AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1411860

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1411860 MtrunA17_Chr3g0127951 99.526 211 1 0 1 211 1 211 2.13e-154 426
Msa1411860 MtrunA17_Chr7g0267321 39.344 183 110 1 8 189 154 336 5.34e-45 153
Msa1411860 MtrunA17_Chr7g0267321 36.111 72 46 0 118 189 24 95 5.94e-11 60.8
Msa1411860 MtrunA17_Chr2g0321801 38.095 189 105 2 10 186 3 191 7.84e-42 140
Msa1411860 MtrunA17_Chr1g0177571 38.798 183 111 1 8 189 2 184 1.71e-38 132
Msa1411860 MtrunA17_Chr4g0025861 38.624 189 106 2 10 188 4 192 2.72e-37 129
Msa1411860 MtrunA17_Chr7g0276371 36.813 182 105 3 29 200 45 226 2.12e-34 122
Msa1411860 MtrunA17_Chr8g0345891 32.692 156 104 1 29 183 101 256 3.34e-20 86.3
Msa1411860 MtrunA17_Chr2g0280851 24.832 149 110 2 39 186 37 184 3.55e-17 76.3
Msa1411860 MtrunA17_Chr1g0206161 25.150 167 125 0 21 187 46 212 9.00e-16 73.2
Msa1411860 MtrunA17_Chr7g0267301 27.517 149 104 2 39 183 56 204 4.21e-14 68.6
Msa1411860 MtrunA17_Chr7g0267281 25.503 149 107 2 39 183 55 203 1.87e-13 67.0
Msa1411860 MtrunA17_Chr2g0330241 27.381 168 112 4 45 210 84 243 9.78e-13 65.5
Msa1411860 MtrunA17_Chr7g0267361 27.624 181 125 5 19 196 65 242 1.54e-12 64.7
Msa1411860 MtrunA17_Chr3g0109121 30.496 141 95 3 44 182 87 226 8.15e-12 62.8
Msa1411860 MtrunA17_Chr5g0440571 21.818 165 118 2 33 186 70 234 1.61e-11 62.0
Msa1411860 MtrunA17_Chr4g0067041 24.675 154 113 3 37 188 65 217 2.13e-11 61.2
Msa1411860 MtrunA17_Chr7g0267291 25.000 168 115 3 30 186 36 203 7.06e-11 60.5
Msa1411860 MtrunA17_Chr7g0267181 29.412 102 70 2 83 183 102 202 9.81e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1411860 AT5G53730.1 58.605 215 83 3 1 211 1 213 1.04e-78 235
Msa1411860 AT3G44220.1 36.585 205 129 1 8 211 2 206 2.87e-47 154
Msa1411860 AT3G52470.1 39.227 181 109 1 10 189 3 183 2.07e-46 152
Msa1411860 AT3G11660.1 39.891 183 107 1 10 189 2 184 4.36e-46 152
Msa1411860 AT2G35960.1 42.857 147 83 1 41 186 36 182 9.26e-43 143
Msa1411860 AT5G06330.1 39.344 183 108 1 10 189 4 186 2.24e-39 134
Msa1411860 AT2G35970.1 39.877 163 97 1 25 186 21 183 5.99e-39 133
Msa1411860 AT5G22200.1 38.095 168 103 1 45 211 43 210 1.62e-38 132
Msa1411860 AT4G09590.1 39.264 163 98 1 25 186 21 183 1.65e-38 132
Msa1411860 AT4G01410.1 32.203 177 119 1 24 199 42 218 1.59e-30 112
Msa1411860 AT4G05220.1 26.875 160 115 1 28 187 50 207 9.00e-21 87.0
Msa1411860 AT1G61760.1 29.412 153 104 1 34 182 48 200 1.07e-18 81.3
Msa1411860 AT5G22870.1 23.602 161 121 2 26 185 29 188 4.55e-18 79.3
Msa1411860 AT2G35980.1 23.810 147 108 3 42 185 57 202 3.45e-14 69.3
Msa1411860 AT2G35460.1 27.891 147 102 3 39 182 67 212 1.95e-13 67.4
