Multiple sequence alignment - TraesCS6A01G166200

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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 TraesCS6A01G166200 chr6A 100.000 5567 0 0 1 5567 169189324 169194890 0.000000e+00 10281.0
1 TraesCS6A01G166200 chr6A 89.076 119 11 2 3786 3904 456719559 456719675 4.490000e-31 147.0
2 TraesCS6A01G166200 chr6D 97.758 4550 96 3 49 4598 130171002 130175545 0.000000e+00 7832.0
3 TraesCS6A01G166200 chr6D 91.292 356 13 3 4985 5326 130176378 130176729 2.350000e-128 470.0
4 TraesCS6A01G166200 chr6D 91.594 345 10 6 4596 4940 130175700 130176025 5.080000e-125 459.0
5 TraesCS6A01G166200 chr6B 97.306 4602 105 11 1 4598 228690109 228694695 0.000000e+00 7793.0
6 TraesCS6A01G166200 chr6B 94.949 297 15 0 4596 4892 228694847 228695143 3.040000e-127 466.0
7 TraesCS6A01G166200 chr6B 94.949 297 10 3 4949 5243 228695882 228696175 1.410000e-125 460.0
8 TraesCS6A01G166200 chr6B 97.727 88 2 0 5239 5326 228696304 228696391 9.660000e-33 152.0
9 TraesCS6A01G166200 chr3A 75.726 2583 588 35 765 3329 665955194 665957755 0.000000e+00 1260.0
10 TraesCS6A01G166200 chr3A 88.889 162 17 1 401 562 726769132 726768972 1.220000e-46 198.0
11 TraesCS6A01G166200 chr3A 86.885 61 5 3 5319 5377 70554255 70554196 1.290000e-06 65.8
12 TraesCS6A01G166200 chr3A 88.679 53 5 1 5325 5377 107648806 107648857 4.660000e-06 63.9
13 TraesCS6A01G166200 chr3D 75.553 2577 591 35 771 3329 426165871 426163316 0.000000e+00 1232.0
14 TraesCS6A01G166200 chr3D 75.347 2592 586 46 765 3329 531348971 531351536 0.000000e+00 1197.0
15 TraesCS6A01G166200 chr3D 75.223 2579 594 41 771 3329 464058178 464055625 0.000000e+00 1181.0
16 TraesCS6A01G166200 chr3D 89.744 156 16 0 407 562 149764782 149764627 3.400000e-47 200.0
17 TraesCS6A01G166200 chr3D 89.744 156 16 0 407 562 598889891 598889736 3.400000e-47 200.0
18 TraesCS6A01G166200 chr3D 97.297 37 1 0 4224 4260 445638711 445638747 4.660000e-06 63.9
19 TraesCS6A01G166200 chr3B 75.339 2583 598 36 765 3329 702682609 702685170 0.000000e+00 1205.0
20 TraesCS6A01G166200 chr3B 78.378 1073 213 13 3440 4507 702685299 702686357 0.000000e+00 678.0
21 TraesCS6A01G166200 chr3B 97.297 37 1 0 4224 4260 584551299 584551335 4.660000e-06 63.9
22 TraesCS6A01G166200 chr2D 75.184 2579 596 40 771 3329 380086803 380084249 0.000000e+00 1177.0
23 TraesCS6A01G166200 chr2D 91.026 156 13 1 407 562 348192917 348192763 5.650000e-50 209.0
24 TraesCS6A01G166200 chr5A 98.319 238 4 0 5330 5567 433490545 433490782 8.630000e-113 418.0
25 TraesCS6A01G166200 chr5A 89.091 55 4 2 5324 5377 106724100 106724153 3.600000e-07 67.6
26 TraesCS6A01G166200 chr1A 95.528 246 7 4 5323 5567 304956652 304956894 1.880000e-104 390.0
