Multiple sequence alignment - TraesCS3A01G330800

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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 TraesCS3A01G330800 chr3A 100.000 2645 0 0 1 2645 575483638 575486282 0.000000e+00 4885.0
1 TraesCS3A01G330800 chr3D 95.231 1887 74 10 1 1881 437474608 437476484 0.000000e+00 2972.0
2 TraesCS3A01G330800 chr3D 92.460 756 54 3 1882 2636 437476517 437477270 0.000000e+00 1077.0
3 TraesCS3A01G330800 chr3B 94.071 1906 80 20 1 1881 572678297 572680194 0.000000e+00 2863.0
4 TraesCS3A01G330800 chrUn 91.610 441 31 5 2189 2627 36545921 36546357 2.910000e-169 604.0
5 TraesCS3A01G330800 chrUn 91.781 438 30 5 2192 2627 275330201 275329768 2.910000e-169 604.0
6 TraesCS3A01G330800 chr7B 91.610 441 31 5 2189 2627 644467502 644467938 2.910000e-169 604.0
7 TraesCS3A01G330800 chr6B 91.781 438 30 5 2192 2627 306995929 306995496 2.910000e-169 604.0
8 TraesCS3A01G330800 chr7D 91.383 441 32 5 2189 2627 203515534 203515970 1.350000e-167 599.0
9 TraesCS3A01G330800 chr4D 91.383 441 32 5 2189 2627 123299948 123300384 1.350000e-167 599.0
10 TraesCS3A01G330800 chr4D 95.349 43 2 0 742 784 455601488 455601530 4.720000e-08 69.4
11 TraesCS3A01G330800 chr1D 91.553 438 31 5 2192 2627 141313075 141312642 1.350000e-167 599.0
12 TraesCS3A01G330800 chr1D 84.496 258 40 0 1228 1485 407878354 407878097 3.380000e-64 255.0
13 TraesCS3A01G330800 chr1D 88.679 53 5 1 736 788 141705967 141706018 2.200000e-06 63.9
14 TraesCS3A01G330800 chr1B 91.383 441 32 5 2189 2627 672479219 672479655 1.350000e-167 599.0
15 TraesCS3A01G330800 chr1B 88.679 53 5 1 736 788 195591191 195591242 2.200000e-06 63.9
16 TraesCS3A01G330800 chr2D 92.000 50 2 2 735 783 649145955 649145907 4.720000e-08 69.4
17 TraesCS3A01G330800 chr5A 91.837 49 3 1 740 788 490326156 490326109 1.700000e-07 67.6
18 TraesCS3A01G330800 chr5A 91.837 49 3 1 740 788 490416186 490416139 1.700000e-07 67.6
19 TraesCS3A01G330800 chr7A 87.719 57 5 2 728 783 717413053 717412998 6.110000e-07 65.8


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 TraesCS3A01G330800 chr3A 575483638 575486282 2644 False 4885.0 4885 100.0000 1 2645 1 chr3A.!!$F1 2644
1 TraesCS3A01G330800 chr3D 437474608 437477270 2662 False 2024.5 2972 93.8455 1 2636 2 chr3D.!!$F1 2635
2 TraesCS3A01G330800 chr3B 572678297 572680194 1897 False 2863.0 2863 94.0710 1 1881 1 chr3B.!!$F1 1880

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
