Multiple sequence alignment - TraesCS1D01G246600

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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 TraesCS1D01G246600 chr1D 100.000 3653 0 0 1 3653 339115869 339112217 0.000000e+00 6746
1 TraesCS1D01G246600 chr1A 95.558 2859 88 7 802 3653 438701343 438698517 0.000000e+00 4540
2 TraesCS1D01G246600 chr1A 87.838 444 30 9 1 427 438702435 438701999 1.960000e-137 499
3 TraesCS1D01G246600 chr1B 96.045 1972 74 2 802 2770 453883085 453881115 0.000000e+00 3206
4 TraesCS1D01G246600 chr1B 95.652 1035 33 6 2622 3653 453880856 453879831 0.000000e+00 1652
5 TraesCS1D01G246600 chr1B 87.363 728 55 20 64 767 453884482 453883768 0.000000e+00 800
6 TraesCS1D01G246600 chr1B 92.105 76 5 1 2754 2828 453880938 453880863 4.990000e-19 106
7 TraesCS1D01G246600 chr2D 75.955 445 80 22 3226 3653 318329100 318329534 1.720000e-48 204


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 TraesCS1D01G246600 chr1D 339112217 339115869 3652 True 6746.0 6746 100.00000 1 3653 1 chr1D.!!$R1 3652
1 TraesCS1D01G246600 chr1A 438698517 438702435 3918 True 2519.5 4540 91.69800 1 3653 2 chr1A.!!$R1 3652
2 TraesCS1D01G246600 chr1B 453879831 453884482 4651 True 1441.0 3206 92.79125 64 3653 4 chr1B.!!$R1 3589

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
868 1652 0.040336 TCTTCTGTCTCACGTCACGC 60.04 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2860 4050 0.391528 GGGCAAATGGGTGCATCAAC 60.392 55.0 0.0 0.0 46.81 3.18 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
29 30 5.869888 GCCTTTACCTTCTATATCATGTCCG 59.130 44.000 0.00 0.00 0.00 4.79
60 61 7.367285 TGTTGGTATTTGCTAATCAACTTCAC 58.633 34.615 18.85 4.04 33.19 3.18
82 83 3.282021 GCCATCCTCATTAACTTGCTCA 58.718 45.455 0.00 0.00 0.00 4.26
84 85 4.261489 GCCATCCTCATTAACTTGCTCATG 60.261 45.833 0.00 0.00 0.00 3.07
98 99 1.990563 GCTCATGCATGCAAGAACAAC 59.009 47.619 26.68 11.30 39.41 3.32
135 137 7.565029 TCTTCATTCATCTCATACCCTAAGTCA 59.435 37.037 0.00 0.00 0.00 3.41
153 156 0.464373 CACCCCCACATCTCCAATCG 60.464 60.000 0.00 0.00 0.00 3.34
174 177 6.235231 TCGATAGAAAAGGGCTATGTTTCT 57.765 37.500 3.63 3.63 46.15 2.52
220 227 6.299023 TGTGCCATCAATTATATGAACGAC 57.701 37.500 0.00 0.00 32.06 4.34
238 245 2.111384 GACTACTCCCAGATCCAGCAA 58.889 52.381 0.00 0.00 0.00 3.91
281 290 4.918583 GCTCCGTATAGAAGCAATGTCTAC 59.081 45.833 0.00 0.00 30.52 2.59
340 349 3.424703 ACTTTTAGAGCACATGCCACAT 58.575 40.909 0.00 0.00 43.38 3.21
415 436 4.037923 ACAAAAGGCTAATCACAGTGTTGG 59.962 41.667 0.00 0.00 0.00 3.77
441 561 6.211384 ACACATTACTATCGATGATGGATGGA 59.789 38.462 8.54 0.00 0.00 3.41
442 562 7.093156 ACACATTACTATCGATGATGGATGGAT 60.093 37.037 8.54 0.00 34.21 3.41
443 563 8.416329 CACATTACTATCGATGATGGATGGATA 58.584 37.037 8.54 0.00 32.24 2.59
