Multiple sequence alignment - TraesCS7B01G018400

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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 TraesCS7B01G018400 chr7B 100.000 2969 0 0 1 2969 15504882 15507850 0.000000e+00 5483.0
1 TraesCS7B01G018400 chr7B 90.789 76 6 1 2607 2682 15507668 15507742 1.880000e-17 100.0
2 TraesCS7B01G018400 chr7D 93.328 2623 146 14 1 2599 72968118 72965501 0.000000e+00 3847.0
3 TraesCS7B01G018400 chr7D 97.561 41 1 0 2892 2932 72965509 72965469 1.480000e-08 71.3
4 TraesCS7B01G018400 chr7A 88.329 2562 181 59 1 2506 77418013 77420512 0.000000e+00 2966.0
5 TraesCS7B01G018400 chr7A 80.147 136 19 7 2607 2742 120998894 120999021 8.760000e-16 95.3
6 TraesCS7B01G018400 chr7A 93.103 58 4 0 2892 2949 77429227 77429284 5.270000e-13 86.1
7 TraesCS7B01G018400 chr7A 100.000 29 0 0 1385 1413 514864690 514864662 1.000000e-03 54.7
8 TraesCS7B01G018400 chr5B 84.411 263 28 5 2607 2869 35248074 35248323 2.290000e-61 246.0
9 TraesCS7B01G018400 chr5B 83.088 136 16 6 2607 2742 49563708 49563580 1.870000e-22 117.0
10 TraesCS7B01G018400 chr5B 96.774 62 2 0 2681 2742 51975737 51975798 1.460000e-18 104.0
11 TraesCS7B01G018400 chr4B 88.571 140 13 3 2741 2879 667898670 667898807 1.830000e-37 167.0
12 TraesCS7B01G018400 chr4B 86.842 76 7 1 2607 2682 667898716 667898788 6.820000e-12 82.4
13 TraesCS7B01G018400 chr1B 85.350 157 13 7 2741 2892 4644983 4645134 1.430000e-33 154.0
14 TraesCS7B01G018400 chr1B 80.882 136 12 9 2607 2742 297302422 297302543 8.760000e-16 95.3
15 TraesCS7B01G018400 chrUn 88.189 127 13 2 2743 2869 75273400 75273524 1.840000e-32 150.0
16 TraesCS7B01G018400 chr5A 89.167 120 11 2 2742 2860 355073657 355073775 6.630000e-32 148.0
17 TraesCS7B01G018400 chr1A 84.177 158 18 4 2741 2893 430181738 430181893 2.380000e-31 147.0
18 TraesCS7B01G018400 chr2A 84.076 157 15 5 2743 2891 59640682 59640836 3.080000e-30 143.0
19 TraesCS7B01G018400 chr2A 80.909 110 18 3 1310 1416 673195659 673195550 1.900000e-12 84.2
20 TraesCS7B01G018400 chr2A 100.000 30 0 0 2865 2894 62287818 62287847 4.130000e-04 56.5
21 TraesCS7B01G018400 chr6A 82.822 163 19 4 2736 2894 60495180 60495023 1.440000e-28 137.0
22 TraesCS7B01G018400 chr3D 82.143 168 20 4 2742 2901 504989335 504989500 5.160000e-28 135.0
23 TraesCS7B01G018400 chr3B 81.065 169 15 7 2743 2895 559375279 559375446 5.200000e-23 119.0
24 TraesCS7B01G018400 chr3B 77.632 152 28 5 1310 1456 526938862 526939012 1.470000e-13 87.9
25 TraesCS7B01G018400 chr3B 94.286 35 2 0 2859 2893 715538861 715538895 1.000000e-03 54.7
26 TraesCS7B01G018400 chr3A 83.088 136 16 7 2607 2742 686989739 686989867 1.870000e-22 117.0
27 TraesCS7B01G018400 chr3A 96.970 33 1 0 1385 1417 50933945 50933977 4.130000e-04 56.5
28 TraesCS7B01G018400 chr2D 82.836 134 11 7 2609 2742 59333946 59333825 3.130000e-20 110.0
29 TraesCS7B01G018400 chr2D 86.047 86 8 3 2660 2742 146467887 146467971 4.080000e-14 89.8
30 TraesCS7B01G018400 chr4A 82.353 136 13 8 2607 2742 648145538 648145414 1.130000e-19 108.0
31 TraesCS7B01G018400 chr4A 80.645 93 18 0 1325 1417 545106786 545106694 4.110000e-09 73.1
32 TraesCS7B01G018400 chr2B 93.333 45 3 0 1377 1421 555385065 555385109 1.910000e-07 67.6
33 TraesCS7B01G018400 chr4D 95.122 41 2 0 1377 1417 51608715 51608755 6.870000e-07 65.8


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 TraesCS7B01G018400 chr7B 15504882 15507850 2968 False 2791.50 5483 95.3945 1 2969 2 chr7B.!!$F1 2968
1 TraesCS7B01G018400 chr7D 72965469 72968118 2649 True 1959.15 3847 95.4445 1 2932 2 chr7D.!!$R1 2931
2 TraesCS7B01G018400 chr7A 77418013 77420512 2499 False 2966.00 2966 88.3290 1 2506 1 chr7A.!!$F1 2505

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
466 479 0.308684 GACCGACCGCGTATGATACA 59.691 55.0 4.92 0.0 35.23 2.29 F
1311 1356 0.170339 CGGAGGAACCCAAATTTCGC 59.830 55.0 0.00 0.0 34.64 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1692 0.034670 ACTCCTCAGGCTTGGCATTC 60.035 55.0 0.0 0.0 0.00 2.67 R
2135 2202 0.458669 GCCCCATGCTCACATCAAAG 59.541 55.0 0.0 0.0 32.87 2.77 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
178 182 1.360820 GTTGTTCGCTAGCTTCCCTC 58.639 55.000 13.93 0.00 0.00 4.30
340 347 2.349249 CGTATCGTGTCCACCGTATCTC 60.349 54.545 0.00 0.00 0.00 2.75
397 404 4.142381 GGAGACACTGCCCAATCAATTTAC 60.142 45.833 0.00 0.00 0.00 2.01
412 425 9.716507 CAATCAATTTACCCTACGTAGATTTTG 57.283 33.333 24.15 16.03 31.16 2.44
422 435 6.238538 CCCTACGTAGATTTTGTTGTTGTTGT 60.239 38.462 24.15 0.00 0.00 3.32
423 436 7.190871 CCTACGTAGATTTTGTTGTTGTTGTT 58.809 34.615 24.15 0.00 0.00 2.83
