AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG033949

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG033949 MtrunA17_Chr6g0481061 95.329 471 18 2 1 471 1 467 0.0 877
MsaG033949 MtrunA17_Chr3g0109791 50.204 245 107 5 38 280 38 269 1.04e-55 189
MsaG033949 MtrunA17_Chr5g0433851 46.800 250 119 5 35 280 21 260 5.58e-47 167
MsaG033949 MtrunA17_Chr1g0181771 56.250 112 38 3 38 149 28 128 1.75e-34 130
MsaG033949 MtrunA17_Chr6g0469431 54.783 115 41 4 46 158 39 144 6.00e-33 124
MsaG033949 MtrunA17_Chr8g0348391 60.638 94 29 2 46 139 53 138 1.07e-32 127
MsaG033949 MtrunA17_Chr7g0276421 68.269 104 31 1 38 139 7 110 1.02e-31 129
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG033949 AT1G18330.1 40.616 357 138 12 46 395 39 328 5.47e-58 195
MsaG033949 AT1G18330.2 43.791 306 104 9 46 345 65 308 7.13e-58 196
MsaG033949 AT5G17300.1 66.250 160 43 3 40 199 38 186 3.00e-52 181
MsaG033949 AT3G10113.1 66.667 135 36 1 46 180 54 179 9.49e-46 162
MsaG033949 AT5G37260.1 55.814 172 61 3 33 204 12 168 1.34e-44 158
MsaG033949 AT3G09600.1 60.638 94 29 2 46 139 32 117 1.84e-32 125
MsaG033949 AT3G09600.7 60.638 94 29 2 46 139 32 117 1.84e-32 125
MsaG033949 AT3G09600.4 60.638 94 29 2 46 139 32 117 1.97e-32 125
MsaG033949 AT3G09600.2 60.638 94 29 2 46 139 32 117 2.01e-32 125
MsaG033949 AT3G09600.6 60.638 94 29 2 46 139 32 117 2.01e-32 125
MsaG033949 AT5G52660.1 59.184 98 32 2 42 139 57 146 1.33e-31 124
MsaG033949 AT5G52660.2 59.184 98 32 2 42 139 57 146 1.41e-31 124
MsaG033949 AT1G01520.1 59.574 94 30 2 46 139 50 135 5.89e-31 121
MsaG033949 AT1G01520.3 59.574 94 30 2 46 139 50 135 7.35e-31 121
MsaG033949 AT1G01520.2 59.574 94 30 2 46 139 50 135 7.88e-31 120
MsaG033949 AT1G01520.4 59.574 94 30 2 46 139 50 135 7.88e-31 120
MsaG033949 AT1G01060.4 58.491 106 42 1 35 138 2 107 1.51e-30 125
MsaG033949 AT1G01060.8 58.491 106 42 1 35 138 2 107 1.62e-30 125
MsaG033949 AT1G01060.2 58.491 106 42 1 35 138 2 107 1.62e-30 125
MsaG033949 AT1G01060.3 58.491 106 42 1 35 138 2 107 1.62e-30 125
MsaG033949 AT1G01060.1 58.491 106 42 1 35 138 2 107 1.62e-30 125
MsaG033949 AT1G01060.7 58.491 106 42 1 35 138 2 107 1.62e-30 125
MsaG033949 AT4G01280.1 60.638 94 29 2 46 139 48 133 1.64e-30 120
MsaG033949 AT5G02840.3 47.015 134 47 4 46 163 37 162 1.73e-30 120
