AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01277

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01277.t1 MTR_2g010650 95.890 146 6 0 3 148 20 165 1.25e-105 298
MS.gene01277.t1 MTR_2g010630 88.000 150 16 2 1 148 16 165 3.68e-95 272
MS.gene01277.t1 MTR_2g010700 71.429 154 37 4 1 148 16 168 1.11e-74 220
MS.gene01277.t1 MTR_2g010600 71.812 149 34 5 4 148 18 162 1.89e-72 214
MS.gene01277.t1 MTR_2g010640 68.456 149 45 2 1 148 16 163 2.65e-72 214
MS.gene01277.t1 MTR_2g010670 69.799 149 44 1 1 148 16 164 3.06e-72 214
MS.gene01277.t1 MTR_4g050762 70.470 149 36 5 4 148 18 162 6.82e-70 208
MS.gene01277.t1 MTR_2g012370 70.470 149 36 5 4 148 18 162 6.82e-70 208
MS.gene01277.t1 MTR_2g010590 66.667 147 42 4 4 148 18 159 8.81e-70 207
MS.gene01277.t1 MTR_2g010690 66.443 149 49 1 1 148 16 164 8.99e-70 207
MS.gene01277.t1 MTR_2g010610 61.224 147 29 5 4 148 18 138 5.95e-56 172
MS.gene01277.t1 MTR_2g435490 54.362 149 60 5 3 148 21 164 2.69e-53 166
MS.gene01277.t1 MTR_2g010580 53.793 145 61 3 5 148 25 164 3.61e-53 166
MS.gene01277.t1 MTR_4g092540 49.333 150 69 4 1 148 15 159 6.10e-48 152
MS.gene01277.t1 MTR_4g128750 55.072 138 53 6 15 148 41 173 7.75e-40 132
MS.gene01277.t1 MTR_4g128770 48.227 141 63 6 14 148 70 206 1.36e-39 132
MS.gene01277.t1 MTR_1g067290 38.571 140 75 6 14 147 73 207 8.70e-27 100
MS.gene01277.t1 MTR_8g078770 34.752 141 82 5 14 148 36 172 6.16e-22 86.7
MS.gene01277.t1 MTR_5g018770 32.168 143 85 5 14 148 47 185 2.35e-20 82.8
MS.gene01277.t1 MTR_4g092515 53.846 78 29 4 6 81 24 96 4.67e-18 75.5
MS.gene01277.t1 MTR_5g018755 34.653 101 59 5 55 148 3 103 6.02e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01277.t1 AT2G14580 62.676 142 46 4 8 148 26 161 1.40e-58 179
MS.gene01277.t1 AT4G33720 60.140 143 50 4 8 148 26 163 9.92e-58 177
MS.gene01277.t1 AT3G19690 58.621 145 51 4 8 148 22 161 3.44e-56 173
MS.gene01277.t1 AT2G14610 57.639 144 54 4 6 148 24 161 9.61e-56 172
MS.gene01277.t1 AT5G26130 58.333 144 53 4 8 148 27 166 3.86e-53 166
MS.gene01277.t1 AT4G33710 57.639 144 54 4 8 148 27 166 7.51e-53 165
MS.gene01277.t1 AT1G50060 58.219 146 53 5 6 148 21 161 7.45e-51 160
MS.gene01277.t1 AT4G33730 52.027 148 64 3 3 148 30 172 1.21e-47 152
MS.gene01277.t1 AT1G50050 53.103 145 61 4 7 148 22 162 1.73e-42 138
MS.gene01277.t1 AT4G25790 48.921 139 62 6 14 148 77 210 6.85e-42 138