444 564 8.981659 ACATTACTATCGATGATGGATGGATAA 58.018 33.333 8.54 3.93 32.95 1.75
445 565 9.822185 CATTACTATCGATGATGGATGGATAAA 57.178 33.333 8.54 0.69 32.95 1.40
469 590 9.505995 AAAACAACATTTTGCAAGAATCAAATC 57.494 25.926 0.00 0.00 36.00 2.17
501 622 7.415086 ACATTGTAAATGTACCCCCTCATTTA 58.585 34.615 3.84 0.00 42.06 1.40
774 900 8.761575 TCTTCCTATTTGTTTTTGAATCATGC 57.238 30.769 0.00 0.00 0.00 4.06
789 1573 0.392193 CATGCGAGTCAAAGAGGCCT 60.392 55.000 3.86 3.86 0.00 5.19
790 1574 1.134699 CATGCGAGTCAAAGAGGCCTA 60.135 52.381 4.42 0.00 0.00 3.93
791 1575 0.532573 TGCGAGTCAAAGAGGCCTAG 59.467 55.000 4.42 0.00 0.00 3.02
792 1576 0.808060 GCGAGTCAAAGAGGCCTAGC 60.808 60.000 4.42 0.00 0.00 3.42
823 1607 8.905702 CCAATATCGTTTCTGAAAAGAAGTTTG 58.094 33.333 19.70 19.59 32.82 2.93
868 1652 0.040336 TCTTCTGTCTCACGTCACGC 60.040 55.000 0.00 0.00 0.00 5.34
871 1655 1.730902 CTGTCTCACGTCACGCCAG 60.731 63.158 0.00 0.00 0.00 4.85
873 1657 1.007734 GTCTCACGTCACGCCAGAA 60.008 57.895 0.00 0.00 0.00 3.02
1027 1814 0.898320 CCTCACTCGTCACATTCCCT 59.102 55.000 0.00 0.00 0.00 4.20
1065 1852 1.684049 CCTCTCCTCCGCTCACCTT 60.684 63.158 0.00 0.00 0.00 3.50
1125 1912 4.200283 GAGCTCTCCGACCAGCCG 62.200 72.222 6.43 0.00 36.17 5.52
1391 2178 2.668550 GGCCTTGGACGGTGTCAC 60.669 66.667 0.00 0.00 33.68 3.67
1444 2231 4.015406 TGTACGCCTGCCACCTGG 62.015 66.667 0.00 0.00 38.53 4.45
1645 2432 0.458260 ACCTATCATGCACGCGTACA 59.542 50.000 15.62 15.62 0.00 2.90
1731 2518 1.463444 CCAAGCACGGCTACTTACAAC 59.537 52.381 0.00 0.00 38.25 3.32
1851 2638 0.973632 ACAGCACTTACATGGACGGA 59.026 50.000 0.00 0.00 0.00 4.69
1855 2642 2.829720 AGCACTTACATGGACGGACTAA 59.170 45.455 0.00 0.00 0.00 2.24
1869 2656 3.215151 CGGACTAAGCAGATCTGGTAGA 58.785 50.000 26.71 16.71 40.87 2.59
2139 2926 3.718956 AGAAGGGCATAGCTCCAAATAGT 59.281 43.478 0.00 0.00 0.00 2.12
2779 3759 5.590530 TTTCCAGTTGCTGTTTATGTTGT 57.409 34.783 0.00 0.00 0.00 3.32
2783 3764 6.039616 TCCAGTTGCTGTTTATGTTGTTTTC 58.960 36.000 0.00 0.00 0.00 2.29
2787 3768 9.081997 CAGTTGCTGTTTATGTTGTTTTCTTTA 57.918 29.630 0.00 0.00 0.00 1.85
2841 4031 6.263617 TGTTTCGTAAGTTTAGGGCTTGAAAT 59.736 34.615 0.00 0.00 39.48 2.17
2951 4141 4.009675 TCCTGTAGCTTGCATTTGTAAGG 58.990 43.478 9.88 0.00 38.05 2.69
3074 4267 7.351223 GCTCAAATCATAATCTTGCAGTAGTC 58.649 38.462 0.00 0.00 0.00 2.59
3075 4268 7.519649 GCTCAAATCATAATCTTGCAGTAGTCC 60.520 40.741 0.00 0.00 0.00 3.85
3093 4286 8.853345 CAGTAGTCCGAAATTTTCAATTTCATG 58.147 33.333 17.79 10.55 37.76 3.07
3256 4450 4.100808 GCATCCTACTGAACTCTCCTTCAT 59.899 45.833 0.00 0.00 29.71 2.57
3257 4451 5.738783 GCATCCTACTGAACTCTCCTTCATC 60.739 48.000 0.00 0.00 29.71 2.92
3294 4488 4.773323 ATTGAACTTGCTTTCTACTGGC 57.227 40.909 0.00 0.00 0.00 4.85
