AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32350

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32350.t1 MTR_1g028470 92.282 298 18 1 1 298 1 293 0.0 530
MS.gene32350.t1 MTR_3g090850 60.550 327 82 12 15 297 5 328 8.03e-113 329
MS.gene32350.t1 MTR_2g022280 50.485 206 81 2 92 297 1 185 1.57e-62 196
MS.gene32350.t1 MTR_0194s0050 37.795 254 135 4 43 295 145 376 2.40e-49 168
MS.gene32350.t1 MTR_7g113830 37.931 232 119 5 66 295 93 301 6.47e-38 136
MS.gene32350.t1 MTR_3g099620 35.391 243 138 4 54 293 79 305 4.65e-37 134
MS.gene32350.t1 MTR_1g082480 38.318 214 102 5 91 296 135 326 1.80e-36 133
MS.gene32350.t1 MTR_1g082480 38.579 197 92 4 91 280 135 309 4.33e-33 124
MS.gene32350.t1 MTR_8g066770 35.468 203 97 5 91 286 113 288 2.84e-32 121
MS.gene32350.t1 MTR_5g064950 30.822 292 152 9 27 295 23 287 2.58e-28 110
MS.gene32350.t1 MTR_8g024210 30.769 273 145 5 40 297 115 358 3.40e-28 112
MS.gene32350.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.gene32350.t1 AT5G53210 47.429 350 113 7 19 297 14 363 2.07e-86 263
MS.gene32350.t1 AT5G53210 44.109 331 114 7 19 278 14 344 1.24e-71 225
MS.gene32350.t1 AT3G06120 46.377 207 95 3 92 297 1 192 3.00e-54 175
MS.gene32350.t1 AT3G24140 41.048 229 123 2 69 297 177 393 4.71e-49 168
MS.gene32350.t1 AT3G24140 41.048 229 123 2 69 297 177 393 5.04e-49 168
MS.gene32350.t1 AT1G72210 34.404 218 97 6 91 295 124 308 1.42e-30 117
MS.gene32350.t1 AT1G72210 35.000 200 85 5 91 278 124 290 2.16e-29 114
MS.gene32350.t1 AT4G01460 35.885 209 112 3 90 297 113 300 5.33e-28 110
MS.gene32350.t1 AT4G01460 35.885 209 112 3 90 297 113 300 5.33e-28 110
MS.gene32350.t1 AT1G22490 34.300 207 111 4 91 296 114 296 6.16e-27 107
MS.gene32350.t1 AT1G22490 35.106 188 98 3 91 278 114 277 2.55e-25 103
MS.gene32350.t1 AT2G46810 33.493 209 106 3 91 297 120 297 5.80e-25 102
MS.gene32350.t1 AT2G46810 33.493 209 106 3 91 297 180 357 2.31e-24 101
MS.gene32350.t1 AT2G46810 33.493 209 106 3 91 297 192 369 2.74e-24 101
MS.gene32350.t1 AT5G65320 33.333 219 120 5 79 295 93 287 2.62e-23 97.4
MS.gene32350.t1 AT3G61950 31.280 211 107 4 91 297 126 302 1.94e-21 92.4
MS.gene32350.t1 AT3G61950 31.280 211 107 4 91 297 177 353 3.68e-21 92.4
MS.gene32350.t1 AT2G46810 32.275 189 96 2 91 278 120 277 1.70e-20 90.1
