AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52491

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52491.t1 MTR_7g035300 87.983 233 20 1 1 225 1 233 4.23e-155 429
MS.gene52491.t1 MTR_7g037260 42.678 239 81 6 42 224 119 357 1.69e-52 173
MS.gene52491.t1 MTR_7g037130 43.220 236 78 6 42 221 119 354 9.07e-49 163
MS.gene52491.t1 MTR_7g451170 39.922 258 91 7 31 224 154 411 3.74e-47 160
MS.gene52491.t1 MTR_4g088015 35.371 229 84 6 57 221 210 438 1.79e-35 130
MS.gene52491.t1 MTR_1g057980 33.466 251 94 6 32 209 44 294 6.36e-32 118
MS.gene52491.t1 MTR_7g035350 30.800 250 96 6 36 208 193 442 3.47e-25 102
MS.gene52491.t1 MTR_7g450950 38.265 196 79 5 37 190 125 320 3.99e-24 98.2
MS.gene52491.t1 MTR_3g077650 44.340 106 47 3 70 163 183 288 3.67e-20 88.6
MS.gene52491.t1 MTR_5g049190 41.284 109 52 3 64 160 15 123 2.65e-19 83.6
MS.gene52491.t1 MTR_3g463400 34.783 115 63 3 70 172 135 249 1.27e-18 84.0
MS.gene52491.t1 MTR_4g105660 37.391 115 60 3 62 164 174 288 2.70e-18 83.2
MS.gene52491.t1 MTR_5g070020 31.373 153 88 4 28 163 77 229 7.49e-18 81.3
MS.gene52491.t1 MTR_6g027340 37.624 101 53 3 91 185 50 146 1.17e-13 67.8
MS.gene52491.t1 MTR_7g061330 40.860 93 43 3 71 151 116 208 2.30e-13 68.9
MS.gene52491.t1 MTR_7g461410 40.860 93 43 3 71 151 116 208 2.30e-13 68.9
MS.gene52491.t1 MTR_7g061330 40.860 93 43 3 71 151 80 172 2.72e-13 68.6
MS.gene52491.t1 MTR_5g010650 38.710 93 45 3 70 150 112 204 2.85e-13 68.6
MS.gene52491.t1 MTR_4g019370 36.522 115 53 5 71 165 41 155 3.94e-13 67.8
MS.gene52491.t1 MTR_6g027360 37.374 99 52 3 93 185 114 208 4.16e-13 67.4
MS.gene52491.t1 MTR_1g026870 31.304 115 66 4 71 172 88 202 9.45e-13 67.4
MS.gene52491.t1 MTR_3g110028 33.043 115 64 4 71 172 88 202 2.19e-12 66.2
MS.gene52491.t1 MTR_4g128190 35.870 92 56 3 65 154 10 100 3.24e-11 61.2
MS.gene52491.t1 MTR_5g041570 31.618 136 72 5 71 185 137 272 4.87e-11 62.0
MS.gene52491.t1 MTR_4g082040 33.621 116 64 4 50 152 86 201 7.26e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52491.t1 AT4G18770 39.130 115 58 3 62 164 211 325 3.44e-20 88.6
MS.gene52491.t1 AT3G27785 39.640 111 55 2 62 160 183 293 3.85e-19 85.5
MS.gene52491.t1 AT5G40360 39.831 118 57 3 60 164 150 266 4.33e-18 82.0
MS.gene52491.t1 AT5G58850 37.615 109 56 3 65 161 102 210 3.66e-17 79.7
MS.gene52491.t1 AT2G25230 39.370 127 64 4 62 175 20 146 3.95e-17 77.8
MS.gene52491.t1 AT5G11050 38.739 111 56 3 63 161 100 210 4.60e-17 79.7
