AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene59042

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59042.t1 MTR_0443s0040 87.821 312 35 2 1 311 1 310 0.0 568
MS.gene59042.t1 MTR_0062s0170 58.013 312 122 6 4 311 3 309 5.11e-111 324
MS.gene59042.t1 MTR_0062s0110 58.013 312 122 6 4 311 3 309 5.11e-111 324
MS.gene59042.t1 MTR_0062s0130 58.013 312 122 6 4 311 3 309 5.11e-111 324
MS.gene59042.t1 MTR_2g036240 58.013 312 122 6 4 311 3 309 5.11e-111 324
MS.gene59042.t1 MTR_2g036260 58.013 312 122 6 4 311 3 309 5.11e-111 324
MS.gene59042.t1 MTR_2g036290 58.013 312 122 6 4 311 3 309 5.11e-111 324
MS.gene59042.t1 MTR_8g046730 58.013 312 122 6 4 311 3 309 5.11e-111 324
MS.gene59042.t1 MTR_0062s0020 48.208 307 136 7 14 308 2 297 1.03e-91 275
MS.gene59042.t1 MTR_0002s1060 48.675 302 138 4 12 310 12 299 1.72e-90 272
MS.gene59042.t1 MTR_0062s0090 46.885 305 137 10 16 308 4 295 1.69e-78 241
MS.gene59042.t1 MTR_0062s0040 46.885 305 137 10 16 308 4 295 1.69e-78 241
MS.gene59042.t1 MTR_0062s0060 46.885 305 137 10 16 308 4 295 1.69e-78 241
MS.gene59042.t1 MTR_0002s0040 42.953 298 149 7 14 309 13 291 1.31e-73 228
MS.gene59042.t1 MTR_0263s0020 43.197 294 146 7 14 305 13 287 9.57e-71 221
MS.gene59042.t1 MTR_1457s0010 38.934 244 116 5 69 311 1 212 8.73e-45 152
MS.gene59042.t1 MTR_6g079630 31.317 281 158 9 16 287 34 288 1.58e-31 120
MS.gene59042.t1 MTR_2g096030 32.270 282 154 10 16 287 31 285 3.96e-29 113
MS.gene59042.t1 MTR_2g096040 30.909 275 155 11 15 279 3 252 2.85e-28 110
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 62 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAAAATCATCTAAAGTTTC+TGG 0.145221 2.1:-54248478 None:intergenic
AATCAATTCCACTTCATTCT+AGG 0.205618 2.1:+54248526 MS.gene59042:CDS
CCCACTACCACAAATTGTTT+TGG 0.245343 2.1:+54248992 MS.gene59042:CDS
TGTAGCTAGTAATCAATTAT+TGG 0.249179 2.1:-54249325 None:intergenic
ATTCAATCCTAAGGAGAAAA+AGG 0.297710 2.1:+54248708 MS.gene59042:CDS
GGACACATATTCCATGGATT+TGG 0.302531 2.1:-54248944 None:intergenic
TTACGGTGAGCTTAAACTTT+TGG 0.347612 2.1:+54249116 MS.gene59042:CDS
ATTTGTGGTAGTGGGCTTGC+AGG 0.350030 2.1:-54248984 None:intergenic
GATATGTCTGATCGAGCTTA+TGG 0.361529 2.1:-54248746 None:intergenic
CCCAAAACAATTTGTGGTAG+TGG 0.365132 2.1:-54248993 None:intergenic
TACCTTGTCAATGATGATTC+TGG 0.380807 2.1:+54248787 MS.gene59042:CDS
CGGGACATTTCGTTCGCGAT+TGG 0.385507 2.1:+54248584 MS.gene59042:CDS
TCATCATTGATGATATTAAC+AGG 0.403312 2.1:-54248499 None:intergenic
CACTGCACTAGCATAATTGA+TGG 0.434540 2.1:+54248817 MS.gene59042:CDS
AATCAACTAATAACGGATTA+CGG 0.451454 2.1:+54249099 MS.gene59042:CDS
