AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42416


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42416.t1 MTR_7g076650 99.412 170 1 0 1 170 1 170 4.21e-126 364
MS.gene42416.t1 MTR_7g076650 99.412 170 1 0 1 170 1 170 3.04e-125 365
MS.gene42416.t1 MTR_7g076650 99.412 170 1 0 1 170 1 170 8.81e-125 365
MS.gene42416.t1 MTR_8g032040 83.237 173 26 1 1 170 1 173 1.47e-106 317
MS.gene42416.t1 MTR_8g009500 67.568 148 48 0 23 170 44 191 1.17e-71 224
MS.gene42416.t1 MTR_8g009500 67.568 148 48 0 23 170 44 191 8.87e-71 225
MS.gene42416.t1 MTR_8g009500 80.769 78 15 0 93 170 20 97 1.13e-43 151
MS.gene42416.t1 MTR_3g110330 41.606 137 70 1 30 166 39 165 1.14e-33 125
MS.gene42416.t1 MTR_8g102620 43.066 137 68 1 30 166 52 178 1.01e-32 122
MS.gene42416.t1 MTR_8g014390 39.007 141 76 1 30 170 49 179 1.25e-30 116
MS.gene42416.t1 MTR_2g101040 39.007 141 76 1 30 170 102 232 4.02e-29 112
MS.gene42416.t1 MTR_2g101040 39.007 141 76 1 30 170 136 266 4.75e-29 112
MS.gene42416.t1 MTR_2g101040 39.007 141 76 1 30 170 102 232 4.96e-29 112
MS.gene42416.t1 MTR_2g101040 39.007 141 76 1 30 170 102 232 5.74e-29 112
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42416.t1 AT4G00570 82.803 157 27 0 14 170 23 179 8.10e-98 295
MS.gene42416.t1 AT2G13560 62.651 166 61 1 6 170 21 186 1.04e-71 227
MS.gene42416.t1 AT2G19900 40.876 137 71 1 30 166 42 168 5.56e-32 120
MS.gene42416.t1 AT5G25880 40.146 137 72 1 30 166 49 175 1.37e-31 119
MS.gene42416.t1 AT5G25880 40.146 137 72 1 30 166 49 175 1.64e-31 119
MS.gene42416.t1 AT5G25880 40.146 137 72 1 30 166 49 175 3.91e-30 115
MS.gene42416.t1 AT5G11670 39.416 137 73 1 30 166 49 175 6.04e-29 112
MS.gene42416.t1 AT1G79750 39.007 141 76 1 30 170 107 237 6.07e-29 112
MS.gene42416.t1 AT2G19900 50.746 67 33 0 100 166 3 69 1.90e-21 90.5

Find 46 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTCGTATCATTTCATTTC+AGG 0.152277 7.2:-87368713 MS.gene42416:CDS
AAACGATCCCTTTCAGTTAA+AGG 0.185284 7.2:+87368757 None:intergenic
TCATGATCCTTGGTTCAATA+AGG 0.276524 7.2:-87369615 MS.gene42416:intron
CATCATCTCTCCTTTATCTT+TGG 0.282849 7.2:+87368188 None:intergenic
CTGATATTCTTCATGATCCT+TGG 0.337382 7.2:-87369625 MS.gene42416:CDS
TCTATTTAAGATCCTCCATT+TGG 0.349893 7.2:+87368454 None:intergenic
TTTAACTGAAAGGGATCGTT+TGG 0.353746 7.2:-87368755 MS.gene42416:CDS
