AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene30918

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene30918.t1 MTR_1g066530 93.694 222 14 0 1 222 1 222 7.68e-157 433
MS.gene30918.t1 MTR_6g073540 50.000 230 106 2 1 221 1 230 1.39e-74 225
MS.gene30918.t1 MTR_6g072470 51.500 200 91 1 1 194 1 200 1.28e-67 207
MS.gene30918.t1 MTR_6g048620 48.649 222 107 5 6 220 5 226 6.78e-65 201
MS.gene30918.t1 MTR_6g045077 45.000 220 116 3 4 220 3 220 4.33e-63 196
MS.gene30918.t1 MTR_6g048910 45.455 220 113 4 6 220 5 222 2.58e-62 194
MS.gene30918.t1 MTR_0695s0030 44.545 220 117 4 6 220 65 284 8.83e-62 195
MS.gene30918.t1 MTR_8g038100 45.000 220 116 4 6 220 281 500 1.48e-59 196
MS.gene30918.t1 MTR_8g038070 44.545 220 117 4 6 220 219 438 2.16e-59 193
MS.gene30918.t1 MTR_0057s0100 41.364 220 124 5 6 220 7 226 9.02e-54 172
MS.gene30918.t1 MTR_0057s0170 41.364 220 124 5 6 220 7 226 9.92e-53 169
MS.gene30918.t1 MTR_7g103990 41.704 223 120 8 6 220 7 227 4.09e-50 163
MS.gene30918.t1 MTR_0216s0030 40.404 198 110 3 4 197 1 194 1.04e-47 155
MS.gene30918.t1 MTR_0807s0020 37.500 224 130 5 1 220 1 218 3.17e-46 152
MS.gene30918.t1 MTR_6g040290 40.359 223 125 6 6 220 7 229 1.59e-45 151
MS.gene30918.t1 MTR_6g048880 40.449 178 96 5 50 220 4 178 1.42e-39 134
MS.gene30918.t1 MTR_7g012000 39.904 208 95 5 6 209 7 188 3.38e-39 134
MS.gene30918.t1 MTR_6g048810 50.355 141 64 4 84 220 162 300 6.79e-37 131
MS.gene30918.t1 MTR_4g102470 40.556 180 84 5 6 182 7 166 2.38e-33 119
MS.gene30918.t1 MTR_6g049040 40.146 137 65 3 1 135 1 122 5.73e-25 95.9
MS.gene30918.t1 MTR_6g049040 35.043 117 65 2 72 187 16 122 3.13e-16 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCGGTACGGTCTTTGAAAA+TGG 0.203555 1.2:+50004349 MS.gene30918:CDS
CTTGAACACGTAACATTCAT+AGG 0.229009 1.2:-50003912 None:intergenic
ATCCGGAGCGAAATCTATTT+TGG 0.242862 1.2:-50004116 None:intergenic
TTTAACAACACGATCCTTCT+TGG 0.279901 1.2:-50003972 None:intergenic
TAGATCTCTAGAAGTTTAAT+AGG 0.303436 1.2:-50004522 None:intergenic
ACTCATTACTCCATTCGTTC+TGG 0.346885 1.2:+50004313 MS.gene30918:CDS
AATGGTGTTTCATCAAGAAA+TGG 0.395080 1.2:-50004022 None:intergenic
TCCAGAGAAGATTATTGCTT+CGG 0.411108 1.2:-50004083 None:intergenic
AACATGGTAGTGATTGGAAC+AGG 0.421529 1.2:-50004163 None:intergenic
GTTACGTGTTCAAGAAGAAA+AGG 0.439700 1.2:+50003921 MS.gene30918:CDS
ACACGATCCTTCTTGGCTCC+TGG 0.452509 1.2:-50003965 None:intergenic
