AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004586

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004586.t1 MTR_2g437090 91.813 171 14 0 69 239 1 171 1.18e-111 318
MS.gene004586.t1 MTR_2g437020 60.924 238 92 1 1 238 146 382 8.26e-100 295
MS.gene004586.t1 MTR_2g436440 60.426 235 91 1 1 235 153 385 5.19e-97 288
MS.gene004586.t1 MTR_2g437060 61.017 236 90 1 1 236 162 395 9.53e-97 288
MS.gene004586.t1 MTR_2g437030 59.916 237 93 1 1 237 233 467 1.36e-96 290
MS.gene004586.t1 MTR_2g437080 57.983 238 98 1 1 238 147 382 3.13e-96 286
MS.gene004586.t1 MTR_2g436400 60.000 230 90 1 1 230 154 381 1.25e-92 277
MS.gene004586.t1 MTR_2g437040 55.085 236 104 1 1 236 147 380 3.58e-87 263
MS.gene004586.t1 MTR_2g438010 48.760 242 119 2 1 239 177 416 2.36e-74 232
MS.gene004586.t1 MTR_4g119550 48.261 230 117 1 1 230 157 384 3.37e-74 230
MS.gene004586.t1 MTR_2g437120 51.502 233 107 3 1 230 158 387 2.11e-72 226
MS.gene004586.t1 MTR_2g437170 48.347 242 120 2 1 239 164 403 1.95e-71 224
MS.gene004586.t1 MTR_2g437200 49.782 229 110 2 1 226 172 398 8.14e-71 222
MS.gene004586.t1 MTR_2g437960 47.934 242 121 3 1 239 160 399 2.72e-70 221
MS.gene004586.t1 MTR_2g438020 49.362 235 110 3 1 230 211 441 3.48e-70 223
MS.gene004586.t1 MTR_2g437150 47.521 242 122 2 1 239 164 403 3.56e-70 221
MS.gene004586.t1 MTR_2g437240 48.927 233 114 2 1 230 172 402 4.97e-70 220
MS.gene004586.t1 MTR_2g437960 47.934 242 121 3 1 239 160 399 5.13e-70 221
MS.gene004586.t1 MTR_2g437100 50.633 237 111 3 1 234 169 402 1.25e-69 219
MS.gene004586.t1 MTR_2g437130 45.607 239 128 1 1 239 148 384 3.26e-68 215
MS.gene004586.t1 MTR_2g437990 46.888 241 124 3 1 239 157 395 2.24e-67 214
MS.gene004586.t1 MTR_2g076320 45.868 242 126 3 1 239 157 396 9.24e-67 211
MS.gene004586.t1 MTR_2g437180 45.455 242 125 4 1 239 156 393 9.67e-66 209
MS.gene004586.t1 MTR_2g437160 46.058 241 126 2 1 239 170 408 2.86e-65 208
MS.gene004586.t1 MTR_2g437260 41.739 230 134 0 1 230 141 370 2.51e-64 205
MS.gene004586.t1 MTR_2g437940 51.724 203 96 1 37 239 167 367 4.44e-64 204
MS.gene004586.t1 MTR_2g437160 48.611 216 105 3 28 239 104 317 1.95e-61 195
MS.gene004586.t1 MTR_2g436460 43.043 230 128 2 1 229 152 379 1.26e-58 190
MS.gene004586.t1 MTR_4g119580 42.601 223 126 1 1 223 149 369 2.43e-55 181
MS.gene004586.t1 MTR_4g120380 41.518 224 129 1 1 224 149 370 5.23e-52 172
