AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene019811

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene019811.t1 MTR_5g053510 88.235 85 10 0 144 228 25 109 1.12e-50 160
MS.gene019811.t1 MTR_4g123470 34.314 204 124 5 11 211 14 210 5.34e-30 111
MS.gene019811.t1 MTR_1g054495 27.876 226 156 6 1 225 1 220 4.66e-25 98.6
MS.gene019811.t1 MTR_0014s0220 30.631 222 131 7 5 225 623 822 1.85e-23 98.6
MS.gene019811.t1 MTR_4g053550 52.113 71 33 1 24 93 47 117 2.65e-19 80.9
MS.gene019811.t1 MTR_4g085790 28.000 225 155 5 1 224 1 219 2.96e-19 83.2
MS.gene019811.t1 MTR_7g025150 28.000 225 155 5 1 224 1 219 1.16e-18 81.6
MS.gene019811.t1 MTR_1g041870 32.778 180 104 5 49 228 13 175 1.23e-16 75.5
MS.gene019811.t1 MTR_1g054485 31.343 134 89 3 1 133 1 132 5.85e-15 70.9
MS.gene019811.t1 MTR_7g039210 21.212 231 152 5 1 203 1 229 1.25e-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 40 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGAATTCTTCAAGAAATTT+TGG 0.074446 6.2:-25532837 None:intergenic
CAGACTTCAATGATTTCTTA+TGG 0.226332 6.2:+25533284 MS.gene019811:CDS
AATGTAACTTTCAACAATTC+AGG 0.262321 6.2:+25532909 MS.gene019811:CDS
GATTTGCATTGCAGAGAAAA+AGG 0.315663 6.2:-25533324 None:intergenic
TGTACTCAAACGACAAGTTT+TGG 0.321936 6.2:+25532637 MS.gene019811:CDS
TGGAATCTGATAGATGTTAA+TGG 0.336468 6.2:+25532876 MS.gene019811:CDS
TCGATGATTTGAAACCAGTT+TGG 0.373591 6.2:+25532856 MS.gene019811:CDS
AACGAATAGTGTCTCCAATC+TGG 0.387174 6.2:-25533450 None:intergenic
AGACTTCAATGATTTCTTAT+GGG 0.387413 6.2:+25533285 MS.gene019811:CDS
AATATATACAAAACCTGATC+TGG 0.390568 6.2:-25532683 None:intergenic
AAATAAAATGATTTGCGGTT+CGG 0.410181 6.2:-25533107 None:intergenic
AACTGTACATCTTCCAGATC+AGG 0.417936 6.2:+25532670 MS.gene019811:CDS
TATTCAGCGATTCATTGCTT+TGG 0.421950 6.2:-25533381 None:intergenic
GATGGCAGAAAGATCTGAAT+TGG 0.422050 6.2:+25533154 MS.gene019811:CDS
GCTGTAACAAACTCTTCATT+CGG 0.423810 6.2:-25533346 None:intergenic
CTCTTTCCACTTCAAATGGC+TGG 0.424705 6.2:+25532605 None:intergenic
AGCCGATTCATACTAACTCT+TGG 0.438013 6.2:+25533026 MS.gene019811:CDS
TCCATCCTGTAGTGAGTAAA+GGG 0.439850 6.2:-25532938 None:intergenic
TTCCAAGAGTTAGTATGAAT+CGG 0.446733 6.2:-25533028 None:intergenic
CATAAGAAATCATTGAAGTC+TGG 0.456714 6.2:-25533283 None:intergenic
TTTGTCTGATGCCTTCGAAA+TGG 0.461961 6.2:-25532980 None:intergenic
TGCTTCTGCTGTGGAAGGGA+GGG 0.473215 6.2:-25533076 None:intergenic
AAATCGTGCTAAACTATGTT+GGG 0.473587 6.2:+25533000 MS.gene019811:CDS
