AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene072946

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene072946.t1 MTR_3g108560 94.512 164 9 0 1 164 83 246 4.11e-112 322
MS.gene072946.t1 MTR_3g108560 94.512 164 9 0 1 164 83 246 5.43e-111 322
MS.gene072946.t1 MTR_3g108150 48.795 166 77 4 1 162 76 237 3.70e-38 135
MS.gene072946.t1 MTR_7g088260 50.595 168 67 7 1 161 154 312 1.57e-37 134
MS.gene072946.t1 MTR_0492s0020 51.497 167 66 7 1 162 149 305 2.81e-37 133
MS.gene072946.t1 MTR_0543s0010 51.497 167 66 7 1 162 149 305 5.03e-37 133
MS.gene072946.t1 MTR_3g087260 51.515 132 57 3 34 162 184 311 2.78e-31 117
MS.gene072946.t1 MTR_3g087260 54.902 102 42 3 19 117 81 181 3.00e-23 95.9
MS.gene072946.t1 MTR_7g056020 44.706 170 79 5 1 166 72 230 5.38e-29 112
MS.gene072946.t1 MTR_3g109982 61.290 93 35 1 51 143 222 313 3.38e-27 107
MS.gene072946.t1 MTR_3g109982 51.261 119 52 3 1 114 76 193 3.21e-25 102
MS.gene072946.t1 MTR_3g110010 61.290 93 35 1 51 143 222 313 3.82e-27 107
MS.gene072946.t1 MTR_3g110010 51.261 119 52 3 1 114 76 193 4.23e-25 101
MS.gene072946.t1 MTR_5g073420 35.762 151 75 4 4 143 82 221 8.54e-18 80.1
MS.gene072946.t1 MTR_5g061680 40.741 108 59 1 8 110 86 193 2.39e-16 75.5
MS.gene072946.t1 MTR_5g012840 34.615 156 85 5 1 144 52 202 8.57e-16 73.9
MS.gene072946.t1 MTR_7g056277 32.298 161 100 3 8 162 334 491 6.83e-15 72.0
MS.gene072946.t1 MTR_7g056287 31.250 160 101 3 8 161 78 234 9.53e-15 71.2
MS.gene072946.t1 MTR_7g098570 41.667 120 61 4 1 112 83 201 1.20e-14 71.2
MS.gene072946.t1 MTR_4g080610 46.154 91 45 2 73 162 121 208 1.93e-14 70.5
MS.gene072946.t1 MTR_8g085430 36.719 128 66 6 1 117 82 205 2.47e-14 70.1
MS.gene072946.t1 MTR_1g041245 33.526 173 95 7 1 161 74 238 3.63e-14 69.7
MS.gene072946.t1 MTR_7g115270 32.278 158 86 4 7 143 81 238 3.94e-14 69.7
MS.gene072946.t1 MTR_1g066830 29.825 171 110 5 1 165 75 241 1.04e-13 68.6
MS.gene072946.t1 MTR_7g098480 35.374 147 78 6 9 144 89 229 1.24e-13 68.6
MS.gene072946.t1 MTR_6g011460 30.303 165 96 6 8 162 120 275 1.40e-13 68.2
MS.gene072946.t1 MTR_3g071850 35.971 139 76 5 12 141 104 238 1.66e-13 68.2
MS.gene072946.t1 MTR_7g056447 36.090 133 73 6 9 133 80 208 3.22e-13 66.6
MS.gene072946.t1 MTR_3g040700 33.333 156 92 5 1 145 106 260 5.11e-13 66.6
MS.gene072946.t1 MTR_7g032370 33.333 153 80 6 4 145 56 197 7.04e-13 65.9
MS.gene072946.t1 MTR_5g058100 35.256 156 86 5 8 148 83 238 1.17e-12 65.5
MS.gene072946.t1 MTR_7g060470 33.125 160 87 5 24 165 101 258 1.93e-12 64.7
MS.gene072946.t1 MTR_4g039440 32.500 120 71 3 49 163 151 265 3.11e-12 64.3
MS.gene072946.t1 MTR_1g108800 37.671 146 80 5 6 142 47 190 3.22e-12 63.9
MS.gene072946.t1 MTR_6g022500 35.099 151 88 5 8 150 175 323 3.28e-12 64.3
