Multiple sequence alignment - TraesCS6D01G216600

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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 TraesCS6D01G216600 chr6D 100.000 2864 0 0 1 2864 306304721 306301858 0.000000e+00 5289
1 TraesCS6D01G216600 chr6B 93.738 2140 75 26 757 2864 473541757 473539645 0.000000e+00 3155
2 TraesCS6D01G216600 chr6B 93.846 715 28 6 16 722 473542604 473541898 0.000000e+00 1062
3 TraesCS6D01G216600 chr6A 90.905 2364 112 42 16 2334 442038764 442036459 0.000000e+00 3079
4 TraesCS6D01G216600 chr6A 92.727 495 21 7 2385 2864 442036450 442035956 0.000000e+00 701
5 TraesCS6D01G216600 chr2A 81.898 453 80 2 1405 1856 617813230 617813681 5.790000e-102 381
6 TraesCS6D01G216600 chr2A 80.220 455 82 7 1405 1855 617731107 617731557 4.570000e-88 335
7 TraesCS6D01G216600 chr2B 81.236 453 83 2 1405 1856 556676602 556677053 5.830000e-97 364
8 TraesCS6D01G216600 chr2B 80.574 453 82 6 1405 1854 556517600 556518049 7.600000e-91 344
9 TraesCS6D01G216600 chr2D 80.899 445 83 2 1405 1848 475985216 475985659 1.630000e-92 350
10 TraesCS6D01G216600 chr2D 80.674 445 82 4 1405 1847 475499558 475500000 2.730000e-90 342
11 TraesCS6D01G216600 chr2D 80.220 455 86 4 1405 1858 475877262 475877713 3.530000e-89 339


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 TraesCS6D01G216600 chr6D 306301858 306304721 2863 True 5289.0 5289 100.000 1 2864 1 chr6D.!!$R1 2863
1 TraesCS6D01G216600 chr6B 473539645 473542604 2959 True 2108.5 3155 93.792 16 2864 2 chr6B.!!$R1 2848
2 TraesCS6D01G216600 chr6A 442035956 442038764 2808 True 1890.0 3079 91.816 16 2864 2 chr6A.!!$R1 2848

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
894 1025 0.102120 ACAACAACCACCGCACATTG 59.898 50.0 0.0 0.0 0.00 2.82 F
1110 1241 0.252284 AGGAGACAACGATCACCCCT 60.252 55.0 0.0 0.0 30.12 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 1889 1.165907 TCCGGCTTGTGCTTGTTCTG 61.166 55.0 0.00 0.0 39.59 3.02 R
2549 2744 1.236616 TGGTGGAGATTGTTGCGCAG 61.237 55.0 11.31 0.0 0.00 5.18 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
168 170 2.245546 TGGGGAGCCATGATTTTGATCT 59.754 45.455 0.00 0.00 0.00 2.75
255 261 3.381908 AGGTATAGGTTCTTCTGTCTGCG 59.618 47.826 0.00 0.00 0.00 5.18
290 296 2.189594 TTCTCTGTCAATGCCACTGG 57.810 50.000 0.00 0.00 0.00 4.00
302 308 1.228063 CCACTGGCTGACTGTGCTT 60.228 57.895 14.42 0.00 44.80 3.91
422 428 2.737376 GGCAGACACCGAACCGAC 60.737 66.667 0.00 0.00 0.00 4.79
431 437 0.459585 ACCGAACCGACGATGGAATG 60.460 55.000 0.00 0.00 35.09 2.67
