AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073374

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073374.t1 MTR_2g437090 92.982 171 12 0 69 239 1 171 7.56e-114 323
MS.gene073374.t1 MTR_2g437020 61.345 238 91 1 1 238 146 382 6.78e-102 301
MS.gene073374.t1 MTR_2g436440 60.426 235 91 1 1 235 153 385 4.54e-98 291
MS.gene073374.t1 MTR_2g437060 61.017 236 90 1 1 236 162 395 9.00e-98 291
MS.gene073374.t1 MTR_2g437030 59.916 237 93 1 1 237 233 467 1.80e-97 292
MS.gene073374.t1 MTR_2g437080 57.983 238 98 1 1 238 147 382 2.27e-97 289
MS.gene073374.t1 MTR_2g436400 60.000 230 90 1 1 230 154 381 9.79e-94 280
MS.gene073374.t1 MTR_2g437040 55.085 236 104 1 1 236 147 380 2.64e-88 266
MS.gene073374.t1 MTR_4g119550 47.234 235 122 1 1 235 157 389 2.52e-75 233
MS.gene073374.t1 MTR_2g438010 47.934 242 121 2 1 239 177 416 1.60e-74 232
MS.gene073374.t1 MTR_2g437120 51.502 233 107 3 1 230 158 387 2.67e-73 229
MS.gene073374.t1 MTR_2g437170 47.934 242 121 2 1 239 164 403 1.50e-72 227
MS.gene073374.t1 MTR_2g437200 49.345 229 111 2 1 226 172 398 1.14e-71 224
MS.gene073374.t1 MTR_2g437960 47.521 242 122 3 1 239 160 399 2.70e-71 223
MS.gene073374.t1 MTR_2g437240 48.498 233 115 2 1 230 172 402 2.92e-71 224
MS.gene073374.t1 MTR_2g437150 47.107 242 123 2 1 239 164 403 3.62e-71 223
MS.gene073374.t1 MTR_2g437960 47.521 242 122 3 1 239 160 399 5.18e-71 223
MS.gene073374.t1 MTR_2g438020 48.936 235 111 3 1 230 211 441 9.23e-71 224
MS.gene073374.t1 MTR_2g437100 50.211 237 112 3 1 234 169 402 1.48e-70 221
MS.gene073374.t1 MTR_2g437130 45.188 239 129 1 1 239 148 384 2.15e-69 218
MS.gene073374.t1 MTR_2g437990 46.058 241 126 3 1 239 157 395 1.11e-67 215
MS.gene073374.t1 MTR_2g076320 45.041 242 128 3 1 239 157 396 5.28e-67 212
MS.gene073374.t1 MTR_2g437180 45.041 242 126 4 1 239 156 393 1.30e-66 211
MS.gene073374.t1 MTR_2g437160 46.058 241 126 2 1 239 170 408 5.58e-66 210
MS.gene073374.t1 MTR_2g437260 41.739 230 134 0 1 230 141 370 8.56e-66 209
MS.gene073374.t1 MTR_2g437940 51.232 203 97 1 37 239 167 367 3.03e-65 207
MS.gene073374.t1 MTR_2g437160 48.611 216 105 3 28 239 104 317 3.07e-62 197
MS.gene073374.t1 MTR_2g436460 42.609 230 129 2 1 229 152 379 1.11e-59 192
MS.gene073374.t1 MTR_4g119580 42.857 224 126 1 1 224 149 370 1.54e-57 187
MS.gene073374.t1 MTR_4g120380 41.071 224 130 1 1 224 149 370 2.32e-53 176
MS.gene073374.t1 MTR_2g019810 42.920 226 127 2 1 226 136 359 4.18e-51 170