CAATGGAACATGGTAGTGAT+TGG 0.462327 1.2:-50004169 None:intergenic
GAATAAGAAAACATTATGTC+CGG 0.469058 1.2:-50004242 None:intergenic
TGATGAAACACCATTTGAAA+AGG 0.482259 1.2:+50004030 MS.gene30918:CDS
ACCGAAGCAATAATCTTCTC+TGG 0.483775 1.2:+50004082 MS.gene30918:CDS
TTTAATAGGCTCTGAAGAGC+AGG 0.498729 1.2:-50004508 None:intergenic
GTTCAAGAAGAAAAGGTTTG+CGG 0.504927 1.2:+50003928 MS.gene30918:CDS
AACAGGGCCATCGAGTAAAT+CGG 0.507747 1.2:-50004146 None:intergenic
TTGAACACGTAACATTCATA+GGG 0.512326 1.2:-50003911 None:intergenic
AGTAAATCGGTATCTGAATC+CGG 0.514277 1.2:-50004133 None:intergenic
GCGGTTGTGAATTATGCTCC+AGG 0.516853 1.2:+50003947 MS.gene30918:CDS
TGTCAATGGTAGAGTAAAGC+TGG 0.518786 1.2:+50004471 MS.gene30918:CDS
GACAATACAGTCGCCTTCGT+TGG 0.522082 1.2:-50004452 None:intergenic
GACGCTGCAATTAAGTGGAC+CGG 0.527798 1.2:+50004223 MS.gene30918:CDS
AAACCATCGGAAGTATGAAT+CGG 0.529141 1.2:-50003998 None:intergenic
TTCGGTGCCTTCTGTCTCAA+AGG 0.532520 1.2:-50004065 None:intergenic
GAATAGACGCTGCAATTAAG+TGG 0.535911 1.2:+50004218 MS.gene30918:CDS
AGGAAATGAGTATGTTCGTA+TGG 0.536361 1.2:+50004267 MS.gene30918:CDS
TACCATGTTCCATTGTCTCA+AGG 0.539896 1.2:+50004177 MS.gene30918:CDS
GAAGAGCAGGCCATTCATCA+TGG 0.540017 1.2:-50004495 None:intergenic
AAGCCGATTCATACTTCCGA+TGG 0.550807 1.2:+50003995 MS.gene30918:CDS
TAAAGCTGGTCCATGATGAA+TGG 0.552708 1.2:+50004485 MS.gene30918:CDS
AAAACGTTCCCTTGAGACAA+TGG 0.561335 1.2:-50004186 None:intergenic
TGCCAAAATAGATTTCGCTC+CGG 0.565519 1.2:+50004114 MS.gene30918:CDS
ATCAAGAAATGGAAAACCAT+CGG 0.570603 1.2:-50004011 None:intergenic
GATTGTGCCTTTGAGACAGA+AGG 0.572261 1.2:+50004058 MS.gene30918:CDS
ACCATGTTCCATTGTCTCAA+GGG 0.576700 1.2:+50004178 MS.gene30918:CDS
GAAATGCAGTATCAATGACT+TGG 0.591249 1.2:-50003877 None:intergenic
TTATGCTCCAGGAGCCAAGA+AGG 0.592184 1.2:+50003958 MS.gene30918:CDS
TCAGATACCGATTTACTCGA+TGG 0.596226 1.2:+50004139 MS.gene30918:CDS
GAAGGCGACTGTATTGTCAA+TGG 0.604836 1.2:+50004457 MS.gene30918:CDS
CGTATTGATATTTCCAACGA+AGG 0.614900 1.2:+50004439 MS.gene30918:CDS
TCCCTTGAGACAATGGAACA+TGG 0.652701 1.2:-50004179 None:intergenic
ACATGGTAGTGATTGGAACA+GGG 0.671114 1.2:-50004162 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CATAATGTTTTCTTATTCAA+AGG + chr1.2:50004247-50004266 MS.gene30918:CDS 20.0%
! GAATAAGAAAACATTATGTC+CGG - chr1.2:50004245-50004264 None:intergenic 25.0%
AATGGTGTTTCATCAAGAAA+TGG - chr1.2:50004025-50004044 None:intergenic 30.0%
