AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene026430

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026430.t1 MTR_1g035640 50.388 129 64 0 2 130 163 291 5.67e-36 129
MS.gene026430.t1 MTR_1g035570 40.909 154 87 2 1 152 167 318 5.99e-33 120
MS.gene026430.t1 MTR_1g035620 45.198 177 69 6 1 152 160 333 1.07e-32 119
MS.gene026430.t1 MTR_6g061070 46.324 136 66 3 3 131 199 334 2.47e-30 114
MS.gene026430.t1 MTR_1g050845 44.444 162 66 4 15 152 159 320 6.73e-30 114
MS.gene026430.t1 MTR_1g035490 44.000 125 62 1 1 125 86 202 1.62e-28 107
MS.gene026430.t1 MTR_5g044670 40.179 112 64 2 22 132 207 316 1.43e-20 86.3
MS.gene026430.t1 MTR_8g103940 41.176 119 60 5 10 125 226 337 6.06e-15 71.2
MS.gene026430.t1 MTR_8g103940 32.787 122 74 3 5 120 377 496 3.12e-11 60.5
MS.gene026430.t1 MTR_1g035540 48.485 66 32 1 85 150 32 95 2.86e-13 63.2
MS.gene026430.t1 MTR_1g108780 36.752 117 64 5 10 123 185 294 5.47e-13 65.5
MS.gene026430.t1 MTR_1g108780 29.839 124 80 2 4 121 338 460 3.34e-11 60.5
MS.gene026430.t1 MTR_1g035460 29.412 102 66 1 22 123 196 291 9.26e-12 62.0
MS.gene026430.t1 MTR_1g034240 26.144 153 97 4 2 141 269 418 1.34e-11 61.6
MS.gene026430.t1 MTR_3g098790 32.039 103 65 3 22 119 197 299 2.24e-11 60.8
MS.gene026430.t1 MTR_4g068320 29.412 102 70 1 32 133 303 402 4.42e-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

