Multiple sequence alignment - TraesCS3D01G108800

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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 TraesCS3D01G108800 chr3D 100.000 2525 0 0 1 2525 61928797 61931321 0 4663
1 TraesCS3D01G108800 chr6A 94.542 2510 112 16 32 2523 162277911 162275409 0 3853
2 TraesCS3D01G108800 chr6A 91.582 1675 122 11 858 2525 395872659 395870997 0 2294
3 TraesCS3D01G108800 chr6D 93.967 2536 101 19 32 2525 15116451 15118976 0 3788
4 TraesCS3D01G108800 chr2B 93.106 2524 109 32 32 2524 77331081 77333570 0 3637
5 TraesCS3D01G108800 chr2B 79.676 1727 238 57 826 2514 16266010 16264359 0 1140
6 TraesCS3D01G108800 chr3B 92.799 2333 97 30 32 2322 766097197 766099500 0 3312
7 TraesCS3D01G108800 chr1A 96.262 1739 55 7 782 2513 565153047 565154782 0 2843
8 TraesCS3D01G108800 chr1A 90.523 707 47 9 32 728 565152336 565153032 0 917
9 TraesCS3D01G108800 chr1A 90.925 573 40 4 32 594 8731030 8731600 0 760
10 TraesCS3D01G108800 chr4D 96.318 1711 54 5 808 2513 386930353 386932059 0 2802
11 TraesCS3D01G108800 chr4B 92.040 1809 95 28 32 1806 483770126 483771919 0 2497
12 TraesCS3D01G108800 chr6B 91.080 1704 118 21 834 2525 171790738 171789057 0 2274
13 TraesCS3D01G108800 chr4A 91.576 1567 105 13 931 2486 12997295 12998845 0 2137
14 TraesCS3D01G108800 chr2A 90.267 637 45 7 32 658 674693697 674693068 0 817
15 TraesCS3D01G108800 chr2A 90.110 637 46 7 32 658 674578699 674578070 0 811
16 TraesCS3D01G108800 chr2A 89.465 636 50 7 32 658 674787388 674786761 0 787


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 TraesCS3D01G108800 chr3D 61928797 61931321 2524 False 4663 4663 100.0000 1 2525 1 chr3D.!!$F1 2524
1 TraesCS3D01G108800 chr6A 162275409 162277911 2502 True 3853 3853 94.5420 32 2523 1 chr6A.!!$R1 2491
2 TraesCS3D01G108800 chr6A 395870997 395872659 1662 True 2294 2294 91.5820 858 2525 1 chr6A.!!$R2 1667
3 TraesCS3D01G108800 chr6D 15116451 15118976 2525 False 3788 3788 93.9670 32 2525 1 chr6D.!!$F1 2493
4 TraesCS3D01G108800 chr2B 77331081 77333570 2489 False 3637 3637 93.1060 32 2524 1 chr2B.!!$F1 2492
5 TraesCS3D01G108800 chr2B 16264359 16266010 1651 True 1140 1140 79.6760 826 2514 1 chr2B.!!$R1 1688
6 TraesCS3D01G108800 chr3B 766097197 766099500 2303 False 3312 3312 92.7990 32 2322 1 chr3B.!!$F1 2290
7 TraesCS3D01G108800 chr1A 565152336 565154782 2446 False 1880 2843 93.3925 32 2513 2 chr1A.!!$F2 2481
8 TraesCS3D01G108800 chr1A 8731030 8731600 570 False 760 760 90.9250 32 594 1 chr1A.!!$F1 562
