AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025085

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025085.t1 MTR_2g038625 98.113 212 4 0 1 212 1 212 1.07e-152 422
MS.gene025085.t1 MTR_2g038580 98.113 212 4 0 1 212 1 212 1.07e-152 422
MS.gene025085.t1 MTR_4g100550 44.886 176 97 0 37 212 75 250 2.76e-42 144
MS.gene025085.t1 MTR_8g006705 61.062 113 44 0 82 194 146 258 5.24e-41 141
MS.gene025085.t1 MTR_5g014890 57.937 126 52 1 72 197 113 237 5.32e-41 140
MS.gene025085.t1 MTR_5g013010 53.077 130 61 0 70 199 124 253 9.34e-41 140
MS.gene025085.t1 MTR_7g093430 56.115 139 57 3 60 195 135 272 1.25e-40 140
MS.gene025085.t1 MTR_1g054285 56.296 135 49 3 66 195 137 266 4.18e-40 139
MS.gene025085.t1 MTR_4g097600 56.061 132 55 2 65 195 110 239 5.36e-40 138
MS.gene025085.t1 MTR_2g061030 60.870 115 42 2 82 195 200 312 8.48e-38 134
MS.gene025085.t1 MTR_1g017090 49.677 155 74 3 49 199 94 248 2.86e-36 129
MS.gene025085.t1 MTR_4g084750 50.847 118 53 1 82 194 65 182 3.77e-34 120
MS.gene025085.t1 MTR_4g126900 42.308 208 100 5 11 201 7 211 5.30e-34 121
MS.gene025085.t1 MTR_3g103590 55.906 127 53 2 69 195 133 256 1.96e-31 116
MS.gene025085.t1 MTR_5g013010 57.812 64 27 0 70 133 124 187 4.19e-16 73.9
MS.gene025085.t1 MTR_1g061660 34.091 132 84 2 40 170 18 147 1.35e-13 67.8
MS.gene025085.t1 MTR_5g039000 37.273 110 66 1 60 169 58 164 4.69e-13 66.6
MS.gene025085.t1 MTR_6g007647 42.045 88 51 0 82 169 33 120 2.16e-12 64.7
MS.gene025085.t1 MTR_6g007647 42.045 88 51 0 82 169 67 154 3.16e-12 64.3
MS.gene025085.t1 MTR_7g010020 42.268 97 52 1 79 171 77 173 4.01e-12 63.9
MS.gene025085.t1 MTR_7g103340 32.667 150 91 4 27 169 4 150 4.64e-12 63.5
MS.gene025085.t1 MTR_3g080100 42.105 95 48 1 82 169 20 114 4.64e-12 63.2
MS.gene025085.t1 MTR_5g038280 40.000 95 50 1 81 168 86 180 5.35e-12 63.9
MS.gene025085.t1 MTR_3g080100 42.105 95 48 1 82 169 59 153 6.74e-12 63.2
MS.gene025085.t1 MTR_8g089895 40.336 119 58 4 76 181 43 161 1.27e-11 62.8
MS.gene025085.t1 MTR_4g107650 40.909 88 52 0 82 169 95 182 4.04e-11 61.6
MS.gene025085.t1 MTR_8g468210 36.697 109 65 2 60 168 59 163 4.47e-11 61.2
MS.gene025085.t1 MTR_8g469430 41.053 95 49 1 81 168 88 182 4.67e-11 61.2
MS.gene025085.t1 MTR_6g011610 40.196 102 57 1 72 169 63 164 6.10e-11 60.5
MS.gene025085.t1 MTR_6g011610 40.196 102 57 1 72 169 82 183 6.31e-11 60.8