ATCATCAAACTCATCCTTTG+AGG 0.453286 2.1:-54249070 None:intergenic
CGGTTCATCTTAGTATCAGC+TGG 0.454457 2.1:-54249156 None:intergenic
GAAAATCATCTAAAGTTTCT+GGG 0.456174 2.1:-54248477 None:intergenic
AGCATTTCCTCCAAGATGTA+AGG 0.467593 2.1:-54249288 None:intergenic
TGTGGTCCCAAAACAATTTG+TGG 0.468651 2.1:-54248999 None:intergenic
GATGTCATTGCTCGGTGGGT+TGG 0.481116 2.1:-54249262 None:intergenic
TATATCGATTCTAGTGTGAC+TGG 0.486159 2.1:+54248859 MS.gene59042:CDS
GCCACTGAGGTGTATAAAGA+TGG 0.489071 2.1:+54248553 MS.gene59042:CDS
AACCGAGAGGTGTTCATTGA+GGG 0.499384 2.1:+54249174 MS.gene59042:CDS
CGCCCTCAATGAACACCTCT+CGG 0.504404 2.1:-54249176 None:intergenic
TGACATCGAGCCTTACATCT+TGG 0.507062 2.1:+54249278 MS.gene59042:CDS
TCTCTACAATCAACTAATAA+CGG 0.510522 2.1:+54249092 MS.gene59042:CDS
CCAAAACAATTTGTGGTAGT+GGG 0.514829 2.1:-54248992 None:intergenic
TATAAAGATGGAAAAGGAAC+GGG 0.518546 2.1:+54248565 MS.gene59042:CDS
CTAGTAATCAATTATTGGTA+AGG 0.518596 2.1:-54249320 None:intergenic
ATCAACAGCAAATCACTCCT+TGG 0.519679 2.1:+54249210 MS.gene59042:CDS
TAAATATCCATTCAATCCTA+AGG 0.520789 2.1:+54248699 MS.gene59042:CDS
GCTGACTTCTCCAACTGCAT+TGG 0.521072 2.1:+54248883 MS.gene59042:CDS
AATAACTTGTCCAATGCAGT+TGG 0.521593 2.1:-54248893 None:intergenic
TGGGCTTGCAGGAGCTCTGT+CGG 0.524861 2.1:-54248973 None:intergenic
GCTCGATGTCATTGCTCGGT+GGG 0.532171 2.1:-54249266 None:intergenic
CAGGAGCTCTGTCGGAGCAA+TGG 0.537676 2.1:-54248965 None:intergenic
ATGAAGGTTATGATAACTAT+CGG 0.552996 2.1:+54248664 MS.gene59042:CDS
CATCGAGCCTTACATCTTGG+AGG 0.554478 2.1:+54249281 MS.gene59042:CDS
TCGAGAATACATTGGCGTGA+AGG 0.556428 2.1:+54248450 MS.gene59042:CDS
GAAAGAACATAAGAATATGA+AGG 0.556511 2.1:+54248648 MS.gene59042:CDS
TAAGCATGTATCCAAATCCA+TGG 0.557313 2.1:+54248933 MS.gene59042:CDS
CATCTTAGTATCAGCTGGAT+CGG 0.557541 2.1:-54249151 None:intergenic
TGAATGGATATTTAGTGCCA+TGG 0.560003 2.1:-54248690 None:intergenic
GAGGTGTATAAAGATGGAAA+AGG 0.564302 2.1:+54248559 MS.gene59042:CDS
GAACCGAGAGGTGTTCATTG+AGG 0.566347 2.1:+54249173 MS.gene59042:CDS
CAATCAAACTATATCCTCAA+AGG 0.567378 2.1:+54249056 MS.gene59042:CDS
AGCAATGGACACATATTCCA+TGG 0.567858 2.1:-54248950 None:intergenic
GGCTCGATGTCATTGCTCGG+TGG 0.574776 2.1:-54249267 None:intergenic
ATATCGATTCTAGTGTGACT+GGG 0.576037 2.1:+54248860 MS.gene59042:CDS
ATGATAACTATCGGAGGCCA+TGG 0.579102 2.1:+54248673 MS.gene59042:CDS
TAAGGCTCGATGTCATTGCT+CGG 0.600452 2.1:-54249270 None:intergenic
AGTTATTAAACATCTCAAGA+AGG 0.601516 2.1:+54248909 MS.gene59042:CDS
GTATAAAGATGGAAAAGGAA+CGG 0.613441 2.1:+54248564 MS.gene59042:CDS
TGGCGAAGCCTAGAATGAAG+TGG 0.614487 2.1:-54248534 None:intergenic
TACCAGAATCATCATTGACA+AGG 0.665409 2.1:-54248789 None:intergenic