TGTCAAAATAAAATGATTTG+CGG 0.475450 6.2:-25533112 None:intergenic
ACATCTATCAGATTCCAAAC+TGG 0.476477 6.2:-25532870 None:intergenic
CAAATCGTGCTAAACTATGT+TGG 0.476784 6.2:+25532999 MS.gene019811:CDS
TTCCTATAGACATGAACAAA+AGG 0.483981 6.2:-25533499 None:intergenic
ATTCGTTTCAAGTTCTTCGA+TGG 0.500169 6.2:+25533466 MS.gene019811:CDS
TTCGTTTCAAGTTCTTCGAT+GGG 0.505866 6.2:+25533467 MS.gene019811:CDS
AACAACAATGCATTCCAGAT+TGG 0.510902 6.2:+25533436 MS.gene019811:CDS
ATCCTCCCTTTACTCACTAC+AGG 0.520199 6.2:+25532933 MS.gene019811:CDS
GTCCATCCTGTAGTGAGTAA+AGG 0.525188 6.2:-25532939 None:intergenic
CACTTTGACTCATTTGCAGA+TGG 0.525652 6.2:+25533136 MS.gene019811:CDS
GTGCTTCTGCTGTGGAAGGG+AGG 0.535843 6.2:-25533077 None:intergenic
TTTGTGCTTCTGCTGTGGAA+GGG 0.552787 6.2:-25533080 None:intergenic
GATTCATACTAACTCTTGGA+AGG 0.611155 6.2:+25533030 MS.gene019811:CDS
TCCCTTTACTCACTACAGGA+TGG 0.611661 6.2:+25532937 MS.gene019811:CDS
AAGAAATCATTGAAGTCTGG+TGG 0.620565 6.2:-25533280 None:intergenic
GAAGGGAGGGAATTCATCAG+TGG 0.689324 6.2:-25533063 None:intergenic
ATCCTGTAGTGAGTAAAGGG+AGG 0.695428 6.2:-25532935 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTATTAAGTTTACAAAC+AGG - chr6.2:25532752-25532771 None:intergenic 15.0%
!! TATTATTAAGTTTACAAACA+GGG - chr6.2:25532751-25532770 None:intergenic 15.0%
!!! AAAATTGGTTTTTGTTAAAT+TGG - chr6.2:25533243-25533262 None:intergenic 15.0%
!! ATACTAAGTTAAAAAATGGT+TGG + chr6.2:25533401-25533420 MS.gene019811:CDS 20.0%
!! CTGAATACTAAGTTAAAAAA+TGG + chr6.2:25533397-25533416 MS.gene019811:CDS 20.0%
!! TACTAAGTTAAAAAATGGTT+GGG + chr6.2:25533402-25533421 MS.gene019811:CDS 20.0%
!! TGTCAAAATAAAATGATTTG+CGG - chr6.2:25533115-25533134 None:intergenic 20.0%
! AATATATACAAAACCTGATC+TGG - chr6.2:25532686-25532705 None:intergenic 25.0%
! AATGTAACTTTCAACAATTC+AGG + chr6.2:25532909-25532928 MS.gene019811:CDS 25.0%
! AGACTTCAATGATTTCTTAT+GGG + chr6.2:25533285-25533304 MS.gene019811:CDS 25.0%
!! AAACCAATTTTGCAAATTAC+AGG + chr6.2:25533252-25533271 MS.gene019811:intron 25.0%
!! AAATAAAATGATTTGCGGTT+CGG - chr6.2:25533110-25533129 None:intergenic 25.0%
!! CGAATTCTTCAAGAAATTTT+GGG - chr6.2:25532839-25532858 None:intergenic 25.0%
!! TCGAATTCTTCAAGAAATTT+TGG - chr6.2:25532840-25532859 None:intergenic 25.0%
AAATCGTGCTAAACTATGTT+GGG + chr6.2:25533000-25533019 MS.gene019811:CDS 30.0%
ACATAGTTTGGTTAGAAAAC+AGG - chr6.2:25533211-25533230 None:intergenic 30.0%
ATCAGATAAAAAACAGCAGT+TGG - chr6.2:25532717-25532736 None:intergenic 30.0%
CAGACTTCAATGATTTCTTA+TGG + chr6.2:25533284-25533303 MS.gene019811:CDS 30.0%
