Multiple sequence alignment - TraesCS3D01G255200

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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 TraesCS3D01G255200 chr3D 100.000 4864 0 0 1419 6282 356853075 356848212 0.000000e+00 8983.0
1 TraesCS3D01G255200 chr3D 100.000 1131 0 0 1 1131 356854493 356853363 0.000000e+00 2089.0
2 TraesCS3D01G255200 chr3D 92.026 627 47 3 1 625 398494804 398494179 0.000000e+00 878.0
3 TraesCS3D01G255200 chr3B 95.685 3615 94 25 2700 6282 457978728 457975144 0.000000e+00 5755.0
4 TraesCS3D01G255200 chr3B 94.937 553 21 5 1427 1975 457980064 457979515 0.000000e+00 859.0
5 TraesCS3D01G255200 chr3B 95.168 476 11 6 2110 2585 457979177 457978714 0.000000e+00 741.0
6 TraesCS3D01G255200 chr3B 94.118 493 18 5 649 1131 457980710 457980219 0.000000e+00 739.0
7 TraesCS3D01G255200 chr3B 98.485 132 1 1 1972 2103 457979356 457979226 1.360000e-56 231.0
8 TraesCS3D01G255200 chr3B 97.619 42 1 0 5875 5916 457975503 457975462 8.740000e-09 73.1
9 TraesCS3D01G255200 chr3B 80.682 88 14 3 4337 4423 780694424 780694339 1.460000e-06 65.8
10 TraesCS3D01G255200 chr3A 97.427 1943 36 8 3728 5666 475734421 475732489 0.000000e+00 3299.0
11 TraesCS3D01G255200 chr3A 98.446 965 13 2 2700 3662 475735381 475734417 0.000000e+00 1698.0
12 TraesCS3D01G255200 chr3A 96.193 683 19 4 1427 2105 475736571 475735892 0.000000e+00 1110.0
13 TraesCS3D01G255200 chr3A 97.071 478 11 3 2110 2585 475735843 475735367 0.000000e+00 802.0
14 TraesCS3D01G255200 chr3A 95.711 443 16 1 627 1066 475737379 475736937 0.000000e+00 710.0
15 TraesCS3D01G255200 chr3A 88.330 437 32 7 5688 6123 475727241 475726823 2.020000e-139 507.0
16 TraesCS3D01G255200 chr3A 85.795 176 11 5 6116 6282 475726275 475726105 2.330000e-39 174.0
17 TraesCS3D01G255200 chr7D 92.675 628 44 2 1 626 619831640 619832267 0.000000e+00 904.0
18 TraesCS3D01G255200 chr7D 92.332 626 46 2 1 624 174523566 174522941 0.000000e+00 889.0
19 TraesCS3D01G255200 chr7D 95.495 111 4 1 2594 2703 569699849 569699739 6.470000e-40 176.0
20 TraesCS3D01G255200 chr7D 92.500 120 9 0 2594 2713 174200678 174200797 8.370000e-39 172.0
21 TraesCS3D01G255200 chr7D 88.889 81 9 0 4347 4427 71362973 71362893 4.010000e-17 100.0
22 TraesCS3D01G255200 chr7D 85.567 97 10 3 4346 4442 621646364 621646456 1.440000e-16 99.0
23 TraesCS3D01G255200 chr2D 92.687 629 41 5 2 626 120887672 120888299 0.000000e+00 902.0
24 TraesCS3D01G255200 chr2D 92.640 625 44 2 1 623 196081634 196081010 0.000000e+00 898.0
25 TraesCS3D01G255200 chr6D 92.492 626 45 2 1 624 124705403 124706028 0.000000e+00 894.0
26 TraesCS3D01G255200 chr6D 92.038 628 48 2 1 626 367645850 367645223 0.000000e+00 881.0
27 TraesCS3D01G255200 chr6D 93.220 118 7 1 2594 2711 132665345 132665229 8.370000e-39 172.0
28 TraesCS3D01G255200 chr5D 92.369 629 46 2 1 627 409944522 409943894 0.000000e+00 894.0
29 TraesCS3D01G255200 chr5D 92.076 631 46 4 1 629 492793119 492792491 0.000000e+00 885.0
30 TraesCS3D01G255200 chr5D 89.286 56 4 2 4388 4442 164606008 164605954 1.130000e-07 69.4
31 TraesCS3D01G255200 chr5A 96.296 108 4 0 2594 2701 36046536 36046429 1.800000e-40 178.0
32 TraesCS3D01G255200 chr7A 95.413 109 5 0 2594 2702 131446066 131445958 2.330000e-39 174.0
33 TraesCS3D01G255200 chr6B 95.413 109 5 0 2594 2702 538391484 538391376 2.330000e-39 174.0
34 TraesCS3D01G255200 chr6B 80.189 106 18 3 4339 4442 212190143 212190039 6.750000e-10 76.8
35 TraesCS3D01G255200 chr6A 95.413 109 5 0 2594 2702 484161811 484161919 2.330000e-39 174.0
36 TraesCS3D01G255200 chr5B 95.370 108 5 0 2594 2701 153073919 153073812 8.370000e-39 172.0
37 TraesCS3D01G255200 chr5B 94.444 36 0 2 4385 4419 426509419 426509453 3.000000e-03 54.7
38 TraesCS3D01G255200 chr1D 94.444 108 6 0 2593 2700 29603266 29603373 3.900000e-37 167.0
39 TraesCS3D01G255200 chr7B 94.118 51 2 1 4401 4451 29374496 29374447 6.750000e-10 76.8
40 TraesCS3D01G255200 chr7B 93.617 47 3 0 4393 4439 718359804 718359850 3.140000e-08 71.3
