Multiple sequence alignment - TraesCS6B01G344400

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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 TraesCS6B01G344400 chr6B 100.000 2498 0 0 1 2498 606945310 606947807 0.000000e+00 4614
1 TraesCS6B01G344400 chr7B 92.262 2520 162 29 2 2496 605410455 605407944 0.000000e+00 3542
2 TraesCS6B01G344400 chr7B 91.855 2517 153 22 1 2496 604707507 604705022 0.000000e+00 3465
3 TraesCS6B01G344400 chr1B 92.228 2522 165 24 1 2498 70008957 70011471 0.000000e+00 3542
4 TraesCS6B01G344400 chr5B 91.855 2517 170 29 1 2496 54182790 54185292 0.000000e+00 3480
5 TraesCS6B01G344400 chr2B 91.799 2512 178 22 1 2498 385899061 385896564 0.000000e+00 3472
6 TraesCS6B01G344400 chr2B 91.107 2530 185 31 1 2496 664480619 664483142 0.000000e+00 3389
7 TraesCS6B01G344400 chr4A 91.657 2517 159 26 2 2496 658427184 658424697 0.000000e+00 3437
8 TraesCS6B01G344400 chr3B 91.397 2534 170 25 1 2498 166547736 166545215 0.000000e+00 3428
9 TraesCS6B01G344400 chr3B 85.850 1576 165 35 941 2498 46771710 46773245 0.000000e+00 1622
10 TraesCS6B01G344400 chr3B 84.177 158 20 5 2345 2498 193587211 193587055 5.570000e-32 148
11 TraesCS6B01G344400 chr3B 79.902 204 26 12 2298 2490 595385063 595384864 4.330000e-28 135
12 TraesCS6B01G344400 chr2D 92.603 2393 151 22 1 2380 28398245 28395866 0.000000e+00 3415


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 TraesCS6B01G344400 chr6B 606945310 606947807 2497 False 4614 4614 100.000 1 2498 1 chr6B.!!$F1 2497
1 TraesCS6B01G344400 chr7B 605407944 605410455 2511 True 3542 3542 92.262 2 2496 1 chr7B.!!$R2 2494
2 TraesCS6B01G344400 chr7B 604705022 604707507 2485 True 3465 3465 91.855 1 2496 1 chr7B.!!$R1 2495
3 TraesCS6B01G344400 chr1B 70008957 70011471 2514 False 3542 3542 92.228 1 2498 1 chr1B.!!$F1 2497
4 TraesCS6B01G344400 chr5B 54182790 54185292 2502 False 3480 3480 91.855 1 2496 1 chr5B.!!$F1 2495
5 TraesCS6B01G344400 chr2B 385896564 385899061 2497 True 3472 3472 91.799 1 2498 1 chr2B.!!$R1 2497
6 TraesCS6B01G344400 chr2B 664480619 664483142 2523 False 3389 3389 91.107 1 2496 1 chr2B.!!$F1 2495
7 TraesCS6B01G344400 chr4A 658424697 658427184 2487 True 3437 3437 91.657 2 2496 1 chr4A.!!$R1 2494
8 TraesCS6B01G344400 chr3B 166545215 166547736 2521 True 3428 3428 91.397 1 2498 1 chr3B.!!$R1 2497
9 TraesCS6B01G344400 chr3B 46771710 46773245 1535 False 1622 1622 85.850 941 2498 1 chr3B.!!$F1 1557
10 TraesCS6B01G344400 chr2D 28395866 28398245 2379 True 3415 3415 92.603 1 2380 1 chr2D.!!$R1 2379

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