424 437 8.336806 CCTACGTAGATTTTGTTGTTGTTGTTA 58.663 33.333 24.15 0.00 0.00 2.41
466 479 0.308684 GACCGACCGCGTATGATACA 59.691 55.000 4.92 0.00 35.23 2.29
516 530 1.359459 CGGAGAAAGGTTGCGGCTAC 61.359 60.000 6.00 6.00 0.00 3.58
784 813 2.821685 CGCGATTCCCTCCATCCA 59.178 61.111 0.00 0.00 0.00 3.41
786 815 1.160329 CGCGATTCCCTCCATCCAAC 61.160 60.000 0.00 0.00 0.00 3.77
789 818 1.226311 GATTCCCTCCATCCAACCCT 58.774 55.000 0.00 0.00 0.00 4.34
873 904 5.183522 GGAGATCCTATAAACGGGTAGAGTG 59.816 48.000 0.00 0.00 0.00 3.51
919 950 2.285368 TTGGCCGATCCACCTCCT 60.285 61.111 0.00 0.00 46.55 3.69
921 952 3.551407 GGCCGATCCACCTCCTCC 61.551 72.222 0.00 0.00 34.01 4.30
922 953 3.551407 GCCGATCCACCTCCTCCC 61.551 72.222 0.00 0.00 0.00 4.30
964 1000 2.704065 TCTTCGTCTTCCAGGACCTTTT 59.296 45.455 0.00 0.00 33.07 2.27
997 1036 2.997897 AGTCCACGAGGAGGGTGC 60.998 66.667 0.21 0.00 46.92 5.01
999 1038 4.631740 TCCACGAGGAGGGTGCCA 62.632 66.667 0.00 0.00 39.61 4.92
1036 1075 3.059982 CCGCTGGGAAGACACTGA 58.940 61.111 0.00 0.00 34.06 3.41
1152 1197 2.043852 ACCGACTCCTCCAGCGAT 60.044 61.111 0.00 0.00 0.00 4.58
1261 1306 3.009115 CTTTCCGGAGAGGGGCCA 61.009 66.667 14.22 0.00 41.52 5.36
1288 1333 3.003173 CCAAGAGGAGGGCCGACA 61.003 66.667 0.00 0.00 39.96 4.35
1311 1356 0.170339 CGGAGGAACCCAAATTTCGC 59.830 55.000 0.00 0.00 34.64 4.70
1431 1476 2.304180 GGCTGCCATGGTCTATGATAGT 59.696 50.000 15.17 0.00 39.21 2.12
1464 1509 3.803082 CGTGGGCCATCTGCAACG 61.803 66.667 10.70 2.04 43.89 4.10
1485 1530 1.997606 ACGAATTTTCCTACTTCGCCG 59.002 47.619 4.04 0.00 44.10 6.46
1494 1539 1.304713 TACTTCGCCGTCCCCTTCT 60.305 57.895 0.00 0.00 0.00 2.85
1508 1553 1.072015 CCCTTCTGCTGATCCTGATCC 59.928 57.143 4.76 0.00 37.02 3.36
1513 1558 0.757512 TGCTGATCCTGATCCTGCTC 59.242 55.000 17.13 1.46 37.27 4.26
1519 1564 2.539432 TCCTGATCCTGCTCTCTTGA 57.461 50.000 0.00 0.00 0.00 3.02
1546 1591 3.296709 GACGGTGATGTCGGCCACT 62.297 63.158 2.24 0.00 33.99 4.00
1553 1598 0.321653 GATGTCGGCCACTTCCTTGT 60.322 55.000 2.24 0.00 0.00 3.16
1647 1692 1.374252 GGTGGTGGCGTCTACAGTG 60.374 63.158 0.00 0.00 0.00 3.66
1662 1710 0.809385 CAGTGAATGCCAAGCCTGAG 59.191 55.000 0.00 0.00 0.00 3.35
1675 1723 0.456628 GCCTGAGGAGTCTACCGTTC 59.543 60.000 0.65 0.00 34.73 3.95
1679 1727 1.075050 TGAGGAGTCTACCGTTCCTGT 59.925 52.381 0.00 0.00 41.32 4.00
1680 1728 2.169330 GAGGAGTCTACCGTTCCTGTT 58.831 52.381 0.00 0.00 41.32 3.16
1703 1751 3.506067 GGTTTGAAGATTTCGGTGGACAT 59.494 43.478 0.00 0.00 0.00 3.06
1785 1833 0.687354 ACGAAGACTGCATGTTCCCT 59.313 50.000 0.00 0.00 0.00 4.20
1848 1896 5.725110 GTATGATGTCATCACACCTTGAC 57.275 43.478 17.74 4.46 43.01 3.18
1873 1921 1.519455 GCAGCTAATGTCGAGCCGT 60.519 57.895 0.00 0.00 41.06 5.68
1902 1950 0.547471 TGGAGATGGGTGAGCTTCCA 60.547 55.000 10.34 8.61 37.46 3.53
1904 1952 0.463474 GAGATGGGTGAGCTTCCAGC 60.463 60.000 10.65 10.65 42.84 4.85
1962 2010 0.972134 CTGCCTCACCTCTCACTGAA 59.028 55.000 0.00 0.00 0.00 3.02
2098 2165 2.642311 TGGTGTTGTGGTAGATGATGGT 59.358 45.455 0.00 0.00 0.00 3.55
2099 2166 3.073798 TGGTGTTGTGGTAGATGATGGTT 59.926 43.478 0.00 0.00 0.00 3.67
2118 2185 5.722263 TGGTTATTTCGTGAAGTCCGATTA 58.278 37.500 0.00 0.00 33.81 1.75
2135 2202 4.553429 CCGATTAAGCAAATTTGTCGACAC 59.447 41.667 19.90 5.54 31.82 3.67
2143 2210 4.739716 GCAAATTTGTCGACACTTTGATGT 59.260 37.500 34.76 15.13 33.77 3.06
2151 2218 2.159612 CGACACTTTGATGTGAGCATGG 60.160 50.000 0.00 0.00 40.12 3.66
2233 2300 5.186996 TGAACTTTTCATCTTTCCACTGC 57.813 39.130 0.00 0.00 34.08 4.40
2397 2466 6.553524 CATTTTGTTTTGTCATGGTTTGCTT 58.446 32.000 0.00 0.00 0.00 3.91
2440 2509 4.900635 ATGGGAAATATTCAGCACGAAC 57.099 40.909 0.00 0.00 36.12 3.95
2531 2600 3.502191 TGGATAAAAAGTGAATGCGGC 57.498 42.857 0.00 0.00 0.00 6.53
2571 2645 5.528600 TCCATCCCCTCAAAAGACATTTA 57.471 39.130 0.00 0.00 0.00 1.40
2573 2647 4.096382 CCATCCCCTCAAAAGACATTTACG 59.904 45.833 0.00 0.00 0.00 3.18
2590 2664 8.193250 ACATTTACGCTTTGTTCTATACGATT 57.807 30.769 0.00 0.00 0.00 3.34
2591 2665 8.662141 ACATTTACGCTTTGTTCTATACGATTT 58.338 29.630 0.00 0.00 0.00 2.17
2592 2666 9.485591 CATTTACGCTTTGTTCTATACGATTTT 57.514 29.630 0.00 0.00 0.00 1.82
2595 2669 7.823149 ACGCTTTGTTCTATACGATTTTAGT 57.177 32.000 0.00 0.00 0.00 2.24
2596 2670 8.248117 ACGCTTTGTTCTATACGATTTTAGTT 57.752 30.769 0.00 0.00 0.00 2.24
2597 2671 9.357652 ACGCTTTGTTCTATACGATTTTAGTTA 57.642 29.630 0.00 0.00 0.00 2.24
2602 2676 9.638239 TTGTTCTATACGATTTTAGTTAACGGT 57.362 29.630 0.00 0.00 0.00 4.83
2603 2677 9.638239 TGTTCTATACGATTTTAGTTAACGGTT 57.362 29.630 0.00 0.00 0.00 4.44
