AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054242

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054242.t1 MTR_3g011990 58.491 318 83 4 1 317 27 296 4.25e-120 347
MS.gene054242.t1 MTR_8g466760 59.248 319 80 5 1 317 27 297 1.12e-118 343
MS.gene054242.t1 MTR_3g011970 56.113 319 96 4 1 317 27 303 1.39e-103 305
MS.gene054242.t1 MTR_3g012010 52.469 324 102 7 1 317 27 305 4.78e-96 286
MS.gene054242.t1 MTR_3g009410 51.084 323 108 8 2 317 28 307 3.09e-83 254
MS.gene054242.t1 MTR_7g026977 44.548 321 140 9 1 300 28 331 1.04e-70 223
MS.gene054242.t1 MTR_5g008310 38.583 381 124 10 1 317 1 335 6.98e-62 200
MS.gene054242.t1 MTR_5g008320 40.263 380 118 11 1 317 1 334 1.71e-61 199
MS.gene054242.t1 MTR_7g022960 42.767 318 127 9 4 317 22 288 3.41e-58 189
MS.gene054242.t1 MTR_7g023010 50.000 216 85 7 106 317 68 264 2.65e-56 183
MS.gene054242.t1 MTR_7g022980 50.926 216 91 6 106 317 68 272 7.42e-56 182
MS.gene054242.t1 MTR_5g008280 35.034 294 92 9 39 279 14 261 1.64e-35 132
MS.gene054242.t1 MTR_5g008280 49.306 144 64 5 180 317 247 387 1.69e-22 97.1
MS.gene054242.t1 MTR_5g008390 40.000 115 40 2 93 206 3 89 4.63e-21 86.3
MS.gene054242.t1 MTR_7g026710 44.371 151 72 8 175 317 14 160 3.04e-20 86.7
MS.gene054242.t1 MTR_7g026700 42.384 151 76 7 175 317 14 161 4.19e-18 80.9
MS.gene054242.t1 MTR_8g466770 52.459 61 19 1 106 166 77 127 6.08e-13 65.5
MS.gene054242.t1 MTR_1g106730 36.471 85 38 1 60 128 69 153 3.92e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 61 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGGTGCTATTATGAAATT+TGG 0.100017 6.1:-26377607 MS.gene054242:CDS
TCTTGTGTCATTGAGAAATA+TGG 0.189284 6.1:-26377710 MS.gene054242:CDS
TTGGCGGCGCAGCTACTTTA+AGG 0.197167 6.1:-26377654 MS.gene054242:CDS
CACGGGAACTGGATCGTCTT+TGG 0.234009 6.1:+26378299 None:intergenic
CCTTATAATTATAGGACAAT+TGG 0.303797 6.1:-26377841 MS.gene054242:CDS
AGGTATGATCGCGGTGCTTT+TGG 0.305418 6.1:-26377919 MS.gene054242:CDS
CCAATTGTCCTATAATTATA+AGG 0.318950 6.1:+26377841 None:intergenic
CTTATAATTATAGGACAATT+GGG 0.334379 6.1:-26377840 MS.gene054242:CDS
GATTGCTTCACAAAATCAAT+AGG 0.350022 6.1:+26378321 None:intergenic
ATGGTTACCCCACACAGTTT+TGG 0.353666 6.1:-26377775 MS.gene054242:CDS
TTCAACTTCGACACGGGAAC+TGG 0.370674 6.1:+26378288 None:intergenic
AATATGGGAAGTGGTAATAA+TGG 0.385817 6.1:-26377694 MS.gene054242:CDS
AGAATATTGTTTATTGCAAA+AGG 0.387301 6.1:+26378140 None:intergenic
GTACTTGAATAACTACGATA+TGG 0.394297 6.1:+26377874 None:intergenic
ACCGTCCGATTGTGACTCTT+CGG 0.405353 6.1:-26377464 MS.gene054242:CDS
AGAATATCGTTTCTTGCAAA+AGG 0.407785 6.1:+26378044 None:intergenic
