AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1425100


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1425100 MtrunA17_Chr1g0179671 94.891 411 21 0 1 411 1 411 0.0 767
Msa1425100 MtrunA17_Chr8g0340991 23.611 360 232 8 12 336 22 373 9.38e-19 88.6
Msa1425100 MtrunA17_Chr2g0330791 21.485 377 224 6 10 336 9 363 9.97e-16 79.0
Msa1425100 MtrunA17_Chr5g0422391 25.155 322 211 6 98 411 125 424 8.78e-14 73.6
Msa1425100 MtrunA17_Chr1g0198861 25.097 259 168 3 96 335 124 375 4.11e-12 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1425100 AT2G36650.1 30.154 325 181 3 11 335 13 291 2.90e-34 131
Msa1425100 AT3G25690.5 25.301 249 186 0 100 348 132 380 2.89e-15 78.6
Msa1425100 AT3G25690.1 25.100 251 188 0 98 348 128 378 2.99e-15 78.6
Msa1425100 AT3G25690.2 25.100 251 188 0 98 348 128 378 2.99e-15 78.6
Msa1425100 AT3G25690.6 25.100 251 188 0 98 348 128 378 2.99e-15 78.6
Msa1425100 AT3G25690.4 25.100 251 188 0 98 348 128 378 2.99e-15 78.6
Msa1425100 AT1G52080.2 26.812 276 180 4 98 366 138 398 4.24e-12 68.2
Msa1425100 AT1G52080.1 26.812 276 180 4 98 366 138 398 4.24e-12 68.2

Find 38 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAAGATTAATGTTTGTTTA+AGG 0.192588 tig0025825:+1293 Msa1425100:CDS
TAGAGAGCTGAAAAGGGTTT+TGG 0.249773 tig0025825:+1057 Msa1425100:CDS
TGACCCTTCTAGTTCCAAAA+AGG 0.258156 tig0025825:+1399 Msa1425100:CDS
GGCTCAATCTCATTTGATTA+AGG 0.274337 tig0025825:+934 Msa1425100:CDS
ACACCAGCTTTGAGGATAAT+AGG 0.296488 tig0025825:-365 None:intergenic
TTTCAATAATCTTAAGGTAT+TGG 0.311191 tig0025825:-841 None:intergenic
TTATTGAAAAGCTTGAATAT+TGG 0.323357 tig0025825:+855 Msa1425100:CDS
CAACAAGATTCTGAATGAAT+TGG 0.330904 tig0025825:+1219 Msa1425100:CDS
ATGAAATTAGAGAGCTGAAA+AGG 0.337337 tig0025825:+1050 Msa1425100:CDS
ACATCATGAGAATTGACTTC+AGG 0.356940 tig0025825:-488 None:intergenic
CTTGAGACATCAGAAGAATA+TGG 0.358484 tig0025825:+1118 Msa1425100:CDS
TCTTTCTGAGAGATTTGGTT+TGG 0.365727 tig0025825:+598 Msa1425100:CDS
AGTGTTCTTTCTGAGAGATT+TGG 0.368051 tig0025825:+593 Msa1425100:CDS
AGTAATGAAATTAAGTGCTT+TGG 0.382181 tig0025825:+1496 Msa1425100:CDS
GAGCAAAACCTTGGAGTAGC+TGG 0.400491 tig0025825:-1532 None:intergenic
TTTGTCAAATTGTAAAGTTA+AGG 0.415691 tig0025825:-678 None:intergenic
