AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060087


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060087.t1 MTR_6g059760 83.568 213 34 1 1 212 1 213 6.08e-126 354
MS.gene060087.t1 MTR_6g059755 83.846 130 20 1 84 212 1 130 1.86e-74 221
MS.gene060087.t1 MTR_6g059650 51.598 219 91 9 1 212 1 211 1.78e-53 171
MS.gene060087.t1 MTR_6g065460 47.368 209 97 8 1 201 1 204 1.71e-46 152
MS.gene060087.t1 MTR_6g044780 43.636 220 113 8 1 212 1 217 3.07e-43 145
MS.gene060087.t1 MTR_6g045097 43.636 220 113 8 1 212 1 217 6.26e-43 144
MS.gene060087.t1 MTR_6g044810 43.119 218 113 8 1 210 1 215 2.21e-42 142
MS.gene060087.t1 MTR_6g045403 41.818 220 115 9 1 212 1 215 6.44e-40 136
MS.gene060087.t1 MTR_6g059410 45.070 213 98 9 1 207 1 200 6.37e-39 133
MS.gene060087.t1 MTR_6g059530 44.749 219 98 11 1 212 1 203 7.10e-38 130
MS.gene060087.t1 MTR_6g045433 40.175 229 113 9 1 212 1 222 4.62e-36 126
MS.gene060087.t1 MTR_6g065460 39.614 207 92 7 1 201 1 180 3.73e-31 112
MS.gene060087.t1 MTR_3g463590 40.415 193 100 9 25 207 22 209 1.72e-30 112
MS.gene060087.t1 MTR_6g066190 39.091 220 115 11 1 210 1 211 1.56e-28 107
MS.gene060087.t1 MTR_1g057110 38.424 203 102 9 1 199 1 184 1.97e-27 103
MS.gene060087.t1 MTR_6g009650 40.094 212 108 11 1 202 1 203 8.22e-27 102
MS.gene060087.t1 MTR_6g059730 37.104 221 125 8 1 212 1 216 1.82e-25 99.0
MS.gene060087.t1 MTR_6g066210 36.771 223 120 12 1 211 1 214 1.78e-23 93.6
MS.gene060087.t1 MTR_6g009563 38.498 213 111 12 1 202 1 204 3.47e-23 92.8
MS.gene060087.t1 MTR_6g017225 35.648 216 116 11 1 201 1 208 1.09e-22 94.4
MS.gene060087.t1 MTR_6g059680 37.755 196 105 10 18 201 18 208 6.23e-22 89.7
MS.gene060087.t1 MTR_6g059810 36.111 216 105 14 6 201 9 211 2.89e-19 82.4
MS.gene060087.t1 MTR_1g035770 35.294 204 113 13 11 200 11 209 7.98e-16 73.6
MS.gene060087.t1 MTR_7g037410 33.918 171 96 8 29 188 27 191 3.64e-14 68.6
MS.gene060087.t1 MTR_6g078070 31.500 200 122 9 9 198 6 200 3.76e-12 63.2
MS.gene060087.t1 MTR_6g065570 44.156 77 37 3 15 85 11 87 4.91e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 57 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGTAAGAAATACTTTATT+TGG 0.169494 6.2:-68437480 MS.gene060087:CDS
ATCAATGATTTCATCTTTAC+TGG 0.216581 6.2:-68437334 MS.gene060087:CDS
GGTATTGGTGGTGGTGTTAA+TGG 0.238618 6.2:-68437214 MS.gene060087:CDS
TATTCAAACTACAGATCTTC+TGG 0.242062 6.2:+68436982 None:intergenic