MS.gene004586.t1 MTR_2g019810 42.478 226 128 2 1 226 136 359 3.48e-49 165
MS.gene004586.t1 MTR_2g019840 41.304 230 133 2 1 230 148 375 7.39e-49 165
MS.gene004586.t1 MTR_4g120380 42.647 204 115 1 1 204 149 350 3.06e-47 161
MS.gene004586.t1 MTR_4g120380 36.667 120 71 2 72 191 302 416 1.35e-13 69.7
MS.gene004586.t1 MTR_4g119570 34.375 224 112 2 1 224 41 229 2.19e-35 125
MS.gene004586.t1 MTR_3g450500 26.087 230 166 1 1 226 143 372 1.32e-25 103
MS.gene004586.t1 MTR_4g007490 26.316 228 164 2 1 224 141 368 9.15e-23 95.5
MS.gene004586.t1 MTR_2g436380 63.333 60 22 0 69 128 1 60 2.08e-18 82.4
MS.gene004586.t1 MTR_3g085240 40.449 89 36 1 128 216 176 247 2.49e-14 70.5
MS.gene004586.t1 MTR_4g119615 46.154 65 30 1 168 232 26 85 1.11e-12 62.4
MS.gene004586.t1 MTR_8g080990 26.630 184 133 2 37 219 185 367 3.78e-11 62.4
MS.gene004586.t1 MTR_2g019830 50.725 69 33 1 161 229 135 202 7.54e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004586.t1 AT5G07900 31.718 227 151 2 1 223 173 399 2.10e-31 119
MS.gene004586.t1 AT1G21150 25.000 220 159 3 1 215 160 378 1.88e-19 86.7
MS.gene004586.t1 AT1G21150 25.000 220 159 3 1 215 124 342 1.95e-19 86.3
MS.gene004586.t1 AT1G21150 25.000 220 159 3 1 215 224 442 2.48e-19 86.7
MS.gene004586.t1 AT5G64950 27.419 248 162 4 1 236 143 384 7.83e-16 76.3
MS.gene004586.t1 AT1G61980 26.425 193 104 4 60 216 216 406 4.20e-14 71.2
MS.gene004586.t1 AT1G61980 26.425 193 104 4 60 216 216 406 4.20e-14 71.2
MS.gene004586.t1 AT1G61980 26.425 193 104 4 60 216 216 406 4.20e-14 71.2
MS.gene004586.t1 AT1G61990 25.967 181 95 3 73 215 220 399 1.79e-11 63.5
MS.gene004586.t1 AT1G61990 25.967 181 95 3 73 215 220 399 1.79e-11 63.5
MS.gene004586.t1 AT1G61970 28.302 106 75 1 105 209 294 399 6.64e-11 62.0
MS.gene004586.t1 AT1G61970 28.302 106 75 1 105 209 294 399 6.64e-11 62.0
MS.gene004586.t1 AT1G61970 28.302 106 75 1 105 209 294 399 6.64e-11 62.0
MS.gene004586.t1 AT1G61970 28.302 106 75 1 105 209 294 399 6.64e-11 62.0
MS.gene004586.t1 AT1G61970 28.302 106 75 1 105 209 294 399 6.64e-11 62.0
MS.gene004586.t1 AT1G61970 28.302 106 75 1 105 209 294 399 6.64e-11 62.0
MS.gene004586.t1 AT1G61970 28.302 106 75 1 105 209 294 399 6.64e-11 62.0

Find 49 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAACAACTTGATGTTATT+TGG 0.104270 2.2:+52153932 None:intergenic
CACTAAATTTAATTTATTAA+TGG 0.141687 2.2:+52153634 None:intergenic
