Multiple sequence alignment - TraesCS3B01G165000

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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 TraesCS3B01G165000 chr3B 100.000 2411 0 0 1 2411 162858432 162860842 0.000000 4453.0
1 TraesCS3B01G165000 chr3B 94.737 38 1 1 65 102 20574556 20574592 0.000093 58.4
2 TraesCS3B01G165000 chr3D 92.488 1491 78 20 101 1578 112320542 112322011 0.000000 2102.0
3 TraesCS3B01G165000 chr3A 89.900 1396 75 24 123 1495 107862392 107863744 0.000000 1736.0
4 TraesCS3B01G165000 chr3A 87.437 796 89 8 1624 2411 594039397 594040189 0.000000 905.0
5 TraesCS3B01G165000 chr1D 91.688 794 57 7 1624 2411 332614969 332615759 0.000000 1092.0
6 TraesCS3B01G165000 chr1D 91.871 775 53 8 1623 2394 35637814 35637047 0.000000 1074.0
7 TraesCS3B01G165000 chr4B 91.436 794 60 7 1621 2411 498882285 498883073 0.000000 1083.0
8 TraesCS3B01G165000 chr7A 88.777 793 81 5 1622 2411 444789300 444790087 0.000000 965.0
9 TraesCS3B01G165000 chr2D 88.457 797 90 2 1617 2411 10149569 10150365 0.000000 961.0
10 TraesCS3B01G165000 chr2D 89.509 753 68 6 1663 2411 32203315 32202570 0.000000 942.0
11 TraesCS3B01G165000 chr6A 89.249 772 66 5 1625 2394 4983847 4984603 0.000000 950.0
12 TraesCS3B01G165000 chr7D 87.196 781 97 3 1624 2402 92110789 92110010 0.000000 885.0


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 TraesCS3B01G165000 chr3B 162858432 162860842 2410 False 4453 4453 100.000 1 2411 1 chr3B.!!$F2 2410
1 TraesCS3B01G165000 chr3D 112320542 112322011 1469 False 2102 2102 92.488 101 1578 1 chr3D.!!$F1 1477
2 TraesCS3B01G165000 chr3A 107862392 107863744 1352 False 1736 1736 89.900 123 1495 1 chr3A.!!$F1 1372
3 TraesCS3B01G165000 chr3A 594039397 594040189 792 False 905 905 87.437 1624 2411 1 chr3A.!!$F2 787
4 TraesCS3B01G165000 chr1D 332614969 332615759 790 False 1092 1092 91.688 1624 2411 1 chr1D.!!$F1 787
5 TraesCS3B01G165000 chr1D 35637047 35637814 767 True 1074 1074 91.871 1623 2394 1 chr1D.!!$R1 771
6 TraesCS3B01G165000 chr4B 498882285 498883073 788 False 1083 1083 91.436 1621 2411 1 chr4B.!!$F1 790
7 TraesCS3B01G165000 chr7A 444789300 444790087 787 False 965 965 88.777 1622 2411 1 chr7A.!!$F1 789
8 TraesCS3B01G165000 chr2D 10149569 10150365 796 False 961 961 88.457 1617 2411 1 chr2D.!!$F1 794
9 TraesCS3B01G165000 chr2D 32202570 32203315 745 True 942 942 89.509 1663 2411 1 chr2D.!!$R1 748
10 TraesCS3B01G165000 chr6A 4983847 4984603 756 False 950 950 89.249 1625 2394 1 chr6A.!!$F1 769
11 TraesCS3B01G165000 chr7D 92110010 92110789 779 True 885 885 87.196 1624 2402 1 chr7D.!!$R1 778

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
111 112 0.038618 GAAAGGCGAAATTTGCGGGT 60.039 50.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1609 0.247814 CAACGCAGCAATTCTAGCCG 60.248 55.0 0.0 0.0 0.0 5.52 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
19 20 1.737838 TGAATGATGTCCTTCCGCAC 58.262 50.000 0.00 0.00 0.00 5.34
20 21 1.017387 GAATGATGTCCTTCCGCACC 58.983 55.000 0.00 0.00 0.00 5.01
21 22 0.394352 AATGATGTCCTTCCGCACCC 60.394 55.000 0.00 0.00 0.00 4.61
22 23 2.511600 GATGTCCTTCCGCACCCG 60.512 66.667 0.00 0.00 0.00 5.28
23 24 3.310860 GATGTCCTTCCGCACCCGT 62.311 63.158 0.00 0.00 0.00 5.28
24 25 3.605749 ATGTCCTTCCGCACCCGTG 62.606 63.158 0.00 0.00 0.00 4.94
