AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180002304.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180002304.01.T01 MTR_1g006650 99.048 105 1 0 1 105 240 344 1.14e-75 227
MsG0180002304.01.T01 MTR_3g109760 80.952 105 19 1 2 105 214 318 4.79e-53 168
MsG0180002304.01.T01 MTR_8g013950 69.091 110 28 3 2 105 233 342 8.24e-41 137
MsG0180002304.01.T01 MTR_1g046680 80.952 63 12 0 2 64 179 241 3.19e-32 113
MsG0180002304.01.T01 MTR_8g076340 79.032 62 13 0 4 65 227 288 2.12e-31 112
MsG0180002304.01.T01 MTR_4g071590 80.328 61 12 0 4 64 220 280 2.48e-30 109
MsG0180002304.01.T01 MTR_4g471590 80.328 61 12 0 4 64 220 280 2.48e-30 109
MsG0180002304.01.T01 MTR_6g032830 77.049 61 14 0 1 61 198 258 5.75e-30 107
MsG0180002304.01.T01 MTR_1g094930 83.929 56 9 0 4 59 156 211 7.08e-30 107
MsG0180002304.01.T01 MTR_1g116010 64.103 78 24 1 4 81 173 246 7.93e-30 107
MsG0180002304.01.T01 MTR_5g007600 77.419 62 14 0 3 64 267 328 8.47e-30 108
MsG0180002304.01.T01 MTR_5g007600 74.603 63 16 0 3 65 165 227 1.73e-26 100
MsG0180002304.01.T01 MTR_2g094600 82.143 56 10 0 4 59 225 280 1.99e-29 107
MsG0180002304.01.T01 MTR_1g094930 83.929 56 9 0 4 59 251 306 2.38e-29 107
MsG0180002304.01.T01 MTR_3g117380 77.419 62 14 0 4 65 238 299 7.84e-29 105
MsG0180002304.01.T01 MTR_7g085410 76.271 59 14 0 1 59 194 252 9.24e-29 104
MsG0180002304.01.T01 MTR_5g021340 75.806 62 15 0 4 65 309 370 1.32e-28 106
MsG0180002304.01.T01 MTR_4g058910 77.586 58 13 0 4 61 323 380 1.54e-28 106
MsG0180002304.01.T01 MTR_7g445980 62.963 54 20 0 3 56 42 95 9.44e-20 77.4
MsG0180002304.01.T01 MTR_7g446110 63.636 55 20 0 2 56 194 248 2.18e-19 80.1
MsG0180002304.01.T01 MTR_7g445950 58.182 55 23 0 2 56 127 181 3.50e-17 72.8
MsG0180002304.01.T01 MTR_7g446070 56.364 55 24 0 2 56 139 193 1.26e-16 71.6
MsG0180002304.01.T01 MTR_7g112330 75.862 29 7 0 2 30 29 57 3.62e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180002304.01.T01 AT5G25830 74.528 106 25 2 2 105 226 331 6.17e-49 158
MsG0180002304.01.T01 AT4G32890 64.815 108 31 3 2 105 204 308 1.51e-44 146
MsG0180002304.01.T01 AT2G45050 81.081 74 12 1 2 75 186 257 6.80e-38 128
MsG0180002304.01.T01 AT3G60530 90.323 62 6 0 2 63 165 226 6.98e-37 125
MsG0180002304.01.T01 AT1G08010 68.056 72 17 1 2 67 227 298 5.13e-31 111
MsG0180002304.01.T01 AT1G08010 68.056 72 17 1 2 67 227 298 5.13e-31 111
MsG0180002304.01.T01 AT1G08010 68.056 72 17 1 2 67 227 298 5.13e-31 111
MsG0180002304.01.T01 AT3G24050 78.333 60 13 0 2 61 201 260 1.49e-30 109
MsG0180002304.01.T01 AT4G34680 77.778 63 14 0 2 64 187 249 3.51e-30 108
MsG0180002304.01.T01 AT4G34680 77.778 63 14 0 2 64 187 249 3.51e-30 108
MsG0180002304.01.T01 AT5G66320 67.568 74 24 0 4 77 258 331 5.31e-30 109
MsG0180002304.01.T01 AT5G66320 67.568 74 24 0 4 77 258 331 5.31e-30 109
MsG0180002304.01.T01 AT1G08000 72.581 62 17 0 2 63 225 286 7.89e-30 108
MsG0180002304.01.T01 AT1G08000 72.581 62 17 0 2 63 225 286 7.89e-30 108
MsG0180002304.01.T01 AT3G54810 77.966 59 13 0 4 62 238 296 6.37e-29 106
MsG0180002304.01.T01 AT3G54810 77.966 59 13 0 4 62 238 296 6.37e-29 106
MsG0180002304.01.T01 AT4G36240 79.661 59 12 0 4 62 173 231 4.30e-28 102
MsG0180002304.01.T01 AT3G51080 76.667 60 14 0 4 63 230 289 8.21e-28 103
MsG0180002304.01.T01 AT2G28340 70.690 58 17 0 2 59 198 255 2.45e-25 96.3
MsG0180002304.01.T01 AT3G45170 64.516 62 22 0 2 63 122 183 8.22e-25 93.2

