Multiple sequence alignment - TraesCS1D01G397600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G397600 chr1D 100.000 3992 0 0 1 3992 465127688 465131679 0.000000e+00 7372
1 TraesCS1D01G397600 chr7B 89.921 3542 232 56 111 3585 504187869 504191352 0.000000e+00 4447
2 TraesCS1D01G397600 chr7B 88.020 409 21 5 3586 3992 504191692 504192074 3.640000e-125 459
3 TraesCS1D01G397600 chr7B 86.381 257 22 9 3202 3448 322488708 322488455 6.580000e-68 268
4 TraesCS1D01G397600 chr1A 94.815 2835 99 10 396 3200 557488442 557491258 0.000000e+00 4377
5 TraesCS1D01G397600 chr1A 94.416 394 16 5 3586 3974 557491447 557491839 5.710000e-168 601
6 TraesCS1D01G397600 chr1A 91.045 268 23 1 108 375 557488103 557488369 1.050000e-95 361
7 TraesCS1D01G397600 chr1A 92.063 126 9 1 3451 3575 557491262 557491387 4.100000e-40 176
8 TraesCS1D01G397600 chr1A 94.231 104 6 0 1 104 557487956 557488059 4.130000e-35 159
9 TraesCS1D01G397600 chr2B 89.649 3362 222 59 287 3585 87924834 87921536 0.000000e+00 4165
10 TraesCS1D01G397600 chr2B 93.955 397 20 3 3599 3992 87921126 87920731 7.380000e-167 597
11 TraesCS1D01G397600 chr4B 93.212 2033 80 19 111 2129 112034938 112036926 0.000000e+00 2937
12 TraesCS1D01G397600 chr4B 93.890 1293 62 5 2128 3406 112037030 112038319 0.000000e+00 1934
13 TraesCS1D01G397600 chr4B 94.595 407 21 1 3586 3992 112038968 112039373 2.620000e-176 628
14 TraesCS1D01G397600 chr4B 89.744 195 16 4 3393 3585 112038720 112038912 3.080000e-61 246
15 TraesCS1D01G397600 chr4B 90.385 104 7 2 1 104 112034787 112034887 2.500000e-27 134
16 TraesCS1D01G397600 chr3A 90.039 763 59 13 2830 3585 22220085 22219333 0.000000e+00 972
17 TraesCS1D01G397600 chr3A 89.815 756 63 11 2836 3585 22222609 22221862 0.000000e+00 957
18 TraesCS1D01G397600 chr3A 90.280 679 47 13 2912 3585 22207061 22206397 0.000000e+00 870
19 TraesCS1D01G397600 chr3A 89.681 407 21 6 3586 3992 22206342 22205957 2.140000e-137 499
20 TraesCS1D01G397600 chr3A 88.698 407 25 4 3586 3992 22219278 22218893 1.000000e-130 477
21 TraesCS1D01G397600 chr3A 88.206 407 27 8 3586 3992 22221807 22221422 2.170000e-127 466
22 TraesCS1D01G397600 chr3A 81.507 146 17 9 114 253 723563480 723563339 1.170000e-20 111
23 TraesCS1D01G397600 chr5B 91.327 196 17 0 3196 3391 447183235 447183430 6.580000e-68 268
24 TraesCS1D01G397600 chr5B 92.045 88 6 1 2359 2445 163260733 163260646 5.420000e-24 122
25 TraesCS1D01G397600 chr2A 85.417 240 30 5 3213 3450 3580456 3580220 1.110000e-60 244


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G397600 chr1D 465127688 465131679 3991 False 7372.0 7372 100.0000 1 3992 1 chr1D.!!$F1 3991
