Multiple sequence alignment - TraesCS5A01G305700

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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 TraesCS5A01G305700 chr5A 100.000 3950 0 0 1 3950 514189180 514193129 0.000000e+00 7295.0
1 TraesCS5A01G305700 chr5A 89.091 495 52 2 3443 3937 514263482 514263974 7.250000e-172 614.0
2 TraesCS5A01G305700 chr5A 95.588 68 3 0 3407 3474 514261302 514261369 4.170000e-20 110.0
3 TraesCS5A01G305700 chr5A 85.714 77 5 5 2439 2511 580685574 580685648 4.230000e-10 76.8
4 TraesCS5A01G305700 chr5D 95.101 2470 83 9 1 2435 408340057 408342523 0.000000e+00 3856.0
5 TraesCS5A01G305700 chr5D 89.598 1317 113 10 2624 3937 408342578 408343873 0.000000e+00 1652.0
6 TraesCS5A01G305700 chr5B 89.502 1848 147 18 624 2435 489842865 489844701 0.000000e+00 2294.0
7 TraesCS5A01G305700 chr5B 90.737 1317 111 8 2624 3937 489844756 489846064 0.000000e+00 1746.0
8 TraesCS5A01G305700 chr5B 91.071 56 4 1 2439 2493 622135525 622135470 1.520000e-09 75.0
9 TraesCS5A01G305700 chr3B 79.074 1123 194 31 2789 3879 17597801 17596688 0.000000e+00 734.0
10 TraesCS5A01G305700 chr3B 79.189 1110 185 33 2790 3864 18246268 18247366 0.000000e+00 728.0
11 TraesCS5A01G305700 chr3D 78.915 1124 194 26 2789 3879 12240282 12239169 0.000000e+00 723.0
12 TraesCS5A01G305700 chr3D 86.486 74 9 1 2439 2511 27938175 27938248 3.270000e-11 80.5
13 TraesCS5A01G305700 chr3A 77.516 1103 221 13 2784 3862 31928944 31930043 4.300000e-179 638.0
14 TraesCS5A01G305700 chr7D 75.993 1108 204 33 2790 3866 603668718 603667642 2.100000e-142 516.0
15 TraesCS5A01G305700 chrUn 76.815 496 111 4 1192 1684 20586244 20586738 3.890000e-70 276.0
16 TraesCS5A01G305700 chr1B 86.076 79 9 2 2441 2517 3656267 3656345 2.530000e-12 84.2
17 TraesCS5A01G305700 chr1B 91.071 56 4 1 2439 2493 163666819 163666764 1.520000e-09 75.0
18 TraesCS5A01G305700 chr7B 86.486 74 7 3 2439 2510 730208548 730208620 1.180000e-10 78.7
19 TraesCS5A01G305700 chr7B 78.947 114 22 2 2793 2905 593293531 593293643 4.230000e-10 76.8
20 TraesCS5A01G305700 chr6B 91.071 56 4 1 2439 2493 680530879 680530824 1.520000e-09 75.0
21 TraesCS5A01G305700 chr1A 91.071 56 4 1 2439 2493 24139851 24139906 1.520000e-09 75.0
22 TraesCS5A01G305700 chr1A 91.071 56 4 1 2439 2493 202293579 202293524 1.520000e-09 75.0
23 TraesCS5A01G305700 chr7A 77.876 113 21 4 2795 2905 634875464 634875574 2.550000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G305700 chr5A 514189180 514193129 3949 False 7295 7295 100.0000 1 3950 1 chr5A.!!$F1 3949