GGGTAACCATAGGGTTATAA+GGG 0.408071 6.1:+26377788 None:intergenic
TTGTTGTTCTCTTCTATCCC+TGG 0.408985 6.1:+26378201 None:intergenic
CCGTCCGATTGTGACTCTTC+GGG 0.440651 6.1:-26377463 MS.gene054242:CDS
AATAATGGAGTTGAAAATCT+AGG 0.441678 6.1:-26377679 MS.gene054242:CDS
GGAGTTGAAAATCTAGGTAT+TGG 0.442823 6.1:-26377673 MS.gene054242:CDS
GATGATGAACCAATTCGAAT+TGG 0.458337 6.1:+26378246 None:intergenic
TGCTCTTTCAACTTCGACAC+GGG 0.461194 6.1:+26378282 None:intergenic
TTGATCATGAATGCCATCCT+TGG 0.475181 6.1:+26377510 None:intergenic
GGGGTAACCATAGGGTTATA+AGG 0.478892 6.1:+26377787 None:intergenic
TATTCTACTGCACAAGCGTT+GGG 0.488486 6.1:-26378027 MS.gene054242:CDS
TATTCTACTGCACAAGCGTT+GGG 0.488486 6.1:-26378123 MS.gene054242:CDS
AAAGGAGCATGAGAAAGATC+TGG 0.489039 6.1:+26378158 None:intergenic
CTTGTGTCATTGAGAAATAT+GGG 0.491632 6.1:-26377709 MS.gene054242:CDS
GGACGGTTCATCTTCAATGT+TGG 0.501871 6.1:+26377480 None:intergenic
GGTAACCATAGGGTTATAAG+GGG 0.503842 6.1:+26377789 None:intergenic
AAACTGTGTGGGGTAACCAT+AGG 0.512662 6.1:+26377778 None:intergenic
TGTGGCTTCTAATTCTTCCA+AGG 0.517229 6.1:-26377527 MS.gene054242:CDS
TCGCCTTCCTATGAGCGCTC+TGG 0.527918 6.1:+26378094 None:intergenic
GAGGACACCAGAGCGCTCAT+AGG 0.532993 6.1:-26378101 MS.gene054242:CDS
TACAGAAAAGCAAATTATTG+TGG 0.538998 6.1:-26377545 MS.gene054242:CDS
AACTGTGTGGGGTAACCATA+GGG 0.541720 6.1:+26377779 None:intergenic
GAGGACACAAGACCGCTCAT+AGG 0.547668 6.1:-26378005 MS.gene054242:CDS
GACTATACCCAAAACTGTGT+GGG 0.547710 6.1:+26377767 None:intergenic
GCTTCTAATTCTTCCAAGGA+TGG 0.549389 6.1:-26377523 MS.gene054242:CDS
ATATTCTACTGCACAAGCGT+TGG 0.555787 6.1:-26378124 MS.gene054242:CDS
ATATTCTACTGCACAAGCGT+TGG 0.562358 6.1:-26378028 MS.gene054242:CDS
ACACCAGAGCGCTCATAGGA+AGG 0.568364 6.1:-26378097 MS.gene054242:CDS
GTTGAAAATCTAGGTATTGG+CGG 0.573766 6.1:-26377670 MS.gene054242:CDS
ACACAAGACCGCTCATAGGA+AGG 0.576634 6.1:-26378001 MS.gene054242:CDS
AAGACCCGAAGAGTCACAAT+CGG 0.595608 6.1:+26377459 None:intergenic
TAGGACAATTGGGGTTAGCA+CGG 0.599922 6.1:-26377830 MS.gene054242:CDS
CGCATGCTCCTTCCTATGAG+CGG 0.602536 6.1:+26377993 None:intergenic
TTATAATTATAGGACAATTG+GGG 0.608675 6.1:-26377839 MS.gene054242:CDS
GCTACTTTAAGGATCGAACA+TGG 0.613690 6.1:-26377643 MS.gene054242:CDS
CGACTATACCCAAAACTGTG+TGG 0.624848 6.1:+26377766 None:intergenic
GTGCTCTTTCAACTTCGACA+CGG 0.625193 6.1:+26378281 None:intergenic
TTCTCAATGACACAAGAGGA+TGG 0.626783 6.1:+26377716 None:intergenic
TCATTGAGAAATATGGGAAG+TGG 0.627718 6.1:-26377703 MS.gene054242:CDS
ATATTTCTCAATGACACAAG+AGG 0.629538 6.1:+26377712 None:intergenic