25 26 4.309950 GTCCTTCCGCACCCGTGT 62.310 66.667 0.00 0.00 0.00 4.49
26 27 3.998672 TCCTTCCGCACCCGTGTC 61.999 66.667 0.00 0.00 0.00 3.67
28 29 4.657824 CTTCCGCACCCGTGTCGT 62.658 66.667 9.60 0.00 0.00 4.34
29 30 4.224274 TTCCGCACCCGTGTCGTT 62.224 61.111 9.60 0.00 0.00 3.85
30 31 3.736732 TTCCGCACCCGTGTCGTTT 62.737 57.895 9.60 0.00 0.00 3.60
31 32 4.007940 CCGCACCCGTGTCGTTTG 62.008 66.667 9.60 0.00 0.00 2.93
32 33 3.266376 CGCACCCGTGTCGTTTGT 61.266 61.111 0.00 0.00 0.00 2.83
33 34 2.326550 GCACCCGTGTCGTTTGTG 59.673 61.111 0.00 0.00 0.00 3.33
34 35 2.174969 GCACCCGTGTCGTTTGTGA 61.175 57.895 0.00 0.00 0.00 3.58
35 36 1.707239 GCACCCGTGTCGTTTGTGAA 61.707 55.000 0.00 0.00 0.00 3.18
36 37 0.941542 CACCCGTGTCGTTTGTGAAT 59.058 50.000 0.00 0.00 0.00 2.57
37 38 0.941542 ACCCGTGTCGTTTGTGAATG 59.058 50.000 0.00 0.00 0.00 2.67
38 39 0.237235 CCCGTGTCGTTTGTGAATGG 59.763 55.000 0.00 0.00 0.00 3.16
39 40 0.941542 CCGTGTCGTTTGTGAATGGT 59.058 50.000 0.00 0.00 0.00 3.55
40 41 1.070175 CCGTGTCGTTTGTGAATGGTC 60.070 52.381 0.00 0.00 0.00 4.02
41 42 1.595328 CGTGTCGTTTGTGAATGGTCA 59.405 47.619 0.00 0.00 0.00 4.02
42 43 2.031068 CGTGTCGTTTGTGAATGGTCAA 59.969 45.455 0.00 0.00 34.87 3.18
43 44 3.359654 GTGTCGTTTGTGAATGGTCAAC 58.640 45.455 0.00 0.00 34.87 3.18
44 45 3.064820 GTGTCGTTTGTGAATGGTCAACT 59.935 43.478 0.00 0.00 34.87 3.16
45 46 3.692101 TGTCGTTTGTGAATGGTCAACTT 59.308 39.130 0.00 0.00 34.87 2.66
46 47 4.201871 TGTCGTTTGTGAATGGTCAACTTC 60.202 41.667 0.00 0.00 34.87 3.01
47 48 3.314080 TCGTTTGTGAATGGTCAACTTCC 59.686 43.478 0.00 0.00 34.87 3.46
48 49 3.315191 CGTTTGTGAATGGTCAACTTCCT 59.685 43.478 0.00 0.00 34.87 3.36
49 50 4.554723 CGTTTGTGAATGGTCAACTTCCTC 60.555 45.833 0.00 0.00 34.87 3.71
50 51 4.437682 TTGTGAATGGTCAACTTCCTCT 57.562 40.909 0.00 0.00 34.87 3.69
51 52 4.008074 TGTGAATGGTCAACTTCCTCTC 57.992 45.455 0.00 0.00 34.87 3.20
52 53 2.996621 GTGAATGGTCAACTTCCTCTCG 59.003 50.000 0.00 0.00 34.87 4.04
53 54 2.003301 GAATGGTCAACTTCCTCTCGC 58.997 52.381 0.00 0.00 0.00 5.03
54 55 0.976641 ATGGTCAACTTCCTCTCGCA 59.023 50.000 0.00 0.00 0.00 5.10
55 56 0.976641 TGGTCAACTTCCTCTCGCAT 59.023 50.000 0.00 0.00 0.00 4.73
56 57 1.066858 TGGTCAACTTCCTCTCGCATC 60.067 52.381 0.00 0.00 0.00 3.91
57 58 1.066858 GGTCAACTTCCTCTCGCATCA 60.067 52.381 0.00 0.00 0.00 3.07
58 59 2.266554 GTCAACTTCCTCTCGCATCAG 58.733 52.381 0.00 0.00 0.00 2.90
59 60 1.005340 CAACTTCCTCTCGCATCAGC 58.995 55.000 0.00 0.00 37.42 4.26
60 61 0.610174 AACTTCCTCTCGCATCAGCA 59.390 50.000 0.00 0.00 42.27 4.41
61 62 0.829333 ACTTCCTCTCGCATCAGCAT 59.171 50.000 0.00 0.00 42.27 3.79
62 63 1.209019 ACTTCCTCTCGCATCAGCATT 59.791 47.619 0.00 0.00 42.27 3.56
63 64 1.598132 CTTCCTCTCGCATCAGCATTG 59.402 52.381 0.00 0.00 42.27 2.82
64 65 0.538584 TCCTCTCGCATCAGCATTGT 59.461 50.000 0.00 0.00 42.27 2.71
65 66 1.065926 TCCTCTCGCATCAGCATTGTT 60.066 47.619 0.00 0.00 42.27 2.83
66 67 2.168313 TCCTCTCGCATCAGCATTGTTA 59.832 45.455 0.00 0.00 42.27 2.41
67 68 2.286294 CCTCTCGCATCAGCATTGTTAC 59.714 50.000 0.00 0.00 42.27 2.50
68 69 2.931969 CTCTCGCATCAGCATTGTTACA 59.068 45.455 0.00 0.00 42.27 2.41
69 70 3.534554 TCTCGCATCAGCATTGTTACAT 58.465 40.909 0.00 0.00 42.27 2.29
70 71 3.310501 TCTCGCATCAGCATTGTTACATG 59.689 43.478 0.00 0.00 42.27 3.21
