AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52393

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52393.t1 MTR_2g437020 92.973 185 13 0 1 185 199 383 4.03e-122 350
MS.gene52393.t1 MTR_2g437090 72.941 170 45 1 16 184 1 170 2.49e-88 256
MS.gene52393.t1 MTR_2g437060 71.585 183 49 2 1 182 215 395 5.96e-86 258
MS.gene52393.t1 MTR_2g437080 69.767 172 51 1 13 183 210 381 8.72e-83 250
MS.gene52393.t1 MTR_2g437030 70.166 181 51 2 6 185 291 469 3.59e-82 251
MS.gene52393.t1 MTR_2g436400 71.779 163 45 1 15 176 219 381 6.11e-80 243
MS.gene52393.t1 MTR_2g436440 68.391 174 54 1 13 185 216 389 3.07e-78 238
MS.gene52393.t1 MTR_2g437040 65.497 171 58 1 13 182 210 380 2.63e-74 228
MS.gene52393.t1 MTR_2g437160 58.889 180 73 1 4 182 135 314 5.95e-68 210
MS.gene52393.t1 MTR_4g119550 57.542 179 75 1 4 181 211 389 9.47e-68 211
MS.gene52393.t1 MTR_2g437200 66.038 159 53 1 15 172 240 398 2.34e-67 211
MS.gene52393.t1 MTR_2g438010 60.345 174 68 1 4 176 234 407 4.21e-67 211
MS.gene52393.t1 MTR_2g437940 63.030 165 60 1 15 178 196 360 4.87e-67 209
MS.gene52393.t1 MTR_2g437160 58.889 180 73 1 4 182 226 405 6.31e-67 210
MS.gene52393.t1 MTR_2g437170 58.333 180 74 1 4 182 221 400 2.07e-66 209
MS.gene52393.t1 MTR_2g437240 60.000 180 71 1 4 182 229 408 2.18e-66 209
MS.gene52393.t1 MTR_2g437150 57.222 180 76 1 4 182 221 400 4.65e-66 207
MS.gene52393.t1 MTR_2g437120 60.335 179 69 2 4 181 215 392 5.02e-66 208
MS.gene52393.t1 MTR_2g437130 60.119 168 66 1 15 181 213 380 1.58e-65 206
MS.gene52393.t1 MTR_2g437960 60.000 170 67 1 15 183 228 397 3.27e-65 206
MS.gene52393.t1 MTR_2g437960 60.000 170 67 1 15 183 228 397 5.21e-65 206
MS.gene52393.t1 MTR_2g437990 56.111 180 78 1 4 182 213 392 1.35e-64 204
MS.gene52393.t1 MTR_2g076320 56.111 180 78 1 4 182 214 393 1.57e-64 204
MS.gene52393.t1 MTR_2g438020 60.606 165 64 1 15 178 279 443 1.01e-62 201
MS.gene52393.t1 MTR_2g437100 61.176 170 65 1 4 172 226 395 3.90e-61 195
MS.gene52393.t1 MTR_2g437180 56.548 168 72 1 15 182 224 390 6.30e-59 189
MS.gene52393.t1 MTR_2g437260 51.266 158 76 1 20 176 213 370 3.40e-53 174
MS.gene52393.t1 MTR_2g436460 51.515 165 78 2 13 175 215 379 1.10e-49 165
MS.gene52393.t1 MTR_4g119580 53.289 152 70 1 20 170 219 370 5.21e-47 158
MS.gene52393.t1 MTR_2g019840 50.303 165 79 3 18 181 218 380 1.10e-43 149
MS.gene52393.t1 MTR_4g120380 47.024 168 88 1 4 170 203 370 2.30e-43 148
MS.gene52393.t1 MTR_2g019810 51.282 156 73 3 18 172 206 359 1.69e-41 143
