AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051558

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051558.t1 MTR_5g070440 68.619 239 74 1 3 240 36 274 2.56e-114 328
MS.gene051558.t1 MTR_3g005480 67.782 239 64 3 3 238 36 264 1.89e-112 323
MS.gene051558.t1 MTR_3g005490 65.833 240 70 3 3 240 36 265 4.75e-107 310
MS.gene051558.t1 MTR_3g005420 63.180 239 87 1 3 240 304 542 1.23e-98 298
MS.gene051558.t1 MTR_3g005420 54.310 232 81 4 3 231 55 264 1.21e-67 218
MS.gene051558.t1 MTR_3g005460 62.348 247 84 3 3 240 277 523 1.09e-95 290
MS.gene051558.t1 MTR_3g005460 49.115 226 93 1 3 228 40 243 2.72e-64 208
MS.gene051558.t1 MTR_3g005440 61.979 192 67 1 3 194 257 442 5.43e-71 224
MS.gene051558.t1 MTR_3g005440 47.436 234 71 4 1 231 33 217 2.29e-54 181
MS.gene051558.t1 MTR_3g005420 51.046 239 81 2 3 240 285 488 1.13e-69 221
MS.gene051558.t1 MTR_3g005420 54.310 232 81 4 3 231 36 245 2.92e-68 218
MS.gene051558.t1 MTR_3g005495 48.319 238 93 2 1 237 26 234 3.31e-66 212
MS.gene051558.t1 MTR_3g005495 49.138 232 100 4 3 232 258 473 5.56e-65 209
MS.gene051558.t1 MTR_1g015350 49.468 188 23 5 31 217 58 174 3.35e-43 144
MS.gene051558.t1 MTR_3g061310 28.947 266 155 6 1 233 21 285 5.54e-24 97.4
MS.gene051558.t1 MTR_1g034240 45.238 84 46 0 3 86 22 105 9.08e-24 99.0
MS.gene051558.t1 MTR_1g034240 33.333 129 76 3 114 235 268 393 7.50e-12 64.7
MS.gene051558.t1 MTR_3g061340 26.953 256 156 5 3 233 25 274 2.32e-23 95.5
MS.gene051558.t1 MTR_1g108780 26.871 294 144 8 1 235 10 291 1.63e-22 95.5
MS.gene051558.t1 MTR_3g061320 28.148 270 140 9 3 233 25 279 2.86e-22 92.8
MS.gene051558.t1 MTR_7g050560 26.838 272 154 7 4 237 29 293 8.03e-22 92.0
MS.gene051558.t1 MTR_1g035460 26.014 296 146 8 4 235 2 288 4.78e-21 90.9
MS.gene051558.t1 MTR_8g103940 23.875 289 154 7 3 235 54 332 6.51e-21 91.3
MS.gene051558.t1 MTR_3g061370 27.969 261 157 5 3 233 22 281 8.23e-21 89.0
MS.gene051558.t1 MTR_5g044670 25.806 279 158 9 4 237 32 306 2.30e-20 88.6
MS.gene051558.t1 MTR_3g098790 24.453 274 167 5 4 237 29 302 4.41e-20 87.4
MS.gene051558.t1 MTR_3g061350 27.170 265 160 6 1 233 21 284 5.58e-20 86.7
MS.gene051558.t1 MTR_4g068320 40.476 84 50 0 3 86 21 104 3.74e-19 85.9
MS.gene051558.t1 MTR_4g068320 35.115 131 75 3 114 237 264 391 2.16e-12 66.2
MS.gene051558.t1 MTR_1g034210 45.946 74 40 0 3 76 22 95 4.69e-19 84.7
MS.gene051558.t1 MTR_7g050710 23.322 283 169 5 3 237 28 310 7.14e-19 84.3
MS.gene051558.t1 MTR_1g034210 45.946 74 40 0 3 76 22 95 9.28e-19 84.3
MS.gene051558.t1 MTR_1g021360 25.806 279 163 6 4 239 198 475 2.46e-16 77.8
