Multiple sequence alignment - TraesCS5D01G327400

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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 TraesCS5D01G327400 chr5D 100.000 3041 0 0 1 3041 420283573 420280533 0.000000e+00 5616.0
1 TraesCS5D01G327400 chr5A 91.267 1649 72 35 585 2194 533949923 533948308 0.000000e+00 2182.0
2 TraesCS5D01G327400 chr5A 91.698 265 21 1 213 476 533950213 533949949 1.720000e-97 366.0
3 TraesCS5D01G327400 chr5A 84.021 194 24 3 2496 2688 626251249 626251062 2.410000e-41 180.0
4 TraesCS5D01G327400 chr5B 93.489 1459 53 11 700 2131 506516074 506514631 0.000000e+00 2130.0
5 TraesCS5D01G327400 chr5B 87.708 602 71 3 10 608 506525349 506524748 0.000000e+00 699.0
6 TraesCS5D01G327400 chr5B 77.199 864 135 37 2192 3024 506514502 506513670 5.980000e-122 448.0
7 TraesCS5D01G327400 chr5B 92.683 82 6 0 2113 2194 506514610 506514529 5.330000e-23 119.0
8 TraesCS5D01G327400 chr2B 82.394 284 32 8 2496 2768 451827709 451827433 6.560000e-57 231.0
9 TraesCS5D01G327400 chr4D 81.786 280 35 6 2496 2764 346467514 346467788 1.420000e-53 220.0
10 TraesCS5D01G327400 chr4D 80.000 280 39 8 2496 2764 248930782 248930509 1.110000e-44 191.0
11 TraesCS5D01G327400 chr2D 82.051 273 34 5 2502 2764 99742743 99743010 5.100000e-53 219.0
12 TraesCS5D01G327400 chr4B 81.071 280 37 6 2496 2764 427507718 427507992 3.070000e-50 209.0
13 TraesCS5D01G327400 chr7D 81.091 275 37 5 2500 2764 466053691 466053422 3.970000e-49 206.0
14 TraesCS5D01G327400 chr7D 84.021 194 23 3 2496 2688 351584861 351584675 2.410000e-41 180.0
15 TraesCS5D01G327400 chr6D 83.333 204 23 7 2496 2697 249450068 249449874 8.660000e-41 178.0
16 TraesCS5D01G327400 chr6D 95.122 41 1 1 2450 2489 464255282 464255242 2.530000e-06 63.9
17 TraesCS5D01G327400 chr7A 82.474 194 28 2 2496 2688 503448286 503448474 6.750000e-37 165.0
18 TraesCS5D01G327400 chr2A 87.234 94 11 1 2354 2447 521516867 521516959 4.150000e-19 106.0
19 TraesCS5D01G327400 chr2A 89.394 66 7 0 2377 2442 27986696 27986761 1.940000e-12 84.2
20 TraesCS5D01G327400 chr4A 87.234 94 9 2 2354 2447 723594813 723594723 1.490000e-18 104.0
21 TraesCS5D01G327400 chr3A 87.778 90 10 1 2358 2447 363177902 363177990 1.490000e-18 104.0
22 TraesCS5D01G327400 chr3B 92.000 50 3 1 2446 2495 11666959 11667007 5.440000e-08 69.4
23 TraesCS5D01G327400 chr6A 89.583 48 4 1 2381 2427 485708166 485708213 3.270000e-05 60.2


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 TraesCS5D01G327400 chr5D 420280533 420283573 3040 True 5616 5616 100.000000 1 3041 1 chr5D.!!$R1 3040
1 TraesCS5D01G327400 chr5A 533948308 533950213 1905 True 1274 2182 91.482500 213 2194 2 chr5A.!!$R2 1981
2 TraesCS5D01G327400 chr5B 506513670 506516074 2404 True 899 2130 87.790333 700 3024 3 chr5B.!!$R2 2324
3 TraesCS5D01G327400 chr5B 506524748 506525349 601 True 699 699 87.708000 10 608 1 chr5B.!!$R1 598

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
608 613 0.106868 CTGGCAATGCATCTCCTCCA 60.107 55.0 7.79 10.47 0.0 3.86 F
609 614 0.554305 TGGCAATGCATCTCCTCCAT 59.446 50.0 7.79 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2049 0.250234 CCCTGAAGATGCCGAAGTGA 59.750 55.0 0.0 0.0 0.0 3.41 R
2383 2519 0.631753 ATCCTCCTCCTTCACTCGGA 59.368 55.0 0.0 0.0 0.0 4.55 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
22 23 3.971150 ACATCGATTCGATTCTCCTGTC 58.029 45.455 18.52 0.00 44.59 3.51
35 36 7.609146 TCGATTCTCCTGTCTAACAAGTAACTA 59.391 37.037 0.00 0.00 0.00 2.24
84 86 0.511221 AGCAACGATCGTTCAAACCG 59.489 50.000 29.64 18.29 36.00 4.44
98 100 3.054166 TCAAACCGACACATACAACTCG 58.946 45.455 0.00 0.00 0.00 4.18
101 103 1.256652 CCGACACATACAACTCGACG 58.743 55.000 0.00 0.00 0.00 5.12
105 107 0.992072 CACATACAACTCGACGCCAG 59.008 55.000 0.00 0.00 0.00 4.85
122 124 1.409521 CCAGACCAAACACACCCAAGA 60.410 52.381 0.00 0.00 0.00 3.02
123 125 1.676006 CAGACCAAACACACCCAAGAC 59.324 52.381 0.00 0.00 0.00 3.01
126 128 1.452145 CCAAACACACCCAAGACCGG 61.452 60.000 0.00 0.00 0.00 5.28
135 137 1.211949 ACCCAAGACCGGATACAATGG 59.788 52.381 9.46 11.35 0.00 3.16
138 140 1.134098 CAAGACCGGATACAATGGGCT 60.134 52.381 9.46 0.00 45.27 5.19
144 146 2.158667 CCGGATACAATGGGCTAAAGGT 60.159 50.000 0.00 0.00 0.00 3.50
158 160 2.271944 AAAGGTCAGCTACAACACCC 57.728 50.000 0.00 0.00 0.00 4.61
169 171 0.333312 ACAACACCCCAAACCACTCA 59.667 50.000 0.00 0.00 0.00 3.41
187 189 5.973565 CCACTCAAAGCAAACTACAAGAAAG 59.026 40.000 0.00 0.00 0.00 2.62
188 190 5.456822 CACTCAAAGCAAACTACAAGAAAGC 59.543 40.000 0.00 0.00 0.00 3.51
209 211 1.363744 CCACTTGAAGTCATCGGAGC 58.636 55.000 0.00 0.00 0.00 4.70
230 232 0.891373 CTCCACCGTGACAGAGTCAT 59.109 55.000 0.00 0.00 44.63 3.06
327 332 1.378762 CACCACCCGATCCAAAGGT 59.621 57.895 0.00 0.00 0.00 3.50
364 369 1.216710 GCAAGACGAGGGACAGAGG 59.783 63.158 0.00 0.00 0.00 3.69
389 394 6.400727 GGTCACCGCGAATTATGTGATATTAC 60.401 42.308 8.23 0.00 39.66 1.89
473 478 3.449322 AAACGATTCGTGATTGAACCG 57.551 42.857 13.22 0.00 40.74 4.44
