AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene33679

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene33679.t1 MTR_4g013330 88.587 184 21 0 39 222 16 199 7.43e-128 359
MS.gene33679.t1 MTR_4g013350 80.500 200 36 2 23 222 1 197 1.23e-116 330
MS.gene33679.t1 MTR_4g013345 78.378 185 37 2 38 222 15 196 1.93e-108 310
MS.gene33679.t1 MTR_4g013320 75.269 186 42 2 39 222 16 199 7.74e-105 301
MS.gene33679.t1 MTR_4g013335 75.500 200 45 1 23 222 1 196 1.47e-104 300
MS.gene33679.t1 MTR_4g013325 71.429 203 51 4 23 222 1 199 1.06e-87 257
MS.gene33679.t1 MTR_4g013310 65.591 186 58 3 39 222 16 197 6.74e-87 255
MS.gene33679.t1 MTR_7g070390 67.630 173 52 2 51 222 23 192 1.60e-78 234
MS.gene33679.t1 MTR_4g013385 55.497 191 77 3 32 222 8 190 5.63e-73 220
MS.gene33679.t1 MTR_0433s0040 55.497 191 77 3 32 222 8 190 5.63e-73 220
MS.gene33679.t1 MTR_1g054525 52.525 198 82 3 25 222 7 192 2.26e-67 206
MS.gene33679.t1 MTR_4g013770 57.895 171 69 2 52 222 24 191 7.93e-67 204
MS.gene33679.t1 MTR_4g013355 49.738 191 79 4 32 222 6 179 6.72e-61 189
MS.gene33679.t1 MTR_4g073950 55.556 153 67 1 70 222 41 192 6.38e-59 184
MS.gene33679.t1 MTR_7g093870 52.564 156 71 1 70 222 38 193 8.18e-55 174
MS.gene33679.t1 MTR_7g093850 53.247 154 69 2 70 222 43 194 1.00e-53 171
MS.gene33679.t1 MTR_7g093820 53.205 156 66 3 70 222 43 194 1.36e-53 171
MS.gene33679.t1 MTR_7g093790 46.429 168 86 3 56 222 27 191 1.67e-52 168
MS.gene33679.t1 MTR_7g093830 51.923 156 68 3 70 222 42 193 3.29e-52 167
MS.gene33679.t1 MTR_1g056370 47.771 157 78 2 66 221 32 185 3.57e-48 156
MS.gene33679.t1 MTR_3g105640 45.062 162 87 2 62 222 28 188 1.34e-46 152
MS.gene33679.t1 MTR_4g078885 46.358 151 77 1 72 222 39 185 1.17e-45 150
MS.gene33679.t1 MTR_3g105630 44.654 159 87 1 65 222 31 189 2.79e-45 149
MS.gene33679.t1 MTR_3g034030 46.358 151 77 1 72 222 39 185 4.07e-45 149
MS.gene33679.t1 MTR_5g096120 41.026 156 82 3 73 222 38 189 1.52e-38 132
MS.gene33679.t1 MTR_4g122110 35.526 152 88 2 75 222 35 180 5.81e-25 97.1
MS.gene33679.t1 MTR_4g122130 35.616 146 88 2 79 222 39 180 4.56e-24 94.7
MS.gene33679.t1 MTR_8g099115 35.862 145 84 5 63 201 27 168 1.89e-16 74.7
MS.gene33679.t1 MTR_4g049550 30.534 131 85 2 69 197 27 153 4.21e-15 70.9
MS.gene33679.t1 MTR_4g049570 28.188 149 105 1 69 217 27 173 1.59e-14 69.3
MS.gene33679.t1 MTR_8g099135 32.967 182 88 8 30 201 7 164 1.29e-13 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene33679.t1 AT1G55210 58.115 191 73 3 32 222 4 187 1.00e-77 232
