Multiple sequence alignment - TraesCS6D01G114900

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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 TraesCS6D01G114900 chr6D 100.000 2522 0 0 1 2522 81748692 81751213 0.000000e+00 4658
1 TraesCS6D01G114900 chr6D 91.614 1574 90 20 178 1748 81919464 81920998 0.000000e+00 2137
2 TraesCS6D01G114900 chr6D 80.686 1429 248 20 1 1413 82963155 82964571 0.000000e+00 1085
3 TraesCS6D01G114900 chr6D 76.723 1422 307 15 1 1413 82236170 82237576 0.000000e+00 771
4 TraesCS6D01G114900 chr6D 76.331 1428 305 27 1 1413 83019355 83020764 0.000000e+00 734
5 TraesCS6D01G114900 chr6D 97.283 184 5 0 1 184 81918874 81919057 1.880000e-81 313
6 TraesCS6D01G114900 chr6B 93.068 2337 124 16 1 2318 156416952 156419269 0.000000e+00 3384
7 TraesCS6D01G114900 chr6B 81.430 1427 239 18 1 1413 157778362 157779776 0.000000e+00 1144
8 TraesCS6D01G114900 chr6B 82.727 1100 176 10 325 1413 157912638 157911542 0.000000e+00 966
9 TraesCS6D01G114900 chr6B 75.466 1394 301 30 36 1413 159403471 159402103 2.120000e-180 641
10 TraesCS6D01G114900 chr6B 93.923 181 11 0 2338 2518 156475518 156475698 8.890000e-70 274
11 TraesCS6D01G114900 chr6A 92.998 2328 126 16 1 2305 98240966 98243279 0.000000e+00 3362
12 TraesCS6D01G114900 chr6A 81.307 1423 249 12 1 1413 99785442 99786857 0.000000e+00 1138
13 TraesCS6D01G114900 chr6A 90.500 200 15 2 2326 2522 98244069 98244267 6.920000e-66 261


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 TraesCS6D01G114900 chr6D 81748692 81751213 2521 False 4658.0 4658 100.0000 1 2522 1 chr6D.!!$F1 2521
1 TraesCS6D01G114900 chr6D 81918874 81920998 2124 False 1225.0 2137 94.4485 1 1748 2 chr6D.!!$F5 1747
2 TraesCS6D01G114900 chr6D 82963155 82964571 1416 False 1085.0 1085 80.6860 1 1413 1 chr6D.!!$F3 1412
3 TraesCS6D01G114900 chr6D 82236170 82237576 1406 False 771.0 771 76.7230 1 1413 1 chr6D.!!$F2 1412
4 TraesCS6D01G114900 chr6D 83019355 83020764 1409 False 734.0 734 76.3310 1 1413 1 chr6D.!!$F4 1412
5 TraesCS6D01G114900 chr6B 156416952 156419269 2317 False 3384.0 3384 93.0680 1 2318 1 chr6B.!!$F1 2317
6 TraesCS6D01G114900 chr6B 157778362 157779776 1414 False 1144.0 1144 81.4300 1 1413 1 chr6B.!!$F3 1412
7 TraesCS6D01G114900 chr6B 157911542 157912638 1096 True 966.0 966 82.7270 325 1413 1 chr6B.!!$R1 1088
8 TraesCS6D01G114900 chr6B 159402103 159403471 1368 True 641.0 641 75.4660 36 1413 1 chr6B.!!$R2 1377
