Multiple sequence alignment - TraesCS5A01G183600

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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 TraesCS5A01G183600 chr5A 100.000 3050 0 0 1 3050 383417336 383420385 0.000000e+00 5633.0
1 TraesCS5A01G183600 chr5D 93.237 2351 86 22 98 2399 291083839 291086165 0.000000e+00 3393.0
2 TraesCS5A01G183600 chr5D 84.515 536 29 30 2517 3038 291086284 291086779 5.910000e-132 481.0
3 TraesCS5A01G183600 chr5B 92.357 2342 114 26 98 2397 331373039 331375357 0.000000e+00 3273.0
4 TraesCS5A01G183600 chr5B 84.369 531 23 22 2517 3038 331375450 331375929 1.660000e-127 466.0
5 TraesCS5A01G183600 chr3D 84.000 125 16 3 1544 1666 329495352 329495474 1.920000e-22 117.0
6 TraesCS5A01G183600 chr7A 83.871 124 16 4 1545 1666 22543196 22543075 6.910000e-22 115.0
7 TraesCS5A01G183600 chr3B 83.200 125 17 3 1544 1666 426995428 426995550 8.940000e-21 111.0
8 TraesCS5A01G183600 chr3A 83.200 125 17 3 1544 1666 444534958 444535080 8.940000e-21 111.0
9 TraesCS5A01G183600 chr7D 87.000 100 10 3 1545 1642 21836566 21836468 3.220000e-20 110.0
10 TraesCS5A01G183600 chr4A 85.047 107 12 4 1539 1642 711880571 711880676 4.160000e-19 106.0
11 TraesCS5A01G183600 chr2A 77.439 164 20 16 1513 1666 280198 280354 7.010000e-12 82.4


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 TraesCS5A01G183600 chr5A 383417336 383420385 3049 False 5633.0 5633 100.000 1 3050 1 chr5A.!!$F1 3049
1 TraesCS5A01G183600 chr5D 291083839 291086779 2940 False 1937.0 3393 88.876 98 3038 2 chr5D.!!$F1 2940
2 TraesCS5A01G183600 chr5B 331373039 331375929 2890 False 1869.5 3273 88.363 98 3038 2 chr5B.!!$F1 2940

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
92 93 0.372334 GTGGCACGTAACATTAGGCG 59.628 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2118 0.749454 AATGGAAGATCACGGCAGCC 60.749 55.0 0.0 0.0 0.0 4.85 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
31 32 4.065281 CCCTGACGTGTCCCCGAC 62.065 72.222 0.00 0.00 0.00 4.79
32 33 4.415332 CCTGACGTGTCCCCGACG 62.415 72.222 0.00 0.00 42.62 5.12
33 34 3.359523 CTGACGTGTCCCCGACGA 61.360 66.667 0.00 0.00 39.21 4.20
34 35 3.606065 CTGACGTGTCCCCGACGAC 62.606 68.421 0.00 0.00 39.21 4.34
35 36 4.410743 GACGTGTCCCCGACGACC 62.411 72.222 0.00 0.00 39.21 4.79
37 38 4.415332 CGTGTCCCCGACGACCAG 62.415 72.222 0.00 0.00 39.21 4.00
38 39 2.987547 GTGTCCCCGACGACCAGA 60.988 66.667 0.00 0.00 34.95 3.86
39 40 2.675423 TGTCCCCGACGACCAGAG 60.675 66.667 0.00 0.00 34.95 3.35
40 41 2.360852 GTCCCCGACGACCAGAGA 60.361 66.667 0.00 0.00 0.00 3.10
41 42 2.360852 TCCCCGACGACCAGAGAC 60.361 66.667 0.00 0.00 0.00 3.36
42 43 3.450115 CCCCGACGACCAGAGACC 61.450 72.222 0.00 0.00 0.00 3.85
43 44 3.450115 CCCGACGACCAGAGACCC 61.450 72.222 0.00 0.00 0.00 4.46
44 45 2.675423 CCGACGACCAGAGACCCA 60.675 66.667 0.00 0.00 0.00 4.51
45 46 2.701780 CCGACGACCAGAGACCCAG 61.702 68.421 0.00 0.00 0.00 4.45
46 47 2.574399 GACGACCAGAGACCCAGC 59.426 66.667 0.00 0.00 0.00 4.85
47 48 3.343788 GACGACCAGAGACCCAGCG 62.344 68.421 0.00 0.00 0.00 5.18
48 49 3.062466 CGACCAGAGACCCAGCGA 61.062 66.667 0.00 0.00 0.00 4.93
49 50 2.888863 GACCAGAGACCCAGCGAG 59.111 66.667 0.00 0.00 0.00 5.03
50 51 3.363844 GACCAGAGACCCAGCGAGC 62.364 68.421 0.00 0.00 0.00 5.03
51 52 4.504916 CCAGAGACCCAGCGAGCG 62.505 72.222 0.00 0.00 0.00 5.03
52 53 4.504916 CAGAGACCCAGCGAGCGG 62.505 72.222 0.00 0.00 0.00 5.52
73 74 4.637771 AAAAATCTCGCCCTCGGG 57.362 55.556 0.00 0.00 37.58 5.14
74 75 1.683441 AAAAATCTCGCCCTCGGGT 59.317 52.632 3.54 0.00 37.48 5.28
75 76 0.676782 AAAAATCTCGCCCTCGGGTG 60.677 55.000 9.29 9.29 46.45 4.61
76 77 2.536997 AAAATCTCGCCCTCGGGTGG 62.537 60.000 15.16 6.68 45.24 4.61
83 84 3.697747 CCCTCGGGTGGCACGTAA 61.698 66.667 12.17 0.00 0.00 3.18
84 85 2.433664 CCTCGGGTGGCACGTAAC 60.434 66.667 12.17 0.90 0.00 2.50
85 86 2.340809 CTCGGGTGGCACGTAACA 59.659 61.111 12.17 0.00 0.00 2.41
86 87 1.079405 CTCGGGTGGCACGTAACAT 60.079 57.895 12.17 0.00 0.00 2.71
87 88 0.672401 CTCGGGTGGCACGTAACATT 60.672 55.000 12.17 0.00 0.00 2.71
88 89 0.607112 TCGGGTGGCACGTAACATTA 59.393 50.000 12.17 0.00 0.00 1.90
89 90 1.003851 CGGGTGGCACGTAACATTAG 58.996 55.000 12.17 0.00 0.00 1.73
90 91 1.375551 GGGTGGCACGTAACATTAGG 58.624 55.000 12.17 0.00 0.00 2.69
91 92 0.730840 GGTGGCACGTAACATTAGGC 59.269 55.000 12.17 0.00 0.00 3.93
92 93 0.372334 GTGGCACGTAACATTAGGCG 59.628 55.000 0.00 0.00 0.00 5.52
93 94 0.741574 TGGCACGTAACATTAGGCGG 60.742 55.000 0.00 0.00 0.00 6.13
94 95 1.350665 GCACGTAACATTAGGCGGC 59.649 57.895 0.00 0.00 0.00 6.53
95 96 2.011453 CACGTAACATTAGGCGGCC 58.989 57.895 12.11 12.11 0.00 6.13
96 97 1.519898 ACGTAACATTAGGCGGCCG 60.520 57.895 24.05 24.05 0.00 6.13
112 113 2.934024 CGATTGCGCGCGAACAAG 60.934 61.111 37.18 17.28 0.00 3.16
138 139 4.415332 CGTGTCACGTCTCCCCCG 62.415 72.222 17.30 0.00 36.74 5.73
168 169 3.916172 GTCGCCGGAGAAATTTAAAAACC 59.084 43.478 10.32 0.00 0.00 3.27
