AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39906

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39906.t1 MTR_1g070480 88.083 193 23 0 1 193 1 193 1.32e-111 317
MS.gene39906.t1 MTR_7g096220 52.747 182 85 1 11 191 18 199 1.09e-61 190
MS.gene39906.t1 MTR_3g012070 77.320 97 21 1 95 191 32 127 2.28e-34 120
MS.gene39906.t1 MTR_2g100260 45.205 146 74 2 30 170 35 179 3.87e-32 114
MS.gene39906.t1 MTR_1g080760 43.617 188 98 3 10 193 10 193 5.90e-30 109
MS.gene39906.t1 MTR_6g092690 36.585 164 98 2 11 168 11 174 1.13e-28 106
MS.gene39906.t1 MTR_4g014060 37.143 140 86 1 32 169 60 199 9.66e-28 104
MS.gene39906.t1 MTR_0562s0010 37.143 140 86 1 32 169 60 199 9.66e-28 104
MS.gene39906.t1 MTR_5g083490 33.163 196 111 2 6 181 8 203 1.16e-26 101
MS.gene39906.t1 MTR_2g100270 43.275 171 87 2 9 169 3 173 1.34e-23 92.8
MS.gene39906.t1 MTR_8g016150 36.970 165 96 1 7 163 2 166 1.34e-22 90.1
MS.gene39906.t1 MTR_1g093090 45.333 75 41 0 30 104 21 95 1.44e-14 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39906.t1 AT1G04260 40.341 176 105 0 18 193 7 182 5.13e-43 142
MS.gene39906.t1 AT1G55190 48.951 143 73 0 26 168 31 173 8.02e-38 129
MS.gene39906.t1 AT3G13710 41.566 166 83 1 17 168 8 173 7.16e-36 124
MS.gene39906.t1 AT1G08770 40.113 177 102 2 17 191 33 207 1.78e-31 114
MS.gene39906.t1 AT3G13720 45.139 144 79 0 25 168 30 173 2.13e-31 112
MS.gene39906.t1 AT5G01640 39.073 151 90 1 32 180 55 205 9.33e-29 107
MS.gene39906.t1 AT2G40380 39.735 151 89 1 32 180 47 197 2.90e-26 100
MS.gene39906.t1 AT2G38360 32.895 152 100 1 32 181 55 206 3.26e-26 100
MS.gene39906.t1 AT3G56110 37.838 148 90 1 32 177 45 192 6.32e-24 94.4
MS.gene39906.t1 AT3G56110 37.838 148 90 1 32 177 45 192 6.32e-24 94.4
MS.gene39906.t1 AT3G56110 37.838 148 90 1 32 177 45 192 6.32e-24 94.4
MS.gene39906.t1 AT3G56110 37.838 148 90 1 32 177 45 192 6.32e-24 94.4
MS.gene39906.t1 AT5G56230 34.104 173 109 3 6 177 14 182 2.30e-23 92.0
MS.gene39906.t1 AT1G17700 38.889 144 88 0 26 169 31 174 6.94e-23 90.9
MS.gene39906.t1 AT5G07110 33.333 147 96 1 31 175 44 190 1.53e-21 88.2
MS.gene39906.t1 AT5G05380 38.514 148 89 1 32 177 48 195 1.89e-21 87.8
MS.gene39906.t1 AT5G05380 38.514 148 89 1 32 177 91 238 4.27e-21 87.8
MS.gene39906.t1 AT5G05380 38.514 148 89 1 32 177 99 246 4.72e-21 87.8
MS.gene39906.t1 AT5G05380 38.514 148 89 1 32 177 115 262 6.56e-21 87.8
MS.gene39906.t1 AT1G55640 29.286 140 98 1 32 170 38 177 6.89e-15 69.7