CATAAGAAATCATTGAAGTC+TGG - chr6.2:25533286-25533305 None:intergenic 30.0%
TGGAATCTGATAGATGTTAA+TGG + chr6.2:25532876-25532895 MS.gene019811:CDS 30.0%
TGGTGAAAAAACACATAGTT+TGG - chr6.2:25533223-25533242 None:intergenic 30.0%
TTCCAAGAGTTAGTATGAAT+CGG - chr6.2:25533031-25533050 None:intergenic 30.0%
TTCCTATAGACATGAACAAA+AGG - chr6.2:25533502-25533521 None:intergenic 30.0%
! AGAGATTTTTACCATTTCGA+AGG + chr6.2:25532969-25532988 MS.gene019811:CDS 30.0%
! GAACCTGTAATTTGCAAAAT+TGG - chr6.2:25533258-25533277 None:intergenic 30.0%
!!! AAGAAATTTTGGGTTCACTT+CGG - chr6.2:25532829-25532848 None:intergenic 30.0%
AACAACAATGCATTCCAGAT+TGG + chr6.2:25533436-25533455 MS.gene019811:CDS 35.0%
AAGAAATCATTGAAGTCTGG+TGG - chr6.2:25533283-25533302 None:intergenic 35.0%
ACATCTATCAGATTCCAAAC+TGG - chr6.2:25532873-25532892 None:intergenic 35.0%
CAAATCGTGCTAAACTATGT+TGG + chr6.2:25532999-25533018 MS.gene019811:CDS 35.0%
GATTCATACTAACTCTTGGA+AGG + chr6.2:25533030-25533049 MS.gene019811:CDS 35.0%
GATTTGCATTGCAGAGAAAA+AGG - chr6.2:25533327-25533346 None:intergenic 35.0%
GCTGTAACAAACTCTTCATT+CGG - chr6.2:25533349-25533368 None:intergenic 35.0%
TATTCAGCGATTCATTGCTT+TGG - chr6.2:25533384-25533403 None:intergenic 35.0%
! CTCCTTTTGTTCATGTCTAT+AGG + chr6.2:25533497-25533516 MS.gene019811:CDS 35.0%
! GTACTCAAACGACAAGTTTT+GGG + chr6.2:25532638-25532657 MS.gene019811:CDS 35.0%
! TCGATGATTTGAAACCAGTT+TGG + chr6.2:25532856-25532875 MS.gene019811:CDS 35.0%
! TGTACTCAAACGACAAGTTT+TGG + chr6.2:25532637-25532656 MS.gene019811:CDS 35.0%
!! ATTCGTTTCAAGTTCTTCGA+TGG + chr6.2:25533466-25533485 MS.gene019811:CDS 35.0%
!! TTCGTTTCAAGTTCTTCGAT+GGG + chr6.2:25533467-25533486 MS.gene019811:CDS 35.0%
AACGAATAGTGTCTCCAATC+TGG - chr6.2:25533453-25533472 None:intergenic 40.0%
AACTGTACATCTTCCAGATC+AGG + chr6.2:25532670-25532689 MS.gene019811:CDS 40.0%
CACTTTGACTCATTTGCAGA+TGG + chr6.2:25533136-25533155 MS.gene019811:CDS 40.0%
GATGGCAGAAAGATCTGAAT+TGG + chr6.2:25533154-25533173 MS.gene019811:CDS 40.0%
TCCATCCTGTAGTGAGTAAA+GGG - chr6.2:25532941-25532960 None:intergenic 40.0%
TTTGTCTGATGCCTTCGAAA+TGG - chr6.2:25532983-25533002 None:intergenic 40.0%
! AGCCGATTCATACTAACTCT+TGG + chr6.2:25533026-25533045 MS.gene019811:CDS 40.0%
ATCCTCCCTTTACTCACTAC+AGG + chr6.2:25532933-25532952 MS.gene019811:CDS 45.0%
ATCCTGTAGTGAGTAAAGGG+AGG - chr6.2:25532938-25532957 None:intergenic 45.0%
GTCCATCCTGTAGTGAGTAA+AGG - chr6.2:25532942-25532961 None:intergenic 45.0%
