AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1185650

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1185650 MtrunA17_Chr7g0258181 85.340 191 28 0 4 194 129 319 2.13e-118 338
Msa1185650 MtrunA17_Chr1g0174271 49.761 209 76 2 7 189 164 369 4.07e-57 184
Msa1185650 MtrunA17_Chr4g0032951 62.376 101 38 0 88 188 325 425 6.41e-39 138
Msa1185650 MtrunA17_Chr2g0329041 62.376 101 37 1 88 188 302 401 2.10e-36 130
Msa1185650 MtrunA17_Chr3g0087771 53.982 113 45 1 77 189 288 393 8.62e-34 124
Msa1185650 MtrunA17_Chr8g0351881 51.613 124 56 1 69 188 263 386 3.79e-27 105
Msa1185650 MtrunA17_Chr4g0014771 61.538 78 30 0 112 189 112 189 4.20e-27 101
Msa1185650 MtrunA17_Chr1g0213791 48.571 105 51 2 85 188 233 335 1.92e-23 95.1
Msa1185650 MtrunA17_Chr1g0152131 49.296 71 36 0 116 186 258 328 1.72e-14 70.9
Msa1185650 MtrunA17_Chr4g0074161 50.000 68 33 1 118 185 206 272 2.64e-14 70.5
Msa1185650 MtrunA17_Chr3g0131771 46.753 77 41 0 108 184 137 213 4.40e-14 69.3
Msa1185650 MtrunA17_Chr5g0421111 46.053 76 41 0 116 191 363 438 9.26e-14 68.9
Msa1185650 MtrunA17_Chr3g0144641 46.053 76 41 0 116 191 189 264 1.96e-13 67.8
Msa1185650 MtrunA17_Chr7g0234761 42.857 84 45 1 111 191 307 390 1.98e-13 67.8
Msa1185650 MtrunA17_Chr1g0190731 46.667 75 39 1 111 185 186 259 2.25e-13 67.4
Msa1185650 MtrunA17_Chr8g0365941 43.421 76 43 0 111 186 298 373 4.24e-13 67.0
Msa1185650 MtrunA17_Chr8g0339091 46.377 69 37 0 116 184 289 357 1.19e-12 65.5
Msa1185650 MtrunA17_Chr4g0035101 43.421 76 43 0 116 191 141 216 2.98e-12 64.3
Msa1185650 MtrunA17_Chr8g0385911 45.070 71 39 0 116 186 143 213 3.46e-12 63.9
Msa1185650 MtrunA17_Chr8g0363921 43.478 69 39 0 116 184 149 217 4.08e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1185650 AT2G42280.1 58.678 121 47 1 77 194 235 355 2.76e-39 137
Msa1185650 AT2G42280.3 63.208 106 36 1 77 179 235 340 2.03e-35 127
Msa1185650 AT1G51140.1 58.252 103 38 2 88 190 279 376 2.66e-33 122
Msa1185650 AT2G43140.1 52.427 103 48 1 87 188 102 204 5.32e-30 110
Msa1185650 AT2G43140.2 52.427 103 48 1 87 188 199 301 1.44e-29 111
Msa1185650 AT1G05805.1 50.980 102 48 2 88 188 253 353 8.24e-26 102
Msa1185650 AT1G35460.1 53.659 82 38 0 110 191 173 254 3.48e-25 98.6
Msa1185650 AT4G09180.1 54.118 85 37 1 104 188 172 254 4.26e-24 95.9
Msa1185650 AT1G35460.2 68.085 47 15 0 110 156 173 219 6.64e-15 70.9
Msa1185650 AT5G58010.1 50.000 68 33 1 118 185 99 165 2.58e-14 70.1
Msa1185650 AT2G24260.2 51.471 68 32 1 118 185 35 101 2.67e-14 69.3
