AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040888

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040888.t1 MTR_1g033600 94.118 136 8 0 1 136 1 136 2.46e-92 263
MS.gene040888.t1 MTR_8g063600 58.462 130 40 1 3 132 1 116 3.14e-44 146
MS.gene040888.t1 MTR_8g063870 50.769 130 36 3 3 132 1 102 5.18e-30 109
MS.gene040888.t1 MTR_4g111975 46.099 141 56 5 12 132 8 148 4.17e-28 105
MS.gene040888.t1 MTR_3g462790 36.434 129 76 1 4 132 35 157 1.19e-26 101
MS.gene040888.t1 MTR_7g067080 39.552 134 60 2 7 132 30 150 1.30e-25 98.6
MS.gene040888.t1 MTR_5g081860 43.902 123 57 4 10 132 25 135 2.61e-24 94.4
MS.gene040888.t1 MTR_1g022290 50.602 83 41 0 6 88 1 83 4.36e-24 89.4
MS.gene040888.t1 MTR_1g111830 43.307 127 54 2 10 132 22 134 2.93e-23 91.3
MS.gene040888.t1 MTR_5g069710 36.434 129 65 2 9 132 26 142 1.39e-21 87.8
MS.gene040888.t1 MTR_3g111880 53.623 69 32 0 9 77 4 72 6.29e-20 78.6
MS.gene040888.t1 MTR_3g116720 48.529 68 35 0 10 77 14 81 6.12e-19 75.9
MS.gene040888.t1 MTR_5g020170 47.368 76 40 0 7 82 14 89 9.74e-19 75.9
MS.gene040888.t1 MTR_7g089210 54.688 64 29 0 15 78 15 78 3.43e-18 73.9
MS.gene040888.t1 MTR_6g004250 49.315 73 37 0 3 75 1 73 4.66e-18 73.6
MS.gene040888.t1 MTR_3g111920 40.299 67 40 0 12 78 3 69 1.54e-15 67.0
MS.gene040888.t1 MTR_8g077360 38.356 73 44 1 9 81 2 73 1.37e-14 64.3
MS.gene040888.t1 MTR_8g077380 38.571 70 42 1 9 78 2 70 4.11e-14 63.2
MS.gene040888.t1 MTR_8g077390 38.571 70 42 1 9 78 2 70 4.11e-14 63.2
MS.gene040888.t1 MTR_3g013440 43.836 73 40 1 3 74 1 73 4.16e-14 63.5
MS.gene040888.t1 MTR_8g077420 42.857 63 35 1 10 72 3 64 3.57e-12 58.2
MS.gene040888.t1 MTR_5g020540 44.444 63 34 1 10 72 2 63 1.14e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040888.t1 AT5G08520 61.364 132 47 4 1 132 1 128 3.93e-47 154
MS.gene040888.t1 AT2G38090 38.281 128 77 1 7 132 24 151 3.25e-25 97.4
MS.gene040888.t1 AT5G05790 41.600 125 61 3 9 132 28 141 2.75e-24 94.7
MS.gene040888.t1 AT5G05790 41.600 125 61 3 9 132 28 141 2.75e-24 94.7
MS.gene040888.t1 AT5G23650 40.625 128 73 2 5 132 6 130 1.61e-23 93.6
MS.gene040888.t1 AT5G58900 40.000 125 68 3 10 132 32 151 2.50e-23 92.4
MS.gene040888.t1 AT3G11280 39.344 122 56 2 12 132 33 137 2.72e-23 91.7
MS.gene040888.t1 AT3G11280 39.344 122 56 2 12 132 33 137 2.72e-23 91.7
MS.gene040888.t1 AT4G39250 50.649 77 38 0 12 88 14 90 6.69e-22 84.0
MS.gene040888.t1 AT1G49010 38.571 140 68 3 10 132 6 144 7.76e-22 88.6
MS.gene040888.t1 AT1G75250 48.649 74 38 0 10 83 10 83 1.52e-20 80.5
MS.gene040888.t1 AT1G75250 48.649 74 38 0 10 83 10 83 4.96e-20 80.1
MS.gene040888.t1 AT1G19510 45.946 74 40 0 15 88 15 88 1.80e-18 75.1
