Multiple sequence alignment - TraesCS6D01G130600

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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 TraesCS6D01G130600 chr6D 100.000 2357 0 0 1 2357 97261985 97264341 0.000000e+00 4353
1 TraesCS6D01G130600 chr6A 92.426 1624 77 21 765 2357 116336148 116337756 0.000000e+00 2276
2 TraesCS6D01G130600 chr6A 86.047 387 41 6 161 540 116335050 116335430 1.010000e-108 403
3 TraesCS6D01G130600 chr6B 91.310 1611 82 32 765 2355 181471799 181473371 0.000000e+00 2146
4 TraesCS6D01G130600 chr6B 86.930 811 67 20 1 777 181469876 181470681 0.000000e+00 874
5 TraesCS6D01G130600 chr3B 93.681 364 20 1 1042 1405 739023592 739023232 2.060000e-150 542
6 TraesCS6D01G130600 chr7B 87.444 223 27 1 1111 1333 635065265 635065486 3.010000e-64 255
7 TraesCS6D01G130600 chr7B 86.547 223 29 1 1111 1333 635170858 635171079 6.510000e-61 244
8 TraesCS6D01G130600 chr7D 87.054 224 28 1 1110 1333 575149325 575149103 3.890000e-63 252
9 TraesCS6D01G130600 chr7D 86.697 218 28 1 1110 1327 575217797 575217581 8.420000e-60 241
10 TraesCS6D01G130600 chr7A 86.547 223 29 1 1111 1333 664873438 664873217 6.510000e-61 244
11 TraesCS6D01G130600 chr7A 87.143 210 23 4 1126 1333 664603389 664603596 3.920000e-58 235


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 TraesCS6D01G130600 chr6D 97261985 97264341 2356 False 4353.0 4353 100.0000 1 2357 1 chr6D.!!$F1 2356
1 TraesCS6D01G130600 chr6A 116335050 116337756 2706 False 1339.5 2276 89.2365 161 2357 2 chr6A.!!$F1 2196
2 TraesCS6D01G130600 chr6B 181469876 181473371 3495 False 1510.0 2146 89.1200 1 2355 2 chr6B.!!$F1 2354

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
74 75 0.462759 CAAGTCGATGGAGGGGAAGC 60.463 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 3625 1.025812 ACAATGTTTTGACCGCGGAA 58.974 45.0 35.9 17.5 36.64 4.3 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
25 26 6.880484 TGTATACAAGTACCCATACCAACAG 58.120 40.000 2.20 0.00 30.88 3.16
28 29 2.747446 CAAGTACCCATACCAACAGCAC 59.253 50.000 0.00 0.00 30.88 4.40
46 47 3.823873 AGCACGACCAATCAACCAAAATA 59.176 39.130 0.00 0.00 0.00 1.40
52 53 5.337578 ACCAATCAACCAAAATATTCGGG 57.662 39.130 8.35 6.37 0.00 5.14
55 56 2.104170 TCAACCAAAATATTCGGGCCC 58.896 47.619 13.57 13.57 0.00 5.80
58 59 2.107366 ACCAAAATATTCGGGCCCAAG 58.893 47.619 24.92 6.44 0.00 3.61
74 75 0.462759 CAAGTCGATGGAGGGGAAGC 60.463 60.000 0.00 0.00 0.00 3.86
94 95 4.134563 AGCGTATTTGGTTGAAACTCAGT 58.865 39.130 0.00 0.00 0.00 3.41
95 96 4.578928 AGCGTATTTGGTTGAAACTCAGTT 59.421 37.500 0.00 0.00 0.00 3.16
