Multiple sequence alignment - TraesCS5B01G539100

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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 TraesCS5B01G539100 chr5B 100.000 3455 0 0 1 3455 694171736 694175190 0.000000e+00 6381.0
1 TraesCS5B01G539100 chr5B 91.304 92 4 3 8 96 599751887 599751977 4.680000e-24 122.0
2 TraesCS5B01G539100 chr5D 94.311 2619 127 11 854 3455 559896500 559899113 0.000000e+00 3991.0
3 TraesCS5B01G539100 chr5D 91.279 172 10 4 113 280 559896248 559896418 2.680000e-56 230.0
4 TraesCS5B01G539100 chr4A 90.754 2282 135 28 790 3043 613417672 613419905 0.000000e+00 2976.0
5 TraesCS5B01G539100 chr4A 85.039 635 40 22 135 728 613417029 613417649 2.300000e-166 595.0
6 TraesCS5B01G539100 chr4A 90.692 419 25 5 3045 3453 613419991 613420405 2.340000e-151 545.0
7 TraesCS5B01G539100 chr6D 91.209 91 5 2 9 96 172744057 172743967 1.680000e-23 121.0
8 TraesCS5B01G539100 chr6D 81.250 112 17 2 669 776 168220622 168220511 1.710000e-13 87.9
9 TraesCS5B01G539100 chr6A 91.209 91 5 2 9 96 53803437 53803347 1.680000e-23 121.0
10 TraesCS5B01G539100 chr3D 91.209 91 5 2 9 96 589264011 589263921 1.680000e-23 121.0
11 TraesCS5B01G539100 chr3D 84.000 100 11 3 669 764 379826246 379826344 1.320000e-14 91.6
12 TraesCS5B01G539100 chr3A 91.209 91 5 2 9 96 695639900 695639990 1.680000e-23 121.0
13 TraesCS5B01G539100 chr3A 91.954 87 4 2 9 92 672889385 672889299 6.060000e-23 119.0
14 TraesCS5B01G539100 chr3A 83.495 103 12 3 669 767 503822388 503822287 1.320000e-14 91.6
15 TraesCS5B01G539100 chrUn 90.110 91 6 2 9 96 388830978 388830888 7.840000e-22 115.0
16 TraesCS5B01G539100 chrUn 90.110 91 6 2 9 96 416410955 416411045 7.840000e-22 115.0
17 TraesCS5B01G539100 chr7D 88.660 97 7 3 9 102 88601120 88601025 7.840000e-22 115.0
18 TraesCS5B01G539100 chr7D 85.714 98 11 1 675 769 432494877 432494780 2.190000e-17 100.0
19 TraesCS5B01G539100 chr6B 83.929 112 14 2 669 776 301608779 301608668 1.700000e-18 104.0
20 TraesCS5B01G539100 chr2A 86.458 96 10 1 675 767 776163171 776163076 6.100000e-18 102.0
21 TraesCS5B01G539100 chr2B 84.848 99 12 1 669 764 353566035 353566133 2.840000e-16 97.1
22 TraesCS5B01G539100 chr3B 83.495 103 12 3 669 767 495475586 495475485 1.320000e-14 91.6


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 TraesCS5B01G539100 chr5B 694171736 694175190 3454 False 6381.0 6381 100.000000 1 3455 1 chr5B.!!$F2 3454
1 TraesCS5B01G539100 chr5D 559896248 559899113 2865 False 2110.5 3991 92.795000 113 3455 2 chr5D.!!$F1 3342
2 TraesCS5B01G539100 chr4A 613417029 613420405 3376 False 1372.0 2976 88.828333 135 3453 3 chr4A.!!$F1 3318

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
47 48 0.818938 CAAGGCACATTAGCATGGCA 59.181 50.0 0.0 0.0 43.55 4.92 F
1398 1474 0.545171 TCTCCGTCTACATCCGGTCT 59.455 55.0 0.0 0.0 44.51 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1684 0.612174 CCTCCCTGACCGAACTCAGA 60.612 60.000 6.36 0.0 40.28 3.27 R
2756 2855 1.351017 AGGGTCATCGCTTCTTTCCAA 59.649 47.619 0.00 0.0 32.92 3.53 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
29 30 3.354948 CCTGAAGGTGTGGATCATTCA 57.645 47.619 0.00 0.00 0.00 2.57
30 31 3.689347 CCTGAAGGTGTGGATCATTCAA 58.311 45.455 0.00 0.00 28.67 2.69
31 32 3.693085 CCTGAAGGTGTGGATCATTCAAG 59.307 47.826 0.00 0.00 28.67 3.02
32 33 3.689347 TGAAGGTGTGGATCATTCAAGG 58.311 45.455 0.00 0.00 0.00 3.61
33 34 2.134789 AGGTGTGGATCATTCAAGGC 57.865 50.000 0.00 0.00 0.00 4.35
34 35 1.355381 AGGTGTGGATCATTCAAGGCA 59.645 47.619 0.00 0.00 0.00 4.75
35 36 1.474077 GGTGTGGATCATTCAAGGCAC 59.526 52.381 0.00 0.00 0.00 5.01
36 37 2.161855 GTGTGGATCATTCAAGGCACA 58.838 47.619 0.00 0.00 0.00 4.57
37 38 2.756760 GTGTGGATCATTCAAGGCACAT 59.243 45.455 0.00 0.00 0.00 3.21
38 39 3.194116 GTGTGGATCATTCAAGGCACATT 59.806 43.478 0.00 0.00 0.00 2.71
39 40 4.398988 GTGTGGATCATTCAAGGCACATTA 59.601 41.667 0.00 0.00 0.00 1.90
40 41 4.641541 TGTGGATCATTCAAGGCACATTAG 59.358 41.667 0.00 0.00 0.00 1.73
41 42 3.633525 TGGATCATTCAAGGCACATTAGC 59.366 43.478 0.00 0.00 0.00 3.09
42 43 3.633525 GGATCATTCAAGGCACATTAGCA 59.366 43.478 0.00 0.00 35.83 3.49
43 44 4.280174 GGATCATTCAAGGCACATTAGCAT 59.720 41.667 0.00 0.00 35.83 3.79
44 45 4.642445 TCATTCAAGGCACATTAGCATG 57.358 40.909 0.00 0.00 35.83 4.06
