Multiple sequence alignment - TraesCS2B01G345700

Loading Multiple Alignment...

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 TraesCS2B01G345700 chr2B 100.000 2753 0 0 1 2753 492616913 492614161 0.000000e+00 5084.0
1 TraesCS2B01G345700 chr2D 94.933 1796 55 14 771 2559 420166139 420164373 0.000000e+00 2780.0
2 TraesCS2B01G345700 chr2D 92.963 739 34 6 6 734 420166970 420166240 0.000000e+00 1061.0
3 TraesCS2B01G345700 chr2A 96.851 1429 39 5 734 2160 570013498 570014922 0.000000e+00 2385.0
4 TraesCS2B01G345700 chr2A 94.580 369 15 3 2207 2572 570014931 570015297 1.430000e-157 566.0
5 TraesCS2B01G345700 chr2A 93.525 278 8 2 457 734 570013151 570013418 3.300000e-109 405.0
6 TraesCS2B01G345700 chr2A 90.157 254 13 9 3 255 570012547 570012789 1.230000e-83 320.0
7 TraesCS2B01G345700 chr2A 92.593 189 14 0 2565 2753 570015856 570016044 3.490000e-69 272.0
8 TraesCS2B01G345700 chr3D 85.294 68 8 1 2446 2511 481576869 481576802 4.920000e-08 69.4


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 TraesCS2B01G345700 chr2B 492614161 492616913 2752 True 5084.0 5084 100.0000 1 2753 1 chr2B.!!$R1 2752
1 TraesCS2B01G345700 chr2D 420164373 420166970 2597 True 1920.5 2780 93.9480 6 2559 2 chr2D.!!$R1 2553
2 TraesCS2B01G345700 chr2A 570012547 570016044 3497 False 789.6 2385 93.5412 3 2753 5 chr2A.!!$F1 2750

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
283 294 1.747709 ATGCCAGACTGCAGATCAAC 58.252 50.000 23.35 7.28 45.93 3.18 F
931 1240 2.062519 GACACTTCTGGTTCGCTCTTC 58.937 52.381 0.00 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1537 1.272807 TAGGTACAGGAAGGTGCACC 58.727 55.0 29.22 29.22 34.41 5.01 R
2301 2617 0.878523 CGACTCGCACACTCCCAAAA 60.879 55.0 0.00 0.00 0.00 2.44 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
80 81 6.969828 AGCATAAACTTGTACAGCTAGAAC 57.030 37.500 1.99 0.00 0.00 3.01
98 99 6.088749 GCTAGAACTATTATGCTCATGTCGTG 59.911 42.308 0.00 0.00 0.00 4.35
259 270 6.183359 CGGTTTGTGCTTTTGAGTAAATATGC 60.183 38.462 0.00 0.00 0.00 3.14
283 294 1.747709 ATGCCAGACTGCAGATCAAC 58.252 50.000 23.35 7.28 45.93 3.18
445 670 4.233789 TGTTTTGCTGTGAAGTTGAACAC 58.766 39.130 0.00 0.00 37.51 3.32
454 679 3.813724 GTGAAGTTGAACACCTACCCTTC 59.186 47.826 0.00 0.00 0.00 3.46
566 791 7.936847 TGGTTGTGACTCAGAAACAAATATAGT 59.063 33.333 4.20 0.00 31.49 2.12
567 792 8.784043 GGTTGTGACTCAGAAACAAATATAGTT 58.216 33.333 0.00 0.00 35.70 2.24
586 811 4.469657 AGTTTCACTTTCCATTACTGCCA 58.530 39.130 0.00 0.00 0.00 4.92
601 826 7.649306 CCATTACTGCCAGTATTATTTGAAAGC 59.351 37.037 5.21 0.00 29.64 3.51
602 827 5.582689 ACTGCCAGTATTATTTGAAAGCC 57.417 39.130 0.00 0.00 0.00 4.35
603 828 5.264395 ACTGCCAGTATTATTTGAAAGCCT 58.736 37.500 0.00 0.00 0.00 4.58
604 829 6.423182 ACTGCCAGTATTATTTGAAAGCCTA 58.577 36.000 0.00 0.00 0.00 3.93
