Multiple sequence alignment - TraesCS6D01G176500

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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 TraesCS6D01G176500 chr6D 100.000 2240 0 0 1 2240 172741110 172738871 0 4137
1 TraesCS6D01G176500 chr6D 94.180 1323 68 5 919 2240 108480828 108482142 0 2008
2 TraesCS6D01G176500 chr6D 97.277 404 11 0 1 404 389243362 389242959 0 686
3 TraesCS6D01G176500 chr2A 94.076 1418 51 5 1 1385 726903995 726902578 0 2122
4 TraesCS6D01G176500 chrUn 95.619 1324 51 4 919 2240 385303176 385301858 0 2117
5 TraesCS6D01G176500 chrUn 93.310 1136 43 5 283 1385 425407386 425408521 0 1646
6 TraesCS6D01G176500 chrUn 95.150 866 41 1 1376 2240 217903726 217904591 0 1365
7 TraesCS6D01G176500 chrUn 96.782 404 13 0 1 404 428084432 428084029 0 675
8 TraesCS6D01G176500 chrUn 96.782 404 13 0 1 404 433990649 433991052 0 675
9 TraesCS6D01G176500 chr7D 95.619 1324 51 4 919 2240 382111675 382112993 0 2117
10 TraesCS6D01G176500 chr7D 97.030 404 12 0 1 404 231543470 231543873 0 680
11 TraesCS6D01G176500 chr7D 97.030 404 11 1 1 404 231605457 231605055 0 678
12 TraesCS6D01G176500 chr5D 93.935 1418 52 6 1 1385 503262316 503260900 0 2111
13 TraesCS6D01G176500 chr5D 93.865 1418 53 6 1 1385 503247732 503249148 0 2106
14 TraesCS6D01G176500 chr3B 93.794 1418 55 5 1 1385 201572327 201570910 0 2100
15 TraesCS6D01G176500 chr7B 93.724 1418 56 7 1 1385 662729374 662730791 0 2095
16 TraesCS6D01G176500 chr7B 97.030 404 12 0 1 404 663096965 663096562 0 680
17 TraesCS6D01G176500 chr2D 93.653 1418 57 5 1 1385 591987069 591988486 0 2089
18 TraesCS6D01G176500 chr3D 93.512 1418 58 6 1 1385 589261067 589259651 0 2078
19 TraesCS6D01G176500 chr4D 94.860 1323 61 4 919 2240 123453366 123452050 0 2060
20 TraesCS6D01G176500 chr1D 93.230 1418 63 5 1 1385 254528066 254529483 0 2056
21 TraesCS6D01G176500 chr1A 92.900 1324 86 5 919 2240 170852452 170851135 0 1917
22 TraesCS6D01G176500 chr5A 95.612 866 37 1 1376 2240 238877077 238876212 0 1387
23 TraesCS6D01G176500 chr6B 95.497 866 37 2 1376 2240 151244325 151245189 0 1382
24 TraesCS6D01G176500 chr6A 95.497 866 38 1 1376 2240 597248786 597249651 0 1382
25 TraesCS6D01G176500 chr3A 97.030 404 12 0 1 404 66002673 66002270 0 680


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 TraesCS6D01G176500 chr6D 172738871 172741110 2239 True 4137 4137 100.000 1 2240 1 chr6D.!!$R1 2239
1 TraesCS6D01G176500 chr6D 108480828 108482142 1314 False 2008 2008 94.180 919 2240 1 chr6D.!!$F1 1321