9 TraesCS6D01G114900 chr6A 98240966 98244267 3301 False 1811.5 3362 91.7490 1 2522 2 chr6A.!!$F2 2521
10 TraesCS6D01G114900 chr6A 99785442 99786857 1415 False 1138.0 1138 81.3070 1 1413 1 chr6A.!!$F1 1412

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
976 1404 1.511318 TTGCCACGTGGATGGAAACG 61.511 55.0 38.3 8.59 43.02 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2612 0.03213 CATCTCCATGCATGCCAAGC 59.968 55.0 21.69 0.0 0.0 4.01 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
27 28 2.902343 GGTATTGGCCCGCTGAGC 60.902 66.667 0.00 0.00 0.00 4.26
108 109 5.772825 TTTTTCCAGACAATGAGGAACTG 57.227 39.130 6.19 0.00 41.55 3.16
477 894 3.497262 CCTTGGTAAGTTCTCCGTTGAAC 59.503 47.826 9.00 9.00 44.67 3.18
602 1021 2.573462 TCTTGAGCTGGCCTATTGAGTT 59.427 45.455 3.32 0.00 0.00 3.01
976 1404 1.511318 TTGCCACGTGGATGGAAACG 61.511 55.000 38.30 8.59 43.02 3.60
1065 1493 1.285078 TCTTCCATGTCTCCTCCGAGA 59.715 52.381 0.00 0.00 43.08 4.04
1198 1626 3.129300 CCAGCGAGGGCGATAAGA 58.871 61.111 0.00 0.00 46.35 2.10
1388 1820 2.416747 CTCCGTGCAAGAACTGATTGA 58.583 47.619 0.00 0.00 0.00 2.57
1418 1853 2.360852 GAGCAGCAGCACCACCAT 60.361 61.111 3.17 0.00 45.49 3.55
1432 1867 0.731417 CACCATAAGAGCAGCAGCAC 59.269 55.000 3.17 0.00 45.49 4.40
1433 1868 0.742281 ACCATAAGAGCAGCAGCACG 60.742 55.000 3.17 0.00 45.49 5.34
1445 1880 1.600636 CAGCACGGCCAAGGAAAGA 60.601 57.895 2.24 0.00 0.00 2.52
1454 1889 1.839424 CCAAGGAAAGACATGGGGAC 58.161 55.000 0.00 0.00 0.00 4.46
1593 2031 1.022903 AGGGTGAGGAGGAAGGAGAT 58.977 55.000 0.00 0.00 0.00 2.75
1655 2093 2.597903 GGTCAAGGATCAGGGGCC 59.402 66.667 0.00 0.00 0.00 5.80
1774 2212 6.626623 GCCCTGCAATAAGCCAATAATCTATG 60.627 42.308 0.00 0.00 44.83 2.23
1795 2234 0.035458 AAAGACCAGACCCTCTTGCG 59.965 55.000 0.00 0.00 0.00 4.85
1893 2333 8.122330 GCATTTGTTTAACGACATGATCTGATA 58.878 33.333 0.00 0.00 0.00 2.15
1917 2357 5.840693 AGATACGATATGATATGCCCCATCA 59.159 40.000 0.00 0.00 36.86 3.07
2005 2446 2.030805 GTCAGTGGTGTTCATTCTTGGC 60.031 50.000 0.00 0.00 0.00 4.52
2024 2469 3.131400 TGGCCTCTTTTTGGTGTGTTTAC 59.869 43.478 3.32 0.00 0.00 2.01
2027 2472 4.803613 GCCTCTTTTTGGTGTGTTTACTTG 59.196 41.667 0.00 0.00 0.00 3.16
2028 2473 5.348164 CCTCTTTTTGGTGTGTTTACTTGG 58.652 41.667 0.00 0.00 0.00 3.61
2030 2475 5.956642 TCTTTTTGGTGTGTTTACTTGGTC 58.043 37.500 0.00 0.00 0.00 4.02
2038 2491 5.277011 GGTGTGTTTACTTGGTCGTTAGTTC 60.277 44.000 0.00 0.00 0.00 3.01
2042 2495 5.580297 TGTTTACTTGGTCGTTAGTTCGTTT 59.420 36.000 0.00 0.00 0.00 3.60
