Multiple sequence alignment - TraesCS5D01G094400

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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 TraesCS5D01G094400 chr5D 100.000 2480 0 0 1 2480 104114146 104111667 0.000000e+00 4580
1 TraesCS5D01G094400 chr5D 85.766 836 79 27 831 1657 104143120 104142316 0.000000e+00 848
2 TraesCS5D01G094400 chr5D 83.750 160 21 4 2320 2476 539846115 539845958 1.990000e-31 147
3 TraesCS5D01G094400 chr5B 93.253 2505 115 18 1 2480 113328982 113326507 0.000000e+00 3640
4 TraesCS5D01G094400 chr5B 87.755 686 57 17 831 1509 113457012 113456347 0.000000e+00 776
5 TraesCS5D01G094400 chr5A 85.962 1382 112 29 977 2300 94310774 94312131 0.000000e+00 1402
6 TraesCS5D01G094400 chr5A 84.838 831 74 29 831 1647 94092227 94093019 0.000000e+00 789
7 TraesCS5D01G094400 chr5A 88.909 541 22 10 442 963 94309836 94310357 1.250000e-177 632
8 TraesCS5D01G094400 chr6A 89.655 493 45 2 1001 1487 10138117 10137625 7.530000e-175 623
9 TraesCS5D01G094400 chr6A 83.871 155 21 4 2320 2473 6272509 6272660 7.150000e-31 145
10 TraesCS5D01G094400 chr6B 84.651 645 67 16 898 1513 17091778 17091137 4.530000e-172 614
11 TraesCS5D01G094400 chr6B 84.578 616 77 11 898 1504 16970491 16971097 1.640000e-166 595
12 TraesCS5D01G094400 chr6D 85.476 599 60 15 898 1480 9147076 9147663 1.270000e-167 599
13 TraesCS5D01G094400 chr2D 85.714 147 18 3 2328 2473 649368177 649368321 4.270000e-33 152
14 TraesCS5D01G094400 chr2D 83.544 158 22 4 2320 2476 39308660 39308506 7.150000e-31 145
15 TraesCS5D01G094400 chr1D 85.714 147 18 3 2328 2473 6667269 6667413 4.270000e-33 152
16 TraesCS5D01G094400 chrUn 84.667 150 20 3 2328 2476 362186933 362187080 1.990000e-31 147
17 TraesCS5D01G094400 chrUn 84.667 150 20 3 2328 2476 462852996 462852849 1.990000e-31 147
18 TraesCS5D01G094400 chr4B 82.911 158 23 4 2320 2476 222603379 222603225 3.330000e-29 139


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 TraesCS5D01G094400 chr5D 104111667 104114146 2479 True 4580 4580 100.0000 1 2480 1 chr5D.!!$R1 2479
1 TraesCS5D01G094400 chr5D 104142316 104143120 804 True 848 848 85.7660 831 1657 1 chr5D.!!$R2 826
2 TraesCS5D01G094400 chr5B 113326507 113328982 2475 True 3640 3640 93.2530 1 2480 1 chr5B.!!$R1 2479
3 TraesCS5D01G094400 chr5B 113456347 113457012 665 True 776 776 87.7550 831 1509 1 chr5B.!!$R2 678