MS.gene52491.t1 AT5G40430 35.542 166 88 7 62 209 48 212 1.67e-16 76.3
MS.gene52491.t1 AT5G11510 36.667 90 45 2 71 148 84 173 1.42e-12 67.0
MS.gene52491.t1 AT5G11510 36.667 90 45 2 71 148 84 173 1.42e-12 67.0
MS.gene52491.t1 AT5G11510 36.667 90 45 2 71 148 84 173 1.42e-12 67.0
MS.gene52491.t1 AT5G11510 36.667 90 45 2 71 148 84 173 1.47e-12 66.6
MS.gene52491.t1 AT5G11510 36.667 90 45 2 71 148 84 173 1.61e-12 66.6
MS.gene52491.t1 AT3G53200 40.278 72 41 2 78 148 1 71 2.25e-12 64.3
MS.gene52491.t1 AT5G02320 35.484 93 48 3 71 151 130 222 4.52e-12 65.1
MS.gene52491.t1 AT5G02320 35.484 93 48 3 71 151 130 222 4.52e-12 65.1
MS.gene52491.t1 AT5G02320 35.484 93 48 3 71 151 70 162 4.79e-12 65.1
MS.gene52491.t1 AT1G69560 25.134 187 115 6 3 169 60 241 4.86e-12 64.7
MS.gene52491.t1 AT1G69560 25.134 187 115 6 3 169 44 225 6.07e-12 64.3
MS.gene52491.t1 AT3G09370 37.634 93 46 3 71 151 138 230 9.96e-12 64.3
MS.gene52491.t1 AT3G09370 37.634 93 46 3 71 151 133 225 1.04e-11 63.9
MS.gene52491.t1 AT3G09370 37.634 93 46 3 71 151 146 238 1.17e-11 63.9
MS.gene52491.t1 AT1G57560 30.769 130 83 4 93 218 51 177 1.29e-11 63.2
MS.gene52491.t1 AT3G28470 31.683 101 56 3 64 151 10 110 2.17e-11 62.8
MS.gene52491.t1 AT4G33450 35.417 96 56 3 93 186 55 146 2.68e-11 62.0
MS.gene52491.t1 AT2G47190 30.275 109 63 3 53 148 7 115 3.36e-11 61.6
MS.gene52491.t1 AT3G53200 43.860 57 31 1 93 148 48 104 4.33e-11 61.2
MS.gene52491.t1 AT1G57560 39.130 69 41 1 93 160 51 119 7.94e-11 60.8
MS.gene52491.t1 AT4G32730 33.333 93 50 3 71 151 90 182 9.51e-11 61.2

Find 43 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATAGTATTCTGCTGTTTA+TGG 0.107084 7.2:-61452938 None:intergenic
GCCTTATGTGGAAACGTTTA+AGG 0.181442 7.2:+61454061 MS.gene52491:CDS
AACGATGATTATGAGTTATA+TGG 0.223163 7.2:+61453986 MS.gene52491:CDS
GGCATTCTCGACTTGCTTAA+TGG 0.229142 7.2:-61453855 None:intergenic
GATCAAGCCCACAACATATT+TGG 0.264284 7.2:+61453761 MS.gene52491:CDS
AAAAGAAACACCTTAATATC+TGG 0.291683 7.2:-61453252 None:intergenic
CCATTGATCAGCATTTATAT+TGG 0.314785 7.2:-61452991 None:intergenic
AAATGATTGTACTCAATATA+AGG 0.322591 7.2:+61452818 MS.gene52491:CDS
CCATCTTAAACCAGATATTA+AGG 0.331529 7.2:+61453242 MS.gene52491:CDS
GAAATTGATTTCCTGCTTCA+TGG 0.333503 7.2:-61454032 None:intergenic
ACCTTAAACGTTTCCACATA+AGG 0.341962 7.2:-61454062 None:intergenic
TAAACAGCAGAATACTATTC+AGG 0.382656 7.2:+61452941 MS.gene52491:CDS
TATCCACCAAGTTCATCTTC+TGG 0.384852 7.2:-61453947 None:intergenic