AGATTTCTTGATAATGAAAA+TGG 0.268782 6.2:-68437079 MS.gene060087:CDS
CCTGGTTTATGTAATAATAT+TGG 0.276379 6.2:-68437103 MS.gene060087:CDS
TCCAAGTGGGTGGTAGTTAA+AGG 0.301512 6.2:-68437259 MS.gene060087:CDS
GGTAAGTAATGTAGGGTTCA+TGG 0.354211 6.2:+68437603 None:intergenic
ACAACTTGAGTAAAGGATAA+TGG 0.359989 6.2:+68437541 None:intergenic
TATTTCTTACTCACAAGAAC+GGG 0.363139 6.2:+68437490 None:intergenic
ATTGAACCATGGGTAGGTAT+TGG 0.417221 6.2:-68437229 MS.gene060087:CDS
TAGAGGGTGGTAAGTAATGT+AGG 0.427202 6.2:+68437595 None:intergenic
AATGGTAAGAGTATTATAGA+TGG 0.435603 6.2:-68437196 MS.gene060087:CDS
ACCTTTAACTACCACCCACT+TGG 0.461157 6.2:+68437258 None:intergenic
GGGCAAAGAGGAAGAAATAG+AGG 0.480997 6.2:+68437578 None:intergenic
ATCAACAAATACAACTTCAA+AGG 0.482143 6.2:+68437024 None:intergenic
TTGGGATAAATGTTAGTGGC+AGG 0.501980 6.2:+68437365 None:intergenic
ACCAGGTGTATCACTGGTGG+TGG 0.503174 6.2:+68437120 None:intergenic
TCAACAAATACAACTTCAAA+GGG 0.504673 6.2:+68437025 None:intergenic
TCTGTTGGGATAAATGTTAG+TGG 0.504722 6.2:+68437361 None:intergenic
TAATGGAAAGTAGGTGGCTA+GGG 0.507074 6.2:+68437558 None:intergenic
TTTAACTACCACCCACTTGG+AGG 0.510750 6.2:+68437261 None:intergenic
AGTAAAGGATAATGGAAAGT+AGG 0.512041 6.2:+68437549 None:intergenic
CAGTCCACCACCACTTTCAC+CGG 0.513171 6.2:+68437453 None:intergenic
GAACCATGGGTAGGTATTGG+TGG 0.518436 6.2:-68437226 MS.gene060087:CDS
AGGTGGTTTCATTGAACCAT+GGG 0.524203 6.2:-68437239 MS.gene060087:CDS
TTGTTCAACAACTTGAGTAA+AGG 0.539696 6.2:+68437534 None:intergenic
CCACCACCACTTTCACCGGC+TGG 0.539880 6.2:+68437457 None:intergenic
AAATACTTTATTTGGCCAGC+CGG 0.543561 6.2:-68437472 MS.gene060087:CDS
ATTTGGCCAGCCGGTGAAAG+TGG 0.544335 6.2:-68437463 MS.gene060087:CDS
CCAGCCGGTGAAAGTGGTGG+TGG 0.546062 6.2:-68437457 MS.gene060087:CDS
ACATAAACCAGGTGTATCAC+TGG 0.553319 6.2:+68437114 None:intergenic
AAAGCTTGCTGTACAACAAG+TGG 0.555218 6.2:+68437406 None:intergenic
ATAATGGAAAGTAGGTGGCT+AGG 0.557559 6.2:+68437557 None:intergenic
CCATGGGTAGGTATTGGTGG+TGG 0.565594 6.2:-68437223 MS.gene060087:CDS
TCAAGTTGTTGAACAAGTGA+AGG 0.568787 6.2:-68437527 MS.gene060087:CDS
AAGGTGGTTTCATTGAACCA+TGG 0.574110 6.2:-68437240 MS.gene060087:CDS
GTATTTCTTACTCACAAGAA+CGG 0.581176 6.2:+68437489 None:intergenic
TTGTTTAAGATTGAGAGAAG+TGG 0.588206 6.2:-68437172 MS.gene060087:CDS
AGAGGGTGGTAAGTAATGTA+GGG 0.588469 6.2:+68437596 None:intergenic