4 TraesCS5D01G094400 chr5A 94309836 94312131 2295 False 1017 1402 87.4355 442 2300 2 chr5A.!!$F2 1858
5 TraesCS5D01G094400 chr5A 94092227 94093019 792 False 789 789 84.8380 831 1647 1 chr5A.!!$F1 816
6 TraesCS5D01G094400 chr6B 17091137 17091778 641 True 614 614 84.6510 898 1513 1 chr6B.!!$R1 615
7 TraesCS5D01G094400 chr6B 16970491 16971097 606 False 595 595 84.5780 898 1504 1 chr6B.!!$F1 606
8 TraesCS5D01G094400 chr6D 9147076 9147663 587 False 599 599 85.4760 898 1480 1 chr6D.!!$F1 582

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
125 126 0.035152 ATGGCTCATGGCGTTTCAGA 60.035 50.0 0.0 0.0 42.94 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2570 1.00006 GCTTCTTCTTTGGCATGTGCA 60.0 47.619 7.36 0.0 44.36 4.57 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
52 53 4.724501 TGGCCCCGCGTGCATTAA 62.725 61.111 17.94 0.16 0.00 1.40
58 59 2.544903 GCCCCGCGTGCATTAATTAATT 60.545 45.455 8.01 5.89 0.00 1.40
71 72 3.508744 AATTAATTCAGGCCAGCAACG 57.491 42.857 5.01 0.00 0.00 4.10
89 90 4.208632 CCATGGTCTCTGGCGTTC 57.791 61.111 2.57 0.00 0.00 3.95
125 126 0.035152 ATGGCTCATGGCGTTTCAGA 60.035 50.000 0.00 0.00 42.94 3.27
138 139 0.396435 TTTCAGACCTGCCACGTCAT 59.604 50.000 0.00 0.00 32.41 3.06
149 150 1.412226 CACGTCATCGAGCAACACG 59.588 57.895 0.00 0.00 40.62 4.49
168 169 4.864334 GCTCGGGCTGACCATGGG 62.864 72.222 18.09 0.00 40.22 4.00
186 187 3.121030 CCAGGGCTGAAACGCGAG 61.121 66.667 15.93 0.00 0.00 5.03
249 250 0.814010 GGCGTTTCTATGTCGGGCAT 60.814 55.000 0.00 0.00 41.42 4.40
255 256 1.860676 TCTATGTCGGGCATAAACGC 58.139 50.000 3.63 0.00 39.36 4.84
277 278 2.740714 GGGCTGCGACGTTGCTAAG 61.741 63.158 27.33 18.40 35.36 2.18
280 281 1.687494 GCTGCGACGTTGCTAAGAGG 61.687 60.000 27.33 11.80 35.36 3.69
283 284 1.077089 GCGACGTTGCTAAGAGGGTC 61.077 60.000 20.81 0.00 0.00 4.46
286 287 0.608640 ACGTTGCTAAGAGGGTCAGG 59.391 55.000 0.00 0.00 0.00 3.86
304 305 5.337009 GGTCAGGTCGTGAAATACTTTCCTA 60.337 44.000 0.00 0.00 38.90 2.94
312 313 7.275123 GTCGTGAAATACTTTCCTATCGAGTTT 59.725 37.037 0.00 0.00 38.90 2.66
319 320 9.939802 AATACTTTCCTATCGAGTTTAGTTTGT 57.060 29.630 0.00 0.00 0.00 2.83
330 331 6.759356 TCGAGTTTAGTTTGTGACAAAGATCA 59.241 34.615 11.54 0.00 0.00 2.92
413 416 6.075046 GCATAGTTTTTCAGTTCGTTTTCCAC 60.075 38.462 0.00 0.00 0.00 4.02
543 546 3.820467 CCAAATTTACTGCCAGTCACTCA 59.180 43.478 0.00 0.00 0.00 3.41
