AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene041071


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene041071.t1 MTR_5g017140 80.916 131 24 1 24 153 144 274 6.02e-74 224
MS.gene041071.t1 MTR_5g017110 64.662 133 44 1 24 153 145 277 2.53e-53 172
MS.gene041071.t1 MTR_0189s0010 59.375 128 47 2 24 148 162 287 3.21e-48 159
MS.gene041071.t1 MTR_0154s0020 57.812 128 49 2 24 148 142 267 4.20e-47 155
MS.gene041071.t1 MTR_0154s0040 57.480 127 49 2 24 147 142 266 2.69e-46 154
MS.gene041071.t1 MTR_2g023890 39.344 122 69 3 26 146 142 259 6.25e-23 92.8
MS.gene041071.t1 MTR_4g049730 40.000 120 68 2 26 144 136 252 6.49e-23 93.2
MS.gene041071.t1 MTR_2g088020 42.017 119 64 2 24 141 142 256 1.73e-22 92.0
MS.gene041071.t1 MTR_3g096230 36.364 121 75 2 24 143 383 502 2.29e-21 89.7
MS.gene041071.t1 MTR_3g096230 36.364 121 75 2 24 143 383 502 3.54e-21 89.4
MS.gene041071.t1 MTR_3g073250 38.843 121 69 3 24 142 407 524 4.15e-20 85.9
MS.gene041071.t1 MTR_2g005290 33.333 141 71 4 24 141 148 288 1.48e-19 84.0
MS.gene041071.t1 MTR_5g059880 39.167 120 68 3 24 141 329 445 1.58e-19 84.3
MS.gene041071.t1 MTR_8g098425 36.975 119 73 2 24 141 547 664 1.64e-19 84.3
MS.gene041071.t1 MTR_1g100250 37.815 119 72 2 24 141 550 667 2.34e-19 84.0
MS.gene041071.t1 MTR_5g071560 41.667 120 67 2 22 141 147 263 3.73e-19 82.8
MS.gene041071.t1 MTR_8g093730 32.558 129 85 2 24 151 438 565 7.59e-19 82.4
MS.gene041071.t1 MTR_0685s0020 39.496 119 67 3 24 140 128 243 3.31e-18 79.0
MS.gene041071.t1 MTR_5g059940 38.017 121 70 3 24 142 262 379 3.36e-18 80.1
MS.gene041071.t1 MTR_5g060350 38.333 120 69 3 24 141 458 574 4.89e-18 80.1
MS.gene041071.t1 MTR_7g113490 36.364 99 61 1 46 142 234 332 6.85e-18 79.7
MS.gene041071.t1 MTR_1g105290 39.394 99 58 1 46 142 221 319 1.31e-17 79.0
MS.gene041071.t1 MTR_1g105290 39.394 99 58 1 46 142 221 319 1.32e-17 79.0
MS.gene041071.t1 MTR_1g105290 39.394 99 58 1 46 142 221 319 2.12e-17 78.2
MS.gene041071.t1 MTR_4g094415 37.500 120 70 3 24 141 301 417 2.82e-17 77.8
MS.gene041071.t1 MTR_3g101210 33.577 137 81 4 21 150 444 577 5.13e-17 77.4
MS.gene041071.t1 MTR_5g017890 33.083 133 79 3 21 146 509 638 5.16e-17 77.4
MS.gene041071.t1 MTR_3g101210 33.577 137 81 4 21 150 444 577 6.20e-17 77.0
MS.gene041071.t1 MTR_4g074875 31.818 132 89 1 16 147 150 280 3.13e-14 69.3
MS.gene041071.t1 MTR_5g059910 36.364 121 72 3 24 142 268 385 3.20e-14 68.9
