AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0751330

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0751330 MtrunA17_Chr5g0394621 93.684 190 12 0 1 190 1 190 9.89e-129 359
Msa0751330 MtrunA17_Chr5g0394631 77.222 180 41 0 1 180 1 180 9.49e-96 283
Msa0751330 MtrunA17_Chr5g0394631 74.227 194 40 5 1 190 214 401 7.49e-91 271
Msa0751330 MtrunA17_Chr1g0204951 64.583 192 64 2 1 190 1 190 3.65e-85 249
Msa0751330 MtrunA17_Chr1g0204971 60.417 192 72 2 1 190 1 190 2.27e-79 234
Msa0751330 MtrunA17_Chr7g0273661 42.038 157 88 1 16 172 3 156 1.81e-43 142
Msa0751330 MtrunA17_Chr7g0223361 39.766 171 99 2 17 187 4 170 5.68e-38 129
Msa0751330 MtrunA17_Chr7g0223351 39.881 168 96 3 20 187 7 169 1.48e-36 125
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0751330 AT2G32030.1 51.190 168 75 3 21 187 24 185 1.22e-57 179
Msa0751330 AT2G32020.1 50.595 168 76 2 21 187 19 180 8.90e-54 169
Msa0751330 AT3G22560.1 38.824 170 99 2 20 187 6 172 9.41e-37 126

Find 48 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAATCAATTCTCTCTTCTT+TGG 0.250774 5_2:-4842030 None:intergenic
ATGTTCTAGGCTCTAAATAT+TGG 0.292142 5_2:+4842312 Msa0751330:CDS
TCCTTAGAACTCCCTCCTTT+TGG 0.297796 5_2:-4842472 None:intergenic
GCAGAACTTGGCTATGTTCT+AGG 0.302641 5_2:+4842299 Msa0751330:CDS
TGTTCTAGGCTCTAAATATT+GGG 0.316974 5_2:+4842313 Msa0751330:CDS
GAAGGGCTCGGAGTGTGATT+TGG 0.319800 5_2:-4842055 None:intergenic
GAGTTCCCAAGAGCAAAATT+TGG 0.339977 5_2:-4842129 None:intergenic
GCTCTAAATATTGGGGTAAA+GGG 0.356917 5_2:+4842321 Msa0751330:CDS
AAGGGCTCGGAGTGTGATTT+GGG 0.367793 5_2:-4842054 None:intergenic
CTAAACAATTGAATTATAGT+TGG 0.392086 5_2:-4842559 None:intergenic
TGCATCAATGATCATGCAAT+TGG 0.393506 5_2:+4842224 Msa0751330:CDS
ATATAGCTACCAAGTTTCTA+TGG 0.402105 5_2:+4842189 Msa0751330:CDS
TCCAAAAGGAGGGAGTTCTA+AGG 0.410439 5_2:+4842471 Msa0751330:CDS
GTTCACCTGGTGATAAATCT+AGG 0.421080 5_2:+4842267 Msa0751330:CDS
GGCTCTAAATATTGGGGTAA+AGG 0.422886 5_2:+4842320 Msa0751330:CDS
GTTGATGCCATCATCCTTGC+TGG 0.429573 5_2:-4842156 None:intergenic
ATTCTGTGAGTTGTCTTACT+TGG 0.446468 5_2:+4842382 Msa0751330:CDS
TGCTGGGTCTCAAAGAGTGC+TGG 0.460731 5_2:+4842436 Msa0751330:CDS
AGGAACAAATGTGCAGAACT+TGG 0.477895 5_2:+4842287 Msa0751330:CDS