TAAAACAATGCATGGAGAAA+TGG 0.391181 7.2:+61453217 MS.gene52491:CDS
TCAATATAAGGAACATCATA+TGG 0.403054 7.2:+61452830 MS.gene52491:CDS
TAATCATCGTTGAATGTCAT+TGG 0.431930 7.2:-61453974 None:intergenic
TTCCTGCTTCATGGGAACCT+CGG 0.444432 7.2:-61454023 None:intergenic
TCCTGCTTCATGGGAACCTC+GGG 0.444652 7.2:-61454022 None:intergenic
ACAACATATTTGGAGACAAC+TGG 0.446422 7.2:+61453771 MS.gene52491:CDS
GTTGTCTCCAAATATGTTGT+GGG 0.463375 7.2:-61453768 None:intergenic
AATTTCATGAAGGCCTTATG+TGG 0.471697 7.2:+61454049 MS.gene52491:CDS
AAATTGATTTCCTGCTTCAT+GGG 0.472609 7.2:-61454031 None:intergenic
TGTTTATGGTAAATGAGAAC+GGG 0.474813 7.2:-61452924 None:intergenic
ATATTTGTATCCAATTTCAC+TGG 0.483235 7.2:-61452883 None:intergenic
CCTTAATATCTGGTTTAAGA+TGG 0.484241 7.2:-61453242 None:intergenic
AATGGACTACAAAAGAGAAT+AGG 0.491834 7.2:+61453009 MS.gene52491:CDS
TCCCGAGGTTCCCATGAAGC+AGG 0.502564 7.2:+61454021 MS.gene52491:CDS
AGTTGTCTCCAAATATGTTG+TGG 0.504440 7.2:-61453769 None:intergenic
GAAATTTCAAGAAGATTGCC+AGG 0.513813 7.2:+61453797 MS.gene52491:CDS
CCAATATAAATGCTGATCAA+TGG 0.515462 7.2:+61452991 MS.gene52491:CDS
TGAGAACGGGTTCTTGATCA+TGG 0.521600 7.2:-61452911 None:intergenic
CTGTTTATGGTAAATGAGAA+CGG 0.529061 7.2:-61452925 None:intergenic
TGGATCTCTTTCTAAATCGA+TGG 0.536456 7.2:+61453190 MS.gene52491:CDS
ACTACTCCAGAAGATGAACT+TGG 0.550371 7.2:+61453941 MS.gene52491:CDS
ATGGACCTTAAAACAATGCA+TGG 0.570560 7.2:+61453209 MS.gene52491:CDS
TAAGGAACATCATATGGATG+AGG 0.593905 7.2:+61452836 MS.gene52491:CDS
GCAGGAAATCAATTTCATGA+AGG 0.597528 7.2:+61454039 MS.gene52491:CDS
ACTCCAGAAGATGAACTTGG+TGG 0.599781 7.2:+61453944 MS.gene52491:CDS
GAATGAGCCATTGAGTGAGG+AGG 0.611909 7.2:+61453724 MS.gene52491:intron
ACATAACTATCGTTACGTCC+TGG 0.612302 7.2:-61453815 None:intergenic
TGGTTGCAAAACTAGAGTGA+TGG 0.623138 7.2:-61452863 None:intergenic
TCGATTTAGAAAGAGATCCA+CGG 0.651610 7.2:-61453187 None:intergenic
GTAGAATGAGCCATTGAGTG+AGG 0.657428 7.2:+61453721 MS.gene52491:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTCATATATAGTTTTATTA+TGG + chr7.2:61453074-61453093 MS.gene52491:intron 10.0%
!! GTCTATATATAATTAAATAG+AGG - chr7.2:61453675-61453694 None:intergenic 15.0%
!! AAACCTTCAAAAATGTAATT+AGG - chr7.2:61453920-61453939 None:intergenic 20.0%
!! AAATGATTGTACTCAATATA+AGG + chr7.2:61452818-61452837 MS.gene52491:CDS 20.0%
!! ATAAAAATATTGCACATGAA+TGG + chr7.2:61453623-61453642 MS.gene52491:intron 20.0%