71 72 2.114056 CGCATCAGCATTGTTACATGC 58.886 47.619 10.30 10.30 42.27 4.06
72 73 2.478200 CGCATCAGCATTGTTACATGCA 60.478 45.455 17.17 0.00 45.59 3.96
73 74 2.855963 GCATCAGCATTGTTACATGCAC 59.144 45.455 17.17 0.00 45.59 4.57
74 75 3.673866 GCATCAGCATTGTTACATGCACA 60.674 43.478 17.17 0.00 45.59 4.57
75 76 3.557577 TCAGCATTGTTACATGCACAC 57.442 42.857 17.17 0.00 45.59 3.82
76 77 2.883386 TCAGCATTGTTACATGCACACA 59.117 40.909 17.17 0.00 45.59 3.72
77 78 3.506844 TCAGCATTGTTACATGCACACAT 59.493 39.130 17.17 0.10 45.59 3.21
78 79 4.022155 TCAGCATTGTTACATGCACACATT 60.022 37.500 17.17 0.00 45.59 2.71
79 80 4.090786 CAGCATTGTTACATGCACACATTG 59.909 41.667 17.17 1.73 45.59 2.82
80 81 3.989167 GCATTGTTACATGCACACATTGT 59.011 39.130 12.42 0.00 42.90 2.71
81 82 4.448395 GCATTGTTACATGCACACATTGTT 59.552 37.500 12.42 0.00 42.90 2.83
82 83 5.612925 GCATTGTTACATGCACACATTGTTG 60.613 40.000 12.42 0.00 42.90 3.33
83 84 3.974912 TGTTACATGCACACATTGTTGG 58.025 40.909 0.00 0.00 32.87 3.77
84 85 3.633986 TGTTACATGCACACATTGTTGGA 59.366 39.130 0.00 0.00 32.87 3.53
85 86 4.280425 TGTTACATGCACACATTGTTGGAT 59.720 37.500 0.00 0.00 32.87 3.41
86 87 3.306917 ACATGCACACATTGTTGGATG 57.693 42.857 20.70 20.70 35.31 3.51
87 88 2.892215 ACATGCACACATTGTTGGATGA 59.108 40.909 25.12 0.00 34.04 2.92
88 89 3.321396 ACATGCACACATTGTTGGATGAA 59.679 39.130 25.12 5.73 34.04 2.57
89 90 3.646611 TGCACACATTGTTGGATGAAG 57.353 42.857 0.00 0.00 0.00 3.02
90 91 2.288334 TGCACACATTGTTGGATGAAGC 60.288 45.455 0.00 0.00 0.00 3.86
91 92 2.029649 GCACACATTGTTGGATGAAGCT 60.030 45.455 0.00 0.00 0.00 3.74
92 93 3.571571 CACACATTGTTGGATGAAGCTG 58.428 45.455 0.00 0.00 0.00 4.24
93 94 3.253921 CACACATTGTTGGATGAAGCTGA 59.746 43.478 0.00 0.00 0.00 4.26
94 95 3.890756 ACACATTGTTGGATGAAGCTGAA 59.109 39.130 0.00 0.00 0.00 3.02
95 96 4.341806 ACACATTGTTGGATGAAGCTGAAA 59.658 37.500 0.00 0.00 0.00 2.69
96 97 4.921515 CACATTGTTGGATGAAGCTGAAAG 59.078 41.667 0.00 0.00 0.00 2.62
97 98 4.021719 ACATTGTTGGATGAAGCTGAAAGG 60.022 41.667 0.00 0.00 0.00 3.11
98 99 1.888512 TGTTGGATGAAGCTGAAAGGC 59.111 47.619 0.00 0.00 0.00 4.35
99 100 1.135575 GTTGGATGAAGCTGAAAGGCG 60.136 52.381 0.00 0.00 37.29 5.52
111 112 0.038618 GAAAGGCGAAATTTGCGGGT 60.039 50.000 0.00 0.00 0.00 5.28
120 121 4.877619 TTTGCGGGTGGGCGTTGA 62.878 61.111 0.00 0.00 35.06 3.18
165 166 0.930310 CGGCCGTGATCAATGTACAG 59.070 55.000 19.50 0.00 0.00 2.74
172 173 1.221414 GATCAATGTACAGGAGCGCC 58.779 55.000 2.29 0.00 0.00 6.53
178 179 0.901114 TGTACAGGAGCGCCCAACTA 60.901 55.000 15.92 1.25 37.41 2.24
244 249 2.872370 CTGAAGCTTGCAAACATAGGC 58.128 47.619 2.10 0.00 0.00 3.93
334 340 9.916397 GTACTGTAAAGATATTGTTTCGATTGG 57.084 33.333 0.00 0.00 0.00 3.16
341 347 6.061441 AGATATTGTTTCGATTGGGCATACA 58.939 36.000 0.00 0.00 0.00 2.29
357 363 5.360714 GGGCATACATCAAATCAAGGAGAAA 59.639 40.000 0.00 0.00 0.00 2.52
366 372 4.568152 AATCAAGGAGAAAAACACACGG 57.432 40.909 0.00 0.00 0.00 4.94
381 387 4.880899 CGGGAAACGGGAAAATGC 57.119 55.556 0.00 0.00 39.42 3.56
383 389 1.248101 CGGGAAACGGGAAAATGCCT 61.248 55.000 0.00 0.00 39.42 4.75
384 390 0.530744 GGGAAACGGGAAAATGCCTC 59.469 55.000 0.00 0.00 0.00 4.70
385 391 1.253100 GGAAACGGGAAAATGCCTCA 58.747 50.000 0.00 0.00 0.00 3.86
