AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene046818

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046818.t1 MTR_1g028470 92.282 298 18 1 1 298 1 293 0.0 530
MS.gene046818.t1 MTR_3g090850 60.550 327 82 12 15 297 5 328 8.03e-113 329
MS.gene046818.t1 MTR_2g022280 50.485 206 81 2 92 297 1 185 1.57e-62 196
MS.gene046818.t1 MTR_0194s0050 37.795 254 135 4 43 295 145 376 2.40e-49 168
MS.gene046818.t1 MTR_7g113830 37.931 232 119 5 66 295 93 301 6.47e-38 136
MS.gene046818.t1 MTR_3g099620 35.391 243 138 4 54 293 79 305 4.65e-37 134
MS.gene046818.t1 MTR_1g082480 38.318 214 102 5 91 296 135 326 1.80e-36 133
MS.gene046818.t1 MTR_1g082480 38.579 197 92 4 91 280 135 309 4.33e-33 124
MS.gene046818.t1 MTR_8g066770 35.468 203 97 5 91 286 113 288 2.84e-32 121
MS.gene046818.t1 MTR_5g064950 30.822 292 152 9 27 295 23 287 2.58e-28 110
MS.gene046818.t1 MTR_8g024210 30.769 273 145 5 40 297 115 358 3.40e-28 112
MS.gene046818.t1 MTR_5g064950 31.752 274 138 8 27 278 23 269 8.49e-28 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046818.t1 AT5G53210 47.429 350 113 7 19 297 14 363 2.07e-86 263
MS.gene046818.t1 AT5G53210 44.109 331 114 7 19 278 14 344 1.24e-71 225
MS.gene046818.t1 AT3G06120 46.377 207 95 3 92 297 1 192 3.00e-54 175
MS.gene046818.t1 AT3G24140 41.048 229 123 2 69 297 177 393 4.71e-49 168
MS.gene046818.t1 AT3G24140 41.048 229 123 2 69 297 177 393 5.04e-49 168
MS.gene046818.t1 AT1G72210 34.404 218 97 6 91 295 124 308 1.42e-30 117
MS.gene046818.t1 AT1G72210 35.000 200 85 5 91 278 124 290 2.16e-29 114
MS.gene046818.t1 AT4G01460 35.885 209 112 3 90 297 113 300 5.33e-28 110
MS.gene046818.t1 AT4G01460 35.885 209 112 3 90 297 113 300 5.33e-28 110
MS.gene046818.t1 AT1G22490 34.300 207 111 4 91 296 114 296 6.16e-27 107
MS.gene046818.t1 AT1G22490 35.106 188 98 3 91 278 114 277 2.55e-25 103
MS.gene046818.t1 AT2G46810 33.493 209 106 3 91 297 120 297 5.80e-25 102
MS.gene046818.t1 AT2G46810 33.493 209 106 3 91 297 180 357 2.31e-24 101
MS.gene046818.t1 AT2G46810 33.493 209 106 3 91 297 192 369 2.74e-24 101
MS.gene046818.t1 AT5G65320 33.333 219 120 5 79 295 93 287 2.62e-23 97.4
MS.gene046818.t1 AT3G61950 31.280 211 107 4 91 297 126 302 1.94e-21 92.4
MS.gene046818.t1 AT3G61950 31.280 211 107 4 91 297 177 353 3.68e-21 92.4
MS.gene046818.t1 AT2G46810 32.275 189 96 2 91 278 120 277 1.70e-20 90.1