MS.gene33679.t1 AT1G55210 58.115 191 73 3 32 222 4 187 1.00e-77 232
MS.gene33679.t1 AT1G58170 57.447 188 71 3 35 222 7 185 1.13e-75 226
MS.gene33679.t1 AT5G49040 52.020 198 87 2 25 222 2 191 3.67e-68 207
MS.gene33679.t1 AT3G13650 50.262 191 87 4 32 222 4 186 4.97e-63 194
MS.gene33679.t1 AT3G13662 54.967 151 63 1 59 209 27 172 1.89e-54 172
MS.gene33679.t1 AT1G65870 49.673 153 75 1 69 221 39 189 5.23e-54 171
MS.gene33679.t1 AT5G49030 50.777 193 85 3 25 217 2 184 1.38e-53 185
MS.gene33679.t1 AT2G21100 49.007 151 75 1 71 221 39 187 9.40e-50 160
MS.gene33679.t1 AT2G21100 49.007 151 75 1 71 221 39 187 9.40e-50 160
MS.gene33679.t1 AT1G22900 49.020 153 74 2 69 221 45 193 1.91e-48 157
MS.gene33679.t1 AT3G13660 57.031 128 52 1 95 222 1 125 8.09e-48 154
MS.gene33679.t1 AT5G42500 43.750 176 90 4 46 221 19 185 3.70e-47 154
MS.gene33679.t1 AT5G42510 46.104 154 77 3 69 221 34 182 1.34e-45 150
MS.gene33679.t1 AT4G38700 38.974 195 105 5 32 222 6 190 5.76e-41 138
MS.gene33679.t1 AT2G21110 40.237 169 87 3 59 222 27 186 1.26e-37 129
MS.gene33679.t1 AT3G58090 50.909 110 54 0 112 221 162 271 5.63e-37 130
MS.gene33679.t1 AT4G23690 34.932 146 83 5 68 209 34 171 1.37e-15 72.4
MS.gene33679.t1 AT4G11210 29.545 176 110 4 30 205 5 166 1.45e-15 72.4
MS.gene33679.t1 AT4G11180 27.225 191 119 5 34 221 10 183 3.77e-12 63.2

Find 50 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATTGAAGGAAAGTATAA+TGG 0.275934 4.3:+84190584 MS.gene33679:CDS
GCTAATAACTTGCGGTCTAT+TGG 0.304831 4.3:-84190296 None:intergenic
CATCTCCCTAACCTTGTTAA+TGG 0.308882 4.3:-84190639 None:intergenic
TCAACCGGCCTTAATGCTTT+TGG 0.320368 4.3:+84190428 MS.gene33679:CDS
ATGGACAGCCCTCTGACTTT+AGG 0.352327 4.3:+84190464 MS.gene33679:CDS
CAAAGTGATGAGGAAATGTT+TGG 0.371335 4.3:-84190192 None:intergenic
ATGCCTGTTGTTGGTGGTAG+TGG 0.375988 4.3:+84190659 MS.gene33679:CDS
TCTGCAACACAGGAAGAAAT+AGG 0.381370 4.3:+84190536 MS.gene33679:CDS
GGACTAAACCAAAAGCATTA+AGG 0.382332 4.3:-84190436 None:intergenic
TGAACAATTGTAATTGTTGT+AGG 0.389348 4.3:-84190386 None:intergenic
GGGAGTACTCTTACTATTGT+AGG 0.399599 4.3:+84190605 MS.gene33679:CDS
CAATTGAGTTCCAAGCTTGT+AGG 0.399871 4.3:+84190491 MS.gene33679:CDS
CATTGGGTTGATCTCAAATC+CGG 0.414046 4.3:+84190722 MS.gene33679:CDS
ATGCTCAAGCTAGTACTCAT+TGG 0.425611 4.3:+84190705 MS.gene33679:CDS
TCATTGAAGGAAAGTATAAT+GGG 0.435892 4.3:+84190585 MS.gene33679:CDS
