AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83588

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83588.t1 MTR_2g104900 97.571 247 6 0 1 247 1 247 0.0 499
MS.gene83588.t1 MTR_4g006575 52.083 240 80 11 19 247 9 224 1.75e-57 182
MS.gene83588.t1 MTR_4g006600 52.083 240 80 11 19 247 9 224 1.75e-57 182
MS.gene83588.t1 MTR_1g013130 35.563 284 124 13 1 247 1 262 1.90e-34 124
MS.gene83588.t1 MTR_3g106230 44.379 169 76 8 34 187 25 190 2.24e-32 118
MS.gene83588.t1 MTR_5g077370 67.532 77 17 3 80 155 86 155 9.59e-27 103
MS.gene83588.t1 MTR_1g033340 64.935 77 22 2 81 157 97 168 2.23e-26 103
MS.gene83588.t1 MTR_3g065020 61.728 81 23 3 76 155 80 153 8.64e-25 98.6
MS.gene83588.t1 MTR_4g128340 54.667 75 23 2 78 152 42 105 1.67e-17 77.8
MS.gene83588.t1 MTR_1g107055 36.232 138 69 4 24 159 12 132 3.61e-16 74.7
MS.gene83588.t1 MTR_7g086860 49.254 67 27 2 60 119 2 68 1.20e-12 64.3
MS.gene83588.t1 MTR_5g008310 40.206 97 39 3 77 164 68 154 2.90e-12 65.9
MS.gene83588.t1 MTR_5g008280 42.000 100 49 3 69 164 34 128 4.75e-12 65.5
MS.gene83588.t1 MTR_3g011990 38.356 146 63 9 34 164 44 177 6.79e-12 64.3
MS.gene83588.t1 MTR_8g466760 44.086 93 34 4 79 164 96 177 8.05e-12 64.3
MS.gene83588.t1 MTR_7g083210 75.758 33 8 0 81 113 39 71 1.08e-11 62.4
MS.gene83588.t1 MTR_5g008320 39.175 97 40 3 77 164 68 154 1.08e-11 63.9
MS.gene83588.t1 MTR_3g012010 41.414 99 46 3 73 164 90 183 6.17e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83588.t1 AT5G10970 39.526 253 120 11 13 247 35 272 6.29e-38 134
MS.gene83588.t1 AT1G80730 41.026 234 93 11 32 247 22 228 4.86e-34 122
MS.gene83588.t1 AT5G25160 41.475 217 97 9 48 247 32 235 1.65e-33 121
MS.gene83588.t1 AT1G24625 41.538 130 40 4 28 157 29 122 2.89e-21 89.0
MS.gene83588.t1 AT1G66140 55.682 88 25 2 81 154 83 170 9.69e-21 88.6
MS.gene83588.t1 AT5G57520 57.143 63 24 1 79 138 48 110 6.10e-17 75.9
MS.gene83588.t1 AT5G14010 76.471 34 8 0 81 114 36 69 7.27e-13 65.1
MS.gene83588.t1 AT5G01860 57.778 45 19 0 70 114 54 98 4.24e-12 63.9

Find 36 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCCAAGAAAGGTGCAAAA+TGG 0.323012 2.2:-1283861 MS.gene83588:CDS
GGCAGCTTCTGCCACTGGTT+TGG 0.325271 2.2:+1283984 None:intergenic
TGAACACAGGTACTCAAGTA+TGG 0.334170 2.2:-1284132 MS.gene83588:CDS
ACCATCATCACTTGGAATTC+AGG 0.350325 2.2:-1284075 MS.gene83588:CDS
