AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76548

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76548.t1 MTR_2g100825 98.065 310 6 0 1 310 1 310 0.0 625
MS.gene76548.t1 MTR_2g100830 74.286 315 76 3 1 310 1 315 9.93e-147 415
MS.gene76548.t1 MTR_8g030670 68.615 325 77 8 5 307 12 333 1.25e-136 391
MS.gene76548.t1 MTR_7g077810 59.813 321 104 8 5 307 12 325 1.39e-113 332
MS.gene76548.t1 MTR_6g053620 52.744 328 129 7 2 308 11 333 3.82e-101 301
MS.gene76548.t1 MTR_8g007185 56.209 306 95 6 1 296 1 277 2.47e-94 281
MS.gene76548.t1 MTR_6g053620 66.667 213 62 5 2 210 11 218 4.57e-94 282
MS.gene76548.t1 MTR_8g007205 55.882 306 96 6 1 296 1 277 9.73e-94 280
MS.gene76548.t1 MTR_8g007195 51.118 313 133 5 1 299 1 307 1.04e-80 248
MS.gene76548.t1 MTR_8g007220 45.955 309 129 8 1 300 1 280 7.92e-72 224
MS.gene76548.t1 MTR_7g036780 55.502 209 75 5 1 202 1 198 5.77e-67 209
MS.gene76548.t1 MTR_3g061700 44.770 239 78 5 60 296 1 187 1.53e-48 161
MS.gene76548.t1 MTR_4g032460 31.915 141 82 4 7 142 3 134 1.05e-14 70.9
MS.gene76548.t1 MTR_5g022710 31.852 135 83 3 13 142 9 139 1.74e-14 70.1
MS.gene76548.t1 MTR_5g022730 32.593 135 82 4 13 142 9 139 2.32e-14 69.7
MS.gene76548.t1 MTR_8g056060 31.507 146 90 3 11 150 8 149 1.91e-13 67.4
MS.gene76548.t1 MTR_8g468480 29.577 142 90 3 13 148 9 146 3.52e-13 66.6
MS.gene76548.t1 MTR_3g110048 29.371 143 90 3 13 148 10 148 4.64e-13 66.2
MS.gene76548.t1 MTR_4g032400 29.787 141 83 4 11 142 14 147 5.15e-13 66.2
MS.gene76548.t1 MTR_4g032510 32.143 140 84 5 11 146 9 141 7.29e-13 65.5
MS.gene76548.t1 MTR_7g094120 32.000 100 61 1 54 146 48 147 9.97e-13 65.5
MS.gene76548.t1 MTR_1g099870 35.484 93 53 2 63 148 1 93 3.14e-12 62.4
MS.gene76548.t1 MTR_7g021400 27.778 144 95 3 4 142 1 140 4.26e-12 63.5
MS.gene76548.t1 MTR_4g032450 28.369 141 91 4 11 145 26 162 5.91e-12 63.5
MS.gene76548.t1 MTR_7g094150 27.778 144 95 3 4 142 1 140 8.33e-12 62.8
MS.gene76548.t1 MTR_7g021380 29.054 148 88 5 4 142 1 140 1.98e-11 61.6
MS.gene76548.t1 MTR_4g032500 29.412 136 92 2 13 148 11 142 2.32e-11 61.2
MS.gene76548.t1 MTR_4g033460 27.007 137 91 3 11 142 12 144 4.25e-11 62.4
MS.gene76548.t1 MTR_4g033455 26.619 139 93 3 13 146 14 148 9.70e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76548.t1 AT3G61415 57.051 312 105 8 5 292 12 318 9.40e-108 317