45 46 3.382227 TCATTCAAGGCACATTAGCATGG 59.618 43.478 0.00 0.00 34.27 3.66
46 47 1.105457 TCAAGGCACATTAGCATGGC 58.895 50.000 0.00 0.00 41.52 4.40
47 48 0.818938 CAAGGCACATTAGCATGGCA 59.181 50.000 0.00 0.00 43.55 4.92
48 49 1.411246 CAAGGCACATTAGCATGGCAT 59.589 47.619 0.00 0.00 43.55 4.40
49 50 2.624364 CAAGGCACATTAGCATGGCATA 59.376 45.455 0.00 0.00 43.55 3.14
50 51 2.948115 AGGCACATTAGCATGGCATAA 58.052 42.857 0.00 0.00 43.55 1.90
51 52 3.503365 AGGCACATTAGCATGGCATAAT 58.497 40.909 0.00 0.00 43.55 1.28
52 53 3.899360 AGGCACATTAGCATGGCATAATT 59.101 39.130 0.00 0.00 43.55 1.40
53 54 4.021719 AGGCACATTAGCATGGCATAATTC 60.022 41.667 0.00 0.00 43.55 2.17
54 55 4.021719 GGCACATTAGCATGGCATAATTCT 60.022 41.667 0.00 0.00 40.91 2.40
55 56 4.921515 GCACATTAGCATGGCATAATTCTG 59.078 41.667 0.00 0.00 34.27 3.02
56 57 5.508489 GCACATTAGCATGGCATAATTCTGT 60.508 40.000 0.00 0.00 34.27 3.41
57 58 6.509656 CACATTAGCATGGCATAATTCTGTT 58.490 36.000 0.00 0.00 34.27 3.16
58 59 6.982141 CACATTAGCATGGCATAATTCTGTTT 59.018 34.615 0.00 0.00 34.27 2.83
59 60 6.982141 ACATTAGCATGGCATAATTCTGTTTG 59.018 34.615 0.00 0.00 34.27 2.93
60 61 6.772360 TTAGCATGGCATAATTCTGTTTGA 57.228 33.333 0.00 0.00 0.00 2.69
61 62 5.664294 AGCATGGCATAATTCTGTTTGAA 57.336 34.783 0.00 0.00 39.24 2.69
62 63 6.229936 AGCATGGCATAATTCTGTTTGAAT 57.770 33.333 0.00 0.00 46.49 2.57
63 64 6.278363 AGCATGGCATAATTCTGTTTGAATC 58.722 36.000 0.00 0.00 43.99 2.52
64 65 5.174398 GCATGGCATAATTCTGTTTGAATCG 59.826 40.000 0.00 0.00 43.99 3.34
65 66 5.247507 TGGCATAATTCTGTTTGAATCGG 57.752 39.130 0.00 0.00 43.99 4.18
66 67 4.946772 TGGCATAATTCTGTTTGAATCGGA 59.053 37.500 0.00 0.00 43.99 4.55
67 68 5.066375 TGGCATAATTCTGTTTGAATCGGAG 59.934 40.000 0.00 0.00 43.99 4.63
68 69 5.066505 GGCATAATTCTGTTTGAATCGGAGT 59.933 40.000 0.00 0.00 43.99 3.85
69 70 6.404734 GGCATAATTCTGTTTGAATCGGAGTT 60.405 38.462 0.00 0.00 43.99 3.01
70 71 7.029563 GCATAATTCTGTTTGAATCGGAGTTT 58.970 34.615 0.00 0.00 43.99 2.66
71 72 7.008628 GCATAATTCTGTTTGAATCGGAGTTTG 59.991 37.037 0.00 0.81 43.99 2.93
72 73 6.633500 AATTCTGTTTGAATCGGAGTTTGA 57.367 33.333 0.00 0.00 43.99 2.69
73 74 6.633500 ATTCTGTTTGAATCGGAGTTTGAA 57.367 33.333 0.00 0.00 41.17 2.69
74 75 6.443934 TTCTGTTTGAATCGGAGTTTGAAA 57.556 33.333 0.00 0.00 0.00 2.69
75 76 5.816919 TCTGTTTGAATCGGAGTTTGAAAC 58.183 37.500 0.00 0.00 0.00 2.78
76 77 4.927422 TGTTTGAATCGGAGTTTGAAACC 58.073 39.130 4.14 0.00 0.00 3.27
77 78 4.399618 TGTTTGAATCGGAGTTTGAAACCA 59.600 37.500 4.14 0.00 0.00 3.67
78 79 5.105716 TGTTTGAATCGGAGTTTGAAACCAA 60.106 36.000 4.14 0.00 0.00 3.67
79 80 5.584253 TTGAATCGGAGTTTGAAACCAAA 57.416 34.783 4.14 0.00 0.00 3.28
91 92 5.993748 TTGAAACCAAACAAACTTCTCCT 57.006 34.783 0.00 0.00 0.00 3.69
92 93 5.993748 TGAAACCAAACAAACTTCTCCTT 57.006 34.783 0.00 0.00 0.00 3.36
93 94 7.469537 TTGAAACCAAACAAACTTCTCCTTA 57.530 32.000 0.00 0.00 0.00 2.69
94 95 7.095695 TGAAACCAAACAAACTTCTCCTTAG 57.904 36.000 0.00 0.00 0.00 2.18
95 96 6.096282 TGAAACCAAACAAACTTCTCCTTAGG 59.904 38.462 0.00 0.00 0.00 2.69
96 97 5.125367 ACCAAACAAACTTCTCCTTAGGT 57.875 39.130 0.00 0.00 0.00 3.08
97 98 4.887655 ACCAAACAAACTTCTCCTTAGGTG 59.112 41.667 0.00 0.00 0.00 4.00
98 99 5.130350 CCAAACAAACTTCTCCTTAGGTGA 58.870 41.667 0.00 0.00 0.00 4.02
99 100 5.239525 CCAAACAAACTTCTCCTTAGGTGAG 59.760 44.000 3.17 0.75 0.00 3.51
100 101 5.888982 AACAAACTTCTCCTTAGGTGAGA 57.111 39.130 3.17 0.00 37.09 3.27
101 102 6.441088 AACAAACTTCTCCTTAGGTGAGAT 57.559 37.500 3.17 0.00 38.58 2.75
102 103 6.043854 ACAAACTTCTCCTTAGGTGAGATC 57.956 41.667 3.17 0.00 38.58 2.75
103 104 5.046231 ACAAACTTCTCCTTAGGTGAGATCC 60.046 44.000 3.17 0.00 38.58 3.36
104 105 3.648739 ACTTCTCCTTAGGTGAGATCCC 58.351 50.000 3.17 0.00 38.58 3.85
105 106 3.012959 ACTTCTCCTTAGGTGAGATCCCA 59.987 47.826 3.17 0.00 38.58 4.37
106 107 4.230455 CTTCTCCTTAGGTGAGATCCCAT 58.770 47.826 3.17 0.00 38.58 4.00
107 108 3.581101 TCTCCTTAGGTGAGATCCCATG 58.419 50.000 0.00 0.00 34.03 3.66
108 109 3.051803 TCTCCTTAGGTGAGATCCCATGT 60.052 47.826 0.00 0.00 34.03 3.21
109 110 4.170053 TCTCCTTAGGTGAGATCCCATGTA 59.830 45.833 0.00 0.00 34.03 2.29
110 111 4.483950 TCCTTAGGTGAGATCCCATGTAG 58.516 47.826 0.00 0.00 0.00 2.74
111 112 4.170053 TCCTTAGGTGAGATCCCATGTAGA 59.830 45.833 0.00 0.00 0.00 2.59
140 141 8.039603 ACTCAAAATGCTGATTAAATACGACA 57.960 30.769 0.00 0.00 0.00 4.35
