AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene069931

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene069931.t1 MTR_4g045977 80.637 408 47 4 1 390 1 394 0.0 641
MS.gene069931.t1 MTR_4g107170 47.500 320 101 5 1 318 1 255 4.96e-87 264
MS.gene069931.t1 MTR_2g049610 43.220 236 129 3 1 234 1 233 7.03e-60 194
MS.gene069931.t1 MTR_1g115290 55.758 165 52 3 38 200 2 147 3.16e-53 174
MS.gene069931.t1 MTR_2g049630 53.892 167 74 3 2 166 4 169 7.10e-51 175
MS.gene069931.t1 MTR_2g049530 49.419 172 84 3 3 172 5 175 3.34e-48 162
MS.gene069931.t1 MTR_6g005440 36.598 194 109 3 1 190 1 184 2.11e-34 129
MS.gene069931.t1 MTR_6g018920 33.679 193 125 1 1 190 1 193 8.53e-31 120
MS.gene069931.t1 MTR_1g114730 34.300 207 132 2 1 204 1 206 3.88e-30 119
MS.gene069931.t1 MTR_6g005450 35.882 170 106 1 1 167 1 170 7.98e-29 115
MS.gene069931.t1 MTR_2g016210 25.641 156 106 2 1 148 1 154 2.17e-12 67.0
MS.gene069931.t1 MTR_3g466980 27.941 136 92 4 1 135 1 131 9.02e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene069931.t1 AT5G55690 34.247 146 85 3 1 142 1 139 3.24e-16 78.6
MS.gene069931.t1 AT5G55690 34.247 146 85 3 1 142 1 139 3.24e-16 78.6

Find 52 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTAGTCGACCTAATGATTT+TGG 0.146545 4.1:+53445479 MS.gene069931:CDS
TGAAGAGGGCAATGCAAATT+TGG 0.258454 4.1:+53445739 MS.gene069931:CDS
TTTACAATTGTAGGGTCTTC+TGG 0.267825 4.1:-53444801 None:intergenic
TTGTGGACATCAAATATTTC+AGG 0.290143 4.1:-53444867 None:intergenic
CAATGCTCTCATGCAAAATA+TGG 0.294005 4.1:+53445112 MS.gene069931:CDS
TCTTCCATGTGAAGGAAATC+TGG 0.330525 4.1:-53444978 None:intergenic
TCTAAATTTGTTAGCAAGAC+TGG 0.334083 4.1:+53444717 MS.gene069931:CDS
CTATTTGTTGATGAATTATG+AGG 0.358221 4.1:-53445263 None:intergenic
AAGTTGGATACTTCTTCTTA+AGG 0.361888 4.1:-53444950 None:intergenic
AGTTGGATACTTCTTCTTAA+GGG 0.378758 4.1:-53444949 None:intergenic
AACCAATAGCCAAAATCATT+AGG 0.388302 4.1:-53445488 None:intergenic
GGGTCTTCTGGCCATGTCAT+TGG 0.398342 4.1:-53444789 None:intergenic
TCTTAATTTCAAAGTATTTG+TGG 0.402565 4.1:-53444884 None:intergenic
TCTTTCCATGCAAACTGATC+AGG 0.410075 4.1:-53445542 None:intergenic
ATTAAAATTTATCTTTCCAT+TGG 0.417218 4.1:-53445772 None:intergenic
TCAACAAATAGTGAGATGAT+TGG 0.421059 4.1:+53445275 MS.gene069931:CDS
TGATGTGTTGTTGCATTTGA+GGG 0.426219 4.1:-53445196 None:intergenic
ATTTGGATGATTTGATCCAA+TGG 0.435367 4.1:+53445756 MS.gene069931:CDS