GAAAATTTCCCTGATCTTGT+AGG 0.357308 2.2:+1283882 None:intergenic
AGAAAGGTGCAAAATGGATT+TGG 0.360298 2.2:-1283855 MS.gene83588:CDS
TTTCCCTGATCTTGTAGGTA+TGG 0.467787 2.2:+1283887 None:intergenic
AACATGGCTCTAATCTTAGA+AGG 0.477004 2.2:+1284498 None:intergenic
ATATAGGCAGCTTCTGCCAC+TGG 0.477130 2.2:+1283979 None:intergenic
ACACAAAAGAGAAAGAACTA+TGG 0.484621 2.2:-1284192 MS.gene83588:CDS
GTAAAAGCACTCAGAGTTTG+AGG 0.499487 2.2:+1283772 None:intergenic
AAGGTGCAAAATGGATTTGG+AGG 0.500419 2.2:-1283852 MS.gene83588:CDS
ACATGAAGATTCCTTGATGC+TGG 0.502045 2.2:+1283948 None:intergenic
TCATCACAAGAATCTTTACT+AGG 0.516480 2.2:+1284389 None:intergenic
GATGCTGGTTGTGAATATAT+AGG 0.519086 2.2:+1283963 None:intergenic
TCTTCATCGGAATCTAATCA+TGG 0.524262 2.2:-1284302 MS.gene83588:CDS
CATGTTGAGGCAGAAACTGA+TGG 0.531135 2.2:-1283930 MS.gene83588:CDS
ATGGCTTCTCTACCTTTGCA+TGG 0.537338 2.2:-1284113 MS.gene83588:CDS
AGTGCCATACCTACAAGATC+AGG 0.538472 2.2:-1283891 MS.gene83588:CDS
CGATGAAGAGTTTATCGACA+TGG 0.551961 2.2:+1284316 None:intergenic
TTCGGTTTGTCGCGTTACTG+TGG 0.557649 2.2:-1284008 MS.gene83588:CDS
ACCTGAATTCCAAGTGATGA+TGG 0.560861 2.2:+1284074 None:intergenic
TATAGTTCACAGGCACTTGG+TGG 0.564578 2.2:-1284227 MS.gene83588:CDS
TGTAGGTATGGCACTAGTCA+AGG 0.572932 2.2:+1283899 None:intergenic
TATATTCACAACCAGCATCA+AGG 0.576962 2.2:-1283959 MS.gene83588:CDS
TAGTTGCATGAGAAAATCCT+TGG 0.584802 2.2:+1284266 None:intergenic
AAAAGATCACCATCATCACT+TGG 0.591415 2.2:-1284083 MS.gene83588:CDS
CATGTCGATAAACTCTTCAT+CGG 0.592241 2.2:-1284315 MS.gene83588:CDS
ATCAAGGAATCTTCATGTTG+AGG 0.598145 2.2:-1283943 MS.gene83588:CDS
TAAAAGCACTCAGAGTTTGA+GGG 0.622554 2.2:+1283773 None:intergenic
ATGGTAATGAATTAGAGCCA+AGG 0.629515 2.2:-1284283 MS.gene83588:CDS
GTTACTGTGGTCCAAACCAG+TGG 0.634342 2.2:-1283995 MS.gene83588:CDS
GAAGAGTTTATCGACATGGA+CGG 0.645110 2.2:+1284320 None:intergenic
TTCAAATTATTAGATAAACA+TGG 0.647436 2.2:+1284482 None:intergenic
AAGTTTGAAGAATAAACAAG+AGG 0.648051 2.2:-1283817 MS.gene83588:CDS
GTGCCATACCTACAAGATCA+GGG 0.648274 2.2:-1283890 MS.gene83588:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCAAATTATTAGATAAACA+TGG + chr2.2:1283806-1283825 None:intergenic 15.0%
! AAGTTTGAAGAATAAACAAG+AGG - chr2.2:1284468-1284487 MS.gene83588:CDS 25.0%
!!! AAGAAAGTTTTATAGTTCAC+AGG - chr2.2:1284048-1284067 MS.gene83588:CDS 25.0%
