AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene67543

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67543.t1 MTR_5g023390 90.526 285 25 2 1 284 1 284 0.0 501
MS.gene67543.t1 MTR_5g023350 91.579 285 22 2 1 284 1 284 1.20e-180 499
MS.gene67543.t1 MTR_5g023550 90.526 285 26 1 1 285 1 284 2.35e-180 498
MS.gene67543.t1 MTR_5g023600 90.877 285 24 2 1 284 1 284 2.61e-179 495
MS.gene67543.t1 MTR_5g023370 89.474 285 28 2 1 284 1 284 6.70e-179 494
MS.gene67543.t1 MTR_5g023520 88.462 286 31 2 1 285 1 285 5.02e-178 492
MS.gene67543.t1 MTR_5g023340 89.123 285 29 2 1 284 1 284 4.04e-177 490
MS.gene67543.t1 MTR_5g023530 88.298 282 33 0 3 284 4 285 1.18e-176 489
MS.gene67543.t1 MTR_5g023470 87.234 282 36 0 3 284 4 285 2.56e-174 483
MS.gene67543.t1 MTR_5g023320 88.153 287 28 4 1 285 1 283 1.57e-172 478
MS.gene67543.t1 MTR_5g023580 83.624 287 41 4 1 282 1 286 4.38e-159 447
MS.gene67543.t1 MTR_8g074450 68.385 291 85 3 1 285 1 290 5.76e-137 388
MS.gene67543.t1 MTR_8g074510 66.323 291 89 4 1 285 1 288 1.11e-132 377
MS.gene67543.t1 MTR_8g074420 67.698 291 87 3 1 285 1 290 1.71e-130 372
MS.gene67543.t1 MTR_5g023460 87.701 187 18 2 99 285 11 192 5.38e-113 324
MS.gene67543.t1 MTR_8g074530 44.138 290 153 5 2 284 17 304 5.59e-67 211
MS.gene67543.t1 MTR_5g023290 37.542 301 169 5 2 284 9 308 2.44e-56 184
MS.gene67543.t1 MTR_5g023410 91.000 100 9 0 1 100 1 100 3.61e-53 172
MS.gene67543.t1 MTR_8g074380 37.063 286 153 7 7 283 14 281 2.06e-47 161
MS.gene67543.t1 MTR_5g023650 35.836 293 171 6 7 284 14 304 9.67e-45 154
MS.gene67543.t1 MTR_4g070530 33.793 290 184 5 1 284 8 295 1.33e-44 153
MS.gene67543.t1 MTR_3g116950 37.113 291 167 10 3 283 10 294 4.10e-42 146
MS.gene67543.t1 MTR_4g070590 36.301 292 170 8 6 285 14 301 5.11e-41 144
MS.gene67543.t1 MTR_4g070540 32.192 292 184 5 3 285 10 296 1.19e-40 143
MS.gene67543.t1 MTR_4g070570 31.633 294 183 9 3 283 13 301 9.85e-39 138
MS.gene67543.t1 MTR_3g116920 34.354 294 173 11 3 283 10 296 2.53e-36 131
MS.gene67543.t1 MTR_3g115150 27.815 302 183 9 5 284 27 315 3.49e-26 105
MS.gene67543.t1 MTR_1g037820 31.915 235 141 5 51 284 9 225 5.26e-26 102
MS.gene67543.t1 MTR_5g023540 60.345 58 20 1 173 230 11 65 2.25e-15 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67543.t1 AT4G35690 37.884 293 160 7 1 284 4 283 1.19e-55 181