796 798 2.426738 TGGCAGTTTGAAAACAGAGGTG 59.573 45.455 8.53 0.0 41.3 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2249 0.249073 ACATTAGCTAGCGCACTCCG 60.249 55.0 11.47 0.0 39.1 4.63 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
122 123 4.393062 AGATGCTACTGGTTGAAATGAACG 59.607 41.667 0.00 0.00 0.00 3.95
140 141 5.172934 TGAACGTAAAAGGAATCGTAGCAT 58.827 37.500 0.00 0.00 35.49 3.79
192 193 5.242171 TCCATGAATAGTGGCAAGCATAATG 59.758 40.000 0.00 0.00 36.66 1.90
197 198 6.324512 TGAATAGTGGCAAGCATAATGGAAAT 59.675 34.615 0.00 0.00 0.00 2.17
274 275 2.755650 GCTCCGATCCAATAACATCGT 58.244 47.619 0.00 0.00 40.28 3.73
510 512 5.339008 TTTGATGCACTTCGGTAGTCTAT 57.661 39.130 0.00 0.00 33.85 1.98
511 513 6.459670 TTTGATGCACTTCGGTAGTCTATA 57.540 37.500 0.00 0.00 33.85 1.31
522 524 6.005583 TCGGTAGTCTATAGGTATTTTGCG 57.994 41.667 0.00 0.00 0.00 4.85
527 529 5.914033 AGTCTATAGGTATTTTGCGCTCAA 58.086 37.500 9.73 0.80 0.00 3.02
751 753 8.612619 CCATTCAATCACTAATAAGTACACACC 58.387 37.037 0.00 0.00 33.48 4.16
784 786 7.867445 AAATATAAGACGTTTTGGCAGTTTG 57.133 32.000 0.83 0.00 0.00 2.93
796 798 2.426738 TGGCAGTTTGAAAACAGAGGTG 59.573 45.455 8.53 0.00 41.30 4.00
816 818 5.043130 AGGTGGTAGTAATCTAGGGGTTACA 60.043 44.000 12.75 0.00 34.14 2.41
896 899 4.417426 TTTATGGAGCAAGCTAGGGTAC 57.583 45.455 0.00 0.00 0.00 3.34
1155 1161 2.666190 CACTCCCACACGTGCCTG 60.666 66.667 17.22 7.38 0.00 4.85
1424 1430 0.598680 GTCCGAGGCAAGATCGATGG 60.599 60.000 0.54 0.00 42.76 3.51
1480 1486 2.876645 GCTTCGGCTCTGTCGTCG 60.877 66.667 0.00 0.00 38.08 5.12
1733 1766 3.464720 TGAATAAATGGTGGCTGGGAA 57.535 42.857 0.00 0.00 0.00 3.97
1840 1873 4.941263 TGTGTTTGTATTGGATGGAGCTAC 59.059 41.667 0.00 0.00 0.00 3.58
1860 1894 4.207891 ACTAGTAAGTTGACCCAGCATG 57.792 45.455 0.00 0.00 29.00 4.06
1904 1970 4.226168 CCTTAGGTTGGTCTTCTCTGGAAT 59.774 45.833 0.00 0.00 0.00 3.01
1909 1975 7.510675 AGGTTGGTCTTCTCTGGAATAATTA 57.489 36.000 0.00 0.00 0.00 1.40
1913 1979 7.265599 TGGTCTTCTCTGGAATAATTAACCA 57.734 36.000 12.19 12.19 0.00 3.67
1955 2021 8.345565 GTTGTGTTCTGTAATGGGATAATGATC 58.654 37.037 0.00 0.00 0.00 2.92
1988 2054 8.165239 TGTGTTATCTTCAGTTAAATGCAACT 57.835 30.769 0.00 0.00 39.34 3.16
2001 2067 8.637986 AGTTAAATGCAACTTGGAAATGTCTTA 58.362 29.630 0.00 0.00 35.16 2.10
2079 2145 9.937175 GATTTTGCTGTTACAGAATTAGGATAC 57.063 33.333 17.40 0.00 32.44 2.24
2080 2146 7.859325 TTTGCTGTTACAGAATTAGGATACC 57.141 36.000 17.40 0.00 32.44 2.73
2114 2180 3.311106 TGTCTAAACGTTTACTCCTGCG 58.689 45.455 16.59 5.84 0.00 5.18
