Multiple sequence alignment - TraesCS6D01G150100

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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 TraesCS6D01G150100 chr6D 100.000 3194 0 0 1 3194 123801069 123797876 0.000000e+00 5899
1 TraesCS6D01G150100 chr6A 94.075 2650 84 16 5 2621 157422721 157425330 0.000000e+00 3956
2 TraesCS6D01G150100 chr6A 96.181 419 16 0 2776 3194 157426284 157426702 0.000000e+00 686
3 TraesCS6D01G150100 chr6A 94.783 115 4 1 2616 2730 157426044 157426156 9.100000e-41 178
4 TraesCS6D01G150100 chr6B 94.870 1696 47 11 887 2577 219015745 219014085 0.000000e+00 2614
5 TraesCS6D01G150100 chr6B 94.177 893 28 8 5 875 219016794 219015904 0.000000e+00 1339
6 TraesCS6D01G150100 chr6B 90.894 593 31 17 2622 3194 219014079 219013490 0.000000e+00 774


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 TraesCS6D01G150100 chr6D 123797876 123801069 3193 True 5899.000000 5899 100.000000 1 3194 1 chr6D.!!$R1 3193
1 TraesCS6D01G150100 chr6A 157422721 157426702 3981 False 1606.666667 3956 95.013000 5 3194 3 chr6A.!!$F1 3189
2 TraesCS6D01G150100 chr6B 219013490 219016794 3304 True 1575.666667 2614 93.313667 5 3194 3 chr6B.!!$R1 3189

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
498 522 0.322277 ACATGGAGCTGCAACTGAGG 60.322 55.0 13.45 0.5 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 2520 1.149288 TGTTCTACCCTGTCCCAGACT 59.851 52.381 0.0 0.0 32.44 3.24 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
23 24 3.381949 GTCACGAGTTCTTGTTGCTACT 58.618 45.455 0.00 0.00 0.00 2.57
25 26 2.476619 CACGAGTTCTTGTTGCTACTGG 59.523 50.000 0.00 0.00 0.00 4.00
26 27 1.461127 CGAGTTCTTGTTGCTACTGGC 59.539 52.381 0.00 0.00 42.22 4.85
48 49 0.833287 ATGATGCTTGGCTCGTAGGT 59.167 50.000 0.00 0.00 0.00 3.08
78 79 1.561717 CGTCGCCGGAATTGAACACA 61.562 55.000 5.05 0.00 0.00 3.72
114 115 1.937223 TGCACGAACACAACAGTTAGG 59.063 47.619 0.00 0.00 0.00 2.69
117 118 2.032894 CACGAACACAACAGTTAGGCAG 60.033 50.000 0.00 0.00 0.00 4.85
128 129 4.330250 ACAGTTAGGCAGAGAGTACGTTA 58.670 43.478 0.00 0.00 0.00 3.18
275 299 7.159201 AGATGGAAGTAATCTTGGATGGAAT 57.841 36.000 0.00 0.00 33.64 3.01
498 522 0.322277 ACATGGAGCTGCAACTGAGG 60.322 55.000 13.45 0.50 0.00 3.86
557 589 2.805671 TCGCATGTTCGTTCTGTTTGAT 59.194 40.909 0.00 0.00 0.00 2.57
824 856 5.961843 CACTAGCACAATTATTTTCAGCTCG 59.038 40.000 0.00 0.00 32.49 5.03
848 880 6.205464 CGGATGCTATTGAACTAATGGTCAAT 59.795 38.462 12.90 12.90 36.80 2.57
901 1080 7.281774 ACATCATACTTCTTGTTCCAGCATAAG 59.718 37.037 0.00 0.00 0.00 1.73
909 1088 6.003326 TCTTGTTCCAGCATAAGTCAAATCA 58.997 36.000 0.00 0.00 0.00 2.57
1065 1244 1.210931 CCAGCACACCATTCTTGCG 59.789 57.895 0.00 0.00 41.33 4.85