169 170 3.822167 TCGCCGGAGAAATTTAAAAACCT 59.178 39.130 5.05 0.00 0.00 3.50
189 190 1.200839 GTCGTTGCGAGGTCAAACG 59.799 57.895 8.08 8.08 36.23 3.60
333 347 4.698276 TCTCTTTTCTTTTCGAATTCGCG 58.302 39.130 22.90 0.00 39.60 5.87
410 424 1.330829 GACCGGCGATGGAAAGAATTC 59.669 52.381 9.30 0.00 34.66 2.17
555 591 2.994186 TTAGGTTGCGGGGTTAGATC 57.006 50.000 0.00 0.00 0.00 2.75
568 604 3.683340 GGGTTAGATCGGACTTTCAACAC 59.317 47.826 2.30 0.00 0.00 3.32
571 607 5.333875 GGTTAGATCGGACTTTCAACACAAC 60.334 44.000 2.30 0.00 0.00 3.32
594 630 8.607459 CAACCACACTAGCTTAGATTTGATTAG 58.393 37.037 0.00 0.00 0.00 1.73
595 631 7.275920 ACCACACTAGCTTAGATTTGATTAGG 58.724 38.462 0.00 0.00 0.00 2.69
677 727 2.438434 GGTGAGCCGTTGATGGGG 60.438 66.667 0.00 0.00 0.00 4.96
847 897 3.122727 TTTATAAGGGGGCCGCCCG 62.123 63.158 33.89 0.00 46.66 6.13
879 929 3.139770 CCTCTCCTCCATTCCATTCCATT 59.860 47.826 0.00 0.00 0.00 3.16
880 930 4.396522 CTCTCCTCCATTCCATTCCATTC 58.603 47.826 0.00 0.00 0.00 2.67
881 931 3.139025 TCTCCTCCATTCCATTCCATTCC 59.861 47.826 0.00 0.00 0.00 3.01
882 932 2.177669 TCCTCCATTCCATTCCATTCCC 59.822 50.000 0.00 0.00 0.00 3.97
883 933 2.601905 CTCCATTCCATTCCATTCCCC 58.398 52.381 0.00 0.00 0.00 4.81
884 934 2.178544 CTCCATTCCATTCCATTCCCCT 59.821 50.000 0.00 0.00 0.00 4.79
953 1011 5.830000 TGCATTTCATCTCAGAATTCAGG 57.170 39.130 8.44 0.00 0.00 3.86
972 1030 0.391263 GCGGTGTTCTTGTCTAGGGG 60.391 60.000 0.00 0.00 0.00 4.79
973 1031 1.263356 CGGTGTTCTTGTCTAGGGGA 58.737 55.000 0.00 0.00 0.00 4.81
974 1032 1.621814 CGGTGTTCTTGTCTAGGGGAA 59.378 52.381 0.00 0.00 0.00 3.97
975 1033 2.353803 CGGTGTTCTTGTCTAGGGGAAG 60.354 54.545 0.00 0.00 0.00 3.46
976 1034 2.904434 GGTGTTCTTGTCTAGGGGAAGA 59.096 50.000 0.00 0.00 0.00 2.87
977 1035 3.326880 GGTGTTCTTGTCTAGGGGAAGAA 59.673 47.826 7.33 7.33 34.17 2.52
978 1036 4.563786 GGTGTTCTTGTCTAGGGGAAGAAG 60.564 50.000 10.30 0.00 36.60 2.85
1236 1294 2.732094 CACGGGTTCACGTCGGTC 60.732 66.667 0.00 0.00 46.75 4.79
1263 1321 1.406860 GCAGGAGGGAGATGGAGGAC 61.407 65.000 0.00 0.00 0.00 3.85
1335 1393 2.101770 CGCGACTTCTACGGGGTC 59.898 66.667 0.00 0.00 39.38 4.46
1344 1402 2.751436 TACGGGGTCTTCGACGGG 60.751 66.667 0.00 0.00 32.65 5.28
1857 1915 1.725557 GCGACGAGTGCCTGATCCTA 61.726 60.000 0.00 0.00 0.00 2.94
1869 1927 3.214250 GATCCTAGCCAGCGACGGG 62.214 68.421 0.00 0.00 0.00 5.28
1886 1944 2.665185 GCTGTGGGACGTGGTCAC 60.665 66.667 0.00 0.00 36.36 3.67
1899 1957 1.668151 GGTCACCAACGAGACAGCC 60.668 63.158 0.00 0.00 36.50 4.85
2053 2111 3.067320 GCCAAGGAATCATTTGTAGGAGC 59.933 47.826 0.00 0.00 0.00 4.70
2059 2117 0.530744 TCATTTGTAGGAGCGCGACT 59.469 50.000 12.10 6.51 0.00 4.18
2060 2118 0.647410 CATTTGTAGGAGCGCGACTG 59.353 55.000 12.10 0.00 0.00 3.51
2088 2146 4.100529 CGTGATCTTCCATTGCAACAATC 58.899 43.478 0.00 0.00 0.00 2.67
2111 2172 9.717942 AATCGTAGTATAGTAGTAACAGTAGGG 57.282 37.037 0.00 0.00 0.00 3.53
2256 2319 6.014584 GTGGGGTTGAGGAAAGAAATAACAAT 60.015 38.462 0.00 0.00 0.00 2.71
2290 2354 6.884280 AAGTTCGATCCTGAAATTGAAACT 57.116 33.333 0.00 0.00 35.12 2.66
2313 2377 5.928976 TGAAGTTCAGTTCATCAGAAGGAA 58.071 37.500 0.08 0.00 33.63 3.36
2342 2406 6.536224 AGTTTTTGTTCAAATTCTGAAGGCTG 59.464 34.615 0.00 0.00 44.83 4.85
2382 2446 2.540515 CGTTCGCATCAGTAATCCTGT 58.459 47.619 0.00 0.00 42.19 4.00
2399 2463 7.878621 AATCCTGTTTAGATGGAGGATGATA 57.121 36.000 0.00 0.00 43.28 2.15
2401 2465 6.143206 TCCTGTTTAGATGGAGGATGATACA 58.857 40.000 0.00 0.00 29.25 2.29
2402 2466 6.615316 TCCTGTTTAGATGGAGGATGATACAA 59.385 38.462 0.00 0.00 29.25 2.41
2403 2467 6.933521 CCTGTTTAGATGGAGGATGATACAAG 59.066 42.308 0.00 0.00 0.00 3.16
2404 2468 6.830912 TGTTTAGATGGAGGATGATACAAGG 58.169 40.000 0.00 0.00 0.00 3.61
2406 2470 2.641815 AGATGGAGGATGATACAAGGCC 59.358 50.000 0.00 0.00 0.00 5.19
2415 2588 4.020128 GGATGATACAAGGCCTTAGTAGGG 60.020 50.000 20.00 7.24 42.25 3.53
2430 2603 8.929487 GCCTTAGTAGGGCTCATATAATAATCT 58.071 37.037 15.80 0.00 45.57 2.40
2433 2606 7.922699 AGTAGGGCTCATATAATAATCTCCC 57.077 40.000 0.00 0.00 0.00 4.30
2434 2607 6.847036 AGTAGGGCTCATATAATAATCTCCCC 59.153 42.308 0.00 0.00 31.75 4.81
2435 2608 5.870984 AGGGCTCATATAATAATCTCCCCT 58.129 41.667 0.00 0.00 34.41 4.79
2436 2609 7.009960 AGGGCTCATATAATAATCTCCCCTA 57.990 40.000 0.00 0.00 37.36 3.53
2437 2610 7.439263 AGGGCTCATATAATAATCTCCCCTAA 58.561 38.462 0.00 0.00 37.36 2.69
2438 2611 7.570607 AGGGCTCATATAATAATCTCCCCTAAG 59.429 40.741 0.00 0.00 37.36 2.18
2439 2612 7.220740 GGCTCATATAATAATCTCCCCTAAGC 58.779 42.308 0.00 0.00 0.00 3.09
2440 2613 7.147479 GGCTCATATAATAATCTCCCCTAAGCA 60.147 40.741 0.00 0.00 0.00 3.91
2441 2614 8.267894 GCTCATATAATAATCTCCCCTAAGCAA 58.732 37.037 0.00 0.00 0.00 3.91
2447 2620 7.410120 AATAATCTCCCCTAAGCAAAAACTG 57.590 36.000 0.00 0.00 0.00 3.16
2448 2621 4.657814 ATCTCCCCTAAGCAAAAACTGA 57.342 40.909 0.00 0.00 0.00 3.41
2449 2622 3.751518 TCTCCCCTAAGCAAAAACTGAC 58.248 45.455 0.00 0.00 0.00 3.51