2126 2192 6.401688 CGTTTACTCCTGCGAATTTATGTTGA 60.402 38.462 0.00 0.00 0.00 3.18
2132 2198 4.082787 CCTGCGAATTTATGTTGACAACCT 60.083 41.667 15.59 8.52 0.00 3.50
2136 2202 5.795441 GCGAATTTATGTTGACAACCTTCTC 59.205 40.000 15.59 4.48 0.00 2.87
2143 2209 4.728772 TGTTGACAACCTTCTCCATCATT 58.271 39.130 15.59 0.00 0.00 2.57
2157 2223 9.731819 CTTCTCCATCATTCATTTAAATGTCTG 57.268 33.333 23.95 20.84 37.77 3.51
2160 2226 7.999679 TCCATCATTCATTTAAATGTCTGGAC 58.000 34.615 23.95 0.00 40.48 4.02
2183 2249 4.840772 CGAAGAAACATCGTCACACAAATC 59.159 41.667 0.00 0.00 35.64 2.17
2202 2268 0.249073 CGGAGTGCGCTAGCTAATGT 60.249 55.000 13.93 0.00 45.42 2.71
2290 2356 1.139853 GGCCTAAGAGTGATGGGACTG 59.860 57.143 0.00 0.00 0.00 3.51
2310 2376 4.214332 ACTGCTTCTTTAAAGAGCCTTTCG 59.786 41.667 24.39 15.32 36.22 3.46
2317 2383 0.185175 AAAGAGCCTTTCGTTGGGGT 59.815 50.000 0.00 0.00 35.91 4.95
2327 2393 4.218686 GTTGGGGTGGCAGGTGGT 62.219 66.667 0.00 0.00 0.00 4.16
2343 2409 3.825328 GGTGGTGCCTTGATCTATCAAT 58.175 45.455 5.88 0.00 44.92 2.57
2381 2448 4.840005 CCGCTTCGCTCCCCCTTC 62.840 72.222 0.00 0.00 0.00 3.46
2386 2453 1.339727 GCTTCGCTCCCCCTTCTTTAA 60.340 52.381 0.00 0.00 0.00 1.52
2387 2454 2.878526 GCTTCGCTCCCCCTTCTTTAAA 60.879 50.000 0.00 0.00 0.00 1.52
2388 2455 2.484742 TCGCTCCCCCTTCTTTAAAC 57.515 50.000 0.00 0.00 0.00 2.01
2396 2463 5.637127 TCCCCCTTCTTTAAACGAAGAAAT 58.363 37.500 20.07 0.00 43.06 2.17
2419 2486 8.824756 AATAAAGAAAGGGGAAGTTTAGATCC 57.175 34.615 0.00 0.00 34.85 3.36
2439 2506 4.801164 TCCCTCATAGTAGTTCTACCCAC 58.199 47.826 6.39 0.00 0.00 4.61
2459 2526 5.125097 CCCACAGAAAAGATCATGAAAGAGG 59.875 44.000 0.00 0.00 0.00 3.69
2461 2528 5.415077 CACAGAAAAGATCATGAAAGAGGCT 59.585 40.000 0.00 0.00 0.00 4.58
2482 2549 3.771577 ATCAGAATGGTACCCGAATCC 57.228 47.619 10.07 0.00 36.16 3.01
2484 2551 3.045634 TCAGAATGGTACCCGAATCCAT 58.954 45.455 10.07 0.00 42.82 3.41
2502 2569 4.266714 TCCATTTACAATCCCGAGTTTCC 58.733 43.478 0.00 0.00 0.00 3.13
2504 2571 4.461081 CCATTTACAATCCCGAGTTTCCAA 59.539 41.667 0.00 0.00 0.00 3.53
2518 2585 3.042887 GTTTCCAAACACATCGCACTTC 58.957 45.455 0.00 0.00 38.74 3.01
2519 2586 1.234821 TCCAAACACATCGCACTTCC 58.765 50.000 0.00 0.00 0.00 3.46
2636 2703 4.740268 TCACACCATCGACTATTGTACAC 58.260 43.478 0.00 0.00 0.00 2.90
2637 2704 3.863424 CACACCATCGACTATTGTACACC 59.137 47.826 0.00 0.00 0.00 4.16
2638 2705 3.118884 ACACCATCGACTATTGTACACCC 60.119 47.826 0.00 0.00 0.00 4.61
2639 2706 3.101437 ACCATCGACTATTGTACACCCA 58.899 45.455 0.00 0.00 0.00 4.51
