AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1342220

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342220 MtrunA17_Chr8g0384451 95.455 220 4 3 1 220 1 214 2.72e-154 426
Msa1342220 MtrunA17_Chr3g0102351 76.364 110 26 0 32 141 13 122 1.62e-60 188
Msa1342220 MtrunA17_Chr5g0446491 75.221 113 28 0 28 140 5 117 9.72e-60 186
Msa1342220 MtrunA17_Chr2g0290491 78.704 108 21 1 45 152 16 121 4.55e-59 183
Msa1342220 MtrunA17_Chr8g0382931 73.913 115 30 0 40 154 22 136 3.57e-58 182
Msa1342220 MtrunA17_Chr7g0263601 70.270 111 32 1 30 139 9 119 5.13e-57 178
Msa1342220 MtrunA17_Chr4g0076321 77.660 94 21 0 47 140 20 113 9.58e-54 169
Msa1342220 MtrunA17_Chr1g0185911 72.917 96 26 0 40 135 23 118 5.95e-53 168
Msa1342220 MtrunA17_Chr1g0195851 66.964 112 37 0 29 140 19 130 1.19e-52 168
Msa1342220 MtrunA17_Chr2g0296321 66.990 103 34 0 45 147 65 167 3.53e-49 161
Msa1342220 MtrunA17_Chr4g0067091 60.345 116 46 0 28 143 4 119 6.98e-49 159
Msa1342220 MtrunA17_Chr4g0076381 58.036 112 47 0 32 143 44 155 2.79e-47 155
Msa1342220 MtrunA17_Chr1g0165041 61.616 99 38 0 45 143 5 103 1.23e-44 147
Msa1342220 MtrunA17_Chr1g0191981 60.606 99 39 0 44 142 2 100 4.00e-40 134
Msa1342220 MtrunA17_Chr1g0159271 52.500 80 38 0 60 139 1 80 5.93e-24 92.0
Msa1342220 MtrunA17_Chr5g0446601 41.053 95 56 0 40 134 18 112 1.11e-19 83.2
Msa1342220 MtrunA17_Chr1g0158951 50.725 69 34 0 76 144 19 87 1.00e-18 78.6
Msa1342220 MtrunA17_Chr1g0159291 39.474 76 46 0 51 126 7 82 4.39e-16 70.9
Msa1342220 MtrunA17_Chr2g0307551 26.241 141 95 2 43 177 8 145 1.05e-15 71.6
Msa1342220 MtrunA17_Chr4g0062271 32.051 78 53 0 47 124 12 89 3.69e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342220 AT2G13570.1 67.391 184 47 6 45 218 35 215 3.66e-72 219
Msa1342220 AT4G14540.1 72.951 122 32 1 27 147 1 122 3.07e-64 196
Msa1342220 AT5G47640.1 73.276 116 30 1 43 158 24 138 8.08e-60 186
Msa1342220 AT3G53340.5 56.081 148 56 2 45 185 28 173 3.22e-55 174
Msa1342220 AT3G53340.1 56.081 148 56 2 45 185 28 173 3.22e-55 174
Msa1342220 AT2G37060.2 78.947 95 20 0 45 139 29 123 3.64e-55 174
Msa1342220 AT2G37060.3 78.947 95 20 0 45 139 29 123 3.64e-55 174
Msa1342220 AT2G37060.1 78.947 95 20 0 45 139 29 123 3.64e-55 174
Msa1342220 AT2G38880.3 68.571 105 33 0 35 139 10 114 2.09e-54 171
Msa1342220 AT2G38880.2 68.571 105 33 0 35 139 10 114 2.59e-54 171
Msa1342220 AT2G38880.1 68.571 105 33 0 35 139 10 114 2.59e-54 171