107 117 2.424684 ACTCAGTTCCCCCTCTCTTT 57.575 50.000 0.00 0.00 0.00 2.52
114 124 5.195960 TCAGTTCCCCCTCTCTTTATCTCTA 59.804 44.000 0.00 0.00 0.00 2.43
117 127 4.063125 TCCCCCTCTCTTTATCTCTACCT 58.937 47.826 0.00 0.00 0.00 3.08
126 136 8.887264 TCTCTTTATCTCTACCTGAAGTCTTT 57.113 34.615 0.00 0.00 0.00 2.52
133 143 5.010314 TCTCTACCTGAAGTCTTTTTACGCA 59.990 40.000 0.00 0.00 0.00 5.24
142 152 7.653647 TGAAGTCTTTTTACGCAAATTACCAT 58.346 30.769 0.00 0.00 0.00 3.55
165 175 8.859156 CCATTTTTCCATGTTAAGTTGATTACG 58.141 33.333 0.00 0.00 0.00 3.18
210 220 5.165961 TCTACCAACCCTCTCAAATCAAG 57.834 43.478 0.00 0.00 0.00 3.02
219 230 3.189287 CCTCTCAAATCAAGGTCAAACGG 59.811 47.826 0.00 0.00 0.00 4.44
227 238 3.292460 TCAAGGTCAAACGGGACAAAAT 58.708 40.909 6.50 0.00 39.59 1.82
313 324 3.425162 AGGTCCTCCTTTGATTCACAC 57.575 47.619 0.00 0.00 42.12 3.82
367 378 3.192001 CCCATTTGGTGAGAATGTCAGTG 59.808 47.826 0.00 0.00 35.13 3.66
378 389 1.722034 ATGTCAGTGTGGTGGACTCT 58.278 50.000 0.00 0.00 32.84 3.24
379 390 0.752658 TGTCAGTGTGGTGGACTCTG 59.247 55.000 0.00 0.00 44.35 3.35
389 400 5.473504 GTGTGGTGGACTCTGACATAATTTT 59.526 40.000 0.00 0.00 0.00 1.82
396 407 9.394477 GTGGACTCTGACATAATTTTAAAACAC 57.606 33.333 1.97 0.00 0.00 3.32
418 435 6.073222 ACACGGTAATTCTCATGTCTTTGAAC 60.073 38.462 0.00 0.00 0.00 3.18
447 464 8.025445 GTCACATGAGAAAAATGCAAATAGAGT 58.975 33.333 0.00 0.00 0.00 3.24
487 505 6.697455 TGATGCACGAGACTATGAAGAAATAC 59.303 38.462 0.00 0.00 0.00 1.89
527 545 2.654749 TTACTCACTGGAGACGCATG 57.345 50.000 0.00 0.00 44.26 4.06
619 1002 9.616156 TCACTTATTTACTGTCCAAAAACACTA 57.384 29.630 0.00 0.00 0.00 2.74
620 1003 9.659830 CACTTATTTACTGTCCAAAAACACTAC 57.340 33.333 0.00 0.00 0.00 2.73
664 1068 4.701956 AAACATCCCTCAAATTACAGCG 57.298 40.909 0.00 0.00 0.00 5.18
684 1090 1.743394 GGGTGTGCACAGTAATAAGGC 59.257 52.381 22.40 4.63 0.00 4.35
737 1269 5.419760 TGTATGAGCGTCTACATCTGTAC 57.580 43.478 0.00 0.00 0.00 2.90
739 1271 3.000684 TGAGCGTCTACATCTGTACCT 57.999 47.619 0.00 0.00 0.00 3.08
741 1273 3.128764 TGAGCGTCTACATCTGTACCTTG 59.871 47.826 0.00 0.00 0.00 3.61
745 1277 5.184479 AGCGTCTACATCTGTACCTTGTTAA 59.816 40.000 0.00 0.00 0.00 2.01
777 2439 9.914923 CAAAAATGTAGCCTTTCTGTTAAAAAC 57.085 29.630 0.00 0.00 0.00 2.43
901 2567 3.335729 CCCCCACCCAGTACCACC 61.336 72.222 0.00 0.00 0.00 4.61
1655 3352 1.988846 TGTGTGAGGGAGAGAGAGAGA 59.011 52.381 0.00 0.00 0.00 3.10
1676 3373 9.264719 GAGAGAGGTAGTAGTAGTATGAGTTTC 57.735 40.741 0.00 0.00 0.00 2.78
1795 3496 3.012959 ACATTGGTCTCCCTCCTTCTCTA 59.987 47.826 0.00 0.00 0.00 2.43