2606 2680 9.638239 TCTATACGATTTTAGTTAACGGTTTGT 57.362 29.630 0.00 0.00 0.00 2.83
2607 2681 9.891535 CTATACGATTTTAGTTAACGGTTTGTC 57.108 33.333 0.00 0.00 0.00 3.18
2608 2682 6.849588 ACGATTTTAGTTAACGGTTTGTCT 57.150 33.333 0.00 0.00 0.00 3.41
2609 2683 7.945033 ACGATTTTAGTTAACGGTTTGTCTA 57.055 32.000 0.00 0.00 0.00 2.59
2610 2684 8.364129 ACGATTTTAGTTAACGGTTTGTCTAA 57.636 30.769 0.00 3.78 0.00 2.10
2611 2685 8.490355 ACGATTTTAGTTAACGGTTTGTCTAAG 58.510 33.333 0.00 0.00 0.00 2.18
2612 2686 7.476492 CGATTTTAGTTAACGGTTTGTCTAAGC 59.524 37.037 0.00 0.00 0.00 3.09
2613 2687 7.790823 TTTTAGTTAACGGTTTGTCTAAGCT 57.209 32.000 0.00 0.00 32.02 3.74
2614 2688 7.412137 TTTAGTTAACGGTTTGTCTAAGCTC 57.588 36.000 0.00 0.00 32.02 4.09
2615 2689 5.211174 AGTTAACGGTTTGTCTAAGCTCT 57.789 39.130 0.00 0.00 32.02 4.09
2616 2690 5.228665 AGTTAACGGTTTGTCTAAGCTCTC 58.771 41.667 0.00 0.00 32.02 3.20
2617 2691 3.746045 AACGGTTTGTCTAAGCTCTCA 57.254 42.857 0.00 0.00 32.02 3.27
2618 2692 3.027974 ACGGTTTGTCTAAGCTCTCAC 57.972 47.619 0.00 0.00 32.02 3.51
2619 2693 2.364324 ACGGTTTGTCTAAGCTCTCACA 59.636 45.455 0.00 0.00 32.02 3.58
2620 2694 3.181469 ACGGTTTGTCTAAGCTCTCACAA 60.181 43.478 0.00 0.00 32.02 3.33
2621 2695 3.807622 CGGTTTGTCTAAGCTCTCACAAA 59.192 43.478 11.19 11.19 36.60 2.83
2622 2696 4.452455 CGGTTTGTCTAAGCTCTCACAAAT 59.548 41.667 15.97 0.00 40.05 2.32
2623 2697 5.637810 CGGTTTGTCTAAGCTCTCACAAATA 59.362 40.000 15.97 0.00 40.05 1.40
2624 2698 6.147164 CGGTTTGTCTAAGCTCTCACAAATAA 59.853 38.462 15.97 0.00 40.05 1.40
2625 2699 7.298854 GGTTTGTCTAAGCTCTCACAAATAAC 58.701 38.462 15.97 7.78 40.05 1.89
2626 2700 7.041372 GGTTTGTCTAAGCTCTCACAAATAACA 60.041 37.037 15.97 0.00 40.05 2.41
2627 2701 7.421530 TTGTCTAAGCTCTCACAAATAACAC 57.578 36.000 0.00 0.00 0.00 3.32
2628 2702 6.521162 TGTCTAAGCTCTCACAAATAACACA 58.479 36.000 0.00 0.00 0.00 3.72
2629 2703 6.646653 TGTCTAAGCTCTCACAAATAACACAG 59.353 38.462 0.00 0.00 0.00 3.66
2630 2704 4.756084 AAGCTCTCACAAATAACACAGC 57.244 40.909 0.00 0.00 0.00 4.40
2631 2705 3.743521 AGCTCTCACAAATAACACAGCA 58.256 40.909 0.00 0.00 0.00 4.41
2632 2706 4.136796 AGCTCTCACAAATAACACAGCAA 58.863 39.130 0.00 0.00 0.00 3.91
2633 2707 4.763793 AGCTCTCACAAATAACACAGCAAT 59.236 37.500 0.00 0.00 0.00 3.56
2634 2708 5.939883 AGCTCTCACAAATAACACAGCAATA 59.060 36.000 0.00 0.00 0.00 1.90
2635 2709 6.600822 AGCTCTCACAAATAACACAGCAATAT 59.399 34.615 0.00 0.00 0.00 1.28
2636 2710 6.690098 GCTCTCACAAATAACACAGCAATATG 59.310 38.462 0.00 0.00 0.00 1.78
2637 2711 7.087409 TCTCACAAATAACACAGCAATATGG 57.913 36.000 0.00 0.00 0.00 2.74
2638 2712 6.883756 TCTCACAAATAACACAGCAATATGGA 59.116 34.615 0.00 0.00 0.00 3.41
2639 2713 7.392953 TCTCACAAATAACACAGCAATATGGAA 59.607 33.333 0.00 0.00 0.00 3.53
2640 2714 7.312154 TCACAAATAACACAGCAATATGGAAC 58.688 34.615 0.00 0.00 0.00 3.62
2711 2785 7.914427 ATAGTGGACAATAGGTTAGATGTGA 57.086 36.000 0.00 0.00 0.00 3.58
2712 2786 5.978814 AGTGGACAATAGGTTAGATGTGAC 58.021 41.667 0.00 0.00 0.00 3.67
2713 2787 5.483937 AGTGGACAATAGGTTAGATGTGACA 59.516 40.000 0.00 0.00 0.00 3.58
2714 2788 6.156949 AGTGGACAATAGGTTAGATGTGACAT 59.843 38.462 0.00 0.00 0.00 3.06
2715 2789 7.344612 AGTGGACAATAGGTTAGATGTGACATA 59.655 37.037 0.00 0.00 0.00 2.29
2716 2790 7.985184 GTGGACAATAGGTTAGATGTGACATAA 59.015 37.037 0.00 0.00 0.00 1.90
2717 2791 8.713971 TGGACAATAGGTTAGATGTGACATAAT 58.286 33.333 0.00 0.00 0.00 1.28
2718 2792 9.561069 GGACAATAGGTTAGATGTGACATAATT 57.439 33.333 0.00 0.00 0.00 1.40
2743 2817 9.807921 TTATGTCACATCTAGATATGTCCTACA 57.192 33.333 10.72 8.07 38.01 2.74
2744 2818 8.712228 ATGTCACATCTAGATATGTCCTACAA 57.288 34.615 10.72 0.00 38.01 2.41
2745 2819 8.712228 TGTCACATCTAGATATGTCCTACAAT 57.288 34.615 10.72 0.00 38.01 2.71
2746 2820 9.147732 TGTCACATCTAGATATGTCCTACAATT 57.852 33.333 10.72 0.00 38.01 2.32
2747 2821 9.988815 GTCACATCTAGATATGTCCTACAATTT 57.011 33.333 10.72 0.00 38.01 1.82
2748 2822 9.987272 TCACATCTAGATATGTCCTACAATTTG 57.013 33.333 10.72 0.00 38.01 2.32
2749 2823 9.770097 CACATCTAGATATGTCCTACAATTTGT 57.230 33.333 4.54 7.30 38.01 2.83
2750 2824 9.988815 ACATCTAGATATGTCCTACAATTTGTC 57.011 33.333 4.54 0.00 35.08 3.18
2759 2833 8.862325 ATGTCCTACAATTTGTCTAATTCACA 57.138 30.769 5.07 1.87 34.19 3.58
2760 2834 8.862325 TGTCCTACAATTTGTCTAATTCACAT 57.138 30.769 5.07 0.00 34.19 3.21
2761 2835 8.946085 TGTCCTACAATTTGTCTAATTCACATC 58.054 33.333 5.07 0.00 34.19 3.06
2762 2836 8.398665 GTCCTACAATTTGTCTAATTCACATCC 58.601 37.037 5.07 0.00 34.19 3.51
2763 2837 8.106462 TCCTACAATTTGTCTAATTCACATCCA 58.894 33.333 5.07 0.00 34.19 3.41
