Multiple sequence alignment - TraesCS6D01G141800

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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 TraesCS6D01G141800 chr6D 100.000 2249 0 0 1 2249 111061187 111063435 0.000000e+00 4154
1 TraesCS6D01G141800 chr6D 89.720 214 21 1 656 868 351137583 351137370 2.850000e-69 272
2 TraesCS6D01G141800 chr6B 89.908 1526 76 35 1 1493 200007732 200009212 0.000000e+00 1893
3 TraesCS6D01G141800 chr6B 93.126 771 16 12 1486 2249 200009271 200010011 0.000000e+00 1096
4 TraesCS6D01G141800 chr6B 90.244 205 20 0 664 868 528285888 528286092 3.680000e-68 268
5 TraesCS6D01G141800 chr6A 87.841 1431 73 43 77 1450 135560399 135561785 0.000000e+00 1585
6 TraesCS6D01G141800 chr6A 92.288 778 32 17 1486 2249 135561878 135562641 0.000000e+00 1079
7 TraesCS6D01G141800 chr6A 90.338 207 19 1 663 868 492283913 492284119 1.020000e-68 270
8 TraesCS6D01G141800 chr7D 91.389 360 29 2 968 1326 593370339 593369981 2.010000e-135 492
9 TraesCS6D01G141800 chr7D 82.014 417 55 14 1846 2249 593369579 593369170 9.950000e-89 337
10 TraesCS6D01G141800 chr7D 94.175 206 12 0 663 868 593371078 593370873 4.660000e-82 315
11 TraesCS6D01G141800 chr7B 90.556 360 32 2 968 1326 667479575 667479933 2.020000e-130 475
12 TraesCS6D01G141800 chr7B 93.333 210 13 1 660 868 667478747 667478956 2.170000e-80 309
13 TraesCS6D01G141800 chr7A 90.251 359 35 0 968 1326 686156681 686156323 9.400000e-129 470
14 TraesCS6D01G141800 chr7A 82.734 417 52 13 1846 2249 686155909 686155500 9.880000e-94 353
15 TraesCS6D01G141800 chr7A 94.203 207 12 0 662 868 686157465 686157259 1.300000e-82 316


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 TraesCS6D01G141800 chr6D 111061187 111063435 2248 False 4154.000000 4154 100.000000 1 2249 1 chr6D.!!$F1 2248
1 TraesCS6D01G141800 chr6B 200007732 200010011 2279 False 1494.500000 1893 91.517000 1 2249 2 chr6B.!!$F2 2248
2 TraesCS6D01G141800 chr6A 135560399 135562641 2242 False 1332.000000 1585 90.064500 77 2249 2 chr6A.!!$F2 2172
3 TraesCS6D01G141800 chr7D 593369170 593371078 1908 True 381.333333 492 89.192667 663 2249 3 chr7D.!!$R1 1586
4 TraesCS6D01G141800 chr7B 667478747 667479933 1186 False 392.000000 475 91.944500 660 1326 2 chr7B.!!$F1 666
5 TraesCS6D01G141800 chr7A 686155500 686157465 1965 True 379.666667 470 89.062667 662 2249 3 chr7A.!!$R1 1587

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
648 696 0.032678 ACGGAAGTGCAGACAGACAG 59.967 55.0 0.0 0.0 46.97 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 2562 1.037493 CGCCCAGCAGGTACTACATA 58.963 55.0 0.0 0.0 36.02 2.29 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