1810 3511 8.043710 CCTCCTTCTCTATGTATGTTTCAGTTT 58.956 37.037 0.00 0.00 0.00 2.66
1884 3589 7.636259 TCCTTGAAATTTTCACGCATTTTAG 57.364 32.000 11.30 4.19 39.87 1.85
1890 3595 8.349245 TGAAATTTTCACGCATTTTAGAGAAGA 58.651 29.630 7.74 0.00 34.08 2.87
1892 3597 9.696917 AAATTTTCACGCATTTTAGAGAAGATT 57.303 25.926 0.00 0.00 0.00 2.40
1915 3620 6.772770 TGTTCAGTTATTTGAAATCGACGA 57.227 33.333 0.00 0.00 38.69 4.20
1916 3621 6.586751 TGTTCAGTTATTTGAAATCGACGAC 58.413 36.000 0.00 0.00 38.69 4.34
1920 3625 1.722011 ATTTGAAATCGACGACGGCT 58.278 45.000 7.55 0.00 40.21 5.52
1922 3627 1.065358 TTGAAATCGACGACGGCTTC 58.935 50.000 7.55 10.64 40.21 3.86
1978 3683 2.462889 ACTGAATTGCACTGCGTTTTG 58.537 42.857 0.00 0.00 0.00 2.44
1989 3694 1.304134 GCGTTTTGGGAGGGGATGT 60.304 57.895 0.00 0.00 0.00 3.06
1997 3702 1.633432 TGGGAGGGGATGTGTTAACAG 59.367 52.381 8.98 0.00 40.39 3.16
2001 3706 0.683179 GGGGATGTGTTAACAGGGGC 60.683 60.000 8.98 0.00 40.39 5.80
2018 3723 2.749044 CGCAAGCTGTGATGGCCT 60.749 61.111 3.32 0.00 0.00 5.19
2020 3725 1.975407 GCAAGCTGTGATGGCCTGT 60.975 57.895 3.32 0.00 0.00 4.00
2067 3773 0.394352 CGGGCAAAGATAGCAAGGGT 60.394 55.000 0.00 0.00 0.00 4.34
2068 3774 1.106285 GGGCAAAGATAGCAAGGGTG 58.894 55.000 0.00 0.00 0.00 4.61
2079 3785 1.364901 CAAGGGTGCTGCTGGTTTG 59.635 57.895 0.00 0.00 0.00 2.93
2103 3809 6.595326 TGAAGCAGGATATATGCCGAATAAAG 59.405 38.462 8.41 0.00 44.97 1.85
2169 3875 4.932200 AGCACTCAAGCAGTACATTTAGAC 59.068 41.667 0.00 0.00 36.85 2.59
2189 3895 1.469251 CCATTTGCACAGCTGATCTGC 60.469 52.381 23.35 20.32 46.76 4.26
2219 3925 2.266554 GAGAACATCTTCAGCCAGACG 58.733 52.381 0.00 0.00 0.00 4.18
2245 3951 1.330234 TCAAGAAAATGCTGCAGCCA 58.670 45.000 34.64 22.77 41.18 4.75
2265 3971 3.379240 CAGGATATGAACTGCAGTCTCG 58.621 50.000 21.95 2.68 0.00 4.04
2300 4006 2.416747 GCTGTTCAGGAAAATTTGGCC 58.583 47.619 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.334960 GGTTGATTGGTCGTGCTGTTG 60.335 52.381 0.00 0.00 0.00 3.33
22 23 0.179032 TGGTTGATTGGTCGTGCTGT 60.179 50.000 0.00 0.00 0.00 4.40
25 26 2.500509 TTTTGGTTGATTGGTCGTGC 57.499 45.000 0.00 0.00 0.00 5.34
28 29 5.034152 CCGAATATTTTGGTTGATTGGTCG 58.966 41.667 0.00 0.00 0.00 4.79
46 47 1.153168 CATCGACTTGGGCCCGAAT 60.153 57.895 19.37 4.33 35.87 3.34
52 53 2.190578 CCCTCCATCGACTTGGGC 59.809 66.667 5.24 0.00 37.37 5.36
55 56 0.462759 GCTTCCCCTCCATCGACTTG 60.463 60.000 0.00 0.00 0.00 3.16
58 59 1.389609 TACGCTTCCCCTCCATCGAC 61.390 60.000 0.00 0.00 0.00 4.20
74 75 5.449304 GGAACTGAGTTTCAACCAAATACG 58.551 41.667 0.00 0.00 0.00 3.06
