AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0153900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0153900 MtrunA17_Chr1g0164121 83.824 136 22 0 4 139 172 307 6.17e-78 233
Msa0153900 MtrunA17_Chr8g0359891 86.131 137 19 0 4 140 2801 2937 1.33e-75 244
Msa0153900 MtrunA17_Chr8g0359891 42.963 135 75 2 5 139 1792 1924 5.69e-23 94.0
Msa0153900 MtrunA17_Chr8g0359891 42.222 135 76 2 5 139 2288 2420 1.62e-21 89.7
Msa0153900 MtrunA17_Chr8g0359891 38.571 140 81 2 2 139 1268 1404 2.43e-20 86.3
Msa0153900 MtrunA17_Chr8g0359891 37.143 140 83 2 2 139 427 563 6.77e-20 85.1
Msa0153900 MtrunA17_Chr1g0164011 85.926 135 19 0 5 139 2361 2495 2.82e-75 243
Msa0153900 MtrunA17_Chr1g0164011 45.185 135 72 2 5 139 1840 1972 1.00e-24 99.0
Msa0153900 MtrunA17_Chr1g0164011 37.143 140 83 2 2 139 1393 1529 2.99e-19 83.2
Msa0153900 MtrunA17_Chr1g0163891 87.500 136 17 0 5 140 2972 3107 2.92e-75 243
Msa0153900 MtrunA17_Chr1g0163891 43.182 132 73 2 8 139 1932 2061 1.02e-21 90.1
Msa0153900 MtrunA17_Chr1g0163891 43.182 132 73 2 8 139 2454 2583 3.29e-21 89.0
Msa0153900 MtrunA17_Chr1g0163891 38.571 140 81 2 2 139 1405 1541 3.80e-20 85.9
Msa0153900 MtrunA17_Chr1g0170881 86.667 135 18 0 5 139 1915 2049 5.34e-75 242
Msa0153900 MtrunA17_Chr1g0170881 40.000 140 79 2 2 139 1390 1526 6.05e-21 88.2
Msa0153900 MtrunA17_Chr1g0163761 87.500 136 17 0 5 140 2439 2574 1.21e-74 241
Msa0153900 MtrunA17_Chr1g0163761 43.704 135 74 2 5 139 1918 2050 1.86e-24 98.2
Msa0153900 MtrunA17_Chr1g0163761 37.857 140 82 2 2 139 1394 1530 1.74e-18 80.9
Msa0153900 MtrunA17_Chr1g0172231 85.401 137 20 0 4 140 1270 1406 3.44e-74 240
Msa0153900 MtrunA17_Chr1g0172231 42.553 141 79 2 5 145 750 888 4.16e-24 97.1
Msa0153900 MtrunA17_Chr1g0172231 37.857 140 82 2 2 139 226 362 6.55e-20 85.1
Msa0153900 MtrunA17_Chr1g0163931 86.765 136 18 0 5 140 1913 2048 5.14e-73 237
Msa0153900 MtrunA17_Chr1g0163931 40.000 140 79 2 2 139 1391 1527 2.47e-21 89.4
Msa0153900 MtrunA17_Chr1g0172051 82.353 136 24 0 5 140 2951 3086 2.74e-70 229
Msa0153900 MtrunA17_Chr1g0172051 42.222 135 76 2 5 139 2432 2564 5.23e-22 91.3
Msa0153900 MtrunA17_Chr1g0172051 37.857 140 82 2 2 139 1391 1527 2.16e-19 83.6
Msa0153900 MtrunA17_Chr1g0172051 34.286 140 87 2 2 139 1908 2044 4.18e-19 82.8
Msa0153900 MtrunA17_Chr1g0167981 80.000 135 27 0 5 139 2955 3089 2.02e-67 221
Msa0153900 MtrunA17_Chr1g0167981 40.426 141 77 2 5 139 1912 2051 2.25e-24 97.8
Msa0153900 MtrunA17_Chr1g0167981 41.549 142 74 3 2 139 1390 1526 6.52e-23 93.6
