Multiple sequence alignment - TraesCS1B01G376600

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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 TraesCS1B01G376600 chr1B 100.000 2642 0 0 1 2642 608336693 608334052 0.000000e+00 4879.0
1 TraesCS1B01G376600 chr1B 92.979 1581 85 11 8 1572 607317818 607316248 0.000000e+00 2281.0
2 TraesCS1B01G376600 chr1B 92.726 1581 86 11 8 1572 607138682 607137115 0.000000e+00 2255.0
3 TraesCS1B01G376600 chr1B 91.174 1167 71 14 429 1572 610892629 610893786 0.000000e+00 1555.0
4 TraesCS1B01G376600 chr1B 97.368 760 18 1 8 767 608044011 608043254 0.000000e+00 1291.0
5 TraesCS1B01G376600 chr1B 89.569 882 56 9 1769 2642 607130229 607129376 0.000000e+00 1086.0
6 TraesCS1B01G376600 chr1B 89.569 882 56 8 1769 2642 607314909 607314056 0.000000e+00 1086.0
7 TraesCS1B01G376600 chr1B 86.871 1013 68 31 790 1744 608043033 608042028 0.000000e+00 1074.0
8 TraesCS1B01G376600 chr1B 87.933 837 58 15 1823 2642 608040956 608040146 0.000000e+00 946.0
9 TraesCS1B01G376600 chr1B 87.846 831 52 12 1823 2642 610898059 610898851 0.000000e+00 929.0
10 TraesCS1B01G376600 chr1D 85.319 1301 116 45 483 1747 446475595 446476856 0.000000e+00 1275.0
11 TraesCS1B01G376600 chr1D 90.268 894 64 8 672 1562 355827694 355828567 0.000000e+00 1147.0
12 TraesCS1B01G376600 chr1D 92.346 797 33 8 800 1572 445367078 445366286 0.000000e+00 1109.0
13 TraesCS1B01G376600 chr1D 89.213 890 52 16 1769 2642 445365013 445364152 0.000000e+00 1072.0
14 TraesCS1B01G376600 chr1D 88.087 831 49 12 1823 2642 446478563 446479354 0.000000e+00 941.0
15 TraesCS1B01G376600 chr1D 87.390 793 76 18 796 1572 388603363 388604147 0.000000e+00 889.0
16 TraesCS1B01G376600 chr1D 84.167 360 54 3 11 368 387422748 387422390 1.950000e-91 346.0
17 TraesCS1B01G376600 chr1D 93.252 163 10 1 1588 1750 445366233 445366072 3.400000e-59 239.0
18 TraesCS1B01G376600 chr1D 87.059 85 11 0 414 498 446443436 446443520 2.160000e-16 97.1
19 TraesCS1B01G376600 chr1A 88.776 980 64 20 796 1747 541343554 541344515 0.000000e+00 1158.0
20 TraesCS1B01G376600 chr1A 86.727 987 84 27 796 1750 541461053 541460082 0.000000e+00 1053.0
21 TraesCS1B01G376600 chr1A 87.130 878 56 21 1769 2611 541458502 541457647 0.000000e+00 942.0
22 TraesCS1B01G376600 chr1A 87.983 724 68 12 796 1503 487604281 487605001 0.000000e+00 837.0
23 TraesCS1B01G376600 chr3A 86.930 834 73 14 1823 2642 111101888 111101077 0.000000e+00 904.0
24 TraesCS1B01G376600 chr3A 82.913 357 59 2 14 368 640842481 640842125 1.180000e-83 320.0