ATCAAGAAATGGAAAACCAT+CGG - chr1.2:50004014-50004033 None:intergenic 30.0%
TGATGAAACACCATTTGAAA+AGG + chr1.2:50004030-50004049 MS.gene30918:CDS 30.0%
TTGAACACGTAACATTCATA+GGG - chr1.2:50003914-50003933 None:intergenic 30.0%
! AATCAAGCTTACGTTTTCAA+AGG + chr1.2:50004403-50004422 MS.gene30918:CDS 30.0%
! CAATCTACTTCCTTTTCAAA+TGG - chr1.2:50004043-50004062 None:intergenic 30.0%
!! AAGGGAACGTTTTTAGAAAA+TGG + chr1.2:50004196-50004215 MS.gene30918:CDS 30.0%
!! TTTTAAAAGTTTGCTCGGTA+CGG + chr1.2:50004336-50004355 MS.gene30918:CDS 30.0%
!!! ACTTTTAAAACCAGAACGAA+TGG - chr1.2:50004326-50004345 None:intergenic 30.0%
!!! TCTGGTTTTAAAAGTTTGCT+CGG + chr1.2:50004331-50004350 MS.gene30918:CDS 30.0%
AGGAAATGAGTATGTTCGTA+TGG + chr1.2:50004267-50004286 MS.gene30918:CDS 35.0%
AGTAAATCGGTATCTGAATC+CGG - chr1.2:50004136-50004155 None:intergenic 35.0%
CTTGAACACGTAACATTCAT+AGG - chr1.2:50003915-50003934 None:intergenic 35.0%
GAAATGCAGTATCAATGACT+TGG - chr1.2:50003880-50003899 None:intergenic 35.0%
GTTACGTGTTCAAGAAGAAA+AGG + chr1.2:50003921-50003940 MS.gene30918:CDS 35.0%
GTTCAAGAAGAAAAGGTTTG+CGG + chr1.2:50003928-50003947 MS.gene30918:CDS 35.0%
TCCAGAGAAGATTATTGCTT+CGG - chr1.2:50004086-50004105 None:intergenic 35.0%
TTTAACAACACGATCCTTCT+TGG - chr1.2:50003975-50003994 None:intergenic 35.0%
! AAACCATCGGAAGTATGAAT+CGG - chr1.2:50004001-50004020 None:intergenic 35.0%
! CGTATTGATATTTCCAACGA+AGG + chr1.2:50004439-50004458 MS.gene30918:CDS 35.0%
AAAACGTTCCCTTGAGACAA+TGG - chr1.2:50004189-50004208 None:intergenic 40.0%
ACCATGTTCCATTGTCTCAA+GGG + chr1.2:50004178-50004197 MS.gene30918:CDS 40.0%
ACCGAAGCAATAATCTTCTC+TGG + chr1.2:50004082-50004101 MS.gene30918:CDS 40.0%
ACTCATTACTCCATTCGTTC+TGG + chr1.2:50004313-50004332 MS.gene30918:CDS 40.0%
GAATAGACGCTGCAATTAAG+TGG + chr1.2:50004218-50004237 MS.gene30918:CDS 40.0%
TAAAGCTGGTCCATGATGAA+TGG + chr1.2:50004485-50004504 MS.gene30918:CDS 40.0%
TACCATGTTCCATTGTCTCA+AGG + chr1.2:50004177-50004196 MS.gene30918:CDS 40.0%
TGCCAAAATAGATTTCGCTC+CGG + chr1.2:50004114-50004133 MS.gene30918:CDS 40.0%
TGTCAATGGTAGAGTAAAGC+TGG + chr1.2:50004471-50004490 MS.gene30918:CDS 40.0%
! AACATGGTAGTGATTGGAAC+AGG - chr1.2:50004166-50004185 None:intergenic 40.0%
! ACATGGTAGTGATTGGAACA+GGG - chr1.2:50004165-50004184 None:intergenic 40.0%
! ATCCGGAGCGAAATCTATTT+TGG - chr1.2:50004119-50004138 None:intergenic 40.0%
! CAATGGAACATGGTAGTGAT+TGG - chr1.2:50004172-50004191 None:intergenic 40.0%
