AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41036

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41036.t1 MTR_1g056910 96.505 372 13 0 1 372 19 390 0.0 737
MS.gene41036.t1 MTR_4g051515 43.915 378 203 7 1 371 19 394 4.26e-95 290
MS.gene41036.t1 MTR_7g106340 41.927 384 206 7 1 371 21 400 1.52e-89 276
MS.gene41036.t1 MTR_1g056880 39.206 403 209 8 1 372 20 417 2.66e-88 273
MS.gene41036.t1 MTR_1g056870 38.710 403 211 8 1 372 20 417 1.97e-85 266
MS.gene41036.t1 MTR_2g087350 42.971 377 199 9 1 371 19 385 3.07e-79 249
MS.gene41036.t1 MTR_1g056840 35.980 403 196 10 1 372 20 391 8.68e-73 232
MS.gene41036.t1 MTR_5g077510 32.208 385 228 12 1 368 48 416 2.15e-44 159
MS.gene41036.t1 MTR_3g065080 30.709 381 238 12 1 368 49 416 1.13e-36 138
MS.gene41036.t1 MTR_6g071340 29.639 388 242 11 1 368 18 394 4.52e-35 133
MS.gene41036.t1 MTR_5g048050 29.124 388 244 11 1 368 38 414 5.85e-34 130
MS.gene41036.t1 MTR_4g085720 29.759 373 245 11 1 368 27 387 5.63e-31 122
MS.gene41036.t1 MTR_8g092870 26.582 395 252 13 1 372 23 402 1.14e-19 90.1
MS.gene41036.t1 MTR_3g095730 23.544 395 262 12 1 372 26 403 3.13e-16 80.1
MS.gene41036.t1 MTR_5g015210 25.067 375 249 14 1 368 80 429 6.40e-16 79.3
MS.gene41036.t1 MTR_3g096370 27.479 353 222 14 1 334 23 360 3.63e-15 76.6
MS.gene41036.t1 MTR_5g083030 25.145 346 198 13 1 310 306 626 2.64e-14 74.7
MS.gene41036.t1 MTR_1g037070 45.122 82 44 1 251 332 1 81 9.55e-14 66.6
MS.gene41036.t1 MTR_4g063800 37.405 131 66 5 1 119 268 394 4.26e-13 70.9
MS.gene41036.t1 MTR_6g462610 32.298 161 95 4 103 259 7 157 1.23e-12 65.9
MS.gene41036.t1 MTR_1g017770 27.000 400 221 16 1 371 58 415 1.47e-12 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41036.t1 AT3G11840 40.291 412 198 6 1 370 23 428 2.91e-99 302
MS.gene41036.t1 AT2G35930 41.799 378 203 9 1 371 25 392 7.22e-86 266
MS.gene41036.t1 AT3G52450 36.881 404 215 10 1 371 20 416 1.81e-74 238
MS.gene41036.t1 AT3G19380 30.133 375 220 11 1 354 27 380 1.29e-38 143
MS.gene41036.t1 AT1G49780 29.474 380 246 11 1 368 27 396 3.25e-32 125
MS.gene41036.t1 AT5G37490 26.500 400 228 14 1 368 44 409 8.25e-27 110
MS.gene41036.t1 AT1G66160 26.562 384 239 13 1 368 46 402 9.88e-26 107
MS.gene41036.t1 AT3G18710 27.865 384 246 13 1 368 25 393 1.33e-22 98.6