1 TraesCS5A01G305700 chr5A 514261302 514263974 2672 False 362 614 92.3395 3407 3937 2 chr5A.!!$F3 530
2 TraesCS5A01G305700 chr5D 408340057 408343873 3816 False 2754 3856 92.3495 1 3937 2 chr5D.!!$F1 3936
3 TraesCS5A01G305700 chr5B 489842865 489846064 3199 False 2020 2294 90.1195 624 3937 2 chr5B.!!$F1 3313
4 TraesCS5A01G305700 chr3B 17596688 17597801 1113 True 734 734 79.0740 2789 3879 1 chr3B.!!$R1 1090
5 TraesCS5A01G305700 chr3B 18246268 18247366 1098 False 728 728 79.1890 2790 3864 1 chr3B.!!$F1 1074
6 TraesCS5A01G305700 chr3D 12239169 12240282 1113 True 723 723 78.9150 2789 3879 1 chr3D.!!$R1 1090
7 TraesCS5A01G305700 chr3A 31928944 31930043 1099 False 638 638 77.5160 2784 3862 1 chr3A.!!$F1 1078
8 TraesCS5A01G305700 chr7D 603667642 603668718 1076 True 516 516 75.9930 2790 3866 1 chr7D.!!$R1 1076


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
462 463 0.546122 ACAAGTCTGTGACAAGGGCA 59.454 50.0 0.46 0.0 34.6 5.36 F
1304 1305 0.486879 AAGGATGGGCTTTTGGGTGA 59.513 50.0 0.00 0.0 0.0 4.02 F
2464 2501 0.104409 AAGTGGTCAGACCCTTCCCT 60.104 55.0 17.59 2.4 37.5 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 1518 0.179089 CTCCATCCTCAGCAACTCGG 60.179 60.0 0.00 0.0 0.00 4.63 R
2467 2504 0.033405 TAGTTCCCTCTAGCGCAGGT 60.033 55.0 11.47 0.0 44.89 4.00 R
3886 6114 0.613260 AAGTAGCGAACATCCAGCCA 59.387 50.0 0.00 0.0 0.00 4.75 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
212 213 5.279384 GTCTCGACTTGACTTGTCACTTAA 58.721 41.667 2.62 0.00 34.37 1.85
253 254 7.335171 TCGAGACATTGTCAAGATGATGATTTT 59.665 33.333 18.57 0.00 34.60 1.82
254 255 7.966753 CGAGACATTGTCAAGATGATGATTTTT 59.033 33.333 18.57 0.00 34.60 1.94
282 283 1.935873 CACAGCACCGTATCAAGATGG 59.064 52.381 0.00 0.00 0.00 3.51
462 463 0.546122 ACAAGTCTGTGACAAGGGCA 59.454 50.000 0.46 0.00 34.60 5.36
478 479 4.436113 AGGGCAAATGTTGATTTTGGTT 57.564 36.364 0.00 0.00 35.18 3.67
813 814 7.608153 TCGTCACAAGGATAATCAAGTTTAGA 58.392 34.615 0.00 0.00 0.00 2.10
896 897 1.891150 CTTTGCAATGACCAGCCTCTT 59.109 47.619 6.48 0.00 0.00 2.85
915 916 3.199946 TCTTCCCATACCACTTGACATCC 59.800 47.826 0.00 0.00 0.00 3.51
949 950 0.947244 CCAAAGCCTCACACACAGTC 59.053 55.000 0.00 0.00 0.00 3.51
963 964 6.070481 TCACACACAGTCCATAAGGCTATTTA 60.070 38.462 0.00 0.00 33.74 1.40
989 990 3.569701 TGCTTGATTGTGGGAAAGAAGAC 59.430 43.478 0.00 0.00 0.00 3.01