2450 2623 3.394606 TCTCCCCTAAGCAAAAACTGACT 59.605 43.478 0.00 0.00 0.00 3.41
2451 2624 4.595781 TCTCCCCTAAGCAAAAACTGACTA 59.404 41.667 0.00 0.00 0.00 2.59
2452 2625 4.906618 TCCCCTAAGCAAAAACTGACTAG 58.093 43.478 0.00 0.00 0.00 2.57
2453 2626 4.010349 CCCCTAAGCAAAAACTGACTAGG 58.990 47.826 0.00 0.00 0.00 3.02
2454 2627 3.440522 CCCTAAGCAAAAACTGACTAGGC 59.559 47.826 0.00 0.00 0.00 3.93
2455 2628 3.440522 CCTAAGCAAAAACTGACTAGGCC 59.559 47.826 0.00 0.00 0.00 5.19
2456 2629 2.959465 AGCAAAAACTGACTAGGCCT 57.041 45.000 11.78 11.78 0.00 5.19
2457 2630 3.229697 AGCAAAAACTGACTAGGCCTT 57.770 42.857 12.58 0.00 0.00 4.35
2458 2631 2.887152 AGCAAAAACTGACTAGGCCTTG 59.113 45.455 12.58 12.86 0.00 3.61
2459 2632 2.623416 GCAAAAACTGACTAGGCCTTGT 59.377 45.455 20.32 20.32 0.00 3.16
2460 2633 3.818773 GCAAAAACTGACTAGGCCTTGTA 59.181 43.478 20.23 7.88 0.00 2.41
2461 2634 4.320275 GCAAAAACTGACTAGGCCTTGTAC 60.320 45.833 20.23 13.52 0.00 2.90
2462 2635 4.699925 AAAACTGACTAGGCCTTGTACA 57.300 40.909 20.23 16.93 0.00 2.90
2463 2636 4.699925 AAACTGACTAGGCCTTGTACAA 57.300 40.909 20.23 8.28 0.00 2.41
2464 2637 4.910458 AACTGACTAGGCCTTGTACAAT 57.090 40.909 20.23 7.29 0.00 2.71
2465 2638 4.207891 ACTGACTAGGCCTTGTACAATG 57.792 45.455 20.23 7.68 0.00 2.82
2466 2639 3.838317 ACTGACTAGGCCTTGTACAATGA 59.162 43.478 20.23 0.00 0.00 2.57
2467 2640 4.081420 ACTGACTAGGCCTTGTACAATGAG 60.081 45.833 20.23 5.81 0.00 2.90
2468 2641 3.198872 GACTAGGCCTTGTACAATGAGC 58.801 50.000 20.23 14.12 0.00 4.26
2469 2642 2.092914 ACTAGGCCTTGTACAATGAGCC 60.093 50.000 25.74 25.74 40.79 4.70
2470 2643 0.034089 AGGCCTTGTACAATGAGCCC 60.034 55.000 27.78 15.35 41.42 5.19
2471 2644 0.034089 GGCCTTGTACAATGAGCCCT 60.034 55.000 23.96 0.00 34.23 5.19
2472 2645 1.211949 GGCCTTGTACAATGAGCCCTA 59.788 52.381 23.96 0.00 34.23 3.53
2473 2646 2.289565 GCCTTGTACAATGAGCCCTAC 58.710 52.381 14.26 0.00 0.00 3.18
2474 2647 2.092914 GCCTTGTACAATGAGCCCTACT 60.093 50.000 14.26 0.00 0.00 2.57
2475 2648 3.134081 GCCTTGTACAATGAGCCCTACTA 59.866 47.826 14.26 0.00 0.00 1.82
2476 2649 4.383770 GCCTTGTACAATGAGCCCTACTAA 60.384 45.833 14.26 0.00 0.00 2.24
2477 2650 5.360591 CCTTGTACAATGAGCCCTACTAAG 58.639 45.833 9.13 0.00 0.00 2.18
2478 2651 4.402056 TGTACAATGAGCCCTACTAAGC 57.598 45.455 0.00 0.00 0.00 3.09
2479 2652 3.772572 TGTACAATGAGCCCTACTAAGCA 59.227 43.478 0.00 0.00 0.00 3.91
2480 2653 3.268023 ACAATGAGCCCTACTAAGCAC 57.732 47.619 0.00 0.00 0.00 4.40
2481 2654 2.092914 ACAATGAGCCCTACTAAGCACC 60.093 50.000 0.00 0.00 0.00 5.01
2482 2655 2.171448 CAATGAGCCCTACTAAGCACCT 59.829 50.000 0.00 0.00 0.00 4.00
2483 2656 1.952621 TGAGCCCTACTAAGCACCTT 58.047 50.000 0.00 0.00 0.00 3.50
2484 2657 1.555075 TGAGCCCTACTAAGCACCTTG 59.445 52.381 0.00 0.00 0.00 3.61
2485 2658 0.253327 AGCCCTACTAAGCACCTTGC 59.747 55.000 0.00 0.00 45.46 4.01
2494 2667 2.980233 GCACCTTGCAGCTTCCGT 60.980 61.111 0.00 0.00 44.26 4.69
2495 2668 2.555547 GCACCTTGCAGCTTCCGTT 61.556 57.895 0.00 0.00 44.26 4.44
2496 2669 1.576421 CACCTTGCAGCTTCCGTTC 59.424 57.895 0.00 0.00 0.00 3.95
2497 2670 1.961277 ACCTTGCAGCTTCCGTTCG 60.961 57.895 0.00 0.00 0.00 3.95
2498 2671 2.174349 CTTGCAGCTTCCGTTCGC 59.826 61.111 0.00 0.00 0.00 4.70
2499 2672 2.590291 TTGCAGCTTCCGTTCGCA 60.590 55.556 0.00 0.00 0.00 5.10
2500 2673 1.915614 CTTGCAGCTTCCGTTCGCAT 61.916 55.000 0.00 0.00 31.67 4.73
2501 2674 1.911293 TTGCAGCTTCCGTTCGCATC 61.911 55.000 0.00 0.00 31.67 3.91
2502 2675 2.390599 GCAGCTTCCGTTCGCATCA 61.391 57.895 0.00 0.00 0.00 3.07
2503 2676 1.712081 CAGCTTCCGTTCGCATCAG 59.288 57.895 0.00 0.00 0.00 2.90
2504 2677 1.016130 CAGCTTCCGTTCGCATCAGT 61.016 55.000 0.00 0.00 0.00 3.41
2505 2678 0.530744 AGCTTCCGTTCGCATCAGTA 59.469 50.000 0.00 0.00 0.00 2.74
2506 2679 0.924090 GCTTCCGTTCGCATCAGTAG 59.076 55.000 0.00 0.00 0.00 2.57
2507 2680 1.736032 GCTTCCGTTCGCATCAGTAGT 60.736 52.381 0.00 0.00 0.00 2.73
2508 2681 2.607187 CTTCCGTTCGCATCAGTAGTT 58.393 47.619 0.00 0.00 0.00 2.24
2509 2682 2.273370 TCCGTTCGCATCAGTAGTTC 57.727 50.000 0.00 0.00 0.00 3.01
2510 2683 1.542472 TCCGTTCGCATCAGTAGTTCA 59.458 47.619 0.00 0.00 0.00 3.18
2511 2684 2.165641 TCCGTTCGCATCAGTAGTTCAT 59.834 45.455 0.00 0.00 0.00 2.57
2512 2685 2.535984 CCGTTCGCATCAGTAGTTCATC 59.464 50.000 0.00 0.00 0.00 2.92
2513 2686 3.179048 CGTTCGCATCAGTAGTTCATCA 58.821 45.455 0.00 0.00 0.00 3.07
2514 2687 3.798878 CGTTCGCATCAGTAGTTCATCAT 59.201 43.478 0.00 0.00 0.00 2.45
2515 2688 4.085363 CGTTCGCATCAGTAGTTCATCATC 60.085 45.833 0.00 0.00 0.00 2.92
2516 2689 4.654091 TCGCATCAGTAGTTCATCATCA 57.346 40.909 0.00 0.00 0.00 3.07
2517 2690 4.614946 TCGCATCAGTAGTTCATCATCAG 58.385 43.478 0.00 0.00 0.00 2.90
2518 2691 4.098501 TCGCATCAGTAGTTCATCATCAGT 59.901 41.667 0.00 0.00 0.00 3.41
2519 2692 5.299279 TCGCATCAGTAGTTCATCATCAGTA 59.701 40.000 0.00 0.00 0.00 2.74
2520 2693 5.628606 CGCATCAGTAGTTCATCATCAGTAG 59.371 44.000 0.00 0.00 0.00 2.57
2521 2694 5.925397 GCATCAGTAGTTCATCATCAGTAGG 59.075 44.000 0.00 0.00 0.00 3.18