562 570 1.226974 CGACTGGATGGCCACGTAG 60.227 63.158 8.16 9.18 39.92 3.51
569 577 2.925078 ATGGCCACGTAGTACCCAT 58.075 52.632 8.16 3.65 41.61 4.00
579 587 5.394443 CCACGTAGTACCCATAGCAAAAGTA 60.394 44.000 0.00 0.00 41.61 2.24
596 608 6.611381 CAAAAGTAACCATGTGATACCAGTG 58.389 40.000 0.00 0.00 0.00 3.66
718 731 3.419915 CGAGGAAACATTTTCTCATGCG 58.580 45.455 12.19 0.00 41.88 4.73
786 808 1.399791 CTCTACCTCGTCGTGGTAACC 59.600 57.143 22.61 0.00 39.29 2.85
893 918 4.268359 CAAAGCCCTAATGAAGCTTCTCT 58.732 43.478 26.09 15.52 45.77 3.10
896 921 2.681976 GCCCTAATGAAGCTTCTCTGCA 60.682 50.000 26.09 7.63 34.08 4.41
965 1002 1.118838 CCAGCCTCTTCTTCCTCGAT 58.881 55.000 0.00 0.00 0.00 3.59
989 1429 4.141018 TCCCTAGTCATAGCACCATACTGA 60.141 45.833 0.00 0.00 0.00 3.41
996 1445 6.151985 AGTCATAGCACCATACTGATAGCTAC 59.848 42.308 0.00 0.00 37.40 3.58
997 1446 6.151985 GTCATAGCACCATACTGATAGCTACT 59.848 42.308 0.00 0.00 37.40 2.57
1039 1499 3.385384 CCCTCCTGCTGCTCGTGA 61.385 66.667 0.00 0.00 0.00 4.35
1122 1588 4.329545 AACCTGTGCGGCCACGAT 62.330 61.111 2.24 0.00 45.04 3.73
1221 1687 2.050714 TCGTTCGACGTGTGCTCC 60.051 61.111 0.00 0.00 43.14 4.70
1494 1960 4.107072 ACCCATAGATCGATCCATCCATT 58.893 43.478 21.66 4.09 0.00 3.16
1554 2024 5.710513 TGAATAATGTTGCAGCTGTTTCT 57.289 34.783 16.64 0.00 0.00 2.52
1573 2060 5.749596 TTCTGGTTAATCTGTTGTGTGTG 57.250 39.130 0.00 0.00 0.00 3.82
1574 2061 4.776349 TCTGGTTAATCTGTTGTGTGTGT 58.224 39.130 0.00 0.00 0.00 3.72
1575 2062 4.574421 TCTGGTTAATCTGTTGTGTGTGTG 59.426 41.667 0.00 0.00 0.00 3.82
1576 2063 4.265893 TGGTTAATCTGTTGTGTGTGTGT 58.734 39.130 0.00 0.00 0.00 3.72
1618 2114 0.040958 GTACCGTCGTCAGTCGTGTT 60.041 55.000 0.00 0.00 40.80 3.32
1672 2168 4.639755 TGTGTTTGCATGGATGTAGTATGG 59.360 41.667 0.00 0.00 0.00 2.74
1707 2203 1.772966 CAAATGTTTGCGTGTCGTGAC 59.227 47.619 0.00 0.00 0.00 3.67
1975 2504 6.930667 AAAACGCCTTCTTTACTTTGTCTA 57.069 33.333 0.00 0.00 0.00 2.59
1996 2525 8.675504 TGTCTACGTAAAAATGAAAAACCTCAA 58.324 29.630 0.00 0.00 0.00 3.02
2004 2533 7.486802 AAAATGAAAAACCTCAATGCTTCTG 57.513 32.000 0.00 0.00 0.00 3.02
2017 2546 7.308770 CCTCAATGCTTCTGAATAGTGTTTCAA 60.309 37.037 0.00 0.00 35.31 2.69
2036 2566 3.856521 TCAAGACACATTTGTTTTGCACG 59.143 39.130 9.74 0.00 44.06 5.34
2037 2567 3.502191 AGACACATTTGTTTTGCACGT 57.498 38.095 0.00 0.00 35.47 4.49
2038 2568 3.843999 AGACACATTTGTTTTGCACGTT 58.156 36.364 0.00 0.00 35.47 3.99