MS.gene025085.t1 MTR_3g086790 36.441 118 65 3 63 173 43 157 8.86e-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
MS.gene025085.t1 AT4G16780 49.032 155 79 0 55 209 102 256 2.16e-43 147
MS.gene025085.t1 AT4G17460 50.336 149 68 1 51 199 110 252 5.67e-42 143
MS.gene025085.t1 AT5G47370 57.627 118 50 0 82 199 130 247 3.07e-40 139
MS.gene025085.t1 AT3G60390 55.738 122 54 0 73 194 153 274 6.36e-40 139
MS.gene025085.t1 AT5G06710 56.452 124 53 1 72 195 180 302 9.38e-40 139
MS.gene025085.t1 AT4G37790 57.143 126 51 2 72 195 114 238 5.81e-39 135
MS.gene025085.t1 AT2G44910 57.895 114 48 0 82 195 163 276 1.02e-38 136
MS.gene025085.t1 AT2G22800 55.556 126 53 2 72 195 101 225 1.58e-37 132
MS.gene025085.t1 AT2G01430 54.386 114 49 1 82 195 139 249 4.35e-35 125
MS.gene025085.t1 AT1G70920 50.000 124 54 2 72 195 59 174 4.50e-29 108
MS.gene025085.t1 AT1G70920 50.000 124 54 2 72 195 29 144 4.82e-29 107
MS.gene025085.t1 AT5G06710 61.290 62 24 0 72 133 180 241 1.94e-18 81.6
MS.gene025085.t1 AT5G03790 42.574 101 58 0 70 170 65 165 1.47e-15 73.2
MS.gene025085.t1 AT2G01430 58.182 55 23 0 82 136 139 193 3.19e-14 68.9
MS.gene025085.t1 AT3G01220 32.738 168 101 3 52 212 57 219 1.70e-13 68.2
MS.gene025085.t1 AT5G03790 41.053 95 56 0 70 164 65 159 1.06e-12 64.7
MS.gene025085.t1 AT2G18550 33.333 144 89 2 69 211 48 185 1.95e-12 64.3
MS.gene025085.t1 AT4G36740 37.374 99 62 0 70 168 44 142 2.14e-12 64.3
MS.gene025085.t1 AT4G36740 37.374 99 62 0 70 168 43 141 2.22e-12 63.9
MS.gene025085.t1 AT3G01470 47.222 72 38 0 82 153 68 139 4.68e-12 63.9
MS.gene025085.t1 AT1G26960 40.909 88 52 0 82 169 71 158 1.45e-11 62.4
MS.gene025085.t1 AT2G46680 39.394 99 56 1 85 179 35 133 8.82e-11 60.1

Find 36 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATACCTTGCTCTTCTGTTC+TGG 0.227517 2.2:+49079002 None:intergenic
GTTCATCATGCAAGAAAATA+TGG 0.268795 2.2:-49078180 MS.gene025085:CDS
GATGATTGAGTTGTGTTTGA+TGG 0.272598 2.2:+49078226 None:intergenic
AATCATCTAAAGCTGCAAAT+TGG 0.315157 2.2:-49078210 MS.gene025085:CDS
CTTAATCTTAAACTTGGATT+AGG 0.319965 2.2:-49079549 MS.gene025085:CDS
CCATTGATTTGAACCATGAT+AGG 0.325695 2.2:-49079470 MS.gene025085:CDS
GGTTGATTCAAAAGAAGAAT+TGG 0.345182 2.2:-49079493 MS.gene025085:CDS
AACTAAGTGAGGAGAATCTT+AGG 0.353207 2.2:-49078291 MS.gene025085:CDS
