AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene05960


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05960.t1 MTR_8g104765 97.222 216 6 0 1 216 1 216 3.97e-158 436
MS.gene05960.t1 MTR_4g120830 93.056 216 6 1 1 216 1 207 1.12e-147 409
MS.gene05960.t1 MTR_4g120825 92.593 216 7 1 1 216 1 207 5.89e-147 407
MS.gene05960.t1 MTR_3g008840 39.888 178 95 4 38 213 19 186 4.29e-38 130
MS.gene05960.t1 MTR_4g101760 34.951 206 118 5 9 213 11 201 6.59e-37 128
MS.gene05960.t1 MTR_4g035905 40.588 170 87 4 44 211 36 193 8.79e-37 127
MS.gene05960.t1 MTR_5g012000 40.351 171 93 4 42 211 46 208 6.10e-36 126
MS.gene05960.t1 MTR_4g035880 40.237 169 89 3 44 211 36 193 1.53e-35 124
MS.gene05960.t1 MTR_4g035870 37.688 199 107 5 11 208 8 190 6.05e-35 123
MS.gene05960.t1 MTR_3g008820 36.932 176 99 4 38 211 18 183 6.40e-34 120
MS.gene05960.t1 MTR_4g025610 34.884 172 107 2 44 213 32 200 5.76e-33 118
MS.gene05960.t1 MTR_7g108790 34.884 172 100 3 45 216 34 193 1.53e-32 117
MS.gene05960.t1 MTR_4g025550 30.952 210 132 4 6 213 2 200 1.29e-31 115
MS.gene05960.t1 MTR_4g025590 34.302 172 108 2 44 213 3 171 1.34e-31 114
MS.gene05960.t1 MTR_3g008760 33.333 183 113 2 28 209 50 224 7.44e-31 113
MS.gene05960.t1 MTR_4g025620 33.721 172 109 2 44 213 32 200 2.02e-30 112
MS.gene05960.t1 MTR_2g043560 36.994 173 89 4 43 212 33 188 6.46e-28 105
MS.gene05960.t1 MTR_1g088540 37.419 155 85 3 61 215 3 145 2.26e-26 99.8
MS.gene05960.t1 MTR_4g035855 31.925 213 132 6 1 211 1 202 4.13e-26 100
MS.gene05960.t1 MTR_4g124855 31.884 207 113 9 7 208 11 194 4.23e-25 97.8
MS.gene05960.t1 MTR_0036s0140 32.317 164 90 6 45 207 78 221 7.49e-17 76.6
MS.gene05960.t1 MTR_3g010780 29.697 165 101 4 45 207 71 222 4.11e-16 76.6
MS.gene05960.t1 MTR_8g042900 29.518 166 101 4 45 207 76 228 3.85e-15 73.9
MS.gene05960.t1 MTR_8g023150 25.150 167 108 3 45 208 77 229 7.58e-14 70.1
MS.gene05960.t1 MTR_8g023310 25.581 172 117 3 44 213 67 229 4.10e-13 68.2
MS.gene05960.t1 MTR_3g091380 25.000 200 140 4 9 206 42 233 2.02e-12 65.9
MS.gene05960.t1 MTR_1g008140 26.506 166 113 4 45 206 82 242 2.54e-12 65.9
MS.gene05960.t1 MTR_7g112580 24.623 199 137 4 10 206 3 190 7.69e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05960.t1 AT2G01610 56.842 190 76 4 33 216 33 222 2.26e-70 214
MS.gene05960.t1 AT1G14890 54.106 207 77 5 9 214 29 218 1.19e-68 209