Find 25 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAAGGGATTGCAAGCATT+AGG 0.348097 1.1:-18706434 MS.gene026430:CDS
CAAAGGGATTGCAAGCATTA+GGG 0.352259 1.1:-18706433 MS.gene026430:CDS
AAAACTTGGATTCTTATCAT+TGG 0.358112 1.1:+18706612 None:intergenic
TATTCTCTTGAAAACTTACT+TGG 0.379463 1.1:+18706468 None:intergenic
GTCAATTTAAGTTCAAAACT+TGG 0.433190 1.1:+18706598 None:intergenic
TGCGTAATAGTTAATCATAC+CGG 0.440953 1.1:+18706022 None:intergenic
GGCTTGATTCCTCTCTAGCT+CGG 0.457584 1.1:+18706238 None:intergenic
AATACTTGAACGAGTTCAAA+GGG 0.491876 1.1:-18706449 MS.gene026430:CDS
CTTTGAGAATTCCTTGTACC+CGG 0.517220 1.1:-18706041 MS.gene026430:CDS
AGTTAATCATACCGGGTACA+AGG 0.518064 1.1:+18706030 None:intergenic
TTTAGAAGTTTCTAATGTGA+GGG 0.522348 1.1:-18706083 MS.gene026430:CDS
GTTCTATTGTGAATGGTGGT+TGG 0.525249 1.1:-18706356 MS.gene026430:CDS
CAAAGGAGGCATGACTAAGA+AGG 0.530395 1.1:-18706674 None:intergenic
GCTTGATTCCTCTCTAGCTC+GGG 0.531379 1.1:+18706239 None:intergenic
GGGTTGATGAAGATAGAACT+TGG 0.534209 1.1:-18706413 MS.gene026430:CDS
TTCTATTTCCCGAGCTAGAG+AGG 0.537691 1.1:-18706247 MS.gene026430:CDS
TGATGAAGATAGAACTTGGA+AGG 0.543162 1.1:-18706409 MS.gene026430:CDS
ATAGAAATATTAAAAGAAAG+AGG 0.543614 1.1:+18706264 None:intergenic
ATTTAGAAGTTTCTAATGTG+AGG 0.550511 1.1:-18706084 MS.gene026430:CDS
GAATACTTGAACGAGTTCAA+AGG 0.559537 1.1:-18706450 MS.gene026430:CDS
AACAGAAGTTCTATTGTGAA+TGG 0.573160 1.1:-18706363 MS.gene026430:CDS
GCGTAATAGTTAATCATACC+GGG 0.602108 1.1:+18706023 None:intergenic
TGGTTGGAATTTATTTACCA+AGG 0.603797 1.1:-18706340 MS.gene026430:CDS
AGAAGTTCTATTGTGAATGG+TGG 0.647616 1.1:-18706360 MS.gene026430:CDS
AAGGAAAATAACTTGCAAGT+CGG 0.656533 1.1:-18706321 MS.gene026430:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGAAATATTAAAAGAAAG+AGG + chr1.1:18706439-18706458 None:intergenic 15.0%
!!! TTTGAAAATGTCTATTATTT+TGG - chr1.1:18706164-18706183 MS.gene026430:intron 15.0%
!! TGTTTGTTTATTAAAGTTTG+TGG - chr1.1:18706522-18706541 MS.gene026430:intron 20.0%
!!! AACTTACAAATAATTTTCCT+TGG + chr1.1:18706140-18706159 None:intergenic 20.0%
!!! ACTTACAAATAATTTTCCTT+GGG + chr1.1:18706139-18706158 None:intergenic 20.0%
!!! TATTAAAGTTTGTGGTTTTT+TGG - chr1.1:18706530-18706549 MS.gene026430:intron 20.0%
! AAAACTTGGATTCTTATCAT+TGG + chr1.1:18706091-18706110 None:intergenic 25.0%
! AAACTTCTAAATCTGTAGAA+GGG + chr1.1:18706608-18706627 None:intergenic 25.0%
! ATTTAGAAGTTTCTAATGTG+AGG - chr1.1:18706616-18706635 MS.gene026430:CDS 25.0%
! TATTCTCTTGAAAACTTACT+TGG + chr1.1:18706235-18706254 None:intergenic 25.0%
! TTTAGAAGTTTCTAATGTGA+GGG - chr1.1:18706617-18706636 MS.gene026430:CDS 25.0%
!! GTCAATTTAAGTTCAAAACT+TGG + chr1.1:18706105-18706124 None:intergenic 25.0%
!!! AAGTAACCTTGCAATTTTTT+AGG + chr1.1:18706487-18706506 None:intergenic 25.0%
!!! AGTAACCTTGCAATTTTTTA+GGG + chr1.1:18706486-18706505 None:intergenic 25.0%
AACAGAAGTTCTATTGTGAA+TGG - chr1.1:18706337-18706356 MS.gene026430:CDS 30.0%
AATACTTGAACGAGTTCAAA+GGG - chr1.1:18706251-18706270 MS.gene026430:CDS 30.0%
GAAACTTCTAAATCTGTAGA+AGG + chr1.1:18706609-18706628 None:intergenic 30.0%
GTATTCTCTGTTTCAATTCA+TGG + chr1.1:18706213-18706232 None:intergenic 30.0%
TGGTTGGAATTTATTTACCA+AGG - chr1.1:18706360-18706379 MS.gene026430:CDS 30.0%
! AAGGAAAATAACTTGCAAGT+CGG - chr1.1:18706379-18706398 MS.gene026430:CDS 30.0%
AGAAGTTCTATTGTGAATGG+TGG - chr1.1:18706340-18706359 MS.gene026430:CDS 35.0%
GAATACTTGAACGAGTTCAA+AGG - chr1.1:18706250-18706269 MS.gene026430:CDS 35.0%
TCAAGCCCTAAAAAATTGCA+AGG - chr1.1:18706478-18706497 MS.gene026430:intron 35.0%
TGATGAAGATAGAACTTGGA+AGG - chr1.1:18706291-18706310 MS.gene026430:CDS 35.0%
! TTGACACAATTTTATGCCCA+AGG - chr1.1:18706120-18706139 MS.gene026430:intron 35.0%
!! GACTTGCAAGTTATTTTCCT+TGG + chr1.1:18706380-18706399 None:intergenic 35.0%
CAAAGGGATTGCAAGCATTA+GGG - chr1.1:18706267-18706286 MS.gene026430:CDS 40.0%
GTTCTATTGTGAATGGTGGT+TGG - chr1.1:18706344-18706363 MS.gene026430:CDS 40.0%
TCAAAGGGATTGCAAGCATT+AGG - chr1.1:18706266-18706285 MS.gene026430:CDS 40.0%
! CTTTGAGAATTCCTTGTACC+CGG - chr1.1:18706659-18706678 MS.gene026430:CDS 40.0%
!! GGGTTGATGAAGATAGAACT+TGG - chr1.1:18706287-18706306 MS.gene026430:CDS 40.0%
TTCTATTTCCCGAGCTAGAG+AGG - chr1.1:18706453-18706472 MS.gene026430:CDS 45.0%
GGCTTGATTCCTCTCTAGCT+CGG + chr1.1:18706465-18706484 None:intergenic 50.0%
! GCTTGATTCCTCTCTAGCTC+GGG + chr1.1:18706464-18706483 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 18706036 18706686 18706036 ID=MS.gene026430
chr1.1 mRNA 18706036 18706686 18706036 ID=MS.gene026430.t1;Parent=MS.gene026430
chr1.1 exon 18706570 18706686 18706570 ID=MS.gene026430.t1.exon1;Parent=MS.gene026430.t1
chr1.1 CDS 18706570 18706686 18706570 ID=cds.MS.gene026430.t1;Parent=MS.gene026430.t1
chr1.1 exon 18706223 18706496 18706223 ID=MS.gene026430.t1.exon2;Parent=MS.gene026430.t1
chr1.1 CDS 18706223 18706496 18706223 ID=cds.MS.gene026430.t1;Parent=MS.gene026430.t1
chr1.1 exon 18706036 18706106 18706036 ID=MS.gene026430.t1.exon3;Parent=MS.gene026430.t1
chr1.1 CDS 18706036 18706106 18706036 ID=cds.MS.gene026430.t1;Parent=MS.gene026430.t1
Gene Sequence

