Multiple sequence alignment - TraesCS2D01G156800

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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 TraesCS2D01G156800 chr2D 100.000 3137 0 0 1 3137 100186859 100183723 0.000000e+00 5794
1 TraesCS2D01G156800 chr2A 94.604 3002 127 19 1 2989 99789746 99786767 0.000000e+00 4614
2 TraesCS2D01G156800 chr2A 100.000 158 0 0 2980 3137 99785865 99785708 3.060000e-75 292
3 TraesCS2D01G156800 chr2B 92.016 2668 137 38 1 2643 151905398 151902782 0.000000e+00 3677
4 TraesCS2D01G156800 chr2B 91.538 260 16 2 2641 2894 151899587 151899328 1.380000e-93 353
5 TraesCS2D01G156800 chr2B 93.427 213 13 1 2925 3137 151899330 151899119 6.530000e-82 315
6 TraesCS2D01G156800 chr4A 88.272 324 36 2 1200 1522 202222054 202221732 1.360000e-103 387


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 TraesCS2D01G156800 chr2D 100183723 100186859 3136 True 5794.000000 5794 100.000 1 3137 1 chr2D.!!$R1 3136
1 TraesCS2D01G156800 chr2A 99785708 99789746 4038 True 2453.000000 4614 97.302 1 3137 2 chr2A.!!$R1 3136
2 TraesCS2D01G156800 chr2B 151899119 151905398 6279 True 1448.333333 3677 92.327 1 3137 3 chr2B.!!$R1 3136

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
806 830 0.963355 GGCACCGTATGAAGGGCAAA 60.963 55.0 0.0 0.0 33.73 3.68 F
1701 1727 0.111061 AATCACCAGCTCCAACTGCA 59.889 50.0 0.0 0.0 36.29 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1889 0.979665 ACTGAGGTGACATGACAGGG 59.020 55.000 0.0 0.0 33.57 4.45 R
2791 6036 2.224185 TGATGTACACAAGGAACGCTGT 60.224 45.455 0.0 0.0 0.00 4.40 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
38 39 4.641989 ACAGTGTCTTTGACTTTGCTCATT 59.358 37.500 0.00 0.00 33.15 2.57
106 108 3.261897 CGAGGTTAGAGAATATGCCCCAT 59.738 47.826 0.00 0.00 0.00 4.00
112 114 2.157880 AGAGAATATGCCCCATCTCCCT 60.158 50.000 0.00 0.00 39.26 4.20
142 147 3.866582 CGCACCCATCTCTCCCCC 61.867 72.222 0.00 0.00 0.00 5.40
148 153 1.284841 CCCATCTCTCCCCCTGCTTT 61.285 60.000 0.00 0.00 0.00 3.51
151 156 1.341156 ATCTCTCCCCCTGCTTTCGG 61.341 60.000 0.00 0.00 0.00 4.30
183 188 8.342634 CCTTCGTGGGTATAACTTTGATTTATG 58.657 37.037 0.00 0.00 0.00 1.90
254 259 5.736813 ACGATACTACTGTGACTTCTCTCT 58.263 41.667 0.00 0.00 0.00 3.10
261 266 5.957842 ACTGTGACTTCTCTCTTCACTAG 57.042 43.478 2.90 0.00 40.34 2.57
313 318 1.664016 CGACAATGCTTGTGAGTTGGC 60.664 52.381 6.31 0.00 45.52 4.52
377 382 4.497473 TGCACTAGGGAAAATCAAAACG 57.503 40.909 0.00 0.00 0.00 3.60