MsaG033949 AT4G01280.2 60.638 94 29 2 46 139 48 133 1.74e-30 120
MsaG033949 AT5G02840.4 47.015 134 47 4 46 163 37 162 1.82e-30 119
MsaG033949 AT5G02840.1 47.015 134 47 4 46 163 37 162 1.96e-30 120
MsaG033949 AT5G02840.2 47.015 134 47 4 46 163 37 162 1.96e-30 120
MsaG033949 AT5G02840.5 47.015 134 47 4 46 163 37 162 2.80e-30 119
MsaG033949 AT2G46830.1 63.529 85 31 0 38 122 5 89 3.51e-30 124
MsaG033949 AT5G17300.2 59.322 118 37 3 82 199 5 111 1.12e-21 95.9
MsaG033949 AT3G09600.3 50.769 65 24 2 75 139 5 61 6.97e-15 74.7
MsaG033949 AT3G09600.8 50.769 65 24 2 75 139 5 61 6.97e-15 74.7
MsaG033949 AT3G09600.5 50.769 65 24 2 75 139 5 61 9.91e-15 73.9
MsaG033949 AT3G09600.9 50.769 65 24 2 75 139 5 61 9.91e-15 73.9

Find 118 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTTCCTCCTCAGATGGTT+TGG 0.248334 6:-103207877 None:intergenic
CATATTTGCAGCATCTTCTT+TGG 0.255626 6:-103208359 None:intergenic
TCGAATCTGAACTGCAGTTT+TGG 0.267753 6:-103207296 None:intergenic
CCTCAGATGGTTTGGATGTC+TGG 0.272930 6:-103207869 None:intergenic
GTTTGGTCGAACACTATCTA+TGG 0.282785 6:+103208405 MsaT033949.1:CDS
AATGCGCAACTTTACCATTA+TGG 0.288861 6:+103208629 MsaT033949.1:CDS
TTCTTAATCCTGTGCCTCTT+AGG 0.290915 6:+103208704 MsaT033949.1:CDS
CTCTGCAACTGATAGGTTAA+TGG 0.293223 6:-103207685 None:intergenic
CTTTGTTTAGTGATGGTATA+CGG 0.298682 6:-103207085 None:intergenic
GATGAAAATTCTTTAATTGC+TGG 0.298848 6:+103208931 MsaT033949.1:CDS
GGAGATGTTTCTGATTCATT+TGG 0.303011 6:-103207660 None:intergenic
CACTGAATCAGTTTGCGATA+TGG 0.310791 6:+103208780 MsaT033949.1:CDS
CACCGACTCAAAACCACTTA+TGG 0.354311 6:+103207929 MsaT033949.1:CDS
GTTGCGCATTCGCCGACATA+TGG 0.355277 6:-103208616 None:intergenic
ACCCTCTTCCAGATTTCTTA+AGG 0.359010 6:-103208876 None:intergenic
AATCTTCATGCAGAACATAT+AGG 0.364568 6:+103207271 MsaT033949.1:intron
GAGATGTTTCTGATTCATTT+GGG 0.373672 6:-103207659 None:intergenic
GGAGTTGTCCTTAAGAAATC+TGG 0.375864 6:+103208868 MsaT033949.1:CDS
AGCTATCAACTCTAATGAAA+TGG 0.384116 6:+103208474 MsaT033949.1:CDS
ATCACTAGTATTAAGCTGTT+TGG 0.389280 6:+103208388 MsaT033949.1:CDS
GGTATGTCAATTGGCTGAAT+AGG 0.403494 6:-103207561 None:intergenic
TTCAGACTGTAATCCACCTT+TGG 0.404938 6:-103206664 None:intergenic
GGATGAAGGGGTTTCCTCTT+CGG 0.405395 6:-103207594 None:intergenic
ATCTCGGTGGTGCAAGAATT+AGG 0.408707 6:-103207804 None:intergenic