AGCAAAGACAGGTTGAAGTT+TGG 0.373329 2.2:-49079027 MS.gene025085:CDS
TGAGCACCCGTTGTTGTCAT+TGG 0.382575 2.2:+49079371 None:intergenic
AATAACAACATCCTCCTCAT+TGG 0.419038 2.2:+49078153 None:intergenic
TCAATTCATTTGCCCTATCA+TGG 0.421387 2.2:+49079457 None:intergenic
AATTGTGCTGTGACGCTTGA+AGG 0.428719 2.2:+49079302 None:intergenic
TTTCTTGCATGATGAACAAA+TGG 0.440678 2.2:+49078186 None:intergenic
ATAACAACATCCTCCTCATT+GGG 0.441004 2.2:+49078154 None:intergenic
ACACCACCAATGACAACAAC+GGG 0.443518 2.2:-49079377 MS.gene025085:CDS
TTGGATCTTAATCTTAAACT+TGG 0.447542 2.2:-49079555 MS.gene025085:CDS
AAACAATGTGAACAAACCTT+TGG 0.458446 2.2:-49079514 MS.gene025085:CDS
ATTGAATTTAAAGCAAAGAC+AGG 0.478696 2.2:-49079038 MS.gene025085:CDS
CCTATCATGGTTCAAATCAA+TGG 0.487751 2.2:+49079470 None:intergenic
GGAGAATCTTAGGTTGAAGA+AGG 0.518622 2.2:-49078281 MS.gene025085:CDS
GCACCCGTTGTTGTCATTGG+TGG 0.522365 2.2:+49079374 None:intergenic
GAACTGCGTGCATTAAAAGT+TGG 0.525263 2.2:-49078250 MS.gene025085:CDS
CATTGATTTGAACCATGATA+GGG 0.530963 2.2:-49079469 MS.gene025085:CDS
AATCTAACTCTATGGTGCTG+TGG 0.578396 2.2:+49078122 None:intergenic
ACGGGTGCTCAAAGAAATTG+AGG 0.587563 2.2:-49079359 MS.gene025085:CDS
TCATCACATGGCATGCACGT+TGG 0.602607 2.2:-49079574 MS.gene025085:CDS
AGGTGAACTGTATATACTTG+AGG 0.616263 2.2:-49078327 MS.gene025085:CDS
GAAAATATGGAAGCCCAATG+AGG 0.640653 2.2:-49078167 MS.gene025085:CDS
GACACCACCAATGACAACAA+CGG 0.643008 2.2:-49079378 MS.gene025085:CDS
GGTTCCAGAACAGAAGAGCA+AGG 0.646687 2.2:-49079006 MS.gene025085:intron
AATATGGAAGCCCAATGAGG+AGG 0.651470 2.2:-49078164 MS.gene025085:CDS
ATGATCTTGATCATCATCCA+TGG 0.675243 2.2:+49079593 None:intergenic
ATGTCATGAGAAACTAAGTG+AGG 0.678157 2.2:-49078302 MS.gene025085:CDS
TGATGATCAAGATCATCACA+TGG 0.696569 2.2:-49079586 MS.gene025085:CDS
GACTAAGCTGAAACAAACAG+AGG 0.748545 2.2:-49078347 MS.gene025085:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTAATTATTAATTTTA+TGG - chr2.2:49078506-49078525 MS.gene025085:intron 0.0%
!! TTTCATTTATCAAAATTTAA+GGG - chr2.2:49078600-49078619 MS.gene025085:intron 10.0%
!!! TTTTATTATTTTTTCTTTCA+TGG - chr2.2:49078780-49078799 MS.gene025085:intron 10.0%
!!! TTTTCATTTATCAAAATTTA+AGG - chr2.2:49078599-49078618 MS.gene025085:intron 10.0%
!! ATAGTCAACAAATAATAAAT+TGG + chr2.2:49078995-49079014 None:intergenic 15.0%