TCCCTTTACTCACTACAGGA+TGG + chr6.2:25532937-25532956 MS.gene019811:CDS 45.0%
TTTGTGCTTCTGCTGTGGAA+GGG - chr6.2:25533083-25533102 None:intergenic 45.0%
! TTTTGTGCTTCTGCTGTGGA+AGG - chr6.2:25533084-25533103 None:intergenic 45.0%
!!! CTCAAACGACAAGTTTTGGG+AGG + chr6.2:25532641-25532660 MS.gene019811:CDS 45.0%
!!! GTAGTTTTGTGCTTCTGCTG+TGG - chr6.2:25533088-25533107 None:intergenic 45.0%
GAAGGGAGGGAATTCATCAG+TGG - chr6.2:25533066-25533085 None:intergenic 50.0%
TGCTTCTGCTGTGGAAGGGA+GGG - chr6.2:25533079-25533098 None:intergenic 55.0%
GTGCTTCTGCTGTGGAAGGG+AGG - chr6.2:25533080-25533099 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 25532620 25533531 25532620 ID=MS.gene019811
chr6.2 mRNA 25532620 25533531 25532620 ID=MS.gene019811.t1;Parent=MS.gene019811
chr6.2 exon 25532620 25532691 25532620 ID=MS.gene019811.t1.exon1;Parent=MS.gene019811.t1
chr6.2 CDS 25532620 25532691 25532620 ID=cds.MS.gene019811.t1;Parent=MS.gene019811.t1
chr6.2 exon 25532819 25533175 25532819 ID=MS.gene019811.t1.exon2;Parent=MS.gene019811.t1
chr6.2 CDS 25532819 25533175 25532819 ID=cds.MS.gene019811.t1;Parent=MS.gene019811.t1
chr6.2 exon 25533274 25533531 25533274 ID=MS.gene019811.t1.exon3;Parent=MS.gene019811.t1
chr6.2 CDS 25533274 25533531 25533274 ID=cds.MS.gene019811.t1;Parent=MS.gene019811.t1
Gene Sequence

>MS.gene019811

ATGGCTGGATATCGTGCTGTACTCAAACGACAAGTTTTGGGAGGTTTTGAAACTGTACATCTTCCAGATCAGGTTTTGTATATATTCATCTTTACCAACTGCTGTTTTTTATCTGATACAATACTATACCCTGTTTGTAAACTTAATAATATTATCGATTGCATTCATCTTCGTTTATAAATGTTGATTATGTGTACAGCAATTCGCCGAAGTGAACCCAAAATTTCTTGAAGAATTCGATGATTTGAAACCAGTTTGGAATCTGATAGATGTTAATGGAAACTATCATAATGTAACTTTCAACAATTCAGGAATCCTCCCTTTACTCACTACAGGATGGACTGACATCAGAGATTTTTACCATTTCGAAGGCATCAGACAAATCGTGCTAAACTATGTTGGGCAAAGCCGATTCATACTAACTCTTGGAAGGACGCTTCAGACCACTGATGAATTCCCTCCCTTCCACAGCAGAAGCACAAAACTACCGAACCGCAAATCATTTTATTTTGACATCACTTTGACTCATTTGCAGATGGCAGAAAGATCTGAATTGGTATAATTTTATTCTAATCACATATATTTGATCCTGTTTTCTAACCAAACTATGTGTTTTTTCACCAATTTAACAAAAACCAATTTTGCAAATTACAGGTTCTGCCACCAGACTTCAATGATTTCTTATGGGATAGTGATTTCGATTACCTTTTTCTCTGCAATGCAAATCCGAATGAAGAGTTTGTTACAGCTGAAATTGAATACCAAAGCAATGAATCGCTGAATACTAAGTTAAAAAATGGTTGGGAGACATTCTGTAACAACAATGCATTCCAGATTGGAGACACTATTCGTTTCAAGTTCTTCGATGGGAAAAACACTCCTTTTGTTCATGTCTATAGGAACAATCCTTAA
Protein sequence

>MS.gene019811.t1

MAGYRAVLKRQVLGGFETVHLPDQQFAEVNPKFLEEFDDLKPVWNLIDVNGNYHNVTFNNSGILPLLTTGWTDIRDFYHFEGIRQIVLNYVGQSRFILTLGRTLQTTDEFPPFHSRSTKLPNRKSFYFDITLTHLQMAERSELVLPPDFNDFLWDSDFDYLFLCNANPNEEFVTAEIEYQSNESLNTKLKNGWETFCNNNAFQIGDTIRFKFFDGKNTPFVHVYRNNP