41 TraesCS3D01G255200 chr7B 88.000 50 4 2 5556 5605 448364114 448364161 2.450000e-04 58.4
42 TraesCS3D01G255200 chr1A 86.765 68 8 1 4376 4442 83823588 83823655 2.430000e-09 75.0
43 TraesCS3D01G255200 chr1A 90.741 54 4 1 4392 4445 508556832 508556780 3.140000e-08 71.3


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 TraesCS3D01G255200 chr3D 356848212 356854493 6281 True 5536.000000 8983 100.0000 1 6282 2 chr3D.!!$R2 6281
1 TraesCS3D01G255200 chr3D 398494179 398494804 625 True 878.000000 878 92.0260 1 625 1 chr3D.!!$R1 624
2 TraesCS3D01G255200 chr3B 457975144 457980710 5566 True 1399.683333 5755 96.0020 649 6282 6 chr3B.!!$R2 5633
3 TraesCS3D01G255200 chr3A 475732489 475737379 4890 True 1523.800000 3299 96.9696 627 5666 5 chr3A.!!$R2 5039
4 TraesCS3D01G255200 chr3A 475726105 475727241 1136 True 340.500000 507 87.0625 5688 6282 2 chr3A.!!$R1 594
5 TraesCS3D01G255200 chr7D 619831640 619832267 627 False 904.000000 904 92.6750 1 626 1 chr7D.!!$F2 625
6 TraesCS3D01G255200 chr7D 174522941 174523566 625 True 889.000000 889 92.3320 1 624 1 chr7D.!!$R2 623
7 TraesCS3D01G255200 chr2D 120887672 120888299 627 False 902.000000 902 92.6870 2 626 1 chr2D.!!$F1 624
8 TraesCS3D01G255200 chr2D 196081010 196081634 624 True 898.000000 898 92.6400 1 623 1 chr2D.!!$R1 622
9 TraesCS3D01G255200 chr6D 124705403 124706028 625 False 894.000000 894 92.4920 1 624 1 chr6D.!!$F1 623
10 TraesCS3D01G255200 chr6D 367645223 367645850 627 True 881.000000 881 92.0380 1 626 1 chr6D.!!$R2 625
11 TraesCS3D01G255200 chr5D 409943894 409944522 628 True 894.000000 894 92.3690 1 627 1 chr5D.!!$R2 626
12 TraesCS3D01G255200 chr5D 492792491 492793119 628 True 885.000000 885 92.0760 1 629 1 chr5D.!!$R3 628

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
592 598 0.763035 ACGCACAGTTTAAGACCCCT 59.237 50.000 0.00 0.0 0.00 4.79 F
1634 1658 0.534203 GCTGTTCCGGTTCCTGTGAA 60.534 55.000 0.00 0.0 0.00 3.18 F
2626 2861 0.331278 CCACCCAGGTTCAAGGCATA 59.669 55.000 0.00 0.0 0.00 3.14 F
2723 2958 0.250295 TTTGTGCCTTCTGGTCCGAG 60.250 55.000 0.00 0.0 35.27 4.63 F
3542 3779 2.745281 TGGCCTTATTGCTGTAAACGAC 59.255 45.455 3.32 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2591 2826 0.550914 GTGGGTGGGAAGGCATCATA 59.449 55.000 0.0 0.0 0.00 2.15 R
2704 2939 0.250295 CTCGGACCAGAAGGCACAAA 60.250 55.000 0.0 0.0 39.06 2.83 R
3542 3779 1.226746 GGTTGCGAAGGATAATCCCG 58.773 55.000 0.0 0.0 37.19 5.14 R
3806 4044 1.662044 CAACAACTGCCCTGAAGCC 59.338 57.895 0.0 0.0 0.00 4.35 R
5503 5746 0.532115 GTCCGCCCTTCAAATTGCAT 59.468 50.000 0.0 0.0 0.00 3.96 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
89 91 1.265454 ATTCGAAGGAGGAACCCGCT 61.265 55.000 3.35 0.00 40.05 5.52
103 105 1.372748 CCGCTTTGCAATGCCGAAA 60.373 52.632 26.20 0.00 0.00 3.46
277 283 1.480954 GATGGGACTCTCCTTTGCGTA 59.519 52.381 0.00 0.00 36.57 4.42
295 301 2.159627 CGTAGATGGCAAGTTTGGTGTC 59.840 50.000 0.00 0.00 0.00 3.67
310 316 2.835156 TGGTGTCCGGATGTGAAGATTA 59.165 45.455 7.81 0.00 0.00 1.75
347 353 1.078989 ACTCTGTACAACCCTAGGCCT 59.921 52.381 11.78 11.78 0.00 5.19
404 410 4.148871 CGTAGAGGCAATCACAATCATACG 59.851 45.833 0.00 0.00 0.00 3.06
460 466 5.446860 TCGAGGTAGATCAACTCTGGTAAT 58.553 41.667 0.00 0.00 35.28 1.89
516 522 8.865244 AAGTAGGGTATTACCTCCATTAAGAA 57.135 34.615 12.54 0.00 42.09 2.52
567 573 1.134788 CGCCTCCTGTTACCTTCGATT 60.135 52.381 0.00 0.00 0.00 3.34
568 574 2.677037 CGCCTCCTGTTACCTTCGATTT 60.677 50.000 0.00 0.00 0.00 2.17
585 591 4.508492 TCGATTTTCAGACGCACAGTTTAA 59.492 37.500 0.00 0.00 0.00 1.52
592 598 0.763035 ACGCACAGTTTAAGACCCCT 59.237 50.000 0.00 0.00 0.00 4.79
845 857 5.008712 GGCATCTCCCGTCCTTAAATAAAAG 59.991 44.000 0.00 0.00 0.00 2.27
1535 1558 4.547406 AACTTTCCTACAAACTCGCAAC 57.453 40.909 0.00 0.00 0.00 4.17
1634 1658 0.534203 GCTGTTCCGGTTCCTGTGAA 60.534 55.000 0.00 0.00 0.00 3.18
1733 1760 3.189702 TGCGAAGTTGCATAAAACCCTAC 59.810 43.478 0.00 0.00 40.62 3.18
1741 1768 6.946009 AGTTGCATAAAACCCTACTGTTACAT 59.054 34.615 0.00 0.00 0.00 2.29
