Multiple sequence alignment - TraesCS1D01G196400

Loading Multiple Alignment...

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 TraesCS1D01G196400 chr1D 100.000 3836 0 0 1 3836 275945002 275941167 0.000000e+00 7084.0
1 TraesCS1D01G196400 chr1B 89.835 3453 137 85 103 3480 375259354 375256041 0.000000e+00 4235.0
2 TraesCS1D01G196400 chr1B 86.828 372 20 13 3471 3836 375256017 375255669 4.650000e-104 388.0
3 TraesCS1D01G196400 chr1A 87.325 3148 142 102 54 3060 348401528 348398497 0.000000e+00 3365.0
4 TraesCS1D01G196400 chr1A 89.106 817 46 8 3044 3836 348398267 348397470 0.000000e+00 976.0
5 TraesCS1D01G196400 chr5B 93.296 179 12 0 1784 1962 681847822 681848000 8.170000e-67 265.0
6 TraesCS1D01G196400 chr2A 82.533 229 18 12 2009 2235 697290087 697290295 8.470000e-42 182.0
7 TraesCS1D01G196400 chr2A 81.373 102 13 4 2369 2464 697290596 697290697 1.140000e-10 78.7
8 TraesCS1D01G196400 chr2A 85.714 56 5 2 2183 2235 727305424 727305479 5.350000e-04 56.5
9 TraesCS1D01G196400 chr2A 85.714 56 5 2 2183 2235 727350696 727350751 5.350000e-04 56.5
10 TraesCS1D01G196400 chr2D 81.553 103 13 4 2368 2464 557259390 557259492 3.180000e-11 80.5
11 TraesCS1D01G196400 chr2B 81.373 102 13 4 2368 2463 664934409 664934510 1.140000e-10 78.7


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 TraesCS1D01G196400 chr1D 275941167 275945002 3835 True 7084.0 7084 100.0000 1 3836 1 chr1D.!!$R1 3835
1 TraesCS1D01G196400 chr1B 375255669 375259354 3685 True 2311.5 4235 88.3315 103 3836 2 chr1B.!!$R1 3733
2 TraesCS1D01G196400 chr1A 348397470 348401528 4058 True 2170.5 3365 88.2155 54 3836 2 chr1A.!!$R1 3782

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
495 525 0.037046 CATTTTGCCTGCCCCTTCAC 60.037 55.0 0.0 0.0 0.0 3.18 F
845 898 0.105504 CCCATTCCCATTCCCCTTCC 60.106 60.0 0.0 0.0 0.0 3.46 F
848 901 0.254784 ATTCCCATTCCCCTTCCCCT 60.255 55.0 0.0 0.0 0.0 4.79 F
849 902 0.481607 TTCCCATTCCCCTTCCCCTT 60.482 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 1659 0.413037 ACCAAATTCCAGGGCATCCA 59.587 50.000 0.00 0.00 34.83 3.41 R
1656 1814 1.843368 AACATTGGCATCCTGACAGG 58.157 50.000 15.99 15.99 36.33 4.00 R
2828 3024 1.873591 CGCATTGCCTGGTATTACCTC 59.126 52.381 13.90 4.35 39.58 3.85 R
2857 3053 7.359933 GCAATTGCTTATTACTCTAGCTAGCTG 60.360 40.741 27.68 16.48 38.21 4.24 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
20 21 3.133141 ACCAAAGTGCTCTCTTTCCTC 57.867 47.619 0.00 0.00 35.77 3.71
21 22 2.708325 ACCAAAGTGCTCTCTTTCCTCT 59.292 45.455 0.00 0.00 35.77 3.69
22 23 3.137360 ACCAAAGTGCTCTCTTTCCTCTT 59.863 43.478 0.00 0.00 35.77 2.85
23 24 4.140536 CCAAAGTGCTCTCTTTCCTCTTT 58.859 43.478 0.00 0.00 35.77 2.52
24 25 5.163195 ACCAAAGTGCTCTCTTTCCTCTTTA 60.163 40.000 0.00 0.00 35.77 1.85
25 26 5.765182 CCAAAGTGCTCTCTTTCCTCTTTAA 59.235 40.000 0.00 0.00 35.77 1.52
26 27 6.263168 CCAAAGTGCTCTCTTTCCTCTTTAAA 59.737 38.462 0.00 0.00 35.77 1.52
27 28 7.040132 CCAAAGTGCTCTCTTTCCTCTTTAAAT 60.040 37.037 0.00 0.00 35.77 1.40
28 29 7.446001 AAGTGCTCTCTTTCCTCTTTAAATG 57.554 36.000 0.00 0.00 0.00 2.32
29 30 5.414144 AGTGCTCTCTTTCCTCTTTAAATGC 59.586 40.000 0.00 0.00 0.00 3.56
30 31 5.414144 GTGCTCTCTTTCCTCTTTAAATGCT 59.586 40.000 0.00 0.00 0.00 3.79
31 32 6.595716 GTGCTCTCTTTCCTCTTTAAATGCTA 59.404 38.462 0.00 0.00 0.00 3.49
32 33 7.281999 GTGCTCTCTTTCCTCTTTAAATGCTAT 59.718 37.037 0.00 0.00 0.00 2.97
