AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene061653

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene061653.t1 MTR_1g035640 50.388 129 64 0 2 130 163 291 5.67e-36 129
MS.gene061653.t1 MTR_1g035570 40.909 154 87 2 1 152 167 318 5.99e-33 120
MS.gene061653.t1 MTR_1g035620 45.198 177 69 6 1 152 160 333 1.07e-32 119
MS.gene061653.t1 MTR_6g061070 46.324 136 66 3 3 131 199 334 2.47e-30 114
MS.gene061653.t1 MTR_1g050845 44.444 162 66 4 15 152 159 320 6.73e-30 114
MS.gene061653.t1 MTR_1g035490 44.000 125 62 1 1 125 86 202 1.62e-28 107
MS.gene061653.t1 MTR_5g044670 40.179 112 64 2 22 132 207 316 1.43e-20 86.3
MS.gene061653.t1 MTR_8g103940 41.176 119 60 5 10 125 226 337 6.06e-15 71.2
MS.gene061653.t1 MTR_8g103940 32.787 122 74 3 5 120 377 496 3.12e-11 60.5
MS.gene061653.t1 MTR_1g035540 48.485 66 32 1 85 150 32 95 2.86e-13 63.2
MS.gene061653.t1 MTR_1g108780 36.752 117 64 5 10 123 185 294 5.47e-13 65.5
MS.gene061653.t1 MTR_1g108780 29.839 124 80 2 4 121 338 460 3.34e-11 60.5
MS.gene061653.t1 MTR_1g035460 29.412 102 66 1 22 123 196 291 9.26e-12 62.0
MS.gene061653.t1 MTR_1g034240 26.144 153 97 4 2 141 269 418 1.34e-11 61.6
MS.gene061653.t1 MTR_3g098790 32.039 103 65 3 22 119 197 299 2.24e-11 60.8
MS.gene061653.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 1.3:-18675252 MS.gene061653:CDS
CAAAGGGATTGCAAGCATTA+GGG 0.352259 1.3:-18675251 MS.gene061653:CDS
AAAACTTGGATTCTTATCAT+TGG 0.358112 1.3:+18675430 None:intergenic
TATTCTCTTGAAAACTTACT+TGG 0.379463 1.3:+18675286 None:intergenic
GTCAATTTAAGTTCAAAACT+TGG 0.433190 1.3:+18675416 None:intergenic
TGCGTAATAGTTAATCATAC+CGG 0.440953 1.3:+18674840 None:intergenic
GGCTTGATTCCTCTCTAGCT+CGG 0.457584 1.3:+18675056 None:intergenic
AATACTTGAACGAGTTCAAA+GGG 0.491876 1.3:-18675267 MS.gene061653:CDS
CAAAGGAGGCATGACTAAGA+AGG 0.500047 1.3:-18675492 None:intergenic
CTTTGAGAATTCCTTGTACC+CGG 0.517220 1.3:-18674859 MS.gene061653:CDS
AGTTAATCATACCGGGTACA+AGG 0.518064 1.3:+18674848 None:intergenic
TTTAGAAGTTTCTAATGTGA+GGG 0.522348 1.3:-18674901 MS.gene061653:CDS
GTTCTATTGTGAATGGTGGT+TGG 0.525249 1.3:-18675174 MS.gene061653:CDS
GCTTGATTCCTCTCTAGCTC+GGG 0.531379 1.3:+18675057 None:intergenic
GGGTTGATGAAGATAGAACT+TGG 0.534209 1.3:-18675231 MS.gene061653:CDS
TTCTATTTCCCGAGCTAGAG+AGG 0.537691 1.3:-18675065 MS.gene061653:CDS
TGATGAAGATAGAACTTGGA+AGG 0.543162 1.3:-18675227 MS.gene061653:CDS
ATAGAAATATTAAAAGAAAG+AGG 0.543614 1.3:+18675082 None:intergenic
ATTTAGAAGTTTCTAATGTG+AGG 0.550511 1.3:-18674902 MS.gene061653:CDS
GAATACTTGAACGAGTTCAA+AGG 0.559537 1.3:-18675268 MS.gene061653:CDS
AACAGAAGTTCTATTGTGAA+TGG 0.573160 1.3:-18675181 MS.gene061653:CDS
GCGTAATAGTTAATCATACC+GGG 0.602108 1.3:+18674841 None:intergenic
TGGTTGGAATTTATTTACCA+AGG 0.603797 1.3:-18675158 MS.gene061653:CDS
AGAAGTTCTATTGTGAATGG+TGG 0.647616 1.3:-18675178 MS.gene061653:CDS
AAGGAAAATAACTTGCAAGT+CGG 0.656533 1.3:-18675139 MS.gene061653:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGAAATATTAAAAGAAAG+AGG + chr1.3:18675257-18675276 None:intergenic 15.0%
!!! TTTGAAAATGTCTATTATTT+TGG - chr1.3:18674982-18675001 MS.gene061653:intron 15.0%