1753 1780 4.464069 ACTGTTACATCTCCTCAAGAGC 57.536 45.455 0.00 0.00 42.90 4.09
2075 2264 3.584406 TGCCAGATATGGATTACAGGGAG 59.416 47.826 11.49 0.00 0.00 4.30
2105 2294 4.778579 ACGAACTCCTGAGCACTACTATA 58.221 43.478 0.00 0.00 0.00 1.31
2106 2295 5.378332 ACGAACTCCTGAGCACTACTATAT 58.622 41.667 0.00 0.00 0.00 0.86
2107 2296 5.239744 ACGAACTCCTGAGCACTACTATATG 59.760 44.000 0.00 0.00 0.00 1.78
2108 2297 5.335269 CGAACTCCTGAGCACTACTATATGG 60.335 48.000 0.00 0.00 0.00 2.74
2132 2366 7.676043 TGGGATTAATGGAACCTTCAAATACAA 59.324 33.333 0.00 0.00 0.00 2.41
2197 2432 4.304110 CGTCTTCTTGTACTTTACTGGCA 58.696 43.478 0.00 0.00 0.00 4.92
2267 2502 3.876309 AAAACTGTCAAGGGCCTCTAA 57.124 42.857 6.46 0.00 0.00 2.10
2459 2694 8.682936 AACTCTTATGCTAGTTAAATGATGGG 57.317 34.615 0.00 0.00 34.23 4.00
2465 2700 5.016173 TGCTAGTTAAATGATGGGTTGCTT 58.984 37.500 0.00 0.00 0.00 3.91
2585 2820 2.007360 TTGCAAGTGTTTGTGCCTTG 57.993 45.000 0.00 0.00 40.14 3.61
2587 2822 3.737127 CAAGTGTTTGTGCCTTGCA 57.263 47.368 0.00 0.00 35.60 4.08
2589 2824 1.134753 CAAGTGTTTGTGCCTTGCAGA 59.865 47.619 0.00 0.00 40.08 4.26
2591 2826 0.740737 GTGTTTGTGCCTTGCAGACT 59.259 50.000 0.00 0.00 40.08 3.24
2592 2827 1.946768 GTGTTTGTGCCTTGCAGACTA 59.053 47.619 0.00 0.00 40.08 2.59
2593 2828 2.554032 GTGTTTGTGCCTTGCAGACTAT 59.446 45.455 0.00 0.00 40.08 2.12
2596 2831 3.354948 TTGTGCCTTGCAGACTATGAT 57.645 42.857 0.00 0.00 40.08 2.45
2597 2832 2.635714 TGTGCCTTGCAGACTATGATG 58.364 47.619 0.00 0.00 40.08 3.07
2598 2833 1.332997 GTGCCTTGCAGACTATGATGC 59.667 52.381 0.00 0.00 40.08 3.91
2599 2834 0.950116 GCCTTGCAGACTATGATGCC 59.050 55.000 0.00 0.00 41.85 4.40
2600 2835 1.476471 GCCTTGCAGACTATGATGCCT 60.476 52.381 0.00 0.00 41.85 4.75
2601 2836 2.928334 CCTTGCAGACTATGATGCCTT 58.072 47.619 0.00 0.00 41.85 4.35
2602 2837 2.877168 CCTTGCAGACTATGATGCCTTC 59.123 50.000 0.00 0.00 41.85 3.46
2603 2838 2.627515 TGCAGACTATGATGCCTTCC 57.372 50.000 0.00 0.00 41.85 3.46
2604 2839 1.141657 TGCAGACTATGATGCCTTCCC 59.858 52.381 0.00 0.00 41.85 3.97
2605 2840 1.141657 GCAGACTATGATGCCTTCCCA 59.858 52.381 0.00 0.00 36.41 4.37
2606 2841 2.843701 CAGACTATGATGCCTTCCCAC 58.156 52.381 0.00 0.00 0.00 4.61
2607 2842 1.771255 AGACTATGATGCCTTCCCACC 59.229 52.381 0.00 0.00 0.00 4.61
2608 2843 0.846693 ACTATGATGCCTTCCCACCC 59.153 55.000 0.00 0.00 0.00 4.61
2609 2844 0.846015 CTATGATGCCTTCCCACCCA 59.154 55.000 0.00 0.00 0.00 4.51
2610 2845 0.550914 TATGATGCCTTCCCACCCAC 59.449 55.000 0.00 0.00 0.00 4.61
2611 2846 2.043953 GATGCCTTCCCACCCACC 60.044 66.667 0.00 0.00 0.00 4.61
2612 2847 3.662117 GATGCCTTCCCACCCACCC 62.662 68.421 0.00 0.00 0.00 4.61
2614 2849 4.366684 GCCTTCCCACCCACCCAG 62.367 72.222 0.00 0.00 0.00 4.45
2615 2850 3.661648 CCTTCCCACCCACCCAGG 61.662 72.222 0.00 0.00 37.03 4.45
2616 2851 2.858974 CTTCCCACCCACCCAGGT 60.859 66.667 0.00 0.00 42.40 4.00
2617 2852 2.370403 TTCCCACCCACCCAGGTT 60.370 61.111 0.00 0.00 38.39 3.50
2618 2853 2.426305 CTTCCCACCCACCCAGGTTC 62.426 65.000 0.00 0.00 38.39 3.62
2619 2854 3.182263 CCCACCCACCCAGGTTCA 61.182 66.667 0.00 0.00 38.39 3.18
2620 2855 2.773527 CCCACCCACCCAGGTTCAA 61.774 63.158 0.00 0.00 38.39 2.69
2621 2856 1.228552 CCACCCACCCAGGTTCAAG 60.229 63.158 0.00 0.00 38.39 3.02
2622 2857 1.228552 CACCCACCCAGGTTCAAGG 60.229 63.158 0.00 0.00 38.39 3.61
2623 2858 2.283173 CCCACCCAGGTTCAAGGC 60.283 66.667 0.00 0.00 34.66 4.35
2624 2859 2.520458 CCACCCAGGTTCAAGGCA 59.480 61.111 0.00 0.00 0.00 4.75
2625 2860 1.077265 CCACCCAGGTTCAAGGCAT 59.923 57.895 0.00 0.00 0.00 4.40
2626 2861 0.331278 CCACCCAGGTTCAAGGCATA 59.669 55.000 0.00 0.00 0.00 3.14
2627 2862 1.272425 CCACCCAGGTTCAAGGCATAA 60.272 52.381 0.00 0.00 0.00 1.90
2628 2863 2.624029 CCACCCAGGTTCAAGGCATAAT 60.624 50.000 0.00 0.00 0.00 1.28
2629 2864 3.372566 CCACCCAGGTTCAAGGCATAATA 60.373 47.826 0.00 0.00 0.00 0.98
2630 2865 3.885297 CACCCAGGTTCAAGGCATAATAG 59.115 47.826 0.00 0.00 0.00 1.73
2631 2866 3.527665 ACCCAGGTTCAAGGCATAATAGT 59.472 43.478 0.00 0.00 0.00 2.12