387 393 2.036604 GGAAACGGGAAAATGCCTCAAA 59.963 45.455 0.00 0.00 0.00 2.69
390 396 3.385193 ACGGGAAAATGCCTCAAAAAG 57.615 42.857 0.00 0.00 0.00 2.27
461 468 4.909880 GGCACTTGTACTTTCGATGAAAAC 59.090 41.667 0.00 0.00 30.84 2.43
466 476 7.165812 CACTTGTACTTTCGATGAAAACAAAGG 59.834 37.037 9.50 4.16 34.24 3.11
701 714 2.417719 GTTTGTCACCGAGAAGCTCAT 58.582 47.619 0.00 0.00 0.00 2.90
713 726 4.681744 GAGAAGCTCATAACAGTCTGGAG 58.318 47.826 4.53 2.34 0.00 3.86
732 745 2.103143 CTCTGAATCGCCGCTCGT 59.897 61.111 0.00 0.00 39.67 4.18
900 926 4.951963 AGGATAGCGCGCGCCTTC 62.952 66.667 46.98 39.46 43.17 3.46
962 988 2.435586 CTCAAGGCTGCGAGGTGG 60.436 66.667 6.35 0.00 0.00 4.61
1308 1343 1.077212 CGAGGAAGGGGAGACGGTA 60.077 63.158 0.00 0.00 0.00 4.02
1467 1502 3.106407 GACGCGACACAGTGGAGC 61.106 66.667 15.93 8.86 0.00 4.70
1497 1532 3.709987 GTTTGCAATTTGAGCTCTGTGT 58.290 40.909 16.19 0.00 0.00 3.72
1498 1533 4.114794 GTTTGCAATTTGAGCTCTGTGTT 58.885 39.130 16.19 1.98 0.00 3.32
1499 1534 4.389890 TTGCAATTTGAGCTCTGTGTTT 57.610 36.364 16.19 0.00 0.00 2.83
1532 1567 2.727123 TTGAGAAAGAGTGGCCACAA 57.273 45.000 36.39 17.22 0.00 3.33
1533 1568 2.727123 TGAGAAAGAGTGGCCACAAA 57.273 45.000 36.39 10.33 0.00 2.83
1540 1575 0.307760 GAGTGGCCACAAAGTTGACG 59.692 55.000 36.39 0.00 0.00 4.35
1546 1581 1.332904 GCCACAAAGTTGACGAGTTCG 60.333 52.381 0.00 0.00 46.33 3.95
1563 1598 3.996614 GTTCCACCGAACATGGGG 58.003 61.111 0.00 0.00 46.49 4.96
1578 1613 2.359011 GGGGGAAATTCCACGGCT 59.641 61.111 14.68 0.00 42.21 5.52
1579 1614 1.610873 GGGGGAAATTCCACGGCTA 59.389 57.895 14.68 0.00 42.21 3.93
1580 1615 0.465642 GGGGGAAATTCCACGGCTAG 60.466 60.000 14.68 0.00 42.21 3.42
1581 1616 0.544697 GGGGAAATTCCACGGCTAGA 59.455 55.000 14.68 0.00 38.64 2.43
1582 1617 1.064979 GGGGAAATTCCACGGCTAGAA 60.065 52.381 14.68 0.00 38.64 2.10
1583 1618 2.422945 GGGGAAATTCCACGGCTAGAAT 60.423 50.000 14.68 0.00 38.64 2.40
1584 1619 3.288092 GGGAAATTCCACGGCTAGAATT 58.712 45.455 14.68 0.00 42.93 2.17
1585 1620 3.066760 GGGAAATTCCACGGCTAGAATTG 59.933 47.826 14.68 0.00 40.84 2.32
1586 1621 3.489229 GGAAATTCCACGGCTAGAATTGC 60.489 47.826 7.23 5.49 40.84 3.56
1587 1622 2.717639 ATTCCACGGCTAGAATTGCT 57.282 45.000 0.00 0.00 28.19 3.91
1588 1623 1.737838 TTCCACGGCTAGAATTGCTG 58.262 50.000 0.00 0.00 42.11 4.41
1589 1624 0.744414 TCCACGGCTAGAATTGCTGC 60.744 55.000 0.00 0.00 40.21 5.25
1590 1625 1.349627 CACGGCTAGAATTGCTGCG 59.650 57.895 0.00 0.00 40.21 5.18
1591 1626 1.079127 ACGGCTAGAATTGCTGCGT 60.079 52.632 0.00 0.00 40.21 5.24
1592 1627 0.673644 ACGGCTAGAATTGCTGCGTT 60.674 50.000 0.00 0.00 40.21 4.84
1593 1628 0.247814 CGGCTAGAATTGCTGCGTTG 60.248 55.000 0.00 0.00 0.00 4.10
1594 1629 0.804989 GGCTAGAATTGCTGCGTTGT 59.195 50.000 0.00 0.00 0.00 3.32
1595 1630 1.200020 GGCTAGAATTGCTGCGTTGTT 59.800 47.619 0.00 0.00 0.00 2.83
1596 1631 2.351738 GGCTAGAATTGCTGCGTTGTTT 60.352 45.455 0.00 0.00 0.00 2.83
1597 1632 2.911102 GCTAGAATTGCTGCGTTGTTTC 59.089 45.455 0.00 0.00 0.00 2.78
1598 1633 3.609175 GCTAGAATTGCTGCGTTGTTTCA 60.609 43.478 0.00 0.00 0.00 2.69
1599 1634 3.648339 AGAATTGCTGCGTTGTTTCAT 57.352 38.095 0.00 0.00 0.00 2.57
1600 1635 3.568538 AGAATTGCTGCGTTGTTTCATC 58.431 40.909 0.00 0.00 0.00 2.92
1601 1636 3.004629 AGAATTGCTGCGTTGTTTCATCA 59.995 39.130 0.00 0.00 0.00 3.07