2039 2569 4.241681 AGACACATTTGTTTTGCACGTTT 58.758 34.783 0.00 0.00 35.47 3.60
2040 2570 4.688413 AGACACATTTGTTTTGCACGTTTT 59.312 33.333 0.00 0.00 35.47 2.43
2041 2571 4.706527 ACACATTTGTTTTGCACGTTTTG 58.293 34.783 0.00 0.00 28.43 2.44
2042 2572 4.900449 ACACATTTGTTTTGCACGTTTTGC 60.900 37.500 0.00 0.00 42.24 3.68
2079 2610 3.913089 AGCTATTTTCCCGCAAAACTTG 58.087 40.909 0.00 0.00 36.78 3.16
2095 2626 5.772825 AAACTTGTGTGCATACATGAACT 57.227 34.783 28.34 13.93 39.39 3.01
2108 2639 7.430992 CATACATGAACTTGGAGATGTATGG 57.569 40.000 17.50 5.26 46.61 2.74
2177 2709 2.370519 TGTGGGTTCATATGTATCCGGG 59.629 50.000 0.00 0.00 0.00 5.73
2183 2715 4.202430 GGTTCATATGTATCCGGGTTCCTT 60.202 45.833 0.00 0.00 0.00 3.36
2227 2759 4.141321 ACCCATAGGACAGTACGTAGATCA 60.141 45.833 0.00 0.00 36.73 2.92
2265 2797 4.955811 ATTTCACGAGGCCTATATGTCA 57.044 40.909 4.42 0.00 0.00 3.58
2277 2809 7.619050 AGGCCTATATGTCATGAAATCACTAG 58.381 38.462 1.29 2.89 0.00 2.57
2300 2832 6.086775 AGTTAAGAGGTACCCCTTACAAAGA 58.913 40.000 14.97 0.00 42.86 2.52
2307 2839 2.702748 ACCCCTTACAAAGAGTCACCT 58.297 47.619 0.00 0.00 0.00 4.00
2334 2866 3.457234 TCTGTGATGTGTGTCACTTGTC 58.543 45.455 4.27 0.42 46.70 3.18
2340 2872 0.027586 GTGTGTCACTTGTCGCAACC 59.972 55.000 4.27 0.00 0.00 3.77
2429 2961 1.874872 GAATTCCGAACCGTTTCACCA 59.125 47.619 0.00 0.00 0.00 4.17
2440 2972 3.506067 ACCGTTTCACCATTGGATTTCTC 59.494 43.478 10.37 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 4.405036 TGCTGGCCTGAATTAATTAATGCA 59.595 37.500 16.52 16.52 30.71 3.96
52 53 1.134946 GCGTTGCTGGCCTGAATTAAT 59.865 47.619 14.77 0.00 0.00 1.40
86 87 4.389576 CGTTGCTGCGGCTGGAAC 62.390 66.667 26.38 26.38 39.59 3.62
125 126 2.573869 CTCGATGACGTGGCAGGT 59.426 61.111 13.36 13.36 40.69 4.00
164 165 2.037847 GTTTCAGCCCTGGCCCAT 59.962 61.111 4.13 0.00 43.17 4.00
188 189 1.956170 ACAAAGACACGCCGAGCAG 60.956 57.895 0.00 0.00 0.00 4.24
262 263 1.078759 CCCTCTTAGCAACGTCGCAG 61.079 60.000 0.00 0.00 0.00 5.18
265 266 0.242825 TGACCCTCTTAGCAACGTCG 59.757 55.000 0.00 0.00 0.00 5.12
267 268 0.608640 CCTGACCCTCTTAGCAACGT 59.391 55.000 0.00 0.00 0.00 3.99
277 278 2.496470 AGTATTTCACGACCTGACCCTC 59.504 50.000 0.00 0.00 0.00 4.30
304 305 7.441157 TGATCTTTGTCACAAACTAAACTCGAT 59.559 33.333 0.00 0.00 0.00 3.59
319 320 8.208224 TGTTCTAACCTTTAGTGATCTTTGTCA 58.792 33.333 0.00 0.00 0.00 3.58