MS.gene041071.t1 MTR_4g074875 31.818 132 89 1 16 147 150 280 3.22e-14 69.3
MS.gene041071.t1 MTR_4g075410 31.250 128 87 1 16 143 150 276 1.05e-13 67.8
MS.gene041071.t1 MTR_4g075410 31.250 128 87 1 16 143 150 276 1.06e-13 67.8
MS.gene041071.t1 MTR_6g005210 37.383 107 60 3 47 149 245 348 2.05e-12 63.9
MS.gene041071.t1 MTR_4g005830 32.168 143 82 5 9 141 202 339 3.65e-12 63.2
MS.gene041071.t1 MTR_6g090470 31.818 132 79 2 24 146 205 334 4.53e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene041071.t1 AT3G50310 53.077 130 54 3 24 146 145 274 1.91e-39 136
MS.gene041071.t1 AT5G67080 50.365 137 58 4 24 152 147 281 1.99e-39 136
MS.gene041071.t1 AT4G36950 50.806 124 54 2 24 142 145 266 2.22e-36 128
MS.gene041071.t1 AT5G55090 42.308 130 72 2 23 151 139 266 6.04e-27 104
MS.gene041071.t1 AT5G55090 42.308 130 72 2 23 151 201 328 8.19e-27 105
MS.gene041071.t1 AT1G07150 38.571 140 82 3 9 148 137 272 7.99e-26 102
MS.gene041071.t1 AT1G07150 39.716 141 79 5 9 148 151 286 8.89e-26 102
MS.gene041071.t1 AT1G05100 40.650 123 68 2 26 145 147 267 9.99e-24 94.7
MS.gene041071.t1 AT2G30040 43.119 109 61 1 46 154 176 283 1.34e-23 95.9
MS.gene041071.t1 AT4G26890 42.000 100 57 1 47 145 158 257 4.35e-23 94.4
MS.gene041071.t1 AT3G46140 38.356 146 82 5 4 141 224 369 2.00e-21 89.0
MS.gene041071.t1 AT2G32510 38.931 131 71 3 26 149 142 270 3.11e-21 88.6
MS.gene041071.t1 AT1G63700 36.885 122 75 2 24 144 539 659 2.84e-20 86.7
MS.gene041071.t1 AT1G63700 36.885 122 75 2 24 144 539 659 2.84e-20 86.7
MS.gene041071.t1 AT3G46160 34.783 138 85 3 9 141 195 332 4.89e-19 82.8
MS.gene041071.t1 AT1G54960 36.364 110 69 1 46 154 234 343 3.12e-18 80.9
MS.gene041071.t1 AT1G54960 36.364 110 69 1 46 154 234 343 3.12e-18 80.9
MS.gene041071.t1 AT4G08500 38.017 121 69 3 24 141 470 587 4.54e-18 80.5
MS.gene041071.t1 AT3G45670 34.641 153 92 3 4 148 220 372 5.31e-18 79.7
MS.gene041071.t1 AT1G09000 38.532 109 66 1 46 153 235 343 9.90e-18 79.3
MS.gene041071.t1 AT1G09000 38.532 109 66 1 46 153 235 343 1.08e-17 79.3
MS.gene041071.t1 AT3G06030 36.735 98 61 1 46 142 234 331 1.65e-17 78.6
MS.gene041071.t1 AT1G53570 34.615 104 67 1 46 148 374 477 2.31e-17 78.2
MS.gene041071.t1 AT1G53570 34.615 104 67 1 46 148 374 477 2.33e-17 78.2
MS.gene041071.t1 AT1G53570 34.615 104 67 1 46 148 374 477 2.71e-17 78.2
