AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42830

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42830.t1 MTR_2g093970 98.068 207 4 0 1 207 87 293 8.54e-147 410
MS.gene42830.t1 MTR_4g059790 68.500 200 55 3 1 199 91 283 4.96e-86 256
MS.gene42830.t1 MTR_4g059840 67.327 202 58 3 1 200 91 286 1.38e-85 255
MS.gene42830.t1 MTR_4g053380 67.500 200 62 1 1 200 95 291 9.22e-82 245
MS.gene42830.t1 MTR_2g017970 54.271 199 79 3 1 198 86 273 5.32e-64 199
MS.gene42830.t1 MTR_2g017960 52.709 203 84 3 1 202 86 277 3.88e-62 194
MS.gene42830.t1 MTR_2g017950 46.635 208 100 3 1 202 89 291 2.07e-56 181
MS.gene42830.t1 MTR_8g087450 62.308 130 49 0 1 130 95 224 2.69e-53 172
MS.gene42830.t1 MTR_2g093980 46.269 201 99 3 1 201 87 278 5.13e-52 169
MS.gene42830.t1 MTR_8g087460 60.902 133 48 3 1 130 111 242 2.42e-48 160
MS.gene42830.t1 MTR_8g087470 60.902 133 48 3 1 130 111 242 2.67e-48 160
MS.gene42830.t1 MTR_4g059780 59.231 130 53 0 1 130 108 237 1.02e-47 158
MS.gene42830.t1 MTR_4g059720 50.314 159 63 2 1 159 60 202 3.36e-45 150
MS.gene42830.t1 MTR_2g093990 53.846 130 59 1 1 130 59 187 1.03e-44 149
MS.gene42830.t1 MTR_7g101080 46.875 128 66 2 1 127 58 184 6.11e-32 116
MS.gene42830.t1 MTR_2g090765 37.662 154 89 1 19 165 73 226 1.25e-24 97.4
MS.gene42830.t1 MTR_7g075453 37.037 135 85 0 21 155 217 351 5.30e-17 79.0
MS.gene42830.t1 MTR_5g098060 33.099 142 87 4 21 160 85 220 3.96e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42830.t1 AT5G60490 50.000 130 63 2 1 129 57 185 3.21e-36 127
MS.gene42830.t1 AT5G03170 44.295 149 74 2 1 148 54 194 9.09e-36 126
MS.gene42830.t1 AT5G44130 35.165 182 101 3 1 180 54 220 5.47e-25 98.2
MS.gene42830.t1 AT2G20520 40.000 150 82 4 1 147 56 200 3.58e-22 90.9
MS.gene42830.t1 AT1G03870 34.637 179 106 4 1 173 57 230 4.75e-22 90.5
MS.gene42830.t1 AT3G46550 33.333 120 75 4 18 132 239 358 2.02e-11 62.8
MS.gene42830.t1 AT3G60900 28.777 139 93 1 21 159 223 355 9.91e-11 60.8

Find 47 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCCAGCAAGTGTTCTTAC+AGG 0.276561 2.3:-7886794 None:intergenic
ATAAATAGCAAGATGTTTAT+CGG 0.320043 2.3:-7886915 None:intergenic
GAAAATTGTTGCTGAGGTTC+CGG 0.329669 2.3:+7886982 MS.gene42830:CDS
TGTTGCTGAGGTTCCGGCTT+TGG 0.331915 2.3:+7886988 MS.gene42830:CDS
AGTGTTAACACCACGATTAA+TGG 0.347939 2.3:+7886881 MS.gene42830:CDS
CATCTTGCTATTTATAAAGT+TGG 0.349855 2.3:+7886923 MS.gene42830:CDS
AACCCTGTAAGAACACTTGC+TGG 0.390538 2.3:+7886791 MS.gene42830:CDS
GAACTTAACGTGATTAGTTA+TGG 0.403328 2.3:+7886833 MS.gene42830:CDS
ACTTGGGTGGCACTTGTTGT+TGG 0.450548 2.3:+7887145 MS.gene42830:CDS