404 409 2.736144 AGATGTTTACGACCAGCGAA 57.264 45.000 0.00 0.00 44.57 4.70
417 422 3.638484 ACCAGCGAAAATTGTTTGTAGC 58.362 40.909 0.00 0.00 0.00 3.58
463 468 6.540189 ACAACAATCTCATGCTAACCACTATC 59.460 38.462 0.00 0.00 0.00 2.08
475 480 7.398829 TGCTAACCACTATCCAAAGAAACATA 58.601 34.615 0.00 0.00 0.00 2.29
498 503 2.738846 GTGTCTACAGTTGCCACATCTG 59.261 50.000 4.52 4.52 37.26 2.90
504 524 3.225104 ACAGTTGCCACATCTGTTGATT 58.775 40.909 5.66 0.00 40.22 2.57
506 526 2.559668 AGTTGCCACATCTGTTGATTGG 59.440 45.455 0.00 0.00 35.69 3.16
507 527 2.557924 GTTGCCACATCTGTTGATTGGA 59.442 45.455 0.00 0.00 35.14 3.53
508 528 2.874014 TGCCACATCTGTTGATTGGAA 58.126 42.857 0.00 0.00 35.14 3.53
509 529 2.557924 TGCCACATCTGTTGATTGGAAC 59.442 45.455 0.00 0.00 35.14 3.62
510 530 2.094545 GCCACATCTGTTGATTGGAACC 60.095 50.000 0.00 0.00 35.14 3.62
511 531 3.156293 CCACATCTGTTGATTGGAACCA 58.844 45.455 0.00 0.00 35.14 3.67
512 532 3.765511 CCACATCTGTTGATTGGAACCAT 59.234 43.478 0.00 0.00 35.14 3.55
513 533 4.142315 CCACATCTGTTGATTGGAACCATC 60.142 45.833 0.00 0.00 35.14 3.51
514 534 4.460034 CACATCTGTTGATTGGAACCATCA 59.540 41.667 0.00 0.00 0.00 3.07
515 535 4.460382 ACATCTGTTGATTGGAACCATCAC 59.540 41.667 0.00 0.00 0.00 3.06
516 536 4.371624 TCTGTTGATTGGAACCATCACT 57.628 40.909 0.00 0.00 0.00 3.41
517 537 4.728772 TCTGTTGATTGGAACCATCACTT 58.271 39.130 0.00 0.00 0.00 3.16
518 538 4.761739 TCTGTTGATTGGAACCATCACTTC 59.238 41.667 0.00 0.00 0.00 3.01
519 539 4.728772 TGTTGATTGGAACCATCACTTCT 58.271 39.130 0.00 0.00 0.00 2.85
520 540 4.761739 TGTTGATTGGAACCATCACTTCTC 59.238 41.667 0.00 0.00 0.00 2.87
521 541 4.639078 TGATTGGAACCATCACTTCTCA 57.361 40.909 0.00 0.00 0.00 3.27
557 577 8.463607 TGATATATTCATTTATGGCATGCAGTG 58.536 33.333 21.36 5.96 0.00 3.66
569 589 1.002990 TGCAGTGTGGCATCCTCAG 60.003 57.895 0.00 0.00 39.25 3.35
581 601 2.159819 ATCCTCAGCGTGTCTTGCGT 62.160 55.000 0.00 0.00 37.44 5.24
584 604 3.716006 CAGCGTGTCTTGCGTGGG 61.716 66.667 0.00 0.00 37.44 4.61
610 630 5.301555 TGTGATTGACGAACCACAAGAATA 58.698 37.500 0.00 0.00 36.69 1.75
616 636 7.688478 TTGACGAACCACAAGAATATATACG 57.312 36.000 0.00 0.00 0.00 3.06
619 639 8.570488 TGACGAACCACAAGAATATATACGTAT 58.430 33.333 13.54 13.54 0.00 3.06
673 694 8.915654 GCAAAGTCAAAGTAATTGGTTTGATAG 58.084 33.333 15.92 9.90 42.91 2.08
735 756 5.932303 TGCTCTAGGTTGACTTTGAATACAC 59.068 40.000 0.00 0.00 0.00 2.90
