AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06157

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06157.t1 MTR_7g100010 99.301 143 1 0 1 143 1 143 4.64e-104 293
MS.gene06157.t1 MTR_8g102180 99.301 143 1 0 1 143 1 143 4.64e-104 293
MS.gene06157.t1 MTR_5g098940 42.029 138 80 0 3 140 2 139 9.50e-39 129
MS.gene06157.t1 MTR_1g025190 47.482 139 73 0 3 141 2 140 1.17e-38 128
MS.gene06157.t1 MTR_5g087820 41.791 134 78 0 3 136 26 159 8.53e-35 119
MS.gene06157.t1 MTR_8g077600 37.162 148 80 3 3 141 2 145 1.15e-30 108
MS.gene06157.t1 MTR_8g077600 35.484 93 47 3 3 86 2 90 1.40e-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
MS.gene06157.t1 AT2G19790 90.141 142 14 0 1 142 1 142 2.48e-96 274
MS.gene06157.t1 AT1G47830 48.201 139 72 0 3 141 2 140 2.48e-39 129
MS.gene06157.t1 AT2G17380 41.727 139 81 0 3 141 2 140 1.62e-38 128
MS.gene06157.t1 AT4G35410 41.727 139 81 0 3 141 2 140 3.23e-37 125
MS.gene06157.t1 AT3G50860 39.583 144 82 1 3 141 2 145 5.28e-35 119
MS.gene06157.t1 AT3G50860 39.583 144 82 1 3 141 2 145 5.57e-35 119
MS.gene06157.t1 AT4G35410 45.361 97 53 0 3 99 2 98 2.05e-25 93.2

Find 23 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGAATGAGCTTGCTATTT+TGG 0.125124 4.2:-3110314 MS.gene06157:intron
GAAACCATGGATCGACATTT+TGG 0.210891 4.2:-3110271 MS.gene06157:CDS
GGGGATCCGATTCGTGTTAA+TGG 0.262612 4.2:-3111727 MS.gene06157:CDS
TACGAACAATTTCGCCTTCA+AGG 0.397557 4.2:+3111637 None:intergenic
GCAACTACAAAATTATATAT+AGG 0.415613 4.2:-3110704 MS.gene06157:CDS
GAAGAACGACGAACCCTTGA+AGG 0.434936 4.2:-3111651 MS.gene06157:CDS
TGTTCACCATTAACACGAAT+CGG 0.437301 4.2:+3111721 None:intergenic
TATCATGTTTCATTTAGAAA+AGG 0.473226 4.2:-3110050 MS.gene06157:CDS
TTCATAATACTGAGCAAGAC+GGG 0.525077 4.2:+3111686 None:intergenic
TCTGACTCCTATTCAGCTGA+TGG 0.529053 4.2:-3109963 MS.gene06157:CDS
ACGAACAATTTCGCCTTCAA+GGG 0.529281 4.2:+3111638 None:intergenic
TTCCTGGTTGGAGTTGATGA+CGG 0.536130 4.2:-3110663 MS.gene06157:CDS
CGCCGTCATCAACTCCAACC+AGG 0.570939 4.2:+3110661 None:intergenic
CCATGGTTTCGACTAAGAGA+TGG 0.572456 4.2:+3110284 None:intergenic
GGTCATGAATGGTTGTATTG+TGG 0.573456 4.2:-3110005 MS.gene06157:CDS
CCTCGCCCGTAATGAAAACC+AGG 0.578527 4.2:-3111610 MS.gene06157:intron
GTTGCCAAAATGTCGATCCA+TGG 0.581731 4.2:+3110267 None:intergenic
GTGTTAATGGTGAACAAACA+AGG 0.589164 4.2:-3111714 MS.gene06157:CDS
TTGGAGGAAATGGTCATGAA+TGG 0.600198 4.2:-3110016 MS.gene06157:CDS
CCATCTCTTAGTCGAAACCA+TGG 0.604583 4.2:-3110284 MS.gene06157:CDS
ATTCATAATACTGAGCAAGA+CGG 0.623435 4.2:+3111685 None:intergenic
TTCGTCGTTCTTCAACAGTG+AGG 0.697820 4.2:+3111661 None:intergenic