MS.gene051558.t1 MTR_0152s0100 38.596 114 68 2 128 240 2 114 3.95e-16 72.4
MS.gene051558.t1 MTR_0152s0100 38.596 114 68 2 128 240 2 114 3.95e-16 72.4
MS.gene051558.t1 MTR_7g050580 27.106 273 152 7 4 237 29 293 7.35e-16 75.9
MS.gene051558.t1 MTR_3g061330 29.586 169 94 2 3 146 25 193 2.69e-15 73.2
MS.gene051558.t1 MTR_7g050590 24.658 292 152 8 4 237 2 283 4.67e-15 73.2
MS.gene051558.t1 MTR_7g050720 23.793 290 162 8 4 234 26 315 2.65e-14 71.2
MS.gene051558.t1 MTR_3g061290 39.286 84 51 0 3 86 25 108 3.83e-14 69.3
MS.gene051558.t1 MTR_4g119990 24.399 291 155 9 3 235 30 313 1.82e-13 69.3
MS.gene051558.t1 MTR_3g061220 38.095 84 39 1 3 86 25 95 4.31e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051558.t1 AT3G18990 29.012 324 138 7 3 238 21 340 4.07e-33 122
MS.gene051558.t1 AT3G18990 29.102 323 137 7 3 237 21 339 1.41e-32 122
MS.gene051558.t1 AT1G49475 39.773 88 52 1 1 88 47 133 1.28e-15 73.2
MS.gene051558.t1 AT4G01580 37.500 88 55 0 1 88 43 130 7.38e-15 70.9
MS.gene051558.t1 AT3G18960 37.500 88 55 0 1 88 43 130 1.05e-14 70.5
MS.gene051558.t1 AT3G18960 37.500 88 55 0 1 88 43 130 1.20e-14 70.9
MS.gene051558.t1 AT3G18960 37.931 87 54 0 2 88 7 93 2.83e-14 68.9
MS.gene051558.t1 AT1G49480 34.091 132 76 4 114 238 98 225 4.25e-12 63.9
MS.gene051558.t1 AT1G49480 34.091 132 76 4 114 238 98 225 4.25e-12 63.9
MS.gene051558.t1 AT1G49480 34.091 132 76 4 114 238 98 225 4.25e-12 63.9

Find 40 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTGGCCCTTTGAAATTT+AGG 0.163069 1.3:-6650362 None:intergenic
CTGTTCCGGATGGTTGTATT+TGG 0.168306 1.3:+6649735 MS.gene051558:CDS
TTTGTTGTCCATGAGAATTT+TGG 0.271399 1.3:-6650277 None:intergenic
AAGTGAGAGCCGTGGGAAAA+AGG 0.303768 1.3:+6650003 MS.gene051558:CDS
AATGAGTTTATCGCAAGGTT+TGG 0.354287 1.3:+6649683 MS.gene051558:CDS
TTCCTTCATAATTGAAAGAA+AGG 0.357561 1.3:-6649850 None:intergenic
GGATGGTTGTATTTGGGAAA+TGG 0.374541 1.3:+6649742 MS.gene051558:CDS
TGTTGCTACAATTACTGTTC+CGG 0.380706 1.3:+6649721 MS.gene051558:CDS
AACCTTGCGATAAACTCATT+TGG 0.384953 1.3:-6649680 None:intergenic
TTTGGTTCTCCACTAGTACT+TGG 0.391271 1.3:-6649938 None:intergenic
TGTTCCGGATGGTTGTATTT+GGG 0.395192 1.3:+6649736 MS.gene051558:CDS
TGGAGCTTGATAGGAACATT+TGG 0.400000 1.3:-6650257 None:intergenic
GAATACTATTCAATAGGATA+TGG 0.402689 1.3:+6649821 MS.gene051558:CDS
TACCTTTCTTTCAATTATGA+AGG 0.405245 1.3:+6649848 MS.gene051558:CDS
ATTATCAATGCAAATGGCAC+TGG 0.434782 1.3:+6650334 MS.gene051558:CDS
GTTTATTGAGTTGAATTCAT+TGG 0.441830 1.3:-6650071 None:intergenic
