AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene065888

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065888.t1 MTR_4g077787 94.944 178 9 0 1 178 1 178 1.44e-126 353
MS.gene065888.t1 MTR_4g111640 85.714 182 24 2 1 181 1 181 8.54e-116 326
MS.gene065888.t1 MTR_4g112310 90.909 132 10 2 51 181 1 131 5.69e-85 246
MS.gene065888.t1 MTR_6g022170 58.879 107 43 1 26 132 28 133 2.04e-43 142
MS.gene065888.t1 MTR_2g101300 40.909 132 75 2 15 144 8 138 1.74e-33 117
MS.gene065888.t1 MTR_3g105930 40.994 161 80 6 29 179 24 179 3.35e-32 114
MS.gene065888.t1 MTR_4g078410 44.186 129 66 2 29 155 22 146 4.30e-32 114
MS.gene065888.t1 MTR_2g090580 38.060 134 75 3 31 162 26 153 2.09e-28 105
MS.gene065888.t1 MTR_8g463180 41.549 142 67 5 12 146 5 137 5.26e-28 106
MS.gene065888.t1 MTR_1g014120 39.189 148 75 6 7 145 4 145 1.44e-27 102
MS.gene065888.t1 MTR_2g079030 39.726 146 77 3 12 155 10 146 1.34e-26 105
MS.gene065888.t1 MTR_8g086360 34.752 141 83 3 12 150 7 140 4.44e-25 96.3
MS.gene065888.t1 MTR_8g095013 36.885 122 69 3 12 131 8 123 6.78e-24 95.5
MS.gene065888.t1 MTR_2g090575 36.508 126 71 3 12 132 2 123 2.43e-23 95.1
MS.gene065888.t1 MTR_8g094990 36.066 122 70 3 12 131 8 123 4.53e-22 90.5
MS.gene065888.t1 MTR_4g124280 36.029 136 63 3 32 145 25 158 1.64e-21 88.2
MS.gene065888.t1 MTR_4g081100 39.423 104 59 2 31 132 31 132 1.96e-21 87.4
MS.gene065888.t1 MTR_7g090170 38.686 137 57 6 29 157 24 141 2.03e-21 85.5
MS.gene065888.t1 MTR_8g095020 40.777 103 54 3 32 132 25 122 4.68e-21 88.2
MS.gene065888.t1 MTR_1g077790 36.190 105 64 2 29 131 26 129 3.71e-20 83.6
MS.gene065888.t1 MTR_2g083250 39.048 105 60 3 31 132 25 128 2.46e-19 82.8
MS.gene065888.t1 MTR_5g006040 32.168 143 89 3 14 152 8 146 8.31e-19 79.7
MS.gene065888.t1 MTR_1g090420 30.857 175 97 5 16 169 8 179 2.61e-18 79.3
MS.gene065888.t1 MTR_4g114870 35.294 102 62 2 32 131 191 290 1.93e-16 76.3
MS.gene065888.t1 MTR_4g114870 31.667 120 76 3 30 145 27 144 3.85e-15 72.4
MS.gene065888.t1 MTR_3g099570 30.137 146 92 4 7 150 2 139 4.64e-16 72.4
MS.gene065888.t1 MTR_1g104800 33.962 106 64 2 32 135 25 126 1.77e-15 70.9
MS.gene065888.t1 MTR_0334s0010 30.833 120 79 2 13 131 9 125 2.14e-15 71.2
MS.gene065888.t1 MTR_4g067200 29.688 128 84 3 13 136 9 134 2.63e-15 70.1
MS.gene065888.t1 MTR_4g066110 29.688 128 84 3 13 136 9 134 2.63e-15 70.1
MS.gene065888.t1 MTR_3g092170 30.400 125 74 4 12 129 2 120 6.31e-15 71.2
MS.gene065888.t1 MTR_6g083240 29.870 154 96 5 14 157 8 159 2.21e-14 67.8