330 331 6.649557 CCGAAATCACTGTTCTAACCTTTAGT 59.350 38.462 0.00 0.00 0.00 2.24
333 334 4.215613 GCCGAAATCACTGTTCTAACCTTT 59.784 41.667 0.00 0.00 0.00 3.11
335 336 3.335579 GCCGAAATCACTGTTCTAACCT 58.664 45.455 0.00 0.00 0.00 3.50
336 337 2.418976 GGCCGAAATCACTGTTCTAACC 59.581 50.000 0.00 0.00 0.00 2.85
337 338 2.093783 CGGCCGAAATCACTGTTCTAAC 59.906 50.000 24.07 0.00 0.00 2.34
338 339 2.343101 CGGCCGAAATCACTGTTCTAA 58.657 47.619 24.07 0.00 0.00 2.10
339 340 1.404986 CCGGCCGAAATCACTGTTCTA 60.405 52.381 30.73 0.00 0.00 2.10
368 371 1.226435 GAGCGACACAGGTAGAGCG 60.226 63.158 0.00 0.00 0.00 5.03
413 416 6.594159 ACCATTAGATTTAGTTCGTCCAACTG 59.406 38.462 0.00 0.00 45.60 3.16
422 425 9.994432 CAGAAATCACACCATTAGATTTAGTTC 57.006 33.333 0.00 0.00 40.83 3.01
543 546 1.945354 CTACGTGGCCATCCAGTCGT 61.945 60.000 19.06 19.06 44.48 4.34
562 570 5.650703 ACATGGTTACTTTTGCTATGGGTAC 59.349 40.000 0.00 0.00 0.00 3.34
569 577 6.477253 TGGTATCACATGGTTACTTTTGCTA 58.523 36.000 0.00 0.00 0.00 3.49
579 587 1.354031 TGGCACTGGTATCACATGGTT 59.646 47.619 0.00 0.00 0.00 3.67
687 700 1.203313 GTTTCCTCGCGTTCGTTGG 59.797 57.895 5.77 0.36 36.96 3.77
718 731 4.176851 GGGACCGAGCTCGACGTC 62.177 72.222 36.59 31.19 43.02 4.34
893 918 3.510531 TTGCGGGGGTATTTATATGCA 57.489 42.857 0.00 0.00 0.00 3.96
896 921 4.105057 TCAGGTTTGCGGGGGTATTTATAT 59.895 41.667 0.00 0.00 0.00 0.86
965 1002 4.588951 CAGTATGGTGCTATGACTAGGGAA 59.411 45.833 0.00 0.00 0.00 3.97
989 1429 0.035458 GGCCGCCATTGAGTAGCTAT 59.965 55.000 3.91 0.00 0.00 2.97
996 1445 2.045045 TTGGAGGCCGCCATTGAG 60.045 61.111 30.16 0.00 37.86 3.02
997 1446 2.045045 CTTGGAGGCCGCCATTGA 60.045 61.111 30.16 13.87 37.86 2.57
1122 1588 1.672854 CCGCGATACCCAGGTTCAGA 61.673 60.000 8.23 0.00 0.00 3.27
1221 1687 4.436998 GACACGCTCCCGGACCAG 62.437 72.222 0.73 0.00 39.22 4.00
1494 1960 3.540751 CAGCTAGCTAGGCGGGCA 61.541 66.667 18.86 0.00 34.67 5.36
1554 2024 4.265893 ACACACACACAACAGATTAACCA 58.734 39.130 0.00 0.00 0.00 3.67
1573 2060 1.069668 ACTGGTACCTCGTTGGAACAC 59.930 52.381 14.36 0.42 39.29 3.32
1574 2061 1.416243 ACTGGTACCTCGTTGGAACA 58.584 50.000 14.36 0.00 39.71 3.18
1575 2062 2.821969 TCTACTGGTACCTCGTTGGAAC 59.178 50.000 14.36 0.00 39.71 3.62
1576 2063 3.159213 TCTACTGGTACCTCGTTGGAA 57.841 47.619 14.36 0.00 39.71 3.53
1618 2114 4.530710 ACTGCAAATCCGACACTAGTAA 57.469 40.909 0.00 0.00 0.00 2.24