2764 2838 8.400947 CCTACAATTTGTCTAATTCACATCCAG 58.599 37.037 5.07 0.00 34.19 3.86
2765 2839 9.166173 CTACAATTTGTCTAATTCACATCCAGA 57.834 33.333 5.07 0.00 34.19 3.86
2766 2840 8.585471 ACAATTTGTCTAATTCACATCCAGAT 57.415 30.769 0.00 0.00 34.19 2.90
2767 2841 8.464404 ACAATTTGTCTAATTCACATCCAGATG 58.536 33.333 6.09 6.09 38.27 2.90
2768 2842 8.464404 CAATTTGTCTAATTCACATCCAGATGT 58.536 33.333 7.47 7.47 42.12 3.06
2794 2868 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
2795 2869 6.798427 TTAAGGATGTCACATCTAAGCTCT 57.202 37.500 17.46 2.09 0.00 4.09
2796 2870 4.935352 AGGATGTCACATCTAAGCTCTC 57.065 45.455 17.46 0.00 0.00 3.20
2797 2871 4.285020 AGGATGTCACATCTAAGCTCTCA 58.715 43.478 17.46 0.00 0.00 3.27
2798 2872 4.099266 AGGATGTCACATCTAAGCTCTCAC 59.901 45.833 17.46 0.00 0.00 3.51
2799 2873 4.142071 GGATGTCACATCTAAGCTCTCACA 60.142 45.833 17.46 0.00 0.00 3.58
2800 2874 4.871933 TGTCACATCTAAGCTCTCACAA 57.128 40.909 0.00 0.00 0.00 3.33
2801 2875 5.213891 TGTCACATCTAAGCTCTCACAAA 57.786 39.130 0.00 0.00 0.00 2.83
2802 2876 5.798132 TGTCACATCTAAGCTCTCACAAAT 58.202 37.500 0.00 0.00 0.00 2.32
2803 2877 6.935167 TGTCACATCTAAGCTCTCACAAATA 58.065 36.000 0.00 0.00 0.00 1.40
2804 2878 7.386059 TGTCACATCTAAGCTCTCACAAATAA 58.614 34.615 0.00 0.00 0.00 1.40
2805 2879 7.331934 TGTCACATCTAAGCTCTCACAAATAAC 59.668 37.037 0.00 0.00 0.00 1.89
2806 2880 7.331934 GTCACATCTAAGCTCTCACAAATAACA 59.668 37.037 0.00 0.00 0.00 2.41
2807 2881 7.331934 TCACATCTAAGCTCTCACAAATAACAC 59.668 37.037 0.00 0.00 0.00 3.32
2808 2882 7.118245 CACATCTAAGCTCTCACAAATAACACA 59.882 37.037 0.00 0.00 0.00 3.72
2809 2883 7.332926 ACATCTAAGCTCTCACAAATAACACAG 59.667 37.037 0.00 0.00 0.00 3.66
2810 2884 4.756084 AAGCTCTCACAAATAACACAGC 57.244 40.909 0.00 0.00 0.00 4.40
2811 2885 3.743521 AGCTCTCACAAATAACACAGCA 58.256 40.909 0.00 0.00 0.00 4.41
2812 2886 4.136796 AGCTCTCACAAATAACACAGCAA 58.863 39.130 0.00 0.00 0.00 3.91
2813 2887 4.763793 AGCTCTCACAAATAACACAGCAAT 59.236 37.500 0.00 0.00 0.00 3.56
2814 2888 4.855388 GCTCTCACAAATAACACAGCAATG 59.145 41.667 0.00 0.00 0.00 2.82
2815 2889 5.335113 GCTCTCACAAATAACACAGCAATGA 60.335 40.000 0.00 0.00 0.00 2.57
2816 2890 6.245115 TCTCACAAATAACACAGCAATGAG 57.755 37.500 0.00 0.00 33.84 2.90
2817 2891 5.181811 TCTCACAAATAACACAGCAATGAGG 59.818 40.000 0.00 0.00 33.46 3.86
2818 2892 5.069318 TCACAAATAACACAGCAATGAGGA 58.931 37.500 0.00 0.00 0.00 3.71
2819 2893 5.534278 TCACAAATAACACAGCAATGAGGAA 59.466 36.000 0.00 0.00 0.00 3.36
2820 2894 5.630680 CACAAATAACACAGCAATGAGGAAC 59.369 40.000 0.00 0.00 0.00 3.62
2821 2895 5.301551 ACAAATAACACAGCAATGAGGAACA 59.698 36.000 0.00 0.00 0.00 3.18
2822 2896 6.183360 ACAAATAACACAGCAATGAGGAACAA 60.183 34.615 0.00 0.00 0.00 2.83
2823 2897 6.403866 AATAACACAGCAATGAGGAACAAA 57.596 33.333 0.00 0.00 0.00 2.83
2824 2898 3.996150 ACACAGCAATGAGGAACAAAG 57.004 42.857 0.00 0.00 0.00 2.77
2825 2899 3.554934 ACACAGCAATGAGGAACAAAGA 58.445 40.909 0.00 0.00 0.00 2.52
2826 2900 3.953612 ACACAGCAATGAGGAACAAAGAA 59.046 39.130 0.00 0.00 0.00 2.52
2827 2901 4.402155 ACACAGCAATGAGGAACAAAGAAA 59.598 37.500 0.00 0.00 0.00 2.52
2828 2902 5.105392 ACACAGCAATGAGGAACAAAGAAAA 60.105 36.000 0.00 0.00 0.00 2.29
2829 2903 5.811613 CACAGCAATGAGGAACAAAGAAAAA 59.188 36.000 0.00 0.00 0.00 1.94
2830 2904 5.812127 ACAGCAATGAGGAACAAAGAAAAAC 59.188 36.000 0.00 0.00 0.00 2.43
2831 2905 6.044682 CAGCAATGAGGAACAAAGAAAAACT 58.955 36.000 0.00 0.00 0.00 2.66
2832 2906 6.019318 CAGCAATGAGGAACAAAGAAAAACTG 60.019 38.462 0.00 0.00 0.00 3.16
2833 2907 5.234972 GCAATGAGGAACAAAGAAAAACTGG 59.765 40.000 0.00 0.00 0.00 4.00
2834 2908 5.535753 ATGAGGAACAAAGAAAAACTGGG 57.464 39.130 0.00 0.00 0.00 4.45
2835 2909 4.605183 TGAGGAACAAAGAAAAACTGGGA 58.395 39.130 0.00 0.00 0.00 4.37
2836 2910 4.401202 TGAGGAACAAAGAAAAACTGGGAC 59.599 41.667 0.00 0.00 0.00 4.46
2837 2911 3.380320 AGGAACAAAGAAAAACTGGGACG 59.620 43.478 0.00 0.00 0.00 4.79
2838 2912 3.379057 GGAACAAAGAAAAACTGGGACGA 59.621 43.478 0.00 0.00 0.00 4.20
2839 2913 4.142337 GGAACAAAGAAAAACTGGGACGAA 60.142 41.667 0.00 0.00 0.00 3.85
2840 2914 5.394224 AACAAAGAAAAACTGGGACGAAA 57.606 34.783 0.00 0.00 0.00 3.46
2841 2915 5.394224 ACAAAGAAAAACTGGGACGAAAA 57.606 34.783 0.00 0.00 0.00 2.29
2842 2916 5.785243 ACAAAGAAAAACTGGGACGAAAAA 58.215 33.333 0.00 0.00 0.00 1.94
2869 2943 9.592196 AATAGGCCACAAATATAATGAACATCT 57.408 29.630 5.01 0.00 0.00 2.90
2871 2945 8.627208 AGGCCACAAATATAATGAACATCTAG 57.373 34.615 5.01 0.00 0.00 2.43
2872 2946 8.439971 AGGCCACAAATATAATGAACATCTAGA 58.560 33.333 5.01 0.00 0.00 2.43