MS.gene065888.t1 MTR_6g023760 36.538 104 58 3 30 131 24 121 7.26e-14 66.6
MS.gene065888.t1 MTR_2g088990 31.618 136 81 4 29 162 22 147 7.80e-14 67.4
MS.gene065888.t1 MTR_3g099580 32.308 130 68 4 9 131 4 120 1.20e-13 66.2
MS.gene065888.t1 MTR_4g130780 30.216 139 87 5 8 140 4 138 8.23e-13 63.9
MS.gene065888.t1 MTR_3g099540 28.125 128 72 4 11 131 7 121 7.17e-12 60.1
MS.gene065888.t1 MTR_3g099680 31.746 126 76 4 11 133 6 124 7.68e-12 62.0
MS.gene065888.t1 MTR_3g099980 31.746 126 76 4 11 133 6 124 8.55e-12 61.6
MS.gene065888.t1 MTR_8g099220 27.200 125 85 3 10 131 6 127 1.41e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065888.t1 AT1G48940 46.512 172 78 2 11 173 10 176 1.50e-55 173
MS.gene065888.t1 AT3G18590 58.400 125 52 0 8 132 3 127 2.58e-53 168
MS.gene065888.t1 AT5G14345 45.455 110 58 2 37 145 21 129 3.96e-32 113
MS.gene065888.t1 AT1G79800 40.000 125 74 1 11 135 13 136 5.57e-31 111
MS.gene065888.t1 AT4G28365 35.948 153 92 2 12 162 9 157 1.15e-30 110
MS.gene065888.t1 AT5G53870 36.517 178 91 7 1 167 1 167 1.56e-27 106
MS.gene065888.t1 AT4G32490 44.860 107 53 2 28 132 27 129 1.70e-27 103
MS.gene065888.t1 AT5G53870 36.517 178 91 7 1 167 1 167 1.92e-27 106
MS.gene065888.t1 AT4G31840 37.107 159 93 5 7 160 2 158 2.59e-27 101
MS.gene065888.t1 AT4G30590 40.323 124 69 3 12 132 8 129 8.47e-26 98.2
MS.gene065888.t1 AT5G57920 40.164 122 64 4 28 142 18 137 2.21e-24 94.4
MS.gene065888.t1 AT2G25060 40.945 127 63 5 24 142 23 145 4.58e-24 93.6
MS.gene065888.t1 AT5G57920 40.336 119 62 4 31 142 22 138 6.65e-24 93.2
MS.gene065888.t1 AT5G57920 40.336 119 62 4 31 142 54 170 9.31e-24 93.6
MS.gene065888.t1 AT4G27520 37.594 133 75 4 17 145 15 143 3.12e-23 94.7
MS.gene065888.t1 AT3G20570 34.426 122 71 3 13 132 15 129 1.02e-20 85.1
MS.gene065888.t1 AT5G25090 37.121 132 70 6 8 132 2 127 1.33e-19 82.0
MS.gene065888.t1 AT2G31050 35.294 136 75 4 11 142 12 138 1.85e-19 82.0
MS.gene065888.t1 AT2G23990 35.556 135 76 5 1 131 1 128 6.50e-19 80.5
MS.gene065888.t1 AT1G64640 31.159 138 78 5 27 151 28 161 2.50e-18 78.6
MS.gene065888.t1 AT2G32300 29.078 141 90 3 8 144 2 136 4.90e-18 79.3
MS.gene065888.t1 AT2G26720 35.484 124 69 3 11 132 12 126 8.88e-18 77.8
MS.gene065888.t1 AT2G32300 29.078 141 90 3 8 144 32 166 9.50e-18 79.0
MS.gene065888.t1 AT5G26330 34.951 103 61 2 32 132 24 122 6.38e-15 69.7
MS.gene065888.t1 AT2G23990 31.818 154 75 6 1 131 1 147 1.06e-14 69.7
MS.gene065888.t1 AT3G60270 32.353 102 62 2 32 132 26 121 1.94e-14 68.2
MS.gene065888.t1 AT5G07475 31.852 135 82 4 14 145 13 140 1.59e-13 65.9
