Multiple sequence alignment - TraesCS7B01G144800

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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 TraesCS7B01G144800 chr7B 100.000 2769 0 0 1 2769 186974631 186977399 0.000000e+00 5114.0
1 TraesCS7B01G144800 chr7D 94.553 1891 58 25 1 1874 214325384 214323522 0.000000e+00 2880.0
2 TraesCS7B01G144800 chr7D 85.778 900 96 21 1881 2769 214133653 214132775 0.000000e+00 924.0
3 TraesCS7B01G144800 chr7A 90.171 1343 66 36 781 2111 226624551 226623263 0.000000e+00 1688.0
4 TraesCS7B01G144800 chr7A 90.909 748 25 9 1 738 226625259 226624545 0.000000e+00 965.0
5 TraesCS7B01G144800 chr7A 86.494 385 49 3 2386 2769 226622793 226622411 1.190000e-113 420.0
6 TraesCS7B01G144800 chr2D 79.861 144 19 9 2065 2202 537722993 537723132 2.270000e-16 97.1


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 TraesCS7B01G144800 chr7B 186974631 186977399 2768 False 5114.000000 5114 100.000000 1 2769 1 chr7B.!!$F1 2768
1 TraesCS7B01G144800 chr7D 214323522 214325384 1862 True 2880.000000 2880 94.553000 1 1874 1 chr7D.!!$R2 1873
2 TraesCS7B01G144800 chr7D 214132775 214133653 878 True 924.000000 924 85.778000 1881 2769 1 chr7D.!!$R1 888
3 TraesCS7B01G144800 chr7A 226622411 226625259 2848 True 1024.333333 1688 89.191333 1 2769 3 chr7A.!!$R1 2768

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
635 654 0.319555 GTCTTCGTGTAGCTGTGCCA 60.32 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 2820 0.038159 CTTCTCGTCTGCCGGTTCTT 60.038 55.0 1.9 0.0 37.11 2.52 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
32 33 0.453950 TTCTCGTGTAAGCTCGACGC 60.454 55.000 7.13 5.03 35.98 5.19
34 35 0.728129 CTCGTGTAAGCTCGACGCAA 60.728 55.000 11.54 0.00 42.61 4.85
269 283 3.735029 GCAGCTGCCTGTGAGTGC 61.735 66.667 28.76 0.00 41.26 4.40
329 343 1.336755 ACGGCAGCAAGTGGTTAAAAG 59.663 47.619 0.00 0.00 0.00 2.27
453 471 1.836999 ATCCACAACAGTGCGCCCTA 61.837 55.000 4.18 0.00 31.87 3.53
635 654 0.319555 GTCTTCGTGTAGCTGTGCCA 60.320 55.000 0.00 0.00 0.00 4.92
682 701 2.419198 CGGGGGCTTCTCGAGATG 59.581 66.667 17.44 19.45 0.00 2.90
778 797 6.176183 GGTTATGGAGTGATTGATATGGGAG 58.824 44.000 0.00 0.00 0.00 4.30
983 1002 6.974048 CAGCTCAGTATATATGCTCTGCTAAG 59.026 42.308 19.33 10.06 31.05 2.18
993 1012 2.501316 TGCTCTGCTAAGTGCTGGAATA 59.499 45.455 2.01 0.00 42.26 1.75
1031 1050 2.820197 GGTTGATCAAAGGACACTTCCC 59.180 50.000 10.35 0.00 44.10 3.97
1056 1076 5.483811 TGGCATGTTTAGATAAACGTCTCA 58.516 37.500 7.13 6.39 46.38 3.27
1072 1092 3.305403 CGTCTCAACCTGCTCTTGACTTA 60.305 47.826 0.00 0.00 0.00 2.24
1262 1282 1.663739 CGACCGACCACAAGAGGAA 59.336 57.895 0.00 0.00 0.00 3.36
1512 1532 3.036577 GGTGACGACGTGAGGACA 58.963 61.111 4.58 0.00 0.00 4.02