483 488 3.181501 CGTGATTGAACCGTATTGCCATT 60.182 43.478 0.00 0.00 0.00 3.16
526 531 1.069513 TCGTGATTCGGACAACCTTGT 59.930 47.619 0.00 0.00 40.36 3.16
530 535 1.606668 GATTCGGACAACCTTGTTGCA 59.393 47.619 6.86 0.00 42.43 4.08
535 540 1.388547 GACAACCTTGTTGCAGACCA 58.611 50.000 6.86 0.00 42.43 4.02
582 587 2.210341 CTCGCTCTGCTCTGCTGACA 62.210 60.000 0.00 0.00 33.27 3.58
586 591 0.108709 CTCTGCTCTGCTGACACCTC 60.109 60.000 0.00 0.00 33.27 3.85
608 613 0.106868 CTGGCAATGCATCTCCTCCA 60.107 55.000 7.79 10.47 0.00 3.86
609 614 0.554305 TGGCAATGCATCTCCTCCAT 59.446 50.000 7.79 0.00 0.00 3.41
611 616 1.245732 GCAATGCATCTCCTCCATCC 58.754 55.000 0.00 0.00 0.00 3.51
612 617 1.202903 GCAATGCATCTCCTCCATCCT 60.203 52.381 0.00 0.00 0.00 3.24
614 619 0.975135 ATGCATCTCCTCCATCCTCG 59.025 55.000 0.00 0.00 0.00 4.63
633 641 4.680237 TCACCGCCGGCAGTCTTG 62.680 66.667 28.98 14.85 0.00 3.02
651 659 2.045438 TGGGGTGCAATAGTGGCG 60.045 61.111 0.00 0.00 0.00 5.69
664 672 4.349503 TGGCGGCTCCAGCAACAT 62.350 61.111 11.43 0.00 44.36 2.71
666 674 3.869272 GCGGCTCCAGCAACATCG 61.869 66.667 0.03 0.00 44.36 3.84
686 694 3.978193 GGGGTGCCACATGGACCA 61.978 66.667 16.53 0.00 37.22 4.02
687 695 2.117206 GGGTGCCACATGGACCAA 59.883 61.111 16.53 0.00 37.22 3.67
688 696 2.275380 GGGTGCCACATGGACCAAC 61.275 63.158 16.53 4.12 37.22 3.77
689 697 2.625823 GGTGCCACATGGACCAACG 61.626 63.158 0.00 0.00 36.24 4.10
690 698 1.896660 GTGCCACATGGACCAACGT 60.897 57.895 0.00 0.00 37.39 3.99
692 700 1.896660 GCCACATGGACCAACGTGT 60.897 57.895 20.30 9.45 41.05 4.49
693 701 1.852067 GCCACATGGACCAACGTGTC 61.852 60.000 20.30 9.01 38.48 3.67
699 707 4.990288 GACCAACGTGTCCTCCTC 57.010 61.111 0.00 0.00 0.00 3.71
700 708 1.292541 GACCAACGTGTCCTCCTCC 59.707 63.158 0.00 0.00 0.00 4.30
701 709 1.458777 ACCAACGTGTCCTCCTCCA 60.459 57.895 0.00 0.00 0.00 3.86
702 710 1.293498 CCAACGTGTCCTCCTCCAG 59.707 63.158 0.00 0.00 0.00 3.86
703 711 1.293498 CAACGTGTCCTCCTCCAGG 59.707 63.158 0.00 0.00 45.15 4.45
704 712 2.584391 AACGTGTCCTCCTCCAGGC 61.584 63.158 0.00 0.00 43.08 4.85
705 713 3.775654 CGTGTCCTCCTCCAGGCC 61.776 72.222 0.00 0.00 43.08 5.19
706 714 2.607750 GTGTCCTCCTCCAGGCCA 60.608 66.667 5.01 0.00 43.08 5.36
707 715 2.284921 TGTCCTCCTCCAGGCCAG 60.285 66.667 5.01 0.00 43.08 4.85
708 716 3.086600 GTCCTCCTCCAGGCCAGG 61.087 72.222 8.15 8.15 43.08 4.45
718 726 3.177884 AGGCCAGGACAGCACCAA 61.178 61.111 5.01 0.00 0.00 3.67
722 730 1.926511 GCCAGGACAGCACCAAATCG 61.927 60.000 0.00 0.00 0.00 3.34
876 898 2.032071 GGCCTGCACCAACGTACT 59.968 61.111 0.00 0.00 0.00 2.73
877 899 1.189524 AGGCCTGCACCAACGTACTA 61.190 55.000 3.11 0.00 0.00 1.82
878 900 1.017701 GGCCTGCACCAACGTACTAC 61.018 60.000 0.00 0.00 0.00 2.73
903 930 1.076485 CCCCTCCTGCCATTCTTGG 60.076 63.158 0.00 0.00 46.66 3.61
977 1010 1.544246 ACATCACGAGATCAACACCGA 59.456 47.619 0.00 0.00 30.20 4.69
1022 1088 4.724697 CACGCTGCGTTTCGGCTG 62.725 66.667 26.77 8.64 44.92 4.85
1326 1392 4.717629 TCCAACGGACTCGCTGCG 62.718 66.667 17.25 17.25 40.63 5.18
2037 2103 2.558359 GGCCTACAACATCAACTTTGCT 59.442 45.455 0.00 0.00 0.00 3.91
2072 2138 3.647113 AGCTGCTTGTATGGAGATGATCT 59.353 43.478 0.00 0.00 0.00 2.75
2148 2253 8.215050 TCCATGTATCTCCCGTTATGTTAATTT 58.785 33.333 0.00 0.00 0.00 1.82
2206 2340 5.997843 TCCTGTTGATCATGATCTCACAAT 58.002 37.500 30.65 0.00 38.60 2.71
2245 2379 6.014242 ACACTGAATCCTCACTGTTCATTCTA 60.014 38.462 0.00 0.00 32.05 2.10
2288 2424 6.946229 ACTCTTTAGTACTATGTTGCAACG 57.054 37.500 23.79 12.70 32.84 4.10
2322 2458 5.450818 ACAGCACCATCTTAGGGAAATTA 57.549 39.130 0.00 0.00 0.00 1.40
2323 2459 5.193679 ACAGCACCATCTTAGGGAAATTAC 58.806 41.667 0.00 0.00 0.00 1.89
2329 2465 6.989169 CACCATCTTAGGGAAATTACTCAGAG 59.011 42.308 0.00 0.00 0.00 3.35
2337 2473 5.422650 AGGGAAATTACTCAGAGGACACTAC 59.577 44.000 1.53 0.00 0.00 2.73
2347 2483 6.207810 ACTCAGAGGACACTACTTTGACTAAG 59.792 42.308 1.53 0.00 39.87 2.18
2352 2488 5.780793 AGGACACTACTTTGACTAAGTCCAT 59.219 40.000 5.53 0.00 43.67 3.41
2360 2496 9.307121 CTACTTTGACTAAGTCCATCTATGTTG 57.693 37.037 5.53 0.00 43.67 3.33
2361 2497 7.680730 ACTTTGACTAAGTCCATCTATGTTGT 58.319 34.615 0.00 0.00 43.67 3.32
2362 2498 7.819900 ACTTTGACTAAGTCCATCTATGTTGTC 59.180 37.037 0.00 0.00 43.67 3.18
2363 2499 6.850752 TGACTAAGTCCATCTATGTTGTCA 57.149 37.500 0.00 0.00 0.00 3.58
2364 2500 6.631016 TGACTAAGTCCATCTATGTTGTCAC 58.369 40.000 0.00 0.00 0.00 3.67
2365 2501 6.210584 TGACTAAGTCCATCTATGTTGTCACA 59.789 38.462 0.00 0.00 37.31 3.58
2367 2503 6.874134 ACTAAGTCCATCTATGTTGTCACAAC 59.126 38.462 14.17 14.17 36.16 3.32
2368 2504 5.227569 AGTCCATCTATGTTGTCACAACA 57.772 39.130 25.30 25.30 36.16 3.33
2369 2505 5.809001 AGTCCATCTATGTTGTCACAACAT 58.191 37.500 33.13 33.13 42.82 2.71
2370 2506 6.946340 AGTCCATCTATGTTGTCACAACATA 58.054 36.000 32.05 32.05 40.87 2.29
2377 2513 5.808042 ATGTTGTCACAACATAGCTGATC 57.192 39.130 30.78 0.00 38.94 2.92
2378 2514 4.898320 TGTTGTCACAACATAGCTGATCT 58.102 39.130 19.75 0.00 34.73 2.75
2383 2519 5.174395 GTCACAACATAGCTGATCTCAAGT 58.826 41.667 0.00 0.00 0.00 3.16