!! TGTTTGTTTATTAAAGTTTG+TGG - chr1.3:18675340-18675359 MS.gene061653:intron 20.0%
!!! AACTTACAAATAATTTTCCT+TGG + chr1.3:18674958-18674977 None:intergenic 20.0%
!!! ACTTACAAATAATTTTCCTT+GGG + chr1.3:18674957-18674976 None:intergenic 20.0%
!!! TATTAAAGTTTGTGGTTTTT+TGG - chr1.3:18675348-18675367 MS.gene061653:intron 20.0%
! AAAACTTGGATTCTTATCAT+TGG + chr1.3:18674909-18674928 None:intergenic 25.0%
! AAACTTCTAAATCTGTAGAA+GGG + chr1.3:18675426-18675445 None:intergenic 25.0%
! ATTTAGAAGTTTCTAATGTG+AGG - chr1.3:18675434-18675453 MS.gene061653:CDS 25.0%
! TATTCTCTTGAAAACTTACT+TGG + chr1.3:18675053-18675072 None:intergenic 25.0%
! TTTAGAAGTTTCTAATGTGA+GGG - chr1.3:18675435-18675454 MS.gene061653:CDS 25.0%
!! GTCAATTTAAGTTCAAAACT+TGG + chr1.3:18674923-18674942 None:intergenic 25.0%
!!! AAGTAACCTTGCAATTTTTT+AGG + chr1.3:18675305-18675324 None:intergenic 25.0%
!!! AGTAACCTTGCAATTTTTTA+GGG + chr1.3:18675304-18675323 None:intergenic 25.0%
AACAGAAGTTCTATTGTGAA+TGG - chr1.3:18675155-18675174 MS.gene061653:CDS 30.0%
AATACTTGAACGAGTTCAAA+GGG - chr1.3:18675069-18675088 MS.gene061653:CDS 30.0%
GAAACTTCTAAATCTGTAGA+AGG + chr1.3:18675427-18675446 None:intergenic 30.0%
GTATTCTCTGTTTCAATTCA+TGG + chr1.3:18675031-18675050 None:intergenic 30.0%
TGGTTGGAATTTATTTACCA+AGG - chr1.3:18675178-18675197 MS.gene061653:CDS 30.0%
! AAGGAAAATAACTTGCAAGT+CGG - chr1.3:18675197-18675216 MS.gene061653:CDS 30.0%
AGAAGTTCTATTGTGAATGG+TGG - chr1.3:18675158-18675177 MS.gene061653:CDS 35.0%
GAATACTTGAACGAGTTCAA+AGG - chr1.3:18675068-18675087 MS.gene061653:CDS 35.0%
TCAAGCCCTAAAAAATTGCA+AGG - chr1.3:18675296-18675315 MS.gene061653:intron 35.0%
TGATGAAGATAGAACTTGGA+AGG - chr1.3:18675109-18675128 MS.gene061653:CDS 35.0%
! TTGACACAATTTTATGCCCA+AGG - chr1.3:18674938-18674957 MS.gene061653:intron 35.0%
!! GACTTGCAAGTTATTTTCCT+TGG + chr1.3:18675198-18675217 None:intergenic 35.0%
CAAAGGGATTGCAAGCATTA+GGG - chr1.3:18675085-18675104 MS.gene061653:CDS 40.0%
GTTCTATTGTGAATGGTGGT+TGG - chr1.3:18675162-18675181 MS.gene061653:CDS 40.0%
TCAAAGGGATTGCAAGCATT+AGG - chr1.3:18675084-18675103 MS.gene061653:CDS 40.0%
! CTTTGAGAATTCCTTGTACC+CGG - chr1.3:18675477-18675496 MS.gene061653:CDS 40.0%
!! GGGTTGATGAAGATAGAACT+TGG - chr1.3:18675105-18675124 MS.gene061653:CDS 40.0%
TTCTATTTCCCGAGCTAGAG+AGG - chr1.3:18675271-18675290 MS.gene061653:CDS 45.0%
GGCTTGATTCCTCTCTAGCT+CGG + chr1.3:18675283-18675302 None:intergenic 50.0%
! GCTTGATTCCTCTCTAGCTC+GGG + chr1.3:18675282-18675301 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 18674854 18675504 18674854 ID=MS.gene061653
chr1.3 mRNA 18674854 18675504 18674854 ID=MS.gene061653.t1;Parent=MS.gene061653
chr1.3 exon 18675388 18675504 18675388 ID=MS.gene061653.t1.exon1;Parent=MS.gene061653.t1
chr1.3 CDS 18675388 18675504 18675388 ID=cds.MS.gene061653.t1;Parent=MS.gene061653.t1
chr1.3 exon 18675041 18675314 18675041 ID=MS.gene061653.t1.exon2;Parent=MS.gene061653.t1
chr1.3 CDS 18675041 18675314 18675041 ID=cds.MS.gene061653.t1;Parent=MS.gene061653.t1
chr1.3 exon 18674854 18674924 18674854 ID=MS.gene061653.t1.exon3;Parent=MS.gene061653.t1
chr1.3 CDS 18674854 18674924 18674854 ID=cds.MS.gene061653.t1;Parent=MS.gene061653.t1
Gene Sequence