751 772 5.408299 TGAATACACAGACACACATGTTAGC 59.592 40.000 0.00 0.00 39.95 3.09
754 775 4.956085 ACACAGACACACATGTTAGCTTA 58.044 39.130 0.00 0.00 39.95 3.09
806 830 0.963355 GGCACCGTATGAAGGGCAAA 60.963 55.000 0.00 0.00 33.73 3.68
834 858 5.869344 GCAAATTCCAAATTTCAGAGGTACC 59.131 40.000 2.73 2.73 0.00 3.34
836 860 7.093945 GCAAATTCCAAATTTCAGAGGTACCTA 60.094 37.037 16.29 0.00 0.00 3.08
850 874 5.958987 AGAGGTACCTAAGTGCAATAGTTCT 59.041 40.000 16.29 0.00 0.00 3.01
854 878 8.057623 AGGTACCTAAGTGCAATAGTTCTAGTA 58.942 37.037 14.41 0.00 0.00 1.82
1005 1031 1.895707 CATCTCCGGCCCAATGCTC 60.896 63.158 0.00 0.00 40.92 4.26
1332 1358 2.270257 CCAGTACGACACGGACCCA 61.270 63.158 2.83 0.00 42.35 4.51
1389 1415 1.188219 TCTCCAAGAGCCAGCTCGTT 61.188 55.000 13.70 6.31 46.90 3.85
1618 1644 1.079819 ACATCTGTCCCTGCGAACG 60.080 57.895 0.00 0.00 0.00 3.95
1687 1713 2.292794 TAGGCGCTCGGTGGAATCAC 62.293 60.000 7.64 0.00 42.91 3.06
1701 1727 0.111061 AATCACCAGCTCCAACTGCA 59.889 50.000 0.00 0.00 36.29 4.41
1726 1752 2.048603 GCTGTCCCTGCCACCATTC 61.049 63.158 0.00 0.00 0.00 2.67
1863 1889 1.149148 GTTCCGAGCCACTCAAGTTC 58.851 55.000 0.00 0.00 0.00 3.01
1866 1892 1.674057 CGAGCCACTCAAGTTCCCT 59.326 57.895 0.00 0.00 0.00 4.20
2074 2100 3.119101 AGTGTACTTGAAGCGGATCGAAT 60.119 43.478 0.00 0.00 0.00 3.34
2246 2273 5.457140 TCCACATTTTCTCGTGCATAAAAC 58.543 37.500 0.00 0.00 0.00 2.43
2523 2555 2.624316 ACTGCTTGTCATCAATTGCG 57.376 45.000 0.00 0.00 32.82 4.85
2604 2646 9.683069 AGTTTAACTTGTGTTTGATCATGATTC 57.317 29.630 10.14 4.08 37.59 2.52
2605 2647 9.462174 GTTTAACTTGTGTTTGATCATGATTCA 57.538 29.630 10.14 6.69 37.59 2.57
2607 2649 9.628746 TTAACTTGTGTTTGATCATGATTCATG 57.371 29.630 18.71 18.71 38.95 3.07
2608 2650 7.888424 AACTTGTGTTTGATCATGATTCATGA 58.112 30.769 26.93 26.93 42.93 3.07
2609 2651 8.528643 AACTTGTGTTTGATCATGATTCATGAT 58.471 29.630 32.38 32.38 46.58 2.45
2705 5944 2.043411 CGCGCCATTGCATTATGTTAC 58.957 47.619 0.00 0.00 37.32 2.50
2791 6036 5.748402 ACCATGCATTGTCATTCTAGAGAA 58.252 37.500 0.00 0.00 38.56 2.87
2807 6052 2.364324 AGAGAACAGCGTTCCTTGTGTA 59.636 45.455 14.85 0.00 0.00 2.90
2840 6085 6.399639 ACAGAAATTTACCCGTCATTTGTT 57.600 33.333 0.00 0.00 0.00 2.83
2903 6148 5.473504 GTGAAACACTGAAATGTAGGTCCAT 59.526 40.000 0.00 0.00 36.32 3.41
2906 6151 6.620877 AACACTGAAATGTAGGTCCATAGA 57.379 37.500 0.00 0.00 30.75 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.142600 GCAAAGTCAAAGACACTGTTCACT 60.143 41.667 0.00 0.00 34.60 3.41