1336 1515 2.560504 TGGTGTGCGCCTATGATTTAG 58.439 47.619 4.18 0.00 0.00 1.85
1516 1695 1.155889 TGAAGTATGCACTGTTGGCG 58.844 50.000 0.00 0.00 34.36 5.69
1674 1853 4.352009 ACCTGACAGATGAGATGTTCTCT 58.648 43.478 3.32 0.00 43.73 3.10
1840 2019 1.163420 GGACCACATGTGCAACGTCA 61.163 55.000 24.85 0.00 42.39 4.35
2037 2216 0.326264 ATTCTGTGACTGGCCTGGTC 59.674 55.000 14.82 16.81 0.00 4.02
2051 2230 3.980583 TGGTCGACTCCAGAACAAC 57.019 52.632 16.46 0.00 31.60 3.32
2087 2266 6.659668 CCTCATGATGCTAGATCATTTCCAAT 59.340 38.462 12.32 0.00 36.69 3.16
2199 2378 2.050144 TGGAGGTTGGCATAGATCTCC 58.950 52.381 9.60 9.60 40.68 3.71
2206 2385 1.230324 GGCATAGATCTCCGCAAACC 58.770 55.000 15.88 0.14 0.00 3.27
2212 2391 0.181350 GATCTCCGCAAACCCCTGAT 59.819 55.000 0.00 0.00 0.00 2.90
2214 2393 1.507140 TCTCCGCAAACCCCTGATAT 58.493 50.000 0.00 0.00 0.00 1.63
2215 2394 1.416401 TCTCCGCAAACCCCTGATATC 59.584 52.381 0.00 0.00 0.00 1.63
2216 2395 0.105964 TCCGCAAACCCCTGATATCG 59.894 55.000 0.00 0.00 0.00 2.92
2217 2396 0.179056 CCGCAAACCCCTGATATCGT 60.179 55.000 0.00 0.00 0.00 3.73
2248 2427 9.988815 ATCCATGAATAGTTCTCTGTTATGTAC 57.011 33.333 0.00 0.00 0.00 2.90
2249 2428 8.977412 TCCATGAATAGTTCTCTGTTATGTACA 58.023 33.333 0.00 0.00 34.95 2.90
2261 2440 3.621268 TGTTATGTACAGCGGATTCAAGC 59.379 43.478 0.33 0.00 31.68 4.01
2262 2441 1.668419 ATGTACAGCGGATTCAAGCC 58.332 50.000 0.33 0.00 0.00 4.35
2263 2442 0.323302 TGTACAGCGGATTCAAGCCA 59.677 50.000 0.00 0.00 0.00 4.75
2264 2443 1.271108 TGTACAGCGGATTCAAGCCAA 60.271 47.619 0.00 0.00 0.00 4.52
2265 2444 2.017049 GTACAGCGGATTCAAGCCAAT 58.983 47.619 0.00 0.00 0.00 3.16
2266 2445 2.418368 ACAGCGGATTCAAGCCAATA 57.582 45.000 0.00 0.00 0.00 1.90
2267 2446 2.017049 ACAGCGGATTCAAGCCAATAC 58.983 47.619 0.00 0.00 0.00 1.89
2268 2447 1.334869 CAGCGGATTCAAGCCAATACC 59.665 52.381 0.00 0.00 0.00 2.73
2269 2448 1.212935 AGCGGATTCAAGCCAATACCT 59.787 47.619 0.00 0.00 0.00 3.08
2270 2449 2.438021 AGCGGATTCAAGCCAATACCTA 59.562 45.455 0.00 0.00 0.00 3.08
2271 2450 2.808543 GCGGATTCAAGCCAATACCTAG 59.191 50.000 0.00 0.00 0.00 3.02
2272 2451 3.744530 GCGGATTCAAGCCAATACCTAGT 60.745 47.826 0.00 0.00 0.00 2.57
2273 2452 4.502604 GCGGATTCAAGCCAATACCTAGTA 60.503 45.833 0.00 0.00 0.00 1.82
2302 2481 7.708998 TCCAATAAAGTTTACTGGTGTTTGTC 58.291 34.615 19.70 0.00 0.00 3.18
2364 2545 3.798515 TGGGACAGGGTAGAACATAAGT 58.201 45.455 0.00 0.00 0.00 2.24
2371 2552 7.548427 GGACAGGGTAGAACATAAGTAAGAAAC 59.452 40.741 0.00 0.00 0.00 2.78
2391 2572 7.167831 GAAACTAAGAAAGTGTCTCTGTGTC 57.832 40.000 0.00 0.00 39.14 3.67
2404 2585 2.983136 CTCTGTGTCAGTAGCTTGTTCG 59.017 50.000 0.00 0.00 32.61 3.95