MS.gene072946.t1 MTR_7g056433 36.054 147 80 6 10 144 84 228 3.83e-12 63.9
MS.gene072946.t1 MTR_4g134150 39.091 110 63 3 7 112 79 188 4.67e-12 62.8
MS.gene072946.t1 MTR_6g045333 36.765 136 79 4 12 141 141 275 8.17e-12 63.2
MS.gene072946.t1 MTR_7g098510 34.177 158 82 7 1 144 81 230 8.86e-12 62.8
MS.gene072946.t1 MTR_7g007080 34.646 127 75 3 23 145 103 225 1.11e-11 62.8
MS.gene072946.t1 MTR_3g036250 32.258 155 95 4 1 145 68 222 3.39e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATACCTTGTCGTGTGTTTC+TGG 0.090694 3.1:-85480665 MS.gene072946:CDS
TCCATCTGTTTCACATATTA+TGG 0.165550 3.1:-85480757 MS.gene072946:CDS
AAATTACTAGTTCAAATTTA+AGG 0.171670 3.1:-85480493 None:intergenic
TTAAATTTGAACTAGTAATT+TGG 0.235482 3.1:+85480495 None:intergenic
CACACGACAAGGTATCTTTA+TGG 0.236534 3.1:+85480672 None:intergenic
TCCCTACGGCTTTCATTCTA+AGG 0.250763 3.1:-85480876 MS.gene072946:CDS
AATTACTAGTTCAAATTTAA+GGG 0.323327 3.1:-85480492 None:intergenic
GCCAACAAGCTTATCCAATT+TGG 0.334639 3.1:-85480632 MS.gene072946:CDS
TCACATATTATGGACATATC+AGG 0.341356 3.1:-85480747 MS.gene072946:CDS
ATGTTATCCTCTTCAATTTG+AGG 0.360335 3.1:+85480836 None:intergenic
TGCTTCCAACTCTTGTAGAA+TGG 0.387005 3.1:+85480705 None:intergenic
AATGTTAGCTCTGACCAAAT+TGG 0.390378 3.1:+85480618 None:intergenic
TGTAGTAGTGACACTTGATA+TGG 0.393009 3.1:+85480980 None:intergenic
ATACCTTGTCGTGTGTTTCT+GGG 0.397938 3.1:-85480664 MS.gene072946:CDS
ATGTGAAACAGATGGATTCC+AGG 0.435339 3.1:+85480764 None:intergenic
GCTTCCAACTCTTGTAGAAT+GGG 0.440611 3.1:+85480706 None:intergenic
TTTGAGGACAGACAAGGTTT+CGG 0.443242 3.1:+85480852 None:intergenic
CGCAAGTAGGCGCATATGTT+GGG 0.450467 3.1:+85480549 None:intergenic
ACCAAATTGGATAAGCTTGT+TGG 0.450733 3.1:+85480631 None:intergenic
TAGCATTAGAAACAAATTTG+TGG 0.474187 3.1:+85480947 None:intergenic
ATTATGCATGGGAGAGATGT+TGG 0.483648 3.1:+85480594 None:intergenic
CCGCAAGTAGGCGCATATGT+TGG 0.484727 3.1:+85480548 None:intergenic
AGCGGGAGAGATCAATGGTT+AGG 0.516583 3.1:+85480905 None:intergenic
GTCGCTCAAACTCCTTCACC+TGG 0.548571 3.1:-85480782 MS.gene072946:CDS
CTTCAATTTGAGGACAGACA+AGG 0.555021 3.1:+85480846 None:intergenic
ATCTGAGCGGGAGAGATCAA+TGG 0.565352 3.1:+85480900 None:intergenic
ATGTCCCATTCTACAAGAGT+TGG 0.565975 3.1:-85480710 MS.gene072946:CDS
CTCCCGCTCAGATTTCCCTA+CGG 0.568994 3.1:-85480890 MS.gene072946:CDS
GCGATCAAGCAAATTATGCA+TGG 0.570982 3.1:+85480582 None:intergenic
AGCCGTAGGGAAATCTGAGC+GGG 0.573586 3.1:+85480888 None:intergenic
TCCATAATATGTGAAACAGA+TGG 0.573720 3.1:+85480756 None:intergenic
GACACTTGATATGGAATGAG+AGG 0.580314 3.1:+85480989 None:intergenic
AGCGACGGAAGATCAACGAC+AGG 0.590697 3.1:+85480799 None:intergenic
CGATCAAGCAAATTATGCAT+GGG 0.597728 3.1:+85480583 None:intergenic