2640 2707 3.118884 ACCATCGACTATTGTACACCCAC 60.119 47.826 0.00 0.00 0.00 4.61
2641 2708 2.925578 TCGACTATTGTACACCCACG 57.074 50.000 0.00 0.00 0.00 4.94
2642 2709 1.473677 TCGACTATTGTACACCCACGG 59.526 52.381 0.00 0.00 0.00 4.94
2643 2710 1.648504 GACTATTGTACACCCACGGC 58.351 55.000 0.00 0.00 0.00 5.68
2644 2711 0.251073 ACTATTGTACACCCACGGCC 59.749 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 193 1.816835 GTTCTCCGTTTCCCCATTTCC 59.183 52.381 0.00 0.00 0.00 3.13
197 198 1.546773 CCAATGTTCTCCGTTTCCCCA 60.547 52.381 0.00 0.00 0.00 4.96
274 275 0.537143 ATGAAGCAAGCGGTGGACAA 60.537 50.000 0.00 0.00 0.00 3.18
452 454 4.100963 TGATGTGTAGACCTGTCAACAACT 59.899 41.667 0.00 0.00 0.00 3.16
527 529 9.342308 TCAGACTGAATCAACAAAAGTAGATTT 57.658 29.630 1.64 0.00 31.35 2.17
722 724 8.540492 GTGTACTTATTAGTGATTGAATGGTCG 58.460 37.037 0.00 0.00 35.78 4.79
751 753 8.395633 CCAAAACGTCTTATATTTAGGAACAGG 58.604 37.037 0.00 0.00 0.00 4.00
784 786 7.266400 CCTAGATTACTACCACCTCTGTTTTC 58.734 42.308 0.00 0.00 0.00 2.29
796 798 7.607615 TTCATGTAACCCCTAGATTACTACC 57.392 40.000 0.00 0.00 33.32 3.18
855 857 8.836413 CCATAAAAGCTTATTACCGATTCAGAA 58.164 33.333 0.00 0.00 0.00 3.02
896 899 5.163754 ACAGTTCAAAAACTCGAGAACTTGG 60.164 40.000 21.68 8.76 46.02 3.61
1141 1147 4.927782 GTGCAGGCACGTGTGGGA 62.928 66.667 18.38 5.38 37.19 4.37
1450 1456 3.123620 GAAGCTGCACCGCTCCTG 61.124 66.667 1.02 0.00 39.86 3.86
1549 1555 1.589993 CGCCATCGATCTCGCAAGT 60.590 57.895 0.00 0.00 39.60 3.16
1710 1743 3.099141 CCCAGCCACCATTTATTCAAGT 58.901 45.455 0.00 0.00 0.00 3.16
1733 1766 2.766263 TGTCTCACTTCCACACTTCTGT 59.234 45.455 0.00 0.00 0.00 3.41
1840 1873 4.471904 TCATGCTGGGTCAACTTACTAG 57.528 45.455 0.00 0.00 0.00 2.57
1860 1894 2.352127 GGCACTTTGGAAAGCACAGATC 60.352 50.000 0.00 0.00 39.63 2.75
1909 1975 7.875554 ACACAACTGAATTTTTAAACAGTGGTT 59.124 29.630 11.95 0.00 42.52 3.67
1913 1979 9.139174 CAGAACACAACTGAATTTTTAAACAGT 57.861 29.630 3.93 3.93 43.92 3.55
1929 1995 7.624360 TCATTATCCCATTACAGAACACAAC 57.376 36.000 0.00 0.00 0.00 3.32
1980 2046 8.907222 AAAATAAGACATTTCCAAGTTGCATT 57.093 26.923 0.00 0.00 0.00 3.56
2008 2074 3.539604 CAGAGAGCCAAGTATTCAAGGG 58.460 50.000 0.00 0.00 0.00 3.95
2052 2118 7.994425 TCCTAATTCTGTAACAGCAAAATCA 57.006 32.000 0.00 0.00 0.00 2.57
2079 2145 6.561614 ACGTTTAGACAGTACATGTGATAGG 58.438 40.000 9.11 0.00 44.17 2.57
2080 2146 8.462143 AAACGTTTAGACAGTACATGTGATAG 57.538 34.615 12.83 0.00 44.17 2.08
2114 2180 7.214467 TGGAGAAGGTTGTCAACATAAATTC 57.786 36.000 17.29 11.69 0.00 2.17