GAAATTGCTGGAGGAATTAA+AGG 0.197979 2.2:-52153825 MS.gene004586:CDS
GCTGGAGGAATTAAAGGTTT+TGG 0.234696 2.2:-52153819 MS.gene004586:CDS
AACTTCTCAGGCACTATAAA+TGG 0.258902 2.2:+52153449 None:intergenic
GTTCACAATCGAAATTTCTT+TGG 0.274752 2.2:-52153968 MS.gene004586:CDS
TAAAGAAAGGTCTGCGAAAA+AGG 0.303287 2.2:-52153490 MS.gene004586:CDS
AGACCAACCCCATTTCTTAA+AGG 0.312139 2.2:+52153709 None:intergenic
CTTTGGCAATTAGTGCTAGA+TGG 0.328181 2.2:+52153771 None:intergenic
AGTTGACACCTTTAAGAAAT+GGG 0.372153 2.2:-52153717 MS.gene004586:CDS
TTGGGTTAATGAGATGGGTT+GGG 0.376912 2.2:-52153603 MS.gene004586:CDS
AAGTTGACACCTTTAAGAAA+TGG 0.378023 2.2:-52153718 MS.gene004586:CDS
TTTAGCAGGAATTGCACAAT+TGG 0.403154 2.2:+52153509 None:intergenic
TTCGCAGACCTTTCTTTAGC+AGG 0.405595 2.2:+52153495 None:intergenic
AGCAATTTCAGCATGTCTCC+TGG 0.410103 2.2:+52153839 None:intergenic
AGGAGACATGCTGAAATTGC+TGG 0.412023 2.2:-52153837 MS.gene004586:CDS
AATGGTACCAACCTATGAAT+TGG 0.419508 2.2:-52154035 MS.gene004586:CDS
TTAGCAGGAATTGCACAATT+GGG 0.419770 2.2:+52153510 None:intergenic
CTGCACAAGCAAGGGTGTCC+CGG 0.429389 2.2:+52153990 None:intergenic
TGCACAAGCAAGGGTGTCCC+GGG 0.430444 2.2:+52153991 None:intergenic
AATTGCACAATTGGGGCCCT+TGG 0.436231 2.2:+52153518 None:intergenic
ATCAAGTTGTTGATCAAGAA+TGG 0.442244 2.2:-52153923 MS.gene004586:CDS
TTTGGGTTAATGAGATGGGT+TGG 0.456967 2.2:-52153604 MS.gene004586:CDS
GAATGTATACGCCAATTCAT+AGG 0.459605 2.2:+52154024 None:intergenic
TGTCAACTTTATCTTTCGAT+AGG 0.471860 2.2:+52153732 None:intergenic
TTAGAAGATTGCTTCGTAGC+AGG 0.479908 2.2:-52153883 MS.gene004586:CDS
CCTGGACCTGAATAGAATAT+CGG 0.484798 2.2:+52153857 None:intergenic
AGGAGTCCGATATTCTATTC+AGG 0.485761 2.2:-52153863 MS.gene004586:CDS
TTATCTGTCAAAGCTGTATG+AGG 0.488477 2.2:-52153384 MS.gene004586:CDS
CACAATTGGGGCCCTTGGAA+TGG 0.496085 2.2:+52153523 None:intergenic
GTCAACTTTATCTTTCGATA+GGG 0.506778 2.2:+52153733 None:intergenic
TTATCAAGAAACAACTTCTC+AGG 0.508607 2.2:+52153437 None:intergenic
CCGATATTCTATTCAGGTCC+AGG 0.510519 2.2:-52153857 MS.gene004586:CDS
GTGCAATTCCTGCTAAAGAA+AGG 0.527981 2.2:-52153503 MS.gene004586:CDS
TACATTCTTGAAATCTCCCC+GGG 0.530135 2.2:-52154008 MS.gene004586:CDS
GATTGTGAACTGCACAAGCA+AGG 0.555573 2.2:+52153981 None:intergenic
TAGCAGGAATTGCACAATTG+GGG 0.567455 2.2:+52153511 None:intergenic
