AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32568

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32568.t1 MTR_3g005495 68.421 209 53 2 11 207 26 233 1.31e-93 281
MS.gene32568.t1 MTR_3g005495 47.005 217 84 4 13 201 258 471 2.12e-56 185
MS.gene32568.t1 MTR_3g005460 65.566 212 53 2 13 205 40 250 4.59e-89 271
MS.gene32568.t1 MTR_3g005460 46.025 239 79 4 13 202 277 514 4.47e-61 199
MS.gene32568.t1 MTR_3g005420 64.455 211 55 2 13 203 36 246 1.12e-82 254
MS.gene32568.t1 MTR_3g005420 44.776 201 104 2 13 207 285 484 9.55e-44 152
MS.gene32568.t1 MTR_3g005420 64.455 211 55 2 13 203 55 265 5.29e-82 253
MS.gene32568.t1 MTR_3g005420 47.458 236 82 2 13 207 304 538 6.03e-63 204
MS.gene32568.t1 MTR_5g070440 52.381 231 68 2 13 202 36 265 1.12e-73 224
MS.gene32568.t1 MTR_3g005490 53.153 222 71 3 13 202 36 256 2.48e-72 220
MS.gene32568.t1 MTR_3g005480 50.862 232 80 3 4 202 27 257 5.14e-70 214
MS.gene32568.t1 MTR_3g005440 56.682 217 47 3 10 206 32 221 2.60e-67 213
MS.gene32568.t1 MTR_3g005440 46.927 179 61 2 13 157 257 435 2.68e-45 155
MS.gene32568.t1 MTR_1g015350 40.690 145 55 2 42 186 59 172 2.17e-23 92.4
MS.gene32568.t1 MTR_1g034240 40.860 93 55 0 4 96 13 105 1.46e-20 89.0
MS.gene32568.t1 MTR_3g061310 46.067 89 46 1 10 96 20 108 1.92e-19 84.3
MS.gene32568.t1 MTR_3g061350 39.474 114 66 2 10 121 20 132 4.00e-18 80.9
MS.gene32568.t1 MTR_7g050560 33.333 105 66 1 14 114 29 133 1.27e-17 79.7
MS.gene32568.t1 MTR_3g061320 44.944 89 47 1 10 96 20 108 2.49e-17 78.6
MS.gene32568.t1 MTR_4g068320 34.615 104 68 0 1 104 9 112 3.81e-17 79.3
MS.gene32568.t1 MTR_7g050710 34.579 107 62 1 13 111 28 134 4.21e-17 78.6
MS.gene32568.t1 MTR_3g061290 43.820 89 48 1 10 96 20 108 8.81e-17 75.5
MS.gene32568.t1 MTR_3g061370 41.667 84 49 0 13 96 22 105 4.60e-16 75.1
MS.gene32568.t1 MTR_3g061330 41.667 84 49 0 13 96 25 108 5.27e-16 74.3
MS.gene32568.t1 MTR_7g050590 34.021 97 62 1 14 108 2 98 1.30e-15 73.9
MS.gene32568.t1 MTR_1g034210 40.476 84 48 1 13 96 22 103 1.43e-15 74.3
MS.gene32568.t1 MTR_1g034210 34.286 105 68 1 1 105 10 113 1.86e-15 74.3
MS.gene32568.t1 MTR_3g061340 45.556 90 46 2 10 96 20 109 5.32e-15 72.0
MS.gene32568.t1 MTR_5g044670 33.735 83 55 0 14 96 32 114 2.19e-14 70.9
MS.gene32568.t1 MTR_7g050580 30.357 112 75 2 14 124 29 138 3.92e-14 70.1
MS.gene32568.t1 MTR_3g098790 34.118 85 56 0 14 98 29 113 4.02e-14 70.1
MS.gene32568.t1 MTR_1g108780 30.909 110 71 1 11 115 10 119 4.21e-14 70.5