2522 2695 6.453943 CATCAGTAGTTCATCATCAGTAGGG 58.546 44.000 0.00 0.00 0.00 3.53
2523 2696 4.342378 TCAGTAGTTCATCATCAGTAGGGC 59.658 45.833 0.00 0.00 0.00 5.19
2524 2697 4.343526 CAGTAGTTCATCATCAGTAGGGCT 59.656 45.833 0.00 0.00 0.00 5.19
2525 2698 4.586841 AGTAGTTCATCATCAGTAGGGCTC 59.413 45.833 0.00 0.00 0.00 4.70
2544 2717 4.928615 GGCTCATATAGTCTTCTGATGTGC 59.071 45.833 0.00 0.00 37.26 4.57
2554 2727 6.705302 AGTCTTCTGATGTGCTCAAATCTAA 58.295 36.000 0.00 0.00 32.14 2.10
2598 2771 1.523758 AGATCGGTGAAGCACAAACC 58.476 50.000 0.00 0.00 35.86 3.27
2617 2791 6.017109 ACAAACCATATCGAATATCTTGTGCC 60.017 38.462 0.00 0.00 0.00 5.01
2659 2833 1.004277 GGGATCTGGGCGCCATATAAA 59.996 52.381 30.85 7.23 30.82 1.40
2660 2834 2.554344 GGGATCTGGGCGCCATATAAAA 60.554 50.000 30.85 6.03 30.82 1.52
2661 2835 3.356290 GGATCTGGGCGCCATATAAAAT 58.644 45.455 30.85 10.99 30.82 1.82
2662 2836 4.523083 GGATCTGGGCGCCATATAAAATA 58.477 43.478 30.85 2.46 30.82 1.40
2663 2837 4.335594 GGATCTGGGCGCCATATAAAATAC 59.664 45.833 30.85 6.94 30.82 1.89
2743 2919 1.040339 ACAGATCCGGGACAGCTCTC 61.040 60.000 0.00 0.00 0.00 3.20
2787 2963 1.211456 AAGATCAGAGGCTCCCAAGG 58.789 55.000 11.71 0.00 0.00 3.61
2788 2964 0.341258 AGATCAGAGGCTCCCAAGGA 59.659 55.000 11.71 1.94 0.00 3.36
2789 2965 1.207791 GATCAGAGGCTCCCAAGGAA 58.792 55.000 11.71 0.00 0.00 3.36
2790 2966 1.561542 GATCAGAGGCTCCCAAGGAAA 59.438 52.381 11.71 0.00 0.00 3.13
2791 2967 1.444933 TCAGAGGCTCCCAAGGAAAA 58.555 50.000 11.71 0.00 0.00 2.29
2792 2968 1.352352 TCAGAGGCTCCCAAGGAAAAG 59.648 52.381 11.71 0.00 0.00 2.27
2793 2969 0.701147 AGAGGCTCCCAAGGAAAAGG 59.299 55.000 11.71 0.00 0.00 3.11
2794 2970 0.967887 GAGGCTCCCAAGGAAAAGGC 60.968 60.000 2.15 0.00 0.00 4.35
2795 2971 1.077445 GGCTCCCAAGGAAAAGGCT 59.923 57.895 0.00 0.00 0.00 4.58
2796 2972 0.542938 GGCTCCCAAGGAAAAGGCTT 60.543 55.000 0.00 0.00 0.00 4.35
2800 2976 1.216678 TCCCAAGGAAAAGGCTTGACA 59.783 47.619 0.00 0.00 0.00 3.58
2814 2990 5.112686 AGGCTTGACACGAGATATTTCTTC 58.887 41.667 0.00 0.00 30.30 2.87
2815 2991 4.271291 GGCTTGACACGAGATATTTCTTCC 59.729 45.833 0.00 0.00 30.30 3.46
2816 2992 5.112686 GCTTGACACGAGATATTTCTTCCT 58.887 41.667 0.00 0.00 30.30 3.36
2817 2993 5.582665 GCTTGACACGAGATATTTCTTCCTT 59.417 40.000 0.00 0.00 30.30 3.36
2818 2994 6.456181 GCTTGACACGAGATATTTCTTCCTTG 60.456 42.308 0.00 0.00 30.30 3.61
2819 2995 6.037786 TGACACGAGATATTTCTTCCTTGT 57.962 37.500 0.00 0.00 30.30 3.16
2820 2996 5.869344 TGACACGAGATATTTCTTCCTTGTG 59.131 40.000 0.00 0.00 43.30 3.33
2821 2997 5.178797 ACACGAGATATTTCTTCCTTGTGG 58.821 41.667 0.00 0.00 42.45 4.17
2822 2998 4.572389 CACGAGATATTTCTTCCTTGTGGG 59.428 45.833 0.00 0.00 37.38 4.61
2823 2999 4.469945 ACGAGATATTTCTTCCTTGTGGGA 59.530 41.667 0.00 0.00 43.41 4.37
2824 3000 5.131142 ACGAGATATTTCTTCCTTGTGGGAT 59.869 40.000 0.00 0.00 44.66 3.85
2825 3001 6.058183 CGAGATATTTCTTCCTTGTGGGATT 58.942 40.000 0.00 0.00 44.66 3.01
2834 3010 3.902218 TCCTTGTGGGATTGATTCATCC 58.098 45.455 6.59 6.59 39.58 3.51
2894 3085 4.436998 GACGGCCGGAGACACCAG 62.437 72.222 31.76 0.00 38.90 4.00
2897 3088 4.767255 GGCCGGAGACACCAGCAG 62.767 72.222 5.05 0.00 43.36 4.24
2898 3089 3.695606 GCCGGAGACACCAGCAGA 61.696 66.667 5.05 0.00 41.38 4.26
2899 3090 3.023949 GCCGGAGACACCAGCAGAT 62.024 63.158 5.05 0.00 41.38 2.90
2929 3120 2.124570 CCATTCCGTCCAGCTGGG 60.125 66.667 32.23 17.17 35.41 4.45
2930 3121 2.124570 CATTCCGTCCAGCTGGGG 60.125 66.667 32.23 25.28 37.22 4.96
2942 3133 2.616458 GCTGGGGTGGGGTTCTCAT 61.616 63.158 0.00 0.00 0.00 2.90
2943 3134 2.087248 CTGGGGTGGGGTTCTCATT 58.913 57.895 0.00 0.00 0.00 2.57
2944 3135 0.034089 CTGGGGTGGGGTTCTCATTC 60.034 60.000 0.00 0.00 0.00 2.67
2945 3136 0.477597 TGGGGTGGGGTTCTCATTCT 60.478 55.000 0.00 0.00 0.00 2.40
3012 3203 7.015292 ACAAATTCCCTCCTTCCTCTTTAAAAC 59.985 37.037 0.00 0.00 0.00 2.43
3028 3220 5.585820 TTAAAACAAGGGTTTGTCACTCC 57.414 39.130 0.00 0.00 46.54 3.85
3029 3221 1.675552 AACAAGGGTTTGTCACTCCG 58.324 50.000 0.00 0.00 46.54 4.63
3038 3230 3.074412 GTTTGTCACTCCGTGATTGGAT 58.926 45.455 0.00 0.00 44.63 3.41
3039 3231 3.417069 TTGTCACTCCGTGATTGGATT 57.583 42.857 0.00 0.00 44.63 3.01
3040 3232 2.698803 TGTCACTCCGTGATTGGATTG 58.301 47.619 0.00 0.00 44.63 2.67
3041 3233 2.009774 GTCACTCCGTGATTGGATTGG 58.990 52.381 0.00 0.00 44.63 3.16
3042 3234 1.905894 TCACTCCGTGATTGGATTGGA 59.094 47.619 1.05 0.00 38.75 3.53
3044 3236 2.698855 CTCCGTGATTGGATTGGAGT 57.301 50.000 0.00 0.00 41.04 3.85
3045 3237 2.283298 CTCCGTGATTGGATTGGAGTG 58.717 52.381 0.00 0.00 41.04 3.51
3046 3238 1.905894 TCCGTGATTGGATTGGAGTGA 59.094 47.619 0.00 0.00 31.53 3.41
3047 3239 2.009774 CCGTGATTGGATTGGAGTGAC 58.990 52.381 0.00 0.00 0.00 3.67
3048 3240 1.660607 CGTGATTGGATTGGAGTGACG 59.339 52.381 0.00 0.00 0.00 4.35
3049 3241 1.398390 GTGATTGGATTGGAGTGACGC 59.602 52.381 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.065281 GTCGGGGACACGTCAGGG 62.065 72.222 0.00 0.00 34.94 4.45