TGAAATTAGAGAGCTGAAAA+GGG 0.459539 tig0025825:+1051 Msa1425100:CDS
CTATAGGAACACCAGCTTTG+AGG 0.462456 tig0025825:-373 None:intergenic
TGCTTAAGAAGCAAGATTGA+AGG 0.471674 tig0025825:+635 Msa1425100:CDS
TTGCTGGTTTGATCTATGCA+TGG 0.476381 tig0025825:+405 Msa1425100:CDS
TGAATCAAGAGATGTTATGA+AGG 0.483238 tig0025825:+1189 Msa1425100:CDS
CCAGCAAAAGAAACAGCTAT+AGG 0.492610 tig0025825:-389 None:intergenic
AAGAACACTACTATCTATAG+AGG 0.498832 tig0025825:-579 None:intergenic
ATCTGCAAATAATATTTCAA+AGG 0.499256 tig0025825:-1166 None:intergenic
TTGGGTGGATGGTAGTGAAA+AGG 0.500899 tig0025825:+1447 Msa1425100:CDS
CATCAAAATGTGTCTTGCAT+TGG 0.501895 tig0025825:+1358 Msa1425100:CDS
ATGAGAGTCAGTTTCTGAAA+AGG 0.515828 tig0025825:-462 None:intergenic
TGAATTGGAGCAAGTTAAGA+AGG 0.519910 tig0025825:+1234 Msa1425100:CDS
CAAACTTTGATGATCAAAGA+AGG 0.530552 tig0025825:+959 Msa1425100:CDS
TTGAAGAACTTATTTACTTG+AGG 0.545043 tig0025825:+1272 Msa1425100:CDS
CATCATGAGAATTGACTTCA+GGG 0.556455 tig0025825:-487 None:intergenic
AAGCCTATTATCCTCAAAGC+TGG 0.568812 tig0025825:+362 Msa1425100:CDS
TCATAGAAACAGAAACTATG+AGG 0.580497 tig0025825:+801 Msa1425100:CDS
GAAGCTACTTAAGAAATCAA+AGG 0.584610 tig0025825:+913 Msa1425100:CDS
ATTCTGCTCCAGCTACTCCA+AGG 0.615340 tig0025825:+1524 Msa1425100:CDS
TAAGCACTAGAGCAAAACCT+TGG 0.616488 tig0025825:-1541 None:intergenic
AAGGTTAAAGTGAAACCAGA+AGG 0.618245 tig0025825:+1466 Msa1425100:CDS
ATCATGAGAATTGACTTCAG+GGG 0.687779 tig0025825:-486 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGATAACTTTTCTTCTA+TGG + tig0025825:529-548 Msa1425100:CDS 20.0%
!! TTTGTCAAATTGTAAAGTTA+AGG - tig0025825:681-700 None:intergenic 20.0%
!! AATCAAAAACATGTTATCAT+TGG + tig0025825:739-758 Msa1425100:CDS 20.0%
!! TTTCAATAATCTTAAGGTAT+TGG - tig0025825:844-863 None:intergenic 20.0%
!! TTATTGAAAAGCTTGAATAT+TGG + tig0025825:855-874 Msa1425100:CDS 20.0%
!! ATCTGCAAATAATATTTCAA+AGG - tig0025825:1169-1188 None:intergenic 20.0%
!! TGATTAAAAAGCTGAAAAAT+TGG + tig0025825:1428-1447 Msa1425100:CDS 20.0%
!! GATTAAAAAGCTGAAAAATT+GGG + tig0025825:1429-1448 Msa1425100:CDS 20.0%
!!! TTTTGATAACTTTTCTTCTA+TGG + tig0025825:529-548 Msa1425100:CDS 20.0%
!! TTTGTCAAATTGTAAAGTTA+AGG - tig0025825:681-700 None:intergenic 20.0%
!! AATCAAAAACATGTTATCAT+TGG + tig0025825:739-758 Msa1425100:CDS 20.0%