1602 1637 2.118228 TTGCTGCGTTGTTTCATCAC 57.882 45.000 0.00 0.00 0.00 3.06
1603 1638 1.020437 TGCTGCGTTGTTTCATCACA 58.980 45.000 0.00 0.00 0.00 3.58
1604 1639 1.002576 TGCTGCGTTGTTTCATCACAG 60.003 47.619 0.00 0.00 0.00 3.66
1605 1640 1.678360 CTGCGTTGTTTCATCACAGC 58.322 50.000 0.00 0.00 0.00 4.40
1606 1641 1.265095 CTGCGTTGTTTCATCACAGCT 59.735 47.619 0.00 0.00 0.00 4.24
1607 1642 2.480037 CTGCGTTGTTTCATCACAGCTA 59.520 45.455 0.00 0.00 0.00 3.32
1608 1643 3.073678 TGCGTTGTTTCATCACAGCTAT 58.926 40.909 0.00 0.00 0.00 2.97
1609 1644 4.249661 TGCGTTGTTTCATCACAGCTATA 58.750 39.130 0.00 0.00 0.00 1.31
1610 1645 4.092821 TGCGTTGTTTCATCACAGCTATAC 59.907 41.667 0.00 0.00 0.00 1.47
1611 1646 4.092821 GCGTTGTTTCATCACAGCTATACA 59.907 41.667 0.00 0.00 0.00 2.29
1612 1647 5.390461 GCGTTGTTTCATCACAGCTATACAA 60.390 40.000 0.00 0.00 0.00 2.41
1613 1648 6.598525 CGTTGTTTCATCACAGCTATACAAA 58.401 36.000 0.00 0.00 0.00 2.83
1614 1649 6.519761 CGTTGTTTCATCACAGCTATACAAAC 59.480 38.462 0.00 0.00 0.00 2.93
1615 1650 7.359595 GTTGTTTCATCACAGCTATACAAACA 58.640 34.615 0.00 0.00 32.19 2.83
1656 1691 2.182181 GTGCAGCTGCGCCATATGA 61.182 57.895 36.52 13.91 45.15 2.15
1747 1784 0.239347 GTTGATGCCAGTGTGTGAGC 59.761 55.000 0.00 0.00 0.00 4.26
1749 1786 0.037160 TGATGCCAGTGTGTGAGCAT 59.963 50.000 3.79 3.79 42.42 3.79
1759 1796 1.528776 TGTGAGCATTGTGCCAGCA 60.529 52.632 0.00 0.00 46.52 4.41
1863 1904 1.757682 ACTTTTGAAGCGGGTGTCAA 58.242 45.000 0.00 2.27 31.99 3.18
1884 1926 0.932399 ACGAAGAACCGTTTTCACCG 59.068 50.000 0.00 0.00 40.17 4.94
1886 1928 1.328374 CGAAGAACCGTTTTCACCGTT 59.672 47.619 0.00 0.00 0.00 4.44
1889 1931 0.029700 GAACCGTTTTCACCGTTGGG 59.970 55.000 0.00 0.00 40.11 4.12
1926 1968 9.561069 GAGCTTTTCAAAACTAGATCCCATATA 57.439 33.333 0.00 0.00 0.00 0.86
2031 2073 2.229792 ACAGGAATTGCATCGTGTGTT 58.770 42.857 13.34 0.00 44.27 3.32
2146 2189 8.726988 GTTTAGTTGCCTATCATACTGTGAAAA 58.273 33.333 0.00 0.00 40.97 2.29
2182 2225 3.662759 TGGAAACTTCTCCAACAAGGT 57.337 42.857 0.00 0.00 42.69 3.50
2185 2228 4.159506 TGGAAACTTCTCCAACAAGGTTTG 59.840 41.667 0.00 0.00 42.69 2.93
2225 2268 0.455633 CGCTACGAAGTTGGCTACGT 60.456 55.000 0.00 0.00 37.78 3.57
2238 2281 3.792401 TGGCTACGTGTAATCCTCAATG 58.208 45.455 0.00 0.00 0.00 2.82
2306 2350 8.024865 GCCTACGATGTTAAAAGGTTTTTATGT 58.975 33.333 0.00 0.00 0.00 2.29
2332 2376 9.852091 TGATCTAAGTCATCTATCATGATTTCG 57.148 33.333 14.65 3.38 31.78 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.998672 GACACGGGTGCGGAAGGA 61.999 66.667 0.00 0.00 0.00 3.36
11 12 4.657824 ACGACACGGGTGCGGAAG 62.658 66.667 0.00 1.20 35.52 3.46
12 13 3.736732 AAACGACACGGGTGCGGAA 62.737 57.895 0.00 0.00 35.52 4.30
13 14 4.224274 AAACGACACGGGTGCGGA 62.224 61.111 0.00 0.00 35.52 5.54
14 15 4.007940 CAAACGACACGGGTGCGG 62.008 66.667 0.00 4.88 35.52 5.69
15 16 3.266376 ACAAACGACACGGGTGCG 61.266 61.111 0.00 0.50 36.62 5.34
16 17 1.707239 TTCACAAACGACACGGGTGC 61.707 55.000 0.00 0.00 31.44 5.01
17 18 0.941542 ATTCACAAACGACACGGGTG 59.058 50.000 0.00 0.00 0.00 4.61
18 19 0.941542 CATTCACAAACGACACGGGT 59.058 50.000 0.00 0.00 0.00 5.28
19 20 0.237235 CCATTCACAAACGACACGGG 59.763 55.000 0.00 0.00 0.00 5.28
20 21 0.941542 ACCATTCACAAACGACACGG 59.058 50.000 0.00 0.00 0.00 4.94
