Multiple sequence alignment - TraesCS7B01G311100

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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 TraesCS7B01G311100 chr7B 100.000 2471 0 0 965 3435 556461609 556464079 0 4564
1 TraesCS7B01G311100 chr7B 100.000 742 0 0 1 742 556460645 556461386 0 1371
2 TraesCS7B01G311100 chr7A 95.885 2479 89 9 965 3435 602809229 602811702 0 4000
3 TraesCS7B01G311100 chr7A 90.546 751 36 8 1 742 602808465 602809189 0 961
4 TraesCS7B01G311100 chr7D 93.961 2484 118 19 965 3432 522513101 522515568 0 3727
5 TraesCS7B01G311100 chr7D 91.501 753 41 6 1 742 522512321 522513061 0 1014


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 TraesCS7B01G311100 chr7B 556460645 556464079 3434 False 2967.5 4564 100.0000 1 3435 2 chr7B.!!$F1 3434
1 TraesCS7B01G311100 chr7A 602808465 602811702 3237 False 2480.5 4000 93.2155 1 3435 2 chr7A.!!$F1 3434
2 TraesCS7B01G311100 chr7D 522512321 522515568 3247 False 2370.5 3727 92.7310 1 3432 2 chr7D.!!$F1 3431

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
22 25 0.251698 TGGCACTGCAAATGGGATCA 60.252 50.0 2.82 0.0 0.00 2.92 F
1023 1050 0.320771 GGAGTGCACGAGTTGGTCAT 60.321 55.0 12.01 0.0 0.00 3.06 F
1987 2019 0.955428 GGACTTGCCTCGTCATTGCA 60.955 55.0 0.00 0.0 33.11 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 1675 0.739462 TAACCGGACATTGCGAGCTG 60.739 55.0 9.46 0.0 30.86 4.24 R
2287 2319 0.812811 CCATCACCATCTCCTGCACG 60.813 60.0 0.00 0.0 0.00 5.34 R
3008 3054 1.119684 TGCACGCTATCAGGTATGGT 58.880 50.0 0.00 0.0 0.00 3.55 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
22 25 0.251698 TGGCACTGCAAATGGGATCA 60.252 50.000 2.82 0.00 0.00 2.92
199 202 7.558161 TGATTTGTAATGTGATGAGGTGATC 57.442 36.000 0.00 0.00 0.00 2.92
214 217 4.290093 AGGTGATCCACATCTACAAGCTA 58.710 43.478 0.00 0.00 38.30 3.32
221 224 5.907207 TCCACATCTACAAGCTATCTGTTC 58.093 41.667 0.00 0.00 0.00 3.18
224 227 4.645136 ACATCTACAAGCTATCTGTTCGGA 59.355 41.667 0.00 0.00 0.00 4.55
253 257 4.627035 GTGTTCGATGATGTGATCAGACAA 59.373 41.667 0.00 0.00 43.53 3.18
413 438 4.082571 GCAAGCTGTTACCAATTGATCTGT 60.083 41.667 7.12 0.00 0.00 3.41
415 440 6.449698 CAAGCTGTTACCAATTGATCTGTTT 58.550 36.000 7.12 0.82 0.00 2.83
416 441 7.592938 CAAGCTGTTACCAATTGATCTGTTTA 58.407 34.615 7.12 0.00 0.00 2.01
417 442 7.759489 AGCTGTTACCAATTGATCTGTTTAA 57.241 32.000 7.12 0.00 0.00 1.52
418 443 8.177119 AGCTGTTACCAATTGATCTGTTTAAA 57.823 30.769 7.12 0.00 0.00 1.52
419 444 8.806146 AGCTGTTACCAATTGATCTGTTTAAAT 58.194 29.630 7.12 0.00 0.00 1.40
420 445 9.423061 GCTGTTACCAATTGATCTGTTTAAATT 57.577 29.630 7.12 0.00 0.00 1.82
