Multiple sequence alignment - TraesCS5D01G157400

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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 TraesCS5D01G157400 chr5D 100.000 2676 0 0 1 2676 245200189 245197514 0.000000e+00 4942.0
1 TraesCS5D01G157400 chr5B 96.321 2664 75 10 2 2657 278469301 278466653 0.000000e+00 4355.0
2 TraesCS5D01G157400 chr5A 94.314 2691 100 23 1 2657 329242045 329239374 0.000000e+00 4072.0
3 TraesCS5D01G157400 chr1A 83.721 172 22 5 1261 1429 391941338 391941170 9.920000e-35 158.0
4 TraesCS5D01G157400 chr1A 80.508 118 21 2 2534 2650 518984401 518984285 3.670000e-14 89.8
5 TraesCS5D01G157400 chr1A 100.000 29 0 0 2422 2450 464115008 464114980 1.000000e-03 54.7
6 TraesCS5D01G157400 chr1B 82.558 172 24 5 1261 1429 422346724 422346556 2.150000e-31 147.0
7 TraesCS5D01G157400 chr2D 83.333 120 19 1 2531 2649 25323377 25323258 2.820000e-20 110.0
8 TraesCS5D01G157400 chr6A 85.714 98 14 0 2552 2649 412850959 412850862 1.310000e-18 104.0
9 TraesCS5D01G157400 chr2B 80.000 145 24 5 2517 2659 27635169 27635028 4.710000e-18 102.0
10 TraesCS5D01G157400 chr2A 80.916 131 21 4 2532 2659 27746403 27746274 1.700000e-17 100.0
11 TraesCS5D01G157400 chr4A 79.528 127 23 3 2534 2659 620748427 620748551 1.320000e-13 87.9
12 TraesCS5D01G157400 chr3D 80.342 117 19 4 2534 2647 254102294 254102409 4.750000e-13 86.1


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 TraesCS5D01G157400 chr5D 245197514 245200189 2675 True 4942 4942 100.000 1 2676 1 chr5D.!!$R1 2675
1 TraesCS5D01G157400 chr5B 278466653 278469301 2648 True 4355 4355 96.321 2 2657 1 chr5B.!!$R1 2655
2 TraesCS5D01G157400 chr5A 329239374 329242045 2671 True 4072 4072 94.314 1 2657 1 chr5A.!!$R1 2656

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
811 835 0.242825 CCAGCAAGCAACATGACAGG 59.757 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 2464 0.251916 CCGTTGGAGATGCCCTAACA 59.748 55.0 0.0 0.0 34.97 2.41 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
74 75 2.842457 TGATGATGATGTAGCAGCACC 58.158 47.619 0.00 0.00 35.98 5.01
124 125 1.202940 GGTTTTCTCCTGGTCTTGGCT 60.203 52.381 0.00 0.00 0.00 4.75
136 137 6.603201 TCCTGGTCTTGGCTTGATTTATTTAG 59.397 38.462 0.00 0.00 0.00 1.85
137 138 6.378280 CCTGGTCTTGGCTTGATTTATTTAGT 59.622 38.462 0.00 0.00 0.00 2.24
138 139 7.556275 CCTGGTCTTGGCTTGATTTATTTAGTA 59.444 37.037 0.00 0.00 0.00 1.82
139 140 9.125026 CTGGTCTTGGCTTGATTTATTTAGTAT 57.875 33.333 0.00 0.00 0.00 2.12
187 188 7.062749 ACTGGTATCTGTTGTTTTCTCACTA 57.937 36.000 0.00 0.00 0.00 2.74
219 220 2.527100 CGGTGCTAGTACTGTAGTTGC 58.473 52.381 18.16 18.16 0.00 4.17
328 330 1.953311 GCCATTTCCCTTGCCGACTTA 60.953 52.381 0.00 0.00 0.00 2.24
329 331 1.743394 CCATTTCCCTTGCCGACTTAC 59.257 52.381 0.00 0.00 0.00 2.34
394 397 6.624352 TCCTCTCTAATTAATGCATGTTGC 57.376 37.500 0.00 0.00 45.29 4.17
578 592 4.641541 TGCAGTGTCAAATATTGATCCAGG 59.358 41.667 0.00 0.00 42.47 4.45
583 597 5.008415 GTGTCAAATATTGATCCAGGCTCTG 59.992 44.000 0.00 0.00 42.47 3.35
716 740 4.853924 AAATACAGACAAACAAGGCAGG 57.146 40.909 0.00 0.00 0.00 4.85