Msa1185650 AT2G24260.1 51.471 68 32 1 118 185 138 204 3.29e-14 70.1
Msa1185650 AT4G30980.1 50.000 68 33 1 118 185 130 196 7.43e-14 68.9
Msa1185650 AT1G10120.2 49.296 71 36 0 116 186 204 274 9.73e-14 68.9
Msa1185650 AT1G10120.1 49.296 71 36 0 116 186 204 274 9.73e-14 68.9
Msa1185650 AT4G30980.2 50.000 68 33 1 118 185 178 244 1.04e-13 68.9
Msa1185650 AT1G68920.3 46.479 71 38 0 116 186 300 370 1.98e-13 68.2
Msa1185650 AT5G50915.3 47.297 74 39 0 111 184 129 202 2.06e-13 67.4
Msa1185650 AT5G50915.4 47.297 74 39 0 111 184 129 202 2.06e-13 67.4
Msa1185650 AT1G68920.1 46.479 71 38 0 116 186 301 371 2.10e-13 68.2
Msa1185650 AT1G68920.4 46.479 71 38 0 116 186 301 371 2.10e-13 68.2
Msa1185650 AT1G68920.2 46.479 71 38 0 116 186 301 371 2.10e-13 68.2
Msa1185650 AT5G50915.1 47.297 74 39 0 111 184 129 202 2.16e-13 67.4
Msa1185650 AT5G50915.2 47.297 74 39 0 111 184 129 202 2.16e-13 67.4
Msa1185650 AT4G34530.1 46.479 71 38 0 116 186 170 240 3.16e-13 67.4
Msa1185650 AT1G26260.4 47.826 69 36 0 116 184 221 289 1.06e-12 65.9
Msa1185650 AT1G26260.1 47.826 69 36 0 116 184 221 289 1.06e-12 65.9
Msa1185650 AT1G26260.6 47.826 69 36 0 116 184 221 289 1.06e-12 65.9
Msa1185650 AT1G26260.2 47.826 69 36 0 116 184 221 289 1.06e-12 65.9
Msa1185650 AT1G26260.5 47.826 69 36 0 116 184 199 267 1.12e-12 65.9
Msa1185650 AT1G26260.3 47.826 69 36 0 116 184 170 238 1.24e-12 65.5
Msa1185650 AT3G07340.1 43.421 76 43 0 116 191 256 331 1.28e-12 65.9
Msa1185650 AT3G07340.2 43.421 76 43 0 116 191 256 331 1.38e-12 65.9
Msa1185650 AT5G48560.2 44.928 69 38 0 116 184 299 367 4.94e-12 64.3
Msa1185650 AT5G48560.1 44.928 69 38 0 116 184 299 367 4.96e-12 64.3
Msa1185650 AT3G23690.1 42.105 76 44 0 116 191 189 264 1.28e-11 62.8
Msa1185650 AT2G42280.2 54.839 62 25 1 77 135 235 296 2.19e-11 62.0
Msa1185650 AT4G36540.1 42.857 77 42 1 108 184 133 207 3.43e-11 61.2
Msa1185650 AT4G36540.2 42.857 77 42 1 108 184 133 207 3.53e-11 61.2
Msa1185650 AT1G25330.1 40.580 69 41 0 116 184 102 170 4.36e-11 60.1
Msa1185650 AT2G18300.2 43.662 71 40 0 116 186 183 253 5.32e-11 60.8
Msa1185650 AT2G18300.1 43.662 71 40 0 116 186 183 253 5.33e-11 60.8
Msa1185650 AT2G18300.3 43.662 71 40 0 116 186 183 253 6.58e-11 60.8

Find 29 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTATCACAGAACTCTAAAA+TGG 0.205272 8_1:+23000993 Msa1185650:CDS
CCGAGTTCTTCTTACTATTT+CGG 0.241324 8_1:-23001375 None:intergenic
ACTATTTCGGCAAGGCTTCT+AGG 0.250386 8_1:-23001362 None:intergenic