27 TraesCS6A01G166200 chr1A 95.417 240 8 3 5329 5567 304954987 304955224 4.070000e-101 379.0
28 TraesCS6A01G166200 chr1A 94.167 240 11 3 5329 5567 304954471 304954708 4.100000e-96 363.0
29 TraesCS6A01G166200 chr2A 91.503 153 11 2 409 561 461700528 461700678 5.650000e-50 209.0
30 TraesCS6A01G166200 chr1D 88.415 164 15 4 407 569 11011786 11011626 1.580000e-45 195.0
31 TraesCS6A01G166200 chr1D 88.415 164 15 4 407 569 11097120 11096960 1.580000e-45 195.0
32 TraesCS6A01G166200 chr4A 91.525 118 7 2 5330 5446 614541932 614542047 5.770000e-35 159.0
33 TraesCS6A01G166200 chr4A 91.509 106 9 0 5460 5565 614542417 614542522 4.490000e-31 147.0
34 TraesCS6A01G166200 chr1B 88.333 60 4 3 5325 5382 188884048 188884106 1.000000e-07 69.4


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 TraesCS6A01G166200 chr6A 169189324 169194890 5566 False 10281.000000 10281 100.000000 1 5567 1 chr6A.!!$F1 5566
1 TraesCS6A01G166200 chr6D 130171002 130176729 5727 False 2920.333333 7832 93.548000 49 5326 3 chr6D.!!$F1 5277
2 TraesCS6A01G166200 chr6B 228690109 228696391 6282 False 2217.750000 7793 96.232750 1 5326 4 chr6B.!!$F1 5325
3 TraesCS6A01G166200 chr3A 665955194 665957755 2561 False 1260.000000 1260 75.726000 765 3329 1 chr3A.!!$F2 2564
4 TraesCS6A01G166200 chr3D 426163316 426165871 2555 True 1232.000000 1232 75.553000 771 3329 1 chr3D.!!$R2 2558
5 TraesCS6A01G166200 chr3D 531348971 531351536 2565 False 1197.000000 1197 75.347000 765 3329 1 chr3D.!!$F2 2564
6 TraesCS6A01G166200 chr3D 464055625 464058178 2553 True 1181.000000 1181 75.223000 771 3329 1 chr3D.!!$R3 2558
7 TraesCS6A01G166200 chr3B 702682609 702686357 3748 False 941.500000 1205 76.858500 765 4507 2 chr3B.!!$F2 3742
8 TraesCS6A01G166200 chr2D 380084249 380086803 2554 True 1177.000000 1177 75.184000 771 3329 1 chr2D.!!$R2 2558
9 TraesCS6A01G166200 chr1A 304954471 304956894 2423 False 377.333333 390 95.037333 5323 5567 3 chr1A.!!$F1 244

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
29 32 0.182299 TTGGCTGTGTGTGGATGTGA 59.818 50.000 0.00 0.0 0.0 3.58 F
413 417 0.250901 TTCTGCCAAGTGCTCCTTCC 60.251 55.000 0.00 0.0 42.0 3.46 F
1000 1004 2.024176 TGGTGAGCTCCCAGAAGTTA 57.976 50.000 17.12 0.0 0.0 2.24 F
2128 2133 3.762407 TGCAAGTTAACCAGCTCTGTA 57.238 42.857 17.50 0.0 0.0 2.74 F
3135 3144 1.689273 GGGAGCCTCGATGTGTCTATT 59.311 52.381 0.00 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 1891 3.973206 TGTTCACCAACGATATGGACT 57.027 42.857 12.38 0.00 43.54 3.85 R
2128 2133 4.965532 AGCCAAGTATTCTGGTATCTCACT 59.034 41.667 0.00 0.00 0.00 3.41 R
2768 2773 1.327303 GTCAATGGTTGCAAGACCCA 58.673 50.000 9.48 9.48 39.01 4.51 R
3135 3144 0.843309 TCAGCCCTGTGAAGTTGGAA 59.157 50.000 0.00 0.00 0.00 3.53 R