MS.gene32350.t1 AT5G65320 33.500 200 109 4 79 278 93 268 3.46e-20 88.6
MS.gene32350.t1 AT5G46690 33.838 198 129 1 91 286 87 284 4.98e-19 86.3
MS.gene32350.t1 AT3G61950 31.638 177 85 2 91 265 126 268 7.56e-19 85.1
MS.gene32350.t1 AT3G61950 31.638 177 85 2 91 265 177 319 1.07e-18 85.5
MS.gene32350.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 1.4:+13867000 None:intergenic
GCTATACTTGTTCACTATTA+AGG 0.194492 1.4:-13866628 MS.gene32350:intron
TATGGAGTTCTTGGACTAAT+TGG 0.233920 1.4:+13866918 None:intergenic
AACCGTTTCGTCACGAATTC+CGG 0.237314 1.4:-13866736 MS.gene32350:CDS
CTCATTGATGTTATCATTGA+TGG 0.240583 1.4:+13866830 None:intergenic
AGCCATTGATATGGAGTTCT+TGG 0.282669 1.4:+13866909 None:intergenic
TTTCTTAATAAAATGTTTGC+TGG 0.293141 1.4:+13866055 None:intergenic
CTAATTGGTAAGATTATTCT+AGG 0.295024 1.4:+13866933 None:intergenic
CATTGTTGTAGCCATTGATA+TGG 0.334687 1.4:+13866900 None:intergenic
ATATTCAATGAAACTGAGTT+TGG 0.348570 1.4:-13867675 MS.gene32350:CDS
AACAAGGTGTCATGATCTAT+TGG 0.372909 1.4:+13867708 None:intergenic
ACCGTTTCGTCACGAATTCC+GGG 0.393233 1.4:-13866735 MS.gene32350:CDS
TGTGACTTCTTCAATTATAG+AGG 0.399402 1.4:-13867502 MS.gene32350:CDS
ATGGAAGAAGCTGAAGAAGT+TGG 0.426375 1.4:+13866849 None:intergenic
GGACTTAGTGGTAAAGGTCT+TGG 0.429539 1.4:+13866954 None:intergenic
TTCGTCACGAATTCCGGGGC+AGG 0.440139 1.4:-13866730 MS.gene32350:CDS
AAGATTATTCTAGGACTTAG+TGG 0.440624 1.4:+13866942 None:intergenic
ATTCTAGGACTTAGTGGTAA+AGG 0.492814 1.4:+13866948 None:intergenic
CCCCGGAATTCGTGACGAAA+CGG 0.495669 1.4:+13866734 None:intergenic
TGTCGCGAATTCAACATCTT+CGG 0.496233 1.4:-13866805 MS.gene32350:CDS
GTACAAAATGGAAACTCAAA+AGG 0.509601 1.4:-13867733 None:intergenic
CAAGTTCTTCAGCACTGAGT+TGG 0.510419 1.4:+13866088 None:intergenic
GTCCAAGAACTCCATATCAA+TGG 0.523072 1.4:-13866911 MS.gene32350:CDS
ATCTTCGGTTGCTGATGTTG+AGG 0.535328 1.4:-13866790 MS.gene32350:CDS
TGAAACTGAGTTTGGTTCAG+AGG 0.550414 1.4:-13867667 MS.gene32350:CDS
TTGGAGATGGCTCAGATGAA+AGG 0.570619 1.4:+13866868 None:intergenic
ACATCGTATGTCGCATATCA+CGG 0.587471 1.4:-13867460 MS.gene32350:CDS
GATCAAGCATCAATAGTTGA+AGG 0.590664 1.4:-13867065 MS.gene32350:CDS
AATAGTGAACAAGTATAGCA+TGG 0.592880 1.4:+13866632 None:intergenic
GAAGCTGAAGAAGTTGGAGA+TGG 0.605113 1.4:+13866855 None:intergenic
ATTATTCTAAGAGCCTGCCC+CGG 0.625886 1.4:+13866717 None:intergenic