MS.gene32568.t1 MTR_3g061220 40.449 89 38 2 10 96 20 95 7.26e-14 65.9
MS.gene32568.t1 MTR_7g050720 32.143 84 57 0 14 97 26 109 1.36e-12 65.9
MS.gene32568.t1 MTR_1g035460 36.471 85 54 0 14 98 2 86 3.53e-12 64.7
MS.gene32568.t1 MTR_8g103940 32.143 84 57 0 13 96 54 137 5.42e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32568.t1 AT3G18990 40.476 84 50 0 13 96 21 104 2.45e-18 82.0
MS.gene32568.t1 AT3G18990 40.476 84 50 0 13 96 21 104 5.17e-18 81.3
MS.gene32568.t1 AT1G49475 38.542 96 58 1 11 106 47 141 7.82e-17 75.5
MS.gene32568.t1 AT4G01580 34.737 95 62 0 4 98 36 130 2.02e-16 74.3
MS.gene32568.t1 AT3G18960 33.684 95 63 0 4 98 36 130 6.14e-16 73.2
MS.gene32568.t1 AT3G18960 33.684 95 63 0 4 98 36 130 1.10e-15 72.8
MS.gene32568.t1 AT3G18960 35.632 87 56 0 12 98 7 93 2.94e-15 70.9

Find 42 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTGCTTTCCTTGAGAATTT+TGG 0.150373 5.1:-61994393 None:intergenic
GACGAGTTTATAACAAGATT+TGG 0.231276 5.1:+61993915 MS.gene32568:CDS
ATTTCCTATCCATTCAAAAC+TGG 0.287220 5.1:+61994149 MS.gene32568:CDS
CTGCAGTGACCAATCTTTAG+AGG 0.292480 5.1:-61993883 None:intergenic
GTTTATTGTGTATTGAATAA+AGG 0.319096 5.1:+61994421 MS.gene32568:CDS
ACGAGTTTATAACAAGATTT+GGG 0.367534 5.1:+61993916 MS.gene32568:CDS
TTCAAAACTGGGAAGACTAA+TGG 0.374313 5.1:+61994161 MS.gene32568:CDS
TGGAGCTTGAACAGAACATT+TGG 0.381563 5.1:-61994373 None:intergenic
AAAGCAATGCGAATAACGTT+TGG 0.420748 5.1:+61994451 MS.gene32568:CDS
GAACACTACTCTATCTGTTA+TGG 0.428310 5.1:+61994053 MS.gene32568:CDS
TATGTAGATTTCAAGTATGA+AGG 0.431237 5.1:+61994080 MS.gene32568:CDS
AATCTTGTTATAAACTCGTC+TGG 0.437746 5.1:-61993912 None:intergenic
TGACGGTTGCGAATGGCATA+TGG 0.455390 5.1:+61993974 MS.gene32568:CDS
ATCACCCTTCCTCTAAAGAT+TGG 0.475124 5.1:+61993874 MS.gene32568:CDS
ATATCGACAGTCAAAGGATT+GGG 0.499850 5.1:-61994216 None:intergenic
TATTCTGCGGCGAATTCAGC+AGG 0.501814 5.1:-61994343 None:intergenic
ATATGCCATTCGCAACCGTC+AGG 0.503250 5.1:-61993972 None:intergenic
TTGGATTCTTTAGATTTGCA+AGG 0.513403 5.1:+61994470 MS.gene32568:CDS
CATATCGACAGTCAAAGGAT+TGG 0.519552 5.1:-61994217 None:intergenic
AAGGATTGGGAACGAAAAGA+AGG 0.522583 5.1:-61994203 None:intergenic
CACCGCATATCGACAGTCAA+AGG 0.544452 5.1:-61994222 None:intergenic
TTTCCTATCCATTCAAAACT+GGG 0.546790 5.1:+61994150 MS.gene32568:CDS
TATTGTGTATTGAATAAAGG+TGG 0.548350 5.1:+61994424 MS.gene32568:CDS
AGGGAAAACAATCTATCAGA+TGG 0.548736 5.1:+61994490 MS.gene32568:CDS
ATGTAGATTTCAAGTATGAA+GGG 0.551054 5.1:+61994081 MS.gene32568:CDS
