Multiple sequence alignment - TraesCS6A01G261600

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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 TraesCS6A01G261600 chr6A 100.000 2742 0 0 1 2742 484856571 484859312 0.000000e+00 5064
1 TraesCS6A01G261600 chr6D 91.118 1610 67 32 1183 2742 344333007 344334590 0.000000e+00 2111
2 TraesCS6A01G261600 chr6D 87.309 654 39 22 545 1177 344332288 344332918 0.000000e+00 708
3 TraesCS6A01G261600 chr6D 90.217 552 26 13 1 552 344309155 344309678 0.000000e+00 695
4 TraesCS6A01G261600 chr6B 90.280 1574 78 31 1157 2671 520086342 520087899 0.000000e+00 1989
5 TraesCS6A01G261600 chr6B 88.350 824 42 21 392 1179 520085497 520086302 0.000000e+00 941
6 TraesCS6A01G261600 chr6B 88.000 400 34 3 1 400 519852708 519853093 6.920000e-126 460


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 TraesCS6A01G261600 chr6A 484856571 484859312 2741 False 5064.0 5064 100.0000 1 2742 1 chr6A.!!$F1 2741
1 TraesCS6A01G261600 chr6D 344332288 344334590 2302 False 1409.5 2111 89.2135 545 2742 2 chr6D.!!$F2 2197
2 TraesCS6A01G261600 chr6D 344309155 344309678 523 False 695.0 695 90.2170 1 552 1 chr6D.!!$F1 551
3 TraesCS6A01G261600 chr6B 520085497 520087899 2402 False 1465.0 1989 89.3150 392 2671 2 chr6B.!!$F2 2279

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
475 477 0.174162 ATTTGCAATGAGGAAGGCGC 59.826 50.0 0.0 0.0 0.0 6.53 F
1252 1394 0.107703 CCTGAATTGCCCGAGCTGTA 60.108 55.0 0.0 0.0 40.8 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1679 0.890996 GGCAACACAACAGAGGGGAG 60.891 60.000 0.0 0.0 0.0 4.30 R
2080 2284 1.591158 GTATGTATGTTCCGTGGCGTG 59.409 52.381 0.0 0.0 0.0 5.34 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
106 107 4.248842 CCCACACGACCTGCACCA 62.249 66.667 0.00 0.00 0.00 4.17
233 234 3.708220 GAGGAGGCGGCTTCGAGTG 62.708 68.421 14.76 0.00 35.61 3.51
234 235 4.070552 GGAGGCGGCTTCGAGTGT 62.071 66.667 14.76 0.00 35.61 3.55
312 313 4.205287 GCCATTGCGGGTTACGTA 57.795 55.556 0.00 0.00 46.52 3.57
313 314 1.717348 GCCATTGCGGGTTACGTAC 59.283 57.895 0.00 0.00 46.52 3.67
314 315 1.020333 GCCATTGCGGGTTACGTACA 61.020 55.000 0.00 0.00 46.52 2.90
315 316 1.440708 CCATTGCGGGTTACGTACAA 58.559 50.000 0.00 0.00 46.52 2.41
316 317 1.395608 CCATTGCGGGTTACGTACAAG 59.604 52.381 0.00 0.00 46.52 3.16
317 318 2.339418 CATTGCGGGTTACGTACAAGA 58.661 47.619 0.00 0.00 46.52 3.02
318 319 2.068837 TTGCGGGTTACGTACAAGAG 57.931 50.000 0.00 0.00 46.52 2.85
319 320 0.388907 TGCGGGTTACGTACAAGAGC 60.389 55.000 0.00 0.00 46.52 4.09
320 321 1.080435 GCGGGTTACGTACAAGAGCC 61.080 60.000 0.00 0.00 46.52 4.70
321 322 0.799534 CGGGTTACGTACAAGAGCCG 60.800 60.000 18.00 18.00 45.06 5.52
