AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40161

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40161.t1 MTR_4g091990 80.791 177 18 1 4 180 39 199 1.01e-95 276
MS.gene40161.t1 MTR_4g091910 51.744 172 81 1 3 174 40 209 2.52e-58 181
MS.gene40161.t1 MTR_1g112680 31.667 180 90 4 9 157 316 493 3.92e-19 84.3
MS.gene40161.t1 MTR_8g064700 32.903 155 96 3 5 151 239 393 4.83e-19 83.6
MS.gene40161.t1 MTR_2g038040 31.928 166 97 4 9 158 51 216 1.49e-13 67.0
MS.gene40161.t1 MTR_3g498695 25.824 182 118 2 9 175 297 476 1.40e-11 62.4
MS.gene40161.t1 MTR_3g498695 26.630 184 115 4 9 175 297 477 1.83e-11 62.0
MS.gene40161.t1 MTR_7g083900 24.051 158 105 1 9 151 285 442 2.08e-11 62.0
MS.gene40161.t1 MTR_7g083900 24.051 158 105 1 9 151 285 442 2.10e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40161.t1 AT4G21330 40.782 179 98 2 7 179 29 205 9.33e-35 121
MS.gene40161.t1 AT2G16910 34.783 161 80 2 9 144 313 473 5.13e-22 92.4
MS.gene40161.t1 AT1G10610 31.293 147 94 1 7 146 164 310 9.23e-15 71.2
MS.gene40161.t1 AT1G10610 31.293 147 94 1 7 146 231 377 9.66e-15 71.6
MS.gene40161.t1 AT1G10610 31.293 147 94 1 7 146 261 407 1.32e-14 71.2
MS.gene40161.t1 AT5G57150 32.298 161 97 3 9 157 53 213 4.18e-13 65.5
MS.gene40161.t1 AT5G57150 32.298 161 97 3 9 157 54 214 4.68e-13 65.1
MS.gene40161.t1 AT1G12860 27.632 152 101 2 9 151 266 417 4.70e-13 66.6
MS.gene40161.t1 AT5G57150 32.298 161 97 3 9 157 54 214 5.57e-13 65.1
MS.gene40161.t1 AT1G12860 27.632 152 101 2 9 151 266 417 6.11e-13 66.2
MS.gene40161.t1 AT5G57150 32.099 162 98 3 9 158 53 214 7.13e-13 65.1
MS.gene40161.t1 AT5G57150 32.298 161 97 3 9 157 54 214 8.96e-13 65.1
MS.gene40161.t1 AT4G29930 27.011 174 103 2 9 158 53 226 1.97e-12 63.9
MS.gene40161.t1 AT4G29930 27.168 173 102 2 9 157 53 225 2.67e-12 63.5
MS.gene40161.t1 AT4G29930 27.168 173 102 2 9 157 53 225 2.67e-12 63.5
MS.gene40161.t1 AT4G29930 27.815 151 105 2 9 158 53 200 3.14e-12 63.2
MS.gene40161.t1 AT4G29930 28.477 151 101 3 9 158 53 197 1.46e-11 61.2
MS.gene40161.t1 AT4G29930 28.667 150 100 3 9 157 53 196 1.87e-11 60.8
MS.gene40161.t1 AT3G26744 26.923 156 101 2 9 151 306 461 1.96e-11 62.0
MS.gene40161.t1 AT3G26744 26.923 156 101 2 9 151 306 461 2.04e-11 62.0
MS.gene40161.t1 AT3G26744 26.923 156 101 2 9 151 306 461 2.04e-11 62.0
MS.gene40161.t1 AT3G26744 26.923 156 101 2 9 151 306 461 2.04e-11 62.0
MS.gene40161.t1 AT4G29930 37.234 94 50 1 9 93 53 146 3.84e-11 59.3

Find 19 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGAGACTATGAATGATTT+AGG 0.220770 4.2:+20571529 MS.gene40161:CDS
AGGAGGGTTCAAGAAATTAA+TGG 0.301353 4.2:+20571510 MS.gene40161:CDS