2632 2867 4.017499 ACCCAGGTTCAAGGCATAATAGTT 60.017 41.667 0.00 0.00 0.00 2.24
2633 2868 4.339247 CCCAGGTTCAAGGCATAATAGTTG 59.661 45.833 0.00 0.00 0.00 3.16
2634 2869 4.202050 CCAGGTTCAAGGCATAATAGTTGC 60.202 45.833 0.00 0.00 39.41 4.17
2635 2870 4.398988 CAGGTTCAAGGCATAATAGTTGCA 59.601 41.667 0.00 0.00 41.95 4.08
2636 2871 5.016173 AGGTTCAAGGCATAATAGTTGCAA 58.984 37.500 0.00 0.00 41.95 4.08
2637 2872 5.658190 AGGTTCAAGGCATAATAGTTGCAAT 59.342 36.000 0.59 0.00 41.95 3.56
2638 2873 6.155049 AGGTTCAAGGCATAATAGTTGCAATT 59.845 34.615 0.59 0.00 41.95 2.32
2639 2874 6.818142 GGTTCAAGGCATAATAGTTGCAATTT 59.182 34.615 0.59 0.00 41.95 1.82
2640 2875 7.201548 GGTTCAAGGCATAATAGTTGCAATTTG 60.202 37.037 0.59 0.00 41.95 2.32
2641 2876 6.339730 TCAAGGCATAATAGTTGCAATTTGG 58.660 36.000 0.59 0.00 41.95 3.28
2642 2877 5.280654 AGGCATAATAGTTGCAATTTGGG 57.719 39.130 0.59 0.00 41.95 4.12
2643 2878 4.716287 AGGCATAATAGTTGCAATTTGGGT 59.284 37.500 0.59 0.00 41.95 4.51
2644 2879 5.189539 AGGCATAATAGTTGCAATTTGGGTT 59.810 36.000 0.59 0.00 41.95 4.11
2645 2880 5.879777 GGCATAATAGTTGCAATTTGGGTTT 59.120 36.000 0.59 0.00 41.95 3.27
2646 2881 6.183360 GGCATAATAGTTGCAATTTGGGTTTG 60.183 38.462 0.59 0.00 41.95 2.93
2647 2882 6.371271 GCATAATAGTTGCAATTTGGGTTTGT 59.629 34.615 0.59 0.00 39.90 2.83
2648 2883 7.094848 GCATAATAGTTGCAATTTGGGTTTGTT 60.095 33.333 0.59 0.00 39.90 2.83
2649 2884 6.616774 AATAGTTGCAATTTGGGTTTGTTG 57.383 33.333 0.59 0.00 0.00 3.33
2650 2885 2.682352 AGTTGCAATTTGGGTTTGTTGC 59.318 40.909 0.59 2.25 45.27 4.17
2652 2887 2.753989 GCAATTTGGGTTTGTTGCAC 57.246 45.000 4.26 0.00 44.63 4.57
2653 2888 1.333308 GCAATTTGGGTTTGTTGCACC 59.667 47.619 4.26 0.00 44.63 5.01
2654 2889 2.636830 CAATTTGGGTTTGTTGCACCA 58.363 42.857 0.00 0.00 35.80 4.17
2655 2890 3.012518 CAATTTGGGTTTGTTGCACCAA 58.987 40.909 0.00 0.00 40.94 3.67
2656 2891 3.574354 ATTTGGGTTTGTTGCACCAAT 57.426 38.095 0.00 0.00 42.09 3.16
2657 2892 3.356529 TTTGGGTTTGTTGCACCAATT 57.643 38.095 0.00 0.00 42.09 2.32
2658 2893 4.487714 TTTGGGTTTGTTGCACCAATTA 57.512 36.364 0.00 0.00 42.09 1.40
2659 2894 4.696479 TTGGGTTTGTTGCACCAATTAT 57.304 36.364 0.00 0.00 38.02 1.28
2660 2895 5.808366 TTGGGTTTGTTGCACCAATTATA 57.192 34.783 0.00 0.00 38.02 0.98
2661 2896 5.140747 TGGGTTTGTTGCACCAATTATAC 57.859 39.130 0.00 0.00 35.80 1.47
2662 2897 4.835615 TGGGTTTGTTGCACCAATTATACT 59.164 37.500 0.00 0.00 35.80 2.12
2663 2898 5.167845 GGGTTTGTTGCACCAATTATACTG 58.832 41.667 0.00 0.00 35.80 2.74
2664 2899 5.279256 GGGTTTGTTGCACCAATTATACTGT 60.279 40.000 0.00 0.00 35.80 3.55
2665 2900 6.071840 GGGTTTGTTGCACCAATTATACTGTA 60.072 38.462 0.00 0.00 35.80 2.74
2666 2901 7.027161 GGTTTGTTGCACCAATTATACTGTAG 58.973 38.462 0.00 0.00 34.04 2.74
2667 2902 6.751514 TTGTTGCACCAATTATACTGTAGG 57.248 37.500 0.00 0.00 0.00 3.18
2668 2903 5.189928 TGTTGCACCAATTATACTGTAGGG 58.810 41.667 0.00 0.00 0.00 3.53
2669 2904 4.431416 TGCACCAATTATACTGTAGGGG 57.569 45.455 0.00 0.00 0.00 4.79
2670 2905 3.137544 TGCACCAATTATACTGTAGGGGG 59.862 47.826 0.00 0.00 0.00 5.40
2671 2906 3.137728 GCACCAATTATACTGTAGGGGGT 59.862 47.826 0.00 0.00 0.00 4.95
2672 2907 4.385977 GCACCAATTATACTGTAGGGGGTT 60.386 45.833 0.00 0.00 0.00 4.11
2673 2908 5.374071 CACCAATTATACTGTAGGGGGTTC 58.626 45.833 0.00 0.00 0.00 3.62
2674 2909 4.414514 ACCAATTATACTGTAGGGGGTTCC 59.585 45.833 0.00 0.00 0.00 3.62
2686 2921 1.359168 GGGGTTCCCTTACAGTCTGT 58.641 55.000 10.99 10.99 41.34 3.41
2687 2922 1.278413 GGGGTTCCCTTACAGTCTGTC 59.722 57.143 9.26 0.00 41.34 3.51
2688 2923 2.258109 GGGTTCCCTTACAGTCTGTCT 58.742 52.381 9.26 0.00 0.00 3.41
2689 2924 2.234168 GGGTTCCCTTACAGTCTGTCTC 59.766 54.545 9.26 0.00 0.00 3.36
2690 2925 3.166679 GGTTCCCTTACAGTCTGTCTCT 58.833 50.000 9.26 0.00 0.00 3.10
2691 2926 3.193903 GGTTCCCTTACAGTCTGTCTCTC 59.806 52.174 9.26 0.00 0.00 3.20
2692 2927 3.808834 TCCCTTACAGTCTGTCTCTCA 57.191 47.619 9.26 0.00 0.00 3.27
2693 2928 4.114015 TCCCTTACAGTCTGTCTCTCAA 57.886 45.455 9.26 0.00 0.00 3.02