432 438 1.636340 CGAACCGACGATGGAATGC 59.364 57.895 0.00 0.00 35.09 3.56
438 444 1.202568 GACGATGGAATGCGCATCG 59.797 57.895 25.53 24.76 43.99 3.84
450 456 3.972537 GCATCGTCTTGCAATGCG 58.027 55.556 14.19 14.19 42.31 4.73
466 480 2.021793 CGTGCGGATTGTGCGATG 59.978 61.111 0.00 0.00 30.86 3.84
471 485 0.794229 GCGGATTGTGCGATGTTGTG 60.794 55.000 0.00 0.00 30.86 3.33
472 486 0.794229 CGGATTGTGCGATGTTGTGC 60.794 55.000 0.00 0.00 30.86 4.57
537 551 2.981140 GACGAGTTGGAGACTTTCTTCG 59.019 50.000 0.00 0.00 39.19 3.79
759 773 4.142945 CGCTCGCGGAATTACTATACTACT 60.143 45.833 6.13 0.00 35.56 2.57
834 965 1.004979 ACCAAGCCGGCCTATAAAACA 59.995 47.619 26.15 0.00 39.03 2.83
894 1025 0.102120 ACAACAACCACCGCACATTG 59.898 50.000 0.00 0.00 0.00 2.82
905 1036 2.871080 CACATTGCTTTCGGCGCG 60.871 61.111 0.00 0.00 45.43 6.86
949 1080 2.178890 GCAGAGCAGCGGATTGGAG 61.179 63.158 0.00 0.00 0.00 3.86
1023 1154 1.749258 GGGGGCAACGAATCAGGAC 60.749 63.158 0.00 0.00 37.60 3.85
1083 1214 2.584873 TAGAGGAGCCCGACTTCCCC 62.585 65.000 0.00 0.00 0.00 4.81
1099 1230 3.068691 CCGCGGAGGAGGAGACAA 61.069 66.667 24.07 0.00 45.00 3.18
1110 1241 0.252284 AGGAGACAACGATCACCCCT 60.252 55.000 0.00 0.00 30.12 4.79
1187 1318 2.798148 GATTCCAACGGCTCCACGGT 62.798 60.000 0.00 0.00 38.39 4.83
1355 1499 7.979444 TGATTTTCTTTCTTCTTGGTCGTAT 57.021 32.000 0.00 0.00 0.00 3.06
1362 1506 4.563337 TCTTCTTGGTCGTATCGTATGG 57.437 45.455 0.00 0.00 0.00 2.74
1411 1574 0.802494 GTTCCCAACGTATGCAGTGG 59.198 55.000 0.00 0.00 0.00 4.00
1804 1967 1.177401 GTTCTGGTTCATGGGCTTCC 58.823 55.000 0.00 0.00 0.00 3.46
1939 2105 3.243805 TGCTTTGTGCCTGTAGTACGTTA 60.244 43.478 0.00 0.00 42.00 3.18
1956 2122 5.864418 ACGTTATTTAGATGGTGCTAGGA 57.136 39.130 0.00 0.00 0.00 2.94
2256 2451 4.731773 GCAAAATCATTCCGTGATCTCACC 60.732 45.833 4.81 0.00 46.80 4.02
2549 2744 6.320171 TCTAACTGTTCAAGTACGTAGCATC 58.680 40.000 0.00 0.00 38.56 3.91
2571 2766 1.227999 CGCAACAATCTCCACCACGT 61.228 55.000 0.00 0.00 0.00 4.49
2643 2840 2.682856 TCCGAATTAATCAGGTTGCTGC 59.317 45.455 8.46 0.00 0.00 5.25
2670 2867 3.658757 TTGACAAATAAACAGCCCAGC 57.341 42.857 0.00 0.00 0.00 4.85
2758 2965 2.176273 GCTGACCTGCGCAATCGAT 61.176 57.895 13.05 0.00 38.10 3.59
2808 3018 5.008331 TCACTCGTCAGTACCAAGTATTCT 58.992 41.667 0.00 0.00 0.00 2.40
2828 3038 4.298626 TCTGCCATTCTTATCCACCTAGT 58.701 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.113774 CAGACACAGGGCAGGCAA 59.886 61.111 0.00 0.00 0.00 4.52