21 22 1.595328 TGACCATTCACAAACGACACG 59.405 47.619 0.00 0.00 0.00 4.49
22 23 3.064820 AGTTGACCATTCACAAACGACAC 59.935 43.478 0.00 0.00 0.00 3.67
23 24 3.275143 AGTTGACCATTCACAAACGACA 58.725 40.909 0.00 0.00 0.00 4.35
24 25 3.963383 AGTTGACCATTCACAAACGAC 57.037 42.857 0.00 0.00 0.00 4.34
25 26 3.314080 GGAAGTTGACCATTCACAAACGA 59.686 43.478 0.00 0.00 0.00 3.85
26 27 3.315191 AGGAAGTTGACCATTCACAAACG 59.685 43.478 0.00 0.00 0.00 3.60
27 28 4.580580 AGAGGAAGTTGACCATTCACAAAC 59.419 41.667 0.00 0.00 0.00 2.93
28 29 4.792068 AGAGGAAGTTGACCATTCACAAA 58.208 39.130 0.00 0.00 0.00 2.83
29 30 4.389374 GAGAGGAAGTTGACCATTCACAA 58.611 43.478 0.00 0.00 0.00 3.33
30 31 3.554960 CGAGAGGAAGTTGACCATTCACA 60.555 47.826 0.00 0.00 0.00 3.58
31 32 2.996621 CGAGAGGAAGTTGACCATTCAC 59.003 50.000 0.00 0.00 0.00 3.18
32 33 2.612972 GCGAGAGGAAGTTGACCATTCA 60.613 50.000 0.00 0.00 0.00 2.57
33 34 2.003301 GCGAGAGGAAGTTGACCATTC 58.997 52.381 0.00 0.00 0.00 2.67
34 35 1.347707 TGCGAGAGGAAGTTGACCATT 59.652 47.619 0.00 0.00 0.00 3.16
35 36 0.976641 TGCGAGAGGAAGTTGACCAT 59.023 50.000 0.00 0.00 0.00 3.55
36 37 0.976641 ATGCGAGAGGAAGTTGACCA 59.023 50.000 0.00 0.00 32.68 4.02
37 38 1.066858 TGATGCGAGAGGAAGTTGACC 60.067 52.381 0.00 0.00 32.68 4.02
38 39 2.266554 CTGATGCGAGAGGAAGTTGAC 58.733 52.381 0.00 0.00 32.68 3.18
39 40 1.404717 GCTGATGCGAGAGGAAGTTGA 60.405 52.381 0.00 0.00 32.68 3.18
40 41 1.005340 GCTGATGCGAGAGGAAGTTG 58.995 55.000 0.00 0.00 32.68 3.16
41 42 0.610174 TGCTGATGCGAGAGGAAGTT 59.390 50.000 0.00 0.00 43.34 2.66
42 43 0.829333 ATGCTGATGCGAGAGGAAGT 59.171 50.000 0.00 0.00 43.34 3.01
43 44 1.598132 CAATGCTGATGCGAGAGGAAG 59.402 52.381 0.00 0.00 43.34 3.46
44 45 1.065926 ACAATGCTGATGCGAGAGGAA 60.066 47.619 0.00 0.00 43.34 3.36
45 46 0.538584 ACAATGCTGATGCGAGAGGA 59.461 50.000 0.00 0.00 43.34 3.71
46 47 1.376543 AACAATGCTGATGCGAGAGG 58.623 50.000 0.00 0.00 43.34 3.69
47 48 2.931969 TGTAACAATGCTGATGCGAGAG 59.068 45.455 0.00 0.00 43.34 3.20
48 49 2.971307 TGTAACAATGCTGATGCGAGA 58.029 42.857 0.00 0.00 43.34 4.04
49 50 3.614588 CATGTAACAATGCTGATGCGAG 58.385 45.455 0.00 0.00 43.34 5.03
50 51 3.678915 CATGTAACAATGCTGATGCGA 57.321 42.857 0.00 0.00 43.34 5.10
59 60 5.107414 CCAACAATGTGTGCATGTAACAATG 60.107 40.000 5.12 7.68 35.15 2.82
60 61 4.989797 CCAACAATGTGTGCATGTAACAAT 59.010 37.500 5.12 0.75 35.15 2.71
61 62 4.098501 TCCAACAATGTGTGCATGTAACAA 59.901 37.500 5.12 0.00 35.15 2.83
62 63 3.633986 TCCAACAATGTGTGCATGTAACA 59.366 39.130 0.00 0.00 35.15 2.41
63 64 4.235939 TCCAACAATGTGTGCATGTAAC 57.764 40.909 0.00 0.00 35.15 2.50
64 65 4.522022 TCATCCAACAATGTGTGCATGTAA 59.478 37.500 0.00 0.00 35.15 2.41
65 66 4.077822 TCATCCAACAATGTGTGCATGTA 58.922 39.130 0.00 0.00 35.15 2.29
66 67 2.892215 TCATCCAACAATGTGTGCATGT 59.108 40.909 0.00 0.00 35.15 3.21
67 68 3.579335 TCATCCAACAATGTGTGCATG 57.421 42.857 0.00 0.00 35.15 4.06
68 69 3.615592 GCTTCATCCAACAATGTGTGCAT 60.616 43.478 0.00 0.00 36.80 3.96
69 70 2.288334 GCTTCATCCAACAATGTGTGCA 60.288 45.455 0.00 0.00 0.00 4.57
70 71 2.029649 AGCTTCATCCAACAATGTGTGC 60.030 45.455 0.00 0.00 0.00 4.57
71 72 3.253921 TCAGCTTCATCCAACAATGTGTG 59.746 43.478 0.00 0.00 0.00 3.82
72 73 3.489355 TCAGCTTCATCCAACAATGTGT 58.511 40.909 0.00 0.00 0.00 3.72