1672 2168 3.853475 ACATTTGCATTTGAGCTAAGCC 58.147 40.909 3.62 0.00 33.11 4.35
1707 2203 5.751990 GGTACTTATATGTCGGACCAACAAG 59.248 44.000 5.55 6.85 0.00 3.16
1967 2496 9.511144 AGGTTTTTCATTTTTACGTAGACAAAG 57.489 29.630 0.00 0.00 0.00 2.77
1975 2504 6.983890 AGCATTGAGGTTTTTCATTTTTACGT 59.016 30.769 0.00 0.00 0.00 3.57
1984 2513 5.850557 TTCAGAAGCATTGAGGTTTTTCA 57.149 34.783 0.00 0.00 38.24 2.69
1996 2525 6.712095 TGTCTTGAAACACTATTCAGAAGCAT 59.288 34.615 0.00 0.00 40.21 3.79
2017 2546 3.502191 ACGTGCAAAACAAATGTGTCT 57.498 38.095 0.00 0.00 36.80 3.41
2036 2566 3.456280 TCTTCTTTGGCATGTGCAAAAC 58.544 40.909 7.36 0.00 38.91 2.43
2037 2567 3.815856 TCTTCTTTGGCATGTGCAAAA 57.184 38.095 7.29 7.29 41.32 2.44
2038 2568 3.719924 CTTCTTCTTTGGCATGTGCAAA 58.280 40.909 7.36 0.00 44.36 3.68
2039 2569 2.546373 GCTTCTTCTTTGGCATGTGCAA 60.546 45.455 7.36 0.00 44.36 4.08
2040 2570 1.000060 GCTTCTTCTTTGGCATGTGCA 60.000 47.619 7.36 0.00 44.36 4.57
2041 2571 1.271656 AGCTTCTTCTTTGGCATGTGC 59.728 47.619 0.00 0.00 41.14 4.57
2042 2572 4.978083 ATAGCTTCTTCTTTGGCATGTG 57.022 40.909 0.00 0.00 0.00 3.21
2043 2573 5.990120 AAATAGCTTCTTCTTTGGCATGT 57.010 34.783 0.00 0.00 0.00 3.21
2044 2574 5.809051 GGAAAATAGCTTCTTCTTTGGCATG 59.191 40.000 0.00 0.00 0.00 4.06
2079 2610 4.002982 TCTCCAAGTTCATGTATGCACAC 58.997 43.478 0.00 0.00 37.54 3.82
2095 2626 4.032960 AGTTGCAACCATACATCTCCAA 57.967 40.909 25.62 0.00 0.00 3.53
2135 2667 9.703892 CCCACATTGAAAACACATTTCTAAATA 57.296 29.630 2.98 0.00 46.27 1.40
2156 2688 2.370519 CCCGGATACATATGAACCCACA 59.629 50.000 10.38 0.00 0.00 4.17
2177 2709 7.410120 AATCCAGGAAAATACATGAAGGAAC 57.590 36.000 0.00 0.00 0.00 3.62
2183 2715 5.656416 GGGTCAAATCCAGGAAAATACATGA 59.344 40.000 0.00 0.00 0.00 3.07
2249 2781 4.955811 TTTCATGACATATAGGCCTCGT 57.044 40.909 9.68 1.83 0.00 4.18
2300 2832 5.163301 ACACATCACAGAAAGTTAGGTGACT 60.163 40.000 6.39 0.00 42.43 3.41
2307 2839 5.984233 GTGACACACATCACAGAAAGTTA 57.016 39.130 0.00 0.00 46.89 2.24
2383 2915 6.129062 GGTCGCACGATTCTAGAGATAAAATG 60.129 42.308 0.00 0.00 0.00 2.32
2393 2925 2.121116 ATTCGGTCGCACGATTCTAG 57.879 50.000 0.00 0.00 43.11 2.43
2429 2961 5.374921 AGATCTTGATGCGAGAAATCCAAT 58.625 37.500 0.00 0.00 0.00 3.16
2440 2972 5.037385 TCTAGTTTCGAAGATCTTGATGCG 58.963 41.667 14.00 10.28 35.04 4.73


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

AutoCloner maintained by Alex Coulton.