ACTGTAGGAGTGTAAATTAT+TGG 0.368268 7.2:+87368273 None:intergenic
AAAACTATTGTGGGTTGTAT+AGG 0.378512 7.2:-87368236 MS.gene42416:CDS
TTATAACTGGCCAGCTCCTC+AGG 0.382199 7.2:-87368157 MS.gene42416:CDS
TAAGATCCTCCATTTGGATA+AGG 0.396615 7.2:+87368460 None:intergenic
CGGATTTCCTTTAACTGAAA+GGG 0.420020 7.2:-87368764 MS.gene42416:CDS
TGATGTCGATGATTTATAAC+TGG 0.420109 7.2:-87368170 MS.gene42416:CDS
GGCGATACCTGCTCCGTGTA+TGG 0.423282 7.2:-87369663 MS.gene42416:CDS
TTAACTGAAAGGGATCGTTT+GGG 0.440854 7.2:-87368754 MS.gene42416:CDS
AAATTGTTTCCTTATCCAAA+TGG 0.443400 7.2:-87368469 MS.gene42416:CDS
CCTTTCAGTTAAAGGAAATC+CGG 0.475100 7.2:+87368765 None:intergenic
AGTGAGCTCATATAGATCAT+TGG 0.482376 7.2:-87368519 MS.gene42416:CDS
CCGGATTTCCTTTAACTGAA+AGG 0.492100 7.2:-87368765 MS.gene42416:CDS
CAATTCATTACCTGAGGAGC+TGG 0.495881 7.2:+87368147 None:intergenic
TAATTTACACTCCTACAGTT+GGG 0.496930 7.2:-87368269 MS.gene42416:CDS
ATAATTTACACTCCTACAGT+TGG 0.500644 7.2:-87368270 MS.gene42416:CDS
AGGGATCGTTTGGGGCTTCG+AGG 0.509582 7.2:-87368745 MS.gene42416:CDS
TAGTGTGTCAAAACTATTGT+GGG 0.517809 7.2:-87368245 MS.gene42416:CDS
ATTCTCGAAATGTAGGATAC+CGG 0.537469 7.2:-87368784 MS.gene42416:intron
ATGAAATGATACGAGGAGGA+AGG 0.570448 7.2:+87368719 None:intergenic
TTATGAACCATACACGGAGC+AGG 0.578199 7.2:+87369656 None:intergenic
TTGTTTCCTTATCCAAATGG+AGG 0.585354 7.2:-87368466 MS.gene42416:CDS
GCGATCGCGGTTGTTCTCGA+CGG 0.600148 7.2:-87369684 MS.gene42416:CDS
TGGCTGCATCATCGCGATCG+CGG 0.605590 7.2:-87369697 MS.gene42416:CDS
TAACTGAAAGGGATCGTTTG+GGG 0.609536 7.2:-87368753 MS.gene42416:CDS
TCTTAAATAGACTACATGAC+AGG 0.611160 7.2:-87368442 MS.gene42416:CDS
CAAGATCAATTCATTACCTG+AGG 0.613037 7.2:+87368141 None:intergenic
TGACACACTAACCCAACTGT+AGG 0.613154 7.2:+87368258 None:intergenic
TTGATTTGGAAGAATGTGGA+AGG 0.621516 7.2:-87369729 None:intergenic
AAATGATACGAGGAGGAAGG+AGG 0.624874 7.2:+87368722 None:intergenic
TTAGTGTGTCAAAACTATTG+TGG 0.625148 7.2:-87368246 MS.gene42416:CDS
AATGTGGAAGGTGACGCGTT+TGG 0.629005 7.2:-87369717 MS.gene42416:CDS
TGATGAACCTTATTGAACCA+AGG 0.639671 7.2:+87369608 None:intergenic
CCACGTTTATGAACCATACA+CGG 0.649265 7.2:+87369650 None:intergenic
CCGTGTATGGTTCATAAACG+TGG 0.657511 7.2:-87369650 MS.gene42416:CDS
TGAAATGAAATGATACGAGG+AGG 0.663233 7.2:+87368715 None:intergenic