CAATCTTCTAATGTTTGAGT+CGG 0.570421 2.2:+52153895 None:intergenic
GATGTTATTTGGCACACGCG+TGG 0.582501 2.2:+52153943 None:intergenic
GTTGACACCTTTAAGAAATG+GGG 0.582694 2.2:-52153716 MS.gene004586:CDS
ATACATTCTTGAAATCTCCC+CGG 0.589953 2.2:-52154009 MS.gene004586:CDS
ATTGTGAACTGCACAAGCAA+GGG 0.590606 2.2:+52153982 None:intergenic
GTATACGCCAATTCATAGGT+TGG 0.610841 2.2:+52154028 None:intergenic
AAAGTGATGGATCTATAGCA+AGG 0.611721 2.2:+52153570 None:intergenic
ACACCTTTAAGAAATGGGGT+TGG 0.612652 2.2:-52153712 MS.gene004586:CDS
AAGTGATGGATCTATAGCAA+GGG 0.614469 2.2:+52153571 None:intergenic
ATGGATACTAACATACACTC+AGG 0.661010 2.2:+52153653 None:intergenic
GCACAAGCAAGGGTGTCCCG+GGG 0.672396 2.2:+52153992 None:intergenic
AGACATGCTGAAATTGCTGG+AGG 0.684530 2.2:-52153834 MS.gene004586:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CACTAAATTTAATTTATTAA+TGG + chr2.2:52153740-52153759 None:intergenic 10.0%
!!! AAATTTAGTGATGAATTTTT+GGG - chr2.2:52153750-52153769 MS.gene004586:CDS 15.0%
!!! TAAATTTAGTGATGAATTTT+TGG - chr2.2:52153749-52153768 MS.gene004586:CDS 15.0%
! ATCAACAACTTGATGTTATT+TGG + chr2.2:52153442-52153461 None:intergenic 25.0%
!!! AATTTTTGGGTTAATGAGAT+GGG - chr2.2:52153763-52153782 MS.gene004586:CDS 25.0%
!!! TTATTTTCGAAGCATTTAGA+AGG - chr2.2:52153692-52153711 MS.gene004586:CDS 25.0%
AAACTGATAGCAAAAAGTGA+TGG + chr2.2:52153817-52153836 None:intergenic 30.0%
CAATCTTCTAATGTTTGAGT+CGG + chr2.2:52153479-52153498 None:intergenic 30.0%
GTCAACTTTATCTTTCGATA+GGG + chr2.2:52153641-52153660 None:intergenic 30.0%
GTTCACAATCGAAATTTCTT+TGG - chr2.2:52153403-52153422 MS.gene004586:CDS 30.0%
TGTCAACTTTATCTTTCGAT+AGG + chr2.2:52153642-52153661 None:intergenic 30.0%
TTATCAAGAAACAACTTCTC+AGG + chr2.2:52153937-52153956 None:intergenic 30.0%
TTGCTATCAGTTTGGAAAAA+AGG - chr2.2:52153824-52153843 MS.gene004586:CDS 30.0%
! AAGTTGACACCTTTAAGAAA+TGG - chr2.2:52153653-52153672 MS.gene004586:CDS 30.0%
! AGTTGACACCTTTAAGAAAT+GGG - chr2.2:52153654-52153673 MS.gene004586:CDS 30.0%
! ATCAAGTTGTTGATCAAGAA+TGG - chr2.2:52153448-52153467 MS.gene004586:CDS 30.0%
!! AGATGGAAAGATGTTTTTGA+AGG + chr2.2:52153586-52153605 None:intergenic 30.0%
!!! ATCACTTTTTGCTATCAGTT+TGG - chr2.2:52153816-52153835 MS.gene004586:CDS 30.0%
!!! GAATTTTTGGGTTAATGAGA+TGG - chr2.2:52153762-52153781 MS.gene004586:CDS 30.0%
!!! GGTTTTGTTTATACTTGCTT+TGG + chr2.2:52153620-52153639 None:intergenic 30.0%
