AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene07342

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene07342.t1 MTR_5g094740 61.947 113 43 0 8 120 709 821 2.24e-43 150
MS.gene07342.t1 MTR_1g019580 54.054 111 51 0 8 118 19 129 3.10e-40 130
MS.gene07342.t1 MTR_1g105780 54.054 111 51 0 8 118 162 272 1.24e-39 133
MS.gene07342.t1 MTR_1g105765 54.054 111 51 0 8 118 162 272 1.31e-39 133
MS.gene07342.t1 MTR_3g452180 49.573 117 59 0 2 118 71 187 1.31e-36 123
MS.gene07342.t1 MTR_7g110090 49.573 117 59 0 2 118 155 271 3.03e-36 124
MS.gene07342.t1 MTR_4g032560 48.276 116 60 0 3 118 185 300 1.43e-35 124
MS.gene07342.t1 MTR_4g032580 48.276 116 60 0 3 118 185 300 1.89e-35 123
MS.gene07342.t1 MTR_1g069260 44.961 129 59 1 3 119 161 289 7.07e-33 116
MS.gene07342.t1 MTR_4g062370 61.290 93 36 0 3 95 160 252 2.07e-32 119
MS.gene07342.t1 MTR_8g042540 53.488 86 40 0 35 120 3 88 4.41e-29 101
MS.gene07342.t1 MTR_1g047540 44.915 118 65 0 2 119 140 257 8.18e-29 108
MS.gene07342.t1 MTR_8g042540 53.571 84 39 0 37 120 17 100 2.13e-28 99.8
MS.gene07342.t1 MTR_1g087870 41.284 109 64 0 9 117 115 223 2.14e-28 104
MS.gene07342.t1 MTR_4g121040 45.133 113 62 0 2 114 59 171 1.46e-27 100
MS.gene07342.t1 MTR_0152s0060 47.191 89 47 0 24 112 228 316 6.37e-23 92.0
MS.gene07342.t1 MTR_1g084880 40.404 99 59 0 20 118 178 276 1.78e-21 86.7
MS.gene07342.t1 MTR_3g048970 40.404 99 59 0 20 118 178 276 1.80e-21 86.7
MS.gene07342.t1 MTR_3g070250 36.792 106 67 0 13 118 176 281 6.56e-20 82.4
MS.gene07342.t1 MTR_3g085990 42.342 111 45 3 4 114 140 231 2.24e-18 77.8
MS.gene07342.t1 MTR_4g057880 43.662 71 40 0 48 118 2 72 8.75e-18 72.0
MS.gene07342.t1 MTR_2g016390 38.710 93 57 0 11 103 602 694 5.27e-17 75.9
MS.gene07342.t1 MTR_4g081330 50.000 62 31 0 38 99 1085 1146 1.01e-14 69.3
MS.gene07342.t1 MTR_2g100360 37.234 94 58 1 4 97 163 255 1.52e-14 67.8
MS.gene07342.t1 MTR_6g016445 50.000 60 30 0 42 101 13 72 2.69e-13 61.6
MS.gene07342.t1 MTR_1g037600 39.326 89 53 1 13 100 71 159 5.65e-13 63.5
MS.gene07342.t1 MTR_4g117740 49.123 57 29 0 6 62 141 197 6.17e-13 62.8
MS.gene07342.t1 MTR_2g072800 57.447 47 20 0 59 105 222 268 5.91e-12 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTTTGTTGAGATCGATTC+TGG 0.241191 1.2:+65119728 MS.gene07342:CDS
TTGATGAATGTGGTTGTATA+TGG 0.268575 1.2:+65119907 MS.gene07342:CDS
ATGCAGGATTTGGCTCATAT+TGG 0.290632 1.2:+65119837 MS.gene07342:intron
TGAGATCGATTCTGGATTCT+TGG 0.324173 1.2:+65119736 MS.gene07342:CDS
TGCAGGATTTGGCTCATATT+GGG 0.361232 1.2:+65119838 MS.gene07342:intron
GGTCAAGGCTAGAAGGTTAA+AGG 0.364042 1.2:+65119998 MS.gene07342:CDS
TTCTCATTGACACCGATATA+TGG 0.377396 1.2:-65120047 None:intergenic
GACGGTGACAGTGTCGTTAT+CGG 0.398058 1.2:+65120020 MS.gene07342:CDS
TGCACAAATGGCACAGGAAA+AGG 0.399613 1.2:-65119665 None:intergenic
GTTATCGGTGCTCCATATAT+CGG 0.401878 1.2:+65120035 MS.gene07342:CDS
CCTCATGCTCACTTTAAGAT+TGG 0.409855 1.2:+65119957 MS.gene07342:CDS
AGATTGGCGGTGGCTGGAAC+AGG 0.416190 1.2:+65119973 MS.gene07342:CDS
ACTTTAAGATTGGCGGTGGC+TGG 0.418939 1.2:+65119967 MS.gene07342:CDS
TGAAACTGAGAATCTGAGTT+TGG 0.418987 1.2:+65119884 MS.gene07342:CDS
TTAAATTCATTATGCACAAA+TGG 0.431684 1.2:-65119677 None:intergenic
CATGAGGGCGTGTAACAAAC+TGG 0.441451 1.2:-65119941 None:intergenic
ACAGGATGGTCAAGGCTAGA+AGG 0.443921 1.2:+65119991 MS.gene07342:CDS
CATGCTCACTTTAAGATTGG+CGG 0.482279 1.2:+65119960 MS.gene07342:CDS
CTGAGTTTGGTTGATGAATG+TGG 0.483514 1.2:+65119897 MS.gene07342:CDS
TGATGAATGTGGTTGTATAT+GGG 0.484155 1.2:+65119908 MS.gene07342:CDS
GCTCACTTTAAGATTGGCGG+TGG 0.568885 1.2:+65119963 MS.gene07342:CDS