33 34 7.281774 TGCTCTCTTTCCTCTTTAAATGCTATG 59.718 37.037 0.00 0.00 0.00 2.23
34 35 7.559590 TCTCTTTCCTCTTTAAATGCTATGC 57.440 36.000 0.00 0.00 0.00 3.14
35 36 6.543831 TCTCTTTCCTCTTTAAATGCTATGCC 59.456 38.462 0.00 0.00 0.00 4.40
36 37 6.186957 TCTTTCCTCTTTAAATGCTATGCCA 58.813 36.000 0.00 0.00 0.00 4.92
37 38 6.835488 TCTTTCCTCTTTAAATGCTATGCCAT 59.165 34.615 0.00 0.00 0.00 4.40
38 39 7.998383 TCTTTCCTCTTTAAATGCTATGCCATA 59.002 33.333 0.00 0.00 0.00 2.74
39 40 8.710749 TTTCCTCTTTAAATGCTATGCCATAT 57.289 30.769 0.00 0.00 0.00 1.78
40 41 8.710749 TTCCTCTTTAAATGCTATGCCATATT 57.289 30.769 0.00 0.00 0.00 1.28
41 42 9.806448 TTCCTCTTTAAATGCTATGCCATATTA 57.194 29.630 0.00 0.00 0.00 0.98
42 43 9.806448 TCCTCTTTAAATGCTATGCCATATTAA 57.194 29.630 0.00 0.00 0.00 1.40
69 70 5.794687 TTCCGCTTATGTGACATGTTTAG 57.205 39.130 8.61 1.85 0.00 1.85
74 75 5.514279 GCTTATGTGACATGTTTAGCATCC 58.486 41.667 8.61 0.00 35.19 3.51
77 78 1.737236 GTGACATGTTTAGCATCCGCA 59.263 47.619 0.00 0.00 42.27 5.69
81 82 0.726827 ATGTTTAGCATCCGCACACG 59.273 50.000 0.00 0.00 42.27 4.49
92 93 2.595707 CGCACACGGTGAAACACTA 58.404 52.632 16.29 0.00 39.98 2.74
94 95 0.234884 GCACACGGTGAAACACTAGC 59.765 55.000 16.29 2.10 39.98 3.42
96 97 1.937223 CACACGGTGAAACACTAGCAA 59.063 47.619 16.29 0.00 39.98 3.91
98 99 2.159014 ACACGGTGAAACACTAGCAAGA 60.159 45.455 16.29 0.00 39.98 3.02
99 100 2.476619 CACGGTGAAACACTAGCAAGAG 59.523 50.000 0.74 0.00 39.98 2.85
100 101 2.102588 ACGGTGAAACACTAGCAAGAGT 59.897 45.455 0.00 0.00 39.98 3.24
101 102 2.731976 CGGTGAAACACTAGCAAGAGTC 59.268 50.000 0.00 0.00 39.98 3.36
107 108 6.647067 GTGAAACACTAGCAAGAGTCTAATGT 59.353 38.462 0.00 0.00 36.32 2.71
113 114 7.090808 CACTAGCAAGAGTCTAATGTGTGTTA 58.909 38.462 0.00 0.00 0.00 2.41
127 128 4.989277 TGTGTGTTACTACTCTACTCCCA 58.011 43.478 0.00 0.00 0.00 4.37
148 155 2.549754 AGCACACACACAAATGAGTAGC 59.450 45.455 0.00 0.00 33.06 3.58
156 165 3.264450 ACACAAATGAGTAGCCTTAGCCT 59.736 43.478 0.00 0.00 41.25 4.58
168 177 2.711542 CCTTAGCCTTCATCAACCGTT 58.288 47.619 0.00 0.00 0.00 4.44
177 186 6.015434 AGCCTTCATCAACCGTTAAAAAGATT 60.015 34.615 0.00 0.00 0.00 2.40
257 275 2.069273 CTAAACCTGTGAAGCACGGAG 58.931 52.381 7.91 1.57 42.79 4.63
265 283 0.315886 TGAAGCACGGAGAAAGCGTA 59.684 50.000 0.00 0.00 0.00 4.42
323 345 4.569180 CACATGCGGGGCTAGGGG 62.569 72.222 0.00 0.00 0.00 4.79
341 363 1.203001 GGGATCAGGACCACCACAAAA 60.203 52.381 0.00 0.00 38.94 2.44
399 429 0.538746 GGTGGGGTGAAATGTCCGTT 60.539 55.000 0.00 0.00 0.00 4.44
430 460 2.835895 AACACGTGCCCAAACCCC 60.836 61.111 17.22 0.00 0.00 4.95
431 461 4.906537 ACACGTGCCCAAACCCCC 62.907 66.667 17.22 0.00 0.00 5.40
433 463 4.144727 ACGTGCCCAAACCCCCAA 62.145 61.111 0.00 0.00 0.00 4.12
435 465 2.922503 GTGCCCAAACCCCCAAGG 60.923 66.667 0.00 0.00 43.78 3.61
437 467 2.202899 GCCCAAACCCCCAAGGAA 59.797 61.111 0.00 0.00 39.89 3.36
438 468 1.913262 GCCCAAACCCCCAAGGAAG 60.913 63.158 0.00 0.00 39.89 3.46
440 470 0.189822 CCCAAACCCCCAAGGAAGAA 59.810 55.000 0.00 0.00 39.89 2.52
443 473 2.425683 CCAAACCCCCAAGGAAGAAGAA 60.426 50.000 0.00 0.00 39.89 2.52
444 474 2.893489 CAAACCCCCAAGGAAGAAGAAG 59.107 50.000 0.00 0.00 39.89 2.85
445 475 1.076438 ACCCCCAAGGAAGAAGAAGG 58.924 55.000 0.00 0.00 39.89 3.46
447 477 1.076438 CCCCAAGGAAGAAGAAGGGT 58.924 55.000 0.00 0.00 34.44 4.34
