AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054127

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054127.t1 MTR_1g028470 92.256 297 19 1 1 297 1 293 0.0 537
MS.gene054127.t1 MTR_3g090850 60.856 327 80 12 15 296 5 328 8.26e-115 334
MS.gene054127.t1 MTR_2g022280 50.000 206 82 2 91 296 1 185 7.86e-64 199
MS.gene054127.t1 MTR_0194s0050 38.793 232 127 2 63 294 160 376 8.32e-49 167
MS.gene054127.t1 MTR_1g082480 34.343 297 139 10 30 295 55 326 7.44e-37 134
MS.gene054127.t1 MTR_3g099620 34.583 240 143 3 54 292 79 305 5.28e-36 131
MS.gene054127.t1 MTR_7g113830 36.364 231 123 5 66 294 93 301 1.43e-35 130
MS.gene054127.t1 MTR_1g082480 34.307 274 137 8 30 279 55 309 1.45e-33 125
MS.gene054127.t1 MTR_8g066770 35.468 203 97 5 90 285 113 288 5.49e-31 118
MS.gene054127.t1 MTR_8g024210 35.885 209 104 3 89 296 179 358 1.70e-28 112
MS.gene054127.t1 MTR_5g064950 28.966 290 159 7 27 294 23 287 7.13e-27 107
MS.gene054127.t1 MTR_5g064950 29.779 272 145 6 27 277 23 269 1.35e-26 106
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054127.t1 AT5G53210 46.629 356 106 8 19 296 14 363 2.77e-82 253
MS.gene054127.t1 AT5G53210 43.323 337 107 8 19 277 14 344 2.65e-67 214
MS.gene054127.t1 AT3G06120 44.928 207 98 3 91 296 1 192 2.56e-54 176
MS.gene054127.t1 AT3G24140 40.351 228 125 2 69 296 177 393 3.46e-48 166
MS.gene054127.t1 AT3G24140 40.351 228 125 2 69 296 177 393 3.81e-48 166
MS.gene054127.t1 AT1G72210 33.486 218 99 6 90 294 124 308 9.02e-30 115
MS.gene054127.t1 AT1G72210 34.000 200 87 5 90 277 124 290 1.63e-28 111
MS.gene054127.t1 AT4G01460 35.885 209 112 3 89 296 113 300 3.08e-28 111
MS.gene054127.t1 AT4G01460 35.885 209 112 3 89 296 113 300 3.08e-28 111
MS.gene054127.t1 AT1G22490 33.816 207 112 4 90 295 114 296 2.51e-26 105
MS.gene054127.t1 AT1G22490 34.574 188 99 3 90 277 114 277 9.07e-25 102
MS.gene054127.t1 AT2G46810 32.536 209 108 3 90 296 120 297 2.55e-24 100
MS.gene054127.t1 AT5G65320 33.333 219 120 5 78 294 93 287 3.99e-24 99.8
MS.gene054127.t1 AT2G46810 33.491 212 102 4 90 296 180 357 8.44e-24 99.8
MS.gene054127.t1 AT2G46810 33.491 212 102 4 90 296 192 369 1.08e-23 99.8
MS.gene054127.t1 AT5G65320 33.500 200 109 4 78 277 93 268 3.69e-21 91.3
MS.gene054127.t1 AT3G61950 31.579 209 109 4 90 296 126 302 4.08e-21 91.7
MS.gene054127.t1 AT3G61950 31.507 219 96 6 90 296 177 353 8.21e-21 91.7
MS.gene054127.t1 AT2G46810 31.217 189 98 2 90 277 120 277 6.39e-20 88.6