MS.gene040888.t1 AT2G21650 50.000 70 35 0 12 81 14 83 1.52e-17 72.8
MS.gene040888.t1 AT5G01200 34.074 135 71 4 10 132 28 156 3.78e-17 75.5
MS.gene040888.t1 AT5G04760 33.871 124 65 3 9 132 3 109 7.32e-16 71.2
MS.gene040888.t1 AT2G18328 49.206 63 32 0 16 78 15 77 9.16e-16 67.8
MS.gene040888.t1 AT3G10580 30.400 125 64 1 12 136 8 109 4.40e-12 61.6
MS.gene040888.t1 AT3G10580 30.400 125 64 1 12 136 8 109 4.66e-12 62.0

Find 42 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCAACAAGACTATGACTA+TGG 0.261298 1.2:-18107291 None:intergenic
ACAATAGCTCCGAGTGGAGC+TGG 0.430828 1.2:-18107259 MS.gene040888:CDS
ATGCTAGTGATGAAGGAGTT+GGG 0.443412 1.2:-18107028 MS.gene040888:CDS
CGAGTCTAACCATGGAACTA+AGG 0.444198 1.2:-18106970 MS.gene040888:CDS
TAAGCAGCATTATGAGCTCT+TGG 0.453346 1.2:-18107129 MS.gene040888:CDS
CGATGTACCGAGGAAGACTA+TGG 0.457934 1.2:-18107159 MS.gene040888:CDS
GCACACAACCAGCTTCAATC+TGG 0.480051 1.2:+18107093 None:intergenic
ACCGTCGTATAATTCTTCTT+CGG 0.482646 1.2:-18107066 MS.gene040888:CDS
ACAAGTCATGCTAGTGATGA+AGG 0.485350 1.2:-18107035 MS.gene040888:CDS
ATTTCTTCCATAGTCTTCCT+CGG 0.496055 1.2:+18107152 None:intergenic
CTGAGGATGATTCGGATCGA+TGG 0.497129 1.2:-18107196 MS.gene040888:CDS
ATCTTGAGCCCTTAGTTCCA+TGG 0.501596 1.2:+18106961 None:intergenic
GACTATGACTATGGATGAAG+TGG 0.502959 1.2:-18107282 None:intergenic
GACGTATCCTGAGGATGATT+CGG 0.503412 1.2:-18107204 MS.gene040888:CDS
GTCGTATAATTCTTCTTCGG+AGG 0.506324 1.2:-18107063 MS.gene040888:CDS
TAAGGCATTTGAAAATGCCT+TGG 0.529052 1.2:-18107228 MS.gene040888:CDS
CATGCTAGTGATGAAGGAGT+TGG 0.531172 1.2:-18107029 MS.gene040888:CDS
ATCTGATCAAGAACGGCGAA+AGG 0.534648 1.2:-18106940 MS.gene040888:CDS
ATCTTGCTCCCAGCTCCACT+CGG 0.536574 1.2:+18107250 None:intergenic
AACGGCGAAAGGGTATTGCT+TGG 0.536741 1.2:-18106929 MS.gene040888:CDS
GAAGAATTATACGACGGTAG+AGG 0.542528 1.2:+18107071 None:intergenic
CAATAGCTCCGAGTGGAGCT+GGG 0.545100 1.2:-18107258 MS.gene040888:CDS
TGAGGATGATTCGGATCGAT+GGG 0.549268 1.2:-18107195 MS.gene040888:CDS
TGCTAGTGATGAAGGAGTTG+GGG 0.551779 1.2:-18107027 MS.gene040888:CDS
CATCGATCCGAATCATCCTC+AGG 0.553968 1.2:+18107197 None:intergenic
GTGGAGCTGGGAGCAAGATA+AGG 0.555622 1.2:-18107246 MS.gene040888:CDS
TCGTATAATTCTTCTTCGGA+GGG 0.557853 1.2:-18107062 MS.gene040888:CDS
GATATTAGCCAGATTGAAGC+TGG 0.559375 1.2:-18107101 MS.gene040888:CDS
CATAGTCTTCCTCGGTACAT+CGG 0.560322 1.2:+18107160 None:intergenic
TCTGATCAAGAACGGCGAAA+GGG 0.569147 1.2:-18106939 MS.gene040888:CDS
GAGTCTAACCATGGAACTAA+GGG 0.584526 1.2:-18106969 MS.gene040888:CDS
GGGAAGAAGGGTGGTCACAA+CGG 0.586497 1.2:-18107005 MS.gene040888:CDS
