AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41971

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41971.t1 MTR_3g011990 59.012 344 92 4 1 343 1 296 5.08e-124 358
MS.gene41971.t1 MTR_8g466760 58.559 333 88 5 13 343 13 297 8.99e-123 355
MS.gene41971.t1 MTR_3g011970 56.456 333 101 4 13 343 13 303 1.62e-108 319
MS.gene41971.t1 MTR_3g012010 52.857 350 113 7 1 343 1 305 2.17e-104 308
MS.gene41971.t1 MTR_3g009410 48.665 337 123 8 14 343 14 307 1.44e-86 263
MS.gene41971.t1 MTR_7g026977 39.211 380 128 9 1 326 1 331 8.90e-67 214
MS.gene41971.t1 MTR_7g022960 43.228 347 134 9 1 343 1 288 1.99e-65 208
MS.gene41971.t1 MTR_5g008310 38.058 381 126 10 27 343 1 335 2.23e-59 194
MS.gene41971.t1 MTR_5g008320 39.737 380 120 11 27 343 1 334 5.34e-59 193
MS.gene41971.t1 MTR_7g023010 39.769 347 122 11 1 343 1 264 2.44e-58 189
MS.gene41971.t1 MTR_7g022980 40.634 347 127 11 1 343 1 272 6.46e-57 186
MS.gene41971.t1 MTR_5g008280 35.034 294 92 9 65 305 14 261 6.38e-35 131
MS.gene41971.t1 MTR_5g008280 48.611 144 65 5 206 343 247 387 1.90e-21 94.4
MS.gene41971.t1 MTR_5g008390 39.130 115 41 2 119 232 3 89 1.05e-19 83.2
MS.gene41971.t1 MTR_7g026710 43.709 151 73 8 201 343 14 160 2.82e-19 84.3
MS.gene41971.t1 MTR_7g026700 41.722 151 77 7 201 343 14 161 4.08e-17 78.2
MS.gene41971.t1 MTR_8g466770 52.459 61 19 1 132 192 77 127 5.82e-13 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 63 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGGTGCTATTATGAAATT+TGG 0.100017 6.4:-18323733 MS.gene41971:CDS
TCTTGTGTCATTGAGAAATA+TGG 0.189284 6.4:-18323836 MS.gene41971:CDS
TTGGCGGCGCAGCTACTTTA+AGG 0.197167 6.4:-18323780 MS.gene41971:CDS
CACGGGAACTGGATCGTCTT+TGG 0.234009 6.4:+18324425 None:intergenic
CCTTATAATTATAGGACAAT+TGG 0.303797 6.4:-18323967 MS.gene41971:CDS
AGGTATGATCGCGGTGCTTT+TGG 0.305418 6.4:-18324045 MS.gene41971:CDS
CCAATTGTCCTATAATTATA+AGG 0.318950 6.4:+18323967 None:intergenic
CTTATAATTATAGGACAATT+GGG 0.334379 6.4:-18323966 MS.gene41971:CDS
GATTGCTTCACAAAATCAAT+AGG 0.350022 6.4:+18324447 None:intergenic
ATGGTTACCCCACACAGTTT+TGG 0.353666 6.4:-18323901 MS.gene41971:CDS
TTCAACTTCGACACGGGAAC+TGG 0.370674 6.4:+18324414 None:intergenic
AATATGGGAAGTGGTAATAA+TGG 0.385817 6.4:-18323820 MS.gene41971:CDS
AGAATATTGTTTATTGCAAA+AGG 0.387301 6.4:+18324266 None:intergenic
GTACTTGAATAACTACGATA+TGG 0.394297 6.4:+18324000 None:intergenic
ACCGTCCGATTGTGACTCTT+CGG 0.405353 6.4:-18323590 MS.gene41971:CDS
AGAATATCGTTTCTTGCAAA+AGG 0.407785 6.4:+18324170 None:intergenic
GGGTAACCATAGGGTTATAA+GGG 0.408071 6.4:+18323914 None:intergenic
TTGTTGTTCTCTTCTATCCC+TGG 0.408985 6.4:+18324327 None:intergenic
GTTAGAGATGCTAGAGGATT+CGG 0.427425 6.4:+18324566 None:intergenic