CCCGAAGAGTCACAATCGGA+CGG 0.656506 6.1:+26377463 None:intergenic
ACTATACCCAAAACTGTGTG+GGG 0.665224 6.1:+26377768 None:intergenic
GTAACCATAGGGTTATAAGG+GGG 0.669111 6.1:+26377790 None:intergenic
TCTACTGCACAAGCGTTGGG+AGG 0.691089 6.1:-26378024 MS.gene054242:CDS
TCTACTGCACAAGCGTTGGG+AGG 0.691089 6.1:-26378120 MS.gene054242:CDS
CATAAACAAAGGTATGATCG+CGG 0.728571 6.1:-26377928 MS.gene054242:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTACACCTTATAATTAT+AGG - chr6.1:26377958-26377977 MS.gene054242:CDS 15.0%
!! AGAATATTGTTTATTGCAAA+AGG + chr6.1:26377670-26377689 None:intergenic 20.0%
!! CATGGTTCAAATAAAAAAAT+TGG - chr6.1:26378182-26378201 MS.gene054242:CDS 20.0%
!! CTTATAATTATAGGACAATT+GGG - chr6.1:26377967-26377986 MS.gene054242:CDS 20.0%
!! TAGAAAAACAACATAAACAA+AGG - chr6.1:26377868-26377887 MS.gene054242:CDS 20.0%
!! TTATAATTATAGGACAATTG+GGG - chr6.1:26377968-26377987 MS.gene054242:CDS 20.0%
! CCAATTGTCCTATAATTATA+AGG + chr6.1:26377969-26377988 None:intergenic 25.0%
! CCTTATAATTATAGGACAAT+TGG - chr6.1:26377966-26377985 MS.gene054242:CDS 25.0%
! TACAGAAAAGCAAATTATTG+TGG - chr6.1:26378262-26378281 MS.gene054242:CDS 25.0%
!! AATAATGGAGTTGAAAATCT+AGG - chr6.1:26378128-26378147 MS.gene054242:CDS 25.0%
!!! ATTGGTGCTATTATGAAATT+TGG - chr6.1:26378200-26378219 MS.gene054242:CDS 25.0%
!!! CTTTTTGGATTTTGATTTCA+AGG + chr6.1:26377466-26377485 None:intergenic 25.0%
AATATGGGAAGTGGTAATAA+TGG - chr6.1:26378113-26378132 MS.gene054242:CDS 30.0%
AGAATATCGTTTCTTGCAAA+AGG + chr6.1:26377766-26377785 None:intergenic 30.0%
ATATTTCTCAATGACACAAG+AGG + chr6.1:26378098-26378117 None:intergenic 30.0%
GATTGCTTCACAAAATCAAT+AGG + chr6.1:26377489-26377508 None:intergenic 30.0%
GTACTTGAATAACTACGATA+TGG + chr6.1:26377936-26377955 None:intergenic 30.0%
! CACAAAATCAATAGGCTTTT+TGG + chr6.1:26377481-26377500 None:intergenic 30.0%
! CTTGTGTCATTGAGAAATAT+GGG - chr6.1:26378098-26378117 MS.gene054242:CDS 30.0%
! TATTTTCAGCCAATTCGAAT+TGG - chr6.1:26377552-26377571 MS.gene054242:CDS 30.0%
! TCTTGTGTCATTGAGAAATA+TGG - chr6.1:26378097-26378116 MS.gene054242:CDS 30.0%
!! ATTTTTGTTGTCAGGAAAAC+AGG + chr6.1:26377586-26377605 None:intergenic 30.0%
GATGATGAACCAATTCGAAT+TGG + chr6.1:26377564-26377583 None:intergenic 35.0%
GGAGTTGAAAATCTAGGTAT+TGG - chr6.1:26378134-26378153 MS.gene054242:CDS 35.0%
TCATTGAGAAATATGGGAAG+TGG - chr6.1:26378104-26378123 MS.gene054242:CDS 35.0%
TTCCTGACAACAAAAATCCA+GGG - chr6.1:26377589-26377608 MS.gene054242:CDS 35.0%
TTTCCTGACAACAAAAATCC+AGG - chr6.1:26377588-26377607 MS.gene054242:CDS 35.0%