25 TraesCS1B01G376600 chr5A 82.418 364 61 3 5 365 539071394 539071757 5.490000e-82 315.0
26 TraesCS1B01G376600 chr3D 80.822 365 48 7 5 366 485230289 485230634 1.560000e-67 267.0
27 TraesCS1B01G376600 chr7A 80.223 359 58 5 11 367 485514310 485514657 9.380000e-65 257.0
28 TraesCS1B01G376600 chr4A 78.747 367 67 5 11 367 329071935 329072300 4.400000e-58 235.0
29 TraesCS1B01G376600 chr5B 75.576 434 86 11 1917 2349 158112616 158113030 2.070000e-46 196.0
30 TraesCS1B01G376600 chr7D 79.323 266 50 5 8 270 26519746 26520009 5.810000e-42 182.0
31 TraesCS1B01G376600 chr2A 84.783 92 9 3 2495 2585 49293129 49293216 1.300000e-13 87.9
32 TraesCS1B01G376600 chr7B 87.500 56 3 4 1656 1708 85298009 85298063 7.900000e-06 62.1


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 TraesCS1B01G376600 chr1B 608334052 608336693 2641 True 4879.000000 4879 100.000000 1 2642 1 chr1B.!!$R3 2641
1 TraesCS1B01G376600 chr1B 607137115 607138682 1567 True 2255.000000 2255 92.726000 8 1572 1 chr1B.!!$R2 1564
2 TraesCS1B01G376600 chr1B 607314056 607317818 3762 True 1683.500000 2281 91.274000 8 2642 2 chr1B.!!$R4 2634
3 TraesCS1B01G376600 chr1B 610892629 610893786 1157 False 1555.000000 1555 91.174000 429 1572 1 chr1B.!!$F1 1143
4 TraesCS1B01G376600 chr1B 608040146 608044011 3865 True 1103.666667 1291 90.724000 8 2642 3 chr1B.!!$R5 2634
5 TraesCS1B01G376600 chr1B 607129376 607130229 853 True 1086.000000 1086 89.569000 1769 2642 1 chr1B.!!$R1 873
6 TraesCS1B01G376600 chr1B 610898059 610898851 792 False 929.000000 929 87.846000 1823 2642 1 chr1B.!!$F2 819
7 TraesCS1B01G376600 chr1D 355827694 355828567 873 False 1147.000000 1147 90.268000 672 1562 1 chr1D.!!$F1 890
8 TraesCS1B01G376600 chr1D 446475595 446479354 3759 False 1108.000000 1275 86.703000 483 2642 2 chr1D.!!$F4 2159
9 TraesCS1B01G376600 chr1D 388603363 388604147 784 False 889.000000 889 87.390000 796 1572 1 chr1D.!!$F2 776
10 TraesCS1B01G376600 chr1D 445364152 445367078 2926 True 806.666667 1109 91.603667 800 2642 3 chr1D.!!$R2 1842
11 TraesCS1B01G376600 chr1A 541343554 541344515 961 False 1158.000000 1158 88.776000 796 1747 1 chr1A.!!$F2 951
12 TraesCS1B01G376600 chr1A 541457647 541461053 3406 True 997.500000 1053 86.928500 796 2611 2 chr1A.!!$R1 1815
13 TraesCS1B01G376600 chr1A 487604281 487605001 720 False 837.000000 837 87.983000 796 1503 1 chr1A.!!$F1 707
14 TraesCS1B01G376600 chr3A 111101077 111101888 811 True 904.000000 904 86.930000 1823 2642 1 chr3A.!!$R1 819