AGGAAATATTTGTTCATGAA+AGG 0.480337 5_2:+4842491 Msa0751330:CDS
GTGAGTTGTCTTACTTGGAA+AGG 0.487957 5_2:+4842387 Msa0751330:CDS
GCTTGAAGCTTTAGTTGATG+TGG 0.488968 5_2:+4842409 Msa0751330:CDS
TGCTTTGCACCATAGAAACT+TGG 0.496119 5_2:-4842198 None:intergenic
ATTCTCTCTTCTTTGGCACA+TGG 0.499559 5_2:-4842023 None:intergenic
TTCTGACCTTGATGATCTCA+TGG 0.505164 5_2:+4842082 Msa0751330:CDS
CATCAAGGTCAGAAAGTTGA+AGG 0.505953 5_2:-4842073 None:intergenic
TGTTGTGAAACAAGTGGTTA+AGG 0.511157 5_2:+4842355 Msa0751330:CDS
CAAAGAGTGCTGGAGAAAGC+TGG 0.517457 5_2:+4842446 Msa0751330:CDS
TTAGTTGATGTGGAAAATGC+TGG 0.527178 5_2:+4842419 Msa0751330:CDS
GGTCAGAAAGTTGAAGGGCT+CGG 0.528148 5_2:-4842067 None:intergenic
TTGTTCCTAGATTTATCACC+AGG 0.541277 5_2:-4842272 None:intergenic
TCTCTATCCTCAAGTTCACC+TGG 0.545696 5_2:+4842254 Msa0751330:CDS
CTCTACACCAGCAAGGATGA+TGG 0.559987 5_2:+4842149 Msa0751330:CDS
GAAAGCTGGTTTCCAAAAGG+AGG 0.562242 5_2:+4842460 Msa0751330:CDS
CTCTAAATATTGGGGTAAAG+GGG 0.564900 5_2:+4842322 Msa0751330:CDS
GGAGAAAGCTGGTTTCCAAA+AGG 0.570344 5_2:+4842457 Msa0751330:CDS
TAGTTGATGTGGAAAATGCT+GGG 0.573363 5_2:+4842420 Msa0751330:CDS
TTTATCACCAGGTGAACTTG+AGG 0.575731 5_2:-4842261 None:intergenic
GCATCAATGATCATGCAATT+GGG 0.576565 5_2:+4842225 Msa0751330:CDS
CACTTGTTTCACAACACATG+TGG 0.594420 5_2:-4842348 None:intergenic
ACCTTGATGATCTCATGGTG+TGG 0.606125 5_2:+4842087 Msa0751330:CDS
GTTCTAGGCTCTAAATATTG+GGG 0.619040 5_2:+4842314 Msa0751330:CDS
TCCACACCATGAGATCATCA+AGG 0.646997 5_2:-4842088 None:intergenic
ATCAAGGTCAGAAAGTTGAA+GGG 0.653293 5_2:-4842072 None:intergenic
AAAGCTGGTTTCCAAAAGGA+GGG 0.657724 5_2:+4842461 Msa0751330:CDS
GAGATCAGTAGAAAGAACAC+TGG 0.658551 5_2:-4842537 None:intergenic
TTGGGAACTCTACACCAGCA+AGG 0.679749 5_2:+4842142 Msa0751330:CDS
CACATGTGTTGTGAAACAAG+TGG 0.736637 5_2:+4842349 Msa0751330:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAAATCAATTCTCTCTTCTT+TGG - chr5_2:4842033-4842052 None:intergenic 25.0%
! AGGAAATATTTGTTCATGAA+AGG + chr5_2:4842491-4842510 Msa0751330:CDS 25.0%
ATATAGCTACCAAGTTTCTA+TGG + chr5_2:4842189-4842208 Msa0751330:CDS 30.0%
!! ATGTTCTAGGCTCTAAATAT+TGG + chr5_2:4842312-4842331 Msa0751330:CDS 30.0%
!! TGTTCTAGGCTCTAAATATT+GGG + chr5_2:4842313-4842332 Msa0751330:CDS 30.0%
ATCAAGGTCAGAAAGTTGAA+GGG - chr5_2:4842075-4842094 None:intergenic 35.0%
