AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83883

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83883.t1 MTR_6g027290 87.970 133 16 0 1 133 44 176 1.57e-83 242
MS.gene83883.t1 MTR_2g030570 49.219 128 65 0 6 133 48 175 2.74e-37 134
MS.gene83883.t1 MTR_2g030600 48.438 128 64 1 6 133 48 173 1.22e-33 124
MS.gene83883.t1 MTR_6g477820 42.373 118 63 2 6 121 53 167 6.38e-26 102
MS.gene83883.t1 MTR_4g047800 36.207 116 73 1 6 121 84 198 3.27e-22 91.3
MS.gene83883.t1 MTR_2g088470 33.621 116 76 1 6 121 91 205 3.46e-20 85.5
MS.gene83883.t1 MTR_0198s0030 37.069 116 72 1 6 121 79 193 6.33e-20 84.7
MS.gene83883.t1 MTR_7g076080 33.333 129 82 2 6 131 115 242 7.67e-19 81.6
MS.gene83883.t1 MTR_1g101280 35.000 120 69 2 6 121 80 194 2.26e-18 80.5
MS.gene83883.t1 MTR_5g046040 37.931 116 69 2 7 121 59 172 1.40e-17 77.4
MS.gene83883.t1 MTR_5g029320 33.333 108 72 0 6 113 113 220 2.49e-17 77.4
MS.gene83883.t1 MTR_7g027265 36.735 98 61 1 5 102 40 136 8.81e-17 72.0
MS.gene83883.t1 MTR_8g432540 31.897 116 78 1 6 121 139 253 1.15e-16 75.5
MS.gene83883.t1 MTR_7g427700 31.746 126 74 1 5 130 39 152 7.04e-16 73.2
MS.gene83883.t1 MTR_7g427710 31.496 127 75 1 5 131 39 153 7.07e-16 73.2
MS.gene83883.t1 MTR_2g101720 32.479 117 72 2 7 119 164 277 6.79e-15 70.5
MS.gene83883.t1 MTR_5g005600 36.634 101 60 3 6 105 69 166 1.01e-13 67.0
MS.gene83883.t1 MTR_2g030720 35.644 101 52 3 7 107 43 130 1.26e-12 61.6
MS.gene83883.t1 MTR_2g030660 32.673 101 59 2 5 104 38 130 3.13e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83883.t1 AT1G73360 46.154 117 60 2 6 121 56 170 8.17e-30 113
MS.gene83883.t1 AT1G17920 41.880 117 65 2 6 121 45 159 5.07e-25 99.4
MS.gene83883.t1 AT1G17920 41.880 117 65 2 6 121 45 159 5.07e-25 99.4
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 8.10e-22 90.1
MS.gene83883.t1 AT3G03260 38.393 112 69 0 6 117 47 158 1.07e-21 89.7
MS.gene83883.t1 AT1G05230 36.207 116 73 1 6 121 88 202 4.02e-21 88.2
MS.gene83883.t1 AT3G03260 38.393 112 69 0 6 117 47 158 1.67e-20 86.3
MS.gene83883.t1 AT4G21750 37.168 113 70 1 6 118 86 197 2.72e-20 85.9
MS.gene83883.t1 AT4G21750 37.168 113 70 1 6 118 86 197 2.72e-20 85.9
MS.gene83883.t1 AT4G21750 37.168 113 70 1 6 118 86 197 2.72e-20 85.9
MS.gene83883.t1 AT4G21750 37.168 113 70 1 6 118 86 197 2.72e-20 85.9
MS.gene83883.t1 AT4G04890 35.398 113 72 1 6 118 86 197 3.90e-19 82.4
MS.gene83883.t1 AT4G04890 35.398 113 72 1 6 118 86 197 3.90e-19 82.4
MS.gene83883.t1 AT3G61150 33.028 109 72 1 5 113 133 240 2.64e-17 77.4
MS.gene83883.t1 AT5G17320 36.207 116 74 0 7 122 51 166 1.31e-16 75.5
MS.gene83883.t1 AT4G00730 32.143 112 67 2 6 113 158 264 1.69e-16 75.1
MS.gene83883.t1 AT5G52170 35.088 114 73 1 6 119 81 193 3.75e-16 73.9
MS.gene83883.t1 AT5G52170 35.088 114 73 1 6 119 81 193 3.75e-16 73.9
MS.gene83883.t1 AT5G52170 35.088 114 73 1 6 119 81 193 3.76e-16 73.9
MS.gene83883.t1 AT4G00730 32.143 112 67 2 6 113 158 264 5.66e-16 73.6
MS.gene83883.t1 AT5G46880 31.579 114 67 2 4 113 133 239 3.02e-15 71.2
MS.gene83883.t1 AT5G46880 31.579 114 67 2 4 113 133 239 3.02e-15 71.2
MS.gene83883.t1 AT5G46880 31.579 114 67 2 4 113 133 239 3.02e-15 71.2
MS.gene83883.t1 AT1G34650 34.259 108 70 1 6 113 40 146 5.00e-15 70.9
MS.gene83883.t1 AT1G79840 33.945 109 60 2 6 112 154 252 7.16e-15 70.5
MS.gene83883.t1 AT1G79840 33.945 109 60 2 6 112 67 165 8.74e-15 70.1
MS.gene83883.t1 AT1G79840 33.945 109 60 2 6 112 67 165 8.74e-15 70.1
MS.gene83883.t1 AT1G79840 33.945 109 60 2 6 112 125 223 8.83e-15 70.1
MS.gene83883.t1 AT1G79840 33.945 109 60 2 6 112 125 223 3.48e-14 68.2
MS.gene83883.t1 AT1G79840 33.945 109 60 2 6 112 125 223 3.49e-14 68.2
MS.gene83883.t1 AT4G17710 30.556 108 62 1 4 111 110 204 6.14e-14 67.8
MS.gene83883.t1 AT2G32370 31.532 111 67 2 6 112 92 197 1.47e-11 60.8