44 45 0.180642 CTGGATCTGTGAGGCAGCAT 59.819 55.0 0.0 0.0 44.66 3.79 F
1032 1072 0.178967 TTGCACCACATGACCCACAT 60.179 50.0 0.0 0.0 40.17 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1502 0.250467 AGCTCAACGACCATTGCAGT 60.250 50.000 0.00 0.00 0.00 4.40 R
1969 2031 1.618837 CTACCATGCTAGCCGGTACAT 59.381 52.381 22.83 3.43 34.12 2.29 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
29 30 0.474854 TTAGAAGTGCCACCCCTGGA 60.475 55.000 0.00 0.00 40.55 3.86
44 45 0.180642 CTGGATCTGTGAGGCAGCAT 59.819 55.000 0.00 0.00 44.66 3.79
45 46 0.622136 TGGATCTGTGAGGCAGCATT 59.378 50.000 0.00 0.00 44.66 3.56
55 58 1.394917 GAGGCAGCATTGTAGTTCACG 59.605 52.381 0.00 0.00 0.00 4.35
60 63 0.871722 GCATTGTAGTTCACGCACCA 59.128 50.000 0.00 0.00 0.00 4.17
61 64 1.468520 GCATTGTAGTTCACGCACCAT 59.531 47.619 0.00 0.00 0.00 3.55
64 67 0.973632 TGTAGTTCACGCACCATCCT 59.026 50.000 0.00 0.00 0.00 3.24
72 75 0.548031 ACGCACCATCCTTGGATGAT 59.452 50.000 26.19 10.79 46.92 2.45
79 82 3.967326 ACCATCCTTGGATGATTACGAGA 59.033 43.478 26.19 0.00 46.92 4.04
81 84 4.202253 CCATCCTTGGATGATTACGAGACA 60.202 45.833 26.19 0.00 46.92 3.41
83 86 3.126831 CCTTGGATGATTACGAGACAGC 58.873 50.000 0.00 0.00 0.00 4.40
85 88 3.885724 TGGATGATTACGAGACAGCAA 57.114 42.857 0.00 0.00 0.00 3.91
101 105 2.235402 CAGCAATCAAGGCCAAAAGGAT 59.765 45.455 5.01 0.00 0.00 3.24
113 117 2.751806 CCAAAAGGATCAGAACCAGCTC 59.248 50.000 0.00 0.00 0.00 4.09
131 135 2.154007 GCTCTACGATATTGTCAAGCGC 59.846 50.000 0.00 0.00 0.00 5.92
210 214 5.243730 CCACACCACATAACCTCTCATTTTT 59.756 40.000 0.00 0.00 0.00 1.94
232 237 7.933728 TTTTATTTGCTCTTTTTACCGTTCC 57.066 32.000 0.00 0.00 0.00 3.62
241 246 6.139048 TCTTTTTACCGTTCCTCCTTTTTG 57.861 37.500 0.00 0.00 0.00 2.44
242 247 3.994204 TTTACCGTTCCTCCTTTTTGC 57.006 42.857 0.00 0.00 0.00 3.68
243 248 2.943036 TACCGTTCCTCCTTTTTGCT 57.057 45.000 0.00 0.00 0.00 3.91
244 249 2.943036 ACCGTTCCTCCTTTTTGCTA 57.057 45.000 0.00 0.00 0.00 3.49
257 267 8.510505 CCTCCTTTTTGCTATTTCTAGATATGC 58.489 37.037 5.99 7.88 0.00 3.14
346 369 2.775890 ACAGCTCATGTTTGGACAGAG 58.224 47.619 0.00 0.00 39.96 3.35
348 371 1.527034 GCTCATGTTTGGACAGAGCA 58.473 50.000 17.79 0.00 45.72 4.26
375 398 4.444388 GTCATACAATGTGATGCGACGTAT 59.556 41.667 0.00 0.00 0.00 3.06
402 425 0.904865 TGGGTGATCTTGCCGAGTCT 60.905 55.000 0.00 0.00 0.00 3.24
590 613 1.470098 GCACGGTGAATTCAAGCTCAT 59.530 47.619 13.29 0.00 0.00 2.90
611 634 8.834465 GCTCATAATGAAGAAATGTGTGAGTAT 58.166 33.333 0.00 0.00 34.56 2.12
619 642 6.126863 AGAAATGTGTGAGTATTCCTTCCA 57.873 37.500 0.00 0.00 0.00 3.53
793 825 2.639839 ACAGGGCAACTCTGTTCATACT 59.360 45.455 0.00 0.00 42.94 2.12
