AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043976

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043976.t1 MTR_1g021320 95.098 204 8 2 1 202 197 400 2.31e-134 397
MS.gene043976.t1 MTR_1g021320 72.868 129 35 0 1 129 40 168 1.82e-59 199
MS.gene043976.t1 MTR_1g021440 66.316 190 53 2 1 188 37 217 8.41e-85 252
MS.gene043976.t1 MTR_1g021440 66.316 190 53 2 1 188 37 217 1.05e-84 253
MS.gene043976.t1 MTR_1g021440 66.316 190 53 2 1 188 37 217 2.96e-83 252
MS.gene043976.t1 MTR_1g021440 66.316 190 53 2 1 188 37 217 5.16e-83 251
MS.gene043976.t1 MTR_1g021350 62.371 194 52 2 1 194 36 208 2.62e-78 238
MS.gene043976.t1 MTR_1g021330 64.706 187 56 3 1 187 41 217 3.59e-76 234
MS.gene043976.t1 MTR_1g021435 60.638 188 40 1 1 188 37 190 3.16e-71 221
MS.gene043976.t1 MTR_1g021290 62.136 206 38 2 1 203 170 338 3.08e-70 217
MS.gene043976.t1 MTR_1g021290 71.287 101 29 0 1 101 42 142 8.51e-47 157
MS.gene043976.t1 MTR_1g021400 65.644 163 49 2 1 163 45 200 1.16e-64 204
MS.gene043976.t1 MTR_1g021410 62.805 164 54 2 1 163 37 194 6.58e-61 194
MS.gene043976.t1 MTR_1g021360 72.868 129 35 0 1 129 40 168 2.46e-59 193
MS.gene043976.t1 MTR_1g021360 53.968 189 31 2 1 189 197 329 3.68e-58 190
MS.gene043976.t1 MTR_1g021380 54.255 188 37 3 1 188 36 174 1.79e-56 182
MS.gene043976.t1 MTR_1g021500 47.556 225 78 6 1 203 41 247 1.53e-53 177
MS.gene043976.t1 MTR_1g021500 47.556 225 78 6 1 203 41 247 3.44e-53 177
MS.gene043976.t1 MTR_1g021270 47.143 70 36 1 18 87 47 115 5.36e-16 75.9
MS.gene043976.t1 MTR_7g050720 32.450 151 85 3 2 136 26 175 5.98e-15 72.4
MS.gene043976.t1 MTR_7g050640 34.177 79 52 0 1 79 28 106 1.60e-13 64.7
MS.gene043976.t1 MTR_7g050710 34.884 86 55 1 2 87 29 113 1.65e-13 68.2
MS.gene043976.t1 MTR_7g050580 37.333 75 47 0 2 76 29 103 1.98e-13 67.8
MS.gene043976.t1 MTR_7g050590 35.443 79 51 0 2 80 2 80 3.78e-13 67.0
MS.gene043976.t1 MTR_3g098790 29.371 143 80 3 1 131 28 161 1.48e-12 65.5
MS.gene043976.t1 MTR_1g034240 40.000 75 45 0 2 76 23 97 1.06e-11 63.5
MS.gene043976.t1 MTR_5g044670 41.333 75 44 0 2 76 32 106 2.55e-11 62.0
MS.gene043976.t1 MTR_1g034210 40.541 74 44 0 2 75 23 96 3.81e-11 61.6
MS.gene043976.t1 MTR_1g034210 40.541 74 44 0 2 75 23 96 4.39e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043976.t1 AT4G33280 45.000 120 64 2 1 118 38 157 7.38e-30 112
MS.gene043976.t1 AT4G33280 49.505 101 50 1 1 100 38 138 1.43e-29 111
MS.gene043976.t1 AT4G33280 49.505 101 50 1 1 100 38 138 5.80e-29 111
MS.gene043976.t1 AT4G34400 42.169 83 48 0 1 83 30 112 8.76e-19 83.6
MS.gene043976.t1 AT4G34400 42.169 83 48 0 1 83 30 112 8.76e-19 83.6
MS.gene043976.t1 AT3G06220 34.146 82 53 1 2 83 25 105 1.26e-15 71.6
MS.gene043976.t1 AT3G06160 34.667 75 49 0 1 75 39 113 1.90e-12 65.1
