AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1347760

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 127 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTAGGAGAGTTTGTGATTA+AGG 0.196287 tig0010114:-731 None:intergenic
TATTTCATCTAGTCTTTGTT+TGG 0.256862 tig0010114:+765 Msa1347760:three_prime_UTR
CGAACTACCTTCTGTGAAAC+TGG 0.280327 tig0010114:-305 None:intergenic
TAATCACAAACTCTCCTAAA+AGG 0.301913 tig0010114:+734 Msa1347760:three_prime_UTR
TTCAATTTGTCACAAGGAAT+AGG 0.340147 tig0010114:-649 None:intergenic
TTCTTCATCTCACAGTGTTC+AGG 0.343603 tig0010114:+339 Msa1347760:three_prime_UTR
GGTAGCCGGTCCCACGTATC+AGG 0.344490 tig0010114:+24 None:intergenic
TTAGGAGAGTTTGTGATTAA+GGG 0.370502 tig0010114:-730 None:intergenic
TCTTTGAGCCTTGCTCTCCC+TGG 0.396650 tig0010114:-73 None:intergenic
TCCTGGGTCTTCCGCAGATC+AGG 0.409087 tig0010114:+140 Msa1347760:three_prime_UTR
GACCTTGAGTTGAAGACTCC+TGG 0.425984 tig0010114:+123 Msa1347760:three_prime_UTR
TTCTTTGAGTTGTGAGGGAA+AGG 0.439952 tig0010114:+600 Msa1347760:three_prime_UTR
TCTGTTCTCTCTTCTTAACT+AGG 0.442611 tig0010114:+537 Msa1347760:three_prime_UTR
TTCACAGAAGGTAGTTCGTT+AGG 0.482876 tig0010114:+310 Msa1347760:three_prime_UTR
ACCTTGAGTTGAAGACTCCT+GGG 0.508601 tig0010114:+124 Msa1347760:three_prime_UTR
AGCTCATCAAGTAGTGTAGT+GGG 0.509577 tig0010114:+364 Msa1347760:three_prime_UTR
GAAAATGTTGAACGTACGTC+TGG 0.514766 tig0010114:+797 Msa1347760:three_prime_UTR
AGACCAGTGTGGCTAAATGT+AGG 0.525327 tig0010114:+698 Msa1347760:three_prime_UTR
ACCCTCACAGTAGCTTCAAA+AGG 0.527695 tig0010114:-440 None:intergenic
TGACAAATTGAAATTGCAGA+TGG 0.531031 tig0010114:+660 Msa1347760:three_prime_UTR
CAAATCATCCAGGGAGAGCA+AGG 0.531527 tig0010114:+65 Msa1347760:five_prime_UTR
GAAAGGCTAGTGAATGAGAA+TGG 0.532624 tig0010114:+392 Msa1347760:three_prime_UTR
TGCAATTTCAATTTGTCACA+AGG 0.534577 tig0010114:-655 None:intergenic
ATCTAGTAAGTCGTCGAGGA+AGG 0.538754 tig0010114:+279 Msa1347760:three_prime_UTR
ACCCAGGAGTCTTCAACTCA+AGG 0.576772 tig0010114:-125 None:intergenic
TAGTGTAGTGGGGAGCAGAA+AGG 0.578575 tig0010114:+375 Msa1347760:three_prime_UTR
TAGCTCATCAAGTAGTGTAG+TGG 0.582065 tig0010114:+363 Msa1347760:three_prime_UTR
AAACCTACATTTAGCCACAC+TGG 0.600095 tig0010114:-701 None:intergenic
TTAAGAAGAGAGAACAGAAG+CGG 0.601746 tig0010114:-532 None:intergenic
GTTGAACGTACGTCTGGACT+CGG 0.603755 tig0010114:+803 Msa1347760:three_prime_UTR
TTCTGCTGCAACTATTGTAG+AGG 0.604657 tig0010114:+474 Msa1347760:three_prime_UTR
AAGGAAACCAGTTTCACAGA+AGG 0.607572 tig0010114:+298 Msa1347760:three_prime_UTR
ACCTGATCTGCGGAAGACCC+AGG 0.614780 tig0010114:-141 None:intergenic
AAGACTAGATGAAATAAGCA+TGG 0.625916 tig0010114:-758 None:intergenic
GAGCAAGGCTCAAAGAAATG+AGG 0.629493 tig0010114:+80 Msa1347760:exon