CCGTCCGATTGTGACTCTTC+GGG 0.440651 6.4:-18323589 MS.gene41971:CDS
AATAATGGAGTTGAAAATCT+AGG 0.441678 6.4:-18323805 MS.gene41971:CDS
GGAGTTGAAAATCTAGGTAT+TGG 0.442823 6.4:-18323799 MS.gene41971:CDS
TGCTCTTTCAACTTCGACAC+GGG 0.451823 6.4:+18324408 None:intergenic
GATGATGAACCAATTCGAAT+TGG 0.458337 6.4:+18324372 None:intergenic
TTGATCATGAATGCCATCCT+TGG 0.475181 6.4:+18323636 None:intergenic
GGGGTAACCATAGGGTTATA+AGG 0.478892 6.4:+18323913 None:intergenic
TATTCTACTGCACAAGCGTT+GGG 0.488486 6.4:-18324153 MS.gene41971:CDS
TATTCTACTGCACAAGCGTT+GGG 0.488486 6.4:-18324249 MS.gene41971:CDS
AAAGGAGCATGAGAAAGATC+TGG 0.489039 6.4:+18324284 None:intergenic
CTTGTGTCATTGAGAAATAT+GGG 0.491632 6.4:-18323835 MS.gene41971:CDS
GGTAACCATAGGGTTATAAG+GGG 0.503842 6.4:+18323915 None:intergenic
AAACTGTGTGGGGTAACCAT+AGG 0.512662 6.4:+18323904 None:intergenic
TGTGGCTTCTAATTCTTCCA+AGG 0.517229 6.4:-18323653 MS.gene41971:CDS
GGACGGTTCATCTTCAATGT+TGG 0.519743 6.4:+18323606 None:intergenic
TCTCCTTCCTATGAGCGCTC+TGG 0.526806 6.4:+18324220 None:intergenic
GAGGACACCAGAGCGCTCAT+AGG 0.532993 6.4:-18324227 MS.gene41971:CDS
AACTGTGTGGGGTAACCATA+GGG 0.541720 6.4:+18323905 None:intergenic
GAGGACACAAGACCGCTCAT+AGG 0.547668 6.4:-18324131 MS.gene41971:CDS
GACTATACCCAAAACTGTGT+GGG 0.547710 6.4:+18323893 None:intergenic
GCTTCTAATTCTTCCAAGGA+TGG 0.549389 6.4:-18323649 MS.gene41971:CDS
ATATTCTACTGCACAAGCGT+TGG 0.555787 6.4:-18324250 MS.gene41971:CDS
TCTAACACTTCACAAGATCA+AGG 0.556382 6.4:-18324549 MS.gene41971:CDS
ATATTCTACTGCACAAGCGT+TGG 0.562358 6.4:-18324154 MS.gene41971:CDS
ACACCAGAGCGCTCATAGGA+AGG 0.562791 6.4:-18324223 MS.gene41971:CDS
GTTGAAAATCTAGGTATTGG+CGG 0.573766 6.4:-18323796 MS.gene41971:CDS
ACACAAGACCGCTCATAGGA+AGG 0.576634 6.4:-18324127 MS.gene41971:CDS
AAGACCCGAAGAGTCACAAT+CGG 0.595608 6.4:+18323585 None:intergenic
TAGGACAATTGGGGTTAGCA+CGG 0.599922 6.4:-18323956 MS.gene41971:CDS
CGCATGCTCCTTCCTATGAG+CGG 0.602536 6.4:+18324119 None:intergenic
TTATAATTATAGGACAATTG+GGG 0.608675 6.4:-18323965 MS.gene41971:CDS
GTGCTCTTTCAACTTCGACA+CGG 0.612007 6.4:+18324407 None:intergenic
GCTACTTTAAGGATCGAACA+TGG 0.613690 6.4:-18323769 MS.gene41971:CDS
CGACTATACCCAAAACTGTG+TGG 0.624848 6.4:+18323892 None:intergenic
TTCTCAATGACACAAGAGGA+TGG 0.626783 6.4:+18323842 None:intergenic
TCATTGAGAAATATGGGAAG+TGG 0.627718 6.4:-18323829 MS.gene41971:CDS
ATATTTCTCAATGACACAAG+AGG 0.629538 6.4:+18323838 None:intergenic
TGAAGTGTTAGAGATGCTAG+AGG 0.648531 6.4:+18324560 None:intergenic
CCCGAAGAGTCACAATCGGA+CGG 0.656506 6.4:+18323589 None:intergenic
ACTATACCCAAAACTGTGTG+GGG 0.665224 6.4:+18323894 None:intergenic
GTAACCATAGGGTTATAAGG+GGG 0.669111 6.4:+18323916 None:intergenic