MS.gene52393.t1 MTR_4g120380 49.324 148 75 0 4 151 203 350 1.33e-40 142
MS.gene52393.t1 MTR_4g120380 40.870 115 54 3 33 138 307 416 2.21e-17 79.3
MS.gene52393.t1 MTR_4g119570 38.690 168 69 2 4 170 95 229 1.44e-26 101
MS.gene52393.t1 MTR_3g450500 32.667 150 101 0 17 166 216 365 2.92e-23 95.1
MS.gene52393.t1 MTR_2g436380 70.492 61 18 0 16 76 1 61 4.69e-23 93.2
MS.gene52393.t1 MTR_4g007490 29.932 147 103 0 20 166 217 363 2.08e-17 79.0
MS.gene52393.t1 MTR_3g085240 44.444 90 33 1 74 163 175 247 2.38e-17 77.4
MS.gene52393.t1 MTR_8g080990 28.221 163 117 0 1 163 202 364 1.28e-13 68.2
MS.gene52393.t1 MTR_8g081000 26.744 172 119 1 6 177 220 384 2.45e-13 67.4
MS.gene52393.t1 MTR_8g081000 26.744 172 119 1 6 177 220 384 2.50e-13 67.4
MS.gene52393.t1 MTR_8g081000 26.744 172 119 1 6 177 220 384 2.57e-13 67.4
MS.gene52393.t1 MTR_4g119615 65.116 43 15 0 115 157 26 68 2.04e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52393.t1 AT5G07900 38.750 160 94 3 13 169 241 399 1.39e-33 123
MS.gene52393.t1 AT1G21150 39.640 111 67 0 27 137 206 316 8.24e-18 80.1
MS.gene52393.t1 AT1G21150 39.640 111 67 0 27 137 242 352 9.59e-18 80.1
MS.gene52393.t1 AT1G21150 39.640 111 67 0 27 137 306 416 1.41e-17 79.7
MS.gene52393.t1 AT5G64950 32.031 128 87 0 1 128 201 328 3.94e-14 69.7
MS.gene52393.t1 AT1G61970 27.358 106 76 1 52 156 294 399 3.69e-12 64.3
MS.gene52393.t1 AT1G61970 27.358 106 76 1 52 156 294 399 3.69e-12 64.3
MS.gene52393.t1 AT1G61970 27.358 106 76 1 52 156 294 399 3.69e-12 64.3
MS.gene52393.t1 AT1G61970 27.358 106 76 1 52 156 294 399 3.69e-12 64.3
MS.gene52393.t1 AT1G61970 27.358 106 76 1 52 156 294 399 3.69e-12 64.3
MS.gene52393.t1 AT1G61970 27.358 106 76 1 52 156 294 399 3.69e-12 64.3
MS.gene52393.t1 AT1G61970 27.358 106 76 1 52 156 294 399 3.69e-12 64.3
MS.gene52393.t1 AT1G61990 27.152 151 75 1 25 140 225 375 1.50e-11 62.4
MS.gene52393.t1 AT1G61990 27.152 151 75 1 25 140 225 375 1.50e-11 62.4
MS.gene52393.t1 AT5G23930 30.476 105 69 1 54 154 329 433 4.01e-11 61.2

Find 42 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATTTAGTGATGAACTTT+TGG 0.234643 2.3:+54837485 MS.gene52393:CDS
GAAATTGGTGGAGGAATTAA+AGG 0.238950 2.3:+54837282 MS.gene52393:CDS
GGTGGAGGAATTAAAGGATT+TGG 0.242361 2.3:+54837288 MS.gene52393:CDS
GTGGAGGAATTAAAGGATTT+GGG 0.314616 2.3:+54837289 MS.gene52393:CDS
AGACCAACCCCACTTCTTAA+AGG 0.324708 2.3:-54837398 None:intergenic
GTTTCTTGATAAGTGTATAA+AGG 0.325915 2.3:+54837681 MS.gene52393:CDS