MS.gene046818.t1 AT5G65320 33.500 200 109 4 79 278 93 268 3.46e-20 88.6
MS.gene046818.t1 AT5G46690 33.838 198 129 1 91 286 87 284 4.98e-19 86.3
MS.gene046818.t1 AT3G61950 31.638 177 85 2 91 265 126 268 7.56e-19 85.1
MS.gene046818.t1 AT3G61950 31.638 177 85 2 91 265 177 319 1.07e-18 85.5
MS.gene046818.t1 AT5G46690 56.164 73 30 1 91 161 87 159 2.10e-18 84.0

Find 36 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTTGTTTCTTGGATTCT+AGG 0.149526 1.2:+14722133 None:intergenic
GCTATACTTGTTCACTATTA+AGG 0.194492 1.2:-14721761 MS.gene046818:intron
TATGGAGTTCTTGGACTAAT+TGG 0.233920 1.2:+14722051 None:intergenic
AACCGTTTCGTCACGAATTC+CGG 0.237314 1.2:-14721869 MS.gene046818:CDS
CTCATTGATGTTATCATTGA+TGG 0.240583 1.2:+14721963 None:intergenic
AGCCATTGATATGGAGTTCT+TGG 0.282669 1.2:+14722042 None:intergenic
TTTCTTAATAAAATGTTTGC+TGG 0.293141 1.2:+14721188 None:intergenic
CTAATTGGTAAGATTATTCT+AGG 0.295024 1.2:+14722066 None:intergenic
CATTGTTGTAGCCATTGATA+TGG 0.334687 1.2:+14722033 None:intergenic
ATATTCAATGAAACTGAGTT+TGG 0.348570 1.2:-14722808 MS.gene046818:CDS
AACAAGGTGTCATGATCTAT+TGG 0.372909 1.2:+14722841 None:intergenic
ACCGTTTCGTCACGAATTCC+GGG 0.393233 1.2:-14721868 MS.gene046818:CDS
TGTGACTTCTTCAATTATAG+AGG 0.399402 1.2:-14722635 MS.gene046818:CDS
ATGGAAGAAGCTGAAGAAGT+TGG 0.426375 1.2:+14721982 None:intergenic
GGACTTAGTGGTAAAGGTCT+TGG 0.429539 1.2:+14722087 None:intergenic
TTCGTCACGAATTCCGGGGC+AGG 0.440139 1.2:-14721863 MS.gene046818:CDS
AAGATTATTCTAGGACTTAG+TGG 0.440624 1.2:+14722075 None:intergenic
ATTCTAGGACTTAGTGGTAA+AGG 0.492814 1.2:+14722081 None:intergenic
CCCCGGAATTCGTGACGAAA+CGG 0.495669 1.2:+14721867 None:intergenic
TGTCGCGAATTCAACATCTT+CGG 0.496233 1.2:-14721938 MS.gene046818:CDS
GTACAAAATGGAAACTCAAA+AGG 0.509601 1.2:-14722866 None:intergenic
CAAGTTCTTCAGCACTGAGT+TGG 0.510419 1.2:+14721221 None:intergenic
GTCCAAGAACTCCATATCAA+TGG 0.523072 1.2:-14722044 MS.gene046818:CDS
ATCTTCGGTTGCTGATGTTG+AGG 0.535328 1.2:-14721923 MS.gene046818:CDS
TGAAACTGAGTTTGGTTCAG+AGG 0.550414 1.2:-14722800 MS.gene046818:CDS
TTGGAGATGGCTCAGATGAA+AGG 0.570619 1.2:+14722001 None:intergenic
ACATCGTATGTCGCATATCA+CGG 0.587471 1.2:-14722593 MS.gene046818:CDS
GATCAAGCATCAATAGTTGA+AGG 0.590664 1.2:-14722198 MS.gene046818:CDS
AATAGTGAACAAGTATAGCA+TGG 0.592880 1.2:+14721765 None:intergenic