MS.gene39906.t1 AT4G29658 28.000 175 113 3 9 170 3 177 1.79e-11 60.8

Find 70 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGAAGAAGAGATCTTTGA+TGG 0.279860 1.4:+57864779 MS.gene39906:CDS
TTGGAAGGTGGGGTGGCGCG+TGG 0.324938 1.4:-57864341 None:intergenic
GGTGATTTGCTTTCAGTTGT+TGG 0.353754 1.4:+57864800 MS.gene39906:CDS
GAAGGGAGAGAGTTGTAAGT+TGG 0.355663 1.4:-57864305 None:intergenic
TCCTCGCCGTCTTCGCCGTT+TGG 0.358765 1.4:+57864549 MS.gene39906:CDS
GTGAGGATGAGTGAAGGATT+GGG 0.361564 1.4:-57864402 None:intergenic
AGTGAGGATGAGTGAAGGAT+TGG 0.368971 1.4:-57864403 None:intergenic
GGAAGGTGGGGTGGCGCGTG+GGG 0.374482 1.4:-57864339 None:intergenic
CACGTGGGGTAGTTGGAAGG+TGG 0.376357 1.4:-57864353 None:intergenic
GTAAGTTGGAGTGGGATAGA+TGG 0.383602 1.4:-57864291 None:intergenic
AGCTTCAATACCAAGCGAAC+GGG 0.394063 1.4:+57864827 MS.gene39906:CDS
CGCTCGTCTTCACCGGCGTC+TGG 0.396795 1.4:+57864672 MS.gene39906:CDS
GGGGTAGTTGGAAGGTGGGG+TGG 0.436768 1.4:-57864348 None:intergenic
TGGGCGGCACGTGGGGTAGT+TGG 0.449041 1.4:-57864360 None:intergenic
CTTCTTCTTCAGTGACCACC+TGG 0.451935 1.4:+57864580 MS.gene39906:CDS
TGAGGGAGAGAGGGTGGTAG+CGG 0.452355 1.4:-57864520 None:intergenic
AGGAAGACGATGAGGGAGAG+AGG 0.457920 1.4:-57864530 None:intergenic
GAGGGTGGTAGCGGAGGCTG+AGG 0.461609 1.4:-57864511 None:intergenic
TGGAAGGTGGGGTGGCGCGT+GGG 0.467570 1.4:-57864340 None:intergenic
GAAGAACCAAACGGCGAAGA+CGG 0.468945 1.4:-57864555 None:intergenic
ACGGAGGGTGGTTTCGGAGA+GGG 0.477533 1.4:-57864426 None:intergenic
CGTGGGGAAGTTGAGTTTGA+AGG 0.477570 1.4:-57864323 None:intergenic
GGTAGCGGAGGCTGAGGAAG+AGG 0.477985 1.4:-57864505 None:intergenic
CGTGGGGTAGTTGGAAGGTG+GGG 0.481724 1.4:-57864351 None:intergenic
GTCCTCGTGTCGGTGCTCTT+CGG 0.484352 1.4:+57864701 MS.gene39906:CDS
GTGGTTTCGGAGAGGGAGTG+AGG 0.487174 1.4:-57864419 None:intergenic
GAGAGAGTTGTAAGTTGGAG+TGG 0.502950 1.4:-57864300 None:intergenic
AGTTGATGCGGAAGTGGTTG+AGG 0.503368 1.4:-57864460 None:intergenic
AGACGATGAGGGAGAGAGGG+TGG 0.503783 1.4:-57864526 None:intergenic
GTCGTCGCGCTCGTCTTCAC+CGG 0.504856 1.4:+57864665 MS.gene39906:CDS
ACGTGGGGTAGTTGGAAGGT+GGG 0.508307 1.4:-57864352 None:intergenic
TGAGGATGAGTGAAGGATTG+GGG 0.510390 1.4:-57864401 None:intergenic
TTTGCCATGGGCGGCACGTG+GGG 0.513786 1.4:-57864367 None:intergenic
AGAGAGTTGTAAGTTGGAGT+GGG 0.514057 1.4:-57864299 None:intergenic
TGTCGATGGTGAAACGGAAG+AGG 0.515612 1.4:-57864607 None:intergenic