MS.gene76548.t1 AT3G61415 57.051 312 105 8 5 292 12 318 1.00e-107 317
MS.gene76548.t1 AT2G45950 59.477 306 101 8 5 292 12 312 4.41e-102 303
MS.gene76548.t1 AT2G45950 59.477 306 101 8 5 292 12 312 4.41e-102 303
MS.gene76548.t1 AT2G45950 59.477 306 101 8 5 292 12 312 4.41e-102 303
MS.gene76548.t1 AT2G45950 59.868 304 99 8 5 290 12 310 1.41e-101 302
MS.gene76548.t1 AT2G45950 59.868 304 99 8 5 290 12 310 1.41e-101 302
MS.gene76548.t1 AT3G21850 29.932 147 91 4 6 146 1 141 6.85e-15 71.2
MS.gene76548.t1 AT1G75950 29.730 148 89 3 6 142 1 144 1.28e-14 70.9
MS.gene76548.t1 AT1G20140 30.000 160 90 5 4 148 1 153 4.53e-14 69.3
MS.gene76548.t1 AT2G03170 30.556 144 90 5 6 146 1 137 1.34e-13 67.8
MS.gene76548.t1 AT4G34210 29.655 145 93 3 6 146 1 140 2.46e-13 67.0
MS.gene76548.t1 AT2G25700 29.299 157 95 4 4 148 1 153 9.48e-13 65.5
MS.gene76548.t1 AT5G42190 27.152 151 85 3 13 142 9 155 1.73e-12 65.1
MS.gene76548.t1 AT4G34470 29.655 145 93 4 6 146 1 140 2.27e-12 64.3

Find 55 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAATTCTTCACATATAAA+TGG 0.142985 2.3:-2986490 None:intergenic
GTCAGCGCAGGAAAGGATTT+TGG 0.246591 2.3:+2987302 MS.gene76548:CDS
CAATATCTTGCTCCACTTGT+TGG 0.288855 2.3:-2986456 None:intergenic
CGCTCCTTGTTTGAGCGGCC+TGG 0.301444 2.3:-2986616 None:intergenic
TCTTACCGAGGAAGAGAAAT+TGG 0.313674 2.3:+2986816 MS.gene76548:CDS
CCTATCAATTCTTGCTTGTA+AGG 0.336967 2.3:-2987214 None:intergenic
TCCTGTTCTCATGTCAGAAA+TGG 0.338825 2.3:+2986387 None:intergenic
AAGACATACTGCACAATTCT+TGG 0.359550 2.3:-2986530 None:intergenic
AAGAAGAATGTGAAGGTAAA+TGG 0.364244 2.3:+2987063 MS.gene76548:CDS
ATATGTGAAGAATTGCAAAA+AGG 0.385772 2.3:+2986496 MS.gene76548:CDS
TGCAGTATGTCTTCCTCAAC+AGG 0.387815 2.3:+2986540 MS.gene76548:CDS
AATATCTTGCTCCACTTGTT+GGG 0.388897 2.3:-2986455 None:intergenic
CCTTCACATTCTTCTTATGT+TGG 0.409567 2.3:-2987056 None:intergenic
CTGCACACAGTCTACAATTC+CGG 0.410788 2.3:+2986701 MS.gene76548:CDS
GCAATTCTTCACATATAAAT+GGG 0.411971 2.3:-2986489 None:intergenic
TCTTCCTCGGTAAGATCATC+AGG 0.427229 2.3:-2986808 None:intergenic
CCTTACAAGCAAGAATTGAT+AGG 0.429208 2.3:+2987214 MS.gene76548:CDS
GAAGTTTGAAGCCACACATA+AGG 0.441329 2.3:-2986421 None:intergenic
