AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene065967

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065967.t1 MTR_8g087530 84.953 319 20 5 18 336 49 339 1.44e-172 483
MS.gene065967.t1 MTR_2g018030 46.484 256 107 6 98 334 112 356 2.18e-57 189
MS.gene065967.t1 MTR_5g075210 42.143 140 62 5 182 320 224 345 1.91e-24 102
MS.gene065967.t1 MTR_7g072875 59.091 66 27 0 255 320 219 284 3.35e-23 97.8
MS.gene065967.t1 MTR_7g072630 59.091 66 27 0 255 320 281 346 7.41e-23 97.8
MS.gene065967.t1 MTR_4g028930 56.716 67 29 0 256 322 315 381 1.86e-21 94.4
MS.gene065967.t1 MTR_8g103520 56.452 62 27 0 255 316 224 285 1.36e-17 82.0
MS.gene065967.t1 MTR_0907s0020 51.562 64 31 0 253 316 100 163 7.02e-15 72.4
MS.gene065967.t1 MTR_7g105790 47.458 59 31 0 258 316 113 171 2.03e-12 65.9
MS.gene065967.t1 MTR_4g052040 43.548 62 35 0 254 315 98 159 1.42e-11 62.8
MS.gene065967.t1 MTR_4g132740 44.068 59 33 0 257 315 83 141 4.18e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065967.t1 AT4G18830 52.555 137 59 3 181 315 210 342 1.16e-36 135
MS.gene065967.t1 AT1G06920 54.430 79 36 0 249 327 237 315 1.59e-24 102
MS.gene065967.t1 AT5G58360 46.296 108 54 1 217 320 182 289 3.35e-24 100
MS.gene065967.t1 AT2G30400 54.795 73 33 0 248 320 245 317 3.98e-22 95.5
MS.gene065967.t1 AT5G01840 61.017 59 23 0 259 317 202 260 1.27e-18 84.7
MS.gene065967.t1 AT5G19650 49.231 65 33 0 255 319 154 218 1.22e-16 78.2
MS.gene065967.t1 AT2G18500 45.455 66 36 0 254 319 225 290 2.45e-14 73.2
MS.gene065967.t1 AT3G52525 49.254 67 34 0 250 316 61 127 2.95e-14 70.1
MS.gene065967.t1 AT2G36026 51.923 52 25 0 265 316 96 147 3.94e-12 64.7
MS.gene065967.t1 AT4G04025 45.763 59 32 0 257 315 115 173 3.44e-11 61.6

Find 61 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAGTTGTGAAGTGTTCTT+TGG 0.266311 4.3:-13377008 MS.gene065967:CDS
GAGGGAAATAATTGGGTTCT+TGG 0.266493 4.3:+13377331 None:intergenic
AACAACTCTTCCATTTCTTC+TGG 0.277466 4.3:+13376923 None:intergenic
CTACATAAGAGGGAAATAAT+TGG 0.293355 4.3:+13377323 None:intergenic
ACATCCAAACTGTACATTAC+TGG 0.306963 4.3:+13377577 None:intergenic
TCGACTTCAGTAGCCATCTT+TGG 0.314341 4.3:+13377136 None:intergenic
GGGTTCTTGGTGATTCAAAT+TGG 0.318117 4.3:+13377344 None:intergenic
TTTCAAAGTGTCGGAGAAAA+TGG 0.336592 4.3:-13377277 MS.gene065967:CDS
GAAGAAAGAAGAAGAGGAAA+TGG 0.347901 4.3:-13377062 MS.gene065967:CDS
GATAAGCCAGCCAGAAGAAA+TGG 0.364577 4.3:-13376933 MS.gene065967:CDS
TATGTAGATGCAGAAAGTTC+TGG 0.372162 4.3:-13377307 MS.gene065967:CDS
CTTACCTTGGAACTCTGCTT+TGG 0.374018 4.3:+13377169 None:intergenic
