AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene86990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86990.t1 MTR_2g104900 97.571 247 6 0 1 247 1 247 0.0 499
MS.gene86990.t1 MTR_4g006575 52.083 240 80 11 19 247 9 224 1.75e-57 182
MS.gene86990.t1 MTR_4g006600 52.083 240 80 11 19 247 9 224 1.75e-57 182
MS.gene86990.t1 MTR_1g013130 35.563 284 124 13 1 247 1 262 1.90e-34 124
MS.gene86990.t1 MTR_3g106230 44.379 169 76 8 34 187 25 190 2.24e-32 118
MS.gene86990.t1 MTR_5g077370 67.532 77 17 3 80 155 86 155 9.59e-27 103
MS.gene86990.t1 MTR_1g033340 64.935 77 22 2 81 157 97 168 2.23e-26 103
MS.gene86990.t1 MTR_3g065020 61.728 81 23 3 76 155 80 153 8.64e-25 98.6
MS.gene86990.t1 MTR_4g128340 54.667 75 23 2 78 152 42 105 1.67e-17 77.8
MS.gene86990.t1 MTR_1g107055 36.232 138 69 4 24 159 12 132 3.61e-16 74.7
MS.gene86990.t1 MTR_7g086860 49.254 67 27 2 60 119 2 68 1.20e-12 64.3
MS.gene86990.t1 MTR_5g008310 40.206 97 39 3 77 164 68 154 2.90e-12 65.9
MS.gene86990.t1 MTR_5g008280 42.000 100 49 3 69 164 34 128 4.75e-12 65.5
MS.gene86990.t1 MTR_3g011990 38.356 146 63 9 34 164 44 177 6.79e-12 64.3
MS.gene86990.t1 MTR_8g466760 44.086 93 34 4 79 164 96 177 8.05e-12 64.3
MS.gene86990.t1 MTR_7g083210 75.758 33 8 0 81 113 39 71 1.08e-11 62.4
MS.gene86990.t1 MTR_5g008320 39.175 97 40 3 77 164 68 154 1.08e-11 63.9
MS.gene86990.t1 MTR_3g012010 41.414 99 46 3 73 164 90 183 6.17e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86990.t1 AT5G10970 39.526 253 120 11 13 247 35 272 6.29e-38 134
MS.gene86990.t1 AT1G80730 41.026 234 93 11 32 247 22 228 4.86e-34 122
MS.gene86990.t1 AT5G25160 41.475 217 97 9 48 247 32 235 1.65e-33 121
MS.gene86990.t1 AT1G24625 41.538 130 40 4 28 157 29 122 2.89e-21 89.0
MS.gene86990.t1 AT1G66140 55.682 88 25 2 81 154 83 170 9.69e-21 88.6
MS.gene86990.t1 AT5G57520 57.143 63 24 1 79 138 48 110 6.10e-17 75.9
MS.gene86990.t1 AT5G14010 76.471 34 8 0 81 114 36 69 7.27e-13 65.1
MS.gene86990.t1 AT5G01860 57.778 45 19 0 70 114 54 98 4.24e-12 63.9

Find 36 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCCAAGAAAGGTGCAAAA+TGG 0.323012 2.3:+175249 MS.gene86990:CDS
GGCAGCTTCTGCCACTGGTT+TGG 0.325271 2.3:-175126 None:intergenic
TGAACACAGGTACTCAAGTA+TGG 0.334170 2.3:+174978 MS.gene86990:CDS
ACCATCATCACTTGGAATTC+AGG 0.350325 2.3:+175035 MS.gene86990:CDS
