AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0061430


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0061430 MtrunA17_Chr1g0161551 91.667 84 6 1 1 84 1 83 1.39e-49 153
Msa0061430 MtrunA17_Chr6g0479181 40.708 113 63 2 9 121 53 161 2.78e-22 86.7
Msa0061430 MtrunA17_Chr5g0413201 31.746 126 68 3 9 119 48 170 6.63e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0061430 AT1G14760.2 42.857 105 49 4 22 119 32 132 9.40e-19 76.6
Msa0061430 AT1G70510.1 35.922 103 58 2 22 119 68 167 1.49e-11 60.1
Msa0061430 AT1G23380.1 34.951 103 59 2 22 119 84 183 5.76e-11 58.5

Find 19 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGATGGAGGGTAAAGAAAT+TGG 0.288718 1_2:+19687152 None:intergenic
GTTTGGACTAGTTGTTGTTT+TGG 0.322855 1_2:-19687839 None:intergenic
TGATCAAGCTCTGGATTGTT+TGG 0.325293 1_2:-19687856 None:intergenic
CCATCCTTTGTTTGAAGCAT+TGG 0.359729 1_2:+19687241 Msa0061430:CDS
TCCAGAGCTTGATCACTTCA+TGG 0.417924 1_2:+19687864 Msa0061430:CDS
AAGTGATGCATGGAAGAAAT+TGG 0.438853 1_2:+19687804 Msa0061430:CDS
GTCTCACATCAATTGTTTGA+AGG 0.470627 1_2:+19687268 Msa0061430:CDS
TATATTCAACTGCAGGAACT+TGG 0.501461 1_2:+19689093 Msa0061430:CDS
GTTCATCAATCACGTCTTTG+AGG 0.505826 1_2:-19689035 None:intergenic
ACCATGAAGTGATCAAGCTC+TGG 0.518397 1_2:-19687865 None:intergenic
AAAAGAAAGTGAAAATGAAG+AGG 0.568561 1_2:+19687196 Msa0061430:CDS
CCAATGCTTCAAACAAAGGA+TGG 0.572089 1_2:-19687241 None:intergenic
TTGATATAACAAGTGATGCA+TGG 0.576358 1_2:+19687794 Msa0061430:CDS
GGAAAGGGAAGTGATGATGT+AGG 0.576930 1_2:+19687173 Msa0061430:CDS
TGCTACGTATATTCAACTGC+AGG 0.578517 1_2:+19689086 Msa0061430:CDS
TCAACCAATGCTTCAAACAA+AGG 0.579326 1_2:-19687245 None:intergenic
GAGGGTAAAGAAATTGGAAA+GGG 0.582588 1_2:+19687158 Msa0061430:CDS
GGAGGGTAAAGAAATTGGAA+AGG 0.606364 1_2:+19687157 Msa0061430:CDS
TATTTCTTAGGTCGGATCTG+AGG 0.611391 1_2:+19687759 Msa0061430:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATATAGTGTATAATTA+TGG + chr1_2:19687415-19687434 Msa0061430:intron 10.0%
!! ATATTAATATATACACAAAA+AGG + chr1_2:19687492-19687511 Msa0061430:intron 10.0%
!! TATTAATATATACACAAAAA+GGG + chr1_2:19687493-19687512 Msa0061430:intron 10.0%
!! ATAGATATATAAATTCTTTA+CGG + chr1_2:19688069-19688088 Msa0061430:intron 10.0%
!! AAATAATAATCTATAAAAGA+TGG - chr1_2:19688607-19688626 None:intergenic 10.0%
!! AAATAATAATCTATAAAAGA+TGG - chr1_2:19688607-19688626 None:intergenic 10.0%
!! AATAATATAGTGTATAATTA+TGG + chr1_2:19687415-19687434 Msa0061430:intron 10.0%
!! ATATTAATATATACACAAAA+AGG + chr1_2:19687492-19687511 Msa0061430:intron 10.0%
!! TATTAATATATACACAAAAA+GGG + chr1_2:19687493-19687512 Msa0061430:intron 10.0%