!! ATTCAAAGAGTAATATATTA+CGG + chr2.2:49078449-49078468 None:intergenic 15.0%
!!! GAATTGATTTTTTTTTGTTT+CGG - chr2.2:49078622-49078641 MS.gene025085:intron 15.0%
!!! TTTCAAAAAATAATTTGTGT+TGG - chr2.2:49078961-49078980 MS.gene025085:intron 15.0%
!!! AATTATACAATTGACTTTTC+AGG - chr2.2:49079352-49079371 MS.gene025085:CDS 20.0%
!!! ATGAAATTTTATAACTTGAG+TGG + chr2.2:49079100-49079119 None:intergenic 20.0%
!!! ATGAATCATTTGGTTTAATT+GGG - chr2.2:49078739-49078758 MS.gene025085:intron 20.0%
!!! TATGAATCATTTGGTTTAAT+TGG - chr2.2:49078738-49078757 MS.gene025085:intron 20.0%
! CTTAATCTTAAACTTGGATT+AGG - chr2.2:49078172-49078191 MS.gene025085:CDS 25.0%
! TTGACAGTTATATGAAATAG+AGG - chr2.2:49079228-49079247 MS.gene025085:intron 25.0%
! TTGGATCTTAATCTTAAACT+TGG - chr2.2:49078166-49078185 MS.gene025085:CDS 25.0%
!! ATTGAATTTAAAGCAAAGAC+AGG - chr2.2:49078683-49078702 MS.gene025085:intron 25.0%
!! TTATGGAAGCTAATTTTGTA+TGG - chr2.2:49078523-49078542 MS.gene025085:intron 25.0%
AAACAATGTGAACAAACCTT+TGG - chr2.2:49078207-49078226 MS.gene025085:CDS 30.0%
GTTCATCATGCAAGAAAATA+TGG - chr2.2:49079541-49079560 MS.gene025085:CDS 30.0%
TTTCTTGCATGATGAACAAA+TGG + chr2.2:49079538-49079557 None:intergenic 30.0%
! AATCATCTAAAGCTGCAAAT+TGG - chr2.2:49079511-49079530 MS.gene025085:CDS 30.0%
! GGTTGATTCAAAAGAAGAAT+TGG - chr2.2:49078228-49078247 MS.gene025085:CDS 30.0%
! TCTTCTTTTGAATCAACCAA+AGG + chr2.2:49078226-49078245 None:intergenic 30.0%
!! CATTGATTTGAACCATGATA+GGG - chr2.2:49078252-49078271 MS.gene025085:CDS 30.0%
AACTAAGTGAGGAGAATCTT+AGG - chr2.2:49079430-49079449 MS.gene025085:CDS 35.0%
AATAACAACATCCTCCTCAT+TGG + chr2.2:49079571-49079590 None:intergenic 35.0%
AATTTCTGACGTAGTAGTCA+GGG + chr2.2:49078925-49078944 None:intergenic 35.0%
AGAGCAAGGTATGAATCATT+TGG - chr2.2:49078729-49078748 MS.gene025085:intron 35.0%
AGGTGAACTGTATATACTTG+AGG - chr2.2:49079394-49079413 MS.gene025085:CDS 35.0%
ATAACAACATCCTCCTCATT+GGG + chr2.2:49079570-49079589 None:intergenic 35.0%
ATGTCATGAGAAACTAAGTG+AGG - chr2.2:49079419-49079438 MS.gene025085:CDS 35.0%
CCTATCATGGTTCAAATCAA+TGG + chr2.2:49078254-49078273 None:intergenic 35.0%
GACTGTTGAACACTACAATT+TGG - chr2.2:49079277-49079296 MS.gene025085:intron 35.0%
TAGTAGTCAGGGTAAAATGA+TGG + chr2.2:49078914-49078933 None:intergenic 35.0%