MS.gene041071.t1 AT1G53570 34.615 104 67 1 46 148 374 477 2.76e-17 78.2
MS.gene041071.t1 AT1G53570 34.615 104 67 1 46 148 374 477 2.76e-17 78.2
MS.gene041071.t1 AT1G53570 34.615 104 67 1 46 148 374 477 2.76e-17 78.2
MS.gene041071.t1 AT1G53570 34.615 104 67 1 46 148 348 451 3.14e-17 77.8
MS.gene041071.t1 AT4G12020 36.134 119 73 2 24 142 1688 1803 6.77e-17 77.0
MS.gene041071.t1 AT4G12020 36.134 119 73 2 24 142 1763 1878 8.63e-17 76.6
MS.gene041071.t1 AT4G12020 36.134 119 73 2 24 142 1755 1870 2.52e-16 75.5
MS.gene041071.t1 AT4G04632 38.776 98 56 2 52 145 1 98 3.63e-16 70.1
MS.gene041071.t1 AT2G42550 33.803 142 86 4 4 141 137 274 1.06e-15 73.2
MS.gene041071.t1 AT5G66850 31.538 130 79 3 21 143 483 609 1.64e-15 73.2
MS.gene041071.t1 AT4G08480 36.066 122 70 4 24 141 638 755 1.82e-15 72.8
MS.gene041071.t1 AT5G66850 31.538 130 79 3 21 143 483 609 2.12e-15 72.8
MS.gene041071.t1 AT3G45790 38.679 106 60 3 26 126 249 354 1.25e-14 70.1
MS.gene041071.t1 AT4G08470 33.884 121 74 3 24 141 358 475 1.45e-14 70.1
MS.gene041071.t1 AT4G08470 33.884 121 74 3 24 141 440 557 1.45e-14 70.1
MS.gene041071.t1 AT2G41930 33.588 131 69 5 26 146 159 281 2.57e-14 69.3
MS.gene041071.t1 AT4G12020 35.294 119 58 3 24 142 1755 1854 4.55e-14 68.9
MS.gene041071.t1 AT4G12020 35.294 119 58 3 24 142 1763 1862 4.60e-14 68.9
MS.gene041071.t1 AT3G13530 31.250 128 87 1 16 143 150 276 1.62e-13 67.4
MS.gene041071.t1 AT5G40440 40.196 102 56 2 47 145 162 261 3.01e-13 66.2
MS.gene041071.t1 AT3G07980 32.031 128 86 1 16 143 150 276 3.12e-13 66.6
MS.gene041071.t1 AT3G07980 32.031 128 86 1 16 143 150 276 3.13e-13 66.6
MS.gene041071.t1 AT5G40440 39.623 106 59 2 47 149 226 329 3.22e-13 66.2
MS.gene041071.t1 AT5G40440 39.623 106 59 2 47 149 226 329 3.22e-13 66.2
MS.gene041071.t1 AT5G40440 39.623 106 59 2 47 149 226 329 3.22e-13 66.2
MS.gene041071.t1 AT5G40440 39.623 106 59 2 47 149 244 347 3.25e-13 66.2
MS.gene041071.t1 AT5G40440 39.623 106 59 2 47 149 244 347 3.25e-13 66.2
MS.gene041071.t1 AT5G12090 28.378 148 100 4 9 153 161 305 3.48e-13 66.2
MS.gene041071.t1 AT2G05060 30.469 128 77 4 26 147 161 282 4.15e-11 60.1
MS.gene041071.t1 AT5G27510 31.148 122 78 3 24 141 150 269 5.38e-11 59.7

Find 37 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAATCGCCGACGGATATA+TGG 0.243489 5.2:-9285627 MS.gene041071:CDS
CCTTCTCGTAATAATTCATC+TGG 0.379686 5.2:+9285493 None:intergenic
