Multiple sequence alignment - TraesCS7B01G138300

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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 TraesCS7B01G138300 chr7B 100.000 2534 0 0 1 2534 173868526 173865993 0.000000e+00 4680
1 TraesCS7B01G138300 chr7D 95.205 2440 86 9 1 2427 224059133 224056712 0.000000e+00 3829
2 TraesCS7B01G138300 chr7D 87.156 109 7 2 3 110 616218804 616218906 1.590000e-22 117
3 TraesCS7B01G138300 chr7D 86.667 105 8 2 6 110 616258545 616258447 7.410000e-21 111
4 TraesCS7B01G138300 chr7A 93.762 2565 111 19 1 2534 237515952 237518498 0.000000e+00 3805


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 TraesCS7B01G138300 chr7B 173865993 173868526 2533 True 4680 4680 100.000 1 2534 1 chr7B.!!$R1 2533
1 TraesCS7B01G138300 chr7D 224056712 224059133 2421 True 3829 3829 95.205 1 2427 1 chr7D.!!$R1 2426
2 TraesCS7B01G138300 chr7A 237515952 237518498 2546 False 3805 3805 93.762 1 2534 1 chr7A.!!$F1 2533

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
753 754 2.5116 GTGCCCAAGATCGTCCGG 60.512 66.667 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2289 0.95396 CAGCCGTGTAAAGGGTCACC 60.954 60.0 0.0 0.0 44.89 4.02 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
753 754 2.511600 GTGCCCAAGATCGTCCGG 60.512 66.667 0.00 0.00 0.00 5.14
774 775 2.736144 ACGCCGTGAACTATCTGAAA 57.264 45.000 0.00 0.00 0.00 2.69
1399 1403 2.523168 TCCTGCAGGTGGACGTCA 60.523 61.111 31.58 7.59 36.34 4.35
1586 1597 1.818060 CCCAATCCAATTTCAGCGTGA 59.182 47.619 0.00 0.00 0.00 4.35
1616 1627 9.807649 AATATGTATTTTTGCATGAAGGTTCTC 57.192 29.630 0.00 0.00 0.00 2.87
1617 1628 6.647334 TGTATTTTTGCATGAAGGTTCTCA 57.353 33.333 0.00 0.00 0.00 3.27
1620 1631 8.149647 TGTATTTTTGCATGAAGGTTCTCATTT 58.850 29.630 0.00 0.00 33.66 2.32
1623 1637 5.381174 TTGCATGAAGGTTCTCATTTCTG 57.619 39.130 0.00 0.00 33.66 3.02
1637 1651 7.377766 TCTCATTTCTGCCAATTACTGTAAC 57.622 36.000 1.73 0.00 0.00 2.50
1638 1652 6.374333 TCTCATTTCTGCCAATTACTGTAACC 59.626 38.462 1.73 0.00 0.00 2.85
1666 1680 6.628844 GCAATAAATCACAGGCCATTTTCTCT 60.629 38.462 5.01 0.00 0.00 3.10
1669 1683 2.426522 TCACAGGCCATTTTCTCTTCG 58.573 47.619 5.01 0.00 0.00 3.79
1716 1730 6.829298 TGTTTTACCACACAACTGGAGATTTA 59.171 34.615 0.00 0.00 35.04 1.40
1718 1732 7.504924 TTTACCACACAACTGGAGATTTAAG 57.495 36.000 0.00 0.00 35.04 1.85
1719 1733 3.821033 ACCACACAACTGGAGATTTAAGC 59.179 43.478 0.00 0.00 35.04 3.09
1720 1734 3.820467 CCACACAACTGGAGATTTAAGCA 59.180 43.478 0.00 0.00 32.30 3.91
1722 1736 5.455392 CACACAACTGGAGATTTAAGCAAG 58.545 41.667 0.00 0.00 0.00 4.01