MS.gene41036.t1 AT1G66160 24.451 364 232 13 21 368 50 386 5.66e-16 79.3
MS.gene41036.t1 AT1G24330 26.434 401 219 19 1 337 288 676 3.21e-11 65.5
MS.gene41036.t1 AT1G24330 26.434 401 219 19 1 337 288 676 3.21e-11 65.5
MS.gene41036.t1 AT1G29340 26.408 284 164 12 1 260 318 580 9.72e-11 63.9

Find 40 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAATTCTTTCGAAGAATT+CGG 0.199521 1.2:+44997630 None:intergenic
ACTAATAGAGATTGAATTAA+TGG 0.226085 1.2:-44997485 MS.gene41036:CDS
TGATTCCTTTGAGAAGCTTT+TGG 0.238517 1.2:+44998019 None:intergenic
TAAAGTGATGGAAATATTTA+AGG 0.243590 1.2:-44997176 MS.gene41036:CDS
TTTACTATGTTGTTGTCCTT+TGG 0.288354 1.2:-44997551 MS.gene41036:CDS
TTACTATGTTGTTGTCCTTT+GGG 0.311153 1.2:-44997550 MS.gene41036:CDS
TTCTGCTACAAAGATGGTTT+TGG 0.311443 1.2:-44997275 MS.gene41036:CDS
ATTTGAAAATAATCAAATAC+TGG 0.314035 1.2:-44997776 MS.gene41036:CDS
ATTCCTGTTATAGCAGTAAC+AGG 0.346346 1.2:+44998249 None:intergenic
GTTGTCCTTTGGGAAGAAAT+AGG 0.365624 1.2:-44997540 MS.gene41036:CDS
GATCCTGTTACTGCTATAAC+AGG 0.386049 1.2:-44998252 MS.gene41036:CDS
GTTGACTGAGAGATTCTTCA+AGG 0.402733 1.2:-44997353 MS.gene41036:CDS
TTGGATGAGATGTTAAAAGT+TGG 0.415505 1.2:-44997256 MS.gene41036:CDS
GGTGTTAAATCAGAATCTAA+TGG 0.418840 1.2:+44998147 None:intergenic
GCTCAAGAGTTTAATGCAGT+TGG 0.418910 1.2:-44997980 MS.gene41036:CDS
ATTGTGAAAGTTCTAAGAAA+TGG 0.433892 1.2:-44997613 MS.gene41036:CDS
ACAATTCTTTCGAAGAATTC+GGG 0.437523 1.2:+44997631 None:intergenic
CATTTGTGTTCTTGTGCAAA+TGG 0.445659 1.2:-44997415 MS.gene41036:CDS
AAACTCTTGAGCTGAACCTT+AGG 0.446427 1.2:+44997991 None:intergenic
GGGAAGAAATAGGTTAATGA+TGG 0.446476 1.2:-44997530 MS.gene41036:CDS
ATGAACATAATCATCTCTTT+CGG 0.450958 1.2:+44997901 None:intergenic
TTCGTCGTTTGATTCAATCT+TGG 0.454949 1.2:-44998113 MS.gene41036:CDS
AGAATCACAGAACTCACATT+TGG 0.479777 1.2:-44997448 MS.gene41036:CDS
GAAGGTATTGAAGAAGCTCT+TGG 0.482882 1.2:-44997847 MS.gene41036:CDS
CAAAGGAATCAAAGATCCTA+AGG 0.507179 1.2:-44998007 MS.gene41036:CDS
AGATTCTTCACTTCTTCTGT+AGG 0.513088 1.2:+44997802 None:intergenic
AAACGACGAAGTGTGTGATT+TGG 0.523610 1.2:+44998126 None:intergenic
GGAAGAGGTTGTTGTGTGAC+AGG 0.532069 1.2:+44998168 None:intergenic
TGCACACAAAATGCTTCACT+TGG 0.539364 1.2:-44998090 MS.gene41036:CDS