!! ATACAAAACATGTTTAGATT+AGG - chr7.2:61453697-61453716 None:intergenic 20.0%
!! TTACGCAATAAAAGATAAAA+AGG - chr7.2:61453310-61453329 None:intergenic 20.0%
!!! TATGATTTTATAACAACAAG+TGG + chr7.2:61453439-61453458 MS.gene52491:intron 20.0%
!!! TGCTAAAAAAAGTGTTAAAA+AGG - chr7.2:61453283-61453302 None:intergenic 20.0%
! AAAAAATACACACATCCATT+AGG - chr7.2:61453564-61453583 None:intergenic 25.0%
! AAAAGAAACACCTTAATATC+TGG - chr7.2:61453255-61453274 None:intergenic 25.0%
! AACGATGATTATGAGTTATA+TGG + chr7.2:61453986-61454005 MS.gene52491:CDS 25.0%
! ATATTTGTATCCAATTTCAC+TGG - chr7.2:61452886-61452905 None:intergenic 25.0%
! CATTTCATTGAAAAACCTAA+TGG + chr7.2:61453546-61453565 MS.gene52491:intron 25.0%
! CTTCAAAAATGTAATTAGGT+TGG - chr7.2:61453916-61453935 None:intergenic 25.0%
! TCAATATAAGGAACATCATA+TGG + chr7.2:61452830-61452849 MS.gene52491:CDS 25.0%
!! CAACCTAATTACATTTTTGA+AGG + chr7.2:61453914-61453933 MS.gene52491:CDS 25.0%
!! TTGTTTCTTACATTTGAGAT+CGG + chr7.2:61453588-61453607 MS.gene52491:intron 25.0%
!!! TGTAAAAGCATTATATGTGT+AGG - chr7.2:61453334-61453353 None:intergenic 25.0%
ATGGAAACAAATTGGTGAAA+TGG + chr7.2:61453642-61453661 MS.gene52491:intron 30.0%
CCAATATAAATGCTGATCAA+TGG + chr7.2:61452991-61453010 MS.gene52491:CDS 30.0%
CCATCTTAAACCAGATATTA+AGG + chr7.2:61453242-61453261 MS.gene52491:CDS 30.0%
CCATTGATCAGCATTTATAT+TGG - chr7.2:61452994-61453013 None:intergenic 30.0%
CTGTTTATGGTAAATGAGAA+CGG - chr7.2:61452928-61452947 None:intergenic 30.0%
TAAAACAATGCATGGAGAAA+TGG + chr7.2:61453217-61453236 MS.gene52491:CDS 30.0%
TAAACAGCAGAATACTATTC+AGG + chr7.2:61452941-61452960 MS.gene52491:CDS 30.0%
TAATCATCGTTGAATGTCAT+TGG - chr7.2:61453977-61453996 None:intergenic 30.0%
TGTTTATGGTAAATGAGAAC+GGG - chr7.2:61452927-61452946 None:intergenic 30.0%
! AAATTGATTTCCTGCTTCAT+GGG - chr7.2:61454034-61454053 None:intergenic 30.0%
! CCTTAATATCTGGTTTAAGA+TGG - chr7.2:61453245-61453264 None:intergenic 30.0%
! GAATAGTATTCTGCTGTTTA+TGG - chr7.2:61452941-61452960 None:intergenic 30.0%
!! AATGGACTACAAAAGAGAAT+AGG + chr7.2:61453009-61453028 MS.gene52491:CDS 30.0%
!! TTTCTCCATGCATTGTTTTA+AGG - chr7.2:61453217-61453236 None:intergenic 30.0%
!!! AGTACAATCATTTTGAGACA+AGG - chr7.2:61452811-61452830 None:intergenic 30.0%
ACAACATATTTGGAGACAAC+TGG + chr7.2:61453771-61453790 MS.gene52491:CDS 35.0%
AGAATGCCAAGAAAAAATCC+AGG + chr7.2:61453870-61453889 MS.gene52491:CDS 35.0%