MS.gene054127.t1 AT5G46690 33.838 198 129 1 90 285 87 284 4.14e-19 86.3
MS.gene054127.t1 AT3G61950 31.892 185 74 4 90 264 126 268 1.43e-18 84.3
MS.gene054127.t1 AT3G61950 31.892 185 74 4 90 264 177 319 2.23e-18 84.3
MS.gene054127.t1 AT5G46690 56.164 73 30 1 90 160 87 159 2.57e-18 83.6

Find 38 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTTGTTTCTTGGATTCT+AGG 0.149526 1.3:+14649646 None:intergenic
GCTATACTTGTTCACTATTA+AGG 0.194492 1.3:-14649274 MS.gene054127:intron
TATGGAGTTCTTGGACTAAT+TGG 0.243592 1.3:+14649564 None:intergenic
AACCGTTTCGTCGCGAATTC+CGG 0.254891 1.3:-14649382 MS.gene054127:CDS
CTCGTTGATGTTATCATTGA+TGG 0.262537 1.3:+14649476 None:intergenic
TTTCTTAATAAAATGTTTGC+TGG 0.293141 1.3:+14648701 None:intergenic
CTAATTGGTAAGATTATTCT+AGG 0.295024 1.3:+14649579 None:intergenic
AGCCATTGGTATGGAGTTCT+TGG 0.318969 1.3:+14649555 None:intergenic
AACAAGGTGTCATGATCTAT+TGG 0.344330 1.3:+14650351 None:intergenic
ATATTCAATGAAACTGAGTT+TGG 0.348570 1.3:-14650318 MS.gene054127:CDS
ACCGTTTCGTCGCGAATTCC+GGG 0.356833 1.3:-14649381 MS.gene054127:CDS
ATGGAAGAAGCTGAAGAAGT+TGG 0.426375 1.3:+14649495 None:intergenic
GGACTTAGTGGTAAAGGTCT+TGG 0.429539 1.3:+14649600 None:intergenic
TTCGTCGCGAATTCCGGGGC+AGG 0.430597 1.3:-14649376 MS.gene054127:CDS
AAGATTATTCTAGGACTTAG+TGG 0.440624 1.3:+14649588 None:intergenic
CACCACATTGTTGCAGCCAT+TGG 0.463771 1.3:+14649541 None:intergenic
CATTGTTGCAGCCATTGGTA+TGG 0.478254 1.3:+14649546 None:intergenic
ATTCTAGGACTTAGTGGTAA+AGG 0.492814 1.3:+14649594 None:intergenic
CCCCGGAATTCGCGACGAAA+CGG 0.496648 1.3:+14649380 None:intergenic
GTACAAAATGGAAACTCAAA+AGG 0.507268 1.3:-14650376 None:intergenic
CAAGTTCTTCAGCACTGAGT+TGG 0.510419 1.3:+14648734 None:intergenic
GTCTTCGCTTGCTGATGTTG+AGG 0.530715 1.3:-14649436 MS.gene054127:CDS
GATTGTGACTACAATTATAG+AGG 0.544599 1.3:-14650148 MS.gene054127:CDS
TGAAACTGAGTTTGGTTCAG+AGG 0.550414 1.3:-14650310 MS.gene054127:CDS
TTGGAGATGGCTCAGATGAA+AGG 0.570619 1.3:+14649514 None:intergenic
ACATCGAATGTCGCATATCA+CGG 0.587471 1.3:-14650106 MS.gene054127:CDS
GATCAAGCATCAATAGTTGA+AGG 0.590664 1.3:-14649711 MS.gene054127:CDS
AATAGTGAACAAGTATAGCA+TGG 0.592880 1.3:+14649278 None:intergenic
ATCTCAGTTTCAGAATCTTG+AGG 0.599342 1.3:+14650204 None:intergenic
ATTATTCGAAGAGCCTGCCC+CGG 0.602185 1.3:+14649363 None:intergenic
GAAGCTGAAGAAGTTGGAGA+TGG 0.605113 1.3:+14649501 None:intergenic
GTCCAAGAACTCCATACCAA+TGG 0.611914 1.3:-14649557 MS.gene054127:CDS