AGCAGCACTAACCTGATCTG+CGG 0.637188 tig0010114:-151 None:intergenic
TGTGAGGGAAAGGCTGCGTG+AGG 0.655698 tig0010114:+610 Msa1347760:three_prime_UTR
AGTCTTCAACTCAAGGTCTG+TGG 0.666361 tig0010114:-118 None:intergenic
GCTCATCAAGTAGTGTAGTG+GGG 0.712201 tig0010114:+365 Msa1347760:three_prime_UTR
TCTTCAAGTTGAGACCAGTG+TGG 0.762333 tig0010114:+687 Msa1347760:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTAAAGCTGTTTTTGTTGT+CGG + tig0010114:224-243 Msa1347760:intron 25.0%
!!! CTTACTAGATTTTTTTTGTG+CGG - tig0010114:269-288 None:intergenic 25.0%
!! TATTTCATCTAGTCTTTGTT+TGG + tig0010114:765-784 Msa1347760:three_prime_UTR 25.0%
!!! ATTAAAGCTGTTTTTGTTGT+CGG + tig0010114:224-243 Msa1347760:intron 25.0%
!!! CTTACTAGATTTTTTTTGTG+CGG - tig0010114:269-288 None:intergenic 25.0%
!! TATTTCATCTAGTCTTTGTT+TGG + tig0010114:765-784 Msa1347760:three_prime_UTR 25.0%
!!! TTTTTTGGACGAGAATAGAA+GGG - tig0010114:507-526 None:intergenic 30.0%
!!! AAACTTTTCTTTGAGTTGTG+AGG + tig0010114:594-613 Msa1347760:three_prime_UTR 30.0%
!!! AACTTTTCTTTGAGTTGTGA+GGG + tig0010114:595-614 Msa1347760:three_prime_UTR 30.0%
TTCAATTTGTCACAAGGAAT+AGG - tig0010114:652-671 None:intergenic 30.0%
TGCAATTTCAATTTGTCACA+AGG - tig0010114:658-677 None:intergenic 30.0%
TGACAAATTGAAATTGCAGA+TGG + tig0010114:660-679 Msa1347760:three_prime_UTR 30.0%
TTAGGAGAGTTTGTGATTAA+GGG - tig0010114:733-752 None:intergenic 30.0%
TTTAGGAGAGTTTGTGATTA+AGG - tig0010114:734-753 None:intergenic 30.0%
TAATCACAAACTCTCCTAAA+AGG + tig0010114:734-753 Msa1347760:three_prime_UTR 30.0%
AAGACTAGATGAAATAAGCA+TGG - tig0010114:761-780 None:intergenic 30.0%
!!! TTTTTTGGACGAGAATAGAA+GGG - tig0010114:507-526 None:intergenic 30.0%
!!! AAACTTTTCTTTGAGTTGTG+AGG + tig0010114:594-613 Msa1347760:three_prime_UTR 30.0%
!!! AACTTTTCTTTGAGTTGTGA+GGG + tig0010114:595-614 Msa1347760:three_prime_UTR 30.0%
TTCAATTTGTCACAAGGAAT+AGG - tig0010114:652-671 None:intergenic 30.0%
TGCAATTTCAATTTGTCACA+AGG - tig0010114:658-677 None:intergenic 30.0%
TGACAAATTGAAATTGCAGA+TGG + tig0010114:660-679 Msa1347760:three_prime_UTR 30.0%
TTAGGAGAGTTTGTGATTAA+GGG - tig0010114:733-752 None:intergenic 30.0%
TTTAGGAGAGTTTGTGATTA+AGG - tig0010114:734-753 None:intergenic 30.0%
TAATCACAAACTCTCCTAAA+AGG + tig0010114:734-753 Msa1347760:three_prime_UTR 30.0%
AAGACTAGATGAAATAAGCA+TGG - tig0010114:761-780 None:intergenic 30.0%
ACTCCAAAAACAAATCATCC+AGG + tig0010114:55-74 Msa1347760:five_prime_UTR 35.0%
CTCCAAAAACAAATCATCCA+GGG + tig0010114:56-75 Msa1347760:five_prime_UTR 35.0%
!!! GTTAGTGCTGCTTTTTTCTT+GGG + tig0010114:162-181 Msa1347760:intron 35.0%
!! TTTTTGTTGTCGGATTTTGC+AGG + tig0010114:234-253 Msa1347760:intron 35.0%
AAAAATCTAGTAAGTCGTCG+AGG + tig0010114:275-294 Msa1347760:three_prime_UTR 35.0%
