AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043070.t1 MTR_4g031910 72.650 234 47 2 1 222 1 229 1.43e-113 324
MS.gene043070.t1 MTR_4g032290 68.033 244 43 2 1 222 1 231 4.35e-107 308
MS.gene043070.t1 MTR_4g032620 57.576 231 89 1 1 222 1 231 9.34e-93 271
MS.gene043070.t1 MTR_8g036130 55.870 247 84 4 1 222 1 247 2.51e-86 256
MS.gene043070.t1 MTR_4g032260 78.981 157 33 0 1 157 1 157 5.69e-79 234
MS.gene043070.t1 MTR_3g065100 48.963 241 98 4 1 219 1 238 1.38e-63 197
MS.gene043070.t1 MTR_3g466980 47.196 214 97 4 1 209 1 203 2.02e-61 191
MS.gene043070.t1 MTR_2g035610 72.951 122 33 0 1 122 1 122 7.64e-52 164
MS.gene043070.t1 MTR_4g063790 45.455 154 84 0 1 154 1 154 2.74e-45 149
MS.gene043070.t1 MTR_5g075380 47.097 155 81 1 1 155 1 154 5.92e-45 147
MS.gene043070.t1 MTR_4g032270 54.745 137 47 2 94 222 2 131 2.22e-44 145
MS.gene043070.t1 MTR_3g466830 47.682 151 78 1 3 153 2 151 3.51e-43 143
MS.gene043070.t1 MTR_3g031100 35.714 224 132 4 1 219 1 217 6.09e-43 145
MS.gene043070.t1 MTR_3g467080 42.949 156 89 0 1 156 1 156 2.63e-42 140
MS.gene043070.t1 MTR_5g047580 46.154 156 82 2 1 156 1 154 8.74e-41 137
MS.gene043070.t1 MTR_2g016210 39.011 182 109 2 1 180 1 182 9.11e-40 137
MS.gene043070.t1 MTR_3g466890 44.737 152 83 1 3 154 2 152 3.35e-38 130
MS.gene043070.t1 MTR_1g077390 42.308 156 88 2 1 156 1 154 6.79e-38 129
MS.gene043070.t1 MTR_3g465410 44.444 126 70 0 29 154 1 126 9.39e-35 121
MS.gene043070.t1 MTR_1g090783 41.558 154 88 2 3 156 2 153 1.51e-34 120
MS.gene043070.t1 MTR_1g077320 43.590 156 86 2 1 156 1 154 7.27e-34 119
MS.gene043070.t1 MTR_7g011950 42.949 156 87 2 1 156 1 154 2.48e-33 117
MS.gene043070.t1 MTR_1g084950 44.872 156 84 2 1 156 1 154 2.99e-33 117
MS.gene043070.t1 MTR_4g028720 43.590 156 86 2 1 156 1 154 3.66e-33 117
MS.gene043070.t1 MTR_1g090710 39.216 153 81 2 1 153 1 141 1.55e-31 113
MS.gene043070.t1 MTR_1g077300 42.949 156 85 2 1 156 1 152 2.18e-31 112
MS.gene043070.t1 MTR_4g028800 75.714 70 15 1 1 70 1 68 2.22e-30 107
MS.gene043070.t1 MTR_1g090697 39.333 150 89 2 1 150 1 148 2.80e-30 110
MS.gene043070.t1 MTR_3g031240 33.974 156 103 0 1 156 1 156 7.50e-29 107
MS.gene043070.t1 MTR_7g055800 49.573 117 31 2 1 117 1 89 7.83e-28 101
MS.gene043070.t1 MTR_3g466900 39.837 123 73 1 32 154 2 123 3.98e-26 98.6
MS.gene043070.t1 MTR_7g055790 52.252 111 35 1 1 111 59 151 6.74e-26 98.6