1592 1613 2.490217 CGAGGCGGGAGTAGTGTG 59.510 66.667 0.00 0.00 0.00 3.82
1602 1623 2.288273 GGGAGTAGTGTGAGTGTGTGAC 60.288 54.545 0.00 0.00 0.00 3.67
1641 1662 3.244665 TGGGCATTGATAGGATGTGCTAG 60.245 47.826 0.00 0.00 36.15 3.42
1645 1666 4.450419 GCATTGATAGGATGTGCTAGTGAC 59.550 45.833 0.00 0.00 33.25 3.67
1883 1921 3.622455 GCTGTGGCCTTAGGTGACTTAAT 60.622 47.826 3.32 0.00 43.67 1.40
1946 1984 6.538381 TGTTATACACGCATTCTTGTCATGAT 59.462 34.615 0.00 0.00 0.00 2.45
1977 2019 6.015434 ACAAAACTAGATGTTGGGGTGATTTC 60.015 38.462 0.00 0.00 39.13 2.17
1993 2035 7.334171 GGGGTGATTTCTTTTTGGTAAATGATG 59.666 37.037 0.00 0.00 30.37 3.07
1994 2036 8.093927 GGGTGATTTCTTTTTGGTAAATGATGA 58.906 33.333 0.00 0.00 30.37 2.92
1995 2037 9.657419 GGTGATTTCTTTTTGGTAAATGATGAT 57.343 29.630 0.00 0.00 30.37 2.45
2004 2046 9.618890 TTTTTGGTAAATGATGATTGTTTCCAA 57.381 25.926 0.00 0.00 34.45 3.53
2012 2054 1.202663 TGATTGTTTCCAACCGACCGA 60.203 47.619 0.00 0.00 32.26 4.69
2013 2055 1.196127 GATTGTTTCCAACCGACCGAC 59.804 52.381 0.00 0.00 32.26 4.79
2014 2056 0.814812 TTGTTTCCAACCGACCGACC 60.815 55.000 0.00 0.00 0.00 4.79
2015 2057 1.227615 GTTTCCAACCGACCGACCA 60.228 57.895 0.00 0.00 0.00 4.02
2016 2058 0.814812 GTTTCCAACCGACCGACCAA 60.815 55.000 0.00 0.00 0.00 3.67
2017 2059 0.107312 TTTCCAACCGACCGACCAAA 60.107 50.000 0.00 0.00 0.00 3.28
2018 2060 0.533308 TTCCAACCGACCGACCAAAG 60.533 55.000 0.00 0.00 0.00 2.77
2019 2061 2.613506 CCAACCGACCGACCAAAGC 61.614 63.158 0.00 0.00 0.00 3.51
2020 2062 1.597027 CAACCGACCGACCAAAGCT 60.597 57.895 0.00 0.00 0.00 3.74
2026 2068 1.003718 ACCGACCAAAGCTAGTGGC 60.004 57.895 14.82 8.04 40.02 5.01
2071 2116 3.991051 CCACACACGCTCGTCCCT 61.991 66.667 0.00 0.00 0.00 4.20
2080 2125 2.032620 ACGCTCGTCCCTCATTATCTT 58.967 47.619 0.00 0.00 0.00 2.40
2091 2136 5.973124 TCCCTCATTATCTTTTCCTCCTCTT 59.027 40.000 0.00 0.00 0.00 2.85
2106 2154 6.074648 TCCTCCTCTTGATTTCTCTCTATCC 58.925 44.000 0.00 0.00 0.00 2.59
2135 2183 4.431524 CCCCTCCCCACCCTGCTA 62.432 72.222 0.00 0.00 0.00 3.49
2204 2519 1.039785 CGAGCTCTCCTCCATGGTCA 61.040 60.000 12.58 0.00 37.27 4.02
2207 2522 1.267574 GCTCTCCTCCATGGTCACCA 61.268 60.000 12.58 0.00 38.19 4.17
2238 2553 0.671781 GAGGCCACATATGCTAGCGG 60.672 60.000 10.77 4.92 0.00 5.52
2248 2563 4.752879 GCTAGCGGCGGTGACCAA 62.753 66.667 23.33 0.00 0.00 3.67
2257 2572 1.463674 GCGGTGACCAAGAATTCCAT 58.536 50.000 1.11 0.00 0.00 3.41
2263 2578 4.265073 GTGACCAAGAATTCCATAGCAGT 58.735 43.478 0.65 0.00 0.00 4.40
2266 2581 3.266772 ACCAAGAATTCCATAGCAGTGGA 59.733 43.478 0.65 6.03 46.28 4.02
2276 2591 3.742882 CCATAGCAGTGGATACGTGATTG 59.257 47.826 0.00 0.00 42.02 2.67
2298 2613 4.205323 GTTACAACCAACGGAAGACTTG 57.795 45.455 0.00 0.00 0.00 3.16