9 TraesCS3D01G108800 chr4D 386930353 386932059 1706 False 2802 2802 96.3180 808 2513 1 chr4D.!!$F1 1705
10 TraesCS3D01G108800 chr4B 483770126 483771919 1793 False 2497 2497 92.0400 32 1806 1 chr4B.!!$F1 1774
11 TraesCS3D01G108800 chr6B 171789057 171790738 1681 True 2274 2274 91.0800 834 2525 1 chr6B.!!$R1 1691
12 TraesCS3D01G108800 chr4A 12997295 12998845 1550 False 2137 2137 91.5760 931 2486 1 chr4A.!!$F1 1555
13 TraesCS3D01G108800 chr2A 674693068 674693697 629 True 817 817 90.2670 32 658 1 chr2A.!!$R2 626
14 TraesCS3D01G108800 chr2A 674578070 674578699 629 True 811 811 90.1100 32 658 1 chr2A.!!$R1 626
15 TraesCS3D01G108800 chr2A 674786761 674787388 627 True 787 787 89.4650 32 658 1 chr2A.!!$R3 626

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
164 165 0.53646 AAAGTACCCGCCCACAACAG 60.536 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2124 1.460504 TCCTAGCACGAGAATGACGT 58.539 50.0 0.0 0.0 44.83 4.34 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
17 18 4.966247 AACCGGGAAAAATGCCCT 57.034 50.000 6.32 0.00 43.72 5.19
18 19 3.157518 AACCGGGAAAAATGCCCTT 57.842 47.368 6.32 0.00 43.72 3.95
19 20 1.429930 AACCGGGAAAAATGCCCTTT 58.570 45.000 6.32 0.00 43.72 3.11
20 21 1.429930 ACCGGGAAAAATGCCCTTTT 58.570 45.000 6.32 0.00 43.72 2.27
51 52 2.489722 GTTGGAAGGCTGGAATCTGAAC 59.510 50.000 0.00 0.00 0.00 3.18
164 165 0.536460 AAAGTACCCGCCCACAACAG 60.536 55.000 0.00 0.00 0.00 3.16
221 223 1.300266 ATCCCGCAAAAACGTACCGG 61.300 55.000 0.00 0.00 38.71 5.28
271 306 1.749638 GAGAGGAACGAGAGGGCGA 60.750 63.158 0.00 0.00 34.83 5.54
332 367 3.841353 CCCGGCCCCCTCCTACTA 61.841 72.222 0.00 0.00 0.00 1.82
347 382 0.901114 TACTACGGCAACCTCCAGCA 60.901 55.000 0.00 0.00 0.00 4.41
396 431 1.395045 CCGCTGCATCTCCTAGGTCA 61.395 60.000 9.08 0.00 0.00 4.02
437 472 2.898840 CTAGGTCGCGGCTCCGTA 60.899 66.667 11.94 0.00 42.09 4.02
520 556 2.036414 TGGGTCGCAGCTCTCTCT 59.964 61.111 0.00 0.00 0.00 3.10
533 569 0.631753 TCTCTCTCCCATCTCCGGTT 59.368 55.000 0.00 0.00 0.00 4.44
547 583 1.590147 CGGTTGGTTCCTAGCTCGT 59.410 57.895 0.00 0.00 0.00 4.18
717 790 4.625083 GCTGCCCTCTGTTCTAAATCTCTT 60.625 45.833 0.00 0.00 0.00 2.85
783 868 4.502105 AGCAGTCTCTGTCTATCTCTCA 57.498 45.455 0.00 0.00 33.43 3.27
800 885 5.386060 TCTCTCAGAAACCTCAACTGTCTA 58.614 41.667 0.00 0.00 33.93 2.59
1105 1214 6.201226 TGTTTGTTGAAACATGTGCTCTTA 57.799 33.333 0.00 0.00 45.26 2.10
1561 1688 3.369471 GCACTTGGAGCACTAGATGGTTA 60.369 47.826 0.00 0.00 39.82 2.85
1620 1747 5.354513 GGAAGGTATAGGAACAGAAAGCAAC 59.645 44.000 0.00 0.00 0.00 4.17