TCAATTCATTTGCCCTATCA+TGG + chr2.2:49078267-49078286 None:intergenic 35.0%
TGATCAGTTGGATTTCTTCT+TGG - chr2.2:49078858-49078877 MS.gene025085:intron 35.0%
TGATGATCAAGATCATCACA+TGG - chr2.2:49078135-49078154 MS.gene025085:CDS 35.0%
TTTACATGCAGGCTCAAAAA+CGG - chr2.2:49078646-49078665 MS.gene025085:intron 35.0%
! ACTTTTCACTTCTGATCAGT+TGG - chr2.2:49078846-49078865 MS.gene025085:intron 35.0%
! GATGATTGAGTTGTGTTTGA+TGG + chr2.2:49079498-49079517 None:intergenic 35.0%
! TTTGTTTCGGTTTTACATGC+AGG - chr2.2:49078635-49078654 MS.gene025085:intron 35.0%
!! CCATTGATTTGAACCATGAT+AGG - chr2.2:49078251-49078270 MS.gene025085:CDS 35.0%
GAAAATATGGAAGCCCAATG+AGG - chr2.2:49079554-49079573 MS.gene025085:CDS 40.0%
GAACTGCGTGCATTAAAAGT+TGG - chr2.2:49079471-49079490 MS.gene025085:CDS 40.0%
GAATTTCTGACGTAGTAGTC+AGG + chr2.2:49078926-49078945 None:intergenic 40.0%
GACTAAGCTGAAACAAACAG+AGG - chr2.2:49079374-49079393 MS.gene025085:CDS 40.0%
TTACATGCAGGCTCAAAAAC+GGG - chr2.2:49078647-49078666 MS.gene025085:intron 40.0%
! AGCAAAGACAGGTTGAAGTT+TGG - chr2.2:49078694-49078713 MS.gene025085:intron 40.0%
!! GGAGAATCTTAGGTTGAAGA+AGG - chr2.2:49079440-49079459 MS.gene025085:CDS 40.0%
!!! CTTGAAGGCATTTTCAAGCT+TGG + chr2.2:49078407-49078426 None:intergenic 40.0%
AATATGGAAGCCCAATGAGG+AGG - chr2.2:49079557-49079576 MS.gene025085:CDS 45.0%
AATTGTGCTGTGACGCTTGA+AGG + chr2.2:49078422-49078441 None:intergenic 45.0%
ACACCACCAATGACAACAAC+GGG - chr2.2:49078344-49078363 MS.gene025085:CDS 45.0%
ACGGGTGCTCAAAGAAATTG+AGG - chr2.2:49078362-49078381 MS.gene025085:intron 45.0%
CATACCTTGCTCTTCTGTTC+TGG + chr2.2:49078722-49078741 None:intergenic 45.0%
GACACCACCAATGACAACAA+CGG - chr2.2:49078343-49078362 MS.gene025085:CDS 45.0%
GGTTCCAGAACAGAAGAGCA+AGG - chr2.2:49078715-49078734 MS.gene025085:intron 50.0%
TCATCACATGGCATGCACGT+TGG - chr2.2:49078147-49078166 MS.gene025085:CDS 50.0%
TGAGCACCCGTTGTTGTCAT+TGG + chr2.2:49078353-49078372 None:intergenic 50.0%
! TCAAAAACGGGCACTTGCTG+AGG - chr2.2:49078659-49078678 MS.gene025085:intron 50.0%
GCACCCGTTGTTGTCATTGG+TGG + chr2.2:49078350-49078369 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 49078130 49079613 49078130 ID=MS.gene025085
chr2.2 mRNA 49078130 49079613 49078130 ID=MS.gene025085.t1;Parent=MS.gene025085