TCACTAAACAAAGGGAGAAA+TGG 0.418116 6:+103207095 MsaT033949.1:CDS
CTTGAGGCTTTGAAACTGTA+TGG 0.421259 6:+103207142 MsaT033949.1:CDS
AAATTCTTTAATTGCTGGCT+TGG 0.424959 6:+103208936 MsaT033949.1:CDS
CCTTGGTACAAACTCCATAA+TGG 0.425270 6:-103208643 None:intergenic
CCTTTCTCTTCCTCCTCAGA+TGG 0.426336 6:-103207882 None:intergenic
ATCTTCATGCAGAACATATA+GGG 0.428042 6:+103207272 MsaT033949.1:intron
TTCCTCTTCGGCCGAGGAGG+AGG 0.434146 6:-103207582 None:intergenic
CTGCTCACTTGAGCTCCATC+AGG 0.436145 6:-103208571 None:intergenic
GGACTTTCAGCACTGCCATC+AGG 0.443949 6:-103207540 None:intergenic
TGTCATTCTCTGCAACTGAT+AGG 0.448195 6:-103207692 None:intergenic
TGTACTATCTGCACTTGGTT+CGG 0.448970 6:+103207731 MsaT033949.1:CDS
TCAACTGATTTGCGAGGGTA+TGG 0.453549 6:-103207615 None:intergenic
GTTCAAGGCACTAAGTCAAC+TGG 0.454976 6:+103206621 MsaT033949.1:CDS
TTTCTCCCTTTGTTTAGTGA+TGG 0.457327 6:-103207092 None:intergenic
CCGACATATGGATTCTCCTT+CGG 0.459009 6:-103208604 None:intergenic
CGAGGAGGAGGTATGTCAAT+TGG 0.460852 6:-103207570 None:intergenic
TGGATGATCTTGAGAAGGTT+GGG 0.471398 6:+103208494 MsaT033949.1:CDS
TGAATGTAGGATCAAGTTCA+AGG 0.473815 6:+103206606 MsaT033949.1:intron
AGCTTAATACTAGTGATTTG+TGG 0.477782 6:-103208382 None:intergenic
GAAGATAATAGCAAGAGAAG+AGG 0.482480 6:+103208735 MsaT033949.1:CDS
CGGAAACAACCTTGCTCCCA+AGG 0.482656 6:+103206719 MsaT033949.1:CDS
GGTGGAAAGCTGGAAGGCCT+TGG 0.485291 6:-103208660 None:intergenic
ATTTGCGAGGGTATGGATGA+AGG 0.487003 6:-103207608 None:intergenic
ATCTTCAAACAAGGCCTAAG+AGG 0.488954 6:-103208718 None:intergenic
GCACTTGGTTCGGAAGCATT+CGG 0.498985 6:+103207741 MsaT033949.1:CDS
AGGGGTTTCCTCTTCGGCCG+AGG 0.499231 6:-103207588 None:intergenic
CATGGCATGAGGTGGAAAGC+TGG 0.502566 6:-103208670 None:intergenic
TATCATACCATGGCCATAAG+TGG 0.502925 6:-103207942 None:intergenic
TACTTGGTTGCAGGTTGTGC+GGG 0.506493 6:+103207515 MsaT033949.1:intron
CGTGGCTGGCGTCAAATTGA+AGG 0.507871 6:+103207166 MsaT033949.1:CDS
TTTGGAAGATTGAGTTTCCT+CGG 0.510593 6:-103208341 None:intergenic
CAACAGGTGACAAGCTGACC+GGG 0.515360 6:-103207830 None:intergenic
ATTTGCTACAATGGAGACTA+AGG 0.515528 6:+103205300 None:intergenic
TCAACAGGTGACAAGCTGAC+CGG 0.517384 6:-103207831 None:intergenic
TGAAACTGTATGGTCGTGGC+TGG 0.519020 6:+103207152 MsaT033949.1:CDS