MS.gene67543.t1 AT2G17680 38.614 303 154 10 1 285 4 292 1.42e-47 160
MS.gene67543.t1 AT2G17080 36.620 284 156 6 1 283 1 261 5.16e-47 158
MS.gene67543.t1 AT2G17070 36.170 282 156 6 1 281 1 259 2.87e-45 154
MS.gene67543.t1 AT4G35710 37.000 300 154 10 1 285 4 283 2.97e-43 149
MS.gene67543.t1 AT4G35200 34.982 283 153 8 1 282 1 253 5.15e-43 147
MS.gene67543.t1 AT4G35210 33.922 283 153 8 1 282 1 250 1.36e-40 141
MS.gene67543.t1 AT4G35680 31.000 300 177 8 7 284 18 309 5.07e-25 102
MS.gene67543.t1 AT4G35720 31.329 316 176 9 5 284 14 324 8.32e-25 101
MS.gene67543.t1 AT4G35660 31.650 297 159 11 7 284 16 287 2.12e-24 99.8
MS.gene67543.t1 AT1G76240 26.207 290 195 7 5 285 29 308 2.02e-23 97.8
MS.gene67543.t1 AT3G51400 30.976 297 169 10 1 284 1 274 7.72e-20 87.4
MS.gene67543.t1 AT1G76210 28.509 228 137 7 61 284 20 225 9.00e-17 77.8
MS.gene67543.t1 AT3G51410 31.673 281 149 8 7 284 39 279 8.46e-16 76.3
MS.gene67543.t1 AT1G20520 26.531 245 146 6 47 284 8 225 4.19e-13 67.8

Find 43 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACATATGGAAACTAAATT+TGG 0.157953 5.4:+15127289 MS.gene67543:CDS
GCAATTGAAAGTATAGAAAA+TGG 0.264764 5.4:+15127610 MS.gene67543:CDS
GCCAACCAAGAAAGACAAAA+TGG 0.341438 5.4:-15127407 None:intergenic
TGAAGATTTGTATATTTCAT+TGG 0.354547 5.4:+15126994 MS.gene67543:CDS
AGAGAACATATTTAGGCGTT+TGG 0.368589 5.4:+15127636 MS.gene67543:CDS
GATCACATCTTTAAAACATA+TGG 0.374642 5.4:+15127276 MS.gene67543:CDS
CACTTCACTCCGCTCTTAGA+AGG 0.374965 5.4:+15127170 MS.gene67543:CDS
ATGGTTTAGAGAACATATTT+AGG 0.402533 5.4:+15127629 MS.gene67543:CDS
CAAAGTCAAAGGCAACAAAA+TGG 0.408302 5.4:+15127437 MS.gene67543:CDS
TGTTCAATTCTAGTGGTGCT+TGG 0.418571 5.4:-15126893 None:intergenic
GAAAATTGTGGAAGAGTTGT+TGG 0.420097 5.4:+15127072 MS.gene67543:CDS
ACATGAAAGATTTGTGGCTT+TGG 0.427553 5.4:+15127582 MS.gene67543:CDS
CATTAGAACCTTCACTTGAA+AGG 0.429263 5.4:-15127555 None:intergenic
GGAAGAGTTGTTGGATGGTT+CGG 0.441396 5.4:+15127081 MS.gene67543:CDS
ATTAGAACCTTCACTTGAAA+GGG 0.442145 5.4:-15127554 None:intergenic
CTCACCTTGATGGTGAGAAA+CGG 0.477848 5.4:-15127050 None:intergenic
CTCCGCTCTTAGAAGGAGAA+AGG 0.483537 5.4:+15127177 MS.gene67543:CDS
TGTTGCACATGAAAGATTTG+TGG 0.489205 5.4:+15127576 MS.gene67543:CDS
ACATATGTCATCAACACAAA+AGG 0.492531 5.4:+15127027 MS.gene67543:CDS
TAACTCTTGTTCAATTCTAG+TGG 0.494436 5.4:-15126900 None:intergenic