TGCTCAAGCTAGTACTCATT+GGG 0.463842 4.3:+84190706 MS.gene33679:CDS
CCGGTTGAGTGTAGTTTCAA+TGG 0.466931 4.3:-84190413 None:intergenic
TCCCTAACCTTGTTAATGGC+AGG 0.468576 4.3:-84190635 None:intergenic
ATCCTGCCATTAACAAGGTT+AGG 0.469301 4.3:+84190633 MS.gene33679:CDS
CCATTGAAACTACACTCAAC+CGG 0.471757 4.3:+84190413 MS.gene33679:CDS
GAACAATTGTAATTGTTGTA+GGG 0.491999 4.3:-84190385 None:intergenic
TTTCTATGCATCTGCAACAC+AGG 0.494727 4.3:+84190526 MS.gene33679:CDS
ACTTTCTGCTTCAACTTCAT+CGG 0.501142 4.3:+84190244 MS.gene33679:CDS
CGTGCCAGTAGAATCTGAAA+TGG 0.504595 4.3:-84190343 None:intergenic
GTTAGGGAGATGCCTGTTGT+TGG 0.505285 4.3:+84190650 MS.gene33679:CDS
AGTCCACTACCACCAACAAC+AGG 0.512977 4.3:-84190662 None:intergenic
TCCTGCCATTAACAAGGTTA+GGG 0.518940 4.3:+84190634 MS.gene33679:CDS
AGGGAGATGCCTGTTGTTGG+TGG 0.521357 4.3:+84190653 MS.gene33679:CDS
ATTGGGTTGATCTCAAATCC+GGG 0.525292 4.3:+84190723 MS.gene33679:CDS
TAAGCCATTTCAGATTCTAC+TGG 0.525620 4.3:+84190339 MS.gene33679:CDS
GGAGTACTCTTACTATTGTA+GGG 0.530187 4.3:+84190606 MS.gene33679:CDS
AAAGTGTCTTGCAAGATATG+AGG 0.558330 4.3:-84190226 None:intergenic
GTACTCAACACATGCATCCC+CGG 0.560211 4.3:-84190741 None:intergenic
GTTATTAGCCCTACACAAGA+AGG 0.567510 4.3:+84190310 MS.gene33679:CDS
GGAAGAAGAACAAAGTGATG+AGG 0.576295 4.3:-84190202 None:intergenic
TACTGGCACGACATACTAAG+TGG 0.585470 4.3:+84190356 MS.gene33679:CDS
GTGATGAGGAAATGTTTGGA+AGG 0.586936 4.3:-84190188 None:intergenic
ATGTTTGGAAGGCATTGTTG+TGG 0.594072 4.3:-84190177 None:intergenic
AAGCTTGTAGGAAAAGCTCA+AGG 0.610963 4.3:+84190503 MS.gene33679:CDS
TAAACCAAAAGCATTAAGGC+CGG 0.621311 4.3:-84190432 None:intergenic
GTTGAGTGTAGTTTCAATGG+TGG 0.624193 4.3:-84190410 None:intergenic
AATTGCGGTCCTAAAGTCAG+AGG 0.626083 4.3:-84190473 None:intergenic
GAGGAATCCTGCCATTAACA+AGG 0.635903 4.3:+84190628 MS.gene33679:CDS
GTGTCTTGCAAGATATGAGG+AGG 0.637513 4.3:-84190223 None:intergenic
ATTGCGGTCCTAAAGTCAGA+GGG 0.650768 4.3:-84190472 None:intergenic
TGTGTAGGGCTAATAACTTG+CGG 0.660123 4.3:-84190304 None:intergenic
ACAAGCTTGGAACTCAATTG+CGG 0.661949 4.3:-84190488 None:intergenic
TCAGAGGGCTGTCCATCATG+CGG 0.670156 4.3:-84190457 None:intergenic
TTGGGTTGATCTCAAATCCG+GGG 0.672473 4.3:+84190724 MS.gene33679:CDS
GTACTCTTACTATTGTAGGG+AGG 0.687219 4.3:+84190609 MS.gene33679:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTAACAAGAAAAAAT+GGG - chr4.3:84189959-84189978 None:intergenic 10.0%
