AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015160

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015160.t1 MTR_5g094680 70.183 218 56 2 1 209 1 218 1.33e-106 306
MS.gene015160.t1 MTR_7g093310 56.774 155 35 3 62 209 6 135 1.01e-48 156
MS.gene015160.t1 MTR_7g092960 65.714 105 27 2 105 209 1 96 2.22e-42 139
MS.gene015160.t1 MTR_5g006240 31.963 219 130 5 7 209 8 223 9.21e-30 110
MS.gene015160.t1 MTR_8g085550 34.932 146 87 3 73 210 3 148 3.96e-18 78.2
MS.gene015160.t1 MTR_8g085520 35.664 143 85 3 74 210 7 148 9.85e-18 77.4
MS.gene015160.t1 MTR_5g037840 34.127 126 63 2 102 209 5 128 1.04e-16 73.9
MS.gene015160.t1 MTR_1g029860 30.827 133 75 4 82 210 57 176 1.24e-16 74.7
MS.gene015160.t1 MTR_5g037810 34.127 126 63 2 102 209 5 128 1.71e-16 73.2
MS.gene015160.t1 MTR_1g029910 28.774 212 109 8 11 210 11 192 7.28e-13 65.1
MS.gene015160.t1 MTR_8g085530 51.923 52 25 0 159 210 245 296 2.57e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 41 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCCAAAAGATTATCCTTT+TGG 0.238623 5.1:+9426790 MS.gene015160:CDS
TTGCCAAAAGGATAATCTTT+TGG 0.239955 5.1:-9426793 None:intergenic
GGTCGTAATGGAAATTAATA+TGG 0.278843 5.1:-9426822 None:intergenic
TTTGATATGTGAGAAGAAAT+AGG 0.329663 5.1:-9426988 None:intergenic
ACGACGAAGATCAGAAAATC+TGG 0.344881 5.1:+9427061 MS.gene015160:CDS
CTTGTGATATCTTATTAGAT+AGG 0.399100 5.1:+9426926 MS.gene015160:CDS
GGACCGGTGTGCAATTTGTT+TGG 0.399227 5.1:+9427206 MS.gene015160:CDS
AAGGATTGAGTTTGAGGCAT+TGG 0.407997 5.1:-9426866 None:intergenic
TTGTCGTGGATAGGTTGAAA+AGG 0.455255 5.1:+9427151 MS.gene015160:CDS
GAAAATTAACAAGGTCGTAA+TGG 0.464601 5.1:-9426834 None:intergenic
CTCAGATTGGTCAACATGCT+AGG 0.500915 5.1:+9427022 MS.gene015160:CDS
TAGGTTGAAAAGGGTTGGAA+TGG 0.524218 5.1:+9427161 MS.gene015160:CDS
GTGGATAGGTTGAAAAGGGT+TGG 0.528714 5.1:+9427156 MS.gene015160:CDS
AAAGAAATACTGCCTCAGAT+TGG 0.530797 5.1:+9427009 MS.gene015160:CDS
ACAGTCAAGGATTGAGTTTG+AGG 0.531545 5.1:-9426872 None:intergenic
TGTCGTGGATAGGTTGAAAA+GGG 0.534622 5.1:+9427152 MS.gene015160:CDS
TCAACCTATCCACGACAAGT+AGG 0.536681 5.1:-9427146 None:intergenic
CAACCTATCCACGACAAGTA+GGG 0.541054 5.1:-9427145 None:intergenic
ATATGGAAATAGTTGCCAAA+AGG 0.543713 5.1:-9426805 None:intergenic
TGTTTGGAAGAGCTCTTCGA+TGG 0.552068 5.1:+9427222 MS.gene015160:CDS
GTTTGAGGCATTGGAATGCA+AGG 0.553544 5.1:-9426857 None:intergenic
GTGAGAAGAAATAGGCAGAG+AGG 0.554494 5.1:-9426980 None:intergenic
TCATTCATCTCGTTACTCTA+CGG 0.565153 5.1:+9427185 MS.gene015160:CDS
CGACGAAGATCAGAAAATCT+GGG 0.572391 5.1:+9427062 MS.gene015160:CDS
TTATAGTAGTCGTACAGTCA+AGG 0.581687 5.1:-9426885 None:intergenic
AGGCCCTACTTGTCGTGGAT+AGG 0.585391 5.1:+9427142 MS.gene015160:CDS
TCAGATTGGTCAACATGCTA+GGG 0.585909 5.1:+9427023 MS.gene015160:CDS
TGGTCAACATGCTAGGGAGA+TGG 0.591832 5.1:+9427029 MS.gene015160:CDS
CTATCTAATAAGATATCACA+AGG 0.605163 5.1:-9426925 None:intergenic
GCGACACAATGGACACGAGA+GGG 0.606474 5.1:-9427340 None:intergenic
TGAAGATAATGATGCTGTGA+AGG 0.607686 5.1:+9427122 MS.gene015160:CDS
TTTGAGGCATTGGAATGCAA+GGG 0.617194 5.1:-9426856 None:intergenic
TGAAGCTTGATGTCAATACA+TGG 0.634786 5.1:+9427094 MS.gene015160:CDS
CATCTCGTTACTCTACGGAC+CGG 0.636560 5.1:+9427190 MS.gene015160:CDS
CTAGCATGTTGACCAATCTG+AGG 0.646175 5.1:-9427021 None:intergenic
TGCGACACAATGGACACGAG+AGG 0.660737 5.1:-9427341 None:intergenic
ACGAGAGGGATGATTGACGA+TGG 0.663362 5.1:-9427326 None:intergenic
TGTGAAGGCCCTACTTGTCG+TGG 0.681329 5.1:+9427137 MS.gene015160:CDS
GATATCACAAGGAATCAACA+AGG 0.723417 5.1:-9426914 None:intergenic
AATGCAAGGGAAAATTAACA+AGG 0.729882 5.1:-9426843 None:intergenic
CTTCCAAACAAATTGCACAC+CGG 0.732526 5.1:-9427209 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAAGAGTGTATTTTTCAA+TGG + chr5.1:9427289-9427308 MS.gene015160:CDS 20.0%