MS.gene01277.t1 AT2G19990 49.286 140 63 5 12 148 42 176 6.02e-41 135
MS.gene01277.t1 AT5G57625 49.275 138 61 6 15 148 75 207 7.83e-41 135
MS.gene01277.t1 AT4G25780 48.936 141 62 5 14 148 54 190 5.24e-39 130
MS.gene01277.t1 AT4G30320 46.763 139 70 4 13 148 24 161 3.25e-38 127
MS.gene01277.t1 AT1G50050 52.555 137 58 4 7 140 22 154 6.43e-38 129
MS.gene01277.t1 AT3G09590 47.143 140 64 6 14 148 52 186 4.16e-37 125
MS.gene01277.t1 AT4G07820 44.056 143 73 4 7 148 24 160 6.16e-37 124
MS.gene01277.t1 AT4G31470 42.029 138 72 5 14 148 53 185 1.25e-35 122
MS.gene01277.t1 AT5G02730 47.518 141 64 6 13 148 58 193 4.88e-35 121
MS.gene01277.t1 AT1G01310 44.928 138 68 5 14 148 87 219 2.06e-32 115
MS.gene01277.t1 AT5G66590 37.589 141 77 5 15 148 49 185 5.42e-27 100
MS.gene01277.t1 AT2G19980 40.278 144 66 6 12 148 35 165 2.52e-23 90.1
MS.gene01277.t1 AT2G19970 37.584 149 75 7 12 148 35 177 1.05e-21 86.3

Find 37 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTGTCCCAAACAATATT+TGG 0.198843 2.2:+70873054 None:intergenic
TTAAAATTCCAAATATTGTT+TGG 0.293275 2.2:-70873062 MS.gene01277:CDS
GATTGTCAATTGGTCCATTC+TGG 0.325775 2.2:-70872991 MS.gene01277:CDS
TCCATTATACTCAGGTGGTT+TGG 0.346423 2.2:-70872837 MS.gene01277:CDS
TAAAATTCCAAATATTGTTT+GGG 0.350860 2.2:-70873061 MS.gene01277:CDS
CTGCCGATCTTGCTTGGTTG+TGG 0.358764 2.2:+70873097 None:intergenic
GATCCACCAGGCAACTATAT+TGG 0.377482 2.2:-70872742 MS.gene01277:CDS
CAAATATGAATCACTTAGTA+TGG 0.381615 2.2:+70872712 None:intergenic
TTACTACTATAATCGTAGTT+TGG 0.383101 2.2:+70872883 None:intergenic
TCCAAACCACCTGAGTATAA+TGG 0.384825 2.2:+70872836 None:intergenic
TGCCGATCTTGCTTGGTTGT+GGG 0.426868 2.2:+70873098 None:intergenic
GCCAAAGTGAAATGTGATAA+TGG 0.434324 2.2:-70872790 MS.gene01277:CDS
TATCAACTGCCGATCTTGCT+TGG 0.450687 2.2:+70873091 None:intergenic
TGGAGAAACACACAACGTAT+TGG 0.459583 2.2:-70872817 MS.gene01277:CDS
ACCATTATCACATTTCACTT+TGG 0.465618 2.2:+70872789 None:intergenic
ACTCATGTCGCCGCTGCTCT+CGG 0.470748 2.2:+70872942 None:intergenic
CATTCTGGTGGTGACCGTTA+CGG 0.493043 2.2:-70872976 MS.gene01277:CDS
TCAACGCAAGGATTGTCAAT+TGG 0.501362 2.2:-70873001 MS.gene01277:CDS
GCATAGAAGCAGTGAAGTTG+TGG 0.504180 2.2:-70872918 MS.gene01277:CDS
CTTTCGCCAATATAGTTGCC+TGG 0.506506 2.2:+70872736 None:intergenic
TGCCCACAACCAAGCAAGAT+CGG 0.521741 2.2:-70873100 MS.gene01277:CDS
TGGGCATTCACGTAGTCTGC+TGG 0.533658 2.2:+70873117 None:intergenic