CCAATATTATTACATAAACC+AGG 0.588965 6.2:+68437103 None:intergenic
CCCACCACCAGTGATACACC+TGG 0.602282 6.2:-68437121 MS.gene060087:CDS
GTGAAAGTGGTGGTGGACTG+AGG 0.603007 6.2:-68437450 MS.gene060087:CDS
AGTAGGTGGCTAGGGCAAAG+AGG 0.612636 6.2:+68437566 None:intergenic
GGTTTCATTGAACCATGGGT+AGG 0.618743 6.2:-68437235 MS.gene060087:CDS
AAGTGGGTGGTAGTTAAAGG+TGG 0.629514 6.2:-68437256 MS.gene060087:CDS
AAAGGATAATGGAAAGTAGG+TGG 0.636765 6.2:+68437552 None:intergenic
GGCAAAGAGGAAGAAATAGA+GGG 0.646580 6.2:+68437579 None:intergenic
AAAGAGGAAGAAATAGAGGG+TGG 0.652446 6.2:+68437582 None:intergenic
CCACCACCAATACCTACCCA+TGG 0.653181 6.2:+68437223 None:intergenic
TGGCCAGCCGGTGAAAGTGG+TGG 0.668540 6.2:-68437460 MS.gene060087:CDS
ATTTCTTACTCACAAGAACG+GGG 0.680212 6.2:+68437491 None:intergenic
TGCTGAATCCTCCAAGTGGG+TGG 0.681258 6.2:-68437269 MS.gene060087:CDS
CCAGGTGTATCACTGGTGGT+GGG 0.686983 6.2:+68437121 None:intergenic
TAAACCAGGTGTATCACTGG+TGG 0.706773 6.2:+68437117 None:intergenic
ATGTGCTGAATCCTCCAAGT+GGG 0.714019 6.2:-68437272 MS.gene060087:CDS
AATGTGCTGAATCCTCCAAG+TGG 0.759346 6.2:-68437273 MS.gene060087:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTTACTAATGATCAAA+CGG + chr6.2:68437536-68437555 None:intergenic 15.0%
!! TGAGTAAGAAATACTTTATT+TGG - chr6.2:68437106-68437125 MS.gene060087:CDS 20.0%
!!! AAATCATTGATATTTTCTGT+TGG + chr6.2:68437243-68437262 None:intergenic 20.0%
!!! AATCATTGATATTTTCTGTT+GGG + chr6.2:68437242-68437261 None:intergenic 20.0%
!!! AGATTTCTTGATAATGAAAA+TGG - chr6.2:68437507-68437526 MS.gene060087:CDS 20.0%
! ATCAACAAATACAACTTCAA+AGG + chr6.2:68437565-68437584 None:intergenic 25.0%
! ATCAATGATTTCATCTTTAC+TGG - chr6.2:68437252-68437271 MS.gene060087:CDS 25.0%
! CCAATATTATTACATAAACC+AGG + chr6.2:68437486-68437505 None:intergenic 25.0%
! CCTGGTTTATGTAATAATAT+TGG - chr6.2:68437483-68437502 MS.gene060087:CDS 25.0%
! TCAACAAATACAACTTCAAA+GGG + chr6.2:68437564-68437583 None:intergenic 25.0%
!!! AATGGTAAGAGTATTATAGA+TGG - chr6.2:68437390-68437409 MS.gene060087:CDS 25.0%
ACAACTTGAGTAAAGGATAA+TGG + chr6.2:68437048-68437067 None:intergenic 30.0%
GAACAAGTGAAGGATAAAAA+TGG - chr6.2:68437069-68437088 MS.gene060087:CDS 30.0%
GTATTTCTTACTCACAAGAA+CGG + chr6.2:68437100-68437119 None:intergenic 30.0%
TATTTCTTACTCACAAGAAC+GGG + chr6.2:68437099-68437118 None:intergenic 30.0%
TTGTTCAACAACTTGAGTAA+AGG + chr6.2:68437055-68437074 None:intergenic 30.0%