MS.gene073374.t1 MTR_2g019840 41.739 230 132 2 1 230 148 375 3.02e-50 168
MS.gene073374.t1 MTR_4g120380 42.157 204 116 1 1 204 149 350 1.98e-48 164
MS.gene073374.t1 MTR_4g120380 35.833 120 72 2 72 191 302 416 2.37e-13 68.9
MS.gene073374.t1 MTR_4g119570 33.929 224 113 2 1 224 41 229 6.54e-37 130
MS.gene073374.t1 MTR_3g450500 26.957 230 164 1 1 226 143 372 2.47e-28 110
MS.gene073374.t1 MTR_4g007490 27.193 228 162 2 1 224 141 368 1.90e-25 102
MS.gene073374.t1 MTR_2g436380 66.667 60 20 0 69 128 1 60 9.61e-21 88.6
MS.gene073374.t1 MTR_3g085240 40.449 89 36 1 128 216 176 247 2.54e-14 70.5
MS.gene073374.t1 MTR_4g119615 46.154 65 30 1 168 232 26 85 1.26e-12 62.4
MS.gene073374.t1 MTR_8g080990 25.137 183 137 0 37 219 185 367 2.23e-11 63.2
MS.gene073374.t1 MTR_2g019830 50.725 69 33 1 161 229 135 202 6.25e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073374.t1 AT5G07900 31.718 227 151 2 1 223 173 399 4.68e-33 124
MS.gene073374.t1 AT1G21150 24.545 220 160 3 1 215 160 378 1.67e-19 86.7
MS.gene073374.t1 AT1G21150 24.545 220 160 3 1 215 124 342 1.73e-19 86.3
MS.gene073374.t1 AT1G21150 24.545 220 160 3 1 215 224 442 2.90e-19 86.3
MS.gene073374.t1 AT5G64950 27.419 248 162 4 1 236 143 384 5.03e-16 76.6
MS.gene073374.t1 AT1G61980 26.131 199 109 4 54 216 210 406 5.58e-14 70.9
MS.gene073374.t1 AT1G61980 26.131 199 109 4 54 216 210 406 5.58e-14 70.9
MS.gene073374.t1 AT1G61980 26.131 199 109 4 54 216 210 406 5.58e-14 70.9
MS.gene073374.t1 AT1G61990 25.731 171 89 2 79 211 226 396 1.46e-11 63.9
MS.gene073374.t1 AT1G61990 25.731 171 89 2 79 211 226 396 1.46e-11 63.9
MS.gene073374.t1 AT1G61970 28.302 106 75 1 105 209 294 399 5.77e-11 62.0
MS.gene073374.t1 AT1G61970 28.302 106 75 1 105 209 294 399 5.77e-11 62.0
MS.gene073374.t1 AT1G61970 28.302 106 75 1 105 209 294 399 5.77e-11 62.0
MS.gene073374.t1 AT1G61970 28.302 106 75 1 105 209 294 399 5.77e-11 62.0
MS.gene073374.t1 AT1G61970 28.302 106 75 1 105 209 294 399 5.77e-11 62.0
MS.gene073374.t1 AT1G61970 28.302 106 75 1 105 209 294 399 5.77e-11 62.0
MS.gene073374.t1 AT1G61970 28.302 106 75 1 105 209 294 399 5.77e-11 62.0
MS.gene073374.t1 AT1G62010 29.464 112 78 1 105 215 278 389 5.90e-11 62.0
MS.gene073374.t1 AT1G62085 27.679 112 80 1 105 215 334 445 9.02e-11 61.6
MS.gene073374.t1 AT1G62085 27.679 112 80 1 105 215 334 445 9.02e-11 61.6

Find 52 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAACAACTTGATGTTATT+TGG 0.104270 2.4:+54610923 None:intergenic
