Multiple sequence alignment - TraesCS6D01G267800

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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 TraesCS6D01G267800 chr6D 100.000 2505 0 0 1 2505 377828339 377825835 0.000000e+00 4626.0
1 TraesCS6D01G267800 chr6B 93.703 1731 59 21 786 2505 564063213 564061522 0.000000e+00 2547.0
2 TraesCS6D01G267800 chr6B 88.268 537 50 5 167 692 564215176 564214642 4.550000e-177 630.0
3 TraesCS6D01G267800 chr6B 87.931 174 11 5 1 169 564215384 564215216 1.970000e-46 196.0
4 TraesCS6D01G267800 chr6B 96.364 55 2 0 691 745 564063262 564063208 9.540000e-15 91.6
5 TraesCS6D01G267800 chr6A 91.608 1692 87 22 167 1826 519220741 519219073 0.000000e+00 2287.0
6 TraesCS6D01G267800 chr6A 90.656 503 24 8 2003 2505 519217793 519217314 0.000000e+00 647.0
7 TraesCS6D01G267800 chr6A 90.184 163 11 2 1859 2017 519219071 519218910 9.080000e-50 207.0


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 TraesCS6D01G267800 chr6D 377825835 377828339 2504 True 4626.0 4626 100.0000 1 2505 1 chr6D.!!$R1 2504
1 TraesCS6D01G267800 chr6B 564061522 564063262 1740 True 1319.3 2547 95.0335 691 2505 2 chr6B.!!$R1 1814
2 TraesCS6D01G267800 chr6B 564214642 564215384 742 True 413.0 630 88.0995 1 692 2 chr6B.!!$R2 691
3 TraesCS6D01G267800 chr6A 519217314 519220741 3427 True 1047.0 2287 90.8160 167 2505 3 chr6A.!!$R1 2338

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
480 529 0.033011 ATCGACTCCACCACCTAGCT 60.033 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 1933 0.742281 CCTGAACATGAGGTGAGCCG 60.742 60.0 0.0 0.0 40.5 5.52 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
21 22 4.972514 CCTTCTTCCTCTTTATTGCCAC 57.027 45.455 0.00 0.00 0.00 5.01
22 23 3.696548 CCTTCTTCCTCTTTATTGCCACC 59.303 47.826 0.00 0.00 0.00 4.61
42 43 0.727398 GGCGTTCTCCCTTTTCATCG 59.273 55.000 0.00 0.00 0.00 3.84
91 97 1.766143 CGGCATCAGCTAAACCGCTC 61.766 60.000 4.04 0.00 38.41 5.03
100 106 3.305177 TAAACCGCTCGCTCCCACC 62.305 63.158 0.00 0.00 0.00 4.61
107 113 2.933287 TCGCTCCCACCACCCATT 60.933 61.111 0.00 0.00 0.00 3.16
111 117 3.188903 TCCCACCACCCATTGCCA 61.189 61.111 0.00 0.00 0.00 4.92
117 123 1.228521 CCACCCATTGCCAGTGTCA 60.229 57.895 0.00 0.00 0.00 3.58
121 127 0.108520 CCCATTGCCAGTGTCAATGC 60.109 55.000 19.11 1.53 45.63 3.56
153 159 0.537653 GTGTCTCTCCCTACCCTTGC 59.462 60.000 0.00 0.00 0.00 4.01
194 242 1.141053 AGTTTCGTCCTTGCCTTCACT 59.859 47.619 0.00 0.00 0.00 3.41