Find 24 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATTTCGTTGGGCTTCATT+TGG 0.279004 6.1:+9263484 None:intergenic
GAACCAAGATTTGATTTGTT+TGG 0.287062 6.1:+9263435 None:intergenic
AACCAAGATTTGATTTGTTT+GGG 0.304941 6.1:+9263436 None:intergenic
AGCCCAAACAAATCAAATCT+TGG 0.386306 6.1:-9263438 MS.gene83883:CDS
GATTTCGTTGGGCTTCATTT+GGG 0.397275 6.1:+9263485 None:intergenic
CTTAGCTAATTGATTTCGTT+GGG 0.409743 6.1:+9263474 None:intergenic
ATCAATTAGCTAAGGAGGTT+GGG 0.412482 6.1:-9263465 MS.gene83883:CDS
CCTTAGCTAATTGATTTCGT+TGG 0.420498 6.1:+9263473 None:intergenic
AACGTTCATGCTCATGCATT+GGG 0.431887 6.1:+9263142 None:intergenic
TCTGTTCGTACTTTGCTAGC+AGG 0.432332 6.1:+9262947 None:intergenic
CTGTTCGTACTTTGCTAGCA+GGG 0.445221 6.1:+9262948 None:intergenic
TTGAATAAAGATTCATGGCA+AGG 0.468284 6.1:-9263516 None:intergenic
AATCAATTAGCTAAGGAGGT+TGG 0.482913 6.1:-9263466 MS.gene83883:CDS
AAACGTTCATGCTCATGCAT+TGG 0.496436 6.1:+9263141 None:intergenic
TTTCATGCAAAAGATGAGAA+TGG 0.506914 6.1:-9263121 MS.gene83883:CDS
TGCTCATGCATTGGGAAAGG+AGG 0.551665 6.1:+9263150 None:intergenic
ACGAAATCAATTAGCTAAGG+AGG 0.581875 6.1:-9263470 MS.gene83883:CDS
GAATGACATGCTGAAAGAGA+AGG 0.584443 6.1:-9263097 MS.gene83883:intron
TCATGCTCATGCATTGGGAA+AGG 0.590182 6.1:+9263147 None:intergenic
CCAACGAAATCAATTAGCTA+AGG 0.600046 6.1:-9263473 MS.gene83883:CDS
GCTAGCAAAGTACGAACAGA+AGG 0.603167 6.1:-9262944 MS.gene83883:CDS
AATCTTGGTTCGATAACAAG+AGG 0.621531 6.1:-9263423 MS.gene83883:CDS
TAACAAGAGGAGTACACTGA+AGG 0.626045 6.1:-9263410 MS.gene83883:intron
TTCGTACTTTGCTAGCAGGG+TGG 0.642156 6.1:+9262951 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACCAAGATTTGATTTGTTT+GGG + chr6.1:9262960-9262979 None:intergenic 25.0%
!!! TTTATTTTTTCAGATCGAGA+AGG - chr6.1:9263416-9263435 MS.gene83883:CDS 25.0%
TTTCATGCAAAAGATGAGAA+TGG - chr6.1:9263272-9263291 MS.gene83883:intron 30.0%
! CTTAGCTAATTGATTTCGTT+GGG + chr6.1:9262922-9262941 None:intergenic 30.0%
!! GAACCAAGATTTGATTTGTT+TGG + chr6.1:9262961-9262980 None:intergenic 30.0%
AATCAATTAGCTAAGGAGGT+TGG - chr6.1:9262927-9262946 MS.gene83883:CDS 35.0%
ACGAAATCAATTAGCTAAGG+AGG - chr6.1:9262923-9262942 MS.gene83883:CDS 35.0%
AGCCCAAACAAATCAAATCT+TGG - chr6.1:9262955-9262974 MS.gene83883:CDS 35.0%
ATCAATTAGCTAAGGAGGTT+GGG - chr6.1:9262928-9262947 MS.gene83883:CDS 35.0%
CCAACGAAATCAATTAGCTA+AGG - chr6.1:9262920-9262939 MS.gene83883:CDS 35.0%
! AATCTTGGTTCGATAACAAG+AGG - chr6.1:9262970-9262989 MS.gene83883:intron 35.0%
! ATGACATTTTGCGAAAGTTG+TGG - chr6.1:9263216-9263235 MS.gene83883:CDS 35.0%
! CCTTAGCTAATTGATTTCGT+TGG + chr6.1:9262923-9262942 None:intergenic 35.0%
! TGACATTTTGCGAAAGTTGT+GGG - chr6.1:9263217-9263236 MS.gene83883:CDS 35.0%
AAACGTTCATGCTCATGCAT+TGG + chr6.1:9263255-9263274 None:intergenic 40.0%
AACGTTCATGCTCATGCATT+GGG + chr6.1:9263254-9263273 None:intergenic 40.0%
GAATGACATGCTGAAAGAGA+AGG - chr6.1:9263296-9263315 MS.gene83883:intron 40.0%
GATTTCGTTGGGCTTCATTT+GGG + chr6.1:9262911-9262930 None:intergenic 40.0%
TGATTTCGTTGGGCTTCATT+TGG + chr6.1:9262912-9262931 None:intergenic 40.0%
! ACATTTTGCGAAAGTTGTGG+GGG - chr6.1:9263219-9263238 MS.gene83883:CDS 40.0%
! GACATTTTGCGAAAGTTGTG+GGG - chr6.1:9263218-9263237 MS.gene83883:CDS 40.0%
! TAACAAGAGGAGTACACTGA+AGG - chr6.1:9262983-9263002 MS.gene83883:intron 40.0%
CTGTTCGTACTTTGCTAGCA+GGG + chr6.1:9263448-9263467 None:intergenic 45.0%
GCTAGCAAAGTACGAACAGA+AGG - chr6.1:9263449-9263468 MS.gene83883:CDS 45.0%
TCATGCTCATGCATTGGGAA+AGG + chr6.1:9263249-9263268 None:intergenic 45.0%
TCTGTTCGTACTTTGCTAGC+AGG + chr6.1:9263449-9263468 None:intergenic 45.0%
!!! AATACTTAATTATTTTTTTA+GGG + chr6.1:9263377-9263396 None:intergenic 5.0%
!!! TAATACTTAATTATTTTTTT+AGG + chr6.1:9263378-9263397 None:intergenic 5.0%
TGCTCATGCATTGGGAAAGG+AGG + chr6.1:9263246-9263265 None:intergenic 50.0%
TTCGTACTTTGCTAGCAGGG+TGG + chr6.1:9263445-9263464 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 9262891 9263524 9262891 ID=MS.gene83883
chr6.1 mRNA 9262891 9263524 9262891 ID=MS.gene83883.t1;Parent=MS.gene83883
chr6.1 exon 9263411 9263524 9263411 ID=MS.gene83883.t1.exon1;Parent=MS.gene83883.t1
chr6.1 CDS 9263411 9263524 9263411 ID=cds.MS.gene83883.t1;Parent=MS.gene83883.t1
chr6.1 exon 9263098 9263289 9263098 ID=MS.gene83883.t1.exon2;Parent=MS.gene83883.t1
chr6.1 CDS 9263098 9263289 9263098 ID=cds.MS.gene83883.t1;Parent=MS.gene83883.t1
chr6.1 exon 9262891 9262986 9262891 ID=MS.gene83883.t1.exon3;Parent=MS.gene83883.t1
chr6.1 CDS 9262891 9262986 9262891 ID=cds.MS.gene83883.t1;Parent=MS.gene83883.t1
Gene Sequence