2 TraesCS6D01G176500 chr2A 726902578 726903995 1417 True 2122 2122 94.076 1 1385 1 chr2A.!!$R1 1384
3 TraesCS6D01G176500 chrUn 385301858 385303176 1318 True 2117 2117 95.619 919 2240 1 chrUn.!!$R1 1321
4 TraesCS6D01G176500 chrUn 425407386 425408521 1135 False 1646 1646 93.310 283 1385 1 chrUn.!!$F2 1102
5 TraesCS6D01G176500 chrUn 217903726 217904591 865 False 1365 1365 95.150 1376 2240 1 chrUn.!!$F1 864
6 TraesCS6D01G176500 chr7D 382111675 382112993 1318 False 2117 2117 95.619 919 2240 1 chr7D.!!$F2 1321
7 TraesCS6D01G176500 chr5D 503260900 503262316 1416 True 2111 2111 93.935 1 1385 1 chr5D.!!$R1 1384
8 TraesCS6D01G176500 chr5D 503247732 503249148 1416 False 2106 2106 93.865 1 1385 1 chr5D.!!$F1 1384
9 TraesCS6D01G176500 chr3B 201570910 201572327 1417 True 2100 2100 93.794 1 1385 1 chr3B.!!$R1 1384
10 TraesCS6D01G176500 chr7B 662729374 662730791 1417 False 2095 2095 93.724 1 1385 1 chr7B.!!$F1 1384
11 TraesCS6D01G176500 chr2D 591987069 591988486 1417 False 2089 2089 93.653 1 1385 1 chr2D.!!$F1 1384
12 TraesCS6D01G176500 chr3D 589259651 589261067 1416 True 2078 2078 93.512 1 1385 1 chr3D.!!$R1 1384
13 TraesCS6D01G176500 chr4D 123452050 123453366 1316 True 2060 2060 94.860 919 2240 1 chr4D.!!$R1 1321
14 TraesCS6D01G176500 chr1D 254528066 254529483 1417 False 2056 2056 93.230 1 1385 1 chr1D.!!$F1 1384
15 TraesCS6D01G176500 chr1A 170851135 170852452 1317 True 1917 1917 92.900 919 2240 1 chr1A.!!$R1 1321
16 TraesCS6D01G176500 chr5A 238876212 238877077 865 True 1387 1387 95.612 1376 2240 1 chr5A.!!$R1 864
17 TraesCS6D01G176500 chr6B 151244325 151245189 864 False 1382 1382 95.497 1376 2240 1 chr6B.!!$F1 864
18 TraesCS6D01G176500 chr6A 597248786 597249651 865 False 1382 1382 95.497 1376 2240 1 chr6A.!!$F1 864

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
971 1005 0.028505 GCGTAACGATCTCGGCACTA 59.971 55.0 4.44 0.0 44.95 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1823 0.401395 ATATGTCATCCACCCGGGGT 60.401 55.0 27.92 14.51 37.22 4.95 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
76 77 0.036952 CACTGATCGAGCACCCTTGT 60.037 55.000 0.00 0.00 0.00 3.16
174 175 1.745489 GAGGGAAGCAACCGCGAAT 60.745 57.895 8.23 0.00 45.49 3.34
237 238 7.012894 TGAGTAACGAAAACATTGGTGAGAATT 59.987 33.333 0.00 0.00 0.00 2.17
405 406 2.359214 GCTAGGTTAGCCAAAAGATGCC 59.641 50.000 0.00 0.00 45.95 4.40
438 470 2.242452 AGAAGGGGTAGAGAAAATGCCC 59.758 50.000 0.00 0.00 41.58 5.36