2384 2520 5.290643 GTCACAACATAGCTGATCTCAAGTC 59.709 44.000 0.00 0.00 0.00 3.01
2385 2521 4.569966 CACAACATAGCTGATCTCAAGTCC 59.430 45.833 0.00 0.00 0.00 3.85
2386 2522 3.724508 ACATAGCTGATCTCAAGTCCG 57.275 47.619 0.00 0.00 0.00 4.79
2387 2523 3.291584 ACATAGCTGATCTCAAGTCCGA 58.708 45.455 0.00 0.00 0.00 4.55
2388 2524 3.317711 ACATAGCTGATCTCAAGTCCGAG 59.682 47.826 0.00 0.00 0.00 4.63
2391 2527 1.474478 GCTGATCTCAAGTCCGAGTGA 59.526 52.381 0.00 0.00 34.46 3.41
2392 2528 2.094494 GCTGATCTCAAGTCCGAGTGAA 60.094 50.000 0.00 0.00 34.46 3.18
2393 2529 3.768406 CTGATCTCAAGTCCGAGTGAAG 58.232 50.000 0.00 0.00 34.46 3.02
2394 2530 2.493675 TGATCTCAAGTCCGAGTGAAGG 59.506 50.000 0.00 0.00 34.46 3.46
2396 2532 2.163509 TCTCAAGTCCGAGTGAAGGAG 58.836 52.381 0.00 0.00 38.65 3.69
2397 2533 1.203523 CTCAAGTCCGAGTGAAGGAGG 59.796 57.143 0.00 0.00 38.65 4.30
2401 2554 0.323542 GTCCGAGTGAAGGAGGAGGA 60.324 60.000 0.00 0.00 38.65 3.71
2412 2565 2.334023 AGGAGGAGGATTGTGATAGGC 58.666 52.381 0.00 0.00 0.00 3.93
2418 2571 3.126831 GAGGATTGTGATAGGCTTGACG 58.873 50.000 0.00 0.00 0.00 4.35
2420 2573 3.126831 GGATTGTGATAGGCTTGACGAG 58.873 50.000 0.00 0.00 0.00 4.18
2428 2581 3.330275 GCTTGACGAGCCAACGTT 58.670 55.556 2.95 0.00 46.52 3.99
2429 2582 2.524300 GCTTGACGAGCCAACGTTA 58.476 52.632 0.00 0.00 46.52 3.18
2430 2583 0.863144 GCTTGACGAGCCAACGTTAA 59.137 50.000 0.00 0.00 46.52 2.01
2431 2584 1.262151 GCTTGACGAGCCAACGTTAAA 59.738 47.619 0.00 0.00 46.52 1.52
2432 2585 2.286536 GCTTGACGAGCCAACGTTAAAA 60.287 45.455 0.00 0.00 46.52 1.52
2433 2586 3.285745 CTTGACGAGCCAACGTTAAAAC 58.714 45.455 0.00 0.00 46.52 2.43
2434 2587 2.553086 TGACGAGCCAACGTTAAAACT 58.447 42.857 0.00 0.00 46.52 2.66
2435 2588 2.540931 TGACGAGCCAACGTTAAAACTC 59.459 45.455 0.00 4.81 46.52 3.01
2436 2589 2.540931 GACGAGCCAACGTTAAAACTCA 59.459 45.455 0.00 0.00 46.52 3.41
2437 2590 2.542595 ACGAGCCAACGTTAAAACTCAG 59.457 45.455 0.00 5.24 44.14 3.35
2438 2591 2.542595 CGAGCCAACGTTAAAACTCAGT 59.457 45.455 0.00 0.00 0.00 3.41
2439 2592 3.362693 CGAGCCAACGTTAAAACTCAGTC 60.363 47.826 0.00 0.00 0.00 3.51
2440 2593 3.537580 AGCCAACGTTAAAACTCAGTCA 58.462 40.909 0.00 0.00 0.00 3.41
2441 2594 3.311596 AGCCAACGTTAAAACTCAGTCAC 59.688 43.478 0.00 0.00 0.00 3.67
2442 2595 3.311596 GCCAACGTTAAAACTCAGTCACT 59.688 43.478 0.00 0.00 0.00 3.41
2443 2596 4.785341 GCCAACGTTAAAACTCAGTCACTG 60.785 45.833 0.00 0.00 0.00 3.66
2444 2597 4.271687 CAACGTTAAAACTCAGTCACTGC 58.728 43.478 0.00 0.00 0.00 4.40
2445 2598 3.793559 ACGTTAAAACTCAGTCACTGCT 58.206 40.909 0.00 0.00 0.00 4.24
2446 2599 4.189231 ACGTTAAAACTCAGTCACTGCTT 58.811 39.130 0.00 0.00 0.00 3.91
2447 2600 4.034048 ACGTTAAAACTCAGTCACTGCTTG 59.966 41.667 0.00 0.00 0.00 4.01
2448 2601 4.270084 CGTTAAAACTCAGTCACTGCTTGA 59.730 41.667 0.00 0.00 0.00 3.02
2467 2620 1.375551 ACGAGCCAACGTCAAAACTT 58.624 45.000 0.00 0.00 43.02 2.66
2468 2621 2.553086 ACGAGCCAACGTCAAAACTTA 58.447 42.857 0.00 0.00 43.02 2.24
2469 2622 2.542595 ACGAGCCAACGTCAAAACTTAG 59.457 45.455 0.00 0.00 43.02 2.18
2472 2625 1.335496 GCCAACGTCAAAACTTAGCCA 59.665 47.619 0.00 0.00 0.00 4.75
2477 2630 3.805207 ACGTCAAAACTTAGCCACTCTT 58.195 40.909 0.00 0.00 0.00 2.85
2481 2634 5.637810 CGTCAAAACTTAGCCACTCTTATGA 59.362 40.000 0.00 0.00 0.00 2.15
2486 2639 7.856145 AAACTTAGCCACTCTTATGAAGATG 57.144 36.000 0.00 0.00 36.82 2.90
2491 2644 4.872691 AGCCACTCTTATGAAGATGAAACG 59.127 41.667 0.00 0.00 36.82 3.60
2519 2673 2.361438 CGGTGGTACCTCAGAAGGATAC 59.639 54.545 14.36 0.00 46.67 2.24
2520 2674 2.699321 GGTGGTACCTCAGAAGGATACC 59.301 54.545 14.36 4.16 46.67 2.73
2525 2679 4.202131 GGTACCTCAGAAGGATACCTTTCG 60.202 50.000 4.06 0.17 44.82 3.46
2544 2698 3.691575 TCGAAATTTGGGGTCAATGCTA 58.308 40.909 0.00 0.00 32.28 3.49
2547 2701 4.142182 CGAAATTTGGGGTCAATGCTACAT 60.142 41.667 0.00 0.00 32.28 2.29
2550 2704 6.469782 AATTTGGGGTCAATGCTACATAAG 57.530 37.500 0.00 0.00 32.28 1.73
2551 2705 3.576078 TGGGGTCAATGCTACATAAGG 57.424 47.619 0.00 0.00 0.00 2.69
2552 2706 3.119319 TGGGGTCAATGCTACATAAGGA 58.881 45.455 0.00 0.00 0.00 3.36
2555 2709 9.665351 TTTGGGGTCAATGCTACATAAGGATGT 62.665 40.741 0.00 0.00 39.96 3.06
2556 2710 4.757149 GGGTCAATGCTACATAAGGATGTC 59.243 45.833 0.00 0.00 43.01 3.06
2563 2717 6.834168 TGCTACATAAGGATGTCGATATCA 57.166 37.500 21.71 4.03 43.01 2.15
2577 2731 5.693555 TGTCGATATCAATGAAGATGTGAGC 59.306 40.000 3.12 0.00 0.00 4.26
2594 2748 1.064060 GAGCCATCGAATCAAAACCGG 59.936 52.381 0.00 0.00 0.00 5.28
2607 2761 1.463674 AAACCGGATGGATGAAGTGC 58.536 50.000 9.46 0.00 39.21 4.40
2610 2764 2.537560 CGGATGGATGAAGTGCCGC 61.538 63.158 0.00 0.00 31.80 6.53
2615 2769 2.700773 GGATGAAGTGCCGCCAACC 61.701 63.158 0.00 0.00 0.00 3.77
2621 2775 2.281484 GTGCCGCCAACCTTCTGA 60.281 61.111 0.00 0.00 0.00 3.27
2625 2779 1.244019 GCCGCCAACCTTCTGACATT 61.244 55.000 0.00 0.00 0.00 2.71
2626 2780 1.948611 GCCGCCAACCTTCTGACATTA 60.949 52.381 0.00 0.00 0.00 1.90
2639 2793 7.173907 ACCTTCTGACATTATTTGTGACAAGAG 59.826 37.037 0.00 0.00 39.18 2.85