94 95 4.486529 AGGTAGAGATAAAGAGAGGGGGAA 59.513 45.833 0.00 0.00 0.00 3.97
95 96 4.063125 AGGTAGAGATAAAGAGAGGGGGA 58.937 47.826 0.00 0.00 0.00 4.81
107 117 7.094075 TGCGTAAAAAGACTTCAGGTAGAGATA 60.094 37.037 0.00 0.00 0.00 1.98
114 124 5.767816 ATTTGCGTAAAAAGACTTCAGGT 57.232 34.783 1.94 0.00 0.00 4.00
117 127 7.028926 TGGTAATTTGCGTAAAAAGACTTCA 57.971 32.000 1.94 0.00 0.00 3.02
126 136 7.657761 ACATGGAAAAATGGTAATTTGCGTAAA 59.342 29.630 0.00 0.00 36.11 2.01
130 140 6.479095 AACATGGAAAAATGGTAATTTGCG 57.521 33.333 0.00 0.00 36.11 4.85
142 152 9.239002 CAACGTAATCAACTTAACATGGAAAAA 57.761 29.630 0.00 0.00 0.00 1.94
165 175 7.433680 AGAATGTTTGGATTTCTAACACCAAC 58.566 34.615 0.00 0.00 42.11 3.77
210 220 3.446310 AACATTTTGTCCCGTTTGACC 57.554 42.857 0.00 0.00 34.25 4.02
227 238 8.268605 TGGCACACTAACATCCTAATTATAACA 58.731 33.333 0.00 0.00 0.00 2.41
313 324 4.168760 GCAATCCTTCATTTTCCTTGTCG 58.831 43.478 0.00 0.00 0.00 4.35
367 378 7.681939 TTAAAATTATGTCAGAGTCCACCAC 57.318 36.000 0.00 0.00 0.00 4.16
389 400 7.972832 AAGACATGAGAATTACCGTGTTTTA 57.027 32.000 0.00 0.00 33.14 1.52
396 407 6.480524 TGTTCAAAGACATGAGAATTACCG 57.519 37.500 0.00 0.00 0.00 4.02
404 415 5.739752 TGTGACTTGTTCAAAGACATGAG 57.260 39.130 0.00 0.00 35.39 2.90
418 435 6.831727 TTTGCATTTTTCTCATGTGACTTG 57.168 33.333 0.00 0.00 0.00 3.16
487 505 8.526218 AGTAATTCAATGCGACATCTATAGTG 57.474 34.615 0.00 0.58 0.00 2.74
630 1013 5.303333 TGAGGGATGTTTTTGGACCTAAAAC 59.697 40.000 27.32 27.32 42.80 2.43
631 1014 5.459505 TGAGGGATGTTTTTGGACCTAAAA 58.540 37.500 9.43 9.43 0.00 1.52
632 1015 5.068215 TGAGGGATGTTTTTGGACCTAAA 57.932 39.130 0.00 0.00 0.00 1.85
633 1016 4.733077 TGAGGGATGTTTTTGGACCTAA 57.267 40.909 0.00 0.00 0.00 2.69
634 1017 4.733077 TTGAGGGATGTTTTTGGACCTA 57.267 40.909 0.00 0.00 0.00 3.08
635 1018 3.611025 TTGAGGGATGTTTTTGGACCT 57.389 42.857 0.00 0.00 0.00 3.85
664 1068 1.743394 GCCTTATTACTGTGCACACCC 59.257 52.381 17.42 0.00 0.00 4.61
763 1295 6.312426 TGGTGCAATGTGTTTTTAACAGAAAG 59.688 34.615 0.00 0.00 43.10 2.62
777 2439 4.931002 CCTTTTATTCCTTGGTGCAATGTG 59.069 41.667 0.00 0.00 0.00 3.21
817 2479 2.297033 TCACTTTTCTGCCATTTCTGCC 59.703 45.455 0.00 0.00 0.00 4.85
818 2480 3.243501 TGTCACTTTTCTGCCATTTCTGC 60.244 43.478 0.00 0.00 0.00 4.26
819 2481 4.572985 TGTCACTTTTCTGCCATTTCTG 57.427 40.909 0.00 0.00 0.00 3.02
901 2567 0.248866 GTTTGTTTGCAGTGGACGGG 60.249 55.000 0.00 0.00 0.00 5.28
952 2627 3.790416 AAGCTGGGTTCTTGGCGCA 62.790 57.895 10.83 0.00 0.00 6.09
1383 3074 2.507992 CAGAGTTCTCCAGCGGCG 60.508 66.667 0.51 0.51 0.00 6.46