439 471 1.987080 AGGGGTAGAGAAAATGCCCT 58.013 50.000 0.00 0.00 41.95 5.19
457 489 1.440938 CTGAGCCGAGGTCCGAGTAG 61.441 65.000 0.00 0.00 41.76 2.57
515 547 0.737715 GCGATTGCTTCTCCACGAGT 60.738 55.000 0.00 0.00 38.39 4.18
696 728 3.861276 GCAAAATAGCCCCGTAACTTT 57.139 42.857 0.00 0.00 0.00 2.66
729 762 2.525592 CCTCACAAAAGGGGGCCA 59.474 61.111 4.39 0.00 32.35 5.36
835 868 0.404040 ATGCGGGAAGGTCAAGGAAA 59.596 50.000 0.00 0.00 0.00 3.13
837 870 1.631388 TGCGGGAAGGTCAAGGAAATA 59.369 47.619 0.00 0.00 0.00 1.40
862 895 1.900351 CTGATGACAGGGAAGCCGA 59.100 57.895 0.00 0.00 40.14 5.54
867 900 0.904865 TGACAGGGAAGCCGATGACT 60.905 55.000 0.00 0.00 0.00 3.41
875 908 1.557269 AAGCCGATGACTGAAGCCCT 61.557 55.000 0.00 0.00 0.00 5.19
901 934 0.031178 CGGCGGCCGTAACTATAACT 59.969 55.000 32.14 0.00 42.73 2.24
964 998 2.110226 CTCGAAAGGCGTAACGATCTC 58.890 52.381 7.95 0.00 41.80 2.75
971 1005 0.028505 GCGTAACGATCTCGGCACTA 59.971 55.000 4.44 0.00 44.95 2.74
1025 1059 3.445450 TCTGTGAAGATGCAGACTACCTC 59.555 47.826 0.00 0.00 36.89 3.85
1036 1070 1.149288 AGACTACCTCCACCTGGACAA 59.851 52.381 0.00 0.00 39.78 3.18
1065 1099 4.200092 CCTATGAAGCTTTACTGTTCCCC 58.800 47.826 0.00 0.00 0.00 4.81
1241 1276 3.518303 GACAGTTTCTATGGGGTGTAGGT 59.482 47.826 0.00 0.00 0.00 3.08
1268 1303 3.116531 GGTAACGGAGGCGTGCAC 61.117 66.667 6.82 6.82 0.00 4.57
1334 1369 1.353694 AGAAGGGAGCTTGACTGCAAT 59.646 47.619 0.00 0.00 38.79 3.56
1356 1391 2.282251 ACCCGTCGAGCAGAGACA 60.282 61.111 0.00 0.00 38.46 3.41
1391 1426 2.987149 GTGATCCGACGGTGCATATTAG 59.013 50.000 14.79 0.00 0.00 1.73
1441 1476 7.042925 GCGATTCATAATACCGTAAAAGTGTCT 60.043 37.037 0.00 0.00 0.00 3.41
1543 1578 1.615883 CAGCGTGCAGATAGATAGGGT 59.384 52.381 0.00 0.00 0.00 4.34
1582 1617 2.613026 TGTCTGAGCGGTTGAAAGAA 57.387 45.000 0.00 0.00 0.00 2.52
1597 1632 6.459710 GGTTGAAAGAATCGGTCTTGAAAACT 60.460 38.462 3.45 0.00 46.36 2.66
1630 1666 1.693606 GGAATACCGGGGGTTCGAATA 59.306 52.381 6.32 0.00 37.09 1.75
1641 1677 2.698797 GGGTTCGAATACCTCTCCATCA 59.301 50.000 12.94 0.00 38.30 3.07
1704 1740 2.159128 ACGAATCTCCTCGACTCGACTA 60.159 50.000 0.00 0.00 41.44 2.59
1766 1802 9.616156 TTGTGTGTTGATTTAGTTAGGACTTTA 57.384 29.630 0.00 0.00 37.33 1.85
1787 1823 9.198475 ACTTTATCTCCCTTTCGTTATCTTCTA 57.802 33.333 0.00 0.00 0.00 2.10
1803 1839 1.687840 CTACCCCGGGTGGATGACA 60.688 63.158 21.85 0.00 36.20 3.58
1805 1841 0.265254 TACCCCGGGTGGATGACATA 59.735 55.000 21.85 0.00 36.19 2.29
1900 1936 2.378547 TCCCAACCCTGTGAAGCTTAAT 59.621 45.455 0.00 0.00 0.00 1.40