1085 1086 3.594134 CCTTGCTGGAGAAGAAGTACAG 58.406 50.000 0.00 0.00 38.35 2.74
1289 1290 1.839354 TGATAGTGCTGATGCCAAGGA 59.161 47.619 0.00 0.00 38.71 3.36
1304 1305 0.486879 AAGGATGGGCTTTTGGGTGA 59.513 50.000 0.00 0.00 0.00 4.02
1344 1345 5.171476 GCTCACTACAAGATTGCTAACAGA 58.829 41.667 0.00 0.00 0.00 3.41
1347 1348 7.148340 GCTCACTACAAGATTGCTAACAGAATT 60.148 37.037 0.00 0.00 0.00 2.17
1356 1357 8.038492 AGATTGCTAACAGAATTGAAGAACTC 57.962 34.615 0.00 0.00 0.00 3.01
1517 1518 0.521735 CGCCCAAAGGACAAGCTTAC 59.478 55.000 0.00 0.00 33.47 2.34
1676 1677 2.472695 TCGGTGTCTCAAAATCCCAG 57.527 50.000 0.00 0.00 0.00 4.45
1681 1682 4.562757 CGGTGTCTCAAAATCCCAGTCTTA 60.563 45.833 0.00 0.00 0.00 2.10
1818 1819 5.651576 TGCTCCTATGACTAGATCAGCTATG 59.348 44.000 0.00 0.00 41.91 2.23
1883 1884 8.652290 GGATAACCTCCATAGAATTGACTAGTT 58.348 37.037 0.00 0.00 44.26 2.24
1909 1910 8.934507 AAGTACTATCACTTCTTTATCTGTGC 57.065 34.615 0.00 0.00 33.41 4.57
1941 1942 1.122227 ACATTTGCATGGCCCCATAC 58.878 50.000 0.00 0.00 34.91 2.39
2000 2023 2.403252 ATCGAACTACTTGGGCTTGG 57.597 50.000 0.00 0.00 0.00 3.61
2013 2036 1.072173 GGGCTTGGTCATTTTTGCCTT 59.928 47.619 0.00 0.00 40.15 4.35
2014 2037 2.487086 GGGCTTGGTCATTTTTGCCTTT 60.487 45.455 0.00 0.00 40.15 3.11
2160 2184 2.047844 CACCAGAGAGCACCACCG 60.048 66.667 0.00 0.00 0.00 4.94
2230 2264 1.265365 GACTTTGAGCACAGAAGGCAC 59.735 52.381 6.91 0.00 0.00 5.01
2238 2273 3.165875 AGCACAGAAGGCACTACTTAGA 58.834 45.455 0.00 0.00 38.49 2.10
2247 2282 2.418884 GGCACTACTTAGAAGTGGAGGC 60.419 54.545 12.18 12.18 43.71 4.70
2257 2292 3.418684 GAAGTGGAGGCCTAAACTTCA 57.581 47.619 34.51 15.76 45.05 3.02
2272 2307 8.082242 GCCTAAACTTCACTGTCATTTATGTTT 58.918 33.333 0.00 0.00 0.00 2.83
2274 2309 9.612620 CTAAACTTCACTGTCATTTATGTTTCC 57.387 33.333 0.00 0.00 0.00 3.13
2278 2313 8.641541 ACTTCACTGTCATTTATGTTTCCAAAT 58.358 29.630 0.00 0.00 0.00 2.32
2280 2315 8.815141 TCACTGTCATTTATGTTTCCAAATTG 57.185 30.769 0.00 0.00 0.00 2.32
2345 2381 8.545229 AACTTCTGATCAGAATTACTCAAGTG 57.455 34.615 32.75 20.83 45.40 3.16
2348 2384 7.244886 TCTGATCAGAATTACTCAAGTGGAA 57.755 36.000 23.17 0.00 33.91 3.53
2349 2385 7.855375 TCTGATCAGAATTACTCAAGTGGAAT 58.145 34.615 23.17 0.00 33.91 3.01
2354 2390 9.739276 ATCAGAATTACTCAAGTGGAATTTACA 57.261 29.630 0.00 0.00 0.00 2.41
2364 2401 9.831737 CTCAAGTGGAATTTACAAGTAATCAAG 57.168 33.333 0.00 0.00 0.00 3.02
2386 2423 8.239314 TCAAGATTCAAACTAAGCTGCAATTAG 58.761 33.333 14.03 14.03 36.51 1.73