426 451 9.865321 ACCAATTGATCTGTTTAAATTGATCTG 57.135 29.630 22.40 16.35 40.73 2.90
427 452 9.309516 CCAATTGATCTGTTTAAATTGATCTGG 57.690 33.333 22.40 19.28 40.73 3.86
428 453 9.309516 CAATTGATCTGTTTAAATTGATCTGGG 57.690 33.333 22.40 12.61 40.73 4.45
497 522 3.993736 ACCAGTTTGTTTCTTTGCACAAC 59.006 39.130 0.00 0.00 32.57 3.32
614 639 4.638421 TCAAAGAAAATGACGTGTCTTGGT 59.362 37.500 0.00 0.00 30.85 3.67
675 700 2.012673 CTTGAGCACCTGAAGCATACC 58.987 52.381 0.00 0.00 0.00 2.73
676 701 1.279496 TGAGCACCTGAAGCATACCT 58.721 50.000 0.00 0.00 0.00 3.08
677 702 2.466846 TGAGCACCTGAAGCATACCTA 58.533 47.619 0.00 0.00 0.00 3.08
678 703 2.837591 TGAGCACCTGAAGCATACCTAA 59.162 45.455 0.00 0.00 0.00 2.69
679 704 3.118629 TGAGCACCTGAAGCATACCTAAG 60.119 47.826 0.00 0.00 0.00 2.18
680 705 2.840651 AGCACCTGAAGCATACCTAAGT 59.159 45.455 0.00 0.00 0.00 2.24
681 706 4.030913 AGCACCTGAAGCATACCTAAGTA 58.969 43.478 0.00 0.00 0.00 2.24
682 707 4.100189 AGCACCTGAAGCATACCTAAGTAG 59.900 45.833 0.00 0.00 0.00 2.57
683 708 4.372656 CACCTGAAGCATACCTAAGTAGC 58.627 47.826 0.00 0.00 0.00 3.58
684 709 3.388350 ACCTGAAGCATACCTAAGTAGCC 59.612 47.826 0.00 0.00 0.00 3.93
685 710 3.553096 CCTGAAGCATACCTAAGTAGCCG 60.553 52.174 0.00 0.00 0.00 5.52
1023 1050 0.320771 GGAGTGCACGAGTTGGTCAT 60.321 55.000 12.01 0.00 0.00 3.06
1035 1062 7.456253 CACGAGTTGGTCATAAAAGAATACAG 58.544 38.462 0.00 0.00 0.00 2.74
1074 1101 4.423913 CCTCAGGATCAGGAGATATCCAA 58.576 47.826 9.50 0.00 43.55 3.53
1076 1103 4.423913 TCAGGATCAGGAGATATCCAAGG 58.576 47.826 9.50 0.00 43.55 3.61
1078 1105 3.407540 AGGATCAGGAGATATCCAAGGGA 59.592 47.826 9.50 0.96 43.55 4.20
1080 1107 2.614259 TCAGGAGATATCCAAGGGAGC 58.386 52.381 9.50 0.00 34.05 4.70
1157 1184 7.425606 ACAAGACAAAGCACGAGATTTTTATT 58.574 30.769 0.00 0.00 29.40 1.40
1166 1197 4.635765 CACGAGATTTTTATTGGCTCAGGA 59.364 41.667 0.00 0.00 0.00 3.86
1199 1230 4.953940 AAGCCTGAGGAGAGATACATTC 57.046 45.455 0.65 0.00 0.00 2.67
1333 1365 3.792047 CGCGTGCATCCACAGGTG 61.792 66.667 0.00 0.00 42.17 4.00
1335 1367 1.965930 GCGTGCATCCACAGGTGAA 60.966 57.895 0.00 0.00 42.17 3.18
1336 1368 1.868997 CGTGCATCCACAGGTGAAC 59.131 57.895 0.00 0.00 42.17 3.18
1389 1421 7.264947 TCTGTTTTCTCTTCCCAAAACAATTC 58.735 34.615 10.30 0.00 46.60 2.17
1413 1445 2.030371 TGGCATGCAGTTCTGTTGAAA 58.970 42.857 21.36 0.00 33.52 2.69
1426 1458 6.912591 AGTTCTGTTGAAATTTAGAGTTTGCG 59.087 34.615 0.00 0.00 33.52 4.85
1449 1481 2.031682 GCTGAAATTCTGCGTGTTCTGT 60.032 45.455 9.01 0.00 31.90 3.41
1456 1488 1.667830 TGCGTGTTCTGTAGCAGGC 60.668 57.895 0.00 0.00 43.97 4.85