TCATTGGAGAAGAATACCCA+TGG 0.676024 7.2:-87368503 MS.gene42416:CDS
GGGTTGTATAGGCGTCCACG+TGG 0.704315 7.2:-87368225 MS.gene42416:CDS
GCACTAAAATACATTCCACG+TGG 0.711731 7.2:+87368210 None:intergenic
TCCTGAAATGAAATGATACG+AGG 0.716494 7.2:+87368712 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAAAAATAAAATCAGTTA+TGG - chr7.2:87368552-87368571 MS.gene42416:intron 10.0%
!!! ATAATAATTTATTTTCATAG+TGG + chr7.2:87368533-87368552 None:intergenic 10.0%
!!! TTAAAAAAATGATGTTTTTA+TGG - chr7.2:87368680-87368699 MS.gene42416:intron 10.0%
!! AAAAAAAAAGCTATAACAAA+TGG - chr7.2:87368707-87368726 MS.gene42416:CDS 15.0%
!! AAAAAAAAGCTATAACAAAT+GGG - chr7.2:87368708-87368727 MS.gene42416:CDS 15.0%
!! AAAAAAAGCTATAACAAATG+GGG - chr7.2:87368709-87368728 MS.gene42416:CDS 20.0%
!! TTGTAACATTTATTTCCAAA+TGG - chr7.2:87369505-87369524 MS.gene42416:intron 20.0%
!!! AAATGTAGTAGTTATTTTGA+AGG - chr7.2:87368428-87368447 MS.gene42416:CDS 20.0%
!!! ATCACAAAATCATCAAATTT+TGG + chr7.2:87368793-87368812 None:intergenic 20.0%
!!! TCACAAAATCATCAAATTTT+GGG + chr7.2:87368792-87368811 None:intergenic 20.0%
! AAATTGTTTCCTTATCCAAA+TGG - chr7.2:87369393-87369412 MS.gene42416:intron 25.0%
! AATGAACCTTAACTAATTTG+AGG + chr7.2:87368916-87368935 None:intergenic 25.0%
! CAGTATTAAATCAAAACCAA+TGG + chr7.2:87369027-87369046 None:intergenic 25.0%
!! TTTTTGAATTCTCGAAATGT+AGG - chr7.2:87369071-87369090 MS.gene42416:intron 25.0%
!!! TATTTTAGTGCCAAAGATAA+AGG - chr7.2:87369664-87369683 MS.gene42416:CDS 25.0%
!!! TTATGGAAAAAGTGTTTTTC+TGG - chr7.2:87368569-87368588 MS.gene42416:intron 25.0%
AACTCACCTCAAATTAGTTA+AGG - chr7.2:87368907-87368926 MS.gene42416:intron 30.0%
ACTATATGCATCTATGTTCT+TGG - chr7.2:87369216-87369235 MS.gene42416:intron 30.0%
ATAATTTACACTCCTACAGT+TGG - chr7.2:87369592-87369611 MS.gene42416:intron 30.0%
CGAAGATAGAAACATAGTAA+TGG + chr7.2:87368308-87368327 None:intergenic 30.0%
GTAACAACATAAGAACCATT+TGG + chr7.2:87369523-87369542 None:intergenic 30.0%
TAATTTACACTCCTACAGTT+GGG - chr7.2:87369593-87369612 MS.gene42416:intron 30.0%
TAGTGTGTCAAAACTATTGT+GGG - chr7.2:87369617-87369636 MS.gene42416:CDS 30.0%
TCTTAAATAGACTACATGAC+AGG - chr7.2:87369420-87369439 MS.gene42416:intron 30.0%
TGATGTCGATGATTTATAAC+TGG - chr7.2:87369692-87369711 MS.gene42416:CDS 30.0%