TGTCTGTCCTCAAATTGAAG+AGG 0.599406 3.1:-85480843 MS.gene072946:CDS
TCCTTAGAATGAAAGCCGTA+GGG 0.602699 3.1:+85480875 None:intergenic
AACAGATGGATTCCAGGTGA+AGG 0.605969 3.1:+85480770 None:intergenic
GCATATGTTGGGCGTTACGA+AGG 0.606778 3.1:+85480560 None:intergenic
CCAACATATGCGCCTACTTG+CGG 0.611512 3.1:-85480548 MS.gene072946:CDS
GTCCTTAGAATGAAAGCCGT+AGG 0.619468 3.1:+85480874 None:intergenic
TTGATATGGAATGAGAGGAT+AGG 0.621762 3.1:+85480994 None:intergenic
GAACCCAGAAACACACGACA+AGG 0.636895 3.1:+85480661 None:intergenic
AGGATAACATTGAACTACGA+AGG 0.654558 3.1:-85480823 MS.gene072946:CDS
AGGTGAAGGAGTTTGAGCGA+CGG 0.665820 3.1:+85480784 None:intergenic
AAGCCGTAGGGAAATCTGAG+CGG 0.734235 3.1:+85480887 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATTTGAACTAGTAATT+TGG + chr3.1:85481021-85481040 None:intergenic 15.0%
! TAGCATTAGAAACAAATTTG+TGG + chr3.1:85480569-85480588 None:intergenic 25.0%
ATGTTATCCTCTTCAATTTG+AGG + chr3.1:85480680-85480699 None:intergenic 30.0%
TCACATATTATGGACATATC+AGG - chr3.1:85480766-85480785 MS.gene072946:CDS 30.0%
TCCATAATATGTGAAACAGA+TGG + chr3.1:85480760-85480779 None:intergenic 30.0%
TCCATCTGTTTCACATATTA+TGG - chr3.1:85480756-85480775 MS.gene072946:CDS 30.0%
! CATATCAGGAAACTTTTATC+TGG - chr3.1:85480780-85480799 MS.gene072946:CDS 30.0%
!!! AGGTTGAGTGTTATTTTGAT+TGG + chr3.1:85480502-85480521 None:intergenic 30.0%
ACCAAATTGGATAAGCTTGT+TGG + chr3.1:85480885-85480904 None:intergenic 35.0%
AGGATAACATTGAACTACGA+AGG - chr3.1:85480690-85480709 MS.gene072946:CDS 35.0%
CGATCAAGCAAATTATGCAT+GGG + chr3.1:85480933-85480952 None:intergenic 35.0%
TGTAGTAGTGACACTTGATA+TGG + chr3.1:85480536-85480555 None:intergenic 35.0%
TTGATATGGAATGAGAGGAT+AGG + chr3.1:85480522-85480541 None:intergenic 35.0%
! TTTTGATACATACCGCAAGT+AGG + chr3.1:85480980-85480999 None:intergenic 35.0%
!! AATGTTAGCTCTGACCAAAT+TGG + chr3.1:85480898-85480917 None:intergenic 35.0%
ATACCTTGTCGTGTGTTTCT+GGG - chr3.1:85480849-85480868 MS.gene072946:CDS 40.0%
ATGTCCCATTCTACAAGAGT+TGG - chr3.1:85480803-85480822 MS.gene072946:CDS 40.0%
ATTATGCATGGGAGAGATGT+TGG + chr3.1:85480922-85480941 None:intergenic 40.0%
CTTCAATTTGAGGACAGACA+AGG + chr3.1:85480670-85480689 None:intergenic 40.0%
GACACTTGATATGGAATGAG+AGG + chr3.1:85480527-85480546 None:intergenic 40.0%
GCCAACAAGCTTATCCAATT+TGG - chr3.1:85480881-85480900 MS.gene072946:CDS 40.0%
GCGATCAAGCAAATTATGCA+TGG + chr3.1:85480934-85480953 None:intergenic 40.0%
GCTTCCAACTCTTGTAGAAT+GGG + chr3.1:85480810-85480829 None:intergenic 40.0%
TCCTTAGAATGAAAGCCGTA+GGG + chr3.1:85480641-85480660 None:intergenic 40.0%
TGCTTCCAACTCTTGTAGAA+TGG + chr3.1:85480811-85480830 None:intergenic 40.0%