AATATTTAAGGCTCATTCTG+AGG 0.547702 1.2:-44997164 None:intergenic
AAATCAGAATCTAATGGAAG+AGG 0.553606 1.2:+44998153 None:intergenic
CTTCAAGGTTTCAATGACAG+TGG 0.556204 1.2:-44997338 MS.gene41036:CDS
AAATACTGGATTCTTTAACA+TGG 0.565062 1.2:-44997762 MS.gene41036:CDS
ATTAACCTATTTCTTCCCAA+AGG 0.586930 1.2:+44997535 None:intergenic
ATCGAGACAGCATTGAACAT+TGG 0.589905 1.2:-44998218 MS.gene41036:CDS
CAAGTCCAAAAGCTTCTCAA+AGG 0.606638 1.2:-44998024 MS.gene41036:CDS
AGGTTAATGATGGTTGAAGC+TGG 0.636668 1.2:-44997520 MS.gene41036:CDS
GTATTTGAAAGATAAAGTGA+TGG 0.642403 1.2:-44997188 MS.gene41036:CDS
GGTTACTGTGAAATCGCATG+CGG 0.706124 1.2:-44997713 MS.gene41036:CDS
AATGGTGTAATAACACAACA+AGG 0.719258 1.2:-44997595 MS.gene41036:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTGAAAATAATCAAATAC+TGG - chr1.2:44997647-44997666 MS.gene41036:CDS 15.0%
!! ACTAATAGAGATTGAATTAA+TGG - chr1.2:44997938-44997957 MS.gene41036:CDS 20.0%
!! ATAGTTGATTGTTACAAAAA+AGG - chr1.2:44997543-44997562 MS.gene41036:CDS 20.0%
!!! TAAAGTGATGGAAATATTTA+AGG - chr1.2:44998247-44998266 MS.gene41036:CDS 20.0%
!!! TGGTTTTTTACAATTTGTTA+AGG - chr1.2:44997596-44997615 MS.gene41036:CDS 20.0%
! AAAAAAGGCGAAATTTATGA+AGG - chr1.2:44997558-44997577 MS.gene41036:CDS 25.0%
! AAATACTGGATTCTTTAACA+TGG - chr1.2:44997661-44997680 MS.gene41036:CDS 25.0%
! ATGAACATAATCATCTCTTT+CGG + chr1.2:44997525-44997544 None:intergenic 25.0%
! GTATTTGAAAGATAAAGTGA+TGG - chr1.2:44998235-44998254 MS.gene41036:CDS 25.0%
!! AGAAAGATTTTGTTGGAAAA+TGG - chr1.2:44997495-44997514 MS.gene41036:CDS 25.0%
!! TAAATTTTCTGCTACAAAGA+TGG - chr1.2:44998142-44998161 MS.gene41036:CDS 25.0%
!!! ATTGTGAAAGTTCTAAGAAA+TGG - chr1.2:44997810-44997829 MS.gene41036:CDS 25.0%
AAATCAGAATCTAATGGAAG+AGG + chr1.2:44997273-44997292 None:intergenic 30.0%
AATGGTGTAATAACACAACA+AGG - chr1.2:44997828-44997847 MS.gene41036:CDS 30.0%
ACAATTCTTTCGAAGAATTC+GGG + chr1.2:44997795-44997814 None:intergenic 30.0%
CACAATTCTTTCGAAGAATT+CGG + chr1.2:44997796-44997815 None:intergenic 30.0%
GGTGTTAAATCAGAATCTAA+TGG + chr1.2:44997279-44997298 None:intergenic 30.0%
TTACTATGTTGTTGTCCTTT+GGG - chr1.2:44997873-44997892 MS.gene41036:CDS 30.0%
TTGGATGAGATGTTAAAAGT+TGG - chr1.2:44998167-44998186 MS.gene41036:CDS 30.0%
TTTACTATGTTGTTGTCCTT+TGG - chr1.2:44997872-44997891 MS.gene41036:CDS 30.0%