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
24 25 1.667724 CCTCACTCATCGCCATTGAAC 59.332 52.381 0.0 0.0 0.00 3.18 F
1011 1225 0.956633 CAAATCACAGCACCAGCAGT 59.043 50.000 0.0 0.0 45.49 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1857 0.107017 AATTCATCCGGGGCTGACAG 60.107 55.000 0.0 0.0 0.0 3.51 R
2203 4531 2.076100 CTTCATGTTCAAGGCGTGCTA 58.924 47.619 0.0 0.0 0.0 3.49 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
24 25 1.667724 CCTCACTCATCGCCATTGAAC 59.332 52.381 0.00 0.0 0.00 3.18
649 652 4.058817 GTTCTCAACAAGAATGTCCTCGT 58.941 43.478 0.00 0.0 45.57 4.18
712 715 4.572985 TTTCAACATTTGAGTGCCTGAG 57.427 40.909 0.00 0.0 41.38 3.35
834 1036 2.433838 CACAGCTCTGACCCAGCG 60.434 66.667 3.60 0.0 42.14 5.18
1011 1225 0.956633 CAAATCACAGCACCAGCAGT 59.043 50.000 0.00 0.0 45.49 4.40
1018 1232 2.111878 GCACCAGCAGTCACCACT 59.888 61.111 0.00 0.0 41.58 4.00
1291 1515 2.652530 GCCGTCACCTACACCGAA 59.347 61.111 0.00 0.0 0.00 4.30
1446 1713 4.202558 CGACTTGTCTAGTTCGCTATTTCG 59.797 45.833 0.00 0.0 37.17 3.46
1480 1753 4.552166 ACTGAATCGTGGAACAAAGTTG 57.448 40.909 0.00 0.0 44.16 3.16
1572 1847 2.634453 TGGTCTTCTGCATCTCTGTTGA 59.366 45.455 0.00 0.0 0.00 3.18
1573 1848 3.071457 TGGTCTTCTGCATCTCTGTTGAA 59.929 43.478 0.00 0.0 0.00 2.69
1575 1850 4.699257 GGTCTTCTGCATCTCTGTTGAAAT 59.301 41.667 0.00 0.0 0.00 2.17
1577 1852 6.294397 GGTCTTCTGCATCTCTGTTGAAATTT 60.294 38.462 0.00 0.0 0.00 1.82
1578 1853 6.581542 GTCTTCTGCATCTCTGTTGAAATTTG 59.418 38.462 0.00 0.0 0.00 2.32
1580 1855 6.005583 TCTGCATCTCTGTTGAAATTTGTC 57.994 37.500 0.00 0.0 0.00 3.18
1581 1856 5.766670 TCTGCATCTCTGTTGAAATTTGTCT 59.233 36.000 0.00 0.0 0.00 3.41
1582 1857 6.005583 TGCATCTCTGTTGAAATTTGTCTC 57.994 37.500 0.00 0.0 0.00 3.36
1586 1861 6.851222 TCTCTGTTGAAATTTGTCTCTGTC 57.149 37.500 0.00 0.0 0.00 3.51
1627 1947 5.772521 ACTTGTTTGCAGGCTAATTTGTAG 58.227 37.500 0.00 0.0 0.00 2.74
1632 1952 3.750371 TGCAGGCTAATTTGTAGTGTGT 58.250 40.909 0.00 0.0 0.00 3.72
1684 2008 5.491070 TCTCGATTCAGGAACATCATTTGT 58.509 37.500 0.00 0.0 41.53 2.83
1738 2062 3.686016 ACTGGACACCATCAATGTTACC 58.314 45.455 0.00 0.0 30.82 2.85
1763 2088 1.847737 TGGTACACCCAAAACTCAGGT 59.152 47.619 0.00 0.0 41.50 4.00
1764 2089 2.158726 TGGTACACCCAAAACTCAGGTC 60.159 50.000 0.00 0.0 41.50 3.85
1766 2091 2.818751 ACACCCAAAACTCAGGTCAA 57.181 45.000 0.00 0.0 0.00 3.18
1774 4075 5.070001 CCAAAACTCAGGTCAAGGATACAA 58.930 41.667 0.00 0.0 41.41 2.41