Msa0153900 MtrunA17_Chr1g0167981 40.146 137 79 2 5 139 2437 2572 7.55e-22 90.5
Msa0153900 MtrunA17_Chr6g0474571 82.353 136 23 1 5 139 2958 3093 5.60e-67 219
Msa0153900 MtrunA17_Chr6g0474571 40.741 135 78 2 5 139 1916 2048 6.78e-22 90.9
Msa0153900 MtrunA17_Chr6g0474571 40.741 135 78 2 5 139 2436 2568 6.78e-22 90.9
Msa0153900 MtrunA17_Chr6g0474571 40.288 139 80 2 2 139 1392 1528 3.95e-21 88.6
Msa0153900 MtrunA17_Chr2g0323691 82.963 135 23 0 5 139 2956 3090 1.21e-64 213
Msa0153900 MtrunA17_Chr2g0323691 39.259 135 80 2 5 139 1916 2048 2.19e-21 89.4
Msa0153900 MtrunA17_Chr2g0323691 39.098 133 78 2 7 139 2438 2567 3.58e-21 88.6
Msa0153900 MtrunA17_Chr2g0323691 33.113 151 93 3 2 147 1392 1539 1.39e-18 81.3
Msa0153900 MtrunA17_Chr1g0163801 86.726 113 15 0 5 117 308 420 3.64e-64 202
Msa0153900 MtrunA17_Chr1g0171091 71.642 134 36 1 8 139 175 308 3.04e-57 181
Msa0153900 MtrunA17_Chr1g0171081 73.469 98 26 0 42 139 1 98 3.57e-48 150
Msa0153900 MtrunA17_Chr2g0313481 37.762 143 88 1 1 142 1413 1555 1.15e-25 101
Msa0153900 MtrunA17_Chr2g0313331 35.664 143 91 1 1 142 1090 1232 4.52e-25 99.8
Msa0153900 MtrunA17_Chr2g0313541 38.519 135 82 1 1 134 1405 1539 8.70e-25 99.0
Msa0153900 MtrunA17_Chr8g0348251 44.056 143 72 4 4 139 126 267 2.14e-24 97.8
Msa0153900 MtrunA17_Chr8g0348251 35.172 145 89 2 5 144 635 779 3.30e-18 80.1
Msa0153900 MtrunA17_Chr1g0174521 43.939 132 72 2 8 139 35 164 2.34e-24 94.4
Msa0153900 MtrunA17_Chr2g0314301 38.235 136 83 1 8 142 1415 1550 2.65e-24 97.8
Msa0153900 MtrunA17_Chr2g0313351 38.060 134 83 0 8 141 1408 1541 4.87e-24 97.1
Msa0153900 MtrunA17_Chr2g0313421 38.060 134 83 0 8 141 515 648 6.49e-24 96.3
Msa0153900 MtrunA17_Chr2g0313591 37.143 140 87 1 1 139 1398 1537 8.38e-24 96.3
Msa0153900 MtrunA17_Chr2g0313311 37.313 134 84 0 8 141 1385 1518 6.51e-23 93.6
Msa0153900 MtrunA17_Chr2g0313471 34.532 139 90 1 5 142 122 260 1.11e-22 90.1
Msa0153900 MtrunA17_Chr8g0348201 40.141 142 79 4 4 139 574 715 7.83e-22 90.5
Msa0153900 MtrunA17_Chr8g0348201 37.143 140 83 3 5 139 1085 1224 7.53e-21 87.8
Msa0153900 MtrunA17_Chr8g0348201 29.801 151 86 2 10 140 1359 1509 3.63e-11 60.1
Msa0153900 MtrunA17_Chr1g0172161 38.571 140 81 2 2 139 431 567 1.18e-20 87.0
Msa0153900 MtrunA17_Chr2g0314151 38.571 140 80 3 2 139 7 142 1.60e-20 82.0
Msa0153900 MtrunA17_Chr1g0163991 35.714 140 85 2 2 139 431 567 2.75e-20 86.3
Msa0153900 MtrunA17_Chr1g0163991 36.170 141 85 2 2 140 1131 1268 4.20e-19 82.8
Msa0153900 MtrunA17_Chr1g0172071 34.286 140 87 2 2 139 125 261 7.32e-20 82.8