AACTTCTCAGGCACTATAAA+TGG + chr2.2:52153925-52153944 None:intergenic 35.0%
ATACATTCTTGAAATCTCCC+CGG - chr2.2:52153362-52153381 MS.gene004586:CDS 35.0%
ATGGATACTAACATACACTC+AGG + chr2.2:52153721-52153740 None:intergenic 35.0%
GAAATTGCTGGAGGAATTAA+AGG - chr2.2:52153546-52153565 MS.gene004586:CDS 35.0%
GAATGTATACGCCAATTCAT+AGG + chr2.2:52153350-52153369 None:intergenic 35.0%
TAAAGAAAGGTCTGCGAAAA+AGG - chr2.2:52153881-52153900 MS.gene004586:CDS 35.0%
TTAGCAGGAATTGCACAATT+GGG + chr2.2:52153864-52153883 None:intergenic 35.0%
TTATCTGTCAAAGCTGTATG+AGG - chr2.2:52153987-52154006 MS.gene004586:CDS 35.0%
TTTAGCAGGAATTGCACAAT+TGG + chr2.2:52153865-52153884 None:intergenic 35.0%
! CTGGAGGAATTAAAGGTTTT+GGG - chr2.2:52153553-52153572 MS.gene004586:CDS 35.0%
! GTTGACACCTTTAAGAAATG+GGG - chr2.2:52153655-52153674 MS.gene004586:CDS 35.0%
!! AAAGTGATGGATCTATAGCA+AGG + chr2.2:52153804-52153823 None:intergenic 35.0%
!! AAGTGATGGATCTATAGCAA+GGG + chr2.2:52153803-52153822 None:intergenic 35.0%
!! TTTTCGAAGCATTTAGAAGG+CGG - chr2.2:52153695-52153714 MS.gene004586:CDS 35.0%
AGACCAACCCCATTTCTTAA+AGG + chr2.2:52153665-52153684 None:intergenic 40.0%
AGGAGTCCGATATTCTATTC+AGG - chr2.2:52153508-52153527 MS.gene004586:CDS 40.0%
ATTGTGAACTGCACAAGCAA+GGG + chr2.2:52153392-52153411 None:intergenic 40.0%
CCTGGACCTGAATAGAATAT+CGG + chr2.2:52153517-52153536 None:intergenic 40.0%
CTTTGGCAATTAGTGCTAGA+TGG + chr2.2:52153603-52153622 None:intergenic 40.0%
GGAAAAAAGGACCATTCCAA+GGG - chr2.2:52153837-52153856 MS.gene004586:CDS 40.0%
GTATACGCCAATTCATAGGT+TGG + chr2.2:52153346-52153365 None:intergenic 40.0%
GTGCAATTCCTGCTAAAGAA+AGG - chr2.2:52153868-52153887 MS.gene004586:CDS 40.0%
TACATTCTTGAAATCTCCCC+GGG - chr2.2:52153363-52153382 MS.gene004586:CDS 40.0%
TAGCAGGAATTGCACAATTG+GGG + chr2.2:52153863-52153882 None:intergenic 40.0%
TGGAAAAAAGGACCATTCCA+AGG - chr2.2:52153836-52153855 MS.gene004586:CDS 40.0%
TTAGAAGATTGCTTCGTAGC+AGG - chr2.2:52153488-52153507 MS.gene004586:CDS 40.0%
! ACACCTTTAAGAAATGGGGT+TGG - chr2.2:52153659-52153678 MS.gene004586:CDS 40.0%
! GCTGGAGGAATTAAAGGTTT+TGG - chr2.2:52153552-52153571 MS.gene004586:CDS 40.0%
! TTGGGTTAATGAGATGGGTT+GGG - chr2.2:52153768-52153787 MS.gene004586:CDS 40.0%
! TTTGGGTTAATGAGATGGGT+TGG - chr2.2:52153767-52153786 MS.gene004586:CDS 40.0%