TTCATAGAATACTATTCAAT+AGG 0.452230 1.3:+6649815 MS.gene051558:CDS
GCTCTCACTTGTTTCAACCT+TGG 0.454890 1.3:-6649990 None:intergenic
ATCTCCACGCGACAAATTGT+TGG 0.473287 1.3:-6650378 None:intergenic
AAACAAAGTATCCTAGTCCT+AGG 0.485163 1.3:+6649960 MS.gene051558:CDS
TGAATCATTATCAATGCAAA+TGG 0.486207 1.3:+6650328 MS.gene051558:CDS
GGGATTTCCTAAATTTCAAA+GGG 0.496954 1.3:+6650355 MS.gene051558:CDS
TGGGATTTCCTAAATTTCAA+AGG 0.501017 1.3:+6650354 MS.gene051558:CDS
ATCAAGCTCCAAAATTCTCA+TGG 0.507903 1.3:+6650269 MS.gene051558:CDS
AGTATCCTAGTCCTAGGAAA+AGG 0.513608 1.3:+6649966 MS.gene051558:CDS
AAATTCTCATGGACAACAAA+GGG 0.515351 1.3:+6650280 MS.gene051558:CDS
AAAATTCTCATGGACAACAA+AGG 0.540935 1.3:+6650279 MS.gene051558:CDS
ATTTCCCAAATACAACCATC+CGG 0.559087 1.3:-6649740 None:intergenic
TTCAAAACTCCAAGTACTAG+TGG 0.562446 1.3:+6649929 MS.gene051558:CDS
AATTGCTAGGGCAAATCGTA+CGG 0.573224 1.3:+6650110 MS.gene051558:CDS
ACTATTCAATAGGATATGGT+TGG 0.585720 1.3:+6649825 MS.gene051558:CDS
TTATCAATGCAAATGGCACT+GGG 0.602081 1.3:+6650335 MS.gene051558:CDS
TTGAAACAAGTGAGAGCCGT+GGG 0.617139 1.3:+6649996 MS.gene051558:CDS
AGGGCCAACAATTTGTCGCG+TGG 0.632739 1.3:+6650374 MS.gene051558:CDS
TTCCAAATGAGTTTATCGCA+AGG 0.633900 1.3:+6649678 MS.gene051558:CDS
GCTACAATTACTGTTCCGGA+TGG 0.637015 1.3:+6649725 MS.gene051558:CDS
TAGTCCTAGGAAAAGGTCCA+AGG 0.639086 1.3:+6649973 MS.gene051558:CDS
AGAAGTCACAATGTTTCGCG+TGG 0.640005 1.3:+6650442 MS.gene051558:CDS
GTTGAAACAAGTGAGAGCCG+TGG 0.675349 1.3:+6649995 MS.gene051558:CDS
GAAATGGAACTGAAGAAATG+CGG 0.682734 1.3:+6649758 MS.gene051558:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCATAGAATACTATTCAAT+AGG + chr1.3:6649815-6649834 MS.gene051558:CDS 20.0%
! GAATACTATTCAATAGGATA+TGG + chr1.3:6649821-6649840 MS.gene051558:CDS 25.0%
! TACCTTTCTTTCAATTATGA+AGG + chr1.3:6649848-6649867 MS.gene051558:CDS 25.0%
! TGAATCATTATCAATGCAAA+TGG + chr1.3:6650328-6650347 MS.gene051558:CDS 25.0%
! TTCCTTCATAATTGAAAGAA+AGG - chr1.3:6649853-6649872 None:intergenic 25.0%
!! ACGTTTTCTTTTGTAACAAA+TGG + chr1.3:6649786-6649805 MS.gene051558:CDS 25.0%
!! AGCAATTTTTGAACGAAAAA+AGG - chr1.3:6650097-6650116 None:intergenic 25.0%
!! GCAATTTTTGAACGAAAAAA+GGG - chr1.3:6650096-6650115 None:intergenic 25.0%
!! TTTTCGTTCAAAAATTGCTA+GGG + chr1.3:6650098-6650117 MS.gene051558:CDS 25.0%
!! TTTTTCGTTCAAAAATTGCT+AGG + chr1.3:6650097-6650116 MS.gene051558:CDS 25.0%
!!! GTTTATTGAGTTGAATTCAT+TGG - chr1.3:6650074-6650093 None:intergenic 25.0%
AAAATTCTCATGGACAACAA+AGG + chr1.3:6650279-6650298 MS.gene051558:CDS 30.0%