CCGTTTCGTCGCGAATTCCG+GGG 0.649169 1.3:-14649380 MS.gene054127:CDS
ATAGAGGAACAAAACAACGA+TGG 0.666577 1.3:-14650132 MS.gene054127:CDS
GAATATATCAGATAATAACA+AGG 0.703731 1.3:+14650335 None:intergenic
GTGATATGCGACATTCGATG+TGG 0.706196 1.3:+14650108 None:intergenic
CAATGGCTGCAACAATGTGG+TGG 0.729603 1.3:-14649540 MS.gene054127:CDS
TACCAATGGCTGCAACAATG+TGG 0.747770 1.3:-14649543 MS.gene054127:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATATAATTAATTATTAA+TGG + chr1.3:14650285-14650304 None:intergenic 0.0%
!! ATGAATTAAATAAACAATAT+TGG + chr1.3:14650197-14650216 None:intergenic 10.0%
!! TACTGTGAAAAAATAAAAAT+TGG - chr1.3:14649947-14649966 MS.gene054127:intron 15.0%
!!! GTTATTTATGTTTTCAATTT+TGG - chr1.3:14650258-14650277 MS.gene054127:CDS 15.0%
!! GAATATATCAGATAATAACA+AGG + chr1.3:14648742-14648761 None:intergenic 20.0%
!!! AGTTTTAAATGAAACTAGTT+AGG - chr1.3:14649127-14649146 MS.gene054127:intron 20.0%
!!! ATTATTGAAGTTTTCCAAAA+TGG + chr1.3:14648799-14648818 None:intergenic 20.0%
!!! GTTTTAAATGAAACTAGTTA+GGG - chr1.3:14649128-14649147 MS.gene054127:intron 20.0%
!!! TTTTAAATGAAACTAGTTAG+GGG - chr1.3:14649129-14649148 MS.gene054127:intron 20.0%
! AAAATTTCTCTTGTGTAGAT+TGG - chr1.3:14650308-14650327 MS.gene054127:CDS 25.0%
! AAACCATATAGAAGAGTAAT+TGG + chr1.3:14649338-14649357 None:intergenic 25.0%
! AGAATCAATATTGAATAGTG+AGG - chr1.3:14649981-14650000 MS.gene054127:intron 25.0%
! ATATTCAATGAAACTGAGTT+TGG - chr1.3:14648756-14648775 MS.gene054127:intron 25.0%
! ATTACTCTTCTATATGGTTT+AGG - chr1.3:14649338-14649357 MS.gene054127:CDS 25.0%
! ATTGAATAGTGAGGTAATAA+TGG - chr1.3:14649990-14650009 MS.gene054127:intron 25.0%
! CTAATTGGTAAGATTATTCT+AGG + chr1.3:14649498-14649517 None:intergenic 25.0%
! GTATATCATAACATCATTCT+GGG - chr1.3:14650130-14650149 MS.gene054127:CDS 25.0%
! TGTATATCATAACATCATTC+TGG - chr1.3:14650129-14650148 MS.gene054127:CDS 25.0%
! TTACTCTTCTATATGGTTTA+GGG - chr1.3:14649339-14649358 MS.gene054127:CDS 25.0%
! TTGGTGAAAAAATCAATGTA+TGG - chr1.3:14650170-14650189 MS.gene054127:CDS 25.0%
!!! AAGATGTTGTTTTTGAGTTT+TGG + chr1.3:14648842-14648861 None:intergenic 25.0%
!!! GATACAAATTTTGATCCTTT+TGG - chr1.3:14649898-14649917 MS.gene054127:intron 25.0%
!!! GTAAACTTTTCTTTGTTTCT+TGG + chr1.3:14649439-14649458 None:intergenic 25.0%
AATAGTGAACAAGTATAGCA+TGG + chr1.3:14649799-14649818 None:intergenic 30.0%
CAACCAATTACTCTTCTATA+TGG - chr1.3:14649332-14649351 MS.gene054127:CDS 30.0%