263 293 3.094572 AGGGTCTCTTTGATTTGCATGG 58.905 45.455 0.00 0.00 0.00 3.66
311 341 3.498774 ATAGGATTGGAGTGGCATGTC 57.501 47.619 0.00 0.00 0.00 3.06
326 356 3.539604 GCATGTCTGCTTCAATCCTAGT 58.460 45.455 0.00 0.00 45.32 2.57
327 357 4.697514 GCATGTCTGCTTCAATCCTAGTA 58.302 43.478 0.00 0.00 45.32 1.82
328 358 5.303971 GCATGTCTGCTTCAATCCTAGTAT 58.696 41.667 0.00 0.00 45.32 2.12
329 359 6.459066 GCATGTCTGCTTCAATCCTAGTATA 58.541 40.000 0.00 0.00 45.32 1.47
330 360 6.931281 GCATGTCTGCTTCAATCCTAGTATAA 59.069 38.462 0.00 0.00 45.32 0.98
331 361 7.095439 GCATGTCTGCTTCAATCCTAGTATAAC 60.095 40.741 0.00 0.00 45.32 1.89
339 369 9.273016 GCTTCAATCCTAGTATAACATTAGCAA 57.727 33.333 0.00 0.00 0.00 3.91
401 457 9.679661 TGTAAAAAGATATTGAAGTGGATGCTA 57.320 29.630 0.00 0.00 0.00 3.49
497 553 6.514012 AAAAATCCCAAGGACCAAAAATCT 57.486 33.333 0.00 0.00 32.98 2.40
537 593 7.833285 AATCAAAGAAGCCCTAGTTAAACAA 57.167 32.000 0.00 0.00 0.00 2.83
538 594 8.422577 AATCAAAGAAGCCCTAGTTAAACAAT 57.577 30.769 0.00 0.00 0.00 2.71
539 595 7.214467 TCAAAGAAGCCCTAGTTAAACAATG 57.786 36.000 0.00 0.00 0.00 2.82
540 596 7.001674 TCAAAGAAGCCCTAGTTAAACAATGA 58.998 34.615 0.00 0.00 0.00 2.57
541 597 7.504238 TCAAAGAAGCCCTAGTTAAACAATGAA 59.496 33.333 0.00 0.00 0.00 2.57
542 598 7.833285 AAGAAGCCCTAGTTAAACAATGAAA 57.167 32.000 0.00 0.00 0.00 2.69
543 599 7.833285 AGAAGCCCTAGTTAAACAATGAAAA 57.167 32.000 0.00 0.00 0.00 2.29
544 600 7.886338 AGAAGCCCTAGTTAAACAATGAAAAG 58.114 34.615 0.00 0.00 0.00 2.27
547 603 7.658261 AGCCCTAGTTAAACAATGAAAAGAAC 58.342 34.615 0.00 0.00 0.00 3.01
550 606 9.244799 CCCTAGTTAAACAATGAAAAGAACAAC 57.755 33.333 0.00 0.00 0.00 3.32
568 624 7.351223 AGAACAACAACAACAACACAAAAATG 58.649 30.769 0.00 0.00 0.00 2.32
576 632 4.385358 ACAACACAAAAATGGAGTGTCC 57.615 40.909 0.00 0.00 44.99 4.02
579 635 5.046663 ACAACACAAAAATGGAGTGTCCTTT 60.047 36.000 0.00 0.00 44.99 3.11
583 639 5.922544 CACAAAAATGGAGTGTCCTTTCATC 59.077 40.000 0.00 0.00 37.46 2.92
584 640 5.598005 ACAAAAATGGAGTGTCCTTTCATCA 59.402 36.000 0.00 0.00 37.46 3.07
592 648 5.529060 GGAGTGTCCTTTCATCATCAATACC 59.471 44.000 0.00 0.00 32.53 2.73
594 650 6.666678 AGTGTCCTTTCATCATCAATACCAT 58.333 36.000 0.00 0.00 0.00 3.55
614 685 4.406069 CATGTAATTTGTGCGTGAGGAAG 58.594 43.478 0.00 0.00 30.83 3.46
661 732 7.682459 AGGTTGGGGTTGATAAAATTTTCCTAT 59.318 33.333 6.72 0.00 0.00 2.57
677 748 3.318313 TCCTATGAAGAACCTCCATCCC 58.682 50.000 0.00 0.00 0.00 3.85
687 758 6.192970 AGAACCTCCATCCCATATTAGTTG 57.807 41.667 0.00 0.00 0.00 3.16
689 760 5.568620 ACCTCCATCCCATATTAGTTGTC 57.431 43.478 0.00 0.00 0.00 3.18
690 761 4.040461 ACCTCCATCCCATATTAGTTGTCG 59.960 45.833 0.00 0.00 0.00 4.35
691 762 3.997021 CTCCATCCCATATTAGTTGTCGC 59.003 47.826 0.00 0.00 0.00 5.19
692 763 3.646162 TCCATCCCATATTAGTTGTCGCT 59.354 43.478 0.00 0.00 0.00 4.93
693 764 3.997021 CCATCCCATATTAGTTGTCGCTC 59.003 47.826 0.00 0.00 0.00 5.03
694 765 4.503123 CCATCCCATATTAGTTGTCGCTCA 60.503 45.833 0.00 0.00 0.00 4.26
697 768 5.680619 TCCCATATTAGTTGTCGCTCAAAT 58.319 37.500 0.00 0.00 37.81 2.32
703 774 2.783135 AGTTGTCGCTCAAATGGATGT 58.217 42.857 0.00 0.00 37.81 3.06
709 780 6.603237 TGTCGCTCAAATGGATGTATTTAG 57.397 37.500 0.00 0.00 0.00 1.85
713 784 5.523369 GCTCAAATGGATGTATTTAGCACC 58.477 41.667 0.00 0.00 32.79 5.01
715 786 4.578516 TCAAATGGATGTATTTAGCACCGG 59.421 41.667 0.00 0.00 0.00 5.28
723 794 4.757594 TGTATTTAGCACCGGAATACGTT 58.242 39.130 9.46 0.00 42.24 3.99
728 799 3.814005 AGCACCGGAATACGTTTAGAT 57.186 42.857 9.46 0.00 42.24 1.98
729 800 4.924305 AGCACCGGAATACGTTTAGATA 57.076 40.909 9.46 0.00 42.24 1.98
730 801 4.614946 AGCACCGGAATACGTTTAGATAC 58.385 43.478 9.46 0.00 42.24 2.24
731 802 3.423206 GCACCGGAATACGTTTAGATACG 59.577 47.826 9.46 0.00 46.52 3.06
743 814 5.653657 CGTTTAGATACGTCCATTTTAGCG 58.346 41.667 0.00 0.00 36.80 4.26
744 815 5.456497 CGTTTAGATACGTCCATTTTAGCGA 59.544 40.000 0.00 0.00 36.80 4.93
745 816 6.559158 CGTTTAGATACGTCCATTTTAGCGAC 60.559 42.308 0.00 0.00 36.80 5.19
746 817 4.650754 AGATACGTCCATTTTAGCGACT 57.349 40.909 0.00 0.00 0.00 4.18
747 818 5.762825 AGATACGTCCATTTTAGCGACTA 57.237 39.130 0.00 0.00 0.00 2.59
748 819 5.517904 AGATACGTCCATTTTAGCGACTAC 58.482 41.667 0.00 0.00 0.00 2.73
749 820 3.863142 ACGTCCATTTTAGCGACTACT 57.137 42.857 0.00 0.00 0.00 2.57