23 24 0.320771 ACAGGTCTGCTAAGGTTGCG 60.321 55.000 0.00 0.00 0.00 4.85
110 111 2.282958 ACGGGAAGTCCTCGCTGA 60.283 61.111 7.78 0.00 34.85 4.26
153 154 1.303643 GGACCTTGGACCAAGCCAG 60.304 63.158 26.34 16.29 39.85 4.85
179 180 1.604278 AGCAACTTCTTTCCACGAAGC 59.396 47.619 0.00 0.00 41.13 3.86
217 218 3.705072 GTGCCCAACTAGTAGGAGTACAT 59.295 47.826 14.61 0.00 0.00 2.29
222 223 6.267014 GCCCAACTAGTAGGAGTACATATCAA 59.733 42.308 14.61 0.00 0.00 2.57
240 241 9.739276 ACATATCAACTTATTTTCCTCTTGTCA 57.261 29.630 0.00 0.00 0.00 3.58
293 314 2.872245 CACATAGAACGGGCCAACATAG 59.128 50.000 4.39 0.00 0.00 2.23
294 315 2.158813 ACATAGAACGGGCCAACATAGG 60.159 50.000 4.39 0.00 0.00 2.57
295 316 1.868713 TAGAACGGGCCAACATAGGA 58.131 50.000 4.39 0.00 0.00 2.94
296 317 0.541863 AGAACGGGCCAACATAGGAG 59.458 55.000 4.39 0.00 0.00 3.69
309 331 7.420800 GCCAACATAGGAGTATGATTTTCTTG 58.579 38.462 0.00 0.00 38.76 3.02
358 383 0.244994 CTCAGGTGAGAACCAGACGG 59.755 60.000 0.22 0.00 44.74 4.79
405 434 2.235016 CCATCCGAGTTGGGAAAAACA 58.765 47.619 0.00 0.00 40.09 2.83
431 460 1.668101 TTTTGGTGGTGGTCGTTGGC 61.668 55.000 0.00 0.00 0.00 4.52
444 473 2.186826 GTTGGCCCCAATCGATCGG 61.187 63.158 16.41 0.00 38.28 4.18
445 474 2.371259 TTGGCCCCAATCGATCGGA 61.371 57.895 16.41 2.25 0.00 4.55
469 502 2.719354 GCACGGACCAACCACAAC 59.281 61.111 0.00 0.00 38.90 3.32
470 503 2.841160 GCACGGACCAACCACAACC 61.841 63.158 0.00 0.00 38.90 3.77
471 504 1.452289 CACGGACCAACCACAACCA 60.452 57.895 0.00 0.00 38.90 3.67
472 505 1.032657 CACGGACCAACCACAACCAA 61.033 55.000 0.00 0.00 38.90 3.67
473 506 0.750182 ACGGACCAACCACAACCAAG 60.750 55.000 0.00 0.00 38.90 3.61
475 508 1.817740 CGGACCAACCACAACCAAGAT 60.818 52.381 0.00 0.00 38.90 2.40
486 519 4.142902 CCACAACCAAGATTAGTAGTTGCG 60.143 45.833 0.00 0.00 41.12 4.85
521 557 1.387084 GCGAGAGTAGCAAGTTTGTCG 59.613 52.381 0.00 0.00 34.19 4.35
615 663 2.498056 GCCAAGTGTGGGGTGGTTG 61.498 63.158 0.00 0.00 46.09 3.77
621 669 0.681564 GTGTGGGGTGGTTGACAACA 60.682 55.000 19.58 3.77 39.06 3.33
630 678 0.102300 GGTTGACAACACCAAGCCAC 59.898 55.000 19.58 0.00 36.38 5.01
632 680 1.380403 TTGACAACACCAAGCCACGG 61.380 55.000 0.00 0.00 0.00 4.94
647 695 2.124293 ACGGAAGTGCAGACAGACA 58.876 52.632 0.00 0.00 46.97 3.41
648 696 0.032678 ACGGAAGTGCAGACAGACAG 59.967 55.000 0.00 0.00 46.97 3.51
649 697 0.315251 CGGAAGTGCAGACAGACAGA 59.685 55.000 0.00 0.00 0.00 3.41
681 734 5.053145 GGTAGTACCTTTCATGATCTGCTG 58.947 45.833 12.41 0.00 34.73 4.41
877 930 1.241165 CGTACCCCTGAAACCAAACC 58.759 55.000 0.00 0.00 0.00 3.27
884 1163 1.136110 CCTGAAACCAAACCAAACGCT 59.864 47.619 0.00 0.00 0.00 5.07
886 1165 2.096248 TGAAACCAAACCAAACGCTCT 58.904 42.857 0.00 0.00 0.00 4.09