MS.gene05960.t1 AT1G23205 53.846 182 74 3 39 215 28 204 6.08e-60 187
MS.gene05960.t1 AT1G70720 44.860 214 106 4 3 215 8 210 1.62e-57 181
MS.gene05960.t1 AT1G70720 47.959 196 90 4 21 215 14 198 1.31e-56 178
MS.gene05960.t1 AT5G62350 40.642 187 103 3 27 212 21 200 5.44e-40 136
MS.gene05960.t1 AT4G25260 37.745 204 115 5 12 213 7 200 3.58e-39 134
MS.gene05960.t1 AT3G47380 39.153 189 105 4 28 213 20 201 2.31e-37 129
MS.gene05960.t1 AT4G12390 41.520 171 93 3 44 213 39 203 4.93e-36 126
MS.gene05960.t1 AT1G62770 37.968 187 106 5 29 213 20 198 5.14e-35 123
MS.gene05960.t1 AT4G25250 32.020 203 127 5 9 210 4 196 1.18e-33 119
MS.gene05960.t1 AT5G20740 36.019 211 114 6 10 216 7 200 8.75e-33 117
MS.gene05960.t1 AT5G20740 35.096 208 120 5 10 216 41 234 3.01e-32 117
MS.gene05960.t1 AT1G62760 37.209 172 97 4 41 211 144 305 3.82e-31 116
MS.gene05960.t1 AT5G51520 31.220 205 121 5 10 207 8 199 4.95e-31 113
MS.gene05960.t1 AT5G62360 35.294 170 97 4 43 211 42 199 7.33e-31 112
MS.gene05960.t1 AT4G00080 30.542 203 122 5 9 207 9 196 9.32e-26 99.8
MS.gene05960.t1 AT2G47670 32.370 173 104 4 44 215 48 208 7.30e-21 87.0
MS.gene05960.t1 AT3G62820 26.829 205 126 5 13 215 12 194 2.36e-20 85.1
MS.gene05960.t1 AT3G14300 27.059 170 108 4 45 207 271 431 9.88e-16 75.9
MS.gene05960.t1 AT3G14300 26.437 174 118 5 42 213 456 621 1.86e-11 63.2
MS.gene05960.t1 AT5G53370 26.066 211 135 7 10 216 78 271 1.08e-14 72.8
MS.gene05960.t1 AT5G53370 26.066 211 135 7 10 216 42 235 1.23e-14 72.4
MS.gene05960.t1 AT3G49220 28.293 205 115 4 10 206 97 277 4.42e-14 70.9
MS.gene05960.t1 AT3G49220 28.293 205 115 4 10 206 52 232 4.62e-14 70.9
MS.gene05960.t1 AT3G49220 28.293 205 115 4 10 206 97 277 5.26e-14 70.5
MS.gene05960.t1 AT5G62340 27.232 224 133 10 1 213 1 205 2.52e-13 66.6
MS.gene05960.t1 AT1G53830 25.301 166 112 4 44 207 61 216 6.44e-11 61.6

Find 60 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGCTTTGGCACTTGTTAA+TGG 0.258713 4.2:+1759712 MS.gene05960:CDS
GTTAATGGTTACGCACAAAA+AGG 0.286538 4.2:+1759727 MS.gene05960:CDS
TCTGCTCCGGTGGCGGTTGT+TGG 0.357625 4.2:-1759184 None:intergenic
CGAAGAAGATGATTGATAAT+AGG 0.374294 4.2:-1759138 None:intergenic
GTCGGAACTGGCGCCGGTGC+CGG 0.392219 4.2:+1759529 MS.gene05960:CDS
ATCTGCTTCGCGAGTGAGAT+TGG 0.399064 4.2:-1759395 None:intergenic