ACAAATCTTCAAGAAAGAAA+AGG 0.508287 5.4:-15126982 None:intergenic
TGACAAAGTTGATGCAAAAG+AGG 0.510512 5.4:+15127467 MS.gene67543:CDS
TTAAGAACCCTTTCAAGTGA+AGG 0.514521 5.4:+15127547 MS.gene67543:CDS
AGATTTGTATATTTCATTGG+AGG 0.519503 5.4:+15126997 MS.gene67543:CDS
TCCGCTCTTAGAAGGAGAAA+GGG 0.536323 5.4:+15127178 MS.gene67543:CDS
TAGATATATGTGGCATCACA+AGG 0.540397 5.4:+15127113 MS.gene67543:CDS
CCATCAAGGTGAGAAAATTG+TGG 0.548327 5.4:+15127060 MS.gene67543:CDS
TTCAAGAAAGAAAAGGCCAT+TGG 0.559275 5.4:-15126975 None:intergenic
GAAAACTATTTGAGCGAACA+TGG 0.573814 5.4:-15126856 None:intergenic
GGTAACATGTGAAGAGAACA+TGG 0.580064 5.4:+15127489 MS.gene67543:CDS
TGGCTCTTCATCAAAGTCAA+AGG 0.589744 5.4:+15127426 MS.gene67543:CDS
GACAAAGTTGATGCAAAAGA+GGG 0.591207 5.4:+15127468 MS.gene67543:CDS
TCCCTTTCTCCTTCTAAGAG+CGG 0.591308 5.4:-15127179 None:intergenic
ATTGTGGAAGAGTTGTTGGA+TGG 0.606512 5.4:+15127076 MS.gene67543:CDS
ATCAGATGTGGATGTTGATG+TGG 0.611639 5.4:-15126945 None:intergenic
ACATCTGATTCAATTACCAA+TGG 0.619749 5.4:+15126959 MS.gene67543:CDS
AGTGATTACAGTTCTTAGAG+AGG 0.621184 5.4:+15127354 MS.gene67543:CDS
ATTGGTAATTGAATCAGATG+TGG 0.626315 5.4:-15126957 None:intergenic
AAGGCCGTTTCTCACCATCA+AGG 0.642576 5.4:+15127046 MS.gene67543:CDS
ATGATCTTGATTCAAAAGTG+AGG 0.650994 5.4:-15127317 None:intergenic
GAACTGTAATCACTGCAACA+AGG 0.656672 5.4:-15127345 None:intergenic
AGATATATGTGGCATCACAA+GGG 0.670882 5.4:+15127114 MS.gene67543:CDS
GTGCTTGGATGAGATTGAGA+AGG 0.684385 5.4:-15126878 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACATATGGAAACTAAATT+TGG + chr5.4:15127289-15127308 MS.gene67543:CDS 20.0%
!! TGAAGATTTGTATATTTCAT+TGG + chr5.4:15126994-15127013 MS.gene67543:CDS 20.0%
!!! ATTTTCTTTAATCTGTAACA+TGG - chr5.4:15127143-15127162 None:intergenic 20.0%
! ACAAATCTTCAAGAAAGAAA+AGG - chr5.4:15126985-15127004 None:intergenic 25.0%
! AGATTTGTATATTTCATTGG+AGG + chr5.4:15126997-15127016 MS.gene67543:CDS 25.0%
! AGTTAACAAAAATGAAGACA+TGG + chr5.4:15126918-15126937 MS.gene67543:CDS 25.0%
! ATGGTTTAGAGAACATATTT+AGG + chr5.4:15127629-15127648 MS.gene67543:CDS 25.0%
! GTTAACAAAAATGAAGACAT+GGG + chr5.4:15126919-15126938 MS.gene67543:CDS 25.0%
!! GCAATTGAAAGTATAGAAAA+TGG + chr5.4:15127610-15127629 MS.gene67543:CDS 25.0%
!! GTGAAACTTTTAGATATATG+TGG + chr5.4:15127103-15127122 MS.gene67543:CDS 25.0%