2646 2800 1.581934 TTTGTGACAAGAGAGTGCCG 58.418 50.000 0.00 0.00 0.00 5.69
2647 2801 0.464036 TTGTGACAAGAGAGTGCCGT 59.536 50.000 0.00 0.00 0.00 5.68
2652 2806 3.184581 GTGACAAGAGAGTGCCGTAAAAG 59.815 47.826 0.00 0.00 0.00 2.27
2653 2807 3.181469 TGACAAGAGAGTGCCGTAAAAGT 60.181 43.478 0.00 0.00 0.00 2.66
2656 2810 5.362263 ACAAGAGAGTGCCGTAAAAGTTAA 58.638 37.500 0.00 0.00 0.00 2.01
2657 2811 5.818857 ACAAGAGAGTGCCGTAAAAGTTAAA 59.181 36.000 0.00 0.00 0.00 1.52
2658 2812 6.316890 ACAAGAGAGTGCCGTAAAAGTTAAAA 59.683 34.615 0.00 0.00 0.00 1.52
2659 2813 6.541111 AGAGAGTGCCGTAAAAGTTAAAAG 57.459 37.500 0.00 0.00 0.00 2.27
2660 2814 5.469084 AGAGAGTGCCGTAAAAGTTAAAAGG 59.531 40.000 0.00 0.00 0.00 3.11
2672 2826 9.525409 GTAAAAGTTAAAAGGAAAGGAAGGTTC 57.475 33.333 0.00 0.00 0.00 3.62
2682 2836 4.202233 GGAAAGGAAGGTTCTATAGGACGG 60.202 50.000 5.05 0.00 0.00 4.79
2688 2842 2.963782 AGGTTCTATAGGACGGCGATTT 59.036 45.455 16.62 0.00 0.00 2.17
2692 2846 1.792949 CTATAGGACGGCGATTTGTGC 59.207 52.381 16.62 0.00 0.00 4.57
2697 2851 2.176546 CGGCGATTTGTGCTGTGG 59.823 61.111 0.00 0.00 33.99 4.17
2698 2852 2.126346 GGCGATTTGTGCTGTGGC 60.126 61.111 0.00 0.00 39.26 5.01
2707 2861 3.554716 TGCTGTGGCAGAGAGTGT 58.445 55.556 16.83 0.00 44.28 3.55
2708 2862 1.832219 TGCTGTGGCAGAGAGTGTT 59.168 52.632 16.83 0.00 44.28 3.32
2709 2863 1.047801 TGCTGTGGCAGAGAGTGTTA 58.952 50.000 16.83 0.00 44.28 2.41
2721 2877 5.411781 CAGAGAGTGTTAGCCGACTAAAAT 58.588 41.667 0.00 0.00 40.04 1.82
2722 2878 5.289675 CAGAGAGTGTTAGCCGACTAAAATG 59.710 44.000 0.00 0.00 40.04 2.32
2724 2880 3.670625 AGTGTTAGCCGACTAAAATGCA 58.329 40.909 0.00 0.00 40.04 3.96
2737 2893 7.540400 CCGACTAAAATGCAACATGTTCAATAA 59.460 33.333 8.48 0.00 0.00 1.40
2745 2901 6.098679 TGCAACATGTTCAATAATTAGGTGC 58.901 36.000 8.48 5.74 0.00 5.01
2746 2902 6.098679 GCAACATGTTCAATAATTAGGTGCA 58.901 36.000 8.48 0.00 0.00 4.57
2749 2905 6.321717 ACATGTTCAATAATTAGGTGCAACG 58.678 36.000 0.00 0.00 38.12 4.10
2750 2906 6.150307 ACATGTTCAATAATTAGGTGCAACGA 59.850 34.615 0.00 0.00 38.12 3.85
2769 2925 4.306600 ACGAAGATGCGCATGTTATGATA 58.693 39.130 30.06 0.00 33.86 2.15
2770 2926 4.749598 ACGAAGATGCGCATGTTATGATAA 59.250 37.500 30.06 0.00 33.86 1.75
2776 2932 4.061596 TGCGCATGTTATGATAAATCCGA 58.938 39.130 5.66 0.00 0.00 4.55
2826 2991 5.472478 GGGTAGAACCGATTGAAGAAAAACT 59.528 40.000 0.00 0.00 39.83 2.66
2843 3008 8.652810 AGAAAAACTTCATTTGAGATGGTTTG 57.347 30.769 0.00 0.00 34.17 2.93
2845 3010 5.473066 AACTTCATTTGAGATGGTTTGGG 57.527 39.130 0.00 0.00 0.00 4.12
2846 3011 4.482990 ACTTCATTTGAGATGGTTTGGGT 58.517 39.130 0.00 0.00 0.00 4.51
2848 3013 5.476945 ACTTCATTTGAGATGGTTTGGGTAC 59.523 40.000 0.00 0.00 0.00 3.34
2854 3019 5.097742 TGAGATGGTTTGGGTACATACAG 57.902 43.478 0.00 0.00 31.18 2.74
2865 3030 3.016736 GGTACATACAGCACATGCCTTT 58.983 45.455 0.00 0.00 43.38 3.11
2867 3032 4.638421 GGTACATACAGCACATGCCTTTAA 59.362 41.667 0.00 0.00 43.38 1.52
2879 3044 4.039124 ACATGCCTTTAAAAGTTCCAGTGG 59.961 41.667 1.40 1.40 0.00 4.00
2880 3045 3.637769 TGCCTTTAAAAGTTCCAGTGGT 58.362 40.909 9.54 0.00 0.00 4.16
2881 3046 3.634910 TGCCTTTAAAAGTTCCAGTGGTC 59.365 43.478 9.54 4.05 0.00 4.02
2883 3048 4.098807 GCCTTTAAAAGTTCCAGTGGTCAA 59.901 41.667 9.54 0.00 0.00 3.18
2884 3049 5.736207 GCCTTTAAAAGTTCCAGTGGTCAAG 60.736 44.000 9.54 3.75 0.00 3.02
2885 3050 5.221244 CCTTTAAAAGTTCCAGTGGTCAAGG 60.221 44.000 9.54 8.44 0.00 3.61
2886 3051 3.382083 AAAAGTTCCAGTGGTCAAGGT 57.618 42.857 9.54 0.00 0.00 3.50
2888 3053 4.724279 AAAGTTCCAGTGGTCAAGGTAT 57.276 40.909 9.54 0.00 0.00 2.73
2889 3054 5.836024 AAAGTTCCAGTGGTCAAGGTATA 57.164 39.130 9.54 0.00 0.00 1.47
2891 3056 4.426704 AGTTCCAGTGGTCAAGGTATACT 58.573 43.478 9.54 0.00 0.00 2.12
2915 3092 9.153479 ACTATGCTAATAATGAGAAGAGAGGTT 57.847 33.333 0.00 0.00 0.00 3.50
2931 3108 5.845065 AGAGAGGTTAAGGTAGACCAAACTT 59.155 40.000 13.51 8.39 38.42 2.66
2932 3109 7.015064 AGAGAGGTTAAGGTAGACCAAACTTA 58.985 38.462 13.51 0.00 38.42 2.24
2933 3110 7.178805 AGAGAGGTTAAGGTAGACCAAACTTAG 59.821 40.741 13.51 0.00 38.42 2.18
2934 3111 7.015064 AGAGGTTAAGGTAGACCAAACTTAGA 58.985 38.462 13.51 0.00 38.42 2.10
2935 3112 7.002250 AGGTTAAGGTAGACCAAACTTAGAC 57.998 40.000 13.51 1.76 38.42 2.59
2936 3113 6.013898 AGGTTAAGGTAGACCAAACTTAGACC 60.014 42.308 13.51 0.00 38.42 3.85
2937 3114 6.239686 GGTTAAGGTAGACCAAACTTAGACCA 60.240 42.308 13.51 0.00 38.89 4.02
2938 3115 5.899631 AAGGTAGACCAAACTTAGACCAA 57.100 39.130 0.66 0.00 38.89 3.67
2939 3116 5.899631 AGGTAGACCAAACTTAGACCAAA 57.100 39.130 0.66 0.00 38.89 3.28
2940 3117 5.618236 AGGTAGACCAAACTTAGACCAAAC 58.382 41.667 0.66 0.00 38.89 2.93
2941 3118 5.368816 AGGTAGACCAAACTTAGACCAAACT 59.631 40.000 0.66 0.00 38.89 2.66
2945 3122 6.365520 AGACCAAACTTAGACCAAACTTGAT 58.634 36.000 0.00 0.00 0.00 2.57
2967 3144 9.947433 TTGATATAAGAAACGTCCCTAAAAAGA 57.053 29.630 0.00 0.00 0.00 2.52
3009 3188 0.467384 CCACAGACCTAGCCATGGAG 59.533 60.000 18.40 4.42 0.00 3.86