TCTACTGCACAAGCGTTGGG+AGG 0.691089 6.4:-18324150 MS.gene41971:CDS
TCTACTGCACAAGCGTTGGG+AGG 0.691089 6.4:-18324246 MS.gene41971:CDS
CATAAACAAAGGTATGATCG+CGG 0.728571 6.4:-18324054 MS.gene41971:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTACACCTTATAATTAT+AGG - chr6.4:18324162-18324181 MS.gene41971:CDS 15.0%
!! AGAATATTGTTTATTGCAAA+AGG + chr6.4:18323874-18323893 None:intergenic 20.0%
!! CATGGTTCAAATAAAAAAAT+TGG - chr6.4:18324386-18324405 MS.gene41971:CDS 20.0%
!! CTTATAATTATAGGACAATT+GGG - chr6.4:18324171-18324190 MS.gene41971:CDS 20.0%
!! TACAGAAAAACAAATTATTG+TGG - chr6.4:18324466-18324485 MS.gene41971:CDS 20.0%
!! TAGAAAAACAACATAAACAA+AGG - chr6.4:18324072-18324091 MS.gene41971:CDS 20.0%
!! TTATAATTATAGGACAATTG+GGG - chr6.4:18324172-18324191 MS.gene41971:CDS 20.0%
! CCAATTGTCCTATAATTATA+AGG + chr6.4:18324173-18324192 None:intergenic 25.0%
! CCTTATAATTATAGGACAAT+TGG - chr6.4:18324170-18324189 MS.gene41971:CDS 25.0%
!! AATAATGGAGTTGAAAATCT+AGG - chr6.4:18324332-18324351 MS.gene41971:CDS 25.0%
!!! AAAAAAAGTAGTGGATATGA+AGG - chr6.4:18323626-18323645 MS.gene41971:CDS 25.0%
!!! ATATCCACTACTTTTTTTGA+GGG + chr6.4:18323624-18323643 None:intergenic 25.0%
!!! ATTGGTGCTATTATGAAATT+TGG - chr6.4:18324404-18324423 MS.gene41971:CDS 25.0%
!!! CTTTTTGGATTTTGATTTCA+AGG + chr6.4:18323670-18323689 None:intergenic 25.0%
AATATGGGAAGTGGTAATAA+TGG - chr6.4:18324317-18324336 MS.gene41971:CDS 30.0%
AGAATATCGTTTCTTGCAAA+AGG + chr6.4:18323970-18323989 None:intergenic 30.0%
ATATTTCTCAATGACACAAG+AGG + chr6.4:18324302-18324321 None:intergenic 30.0%
GATTGCTTCACAAAATCAAT+AGG + chr6.4:18323693-18323712 None:intergenic 30.0%
GTACTTGAATAACTACGATA+TGG + chr6.4:18324140-18324159 None:intergenic 30.0%
! CACAAAATCAATAGGCTTTT+TGG + chr6.4:18323685-18323704 None:intergenic 30.0%
! CTTGTGTCATTGAGAAATAT+GGG - chr6.4:18324302-18324321 MS.gene41971:CDS 30.0%
! TATTTTCAGCCAATTCGAAT+TGG - chr6.4:18323756-18323775 MS.gene41971:CDS 30.0%
! TCTTGTGTCATTGAGAAATA+TGG - chr6.4:18324301-18324320 MS.gene41971:CDS 30.0%
!! ATTTTTGTTGTCAGGAAAAC+AGG + chr6.4:18323790-18323809 None:intergenic 30.0%
!!! CATATCCACTACTTTTTTTG+AGG + chr6.4:18323625-18323644 None:intergenic 30.0%
GATGATGAACCAATTCGAAT+TGG + chr6.4:18323768-18323787 None:intergenic 35.0%
GGAGTTGAAAATCTAGGTAT+TGG - chr6.4:18324338-18324357 MS.gene41971:CDS 35.0%
TCATTGAGAAATATGGGAAG+TGG - chr6.4:18324308-18324327 MS.gene41971:CDS 35.0%
TCTAACACTTCACAAGATCA+AGG - chr6.4:18323588-18323607 MS.gene41971:CDS 35.0%
TTCCTGACAACAAAAATCCA+GGG - chr6.4:18323793-18323812 MS.gene41971:CDS 35.0%
TTCTCCCTCAAAAAAAGTAG+TGG - chr6.4:18323617-18323636 MS.gene41971:CDS 35.0%
TTTCCTGACAACAAAAATCC+AGG - chr6.4:18323792-18323811 MS.gene41971:CDS 35.0%