2049 2502 5.455392 TGGTCGTTAGTTCGTTTCTTCTAG 58.545 41.667 0.00 0.00 0.00 2.43
2050 2503 4.323070 GGTCGTTAGTTCGTTTCTTCTAGC 59.677 45.833 0.00 0.00 0.00 3.42
2116 2569 1.827789 GGTGCTGGTTGGCTGTCAA 60.828 57.895 0.00 0.00 0.00 3.18
2153 2606 4.920640 AGTCGAGTCTTCAGTTTCAGAA 57.079 40.909 0.00 0.00 0.00 3.02
2154 2607 4.612943 AGTCGAGTCTTCAGTTTCAGAAC 58.387 43.478 0.00 0.00 35.97 3.01
2155 2608 3.422546 GTCGAGTCTTCAGTTTCAGAACG 59.577 47.826 0.00 0.00 40.75 3.95
2156 2609 3.066342 TCGAGTCTTCAGTTTCAGAACGT 59.934 43.478 0.00 0.00 40.75 3.99
2158 2611 4.613448 CGAGTCTTCAGTTTCAGAACGTAG 59.387 45.833 0.00 0.00 40.75 3.51
2159 2612 4.872664 AGTCTTCAGTTTCAGAACGTAGG 58.127 43.478 0.00 0.00 40.75 3.18
2227 2686 0.326238 CTACCACCTAGGCCTTGGGA 60.326 60.000 32.76 20.88 43.14 4.37
2228 2687 0.326238 TACCACCTAGGCCTTGGGAG 60.326 60.000 32.76 25.35 43.14 4.30
2229 2688 1.616628 CCACCTAGGCCTTGGGAGT 60.617 63.158 32.76 13.12 0.00 3.85
2231 2690 2.301738 ACCTAGGCCTTGGGAGTGC 61.302 63.158 32.76 0.00 0.00 4.40
2235 2694 2.272471 GGCCTTGGGAGTGCCTAC 59.728 66.667 1.06 0.00 42.01 3.18
2236 2695 2.125106 GCCTTGGGAGTGCCTACG 60.125 66.667 1.06 0.00 0.00 3.51
2237 2696 2.955881 GCCTTGGGAGTGCCTACGT 61.956 63.158 1.06 0.00 0.00 3.57
2238 2697 1.079127 CCTTGGGAGTGCCTACGTG 60.079 63.158 1.06 0.00 0.00 4.49
2239 2698 1.079127 CTTGGGAGTGCCTACGTGG 60.079 63.158 1.06 0.00 39.35 4.94
2265 2724 1.259609 CATGGCCACCTTGTGATGTT 58.740 50.000 8.16 0.00 35.23 2.71
2281 2740 7.099266 TGTGATGTTATGGGCAGAAATTTAG 57.901 36.000 0.00 0.00 0.00 1.85
2291 2751 5.721000 TGGGCAGAAATTTAGATGGTGATTT 59.279 36.000 0.00 0.00 0.00 2.17
2354 3583 3.187227 CAGTGTTCATGTGCACCTAAGAC 59.813 47.826 15.69 13.66 36.35 3.01
2409 3638 6.291377 TGGGCATTTTATAAGTTTTGTTGCA 58.709 32.000 0.00 0.00 0.00 4.08
2421 3650 6.220726 AGTTTTGTTGCAACCTTGTTATCT 57.779 33.333 26.14 10.77 0.00 1.98
2444 3676 5.036117 TGTATCCACCTATCAAGCCTTTC 57.964 43.478 0.00 0.00 0.00 2.62
2459 3691 8.193953 TCAAGCCTTTCCATTTTAGAGAAAAT 57.806 30.769 0.00 0.00 44.44 1.82
2460 3692 8.650490 TCAAGCCTTTCCATTTTAGAGAAAATT 58.350 29.630 0.00 0.00 41.53 1.82
2462 3694 6.875726 AGCCTTTCCATTTTAGAGAAAATTGC 59.124 34.615 0.00 0.00 41.53 3.56
2478 3710 0.847373 TTGCACTGTGGGTCCCTTAA 59.153 50.000 10.00 0.00 0.00 1.85
2491 3723 2.038557 GTCCCTTAACTTGGCACTGAGA 59.961 50.000 0.00 0.00 0.00 3.27
