AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01356

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01356.t1 MTR_4g050762 74.457 184 38 4 1 178 1 181 1.12e-92 268
MS.gene01356.t1 MTR_2g012370 74.457 184 38 4 1 178 1 181 1.12e-92 268
MS.gene01356.t1 MTR_2g010590 74.074 162 36 2 1 159 1 159 1.15e-86 251
MS.gene01356.t1 MTR_2g010600 74.545 165 33 4 1 159 1 162 1.68e-84 246
MS.gene01356.t1 MTR_2g010650 66.471 170 41 7 1 159 1 165 2.51e-73 218
MS.gene01356.t1 MTR_2g010630 67.949 156 40 4 10 159 14 165 4.73e-73 217
MS.gene01356.t1 MTR_2g010610 70.552 163 19 4 1 159 1 138 3.23e-71 212
MS.gene01356.t1 MTR_2g010700 62.209 172 48 7 1 159 1 168 6.03e-65 197
MS.gene01356.t1 MTR_2g010640 61.818 165 52 6 1 159 4 163 8.19e-63 191
MS.gene01356.t1 MTR_2g010670 62.130 169 49 7 1 159 1 164 2.82e-61 187
MS.gene01356.t1 MTR_2g010690 60.355 169 52 7 1 159 1 164 6.55e-61 187
MS.gene01356.t1 MTR_2g435490 52.976 168 71 4 4 166 10 174 8.85e-61 187
MS.gene01356.t1 MTR_2g010580 48.428 159 73 3 6 159 10 164 2.04e-52 165
MS.gene01356.t1 MTR_4g092540 47.853 163 77 4 1 159 1 159 5.98e-49 156
MS.gene01356.t1 MTR_4g128750 48.529 136 65 3 26 159 41 173 1.77e-38 130
MS.gene01356.t1 MTR_4g128770 42.857 140 72 3 25 159 70 206 2.15e-37 128
MS.gene01356.t1 MTR_1g067290 38.931 131 76 3 25 151 73 203 4.11e-30 109
MS.gene01356.t1 MTR_4g092515 51.485 101 44 2 3 98 6 106 1.68e-26 98.2
MS.gene01356.t1 MTR_8g078770 31.765 170 99 6 4 159 6 172 9.07e-22 87.0
MS.gene01356.t1 MTR_5g018770 35.075 134 80 4 25 151 47 180 2.47e-21 86.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01356.t1 AT2G14580 60.366 164 55 4 1 159 3 161 6.13e-65 197
MS.gene01356.t1 AT4G33720 58.974 156 60 2 4 159 12 163 1.62e-64 196
MS.gene01356.t1 AT5G26130 59.060 149 59 1 4 150 12 160 8.46e-60 184
MS.gene01356.t1 AT2G14610 56.688 157 60 3 6 159 10 161 4.47e-59 182
MS.gene01356.t1 AT4G33710 61.538 143 50 2 19 159 27 166 8.05e-58 179
MS.gene01356.t1 AT3G19690 53.205 156 66 3 6 159 11 161 1.84e-56 175
MS.gene01356.t1 AT1G50060 49.057 159 77 2 2 159 6 161 8.31e-51 161
MS.gene01356.t1 AT2G19990 49.306 144 69 2 17 159 36 176 5.34e-46 149
MS.gene01356.t1 AT4G33730 52.113 142 63 3 19 159 35 172 1.38e-45 148
MS.gene01356.t1 AT4G25790 48.905 137 65 3 25 159 77 210 2.36e-43 144
MS.gene01356.t1 AT5G57625 50.000 136 63 3 26 159 75 207 5.93e-43 142
MS.gene01356.t1 AT4G07820 46.479 142 71 2 18 159 24 160 7.91e-43 140