18 19 6.892310 AAAAATGAGCAAAGTCAAAGACAC 57.108 33.333 0.00 0.00 34.60 3.67
59 60 4.579869 AGCATCCGTTTTAGACTGACAAT 58.420 39.130 0.00 0.00 0.00 2.71
70 71 2.467566 ACCTCGTTAGCATCCGTTTT 57.532 45.000 0.00 0.00 0.00 2.43
106 108 0.548031 GGGATGTGCATTCAGGGAGA 59.452 55.000 0.00 0.00 0.00 3.71
112 114 2.045708 GGTGCGGGATGTGCATTCA 61.046 57.895 0.00 0.00 45.34 2.57
142 147 0.449388 GAAGGCATGACCGAAAGCAG 59.551 55.000 0.00 0.00 46.52 4.24
148 153 2.264480 CCACGAAGGCATGACCGA 59.736 61.111 4.09 0.00 46.52 4.69
151 156 2.870411 GTTATACCCACGAAGGCATGAC 59.130 50.000 0.00 0.00 35.39 3.06
377 382 6.363473 GCTGGTCGTAAACATCTATTTATGC 58.637 40.000 0.00 0.00 33.04 3.14
393 398 2.098443 ACAAACAATTTTCGCTGGTCGT 59.902 40.909 0.00 0.00 39.67 4.34
404 409 5.061179 ACTAGTCACCGCTACAAACAATTT 58.939 37.500 0.00 0.00 0.00 1.82
417 422 2.559668 TCCACCAACTTACTAGTCACCG 59.440 50.000 0.00 0.00 31.99 4.94
447 452 5.692115 TCTTTGGATAGTGGTTAGCATGA 57.308 39.130 0.00 0.00 0.00 3.07
463 468 7.672983 ACTGTAGACACATATGTTTCTTTGG 57.327 36.000 25.33 17.70 39.95 3.28
475 480 2.928801 TGTGGCAACTGTAGACACAT 57.071 45.000 0.00 0.00 37.16 3.21
498 503 4.761739 TGAGAAGTGATGGTTCCAATCAAC 59.238 41.667 0.00 0.00 0.00 3.18
504 524 4.916041 AGATTGAGAAGTGATGGTTCCA 57.084 40.909 0.00 0.00 0.00 3.53
506 526 8.610896 CATTTCTAGATTGAGAAGTGATGGTTC 58.389 37.037 0.00 0.00 42.68 3.62
507 527 8.324306 TCATTTCTAGATTGAGAAGTGATGGTT 58.676 33.333 7.13 0.00 43.35 3.67
508 528 7.855375 TCATTTCTAGATTGAGAAGTGATGGT 58.145 34.615 7.13 0.00 43.35 3.55
540 560 2.816689 CCACACTGCATGCCATAAATG 58.183 47.619 16.68 6.80 0.00 2.32
555 575 2.046892 ACGCTGAGGATGCCACAC 60.047 61.111 0.00 0.00 0.00 3.82
557 577 2.046892 ACACGCTGAGGATGCCAC 60.047 61.111 0.00 0.00 0.00 5.01
569 589 2.325082 AATCCCACGCAAGACACGC 61.325 57.895 0.00 0.00 43.62 5.34
581 601 2.224646 TGGTTCGTCAATCACAATCCCA 60.225 45.455 0.00 0.00 0.00 4.37
673 694 8.417176 CACGAAACTGCAACATAATCTTAAAAC 58.583 33.333 0.00 0.00 0.00 2.43
735 756 9.891828 TTATTTTTAAGCTAACATGTGTGTCTG 57.108 29.630 0.00 0.00 37.67 3.51
806 830 5.993441 CCTCTGAAATTTGGAATTTGCAAGT 59.007 36.000 0.00 0.00 0.00 3.16
822 846 4.967084 TTGCACTTAGGTACCTCTGAAA 57.033 40.909 20.32 10.40 0.00 2.69
825 849 5.599999 ACTATTGCACTTAGGTACCTCTG 57.400 43.478 20.32 14.79 0.00 3.35
826 850 5.958987 AGAACTATTGCACTTAGGTACCTCT 59.041 40.000 20.32 0.74 0.00 3.69
834 858 9.856488 TCAGTTTACTAGAACTATTGCACTTAG 57.144 33.333 0.00 0.00 37.76 2.18