AAGGGTATCTTTCCTCACTT+TGG 0.441633 4.1:-53444931 None:intergenic
AGCATGGAGTTTACAATTGT+AGG 0.450184 4.1:-53444810 None:intergenic
AGTTGCTTTGTTGATGAACT+AGG 0.453927 4.1:-53445623 None:intergenic
ATGAGGCAAATCAATATGAT+TGG 0.457882 4.1:-53445246 None:intergenic
TGCTATGCATGACATTAGCT+TGG 0.463751 4.1:-53445166 None:intergenic
GCATGGAGTTTACAATTGTA+GGG 0.478326 4.1:-53444809 None:intergenic
TTGATGTGTTGTTGCATTTG+AGG 0.480724 4.1:-53445197 None:intergenic
TCATCTACAAAGCAACTAGA+TGG 0.483503 4.1:+53445329 MS.gene069931:CDS
GATGGCAATGCAAGTTATCT+TGG 0.483510 4.1:+53445590 MS.gene069931:CDS
TTTGGCTATTGGTTAAATGA+TGG 0.505634 4.1:+53445497 MS.gene069931:CDS
AGGAAATCTGGATGCCAAGT+TGG 0.519137 4.1:-53444966 None:intergenic
TTGATTGTGTATGATGATGA+TGG 0.536425 4.1:+53444753 MS.gene069931:CDS
ATATGAGCATAAGAAGATTG+AGG 0.538047 4.1:+53444839 MS.gene069931:CDS
CGGTTAAATCAACTAGATGA+TGG 0.538310 4.1:+53445671 MS.gene069931:CDS
GGTGATCAGTTTGCCTCGAA+AGG 0.542852 4.1:+53445695 MS.gene069931:CDS
GATCGTCAAAATCATGAGGT+TGG 0.544039 4.1:-53445649 None:intergenic
GTCAACCTGATCAGTTTGCA+TGG 0.549898 4.1:+53445537 MS.gene069931:CDS
CAAATGCAACAACACATCAA+TGG 0.552382 4.1:+53445200 MS.gene069931:CDS
GCATCCAGATTTCCTTCACA+TGG 0.557364 4.1:+53444974 MS.gene069931:CDS
ATGCTCATATTCTTGAAGCA+TGG 0.569236 4.1:-53444826 None:intergenic
TGATGATGATGGTAATAATG+TGG 0.569879 4.1:+53444764 MS.gene069931:CDS
ATTAGCTTGGCTTGAATGTG+AGG 0.604587 4.1:-53445153 None:intergenic
AACCGATCGTCAAAATCATG+AGG 0.617532 4.1:-53445653 None:intergenic
TGCTTTGTTGATGAACTAGG+AGG 0.622470 4.1:-53445620 None:intergenic
GATGATGATGGTAATAATGT+GGG 0.631187 4.1:+53444765 MS.gene069931:CDS
CATCAATGGTACTAATGTGA+TGG 0.636457 4.1:+53445214 MS.gene069931:CDS
TTAAGAAGAAGTATCCAACT+TGG 0.637255 4.1:+53444952 MS.gene069931:CDS
CAATGGTACTAATGTGATGG+TGG 0.643866 4.1:+53445217 MS.gene069931:CDS
ATAATGTGGGACCAATGACA+TGG 0.658982 4.1:+53444778 MS.gene069931:CDS
AAGCTAAGATAACCAAAGTG+AGG 0.659175 4.1:+53444919 MS.gene069931:CDS
TTAAATCAACTAGATGATGG+TGG 0.672684 4.1:+53445674 MS.gene069931:CDS
AGTTGCTTTGTAGATGAACG+AGG 0.683394 4.1:-53445323 None:intergenic
TCTACAAAGCAACTAGATGG+TGG 0.684272 4.1:+53445332 MS.gene069931:CDS
TGCTTTGTAGATGAACGAGG+AGG 0.699199 4.1:-53445320 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCATTTTGAATGTATTTCAT+TGG - chr4.1:53444642-53444661 None:intergenic 20.0%
!!! TCTTAATTTCAAAGTATTTG+TGG - chr4.1:53444887-53444906 None:intergenic 20.0%