Msa1411860 AT2G27080.1 25.405 185 128 4 18 193 63 246 2.26e-12 64.7
Msa1411860 AT2G27080.2 25.405 185 128 4 18 193 63 246 2.26e-12 64.7
Msa1411860 AT5G06320.1 25.000 160 113 4 30 183 49 207 3.42e-12 63.9
Msa1411860 AT1G65690.1 24.845 161 113 2 34 186 70 230 1.70e-11 62.0
Msa1411860 AT5G36970.1 22.876 153 113 2 40 187 79 231 5.86e-11 60.5

Find 38 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGAGGTTTGGAGGGTTTA+AGG 0.111111 tig0023844:-47754 None:intergenic
AAAATTGGTACTTGGGTTTC+TGG 0.142311 tig0023844:+48112 Msa1411860:CDS
GGAAAACTTCGTTGGAAAAT+TGG 0.175584 tig0023844:+48097 Msa1411860:CDS
CTTGGGTTTCTGGTCGTTAC+AGG 0.188562 tig0023844:+48122 Msa1411860:CDS
TCTTGTGTTCCTTGGTAAAA+AGG 0.219373 tig0023844:-47956 None:intergenic
TTACCTGTTGCTCCTTCTAT+TGG 0.247943 tig0023844:+48016 Msa1411860:CDS
ATGAGTCGTGATCAAGTTTC+TGG 0.250971 tig0023844:+48046 Msa1411860:CDS
GTTGATAGATGTCAAGTTCT+TGG 0.269336 tig0023844:-47784 None:intergenic
TGTGATTCTATAGTGGCTTT+TGG 0.272766 tig0023844:+48157 Msa1411860:CDS
AGATGAGAAGTATGAGTAAT+AGG 0.289246 tig0023844:-47724 None:intergenic
GCCTCCTCTGAATTCAAAAC+TGG 0.322386 tig0023844:+48201 Msa1411860:CDS
GGTTTGAGTCTTAAAGCTAA+TGG 0.350685 tig0023844:+48076 Msa1411860:CDS
TCATCTTCTTTGATTGGAAA+TGG 0.358731 tig0023844:+47992 Msa1411860:CDS
AATTACTCTCTTGTGTTCCT+TGG 0.384175 tig0023844:-47964 None:intergenic
TGATCAAGTTTCTGGAAGAT+TGG 0.393770 tig0023844:+48054 Msa1411860:CDS
TTGGAGGGAGAATTGAGGTT+TGG 0.394952 tig0023844:-47765 None:intergenic
TGTTAATTGTGATTCTATAG+TGG 0.400079 tig0023844:+48150 Msa1411860:CDS
TTCGTTGGAAAATTGGTACT+TGG 0.400314 tig0023844:+48104 Msa1411860:CDS
AAGCTAATGGAAAACTTCGT+TGG 0.433071 tig0023844:+48089 Msa1411860:CDS
GATCAAGTTTCTGGAAGATT+GGG 0.435233 tig0023844:+48055 Msa1411860:CDS
CTCATTTCGTAACCAATAGA+AGG 0.441144 tig0023844:-48028 None:intergenic
ATCTATCAACTAAACCTCTC+TGG 0.462378 tig0023844:+47797 Msa1411860:CDS
TGAGTTGGATTGAGGAGTTG+AGG 0.468057 tig0023844:-47826 None:intergenic
GAGAAGAGTGAGTTGGATTG+AGG 0.472613 tig0023844:-47834 None:intergenic
TAACCAATAGAAGGAGCAAC+AGG 0.479843 tig0023844:-48019 None:intergenic
GAGGGAGAATTGAGGTTTGG+AGG 0.495433 tig0023844:-47762 None:intergenic
TGGATTGAGGAGTTGAGGAT+TGG 0.498080 tig0023844:-47821 None:intergenic
CTTAATCTATGTTTAAATTG+TGG 0.511484 tig0023844:-48239 None:intergenic
AGGGAGAATTGAGGTTTGGA+GGG 0.537404 tig0023844:-47761 None:intergenic
TCGTTGGAAAATTGGTACTT+GGG 0.552290 tig0023844:+48105 Msa1411860:CDS
AGTTCTTGGAGGGAGAATTG+AGG 0.555673 tig0023844:-47770 None:intergenic
GATAGATGTCAAGTTCTTGG+AGG 0.569584 tig0023844:-47781 None:intergenic
CCTCCTCTGAATTCAAAACT+GGG 0.578180 tig0023844:+48202 Msa1411860:CDS