CCATCTGAGGAGGAAGAGAA+AGG 0.527813 6:+103207882 MsaT033949.1:CDS
CAAGCTGACCGGGTGAATCT+CGG 0.528860 6:-103207820 None:intergenic
TTAAGAATTTGATGATTGCA+TGG 0.529235 6:-103208688 None:intergenic
ATGGATGATCTTGAGAAGGT+TGG 0.536503 6:+103208493 MsaT033949.1:CDS
TTTGGTCGAACACTATCTAT+GGG 0.537064 6:+103208406 MsaT033949.1:CDS
GCAAGGTTGTTTCCGACAGA+AGG 0.537798 6:-103206711 None:intergenic
TTGCGAGGGTATGGATGAAG+GGG 0.537852 6:-103207606 None:intergenic
TTTGCGAGGGTATGGATGAA+GGG 0.538270 6:-103207607 None:intergenic
GTCCTTAAGAAATCTGGAAG+AGG 0.539236 6:+103208874 MsaT033949.1:CDS
GTATACCATCACTAAACAAA+GGG 0.540490 6:+103207087 MsaT033949.1:CDS
GTAAAACAACCTTGGGAGCA+AGG 0.542630 6:-103206728 None:intergenic
CTCAAAACCACTTATGGCCA+TGG 0.544250 6:+103207935 MsaT033949.1:CDS
TGACTCTTTCAAAGGACAGT+TGG 0.545667 6:+103207635 MsaT033949.1:CDS
ACCTCTGTACTATCTGCACT+TGG 0.545955 6:+103207726 MsaT033949.1:CDS
CTACTTGGTTGCAGGTTGTG+CGG 0.548743 6:+103207514 MsaT033949.1:intron
CTTGCTATTATCTTCAAACA+AGG 0.551156 6:-103208727 None:intergenic
AAACAAGGCCTAAGAGGCAC+AGG 0.552171 6:-103208712 None:intergenic
CTAGGCATGTGTACACCTGA+TGG 0.552985 6:+103208556 MsaT033949.1:CDS
GTCCGAGATTATTTCTTCCG+AGG 0.553467 6:+103208324 MsaT033949.1:CDS
GGTTTCCTCTTCGGCCGAGG+AGG 0.557391 6:-103207585 None:intergenic
AAATCAGTTGACTCTTTCAA+AGG 0.561001 6:+103207627 MsaT033949.1:CDS
TGAAAATGATGCTAAGTCGC+AGG 0.563551 6:+103206683 MsaT033949.1:CDS
TCCTTAAGAAATCTGGAAGA+GGG 0.563781 6:+103208875 MsaT033949.1:CDS
TTCCTCGGAAGAAATAATCT+CGG 0.576521 6:-103208326 None:intergenic
GAAGAGGAAAGCTCTTGCAC+TGG 0.577825 6:+103208751 MsaT033949.1:CDS
TACCTCCTCCTCGGCCGAAG+AGG 0.581749 6:+103207580 MsaT033949.1:CDS
CGTATACCATCACTAAACAA+AGG 0.584691 6:+103207086 MsaT033949.1:CDS
ATCGCAAACTGATTCAGTGT+TGG 0.585409 6:-103208776 None:intergenic
TGCTGGCTTGGAAGAAAGAG+AGG 0.586743 6:+103208948 MsaT033949.1:CDS
ACTGTAATCCACCTTTGGAA+TGG 0.588366 6:-103206659 None:intergenic
GGGTTCTCAGAAGTCAATGA+AGG 0.589070 6:+103208426 MsaT033949.1:CDS
CCAGACATCCAAACCATCTG+AGG 0.593425 6:+103207869 MsaT033949.1:CDS
CAGGTTGTGCGGGAACCTGA+TGG 0.598426 6:+103207525 MsaT033949.1:intron
TTGCACCACCGAGATTCACC+CGG 0.599354 6:+103207812 MsaT033949.1:CDS
CTTGATACAGAATTATCACT+AGG 0.603577 6:+103208538 MsaT033949.1:CDS
GCTTTGAAACTGTATGGTCG+TGG 0.606371 6:+103207148 MsaT033949.1:CDS