Msa0153900 MtrunA17_Chr1g0172141 37.143 140 83 2 2 139 1394 1530 7.82e-20 84.7
Msa0153900 MtrunA17_Chr1g0172101 36.429 140 84 2 2 139 199 335 4.05e-19 82.0
Msa0153900 MtrunA17_Chr1g0174511 37.143 140 83 2 2 139 1389 1525 2.54e-18 80.5
Msa0153900 MtrunA17_Chr3g0081941 34.722 144 88 4 3 142 1133 1274 1.86e-17 78.2
Msa0153900 MtrunA17_Chr2g0313491 33.099 142 92 1 4 142 1366 1507 2.28e-17 77.8
Msa0153900 MtrunA17_Chr1g0163791 33.571 140 88 2 2 139 1389 1525 2.07e-16 75.1
Msa0153900 MtrunA17_Chr7g0255111 29.134 127 88 1 5 131 1289 1413 2.22e-14 69.3
Msa0153900 MtrunA17_Chr2g0314131 45.122 82 44 1 5 86 74 154 3.27e-13 63.2
Msa0153900 MtrunA17_Chr4g0011631 35.075 134 85 1 3 136 251 382 1.78e-12 63.5
Msa0153900 MtrunA17_Chr4g0011661 33.099 142 88 2 3 142 251 387 1.80e-11 60.8
Msa0153900 MtrunA17_Chr7g0255401 31.206 141 88 3 3 134 1110 1250 7.88e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTCGTTTCGTCGTTAA+AGG 0.182894 1_4:+17932470 Msa0153900:CDS
GAACAAATGTTCACAGAAAA+AGG 0.255110 1_4:+17932605 Msa0153900:CDS
AAGTAAATTCCAAGTATTCC+AGG 0.346947 1_4:-17932391 None:intergenic
ATTTGAAAACCTGGAATACT+TGG 0.360265 1_4:+17932382 Msa0153900:CDS
ACGACGAAACGAAGCAAAGA+TGG 0.445701 1_4:-17932464 None:intergenic
GTTTGAGAAGCTTCTGCTAT+GGG 0.448087 1_4:+17932423 Msa0153900:CDS
GATGAGAAGATCTTCATTTG+AGG 0.504619 1_4:-17932497 None:intergenic
AGTTTGAGAAGCTTCTGCTA+TGG 0.535941 1_4:+17932422 Msa0153900:CDS
CAGGTTGATCTATTTGAAAG+TGG 0.540090 1_4:+17932217 Msa0153900:CDS
TGACGATTGCGATGATGCAC+AGG 0.541212 1_4:+17932198 None:intergenic
CGACGAAACGAAGCAAAGAT+GGG 0.541623 1_4:-17932463 None:intergenic
AAACATCGTATTTGAAAACC+TGG 0.549598 1_4:+17932373 Msa0153900:CDS
ACAGTAGCACCGTGCCTCAC+AGG 0.560430 1_4:+17932527 Msa0153900:CDS
GAAGAAAATATGCGATGGAA+AGG 0.574852 1_4:+17932563 Msa0153900:CDS
TGGGAGAAGAAAATATGCGA+TGG 0.606913 1_4:+17932558 Msa0153900:CDS
AACTAACTGTGAGAAGATGT+TGG 0.608661 1_4:+17932316 Msa0153900:CDS
ACATCAATTCCTGTGAGGCA+CGG 0.617104 1_4:-17932536 None:intergenic
TGCCTCACAGGAATTGATGT+GGG 0.634743 1_4:+17932539 Msa0153900:CDS
GAAGCTTCTCAAACTTGACA+AGG 0.638660 1_4:-17932414 None:intergenic
GTGCCTCACAGGAATTGATG+TGG 0.642171 1_4:+17932538 Msa0153900:CDS
CTCCCACATCAATTCCTGTG+AGG 0.674296 1_4:-17932541 None:intergenic
GCACGGTGCTACTGTGAGTG+CGG 0.676471 1_4:-17932519 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GATTGATGAAGAAAAAACAG+AGG + chr1_4:17932349-17932368 Msa0153900:CDS 30.0%
AAACATCGTATTTGAAAACC+TGG + chr1_4:17932373-17932392 Msa0153900:CDS 30.0%
ATTTGAAAACCTGGAATACT+TGG + chr1_4:17932382-17932401 Msa0153900:CDS 30.0%