GCTATTGTGGAAATGGTTAC+TGG 0.394847 5.2:-9285592 MS.gene041071:CDS
TTAAGGATCCTTTGAGAAGA+TGG 0.405417 5.2:-9285444 MS.gene041071:CDS
ACACTATCATTCACCGCTTC+TGG 0.411589 5.2:+9285652 None:intergenic
TGATGTTGACGATTCGAATT+GGG 0.421148 5.2:-9285540 MS.gene041071:CDS
TCTTGAAAAGTGTTTCGTTA+AGG 0.422240 5.2:-9285461 MS.gene041071:CDS
TTGATGTTGACGATTCGAAT+TGG 0.426586 5.2:-9285541 MS.gene041071:CDS
TGGTTGCGCTATTGTGGAAA+TGG 0.430722 5.2:-9285599 MS.gene041071:CDS
TGAATCGCCGACGGATATAT+GGG 0.431895 5.2:-9285626 MS.gene041071:CDS
GCTTCTGGTGACATAATTAC+CGG 0.459669 5.2:+9285667 None:intergenic
TTGACGATTCGAATTGGGGT+TGG 0.467699 5.2:-9285535 MS.gene041071:CDS
GGCTCTTGGTTGCGCTATTG+TGG 0.495111 5.2:-9285605 MS.gene041071:CDS
CCGACGGATATATGGGCTCT+TGG 0.500419 5.2:-9285619 MS.gene041071:CDS
CAGATGAATTATTACGAGAA+GGG 0.520167 5.2:-9285492 MS.gene041071:CDS
GAACGACAGTGGTGAGCTCT+CGG 0.525648 5.2:-9285888 MS.gene041071:CDS
CCAGATGAATTATTACGAGA+AGG 0.525954 5.2:-9285493 MS.gene041071:CDS
TTTCTAGAATATGTCAGTGG+TGG 0.546933 5.2:-9285932 None:intergenic
GGTAATTATGTCACCAGAAG+CGG 0.557800 5.2:-9285665 MS.gene041071:CDS
GGTGAAAAGTGGCGATCAAG+AGG 0.575193 5.2:-9285694 MS.gene041071:CDS
GTTGTAACAGAGTTAAGTTG+AGG 0.584853 5.2:-9285367 None:intergenic
GGGTTGAACAAGGTGAAAAG+TGG 0.592877 5.2:-9285705 MS.gene041071:CDS
TCAGTCTTGCGAAAGAGACA+AGG 0.595495 5.2:-9285726 MS.gene041071:CDS
GATGTTGACGATTCGAATTG+GGG 0.607028 5.2:-9285539 MS.gene041071:CDS
GTGGCGATCAAGAGGAACTC+CGG 0.608502 5.2:-9285686 MS.gene041071:CDS
TCTATCGTCCATCTTCTCAA+AGG 0.609523 5.2:+9285436 None:intergenic
CAGTCTTGCGAAAGAGACAA+GGG 0.612424 5.2:-9285725 MS.gene041071:CDS
ACTGTCGTTCTCGAGTTGAT+CGG 0.619509 5.2:+9285901 None:intergenic
ACCTCGTATAACGACTAATG+AGG 0.627651 5.2:+9285861 None:intergenic
AGAATCCGCATGGAATGTGT+CGG 0.631308 5.2:-9285569 MS.gene041071:CDS
TGGTTACTGGAGAATCCGCA+TGG 0.636768 5.2:-9285579 MS.gene041071:CDS
CCAAGAGCCCATATATCCGT+CGG 0.644209 5.2:+9285619 None:intergenic
GATCAACTCGAGAACGACAG+TGG 0.656688 5.2:-9285899 MS.gene041071:CDS
AAAGAGACAAGGGTTGAACA+AGG 0.656891 5.2:-9285715 MS.gene041071:CDS
ACCTCATTAGTCGTTATACG+AGG 0.719200 5.2:-9285862 MS.gene041071:intron
TAGTGTGTATGAATCGCCGA+CGG 0.726925 5.2:-9285635 MS.gene041071:CDS
CATATCCGACACATTCCATG+CGG 0.747815 5.2:+9285564 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAGTATATTCACAAAAAA+GGG - chr5.2:9285468-9285487 MS.gene041071:CDS 20.0%