! ATGAAAAACATGCAAACAAT+TGG - chr5.1:9427271-9427290 None:intergenic 25.0%
! CTATCTAATAAGATATCACA+AGG - chr5.1:9426928-9426947 None:intergenic 25.0%
! CTTGTGATATCTTATTAGAT+AGG + chr5.1:9426926-9426945 MS.gene015160:CDS 25.0%
! TTTGATATGTGAGAAGAAAT+AGG - chr5.1:9426991-9427010 None:intergenic 25.0%
!!! ATAATCTTTTGGGATTGTAA+AGG - chr5.1:9426785-9426804 None:intergenic 25.0%
AATGCAAGGGAAAATTAACA+AGG - chr5.1:9426846-9426865 None:intergenic 30.0%
ATATGGAAATAGTTGCCAAA+AGG - chr5.1:9426808-9426827 None:intergenic 30.0%
GAAAATTAACAAGGTCGTAA+TGG - chr5.1:9426837-9426856 None:intergenic 30.0%
! ATCCCAAAAGATTATCCTTT+TGG + chr5.1:9426790-9426809 MS.gene015160:CDS 30.0%
! GGTCGTAATGGAAATTAATA+TGG - chr5.1:9426825-9426844 None:intergenic 30.0%
! TGCCAAAAGGATAATCTTTT+GGG - chr5.1:9426795-9426814 None:intergenic 30.0%
! TTGCCAAAAGGATAATCTTT+TGG - chr5.1:9426796-9426815 None:intergenic 30.0%
AAAGAAATACTGCCTCAGAT+TGG + chr5.1:9427009-9427028 MS.gene015160:CDS 35.0%
GATATCACAAGGAATCAACA+AGG - chr5.1:9426917-9426936 None:intergenic 35.0%
TCATTCATCTCGTTACTCTA+CGG + chr5.1:9427185-9427204 MS.gene015160:CDS 35.0%
TGAAGATAATGATGCTGTGA+AGG + chr5.1:9427122-9427141 MS.gene015160:CDS 35.0%
TGAAGCTTGATGTCAATACA+TGG + chr5.1:9427094-9427113 MS.gene015160:CDS 35.0%
TTATAGTAGTCGTACAGTCA+AGG - chr5.1:9426888-9426907 None:intergenic 35.0%
!!! TCTTTTGGGATTGTAAAGGT+TGG - chr5.1:9426781-9426800 None:intergenic 35.0%
ACAGTCAAGGATTGAGTTTG+AGG - chr5.1:9426875-9426894 None:intergenic 40.0%
ACGACGAAGATCAGAAAATC+TGG + chr5.1:9427061-9427080 MS.gene015160:CDS 40.0%
CGACGAAGATCAGAAAATCT+GGG + chr5.1:9427062-9427081 MS.gene015160:CDS 40.0%
CTTCCAAACAAATTGCACAC+CGG - chr5.1:9427212-9427231 None:intergenic 40.0%
! AAGGATTGAGTTTGAGGCAT+TGG - chr5.1:9426869-9426888 None:intergenic 40.0%
! TAGGTTGAAAAGGGTTGGAA+TGG + chr5.1:9427161-9427180 MS.gene015160:CDS 40.0%
! TCAGATTGGTCAACATGCTA+GGG + chr5.1:9427023-9427042 MS.gene015160:CDS 40.0%
! TCATCAGTTTTGCGACACAA+TGG - chr5.1:9427354-9427373 None:intergenic 40.0%
! TGTCGTGGATAGGTTGAAAA+GGG + chr5.1:9427152-9427171 MS.gene015160:CDS 40.0%
! TTGTCGTGGATAGGTTGAAA+AGG + chr5.1:9427151-9427170 MS.gene015160:CDS 40.0%
!! TTTGAGGCATTGGAATGCAA+GGG - chr5.1:9426859-9426878 None:intergenic 40.0%
CAACCTATCCACGACAAGTA+GGG - chr5.1:9427148-9427167 None:intergenic 45.0%
CTAGCATGTTGACCAATCTG+AGG - chr5.1:9427024-9427043 None:intergenic 45.0%
GTGAGAAGAAATAGGCAGAG+AGG - chr5.1:9426983-9427002 None:intergenic 45.0%
TCAACCTATCCACGACAAGT+AGG - chr5.1:9427149-9427168 None:intergenic 45.0%
TGTTTGGAAGAGCTCTTCGA+TGG + chr5.1:9427222-9427241 MS.gene015160:CDS 45.0%
! CTCAGATTGGTCAACATGCT+AGG + chr5.1:9427022-9427041 MS.gene015160:CDS 45.0%
! GTGGATAGGTTGAAAAGGGT+TGG + chr5.1:9427156-9427175 MS.gene015160:CDS 45.0%
!! GTTTGAGGCATTGGAATGCA+AGG - chr5.1:9426860-9426879 None:intergenic 45.0%
ACGAGAGGGATGATTGACGA+TGG - chr5.1:9427329-9427348 None:intergenic 50.0%
CATCTCGTTACTCTACGGAC+CGG + chr5.1:9427190-9427209 MS.gene015160:CDS 50.0%
TGGTCAACATGCTAGGGAGA+TGG + chr5.1:9427029-9427048 MS.gene015160:CDS 50.0%
! GGACCGGTGTGCAATTTGTT+TGG + chr5.1:9427206-9427225 MS.gene015160:CDS 50.0%
AGGCCCTACTTGTCGTGGAT+AGG + chr5.1:9427142-9427161 MS.gene015160:CDS 55.0%
GCGACACAATGGACACGAGA+GGG - chr5.1:9427343-9427362 None:intergenic 55.0%
TGCGACACAATGGACACGAG+AGG - chr5.1:9427344-9427363 None:intergenic 55.0%
TGTGAAGGCCCTACTTGTCG+TGG + chr5.1:9427137-9427156 MS.gene015160:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 9426736 9427386 9426736 ID=MS.gene015160
chr5.1 mRNA 9426736 9427386 9426736 ID=MS.gene015160.t1;Parent=MS.gene015160
chr5.1 exon 9426736 9427386 9426736 ID=MS.gene015160.t1.exon1;Parent=MS.gene015160.t1
chr5.1 CDS 9426736 9427386 9426736 ID=cds.MS.gene015160.t1;Parent=MS.gene015160.t1
Gene Sequence