ATTTATTACACAAACTTGAA+TGG 0.396706 4.3:+13376819 None:intergenic
AATGATATCATGGTATTCAT+TGG 0.398859 4.3:+13376877 None:intergenic
GTGGTGAGGATGATGCATTC+TGG 0.406825 4.3:-13377663 MS.gene065967:CDS
GAAGCCAGTAATGTACAGTT+TGG 0.411136 4.3:-13377581 MS.gene065967:CDS
GATGCAGAAAGTTCTGGTCT+TGG 0.420949 4.3:-13377301 MS.gene065967:CDS
CAATTTCCTTGTGGGAATAG+AGG 0.421459 4.3:-13377700 MS.gene065967:CDS
ACTTTCTGCATCTACATAAG+AGG 0.429055 4.3:+13377312 None:intergenic
GTTCATCACAATTTCCTTGT+GGG 0.429553 4.3:-13377708 MS.gene065967:CDS
TGGAGAATGTACTCTTACCT+TGG 0.430524 4.3:+13377156 None:intergenic
ACTCTTCCATTTCTTCTGGC+TGG 0.432481 4.3:+13376927 None:intergenic
TACATAAGAGGGAAATAATT+GGG 0.446625 4.3:+13377324 None:intergenic
GAAAGAAGAAGAGGAAATGG+TGG 0.463652 4.3:-13377059 MS.gene065967:CDS
GCATTCTGGAGATTGTCATT+TGG 0.470215 4.3:-13377649 MS.gene065967:CDS
TTCCTTGTGGGAATAGAGGC+AGG 0.471947 4.3:-13377696 MS.gene065967:CDS
AAAGATGAAGAAAGAAGAAG+AGG 0.484787 4.3:-13377068 MS.gene065967:CDS
TCAAAGCATTTCGACAGGTA+TGG 0.486694 4.3:-13376853 MS.gene065967:CDS
AGAAGAAGAGGAAATGGTGG+AGG 0.494303 4.3:-13377056 MS.gene065967:CDS
TTAAAGCAAAGGTTAACAAA+AGG 0.494673 4.3:-13377234 MS.gene065967:CDS
TAAATGTAAATCCTTAGAAA+AGG 0.497808 4.3:-13377374 MS.gene065967:CDS
ATGCTTTGATAATGATATCA+TGG 0.506592 4.3:+13376867 None:intergenic
AAGAGTACATTCTCCAAAGA+TGG 0.518216 4.3:-13377149 MS.gene065967:CDS
AAGCAAAGGTTAACAAAAGG+AGG 0.522101 4.3:-13377231 MS.gene065967:CDS
GGTCTTGGATTTCAAAGTGT+CGG 0.531784 4.3:-13377286 MS.gene065967:CDS
ACTCAGAACTCCCCGTCTGA+TGG 0.532872 4.3:-13377730 MS.gene065967:CDS
ATGGTGGAGGAAACAGAAGA+AGG 0.542284 4.3:-13377043 MS.gene065967:CDS
CATTATCAAAGCATTTCGAC+AGG 0.549940 4.3:-13376858 MS.gene065967:CDS
TGGTGGAGGAAACAGAAGAA+GGG 0.553251 4.3:-13377042 MS.gene065967:CDS
AGTCGAAATACGCAAAATGA+AGG 0.561509 4.3:-13377119 MS.gene065967:CDS
ATGTGAGGAGTTTAAAGCAA+AGG 0.562245 4.3:-13377245 MS.gene065967:CDS
CTTTCTGCATCTACATAAGA+GGG 0.562393 4.3:+13377313 None:intergenic
GAATCTCTAAAATCTTGTTG+TGG 0.573719 4.3:+13376983 None:intergenic
AGGAAGTTGAGTGCTTAAAG+AGG 0.596150 4.3:-13377486 MS.gene065967:CDS
GCTTAAAGAGGAGATATGAG+AGG 0.596446 4.3:-13377474 MS.gene065967:CDS
GGTTCATCACAATTTCCTTG+TGG 0.598854 4.3:-13377709 MS.gene065967:CDS
AGCAAAGGTTAACAAAAGGA+GGG 0.601137 4.3:-13377230 MS.gene065967:CDS
AATTGTGATGAACCATCAGA+CGG 0.617022 4.3:+13377718 None:intergenic
ATTGTGATGAACCATCAGAC+GGG 0.626786 4.3:+13377719 None:intergenic
GAAACCAAAGCAGAGTTCCA+AGG 0.627313 4.3:-13377173 MS.gene065967:CDS
AGTTTGGATGTGAAAAGACA+TGG 0.628614 4.3:-13377565 MS.gene065967:CDS