chr2.2 exon 49079296 49079613 49079296 ID=MS.gene025085.t1.exon1;Parent=MS.gene025085.t1
chr2.2 CDS 49079296 49079613 49079296 ID=cds.MS.gene025085.t1;Parent=MS.gene025085.t1
chr2.2 exon 49079007 49079086 49079007 ID=MS.gene025085.t1.exon2;Parent=MS.gene025085.t1
chr2.2 CDS 49079007 49079086 49079007 ID=cds.MS.gene025085.t1;Parent=MS.gene025085.t1
chr2.2 exon 49078130 49078369 49078130 ID=MS.gene025085.t1.exon3;Parent=MS.gene025085.t1
chr2.2 CDS 49078130 49078369 49078130 ID=cds.MS.gene025085.t1;Parent=MS.gene025085.t1
Gene Sequence

>MS.gene025085

ATGGATGATGATCAAGATCATCACATGGCATGCACGTTGGATCTTAATCTTAAACTTGGATTAGGAAGTTATGTGCAAAACAATGTGAACAAACCTTTGGTTGATTCAAAAGAAGAATTGGCCATTGATTTGAACCATGATAGGGCAAATGAATTGAGTTTGAAGAGAGTGCATGAAGAACAAGCAAACACAGTTGAAGAAGAAATTGCTATTGACACCACCAATGACAACAACGGGTGCTCAAAGAAATTGAGGCTTACAACTGAGCAATCAACCAAGCTTGAAAATGCCTTCAAGCGTCACAGCACAATTAACACCGTAATATATTACTCTTTGAATTTTCTTTTCATTTTTCATTAGCTTGAAATTTTTTTTTTTTATTAATTATTAATTTTATGGAAGCTAATTTTGTATGGTTTATAATTTATCATGTATTTTATTCGTTACTGTTTTATATATCATTGTTAAATTTTCATTTATCAAAATTTAAGGGAATTGATTTTTTTTTGTTTCGGTTTTACATGCAGGCTCAAAAACGGGCACTTGCTGAGGAATTGAATTTAAAGCAAAGACAGGTTGAAGTTTGGTTCCAGAACAGAAGAGCAAGGTATGAATCATTTGGTTTAATTGGGTCATTTCAATTTTAAAATTTTTATTATTTTTTCTTTCATGGCTCAATATTTGTTTGATCTTAATCTAACATATTTTCTTCATCAACTTTTCACTTCTGATCAGTTGGATTTCTTCTTGGTTTTTTTTTTTTTTTTTTTTTTAATGTGTTCCATCATTTTACCCTGACTACTACGTCAGAAATTCTTGACAAAATTGTCTTTTCAAAAAATAATTTGTGTTGGTAAATCATCCAATTTATTATTTGTTGACTATTTCAAAGAGATATATCTCGTTTTTGCAAAAATAATTTATCTCAAAAAAGCTAATTTTTAATGTAATTTTAATATTATGTATACCACTCAAGTTATAAAATTTCATATTGTATTTATGATATTAAAAATACATCAATAATTAATAATAATATTTTTATAAAATACTATTATCTTTCATTTATCATTTTTCTTATTCTGTGTGAAGTGAACAAAGTTGACAGTTATATGAAATAGAGGATAAAAAATGTATTTTTTATTGATTAGACTGTTGAACACTACAATTTGGAGACTAAAAATTGAATATTTTTTGTTTGACTTGACTATACTACTTTCTAAGCAATTATACAATTGACTTTTCAGGACTAAGCTGAAACAAACAGAGGTGAACTGTATATACTTGAGGAAATGTCATGAGAAACTAAGTGAGGAGAATCTTAGGTTGAAGAAGGAATTAGAAGAACTGCGTGCATTAAAAGTTGGACCATCAAACACAACTCAATCATCTAAAGCTGCAAATTGGACCATTTGTTCATCATGCAAGAAAATATGGAAGCCCAATGAGGAGGATGTTGTTATTAAGAGCAGCCACAGCACCATAGA
Protein sequence

>MS.gene025085.t1

MDDDQDHHMACTLDLNLKLGLGSYVQNNVNKPLVDSKEELAIDLNHDRANELSLKRVHEEQANTVEEEIAIDTTNDNNGCSKKLRLTTEQSTKLENAFKRHSTINTAQKRALAEELNLKQRQVEVWFQNRRARTKLKQTEVNCIYLRKCHEKLSEENLRLKKELEELRALKVGPSNTTQSSKAANWTICSSCKKIWKPNEEDVVIKSSHSTI