AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073497

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073497.t1 MTR_4g021790 86.387 191 26 0 1 191 1 191 9.59e-122 345
MS.gene073497.t1 MTR_4g021845 84.293 191 30 0 1 191 1 191 1.03e-120 341
MS.gene073497.t1 MTR_4g021855 84.817 191 29 0 1 191 1 191 4.26e-119 340
MS.gene073497.t1 MTR_4g021760 78.974 195 40 1 1 194 1 195 2.99e-114 328
MS.gene073497.t1 MTR_5g055260 69.591 171 42 2 1 171 1 161 7.56e-81 241
MS.gene073497.t1 MTR_4g023980 76.056 142 34 0 55 196 35 176 1.89e-79 234
MS.gene073497.t1 MTR_1g032570 43.750 224 89 4 2 191 3 223 4.69e-54 182
MS.gene073497.t1 MTR_6g016850 44.172 163 88 2 10 169 9 171 4.27e-44 145
MS.gene073497.t1 MTR_8g105600 41.206 199 97 2 10 188 9 207 2.01e-41 147
MS.gene073497.t1 MTR_3g086100 38.679 212 102 5 10 193 13 224 1.37e-40 145
MS.gene073497.t1 MTR_4g121020 37.559 213 103 3 7 191 28 238 4.61e-40 144
MS.gene073497.t1 MTR_4g121020 37.559 213 103 3 7 191 28 238 4.63e-40 144
MS.gene073497.t1 MTR_6g045327 43.784 185 100 3 10 192 14 196 1.29e-39 139
MS.gene073497.t1 MTR_8g079940 36.967 211 107 4 9 193 24 234 1.36e-39 142
MS.gene073497.t1 MTR_2g034960 38.278 209 105 2 7 191 26 234 1.39e-39 142
MS.gene073497.t1 MTR_8g093040 47.205 161 78 3 1 156 1 159 1.45e-39 136
MS.gene073497.t1 MTR_4g131600 34.951 206 111 4 9 191 19 224 8.17e-34 126
MS.gene073497.t1 MTR_3g106220 34.562 217 104 4 10 191 8 221 3.72e-33 125
MS.gene073497.t1 MTR_1g013170 34.762 210 109 3 10 191 5 214 5.23e-33 123
MS.gene073497.t1 MTR_7g117705 30.516 213 120 3 10 194 5 217 8.51e-32 119
MS.gene073497.t1 MTR_1g013180 31.905 210 115 3 10 191 156 365 1.08e-30 118
MS.gene073497.t1 MTR_1g032570 40.127 157 58 3 68 191 1 154 1.16e-29 114
MS.gene073497.t1 MTR_4g131570 31.429 210 116 4 10 191 17 226 7.86e-29 112
MS.gene073497.t1 MTR_4g131580 30.918 207 118 3 10 191 17 223 9.64e-28 109
MS.gene073497.t1 MTR_2g450070 30.137 219 116 4 10 191 18 236 6.10e-27 107
MS.gene073497.t1 MTR_2g450070 30.137 219 116 4 10 191 18 236 6.96e-27 107
MS.gene073497.t1 MTR_3g102600 32.258 186 90 2 7 191 5 155 8.57e-26 98.6
MS.gene073497.t1 MTR_3g102590 33.155 187 98 4 7 191 5 166 1.29e-25 98.2
MS.gene073497.t1 MTR_3g102600 32.258 186 90 2 7 191 5 155 2.26e-25 98.6
MS.gene073497.t1 MTR_3g102590 33.155 187 98 4 7 191 5 166 2.71e-25 98.6
MS.gene073497.t1 MTR_3g086100 36.601 153 70 4 68 193 1 153 2.52e-23 96.7
MS.gene073497.t1 MTR_3g102600 31.206 141 62 1 52 192 2 107 1.55e-18 78.2
MS.gene073497.t1 MTR_3g102600 31.429 140 61 1 52 191 2 106 2.12e-18 79.0