3011 3190 1.411977 CACAGACCTAGCCATGGAGAG 59.588 57.143 18.40 11.24 0.00 3.20
3012 3191 1.047002 CAGACCTAGCCATGGAGAGG 58.953 60.000 24.16 24.16 35.05 3.69
3024 3203 1.078143 GGAGAGGGCGCATGAAAGT 60.078 57.895 10.83 0.00 0.00 2.66
3025 3204 0.678048 GGAGAGGGCGCATGAAAGTT 60.678 55.000 10.83 0.00 0.00 2.66
3026 3205 0.449388 GAGAGGGCGCATGAAAGTTG 59.551 55.000 10.83 0.00 0.00 3.16
3027 3206 0.962356 AGAGGGCGCATGAAAGTTGG 60.962 55.000 10.83 0.00 0.00 3.77
3028 3207 2.125952 GGGCGCATGAAAGTTGGC 60.126 61.111 10.83 0.00 0.00 4.52
3029 3208 2.639327 GGGCGCATGAAAGTTGGCT 61.639 57.895 10.83 0.00 0.00 4.75
3030 3209 1.312371 GGGCGCATGAAAGTTGGCTA 61.312 55.000 10.83 0.00 0.00 3.93
3031 3210 0.740737 GGCGCATGAAAGTTGGCTAT 59.259 50.000 10.83 0.00 0.00 2.97
3032 3211 1.268743 GGCGCATGAAAGTTGGCTATC 60.269 52.381 10.83 0.00 0.00 2.08
3033 3212 1.268743 GCGCATGAAAGTTGGCTATCC 60.269 52.381 0.30 0.00 0.00 2.59
3034 3213 2.016318 CGCATGAAAGTTGGCTATCCA 58.984 47.619 0.00 0.00 41.55 3.41
3035 3214 2.223340 CGCATGAAAGTTGGCTATCCAC 60.223 50.000 0.00 0.00 43.33 4.02
3036 3215 2.754552 GCATGAAAGTTGGCTATCCACA 59.245 45.455 0.00 0.00 43.33 4.17
3037 3216 3.428045 GCATGAAAGTTGGCTATCCACAC 60.428 47.826 0.00 0.00 43.33 3.82
3038 3217 2.790433 TGAAAGTTGGCTATCCACACC 58.210 47.619 0.00 0.00 43.33 4.16
3039 3218 2.107378 TGAAAGTTGGCTATCCACACCA 59.893 45.455 0.00 0.00 43.33 4.17
3040 3219 2.969821 AAGTTGGCTATCCACACCAA 57.030 45.000 0.00 0.00 43.33 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.822350 AGACAGGAGAATCGAATCGATGTA 59.178 41.667 19.44 0.00 46.30 2.29
1 2 3.634448 AGACAGGAGAATCGAATCGATGT 59.366 43.478 19.44 12.72 46.30 3.06
2 3 4.235939 AGACAGGAGAATCGAATCGATG 57.764 45.455 19.44 9.42 46.30 3.84
4 5 4.638865 TGTTAGACAGGAGAATCGAATCGA 59.361 41.667 8.12 8.12 41.13 3.59
5 6 4.921547 TGTTAGACAGGAGAATCGAATCG 58.078 43.478 0.00 0.00 34.37 3.34
6 7 6.334202 ACTTGTTAGACAGGAGAATCGAATC 58.666 40.000 0.00 0.00 34.37 2.52
7 8 6.287589 ACTTGTTAGACAGGAGAATCGAAT 57.712 37.500 0.00 0.00 34.37 3.34
8 9 5.723672 ACTTGTTAGACAGGAGAATCGAA 57.276 39.130 0.00 0.00 34.37 3.71
70 72 1.133407 TGTGTCGGTTTGAACGATCG 58.867 50.000 14.88 14.88 42.82 3.69
75 77 4.607557 CGAGTTGTATGTGTCGGTTTGAAC 60.608 45.833 0.00 0.00 0.00 3.18
77 79 3.054166 CGAGTTGTATGTGTCGGTTTGA 58.946 45.455 0.00 0.00 0.00 2.69
84 86 0.989890 GGCGTCGAGTTGTATGTGTC 59.010 55.000 0.00 0.00 0.00 3.67
98 100 1.647084 GTGTGTTTGGTCTGGCGTC 59.353 57.895 0.00 0.00 0.00 5.19
101 103 1.040339 TTGGGTGTGTTTGGTCTGGC 61.040 55.000 0.00 0.00 0.00 4.85
105 107 1.029681 GGTCTTGGGTGTGTTTGGTC 58.970 55.000 0.00 0.00 0.00 4.02
122 124 2.158667 CCTTTAGCCCATTGTATCCGGT 60.159 50.000 0.00 0.00 0.00 5.28
123 125 2.158667 ACCTTTAGCCCATTGTATCCGG 60.159 50.000 0.00 0.00 0.00 5.14
126 128 3.565902 GCTGACCTTTAGCCCATTGTATC 59.434 47.826 0.00 0.00 35.15 2.24
135 137 2.742589 GTGTTGTAGCTGACCTTTAGCC 59.257 50.000 0.00 0.00 42.07 3.93
138 140 2.039348 GGGGTGTTGTAGCTGACCTTTA 59.961 50.000 0.00 0.00 0.00 1.85
144 146 1.477923 GGTTTGGGGTGTTGTAGCTGA 60.478 52.381 0.00 0.00 0.00 4.26
158 160 3.525268 AGTTTGCTTTGAGTGGTTTGG 57.475 42.857 0.00 0.00 0.00 3.28
169 171 3.069586 GGGGCTTTCTTGTAGTTTGCTTT 59.930 43.478 0.00 0.00 0.00 3.51
187 189 1.026718 CCGATGACTTCAAGTGGGGC 61.027 60.000 0.00 0.00 0.00 5.80
188 190 0.613260 TCCGATGACTTCAAGTGGGG 59.387 55.000 0.00 0.00 0.00 4.96
209 211 1.878656 GACTCTGTCACGGTGGAGGG 61.879 65.000 8.50 7.30 32.09 4.30
230 232 1.287191 GCGCGGCTCATCTCTATGA 59.713 57.895 8.83 0.00 39.87 2.15
327 332 1.975660 CTCCGGGTGAAAACCTTGAA 58.024 50.000 0.00 0.00 0.00 2.69
364 369 1.647346 TCACATAATTCGCGGTGACC 58.353 50.000 6.13 0.00 35.51 4.02
368 373 5.463286 TCGTAATATCACATAATTCGCGGT 58.537 37.500 6.13 0.00 0.00 5.68
389 394 7.872881 AGAATCATTCCAATCAATTCAGATCG 58.127 34.615 0.00 0.00 0.00 3.69
453 458 3.449322 CGGTTCAATCACGAATCGTTT 57.551 42.857 5.20 0.00 43.04 3.60
461 466 1.735018 TGGCAATACGGTTCAATCACG 59.265 47.619 0.00 0.00 0.00 4.35
473 478 7.624360 TGGATCGGAATTATAATGGCAATAC 57.376 36.000 0.00 0.00 0.00 1.89
483 488 9.062524 ACGATTTTGAATTGGATCGGAATTATA 57.937 29.630 9.07 0.00 44.02 0.98
526 531 3.055385 GTGTTACCCTCTATGGTCTGCAA 60.055 47.826 0.00 0.00 39.91 4.08
530 535 2.766828 GCAGTGTTACCCTCTATGGTCT 59.233 50.000 0.00 0.00 39.91 3.85
535 540 3.197983 GTCTTGGCAGTGTTACCCTCTAT 59.802 47.826 0.00 0.00 0.00 1.98
582 587 0.745845 GATGCATTGCCAGACGAGGT 60.746 55.000 6.12 0.00 0.00 3.85
586 591 0.463295 AGGAGATGCATTGCCAGACG 60.463 55.000 17.76 0.00 0.00 4.18
624 632 2.985847 GCACCCCACAAGACTGCC 60.986 66.667 0.00 0.00 0.00 4.85
633 641 2.406616 CGCCACTATTGCACCCCAC 61.407 63.158 0.00 0.00 0.00 4.61
651 659 3.512516 GCCGATGTTGCTGGAGCC 61.513 66.667 0.00 0.00 41.18 4.70
675 683 2.244000 GACACGTTGGTCCATGTGG 58.756 57.895 22.12 9.67 36.67 4.17
683 691 1.458777 TGGAGGAGGACACGTTGGT 60.459 57.895 0.00 0.00 0.00 3.67
685 693 1.293498 CCTGGAGGAGGACACGTTG 59.707 63.158 0.00 0.00 46.33 4.10
686 694 2.584391 GCCTGGAGGAGGACACGTT 61.584 63.158 0.00 0.00 46.33 3.99