1641 1768 4.777463 ACCCATTACCACTAACATGCTAC 58.223 43.478 0.00 0.00 0.00 3.58
1708 1835 1.071857 GGAGGGTTCGGTTTCAGACTT 59.928 52.381 0.00 0.00 0.00 3.01
2263 2416 5.887598 AGTGGATAGTGAATTAGCAAATGCA 59.112 36.000 8.28 0.00 45.16 3.96
2288 2441 4.254402 ACTGATGATCCAGATGATGACG 57.746 45.455 6.04 0.00 37.59 4.35
2372 2525 6.763135 TGATGATATGTTTGCTGAGTACCTTC 59.237 38.462 0.00 0.00 0.00 3.46
2429 2607 6.721208 TGAGAGTATGATATGTAGATGTGGCA 59.279 38.462 0.00 0.00 0.00 4.92
2488 2666 5.235401 GTCTTCTTTTGTATAGCTAGCTGCC 59.765 44.000 27.68 14.41 44.23 4.85
2514 2692 4.095036 GGTGGTCTTCTTTTGTATAGCTGC 59.905 45.833 0.00 0.00 0.00 5.25
2515 2693 3.932710 TGGTCTTCTTTTGTATAGCTGCG 59.067 43.478 0.00 0.00 0.00 5.18
2516 2694 3.309954 GGTCTTCTTTTGTATAGCTGCGG 59.690 47.826 0.00 0.00 0.00 5.69
2518 2696 3.932710 TCTTCTTTTGTATAGCTGCGGTG 59.067 43.478 0.00 0.00 0.00 4.94
2520 2698 2.027561 TCTTTTGTATAGCTGCGGTGGT 60.028 45.455 0.00 0.00 0.00 4.16
2521 2699 1.732941 TTTGTATAGCTGCGGTGGTG 58.267 50.000 0.00 0.00 0.00 4.17
2523 2701 1.261938 TGTATAGCTGCGGTGGTGGT 61.262 55.000 0.00 0.00 0.00 4.16
2524 2702 0.529992 GTATAGCTGCGGTGGTGGTC 60.530 60.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.173782 AAAAAGGGCATTTTTCCCGGTT 59.826 40.909 16.07 0.00 45.87 4.44
1 2 1.771854 AAAAAGGGCATTTTTCCCGGT 59.228 42.857 16.07 0.00 45.87 5.28
2 3 2.559698 AAAAAGGGCATTTTTCCCGG 57.440 45.000 16.07 0.00 45.87 5.73
8 9 7.433680 CAACACTAGTAGAAAAAGGGCATTTT 58.566 34.615 3.70 3.70 43.04 1.82
9 10 6.015434 CCAACACTAGTAGAAAAAGGGCATTT 60.015 38.462 3.59 0.00 0.00 2.32
10 11 5.476945 CCAACACTAGTAGAAAAAGGGCATT 59.523 40.000 3.59 0.00 0.00 3.56
11 12 5.010282 CCAACACTAGTAGAAAAAGGGCAT 58.990 41.667 3.59 0.00 0.00 4.40
12 13 4.103469 TCCAACACTAGTAGAAAAAGGGCA 59.897 41.667 3.59 0.00 0.00 5.36
13 14 4.648651 TCCAACACTAGTAGAAAAAGGGC 58.351 43.478 3.59 0.00 0.00 5.19
14 15 5.705905 CCTTCCAACACTAGTAGAAAAAGGG 59.294 44.000 3.59 0.00 0.00 3.95
15 16 5.181433 GCCTTCCAACACTAGTAGAAAAAGG 59.819 44.000 15.89 15.89 0.00 3.11
16 17 5.998363 AGCCTTCCAACACTAGTAGAAAAAG 59.002 40.000 3.59 0.00 0.00 2.27
17 18 5.763204 CAGCCTTCCAACACTAGTAGAAAAA 59.237 40.000 3.59 0.00 0.00 1.94
18 19 5.305585 CAGCCTTCCAACACTAGTAGAAAA 58.694 41.667 3.59 0.00 0.00 2.29
19 20 4.262894 CCAGCCTTCCAACACTAGTAGAAA 60.263 45.833 3.59 0.00 0.00 2.52
20 21 3.260884 CCAGCCTTCCAACACTAGTAGAA 59.739 47.826 3.59 0.00 0.00 2.10
21 22 2.832129 CCAGCCTTCCAACACTAGTAGA 59.168 50.000 3.59 0.00 0.00 2.59
22 23 2.832129 TCCAGCCTTCCAACACTAGTAG 59.168 50.000 0.00 0.00 0.00 2.57