2873 2947 9.236006 GGCCACAAATATAATGAACATCTAGAT 57.764 33.333 0.00 0.00 0.00 1.98
2888 2962 6.312399 CATCTAGATGTGTCCTAGACAGAC 57.688 45.833 22.42 0.00 43.57 3.51
2889 2963 4.783055 TCTAGATGTGTCCTAGACAGACC 58.217 47.826 0.00 0.00 43.57 3.85
2890 2964 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
2929 3003 5.761726 TCTCATGCTGCCTATTCATTAAGTG 59.238 40.000 0.00 0.00 0.00 3.16
2944 3018 7.722795 TCATTAAGTGAAAAATGAGACGACA 57.277 32.000 0.00 0.00 37.23 4.35
2945 3019 8.322906 TCATTAAGTGAAAAATGAGACGACAT 57.677 30.769 0.00 0.00 37.23 3.06
2946 3020 8.783093 TCATTAAGTGAAAAATGAGACGACATT 58.217 29.630 0.00 0.00 37.23 2.71
2950 3024 8.782533 AAGTGAAAAATGAGACGACATTTAAC 57.217 30.769 15.48 14.06 45.71 2.01
2951 3025 7.925993 AGTGAAAAATGAGACGACATTTAACA 58.074 30.769 15.48 14.82 45.71 2.41
2952 3026 8.402472 AGTGAAAAATGAGACGACATTTAACAA 58.598 29.630 15.48 5.14 45.71 2.83
2953 3027 9.015577 GTGAAAAATGAGACGACATTTAACAAA 57.984 29.630 15.48 0.00 45.71 2.83
2954 3028 9.015577 TGAAAAATGAGACGACATTTAACAAAC 57.984 29.630 15.48 8.18 45.71 2.93
2955 3029 8.918961 AAAAATGAGACGACATTTAACAAACA 57.081 26.923 15.48 0.00 45.71 2.83
2956 3030 9.528018 AAAAATGAGACGACATTTAACAAACAT 57.472 25.926 15.48 0.00 45.71 2.71
2957 3031 9.528018 AAAATGAGACGACATTTAACAAACATT 57.472 25.926 15.48 0.00 45.71 2.71
2959 3033 9.825972 AATGAGACGACATTTAACAAACATTAG 57.174 29.630 0.00 0.00 37.20 1.73
2960 3034 7.295201 TGAGACGACATTTAACAAACATTAGC 58.705 34.615 0.00 0.00 0.00 3.09
2961 3035 7.041712 TGAGACGACATTTAACAAACATTAGCA 60.042 33.333 0.00 0.00 0.00 3.49
2962 3036 7.075741 AGACGACATTTAACAAACATTAGCAC 58.924 34.615 0.00 0.00 0.00 4.40
2963 3037 6.146898 ACGACATTTAACAAACATTAGCACC 58.853 36.000 0.00 0.00 0.00 5.01
2964 3038 6.146216 CGACATTTAACAAACATTAGCACCA 58.854 36.000 0.00 0.00 0.00 4.17
2965 3039 6.638873 CGACATTTAACAAACATTAGCACCAA 59.361 34.615 0.00 0.00 0.00 3.67
2966 3040 7.168302 CGACATTTAACAAACATTAGCACCAAA 59.832 33.333 0.00 0.00 0.00 3.28
2967 3041 8.900983 ACATTTAACAAACATTAGCACCAAAT 57.099 26.923 0.00 0.00 0.00 2.32
2968 3042 9.336171 ACATTTAACAAACATTAGCACCAAATT 57.664 25.926 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.205657 ACTGTCGTTACGCTGTGTTG 58.794 50.000 0.00 0.00 0.00 3.33
94 95 1.404391 GCGAGAGATACCGGACAGAAA 59.596 52.381 9.46 0.00 0.00 2.52
178 182 2.389713 CAAGAGACCAAACTGTTGCG 57.610 50.000 0.00 0.00 35.16 4.85
372 379 0.036732 TGATTGGGCAGTGTCTCCAC 59.963 55.000 0.00 0.00 42.17 4.02
373 380 0.770499 TTGATTGGGCAGTGTCTCCA 59.230 50.000 0.00 0.00 0.00 3.86
397 404 5.934935 ACAACAACAAAATCTACGTAGGG 57.065 39.130 22.01 9.54 0.00 3.53
412 425 5.997385 AGGATTCGATGTAACAACAACAAC 58.003 37.500 0.00 0.00 0.00 3.32
422 435 7.975058 TCAATTTGTACGTAGGATTCGATGTAA 59.025 33.333 0.00 0.00 0.00 2.41
423 436 7.433131 GTCAATTTGTACGTAGGATTCGATGTA 59.567 37.037 0.00 0.00 0.00 2.29
424 437 6.255020 GTCAATTTGTACGTAGGATTCGATGT 59.745 38.462 0.00 0.00 0.00 3.06
516 530 1.286501 CAACCGATCCACCGTATGTG 58.713 55.000 0.00 0.00 45.01 3.21
647 668 2.203126 GCCTTCTCTGCCGGATGG 60.203 66.667 5.05 0.00 38.77 3.51
681 707 1.712018 GACGCTTCCCCCATTTACGC 61.712 60.000 0.00 0.00 0.00 4.42
784 813 9.201989 GGAGATATTCTTTATTTTTGGAGGGTT 57.798 33.333 0.00 0.00 0.00 4.11
786 815 8.007153 AGGGAGATATTCTTTATTTTTGGAGGG 58.993 37.037 0.00 0.00 0.00 4.30
789 818 7.228706 GCGAGGGAGATATTCTTTATTTTTGGA 59.771 37.037 0.00 0.00 0.00 3.53
827 857 3.533547 TGCGTAATAGGCAACGGTTTAT 58.466 40.909 5.07 0.00 46.39 1.40
873 904 1.838073 TTGGGAAGGGGAGAAGACGC 61.838 60.000 0.00 0.00 0.00 5.19
922 953 3.347590 GGGGAGGTGGAAAGGGGG 61.348 72.222 0.00 0.00 0.00 5.40
1022 1061 1.879796 GCTGGTTCAGTGTCTTCCCAG 60.880 57.143 0.00 0.00 41.87 4.45
1036 1075 3.322466 CCTCCTCCGGTGCTGGTT 61.322 66.667 0.00 0.00 0.00 3.67
1098 1143 1.081376 CGTGACGCGAAGGACTCTT 60.081 57.895 15.93 0.00 44.77 2.85
1178 1223 2.101415 TCGATGCAGATTTCCTCGATGT 59.899 45.455 2.37 0.00 33.80 3.06
1180 1225 2.865670 GCTCGATGCAGATTTCCTCGAT 60.866 50.000 6.76 0.00 42.31 3.59
1288 1333 0.112412 AATTTGGGTTCCTCCGCAGT 59.888 50.000 0.00 0.00 37.00 4.40
1323 1368 4.700448 TACTTCCCCCACGGCCGA 62.700 66.667 35.90 4.54 0.00 5.54
1464 1509 2.028883 CGGCGAAGTAGGAAAATTCGTC 59.971 50.000 0.00 5.89 45.66 4.20
1485 1530 0.179936 CAGGATCAGCAGAAGGGGAC 59.820 60.000 0.00 0.00 0.00 4.46
1494 1539 0.757512 GAGCAGGATCAGGATCAGCA 59.242 55.000 20.54 0.00 40.52 4.41
1497 1542 2.699321 CAAGAGAGCAGGATCAGGATCA 59.301 50.000 11.12 0.00 39.54 2.92
1508 1553 0.175302 AGCATCGGTCAAGAGAGCAG 59.825 55.000 0.00 0.00 42.32 4.24