1 TraesCS1D01G397600 chr7B 504187869 504192074 4205 False 2453.0 4447 88.9705 111 3992 2 chr7B.!!$F1 3881
2 TraesCS1D01G397600 chr1A 557487956 557491839 3883 False 1134.8 4377 93.3140 1 3974 5 chr1A.!!$F1 3973
3 TraesCS1D01G397600 chr2B 87920731 87924834 4103 True 2381.0 4165 91.8020 287 3992 2 chr2B.!!$R1 3705
4 TraesCS1D01G397600 chr4B 112034787 112039373 4586 False 1175.8 2937 92.3652 1 3992 5 chr4B.!!$F1 3991
5 TraesCS1D01G397600 chr3A 22218893 22222609 3716 True 718.0 972 89.1895 2830 3992 4 chr3A.!!$R3 1162
6 TraesCS1D01G397600 chr3A 22205957 22207061 1104 True 684.5 870 89.9805 2912 3992 2 chr3A.!!$R2 1080

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
425 525 0.386858 CAGCACAGCAGCAACATCAC 60.387 55.000 0.0 0.0 36.85 3.06 F
493 593 1.355066 GACTCTGTACGGCAGCAAGC 61.355 60.000 0.0 0.0 44.66 4.01 F
1878 1981 1.271707 CCACCCGTAAACAATGGACCT 60.272 52.381 0.0 0.0 36.17 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1647 1.294659 CTGCTTCCGAGTCTGCAACC 61.295 60.000 0.0 0.0 34.90 3.77 R
1953 2056 1.829222 CCAAATGCCCATGAAGAGCTT 59.171 47.619 0.0 0.0 0.00 3.74 R
3174 5956 1.229428 TCTGCCTTGAAGACGCAAAG 58.771 50.000 0.0 0.0 30.85 2.77 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.962356 CGAGCAGCCCAAAATGGTCT 60.962 55.000 3.30 0.00 40.82 3.85
104 105 3.926616 GGATACAAGGACGTGGGATATG 58.073 50.000 0.00 0.00 0.00 1.78
107 108 0.880278 CAAGGACGTGGGATATGGCG 60.880 60.000 0.00 0.00 0.00 5.69
109 110 1.006102 GGACGTGGGATATGGCGAG 60.006 63.158 0.00 0.00 0.00 5.03
111 112 0.956633 GACGTGGGATATGGCGAGTA 59.043 55.000 0.00 0.00 0.00 2.59
192 237 1.003464 GCCCCATTTGTTGCTTCCATT 59.997 47.619 0.00 0.00 0.00 3.16
203 248 4.039124 TGTTGCTTCCATTCCTCCTTTTTC 59.961 41.667 0.00 0.00 0.00 2.29
204 249 2.819608 TGCTTCCATTCCTCCTTTTTCG 59.180 45.455 0.00 0.00 0.00 3.46
206 251 1.834188 TCCATTCCTCCTTTTTCGGC 58.166 50.000 0.00 0.00 0.00 5.54
207 252 1.354368 TCCATTCCTCCTTTTTCGGCT 59.646 47.619 0.00 0.00 0.00 5.52
218 263 4.766891 TCCTTTTTCGGCTTCTTTGATGAT 59.233 37.500 0.00 0.00 0.00 2.45
254 299 5.180117 CGATTTCCTCAATCATCATGGTACC 59.820 44.000 4.43 4.43 41.51 3.34
269 314 9.226606 CATCATGGTACCTTTAAGTTGTAGAAA 57.773 33.333 14.36 0.00 0.00 2.52
276 321 5.163131 ACCTTTAAGTTGTAGAAAGAGCCCA 60.163 40.000 0.00 0.00 32.94 5.36
285 330 4.590647 TGTAGAAAGAGCCCATAGAGGATG 59.409 45.833 0.00 0.00 41.22 3.51
296 341 5.068636 CCCATAGAGGATGTTTCTGATTGG 58.931 45.833 0.00 0.00 41.22 3.16
425 525 0.386858 CAGCACAGCAGCAACATCAC 60.387 55.000 0.00 0.00 36.85 3.06