MS.gene065888.t1 AT1G45063 31.579 114 71 3 32 142 149 258 2.74e-11 60.8
MS.gene065888.t1 AT1G45063 31.250 112 69 2 24 132 21 127 3.24e-11 60.8
MS.gene065888.t1 AT1G45063 31.579 114 71 3 32 142 149 258 4.11e-11 60.8
MS.gene065888.t1 AT1G45063 31.250 112 69 2 24 132 21 127 4.48e-11 60.8

Find 27 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATGATCATCAAGGTTT+TGG 0.254697 4.2:-32022565 MS.gene065888:CDS
CTCTTTACTTTGTCATTCCT+TGG 0.308362 4.2:-32022432 MS.gene065888:CDS
GTGCATGATGTGATGGTAAT+AGG 0.357195 4.2:+32022456 None:intergenic
TGTGGTGATGGTGCTGTAAT+TGG 0.357901 4.2:+32022534 None:intergenic
TACTTCATCAGTGGAGTTAG+TGG 0.390509 4.2:-32022606 MS.gene065888:CDS
GCTTTAGAATGTTGTGCTAT+TGG 0.403786 4.2:+32022492 None:intergenic
TCATCTTTGTCCTTTGAGTC+AGG 0.404812 4.2:+32023095 None:intergenic
TTTGAAGTTGGTGGTAGAAT+TGG 0.429149 4.2:-32023128 MS.gene065888:CDS
CTGATGAAGTAGAACATTCC+TGG 0.429651 4.2:+32022618 None:intergenic
AGTTGGTGGTAGAATTGGTT+GGG 0.458216 4.2:-32023123 MS.gene065888:CDS
AGATGATATGTACAACCAAT+GGG 0.511828 4.2:-32023078 MS.gene065888:CDS
AATTGTACTGAATTTGAAGT+TGG 0.513642 4.2:-32023140 MS.gene065888:CDS
TCATTTGCAGATTGTGGTGA+TGG 0.516343 4.2:+32022522 None:intergenic
AAGATGATATGTACAACCAA+TGG 0.516678 4.2:-32023079 MS.gene065888:CDS
GCACTCTCATTTGCAGATTG+TGG 0.519361 4.2:+32022516 None:intergenic
TTGGGTTGTGCCTGACTCAA+AGG 0.571720 4.2:-32023105 MS.gene065888:CDS
TGTACTGAATTTGAAGTTGG+TGG 0.573218 4.2:-32023137 MS.gene065888:CDS
AAGTTGGTGGTAGAATTGGT+TGG 0.575738 4.2:-32023124 MS.gene065888:CDS
TGAGAAAGATTCAGTGATGG+TGG 0.580149 4.2:-32022727 MS.gene065888:CDS
GTGTGAGGCAGCTTTGAAGA+TGG 0.582821 4.2:+32023214 None:intergenic
TTCAAGCATAAATCATGCCA+AGG 0.596027 4.2:+32022415 None:intergenic
GCAAAGTAAAAGTGAGTGTG+AGG 0.606729 4.2:+32023199 None:intergenic
AGGACAGAAAATGATCATCA+AGG 0.610451 4.2:-32022571 MS.gene065888:CDS
AAAGAGTGTGCATGATGTGA+TGG 0.616291 4.2:+32022449 None:intergenic
GGAATGTTCTACTTCATCAG+TGG 0.644882 4.2:-32022615 MS.gene065888:CDS
GTTAGTGGTCATTGTACGAG+AGG 0.648683 4.2:-32022591 MS.gene065888:CDS
GTATGAGAAAGATTCAGTGA+TGG 0.665783 4.2:-32022730 MS.gene065888:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAAAAAAAAAAAAAAAAA+TGG + chr4.2:32022795-32022814 None:intergenic 0.0%
!! TATATATGAGAAAATTAAAT+TGG + chr4.2:32022638-32022657 None:intergenic 10.0%
!!! TTTTTTTTTATAAATGAAGA+TGG - chr4.2:32022803-32022822 MS.gene065888:intron 10.0%
!! AAAATTAAATTGGTAAGAAA+TGG + chr4.2:32022628-32022647 None:intergenic 15.0%