CACTAAATTTAATTTATTAA+TGG 0.141687 2.4:+54610625 None:intergenic
GAAATTGGTGGAGGAATTAA+AGG 0.214341 2.4:-54610816 MS.gene073374:CDS
GGTGGAGGAATTAAAGGTTT+TGG 0.244368 2.4:-54610810 MS.gene073374:CDS
AACTTCTCAGGCACTATAAA+TGG 0.258902 2.4:+54610440 None:intergenic
GTTCACAATCGAAATTTCTT+TGG 0.274752 2.4:-54610959 MS.gene073374:CDS
TAAAGAAAGGTCTGCGAAAA+AGG 0.303287 2.4:-54610481 MS.gene073374:CDS
AGACCAACCCCATTTCTTAA+AGG 0.312139 2.4:+54610700 None:intergenic
TCCAGGAGACATGCTGAAAT+TGG 0.363602 2.4:-54610831 MS.gene073374:CDS
CCTGGACCTGAATAGAATAT+TGG 0.371161 2.4:+54610848 None:intergenic
AGTTGACACCTTTAAGAAAT+GGG 0.372153 2.4:-54610708 MS.gene073374:CDS
TTGGGTTAATGAGATGGGTT+GGG 0.376912 2.4:-54610594 MS.gene073374:CDS
AAGTTGACACCTTTAAGAAA+TGG 0.378023 2.4:-54610709 MS.gene073374:CDS
ACCAATTTCAGCATGTCTCC+TGG 0.389411 2.4:+54610830 None:intergenic
TTTAGCAGGAATTGCACAAT+TGG 0.403154 2.4:+54610500 None:intergenic
TTCGCAGACCTTTCTTTAGC+AGG 0.405595 2.4:+54610486 None:intergenic
AATGGTACCAACCTATGAAT+TGG 0.419508 2.4:-54611026 MS.gene073374:CDS
TTAGCAGGAATTGCACAATT+GGG 0.419770 2.4:+54610501 None:intergenic
CTGCACAAGCAAGGGTGTCC+CGG 0.429389 2.4:+54610981 None:intergenic
TGCACAAGCAAGGGTGTCCC+GGG 0.430444 2.4:+54610982 None:intergenic
AATTGCACAATTGGGGCCCT+TGG 0.436231 2.4:+54610509 None:intergenic
TGTCAACTTTATCTTTCCAT+AGG 0.441802 2.4:+54610723 None:intergenic
ATCAAGTTGTTGATCAAGAA+TGG 0.442244 2.4:-54610914 MS.gene073374:CDS
AGGAGTCCAATATTCTATTC+AGG 0.455375 2.4:-54610854 MS.gene073374:CDS
TTTGGGTTAATGAGATGGGT+TGG 0.456967 2.4:-54610595 MS.gene073374:CDS
GAATGTATACGCCAATTCAT+AGG 0.459605 2.4:+54611015 None:intergenic
TTATCTGTCAAAGCTGTATG+AGG 0.488477 2.4:-54610375 MS.gene073374:CDS
CACAATTGGGGCCCTTGGAA+TGG 0.496085 2.4:+54610514 None:intergenic
CCAATATTCTATTCAGGTCC+AGG 0.500936 2.4:-54610848 MS.gene073374:CDS
TTGCTTTGGCAATTAGTGCT+AGG 0.502653 2.4:+54610759 None:intergenic
TTATCAAGAAACAACTTCTC+AGG 0.508607 2.4:+54610428 None:intergenic
GTCAACTTTATCTTTCCATA+GGG 0.508818 2.4:+54610724 None:intergenic
CAAGTATAAACAAAACCCTA+TGG 0.520595 2.4:-54610739 MS.gene073374:CDS
TTAGAAGATTGATTCATAGC+AGG 0.520763 2.4:-54610874 MS.gene073374:CDS
GTGCAATTCCTGCTAAAGAA+AGG 0.527981 2.4:-54610494 MS.gene073374:CDS
TACATTCTTGAAATCTCCCC+GGG 0.530135 2.4:-54610999 MS.gene073374:CDS
CAATCTTCTAATATTTGAGT+CGG 0.547437 2.4:+54610886 None:intergenic
GATTGTGAACTGCACAAGCA+AGG 0.555573 2.4:+54610972 None:intergenic
AGGAGACATGCTGAAATTGG+TGG 0.557623 2.4:-54610828 MS.gene073374:CDS