AAAGGGTATTGCTTGGACTG+AGG 0.610320 1.2:-18106922 MS.gene040888:CDS
GCTCAAGATCTGATCAAGAA+CGG 0.629483 1.2:-18106947 MS.gene040888:CDS
TGCCTTGGCGACGTATCCTG+AGG 0.642436 1.2:-18107213 MS.gene040888:CDS
ATCCTCAGGATACGTCGCCA+AGG 0.650046 1.2:+18107211 None:intergenic
GCTAGTGATGAAGGAGTTGG+GGG 0.665624 1.2:-18107026 MS.gene040888:CDS
AGATTGCAGCCGATGTACCG+AGG 0.668392 1.2:-18107169 MS.gene040888:CDS
CTTGGACTGAGGAAGAACAC+AGG 0.712971 1.2:-18106911 MS.gene040888:CDS
AAGTGGACAATAGCTCCGAG+TGG 0.719804 1.2:-18107265 MS.gene040888:CDS
TCCGAAGAAGAATTATACGA+CGG 0.741107 1.2:+18107065 None:intergenic
CTAGTGATGAAGGAGTTGGG+GGG 0.784191 1.2:-18107025 MS.gene040888:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTTAAAAGTAATCAAAAT+TGG + chr1.2:18106852-18106871 None:intergenic 15.0%
!! TGTTAATTAATACAGATAAA+TGG + chr1.2:18107056-18107075 None:intergenic 15.0%
!!! TTCTTTAATTGTCATTTTTT+TGG - chr1.2:18107028-18107047 MS.gene040888:CDS 15.0%
!! AATAATTACAATAGCTAAGA+TGG + chr1.2:18107254-18107273 None:intergenic 20.0%
! AGTAATCAAAATTGGCATAA+AGG + chr1.2:18106844-18106863 None:intergenic 25.0%
!! AAAGCATTCAAAAGAGTTTA+AGG + chr1.2:18107010-18107029 None:intergenic 25.0%
!!! AGTTTAAGCTTATAGTTTTG+TGG - chr1.2:18106898-18106917 MS.gene040888:intron 25.0%
ATGTTCAGATTTCATATGAC+AGG + chr1.2:18106953-18106972 None:intergenic 30.0%
! TGCATGCATCAACTATTTTA+AGG + chr1.2:18107129-18107148 None:intergenic 30.0%
AAAAATGACGAGTCTAACCA+TGG - chr1.2:18106717-18106736 MS.gene040888:intron 35.0%
AAGAGTGGTAAAAGATAGTG+GGG - chr1.2:18107170-18107189 MS.gene040888:CDS 35.0%
ACCGTCGTATAATTCTTCTT+CGG - chr1.2:18106629-18106648 MS.gene040888:intron 35.0%
ATTTCTTCCATAGTCTTCCT+CGG + chr1.2:18106546-18106565 None:intergenic 35.0%
GAAGAGTGGTAAAAGATAGT+GGG - chr1.2:18107169-18107188 MS.gene040888:CDS 35.0%
TCCGAAGAAGAATTATACGA+CGG + chr1.2:18106633-18106652 None:intergenic 35.0%
TCGTATAATTCTTCTTCGGA+GGG - chr1.2:18106633-18106652 MS.gene040888:intron 35.0%
TGAAGAGTGGTAAAAGATAG+TGG - chr1.2:18107168-18107187 MS.gene040888:CDS 35.0%
TTTAAGGACTAACAGATGAC+AGG + chr1.2:18107113-18107132 None:intergenic 35.0%
! AATAGTTGATGCATGCATTG+AGG - chr1.2:18107132-18107151 MS.gene040888:CDS 35.0%
! ACGTTCTTTTTACCAAACCA+TGG - chr1.2:18107087-18107106 MS.gene040888:CDS 35.0%
! TAAGGCATTTGAAAATGCCT+TGG - chr1.2:18106467-18106486 MS.gene040888:intron 35.0%
ACAAGTCATGCTAGTGATGA+AGG - chr1.2:18106660-18106679 MS.gene040888:intron 40.0%
ATGCTAGTGATGAAGGAGTT+GGG - chr1.2:18106667-18106686 MS.gene040888:intron 40.0%
GAACTAGCAGAGTACAGAAT+TGG + chr1.2:18107232-18107251 None:intergenic 40.0%