CTGACCCAGTGTTCTTTGAT+AGG 0.310935 4.2:-20570961 None:intergenic
CCCAACGTAACAACCATAAA+AGG 0.335966 4.2:+20571568 MS.gene40161:CDS
TCTGATTACAACTTTCATAA+AGG 0.355929 4.2:+20571597 MS.gene40161:CDS
AGACCGAAGCATGAAGAGTT+TGG 0.389720 4.2:-20571011 None:intergenic
GTGGTTACATTTGTGACCAT+TGG 0.476973 4.2:-20571040 None:intergenic
ATACCAAACTCTTCATGCTT+CGG 0.491967 4.2:+20571008 MS.gene40161:CDS
AAGAAGTACTATAATGAAGA+TGG 0.534455 4.2:+20570928 None:intergenic
CACGCAAGAGCTTCAAGCAA+TGG 0.537500 4.2:+20571265 MS.gene40161:CDS
GCTTCGGTCTTTAGTACCAA+TGG 0.541325 4.2:+20571024 MS.gene40161:CDS
ATCTTTGAGAACAAGAGAGG+AGG 0.564401 4.2:+20571493 MS.gene40161:CDS
GTGTTCCTATCAAAGAACAC+TGG 0.568463 4.2:+20570956 MS.gene40161:CDS
TAATAAGGAAGAGGTTCAAG+TGG 0.575955 4.2:+20571435 MS.gene40161:intron
TCTTTGAGAACAAGAGAGGA+GGG 0.579294 4.2:+20571494 MS.gene40161:CDS
ATGATCTTTGAGAACAAGAG+AGG 0.626104 4.2:+20571490 MS.gene40161:CDS
TTGACTTGATGAACATCAAG+TGG 0.631805 4.2:-20571997 None:intergenic
TGTTCCTATCAAAGAACACT+GGG 0.634820 4.2:+20570957 MS.gene40161:CDS
GGTCAGAAAGAAAGATGAGA+CGG 0.638514 4.2:+20570978 MS.gene40161:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCTATAACTTCTATTAATA+AGG + chr4.2:20571420-20571439 MS.gene40161:intron 15.0%
!! TAGTTATATGATATTAATTG+TGG - chr4.2:20571644-20571663 None:intergenic 15.0%
!!! AAACGAAATCAATTTTAATA+TGG - chr4.2:20571760-20571779 None:intergenic 15.0%
!!! GATTTTATGAATCTTAATTT+TGG + chr4.2:20571165-20571184 MS.gene40161:intron 15.0%
!! ATAACTATTAGAAAAGACTA+TGG + chr4.2:20571657-20571676 MS.gene40161:intron 20.0%
!! TAACTATTAGAAAAGACTAT+GGG + chr4.2:20571658-20571677 MS.gene40161:intron 20.0%
!! TCATTTAGTTAATTCATGAA+AGG - chr4.2:20571394-20571413 None:intergenic 20.0%
!! TTTCTATATATTCATTTCCT+TGG + chr4.2:20571101-20571120 MS.gene40161:intron 20.0%
!!! ACAATTTTTAGGCTTTAAAA+AGG - chr4.2:20571696-20571715 None:intergenic 20.0%
!!! CAATTTTTAGGCTTTAAAAA+GGG - chr4.2:20571695-20571714 None:intergenic 20.0%
!!! CCTAAAAATTGTTTTTTTAG+AGG + chr4.2:20571704-20571723 MS.gene40161:intron 20.0%
!!! CCTCTAAAAAAACAATTTTT+AGG - chr4.2:20571707-20571726 None:intergenic 20.0%
! AACTTCTATTAATAAGGAAG+AGG + chr4.2:20571426-20571445 MS.gene40161:intron 25.0%
! ACAAACTAAAAACTAAACCA+AGG - chr4.2:20571121-20571140 None:intergenic 25.0%
! GGAAGAAAAAGAAAAATATG+AGG + chr4.2:20571286-20571305 MS.gene40161:CDS 25.0%
! TCTGATTACAACTTTCATAA+AGG + chr4.2:20571597-20571616 MS.gene40161:CDS 25.0%
! TTACGAGTAAATATCACATT+TGG - chr4.2:20571828-20571847 None:intergenic 25.0%
!! GCAGAAAAATCATCTAATTT+TGG - chr4.2:20571323-20571342 None:intergenic 25.0%