GAAATTACAGAATGCAGCAG+AGG 0.634808 4.3:-13377419 MS.gene065967:CDS
TAATGAAACAAAGAGTGCAA+AGG 0.636359 4.3:-13377506 MS.gene065967:CDS
TGTTGTCGTTGCATCAGACG+AGG 0.644231 4.3:+13377768 None:intergenic
ATCAGACGGGGAGTTCTGAG+TGG 0.651626 4.3:+13377732 None:intergenic
TGAGCAGAGAATTACAGAGG+AGG 0.661098 4.3:-13377195 MS.gene065967:CDS
TCAGACGGGGAGTTCTGAGT+GGG 0.663234 4.3:+13377733 None:intergenic
AACCTGCCTCTATTCCCACA+AGG 0.669707 4.3:+13377694 None:intergenic
ATGTGAGCAGAGAATTACAG+AGG 0.684434 4.3:-13377198 MS.gene065967:CDS
AAATGGTGTGAATCAATGTG+AGG 0.711307 4.3:-13377260 MS.gene065967:CDS
TTGTGATGAACCATCAGACG+GGG 0.714122 4.3:+13377720 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATTACACAAACTTGAA+TGG + chr4.3:13377752-13377771 None:intergenic 20.0%
!! TAAATGTAAATCCTTAGAAA+AGG - chr4.3:13377194-13377213 MS.gene065967:CDS 20.0%
!!! TATCTTTACTTTTCTTCTTT+TGG + chr4.3:13376963-13376982 None:intergenic 20.0%
! AATGATATCATGGTATTCAT+TGG + chr4.3:13377694-13377713 None:intergenic 25.0%
! TACATAAGAGGGAAATAATT+GGG + chr4.3:13377247-13377266 None:intergenic 25.0%
! TTAAAGCAAAGGTTAACAAA+AGG - chr4.3:13377334-13377353 MS.gene065967:CDS 25.0%
!!! ATGCTTTGATAATGATATCA+TGG + chr4.3:13377704-13377723 None:intergenic 25.0%
AAAGATGAAGAAAGAAGAAG+AGG - chr4.3:13377500-13377519 MS.gene065967:CDS 30.0%
CTACATAAGAGGGAAATAAT+TGG + chr4.3:13377248-13377267 None:intergenic 30.0%
! TAATGAAACAAAGAGTGCAA+AGG - chr4.3:13377062-13377081 MS.gene065967:CDS 30.0%
!! GAATCTCTAAAATCTTGTTG+TGG + chr4.3:13377588-13377607 None:intergenic 30.0%
AAATGGTGTGAATCAATGTG+AGG - chr4.3:13377308-13377327 MS.gene065967:CDS 35.0%
AACAACTCTTCCATTTCTTC+TGG + chr4.3:13377648-13377667 None:intergenic 35.0%
AAGCAAAGGTTAACAAAAGG+AGG - chr4.3:13377337-13377356 MS.gene065967:CDS 35.0%
AATTGTGATGAACCATCAGA+CGG + chr4.3:13376853-13376872 None:intergenic 35.0%
ACATCCAAACTGTACATTAC+TGG + chr4.3:13376994-13377013 None:intergenic 35.0%
ACTTTCTGCATCTACATAAG+AGG + chr4.3:13377259-13377278 None:intergenic 35.0%
AGCAAAGGTTAACAAAAGGA+GGG - chr4.3:13377338-13377357 MS.gene065967:CDS 35.0%
AGTCGAAATACGCAAAATGA+AGG - chr4.3:13377449-13377468 MS.gene065967:CDS 35.0%
AGTTTGGATGTGAAAAGACA+TGG - chr4.3:13377003-13377022 MS.gene065967:CDS 35.0%
CTTTCTGCATCTACATAAGA+GGG + chr4.3:13377258-13377277 None:intergenic 35.0%
GAAGAAAGAAGAAGAGGAAA+TGG - chr4.3:13377506-13377525 MS.gene065967:CDS 35.0%
GTTCATCACAATTTCCTTGT+GGG - chr4.3:13376860-13376879 MS.gene065967:CDS 35.0%
TATGTAGATGCAGAAAGTTC+TGG - chr4.3:13377261-13377280 MS.gene065967:CDS 35.0%