251 299 2.966732 GCCCTCCGTCCACCATCAA 61.967 63.158 0.00 0.00 0.00 2.57
266 314 2.412870 CATCAACTACGCCTCACAACA 58.587 47.619 0.00 0.00 0.00 3.33
277 325 1.609061 CCTCACAACAATCGCTCCACT 60.609 52.381 0.00 0.00 0.00 4.00
279 327 1.202639 TCACAACAATCGCTCCACTGT 60.203 47.619 0.00 0.00 0.00 3.55
280 328 1.195448 CACAACAATCGCTCCACTGTC 59.805 52.381 0.00 0.00 0.00 3.51
293 341 4.379143 CTGTCGCGTCGTCACCGA 62.379 66.667 5.77 0.00 41.73 4.69
311 359 0.390998 GACTCAGGCTCAGTGCTTCC 60.391 60.000 0.00 0.00 42.39 3.46
322 370 1.519455 GTGCTTCCTCATCCGTCCG 60.519 63.158 0.00 0.00 0.00 4.79
341 389 4.208686 CACCTCCTACGCCTCGCC 62.209 72.222 0.00 0.00 0.00 5.54
444 493 1.906574 ACTACTCCGAGGATGCCAAAA 59.093 47.619 0.00 0.00 0.00 2.44
480 529 0.033011 ATCGACTCCACCACCTAGCT 60.033 55.000 0.00 0.00 0.00 3.32
481 530 0.251653 TCGACTCCACCACCTAGCTT 60.252 55.000 0.00 0.00 0.00 3.74
504 553 2.283966 AGGACGCAGCTACCAGGT 60.284 61.111 0.00 0.00 0.00 4.00
560 614 2.361737 GCAAGCCCCCTCAAGGAC 60.362 66.667 0.00 0.00 38.24 3.85
565 619 2.993853 CCCCCTCAAGGACTGCTC 59.006 66.667 0.00 0.00 38.24 4.26
582 642 8.207545 AGGACTGCTCCTAATTTTACTTATGAG 58.792 37.037 0.00 0.00 46.16 2.90
588 648 6.601332 TCCTAATTTTACTTATGAGCAGGGG 58.399 40.000 0.00 0.00 0.00 4.79
669 732 2.296945 TTTGACAGCACTTGGCCCCT 62.297 55.000 0.00 0.00 46.50 4.79
787 851 5.812127 GCTGGGAAATGTGCTTAATTTTAGG 59.188 40.000 0.00 0.00 0.00 2.69
931 1010 2.549754 CCGAAGCGCTTCATATCCATTT 59.450 45.455 40.22 10.29 39.46 2.32
995 1074 1.600107 GCCACCCCGTCAAGACATA 59.400 57.895 0.72 0.00 0.00 2.29
1130 1212 6.898451 TTAATGTCGTCGCAAACAAATAAC 57.102 33.333 0.00 0.00 0.00 1.89
1159 1245 6.289834 TGATGCATTGAAACAAGAAAATGGT 58.710 32.000 0.00 0.00 31.97 3.55
1381 1467 2.590114 GGCCCAACACCTCGGTACT 61.590 63.158 0.00 0.00 0.00 2.73
1382 1468 1.079336 GCCCAACACCTCGGTACTC 60.079 63.158 0.00 0.00 0.00 2.59
1384 1470 0.974383 CCCAACACCTCGGTACTCTT 59.026 55.000 0.00 0.00 0.00 2.85
1385 1471 1.346722 CCCAACACCTCGGTACTCTTT 59.653 52.381 0.00 0.00 0.00 2.52
1386 1472 2.224450 CCCAACACCTCGGTACTCTTTT 60.224 50.000 0.00 0.00 0.00 2.27
1387 1473 3.064931 CCAACACCTCGGTACTCTTTTC 58.935 50.000 0.00 0.00 0.00 2.29
1388 1474 3.244112 CCAACACCTCGGTACTCTTTTCT 60.244 47.826 0.00 0.00 0.00 2.52
1389 1475 4.377897 CAACACCTCGGTACTCTTTTCTT 58.622 43.478 0.00 0.00 0.00 2.52
1390 1476 4.254402 ACACCTCGGTACTCTTTTCTTC 57.746 45.455 0.00 0.00 0.00 2.87
1391 1477 3.896272 ACACCTCGGTACTCTTTTCTTCT 59.104 43.478 0.00 0.00 0.00 2.85