GGAGGCTGAGGAAGAGGATG+AGG 0.518385 1.4:-57864499 None:intergenic
GAGGATGAGGAGGATGATGA+TGG 0.521356 1.4:-57864486 None:intergenic
AGAGTAGAATGAGGAGGAAG+CGG 0.522523 1.4:-57864631 None:intergenic
GGGAGAGAGGGTGGTAGCGG+AGG 0.523307 1.4:-57864517 None:intergenic
AGCGGTTGTCGATGGTGAAA+CGG 0.524582 1.4:-57864613 None:intergenic
TCTAGTGTACCCCGTTCGCT+TGG 0.526290 1.4:-57864837 None:intergenic
CGGCACGTGGGGTAGTTGGA+AGG 0.532393 1.4:-57864356 None:intergenic
GAGGGAGTGAGGATGAGTGA+AGG 0.534577 1.4:-57864408 None:intergenic
GGCTGAGGAAGAGGATGAGG+AGG 0.555428 1.4:-57864496 None:intergenic
GTGGGGAAGTTGAGTTTGAA+GGG 0.558559 1.4:-57864322 None:intergenic
ACTACCCCACGTGCCGCCCA+TGG 0.561155 1.4:+57864363 MS.gene39906:CDS
GTCGGTGCTCTTCGGTGCTG+CGG 0.562357 1.4:+57864709 MS.gene39906:CDS
GAGGAGGAAGCGGTTGTCGA+TGG 0.562502 1.4:-57864621 None:intergenic
GAAGAAGAGGAAGAACCAAA+CGG 0.572756 1.4:-57864564 None:intergenic
CTGGCTTAACGTCCTCGTGT+CGG 0.579627 1.4:+57864691 MS.gene39906:CDS
GGTGGTCACTGAAGAAGAAG+AGG 0.581883 1.4:-57864577 None:intergenic
GGTGCTCTTCGGTGCTGCGG+TGG 0.582059 1.4:+57864712 MS.gene39906:CDS
TGGCGTAGTTGATGCGGAAG+TGG 0.582115 1.4:-57864466 None:intergenic
GGAAGACGATGAGGGAGAGA+GGG 0.595788 1.4:-57864529 None:intergenic
GGGCAGAGAGTAGAATGAGG+AGG 0.599319 1.4:-57864637 None:intergenic
CACCGAAGAGCACCGACACG+AGG 0.603948 1.4:-57864703 None:intergenic
TAGCTTCAATACCAAGCGAA+CGG 0.609099 1.4:+57864826 MS.gene39906:CDS
GACGAGCGCGACGACTGTGA+GGG 0.612183 1.4:-57864657 None:intergenic
TACGGAGGGTGGTTTCGGAG+AGG 0.616601 1.4:-57864427 None:intergenic
TGAGGGCAGAGAGTAGAATG+AGG 0.616996 1.4:-57864640 None:intergenic
TGAAACGGAAGAGGATGACC+AGG 0.620279 1.4:-57864598 None:intergenic
ACCAAACGGCGAAGACGGCG+AGG 0.625480 1.4:-57864550 None:intergenic
AGACGGCGAGGAAGACGATG+AGG 0.634290 1.4:-57864538 None:intergenic
GATTTGCTTTCAGTTGTTGG+TGG 0.638304 1.4:+57864803 MS.gene39906:CDS
GACGGCGAGGAAGACGATGA+GGG 0.639915 1.4:-57864537 None:intergenic
AGACGAGCGCGACGACTGTG+AGG 0.675858 1.4:-57864658 None:intergenic
TGATGATGGCGTAGTTGATG+CGG 0.679858 1.4:-57864472 None:intergenic
GCTTCAATACCAAGCGAACG+GGG 0.692098 1.4:+57864828 MS.gene39906:CDS
GAGGACGTTAAGCCAGACGC+CGG 0.719336 1.4:-57864684 None:intergenic
AACGGAAGAGGATGACCAGG+TGG 0.730030 1.4:-57864595 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GATGAAGAAGAGATCTTTGA+TGG + chr1.4:57864779-57864798 MS.gene39906:CDS 35.0%
GAAGAAGAGGAAGAACCAAA+CGG - chr1.4:57864567-57864586 None:intergenic 40.0%