448 478 1.429299 CCCCAAGGAAGAAGAAGGGTT 59.571 52.381 0.00 0.00 34.44 4.11
449 479 2.158310 CCCCAAGGAAGAAGAAGGGTTT 60.158 50.000 0.00 0.00 34.44 3.27
485 515 2.992164 GCCCCATGCATTTTGCCT 59.008 55.556 0.00 0.00 44.23 4.75
486 516 1.450669 GCCCCATGCATTTTGCCTG 60.451 57.895 0.00 0.00 44.23 4.85
487 517 1.450669 CCCCATGCATTTTGCCTGC 60.451 57.895 0.00 0.00 44.23 4.85
488 518 1.450669 CCCATGCATTTTGCCTGCC 60.451 57.895 0.00 0.00 44.23 4.85
491 521 1.614226 ATGCATTTTGCCTGCCCCT 60.614 52.632 0.00 0.00 44.23 4.79
492 522 1.202769 ATGCATTTTGCCTGCCCCTT 61.203 50.000 0.00 0.00 44.23 3.95
493 523 1.078918 GCATTTTGCCTGCCCCTTC 60.079 57.895 0.00 0.00 37.42 3.46
494 524 1.829523 GCATTTTGCCTGCCCCTTCA 61.830 55.000 0.00 0.00 37.42 3.02
495 525 0.037046 CATTTTGCCTGCCCCTTCAC 60.037 55.000 0.00 0.00 0.00 3.18
496 526 0.178924 ATTTTGCCTGCCCCTTCACT 60.179 50.000 0.00 0.00 0.00 3.41
497 527 0.480690 TTTTGCCTGCCCCTTCACTA 59.519 50.000 0.00 0.00 0.00 2.74
498 528 0.480690 TTTGCCTGCCCCTTCACTAA 59.519 50.000 0.00 0.00 0.00 2.24
499 529 0.251165 TTGCCTGCCCCTTCACTAAC 60.251 55.000 0.00 0.00 0.00 2.34
500 530 1.378646 GCCTGCCCCTTCACTAACC 60.379 63.158 0.00 0.00 0.00 2.85
501 531 2.074967 CCTGCCCCTTCACTAACCA 58.925 57.895 0.00 0.00 0.00 3.67
502 532 0.625849 CCTGCCCCTTCACTAACCAT 59.374 55.000 0.00 0.00 0.00 3.55
503 533 1.408822 CCTGCCCCTTCACTAACCATC 60.409 57.143 0.00 0.00 0.00 3.51
504 534 1.281867 CTGCCCCTTCACTAACCATCA 59.718 52.381 0.00 0.00 0.00 3.07
505 535 1.281867 TGCCCCTTCACTAACCATCAG 59.718 52.381 0.00 0.00 0.00 2.90
506 536 1.559682 GCCCCTTCACTAACCATCAGA 59.440 52.381 0.00 0.00 0.00 3.27
507 537 2.681097 GCCCCTTCACTAACCATCAGAC 60.681 54.545 0.00 0.00 0.00 3.51
508 538 2.092914 CCCCTTCACTAACCATCAGACC 60.093 54.545 0.00 0.00 0.00 3.85
509 539 2.571653 CCCTTCACTAACCATCAGACCA 59.428 50.000 0.00 0.00 0.00 4.02
510 540 3.600388 CCTTCACTAACCATCAGACCAC 58.400 50.000 0.00 0.00 0.00 4.16
525 555 0.179056 ACCACAAACCTGAGGTCACG 60.179 55.000 3.76 0.00 42.25 4.35
554 588 7.811713 GCAGGAGGCTTAATCAATCAATTAATC 59.188 37.037 0.00 0.00 40.25 1.75
585 619 4.003648 ACTTCGCTTTCAATCCCTGTTAG 58.996 43.478 0.00 0.00 0.00 2.34
841 894 1.543690 CCTCCCATTCCCATTCCCC 59.456 63.158 0.00 0.00 0.00 4.81
845 898 0.105504 CCCATTCCCATTCCCCTTCC 60.106 60.000 0.00 0.00 0.00 3.46
846 899 0.105504 CCATTCCCATTCCCCTTCCC 60.106 60.000 0.00 0.00 0.00 3.97
847 900 0.105504 CATTCCCATTCCCCTTCCCC 60.106 60.000 0.00 0.00 0.00 4.81
848 901 0.254784 ATTCCCATTCCCCTTCCCCT 60.255 55.000 0.00 0.00 0.00 4.79
849 902 0.481607 TTCCCATTCCCCTTCCCCTT 60.482 55.000 0.00 0.00 0.00 3.95
899 956 3.622630 GTCTACTTCTAGACTCCCAGCA 58.377 50.000 0.00 0.00 44.02 4.41
1143 1247 2.188947 TAACCCACCCTCCTCCCCT 61.189 63.158 0.00 0.00 0.00 4.79
1227 1336 7.628769 AGTAGTAGTAGTAGTTTCTTGGCTC 57.371 40.000 0.00 0.00 0.00 4.70
1230 1339 4.175787 AGTAGTAGTTTCTTGGCTCGTG 57.824 45.455 0.00 0.00 0.00 4.35
1233 1342 1.194772 GTAGTTTCTTGGCTCGTGTGC 59.805 52.381 0.00 0.00 0.00 4.57
1234 1343 1.082756 GTTTCTTGGCTCGTGTGCG 60.083 57.895 0.00 0.00 39.92 5.34
1317 1464 2.202349 GCGTGCGGATTGCTGTTC 60.202 61.111 0.00 0.00 46.63 3.18
1321 1468 2.334946 TGCGGATTGCTGTTCCTGC 61.335 57.895 0.00 0.00 46.63 4.85
1328 1475 4.099170 GCTGTTCCTGCTGCTGCG 62.099 66.667 11.21 5.84 43.34 5.18
1389 1538 4.107622 CGGTCAAAGCATTGATTGATTCC 58.892 43.478 7.74 2.44 46.67 3.01