322 323 0.527565 GGGTTACGTACAAGAGCCGA 59.472 55.000 0.00 0.00 0.00 5.54
323 324 1.468736 GGGTTACGTACAAGAGCCGAG 60.469 57.143 0.00 0.00 0.00 4.63
324 325 1.468736 GGTTACGTACAAGAGCCGAGG 60.469 57.143 0.00 0.00 0.00 4.63
325 326 0.813184 TTACGTACAAGAGCCGAGGG 59.187 55.000 0.00 0.00 0.00 4.30
326 327 1.033746 TACGTACAAGAGCCGAGGGG 61.034 60.000 0.00 0.00 0.00 4.79
327 328 2.901042 GTACAAGAGCCGAGGGGG 59.099 66.667 0.00 0.00 39.58 5.40
358 359 2.356793 GTGCGCTGACTGCTGAGT 60.357 61.111 9.73 0.00 40.11 3.41
364 365 1.011451 GCTGACTGCTGAGTTCGGTC 61.011 60.000 0.00 0.00 39.61 4.79
448 450 2.284288 CGTAAACGAATCTCGAAAGCGG 60.284 50.000 2.59 0.00 43.74 5.52
464 466 1.344114 AGCGGAAACCACATTTGCAAT 59.656 42.857 0.00 0.00 38.49 3.56
470 472 4.502950 GGAAACCACATTTGCAATGAGGAA 60.503 41.667 22.33 1.33 38.45 3.36
472 474 2.564062 ACCACATTTGCAATGAGGAAGG 59.436 45.455 22.33 12.10 34.51 3.46
473 475 2.613691 CACATTTGCAATGAGGAAGGC 58.386 47.619 0.00 0.00 0.00 4.35
474 476 1.203052 ACATTTGCAATGAGGAAGGCG 59.797 47.619 0.00 0.00 0.00 5.52
475 477 0.174162 ATTTGCAATGAGGAAGGCGC 59.826 50.000 0.00 0.00 0.00 6.53
476 478 1.876497 TTTGCAATGAGGAAGGCGCC 61.876 55.000 21.89 21.89 0.00 6.53
477 479 2.439156 GCAATGAGGAAGGCGCCT 60.439 61.111 27.08 27.08 42.17 5.52
478 480 1.153168 GCAATGAGGAAGGCGCCTA 60.153 57.895 33.07 15.07 38.73 3.93
479 481 1.440145 GCAATGAGGAAGGCGCCTAC 61.440 60.000 33.07 25.58 38.73 3.18
480 482 1.144057 AATGAGGAAGGCGCCTACG 59.856 57.895 33.07 0.00 38.73 3.51
481 483 2.311688 AATGAGGAAGGCGCCTACGG 62.312 60.000 33.07 0.00 38.73 4.02
495 497 1.673168 CTACGGCCTACCTACGAACT 58.327 55.000 0.00 0.00 0.00 3.01
505 507 0.811616 CCTACGAACTGCCATGGAGC 60.812 60.000 18.40 0.45 0.00 4.70
543 545 0.530211 CGGAGATGGAGCAAGAGCAG 60.530 60.000 0.00 0.00 45.49 4.24
712 714 2.811317 GACGCAGGCCGAGACAAG 60.811 66.667 0.00 0.00 41.02 3.16
869 899 1.700955 TCTATCTAACCACCGGGAGC 58.299 55.000 6.32 0.00 38.05 4.70
1105 1141 2.656651 CTCGCCGCCTTCGATCAG 60.657 66.667 0.00 0.00 38.10 2.90
1117 1153 1.380524 TCGATCAGAACTCCTCCGTC 58.619 55.000 0.00 0.00 0.00 4.79
1152 1192 5.648526 TCGACATCCTATTATCAGCTACTCC 59.351 44.000 0.00 0.00 0.00 3.85
1177 1316 4.020839 CCAAAAGTCCTCCGTTACTCCTTA 60.021 45.833 0.00 0.00 0.00 2.69
1178 1317 5.338137 CCAAAAGTCCTCCGTTACTCCTTAT 60.338 44.000 0.00 0.00 0.00 1.73
1179 1318 6.127253 CCAAAAGTCCTCCGTTACTCCTTATA 60.127 42.308 0.00 0.00 0.00 0.98
1190 1329 9.304335 TCCGTTACTCCTTATATGTTATCATGA 57.696 33.333 0.00 0.00 35.70 3.07
1252 1394 0.107703 CCTGAATTGCCCGAGCTGTA 60.108 55.000 0.00 0.00 40.80 2.74
1430 1572 1.474017 CGATACGGCCTGTAAGTTCG 58.526 55.000 0.00 7.84 36.44 3.95
1435 1577 1.001633 ACGGCCTGTAAGTTCGTCAAT 59.998 47.619 0.00 0.00 36.26 2.57