1509 1541 4.749099 CCTGAACATAGAGCAAGAGTATGC 59.251 45.833 0.00 0.00 46.78 3.14
1614 1646 3.349927 TCATCCTTCCAATGCTTCACAG 58.650 45.455 0.00 0.00 0.00 3.66
1634 1666 1.726853 CACGAGGCGGAGAAAATCTT 58.273 50.000 0.00 0.00 0.00 2.40
1643 1675 5.124617 AGGCGGAGAAAATCTTCTGAAATTC 59.875 40.000 0.00 0.00 42.19 2.17
1852 1884 1.679139 CTTTCAGCACCACCACAAGA 58.321 50.000 0.00 0.00 0.00 3.02
1987 2019 0.955428 GGACTTGCCTCGTCATTGCA 60.955 55.000 0.00 0.00 33.11 4.08
2078 2110 2.190578 GGCTCTGCCCTATTGCGT 59.809 61.111 0.00 0.00 44.06 5.24
2203 2235 2.022129 CTTCGACACGGTGAGCCAC 61.022 63.158 16.29 0.00 34.09 5.01
2221 2253 3.485431 CTTGCAGTGCGCCTCTCG 61.485 66.667 11.20 0.34 41.33 4.04
2287 2319 3.906846 AGATGGTGGATGAGAAGTATCCC 59.093 47.826 0.00 0.00 42.79 3.85
2303 2335 2.659063 CCCGTGCAGGAGATGGTGA 61.659 63.158 8.24 0.00 45.00 4.02
2571 2607 1.871080 AGGGCGATTTAGCTTCATCG 58.129 50.000 18.35 18.35 44.24 3.84
2659 2695 7.383102 AGAAATATCAACTGCAATTTCTCGT 57.617 32.000 13.54 0.00 42.24 4.18
2660 2696 7.246311 AGAAATATCAACTGCAATTTCTCGTG 58.754 34.615 13.54 0.00 42.24 4.35
2839 2878 5.578005 ATTGAAGTTCAATCTGATGGCTG 57.422 39.130 22.70 0.00 43.03 4.85
2846 2885 4.426736 TCAATCTGATGGCTGCTATTCA 57.573 40.909 0.00 0.15 0.00 2.57
2862 2901 5.105797 TGCTATTCAAAGGTAACATGCTTGG 60.106 40.000 4.44 0.00 41.41 3.61
2921 2960 2.092968 TCAGGGGACTATGCAACATGAC 60.093 50.000 0.00 0.00 40.21 3.06
3420 3466 9.078990 TGTATAAACCATCCACATTGTGTTTAA 57.921 29.630 15.34 0.00 33.46 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 70 4.878968 TCATCAGGTAGTAGGATTCCACA 58.121 43.478 5.29 0.00 0.00 4.17
72 75 4.078571 TGGTCCTCATCAGGTAGTAGGATT 60.079 45.833 0.00 0.00 41.28 3.01
178 181 5.647658 GTGGATCACCTCATCACATTACAAA 59.352 40.000 0.00 0.00 37.04 2.83
179 182 5.185454 GTGGATCACCTCATCACATTACAA 58.815 41.667 0.00 0.00 37.04 2.41
199 202 4.742167 CGAACAGATAGCTTGTAGATGTGG 59.258 45.833 0.00 0.00 0.00 4.17
224 227 4.118093 TCACATCATCGAACACGGTATT 57.882 40.909 0.00 0.00 0.00 1.89
236 239 6.922247 ACATCTTTGTCTGATCACATCATC 57.078 37.500 0.00 0.00 38.85 2.92
253 257 1.612726 GCTTGCACAGGAGGACATCTT 60.613 52.381 0.00 0.00 0.00 2.40
343 354 8.506168 AACAGTGACTTAACAAAAATGAGAGA 57.494 30.769 0.00 0.00 0.00 3.10
375 386 3.437049 CAGCTTGCTTAAACTACTGGACC 59.563 47.826 0.00 0.00 0.00 4.46
413 438 3.197549 GCAAGCCCCCAGATCAATTTAAA 59.802 43.478 0.00 0.00 0.00 1.52
415 440 2.292126 TGCAAGCCCCCAGATCAATTTA 60.292 45.455 0.00 0.00 0.00 1.40
416 441 1.197812 GCAAGCCCCCAGATCAATTT 58.802 50.000 0.00 0.00 0.00 1.82