1903 1939 4.567747 CCCAACCCTGTGAAGCTTAATAGT 60.568 45.833 0.00 0.00 0.00 2.12
1929 1965 3.762823 AGAAAACGATAGAGACTTCCGGT 59.237 43.478 0.00 0.00 41.38 5.28
2003 2039 4.750098 GCTACATAAGCGCTCAAATTCCTA 59.250 41.667 12.06 0.00 42.53 2.94
2019 2055 8.691797 TCAAATTCCTAAATACTTATTGCCCAC 58.308 33.333 0.00 0.00 0.00 4.61
2036 2072 3.706086 GCCCACAAAATATGATCAACCCT 59.294 43.478 0.00 0.00 0.00 4.34
2055 2091 9.504705 TCAACCCTAGGTACATTTATTAGGTTA 57.495 33.333 8.29 0.00 33.12 2.85
2147 2184 2.973945 CGAAAGGTTACCCTCTTCCAG 58.026 52.381 0.00 0.00 41.56 3.86
2224 2261 3.734463 TCGACATCTTGTTTGGTAAGCA 58.266 40.909 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.019174 CCATTCATCTTTAGCACAAGGGT 58.981 43.478 0.00 0.00 0.00 4.34
76 77 4.464008 CTTAGCCCCATTCATCTTTAGCA 58.536 43.478 0.00 0.00 0.00 3.49
80 81 2.092429 TCGCTTAGCCCCATTCATCTTT 60.092 45.455 0.00 0.00 0.00 2.52
89 90 2.505982 GCAGATCGCTTAGCCCCA 59.494 61.111 0.00 0.00 37.77 4.96
174 175 4.467084 GCTTCATCGACCCCCGCA 62.467 66.667 0.00 0.00 38.37 5.69
206 207 4.261405 CCAATGTTTTCGTTACTCAAGCCA 60.261 41.667 0.00 0.00 0.00 4.75
237 238 0.470080 TTGGGTTTTCGGGGCATTGA 60.470 50.000 0.00 0.00 0.00 2.57
405 406 3.808834 ACCCCTTCTTACCCTGAAAAG 57.191 47.619 0.00 0.00 0.00 2.27
438 470 1.440938 CTACTCGGACCTCGGCTCAG 61.441 65.000 0.00 0.00 39.77 3.35
439 471 1.451567 CTACTCGGACCTCGGCTCA 60.452 63.158 0.00 0.00 39.77 4.26
515 547 1.452953 CCGTAGCGCCTGGTATGAGA 61.453 60.000 2.29 0.00 37.27 3.27
602 634 1.005294 CTGTGTCGGTTTCGGGTACG 61.005 60.000 0.00 0.00 42.74 3.67
629 661 2.818593 GCGCCCCTAGGTATTCTCTACT 60.819 54.545 8.29 0.00 34.57 2.57
816 849 0.404040 TTTCCTTGACCTTCCCGCAT 59.596 50.000 0.00 0.00 0.00 4.73
820 853 3.265995 TCACCTATTTCCTTGACCTTCCC 59.734 47.826 0.00 0.00 0.00 3.97
835 868 3.724478 TCCCTGTCATCAGTTCACCTAT 58.276 45.455 0.00 0.00 39.82 2.57
837 870 2.030027 TCCCTGTCATCAGTTCACCT 57.970 50.000 0.00 0.00 39.82 4.00
862 895 1.067295 TTCACCAGGGCTTCAGTCAT 58.933 50.000 0.00 0.00 0.00 3.06
867 900 2.429930 CCGTTCACCAGGGCTTCA 59.570 61.111 0.00 0.00 0.00 3.02
945 979 1.530441 CGAGATCGTTACGCCTTTCGA 60.530 52.381 12.07 0.00 36.92 3.71
964 998 1.529226 ATCTCTCCGAGATAGTGCCG 58.471 55.000 4.64 0.00 46.15 5.69
983 1017 3.517901 AGACATGTCTATTTCACCGGGAA 59.482 43.478 26.87 3.52 38.35 3.97
984 1018 3.104512 AGACATGTCTATTTCACCGGGA 58.895 45.455 26.87 0.00 38.35 5.14
986 1020 3.618594 CACAGACATGTCTATTTCACCGG 59.381 47.826 27.44 14.24 37.65 5.28