1437 1579 3.255725 CGGCCTGTAAGTTCGTCAATAA 58.744 45.455 0.00 0.00 0.00 1.40
1438 1580 3.306166 CGGCCTGTAAGTTCGTCAATAAG 59.694 47.826 0.00 0.00 0.00 1.73
1488 1655 4.924305 ACGTGAGTGAGTTTTACAGGTA 57.076 40.909 0.00 0.00 46.97 3.08
1495 1662 8.020244 GTGAGTGAGTTTTACAGGTAGTAGTAC 58.980 40.741 0.00 0.00 33.43 2.73
1512 1679 0.168348 TACGTGAGCGACTCTGAAGC 59.832 55.000 0.00 0.00 42.00 3.86
1521 1695 0.823460 GACTCTGAAGCTCCCCTCTG 59.177 60.000 0.00 0.00 0.00 3.35
1717 1892 0.543749 ACCTGGAGACTGCTTATGCC 59.456 55.000 0.00 0.00 38.71 4.40
1795 1971 7.823745 ATGTCTGTAAAATTCTTGTCCTTGT 57.176 32.000 0.00 0.00 0.00 3.16
1796 1972 8.918202 ATGTCTGTAAAATTCTTGTCCTTGTA 57.082 30.769 0.00 0.00 0.00 2.41
1821 1997 1.651987 TAGCTCGTGCATAAGGTTGC 58.348 50.000 12.58 0.00 42.74 4.17
1833 2009 6.442513 GCATAAGGTTGCATTTAGTCTTCT 57.557 37.500 0.00 0.00 42.31 2.85
1859 2035 3.861840 ACAGACATCCCATAGTGTTTCG 58.138 45.455 0.00 0.00 0.00 3.46
1874 2050 1.987770 GTTTCGCCGTCGTATTCTTCA 59.012 47.619 0.00 0.00 36.96 3.02
1880 2056 2.743938 CCGTCGTATTCTTCATCTGGG 58.256 52.381 0.00 0.00 0.00 4.45
1883 2059 3.797256 CGTCGTATTCTTCATCTGGGAAC 59.203 47.826 0.00 0.00 0.00 3.62
1885 2061 5.044558 GTCGTATTCTTCATCTGGGAACTC 58.955 45.833 0.00 0.00 0.00 3.01
1906 2101 8.541133 AACTCTTACTAATCTTCTTGCAGTTC 57.459 34.615 0.00 0.00 0.00 3.01
1907 2102 6.809196 ACTCTTACTAATCTTCTTGCAGTTCG 59.191 38.462 0.00 0.00 0.00 3.95
1908 2103 6.100004 TCTTACTAATCTTCTTGCAGTTCGG 58.900 40.000 0.00 0.00 0.00 4.30
1933 2128 7.223971 GGAAACTGCAGATAATGTACGATACAA 59.776 37.037 23.35 0.00 42.76 2.41
2018 2216 8.303396 CGAGTTTCATCGTCTTTAATCAAATG 57.697 34.615 0.00 0.00 37.91 2.32
2080 2284 4.517285 TCTGCTAATCAGGTGGATGTTTC 58.483 43.478 0.00 0.00 43.06 2.78
2093 2297 0.816018 ATGTTTCACGCCACGGAACA 60.816 50.000 7.79 7.79 34.75 3.18
2100 2304 1.591158 CACGCCACGGAACATACATAC 59.409 52.381 0.00 0.00 0.00 2.39
2107 2311 5.756347 GCCACGGAACATACATACTCAAATA 59.244 40.000 0.00 0.00 0.00 1.40
2470 2677 8.156820 AGTTATGCAGAAGCCAACATATGTATA 58.843 33.333 9.21 0.00 41.13 1.47
2475 2683 9.348476 TGCAGAAGCCAACATATGTATAAAATA 57.652 29.630 9.21 0.00 41.13 1.40
2551 2761 4.391216 ACATGAGAAGAAAGTTGATCGCAG 59.609 41.667 0.00 0.00 0.00 5.18
2606 2816 5.997385 ACTTTAAAGCATTACACCACTTCG 58.003 37.500 15.24 0.00 0.00 3.79
2644 2854 4.917385 TCTTGGTGGTTACTATGCACAAT 58.083 39.130 0.00 0.00 0.00 2.71
2674 2884 6.049149 TCACACTGTCCAAAGAAAACTAGAG 58.951 40.000 0.00 0.00 0.00 2.43
2734 2944 4.947388 GGCCACATTTCTTACCTCATACAA 59.053 41.667 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
310 311 2.901042 CCCCCTCGGCTCTTGTAC 59.099 66.667 0.00 0.00 0.00 2.90
364 365 0.307760 GAACACTTTCACACTGGGCG 59.692 55.000 0.00 0.00 0.00 6.13