Find 28 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACTCTGATGTTGTAAAATC+TGG 0.292416 1:-36490614 None:intergenic
CTAGCTGCAGGCCTGTATTC+AGG 0.333508 1:-36490492 None:intergenic
AAGACACCACAATGGCGAAC+CGG 0.386976 1:+36490405 MsG0180002304.01.T01:CDS
TTACTTGATTCACCAACATA+TGG 0.405233 1:+36490665 MsG0180002304.01.T01:CDS
ACGATGCGAGTTAGAGTGTT+TGG 0.406152 1:-36490532 None:intergenic
CAATGGCGAACCGGGCCTAA+TGG 0.414512 1:+36490414 MsG0180002304.01.T01:CDS
TACATCATCTGCCTAAAATC+AGG 0.450652 1:-36490690 None:intergenic
GAGGCAGAAGGAAATGTTGC+GGG 0.466463 1:+36490572 MsG0180002304.01.T01:CDS
TACTTGATTCACCAACATAT+GGG 0.466490 1:+36490666 MsG0180002304.01.T01:CDS
GTCGATTGGTGCCTGAATAC+AGG 0.470023 1:+36490481 MsG0180002304.01.T01:CDS
AGACACCACAATGGCGAACC+GGG 0.471491 1:+36490406 MsG0180002304.01.T01:CDS
TGTTTGGTCAGCACAAATGT+AGG 0.504596 1:-36490516 None:intergenic
ATCGTAAAGTGTTGGAGCTA+CGG 0.505579 1:+36490550 MsG0180002304.01.T01:CDS
AAGATACAAGTCGGGTCGAT+TGG 0.534399 1:+36490467 MsG0180002304.01.T01:CDS
AATCAAGTAATCATCATGGT+TGG 0.550610 1:-36490652 None:intergenic
ACAAATGTAGGGCTAGCTGC+AGG 0.560737 1:-36490504 None:intergenic
TAAAATCAGGTCCCATATGT+TGG 0.573858 1:-36490677 None:intergenic
GTTTGGTCAGCACAAATGTA+GGG 0.574012 1:-36490515 None:intergenic
TTAGGCCCGGTTCGCCATTG+TGG 0.587065 1:-36490411 None:intergenic
TTGTGGTGTAAGATACAAGT+CGG 0.589234 1:+36490458 MsG0180002304.01.T01:CDS
TAACTCGCATCGTAAAGTGT+TGG 0.602752 1:+36490542 MsG0180002304.01.T01:CDS
TGTGGTGTAAGATACAAGTC+GGG 0.608929 1:+36490459 MsG0180002304.01.T01:CDS
GTTGGAGCTACGGAGGCAGA+AGG 0.611025 1:+36490560 MsG0180002304.01.T01:CDS
AAAACATTATGCAACGCTTG+TGG 0.638941 1:+36490441 MsG0180002304.01.T01:CDS
GGTGAATCAAGTAATCATCA+TGG 0.660405 1:-36490656 None:intergenic
GTAAAGTGTTGGAGCTACGG+AGG 0.667005 1:+36490553 MsG0180002304.01.T01:CDS
GGAGGCAGAAGGAAATGTTG+CGG 0.675658 1:+36490571 MsG0180002304.01.T01:CDS
TGACAGACAAGACACCACAA+TGG 0.724676 1:+36490397 MsG0180002304.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AATCAAGTAATCATCATGGT+TGG - Chr1:36490655-36490674 None:intergenic 30.0%
TACTCTGATGTTGTAAAATC+TGG - Chr1:36490617-36490636 None:intergenic 30.0%
TACTTGATTCACCAACATAT+GGG + Chr1:36490666-36490685 MsG0180002304.01.T01:CDS 30.0%
TTACTTGATTCACCAACATA+TGG + Chr1:36490665-36490684 MsG0180002304.01.T01:CDS 30.0%
!!! GTTGTAAAATCTGGTTTTGT+TGG - Chr1:36490608-36490627 None:intergenic 30.0%
AAAACATTATGCAACGCTTG+TGG + Chr1:36490441-36490460 MsG0180002304.01.T01:CDS 35.0%
GGTGAATCAAGTAATCATCA+TGG - Chr1:36490659-36490678 None:intergenic 35.0%
TAAAATCAGGTCCCATATGT+TGG - Chr1:36490680-36490699 None:intergenic 35.0%
TACATCATCTGCCTAAAATC+AGG - Chr1:36490693-36490712 None:intergenic 35.0%
TTGTGGTGTAAGATACAAGT+CGG + Chr1:36490458-36490477 MsG0180002304.01.T01:CDS 35.0%
! AACATATGGGACCTGATTTT+AGG + Chr1:36490679-36490698 MsG0180002304.01.T01:CDS 35.0%