MS.gene01356.t1 AT1G50050 48.750 160 77 3 2 159 6 162 8.15e-42 138
MS.gene01356.t1 AT4G25780 47.143 140 66 4 25 159 54 190 1.59e-40 135
MS.gene01356.t1 AT1G50050 50.000 146 71 2 2 145 6 151 1.66e-39 134
MS.gene01356.t1 AT3G09590 43.478 138 72 3 25 159 52 186 1.06e-38 131
MS.gene01356.t1 AT4G30320 40.881 159 87 5 3 159 8 161 1.98e-38 129
MS.gene01356.t1 AT1G01310 45.669 127 68 1 25 150 87 213 5.27e-38 130
MS.gene01356.t1 AT4G31470 46.094 128 68 1 25 151 53 180 1.20e-37 128
MS.gene01356.t1 AT5G02730 41.538 130 73 2 24 150 58 187 2.39e-34 120
MS.gene01356.t1 AT2G19970 45.522 134 61 5 23 146 35 166 1.74e-29 107
MS.gene01356.t1 AT5G66590 40.714 140 74 5 26 159 49 185 1.55e-28 105
MS.gene01356.t1 AT2G19980 36.076 158 77 6 3 146 7 154 2.17e-21 86.3

Find 52 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGCCTTATTACTCATTAT+TGG 0.249523 2.2:+69962401 MS.gene01356:CDS
TCCACTCCGGTGGCCGTTAC+GGG 0.266655 2.2:+69962579 MS.gene01356:CDS
CCCAAACCACCTGGGTATAA+TGG 0.278371 2.2:-69962721 None:intergenic
GCCATTATACCCAGGTGGTT+TGG 0.295458 2.2:+69962720 MS.gene01356:CDS
CCATTATACCCAGGTGGTTT+GGG 0.311099 2.2:+69962721 MS.gene01356:CDS
CTCGGATCTTGCTGCGTTGT+GGG 0.314469 2.2:-69962468 None:intergenic
ATCCACTCCGGTGGCCGTTA+CGG 0.319599 2.2:+69962578 MS.gene01356:CDS
ATGACCAATAATGAGTAATA+AGG 0.340498 2.2:-69962405 None:intergenic
CATAGTCTGCCGGTGAGTCT+TGG 0.370268 2.2:-69962439 None:intergenic
TTGGTGTTCCAAATATTGTT+TGG 0.373768 2.2:+69962492 MS.gene01356:CDS
AGTGGTTGTTCTACCAAGTA+TGG 0.397157 2.2:-69962854 None:intergenic
ATAGTCTGCCGGTGAGTCTT+GGG 0.404268 2.2:-69962438 None:intergenic
GTTACTATTAGAATCATAAT+CGG 0.431949 2.2:-69962672 None:intergenic
GCACAGATGCAGTGAGGTTG+TGG 0.462999 2.2:+69962636 MS.gene01356:CDS
CCTCGGATCTTGCTGCGTTG+TGG 0.470167 2.2:-69962469 None:intergenic
ATCTGTGCCACTCAAGTCTC+CGG 0.487855 2.2:-69962621 None:intergenic
TGGGAAAATTCACTACGTCT+TGG 0.491620 2.2:+69962740 MS.gene01356:CDS
TGTTGCTCAAAGACCATACT+TGG 0.498663 2.2:+69962841 MS.gene01356:CDS
AATAGTAACTCATGTGCTGC+TGG 0.499793 2.2:+69962686 MS.gene01356:CDS
GAGAATCTTGCGGGTAGCAC+CGG 0.500030 2.2:+69962602 MS.gene01356:CDS
GGCAAAGTGAGATGTGATAA+TGG 0.512407 2.2:+69962767 MS.gene01356:CDS
TATACTATCACTCACAAGAA+AGG 0.514969 2.2:+69962901 MS.gene01356:CDS
ATTCTCCCCGTAACGGCCAC+CGG 0.523807 2.2:-69962585 None:intergenic
CGTTACGGGGAGAATCTTGC+GGG 0.525657 2.2:+69962593 MS.gene01356:CDS