1392 1478 4.344390 ACACCTCGGTACTCTTTTCTTCTT 59.656 41.667 0.00 0.00 0.00 2.52
1393 1479 4.924462 CACCTCGGTACTCTTTTCTTCTTC 59.076 45.833 0.00 0.00 0.00 2.87
1412 1498 8.147704 TCTTCTTCTTCTTCTTCTTCTTCTTCC 58.852 37.037 0.00 0.00 0.00 3.46
1527 1626 3.446873 GCTAGGACGAGGATGATGATGAT 59.553 47.826 0.00 0.00 0.00 2.45
1532 1631 3.504375 ACGAGGATGATGATGATGAGGA 58.496 45.455 0.00 0.00 0.00 3.71
1535 1634 4.095211 GAGGATGATGATGATGAGGAGGA 58.905 47.826 0.00 0.00 0.00 3.71
1536 1635 4.098155 AGGATGATGATGATGAGGAGGAG 58.902 47.826 0.00 0.00 0.00 3.69
1537 1636 3.198200 GGATGATGATGATGAGGAGGAGG 59.802 52.174 0.00 0.00 0.00 4.30
1696 1801 8.893219 ATGAGACGATGTTGATGTAATTATGT 57.107 30.769 0.00 0.00 0.00 2.29
1699 1804 8.893219 AGACGATGTTGATGTAATTATGTGAT 57.107 30.769 0.00 0.00 0.00 3.06
1706 1811 6.843069 TGATGTAATTATGTGATGGTCGTG 57.157 37.500 0.00 0.00 0.00 4.35
1826 1933 1.897398 CTCAGGTGCGTGCGTAAACC 61.897 60.000 5.52 5.52 0.00 3.27
1914 2021 1.451387 GCCCCGTTCGATGTGGAAT 60.451 57.895 0.00 0.00 0.00 3.01
1929 2036 1.598701 GGAATCTGCCCTGCACAACC 61.599 60.000 0.00 0.00 33.79 3.77
1945 2056 1.492176 CAACCACCAGATGATAGGGCT 59.508 52.381 0.00 0.00 0.00 5.19
1950 2061 4.141390 ACCACCAGATGATAGGGCTAAAAG 60.141 45.833 0.00 0.00 0.00 2.27
2039 3282 1.532505 CGCAGCTGTCCAATAACATGC 60.533 52.381 16.64 0.00 33.72 4.06
2052 3295 1.985473 AACATGCAAGTTCAGAGCCA 58.015 45.000 0.51 0.00 0.00 4.75
2130 3374 4.742167 CCACATTCATGTCTGTCTATCGTC 59.258 45.833 0.00 0.00 39.39 4.20
2137 3381 2.223272 TGTCTGTCTATCGTCATCACGC 60.223 50.000 0.00 0.00 46.28 5.34
2218 3462 0.733150 GTGACGAAATAAGGCAGGCC 59.267 55.000 0.97 0.97 0.00 5.19
2267 3511 0.600255 CGTAGACCGGGGCATTGATC 60.600 60.000 6.32 0.00 0.00 2.92
2282 3526 0.177836 TGATCACCACTATGGCCACG 59.822 55.000 8.16 4.61 42.67 4.94
2305 3549 0.250640 AGGACAGCCTGCAGAAACAG 60.251 55.000 17.39 3.73 44.90 3.16
2306 3550 0.536006 GGACAGCCTGCAGAAACAGT 60.536 55.000 17.39 7.20 35.83 3.55
2309 3553 1.900498 AGCCTGCAGAAACAGTGGC 60.900 57.895 17.39 8.43 35.83 5.01
2314 3558 2.270986 GCAGAAACAGTGGCCCCAG 61.271 63.158 0.00 0.00 0.00 4.45
2468 3712 2.283173 TCCAGAGCCTGCGACTCA 60.283 61.111 3.64 0.00 36.58 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.546714 AAAGGGAGAACGCCGGTGG 62.547 63.158 21.14 6.53 0.00 4.61
19 20 1.574702 GAAAAGGGAGAACGCCGGTG 61.575 60.000 14.93 14.93 0.00 4.94
20 21 1.302271 GAAAAGGGAGAACGCCGGT 60.302 57.895 1.90 0.00 0.00 5.28