>MS.gene83883

ATGGCAAGGAACTCTAACCCAAATGAAGCCCAACGAAATCAATTAGCTAAGGAGGTTGGGCTTGAGCCCAAACAAATCAAATCTTGGTTCGATAACAAGAGGAGTACACTGAAGGTAATTGTCTTCAAATAGATGTACATATATCACTACTCATTTTCTTTTCACTAACTCGTATCACATGCTTTCATATAACTAGTACTAATTATTTATATATATTTTTTACATTATTATTAAGAAAAAACACATGAGAGAAGATAACAAAGCTCTTCATGCTGCAAGAAAAGAGCTCATTACTGAAAATATCGTTGTGAAAAAGATATTCAAGATGACATTTTGCGAAAGTTGTGGGGGTCCTCCTTTCCCAATGCATGAGCATGAACGTTTCATGCAAAAGATGAGAATGGAGAATGACATGCTGAAAGAGAAGGTTAGTGAATATTTTAATTTTATCAAATATCGATGATAATTTTTTAATTAAATATTCCCTAAAAAAATAATTAAGTATTATTTATTTATGAATCAAATTTTATTTTTTCAGATCGAGAAGGTGTCCACCCTGCTAGCAAAGTACGAACAGAAGGAAATCTCGCAGTTTGAATTTGAATACACTTTTGCTCGTTTAAATGCTTTTTGA
Protein sequence

>MS.gene83883.t1

MARNSNPNEAQRNQLAKEVGLEPKQIKSWFDNKRSTLKKKHMREDNKALHAARKELITENIVVKKIFKMTFCESCGGPPFPMHEHERFMQKMRMENDMLKEKIEKVSTLLAKYEQKEISQFEFEYTFARLNAF