MS.gene073497.t1 MTR_7g026400 33.333 171 81 5 45 191 19 180 2.17e-18 82.8
MS.gene073497.t1 MTR_0450s0040 26.316 190 125 3 12 190 6 191 8.44e-17 77.4
MS.gene073497.t1 MTR_1g013160 31.544 149 75 2 71 192 1 149 1.19e-16 73.9
MS.gene073497.t1 MTR_4g121020 32.558 129 62 1 88 191 6 134 5.07e-13 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073497.t1 AT2G01760 37.788 217 100 5 10 191 7 223 6.04e-39 137
MS.gene073497.t1 AT1G67710 37.321 209 103 3 11 191 8 216 8.88e-38 136
MS.gene073497.t1 AT3G16857 35.088 228 102 4 10 191 33 260 1.01e-34 129
MS.gene073497.t1 AT3G16857 35.088 228 102 4 10 191 33 260 1.23e-34 129
MS.gene073497.t1 AT2G01760 33.469 245 100 6 10 191 7 251 3.52e-33 122
MS.gene073497.t1 AT4G31920 36.041 197 108 5 10 191 13 206 8.19e-33 123
MS.gene073497.t1 AT2G25180 33.014 209 116 3 10 194 13 221 5.55e-31 118
MS.gene073497.t1 AT5G58080 33.493 209 107 6 10 191 14 217 1.02e-25 103
MS.gene073497.t1 AT3G16857 32.804 189 81 4 49 191 2 190 3.28e-23 96.7
MS.gene073497.t1 AT5G49240 29.717 212 122 5 7 191 35 246 3.43e-23 94.4
MS.gene073497.t1 AT3G62670 26.519 181 115 3 27 189 52 232 1.41e-22 94.4
MS.gene073497.t1 AT1G49190 27.053 207 124 3 10 189 30 236 4.89e-21 89.7
MS.gene073497.t1 AT1G67710 35.762 151 70 2 68 191 1 151 9.09e-21 89.4
MS.gene073497.t1 AT2G01760 34.810 158 69 4 68 191 1 158 2.44e-19 84.3
MS.gene073497.t1 AT1G49190 31.200 125 85 1 10 133 30 154 1.44e-16 77.4

Find 45 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCTTTCCAACAAATTAA+AGG 0.201740 4.1:+76313841 None:intergenic
AACTGCATCAACGATTTCTA+TGG 0.292867 4.1:-76313372 MS.gene073497:CDS
TTCTGATGCCTTTAATTTGT+TGG 0.335924 4.1:-76313849 MS.gene073497:CDS
CTTTAATTTGTTGGAAAGAA+AGG 0.348441 4.1:-76313840 MS.gene073497:CDS
TAAGTGACTAACCTTGATAA+TGG 0.362032 4.1:+76314007 None:intergenic
AGAAATCGTTGATGCAGTTC+TGG 0.372917 4.1:+76313376 None:intergenic
TGAGTTGTAGGGTAACATTT+TGG 0.376494 4.1:+76313756 None:intergenic
TACATATTGGACTAAGCCTT+TGG 0.386876 4.1:-76313572 MS.gene073497:CDS
TGACAGGAATGTTGAGTTGT+AGG 0.408636 4.1:+76313744 None:intergenic
GGTTGAAGAAAATAGAAAAC+GGG 0.411991 4.1:-76313461 MS.gene073497:CDS
ATCAGAAGCTGTGTTACATT+TGG 0.412873 4.1:+76313865 None:intergenic
AATAAAGAATATGAAATTGT+TGG 0.416766 4.1:-76313493 MS.gene073497:CDS
TGCAATCGATTCCATTATCA+AGG 0.445235 4.1:-76314018 MS.gene073497:intron
AAGTTATAAACATCCATGTT+TGG 0.449631 4.1:+76313782 None:intergenic
TTCTGGCGACCAAGACAAAC+GGG 0.460294 4.1:+76313393 None:intergenic
AATAAATTCTTACTAATGAC+AGG 0.461511 4.1:+76313728 None:intergenic
