AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41035

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41035.t1 MTR_1g056910 90.591 372 11 1 1 348 19 390 0.0 678
MS.gene41035.t1 MTR_1g056880 38.060 402 191 8 1 348 20 417 2.90e-81 254
MS.gene41035.t1 MTR_4g051515 40.476 378 192 7 1 347 19 394 4.40e-80 250
MS.gene41035.t1 MTR_1g056870 37.562 402 193 8 1 348 20 417 2.05e-78 247
MS.gene41035.t1 MTR_7g106340 39.426 383 193 8 1 347 21 400 4.04e-78 246
MS.gene41035.t1 MTR_2g087350 39.894 376 188 9 1 347 19 385 2.57e-72 230
MS.gene41035.t1 MTR_1g056840 35.884 379 205 8 1 348 20 391 5.50e-69 222
MS.gene41035.t1 MTR_5g077510 30.809 383 212 13 1 344 48 416 3.60e-42 152
MS.gene41035.t1 MTR_3g065080 29.365 378 223 11 1 344 49 416 3.18e-35 133
MS.gene41035.t1 MTR_6g071340 29.016 386 223 12 1 344 18 394 6.45e-32 124
MS.gene41035.t1 MTR_5g048050 28.497 386 225 12 1 344 38 414 8.50e-31 121
MS.gene41035.t1 MTR_4g085720 29.867 375 218 15 1 344 27 387 1.75e-25 106
MS.gene41035.t1 MTR_8g092870 25.641 390 238 15 1 348 23 402 1.89e-16 80.5
MS.gene41035.t1 MTR_3g095730 23.896 385 249 13 1 348 26 403 4.82e-16 79.0
MS.gene41035.t1 MTR_5g015210 25.401 374 231 14 1 347 80 432 7.35e-14 72.8
MS.gene41035.t1 MTR_4g063800 37.405 131 66 5 1 119 268 394 2.56e-13 71.2
MS.gene41035.t1 MTR_1g037070 44.444 81 44 1 228 308 2 81 2.93e-13 65.1
MS.gene41035.t1 MTR_7g078330 35.484 124 71 5 1 118 287 407 1.45e-12 68.9
MS.gene41035.t1 MTR_3g096370 39.167 120 55 4 1 112 23 132 2.76e-12 67.8
MS.gene41035.t1 MTR_7g059405 34.783 138 78 5 1 128 277 412 2.42e-11 65.5
MS.gene41035.t1 MTR_1g017770 40.164 122 60 6 1 118 58 170 3.17e-11 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41035.t1 AT3G11840 36.893 412 188 8 1 346 23 428 2.86e-85 265
MS.gene41035.t1 AT2G35930 38.727 377 192 10 1 347 25 392 4.68e-73 232
MS.gene41035.t1 AT3G52450 34.653 404 200 11 1 347 20 416 1.21e-62 206
MS.gene41035.t1 AT3G19380 30.769 364 208 12 1 330 27 380 2.41e-32 125
MS.gene41035.t1 AT5G37490 26.131 398 208 15 1 344 44 409 8.55e-28 113
MS.gene41035.t1 AT1G66160 27.688 372 226 10 1 344 46 402 9.78e-28 112
MS.gene41035.t1 AT1G49780 31.701 388 203 15 1 344 27 396 2.36e-26 108
MS.gene41035.t1 AT3G18710 28.084 381 225 14 1 344 25 393 1.08e-20 92.8
MS.gene41035.t1 AT1G66160 25.568 352 219 10 21 344 50 386 8.05e-18 84.3

Find 34 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:+44954167 None:intergenic
ACTAATAGAGATTGAATTAA+TGG 0.226085 1.2:-44954022 MS.gene41035:CDS
TGATTCCTTTGAGAAGCTTT+TGG 0.238517 1.2:+44954556 None:intergenic
TAAAGTGATGGAAATATTTA+AGG 0.243590 1.2:-44953713 MS.gene41035:CDS
TTCTGCTACAAAGATGGTTT+TGG 0.311443 1.2:-44953812 MS.gene41035:CDS