!! TTTCAATAATCTTAAGGTAT+TGG - tig0025825:844-863 None:intergenic 20.0%
!! TTATTGAAAAGCTTGAATAT+TGG + tig0025825:855-874 Msa1425100:CDS 20.0%
!! ATCTGCAAATAATATTTCAA+AGG - tig0025825:1169-1188 None:intergenic 20.0%
!! TGATTAAAAAGCTGAAAAAT+TGG + tig0025825:1428-1447 Msa1425100:CDS 20.0%
!! GATTAAAAAGCTGAAAAATT+GGG + tig0025825:1429-1448 Msa1425100:CDS 20.0%
!! CAAGCTTTTCAATAATCTTA+AGG - tig0025825:850-869 None:intergenic 25.0%
! ACTATGATGAATTGCAAAAA+AGG + tig0025825:1002-1021 Msa1425100:CDS 25.0%
! CTATGATGAATTGCAAAAAA+GGG + tig0025825:1003-1022 Msa1425100:CDS 25.0%
! TTGAAGAACTTATTTACTTG+AGG + tig0025825:1272-1291 Msa1425100:CDS 25.0%
! GGAAGATTAATGTTTGTTTA+AGG + tig0025825:1293-1312 Msa1425100:CDS 25.0%
!!! TGAATTGCATTGTTCTTTTT+TGG + tig0025825:1333-1352 Msa1425100:CDS 25.0%
!! TTTAATCAACTTTCCCTTTT+TGG - tig0025825:1416-1435 None:intergenic 25.0%
! AGTAATGAAATTAAGTGCTT+TGG + tig0025825:1496-1515 Msa1425100:CDS 25.0%
!! CAAGCTTTTCAATAATCTTA+AGG - tig0025825:850-869 None:intergenic 25.0%
! ACTATGATGAATTGCAAAAA+AGG + tig0025825:1002-1021 Msa1425100:CDS 25.0%
! CTATGATGAATTGCAAAAAA+GGG + tig0025825:1003-1022 Msa1425100:CDS 25.0%
! TTGAAGAACTTATTTACTTG+AGG + tig0025825:1272-1291 Msa1425100:CDS 25.0%
! GGAAGATTAATGTTTGTTTA+AGG + tig0025825:1293-1312 Msa1425100:CDS 25.0%
!!! TGAATTGCATTGTTCTTTTT+TGG + tig0025825:1333-1352 Msa1425100:CDS 25.0%
!! TTTAATCAACTTTCCCTTTT+TGG - tig0025825:1416-1435 None:intergenic 25.0%
! AGTAATGAAATTAAGTGCTT+TGG + tig0025825:1496-1515 Msa1425100:CDS 25.0%
AAGAACACTACTATCTATAG+AGG - tig0025825:582-601 None:intergenic 30.0%
TCATAGAAACAGAAACTATG+AGG + tig0025825:801-820 Msa1425100:CDS 30.0%
GAAGCTACTTAAGAAATCAA+AGG + tig0025825:913-932 Msa1425100:CDS 30.0%
! CAAACTTTGATGATCAAAGA+AGG + tig0025825:959-978 Msa1425100:CDS 30.0%
ATGAAATTAGAGAGCTGAAA+AGG + tig0025825:1050-1069 Msa1425100:CDS 30.0%
TGAAATTAGAGAGCTGAAAA+GGG + tig0025825:1051-1070 Msa1425100:CDS 30.0%
TGAATCAAGAGATGTTATGA+AGG + tig0025825:1189-1208 Msa1425100:CDS 30.0%
CAACAAGATTCTGAATGAAT+TGG + tig0025825:1219-1238 Msa1425100:CDS 30.0%
TAAAAAGCTGAAAAATTGGG+TGG + tig0025825:1432-1451 Msa1425100:CDS 30.0%
AAGAACACTACTATCTATAG+AGG - tig0025825:582-601 None:intergenic 30.0%