2299 2614 2.413310 ACAACCAACGGAAGACTTGT 57.587 45.000 0.00 0.00 0.00 3.16
2301 2616 3.200483 ACAACCAACGGAAGACTTGTAC 58.800 45.455 0.00 0.00 0.00 2.90
2315 2630 7.715686 GGAAGACTTGTACTGAAATAATAGGGG 59.284 40.741 0.00 0.00 0.00 4.79
2356 2671 2.029649 TGGGACGACCTCTTTCTTAACG 60.030 50.000 3.44 0.00 41.11 3.18
2358 2673 2.029560 GGACGACCTCTTTCTTAACGGT 60.030 50.000 0.00 0.00 0.00 4.83
2362 2677 3.366679 CGACCTCTTTCTTAACGGTGCTA 60.367 47.826 0.00 0.00 0.00 3.49
2372 2687 6.956299 TCTTAACGGTGCTATTAACACTTC 57.044 37.500 0.00 0.00 38.14 3.01
2378 2693 4.142902 CGGTGCTATTAACACTTCAACCTG 60.143 45.833 0.00 0.00 38.14 4.00
2381 2696 4.688879 TGCTATTAACACTTCAACCTGACG 59.311 41.667 0.00 0.00 0.00 4.35
2382 2697 4.092968 GCTATTAACACTTCAACCTGACGG 59.907 45.833 0.00 0.00 0.00 4.79
2384 2699 0.179029 AACACTTCAACCTGACGGGG 60.179 55.000 5.03 0.00 40.03 5.73
2392 2707 1.956629 AACCTGACGGGGCATCTACG 61.957 60.000 5.03 0.00 40.03 3.51
2414 2729 3.707458 TTGCGACCGGTGGCCATA 61.707 61.111 34.59 19.36 33.12 2.74
2470 2785 1.595382 GACAACGACCAGCAGCTGT 60.595 57.895 21.26 9.30 0.00 4.40
2505 2820 0.678395 AACCGGCATGTCATTTTGCA 59.322 45.000 0.00 0.00 40.66 4.08
2511 2826 2.738314 GGCATGTCATTTTGCAAGAACC 59.262 45.455 0.00 0.00 40.66 3.62
2515 2830 1.035923 TCATTTTGCAAGAACCGGCA 58.964 45.000 0.00 0.00 38.46 5.69
2619 2934 3.252215 TGCTGGAACCGACTACATTTTTG 59.748 43.478 0.00 0.00 0.00 2.44
2730 3047 2.473984 GGAGTTGTACTTTTGGACGACG 59.526 50.000 0.00 0.00 35.46 5.12
2731 3048 3.374745 GAGTTGTACTTTTGGACGACGA 58.625 45.455 0.00 0.00 35.46 4.20
2734 3051 5.717119 AGTTGTACTTTTGGACGACGATAT 58.283 37.500 0.00 0.00 35.46 1.63
2736 3053 5.313520 TGTACTTTTGGACGACGATATCA 57.686 39.130 0.00 0.00 0.00 2.15
2748 3065 4.624024 ACGACGATATCACACGATTTTTGT 59.376 37.500 16.17 0.00 32.73 2.83
2758 3075 0.506506 CGATTTTTGTTGCAACCCGC 59.493 50.000 26.14 9.08 42.89 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.869767 GGGTGCTAGATGCTCGATTTG 59.130 52.381 0.00 0.00 43.37 2.32
34 35 0.032678 CGGGTGCTAGATGCTCGATT 59.967 55.000 0.00 0.00 43.37 3.34
67 68 3.071206 TCAGAGCCGCCTCACCTC 61.071 66.667 0.00 0.00 40.68 3.85
89 90 3.388024 TGTACAAGTGACTTTCCTCTGCT 59.612 43.478 0.00 0.00 0.00 4.24
269 283 1.869574 CGCCGATCACTCACACTCG 60.870 63.158 0.00 0.00 0.00 4.18
329 343 1.683790 CGCGACAAATCTCACCGGAC 61.684 60.000 9.46 0.00 0.00 4.79
635 654 1.714794 CTCCGAAACAATCTCGCACT 58.285 50.000 0.00 0.00 34.95 4.40
670 689 2.223782 ACATCAGCTCATCTCGAGAAGC 60.224 50.000 25.16 25.16 45.45 3.86
682 701 2.887568 CCCACGCGACATCAGCTC 60.888 66.667 15.93 0.00 0.00 4.09
778 797 1.194772 GAACGCTGAGGTAAGCACAAC 59.805 52.381 0.00 0.00 43.73 3.32