GAAGCTGAAGAAGTTGGAGA+TGG 0.605113 1.2:+14721988 None:intergenic
ATTATTCTAAGAGCCTGCCC+CGG 0.625886 1.2:+14721850 None:intergenic
CCGTTTCGTCACGAATTCCG+GGG 0.670932 1.2:-14721867 MS.gene046818:CDS
ATAGAGGAACAAAACAACGA+TGG 0.690625 1.2:-14722619 MS.gene046818:CDS
CAATGGCTACAACAATGTGG+TGG 0.701552 1.2:-14722027 MS.gene046818:CDS
TATCAATGGCTACAACAATG+TGG 0.711948 1.2:-14722030 MS.gene046818:CDS
GAATATATCAGATAACAACA+AGG 0.741545 1.2:+14722825 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATATAATTAATTATTAA+TGG + chr1.2:14722775-14722794 None:intergenic 0.0%
!! ATGAATTAAATAAACAATAT+TGG + chr1.2:14722687-14722706 None:intergenic 10.0%
!! TTACTGTAAAAAATAAAAAT+TGG - chr1.2:14722436-14722455 MS.gene046818:intron 10.0%
!!! GTTATTTATGTTTTCAATTT+TGG - chr1.2:14722748-14722767 MS.gene046818:CDS 15.0%
!!! AGTTTTAAATGAAACTAGTT+AGG - chr1.2:14721617-14721636 MS.gene046818:intron 20.0%
!!! ATTATTGAAGTTTTCCAAAA+TGG + chr1.2:14721286-14721305 None:intergenic 20.0%
!!! GTTTTAAATGAAACTAGTTA+GGG - chr1.2:14721618-14721637 MS.gene046818:intron 20.0%
!!! TTTTAAATGAAACTAGTTAG+GGG - chr1.2:14721619-14721638 MS.gene046818:intron 20.0%
! AAAATTTCTCTTGTGTAGAT+TGG - chr1.2:14722798-14722817 MS.gene046818:CDS 25.0%
! AGAATCAATATTGAATACTG+TGG - chr1.2:14722470-14722489 MS.gene046818:intron 25.0%
! ATATTCAATGAAACTGAGTT+TGG - chr1.2:14721243-14721262 MS.gene046818:intron 25.0%
! ATTACTCTTCTATATGGTTT+AGG - chr1.2:14721828-14721847 MS.gene046818:CDS 25.0%
! ATTGAATACTGTGGTAATAA+TGG - chr1.2:14722479-14722498 MS.gene046818:intron 25.0%
! CAACTAATTACTCTTCTATA+TGG - chr1.2:14721822-14721841 MS.gene046818:CDS 25.0%
! CATAACAATTAACATCATTC+TGG - chr1.2:14722625-14722644 MS.gene046818:CDS 25.0%
! CTAATTGGTAAGATTATTCT+AGG + chr1.2:14721988-14722007 None:intergenic 25.0%
! GAATATATCAGATAACAACA+AGG + chr1.2:14721229-14721248 None:intergenic 25.0%
! TTACTCTTCTATATGGTTTA+GGG - chr1.2:14721829-14721848 MS.gene046818:CDS 25.0%
! TTGGTGAAAAAATCAATGTA+TGG - chr1.2:14722660-14722679 MS.gene046818:CDS 25.0%
!!! AAGATGTTGTTTTTGAGTTT+TGG + chr1.2:14721329-14721348 None:intergenic 25.0%
!!! GATACAAATTTTGATCCTTT+TGG - chr1.2:14722388-14722407 MS.gene046818:intron 25.0%
!!! GTAAACTTTTCTTTGTTTCT+TGG + chr1.2:14721929-14721948 None:intergenic 25.0%
AATAGTGAACAAGTATAGCA+TGG + chr1.2:14722289-14722308 None:intergenic 30.0%