>MS.gene026430

ATGACTAAGAAGGCTAAGAAATGTTCAATAACTGAAGCAAATAATAAGAAATCCAATGATAAGAATCCAAGTTTTGAACTTAAATTGACACAATTTTATGCCCAAGGAAAATTATTTGTAAGTTTACTTTTGAAAATGTCTATTATTTTGGCTTTAATTAATATCTCTAATAAACCATGAATTGAAACAGAGAATACCAAGTAAGTTTTCAAGAGAATACTTGAACGAGTTCAAAGGGATTGCAAGCATTAGGGTTGATGAAGATAGAACTTGGAAGGTGAATGTGAAGTTTGATTATGCAAACAGAAGTTCTATTGTGAATGGTGGTTGGAATTTATTTACCAAGGAAAATAACTTGCAAGTCGGCGATGTGTGTAAATTTGAGATGACTCGATCTGAGCCTCTTTCTTTTAATATTTCTATTTCCCGAGCTAGAGAGGAATCAAGCCCTAAAAAATTGCAAGGTTACTTTCTTTCTTCATTATTTGTTTGTTTATTAAAGTTTGTGGTTTTTTGGTCATTGATGTTTGATTAACATTTATCAATCAGTTTTTCACTAACTTCTTAATCCCTTCTACAGATTTAGAAGTTTCTAATGTGAGGGAACATAACACATTTGAGCTCTTTGAGAATTCCTTGTACCCGGTATGA
Protein sequence

>MS.gene026430.t1

MTKKAKKCSITEANNKKSNDKNPSFELKLTQFYAQGKLFRIPSKFSREYLNEFKGIASIRVDEDRTWKVNVKFDYANRSSIVNGGWNLFTKENNLQVGDVCKFEMTRSEPLSFNISISRAREESSPKKLQDLEVSNVREHNTFELFENSLYPV