! ATTAACCTATTTCTTCCCAA+AGG + chr1.2:44997891-44997910 None:intergenic 30.0%
! GAGCAATAGAAAGATTTTGT+TGG - chr1.2:44997488-44997507 MS.gene41036:CDS 30.0%
!!! TTTCAGTTTTTGAGTCATCA+AGG - chr1.2:44998035-44998054 MS.gene41036:CDS 30.0%
AGAATCACAGAACTCACATT+TGG - chr1.2:44997975-44997994 MS.gene41036:CDS 35.0%
AGATTCTTCACTTCTTCTGT+AGG + chr1.2:44997624-44997643 None:intergenic 35.0%
AGTTTCCGAGATGAAAAACT+CGG - chr1.2:44997689-44997708 MS.gene41036:CDS 35.0%
ATTCCTGTTATAGCAGTAAC+AGG + chr1.2:44997177-44997196 None:intergenic 35.0%
CAAAGGAATCAAAGATCCTA+AGG - chr1.2:44997416-44997435 MS.gene41036:CDS 35.0%
CATTTGTGTTCTTGTGCAAA+TGG - chr1.2:44998008-44998027 MS.gene41036:CDS 35.0%
GGGAAGAAATAGGTTAATGA+TGG - chr1.2:44997893-44997912 MS.gene41036:CDS 35.0%
TTCGTCGTTTGATTCAATCT+TGG - chr1.2:44997310-44997329 MS.gene41036:CDS 35.0%
! ACTTGAATTTTTGTGAGTGG+TGG + chr1.2:44997384-44997403 None:intergenic 35.0%
! AGTAACCGAGTTTTTCATCT+CGG + chr1.2:44997697-44997716 None:intergenic 35.0%
! ATTTTTGTGAGTGGTGGTTT+TGG + chr1.2:44997378-44997397 None:intergenic 35.0%
! TGGACTTGAATTTTTGTGAG+TGG + chr1.2:44997387-44997406 None:intergenic 35.0%
! TTCTGCTACAAAGATGGTTT+TGG - chr1.2:44998148-44998167 MS.gene41036:CDS 35.0%
!! TGATTCCTTTGAGAAGCTTT+TGG + chr1.2:44997407-44997426 None:intergenic 35.0%
AAACGACGAAGTGTGTGATT+TGG + chr1.2:44997300-44997319 None:intergenic 40.0%
AAACTCTTGAGCTGAACCTT+AGG + chr1.2:44997435-44997454 None:intergenic 40.0%
AGGTTAATGATGGTTGAAGC+TGG - chr1.2:44997903-44997922 MS.gene41036:CDS 40.0%
CAAGTCCAAAAGCTTCTCAA+AGG - chr1.2:44997399-44997418 MS.gene41036:CDS 40.0%
CTTCAAGGTTTCAATGACAG+TGG - chr1.2:44998085-44998104 MS.gene41036:CDS 40.0%
GATCCTGTTACTGCTATAAC+AGG - chr1.2:44997171-44997190 MS.gene41036:CDS 40.0%
GCTCAAGAGTTTAATGCAGT+TGG - chr1.2:44997443-44997462 MS.gene41036:CDS 40.0%
GTTGACTGAGAGATTCTTCA+AGG - chr1.2:44998070-44998089 MS.gene41036:CDS 40.0%
TGCACACAAAATGCTTCACT+TGG - chr1.2:44997333-44997352 MS.gene41036:CDS 40.0%
! ATCGAGACAGCATTGAACAT+TGG - chr1.2:44997205-44997224 MS.gene41036:CDS 40.0%
! GTTGTCCTTTGGGAAGAAAT+AGG - chr1.2:44997883-44997902 MS.gene41036:CDS 40.0%
!! GAAGGTATTGAAGAAGCTCT+TGG - chr1.2:44997576-44997595 MS.gene41036:CDS 40.0%