ATTCTGGCATTGTATGTATT+TGG - chr1.2:14722641-14722660 MS.gene046818:CDS 30.0%
ATTGTTATGATATACATCCC+TGG + chr1.2:14722614-14722633 None:intergenic 30.0%
CATAAACCAGACCAAATTTA+TGG - chr1.2:14721653-14721672 MS.gene046818:intron 30.0%
CTCATTGATGTTATCATTGA+TGG + chr1.2:14722091-14722110 None:intergenic 30.0%
GCTATACTTGTTCACTATTA+AGG - chr1.2:14722290-14722309 MS.gene046818:intron 30.0%
TGTGACTTCTTCAATTATAG+AGG - chr1.2:14721416-14721435 MS.gene046818:intron 30.0%
TTGTATCTCTTGTTAGCATA+AGG + chr1.2:14722375-14722394 None:intergenic 30.0%
! ACTCTTTTGACATAAAAGCA+AGG + chr1.2:14721543-14721562 None:intergenic 30.0%
! AGAGGATCTATTTTCCATTT+TGG - chr1.2:14721269-14721288 MS.gene046818:intron 30.0%
! TTCTTTGTTTCTTGGATTCT+AGG + chr1.2:14721921-14721940 None:intergenic 30.0%
!! AAGATTATTCTAGGACTTAG+TGG + chr1.2:14721979-14721998 None:intergenic 30.0%
!! GAGTTTTGGTCATTGATAAT+GGG + chr1.2:14721315-14721334 None:intergenic 30.0%
!! TGAGTTTTGGTCATTGATAA+TGG + chr1.2:14721316-14721335 None:intergenic 30.0%
ATAGAGGAACAAAACAACGA+TGG - chr1.2:14721432-14721451 MS.gene046818:intron 35.0%
CAAAAAATGACAGCTACTAG+AGG + chr1.2:14722416-14722435 None:intergenic 35.0%
CATTGTTGTAGCCATTGATA+TGG + chr1.2:14722021-14722040 None:intergenic 35.0%
GATCAAGCATCAATAGTTGA+AGG - chr1.2:14721853-14721872 MS.gene046818:CDS 35.0%
GTAATGTACTTCACTACTGT+AGG + chr1.2:14722523-14722542 None:intergenic 35.0%
TATCAATGGCTACAACAATG+TGG - chr1.2:14722021-14722040 MS.gene046818:CDS 35.0%
TATGGAGTTCTTGGACTAAT+TGG + chr1.2:14722003-14722022 None:intergenic 35.0%
! AACAAGGTGTCATGATCTAT+TGG + chr1.2:14721213-14721232 None:intergenic 35.0%
! GATGTTGAGGTTAAGTTTTG+TGG - chr1.2:14722141-14722160 MS.gene046818:CDS 35.0%
! TGCTCATTTTCAGAAACTTG+AGG + chr1.2:14721360-14721379 None:intergenic 35.0%
!! ATTCTAGGACTTAGTGGTAA+AGG + chr1.2:14721973-14721992 None:intergenic 35.0%
ACATCGTATGTCGCATATCA+CGG - chr1.2:14721458-14721477 MS.gene046818:intron 40.0%
ACCAGACCAAATTTATGGTC+TGG - chr1.2:14721658-14721677 MS.gene046818:intron 40.0%
ACCAGACCATAAATTTGGTC+TGG + chr1.2:14721662-14721681 None:intergenic 40.0%
ACTGGACCAGACCATAAATT+TGG + chr1.2:14721667-14721686 None:intergenic 40.0%
AGCCATTGATATGGAGTTCT+TGG + chr1.2:14722012-14722031 None:intergenic 40.0%
ATGGAAGAAGCTGAAGAAGT+TGG + chr1.2:14722072-14722091 None:intergenic 40.0%