CAGATTGGAGCCGTCGGAAC+TGG 0.401781 4.2:+1759517 MS.gene05960:CDS
GGCGGTTGTTGGACGGAGAT+TGG 0.404587 4.2:-1759173 None:intergenic
AGGGAAGTGTAGCATATGTC+AGG 0.436656 4.2:-1759271 None:intergenic
GTGGACTTTGGAGAAGCTTA+CGG 0.443650 4.2:-1759353 None:intergenic
GAAGTTCACGAGTAATGCTT+TGG 0.455722 4.2:+1759699 MS.gene05960:CDS
TTTGGAGAAGCTTACGGCTA+TGG 0.464721 4.2:-1759347 None:intergenic
GGGATTCTGTTGAACTGCAT+TGG 0.465344 4.2:-1759305 None:intergenic
AGAGGCGGTTCGGTGGACTT+TGG 0.468926 4.2:-1759365 None:intergenic
CTTAAACAGATGCGACAGAT+TGG 0.471352 4.2:+1759502 MS.gene05960:CDS
CTCCGGTGGCGGTTGTTGGA+CGG 0.475048 4.2:-1759180 None:intergenic
GGCGATGCGAGCGAGTTGGC+CGG 0.484500 4.2:-1759326 None:intergenic
GAGGAAACTGTGAGAGTGTT+GGG 0.489323 4.2:-1759116 None:intergenic
TGGAGGTTCTGCTCCGGTGG+CGG 0.492157 4.2:-1759191 None:intergenic
GGAGGAAACTGTGAGAGTGT+TGG 0.492920 4.2:-1759117 None:intergenic
AAACGAATCTGCTCCGGCAC+CGG 0.499792 4.2:-1759542 None:intergenic
TTCTGTACATCCGCTTTCAC+AGG 0.501048 4.2:-1759658 None:intergenic
TCGTCGTTGGTGGTGGTTGG+AGG 0.502344 4.2:-1759208 None:intergenic
GCGTCGTCGTTGGTGGTGGT+TGG 0.506567 4.2:-1759211 None:intergenic
CTCCGTCCAACAACCGCCAC+CGG 0.510383 4.2:+1759178 MS.gene05960:CDS
TGGAGAGATAAGAGGCGGTT+CGG 0.511261 4.2:-1759375 None:intergenic
GGTGGTTGGAGGTTCTGCTC+CGG 0.513292 4.2:-1759197 None:intergenic
TTCCGCGTCGTCGTTGGTGG+TGG 0.522970 4.2:-1759215 None:intergenic
AGTGAGATTGGAGAGATAAG+AGG 0.523775 4.2:-1759383 None:intergenic
GATGAATTCCGCGTCGTCGT+TGG 0.527488 4.2:-1759221 None:intergenic
GAATTCCGCGTCGTCGTTGG+TGG 0.529270 4.2:-1759218 None:intergenic
GGCACCGGCGCCAGTTCCGA+CGG 0.530037 4.2:-1759527 None:intergenic
CTGCATTGGCGTAGCGAGAG+AGG 0.532228 4.2:-1759291 None:intergenic
AGAAGATGATTGATAATAGG+AGG 0.540415 4.2:-1759135 None:intergenic
AAACAGAAACGAATCTGCTC+CGG 0.547260 4.2:-1759548 None:intergenic
GGTTGGAGGTTCTGCTCCGG+TGG 0.548791 4.2:-1759194 None:intergenic
GCGATGCGAGCGAGTTGGCC+GGG 0.559441 4.2:-1759325 None:intergenic
GGAGCCGTCGGAACTGGCGC+CGG 0.568149 4.2:+1759523 MS.gene05960:CDS
TGCATTGGCGTAGCGAGAGA+GGG 0.576173 4.2:-1759290 None:intergenic
TGTACAGAATCGTGTCTCGA+AGG 0.577511 4.2:+1759672 MS.gene05960:CDS
CTATGGCGATGCGAGCGAGT+TGG 0.577700 4.2:-1759330 None:intergenic
TACTGATGAAGAAACGTGTA+CGG 0.583108 4.2:+1759609 MS.gene05960:CDS