1399 1548 5.126707 GCATTGATTGATTCCTGAGGTTTCT 59.873 40.000 0.00 0.00 0.00 2.52
1403 1552 3.340814 TGATTCCTGAGGTTTCTCTGC 57.659 47.619 0.00 0.00 40.58 4.26
1418 1567 0.887387 TCTGCCTTGTGCGTTAACCC 60.887 55.000 0.00 0.00 45.60 4.11
1419 1568 1.862602 CTGCCTTGTGCGTTAACCCC 61.863 60.000 0.00 0.00 45.60 4.95
1420 1569 2.973316 GCCTTGTGCGTTAACCCCG 61.973 63.158 0.00 0.00 0.00 5.73
1421 1570 2.329614 CCTTGTGCGTTAACCCCGG 61.330 63.158 0.00 0.00 0.00 5.73
1422 1571 2.973316 CTTGTGCGTTAACCCCGGC 61.973 63.158 0.00 0.00 0.00 6.13
1457 1606 2.194868 CCCCGCCCCCTGATTAAC 59.805 66.667 0.00 0.00 0.00 2.01
1463 1612 1.453197 CCCCCTGATTAACGGTGGC 60.453 63.158 0.00 0.00 0.00 5.01
1480 1629 2.096248 TGGCGTTTCTGTTTTGGTTCT 58.904 42.857 0.00 0.00 0.00 3.01
1486 1635 1.305201 TCTGTTTTGGTTCTGCGTCC 58.695 50.000 0.00 0.00 0.00 4.79
1517 1666 2.234300 CAGCATTTGGATTGGATGCC 57.766 50.000 4.12 0.00 45.50 4.40
1518 1667 1.125633 AGCATTTGGATTGGATGCCC 58.874 50.000 4.12 0.00 45.50 5.36
1556 1709 6.094186 CCAGTCCTAGCCTTTATGTTTTCTTC 59.906 42.308 0.00 0.00 0.00 2.87
1588 1741 9.784680 CTTCTCTTTGGTTGATTGATTGATAAG 57.215 33.333 0.00 0.00 0.00 1.73
1590 1743 9.958180 TCTCTTTGGTTGATTGATTGATAAGTA 57.042 29.630 0.00 0.00 0.00 2.24
1595 1748 8.196802 TGGTTGATTGATTGATAAGTAAGTCG 57.803 34.615 0.00 0.00 0.00 4.18
1596 1749 7.822334 TGGTTGATTGATTGATAAGTAAGTCGT 59.178 33.333 0.00 0.00 0.00 4.34
1597 1750 9.309516 GGTTGATTGATTGATAAGTAAGTCGTA 57.690 33.333 0.00 0.00 0.00 3.43
1630 1787 2.417933 GCAATCTTGTCAGCGTTCAGAT 59.582 45.455 0.00 0.00 0.00 2.90
1647 1805 6.074941 CGTTCAGATGAGATCGATTTCTTGAG 60.075 42.308 16.09 5.86 33.72 3.02
1648 1806 5.840715 TCAGATGAGATCGATTTCTTGAGG 58.159 41.667 16.09 3.88 0.00 3.86
1649 1807 5.362143 TCAGATGAGATCGATTTCTTGAGGT 59.638 40.000 16.09 0.00 0.00 3.85
1650 1808 6.047870 CAGATGAGATCGATTTCTTGAGGTT 58.952 40.000 16.09 0.00 0.00 3.50
1651 1809 6.200665 CAGATGAGATCGATTTCTTGAGGTTC 59.799 42.308 16.09 3.64 0.00 3.62
1652 1810 4.759782 TGAGATCGATTTCTTGAGGTTCC 58.240 43.478 16.09 0.00 0.00 3.62
1653 1811 4.467795 TGAGATCGATTTCTTGAGGTTCCT 59.532 41.667 16.09 0.00 0.00 3.36
1654 1812 5.046304 TGAGATCGATTTCTTGAGGTTCCTT 60.046 40.000 16.09 0.00 0.00 3.36
1655 1813 5.810095 AGATCGATTTCTTGAGGTTCCTTT 58.190 37.500 0.00 0.00 0.00 3.11
1656 1814 5.877564 AGATCGATTTCTTGAGGTTCCTTTC 59.122 40.000 0.00 0.00 0.00 2.62
1657 1815 4.324267 TCGATTTCTTGAGGTTCCTTTCC 58.676 43.478 0.00 0.00 0.00 3.13
1686 1844 0.810648 GCCAATGTTTCCATCGCTGA 59.189 50.000 0.00 0.00 0.00 4.26
1730 1890 1.668751 TCTTTCTTGTGGTTGTCGTGC 59.331 47.619 0.00 0.00 0.00 5.34
2471 2643 1.293924 GGCAACCTCATCATCGACTG 58.706 55.000 0.00 0.00 0.00 3.51
2512 2687 0.537143 ATTGACAAAGCTGCGACCCA 60.537 50.000 0.00 0.00 0.00 4.51
2662 2837 0.926293 GGGAGGTGGATGGATGGAAA 59.074 55.000 0.00 0.00 0.00 3.13
2966 3170 3.431486 GGGAGAGGATGACTGCTTGTTAG 60.431 52.174 0.00 0.00 0.00 2.34
2967 3171 3.449018 GGAGAGGATGACTGCTTGTTAGA 59.551 47.826 0.00 0.00 0.00 2.10
3018 3222 2.380064 TTCCATATGGGTCAATGGCC 57.620 50.000 21.78 0.00 42.08 5.36
3019 3223 1.230074 TCCATATGGGTCAATGGCCA 58.770 50.000 21.78 8.56 42.08 5.36
3021 3225 1.133388 CCATATGGGTCAATGGCCAGT 60.133 52.381 13.05 5.37 36.50 4.00
3150 3598 3.723922 ACGTTAATGCCGCCCCCT 61.724 61.111 0.00 0.00 0.00 4.79
3183 3631 1.000233 CACAGCTTGCGTTGATGCAC 61.000 55.000 0.00 0.00 46.25 4.57