! GCTTTCAAAGAAAGAAAAAA+TGG + chr4.1:53444678-53444697 MS.gene069931:CDS 25.0%
!! CTATTTGTTGATGAATTATG+AGG - chr4.1:53445266-53445285 None:intergenic 25.0%
!! TTTTCATCTCAAAGTGAAAA+GGG + chr4.1:53445407-53445426 MS.gene069931:CDS 25.0%
!! TTTTTCATCTCAAAGTGAAA+AGG + chr4.1:53445406-53445425 MS.gene069931:CDS 25.0%
!!! AAAGAAAAAATGGATTAGCA+AGG + chr4.1:53444688-53444707 MS.gene069931:CDS 25.0%
AACCAATAGCCAAAATCATT+AGG - chr4.1:53445491-53445510 None:intergenic 30.0%
AAGTTGGATACTTCTTCTTA+AGG - chr4.1:53444953-53444972 None:intergenic 30.0%
AGTTGGATACTTCTTCTTAA+GGG - chr4.1:53444952-53444971 None:intergenic 30.0%
ATATGAGCATAAGAAGATTG+AGG + chr4.1:53444839-53444858 MS.gene069931:CDS 30.0%
ATGAGGCAAATCAATATGAT+TGG - chr4.1:53445249-53445268 None:intergenic 30.0%
ATTTGGATGATTTGATCCAA+TGG + chr4.1:53445756-53445775 MS.gene069931:CDS 30.0%
TCAACAAATAGTGAGATGAT+TGG + chr4.1:53445275-53445294 MS.gene069931:CDS 30.0%
TTGTGGACATCAAATATTTC+AGG - chr4.1:53444870-53444889 None:intergenic 30.0%
! TTAAATCAACTAGATGATGG+TGG + chr4.1:53445674-53445693 MS.gene069931:CDS 30.0%
! TTGATTGTGTATGATGATGA+TGG + chr4.1:53444753-53444772 MS.gene069931:CDS 30.0%
! TTTGGCTATTGGTTAAATGA+TGG + chr4.1:53445497-53445516 MS.gene069931:CDS 30.0%
! TTTTCATCTCAAAGTGAAGA+GGG + chr4.1:53445572-53445591 MS.gene069931:CDS 30.0%
! TTTTCATCTCAAAGTGAAGA+TGG + chr4.1:53445572-53445591 MS.gene069931:CDS 30.0%
! TTTTTCATCTCAAAGTGAAG+AGG + chr4.1:53445571-53445590 MS.gene069931:CDS 30.0%
!! GATGATGATGGTAATAATGT+GGG + chr4.1:53444765-53444784 MS.gene069931:CDS 30.0%
!! TCTAAATTTGTTAGCAAGAC+TGG + chr4.1:53444717-53444736 MS.gene069931:CDS 30.0%
!! TGATGATGATGGTAATAATG+TGG + chr4.1:53444764-53444783 MS.gene069931:CDS 30.0%
!! TTAAGAAGAAGTATCCAACT+TGG + chr4.1:53444952-53444971 MS.gene069931:CDS 30.0%
AAGCTAAGATAACCAAAGTG+AGG + chr4.1:53444919-53444938 MS.gene069931:CDS 35.0%
AGCATGGAGTTTACAATTGT+AGG - chr4.1:53444813-53444832 None:intergenic 35.0%
ATGCTCATATTCTTGAAGCA+TGG - chr4.1:53444829-53444848 None:intergenic 35.0%
CAAATGCAACAACACATCAA+TGG + chr4.1:53445200-53445219 MS.gene069931:CDS 35.0%
CAATGCTCTCATGCAAAATA+TGG + chr4.1:53445112-53445131 MS.gene069931:CDS 35.0%
CATCAATGGTACTAATGTGA+TGG + chr4.1:53445214-53445233 MS.gene069931:CDS 35.0%
CGGTTAAATCAACTAGATGA+TGG + chr4.1:53445671-53445690 MS.gene069931:CDS 35.0%