1723 1737 4.022849 ACACAACTGGAGATTTAAGCAAGC 60.023 41.667 0.00 0.00 0.00 4.01
1724 1738 4.022935 CACAACTGGAGATTTAAGCAAGCA 60.023 41.667 0.00 0.00 0.00 3.91
1784 1807 5.012251 TCACATACTACAAGCCAAACCACTA 59.988 40.000 0.00 0.00 0.00 2.74
1785 1808 5.880332 CACATACTACAAGCCAAACCACTAT 59.120 40.000 0.00 0.00 0.00 2.12
2017 2044 4.280677 CCAAGTTATGGTTTCTTCCTTGCA 59.719 41.667 0.00 0.00 44.85 4.08
2028 2055 6.218746 GTTTCTTCCTTGCAGATGAATTTGT 58.781 36.000 5.47 0.00 32.05 2.83
2143 2176 1.956477 GCAAAGCACAGGGAAGAAAGA 59.044 47.619 0.00 0.00 0.00 2.52
2148 2181 4.313020 AGCACAGGGAAGAAAGATTGAT 57.687 40.909 0.00 0.00 0.00 2.57
2150 2183 5.819991 AGCACAGGGAAGAAAGATTGATTA 58.180 37.500 0.00 0.00 0.00 1.75
2215 2248 3.377759 AGCTGCTCGACTCGGCTT 61.378 61.111 9.75 0.00 43.10 4.35
2224 2257 1.856012 GACTCGGCTTGCGATATGC 59.144 57.895 0.00 0.00 46.70 3.14
2247 2280 3.178046 TGCCATAGGTGTACTTCCTCAA 58.822 45.455 12.16 0.00 36.60 3.02
2256 2289 3.076621 TGTACTTCCTCAATGCTTGCAG 58.923 45.455 0.87 0.00 0.00 4.41
2311 2344 1.136000 TGCTCATCGTTGCATGTTTCG 60.136 47.619 0.00 0.00 33.94 3.46
2370 2403 6.550481 TCCTTCATCATTGCCTAATTGCATAA 59.450 34.615 0.00 0.00 41.70 1.90
2384 2417 4.764679 TTGCATAACAAGTGGTTAGCAG 57.235 40.909 11.77 0.89 44.74 4.24
2408 2441 8.341173 CAGATGAACTCACAGGAATTTAATAGC 58.659 37.037 0.00 0.00 0.00 2.97
2428 2461 4.688021 AGCGAACAAGCTTAGAATCTAGG 58.312 43.478 0.00 0.00 46.80 3.02
2435 2468 7.187824 ACAAGCTTAGAATCTAGGATCAACA 57.812 36.000 0.00 0.00 0.00 3.33
2439 2472 8.083828 AGCTTAGAATCTAGGATCAACAGAAA 57.916 34.615 3.42 0.00 0.00 2.52
2443 2476 7.487822 AGAATCTAGGATCAACAGAAACAGA 57.512 36.000 0.00 0.00 0.00 3.41
2445 2478 8.040132 AGAATCTAGGATCAACAGAAACAGAAG 58.960 37.037 0.00 0.00 0.00 2.85
2452 2485 5.362556 TCAACAGAAACAGAAGCAATAGC 57.637 39.130 0.00 0.00 42.56 2.97
2457 2490 2.200373 AACAGAAGCAATAGCCGGTT 57.800 45.000 1.90 0.00 43.56 4.44
2469 2502 2.403252 AGCCGGTTCAAAGATACAGG 57.597 50.000 1.90 0.00 33.45 4.00
2470 2503 1.906574 AGCCGGTTCAAAGATACAGGA 59.093 47.619 1.90 0.00 32.20 3.86
2471 2504 2.007608 GCCGGTTCAAAGATACAGGAC 58.992 52.381 1.90 0.00 32.20 3.85
2472 2505 2.354805 GCCGGTTCAAAGATACAGGACT 60.355 50.000 1.90 0.00 32.20 3.85
2473 2506 3.522553 CCGGTTCAAAGATACAGGACTC 58.477 50.000 0.00 0.00 32.20 3.36
2474 2507 3.056107 CCGGTTCAAAGATACAGGACTCA 60.056 47.826 0.00 0.00 32.20 3.41
2479 2512 6.314896 GGTTCAAAGATACAGGACTCAGATTG 59.685 42.308 0.00 0.00 0.00 2.67
2482 2515 5.690464 AAGATACAGGACTCAGATTGCTT 57.310 39.130 0.00 0.00 0.00 3.91
2495 2528 2.573462 AGATTGCTTAGTCAGGCTTGGA 59.427 45.455 0.00 0.00 0.00 3.53