GAAAATTTCCCTGATCTTGT+AGG 0.357308 2.3:-175228 None:intergenic
AGAAAGGTGCAAAATGGATT+TGG 0.360298 2.3:+175255 MS.gene86990:CDS
TTTCCCTGATCTTGTAGGTA+TGG 0.467787 2.3:-175223 None:intergenic
AACATGGCTCTAATCTTAGA+AGG 0.477004 2.3:-174612 None:intergenic
ATATAGGCAGCTTCTGCCAC+TGG 0.477130 2.3:-175131 None:intergenic
ACACAAAAGAGAAAGAACTA+TGG 0.484621 2.3:+174918 MS.gene86990:CDS
GTAAAAGCACTCAGAGTTTG+AGG 0.499487 2.3:-175338 None:intergenic
AAGGTGCAAAATGGATTTGG+AGG 0.500419 2.3:+175258 MS.gene86990:CDS
ACATGAAGATTCCTTGATGC+TGG 0.502045 2.3:-175162 None:intergenic
TCATCACAAGAATCTTTACT+AGG 0.516480 2.3:-174721 None:intergenic
GATGCTGGTTGTGAATATAT+AGG 0.519086 2.3:-175147 None:intergenic
TCTTCATCGGAATCTAATCA+TGG 0.524262 2.3:+174808 MS.gene86990:CDS
CATGTTGAGGCAGAAACTGA+TGG 0.531135 2.3:+175180 MS.gene86990:CDS
ATGGCTTCTCTACCTTTGCA+TGG 0.537338 2.3:+174997 MS.gene86990:CDS
AGTGCCATACCTACAAGATC+AGG 0.538472 2.3:+175219 MS.gene86990:CDS
CGATGAAGAGTTTATCGACA+TGG 0.551961 2.3:-174794 None:intergenic
TTCGGTTTGTCGCGTTACTG+TGG 0.557649 2.3:+175102 MS.gene86990:CDS
ACCTGAATTCCAAGTGATGA+TGG 0.560861 2.3:-175036 None:intergenic
TATAGTTCACAGGCACTTGG+TGG 0.564578 2.3:+174883 MS.gene86990:CDS
TGTAGGTATGGCACTAGTCA+AGG 0.572932 2.3:-175211 None:intergenic
TATATTCACAACCAGCATCA+AGG 0.576962 2.3:+175151 MS.gene86990:CDS
TAGTTGCATGAGAAAATCCT+TGG 0.584802 2.3:-174844 None:intergenic
AAAAGATCACCATCATCACT+TGG 0.591415 2.3:+175027 MS.gene86990:CDS
CATGTCGATAAACTCTTCAT+CGG 0.592241 2.3:+174795 MS.gene86990:CDS
ATCAAGGAATCTTCATGTTG+AGG 0.598145 2.3:+175167 MS.gene86990:CDS
TAAAAGCACTCAGAGTTTGA+GGG 0.622554 2.3:-175337 None:intergenic
ATGGTAATGAATTAGAGCCA+AGG 0.629515 2.3:+174827 MS.gene86990:CDS
GTTACTGTGGTCCAAACCAG+TGG 0.634342 2.3:+175115 MS.gene86990:CDS
GAAGAGTTTATCGACATGGA+CGG 0.645110 2.3:-174790 None:intergenic
TTCAAATTATTAGATAAACA+TGG 0.647436 2.3:-174628 None:intergenic
AAGTTTGAAGAATAAACAAG+AGG 0.648051 2.3:+175293 MS.gene86990:CDS
GTGCCATACCTACAAGATCA+GGG 0.648274 2.3:+175220 MS.gene86990:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCAAATTATTAGATAAACA+TGG - chr2.3:174631-174650 None:intergenic 15.0%
! AAGTTTGAAGAATAAACAAG+AGG + chr2.3:175293-175312 MS.gene86990:CDS 25.0%
!!! AAGAAAGTTTTATAGTTCAC+AGG + chr2.3:174873-174892 MS.gene86990:CDS 25.0%