TTCTGAGAAGGCGGAATCGT+CGG 0.454414 2.3:-7886660 None:intergenic
TCTGAGAAGGCGGAATCGTC+GGG 0.465451 2.3:-7886659 None:intergenic
GCTGGTGCAGGCGCCAAAGC+CGG 0.482022 2.3:-7887001 None:intergenic
GCCTTAGCATCAGCAATAGC+TGG 0.484689 2.3:-7887019 None:intergenic
GGAAATGTGAACATTTCAAC+GGG 0.489369 2.3:+7886857 MS.gene42830:CDS
ACCAGCTATTGCTGATGCTA+AGG 0.493657 2.3:+7887018 MS.gene42830:CDS
TTAGGAGCTGTGAGTTGAGC+TGG 0.506453 2.3:-7886604 None:intergenic
GCCTTCTCAGAACTCAAACC+AGG 0.511146 2.3:+7886671 MS.gene42830:CDS
AGCAAGTGTTCTTACAGGGT+TGG 0.512112 2.3:-7886789 None:intergenic
GTTGAATCTTCAGATGATGA+TGG 0.519092 2.3:-7887064 None:intergenic
GGATTGACATGAGTGGAACT+TGG 0.521312 2.3:+7887128 MS.gene42830:CDS
TGCGAGGATCGTCAAGCCGC+CGG 0.521917 2.3:-7886636 None:intergenic
GCATCAGCAATAGCTGGTGC+AGG 0.524825 2.3:-7887013 None:intergenic
TGCTAAGAAAATTGTTGCTG+AGG 0.530469 2.3:+7886976 MS.gene42830:CDS
ACACTTGCTGGAAACAAACC+TGG 0.537319 2.3:+7886803 MS.gene42830:CDS
GTTGTTGGAATTGTCTTCGT+GGG 0.546805 2.3:+7887160 MS.gene42830:CDS
TTAGCAGGAGAAAATTCTGA+TGG 0.547442 2.3:-7886959 None:intergenic
GAGAGTGAGTTGAGGAACCC+TGG 0.549587 2.3:-7886689 None:intergenic
CAGCTCCTAACCATAAAATC+CGG 0.551779 2.3:+7886617 MS.gene42830:CDS
TTCCAGCAAGTGTTCTTACA+GGG 0.554792 2.3:-7886793 None:intergenic
TGAAGATTCAACAACGTCGC+AGG 0.554836 2.3:+7887075 MS.gene42830:CDS
CCCTGGTTTGAGTTCTGAGA+AGG 0.557457 2.3:-7886672 None:intergenic
TGTTGTTGGAATTGTCTTCG+TGG 0.560250 2.3:+7887159 MS.gene42830:CDS
CTTAACGTGATTAGTTATGG+TGG 0.562819 2.3:+7886836 MS.gene42830:CDS
AGGCGGAATCGTCGGGTGCG+AGG 0.569498 2.3:-7886652 None:intergenic
CTGTGACTTCTAGTGCTATG+AGG 0.580983 2.3:+7887107 MS.gene42830:CDS
CCTTCTCAGAACTCAAACCA+GGG 0.601582 2.3:+7886672 MS.gene42830:CDS
TGGAAATGTGAACATTTCAA+CGG 0.610164 2.3:+7886856 MS.gene42830:CDS
TTTCATTGGAGAGTGAGTTG+AGG 0.614496 2.3:-7886697 None:intergenic
GTTGGAATTGTCTTCGTGGG+AGG 0.620149 2.3:+7887163 MS.gene42830:CDS
TGGTTTGAGTTCTGAGAAGG+CGG 0.623094 2.3:-7886669 None:intergenic
GATTGACATGAGTGGAACTT+GGG 0.631120 2.3:+7887129 MS.gene42830:CDS
ATACAAAATCAGAAATAACA+TGG 0.635906 2.3:-7886742 None:intergenic
ATAGCACTAGAAGTCACAGC+AGG 0.654697 2.3:-7887103 None:intergenic
ATATATGATTCCATTAATCG+TGG 0.660112 2.3:-7886891 None:intergenic
CTCCTAACCATAAAATCCGG+CGG 0.662023 2.3:+7886620 MS.gene42830:CDS
TGACATGAGTGGAACTTGGG+TGG 0.707155 2.3:+7887132 MS.gene42830:CDS
GCTATGAGGATTGACATGAG+TGG 0.723158 2.3:+7887121 MS.gene42830:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAATAGCAAGATGTTTAT+CGG - chr2.3:7886918-7886937 None:intergenic 20.0%