CGAGATTTGAGAAACAGTCA+TGG 0.583249 4.2:-1759450 None:intergenic
GATGAAGAAACGTGTACGGA+TGG 0.588482 4.2:+1759613 MS.gene05960:CDS
ACAGTCATGGAGAGCGAGTG+CGG 0.590149 4.2:-1759437 None:intergenic
AATGCAGTTCAACAGAATCC+CGG 0.598872 4.2:+1759307 MS.gene05960:CDS
AGATGAGTAACGTGCAGACG+TGG 0.606703 4.2:+1759572 MS.gene05960:CDS
AGAGATAAGAGGCGGTTCGG+TGG 0.627950 4.2:-1759372 None:intergenic
GGGAAGTGTAGCATATGTCA+GGG 0.632502 4.2:-1759270 None:intergenic
GCATCTGTTTAAGCGAGCCA+CGG 0.637289 4.2:-1759492 None:intergenic
GTGTTGCGTTGCAACTTGAA+CGG 0.641224 4.2:-1759243 None:intergenic
ATGCGACAGATTGGAGCCGT+CGG 0.644503 4.2:+1759511 MS.gene05960:CDS
TGGACGGAGATTGGAGAATG+TGG 0.645484 4.2:-1759164 None:intergenic
AACCACCACCAACGACGACG+CGG 0.663044 4.2:+1759213 MS.gene05960:CDS
CGTGCAGACGTGGATGAGTG+CGG 0.674734 4.2:+1759582 MS.gene05960:CDS
GAGATTGGAGAGATAAGAGG+CGG 0.675120 4.2:-1759380 None:intergenic
AGAAGATTGTCCTGTGAAAG+CGG 0.686477 4.2:+1759648 MS.gene05960:CDS
ACGGAGATTGGAGAATGTGG+CGG 0.690066 4.2:-1759161 None:intergenic
GATGCTGTTGATGAAATCCG+TGG 0.736309 4.2:+1759475 MS.gene05960:CDS
ACTCGCGAAGCAGATTACAG+CGG 0.792244 4.2:+1759403 MS.gene05960:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAAGATGATTGATAATAGG+AGG - chr4.2:1759138-1759157 None:intergenic 30.0%
! CGAAGAAGATGATTGATAAT+AGG - chr4.2:1759141-1759160 None:intergenic 30.0%
GTTAATGGTTACGCACAAAA+AGG + chr4.2:1759727-1759746 MS.gene05960:CDS 35.0%
TACTGATGAAGAAACGTGTA+CGG + chr4.2:1759609-1759628 MS.gene05960:CDS 35.0%
! AATGCTTTGGCACTTGTTAA+TGG + chr4.2:1759712-1759731 MS.gene05960:CDS 35.0%
AAACAGAAACGAATCTGCTC+CGG - chr4.2:1759551-1759570 None:intergenic 40.0%
AATGCAGTTCAACAGAATCC+CGG + chr4.2:1759307-1759326 MS.gene05960:CDS 40.0%
AGAAGATTGTCCTGTGAAAG+CGG + chr4.2:1759648-1759667 MS.gene05960:CDS 40.0%
AGTGAGATTGGAGAGATAAG+AGG - chr4.2:1759386-1759405 None:intergenic 40.0%
CGAGATTTGAGAAACAGTCA+TGG - chr4.2:1759453-1759472 None:intergenic 40.0%
CTTAAACAGATGCGACAGAT+TGG + chr4.2:1759502-1759521 MS.gene05960:CDS 40.0%
GAAGTTCACGAGTAATGCTT+TGG + chr4.2:1759699-1759718 MS.gene05960:CDS 40.0%
GAGATTGGAGAGATAAGAGG+CGG - chr4.2:1759383-1759402 None:intergenic 45.0%
GATGAAGAAACGTGTACGGA+TGG + chr4.2:1759613-1759632 MS.gene05960:CDS 45.0%
GGGATTCTGTTGAACTGCAT+TGG - chr4.2:1759308-1759327 None:intergenic 45.0%