!! ATAGATATATAAATTCTTTA+CGG + chr1_2:19688069-19688088 Msa0061430:intron 10.0%
!! AAATAATAATCTATAAAAGA+TGG - chr1_2:19688607-19688626 None:intergenic 10.0%
!! AAATAATAATCTATAAAAGA+TGG - chr1_2:19688607-19688626 None:intergenic 10.0%
!! ACAACTTAAATTTATTTAAG+AGG + chr1_2:19687314-19687333 Msa0061430:intron 15.0%
!! GTATTACATACATTAATTAA+TGG + chr1_2:19687886-19687905 Msa0061430:intron 15.0%
!!! TTGTTACTTAGTAATTAATT+TGG - chr1_2:19688106-19688125 None:intergenic 15.0%
!!! TTACTAAGTAACAATTTTTA+TGG + chr1_2:19688112-19688131 Msa0061430:intron 15.0%
!! ACAACTTAAATTTATTTAAG+AGG + chr1_2:19687314-19687333 Msa0061430:intron 15.0%
!! GTATTACATACATTAATTAA+TGG + chr1_2:19687886-19687905 Msa0061430:intron 15.0%
!!! TTGTTACTTAGTAATTAATT+TGG - chr1_2:19688106-19688125 None:intergenic 15.0%
!!! TTACTAAGTAACAATTTTTA+TGG + chr1_2:19688112-19688131 Msa0061430:intron 15.0%
!! TAATTATGGAAAGATAGTTT+AGG + chr1_2:19687429-19687448 Msa0061430:intron 20.0%
!!! TCTTTTTTGCAAAAGAAAAA+TGG + chr1_2:19687675-19687694 Msa0061430:intron 20.0%
!!! AAGAAAAATGGATTAATCAA+AGG + chr1_2:19687687-19687706 Msa0061430:intron 20.0%
!!! AGTAATTAATTTGGATGTTT+TGG - chr1_2:19688097-19688116 None:intergenic 20.0%
!! AAAATAATAGAGAGAGAAAA+AGG - chr1_2:19688239-19688258 None:intergenic 20.0%
!! AATCATATTATATGTGAACT+AGG - chr1_2:19688974-19688993 None:intergenic 20.0%
!! TATGATTCATTTATGTACAT+AGG + chr1_2:19688987-19689006 Msa0061430:intron 20.0%
!! TAATTATGGAAAGATAGTTT+AGG + chr1_2:19687429-19687448 Msa0061430:intron 20.0%
!!! TCTTTTTTGCAAAAGAAAAA+TGG + chr1_2:19687675-19687694 Msa0061430:intron 20.0%
!!! AAGAAAAATGGATTAATCAA+AGG + chr1_2:19687687-19687706 Msa0061430:intron 20.0%
!!! AGTAATTAATTTGGATGTTT+TGG - chr1_2:19688097-19688116 None:intergenic 20.0%
!! AAAATAATAGAGAGAGAAAA+AGG - chr1_2:19688239-19688258 None:intergenic 20.0%
!! AATCATATTATATGTGAACT+AGG - chr1_2:19688974-19688993 None:intergenic 20.0%
!! TATGATTCATTTATGTACAT+AGG + chr1_2:19688987-19689006 Msa0061430:intron 20.0%
! AAAAGAAAGTGAAAATGAAG+AGG + chr1_2:19687196-19687215 Msa0061430:CDS 25.0%
! TAATTTCATTCCATACATGT+TGG - chr1_2:19687719-19687738 None:intergenic 25.0%
!! TCTTCATTCCTTTATTTCTT+AGG + chr1_2:19687747-19687766 Msa0061430:intron 25.0%
! CATACATTAATTAATGGTCA+TGG + chr1_2:19687892-19687911 Msa0061430:intron 25.0%
!! AATCAAATTTGTTCACTCAA+TGG + chr1_2:19687977-19687996 Msa0061430:intron 25.0%
! TGTGTGTAAAATAGATATTG+TGG + chr1_2:19688025-19688044 Msa0061430:intron 25.0%
! TCATGAAAGTTGTCTATTAA+TGG + chr1_2:19688290-19688309 Msa0061430:intron 25.0%
!!! ACGTAAATTGAAAGTTTTGA+AGG - chr1_2:19688359-19688378 None:intergenic 25.0%