TTAGTGTGTCAAAACTATTG+TGG - chr7.2:87369616-87369635 MS.gene42416:CDS 30.0%
! AAAACTATTGTGGGTTGTAT+AGG - chr7.2:87369626-87369645 MS.gene42416:CDS 30.0%
! AATTTTATCTGACTGACCAT+GGG + chr7.2:87369378-87369397 None:intergenic 30.0%
! ACTGTAGGAGTGTAAATTAT+TGG + chr7.2:87369592-87369611 None:intergenic 30.0%
! TCTATTTAAGATCCTCCATT+TGG + chr7.2:87369411-87369430 None:intergenic 30.0%
! TTAAGGTTCATTGTCATTTC+TGG - chr7.2:87368924-87368943 MS.gene42416:intron 30.0%
AAACGATCCCTTTCAGTTAA+AGG + chr7.2:87369108-87369127 None:intergenic 35.0%
AATGATCTATATGAGCTCAC+TGG + chr7.2:87369344-87369363 None:intergenic 35.0%
AGTGAGCTCATATAGATCAT+TGG - chr7.2:87369343-87369362 MS.gene42416:intron 35.0%
ATGCATGAGAAAATAGACAC+TGG - chr7.2:87368855-87368874 MS.gene42416:intron 35.0%
ATTCTCGAAATGTAGGATAC+CGG - chr7.2:87369078-87369097 MS.gene42416:intron 35.0%
CAAAACCAATGGTTAAGAAC+AGG + chr7.2:87369016-87369035 None:intergenic 35.0%
CAGAAACTTGAAATTCTACG+CGG + chr7.2:87368990-87369009 None:intergenic 35.0%
CATCATCTCTCCTTTATCTT+TGG + chr7.2:87369677-87369696 None:intergenic 35.0%
CCTTTCAGTTAAAGGAAATC+CGG + chr7.2:87369100-87369119 None:intergenic 35.0%
CGGATTTCCTTTAACTGAAA+GGG - chr7.2:87369098-87369117 MS.gene42416:intron 35.0%
CTGATATTCTTCATGATCCT+TGG - chr7.2:87368237-87368256 MS.gene42416:CDS 35.0%
TAAGATCCTCCATTTGGATA+AGG + chr7.2:87369405-87369424 None:intergenic 35.0%
TATCTAAATCCTCAGTATCC+AGG + chr7.2:87368951-87368970 None:intergenic 35.0%
TCATGATCCTTGGTTCAATA+AGG - chr7.2:87368247-87368266 MS.gene42416:CDS 35.0%
TCCTCGTATCATTTCATTTC+AGG - chr7.2:87369149-87369168 MS.gene42416:intron 35.0%
TCCTGAAATGAAATGATACG+AGG + chr7.2:87369153-87369172 None:intergenic 35.0%
TGAAATGAAATGATACGAGG+AGG + chr7.2:87369150-87369169 None:intergenic 35.0%
TGATGAACCTTATTGAACCA+AGG + chr7.2:87368257-87368276 None:intergenic 35.0%
TGCATGAGAAAATAGACACT+GGG - chr7.2:87368856-87368875 MS.gene42416:intron 35.0%
TGTTACCTTTCATTCTCTTC+AGG - chr7.2:87369537-87369556 MS.gene42416:intron 35.0%
TTAACTGAAAGGGATCGTTT+GGG - chr7.2:87369108-87369127 MS.gene42416:intron 35.0%
TTGTTTCCTTATCCAAATGG+AGG - chr7.2:87369396-87369415 MS.gene42416:intron 35.0%
TTTAACTGAAAGGGATCGTT+TGG - chr7.2:87369107-87369126 MS.gene42416:intron 35.0%
! CAATTTTATCTGACTGACCA+TGG + chr7.2:87369379-87369398 None:intergenic 35.0%