750 821 4.970662 ACGTCCATTTTAGCGACTACTA 57.029 40.909 0.00 0.00 0.00 1.82
751 822 5.511234 ACGTCCATTTTAGCGACTACTAT 57.489 39.130 0.00 0.00 0.00 2.12
752 823 5.279384 ACGTCCATTTTAGCGACTACTATG 58.721 41.667 0.00 0.00 0.00 2.23
753 824 5.066893 ACGTCCATTTTAGCGACTACTATGA 59.933 40.000 0.00 0.00 0.00 2.15
754 825 5.625721 CGTCCATTTTAGCGACTACTATGAG 59.374 44.000 0.00 0.00 0.00 2.90
755 826 6.512903 CGTCCATTTTAGCGACTACTATGAGA 60.513 42.308 0.00 0.00 0.00 3.27
756 827 7.371936 GTCCATTTTAGCGACTACTATGAGAT 58.628 38.462 0.00 0.00 0.00 2.75
757 828 7.327275 GTCCATTTTAGCGACTACTATGAGATG 59.673 40.741 0.00 0.00 0.00 2.90
758 829 6.587990 CCATTTTAGCGACTACTATGAGATGG 59.412 42.308 0.00 0.00 0.00 3.51
776 847 8.150827 TGAGATGGAGGGAATAGTATAAATGG 57.849 38.462 0.00 0.00 0.00 3.16
779 850 6.697641 TGGAGGGAATAGTATAAATGGGTC 57.302 41.667 0.00 0.00 0.00 4.46
780 851 5.247564 TGGAGGGAATAGTATAAATGGGTCG 59.752 44.000 0.00 0.00 0.00 4.79
781 852 5.247792 GGAGGGAATAGTATAAATGGGTCGT 59.752 44.000 0.00 0.00 0.00 4.34
782 853 6.438425 GGAGGGAATAGTATAAATGGGTCGTA 59.562 42.308 0.00 0.00 0.00 3.43
783 854 7.038799 GGAGGGAATAGTATAAATGGGTCGTAA 60.039 40.741 0.00 0.00 0.00 3.18
784 855 7.904205 AGGGAATAGTATAAATGGGTCGTAAG 58.096 38.462 0.00 0.00 0.00 2.34
831 902 3.128589 CCTAACGGATCAAACAACCCATG 59.871 47.826 0.00 0.00 0.00 3.66
839 910 5.067805 GGATCAAACAACCCATGTAGGAATC 59.932 44.000 0.00 0.00 42.99 2.52
840 911 4.340617 TCAAACAACCCATGTAGGAATCC 58.659 43.478 0.00 0.00 42.99 3.01
842 913 5.251932 TCAAACAACCCATGTAGGAATCCTA 59.748 40.000 4.61 4.61 42.99 2.94
844 915 5.789574 ACAACCCATGTAGGAATCCTAAA 57.210 39.130 11.12 6.05 41.63 1.85
845 916 5.755849 ACAACCCATGTAGGAATCCTAAAG 58.244 41.667 11.12 3.95 41.63 1.85
846 917 5.253096 ACAACCCATGTAGGAATCCTAAAGT 59.747 40.000 11.12 0.00 41.63 2.66
848 919 5.755849 ACCCATGTAGGAATCCTAAAGTTG 58.244 41.667 11.12 1.90 37.91 3.16
926 999 7.565323 TCAAACCAAATTCAAATTCCCAAAG 57.435 32.000 0.00 0.00 0.00 2.77
944 1017 5.182487 CCAAAGGTTTTTAAGCCACAGTTT 58.818 37.500 0.00 0.00 0.00 2.66
945 1018 5.645929 CCAAAGGTTTTTAAGCCACAGTTTT 59.354 36.000 0.00 0.00 0.00 2.43
959 1032 1.135972 CAGTTTTTGAGGCATCGTCGG 60.136 52.381 0.00 0.00 0.00 4.79
986 1059 4.214327 GCCCTCCTCCGCTCGAAG 62.214 72.222 0.00 0.00 0.00 3.79
990 1063 2.754658 TCCTCCGCTCGAAGACCC 60.755 66.667 0.00 0.00 0.00 4.46
1260 1336 4.785453 GGCCTCCTCAGCAACCCG 62.785 72.222 0.00 0.00 0.00 5.28
1299 1375 1.815421 CACCTCCTACGGTGCATGC 60.815 63.158 11.82 11.82 46.98 4.06
1390 1466 0.668535 CGCCATGATCTCCGTCTACA 59.331 55.000 0.00 0.00 0.00 2.74
1398 1474 0.545171 TCTCCGTCTACATCCGGTCT 59.455 55.000 0.00 0.00 44.51 3.85
1444 1520 2.748647 TCGGCGAGATGGACGTCA 60.749 61.111 18.91 3.91 40.06 4.35
1445 1521 2.579787 CGGCGAGATGGACGTCAC 60.580 66.667 18.91 7.49 34.98 3.67
1449 1525 2.202756 GAGATGGACGTCACGCCC 60.203 66.667 18.91 0.00 0.00 6.13
1470 1546 1.301677 CCGCTTCCTGCTTCAACTCC 61.302 60.000 0.00 0.00 40.11 3.85
1614 1690 4.400961 GCCCTTGGCGCTCTGAGT 62.401 66.667 7.64 0.00 39.62 3.41
2193 2269 2.492088 AGGGAACTTTATTTCGCTTGCC 59.508 45.455 0.00 0.00 44.10 4.52
2230 2306 0.536006 GGGTATGCATGAGGAGGCAC 60.536 60.000 10.16 0.00 42.75 5.01
2335 2418 5.716228 TGCTTGACCATGTCCAATAAATTCT 59.284 36.000 0.00 0.00 0.00 2.40
2363 2446 0.322546 CCACTTCCTTGCCTGTACCC 60.323 60.000 0.00 0.00 0.00 3.69
2457 2542 2.547211 CTGCAGTGAACTTGTCTGAAGG 59.453 50.000 5.25 0.00 32.79 3.46
2749 2848 7.820872 CCTGCATAAACATCAAATTTCCTTCTT 59.179 33.333 0.00 0.00 0.00 2.52
2809 2908 9.950496 AGTCATGTCTATTATCAAAGTTCAGTT 57.050 29.630 0.00 0.00 0.00 3.16
3026 3132 5.772825 TGGAATTCAAGTTCAAAGGACTG 57.227 39.130 7.93 0.00 0.00 3.51
3105 3295 3.957468 GCAGTAGGCATTTGCAACTATC 58.043 45.455 0.00 0.00 44.36 2.08
3124 3314 5.777223 ACTATCATCTAATGCCACTCTGCTA 59.223 40.000 0.00 0.00 0.00 3.49
3149 3349 1.134401 ACATAGCTGTCCACAATCCCG 60.134 52.381 0.00 0.00 0.00 5.14
3264 3464 4.768448 TCTTATGTCAGTTTCTACGGACCA 59.232 41.667 6.20 0.00 45.35 4.02
3296 3496 5.365619 TCTTTAGCTTTCCAACGAGACTTT 58.634 37.500 0.00 0.00 0.00 2.66
3341 3541 4.801891 CATATGATGCTAATGTTGGTGCC 58.198 43.478 0.00 0.00 0.00 5.01
3374 3574 8.956426 CCAAAGGCACATCTTATTAGAAAACTA 58.044 33.333 0.00 0.00 33.20 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.354948 TGAATGATCCACACCTTCAGG 57.645 47.619 0.00 0.00 42.17 3.86