AAATTCTCATGGACAACAAA+GGG + chr1.3:6650280-6650299 MS.gene051558:CDS 30.0%
ACTATTCAATAGGATATGGT+TGG + chr1.3:6649825-6649844 MS.gene051558:CDS 30.0%
GAAAGAGAGATCAATTTAAG+TGG - chr1.3:6650192-6650211 None:intergenic 30.0%
GGGATTTCCTAAATTTCAAA+GGG + chr1.3:6650355-6650374 MS.gene051558:CDS 30.0%
TGGGATTTCCTAAATTTCAA+AGG + chr1.3:6650354-6650373 MS.gene051558:CDS 30.0%
! TTGATCTCTCTTTCATTTTG+CGG + chr1.3:6650198-6650217 MS.gene051558:intron 30.0%
!! TTTGTTGTCCATGAGAATTT+TGG - chr1.3:6650280-6650299 None:intergenic 30.0%
!!! GGATTTTACTTTGGAGTTTT+TGG + chr1.3:6650136-6650155 MS.gene051558:intron 30.0%
AACCTTGCGATAAACTCATT+TGG - chr1.3:6649683-6649702 None:intergenic 35.0%
AATGAGTTTATCGCAAGGTT+TGG + chr1.3:6649683-6649702 MS.gene051558:CDS 35.0%
ATCAAGCTCCAAAATTCTCA+TGG + chr1.3:6650269-6650288 MS.gene051558:CDS 35.0%
ATTATCAATGCAAATGGCAC+TGG + chr1.3:6650334-6650353 MS.gene051558:CDS 35.0%
ATTTCCCAAATACAACCATC+CGG - chr1.3:6649743-6649762 None:intergenic 35.0%
GAAATGGAACTGAAGAAATG+CGG + chr1.3:6649758-6649777 MS.gene051558:CDS 35.0%
TGTTGCTACAATTACTGTTC+CGG + chr1.3:6649721-6649740 MS.gene051558:CDS 35.0%
TTATCAATGCAAATGGCACT+GGG + chr1.3:6650335-6650354 MS.gene051558:CDS 35.0%
TTCAAAACTCCAAGTACTAG+TGG + chr1.3:6649929-6649948 MS.gene051558:CDS 35.0%
TTCCAAATGAGTTTATCGCA+AGG + chr1.3:6649678-6649697 MS.gene051558:CDS 35.0%
! AAACAAAGTATCCTAGTCCT+AGG + chr1.3:6649960-6649979 MS.gene051558:CDS 35.0%
! TGCTTCTAAAAAAGCAGAGA+AGG + chr1.3:6650045-6650064 MS.gene051558:CDS 35.0%
!! TGTTTTTGTCCTTTTTCCCA+CGG - chr1.3:6650015-6650034 None:intergenic 35.0%
!! TTGTTGGCCCTTTGAAATTT+AGG - chr1.3:6650365-6650384 None:intergenic 35.0%
!!! CTAGTACTTGGAGTTTTGAA+CGG - chr1.3:6649929-6649948 None:intergenic 35.0%
!!! GGACTAGGATACTTTGTTTT+TGG - chr1.3:6649959-6649978 None:intergenic 35.0%
!!! TGAGAATTTTGGAGCTTGAT+AGG - chr1.3:6650269-6650288 None:intergenic 35.0%
AATTGCTAGGGCAAATCGTA+CGG + chr1.3:6650110-6650129 MS.gene051558:CDS 40.0%
AGTATCCTAGTCCTAGGAAA+AGG + chr1.3:6649966-6649985 MS.gene051558:CDS 40.0%
GGATGGTTGTATTTGGGAAA+TGG + chr1.3:6649742-6649761 MS.gene051558:CDS 40.0%
TGGAGCTTGATAGGAACATT+TGG - chr1.3:6650260-6650279 None:intergenic 40.0%
TGTTCCGGATGGTTGTATTT+GGG + chr1.3:6649736-6649755 MS.gene051558:CDS 40.0%
! GTACGGTGAGGATTTTACTT+TGG + chr1.3:6650127-6650146 MS.gene051558:intron 40.0%
!! TTTGGTTCTCCACTAGTACT+TGG - chr1.3:6649941-6649960 None:intergenic 40.0%
AGAAGTCACAATGTTTCGCG+TGG + chr1.3:6650442-6650461 MS.gene051558:CDS 45.0%