ATACTGATTGGAACAGAATC+TGG 0.286669 8_1:-23001311 None:intergenic
AACATCTCTGATGACTTTCT+TGG 0.289008 8_1:-23001263 None:intergenic
CTCTTTGCTTTGATACTGAT+TGG 0.293586 8_1:-23001323 None:intergenic
AACATATCGAACAATCAAAT+TGG 0.332870 8_1:+23000937 Msa1185650:CDS
TCAAGGAAGAAGGACTTCTA+AGG 0.338864 8_1:-23000966 None:intergenic
AATGAGGATGCTCAATATTA+TGG 0.342968 8_1:+23001069 Msa1185650:CDS
TTGGTTTCTCCATCTGCACT+TGG 0.402536 8_1:-23001735 None:intergenic
TTATCACAGAACTCTAAAAT+GGG 0.430915 8_1:+23000994 Msa1185650:CDS
CAAAATAGAAATGTTAGACT+TGG 0.447335 8_1:+23001556 Msa1185650:CDS
TGCTGTTGTACTCAGAATGT+AGG 0.493929 8_1:+23001197 Msa1185650:intron
GATTGTTCGAAACATTGATA+AGG 0.501005 8_1:+23001427 Msa1185650:CDS
GTAAGTTCACCATCACTGTC+AGG 0.511286 8_1:-23000904 None:intergenic
AACTCTAAAATGGGGAGTGA+TGG 0.522219 8_1:+23001003 Msa1185650:CDS
CCGAAATAGTAAGAAGAACT+CGG 0.523931 8_1:+23001375 Msa1185650:CDS
CATTTATGAATCTAATAACC+AGG 0.533143 8_1:+23001101 Msa1185650:CDS
GTCATCAGAGATGTTTGTTG+TGG 0.533598 8_1:+23001271 Msa1185650:CDS
GATAACATTCTCAAGGAAGA+AGG 0.536765 8_1:-23000976 None:intergenic
TTCTTCTTACTATTTCGGCA+AGG 0.571571 8_1:-23001370 None:intergenic
CAAGGAAGAAGGACTTCTAA+GGG 0.573960 8_1:-23000965 None:intergenic
GTTCTGTGATAACATTCTCA+AGG 0.609917 8_1:-23000983 None:intergenic
ATCAGTATCAAAGCAAAGAG+AGG 0.613324 8_1:+23001326 Msa1185650:CDS
AAAATGGGGAGTGATGGCAT+TGG 0.649328 8_1:+23001009 Msa1185650:CDS
TATCACAGAACTCTAAAATG+GGG 0.685073 8_1:+23000995 Msa1185650:CDS
ATCATTATACCTGACAGTGA+TGG 0.687741 8_1:+23000895 Msa1185650:CDS
AAGACAAGTAGTTAGCAATG+AGG 0.698590 8_1:+23001053 Msa1185650:CDS
CTACTTGTCTTCGATCATCG+CGG 0.730474 8_1:-23001041 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTATACATTGTTTAATTAT+TGG + chr8_1:23001522-23001541 Msa1185650:intron 15.0%
!! AGGTACATAATTAAATTTAT+AGG + chr8_1:23001615-23001634 Msa1185650:intron 15.0%
!! GTTATACATTGTTTAATTAT+TGG + chr8_1:23001522-23001541 Msa1185650:intron 15.0%
!! AGGTACATAATTAAATTTAT+AGG + chr8_1:23001615-23001634 Msa1185650:intron 15.0%
!!! AACATGTTCATTTTTTTATC+AGG + chr8_1:23001129-23001148 Msa1185650:intron 20.0%
!! AGATCTTCAAAAACAATTAA+AGG + chr8_1:23001595-23001614 Msa1185650:CDS 20.0%
!!! AACATGTTCATTTTTTTATC+AGG + chr8_1:23001129-23001148 Msa1185650:intron 20.0%
!! AGATCTTCAAAAACAATTAA+AGG + chr8_1:23001595-23001614 Msa1185650:CDS 20.0%
! AACATATCGAACAATCAAAT+TGG + chr8_1:23000937-23000956 Msa1185650:CDS 25.0%
!!! TTATCACAGAACTCTAAAAT+GGG + chr8_1:23000994-23001013 Msa1185650:CDS 25.0%