GAGAATATCGCCGAGAGCAG+CGG 0.550660 2.2:-70872952 MS.gene01277:CDS
CGTAACGGTCACCACCAGAA+TGG 0.554171 2.2:+70872977 None:intergenic
TATAGTAGTAACTCATGTGT+TGG 0.568160 2.2:-70872871 MS.gene01277:CDS
CATAGAAGCAGTGAAGTTGT+GGG 0.603029 2.2:-70872917 MS.gene01277:CDS
TGTCAATTGGTCCATTCTGG+TGG 0.605326 2.2:-70872988 MS.gene01277:CDS
GAGAGCAGCGGCGACATGAG+TGG 0.607916 2.2:-70872940 MS.gene01277:CDS
AAATTATGCTAATCAACGCA+AGG 0.622269 2.2:-70873013 MS.gene01277:CDS
CGGCGATATTCTCTCCGTAA+CGG 0.622517 2.2:+70872962 None:intergenic
ATGCCTCCATTATACTCAGG+TGG 0.625424 2.2:-70872842 MS.gene01277:CDS
TGAATGCCTCCATTATACTC+AGG 0.648037 2.2:-70872845 MS.gene01277:CDS
ACTTGCAATTACGATCCACC+AGG 0.648548 2.2:-70872754 MS.gene01277:CDS
TCGCCAATATAGTTGCCTGG+TGG 0.651539 2.2:+70872739 None:intergenic
AGTAGTAACTCATGTGTTGG+TGG 0.657995 2.2:-70872868 MS.gene01277:CDS
AAACCACCTGAGTATAATGG+AGG 0.693168 2.2:+70872839 None:intergenic
AAAGTGAAATGTGATAATGG+TGG 0.767769 2.2:-70872787 MS.gene01277:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATTCCAAATATTGTTT+GGG - chr2.2:70872815-70872834 MS.gene01277:CDS 15.0%
!! TTAAAATTCCAAATATTGTT+TGG - chr2.2:70872814-70872833 MS.gene01277:CDS 15.0%
! TTACTACTATAATCGTAGTT+TGG + chr2.2:70872996-70873015 None:intergenic 25.0%
AAATTATGCTAATCAACGCA+AGG - chr2.2:70872863-70872882 MS.gene01277:CDS 30.0%
ACCATTATCACATTTCACTT+TGG + chr2.2:70873090-70873109 None:intergenic 30.0%
TATAGTAGTAACTCATGTGT+TGG - chr2.2:70873005-70873024 MS.gene01277:CDS 30.0%
TTGTTGTCCCAAACAATATT+TGG + chr2.2:70872825-70872844 None:intergenic 30.0%
!! AAAGTGAAATGTGATAATGG+TGG - chr2.2:70873089-70873108 MS.gene01277:CDS 30.0%
GCCAAAGTGAAATGTGATAA+TGG - chr2.2:70873086-70873105 MS.gene01277:CDS 35.0%
AAACCACCTGAGTATAATGG+AGG + chr2.2:70873040-70873059 None:intergenic 40.0%
AGTAGTAACTCATGTGTTGG+TGG - chr2.2:70873008-70873027 MS.gene01277:CDS 40.0%
CATAGAAGCAGTGAAGTTGT+GGG - chr2.2:70872959-70872978 MS.gene01277:CDS 40.0%
GATTGTCAATTGGTCCATTC+TGG - chr2.2:70872885-70872904 MS.gene01277:CDS 40.0%
TCAACGCAAGGATTGTCAAT+TGG - chr2.2:70872875-70872894 MS.gene01277:CDS 40.0%
TCCAAACCACCTGAGTATAA+TGG + chr2.2:70873043-70873062 None:intergenic 40.0%
TCCATTATACTCAGGTGGTT+TGG - chr2.2:70873039-70873058 MS.gene01277:CDS 40.0%
TGAATGCCTCCATTATACTC+AGG - chr2.2:70873031-70873050 MS.gene01277:CDS 40.0%
TGGAGAAACACACAACGTAT+TGG - chr2.2:70873059-70873078 MS.gene01277:CDS 40.0%