ATGGAGACTATGAATGATTT+AGG + chr4.2:20571529-20571548 MS.gene40161:CDS 30.0%
TAAGAAGATGAGTGAAGTTT+AGG - chr4.2:20571065-20571084 None:intergenic 30.0%
! AATCAGATATGCTCCTTTTA+TGG - chr4.2:20571584-20571603 None:intergenic 30.0%
! ATAAATGCAACGTTTTTGTG+TGG + chr4.2:20571936-20571955 MS.gene40161:intron 30.0%
! ATTAGATGATTTTTCTGCTG+CGG + chr4.2:20571325-20571344 MS.gene40161:CDS 30.0%
! TTTTTGTGTGGATTCAATGT+TGG + chr4.2:20571948-20571967 MS.gene40161:intron 30.0%
!!! TCAATGTTGGTAATTTTCCA+GGG + chr4.2:20571961-20571980 MS.gene40161:intron 30.0%
!!! TTCAATGTTGGTAATTTTCC+AGG + chr4.2:20571960-20571979 MS.gene40161:intron 30.0%
AGAGGTTCAAGTGGAAAAAA+TGG + chr4.2:20571444-20571463 MS.gene40161:CDS 35.0%
AGGAGGGTTCAAGAAATTAA+TGG + chr4.2:20571510-20571529 MS.gene40161:CDS 35.0%
ATACCAAACTCTTCATGCTT+CGG + chr4.2:20571008-20571027 MS.gene40161:CDS 35.0%
GTTCAAGTGGAAAAAATGGA+TGG + chr4.2:20571448-20571467 MS.gene40161:CDS 35.0%
TAATAAGGAAGAGGTTCAAG+TGG + chr4.2:20571435-20571454 MS.gene40161:intron 35.0%
TGCGGAAGAGATGAAAAAAT+GGG + chr4.2:20571343-20571362 MS.gene40161:CDS 35.0%
TGTTCCTATCAAAGAACACT+GGG + chr4.2:20570957-20570976 MS.gene40161:CDS 35.0%
! ATGATCTTTGAGAACAAGAG+AGG + chr4.2:20571490-20571509 MS.gene40161:CDS 35.0%
! CCTTTTATGGTTGTTACGTT+GGG - chr4.2:20571571-20571590 None:intergenic 35.0%
! TCCTTTTATGGTTGTTACGT+TGG - chr4.2:20571572-20571591 None:intergenic 35.0%
! TTGACTTGATGAACATCAAG+TGG - chr4.2:20572000-20572019 None:intergenic 35.0%
!! TTGGTAATTTTCCAGGGAAT+GGG + chr4.2:20571967-20571986 MS.gene40161:intron 35.0%
CCCAACGTAACAACCATAAA+AGG + chr4.2:20571568-20571587 MS.gene40161:CDS 40.0%
CGGAAGAGATGAAAAAATGG+GGG + chr4.2:20571345-20571364 MS.gene40161:CDS 40.0%
CTGCGGAAGAGATGAAAAAA+TGG + chr4.2:20571342-20571361 MS.gene40161:CDS 40.0%
GAAGATGAGTGAAGTTTAGG+TGG - chr4.2:20571062-20571081 None:intergenic 40.0%
GATGAAAAAATGGGGGATAC+AGG + chr4.2:20571352-20571371 MS.gene40161:CDS 40.0%
GCGGAAGAGATGAAAAAATG+GGG + chr4.2:20571344-20571363 MS.gene40161:CDS 40.0%
GGTCAGAAAGAAAGATGAGA+CGG + chr4.2:20570978-20570997 MS.gene40161:CDS 40.0%
GTGGTTACATTTGTGACCAT+TGG - chr4.2:20571043-20571062 None:intergenic 40.0%
GTGTTCCTATCAAAGAACAC+TGG + chr4.2:20570956-20570975 MS.gene40161:CDS 40.0%
! ATCTTTGAGAACAAGAGAGG+AGG + chr4.2:20571493-20571512 MS.gene40161:CDS 40.0%
! TCTTTGAGAACAAGAGAGGA+GGG + chr4.2:20571494-20571513 MS.gene40161:CDS 40.0%
!!! GTTGGTAATTTTCCAGGGAA+TGG + chr4.2:20571966-20571985 MS.gene40161:intron 40.0%
AGACCGAAGCATGAAGAGTT+TGG - chr4.2:20571014-20571033 None:intergenic 45.0%