10 11 3.693085 CCTTGAATGATCCACACCTTCAG 59.307 47.826 0.00 0.00 31.82 3.02
11 12 3.689347 CCTTGAATGATCCACACCTTCA 58.311 45.455 0.00 0.00 0.00 3.02
12 13 2.424956 GCCTTGAATGATCCACACCTTC 59.575 50.000 0.00 0.00 0.00 3.46
13 14 2.225091 TGCCTTGAATGATCCACACCTT 60.225 45.455 0.00 0.00 0.00 3.50
14 15 1.355381 TGCCTTGAATGATCCACACCT 59.645 47.619 0.00 0.00 0.00 4.00
15 16 1.474077 GTGCCTTGAATGATCCACACC 59.526 52.381 0.00 0.00 0.00 4.16
16 17 2.161855 TGTGCCTTGAATGATCCACAC 58.838 47.619 0.00 0.00 0.00 3.82
17 18 2.583024 TGTGCCTTGAATGATCCACA 57.417 45.000 0.00 0.00 0.00 4.17
18 19 4.498682 GCTAATGTGCCTTGAATGATCCAC 60.499 45.833 0.00 0.00 0.00 4.02
19 20 3.633525 GCTAATGTGCCTTGAATGATCCA 59.366 43.478 0.00 0.00 0.00 3.41
20 21 3.633525 TGCTAATGTGCCTTGAATGATCC 59.366 43.478 0.00 0.00 0.00 3.36
21 22 4.906065 TGCTAATGTGCCTTGAATGATC 57.094 40.909 0.00 0.00 0.00 2.92
22 23 4.038763 CCATGCTAATGTGCCTTGAATGAT 59.961 41.667 0.00 0.00 31.27 2.45
23 24 3.382227 CCATGCTAATGTGCCTTGAATGA 59.618 43.478 0.00 0.00 31.27 2.57
24 25 3.713288 CCATGCTAATGTGCCTTGAATG 58.287 45.455 0.00 0.00 31.27 2.67
25 26 2.101917 GCCATGCTAATGTGCCTTGAAT 59.898 45.455 0.00 0.00 31.27 2.57
26 27 1.477700 GCCATGCTAATGTGCCTTGAA 59.522 47.619 0.00 0.00 31.27 2.69
27 28 1.105457 GCCATGCTAATGTGCCTTGA 58.895 50.000 0.00 0.00 31.27 3.02
28 29 0.818938 TGCCATGCTAATGTGCCTTG 59.181 50.000 0.00 0.00 32.24 3.61
29 30 1.784358 ATGCCATGCTAATGTGCCTT 58.216 45.000 0.00 0.00 32.24 4.35
30 31 2.662535 TATGCCATGCTAATGTGCCT 57.337 45.000 0.00 0.00 32.24 4.75
31 32 3.947910 ATTATGCCATGCTAATGTGCC 57.052 42.857 0.00 0.00 32.24 5.01
32 33 4.921515 CAGAATTATGCCATGCTAATGTGC 59.078 41.667 0.00 0.00 33.23 4.57
33 34 6.080648 ACAGAATTATGCCATGCTAATGTG 57.919 37.500 0.00 0.00 31.27 3.21
34 35 6.720112 AACAGAATTATGCCATGCTAATGT 57.280 33.333 0.00 0.00 31.27 2.71
35 36 7.204604 TCAAACAGAATTATGCCATGCTAATG 58.795 34.615 0.00 0.00 0.00 1.90
36 37 7.350744 TCAAACAGAATTATGCCATGCTAAT 57.649 32.000 0.00 0.00 0.00 1.73
37 38 6.772360 TCAAACAGAATTATGCCATGCTAA 57.228 33.333 0.00 0.00 0.00 3.09
38 39 6.772360 TTCAAACAGAATTATGCCATGCTA 57.228 33.333 0.00 0.00 0.00 3.49
39 40 5.664294 TTCAAACAGAATTATGCCATGCT 57.336 34.783 0.00 0.00 0.00 3.79
40 41 5.174398 CGATTCAAACAGAATTATGCCATGC 59.826 40.000 0.00 0.00 46.76 4.06
41 42 5.688621 CCGATTCAAACAGAATTATGCCATG 59.311 40.000 0.00 0.00 46.76 3.66
42 43 5.593909 TCCGATTCAAACAGAATTATGCCAT 59.406 36.000 0.00 0.00 46.76 4.40
43 44 4.946772 TCCGATTCAAACAGAATTATGCCA 59.053 37.500 0.00 0.00 46.76 4.92
44 45 5.066505 ACTCCGATTCAAACAGAATTATGCC 59.933 40.000 0.00 0.00 46.76 4.40
45 46 6.124088 ACTCCGATTCAAACAGAATTATGC 57.876 37.500 0.00 0.00 46.76 3.14
46 47 8.236586 TCAAACTCCGATTCAAACAGAATTATG 58.763 33.333 0.00 0.00 46.76 1.90
47 48 8.335532 TCAAACTCCGATTCAAACAGAATTAT 57.664 30.769 0.00 0.00 46.76 1.28
48 49 7.737972 TCAAACTCCGATTCAAACAGAATTA 57.262 32.000 0.00 0.00 46.76 1.40
49 50 6.633500 TCAAACTCCGATTCAAACAGAATT 57.367 33.333 0.00 0.00 46.76 2.17
51 52 6.262601 GTTTCAAACTCCGATTCAAACAGAA 58.737 36.000 0.00 0.00 41.28 3.02
52 53 5.220970 GGTTTCAAACTCCGATTCAAACAGA 60.221 40.000 0.00 0.00 0.00 3.41
53 54 4.976116 GGTTTCAAACTCCGATTCAAACAG 59.024 41.667 0.00 0.00 0.00 3.16
54 55 4.399618 TGGTTTCAAACTCCGATTCAAACA 59.600 37.500 0.00 0.00 0.00 2.83
55 56 4.927422 TGGTTTCAAACTCCGATTCAAAC 58.073 39.130 0.00 0.00 0.00 2.93
56 57 5.584253 TTGGTTTCAAACTCCGATTCAAA 57.416 34.783 0.00 0.00 0.00 2.69
57 58 5.584253 TTTGGTTTCAAACTCCGATTCAA 57.416 34.783 0.00 0.00 37.89 2.69
68 69 6.353404 AGGAGAAGTTTGTTTGGTTTCAAA 57.647 33.333 0.00 0.00 40.23 2.69
69 70 5.993748 AGGAGAAGTTTGTTTGGTTTCAA 57.006 34.783 0.00 0.00 0.00 2.69
70 71 5.993748 AAGGAGAAGTTTGTTTGGTTTCA 57.006 34.783 0.00 0.00 0.00 2.69
71 72 6.096423 ACCTAAGGAGAAGTTTGTTTGGTTTC 59.904 38.462 0.00 0.00 0.00 2.78
72 73 5.955959 ACCTAAGGAGAAGTTTGTTTGGTTT 59.044 36.000 0.00 0.00 0.00 3.27
73 74 5.359860 CACCTAAGGAGAAGTTTGTTTGGTT 59.640 40.000 0.00 0.00 0.00 3.67
74 75 4.887655 CACCTAAGGAGAAGTTTGTTTGGT 59.112 41.667 0.00 0.00 0.00 3.67
75 76 5.130350 TCACCTAAGGAGAAGTTTGTTTGG 58.870 41.667 0.00 0.00 0.00 3.28
76 77 6.055588 TCTCACCTAAGGAGAAGTTTGTTTG 58.944 40.000 0.00 0.00 38.40 2.93