GAAGAATTATACGACGGTAG+AGG + chr1.2:18106627-18106646 None:intergenic 40.0%
GAGTCTAACCATGGAACTAA+GGG - chr1.2:18106726-18106745 MS.gene040888:intron 40.0%
GATATTAGCCAGATTGAAGC+TGG - chr1.2:18106594-18106613 MS.gene040888:intron 40.0%
GCTCAAGATCTGATCAAGAA+CGG - chr1.2:18106748-18106767 MS.gene040888:intron 40.0%
GTCGTATAATTCTTCTTCGG+AGG - chr1.2:18106632-18106651 MS.gene040888:intron 40.0%
TAAGCAGCATTATGAGCTCT+TGG - chr1.2:18106566-18106585 MS.gene040888:intron 40.0%
! GATGCATGCATTGAGGTTTT+AGG - chr1.2:18107139-18107158 MS.gene040888:CDS 40.0%
!! AAAAGATAGTGGGGAGAGAA+GGG - chr1.2:18107179-18107198 MS.gene040888:CDS 40.0%
!! TAAAAGATAGTGGGGAGAGA+AGG - chr1.2:18107178-18107197 MS.gene040888:CDS 40.0%
!!! GGTTAGACTCGTCATTTTTG+TGG + chr1.2:18106716-18106735 None:intergenic 40.0%
ATCTGATCAAGAACGGCGAA+AGG - chr1.2:18106755-18106774 MS.gene040888:intron 45.0%
ATCTTGAGCCCTTAGTTCCA+TGG + chr1.2:18106737-18106756 None:intergenic 45.0%
CATAGTCTTCCTCGGTACAT+CGG + chr1.2:18106538-18106557 None:intergenic 45.0%
CATGCTAGTGATGAAGGAGT+TGG - chr1.2:18106666-18106685 MS.gene040888:intron 45.0%
CGAGTCTAACCATGGAACTA+AGG - chr1.2:18106725-18106744 MS.gene040888:intron 45.0%
GACGTATCCTGAGGATGATT+CGG - chr1.2:18106491-18106510 MS.gene040888:intron 45.0%
TCTGATCAAGAACGGCGAAA+GGG - chr1.2:18106756-18106775 MS.gene040888:intron 45.0%
TGCTAGTGATGAAGGAGTTG+GGG - chr1.2:18106668-18106687 MS.gene040888:intron 45.0%
! TGAGGATGATTCGGATCGAT+GGG - chr1.2:18106500-18106519 MS.gene040888:intron 45.0%
! TTTTAGGCGAGGATGAAGAG+TGG - chr1.2:18107155-18107174 MS.gene040888:CDS 45.0%
!! AAAGGGTATTGCTTGGACTG+AGG - chr1.2:18106773-18106792 MS.gene040888:intron 45.0%
!!! ATGCATTGAGGTTTTAGGCG+AGG - chr1.2:18107144-18107163 MS.gene040888:CDS 45.0%
AAGTGGACAATAGCTCCGAG+TGG - chr1.2:18106430-18106449 MS.gene040888:intron 50.0%
ACAGATGACAGGCCATGGTT+TGG + chr1.2:18107102-18107121 None:intergenic 50.0%
CATCGATCCGAATCATCCTC+AGG + chr1.2:18106501-18106520 None:intergenic 50.0%
CGATGTACCGAGGAAGACTA+TGG - chr1.2:18106536-18106555 MS.gene040888:intron 50.0%
CTAGTGATGAAGGAGTTGGG+GGG - chr1.2:18106670-18106689 MS.gene040888:intron 50.0%
CTTGGACTGAGGAAGAACAC+AGG - chr1.2:18106784-18106803 MS.gene040888:intron 50.0%
GACTAACAGATGACAGGCCA+TGG + chr1.2:18107107-18107126 None:intergenic 50.0%
GCACACAACCAGCTTCAATC+TGG + chr1.2:18106605-18106624 None:intergenic 50.0%
GCTAGTGATGAAGGAGTTGG+GGG - chr1.2:18106669-18106688 MS.gene040888:intron 50.0%
! CTGAGGATGATTCGGATCGA+TGG - chr1.2:18106499-18106518 MS.gene040888:intron 50.0%
! GTGGGGAGAGAAGGGAATTT+TGG - chr1.2:18107187-18107206 MS.gene040888:CDS 50.0%