TTCAAGCTCCAAAATTCTCA+AGG 0.552648 5.1:+61994385 MS.gene32568:CDS
TGGATTCTTTAGATTTGCAA+GGG 0.565236 5.1:+61994471 MS.gene32568:CDS
TGTGTATTGAATAAAGGTGG+CGG 0.569727 5.1:+61994427 MS.gene32568:CDS
CTGTTCCTGACGGTTGCGAA+TGG 0.576577 5.1:+61993967 MS.gene32568:CDS
AGTGACCAATCTTTAGAGGA+AGG 0.582133 5.1:-61993879 None:intergenic
AAAATTCTCAAGGAAAGCAG+TGG 0.599450 5.1:+61994395 MS.gene32568:CDS
ATAGAGTAGTGTTCTGCGAA+CGG 0.599484 5.1:-61994044 None:intergenic
AGGATTGGGAACGAAAAGAA+GGG 0.605751 5.1:-61994202 None:intergenic
GTGACCAATCTTTAGAGGAA+GGG 0.612342 5.1:-61993878 None:intergenic
GCTACGATTACTGTTCCTGA+CGG 0.625910 5.1:+61993957 MS.gene32568:CDS
ATTTGGCTTCAAATATTCTG+CGG 0.631419 5.1:-61994356 None:intergenic
ATCCTTTGACTGTCGATATG+CGG 0.632326 5.1:+61994220 MS.gene32568:CDS
AAATTCTCAAGGAAAGCAGT+GGG 0.637805 5.1:+61994396 MS.gene32568:CDS
ACAAGTTACAGCTTCTCACA+CGG 0.646742 5.1:+61994561 MS.gene32568:CDS
ATGAGTTTGAGCTTATCAAG+AGG 0.652349 5.1:+61994521 MS.gene32568:CDS
CATATGGAAGTGAAGAAATG+TGG 0.695642 5.1:+61993990 MS.gene32568:CDS
GTAACTTGTAACACAACACG+CGG 0.711770 5.1:-61994547 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTTGAGTTATATATTTA+TGG + chr5.1:61994280-61994299 MS.gene32568:intron 15.0%
!! GTTTATTGTGTATTGAATAA+AGG + chr5.1:61994421-61994440 MS.gene32568:CDS 20.0%
!! TGTTGTATTGTAATTCATAT+AGG + chr5.1:61994655-61994674 MS.gene32568:intron 20.0%
!!! AAGTTTTCTTTTGCAAAAAT+TGG + chr5.1:61994018-61994037 MS.gene32568:CDS 20.0%
!!! GGATTTTACTATACATTATT+TGG + chr5.1:61994246-61994265 MS.gene32568:intron 20.0%
! ACGAGTTTATAACAAGATTT+GGG + chr5.1:61993916-61993935 MS.gene32568:CDS 25.0%
! TATTGTGTATTGAATAAAGG+TGG + chr5.1:61994424-61994443 MS.gene32568:CDS 25.0%
!! ATGTAGATTTCAAGTATGAA+GGG + chr5.1:61994081-61994100 MS.gene32568:CDS 25.0%
!! TATGTAGATTTCAAGTATGA+AGG + chr5.1:61994080-61994099 MS.gene32568:CDS 25.0%
!!! ATTCATATAGGTAGTTTTGT+TGG + chr5.1:61994667-61994686 MS.gene32568:intron 25.0%
AATGGAGGAACAATCTATTT+AGG - chr5.1:61994311-61994330 None:intergenic 30.0%
ATTTCCTATCCATTCAAAAC+TGG + chr5.1:61994149-61994168 MS.gene32568:CDS 30.0%
GACGAGTTTATAACAAGATT+TGG + chr5.1:61993915-61993934 MS.gene32568:CDS 30.0%
TGGATTCTTTAGATTTGCAA+GGG + chr5.1:61994471-61994490 MS.gene32568:CDS 30.0%
TTGGATTCTTTAGATTTGCA+AGG + chr5.1:61994470-61994489 MS.gene32568:CDS 30.0%
TTTCCTATCCATTCAAAACT+GGG + chr5.1:61994150-61994169 MS.gene32568:CDS 30.0%