! CTAATTTGAGGTGAGTTGAA+TGG + chr7.2:87368904-87368923 None:intergenic 35.0%
! GTGAGTCTGATGATGAAATT+AGG - chr7.2:87369464-87369483 MS.gene42416:intron 35.0%
AAGTGCCTGAAGAGAATGAA+AGG + chr7.2:87369545-87369564 None:intergenic 40.0%
ATGAAATGATACGAGGAGGA+AGG + chr7.2:87369146-87369165 None:intergenic 40.0%
CCACGTTTATGAACCATACA+CGG + chr7.2:87368215-87368234 None:intergenic 40.0%
CCGGATTTCCTTTAACTGAA+AGG - chr7.2:87369097-87369116 MS.gene42416:intron 40.0%
GCACTAAAATACATTCCACG+TGG + chr7.2:87369655-87369674 None:intergenic 40.0%
TAACTGAAAGGGATCGTTTG+GGG - chr7.2:87369109-87369128 MS.gene42416:intron 40.0%
TCATTGGAGAAGAATACCCA+TGG - chr7.2:87369359-87369378 MS.gene42416:intron 40.0%
TGATGCCTGTTCTTAACCAT+TGG - chr7.2:87369008-87369027 MS.gene42416:intron 40.0%
!! TTCATTGTCATTTCTGGTCC+TGG - chr7.2:87368930-87368949 MS.gene42416:intron 40.0%
AAATGATACGAGGAGGAAGG+AGG + chr7.2:87369143-87369162 None:intergenic 45.0%
CAATTCATTACCTGAGGAGC+TGG + chr7.2:87369718-87369737 None:intergenic 45.0%
CCGTGTATGGTTCATAAACG+TGG - chr7.2:87368212-87368231 MS.gene42416:CDS 45.0%
TGACACACTAACCCAACTGT+AGG + chr7.2:87369607-87369626 None:intergenic 45.0%
TTATGAACCATACACGGAGC+AGG + chr7.2:87368209-87368228 None:intergenic 45.0%
!! ATTTCTGGTCCTGGATACTG+AGG - chr7.2:87368939-87368958 MS.gene42416:intron 45.0%
!! ATTAAAATAATAATATGTTA+TGG + chr7.2:87369318-87369337 None:intergenic 5.0%
TTATAACTGGCCAGCTCCTC+AGG - chr7.2:87369705-87369724 MS.gene42416:CDS 50.0%
GCGATCGCGGTTGTTCTCGA+CGG - chr7.2:87368178-87368197 MS.gene42416:CDS 60.0%
GGCGATACCTGCTCCGTGTA+TGG - chr7.2:87368199-87368218 MS.gene42416:CDS 60.0%
GGGTTGTATAGGCGTCCACG+TGG - chr7.2:87369637-87369656 MS.gene42416:CDS 60.0%
TGGCTGCATCATCGCGATCG+CGG - chr7.2:87368165-87368184 MS.gene42416:CDS 60.0%
! AGGGATCGTTTGGGGCTTCG+AGG - chr7.2:87369117-87369136 MS.gene42416:intron 60.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 87368146 87369738 87368146 ID=MS.gene42416
chr7.2 mRNA 87368146 87369738 87368146 ID=MS.gene42416.t1;Parent=MS.gene42416
chr7.2 exon 87369616 87369738 87369616 ID=MS.gene42416.t1.exon1;Parent=MS.gene42416.t1
chr7.2 CDS 87369616 87369738 87369616 ID=cds.MS.gene42416.t1;Parent=MS.gene42416.t1
chr7.2 exon 87368695 87368791 87368695 ID=MS.gene42416.t1.exon2;Parent=MS.gene42416.t1