742 766 1.522668 TTACACACACTGCATCCAGC 58.477 50.000 0.00 0.00 43.02 4.85
811 835 0.242825 CCAGCAAGCAACATGACAGG 59.757 55.000 0.00 0.00 0.00 4.00
857 881 8.267894 ACCATCACTAAACTAGTTTATCATGCT 58.732 33.333 24.61 13.85 36.76 3.79
858 882 9.113838 CCATCACTAAACTAGTTTATCATGCTT 57.886 33.333 24.61 12.89 36.76 3.91
859 883 9.926751 CATCACTAAACTAGTTTATCATGCTTG 57.073 33.333 24.61 18.11 36.76 4.01
860 884 9.672673 ATCACTAAACTAGTTTATCATGCTTGT 57.327 29.630 24.61 15.02 36.76 3.16
1055 1087 8.964476 TCTATCTTCTCTTCTCTTCTCTTCTC 57.036 38.462 0.00 0.00 0.00 2.87
1056 1088 8.772250 TCTATCTTCTCTTCTCTTCTCTTCTCT 58.228 37.037 0.00 0.00 0.00 3.10
1057 1089 9.401058 CTATCTTCTCTTCTCTTCTCTTCTCTT 57.599 37.037 0.00 0.00 0.00 2.85
1058 1090 7.687941 TCTTCTCTTCTCTTCTCTTCTCTTC 57.312 40.000 0.00 0.00 0.00 2.87
1059 1091 7.461749 TCTTCTCTTCTCTTCTCTTCTCTTCT 58.538 38.462 0.00 0.00 0.00 2.85
1060 1092 7.607991 TCTTCTCTTCTCTTCTCTTCTCTTCTC 59.392 40.741 0.00 0.00 0.00 2.87
1138 1174 4.961511 ACACCGTGCGCGTCATGT 62.962 61.111 19.61 16.18 36.15 3.21
1447 1483 2.360350 CAGCGCATCAACCACCCT 60.360 61.111 11.47 0.00 0.00 4.34
1480 1516 1.334243 GCATTTCATCTGCAGGAGCTC 59.666 52.381 15.13 4.71 42.74 4.09
1738 1774 5.443185 TGAGAAGAAAGTTGATTGCTTGG 57.557 39.130 0.00 0.00 36.85 3.61
1835 1880 6.849697 AGTACCTCCATTTCTATTCATGGGTA 59.150 38.462 0.00 0.00 40.53 3.69
1837 1882 6.365520 ACCTCCATTTCTATTCATGGGTAAC 58.634 40.000 0.00 0.00 40.53 2.50
2257 2302 3.157949 TGAGTGCCCCGTGTCACA 61.158 61.111 3.42 0.00 35.76 3.58
2453 2498 0.869730 AACGGTGTACATCAAACGGC 59.130 50.000 6.97 0.00 34.51 5.68
2485 2530 0.320771 GCGGACACTTGACATCAGGT 60.321 55.000 0.00 0.00 36.56 4.00
2494 2539 2.764128 ACATCAGGTCGGGCGGAT 60.764 61.111 0.00 0.00 0.00 4.18
2522 2567 4.394920 TCCAGTGCTATCCGTCAAATTTTC 59.605 41.667 0.00 0.00 0.00 2.29
2523 2568 4.438744 CCAGTGCTATCCGTCAAATTTTCC 60.439 45.833 0.00 0.00 0.00 3.13
2657 2702 9.104965 TGTTCAATAAGTTTTATACCTCCATCG 57.895 33.333 0.00 0.00 0.00 3.84
2658 2703 9.321562 GTTCAATAAGTTTTATACCTCCATCGA 57.678 33.333 0.00 0.00 0.00 3.59
2659 2704 9.542462 TTCAATAAGTTTTATACCTCCATCGAG 57.458 33.333 0.00 0.00 35.72 4.04
2660 2705 7.656137 TCAATAAGTTTTATACCTCCATCGAGC 59.344 37.037 0.00 0.00 34.49 5.03
2661 2706 5.615925 AAGTTTTATACCTCCATCGAGCT 57.384 39.130 0.00 0.00 34.49 4.09
2662 2707 5.615925 AGTTTTATACCTCCATCGAGCTT 57.384 39.130 0.00 0.00 34.49 3.74
2663 2708 5.602628 AGTTTTATACCTCCATCGAGCTTC 58.397 41.667 0.00 0.00 34.49 3.86
2664 2709 5.364157 AGTTTTATACCTCCATCGAGCTTCT 59.636 40.000 0.00 0.00 34.49 2.85
2665 2710 5.871396 TTTATACCTCCATCGAGCTTCTT 57.129 39.130 0.00 0.00 34.49 2.52
2666 2711 5.871396 TTATACCTCCATCGAGCTTCTTT 57.129 39.130 0.00 0.00 34.49 2.52
2667 2712 2.682155 ACCTCCATCGAGCTTCTTTC 57.318 50.000 0.00 0.00 34.49 2.62
2668 2713 1.208293 ACCTCCATCGAGCTTCTTTCC 59.792 52.381 0.00 0.00 34.49 3.13
2669 2714 1.474143 CCTCCATCGAGCTTCTTTCCC 60.474 57.143 0.00 0.00 34.49 3.97
2670 2715 0.541863 TCCATCGAGCTTCTTTCCCC 59.458 55.000 0.00 0.00 0.00 4.81
2671 2716 0.811616 CCATCGAGCTTCTTTCCCCG 60.812 60.000 0.00 0.00 0.00 5.73