CACAGATGCAGTGAGGTTGT+GGG 0.544377 2.2:+69962637 MS.gene01356:CDS
CCCCGTAACGGCCACCGGAG+TGG 0.561545 2.2:-69962580 None:intergenic
AATTCACTACGTCTTGGATG+TGG 0.564502 2.2:+69962746 MS.gene01356:CDS
TGGGCGTTCACATAGTCTGC+CGG 0.578916 2.2:-69962449 None:intergenic
CCGTTACGGGGAGAATCTTG+CGG 0.579184 2.2:+69962592 MS.gene01356:CDS
AGCACATGCCCAAGACTCAC+CGG 0.583038 2.2:+69962430 MS.gene01356:CDS
ACTTGCAATTACGACCCACC+TGG 0.587462 2.2:+69962803 MS.gene01356:CDS
AATATTTGGAACACCAACCT+CGG 0.594900 2.2:-69962486 None:intergenic
CCACTCCGGTGGCCGTTACG+GGG 0.608356 2.2:+69962580 MS.gene01356:CDS
CCGCAAGATTCTCCCCGTAA+CGG 0.617173 2.2:-69962592 None:intergenic
GGTAGCACCGGAGACTTGAG+TGG 0.629873 2.2:+69962614 MS.gene01356:CDS
GTGTGACCACCGCAAGTGAG+TGG 0.635753 2.2:-69962872 None:intergenic
GTAGAACAACCACTCACTTG+CGG 0.636306 2.2:+69962863 MS.gene01356:CDS
ACATAGACTACATAGTTACC+AGG 0.639271 2.2:-69962821 None:intergenic
TGTGCTGCTGGTAAAGTGTG+TGG 0.641579 2.2:+69962698 MS.gene01356:CDS
TGTCAACTTATCCACTCCGG+TGG 0.651321 2.2:+69962569 MS.gene01356:CDS
AAACTATGCTAATCAACACA+AGG 0.652986 2.2:+69962541 MS.gene01356:CDS
AACGCAGCAAGATCCGAGGT+TGG 0.657560 2.2:+69962473 MS.gene01356:CDS
AACTATGCTAATCAACACAA+GGG 0.673499 2.2:+69962542 MS.gene01356:CDS
AGACTACATAGTTACCAGGT+GGG 0.675658 2.2:-69962817 None:intergenic
CCACAACGCAGCAAGATCCG+AGG 0.679159 2.2:+69962469 MS.gene01356:CDS
GAACAACCACTCACTTGCGG+TGG 0.680754 2.2:+69962866 MS.gene01356:CDS
TAGACTACATAGTTACCAGG+TGG 0.686439 2.2:-69962818 None:intergenic
GATTGTCAACTTATCCACTC+CGG 0.689104 2.2:+69962566 MS.gene01356:CDS
AGTGTGTGGCCATTATACCC+AGG 0.694274 2.2:+69962712 MS.gene01356:CDS
GTGTGGCCATTATACCCAGG+TGG 0.699736 2.2:+69962715 MS.gene01356:CDS
TGAGTGGCACAGATGCAGTG+AGG 0.786885 2.2:+69962630 MS.gene01356:CDS
AAAGTGAGATGTGATAATGG+TGG 0.798728 2.2:+69962770 MS.gene01356:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTACTATTAGAATCATAAT+CGG - chr2.2:69962675-69962694 None:intergenic 20.0%
! ATGACCAATAATGAGTAATA+AGG - chr2.2:69962408-69962427 None:intergenic 25.0%
!!! GTTTTGTTCCAAACAATATT+TGG - chr2.2:69962503-69962522 None:intergenic 25.0%
AAACTATGCTAATCAACACA+AGG + chr2.2:69962541-69962560 MS.gene01356:CDS 30.0%
AACTATGCTAATCAACACAA+GGG + chr2.2:69962542-69962561 MS.gene01356:CDS 30.0%
TATACTATCACTCACAAGAA+AGG + chr2.2:69962901-69962920 MS.gene01356:CDS 30.0%
! TTGGTGTTCCAAATATTGTT+TGG + chr2.2:69962492-69962511 MS.gene01356:CDS 30.0%