TGCATCAATGATCATGCAAT+TGG + chr5_2:4842224-4842243 Msa0751330:CDS 35.0%
GCATCAATGATCATGCAATT+GGG + chr5_2:4842225-4842244 Msa0751330:CDS 35.0%
TTGTTCCTAGATTTATCACC+AGG - chr5_2:4842275-4842294 None:intergenic 35.0%
!! GTTCTAGGCTCTAAATATTG+GGG + chr5_2:4842314-4842333 Msa0751330:CDS 35.0%
! GCTCTAAATATTGGGGTAAA+GGG + chr5_2:4842321-4842340 Msa0751330:CDS 35.0%
CTCTAAATATTGGGGTAAAG+GGG + chr5_2:4842322-4842341 Msa0751330:CDS 35.0%
TGTTGTGAAACAAGTGGTTA+AGG + chr5_2:4842355-4842374 Msa0751330:CDS 35.0%
ATTCTGTGAGTTGTCTTACT+TGG + chr5_2:4842382-4842401 Msa0751330:CDS 35.0%
! TTAGTTGATGTGGAAAATGC+TGG + chr5_2:4842419-4842438 Msa0751330:CDS 35.0%
! TAGTTGATGTGGAAAATGCT+GGG + chr5_2:4842420-4842439 Msa0751330:CDS 35.0%
ATTCTCTCTTCTTTGGCACA+TGG - chr5_2:4842026-4842045 None:intergenic 40.0%
CATCAAGGTCAGAAAGTTGA+AGG - chr5_2:4842076-4842095 None:intergenic 40.0%
! TTCTGACCTTGATGATCTCA+TGG + chr5_2:4842082-4842101 Msa0751330:CDS 40.0%
GTGGACAACTGATGAAAAAG+TGG + chr5_2:4842106-4842125 Msa0751330:CDS 40.0%
! AAGTGGCCAAATTTTGCTCT+TGG + chr5_2:4842123-4842142 Msa0751330:CDS 40.0%
! AGTGGCCAAATTTTGCTCTT+GGG + chr5_2:4842124-4842143 Msa0751330:CDS 40.0%
GAGTTCCCAAGAGCAAAATT+TGG - chr5_2:4842132-4842151 None:intergenic 40.0%
TGCTTTGCACCATAGAAACT+TGG - chr5_2:4842201-4842220 None:intergenic 40.0%
TTTATCACCAGGTGAACTTG+AGG - chr5_2:4842264-4842283 None:intergenic 40.0%
GTTCACCTGGTGATAAATCT+AGG + chr5_2:4842267-4842286 Msa0751330:CDS 40.0%
AGGAACAAATGTGCAGAACT+TGG + chr5_2:4842287-4842306 Msa0751330:CDS 40.0%
!! GGCTCTAAATATTGGGGTAA+AGG + chr5_2:4842320-4842339 Msa0751330:CDS 40.0%
CACTTGTTTCACAACACATG+TGG - chr5_2:4842351-4842370 None:intergenic 40.0%
CACATGTGTTGTGAAACAAG+TGG + chr5_2:4842349-4842368 Msa0751330:CDS 40.0%
GTGAGTTGTCTTACTTGGAA+AGG + chr5_2:4842387-4842406 Msa0751330:CDS 40.0%
! GCTTGAAGCTTTAGTTGATG+TGG + chr5_2:4842409-4842428 Msa0751330:CDS 40.0%
! AAAGCTGGTTTCCAAAAGGA+GGG + chr5_2:4842461-4842480 Msa0751330:CDS 40.0%
GAGATCAGTAGAAAGAACAC+TGG - chr5_2:4842540-4842559 None:intergenic 40.0%
! ACCTTGATGATCTCATGGTG+TGG + chr5_2:4842087-4842106 Msa0751330:CDS 45.0%
TCCACACCATGAGATCATCA+AGG - chr5_2:4842091-4842110 None:intergenic 45.0%
TCTCTATCCTCAAGTTCACC+TGG + chr5_2:4842254-4842273 Msa0751330:CDS 45.0%