TGTCTGTCCTCAAATTGAAG+AGG - chr3.1:85480670-85480689 MS.gene072946:CDS 40.0%
TTTGAGGACAGACAAGGTTT+CGG + chr3.1:85480664-85480683 None:intergenic 40.0%
! ATGTGAAACAGATGGATTCC+AGG + chr3.1:85480752-85480771 None:intergenic 40.0%
! CACACGACAAGGTATCTTTA+TGG + chr3.1:85480844-85480863 None:intergenic 40.0%
GATACCTTGTCGTGTGTTTC+TGG - chr3.1:85480848-85480867 MS.gene072946:CDS 45.0%
GTCCTTAGAATGAAAGCCGT+AGG + chr3.1:85480642-85480661 None:intergenic 45.0%
TCCCTACGGCTTTCATTCTA+AGG - chr3.1:85480637-85480656 MS.gene072946:CDS 45.0%
! AACAGATGGATTCCAGGTGA+AGG + chr3.1:85480746-85480765 None:intergenic 45.0%
AAGCCGTAGGGAAATCTGAG+CGG + chr3.1:85480629-85480648 None:intergenic 50.0%
AGCGGGAGAGATCAATGGTT+AGG + chr3.1:85480611-85480630 None:intergenic 50.0%
AGGTGAAGGAGTTTGAGCGA+CGG + chr3.1:85480732-85480751 None:intergenic 50.0%
ATCTGAGCGGGAGAGATCAA+TGG + chr3.1:85480616-85480635 None:intergenic 50.0%
CCAACATATGCGCCTACTTG+CGG - chr3.1:85480965-85480984 MS.gene072946:CDS 50.0%
CGCAAGTAGGCGCATATGTT+GGG + chr3.1:85480967-85480986 None:intergenic 50.0%
GAACCCAGAAACACACGACA+AGG + chr3.1:85480855-85480874 None:intergenic 50.0%
GCATATGTTGGGCGTTACGA+AGG + chr3.1:85480956-85480975 None:intergenic 50.0%
AGCCGTAGGGAAATCTGAGC+GGG + chr3.1:85480628-85480647 None:intergenic 55.0%
AGCGACGGAAGATCAACGAC+AGG + chr3.1:85480717-85480736 None:intergenic 55.0%
CCGCAAGTAGGCGCATATGT+TGG + chr3.1:85480968-85480987 None:intergenic 55.0%
CTCCCGCTCAGATTTCCCTA+CGG - chr3.1:85480623-85480642 MS.gene072946:CDS 55.0%
GTCGCTCAAACTCCTTCACC+TGG - chr3.1:85480731-85480750 MS.gene072946:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 85480495 85481040 85480495 ID=MS.gene072946
chr3.1 mRNA 85480495 85481040 85480495 ID=MS.gene072946.t1;Parent=MS.gene072946
chr3.1 exon 85480495 85481040 85480495 ID=MS.gene072946.t1.exon1;Parent=MS.gene072946.t1
chr3.1 CDS 85480495 85481040 85480495 ID=cds.MS.gene072946.t1;Parent=MS.gene072946.t1
Gene Sequence

>MS.gene072946

ATGGCCAATCAAAATAACACTCAACCTATCCTCTCATTCCATATCAAGTGTCACTACTACAATTGTGATATCCACAAATTTGTTTCTAATGCTATTCAACGACGAGTTCAAAACCTAACCATTGATCTCTCCCGCTCAGATTTCCCTACGGCTTTCATTCTAAGGACCGAAACCTTGTCTGTCCTCAAATTGAAGAGGATAACATTGAACTACGAAGGTCCTGTCGTTGATCTTCCGTCGCTCAAACTCCTTCACCTGGAATCCATCTGTTTCACATATTATGGACATATCAGGAAACTTTTATCTGGATGTCCCATTCTACAAGAGTTGGAAGCAAATGATCTAACCATAAAGATACCTTGTCGTGTGTTTCTGGGTTCTTCACAGCCAACAAGCTTATCCAATTTGGTCAGAGCTAACATTTCCAACATCTCTCCCATGCATAATTTGCTTGATCGCCTTCGTAACGCCCAACATATGCGCCTACTTGCGGTATGTATCAAAATATTTTCTGCTTATATGACCAAATTACTAGTTCAAATTTAA
Protein sequence

>MS.gene072946.t1

MANQNNTQPILSFHIKCHYYNCDIHKFVSNAIQRRVQNLTIDLSRSDFPTAFILRTETLSVLKLKRITLNYEGPVVDLPSLKLLHLESICFTYYGHIRKLLSGCPILQELEANDLTIKIPCRVFLGSSQPTSLSNLVRANISNISPMHNLLDRLRNAQHMRLLAVCIKIFSAYMTKLLVQI