!! AACGGCGAAAGGGTATTGCT+TGG - chr1.2:18106766-18106785 MS.gene040888:intron 50.0%
ACAATAGCTCCGAGTGGAGC+TGG - chr1.2:18106436-18106455 MS.gene040888:intron 55.0%
AGATTGCAGCCGATGTACCG+AGG - chr1.2:18106526-18106545 MS.gene040888:intron 55.0%
ATCCTCAGGATACGTCGCCA+AGG + chr1.2:18106487-18106506 None:intergenic 55.0%
ATCTTGCTCCCAGCTCCACT+CGG + chr1.2:18106448-18106467 None:intergenic 55.0%
CAATAGCTCCGAGTGGAGCT+GGG - chr1.2:18106437-18106456 MS.gene040888:intron 55.0%
GAAGGAGTTGGGGGGAAGAA+GGG - chr1.2:18106678-18106697 MS.gene040888:intron 55.0%
GGGAAGAAGGGTGGTCACAA+CGG - chr1.2:18106690-18106709 MS.gene040888:intron 55.0%
GTGGAGCTGGGAGCAAGATA+AGG - chr1.2:18106449-18106468 MS.gene040888:intron 55.0%
TGAAGGAGTTGGGGGGAAGA+AGG - chr1.2:18106677-18106696 MS.gene040888:intron 55.0%
TGCCTTGGCGACGTATCCTG+AGG - chr1.2:18106482-18106501 MS.gene040888:intron 60.0%
GGAGTTGGGGGGAAGAAGGG+TGG - chr1.2:18106681-18106700 MS.gene040888:intron 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 18106417 18107300 18106417 ID=MS.gene040888
chr1.2 mRNA 18106417 18107300 18106417 ID=MS.gene040888.t1;Parent=MS.gene040888
chr1.2 exon 18106908 18107300 18106908 ID=MS.gene040888.t1.exon1;Parent=MS.gene040888.t1
chr1.2 CDS 18106908 18107300 18106908 ID=cds.MS.gene040888.t1;Parent=MS.gene040888.t1
chr1.2 exon 18106417 18106434 18106417 ID=MS.gene040888.t1.exon2;Parent=MS.gene040888.t1
chr1.2 CDS 18106417 18106434 18106417 ID=cds.MS.gene040888.t1;Parent=MS.gene040888.t1
Gene Sequence

>MS.gene040888

ATGACTATGGATGAAGTGGACAATAGCTCCGAGTGGAGCTGGGAGCAAGATAAGGCATTTGAAAATGCCTTGGCGACGTATCCTGAGGATGATTCGGATCGATGGGAGAAGATTGCAGCCGATGTACCGAGGAAGACTATGGAAGAAATTAAGCAGCATTATGAGCTCTTGGTTGATGATATTAGCCAGATTGAAGCTGGTTGTGTGCCTCTACCGTCGTATAATTCTTCTTCGGAGGGTTCAACAAGTCATGCTAGTGATGAAGGAGTTGGGGGGAAGAAGGGTGGTCACAACGGCCACAAAAATGACGAGTCTAACCATGGAACTAAGGGCTCAAGATCTGATCAAGAACGGCGAAAGGGTATTGCTTGGACTGAGGAAGAACACAGGCAAGTTTATCTTTTGCTTATCTGTTTTGATTAAACCTTTATGCCAATTTTGATTACTTTTAACTTTTAATTCTTTCTTTTCAAGCTAATGAAGTTTAAGCTTATAGTTTTGTGGTTAGTTGTATTCGATTGTTGACTCTAATTCCTGTCATATGAAATCTGAACATCTTGATATTTTCAAAATTACTGTTTGATTGTGAACCTTAAACTCTTTTGAATGCTTTCTTTAATTGTCATTTTTTTGGTACCATTTATCTGTATTAATTAACAACTATCTTAGCACGTTCTTTTTACCAAACCATGGCCTGTCATCTGTTAGTCCTTAAAATAGTTGATGCATGCATTGAGGTTTTAGGCGAGGATGAAGAGTGGTAAAAGATAGTGGGGAGAGAAGGGAATTTTGGTATTGAACTGAATTTTGATCCAATTCTGTACTCTGCTAGTTCCATCTTAGCTATTGTAATTATTAAATGCTAGTATAGTGATTTCCTCTGA
Protein sequence

>MS.gene040888.t1

MTMDEVDNSSEWSWEQDKAFENALATYPEDDSDRWEKIAADVPRKTMEEIKQHYELLVDDISQIEAGCVPLPSYNSSSEGSTSHASDEGVGGKKGGHNGHKNDESNHGTKGSRSDQERRKGIAWTEEEHRQYSDFL