77 78 6.248569 TCTCACCTAAGGAGAAGTTTGTTT 57.751 37.500 0.00 0.00 38.40 2.83
78 79 5.888982 TCTCACCTAAGGAGAAGTTTGTT 57.111 39.130 0.00 0.00 38.40 2.83
79 80 5.046231 GGATCTCACCTAAGGAGAAGTTTGT 60.046 44.000 0.00 0.00 44.01 2.83
80 81 5.423886 GGATCTCACCTAAGGAGAAGTTTG 58.576 45.833 0.00 0.00 44.01 2.93
81 82 4.471747 GGGATCTCACCTAAGGAGAAGTTT 59.528 45.833 0.00 0.00 44.01 2.66
82 83 4.034410 GGGATCTCACCTAAGGAGAAGTT 58.966 47.826 0.00 0.00 44.01 2.66
83 84 3.012959 TGGGATCTCACCTAAGGAGAAGT 59.987 47.826 0.00 0.00 44.01 3.01
84 85 3.647636 TGGGATCTCACCTAAGGAGAAG 58.352 50.000 0.00 0.00 44.01 2.85
85 86 3.776731 TGGGATCTCACCTAAGGAGAA 57.223 47.619 0.00 0.00 44.01 2.87
86 87 3.051803 ACATGGGATCTCACCTAAGGAGA 60.052 47.826 0.00 0.00 44.83 3.71
87 88 3.312890 ACATGGGATCTCACCTAAGGAG 58.687 50.000 0.00 0.00 0.00 3.69
88 89 3.421394 ACATGGGATCTCACCTAAGGA 57.579 47.619 0.00 0.00 0.00 3.36
89 90 4.282195 GTCTACATGGGATCTCACCTAAGG 59.718 50.000 0.00 0.00 0.00 2.69
90 91 4.282195 GGTCTACATGGGATCTCACCTAAG 59.718 50.000 0.00 0.00 0.00 2.18
91 92 4.223953 GGTCTACATGGGATCTCACCTAA 58.776 47.826 0.00 0.00 0.00 2.69
92 93 3.206639 TGGTCTACATGGGATCTCACCTA 59.793 47.826 0.00 0.00 0.00 3.08
93 94 2.023015 TGGTCTACATGGGATCTCACCT 60.023 50.000 0.00 0.00 0.00 4.00
94 95 2.398588 TGGTCTACATGGGATCTCACC 58.601 52.381 0.00 0.00 0.00 4.02
95 96 3.452627 AGTTGGTCTACATGGGATCTCAC 59.547 47.826 0.00 0.00 0.00 3.51
96 97 3.706594 GAGTTGGTCTACATGGGATCTCA 59.293 47.826 0.00 0.00 0.00 3.27
97 98 3.706594 TGAGTTGGTCTACATGGGATCTC 59.293 47.826 0.00 0.00 0.00 2.75
98 99 3.724478 TGAGTTGGTCTACATGGGATCT 58.276 45.455 0.00 0.00 0.00 2.75
99 100 4.487714 TTGAGTTGGTCTACATGGGATC 57.512 45.455 0.00 0.00 0.00 3.36
100 101 4.927267 TTTGAGTTGGTCTACATGGGAT 57.073 40.909 0.00 0.00 0.00 3.85
101 102 4.715534 TTTTGAGTTGGTCTACATGGGA 57.284 40.909 0.00 0.00 0.00 4.37
102 103 4.380867 GCATTTTGAGTTGGTCTACATGGG 60.381 45.833 0.00 0.00 0.00 4.00
103 104 4.460382 AGCATTTTGAGTTGGTCTACATGG 59.540 41.667 0.00 0.00 0.00 3.66
104 105 5.181811 TCAGCATTTTGAGTTGGTCTACATG 59.818 40.000 0.00 0.00 0.00 3.21
105 106 5.316167 TCAGCATTTTGAGTTGGTCTACAT 58.684 37.500 0.00 0.00 0.00 2.29
106 107 4.713553 TCAGCATTTTGAGTTGGTCTACA 58.286 39.130 0.00 0.00 0.00 2.74
107 108 5.886960 ATCAGCATTTTGAGTTGGTCTAC 57.113 39.130 0.00 0.00 0.00 2.59
108 109 7.994425 TTAATCAGCATTTTGAGTTGGTCTA 57.006 32.000 0.00 0.00 0.00 2.59
109 110 6.899393 TTAATCAGCATTTTGAGTTGGTCT 57.101 33.333 0.00 0.00 0.00 3.85
110 111 9.076596 GTATTTAATCAGCATTTTGAGTTGGTC 57.923 33.333 0.00 0.00 0.00 4.02
111 112 7.754924 CGTATTTAATCAGCATTTTGAGTTGGT 59.245 33.333 0.00 0.00 0.00 3.67
140 141 8.474025 TGTTTCTACATTTCCAATTTCTTGTGT 58.526 29.630 0.00 0.00 0.00 3.72
177 178 6.899393 TGCTTAGAAATTTGTTCCATGTCT 57.101 33.333 0.00 0.00 0.00 3.41
225 229 4.104738 AGACCCTCAAATGTTTCTCCTTCA 59.895 41.667 0.00 0.00 0.00 3.02
263 293 9.887406 TTTTTCATATTCCTACGTTTTGAGAAC 57.113 29.630 0.00 0.00 0.00 3.01
311 341 8.930760 GCTAATGTTATACTAGGATTGAAGCAG 58.069 37.037 0.00 0.00 0.00 4.24
321 351 9.162764 ACACAACTTTGCTAATGTTATACTAGG 57.837 33.333 0.00 0.00 0.00 3.02
325 355 9.672086 TCAAACACAACTTTGCTAATGTTATAC 57.328 29.630 0.00 0.00 32.10 1.47
327 357 9.195411 CATCAAACACAACTTTGCTAATGTTAT 57.805 29.630 0.00 0.00 32.10 1.89
328 358 7.651304 CCATCAAACACAACTTTGCTAATGTTA 59.349 33.333 0.00 0.00 32.10 2.41
329 359 6.479660 CCATCAAACACAACTTTGCTAATGTT 59.520 34.615 0.00 0.00 32.10 2.71
330 360 5.984926 CCATCAAACACAACTTTGCTAATGT 59.015 36.000 0.00 0.00 32.10 2.71
331 361 5.107375 GCCATCAAACACAACTTTGCTAATG 60.107 40.000 0.00 0.00 32.10 1.90
339 369 5.789643 ACTTATGCCATCAAACACAACTT 57.210 34.783 0.00 0.00 0.00 2.66
373 403 9.638239 GCATCCACTTCAATATCTTTTTACAAA 57.362 29.630 0.00 0.00 0.00 2.83
380 436 9.638176 AAATCTAGCATCCACTTCAATATCTTT 57.362 29.630 0.00 0.00 0.00 2.52
452 508 5.705609 TTCTTAAGTTGGTTGCTTGATCC 57.294 39.130 1.63 0.00 0.00 3.36
521 577 7.833285 TCTTTTCATTGTTTAACTAGGGCTT 57.167 32.000 0.00 0.00 0.00 4.35
533 589 7.721286 TGTTGTTGTTGTTCTTTTCATTGTT 57.279 28.000 0.00 0.00 0.00 2.83
535 591 7.530190 GTGTTGTTGTTGTTGTTCTTTTCATTG 59.470 33.333 0.00 0.00 0.00 2.82
537 593 6.703607 TGTGTTGTTGTTGTTGTTCTTTTCAT 59.296 30.769 0.00 0.00 0.00 2.57
538 594 6.042777 TGTGTTGTTGTTGTTGTTCTTTTCA 58.957 32.000 0.00 0.00 0.00 2.69