!!! CTTTTTTGGACGAGAATAGA+AGG - tig0010114:508-527 None:intergenic 35.0%
TTAAGAAGAGAGAACAGAAG+CGG - tig0010114:535-554 None:intergenic 35.0%
TCTGTTCTCTCTTCTTAACT+AGG + tig0010114:537-556 Msa1347760:three_prime_UTR 35.0%
! GAAATAAGCATGGTCCTTTT+AGG - tig0010114:751-770 None:intergenic 35.0%
ACTCCAAAAACAAATCATCC+AGG + tig0010114:55-74 Msa1347760:five_prime_UTR 35.0%
CTCCAAAAACAAATCATCCA+GGG + tig0010114:56-75 Msa1347760:five_prime_UTR 35.0%
!!! GTTAGTGCTGCTTTTTTCTT+GGG + tig0010114:162-181 Msa1347760:intron 35.0%
!! TTTTTGTTGTCGGATTTTGC+AGG + tig0010114:234-253 Msa1347760:intron 35.0%
AAAAATCTAGTAAGTCGTCG+AGG + tig0010114:275-294 Msa1347760:three_prime_UTR 35.0%
!!! CTTTTTTGGACGAGAATAGA+AGG - tig0010114:508-527 None:intergenic 35.0%
TTAAGAAGAGAGAACAGAAG+CGG - tig0010114:535-554 None:intergenic 35.0%
TCTGTTCTCTCTTCTTAACT+AGG + tig0010114:537-556 Msa1347760:three_prime_UTR 35.0%
! GAAATAAGCATGGTCCTTTT+AGG - tig0010114:751-770 None:intergenic 35.0%
!!! GTCTTGTTTTCCTGATACGT+GGG - tig0010114:37-56 None:intergenic 40.0%
!!! AGTCTTGTTTTCCTGATACG+TGG - tig0010114:38-57 None:intergenic 40.0%
!!! CTCCCTGGATGATTTGTTTT+TGG - tig0010114:61-80 None:intergenic 40.0%
!!! GGTTAGTGCTGCTTTTTTCT+TGG + tig0010114:161-180 Msa1347760:intron 40.0%
ACCTATAGATGCAGTAGAAG+AGG + tig0010114:195-214 Msa1347760:intron 40.0%
ACCTCTTCTACTGCATCTAT+AGG - tig0010114:199-218 None:intergenic 40.0%
AAGGAAACCAGTTTCACAGA+AGG + tig0010114:298-317 Msa1347760:three_prime_UTR 40.0%
TTCACAGAAGGTAGTTCGTT+AGG + tig0010114:310-329 Msa1347760:three_prime_UTR 40.0%
TTCTTCATCTCACAGTGTTC+AGG + tig0010114:339-358 Msa1347760:three_prime_UTR 40.0%
TAGCTCATCAAGTAGTGTAG+TGG + tig0010114:363-382 Msa1347760:three_prime_UTR 40.0%
AGCTCATCAAGTAGTGTAGT+GGG + tig0010114:364-383 Msa1347760:three_prime_UTR 40.0%
GAAAGGCTAGTGAATGAGAA+TGG + tig0010114:392-411 Msa1347760:three_prime_UTR 40.0%
! CTACTGTGAGGGTTTTCATT+GGG + tig0010114:450-469 Msa1347760:three_prime_UTR 40.0%
TTCTGCTGCAACTATTGTAG+AGG + tig0010114:474-493 Msa1347760:three_prime_UTR 40.0%
!!! ACAGAAGCGGCTTTCTTTTT+TGG - tig0010114:522-541 None:intergenic 40.0%
!! TTCTTTGAGTTGTGAGGGAA+AGG + tig0010114:600-619 Msa1347760:three_prime_UTR 40.0%
AAACCTACATTTAGCCACAC+TGG - tig0010114:704-723 None:intergenic 40.0%
GAAAATGTTGAACGTACGTC+TGG + tig0010114:797-816 Msa1347760:three_prime_UTR 40.0%
!!! GTCTTGTTTTCCTGATACGT+GGG - tig0010114:37-56 None:intergenic 40.0%
!!! AGTCTTGTTTTCCTGATACG+TGG - tig0010114:38-57 None:intergenic 40.0%
!!! CTCCCTGGATGATTTGTTTT+TGG - tig0010114:61-80 None:intergenic 40.0%
!!! GGTTAGTGCTGCTTTTTTCT+TGG + tig0010114:161-180 Msa1347760:intron 40.0%
ACCTATAGATGCAGTAGAAG+AGG + tig0010114:195-214 Msa1347760:intron 40.0%