TAGCTTCAATACCAAGCGAA+CGG + chr1.4:57864826-57864845 MS.gene39906:CDS 40.0%
! AGAGAGTTGTAAGTTGGAGT+GGG - chr1.4:57864302-57864321 None:intergenic 40.0%
! GAGTGAAGAAGTTTTGCCAT+GGG - chr1.4:57864382-57864401 None:intergenic 40.0%
! GATTTGCTTTCAGTTGTTGG+TGG + chr1.4:57864803-57864822 MS.gene39906:CDS 40.0%
! GGTTGAGGTTGCGTTTTATA+CGG - chr1.4:57864448-57864467 None:intergenic 40.0%
! TTTTATACGGAGGGTGGTTT+CGG - chr1.4:57864435-57864454 None:intergenic 40.0%
!! GGTGATTTGCTTTCAGTTGT+TGG + chr1.4:57864800-57864819 MS.gene39906:CDS 40.0%
!! TTGTTTTGCATGCGGCATTT+CGG + chr1.4:57864735-57864754 MS.gene39906:CDS 40.0%
AGAGTAGAATGAGGAGGAAG+CGG - chr1.4:57864634-57864653 None:intergenic 45.0%
AGCTTCAATACCAAGCGAAC+GGG + chr1.4:57864827-57864846 MS.gene39906:CDS 45.0%
AGTGAGGATGAGTGAAGGAT+TGG - chr1.4:57864406-57864425 None:intergenic 45.0%
GAAGGGAGAGAGTTGTAAGT+TGG - chr1.4:57864308-57864327 None:intergenic 45.0%
GTGAGGATGAGTGAAGGATT+GGG - chr1.4:57864405-57864424 None:intergenic 45.0%
GTGGGGAAGTTGAGTTTGAA+GGG - chr1.4:57864325-57864344 None:intergenic 45.0%
TGAGGATGAGTGAAGGATTG+GGG - chr1.4:57864404-57864423 None:intergenic 45.0%
! GAGAGAGTTGTAAGTTGGAG+TGG - chr1.4:57864303-57864322 None:intergenic 45.0%
! GAGGTTGCGTTTTATACGGA+GGG - chr1.4:57864444-57864463 None:intergenic 45.0%
! GGAGTGAAGAAGTTTTGCCA+TGG - chr1.4:57864383-57864402 None:intergenic 45.0%
! GTAAGTTGGAGTGGGATAGA+TGG - chr1.4:57864294-57864313 None:intergenic 45.0%
! TGAAGAAGTTTTGCCATGGG+CGG - chr1.4:57864379-57864398 None:intergenic 45.0%
! TGAGGTTGCGTTTTATACGG+AGG - chr1.4:57864445-57864464 None:intergenic 45.0%
!! TGATGATGGCGTAGTTGATG+CGG - chr1.4:57864475-57864494 None:intergenic 45.0%
AGCGGTTGTCGATGGTGAAA+CGG - chr1.4:57864616-57864635 None:intergenic 50.0%
CGTGGGGAAGTTGAGTTTGA+AGG - chr1.4:57864326-57864345 None:intergenic 50.0%
CTTCTTCTTCAGTGACCACC+TGG + chr1.4:57864580-57864599 MS.gene39906:CDS 50.0%
GAAGAACCAAACGGCGAAGA+CGG - chr1.4:57864558-57864577 None:intergenic 50.0%
GAGGATGAGGAGGATGATGA+TGG - chr1.4:57864489-57864508 None:intergenic 50.0%
GCTTCAATACCAAGCGAACG+GGG + chr1.4:57864828-57864847 MS.gene39906:CDS 50.0%
GGTGGTCACTGAAGAAGAAG+AGG - chr1.4:57864580-57864599 None:intergenic 50.0%
TGAAACGGAAGAGGATGACC+AGG - chr1.4:57864601-57864620 None:intergenic 50.0%
TGAGGGCAGAGAGTAGAATG+AGG - chr1.4:57864643-57864662 None:intergenic 50.0%
TGTCGATGGTGAAACGGAAG+AGG - chr1.4:57864610-57864629 None:intergenic 50.0%