MS.gene043976.t1 AT3G06160 34.667 75 49 0 1 75 24 98 2.38e-12 65.1
MS.gene043976.t1 AT3G06160 34.667 75 49 0 1 75 24 98 2.38e-12 65.1
MS.gene043976.t1 AT3G06160 34.667 75 49 0 1 75 24 98 2.38e-12 65.1
MS.gene043976.t1 AT3G06160 34.667 75 49 0 1 75 83 157 2.43e-12 65.1
MS.gene043976.t1 AT5G60130 40.909 88 47 2 1 83 28 115 5.37e-12 63.2
MS.gene043976.t1 AT5G60130 40.909 88 47 2 1 83 28 115 6.72e-12 63.5
MS.gene043976.t1 AT5G60130 40.909 88 47 2 1 83 2 89 7.41e-12 63.5
MS.gene043976.t1 AT3G18990 37.333 75 47 0 2 76 22 96 7.47e-12 63.5
MS.gene043976.t1 AT5G66980 40.449 89 48 2 1 85 24 111 7.61e-12 63.5
MS.gene043976.t1 AT3G18990 37.333 75 47 0 2 76 22 96 8.35e-12 63.5
MS.gene043976.t1 AT5G60130 40.909 88 47 2 1 83 25 112 1.04e-11 63.2
MS.gene043976.t1 AT5G60130 40.909 88 47 2 1 83 28 115 1.12e-11 63.2
MS.gene043976.t1 AT3G53310 36.000 75 48 0 2 76 26 100 8.41e-11 60.5

Find 34 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACACCACCGGGACCTTTA+AGG 0.159160 1.3:+3404840 None:intergenic
CCAGAAAATGTGACCCTTAA+AGG 0.236805 1.3:-3404854 MS.gene043976:CDS
GGTGGTGTTGCATGGAAAAT+AGG 0.237795 1.3:-3404827 MS.gene043976:CDS
TGGTTTATATGAGAAATTTC+AGG 0.307206 1.3:-3404525 MS.gene043976:CDS
CCTACCAACCAACCGGAAAA+AGG 0.307983 1.3:-3404364 MS.gene043976:CDS
TTTCAGGATCTTAACAATAT+AGG 0.337128 1.3:-3404509 MS.gene043976:CDS
CCCCTAGTTCAGTTTGAGTA+TGG 0.362232 1.3:+3404618 None:intergenic
CGACATCAGCTAATTGTTGT+TGG 0.381642 1.3:-3404325 MS.gene043976:CDS
GTGGTGTTGCATGGAAAATA+GGG 0.415820 1.3:-3404826 MS.gene043976:CDS
AACACCACCGGGACCTTTAA+GGG 0.419570 1.3:+3404841 None:intergenic
GTATCAGCTATGAACTGCTC+AGG 0.438283 1.3:+3404416 None:intergenic
GTTGTTGGAGAGCACTTGAC+TGG 0.446323 1.3:-3404310 MS.gene043976:CDS
CCAACCGTCCACGAAGTAAA+CGG 0.457669 1.3:+3404784 None:intergenic
GAAGTCAATACTGCTTCTAA+TGG 0.478633 1.3:-3404560 MS.gene043976:CDS
GTTTCAACAGGTACAGCTAA+TGG 0.493162 1.3:+3404482 None:intergenic
TTCCTTGTCTTTAATTACAA+TGG 0.493431 1.3:-3404722 MS.gene043976:CDS
CCGTTTACTTCGTGGACGGT+TGG 0.508441 1.3:-3404784 MS.gene043976:CDS
GCCATACTCAAACTGAACTA+GGG 0.513331 1.3:-3404619 MS.gene043976:CDS
GGCCATACTCAAACTGAACT+AGG 0.514000 1.3:-3404620 MS.gene043976:CDS
AGACGATACCGTTTACTTCG+TGG 0.517967 1.3:-3404792 MS.gene043976:CDS
CAGTTTCCCTACCAACCAAC+CGG 0.519266 1.3:-3404371 MS.gene043976:CDS
CACCATTGTAATTAAAGACA+AGG 0.542064 1.3:+3404720 None:intergenic
TATCAGCTATGAACTGCTCA+GGG 0.548226 1.3:+3404417 None:intergenic
AAGGTCCCGGTGGTGTTGCA+TGG 0.549921 1.3:-3404835 MS.gene043976:CDS
TCTAATGGTGGTGTTGAATG+TGG 0.555737 1.3:-3404545 MS.gene043976:CDS
AATGTGACCCTTAAAGGTCC+CGG 0.577654 1.3:-3404848 MS.gene043976:CDS
TTGTTGGAGAGCACTTGACT+GGG 0.586591 1.3:-3404309 None:intergenic