ACCTCTTCTACTGCATCTAT+AGG - tig0010114:199-218 None:intergenic 40.0%
AAGGAAACCAGTTTCACAGA+AGG + tig0010114:298-317 Msa1347760:three_prime_UTR 40.0%
TTCACAGAAGGTAGTTCGTT+AGG + tig0010114:310-329 Msa1347760:three_prime_UTR 40.0%
TTCTTCATCTCACAGTGTTC+AGG + tig0010114:339-358 Msa1347760:three_prime_UTR 40.0%
TAGCTCATCAAGTAGTGTAG+TGG + tig0010114:363-382 Msa1347760:three_prime_UTR 40.0%
AGCTCATCAAGTAGTGTAGT+GGG + tig0010114:364-383 Msa1347760:three_prime_UTR 40.0%
GAAAGGCTAGTGAATGAGAA+TGG + tig0010114:392-411 Msa1347760:three_prime_UTR 40.0%
! CTACTGTGAGGGTTTTCATT+GGG + tig0010114:450-469 Msa1347760:three_prime_UTR 40.0%
TTCTGCTGCAACTATTGTAG+AGG + tig0010114:474-493 Msa1347760:three_prime_UTR 40.0%
!!! ACAGAAGCGGCTTTCTTTTT+TGG - tig0010114:522-541 None:intergenic 40.0%
!! TTCTTTGAGTTGTGAGGGAA+AGG + tig0010114:600-619 Msa1347760:three_prime_UTR 40.0%
AAACCTACATTTAGCCACAC+TGG - tig0010114:704-723 None:intergenic 40.0%
GAAAATGTTGAACGTACGTC+TGG + tig0010114:797-816 Msa1347760:three_prime_UTR 40.0%
GAGCAAGGCTCAAAGAAATG+AGG + tig0010114:80-99 Msa1347760:exon 45.0%
AGTCTTCAACTCAAGGTCTG+TGG - tig0010114:121-140 None:intergenic 45.0%
!! ACCTTGAGTTGAAGACTCCT+GGG + tig0010114:124-143 Msa1347760:three_prime_UTR 45.0%
ATCTAGTAAGTCGTCGAGGA+AGG + tig0010114:279-298 Msa1347760:three_prime_UTR 45.0%
CGAACTACCTTCTGTGAAAC+TGG - tig0010114:308-327 None:intergenic 45.0%
GCTCATCAAGTAGTGTAGTG+GGG + tig0010114:365-384 Msa1347760:three_prime_UTR 45.0%
!!! TGCCTTTTGAAGCTACTGTG+AGG + tig0010114:438-457 Msa1347760:three_prime_UTR 45.0%
!!! GCCTTTTGAAGCTACTGTGA+GGG + tig0010114:439-458 Msa1347760:three_prime_UTR 45.0%
ACCCTCACAGTAGCTTCAAA+AGG - tig0010114:443-462 None:intergenic 45.0%
! GCTACTGTGAGGGTTTTCAT+TGG + tig0010114:449-468 Msa1347760:three_prime_UTR 45.0%
!! TCTTCAAGTTGAGACCAGTG+TGG + tig0010114:687-706 Msa1347760:three_prime_UTR 45.0%
AGACCAGTGTGGCTAAATGT+AGG + tig0010114:698-717 Msa1347760:three_prime_UTR 45.0%
GAGCAAGGCTCAAAGAAATG+AGG + tig0010114:80-99 Msa1347760:exon 45.0%
AGTCTTCAACTCAAGGTCTG+TGG - tig0010114:121-140 None:intergenic 45.0%
!! ACCTTGAGTTGAAGACTCCT+GGG + tig0010114:124-143 Msa1347760:three_prime_UTR 45.0%
ATCTAGTAAGTCGTCGAGGA+AGG + tig0010114:279-298 Msa1347760:three_prime_UTR 45.0%
CGAACTACCTTCTGTGAAAC+TGG - tig0010114:308-327 None:intergenic 45.0%
GCTCATCAAGTAGTGTAGTG+GGG + tig0010114:365-384 Msa1347760:three_prime_UTR 45.0%
!!! TGCCTTTTGAAGCTACTGTG+AGG + tig0010114:438-457 Msa1347760:three_prime_UTR 45.0%
!!! GCCTTTTGAAGCTACTGTGA+GGG + tig0010114:439-458 Msa1347760:three_prime_UTR 45.0%
ACCCTCACAGTAGCTTCAAA+AGG - tig0010114:443-462 None:intergenic 45.0%
! GCTACTGTGAGGGTTTTCAT+TGG + tig0010114:449-468 Msa1347760:three_prime_UTR 45.0%