417 442 0.041535 TGCAAGCCCCCAGATCAATT 59.958 50.000 0.00 0.00 0.00 2.32
418 443 0.263765 ATGCAAGCCCCCAGATCAAT 59.736 50.000 0.00 0.00 0.00 2.57
419 444 0.396139 GATGCAAGCCCCCAGATCAA 60.396 55.000 0.00 0.00 0.00 2.57
420 445 1.228228 GATGCAAGCCCCCAGATCA 59.772 57.895 0.00 0.00 0.00 2.92
421 446 1.530183 GGATGCAAGCCCCCAGATC 60.530 63.158 0.00 0.00 35.29 2.75
422 447 1.661990 ATGGATGCAAGCCCCCAGAT 61.662 55.000 6.52 0.00 46.54 2.90
423 448 1.877672 AATGGATGCAAGCCCCCAGA 61.878 55.000 6.52 0.00 46.54 3.86
424 449 0.979187 AAATGGATGCAAGCCCCCAG 60.979 55.000 6.52 0.00 46.54 4.45
425 450 1.080722 AAATGGATGCAAGCCCCCA 59.919 52.632 6.52 5.24 46.54 4.96
426 451 0.977108 TCAAATGGATGCAAGCCCCC 60.977 55.000 6.52 0.00 46.54 5.40
427 452 1.069668 GATCAAATGGATGCAAGCCCC 59.930 52.381 6.52 0.00 46.54 5.80
428 453 2.037144 AGATCAAATGGATGCAAGCCC 58.963 47.619 6.52 1.78 46.54 5.19
464 489 4.584327 AACAAACTGGTGGTTTAGATGC 57.416 40.909 0.00 0.00 45.26 3.91
497 522 4.802039 GCCATCACATTTTAGAACATGCAG 59.198 41.667 0.00 0.00 0.00 4.41
590 615 5.299279 ACCAAGACACGTCATTTTCTTTGAT 59.701 36.000 0.00 0.00 0.00 2.57
604 629 2.121564 CTTGCCTGCACCAAGACACG 62.122 60.000 14.32 0.00 41.64 4.49
675 700 3.207778 AGAGACACTAGCGGCTACTTAG 58.792 50.000 5.42 0.29 0.00 2.18
676 701 3.278668 AGAGACACTAGCGGCTACTTA 57.721 47.619 5.42 0.00 0.00 2.24
677 702 2.131776 AGAGACACTAGCGGCTACTT 57.868 50.000 5.42 0.00 0.00 2.24
678 703 2.563702 GTAGAGACACTAGCGGCTACT 58.436 52.381 5.42 1.33 0.00 2.57
679 704 1.261089 CGTAGAGACACTAGCGGCTAC 59.739 57.143 5.42 0.00 0.00 3.58
680 705 1.579698 CGTAGAGACACTAGCGGCTA 58.420 55.000 9.71 9.71 0.00 3.93
681 706 1.096386 CCGTAGAGACACTAGCGGCT 61.096 60.000 7.98 7.98 38.15 5.52
682 707 1.355916 CCGTAGAGACACTAGCGGC 59.644 63.158 0.00 0.00 38.15 6.53
683 708 1.096386 AGCCGTAGAGACACTAGCGG 61.096 60.000 12.87 12.87 42.62 5.52
684 709 0.733729 AAGCCGTAGAGACACTAGCG 59.266 55.000 0.00 0.00 30.70 4.26
685 710 4.571372 AATAAGCCGTAGAGACACTAGC 57.429 45.455 0.00 0.00 0.00 3.42
982 1007 1.995484 CATCACTGTAGCAGTCCAACG 59.005 52.381 0.00 0.00 43.43 4.10
1023 1050 4.153475 GCAGTTCCACGCTGTATTCTTTTA 59.847 41.667 0.00 0.00 36.42 1.52
1080 1107 2.162681 CTTAAGTTTGCCACTCCCTGG 58.837 52.381 0.00 0.00 44.08 4.45
1090 1117 2.863739 CGGCTTAAGGCTTAAGTTTGC 58.136 47.619 35.08 25.98 43.52 3.68
1166 1197 5.841237 TCTCCTCAGGCTTTATATACAAGCT 59.159 40.000 19.77 10.08 45.18 3.74
1264 1295 5.928976 TCAAGTTCTTGATCCTTTGAGACA 58.071 37.500 10.67 0.00 0.00 3.41
1333 1365 4.502282 CACATGTAGAGAAGCTCGATGTTC 59.498 45.833 0.00 0.00 35.36 3.18