Msa1342220 AT2G38880.5 68.571 105 33 0 35 139 10 114 2.59e-54 171
Msa1342220 AT3G53340.4 77.174 92 21 0 45 136 28 119 4.64e-53 167
Msa1342220 AT3G53340.3 77.419 93 21 0 45 137 28 120 1.32e-52 167
Msa1342220 AT3G53340.2 77.419 93 21 0 45 137 28 120 1.32e-52 167
Msa1342220 AT2G38880.4 69.307 101 31 0 36 136 11 111 1.71e-52 165
Msa1342220 AT2G38880.7 69.307 101 31 0 35 135 10 110 3.21e-52 165
Msa1342220 AT2G38880.11 69.307 101 31 0 36 136 11 111 5.85e-52 166
Msa1342220 AT2G38880.8 69.307 101 31 0 36 136 11 111 5.85e-52 166
Msa1342220 AT2G38880.9 69.307 101 31 0 36 136 11 111 1.78e-51 164
Msa1342220 AT2G38880.10 69.307 101 31 0 36 136 11 111 1.78e-51 164
Msa1342220 AT2G38880.6 69.307 101 31 0 36 136 11 111 1.78e-51 164
Msa1342220 AT2G47810.1 74.490 98 25 0 45 142 50 147 8.01e-51 162
Msa1342220 AT5G47670.2 57.143 112 48 0 29 140 12 123 4.34e-47 154
Msa1342220 AT5G47670.1 57.143 112 48 0 29 140 41 152 9.09e-47 154
Msa1342220 AT5G47670.3 57.143 112 48 0 29 140 41 152 9.09e-47 154
Msa1342220 AT1G09030.1 61.458 96 37 0 46 141 3 98 6.28e-42 139
Msa1342220 AT1G21970.1 60.417 96 38 0 45 140 58 153 1.56e-41 141
Msa1342220 AT5G23090.5 28.758 153 97 4 47 194 12 157 1.53e-14 68.9
Msa1342220 AT5G23090.2 28.758 153 97 4 47 194 12 157 1.53e-14 68.9
Msa1342220 AT5G23090.1 28.758 153 97 4 47 194 12 157 1.53e-14 68.9
Msa1342220 AT5G23090.4 34.615 78 51 0 47 124 12 89 2.43e-14 68.6
Msa1342220 AT5G08190.1 33.333 81 54 0 46 126 11 91 2.78e-14 68.6
Msa1342220 AT5G08190.2 33.333 81 54 0 46 126 11 91 3.12e-14 68.2

Find 22 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAATGGTGATGATATTATT+TGG 0.131471 tig0005289:-67370 Msa1342220:CDS
TGTTCAGATCTTTGTTGTTT+TGG 0.178571 tig0005289:+67254 None:intergenic
CAATGGTGATGATATTATTT+GGG 0.366036 tig0005289:-67369 Msa1342220:CDS
TGAATGGAATTTGGAGAGAA+AGG 0.382069 tig0005289:+67098 None:intergenic
ATTCTACCAACATTTGCTAT+AGG 0.386839 tig0005289:+67530 None:intergenic
GGTTGATCAGTAGTCATATA+AGG 0.405322 tig0005289:+67131 None:intergenic
CATAGTAATAATTTGCCAAA+TGG 0.423743 tig0005289:-67668 Msa1342220:CDS
GGAGAGAAAGGAAGTGGAAA+TGG 0.431632 tig0005289:+67110 None:intergenic
GTTAGGCTTTGAAGATTATG+TGG 0.475398 tig0005289:-67336 Msa1342220:CDS
ACATTTATCCGATGCTTCCC+CGG 0.490805 tig0005289:+67415 None:intergenic
ATTTGGGCTATTACAACGTT+AGG 0.507634 tig0005289:-67353 Msa1342220:CDS
CAAGATCAGATTGATTCCAT+AGG 0.513351 tig0005289:-67059 Msa1342220:CDS