!! TCAGATACCGATTTACTCGA+TGG + chr1.2:50004139-50004158 MS.gene30918:CDS 40.0%
!! TTTAATAGGCTCTGAAGAGC+AGG - chr1.2:50004511-50004530 None:intergenic 40.0%
AACAGGGCCATCGAGTAAAT+CGG - chr1.2:50004149-50004168 None:intergenic 45.0%
GAAGGCGACTGTATTGTCAA+TGG + chr1.2:50004457-50004476 MS.gene30918:CDS 45.0%
TCCCTTGAGACAATGGAACA+TGG - chr1.2:50004182-50004201 None:intergenic 45.0%
! AAGCCGATTCATACTTCCGA+TGG + chr1.2:50003995-50004014 MS.gene30918:CDS 45.0%
! CTCGGTACGGTCTTTGAAAA+TGG + chr1.2:50004349-50004368 MS.gene30918:CDS 45.0%
!! GATTGTGCCTTTGAGACAGA+AGG + chr1.2:50004058-50004077 MS.gene30918:CDS 45.0%
GAAGAGCAGGCCATTCATCA+TGG - chr1.2:50004498-50004517 None:intergenic 50.0%
GACAATACAGTCGCCTTCGT+TGG - chr1.2:50004455-50004474 None:intergenic 50.0%
GACGCTGCAATTAAGTGGAC+CGG + chr1.2:50004223-50004242 MS.gene30918:CDS 50.0%
GCGGTTGTGAATTATGCTCC+AGG + chr1.2:50003947-50003966 MS.gene30918:CDS 50.0%
TTATGCTCCAGGAGCCAAGA+AGG + chr1.2:50003958-50003977 MS.gene30918:CDS 50.0%
!! TTCGGTGCCTTCTGTCTCAA+AGG - chr1.2:50004068-50004087 None:intergenic 50.0%
ACACGATCCTTCTTGGCTCC+TGG - chr1.2:50003968-50003987 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 50003869 50004537 50003869 ID=MS.gene30918
chr1.2 mRNA 50003869 50004537 50003869 ID=MS.gene30918.t1;Parent=MS.gene30918
chr1.2 exon 50003869 50004537 50003869 ID=MS.gene30918.t1.exon1;Parent=MS.gene30918.t1
chr1.2 CDS 50003869 50004537 50003869 ID=cds.MS.gene30918.t1;Parent=MS.gene30918.t1
Gene Sequence

>MS.gene30918

ATGTCAATCCAAGTCATTGATACTGCATTTCGTTCATCTAAGCCCTATGAATGTTACGTGTTCAAGAAGAAAAGGTTTGCGGTTGTGAATTATGCTCCAGGAGCCAAGAAGGATCGTGTTGTTAAAAAGCCGATTCATACTTCCGATGGTTTTCCATTTCTTGATGAAACACCATTTGAAAAGGAAGTAGATTGTGCCTTTGAGACAGAAGGCACCGAAGCAATAATCTTCTCTGGAAAGCAATGTGCCAAAATAGATTTCGCTCCGGATTCAGATACCGATTTACTCGATGGCCCTGTTCCAATCACTACCATGTTCCATTGTCTCAAGGGAACGTTTTTAGAAAATGGAATAGACGCTGCAATTAAGTGGACCGGACATAATGTTTTCTTATTCAAAGGAAATGAGTATGTTCGTATGGACTATCACAAGAAGACTATTGTGACTCATTACTCCATTCGTTCTGGTTTTAAAAGTTTGCTCGGTACGGTCTTTGAAAATGGAATTGATGCAGCATTTGCTTCTCATGTTGCAAATCAAGCTTACGTTTTCAAAGGAGAATACTATGCACGTATTGATATTTCCAACGAAGGCGACTGTATTGTCAATGGTAGAGTAAAGCTGGTCCATGATGAATGGCCTGCTCTTCAGAGCCTATTAAACTTCTAG
Protein sequence

>MS.gene30918.t1

MSIQVIDTAFRSSKPYECYVFKKKRFAVVNYAPGAKKDRVVKKPIHTSDGFPFLDETPFEKEVDCAFETEGTEAIIFSGKQCAKIDFAPDSDTDLLDGPVPITTMFHCLKGTFLENGIDAAIKWTGHNVFLFKGNEYVRMDYHKKTIVTHYSIRSGFKSLLGTVFENGIDAAFASHVANQAYVFKGEYYARIDISNEGDCIVNGRVKLVHDEWPALQSLLNF