>MS.gene061653

ATGACTAAGAAGGCTAAGAAATGTTCAATAACTGAAGCAAATAATAAGAAATCCAATGATAAGAATCCAAGTTTTGAACTTAAATTGACACAATTTTATGCCCAAGGAAAATTATTTGTAAGTTTACTTTTGAAAATGTCTATTATTTTGGCTTTAATTAATATCTCTAATAAACCATGAATTGAAACAGAGAATACCAAGTAAGTTTTCAAGAGAATACTTGAACGAGTTCAAAGGGATTGCAAGCATTAGGGTTGATGAAGATAGAACTTGGAAGGTGAATGTGAAGTTTGATTATGCAAACAGAAGTTCTATTGTGAATGGTGGTTGGAATTTATTTACCAAGGAAAATAACTTGCAAGTCGGCGATGTGTGTAAATTTGAGATGACTCGATCTGAGCCTCTTTCTTTTAATATTTCTATTTCCCGAGCTAGAGAGGAATCAAGCCCTAAAAAATTGCAAGGTTACTTTCTTTCTTCATTATTTGTTTGTTTATTAAAGTTTGTGGTTTTTTGGTCATTGATGTTTGATTAACATTTATCAATCAGTTTTTCACTAACTTCTTAATCCCTTCTACAGATTTAGAAGTTTCTAATGTGAGGGAACATAACACATTTGAGCTCTTTGAGAATTCCTTGTACCCGGTATGA
Protein sequence

>MS.gene061653.t1

MTKKAKKCSITEANNKKSNDKNPSFELKLTQFYAQGKLFRIPSKFSREYLNEFKGIASIRVDEDRTWKVNVKFDYANRSSIVNGGWNLFTKENNLQVGDVCKFEMTRSEPLSFNISISRAREESSPKKLQDLEVSNVREHNTFELFENSLYPV