15 16 4.415332 CGTCGGGGACACGTCAGG 62.415 72.222 0.00 0.00 34.94 3.86
16 17 3.359523 TCGTCGGGGACACGTCAG 61.360 66.667 0.00 0.00 36.62 3.51
17 18 3.663176 GTCGTCGGGGACACGTCA 61.663 66.667 0.00 0.00 36.91 4.35
18 19 4.410743 GGTCGTCGGGGACACGTC 62.411 72.222 8.63 0.00 38.70 4.34
20 21 4.415332 CTGGTCGTCGGGGACACG 62.415 72.222 8.63 0.00 38.70 4.49
21 22 2.987547 TCTGGTCGTCGGGGACAC 60.988 66.667 8.63 0.62 38.70 3.67
22 23 2.675423 CTCTGGTCGTCGGGGACA 60.675 66.667 8.63 0.00 38.70 4.02
23 24 2.360852 TCTCTGGTCGTCGGGGAC 60.361 66.667 0.00 0.00 36.18 4.46
24 25 2.360852 GTCTCTGGTCGTCGGGGA 60.361 66.667 0.00 0.00 0.00 4.81
25 26 3.450115 GGTCTCTGGTCGTCGGGG 61.450 72.222 0.00 0.00 0.00 5.73
26 27 3.450115 GGGTCTCTGGTCGTCGGG 61.450 72.222 0.00 0.00 0.00 5.14
27 28 2.675423 TGGGTCTCTGGTCGTCGG 60.675 66.667 0.00 0.00 0.00 4.79
28 29 2.878429 CTGGGTCTCTGGTCGTCG 59.122 66.667 0.00 0.00 0.00 5.12
29 30 2.574399 GCTGGGTCTCTGGTCGTC 59.426 66.667 0.00 0.00 0.00 4.20
30 31 3.374402 CGCTGGGTCTCTGGTCGT 61.374 66.667 0.00 0.00 0.00 4.34
31 32 3.057547 CTCGCTGGGTCTCTGGTCG 62.058 68.421 0.00 0.00 0.00 4.79
32 33 2.888863 CTCGCTGGGTCTCTGGTC 59.111 66.667 0.00 0.00 0.00 4.02
33 34 3.386237 GCTCGCTGGGTCTCTGGT 61.386 66.667 0.00 0.00 0.00 4.00
34 35 4.504916 CGCTCGCTGGGTCTCTGG 62.505 72.222 0.00 0.00 0.00 3.86
35 36 4.504916 CCGCTCGCTGGGTCTCTG 62.505 72.222 0.00 0.00 0.00 3.35
40 41 4.947147 TTTTGCCGCTCGCTGGGT 62.947 61.111 0.00 0.00 38.78 4.51
41 42 3.669344 TTTTTGCCGCTCGCTGGG 61.669 61.111 0.00 0.00 38.78 4.45
56 57 0.676782 CACCCGAGGGCGAGATTTTT 60.677 55.000 8.33 0.00 40.82 1.94
57 58 1.078426 CACCCGAGGGCGAGATTTT 60.078 57.895 8.33 0.00 40.82 1.82
58 59 2.584608 CACCCGAGGGCGAGATTT 59.415 61.111 8.33 0.00 40.82 2.17
59 60 3.470888 CCACCCGAGGGCGAGATT 61.471 66.667 8.33 0.00 40.82 2.40
66 67 3.697747 TTACGTGCCACCCGAGGG 61.698 66.667 6.63 6.63 42.03 4.30
67 68 2.433664 GTTACGTGCCACCCGAGG 60.434 66.667 0.00 0.00 0.00 4.63
68 69 0.672401 AATGTTACGTGCCACCCGAG 60.672 55.000 0.00 0.00 0.00 4.63
69 70 0.607112 TAATGTTACGTGCCACCCGA 59.393 50.000 0.00 0.00 0.00 5.14
70 71 1.003851 CTAATGTTACGTGCCACCCG 58.996 55.000 0.00 0.00 0.00 5.28
71 72 1.375551 CCTAATGTTACGTGCCACCC 58.624 55.000 0.00 0.00 0.00 4.61
72 73 0.730840 GCCTAATGTTACGTGCCACC 59.269 55.000 0.00 0.00 0.00 4.61
73 74 0.372334 CGCCTAATGTTACGTGCCAC 59.628 55.000 0.00 0.00 0.00 5.01
74 75 0.741574 CCGCCTAATGTTACGTGCCA 60.742 55.000 0.00 0.00 0.00 4.92
75 76 2.011453 CCGCCTAATGTTACGTGCC 58.989 57.895 0.00 0.00 0.00 5.01
76 77 1.350665 GCCGCCTAATGTTACGTGC 59.649 57.895 0.00 0.00 0.00 5.34
77 78 1.758319 CGGCCGCCTAATGTTACGTG 61.758 60.000 14.67 0.00 0.00 4.49
78 79 1.519898 CGGCCGCCTAATGTTACGT 60.520 57.895 14.67 0.00 0.00 3.57
79 80 0.599204 ATCGGCCGCCTAATGTTACG 60.599 55.000 23.51 0.00 0.00 3.18
80 81 1.263217 CAATCGGCCGCCTAATGTTAC 59.737 52.381 23.51 0.00 0.00 2.50
81 82 1.588674 CAATCGGCCGCCTAATGTTA 58.411 50.000 23.51 0.00 0.00 2.41
82 83 1.724582 GCAATCGGCCGCCTAATGTT 61.725 55.000 23.51 3.21 36.11 2.71
83 84 2.186826 GCAATCGGCCGCCTAATGT 61.187 57.895 23.51 0.00 36.11 2.71
84 85 2.639286 GCAATCGGCCGCCTAATG 59.361 61.111 23.51 15.03 36.11 1.90
85 86 2.972505 CGCAATCGGCCGCCTAAT 60.973 61.111 23.51 5.58 40.31 1.73
94 95 4.437959 TTGTTCGCGCGCAATCGG 62.438 61.111 32.61 14.68 35.95 4.18
95 96 2.934024 CTTGTTCGCGCGCAATCG 60.934 61.111 32.61 15.11 39.07 3.34
96 97 2.574212 CCTTGTTCGCGCGCAATC 60.574 61.111 32.61 19.53 0.00 2.67
106 107 2.027625 CACGTCCCGCTCCTTGTTC 61.028 63.158 0.00 0.00 0.00 3.18
155 156 5.385615 CGCAACGACGAGGTTTTTAAATTTC 60.386 40.000 0.00 0.00 34.06 2.17
169 170 1.066093 TTTGACCTCGCAACGACGA 59.934 52.632 0.00 0.00 40.36 4.20
298 301 1.179174 AAAGAGAAAGCGGGGGTTGC 61.179 55.000 0.00 0.00 0.00 4.17
312 326 4.455124 ACGCGAATTCGAAAAGAAAAGAG 58.545 39.130 31.01 8.62 42.91 2.85
339 353 1.156645 GGTCTGATGCTGATGCCGAC 61.157 60.000 0.00 0.00 38.71 4.79
341 355 1.890979 GGGTCTGATGCTGATGCCG 60.891 63.158 0.00 0.00 38.71 5.69
342 356 1.890979 CGGGTCTGATGCTGATGCC 60.891 63.158 0.00 0.00 38.71 4.40
343 357 1.144716 TCGGGTCTGATGCTGATGC 59.855 57.895 0.00 0.00 40.20 3.91
344 358 0.873312 CGTCGGGTCTGATGCTGATG 60.873 60.000 0.00 0.00 0.00 3.07
345 359 1.439228 CGTCGGGTCTGATGCTGAT 59.561 57.895 0.00 0.00 0.00 2.90
346 360 2.710902 CCGTCGGGTCTGATGCTGA 61.711 63.158 2.34 0.00 0.00 4.26
347 361 2.202797 CCGTCGGGTCTGATGCTG 60.203 66.667 2.34 0.00 0.00 4.41
348 362 1.982395 TTCCGTCGGGTCTGATGCT 60.982 57.895 12.29 0.00 33.83 3.79
349 363 1.810030 GTTCCGTCGGGTCTGATGC 60.810 63.158 12.29 0.00 33.83 3.91
444 467 1.673337 GTGGCCCGGGAGTGTAAAC 60.673 63.158 29.31 2.59 0.00 2.01
555 591 1.740585 TGTGGTTGTGTTGAAAGTCCG 59.259 47.619 0.00 0.00 0.00 4.79
568 604 6.992063 ATCAAATCTAAGCTAGTGTGGTTG 57.008 37.500 0.00 0.00 0.00 3.77
571 607 6.203723 GCCTAATCAAATCTAAGCTAGTGTGG 59.796 42.308 0.00 0.00 0.00 4.17