CTGACCCAGTGTTCTTTGAT+AGG - chr4.2:20570964-20570983 None:intergenic 45.0%
GCTTCGGTCTTTAGTACCAA+TGG + chr4.2:20571024-20571043 MS.gene40161:CDS 45.0%
! GTAATTTTCCAGGGAATGGG+TGG + chr4.2:20571970-20571989 MS.gene40161:intron 45.0%
CACGCAAGAGCTTCAAGCAA+TGG + chr4.2:20571265-20571284 MS.gene40161:CDS 50.0%
GTGGCTGACCACCCATTCCC+TGG - chr4.2:20571981-20572000 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 20570941 20572053 20570941 ID=MS.gene40161
chr4.2 mRNA 20570941 20572053 20570941 ID=MS.gene40161.t1;Parent=MS.gene40161
chr4.2 exon 20570941 20571054 20570941 ID=MS.gene40161.t1.exon1;Parent=MS.gene40161.t1
chr4.2 CDS 20570941 20571054 20570941 ID=cds.MS.gene40161.t1;Parent=MS.gene40161.t1
chr4.2 exon 20571194 20571373 20571194 ID=MS.gene40161.t1.exon2;Parent=MS.gene40161.t1
chr4.2 CDS 20571194 20571373 20571194 ID=cds.MS.gene40161.t1;Parent=MS.gene40161.t1
chr4.2 exon 20571442 20571618 20571442 ID=MS.gene40161.t1.exon3;Parent=MS.gene40161.t1
chr4.2 CDS 20571442 20571618 20571442 ID=cds.MS.gene40161.t1;Parent=MS.gene40161.t1
chr4.2 exon 20571982 20572053 20571982 ID=MS.gene40161.t1.exon4;Parent=MS.gene40161.t1
chr4.2 CDS 20571982 20572053 20571982 ID=cds.MS.gene40161.t1;Parent=MS.gene40161.t1
Gene Sequence

>MS.gene40161

ATGAAGATGGCACAAGTGTTCCTATCAAAGAACACTGGGTCAGAAAGAAAGATGAGACGGAAACTCAATACCAAACTCTTCATGCTTCGGTCTTTAGTACCAATGGTCACAAATGTAACCACCTAAACTTCACTCATCTTCTTAAATAGTCTTTTATAATTTTCTATATATTCATTTCCTTGGTTTAGTTTTTAGTTTGTATAATAATATTAGACAGTTAAACTGATTTTATGAATCTTAATTTTGGTTTCAGATGACAAAAGAAAGCATTTTTGACGATGCTATTACTTATATCAAGAAGCTTAAAGATGAAGTTAAGAGTCGCACGCAAGAGCTTCAAGCAATGGAAGAAAAAGAAAAATATGAGGAAAGAGCTGAGCCAAAATTAGATGATTTTTCTGCTGCGGAAGAGATGAAAAAATGGGGGATACAGGTTTTATATAAATTATTCCTTTCATGAATTAACTAAATGAATTTTCATCTATAACTTCTATTAATAAGGAAGAGGTTCAAGTGGAAAAAATGGATGGAAATAAGCTATATGTTAAGATGATCTTTGAGAACAAGAGAGGAGGGTTCAAGAAATTAATGGAGACTATGAATGATTTAGGACTTGAAATGATAGAACCCAACGTAACAACCATAAAAGGAGCATATCTGATTACAACTTTCATAAAGGTAATCTAAATCAAAAGCTCAACCACAATTAATATCATATAACTATTAGAAAAGACTATGGGTATGTTTAGTTCCCTTTTTAAAGCCTAAAAATTGTTTTTTTAGAGGTGTAGAATTATTTGATATGTTTGAATGTTTCCATATTAAAATTGATTTCGTTTTTAGAATTGATTATAATTTAAAGTTAAAATTTGTAGCTTTCGATTCCAAATGTGATATTTACTCGTAAATTTATTGTTCAACTCATTTTGCTTATATTTTATAATTGATGAAATACATGCTAATATTTTTTATTTGCTTTTTATTTGAAAGTTTGAATAAATGCAACGTTTTTGTGTGGATTCAATGTTGGTAATTTTCCAGGGAATGGGTGGTCAGCCACTTGATGTTCATCAAGTCAAACATTTGTTGCAAGATATAATCAAGAGCATTTAG
Protein sequence

>MS.gene40161.t1

MKMAQVFLSKNTGSERKMRRKLNTKLFMLRSLVPMVTNMTKESIFDDAITYIKKLKDEVKSRTQELQAMEEKEKYEERAEPKLDDFSAAEEMKKWGIQEEVQVEKMDGNKLYVKMIFENKRGGFKKLMETMNDLGLEMIEPNVTTIKGAYLITTFIKGMGGQPLDVHQVKHLLQDIIKSI