!!! TTTTTTTTAACAAGAAAAAA+TGG - chr4.3:84189960-84189979 None:intergenic 10.0%
!!! AAAAAAAAGTACATACAATG+TGG - chr4.3:84189863-84189882 None:intergenic 20.0%
! AGGAACAAAAATATAAGAAG+AGG - chr4.3:84190051-84190070 None:intergenic 25.0%
! GAACAATTGTAATTGTTGTA+GGG - chr4.3:84190388-84190407 None:intergenic 25.0%
! TGAACAATTGTAATTGTTGT+AGG - chr4.3:84190389-84190408 None:intergenic 25.0%
!! ATGAATTTTGCTTTCATTGA+AGG + chr4.3:84190572-84190591 MS.gene33679:CDS 25.0%
!! TCATTGAAGGAAAGTATAAT+GGG + chr4.3:84190585-84190604 MS.gene33679:CDS 25.0%
!! TTCATTGAAGGAAAGTATAA+TGG + chr4.3:84190584-84190603 MS.gene33679:CDS 25.0%
AAGTGAAGTTAAAGAAAGTG+AGG - chr4.3:84190071-84190090 None:intergenic 30.0%
AGGAGAGAAGAGAATAATAA+TGG - chr4.3:84190104-84190123 None:intergenic 30.0%
ATATAAGAAGAGGAAAGTGA+AGG - chr4.3:84190041-84190060 None:intergenic 30.0%
! TAGTTTTTCCTTCTTGTGTA+GGG - chr4.3:84190321-84190340 None:intergenic 30.0%
!! TTAGTTTTTCCTTCTTGTGT+AGG - chr4.3:84190322-84190341 None:intergenic 30.0%
AAGAGGAAAGTGAAGGAAAA+AGG - chr4.3:84190034-84190053 None:intergenic 35.0%
ACTTTCTGCTTCAACTTCAT+CGG + chr4.3:84190244-84190263 MS.gene33679:CDS 35.0%
AGTGAAGGAAAAAGGACAAA+TGG - chr4.3:84190026-84190045 None:intergenic 35.0%
CAAAGTGATGAGGAAATGTT+TGG - chr4.3:84190195-84190214 None:intergenic 35.0%
TAAGCCATTTCAGATTCTAC+TGG + chr4.3:84190339-84190358 MS.gene33679:CDS 35.0%
! AAAGTGTCTTGCAAGATATG+AGG - chr4.3:84190229-84190248 None:intergenic 35.0%
! GGAGTACTCTTACTATTGTA+GGG + chr4.3:84190606-84190625 MS.gene33679:CDS 35.0%
!! GGACTAAACCAAAAGCATTA+AGG - chr4.3:84190439-84190458 None:intergenic 35.0%
!! TAAACCAAAAGCATTAAGGC+CGG - chr4.3:84190435-84190454 None:intergenic 35.0%
AAGCTTGTAGGAAAAGCTCA+AGG + chr4.3:84190503-84190522 MS.gene33679:CDS 40.0%
ACAAGCTTGGAACTCAATTG+CGG - chr4.3:84190491-84190510 None:intergenic 40.0%
AGGAAAAAGGACAAATGGAG+TGG - chr4.3:84190021-84190040 None:intergenic 40.0%
ATCCTGCCATTAACAAGGTT+AGG + chr4.3:84190633-84190652 MS.gene33679:CDS 40.0%
ATGCTCAAGCTAGTACTCAT+TGG + chr4.3:84190705-84190724 MS.gene33679:CDS 40.0%
CAATTGAGTTCCAAGCTTGT+AGG + chr4.3:84190491-84190510 MS.gene33679:CDS 40.0%
CATCTCCCTAACCTTGTTAA+TGG - chr4.3:84190642-84190661 None:intergenic 40.0%
CCATTGAAACTACACTCAAC+CGG + chr4.3:84190413-84190432 MS.gene33679:CDS 40.0%
GATTGTTGTGATGCTAACTG+TGG - chr4.3:84190149-84190168 None:intergenic 40.0%
GGAAAAAGGACAAATGGAGT+GGG - chr4.3:84190020-84190039 None:intergenic 40.0%