437 537 2.613977 GCAACATCACTAGGTCAGCAGT 60.614 50.000 0.00 0.00 0.00 4.40
481 581 3.668447 CAAAGCATAGTGGTGACTCTGT 58.332 45.455 0.00 0.00 35.43 3.41
493 593 1.355066 GACTCTGTACGGCAGCAAGC 61.355 60.000 0.00 0.00 44.66 4.01
557 657 3.349927 CCAGTTGCTCTTGATCCAATCA 58.650 45.455 0.00 0.00 37.55 2.57
566 666 1.530183 GATCCAATCAGCCTGCCCC 60.530 63.158 0.00 0.00 0.00 5.80
607 707 3.264193 AGCAAGTGAGAGAGAGAGAGAGA 59.736 47.826 0.00 0.00 0.00 3.10
608 708 3.624861 GCAAGTGAGAGAGAGAGAGAGAG 59.375 52.174 0.00 0.00 0.00 3.20
609 709 4.623886 GCAAGTGAGAGAGAGAGAGAGAGA 60.624 50.000 0.00 0.00 0.00 3.10
613 713 3.776969 TGAGAGAGAGAGAGAGAGAGCTT 59.223 47.826 0.00 0.00 0.00 3.74
668 768 2.654289 CATGTCCCCGACGTGTCA 59.346 61.111 0.00 0.00 42.57 3.58
711 811 1.902508 GTCTTCCCATGTCACTCTGGA 59.097 52.381 0.00 0.00 34.24 3.86
958 1060 3.240302 AGGCAGTCTGGTGGTATATACC 58.760 50.000 22.97 22.97 46.62 2.73
1545 1647 2.778299 TCAACCGGTGAAAATGAGGAG 58.222 47.619 8.52 0.00 31.51 3.69
1878 1981 1.271707 CCACCCGTAAACAATGGACCT 60.272 52.381 0.00 0.00 36.17 3.85
2075 2192 7.831193 AGGTTAGTTCACCTCGTAATACTCTAA 59.169 37.037 0.00 0.00 44.63 2.10
2132 2249 7.176165 TGTTGCTACGGTACTCTAATATATGCT 59.824 37.037 0.00 0.00 0.00 3.79
2192 2414 7.252612 TGACATCTGGATTTGTTAGGTTAGA 57.747 36.000 0.00 0.00 0.00 2.10
2334 2556 1.816835 TGGAGGTGTGTAGTTAGCTCG 59.183 52.381 0.00 0.00 41.16 5.03
2382 2604 4.855298 ACTCCCTCCGATCCAAAATAAA 57.145 40.909 0.00 0.00 0.00 1.40
2415 2663 3.955771 GAACAACCTTAGTTCAACGCA 57.044 42.857 0.00 0.00 43.64 5.24
2565 2813 2.972625 TGTGTGCACAGCTATACCTTC 58.027 47.619 22.40 4.69 36.21 3.46
2570 2818 4.003648 GTGCACAGCTATACCTTCTGTTT 58.996 43.478 13.17 0.00 38.85 2.83
2760 3011 3.479979 GGGTCCGGATCATACCCC 58.520 66.667 18.43 13.65 46.12 4.95
2853 3104 2.480419 CGGCAGAAACGAAGTGAAGATT 59.520 45.455 0.00 0.00 45.00 2.40
2886 3137 3.737172 GGCACACACATGACGCCC 61.737 66.667 0.00 0.00 40.16 6.13
2976 3227 0.674581 CTGTCGGGAATCAAGCAGCA 60.675 55.000 0.00 0.00 0.00 4.41
2994 5776 4.824289 CAGCATCAGCCCAAAACTAATTT 58.176 39.130 0.00 0.00 43.56 1.82
3179 5961 9.231297 TGATGTATTTATTATAGCTCCCTTTGC 57.769 33.333 0.00 0.00 0.00 3.68
3200 5982 4.811024 TGCGTCTTCAAGGCAGAATAATAG 59.189 41.667 0.00 0.00 43.50 1.73
3211 5993 5.071115 AGGCAGAATAATAGTCCCTCTGTTC 59.929 44.000 0.00 0.00 36.67 3.18
3462 6677 3.292460 GGAGTATCAGACTACAGCCAGT 58.708 50.000 0.00 0.00 39.11 4.00
3463 6678 3.067461 GGAGTATCAGACTACAGCCAGTG 59.933 52.174 0.00 0.00 39.11 3.66
3476 6691 3.244875 ACAGCCAGTGAAATGGTGTGATA 60.245 43.478 7.88 0.00 42.75 2.15