2694 2929 4.480115 TCCCTTACAGTCTGTCTCTCAAA 58.520 43.478 9.26 0.00 0.00 2.69
2695 2930 4.899457 TCCCTTACAGTCTGTCTCTCAAAA 59.101 41.667 9.26 0.00 0.00 2.44
2696 2931 5.365605 TCCCTTACAGTCTGTCTCTCAAAAA 59.634 40.000 9.26 0.00 0.00 1.94
2717 2952 3.525268 AAAAGTGTTTGTGCCTTCTGG 57.475 42.857 0.00 0.00 0.00 3.86
2718 2953 2.143876 AAGTGTTTGTGCCTTCTGGT 57.856 45.000 0.00 0.00 35.27 4.00
2719 2954 1.680338 AGTGTTTGTGCCTTCTGGTC 58.320 50.000 0.00 0.00 35.27 4.02
2720 2955 0.668535 GTGTTTGTGCCTTCTGGTCC 59.331 55.000 0.00 0.00 35.27 4.46
2721 2956 0.817634 TGTTTGTGCCTTCTGGTCCG 60.818 55.000 0.00 0.00 35.27 4.79
2722 2957 0.534203 GTTTGTGCCTTCTGGTCCGA 60.534 55.000 0.00 0.00 35.27 4.55
2723 2958 0.250295 TTTGTGCCTTCTGGTCCGAG 60.250 55.000 0.00 0.00 35.27 4.63
2862 3097 6.036577 ACCTTTCAAGCTTGTTTCTTTCAA 57.963 33.333 25.19 7.55 0.00 2.69
3371 3608 8.028354 CCTAATTTCATGCTTCATGTTTGTACA 58.972 33.333 6.68 0.00 41.98 2.90
3542 3779 2.745281 TGGCCTTATTGCTGTAAACGAC 59.255 45.455 3.32 0.00 0.00 4.34
3806 4044 4.811555 TGTCAAGGTTGAATTCAAGACG 57.188 40.909 21.05 10.18 39.21 4.18
3898 4136 3.624326 TGTGTAAGTTCATGTTGCAGC 57.376 42.857 0.00 0.00 0.00 5.25
4027 4265 8.717821 TGTTTGCATTATGTCTTTAGTACTGTC 58.282 33.333 5.39 0.00 0.00 3.51
4251 4489 5.414765 GTCGGGTGAGAATTTGGATAACTTT 59.585 40.000 0.00 0.00 0.00 2.66
4310 4548 8.336801 ACATACTTTCAAGTTCAGGTAAATCC 57.663 34.615 0.00 0.00 40.37 3.01
4333 4571 7.351166 TCCCTTTCTTTGGAAGAGAAAAGTAA 58.649 34.615 1.57 0.00 41.21 2.24
4545 4785 9.181061 AGGTTAGTGTGTTTGTACTTGTTTTAT 57.819 29.630 0.00 0.00 0.00 1.40
5015 5256 7.648770 ACCCTGATTATAACAAAACCCTACAT 58.351 34.615 0.00 0.00 0.00 2.29
5035 5276 0.242017 GTGACTGGTGCTCATTTGGC 59.758 55.000 0.00 0.00 0.00 4.52
5336 5577 2.601266 CGTGCTTTGGTAACTTGTTCCG 60.601 50.000 0.00 0.00 37.61 4.30
5477 5720 7.986085 TTGAAGCTCTAATGTTTTTCTAGCT 57.014 32.000 0.00 0.00 40.38 3.32
5519 5762 0.390078 TGCATGCAATTTGAAGGGCG 60.390 50.000 20.30 0.00 0.00 6.13
5541 5786 5.390613 CGGACATTTGGTTCAGTTGTATTC 58.609 41.667 0.00 0.00 0.00 1.75
5544 5789 7.065803 CGGACATTTGGTTCAGTTGTATTCTAT 59.934 37.037 0.00 0.00 0.00 1.98
5545 5790 9.391006 GGACATTTGGTTCAGTTGTATTCTATA 57.609 33.333 0.00 0.00 0.00 1.31
5605 5850 2.282887 GCACCGGGTTGGATGGTT 60.283 61.111 6.32 0.00 42.00 3.67
5610 5855 2.445155 GGGTTGGATGGTTGCCCT 59.555 61.111 0.00 0.00 36.49 5.19
5615 5860 2.456577 GTTGGATGGTTGCCCTGTATT 58.543 47.619 0.00 0.00 0.00 1.89
5623 5868 3.245229 TGGTTGCCCTGTATTTGATGTCT 60.245 43.478 0.00 0.00 0.00 3.41
5634 5879 5.877564 TGTATTTGATGTCTGCGGAAACATA 59.122 36.000 0.00 0.00 36.28 2.29
5666 5936 5.236911 GTGGACGTTTGGTGTGTCTATTTTA 59.763 40.000 0.00 0.00 33.21 1.52
5675 5945 8.780846 TTGGTGTGTCTATTTTAATGTACGAT 57.219 30.769 0.00 0.00 0.00 3.73
5682 5952 9.093970 TGTCTATTTTAATGTACGATGTTGGAG 57.906 33.333 0.00 0.00 0.00 3.86
5754 6024 6.539173 TCTCTCCTCTCTAACATACTCCATC 58.461 44.000 0.00 0.00 0.00 3.51
5762 6032 6.263392 TCTCTAACATACTCCATCTGTAGTGC 59.737 42.308 0.00 0.00 0.00 4.40
5778 6048 4.819088 TGTAGTGCTGAATTTTGCTGTGTA 59.181 37.500 5.46 0.00 0.00 2.90
5779 6049 4.916983 AGTGCTGAATTTTGCTGTGTAA 57.083 36.364 5.46 0.00 0.00 2.41
5953 6223 2.543653 CCAAGTTCAGTTTTTGGCTCCG 60.544 50.000 0.00 0.00 35.41 4.63
5964 6234 0.535335 TTGGCTCCGCGTAGAAATCT 59.465 50.000 1.57 0.00 0.00 2.40
5996 6266 1.000274 GAGTTTGCCATCCACAACCAC 60.000 52.381 0.00 0.00 0.00 4.16
6047 6318 4.970611 CGATCTCACTATTACTTGGACACG 59.029 45.833 0.00 0.00 0.00 4.49
6124 6950 4.041198 CCACACCACTTCTAAACCTTAGGA 59.959 45.833 4.77 0.00 0.00 2.94
6142 6968 3.594134 AGGATTCACTTGAGCTTCTTCG 58.406 45.455 0.00 0.00 0.00 3.79
6151 6979 1.532437 TGAGCTTCTTCGTTGCATGTG 59.468 47.619 0.00 0.00 0.00 3.21
6152 6980 1.532868 GAGCTTCTTCGTTGCATGTGT 59.467 47.619 0.00 0.00 0.00 3.72
6202 7039 1.298667 GCTGGGTCATGGGTACGTT 59.701 57.895 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 7.603024 CCTCCTTCGAATACTTCAAAGTAGTTT 59.397 37.037 0.00 0.00 44.06 2.66