GCATGGAGTTTACAATTGTA+GGG - chr4.1:53444812-53444831 None:intergenic 35.0%
TCATCTACAAAGCAACTAGA+TGG + chr4.1:53445329-53445348 MS.gene069931:CDS 35.0%
TCTTTCCAGAAAAACTGATC+AGG - chr4.1:53445380-53445399 None:intergenic 35.0%
TGAAAAAGAAAGACCTTTCG+AGG - chr4.1:53445711-53445730 None:intergenic 35.0%
TTTACAATTGTAGGGTCTTC+TGG - chr4.1:53444804-53444823 None:intergenic 35.0%
! AGTTGCTTTGTTGATGAACT+AGG - chr4.1:53445626-53445645 None:intergenic 35.0%
! CTTAGTCGACCTAATGATTT+TGG + chr4.1:53445479-53445498 MS.gene069931:CDS 35.0%
! GTTATCCTGATCAGTTTTTC+TGG + chr4.1:53445372-53445391 MS.gene069931:CDS 35.0%
! TGATGTGTTGTTGCATTTGA+GGG - chr4.1:53445199-53445218 None:intergenic 35.0%
! TGATTTTGTGATCACAAGCT+TGG - chr4.1:53445046-53445065 None:intergenic 35.0%
! TTGATGTGTTGTTGCATTTG+AGG - chr4.1:53445200-53445219 None:intergenic 35.0%
!! AAATGATGGCGTTTTGAACT+GGG + chr4.1:53445511-53445530 MS.gene069931:CDS 35.0%
!! AACCTCATGATTTTGACGAT+CGG + chr4.1:53445651-53445670 MS.gene069931:CDS 35.0%
!! GTTGATTTTCTTCCATGTGA+AGG - chr4.1:53444989-53445008 None:intergenic 35.0%
!! TAAATGATGGCGTTTTGAAC+TGG + chr4.1:53445510-53445529 MS.gene069931:CDS 35.0%
!!! GACCTAATGATTTTGGCTAT+TGG + chr4.1:53445486-53445505 MS.gene069931:CDS 35.0%
AACCGATCGTCAAAATCATG+AGG - chr4.1:53445656-53445675 None:intergenic 40.0%
ATAATGTGGGACCAATGACA+TGG + chr4.1:53444778-53444797 MS.gene069931:CDS 40.0%
CAATGGTACTAATGTGATGG+TGG + chr4.1:53445217-53445236 MS.gene069931:CDS 40.0%
GATCGTCAAAATCATGAGGT+TGG - chr4.1:53445652-53445671 None:intergenic 40.0%
GATGGCAATGCAAGTTATCT+TGG + chr4.1:53445590-53445609 MS.gene069931:CDS 40.0%
TCTACAAAGCAACTAGATGG+TGG + chr4.1:53445332-53445351 MS.gene069931:CDS 40.0%
TCTTCCATGTGAAGGAAATC+TGG - chr4.1:53444981-53445000 None:intergenic 40.0%
TCTTTCCATGCAAACTGATC+AGG - chr4.1:53445545-53445564 None:intergenic 40.0%
TGAAGAGGGCAATGCAAATT+TGG + chr4.1:53445739-53445758 MS.gene069931:CDS 40.0%
TGCTATGCATGACATTAGCT+TGG - chr4.1:53445169-53445188 None:intergenic 40.0%
! AGTTGCTTTGTAGATGAACG+AGG - chr4.1:53445326-53445345 None:intergenic 40.0%
! ATTAGCTTGGCTTGAATGTG+AGG - chr4.1:53445156-53445175 None:intergenic 40.0%
! TGCTTTGTTGATGAACTAGG+AGG - chr4.1:53445623-53445642 None:intergenic 40.0%
!! AAGGGTATCTTTCCTCACTT+TGG - chr4.1:53444934-53444953 None:intergenic 40.0%
!! AGATGGTGGTGTTTTGAATC+AGG + chr4.1:53445346-53445365 MS.gene069931:CDS 40.0%
AGGAAATCTGGATGCCAAGT+TGG - chr4.1:53444969-53444988 None:intergenic 45.0%