! AAGAGTACATTCTCCAAAGA+TGG - chr4.3:13377419-13377438 MS.gene065967:CDS 35.0%
! ATGTGAGGAGTTTAAAGCAA+AGG - chr4.3:13377323-13377342 MS.gene065967:CDS 35.0%
! CATTATCAAAGCATTTCGAC+AGG - chr4.3:13377710-13377729 MS.gene065967:CDS 35.0%
!! TTTCAAAGTGTCGGAGAAAA+TGG - chr4.3:13377291-13377310 MS.gene065967:CDS 35.0%
AGGAAGTTGAGTGCTTAAAG+AGG - chr4.3:13377082-13377101 MS.gene065967:CDS 40.0%
ATGTGAGCAGAGAATTACAG+AGG - chr4.3:13377370-13377389 MS.gene065967:CDS 40.0%
ATTGTGATGAACCATCAGAC+GGG + chr4.3:13376852-13376871 None:intergenic 40.0%
CAATTTCCTTGTGGGAATAG+AGG - chr4.3:13376868-13376887 MS.gene065967:CDS 40.0%
GAAAGAAGAAGAGGAAATGG+TGG - chr4.3:13377509-13377528 MS.gene065967:CDS 40.0%
GAAATTACAGAATGCAGCAG+AGG - chr4.3:13377149-13377168 MS.gene065967:CDS 40.0%
GAAGCCAGTAATGTACAGTT+TGG - chr4.3:13376987-13377006 MS.gene065967:CDS 40.0%
GAGGGAAATAATTGGGTTCT+TGG + chr4.3:13377240-13377259 None:intergenic 40.0%
GCTTAAAGAGGAGATATGAG+AGG - chr4.3:13377094-13377113 MS.gene065967:CDS 40.0%
GGTCTTGGATTTCAAAGTGT+CGG - chr4.3:13377282-13377301 MS.gene065967:CDS 40.0%
GGTTCATCACAATTTCCTTG+TGG - chr4.3:13376859-13376878 MS.gene065967:CDS 40.0%
TGGAGAATGTACTCTTACCT+TGG + chr4.3:13377415-13377434 None:intergenic 40.0%
! GCATTCTGGAGATTGTCATT+TGG - chr4.3:13376919-13376938 MS.gene065967:CDS 40.0%
! GGGTTCTTGGTGATTCAAAT+TGG + chr4.3:13377227-13377246 None:intergenic 40.0%
! TCAAAGCATTTCGACAGGTA+TGG - chr4.3:13377715-13377734 MS.gene065967:CDS 40.0%
! TGCAGTTGTGAAGTGTTCTT+TGG - chr4.3:13377560-13377579 MS.gene065967:CDS 40.0%
! TTGGAGCTCATCCTTTTCTA+AGG + chr4.3:13377208-13377227 None:intergenic 40.0%
!! AATAGAGGCAGGTTTTATGG+AGG - chr4.3:13376883-13376902 MS.gene065967:CDS 40.0%
ACTCTTCCATTTCTTCTGGC+TGG + chr4.3:13377644-13377663 None:intergenic 45.0%
AGAAGAAGAGGAAATGGTGG+AGG - chr4.3:13377512-13377531 MS.gene065967:CDS 45.0%
CTTACCTTGGAACTCTGCTT+TGG + chr4.3:13377402-13377421 None:intergenic 45.0%
GAAACCAAAGCAGAGTTCCA+AGG - chr4.3:13377395-13377414 MS.gene065967:CDS 45.0%
GATAAGCCAGCCAGAAGAAA+TGG - chr4.3:13377635-13377654 MS.gene065967:CDS 45.0%
TCGACTTCAGTAGCCATCTT+TGG + chr4.3:13377435-13377454 None:intergenic 45.0%
TGAGCAGAGAATTACAGAGG+AGG - chr4.3:13377373-13377392 MS.gene065967:CDS 45.0%
TGGTGGAGGAAACAGAAGAA+GGG - chr4.3:13377526-13377545 MS.gene065967:CDS 45.0%
TTGTGATGAACCATCAGACG+GGG + chr4.3:13376851-13376870 None:intergenic 45.0%
! ATGGTGGAGGAAACAGAAGA+AGG - chr4.3:13377525-13377544 MS.gene065967:CDS 45.0%
! GATGCAGAAAGTTCTGGTCT+TGG - chr4.3:13377267-13377286 MS.gene065967:CDS 45.0%