594 630 5.164954 CCTCGCTAATCAACTAATCTAGCC 58.835 45.833 0.00 0.00 33.02 3.93
595 631 5.164954 CCCTCGCTAATCAACTAATCTAGC 58.835 45.833 0.00 0.00 33.24 3.42
650 689 3.086600 GGCTCACCCTCTCCCCAG 61.087 72.222 0.00 0.00 0.00 4.45
822 872 1.040646 GCCCCCTTATAAAGCTTGGC 58.959 55.000 0.00 1.44 0.00 4.52
847 897 2.363147 AGGAGAGGAGTCCGTGGC 60.363 66.667 2.76 0.00 42.05 5.01
879 929 0.725133 AGAAGATGAAGGGGAGGGGA 59.275 55.000 0.00 0.00 0.00 4.81
880 930 1.213926 CAAGAAGATGAAGGGGAGGGG 59.786 57.143 0.00 0.00 0.00 4.79
881 931 1.918957 ACAAGAAGATGAAGGGGAGGG 59.081 52.381 0.00 0.00 0.00 4.30
882 932 3.432890 GCTACAAGAAGATGAAGGGGAGG 60.433 52.174 0.00 0.00 0.00 4.30
883 933 3.432890 GGCTACAAGAAGATGAAGGGGAG 60.433 52.174 0.00 0.00 0.00 4.30
884 934 2.505819 GGCTACAAGAAGATGAAGGGGA 59.494 50.000 0.00 0.00 0.00 4.81
932 990 4.608951 GCCTGAATTCTGAGATGAAATGC 58.391 43.478 13.45 2.03 0.00 3.56
953 1011 0.391263 CCCCTAGACAAGAACACCGC 60.391 60.000 0.00 0.00 0.00 5.68
972 1030 4.075682 CCAAGAAACCCCTCTTCTTCTTC 58.924 47.826 0.00 0.00 40.37 2.87
973 1031 3.752218 GCCAAGAAACCCCTCTTCTTCTT 60.752 47.826 0.00 0.00 40.37 2.52
974 1032 2.224892 GCCAAGAAACCCCTCTTCTTCT 60.225 50.000 0.00 0.00 40.37 2.85
975 1033 2.163509 GCCAAGAAACCCCTCTTCTTC 58.836 52.381 0.00 0.00 40.37 2.87
976 1034 1.545651 CGCCAAGAAACCCCTCTTCTT 60.546 52.381 0.00 0.00 42.52 2.52
977 1035 0.036875 CGCCAAGAAACCCCTCTTCT 59.963 55.000 0.00 0.00 33.25 2.85
978 1036 0.250770 ACGCCAAGAAACCCCTCTTC 60.251 55.000 0.00 0.00 33.25 2.87
1115 1173 2.449518 TGACCTTCCACCTGGCCA 60.450 61.111 4.71 4.71 34.44 5.36
1245 1303 1.112315 CGTCCTCCATCTCCCTCCTG 61.112 65.000 0.00 0.00 0.00 3.86
1377 1435 4.521062 AGCTCGTGCATCCGCTCC 62.521 66.667 12.58 0.00 42.74 4.70
1422 1480 2.997897 GTCCAGGACTCGGGCTGT 60.998 66.667 12.94 0.00 0.00 4.40
1641 1699 2.271497 TCGGAGGAGAGGACGACC 59.729 66.667 0.00 0.00 0.00 4.79
1869 1927 2.665185 GTGACCACGTCCCACAGC 60.665 66.667 6.61 0.00 0.00 4.40
1886 1944 3.114616 CGCAGGCTGTCTCGTTGG 61.115 66.667 17.16 0.00 0.00 3.77
1986 2044 1.865865 TGTTGTCCGAGCTGTTCTTC 58.134 50.000 0.00 0.00 0.00 2.87
2059 2117 1.913951 ATGGAAGATCACGGCAGCCA 61.914 55.000 13.30 0.00 0.00 4.75
2060 2118 0.749454 AATGGAAGATCACGGCAGCC 60.749 55.000 0.00 0.00 0.00 4.85
2088 2146 8.144478 TGACCCTACTGTTACTACTATACTACG 58.856 40.741 0.00 0.00 0.00 3.51
2111 2172 8.198109 TCACTATAGAGCTAGTTTTGGATTGAC 58.802 37.037 6.78 0.00 29.41 3.18
2179 2242 6.284891 TCCAGGGAGAAATATTGCAAAAAG 57.715 37.500 1.71 0.00 0.00 2.27
2290 2354 5.551305 TCCTTCTGATGAACTGAACTTCA 57.449 39.130 0.00 0.00 34.65 3.02
2313 2377 7.761249 CCTTCAGAATTTGAACAAAAACTGACT 59.239 33.333 23.83 9.93 40.82 3.41
2342 2406 2.220313 GGAAGCTGCAGATCTGAATCC 58.780 52.381 27.04 15.89 31.78 3.01
2382 2446 5.221925 GGCCTTGTATCATCCTCCATCTAAA 60.222 44.000 0.00 0.00 0.00 1.85
2415 2588 7.796054 TGCTTAGGGGAGATTATTATATGAGC 58.204 38.462 0.00 0.00 0.00 4.26
2421 2594 9.136323 CAGTTTTTGCTTAGGGGAGATTATTAT 57.864 33.333 0.00 0.00 0.00 1.28
2422 2595 8.333235 TCAGTTTTTGCTTAGGGGAGATTATTA 58.667 33.333 0.00 0.00 0.00 0.98
2423 2596 7.122799 GTCAGTTTTTGCTTAGGGGAGATTATT 59.877 37.037 0.00 0.00 0.00 1.40
2424 2597 6.603599 GTCAGTTTTTGCTTAGGGGAGATTAT 59.396 38.462 0.00 0.00 0.00 1.28
2425 2598 5.944007 GTCAGTTTTTGCTTAGGGGAGATTA 59.056 40.000 0.00 0.00 0.00 1.75
2426 2599 4.767409 GTCAGTTTTTGCTTAGGGGAGATT 59.233 41.667 0.00 0.00 0.00 2.40
2427 2600 4.043435 AGTCAGTTTTTGCTTAGGGGAGAT 59.957 41.667 0.00 0.00 0.00 2.75
2428 2601 3.394606 AGTCAGTTTTTGCTTAGGGGAGA 59.605 43.478 0.00 0.00 0.00 3.71
2429 2602 3.756117 AGTCAGTTTTTGCTTAGGGGAG 58.244 45.455 0.00 0.00 0.00 4.30
2430 2603 3.876309 AGTCAGTTTTTGCTTAGGGGA 57.124 42.857 0.00 0.00 0.00 4.81
2431 2604 4.010349 CCTAGTCAGTTTTTGCTTAGGGG 58.990 47.826 0.00 0.00 32.94 4.79
2432 2605 3.440522 GCCTAGTCAGTTTTTGCTTAGGG 59.559 47.826 0.00 0.00 35.15 3.53
2433 2606 3.440522 GGCCTAGTCAGTTTTTGCTTAGG 59.559 47.826 0.00 0.00 36.48 2.69
2434 2607 4.327680 AGGCCTAGTCAGTTTTTGCTTAG 58.672 43.478 1.29 0.00 0.00 2.18
2435 2608 4.367039 AGGCCTAGTCAGTTTTTGCTTA 57.633 40.909 1.29 0.00 0.00 3.09
2436 2609 3.229697 AGGCCTAGTCAGTTTTTGCTT 57.770 42.857 1.29 0.00 0.00 3.91
2437 2610 2.887152 CAAGGCCTAGTCAGTTTTTGCT 59.113 45.455 5.16 0.00 0.00 3.91
2438 2611 2.623416 ACAAGGCCTAGTCAGTTTTTGC 59.377 45.455 5.16 0.00 0.00 3.68
2439 2612 4.819630 TGTACAAGGCCTAGTCAGTTTTTG 59.180 41.667 5.16 0.00 0.00 2.44
2440 2613 5.043737 TGTACAAGGCCTAGTCAGTTTTT 57.956 39.130 5.16 0.00 0.00 1.94
2441 2614 4.699925 TGTACAAGGCCTAGTCAGTTTT 57.300 40.909 5.16 0.00 0.00 2.43
2442 2615 4.699925 TTGTACAAGGCCTAGTCAGTTT 57.300 40.909 5.16 0.00 0.00 2.66
2443 2616 4.286032 TCATTGTACAAGGCCTAGTCAGTT 59.714 41.667 15.24 0.00 0.00 3.16
2444 2617 3.838317 TCATTGTACAAGGCCTAGTCAGT 59.162 43.478 15.24 2.59 0.00 3.41
2445 2618 4.437239 CTCATTGTACAAGGCCTAGTCAG 58.563 47.826 15.24 2.26 0.00 3.51
2446 2619 3.369471 GCTCATTGTACAAGGCCTAGTCA 60.369 47.826 15.24 0.03 0.00 3.41
