Multiple sequence alignment - TraesCS3A01G173800

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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 TraesCS3A01G173800 chr3A 100.000 2495 0 0 1 2495 191856329 191858823 0.000000e+00 4608
1 TraesCS3A01G173800 chr3A 96.981 265 8 0 2219 2483 227634228 227634492 1.760000e-121 446
2 TraesCS3A01G173800 chr5B 98.493 1725 15 2 1 1725 127854013 127855726 0.000000e+00 3031
3 TraesCS3A01G173800 chr5B 98.897 725 8 0 1759 2483 127855895 127856619 0.000000e+00 1295
4 TraesCS3A01G173800 chr7A 98.134 1608 29 1 1 1608 563530701 563529095 0.000000e+00 2802
5 TraesCS3A01G173800 chr7A 99.186 1105 9 0 1 1105 60328230 60327126 0.000000e+00 1991
6 TraesCS3A01G173800 chr7A 98.473 262 4 0 2222 2483 211363364 211363103 1.750000e-126 462
7 TraesCS3A01G173800 chr1A 98.246 1596 27 1 1 1595 278507126 278508721 0.000000e+00 2791
8 TraesCS3A01G173800 chr1A 99.457 1105 6 0 1 1105 238108965 238107861 0.000000e+00 2008
9 TraesCS3A01G173800 chr1A 99.276 1105 8 0 1 1105 238154350 238153246 0.000000e+00 1997
10 TraesCS3A01G173800 chr1A 98.113 265 5 0 2219 2483 94581955 94582219 1.750000e-126 462
11 TraesCS3A01G173800 chr1A 98.431 255 4 0 2229 2483 94663018 94662764 1.360000e-122 449
12 TraesCS3A01G173800 chr5A 99.186 1105 9 0 1 1105 16577140 16576036 0.000000e+00 1991
13 TraesCS3A01G173800 chr6B 99.186 1105 8 1 1 1105 596656526 596655423 0.000000e+00 1989
14 TraesCS3A01G173800 chr2D 99.095 1105 10 0 1 1105 642938564 642939668 0.000000e+00 1986
15 TraesCS3A01G173800 chr2D 91.667 132 7 4 1502 1631 604396461 604396332 1.970000e-41 180
16 TraesCS3A01G173800 chr2D 91.667 132 7 4 1502 1631 604404683 604404554 1.970000e-41 180
17 TraesCS3A01G173800 chr4A 97.032 539 15 1 1070 1608 275502889 275502352 0.000000e+00 905
18 TraesCS3A01G173800 chrUn 86.851 578 61 11 1601 2169 229490765 229491336 1.260000e-177 632
19 TraesCS3A01G173800 chrUn 97.738 221 5 0 2263 2483 406859804 406860024 5.040000e-102 381
20 TraesCS3A01G173800 chrUn 96.296 81 3 0 2222 2302 369464447 369464367 1.560000e-27 134
21 TraesCS3A01G173800 chrUn 96.296 81 3 0 2222 2302 443029488 443029408 1.560000e-27 134
22 TraesCS3A01G173800 chrUn 84.496 129 11 7 2170 2296 229491317 229491438 4.360000e-23 119
23 TraesCS3A01G173800 chr1D 94.444 324 14 2 1292 1615 461637087 461636768 1.720000e-136 496
24 TraesCS3A01G173800 chr2A 97.710 262 6 0 2222 2483 423417788 423417527 3.780000e-123 451
25 TraesCS3A01G173800 chr2A 98.438 256 4 0 1018 1273 588457946 588458201 3.780000e-123 451
26 TraesCS3A01G173800 chr2A 97.854 233 5 0 2263 2495 755518488 755518256 1.070000e-108 403
27 TraesCS3A01G173800 chr7B 97.425 233 6 0 2263 2495 743103523 743103291 5.000000e-107 398
28 TraesCS3A01G173800 chr7B 100.000 119 0 0 1323 1441 740000501 740000383 1.160000e-53 220
29 TraesCS3A01G173800 chr2B 96.154 130 2 1 1502 1631 357443756 357443630 2.510000e-50 209
30 TraesCS3A01G173800 chr2B 94.615 130 4 1 1502 1631 357569666 357569792 5.440000e-47 198
31 TraesCS3A01G173800 chr6D 96.296 81 3 0 2222 2302 246666786 246666706 1.560000e-27 134


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 TraesCS3A01G173800 chr3A 191856329 191858823 2494 False 4608.0 4608 100.0000 1 2495 1 chr3A.!!$F1 2494
1 TraesCS3A01G173800 chr5B 127854013 127856619 2606 False 2163.0 3031 98.6950 1 2483 2 chr5B.!!$F1 2482
2 TraesCS3A01G173800 chr7A 563529095 563530701 1606 True 2802.0 2802 98.1340 1 1608 1 chr7A.!!$R3 1607
3 TraesCS3A01G173800 chr7A 60327126 60328230 1104 True 1991.0 1991 99.1860 1 1105 1 chr7A.!!$R1 1104
4 TraesCS3A01G173800 chr1A 278507126 278508721 1595 False 2791.0 2791 98.2460 1 1595 1 chr1A.!!$F2 1594
5 TraesCS3A01G173800 chr1A 238107861 238108965 1104 True 2008.0 2008 99.4570 1 1105 1 chr1A.!!$R2 1104
6 TraesCS3A01G173800 chr1A 238153246 238154350 1104 True 1997.0 1997 99.2760 1 1105 1 chr1A.!!$R3 1104
7 TraesCS3A01G173800 chr5A 16576036 16577140 1104 True 1991.0 1991 99.1860 1 1105 1 chr5A.!!$R1 1104
8 TraesCS3A01G173800 chr6B 596655423 596656526 1103 True 1989.0 1989 99.1860 1 1105 1 chr6B.!!$R1 1104
9 TraesCS3A01G173800 chr2D 642938564 642939668 1104 False 1986.0 1986 99.0950 1 1105 1 chr2D.!!$F1 1104
10 TraesCS3A01G173800 chr4A 275502352 275502889 537 True 905.0 905 97.0320 1070 1608 1 chr4A.!!$R1 538
11 TraesCS3A01G173800 chrUn 229490765 229491438 673 False 375.5 632 85.6735 1601 2296 2 chrUn.!!$F2 695