2505 2538 4.469657 AGTCAGGCTTGGAAAATGTAACA 58.530 39.130 0.00 0.00 0.00 2.41
2508 2541 4.278170 TCAGGCTTGGAAAATGTAACACTG 59.722 41.667 0.00 0.00 0.00 3.66
2511 2544 4.219033 GCTTGGAAAATGTAACACTGACG 58.781 43.478 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
567 568 4.856607 CCGGAGAAGAGCGCGTCC 62.857 72.222 8.43 4.29 0.00 4.79
651 652 4.992511 TAAAACACGCCGGCCGCT 62.993 61.111 22.85 0.00 41.76 5.52
684 685 1.977188 CGATGTAGTGCGTCTCAACA 58.023 50.000 0.00 0.00 0.00 3.33
753 754 2.838386 TCAGATAGTTCACGGCGTAC 57.162 50.000 14.22 8.83 0.00 3.67
913 917 2.651361 CTCCAGCACGTTCGAGGT 59.349 61.111 0.00 0.00 0.00 3.85
915 919 2.811317 GCCTCCAGCACGTTCGAG 60.811 66.667 0.00 0.00 42.97 4.04
1217 1221 2.283173 TCTCCTCCAGCACGCTGA 60.283 61.111 20.42 5.89 46.30 4.26
1219 1223 3.073735 CCTCTCCTCCAGCACGCT 61.074 66.667 0.00 0.00 0.00 5.07
1282 1286 4.496336 GGCCTTGATCTGCGCCCT 62.496 66.667 4.18 0.00 35.23 5.19
1338 1342 0.243907 CCTTCTCGTTCGCCTTCAGA 59.756 55.000 0.00 0.00 0.00 3.27
1339 1343 1.355066 GCCTTCTCGTTCGCCTTCAG 61.355 60.000 0.00 0.00 0.00 3.02
1399 1403 1.445095 GCCTCACCATGCTCTCGAT 59.555 57.895 0.00 0.00 0.00 3.59
1567 1578 3.574284 TTCACGCTGAAATTGGATTGG 57.426 42.857 0.00 0.00 32.71 3.16
1595 1606 8.538409 AAATGAGAACCTTCATGCAAAAATAC 57.462 30.769 0.00 0.00 37.83 1.89
1596 1607 8.587608 AGAAATGAGAACCTTCATGCAAAAATA 58.412 29.630 0.00 0.00 37.83 1.40
1597 1608 7.386848 CAGAAATGAGAACCTTCATGCAAAAAT 59.613 33.333 0.00 0.00 37.83 1.82
1598 1609 6.702723 CAGAAATGAGAACCTTCATGCAAAAA 59.297 34.615 0.00 0.00 37.83 1.94
1616 1627 5.418840 AGGGTTACAGTAATTGGCAGAAATG 59.581 40.000 0.00 0.00 0.00 2.32
1617 1628 5.418840 CAGGGTTACAGTAATTGGCAGAAAT 59.581 40.000 0.00 0.00 0.00 2.17
1620 1631 3.872240 GCAGGGTTACAGTAATTGGCAGA 60.872 47.826 0.00 0.00 0.00 4.26
1623 1637 2.442413 TGCAGGGTTACAGTAATTGGC 58.558 47.619 0.00 0.04 0.00 4.52
1637 1651 1.410153 GGCCTGTGATTTATTGCAGGG 59.590 52.381 10.86 0.00 46.23 4.45
1716 1730 5.170748 GCTTGGTAATGTAATTGCTTGCTT 58.829 37.500 0.00 0.00 39.06 3.91
1718 1732 4.493547 TGCTTGGTAATGTAATTGCTTGC 58.506 39.130 0.00 0.00 39.06 4.01
1719 1733 5.713025 ACTGCTTGGTAATGTAATTGCTTG 58.287 37.500 0.00 0.00 39.06 4.01
1720 1734 5.476599 TGACTGCTTGGTAATGTAATTGCTT 59.523 36.000 0.00 0.00 39.06 3.91
1722 1736 5.309323 TGACTGCTTGGTAATGTAATTGC 57.691 39.130 0.00 0.00 36.99 3.56
1723 1737 7.144722 TCTTGACTGCTTGGTAATGTAATTG 57.855 36.000 0.00 0.00 36.99 2.32
1724 1738 7.944729 ATCTTGACTGCTTGGTAATGTAATT 57.055 32.000 0.00 0.00 41.28 1.40
1765 1788 7.248743 AGTAATAGTGGTTTGGCTTGTAGTA 57.751 36.000 0.00 0.00 0.00 1.82