TCCATCTTTATACACCTCAG+TGG 0.670679 2.1:-54248554 None:intergenic
CATCAATTATGCTAGTGCAG+TGG 0.677859 2.1:-54248816 None:intergenic
CATTCTAGGCTTCGCCACTG+AGG 0.701525 2.1:+54248540 MS.gene59042:CDS
AAGGTTATGATAACTATCGG+AGG 0.701816 2.1:+54248667 MS.gene59042:CDS
TATCGATTCTAGTGTGACTG+GGG 0.708158 2.1:+54248861 MS.gene59042:CDS
TGATACTAAGATGAACCGAG+AGG 0.777827 2.1:+54249161 MS.gene59042:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGTTATTAAACATCTCAAGA+AGG + chr2.1:54248909-54248928 MS.gene59042:CDS 25.0%
! ATGAAGGTTATGATAACTAT+CGG + chr2.1:54248664-54248683 MS.gene59042:CDS 25.0%
! ATGTATTCTCGAAAAATTGT+TGG - chr2.1:54248442-54248461 None:intergenic 25.0%
! GAAAGAACATAAGAATATGA+AGG + chr2.1:54248648-54248667 MS.gene59042:CDS 25.0%
! TAAATATCCATTCAATCCTA+AGG + chr2.1:54248699-54248718 MS.gene59042:CDS 25.0%
! TCTCTACAATCAACTAATAA+CGG + chr2.1:54249092-54249111 MS.gene59042:CDS 25.0%
!! GAAAATCATCTAAAGTTTCT+GGG - chr2.1:54248480-54248499 None:intergenic 25.0%
!! TCATCATTGATGATATTAAC+AGG - chr2.1:54248502-54248521 None:intergenic 25.0%
!!! AATCAACTAATAACGGATTA+CGG + chr2.1:54249099-54249118 MS.gene59042:CDS 25.0%
!!! ACAATTTTTCGAGAATACAT+TGG + chr2.1:54248442-54248461 MS.gene59042:CDS 25.0%
AATCAATTCCACTTCATTCT+AGG + chr2.1:54248526-54248545 MS.gene59042:CDS 30.0%
ATTCAATCCTAAGGAGAAAA+AGG + chr2.1:54248708-54248727 MS.gene59042:CDS 30.0%
CAATCAAACTATATCCTCAA+AGG + chr2.1:54249056-54249075 MS.gene59042:CDS 30.0%
GTATAAAGATGGAAAAGGAA+CGG + chr2.1:54248564-54248583 MS.gene59042:CDS 30.0%
TATAAAGATGGAAAAGGAAC+GGG + chr2.1:54248565-54248584 MS.gene59042:CDS 30.0%
! AAAAATTGTTGGCCTCAAAA+CGG - chr2.1:54248431-54248450 None:intergenic 30.0%
! GGAAAATCATCTAAAGTTTC+TGG - chr2.1:54248481-54248500 None:intergenic 30.0%
! TTTTTCTCCTTAGGATTGAA+TGG - chr2.1:54248709-54248728 None:intergenic 30.0%
!! CATAGTTGATATCCATTTTG+TGG - chr2.1:54249020-54249039 None:intergenic 30.0%
!!! TGTGTTTGAACACTTTTTCT+GGG - chr2.1:54248627-54248646 None:intergenic 30.0%
!!! TTGTGTTTGAACACTTTTTC+TGG - chr2.1:54248628-54248647 None:intergenic 30.0%
AAGGTTATGATAACTATCGG+AGG + chr2.1:54248667-54248686 MS.gene59042:CDS 35.0%
ATCATCAAACTCATCCTTTG+AGG - chr2.1:54249073-54249092 None:intergenic 35.0%
ATCCTAAGGAGAAAAAGGTA+TGG + chr2.1:54248713-54248732 MS.gene59042:CDS 35.0%
CCAAAACAATTTGTGGTAGT+GGG - chr2.1:54248995-54249014 None:intergenic 35.0%
GAGGTGTATAAAGATGGAAA+AGG + chr2.1:54248559-54248578 MS.gene59042:CDS 35.0%
TAAGCATGTATCCAAATCCA+TGG + chr2.1:54248933-54248952 MS.gene59042:CDS 35.0%
TACCAGAATCATCATTGACA+AGG - chr2.1:54248792-54248811 None:intergenic 35.0%