75 77 1.603739 GCAAAGCGGGTTCCTCCTT 60.604 57.895 0.00 0.00 36.25 3.36
89 91 4.595116 CAAATTGTTTTCGGCATTGCAAA 58.405 34.783 11.39 0.36 0.00 3.68
103 105 3.665226 TCCGGCGCGCAAATTGTT 61.665 55.556 34.42 0.00 0.00 2.83
277 283 1.620822 GGACACCAAACTTGCCATCT 58.379 50.000 0.00 0.00 0.00 2.90
295 301 5.521735 CAGAGAAAGTAATCTTCACATCCGG 59.478 44.000 0.00 0.00 32.90 5.14
310 316 6.472686 ACAGAGTCAGTTTACAGAGAAAGT 57.527 37.500 0.00 0.00 0.00 2.66
404 410 3.007074 GCTAAACCCTAGATGTCTAGCCC 59.993 52.174 10.84 0.00 43.47 5.19
567 573 3.558418 GGTCTTAAACTGTGCGTCTGAAA 59.442 43.478 0.00 0.00 0.00 2.69
568 574 3.128349 GGTCTTAAACTGTGCGTCTGAA 58.872 45.455 0.00 0.00 0.00 3.02
585 591 0.467659 CGATCTCGGGTAAGGGGTCT 60.468 60.000 0.00 0.00 35.37 3.85
692 698 2.188161 GTGCCCCGAAACGTTGGAA 61.188 57.895 0.00 0.00 0.00 3.53
765 772 1.440145 GCTGGAAAGGGCGATGCTAC 61.440 60.000 0.00 0.00 0.00 3.58
845 857 3.508840 CAGATTTCCGGGCACGCC 61.509 66.667 0.58 0.00 39.22 5.68
1418 1433 4.300803 GGGAAAATTTTACCGTCACAACC 58.699 43.478 16.48 3.22 30.03 3.77
1634 1658 1.355381 TGGATTGGCTGGATCAGTGTT 59.645 47.619 0.00 0.00 33.43 3.32
1733 1760 4.734398 AGCTCTTGAGGAGATGTAACAG 57.266 45.455 0.00 0.00 44.45 3.16
1741 1768 2.705658 TGGTTTGAAGCTCTTGAGGAGA 59.294 45.455 0.00 0.00 44.45 3.71
1753 1780 5.399301 CGTTTCATAGCTTGTTGGTTTGAAG 59.601 40.000 0.00 0.00 42.06 3.02
2013 2202 8.323567 ACTCCACCCGATTTAAGATTTTAGTTA 58.676 33.333 0.00 0.00 0.00 2.24
2075 2264 2.930682 GCTCAGGAGTTCGTTTATCACC 59.069 50.000 0.00 0.00 0.00 4.02
2105 2294 7.843760 TGTATTTGAAGGTTCCATTAATCCCAT 59.156 33.333 0.00 0.00 0.00 4.00
2106 2295 7.185565 TGTATTTGAAGGTTCCATTAATCCCA 58.814 34.615 0.00 0.00 0.00 4.37
2107 2296 7.654022 TGTATTTGAAGGTTCCATTAATCCC 57.346 36.000 0.00 0.00 0.00 3.85
2267 2502 3.107402 TCCAGTCTTCAGGATGTAGCT 57.893 47.619 0.00 0.00 37.40 3.32
2459 2694 1.672881 ACAGCAGACAACAGAAGCAAC 59.327 47.619 0.00 0.00 0.00 4.17
2465 2700 2.158971 TGCACTAACAGCAGACAACAGA 60.159 45.455 0.00 0.00 37.02 3.41
2585 2820 1.141657 TGGGAAGGCATCATAGTCTGC 59.858 52.381 0.00 0.00 37.66 4.26
2586 2821 2.486191 GGTGGGAAGGCATCATAGTCTG 60.486 54.545 0.00 0.00 0.00 3.51
2587 2822 1.771255 GGTGGGAAGGCATCATAGTCT 59.229 52.381 0.00 0.00 0.00 3.24
2589 2824 0.846693 GGGTGGGAAGGCATCATAGT 59.153 55.000 0.00 0.00 0.00 2.12
2591 2826 0.550914 GTGGGTGGGAAGGCATCATA 59.449 55.000 0.00 0.00 0.00 2.15
2592 2827 1.307647 GTGGGTGGGAAGGCATCAT 59.692 57.895 0.00 0.00 0.00 2.45
2593 2828 2.763215 GTGGGTGGGAAGGCATCA 59.237 61.111 0.00 0.00 0.00 3.07
2597 2832 4.366684 CTGGGTGGGTGGGAAGGC 62.367 72.222 0.00 0.00 0.00 4.35
2598 2833 3.661648 CCTGGGTGGGTGGGAAGG 61.662 72.222 0.00 0.00 0.00 3.46
2599 2834 2.426305 GAACCTGGGTGGGTGGGAAG 62.426 65.000 0.00 0.00 39.85 3.46
2600 2835 2.370403 AACCTGGGTGGGTGGGAA 60.370 61.111 0.00 0.00 39.85 3.97
2601 2836 2.856988 GAACCTGGGTGGGTGGGA 60.857 66.667 0.00 0.00 39.85 4.37
2602 2837 2.713531 CTTGAACCTGGGTGGGTGGG 62.714 65.000 0.00 0.00 39.85 4.61
2603 2838 1.228552 CTTGAACCTGGGTGGGTGG 60.229 63.158 0.00 0.00 39.85 4.61
2604 2839 1.228552 CCTTGAACCTGGGTGGGTG 60.229 63.158 0.00 0.00 39.85 4.61
2605 2840 3.146828 GCCTTGAACCTGGGTGGGT 62.147 63.158 0.00 0.00 42.05 4.51
2606 2841 2.283173 GCCTTGAACCTGGGTGGG 60.283 66.667 0.00 0.00 41.11 4.61
2607 2842 0.331278 TATGCCTTGAACCTGGGTGG 59.669 55.000 0.00 0.00 42.93 4.61
2608 2843 2.214376 TTATGCCTTGAACCTGGGTG 57.786 50.000 0.00 0.00 0.00 4.61
2609 2844 3.527665 ACTATTATGCCTTGAACCTGGGT 59.472 43.478 0.00 0.00 0.00 4.51
2610 2845 4.170468 ACTATTATGCCTTGAACCTGGG 57.830 45.455 0.00 0.00 0.00 4.45
2611 2846 4.202050 GCAACTATTATGCCTTGAACCTGG 60.202 45.833 0.00 0.00 37.85 4.45
2612 2847 4.398988 TGCAACTATTATGCCTTGAACCTG 59.601 41.667 0.00 0.00 43.16 4.00
2613 2848 4.599041 TGCAACTATTATGCCTTGAACCT 58.401 39.130 0.00 0.00 43.16 3.50
2614 2849 4.981806 TGCAACTATTATGCCTTGAACC 57.018 40.909 0.00 0.00 43.16 3.62
2615 2850 7.201548 CCAAATTGCAACTATTATGCCTTGAAC 60.202 37.037 0.00 0.00 43.16 3.18