CCGTTTCGTCACGAATTCCG+GGG 0.670932 1.4:-13866734 MS.gene32350:CDS
ATAGAGGAACAAAACAACGA+TGG 0.690625 1.4:-13867486 MS.gene32350:CDS
CAATGGCTACAACAATGTGG+TGG 0.701552 1.4:-13866894 MS.gene32350:CDS
TATCAATGGCTACAACAATG+TGG 0.711948 1.4:-13866897 MS.gene32350:CDS
GAATATATCAGATAACAACA+AGG 0.741545 1.4:+13867692 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATATAATTAATTATTAA+TGG + chr1.4:13867642-13867661 None:intergenic 0.0%
!! ATGAATTAAATAAACAATAT+TGG + chr1.4:13867554-13867573 None:intergenic 10.0%
!! TTACTGTAAAAAATAAAAAT+TGG - chr1.4:13867303-13867322 MS.gene32350:intron 10.0%
!!! GTTATTTATGTTTTCAATTT+TGG - chr1.4:13867615-13867634 MS.gene32350:CDS 15.0%
!!! AGTTTTAAATGAAACTAGTT+AGG - chr1.4:13866484-13866503 MS.gene32350:intron 20.0%
!!! ATTATTGAAGTTTTCCAAAA+TGG + chr1.4:13866153-13866172 None:intergenic 20.0%
!!! GTTTTAAATGAAACTAGTTA+GGG - chr1.4:13866485-13866504 MS.gene32350:intron 20.0%
!!! TTTTAAATGAAACTAGTTAG+GGG - chr1.4:13866486-13866505 MS.gene32350:intron 20.0%
! AAAATTTCTCTTGTGTAGAT+TGG - chr1.4:13867665-13867684 MS.gene32350:CDS 25.0%
! AGAATCAATATTGAATACTG+TGG - chr1.4:13867337-13867356 MS.gene32350:intron 25.0%
! ATATTCAATGAAACTGAGTT+TGG - chr1.4:13866110-13866129 MS.gene32350:intron 25.0%
! ATTACTCTTCTATATGGTTT+AGG - chr1.4:13866695-13866714 MS.gene32350:CDS 25.0%
! ATTGAATACTGTGGTAATAA+TGG - chr1.4:13867346-13867365 MS.gene32350:intron 25.0%
! CAACTAATTACTCTTCTATA+TGG - chr1.4:13866689-13866708 MS.gene32350:CDS 25.0%
! CATAACAATTAACATCATTC+TGG - chr1.4:13867492-13867511 MS.gene32350:CDS 25.0%
! CTAATTGGTAAGATTATTCT+AGG + chr1.4:13866855-13866874 None:intergenic 25.0%
! GAATATATCAGATAACAACA+AGG + chr1.4:13866096-13866115 None:intergenic 25.0%
! TTACTCTTCTATATGGTTTA+GGG - chr1.4:13866696-13866715 MS.gene32350:CDS 25.0%
! TTGGTGAAAAAATCAATGTA+TGG - chr1.4:13867527-13867546 MS.gene32350:CDS 25.0%
!!! AAGATGTTGTTTTTGAGTTT+TGG + chr1.4:13866196-13866215 None:intergenic 25.0%
!!! GATACAAATTTTGATCCTTT+TGG - chr1.4:13867255-13867274 MS.gene32350:intron 25.0%
!!! GTAAACTTTTCTTTGTTTCT+TGG + chr1.4:13866796-13866815 None:intergenic 25.0%
AATAGTGAACAAGTATAGCA+TGG + chr1.4:13867156-13867175 None:intergenic 30.0%
ATTCTGGCATTGTATGTATT+TGG - chr1.4:13867508-13867527 MS.gene32350:CDS 30.0%