756 1065 9.090103 ACTAGTATGTTCTAGCAATAGCCATTA 57.910 33.333 0.00 0.00 43.56 1.90
925 1234 9.239002 CTCTTATTAATAGACACTTCTGGTTCG 57.761 37.037 0.00 0.00 32.75 3.95
931 1240 2.062519 GACACTTCTGGTTCGCTCTTC 58.937 52.381 0.00 0.00 0.00 2.87
1041 1351 3.489229 GCGAAGTTCTGAAGGCTGTTTTT 60.489 43.478 0.56 0.00 0.00 1.94
1587 1897 7.289310 TGGCATATGAATATCTCAGGTTTTCA 58.711 34.615 6.97 0.00 37.52 2.69
1620 1930 2.015456 TCATATCAGACATCCGGGCT 57.985 50.000 0.00 0.00 0.00 5.19
1629 1939 2.505982 ATCCGGGCTTGGATGTCG 59.494 61.111 0.00 0.00 47.00 4.35
1788 2099 3.228188 TGTGATTTGAGCCTTTGAGGT 57.772 42.857 0.00 0.00 37.80 3.85
1806 2117 9.994432 CTTTGAGGTATGTAAAGAATGTTCATC 57.006 33.333 0.00 0.00 34.23 2.92
1838 2149 7.986562 TGATCATCTACTGTTGTAGTACTGAC 58.013 38.462 5.39 2.38 44.74 3.51
1856 2167 9.429359 AGTACTGACATATATGCTTTAAGATGC 57.571 33.333 12.79 0.00 0.00 3.91
1889 2200 1.139520 GATGTGCGCCCATTGGTTC 59.860 57.895 6.86 0.00 0.00 3.62
1927 2238 8.627403 CATGATTTGGTATTGACTGATTTAGCT 58.373 33.333 0.00 0.00 0.00 3.32
2004 2315 7.221452 GGATAATTGCTTGTGCTAAATCAACAG 59.779 37.037 0.00 0.00 40.48 3.16
2020 2332 5.029807 TCAACAGCATTAATATGGGTCGA 57.970 39.130 5.19 0.00 32.15 4.20
2028 2340 4.682778 TTAATATGGGTCGAAGGGAGTG 57.317 45.455 0.00 0.00 0.00 3.51
2054 2367 4.617253 ATATTAGCCCGCTATTGTGTGA 57.383 40.909 0.00 0.00 0.00 3.58
2089 2404 6.724694 TCATTGGTGCATTCAAATTTTAGC 57.275 33.333 9.04 0.00 0.00 3.09
2090 2405 5.348179 TCATTGGTGCATTCAAATTTTAGCG 59.652 36.000 9.04 0.00 0.00 4.26
2163 2479 9.936759 AAGGATTTCTAGCTTAGTATATTGCTC 57.063 33.333 0.00 0.00 33.80 4.26
2170 2486 9.355916 TCTAGCTTAGTATATTGCTCTTTCTCA 57.644 33.333 0.00 0.00 33.80 3.27
2194 2510 2.124996 TTGGTGGAGAGGGGAGGG 59.875 66.667 0.00 0.00 0.00 4.30
2301 2617 2.048444 ATGAAGCGTGCTCCATCAAT 57.952 45.000 0.00 0.00 0.00 2.57
2318 2634 1.608590 CAATTTTGGGAGTGTGCGAGT 59.391 47.619 0.00 0.00 0.00 4.18
2412 2730 9.019764 CACATTTGGATTAAACGTTTCATATCC 57.980 33.333 26.81 26.81 33.71 2.59
2488 2806 5.461737 ACAAAACAATAAGCACATTCAACCG 59.538 36.000 0.00 0.00 0.00 4.44
2489 2807 5.446143 AAACAATAAGCACATTCAACCGA 57.554 34.783 0.00 0.00 0.00 4.69
2589 3476 2.327343 TGTGCTCAACGCTCCATGC 61.327 57.895 0.00 0.00 40.11 4.06
2613 3500 2.407846 CTAGGACGCATGATCGCCGT 62.408 60.000 0.00 5.03 37.99 5.68
2648 3535 9.125026 ACTCCCAAAATGATATTGACATTAGAC 57.875 33.333 0.00 0.00 37.04 2.59
2654 3541 7.458409 AATGATATTGACATTAGACCCATGC 57.542 36.000 0.00 0.00 36.40 4.06
2655 3542 5.316167 TGATATTGACATTAGACCCATGCC 58.684 41.667 0.00 0.00 0.00 4.40
2682 3569 6.299141 TGGGCTCCAATATCAATAGTTTCTC 58.701 40.000 0.00 0.00 0.00 2.87
2685 3572 6.299141 GCTCCAATATCAATAGTTTCTCCCA 58.701 40.000 0.00 0.00 0.00 4.37
2686 3573 6.429385 GCTCCAATATCAATAGTTTCTCCCAG 59.571 42.308 0.00 0.00 0.00 4.45
2696 3583 3.185455 AGTTTCTCCCAGGCTATCTTGT 58.815 45.455 0.00 0.00 0.00 3.16