TACCTTGTCAATGATGATTC+TGG + chr2.1:54248787-54248806 MS.gene59042:CDS 35.0%
TGAATGGATATTTAGTGCCA+TGG - chr2.1:54248693-54248712 None:intergenic 35.0%
! AATAACTTGTCCAATGCAGT+TGG - chr2.1:54248896-54248915 None:intergenic 35.0%
! ATCCATACCTTTTTCTCCTT+AGG - chr2.1:54248718-54248737 None:intergenic 35.0%
! CCACTACCACAAATTGTTTT+GGG + chr2.1:54248993-54249012 MS.gene59042:CDS 35.0%
! TTACGGTGAGCTTAAACTTT+TGG + chr2.1:54249116-54249135 MS.gene59042:CDS 35.0%
!! ATATCGATTCTAGTGTGACT+GGG + chr2.1:54248860-54248879 MS.gene59042:CDS 35.0%
!! TATATCGATTCTAGTGTGAC+TGG + chr2.1:54248859-54248878 MS.gene59042:CDS 35.0%
!!! ACAATATCAATGCCGTTTTG+AGG + chr2.1:54248416-54248435 MS.gene59042:CDS 35.0%
!!! ATTGTTTTGGGACCACAAAA+TGG + chr2.1:54249005-54249024 MS.gene59042:CDS 35.0%
AGCAATGGACACATATTCCA+TGG - chr2.1:54248953-54248972 None:intergenic 40.0%
AGCATTTCCTCCAAGATGTA+AGG - chr2.1:54249291-54249310 None:intergenic 40.0%
ATCAACAGCAAATCACTCCT+TGG + chr2.1:54249210-54249229 MS.gene59042:CDS 40.0%
CACTCCAAACAAAAAGTCCA+AGG - chr2.1:54249230-54249249 None:intergenic 40.0%
CACTGCACTAGCATAATTGA+TGG + chr2.1:54248817-54248836 MS.gene59042:CDS 40.0%
CATCAATTATGCTAGTGCAG+TGG - chr2.1:54248819-54248838 None:intergenic 40.0%
CATCTTAGTATCAGCTGGAT+CGG - chr2.1:54249154-54249173 None:intergenic 40.0%
CCCAAAACAATTTGTGGTAG+TGG - chr2.1:54248996-54249015 None:intergenic 40.0%
GATATGTCTGATCGAGCTTA+TGG - chr2.1:54248749-54248768 None:intergenic 40.0%
GGACACATATTCCATGGATT+TGG - chr2.1:54248947-54248966 None:intergenic 40.0%
TCCATCTTTATACACCTCAG+TGG - chr2.1:54248557-54248576 None:intergenic 40.0%
TGATACTAAGATGAACCGAG+AGG + chr2.1:54249161-54249180 MS.gene59042:CDS 40.0%
TGTGGTCCCAAAACAATTTG+TGG - chr2.1:54249002-54249021 None:intergenic 40.0%
! CACTCCTTGGACTTTTTGTT+TGG + chr2.1:54249223-54249242 MS.gene59042:CDS 40.0%
! CCCACTACCACAAATTGTTT+TGG + chr2.1:54248992-54249011 MS.gene59042:CDS 40.0%
!! TATCGATTCTAGTGTGACTG+GGG + chr2.1:54248861-54248880 MS.gene59042:CDS 40.0%
ATGATAACTATCGGAGGCCA+TGG + chr2.1:54248673-54248692 MS.gene59042:CDS 45.0%
CGGTTCATCTTAGTATCAGC+TGG - chr2.1:54249159-54249178 None:intergenic 45.0%
GCCACTGAGGTGTATAAAGA+TGG + chr2.1:54248553-54248572 MS.gene59042:CDS 45.0%
TAAGGCTCGATGTCATTGCT+CGG - chr2.1:54249273-54249292 None:intergenic 45.0%
TCGAGAATACATTGGCGTGA+AGG + chr2.1:54248450-54248469 MS.gene59042:CDS 45.0%
TGACATCGAGCCTTACATCT+TGG + chr2.1:54249278-54249297 MS.gene59042:CDS 45.0%
! GGTGAGCTTAAACTTTTGGC+AGG + chr2.1:54249120-54249139 MS.gene59042:CDS 45.0%
!! AACCGAGAGGTGTTCATTGA+GGG + chr2.1:54249174-54249193 MS.gene59042:CDS 45.0%