!! TTGGCCTTATTACTCATTAT+TGG + chr2.2:69962401-69962420 MS.gene01356:CDS 30.0%
ACATAGACTACATAGTTACC+AGG - chr2.2:69962824-69962843 None:intergenic 35.0%
! AATATTTGGAACACCAACCT+CGG - chr2.2:69962489-69962508 None:intergenic 35.0%
!! AAAGTGAGATGTGATAATGG+TGG + chr2.2:69962770-69962789 MS.gene01356:CDS 35.0%
AATAGTAACTCATGTGCTGC+TGG + chr2.2:69962686-69962705 MS.gene01356:CDS 40.0%
AATTCACTACGTCTTGGATG+TGG + chr2.2:69962746-69962765 MS.gene01356:CDS 40.0%
AGACTACATAGTTACCAGGT+GGG - chr2.2:69962820-69962839 None:intergenic 40.0%
AGTGGTTGTTCTACCAAGTA+TGG - chr2.2:69962857-69962876 None:intergenic 40.0%
GATTGTCAACTTATCCACTC+CGG + chr2.2:69962566-69962585 MS.gene01356:CDS 40.0%
GGCAAAGTGAGATGTGATAA+TGG + chr2.2:69962767-69962786 MS.gene01356:CDS 40.0%
TAGACTACATAGTTACCAGG+TGG - chr2.2:69962821-69962840 None:intergenic 40.0%
TGGGAAAATTCACTACGTCT+TGG + chr2.2:69962740-69962759 MS.gene01356:CDS 40.0%
TGTTGCTCAAAGACCATACT+TGG + chr2.2:69962841-69962860 MS.gene01356:CDS 40.0%
! TGAATTTTCCCAAACCACCT+GGG - chr2.2:69962732-69962751 None:intergenic 40.0%
CCATTATACCCAGGTGGTTT+GGG + chr2.2:69962721-69962740 MS.gene01356:CDS 45.0%
GTAGAACAACCACTCACTTG+CGG + chr2.2:69962863-69962882 MS.gene01356:CDS 45.0%
! GTGAATTTTCCCAAACCACC+TGG - chr2.2:69962733-69962752 None:intergenic 45.0%
ACTTGCAATTACGACCCACC+TGG + chr2.2:69962803-69962822 MS.gene01356:CDS 50.0%
AGTGTGTGGCCATTATACCC+AGG + chr2.2:69962712-69962731 MS.gene01356:CDS 50.0%
ATAGTCTGCCGGTGAGTCTT+GGG - chr2.2:69962441-69962460 None:intergenic 50.0%
CACAGATGCAGTGAGGTTGT+GGG + chr2.2:69962637-69962656 MS.gene01356:CDS 50.0%
CCCAAACCACCTGGGTATAA+TGG - chr2.2:69962724-69962743 None:intergenic 50.0%
GCCATTATACCCAGGTGGTT+TGG + chr2.2:69962720-69962739 MS.gene01356:CDS 50.0%
TGTCAACTTATCCACTCCGG+TGG + chr2.2:69962569-69962588 MS.gene01356:CDS 50.0%
! ATCTGTGCCACTCAAGTCTC+CGG - chr2.2:69962624-69962643 None:intergenic 50.0%
! TGTGCTGCTGGTAAAGTGTG+TGG + chr2.2:69962698-69962717 MS.gene01356:CDS 50.0%
AACGCAGCAAGATCCGAGGT+TGG + chr2.2:69962473-69962492 MS.gene01356:CDS 55.0%
AGCACATGCCCAAGACTCAC+CGG + chr2.2:69962430-69962449 MS.gene01356:CDS 55.0%
CATAGTCTGCCGGTGAGTCT+TGG - chr2.2:69962442-69962461 None:intergenic 55.0%
CCGCAAGATTCTCCCCGTAA+CGG - chr2.2:69962595-69962614 None:intergenic 55.0%
CCGTTACGGGGAGAATCTTG+CGG + chr2.2:69962592-69962611 MS.gene01356:CDS 55.0%