GGAAGAAGAACAAAGTGATG+AGG - chr4.3:84190205-84190224 None:intergenic 40.0%
GTACTCTTACTATTGTAGGG+AGG + chr4.3:84190609-84190628 MS.gene33679:CDS 40.0%
GTGATGAGGAAATGTTTGGA+AGG - chr4.3:84190191-84190210 None:intergenic 40.0%
GTTATTAGCCCTACACAAGA+AGG + chr4.3:84190310-84190329 MS.gene33679:CDS 40.0%
GTTGAGTGTAGTTTCAATGG+TGG - chr4.3:84190413-84190432 None:intergenic 40.0%
TCCTGCCATTAACAAGGTTA+GGG + chr4.3:84190634-84190653 MS.gene33679:CDS 40.0%
TCTGCAACACAGGAAGAAAT+AGG + chr4.3:84190536-84190555 MS.gene33679:CDS 40.0%
TGCTCAAGCTAGTACTCATT+GGG + chr4.3:84190706-84190725 MS.gene33679:CDS 40.0%
TGTGTAGGGCTAATAACTTG+CGG - chr4.3:84190307-84190326 None:intergenic 40.0%
TTTCTATGCATCTGCAACAC+AGG + chr4.3:84190526-84190545 MS.gene33679:CDS 40.0%
! GCTAATAACTTGCGGTCTAT+TGG - chr4.3:84190299-84190318 None:intergenic 40.0%
! TTGAGCTTTTCCTACAAGCT+TGG - chr4.3:84190504-84190523 None:intergenic 40.0%
!! ATGTTTGGAAGGCATTGTTG+TGG - chr4.3:84190180-84190199 None:intergenic 40.0%
!! ATTGGGTTGATCTCAAATCC+GGG + chr4.3:84190723-84190742 MS.gene33679:CDS 40.0%
!! CATTGGGTTGATCTCAAATC+CGG + chr4.3:84190722-84190741 MS.gene33679:CDS 40.0%
!! GGGAGTACTCTTACTATTGT+AGG + chr4.3:84190605-84190624 MS.gene33679:CDS 40.0%
!!! GGACTTTTCAGATTTGCTAG+AGG + chr4.3:84190680-84190699 MS.gene33679:CDS 40.0%
!!! TTTTGGTTTAGTCCGCATGA+TGG + chr4.3:84190445-84190464 MS.gene33679:CDS 40.0%
AATTGCGGTCCTAAAGTCAG+AGG - chr4.3:84190476-84190495 None:intergenic 45.0%
ATTGCGGTCCTAAAGTCAGA+GGG - chr4.3:84190475-84190494 None:intergenic 45.0%
CCGGTTGAGTGTAGTTTCAA+TGG - chr4.3:84190416-84190435 None:intergenic 45.0%
CGTGCCAGTAGAATCTGAAA+TGG - chr4.3:84190346-84190365 None:intergenic 45.0%
CTGTGGAGACAGTAAAGTAG+TGG - chr4.3:84190132-84190151 None:intergenic 45.0%
GACAAATGGAGTGGGATGTA+GGG - chr4.3:84190012-84190031 None:intergenic 45.0%
GAGGAATCCTGCCATTAACA+AGG + chr4.3:84190628-84190647 MS.gene33679:CDS 45.0%
GTGTCTTGCAAGATATGAGG+AGG - chr4.3:84190226-84190245 None:intergenic 45.0%
TACTGGCACGACATACTAAG+TGG + chr4.3:84190356-84190375 MS.gene33679:CDS 45.0%
TCCCTAACCTTGTTAATGGC+AGG - chr4.3:84190638-84190657 None:intergenic 45.0%
TGGAGACAGTAAAGTAGTGG+AGG - chr4.3:84190129-84190148 None:intergenic 45.0%
! ACAGTAAAGTAGTGGAGGAG+AGG - chr4.3:84190124-84190143 None:intergenic 45.0%
! TCAACCGGCCTTAATGCTTT+TGG + chr4.3:84190428-84190447 MS.gene33679:CDS 45.0%