CCAATCTTAAAGTGAGCATG+AGG 0.578221 1.2:-65119957 None:intergenic
TCATTATGCACAAATGGCAC+AGG 0.601819 1.2:-65119671 None:intergenic
TGGCGGTGGCTGGAACAGGA+TGG 0.649155 1.2:+65119977 MS.gene07342:CDS
TGGCTGGAACAGGATGGTCA+AGG 0.676417 1.2:+65119983 MS.gene07342:CDS
AGGGCGTGTAACAAACTGGA+GGG 0.676724 1.2:-65119937 None:intergenic
CAATCTTAAAGTGAGCATGA+GGG 0.680650 1.2:-65119956 None:intergenic
AAGGCTAGAAGGTTAAAGGA+CGG 0.693112 1.2:+65120002 MS.gene07342:CDS
GAGGGCGTGTAACAAACTGG+AGG 0.699235 1.2:-65119938 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATTCATTATGCACAAA+TGG - chr1.2:65119680-65119699 None:intergenic 20.0%
!!! TGTTAAAAAAGATATTGACT+TGG + chr1.2:65119770-65119789 MS.gene07342:intron 20.0%
!!! ATATGATGTTTTGATTATGC+AGG + chr1.2:65119821-65119840 MS.gene07342:intron 25.0%
TGATGAATGTGGTTGTATAT+GGG + chr1.2:65119908-65119927 MS.gene07342:CDS 30.0%
TTGATGAATGTGGTTGTATA+TGG + chr1.2:65119907-65119926 MS.gene07342:CDS 30.0%
!!! TGTTTTGATTATGCAGGATT+TGG + chr1.2:65119827-65119846 MS.gene07342:intron 30.0%
CAATCTTAAAGTGAGCATGA+GGG - chr1.2:65119959-65119978 None:intergenic 35.0%
TGAAACTGAGAATCTGAGTT+TGG + chr1.2:65119884-65119903 MS.gene07342:CDS 35.0%
TTCTCATTGACACCGATATA+TGG - chr1.2:65120050-65120069 None:intergenic 35.0%
AAGGCTAGAAGGTTAAAGGA+CGG + chr1.2:65120002-65120021 MS.gene07342:CDS 40.0%
CCAATCTTAAAGTGAGCATG+AGG - chr1.2:65119960-65119979 None:intergenic 40.0%
TCATTATGCACAAATGGCAC+AGG - chr1.2:65119674-65119693 None:intergenic 40.0%
! ATGCAGGATTTGGCTCATAT+TGG + chr1.2:65119837-65119856 MS.gene07342:intron 40.0%
! GACTTTGTTGAGATCGATTC+TGG + chr1.2:65119728-65119747 MS.gene07342:CDS 40.0%
! GTTATCGGTGCTCCATATAT+CGG + chr1.2:65120035-65120054 MS.gene07342:CDS 40.0%
! TGAGATCGATTCTGGATTCT+TGG + chr1.2:65119736-65119755 MS.gene07342:CDS 40.0%
! TGCAGGATTTGGCTCATATT+GGG + chr1.2:65119838-65119857 MS.gene07342:intron 40.0%
!! CATGCTCACTTTAAGATTGG+CGG + chr1.2:65119960-65119979 MS.gene07342:CDS 40.0%
!! CCTCATGCTCACTTTAAGAT+TGG + chr1.2:65119957-65119976 MS.gene07342:CDS 40.0%
!! CTGAGTTTGGTTGATGAATG+TGG + chr1.2:65119897-65119916 MS.gene07342:CDS 40.0%
GGTCAAGGCTAGAAGGTTAA+AGG + chr1.2:65119998-65120017 MS.gene07342:CDS 45.0%
TGCACAAATGGCACAGGAAA+AGG - chr1.2:65119668-65119687 None:intergenic 45.0%
ACAGGATGGTCAAGGCTAGA+AGG + chr1.2:65119991-65120010 MS.gene07342:CDS 50.0%
AGGGCGTGTAACAAACTGGA+GGG - chr1.2:65119940-65119959 None:intergenic 50.0%
! CATGAGGGCGTGTAACAAAC+TGG - chr1.2:65119944-65119963 None:intergenic 50.0%
! GACGGTGACAGTGTCGTTAT+CGG + chr1.2:65120020-65120039 MS.gene07342:CDS 50.0%
!! ACTTTAAGATTGGCGGTGGC+TGG + chr1.2:65119967-65119986 MS.gene07342:CDS 50.0%
!! GCTCACTTTAAGATTGGCGG+TGG + chr1.2:65119963-65119982 MS.gene07342:CDS 50.0%
TGGCTGGAACAGGATGGTCA+AGG + chr1.2:65119983-65120002 MS.gene07342:CDS 55.0%
! GAGGGCGTGTAACAAACTGG+AGG - chr1.2:65119941-65119960 None:intergenic 55.0%
AGATTGGCGGTGGCTGGAAC+AGG + chr1.2:65119973-65119992 MS.gene07342:CDS 60.0%
TGGCGGTGGCTGGAACAGGA+TGG + chr1.2:65119977-65119996 MS.gene07342:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 65119650 65120097 65119650 ID=MS.gene07342
chr1.2 mRNA 65119650 65120097 65119650 ID=MS.gene07342.t1;Parent=MS.gene07342
chr1.2 exon 65119650 65119757 65119650 ID=MS.gene07342.t1.exon1;Parent=MS.gene07342.t1
chr1.2 CDS 65119650 65119757 65119650 ID=cds.MS.gene07342.t1;Parent=MS.gene07342.t1
chr1.2 exon 65119843 65120097 65119843 ID=MS.gene07342.t1.exon2;Parent=MS.gene07342.t1
chr1.2 CDS 65119843 65120097 65119843 ID=cds.MS.gene07342.t1;Parent=MS.gene07342.t1
Gene Sequence