1513 1558 0.803768 CCGTCAGCATCGGTCAAGAG 60.804 60.000 6.16 0.00 42.62 2.85
1553 1598 4.155733 CCTCGTATGTGGCCGCCA 62.156 66.667 15.15 8.43 0.00 5.69
1647 1692 0.034670 ACTCCTCAGGCTTGGCATTC 60.035 55.000 0.00 0.00 0.00 2.67
1662 1710 1.067071 CCAACAGGAACGGTAGACTCC 60.067 57.143 0.00 0.00 34.27 3.85
1675 1723 3.317993 ACCGAAATCTTCAAACCAACAGG 59.682 43.478 0.00 0.00 0.00 4.00
1679 1727 3.316868 GTCCACCGAAATCTTCAAACCAA 59.683 43.478 0.00 0.00 0.00 3.67
1680 1728 2.882137 GTCCACCGAAATCTTCAAACCA 59.118 45.455 0.00 0.00 0.00 3.67
1785 1833 1.075305 TGCAGCAAATGAGAGGCCA 59.925 52.632 5.01 0.00 0.00 5.36
1848 1896 3.917380 GCTCGACATTAGCTGCATAGTAG 59.083 47.826 1.02 0.00 37.01 2.57
1873 1921 5.500234 CTCACCCATCTCCAATAAACTCAA 58.500 41.667 0.00 0.00 0.00 3.02
1904 1952 2.202797 CATCCACCTCTCGCCACG 60.203 66.667 0.00 0.00 0.00 4.94
1962 2010 7.215789 GTGATGAACTCCTGATCAATCATAGT 58.784 38.462 7.14 0.00 35.62 2.12
2007 2055 8.248117 AGTAGTAACGCGAAATAAAGAATTGT 57.752 30.769 15.93 0.00 0.00 2.71
2085 2152 6.228616 TCACGAAATAACCATCATCTACCA 57.771 37.500 0.00 0.00 0.00 3.25
2098 2165 5.870433 TGCTTAATCGGACTTCACGAAATAA 59.130 36.000 0.00 0.00 44.20 1.40
2099 2166 5.412640 TGCTTAATCGGACTTCACGAAATA 58.587 37.500 0.00 0.00 44.20 1.40
2118 2185 4.992688 TCAAAGTGTCGACAAATTTGCTT 58.007 34.783 32.59 23.33 36.00 3.91
2135 2202 0.458669 GCCCCATGCTCACATCAAAG 59.541 55.000 0.00 0.00 32.87 2.77
2143 2210 1.281199 ACTGGTATGCCCCATGCTCA 61.281 55.000 0.00 0.00 42.00 4.26
2227 2294 7.255242 CCCAAGTATAATGATGTAAAGCAGTGG 60.255 40.741 0.00 0.00 0.00 4.00
2326 2395 8.981647 GTGGTCTTTACGAATTTAGTTTACTCA 58.018 33.333 0.00 0.00 0.00 3.41
2370 2439 5.738118 AACCATGACAAAACAAAATGCAG 57.262 34.783 0.00 0.00 0.00 4.41
2397 2466 1.968704 TACAAATGTTGTGCGGACCA 58.031 45.000 4.04 0.00 45.03 4.02
2440 2509 1.033746 AGCTGATGTGCCCATTTCCG 61.034 55.000 0.00 0.00 0.00 4.30
2510 2579 3.489059 CGCCGCATTCACTTTTTATCCAT 60.489 43.478 0.00 0.00 0.00 3.41
2512 2581 2.159435 ACGCCGCATTCACTTTTTATCC 60.159 45.455 0.00 0.00 0.00 2.59
2531 2600 3.550820 TGGAAATATGATGGGTCCAACG 58.449 45.455 0.00 0.00 35.45 4.10
2571 2645 7.823149 ACTAAAATCGTATAGAACAAAGCGT 57.177 32.000 0.00 0.00 0.00 5.07
2590 2664 7.212274 AGAGCTTAGACAAACCGTTAACTAAA 58.788 34.615 3.71 0.00 0.00 1.85
2591 2665 6.752168 AGAGCTTAGACAAACCGTTAACTAA 58.248 36.000 3.71 0.00 0.00 2.24
2592 2666 6.016024 TGAGAGCTTAGACAAACCGTTAACTA 60.016 38.462 3.71 0.00 0.00 2.24
2593 2667 5.211174 AGAGCTTAGACAAACCGTTAACT 57.789 39.130 3.71 0.00 0.00 2.24
2594 2668 4.986659 TGAGAGCTTAGACAAACCGTTAAC 59.013 41.667 0.00 0.00 0.00 2.01
2595 2669 4.986659 GTGAGAGCTTAGACAAACCGTTAA 59.013 41.667 0.00 0.00 0.00 2.01
2596 2670 4.038282 TGTGAGAGCTTAGACAAACCGTTA 59.962 41.667 0.00 0.00 0.00 3.18
2597 2671 3.181469 TGTGAGAGCTTAGACAAACCGTT 60.181 43.478 0.00 0.00 0.00 4.44
2598 2672 2.364324 TGTGAGAGCTTAGACAAACCGT 59.636 45.455 0.00 0.00 0.00 4.83
2599 2673 3.026630 TGTGAGAGCTTAGACAAACCG 57.973 47.619 0.00 0.00 0.00 4.44
2600 2674 5.948992 ATTTGTGAGAGCTTAGACAAACC 57.051 39.130 16.00 0.00 40.19 3.27
2601 2675 7.798982 GTGTTATTTGTGAGAGCTTAGACAAAC 59.201 37.037 16.00 8.62 40.19 2.93
2602 2676 7.497579 TGTGTTATTTGTGAGAGCTTAGACAAA 59.502 33.333 16.01 16.01 41.27 2.83
2603 2677 6.989759 TGTGTTATTTGTGAGAGCTTAGACAA 59.010 34.615 0.00 0.00 0.00 3.18
2604 2678 6.521162 TGTGTTATTTGTGAGAGCTTAGACA 58.479 36.000 0.00 0.00 0.00 3.41
2605 2679 6.401581 GCTGTGTTATTTGTGAGAGCTTAGAC 60.402 42.308 0.00 0.00 0.00 2.59
2606 2680 5.639506 GCTGTGTTATTTGTGAGAGCTTAGA 59.360 40.000 0.00 0.00 0.00 2.10
2607 2681 5.409520 TGCTGTGTTATTTGTGAGAGCTTAG 59.590 40.000 0.00 0.00 0.00 2.18
2608 2682 5.304778 TGCTGTGTTATTTGTGAGAGCTTA 58.695 37.500 0.00 0.00 0.00 3.09
2609 2683 4.136796 TGCTGTGTTATTTGTGAGAGCTT 58.863 39.130 0.00 0.00 0.00 3.74
2610 2684 3.743521 TGCTGTGTTATTTGTGAGAGCT 58.256 40.909 0.00 0.00 0.00 4.09
2611 2685 4.488126 TTGCTGTGTTATTTGTGAGAGC 57.512 40.909 0.00 0.00 0.00 4.09
2612 2686 7.066163 TCCATATTGCTGTGTTATTTGTGAGAG 59.934 37.037 0.00 0.00 0.00 3.20
2613 2687 6.883756 TCCATATTGCTGTGTTATTTGTGAGA 59.116 34.615 0.00 0.00 0.00 3.27
2614 2688 7.087409 TCCATATTGCTGTGTTATTTGTGAG 57.913 36.000 0.00 0.00 0.00 3.51
2615 2689 7.040132 TGTTCCATATTGCTGTGTTATTTGTGA 60.040 33.333 0.00 0.00 0.00 3.58
2616 2690 7.089538 TGTTCCATATTGCTGTGTTATTTGTG 58.910 34.615 0.00 0.00 0.00 3.33
2617 2691 7.225784 TGTTCCATATTGCTGTGTTATTTGT 57.774 32.000 0.00 0.00 0.00 2.83
2618 2692 8.531622 TTTGTTCCATATTGCTGTGTTATTTG 57.468 30.769 0.00 0.00 0.00 2.32
2619 2693 9.553064 TTTTTGTTCCATATTGCTGTGTTATTT 57.447 25.926 0.00 0.00 0.00 1.40