MS.gene043070.t1 MTR_2g035580 37.580 157 97 1 1 157 1 156 4.82e-25 96.7
MS.gene043070.t1 MTR_3g466930 37.600 125 73 2 32 154 2 123 1.06e-23 92.4
MS.gene043070.t1 MTR_7g106510 38.583 127 78 0 3 129 6 132 1.67e-23 98.2
MS.gene043070.t1 MTR_4g019670 39.370 127 77 0 3 129 6 132 3.16e-23 97.4
MS.gene043070.t1 MTR_5g047560 36.538 156 81 3 1 156 1 138 6.07e-23 90.5
MS.gene043070.t1 MTR_7g055940 48.113 106 27 2 1 106 1 78 1.14e-22 87.8
MS.gene043070.t1 MTR_3g093900 33.858 127 84 0 3 129 6 132 2.88e-20 89.0
MS.gene043070.t1 MTR_2g035590 56.790 81 35 0 74 154 1 81 2.32e-18 77.4
MS.gene043070.t1 MTR_1g114730 31.858 113 70 3 1 107 1 112 1.73e-13 68.9
MS.gene043070.t1 MTR_6g018920 32.743 113 69 4 1 107 1 112 2.66e-13 68.2
MS.gene043070.t1 MTR_6g005450 33.628 113 68 4 1 107 1 112 1.19e-12 66.2
MS.gene043070.t1 MTR_6g005440 35.398 113 66 3 1 107 1 112 2.06e-11 62.8
MS.gene043070.t1 MTR_4g084780 55.769 52 23 0 74 125 1 52 3.27e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043070.t1 AT5G48670 55.195 154 68 1 1 154 1 153 9.97e-46 154
MS.gene043070.t1 AT5G26630 44.503 191 95 2 1 181 1 190 3.77e-40 137
MS.gene043070.t1 AT1G65330 41.711 187 95 3 3 176 2 187 4.66e-40 139
MS.gene043070.t1 AT1G65300 40.884 181 98 2 3 175 2 181 1.13e-39 137
MS.gene043070.t1 AT5G26650 36.190 210 115 4 5 204 3 203 1.16e-34 127
MS.gene043070.t1 AT5G27960 40.476 168 89 3 5 162 3 169 1.24e-34 125
MS.gene043070.t1 AT1G31630 36.310 168 96 3 3 161 2 167 2.76e-33 122
MS.gene043070.t1 AT1G31640 39.073 151 90 2 3 153 2 150 1.11e-31 120
MS.gene043070.t1 AT5G27810 55.914 93 41 0 29 121 1 93 8.63e-31 110
MS.gene043070.t1 AT3G05860 38.667 150 91 1 1 150 1 149 4.79e-30 110
MS.gene043070.t1 AT3G05860 42.975 121 69 0 1 121 1 121 7.02e-30 111
MS.gene043070.t1 AT3G05860 42.975 121 69 0 1 121 1 121 9.15e-30 111
MS.gene043070.t1 AT2G28700 37.423 163 97 2 1 161 1 160 1.47e-29 112
MS.gene043070.t1 AT1G22590 32.099 162 106 1 1 162 1 158 1.68e-26 100
MS.gene043070.t1 AT5G26580 36.029 136 72 2 1 136 1 121 1.03e-22 94.7
MS.gene043070.t1 AT5G06500 37.984 129 79 1 1 129 1 128 9.13e-21 87.4
MS.gene043070.t1 AT2G40210 37.209 129 80 1 1 129 1 128 1.45e-16 77.8
MS.gene043070.t1 AT5G58890 37.795 127 68 5 6 123 6 130 2.04e-15 73.9
MS.gene043070.t1 AT5G55690 42.308 78 38 2 1 71 1 78 1.27e-12 65.9
MS.gene043070.t1 AT5G55690 42.308 78 38 2 1 71 1 78 1.27e-12 65.9