21 22 0.676782 ATGAAAAGGGAGAACGCCGG 60.677 55.000 0.00 0.00 0.00 6.13
22 23 0.727398 GATGAAAAGGGAGAACGCCG 59.273 55.000 0.00 0.00 0.00 6.46
42 43 1.558383 GTTGACGCGCGGATATGTC 59.442 57.895 35.22 21.23 0.00 3.06
83 89 4.699522 GGTGGGAGCGAGCGGTTT 62.700 66.667 0.00 0.00 0.00 3.27
91 97 2.751436 CAATGGGTGGTGGGAGCG 60.751 66.667 0.00 0.00 0.00 5.03
100 106 1.067425 CATTGACACTGGCAATGGGTG 60.067 52.381 24.86 5.73 45.42 4.61
101 107 1.259609 CATTGACACTGGCAATGGGT 58.740 50.000 24.86 0.00 45.42 4.51
107 113 1.528776 TGCAGCATTGACACTGGCA 60.529 52.632 0.00 0.00 34.38 4.92
111 117 1.174712 GGTGGTGCAGCATTGACACT 61.175 55.000 23.18 0.00 34.16 3.55
117 123 2.360350 CCGAGGTGGTGCAGCATT 60.360 61.111 23.18 13.62 33.95 3.56
194 242 1.885388 CTGACAACGCCCGACACAA 60.885 57.895 0.00 0.00 0.00 3.33
216 264 1.161563 GGCGAAACACTGAACCCGAA 61.162 55.000 0.00 0.00 0.00 4.30
248 296 2.605837 TTGTTGTGAGGCGTAGTTGA 57.394 45.000 0.00 0.00 0.00 3.18
251 299 1.710013 CGATTGTTGTGAGGCGTAGT 58.290 50.000 0.00 0.00 0.00 2.73
311 359 3.432051 GAGGTGGCGGACGGATGAG 62.432 68.421 0.00 0.00 0.00 2.90
322 370 4.208686 CGAGGCGTAGGAGGTGGC 62.209 72.222 0.00 0.00 0.00 5.01
341 389 1.927174 CAAGAAGATGGAGTAACGGCG 59.073 52.381 4.80 4.80 0.00 6.46
348 396 0.909610 TCGGGCCAAGAAGATGGAGT 60.910 55.000 4.39 0.00 43.54 3.85
394 442 1.355210 CGAGCAAACACGCACCTTT 59.645 52.632 0.00 0.00 0.00 3.11
444 493 3.129287 GTCGATGGATCACATGCCTTTTT 59.871 43.478 0.00 0.00 40.72 1.94
462 511 0.251653 AAGCTAGGTGGTGGAGTCGA 60.252 55.000 0.00 0.00 0.00 4.20
480 529 1.508632 GTAGCTGCGTCCTGTTTGAA 58.491 50.000 0.00 0.00 0.00 2.69
481 530 0.320421 GGTAGCTGCGTCCTGTTTGA 60.320 55.000 0.00 0.00 0.00 2.69
508 557 4.373116 GTCACTGCTTCCGCCGGA 62.373 66.667 5.05 0.00 34.43 5.14
565 619 5.770162 CCCCCTGCTCATAAGTAAAATTAGG 59.230 44.000 0.00 0.00 0.00 2.69
582 642 2.808906 AGTGACTATTTTCCCCCTGC 57.191 50.000 0.00 0.00 0.00 4.85
741 804 7.417116 CCAGCGGATTTAGTTTACTCCTACTAA 60.417 40.741 0.00 0.00 35.62 2.24
745 808 4.100498 CCCAGCGGATTTAGTTTACTCCTA 59.900 45.833 0.00 0.00 0.00 2.94
746 809 3.118371 CCCAGCGGATTTAGTTTACTCCT 60.118 47.826 0.00 0.00 0.00 3.69
756 820 1.748493 GCACATTTCCCAGCGGATTTA 59.252 47.619 0.00 0.00 38.24 1.40
846 910 1.202627 GCAGGAGGAGAAGATCGCAAT 60.203 52.381 0.00 0.00 0.00 3.56
931 1010 3.761752 CGAGAGAAAATTTTGCCCCCTTA 59.238 43.478 8.47 0.00 0.00 2.69
991 1070 5.060506 TCAACTCACCGACATGTTTTATGT 58.939 37.500 0.00 0.00 34.52 2.29