3353 4550 4.141298 GGGATTCTTCTCTTCATCCATGGT 60.141 45.833 12.58 0.00 37.52 3.55
3428 4625 6.071108 TCCTTCAGGTATTCTCTCAAACTCAG 60.071 42.308 0.00 0.00 36.34 3.35
3556 4753 7.503549 TGCTATGCTGAAGATCTTAATGAAGA 58.496 34.615 8.25 0.00 45.75 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.742012 ACTCCGGACATGATATAGAAGGT 58.258 43.478 0.00 0.00 0.00 3.50
29 30 6.919721 TGATTAGCAAATACCAACAAACTCC 58.080 36.000 0.00 0.00 0.00 3.85
60 61 2.289002 GAGCAAGTTAATGAGGATGGCG 59.711 50.000 0.00 0.00 0.00 5.69
82 83 3.132925 GGTTTGTTGTTCTTGCATGCAT 58.867 40.909 23.37 0.00 0.00 3.96
84 85 2.825205 AGGTTTGTTGTTCTTGCATGC 58.175 42.857 11.82 11.82 0.00 4.06
98 99 6.429078 TGAGATGAATGAAGAGTGAAGGTTTG 59.571 38.462 0.00 0.00 0.00 2.93
135 137 0.620410 TCGATTGGAGATGTGGGGGT 60.620 55.000 0.00 0.00 0.00 4.95
153 156 8.910351 ACATAGAAACATAGCCCTTTTCTATC 57.090 34.615 11.21 0.00 44.88 2.08
174 177 8.729756 CACATTTCACTTGTTCCATTAGACATA 58.270 33.333 0.00 0.00 0.00 2.29
220 227 3.634397 TTTTGCTGGATCTGGGAGTAG 57.366 47.619 0.00 0.00 0.00 2.57
281 290 6.625362 TCTAACTTCATGTTGTAGCTGAGAG 58.375 40.000 0.00 0.00 39.55 3.20
319 328 2.862541 TGTGGCATGTGCTCTAAAAGT 58.137 42.857 4.84 0.00 41.70 2.66
415 436 6.533012 CCATCCATCATCGATAGTAATGTGTC 59.467 42.308 0.00 0.00 37.40 3.67
443 563 9.505995 GATTTGATTCTTGCAAAATGTTGTTTT 57.494 25.926 0.00 0.00 38.57 2.43
444 564 7.851963 CGATTTGATTCTTGCAAAATGTTGTTT 59.148 29.630 0.00 0.00 38.57 2.83
445 565 7.011295 ACGATTTGATTCTTGCAAAATGTTGTT 59.989 29.630 0.00 0.00 38.57 2.83
469 590 5.220777 GGGGTACATTTACAATGTCATGACG 60.221 44.000 20.54 9.32 33.76 4.35
543 665 8.188531 TCCCGTAATCTTAGTCAAATTTTACG 57.811 34.615 0.00 0.00 37.45 3.18
685 808 9.787532 TTTCTTAAATCAAGCCTCATAAATTCG 57.212 29.630 0.00 0.00 33.94 3.34
756 882 6.215121 TGACTCGCATGATTCAAAAACAAAT 58.785 32.000 0.00 0.00 31.58 2.32
760 886 5.914635 TCTTTGACTCGCATGATTCAAAAAC 59.085 36.000 0.00 0.00 46.56 2.43
768 894 1.661341 GCCTCTTTGACTCGCATGAT 58.339 50.000 0.00 0.00 0.00 2.45
769 895 0.391661 GGCCTCTTTGACTCGCATGA 60.392 55.000 0.00 0.00 0.00 3.07
773 899 0.808060 GCTAGGCCTCTTTGACTCGC 60.808 60.000 9.68 0.00 0.00 5.03
774 900 0.179097 GGCTAGGCCTCTTTGACTCG 60.179 60.000 9.68 0.00 46.69 4.18
789 1573 6.474140 TCAGAAACGATATTGGTTAGGCTA 57.526 37.500 0.00 0.00 0.00 3.93
790 1574 5.353394 TCAGAAACGATATTGGTTAGGCT 57.647 39.130 0.00 0.00 0.00 4.58
791 1575 6.431198 TTTCAGAAACGATATTGGTTAGGC 57.569 37.500 0.00 0.00 0.00 3.93
792 1576 8.263940 TCTTTTCAGAAACGATATTGGTTAGG 57.736 34.615 0.00 0.00 0.00 2.69
793 1577 9.760660 CTTCTTTTCAGAAACGATATTGGTTAG 57.239 33.333 3.07 0.00 38.63 2.34
794 1578 9.280174 ACTTCTTTTCAGAAACGATATTGGTTA 57.720 29.630 3.07 0.00 38.63 2.85
795 1579 8.166422 ACTTCTTTTCAGAAACGATATTGGTT 57.834 30.769 3.07 0.00 38.63 3.67