AAAAACGGTGTTTGATAAGA+AGG - chr2.3:175084-175103 None:intergenic 30.0%
AAAGAACTATGGCAAAAAGA+GGG + chr2.3:174929-174948 MS.gene86990:CDS 30.0%
ACACAAAAGAGAAAGAACTA+TGG + chr2.3:174918-174937 MS.gene86990:CDS 30.0%
TCATCACAAGAATCTTTACT+AGG - chr2.3:174724-174743 None:intergenic 30.0%
! TTTCTCTTTTGTGTGCATTT+TGG - chr2.3:174912-174931 None:intergenic 30.0%
!! TCTTATCAAACACCGTTTTT+CGG + chr2.3:175084-175103 MS.gene86990:CDS 30.0%
AAAAGATCACCATCATCACT+TGG + chr2.3:175027-175046 MS.gene86990:CDS 35.0%
ATCAAGGAATCTTCATGTTG+AGG + chr2.3:175167-175186 MS.gene86990:CDS 35.0%
CATGTCGATAAACTCTTCAT+CGG + chr2.3:174795-174814 MS.gene86990:CDS 35.0%
GAAAATTTCCCTGATCTTGT+AGG - chr2.3:175231-175250 None:intergenic 35.0%
GAAAGAACTATGGCAAAAAG+AGG + chr2.3:174928-174947 MS.gene86990:CDS 35.0%
TAGTTGCATGAGAAAATCCT+TGG - chr2.3:174847-174866 None:intergenic 35.0%
TATATTCACAACCAGCATCA+AGG + chr2.3:175151-175170 MS.gene86990:CDS 35.0%
TCTTCATCGGAATCTAATCA+TGG + chr2.3:174808-174827 MS.gene86990:CDS 35.0%
! AATCCATTTTGCACCTTTCT+TGG - chr2.3:175255-175274 None:intergenic 35.0%
! AGAAAGGTGCAAAATGGATT+TGG + chr2.3:175255-175274 MS.gene86990:CDS 35.0%
! AGGGAAATTTTCTCCAAGAA+AGG + chr2.3:175239-175258 MS.gene86990:CDS 35.0%
! ATGGTAATGAATTAGAGCCA+AGG + chr2.3:174827-174846 MS.gene86990:CDS 35.0%
! CTTTTATAAGAGCCATGCAA+AGG - chr2.3:175012-175031 None:intergenic 35.0%
! GATGCTGGTTGTGAATATAT+AGG - chr2.3:175150-175169 None:intergenic 35.0%
! TTTTATAGTTCACAGGCACT+TGG + chr2.3:174880-174899 MS.gene86990:CDS 35.0%
!! AACATGGCTCTAATCTTAGA+AGG - chr2.3:174615-174634 None:intergenic 35.0%
ACATGAAGATTCCTTGATGC+TGG - chr2.3:175165-175184 None:intergenic 40.0%
ACCATCATCACTTGGAATTC+AGG + chr2.3:175035-175054 MS.gene86990:CDS 40.0%
ACCTGAATTCCAAGTGATGA+TGG - chr2.3:175039-175058 None:intergenic 40.0%
CGATGAAGAGTTTATCGACA+TGG - chr2.3:174797-174816 None:intergenic 40.0%
GAAGAGTTTATCGACATGGA+CGG - chr2.3:174793-174812 None:intergenic 40.0%
TAACGCGACAAACCGAAAAA+CGG - chr2.3:175099-175118 None:intergenic 40.0%
TGAACACAGGTACTCAAGTA+TGG + chr2.3:174978-174997 MS.gene86990:CDS 40.0%
TTTCCCTGATCTTGTAGGTA+TGG - chr2.3:175226-175245 None:intergenic 40.0%
! AAAAAGAGGGCACAAATCTG+TGG + chr2.3:174942-174961 MS.gene86990:CDS 40.0%