ATATGAAATTGTTGGAAGCT+TGG 0.461542 4.1:-76313485 MS.gene073497:CDS
TTGAGACCAGCAGGGAATGA+TGG 0.464643 4.1:+76314093 None:intergenic
AAAAGATACACATGCAAAGA+AGG 0.470493 4.1:-76313416 MS.gene073497:CDS
CAAAGAAGGCCCGTTTGTCT+TGG 0.473177 4.1:-76313402 MS.gene073497:CDS
CACTGTTCTTAACACTATTG+AGG 0.478157 4.1:-76314046 MS.gene073497:CDS
ATCATTCCCTGCTGGTCTCA+AGG 0.485183 4.1:-76314091 MS.gene073497:CDS
AATGTGGGGCTTGTACATAT+TGG 0.487863 4.1:-76313585 MS.gene073497:CDS
GTTCTGGCGACCAAGACAAA+CGG 0.493157 4.1:+76313392 None:intergenic
GCAATAACCTTGAGACCAGC+AGG 0.494358 4.1:+76314084 None:intergenic
TGGCACCATGTTGCAAGAAA+CGG 0.499982 4.1:-76313526 MS.gene073497:CDS
AACAGTGATGTCATGATCAA+TGG 0.502328 4.1:+76314062 None:intergenic
GACAGCCCATCATTCCCTGC+TGG 0.504637 4.1:-76314099 MS.gene073497:CDS
TGGTTGAAGAAAATAGAAAA+CGG 0.506154 4.1:-76313462 MS.gene073497:CDS
TGATGGGCTGTCAACGAAAA+CGG 0.507263 4.1:+76314110 None:intergenic
ATTATGAAGTCTATTGAATG+TGG 0.513075 4.1:-76313601 MS.gene073497:CDS
CTATGGGCTGTCAATCAACT+AGG 0.518108 4.1:-76313355 MS.gene073497:CDS
GACAGGAATGTTGAGTTGTA+GGG 0.519779 4.1:+76313745 None:intergenic
TTGAACTCTTCTTCAACCAA+AGG 0.521847 4.1:+76313556 None:intergenic
AGGAAAGAAGCATACTATCA+AGG 0.524721 4.1:+76313332 None:intergenic
TGAGACCAGCAGGGAATGAT+GGG 0.532165 4.1:+76314094 None:intergenic
TTATGAAGTCTATTGAATGT+GGG 0.532174 4.1:-76313600 MS.gene073497:CDS
TGAAATTGTTGGAAGCTTGG+TGG 0.576315 4.1:-76313482 MS.gene073497:CDS
ACTGCATCAACGATTTCTAT+GGG 0.587946 4.1:-76313371 MS.gene073497:CDS
TATGAAGTCTATTGAATGTG+GGG 0.598969 4.1:-76313599 MS.gene073497:CDS
TGATGCTCATATGCCAAACA+TGG 0.604750 4.1:-76313795 MS.gene073497:CDS
TCAAACCGTTTCTTGCAACA+TGG 0.613360 4.1:+76313521 None:intergenic
AAGAAGAGTTCAAGATCATG+TGG 0.629722 4.1:-76313546 MS.gene073497:CDS
CAATAACCTTGAGACCAGCA+GGG 0.699486 4.1:+76314085 None:intergenic
GTTGAAGAAAATAGAAAACG+GGG 0.712341 4.1:-76313460 MS.gene073497:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAGAATATGAAATTGT+TGG - chr4.1:76313951-76313970 MS.gene073497:intron 15.0%
!! AATAAATTCTTACTAATGAC+AGG + chr4.1:76313719-76313738 None:intergenic 20.0%
!!! TTATTTCTTTTTTGTAGTGA+TGG - chr4.1:76313797-76313816 MS.gene073497:CDS 20.0%
! AAGTTATAAACATCCATGTT+TGG + chr4.1:76313665-76313684 None:intergenic 25.0%
! ATTATGAAGTCTATTGAATG+TGG - chr4.1:76313843-76313862 MS.gene073497:CDS 25.0%
! CTTTCTTTCCAACAAATTAA+AGG + chr4.1:76313606-76313625 None:intergenic 25.0%
! TGGTTGAAGAAAATAGAAAA+CGG - chr4.1:76313982-76314001 MS.gene073497:intron 25.0%