403 404 0.107081 TTCGTTCTTTCCGCCTTCCA 59.893 50.000 0.00 0.00 0.00 3.53
416 417 4.325472 AGATTCGTTTACGGACATTCGTTC 59.675 41.667 2.09 0.00 43.59 3.95
448 450 4.255833 TCCTCATTGCAAATGTGGTTTC 57.744 40.909 19.90 0.00 35.04 2.78
464 466 3.458163 CCGTAGGCGCCTTCCTCA 61.458 66.667 37.74 14.26 46.14 3.86
476 478 1.332997 CAGTTCGTAGGTAGGCCGTAG 59.667 57.143 0.00 0.00 40.50 3.51
477 479 1.382522 CAGTTCGTAGGTAGGCCGTA 58.617 55.000 0.00 0.00 40.50 4.02
478 480 1.941999 GCAGTTCGTAGGTAGGCCGT 61.942 60.000 0.00 0.00 40.50 5.68
479 481 1.226888 GCAGTTCGTAGGTAGGCCG 60.227 63.158 0.00 0.00 40.50 6.13
480 482 1.143401 GGCAGTTCGTAGGTAGGCC 59.857 63.158 0.00 0.00 0.00 5.19
481 483 0.464452 ATGGCAGTTCGTAGGTAGGC 59.536 55.000 0.00 0.00 0.00 3.93
482 484 1.202533 CCATGGCAGTTCGTAGGTAGG 60.203 57.143 0.00 0.00 0.00 3.18
483 485 1.754803 TCCATGGCAGTTCGTAGGTAG 59.245 52.381 6.96 0.00 0.00 3.18
484 486 1.754803 CTCCATGGCAGTTCGTAGGTA 59.245 52.381 6.96 0.00 0.00 3.08
485 487 0.537188 CTCCATGGCAGTTCGTAGGT 59.463 55.000 6.96 0.00 0.00 3.08
655 657 1.664965 GAGCGGCGATATGACACCC 60.665 63.158 12.98 0.00 0.00 4.61
704 706 0.105039 GTCATAGGGGCCTTGTCTCG 59.895 60.000 0.84 0.00 0.00 4.04
705 707 0.470341 GGTCATAGGGGCCTTGTCTC 59.530 60.000 0.84 0.00 0.00 3.36
707 709 1.146263 CGGTCATAGGGGCCTTGTC 59.854 63.158 0.84 0.00 0.00 3.18
708 710 3.043999 GCGGTCATAGGGGCCTTGT 62.044 63.158 0.84 0.00 0.00 3.16
709 711 2.203209 GCGGTCATAGGGGCCTTG 60.203 66.667 0.84 0.00 0.00 3.61
710 712 3.489513 GGCGGTCATAGGGGCCTT 61.490 66.667 0.84 0.00 42.29 4.35
712 714 4.256180 CTGGCGGTCATAGGGGCC 62.256 72.222 0.00 0.00 45.76 5.80
774 790 1.450312 GATCTGTGCACCTTCCCGG 60.450 63.158 15.69 0.00 39.35 5.73
786 802 5.760253 ACATTCACAAAAGAAGACGATCTGT 59.240 36.000 0.00 0.00 0.00 3.41
869 899 4.653888 AAAGGTCGTTGGCCCCGG 62.654 66.667 11.51 0.00 0.00 5.73
989 1025 1.069765 CCGTCCATGGGAGGAATCG 59.930 63.158 18.09 9.18 39.66 3.34
1105 1141 4.082136 ACATAAGAAGTGACGGAGGAGTTC 60.082 45.833 0.00 0.00 0.00 3.01
1117 1153 9.347934 GATAATAGGATGTCGACATAAGAAGTG 57.652 37.037 30.04 0.00 36.57 3.16
1152 1192 3.064931 GAGTAACGGAGGACTTTTGGTG 58.935 50.000 0.00 0.00 0.00 4.17
1247 1389 3.452474 CACTTCCTGCAGACTATACAGC 58.548 50.000 17.39 0.00 0.00 4.40
1252 1394 2.093973 CGTTCCACTTCCTGCAGACTAT 60.094 50.000 17.39 0.00 0.00 2.12
1437 1579 4.827835 TGCTGAACTCTGAAGTACAGTACT 59.172 41.667 7.48 7.48 45.86 2.73
1438 1580 5.048643 TCTGCTGAACTCTGAAGTACAGTAC 60.049 44.000 2.05 2.05 45.86 2.73
1461 1628 4.921515 TGTAAAACTCACTCACGTATGCTC 59.078 41.667 0.00 0.00 0.00 4.26
1488 1655 2.001159 CAGAGTCGCTCACGTACTACT 58.999 52.381 9.09 0.00 41.18 2.57
1495 1662 1.211449 AGCTTCAGAGTCGCTCACG 59.789 57.895 9.09 0.00 42.01 4.35