TCATAGAAACAGAAACTATG+AGG + tig0025825:801-820 Msa1425100:CDS 30.0%
GAAGCTACTTAAGAAATCAA+AGG + tig0025825:913-932 Msa1425100:CDS 30.0%
! CAAACTTTGATGATCAAAGA+AGG + tig0025825:959-978 Msa1425100:CDS 30.0%
ATGAAATTAGAGAGCTGAAA+AGG + tig0025825:1050-1069 Msa1425100:CDS 30.0%
TGAAATTAGAGAGCTGAAAA+GGG + tig0025825:1051-1070 Msa1425100:CDS 30.0%
TGAATCAAGAGATGTTATGA+AGG + tig0025825:1189-1208 Msa1425100:CDS 30.0%
CAACAAGATTCTGAATGAAT+TGG + tig0025825:1219-1238 Msa1425100:CDS 30.0%
TAAAAAGCTGAAAAATTGGG+TGG + tig0025825:1432-1451 Msa1425100:CDS 30.0%
! ATGAGAGTCAGTTTCTGAAA+AGG - tig0025825:465-484 None:intergenic 35.0%
! ATCATGAGAATTGACTTCAG+GGG - tig0025825:489-508 None:intergenic 35.0%
! CATCATGAGAATTGACTTCA+GGG - tig0025825:490-509 None:intergenic 35.0%
! ACATCATGAGAATTGACTTC+AGG - tig0025825:491-510 None:intergenic 35.0%
! AGTGTTCTTTCTGAGAGATT+TGG + tig0025825:593-612 Msa1425100:CDS 35.0%
! TCTTTCTGAGAGATTTGGTT+TGG + tig0025825:598-617 Msa1425100:CDS 35.0%
TGCTTAAGAAGCAAGATTGA+AGG + tig0025825:635-654 Msa1425100:CDS 35.0%
GGCTCAATCTCATTTGATTA+AGG + tig0025825:934-953 Msa1425100:CDS 35.0%
CTTGAGACATCAGAAGAATA+TGG + tig0025825:1118-1137 Msa1425100:CDS 35.0%
TGAATTGGAGCAAGTTAAGA+AGG + tig0025825:1234-1253 Msa1425100:CDS 35.0%
CATCAAAATGTGTCTTGCAT+TGG + tig0025825:1358-1377 Msa1425100:CDS 35.0%
!!! TTCCCTTTTTGGAACTAGAA+GGG - tig0025825:1405-1424 None:intergenic 35.0%
!!! TTTCCCTTTTTGGAACTAGA+AGG - tig0025825:1406-1425 None:intergenic 35.0%
AAGGTTAAAGTGAAACCAGA+AGG + tig0025825:1466-1485 Msa1425100:CDS 35.0%
!! TCATTACTGCTTTTACCTTC+TGG - tig0025825:1484-1503 None:intergenic 35.0%
! ATGAGAGTCAGTTTCTGAAA+AGG - tig0025825:465-484 None:intergenic 35.0%
! ATCATGAGAATTGACTTCAG+GGG - tig0025825:489-508 None:intergenic 35.0%
! CATCATGAGAATTGACTTCA+GGG - tig0025825:490-509 None:intergenic 35.0%
! ACATCATGAGAATTGACTTC+AGG - tig0025825:491-510 None:intergenic 35.0%
! AGTGTTCTTTCTGAGAGATT+TGG + tig0025825:593-612 Msa1425100:CDS 35.0%
! TCTTTCTGAGAGATTTGGTT+TGG + tig0025825:598-617 Msa1425100:CDS 35.0%
TGCTTAAGAAGCAAGATTGA+AGG + tig0025825:635-654 Msa1425100:CDS 35.0%
GGCTCAATCTCATTTGATTA+AGG + tig0025825:934-953 Msa1425100:CDS 35.0%
CTTGAGACATCAGAAGAATA+TGG + tig0025825:1118-1137 Msa1425100:CDS 35.0%
TGAATTGGAGCAAGTTAAGA+AGG + tig0025825:1234-1253 Msa1425100:CDS 35.0%