! CATAAACAAAGGTATGATCG+CGG - chr6.4:18324083-18324102 MS.gene41971:CDS 35.0%
!! GTTGAAAATCTAGGTATTGG+CGG - chr6.4:18324341-18324360 MS.gene41971:CDS 35.0%
ACTATACCCAAAACTGTGTG+GGG + chr6.4:18324246-18324265 None:intergenic 40.0%
ATATTCTACTGCACAAGCGT+TGG - chr6.4:18323887-18323906 MS.gene41971:CDS 40.0%
GACTATACCCAAAACTGTGT+GGG + chr6.4:18324247-18324266 None:intergenic 40.0%
GCTTCTAATTCTTCCAAGGA+TGG - chr6.4:18324488-18324507 MS.gene41971:CDS 40.0%
GGGTAACCATAGGGTTATAA+GGG + chr6.4:18324226-18324245 None:intergenic 40.0%
GGTAACCATAGGGTTATAAG+GGG + chr6.4:18324225-18324244 None:intergenic 40.0%
GTAACCATAGGGTTATAAGG+GGG + chr6.4:18324224-18324243 None:intergenic 40.0%
GTTAGAGATGCTAGAGGATT+CGG + chr6.4:18323574-18323593 None:intergenic 40.0%
TATTCTACTGCACAAGCGTT+GGG - chr6.4:18323888-18323907 MS.gene41971:CDS 40.0%
TGTGGCTTCTAATTCTTCCA+AGG - chr6.4:18324484-18324503 MS.gene41971:CDS 40.0%
TTCTCAATGACACAAGAGGA+TGG + chr6.4:18324298-18324317 None:intergenic 40.0%
TTGATCATGAATGCCATCCT+TGG + chr6.4:18324504-18324523 None:intergenic 40.0%
! AAAGGAGCATGAGAAAGATC+TGG + chr6.4:18323856-18323875 None:intergenic 40.0%
! GCTACTTTAAGGATCGAACA+TGG - chr6.4:18324368-18324387 MS.gene41971:CDS 40.0%
! TGAAGTGTTAGAGATGCTAG+AGG + chr6.4:18323580-18323599 None:intergenic 40.0%
! TTGTTGTTCTCTTCTATCCC+TGG + chr6.4:18323813-18323832 None:intergenic 40.0%
!! ATCCCTGGATTTTTGTTGTC+AGG + chr6.4:18323798-18323817 None:intergenic 40.0%
AAACTGTGTGGGGTAACCAT+AGG + chr6.4:18324236-18324255 None:intergenic 45.0%
AACTGTGTGGGGTAACCATA+GGG + chr6.4:18324235-18324254 None:intergenic 45.0%
AAGACCCCCTTATAACCCTA+TGG - chr6.4:18324217-18324236 MS.gene41971:CDS 45.0%
AAGACCCGAAGAGTCACAAT+CGG + chr6.4:18324555-18324574 None:intergenic 45.0%
CGACTATACCCAAAACTGTG+TGG + chr6.4:18324248-18324267 None:intergenic 45.0%
GGACGGTTCATCTTCAATGT+TGG + chr6.4:18324534-18324553 None:intergenic 45.0%
GGGGTAACCATAGGGTTATA+AGG + chr6.4:18324227-18324246 None:intergenic 45.0%
GTGCTCTTTCAACTTCGACA+CGG + chr6.4:18323733-18323752 None:intergenic 45.0%
TGCTCTTTCAACTTCGACAC+GGG + chr6.4:18323732-18323751 None:intergenic 45.0%
! ATGGTTACCCCACACAGTTT+TGG - chr6.4:18324236-18324255 MS.gene41971:CDS 45.0%
! TAGGACAATTGGGGTTAGCA+CGG - chr6.4:18324181-18324200 MS.gene41971:CDS 45.0%
! TGGTTACCCCACACAGTTTT+GGG - chr6.4:18324237-18324256 MS.gene41971:CDS 45.0%
!!! ATCGCGGTGCTTTTGGTTTA+GGG - chr6.4:18324099-18324118 MS.gene41971:CDS 45.0%
ACACAAGACCGCTCATAGGA+AGG - chr6.4:18324010-18324029 MS.gene41971:CDS 50.0%
ACCGTCCGATTGTGACTCTT+CGG - chr6.4:18324547-18324566 MS.gene41971:CDS 50.0%
TTCAACTTCGACACGGGAAC+TGG + chr6.4:18323726-18323745 None:intergenic 50.0%