MS.gene043070.t1 AT5G27090 34.444 90 58 1 7 95 23 112 7.78e-11 59.7
MS.gene043070.t1 AT5G27944 39.726 73 43 1 24 95 41 113 9.32e-11 60.1

Find 52 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGTGAGGAAATGGGAATTT+TGG 0.183275 4.2:-73221111 MS.gene043070:CDS
AGAAACAAAGAAAAGAAAAT+AGG 0.231520 4.2:-73221307 MS.gene043070:CDS
CCCTTTGGTGAGATCAATTA+TGG 0.234667 4.2:-73220990 MS.gene043070:CDS
TACCAATGTCCTTCAGATTA+TGG 0.267347 4.2:+73221180 None:intergenic
ATAATTTCATCATCATTAAT+AGG 0.285530 4.2:+73221068 None:intergenic
AACAAAGGGTCTATTGAAAA+AGG 0.314581 4.2:-73221540 MS.gene043070:CDS
GTGAGATCAATTATGGAGTT+TGG 0.319353 4.2:-73220983 MS.gene043070:CDS
AGCATCTAGGAGTGAGGAAA+TGG 0.344298 4.2:-73221120 MS.gene043070:CDS
ATGAGCCTCAACCTGAGATT+TGG 0.345571 4.2:-73221460 MS.gene043070:CDS
TATGCAAAGTCAATTATTGA+TGG 0.385590 4.2:-73221048 MS.gene043070:CDS
CTAGATGCTGTTGGAGGTGG+TGG 0.417295 4.2:+73221134 None:intergenic
GAAACAAAGAAAAGAAAATA+GGG 0.419680 4.2:-73221306 MS.gene043070:CDS
GGTCTGATTTACTACCTTGA+AGG 0.436579 4.2:-73220962 None:intergenic
GAAGGACATTGGTAGACGTT+TGG 0.439260 4.2:-73221171 MS.gene043070:CDS
CACAACCATGGCTAGAAGTA+AGG 0.457305 4.2:-73221618 None:intergenic
CTCATAAGAGCCATACACTA+TGG 0.467809 4.2:+73221478 None:intergenic
TCTGATGAAGGCCAAATCTC+AGG 0.474702 4.2:+73221449 None:intergenic
CTCCTAGATGCTGTTGGAGG+TGG 0.476689 4.2:+73221131 None:intergenic
TTGATTTGAGTTATCATACT+TGG 0.482235 4.2:-73221211 MS.gene043070:CDS
TCAATTATTGATGGACTCAA+TGG 0.482426 4.2:-73221039 MS.gene043070:CDS
TCCTCACTCCTAGATGCTGT+TGG 0.486555 4.2:+73221125 None:intergenic
TGCAGCATCATTGACAATGA+AGG 0.502295 4.2:+73221586 None:intergenic
GATGCTGTTGGAGGTGGTGG+TGG 0.513228 4.2:+73221137 None:intergenic
GGACATTGGTAGACGTTTGG+CGG 0.524285 4.2:-73221168 MS.gene043070:CDS
GAGATTTGGCCTTCATCAGA+GGG 0.524738 4.2:-73221446 MS.gene043070:CDS
TCACTCCTAGATGCTGTTGG+AGG 0.527908 4.2:+73221128 None:intergenic
TTTGTGTTAAGAAAGTCTCT+TGG 0.530215 4.2:+73221357 None:intergenic
CACCACCTCCAACAGCATCT+AGG 0.540352 4.2:-73221133 MS.gene043070:CDS
ATGTCTCATTGTCTCAATGA+AGG 0.542205 4.2:-73221263 MS.gene043070:CDS
GCATCTAGGAGTGAGGAAAT+GGG 0.544227 4.2:-73221119 MS.gene043070:CDS
CCATAATTGATCTCACCAAA+GGG 0.558369 4.2:+73220990 None:intergenic
GAAGCCTGTGCCATAGTGTA+TGG 0.560968 4.2:-73221488 MS.gene043070:CDS
GAAGGCCAAATCTCAGGTTG+AGG 0.568672 4.2:+73221455 None:intergenic