5104 6014 0.038744 CCCCTCAGGTTCAGCATTGT 59.961 55.000 0.00 0.00 0.00 2.71 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
29 32 0.182299 TTGGCTGTGTGTGGATGTGA 59.818 50.000 0.00 0.00 0.00 3.58
37 40 3.507622 TGTGTGTGGATGTGAAAACAACA 59.492 39.130 0.00 0.00 0.00 3.33
39 42 3.115554 GTGTGGATGTGAAAACAACAGC 58.884 45.455 0.00 0.00 33.21 4.40
70 74 4.233789 GGCATTTCGCTACAAATGTGAAA 58.766 39.130 11.87 5.20 43.16 2.69
107 111 3.382083 TGACCCTGACAGAGTAGCATA 57.618 47.619 3.32 0.00 0.00 3.14
145 149 4.558095 GCAAATGGCATGACATATCTGGAC 60.558 45.833 16.16 0.00 43.97 4.02
259 263 4.721776 TGCCTGGGACTCTTAATCTTACAT 59.278 41.667 0.00 0.00 0.00 2.29
387 391 2.752154 GCTCATGGAAGATGCCCTGATT 60.752 50.000 0.00 0.00 33.10 2.57
410 414 2.071778 TTTTTCTGCCAAGTGCTCCT 57.928 45.000 0.00 0.00 42.00 3.69
412 416 1.609208 TTTCTGCCAAGTGCTCCTTC 58.391 50.000 0.00 0.00 42.00 3.46
413 417 0.250901 TTCTGCCAAGTGCTCCTTCC 60.251 55.000 0.00 0.00 42.00 3.46
429 433 7.709613 GTGCTCCTTCCGTTTCTAAATATAAGA 59.290 37.037 0.00 0.00 0.00 2.10
1000 1004 2.024176 TGGTGAGCTCCCAGAAGTTA 57.976 50.000 17.12 0.00 0.00 2.24
1456 1460 4.714632 TGGTCAACTAGAAAACCTGGAAG 58.285 43.478 0.00 0.00 32.82 3.46
1886 1891 5.423931 GGCTTCAAAACTGGGGGAATATTAA 59.576 40.000 0.00 0.00 0.00 1.40
1890 1895 6.192044 TCAAAACTGGGGGAATATTAAGTCC 58.808 40.000 0.00 0.00 39.22 3.85
1901 1906 7.166167 GGGAATATTAAGTCCATATCGTTGGT 58.834 38.462 5.31 0.00 41.83 3.67
2128 2133 3.762407 TGCAAGTTAACCAGCTCTGTA 57.238 42.857 17.50 0.00 0.00 2.74
3135 3144 1.689273 GGGAGCCTCGATGTGTCTATT 59.311 52.381 0.00 0.00 0.00 1.73
3398 3425 1.002430 GGCGGCTCATCCATCTTATCA 59.998 52.381 0.00 0.00 34.01 2.15
3411 3438 6.042777 TCCATCTTATCAAGTTTCACTAGCG 58.957 40.000 0.00 0.00 0.00 4.26
3468 3498 2.963599 TGGTTCTTCTGGGGGTTTAC 57.036 50.000 0.00 0.00 0.00 2.01
3501 3531 4.642885 AGACTATTGAAGAGAAGGTCCTCG 59.357 45.833 0.00 0.00 38.19 4.63
3955 3985 2.701780 CGGACTGACGCAGCCTACT 61.702 63.158 6.74 0.00 34.37 2.57
4519 4549 2.349590 CGACACAGATGATGGAAAGCA 58.650 47.619 0.00 0.00 0.00 3.91
4553 4583 2.888863 GACACTCTCCAGAGCGGG 59.111 66.667 3.33 0.00 45.79 6.13
4570 4600 4.394712 GCCTCCGGTGGTGACAGG 62.395 72.222 23.03 11.39 44.46 4.00
4688 4875 2.921121 TCGTTGTAAGCTTGTATCAGCG 59.079 45.455 9.86 15.28 45.24 5.18
4725 4912 1.468914 TCTGGAGAATGTGACGAGTCG 59.531 52.381 11.85 11.85 0.00 4.18
4755 4942 0.959372 GGTGCTGCTGAAGTGCTGAT 60.959 55.000 0.00 0.00 34.47 2.90
4771 4958 2.274437 CTGATCAAGCTGCGTACATGT 58.726 47.619 2.69 2.69 0.00 3.21
4786 4973 6.073276 TGCGTACATGTATCCTCAAATAATGC 60.073 38.462 9.18 1.57 0.00 3.56
4863 5050 7.290014 TCTCCTTGATCTGGCAGTTTATATGTA 59.710 37.037 15.27 0.00 0.00 2.29