!! TTGGGTTGATCTCAAATCCG+GGG + chr4.3:84190724-84190743 MS.gene33679:CDS 45.0%
AGTCCACTACCACCAACAAC+AGG - chr4.3:84190665-84190684 None:intergenic 50.0%
ATGGACAGCCCTCTGACTTT+AGG + chr4.3:84190464-84190483 MS.gene33679:CDS 50.0%
GGACAAATGGAGTGGGATGT+AGG - chr4.3:84190013-84190032 None:intergenic 50.0%
GTACTCAACACATGCATCCC+CGG - chr4.3:84190744-84190763 None:intergenic 50.0%
GTTAGGGAGATGCCTGTTGT+TGG + chr4.3:84190650-84190669 MS.gene33679:CDS 50.0%
!! ATGCCTGTTGTTGGTGGTAG+TGG + chr4.3:84190659-84190678 MS.gene33679:CDS 50.0%
AGGGAGATGCCTGTTGTTGG+TGG + chr4.3:84190653-84190672 MS.gene33679:CDS 55.0%
TCAGAGGGCTGTCCATCATG+CGG - chr4.3:84190460-84190479 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 84189834 84190787 84189834 ID=MS.gene33679
chr4.3 mRNA 84189834 84190787 84189834 ID=MS.gene33679.t1;Parent=MS.gene33679
chr4.3 exon 84189834 84189866 84189834 ID=MS.gene33679.t1.exon1;Parent=MS.gene33679.t1
chr4.3 CDS 84189834 84189866 84189834 ID=cds.MS.gene33679.t1;Parent=MS.gene33679.t1
chr4.3 exon 84190152 84190787 84190152 ID=MS.gene33679.t1.exon2;Parent=MS.gene33679.t1
chr4.3 CDS 84190152 84190787 84190152 ID=cds.MS.gene33679.t1;Parent=MS.gene33679.t1
Gene Sequence

>MS.gene33679

ATGAACATCAAAATACAGAAATTATACCACATTGTATGTACTTTTTTTTTTTTTAACATTTTATCTTCTACACACTAATTTAAAAAATTAACGTAAAAATAAAAATACACTTTATATATAATCCCATTTTTTCTTGTTAAAAAAAAAAAGAATGAAATAATTAGAAAAATACTTACCCTACATCCCACTCCATTTGTCCTTTTTCCTTCACTTTCCTCTTCTTATATTTTTGTTCCTCACTTTCTTTAACTTCACTTCATTAAGCTTCCATTATTATTCTCTTCTCTCCTCTCCTCCACTACTTTACTGTCTCCACAGTTAGCATCACAACAATCTCTTGCATCCACAACAATGCCTTCCAAACATTTCCTCATCACTTTGTTCTTCTTCCTCCTCATATCTTGCAAGACACTTTCTGCTTCAACTTCATCGGAAAAAGAAGACACTTATGATTTTGTTCGTCCAATAGACCGCAAGTTATTAGCCCTACACAAGAAGGAAAAACTAAGCCATTTCAGATTCTACTGGCACGACATACTAAGTGGAAATAACCCTACAACAATTACAATTGTTCAACCACCATTGAAACTACACTCAACCGGCCTTAATGCTTTTGGTTTAGTCCGCATGATGGACAGCCCTCTGACTTTAGGACCGCAATTGAGTTCCAAGCTTGTAGGAAAAGCTCAAGGTTTCTATGCATCTGCAACACAGGAAGAAATAGGTTTTCTTATGACAATGAATTTTGCTTTCATTGAAGGAAAGTATAATGGGAGTACTCTTACTATTGTAGGGAGGAATCCTGCCATTAACAAGGTTAGGGAGATGCCTGTTGTTGGTGGTAGTGGACTTTTCAGATTTGCTAGAGGATATGCTCAAGCTAGTACTCATTGGGTTGATCTCAAATCCGGGGATGCATGTGTTGAGTACAATCTTCATGTTTTTCACTATTGA
Protein sequence

>MS.gene33679.t1

MNIKIQKLYHILASQQSLASTTMPSKHFLITLFFFLLISCKTLSASTSSEKEDTYDFVRPIDRKLLALHKKEKLSHFRFYWHDILSGNNPTTITIVQPPLKLHSTGLNAFGLVRMMDSPLTLGPQLSSKLVGKAQGFYASATQEEIGFLMTMNFAFIEGKYNGSTLTIVGRNPAINKVREMPVVGGSGLFRFARGYAQASTHWVDLKSGDACVEYNLHVFHY