GTGTTGCGTTGCAACTTGAA+CGG - chr4.2:1759246-1759265 None:intergenic 45.0%
TGTACAGAATCGTGTCTCGA+AGG + chr4.2:1759672-1759691 MS.gene05960:CDS 45.0%
TTCTGTACATCCGCTTTCAC+AGG - chr4.2:1759661-1759680 None:intergenic 45.0%
TTTGGAGAAGCTTACGGCTA+TGG - chr4.2:1759350-1759369 None:intergenic 45.0%
! AGGGAAGTGTAGCATATGTC+AGG - chr4.2:1759274-1759293 None:intergenic 45.0%
! GATGCTGTTGATGAAATCCG+TGG + chr4.2:1759475-1759494 MS.gene05960:CDS 45.0%
! GGGAAGTGTAGCATATGTCA+GGG - chr4.2:1759273-1759292 None:intergenic 45.0%
! GTGGACTTTGGAGAAGCTTA+CGG - chr4.2:1759356-1759375 None:intergenic 45.0%
!! GAGGAAACTGTGAGAGTGTT+GGG - chr4.2:1759119-1759138 None:intergenic 45.0%
ACGGAGATTGGAGAATGTGG+CGG - chr4.2:1759164-1759183 None:intergenic 50.0%
ACTCGCGAAGCAGATTACAG+CGG + chr4.2:1759403-1759422 MS.gene05960:CDS 50.0%
AGATGAGTAACGTGCAGACG+TGG + chr4.2:1759572-1759591 MS.gene05960:CDS 50.0%
ATCTGCTTCGCGAGTGAGAT+TGG - chr4.2:1759398-1759417 None:intergenic 50.0%
GCATCTGTTTAAGCGAGCCA+CGG - chr4.2:1759495-1759514 None:intergenic 50.0%
TGGACGGAGATTGGAGAATG+TGG - chr4.2:1759167-1759186 None:intergenic 50.0%
TGGAGAGATAAGAGGCGGTT+CGG - chr4.2:1759378-1759397 None:intergenic 50.0%
! GGAGGAAACTGTGAGAGTGT+TGG - chr4.2:1759120-1759139 None:intergenic 50.0%
AAACGAATCTGCTCCGGCAC+CGG - chr4.2:1759545-1759564 None:intergenic 55.0%
ACAGTCATGGAGAGCGAGTG+CGG - chr4.2:1759440-1759459 None:intergenic 55.0%
ATGCGACAGATTGGAGCCGT+CGG + chr4.2:1759511-1759530 MS.gene05960:CDS 55.0%
GATGAATTCCGCGTCGTCGT+TGG - chr4.2:1759224-1759243 None:intergenic 55.0%
! AGAGATAAGAGGCGGTTCGG+TGG - chr4.2:1759375-1759394 None:intergenic 55.0%
! TGCATTGGCGTAGCGAGAGA+GGG - chr4.2:1759293-1759312 None:intergenic 55.0%
AACCACCACCAACGACGACG+CGG + chr4.2:1759213-1759232 MS.gene05960:CDS 60.0%
CAGATTGGAGCCGTCGGAAC+TGG + chr4.2:1759517-1759536 MS.gene05960:CDS 60.0%
CGTGCAGACGTGGATGAGTG+CGG + chr4.2:1759582-1759601 MS.gene05960:CDS 60.0%
CTATGGCGATGCGAGCGAGT+TGG - chr4.2:1759333-1759352 None:intergenic 60.0%
GAATTCCGCGTCGTCGTTGG+TGG - chr4.2:1759221-1759240 None:intergenic 60.0%
GGCGGTTGTTGGACGGAGAT+TGG - chr4.2:1759176-1759195 None:intergenic 60.0%
GGTGGTTGGAGGTTCTGCTC+CGG - chr4.2:1759200-1759219 None:intergenic 60.0%
! CTGCATTGGCGTAGCGAGAG+AGG - chr4.2:1759294-1759313 None:intergenic 60.0%