AGTTGTCTCCAAATATGTTG+TGG - chr7.2:61453772-61453791 None:intergenic 35.0%
ATGGACCTTAAAACAATGCA+TGG + chr7.2:61453209-61453228 MS.gene52491:CDS 35.0%
CAAGAAAAAATCCAGGAACA+TGG + chr7.2:61453877-61453896 MS.gene52491:CDS 35.0%
GAAATTTCAAGAAGATTGCC+AGG + chr7.2:61453797-61453816 MS.gene52491:CDS 35.0%
GCACATGAATGGAAACAAAT+TGG + chr7.2:61453634-61453653 MS.gene52491:intron 35.0%
GCAGGAAATCAATTTCATGA+AGG + chr7.2:61454039-61454058 MS.gene52491:CDS 35.0%
GTTGTCTCCAAATATGTTGT+GGG - chr7.2:61453771-61453790 None:intergenic 35.0%
TAAGGAACATCATATGGATG+AGG + chr7.2:61452836-61452855 MS.gene52491:CDS 35.0%
TCGATTTAGAAAGAGATCCA+CGG - chr7.2:61453190-61453209 None:intergenic 35.0%
TGGATCTCTTTCTAAATCGA+TGG + chr7.2:61453190-61453209 MS.gene52491:CDS 35.0%
! AATTTCATGAAGGCCTTATG+TGG + chr7.2:61454049-61454068 MS.gene52491:CDS 35.0%
! AGTTTTGCAACCAGTGAAAT+TGG + chr7.2:61452873-61452892 MS.gene52491:CDS 35.0%
! GAAATTGATTTCCTGCTTCA+TGG - chr7.2:61454035-61454054 None:intergenic 35.0%
! TTCTTACATTTGAGATCGGA+GGG + chr7.2:61453592-61453611 MS.gene52491:intron 35.0%
! TTTCTTACATTTGAGATCGG+AGG + chr7.2:61453591-61453610 MS.gene52491:intron 35.0%
!!! CATGTTCCTGGATTTTTTCT+TGG - chr7.2:61453879-61453898 None:intergenic 35.0%
ACATAACTATCGTTACGTCC+TGG - chr7.2:61453818-61453837 None:intergenic 40.0%
ACTACTCCAGAAGATGAACT+TGG + chr7.2:61453941-61453960 MS.gene52491:CDS 40.0%
GATCAAGCCCACAACATATT+TGG + chr7.2:61453761-61453780 MS.gene52491:CDS 40.0%
TATCCACCAAGTTCATCTTC+TGG - chr7.2:61453950-61453969 None:intergenic 40.0%
TGGTTGCAAAACTAGAGTGA+TGG - chr7.2:61452866-61452885 None:intergenic 40.0%
! CTCAATTTTCACCATGTTCC+TGG - chr7.2:61453891-61453910 None:intergenic 40.0%
! TAGCATTTTTGTCGAATCCG+TGG + chr7.2:61453170-61453189 MS.gene52491:intron 40.0%
!! TGGATTAGAGTTTTATCCCG+AGG + chr7.2:61454006-61454025 MS.gene52491:CDS 40.0%
ACTCCAGAAGATGAACTTGG+TGG + chr7.2:61453944-61453963 MS.gene52491:CDS 45.0%
GTAGAATGAGCCATTGAGTG+AGG + chr7.2:61453721-61453740 MS.gene52491:intron 45.0%
! GGCATTCTCGACTTGCTTAA+TGG - chr7.2:61453858-61453877 None:intergenic 45.0%
! TGAGAACGGGTTCTTGATCA+TGG - chr7.2:61452914-61452933 None:intergenic 45.0%
! TTTTGCTCCTCCTCACTCAA+TGG - chr7.2:61453734-61453753 None:intergenic 45.0%
!!! TTTTTTTTATTTATTTTATG+CGG - chr7.2:61453368-61453387 None:intergenic 5.0%
GAATGAGCCATTGAGTGAGG+AGG + chr7.2:61453724-61453743 MS.gene52491:intron 50.0%
TTCCTGCTTCATGGGAACCT+CGG - chr7.2:61454026-61454045 None:intergenic 50.0%