! TTATGAAGTCTATTGAATGT+GGG - chr4.1:76313844-76313863 MS.gene073497:CDS 25.0%
!!! CTTTAATTTGTTGGAAAGAA+AGG - chr4.1:76313604-76313623 MS.gene073497:CDS 25.0%
AAAAGATACACATGCAAAGA+AGG - chr4.1:76314028-76314047 MS.gene073497:CDS 30.0%
ATATGAAATTGTTGGAAGCT+TGG - chr4.1:76313959-76313978 MS.gene073497:intron 30.0%
GGTTGAAGAAAATAGAAAAC+GGG - chr4.1:76313983-76314002 MS.gene073497:intron 30.0%
GTTGAAGAAAATAGAAAACG+GGG - chr4.1:76313984-76314003 MS.gene073497:intron 30.0%
TAAGTGACTAACCTTGATAA+TGG + chr4.1:76313440-76313459 None:intergenic 30.0%
TATGAAGTCTATTGAATGTG+GGG - chr4.1:76313845-76313864 MS.gene073497:CDS 30.0%
! TTTGCATGTGTATCTTTTGA+GGG + chr4.1:76314026-76314045 None:intergenic 30.0%
!! TTCTGATGCCTTTAATTTGT+TGG - chr4.1:76313595-76313614 MS.gene073497:CDS 30.0%
AACAGTGATGTCATGATCAA+TGG + chr4.1:76313385-76313404 None:intergenic 35.0%
AACTGCATCAACGATTTCTA+TGG - chr4.1:76314072-76314091 MS.gene073497:CDS 35.0%
AAGAAGAGTTCAAGATCATG+TGG - chr4.1:76313898-76313917 MS.gene073497:intron 35.0%
ACTGCATCAACGATTTCTAT+GGG - chr4.1:76314073-76314092 MS.gene073497:CDS 35.0%
ATCAGAAGCTGTGTTACATT+TGG + chr4.1:76313582-76313601 None:intergenic 35.0%
CACTGTTCTTAACACTATTG+AGG - chr4.1:76313398-76313417 MS.gene073497:CDS 35.0%
TACATATTGGACTAAGCCTT+TGG - chr4.1:76313872-76313891 MS.gene073497:intron 35.0%
TTGAACTCTTCTTCAACCAA+AGG + chr4.1:76313891-76313910 None:intergenic 35.0%
! AGGAAAGAAGCATACTATCA+AGG + chr4.1:76314115-76314134 None:intergenic 35.0%
! CTTTGCATGTGTATCTTTTG+AGG + chr4.1:76314027-76314046 None:intergenic 35.0%
! TGAGTTGTAGGGTAACATTT+TGG + chr4.1:76313691-76313710 None:intergenic 35.0%
! TGCAATCGATTCCATTATCA+AGG - chr4.1:76313426-76313445 MS.gene073497:CDS 35.0%
! TTGCATGTGTATCTTTTGAG+GGG + chr4.1:76314025-76314044 None:intergenic 35.0%
AATGTGGGGCTTGTACATAT+TGG - chr4.1:76313859-76313878 MS.gene073497:CDS 40.0%
AGAAATCGTTGATGCAGTTC+TGG + chr4.1:76314071-76314090 None:intergenic 40.0%
TCAAACCGTTTCTTGCAACA+TGG + chr4.1:76313926-76313945 None:intergenic 40.0%
TGAAATTGTTGGAAGCTTGG+TGG - chr4.1:76313962-76313981 MS.gene073497:intron 40.0%
TGATGCTCATATGCCAAACA+TGG - chr4.1:76313649-76313668 MS.gene073497:intron 40.0%
! GACAGGAATGTTGAGTTGTA+GGG + chr4.1:76313702-76313721 None:intergenic 40.0%
! TGACAGGAATGTTGAGTTGT+AGG + chr4.1:76313703-76313722 None:intergenic 40.0%
CAATAACCTTGAGACCAGCA+GGG + chr4.1:76313362-76313381 None:intergenic 45.0%
TGGCACCATGTTGCAAGAAA+CGG - chr4.1:76313918-76313937 MS.gene073497:intron 45.0%