!! AAGCGTTGCATAATGTTTTC+GGG - Chr1:36490440-36490459 None:intergenic 35.0%
!! CAAGCGTTGCATAATGTTTT+CGG - Chr1:36490441-36490460 None:intergenic 35.0%
!!! AAATCTGGTTTTGTTGGTGT+TGG - Chr1:36490602-36490621 None:intergenic 35.0%
GTTTGGTCAGCACAAATGTA+GGG - Chr1:36490518-36490537 None:intergenic 40.0%
TAACTCGCATCGTAAAGTGT+TGG + Chr1:36490542-36490561 MsG0180002304.01.T01:CDS 40.0%
TGTGGTGTAAGATACAAGTC+GGG + Chr1:36490459-36490478 MsG0180002304.01.T01:CDS 40.0%
TGTTTGGTCAGCACAAATGT+AGG - Chr1:36490519-36490538 None:intergenic 40.0%
!! ATCGTAAAGTGTTGGAGCTA+CGG + Chr1:36490550-36490569 MsG0180002304.01.T01:CDS 40.0%
!! CATAATGTTTTCGGGCCATT+AGG - Chr1:36490432-36490451 None:intergenic 40.0%
AAGATACAAGTCGGGTCGAT+TGG + Chr1:36490467-36490486 MsG0180002304.01.T01:CDS 45.0%
TGACAGACAAGACACCACAA+TGG + Chr1:36490397-36490416 MsG0180002304.01.T01:CDS 45.0%
! ACGATGCGAGTTAGAGTGTT+TGG - Chr1:36490535-36490554 None:intergenic 45.0%
AAGACACCACAATGGCGAAC+CGG + Chr1:36490405-36490424 MsG0180002304.01.T01:CDS 50.0%
GAGGCAGAAGGAAATGTTGC+GGG + Chr1:36490572-36490591 MsG0180002304.01.T01:CDS 50.0%
GGAGGCAGAAGGAAATGTTG+CGG + Chr1:36490571-36490590 MsG0180002304.01.T01:CDS 50.0%
! GTCGATTGGTGCCTGAATAC+AGG + Chr1:36490481-36490500 MsG0180002304.01.T01:CDS 50.0%
!! ACAAATGTAGGGCTAGCTGC+AGG - Chr1:36490507-36490526 None:intergenic 50.0%
!! GTAAAGTGTTGGAGCTACGG+AGG + Chr1:36490553-36490572 MsG0180002304.01.T01:CDS 50.0%
AGACACCACAATGGCGAACC+GGG + Chr1:36490406-36490425 MsG0180002304.01.T01:CDS 55.0%
CTAGCTGCAGGCCTGTATTC+AGG - Chr1:36490495-36490514 None:intergenic 55.0%
!! TGTTTTCGGGCCATTAGGCC+CGG - Chr1:36490427-36490446 None:intergenic 55.0%
CAATGGCGAACCGGGCCTAA+TGG + Chr1:36490414-36490433 MsG0180002304.01.T01:CDS 60.0%
GTTGGAGCTACGGAGGCAGA+AGG + Chr1:36490560-36490579 MsG0180002304.01.T01:CDS 60.0%
! TTAGGCCCGGTTCGCCATTG+TGG - Chr1:36490414-36490433 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 36490396 36490713 36490396 ID=MsG0180002304.01;Name=MsG0180002304.01
Chr1 mRNA 36490396 36490713 36490396 ID=MsG0180002304.01.T01;Parent=MsG0180002304.01;Name=MsG0180002304.01.T01;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|105
Chr1 exon 36490396 36490713 36490396 ID=MsG0180002304.01.T01:exon:142;Parent=MsG0180002304.01.T01
Chr1 CDS 36490396 36490713 36490396 ID=MsG0180002304.01.T01:cds;Parent=MsG0180002304.01.T01
Gene Sequence

>MsG0180002304.01.T01

ATGACAGACAAGACACCACAATGGCGAACCGGGCCTAATGGCCCGAAAACATTATGCAACGCTTGTGGTGTAAGATACAAGTCGGGTCGATTGGTGCCTGAATACAGGCCTGCAGCTAGCCCTACATTTGTGCTGACCAAACACTCTAACTCGCATCGTAAAGTGTTGGAGCTACGGAGGCAGAAGGAAATGTTGCGGGCACACCAACACCAACAAAACCAGATTTTACAACATCAGAGTATGATGTTTGATATGTCCAACCATGATGATTACTTGATTCACCAACATATGGGACCTGATTTTAGGCAGATGATGTAG
Protein sequence

>MsG0180002304.01.T01

MTDKTPQWRTGPNGPKTLCNACGVRYKSGRLVPEYRPAASPTFVLTKHSNSHRKVLELRRQKEMLRAHQHQQNQILQHQSMMFDMSNHDDYLIHQHMGPDFRQMM*