1767 1790 9.257651 GTATAGTAATAGTGGTTTGGCTTGTAG 57.742 37.037 0.00 0.00 0.00 2.74
1784 1807 8.846211 AGCCGTTTGCAAAATATGTATAGTAAT 58.154 29.630 14.67 0.00 44.83 1.89
1785 1808 8.215926 AGCCGTTTGCAAAATATGTATAGTAA 57.784 30.769 14.67 0.00 44.83 2.24
1804 1827 3.057033 CACTGTACTAGTTGGTAGCCGTT 60.057 47.826 0.00 0.00 37.60 4.44
2017 2044 1.468520 CAACGCCCGACAAATTCATCT 59.531 47.619 0.00 0.00 0.00 2.90
2028 2055 4.373116 GAGTGCCTCAACGCCCGA 62.373 66.667 0.00 0.00 0.00 5.14
2148 2181 9.740239 AACTAGCGATACTTTACGATGAATTAA 57.260 29.630 0.00 0.00 0.00 1.40
2150 2183 7.919091 TGAACTAGCGATACTTTACGATGAATT 59.081 33.333 0.00 0.00 0.00 2.17
2215 2248 1.072173 ACCTATGGCAAGCATATCGCA 59.928 47.619 0.00 0.00 46.13 5.10
2224 2257 3.197766 TGAGGAAGTACACCTATGGCAAG 59.802 47.826 10.82 0.00 37.93 4.01
2256 2289 0.953960 CAGCCGTGTAAAGGGTCACC 60.954 60.000 0.00 0.00 44.89 4.02
2370 2403 4.202357 TGAGTTCATCTGCTAACCACTTGT 60.202 41.667 0.00 0.00 0.00 3.16
2384 2417 7.224753 TCGCTATTAAATTCCTGTGAGTTCATC 59.775 37.037 0.00 0.00 0.00 2.92
2408 2441 6.507900 TGATCCTAGATTCTAAGCTTGTTCG 58.492 40.000 9.86 0.00 0.00 3.95
2428 2461 6.026513 GCTATTGCTTCTGTTTCTGTTGATC 58.973 40.000 0.00 0.00 36.03 2.92
2435 2468 2.290323 ACCGGCTATTGCTTCTGTTTCT 60.290 45.455 0.00 0.00 39.59 2.52
2439 2472 1.003118 TGAACCGGCTATTGCTTCTGT 59.997 47.619 0.00 0.00 39.59 3.41
2443 2476 2.790433 TCTTTGAACCGGCTATTGCTT 58.210 42.857 0.00 0.00 39.59 3.91
2445 2478 3.625764 TGTATCTTTGAACCGGCTATTGC 59.374 43.478 0.00 0.00 38.76 3.56
2452 2485 3.056107 TGAGTCCTGTATCTTTGAACCGG 60.056 47.826 0.00 0.00 0.00 5.28
2457 2490 5.188555 AGCAATCTGAGTCCTGTATCTTTGA 59.811 40.000 0.00 0.00 0.00 2.69
2469 2502 3.118811 AGCCTGACTAAGCAATCTGAGTC 60.119 47.826 3.41 3.41 46.70 3.36
2470 2503 2.836981 AGCCTGACTAAGCAATCTGAGT 59.163 45.455 0.00 0.00 36.71 3.41
2471 2504 3.540314 AGCCTGACTAAGCAATCTGAG 57.460 47.619 0.00 0.00 0.00 3.35
2472 2505 3.603532 CAAGCCTGACTAAGCAATCTGA 58.396 45.455 0.00 0.00 0.00 3.27
2473 2506 2.681848 CCAAGCCTGACTAAGCAATCTG 59.318 50.000 0.00 0.00 0.00 2.90
2474 2507 2.573462 TCCAAGCCTGACTAAGCAATCT 59.427 45.455 0.00 0.00 0.00 2.40
2479 2512 3.507622 ACATTTTCCAAGCCTGACTAAGC 59.492 43.478 0.00 0.00 0.00 3.09
2482 2515 5.472137 GTGTTACATTTTCCAAGCCTGACTA 59.528 40.000 0.00 0.00 0.00 2.59
2495 2528 6.569179 ATTTAGCCGTCAGTGTTACATTTT 57.431 33.333 0.00 0.00 0.00 1.82
2505 2538 6.258727 CAGATAATGACAATTTAGCCGTCAGT 59.741 38.462 0.00 0.00 42.53 3.41
2508 2541 6.844696 TCAGATAATGACAATTTAGCCGTC 57.155 37.500 0.00 0.00 31.12 4.79


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

AutoCloner maintained by Alex Coulton.