687 695 2.997897 GCCTGGAGGAGGACACGT 60.998 66.667 0.00 0.00 46.33 4.49
692 700 3.284251 TCCTGGCCTGGAGGAGGA 61.284 66.667 26.46 15.06 46.33 3.71
693 701 3.086600 GTCCTGGCCTGGAGGAGG 61.087 72.222 30.23 14.87 46.13 4.30
694 702 2.284921 TGTCCTGGCCTGGAGGAG 60.285 66.667 30.23 4.95 40.42 3.69
695 703 2.284921 CTGTCCTGGCCTGGAGGA 60.285 66.667 30.23 18.66 37.27 3.71
696 704 4.106925 GCTGTCCTGGCCTGGAGG 62.107 72.222 30.23 24.47 36.69 4.30
697 705 3.324930 TGCTGTCCTGGCCTGGAG 61.325 66.667 30.23 20.48 36.69 3.86
698 706 3.640407 GTGCTGTCCTGGCCTGGA 61.640 66.667 26.46 26.46 0.00 3.86
699 707 4.729918 GGTGCTGTCCTGGCCTGG 62.730 72.222 22.36 22.36 0.00 4.45
700 708 2.981914 TTTGGTGCTGTCCTGGCCTG 62.982 60.000 3.32 2.54 0.00 4.85
701 709 2.085343 ATTTGGTGCTGTCCTGGCCT 62.085 55.000 3.32 0.00 0.00 5.19
702 710 1.598701 GATTTGGTGCTGTCCTGGCC 61.599 60.000 0.00 0.00 0.00 5.36
703 711 1.885871 GATTTGGTGCTGTCCTGGC 59.114 57.895 0.00 0.00 0.00 4.85
704 712 0.606401 ACGATTTGGTGCTGTCCTGG 60.606 55.000 0.00 0.00 0.00 4.45
705 713 1.238439 AACGATTTGGTGCTGTCCTG 58.762 50.000 0.00 0.00 0.00 3.86
706 714 1.608590 CAAACGATTTGGTGCTGTCCT 59.391 47.619 0.00 0.00 37.01 3.85
707 715 1.606668 TCAAACGATTTGGTGCTGTCC 59.393 47.619 9.54 0.00 40.98 4.02
708 716 3.236816 CATCAAACGATTTGGTGCTGTC 58.763 45.455 9.66 0.00 43.94 3.51
718 726 1.129251 CGAGCTGCACATCAAACGATT 59.871 47.619 1.02 0.00 0.00 3.34
722 730 1.267235 CGATCGAGCTGCACATCAAAC 60.267 52.381 10.26 0.00 0.00 2.93
903 930 5.047847 TCGGTTATATAGAGCTTGTGTTGC 58.952 41.667 0.00 0.00 0.00 4.17
950 983 4.574421 TGTTGATCTCGTGATGTTTGTGTT 59.426 37.500 4.41 0.00 32.19 3.32
952 985 4.457810 GTGTTGATCTCGTGATGTTTGTG 58.542 43.478 4.41 0.00 32.19 3.33
1296 1362 4.641645 TTGGACCGCAGCCACTGG 62.642 66.667 0.00 0.00 34.56 4.00
1494 1560 2.045242 TAGGAGGACGCGAGCACT 60.045 61.111 15.93 4.49 0.00 4.40
1530 1596 4.814294 ATCTGGGCGGCGTCGAAC 62.814 66.667 16.53 4.94 39.00 3.95
1929 1995 2.227388 GTCGTAGAGGTCGAACAGGAAA 59.773 50.000 1.87 0.00 36.95 3.13
1983 2049 0.250234 CCCTGAAGATGCCGAAGTGA 59.750 55.000 0.00 0.00 0.00 3.41
2037 2103 7.228906 CCATACAAGCAGCTCTACTAGTACTAA 59.771 40.741 3.76 0.00 0.00 2.24
2072 2138 0.943673 CCACAGATCAACAACGTGCA 59.056 50.000 0.00 0.00 0.00 4.57
2148 2253 9.653287 ATGAAATCATAAAGTTCAAGTCGTAGA 57.347 29.630 0.00 0.00 35.07 2.59
2176 2281 4.224991 TCATGATCAACAGGAGAATGCA 57.775 40.909 0.00 0.00 34.30 3.96
2206 2340 5.470098 GGATTCAGTGTAAGTTTCTTCAGCA 59.530 40.000 0.00 0.00 0.00 4.41
2262 2396 9.084164 CGTTGCAACATAGTACTAAAGAGTTAT 57.916 33.333 28.01 0.00 37.10 1.89
2263 2397 7.062605 GCGTTGCAACATAGTACTAAAGAGTTA 59.937 37.037 28.01 0.00 37.10 2.24
2268 2402 4.201783 GGGCGTTGCAACATAGTACTAAAG 60.202 45.833 28.01 9.08 0.00 1.85
2270 2404 3.055675 AGGGCGTTGCAACATAGTACTAA 60.056 43.478 28.01 0.00 0.00 2.24
2271 2405 2.498481 AGGGCGTTGCAACATAGTACTA 59.502 45.455 28.01 4.77 0.00 1.82
2272 2406 1.278127 AGGGCGTTGCAACATAGTACT 59.722 47.619 28.01 13.87 0.00 2.73
2273 2407 1.396996 CAGGGCGTTGCAACATAGTAC 59.603 52.381 28.01 11.97 0.00 2.73
2274 2408 1.677518 CCAGGGCGTTGCAACATAGTA 60.678 52.381 28.01 0.00 0.00 1.82
2275 2409 0.960364 CCAGGGCGTTGCAACATAGT 60.960 55.000 28.01 7.95 0.00 2.12
2276 2410 1.802636 CCAGGGCGTTGCAACATAG 59.197 57.895 28.01 13.80 0.00 2.23
2299 2435 5.450818 AATTTCCCTAAGATGGTGCTGTA 57.549 39.130 0.00 0.00 0.00 2.74
2308 2444 6.903534 TGTCCTCTGAGTAATTTCCCTAAGAT 59.096 38.462 3.66 0.00 0.00 2.40
2322 2458 4.475345 AGTCAAAGTAGTGTCCTCTGAGT 58.525 43.478 3.66 0.00 0.00 3.41
2323 2459 6.207810 ACTTAGTCAAAGTAGTGTCCTCTGAG 59.792 42.308 0.00 0.00 46.85 3.35
2337 2473 7.819415 TGACAACATAGATGGACTTAGTCAAAG 59.181 37.037 14.72 0.00 41.33 2.77
2360 2496 5.174395 ACTTGAGATCAGCTATGTTGTGAC 58.826 41.667 0.00 0.00 0.00 3.67
2361 2497 5.411831 ACTTGAGATCAGCTATGTTGTGA 57.588 39.130 0.00 0.00 0.00 3.58
2362 2498 4.569966 GGACTTGAGATCAGCTATGTTGTG 59.430 45.833 0.00 0.00 0.00 3.33
2363 2499 4.679106 CGGACTTGAGATCAGCTATGTTGT 60.679 45.833 0.00 0.00 0.00 3.32
2364 2500 3.801050 CGGACTTGAGATCAGCTATGTTG 59.199 47.826 0.00 0.00 0.00 3.33
2365 2501 3.701542 TCGGACTTGAGATCAGCTATGTT 59.298 43.478 0.00 0.00 0.00 2.71
2367 2503 3.317711 ACTCGGACTTGAGATCAGCTATG 59.682 47.826 0.00 0.00 39.35 2.23
2368 2504 3.317711 CACTCGGACTTGAGATCAGCTAT 59.682 47.826 0.00 0.00 39.35 2.97
2369 2505 2.685388 CACTCGGACTTGAGATCAGCTA 59.315 50.000 0.00 0.00 39.35 3.32
2370 2506 1.476085 CACTCGGACTTGAGATCAGCT 59.524 52.381 0.00 0.00 39.35 4.24
2371 2507 1.474478 TCACTCGGACTTGAGATCAGC 59.526 52.381 0.00 0.00 39.35 4.26
2372 2508 3.428725 CCTTCACTCGGACTTGAGATCAG 60.429 52.174 0.00 0.00 39.35 2.90
2373 2509 2.493675 CCTTCACTCGGACTTGAGATCA 59.506 50.000 0.00 0.00 39.35 2.92
2374 2510 2.755655 TCCTTCACTCGGACTTGAGATC 59.244 50.000 0.00 0.00 39.35 2.75
2375 2511 2.757868 CTCCTTCACTCGGACTTGAGAT 59.242 50.000 0.00 0.00 39.35 2.75
2376 2512 2.163509 CTCCTTCACTCGGACTTGAGA 58.836 52.381 0.00 0.00 39.35 3.27