ATTGTTATGATATACATCCC+TGG + chr1.4:13867481-13867500 None:intergenic 30.0%
CATAAACCAGACCAAATTTA+TGG - chr1.4:13866520-13866539 MS.gene32350:intron 30.0%
CTCATTGATGTTATCATTGA+TGG + chr1.4:13866958-13866977 None:intergenic 30.0%
GCTATACTTGTTCACTATTA+AGG - chr1.4:13867157-13867176 MS.gene32350:intron 30.0%
TGTGACTTCTTCAATTATAG+AGG - chr1.4:13866283-13866302 MS.gene32350:intron 30.0%
TTGTATCTCTTGTTAGCATA+AGG + chr1.4:13867242-13867261 None:intergenic 30.0%
! ACTCTTTTGACATAAAAGCA+AGG + chr1.4:13866410-13866429 None:intergenic 30.0%
! AGAGGATCTATTTTCCATTT+TGG - chr1.4:13866136-13866155 MS.gene32350:intron 30.0%
! TTCTTTGTTTCTTGGATTCT+AGG + chr1.4:13866788-13866807 None:intergenic 30.0%
!! AAGATTATTCTAGGACTTAG+TGG + chr1.4:13866846-13866865 None:intergenic 30.0%
!! GAGTTTTGGTCATTGATAAT+GGG + chr1.4:13866182-13866201 None:intergenic 30.0%
!! TGAGTTTTGGTCATTGATAA+TGG + chr1.4:13866183-13866202 None:intergenic 30.0%
ATAGAGGAACAAAACAACGA+TGG - chr1.4:13866299-13866318 MS.gene32350:intron 35.0%
CAAAAAATGACAGCTACTAG+AGG + chr1.4:13867283-13867302 None:intergenic 35.0%
CATTGTTGTAGCCATTGATA+TGG + chr1.4:13866888-13866907 None:intergenic 35.0%
GATCAAGCATCAATAGTTGA+AGG - chr1.4:13866720-13866739 MS.gene32350:CDS 35.0%
GTAATGTACTTCACTACTGT+AGG + chr1.4:13867390-13867409 None:intergenic 35.0%
TATCAATGGCTACAACAATG+TGG - chr1.4:13866888-13866907 MS.gene32350:CDS 35.0%
TATGGAGTTCTTGGACTAAT+TGG + chr1.4:13866870-13866889 None:intergenic 35.0%
! AACAAGGTGTCATGATCTAT+TGG + chr1.4:13866080-13866099 None:intergenic 35.0%
! GATGTTGAGGTTAAGTTTTG+TGG - chr1.4:13867008-13867027 MS.gene32350:CDS 35.0%
! TGCTCATTTTCAGAAACTTG+AGG + chr1.4:13866227-13866246 None:intergenic 35.0%
!! ATTCTAGGACTTAGTGGTAA+AGG + chr1.4:13866840-13866859 None:intergenic 35.0%
ACATCGTATGTCGCATATCA+CGG - chr1.4:13866325-13866344 MS.gene32350:intron 40.0%
ACCAGACCAAATTTATGGTC+TGG - chr1.4:13866525-13866544 MS.gene32350:intron 40.0%
ACCAGACCATAAATTTGGTC+TGG + chr1.4:13866529-13866548 None:intergenic 40.0%
ACTGGACCAGACCATAAATT+TGG + chr1.4:13866534-13866553 None:intergenic 40.0%
AGCCATTGATATGGAGTTCT+TGG + chr1.4:13866879-13866898 None:intergenic 40.0%
ATGGAAGAAGCTGAAGAAGT+TGG + chr1.4:13866939-13866958 None:intergenic 40.0%
ATTGCATCAACCGTAGACTA+CGG + chr1.4:13866582-13866601 None:intergenic 40.0%