AAGTAAATTCCAAGTATTCC+AGG - chr1_4:17932394-17932413 None:intergenic 30.0%
GAACAAATGTTCACAGAAAA+AGG + chr1_4:17932605-17932624 Msa0153900:CDS 30.0%
!! CAGGTTGATCTATTTGAAAG+TGG + chr1_4:17932217-17932236 Msa0153900:CDS 35.0%
AACTAACTGTGAGAAGATGT+TGG + chr1_4:17932316-17932335 Msa0153900:CDS 35.0%
GATGAGAAGATCTTCATTTG+AGG - chr1_4:17932500-17932519 None:intergenic 35.0%
GAAGAAAATATGCGATGGAA+AGG + chr1_4:17932563-17932582 Msa0153900:CDS 35.0%
GAAGCTTCTCAAACTTGACA+AGG - chr1_4:17932417-17932436 None:intergenic 40.0%
AGTTTGAGAAGCTTCTGCTA+TGG + chr1_4:17932422-17932441 Msa0153900:CDS 40.0%
GTTTGAGAAGCTTCTGCTAT+GGG + chr1_4:17932423-17932442 Msa0153900:CDS 40.0%
TTGCTTCGTTTCGTCGTTAA+AGG + chr1_4:17932470-17932489 Msa0153900:CDS 40.0%
TGGGAGAAGAAAATATGCGA+TGG + chr1_4:17932558-17932577 Msa0153900:CDS 40.0%
CGACGAAACGAAGCAAAGAT+GGG - chr1_4:17932466-17932485 None:intergenic 45.0%
ACGACGAAACGAAGCAAAGA+TGG - chr1_4:17932467-17932486 None:intergenic 45.0%
ACATCAATTCCTGTGAGGCA+CGG - chr1_4:17932539-17932558 None:intergenic 45.0%
TGCCTCACAGGAATTGATGT+GGG + chr1_4:17932539-17932558 Msa0153900:CDS 45.0%
GTGCCTCACAGGAATTGATG+TGG + chr1_4:17932538-17932557 Msa0153900:CDS 50.0%
CTCCCACATCAATTCCTGTG+AGG - chr1_4:17932544-17932563 None:intergenic 50.0%
!! GCACGGTGCTACTGTGAGTG+CGG - chr1_4:17932522-17932541 None:intergenic 60.0%
ACAGTAGCACCGTGCCTCAC+AGG + chr1_4:17932527-17932546 Msa0153900:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 17932209 17932652 17932209 ID=Msa0153900;Name=Msa0153900
chr1_4 mRNA 17932209 17932652 17932209 ID=Msa0153900-mRNA-1;Parent=Msa0153900;Name=Msa0153900-mRNA-1;_AED=0.48;_eAED=0.49;_QI=0|-1|0|1|-1|1|1|0|147
chr1_4 exon 17932209 17932652 17932209 ID=Msa0153900-mRNA-1:exon:6748;Parent=Msa0153900-mRNA-1
chr1_4 CDS 17932209 17932652 17932209 ID=Msa0153900-mRNA-1:cds;Parent=Msa0153900-mRNA-1
Gene Sequence

>Msa0153900

ATGATGCACAGGTTGATCTATTTGAAAGTGGACAACTGCAAAGAGTTGATCTATTTGATAACAATTTCAACAGCTAAAAGTCTAGTTCAACTCAAAGCATTAGAAGTAACTAACTGTGAGAAGATGTTGGATGTCGTGAAGATTGATGAAGAAAAAACAGAGGAAAACATCGTATTTGAAAACCTGGAATACTTGGAATTTACTTCCTTGTCAAGTTTGAGAAGCTTCTGCTATGGGAAACAAGCATTCATATTCCCATCTTTGCTTCGTTTCGTCGTTAAAGGATGTCCTCAAATGAAGATCTTCTCATCCGCACTCACAGTAGCACCGTGCCTCACAGGAATTGATGTGGGAGAAGAAAATATGCGATGGAAAGGTGATCTTAACACAACTATTGAACAAATGTTCACAGAAAAAGGTACACAATGTCATTATTATTTATGA
Protein sequence

>Msa0153900

MMHRLIYLKVDNCKELIYLITISTAKSLVQLKALEVTNCEKMLDVVKIDEEKTEENIVFENLEYLEFTSLSSLRSFCYGKQAFIFPSLLRFVVKGCPQMKIFSSALTVAPCLTGIDVGEENMRWKGDLNTTIEQMFTEKGTQCHYYL*