888 1167 1.757682 AACCAAACCAAACGCTCTCA 58.242 45.000 0.00 0.00 0.00 3.27
898 1177 2.050077 CGCTCTCACGTGTCAGCA 60.050 61.111 28.64 7.78 0.00 4.41
946 1233 4.259356 CAGAAGCAACCTGATCATCAAGA 58.741 43.478 0.00 0.00 33.65 3.02
948 1235 3.278668 AGCAACCTGATCATCAAGAGG 57.721 47.619 0.00 0.00 0.00 3.69
950 1237 2.941720 GCAACCTGATCATCAAGAGGAC 59.058 50.000 0.00 0.00 0.00 3.85
951 1238 3.620719 GCAACCTGATCATCAAGAGGACA 60.621 47.826 0.00 0.00 0.00 4.02
952 1239 4.190001 CAACCTGATCATCAAGAGGACAG 58.810 47.826 0.00 0.00 0.00 3.51
953 1240 3.717576 ACCTGATCATCAAGAGGACAGA 58.282 45.455 0.00 0.00 31.85 3.41
955 1242 4.101274 ACCTGATCATCAAGAGGACAGATG 59.899 45.833 0.00 0.00 40.29 2.90
1380 1998 1.867363 AAGGTTCTAGCGATCAGGGT 58.133 50.000 0.00 0.00 0.00 4.34
1381 1999 1.115467 AGGTTCTAGCGATCAGGGTG 58.885 55.000 0.00 0.00 0.00 4.61
1400 2018 2.808543 GTGCAATTCGAAACCTCTGACT 59.191 45.455 0.00 0.00 0.00 3.41
1459 2092 2.997315 TGGGTCAGACTCGCCCAG 60.997 66.667 9.01 0.00 46.59 4.45
1478 2111 3.066190 CATGCACCTGGCCCTGTG 61.066 66.667 15.51 15.51 43.89 3.66
1602 2316 1.566018 CTGACCACGCGGAGGAAAAC 61.566 60.000 24.06 13.01 35.59 2.43
1604 2318 1.153127 ACCACGCGGAGGAAAACAA 60.153 52.632 24.06 0.00 35.59 2.83
1679 2398 2.740055 CCACCTGTCGTGCTCTGC 60.740 66.667 0.00 0.00 41.53 4.26
1680 2399 2.341543 CACCTGTCGTGCTCTGCT 59.658 61.111 0.00 0.00 35.18 4.24
1681 2400 2.025969 CACCTGTCGTGCTCTGCTG 61.026 63.158 0.00 0.00 35.18 4.41
1768 2489 1.533033 TGAGAGCTCCGTTGACCCA 60.533 57.895 10.93 0.00 0.00 4.51
1816 2541 0.463620 GAGCTCGGAGCAGAGGAATT 59.536 55.000 29.88 8.27 45.56 2.17
1817 2542 0.463620 AGCTCGGAGCAGAGGAATTC 59.536 55.000 29.88 0.00 45.56 2.17
1822 2547 0.541863 GGAGCAGAGGAATTCGGGAA 59.458 55.000 0.00 0.00 0.00 3.97
1823 2548 1.141858 GGAGCAGAGGAATTCGGGAAT 59.858 52.381 0.00 0.00 0.00 3.01
1824 2549 2.216898 GAGCAGAGGAATTCGGGAATG 58.783 52.381 0.00 0.00 0.00 2.67
1839 2564 3.338275 AATGGCGTGCGGGTGGTAT 62.338 57.895 0.00 0.00 0.00 2.73
1840 2565 4.769063 TGGCGTGCGGGTGGTATG 62.769 66.667 0.00 0.00 0.00 2.39
1841 2566 4.770874 GGCGTGCGGGTGGTATGT 62.771 66.667 0.00 0.00 0.00 2.29
1842 2567 2.184836 GCGTGCGGGTGGTATGTA 59.815 61.111 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.296715 CCGCAACCTTAGCAGACCT 59.703 57.895 0.00 0.00 0.00 3.85
23 24 2.661866 ACGACACGCTCAACTGCC 60.662 61.111 0.00 0.00 0.00 4.85
73 74 1.340248 TCAGTTCCACTCCACGTTCTC 59.660 52.381 0.00 0.00 0.00 2.87
110 111 7.608761 CCATTCTGAATTCCCAATGATTGTTTT 59.391 33.333 20.46 0.00 0.00 2.43
153 154 2.297701 TGGAAAGAAGTTGCTGTCCAC 58.702 47.619 9.11 0.00 45.29 4.02
179 180 1.534729 GCACTTTAAGGTGGTGGAGG 58.465 55.000 18.26 0.00 37.65 4.30