AGTAAGTGCCATTCCAAAGG+TGG 0.606494 6:+103206651 MsaT033949.1:CDS
GCATGAGGTGGAAAGCTGGA+AGG 0.615795 6:-103208666 None:intergenic
GCAACTGATAGGTTAATGGA+TGG 0.620506 6:-103207681 None:intergenic
GATGATTGCATGGCATGAGG+TGG 0.625757 6:-103208678 None:intergenic
AAGAGTCAACTGATTTGCGA+GGG 0.626425 6:-103207620 None:intergenic
GCTAGTAAGTGCCATTCCAA+AGG 0.631426 6:+103206648 MsaT033949.1:CDS
AGTGCAGATAGTACAGAGGT+TGG 0.636802 6:-103207723 None:intergenic
AAAGAGTCAACTGATTTGCG+AGG 0.637562 6:-103207621 None:intergenic
GACATCCAAACCATCTGAGG+AGG 0.638275 6:+103207872 MsaT033949.1:CDS
TGGAGCTCAAGTGAGCAGCA+TGG 0.641800 6:+103208576 MsaT033949.1:CDS
TCGCAGGATATACCTTCTGT+CGG 0.642530 6:+103206699 MsaT033949.1:CDS
CAATTGACATACCTCCTCCT+CGG 0.655187 6:+103207571 MsaT033949.1:CDS
AAGAATTAGGAGAAAGACAT+CGG 0.655270 6:-103207791 None:intergenic
TGAAATGGATGATCTTGAGA+AGG 0.659901 6:+103208489 MsaT033949.1:CDS
TTTGATGATTGCATGGCATG+AGG 0.660991 6:-103208681 None:intergenic
CCGAAGGAGAATCCATATGT+CGG 0.663355 6:+103208604 MsaT033949.1:CDS
CCATTATGGAGTTTGTACCA+AGG 0.666026 6:+103208643 MsaT033949.1:CDS
GAGCAGCATGGAACAACCGA+AGG 0.671244 6:+103208588 MsaT033949.1:CDS
CATACAGTTTCAAAGCCTCA+AGG 0.678034 6:-103207141 None:intergenic
GCTGGCTTGGAAGAAAGAGA+GGG 0.682057 6:+103208949 MsaT033949.1:CDS
AGAGCATCAAAAGTTCCTTG+AGG 0.714656 6:+103207126 MsaT033949.1:CDS
GCTGACCGGGTGAATCTCGG+TGG 0.721988 6:-103207817 None:intergenic
ACCAAGTGCAGATAGTACAG+AGG 0.725278 6:-103207727 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 103205310 103208996 103205310 ID=MsaG033949
Chr6 mRNA 103205310 103208996 103205310 ID=MsaT033949.1;Parent=MsaG033949
Chr6 exon 103205310 103205321 103205310 ID=MsaT033949.1.exon1;Parent=MsaT033949.1
Chr6 CDS 103205310 103205321 103205310 ID=cds.MsaT033949.1;Parent=MsaT033949.1
Chr6 exon 103206615 103206740 103206615 ID=MsaT033949.1.exon2;Parent=MsaT033949.1
Chr6 CDS 103206615 103206740 103206615 ID=cds.MsaT033949.1;Parent=MsaT033949.1
Chr6 exon 103207076 103207187 103207076 ID=MsaT033949.1.exon3;Parent=MsaT033949.1
Chr6 CDS 103207076 103207187 103207076 ID=cds.MsaT033949.1;Parent=MsaT033949.1
Chr6 exon 103207284 103207345 103207284 ID=MsaT033949.1.exon4;Parent=MsaT033949.1
Chr6 CDS 103207284 103207345 103207284 ID=cds.MsaT033949.1;Parent=MsaT033949.1