AAAAACGGTGTTTGATAAGA+AGG + chr2.2:1284259-1284278 None:intergenic 30.0%
AAAGAACTATGGCAAAAAGA+GGG - chr2.2:1284104-1284123 MS.gene83588:CDS 30.0%
ACACAAAAGAGAAAGAACTA+TGG - chr2.2:1284093-1284112 MS.gene83588:CDS 30.0%
TCATCACAAGAATCTTTACT+AGG + chr2.2:1283899-1283918 None:intergenic 30.0%
! TTTCTCTTTTGTGTGCATTT+TGG + chr2.2:1284087-1284106 None:intergenic 30.0%
!! TCTTATCAAACACCGTTTTT+CGG - chr2.2:1284259-1284278 MS.gene83588:CDS 30.0%
AAAAGATCACCATCATCACT+TGG - chr2.2:1284202-1284221 MS.gene83588:CDS 35.0%
ATCAAGGAATCTTCATGTTG+AGG - chr2.2:1284342-1284361 MS.gene83588:CDS 35.0%
CATGTCGATAAACTCTTCAT+CGG - chr2.2:1283970-1283989 MS.gene83588:CDS 35.0%
GAAAATTTCCCTGATCTTGT+AGG + chr2.2:1284406-1284425 None:intergenic 35.0%
GAAAGAACTATGGCAAAAAG+AGG - chr2.2:1284103-1284122 MS.gene83588:CDS 35.0%
TAGTTGCATGAGAAAATCCT+TGG + chr2.2:1284022-1284041 None:intergenic 35.0%
TATATTCACAACCAGCATCA+AGG - chr2.2:1284326-1284345 MS.gene83588:CDS 35.0%
TCTTCATCGGAATCTAATCA+TGG - chr2.2:1283983-1284002 MS.gene83588:CDS 35.0%
! AATCCATTTTGCACCTTTCT+TGG + chr2.2:1284430-1284449 None:intergenic 35.0%
! AGAAAGGTGCAAAATGGATT+TGG - chr2.2:1284430-1284449 MS.gene83588:CDS 35.0%
! AGGGAAATTTTCTCCAAGAA+AGG - chr2.2:1284414-1284433 MS.gene83588:CDS 35.0%
! ATGGTAATGAATTAGAGCCA+AGG - chr2.2:1284002-1284021 MS.gene83588:CDS 35.0%
! CTTTTATAAGAGCCATGCAA+AGG + chr2.2:1284187-1284206 None:intergenic 35.0%
! GATGCTGGTTGTGAATATAT+AGG + chr2.2:1284325-1284344 None:intergenic 35.0%
! TTTTATAGTTCACAGGCACT+TGG - chr2.2:1284055-1284074 MS.gene83588:CDS 35.0%
!! AACATGGCTCTAATCTTAGA+AGG + chr2.2:1283790-1283809 None:intergenic 35.0%
ACATGAAGATTCCTTGATGC+TGG + chr2.2:1284340-1284359 None:intergenic 40.0%
ACCATCATCACTTGGAATTC+AGG - chr2.2:1284210-1284229 MS.gene83588:CDS 40.0%
ACCTGAATTCCAAGTGATGA+TGG + chr2.2:1284214-1284233 None:intergenic 40.0%
CGATGAAGAGTTTATCGACA+TGG + chr2.2:1283972-1283991 None:intergenic 40.0%
GAAGAGTTTATCGACATGGA+CGG + chr2.2:1283968-1283987 None:intergenic 40.0%
TAACGCGACAAACCGAAAAA+CGG + chr2.2:1284274-1284293 None:intergenic 40.0%
TGAACACAGGTACTCAAGTA+TGG - chr2.2:1284153-1284172 MS.gene83588:CDS 40.0%
TTTCCCTGATCTTGTAGGTA+TGG + chr2.2:1284401-1284420 None:intergenic 40.0%
! AAAAAGAGGGCACAAATCTG+TGG - chr2.2:1284117-1284136 MS.gene83588:CDS 40.0%