CATAAACCAGACCAAATTTA+TGG - chr1.3:14649163-14649182 MS.gene054127:intron 30.0%
GATTGTGACTACAATTATAG+AGG - chr1.3:14648926-14648945 MS.gene054127:intron 30.0%
GCTATACTTGTTCACTATTA+AGG - chr1.3:14649800-14649819 MS.gene054127:intron 30.0%
TTGTATCTCTTGTTAGCATA+AGG + chr1.3:14649885-14649904 None:intergenic 30.0%
! ACTCTTTTGACATAAAAGCA+AGG + chr1.3:14649053-14649072 None:intergenic 30.0%
! TTCTTTGTTTCTTGGATTCT+AGG + chr1.3:14649431-14649450 None:intergenic 30.0%
!! AAGATTATTCTAGGACTTAG+TGG + chr1.3:14649489-14649508 None:intergenic 30.0%
!! GAGTTTTGGTCATTGATAAT+GGG + chr1.3:14648828-14648847 None:intergenic 30.0%
!! TGAGTTTTGGTCATTGATAA+TGG + chr1.3:14648829-14648848 None:intergenic 30.0%
ATAGAGGAACAAAACAACGA+TGG - chr1.3:14648942-14648961 MS.gene054127:intron 35.0%
ATCTCAGTTTCAGAATCTTG+AGG + chr1.3:14648873-14648892 None:intergenic 35.0%
CAAAAAATGACAGCTACTAG+AGG + chr1.3:14649926-14649945 None:intergenic 35.0%
CTCGTTGATGTTATCATTGA+TGG + chr1.3:14649601-14649620 None:intergenic 35.0%
GATCAAGCATCAATAGTTGA+AGG - chr1.3:14649363-14649382 MS.gene054127:CDS 35.0%
GATGTTATGATATACATCCC+TGG + chr1.3:14650125-14650144 None:intergenic 35.0%
GTAATGTACTTCACTACTGT+AGG + chr1.3:14650034-14650053 None:intergenic 35.0%
TATGGAGTTCTTGGACTAAT+TGG + chr1.3:14649513-14649532 None:intergenic 35.0%
! AACAAGGTGTCATGATCTAT+TGG + chr1.3:14648726-14648745 None:intergenic 35.0%
! AGAGGATCTCTTTTCCATTT+TGG - chr1.3:14648782-14648801 MS.gene054127:intron 35.0%
! GATGTTGAGGTTAAGTTTTG+TGG - chr1.3:14649651-14649670 MS.gene054127:CDS 35.0%
!! ATTCTAGGACTTAGTGGTAA+AGG + chr1.3:14649483-14649502 None:intergenic 35.0%
!!! TTTTGGTCATTGATAATGGG+AGG + chr1.3:14648825-14648844 None:intergenic 35.0%
ACATCGAATGTCGCATATCA+CGG - chr1.3:14648968-14648987 MS.gene054127:intron 40.0%
ACCAGACCAAATTTATGGTC+TGG - chr1.3:14649168-14649187 MS.gene054127:intron 40.0%
ACCAGACCATAAATTTGGTC+TGG + chr1.3:14649172-14649191 None:intergenic 40.0%
ACTGGACCAGACCATAAATT+TGG + chr1.3:14649177-14649196 None:intergenic 40.0%
ATGGAAGAAGCTGAAGAAGT+TGG + chr1.3:14649582-14649601 None:intergenic 40.0%
ATTGCATCAACCGTAGACTA+CGG + chr1.3:14649225-14649244 None:intergenic 40.0%
GGTCTGGCATTGTATGTATT+TGG - chr1.3:14650151-14650170 MS.gene054127:CDS 40.0%
TAACTACGAACCGTAGTCTA+CGG - chr1.3:14649212-14649231 MS.gene054127:intron 40.0%
TAGACTACGGTTCGTAGTTA+GGG + chr1.3:14649212-14649231 None:intergenic 40.0%
TCATAACATCATTCTGGGTC+TGG - chr1.3:14650135-14650154 MS.gene054127:CDS 40.0%