GTCCAAGAACTCCATATCAA+TGG - chr1.4:13866874-13866893 MS.gene32350:CDS 40.0%
TAACTACGAACCGTAGTCTA+CGG - chr1.4:13866569-13866588 MS.gene32350:intron 40.0%
TAGACTACGGTTCGTAGTTA+GGG + chr1.4:13866569-13866588 None:intergenic 40.0%
TGTCGCGAATTCAACATCTT+CGG - chr1.4:13866980-13866999 MS.gene32350:CDS 40.0%
! TGAAACTGAGTTTGGTTCAG+AGG - chr1.4:13866118-13866137 MS.gene32350:intron 40.0%
!! TTCACATTTCTGAGACACCA+GGG - chr1.4:13867461-13867480 MS.gene32350:CDS 40.0%
!! TTTCACATTTCTGAGACACC+AGG - chr1.4:13867460-13867479 MS.gene32350:CDS 40.0%
AACCGTTTCGTCACGAATTC+CGG - chr1.4:13867049-13867068 MS.gene32350:CDS 45.0%
AGACTACGGTTCGTAGTTAG+GGG + chr1.4:13866568-13866587 None:intergenic 45.0%
ATCTTCGGTTGCTGATGTTG+AGG - chr1.4:13866995-13867014 MS.gene32350:CDS 45.0%
CAATGGCTACAACAATGTGG+TGG - chr1.4:13866891-13866910 MS.gene32350:CDS 45.0%
GAAGCTGAAGAAGTTGGAGA+TGG + chr1.4:13866933-13866952 None:intergenic 45.0%
GGACTTAGTGGTAAAGGTCT+TGG + chr1.4:13866834-13866853 None:intergenic 45.0%
GTAGACTACGGTTCGTAGTT+AGG + chr1.4:13866570-13866589 None:intergenic 45.0%
TTGGAGATGGCTCAGATGAA+AGG + chr1.4:13866920-13866939 None:intergenic 45.0%
! ATTATTCTAAGAGCCTGCCC+CGG + chr1.4:13867071-13867090 None:intergenic 45.0%
! CAAGTTCTTCAGCACTGAGT+TGG + chr1.4:13867700-13867719 None:intergenic 45.0%
! TTAGGGGTGTGCAAAAGAAC+TGG + chr1.4:13866552-13866571 None:intergenic 45.0%
!!! TAATTTTAATCTTAATAAAA+AGG + chr1.4:13866626-13866645 None:intergenic 5.0%
ACCGTTTCGTCACGAATTCC+GGG - chr1.4:13867050-13867069 MS.gene32350:CDS 50.0%
CAGCTACTAGAGGCTCCAAA+AGG + chr1.4:13867273-13867292 None:intergenic 50.0%
CCCCGGAATTCGTGACGAAA+CGG + chr1.4:13867054-13867073 None:intergenic 55.0%
CCGTTTCGTCACGAATTCCG+GGG - chr1.4:13867051-13867070 MS.gene32350:CDS 55.0%
TTCGTCACGAATTCCGGGGC+AGG - chr1.4:13867055-13867074 MS.gene32350:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 13866059 13867748 13866059 ID=MS.gene32350
chr1.4 mRNA 13866059 13867748 13866059 ID=MS.gene32350.t1;Parent=MS.gene32350
chr1.4 exon 13867380 13867748 13867380 ID=MS.gene32350.t1.exon1;Parent=MS.gene32350.t1
chr1.4 CDS 13867380 13867748 13867380 ID=cds.MS.gene32350.t1;Parent=MS.gene32350.t1
chr1.4 exon 13866629 13867090 13866629 ID=MS.gene32350.t1.exon2;Parent=MS.gene32350.t1