!!! GCGATTCAATCGTTTTAGAG+AGG - chr1.2:44997763-44997782 MS.gene41036:CDS 40.0%
GGTTACTGTGAAATCGCATG+CGG - chr1.2:44997710-44997729 MS.gene41036:CDS 45.0%
!!! TGAGTGGTGGTTTTGGTGTT+GGG + chr1.2:44997371-44997390 None:intergenic 45.0%
GGAAGAGGTTGTTGTGTGAC+AGG + chr1.2:44997258-44997277 None:intergenic 50.0%
!!! GTGAGTGGTGGTTTTGGTGT+TGG + chr1.2:44997372-44997391 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 44997165 44998280 44997165 ID=MS.gene41036
chr1.2 mRNA 44997165 44998280 44997165 ID=MS.gene41036.t1;Parent=MS.gene41036
chr1.2 exon 44997165 44998280 44997165 ID=MS.gene41036.t1.exon1;Parent=MS.gene41036.t1
chr1.2 CDS 44997165 44998280 44997165 ID=cds.MS.gene41036.t1;Parent=MS.gene41036.t1
Gene Sequence

>MS.gene41036

ATGAAAGATCCTGTTACTGCTATAACAGGAATAACATATGATCGAGACAGCATTGAACATTGGTTATTCACAAACAAGAACACAACATGTCCTGTCACACAACAACCTCTTCCATTAGATTCTGATTTAACACCAAATCACACACTTCGTCGTTTGATTCAATCTTGGTGCACACAAAATGCTTCACTTGGTATTGATAGAATCCCAACACCAAAACCACCACTCACAAAAATTCAAGTCCAAAAGCTTCTCAAAGGAATCAAAGATCCTAAGGTTCAGCTCAAGAGTTTAATGCAGTTGGAATTGCTTGCTGCTGAGAAAGAGAGCAATAGAAAGATTTTGTTGGAAAATGGTGTGCCGAAAGAGATGATTATGTTCATAGTTGATTGTTACAAAAAAGGCGAAATTTATGAAGGTATTGAAGAAGCTCTTGGTTTTTTACAATTTGTTAAGGTTCCTACAGAAGAAGTGAAGAATCTTCTATTTGAAAATAATCAAATACTGGATTCTTTAACATGGATTTTAGTTTCCGAGATGAAAAACTCGGTTACTGTGAAATCGCATGCGGTTTTAGTGCTTAAAAAATTCATAAACAAATGCGATTCAATCGTTTTAGAGAGGCTAAAACCCGAATTCTTCGAAAGAATTGTGAAAGTTCTAAGAAATGGTGTAATAACACAACAAGGTTTGTCTTCTGCTTTACATATTTTACTATGTTGTTGTCCTTTGGGAAGAAATAGGTTAATGATGGTTGAAGCTGGTGCAATTCATGAACTAATAGAGATTGAATTAATGGCAATACATGAAAAGAGAATCACAGAACTCACATTTGGTATATTGTTTCATTTGTGTTCTTGTGCAAATGGAAGATTTCAGTTTTTGAGTCATCAAGGTTCAATTGCAATGTTGACTGAGAGATTCTTCAAGGTTTCAATGACAGTGGATGATAGAGCTGTTTTTATACTCTCATTGATATCTAAATTTTCTGCTACAAAGATGGTTTTGGATGAGATGTTAAAAGTTGGAACTGTTGCAAAGCTTTTTGTTTTGCTTCAAAGTGATCATGCTAAGTATTTGAAAGATAAAGTGATGGAAATATTTAAGGCTCATTCTGAG
Protein sequence

>MS.gene41036.t1

MKDPVTAITGITYDRDSIEHWLFTNKNTTCPVTQQPLPLDSDLTPNHTLRRLIQSWCTQNASLGIDRIPTPKPPLTKIQVQKLLKGIKDPKVQLKSLMQLELLAAEKESNRKILLENGVPKEMIMFIVDCYKKGEIYEGIEEALGFLQFVKVPTEEVKNLLFENNQILDSLTWILVSEMKNSVTVKSHAVLVLKKFINKCDSIVLERLKPEFFERIVKVLRNGVITQQGLSSALHILLCCCPLGRNRLMMVEAGAIHELIEIELMAIHEKRITELTFGILFHLCSCANGRFQFLSHQGSIAMLTERFFKVSMTVDDRAVFILSLISKFSATKMVLDEMLKVGTVAKLFVLLQSDHAKYLKDKVMEIFKAHSE