GCATCCAGATTTCCTTCACA+TGG + chr4.1:53444974-53444993 MS.gene069931:CDS 45.0%
GTCAACCTGATCAGTTTGCA+TGG + chr4.1:53445537-53445556 MS.gene069931:CDS 45.0%
TGCTTTGTAGATGAACGAGG+AGG - chr4.1:53445323-53445342 None:intergenic 45.0%
GGTGATCAGTTTGCCTCGAA+AGG + chr4.1:53445695-53445714 MS.gene069931:CDS 50.0%
GGGTCTTCTGGCCATGTCAT+TGG - chr4.1:53444792-53444811 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 53444621 53445793 53444621 ID=MS.gene069931
chr4.1 mRNA 53444621 53445793 53444621 ID=MS.gene069931.t1;Parent=MS.gene069931
chr4.1 exon 53444621 53445793 53444621 ID=MS.gene069931.t1.exon1;Parent=MS.gene069931.t1
chr4.1 CDS 53444621 53445793 53444621 ID=cds.MS.gene069931.t1;Parent=MS.gene069931.t1
Gene Sequence

>MS.gene069931

ATGGGTCGTAAAAAAATACCAATGAAATACATTCAAAATGAGAAATCTCGCAAAATAGCTTTCAAAGAAAGAAAAAATGGATTAGCAAGGAAACTTTCTAAATTTGTTAGCAAGACTGGAGCAAGAGCTTGTTTGATTGTGTATGATGATGATGGTAATAATGTGGGACCAATGACATGGCCAGAAGACCCTACAATTGTAAACTCCATGCTTCAAGAATATGAGCATAAGAAGATTGAGGAAGCTCCTGAAATATTTGATGTCCACAAATACTTTGAAATTAAGAAAAAAAATGTTGAAGCTAAGATAACCAAAGTGAGGAAAGATACCCTTAAGAAGAAGTATCCAACTTGGCATCCAGATTTCCTTCACATGGAAGAAAATCAACTCAGAGATTTCATTGCTACTGTAAATGATAAGATCCAAGCTTGTGATCACAAAATCAGCATGTTGAAAAATATGCAACATAGTGAAACTAGTTTCTTGCAAAACAATGCTCTCATGCAAAATATGGTTCAAGAGAGTGTTGTTTCCTCACATTCAAGCCAAGCTAATGTCATGCATAGCAATAGCATCCCTCAAATGCAACAACACATCAATGGTACTAATGTGATGGTGGATTTGACCAATCATATTGATTTGCCTCATAATTCATCAACAAATAGTGAGATGATTGGTTTCACTGATCTTTGTGATTTGCCTCCTCGTTCATCTACAAAGCAACTAGATGGTGGTGTTTTGAATCAGGCTAGTTATCCTGATCAGTTTTTCTGGAAAGATCATTCTTTTTCATCTCAAAGTGAAAAGGGAAATGCAAGTTATCTTATTGATTTGCATCGTAGTTCGTCAACAAAGCAACTTAGTCGACCTAATGATTTTGGCTATTGGTTAAATGATGGCGTTTTGAACTGGGTTAGTCAACCTGATCAGTTTGCATGGAAAGATCTTTCTTTTTCATCTCAAAGTGAAGATGGCAATGCAAGTTATCTTGGTGATTTTCCTCCTAGTTCATCAACAAAGCAACTTAGCCAACCTCATGATTTTGACGATCGGTTAAATCAACTAGATGATGGTGGTGATCAGTTTGCCTCGAAAGGTCTTTCTTTTTCATCTCAAAGTGAAGAGGGCAATGCAAATTTGGATGATTTGATCCAATGGAAAGATAAATTTTAA
Protein sequence

>MS.gene069931.t1

MGRKKIPMKYIQNEKSRKIAFKERKNGLARKLSKFVSKTGARACLIVYDDDGNNVGPMTWPEDPTIVNSMLQEYEHKKIEEAPEIFDVHKYFEIKKKNVEAKITKVRKDTLKKKYPTWHPDFLHMEENQLRDFIATVNDKIQACDHKISMLKNMQHSETSFLQNNALMQNMVQESVVSSHSSQANVMHSNSIPQMQQHINGTNVMVDLTNHIDLPHNSSTNSEMIGFTDLCDLPPRSSTKQLDGGVLNQASYPDQFFWKDHSFSSQSEKGNASYLIDLHRSSSTKQLSRPNDFGYWLNDGVLNWVSQPDQFAWKDLSFSSQSEDGNASYLGDFPPSSSTKQLSQPHDFDDRLNQLDDGGDQFASKGLSFSSQSEEGNANLDDLIQWKDKF