Multiple sequence alignment - TraesCS5D01G268400

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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 TraesCS5D01G268400 chr5D 100.000 2567 0 0 1 2567 371796309 371798875 0.000000e+00 4741
1 TraesCS5D01G268400 chr5A 95.914 2570 91 10 1 2567 474827814 474830372 0.000000e+00 4152
2 TraesCS5D01G268400 chr5B 94.094 1507 64 13 1065 2567 441646868 441648353 0.000000e+00 2266
3 TraesCS5D01G268400 chr5B 93.484 1197 51 15 1 1186 441645767 441646947 0.000000e+00 1753
4 TraesCS5D01G268400 chr5B 92.405 79 6 0 1108 1186 441646827 441646905 2.090000e-21 113
5 TraesCS5D01G268400 chr3A 94.624 93 5 0 1 93 251035865 251035773 7.400000e-31 145
6 TraesCS5D01G268400 chr2B 94.624 93 5 0 1 93 288939819 288939911 7.400000e-31 145
7 TraesCS5D01G268400 chr6A 93.548 93 6 0 1 93 538097728 538097820 3.440000e-29 139
8 TraesCS5D01G268400 chr4B 93.548 93 6 0 1 93 146469265 146469357 3.440000e-29 139
9 TraesCS5D01G268400 chr3B 93.548 93 6 0 1 93 521797874 521797782 3.440000e-29 139
10 TraesCS5D01G268400 chr1D 91.176 102 9 0 1 102 81742290 81742189 3.440000e-29 139
11 TraesCS5D01G268400 chr1B 93.548 93 6 0 1 93 136627474 136627382 3.440000e-29 139
12 TraesCS5D01G268400 chr1B 93.548 93 6 0 1 93 388762421 388762329 3.440000e-29 139


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 TraesCS5D01G268400 chr5D 371796309 371798875 2566 False 4741.000000 4741 100.000000 1 2567 1 chr5D.!!$F1 2566
1 TraesCS5D01G268400 chr5A 474827814 474830372 2558 False 4152.000000 4152 95.914000 1 2567 1 chr5A.!!$F1 2566
2 TraesCS5D01G268400 chr5B 441645767 441648353 2586 False 1377.333333 2266 93.327667 1 2567 3 chr5B.!!$F1 2566

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
564 574 0.819259 TCAGCCACAAGAACACAGGC 60.819 55.0 0.0 0.0 45.54 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1624 0.179084 TTGTACCAGATAGCAGGCGC 60.179 55.0 0.0 0.0 38.99 6.53 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
46 47 5.053145 GTGTCTGTTCACTCATTTCAGTCT 58.947 41.667 0.00 0.00 35.68 3.24
289 298 2.175715 AGAAGGCAAGAACAGAAAGGGT 59.824 45.455 0.00 0.00 0.00 4.34
405 415 9.974980 TCACTATCCAACAATTTTAAAACTTCC 57.025 29.630 1.97 0.00 0.00 3.46
411 421 7.066404 TCCAACAATTTTAAAACTTCCAAAGGC 59.934 33.333 1.97 0.00 0.00 4.35
445 455 3.146618 AGACTAGATAACAACGGCGTG 57.853 47.619 15.70 10.75 0.00 5.34
473 483 6.238648 ACAGTGAAGAAACCTATACTTTGGG 58.761 40.000 0.00 0.00 0.00 4.12
549 559 3.072476 TGGGAGTTCCAGCTCAGC 58.928 61.111 0.00 0.00 41.46 4.26
564 574 0.819259 TCAGCCACAAGAACACAGGC 60.819 55.000 0.00 0.00 45.54 4.85
586 597 5.001237 CAATGACAAGATTGCATAGCCAA 57.999 39.130 0.00 0.00 0.00 4.52
815 826 4.620086 TCTCTATGTCCCCTTCTTGGTA 57.380 45.455 0.00 0.00 0.00 3.25
872 883 1.808945 GCATGACCAAGGTCTGACAAG 59.191 52.381 19.20 5.18 44.80 3.16
921 932 5.215252 AGCACATGCCGTATCTATAAACT 57.785 39.130 0.00 0.00 43.38 2.66
1089 1101 2.747855 CTTGGAGGGAAGCCGCAC 60.748 66.667 0.00 0.00 0.00 5.34