TTAAAAGAATGCTTTGGTTA+AGG 0.353006 2.3:+54837224 None:intergenic
GACACATGACATGCTGAAAT+TGG 0.353711 2.3:+54837267 MS.gene52393:CDS
TTTCTTGATAAGTGTATAAA+GGG 0.396797 2.3:+54837682 MS.gene52393:CDS
ATGTTCTACAAGCATTTAGA+AGG 0.400394 2.3:+54837428 MS.gene52393:CDS
TTGCAATATCTTCTGAAGAA+AGG 0.412458 2.3:+54837604 MS.gene52393:CDS
TAAGTGTATAAAGGGTATTA+AGG 0.419835 2.3:+54837690 MS.gene52393:CDS
CAAACATTAAAAGAATGCTT+TGG 0.436839 2.3:+54837218 None:intergenic
TTATCTATTAAAGTTGTATG+AGG 0.446208 2.3:+54837720 MS.gene52393:CDS
TTGGGTCAATCAGTTAGGTT+GGG 0.447898 2.3:+54837504 MS.gene52393:CDS
TTTCTTTAAGTTTCGAAAAG+AGG 0.455763 2.3:+54837560 MS.gene52393:CDS
TTTGGGTCAATCAGTTAGGT+TGG 0.464253 2.3:+54837503 MS.gene52393:CDS
AATGCTTTGGTTAAGGAGTC+GGG 0.471203 2.3:+54837231 None:intergenic
GAATGCTTTGGTTAAGGAGT+CGG 0.487572 2.3:+54837230 None:intergenic
ATCTGTAAGGAAAACATTGT+GGG 0.488825 2.3:+54837360 MS.gene52393:CDS
TTCTTTAAGTTTCGAAAAGA+GGG 0.495393 2.3:+54837561 MS.gene52393:CDS
TGCATGCCAAACTATCTGTA+AGG 0.519763 2.3:+54837347 MS.gene52393:CDS
TCGAAAAGAGGGTCCTTCCA+AGG 0.522254 2.3:+54837572 MS.gene52393:CDS
AAACTGATGGTCCTTTGGCA+AGG 0.547751 2.3:-54837537 None:intergenic
AGTCGATGCCTTTAAGAAGT+GGG 0.559365 2.3:+54837390 MS.gene52393:CDS
GATGCACTTGCCCTTGCCAA+AGG 0.563336 2.3:+54837526 MS.gene52393:CDS
TATTGCAATACAGAGGCCCT+TGG 0.565124 2.3:-54837589 None:intergenic
AACTGATGGTCCTTTGGCAA+GGG 0.571808 2.3:-54837536 None:intergenic
CGAAAAGAGGGTCCTTCCAA+GGG 0.576545 2.3:+54837573 MS.gene52393:CDS
AAGTCGATGCCTTTAAGAAG+TGG 0.577016 2.3:+54837389 MS.gene52393:CDS
TATCTGTAAGGAAAACATTG+TGG 0.577111 2.3:+54837359 MS.gene52393:CDS
AAGGCAACCACATTGTATGT+TGG 0.594814 2.3:+54837447 MS.gene52393:CDS
GCAATACAGAGGCCCTTGGA+AGG 0.596897 2.3:-54837585 None:intergenic
ATGCCTTTAAGAAGTGGGGT+TGG 0.598873 2.3:+54837395 MS.gene52393:CDS
GTCGATGCCTTTAAGAAGTG+GGG 0.602513 2.3:+54837391 MS.gene52393:CDS
GGCATGCAATGCTACACCAA+AGG 0.603475 2.3:-54837332 None:intergenic
ACATGACATGCTGAAATTGG+TGG 0.610610 2.3:+54837270 MS.gene52393:CDS
TGACATGCTGAAATTGGTGG+AGG 0.631062 2.3:+54837273 MS.gene52393:CDS
ACTCAATCTTGCTTACACCA+TGG 0.635583 2.3:+54837747 MS.gene52393:CDS
AATTTCAGCATGTCATGTGT+CGG 0.639746 2.3:-54837265 None:intergenic
CAGAAGATATTGCAATACAG+AGG 0.669772 2.3:-54837596 None:intergenic
ATGGATACCAACATACAATG+TGG 0.711327 2.3:-54837454 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CACTAAATTAATTTTATCAA+TGG - chr2.3:54837476-54837495 None:intergenic 15.0%