1901 4202 7.384932 TCAGAATGGTCACATATTGCTATTACG 59.615 37.037 0.00 0.0 35.94 3.18
1945 4246 4.654262 AGGTTCAACTTACTCTCCACTTCA 59.346 41.667 0.00 0.0 0.00 3.02
1971 4272 2.013563 GCATGGAATTGACTCGCCTCA 61.014 52.381 0.00 0.0 0.00 3.86
1979 4288 4.613925 ATTGACTCGCCTCATGATACAT 57.386 40.909 0.00 0.0 0.00 2.29
2005 4315 6.410540 TCTAGCTTTCTGAATTTCTCTTCCC 58.589 40.000 0.00 0.0 0.00 3.97
2013 4323 2.514458 ATTTCTCTTCCCGTTGCCAT 57.486 45.000 0.00 0.0 0.00 4.40
2141 4451 0.034186 TGCTGGGCTTGGATAACTGG 60.034 55.000 0.00 0.0 0.00 4.00
2203 4531 4.019174 CACTTGCATGGGAGGTTTATTCT 58.981 43.478 4.44 0.0 0.00 2.40
2211 4539 2.210961 GGAGGTTTATTCTAGCACGCC 58.789 52.381 0.00 0.0 0.00 5.68
2251 4602 2.166459 ACATACAGTGGGTGATGTCTCG 59.834 50.000 0.00 0.0 0.00 4.04
2275 4626 7.305474 CGTAAGAAAAAGTAAGCCACATGAAT 58.695 34.615 0.00 0.0 43.02 2.57
2596 4976 5.324409 AGACTTGATTTTCCTGGCACATAA 58.676 37.500 0.00 0.0 38.20 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.689080 ATGGCGATGAGTGAGGGAGT 60.689 55.000 0.00 0.0 0.00 3.85
2 3 0.178767 CAATGGCGATGAGTGAGGGA 59.821 55.000 0.00 0.0 0.00 4.20
4 5 1.667724 GTTCAATGGCGATGAGTGAGG 59.332 52.381 0.00 0.0 0.00 3.86
5 6 2.606725 GAGTTCAATGGCGATGAGTGAG 59.393 50.000 0.00 0.0 0.00 3.51
6 7 2.234661 AGAGTTCAATGGCGATGAGTGA 59.765 45.455 0.00 0.0 0.00 3.41
24 25 4.493547 AGTTCTTCAGCTCGATTCAAGAG 58.506 43.478 0.00 0.0 38.68 2.85
834 1036 3.279875 GGACCGATGGATTGGCGC 61.280 66.667 0.00 0.0 34.49 6.53
845 1047 2.358247 GCCGAAAGCTTGGACCGA 60.358 61.111 0.00 0.0 38.99 4.69
905 1107 1.608717 GCGGATGGAGTGGACAGTCT 61.609 60.000 0.00 0.0 0.00 3.24
909 1111 1.522092 GATGCGGATGGAGTGGACA 59.478 57.895 0.00 0.0 0.00 4.02
1011 1225 1.275291 GAATCGGAGGAACAGTGGTGA 59.725 52.381 0.00 0.0 0.00 4.02
1018 1232 2.093500 CAGATGTGGAATCGGAGGAACA 60.093 50.000 0.00 0.0 0.00 3.18
1132 1356 2.741985 TGGATGTTGTCGCGCAGG 60.742 61.111 8.75 0.0 0.00 4.85
1446 1713 3.979495 ACGATTCAGTTCGAACTACACAC 59.021 43.478 29.28 17.7 41.62 3.82
1480 1753 2.483583 TCCAACAAACACATGCGAAC 57.516 45.000 0.00 0.0 0.00 3.95
1572 1847 2.519013 GGGGCTGACAGAGACAAATTT 58.481 47.619 6.65 0.0 0.00 1.82
1573 1848 1.611673 CGGGGCTGACAGAGACAAATT 60.612 52.381 6.65 0.0 0.00 1.82
1575 1850 1.371183 CGGGGCTGACAGAGACAAA 59.629 57.895 6.65 0.0 0.00 2.83
1577 1852 2.805313 ATCCGGGGCTGACAGAGACA 62.805 60.000 6.65 0.0 0.00 3.41
1578 1853 2.060980 ATCCGGGGCTGACAGAGAC 61.061 63.158 6.65 0.0 0.00 3.36
1580 1855 1.617018 TTCATCCGGGGCTGACAGAG 61.617 60.000 6.65 0.0 0.00 3.35