2407 2588 2.863740 TGTGTCAGTAGCTTGTTCGTTG 59.136 45.455 0.00 0.00 0.00 4.10
2428 2610 6.608610 GTTGTTATCGTATGGGGATTTATGC 58.391 40.000 0.00 0.00 0.00 3.14
2541 2727 5.747197 GCATTTCTGAAAGTTATGATGCCAG 59.253 40.000 8.95 0.00 34.21 4.85
2556 2742 4.402155 TGATGCCAGGACCAATAATTCAAC 59.598 41.667 0.00 0.00 0.00 3.18
2562 2748 4.463891 CAGGACCAATAATTCAACCTGCTT 59.536 41.667 0.00 0.00 37.27 3.91
2589 2775 3.381272 CGGTGGTTGCATTTATGAGGATT 59.619 43.478 0.00 0.00 0.00 3.01
2613 2799 2.126467 GCGCTGTGCTGAAAAATGAAA 58.874 42.857 5.84 0.00 41.73 2.69
2666 3571 2.460534 TCGGTTTGCTGTACGAACTGC 61.461 52.381 0.00 0.99 45.42 4.40
2695 3606 8.049117 TCCTGCACTGTATTTCTGAATATTCTT 58.951 33.333 16.24 0.09 30.84 2.52
2696 3607 9.330063 CCTGCACTGTATTTCTGAATATTCTTA 57.670 33.333 16.24 1.98 30.84 2.10
2740 3744 1.274167 TCGCCTCCAGTTACATTCGTT 59.726 47.619 0.00 0.00 0.00 3.85
2753 3757 2.367567 ACATTCGTTCCACACCAGTACT 59.632 45.455 0.00 0.00 0.00 2.73
2754 3758 3.575256 ACATTCGTTCCACACCAGTACTA 59.425 43.478 0.00 0.00 0.00 1.82
2755 3759 3.648339 TTCGTTCCACACCAGTACTAC 57.352 47.619 0.00 0.00 0.00 2.73
2757 3761 3.159472 TCGTTCCACACCAGTACTACAT 58.841 45.455 0.00 0.00 0.00 2.29
2759 3763 4.156556 TCGTTCCACACCAGTACTACATAC 59.843 45.833 0.00 0.00 0.00 2.39
2760 3764 4.082625 CGTTCCACACCAGTACTACATACA 60.083 45.833 0.00 0.00 36.09 2.29
2773 3796 3.938963 ACTACATACACCTGCGGAATTTG 59.061 43.478 0.00 0.00 0.00 2.32
2774 3797 3.066291 ACATACACCTGCGGAATTTGA 57.934 42.857 0.00 0.00 0.00 2.69
2778 3801 2.795329 ACACCTGCGGAATTTGAGAAT 58.205 42.857 0.00 0.00 0.00 2.40
2800 3823 3.823281 TCCCGAAAGTATTTGGCGATA 57.177 42.857 0.00 0.00 39.27 2.92
2802 3825 2.546789 CCCGAAAGTATTTGGCGATACC 59.453 50.000 7.08 0.00 39.27 2.73
3139 4162 3.022406 GGGATCGTGTAGTAGTTGAGGT 58.978 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.586802 GCAACAAGAACTCGTGACCC 59.413 55.000 0.00 0.00 0.00 4.46
1 2 1.583054 AGCAACAAGAACTCGTGACC 58.417 50.000 0.00 0.00 0.00 4.02
2 3 3.182572 CAGTAGCAACAAGAACTCGTGAC 59.817 47.826 0.00 0.00 0.00 3.67
3 4 3.381045 CAGTAGCAACAAGAACTCGTGA 58.619 45.455 0.00 0.00 0.00 4.35
26 27 2.032550 CCTACGAGCCAAGCATCATTTG 59.967 50.000 0.00 0.00 0.00 2.32
28 29 1.210478 ACCTACGAGCCAAGCATCATT 59.790 47.619 0.00 0.00 0.00 2.57
29 30 0.833287 ACCTACGAGCCAAGCATCAT 59.167 50.000 0.00 0.00 0.00 2.45
30 31 0.108186 CACCTACGAGCCAAGCATCA 60.108 55.000 0.00 0.00 0.00 3.07
31 32 0.108138 ACACCTACGAGCCAAGCATC 60.108 55.000 0.00 0.00 0.00 3.91
32 33 1.137086 CTACACCTACGAGCCAAGCAT 59.863 52.381 0.00 0.00 0.00 3.79
34 35 0.531200 ACTACACCTACGAGCCAAGC 59.469 55.000 0.00 0.00 0.00 4.01
35 36 1.816835 TGACTACACCTACGAGCCAAG 59.183 52.381 0.00 0.00 0.00 3.61