!!! GATCACATCTTTAAAACATA+TGG + chr5.4:15127276-15127295 MS.gene67543:CDS 25.0%
ACATATGTCATCAACACAAA+AGG + chr5.4:15127027-15127046 MS.gene67543:CDS 30.0%
ACATCTGATTCAATTACCAA+TGG + chr5.4:15126959-15126978 MS.gene67543:CDS 30.0%
ATGATCTTGATTCAAAAGTG+AGG - chr5.4:15127320-15127339 None:intergenic 30.0%
ATTAGAACCTTCACTTGAAA+GGG - chr5.4:15127557-15127576 None:intergenic 30.0%
TAACTCTTGTTCAATTCTAG+TGG - chr5.4:15126903-15126922 None:intergenic 30.0%
! ATTGGTAATTGAATCAGATG+TGG - chr5.4:15126960-15126979 None:intergenic 30.0%
! TCAATCCATTTTGTCTTTCT+TGG + chr5.4:15127402-15127421 MS.gene67543:CDS 30.0%
ACATGAAAGATTTGTGGCTT+TGG + chr5.4:15127582-15127601 MS.gene67543:CDS 35.0%
AGAGAACATATTTAGGCGTT+TGG + chr5.4:15127636-15127655 MS.gene67543:CDS 35.0%
AGATATATGTGGCATCACAA+GGG + chr5.4:15127114-15127133 MS.gene67543:CDS 35.0%
AGTGATTACAGTTCTTAGAG+AGG + chr5.4:15127354-15127373 MS.gene67543:CDS 35.0%
CAAAGTCAAAGGCAACAAAA+TGG + chr5.4:15127437-15127456 MS.gene67543:CDS 35.0%
CATTAGAACCTTCACTTGAA+AGG - chr5.4:15127558-15127577 None:intergenic 35.0%
GAAAACTATTTGAGCGAACA+TGG - chr5.4:15126859-15126878 None:intergenic 35.0%
GAAAATTGTGGAAGAGTTGT+TGG + chr5.4:15127072-15127091 MS.gene67543:CDS 35.0%
TAGATATATGTGGCATCACA+AGG + chr5.4:15127113-15127132 MS.gene67543:CDS 35.0%
TGTTGCACATGAAAGATTTG+TGG + chr5.4:15127576-15127595 MS.gene67543:CDS 35.0%
TTCAAGAAAGAAAAGGCCAT+TGG - chr5.4:15126978-15126997 None:intergenic 35.0%
! TCCATTTTGTCTTTCTTGGT+TGG + chr5.4:15127406-15127425 MS.gene67543:CDS 35.0%
! TTAAGAACCCTTTCAAGTGA+AGG + chr5.4:15127547-15127566 MS.gene67543:CDS 35.0%
!! GACAAAGTTGATGCAAAAGA+GGG + chr5.4:15127468-15127487 MS.gene67543:CDS 35.0%
!! TGACAAAGTTGATGCAAAAG+AGG + chr5.4:15127467-15127486 MS.gene67543:CDS 35.0%
ATCAGATGTGGATGTTGATG+TGG - chr5.4:15126948-15126967 None:intergenic 40.0%
ATTGTGGAAGAGTTGTTGGA+TGG + chr5.4:15127076-15127095 MS.gene67543:CDS 40.0%
CCATCAAGGTGAGAAAATTG+TGG + chr5.4:15127060-15127079 MS.gene67543:CDS 40.0%
GAACTGTAATCACTGCAACA+AGG - chr5.4:15127348-15127367 None:intergenic 40.0%
GCCAACCAAGAAAGACAAAA+TGG - chr5.4:15127410-15127429 None:intergenic 40.0%
GGTAACATGTGAAGAGAACA+TGG + chr5.4:15127489-15127508 MS.gene67543:CDS 40.0%
TGGCTCTTCATCAAAGTCAA+AGG + chr5.4:15127426-15127445 MS.gene67543:CDS 40.0%