TCAATTCTTGCTTGTAAGGC+CGG 0.456857 2.3:-2987210 None:intergenic
TCACTGATGACCCAAGCATT+AGG 0.467031 2.3:+2986854 MS.gene76548:CDS
CAAGGAACAATTTAATCTGC+GGG 0.474777 2.3:-2987253 None:intergenic
GTGTGGCTTCAAACTTCTGA+TGG 0.483405 2.3:+2986427 MS.gene76548:CDS
GTTTATCTGTTTCCGCACTT+TGG 0.495351 2.3:-2987104 None:intergenic
GGGCTCCAATTTCTCTTCCT+CGG 0.502445 2.3:-2986821 None:intergenic
CACAAATATGCTCTGTGAGT+TGG 0.512352 2.3:+2986672 MS.gene76548:CDS
GGTTCAAAAGCCTAATGCTT+GGG 0.515510 2.3:-2986864 None:intergenic
AATATGCTGCGTATTTCCTC+TGG 0.531066 2.3:-2986778 None:intergenic
AGCAAGAATTGATAGGGAAG+TGG 0.533628 2.3:+2987221 MS.gene76548:CDS
TGTCGATTTCATCAAGCACC+AGG 0.534958 2.3:+2986598 MS.gene76548:CDS
TTTCTTCGTCAGCGCAGGAA+AGG 0.538827 2.3:+2987295 MS.gene76548:CDS
CGGTTCAAAAGCCTAATGCT+TGG 0.541710 2.3:-2986865 None:intergenic
TTCTCTTCTTGGCATACAAG+CGG 0.552561 2.3:-2986885 None:intergenic
GTCTTGTATTCTCTCTTGCA+AGG 0.555467 2.3:-2987271 None:intergenic
CTTACAAGCAAGAATTGATA+GGG 0.556753 2.3:+2987215 MS.gene76548:CDS
AAAATCACCTTGTAAACTTG+AGG 0.557760 2.3:-2987136 None:intergenic
ATTGGAGAACTGACCTGTTG+AGG 0.564195 2.3:-2986553 None:intergenic
TGTGAGACCTCAAGTTTACA+AGG 0.569835 2.3:+2987129 MS.gene76548:CDS
TTGTGAGATCAATCAATGGC+CGG 0.572234 2.3:-2986720 None:intergenic
TTAAGAATTAAGCTCCACAT+TGG 0.575341 2.3:-2986571 None:intergenic
GTCATCAGTGATGTTTAACA+AGG 0.579418 2.3:-2986842 None:intergenic
CTCCATTAATAAAAGACAGA+AGG 0.582081 2.3:-2986981 None:intergenic
AGCACCAGGCCGCTCAAACA+AGG 0.585987 2.3:+2986612 MS.gene76548:CDS
GCAAGGAACAATTTAATCTG+CGG 0.587576 2.3:-2987254 None:intergenic
TATTGATGATGAGATTGATC+CGG 0.591105 2.3:+2987191 MS.gene76548:CDS
CGACTTGTGAGATCAATCAA+TGG 0.592768 2.3:-2986724 None:intergenic
TGTAAACTTGAGGTCTCACA+AGG 0.600049 2.3:-2987126 None:intergenic
TGATGGTTCAACCCAACAAG+TGG 0.601578 2.3:+2986444 MS.gene76548:CDS
AACAGGTCAGTTCTCCAATG+TGG 0.631635 2.3:+2986557 MS.gene76548:CDS
CCAACATAAGAAGAATGTGA+AGG 0.658942 2.3:+2987056 MS.gene76548:CDS
ACTTTCGCTCCTTGTTTGAG+CGG 0.668556 2.3:-2986621 None:intergenic
GTAAATGGTCATGACGACAT+CGG 0.684541 2.3:+2987078 MS.gene76548:CDS
TCATCAGTGATGTTTAACAA+GGG 0.698660 2.3:-2986841 None:intergenic
CGACATCGGACACCAAAGTG+CGG 0.709958 2.3:+2987092 MS.gene76548:CDS