2447 2620 3.198872 GCTCATTGTACAAGGCCTAGTC 58.801 50.000 15.24 0.00 0.00 2.59
2448 2621 2.092914 GGCTCATTGTACAAGGCCTAGT 60.093 50.000 27.88 6.35 36.96 2.57
2449 2622 2.565841 GGCTCATTGTACAAGGCCTAG 58.434 52.381 27.88 17.73 36.96 3.02
2450 2623 2.710096 GGCTCATTGTACAAGGCCTA 57.290 50.000 27.88 10.15 36.96 3.93
2451 2624 3.577389 GGCTCATTGTACAAGGCCT 57.423 52.632 27.88 0.00 36.96 5.19
2452 2625 2.493547 GGGCTCATTGTACAAGGCC 58.506 57.895 27.55 27.55 46.79 5.19
2453 2626 2.092914 AGTAGGGCTCATTGTACAAGGC 60.093 50.000 15.24 16.42 35.02 4.35
2454 2627 3.914426 AGTAGGGCTCATTGTACAAGG 57.086 47.619 13.96 13.96 0.00 3.61
2455 2628 4.811557 GCTTAGTAGGGCTCATTGTACAAG 59.188 45.833 14.65 6.58 0.00 3.16
2456 2629 4.224147 TGCTTAGTAGGGCTCATTGTACAA 59.776 41.667 11.41 11.41 0.00 2.41
2457 2630 3.772572 TGCTTAGTAGGGCTCATTGTACA 59.227 43.478 0.00 0.00 0.00 2.90
2458 2631 4.120589 GTGCTTAGTAGGGCTCATTGTAC 58.879 47.826 0.00 0.00 0.00 2.90
2459 2632 3.134081 GGTGCTTAGTAGGGCTCATTGTA 59.866 47.826 0.00 0.00 0.00 2.41
2460 2633 2.092914 GGTGCTTAGTAGGGCTCATTGT 60.093 50.000 0.00 0.00 0.00 2.71
2461 2634 2.171448 AGGTGCTTAGTAGGGCTCATTG 59.829 50.000 0.00 0.00 0.00 2.82
2462 2635 2.482494 AGGTGCTTAGTAGGGCTCATT 58.518 47.619 0.00 0.00 0.00 2.57
2463 2636 2.171448 CAAGGTGCTTAGTAGGGCTCAT 59.829 50.000 0.00 0.00 0.00 2.90
2464 2637 1.555075 CAAGGTGCTTAGTAGGGCTCA 59.445 52.381 0.00 0.00 0.00 4.26
2465 2638 1.744114 GCAAGGTGCTTAGTAGGGCTC 60.744 57.143 0.00 0.00 40.96 4.70
2466 2639 0.253327 GCAAGGTGCTTAGTAGGGCT 59.747 55.000 0.00 0.00 40.96 5.19
2467 2640 0.035439 TGCAAGGTGCTTAGTAGGGC 60.035 55.000 1.43 0.00 45.31 5.19
2468 2641 2.014068 GCTGCAAGGTGCTTAGTAGGG 61.014 57.143 1.43 0.00 45.31 3.53
2469 2642 1.373570 GCTGCAAGGTGCTTAGTAGG 58.626 55.000 1.43 0.00 45.31 3.18
2480 2653 2.863153 CGAACGGAAGCTGCAAGG 59.137 61.111 1.02 0.00 0.00 3.61
2481 2654 1.915614 ATGCGAACGGAAGCTGCAAG 61.916 55.000 1.02 0.00 38.84 4.01
2482 2655 1.911293 GATGCGAACGGAAGCTGCAA 61.911 55.000 1.02 0.00 38.84 4.08
2483 2656 2.358615 ATGCGAACGGAAGCTGCA 60.359 55.556 1.02 0.00 39.50 4.41
2484 2657 2.301902 CTGATGCGAACGGAAGCTGC 62.302 60.000 0.00 0.00 0.00 5.25
2485 2658 1.016130 ACTGATGCGAACGGAAGCTG 61.016 55.000 0.00 0.00 0.00 4.24
2486 2659 0.530744 TACTGATGCGAACGGAAGCT 59.469 50.000 0.00 0.00 0.00 3.74
2487 2660 0.924090 CTACTGATGCGAACGGAAGC 59.076 55.000 0.00 0.00 0.00 3.86
2488 2661 2.279582 ACTACTGATGCGAACGGAAG 57.720 50.000 0.00 0.00 0.00 3.46
2489 2662 2.029739 TGAACTACTGATGCGAACGGAA 60.030 45.455 0.00 0.00 0.00 4.30
2490 2663 1.542472 TGAACTACTGATGCGAACGGA 59.458 47.619 0.00 0.00 0.00 4.69
2491 2664 1.990799 TGAACTACTGATGCGAACGG 58.009 50.000 0.00 0.00 0.00 4.44
2492 2665 3.179048 TGATGAACTACTGATGCGAACG 58.821 45.455 0.00 0.00 0.00 3.95
2493 2666 4.805719 TGATGATGAACTACTGATGCGAAC 59.194 41.667 0.00 0.00 0.00 3.95
2494 2667 5.009854 TGATGATGAACTACTGATGCGAA 57.990 39.130 0.00 0.00 0.00 4.70
2495 2668 4.098501 ACTGATGATGAACTACTGATGCGA 59.901 41.667 0.00 0.00 0.00 5.10
2496 2669 4.366586 ACTGATGATGAACTACTGATGCG 58.633 43.478 0.00 0.00 0.00 4.73
2497 2670 5.925397 CCTACTGATGATGAACTACTGATGC 59.075 44.000 0.00 0.00 0.00 3.91
2498 2671 6.453943 CCCTACTGATGATGAACTACTGATG 58.546 44.000 0.00 0.00 0.00 3.07
2499 2672 5.011533 GCCCTACTGATGATGAACTACTGAT 59.988 44.000 0.00 0.00 0.00 2.90
2500 2673 4.342378 GCCCTACTGATGATGAACTACTGA 59.658 45.833 0.00 0.00 0.00 3.41
2501 2674 4.343526 AGCCCTACTGATGATGAACTACTG 59.656 45.833 0.00 0.00 0.00 2.74
2502 2675 4.551671 AGCCCTACTGATGATGAACTACT 58.448 43.478 0.00 0.00 0.00 2.57
2503 2676 4.342378 TGAGCCCTACTGATGATGAACTAC 59.658 45.833 0.00 0.00 0.00 2.73
2504 2677 4.546674 TGAGCCCTACTGATGATGAACTA 58.453 43.478 0.00 0.00 0.00 2.24
2505 2678 3.378512 TGAGCCCTACTGATGATGAACT 58.621 45.455 0.00 0.00 0.00 3.01
2506 2679 3.827008 TGAGCCCTACTGATGATGAAC 57.173 47.619 0.00 0.00 0.00 3.18
2507 2680 6.956435 ACTATATGAGCCCTACTGATGATGAA 59.044 38.462 0.00 0.00 0.00 2.57
2508 2681 6.497640 ACTATATGAGCCCTACTGATGATGA 58.502 40.000 0.00 0.00 0.00 2.92
2509 2682 6.606796 AGACTATATGAGCCCTACTGATGATG 59.393 42.308 0.00 0.00 0.00 3.07
2510 2683 6.740693 AGACTATATGAGCCCTACTGATGAT 58.259 40.000 0.00 0.00 0.00 2.45
2511 2684 6.146140 AGACTATATGAGCCCTACTGATGA 57.854 41.667 0.00 0.00 0.00 2.92
2512 2685 6.663093 AGAAGACTATATGAGCCCTACTGATG 59.337 42.308 0.00 0.00 0.00 3.07
2513 2686 6.663093 CAGAAGACTATATGAGCCCTACTGAT 59.337 42.308 0.00 0.00 0.00 2.90
2514 2687 6.007076 CAGAAGACTATATGAGCCCTACTGA 58.993 44.000 0.00 0.00 0.00 3.41
2515 2688 6.007076 TCAGAAGACTATATGAGCCCTACTG 58.993 44.000 0.00 0.00 0.00 2.74
2516 2689 6.207509 TCAGAAGACTATATGAGCCCTACT 57.792 41.667 0.00 0.00 0.00 2.57
2517 2690 6.435904 ACATCAGAAGACTATATGAGCCCTAC 59.564 42.308 0.00 0.00 0.00 3.18
2518 2691 6.435591 CACATCAGAAGACTATATGAGCCCTA 59.564 42.308 0.00 0.00 0.00 3.53
2519 2692 5.245751 CACATCAGAAGACTATATGAGCCCT 59.754 44.000 0.00 0.00 0.00 5.19