1025 1059 1.133482 AGGGTCTTTTTGTCCAGGTGG 60.133 52.381 0.00 0.00 0.00 4.61
1036 1070 6.543735 ACAGTAAAGCTTCATAGGGTCTTTT 58.456 36.000 0.00 0.00 0.00 2.27
1241 1276 1.626825 CCTCCGTTACCTTTTGGGAGA 59.373 52.381 6.95 0.00 45.66 3.71
1268 1303 2.045926 CTGGCCCGAGGAAACCTG 60.046 66.667 0.00 0.00 31.76 4.00
1334 1369 1.002990 TCTGCTCGACGGGTGAGTA 60.003 57.895 0.00 0.00 35.85 2.59
1356 1391 2.677037 CGGATCACTAAGGCCGACTTTT 60.677 50.000 0.00 0.00 46.29 2.27
1391 1426 3.491267 ACGCTTCGCTTCTTTCTATATGC 59.509 43.478 0.00 0.00 0.00 3.14
1422 1457 7.917505 CGGTTAGAGACACTTTTACGGTATTAT 59.082 37.037 0.00 0.00 0.00 1.28
1425 1460 5.644644 CGGTTAGAGACACTTTTACGGTAT 58.355 41.667 0.00 0.00 0.00 2.73
1431 1466 4.381292 GCCTAGCGGTTAGAGACACTTTTA 60.381 45.833 0.00 0.00 0.00 1.52
1441 1476 3.563223 ACTCTATTGCCTAGCGGTTAGA 58.437 45.455 0.00 0.00 0.00 2.10
1528 1563 1.352083 GCCCACCCTATCTATCTGCA 58.648 55.000 0.00 0.00 0.00 4.41
1582 1617 6.934645 TCAATACTTCAGTTTTCAAGACCGAT 59.065 34.615 0.00 0.00 0.00 4.18
1597 1632 5.247564 CCCCGGTATTCCTATCAATACTTCA 59.752 44.000 0.00 0.00 38.70 3.02
1641 1677 3.626930 AGAGAGAACTTATGACCTCGCT 58.373 45.455 0.00 0.00 32.35 4.93
1704 1740 6.975471 TCTACCCATTCCATCCATCATATT 57.025 37.500 0.00 0.00 0.00 1.28
1766 1802 5.304871 GGGTAGAAGATAACGAAAGGGAGAT 59.695 44.000 0.00 0.00 0.00 2.75
1787 1823 0.401395 ATATGTCATCCACCCGGGGT 60.401 55.000 27.92 14.51 37.22 4.95
1803 1839 5.329399 AGATCTTCGACTTAGCTCCCATAT 58.671 41.667 0.00 0.00 0.00 1.78
1805 1841 3.571590 AGATCTTCGACTTAGCTCCCAT 58.428 45.455 0.00 0.00 0.00 4.00
1833 1869 4.061357 TGTTTATCAACCACTCACGACA 57.939 40.909 0.00 0.00 31.02 4.35
1862 1898 5.280830 GGTTGGGACTCCCTAAATCAAACTA 60.281 44.000 15.64 0.00 45.70 2.24
1900 1936 8.027771 GGAAGTCTCTATCGTTTTCTTTGACTA 58.972 37.037 0.00 0.00 32.81 2.59
1903 1939 5.862323 CGGAAGTCTCTATCGTTTTCTTTGA 59.138 40.000 0.00 0.00 0.00 2.69
1929 1965 6.795144 TTCATTAAGGTCGTCACCCTATAA 57.205 37.500 0.00 0.00 45.12 0.98
1964 2000 4.351874 TGTAGCTAAAAACTCTGCCACT 57.648 40.909 0.00 0.00 0.00 4.00
2019 2055 8.924511 ATGTACCTAGGGTTGATCATATTTTG 57.075 34.615 14.81 0.00 37.09 2.44
2055 2091 3.172339 GACCAGGATAGCCTCAGATCAT 58.828 50.000 0.00 0.00 44.80 2.45
2090 2127 8.511604 TTCAGATTGGAAAGGATGAATACTTC 57.488 34.615 0.00 0.00 28.61 3.01
2147 2184 2.071844 TAGCGGCTGTAGCATCCGTC 62.072 60.000 13.86 5.77 43.81 4.79
2167 2204 0.555769 TTCCCCTCCTGCAAAAGTGT 59.444 50.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.