! GTAACTAAAACTTGTCATTA+TGG - chr1_2:19688384-19688403 None:intergenic 25.0%
!!! TTTTTAAGCAAGCATAAACT+AGG + chr1_2:19688868-19688887 Msa0061430:intron 25.0%
! AAAAGAAAGTGAAAATGAAG+AGG + chr1_2:19687196-19687215 Msa0061430:CDS 25.0%
! TAATTTCATTCCATACATGT+TGG - chr1_2:19687719-19687738 None:intergenic 25.0%
!! TCTTCATTCCTTTATTTCTT+AGG + chr1_2:19687747-19687766 Msa0061430:intron 25.0%
! CATACATTAATTAATGGTCA+TGG + chr1_2:19687892-19687911 Msa0061430:intron 25.0%
!! AATCAAATTTGTTCACTCAA+TGG + chr1_2:19687977-19687996 Msa0061430:intron 25.0%
! TGTGTGTAAAATAGATATTG+TGG + chr1_2:19688025-19688044 Msa0061430:intron 25.0%
! TCATGAAAGTTGTCTATTAA+TGG + chr1_2:19688290-19688309 Msa0061430:intron 25.0%
!!! ACGTAAATTGAAAGTTTTGA+AGG - chr1_2:19688359-19688378 None:intergenic 25.0%
! GTAACTAAAACTTGTCATTA+TGG - chr1_2:19688384-19688403 None:intergenic 25.0%
!!! TTTTTAAGCAAGCATAAACT+AGG + chr1_2:19688868-19688887 Msa0061430:intron 25.0%
TGTAAGTAATGTATTCCTCA+TGG - chr1_2:19687465-19687484 None:intergenic 30.0%
AGGGTAAAAAAGACAACAAA+AGG + chr1_2:19687512-19687531 Msa0061430:intron 30.0%
GGGTAAAAAAGACAACAAAA+GGG + chr1_2:19687513-19687532 Msa0061430:intron 30.0%
AAGGATATATCCAACATGTA+TGG + chr1_2:19687706-19687725 Msa0061430:intron 30.0%
! CATTCCTTTATTTCTTAGGT+CGG + chr1_2:19687751-19687770 Msa0061430:intron 30.0%
TTGATATAACAAGTGATGCA+TGG + chr1_2:19687794-19687813 Msa0061430:CDS 30.0%
GTCAAAAAGTTGTTGCAAAA+TGG - chr1_2:19688172-19688191 None:intergenic 30.0%
! AAAGCTTTTGCTTCTTTTGT+TGG - chr1_2:19689060-19689079 None:intergenic 30.0%
TGTAAGTAATGTATTCCTCA+TGG - chr1_2:19687465-19687484 None:intergenic 30.0%
AGGGTAAAAAAGACAACAAA+AGG + chr1_2:19687512-19687531 Msa0061430:intron 30.0%
GGGTAAAAAAGACAACAAAA+GGG + chr1_2:19687513-19687532 Msa0061430:intron 30.0%
AAGGATATATCCAACATGTA+TGG + chr1_2:19687706-19687725 Msa0061430:intron 30.0%
! CATTCCTTTATTTCTTAGGT+CGG + chr1_2:19687751-19687770 Msa0061430:intron 30.0%
TTGATATAACAAGTGATGCA+TGG + chr1_2:19687794-19687813 Msa0061430:CDS 30.0%
GTCAAAAAGTTGTTGCAAAA+TGG - chr1_2:19688172-19688191 None:intergenic 30.0%
! AAAGCTTTTGCTTCTTTTGT+TGG - chr1_2:19689060-19689079 None:intergenic 30.0%
GAGGGTAAAGAAATTGGAAA+GGG + chr1_2:19687158-19687177 Msa0061430:CDS 35.0%
TCAACCAATGCTTCAAACAA+AGG - chr1_2:19687248-19687267 None:intergenic 35.0%
GTCTCACATCAATTGTTTGA+AGG + chr1_2:19687268-19687287 Msa0061430:CDS 35.0%
AGATCCGACCTAAGAAATAA+AGG - chr1_2:19687758-19687777 None:intergenic 35.0%
AAGTGATGCATGGAAGAAAT+TGG + chr1_2:19687804-19687823 Msa0061430:CDS 35.0%
!!! GTTTGGACTAGTTGTTGTTT+TGG - chr1_2:19687842-19687861 None:intergenic 35.0%
!!! TACATAGGAAGCATTTTGCA+TGG + chr1_2:19689002-19689021 Msa0061430:intron 35.0%