239 240 7.061441 CCTCATCACGACTTCATCAAAAATTTG 59.939 37.037 0.00 0.00 39.48 2.32
240 241 7.040478 TCCTCATCACGACTTCATCAAAAATTT 60.040 33.333 0.00 0.00 0.00 1.82
241 242 6.430925 TCCTCATCACGACTTCATCAAAAATT 59.569 34.615 0.00 0.00 0.00 1.82
248 249 3.119316 ACTGTCCTCATCACGACTTCATC 60.119 47.826 0.00 0.00 0.00 2.92
249 250 2.828520 ACTGTCCTCATCACGACTTCAT 59.171 45.455 0.00 0.00 0.00 2.57
256 277 2.438868 TGTGAACTGTCCTCATCACG 57.561 50.000 5.41 0.00 43.91 4.35
309 331 5.900865 ACAGCTGACCTAGTAGTTCTAAC 57.099 43.478 23.35 0.00 0.00 2.34
358 383 1.177401 GATGAGCAACCCAAAGACCC 58.823 55.000 0.00 0.00 0.00 4.46
403 432 2.640332 ACCACCACCAAAACCTTTTTGT 59.360 40.909 9.82 0.00 0.00 2.83
404 433 3.266636 GACCACCACCAAAACCTTTTTG 58.733 45.455 4.68 4.68 0.00 2.44
405 434 2.093921 CGACCACCACCAAAACCTTTTT 60.094 45.455 0.00 0.00 0.00 1.94
431 460 2.029073 CCGTCCGATCGATTGGGG 59.971 66.667 28.01 19.46 31.87 4.96
455 488 0.464735 TCTTGGTTGTGGTTGGTCCG 60.465 55.000 0.00 0.00 39.52 4.79
466 499 4.092968 GGTCGCAACTACTAATCTTGGTTG 59.907 45.833 0.00 0.00 39.83 3.77
467 500 4.020485 AGGTCGCAACTACTAATCTTGGTT 60.020 41.667 0.00 0.00 0.00 3.67
469 502 4.124851 AGGTCGCAACTACTAATCTTGG 57.875 45.455 0.00 0.00 0.00 3.61
470 503 6.199154 CACATAGGTCGCAACTACTAATCTTG 59.801 42.308 0.00 0.00 0.00 3.02
471 504 6.273825 CACATAGGTCGCAACTACTAATCTT 58.726 40.000 0.00 0.00 0.00 2.40
472 505 5.736492 GCACATAGGTCGCAACTACTAATCT 60.736 44.000 0.00 0.00 0.00 2.40
473 506 4.444720 GCACATAGGTCGCAACTACTAATC 59.555 45.833 0.00 0.00 0.00 1.75
475 508 3.446161 AGCACATAGGTCGCAACTACTAA 59.554 43.478 5.10 0.00 0.00 2.24
486 519 1.676529 TCTCGCTACAGCACATAGGTC 59.323 52.381 1.61 0.00 42.21 3.85
615 663 1.098712 TTCCGTGGCTTGGTGTTGTC 61.099 55.000 0.00 0.00 0.00 3.18
621 669 2.594592 GCACTTCCGTGGCTTGGT 60.595 61.111 0.00 0.00 41.51 3.67
630 678 0.315251 TCTGTCTGTCTGCACTTCCG 59.685 55.000 0.00 0.00 0.00 4.30
632 680 2.810439 ACTCTGTCTGTCTGCACTTC 57.190 50.000 0.00 0.00 0.00 3.01
637 685 3.366883 CCAACTCTACTCTGTCTGTCTGC 60.367 52.174 0.00 0.00 0.00 4.26
639 687 4.107127 ACCAACTCTACTCTGTCTGTCT 57.893 45.455 0.00 0.00 0.00 3.41
640 688 5.005094 ACTACCAACTCTACTCTGTCTGTC 58.995 45.833 0.00 0.00 0.00 3.51
641 689 4.988029 ACTACCAACTCTACTCTGTCTGT 58.012 43.478 0.00 0.00 0.00 3.41
642 690 5.354792 GGTACTACCAACTCTACTCTGTCTG 59.645 48.000 0.00 0.00 38.42 3.51
643 691 5.251237 AGGTACTACCAACTCTACTCTGTCT 59.749 44.000 8.01 0.00 41.95 3.41
644 692 5.499313 AGGTACTACCAACTCTACTCTGTC 58.501 45.833 8.01 0.00 41.95 3.51
645 693 5.517620 AGGTACTACCAACTCTACTCTGT 57.482 43.478 8.01 0.00 41.95 3.41
646 694 6.433404 TGAAAGGTACTACCAACTCTACTCTG 59.567 42.308 8.01 0.00 41.95 3.35