CATCAAAATGTGTCTTGCAT+TGG + tig0025825:1358-1377 Msa1425100:CDS 35.0%
!!! TTCCCTTTTTGGAACTAGAA+GGG - tig0025825:1405-1424 None:intergenic 35.0%
!!! TTTCCCTTTTTGGAACTAGA+AGG - tig0025825:1406-1425 None:intergenic 35.0%
AAGGTTAAAGTGAAACCAGA+AGG + tig0025825:1466-1485 Msa1425100:CDS 35.0%
!! TCATTACTGCTTTTACCTTC+TGG - tig0025825:1484-1503 None:intergenic 35.0%
AAGCCTATTATCCTCAAAGC+TGG + tig0025825:362-381 Msa1425100:CDS 40.0%
!! ACACCAGCTTTGAGGATAAT+AGG - tig0025825:368-387 None:intergenic 40.0%
CCAGCAAAAGAAACAGCTAT+AGG - tig0025825:392-411 None:intergenic 40.0%
!!! CCTATAGCTGTTTCTTTTGC+TGG + tig0025825:389-408 Msa1425100:CDS 40.0%
!! TTGCTGGTTTGATCTATGCA+TGG + tig0025825:405-424 Msa1425100:CDS 40.0%
! TAGAGAGCTGAAAAGGGTTT+TGG + tig0025825:1057-1076 Msa1425100:CDS 40.0%
!! TGACCCTTCTAGTTCCAAAA+AGG + tig0025825:1399-1418 Msa1425100:CDS 40.0%
!! GACCCTTCTAGTTCCAAAAA+GGG + tig0025825:1400-1419 Msa1425100:CDS 40.0%
AAGCTGAAAAATTGGGTGGA+TGG + tig0025825:1436-1455 Msa1425100:CDS 40.0%
TAAGCACTAGAGCAAAACCT+TGG - tig0025825:1544-1563 None:intergenic 40.0%
AAGCCTATTATCCTCAAAGC+TGG + tig0025825:362-381 Msa1425100:CDS 40.0%
!! ACACCAGCTTTGAGGATAAT+AGG - tig0025825:368-387 None:intergenic 40.0%
CCAGCAAAAGAAACAGCTAT+AGG - tig0025825:392-411 None:intergenic 40.0%
!!! CCTATAGCTGTTTCTTTTGC+TGG + tig0025825:389-408 Msa1425100:CDS 40.0%
!! TTGCTGGTTTGATCTATGCA+TGG + tig0025825:405-424 Msa1425100:CDS 40.0%
! TAGAGAGCTGAAAAGGGTTT+TGG + tig0025825:1057-1076 Msa1425100:CDS 40.0%
!! TGACCCTTCTAGTTCCAAAA+AGG + tig0025825:1399-1418 Msa1425100:CDS 40.0%
!! GACCCTTCTAGTTCCAAAAA+GGG + tig0025825:1400-1419 Msa1425100:CDS 40.0%
AAGCTGAAAAATTGGGTGGA+TGG + tig0025825:1436-1455 Msa1425100:CDS 40.0%
TAAGCACTAGAGCAAAACCT+TGG - tig0025825:1544-1563 None:intergenic 40.0%
CTATAGGAACACCAGCTTTG+AGG - tig0025825:376-395 None:intergenic 45.0%
! TTGGGTGGATGGTAGTGAAA+AGG + tig0025825:1447-1466 Msa1425100:CDS 45.0%
CTATAGGAACACCAGCTTTG+AGG - tig0025825:376-395 None:intergenic 45.0%
! TTGGGTGGATGGTAGTGAAA+AGG + tig0025825:1447-1466 Msa1425100:CDS 45.0%
ATTCTGCTCCAGCTACTCCA+AGG + tig0025825:1524-1543 Msa1425100:CDS 50.0%
GAGCAAAACCTTGGAGTAGC+TGG - tig0025825:1535-1554 None:intergenic 50.0%