Chr6 exon 103207528 103207956 103207528 ID=MsaT033949.1.exon5;Parent=MsaT033949.1
Chr6 CDS 103207528 103207956 103207528 ID=cds.MsaT033949.1;Parent=MsaT033949.1
Chr6 exon 103208322 103208996 103208322 ID=MsaT033949.1.exon6;Parent=MsaT033949.1
Chr6 CDS 103208322 103208996 103208322 ID=cds.MsaT033949.1;Parent=MsaT033949.1
Gene Sequence

>MsaT033949.1

ATGGAGACTAAGGATCAAGTTCAAGGCACTAAGTCAACTGGAACAGCTAGTAAGTGCCATTCCAAAGGTGGATTACAGTCTGAAAATGATGCTAAGTCGCAGGATATACCTTCTGTCGGAAACAACCTTGCTCCCAAGGTTAGGAAACCGTATACCATCACTAAACAAAGGGAGAAATGGACCGACGAAGAGCATCAAAAGTTCCTTGAGGCTTTGAAACTGTATGGTCGTGGCTGGCGTCAAATTGAAGAACATATAGGGTCCAAAACTGCAGTTCAGATTCGAAGCCATGCTCAAAAGTTTTTCTCTAAGGTTGTGCGGGAACCTGATGGCAGTGCTGAAAGTCCTATTCAGCCAATTGACATACCTCCTCCTCGGCCGAAGAGGAAACCCCTTCATCCATACCCTCGCAAATCAGTTGACTCTTTCAAAGGACAGTTGGTCCCAAATGAATCAGAAACATCTCCATCCATTAACCTATCAGTTGCAGAGAATGACACTCAATCGCCAACCTCTGTACTATCTGCACTTGGTTCGGAAGCATTCGGCTCAGCAGCTTTTTCTGAGCAGACTAACCGATGTCTTTCTCCTAATTCTTGCACCACCGAGATTCACCCGGTCAGCTTGTCACCTGTTGAAAAAGAAAACGATTGCCAGACATCCAAACCATCTGAGGAGGAAGAGAAAGGATCTTTAGCTTCAATTCCTTTATCCACCGACTCAAAACCACTTATGGCCATGAAGTCCGAGATTATTTCTTCCGAGGAAACTCAATCTTCCAAAGAAGATGCTGCAAATATGCCACAAATCACTAGTATTAAGCTGTTTGGTCGAACACTATCTATGGGTTCTCAGAAGTCAATGAAGGATGATGACGAAAATACTAAGCTAATAGCTATCAACTCTAATGAAATGGATGATCTTGAGAAGGTTGGGCAAAAAGAGGTATCAGAGCAACTTGATACAGAATTATCACTAGGCATGTGTACACCTGATGGAGCTCAAGTGAGCAGCATGGAACAACCGAAGGAGAATCCATATGTCGGCGAATGCGCAACTTTACCATTATGGAGTTTGTACCAAGGCCTTCCAGCTTTCCACCTCATGCCATGCAATCATCAAATTCTTAATCCTGTGCCTCTTAGGCCTTGTTTGAAGATAATAGCAAGAGAAGAGGAAAGCTCTTGCACTGGTTCCAACACTGAATCAGTTTGCGATATGGAAAATCAAAGCAAGAACAACTCATCAGATACCGATGATTCTCAAACTCAAAAACATCGTCAGGAAGGAGTTGTCCTTAAGAAATCTGGAAGAGGGTTTGTTCCATATAAAAGATGTTTAGCTGAAAGAGATGAAAATTCTTTAATTGCTGGCTTGGAAGAAAGAGAGGGACAAAGAGCTCGTGTGTGTTCATAG
Protein sequence

>MsaT033949.1

METKDQVQGTKSTGTASKCHSKGGLQSENDAKSQDIPSVGNNLAPKVRKPYTITKQREKWTDEEHQKFLEALKLYGRGWRQIEEHIGSKTAVQIRSHAQKFFSKVVREPDGSAESPIQPIDIPPPRPKRKPLHPYPRKSVDSFKGQLVPNESETSPSINLSVAENDTQSPTSVLSALGSEAFGSAAFSEQTNRCLSPNSCTTEIHPVSLSPVEKENDCQTSKPSEEEEKGSLASIPLSTDSKPLMAMKSEIISSEETQSSKEDAANMPQITSIKLFGRTLSMGSQKSMKDDDENTKLIAINSNEMDDLEKVGQKEVSEQLDTELSLGMCTPDGAQVSSMEQPKENPYVGECATLPLWSLYQGLPAFHLMPCNHQILNPVPLRPCLKIIAREEESSCTGSNTESVCDMENQSKNNSSDTDDSQTQKHRQEGVVLKKSGRGFVPYKRCLAERDENSLIAGLEEREGQRARVCS*