>MS.gene07342

ATGCATTTGTTCAATCCTTTTCCTGTGCCATTTGTGCATAATGAATTTAACTTTCAACTGACATATGAGAAAAAGCTTGACTTTGTTGAGATCGATTCTGGATTCTTGGTATGTTTTATGTGTTAAAAAAGATATTGACTTGGTGTTGCAATTGATTCGACTTCAACTAATATATGATGTTTTGATTATGCAGGATTTGGCTCATATTGGGTTCTGTCAGCTTGCTTTGAACACTGAAACTGAGAATCTGAGTTTGGTTGATGAATGTGGTTGTATATGGGATTGCACCCTCCAGTTTGTTACACGCCCTCATGCTCACTTTAAGATTGGCGGTGGCTGGAACAGGATGGTCAAGGCTAGAAGGTTAAAGGACGGTGACAGTGTCGTTATCGGTGCTCCATATATCGGTGTCAATGAGAAGCTCTTTTTTTTTGTTGTTTGTTATTAG
Protein sequence

>MS.gene07342.t1

MHLFNPFPVPFVHNEFNFQLTYEKKLDFVEIDSGFLDLAHIGFCQLALNTETENLSLVDECGCIWDCTLQFVTRPHAHFKIGGGWNRMVKARRLKDGDSVVIGAPYIGVNEKLFFFVVCY