! CTATGGGCTGTCAATCAACT+AGG - chr4.1:76314089-76314108 MS.gene073497:CDS 45.0%
!! TGATGGGCTGTCAACGAAAA+CGG + chr4.1:76313337-76313356 None:intergenic 45.0%
CAAAGAAGGCCCGTTTGTCT+TGG - chr4.1:76314042-76314061 MS.gene073497:CDS 50.0%
GCAATAACCTTGAGACCAGC+AGG + chr4.1:76313363-76313382 None:intergenic 50.0%
GTTCTGGCGACCAAGACAAA+CGG + chr4.1:76314055-76314074 None:intergenic 50.0%
TGAGACCAGCAGGGAATGAT+GGG + chr4.1:76313353-76313372 None:intergenic 50.0%
TTCTGGCGACCAAGACAAAC+GGG + chr4.1:76314054-76314073 None:intergenic 50.0%
TTGAGACCAGCAGGGAATGA+TGG + chr4.1:76313354-76313373 None:intergenic 50.0%
! ATCATTCCCTGCTGGTCTCA+AGG - chr4.1:76313353-76313372 MS.gene073497:CDS 50.0%
GACAGCCCATCATTCCCTGC+TGG - chr4.1:76313345-76313364 MS.gene073497:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 76313330 76314136 76313330 ID=MS.gene073497
chr4.1 mRNA 76313330 76314136 76313330 ID=MS.gene073497.t1;Parent=MS.gene073497
chr4.1 exon 76314019 76314136 76314019 ID=MS.gene073497.t1.exon1;Parent=MS.gene073497.t1
chr4.1 CDS 76314019 76314136 76314019 ID=cds.MS.gene073497.t1;Parent=MS.gene073497.t1
chr4.1 exon 76313741 76313890 76313741 ID=MS.gene073497.t1.exon2;Parent=MS.gene073497.t1
chr4.1 CDS 76313741 76313890 76313741 ID=cds.MS.gene073497.t1;Parent=MS.gene073497.t1
chr4.1 exon 76313330 76313652 76313330 ID=MS.gene073497.t1.exon3;Parent=MS.gene073497.t1
chr4.1 CDS 76313330 76313652 76313330 ID=cds.MS.gene073497.t1;Parent=MS.gene073497.t1
Gene Sequence

>MS.gene073497

ATGGCCGTTTTCGTTGACAGCCCATCATTCCCTGCTGGTCTCAAGGTTATTGCCATTGATCATGACATCACTGTTCTTAACACTATTGAGGATATGTGCAATCGATTCCATTATCAAGGTTAGTCACTTAGTTAATTGCACTTTATTCAATTCTGAAGTTTCTATCTATGTTATTACTTTTATGTATTTTCATGTTTGTTTGTTTCTTCATTCTTATGCATATTTTTATATGTTTCTTTATTTCAGTTACCAAATGTAACACAGCTTCTGATGCCTTTAATTTGTTGGAAAGAAAGGACTGTTTTGATGTAATGTTGATTGATGCTCATATGCCAAACATGGATGTTTATAACTTTGTCCAAAATGTTACCCTACAACTCAACATTCCTGTCATTAGTAAGAATTTATTCAACTTTACATGATTCATTCATATATATGTACTTAATTAGTGTGAACTGACATTATTATTATTTCTTTTTTGTAGTGATGGCTGTTGATTTCGCAAAAAGTTCTATTATGAAGTCTATTGAATGTGGGGCTTGTACATATTGGACTAAGCCTTTGGTTGAAGAAGAGTTCAAGATCATGTGGCACCATGTTGCAAGAAACGGTTTGACTGAAAATAAAGAATATGAAATTGTTGGAAGCTTGGTGGTTGAAGAAAATAGAAAACGGGGTAGAGAAGATGATAACCCCTCAAAAGATACACATGCAAAGAAGGCCCGTTTGTCTTGGTCGCCAGAACTGCATCAACGATTTCTATGGGCTGTCAATCAACTAGGCCTTGATAGTATGCTTCTTTCCTAA
Protein sequence

>MS.gene073497.t1

MAVFVDSPSFPAGLKVIAIDHDITVLNTIEDMCNRFHYQVTKCNTASDAFNLLERKDCFDVMLIDAHMPNMDVYNFVQNVTLQLNIPVIMMAVDFAKSSIMKSIECGACTYWTKPLVEEEFKIMWHHVARNGLTENKEYEIVGSLVVEENRKRGREDDNPSKDTHAKKARLSWSPELHQRFLWAVNQLGLDSMLLS