2497 3729 3.281727 AACTTGGCACTGAGAGAACAA 57.718 42.857 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.294030 GAGATGTTATTTTTGCAAGATAACCAG 57.706 33.333 27.35 0.00 36.10 4.00
108 109 6.601217 AGAATCTTCAGGTTCTTTCAATAGCC 59.399 38.462 0.00 0.00 30.84 3.93
195 612 2.541466 AGGAACCTCACTTCCCTACTG 58.459 52.381 0.00 0.00 40.78 2.74
976 1404 1.265365 GAGCAACTTGTTCACAGGAGC 59.735 52.381 1.00 0.40 0.00 4.70
1065 1493 2.146342 CTTGATGTCAGCTTCAACCGT 58.854 47.619 0.00 0.00 35.69 4.83
1128 1556 1.367471 CCACAACTCGCTGTCTGGA 59.633 57.895 0.00 0.00 31.40 3.86
1326 1757 3.650950 TTCCTGGCTGGGCTGTCC 61.651 66.667 10.79 0.00 36.20 4.02
1360 1791 0.967887 TCTTGCACGGAGGAGGAGAG 60.968 60.000 0.00 0.00 0.00 3.20
1388 1820 1.913722 CTGCTCTCCATGGCCTCTT 59.086 57.895 6.96 0.00 0.00 2.85
1418 1853 2.434884 GCCGTGCTGCTGCTCTTA 60.435 61.111 17.00 0.00 40.48 2.10
1432 1867 1.315257 CCCATGTCTTTCCTTGGCCG 61.315 60.000 0.00 0.00 0.00 6.13
1433 1868 0.972471 CCCCATGTCTTTCCTTGGCC 60.972 60.000 0.00 0.00 0.00 5.36
1454 1889 0.809385 CAAGGAGTGCAGCAATGGAG 59.191 55.000 0.00 0.00 0.00 3.86
1593 2031 2.325661 TGTGAGAGTCCAATCCTCCA 57.674 50.000 0.00 0.00 0.00 3.86
1774 2212 2.155279 GCAAGAGGGTCTGGTCTTTTC 58.845 52.381 0.00 0.00 30.31 2.29
1893 2333 5.840693 TGATGGGGCATATCATATCGTATCT 59.159 40.000 0.00 0.00 30.03 1.98
1960 2400 1.709147 GCCACCTGCTGCGATTAGTG 61.709 60.000 0.00 0.00 36.87 2.74
1995 2436 3.321682 CACCAAAAAGAGGCCAAGAATGA 59.678 43.478 5.01 0.00 0.00 2.57
1997 2438 3.070015 CACACCAAAAAGAGGCCAAGAAT 59.930 43.478 5.01 0.00 0.00 2.40
2005 2446 5.105513 ACCAAGTAAACACACCAAAAAGAGG 60.106 40.000 0.00 0.00 0.00 3.69
2024 2469 4.743644 AGAAGAAACGAACTAACGACCAAG 59.256 41.667 0.00 0.00 37.03 3.61
2027 2472 4.323070 GCTAGAAGAAACGAACTAACGACC 59.677 45.833 0.00 0.00 37.03 4.79
2028 2473 5.152804 AGCTAGAAGAAACGAACTAACGAC 58.847 41.667 0.00 0.00 37.03 4.34
2030 2475 7.737525 ATAAGCTAGAAGAAACGAACTAACG 57.262 36.000 0.00 0.00 39.31 3.18
2038 2491 7.276658 ACATGAGTGAATAAGCTAGAAGAAACG 59.723 37.037 0.00 0.00 0.00 3.60
2042 2495 9.755804 CATTACATGAGTGAATAAGCTAGAAGA 57.244 33.333 0.00 0.00 0.00 2.87
2049 2502 7.066284 AGGAACACATTACATGAGTGAATAAGC 59.934 37.037 15.36 0.00 34.32 3.09
2050 2503 8.498054 AGGAACACATTACATGAGTGAATAAG 57.502 34.615 15.36 3.28 34.32 1.73
2116 2569 3.990092 TCGACTATGCAAAGTTGACACT 58.010 40.909 0.00 0.00 35.40 3.55
2153 2606 1.077501 ATGCATGCCAAGCCTACGT 60.078 52.632 16.68 0.00 0.00 3.57
2154 2607 1.357690 CATGCATGCCAAGCCTACG 59.642 57.895 14.93 0.00 0.00 3.51
