AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25756

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25756.t1 MTR_3g080680 72.222 198 40 3 1 183 1 198 1.10e-97 281
MS.gene25756.t1 MTR_3g082420 44.920 187 96 5 2 183 37 221 9.73e-37 127
MS.gene25756.t1 MTR_3g082340 46.626 163 81 4 25 183 62 222 9.39e-36 124
MS.gene25756.t1 MTR_8g461300 44.048 168 78 5 28 183 35 198 4.98e-33 117
MS.gene25756.t1 MTR_3g083080 41.714 175 90 6 16 185 40 207 9.62e-29 106
MS.gene25756.t1 MTR_3g083050 41.477 176 88 8 16 185 42 208 6.14e-25 96.7
MS.gene25756.t1 MTR_3g083030 41.477 176 88 8 16 185 65 231 1.19e-24 96.3
MS.gene25756.t1 MTR_4g055800 39.437 142 69 5 30 167 145 273 1.70e-20 86.7
MS.gene25756.t1 MTR_3g083150 35.897 195 110 7 2 184 21 212 1.11e-18 80.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 42 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAACAGAAACAGGTGAAAA+AGG 0.230480 3.2:+71135979 MS.gene25756:CDS
TTACCACGTTTGCCGTAATA+AGG 0.262079 3.2:-71136085 None:intergenic
AATAGATTCTACCATTAATA+AGG 0.262811 3.2:-71136576 None:intergenic
TGTACCCATGCCCTTATTAA+TGG 0.282280 3.2:+71136565 MS.gene25756:CDS
ATTAAAATTAAATGTGATCT+TGG 0.329794 3.2:-71136318 None:intergenic
AAGGGATCGGGATCGGGATC+GGG 0.362198 3.2:+71135998 MS.gene25756:CDS
AAAGGGATCGGGATCGGGAT+CGG 0.404103 3.2:+71135997 MS.gene25756:CDS
ATCGGGATCGGGATCGGGAT+TGG 0.407528 3.2:+71136003 MS.gene25756:CDS
TGGAGTGTCCTTCGAGAATA+GGG 0.410247 3.2:-71136380 None:intergenic
ACAGAGAATGGAACAGAAAC+AGG 0.416228 3.2:+71135970 None:intergenic
GGCTCAAATTCAAATCTATA+CGG 0.426055 3.2:+71136144 MS.gene25756:CDS
TTGGAGTGTCCTTCGAGAAT+AGG 0.428317 3.2:-71136381 None:intergenic
AGTATAAGAATGAGGCATAT+AGG 0.441135 3.2:+71136113 MS.gene25756:CDS
GATTCCGACTTTCCTTATTA+CGG 0.458848 3.2:+71136073 MS.gene25756:CDS
GCTTGGAAAGTTGTTAAAGC+AGG 0.466031 3.2:-71136643 None:intergenic
ATAGATTCTACCATTAATAA+GGG 0.476198 3.2:-71136575 None:intergenic
GAGAATAGGGCGAACATCAT+CGG 0.483809 3.2:-71136367 None:intergenic
GTACGTCACAAGATCTTCAA+TGG 0.490169 3.2:-71136035 None:intergenic
TTCTACCATTAATAAGGGCA+TGG 0.508172 3.2:-71136570 None:intergenic
AGGCCATGAAACACAAAAGC+TGG 0.508489 3.2:-71136535 None:intergenic
ATTAAATGTGATCTTGGTGG+AGG 0.515471 3.2:-71136312 None:intergenic
AGGACACTCCAAGCTTGCAT+TGG 0.517715 3.2:+71136392 MS.gene25756:CDS
AAAATTAAATGTGATCTTGG+TGG 0.523290 3.2:-71136315 None:intergenic
GTAATAGTCCAATGCAAGCT+TGG 0.525102 3.2:-71136400 None:intergenic
TACGTCACAAGATCTTCAAT+GGG 0.528436 3.2:-71136034 None:intergenic