! TTGTTTAAGATTGAGAGAAG+TGG - chr6.2:68437414-68437433 MS.gene060087:CDS 30.0%
!! AGTAAAGGATAATGGAAAGT+AGG + chr6.2:68437040-68437059 None:intergenic 30.0%
!!! ATTGAGAGAAGTGGTTTTTT+TGG - chr6.2:68437423-68437442 MS.gene060087:CDS 30.0%
ATTTCTTACTCACAAGAACG+GGG + chr6.2:68437098-68437117 None:intergenic 35.0%
TCTGTTGGGATAAATGTTAG+TGG + chr6.2:68437228-68437247 None:intergenic 35.0%
! AAATACTTTATTTGGCCAGC+CGG - chr6.2:68437114-68437133 MS.gene060087:CDS 35.0%
! TCAAGTTGTTGAACAAGTGA+AGG - chr6.2:68437059-68437078 MS.gene060087:CDS 35.0%
!! AAAGGATAATGGAAAGTAGG+TGG + chr6.2:68437037-68437056 None:intergenic 35.0%
!! TGTACAGCAAGCTTTTTCTA+AGG - chr6.2:68437188-68437207 MS.gene060087:CDS 35.0%
AAAGAGGAAGAAATAGAGGG+TGG + chr6.2:68437007-68437026 None:intergenic 40.0%
AAGGTGGTTTCATTGAACCA+TGG - chr6.2:68437346-68437365 MS.gene060087:CDS 40.0%
ACATAAACCAGGTGTATCAC+TGG + chr6.2:68437475-68437494 None:intergenic 40.0%
AGAGGGTGGTAAGTAATGTA+GGG + chr6.2:68436993-68437012 None:intergenic 40.0%
AGGTGGTTTCATTGAACCAT+GGG - chr6.2:68437347-68437366 MS.gene060087:CDS 40.0%
ATTGAACCATGGGTAGGTAT+TGG - chr6.2:68437357-68437376 MS.gene060087:CDS 40.0%
GGCAAAGAGGAAGAAATAGA+GGG + chr6.2:68437010-68437029 None:intergenic 40.0%
TAATGGAAAGTAGGTGGCTA+GGG + chr6.2:68437031-68437050 None:intergenic 40.0%
TAGAGGGTGGTAAGTAATGT+AGG + chr6.2:68436994-68437013 None:intergenic 40.0%
TTGGGATAAATGTTAGTGGC+AGG + chr6.2:68437224-68437243 None:intergenic 40.0%
! ATAATGGAAAGTAGGTGGCT+AGG + chr6.2:68437032-68437051 None:intergenic 40.0%
!! AAAGCTTGCTGTACAACAAG+TGG + chr6.2:68437183-68437202 None:intergenic 40.0%
AAGTGGGTGGTAGTTAAAGG+TGG - chr6.2:68437330-68437349 MS.gene060087:CDS 45.0%
AATGTGCTGAATCCTCCAAG+TGG - chr6.2:68437313-68437332 MS.gene060087:CDS 45.0%
ACCTTTAACTACCACCCACT+TGG + chr6.2:68437331-68437350 None:intergenic 45.0%
ATGTGCTGAATCCTCCAAGT+GGG - chr6.2:68437314-68437333 MS.gene060087:CDS 45.0%
GGGCAAAGAGGAAGAAATAG+AGG + chr6.2:68437011-68437030 None:intergenic 45.0%
GGTTTCATTGAACCATGGGT+AGG - chr6.2:68437351-68437370 MS.gene060087:CDS 45.0%
TAAACCAGGTGTATCACTGG+TGG + chr6.2:68437472-68437491 None:intergenic 45.0%
TCCAAGTGGGTGGTAGTTAA+AGG - chr6.2:68437327-68437346 MS.gene060087:CDS 45.0%
TTTAACTACCACCCACTTGG+AGG + chr6.2:68437328-68437347 None:intergenic 45.0%
!! GGTATTGGTGGTGGTGTTAA+TGG - chr6.2:68437372-68437391 MS.gene060087:CDS 45.0%