! CATAAACAAAGGTATGATCG+CGG - chr6.1:26377879-26377898 MS.gene054242:CDS 35.0%
!! GTTGAAAATCTAGGTATTGG+CGG - chr6.1:26378137-26378156 MS.gene054242:CDS 35.0%
ACTATACCCAAAACTGTGTG+GGG + chr6.1:26378042-26378061 None:intergenic 40.0%
ATATTCTACTGCACAAGCGT+TGG - chr6.1:26377683-26377702 MS.gene054242:CDS 40.0%
GACTATACCCAAAACTGTGT+GGG + chr6.1:26378043-26378062 None:intergenic 40.0%
GCTTCTAATTCTTCCAAGGA+TGG - chr6.1:26378284-26378303 MS.gene054242:CDS 40.0%
GGGTAACCATAGGGTTATAA+GGG + chr6.1:26378022-26378041 None:intergenic 40.0%
GGTAACCATAGGGTTATAAG+GGG + chr6.1:26378021-26378040 None:intergenic 40.0%
GTAACCATAGGGTTATAAGG+GGG + chr6.1:26378020-26378039 None:intergenic 40.0%
TATTCTACTGCACAAGCGTT+GGG - chr6.1:26377684-26377703 MS.gene054242:CDS 40.0%
TGTGGCTTCTAATTCTTCCA+AGG - chr6.1:26378280-26378299 MS.gene054242:CDS 40.0%
TTCTCAATGACACAAGAGGA+TGG + chr6.1:26378094-26378113 None:intergenic 40.0%
TTGATCATGAATGCCATCCT+TGG + chr6.1:26378300-26378319 None:intergenic 40.0%
! AAAGGAGCATGAGAAAGATC+TGG + chr6.1:26377652-26377671 None:intergenic 40.0%
! GCTACTTTAAGGATCGAACA+TGG - chr6.1:26378164-26378183 MS.gene054242:CDS 40.0%
! TTGTTGTTCTCTTCTATCCC+TGG + chr6.1:26377609-26377628 None:intergenic 40.0%
!! ATCCCTGGATTTTTGTTGTC+AGG + chr6.1:26377594-26377613 None:intergenic 40.0%
AAACTGTGTGGGGTAACCAT+AGG + chr6.1:26378032-26378051 None:intergenic 45.0%
AACTGTGTGGGGTAACCATA+GGG + chr6.1:26378031-26378050 None:intergenic 45.0%
AAGACCCCCTTATAACCCTA+TGG - chr6.1:26378013-26378032 MS.gene054242:CDS 45.0%
AAGACCCGAAGAGTCACAAT+CGG + chr6.1:26378351-26378370 None:intergenic 45.0%
CGACTATACCCAAAACTGTG+TGG + chr6.1:26378044-26378063 None:intergenic 45.0%
GGACGGTTCATCTTCAATGT+TGG + chr6.1:26378330-26378349 None:intergenic 45.0%
GGGGTAACCATAGGGTTATA+AGG + chr6.1:26378023-26378042 None:intergenic 45.0%
GTGCTCTTTCAACTTCGACA+CGG + chr6.1:26377529-26377548 None:intergenic 45.0%
TGCTCTTTCAACTTCGACAC+GGG + chr6.1:26377528-26377547 None:intergenic 45.0%
! ATGGTTACCCCACACAGTTT+TGG - chr6.1:26378032-26378051 MS.gene054242:CDS 45.0%
! TAGGACAATTGGGGTTAGCA+CGG - chr6.1:26377977-26377996 MS.gene054242:CDS 45.0%
! TGGTTACCCCACACAGTTTT+GGG - chr6.1:26378033-26378052 MS.gene054242:CDS 45.0%
!!! ATCGCGGTGCTTTTGGTTTA+GGG - chr6.1:26377895-26377914 MS.gene054242:CDS 45.0%
ACACAAGACCGCTCATAGGA+AGG - chr6.1:26377806-26377825 MS.gene054242:CDS 50.0%
ACCGTCCGATTGTGACTCTT+CGG - chr6.1:26378343-26378362 MS.gene054242:CDS 50.0%
TTCAACTTCGACACGGGAAC+TGG + chr6.1:26377522-26377541 None:intergenic 50.0%
! AGGTATGATCGCGGTGCTTT+TGG - chr6.1:26377888-26377907 MS.gene054242:CDS 50.0%