CATCGAGCCTTACATCTTGG+AGG + chr2.1:54249281-54249300 MS.gene59042:CDS 50.0%
TGGCGAAGCCTAGAATGAAG+TGG - chr2.1:54248537-54248556 None:intergenic 50.0%
! GCTGACTTCTCCAACTGCAT+TGG + chr2.1:54248883-54248902 MS.gene59042:CDS 50.0%
!! ATTTGTGGTAGTGGGCTTGC+AGG - chr2.1:54248987-54249006 None:intergenic 50.0%
!! GAACCGAGAGGTGTTCATTG+AGG + chr2.1:54249173-54249192 MS.gene59042:CDS 50.0%
CATTCTAGGCTTCGCCACTG+AGG + chr2.1:54248540-54248559 MS.gene59042:CDS 55.0%
CGCCCTCAATGAACACCTCT+CGG - chr2.1:54249179-54249198 None:intergenic 55.0%
CGGGACATTTCGTTCGCGAT+TGG + chr2.1:54248584-54248603 MS.gene59042:CDS 55.0%
GCTCGATGTCATTGCTCGGT+GGG - chr2.1:54249269-54249288 None:intergenic 55.0%
! GATGTCATTGCTCGGTGGGT+TGG - chr2.1:54249265-54249284 None:intergenic 55.0%
CAGGAGCTCTGTCGGAGCAA+TGG - chr2.1:54248968-54248987 None:intergenic 60.0%
GGCTCGATGTCATTGCTCGG+TGG - chr2.1:54249270-54249289 None:intergenic 60.0%
TGGGCTTGCAGGAGCTCTGT+CGG - chr2.1:54248976-54248995 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 54248400 54249335 54248400 ID=MS.gene59042
chr2.1 mRNA 54248400 54249335 54248400 ID=MS.gene59042.t1;Parent=MS.gene59042
chr2.1 exon 54248400 54249335 54248400 ID=MS.gene59042.t1.exon1;Parent=MS.gene59042.t1
chr2.1 CDS 54248400 54249335 54248400 ID=cds.MS.gene59042.t1;Parent=MS.gene59042.t1
Gene Sequence

>MS.gene59042

ATGTCTGATCACTCTCACAATATCAATGCCGTTTTGAGGCCAACAATTTTTCGAGAATACATTGGCGTGAAGGATGACCCAGAAACTTTAGATGATTTTCCTGTTAATATCATCAATGATGATGTCAATCAATTCCACTTCATTCTAGGCTTCGCCACTGAGGTGTATAAAGATGGAAAAGGAACGGGACATTTCGTTCGCGATTGGAACTTTGATTACTTCAGCCCAGAAAAAGTGTTCAAACACAAGAAAGAACATAAGAATATGAAGGTTATGATAACTATCGGAGGCCATGGCACTAAATATCCATTCAATCCTAAGGAGAAAAAGGTATGGATTTTCAATGCCATAAGCTCGATCAGACATATCATTCAAGACTATGAGAACTACCTTGTCAATGATGATTCTGGTAGCTGCCACTGCACTAGCATAATTGATGGTATTGATATTAACTATGAGTATATCGATTCTAGTGTGACTGGGGCTGACTTCTCCAACTGCATTGGACAAGTTATTAAACATCTCAAGAAGGATAAGCATGTATCCAAATCCATGGAATATGTGTCCATTGCTCCGACAGAGCTCCTGCAAGCCCACTACCACAAATTGTTTTGGGACCACAAAATGGATATCAACTATGTTGACTACAAGTTCTACAATCAAACTATATCCTCAAAGGATGAGTTTGATGATCTCTACAATCAACTAATAACGGATTACGGTGAGCTTAAACTTTTGGCAGGTGTTAGTACCGATCCAGCTGATACTAAGATGAACCGAGAGGTGTTCATTGAGGGCGTCACAAGACTGATCAACAGCAAATCACTCCTTGGACTTTTTGTTTGGAGTGCTAATGACTCTGCCAACCCACCGAGCAATGACATCGAGCCTTACATCTTGGAGGAAATGCTACAAGATCTCCTTACCAATAATTGA
Protein sequence

>MS.gene59042.t1

MSDHSHNINAVLRPTIFREYIGVKDDPETLDDFPVNIINDDVNQFHFILGFATEVYKDGKGTGHFVRDWNFDYFSPEKVFKHKKEHKNMKVMITIGGHGTKYPFNPKEKKVWIFNAISSIRHIIQDYENYLVNDDSGSCHCTSIIDGIDINYEYIDSSVTGADFSNCIGQVIKHLKKDKHVSKSMEYVSIAPTELLQAHYHKLFWDHKMDINYVDYKFYNQTISSKDEFDDLYNQLITDYGELKLLAGVSTDPADTKMNREVFIEGVTRLINSKSLLGLFVWSANDSANPPSNDIEPYILEEMLQDLLTNN