539 595 6.517914 TGTGTTGTTGTTGTTGTTCTTTTC 57.482 33.333 0.00 0.00 0.00 2.29
540 596 6.910536 TTGTGTTGTTGTTGTTGTTCTTTT 57.089 29.167 0.00 0.00 0.00 2.27
541 597 6.910536 TTTGTGTTGTTGTTGTTGTTCTTT 57.089 29.167 0.00 0.00 0.00 2.52
542 598 6.910536 TTTTGTGTTGTTGTTGTTGTTCTT 57.089 29.167 0.00 0.00 0.00 2.52
543 599 6.910536 TTTTTGTGTTGTTGTTGTTGTTCT 57.089 29.167 0.00 0.00 0.00 3.01
544 600 6.576684 CCATTTTTGTGTTGTTGTTGTTGTTC 59.423 34.615 0.00 0.00 0.00 3.18
547 603 6.073331 ACTCCATTTTTGTGTTGTTGTTGTTG 60.073 34.615 0.00 0.00 0.00 3.33
550 606 5.407995 ACACTCCATTTTTGTGTTGTTGTTG 59.592 36.000 0.00 0.00 41.45 3.33
553 609 4.566360 GGACACTCCATTTTTGTGTTGTTG 59.434 41.667 0.00 0.00 43.81 3.33
568 624 5.529060 GGTATTGATGATGAAAGGACACTCC 59.471 44.000 0.00 0.00 36.58 3.85
579 635 8.136800 GCACAAATTACATGGTATTGATGATGA 58.863 33.333 0.00 0.00 0.00 2.92
583 639 6.196910 CACGCACAAATTACATGGTATTGATG 59.803 38.462 0.00 0.52 0.00 3.07
584 640 6.094742 TCACGCACAAATTACATGGTATTGAT 59.905 34.615 0.00 0.00 0.00 2.57
592 648 4.154015 TCTTCCTCACGCACAAATTACATG 59.846 41.667 0.00 0.00 0.00 3.21
594 650 3.734463 TCTTCCTCACGCACAAATTACA 58.266 40.909 0.00 0.00 0.00 2.41
614 685 8.969267 CAACCTTATGTGTAGAATCTTACGATC 58.031 37.037 0.00 0.00 0.00 3.69
624 695 4.351407 TCAACCCCAACCTTATGTGTAGAA 59.649 41.667 0.00 0.00 0.00 2.10
661 732 5.911178 ACTAATATGGGATGGAGGTTCTTCA 59.089 40.000 0.00 0.00 0.00 3.02
677 748 6.603237 TCCATTTGAGCGACAACTAATATG 57.397 37.500 0.00 1.63 38.29 1.78
687 758 5.007626 TGCTAAATACATCCATTTGAGCGAC 59.992 40.000 0.00 0.00 32.80 5.19
689 760 5.207768 GTGCTAAATACATCCATTTGAGCG 58.792 41.667 0.00 0.00 32.80 5.03
690 761 5.523369 GGTGCTAAATACATCCATTTGAGC 58.477 41.667 0.00 0.00 31.88 4.26
691 762 5.277974 CCGGTGCTAAATACATCCATTTGAG 60.278 44.000 0.00 0.00 30.84 3.02
692 763 4.578516 CCGGTGCTAAATACATCCATTTGA 59.421 41.667 0.00 0.00 30.84 2.69
693 764 4.578516 TCCGGTGCTAAATACATCCATTTG 59.421 41.667 0.00 0.00 30.84 2.32
694 765 4.787551 TCCGGTGCTAAATACATCCATTT 58.212 39.130 0.00 0.00 32.91 2.32
697 768 3.916359 TTCCGGTGCTAAATACATCCA 57.084 42.857 0.00 0.00 0.00 3.41
703 774 6.804677 TCTAAACGTATTCCGGTGCTAAATA 58.195 36.000 0.00 0.00 42.24 1.40
709 780 3.423206 CGTATCTAAACGTATTCCGGTGC 59.577 47.826 0.00 0.00 42.24 5.01
723 794 6.140303 AGTCGCTAAAATGGACGTATCTAA 57.860 37.500 0.00 0.00 35.87 2.10
728 799 4.970662 AGTAGTCGCTAAAATGGACGTA 57.029 40.909 0.00 0.00 35.87 3.57
729 800 3.863142 AGTAGTCGCTAAAATGGACGT 57.137 42.857 0.00 0.00 35.87 4.34
730 801 5.516996 TCATAGTAGTCGCTAAAATGGACG 58.483 41.667 0.00 0.00 35.87 4.79
731 802 6.736123 TCTCATAGTAGTCGCTAAAATGGAC 58.264 40.000 8.47 0.00 0.00 4.02
732 803 6.954487 TCTCATAGTAGTCGCTAAAATGGA 57.046 37.500 8.47 0.00 0.00 3.41
733 804 6.587990 CCATCTCATAGTAGTCGCTAAAATGG 59.412 42.308 0.00 0.00 0.00 3.16
734 805 7.371159 TCCATCTCATAGTAGTCGCTAAAATG 58.629 38.462 0.00 0.00 0.00 2.32
735 806 7.309499 CCTCCATCTCATAGTAGTCGCTAAAAT 60.309 40.741 0.00 0.00 0.00 1.82
736 807 6.016192 CCTCCATCTCATAGTAGTCGCTAAAA 60.016 42.308 0.00 0.00 0.00 1.52
737 808 5.473846 CCTCCATCTCATAGTAGTCGCTAAA 59.526 44.000 0.00 0.00 0.00 1.85
738 809 5.004448 CCTCCATCTCATAGTAGTCGCTAA 58.996 45.833 0.00 0.00 0.00 3.09
739 810 4.565861 CCCTCCATCTCATAGTAGTCGCTA 60.566 50.000 0.00 0.00 0.00 4.26
740 811 3.417101 CCTCCATCTCATAGTAGTCGCT 58.583 50.000 0.00 0.00 0.00 4.93
741 812 2.490115 CCCTCCATCTCATAGTAGTCGC 59.510 54.545 0.00 0.00 0.00 5.19
742 813 4.022413 TCCCTCCATCTCATAGTAGTCG 57.978 50.000 0.00 0.00 0.00 4.18
743 814 7.179269 ACTATTCCCTCCATCTCATAGTAGTC 58.821 42.308 0.00 0.00 0.00 2.59
744 815 7.109901 ACTATTCCCTCCATCTCATAGTAGT 57.890 40.000 0.00 0.00 0.00 2.73
750 821 8.776119 CCATTTATACTATTCCCTCCATCTCAT 58.224 37.037 0.00 0.00 0.00 2.90
751 822 7.182749 CCCATTTATACTATTCCCTCCATCTCA 59.817 40.741 0.00 0.00 0.00 3.27
752 823 7.182930 ACCCATTTATACTATTCCCTCCATCTC 59.817 40.741 0.00 0.00 0.00 2.75
753 824 7.031917 ACCCATTTATACTATTCCCTCCATCT 58.968 38.462 0.00 0.00 0.00 2.90
754 825 7.272144 ACCCATTTATACTATTCCCTCCATC 57.728 40.000 0.00 0.00 0.00 3.51
755 826 6.070194 CGACCCATTTATACTATTCCCTCCAT 60.070 42.308 0.00 0.00 0.00 3.41
756 827 5.247564 CGACCCATTTATACTATTCCCTCCA 59.752 44.000 0.00 0.00 0.00 3.86
757 828 5.247792 ACGACCCATTTATACTATTCCCTCC 59.752 44.000 0.00 0.00 0.00 4.30