ATCTCCACGCGACAAATTGT+TGG - chr1.3:6650381-6650400 None:intergenic 45.0%
CTGTTCCGGATGGTTGTATT+TGG + chr1.3:6649735-6649754 MS.gene051558:CDS 45.0%
GCTACAATTACTGTTCCGGA+TGG + chr1.3:6649725-6649744 MS.gene051558:CDS 45.0%
GCTCTCACTTGTTTCAACCT+TGG - chr1.3:6649993-6650012 None:intergenic 45.0%
TAGTCCTAGGAAAAGGTCCA+AGG + chr1.3:6649973-6649992 MS.gene051558:CDS 45.0%
TTGAAACAAGTGAGAGCCGT+GGG + chr1.3:6649996-6650015 MS.gene051558:CDS 45.0%
! TCAACCTTGGACCTTTTCCT+AGG - chr1.3:6649980-6649999 None:intergenic 45.0%
! TTGGACCTTTTCCTAGGACT+AGG - chr1.3:6649974-6649993 None:intergenic 45.0%
AAGTGAGAGCCGTGGGAAAA+AGG + chr1.3:6650003-6650022 MS.gene051558:CDS 50.0%
GTTGAAACAAGTGAGAGCCG+TGG + chr1.3:6649995-6650014 MS.gene051558:CDS 50.0%
AGGGCCAACAATTTGTCGCG+TGG + chr1.3:6650374-6650393 MS.gene051558:CDS 55.0%
CTAGGGCAAATCGTACGGTG+AGG + chr1.3:6650115-6650134 MS.gene051558:intron 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 6649668 6650481 6649668 ID=MS.gene051558
chr1.3 mRNA 6649668 6650481 6649668 ID=MS.gene051558.t1;Parent=MS.gene051558
chr1.3 exon 6649668 6650131 6649668 ID=MS.gene051558.t1.exon1;Parent=MS.gene051558.t1
chr1.3 CDS 6649668 6650131 6649668 ID=cds.MS.gene051558.t1;Parent=MS.gene051558.t1
chr1.3 exon 6650223 6650481 6650223 ID=MS.gene051558.t1.exon2;Parent=MS.gene051558.t1
chr1.3 CDS 6650223 6650481 6650223 ID=cds.MS.gene051558.t1;Parent=MS.gene051558.t1
Gene Sequence

>MS.gene051558

ATGCAGAGAATTCCAAATGAGTTTATCGCAAGGTTTGGAAATGAACTTAAGAATGTTGCTACAATTACTGTTCCGGATGGTTGTATTTGGGAAATGGAACTGAAGAAATGCGGCAACGACGTTTTCTTTTGTAACAAATGGCAAGAGTTCATAGAATACTATTCAATAGGATATGGTTGGTACCTTTCTTTCAATTATGAAGGAAATTCAAAGTTTAGTGTTACTATAATTGATGTAACTTCTGTTGAGATTTGCTATCCGTTCAAAACTCCAAGTACTAGTGGAGAACCAAAAACAAAGTATCCTAGTCCTAGGAAAAGGTCCAAGGTTGAAACAAGTGAGAGCCGTGGGAAAAAGGACAAAAACATGTCTAAGCGTGCTTCTAAAAAAGCAGAGAAGGCTGCCAATGAATTCAACTCAATAAACCCTTTTTTCGTTCAAAAATTGCTAGGGCAAATCGTACGGTGAGGATTTTACTTTGGAGTTTTTGGTTTAAACTAAATGTTGACTTATTTATGTTGCCACTTAAATTGATCTCTCTTTCATTTTGCGGAGTGTTGCTTCTAAATTTGCTCAAAAGTACTTGAAGCCAAATGTTCCTATCAAGCTCCAAAATTCTCATGGACAACAAAGGGAAGTTTCTTGTATATTCTCTAATGCTGAATCATTATCAATGCAAATGGCACTGGGATTTCCTAAATTTCAAAGGGCCAACAATTTGTCGCGTGGAGATTATTGTGTGTTTGAGCTGATAAAAAAGAAGTCAATTGTGCTAGAAGTCACAATGTTTCGCGTGGTTGATTATCGTGATTAA
Protein sequence

>MS.gene051558.t1

MQRIPNEFIARFGNELKNVATITVPDGCIWEMELKKCGNDVFFCNKWQEFIEYYSIGYGWYLSFNYEGNSKFSVTIIDVTSVEICYPFKTPSTSGEPKTKYPSPRKRSKVETSESRGKKDKNMSKRASKKAEKAANEFNSINPFFVQKLLGQIVRVASKFAQKYLKPNVPIKLQNSHGQQREVSCIFSNAESLSMQMALGFPKFQRANNLSRGDYCVFELIKKKSIVLEVTMFRVVDYRD