TAGCAGGAATTGCACAATTG+GGG 0.567455 2.4:+54610502 None:intergenic
GATGTTATTTGGCACACGCG+TGG 0.582501 2.4:+54610934 None:intergenic
GTTGACACCTTTAAGAAATG+GGG 0.582694 2.4:-54610707 MS.gene073374:CDS
CTTTGGCAATTAGTGCTAGG+TGG 0.586175 2.4:+54610762 None:intergenic
ATACATTCTTGAAATCTCCC+CGG 0.589953 2.4:-54611000 MS.gene073374:CDS
ATTGTGAACTGCACAAGCAA+GGG 0.590606 2.4:+54610973 None:intergenic
AGACATGCTGAAATTGGTGG+AGG 0.596916 2.4:-54610825 MS.gene073374:CDS
GTATACGCCAATTCATAGGT+TGG 0.610841 2.4:+54611019 None:intergenic
AAAGTGATGGATCTATAGCA+AGG 0.611721 2.4:+54610561 None:intergenic
ACACCTTTAAGAAATGGGGT+TGG 0.612652 2.4:-54610703 MS.gene073374:CDS
AAGTGATGGATCTATAGCAA+GGG 0.614469 2.4:+54610562 None:intergenic
ATGGATACTAACATACACTC+AGG 0.661010 2.4:+54610644 None:intergenic
GCACAAGCAAGGGTGTCCCG+GGG 0.672396 2.4:+54610983 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CACTAAATTTAATTTATTAA+TGG + chr2.4:54610731-54610750 None:intergenic 10.0%
!!! AAATTTAGTGATGAATTTTT+GGG - chr2.4:54610741-54610760 MS.gene073374:CDS 15.0%
!!! TAAATTTAGTGATGAATTTT+TGG - chr2.4:54610740-54610759 MS.gene073374:CDS 15.0%
! AAACTTATAGCAAAAAGTGA+TGG + chr2.4:54610808-54610827 None:intergenic 25.0%
! ATCAACAACTTGATGTTATT+TGG + chr2.4:54610433-54610452 None:intergenic 25.0%
! CAATCTTCTAATATTTGAGT+CGG + chr2.4:54610470-54610489 None:intergenic 25.0%
! TTGCTATAAGTTTGGAAAAA+AGG - chr2.4:54610815-54610834 MS.gene073374:CDS 25.0%
!!! AATTTTTGGGTTAATGAGAT+GGG - chr2.4:54610754-54610773 MS.gene073374:CDS 25.0%
!!! ATCACTTTTTGCTATAAGTT+TGG - chr2.4:54610807-54610826 MS.gene073374:CDS 25.0%
!!! TTATTTTCGAAGCATTTAGA+AGG - chr2.4:54610683-54610702 MS.gene073374:CDS 25.0%
CAAGTATAAACAAAACCCTA+TGG - chr2.4:54610614-54610633 MS.gene073374:CDS 30.0%
GTCAACTTTATCTTTCCATA+GGG + chr2.4:54610632-54610651 None:intergenic 30.0%
GTTCACAATCGAAATTTCTT+TGG - chr2.4:54610394-54610413 MS.gene073374:CDS 30.0%
TGTCAACTTTATCTTTCCAT+AGG + chr2.4:54610633-54610652 None:intergenic 30.0%
TTATCAAGAAACAACTTCTC+AGG + chr2.4:54610928-54610947 None:intergenic 30.0%
! AAGTTGACACCTTTAAGAAA+TGG - chr2.4:54610644-54610663 MS.gene073374:CDS 30.0%
! AGTTGACACCTTTAAGAAAT+GGG - chr2.4:54610645-54610664 MS.gene073374:CDS 30.0%
! ATCAAGTTGTTGATCAAGAA+TGG - chr2.4:54610439-54610458 MS.gene073374:CDS 30.0%
! TTAGAAGATTGATTCATAGC+AGG - chr2.4:54610479-54610498 MS.gene073374:CDS 30.0%
!!! GAATTTTTGGGTTAATGAGA+TGG - chr2.4:54610753-54610772 MS.gene073374:CDS 30.0%