GGTTGGAGTTGATGACGGCG+AGG 0.701215 4.2:-3110658 MS.gene06157:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATAAAATCAATTTGTTT+TGG + chr4.2:3110392-3110411 None:intergenic 10.0%
!! ATGAAAATAAAAGAAAAGAA+TGG + chr4.2:3110101-3110120 None:intergenic 15.0%
!! ATATTTATCTACAATGAAAG+TGG + chr4.2:3111285-3111304 None:intergenic 20.0%
!! ATTTAAACATGTGATGAAAT+TGG + chr4.2:3110667-3110686 None:intergenic 20.0%
!! GCAACTACAAAATTATATAT+AGG - chr4.2:3110974-3110993 MS.gene06157:intron 20.0%
!! TATCATGTTTCATTTAGAAA+AGG - chr4.2:3111628-3111647 MS.gene06157:CDS 20.0%
!! TGAAATTGGAAAGAAAAAAA+AGG + chr4.2:3110653-3110672 None:intergenic 20.0%
!!! ATTCTAGTTGATTTATACAA+AGG - chr4.2:3111067-3111086 MS.gene06157:intron 20.0%
!!! TGAATATTTTTACTATAGAC+AGG - chr4.2:3110529-3110548 MS.gene06157:intron 20.0%
! AAACAATGACAATGTGAATT+AGG + chr4.2:3110156-3110175 None:intergenic 25.0%
! AGAAACAAAAAATCAGTGTT+TGG + chr4.2:3111566-3111585 None:intergenic 25.0%
! ATTAGGTAAAATTGAAGGTA+AGG + chr4.2:3110139-3110158 None:intergenic 25.0%
! GGAAGAAAACAATAGAATTA+TGG + chr4.2:3111518-3111537 None:intergenic 25.0%
! TAAATAAGACATAGATGTCT+TGG - chr4.2:3110494-3110513 MS.gene06157:intron 25.0%
! TAGATTATATAATCTGTGAG+TGG - chr4.2:3110712-3110731 MS.gene06157:CDS 25.0%
! TGTGAATTAGGTAAAATTGA+AGG + chr4.2:3110144-3110163 None:intergenic 25.0%
! TGTTTATTATTATTCAACCC+TGG - chr4.2:3110171-3110190 MS.gene06157:intron 25.0%
! TTGAATAATAAAGAATGACG+AGG + chr4.2:3110755-3110774 None:intergenic 25.0%
!!! AGAAAAGGTACATTTTATGT+TGG - chr4.2:3111643-3111662 MS.gene06157:CDS 25.0%
!!! CACTGTGTTATATTTTAGTT+GGG - chr4.2:3110625-3110644 MS.gene06157:intron 25.0%
AGAATTATGGAAGTAATGTG+AGG + chr4.2:3111505-3111524 None:intergenic 30.0%
AGTAAGAGAAAGTCAAAAGA+TGG + chr4.2:3110829-3110848 None:intergenic 30.0%
ATTCATAATACTGAGCAAGA+CGG + chr4.2:3109996-3110015 None:intergenic 30.0%
CATTCTTTATTATTCAACCG+AGG - chr4.2:3110758-3110777 MS.gene06157:intron 30.0%
CCAACTAAAATATAACACAG+TGG + chr4.2:3110627-3110646 None:intergenic 30.0%
GCATATTGTGTTAAATAGTC+TGG - chr4.2:3111110-3111129 MS.gene06157:intron 30.0%
GGTTTATACCAGAAACATAA+GGG - chr4.2:3110863-3110882 MS.gene06157:intron 30.0%
TATAGACAGGAGATAATTGT+TGG - chr4.2:3110542-3110561 MS.gene06157:intron 30.0%
TGAGTGGAATGAAATTGAAA+TGG - chr4.2:3110728-3110747 MS.gene06157:intron 30.0%
TGGTTTATACCAGAAACATA+AGG - chr4.2:3110862-3110881 MS.gene06157:intron 30.0%
TTAACAAGACTAAGAACTTC+AGG + chr4.2:3111231-3111250 None:intergenic 30.0%
TTATTATTATTCAACCCTGG+AGG - chr4.2:3110174-3110193 MS.gene06157:intron 30.0%
TTTCATAATCTATCATGGAG+AGG + chr4.2:3110346-3110365 None:intergenic 30.0%