836 860 7.819900 CCTCAGTTTACTAGAACTATTGCACTT 59.180 37.037 0.00 0.00 37.76 3.16
918 944 0.909623 ATCGACGGGGACTGGATTTT 59.090 50.000 0.00 0.00 40.47 1.82
1032 1058 3.296709 GAAAGAGAGGGCGGCGACA 62.297 63.158 17.61 0.00 0.00 4.35
1077 1103 2.657066 GGTGAAGTCCCCGTCCTCC 61.657 68.421 0.00 0.00 0.00 4.30
1230 1256 1.303615 GTCCTCCTCCGTCCAGAGA 59.696 63.158 0.00 0.00 35.82 3.10
1332 1358 1.135373 CGGCGCATATCCTCGTAGAAT 60.135 52.381 10.83 0.00 34.09 2.40
1687 1713 2.433446 AGGTGCAGTTGGAGCTGG 59.567 61.111 4.52 0.00 42.54 4.85
1701 1727 4.341783 GCAGGGACAGCAGCAGGT 62.342 66.667 0.00 0.00 41.82 4.00
1726 1752 4.421515 CTGAGGGGGCTGCACCAG 62.422 72.222 24.50 7.92 42.05 4.00
1863 1889 0.979665 ACTGAGGTGACATGACAGGG 59.020 55.000 0.00 0.00 33.57 4.45
1866 1892 1.620323 CCTGACTGAGGTGACATGACA 59.380 52.381 0.00 0.00 37.02 3.58
2074 2100 1.993701 TTCACCTGGTCCTGCAGCAA 61.994 55.000 8.66 0.00 30.08 3.91
2225 2252 5.058008 GTCGTTTTATGCACGAGAAAATGTG 59.942 40.000 12.93 0.00 46.90 3.21
2246 2273 1.266718 CCAACCCAGTCAACAATGTCG 59.733 52.381 0.00 0.00 0.00 4.35
2502 2534 3.065786 CCGCAATTGATGACAAGCAGTAT 59.934 43.478 10.34 0.00 39.46 2.12
2523 2555 9.227777 GTTTACTATACCATAATTCCATGACCC 57.772 37.037 0.00 0.00 0.00 4.46
2604 2646 6.851609 TCACGGAAAATAAACAAGGATCATG 58.148 36.000 0.00 0.00 0.00 3.07
2605 2647 7.362920 CCTTCACGGAAAATAAACAAGGATCAT 60.363 37.037 0.00 0.00 32.37 2.45
2606 2648 6.072175 CCTTCACGGAAAATAAACAAGGATCA 60.072 38.462 0.00 0.00 32.37 2.92
2607 2649 6.322491 CCTTCACGGAAAATAAACAAGGATC 58.678 40.000 0.00 0.00 32.37 3.36
2608 2650 5.336451 GCCTTCACGGAAAATAAACAAGGAT 60.336 40.000 0.00 0.00 32.37 3.24
2609 2651 4.022676 GCCTTCACGGAAAATAAACAAGGA 60.023 41.667 0.00 0.00 32.37 3.36
2612 2654 4.580995 TCAGCCTTCACGGAAAATAAACAA 59.419 37.500 0.00 0.00 33.16 2.83
2724 5969 4.430007 TGTTCACATACGCTGACCTTATC 58.570 43.478 0.00 0.00 0.00 1.75
2791 6036 2.224185 TGATGTACACAAGGAACGCTGT 60.224 45.455 0.00 0.00 0.00 4.40
2807 6052 5.646360 CGGGTAAATTTCTGTAACCTGATGT 59.354 40.000 9.46 0.00 38.63 3.06
2903 6148 8.076781 CGCATTAACTTAGAAGCAGTAGATCTA 58.923 37.037 0.00 0.00 0.00 1.98
2906 6151 6.574350 ACGCATTAACTTAGAAGCAGTAGAT 58.426 36.000 0.00 0.00 0.00 1.98
2927 6172 6.598753 ATGGACAAATAATGTAGTGTACGC 57.401 37.500 0.00 0.00 44.12 4.42
2966 6211 3.290710 AGTTGTGCACCTTGATTGAAGT 58.709 40.909 15.69 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.