2377 2513 1.203523 CCTCCTTCACTCGGACTTGAG 59.796 57.143 0.00 0.00 41.86 3.02
2378 2514 1.203013 TCCTCCTTCACTCGGACTTGA 60.203 52.381 0.00 0.00 0.00 3.02
2383 2519 0.631753 ATCCTCCTCCTTCACTCGGA 59.368 55.000 0.00 0.00 0.00 4.55
2384 2520 1.137872 CAATCCTCCTCCTTCACTCGG 59.862 57.143 0.00 0.00 0.00 4.63
2385 2521 1.827969 ACAATCCTCCTCCTTCACTCG 59.172 52.381 0.00 0.00 0.00 4.18
2386 2522 2.834549 TCACAATCCTCCTCCTTCACTC 59.165 50.000 0.00 0.00 0.00 3.51
2387 2523 2.907892 TCACAATCCTCCTCCTTCACT 58.092 47.619 0.00 0.00 0.00 3.41
2388 2524 3.922171 ATCACAATCCTCCTCCTTCAC 57.078 47.619 0.00 0.00 0.00 3.18
2391 2527 2.708325 GCCTATCACAATCCTCCTCCTT 59.292 50.000 0.00 0.00 0.00 3.36
2392 2528 2.090267 AGCCTATCACAATCCTCCTCCT 60.090 50.000 0.00 0.00 0.00 3.69
2393 2529 2.334023 AGCCTATCACAATCCTCCTCC 58.666 52.381 0.00 0.00 0.00 4.30
2394 2530 3.389329 TCAAGCCTATCACAATCCTCCTC 59.611 47.826 0.00 0.00 0.00 3.71
2396 2532 3.471680 GTCAAGCCTATCACAATCCTCC 58.528 50.000 0.00 0.00 0.00 4.30
2397 2533 3.126831 CGTCAAGCCTATCACAATCCTC 58.873 50.000 0.00 0.00 0.00 3.71
2401 2554 2.555199 GCTCGTCAAGCCTATCACAAT 58.445 47.619 0.00 0.00 45.92 2.71
2412 2565 3.001939 AGTTTTAACGTTGGCTCGTCAAG 59.998 43.478 11.99 0.00 43.38 3.02
2418 2571 3.558418 TGACTGAGTTTTAACGTTGGCTC 59.442 43.478 11.99 12.56 0.00 4.70
2420 2573 3.311596 AGTGACTGAGTTTTAACGTTGGC 59.688 43.478 11.99 0.00 0.00 4.52
2424 2577 3.793559 AGCAGTGACTGAGTTTTAACGT 58.206 40.909 18.18 0.00 32.44 3.99
2425 2578 4.270084 TCAAGCAGTGACTGAGTTTTAACG 59.730 41.667 18.18 0.00 32.44 3.18
2426 2579 5.734855 TCAAGCAGTGACTGAGTTTTAAC 57.265 39.130 18.18 0.00 32.44 2.01
2448 2601 1.375551 AAGTTTTGACGTTGGCTCGT 58.624 45.000 7.85 7.85 46.88 4.18
2449 2602 2.661979 GCTAAGTTTTGACGTTGGCTCG 60.662 50.000 0.00 1.70 0.00 5.03
2450 2603 2.350484 GGCTAAGTTTTGACGTTGGCTC 60.350 50.000 0.00 0.00 0.00 4.70
2467 2620 6.042777 CGTTTCATCTTCATAAGAGTGGCTA 58.957 40.000 0.00 0.00 41.61 3.93
2468 2621 4.872691 CGTTTCATCTTCATAAGAGTGGCT 59.127 41.667 0.00 0.00 41.61 4.75
2469 2622 4.494855 GCGTTTCATCTTCATAAGAGTGGC 60.495 45.833 0.00 0.00 41.61 5.01
2472 2625 4.872691 CCTGCGTTTCATCTTCATAAGAGT 59.127 41.667 0.00 0.00 41.61 3.24
2477 2630 2.917933 CCCCTGCGTTTCATCTTCATA 58.082 47.619 0.00 0.00 0.00 2.15
2481 2634 4.002797 GCCCCTGCGTTTCATCTT 57.997 55.556 0.00 0.00 0.00 2.40
2501 2654 4.348020 AAGGTATCCTTCTGAGGTACCA 57.652 45.455 15.94 0.00 40.17 3.25
2502 2655 4.202131 CGAAAGGTATCCTTCTGAGGTACC 60.202 50.000 2.73 2.73 43.92 3.34
2503 2656 4.643784 TCGAAAGGTATCCTTCTGAGGTAC 59.356 45.833 1.36 0.00 43.92 3.34
2508 2662 6.374333 CCAAATTTCGAAAGGTATCCTTCTGA 59.626 38.462 16.80 0.94 43.92 3.27
2515 2669 4.703093 TGACCCCAAATTTCGAAAGGTATC 59.297 41.667 16.80 11.24 0.00 2.24
2519 2673 4.244862 CATTGACCCCAAATTTCGAAAGG 58.755 43.478 16.80 13.39 35.67 3.11
2520 2674 3.679502 GCATTGACCCCAAATTTCGAAAG 59.320 43.478 16.80 3.96 35.67 2.62
2525 2679 4.799564 TGTAGCATTGACCCCAAATTTC 57.200 40.909 0.00 0.00 35.67 2.17
2547 2701 8.588472 ACATCTTCATTGATATCGACATCCTTA 58.412 33.333 0.32 0.00 0.00 2.69
2550 2704 6.870439 TCACATCTTCATTGATATCGACATCC 59.130 38.462 0.32 0.00 0.00 3.51
2551 2705 7.411696 GCTCACATCTTCATTGATATCGACATC 60.412 40.741 0.00 0.00 0.00 3.06
2552 2706 6.368243 GCTCACATCTTCATTGATATCGACAT 59.632 38.462 0.00 0.00 0.00 3.06
2555 2709 5.221501 TGGCTCACATCTTCATTGATATCGA 60.222 40.000 0.00 0.00 0.00 3.59
2556 2710 4.992951 TGGCTCACATCTTCATTGATATCG 59.007 41.667 0.00 0.00 0.00 2.92
2577 2731 2.033299 CCATCCGGTTTTGATTCGATGG 59.967 50.000 0.00 0.00 33.44 3.51
2594 2748 1.031571 TTGGCGGCACTTCATCCATC 61.032 55.000 12.92 0.00 0.00 3.51
2607 2761 2.107950 TAATGTCAGAAGGTTGGCGG 57.892 50.000 0.00 0.00 0.00 6.13
2610 2764 6.016360 TGTCACAAATAATGTCAGAAGGTTGG 60.016 38.462 0.00 0.00 41.46 3.77
2615 2769 8.315391 TCTCTTGTCACAAATAATGTCAGAAG 57.685 34.615 0.00 0.00 41.46 2.85
2621 2775 5.182001 GGCACTCTCTTGTCACAAATAATGT 59.818 40.000 0.00 0.00 45.34 2.71
2625 2779 3.244078 ACGGCACTCTCTTGTCACAAATA 60.244 43.478 0.00 0.00 0.00 1.40
2626 2780 2.146342 CGGCACTCTCTTGTCACAAAT 58.854 47.619 0.00 0.00 0.00 2.32
2639 2793 5.678132 TCCTTTTAACTTTTACGGCACTC 57.322 39.130 0.00 0.00 0.00 3.51
2646 2800 9.525409 GAACCTTCCTTTCCTTTTAACTTTTAC 57.475 33.333 0.00 0.00 0.00 2.01
2647 2801 9.483489 AGAACCTTCCTTTCCTTTTAACTTTTA 57.517 29.630 0.00 0.00 0.00 1.52
2652 2806 9.175312 CCTATAGAACCTTCCTTTCCTTTTAAC 57.825 37.037 0.00 0.00 0.00 2.01
2653 2807 9.119512 TCCTATAGAACCTTCCTTTCCTTTTAA 57.880 33.333 0.00 0.00 0.00 1.52
2656 2810 6.351966 CGTCCTATAGAACCTTCCTTTCCTTT 60.352 42.308 0.00 0.00 0.00 3.11
2657 2811 5.128991 CGTCCTATAGAACCTTCCTTTCCTT 59.871 44.000 0.00 0.00 0.00 3.36
2658 2812 4.650131 CGTCCTATAGAACCTTCCTTTCCT 59.350 45.833 0.00 0.00 0.00 3.36
2659 2813 4.202233 CCGTCCTATAGAACCTTCCTTTCC 60.202 50.000 0.00 0.00 0.00 3.13
2660 2814 4.740034 GCCGTCCTATAGAACCTTCCTTTC 60.740 50.000 0.00 0.00 0.00 2.62
2672 2826 1.792949 GCACAAATCGCCGTCCTATAG 59.207 52.381 0.00 0.00 0.00 1.31