GCAGAACTTGGCTATGTTCT+AGG + chr5_2:4842299-4842318 Msa0751330:CDS 45.0%
! GGAGAAAGCTGGTTTCCAAA+AGG + chr5_2:4842457-4842476 Msa0751330:CDS 45.0%
! GAAAGCTGGTTTCCAAAAGG+AGG + chr5_2:4842460-4842479 Msa0751330:CDS 45.0%
TCCAAAAGGAGGGAGTTCTA+AGG + chr5_2:4842471-4842490 Msa0751330:CDS 45.0%
! TCCTTAGAACTCCCTCCTTT+TGG - chr5_2:4842475-4842494 None:intergenic 45.0%
AAGGGCTCGGAGTGTGATTT+GGG - chr5_2:4842057-4842076 None:intergenic 50.0%
GGTCAGAAAGTTGAAGGGCT+CGG - chr5_2:4842070-4842089 None:intergenic 50.0%
TTGGGAACTCTACACCAGCA+AGG + chr5_2:4842142-4842161 Msa0751330:CDS 50.0%
CTCTACACCAGCAAGGATGA+TGG + chr5_2:4842149-4842168 Msa0751330:CDS 50.0%
GTTGATGCCATCATCCTTGC+TGG - chr5_2:4842159-4842178 None:intergenic 50.0%
!! CAAAGAGTGCTGGAGAAAGC+TGG + chr5_2:4842446-4842465 Msa0751330:CDS 50.0%
GAAGGGCTCGGAGTGTGATT+TGG - chr5_2:4842058-4842077 None:intergenic 55.0%
! TGCTGGGTCTCAAAGAGTGC+TGG + chr5_2:4842436-4842455 Msa0751330:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 4841996 4842568 4841996 ID=Msa0751330;Name=Msa0751330
chr5_2 mRNA 4841996 4842568 4841996 ID=Msa0751330-mRNA-1;Parent=Msa0751330;Name=Msa0751330-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|-1|0|1|-1|1|1|0|190
chr5_2 exon 4841996 4842568 4841996 ID=Msa0751330-mRNA-1:exon:1903;Parent=Msa0751330-mRNA-1
chr5_2 CDS 4841996 4842568 4841996 ID=Msa0751330-mRNA-1:cds;Parent=Msa0751330-mRNA-1
Gene Sequence

>Msa0751330

ATGGAAAGAACTTCTATTTCTTTCGAACCATGTGCCAAAGAAGAGAGAATTGATTTAACCCAAATCACACTCCGAGCCCTTCAACTTTCTGACCTTGATGATCTCATGGTGTGGACAACTGATGAAAAAGTGGCCAAATTTTGCTCTTGGGAACTCTACACCAGCAAGGATGATGGCATCAACTTCATTGAAAATATAGCTACCAAGTTTCTATGGTGCAAAGCAATATGCATCAATGATCATGCAATTGGGTGTGTTTCTCTATCCTCAAGTTCACCTGGTGATAAATCTAGGAACAAATGTGCAGAACTTGGCTATGTTCTAGGCTCTAAATATTGGGGTAAAGGGGTTGCCACATGTGTTGTGAAACAAGTGGTTAAGGTTGCATTCTGTGAGTTGTCTTACTTGGAAAGGCTTGAAGCTTTAGTTGATGTGGAAAATGCTGGGTCTCAAAGAGTGCTGGAGAAAGCTGGTTTCCAAAAGGAGGGAGTTCTAAGGAAATATTTGTTCATGAAAGGAAAAAGTAGAGATATGATCATGTCCAGTGTTCTTTCTACTGATCTCCAACTATAA
Protein sequence

>Msa0751330

MERTSISFEPCAKEERIDLTQITLRALQLSDLDDLMVWTTDEKVAKFCSWELYTSKDDGINFIENIATKFLWCKAICINDHAIGCVSLSSSSPGDKSRNKCAELGYVLGSKYWGKGVATCVVKQVVKVAFCELSYLERLEALVDVENAGSQRVLEKAGFQKEGVLRKYLFMKGKSRDMIMSSVLSTDLQL*