! GGGAATAGAGGCAGGTTTTA+TGG - chr4.3:13376880-13376899 MS.gene065967:CDS 45.0%
AACCTGCCTCTATTCCCACA+AGG + chr4.3:13376877-13376896 None:intergenic 50.0%
GTGGTGAGGATGATGCATTC+TGG - chr4.3:13376905-13376924 MS.gene065967:CDS 50.0%
TGTTGTCGTTGCATCAGACG+AGG + chr4.3:13376803-13376822 None:intergenic 50.0%
TTCCTTGTGGGAATAGAGGC+AGG - chr4.3:13376872-13376891 MS.gene065967:CDS 50.0%
!! AGAGGCAGGTTTTATGGAGG+TGG - chr4.3:13376886-13376905 MS.gene065967:CDS 50.0%
!! CAGGTTTTATGGAGGTGGTG+AGG - chr4.3:13376891-13376910 MS.gene065967:CDS 50.0%
ACTCAGAACTCCCCGTCTGA+TGG - chr4.3:13376838-13376857 MS.gene065967:CDS 55.0%
!! ATCAGACGGGGAGTTCTGAG+TGG + chr4.3:13376839-13376858 None:intergenic 55.0%
!! TCAGACGGGGAGTTCTGAGT+GGG + chr4.3:13376838-13376857 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 13376790 13377800 13376790 ID=MS.gene065967
chr4.3 mRNA 13376790 13377800 13376790 ID=MS.gene065967.t1;Parent=MS.gene065967
chr4.3 exon 13376790 13377800 13376790 ID=MS.gene065967.t1.exon1;Parent=MS.gene065967.t1
chr4.3 CDS 13376790 13377800 13376790 ID=cds.MS.gene065967.t1;Parent=MS.gene065967.t1
Gene Sequence

>MS.gene065967

ATGCAGAACTCCTCGTCTGATGCAACGACAACAATCAAGCATTATCCCACTCAGAACTCCCCGTCTGATGGTTCATCACAATTTCCTTGTGGGAATAGAGGCAGGTTTTATGGAGGTGGTGAGGATGATGCATTCTGGAGATTGTCATTTGGTGAAGAGTTTACTAATGACCAAAAGAAGAAAAGTAAAGATATTCTGAAGCCAGTAATGTACAGTTTGGATGTGAAAAGACATGGAAGAAGAAGAAGAAGAAGAGAAGATAGAAAATTGCTTAATGAAACAAAGAGTGCAAAGGAAGTTGAGTGCTTAAAGAGGAGATATGAGAGGAAAGCACAAAGAGCTTTACAAGAGCAGCTCTTGAAATTACAGAATGCAGCAGAGGAAGCTGAATTTGTTGCATCAAGTAAATGTAAATCCTTAGAAAAGGATGAGCTCCAATTTGAATCACCAAGAACCCAATTATTTCCCTCTTATGTAGATGCAGAAAGTTCTGGTCTTGGATTTCAAAGTGTCGGAGAAAATGGTGTGAATCAATGTGAGGAGTTTAAAGCAAAGGTTAACAAAAGGAGGGAATCAGTTCATGTGAGCAGAGAATTACAGAGGAGGAAACCAAAGCAGAGTTCCAAGGTAAGAGTACATTCTCCAAAGATGGCTACTGAAGTCGAAATACGCAAAATGAAGGCGATAGAAGACAAAAAGAAAGCAAAACTAAAGATGAAGAAAGAAGAAGAGGAAATGGTGGAGGAAACAGAAGAAGGGTTAGATAGTTTTGCAGTTGTGAAGTGTTCTTTGGATCCACAACAAGATTTTAGAGATTCAATGATTGAGATGATCAAAGAGAAAGAGATAAGCCAGCCAGAAGAAATGGAAGAGTTGTTAGCATGCTATTTGAGTTTGAATTCCAATGAATACCATGATATCATTATCAAAGCATTTCGACAGGTATGGTTATGCATGAGCCATTCAAGTTTGTGTAATAAATCAGAGAAACAATGTTGTTACTATGATTAG
Protein sequence

>MS.gene065967.t1

MQNSSSDATTTIKHYPTQNSPSDGSSQFPCGNRGRFYGGGEDDAFWRLSFGEEFTNDQKKKSKDILKPVMYSLDVKRHGRRRRRREDRKLLNETKSAKEVECLKRRYERKAQRALQEQLLKLQNAAEEAEFVASSKCKSLEKDELQFESPRTQLFPSYVDAESSGLGFQSVGENGVNQCEEFKAKVNKRRESVHVSRELQRRKPKQSSKVRVHSPKMATEVEIRKMKAIEDKKKAKLKMKKEEEEMVEETEEGLDSFAVVKCSLDPQQDFRDSMIEMIKEKEISQPEEMEELLACYLSLNSNEYHDIIIKAFRQVWLCMSHSSLCNKSEKQCCYYD