chr1.4 CDS 13866629 13867090 13866629 ID=cds.MS.gene32350.t1;Parent=MS.gene32350.t1
chr1.4 exon 13866059 13866124 13866059 ID=MS.gene32350.t1.exon3;Parent=MS.gene32350.t1
chr1.4 CDS 13866059 13866124 13866059 ID=cds.MS.gene32350.t1;Parent=MS.gene32350.t1
Gene Sequence

>MS.gene32350

ATGGAAACTCAAAAGGCTCCAATAGATCATGACACCTTGTTGTTATCTGATATATTCAATGAAACTGAGTTTGGTTCAGAGGATCTATTTTCCATTTTGGAAAACTTCAATAATTTTTCTCCCATTATCAATGACCAAAACTCAAAAACAACATCTTCAAGTGCTCCTCAAGTTTCTGAAAATGAGCATGCTGAGACATCACAGAAATGCAAGAGACAGAAGATTGTGACTTCTTCAATTATAGAGGAACAAAACAACGATGGACAACATCGTATGTCGCATATCACGGTCGAACGCAATCGAAGAAAGCAAATGAATGAGCAGCTATCTATCTTGAAGTCACTTATGCCTTGCTTTTATGTCAAAAGAGTGAGTACATATTAACTAACTTGTCACAAATTCAAATTCTAAATAATTTTTTTCAAAGTTTTAAATGAAACTAGTTAGGGGTGTGCATGATTCATAAACCAGACCAAATTTATGGTCTGGTCCAGTTCTTTTGCACACCCCTAACTACGAACCGTAGTCTACGGTTGATGCAATAACAATTGCAATTGTTTGAAACCTTTTTATTAAGATTAAAATTATGTTTATCTTTCTTTAAAATTATTATTTTTTGCATAAAAAATGCAACTAATTACTCTTCTATATGGTTTAGGGAGATCAAGCATCAATAGTTGAAGGTGTAATTGATTACATCAACGAGTTACATCAACTACTACAATGCCTAGAATCCAAGAAACAAAGAAAAGTTTACAGTGAAGTAACAAGTCCAAGACCTTTACCACTAAGTCCTAGAATAATCTTACCAATTAGTCCAAGAACTCCATATCAATGGCTACAACAATGTGGTGGTTACCTTTCATCTGAGCCATCTCCAACTTCTTCAGCTTCTTCCATCAATGATAACATCAATGAGCTTGTCGCGAATTCAACATCTTCGGTTGCTGATGTTGAGGTTAAGTTTTGTGGTTCACATGTGCTTTTGAAAACCGTTTCGTCACGAATTCCGGGGCAGGCTCTTAGAATAATGTCTGTTCTTGAAGATCTAATGCTTGAGATTGTTCATGTTAGAGTTAATACTGCTGATGAAACCATGCTATACTTGTTCACTATTAAGGTAACTTAATCTTTTGTTTATGCTTAATTAATTACTATTATTTACAACTACATTGATGATCCTTATGCTAACAAGAGATACAAATTTTGATCCTTTTGGAGCCTCTAGTAGCTGTCATTTTTTGTTACTGTAAAAAATAAAAATTGGTAACTTTGATGAGAATCAATATTGAATACTGTGGTAATAATGGTAAATTCTTTGCTAAAAGCCTACAGTAGTGAAGTACATTACTACTGTATAGTATAATAATTAATCAATGACATGCAGTACACAAAGCATCTTTTCACATTTCTGAGACACCAGGGATGTATATCATAACAATTAACATCATTCTGGCATTGTATGTATTTGGTGAAAAAATCAATGTATGGTCCAATATTGTTTATTTAATTCATAGCAGCTAATGATTGAGTATGCATGTATCATATGTGTTAATGTTATTTATGTTTTCAATTTTGGTCCATTAATAATTAATTATATTTTCTTAAAATTTCTCTTGTGTAGATTGGAATTGAATGCCAACTCAGTGCTGAAGAACTTGCTCAACAAATCCAGCAAACATTTTATTAA
Protein sequence

>MS.gene32350.t1

METQKAPIDHDTLLLSDIFNETEFGSEDLFSILENFNNFSPIINDQNSKTTSSSAPQVSENEHAETSQKCKRQKIVTSSIIEEQNNDGQHRMSHITVERNRRKQMNEQLSILKSLMPCFYVKRGDQASIVEGVIDYINELHQLLQCLESKKQRKVYSEVTSPRPLPLSPRIILPISPRTPYQWLQQCGGYLSSEPSPTSSASSINDNINELVANSTSSVADVEVKFCGSHVLLKTVSSRIPGQALRIMSVLEDLMLEIVHVRVNTADETMLYLFTIKIGIECQLSAEELAQQIQQTFY