!!! GGTTTTGTTTATACTTGCTT+TGG + chr2.4:54610611-54610630 None:intergenic 30.0%
AACTTCTCAGGCACTATAAA+TGG + chr2.4:54610916-54610935 None:intergenic 35.0%
AGGAGTCCAATATTCTATTC+AGG - chr2.4:54610499-54610518 MS.gene073374:CDS 35.0%
ATACATTCTTGAAATCTCCC+CGG - chr2.4:54610353-54610372 MS.gene073374:CDS 35.0%
ATGGATACTAACATACACTC+AGG + chr2.4:54610712-54610731 None:intergenic 35.0%
GAAATTGGTGGAGGAATTAA+AGG - chr2.4:54610537-54610556 MS.gene073374:CDS 35.0%
GAATGTATACGCCAATTCAT+AGG + chr2.4:54610341-54610360 None:intergenic 35.0%
TAAAGAAAGGTCTGCGAAAA+AGG - chr2.4:54610872-54610891 MS.gene073374:CDS 35.0%
TTAGCAGGAATTGCACAATT+GGG + chr2.4:54610855-54610874 None:intergenic 35.0%
TTATCTGTCAAAGCTGTATG+AGG - chr2.4:54610978-54610997 MS.gene073374:CDS 35.0%
TTTAGCAGGAATTGCACAAT+TGG + chr2.4:54610856-54610875 None:intergenic 35.0%
! GTGGAGGAATTAAAGGTTTT+GGG - chr2.4:54610544-54610563 MS.gene073374:CDS 35.0%
! GTTGACACCTTTAAGAAATG+GGG - chr2.4:54610646-54610665 MS.gene073374:CDS 35.0%
!! AAAGTGATGGATCTATAGCA+AGG + chr2.4:54610795-54610814 None:intergenic 35.0%
!! AAGTGATGGATCTATAGCAA+GGG + chr2.4:54610794-54610813 None:intergenic 35.0%
!! AGGTGGAAAGATGTTTTTGA+AGG + chr2.4:54610577-54610596 None:intergenic 35.0%
!! TTTTCGAAGCATTTAGAAGG+CGG - chr2.4:54610686-54610705 MS.gene073374:CDS 35.0%
AGACCAACCCCATTTCTTAA+AGG + chr2.4:54610656-54610675 None:intergenic 40.0%
ATTGTGAACTGCACAAGCAA+GGG + chr2.4:54610383-54610402 None:intergenic 40.0%
CCAATATTCTATTCAGGTCC+AGG - chr2.4:54610505-54610524 MS.gene073374:CDS 40.0%
CCTGGACCTGAATAGAATAT+TGG + chr2.4:54610508-54610527 None:intergenic 40.0%
GGAAAAAAGGACCATTCCAA+GGG - chr2.4:54610828-54610847 MS.gene073374:CDS 40.0%
GTATACGCCAATTCATAGGT+TGG + chr2.4:54610337-54610356 None:intergenic 40.0%
GTGCAATTCCTGCTAAAGAA+AGG - chr2.4:54610859-54610878 MS.gene073374:CDS 40.0%
TACATTCTTGAAATCTCCCC+GGG - chr2.4:54610354-54610373 MS.gene073374:CDS 40.0%
TAGCAGGAATTGCACAATTG+GGG + chr2.4:54610854-54610873 None:intergenic 40.0%
TGGAAAAAAGGACCATTCCA+AGG - chr2.4:54610827-54610846 MS.gene073374:CDS 40.0%
TTGCTTTGGCAATTAGTGCT+AGG + chr2.4:54610597-54610616 None:intergenic 40.0%
! ACACCTTTAAGAAATGGGGT+TGG - chr2.4:54610650-54610669 MS.gene073374:CDS 40.0%
! GGTGGAGGAATTAAAGGTTT+TGG - chr2.4:54610543-54610562 MS.gene073374:CDS 40.0%
! TTGGGTTAATGAGATGGGTT+GGG - chr2.4:54610759-54610778 MS.gene073374:CDS 40.0%
! TTTGGGTTAATGAGATGGGT+TGG - chr2.4:54610758-54610777 MS.gene073374:CDS 40.0%