807 839 4.218200 TGTTCATACTTGGATGGCAACTTG 59.782 41.667 0.00 0.00 37.61 3.16
823 855 5.221362 GGCAACTTGTTTTAACTACCCACAT 60.221 40.000 0.00 0.00 0.00 3.21
824 856 6.016108 GGCAACTTGTTTTAACTACCCACATA 60.016 38.462 0.00 0.00 0.00 2.29
826 858 7.380333 GCAACTTGTTTTAACTACCCACATAAC 59.620 37.037 0.00 0.00 0.00 1.89
827 859 8.626526 CAACTTGTTTTAACTACCCACATAACT 58.373 33.333 0.00 0.00 0.00 2.24
942 981 2.562298 TCCCAATCACACCATTTTCTGC 59.438 45.455 0.00 0.00 0.00 4.26
1032 1072 0.178967 TTGCACCACATGACCCACAT 60.179 50.000 0.00 0.00 40.17 3.21
1145 1185 4.870426 AGTCCTTACTACGCATGTTGAATG 59.130 41.667 0.00 0.00 32.84 2.67
1185 1225 3.366396 AGAGACATGGAACCGTCACTAT 58.634 45.455 0.00 0.00 31.39 2.12
1232 1272 5.067273 ACATTTTCCAATTGAGTACGTGGA 58.933 37.500 7.12 0.00 38.39 4.02
1238 1278 4.954202 TCCAATTGAGTACGTGGAGACTAT 59.046 41.667 7.12 0.00 35.22 2.12
1389 1438 4.884668 TCTTTTCTTGTACAGGACGGAT 57.115 40.909 7.26 0.00 0.00 4.18
1442 1491 1.975680 GTGGGAAGGTAGACTGGTTCA 59.024 52.381 0.00 0.00 0.00 3.18
1447 1496 4.254492 GGAAGGTAGACTGGTTCATGTTC 58.746 47.826 0.00 0.00 0.00 3.18
1453 1502 4.422073 AGACTGGTTCATGTTCTCACAA 57.578 40.909 0.00 0.00 36.16 3.33
1473 1522 0.167470 CTGCAATGGTCGTTGAGCTG 59.833 55.000 7.06 0.00 0.00 4.24
1497 1546 5.563867 GCGGAAAATTTACACATGGAACTGA 60.564 40.000 0.00 0.00 0.00 3.41
1526 1575 6.183360 ACGAATGAAGATTTCAACAAGTGGTT 60.183 34.615 0.00 0.00 43.95 3.67
1613 1662 1.592669 CTCCATGCCGAACGCCTAG 60.593 63.158 0.00 0.00 36.24 3.02
1678 1729 7.331440 TGTTCTTTTCAAAACTACGTCTGTGTA 59.669 33.333 0.00 0.00 0.00 2.90
1737 1788 1.522806 GTGGTGGTGTGTGAGCGAA 60.523 57.895 0.00 0.00 0.00 4.70
1784 1836 9.693739 ATATGTGTGGATGTGAACCTATTTTAA 57.306 29.630 0.00 0.00 0.00 1.52
1800 1852 6.257849 CCTATTTTAAGCGTGACAGCAGATAA 59.742 38.462 2.68 0.00 40.15 1.75
2136 2202 2.791560 CGCGATGGAGAGTCATTACAAG 59.208 50.000 0.00 0.00 0.00 3.16
2164 2230 9.632638 AACATGGCATATTTCAGTAGAACTAAT 57.367 29.630 0.00 0.00 32.39 1.73
2192 2258 5.121768 GCAGATTCAGTATAAACAACACGGT 59.878 40.000 0.00 0.00 0.00 4.83
2263 2352 1.952990 CCAGTACACACAACATGGCAA 59.047 47.619 0.00 0.00 0.00 4.52
2264 2353 2.360483 CCAGTACACACAACATGGCAAA 59.640 45.455 0.00 0.00 0.00 3.68
2265 2354 3.005684 CCAGTACACACAACATGGCAAAT 59.994 43.478 0.00 0.00 0.00 2.32
2266 2355 4.501229 CCAGTACACACAACATGGCAAATT 60.501 41.667 0.00 0.00 0.00 1.82
2267 2356 5.049167 CAGTACACACAACATGGCAAATTT 58.951 37.500 0.00 0.00 0.00 1.82
2268 2357 6.212235 CAGTACACACAACATGGCAAATTTA 58.788 36.000 0.00 0.00 0.00 1.40
2269 2358 6.363088 CAGTACACACAACATGGCAAATTTAG 59.637 38.462 0.00 0.00 0.00 1.85