3217 3665 6.367695 CGAATGTGACGGCCTGATTAATTATA 59.632 38.462 0.00 0.00 0.00 0.98
3219 3667 8.635765 AATGTGACGGCCTGATTAATTATAAT 57.364 30.769 0.00 0.00 34.40 1.28
3220 3668 8.635765 ATGTGACGGCCTGATTAATTATAATT 57.364 30.769 14.86 14.86 31.83 1.40
3221 3669 9.733556 ATGTGACGGCCTGATTAATTATAATTA 57.266 29.630 12.90 12.90 31.83 1.40
3224 3672 9.952030 TGACGGCCTGATTAATTATAATTATCA 57.048 29.630 16.71 17.99 31.83 2.15
3226 3674 9.959721 ACGGCCTGATTAATTATAATTATCACT 57.040 29.630 16.71 4.82 31.83 3.41
3253 3701 6.381801 CAATTAATCGGCTTCTTGTTCTTGT 58.618 36.000 0.00 0.00 0.00 3.16
3297 3745 7.008628 CGGCATTAAACTAAGCTGAATTTGAAG 59.991 37.037 0.00 0.00 35.42 3.02
3417 3876 3.118992 GGGGAGATGCCACATTTTTCTTC 60.119 47.826 0.00 0.00 41.00 2.87
3419 3878 4.021192 GGGAGATGCCACATTTTTCTTCAA 60.021 41.667 0.00 0.00 38.95 2.69
3428 3887 6.054295 CCACATTTTTCTTCAATTGGAACCA 58.946 36.000 5.42 0.00 0.00 3.67
3460 3922 0.463295 AGCATCTTGCCATCTCCGTG 60.463 55.000 0.00 0.00 46.52 4.94
3583 4078 5.673068 GCAAATTGCAATGTGTTTGTGTGAA 60.673 36.000 26.59 0.00 44.26 3.18
3589 4084 4.569966 GCAATGTGTTTGTGTGAATTGGAA 59.430 37.500 0.00 0.00 37.65 3.53
3604 4099 0.768622 TGGAACGAACATTGGGAGGT 59.231 50.000 0.00 0.00 0.00 3.85
3620 4115 3.262151 GGGAGGTAGCAGAGACTTTTTCT 59.738 47.826 0.00 0.00 37.23 2.52
3622 4117 4.932799 GGAGGTAGCAGAGACTTTTTCTTC 59.067 45.833 0.00 0.00 33.22 2.87
3674 4178 2.196595 CCTCTTTCAGTGGGGTGGATA 58.803 52.381 0.00 0.00 0.00 2.59
3796 4302 1.913403 GTGCAAAATCGAGCGGAAATG 59.087 47.619 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.708325 AGAGGAAAGAGAGCACTTTGGT 59.292 45.455 7.96 0.00 39.71 3.67
1 2 3.415457 AGAGGAAAGAGAGCACTTTGG 57.585 47.619 7.96 0.00 39.71 3.28
2 3 6.867662 TTAAAGAGGAAAGAGAGCACTTTG 57.132 37.500 7.96 0.00 39.71 2.77
3 4 7.522889 GCATTTAAAGAGGAAAGAGAGCACTTT 60.523 37.037 0.00 0.00 41.86 2.66
4 5 6.072230 GCATTTAAAGAGGAAAGAGAGCACTT 60.072 38.462 0.00 0.00 0.00 3.16
5 6 5.414144 GCATTTAAAGAGGAAAGAGAGCACT 59.586 40.000 0.00 0.00 0.00 4.40
6 7 5.414144 AGCATTTAAAGAGGAAAGAGAGCAC 59.586 40.000 0.00 0.00 0.00 4.40
7 8 5.564550 AGCATTTAAAGAGGAAAGAGAGCA 58.435 37.500 0.00 0.00 0.00 4.26
8 9 7.638134 CATAGCATTTAAAGAGGAAAGAGAGC 58.362 38.462 0.00 0.00 0.00 4.09
9 10 7.255070 GGCATAGCATTTAAAGAGGAAAGAGAG 60.255 40.741 0.00 0.00 0.00 3.20
10 11 6.543831 GGCATAGCATTTAAAGAGGAAAGAGA 59.456 38.462 0.00 0.00 0.00 3.10
11 12 6.319658 TGGCATAGCATTTAAAGAGGAAAGAG 59.680 38.462 0.00 0.00 0.00 2.85
12 13 6.186957 TGGCATAGCATTTAAAGAGGAAAGA 58.813 36.000 0.00 0.00 0.00 2.52
13 14 6.455360 TGGCATAGCATTTAAAGAGGAAAG 57.545 37.500 0.00 0.00 0.00 2.62
14 15 8.710749 ATATGGCATAGCATTTAAAGAGGAAA 57.289 30.769 13.39 0.00 0.00 3.13
15 16 8.710749 AATATGGCATAGCATTTAAAGAGGAA 57.289 30.769 13.39 0.00 0.00 3.36
16 17 9.806448 TTAATATGGCATAGCATTTAAAGAGGA 57.194 29.630 13.39 0.00 0.00 3.71
44 45 5.446143 AACATGTCACATAAGCGGAAAAA 57.554 34.783 0.00 0.00 0.00 1.94
45 46 5.446143 AAACATGTCACATAAGCGGAAAA 57.554 34.783 0.00 0.00 0.00 2.29
46 47 5.391523 GCTAAACATGTCACATAAGCGGAAA 60.392 40.000 0.00 0.00 0.00 3.13
47 48 4.094294 GCTAAACATGTCACATAAGCGGAA 59.906 41.667 0.00 0.00 0.00 4.30
48 49 3.621268 GCTAAACATGTCACATAAGCGGA 59.379 43.478 0.00 0.00 0.00 5.54
49 50 3.373748 TGCTAAACATGTCACATAAGCGG 59.626 43.478 0.00 0.00 0.00 5.52
50 51 4.598406 TGCTAAACATGTCACATAAGCG 57.402 40.909 0.00 0.00 0.00 4.68