! AGTTGATGCGGAAGTGGTTG+AGG - chr1.4:57864463-57864482 None:intergenic 50.0%
! GTTGCGTTTTATACGGAGGG+TGG - chr1.4:57864441-57864460 None:intergenic 50.0%
!! TGCGGTGGTTGTTTTGCATG+CGG + chr1.4:57864727-57864746 MS.gene39906:CDS 50.0%
AACGGAAGAGGATGACCAGG+TGG - chr1.4:57864598-57864617 None:intergenic 55.0%
ACGTGGGGTAGTTGGAAGGT+GGG - chr1.4:57864355-57864374 None:intergenic 55.0%
AGGAAGACGATGAGGGAGAG+AGG - chr1.4:57864533-57864552 None:intergenic 55.0%
CTGGCTTAACGTCCTCGTGT+CGG + chr1.4:57864691-57864710 MS.gene39906:CDS 55.0%
GAGGGAGTGAGGATGAGTGA+AGG - chr1.4:57864411-57864430 None:intergenic 55.0%
GGAAGACGATGAGGGAGAGA+GGG - chr1.4:57864532-57864551 None:intergenic 55.0%
GGGCAGAGAGTAGAATGAGG+AGG - chr1.4:57864640-57864659 None:intergenic 55.0%
TCTAGTGTACCCCGTTCGCT+TGG - chr1.4:57864840-57864859 None:intergenic 55.0%
! TGGCGTAGTTGATGCGGAAG+TGG - chr1.4:57864469-57864488 None:intergenic 55.0%
ACGGAGGGTGGTTTCGGAGA+GGG - chr1.4:57864429-57864448 None:intergenic 60.0%
AGACGATGAGGGAGAGAGGG+TGG - chr1.4:57864529-57864548 None:intergenic 60.0%
AGACGGCGAGGAAGACGATG+AGG - chr1.4:57864541-57864560 None:intergenic 60.0%
CACGTGGGGTAGTTGGAAGG+TGG - chr1.4:57864356-57864375 None:intergenic 60.0%
CGTGGGGTAGTTGGAAGGTG+GGG - chr1.4:57864354-57864373 None:intergenic 60.0%
GACGGCGAGGAAGACGATGA+GGG - chr1.4:57864540-57864559 None:intergenic 60.0%
GAGGACGTTAAGCCAGACGC+CGG - chr1.4:57864687-57864706 None:intergenic 60.0%
GAGGAGGAAGCGGTTGTCGA+TGG - chr1.4:57864624-57864643 None:intergenic 60.0%
GGAGGCTGAGGAAGAGGATG+AGG - chr1.4:57864502-57864521 None:intergenic 60.0%
GGCTGAGGAAGAGGATGAGG+AGG - chr1.4:57864499-57864518 None:intergenic 60.0%
GTGGTTTCGGAGAGGGAGTG+AGG - chr1.4:57864422-57864441 None:intergenic 60.0%
TACGGAGGGTGGTTTCGGAG+AGG - chr1.4:57864430-57864449 None:intergenic 60.0%
TGAGGGAGAGAGGGTGGTAG+CGG - chr1.4:57864523-57864542 None:intergenic 60.0%
! GTCCTCGTGTCGGTGCTCTT+CGG + chr1.4:57864701-57864720 MS.gene39906:CDS 60.0%
! TTTTGCCATGGGCGGCACGT+GGG - chr1.4:57864371-57864390 None:intergenic 60.0%
ACCAAACGGCGAAGACGGCG+AGG - chr1.4:57864553-57864572 None:intergenic 65.0%
AGACGAGCGCGACGACTGTG+AGG - chr1.4:57864661-57864680 None:intergenic 65.0%
CGGCACGTGGGGTAGTTGGA+AGG - chr1.4:57864359-57864378 None:intergenic 65.0%
GACGAGCGCGACGACTGTGA+GGG - chr1.4:57864660-57864679 None:intergenic 65.0%
GGGGTAGTTGGAAGGTGGGG+TGG - chr1.4:57864351-57864370 None:intergenic 65.0%