4868 5055 4.314961 TCTGGCAGTTTATATGTATGGCG 58.685 43.478 15.27 0.00 39.13 5.69
4878 5065 1.188219 ATGTATGGCGAGCTCGGGAT 61.188 55.000 35.10 3.42 40.23 3.85
5042 5952 3.951306 TCTTTCACTTGTGTCAAATGCG 58.049 40.909 0.46 0.00 0.00 4.73
5051 5961 3.142174 TGTGTCAAATGCGTGGATGTAA 58.858 40.909 0.00 0.00 0.00 2.41
5087 5997 3.501445 AGAGTTGCTGAGATGCTGTTTTC 59.499 43.478 0.00 0.00 0.00 2.29
5102 6012 7.246674 TGCTGTTTTCAAGAACAAGTACTAG 57.753 36.000 0.00 0.00 38.90 2.57
5103 6013 6.821665 TGCTGTTTTCAAGAACAAGTACTAGT 59.178 34.615 0.00 0.00 38.90 2.57
5104 6014 7.982919 TGCTGTTTTCAAGAACAAGTACTAGTA 59.017 33.333 0.00 0.00 38.90 1.82
5257 6300 1.081376 CTTCGAGTGACGCGTCCTT 60.081 57.895 34.34 22.93 42.26 3.36
5326 6369 6.591313 GAAATTCTGGTTCGAGTCCTTATC 57.409 41.667 9.52 0.00 0.00 1.75
5327 6370 5.941555 AATTCTGGTTCGAGTCCTTATCT 57.058 39.130 9.52 0.00 0.00 1.98
5345 6388 8.503573 TCCTTATCTTCTACTCCTAATGTCTCA 58.496 37.037 0.00 0.00 0.00 3.27
5376 6419 0.111398 GTTCGTTCGTTGGTTCGCTC 60.111 55.000 0.00 0.00 0.00 5.03
5386 6429 2.100603 GTTCGCTCGCTCGCTACT 59.899 61.111 0.00 0.00 0.00 2.57
5401 6444 2.359531 CGCTACTTCCTTTCGATCTCCT 59.640 50.000 0.00 0.00 0.00 3.69
5493 6537 9.541884 AATTAGGTGGTCAAATAAGTAACCAAT 57.458 29.630 0.00 0.00 43.09 3.16
5524 6568 2.160205 GTCCAAGCAAACCCTAACTCC 58.840 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 32 1.762370 CCCTTCCTTGGCTGTTGTTTT 59.238 47.619 0.00 0.00 0.00 2.43
39 42 1.512694 GCGAAATGCCCTTCCTTGG 59.487 57.895 0.00 0.00 37.76 3.61
70 74 7.872483 GTCAGGGTCAAAATGTTCATTTTACAT 59.128 33.333 18.82 10.25 37.82 2.29
83 87 3.327757 TGCTACTCTGTCAGGGTCAAAAT 59.672 43.478 9.15 0.00 0.00 1.82
107 111 4.561326 GCCATTTGCAACACTTACCTGAAT 60.561 41.667 0.00 0.00 40.77 2.57
287 291 8.314751 GCTGGTGTTCTAGATTGGTATATACAT 58.685 37.037 14.70 0.47 0.00 2.29
405 409 7.927092 AGTCTTATATTTAGAAACGGAAGGAGC 59.073 37.037 0.00 0.00 0.00 4.70
441 445 8.954950 ACATCTGAATGTAGTCCTTATTGAAG 57.045 34.615 0.00 0.00 44.38 3.02
1000 1004 1.218854 GCTGCCGCAAATTTCCCAT 59.781 52.632 0.00 0.00 35.78 4.00
1688 1693 4.729918 CCCCAGTGAGCCCTGCAC 62.730 72.222 0.00 0.00 36.53 4.57
1886 1891 3.973206 TGTTCACCAACGATATGGACT 57.027 42.857 12.38 0.00 43.54 3.85
2128 2133 4.965532 AGCCAAGTATTCTGGTATCTCACT 59.034 41.667 0.00 0.00 0.00 3.41
2698 2703 2.545322 GCAGGTATAGTTCCGCCACTAC 60.545 54.545 0.00 0.00 31.92 2.73
2768 2773 1.327303 GTCAATGGTTGCAAGACCCA 58.673 50.000 9.48 9.48 39.01 4.51
3070 3079 3.414700 CGTGTTCAGGGCACTCGC 61.415 66.667 0.00 0.00 34.91 5.03
3135 3144 0.843309 TCAGCCCTGTGAAGTTGGAA 59.157 50.000 0.00 0.00 0.00 3.53
3398 3425 2.870435 ACGATTGCCGCTAGTGAAACTT 60.870 45.455 4.44 0.00 44.65 2.66
3411 3438 1.064060 GTAATGCCACAGACGATTGCC 59.936 52.381 0.00 0.00 0.00 4.52