3551 6767 8.725148 ACATATGCTTTCTTCTACAGAGTTTTG 58.275 33.333 1.58 0.00 31.12 2.44
3630 7266 7.588143 TTGCACCATATTAAAACATTTTCGG 57.412 32.000 0.00 0.00 0.00 4.30
3722 7358 4.080526 ACAGCATTTACGTTAGGAGGGAAT 60.081 41.667 0.00 0.00 0.00 3.01
3734 7370 3.892031 AGGAGGGAATATGATGGTCCAT 58.108 45.455 3.26 3.26 32.70 3.41
3751 7387 5.222027 TGGTCCATCAATCTTTGACAGGTTA 60.222 40.000 9.20 0.00 43.48 2.85
3968 7608 4.661222 TCAGCATTCAGGTTCCATACAAA 58.339 39.130 0.00 0.00 0.00 2.83
3969 7609 5.263599 TCAGCATTCAGGTTCCATACAAAT 58.736 37.500 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.560896 GCTAAACCACTACGTTTTGGACA 59.439 43.478 19.18 5.43 37.20 4.02
95 96 4.595762 TTAAGTACTCGCCATATCCCAC 57.404 45.455 0.00 0.00 0.00 4.61
104 105 2.608090 GGCACTTCATTAAGTACTCGCC 59.392 50.000 0.00 3.81 44.28 5.54
107 108 4.833390 ACAGGGCACTTCATTAAGTACTC 58.167 43.478 0.00 0.00 44.28 2.59
109 110 8.726870 TTATTACAGGGCACTTCATTAAGTAC 57.273 34.615 0.00 0.00 44.28 2.73
192 237 2.884639 CAAAGAAGCCGAAAAAGGAGGA 59.115 45.455 0.00 0.00 0.00 3.71
203 248 5.239359 TCATTCAATCATCAAAGAAGCCG 57.761 39.130 0.00 0.00 0.00 5.52
204 249 6.802608 TGATCATTCAATCATCAAAGAAGCC 58.197 36.000 0.00 0.00 30.76 4.35
218 263 7.499895 TGATTGAGGAAATCGATGATCATTCAA 59.500 33.333 10.14 20.37 46.68 2.69
254 299 8.041323 TCTATGGGCTCTTTCTACAACTTAAAG 58.959 37.037 0.00 0.00 0.00 1.85
269 314 3.390639 CAGAAACATCCTCTATGGGCTCT 59.609 47.826 0.00 0.00 40.16 4.09
276 321 5.378230 TGCCAATCAGAAACATCCTCTAT 57.622 39.130 0.00 0.00 0.00 1.98
296 341 1.133668 AGAGAATGGGGCTGGTATTGC 60.134 52.381 0.00 0.00 0.00 3.56
425 525 1.205655 TGCTTGCTACTGCTGACCTAG 59.794 52.381 0.00 0.00 40.48 3.02
437 537 4.635223 CTGTATAATGCTCCTGCTTGCTA 58.365 43.478 0.00 0.00 40.48 3.49
530 630 1.302033 CAAGAGCAACTGGGCGACT 60.302 57.895 0.00 0.00 39.27 4.18
557 657 3.661648 AATTGACCGGGGCAGGCT 61.662 61.111 6.32 0.00 33.69 4.58
566 666 2.219674 GCTCTATTCGCTCAATTGACCG 59.780 50.000 15.50 15.50 0.00 4.79
607 707 3.583086 TCCTAAACCTAACAGCAAGCTCT 59.417 43.478 0.00 0.00 0.00 4.09
608 708 3.935828 CTCCTAAACCTAACAGCAAGCTC 59.064 47.826 0.00 0.00 0.00 4.09
609 709 3.328050 ACTCCTAAACCTAACAGCAAGCT 59.672 43.478 0.00 0.00 0.00 3.74
613 713 2.304761 CCCACTCCTAAACCTAACAGCA 59.695 50.000 0.00 0.00 0.00 4.41
652 752 2.970639 CTGACACGTCGGGGACAT 59.029 61.111 0.00 0.00 32.09 3.06
686 786 4.038522 CAGAGTGACATGGGAAGACGATAT 59.961 45.833 0.00 0.00 0.00 1.63
1545 1647 1.294659 CTGCTTCCGAGTCTGCAACC 61.295 60.000 0.00 0.00 34.90 3.77