ATAGATGTCAAGTTCTTGGA+GGG 0.593208 tig0023844:-47780 None:intergenic
CAGAGGAGGCACATTCAAAG+TGG 0.616810 tig0023844:-48188 None:intergenic
AAGTATGAGTAATAGGATTG+TGG 0.630352 tig0023844:-47717 None:intergenic
AGTTGAGGATTGGTCCAGAG+AGG 0.632708 tig0023844:-47811 None:intergenic
AGAGGAGGCACATTCAAAGT+GGG 0.650069 tig0023844:-48187 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTATCATCTTCTTTGAT+TGG + tig0023844:47986-48005 Msa1411860:CDS 20.0%
!!! AACTTTTTGGTTTGGATTTT+TGG - tig0023844:47861-47880 None:intergenic 25.0%
!!! TAAATGCTAACTTTTTGGTT+TGG - tig0023844:47869-47888 None:intergenic 25.0%
! TGTTAATTGTGATTCTATAG+TGG + tig0023844:48150-48169 Msa1411860:CDS 25.0%
!!! CTCTATTCTTACTTGTTTTG+TGG - tig0023844:47654-47673 None:intergenic 30.0%
AAGTATGAGTAATAGGATTG+TGG - tig0023844:47720-47739 None:intergenic 30.0%
! AGATGAGAAGTATGAGTAAT+AGG - tig0023844:47727-47746 None:intergenic 30.0%
! CGTAGTAAATGCTAACTTTT+TGG - tig0023844:47874-47893 None:intergenic 30.0%
TCATCTTCTTTGATTGGAAA+TGG + tig0023844:47992-48011 Msa1411860:CDS 30.0%
ATAGATGTCAAGTTCTTGGA+GGG - tig0023844:47783-47802 None:intergenic 35.0%
! GTTGATAGATGTCAAGTTCT+TGG - tig0023844:47787-47806 None:intergenic 35.0%
ATCTATCAACTAAACCTCTC+TGG + tig0023844:47797-47816 Msa1411860:CDS 35.0%
TCTTGTGTTCCTTGGTAAAA+AGG - tig0023844:47959-47978 None:intergenic 35.0%
AATTACTCTCTTGTGTTCCT+TGG - tig0023844:47967-47986 None:intergenic 35.0%
CTCATTTCGTAACCAATAGA+AGG - tig0023844:48031-48050 None:intergenic 35.0%
! TGATCAAGTTTCTGGAAGAT+TGG + tig0023844:48054-48073 Msa1411860:CDS 35.0%
! GATCAAGTTTCTGGAAGATT+GGG + tig0023844:48055-48074 Msa1411860:CDS 35.0%
GGTTTGAGTCTTAAAGCTAA+TGG + tig0023844:48076-48095 Msa1411860:CDS 35.0%
AAGCTAATGGAAAACTTCGT+TGG + tig0023844:48089-48108 Msa1411860:CDS 35.0%
GGAAAACTTCGTTGGAAAAT+TGG + tig0023844:48097-48116 Msa1411860:CDS 35.0%
TTCGTTGGAAAATTGGTACT+TGG + tig0023844:48104-48123 Msa1411860:CDS 35.0%
TCGTTGGAAAATTGGTACTT+GGG + tig0023844:48105-48124 Msa1411860:CDS 35.0%
AAAATTGGTACTTGGGTTTC+TGG + tig0023844:48112-48131 Msa1411860:CDS 35.0%
! TGTGATTCTATAGTGGCTTT+TGG + tig0023844:48157-48176 Msa1411860:CDS 35.0%
!!! TCTATAGTGGCTTTTGGAAT+TGG + tig0023844:48163-48182 Msa1411860:CDS 35.0%
! TGTTTTGTGGCACAGTGTTT+TGG - tig0023844:47641-47660 None:intergenic 40.0%
ATTGAGGTTTGGAGGGTTTA+AGG - tig0023844:47757-47776 None:intergenic 40.0%
GATAGATGTCAAGTTCTTGG+AGG - tig0023844:47784-47803 None:intergenic 40.0%
!! TTTTGGAGAGAAGAGTGAGT+TGG - tig0023844:47844-47863 None:intergenic 40.0%
! TTTGTGCCACCTTTTTACCA+AGG + tig0023844:47947-47966 Msa1411860:CDS 40.0%
TGTGTTCCTTGGTAAAAAGG+TGG - tig0023844:47956-47975 None:intergenic 40.0%