GTCAATACTGCTTCTAATGG+TGG 0.593959 1.3:-3404557 MS.gene043976:CDS
CCATACTCAAACTGAACTAG+GGG 0.634393 1.3:-3404618 MS.gene043976:CDS
GTAGGGAAACTGTATAGCTG+TGG 0.649466 1.3:+3404382 None:intergenic
GATACCGTTTACTTCGTGGA+CGG 0.682240 1.3:-3404788 MS.gene043976:CDS
GTGACCCTTAAAGGTCCCGG+TGG 0.715661 1.3:-3404845 MS.gene043976:CDS
ATCAGCTATGAACTGCTCAG+GGG 0.739451 1.3:+3404418 None:intergenic
CATACTCAAACTGAACTAGG+GGG 0.777970 1.3:-3404617 MS.gene043976:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTGTCTGAAAATGTTTT+AGG + chr1.3:3404319-3404338 None:intergenic 20.0%
! TGGTTTATATGAGAAATTTC+AGG - chr1.3:3404681-3404700 MS.gene043976:CDS 25.0%
! TTCCTTGTCTTTAATTACAA+TGG - chr1.3:3404484-3404503 MS.gene043976:CDS 25.0%
! TTTCAGGATCTTAACAATAT+AGG - chr1.3:3404697-3404716 MS.gene043976:CDS 25.0%
!! AATGAAAAGACTTTTAATGC+TGG - chr1.3:3404751-3404770 MS.gene043976:CDS 25.0%
!! AGCATTAAAAGTCTTTTCAT+TGG + chr1.3:3404752-3404771 None:intergenic 25.0%
!!! AAAGAAGCTTCTTATTTTGT+CGG - chr1.3:3404556-3404575 MS.gene043976:CDS 25.0%
!!! TTTGATGTTTTGATCTTTGA+TGG - chr1.3:3404517-3404536 MS.gene043976:CDS 25.0%
CACCATTGTAATTAAAGACA+AGG + chr1.3:3404489-3404508 None:intergenic 30.0%
!! TTTTCATTGGTAGTTTCAAC+AGG + chr1.3:3404739-3404758 None:intergenic 30.0%
!!! TCTTATTTTGTCGGAAAATG+CGG - chr1.3:3404565-3404584 MS.gene043976:CDS 30.0%
GAAGTCAATACTGCTTCTAA+TGG - chr1.3:3404646-3404665 MS.gene043976:CDS 35.0%
CATACTCAAACTGAACTAGG+GGG - chr1.3:3404589-3404608 MS.gene043976:CDS 40.0%
CCAGAAAATGTGACCCTTAA+AGG - chr1.3:3404352-3404371 MS.gene043976:CDS 40.0%
CCATACTCAAACTGAACTAG+GGG - chr1.3:3404588-3404607 MS.gene043976:CDS 40.0%
CGACATCAGCTAATTGTTGT+TGG - chr1.3:3404881-3404900 MS.gene043976:CDS 40.0%
GCCATACTCAAACTGAACTA+GGG - chr1.3:3404587-3404606 MS.gene043976:CDS 40.0%
GTCAATACTGCTTCTAATGG+TGG - chr1.3:3404649-3404668 MS.gene043976:CDS 40.0%
GTTTCAACAGGTACAGCTAA+TGG + chr1.3:3404727-3404746 None:intergenic 40.0%
TATCAGCTATGAACTGCTCA+GGG + chr1.3:3404792-3404811 None:intergenic 40.0%
! TATTTTCCATGCAACACCAC+CGG + chr1.3:3404380-3404399 None:intergenic 40.0%
! TCTAATGGTGGTGTTGAATG+TGG - chr1.3:3404661-3404680 MS.gene043976:CDS 40.0%
! TCTTCTCTTGCTCCTTTTTC+CGG + chr1.3:3404857-3404876 None:intergenic 40.0%
!! CCTTTAAGGGTCACATTTTC+TGG + chr1.3:3404355-3404374 None:intergenic 40.0%
!! GTGGTGTTGCATGGAAAATA+GGG - chr1.3:3404380-3404399 MS.gene043976:CDS 40.0%
AATGTGACCCTTAAAGGTCC+CGG - chr1.3:3404358-3404377 MS.gene043976:CDS 45.0%
AGACGATACCGTTTACTTCG+TGG - chr1.3:3404414-3404433 MS.gene043976:CDS 45.0%
ATCAGCTATGAACTGCTCAG+GGG + chr1.3:3404791-3404810 None:intergenic 45.0%
CCCCTAGTTCAGTTTGAGTA+TGG + chr1.3:3404591-3404610 None:intergenic 45.0%
GATACCGTTTACTTCGTGGA+CGG - chr1.3:3404418-3404437 MS.gene043976:CDS 45.0%