2682 2836 1.443194 CTGCCACAGCACAAATCGC 60.443 57.895 0.00 0.00 46.52 4.58
2688 2842 1.070275 CACTCTCTGCCACAGCACA 59.930 57.895 0.00 0.00 46.52 4.57
2692 2846 1.674221 GGCTAACACTCTCTGCCACAG 60.674 57.143 0.00 0.00 42.79 3.66
2696 2850 0.458716 GTCGGCTAACACTCTCTGCC 60.459 60.000 0.00 0.00 40.14 4.85
2697 2851 0.528470 AGTCGGCTAACACTCTCTGC 59.472 55.000 0.00 0.00 0.00 4.26
2698 2852 4.436242 TTTAGTCGGCTAACACTCTCTG 57.564 45.455 9.45 0.00 36.96 3.35
2699 2853 5.411781 CATTTTAGTCGGCTAACACTCTCT 58.588 41.667 9.45 0.00 36.96 3.10
2700 2854 4.033014 GCATTTTAGTCGGCTAACACTCTC 59.967 45.833 9.45 0.00 36.96 3.20
2702 2856 3.682858 TGCATTTTAGTCGGCTAACACTC 59.317 43.478 9.45 0.00 36.96 3.51
2703 2857 3.670625 TGCATTTTAGTCGGCTAACACT 58.329 40.909 9.45 0.00 36.96 3.55
2705 2859 3.815962 TGTTGCATTTTAGTCGGCTAACA 59.184 39.130 9.45 3.04 36.96 2.41
2707 2861 4.457603 ACATGTTGCATTTTAGTCGGCTAA 59.542 37.500 5.12 5.12 35.57 3.09
2708 2862 4.006989 ACATGTTGCATTTTAGTCGGCTA 58.993 39.130 0.00 0.00 0.00 3.93
2709 2863 2.819608 ACATGTTGCATTTTAGTCGGCT 59.180 40.909 0.00 0.00 0.00 5.52
2721 2877 6.098679 GCACCTAATTATTGAACATGTTGCA 58.901 36.000 17.58 10.93 0.00 4.08
2722 2878 6.098679 TGCACCTAATTATTGAACATGTTGC 58.901 36.000 17.58 9.53 0.00 4.17
2724 2880 6.806249 CGTTGCACCTAATTATTGAACATGTT 59.194 34.615 11.78 11.78 0.00 2.71
2737 2893 1.665679 CGCATCTTCGTTGCACCTAAT 59.334 47.619 0.00 0.00 40.14 1.73
2741 2897 2.202349 GCGCATCTTCGTTGCACC 60.202 61.111 0.30 0.00 40.14 5.01
2745 2901 2.804421 TAACATGCGCATCTTCGTTG 57.196 45.000 25.56 16.35 0.00 4.10
2746 2902 2.935849 TCATAACATGCGCATCTTCGTT 59.064 40.909 22.51 22.46 0.00 3.85
2749 2905 6.744537 GGATTTATCATAACATGCGCATCTTC 59.255 38.462 22.51 0.00 0.00 2.87
2750 2906 6.615088 GGATTTATCATAACATGCGCATCTT 58.385 36.000 22.51 18.44 0.00 2.40
2757 2913 9.069078 CATCATTTCGGATTTATCATAACATGC 57.931 33.333 0.00 0.00 0.00 4.06
2792 2948 3.716431 TCGGTTCTACCCCAACTCTATT 58.284 45.455 0.00 0.00 33.75 1.73
2798 2954 2.773993 TCAATCGGTTCTACCCCAAC 57.226 50.000 0.00 0.00 33.75 3.77
2826 2991 5.389520 TGTACCCAAACCATCTCAAATGAA 58.610 37.500 0.00 0.00 0.00 2.57
2831 2996 5.496556 CTGTATGTACCCAAACCATCTCAA 58.503 41.667 0.00 0.00 0.00 3.02
2843 3008 1.134098 AGGCATGTGCTGTATGTACCC 60.134 52.381 4.84 0.00 41.70 3.69
2845 3010 5.811399 TTAAAGGCATGTGCTGTATGTAC 57.189 39.130 4.84 0.00 41.70 2.90
2846 3011 6.432783 ACTTTTAAAGGCATGTGCTGTATGTA 59.567 34.615 9.64 0.00 41.70 2.29
2848 3013 5.713025 ACTTTTAAAGGCATGTGCTGTATG 58.287 37.500 9.64 0.00 41.70 2.39
2854 3019 3.988819 TGGAACTTTTAAAGGCATGTGC 58.011 40.909 9.64 0.00 41.14 4.57
2865 3030 4.513406 ACCTTGACCACTGGAACTTTTA 57.487 40.909 0.71 0.00 0.00 1.52
2867 3032 4.724279 ATACCTTGACCACTGGAACTTT 57.276 40.909 0.71 0.00 0.00 2.66
2888 3053 9.815306 ACCTCTCTTCTCATTATTAGCATAGTA 57.185 33.333 0.00 0.00 0.00 1.82
2889 3054 8.719645 ACCTCTCTTCTCATTATTAGCATAGT 57.280 34.615 0.00 0.00 0.00 2.12
2905 3082 5.997384 TTGGTCTACCTTAACCTCTCTTC 57.003 43.478 0.02 0.00 36.47 2.87
2912 3089 6.169094 GGTCTAAGTTTGGTCTACCTTAACC 58.831 44.000 11.57 0.00 34.22 2.85
2915 3092 6.999705 TTGGTCTAAGTTTGGTCTACCTTA 57.000 37.500 0.02 0.00 36.82 2.69
2916 3093 5.899631 TTGGTCTAAGTTTGGTCTACCTT 57.100 39.130 0.02 0.00 36.82 3.50
2931 3108 9.362539 GACGTTTCTTATATCAAGTTTGGTCTA 57.637 33.333 0.00 0.00 0.00 2.59
2932 3109 7.333672 GGACGTTTCTTATATCAAGTTTGGTCT 59.666 37.037 0.00 0.00 0.00 3.85
2933 3110 7.413767 GGGACGTTTCTTATATCAAGTTTGGTC 60.414 40.741 0.00 0.00 0.00 4.02
2934 3111 6.373495 GGGACGTTTCTTATATCAAGTTTGGT 59.627 38.462 0.00 0.00 0.00 3.67
2935 3112 6.598064 AGGGACGTTTCTTATATCAAGTTTGG 59.402 38.462 0.00 0.00 0.00 3.28
2936 3113 7.611213 AGGGACGTTTCTTATATCAAGTTTG 57.389 36.000 0.00 0.00 0.00 2.93
2937 3114 9.729281 TTTAGGGACGTTTCTTATATCAAGTTT 57.271 29.630 0.00 0.00 0.00 2.66
2938 3115 9.729281 TTTTAGGGACGTTTCTTATATCAAGTT 57.271 29.630 0.00 0.00 0.00 2.66
2939 3116 9.729281 TTTTTAGGGACGTTTCTTATATCAAGT 57.271 29.630 0.00 0.00 0.00 3.16
2941 3118 9.947433 TCTTTTTAGGGACGTTTCTTATATCAA 57.053 29.630 0.00 0.00 0.00 2.57
2951 3128 7.174426 CCTTCAGTTATCTTTTTAGGGACGTTT 59.826 37.037 0.00 0.00 0.00 3.60
2952 3129 6.653740 CCTTCAGTTATCTTTTTAGGGACGTT 59.346 38.462 0.00 0.00 0.00 3.99
2953 3130 6.013984 TCCTTCAGTTATCTTTTTAGGGACGT 60.014 38.462 0.00 0.00 0.00 4.34
2954 3131 6.313164 GTCCTTCAGTTATCTTTTTAGGGACG 59.687 42.308 0.00 0.00 31.01 4.79
2987 3166 0.615331 CATGGCTAGGTCTGTGGTGT 59.385 55.000 0.00 0.00 0.00 4.16
2993 3172 1.047002 CCTCTCCATGGCTAGGTCTG 58.953 60.000 19.25 0.21 0.00 3.51
2997 3176 2.876945 CGCCCTCTCCATGGCTAGG 61.877 68.421 20.15 20.15 45.71 3.02
3009 3188 1.508088 CCAACTTTCATGCGCCCTC 59.492 57.895 4.18 0.00 0.00 4.30
3011 3190 1.312371 TAGCCAACTTTCATGCGCCC 61.312 55.000 4.18 0.00 0.00 6.13
3012 3191 0.740737 ATAGCCAACTTTCATGCGCC 59.259 50.000 4.18 0.00 0.00 6.53
3014 3193 2.016318 TGGATAGCCAACTTTCATGCG 58.984 47.619 0.00 0.00 42.49 4.73


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

AutoCloner maintained by Alex Coulton.