2270 2359 5.275067 ACACACAACATGGCAAATTTAGT 57.725 34.783 0.00 0.00 0.00 2.24
2271 2360 6.398234 ACACACAACATGGCAAATTTAGTA 57.602 33.333 0.00 0.00 0.00 1.82
2272 2361 6.991938 ACACACAACATGGCAAATTTAGTAT 58.008 32.000 0.00 0.00 0.00 2.12
2273 2362 8.116651 ACACACAACATGGCAAATTTAGTATA 57.883 30.769 0.00 0.00 0.00 1.47
2274 2363 8.580720 ACACACAACATGGCAAATTTAGTATAA 58.419 29.630 0.00 0.00 0.00 0.98
2275 2364 9.416794 CACACAACATGGCAAATTTAGTATAAA 57.583 29.630 0.00 0.00 0.00 1.40
2276 2365 9.988815 ACACAACATGGCAAATTTAGTATAAAA 57.011 25.926 0.00 0.00 0.00 1.52
2284 2373 9.979578 TGGCAAATTTAGTATAAAATAGCATGG 57.020 29.630 0.00 0.00 34.35 3.66
2285 2374 9.981114 GGCAAATTTAGTATAAAATAGCATGGT 57.019 29.630 1.62 1.62 34.35 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.346395 AGGATGGTGCGTGAACTACAA 59.654 47.619 0.00 0.00 0.00 2.41
45 46 0.973632 AGGATGGTGCGTGAACTACA 59.026 50.000 0.00 0.00 0.00 2.74
55 58 2.549754 CGTAATCATCCAAGGATGGTGC 59.450 50.000 24.70 16.47 44.36 5.01
60 63 4.502259 GCTGTCTCGTAATCATCCAAGGAT 60.502 45.833 0.00 0.00 34.81 3.24
61 64 3.181475 GCTGTCTCGTAATCATCCAAGGA 60.181 47.826 0.00 0.00 0.00 3.36
64 67 3.885724 TGCTGTCTCGTAATCATCCAA 57.114 42.857 0.00 0.00 0.00 3.53
72 75 2.346803 GCCTTGATTGCTGTCTCGTAA 58.653 47.619 0.00 0.00 0.00 3.18
79 82 1.345415 CCTTTTGGCCTTGATTGCTGT 59.655 47.619 3.32 0.00 0.00 4.40
81 84 2.014010 TCCTTTTGGCCTTGATTGCT 57.986 45.000 3.32 0.00 40.12 3.91
83 86 3.765511 TCTGATCCTTTTGGCCTTGATTG 59.234 43.478 3.32 0.00 40.12 2.67
85 88 3.744940 TCTGATCCTTTTGGCCTTGAT 57.255 42.857 3.32 0.00 40.12 2.57
101 105 4.645136 ACAATATCGTAGAGCTGGTTCTGA 59.355 41.667 0.00 0.00 43.63 3.27
113 117 4.508971 CAAAGCGCTTGACAATATCGTAG 58.491 43.478 25.80 0.00 37.17 3.51
131 135 1.533625 TGGACCTCGCATTTCCAAAG 58.466 50.000 0.00 0.00 36.45 2.77
210 214 6.072342 GGAGGAACGGTAAAAAGAGCAAATAA 60.072 38.462 0.00 0.00 0.00 1.40
211 215 5.413523 GGAGGAACGGTAAAAAGAGCAAATA 59.586 40.000 0.00 0.00 0.00 1.40
228 233 7.923414 TCTAGAAATAGCAAAAAGGAGGAAC 57.077 36.000 0.00 0.00 0.00 3.62
232 237 9.282569 AGCATATCTAGAAATAGCAAAAAGGAG 57.717 33.333 0.00 0.00 0.00 3.69
241 246 7.008447 CGTAAACGGAGCATATCTAGAAATAGC 59.992 40.741 0.00 0.00 35.37 2.97
242 247 8.021973 ACGTAAACGGAGCATATCTAGAAATAG 58.978 37.037 7.50 0.00 44.95 1.73
243 248 7.879070 ACGTAAACGGAGCATATCTAGAAATA 58.121 34.615 7.50 0.00 44.95 1.40
244 249 6.746120 ACGTAAACGGAGCATATCTAGAAAT 58.254 36.000 7.50 0.00 44.95 2.17
314 337 8.021396 CCAAACATGAGCTGTATGATAATGATG 58.979 37.037 13.05 0.00 36.98 3.07
321 344 4.847198 TGTCCAAACATGAGCTGTATGAT 58.153 39.130 13.05 0.47 36.98 2.45