!!! AATAATTCATCTGGAATTTT+TGG + chr5.2:9285792-9285811 None:intergenic 20.0%
! CTCAAGTATATTCACAAAAA+AGG - chr5.2:9285467-9285486 MS.gene041071:CDS 25.0%
!! AACTGAAACATTTTCAACAT+CGG + chr5.2:9285907-9285926 None:intergenic 25.0%
CAGATGAATTATTACGAGAA+GGG - chr5.2:9285799-9285818 MS.gene041071:intron 30.0%
! TTTTCAACATCGGAGATAAA+CGG + chr5.2:9285897-9285916 None:intergenic 30.0%
!! TCTTGAAAAGTGTTTCGTTA+AGG - chr5.2:9285830-9285849 MS.gene041071:intron 30.0%
AACATTCTCGTATTCGAGAA+TGG - chr5.2:9285522-9285541 MS.gene041071:CDS 35.0%
ATTCTCGAATACGAGAATGT+TGG + chr5.2:9285523-9285542 None:intergenic 35.0%
CCAGATGAATTATTACGAGA+AGG - chr5.2:9285798-9285817 MS.gene041071:intron 35.0%
CCTTCTCGTAATAATTCATC+TGG + chr5.2:9285801-9285820 None:intergenic 35.0%
TGATGTTGACGATTCGAATT+GGG - chr5.2:9285751-9285770 MS.gene041071:intron 35.0%
TTCTCGAATACGAGAATGTT+GGG + chr5.2:9285522-9285541 None:intergenic 35.0%
TTGATGTTGACGATTCGAAT+TGG - chr5.2:9285750-9285769 MS.gene041071:intron 35.0%
! TGTTCATTGCGATTTGAAGT+TGG - chr5.2:9285493-9285512 MS.gene041071:CDS 35.0%
! TTAAGGATCCTTTGAGAAGA+TGG - chr5.2:9285847-9285866 MS.gene041071:intron 35.0%
AAAGAGACAAGGGTTGAACA+AGG - chr5.2:9285576-9285595 MS.gene041071:CDS 40.0%
ACCTCATTAGTCGTTATACG+AGG - chr5.2:9285429-9285448 MS.gene041071:CDS 40.0%
ACCTCGTATAACGACTAATG+AGG + chr5.2:9285433-9285452 None:intergenic 40.0%
CATTAGTCGTTATACGAGGT+CGG - chr5.2:9285433-9285452 MS.gene041071:CDS 40.0%
GATGTTGACGATTCGAATTG+GGG - chr5.2:9285752-9285771 MS.gene041071:intron 40.0%
GCTATTGTGGAAATGGTTAC+TGG - chr5.2:9285699-9285718 MS.gene041071:CDS 40.0%
GCTTCTGGTGACATAATTAC+CGG + chr5.2:9285627-9285646 None:intergenic 40.0%
GGTAATTATGTCACCAGAAG+CGG - chr5.2:9285626-9285645 MS.gene041071:CDS 40.0%
TCTATCGTCCATCTTCTCAA+AGG + chr5.2:9285858-9285877 None:intergenic 40.0%
ACACTATCATTCACCGCTTC+TGG + chr5.2:9285642-9285661 None:intergenic 45.0%
AGAATCCGCATGGAATGTGT+CGG - chr5.2:9285722-9285741 MS.gene041071:CDS 45.0%
ATGAATCGCCGACGGATATA+TGG - chr5.2:9285664-9285683 MS.gene041071:CDS 45.0%
CAGTCTTGCGAAAGAGACAA+GGG - chr5.2:9285566-9285585 MS.gene041071:CDS 45.0%
CATATCCGACACATTCCATG+CGG + chr5.2:9285730-9285749 None:intergenic 45.0%
GGGTTGAACAAGGTGAAAAG+TGG - chr5.2:9285586-9285605 MS.gene041071:CDS 45.0%
TAGTGTGTATGAATCGCCGA+CGG - chr5.2:9285656-9285675 MS.gene041071:CDS 45.0%