993 1012 3.346426 CCAGCTGGTTTTAGTGCCT 57.654 52.632 25.53 0.00 0.00 4.75
1031 1050 6.092122 TGAGACGTTTATCTAAACATGCCAAG 59.908 38.462 12.05 0.00 44.29 3.61
1056 1076 7.428826 CAAAGAAATTAAGTCAAGAGCAGGTT 58.571 34.615 0.00 0.00 0.00 3.50
1072 1092 3.118298 ACTGCAAAGTGGCCAAAGAAATT 60.118 39.130 7.24 0.00 0.00 1.82
1262 1282 2.659610 GCTTCAGAGGACTGCCGT 59.340 61.111 0.00 0.00 43.17 5.68
1512 1532 1.579964 GCCGGAACCCGTTCGATTTT 61.580 55.000 5.05 0.00 46.80 1.82
1592 1613 2.030562 CCCACCGGTCACACACTC 59.969 66.667 2.59 0.00 0.00 3.51
1602 1623 0.530288 CCATTTGCTAAACCCACCGG 59.470 55.000 0.00 0.00 0.00 5.28
1641 1662 4.547406 AAAAGTAAAAGACCAGCGTCAC 57.453 40.909 0.00 0.00 41.87 3.67
1645 1666 7.803724 AGTAACATAAAAGTAAAAGACCAGCG 58.196 34.615 0.00 0.00 0.00 5.18
1697 1718 6.861055 CGCTAGTAGAGTACCAGTACTAGTAC 59.139 46.154 23.03 23.03 45.63 2.73
1698 1719 6.015856 CCGCTAGTAGAGTACCAGTACTAGTA 60.016 46.154 22.62 0.00 45.63 1.82
1699 1720 5.221422 CCGCTAGTAGAGTACCAGTACTAGT 60.221 48.000 22.62 0.00 45.63 2.57
1700 1721 5.221422 ACCGCTAGTAGAGTACCAGTACTAG 60.221 48.000 20.02 20.02 45.63 2.57
1701 1722 4.651503 ACCGCTAGTAGAGTACCAGTACTA 59.348 45.833 10.37 6.49 45.63 1.82
1703 1724 3.802866 ACCGCTAGTAGAGTACCAGTAC 58.197 50.000 0.00 0.00 36.35 2.73
1704 1725 4.651503 AGTACCGCTAGTAGAGTACCAGTA 59.348 45.833 19.54 5.52 36.56 2.74
1705 1726 3.454082 AGTACCGCTAGTAGAGTACCAGT 59.546 47.826 19.54 6.28 36.56 4.00
1706 1727 4.070630 AGTACCGCTAGTAGAGTACCAG 57.929 50.000 19.54 1.47 36.56 4.00
1707 1728 4.494091 AAGTACCGCTAGTAGAGTACCA 57.506 45.455 19.54 0.00 36.56 3.25
1708 1729 4.637977 ACAAAGTACCGCTAGTAGAGTACC 59.362 45.833 19.54 8.57 36.56 3.34
1709 1730 5.809719 ACAAAGTACCGCTAGTAGAGTAC 57.190 43.478 17.15 17.15 36.23 2.73
1710 1731 5.392380 GCAACAAAGTACCGCTAGTAGAGTA 60.392 44.000 0.00 0.00 0.00 2.59
1711 1732 4.617762 GCAACAAAGTACCGCTAGTAGAGT 60.618 45.833 0.00 0.00 0.00 3.24
1883 1921 3.576982 AGTAACAGTAGCAGCCAGTACAA 59.423 43.478 0.00 0.00 0.00 2.41
1946 1984 7.013846 CACCCCAACATCTAGTTTTGTTTCTAA 59.986 37.037 5.96 0.00 38.74 2.10
1977 2019 9.270640 TGGAAACAATCATCATTTACCAAAAAG 57.729 29.630 0.00 0.00 37.44 2.27
2004 2046 1.183676 ACTAGCTTTGGTCGGTCGGT 61.184 55.000 0.00 0.00 0.00 4.69
2012 2054 1.003718 GACCGCCACTAGCTTTGGT 60.004 57.895 14.00 3.92 40.39 3.67
2013 2055 1.003839 TGACCGCCACTAGCTTTGG 60.004 57.895 9.29 9.29 40.39 3.28
2014 2056 2.162716 GTGACCGCCACTAGCTTTG 58.837 57.895 0.00 0.00 42.44 2.77
2015 2057 4.695560 GTGACCGCCACTAGCTTT 57.304 55.556 0.00 0.00 42.44 3.51
2066 2109 5.368230 AGAGGAGGAAAAGATAATGAGGGAC 59.632 44.000 0.00 0.00 0.00 4.46
2071 2116 9.401058 GAAATCAAGAGGAGGAAAAGATAATGA 57.599 33.333 0.00 0.00 0.00 2.57
2080 2125 7.070571 GGATAGAGAGAAATCAAGAGGAGGAAA 59.929 40.741 0.00 0.00 0.00 3.13