647 695 6.550163 TGAAAGGTACTACCAACTCTACTCT 58.450 40.000 8.01 0.00 41.95 3.24
648 696 6.830873 TGAAAGGTACTACCAACTCTACTC 57.169 41.667 8.01 0.00 41.95 2.59
649 697 6.952358 TCATGAAAGGTACTACCAACTCTACT 59.048 38.462 8.01 0.00 41.95 2.57
681 734 4.615815 AGATCTGCATCCGCGGCC 62.616 66.667 23.51 11.95 44.81 6.13
877 930 0.504384 CTGACACGTGAGAGCGTTTG 59.496 55.000 25.01 0.00 43.83 2.93
884 1163 1.661509 CGCTTGCTGACACGTGAGA 60.662 57.895 25.01 6.83 0.00 3.27
886 1165 2.661537 CCGCTTGCTGACACGTGA 60.662 61.111 25.01 0.00 0.00 4.35
888 1167 4.908687 TGCCGCTTGCTGACACGT 62.909 61.111 0.00 0.00 42.00 4.49
946 1233 2.362503 TCCGGTCGCATCTGTCCT 60.363 61.111 0.00 0.00 0.00 3.85
948 1235 2.202756 GGTCCGGTCGCATCTGTC 60.203 66.667 0.00 0.00 0.00 3.51
950 1237 3.822192 TCGGTCCGGTCGCATCTG 61.822 66.667 12.29 0.16 0.00 2.90
951 1238 3.823330 GTCGGTCCGGTCGCATCT 61.823 66.667 12.29 0.00 0.00 2.90
952 1239 4.867599 GGTCGGTCCGGTCGCATC 62.868 72.222 12.29 7.64 0.00 3.91
1364 1982 0.175760 TGCACCCTGATCGCTAGAAC 59.824 55.000 0.00 0.00 0.00 3.01
1366 1984 1.123077 ATTGCACCCTGATCGCTAGA 58.877 50.000 0.00 0.00 0.00 2.43
1380 1998 3.126001 AGTCAGAGGTTTCGAATTGCA 57.874 42.857 0.00 0.00 0.00 4.08
1381 1999 4.489679 AAAGTCAGAGGTTTCGAATTGC 57.510 40.909 0.00 0.00 0.00 3.56
1431 2064 4.680237 TGACCCACGCGCCAAGAG 62.680 66.667 5.73 0.00 0.00 2.85
1575 2289 2.653702 GCGTGGTCAGAGCTCTGT 59.346 61.111 36.32 6.64 44.12 3.41
1602 2316 3.131396 GTCGGTGCCACTTAGGATATTG 58.869 50.000 0.00 0.00 41.22 1.90
1604 2318 2.365617 CTGTCGGTGCCACTTAGGATAT 59.634 50.000 0.00 0.00 41.22 1.63
1679 2398 2.508887 GCTCCTCACTCGCAGCAG 60.509 66.667 0.00 0.00 0.00 4.24
1680 2399 3.292500 CTGCTCCTCACTCGCAGCA 62.293 63.158 0.00 0.00 43.75 4.41
1681 2400 2.508887 CTGCTCCTCACTCGCAGC 60.509 66.667 0.00 0.00 43.75 5.25
1768 2489 2.586079 CGATCATTCGCCACGCCT 60.586 61.111 0.00 0.00 38.75 5.52
1822 2547 3.792736 ATACCACCCGCACGCCAT 61.793 61.111 0.00 0.00 0.00 4.40
1823 2548 4.769063 CATACCACCCGCACGCCA 62.769 66.667 0.00 0.00 0.00 5.69
1824 2549 3.374012 TACATACCACCCGCACGCC 62.374 63.158 0.00 0.00 0.00 5.68
1836 2561 1.269621 CGCCCAGCAGGTACTACATAC 60.270 57.143 0.00 0.00 36.02 2.39
1837 2562 1.037493 CGCCCAGCAGGTACTACATA 58.963 55.000 0.00 0.00 36.02 2.29
1839 2564 1.304630 TCGCCCAGCAGGTACTACA 60.305 57.895 0.00 0.00 36.02 2.74
1840 2565 1.141234 GTCGCCCAGCAGGTACTAC 59.859 63.158 0.00 0.00 36.02 2.73
1841 2566 2.412323 CGTCGCCCAGCAGGTACTA 61.412 63.158 0.00 0.00 36.02 1.82
1842 2567 3.760035 CGTCGCCCAGCAGGTACT 61.760 66.667 0.00 0.00 43.88 2.73
2099 2951 1.520120 CGCCATGCTGATCGTCACT 60.520 57.895 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.