!! GAACCATGGGTAGGTATTGG+TGG - chr6.2:68437360-68437379 MS.gene060087:CDS 50.0%
ACCAGGTGTATCACTGGTGG+TGG + chr6.2:68437469-68437488 None:intergenic 55.0%
AGTAGGTGGCTAGGGCAAAG+AGG + chr6.2:68437023-68437042 None:intergenic 55.0%
ATTTGGCCAGCCGGTGAAAG+TGG - chr6.2:68437123-68437142 MS.gene060087:CDS 55.0%
CAGTCCACCACCACTTTCAC+CGG + chr6.2:68437136-68437155 None:intergenic 55.0%
CCACCACCAATACCTACCCA+TGG + chr6.2:68437366-68437385 None:intergenic 55.0%
CCAGGTGTATCACTGGTGGT+GGG + chr6.2:68437468-68437487 None:intergenic 55.0%
TGCTGAATCCTCCAAGTGGG+TGG - chr6.2:68437317-68437336 MS.gene060087:CDS 55.0%
!! CCATGGGTAGGTATTGGTGG+TGG - chr6.2:68437363-68437382 MS.gene060087:CDS 55.0%
!! GTGAAAGTGGTGGTGGACTG+AGG - chr6.2:68437136-68437155 MS.gene060087:CDS 55.0%
CCCACCACCAGTGATACACC+TGG - chr6.2:68437465-68437484 MS.gene060087:CDS 60.0%
CCACCACCACTTTCACCGGC+TGG + chr6.2:68437132-68437151 None:intergenic 65.0%
CCAGCCGGTGAAAGTGGTGG+TGG - chr6.2:68437129-68437148 MS.gene060087:CDS 65.0%
TGGCCAGCCGGTGAAAGTGG+TGG - chr6.2:68437126-68437145 MS.gene060087:CDS 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 68436985 68437623 68436985 ID=MS.gene060087
chr6.2 mRNA 68436985 68437623 68436985 ID=MS.gene060087.t1;Parent=MS.gene060087
chr6.2 exon 68436985 68437623 68436985 ID=MS.gene060087.t1.exon1;Parent=MS.gene060087.t1
chr6.2 CDS 68436985 68437623 68436985 ID=cds.MS.gene060087.t1;Parent=MS.gene060087.t1
Gene Sequence

>MS.gene060087

ATGAACCCTACATTACTTACCACCCTCTATTTCTTCCTCTTTGCCCTAGCCACCTACTTTCCATTATCCTTTACTCAAGTTGTTGAACAAGTGAAGGATAAAAATGGAAACCCCGTTCTTGTGAGTAAGAAATACTTTATTTGGCCAGCCGGTGAAAGTGGTGGTGGACTGAGGCTTAATGAGACAGAAGAATGTCCACTTGTTGTACAGCAAGCTTTTTCTAAGGATGTTAAAAGCCTGCCACTAACATTTATCCCAACAGAAAATATCAATGATTTCATCTTTACTGGCTTCACATCACTAGATATTGTATTTGAAAAGAAGACAAAATGTGCTGAATCCTCCAAGTGGGTGGTAGTTAAAGGTGGTTTCATTGAACCATGGGTAGGTATTGGTGGTGGTGTTAATGGTAAGAGTATTATAGATGGTTTGTTTAAGATTGAGAGAAGTGGTTTTTTTGGATACAAGCTTGTGTTTTGTCCCACCACCAGTGATACACCTGGTTTATGTAATAATATTGGAAGATTTCTTGATAATGAAAATGGAGTCCGTTTGATCATTAGTAAAAATTTTCAACCCTTTGAAGTTGTATTTGTTGATGTTGAAGATGTTGCTCGATCCAGAAGATCTGTAGTTTGA

Protein sequence

>MS.gene060087.t1

MNPTLLTTLYFFLFALATYFPLSFTQVVEQVKDKNGNPVLVSKKYFIWPAGESGGGLRLNETEECPLVVQQAFSKDVKSLPLTFIPTENINDFIFTGFTSLDIVFEKKTKCAESSKWVVVKGGFIEPWVGIGGGVNGKSIIDGLFKIERSGFFGYKLVFCPTTSDTPGLCNNIGRFLDNENGVRLIISKNFQPFEVVFVDVEDVARSRRSVV