TGTGCCTGATGATCTTACCG+AGG 0.742578 2.3:+2986804 MS.gene76548:CDS
AGATGACAAAGCCTTATGTG+TGG 0.770261 2.3:+2986410 MS.gene76548:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAAAAAAGAGGAAAAA+AGG + chr2.3:2987033-2987052 MS.gene76548:CDS 15.0%
!!! CTTCTAAGAATAAAAAAAAG+AGG + chr2.3:2987025-2987044 MS.gene76548:CDS 20.0%
! ATATGTGAAGAATTGCAAAA+AGG + chr2.3:2986496-2986515 MS.gene76548:CDS 25.0%
! GCAATTCTTCACATATAAAT+GGG - chr2.3:2986492-2986511 None:intergenic 25.0%
! TAGCTCGAATAATTGAAAAA+AGG + chr2.3:2986752-2986771 MS.gene76548:CDS 25.0%
! TGCAATTCTTCACATATAAA+TGG - chr2.3:2986493-2986512 None:intergenic 25.0%
!! AAGTTTACAAGGTGATTTTA+TGG + chr2.3:2987140-2987159 MS.gene76548:CDS 25.0%
AAAATCACCTTGTAAACTTG+AGG - chr2.3:2987139-2987158 None:intergenic 30.0%
AAGAAGAATGTGAAGGTAAA+TGG + chr2.3:2987063-2987082 MS.gene76548:CDS 30.0%
CTCCATTAATAAAAGACAGA+AGG - chr2.3:2986984-2987003 None:intergenic 30.0%
CTTACAAGCAAGAATTGATA+GGG + chr2.3:2987215-2987234 MS.gene76548:CDS 30.0%
TCATCAGTGATGTTTAACAA+GGG - chr2.3:2986844-2986863 None:intergenic 30.0%
TTAAGAATTAAGCTCCACAT+TGG - chr2.3:2986574-2986593 None:intergenic 30.0%
! AAGTAGTTCTTTTCTCTTCT+TGG - chr2.3:2986899-2986918 None:intergenic 30.0%
! GACCTTCTGTCTTTTATTAA+TGG + chr2.3:2986979-2986998 MS.gene76548:CDS 30.0%
! TTTTATTAATGGAGATCCGA+AGG + chr2.3:2986990-2987009 MS.gene76548:CDS 30.0%
!! TATTGATGATGAGATTGATC+CGG + chr2.3:2987191-2987210 MS.gene76548:CDS 30.0%
!!! GAAGTAGTTTTAATCTCCTT+CGG - chr2.3:2987009-2987028 None:intergenic 30.0%
AAGACATACTGCACAATTCT+TGG - chr2.3:2986533-2986552 None:intergenic 35.0%
AATATCTTGCTCCACTTGTT+GGG - chr2.3:2986458-2986477 None:intergenic 35.0%
CAAGGAACAATTTAATCTGC+GGG - chr2.3:2987256-2987275 None:intergenic 35.0%
CCAACATAAGAAGAATGTGA+AGG + chr2.3:2987056-2987075 MS.gene76548:CDS 35.0%
CCTATCAATTCTTGCTTGTA+AGG - chr2.3:2987217-2987236 None:intergenic 35.0%
CCTTACAAGCAAGAATTGAT+AGG + chr2.3:2987214-2987233 MS.gene76548:CDS 35.0%
CCTTCACATTCTTCTTATGT+TGG - chr2.3:2987059-2987078 None:intergenic 35.0%
GCAAGGAACAATTTAATCTG+CGG - chr2.3:2987257-2987276 None:intergenic 35.0%
GTCATCAGTGATGTTTAACA+AGG - chr2.3:2986845-2986864 None:intergenic 35.0%
TGAAGAATTGCAAAAAGGCA+TGG + chr2.3:2986501-2986520 MS.gene76548:CDS 35.0%