CGTTACGGGGAGAATCTTGC+GGG + chr2.2:69962593-69962612 MS.gene01356:CDS 55.0%
CTCGGATCTTGCTGCGTTGT+GGG - chr2.2:69962471-69962490 None:intergenic 55.0%
GAACAACCACTCACTTGCGG+TGG + chr2.2:69962866-69962885 MS.gene01356:CDS 55.0%
GAGAATCTTGCGGGTAGCAC+CGG + chr2.2:69962602-69962621 MS.gene01356:CDS 55.0%
GCACAGATGCAGTGAGGTTG+TGG + chr2.2:69962636-69962655 MS.gene01356:CDS 55.0%
GTGTGGCCATTATACCCAGG+TGG + chr2.2:69962715-69962734 MS.gene01356:CDS 55.0%
TGAGTGGCACAGATGCAGTG+AGG + chr2.2:69962630-69962649 MS.gene01356:CDS 55.0%
TGGGCGTTCACATAGTCTGC+CGG - chr2.2:69962452-69962471 None:intergenic 55.0%
ATCCACTCCGGTGGCCGTTA+CGG + chr2.2:69962578-69962597 MS.gene01356:CDS 60.0%
ATTCTCCCCGTAACGGCCAC+CGG - chr2.2:69962588-69962607 None:intergenic 60.0%
CCACAACGCAGCAAGATCCG+AGG + chr2.2:69962469-69962488 MS.gene01356:CDS 60.0%
CCTCGGATCTTGCTGCGTTG+TGG - chr2.2:69962472-69962491 None:intergenic 60.0%
GTGTGACCACCGCAAGTGAG+TGG - chr2.2:69962875-69962894 None:intergenic 60.0%
! GGTAGCACCGGAGACTTGAG+TGG + chr2.2:69962614-69962633 MS.gene01356:CDS 60.0%
TCCACTCCGGTGGCCGTTAC+GGG + chr2.2:69962579-69962598 MS.gene01356:CDS 65.0%
CCACTCCGGTGGCCGTTACG+GGG + chr2.2:69962580-69962599 MS.gene01356:CDS 70.0%
CCCCGTAACGGCCACCGGAG+TGG - chr2.2:69962583-69962602 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 69962383 69962928 69962383 ID=MS.gene01356
chr2.2 mRNA 69962383 69962928 69962383 ID=MS.gene01356.t1;Parent=MS.gene01356
chr2.2 exon 69962383 69962928 69962383 ID=MS.gene01356.t1.exon1;Parent=MS.gene01356.t1
chr2.2 CDS 69962383 69962928 69962383 ID=cds.MS.gene01356.t1;Parent=MS.gene01356.t1
Gene Sequence

>MS.gene01356

ATGAGTTCATTTTCTCTATTGGCCTTATTACTCATTATTGGTCATGTAGCACATGCCCAAGACTCACCGGCAGACTATGTGAACGCCCACAACGCAGCAAGATCCGAGGTTGGTGTTCCAAATATTGTTTGGAACAAAACTGTTGCTGCTTATGCACAAAACTATGCTAATCAACACAAGGGTGATTGTCAACTTATCCACTCCGGTGGCCGTTACGGGGAGAATCTTGCGGGTAGCACCGGAGACTTGAGTGGCACAGATGCAGTGAGGTTGTGGGTGAATGAGAAAGCCGATTATGATTCTAATAGTAACTCATGTGCTGCTGGTAAAGTGTGTGGCCATTATACCCAGGTGGTTTGGGAAAATTCACTACGTCTTGGATGTGGCAAAGTGAGATGTGATAATGGTGGCACATTCATTACTTGCAATTACGACCCACCTGGTAACTATGTAGTCTATGTTGCTCAAAGACCATACTTGGTAGAACAACCACTCACTTGCGGTGGTCACACACGAATTATACTATCACTCACAAGAAAGGATTAG
Protein sequence

>MS.gene01356.t1

MSSFSLLALLLIIGHVAHAQDSPADYVNAHNAARSEVGVPNIVWNKTVAAYAQNYANQHKGDCQLIHSGGRYGENLAGSTGDLSGTDAVRLWVNEKADYDSNSNSCAAGKVCGHYTQVVWENSLRLGCGKVRCDNGGTFITCNYDPPGNYVVYVAQRPYLVEQPLTCGGHTRIILSLTRKD