! ACATTTTATGTTGGAGGAAA+TGG - chr4.2:3111652-3111671 MS.gene06157:CDS 30.0%
! CATAAACACTTCTGAGAATA+TGG - chr4.2:3110272-3110291 MS.gene06157:CDS 30.0%
! CTAGTTGATTTATACAAAGG+CGG - chr4.2:3111070-3111089 MS.gene06157:intron 30.0%
! GCTGATTTCATAATCTATCA+TGG + chr4.2:3110351-3110370 None:intergenic 30.0%
! TATTATTCAACCGAGGTTTT+AGG - chr4.2:3110765-3110784 MS.gene06157:intron 30.0%
!! AAAGGTACATTTTATGTTGG+AGG - chr4.2:3111646-3111665 MS.gene06157:CDS 30.0%
!! AACATACCTGGTTTTCATTA+CGG + chr4.2:3110077-3110096 None:intergenic 30.0%
!!! CCACTGTGTTATATTTTAGT+TGG - chr4.2:3110624-3110643 MS.gene06157:intron 30.0%
AAGTCAATCCCTTATGTTTC+TGG + chr4.2:3110874-3110893 None:intergenic 35.0%
AATCTATCATGGAGAGGTTA+TGG + chr4.2:3110340-3110359 None:intergenic 35.0%
AGCAAACTTGAATCCAAAGA+TGG + chr4.2:3110791-3110810 None:intergenic 35.0%
AGGTAAAATTGAAGGTAAGG+AGG + chr4.2:3110136-3110155 None:intergenic 35.0%
GAAAAGAATGGAAACATACC+TGG + chr4.2:3110089-3110108 None:intergenic 35.0%
GTGTTAATGGTGAACAAACA+AGG - chr4.2:3109964-3109983 MS.gene06157:CDS 35.0%
TCTACAATGAAAGTGGTACA+TGG + chr4.2:3111278-3111297 None:intergenic 35.0%
TCTTACTCATATTGATGCGT+TGG - chr4.2:3110842-3110861 MS.gene06157:intron 35.0%
TGTTCACCATTAACACGAAT+CGG + chr4.2:3109960-3109979 None:intergenic 35.0%
TTCATAATACTGAGCAAGAC+GGG + chr4.2:3109995-3110014 None:intergenic 35.0%
TTGAAGCTAAGTTCAGAAGA+TGG + chr4.2:3111543-3111562 None:intergenic 35.0%
! GTTTTATCCATCAGCTGAAT+AGG + chr4.2:3111725-3111744 None:intergenic 35.0%
! TGGCTGATACATTTTTGTCA+TGG - chr4.2:3110928-3110947 MS.gene06157:intron 35.0%
!! ACATACCTGGTTTTCATTAC+GGG + chr4.2:3110076-3110095 None:intergenic 35.0%
!!! CTATGCATCTTTGTTTTTCC+TGG - chr4.2:3110999-3111018 MS.gene06157:intron 35.0%
AAAAGATGGCCTAAAACCTC+GGG + chr4.2:3110815-3110834 None:intergenic 40.0%
ACGAACAATTTCGCCTTCAA+GGG + chr4.2:3110043-3110062 None:intergenic 40.0%
ACTTTCTCTTCCCCAATTCT+GGG + chr4.2:3110580-3110599 None:intergenic 40.0%
AGCTAAGTTCAGAAGATGGA+AGG + chr4.2:3111539-3111558 None:intergenic 40.0%
AGTGGTCATCACTATGTGAT+CGG - chr4.2:3111150-3111169 MS.gene06157:intron 40.0%
CAAAAGATGGCCTAAAACCT+CGG + chr4.2:3110816-3110835 None:intergenic 40.0%
CAATCTAATTGCTACCTCCA+GGG + chr4.2:3110191-3110210 None:intergenic 40.0%
CCAGTTTCTTTAGACAAGCA+AGG + chr4.2:3111181-3111200 None:intergenic 40.0%
CCTTGCTTGTCTAAAGAAAC+TGG - chr4.2:3111178-3111197 MS.gene06157:intron 40.0%
GGTCATGAATGGTTGTATTG+TGG - chr4.2:3111673-3111692 MS.gene06157:CDS 40.0%
TACGAACAATTTCGCCTTCA+AGG + chr4.2:3110044-3110063 None:intergenic 40.0%
TACTTTCTCTTCCCCAATTC+TGG + chr4.2:3110581-3110600 None:intergenic 40.0%
TCAATCTAATTGCTACCTCC+AGG + chr4.2:3110192-3110211 None:intergenic 40.0%