! TTTTGTCTGTGATGCATGCA+AGG + chr2.4:54611014-54611033 None:intergenic 40.0%
ACCAATTTCAGCATGTCTCC+TGG + chr2.4:54610526-54610545 None:intergenic 45.0%
AGACATGCTGAAATTGGTGG+AGG - chr2.4:54610528-54610547 MS.gene073374:CDS 45.0%
AGGAGACATGCTGAAATTGG+TGG - chr2.4:54610525-54610544 MS.gene073374:CDS 45.0%
CTTTGGCAATTAGTGCTAGG+TGG + chr2.4:54610594-54610613 None:intergenic 45.0%
GATTGTGAACTGCACAAGCA+AGG + chr2.4:54610384-54610403 None:intergenic 45.0%
TCCAGGAGACATGCTGAAAT+TGG - chr2.4:54610522-54610541 MS.gene073374:CDS 45.0%
TTCGCAGACCTTTCTTTAGC+AGG + chr2.4:54610870-54610889 None:intergenic 45.0%
AATTGCACAATTGGGGCCCT+TGG + chr2.4:54610847-54610866 None:intergenic 50.0%
! GATGTTATTTGGCACACGCG+TGG + chr2.4:54610422-54610441 None:intergenic 50.0%
CACAATTGGGGCCCTTGGAA+TGG + chr2.4:54610842-54610861 None:intergenic 55.0%
!! CTGCACAAGCAAGGGTGTCC+CGG + chr2.4:54610375-54610394 None:intergenic 60.0%
!! TGCACAAGCAAGGGTGTCCC+GGG + chr2.4:54610374-54610393 None:intergenic 60.0%
!! GCACAAGCAAGGGTGTCCCG+GGG + chr2.4:54610373-54610392 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 54610328 54611047 54610328 ID=MS.gene073374
chr2.4 mRNA 54610328 54611047 54610328 ID=MS.gene073374.t1;Parent=MS.gene073374
chr2.4 exon 54610328 54611047 54610328 ID=MS.gene073374.t1.exon1;Parent=MS.gene073374.t1
chr2.4 CDS 54610328 54611047 54610328 ID=cds.MS.gene073374.t1;Parent=MS.gene073374.t1
Gene Sequence

>MS.gene073374

ATGGTACCAACCTATGAATTGGCGTATACATTCTTGAAATCTCCCCGGGACACCCTTGCTTGTGCAGTTCACAATCGAAATTTCTTTGGAGCCACGCGTGTGCCAAATAACATCAAGTTGTTGATCAAGAATGGAGTGTCCGACTCAAATATTAGAAGATTGATTCATAGCAGGAGTCCAATATTCTATTCAGGTCCAGGAGACATGCTGAAATTGGTGGAGGAATTAAAGGTTTTGGGTTTTAATCCTTCAAAAACATCTTTCCACCTAGCACTAATTGCCAAAGCAAGTATAAACAAAACCCTATGGAAAGATAAAGTTGACACCTTTAAGAAATGGGGTTGGTCTGAACAAGTTATTTTCGAAGCATTTAGAAGGCGGCCTGAGTGTATGTTAGTATCCATTAATAAATTAAATTTAGTGATGAATTTTTGGGTTAATGAGATGGGTTGGGATGCTCTTGCCCTTGCTATAGATCCATCACTTTTTGCTATAAGTTTGGAAAAAAGGACCATTCCAAGGGCCCCAATTGTGCAATTCCTGCTAAAGAAAGGTCTGCGAAAAAGGACTGCAAGCTTAACTTCTCCATTTATAGTGCCTGAGAAGTTGTTTCTTGATAAGTTTATAAAACGTTTTGAGAACGAGTCTTCTTATCTGTCAAAGCTGTATGAGGAAAAACTCAACCTTGCATGCATCACAGACAAAACTTGCACACCATAG
Protein sequence

>MS.gene073374.t1

MVPTYELAYTFLKSPRDTLACAVHNRNFFGATRVPNNIKLLIKNGVSDSNIRRLIHSRSPIFYSGPGDMLKLVEELKVLGFNPSKTSFHLALIAKASINKTLWKDKVDTFKKWGWSEQVIFEAFRRRPECMLVSINKLNLVMNFWVNEMGWDALALAIDPSLFAISLEKRTIPRAPIVQFLLKKGLRKRTASLTSPFIVPEKLFLDKFIKRFENESSYLSKLYEEKLNLACITDKTCTP