! TGAAACTGAGTTTGGTTCAG+AGG - chr1.3:14648764-14648783 MS.gene054127:intron 40.0%
!! ACGGTTTTCAAAAGCACATG+TGG + chr1.3:14649678-14649697 None:intergenic 40.0%
!! TTCACATTTCTGAGACACCA+GGG - chr1.3:14650105-14650124 MS.gene054127:CDS 40.0%
!! TTTCACATTTCTGAGACACC+AGG - chr1.3:14650104-14650123 MS.gene054127:CDS 40.0%
AGACTACGGTTCGTAGTTAG+GGG + chr1.3:14649211-14649230 None:intergenic 45.0%
AGCCATTGGTATGGAGTTCT+TGG + chr1.3:14649522-14649541 None:intergenic 45.0%
CATTGTTGCAGCCATTGGTA+TGG + chr1.3:14649531-14649550 None:intergenic 45.0%
GAAGCTGAAGAAGTTGGAGA+TGG + chr1.3:14649576-14649595 None:intergenic 45.0%
GGACTTAGTGGTAAAGGTCT+TGG + chr1.3:14649477-14649496 None:intergenic 45.0%
GTAGACTACGGTTCGTAGTT+AGG + chr1.3:14649213-14649232 None:intergenic 45.0%
GTCCAAGAACTCCATACCAA+TGG - chr1.3:14649517-14649536 MS.gene054127:CDS 45.0%
GTGATATGCGACATTCGATG+TGG + chr1.3:14648969-14648988 None:intergenic 45.0%
TACCAATGGCTGCAACAATG+TGG - chr1.3:14649531-14649550 MS.gene054127:CDS 45.0%
TTGGAGATGGCTCAGATGAA+AGG + chr1.3:14649563-14649582 None:intergenic 45.0%
! CAAGTTCTTCAGCACTGAGT+TGG + chr1.3:14650343-14650362 None:intergenic 45.0%
! TTAGGGGTGTGCAAAAGAAC+TGG + chr1.3:14649195-14649214 None:intergenic 45.0%
!!! TAATTTTAATCTTAATAAAA+AGG + chr1.3:14649269-14649288 None:intergenic 5.0%
AACCGTTTCGTCGCGAATTC+CGG - chr1.3:14649692-14649711 MS.gene054127:CDS 50.0%
ATTATTCGAAGAGCCTGCCC+CGG + chr1.3:14649714-14649733 None:intergenic 50.0%
CAATGGCTGCAACAATGTGG+TGG - chr1.3:14649534-14649553 MS.gene054127:CDS 50.0%
CACCACATTGTTGCAGCCAT+TGG + chr1.3:14649536-14649555 None:intergenic 50.0%
CAGCTACTAGAGGCTCCAAA+AGG + chr1.3:14649916-14649935 None:intergenic 50.0%
! GTCTTCGCTTGCTGATGTTG+AGG - chr1.3:14649638-14649657 MS.gene054127:CDS 50.0%
ACCGTTTCGTCGCGAATTCC+GGG - chr1.3:14649693-14649712 MS.gene054127:CDS 55.0%
CCCCGGAATTCGCGACGAAA+CGG + chr1.3:14649697-14649716 None:intergenic 60.0%
CCGTTTCGTCGCGAATTCCG+GGG - chr1.3:14649694-14649713 MS.gene054127:CDS 60.0%
TTCGTCGCGAATTCCGGGGC+AGG - chr1.3:14649698-14649717 MS.gene054127:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 14648705 14650391 14648705 ID=MS.gene054127
chr1.3 mRNA 14648705 14650391 14648705 ID=MS.gene054127.t1;Parent=MS.gene054127
chr1.3 exon 14650026 14650391 14650026 ID=MS.gene054127.t1.exon1;Parent=MS.gene054127.t1
chr1.3 CDS 14650026 14650391 14650026 ID=cds.MS.gene054127.t1;Parent=MS.gene054127.t1