78 79 2.429478 GTGCAAACCCCACTAACGTAT 58.571 47.619 0.00 0.00 0.00 3.06
114 115 5.399858 TGTGATCTTTAACGTACTCTCTGC 58.600 41.667 0.00 0.00 0.00 4.26
117 118 5.399858 TGCTGTGATCTTTAACGTACTCTC 58.600 41.667 0.00 0.00 0.00 3.20
275 299 1.581934 CAGAACAGAACGGCACAAGA 58.418 50.000 0.00 0.00 0.00 3.02
557 589 7.947782 ATATTGTCTTCCTAACATAAGGGGA 57.052 36.000 0.00 0.00 37.24 4.81
694 726 7.981225 AGCACTTGTCAAATGTAAAACTGAAAT 59.019 29.630 0.00 0.00 0.00 2.17
824 856 6.942532 TTGACCATTAGTTCAATAGCATCC 57.057 37.500 0.00 0.00 0.00 3.51
848 880 9.877178 ATAACAAAACAAACAGTATTTGTCCAA 57.123 25.926 0.00 0.00 41.30 3.53
925 1104 3.769536 AGCGACAAGGAAAACAACAAAG 58.230 40.909 0.00 0.00 0.00 2.77
976 1155 3.609807 GCTAGCTTGCAAATTACAACTGC 59.390 43.478 15.53 0.00 36.60 4.40
1065 1244 1.900486 ACAACCCTAGCAGGTAGTGAC 59.100 52.381 5.91 0.00 40.05 3.67
1336 1515 1.166531 AACACCTCAACAGCGCCTTC 61.167 55.000 2.29 0.00 0.00 3.46
1367 1546 4.517285 TGGCAGTCTCAAATGTATCCTTC 58.483 43.478 0.00 0.00 0.00 3.46
1516 1695 1.748122 CTGCCCTCCATGACTGTGC 60.748 63.158 0.00 0.00 0.00 4.57
1840 2019 1.686587 GCCCAAAGGTAGCACAAAAGT 59.313 47.619 0.00 0.00 34.57 2.66
2037 2216 1.335597 TGTAGCGTTGTTCTGGAGTCG 60.336 52.381 0.00 0.00 0.00 4.18
2051 2230 2.286294 GCATCATGAGGACTTTGTAGCG 59.714 50.000 12.39 0.00 0.00 4.26
2087 2266 2.731571 GCAGATGGTCCACGCCCTA 61.732 63.158 0.00 0.00 0.00 3.53
2199 2378 1.597663 GAACGATATCAGGGGTTTGCG 59.402 52.381 3.12 0.00 0.00 4.85
2206 2385 4.157840 TCATGGATACGAACGATATCAGGG 59.842 45.833 3.12 0.00 42.51 4.45
2212 2391 8.107399 AGAACTATTCATGGATACGAACGATA 57.893 34.615 0.14 0.00 42.51 2.92
2214 2393 6.262496 AGAGAACTATTCATGGATACGAACGA 59.738 38.462 0.14 0.00 42.51 3.85
2215 2394 6.360947 CAGAGAACTATTCATGGATACGAACG 59.639 42.308 0.00 0.00 42.51 3.95
2216 2395 7.203910 ACAGAGAACTATTCATGGATACGAAC 58.796 38.462 0.00 0.00 42.51 3.95
2217 2396 7.348080 ACAGAGAACTATTCATGGATACGAA 57.652 36.000 0.00 0.00 42.51 3.85
2248 2427 1.334869 GGTATTGGCTTGAATCCGCTG 59.665 52.381 0.00 0.00 0.00 5.18
2249 2428 1.212935 AGGTATTGGCTTGAATCCGCT 59.787 47.619 0.00 0.00 0.00 5.52
2250 2429 1.680338 AGGTATTGGCTTGAATCCGC 58.320 50.000 0.00 0.00 0.00 5.54
2251 2430 4.073293 ACTAGGTATTGGCTTGAATCCG 57.927 45.455 0.00 0.00 0.00 4.18
2252 2431 5.925509 TGTACTAGGTATTGGCTTGAATCC 58.074 41.667 0.00 0.00 0.00 3.01
2253 2432 7.173390 GGATTGTACTAGGTATTGGCTTGAATC 59.827 40.741 0.00 0.00 0.00 2.52
2254 2433 6.998673 GGATTGTACTAGGTATTGGCTTGAAT 59.001 38.462 0.00 0.00 0.00 2.57
2255 2434 6.069905 TGGATTGTACTAGGTATTGGCTTGAA 60.070 38.462 0.00 0.00 0.00 2.69
2256 2435 5.427157 TGGATTGTACTAGGTATTGGCTTGA 59.573 40.000 0.00 0.00 0.00 3.02
2257 2436 5.680619 TGGATTGTACTAGGTATTGGCTTG 58.319 41.667 0.00 0.00 0.00 4.01