73 74 4.508461 TTCAGCTTCATCCAACAATGTG 57.492 40.909 0.00 0.00 0.00 3.21
74 75 4.021719 CCTTTCAGCTTCATCCAACAATGT 60.022 41.667 0.00 0.00 0.00 2.71
75 76 4.491676 CCTTTCAGCTTCATCCAACAATG 58.508 43.478 0.00 0.00 0.00 2.82
76 77 3.056322 GCCTTTCAGCTTCATCCAACAAT 60.056 43.478 0.00 0.00 0.00 2.71
77 78 2.297033 GCCTTTCAGCTTCATCCAACAA 59.703 45.455 0.00 0.00 0.00 2.83
78 79 1.888512 GCCTTTCAGCTTCATCCAACA 59.111 47.619 0.00 0.00 0.00 3.33
79 80 1.135575 CGCCTTTCAGCTTCATCCAAC 60.136 52.381 0.00 0.00 0.00 3.77
80 81 1.167851 CGCCTTTCAGCTTCATCCAA 58.832 50.000 0.00 0.00 0.00 3.53
81 82 0.324614 TCGCCTTTCAGCTTCATCCA 59.675 50.000 0.00 0.00 0.00 3.41
82 83 1.453155 TTCGCCTTTCAGCTTCATCC 58.547 50.000 0.00 0.00 0.00 3.51
83 84 3.772060 ATTTCGCCTTTCAGCTTCATC 57.228 42.857 0.00 0.00 0.00 2.92
84 85 4.240096 CAAATTTCGCCTTTCAGCTTCAT 58.760 39.130 0.00 0.00 0.00 2.57
85 86 3.641648 CAAATTTCGCCTTTCAGCTTCA 58.358 40.909 0.00 0.00 0.00 3.02
86 87 2.409715 GCAAATTTCGCCTTTCAGCTTC 59.590 45.455 0.00 0.00 0.00 3.86
87 88 2.407090 GCAAATTTCGCCTTTCAGCTT 58.593 42.857 0.00 0.00 0.00 3.74
88 89 1.666888 CGCAAATTTCGCCTTTCAGCT 60.667 47.619 6.92 0.00 0.00 4.24
89 90 0.710017 CGCAAATTTCGCCTTTCAGC 59.290 50.000 6.92 0.00 0.00 4.26
90 91 1.339711 CCGCAAATTTCGCCTTTCAG 58.660 50.000 6.92 0.00 0.00 3.02
91 92 0.038709 CCCGCAAATTTCGCCTTTCA 60.039 50.000 6.92 0.00 0.00 2.69
92 93 0.038618 ACCCGCAAATTTCGCCTTTC 60.039 50.000 6.92 0.00 0.00 2.62
93 94 0.319469 CACCCGCAAATTTCGCCTTT 60.319 50.000 6.92 0.00 0.00 3.11
94 95 1.288752 CACCCGCAAATTTCGCCTT 59.711 52.632 6.92 0.00 0.00 4.35
95 96 2.635443 CCACCCGCAAATTTCGCCT 61.635 57.895 6.92 0.00 0.00 5.52
96 97 2.126110 CCACCCGCAAATTTCGCC 60.126 61.111 6.92 0.00 0.00 5.54
97 98 2.126110 CCCACCCGCAAATTTCGC 60.126 61.111 0.00 0.00 0.00 4.70
98 99 2.126110 GCCCACCCGCAAATTTCG 60.126 61.111 0.00 0.00 0.00 3.46
99 100 2.126110 CGCCCACCCGCAAATTTC 60.126 61.111 0.00 0.00 0.00 2.17
165 166 2.512515 CAGCTAGTTGGGCGCTCC 60.513 66.667 3.94 6.36 34.52 4.70
172 173 3.988379 TTGCAAACTTCAGCTAGTTGG 57.012 42.857 6.75 1.26 38.33 3.77
334 340 6.455360 TTTCTCCTTGATTTGATGTATGCC 57.545 37.500 0.00 0.00 0.00 4.40
341 347 6.208644 CGTGTGTTTTTCTCCTTGATTTGAT 58.791 36.000 0.00 0.00 0.00 2.57
357 363 0.394080 TTCCCGTTTCCCGTGTGTTT 60.394 50.000 0.00 0.00 33.66 2.83
366 372 1.253100 TGAGGCATTTTCCCGTTTCC 58.747 50.000 0.00 0.00 0.00 3.13
379 385 5.645929 GGGTTTTTCTTTTCTTTTTGAGGCA 59.354 36.000 0.00 0.00 0.00 4.75
380 386 5.645929 TGGGTTTTTCTTTTCTTTTTGAGGC 59.354 36.000 0.00 0.00 0.00 4.70
381 387 7.864108 ATGGGTTTTTCTTTTCTTTTTGAGG 57.136 32.000 0.00 0.00 0.00 3.86
383 389 9.161629 GAGAATGGGTTTTTCTTTTCTTTTTGA 57.838 29.630 0.00 0.00 33.65 2.69
384 390 8.397906 GGAGAATGGGTTTTTCTTTTCTTTTTG 58.602 33.333 0.00 0.00 33.65 2.44
385 391 8.106462 TGGAGAATGGGTTTTTCTTTTCTTTTT 58.894 29.630 0.00 0.00 33.65 1.94
387 393 7.047891 GTGGAGAATGGGTTTTTCTTTTCTTT 58.952 34.615 0.00 0.00 33.65 2.52
390 396 4.982295 CGTGGAGAATGGGTTTTTCTTTTC 59.018 41.667 0.00 0.00 33.65 2.29
461 468 5.590259 CAGTATATTTGGTGGGAGTCCTTTG 59.410 44.000 9.58 0.00 0.00 2.77
466 476 5.123936 GGAACAGTATATTTGGTGGGAGTC 58.876 45.833 0.00 0.00 0.00 3.36
713 726 1.941734 CGAGCGGCGATTCAGAGTC 60.942 63.158 12.98 0.00 44.57 3.36