! TTTTGTCTGTGATGCATGCA+AGG + chr2.2:52154023-52154042 None:intergenic 40.0%
AGACATGCTGAAATTGCTGG+AGG - chr2.2:52153537-52153556 MS.gene004586:CDS 45.0%
AGCAATTTCAGCATGTCTCC+TGG + chr2.2:52153535-52153554 None:intergenic 45.0%
AGGAGACATGCTGAAATTGC+TGG - chr2.2:52153534-52153553 MS.gene004586:CDS 45.0%
CCGATATTCTATTCAGGTCC+AGG - chr2.2:52153514-52153533 MS.gene004586:CDS 45.0%
GATTGTGAACTGCACAAGCA+AGG + chr2.2:52153393-52153412 None:intergenic 45.0%
TTCGCAGACCTTTCTTTAGC+AGG + chr2.2:52153879-52153898 None:intergenic 45.0%
AATTGCACAATTGGGGCCCT+TGG + chr2.2:52153856-52153875 None:intergenic 50.0%
! GATGTTATTTGGCACACGCG+TGG + chr2.2:52153431-52153450 None:intergenic 50.0%
CACAATTGGGGCCCTTGGAA+TGG + chr2.2:52153851-52153870 None:intergenic 55.0%
!! CTGCACAAGCAAGGGTGTCC+CGG + chr2.2:52153384-52153403 None:intergenic 60.0%
!! TGCACAAGCAAGGGTGTCCC+GGG + chr2.2:52153383-52153402 None:intergenic 60.0%
!! GCACAAGCAAGGGTGTCCCG+GGG + chr2.2:52153382-52153401 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 52153337 52154056 52153337 ID=MS.gene004586
chr2.2 mRNA 52153337 52154056 52153337 ID=MS.gene004586.t1;Parent=MS.gene004586
chr2.2 exon 52153337 52154056 52153337 ID=MS.gene004586.t1.exon1;Parent=MS.gene004586.t1
chr2.2 CDS 52153337 52154056 52153337 ID=cds.MS.gene004586.t1;Parent=MS.gene004586.t1
Gene Sequence

>MS.gene004586

ATGGTACCAACCTATGAATTGGCGTATACATTCTTGAAATCTCCCCGGGACACCCTTGCTTGTGCAGTTCACAATCGAAATTTCTTTGGAGCCACGCGTGTGCCAAATAACATCAAGTTGTTGATCAAGAATGGAGTGTCCGACTCAAACATTAGAAGATTGCTTCGTAGCAGGAGTCCGATATTCTATTCAGGTCCAGGAGACATGCTGAAATTGCTGGAGGAATTAAAGGTTTTGGGTTTTAATCCTTCAAAAACATCTTTCCATCTAGCACTAATTGCCAAAGCAAGTATAAACAAAACCCTATCGAAAGATAAAGTTGACACCTTTAAGAAATGGGGTTGGTCTGAACAAGTTATTTTCGAAGCATTTAGAAGGCGGCCTGAGTGTATGTTAGTATCCATTAATAAATTAAATTTAGTGATGAATTTTTGGGTTAATGAGATGGGTTGGGATGCTCTTGCCCTTGCTATAGATCCATCACTTTTTGCTATCAGTTTGGAAAAAAGGACCATTCCAAGGGCCCCAATTGTGCAATTCCTGCTAAAGAAAGGTCTGCGAAAAAGGACTGCAAGCTTAACTTCTCCATTTATAGTGCCTGAGAAGTTGTTTCTTGATAAGTTTATAAAACGTTTTGAGAACGAGTCTTCTTATCTGTCAAAGCTGTATGAGGAAAAACTCAACCTTGCATGCATCACAGACAAAACTTGCACACCATAG
Protein sequence

>MS.gene004586.t1

MVPTYELAYTFLKSPRDTLACAVHNRNFFGATRVPNNIKLLIKNGVSDSNIRRLLRSRSPIFYSGPGDMLKLLEELKVLGFNPSKTSFHLALIAKASINKTLSKDKVDTFKKWGWSEQVIFEAFRRRPECMLVSINKLNLVMNFWVNEMGWDALALAIDPSLFAISLEKRTIPRAPIVQFLLKKGLRKRTASLTSPFIVPEKLFLDKFIKRFENESSYLSKLYEEKLNLACITDKTCTP