23 24 2.897350 TCCAGCCTTCCAACACTAGTA 58.103 47.619 0.00 0.00 0.00 1.82
24 25 1.729586 TCCAGCCTTCCAACACTAGT 58.270 50.000 0.00 0.00 0.00 2.57
25 26 2.859165 TTCCAGCCTTCCAACACTAG 57.141 50.000 0.00 0.00 0.00 2.57
26 27 2.912956 AGATTCCAGCCTTCCAACACTA 59.087 45.455 0.00 0.00 0.00 2.74
27 28 1.707427 AGATTCCAGCCTTCCAACACT 59.293 47.619 0.00 0.00 0.00 3.55
28 29 1.815003 CAGATTCCAGCCTTCCAACAC 59.185 52.381 0.00 0.00 0.00 3.32
29 30 1.704628 TCAGATTCCAGCCTTCCAACA 59.295 47.619 0.00 0.00 0.00 3.33
30 31 2.489722 GTTCAGATTCCAGCCTTCCAAC 59.510 50.000 0.00 0.00 0.00 3.77
51 52 8.286800 TGTGAATTGAAAGTTTACCAATACGAG 58.713 33.333 3.66 0.00 31.07 4.18
332 367 4.643387 GGTGCTGGAGGTTGCCGT 62.643 66.667 0.00 0.00 0.00 5.68
355 390 1.003573 AGGATGGACCAGGGGAGAC 59.996 63.158 0.00 0.00 42.04 3.36
396 431 3.083997 GATGGAGGAGGGTGGCGT 61.084 66.667 0.00 0.00 0.00 5.68
437 472 0.690077 GGACCTAACCGGAGATGGGT 60.690 60.000 9.46 11.67 40.20 4.51
520 556 1.559065 GGAACCAACCGGAGATGGGA 61.559 60.000 23.08 0.00 38.37 4.37
533 569 2.978824 GCCACGAGCTAGGAACCA 59.021 61.111 0.00 0.00 38.99 3.67
547 583 2.043248 GGACTACGGAGGGAGCCA 60.043 66.667 0.00 0.00 0.00 4.75
717 790 0.631753 TTGTGGGTTCAGGGGTTCAA 59.368 50.000 0.00 0.00 0.00 2.69
748 833 5.356751 CAGAGACTGCTAGTTCAGACTACAT 59.643 44.000 4.57 0.00 38.74 2.29
856 948 5.056480 TCGATGAACACTTCACAAATCTGT 58.944 37.500 0.00 0.00 43.48 3.41
1105 1214 8.296713 CCTTTGTGTAGTAACAAATGCTAATGT 58.703 33.333 3.21 0.00 46.12 2.71
1454 1577 5.174775 ACTCCCCATATAGAGAGAGTAGGT 58.825 45.833 4.15 0.00 33.01 3.08
1561 1688 5.355071 ACATCAACAAGCACGTCAATATGAT 59.645 36.000 0.00 0.00 0.00 2.45
1620 1747 3.807622 CGTAGCATGTTAGTGGTAATGGG 59.192 47.826 0.00 0.00 34.25 4.00
1641 1768 4.221926 TCATGTTCCAATCAACAACACG 57.778 40.909 0.00 0.00 39.69 4.49
1937 2089 3.815401 TCTTTAGCTGTTTGAGGCTGTTC 59.185 43.478 0.00 0.00 39.31 3.18
1972 2124 1.460504 TCCTAGCACGAGAATGACGT 58.539 50.000 0.00 0.00 44.83 4.34
2102 2255 9.229784 GCAATTGTCATCTCACATACTAATTTG 57.770 33.333 7.40 0.00 0.00 2.32
2263 2416 4.411212 TCATCATCTGGATCATCAGTTGGT 59.589 41.667 0.00 0.00 35.98 3.67
2372 2525 0.603707 TCTTGTTCTCCTTGCGCCAG 60.604 55.000 4.18 2.17 0.00 4.85
2422 2575 2.624838 CAAAAGAAGACCACTGCCACAT 59.375 45.455 0.00 0.00 0.00 3.21
2429 2607 6.155393 AGCTAGCTATACAAAAGAAGACCACT 59.845 38.462 17.69 0.00 0.00 4.00
2461 2639 6.989169 CAGCTAGCTATACAAAAGAAGACCAT 59.011 38.462 18.86 0.00 0.00 3.55
2488 2666 4.092968 GCTATACAAAAGAAGACCACCACG 59.907 45.833 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.