1118 1172 2.809174 CGGCGTCAGATGCGTTGA 60.809 61.111 8.57 0.00 0.00 3.18
1422 1476 0.536260 CCAGGAGAGTCAGCTTCAGG 59.464 60.000 0.00 0.00 0.00 3.86
1544 1598 1.466167 CATTGGTGCAAAGAGACCTCG 59.534 52.381 0.00 0.00 32.98 4.63
1546 1600 0.249868 TGGTGCAAAGAGACCTCGTG 60.250 55.000 0.00 0.00 32.98 4.35
1548 1602 1.301716 TGCAAAGAGACCTCGTGGC 60.302 57.895 2.76 5.54 38.30 5.01
1570 1624 4.213482 GCGCCATAACCAGATACTAAAAGG 59.787 45.833 0.00 0.00 0.00 3.11
1571 1625 4.213482 CGCCATAACCAGATACTAAAAGGC 59.787 45.833 0.00 0.00 0.00 4.35
1586 1640 1.048724 AAGGCGCCTGCTATCTGGTA 61.049 55.000 33.60 0.00 42.25 3.25
1599 1653 6.908825 TGCTATCTGGTACAACATCAAAAAC 58.091 36.000 0.00 0.00 38.70 2.43
1636 1690 6.005060 CTGGAAGAAAAGGGGTTCACAACC 62.005 50.000 0.00 0.00 44.48 3.77
1708 1775 4.954875 ACTGAAGCAATAGACTAGATGGC 58.045 43.478 0.00 0.00 0.00 4.40
1765 1832 6.431234 ACTCTCGAAAAGATATTTGCCACTTT 59.569 34.615 1.70 0.00 34.67 2.66
1866 1935 3.012518 CCACCTTGCTATTCTGAACTGG 58.987 50.000 0.00 0.00 0.00 4.00
2003 2072 2.572104 AGGGGCAAAAGATAAGAGACGT 59.428 45.455 0.00 0.00 0.00 4.34
2129 2198 4.281182 ACCAGGTGTTCTACTTCTGTACAG 59.719 45.833 17.17 17.17 0.00 2.74
2256 2325 5.581085 AGTTTTGGTCAGATATGTAGCGTTC 59.419 40.000 0.00 0.00 0.00 3.95
2262 2331 4.735822 GTCAGATATGTAGCGTTCTCACAC 59.264 45.833 0.00 0.00 0.00 3.82
2263 2332 4.398044 TCAGATATGTAGCGTTCTCACACA 59.602 41.667 0.00 0.00 0.00 3.72
2282 2351 7.269316 TCACACAACAGTTTGATAGTTCACTA 58.731 34.615 3.39 0.00 36.48 2.74
2410 2479 9.517609 GGTTTATGTTAGTGACTGATAGTACAG 57.482 37.037 0.00 0.00 42.78 2.74
2467 2536 4.464008 CCAAAGCTCATTAGGATGGCTAA 58.536 43.478 0.00 0.00 38.21 3.09
2474 2544 3.785887 TCATTAGGATGGCTAAGGGTGTT 59.214 43.478 0.00 0.00 33.93 3.32
2478 2548 2.772515 AGGATGGCTAAGGGTGTTAGTC 59.227 50.000 0.00 0.00 0.00 2.59
2537 2607 2.735823 TCTCGAGCATGATCAACATCG 58.264 47.619 12.15 16.36 37.07 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.677148 AGTGAACAGACACACTAAAATATGTT 57.323 30.769 0.00 0.00 44.06 2.71
27 28 6.648310 ACATACAGACTGAAATGAGTGAACAG 59.352 38.462 21.47 0.00 35.14 3.16
46 47 8.443979 TGGATATTTCAATATGGACCACATACA 58.556 33.333 0.00 0.00 44.41 2.29
289 298 5.056480 ACTCTGACATCATCGTTGTTTGAA 58.944 37.500 6.30 0.00 0.00 2.69
402 412 4.227197 TCCTGGTATTTTTGCCTTTGGAA 58.773 39.130 0.00 0.00 0.00 3.53
405 415 5.011023 AGTCTTCCTGGTATTTTTGCCTTTG 59.989 40.000 0.00 0.00 0.00 2.77
411 421 9.667107 TGTTATCTAGTCTTCCTGGTATTTTTG 57.333 33.333 0.00 0.00 0.00 2.44
445 455 6.532988 AGTATAGGTTTCTTCACTGTCCTC 57.467 41.667 0.00 0.00 0.00 3.71
473 483 4.760204 ACAGGGTGTATACAAAAACAGAGC 59.240 41.667 7.25 0.00 0.00 4.09
549 559 1.955778 TCATTGCCTGTGTTCTTGTGG 59.044 47.619 0.00 0.00 0.00 4.17
564 574 4.642445 TGGCTATGCAATCTTGTCATTG 57.358 40.909 0.00 0.00 36.91 2.82
579 589 0.261696 GGATGGTGGGGTTTGGCTAT 59.738 55.000 0.00 0.00 0.00 2.97
586 597 1.432807 AGAATTGTGGATGGTGGGGTT 59.567 47.619 0.00 0.00 0.00 4.11