1581 1856 0.982852 ATTCATCCGGGGCTGACAGA 60.983 55.000 6.65 0.0 0.00 3.41
1582 1857 0.107017 AATTCATCCGGGGCTGACAG 60.107 55.000 0.00 0.0 0.00 3.51
1586 1861 0.740737 GTTCAATTCATCCGGGGCTG 59.259 55.000 0.00 0.0 0.00 4.85
1684 2008 6.101650 TCAGATCAAGTAGCAGAAACAGAA 57.898 37.500 0.00 0.0 0.00 3.02
1747 2072 2.654863 CTTGACCTGAGTTTTGGGTGT 58.345 47.619 0.00 0.0 33.01 4.16
1750 2075 2.656947 TCCTTGACCTGAGTTTTGGG 57.343 50.000 0.00 0.0 0.00 4.12
1751 2076 4.651778 TGTATCCTTGACCTGAGTTTTGG 58.348 43.478 0.00 0.0 0.00 3.28
1752 2077 6.207417 ACATTGTATCCTTGACCTGAGTTTTG 59.793 38.462 0.00 0.0 0.00 2.44
1754 2079 5.880901 ACATTGTATCCTTGACCTGAGTTT 58.119 37.500 0.00 0.0 0.00 2.66
1755 2080 5.013079 TGACATTGTATCCTTGACCTGAGTT 59.987 40.000 0.00 0.0 0.00 3.01
1756 2081 4.532126 TGACATTGTATCCTTGACCTGAGT 59.468 41.667 0.00 0.0 0.00 3.41
1757 2082 4.872691 GTGACATTGTATCCTTGACCTGAG 59.127 45.833 0.00 0.0 0.00 3.35
1758 2083 4.285775 TGTGACATTGTATCCTTGACCTGA 59.714 41.667 0.00 0.0 0.00 3.86
1759 2084 4.578871 TGTGACATTGTATCCTTGACCTG 58.421 43.478 0.00 0.0 0.00 4.00
1760 2085 4.908601 TGTGACATTGTATCCTTGACCT 57.091 40.909 0.00 0.0 0.00 3.85
1763 2088 7.563906 TGTATCATGTGACATTGTATCCTTGA 58.436 34.615 0.00 0.0 0.00 3.02
1764 2089 7.790823 TGTATCATGTGACATTGTATCCTTG 57.209 36.000 0.00 0.0 0.00 3.61
1766 2091 6.994496 CCTTGTATCATGTGACATTGTATCCT 59.006 38.462 0.00 0.0 0.00 3.24
1774 4075 5.195185 TCAATGCCTTGTATCATGTGACAT 58.805 37.500 0.00 0.0 33.87 3.06
1840 4141 9.084164 GTAGCTAAGATCATTTACAAGTTCGAA 57.916 33.333 0.00 0.0 0.00 3.71
1901 4202 2.554142 GCAATAGCAAAAGCATTCCCC 58.446 47.619 0.00 0.0 41.58 4.81
1945 4246 3.612479 GCGAGTCAATTCCATGCAAAACT 60.612 43.478 0.00 0.0 0.00 2.66
1979 4288 7.391833 GGGAAGAGAAATTCAGAAAGCTAGAAA 59.608 37.037 0.00 0.0 0.00 2.52
2203 4531 2.076100 CTTCATGTTCAAGGCGTGCTA 58.924 47.619 0.00 0.0 0.00 3.49
2251 4602 9.476202 AAATTCATGTGGCTTACTTTTTCTTAC 57.524 29.630 0.00 0.0 0.00 2.34
2275 4626 8.723311 CGGAATGGTAAATTGTGAGTTACTAAA 58.277 33.333 0.00 0.0 36.74 1.85
2445 4801 6.339730 TGTTGTTCTTTTCAGCATTCAACAT 58.660 32.000 0.00 0.0 38.84 2.71
2446 4802 5.718146 TGTTGTTCTTTTCAGCATTCAACA 58.282 33.333 0.00 0.0 40.53 3.33
2447 4803 6.256321 ACATGTTGTTCTTTTCAGCATTCAAC 59.744 34.615 0.00 0.0 35.27 3.18
2449 4805 5.904941 ACATGTTGTTCTTTTCAGCATTCA 58.095 33.333 0.00 0.0 35.27 2.57


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

AutoCloner maintained by Alex Coulton.