! AGGTATGATCGCGGTGCTTT+TGG - chr6.4:18324092-18324111 MS.gene41971:CDS 50.0%
!!! GATCGCGGTGCTTTTGGTTT+AGG - chr6.4:18324098-18324117 MS.gene41971:CDS 50.0%
CACGGGAACTGGATCGTCTT+TGG + chr6.4:18323715-18323734 None:intergenic 55.0%
CCCGAAGAGTCACAATCGGA+CGG + chr6.4:18324551-18324570 None:intergenic 55.0%
CCGTCCGATTGTGACTCTTC+GGG - chr6.4:18324548-18324567 MS.gene41971:CDS 55.0%
CGCATGCTCCTTCCTATGAG+CGG + chr6.4:18324021-18324040 None:intergenic 55.0%
GAGGACACAAGACCGCTCAT+AGG - chr6.4:18324006-18324025 MS.gene41971:CDS 55.0%
TCTCCTTCCTATGAGCGCTC+TGG + chr6.4:18323920-18323939 None:intergenic 55.0%
! ACACCAGAGCGCTCATAGGA+AGG - chr6.4:18323914-18323933 MS.gene41971:CDS 55.0%
! TTGGCGGCGCAGCTACTTTA+AGG - chr6.4:18324357-18324376 MS.gene41971:CDS 55.0%
!! TCTACTGCACAAGCGTTGGG+AGG - chr6.4:18323891-18323910 MS.gene41971:CDS 55.0%
! GAGGACACCAGAGCGCTCAT+AGG - chr6.4:18323910-18323929 MS.gene41971:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 18323564 18324595 18323564 ID=MS.gene41971
chr6.4 mRNA 18323564 18324595 18323564 ID=MS.gene41971.t1;Parent=MS.gene41971
chr6.4 exon 18323564 18324595 18323564 ID=MS.gene41971.t1.exon1;Parent=MS.gene41971.t1
chr6.4 CDS 18323564 18324595 18323564 ID=cds.MS.gene41971.t1;Parent=MS.gene41971.t1
Gene Sequence

>MS.gene41971

ATGGTATCCGAATCCTCTAGCATCTCTAACACTTCACAAGATCAAGGTGATGCTTCTCCCTCAAAAAAAGTAGTGGATATGAAGGAGAAAGAACAAGTTCAATCCTTGAAATCAAAATCCAAAAAGCCTATTGATTTTGTGAAGCAATCCAAAGACGATCCAGTTCCCGTGTCGAAGTTGAAAGAGCACAATTATTTTCAGCCAATTCGAATTGGTTCATCATCCTGTTTTCCTGACAACAAAAATCCAGGGATAGAAGAGAACAACAAAAAAGAGAAGAATTCGTATTCCAGATCTTTCTCATGCTCCTTTTGCAATAAACAATATTCTACTGCACAAGCGTTGGGAGGACACCAGAGCGCTCATAGGAAGGAGAATTCATATTCAAGATCTTTCTCTTGCTCCTTTTGCAAGAAACGATATTCTACTGCACAAGCGTTGGGAGGACACAAGACCGCTCATAGGAAGGAGCATGCGTTAGAAAAATCTCAGAAGAAGAAACAAGCTTTAGAAAAACAACATAAACAAAGGTATGATCGCGGTGCTTTTGGTTTAGGGAAATCTTACTTTGATCCATATCGTAGTTATTCAAGTACTCTTTTTACACCTTATAATTATAGGACAATTGGGGTTAGCACGGACTCAATGATTCGAAGACCCCCTTATAACCCTATGGTTACCCCACACAGTTTTGGGTATAGTCGTTCTGCATTGTTGCAAGAGATAACACACCATCCTCTTGTGTCATTGAGAAATATGGGAAGTGGTAATAATGGAGTTGAAAATCTAGGTATTGGCGGCGCAGCTACTTTAAGGATCGAACATGGTTCAAATAAAAAAATTGGTGCTATTATGAAATTTGGAGATTCGTCTACAAATATTGCTACAAGTTCAAATTCAAATACAGAAAAACAAATTATTGTGGCTTCTAATTCTTCCAAGGATGGCATTCATGATCAATCAAACTCCAACATTGAAGATGAACCGTCCGATTGTGACTCTTCGGGTCTTGATTTATCACTTAAGCTTTAA
Protein sequence

>MS.gene41971.t1

MVSESSSISNTSQDQGDASPSKKVVDMKEKEQVQSLKSKSKKPIDFVKQSKDDPVPVSKLKEHNYFQPIRIGSSSCFPDNKNPGIEENNKKEKNSYSRSFSCSFCNKQYSTAQALGGHQSAHRKENSYSRSFSCSFCKKRYSTAQALGGHKTAHRKEHALEKSQKKKQALEKQHKQRYDRGAFGLGKSYFDPYRSYSSTLFTPYNYRTIGVSTDSMIRRPPYNPMVTPHSFGYSRSALLQEITHHPLVSLRNMGSGNNGVENLGIGGAATLRIEHGSNKKIGAIMKFGDSSTNIATSSNSNTEKQIIVASNSSKDGIHDQSNSNIEDEPSDCDSSGLDLSLKL