2126 2192 8.421249 TTTAAATGAATGATGGAGAAGGTTGT 57.579 30.769 0.00 0.00 0.00 3.32
2132 2198 8.689061 CCAGACATTTAAATGAATGATGGAGAA 58.311 33.333 30.18 0.00 42.86 2.87
2136 2202 6.914215 CGTCCAGACATTTAAATGAATGATGG 59.086 38.462 30.18 25.12 42.30 3.51
2143 2209 7.227711 TGTTTCTTCGTCCAGACATTTAAATGA 59.772 33.333 30.18 8.58 39.67 2.57
2160 2226 3.852471 TTGTGTGACGATGTTTCTTCG 57.148 42.857 0.00 4.07 42.20 3.79
2183 2249 0.249073 ACATTAGCTAGCGCACTCCG 60.249 55.000 11.47 0.00 39.10 4.63
2228 2294 1.773653 GGGGCTCTCTCCAATCATTCT 59.226 52.381 0.00 0.00 0.00 2.40
2275 2341 2.264455 AGAAGCAGTCCCATCACTCTT 58.736 47.619 0.00 0.00 0.00 2.85
2290 2356 4.750952 ACGAAAGGCTCTTTAAAGAAGC 57.249 40.909 18.25 20.26 34.03 3.86
2310 2376 4.218686 ACCACCTGCCACCCCAAC 62.219 66.667 0.00 0.00 0.00 3.77
2333 2399 6.949352 TTTTGCTCCCTCAATTGATAGATC 57.051 37.500 8.96 5.33 0.00 2.75
2370 2437 1.084289 CGTTTAAAGAAGGGGGAGCG 58.916 55.000 0.00 0.00 0.00 5.03
2381 2448 9.406828 CCCCTTTCTTTATTTCTTCGTTTAAAG 57.593 33.333 0.00 0.00 34.47 1.85
2386 2453 6.776116 ACTTCCCCTTTCTTTATTTCTTCGTT 59.224 34.615 0.00 0.00 0.00 3.85
2387 2454 6.304624 ACTTCCCCTTTCTTTATTTCTTCGT 58.695 36.000 0.00 0.00 0.00 3.85
2388 2455 6.819397 ACTTCCCCTTTCTTTATTTCTTCG 57.181 37.500 0.00 0.00 0.00 3.79
2396 2463 6.728411 GGGATCTAAACTTCCCCTTTCTTTA 58.272 40.000 0.00 0.00 45.08 1.85
2406 2473 7.842887 ACTACTATGAGGGATCTAAACTTCC 57.157 40.000 0.00 0.00 0.00 3.46
2417 2484 4.231195 TGTGGGTAGAACTACTATGAGGGA 59.769 45.833 11.04 0.00 36.36 4.20
2419 2486 5.446860 TCTGTGGGTAGAACTACTATGAGG 58.553 45.833 11.04 0.71 36.36 3.86
2439 2506 7.498239 TGATAGCCTCTTTCATGATCTTTTCTG 59.502 37.037 0.00 0.00 0.00 3.02
2482 2549 5.637006 TTGGAAACTCGGGATTGTAAATG 57.363 39.130 0.00 0.00 0.00 2.32
2484 2551 4.888239 TGTTTGGAAACTCGGGATTGTAAA 59.112 37.500 0.00 0.00 39.59 2.01
2502 2569 0.725784 GCGGAAGTGCGATGTGTTTG 60.726 55.000 0.00 0.00 0.00 2.93
2504 2571 1.291877 GAGCGGAAGTGCGATGTGTT 61.292 55.000 0.00 0.00 40.67 3.32
2539 2606 1.117749 TGATCCATCTGAGGGCCGAG 61.118 60.000 2.89 0.00 0.00 4.63
2542 2609 1.492176 TCTTTGATCCATCTGAGGGCC 59.508 52.381 2.89 0.00 0.00 5.80
2577 2644 7.869937 TGATGTCGAATTCCAAAAATAAGCAAA 59.130 29.630 0.00 0.00 0.00 3.68
2583 2650 8.792633 ACTTCTTGATGTCGAATTCCAAAAATA 58.207 29.630 0.00 0.00 0.00 1.40
2584 2651 7.596248 CACTTCTTGATGTCGAATTCCAAAAAT 59.404 33.333 0.00 0.00 0.00 1.82
2624 2691 1.648504 GCCGTGGGTGTACAATAGTC 58.351 55.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.