51 52 5.514279 GGATGCTAAACATGTCACATAAGC 58.486 41.667 0.00 3.15 39.84 3.09
52 53 5.741425 CGGATGCTAAACATGTCACATAAG 58.259 41.667 0.00 0.00 39.84 1.73
56 57 1.737236 GCGGATGCTAAACATGTCACA 59.263 47.619 0.00 0.00 39.84 3.58
74 75 0.506932 CTAGTGTTTCACCGTGTGCG 59.493 55.000 0.00 0.00 34.49 5.34
77 78 2.159014 TCTTGCTAGTGTTTCACCGTGT 60.159 45.455 0.00 0.00 34.49 4.49
81 82 3.996480 AGACTCTTGCTAGTGTTTCACC 58.004 45.455 4.43 0.00 34.49 4.02
85 86 6.425114 CACACATTAGACTCTTGCTAGTGTTT 59.575 38.462 4.43 2.01 36.88 2.83
90 91 7.316640 AGTAACACACATTAGACTCTTGCTAG 58.683 38.462 0.00 0.00 0.00 3.42
92 93 6.102897 AGTAACACACATTAGACTCTTGCT 57.897 37.500 0.00 0.00 0.00 3.91
94 95 8.516234 AGAGTAGTAACACACATTAGACTCTTG 58.484 37.037 0.00 0.00 36.26 3.02
96 97 9.165035 GTAGAGTAGTAACACACATTAGACTCT 57.835 37.037 0.00 0.00 39.55 3.24
98 99 9.165035 GAGTAGAGTAGTAACACACATTAGACT 57.835 37.037 0.00 0.00 0.00 3.24
99 100 8.397148 GGAGTAGAGTAGTAACACACATTAGAC 58.603 40.741 0.00 0.00 0.00 2.59
100 101 7.555554 GGGAGTAGAGTAGTAACACACATTAGA 59.444 40.741 0.00 0.00 0.00 2.10
101 102 7.338703 TGGGAGTAGAGTAGTAACACACATTAG 59.661 40.741 0.00 0.00 0.00 1.73
107 108 4.015084 GCTGGGAGTAGAGTAGTAACACA 58.985 47.826 0.00 0.00 0.00 3.72
113 114 2.225041 TGTGTGCTGGGAGTAGAGTAGT 60.225 50.000 0.00 0.00 0.00 2.73
127 128 2.549754 GCTACTCATTTGTGTGTGTGCT 59.450 45.455 0.00 0.00 0.00 4.40
148 155 2.403252 ACGGTTGATGAAGGCTAAGG 57.597 50.000 0.00 0.00 0.00 2.69
187 196 9.647797 TCGAATAAATATATGTCACGGCTATTT 57.352 29.630 0.00 0.00 0.00 1.40
188 197 9.647797 TTCGAATAAATATATGTCACGGCTATT 57.352 29.630 0.00 0.00 0.00 1.73
189 198 9.817809 ATTCGAATAAATATATGTCACGGCTAT 57.182 29.630 9.39 0.00 0.00 2.97
257 275 4.534168 GTTTCTCTTTGGGTTACGCTTTC 58.466 43.478 0.36 0.00 0.00 2.62
265 283 1.652563 GCGCGTTTCTCTTTGGGTT 59.347 52.632 8.43 0.00 0.00 4.11
323 345 2.293399 GTGTTTTGTGGTGGTCCTGATC 59.707 50.000 0.00 0.00 34.23 2.92
399 429 0.599558 CGTGTTCCCTACTTGGACGA 59.400 55.000 0.00 0.00 35.22 4.20
430 460 2.893489 CCAAACCCTTCTTCTTCCTTGG 59.107 50.000 0.00 0.00 0.00 3.61
431 461 2.893489 CCCAAACCCTTCTTCTTCCTTG 59.107 50.000 0.00 0.00 0.00 3.61
433 463 2.144450 ACCCAAACCCTTCTTCTTCCT 58.856 47.619 0.00 0.00 0.00 3.36
435 465 1.613925 GCACCCAAACCCTTCTTCTTC 59.386 52.381 0.00 0.00 0.00 2.87
437 467 0.555769 TGCACCCAAACCCTTCTTCT 59.444 50.000 0.00 0.00 0.00 2.85
438 468 0.673985 GTGCACCCAAACCCTTCTTC 59.326 55.000 5.22 0.00 0.00 2.87
440 470 1.152546 GGTGCACCCAAACCCTTCT 60.153 57.895 26.31 0.00 0.00 2.85
481 511 1.378762 GTTAGTGAAGGGGCAGGCA 59.621 57.895 0.00 0.00 0.00 4.75
484 514 1.281867 TGATGGTTAGTGAAGGGGCAG 59.718 52.381 0.00 0.00 0.00 4.85
485 515 1.281867 CTGATGGTTAGTGAAGGGGCA 59.718 52.381 0.00 0.00 0.00 5.36
486 516 1.559682 TCTGATGGTTAGTGAAGGGGC 59.440 52.381 0.00 0.00 0.00 5.80
487 517 2.092914 GGTCTGATGGTTAGTGAAGGGG 60.093 54.545 0.00 0.00 0.00 4.79
488 518 2.571653 TGGTCTGATGGTTAGTGAAGGG 59.428 50.000 0.00 0.00 0.00 3.95
491 521 4.698201 TTGTGGTCTGATGGTTAGTGAA 57.302 40.909 0.00 0.00 0.00 3.18
492 522 4.385825 GTTTGTGGTCTGATGGTTAGTGA 58.614 43.478 0.00 0.00 0.00 3.41
493 523 3.502211 GGTTTGTGGTCTGATGGTTAGTG 59.498 47.826 0.00 0.00 0.00 2.74
494 524 3.394606 AGGTTTGTGGTCTGATGGTTAGT 59.605 43.478 0.00 0.00 0.00 2.24
495 525 3.753272 CAGGTTTGTGGTCTGATGGTTAG 59.247 47.826 0.00 0.00 0.00 2.34