2388 2425 8.340618 AGATTCAAACTAAGCTGCAATTAGAA 57.659 30.769 19.92 8.47 34.86 2.10
2450 2487 3.754965 TCTCAATTGAGACCCAAAGTGG 58.245 45.455 30.05 5.43 45.48 4.00
2451 2488 3.138283 TCTCAATTGAGACCCAAAGTGGT 59.862 43.478 30.05 0.00 45.48 4.16
2458 2495 1.844130 ACCCAAAGTGGTCAGACCC 59.156 57.895 17.59 8.45 37.50 4.46
2459 2496 0.697854 ACCCAAAGTGGTCAGACCCT 60.698 55.000 17.59 10.65 37.50 4.34
2460 2497 0.478507 CCCAAAGTGGTCAGACCCTT 59.521 55.000 17.59 15.76 37.50 3.95
2461 2498 1.545651 CCCAAAGTGGTCAGACCCTTC 60.546 57.143 17.59 7.68 37.50 3.46
2462 2499 1.545651 CCAAAGTGGTCAGACCCTTCC 60.546 57.143 17.59 2.54 37.50 3.46
2463 2500 0.771755 AAAGTGGTCAGACCCTTCCC 59.228 55.000 17.59 0.05 37.50 3.97
2464 2501 0.104409 AAGTGGTCAGACCCTTCCCT 60.104 55.000 17.59 2.40 37.50 4.20
2465 2502 0.838122 AGTGGTCAGACCCTTCCCTG 60.838 60.000 17.59 0.00 37.50 4.45
2466 2503 1.538876 TGGTCAGACCCTTCCCTGG 60.539 63.158 17.59 0.00 37.50 4.45
2467 2504 1.229529 GGTCAGACCCTTCCCTGGA 60.230 63.158 8.65 0.00 30.04 3.86
2468 2505 1.554583 GGTCAGACCCTTCCCTGGAC 61.555 65.000 8.65 0.00 30.04 4.02
2469 2506 1.229529 TCAGACCCTTCCCTGGACC 60.230 63.158 0.00 0.00 0.00 4.46
2470 2507 1.229658 CAGACCCTTCCCTGGACCT 60.230 63.158 0.00 0.00 0.00 3.85
2471 2508 1.229658 AGACCCTTCCCTGGACCTG 60.230 63.158 0.00 0.00 0.00 4.00
2472 2509 2.936032 ACCCTTCCCTGGACCTGC 60.936 66.667 0.00 0.00 0.00 4.85
2473 2510 4.101448 CCCTTCCCTGGACCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2474 2511 4.785453 CCTTCCCTGGACCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2475 2512 3.710722 CTTCCCTGGACCTGCGCT 61.711 66.667 9.73 0.00 0.00 5.92
2476 2513 2.284331 TTCCCTGGACCTGCGCTA 60.284 61.111 9.73 0.00 0.00 4.26
2477 2514 2.303549 CTTCCCTGGACCTGCGCTAG 62.304 65.000 9.73 4.25 0.00 3.42
2478 2515 2.759973 CCCTGGACCTGCGCTAGA 60.760 66.667 9.73 0.00 0.00 2.43
2479 2516 2.790791 CCCTGGACCTGCGCTAGAG 61.791 68.421 9.73 0.00 0.00 2.43
2480 2517 2.790791 CCTGGACCTGCGCTAGAGG 61.791 68.421 9.73 10.21 36.57 3.69
2481 2518 2.759973 TGGACCTGCGCTAGAGGG 60.760 66.667 15.94 9.24 34.56 4.30
2482 2519 2.442272 GGACCTGCGCTAGAGGGA 60.442 66.667 15.94 0.00 34.56 4.20
2483 2520 2.058595 GGACCTGCGCTAGAGGGAA 61.059 63.158 15.94 0.00 34.56 3.97
2484 2521 1.142097 GACCTGCGCTAGAGGGAAC 59.858 63.158 15.94 4.40 34.56 3.62
2486 2523 0.033405 ACCTGCGCTAGAGGGAACTA 60.033 55.000 15.94 0.00 44.43 2.24
2487 2524 0.386113 CCTGCGCTAGAGGGAACTAC 59.614 60.000 9.73 0.00 44.43 2.73