! GAAGAATTGCAAAAAGGCAT+GGG + chr2.3:2986502-2986521 MS.gene76548:CDS 35.0%
AATATGCTGCGTATTTCCTC+TGG - chr2.3:2986781-2986800 None:intergenic 40.0%
AATTGAAAAAAGGTCGCCAG+AGG + chr2.3:2986762-2986781 MS.gene76548:CDS 40.0%
AGCAAGAATTGATAGGGAAG+TGG + chr2.3:2987221-2987240 MS.gene76548:CDS 40.0%
CAATATCTTGCTCCACTTGT+TGG - chr2.3:2986459-2986478 None:intergenic 40.0%
CACAAATATGCTCTGTGAGT+TGG + chr2.3:2986672-2986691 MS.gene76548:CDS 40.0%
CGACTTGTGAGATCAATCAA+TGG - chr2.3:2986727-2986746 None:intergenic 40.0%
GGTTCAAAAGCCTAATGCTT+GGG - chr2.3:2986867-2986886 None:intergenic 40.0%
GTAAATGGTCATGACGACAT+CGG + chr2.3:2987078-2987097 MS.gene76548:CDS 40.0%
GTCTTGTATTCTCTCTTGCA+AGG - chr2.3:2987274-2987293 None:intergenic 40.0%
GTTTATCTGTTTCCGCACTT+TGG - chr2.3:2987107-2987126 None:intergenic 40.0%
TCAATTCTTGCTTGTAAGGC+CGG - chr2.3:2987213-2987232 None:intergenic 40.0%
TCTTACCGAGGAAGAGAAAT+TGG + chr2.3:2986816-2986835 MS.gene76548:CDS 40.0%
TGTAAACTTGAGGTCTCACA+AGG - chr2.3:2987129-2987148 None:intergenic 40.0%
TGTGAGACCTCAAGTTTACA+AGG + chr2.3:2987129-2987148 MS.gene76548:CDS 40.0%
TTCTCTTCTTGGCATACAAG+CGG - chr2.3:2986888-2986907 None:intergenic 40.0%
TTGTGAGATCAATCAATGGC+CGG - chr2.3:2986723-2986742 None:intergenic 40.0%
! AGATGACAAAGCCTTATGTG+TGG + chr2.3:2986410-2986429 MS.gene76548:CDS 40.0%
! GAAGTTTGAAGCCACACATA+AGG - chr2.3:2986424-2986443 None:intergenic 40.0%
AACAGGTCAGTTCTCCAATG+TGG + chr2.3:2986557-2986576 MS.gene76548:CDS 45.0%
ATTGGAGAACTGACCTGTTG+AGG - chr2.3:2986556-2986575 None:intergenic 45.0%
CGGTTCAAAAGCCTAATGCT+TGG - chr2.3:2986868-2986887 None:intergenic 45.0%
CTGCACACAGTCTACAATTC+CGG + chr2.3:2986701-2986720 MS.gene76548:CDS 45.0%
GTGTGGCTTCAAACTTCTGA+TGG + chr2.3:2986427-2986446 MS.gene76548:CDS 45.0%
TCACTGATGACCCAAGCATT+AGG + chr2.3:2986854-2986873 MS.gene76548:CDS 45.0%
TCTTCCTCGGTAAGATCATC+AGG - chr2.3:2986811-2986830 None:intergenic 45.0%
TGATGGTTCAACCCAACAAG+TGG + chr2.3:2986444-2986463 MS.gene76548:CDS 45.0%
TGCAGTATGTCTTCCTCAAC+AGG + chr2.3:2986540-2986559 MS.gene76548:CDS 45.0%
! ACTTTCGCTCCTTGTTTGAG+CGG - chr2.3:2986624-2986643 None:intergenic 45.0%
!! TGTCGATTTCATCAAGCACC+AGG + chr2.3:2986598-2986617 MS.gene76548:CDS 45.0%