496 526 3.392947 TCAGGTTTGTGGTCTGATGGTTA 59.607 43.478 0.00 0.00 33.21 2.85
497 527 2.174639 TCAGGTTTGTGGTCTGATGGTT 59.825 45.455 0.00 0.00 33.21 3.67
498 528 1.774254 TCAGGTTTGTGGTCTGATGGT 59.226 47.619 0.00 0.00 33.21 3.55
499 529 2.430465 CTCAGGTTTGTGGTCTGATGG 58.570 52.381 0.00 0.00 36.99 3.51
500 530 2.224621 ACCTCAGGTTTGTGGTCTGATG 60.225 50.000 0.00 0.00 45.59 3.07
501 531 2.057922 ACCTCAGGTTTGTGGTCTGAT 58.942 47.619 0.00 0.00 45.59 2.90
502 532 1.507140 ACCTCAGGTTTGTGGTCTGA 58.493 50.000 0.00 0.00 45.59 3.27
507 537 0.884704 CCGTGACCTCAGGTTTGTGG 60.885 60.000 0.00 0.00 42.41 4.17
508 538 0.105964 TCCGTGACCTCAGGTTTGTG 59.894 55.000 0.00 0.00 35.25 3.33
509 539 0.393077 CTCCGTGACCTCAGGTTTGT 59.607 55.000 0.00 0.00 35.25 2.83
510 540 0.951040 GCTCCGTGACCTCAGGTTTG 60.951 60.000 0.00 0.00 35.25 2.93
585 619 2.158813 TCCCTCCCTCGCATTTGATTAC 60.159 50.000 0.00 0.00 0.00 1.89
655 704 6.569179 AACCCCGGATTAATTAATTGATCG 57.431 37.500 20.54 16.51 34.63 3.69
769 822 0.247736 ATCGTCCCAAGTCAGTCAGC 59.752 55.000 0.00 0.00 0.00 4.26
1124 1224 1.693103 GGGGAGGAGGGTGGGTTAG 60.693 68.421 0.00 0.00 0.00 2.34
1143 1247 1.335132 CGCAGCTAGGTAGGGGGAAA 61.335 60.000 0.00 0.00 0.00 3.13
1178 1284 0.707024 TCAAGCAGGAGAGGAGAGGA 59.293 55.000 0.00 0.00 0.00 3.71
1179 1285 1.792115 ATCAAGCAGGAGAGGAGAGG 58.208 55.000 0.00 0.00 0.00 3.69
1180 1286 2.158928 CCAATCAAGCAGGAGAGGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
1181 1287 1.836166 CCAATCAAGCAGGAGAGGAGA 59.164 52.381 0.00 0.00 0.00 3.71
1182 1288 1.558756 ACCAATCAAGCAGGAGAGGAG 59.441 52.381 0.00 0.00 0.00 3.69
1227 1336 0.223513 CAAAAAGAAACGCGCACACG 59.776 50.000 5.73 0.00 44.07 4.49
1230 1339 0.920664 AAGCAAAAAGAAACGCGCAC 59.079 45.000 5.73 0.00 0.00 5.34
1233 1342 1.443176 GACGAAGCAAAAAGAAACGCG 59.557 47.619 3.53 3.53 0.00 6.01
1234 1343 1.779157 GGACGAAGCAAAAAGAAACGC 59.221 47.619 0.00 0.00 0.00 4.84
1328 1475 2.107141 CGAACTGATCCCGCTCCC 59.893 66.667 0.00 0.00 0.00 4.30
1389 1538 2.149578 CACAAGGCAGAGAAACCTCAG 58.850 52.381 0.00 0.00 34.31 3.35
1399 1548 0.887387 GGGTTAACGCACAAGGCAGA 60.887 55.000 17.07 0.00 45.17 4.26
1403 1552 2.329614 CCGGGGTTAACGCACAAGG 61.330 63.158 22.45 15.44 0.00 3.61
1419 1568 3.920093 GAAGAAGGGTGGGTGGCCG 62.920 68.421 0.00 0.00 0.00 6.13
1420 1569 2.035783 GAAGAAGGGTGGGTGGCC 59.964 66.667 0.00 0.00 0.00 5.36
1421 1570 1.002011 GAGAAGAAGGGTGGGTGGC 60.002 63.158 0.00 0.00 0.00 5.01
1422 1571 1.685820 GGAGAAGAAGGGTGGGTGG 59.314 63.158 0.00 0.00 0.00 4.61
1457 1606 0.593773 CCAAAACAGAAACGCCACCG 60.594 55.000 0.00 0.00 41.14 4.94
1463 1612 2.108700 CGCAGAACCAAAACAGAAACG 58.891 47.619 0.00 0.00 0.00 3.60
1480 1629 2.049185 GGAGCAGAGAGAGGACGCA 61.049 63.158 0.00 0.00 0.00 5.24
1510 1659 0.413037 ACCAAATTCCAGGGCATCCA 59.587 50.000 0.00 0.00 34.83 3.41
1511 1660 2.031870 GTACCAAATTCCAGGGCATCC 58.968 52.381 0.00 0.00 0.00 3.51
1513 1662 1.360852 TGGTACCAAATTCCAGGGCAT 59.639 47.619 13.60 0.00 0.00 4.40
1514 1663 0.780637 TGGTACCAAATTCCAGGGCA 59.219 50.000 13.60 0.00 0.00 5.36
1515 1664 1.474330 CTGGTACCAAATTCCAGGGC 58.526 55.000 17.11 0.00 43.30 5.19
1556 1709 7.031226 TCAATCAACCAAAGAGAAGAAACAG 57.969 36.000 0.00 0.00 0.00 3.16
1588 1741 5.888105 TGCCAGAAATCTAGTACGACTTAC 58.112 41.667 0.00 0.00 0.00 2.34
1590 1743 5.401531 TTGCCAGAAATCTAGTACGACTT 57.598 39.130 0.00 0.00 0.00 3.01