TCCTGCTTCATGGGAACCTC+GGG - chr7.2:61454025-61454044 None:intergenic 55.0%
TCCCGAGGTTCCCATGAAGC+AGG + chr7.2:61454021-61454040 MS.gene52491:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 61452801 61454081 61452801 ID=MS.gene52491
chr7.2 mRNA 61452801 61454081 61452801 ID=MS.gene52491.t1;Parent=MS.gene52491
chr7.2 exon 61452801 61453030 61452801 ID=MS.gene52491.t1.exon1;Parent=MS.gene52491.t1
chr7.2 CDS 61452801 61453030 61452801 ID=cds.MS.gene52491.t1;Parent=MS.gene52491.t1
chr7.2 exon 61453173 61453263 61453173 ID=MS.gene52491.t1.exon2;Parent=MS.gene52491.t1
chr7.2 CDS 61453173 61453263 61453173 ID=cds.MS.gene52491.t1;Parent=MS.gene52491.t1
chr7.2 exon 61453725 61454081 61453725 ID=MS.gene52491.t1.exon3;Parent=MS.gene52491.t1
chr7.2 CDS 61453725 61454081 61453725 ID=cds.MS.gene52491.t1;Parent=MS.gene52491.t1
Gene Sequence

>MS.gene52491

ATGTTTTCCTTGTCTCAAAATGATTGTACTCAATATAAGGAACATCATATGGATGAGGTTAACCATCACTCTAGTTTTGCAACCAGTGAAATTGGATACAAATATCAAGACCATGATCAAGAACCCGTTCTCATTTACCATAAACAGCAGAATACTATTCAGGAGAATAATGAAATTCATCACAAATATTCCAATATAAATGCTGATCAATGGACTACAAAAGAGAATAGGTACATAAAATCATTTATAATTTCTATACTTCGTACTACATGTTTTCATATATAGTTTTATTATGGTTCAAGTTCAATATATGTTTAACTCTTTTGTTTTGCAATTTGATTAATCTTATCTTGTTTTTATATATATTTTTAGCATTTTTGTCGAATCCGTGGATCTCTTTCTAAATCGATGGACCTTAAAACAATGCATGGAGAAATGGTACCATCTTAAACCAGATATTAAGGTGTTTCTTTTTAAATCCTTTTTAACACTTTTTTTAGCAAAATCCTTTTTATCTTTTATTGCGTAAACCTACACATATAATGCTTTTACATGTACATAAAACCGCATAAAATAAATAAAAAAAATAGAAATGCTTATCAGTTAAATGCATAAATGCAATTGAATCATCATTTGTATATGATTTTATAACAACAAGTGGAATTCGTAGCTAACATTTATTTTATATTCATTGATGCAAGTTCTTATAGATTGTACAATATTGACATAATAGTTTTAGTTATTACATTTCATTGAAAAACCTAATGGATGTGTGTATTTTTTTTTTTTGTTTCTTACATTTGAGATCGGAGGGAGTACATAATAAAAATATTGCACATGAATGGAAACAAATTGGTGAAATGGAAATCTTCCTCTATTTAATTATATATAGACCTAATCTAAACATGTTTTGTATAATTGTAGAATGAGCCATTGAGTGAGGAGGAGCAAAACATACTAGATCAAGCCCACAACATATTTGGAGACAACTGGACTGAAATTTCAAGAAGATTGCCAGGACGTAACGATAGTTATGTTAAGAATCATTTGAACGCCATTAAGCAAGTCGAGAATGCCAAGAAAAAATCCAGGAACATGGTGAAAATTGAGAACCAACCTAATTACATTTTTGAAGGTTTGACTACTCCAGAAGATGAACTTGGTGGATATGTGCCAATGACATTCAACGATGATTATGAGTTATATGGATTAGAGTTTTATCCCGAGGTTCCCATGAAGCAGGAAATCAATTTCATGAAGGCCTTATGTGGAAACGTTTAA
Protein sequence

>MS.gene52491.t1

MFSLSQNDCTQYKEHHMDEVNHHSSFATSEIGYKYQDHDQEPVLIYHKQQNTIQENNEIHHKYSNINADQWTTKENSIFVESVDLFLNRWTLKQCMEKWYHLKPDIKNEPLSEEEQNILDQAHNIFGDNWTEISRRLPGRNDSYVKNHLNAIKQVENAKKKSRNMVKIENQPNYIFEGLTTPEDELGGYVPMTFNDDYELYGLEFYPEVPMKQEINFMKALCGNV