! AAGGTGCAAAATGGATTTGG+AGG - chr2.2:1284433-1284452 MS.gene83588:CDS 40.0%
! CTTCGCTAGATTTTGAACAC+AGG - chr2.2:1284140-1284159 MS.gene83588:CDS 40.0%
! TCTCCAAGAAAGGTGCAAAA+TGG - chr2.2:1284424-1284443 MS.gene83588:CDS 40.0%
AGTGCCATACCTACAAGATC+AGG - chr2.2:1284394-1284413 MS.gene83588:CDS 45.0%
ATGGCTTCTCTACCTTTGCA+TGG - chr2.2:1284172-1284191 MS.gene83588:CDS 45.0%
CATGTTGAGGCAGAAACTGA+TGG - chr2.2:1284355-1284374 MS.gene83588:CDS 45.0%
GTGCCATACCTACAAGATCA+GGG - chr2.2:1284395-1284414 MS.gene83588:CDS 45.0%
TATAGTTCACAGGCACTTGG+TGG - chr2.2:1284058-1284077 MS.gene83588:CDS 45.0%
TGTAGGTATGGCACTAGTCA+AGG + chr2.2:1284389-1284408 None:intergenic 45.0%
ATATAGGCAGCTTCTGCCAC+TGG + chr2.2:1284309-1284328 None:intergenic 50.0%
GTTACTGTGGTCCAAACCAG+TGG - chr2.2:1284290-1284309 MS.gene83588:CDS 50.0%
! TTCGGTTTGTCGCGTTACTG+TGG - chr2.2:1284277-1284296 MS.gene83588:CDS 50.0%
! GGCAGCTTCTGCCACTGGTT+TGG + chr2.2:1284304-1284323 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 1283782 1284525 1283782 ID=MS.gene83588
chr2.2 mRNA 1283782 1284525 1283782 ID=MS.gene83588.t1;Parent=MS.gene83588
chr2.2 exon 1283782 1284525 1283782 ID=MS.gene83588.t1.exon1;Parent=MS.gene83588.t1
chr2.2 CDS 1283782 1284525 1283782 ID=cds.MS.gene83588.t1;Parent=MS.gene83588.t1
Gene Sequence

>MS.gene83588

ATGGACCTTCTAAGATTAGAGCCATGTTTATCTAATAATTTGAACATCTCATTTTCTGAGAAGAGACAAACAGAAAATGAAGAGAAAAAACATCTTGTACTAGATTTAACTCTTCCTAGTAAAGATTCTTGTGATGATGAGTCAAAACAAGAACTCAATCTCATAAACTGTTTCGATACAGAACCGTCCATGTCGATAAACTCTTCATCGGAATCTAATCATGGTAATGAATTAGAGCCAAGGATTTTCTCATGCAACTATTGTCAAAGAAAGTTTTATAGTTCACAGGCACTTGGTGGACACCAAAATGCACACAAAAGAGAAAGAACTATGGCAAAAAGAGGGCACAAATCTGTGGCTTCGCTAGATTTTGAACACAGGTACTCAAGTATGGCTTCTCTACCTTTGCATGGCTCTTATAAAAGATCACCATCATCACTTGGAATTCAGGTGCACTCTTCTATGATTCAAAAACCTTCTTATCAAACACCGTTTTTCGGTTTGTCGCGTTACTGTGGTCCAAACCAGTGGCAGAAGCTGCCTATATATTCACAACCAGCATCAAGGAATCTTCATGTTGAGGCAGAAACTGATGGATCATCATCCTTGACTAGTGCCATACCTACAAGATCAGGGAAATTTTCTCCAAGAAAGGTGCAAAATGGATTTGGAGGTTATAATGCTACAAGTTTGAAGAATAAACAAGAGGAGTTGCAGAAGCTTGACTTGTCCCTCAAACTCTGA
Protein sequence

>MS.gene83588.t1

MDLLRLEPCLSNNLNISFSEKRQTENEEKKHLVLDLTLPSKDSCDDESKQELNLINCFDTEPSMSINSSSESNHGNELEPRIFSCNYCQRKFYSSQALGGHQNAHKRERTMAKRGHKSVASLDFEHRYSSMASLPLHGSYKRSPSSLGIQVHSSMIQKPSYQTPFFGLSRYCGPNQWQKLPIYSQPASRNLHVEAETDGSSSLTSAIPTRSGKFSPRKVQNGFGGYNATSLKNKQEELQKLDLSLKL