732 745 2.659016 CTGCTCCACTTGGCTCGA 59.341 61.111 0.00 0.00 34.44 4.04
946 972 4.020617 CCCACCTCGCAGCCTTGA 62.021 66.667 0.00 0.00 0.00 3.02
1448 1483 4.994201 TCCACTGTGTCGCGTCGC 62.994 66.667 7.29 7.29 0.00 5.19
1449 1484 2.801162 CTCCACTGTGTCGCGTCG 60.801 66.667 5.77 0.00 0.00 5.12
1450 1485 3.106407 GCTCCACTGTGTCGCGTC 61.106 66.667 5.77 0.00 0.00 5.19
1467 1502 0.664166 AAATTGCAAACGAGCAGCCG 60.664 50.000 1.71 2.15 46.54 5.52
1470 1505 1.717645 GCTCAAATTGCAAACGAGCAG 59.282 47.619 28.89 13.31 46.54 4.24
1506 1541 4.339247 TGGCCACTCTTTCTCAAAGAAAAG 59.661 41.667 0.00 6.77 46.13 2.27
1526 1561 1.332904 CGAACTCGTCAACTTTGTGGC 60.333 52.381 0.00 0.00 34.11 5.01
1563 1598 2.413310 TTCTAGCCGTGGAATTTCCC 57.587 50.000 12.90 3.74 35.03 3.97
1566 1601 3.129287 CAGCAATTCTAGCCGTGGAATTT 59.871 43.478 0.00 0.00 40.04 1.82
1569 1604 1.737838 CAGCAATTCTAGCCGTGGAA 58.262 50.000 0.00 0.00 0.00 3.53
1571 1606 1.723870 GCAGCAATTCTAGCCGTGG 59.276 57.895 0.00 0.00 0.00 4.94
1574 1609 0.247814 CAACGCAGCAATTCTAGCCG 60.248 55.000 0.00 0.00 0.00 5.52
1575 1610 0.804989 ACAACGCAGCAATTCTAGCC 59.195 50.000 0.00 0.00 0.00 3.93
1577 1612 4.145876 TGAAACAACGCAGCAATTCTAG 57.854 40.909 0.00 0.00 0.00 2.43
1578 1613 4.215185 TGATGAAACAACGCAGCAATTCTA 59.785 37.500 0.00 0.00 0.00 2.10
1579 1614 3.004629 TGATGAAACAACGCAGCAATTCT 59.995 39.130 0.00 0.00 0.00 2.40
1580 1615 3.120121 GTGATGAAACAACGCAGCAATTC 59.880 43.478 0.00 0.00 31.67 2.17
1581 1616 3.052036 GTGATGAAACAACGCAGCAATT 58.948 40.909 0.00 0.00 31.67 2.32
1582 1617 2.034432 TGTGATGAAACAACGCAGCAAT 59.966 40.909 0.00 0.00 31.67 3.56
1583 1618 1.403323 TGTGATGAAACAACGCAGCAA 59.597 42.857 0.00 0.00 31.67 3.91
1584 1619 1.002576 CTGTGATGAAACAACGCAGCA 60.003 47.619 8.95 0.00 37.78 4.41
1585 1620 1.678360 CTGTGATGAAACAACGCAGC 58.322 50.000 8.95 0.00 37.78 5.25
1586 1621 1.265095 AGCTGTGATGAAACAACGCAG 59.735 47.619 14.82 14.82 43.99 5.18
1587 1622 1.308047 AGCTGTGATGAAACAACGCA 58.692 45.000 0.00 0.00 0.00 5.24
1588 1623 3.747099 ATAGCTGTGATGAAACAACGC 57.253 42.857 0.00 0.00 0.00 4.84
1589 1624 5.778161 TGTATAGCTGTGATGAAACAACG 57.222 39.130 0.00 0.00 0.00 4.10
1590 1625 7.359595 TGTTTGTATAGCTGTGATGAAACAAC 58.640 34.615 0.00 0.00 31.11 3.32
1591 1626 7.503521 TGTTTGTATAGCTGTGATGAAACAA 57.496 32.000 0.00 0.00 31.11 2.83
1592 1627 7.686438 ATGTTTGTATAGCTGTGATGAAACA 57.314 32.000 0.00 4.88 36.72 2.83
1593 1628 8.970691 AAATGTTTGTATAGCTGTGATGAAAC 57.029 30.769 0.00 0.00 0.00 2.78
1594 1629 9.979578 AAAAATGTTTGTATAGCTGTGATGAAA 57.020 25.926 0.00 0.00 0.00 2.69
1839 1880 3.219281 ACACCCGCTTCAAAAGTTGTAT 58.781 40.909 0.00 0.00 0.00 2.29
1884 1926 4.047059 TCGTCGCGAGGACCCAAC 62.047 66.667 26.15 3.73 42.99 3.77
1974 2016 5.904080 GCTGATATTTAGCACTAAAGTTGCG 59.096 40.000 8.66 0.07 40.81 4.85
2031 2073 4.404715 AGGCTACTAGGCGAATTCACTAAA 59.595 41.667 6.22 0.00 46.58 1.85
2225 2268 8.319057 AGTATTGTAGGACATTGAGGATTACA 57.681 34.615 0.00 0.00 0.00 2.41
2238 2281 6.148976 GGACAACTTCCAAAGTATTGTAGGAC 59.851 42.308 0.00 0.00 45.10 3.85
2306 2350 9.852091 CGAAATCATGATAGATGACTTAGATCA 57.148 33.333 9.04 0.00 0.00 2.92
2332 2376 5.221048 CCATCCCCACATAGTTTCGAAATTC 60.221 44.000 14.69 1.86 0.00 2.17


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

AutoCloner maintained by Alex Coulton.