1512 1679 0.890996 GGCAACACAACAGAGGGGAG 60.891 60.000 0.00 0.00 0.00 4.30
1521 1695 1.903404 CCCCTGGAGGCAACACAAC 60.903 63.158 0.00 0.00 41.41 3.32
1821 1997 7.644551 GGATGTCTGTACGTAGAAGACTAAATG 59.355 40.741 26.64 2.75 40.79 2.32
1824 2000 5.587844 GGGATGTCTGTACGTAGAAGACTAA 59.412 44.000 26.64 15.45 40.79 2.24
1831 2007 4.820173 CACTATGGGATGTCTGTACGTAGA 59.180 45.833 0.00 0.00 0.00 2.59
1832 2008 4.579340 ACACTATGGGATGTCTGTACGTAG 59.421 45.833 0.00 0.00 0.00 3.51
1833 2009 4.529897 ACACTATGGGATGTCTGTACGTA 58.470 43.478 0.00 0.00 0.00 3.57
1859 2035 2.128035 CCAGATGAAGAATACGACGGC 58.872 52.381 0.00 0.00 0.00 5.68
1874 2050 8.482128 CAAGAAGATTAGTAAGAGTTCCCAGAT 58.518 37.037 0.00 0.00 0.00 2.90
1880 2056 8.541133 AACTGCAAGAAGATTAGTAAGAGTTC 57.459 34.615 0.00 0.00 37.43 3.01
1883 2059 6.254589 CCGAACTGCAAGAAGATTAGTAAGAG 59.745 42.308 0.00 0.00 37.43 2.85
1885 2061 6.100004 TCCGAACTGCAAGAAGATTAGTAAG 58.900 40.000 0.00 0.00 37.43 2.34
1906 2101 4.109766 TCGTACATTATCTGCAGTTTCCG 58.890 43.478 14.67 6.80 0.00 4.30
1907 2102 6.700081 TGTATCGTACATTATCTGCAGTTTCC 59.300 38.462 14.67 0.00 32.89 3.13
1908 2103 7.694388 TGTATCGTACATTATCTGCAGTTTC 57.306 36.000 14.67 0.00 32.89 2.78
1969 2167 6.420604 CGTTAATTTGTTGCTCTTCACCATTT 59.579 34.615 0.00 0.00 0.00 2.32
1971 2169 5.240623 TCGTTAATTTGTTGCTCTTCACCAT 59.759 36.000 0.00 0.00 0.00 3.55
1980 2178 5.851177 CGATGAAACTCGTTAATTTGTTGCT 59.149 36.000 0.00 0.00 34.00 3.91
1993 2191 8.168626 TCATTTGATTAAAGACGATGAAACTCG 58.831 33.333 0.00 0.00 44.14 4.18
2016 2214 8.256356 AGGCTGAACAAGTAGAGTTATATCAT 57.744 34.615 0.00 0.00 0.00 2.45
2017 2215 7.342026 TGAGGCTGAACAAGTAGAGTTATATCA 59.658 37.037 0.00 0.00 0.00 2.15
2018 2216 7.717568 TGAGGCTGAACAAGTAGAGTTATATC 58.282 38.462 0.00 0.00 0.00 1.63
2080 2284 1.591158 GTATGTATGTTCCGTGGCGTG 59.409 52.381 0.00 0.00 0.00 5.34
2100 2304 8.786826 TTACCATTGACTAGTTGGTATTTGAG 57.213 34.615 20.56 0.00 43.56 3.02
2149 2353 3.183172 CGACTGATTGAGGTTCATATGCG 59.817 47.826 0.00 0.00 0.00 4.73
2470 2677 7.173047 GGCATGTTTCTTGTTTCACCATATTTT 59.827 33.333 0.00 0.00 0.00 1.82
2475 2683 3.387374 TGGCATGTTTCTTGTTTCACCAT 59.613 39.130 0.00 0.00 0.00 3.55
2533 2743 2.481952 GCACTGCGATCAACTTTCTTCT 59.518 45.455 0.00 0.00 0.00 2.85
2606 2816 6.096846 ACCACCAAGAATGCTAATATGGAAAC 59.903 38.462 0.00 0.00 0.00 2.78
2644 2854 4.746535 TCTTTGGACAGTGTGAGTACAA 57.253 40.909 0.00 0.00 38.01 2.41
2674 2884 7.548196 TCCAATATGAATTTCGTTGAGTACC 57.452 36.000 0.00 0.00 0.00 3.34
2681 2891 6.016610 CCGGGTTATCCAATATGAATTTCGTT 60.017 38.462 0.00 0.00 34.36 3.85


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

AutoCloner maintained by Alex Coulton.