! AATCTTGTTATAAACTCGTC+TGG - chr5.1:61993915-61993934 None:intergenic 30.0%
! ATTTGGCTTCAAATATTCTG+CGG - chr5.1:61994359-61994378 None:intergenic 30.0%
!!! AACGAAAAGAAGGGTTTTTT+GGG - chr5.1:61994196-61994215 None:intergenic 30.0%
AAAATTCTCAAGGAAAGCAG+TGG + chr5.1:61994395-61994414 MS.gene32568:CDS 35.0%
AAAGCAATGCGAATAACGTT+TGG + chr5.1:61994451-61994470 MS.gene32568:CDS 35.0%
AAATTCTCAAGGAAAGCAGT+GGG + chr5.1:61994396-61994415 MS.gene32568:CDS 35.0%
AGGGAAAACAATCTATCAGA+TGG + chr5.1:61994490-61994509 MS.gene32568:CDS 35.0%
ATATCGACAGTCAAAGGATT+GGG - chr5.1:61994219-61994238 None:intergenic 35.0%
ATGAGTTTGAGCTTATCAAG+AGG + chr5.1:61994521-61994540 MS.gene32568:CDS 35.0%
CATATGGAAGTGAAGAAATG+TGG + chr5.1:61993990-61994009 MS.gene32568:CDS 35.0%
GAACACTACTCTATCTGTTA+TGG + chr5.1:61994053-61994072 MS.gene32568:CDS 35.0%
TGTGTATTGAATAAAGGTGG+CGG + chr5.1:61994427-61994446 MS.gene32568:CDS 35.0%
TTCAAAACTGGGAAGACTAA+TGG + chr5.1:61994161-61994180 MS.gene32568:CDS 35.0%
TTCAAGCTCCAAAATTCTCA+AGG + chr5.1:61994385-61994404 MS.gene32568:CDS 35.0%
! ACTGCTTTCCTTGAGAATTT+TGG - chr5.1:61994396-61994415 None:intergenic 35.0%
!!! AAAGAAGGGTTTTTTGGGTT+TGG - chr5.1:61994191-61994210 None:intergenic 35.0%
!!! AGGTAGTTTTGTTGGTTGTT+AGG + chr5.1:61994675-61994694 MS.gene32568:intron 35.0%
!!! GAACGAAAAGAAGGGTTTTT+TGG - chr5.1:61994197-61994216 None:intergenic 35.0%
!!! TTAGTCTTCCCAGTTTTGAA+TGG - chr5.1:61994161-61994180 None:intergenic 35.0%
AAGGATTGGGAACGAAAAGA+AGG - chr5.1:61994206-61994225 None:intergenic 40.0%
ACAAGTTACAGCTTCTCACA+CGG + chr5.1:61994561-61994580 MS.gene32568:CDS 40.0%
AGCAGGAACATACTACACAA+TGG - chr5.1:61994329-61994348 None:intergenic 40.0%
AGGAACATACTACACAATGG+AGG - chr5.1:61994326-61994345 None:intergenic 40.0%
AGGATTGGGAACGAAAAGAA+GGG - chr5.1:61994205-61994224 None:intergenic 40.0%
ATAGAGTAGTGTTCTGCGAA+CGG - chr5.1:61994047-61994066 None:intergenic 40.0%
ATCCTTTGACTGTCGATATG+CGG + chr5.1:61994220-61994239 MS.gene32568:CDS 40.0%
CATATCGACAGTCAAAGGAT+TGG - chr5.1:61994220-61994239 None:intergenic 40.0%
TGGAGCTTGAACAGAACATT+TGG - chr5.1:61994376-61994395 None:intergenic 40.0%
! AGTGACCAATCTTTAGAGGA+AGG - chr5.1:61993882-61993901 None:intergenic 40.0%
! ATCACCCTTCCTCTAAAGAT+TGG + chr5.1:61993874-61993893 MS.gene32568:CDS 40.0%
! GTAACTTGTAACACAACACG+CGG - chr5.1:61994550-61994569 None:intergenic 40.0%
! GTGACCAATCTTTAGAGGAA+GGG - chr5.1:61993881-61993900 None:intergenic 40.0%
!!! CTTCCCAGTTTTGAATGGAT+AGG - chr5.1:61994156-61994175 None:intergenic 40.0%