1591 1744 5.361285 AGATTGCCAGAAATCTAGTACGACT 59.639 40.000 0.00 0.00 43.52 4.18
1592 1745 5.593010 AGATTGCCAGAAATCTAGTACGAC 58.407 41.667 0.00 0.00 43.52 4.34
1593 1746 5.854010 AGATTGCCAGAAATCTAGTACGA 57.146 39.130 0.00 0.00 43.52 3.43
1595 1748 6.818644 TGACAAGATTGCCAGAAATCTAGTAC 59.181 38.462 1.17 0.00 44.35 2.73
1596 1749 6.946340 TGACAAGATTGCCAGAAATCTAGTA 58.054 36.000 1.17 0.00 44.35 1.82
1597 1750 5.809001 TGACAAGATTGCCAGAAATCTAGT 58.191 37.500 1.17 0.00 44.35 2.57
1598 1751 5.220815 GCTGACAAGATTGCCAGAAATCTAG 60.221 44.000 12.37 0.00 44.35 2.43
1630 1787 4.467795 AGGAACCTCAAGAAATCGATCTCA 59.532 41.667 0.82 0.00 0.00 3.27
1656 1814 1.843368 AACATTGGCATCCTGACAGG 58.157 50.000 15.99 15.99 36.33 4.00
1657 1815 2.165030 GGAAACATTGGCATCCTGACAG 59.835 50.000 0.00 0.00 36.33 3.51
1686 1844 3.754323 TGGTCAGTTCAACAAGAAACGTT 59.246 39.130 0.00 0.00 38.13 3.99
2486 2661 1.978617 AGCTTTGTCAATGGCGGGG 60.979 57.895 1.08 0.00 0.00 5.73
2512 2687 2.281070 CTCTGCAACTGGGCGTGT 60.281 61.111 0.00 0.00 36.28 4.49
2711 2886 5.762179 TTGGTTTCTGTCCTAGTGATGAT 57.238 39.130 0.00 0.00 0.00 2.45
2828 3024 1.873591 CGCATTGCCTGGTATTACCTC 59.126 52.381 13.90 4.35 39.58 3.85
2857 3053 7.359933 GCAATTGCTTATTACTCTAGCTAGCTG 60.360 40.741 27.68 16.48 38.21 4.24
2966 3170 5.391312 AGGTTGAGCAACACCATATTTTC 57.609 39.130 14.55 0.00 42.85 2.29
2967 3171 5.304101 TGAAGGTTGAGCAACACCATATTTT 59.696 36.000 14.55 0.00 42.85 1.82
3150 3598 1.948508 CTGTGCGGCTTTGCTTGTA 59.051 52.632 0.00 0.00 35.36 2.41
3183 3631 2.741985 TCACATTCGTGCTGCCCG 60.742 61.111 0.00 0.00 43.28 6.13
3217 3665 8.691661 AAGCCGATTAATTGGTAGTGATAATT 57.308 30.769 20.81 0.00 33.62 1.40
3219 3667 7.506114 AGAAGCCGATTAATTGGTAGTGATAA 58.494 34.615 20.81 0.00 33.62 1.75
3220 3668 7.062749 AGAAGCCGATTAATTGGTAGTGATA 57.937 36.000 20.81 0.00 33.62 2.15
3221 3669 5.930135 AGAAGCCGATTAATTGGTAGTGAT 58.070 37.500 20.81 3.85 33.62 3.06
3223 3671 5.354234 ACAAGAAGCCGATTAATTGGTAGTG 59.646 40.000 20.81 14.33 33.62 2.74
3224 3672 5.497474 ACAAGAAGCCGATTAATTGGTAGT 58.503 37.500 20.81 8.28 33.62 2.73
3225 3673 6.316390 AGAACAAGAAGCCGATTAATTGGTAG 59.684 38.462 20.81 8.84 33.62 3.18
3226 3674 6.177610 AGAACAAGAAGCCGATTAATTGGTA 58.822 36.000 20.81 0.00 33.62 3.25
3227 3675 5.010282 AGAACAAGAAGCCGATTAATTGGT 58.990 37.500 20.81 4.25 33.62 3.67
3228 3676 5.567138 AGAACAAGAAGCCGATTAATTGG 57.433 39.130 16.52 16.52 0.00 3.16
3229 3677 6.381801 ACAAGAACAAGAAGCCGATTAATTG 58.618 36.000 0.00 0.00 0.00 2.32
3253 3701 2.594303 CAACCGCAGCCACAGGAA 60.594 61.111 0.00 0.00 0.00 3.36
3297 3745 2.462456 TCGCCATCATATCAGAAGCC 57.538 50.000 0.00 0.00 0.00 4.35
3373 3826 2.293122 TCTTGGGTGCAAACAATTCTCG 59.707 45.455 4.95 0.00 0.00 4.04
3417 3876 4.165779 GTGCGATTACTTGGTTCCAATTG 58.834 43.478 4.67 0.00 0.00 2.32
3419 3878 3.417101 TGTGCGATTACTTGGTTCCAAT 58.583 40.909 4.67 0.00 0.00 3.16
3428 3887 3.426695 GCAAGATGCTTGTGCGATTACTT 60.427 43.478 8.74 0.00 40.96 2.24
3583 4078 2.225017 ACCTCCCAATGTTCGTTCCAAT 60.225 45.455 0.00 0.00 0.00 3.16
3589 4084 0.981183 TGCTACCTCCCAATGTTCGT 59.019 50.000 0.00 0.00 0.00 3.85
3622 4117 9.586150 CGTTGCTGCTTTCATATATAAAACTAG 57.414 33.333 0.00 0.00 0.00 2.57
3674 4178 3.547868 CGTCTTGATCAATCAACGTCGAT 59.452 43.478 20.98 0.00 41.51 3.59


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

AutoCloner maintained by Alex Coulton.