TATATTCAACTGCAGGAACT+TGG + chr1_2:19689093-19689112 Msa0061430:CDS 35.0%
GAGGGTAAAGAAATTGGAAA+GGG + chr1_2:19687158-19687177 Msa0061430:CDS 35.0%
TCAACCAATGCTTCAAACAA+AGG - chr1_2:19687248-19687267 None:intergenic 35.0%
GTCTCACATCAATTGTTTGA+AGG + chr1_2:19687268-19687287 Msa0061430:CDS 35.0%
AGATCCGACCTAAGAAATAA+AGG - chr1_2:19687758-19687777 None:intergenic 35.0%
AAGTGATGCATGGAAGAAAT+TGG + chr1_2:19687804-19687823 Msa0061430:CDS 35.0%
!!! GTTTGGACTAGTTGTTGTTT+TGG - chr1_2:19687842-19687861 None:intergenic 35.0%
!!! TACATAGGAAGCATTTTGCA+TGG + chr1_2:19689002-19689021 Msa0061430:intron 35.0%
TATATTCAACTGCAGGAACT+TGG + chr1_2:19689093-19689112 Msa0061430:CDS 35.0%
GGAGGGTAAAGAAATTGGAA+AGG + chr1_2:19687157-19687176 Msa0061430:CDS 40.0%
CCAATGCTTCAAACAAAGGA+TGG - chr1_2:19687244-19687263 None:intergenic 40.0%
! CCATCCTTTGTTTGAAGCAT+TGG + chr1_2:19687241-19687260 Msa0061430:CDS 40.0%
! GGAAAGATAGTTTAGGACCA+CGG + chr1_2:19687436-19687455 Msa0061430:intron 40.0%
TATTTCTTAGGTCGGATCTG+AGG + chr1_2:19687759-19687778 Msa0061430:intron 40.0%
!! TGATCAAGCTCTGGATTGTT+TGG - chr1_2:19687859-19687878 None:intergenic 40.0%
!! GTACGTATGGTTTTGCATGT+GGG - chr1_2:19688422-19688441 None:intergenic 40.0%
AATACGTTGTGACGTACGTA+TGG - chr1_2:19688435-19688454 None:intergenic 40.0%
AATACGTTGTGACGTACGTA+TGG - chr1_2:19688435-19688454 None:intergenic 40.0%
GTTCATCAATCACGTCTTTG+AGG - chr1_2:19689038-19689057 None:intergenic 40.0%
TGCTACGTATATTCAACTGC+AGG + chr1_2:19689086-19689105 Msa0061430:CDS 40.0%
GGAGGGTAAAGAAATTGGAA+AGG + chr1_2:19687157-19687176 Msa0061430:CDS 40.0%
CCAATGCTTCAAACAAAGGA+TGG - chr1_2:19687244-19687263 None:intergenic 40.0%
! CCATCCTTTGTTTGAAGCAT+TGG + chr1_2:19687241-19687260 Msa0061430:CDS 40.0%
! GGAAAGATAGTTTAGGACCA+CGG + chr1_2:19687436-19687455 Msa0061430:intron 40.0%
TATTTCTTAGGTCGGATCTG+AGG + chr1_2:19687759-19687778 Msa0061430:intron 40.0%
!! TGATCAAGCTCTGGATTGTT+TGG - chr1_2:19687859-19687878 None:intergenic 40.0%
!! GTACGTATGGTTTTGCATGT+GGG - chr1_2:19688422-19688441 None:intergenic 40.0%
AATACGTTGTGACGTACGTA+TGG - chr1_2:19688435-19688454 None:intergenic 40.0%
AATACGTTGTGACGTACGTA+TGG - chr1_2:19688435-19688454 None:intergenic 40.0%
GTTCATCAATCACGTCTTTG+AGG - chr1_2:19689038-19689057 None:intergenic 40.0%
TGCTACGTATATTCAACTGC+AGG + chr1_2:19689086-19689105 Msa0061430:CDS 40.0%
! GGAAAGGGAAGTGATGATGT+AGG + chr1_2:19687173-19687192 Msa0061430:CDS 45.0%
TCCAGAGCTTGATCACTTCA+TGG + chr1_2:19687864-19687883 Msa0061430:CDS 45.0%
ACCATGAAGTGATCAAGCTC+TGG - chr1_2:19687868-19687887 None:intergenic 45.0%
!! TGGTTTTGCATGTGGGTTGA+GGG - chr1_2:19688415-19688434 None:intergenic 45.0%