chr7.2 CDS 87368695 87368791 87368695 ID=cds.MS.gene42416.t1;Parent=MS.gene42416.t1
chr7.2 exon 87368421 87368539 87368421 ID=MS.gene42416.t1.exon3;Parent=MS.gene42416.t1
chr7.2 CDS 87368421 87368539 87368421 ID=cds.MS.gene42416.t1;Parent=MS.gene42416.t1
chr7.2 exon 87368146 87368325 87368146 ID=MS.gene42416.t1.exon4;Parent=MS.gene42416.t1
chr7.2 CDS 87368146 87368325 87368146 ID=cds.MS.gene42416.t1;Parent=MS.gene42416.t1
Gene Sequence

>MS.gene42416

ATGTGGAAGGTGACGCGTTTGGCTGCATCATCGCGATCGCGGTTGTTCTCGACGGCGATACCTGCTCCGTGTATGGTTCATAAACGTGGTGCTGATATTCTTCATGATCCTTGGTTCAATAAGGTTCATCATCTTTAACTTCACTTGTTTTTGAGTTCTCCATTACTATGTTTCTATCTTCGTTTTTATCTTTTGATTACTGTTTTGAGATTGTAATTGTTTTAATTTTAGTTCTTGATTACGTTGATGAATGAATTTCTATTGTTAATTGATTTGATAGAAAAATGTAGTAGTTATTTTGAAGGTTTGTCTGTTGCAGATTCTAAAAAAAAAATGTGATTTTGATAGATTTTTAGAATGTTGAAGTTGTTTTGTGTTTGTTTACCACTATGAAAATAAATTATTATTTAAAAATAAAATCAGTTATGGAAAAAGTGTTTTTCTGGAGAAGCTATTCAAAACAGTTTATTTGAAGCAGTTTTTAGATTAAAACAAACATATGATTATGAAAGCATCTAAAAATGACTATTTTGTTTAAAAAAATGATGTTTTTATGGAAGAAAAAAAAAAGCTATAACAAATGGGGCTCTGAGTGTTGTTTGTCGATAATCACTTTTGTTTTTTGTCAATGTTCATTTGAAGTCCCAAAATTTGATGATTTTGTGATTTGATTCAGCTGATTTGAAGTTTGAACACTGATATTAGTTTTATGCATGAGAAAATAGACACTGGGAAAGTTCTACTATTATATGTGTCCATTCAACTCACCTCAAATTAGTTAAGGTTCATTGTCATTTCTGGTCCTGGATACTGAGGATTTAGATAAACAAATATGTACTATCCGCGTAGAATTTCAAGTTTCTGATGCCTGTTCTTAACCATTGGTTTTGATTTAATACTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAATTCTCGAAATGTAGGATACCGGATTTCCTTTAACTGAAAGGGATCGTTTGGGGCTTCGAGGCCTCCTTCCTCCTCGTATCATTTCATTTCAGGAGCAATATGATCGTTTTAGTAAGTTTTATTCATCATCTTCTAATACTATATGCATCTATGTTCTTGGCTATCTTAAAGTTGCATTATCTACATTGCTAGTGTCATTATCTTCATGTTTATTTTTAATATTTATTGTTTGATAGCCATAACATATTATTATTTTAATTTTCCAGTGAGCTCATATAGATCATTGGAGAAGAATACCCATGGTCAGTCAGATAAAATTGTTTCCTTATCCAAATGGAGGATCTTAAATAGACTACATGACAGGAATGAGACATTGTACTACAGAGTGAGTCTGATGATGAAATTAGGTTGTTATGTGACAAAATTTTGTAACATTTATTTCCAAATGGTTCTTATGTTGTTACCTTTCATTCTCTTCAGGCACTTATTGATAACATCAAAGAATTTGCTCCAATAATTTACACTCCTACAGTTGGGTTAGTGTGTCAAAACTATTGTGGGTTGTATAGGCGTCCACGTGGAATGTATTTTAGTGCCAAAGATAAAGGAGAGATGATGTCGATGATTTATAACTGGCCAGCTCCTCAGGTAATGAATTGA

Protein sequence

>MS.gene42416.t1

MWKVTRLAASSRSRLFSTAIPAPCMVHKRGADILHDPWFNKDTGFPLTERDRLGLRGLLPPRIISFQEQYDRFMSSYRSLEKNTHGQSDKIVSLSKWRILNRLHDRNETLYYRALIDNIKEFAPIIYTPTVGLVCQNYCGLYRRPRGMYFSAKDKGEMMSMIYNWPAPQVMN