ATTCTGCTCCAGCTACTCCA+AGG + tig0025825:1524-1543 Msa1425100:CDS 50.0%
GAGCAAAACCTTGGAGTAGC+TGG - tig0025825:1535-1554 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0025825 gene 329 1564 329 ID=Msa1425100;Name=Msa1425100
tig0025825 mRNA 329 1564 329 ID=Msa1425100-mRNA-1;Parent=Msa1425100;Name=Msa1425100-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|411
tig0025825 exon 329 1564 329 ID=Msa1425100-mRNA-1:exon:4131;Parent=Msa1425100-mRNA-1
tig0025825 CDS 329 1564 329 ID=Msa1425100-mRNA-1:cds;Parent=Msa1425100-mRNA-1
Gene Sequence

>Msa1425100

ATGGAAAACTCAACGCTTAAAGCTGAGAATCTAAAGCCTATTATCCTCAAAGCTGGTGTTCCTATAGCTGTTTCTTTTGCTGGTTTGATCTATGCATGGATCATAACAAAGAAAAGCTTATCAAATGTCTCTTCCTTTTCAGAAACTGACTCTCATACCCCTGAAGTCAATTCTCATGATGTAACTCAACATGAAGAAAGTTTTGATAACTTTTCTTCTATGGAAGATGAAGAAAAAGAAGAATACACTACCTCTATAGATAGTAGTGTTCTTTCTGAGAGATTTGGTTTGGAACAAGAGATTGCTTGCTTAAGAAGCAAGATTGAAGGTATGCAAATGAGAGAATTAGCCTTAACTTTACAATTTGACAAATATTGTGAAATGAAAGAAAAAGAATCTATGCTTAGAGAAATCAAAAACATGTTATCATTGGAGACATCTCGTGTCGAATTCTTCGATAGAGAGATTTCATTCATAGAAACAGAAACTATGAGGTTAGAGAATTTTGTAATCCAATACCTTAAGATTATTGAAAAGCTTGAATATTGGAAATCAGAGAATAGATTGCTTCAGAAGAAAGTTCAGAAGCTACTTAAGAAATCAAAGGCTCAATCTCATTTGATTAAGGAGCAAACTTTGATGATCAAAGAAGGAGAAGAAGAAATCTTGAGAAACTATGATGAATTGCAAAAAAGGGCTAATATGATTCATAAGTTAGAAGATGAAATTAGAGAGCTGAAAAGGGTTTTGGATGATTTTCAAGATGAGAAGAATGAACTTGTGAAGAAGCTTGAGACATCAGAAGAATATGGATGTAAAGAAGAGCTACATAAAAAGCCTTTGAAATATTATTTGCAGATTGAATCAAGAGATGTTATGAAGGAAGATTACAACAAGATTCTGAATGAATTGGAGCAAGTTAAGAAGGAACATGAAAATGAAATTGAAGAACTTATTTACTTGAGGAAGATTAATGTTTGTTTAAGGCAAGAGTTAATGAAGCATGAATTGCATTGTTCTTTTTTGGATCATCAAAATGTGTCTTGCATTGGTTCTTCTACTTTTCATTGTGACCCTTCTAGTTCCAAAAAGGGAAAGTTGATTAAAAAGCTGAAAAATTGGGTGGATGGTAGTGAAAAGGTTAAAGTGAAACCAGAAGGTAAAAGCAGTAATGAAATTAAGTGCTTTGGTATGAATTCTGCTCCAGCTACTCCAAGGTTTTGCTCTAGTGCTTAG

Protein sequence

>Msa1425100

MENSTLKAENLKPIILKAGVPIAVSFAGLIYAWIITKKSLSNVSSFSETDSHTPEVNSHDVTQHEESFDNFSSMEDEEKEEYTTSIDSSVLSERFGLEQEIACLRSKIEGMQMRELALTLQFDKYCEMKEKESMLREIKNMLSLETSRVEFFDREISFIETETMRLENFVIQYLKIIEKLEYWKSENRLLQKKVQKLLKKSKAQSHLIKEQTLMIKEGEEEILRNYDELQKRANMIHKLEDEIRELKRVLDDFQDEKNELVKKLETSEEYGCKEELHKKPLKYYLQIESRDVMKEDYNKILNELEQVKKEHENEIEELIYLRKINVCLRQELMKHELHCSFLDHQNVSCIGSSTFHCDPSSSKKGKLIKKLKNWVDGSEKVKVKPEGKSSNEIKCFGMNSAPATPRFCSSA*