995 1074 4.133820 TGATCAACTCACCGACATGTTTT 58.866 39.130 0.00 0.00 0.00 2.43
1130 1212 4.725359 TCTTGTTTCAATGCATCATCACG 58.275 39.130 0.00 0.00 0.00 4.35
1159 1245 3.706373 GGCCAGCCTCCGTCTGAA 61.706 66.667 0.00 0.00 33.54 3.02
1334 1420 4.517285 TGCTGTAGGATTGGTTCATCTTC 58.483 43.478 0.00 0.00 0.00 2.87
1381 1467 9.898152 AAGAAGAAGAAGAAGAAGAAGAAAAGA 57.102 29.630 0.00 0.00 0.00 2.52
1384 1470 9.898152 AAGAAGAAGAAGAAGAAGAAGAAGAAA 57.102 29.630 0.00 0.00 0.00 2.52
1385 1471 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1386 1472 8.147704 GGAAGAAGAAGAAGAAGAAGAAGAAGA 58.852 37.037 0.00 0.00 0.00 2.87
1387 1473 8.150296 AGGAAGAAGAAGAAGAAGAAGAAGAAG 58.850 37.037 0.00 0.00 0.00 2.85
1388 1474 8.028652 AGGAAGAAGAAGAAGAAGAAGAAGAA 57.971 34.615 0.00 0.00 0.00 2.52
1389 1475 7.256154 GGAGGAAGAAGAAGAAGAAGAAGAAGA 60.256 40.741 0.00 0.00 0.00 2.87
1390 1476 6.873605 GGAGGAAGAAGAAGAAGAAGAAGAAG 59.126 42.308 0.00 0.00 0.00 2.85
1391 1477 6.556874 AGGAGGAAGAAGAAGAAGAAGAAGAA 59.443 38.462 0.00 0.00 0.00 2.52
1392 1478 6.081356 AGGAGGAAGAAGAAGAAGAAGAAGA 58.919 40.000 0.00 0.00 0.00 2.87
1393 1479 6.358974 AGGAGGAAGAAGAAGAAGAAGAAG 57.641 41.667 0.00 0.00 0.00 2.85
1434 1533 5.479027 TGCAATATCAGATGGGAATGAATGG 59.521 40.000 0.00 0.00 0.00 3.16
1507 1606 4.666512 TCATCATCATCATCCTCGTCCTA 58.333 43.478 0.00 0.00 0.00 2.94
1527 1626 2.609339 CCGATCCCCTCCTCCTCA 59.391 66.667 0.00 0.00 0.00 3.86
1537 1636 4.222847 GACACTCCGCCCGATCCC 62.223 72.222 0.00 0.00 0.00 3.85
1578 1677 1.755008 GACACTCCCCTCTCCTCCG 60.755 68.421 0.00 0.00 0.00 4.63
1826 1933 0.742281 CCTGAACATGAGGTGAGCCG 60.742 60.000 0.00 0.00 40.50 5.52
1888 1995 3.833645 CGAACGGGGCATCTCGGA 61.834 66.667 0.00 0.00 0.00 4.55
1914 2021 2.203337 GTGGTTGTGCAGGGCAGA 60.203 61.111 0.00 0.00 40.08 4.26
1929 2036 5.041191 ACTTTTAGCCCTATCATCTGGTG 57.959 43.478 0.00 0.00 0.00 4.17
2039 3282 7.798596 ATCTATTTACATGGCTCTGAACTTG 57.201 36.000 0.00 0.00 0.00 3.16
2078 3321 3.370527 GGGTTTGAGCCTTGCTATGAGTA 60.371 47.826 0.00 0.00 39.88 2.59
2130 3374 2.355756 AGAAATGAATTCGGGCGTGATG 59.644 45.455 0.04 0.00 43.15 3.07
2137 3381 5.641209 CAGGCTATCTAGAAATGAATTCGGG 59.359 44.000 0.00 0.00 43.15 5.14
2267 3511 2.046411 TGCGTGGCCATAGTGGTG 60.046 61.111 9.72 0.00 40.46 4.17
2328 3572 2.856032 CAGAGTTCTGTTGCGCGG 59.144 61.111 8.83 0.00 39.09 6.46
2468 3712 1.194781 AGCTGACGGTGAAGGTGGAT 61.195 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.