TTACCTGTTGCTCCTTCTAT+TGG + tig0023844:48016-48035 Msa1411860:CDS 40.0%
TAACCAATAGAAGGAGCAAC+AGG - tig0023844:48022-48041 None:intergenic 40.0%
ATGAGTCGTGATCAAGTTTC+TGG + tig0023844:48046-48065 Msa1411860:CDS 40.0%
CCTCCTCTGAATTCAAAACT+GGG + tig0023844:48202-48221 Msa1411860:CDS 40.0%
AGGGAGAATTGAGGTTTGGA+GGG - tig0023844:47764-47783 None:intergenic 45.0%
TTGGAGGGAGAATTGAGGTT+TGG - tig0023844:47768-47787 None:intergenic 45.0%
AGTTCTTGGAGGGAGAATTG+AGG - tig0023844:47773-47792 None:intergenic 45.0%
TGGATTGAGGAGTTGAGGAT+TGG - tig0023844:47824-47843 None:intergenic 45.0%
! TGAGTTGGATTGAGGAGTTG+AGG - tig0023844:47829-47848 None:intergenic 45.0%
! GAGAAGAGTGAGTTGGATTG+AGG - tig0023844:47837-47856 None:intergenic 45.0%
! AGAGGAGGCACATTCAAAGT+GGG - tig0023844:48190-48209 None:intergenic 45.0%
GCCTCCTCTGAATTCAAAAC+TGG + tig0023844:48201-48220 Msa1411860:CDS 45.0%
!!! CCCAGTTTTGAATTCAGAGG+AGG - tig0023844:48205-48224 None:intergenic 45.0%
!!! GCACCCAGTTTTGAATTCAG+AGG - tig0023844:48208-48227 None:intergenic 45.0%
GAGGGAGAATTGAGGTTTGG+AGG - tig0023844:47765-47784 None:intergenic 50.0%
!! AGTTGAGGATTGGTCCAGAG+AGG - tig0023844:47814-47833 None:intergenic 50.0%
!! CTTGGGTTTCTGGTCGTTAC+AGG + tig0023844:48122-48141 Msa1411860:CDS 50.0%
! CAGAGGAGGCACATTCAAAG+TGG - tig0023844:48191-48210 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0023844 gene 47614 48249 47614 ID=Msa1411860;Name=Msa1411860
tig0023844 mRNA 47614 48249 47614 ID=Msa1411860-mRNA-1;Parent=Msa1411860;Name=Msa1411860-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|211
tig0023844 exon 47614 48249 47614 ID=Msa1411860-mRNA-1:exon:20325;Parent=Msa1411860-mRNA-1
tig0023844 CDS 47614 48249 47614 ID=Msa1411860-mRNA-1:cds;Parent=Msa1411860-mRNA-1
Gene Sequence

>Msa1411860

ATGTCTCAAATCACAATAAAATCTCCAAAACACTGTGCCACAAAACAAGTAAGAATAGAGAGAAACTACAAGAAAATCTTCTTTGCTTTCTCAACATTTTTCACCACAATCCTATTACTCATACTTCTCATCTATTTCATCCTTAAACCCTCCAAACCTCAATTCTCCCTCCAAGAACTTGACATCTATCAACTAAACCTCTCTGGACCAATCCTCAACTCCTCAATCCAACTCACTCTTCTCTCCAAAAATCCAAACCAAAAAGTTAGCATTTACTACGACGAGTTTCAAGTTTATGCAACTTACAAGAATCAACAAATAACTAGTGATTCATTTGTGCCACCTTTTTACCAAGGAACACAAGAGAGTAATTTTTTATCATCTTCTTTGATTGGAAATGGTTTACCTGTTGCTCCTTCTATTGGTTACGAAATGAGTCGTGATCAAGTTTCTGGAAGATTGGGTTTGAGTCTTAAAGCTAATGGAAAACTTCGTTGGAAAATTGGTACTTGGGTTTCTGGTCGTTACAGGTTTAATGTTAATTGTGATTCTATAGTGGCTTTTGGAATTGGACCCACTTTGAATGTGCCTCCTCTGAATTCAAAACTGGGTGCTTTGTGTTCTACCACAATTTAA
Protein sequence

>Msa1411860

MSQITIKSPKHCATKQVRIERNYKKIFFAFSTFFTTILLLILLIYFILKPSKPQFSLQELDIYQLNLSGPILNSSIQLTLLSKNPNQKVSIYYDEFQVYATYKNQQITSDSFVPPFYQGTQESNFLSSSLIGNGLPVAPSIGYEMSRDQVSGRLGLSLKANGKLRWKIGTWVSGRYRFNVNCDSIVAFGIGPTLNVPPLNSKLGALCSTTI*