2258 2437 5.968676 TGGATTGTACTAGGTATTGGCTT 57.031 39.130 0.00 0.00 0.00 4.35
2259 2438 5.968676 TTGGATTGTACTAGGTATTGGCT 57.031 39.130 0.00 0.00 0.00 4.75
2260 2439 8.685838 TTTATTGGATTGTACTAGGTATTGGC 57.314 34.615 0.00 0.00 0.00 4.52
2261 2440 9.847224 ACTTTATTGGATTGTACTAGGTATTGG 57.153 33.333 0.00 0.00 0.00 3.16
2270 2449 9.010029 CACCAGTAAACTTTATTGGATTGTACT 57.990 33.333 23.26 3.24 33.19 2.73
2271 2450 8.789762 ACACCAGTAAACTTTATTGGATTGTAC 58.210 33.333 23.26 0.00 33.19 2.90
2272 2451 8.927675 ACACCAGTAAACTTTATTGGATTGTA 57.072 30.769 23.26 0.00 33.19 2.41
2273 2452 7.833285 ACACCAGTAAACTTTATTGGATTGT 57.167 32.000 23.26 16.72 33.19 2.71
2302 2481 9.515020 GTCTATTTCTTCTTCATCTCTACACAG 57.485 37.037 0.00 0.00 0.00 3.66
2339 2520 1.149288 TGTTCTACCCTGTCCCAGACT 59.851 52.381 0.00 0.00 32.44 3.24
2364 2545 8.475639 ACACAGAGACACTTTCTTAGTTTCTTA 58.524 33.333 0.00 0.00 42.53 2.10
2371 2552 5.837437 ACTGACACAGAGACACTTTCTTAG 58.163 41.667 5.76 0.00 33.22 2.18
2389 2570 5.442909 CGATAACAACGAACAAGCTACTGAC 60.443 44.000 0.00 0.00 0.00 3.51
2390 2571 4.619760 CGATAACAACGAACAAGCTACTGA 59.380 41.667 0.00 0.00 0.00 3.41
2391 2572 4.384846 ACGATAACAACGAACAAGCTACTG 59.615 41.667 0.00 0.00 34.70 2.74
2404 2585 6.608610 GCATAAATCCCCATACGATAACAAC 58.391 40.000 0.00 0.00 0.00 3.32
2407 2588 4.201783 GCGCATAAATCCCCATACGATAAC 60.202 45.833 0.30 0.00 0.00 1.89
2428 2610 8.514136 TTTCATTTTTATTTTCCAGTACAGCG 57.486 30.769 0.00 0.00 0.00 5.18
2541 2727 5.185828 AGAAAGCAGGTTGAATTATTGGTCC 59.814 40.000 0.00 0.00 0.00 4.46
2556 2742 1.073199 AACCACCGGAGAAAGCAGG 59.927 57.895 9.46 0.00 0.00 4.85
2562 2748 2.570415 TAAATGCAACCACCGGAGAA 57.430 45.000 9.46 0.00 0.00 2.87
2589 2775 3.057666 TCATTTTTCAGCACAGCGCATAA 60.058 39.130 11.47 0.00 46.13 1.90
2613 2799 9.251440 TGTACAGTATATAACAGGTTCAGAGTT 57.749 33.333 0.00 0.00 0.00 3.01
2666 3571 3.930336 TCAGAAATACAGTGCAGGAGTG 58.070 45.455 0.00 0.00 0.00 3.51
2695 3606 9.826574 GACAGTTTGTATTGGTCTTGGTATATA 57.173 33.333 0.00 0.00 0.00 0.86
2696 3607 7.494625 CGACAGTTTGTATTGGTCTTGGTATAT 59.505 37.037 0.00 0.00 0.00 0.86
2740 3744 3.765511 GGTGTATGTAGTACTGGTGTGGA 59.234 47.826 5.39 0.00 34.27 4.02
2773 3796 5.340803 GCCAAATACTTTCGGGAAATTCTC 58.659 41.667 0.00 0.00 0.00 2.87
2774 3797 4.142469 CGCCAAATACTTTCGGGAAATTCT 60.142 41.667 0.00 0.00 0.00 2.40
2778 3801 2.780714 TCGCCAAATACTTTCGGGAAA 58.219 42.857 0.00 0.00 0.00 3.13
2800 3823 1.750778 CTTGCCAACTGTTTGAGTGGT 59.249 47.619 0.00 0.00 34.02 4.16
2802 3825 1.406539 AGCTTGCCAACTGTTTGAGTG 59.593 47.619 0.00 0.00 34.02 3.51


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

AutoCloner maintained by Alex Coulton.