ATTTGAAAATAATCAAATAC+TGG 0.314035 1.2:-44954313 MS.gene41035:CDS
ATTCCTGTTATAGCAGTAAC+AGG 0.346346 1.2:+44954786 None:intergenic
GATCCTGTTACTGCTATAAC+AGG 0.386049 1.2:-44954789 MS.gene41035:CDS
GTTGACTGAGAGATTCTTCA+AGG 0.402733 1.2:-44953890 MS.gene41035:CDS
TTGGATGAGATGTTAAAAGT+TGG 0.415505 1.2:-44953793 MS.gene41035:CDS
GGTGTTAAATCAGAATCTAA+TGG 0.418840 1.2:+44954684 None:intergenic
GCTCAAGAGTTTAATGCAGT+TGG 0.418910 1.2:-44954517 MS.gene41035:CDS
ATTGTGAAAGTTCTAAGAAA+TGG 0.433892 1.2:-44954150 MS.gene41035:CDS
ACAATTCTTTCGAAGAATTC+GGG 0.437523 1.2:+44954168 None:intergenic
CATTTGTGTTCTTGTGCAAA+TGG 0.445659 1.2:-44953952 MS.gene41035:CDS
AAACTCTTGAGCTGAACCTT+AGG 0.446427 1.2:+44954528 None:intergenic
ATGAACATAATCATCTCTTT+CGG 0.450958 1.2:+44954438 None:intergenic
TTCGTCGTTTGATTCAATCT+TGG 0.454949 1.2:-44954650 MS.gene41035:CDS
AGAATCACAGAACTCACATT+TGG 0.479777 1.2:-44953985 MS.gene41035:CDS
GAAGGTATTGAAGAAGCTCT+TGG 0.482882 1.2:-44954384 MS.gene41035:CDS
CAAAGGAATCAAAGATCCTA+AGG 0.507179 1.2:-44954544 MS.gene41035:CDS
AGATTCTTCACTTCTTCTGT+AGG 0.513088 1.2:+44954339 None:intergenic
AAACGACGAAGTGTGTGATT+TGG 0.523610 1.2:+44954663 None:intergenic
GGAAGAGGTTGTTGTGTGAC+AGG 0.532069 1.2:+44954705 None:intergenic
TGCACACAAAATGCTTCACT+TGG 0.539364 1.2:-44954627 MS.gene41035:CDS
AATATTTAAGGCTCATTCTG+AGG 0.547702 1.2:-44953701 None:intergenic
AAATCAGAATCTAATGGAAG+AGG 0.553606 1.2:+44954690 None:intergenic
CTTCAAGGTTTCAATGACAG+TGG 0.556204 1.2:-44953875 MS.gene41035:CDS
AAATACTGGATTCTTTAACA+TGG 0.565062 1.2:-44954299 MS.gene41035:CDS
ATCGAGACAGCATTGAACAT+TGG 0.589905 1.2:-44954755 MS.gene41035:CDS
CAAGTCCAAAAGCTTCTCAA+AGG 0.606638 1.2:-44954561 MS.gene41035:CDS
GTATTTGAAAGATAAAGTGA+TGG 0.642403 1.2:-44953725 MS.gene41035:CDS
GGTTACTGTGAAATCGCATG+CGG 0.706124 1.2:-44954250 MS.gene41035:CDS
AATGGTGTAATAACACAACA+AGG 0.719258 1.2:-44954132 MS.gene41035:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTGAAAATAATCAAATAC+TGG - chr1.2:44954184-44954203 MS.gene41035:CDS 15.0%
!! ACTAATAGAGATTGAATTAA+TGG - chr1.2:44954475-44954494 MS.gene41035:CDS 20.0%
!! ATAGTTGATTGTTACAAAAA+AGG - chr1.2:44954080-44954099 MS.gene41035:intron 20.0%
!!! TAAAGTGATGGAAATATTTA+AGG - chr1.2:44954784-44954803 MS.gene41035:CDS 20.0%
!!! TGGTTTTTTACAATTTGTTA+AGG - chr1.2:44954133-44954152 MS.gene41035:CDS 20.0%
! AAAAAAGGCGAAATTTATGA+AGG - chr1.2:44954095-44954114 MS.gene41035:intron 25.0%
! AAATACTGGATTCTTTAACA+TGG - chr1.2:44954198-44954217 MS.gene41035:CDS 25.0%
! ATGAACATAATCATCTCTTT+CGG + chr1.2:44954062-44954081 None:intergenic 25.0%
! GTATTTGAAAGATAAAGTGA+TGG - chr1.2:44954772-44954791 MS.gene41035:CDS 25.0%
!! AGAAAGATTTTGTTGGAAAA+TGG - chr1.2:44954032-44954051 MS.gene41035:CDS 25.0%