ATTGCATCAACCGTAGACTA+CGG + chr1.2:14721715-14721734 None:intergenic 40.0%
GTCCAAGAACTCCATATCAA+TGG - chr1.2:14722007-14722026 MS.gene046818:CDS 40.0%
TAACTACGAACCGTAGTCTA+CGG - chr1.2:14721702-14721721 MS.gene046818:intron 40.0%
TAGACTACGGTTCGTAGTTA+GGG + chr1.2:14721702-14721721 None:intergenic 40.0%
TGTCGCGAATTCAACATCTT+CGG - chr1.2:14722113-14722132 MS.gene046818:CDS 40.0%
! TGAAACTGAGTTTGGTTCAG+AGG - chr1.2:14721251-14721270 MS.gene046818:intron 40.0%
!! TTCACATTTCTGAGACACCA+GGG - chr1.2:14722594-14722613 MS.gene046818:CDS 40.0%
!! TTTCACATTTCTGAGACACC+AGG - chr1.2:14722593-14722612 MS.gene046818:CDS 40.0%
AACCGTTTCGTCACGAATTC+CGG - chr1.2:14722182-14722201 MS.gene046818:CDS 45.0%
AGACTACGGTTCGTAGTTAG+GGG + chr1.2:14721701-14721720 None:intergenic 45.0%
ATCTTCGGTTGCTGATGTTG+AGG - chr1.2:14722128-14722147 MS.gene046818:CDS 45.0%
CAATGGCTACAACAATGTGG+TGG - chr1.2:14722024-14722043 MS.gene046818:CDS 45.0%
GAAGCTGAAGAAGTTGGAGA+TGG + chr1.2:14722066-14722085 None:intergenic 45.0%
GGACTTAGTGGTAAAGGTCT+TGG + chr1.2:14721967-14721986 None:intergenic 45.0%
GTAGACTACGGTTCGTAGTT+AGG + chr1.2:14721703-14721722 None:intergenic 45.0%
TTGGAGATGGCTCAGATGAA+AGG + chr1.2:14722053-14722072 None:intergenic 45.0%
! ATTATTCTAAGAGCCTGCCC+CGG + chr1.2:14722204-14722223 None:intergenic 45.0%
! CAAGTTCTTCAGCACTGAGT+TGG + chr1.2:14722833-14722852 None:intergenic 45.0%
! TTAGGGGTGTGCAAAAGAAC+TGG + chr1.2:14721685-14721704 None:intergenic 45.0%
!!! TAATTTTAATCTTAATAAAA+AGG + chr1.2:14721759-14721778 None:intergenic 5.0%
ACCGTTTCGTCACGAATTCC+GGG - chr1.2:14722183-14722202 MS.gene046818:CDS 50.0%
CAGCTACTAGAGGCTCCAAA+AGG + chr1.2:14722406-14722425 None:intergenic 50.0%
CCCCGGAATTCGTGACGAAA+CGG + chr1.2:14722187-14722206 None:intergenic 55.0%
CCGTTTCGTCACGAATTCCG+GGG - chr1.2:14722184-14722203 MS.gene046818:CDS 55.0%
TTCGTCACGAATTCCGGGGC+AGG - chr1.2:14722188-14722207 MS.gene046818:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 14721192 14722881 14721192 ID=MS.gene046818
chr1.2 mRNA 14721192 14722881 14721192 ID=MS.gene046818.t1;Parent=MS.gene046818
chr1.2 exon 14722513 14722881 14722513 ID=MS.gene046818.t1.exon1;Parent=MS.gene046818.t1
chr1.2 CDS 14722513 14722881 14722513 ID=cds.MS.gene046818.t1;Parent=MS.gene046818.t1
chr1.2 exon 14721762 14722223 14721762 ID=MS.gene046818.t1.exon2;Parent=MS.gene046818.t1