3468 3498 5.355630 TCTCTTCAATAGTCTCCGTCTCAAG 59.644 44.000 0.00 0.00 0.00 3.02
3501 3531 1.741770 CGCAGGTACAAGAGCCCAC 60.742 63.158 0.00 0.00 0.00 4.61
4218 4248 3.003113 GCTGTAGACGTCGCCCCTT 62.003 63.158 10.46 0.00 0.00 3.95
4315 4345 4.415150 CCACTGCACCCAGCCGAT 62.415 66.667 0.00 0.00 43.02 4.18
4529 4559 1.132844 CTGGAGAGTGTCGTCGTCG 59.867 63.158 0.00 0.00 38.55 5.12
4530 4560 0.444651 CTCTGGAGAGTGTCGTCGTC 59.555 60.000 0.00 0.00 37.40 4.20
4531 4561 1.579084 GCTCTGGAGAGTGTCGTCGT 61.579 60.000 5.57 0.00 43.85 4.34
4659 4846 3.006940 CAAGCTTACAACGATTGGGCTA 58.993 45.455 0.00 0.00 35.35 3.93
4688 4875 5.361285 TCTCCAGATAACTGAAGCTTACTCC 59.639 44.000 0.00 0.00 46.03 3.85
4755 4942 2.430694 AGGATACATGTACGCAGCTTGA 59.569 45.455 7.96 0.00 41.41 3.02
4764 4951 8.285394 CACAGCATTATTTGAGGATACATGTAC 58.715 37.037 7.96 2.44 41.41 2.90
4771 4958 7.129457 AGAGTCACAGCATTATTTGAGGATA 57.871 36.000 0.00 0.00 0.00 2.59
4786 4973 7.641802 GCTAAAAACTCAAAAGAAGAGTCACAG 59.358 37.037 0.00 0.00 45.11 3.66
4863 5050 1.593787 CATATCCCGAGCTCGCCAT 59.406 57.895 30.49 23.58 38.18 4.40
4868 5055 0.801251 GCATTGCATATCCCGAGCTC 59.199 55.000 2.73 2.73 0.00 4.09
4878 5065 1.526686 CGCTCCCAGGCATTGCATA 60.527 57.895 11.39 0.00 0.00 3.14
4904 5091 3.883180 GCAACCAACACACCGCGT 61.883 61.111 4.92 0.00 0.00 6.01
4908 5095 2.884639 AGTATGAAGCAACCAACACACC 59.115 45.455 0.00 0.00 0.00 4.16
5042 5952 2.100418 GACCCCTACGACTTACATCCAC 59.900 54.545 0.00 0.00 0.00 4.02
5051 5961 2.944991 GCAACTCTAGACCCCTACGACT 60.945 54.545 0.00 0.00 0.00 4.18
5087 5997 7.598869 TCAGCATTGTACTAGTACTTGTTCTTG 59.401 37.037 28.56 20.41 37.00 3.02
5102 6012 2.359900 CCCTCAGGTTCAGCATTGTAC 58.640 52.381 0.00 0.00 0.00 2.90
5103 6013 1.281867 CCCCTCAGGTTCAGCATTGTA 59.718 52.381 0.00 0.00 0.00 2.41
5104 6014 0.038744 CCCCTCAGGTTCAGCATTGT 59.961 55.000 0.00 0.00 0.00 2.71
5129 6039 7.229306 TGCAAAGTCACAAAGATAAGTTCTGAT 59.771 33.333 0.00 0.00 33.93 2.90
5257 6300 4.180057 GTGTGGACAGAAACATTTGCAAA 58.820 39.130 15.44 15.44 0.00 3.68
5326 6369 5.008217 CGGACTGAGACATTAGGAGTAGAAG 59.992 48.000 0.00 0.00 0.00 2.85
5327 6370 4.882427 CGGACTGAGACATTAGGAGTAGAA 59.118 45.833 0.00 0.00 0.00 2.10
5376 6419 0.179171 TCGAAAGGAAGTAGCGAGCG 60.179 55.000 0.00 0.00 0.00 5.03
5386 6429 2.700897 GGATGGAGGAGATCGAAAGGAA 59.299 50.000 0.00 0.00 0.00 3.36
5429 6473 2.092646 CCACCGGTTTTCATAGGGATGA 60.093 50.000 2.97 0.00 40.45 2.92
5482 6526 5.321102 ACCTGATTGTGCATTGGTTACTTA 58.679 37.500 0.00 0.00 0.00 2.24
5493 6537 0.178995 TGCTTGGACCTGATTGTGCA 60.179 50.000 0.00 0.00 34.56 4.57
5524 6568 1.817099 GATGCGTGAGAAGGGGCTG 60.817 63.158 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.