!! TAAATTTTCTGCTACAAAGA+TGG - chr1.2:44954679-44954698 MS.gene41035:CDS 25.0%
!!! ATTGTGAAAGTTCTAAGAAA+TGG - chr1.2:44954347-44954366 MS.gene41035:CDS 25.0%
AAATCAGAATCTAATGGAAG+AGG + chr1.2:44953810-44953829 None:intergenic 30.0%
AATGGTGTAATAACACAACA+AGG - chr1.2:44954365-44954384 MS.gene41035:CDS 30.0%
ACAATTCTTTCGAAGAATTC+GGG + chr1.2:44954332-44954351 None:intergenic 30.0%
CACAATTCTTTCGAAGAATT+CGG + chr1.2:44954333-44954352 None:intergenic 30.0%
GGTGTTAAATCAGAATCTAA+TGG + chr1.2:44953816-44953835 None:intergenic 30.0%
TTACTATGTTGTTGTCCTTT+GGG - chr1.2:44954410-44954429 MS.gene41035:CDS 30.0%
TTGGATGAGATGTTAAAAGT+TGG - chr1.2:44954704-44954723 MS.gene41035:CDS 30.0%
TTTACTATGTTGTTGTCCTT+TGG - chr1.2:44954409-44954428 MS.gene41035:CDS 30.0%
! ATTAACCTATTTCTTCCCAA+AGG + chr1.2:44954428-44954447 None:intergenic 30.0%
! GAGCAATAGAAAGATTTTGT+TGG - chr1.2:44954025-44954044 MS.gene41035:CDS 30.0%
!!! TTTCAGTTTTTGAGTCATCA+AGG - chr1.2:44954572-44954591 MS.gene41035:CDS 30.0%
AGAATCACAGAACTCACATT+TGG - chr1.2:44954512-44954531 MS.gene41035:CDS 35.0%
AGATTCTTCACTTCTTCTGT+AGG + chr1.2:44954161-44954180 None:intergenic 35.0%
AGTTTCCGAGATGAAAAACT+CGG - chr1.2:44954226-44954245 MS.gene41035:CDS 35.0%
ATTCCTGTTATAGCAGTAAC+AGG + chr1.2:44953714-44953733 None:intergenic 35.0%
CAAAGGAATCAAAGATCCTA+AGG - chr1.2:44953953-44953972 MS.gene41035:CDS 35.0%
CATTTGTGTTCTTGTGCAAA+TGG - chr1.2:44954545-44954564 MS.gene41035:CDS 35.0%
GGGAAGAAATAGGTTAATGA+TGG - chr1.2:44954430-44954449 MS.gene41035:CDS 35.0%
TTCGTCGTTTGATTCAATCT+TGG - chr1.2:44953847-44953866 MS.gene41035:CDS 35.0%
! ACTTGAATTTTTGTGAGTGG+TGG + chr1.2:44953921-44953940 None:intergenic 35.0%
! AGTAACCGAGTTTTTCATCT+CGG + chr1.2:44954234-44954253 None:intergenic 35.0%
! ATTTTTGTGAGTGGTGGTTT+TGG + chr1.2:44953915-44953934 None:intergenic 35.0%
! TGGACTTGAATTTTTGTGAG+TGG + chr1.2:44953924-44953943 None:intergenic 35.0%
! TTCTGCTACAAAGATGGTTT+TGG - chr1.2:44954685-44954704 MS.gene41035:CDS 35.0%
!! TGATTCCTTTGAGAAGCTTT+TGG + chr1.2:44953944-44953963 None:intergenic 35.0%
AAACGACGAAGTGTGTGATT+TGG + chr1.2:44953837-44953856 None:intergenic 40.0%
AAACTCTTGAGCTGAACCTT+AGG + chr1.2:44953972-44953991 None:intergenic 40.0%
AGGTTAATGATGGTTGAAGC+TGG - chr1.2:44954440-44954459 MS.gene41035:CDS 40.0%
CAAGTCCAAAAGCTTCTCAA+AGG - chr1.2:44953936-44953955 MS.gene41035:CDS 40.0%
CTTCAAGGTTTCAATGACAG+TGG - chr1.2:44954622-44954641 MS.gene41035:CDS 40.0%
GATCCTGTTACTGCTATAAC+AGG - chr1.2:44953708-44953727 MS.gene41035:CDS 40.0%
GCTCAAGAGTTTAATGCAGT+TGG - chr1.2:44953980-44953999 MS.gene41035:CDS 40.0%
GTTGACTGAGAGATTCTTCA+AGG - chr1.2:44954607-44954626 MS.gene41035:CDS 40.0%
TGCACACAAAATGCTTCACT+TGG - chr1.2:44953870-44953889 MS.gene41035:CDS 40.0%