2713 3600 3.004944 TCTTGTTTTGCATTAACCGGTCC 59.995 43.478 8.04 0.00 0.00 4.46
2734 3621 2.331194 TCGTCAAGTTTAAGCCTACGC 58.669 47.619 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.755266 AACCTACGTATGATTGCTCCTT 57.245 40.909 4.77 0.00 0.00 3.36
1 2 4.161565 TGAAACCTACGTATGATTGCTCCT 59.838 41.667 4.77 0.00 0.00 3.69
4 5 7.391148 AAAATGAAACCTACGTATGATTGCT 57.609 32.000 4.77 0.00 0.00 3.91
5 6 7.753132 TGAAAAATGAAACCTACGTATGATTGC 59.247 33.333 4.77 0.00 0.00 3.56
6 7 9.787532 ATGAAAAATGAAACCTACGTATGATTG 57.212 29.630 4.77 0.00 0.00 2.67
7 8 9.787532 CATGAAAAATGAAACCTACGTATGATT 57.212 29.630 4.77 0.00 0.00 2.57
8 9 8.956426 ACATGAAAAATGAAACCTACGTATGAT 58.044 29.630 0.00 0.00 0.00 2.45
9 10 8.330466 ACATGAAAAATGAAACCTACGTATGA 57.670 30.769 0.00 0.00 0.00 2.15
10 11 8.964420 AACATGAAAAATGAAACCTACGTATG 57.036 30.769 0.00 0.00 0.00 2.39
11 12 9.974980 AAAACATGAAAAATGAAACCTACGTAT 57.025 25.926 0.00 0.00 0.00 3.06
13 14 7.223777 CCAAAACATGAAAAATGAAACCTACGT 59.776 33.333 0.00 0.00 0.00 3.57
14 15 7.307101 CCCAAAACATGAAAAATGAAACCTACG 60.307 37.037 0.00 0.00 0.00 3.51
56 57 7.162082 AGTTCTAGCTGTACAAGTTTATGCTT 58.838 34.615 8.58 0.00 0.00 3.91
80 81 8.023706 ACTGTATACACGACATGAGCATAATAG 58.976 37.037 0.08 0.00 0.00 1.73
85 86 4.655762 ACTGTATACACGACATGAGCAT 57.344 40.909 0.08 0.00 0.00 3.79
202 213 8.553153 TGACACCCCAACTCTTTATTGATAATA 58.447 33.333 0.00 0.00 0.00 0.98
259 270 2.975732 TCTGCAGTCTGGCATAAGAG 57.024 50.000 14.67 0.00 43.97 2.85
416 641 1.327303 TCACAGCAAAACATGGTCCC 58.673 50.000 0.00 0.00 37.77 4.46
445 670 0.625849 ATGGTGCCTTGAAGGGTAGG 59.374 55.000 13.99 0.00 35.37 3.18
454 679 2.372264 AGCATTCACTATGGTGCCTTG 58.628 47.619 3.97 3.28 43.11 3.61
566 791 4.469657 ACTGGCAGTAATGGAAAGTGAAA 58.530 39.130 20.61 0.00 0.00 2.69
567 792 4.098914 ACTGGCAGTAATGGAAAGTGAA 57.901 40.909 20.61 0.00 0.00 3.18
568 793 3.788227 ACTGGCAGTAATGGAAAGTGA 57.212 42.857 20.61 0.00 0.00 3.41
569 794 7.807977 ATAATACTGGCAGTAATGGAAAGTG 57.192 36.000 29.35 0.00 33.89 3.16
570 795 8.686334 CAAATAATACTGGCAGTAATGGAAAGT 58.314 33.333 29.35 10.25 33.89 2.66
571 796 8.902806 TCAAATAATACTGGCAGTAATGGAAAG 58.097 33.333 29.35 16.76 33.89 2.62
659 888 1.073763 TGATGTCTGTTGGAGTTGGGG 59.926 52.381 0.00 0.00 0.00 4.96
698 927 7.968014 AAAAATAGCTTCCATCTTCCAGATT 57.032 32.000 0.00 0.00 31.32 2.40
756 1065 4.404073 CCTAGACTAAGCAGAACATGGACT 59.596 45.833 0.00 0.00 0.00 3.85
912 1221 1.603172 CGAAGAGCGAACCAGAAGTGT 60.603 52.381 0.00 0.00 44.57 3.55
925 1234 2.080286 TCAGCTACAAACCGAAGAGC 57.920 50.000 0.00 0.00 0.00 4.09
931 1240 2.288825 TGGAGACTTCAGCTACAAACCG 60.289 50.000 0.00 0.00 0.00 4.44
1041 1351 5.208294 AGTCTTTACCATCCAGTAGAGGA 57.792 43.478 0.00 0.00 43.01 3.71
1227 1537 1.272807 TAGGTACAGGAAGGTGCACC 58.727 55.000 29.22 29.22 34.41 5.01