!! TCTTCAAGTTGAGACCAGTG+TGG + tig0010114:687-706 Msa1347760:three_prime_UTR 45.0%
AGACCAGTGTGGCTAAATGT+AGG + tig0010114:698-717 Msa1347760:three_prime_UTR 45.0%
! GTTTTCCTGATACGTGGGAC+CGG - tig0010114:32-51 None:intergenic 50.0%
CAAATCATCCAGGGAGAGCA+AGG + tig0010114:65-84 Msa1347760:five_prime_UTR 50.0%
!! GACCTTGAGTTGAAGACTCC+TGG + tig0010114:123-142 Msa1347760:three_prime_UTR 50.0%
ACCCAGGAGTCTTCAACTCA+AGG - tig0010114:128-147 None:intergenic 50.0%
AGCAGCACTAACCTGATCTG+CGG - tig0010114:154-173 None:intergenic 50.0%
! TAGTGTAGTGGGGAGCAGAA+AGG + tig0010114:375-394 Msa1347760:three_prime_UTR 50.0%
GTTGAACGTACGTCTGGACT+CGG + tig0010114:803-822 Msa1347760:three_prime_UTR 50.0%
! GTACGTCTGGACTCGGTATA+TGG + tig0010114:810-829 Msa1347760:three_prime_UTR 50.0%
! GTTTTCCTGATACGTGGGAC+CGG - tig0010114:32-51 None:intergenic 50.0%
CAAATCATCCAGGGAGAGCA+AGG + tig0010114:65-84 Msa1347760:five_prime_UTR 50.0%
!! GACCTTGAGTTGAAGACTCC+TGG + tig0010114:123-142 Msa1347760:three_prime_UTR 50.0%
ACCCAGGAGTCTTCAACTCA+AGG - tig0010114:128-147 None:intergenic 50.0%
AGCAGCACTAACCTGATCTG+CGG - tig0010114:154-173 None:intergenic 50.0%
! TAGTGTAGTGGGGAGCAGAA+AGG + tig0010114:375-394 Msa1347760:three_prime_UTR 50.0%
GTTGAACGTACGTCTGGACT+CGG + tig0010114:803-822 Msa1347760:three_prime_UTR 50.0%
TCTTTGAGCCTTGCTCTCCC+TGG - tig0010114:76-95 None:intergenic 55.0%
TCTTTGAGCCTTGCTCTCCC+TGG - tig0010114:76-95 None:intergenic 55.0%
TCCTGGGTCTTCCGCAGATC+AGG + tig0010114:140-159 Msa1347760:three_prime_UTR 60.0%
ACCTGATCTGCGGAAGACCC+AGG - tig0010114:144-163 None:intergenic 60.0%
TGTGAGGGAAAGGCTGCGTG+AGG + tig0010114:610-629 Msa1347760:three_prime_UTR 60.0%
TCCTGGGTCTTCCGCAGATC+AGG + tig0010114:140-159 Msa1347760:three_prime_UTR 60.0%
ACCTGATCTGCGGAAGACCC+AGG - tig0010114:144-163 None:intergenic 60.0%
TGTGAGGGAAAGGCTGCGTG+AGG + tig0010114:610-629 Msa1347760:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
tig0010114 gene 28 831 28 ID=Msa1347760;Name=Msa1347760
tig0010114 mRNA 28 831 28 ID=Msa1347760-mRNA-1;Parent=Msa1347760;Name=Msa1347760-mRNA-1;_AED=0.00;_eAED=0.00;_QI=69|1|1|1|1|1|2|620|6
tig0010114 exon 28 161 28 ID=Msa1347760-mRNA-1:exon:6034;Parent=Msa1347760-mRNA-1
tig0010114 exon 256 831 256 ID=Msa1347760-mRNA-1:exon:6035;Parent=Msa1347760-mRNA-1
tig0010114 five_prime_UTR 28 96 28 ID=Msa1347760-mRNA-1:five_prime_utr;Parent=Msa1347760-mRNA-1
tig0010114 CDS 97 117 97 ID=Msa1347760-mRNA-1:cds;Parent=Msa1347760-mRNA-1
tig0010114 three_prime_UTR 118 161 118 ID=Msa1347760-mRNA-1:three_prime_utr;Parent=Msa1347760-mRNA-1
tig0010114 three_prime_UTR 256 831 256 ID=Msa1347760-mRNA-1:three_prime_utr;Parent=Msa1347760-mRNA-1
Gene Sequence

>Msa1347760

ATGAGGATTCTAATGATGTAG
Protein sequence

>Msa1347760

MRILMM*