! AAGGTGCAAAATGGATTTGG+AGG + chr2.3:175258-175277 MS.gene86990:CDS 40.0%
! CTTCGCTAGATTTTGAACAC+AGG + chr2.3:174965-174984 MS.gene86990:CDS 40.0%
! TCTCCAAGAAAGGTGCAAAA+TGG + chr2.3:175249-175268 MS.gene86990:CDS 40.0%
AGTGCCATACCTACAAGATC+AGG + chr2.3:175219-175238 MS.gene86990:CDS 45.0%
ATGGCTTCTCTACCTTTGCA+TGG + chr2.3:174997-175016 MS.gene86990:CDS 45.0%
CATGTTGAGGCAGAAACTGA+TGG + chr2.3:175180-175199 MS.gene86990:CDS 45.0%
GTGCCATACCTACAAGATCA+GGG + chr2.3:175220-175239 MS.gene86990:CDS 45.0%
TATAGTTCACAGGCACTTGG+TGG + chr2.3:174883-174902 MS.gene86990:CDS 45.0%
TGTAGGTATGGCACTAGTCA+AGG - chr2.3:175214-175233 None:intergenic 45.0%
ATATAGGCAGCTTCTGCCAC+TGG - chr2.3:175134-175153 None:intergenic 50.0%
GTTACTGTGGTCCAAACCAG+TGG + chr2.3:175115-175134 MS.gene86990:CDS 50.0%
! TTCGGTTTGTCGCGTTACTG+TGG + chr2.3:175102-175121 MS.gene86990:CDS 50.0%
! GGCAGCTTCTGCCACTGGTT+TGG - chr2.3:175129-175148 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 174607 175350 174607 ID=MS.gene86990
chr2.3 mRNA 174607 175350 174607 ID=MS.gene86990.t1;Parent=MS.gene86990
chr2.3 exon 174607 175350 174607 ID=MS.gene86990.t1.exon1;Parent=MS.gene86990.t1
chr2.3 CDS 174607 175350 174607 ID=cds.MS.gene86990.t1;Parent=MS.gene86990.t1
Gene Sequence

>MS.gene86990

ATGGACCTTCTAAGATTAGAGCCATGTTTATCTAATAATTTGAACATCTCATTTTCTGAGAAGAGACAAACAGAAAATGAAGAGAAAAAACATCTTGTACTAGATTTAACTCTTCCTAGTAAAGATTCTTGTGATGATGAGTCAAAACAAGAACTCAATCTCATAAACTGTTTCGATACAGAACCGTCCATGTCGATAAACTCTTCATCGGAATCTAATCATGGTAATGAATTAGAGCCAAGGATTTTCTCATGCAACTATTGTCAAAGAAAGTTTTATAGTTCACAGGCACTTGGTGGACACCAAAATGCACACAAAAGAGAAAGAACTATGGCAAAAAGAGGGCACAAATCTGTGGCTTCGCTAGATTTTGAACACAGGTACTCAAGTATGGCTTCTCTACCTTTGCATGGCTCTTATAAAAGATCACCATCATCACTTGGAATTCAGGTGCACTCTTCTATGATTCAAAAACCTTCTTATCAAACACCGTTTTTCGGTTTGTCGCGTTACTGTGGTCCAAACCAGTGGCAGAAGCTGCCTATATATTCACAACCAGCATCAAGGAATCTTCATGTTGAGGCAGAAACTGATGGATCATCATCCTTGACTAGTGCCATACCTACAAGATCAGGGAAATTTTCTCCAAGAAAGGTGCAAAATGGATTTGGAGGTTATAATGCTACAAGTTTGAAGAATAAACAAGAGGAGTTGCAGAAGCTTGACTTGTCCCTCAAACTCTGA
Protein sequence

>MS.gene86990.t1

MDLLRLEPCLSNNLNISFSEKRQTENEEKKHLVLDLTLPSKDSCDDESKQELNLINCFDTEPSMSINSSSESNHGNELEPRIFSCNYCQRKFYSSQALGGHQNAHKRERTMAKRGHKSVASLDFEHRYSSMASLPLHGSYKRSPSSLGIQVHSSMIQKPSYQTPFFGLSRYCGPNQWQKLPIYSQPASRNLHVEAETDGSSSLTSAIPTRSGKFSPRKVQNGFGGYNATSLKNKQEELQKLDLSLKL