chr1.2 CDS 14721762 14722223 14721762 ID=cds.MS.gene046818.t1;Parent=MS.gene046818.t1
chr1.2 exon 14721192 14721257 14721192 ID=MS.gene046818.t1.exon3;Parent=MS.gene046818.t1
chr1.2 CDS 14721192 14721257 14721192 ID=cds.MS.gene046818.t1;Parent=MS.gene046818.t1
Gene Sequence

>MS.gene046818

ATGGAAACTCAAAAGGCTCCAATAGATCATGACACCTTGTTGTTATCTGATATATTCAATGAAACTGAGTTTGGTTCAGAGGATCTATTTTCCATTTTGGAAAACTTCAATAATTTTTCTCCCATTATCAATGACCAAAACTCAAAAACAACATCTTCAAGTGCTCCTCAAGTTTCTGAAAATGAGCATGCTGAGACATCACAGAAATGCAAGAGACAGAAGATTGTGACTTCTTCAATTATAGAGGAACAAAACAACGATGGACAACATCGTATGTCGCATATCACGGTCGAACGCAATCGAAGAAAGCAAATGAATGAGCAGCTATCTATCTTGAAGTCACTTATGCCTTGCTTTTATGTCAAAAGAGTGAGTACATATTAACTAACTTGTCACAAATTCAAATTCTAAATAATTTTTTTCAAAGTTTTAAATGAAACTAGTTAGGGGTGTGCATGATTCATAAACCAGACCAAATTTATGGTCTGGTCCAGTTCTTTTGCACACCCCTAACTACGAACCGTAGTCTACGGTTGATGCAATAACAATTGCAATTGTTTGAAACCTTTTTATTAAGATTAAAATTATGTTTATCTTTCTTTAAAATTATTATTTTTTGCATAAAAAATGCAACTAATTACTCTTCTATATGGTTTAGGGAGATCAAGCATCAATAGTTGAAGGTGTAATTGATTACATCAACGAGTTACATCAACTACTACAATGCCTAGAATCCAAGAAACAAAGAAAAGTTTACAGTGAAGTAACAAGTCCAAGACCTTTACCACTAAGTCCTAGAATAATCTTACCAATTAGTCCAAGAACTCCATATCAATGGCTACAACAATGTGGTGGTTACCTTTCATCTGAGCCATCTCCAACTTCTTCAGCTTCTTCCATCAATGATAACATCAATGAGCTTGTCGCGAATTCAACATCTTCGGTTGCTGATGTTGAGGTTAAGTTTTGTGGTTCACATGTGCTTTTGAAAACCGTTTCGTCACGAATTCCGGGGCAGGCTCTTAGAATAATGTCTGTTCTTGAAGATCTAATGCTTGAGATTGTTCATGTTAGAGTTAATACTGCTGATGAAACCATGCTATACTTGTTCACTATTAAGGTAACTTAATCTTTTGTTTATGCTTAATTAATTACTATTATTTACAACTACATTGATGATCCTTATGCTAACAAGAGATACAAATTTTGATCCTTTTGGAGCCTCTAGTAGCTGTCATTTTTTGTTACTGTAAAAAATAAAAATTGGTAACTTTGATGAGAATCAATATTGAATACTGTGGTAATAATGGTAAATTCTTTGCTAAAAGCCTACAGTAGTGAAGTACATTACTACTGTATAGTATAATAATTAATCAATGACATGCAGTACACAAAGCATCTTTTCACATTTCTGAGACACCAGGGATGTATATCATAACAATTAACATCATTCTGGCATTGTATGTATTTGGTGAAAAAATCAATGTATGGTCCAATATTGTTTATTTAATTCATAGCAGCTAATGATTGAGTATGCATGTATCATATGTGTTAATGTTATTTATGTTTTCAATTTTGGTCCATTAATAATTAATTATATTTTCTTAAAATTTCTCTTGTGTAGATTGGAATTGAATGCCAACTCAGTGCTGAAGAACTTGCTCAACAAATCCAGCAAACATTTTATTAA
Protein sequence

>MS.gene046818.t1

METQKAPIDHDTLLLSDIFNETEFGSEDLFSILENFNNFSPIINDQNSKTTSSSAPQVSENEHAETSQKCKRQKIVTSSIIEEQNNDGQHRMSHITVERNRRKQMNEQLSILKSLMPCFYVKRGDQASIVEGVIDYINELHQLLQCLESKKQRKVYSEVTSPRPLPLSPRIILPISPRTPYQWLQQCGGYLSSEPSPTSSASSINDNINELVANSTSSVADVEVKFCGSHVLLKTVSSRIPGQALRIMSVLEDLMLEIVHVRVNTADETMLYLFTIKIGIECQLSAEELAQQIQQTFY