!! ACATATACTCCTAAAAAAAA+TGG + chr4.2:32022700-32022719 None:intergenic 20.0%
!!! ACAATTGATGACAAAAAATT+GGG + chr4.2:32022483-32022502 None:intergenic 20.0%
!!! TACAATTGATGACAAAAAAT+TGG + chr4.2:32022484-32022503 None:intergenic 20.0%
!!! TATATGTCACCATTTTTTTT+AGG - chr4.2:32022688-32022707 MS.gene065888:CDS 20.0%
! CATATATATGCTATAGTTGT+TGG - chr4.2:32022650-32022669 MS.gene065888:CDS 25.0%
!! AATTGTACTGAATTTGAAGT+TGG - chr4.2:32022497-32022516 MS.gene065888:CDS 25.0%
AAGATGATATGTACAACCAA+TGG - chr4.2:32022558-32022577 MS.gene065888:CDS 30.0%
AGATGATATGTACAACCAAT+GGG - chr4.2:32022559-32022578 MS.gene065888:CDS 30.0%
CCATTGTTGCCAAAAAATAA+TGG + chr4.2:32022974-32022993 None:intergenic 30.0%
GTACACAATACAACATAGAA+AGG - chr4.2:32022840-32022859 MS.gene065888:intron 30.0%
TTGGTAAGAAATGGTACTTA+CGG + chr4.2:32022619-32022638 None:intergenic 30.0%
! ATTGATGACAAAAAATTGGG+AGG + chr4.2:32022480-32022499 None:intergenic 30.0%
! GAAAATGATCATCAAGGTTT+TGG - chr4.2:32023072-32023091 MS.gene065888:CDS 30.0%
! TATATCCATTACGAAAGTGT+TGG + chr4.2:32022759-32022778 None:intergenic 30.0%
!! ATATCCATTACGAAAGTGTT+GGG + chr4.2:32022758-32022777 None:intergenic 30.0%
!!! CCATTATTTTTTGGCAACAA+TGG - chr4.2:32022971-32022990 MS.gene065888:intron 30.0%
AGGACAGAAAATGATCATCA+AGG - chr4.2:32023066-32023085 MS.gene065888:CDS 35.0%
ATATCCCAACACTTTCGTAA+TGG - chr4.2:32022751-32022770 MS.gene065888:intron 35.0%
CTCTTTACTTTGTCATTCCT+TGG - chr4.2:32023205-32023224 MS.gene065888:CDS 35.0%
GTATGAGAAAGATTCAGTGA+TGG - chr4.2:32022907-32022926 MS.gene065888:intron 35.0%
! ATCTATTTTGTGAAGCCCAT+TGG + chr4.2:32022577-32022596 None:intergenic 35.0%
! TGTACTGAATTTGAAGTTGG+TGG - chr4.2:32022500-32022519 MS.gene065888:CDS 35.0%
!! GCTTTAGAATGTTGTGCTAT+TGG + chr4.2:32023148-32023167 None:intergenic 35.0%
!! TTTGAAGTTGGTGGTAGAAT+TGG - chr4.2:32022509-32022528 MS.gene065888:CDS 35.0%
!!! TCCACTCGTCCATTATTTTT+TGG - chr4.2:32022962-32022981 MS.gene065888:intron 35.0%
CTGATGAAGTAGAACATTCC+TGG + chr4.2:32023022-32023041 None:intergenic 40.0%
GCAAAGTAAAAGTGAGTGTG+AGG + chr4.2:32022441-32022460 None:intergenic 40.0%
GGAATGTTCTACTTCATCAG+TGG - chr4.2:32023022-32023041 MS.gene065888:intron 40.0%
GTGCATGATGTGATGGTAAT+AGG + chr4.2:32023184-32023203 None:intergenic 40.0%
TACTTCATCAGTGGAGTTAG+TGG - chr4.2:32023031-32023050 MS.gene065888:intron 40.0%
TCATCTTTGTCCTTTGAGTC+AGG + chr4.2:32022545-32022564 None:intergenic 40.0%
TCATTTGCAGATTGTGGTGA+TGG + chr4.2:32023118-32023137 None:intergenic 40.0%