2672 2717 1.153349 ATCGAGCTTCTTTCCCCGC 60.153 57.895 0.00 0.00 0.00 6.13
2673 2718 2.595009 ATCGAGCTTCTTTCCCCGCC 62.595 60.000 0.00 0.00 0.00 6.13
2674 2719 2.671682 GAGCTTCTTTCCCCGCCT 59.328 61.111 0.00 0.00 0.00 5.52
2675 2720 1.450491 GAGCTTCTTTCCCCGCCTC 60.450 63.158 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.976641 TGCGGACAAGGAGAGATTGT 59.023 50.000 0.00 0.00 43.38 2.71
187 188 6.868864 CAGTACTAGCACCGCTAATCAAATAT 59.131 38.462 0.00 0.00 40.82 1.28
199 200 2.163815 AGCAACTACAGTACTAGCACCG 59.836 50.000 0.00 0.00 0.00 4.94
200 201 3.870633 AGCAACTACAGTACTAGCACC 57.129 47.619 0.00 0.00 0.00 5.01
219 220 7.974501 AGCTTCAATTCAATCTTCAATGCTAAG 59.025 33.333 0.00 0.00 0.00 2.18
258 260 6.826668 TCACTCTTCTCTACAAATTGGTGAA 58.173 36.000 0.00 0.00 0.00 3.18
328 330 5.604650 AGCTAGCCTAGAGGTGAATAATTGT 59.395 40.000 12.13 0.00 37.57 2.71
329 331 6.014669 AGAGCTAGCCTAGAGGTGAATAATTG 60.015 42.308 12.13 0.00 37.57 2.32
394 397 4.109050 GGTGAAGATCGAAGACTTAGCAG 58.891 47.826 0.00 0.00 42.51 4.24
578 592 1.078567 ACTTAGCTGGCTGCAGAGC 60.079 57.895 20.43 18.67 45.94 4.09
583 597 3.583383 CCACACTTAGCTGGCTGC 58.417 61.111 8.47 8.47 43.29 5.25
669 687 7.338710 AGCAGCAAAGGTTGATTATTAGTCTA 58.661 34.615 0.00 0.00 0.00 2.59
716 740 0.875059 GCAGTGTGTGTAAAGGCCTC 59.125 55.000 5.23 0.00 0.00 4.70
811 835 5.719173 TGGTTTTGTGCTAATTAATGAGCC 58.281 37.500 20.23 12.72 37.94 4.70
857 881 7.062371 CGTTAATCAGGACAAACAAACAAACAA 59.938 33.333 0.00 0.00 0.00 2.83
858 882 6.528423 CGTTAATCAGGACAAACAAACAAACA 59.472 34.615 0.00 0.00 0.00 2.83
859 883 6.748198 TCGTTAATCAGGACAAACAAACAAAC 59.252 34.615 0.00 0.00 0.00 2.93
860 884 6.853720 TCGTTAATCAGGACAAACAAACAAA 58.146 32.000 0.00 0.00 0.00 2.83
1055 1087 2.961526 TTGCTACGGGCTTAGAGAAG 57.038 50.000 4.43 0.00 42.39 2.85
1056 1088 2.829720 TCTTTGCTACGGGCTTAGAGAA 59.170 45.455 4.43 0.00 42.39 2.87
1057 1089 2.427453 CTCTTTGCTACGGGCTTAGAGA 59.573 50.000 19.04 10.44 44.26 3.10
1058 1090 2.482142 CCTCTTTGCTACGGGCTTAGAG 60.482 54.545 17.94 17.94 42.79 2.43
1059 1091 1.480954 CCTCTTTGCTACGGGCTTAGA 59.519 52.381 4.43 5.91 42.39 2.10
1060 1092 1.480954 TCCTCTTTGCTACGGGCTTAG 59.519 52.381 4.43 2.42 42.39 2.18
1357 1393 0.762461 GCTGGAGGTAGGAGATGGCT 60.762 60.000 0.00 0.00 0.00 4.75
1447 1483 3.521765 AAATGCAGTGGCCGGGGAA 62.522 57.895 2.18 0.00 40.13 3.97
1738 1774 5.348451 GCATTATCCAAAACAACATGTGTCC 59.652 40.000 0.00 0.00 40.60 4.02
1835 1880 4.887655 CCTCAACCAGTTTTTGTCTAGGTT 59.112 41.667 0.00 0.00 39.76 3.50
1837 1882 4.461198 ACCTCAACCAGTTTTTGTCTAGG 58.539 43.478 0.00 0.00 0.00 3.02
2419 2464 0.251916 CCGTTGGAGATGCCCTAACA 59.748 55.000 0.00 0.00 34.97 2.41
2494 2539 1.409064 GACGGATAGCACTGGATGACA 59.591 52.381 0.00 0.00 0.00 3.58
2522 2567 2.194868 GGCCGGACAAATAGGGGG 59.805 66.667 5.05 0.00 0.00 5.40
2523 2568 1.148498 GAGGCCGGACAAATAGGGG 59.852 63.158 11.69 0.00 0.00 4.79
2657 2702 1.450491 GAGGCGGGGAAAGAAGCTC 60.450 63.158 0.00 0.00 0.00 4.09
2658 2703 2.671682 GAGGCGGGGAAAGAAGCT 59.328 61.111 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.