1 2 3.170672 ACAGACACAGGGCAGGCA 61.171 61.111 0.00 0.00 0.00 4.75
2 3 2.670934 CACAGACACAGGGCAGGC 60.671 66.667 0.00 0.00 0.00 4.85
3 4 1.598962 CACACAGACACAGGGCAGG 60.599 63.158 0.00 0.00 0.00 4.85
4 5 0.392706 TACACACAGACACAGGGCAG 59.607 55.000 0.00 0.00 0.00 4.85
5 6 1.055849 ATACACACAGACACAGGGCA 58.944 50.000 0.00 0.00 0.00 5.36
6 7 1.442769 CATACACACAGACACAGGGC 58.557 55.000 0.00 0.00 0.00 5.19
7 8 1.270785 TGCATACACACAGACACAGGG 60.271 52.381 0.00 0.00 0.00 4.45
8 9 2.071540 CTGCATACACACAGACACAGG 58.928 52.381 0.00 0.00 35.90 4.00
9 10 1.462283 GCTGCATACACACAGACACAG 59.538 52.381 0.00 0.00 35.90 3.66
10 11 1.511850 GCTGCATACACACAGACACA 58.488 50.000 0.00 0.00 35.90 3.72
11 12 0.439985 CGCTGCATACACACAGACAC 59.560 55.000 0.00 0.00 35.90 3.67
12 13 0.033366 ACGCTGCATACACACAGACA 59.967 50.000 0.00 0.00 35.90 3.41
13 14 1.920574 CTACGCTGCATACACACAGAC 59.079 52.381 0.00 0.00 35.90 3.51
14 15 1.135112 CCTACGCTGCATACACACAGA 60.135 52.381 0.00 0.00 35.90 3.41
168 170 0.104855 GCACACCTAGATCCGCATCA 59.895 55.000 0.00 0.00 0.00 3.07
255 261 2.498078 AGAGAAAGGAATCCACGGAGAC 59.502 50.000 0.61 0.00 0.00 3.36
290 296 1.450531 AACCTGCAAGCACAGTCAGC 61.451 55.000 0.00 0.00 35.83 4.26
296 302 2.051334 ACTACAAACCTGCAAGCACA 57.949 45.000 0.00 0.00 0.00 4.57
302 308 5.278266 GCAAACAGAATACTACAAACCTGCA 60.278 40.000 0.00 0.00 0.00 4.41
365 371 2.497792 AAATGGCCGATCCCAGCACA 62.498 55.000 0.00 0.00 38.50 4.57
450 456 0.794229 CAACATCGCACAATCCGCAC 60.794 55.000 0.00 0.00 0.00 5.34
472 486 3.140149 CATTTTGTGCTGCACGCG 58.860 55.556 25.88 3.53 43.27 6.01
501 515 2.032681 GTCCAGCCGGTTCAGCTT 59.967 61.111 1.90 0.00 38.95 3.74
503 517 4.373116 TCGTCCAGCCGGTTCAGC 62.373 66.667 1.90 0.00 0.00 4.26
563 577 5.333513 GTGTGTCATCCGTTTGTGTTTTAA 58.666 37.500 0.00 0.00 0.00 1.52
564 578 4.201930 GGTGTGTCATCCGTTTGTGTTTTA 60.202 41.667 0.00 0.00 0.00 1.52
759 773 6.643388 TGGCGGTCTATACTATACGAATAGA 58.357 40.000 0.00 0.00 37.84 1.98
799 930 4.083862 GGTGGCCACTCGACTCCC 62.084 72.222 33.91 12.56 0.00 4.30
834 965 0.045469 ATTGAGAAGGGGGAGAGCCT 59.955 55.000 0.00 0.00 0.00 4.58
949 1080 2.517166 GGAATCCCTCGCCCTTGC 60.517 66.667 0.00 0.00 0.00 4.01
1023 1154 0.538057 CCGGGATCCCAATCACATGG 60.538 60.000 30.42 16.43 34.76 3.66
1083 1214 2.182030 GTTGTCTCCTCCTCCGCG 59.818 66.667 0.00 0.00 0.00 6.46
1085 1216 0.382515 GATCGTTGTCTCCTCCTCCG 59.617 60.000 0.00 0.00 0.00 4.63
1088 1219 1.187087 GGTGATCGTTGTCTCCTCCT 58.813 55.000 0.00 0.00 0.00 3.69
1096 1227 0.544357 TCAGGAGGGGTGATCGTTGT 60.544 55.000 0.00 0.00 0.00 3.32