GGGCTCCAATTTCTCTTCCT+CGG - chr2.3:2986824-2986843 None:intergenic 50.0%
TGTGCCTGATGATCTTACCG+AGG + chr2.3:2986804-2986823 MS.gene76548:CDS 50.0%
TTTCTTCGTCAGCGCAGGAA+AGG + chr2.3:2987295-2987314 MS.gene76548:CDS 50.0%
! AGACTTTTCTTCGTCAGCGC+AGG + chr2.3:2987290-2987309 MS.gene76548:CDS 50.0%
! GTCAGCGCAGGAAAGGATTT+TGG + chr2.3:2987302-2987321 MS.gene76548:CDS 50.0%
CGACATCGGACACCAAAGTG+CGG + chr2.3:2987092-2987111 MS.gene76548:CDS 55.0%
AGCACCAGGCCGCTCAAACA+AGG + chr2.3:2986612-2986631 MS.gene76548:CDS 60.0%
! CGCTCCTTGTTTGAGCGGCC+TGG - chr2.3:2986619-2986638 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 2986397 2987329 2986397 ID=MS.gene76548
chr2.3 mRNA 2986397 2987329 2986397 ID=MS.gene76548.t1;Parent=MS.gene76548
chr2.3 exon 2986397 2987329 2986397 ID=MS.gene76548.t1.exon1;Parent=MS.gene76548.t1
chr2.3 CDS 2986397 2987329 2986397 ID=cds.MS.gene76548.t1;Parent=MS.gene76548.t1
Gene Sequence

>MS.gene76548

ATGTCAGAAATGGAGATGACAAAGCCTTATGTGTGGCTTCAAACTTCTGATGGTTCAACCCAACAAGTGGAGCAAGATATTGCAATGTTTTGCCCATTTATATGTGAAGAATTGCAAAAAGGCATGGGATCTTCCAAGAATTGTGCAGTATGTCTTCCTCAACAGGTCAGTTCTCCAATGTGGAGCTTAATTCTTAATTATTGTCGATTTCATCAAGCACCAGGCCGCTCAAACAAGGAGCGAAAGTCGTATGATGATAGTTTCGTTAAGATAGACACAAATATGCTCTGTGAGTTGGCGTGTGCTGCACACAGTCTACAATTCCGGCCATTGATTGATCTCACAAGTCGTGCACTAGCTCGAATAATTGAAAAAAGGTCGCCAGAGGAAATACGCAGCATATTTCGTGTGCCTGATGATCTTACCGAGGAAGAGAAATTGGAGCCCTTGTTAAACATCACTGATGACCCAAGCATTAGGCTTTTGAACCGCTTGTATGCCAAGAAGAGAAAAGAACTACTTAAAGAGCGTGAAAGCATAAAGAAGAATGTTGATGTTGAAGAAGATGAACGTTCAGTTGACGACCTTCTGTCTTTTATTAATGGAGATCCGAAGGAGATTAAAACTACTTCTAAGAATAAAAAAAAGAGGAAAAAAGGCCAACATAAGAAGAATGTGAAGGTAAATGGTCATGACGACATCGGACACCAAAGTGCGGAAACAGATAAACCTTGTGAGACCTCAAGTTTACAAGGTGATTTTATGGTTGAGTTTGATGATGATAATAATGATGATATTGATGATGAGATTGATCCGGCCTTACAAGCAAGAATTGATAGGGAAGTGGAAGAATTTGCCCGCAGATTAAATTGTTCCTTGCAAGAGAGAATACAAGACTTTTCTTCGTCAGCGCAGGAAAGGATTTTGGCTTGA
Protein sequence

>MS.gene76548.t1

MSEMEMTKPYVWLQTSDGSTQQVEQDIAMFCPFICEELQKGMGSSKNCAVCLPQQVSSPMWSLILNYCRFHQAPGRSNKERKSYDDSFVKIDTNMLCELACAAHSLQFRPLIDLTSRALARIIEKRSPEEIRSIFRVPDDLTEEEKLEPLLNITDDPSIRLLNRLYAKKRKELLKERESIKKNVDVEEDERSVDDLLSFINGDPKEIKTTSKNKKKRKKGQHKKNVKVNGHDDIGHQSAETDKPCETSSLQGDFMVEFDDDNNDDIDDEIDPALQARIDREVEEFARRLNCSLQERIQDFSSSAQERILA