GTCGTCGCGCTCGTCTTCAC+CGG + chr1.4:57864665-57864684 MS.gene39906:CDS 65.0%
TCCTCGCCGTCTTCGCCGTT+TGG + chr1.4:57864549-57864568 MS.gene39906:CDS 65.0%
TTTGCCATGGGCGGCACGTG+GGG - chr1.4:57864370-57864389 None:intergenic 65.0%
! GTTTTGCCATGGGCGGCACG+TGG - chr1.4:57864372-57864391 None:intergenic 65.0%
!! CACCGAAGAGCACCGACACG+AGG - chr1.4:57864706-57864725 None:intergenic 65.0%
!! GGTAGCGGAGGCTGAGGAAG+AGG - chr1.4:57864508-57864527 None:intergenic 65.0%
!! GTCGGTGCTCTTCGGTGCTG+CGG + chr1.4:57864709-57864728 MS.gene39906:CDS 65.0%
ACTACCCCACGTGCCGCCCA+TGG + chr1.4:57864363-57864382 MS.gene39906:CDS 70.0%
CGCTCGTCTTCACCGGCGTC+TGG + chr1.4:57864672-57864691 MS.gene39906:CDS 70.0%
TGGAAGGTGGGGTGGCGCGT+GGG - chr1.4:57864343-57864362 None:intergenic 70.0%
TGGGCGGCACGTGGGGTAGT+TGG - chr1.4:57864363-57864382 None:intergenic 70.0%
TTGGAAGGTGGGGTGGCGCG+TGG - chr1.4:57864344-57864363 None:intergenic 70.0%
!! GAGGGTGGTAGCGGAGGCTG+AGG - chr1.4:57864514-57864533 None:intergenic 70.0%
!! GGGAGAGAGGGTGGTAGCGG+AGG - chr1.4:57864520-57864539 None:intergenic 70.0%
!! GGTGCTCTTCGGTGCTGCGG+TGG + chr1.4:57864712-57864731 MS.gene39906:CDS 70.0%
GGAAGGTGGGGTGGCGCGTG+GGG - chr1.4:57864342-57864361 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 57864284 57864865 57864284 ID=MS.gene39906
chr1.4 mRNA 57864284 57864865 57864284 ID=MS.gene39906.t1;Parent=MS.gene39906
chr1.4 exon 57864284 57864865 57864284 ID=MS.gene39906.t1.exon1;Parent=MS.gene39906.t1
chr1.4 CDS 57864284 57864865 57864284 ID=cds.MS.gene39906.t1;Parent=MS.gene39906.t1
Gene Sequence

>MS.gene39906

ATGTCTTCCATCTATCCCACTCCAACTTACAACTCTCTCCCTTCAAACTCAACTTCCCCACGCGCCACCCCACCTTCCAACTACCCCACGTGCCGCCCATGGCAAAACTTCTTCACTCCCCAATCCTTCACTCATCCTCACTCCCTCTCCGAAACCACCCTCCGTATAAAACGCAACCTCAACCACTTCCGCATCAACTACGCCATCATCATCCTCCTCATCCTCTTCCTCAGCCTCCGCTACCACCCTCTCTCCCTCATCGTCTTCCTCGCCGTCTTCGCCGTTTGGTTCTTCCTCTTCTTCTTCAGTGACCACCTGGTCATCCTCTTCCGTTTCACCATCGACAACCGCTTCCTCCTCATTCTACTCTCTGCCCTCACAGTCGTCGCGCTCGTCTTCACCGGCGTCTGGCTTAACGTCCTCGTGTCGGTGCTCTTCGGTGCTGCGGTGGTTGTTTTGCATGCGGCATTTCGGAGTATTGATGATTTGTATTTAGATGAAGAAGAGATCTTTGATGGTGATTTGCTTTCAGTTGTTGGTGGTAGCTTCAATACCAAGCGAACGGGGTACACTAGAATGTAG
Protein sequence

>MS.gene39906.t1

MSSIYPTPTYNSLPSNSTSPRATPPSNYPTCRPWQNFFTPQSFTHPHSLSETTLRIKRNLNHFRINYAIIILLILFLSLRYHPLSLIVFLAVFAVWFFLFFFSDHLVILFRFTIDNRFLLILLSALTVVALVFTGVWLNVLVSVLFGAAVVVLHAAFRSIDDLYLDEEEIFDGDLLSVVGGSFNTKRTGYTRM