! ATCGAGACAGCATTGAACAT+TGG - chr1.2:44953742-44953761 MS.gene41035:CDS 40.0%
! GTTGTCCTTTGGGAAGAAAT+AGG - chr1.2:44954420-44954439 MS.gene41035:CDS 40.0%
!! GAAGGTATTGAAGAAGCTCT+TGG - chr1.2:44954113-44954132 MS.gene41035:intron 40.0%
!!! GCGATTCAATCGTTTTAGAG+AGG - chr1.2:44954300-44954319 MS.gene41035:CDS 40.0%
GGTTACTGTGAAATCGCATG+CGG - chr1.2:44954247-44954266 MS.gene41035:CDS 45.0%
!!! TGAGTGGTGGTTTTGGTGTT+GGG + chr1.2:44953908-44953927 None:intergenic 45.0%
GGAAGAGGTTGTTGTGTGAC+AGG + chr1.2:44953795-44953814 None:intergenic 50.0%
!!! GTGAGTGGTGGTTTTGGTGT+TGG + chr1.2:44953909-44953928 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 44953702 44954817 44953702 ID=MS.gene41035
chr1.2 mRNA 44953702 44954817 44953702 ID=MS.gene41035.t1;Parent=MS.gene41035
chr1.2 exon 44954133 44954817 44954133 ID=MS.gene41035.t1.exon1;Parent=MS.gene41035.t1
chr1.2 CDS 44954133 44954817 44954133 ID=cds.MS.gene41035.t1;Parent=MS.gene41035.t1
chr1.2 exon 44953702 44954060 44953702 ID=MS.gene41035.t1.exon2;Parent=MS.gene41035.t1
chr1.2 CDS 44953702 44954060 44953702 ID=cds.MS.gene41035.t1;Parent=MS.gene41035.t1
Gene Sequence

>MS.gene41035

ATGAAAGATCCTGTTACTGCTATAACAGGAATAACATATGATCGAGACAGCATTGAACATTGGTTATTCACAAACAAGAACACAACATGTCCTGTCACACAACAACCTCTTCCATTAGATTCTGATTTAACACCAAATCACACACTTCGTCGTTTGATTCAATCTTGGTGCACACAAAATGCTTCACTTGGTATTGATAGAATCCCAACACCAAAACCACCACTCACAAAAATTCAAGTCCAAAAGCTTCTCAAAGGAATCAAAGATCCTAAGGTTCAGCTCAAGAGTTTAATGCAGTTGGAATTGCTTGCTGCTGAGAAAGAGAGCAATAGAAAGATTTTGTTGGAAAATGGTGTGCCGAAAGAGATGATTATGTTCATAGTTGATTGTTACAAAAAAGGCGAAATTTATGAAGGTATTGAAGAAGCTCTTGGTTTTTTACAATTTGTTAAGGTTCCTACAGAAGAAGTGAAGAATCTTCTATTTGAAAATAATCAAATACTGGATTCTTTAACATGGATTTTAGTTTCCGAGATGAAAAACTCGGTTACTGTGAAATCGCATGCGGTTTTAGTGCTTAAAAAATTCATAAACAAATGCGATTCAATCGTTTTAGAGAGGCTAAAACCCGAATTCTTCGAAAGAATTGTGAAAGTTCTAAGAAATGGTGTAATAACACAACAAGGTTTGTCTTCTGCTTTACATATTTTACTATGTTGTTGTCCTTTGGGAAGAAATAGGTTAATGATGGTTGAAGCTGGTGCAATTCATGAACTAATAGAGATTGAATTAATGGCAATACATGAAAAGAGAATCACAGAACTCACATTTGGTATATTGTTTCATTTGTGTTCTTGTGCAAATGGAAGATTTCAGTTTTTGAGTCATCAAGGTTCAATTGCAATGTTGACTGAGAGATTCTTCAAGGTTTCAATGACAGTGGATGATAGAGCTGTTTTTATACTCTCATTGATATCTAAATTTTCTGCTACAAAGATGGTTTTGGATGAGATGTTAAAAGTTGGAACTGTTGCAAAGCTTTTTGTTTTGCTTCAAAGTGATCATGCTAAGTATTTGAAAGATAAAGTGATGGAAATATTTAAGGCTCATTCTGAG
Protein sequence

>MS.gene41035.t1

MKDPVTAITGITYDRDSIEHWLFTNKNTTCPVTQQPLPLDSDLTPNHTLRRLIQSWCTQNASLGIDRIPTPKPPLTKIQVQKLLKGIKDPKVQLKSLMQLELLAAEKESNRKILLENGVPKEMIMFIVDCYKKGEIYEGIEEALGFLQFVKVPTEEVKNLLFENNQILDSLTWILVSEMKNSVTVKSHAVLVLKKFINKCDSIVLERLKPEFFERIVKVLRNGVITQQAGAIHELIEIELMAIHEKRITELTFGILFHLCSCANGRFQFLSHQGSIAMLTERFFKVSMTVDDRAVFILSLISKFSATKMVLDEMLKVGTVAKLFVLLQSDHAKYLKDKVMEIFKAHSE