TCTGCAAAATTGTCGACAGA+AGG + chr4.2:3111349-3111368 None:intergenic 40.0%
TGTATCAGCCAGATGAATCA+TGG + chr4.2:3110919-3110938 None:intergenic 40.0%
TTCCTTTCACACCCAGAATT+GGG - chr4.2:3110566-3110585 MS.gene06157:intron 40.0%
TTGGAGGAAATGGTCATGAA+TGG - chr4.2:3111662-3111681 MS.gene06157:CDS 40.0%
TTTCCTTTCACACCCAGAAT+TGG - chr4.2:3110565-3110584 MS.gene06157:intron 40.0%
! GAAACCATGGATCGACATTT+TGG - chr4.2:3111407-3111426 MS.gene06157:intron 40.0%
!!! GCAGAATGAGCTTGCTATTT+TGG - chr4.2:3111364-3111383 MS.gene06157:intron 40.0%
!!! GCATCTTTGTTTTTCCTGGT+TGG - chr4.2:3111003-3111022 MS.gene06157:intron 40.0%
CCAAAGATGGCCTAAAACCT+CGG + chr4.2:3110778-3110797 None:intergenic 45.0%
CCATCTCTTAGTCGAAACCA+TGG - chr4.2:3111394-3111413 MS.gene06157:intron 45.0%
CCATGGTTTCGACTAAGAGA+TGG + chr4.2:3111397-3111416 None:intergenic 45.0%
GATCACATAGTGATGACCAC+TGG + chr4.2:3111151-3111170 None:intergenic 45.0%
GCTTTGATCTTACTGACCAG+TGG - chr4.2:3111132-3111151 MS.gene06157:intron 45.0%
GTTGCCAAAATGTCGATCCA+TGG + chr4.2:3111414-3111433 None:intergenic 45.0%
TCCTTTCACACCCAGAATTG+GGG - chr4.2:3110567-3110586 MS.gene06157:intron 45.0%
TCTGACTCCTATTCAGCTGA+TGG - chr4.2:3111715-3111734 MS.gene06157:CDS 45.0%
TCTGCTCACCATGATTCATC+TGG - chr4.2:3110908-3110927 MS.gene06157:intron 45.0%
TTCGTCGTTCTTCAACAGTG+AGG + chr4.2:3110020-3110039 None:intergenic 45.0%
!! TTCCTGGTTGGAGTTGATGA+CGG - chr4.2:3111015-3111034 MS.gene06157:intron 45.0%
!!! AGTTTGCTACCCGAGGTTTT+AGG - chr4.2:3110803-3110822 MS.gene06157:intron 45.0%
ACAGAGACTCTAGTCACAGC+AGG + chr4.2:3111446-3111465 None:intergenic 50.0%
GAAGAACGACGAACCCTTGA+AGG - chr4.2:3110027-3110046 MS.gene06157:CDS 50.0%
TCCCCAATTCTGGGTGTGAA+AGG + chr4.2:3110571-3110590 None:intergenic 50.0%
! GGGGATCCGATTCGTGTTAA+TGG - chr4.2:3109951-3109970 MS.gene06157:CDS 50.0%
!! GGATCGACATTTTGGCAACG+TGG - chr4.2:3111415-3111434 MS.gene06157:intron 50.0%
!! GGATTCAAGTTTGCTACCCG+AGG - chr4.2:3110796-3110815 MS.gene06157:intron 50.0%
!!! CCGAGGTTTTAGGCCATCTT+TGG - chr4.2:3110775-3110794 MS.gene06157:intron 50.0%
CCTCGCCCGTAATGAAAACC+AGG - chr4.2:3110068-3110087 MS.gene06157:intron 55.0%
!! CCTGGTTTTCATTACGGGCG+AGG + chr4.2:3110071-3110090 None:intergenic 55.0%
CGCCGTCATCAACTCCAACC+AGG + chr4.2:3111020-3111039 None:intergenic 60.0%
!! GGTTGGAGTTGATGACGGCG+AGG - chr4.2:3111020-3111039 MS.gene06157:intron 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 3109949 3111751 3109949 ID=MS.gene06157
chr4.2 mRNA 3109949 3111751 3109949 ID=MS.gene06157.t1;Parent=MS.gene06157
chr4.2 exon 3111611 3111751 3111611 ID=MS.gene06157.t1.exon1;Parent=MS.gene06157.t1