GAATTTGGAGAGAAAGGAAG+TGG 0.527073 tig0005289:+67104 None:intergenic
CTATGACTCTCATCATCCAT+TGG 0.535551 tig0005289:+67686 None:intergenic
TCATTCATACCAATGCCCTA+TGG 0.542150 tig0005289:+67043 None:intergenic
AGATTGATTCCATAGGGCAT+TGG 0.544180 tig0005289:-67052 Msa1342220:CDS
TTTCTTCCTATAGCAAATGT+TGG 0.557368 tig0005289:-67536 Msa1342220:CDS
AAGATCAGATTGATTCCATA+GGG 0.573421 tig0005289:-67058 Msa1342220:CDS
GACAGTTCAAGAATGTGTGT+CGG 0.617021 tig0005289:-67456 Msa1342220:CDS
ATGGAATCAATCTGATCTTG+CGG 0.627874 tig0005289:+67062 None:intergenic
AACAACAAAGATCTGAACAA+AGG 0.635439 tig0005289:-67250 Msa1342220:CDS
TGATCAGTAGTCATATAAGG+AGG 0.682713 tig0005289:+67134 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTAAACAATGACTTTCA+GGG + tig0005289:67099-67118 None:intergenic 20.0%
!!! TTTTGAAGGTAACATTTTAA+TGG + tig0005289:67418-67437 None:intergenic 20.0%
!!! CAATATCTCTATATTTTTGA+AGG + tig0005289:67432-67451 None:intergenic 20.0%
!! CAAAAATATAGAGATATTGA+AGG - tig0005289:67433-67452 Msa1342220:CDS 20.0%
!!! AATTGTTTTTGAATGGAATT+TGG + tig0005289:67640-67659 None:intergenic 20.0%
!! CATAGTAATAATTTGCCAAA+TGG - tig0005289:67058-67077 Msa1342220:CDS 25.0%
!! GTTTTTAAACAATGACTTTC+AGG + tig0005289:67100-67119 None:intergenic 25.0%
! AAAAAAGTTATTCCTGCAAA+TGG - tig0005289:67223-67242 Msa1342220:CDS 25.0%
! GAAAAAAGAAAGACAATCAA+TGG - tig0005289:67340-67359 Msa1342220:CDS 25.0%
!! TCAATGGTGATGATATTATT+TGG - tig0005289:67356-67375 Msa1342220:CDS 25.0%
!! CAATGGTGATGATATTATTT+GGG - tig0005289:67357-67376 Msa1342220:CDS 25.0%
! TTTTCTGTGTTGAATCCATT+TGG + tig0005289:67076-67095 None:intergenic 30.0%
TTTCTTCCTATAGCAAATGT+TGG - tig0005289:67190-67209 Msa1342220:CDS 30.0%
!! ATTCTACCAACATTTGCTAT+AGG + tig0005289:67199-67218 None:intergenic 30.0%
!! TTTGAGATTTTTCCATTTGC+AGG + tig0005289:67238-67257 None:intergenic 30.0%
TGCAAATGGAAAAATCTCAA+AGG - tig0005289:67237-67256 Msa1342220:CDS 30.0%
!!! TGTTCAGATCTTTGTTGTTT+TGG + tig0005289:67475-67494 None:intergenic 30.0%
AACAACAAAGATCTGAACAA+AGG - tig0005289:67476-67495 Msa1342220:CDS 30.0%
! AAGATCAGATTGATTCCATA+GGG - tig0005289:67668-67687 Msa1342220:CDS 30.0%
!! GAGTTCATAAGTTTTGTCAC+CGG - tig0005289:67292-67311 Msa1342220:CDS 35.0%
!! AGTTCATAAGTTTTGTCACC+GGG - tig0005289:67293-67312 Msa1342220:CDS 35.0%
ATTTGGGCTATTACAACGTT+AGG - tig0005289:67373-67392 Msa1342220:CDS 35.0%
!! GTTAGGCTTTGAAGATTATG+TGG - tig0005289:67390-67409 Msa1342220:CDS 35.0%