2616 2851 6.817641 CCAAATTGCAACTATTATGCCTTGAA 59.182 34.615 0.00 0.00 43.16 2.69
2617 2852 6.339730 CCAAATTGCAACTATTATGCCTTGA 58.660 36.000 0.00 0.00 43.16 3.02
2618 2853 5.524646 CCCAAATTGCAACTATTATGCCTTG 59.475 40.000 0.00 0.00 43.16 3.61
2619 2854 5.189539 ACCCAAATTGCAACTATTATGCCTT 59.810 36.000 0.00 0.00 43.16 4.35
2620 2855 4.716287 ACCCAAATTGCAACTATTATGCCT 59.284 37.500 0.00 0.00 43.16 4.75
2621 2856 5.022282 ACCCAAATTGCAACTATTATGCC 57.978 39.130 0.00 0.00 43.16 4.40
2622 2857 6.371271 ACAAACCCAAATTGCAACTATTATGC 59.629 34.615 0.00 0.00 44.08 3.14
2623 2858 7.903995 ACAAACCCAAATTGCAACTATTATG 57.096 32.000 0.00 0.00 0.00 1.90
2624 2859 7.094848 GCAACAAACCCAAATTGCAACTATTAT 60.095 33.333 0.00 0.00 45.38 1.28
2625 2860 6.203723 GCAACAAACCCAAATTGCAACTATTA 59.796 34.615 0.00 0.00 45.38 0.98
2626 2861 5.008514 GCAACAAACCCAAATTGCAACTATT 59.991 36.000 0.00 0.00 45.38 1.73
2627 2862 4.514816 GCAACAAACCCAAATTGCAACTAT 59.485 37.500 0.00 0.00 45.38 2.12
2628 2863 3.873952 GCAACAAACCCAAATTGCAACTA 59.126 39.130 0.00 0.00 45.38 2.24
2629 2864 2.682352 GCAACAAACCCAAATTGCAACT 59.318 40.909 0.00 0.00 45.38 3.16
2630 2865 3.063670 GCAACAAACCCAAATTGCAAC 57.936 42.857 0.00 0.00 45.38 4.17
2633 2868 1.333308 GGTGCAACAAACCCAAATTGC 59.667 47.619 0.00 0.94 46.08 3.56
2634 2869 2.636830 TGGTGCAACAAACCCAAATTG 58.363 42.857 0.00 0.00 39.98 2.32
2635 2870 3.356529 TTGGTGCAACAAACCCAAATT 57.643 38.095 16.46 0.00 39.98 1.82
2636 2871 3.574354 ATTGGTGCAACAAACCCAAAT 57.426 38.095 23.14 0.00 40.16 2.32
2637 2872 3.356529 AATTGGTGCAACAAACCCAAA 57.643 38.095 23.14 0.00 40.16 3.28
2638 2873 4.696479 ATAATTGGTGCAACAAACCCAA 57.304 36.364 23.14 14.03 39.98 4.12
2639 2874 4.835615 AGTATAATTGGTGCAACAAACCCA 59.164 37.500 23.14 3.95 39.98 4.51
2640 2875 5.167845 CAGTATAATTGGTGCAACAAACCC 58.832 41.667 23.14 7.99 39.98 4.11
2641 2876 5.778862 ACAGTATAATTGGTGCAACAAACC 58.221 37.500 23.14 7.62 39.98 3.27
2642 2877 7.027161 CCTACAGTATAATTGGTGCAACAAAC 58.973 38.462 23.14 15.04 39.98 2.93
2643 2878 6.151985 CCCTACAGTATAATTGGTGCAACAAA 59.848 38.462 23.14 6.25 39.98 2.83
2644 2879 5.650266 CCCTACAGTATAATTGGTGCAACAA 59.350 40.000 21.46 21.46 39.98 2.83
2645 2880 5.189928 CCCTACAGTATAATTGGTGCAACA 58.810 41.667 0.00 0.00 39.98 3.33
2646 2881 4.578928 CCCCTACAGTATAATTGGTGCAAC 59.421 45.833 0.00 0.00 0.00 4.17
2647 2882 4.385865 CCCCCTACAGTATAATTGGTGCAA 60.386 45.833 0.00 0.00 0.00 4.08
2648 2883 3.137544 CCCCCTACAGTATAATTGGTGCA 59.862 47.826 0.00 0.00 0.00 4.57
2649 2884 3.137728 ACCCCCTACAGTATAATTGGTGC 59.862 47.826 0.00 0.00 0.00 5.01
2650 2885 5.374071 GAACCCCCTACAGTATAATTGGTG 58.626 45.833 0.00 0.00 0.00 4.17
2651 2886 4.414514 GGAACCCCCTACAGTATAATTGGT 59.585 45.833 0.00 0.00 0.00 3.67
2652 2887 4.981812 GGAACCCCCTACAGTATAATTGG 58.018 47.826 0.00 0.00 0.00 3.16
2670 2905 3.827302 TGAGAGACAGACTGTAAGGGAAC 59.173 47.826 8.41 0.00 39.30 3.62
2671 2906 4.114015 TGAGAGACAGACTGTAAGGGAA 57.886 45.455 8.41 0.00 39.30 3.97
2672 2907 3.808834 TGAGAGACAGACTGTAAGGGA 57.191 47.619 8.41 0.00 39.30 4.20
2673 2908 4.873746 TTTGAGAGACAGACTGTAAGGG 57.126 45.455 8.41 0.00 39.30 3.95
2696 2931 3.260632 ACCAGAAGGCACAAACACTTTTT 59.739 39.130 0.00 0.00 39.06 1.94
2697 2932 2.831526 ACCAGAAGGCACAAACACTTTT 59.168 40.909 0.00 0.00 39.06 2.27
2698 2933 2.427095 GACCAGAAGGCACAAACACTTT 59.573 45.455 0.00 0.00 39.06 2.66
2699 2934 2.024414 GACCAGAAGGCACAAACACTT 58.976 47.619 0.00 0.00 39.06 3.16
2700 2935 1.680338 GACCAGAAGGCACAAACACT 58.320 50.000 0.00 0.00 39.06 3.55
2701 2936 0.668535 GGACCAGAAGGCACAAACAC 59.331 55.000 0.00 0.00 39.06 3.32
2702 2937 0.817634 CGGACCAGAAGGCACAAACA 60.818 55.000 0.00 0.00 39.06 2.83
2703 2938 0.534203 TCGGACCAGAAGGCACAAAC 60.534 55.000 0.00 0.00 39.06 2.93
2704 2939 0.250295 CTCGGACCAGAAGGCACAAA 60.250 55.000 0.00 0.00 39.06 2.83
2705 2940 1.118965 TCTCGGACCAGAAGGCACAA 61.119 55.000 0.00 0.00 39.06 3.33
2706 2941 1.533033 TCTCGGACCAGAAGGCACA 60.533 57.895 0.00 0.00 39.06 4.57