1098 1229 1.123928 GATCAGGAGGGGTGATCGTT 58.876 55.000 0.00 0.00 40.64 3.85
1099 1230 2.827715 GATCAGGAGGGGTGATCGT 58.172 57.895 0.00 0.00 40.64 3.73
1110 1241 0.033920 CGAATCCGCCATGATCAGGA 59.966 55.000 9.37 6.40 37.17 3.86
1187 1318 3.131478 TCTGCTCGCGATCGGTCA 61.131 61.111 18.30 6.79 36.13 4.02
1283 1427 7.148771 CGTTCCGTGTTGAATTGTATACAGTAA 60.149 37.037 5.56 0.00 0.00 2.24
1285 1429 5.119588 CGTTCCGTGTTGAATTGTATACAGT 59.880 40.000 5.56 0.00 0.00 3.55
1287 1431 4.143073 GCGTTCCGTGTTGAATTGTATACA 60.143 41.667 0.08 0.08 0.00 2.29
1288 1432 4.328667 GCGTTCCGTGTTGAATTGTATAC 58.671 43.478 0.00 0.00 0.00 1.47
1289 1433 3.371591 GGCGTTCCGTGTTGAATTGTATA 59.628 43.478 0.00 0.00 0.00 1.47
1290 1434 2.160813 GGCGTTCCGTGTTGAATTGTAT 59.839 45.455 0.00 0.00 0.00 2.29
1291 1435 1.532007 GGCGTTCCGTGTTGAATTGTA 59.468 47.619 0.00 0.00 0.00 2.41
1292 1436 0.309612 GGCGTTCCGTGTTGAATTGT 59.690 50.000 0.00 0.00 0.00 2.71
1293 1437 0.309302 TGGCGTTCCGTGTTGAATTG 59.691 50.000 0.00 0.00 34.14 2.32
1294 1438 1.025812 TTGGCGTTCCGTGTTGAATT 58.974 45.000 0.00 0.00 34.14 2.17
1355 1499 4.873827 GTCTAACAATCCAAAGCCATACGA 59.126 41.667 0.00 0.00 0.00 3.43
1362 1506 7.150783 AGAATTCAGTCTAACAATCCAAAGC 57.849 36.000 8.44 0.00 0.00 3.51
1726 1889 1.165907 TCCGGCTTGTGCTTGTTCTG 61.166 55.000 0.00 0.00 39.59 3.02
1919 2085 6.476243 AAATAACGTACTACAGGCACAAAG 57.524 37.500 0.00 0.00 0.00 2.77
1939 2105 6.126652 ACACAGATTCCTAGCACCATCTAAAT 60.127 38.462 0.00 0.00 0.00 1.40
1956 2122 8.154856 ACAACTTAACCTACACATACACAGATT 58.845 33.333 0.00 0.00 0.00 2.40
2066 2232 2.306847 TCCTTTCCCAAGCTTGTTCAC 58.693 47.619 24.35 0.00 0.00 3.18
2256 2451 8.400947 CAAACAATCTCACATAACAGATAAGGG 58.599 37.037 0.00 0.00 0.00 3.95
2383 2578 5.188948 TGGAACTACAGGTGCTGTGTAATAT 59.811 40.000 0.00 0.00 45.01 1.28
2549 2744 1.236616 TGGTGGAGATTGTTGCGCAG 61.237 55.000 11.31 0.00 0.00 5.18
2571 2766 7.290110 TGAATTCAGTCTCTTTCAGTGAGTA 57.710 36.000 3.38 0.00 33.59 2.59
2643 2840 5.106987 GGGCTGTTTATTTGTCAAAGCAATG 60.107 40.000 4.03 0.00 0.00 2.82
2717 2920 4.731000 CGACGTTGTTGCACATTTTCTTTA 59.269 37.500 0.00 0.00 0.00 1.85
2758 2965 7.095695 ACTGAAAGCTTAGTTTGCAAGTTAA 57.904 32.000 0.00 2.10 37.60 2.01
2808 3018 6.328934 TGATTACTAGGTGGATAAGAATGGCA 59.671 38.462 0.00 0.00 0.00 4.92
2828 3038 9.778741 ATTTCTCCTGCGAGTAAAATATGATTA 57.221 29.630 0.00 0.00 37.40 1.75


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

AutoCloner maintained by Alex Coulton.