2155 2608 0.752743 TCCATGCATGCCAAGCCTAC 60.753 55.000 21.69 0.00 0.00 3.18
2156 2609 0.466739 CTCCATGCATGCCAAGCCTA 60.467 55.000 21.69 0.00 0.00 3.93
2158 2611 1.113517 ATCTCCATGCATGCCAAGCC 61.114 55.000 21.69 0.00 0.00 4.35
2159 2612 0.032130 CATCTCCATGCATGCCAAGC 59.968 55.000 21.69 0.00 0.00 4.01
2184 2642 1.493772 TTCGTTGCTTAGGTGACGTG 58.506 50.000 0.00 0.00 36.89 4.49
2210 2669 1.616628 CTCCCAAGGCCTAGGTGGT 60.617 63.158 18.73 0.00 38.35 4.16
2227 2686 3.319198 CCCACCCACGTAGGCACT 61.319 66.667 0.00 0.00 46.37 4.40
2228 2687 3.315949 TCCCACCCACGTAGGCAC 61.316 66.667 0.00 0.00 35.39 5.01
2229 2688 3.315949 GTCCCACCCACGTAGGCA 61.316 66.667 0.00 0.00 35.39 4.75
2231 2690 1.220749 CATGTCCCACCCACGTAGG 59.779 63.158 0.00 0.00 37.03 3.18
2233 2692 2.961893 GCCATGTCCCACCCACGTA 61.962 63.158 0.00 0.00 0.00 3.57
2234 2693 4.344865 GCCATGTCCCACCCACGT 62.345 66.667 0.00 0.00 0.00 4.49
2236 2695 3.978193 TGGCCATGTCCCACCCAC 61.978 66.667 0.00 0.00 0.00 4.61
2237 2696 3.978193 GTGGCCATGTCCCACCCA 61.978 66.667 9.72 1.18 45.51 4.51
2247 2706 2.897271 TAACATCACAAGGTGGCCAT 57.103 45.000 9.72 0.00 33.87 4.40
2265 2724 6.012337 TCACCATCTAAATTTCTGCCCATA 57.988 37.500 0.00 0.00 0.00 2.74
2281 2740 5.947228 TCACAGAAACTCAAATCACCATC 57.053 39.130 0.00 0.00 0.00 3.51
2321 2792 6.539826 TGCACATGAACACTGAATAATAGGAG 59.460 38.462 0.00 0.00 0.00 3.69
2323 2794 6.458751 GGTGCACATGAACACTGAATAATAGG 60.459 42.308 20.43 0.00 36.99 2.57
2324 2795 6.317140 AGGTGCACATGAACACTGAATAATAG 59.683 38.462 20.43 0.00 36.99 1.73
2335 3564 2.412870 CGTCTTAGGTGCACATGAACA 58.587 47.619 20.43 0.00 0.00 3.18
2336 3565 1.128692 GCGTCTTAGGTGCACATGAAC 59.871 52.381 20.43 10.53 0.00 3.18
2354 3583 8.175069 AGTACATAATGTTGTTTAAGTGATGCG 58.825 33.333 0.00 0.00 0.00 4.73
2383 3612 8.097038 TGCAACAAAACTTATAAAATGCCCATA 58.903 29.630 0.00 0.00 0.00 2.74
2404 3633 6.322491 GGATACAAGATAACAAGGTTGCAAC 58.678 40.000 21.59 21.59 0.00 4.17
2444 3676 6.366877 CCACAGTGCAATTTTCTCTAAAATGG 59.633 38.462 0.00 0.00 43.04 3.16
2459 3691 0.847373 TTAAGGGACCCACAGTGCAA 59.153 50.000 14.60 0.00 38.89 4.08
2460 3692 0.109723 GTTAAGGGACCCACAGTGCA 59.890 55.000 14.60 0.00 38.89 4.57
2462 3694 2.504367 CAAGTTAAGGGACCCACAGTG 58.496 52.381 14.60 1.31 0.00 3.66
2478 3710 3.498774 ATTGTTCTCTCAGTGCCAAGT 57.501 42.857 0.00 0.00 0.00 3.16
2497 3729 7.883229 CGGCTTTCAGGTTGTTAAATTAAAT 57.117 32.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.