ACTTGCAATTACGATCCACC+AGG - chr2.2:70873122-70873141 MS.gene01277:CDS 45.0%
ATGCCTCCATTATACTCAGG+TGG - chr2.2:70873034-70873053 MS.gene01277:CDS 45.0%
CTTTCGCCAATATAGTTGCC+TGG + chr2.2:70873143-70873162 None:intergenic 45.0%
GATCCACCAGGCAACTATAT+TGG - chr2.2:70873134-70873153 MS.gene01277:CDS 45.0%
GCATAGAAGCAGTGAAGTTG+TGG - chr2.2:70872958-70872977 MS.gene01277:CDS 45.0%
TATCAACTGCCGATCTTGCT+TGG + chr2.2:70872788-70872807 None:intergenic 45.0%
TGTCAATTGGTCCATTCTGG+TGG - chr2.2:70872888-70872907 MS.gene01277:CDS 45.0%
CGGCGATATTCTCTCCGTAA+CGG + chr2.2:70872917-70872936 None:intergenic 50.0%
TCGCCAATATAGTTGCCTGG+TGG + chr2.2:70873140-70873159 None:intergenic 50.0%
TGCCCACAACCAAGCAAGAT+CGG - chr2.2:70872776-70872795 MS.gene01277:CDS 50.0%
TGCCGATCTTGCTTGGTTGT+GGG + chr2.2:70872781-70872800 None:intergenic 50.0%
! CATTCTGGTGGTGACCGTTA+CGG - chr2.2:70872900-70872919 MS.gene01277:CDS 50.0%
CGTAACGGTCACCACCAGAA+TGG + chr2.2:70872902-70872921 None:intergenic 55.0%
CTGCCGATCTTGCTTGGTTG+TGG + chr2.2:70872782-70872801 None:intergenic 55.0%
GAGAATATCGCCGAGAGCAG+CGG - chr2.2:70872924-70872943 MS.gene01277:CDS 55.0%
TGGGCATTCACGTAGTCTGC+TGG + chr2.2:70872762-70872781 None:intergenic 55.0%
ACTCATGTCGCCGCTGCTCT+CGG + chr2.2:70872937-70872956 None:intergenic 60.0%
GAGAGCAGCGGCGACATGAG+TGG - chr2.2:70872936-70872955 MS.gene01277:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 70872726 70873172 70872726 ID=MS.gene01277
chr2.2 mRNA 70872726 70873172 70872726 ID=MS.gene01277.t1;Parent=MS.gene01277
chr2.2 exon 70872726 70873172 70872726 ID=MS.gene01277.t1.exon1;Parent=MS.gene01277.t1
chr2.2 CDS 70872726 70873172 70872726 ID=cds.MS.gene01277.t1;Parent=MS.gene01277.t1
Gene Sequence

>MS.gene01277

ATGGATAGTCACGTTGCACATGCACAAGACTCACCAGCAGACTACGTGAATGCCCACAACCAAGCAAGATCGGCAGTTGATACAAACATTAAAATTCCAAATATTGTTTGGGACAACAACGTCGCTGCTTTTGCACAAAATTATGCTAATCAACGCAAGGATTGTCAATTGGTCCATTCTGGTGGTGACCGTTACGGAGAGAATATCGCCGAGAGCAGCGGCGACATGAGTGGCATAGAAGCAGTGAAGTTGTGGGTTGATGAAAAACCAAACTACGATTATAGTAGTAACTCATGTGTTGGTGGTGAATGCCTCCATTATACTCAGGTGGTTTGGAGAAACACACAACGTATTGGATGTGCCAAAGTGAAATGTGATAATGGTGGCACATTTGTTACTTGCAATTACGATCCACCAGGCAACTATATTGGCGAAAGACCATACTAA
Protein sequence

>MS.gene01277.t1

MDSHVAHAQDSPADYVNAHNQARSAVDTNIKIPNIVWDNNVAAFAQNYANQRKDCQLVHSGGDRYGENIAESSGDMSGIEAVKLWVDEKPNYDYSSNSCVGGECLHYTQVVWRNTQRIGCAKVKCDNGGTFVTCNYDPPGNYIGERPY