!! AAACTTAAAGAAAAAACTGA+TGG - chr2.3:54837553-54837572 None:intergenic 20.0%
!! TTATCTATTAAAGTTGTATG+AGG + chr2.3:54837720-54837739 MS.gene52393:CDS 20.0%
!! TTTCTTGATAAGTGTATAAA+GGG + chr2.3:54837682-54837701 MS.gene52393:CDS 20.0%
!!! TAATTTAGTGATGAACTTTT+GGG + chr2.3:54837486-54837505 MS.gene52393:CDS 20.0%
!!! TTAATTTAGTGATGAACTTT+TGG + chr2.3:54837485-54837504 MS.gene52393:CDS 20.0%
! GTTTCTTGATAAGTGTATAA+AGG + chr2.3:54837681-54837700 MS.gene52393:CDS 25.0%
!! TTCTTTAAGTTTCGAAAAGA+GGG + chr2.3:54837561-54837580 MS.gene52393:CDS 25.0%
!! TTTCTTTAAGTTTCGAAAAG+AGG + chr2.3:54837560-54837579 MS.gene52393:CDS 25.0%
!!! TAAGTGTATAAAGGGTATTA+AGG + chr2.3:54837690-54837709 MS.gene52393:CDS 25.0%
ATCTGTAAGGAAAACATTGT+GGG + chr2.3:54837360-54837379 MS.gene52393:CDS 30.0%
ATGTTCTACAAGCATTTAGA+AGG + chr2.3:54837428-54837447 MS.gene52393:CDS 30.0%
TATCTGTAAGGAAAACATTG+TGG + chr2.3:54837359-54837378 MS.gene52393:CDS 30.0%
! TGTTTTCCTTACAGATAGTT+TGG - chr2.3:54837356-54837375 None:intergenic 30.0%
! TTATCAAGAAACAGCTTTTC+AGG - chr2.3:54837673-54837692 None:intergenic 30.0%
! TTGCAATATCTTCTGAAGAA+AGG + chr2.3:54837604-54837623 MS.gene52393:CDS 30.0%
AATTTCAGCATGTCATGTGT+CGG - chr2.3:54837268-54837287 None:intergenic 35.0%
AGAAAAAACTGATGGTCCTT+TGG - chr2.3:54837545-54837564 None:intergenic 35.0%
ATGGATACCAACATACAATG+TGG - chr2.3:54837457-54837476 None:intergenic 35.0%
CAGAAGATATTGCAATACAG+AGG - chr2.3:54837599-54837618 None:intergenic 35.0%
GAAATTGGTGGAGGAATTAA+AGG + chr2.3:54837282-54837301 MS.gene52393:CDS 35.0%
GAAGAAAGGTTTGCGAAAAA+AGG + chr2.3:54837618-54837637 MS.gene52393:CDS 35.0%
GCTACTTCAAAAACAACCTT+TGG + chr2.3:54837316-54837335 MS.gene52393:CDS 35.0%
GTGGAGGAATTAAAGGATTT+GGG + chr2.3:54837289-54837308 MS.gene52393:CDS 35.0%
!! AACTTTTGGGTCAATCAGTT+AGG + chr2.3:54837499-54837518 MS.gene52393:CDS 35.0%
AAGGCAACCACATTGTATGT+TGG + chr2.3:54837447-54837466 MS.gene52393:CDS 40.0%
ACATGACATGCTGAAATTGG+TGG + chr2.3:54837270-54837289 MS.gene52393:CDS 40.0%
ACTCAATCTTGCTTACACCA+TGG + chr2.3:54837747-54837766 MS.gene52393:CDS 40.0%
GACACATGACATGCTGAAAT+TGG + chr2.3:54837267-54837286 MS.gene52393:CDS 40.0%
GGTGGAGGAATTAAAGGATT+TGG + chr2.3:54837288-54837307 MS.gene52393:CDS 40.0%
TGCATGCCAAACTATCTGTA+AGG + chr2.3:54837347-54837366 MS.gene52393:CDS 40.0%
TTGGGTCAATCAGTTAGGTT+GGG + chr2.3:54837504-54837523 MS.gene52393:CDS 40.0%