CTTGGAAAGTTGTTAAAGCA+GGG 0.540365 3.2:-71136642 None:intergenic
TTTCCTTATTACGGCAAACG+TGG 0.562249 3.2:+71136082 MS.gene25756:CDS
AACATCATCGGAAATGTGAA+GGG 0.573072 3.2:-71136355 None:intergenic
GAACATCATCGGAAATGTGA+AGG 0.574469 3.2:-71136356 None:intergenic
GAACACAGCATACTTCAGCT+TGG 0.589049 3.2:-71136660 None:intergenic
TCTACCATTAATAAGGGCAT+GGG 0.593250 3.2:-71136569 None:intergenic
TAAATGTGATCTTGGTGGAG+GGG 0.597056 3.2:-71136310 None:intergenic
AGTTGTTAAAGCAGGGGTGT+CGG 0.599691 3.2:-71136635 None:intergenic
TTAAATGTGATCTTGGTGGA+GGG 0.609839 3.2:-71136311 None:intergenic
GCACACTCTCTGATCTCAGG+TGG 0.621362 3.2:-71136722 None:intergenic
TTGGAAAGTTGTTAAAGCAG+GGG 0.623852 3.2:-71136641 None:intergenic
GATGTTCGCCCTATTCTCGA+AGG 0.637823 3.2:+71136372 MS.gene25756:CDS
GGGCATGGGTACACTTAACA+AGG 0.642669 3.2:-71136555 None:intergenic
TTTGCCGTAATAAGGAAAGT+CGG 0.657780 3.2:-71136077 None:intergenic
TGAGGCATATAGGATGCTTG+AGG 0.663425 3.2:+71136123 MS.gene25756:CDS
TGTTCGAGATAAACAACCTG+TGG 0.664849 3.2:+71136678 MS.gene25756:CDS
ACATCATCGGAAATGTGAAG+GGG 0.674764 3.2:-71136354 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAAATTAAATGTGATCT+TGG - chr3.2:71136321-71136340 None:intergenic 15.0%
!!! AAGATCACATTTAATTTTAA+TGG + chr3.2:71136320-71136339 MS.gene25756:CDS 15.0%
!!! AGATCACATTTAATTTTAAT+GGG + chr3.2:71136321-71136340 MS.gene25756:CDS 15.0%
!! AATAGATTCTACCATTAATA+AGG - chr3.2:71136579-71136598 None:intergenic 20.0%
!! AGAAGAACAATTAATTAGTT+TGG - chr3.2:71136495-71136514 None:intergenic 20.0%
!! ATAGATTCTACCATTAATAA+GGG - chr3.2:71136578-71136597 None:intergenic 20.0%
!! TTAATTCATTCATTCATTCT+TGG + chr3.2:71136252-71136271 MS.gene25756:intron 20.0%
!! TTCTTCACTATGTTATATTA+GGG + chr3.2:71136511-71136530 MS.gene25756:intron 20.0%
!!! TAATTTTGAGTATAAGAATG+AGG + chr3.2:71136105-71136124 MS.gene25756:CDS 20.0%
! AAAATTAAATGTGATCTTGG+TGG - chr3.2:71136318-71136337 None:intergenic 25.0%
! CTTCTTCACTATGTTATATT+AGG + chr3.2:71136510-71136529 MS.gene25756:intron 25.0%
!!! TCACATTTAATTTTAATGGG+CGG + chr3.2:71136324-71136343 MS.gene25756:CDS 25.0%
AGTATAAGAATGAGGCATAT+AGG + chr3.2:71136113-71136132 MS.gene25756:CDS 30.0%
GGCTCAAATTCAAATCTATA+CGG + chr3.2:71136144-71136163 MS.gene25756:CDS 30.0%
!!! CCTGATTACTGTTTTTTTCA+CGG - chr3.2:71136425-71136444 None:intergenic 30.0%
AACATCATCGGAAATGTGAA+GGG - chr3.2:71136358-71136377 None:intergenic 35.0%
ATAGATAGATGCGTACACTT+AGG - chr3.2:71136183-71136202 None:intergenic 35.0%