2685 2759 9.601810 TCACATCTAACCTATTGTCCACTATAT 57.398 33.333 0.00 0.00 0.00 0.86
2686 2760 8.857098 GTCACATCTAACCTATTGTCCACTATA 58.143 37.037 0.00 0.00 0.00 1.31
2687 2761 7.344612 TGTCACATCTAACCTATTGTCCACTAT 59.655 37.037 0.00 0.00 0.00 2.12
2688 2762 6.666113 TGTCACATCTAACCTATTGTCCACTA 59.334 38.462 0.00 0.00 0.00 2.74
2689 2763 5.483937 TGTCACATCTAACCTATTGTCCACT 59.516 40.000 0.00 0.00 0.00 4.00
2690 2764 5.730550 TGTCACATCTAACCTATTGTCCAC 58.269 41.667 0.00 0.00 0.00 4.02
2691 2765 6.560003 ATGTCACATCTAACCTATTGTCCA 57.440 37.500 0.00 0.00 0.00 4.02
2692 2766 9.561069 AATTATGTCACATCTAACCTATTGTCC 57.439 33.333 0.00 0.00 0.00 4.02
2717 2791 9.807921 TGTAGGACATATCTAGATGTGACATAA 57.192 33.333 29.72 15.67 40.18 1.90
2718 2792 9.807921 TTGTAGGACATATCTAGATGTGACATA 57.192 33.333 29.72 23.14 40.18 2.29
2719 2793 8.712228 TTGTAGGACATATCTAGATGTGACAT 57.288 34.615 29.72 24.02 40.18 3.06
2720 2794 8.712228 ATTGTAGGACATATCTAGATGTGACA 57.288 34.615 29.72 21.33 40.18 3.58
2721 2795 9.988815 AAATTGTAGGACATATCTAGATGTGAC 57.011 33.333 29.72 24.07 40.18 3.67
2722 2796 9.987272 CAAATTGTAGGACATATCTAGATGTGA 57.013 33.333 29.72 10.87 40.18 3.58
2723 2797 9.770097 ACAAATTGTAGGACATATCTAGATGTG 57.230 33.333 23.54 23.54 40.18 3.21
2724 2798 9.988815 GACAAATTGTAGGACATATCTAGATGT 57.011 33.333 15.79 7.11 42.82 3.06
2733 2807 9.952030 TGTGAATTAGACAAATTGTAGGACATA 57.048 29.630 0.00 0.00 37.93 2.29
2734 2808 8.862325 TGTGAATTAGACAAATTGTAGGACAT 57.138 30.769 0.00 0.00 37.93 3.06
2735 2809 8.862325 ATGTGAATTAGACAAATTGTAGGACA 57.138 30.769 0.00 0.00 37.93 4.02
2736 2810 8.398665 GGATGTGAATTAGACAAATTGTAGGAC 58.601 37.037 0.00 0.00 37.93 3.85
2737 2811 8.106462 TGGATGTGAATTAGACAAATTGTAGGA 58.894 33.333 0.00 0.00 37.93 2.94
2738 2812 8.279970 TGGATGTGAATTAGACAAATTGTAGG 57.720 34.615 0.00 0.00 37.93 3.18
2739 2813 9.166173 TCTGGATGTGAATTAGACAAATTGTAG 57.834 33.333 0.00 0.00 37.93 2.74
2740 2814 9.685276 ATCTGGATGTGAATTAGACAAATTGTA 57.315 29.630 0.00 0.00 37.93 2.41
2741 2815 8.464404 CATCTGGATGTGAATTAGACAAATTGT 58.536 33.333 0.00 0.00 34.75 2.71
2742 2816 8.851960 CATCTGGATGTGAATTAGACAAATTG 57.148 34.615 2.69 0.00 34.75 2.32
2769 2843 8.103305 AGAGCTTAGATGTGACATCCTTAAAAA 58.897 33.333 21.05 6.46 0.00 1.94
2770 2844 7.624549 AGAGCTTAGATGTGACATCCTTAAAA 58.375 34.615 21.05 8.00 0.00 1.52
2771 2845 7.093333 TGAGAGCTTAGATGTGACATCCTTAAA 60.093 37.037 21.05 10.18 0.00 1.52
2772 2846 6.381133 TGAGAGCTTAGATGTGACATCCTTAA 59.619 38.462 21.05 13.11 0.00 1.85
2773 2847 5.893824 TGAGAGCTTAGATGTGACATCCTTA 59.106 40.000 21.05 6.22 0.00 2.69
2774 2848 4.713814 TGAGAGCTTAGATGTGACATCCTT 59.286 41.667 21.05 7.22 0.00 3.36
2775 2849 4.099266 GTGAGAGCTTAGATGTGACATCCT 59.901 45.833 21.05 11.37 0.00 3.24
2776 2850 4.142071 TGTGAGAGCTTAGATGTGACATCC 60.142 45.833 21.05 6.69 0.00 3.51
2777 2851 5.003692 TGTGAGAGCTTAGATGTGACATC 57.996 43.478 17.46 17.46 0.00 3.06
2778 2852 5.411831 TTGTGAGAGCTTAGATGTGACAT 57.588 39.130 0.00 0.00 0.00 3.06
2779 2853 4.871933 TTGTGAGAGCTTAGATGTGACA 57.128 40.909 0.00 0.00 0.00 3.58
2780 2854 7.331934 TGTTATTTGTGAGAGCTTAGATGTGAC 59.668 37.037 0.00 0.00 0.00 3.67
2781 2855 7.331934 GTGTTATTTGTGAGAGCTTAGATGTGA 59.668 37.037 0.00 0.00 0.00 3.58
2782 2856 7.118245 TGTGTTATTTGTGAGAGCTTAGATGTG 59.882 37.037 0.00 0.00 0.00 3.21
2783 2857 7.161404 TGTGTTATTTGTGAGAGCTTAGATGT 58.839 34.615 0.00 0.00 0.00 3.06
2784 2858 7.601073 TGTGTTATTTGTGAGAGCTTAGATG 57.399 36.000 0.00 0.00 0.00 2.90
2785 2859 6.314896 GCTGTGTTATTTGTGAGAGCTTAGAT 59.685 38.462 0.00 0.00 0.00 1.98
2786 2860 5.639506 GCTGTGTTATTTGTGAGAGCTTAGA 59.360 40.000 0.00 0.00 0.00 2.10
2787 2861 5.409520 TGCTGTGTTATTTGTGAGAGCTTAG 59.590 40.000 0.00 0.00 0.00 2.18
2788 2862 5.304778 TGCTGTGTTATTTGTGAGAGCTTA 58.695 37.500 0.00 0.00 0.00 3.09
2789 2863 4.136796 TGCTGTGTTATTTGTGAGAGCTT 58.863 39.130 0.00 0.00 0.00 3.74
2790 2864 3.743521 TGCTGTGTTATTTGTGAGAGCT 58.256 40.909 0.00 0.00 0.00 4.09
2791 2865 4.488126 TTGCTGTGTTATTTGTGAGAGC 57.512 40.909 0.00 0.00 0.00 4.09
2792 2866 6.245115 TCATTGCTGTGTTATTTGTGAGAG 57.755 37.500 0.00 0.00 0.00 3.20
2793 2867 5.181811 CCTCATTGCTGTGTTATTTGTGAGA 59.818 40.000 0.00 0.00 34.10 3.27
2794 2868 5.181811 TCCTCATTGCTGTGTTATTTGTGAG 59.818 40.000 0.00 0.00 0.00 3.51
2795 2869 5.069318 TCCTCATTGCTGTGTTATTTGTGA 58.931 37.500 0.00 0.00 0.00 3.58
2796 2870 5.375417 TCCTCATTGCTGTGTTATTTGTG 57.625 39.130 0.00 0.00 0.00 3.33
2797 2871 5.301551 TGTTCCTCATTGCTGTGTTATTTGT 59.698 36.000 0.00 0.00 0.00 2.83
2798 2872 5.771469 TGTTCCTCATTGCTGTGTTATTTG 58.229 37.500 0.00 0.00 0.00 2.32