796 1580 7.745620 ACTTCTTTTCAGAAACGATATTGGT 57.254 32.000 3.07 0.00 38.63 3.67
797 1581 8.905702 CAAACTTCTTTTCAGAAACGATATTGG 58.094 33.333 3.07 0.00 38.63 3.16
798 1582 8.905702 CCAAACTTCTTTTCAGAAACGATATTG 58.094 33.333 3.07 8.39 38.63 1.90
799 1583 8.082242 CCCAAACTTCTTTTCAGAAACGATATT 58.918 33.333 3.07 0.00 38.63 1.28
800 1584 7.593825 CCCAAACTTCTTTTCAGAAACGATAT 58.406 34.615 3.07 0.00 38.63 1.63
841 1625 2.663602 CGTGAGACAGAAGAACGGATTG 59.336 50.000 0.00 0.00 0.00 2.67
868 1652 2.438434 GGCGTGTGGGGATTCTGG 60.438 66.667 0.00 0.00 0.00 3.86
871 1655 3.912745 AACGGGCGTGTGGGGATTC 62.913 63.158 0.00 0.00 0.00 2.52
873 1657 4.715523 CAACGGGCGTGTGGGGAT 62.716 66.667 0.00 0.00 0.00 3.85
1065 1852 0.898789 GGAGGAAGTGGTGGTCTCGA 60.899 60.000 0.00 0.00 0.00 4.04
1323 2110 2.757508 CGGGAGGCAGCTGAGAGA 60.758 66.667 20.43 0.00 0.00 3.10
1353 2140 2.490217 GCTTCTAGCACGGCGAGA 59.510 61.111 16.62 2.08 41.89 4.04
1371 2158 1.303317 GACACCGTCCAAGGCCATT 60.303 57.895 5.01 0.00 33.69 3.16
1401 2188 4.722700 AGGACCGTGCATGCCACC 62.723 66.667 16.68 10.97 41.53 4.61
1473 2260 0.530650 CATTCTCCGTCATCCACCCG 60.531 60.000 0.00 0.00 0.00 5.28
1645 2432 1.123077 TGAATCATCCCAGTAGCGCT 58.877 50.000 17.26 17.26 0.00 5.92
1648 2435 3.672808 CCTCATGAATCATCCCAGTAGC 58.327 50.000 0.00 0.00 0.00 3.58
1651 2438 1.144503 GGCCTCATGAATCATCCCAGT 59.855 52.381 0.00 0.00 0.00 4.00
1731 2518 5.034554 TGCAAAGAGCTTTAATCAAGACG 57.965 39.130 0.00 0.00 45.94 4.18
1851 2638 9.815306 TTATCTAATCTACCAGATCTGCTTAGT 57.185 33.333 17.76 11.89 32.89 2.24
1855 2642 7.122650 GCTCTTATCTAATCTACCAGATCTGCT 59.877 40.741 17.76 6.48 32.89 4.24
1869 2656 6.017605 CGACCAATGCAAAGCTCTTATCTAAT 60.018 38.462 0.00 0.00 0.00 1.73
2669 3456 6.127730 ACAGAACTGGAATTTCTTTCGTGTTT 60.128 34.615 6.76 0.00 33.53 2.83
2751 3538 3.801114 AACAGCAACTGGAAAAAGGAC 57.199 42.857 0.00 0.00 35.51 3.85
2831 4021 7.554476 AGAACTTCTACTGATAATTTCAAGCCC 59.446 37.037 0.00 0.00 32.78 5.19
2841 4031 7.761704 GCATCAACTCAGAACTTCTACTGATAA 59.238 37.037 0.00 0.00 41.35 1.75
2860 4050 0.391528 GGGCAAATGGGTGCATCAAC 60.392 55.000 0.00 0.00 46.81 3.18
3074 4267 4.201705 CCGCCATGAAATTGAAAATTTCGG 60.202 41.667 16.52 14.03 40.02 4.30
3075 4268 4.724602 GCCGCCATGAAATTGAAAATTTCG 60.725 41.667 16.52 8.09 40.02 3.46
3239 4433 4.081972 GCACTGATGAAGGAGAGTTCAGTA 60.082 45.833 3.79 0.00 43.76 2.74
3294 4488 0.853224 GTCAATCGCGCATGAACACG 60.853 55.000 8.75 0.00 0.00 4.49
3353 4550 6.239217 AGGATGACATGTATGAGCTTGTTA 57.761 37.500 0.00 0.00 0.00 2.41
3428 4625 1.523758 ACGAGCAAATGACCCAACTC 58.476 50.000 0.00 0.00 0.00 3.01
3531 4728 7.503549 TCTTCATTAAGATCTTCAGCATAGCA 58.496 34.615 12.24 0.00 36.80 3.49
3556 4753 5.499004 TGCAGGTAGGATTGAAACTTACT 57.501 39.130 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.