ATTAAATGTGATCTTGGTGG+AGG - chr3.2:71136315-71136334 None:intergenic 35.0%
CCGTGAAAAAAACAGTAATC+AGG + chr3.2:71136422-71136441 MS.gene25756:CDS 35.0%
CTTGGAAAGTTGTTAAAGCA+GGG - chr3.2:71136645-71136664 None:intergenic 35.0%
GAACAGAAACAGGTGAAAAA+GGG + chr3.2:71135980-71135999 MS.gene25756:CDS 35.0%
GATTCCGACTTTCCTTATTA+CGG + chr3.2:71136073-71136092 MS.gene25756:CDS 35.0%
TACGTCACAAGATCTTCAAT+GGG - chr3.2:71136037-71136056 None:intergenic 35.0%
TTAAATGTGATCTTGGTGGA+GGG - chr3.2:71136314-71136333 None:intergenic 35.0%
TTCTACCATTAATAAGGGCA+TGG - chr3.2:71136573-71136592 None:intergenic 35.0%
TTGGAAAGTTGTTAAAGCAG+GGG - chr3.2:71136644-71136663 None:intergenic 35.0%
TTTGCCGTAATAAGGAAAGT+CGG - chr3.2:71136080-71136099 None:intergenic 35.0%
! AAGATCATCTTCAGCTTTTG+TGG - chr3.2:71136614-71136633 None:intergenic 35.0%
! ATCTTCAGCTTTTGTGGTAA+AGG - chr3.2:71136608-71136627 None:intergenic 35.0%
! TCTACCATTAATAAGGGCAT+GGG - chr3.2:71136572-71136591 None:intergenic 35.0%
AAACAGGTGAAAAAGGGATC+GGG + chr3.2:71135986-71136005 MS.gene25756:CDS 40.0%
ACATCATCGGAAATGTGAAG+GGG - chr3.2:71136357-71136376 None:intergenic 40.0%
GAAACAGGTGAAAAAGGGAT+CGG + chr3.2:71135985-71136004 MS.gene25756:CDS 40.0%
GAACATCATCGGAAATGTGA+AGG - chr3.2:71136359-71136378 None:intergenic 40.0%
GCTTGGAAAGTTGTTAAAGC+AGG - chr3.2:71136646-71136665 None:intergenic 40.0%
GGAACAGAAACAGGTGAAAA+AGG + chr3.2:71135979-71135998 MS.gene25756:CDS 40.0%
GTAATAGTCCAATGCAAGCT+TGG - chr3.2:71136403-71136422 None:intergenic 40.0%
GTACGTCACAAGATCTTCAA+TGG - chr3.2:71136038-71136057 None:intergenic 40.0%
TAAATGTGATCTTGGTGGAG+GGG - chr3.2:71136313-71136332 None:intergenic 40.0%
TGTACCCATGCCCTTATTAA+TGG + chr3.2:71136565-71136584 MS.gene25756:CDS 40.0%
TGTTCGAGATAAACAACCTG+TGG + chr3.2:71136678-71136697 MS.gene25756:CDS 40.0%
TTACCACGTTTGCCGTAATA+AGG - chr3.2:71136088-71136107 None:intergenic 40.0%
TTTCCTTATTACGGCAAACG+TGG + chr3.2:71136082-71136101 MS.gene25756:CDS 40.0%
AGGCCATGAAACACAAAAGC+TGG - chr3.2:71136538-71136557 None:intergenic 45.0%
GAACACAGCATACTTCAGCT+TGG - chr3.2:71136663-71136682 None:intergenic 45.0%
GAGAATAGGGCGAACATCAT+CGG - chr3.2:71136370-71136389 None:intergenic 45.0%
TGAGGCATATAGGATGCTTG+AGG + chr3.2:71136123-71136142 MS.gene25756:CDS 45.0%
TGGATAACACAACACAACGC+AGG + chr3.2:71136272-71136291 MS.gene25756:intron 45.0%
! AGTTGTTAAAGCAGGGGTGT+CGG - chr3.2:71136638-71136657 None:intergenic 45.0%
! GGTCCAGCTTTTGTGTTTCA+TGG + chr3.2:71136532-71136551 MS.gene25756:CDS 45.0%
! TGGAGTGTCCTTCGAGAATA+GGG - chr3.2:71136383-71136402 None:intergenic 45.0%