TATACGAGGTCGGTTGTTGA+AGG - chr5.2:9285443-9285462 MS.gene041071:CDS 45.0%
TCAGTCTTGCGAAAGAGACA+AGG - chr5.2:9285565-9285584 MS.gene041071:CDS 45.0%
TGAATCGCCGACGGATATAT+GGG - chr5.2:9285665-9285684 MS.gene041071:CDS 45.0%
TGGTTGCGCTATTGTGGAAA+TGG - chr5.2:9285692-9285711 MS.gene041071:CDS 45.0%
TTGACGATTCGAATTGGGGT+TGG - chr5.2:9285756-9285775 MS.gene041071:intron 45.0%
!! ACTGTCGTTCTCGAGTTGAT+CGG + chr5.2:9285393-9285412 None:intergenic 45.0%
CCAAGAGCCCATATATCCGT+CGG + chr5.2:9285675-9285694 None:intergenic 50.0%
GATCAACTCGAGAACGACAG+TGG - chr5.2:9285392-9285411 MS.gene041071:CDS 50.0%
GGTGAAAAGTGGCGATCAAG+AGG - chr5.2:9285597-9285616 MS.gene041071:CDS 50.0%
TGGTTACTGGAGAATCCGCA+TGG - chr5.2:9285712-9285731 MS.gene041071:CDS 50.0%
CCGACGGATATATGGGCTCT+TGG - chr5.2:9285672-9285691 MS.gene041071:CDS 55.0%
GAACGACAGTGGTGAGCTCT+CGG - chr5.2:9285403-9285422 MS.gene041071:CDS 55.0%
GGCTCTTGGTTGCGCTATTG+TGG - chr5.2:9285686-9285705 MS.gene041071:CDS 55.0%
GTGGCGATCAAGAGGAACTC+CGG - chr5.2:9285605-9285624 MS.gene041071:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 9285369 9285944 9285369 ID=MS.gene041071
chr5.2 mRNA 9285369 9285944 9285369 ID=MS.gene041071.t1;Parent=MS.gene041071
chr5.2 exon 9285863 9285944 9285863 ID=MS.gene041071.t1.exon1;Parent=MS.gene041071.t1
chr5.2 CDS 9285863 9285944 9285863 ID=cds.MS.gene041071.t1;Parent=MS.gene041071.t1
chr5.2 exon 9285369 9285751 9285369 ID=MS.gene041071.t1.exon2;Parent=MS.gene041071.t1
chr5.2 CDS 9285369 9285751 9285369 ID=cds.MS.gene041071.t1;Parent=MS.gene041071.t1
Gene Sequence

>MS.gene041071

ATGTCAGTGGTGGAACTCTCTCCGATCAACTCGAGAACGACAGTGGTGAGCTCTCGGAGAACCTCATTAGTCGTTATACGAGGTCGGTTGTTGAAGGACTCAAGTATATTCACAAAAAAGGGTTTGTTCATTGCGATTTGAAGTTGGTTGCCCAACATTCTCGTATTCGAGAATGGAAACATTAAAATTTCAGATTTCAGTCTTGCGAAAGAGACAAGGGTTGAACAAGGTGAAAAGTGGCGATCAAGAGGAACTCCGGTAATTATGTCACCAGAAGCGGTGAATGATAGTGTGTATGAATCGCCGACGGATATATGGGCTCTTGGTTGCGCTATTGTGGAAATGGTTACTGGAGAATCCGCATGGAATGTGTCGGATATGTTGATGTTGACGATTCGAATTGGGGTTGGAGAAGAATTACCAAAAATTCCAGATGAATTATTACGAGAAGGGATAGATTTTCTTGAAAAGTGTTTCGTTAAGGATCCTTTGAGAAGATGGACGATAGATCTGCTTTTGAAACATCCGTTTATCTCCGATGTTGAAAATGTTTCAGTTGTAACAGAGTTAAGTTGA

Protein sequence

>MS.gene041071.t1

MSVVELSPINSRTTVVSSRRTSLVVIRDFSLAKETRVEQGEKWRSRGTPVIMSPEAVNDSVYESPTDIWALGCAIVEMVTGESAWNVSDMLMLTIRIGVGEELPKIPDELLREGIDFLEKCFVKDPLRRWTIDLLLKHPFISDVENVSVVTELS