2520 2693 5.477510 CACATCAGAAGACTATATGAGCCC 58.522 45.833 0.00 0.00 0.00 5.19
2521 2694 4.928615 GCACATCAGAAGACTATATGAGCC 59.071 45.833 0.00 0.00 33.60 4.70
2522 2695 5.782047 AGCACATCAGAAGACTATATGAGC 58.218 41.667 0.00 0.00 36.52 4.26
2523 2696 6.979465 TGAGCACATCAGAAGACTATATGAG 58.021 40.000 0.00 0.00 32.77 2.90
2524 2697 6.966534 TGAGCACATCAGAAGACTATATGA 57.033 37.500 0.00 0.00 32.77 2.15
2525 2698 8.604640 ATTTGAGCACATCAGAAGACTATATG 57.395 34.615 0.00 0.00 39.68 1.78
2554 2727 9.270640 CTAACGATCAGTACCTAGTGTAATACT 57.729 37.037 0.00 0.00 43.56 2.12
2575 2748 1.990799 TGTGCTTCACCGATCTAACG 58.009 50.000 0.00 0.00 32.73 3.18
2598 2771 4.091945 CGGTGGCACAAGATATTCGATATG 59.908 45.833 20.82 0.00 44.16 1.78
2617 2791 4.911901 TTTTTGGGTCCTCCGGTG 57.088 55.556 0.00 0.00 38.76 4.94
2695 2869 9.007901 CCTTTGATTTCATCTCTTTTCTGTAGT 57.992 33.333 0.00 0.00 0.00 2.73
2696 2870 8.457261 CCCTTTGATTTCATCTCTTTTCTGTAG 58.543 37.037 0.00 0.00 0.00 2.74
2697 2871 8.163408 TCCCTTTGATTTCATCTCTTTTCTGTA 58.837 33.333 0.00 0.00 0.00 2.74
2698 2872 7.006509 TCCCTTTGATTTCATCTCTTTTCTGT 58.993 34.615 0.00 0.00 0.00 3.41
2699 2873 7.458409 TCCCTTTGATTTCATCTCTTTTCTG 57.542 36.000 0.00 0.00 0.00 3.02
2700 2874 7.506938 TGTTCCCTTTGATTTCATCTCTTTTCT 59.493 33.333 0.00 0.00 0.00 2.52
2701 2875 7.661040 TGTTCCCTTTGATTTCATCTCTTTTC 58.339 34.615 0.00 0.00 0.00 2.29
2702 2876 7.506938 TCTGTTCCCTTTGATTTCATCTCTTTT 59.493 33.333 0.00 0.00 0.00 2.27
2703 2877 7.006509 TCTGTTCCCTTTGATTTCATCTCTTT 58.993 34.615 0.00 0.00 0.00 2.52
2706 2880 6.039159 GGATCTGTTCCCTTTGATTTCATCTC 59.961 42.308 0.00 0.00 38.75 2.75
2721 2897 1.153349 GCTGTCCCGGATCTGTTCC 60.153 63.158 0.73 0.00 41.59 3.62
2743 2919 4.430423 GTCTTCACGCAAGCGCCG 62.430 66.667 15.09 2.67 44.19 6.46
2745 2921 2.802346 CTTCGTCTTCACGCAAGCGC 62.802 60.000 15.09 0.00 46.28 5.92
2767 2943 1.563410 CCTTGGGAGCCTCTGATCTTT 59.437 52.381 0.00 0.00 0.00 2.52
2787 2963 5.803020 AATATCTCGTGTCAAGCCTTTTC 57.197 39.130 0.00 0.00 0.00 2.29
2788 2964 5.940470 AGAAATATCTCGTGTCAAGCCTTTT 59.060 36.000 0.00 0.00 0.00 2.27
2789 2965 5.491982 AGAAATATCTCGTGTCAAGCCTTT 58.508 37.500 0.00 0.00 0.00 3.11
2790 2966 5.091261 AGAAATATCTCGTGTCAAGCCTT 57.909 39.130 0.00 0.00 0.00 4.35
2791 2967 4.744795 AGAAATATCTCGTGTCAAGCCT 57.255 40.909 0.00 0.00 0.00 4.58
2792 2968 4.271291 GGAAGAAATATCTCGTGTCAAGCC 59.729 45.833 0.00 0.00 33.77 4.35
2793 2969 5.112686 AGGAAGAAATATCTCGTGTCAAGC 58.887 41.667 0.00 0.00 33.77 4.01
2794 2970 6.591834 ACAAGGAAGAAATATCTCGTGTCAAG 59.408 38.462 0.00 0.00 33.77 3.02
2795 2971 6.368791 CACAAGGAAGAAATATCTCGTGTCAA 59.631 38.462 0.00 0.00 33.77 3.18
2796 2972 5.869344 CACAAGGAAGAAATATCTCGTGTCA 59.131 40.000 0.00 0.00 33.77 3.58
2800 2976 4.469945 TCCCACAAGGAAGAAATATCTCGT 59.530 41.667 0.00 0.00 43.78 4.18
2814 2990 2.620115 CGGATGAATCAATCCCACAAGG 59.380 50.000 0.00 0.00 42.86 3.61
2815 2991 2.620115 CCGGATGAATCAATCCCACAAG 59.380 50.000 0.00 0.00 42.86 3.16
2816 2992 2.240921 TCCGGATGAATCAATCCCACAA 59.759 45.455 0.00 0.00 42.86 3.33
2817 2993 1.843206 TCCGGATGAATCAATCCCACA 59.157 47.619 0.00 0.00 42.86 4.17
2818 2994 2.638480 TCCGGATGAATCAATCCCAC 57.362 50.000 0.00 0.00 42.86 4.61
2819 2995 2.749466 GCTTCCGGATGAATCAATCCCA 60.749 50.000 20.87 0.00 42.86 4.37
2820 2996 1.882623 GCTTCCGGATGAATCAATCCC 59.117 52.381 20.87 0.00 42.86 3.85
2821 2997 2.291741 GTGCTTCCGGATGAATCAATCC 59.708 50.000 20.87 1.40 42.46 3.01
2822 2998 2.032549 CGTGCTTCCGGATGAATCAATC 60.033 50.000 20.87 2.10 31.34 2.67
2823 2999 1.942657 CGTGCTTCCGGATGAATCAAT 59.057 47.619 20.87 0.00 31.34 2.57
2824 3000 1.066502 TCGTGCTTCCGGATGAATCAA 60.067 47.619 20.87 0.00 31.34 2.57
2825 3001 0.534873 TCGTGCTTCCGGATGAATCA 59.465 50.000 20.87 6.77 31.06 2.57
2834 3010 3.414700 GCAGGTGTCGTGCTTCCG 61.415 66.667 7.09 0.00 41.29 4.30
2895 3086 2.202987 GCCTGGACCGCAGATCTG 60.203 66.667 18.84 18.84 0.00 2.90
2896 3087 3.474570 GGCCTGGACCGCAGATCT 61.475 66.667 0.00 0.00 0.00 2.75
2897 3088 2.615227 AATGGCCTGGACCGCAGATC 62.615 60.000 3.32 0.00 0.00 2.75
2898 3089 2.615227 GAATGGCCTGGACCGCAGAT 62.615 60.000 3.32 0.00 0.00 2.90
2899 3090 3.329542 GAATGGCCTGGACCGCAGA 62.330 63.158 3.32 0.00 0.00 4.26
2929 3120 3.441500 AGAAAGAATGAGAACCCCACC 57.558 47.619 0.00 0.00 0.00 4.61
2930 3121 3.759086 GGAAGAAAGAATGAGAACCCCAC 59.241 47.826 0.00 0.00 0.00 4.61
2942 3133 1.512156 GCGTTGCCGGGAAGAAAGAA 61.512 55.000 9.39 0.00 33.68 2.52
2943 3134 1.964373 GCGTTGCCGGGAAGAAAGA 60.964 57.895 9.39 0.00 33.68 2.52
2944 3135 2.258013 TGCGTTGCCGGGAAGAAAG 61.258 57.895 9.39 2.14 33.68 2.62
2945 3136 2.203224 TGCGTTGCCGGGAAGAAA 60.203 55.556 9.39 0.00 33.68 2.52
3012 3203 3.396951 ACGGAGTGACAAACCCTTG 57.603 52.632 0.00 0.00 42.51 3.61
3028 3220 1.660607 CGTCACTCCAATCCAATCACG 59.339 52.381 0.00 0.00 0.00 4.35
3029 3221 1.398390 GCGTCACTCCAATCCAATCAC 59.602 52.381 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.