GTTGATTGACCATAATCTGA+AGG 0.571124 4.2:-73221189 MS.gene043070:CDS
TTTAACCTTACTTCTAGCCA+TGG 0.572129 4.2:+73221613 None:intergenic
TCCATAATTGATCTCACCAA+AGG 0.580970 4.2:+73220989 None:intergenic
GTGCACGAGACAGTGCCCTT+TGG 0.582311 4.2:-73221005 MS.gene043070:CDS
CATTAATAGGTATCCCAACA+TGG 0.589301 4.2:+73221081 None:intergenic
AAGAGACTTTCTTAACACAA+AGG 0.590392 4.2:-73221355 MS.gene043070:CDS
TGAGATTTGGCCTTCATCAG+AGG 0.593649 4.2:-73221447 MS.gene043070:CDS
GACCATAATCTGAAGGACAT+TGG 0.595565 4.2:-73221182 MS.gene043070:CDS
ACAGGCTTCAATGCCACAGA+GGG 0.601811 4.2:+73221502 None:intergenic
TTGATGGACTCAATGGTGGC+TGG 0.607204 4.2:-73221032 MS.gene043070:CDS
GATTTGGCCTTCATCAGAGG+GGG 0.615187 4.2:-73221444 MS.gene043070:CDS
TCCAACAGCATCTAGGAGTG+AGG 0.643310 4.2:-73221126 MS.gene043070:CDS
TCATTGTCAATGATGCTGCA+AGG 0.652548 4.2:-73221583 MS.gene043070:CDS
AGAGCCATACACTATGGCAC+AGG 0.656790 4.2:+73221484 None:intergenic
ATTATTGATGGACTCAATGG+TGG 0.666274 4.2:-73221036 MS.gene043070:CDS
AGATTTGGCCTTCATCAGAG+GGG 0.672121 4.2:-73221445 MS.gene043070:CDS
GCTGAACTTAGCACCCTCTG+TGG 0.677042 4.2:-73221515 MS.gene043070:CDS
TGTGCACGACAATATGTCAA+CGG 0.688304 4.2:-73221234 MS.gene043070:CDS
CACAGGCTTCAATGCCACAG+AGG 0.696692 4.2:+73221501 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATTTCATCATCATTAAT+AGG + chr4.2:73221511-73221530 None:intergenic 15.0%
!! AACATACAAAAAAAGAACAA+AGG - chr4.2:73221021-73221040 MS.gene043070:CDS 20.0%
!! ACATACAAAAAAAGAACAAA+GGG - chr4.2:73221022-73221041 MS.gene043070:CDS 20.0%
!! AGAAACAAAGAAAAGAAAAT+AGG - chr4.2:73221269-73221288 MS.gene043070:CDS 20.0%
!! GAAACAAAGAAAAGAAAATA+GGG - chr4.2:73221270-73221289 MS.gene043070:CDS 20.0%
! TATGCAAAGTCAATTATTGA+TGG - chr4.2:73221528-73221547 MS.gene043070:CDS 25.0%
!! TTGATTTGAGTTATCATACT+TGG - chr4.2:73221365-73221384 MS.gene043070:CDS 25.0%
AACAAAGGGTCTATTGAAAA+AGG - chr4.2:73221036-73221055 MS.gene043070:CDS 30.0%
AAGAGACTTTCTTAACACAA+AGG - chr4.2:73221221-73221240 MS.gene043070:CDS 30.0%
TTTGTGTTAAGAAAGTCTCT+TGG + chr4.2:73221222-73221241 None:intergenic 30.0%
! CTTAACACAAAGGATTTTGA+AGG - chr4.2:73221231-73221250 MS.gene043070:CDS 30.0%
!! TCAATTATTGATGGACTCAA+TGG - chr4.2:73221537-73221556 MS.gene043070:CDS 30.0%
ATGTCTCATTGTCTCAATGA+AGG - chr4.2:73221313-73221332 MS.gene043070:CDS 35.0%
CATTAATAGGTATCCCAACA+TGG + chr4.2:73221498-73221517 None:intergenic 35.0%