CTGCAGTGACCAATCTTTAG+AGG - chr5.1:61993886-61993905 None:intergenic 45.0%
GCTACGATTACTGTTCCTGA+CGG + chr5.1:61993957-61993976 MS.gene32568:CDS 45.0%
ATATGCCATTCGCAACCGTC+AGG - chr5.1:61993975-61993994 None:intergenic 50.0%
CACCGCATATCGACAGTCAA+AGG - chr5.1:61994225-61994244 None:intergenic 50.0%
TATTCTGCGGCGAATTCAGC+AGG - chr5.1:61994346-61994365 None:intergenic 50.0%
TGACGGTTGCGAATGGCATA+TGG + chr5.1:61993974-61993993 MS.gene32568:CDS 50.0%
TTGACTGTCGATATGCGGTG+AGG + chr5.1:61994225-61994244 MS.gene32568:intron 50.0%
CTGTTCCTGACGGTTGCGAA+TGG + chr5.1:61993967-61993986 MS.gene32568:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 61993870 61994705 61993870 ID=MS.gene32568
chr5.1 mRNA 61993870 61994705 61993870 ID=MS.gene32568.t1;Parent=MS.gene32568
chr5.1 exon 61993870 61994241 61993870 ID=MS.gene32568.t1.exon1;Parent=MS.gene32568.t1
chr5.1 CDS 61993870 61994241 61993870 ID=cds.MS.gene32568.t1;Parent=MS.gene32568.t1
chr5.1 exon 61994337 61994582 61994337 ID=MS.gene32568.t1.exon2;Parent=MS.gene32568.t1
chr5.1 CDS 61994337 61994582 61994337 ID=cds.MS.gene32568.t1;Parent=MS.gene32568.t1
chr5.1 exon 61994697 61994705 61994697 ID=MS.gene32568.t1.exon3;Parent=MS.gene32568.t1
chr5.1 CDS 61994697 61994705 61994697 ID=cds.MS.gene32568.t1;Parent=MS.gene32568.t1
Gene Sequence

>MS.gene32568

ATGTATCACCCTTCCTCTAAAGATTGGTCACTGCAGAGAATTCCAGACGAGTTTATAACAAGATTTGGGAATGAACTCAACAGTGTTGCTACGATTACTGTTCCTGACGGTTGCGAATGGCATATGGAAGTGAAGAAATGTGGCAGCGAAGTTTTCTTTTGCAAAAATTGGCAACCGTTCGCAGAACACTACTCTATCTGTTATGGTTGTTATGTAGATTTCAAGTATGAAGGGAATTCAAAGTTTAATGTTGTTATATATGATACAAATTCTGTCGAGATTTCCTATCCATTCAAAACTGGGAAGACTAATGGAGAACCAAACCCAAAAAACCCTTCTTTTCGTTCCCAATCCTTTGACTGTCGATATGCGGTGAGGATTTTACTATACATTATTTGGTTTAAAAGTAAATGTTTGAGTTATATATTTATGGTGTCACCTAAATAGATTGTTCCTCCATTGTGTAGTATGTTCCTGCTGAATTCGCCGCAGAATATTTGAAGCCAAATGTTCTGTTCAAGCTCCAAAATTCTCAAGGAAAGCAGTGGGAAGTTTATTGTGTATTGAATAAAGGTGGCGGAAAAGCAATGCGAATAACGTTTGGATTCTTTAGATTTGCAAGGGAAAACAATCTATCAGATGGAGTTATGTATGAGTTTGAGCTTATCAAGAGGAAACCGCGTGTTGTGTTACAAGTTACAGCTTCTCACACGGTAAAGAGCTGTTTCACATTCGTGTATGCGTCAGTTCTATTTTCTTACAATTTTTTCTTCTAATGTTGTAACTGTTGTATTGTAATTCATATAGGTAGTTTTGTTGGTTGTTAGGTTTTTTAG
Protein sequence

>MS.gene32568.t1

MYHPSSKDWSLQRIPDEFITRFGNELNSVATITVPDGCEWHMEVKKCGSEVFFCKNWQPFAEHYSICYGCYVDFKYEGNSKFNVVIYDTNSVEISYPFKTGKTNGEPNPKNPSFRSQSFDCRYAYVPAEFAAEYLKPNVLFKLQNSQGKQWEVYCVLNKGGGKAMRITFGFFRFARENNLSDGVMYEFELIKRKPRVVLQVTASHTVF