!! ATGGTTTTGCATGTGGGTTG+AGG - chr1_2:19688416-19688435 None:intergenic 45.0%
!! CGTACGTATGGTTTTGCATG+TGG - chr1_2:19688423-19688442 None:intergenic 45.0%
! GGAAAGGGAAGTGATGATGT+AGG + chr1_2:19687173-19687192 Msa0061430:CDS 45.0%
TCCAGAGCTTGATCACTTCA+TGG + chr1_2:19687864-19687883 Msa0061430:CDS 45.0%
ACCATGAAGTGATCAAGCTC+TGG - chr1_2:19687868-19687887 None:intergenic 45.0%
!! TGGTTTTGCATGTGGGTTGA+GGG - chr1_2:19688415-19688434 None:intergenic 45.0%
!! ATGGTTTTGCATGTGGGTTG+AGG - chr1_2:19688416-19688435 None:intergenic 45.0%
!! CGTACGTATGGTTTTGCATG+TGG - chr1_2:19688423-19688442 None:intergenic 45.0%
TGTATTCCTCATGGTGACCG+TGG - chr1_2:19687456-19687475 None:intergenic 50.0%
! TTGCATGTGGGTTGAGGGTT+CGG - chr1_2:19688410-19688429 None:intergenic 50.0%
! GACGTACGTATGGTTCTGCT+AGG - chr1_2:19688656-19688675 None:intergenic 50.0%
TGTATTCCTCATGGTGACCG+TGG - chr1_2:19687456-19687475 None:intergenic 50.0%
! TTGCATGTGGGTTGAGGGTT+CGG - chr1_2:19688410-19688429 None:intergenic 50.0%
! GACGTACGTATGGTTCTGCT+AGG - chr1_2:19688656-19688675 None:intergenic 50.0%
TTAGGACCACGGTCACCATG+AGG + chr1_2:19687447-19687466 Msa0061430:intron 55.0%
TTAGGACCACGGTCACCATG+AGG + chr1_2:19687447-19687466 Msa0061430:intron 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 19687155 19689131 19687155 ID=Msa0061430;Name=Msa0061430
chr1_2 mRNA 19687155 19689131 19687155 ID=Msa0061430-mRNA-1;Parent=Msa0061430;Name=Msa0061430-mRNA-1;_AED=0.03;_eAED=0.04;_QI=0|0|0|1|1|1|3|0|124
chr1_2 exon 19687155 19687289 19687155 ID=Msa0061430-mRNA-1:exon:7575;Parent=Msa0061430-mRNA-1
chr1_2 exon 19687769 19687885 19687769 ID=Msa0061430-mRNA-1:exon:7576;Parent=Msa0061430-mRNA-1
chr1_2 exon 19689009 19689131 19689009 ID=Msa0061430-mRNA-1:exon:7577;Parent=Msa0061430-mRNA-1
chr1_2 CDS 19687155 19687289 19687155 ID=Msa0061430-mRNA-1:cds;Parent=Msa0061430-mRNA-1
chr1_2 CDS 19687769 19687885 19687769 ID=Msa0061430-mRNA-1:cds;Parent=Msa0061430-mRNA-1
chr1_2 CDS 19689009 19689131 19689009 ID=Msa0061430-mRNA-1:cds;Parent=Msa0061430-mRNA-1
Gene Sequence

>Msa0061430

ATGGAGGGTAAAGAAATTGGAAAGGGAAGTGATGATGTAGGAAAAGAAAGTGAAAATGAAGAGGTTCTAAAGAAGATTATTGCAAGCCATCCTTTGTTTGAAGCATTGGTTGAGTCTCACATCAATTGTTTGAAGGTCGGATCTGAGGATGCAAAAGAGTTTGATATAACAAGTGATGCATGGAAGAAATTGGTCAACACAAAGTCCAAAACAACAACTAGTCCAAACAATCCAGAGCTTGATCACTTCATGGAAGCATTTTGCATGGCACTGAGCAACCTCAAAGACGTGATTGATGAACCAACAAAAGAAGCAAAAGCTTTCATCAATGCTACGTATATTCAACTGCAGGAACTTGGTGAAGAAAATAATTAA

Protein sequence

>Msa0061430

MEGKEIGKGSDDVGKESENEEVLKKIIASHPLFEALVESHINCLKVGSEDAKEFDITSDAWKKLVNTKSKTTTSPNNPELDHFMEAFCMALSNLKDVIDEPTKEAKAFINATYIQLQELGEENN*