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
346 358 3.963129 TCCAGAAAAATTGTCGGCCTAT 58.037 40.909 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1989 2.156098 CTTCGAAATCCGGGTTTTCCA 58.844 47.619 15.27 4.17 42.91 3.53 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
346 358 3.963129 TCCAGAAAAATTGTCGGCCTAT 58.037 40.909 0.00 0.0 0.00 2.57
916 928 4.640201 CAGGTGTGAAATCCCATCGTATTT 59.360 41.667 0.00 0.0 0.00 1.40
1272 1284 6.128902 GCGTCGAGATTAATAAAATCGTGGAT 60.129 38.462 0.00 0.0 35.05 3.41
1729 1741 9.826574 TCACCTGTACACTTATTTATGTATTCC 57.173 33.333 0.00 0.0 34.00 3.01
1730 1742 8.761497 CACCTGTACACTTATTTATGTATTCCG 58.239 37.037 0.00 0.0 34.00 4.30
1836 1989 3.569250 ACAAACAACAACAAGAACGCT 57.431 38.095 0.00 0.0 0.00 5.07
1837 1990 3.241701 ACAAACAACAACAAGAACGCTG 58.758 40.909 0.00 0.0 0.00 5.18
1863 2016 4.258702 ACCCGGATTTCGAAGATGATAG 57.741 45.455 0.73 0.0 42.43 2.08
1919 2072 1.625818 AGAGAGTCCGACAGGCAAAAT 59.374 47.619 0.40 0.0 37.47 1.82
2008 2161 1.107538 CCGAGGGCGACATCCTTCTA 61.108 60.000 0.00 0.0 38.06 2.10
2342 2495 2.563620 TGTGGAAACGCTGTCTATGGTA 59.436 45.455 0.00 0.0 42.82 3.25
2483 2636 0.629571 TAGGTAGGAGGGAGGGAGCA 60.630 60.000 0.00 0.0 0.00 4.26
2484 2637 1.762858 GGTAGGAGGGAGGGAGCAC 60.763 68.421 0.00 0.0 0.00 4.40
2485 2638 1.311747 GTAGGAGGGAGGGAGCACT 59.688 63.158 0.00 0.0 0.00 4.40
2486 2639 0.325765 GTAGGAGGGAGGGAGCACTT 60.326 60.000 0.00 0.0 0.00 3.16
2487 2640 0.032017 TAGGAGGGAGGGAGCACTTC 60.032 60.000 0.00 0.0 0.00 3.01
2488 2641 2.726351 GGAGGGAGGGAGCACTTCG 61.726 68.421 0.00 0.0 0.00 3.79
2489 2642 1.985116 GAGGGAGGGAGCACTTCGT 60.985 63.158 0.00 0.0 0.00 3.85
2490 2643 1.536662 AGGGAGGGAGCACTTCGTT 60.537 57.895 0.00 0.0 0.00 3.85
2491 2644 0.252103 AGGGAGGGAGCACTTCGTTA 60.252 55.000 0.00 0.0 0.00 3.18
2492 2645 0.175989 GGGAGGGAGCACTTCGTTAG 59.824 60.000 0.00 0.0 0.00 2.34
2493 2646 1.183549 GGAGGGAGCACTTCGTTAGA 58.816 55.000 0.00 0.0 0.00 2.10
2494 2647 1.757699 GGAGGGAGCACTTCGTTAGAT 59.242 52.381 0.00 0.0 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
346 358 1.209504 GAGGGATCGGAACCACATTCA 59.790 52.381 6.63 0.00 39.30 2.57
916 928 2.290514 CCAGCAAATCCTTGACTCCTCA 60.291 50.000 0.00 0.00 34.14 3.86
1272 1284 5.393787 GGTTAGCCAATACGGATCGATATCA 60.394 44.000 0.00 0.00 36.56 2.15
1836 1989 2.156098 CTTCGAAATCCGGGTTTTCCA 58.844 47.619 15.27 4.17 42.91 3.53
1837 1990 2.429478 TCTTCGAAATCCGGGTTTTCC 58.571 47.619 15.27 1.04 39.14 3.13
1863 2016 7.180748 GCGGAATTCTTGATTTACAGAACTAC 58.819 38.462 5.23 0.00 0.00 2.73
1919 2072 4.877378 TTAGTCTTTCTAACTCCCGCAA 57.123 40.909 0.00 0.00 34.17 4.85
2008 2161 4.473520 CCGCCCTTCATGCTCGGT 62.474 66.667 0.00 0.00 35.75 4.69
2342 2495 4.665009 TGAGAAAGGGGATGCTATAACCAT 59.335 41.667 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.