1560 1870 8.716674 AAAACCTGAGATATTCATATGCCAAT 57.283 30.769 0.00 0.00 34.68 3.16
1587 1897 3.189606 TGATATGAAAGGGTGTCTGGGT 58.810 45.455 0.00 0.00 0.00 4.51
1620 1930 2.293122 CAGGAAAAGCAACGACATCCAA 59.707 45.455 0.00 0.00 0.00 3.53
1775 2086 5.755409 TCTTTACATACCTCAAAGGCTCA 57.245 39.130 0.00 0.00 39.63 4.26
1806 2117 9.755804 ACTACAACAGTAGATGATCAACATATG 57.244 33.333 0.00 0.00 38.83 1.78
1856 2167 3.374745 GCACATCGCCATTTTATTCCAG 58.625 45.455 0.00 0.00 32.94 3.86
1889 2200 8.712363 CAATACCAAATCATGAACGGTATAGAG 58.288 37.037 23.75 16.68 41.08 2.43
1927 2238 1.872237 GCAGTCTTCAACACCGTGCTA 60.872 52.381 0.00 0.00 0.00 3.49
2004 2315 4.003648 CTCCCTTCGACCCATATTAATGC 58.996 47.826 0.00 0.00 0.00 3.56
2020 2332 5.338137 GCGGGCTAATATAATACACTCCCTT 60.338 44.000 0.00 0.00 0.00 3.95
2028 2340 7.762615 TCACACAATAGCGGGCTAATATAATAC 59.237 37.037 4.26 0.00 31.73 1.89
2054 2367 3.324268 TGCACCAATGAACAAATGATGGT 59.676 39.130 0.00 0.00 41.65 3.55
2102 2417 6.506500 AAAACAACAACAATGAAATGCCAA 57.493 29.167 0.00 0.00 0.00 4.52
2170 2486 1.355720 CCCCTCTCCACCAACTTTCAT 59.644 52.381 0.00 0.00 0.00 2.57
2176 2492 2.301738 CCCTCCCCTCTCCACCAAC 61.302 68.421 0.00 0.00 0.00 3.77
2194 2510 3.459063 ACTCCTAACGCTCCCGCC 61.459 66.667 0.00 0.00 38.22 6.13
2301 2617 0.878523 CGACTCGCACACTCCCAAAA 60.879 55.000 0.00 0.00 0.00 2.44
2318 2634 5.778862 TGTGACTCTGATTTTGTACATCGA 58.221 37.500 0.00 0.00 0.00 3.59
2373 2691 7.447374 AATCCAAATGTGTGAACGAATAGAA 57.553 32.000 0.00 0.00 0.00 2.10
2375 2693 9.061610 GTTTAATCCAAATGTGTGAACGAATAG 57.938 33.333 0.00 0.00 0.00 1.73
2376 2694 7.746916 CGTTTAATCCAAATGTGTGAACGAATA 59.253 33.333 0.00 0.00 0.00 1.75
2377 2695 6.580791 CGTTTAATCCAAATGTGTGAACGAAT 59.419 34.615 0.00 0.00 0.00 3.34
2412 2730 2.912967 GTGTGCATGATGCTTTCGAAAG 59.087 45.455 29.45 29.45 45.31 2.62
2472 2790 4.009675 ACATGTCGGTTGAATGTGCTTAT 58.990 39.130 0.00 0.00 33.37 1.73
2475 2793 1.896220 ACATGTCGGTTGAATGTGCT 58.104 45.000 0.00 0.00 33.37 4.40
2589 3476 1.403382 CGATCATGCGTCCTAGGATGG 60.403 57.143 28.51 18.35 39.88 3.51
2613 3500 1.265635 CATTTTGGGAGTTCACGCGAA 59.734 47.619 15.93 0.00 0.00 4.70
2661 3548 6.299141 TGGGAGAAACTATTGATATTGGAGC 58.701 40.000 0.00 0.00 0.00 4.70
2674 3561 4.362677 ACAAGATAGCCTGGGAGAAACTA 58.637 43.478 0.00 0.00 0.00 2.24
2682 3569 2.170166 TGCAAAACAAGATAGCCTGGG 58.830 47.619 0.00 0.00 0.00 4.45
2685 3572 5.393027 CGGTTAATGCAAAACAAGATAGCCT 60.393 40.000 14.94 0.00 0.00 4.58
2686 3573 4.798387 CGGTTAATGCAAAACAAGATAGCC 59.202 41.667 14.94 0.44 0.00 3.93
2696 3583 1.807742 CGAGGACCGGTTAATGCAAAA 59.192 47.619 9.42 0.00 33.91 2.44
2713 3600 2.344741 GCGTAGGCTTAAACTTGACGAG 59.655 50.000 6.39 0.00 35.83 4.18
2734 3621 1.361993 CGAGGAAGAGATGGAGGCG 59.638 63.158 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.