! CATTTATGAATCTAATAACC+AGG + chr8_1:23001101-23001120 Msa1185650:CDS 25.0%
! CAAACAAAATTGTCTCAAAA+GGG - chr8_1:23001492-23001511 None:intergenic 25.0%
! ACAAACAAAATTGTCTCAAA+AGG - chr8_1:23001493-23001512 None:intergenic 25.0%
! CAAAATAGAAATGTTAGACT+TGG + chr8_1:23001556-23001575 Msa1185650:CDS 25.0%
! AACTAATCATGATTAACTGA+GGG - chr8_1:23001657-23001676 None:intergenic 25.0%
! AACATATCGAACAATCAAAT+TGG + chr8_1:23000937-23000956 Msa1185650:CDS 25.0%
!!! TTATCACAGAACTCTAAAAT+GGG + chr8_1:23000994-23001013 Msa1185650:CDS 25.0%
! CATTTATGAATCTAATAACC+AGG + chr8_1:23001101-23001120 Msa1185650:CDS 25.0%
! CAAACAAAATTGTCTCAAAA+GGG - chr8_1:23001492-23001511 None:intergenic 25.0%
! ACAAACAAAATTGTCTCAAA+AGG - chr8_1:23001493-23001512 None:intergenic 25.0%
! CAAAATAGAAATGTTAGACT+TGG + chr8_1:23001556-23001575 Msa1185650:CDS 25.0%
! AACTAATCATGATTAACTGA+GGG - chr8_1:23001657-23001676 None:intergenic 25.0%
! GTTATCACAGAACTCTAAAA+TGG + chr8_1:23000993-23001012 Msa1185650:CDS 30.0%
!! TATCACAGAACTCTAAAATG+GGG + chr8_1:23000995-23001014 Msa1185650:CDS 30.0%
AATGAGGATGCTCAATATTA+TGG + chr8_1:23001069-23001088 Msa1185650:CDS 30.0%
AAATGAACATGTTACATACC+TGG - chr8_1:23001122-23001141 None:intergenic 30.0%
GATTGTTCGAAACATTGATA+AGG + chr8_1:23001427-23001446 Msa1185650:CDS 30.0%
GAACTAATCATGATTAACTG+AGG - chr8_1:23001658-23001677 None:intergenic 30.0%
! GTTATCACAGAACTCTAAAA+TGG + chr8_1:23000993-23001012 Msa1185650:CDS 30.0%
!! TATCACAGAACTCTAAAATG+GGG + chr8_1:23000995-23001014 Msa1185650:CDS 30.0%
AATGAGGATGCTCAATATTA+TGG + chr8_1:23001069-23001088 Msa1185650:CDS 30.0%
AAATGAACATGTTACATACC+TGG - chr8_1:23001122-23001141 None:intergenic 30.0%
GATTGTTCGAAACATTGATA+AGG + chr8_1:23001427-23001446 Msa1185650:CDS 30.0%
GAACTAATCATGATTAACTG+AGG - chr8_1:23001658-23001677 None:intergenic 30.0%
ATCATTATACCTGACAGTGA+TGG + chr8_1:23000895-23000914 Msa1185650:CDS 35.0%
GATAACATTCTCAAGGAAGA+AGG - chr8_1:23000979-23000998 None:intergenic 35.0%
GTTCTGTGATAACATTCTCA+AGG - chr8_1:23000986-23001005 None:intergenic 35.0%
AAGACAAGTAGTTAGCAATG+AGG + chr8_1:23001053-23001072 Msa1185650:CDS 35.0%
TAGGAGGCAAAATTGCATTT+AGG - chr8_1:23001155-23001174 None:intergenic 35.0%
AACATCTCTGATGACTTTCT+TGG - chr8_1:23001266-23001285 None:intergenic 35.0%
! ATACTGATTGGAACAGAATC+TGG - chr8_1:23001314-23001333 None:intergenic 35.0%
CTCTTTGCTTTGATACTGAT+TGG - chr8_1:23001326-23001345 None:intergenic 35.0%
ATCAGTATCAAAGCAAAGAG+AGG + chr8_1:23001326-23001345 Msa1185650:CDS 35.0%