TGATCAGTAGTCATATAAGG+AGG + tig0005289:67595-67614 None:intergenic 35.0%
GGTTGATCAGTAGTCATATA+AGG + tig0005289:67598-67617 None:intergenic 35.0%
TGAATGGAATTTGGAGAGAA+AGG + tig0005289:67631-67650 None:intergenic 35.0%
!!! CGGTCGTAATTGTTTTTGAA+TGG + tig0005289:67647-67666 None:intergenic 35.0%
ATGGAATCAATCTGATCTTG+CGG + tig0005289:67667-67686 None:intergenic 35.0%
! CAAGATCAGATTGATTCCAT+AGG - tig0005289:67667-67686 Msa1342220:CDS 35.0%
GACAGTTCAAGAATGTGTGT+CGG - tig0005289:67270-67289 Msa1342220:CDS 40.0%
!! GTTCATAAGTTTTGTCACCG+GGG - tig0005289:67294-67313 Msa1342220:CDS 40.0%
GAATTTGGAGAGAAAGGAAG+TGG + tig0005289:67625-67644 None:intergenic 40.0%
! AGATTGATTCCATAGGGCAT+TGG - tig0005289:67674-67693 Msa1342220:CDS 40.0%
TCATTCATACCAATGCCCTA+TGG + tig0005289:67686-67705 None:intergenic 40.0%
ACATTTATCCGATGCTTCCC+CGG + tig0005289:67314-67333 None:intergenic 45.0%
GGAGAGAAAGGAAGTGGAAA+TGG + tig0005289:67619-67638 None:intergenic 45.0%
!! TTTTGTCACCGGGGAAGCAT+CGG - tig0005289:67303-67322 Msa1342220:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0005289 gene 67043 67705 67043 ID=Msa1342220;Name=Msa1342220
tig0005289 mRNA 67043 67705 67043 ID=Msa1342220-mRNA-1;Parent=Msa1342220;Name=Msa1342220-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|220
tig0005289 exon 67043 67705 67043 ID=Msa1342220-mRNA-1:exon:3503;Parent=Msa1342220-mRNA-1
tig0005289 CDS 67043 67705 67043 ID=Msa1342220-mRNA-1:cds;Parent=Msa1342220-mRNA-1
Gene Sequence

>Msa1342220

ATGGATGATGAGAGTCATAGTAATAATTTGCCAAATGGATTCAACACAGAAAACCCTGAAAGTCATTGTTTAAAAACAATCAACAACAACAACAACAATAATCATAATCATCATCACAATAGCAATAGCAATAAAGAACAAGATCGTTTTCTTCCTATAGCAAATGTTGGTAGAATAATGAAAAAAGTTATTCCTGCAAATGGAAAAATCTCAAAGGATGCAAAAGAGACAGTTCAAGAATGTGTGTCGGAGTTCATAAGTTTTGTCACCGGGGAAGCATCGGATAAATGTCAAAGAGAAAAAAGAAAGACAATCAATGGTGATGATATTATTTGGGCTATTACAACGTTAGGCTTTGAAGATTATGTGGAACCATTAAAATGTTACCTTCAAAAATATAGAGATATTGAAGGTGAAAAAGTCAATGTTCCAAAACAACAAAGATCTGAACAAAGGCTACATCAACATCAACATCAACATAATCAAGATGAATTAAATAATCAACATTTCAACAATAGTGTATATACATCTACAAATCTCATGTCTCAACCTCCTTATATGACTACTGATCAACCATTTCCACTTCCTTTCTCTCCAAATTCCATTCAAAAACAATTACGACCGCAAGATCAGATTGATTCCATAGGGCATTGGTATGAATGA
Protein sequence

>Msa1342220

MDDESHSNNLPNGFNTENPESHCLKTINNNNNNNHNHHHNSNSNKEQDRFLPIANVGRIMKKVIPANGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVEPLKCYLQKYRDIEGEKVNVPKQQRSEQRLHQHQHQHNQDELNNQHFNNSVYTSTNLMSQPPYMTTDQPFPLPFSPNSIQKQLRPQDQIDSIGHWYE*