CCATAATTGATCTCACCAAA+GGG + chr4.2:73221589-73221608 None:intergenic 35.0%
GTGAGATCAATTATGGAGTT+TGG - chr4.2:73221593-73221612 MS.gene043070:CDS 35.0%
GTTGATTGACCATAATCTGA+AGG - chr4.2:73221387-73221406 MS.gene043070:CDS 35.0%
TACCAATGTCCTTCAGATTA+TGG + chr4.2:73221399-73221418 None:intergenic 35.0%
TCCATAATTGATCTCACCAA+AGG + chr4.2:73221590-73221609 None:intergenic 35.0%
! AGTGAGGAAATGGGAATTTT+GGG - chr4.2:73221466-73221485 MS.gene043070:CDS 35.0%
!! ATTATTGATGGACTCAATGG+TGG - chr4.2:73221540-73221559 MS.gene043070:CDS 35.0%
!! TGAATTTTGAGAGCACAGAT+TGG + chr4.2:73221159-73221178 None:intergenic 35.0%
CCCTTTGGTGAGATCAATTA+TGG - chr4.2:73221586-73221605 MS.gene043070:CDS 40.0%
CTCATAAGAGCCATACACTA+TGG + chr4.2:73221101-73221120 None:intergenic 40.0%
GACCATAATCTGAAGGACAT+TGG - chr4.2:73221394-73221413 MS.gene043070:CDS 40.0%
TCATTGTCAATGATGCTGCA+AGG - chr4.2:73220993-73221012 MS.gene043070:CDS 40.0%
TGCAGCATCATTGACAATGA+AGG + chr4.2:73220993-73221012 None:intergenic 40.0%
TGTGCACGACAATATGTCAA+CGG - chr4.2:73221342-73221361 MS.gene043070:CDS 40.0%
! GAGTGAGGAAATGGGAATTT+TGG - chr4.2:73221465-73221484 MS.gene043070:CDS 40.0%
!! GAAATGGGAATTTTGGGTCA+TGG - chr4.2:73221472-73221491 MS.gene043070:CDS 40.0%
AGCATCTAGGAGTGAGGAAA+TGG - chr4.2:73221456-73221475 MS.gene043070:CDS 45.0%
ATGAGCCTCAACCTGAGATT+TGG - chr4.2:73221116-73221135 MS.gene043070:CDS 45.0%
GAAGGACATTGGTAGACGTT+TGG - chr4.2:73221405-73221424 MS.gene043070:CDS 45.0%
GCATCTAGGAGTGAGGAAAT+GGG - chr4.2:73221457-73221476 MS.gene043070:CDS 45.0%
TCTGATGAAGGCCAAATCTC+AGG + chr4.2:73221130-73221149 None:intergenic 45.0%
! AGATTTGGCCTTCATCAGAG+GGG - chr4.2:73221131-73221150 MS.gene043070:CDS 45.0%
! GAGATTTGGCCTTCATCAGA+GGG - chr4.2:73221130-73221149 MS.gene043070:CDS 45.0%
! TGAGATTTGGCCTTCATCAG+AGG - chr4.2:73221129-73221148 MS.gene043070:CDS 45.0%
!! ATTTTGGGTCATGGCCATGT+TGG - chr4.2:73221481-73221500 MS.gene043070:CDS 45.0%
!! TTTTGGGTCATGGCCATGTT+GGG - chr4.2:73221482-73221501 MS.gene043070:CDS 45.0%
ACAGGCTTCAATGCCACAGA+GGG + chr4.2:73221077-73221096 None:intergenic 50.0%
AGAGCCATACACTATGGCAC+AGG + chr4.2:73221095-73221114 None:intergenic 50.0%
GAAGCCTGTGCCATAGTGTA+TGG - chr4.2:73221088-73221107 MS.gene043070:CDS 50.0%
GGACATTGGTAGACGTTTGG+CGG - chr4.2:73221408-73221427 MS.gene043070:CDS 50.0%