1418 3109 1.134491 CCGGGGGTAAATCTGTCAGAC 60.134 57.143 4.21 0.00 0.00 3.51
1452 3143 3.009026 TGCCACTGTATGTACATTGCAG 58.991 45.455 25.61 25.61 36.07 4.41
1611 3306 1.330521 ACGCACACACACACTGAAATC 59.669 47.619 0.00 0.00 0.00 2.17
1655 3352 7.348033 AGCAGAAACTCATACTACTACTACCT 58.652 38.462 0.00 0.00 0.00 3.08
1676 3373 3.356529 ACACCTCAAAATCCCTAGCAG 57.643 47.619 0.00 0.00 0.00 4.24
1759 3458 6.258947 GGAGACCAATGTAGTGCTAAAAGATC 59.741 42.308 0.00 0.00 0.00 2.75
1760 3459 6.116126 GGAGACCAATGTAGTGCTAAAAGAT 58.884 40.000 0.00 0.00 0.00 2.40
1761 3460 5.488341 GGAGACCAATGTAGTGCTAAAAGA 58.512 41.667 0.00 0.00 0.00 2.52
1864 3565 8.349245 TCTTCTCTAAAATGCGTGAAAATTTCA 58.651 29.630 4.03 4.03 37.33 2.69
1869 3570 7.648142 ACAATCTTCTCTAAAATGCGTGAAAA 58.352 30.769 0.00 0.00 0.00 2.29
1873 3574 6.602179 TGAACAATCTTCTCTAAAATGCGTG 58.398 36.000 0.00 0.00 0.00 5.34
1890 3595 7.744715 GTCGTCGATTTCAAATAACTGAACAAT 59.255 33.333 0.00 0.00 35.07 2.71
1892 3597 6.586751 GTCGTCGATTTCAAATAACTGAACA 58.413 36.000 0.00 0.00 35.07 3.18
1920 3625 1.025812 ACAATGTTTTGACCGCGGAA 58.974 45.000 35.90 17.50 36.64 4.30
1922 3627 2.690173 TAACAATGTTTTGACCGCGG 57.310 45.000 26.86 26.86 36.64 6.46
1927 3632 6.575162 ACCAGAGGATAACAATGTTTTGAC 57.425 37.500 3.17 0.00 36.64 3.18
1929 3634 6.980593 TGAACCAGAGGATAACAATGTTTTG 58.019 36.000 3.17 0.00 38.86 2.44
1930 3635 7.781324 ATGAACCAGAGGATAACAATGTTTT 57.219 32.000 3.17 0.00 0.00 2.43
1978 3683 1.064685 CCTGTTAACACATCCCCTCCC 60.065 57.143 3.59 0.00 30.39 4.30
1989 3694 2.265182 GCTTGCGCCCCTGTTAACA 61.265 57.895 4.18 8.28 0.00 2.41
1997 3702 3.818787 CATCACAGCTTGCGCCCC 61.819 66.667 4.18 0.00 36.60 5.80
2001 3706 2.749044 AGGCCATCACAGCTTGCG 60.749 61.111 5.01 0.00 0.00 4.85
2067 3773 4.256462 TGCTTCAAACCAGCAGCA 57.744 50.000 0.00 0.00 42.49 4.41
2079 3785 6.037610 CCTTTATTCGGCATATATCCTGCTTC 59.962 42.308 9.36 0.00 39.60 3.86
2103 3809 6.529220 AGTTGATATCTGCAGTATCCTTTCC 58.471 40.000 22.56 12.23 0.00 3.13
2169 3875 1.469251 GCAGATCAGCTGTGCAAATGG 60.469 52.381 19.68 3.09 46.62 3.16
2189 3895 5.576384 GCTGAAGATGTTCTCACTCTTACAG 59.424 44.000 4.03 0.00 33.38 2.74
2219 3925 5.163982 GCTGCAGCATTTTCTTGAATCTTTC 60.164 40.000 33.36 0.00 41.59 2.62
2245 3951 2.223923 GCGAGACTGCAGTTCATATCCT 60.224 50.000 22.65 11.41 34.15 3.24
2265 3971 2.282040 AGCCTGTGACAAGCCAGC 60.282 61.111 1.97 0.00 0.00 4.85
2300 4006 4.825546 AAGAACACTGCTGAAGATGTTG 57.174 40.909 7.91 0.00 33.24 3.33


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

AutoCloner maintained by Alex Coulton.