chr4.2 CDS 3111611 3111751 3111611 ID=cds.MS.gene06157.t1;Parent=MS.gene06157.t1
chr4.2 exon 3110659 3110745 3110659 ID=MS.gene06157.t1.exon2;Parent=MS.gene06157.t1
chr4.2 CDS 3110659 3110745 3110659 ID=cds.MS.gene06157.t1;Parent=MS.gene06157.t1
chr4.2 exon 3110264 3110332 3110264 ID=MS.gene06157.t1.exon3;Parent=MS.gene06157.t1
chr4.2 CDS 3110264 3110332 3110264 ID=cds.MS.gene06157.t1;Parent=MS.gene06157.t1
chr4.2 exon 3109949 3110083 3109949 ID=MS.gene06157.t1.exon4;Parent=MS.gene06157.t1
chr4.2 CDS 3109949 3110083 3109949 ID=cds.MS.gene06157.t1;Parent=MS.gene06157.t1
Gene Sequence

>MS.gene06157

ATGGGGATCCGATTCGTGTTAATGGTGAACAAACAAGGACAGACCCGTCTTGCTCAGTATTATGAATACCTCACTGTTGAAGAACGACGAACCCTTGAAGGCGAAATTGTTCGTAAATGCCTCGCCCGTAATGAAAACCAGGTATGTTTCCATTCTTTTCTTTTATTTTCATCAGATCTTCATACCTCCTTACCTTCAATTTTACCTAATTCACATTGTCATTGTTTATTATTATTCAACCCTGGAGGTAGCAATTAGATTGAGAGCTTAATTCAAAATTTAAGACAATCTTAGTTTACAATTTGACTCAACTGAATATCAAACATAAACACTTCTGAGAATATGGAAACAGCTTACAACATGTTCATAAGTTACTTGCAGATTATTTCCATAACCTCTCCATGATAGATTATGAAATCAGCTTATAGTTATAGCTTATTCCAAAACAAATTGATTTTATTTTGTCTTTTGTTTTAGAAATAGCATATGCATAAGTACTCATATGATAAATGTCATGTTGTAAGCGCTTAATTAATTTGTTTATCTAAATAAGACATAGATGTCTTGGAAAGTTATTATTTGAATATTTTTACTATAGACAGGAGATAATTGTTGGTTTCCTTTCACACCCAGAATTGGGGAAGAGAAAGTAGTTAGTGAGATATTGAATGCATTCCACTGTGTTATATTTTAGTTGGGAACCTTTTTTTTCTTTCCAATTTCATCACATGTTTAAATCTTAGCTTAGATTTTGTGTTATTATTAGATTATATAATCTGTGAGTGGAATGAAATTGAAATGGACCTCGTCATTCTTTATTATTCAACCGAGGTTTTAGGCCATCTTTGGATTCAAGTTTGCTACCCGAGGTTTTAGGCCATCTTTTGACTTTCTCTTACTCATATTGATGCGTTGGTTTATACCAGAAACATAAGGGATTGACTTGTCTTATTGTTGTTTCTGCTCACCATGATTCATCTGGCTGATACATTTTTGTCATGGACAGTGTTCATTTGTTGAGCATCGCAACTACAAAATTATATATAGGCGCTATGCATCTTTGTTTTTCCTGGTTGGAGTTGATGACGGCGAGGTAATTCATTGTTTCTATATTTCTCATTCTAGTTGATTTATACAAAGGCGGTGAATAATTTGAAATGAGCATATTGTGTTAAATAGTCTGGCTTTGATCTTACTGACCAGTGGTCATCACTATGTGATCGGCTTAGCCTTGCTTGTCTAAAGAAACTGGAAGAATTATCTGTTGTAAACTCAGAAACCTGAAGTTCTTAGTCTTGTTAAACACTTCAGCTTCAGCAAAATTTTCCATGTACCACTTTCATTGTAGATAAATATGATATCATTTCAATTCTGCTTCTACTTGATTGTTCATTCTACCTTCTGTCGACAATTTTGCAGAATGAGCTTGCTATTTTGGAATTTATCCATCTCTTAGTCGAAACCATGGATCGACATTTTGGCAACGTGGTAAGTCCTGCTGTGACTAGAGTCTCTGTAGTTTTGTGTTTGTTGAAATTGAAAGTAATGTGTCTCCTCACATTACTTCCATAATTCTATTGTTTTCTTCCTTCCATCTTCTGAACTTAGCTTCAACCAAACACTGATTTTTTGTTTCTCAAATTTCTTCTTGTCTGCTTAAATTTGCAGTGTGAGCTAGATATCATGTTTCATTTAGAAAAGGTACATTTTATGTTGGAGGAAATGGTCATGAATGGTTGTATTGTGGAGACAAGCAAATCAAATATTCTGACTCCTATTCAGCTGATGGATAAAACATCATAA
Protein sequence

>MS.gene06157.t1

MGIRFVLMVNKQGQTRLAQYYEYLTVEERRTLEGEIVRKCLARNENQCSFVEHRNYKIIYRRYASLFFLVGVDDGENELAILEFIHLLVETMDRHFGNVCELDIMFHLEKVHFMLEEMVMNGCIVETSKSNILTPIQLMDKTS