!! AGAGGCGGTTCGGTGGACTT+TGG - chr4.2:1759368-1759387 None:intergenic 60.0%
!! TCGTCGTTGGTGGTGGTTGG+AGG - chr4.2:1759211-1759230 None:intergenic 60.0%
CTCCGTCCAACAACCGCCAC+CGG + chr4.2:1759178-1759197 MS.gene05960:CDS 65.0%
GGTTGGAGGTTCTGCTCCGG+TGG - chr4.2:1759197-1759216 None:intergenic 65.0%
TGGAGGTTCTGCTCCGGTGG+CGG - chr4.2:1759194-1759213 None:intergenic 65.0%
! CTCCGGTGGCGGTTGTTGGA+CGG - chr4.2:1759183-1759202 None:intergenic 65.0%
! TCTGCTCCGGTGGCGGTTGT+TGG - chr4.2:1759187-1759206 None:intergenic 65.0%
! TTCCGCGTCGTCGTTGGTGG+TGG - chr4.2:1759218-1759237 None:intergenic 65.0%
!! GCGTCGTCGTTGGTGGTGGT+TGG - chr4.2:1759214-1759233 None:intergenic 65.0%
! GCGATGCGAGCGAGTTGGCC+GGG - chr4.2:1759328-1759347 None:intergenic 70.0%
! GGCGATGCGAGCGAGTTGGC+CGG - chr4.2:1759329-1759348 None:intergenic 70.0%
GGAGCCGTCGGAACTGGCGC+CGG + chr4.2:1759523-1759542 MS.gene05960:CDS 75.0%
!! GGCACCGGCGCCAGTTCCGA+CGG - chr4.2:1759530-1759549 None:intergenic 75.0%
!! GTCGGAACTGGCGCCGGTGC+CGG + chr4.2:1759529-1759548 MS.gene05960:CDS 75.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 1759109 1759759 1759109 ID=MS.gene05960
chr4.2 mRNA 1759109 1759759 1759109 ID=MS.gene05960.t1;Parent=MS.gene05960
chr4.2 exon 1759109 1759759 1759109 ID=MS.gene05960.t1.exon1;Parent=MS.gene05960.t1
chr4.2 CDS 1759109 1759759 1759109 ID=cds.MS.gene05960.t1;Parent=MS.gene05960.t1
Gene Sequence

>MS.gene05960

ATGACAACCCAACACTCTCACAGTTTCCTCCTATTATCAATCATCTTCTTCGCCGCCACATTCTCCAATCTCCGTCCAACAACCGCCACCGGAGCAGAACCTCCAACCACCACCAACGACGACGCGGAATTCATCCGTTCAAGTTGCAACGCAACACTCTACCCTGACATATGCTACACTTCCCTCTCTCGCTACGCCAATGCAGTTCAACAGAATCCCGGCCAACTCGCTCGCATCGCCATAGCCGTAAGCTTCTCCAAAGTCCACCGAACCGCCTCTTATCTCTCCAATCTCACTCGCGAAGCAGATTACAGCGGTAGTTCACGCGCCGCACTCGCTCTCCATGACTGTTTCTCAAATCTCGACGATGCTGTTGATGAAATCCGTGGCTCGCTTAAACAGATGCGACAGATTGGAGCCGTCGGAACTGGCGCCGGTGCCGGAGCAGATTCGTTTCTGTTTCAGATGAGTAACGTGCAGACGTGGATGAGTGCGGCACTTACTGATGAAGAAACGTGTACGGATGGATTTCAAGATGTAGAAGATTGTCCTGTGAAAGCGGATGTACAGAATCGTGTCTCGAAGGTGAAGAAGTTCACGAGTAATGCTTTGGCACTTGTTAATGGTTACGCACAAAAAGGAATGCCATGA

Protein sequence

>MS.gene05960.t1

MTTQHSHSFLLLSIIFFAATFSNLRPTTATGAEPPTTTNDDAEFIRSSCNATLYPDICYTSLSRYANAVQQNPGQLARIAIAVSFSKVHRTASYLSNLTREADYSGSSRAALALHDCFSNLDDAVDEIRGSLKQMRQIGAVGTGAGAGADSFLFQMSNVQTWMSAALTDEETCTDGFQDVEDCPVKADVQNRVSKVKKFTSNALALVNGYAQKGMP