! TTGGAGTGTCCTTCGAGAAT+AGG - chr3.2:71136384-71136403 None:intergenic 45.0%
!! ATGGCACACTTTTTGACCAC+AGG - chr3.2:71136697-71136716 None:intergenic 45.0%
AGGACACTCCAAGCTTGCAT+TGG + chr3.2:71136392-71136411 MS.gene25756:CDS 50.0%
GATGTTCGCCCTATTCTCGA+AGG + chr3.2:71136372-71136391 MS.gene25756:CDS 50.0%
GGGCATGGGTACACTTAACA+AGG - chr3.2:71136558-71136577 None:intergenic 50.0%
GGTGAAAAAGGGATCGGGAT+CGG + chr3.2:71135991-71136010 MS.gene25756:CDS 50.0%
GTGAAAAAGGGATCGGGATC+GGG + chr3.2:71135992-71136011 MS.gene25756:CDS 50.0%
AAAGGGATCGGGATCGGGAT+CGG + chr3.2:71135997-71136016 MS.gene25756:CDS 55.0%
AAGGGATCGGGATCGGGATC+GGG + chr3.2:71135998-71136017 MS.gene25756:CDS 60.0%
ATCGGGATCGGGATCGGGAT+TGG + chr3.2:71136003-71136022 MS.gene25756:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 71135977 71136729 71135977 ID=MS.gene25756
chr3.2 mRNA 71135977 71136729 71135977 ID=MS.gene25756.t1;Parent=MS.gene25756
chr3.2 exon 71135977 71136186 71135977 ID=MS.gene25756.t1.exon1;Parent=MS.gene25756.t1
chr3.2 CDS 71135977 71136186 71135977 ID=cds.MS.gene25756.t1;Parent=MS.gene25756.t1
chr3.2 exon 71136294 71136443 71136294 ID=MS.gene25756.t1.exon2;Parent=MS.gene25756.t1
chr3.2 CDS 71136294 71136443 71136294 ID=cds.MS.gene25756.t1;Parent=MS.gene25756.t1
chr3.2 exon 71136532 71136729 71136532 ID=MS.gene25756.t1.exon3;Parent=MS.gene25756.t1
chr3.2 CDS 71136532 71136729 71136532 ID=cds.MS.gene25756.t1;Parent=MS.gene25756.t1
Gene Sequence

>MS.gene25756

ATGGAACAGAAACAGGTGAAAAAGGGATCGGGATCGGGATCGGGATTGGAAGAGAAACCCATTGAAGATCTTGTGACGTACTTCTCTAAGCATGACGATTCCGACTTTCCTTATTACGGCAAACGTGGTAATTTTGAGTATAAGAATGAGGCATATAGGATGCTTGAGGCTCAAATTCAAATCTATACGGAGAAGTCTCGCAACCTAAGTGTACGCATCTATCTATCTATCTATCTATCTATTTCAATTTTGTTTTTAATTTCACTCTCTTCATTTTAATTCATTCATTCATTCTTGGATAACACAACACAACGCAGGAGTACGATGCTATCGCCCCTCCACCAAGATCACATTTAATTTTAATGGGCGGTATCATACCCCTTCACATTTCCGATGATGTTCGCCCTATTCTCGAAGGACACTCCAAGCTTGCATTGGACTATTACCGTGAAAAAAACAGTAATCAGGTTCGATACTAAGAGAATGAATTTTTTTGTATGTTGTTTATTCATTAACCAAACTAATTAATTGTTCTTCTTCACTATGTTATATTAGGGTCCAGCTTTTGTGTTTCATGGCCTTGTTAAGTGTACCCATGCCCTTATTAATGGTAGAATCTATTACATTACCTTTACCACAAAAGCTGAAGATGATCTTTCCGACACCCCTGCTTTAACAACTTTCCAAGCTGAAGTATGCTGTGTTCGAGATAAACAACCTGTGGTCAAAAAGTGTGCCATTAAAACCACCTGA
Protein sequence

>MS.gene25756.t1

MEQKQVKKGSGSGSGLEEKPIEDLVTYFSKHDDSDFPYYGKRGNFEYKNEAYRMLEAQIQIYTEKSRNLSEYDAIAPPPRSHLILMGGIIPLHISDDVRPILEGHSKLALDYYREKNSNQGPAFVFHGLVKCTHALINGRIYYITFTTKAEDDLSDTPALTTFQAEVCCVRDKQPVVKKCAIKTT