TTCTTCTTACTATTTCGGCA+AGG - chr8_1:23001373-23001392 None:intergenic 35.0%
CCGAGTTCTTCTTACTATTT+CGG - chr8_1:23001378-23001397 None:intergenic 35.0%
CCGAAATAGTAAGAAGAACT+CGG + chr8_1:23001375-23001394 Msa1185650:CDS 35.0%
ATCATTATACCTGACAGTGA+TGG + chr8_1:23000895-23000914 Msa1185650:CDS 35.0%
GATAACATTCTCAAGGAAGA+AGG - chr8_1:23000979-23000998 None:intergenic 35.0%
GTTCTGTGATAACATTCTCA+AGG - chr8_1:23000986-23001005 None:intergenic 35.0%
AAGACAAGTAGTTAGCAATG+AGG + chr8_1:23001053-23001072 Msa1185650:CDS 35.0%
TAGGAGGCAAAATTGCATTT+AGG - chr8_1:23001155-23001174 None:intergenic 35.0%
AACATCTCTGATGACTTTCT+TGG - chr8_1:23001266-23001285 None:intergenic 35.0%
! ATACTGATTGGAACAGAATC+TGG - chr8_1:23001314-23001333 None:intergenic 35.0%
CTCTTTGCTTTGATACTGAT+TGG - chr8_1:23001326-23001345 None:intergenic 35.0%
ATCAGTATCAAAGCAAAGAG+AGG + chr8_1:23001326-23001345 Msa1185650:CDS 35.0%
TTCTTCTTACTATTTCGGCA+AGG - chr8_1:23001373-23001392 None:intergenic 35.0%
CCGAGTTCTTCTTACTATTT+CGG - chr8_1:23001378-23001397 None:intergenic 35.0%
CCGAAATAGTAAGAAGAACT+CGG + chr8_1:23001375-23001394 Msa1185650:CDS 35.0%
CAAGGAAGAAGGACTTCTAA+GGG - chr8_1:23000968-23000987 None:intergenic 40.0%
TCAAGGAAGAAGGACTTCTA+AGG - chr8_1:23000969-23000988 None:intergenic 40.0%
!! AACTCTAAAATGGGGAGTGA+TGG + chr8_1:23001003-23001022 Msa1185650:CDS 40.0%
TCACGCGAATCAGCAAAATT+AGG - chr8_1:23001174-23001193 None:intergenic 40.0%
TGCTGTTGTACTCAGAATGT+AGG + chr8_1:23001197-23001216 Msa1185650:intron 40.0%
! GTCATCAGAGATGTTTGTTG+TGG + chr8_1:23001271-23001290 Msa1185650:CDS 40.0%
TAAAAAGAGCCAAGTGCAGA+TGG + chr8_1:23001726-23001745 Msa1185650:CDS 40.0%
CAAGGAAGAAGGACTTCTAA+GGG - chr8_1:23000968-23000987 None:intergenic 40.0%
TCAAGGAAGAAGGACTTCTA+AGG - chr8_1:23000969-23000988 None:intergenic 40.0%
!! AACTCTAAAATGGGGAGTGA+TGG + chr8_1:23001003-23001022 Msa1185650:CDS 40.0%
TCACGCGAATCAGCAAAATT+AGG - chr8_1:23001174-23001193 None:intergenic 40.0%
TGCTGTTGTACTCAGAATGT+AGG + chr8_1:23001197-23001216 Msa1185650:intron 40.0%
! GTCATCAGAGATGTTTGTTG+TGG + chr8_1:23001271-23001290 Msa1185650:CDS 40.0%
TAAAAAGAGCCAAGTGCAGA+TGG + chr8_1:23001726-23001745 Msa1185650:CDS 40.0%
GTAAGTTCACCATCACTGTC+AGG - chr8_1:23000907-23000926 None:intergenic 45.0%
AAAATGGGGAGTGATGGCAT+TGG + chr8_1:23001009-23001028 Msa1185650:CDS 45.0%
CTACTTGTCTTCGATCATCG+CGG - chr8_1:23001044-23001063 None:intergenic 45.0%
CGCGAATCAGCAAAATTAGG+AGG - chr8_1:23001171-23001190 None:intergenic 45.0%