2707 2942 1.216710 CTCTCGGACCAGAAGGCAC 59.783 63.158 0.00 0.00 39.06 5.01
2708 2943 0.541998 TTCTCTCGGACCAGAAGGCA 60.542 55.000 0.00 0.00 39.06 4.75
2709 2944 0.608640 TTTCTCTCGGACCAGAAGGC 59.391 55.000 0.00 0.00 39.06 4.35
2710 2945 4.946478 ATATTTCTCTCGGACCAGAAGG 57.054 45.455 0.00 0.00 42.21 3.46
2711 2946 6.392625 TGTATATTTCTCTCGGACCAGAAG 57.607 41.667 0.00 0.00 30.32 2.85
2712 2947 6.549736 TCATGTATATTTCTCTCGGACCAGAA 59.450 38.462 0.00 0.00 0.00 3.02
2713 2948 6.068670 TCATGTATATTTCTCTCGGACCAGA 58.931 40.000 0.00 0.00 0.00 3.86
2714 2949 6.332735 TCATGTATATTTCTCTCGGACCAG 57.667 41.667 0.00 0.00 0.00 4.00
2715 2950 6.724893 TTCATGTATATTTCTCTCGGACCA 57.275 37.500 0.00 0.00 0.00 4.02
2716 2951 7.711339 ACTTTTCATGTATATTTCTCTCGGACC 59.289 37.037 0.00 0.00 0.00 4.46
2717 2952 8.649973 ACTTTTCATGTATATTTCTCTCGGAC 57.350 34.615 0.00 0.00 0.00 4.79
2749 2984 7.473735 TGGCACAAATTGAATAAAGATACCA 57.526 32.000 0.00 0.00 31.92 3.25
2862 3097 5.894298 TGTAATCCAGCATCTACTCCAAT 57.106 39.130 0.00 0.00 0.00 3.16
3342 3579 8.584157 ACAAACATGAAGCATGAAATTAGGTTA 58.416 29.630 13.79 0.00 43.81 2.85
3542 3779 1.226746 GGTTGCGAAGGATAATCCCG 58.773 55.000 0.00 0.00 37.19 5.14
3806 4044 1.662044 CAACAACTGCCCTGAAGCC 59.338 57.895 0.00 0.00 0.00 4.35
3898 4136 4.999950 AGGAATCTAAGTGTGCAGAAGTTG 59.000 41.667 0.00 0.00 0.00 3.16
4027 4265 5.230726 GTGCCAAGCATTAAAGAAATCATCG 59.769 40.000 0.00 0.00 41.91 3.84
4251 4489 4.759693 ACAAGAATGTTCTTTACATCGCCA 59.240 37.500 5.30 0.00 46.75 5.69
4333 4571 5.892686 GGCGGAGGGAGTAGATATAAACTAT 59.107 44.000 0.00 0.00 0.00 2.12
4545 4785 7.762615 CGTGATACTTCTACCCATTCAAGTTAA 59.237 37.037 0.00 0.00 31.52 2.01
4564 4804 4.496341 CCTGGAATGCAATCAACGTGATAC 60.496 45.833 3.77 0.00 35.76 2.24
5015 5256 1.608055 CCAAATGAGCACCAGTCACA 58.392 50.000 0.00 0.00 0.00 3.58
5035 5276 6.115446 TGGATACTGTTTAAGGCATCTTCAG 58.885 40.000 0.00 0.00 33.91 3.02
5336 5577 2.838736 AGACCATCACACACAGAACAC 58.161 47.619 0.00 0.00 0.00 3.32
5503 5746 0.532115 GTCCGCCCTTCAAATTGCAT 59.468 50.000 0.00 0.00 0.00 3.96
5519 5762 6.575162 AGAATACAACTGAACCAAATGTCC 57.425 37.500 0.00 0.00 0.00 4.02
5552 5797 9.898152 CTGCCCCTTTTCCAAAATAAATAAATA 57.102 29.630 0.00 0.00 0.00 1.40
5553 5798 8.610369 TCTGCCCCTTTTCCAAAATAAATAAAT 58.390 29.630 0.00 0.00 0.00 1.40
5605 5850 2.368439 GCAGACATCAAATACAGGGCA 58.632 47.619 0.00 0.00 0.00 5.36
5610 5855 4.068599 TGTTTCCGCAGACATCAAATACA 58.931 39.130 0.00 0.00 0.00 2.29
5615 5860 4.094739 CACATATGTTTCCGCAGACATCAA 59.905 41.667 5.37 0.00 37.62 2.57
5634 5879 0.882927 CCAAACGTCCACGGACACAT 60.883 55.000 16.23 0.00 44.77 3.21
5666 5936 3.206150 GGCATCTCCAACATCGTACATT 58.794 45.455 0.00 0.00 34.01 2.71
5675 5945 4.421365 GCAAGGGCATCTCCAACA 57.579 55.556 0.00 0.00 40.72 3.33
5731 6001 6.430925 CAGATGGAGTATGTTAGAGAGGAGAG 59.569 46.154 0.00 0.00 0.00 3.20
5732 6002 6.126332 ACAGATGGAGTATGTTAGAGAGGAGA 60.126 42.308 0.00 0.00 0.00 3.71
5733 6003 6.068010 ACAGATGGAGTATGTTAGAGAGGAG 58.932 44.000 0.00 0.00 0.00 3.69
5734 6004 6.019656 ACAGATGGAGTATGTTAGAGAGGA 57.980 41.667 0.00 0.00 0.00 3.71
5735 6005 7.001674 ACTACAGATGGAGTATGTTAGAGAGG 58.998 42.308 0.00 0.00 33.56 3.69
5736 6006 7.521423 GCACTACAGATGGAGTATGTTAGAGAG 60.521 44.444 0.00 0.00 33.56 3.20
5737 6007 6.263392 GCACTACAGATGGAGTATGTTAGAGA 59.737 42.308 0.00 0.00 33.56 3.10
5754 6024 4.224433 CACAGCAAAATTCAGCACTACAG 58.776 43.478 5.08 0.00 0.00 2.74
5762 6032 5.695851 ACTCCTTACACAGCAAAATTCAG 57.304 39.130 0.00 0.00 0.00 3.02
5964 6234 4.350368 TGGCAAACTCTGTAGATTCACA 57.650 40.909 0.00 0.00 0.00 3.58
5996 6266 6.019479 GTGTCAGTATTTCTTAGATGCGGAAG 60.019 42.308 0.00 0.00 0.00 3.46
6047 6318 2.696187 GGTCTTCTATGGTGGAGAGACC 59.304 54.545 4.76 4.76 35.75 3.85
6124 6950 3.058639 GCAACGAAGAAGCTCAAGTGAAT 60.059 43.478 0.00 0.00 0.00 2.57
6142 6968 5.348451 ACACAAAGAAAAAGACACATGCAAC 59.652 36.000 0.00 0.00 0.00 4.17
6202 7039 1.483004 TGACAAACTTCGTGACCTGGA 59.517 47.619 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.