!! ATACAAAATCAGAAATAACA+TGG - chr2.3:7886745-7886764 None:intergenic 20.0%
!!! TAGTTCAAGTTTTTTTTCAT+TGG - chr2.3:7886714-7886733 None:intergenic 20.0%
! ATATATGATTCCATTAATCG+TGG - chr2.3:7886894-7886913 None:intergenic 25.0%
!!! CATCTTGCTATTTATAAAGT+TGG + chr2.3:7886923-7886942 MS.gene42830:CDS 25.0%
TGGAAATGTGAACATTTCAA+CGG + chr2.3:7886856-7886875 MS.gene42830:CDS 30.0%
! GAACTTAACGTGATTAGTTA+TGG + chr2.3:7886833-7886852 MS.gene42830:CDS 30.0%
!! GATGATGGTTTTTCTTTTTC+AGG - chr2.3:7887052-7887071 None:intergenic 30.0%
AGTGTTAACACCACGATTAA+TGG + chr2.3:7886881-7886900 MS.gene42830:CDS 35.0%
GGAAATGTGAACATTTCAAC+GGG + chr2.3:7886857-7886876 MS.gene42830:CDS 35.0%
GTTGAATCTTCAGATGATGA+TGG - chr2.3:7887067-7887086 None:intergenic 35.0%
TGCTAAGAAAATTGTTGCTG+AGG + chr2.3:7886976-7886995 MS.gene42830:CDS 35.0%
TTAGCAGGAGAAAATTCTGA+TGG - chr2.3:7886962-7886981 None:intergenic 35.0%
! ACGTTAAGTTCAACTTTTCC+AGG - chr2.3:7886824-7886843 None:intergenic 35.0%
! CTTAACGTGATTAGTTATGG+TGG + chr2.3:7886836-7886855 MS.gene42830:CDS 35.0%
! TCAGCAACAATTTTCTTAGC+AGG - chr2.3:7886977-7886996 None:intergenic 35.0%
CAGCTCCTAACCATAAAATC+CGG + chr2.3:7886617-7886636 MS.gene42830:CDS 40.0%
GAAAATTGTTGCTGAGGTTC+CGG + chr2.3:7886982-7887001 MS.gene42830:CDS 40.0%
GATTGACATGAGTGGAACTT+GGG + chr2.3:7887129-7887148 MS.gene42830:CDS 40.0%
GTTGTTGGAATTGTCTTCGT+GGG + chr2.3:7887160-7887179 MS.gene42830:CDS 40.0%
TGTTGTTGGAATTGTCTTCG+TGG + chr2.3:7887159-7887178 MS.gene42830:CDS 40.0%
TTCCAGCAAGTGTTCTTACA+GGG - chr2.3:7886796-7886815 None:intergenic 40.0%
TTTCATTGGAGAGTGAGTTG+AGG - chr2.3:7886700-7886719 None:intergenic 40.0%
TTTCCAGCAAGTGTTCTTAC+AGG - chr2.3:7886797-7886816 None:intergenic 40.0%
!!! GGTTTTTCTTTTTCAGGCGT+CGG - chr2.3:7887046-7887065 None:intergenic 40.0%
AACCCTGTAAGAACACTTGC+TGG + chr2.3:7886791-7886810 MS.gene42830:CDS 45.0%
ACCAGCTATTGCTGATGCTA+AGG + chr2.3:7887018-7887037 MS.gene42830:CDS 45.0%
AGCAAGTGTTCTTACAGGGT+TGG - chr2.3:7886792-7886811 None:intergenic 45.0%
ATAGCACTAGAAGTCACAGC+AGG - chr2.3:7887106-7887125 None:intergenic 45.0%
CCTTCTCAGAACTCAAACCA+GGG + chr2.3:7886672-7886691 MS.gene42830:CDS 45.0%
CTCCTAACCATAAAATCCGG+CGG + chr2.3:7886620-7886639 MS.gene42830:CDS 45.0%
CTGTGACTTCTAGTGCTATG+AGG + chr2.3:7887107-7887126 MS.gene42830:CDS 45.0%
GCTATGAGGATTGACATGAG+TGG + chr2.3:7887121-7887140 MS.gene42830:CDS 45.0%
GGATTGACATGAGTGGAACT+TGG + chr2.3:7887128-7887147 MS.gene42830:CDS 45.0%
TGAAGATTCAACAACGTCGC+AGG + chr2.3:7887075-7887094 MS.gene42830:CDS 45.0%
! ACACTTGCTGGAAACAAACC+TGG + chr2.3:7886803-7886822 MS.gene42830:CDS 45.0%