TTTGGGTCAATCAGTTAGGT+TGG + chr2.3:54837503-54837522 MS.gene52393:CDS 40.0%
! AAGTCGATGCCTTTAAGAAG+TGG + chr2.3:54837389-54837408 MS.gene52393:CDS 40.0%
! AGTCGATGCCTTTAAGAAGT+GGG + chr2.3:54837390-54837409 MS.gene52393:CDS 40.0%
!! AGCTTTTCAGGCACTACAAA+TGG - chr2.3:54837661-54837680 None:intergenic 40.0%
AAACTGATGGTCCTTTGGCA+AGG - chr2.3:54837540-54837559 None:intergenic 45.0%
AACTGATGGTCCTTTGGCAA+GGG - chr2.3:54837539-54837558 None:intergenic 45.0%
AGACCAACCCCACTTCTTAA+AGG - chr2.3:54837401-54837420 None:intergenic 45.0%
TATTGCAATACAGAGGCCCT+TGG - chr2.3:54837592-54837611 None:intergenic 45.0%
TGACATGCTGAAATTGGTGG+AGG + chr2.3:54837273-54837292 MS.gene52393:CDS 45.0%
! ATGCCTTTAAGAAGTGGGGT+TGG + chr2.3:54837395-54837414 MS.gene52393:CDS 45.0%
! CGATGTGCATGTTTTGTCCA+TGG - chr2.3:54837767-54837786 None:intergenic 45.0%
! GTCGATGCCTTTAAGAAGTG+GGG + chr2.3:54837391-54837410 MS.gene52393:CDS 45.0%
CGAAAAGAGGGTCCTTCCAA+GGG + chr2.3:54837573-54837592 MS.gene52393:CDS 50.0%
GGCATGCAATGCTACACCAA+AGG - chr2.3:54837335-54837354 None:intergenic 50.0%
TCGAAAAGAGGGTCCTTCCA+AGG + chr2.3:54837572-54837591 MS.gene52393:CDS 50.0%
GATGCACTTGCCCTTGCCAA+AGG + chr2.3:54837526-54837545 MS.gene52393:CDS 55.0%
GCAATACAGAGGCCCTTGGA+AGG - chr2.3:54837588-54837607 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 54837232 54837789 54837232 ID=MS.gene52393
chr2.3 mRNA 54837232 54837789 54837232 ID=MS.gene52393.t1;Parent=MS.gene52393
chr2.3 exon 54837232 54837789 54837232 ID=MS.gene52393.t1.exon1;Parent=MS.gene52393.t1
chr2.3 CDS 54837232 54837789 54837232 ID=cds.MS.gene52393.t1;Parent=MS.gene52393.t1
Gene Sequence

>MS.gene52393

ATGCTTTGGTTAAGGAGTCGGGCATTTCAGACACCGACACATGACATGCTGAAATTGGTGGAGGAATTAAAGGATTTGGGTTTTGCTACTTCAAAAACAACCTTTGGTGTAGCATTGCATGCCAAACTATCTGTAAGGAAAACATTGTGGGAAGAGAAAGTCGATGCCTTTAAGAAGTGGGGTTGGTCTGATGAAGATGTTCTACAAGCATTTAGAAGGCAACCACATTGTATGTTGGTATCCATTGATAAAATTAATTTAGTGATGAACTTTTGGGTCAATCAGTTAGGTTGGGATGCACTTGCCCTTGCCAAAGGACCATCAGTTTTTTCTTTAAGTTTCGAAAAGAGGGTCCTTCCAAGGGCCTCTGTATTGCAATATCTTCTGAAGAAAGGTTTGCGAAAAAAGGATGCAAGCTTAACTTGTCCATTTGTAGTGCCTGAAAAGCTGTTTCTTGATAAGTGTATAAAGGGTATTAAGGAGTCTTCTTATCTATTAAAGTTGTATGAGGAAAAACTCAATCTTGCTTACACCATGGACAAAACATGCACATCGTGA
Protein sequence

>MS.gene52393.t1

MLWLRSRAFQTPTHDMLKLVEELKDLGFATSKTTFGVALHAKLSVRKTLWEEKVDAFKKWGWSDEDVLQAFRRQPHCMLVSIDKINLVMNFWVNQLGWDALALAKGPSVFSLSFEKRVLPRASVLQYLLKKGLRKKDASLTCPFVVPEKLFLDKCIKGIKESSYLLKLYEEKLNLAYTMDKTCTS