2091 2136 3.900601 GCCAGAGGGATAGAGAGAAATCA 59.099 47.826 0.00 0.00 35.59 2.57
2122 2170 0.326238 CTAGGTTAGCAGGGTGGGGA 60.326 60.000 0.00 0.00 0.00 4.81
2133 2181 1.144057 CGTGGCTGGGCTAGGTTAG 59.856 63.158 0.00 0.00 0.00 2.34
2134 2182 3.026431 GCGTGGCTGGGCTAGGTTA 62.026 63.158 0.00 0.00 0.00 2.85
2135 2183 4.410400 GCGTGGCTGGGCTAGGTT 62.410 66.667 0.00 0.00 0.00 3.50
2178 2492 1.145945 TGGAGGAGAGCTCGTATGGAT 59.854 52.381 8.37 0.00 0.00 3.41
2204 2519 4.425099 CTCTGTCGAGGAGGTGGT 57.575 61.111 7.28 0.00 33.51 4.16
2228 2543 2.415843 GTCACCGCCGCTAGCATA 59.584 61.111 16.45 0.00 44.04 3.14
2238 2553 1.463674 ATGGAATTCTTGGTCACCGC 58.536 50.000 5.23 0.00 0.00 5.68
2257 2572 2.764010 ACCAATCACGTATCCACTGCTA 59.236 45.455 0.00 0.00 0.00 3.49
2298 2613 9.000486 GTGCTAAATCCCCTATTATTTCAGTAC 58.000 37.037 0.00 0.00 0.00 2.73
2299 2614 8.945193 AGTGCTAAATCCCCTATTATTTCAGTA 58.055 33.333 0.00 0.00 0.00 2.74
2301 2616 7.391833 GGAGTGCTAAATCCCCTATTATTTCAG 59.608 40.741 0.00 0.00 0.00 3.02
2315 2630 4.321230 CCCAAACTTGTGGAGTGCTAAATC 60.321 45.833 0.00 0.00 41.65 2.17
2356 2671 5.001232 TCAGGTTGAAGTGTTAATAGCACC 58.999 41.667 3.62 0.00 37.56 5.01
2358 2673 4.688879 CGTCAGGTTGAAGTGTTAATAGCA 59.311 41.667 0.00 0.00 0.00 3.49
2362 2677 3.408634 CCCGTCAGGTTGAAGTGTTAAT 58.591 45.455 0.00 0.00 35.12 1.40
2372 2687 0.462047 GTAGATGCCCCGTCAGGTTG 60.462 60.000 0.00 0.00 35.12 3.77
2378 2693 1.006102 CATCCGTAGATGCCCCGTC 60.006 63.158 0.00 0.00 43.35 4.79
2392 2707 3.124921 CCACCGGTCGCAACATCC 61.125 66.667 2.59 0.00 0.00 3.51
2430 2745 2.726555 CTCATGCAACATGAGTACGC 57.273 50.000 23.34 0.00 40.34 4.42
2436 2751 2.453983 TGTCGACTCATGCAACATGA 57.546 45.000 17.92 9.72 0.00 3.07
2438 2753 1.460743 CGTTGTCGACTCATGCAACAT 59.539 47.619 17.92 0.00 40.63 2.71
2484 2799 1.605202 GCAAAATGACATGCCGGTTGT 60.605 47.619 11.36 11.36 36.56 3.32
2505 2820 0.038159 CTTCTCGTCTGCCGGTTCTT 60.038 55.000 1.90 0.00 37.11 2.52
2511 2826 1.221466 TTGCAACTTCTCGTCTGCCG 61.221 55.000 0.00 0.00 32.36 5.69
2515 2830 1.134521 TGTGGTTGCAACTTCTCGTCT 60.135 47.619 27.64 0.00 0.00 4.18
2567 2882 0.237235 GATCGCAGCAAAAACGACCA 59.763 50.000 0.00 0.00 38.85 4.02
2699 3016 3.685139 AGTACAACTCCCACTGATGTG 57.315 47.619 0.00 0.00 43.45 3.21
2706 3023 2.546789 CGTCCAAAAGTACAACTCCCAC 59.453 50.000 0.00 0.00 0.00 4.61
2730 3047 6.183359 GGTTGCAACAAAAATCGTGTGATATC 60.183 38.462 29.55 3.17 33.40 1.63
2731 3048 5.633182 GGTTGCAACAAAAATCGTGTGATAT 59.367 36.000 29.55 0.00 33.40 1.63
2734 3051 3.182967 GGTTGCAACAAAAATCGTGTGA 58.817 40.909 29.55 0.00 0.00 3.58
2736 3053 2.545731 GGGTTGCAACAAAAATCGTGT 58.454 42.857 29.55 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.