ACTATTTCGGCAAGGCTTCT+AGG - chr8_1:23001365-23001384 None:intergenic 45.0%
TTGGTTTCTCCATCTGCACT+TGG - chr8_1:23001738-23001757 None:intergenic 45.0%
GTAAGTTCACCATCACTGTC+AGG - chr8_1:23000907-23000926 None:intergenic 45.0%
AAAATGGGGAGTGATGGCAT+TGG + chr8_1:23001009-23001028 Msa1185650:CDS 45.0%
CTACTTGTCTTCGATCATCG+CGG - chr8_1:23001044-23001063 None:intergenic 45.0%
CGCGAATCAGCAAAATTAGG+AGG - chr8_1:23001171-23001190 None:intergenic 45.0%
ACTATTTCGGCAAGGCTTCT+AGG - chr8_1:23001365-23001384 None:intergenic 45.0%
TTGGTTTCTCCATCTGCACT+TGG - chr8_1:23001738-23001757 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 23000892 23001763 23000892 ID=Msa1185650;Name=Msa1185650
chr8_1 mRNA 23000892 23001763 23000892 ID=Msa1185650-mRNA-1;Parent=Msa1185650;Name=Msa1185650-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|0|0|1|1|1|4|0|194
chr8_1 exon 23000892 23001122 23000892 ID=Msa1185650-mRNA-1:exon:8487;Parent=Msa1185650-mRNA-1
chr8_1 exon 23001212 23001448 23001212 ID=Msa1185650-mRNA-1:exon:8488;Parent=Msa1185650-mRNA-1
chr8_1 exon 23001548 23001616 23001548 ID=Msa1185650-mRNA-1:exon:8489;Parent=Msa1185650-mRNA-1
chr8_1 exon 23001716 23001763 23001716 ID=Msa1185650-mRNA-1:exon:8490;Parent=Msa1185650-mRNA-1
chr8_1 CDS 23000892 23001122 23000892 ID=Msa1185650-mRNA-1:cds;Parent=Msa1185650-mRNA-1
chr8_1 CDS 23001212 23001448 23001212 ID=Msa1185650-mRNA-1:cds;Parent=Msa1185650-mRNA-1
chr8_1 CDS 23001548 23001616 23001548 ID=Msa1185650-mRNA-1:cds;Parent=Msa1185650-mRNA-1
chr8_1 CDS 23001716 23001763 23001716 ID=Msa1185650-mRNA-1:cds;Parent=Msa1185650-mRNA-1
Gene Sequence

>Msa1185650

TTGATCATTATACCTGACAGTGATGGTGAACTTACTCTATCTATGAACATATCGAACAATCAAATTGGCTTCTCCCTTAGAAGTCCTTCTTCCTTGAGAATGTTATCACAGAACTCTAAAATGGGGAGTGATGGCATTGGAACAACTAGCCGCGATGATCGAAGACAAGTAGTTAGCAATGAGGATGCTCAATATTATGGTCATAAATTCATTTATGAATCTAATAACCAGAATGTAGGCGTACGAAATCAAATTGATACACTATCACATCACTTGAGTTTGCCAAGAAAGTCATCAGAGATGTTTGTTGTGGAGAATTTGCTTCAGTTTCCAGATTCTGTTCCAATCAGTATCAAAGCAAAGAGAGGCTTTGAAACACATCCTAGAAGCCTTGCCGAAATAGTAAGAAGAACTCGGATAAGTGAACGAATGAGAAAATTGCAAGAGATTGTTCGAAACATTGATAAGCAAACTTGCAAAATAGAAATGTTAGACTTGGTTGTAGAGTACATTAAAGATCTTCAAAAACAATTAAAGACTATGAGTGTAAAAAGAGCCAAGTGCAGATGGAGAAACCAAAAATGA
Protein sequence

>Msa1185650

LIIIPDSDGELTLSMNISNNQIGFSLRSPSSLRMLSQNSKMGSDGIGTTSRDDRRQVVSNEDAQYYGHKFIYESNNQNVGVRNQIDTLSHHLSLPRKSSEMFVVENLLQFPDSVPISIKAKRGFETHPRSLAEIVRRTRISERMRKLQEIVRNIDKQTCKIEMLDLVVEYIKDLQKQLKTMSVKRAKCRWRNQK*