!! TGGTTTGAGTTCTGAGAAGG+CGG - chr2.3:7886672-7886691 None:intergenic 45.0%
GCCTTAGCATCAGCAATAGC+TGG - chr2.3:7887022-7887041 None:intergenic 50.0%
GCCTTCTCAGAACTCAAACC+AGG + chr2.3:7886671-7886690 MS.gene42830:CDS 50.0%
GTTGGAATTGTCTTCGTGGG+AGG + chr2.3:7887163-7887182 MS.gene42830:CDS 50.0%
TGACATGAGTGGAACTTGGG+TGG + chr2.3:7887132-7887151 MS.gene42830:CDS 50.0%
! AGCCGCCGGATTTTATGGTT+AGG - chr2.3:7886625-7886644 None:intergenic 50.0%
! TTAGGAGCTGTGAGTTGAGC+TGG - chr2.3:7886607-7886626 None:intergenic 50.0%
! TTCTGAGAAGGCGGAATCGT+CGG - chr2.3:7886663-7886682 None:intergenic 50.0%
!! ACTTGGGTGGCACTTGTTGT+TGG + chr2.3:7887145-7887164 MS.gene42830:CDS 50.0%
!! CCCTGGTTTGAGTTCTGAGA+AGG - chr2.3:7886675-7886694 None:intergenic 50.0%
GCATCAGCAATAGCTGGTGC+AGG - chr2.3:7887016-7887035 None:intergenic 55.0%
TCTGAGAAGGCGGAATCGTC+GGG - chr2.3:7886662-7886681 None:intergenic 55.0%
TGTTGCTGAGGTTCCGGCTT+TGG + chr2.3:7886988-7887007 MS.gene42830:CDS 55.0%
! CGTCAAGCCGCCGGATTTTA+TGG - chr2.3:7886630-7886649 None:intergenic 55.0%
! GAGAGTGAGTTGAGGAACCC+TGG - chr2.3:7886692-7886711 None:intergenic 55.0%
TGCGAGGATCGTCAAGCCGC+CGG - chr2.3:7886639-7886658 None:intergenic 65.0%
AGGCGGAATCGTCGGGTGCG+AGG - chr2.3:7886655-7886674 None:intergenic 70.0%
GCTGGTGCAGGCGCCAAAGC+CGG - chr2.3:7887004-7887023 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 7886581 7887204 7886581 ID=MS.gene42830
chr2.3 mRNA 7886581 7887204 7886581 ID=MS.gene42830.t1;Parent=MS.gene42830
chr2.3 exon 7886581 7887204 7886581 ID=MS.gene42830.t1.exon1;Parent=MS.gene42830.t1
chr2.3 CDS 7886581 7887204 7886581 ID=cds.MS.gene42830.t1;Parent=MS.gene42830.t1
Gene Sequence

>MS.gene42830

ATGAAAACAACTCAACTAATCAGCCAGCTCAACTCACAGCTCCTAACCATAAAATCCGGCGGCTTGACGATCCTCGCACCCGACGATTCCGCCTTCTCAGAACTCAAACCAGGGTTCCTCAACTCACTCTCCAATGAAAAAAAACTTGAACTACTTCAATTCCATGTTATTTCTGATTTTGTATCTAGCTCAAACTTTGATACTTTAACCAACCCTGTAAGAACACTTGCTGGAAACAAACCTGGAAAAGTTGAACTTAACGTGATTAGTTATGGTGGAAATGTGAACATTTCAACGGGAAGTGTTAACACCACGATTAATGGAATCATATATACCGATAAACATCTTGCTATTTATAAAGTTGGTAAAGTGCTTATTCCATCAGAATTTTCTCCTGCTAAGAAAATTGTTGCTGAGGTTCCGGCTTTGGCGCCTGCACCAGCTATTGCTGATGCTAAGGCGCCGACGCCTGAAAAAGAAAAACCATCATCATCTGAAGATTCAACAACGTCGCAGGTTGTTCCTGCTGTGACTTCTAGTGCTATGAGGATTGACATGAGTGGAACTTGGGTGGCACTTGTTGTTGGAATTGTCTTCGTGGGAGGTTTTTACAACAAAAACTAA
Protein sequence

>MS.gene42830.t1

MKTTQLISQLNSQLLTIKSGGLTILAPDDSAFSELKPGFLNSLSNEKKLELLQFHVISDFVSSSNFDTLTNPVRTLAGNKPGKVELNVISYGGNVNISTGSVNTTINGIIYTDKHLAIYKVGKVLIPSEFSPAKKIVAEVPALAPAPAIADAKAPTPEKEKPSSSEDSTTSQVVPAVTSSAMRIDMSGTWVALVVGIVFVGGFYNKN