781 792 5.221165 GGGACATAGAGAACTTAGCTCAGAC 60.221 48.000 0.90 0.00 34.85 3.51
787 798 4.651962 AGAAGGGGACATAGAGAACTTAGC 59.348 45.833 0.00 0.00 0.00 3.09
815 826 1.713078 AGGGAGGTTGGAGCAAAGAAT 59.287 47.619 0.00 0.00 0.00 2.40
1047 1059 1.483827 CTGGGCTTGAGTCTGCTGATA 59.516 52.381 0.00 0.00 0.00 2.15
1095 1149 2.653448 CATCTGACGCCGCTCTCG 60.653 66.667 0.00 0.00 0.00 4.04
1106 1160 1.945819 GCTTCCCTTCAACGCATCTGA 60.946 52.381 0.00 0.00 0.00 3.27
1118 1172 4.643387 AACGCTGCGGCTTCCCTT 62.643 61.111 26.95 6.49 36.09 3.95
1144 1198 2.741985 TCCAACGCATCTGGCACG 60.742 61.111 0.00 0.00 45.17 5.34
1146 1200 2.046023 CCTCCAACGCATCTGGCA 60.046 61.111 0.00 0.00 45.17 4.92
1346 1400 4.142271 CGATGGAGAAGCTATCCTGGATAC 60.142 50.000 12.38 9.61 37.74 2.24
1422 1476 1.464734 TGTCGGAGTGATCAGGAGAC 58.535 55.000 0.00 4.69 0.00 3.36
1544 1598 1.202651 AGTATCTGGTTATGGCGCCAC 60.203 52.381 35.50 20.34 0.00 5.01
1546 1600 3.396260 TTAGTATCTGGTTATGGCGCC 57.604 47.619 22.73 22.73 0.00 6.53
1548 1602 4.213482 GCCTTTTAGTATCTGGTTATGGCG 59.787 45.833 0.00 0.00 0.00 5.69
1570 1624 0.179084 TTGTACCAGATAGCAGGCGC 60.179 55.000 0.00 0.00 38.99 6.53
1571 1625 1.134818 TGTTGTACCAGATAGCAGGCG 60.135 52.381 0.00 0.00 0.00 5.52
1586 1640 5.799213 TCCTGTTTTGGTTTTTGATGTTGT 58.201 33.333 0.00 0.00 0.00 3.32
1599 1653 1.615392 CTTCCAGCCTTCCTGTTTTGG 59.385 52.381 0.00 0.00 40.06 3.28
1708 1775 6.947733 TGGCAAATATCATATTCCTGGGTAAG 59.052 38.462 0.00 0.00 0.00 2.34
1741 1808 6.428385 AAGTGGCAAATATCTTTTCGAGAG 57.572 37.500 0.00 0.00 37.93 3.20
1744 1811 7.535139 CCTTAAAGTGGCAAATATCTTTTCGA 58.465 34.615 5.51 0.00 33.22 3.71
1765 1832 9.890629 CTACTGCATGAAATATATTAGGCCTTA 57.109 33.333 12.58 0.11 0.00 2.69
1843 1912 3.686726 CAGTTCAGAATAGCAAGGTGGAC 59.313 47.826 0.00 0.00 0.00 4.02
2003 2072 5.066375 GCTGTTTTATGAGGTCATATGTGCA 59.934 40.000 1.90 0.00 38.49 4.57
2048 2117 2.949447 AGGAACTGCCACTTTGTTGAT 58.051 42.857 0.00 0.00 37.18 2.57
2129 2198 8.614469 AGGCTTCAAATCTGAATATAGCTAAC 57.386 34.615 0.00 0.00 40.78 2.34
2256 2325 6.258727 AGTGAACTATCAAACTGTTGTGTGAG 59.741 38.462 0.00 0.99 43.01 3.51
2262 2331 7.598869 TGTAGCTAGTGAACTATCAAACTGTTG 59.401 37.037 0.00 0.00 37.30 3.33
2263 2332 7.667557 TGTAGCTAGTGAACTATCAAACTGTT 58.332 34.615 0.00 0.00 37.30 3.16
2282 2351 7.395617 TCGATATAGTCTTGAGGTATGTAGCT 58.604 38.462 0.00 0.00 36.62 3.32
2410 2479 9.106070 TGATGATGAGTAGATATTTGCATATGC 57.894 33.333 21.09 21.09 42.50 3.14
2426 2495 3.176411 TGGGACAGTTCTGATGATGAGT 58.824 45.455 6.83 0.00 0.00 3.41
2467 2536 1.359168 GGTTCCCAGACTAACACCCT 58.641 55.000 0.00 0.00 0.00 4.34
2474 2544 4.030913 CTGAGGTAATGGTTCCCAGACTA 58.969 47.826 0.00 0.00 36.75 2.59
2478 2548 2.571653 TGTCTGAGGTAATGGTTCCCAG 59.428 50.000 0.00 0.00 36.75 4.45
2516 2586 3.118542 CGATGTTGATCATGCTCGAGAA 58.881 45.455 18.75 5.90 36.83 2.87
2537 2607 4.508662 CAACCTTCCTAGATGACCAAGTC 58.491 47.826 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.