TCACTCCTAGATGCTGTTGG+AGG + chr4.2:73221451-73221470 None:intergenic 50.0%
TCCAACAGCATCTAGGAGTG+AGG - chr4.2:73221450-73221469 MS.gene043070:CDS 50.0%
TCCTCACTCCTAGATGCTGT+TGG + chr4.2:73221454-73221473 None:intergenic 50.0%
! GAAGGCCAAATCTCAGGTTG+AGG + chr4.2:73221124-73221143 None:intergenic 50.0%
! GATTTGGCCTTCATCAGAGG+GGG - chr4.2:73221132-73221151 MS.gene043070:CDS 50.0%
!! TTGATGGACTCAATGGTGGC+TGG - chr4.2:73221544-73221563 MS.gene043070:CDS 50.0%
CACAGGCTTCAATGCCACAG+AGG + chr4.2:73221078-73221097 None:intergenic 55.0%
CACCACCTCCAACAGCATCT+AGG - chr4.2:73221443-73221462 MS.gene043070:CDS 55.0%
CTAGATGCTGTTGGAGGTGG+TGG + chr4.2:73221445-73221464 None:intergenic 55.0%
CTCCTAGATGCTGTTGGAGG+TGG + chr4.2:73221448-73221467 None:intergenic 55.0%
GATTGGACCCCCTCTGATGA+AGG + chr4.2:73221142-73221161 None:intergenic 55.0%
GCTGAACTTAGCACCCTCTG+TGG - chr4.2:73221061-73221080 MS.gene043070:CDS 55.0%
GTGCACGAGACAGTGCCCTT+TGG - chr4.2:73221571-73221590 MS.gene043070:CDS 60.0%
! GATGCTGTTGGAGGTGGTGG+TGG + chr4.2:73221442-73221461 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 73220965 73221633 73220965 ID=MS.gene043070
chr4.2 mRNA 73220965 73221633 73220965 ID=MS.gene043070.t1;Parent=MS.gene043070
chr4.2 exon 73220965 73221633 73220965 ID=MS.gene043070.t1.exon1;Parent=MS.gene043070.t1
chr4.2 CDS 73220965 73221633 73220965 ID=cds.MS.gene043070.t1;Parent=MS.gene043070.t1
Gene Sequence

>MS.gene043070

ATGGCTAGAAGTAAGGTTAAACTCGCCTTCATTGTCAATGATGCTGCAAGGAAAGCAACATACAAAAAAAGAACAAAGGGTCTATTGAAAAAGGTTGCTGAACTTAGCACCCTCTGTGGCATTGAAGCCTGTGCCATAGTGTATGGCTCTTATGAGCCTCAACCTGAGATTTGGCCTTCATCAGAGGGGGTCCAATCTGTGCTCTCAAAATTCATGACGATGCACGAGTTTCAAAAGTGCAAGAAAATGCTGAACCAAGAGACTTTCTTAACACAAAGGATTTTGAAGGCTGAAGAGAAATTGAAGAAACAAAGAAAAGAAAATAGGGAGCAAGAGATGACAATACTCATGTCTCATTGTCTCAATGAAGGTAGAGTTGTGCACGACAATATGTCAACGGTTGATTTGAGTTATCATACTTGGTTGATTGACCATAATCTGAAGGACATTGGTAGACGTTTGGCGGCAACAGTGCCACCACCACCTCCAACAGCATCTAGGAGTGAGGAAATGGGAATTTTGGGTCATGGCCATGTTGGGATACCTATTAATGATGATGAAATTATGCAAAGTCAATTATTGATGGACTCAATGGTGGCTGGTAATGTGCACGAGACAGTGCCCTTTGGTGAGATCAATTATGGAGTTTGGTCTGATTTACTACCTTGA
Protein sequence

>MS.gene043070.t1

MARSKVKLAFIVNDAARKATYKKRTKGLLKKVAELSTLCGIEACAIVYGSYEPQPEIWPSSEGVQSVLSKFMTMHEFQKCKKMLNQETFLTQRILKAEEKLKKQRKENREQEMTILMSHCLNEGRVVHDNMSTVDLSYHTWLIDHNLKDIGRRLAATVPPPPPTASRSEEMGILGHGHVGIPINDDEIMQSQLLMDSMVAGNVHETVPFGEINYGVWSDLLP