>MS.gene015160

ATGAATTATAATTTTCGCTTGAAAATAAGTTCAATCGAAGAACCAACCTTTACAATCCCAAAAGATTATCCTTTTGGCAACTATTTCCATATTAATTTCCATTACGACCTTGTTAATTTTCCCTTGCATTCCAATGCCTCAAACTCAATCCTTGACTGTACGACTACTATAAATCGAACCTTGTTGATTCCTTGTGATATCTTATTAGATAGGAAAGACAACATCTTATATGAGTACTATATTTCCTCTCTGCCTATTTCTTCTCACATATCAAAAGAAATACTGCCTCAGATTGGTCAACATGCTAGGGAGATGGTCGCTAATGACGACGAAGATCAGAAAATCTGGGAGATAGACGTGAAGCTTGATGTCAATACATGGTATATTGAAGATAATGATGCTGTGAAGGCCCTACTTGTCGTGGATAGGTTGAAAAGGGTTGGAATGGATCATTCATCTCGTTACTCTACGGACCGGTGTGCAATTTGTTTGGAAGAGCTCTTCGATGGATCAAAGTCAGAACATGTTATGACCAATTGTTTGCATGTTTTTCATAAAGAGTGTATTTTTCAATGGCTCAAAAGATGCTTCCATCGTCAATCATCCCTCTCGTGTCCATTGTGTCGCAAAACTGATGAAGCTTTTGAATGA
Protein sequence

>MS.gene015160.t1

MNYNFRLKISSIEEPTFTIPKDYPFGNYFHINFHYDLVNFPLHSNASNSILDCTTTINRTLLIPCDILLDRKDNILYEYYISSLPISSHISKEILPQIGQHAREMVANDDEDQKIWEIDVKLDVNTWYIEDNDAVKALLVVDRLKRVGMDHSSRYSTDRCAICLEELFDGSKSEHVMTNCLHVFHKECIFQWLKRCFHRQSSLSCPLCRKTDEAFE