346 369 4.107622 GCATCACATTGTATGACCTTTGC 58.892 43.478 9.18 0.00 0.00 3.68
348 371 4.094887 GTCGCATCACATTGTATGACCTTT 59.905 41.667 9.18 0.00 0.00 3.11
375 398 0.608130 CAAGATCACCCAGGTCGACA 59.392 55.000 18.91 0.00 0.00 4.35
402 425 0.759959 TTTTACCGAGTGGCCTCACA 59.240 50.000 3.32 0.00 45.91 3.58
465 488 7.733773 TTTGTCGGGAGATATATCCATATGT 57.266 36.000 17.94 0.00 41.52 2.29
477 500 3.129287 GCATGATTGTTTTGTCGGGAGAT 59.871 43.478 0.00 0.00 43.27 2.75
590 613 9.739276 AAGGAATACTCACACATTTCTTCATTA 57.261 29.630 0.00 0.00 25.67 1.90
793 825 5.606348 AGTTAAAACAAGTTGCCATCCAA 57.394 34.783 1.81 0.00 0.00 3.53
942 981 3.055963 AGAAGCAGAGTCCACATGAAGAG 60.056 47.826 0.00 0.00 0.00 2.85
983 1023 1.542375 ATGGGGAACAGGACCTGCT 60.542 57.895 21.95 9.66 34.37 4.24
1124 1164 3.621268 GCATTCAACATGCGTAGTAAGGA 59.379 43.478 0.00 0.00 35.17 3.36
1145 1185 4.516698 TCTCTTTGAGGTTGTTGATGAAGC 59.483 41.667 0.00 0.00 0.00 3.86
1185 1225 3.390967 TGATCTGGACCTTTGAGTGTTCA 59.609 43.478 0.00 0.00 0.00 3.18
1232 1272 4.042187 ACTTGTTCCCTTGCTTCATAGTCT 59.958 41.667 0.00 0.00 0.00 3.24
1238 1278 5.010617 GGAAATTACTTGTTCCCTTGCTTCA 59.989 40.000 0.00 0.00 37.87 3.02
1335 1381 4.142138 ACTCGCGAAAAGGACAGAGATAAT 60.142 41.667 11.33 0.00 0.00 1.28
1352 1399 1.714794 AAGAATCAGGTGAACTCGCG 58.285 50.000 0.00 0.00 0.00 5.87
1442 1491 3.225104 ACCATTGCAGTTGTGAGAACAT 58.775 40.909 0.00 0.00 0.00 2.71
1447 1496 1.229428 ACGACCATTGCAGTTGTGAG 58.771 50.000 0.00 0.00 30.46 3.51
1453 1502 0.250467 AGCTCAACGACCATTGCAGT 60.250 50.000 0.00 0.00 0.00 4.40
1473 1522 4.621034 CAGTTCCATGTGTAAATTTTCCGC 59.379 41.667 0.00 0.00 0.00 5.54
1497 1546 7.592533 CACTTGTTGAAATCTTCATTCGTCAAT 59.407 33.333 0.00 0.00 39.84 2.57
1526 1575 2.560981 TCTACAAACTCACATGCTCCGA 59.439 45.455 0.00 0.00 0.00 4.55
1601 1650 0.529992 ATGTAAGCTAGGCGTTCGGC 60.530 55.000 10.65 10.65 42.51 5.54
1678 1729 3.371595 GGGGGTTGCAGTCATAACATAGT 60.372 47.826 0.00 0.00 0.00 2.12
1784 1836 2.751166 AACTTATCTGCTGTCACGCT 57.249 45.000 0.00 0.00 0.00 5.07
1962 2024 2.498481 TGCTAGCCGGTACATTTAGTGT 59.502 45.455 13.29 0.00 44.95 3.55
1969 2031 1.618837 CTACCATGCTAGCCGGTACAT 59.381 52.381 22.83 3.43 34.12 2.29
2136 2202 8.438676 AGTTCTACTGAAATATGCCATGTTAC 57.561 34.615 0.00 0.00 33.52 2.50
2164 2230 7.011016 CGTGTTGTTTATACTGAATCTGCCATA 59.989 37.037 0.00 0.00 0.00 2.74
2300 2389 6.173427 TGTATACTGAATCTGCCATGCTAA 57.827 37.500 4.17 0.00 0.00 3.09
2477 2642 3.581024 CATGGTCCTTGGTGACATTTG 57.419 47.619 0.00 0.00 42.32 2.32


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

AutoCloner maintained by Alex Coulton.