TGTTCAATTCTAGTGGTGCT+TGG - chr5.4:15126896-15126915 None:intergenic 40.0%
! CCACAATTTTCTCACCTTGA+TGG - chr5.4:15127063-15127082 None:intergenic 40.0%
GGAAGAGTTGTTGGATGGTT+CGG + chr5.4:15127081-15127100 MS.gene67543:CDS 45.0%
GTGCTTGGATGAGATTGAGA+AGG - chr5.4:15126881-15126900 None:intergenic 45.0%
TCCGCTCTTAGAAGGAGAAA+GGG + chr5.4:15127178-15127197 MS.gene67543:CDS 45.0%
! TCCCTTTCTCCTTCTAAGAG+CGG - chr5.4:15127182-15127201 None:intergenic 45.0%
!! CTCACCTTGATGGTGAGAAA+CGG - chr5.4:15127053-15127072 None:intergenic 45.0%
AAGGCCGTTTCTCACCATCA+AGG + chr5.4:15127046-15127065 MS.gene67543:CDS 50.0%
CACTTCACTCCGCTCTTAGA+AGG + chr5.4:15127170-15127189 MS.gene67543:CDS 50.0%
CTCCGCTCTTAGAAGGAGAA+AGG + chr5.4:15127177-15127196 MS.gene67543:CDS 50.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 15126842 15127699 15126842 ID=MS.gene67543
chr5.4 mRNA 15126842 15127699 15126842 ID=MS.gene67543.t1;Parent=MS.gene67543
chr5.4 exon 15126842 15127699 15126842 ID=MS.gene67543.t1.exon1;Parent=MS.gene67543.t1
chr5.4 CDS 15126842 15127699 15126842 ID=cds.MS.gene67543.t1;Parent=MS.gene67543.t1
Gene Sequence

>MS.gene67543

ATGGCAAGCAAATACCATGTTCGCTCAAATAGTTTTCCTTCTCAATCTCATCCAAGCACCACTAGAATTGAACAAGAGTTAACAAAAATGAAGACATGGGAAGCCACATCAACATCCACATCTGATTCAATTACCAATGGCCTTTTCTTTCTTGAAGATTTGTATATTTCATTGGAGGATCTTCTACATATGTCATCAACACAAAAGGCCGTTTCTCACCATCAAGGTGAGAAAATTGTGGAAGAGTTGTTGGATGGTTCGGTGAAACTTTTAGATATATGTGGCATCACAAGGGACACCATGTTACAGATTAAAGAAAATGTTCAATCACTTCACTCCGCTCTTAGAAGGAGAAAGGGAGATTCAAGCATCGAAACAAGTGTAGTTGAATATAAATTATTCACAAAGAAAATGAAGAAGAATGTCACAAAGTTGATCACATCTTTAAAACATATGGAAACTAAATTTGGAGCATCCTCACTTTTGAATCAAGATCATCAAGACCTTGTTGCAGTGATTACAGTTCTTAGAGAGGTGATTGCAATGAACATCTCTATCTTTCAATCCATTTTGTCTTTCTTGGTTGGCTCTTCATCAAAGTCAAAGGCAACAAAATGGTTGAAAGTGACAAAGTTGATGCAAAAGAGGGTAACATGTGAAGAGAACATGGAGAATTTCAATGAATTGCAGTGTGTCGAAGCATCTTTAAGAACCCTTTCAAGTGAAGGTTCTAATGTTGCACATGAAAGATTTGTGGCTTTGGAGAATGCAATTGAAAGTATAGAAAATGGTTTAGAGAACATATTTAGGCGTTTGGTTAAAACTAGAGTCTGTCTTTTGAACATCATGACTCAATAG
Protein sequence

>MS.gene67543.t1

MASKYHVRSNSFPSQSHPSTTRIEQELTKMKTWEATSTSTSDSITNGLFFLEDLYISLEDLLHMSSTQKAVSHHQGEKIVEELLDGSVKLLDICGITRDTMLQIKENVQSLHSALRRRKGDSSIETSVVEYKLFTKKMKKNVTKLITSLKHMETKFGASSLLNQDHQDLVAVITVLREVIAMNISIFQSILSFLVGSSSKSKATKWLKVTKLMQKRVTCEENMENFNELQCVEASLRTLSSEGSNVAHERFVALENAIESIENGLENIFRRLVKTRVCLLNIMTQ