1572 1674 2.948979 CTGTGCAACCAACCAAGAGTTA 59.051 45.455 0.00 0.00 33.60 2.24
1953 2056 1.829222 CCAAATGCCCATGAAGAGCTT 59.171 47.619 0.00 0.00 0.00 3.74
2093 2210 4.250464 CGTAGCAACATGACCTTTTCCTA 58.750 43.478 0.00 0.00 0.00 2.94
2140 2362 7.156694 AGAGAGGTAGACACATATAGGAGTT 57.843 40.000 0.00 0.00 0.00 3.01
2192 2414 9.003658 CCAAGTATTTCAACTCAGTGTTCTTAT 57.996 33.333 0.00 0.00 36.63 1.73
2382 2604 2.687935 AGGTTGTTCAAAACTGCGACAT 59.312 40.909 0.00 0.00 0.00 3.06
2415 2663 3.572682 TCCGATCCATAATAAGTGTCGCT 59.427 43.478 0.00 0.00 0.00 4.93
2706 2957 3.357079 GCGATGCCCGGCCTTATG 61.357 66.667 7.03 0.00 39.04 1.90
2727 2978 3.089284 GGACCCTCCGAATTTGACATTT 58.911 45.455 0.00 0.00 0.00 2.32
2760 3011 1.344763 GTGGATACCCAGGGAAGATCG 59.655 57.143 14.54 0.00 44.55 3.69
2814 3065 2.613691 CCGAAGTTGTATGTTACGCCT 58.386 47.619 0.00 0.00 0.00 5.52
2853 3104 2.858862 GCCATGGCAAGCACACACA 61.859 57.895 32.08 0.00 41.49 3.72
2886 3137 2.081212 GTGTCGCGTGAACTCCTCG 61.081 63.158 5.77 0.00 35.12 4.63
3174 5956 1.229428 TCTGCCTTGAAGACGCAAAG 58.771 50.000 0.00 0.00 30.85 2.77
3179 5961 5.463724 GGACTATTATTCTGCCTTGAAGACG 59.536 44.000 0.00 0.00 0.00 4.18
3200 5982 7.981102 ACAAAGTAAATAAGAACAGAGGGAC 57.019 36.000 0.00 0.00 0.00 4.46
3438 6653 3.301274 GGCTGTAGTCTGATACTCCCTT 58.699 50.000 0.00 0.00 39.80 3.95
3448 6663 3.005554 CCATTTCACTGGCTGTAGTCTG 58.994 50.000 0.00 0.00 0.00 3.51
3449 6664 2.639839 ACCATTTCACTGGCTGTAGTCT 59.360 45.455 0.00 0.00 40.15 3.24
3462 6677 3.273434 GCAGCTCTATCACACCATTTCA 58.727 45.455 0.00 0.00 0.00 2.69
3463 6678 2.286294 CGCAGCTCTATCACACCATTTC 59.714 50.000 0.00 0.00 0.00 2.17
3476 6691 1.582968 CAAATGGCAACGCAGCTCT 59.417 52.632 0.00 0.00 42.51 4.09
3542 6757 6.651755 AATTTGTTTGACTGCAAAACTCTG 57.348 33.333 12.41 0.00 44.91 3.35
3551 6767 7.041916 TGGATGATGAAAAATTTGTTTGACTGC 60.042 33.333 0.00 0.00 0.00 4.40
3615 7251 9.974980 ATGTTGTACTTCCGAAAATGTTTTAAT 57.025 25.926 0.00 0.00 0.00 1.40
3629 7265 5.497474 ACTTGGTATCCATGTTGTACTTCC 58.503 41.667 0.00 0.00 38.49 3.46
3630 7266 6.653320 TGAACTTGGTATCCATGTTGTACTTC 59.347 38.462 19.61 8.86 46.89 3.01
3734 7370 6.353323 TGACACTTAACCTGTCAAAGATTGA 58.647 36.000 8.25 0.00 43.99 2.57
3751 7387 6.645790 AGCATTGAGAGAAAATTGACACTT 57.354 33.333 0.00 0.00 0.00 3.16
3759 7395 4.575645 GCAGAGCTAGCATTGAGAGAAAAT 59.424 41.667 18.83 0.00 0.00 1.82
3968 7608 3.523157 TGTGTACACCAATGATCTCCCAT 59.477 43.478 22.91 0.00 0.00 4.00
3969 7609 2.909662 TGTGTACACCAATGATCTCCCA 59.090 45.455 22.91 0.00 0.00 4.37


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.