758 829 6.356186 ACGACCCATTTATACTATTCCCTC 57.644 41.667 0.00 0.00 0.00 4.30
776 847 5.007724 CCATAGGCATTTCTTTCTTACGACC 59.992 44.000 0.00 0.00 0.00 4.79
779 850 6.867662 ATCCATAGGCATTTCTTTCTTACG 57.132 37.500 0.00 0.00 0.00 3.18
780 851 8.000780 ACAATCCATAGGCATTTCTTTCTTAC 57.999 34.615 0.00 0.00 0.00 2.34
781 852 9.693739 TTACAATCCATAGGCATTTCTTTCTTA 57.306 29.630 0.00 0.00 0.00 2.10
782 853 8.593945 TTACAATCCATAGGCATTTCTTTCTT 57.406 30.769 0.00 0.00 0.00 2.52
783 854 8.773033 ATTACAATCCATAGGCATTTCTTTCT 57.227 30.769 0.00 0.00 0.00 2.52
813 884 2.286365 ACATGGGTTGTTTGATCCGT 57.714 45.000 0.00 0.00 33.74 4.69
831 902 5.099042 TGGAGCAACTTTAGGATTCCTAC 57.901 43.478 12.12 0.13 35.63 3.18
839 910 5.728637 AGGAATTTTGGAGCAACTTTAGG 57.271 39.130 0.00 0.00 0.00 2.69
840 911 5.858581 CGAAGGAATTTTGGAGCAACTTTAG 59.141 40.000 0.00 0.00 0.00 1.85
842 913 4.340950 TCGAAGGAATTTTGGAGCAACTTT 59.659 37.500 0.00 0.00 0.00 2.66
844 915 3.486383 TCGAAGGAATTTTGGAGCAACT 58.514 40.909 0.00 0.00 0.00 3.16
845 916 3.915437 TCGAAGGAATTTTGGAGCAAC 57.085 42.857 0.00 0.00 0.00 4.17
846 917 4.927978 TTTCGAAGGAATTTTGGAGCAA 57.072 36.364 0.00 0.00 30.88 3.91
848 919 5.714047 AGATTTTCGAAGGAATTTTGGAGC 58.286 37.500 0.00 0.00 30.88 4.70
926 999 5.293324 CCTCAAAAACTGTGGCTTAAAAACC 59.707 40.000 0.00 0.00 32.10 3.27
944 1017 1.298157 CTTGCCGACGATGCCTCAAA 61.298 55.000 0.00 0.00 0.00 2.69
945 1018 1.741401 CTTGCCGACGATGCCTCAA 60.741 57.895 0.00 0.00 0.00 3.02
959 1032 4.372999 AGGAGGGCCCAAGCTTGC 62.373 66.667 27.56 8.18 39.73 4.01
986 1059 2.511600 CCATCGCTCCGTTGGGTC 60.512 66.667 6.79 0.00 41.37 4.46
990 1063 1.519455 GGAGTCCATCGCTCCGTTG 60.519 63.158 3.60 0.00 42.46 4.10
1029 1105 2.529744 GGTCAGGGCCTTGGTCAGT 61.530 63.158 15.86 0.00 0.00 3.41
1327 1403 1.298859 GGCAATTCGTCGAACAGGCT 61.299 55.000 20.72 0.86 0.00 4.58
1353 1429 4.052229 CTCCAGACGACGGCGGTT 62.052 66.667 18.49 0.00 43.17 4.44
1390 1466 2.758737 GACGTCCCCAGACCGGAT 60.759 66.667 9.46 0.00 40.12 4.18
1455 1531 0.756294 TCACGGAGTTGAAGCAGGAA 59.244 50.000 0.00 0.00 41.61 3.36
1509 1585 4.478371 TAGAGCTCGACGGCCCGA 62.478 66.667 11.71 0.00 37.03 5.14
1599 1675 2.097038 CGAACTCAGAGCGCCAAGG 61.097 63.158 2.29 0.00 0.00 3.61
1602 1678 3.282745 GACCGAACTCAGAGCGCCA 62.283 63.158 2.29 0.00 0.00 5.69
1608 1684 0.612174 CCTCCCTGACCGAACTCAGA 60.612 60.000 6.36 0.00 40.28 3.27
1614 1690 2.525629 TGCACCTCCCTGACCGAA 60.526 61.111 0.00 0.00 0.00 4.30
1643 1719 3.027170 GAGAACATGCCGTGCCGTG 62.027 63.158 0.00 0.00 0.00 4.94
1644 1720 2.742372 GAGAACATGCCGTGCCGT 60.742 61.111 0.00 0.00 0.00 5.68
1747 1823 2.105528 AACCACGTCACGCTCGTT 59.894 55.556 0.00 0.00 39.55 3.85
2193 2269 4.021102 ACCCAAGCCCGAATAGATATTG 57.979 45.455 0.00 0.00 0.00 1.90
2230 2306 1.903877 ATGTCCCTTCTCACCCGCTG 61.904 60.000 0.00 0.00 0.00 5.18
2312 2388 6.212888 AGAATTTATTGGACATGGTCAAGC 57.787 37.500 0.00 0.00 33.68 4.01
2355 2438 1.745489 GAAGCTTGGCGGGTACAGG 60.745 63.158 2.10 0.00 0.00 4.00
2410 2495 8.243426 GCAAACAAATAAGTCAGTCCATTCATA 58.757 33.333 0.00 0.00 0.00 2.15
2457 2542 2.879103 TCCCAAATGTCAACCTCCTC 57.121 50.000 0.00 0.00 0.00 3.71
2511 2609 3.417069 TCCCGCTTACATTATCATGGG 57.583 47.619 0.00 0.00 34.27 4.00
2518 2616 4.359434 TTGGCATATCCCGCTTACATTA 57.641 40.909 0.00 0.00 0.00 1.90
2749 2848 2.857483 TCGCTTCTTTCCAACATTCCA 58.143 42.857 0.00 0.00 0.00 3.53
2756 2855 1.351017 AGGGTCATCGCTTCTTTCCAA 59.649 47.619 0.00 0.00 32.92 3.53
2809 2908 9.775539 ATAAGATGGTAATAAGATCAGGCTAGA 57.224 33.333 0.00 0.00 0.00 2.43
3062 3252 7.059448 TGCTTTGCTGAAAAACTTGTAAAAG 57.941 32.000 0.00 0.00 0.00 2.27
3103 3293 5.557576 TTAGCAGAGTGGCATTAGATGAT 57.442 39.130 0.00 0.00 35.83 2.45
3104 3294 5.303165 CATTAGCAGAGTGGCATTAGATGA 58.697 41.667 0.00 0.00 35.83 2.92
3105 3295 4.083431 GCATTAGCAGAGTGGCATTAGATG 60.083 45.833 0.00 0.00 41.58 2.90
3149 3349 6.371548 TGAAGTTAATATCCACTGACAGCAAC 59.628 38.462 1.25 0.00 0.00 4.17
3179 3379 7.380536 AGTTCAGTACACGGATGTAATTAACA 58.619 34.615 11.99 0.00 42.12 2.41
3264 3464 6.371825 CGTTGGAAAGCTAAAGATAGTTCCTT 59.628 38.462 10.15 0.00 36.20 3.36
3341 3541 4.853924 AAGATGTGCCTTTGGTAAAGTG 57.146 40.909 0.00 0.00 36.77 3.16


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

AutoCloner maintained by Alex Coulton.