!!! GATCGCGGTGCTTTTGGTTT+AGG - chr6.1:26377894-26377913 MS.gene054242:CDS 50.0%
CACGGGAACTGGATCGTCTT+TGG + chr6.1:26377511-26377530 None:intergenic 55.0%
CCCGAAGAGTCACAATCGGA+CGG + chr6.1:26378347-26378366 None:intergenic 55.0%
CCGTCCGATTGTGACTCTTC+GGG - chr6.1:26378344-26378363 MS.gene054242:CDS 55.0%
CGCATGCTCCTTCCTATGAG+CGG + chr6.1:26377817-26377836 None:intergenic 55.0%
GAGGACACAAGACCGCTCAT+AGG - chr6.1:26377802-26377821 MS.gene054242:CDS 55.0%
! ACACCAGAGCGCTCATAGGA+AGG - chr6.1:26377710-26377729 MS.gene054242:CDS 55.0%
! TTGGCGGCGCAGCTACTTTA+AGG - chr6.1:26378153-26378172 MS.gene054242:CDS 55.0%
!! TCTACTGCACAAGCGTTGGG+AGG - chr6.1:26377687-26377706 MS.gene054242:CDS 55.0%
TCGCCTTCCTATGAGCGCTC+TGG + chr6.1:26377716-26377735 None:intergenic 60.0%
! GAGGACACCAGAGCGCTCAT+AGG - chr6.1:26377706-26377725 MS.gene054242:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 26377438 26378391 26377438 ID=MS.gene054242
chr6.1 mRNA 26377438 26378391 26377438 ID=MS.gene054242.t1;Parent=MS.gene054242
chr6.1 exon 26377438 26378391 26377438 ID=MS.gene054242.t1.exon1;Parent=MS.gene054242.t1
chr6.1 CDS 26377438 26378391 26377438 ID=cds.MS.gene054242.t1;Parent=MS.gene054242.t1
Gene Sequence

>MS.gene054242

ATGAAGGAGAAAGAACAAGTTCAATCCTTGAAATCAAAATCCAAAAAGCCTATTGATTTTGTGAAGCAATCCAAAGACGATCCAGTTCCCGTGTCGAAGTTGAAAGAGCACAGTTATTTTCAGCCAATTCGAATTGGTTCATCATCCTGTTTTCCTGACAACAAAAATCCAGGGATAGAAGAGAACAACAAAAAAGAGAAGAATTCGTATTCCAGATCTTTCTCATGCTCCTTTTGCAATAAACAATATTCTACTGCACAAGCGTTGGGAGGACACCAGAGCGCTCATAGGAAGGCGAATTCAGATTCAAGATCTTTCTCTTGCTCCTTTTGCAAGAAACGATATTCTACTGCACAAGCGTTGGGAGGACACAAGACCGCTCATAGGAAGGAGCATGCGTTAGAAAAATCTCAGAAGAAGAAACAAGCTTTAGAAAAACAACATAAACAAAGGTATGATCGCGGTGCTTTTGGTTTAGGGAAATCTTACTTTGATCCATATCGTAGTTATTCAAGTACTCTTTTTACACCTTATAATTATAGGACAATTGGGGTTAGCACGGACTCAATGATTCGAAGACCCCCTTATAACCCTATGGTTACCCCACACAGTTTTGGGTATAGTCGTTCTGCATTGTTGCAAGAGATAACACACCATCCTCTTGTGTCATTGAGAAATATGGGAAGTGGTAATAATGGAGTTGAAAATCTAGGTATTGGCGGCGCAGCTACTTTAAGGATCGAACATGGTTCAAATAAAAAAATTGGTGCTATTATGAAATTTGGAGATTCGTCTACAAATATTGCTACAAGTTCAAATTCAAATACAGAAAAGCAAATTATTGTGGCTTCTAATTCTTCCAAGGATGGCATTCATGATCAATCAAAGTCCAACATTGAAGATGAACCGTCCGATTGTGACTCTTCGGGTCTTGATTTATCTCTTAAGCTTTAA
Protein sequence

>MS.gene054242.t1

MKEKEQVQSLKSKSKKPIDFVKQSKDDPVPVSKLKEHSYFQPIRIGSSSCFPDNKNPGIEENNKKEKNSYSRSFSCSFCNKQYSTAQALGGHQSAHRKANSDSRSFSCSFCKKRYSTAQALGGHKTAHRKEHALEKSQKKKQALEKQHKQRYDRGAFGLGKSYFDPYRSYSSTLFTPYNYRTIGVSTDSMIRRPPYNPMVTPHSFGYSRSALLQEITHHPLVSLRNMGSGNNGVENLGIGGAATLRIEHGSNKKIGAIMKFGDSSTNIATSSNSNTEKQIIVASNSSKDGIHDQSKSNIEDEPSDCDSSGLDLSLKL