GGCCATACTCAAACTGAACT+AGG - chr1.3:3404586-3404605 MS.gene043976:CDS 45.0%
GTAGGGAAACTGTATAGCTG+TGG + chr1.3:3404827-3404846 None:intergenic 45.0%
GTATCAGCTATGAACTGCTC+AGG + chr1.3:3404793-3404812 None:intergenic 45.0%
! ATTTTCCATGCAACACCACC+GGG + chr1.3:3404379-3404398 None:intergenic 45.0%
!! CTTTTTCCGGTTGGTTGGTA+GGG + chr1.3:3404844-3404863 None:intergenic 45.0%
!! GGTGGTGTTGCATGGAAAAT+AGG - chr1.3:3404379-3404398 MS.gene043976:CDS 45.0%
!! TTGTTGGAGAGCACTTGACT+GGG - chr1.3:3404897-3404916 MS.gene043976:CDS 45.0%
AACACCACCGGGACCTTTAA+GGG + chr1.3:3404368-3404387 None:intergenic 50.0%
ACTAGGGGGTAGCAAAGCAA+AGG - chr1.3:3404603-3404622 MS.gene043976:CDS 50.0%
CAGTTTCCCTACCAACCAAC+CGG - chr1.3:3404835-3404854 MS.gene043976:CDS 50.0%
CCAACCGTCCACGAAGTAAA+CGG + chr1.3:3404425-3404444 None:intergenic 50.0%
CCTACCAACCAACCGGAAAA+AGG - chr1.3:3404842-3404861 MS.gene043976:CDS 50.0%
! CTCTTGCTCCTTTTTCCGGT+TGG + chr1.3:3404853-3404872 None:intergenic 50.0%
! TGCTCCTTTTTCCGGTTGGT+TGG + chr1.3:3404849-3404868 None:intergenic 50.0%
!! CCTTTTTCCGGTTGGTTGGT+AGG + chr1.3:3404845-3404864 None:intergenic 50.0%
!! GTTGTTGGAGAGCACTTGAC+TGG - chr1.3:3404896-3404915 MS.gene043976:CDS 50.0%
CAACACCACCGGGACCTTTA+AGG + chr1.3:3404369-3404388 None:intergenic 55.0%
CCGTTTACTTCGTGGACGGT+TGG - chr1.3:3404422-3404441 MS.gene043976:CDS 55.0%
GTGACCCTTAAAGGTCCCGG+TGG - chr1.3:3404361-3404380 MS.gene043976:CDS 60.0%
!! AAGGTCCCGGTGGTGTTGCA+TGG - chr1.3:3404371-3404390 MS.gene043976:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 3404310 3404918 3404310 ID=MS.gene043976
chr1.3 mRNA 3404310 3404918 3404310 ID=MS.gene043976.t1;Parent=MS.gene043976
chr1.3 exon 3404310 3404918 3404310 ID=MS.gene043976.t1.exon1;Parent=MS.gene043976.t1
chr1.3 CDS 3404310 3404918 3404310 ID=cds.MS.gene043976.t1;Parent=MS.gene043976.t1
Gene Sequence

>MS.gene043976

GCACTTCCTAAAACATTTTCAGACAATTTAAATAAGAAGTTGCCAGAAAATGTGACCCTTAAAGGTCCCGGTGGTGTTGCATGGAAAATAGGGCTCATAACTAGAGACGATACCGTTTACTTCGTGGACGGTTGGCAACGATTCGTGAACGATCACTCTTTGAAAGATAATGATTTCCTTGTCTTTAATTACAATGGTGAATCACACTTTGATGTTTTGATCTTTGATGGAGAAAGCTTCTGTGAGAAAGAAGCTTCTTATTTTGTCGGAAAATGCGGCCATACTCAAACTGAACTAGGGGGTAGCAAAGCAAAGGAAACAAACAATTCTATTGAAGAAGTCAATACTGCTTCTAATGGTGGTGTTGAATGTGGTTTATATGAGAAATTTCAGGATCTTAACAATATAGGAACACCATTAGCTGTACCTGTTGAAACTACCAATGAAAAGACTTTTAATGCTGGTGTCAAATCTGATTCCCCTGAGCAGTTCATAGCTGATACAGTCACTAAGACCACAGCTATACAGTTTCCCTACCAACCAACCGGAAAAAGGAGCAAGAGAAGATCATCGACATCAGCTAATTGTTGTTGGAGAGCACTTGACTGG
Protein sequence

>MS.gene043976.t1

ALPKTFSDNLNKKLPENVTLKGPGGVAWKIGLITRDDTVYFVDGWQRFVNDHSLKDNDFLVFNYNGESHFDVLIFDGESFCEKEASYFVGKCGHTQTELGGSKAKETNNSIEEVNTASNGGVECGLYEKFQDLNNIGTPLAVPVETTNEKTFNAGVKSDSPEQFIADTVTKTTAIQFPYQPTGKRSKRRSSTSANCCWRALDW