TGAGAAAGATTCAGTGATGG+TGG - chr4.2:32022910-32022929 MS.gene065888:intron 40.0%
! AAAGAGTGTGCATGATGTGA+TGG + chr4.2:32023191-32023210 None:intergenic 40.0%
! GTTTTCAAATTTGAGCGACC+AGG - chr4.2:32023001-32023020 MS.gene065888:intron 40.0%
!! AAGTTGGTGGTAGAATTGGT+TGG - chr4.2:32022513-32022532 MS.gene065888:CDS 40.0%
!! AGTTGGTGGTAGAATTGGTT+GGG - chr4.2:32022514-32022533 MS.gene065888:CDS 40.0%
!! GCCAAAAAATAATGGACGAG+TGG + chr4.2:32022966-32022985 None:intergenic 40.0%
GCACTCTCATTTGCAGATTG+TGG + chr4.2:32023124-32023143 None:intergenic 45.0%
GTTAGTGGTCATTGTACGAG+AGG - chr4.2:32023046-32023065 MS.gene065888:CDS 45.0%
!! TGTGGTGATGGTGCTGTAAT+TGG + chr4.2:32023106-32023125 None:intergenic 45.0%
! TTGGGTTGTGCCTGACTCAA+AGG - chr4.2:32022532-32022551 MS.gene065888:CDS 50.0%
!! GTGTGAGGCAGCTTTGAAGA+TGG + chr4.2:32022426-32022445 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 32022416 32023243 32022416 ID=MS.gene065888
chr4.2 mRNA 32022416 32023243 32022416 ID=MS.gene065888.t1;Parent=MS.gene065888
chr4.2 exon 32023042 32023243 32023042 ID=MS.gene065888.t1.exon1;Parent=MS.gene065888.t1
chr4.2 CDS 32023042 32023243 32023042 ID=cds.MS.gene065888.t1;Parent=MS.gene065888.t1
chr4.2 exon 32022416 32022759 32022416 ID=MS.gene065888.t1.exon2;Parent=MS.gene065888.t1
chr4.2 CDS 32022416 32022759 32022416 ID=cds.MS.gene065888.t1;Parent=MS.gene065888.t1
Gene Sequence

>MS.gene065888

ATGGCTTCCATCTTCAAAGCTGCCTCACACTCACTTTTACTTTGCTTCATTCTTTTCTCAGCCTCCCAATTTTTTGTCATCAATTGTACTGAATTTGAAGTTGGTGGTAGAATTGGTTGGGTTGTGCCTGACTCAAAGGACAAAGATGATATGTACAACCAATGGGCTTCACAAAATAGATTCAAAATCGATGACACTGTCCGTAAGTACCATTTCTTACCAATTTAATTTTCTCATATATATGCTATAGTTGTTGGAATACAAATGCATGATATATGTCACCATTTTTTTTAGGAGTATATGTTAACATTTCAAAATATGTGTGCATTTATATTATATCCCAACACTTTCGTAATGGATATATTTACTTCTCAATCCATTTTTTTTTTTTTTTTTATAAATGAAGATGGTGTCAACTTGTTATGTACACAATACAACATAGAAAGGCTCTAAATTACAATTCTAAATGTGTTGCGATTTTTAGATTTCAAGTATGAGAAAGATTCAGTGATGGTGGTAAGTGAAGAAGAGTATGAACAATGCAAATCCACTCGTCCATTATTTTTTGGCAACAATGGCAACACAGTTTTCAAATTTGAGCGACCAGGAATGTTCTACTTCATCAGTGGAGTTAGTGGTCATTGTACGAGAGGACAGAAAATGATCATCAAGGTTTTGGATGTCGAACCAATTACAGCACCATCACCACAATCTGCAAATGAGAGTGCACCAATAGCACAACATTCTAAAGCTGCTCAAATTACTCCTATTACCATCACATCATGCACACTCTTTACTTTGTCATTCCTTGGCATGATTTATGCTTGA
Protein sequence

>MS.gene065888.t1

MASIFKAASHSLLLCFILFSASQFFVINCTEFEVGGRIGWVVPDSKDKDDMYNQWASQNRFKIDDTVHFKYEKDSVMVVSEEEYEQCKSTRPLFFGNNGNTVFKFERPGMFYFISGVSGHCTRGQKMIIKVLDVEPITAPSPQSANESAPIAQHSKAAQITPITITSCTLFTLSFLGMIYA