chr1.3 exon 14649275 14649736 14649275 ID=MS.gene054127.t1.exon2;Parent=MS.gene054127.t1
chr1.3 CDS 14649275 14649736 14649275 ID=cds.MS.gene054127.t1;Parent=MS.gene054127.t1
chr1.3 exon 14648705 14648770 14648705 ID=MS.gene054127.t1.exon3;Parent=MS.gene054127.t1
chr1.3 CDS 14648705 14648770 14648705 ID=cds.MS.gene054127.t1;Parent=MS.gene054127.t1
Gene Sequence

>MS.gene054127

ATGGAAACTCAAAAGGTTCCAATAGATCATGACACCTTGTTATTATCTGATATATTCAATGAAACTGAGTTTGGTTCAGAGGATCTCTTTTCCATTTTGGAAAACTTCAATAATTTTCCTCCCATTATCAATGACCAAAACTCAAAAACAACATCTTCAAGTGCTCCTCAAGATTCTGAAACTGAGATTGCTGAAACATCACATAAATGCAAGAGACAGAAGATTGTGACTACAATTATAGAGGAACAAAACAACGATGGACCACATCGAATGTCGCATATCACGGTCGAACGCAATCGAAGAAAGCAAATGAATGAGCAGCTATCTATCTTGAAGTCACTTATGCCTTGCTTTTATGTCAAAAGAGTGAGTACATATTAACTAACTTGTCACAAATTCAAATTCTAAATAATTTTTTTCAAAGTTTTAAATGAAACTAGTTAGGGGTGTGCATGATTCATAAACCAGACCAAATTTATGGTCTGGTCCAGTTCTTTTGCACACCCCTAACTACGAACCGTAGTCTACGGTTGATGCAATAACAATTGCAATTGTTTGAAACCTTTTTATTAAGATTAAAATTATGTTTATCTTACTTTAAAATTATTATTTTTTGCATAAAAAATGCAACCAATTACTCTTCTATATGGTTTAGGGAGATCAAGCATCAATAGTTGAAGGTGTAATTGATTACATCAACGAGTTACATCAACTACTACAATGCCTAGAATCCAAGAAACAAAGAAAAGTTTACAATGAAGTAACAAGTCCAAGACCTTTACCACTAAGTCCTAGAATAATCTTACCAATTAGTCCAAGAACTCCATACCAATGGCTGCAACAATGTGGTGGTTACCTTTCATCTGAGCCATCTCCAACTTCTTCAGCTTCTTCCATCAATGATAACATCAACGAGCTTGTCGCGAATTCAACGTCTTCGCTTGCTGATGTTGAGGTTAAGTTTTGTGGTCCACATGTGCTTTTGAAAACCGTTTCGTCGCGAATTCCGGGGCAGGCTCTTCGAATAATGTCTGTTCTTGATGATCTAAAGCTTGAGATTGTTCATGTTAGAGTTAATACTGCTGATGAAACCATGCTATACTTGTTCACTATTAAGGTAACTTAATCTTTTGTTTATGTTTAGTTAATTACTATTATTTACAACTACATTGATGATCCTTATGCTAACAAGAGATACAAATTTTGATCCTTTTGGAGCCTCTAGTAGCTGTCATTTTTTGTTACTGTGAAAAAATAAAAATTGGTAACTTTGATGAGAATCAATATTGAATAGTGAGGTAATAATGGTAAATTCTTTGCTGAAAGCCTACAGTAGTGAAGTACATTACTACTGTATAGTATAATAATTAATCAATGACATGCAGTACACAAAGCATCTTTTCACATTTCTGAGACACCAGGGATGTATATCATAACATCATTCTGGGTCTGGCATTGTATGTATTTGGTGAAAAAATCAATGTATGGTCCAATATTGTTTATTTAATTCATAGCAGCTAATGATTGAGTATGCATGTATCATATGTGTTAATGTTATTTATGTTTTCAATTTTGGTCCATTAATAATTAATTATATTTTCTTAAAATTTCTCTTGTGTAGATTGGAATTGAATGCCAACTCAGTGCTGAAGAACTTGCTCAACAAATCCAGCAAACATTTTATTAA
Protein sequence

>MS.gene054127.t1

METQKVPIDHDTLLLSDIFNETEFGSEDLFSILENFNNFPPIINDQNSKTTSSSAPQDSETEIAETSHKCKRQKIVTTIIEEQNNDGPHRMSHITVERNRRKQMNEQLSILKSLMPCFYVKRGDQASIVEGVIDYINELHQLLQCLESKKQRKVYNEVTSPRPLPLSPRIILPISPRTPYQWLQQCGGYLSSEPSPTSSASSINDNINELVANSTSSLADVEVKFCGPHVLLKTVSSRIPGQALRIMSVLDDLKLEIVHVRVNTADETMLYLFTIKIGIECQLSAEELAQQIQQTFY