2799 2873 6.403866 TTGTTCCTCATTGCTGTGTTATTT 57.596 33.333 0.00 0.00 0.00 1.40
2800 2874 6.265196 TCTTTGTTCCTCATTGCTGTGTTATT 59.735 34.615 0.00 0.00 0.00 1.40
2801 2875 5.769662 TCTTTGTTCCTCATTGCTGTGTTAT 59.230 36.000 0.00 0.00 0.00 1.89
2802 2876 5.129634 TCTTTGTTCCTCATTGCTGTGTTA 58.870 37.500 0.00 0.00 0.00 2.41
2803 2877 3.953612 TCTTTGTTCCTCATTGCTGTGTT 59.046 39.130 0.00 0.00 0.00 3.32
2804 2878 3.554934 TCTTTGTTCCTCATTGCTGTGT 58.445 40.909 0.00 0.00 0.00 3.72
2805 2879 4.572985 TTCTTTGTTCCTCATTGCTGTG 57.427 40.909 0.00 0.00 0.00 3.66
2806 2880 5.596836 TTTTCTTTGTTCCTCATTGCTGT 57.403 34.783 0.00 0.00 0.00 4.40
2807 2881 6.019318 CAGTTTTTCTTTGTTCCTCATTGCTG 60.019 38.462 0.00 0.00 0.00 4.41
2808 2882 6.044682 CAGTTTTTCTTTGTTCCTCATTGCT 58.955 36.000 0.00 0.00 0.00 3.91
2809 2883 5.234972 CCAGTTTTTCTTTGTTCCTCATTGC 59.765 40.000 0.00 0.00 0.00 3.56
2810 2884 5.754890 CCCAGTTTTTCTTTGTTCCTCATTG 59.245 40.000 0.00 0.00 0.00 2.82
2811 2885 5.660864 TCCCAGTTTTTCTTTGTTCCTCATT 59.339 36.000 0.00 0.00 0.00 2.57
2812 2886 5.069119 GTCCCAGTTTTTCTTTGTTCCTCAT 59.931 40.000 0.00 0.00 0.00 2.90
2813 2887 4.401202 GTCCCAGTTTTTCTTTGTTCCTCA 59.599 41.667 0.00 0.00 0.00 3.86
2814 2888 4.497507 CGTCCCAGTTTTTCTTTGTTCCTC 60.498 45.833 0.00 0.00 0.00 3.71
2815 2889 3.380320 CGTCCCAGTTTTTCTTTGTTCCT 59.620 43.478 0.00 0.00 0.00 3.36
2816 2890 3.379057 TCGTCCCAGTTTTTCTTTGTTCC 59.621 43.478 0.00 0.00 0.00 3.62
2817 2891 4.625972 TCGTCCCAGTTTTTCTTTGTTC 57.374 40.909 0.00 0.00 0.00 3.18
2818 2892 5.394224 TTTCGTCCCAGTTTTTCTTTGTT 57.606 34.783 0.00 0.00 0.00 2.83
2819 2893 5.394224 TTTTCGTCCCAGTTTTTCTTTGT 57.606 34.783 0.00 0.00 0.00 2.83
2843 2917 9.592196 AGATGTTCATTATATTTGTGGCCTATT 57.408 29.630 3.32 0.00 0.00 1.73
2845 2919 9.725019 CTAGATGTTCATTATATTTGTGGCCTA 57.275 33.333 3.32 0.00 0.00 3.93
2846 2920 8.439971 TCTAGATGTTCATTATATTTGTGGCCT 58.560 33.333 3.32 0.00 0.00 5.19
2847 2921 8.621532 TCTAGATGTTCATTATATTTGTGGCC 57.378 34.615 0.00 0.00 0.00 5.36
2865 2939 5.240623 GGTCTGTCTAGGACACATCTAGATG 59.759 48.000 27.63 27.63 43.25 2.90
2866 2940 5.381757 GGTCTGTCTAGGACACATCTAGAT 58.618 45.833 0.00 0.00 43.25 1.98
2867 2941 4.385421 GGGTCTGTCTAGGACACATCTAGA 60.385 50.000 0.00 0.00 37.67 2.43
2868 2942 3.886505 GGGTCTGTCTAGGACACATCTAG 59.113 52.174 0.00 0.00 37.67 2.43
2869 2943 3.528078 AGGGTCTGTCTAGGACACATCTA 59.472 47.826 3.18 0.00 39.36 1.98
2870 2944 2.313342 AGGGTCTGTCTAGGACACATCT 59.687 50.000 3.18 0.00 39.36 2.90
2871 2945 2.741145 AGGGTCTGTCTAGGACACATC 58.259 52.381 3.18 0.00 39.36 3.06
2872 2946 2.930109 AGGGTCTGTCTAGGACACAT 57.070 50.000 3.18 0.00 39.36 3.21
2873 2947 2.696526 AAGGGTCTGTCTAGGACACA 57.303 50.000 3.18 0.00 39.36 3.72
2874 2948 4.087907 ACTAAAGGGTCTGTCTAGGACAC 58.912 47.826 0.00 0.00 37.67 3.67
2875 2949 4.399483 ACTAAAGGGTCTGTCTAGGACA 57.601 45.455 0.43 0.43 40.50 4.02
2876 2950 6.847421 TTAACTAAAGGGTCTGTCTAGGAC 57.153 41.667 0.00 0.00 0.00 3.85
2877 2951 6.070938 GCTTTAACTAAAGGGTCTGTCTAGGA 60.071 42.308 10.45 0.00 42.17 2.94
2878 2952 6.107343 GCTTTAACTAAAGGGTCTGTCTAGG 58.893 44.000 10.45 0.00 42.17 3.02
2879 2953 5.805994 CGCTTTAACTAAAGGGTCTGTCTAG 59.194 44.000 14.82 0.00 45.56 2.43
2880 2954 5.717119 CGCTTTAACTAAAGGGTCTGTCTA 58.283 41.667 14.82 0.00 45.56 2.59
2881 2955 4.566987 CGCTTTAACTAAAGGGTCTGTCT 58.433 43.478 14.82 0.00 45.56 3.41
2882 2956 4.923264 CGCTTTAACTAAAGGGTCTGTC 57.077 45.455 14.82 0.00 45.56 3.51
2889 2963 4.201822 GCATGAGACCGCTTTAACTAAAGG 60.202 45.833 10.45 0.02 42.17 3.11
2890 2964 4.631813 AGCATGAGACCGCTTTAACTAAAG 59.368 41.667 0.00 5.07 44.14 1.85
2929 3003 9.015577 TGTTTGTTAAATGTCGTCTCATTTTTC 57.984 29.630 16.01 11.84 42.88 2.29
2933 3007 9.825972 CTAATGTTTGTTAAATGTCGTCTCATT 57.174 29.630 0.00 0.00 39.35 2.57
2934 3008 7.962918 GCTAATGTTTGTTAAATGTCGTCTCAT 59.037 33.333 0.00 0.00 0.00 2.90
2935 3009 7.041712 TGCTAATGTTTGTTAAATGTCGTCTCA 60.042 33.333 0.00 0.00 0.00 3.27
2936 3010 7.268447 GTGCTAATGTTTGTTAAATGTCGTCTC 59.732 37.037 0.00 0.00 0.00 3.36
2937 3011 7.075741 GTGCTAATGTTTGTTAAATGTCGTCT 58.924 34.615 0.00 0.00 0.00 4.18
2938 3012 6.304683 GGTGCTAATGTTTGTTAAATGTCGTC 59.695 38.462 0.00 0.00 0.00 4.20
2939 3013 6.146898 GGTGCTAATGTTTGTTAAATGTCGT 58.853 36.000 0.00 0.00 0.00 4.34
2940 3014 6.146216 TGGTGCTAATGTTTGTTAAATGTCG 58.854 36.000 0.00 0.00 0.00 4.35
2941 3015 7.938563 TTGGTGCTAATGTTTGTTAAATGTC 57.061 32.000 0.00 0.00 0.00 3.06
2942 3016 8.900983 ATTTGGTGCTAATGTTTGTTAAATGT 57.099 26.923 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.