1335 1367 3.736433 GCACATGTAGAGAAGCTCGATGT 60.736 47.826 0.00 0.00 35.36 3.06
1336 1368 2.793790 GCACATGTAGAGAAGCTCGATG 59.206 50.000 0.00 0.00 35.36 3.84
1389 1421 1.028330 ACAGAACTGCATGCCATCGG 61.028 55.000 16.68 13.26 0.00 4.18
1413 1445 5.886960 ATTTCAGCTCGCAAACTCTAAAT 57.113 34.783 0.00 0.00 0.00 1.40
1426 1458 2.481952 AGAACACGCAGAATTTCAGCTC 59.518 45.455 11.38 3.18 0.00 4.09
1456 1488 2.593725 CCCGCCAGCATCTCCATG 60.594 66.667 0.00 0.00 0.00 3.66
1614 1646 0.741221 AGATTTTCTCCGCCTCGTGC 60.741 55.000 0.00 0.00 0.00 5.34
1617 1649 1.929836 CAGAAGATTTTCTCCGCCTCG 59.070 52.381 0.00 0.00 41.71 4.63
1643 1675 0.739462 TAACCGGACATTGCGAGCTG 60.739 55.000 9.46 0.00 30.86 4.24
1819 1851 2.884639 GCTGAAAGGGTTGCTTCTAACA 59.115 45.455 0.00 0.00 32.22 2.41
1821 1853 2.884639 GTGCTGAAAGGGTTGCTTCTAA 59.115 45.455 0.00 0.00 0.00 2.10
1852 1884 6.208007 TGTCATGAATCTGTCTGAAATTGCTT 59.792 34.615 0.00 0.00 0.00 3.91
1987 2019 4.284550 ATGGCAACCGCACCACCT 62.285 61.111 0.00 0.00 39.19 4.00
2078 2110 1.257743 CTCGTGACCCTCCTCTTGAA 58.742 55.000 0.00 0.00 0.00 2.69
2167 2199 2.789409 AGTCCCTGCCAAGAACATAC 57.211 50.000 0.00 0.00 0.00 2.39
2221 2253 1.067582 CTCCCGCTCAATACCGTCC 59.932 63.158 0.00 0.00 0.00 4.79
2287 2319 0.812811 CCATCACCATCTCCTGCACG 60.813 60.000 0.00 0.00 0.00 5.34
2303 2335 1.202330 CAACTCCTCCTCAGCTCCAT 58.798 55.000 0.00 0.00 0.00 3.41
2368 2400 1.350684 TGGATTGTAGCAAGGCACAGA 59.649 47.619 0.00 0.00 0.00 3.41
2571 2607 7.320399 TGTTTTGTCTTCCTTTTCCTTCTTTC 58.680 34.615 0.00 0.00 0.00 2.62
2606 2642 3.817647 GCTCAAACTCTCACAAACCATCT 59.182 43.478 0.00 0.00 0.00 2.90
2657 2693 2.493278 AGAAAGCATCAATTTCCCCACG 59.507 45.455 0.00 0.00 37.37 4.94
2659 2695 3.903090 ACAAGAAAGCATCAATTTCCCCA 59.097 39.130 0.00 0.00 37.37 4.96
2660 2696 4.541973 ACAAGAAAGCATCAATTTCCCC 57.458 40.909 0.00 0.00 37.37 4.81
2747 2786 7.006509 CAGGATAATTTGTAGGATGGGTGAAT 58.993 38.462 0.00 0.00 0.00 2.57
2749 2788 5.431731 ACAGGATAATTTGTAGGATGGGTGA 59.568 40.000 0.00 0.00 0.00 4.02
2839 2878 5.343249 CCAAGCATGTTACCTTTGAATAGC 58.657 41.667 0.00 0.00 0.00 2.97
2846 2885 1.266178 GCCCCAAGCATGTTACCTTT 58.734 50.000 0.00 0.00 42.97 3.11
2862 2901 2.829741 TAATGCTGTTTGGTTTGCCC 57.170 45.000 0.00 0.00 0.00 5.36
2921 2960 6.375455 AGGAAGCCTTATGTGTAAACAGAATG 59.625 38.462 0.00 0.00 46.00 2.67
2997 3043 7.856398 CGCTATCAGGTATGGTCTAAATATACG 59.144 40.741 0.00 0.00 0.00 3.06
3000 3046 7.548097 CACGCTATCAGGTATGGTCTAAATAT 58.452 38.462 0.00 0.00 0.00 1.28
3008 3054 1.119684 TGCACGCTATCAGGTATGGT 58.880 50.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.