2488 2525 0.386113 CTGCGCTAGAGGGAACTACC 59.614 60.000 9.73 0.00 44.43 3.18
2489 2526 0.033405 TGCGCTAGAGGGAACTACCT 60.033 55.000 9.73 0.00 44.43 3.08
2490 2527 0.386113 GCGCTAGAGGGAACTACCTG 59.614 60.000 0.00 0.00 44.43 4.00
2491 2528 0.386113 CGCTAGAGGGAACTACCTGC 59.614 60.000 0.00 0.00 44.43 4.85
2492 2529 1.486211 GCTAGAGGGAACTACCTGCA 58.514 55.000 0.00 0.00 44.43 4.41
2493 2530 2.043227 GCTAGAGGGAACTACCTGCAT 58.957 52.381 0.00 0.00 44.43 3.96
2494 2531 2.036604 GCTAGAGGGAACTACCTGCATC 59.963 54.545 0.00 0.00 44.43 3.91
2495 2532 1.115467 AGAGGGAACTACCTGCATCG 58.885 55.000 0.00 0.00 44.43 3.84
2496 2533 0.105039 GAGGGAACTACCTGCATCGG 59.895 60.000 0.00 0.00 44.43 4.18
2497 2534 1.146263 GGGAACTACCTGCATCGGG 59.854 63.158 0.00 0.00 38.98 5.14
2498 2535 1.523938 GGAACTACCTGCATCGGGC 60.524 63.158 0.00 0.00 45.13 6.13
2499 2536 1.523938 GAACTACCTGCATCGGGCC 60.524 63.158 0.00 0.00 43.89 5.80
2500 2537 3.385749 AACTACCTGCATCGGGCCG 62.386 63.158 22.51 22.51 43.89 6.13
2505 2542 3.520862 CTGCATCGGGCCGCATTT 61.521 61.111 23.83 2.49 43.89 2.32
2506 2543 3.067439 TGCATCGGGCCGCATTTT 61.067 55.556 23.83 0.00 43.89 1.82
2507 2544 2.184066 GCATCGGGCCGCATTTTT 59.816 55.556 23.83 0.00 36.11 1.94
2543 2580 3.764972 TCTCAATCATGCATGCTGGAAAA 59.235 39.130 22.25 2.92 0.00 2.29
2544 2581 4.221041 TCTCAATCATGCATGCTGGAAAAA 59.779 37.500 22.25 2.12 0.00 1.94
2548 2585 4.811969 TCATGCATGCTGGAAAAATTCT 57.188 36.364 22.25 0.00 0.00 2.40
2557 2594 5.385198 TGCTGGAAAAATTCTAGTGGTCTT 58.615 37.500 5.54 0.00 40.08 3.01
2558 2595 5.833131 TGCTGGAAAAATTCTAGTGGTCTTT 59.167 36.000 5.54 0.00 40.08 2.52
2559 2596 6.323739 TGCTGGAAAAATTCTAGTGGTCTTTT 59.676 34.615 5.54 0.00 40.08 2.27
2560 2597 7.147742 TGCTGGAAAAATTCTAGTGGTCTTTTT 60.148 33.333 5.54 0.00 40.08 1.94
2583 2620 5.705609 TTTTCTTAACCATGCAGGAGAAC 57.294 39.130 0.00 0.00 41.22 3.01
2584 2621 4.640771 TTCTTAACCATGCAGGAGAACT 57.359 40.909 0.00 0.00 41.22 3.01
2598 2635 6.422776 CAGGAGAACTGCACGTATAAAATT 57.577 37.500 0.00 0.00 40.97 1.82
2599 2636 6.478588 CAGGAGAACTGCACGTATAAAATTC 58.521 40.000 0.00 0.00 40.97 2.17
2600 2637 5.585047 AGGAGAACTGCACGTATAAAATTCC 59.415 40.000 0.00 0.00 0.00 3.01
2601 2638 5.353123 GGAGAACTGCACGTATAAAATTCCA 59.647 40.000 0.00 0.00 0.00 3.53
2602 2639 6.422776 AGAACTGCACGTATAAAATTCCAG 57.577 37.500 0.00 0.00 0.00 3.86
2603 2640 5.938125 AGAACTGCACGTATAAAATTCCAGT 59.062 36.000 0.00 0.00 34.10 4.00
2604 2641 5.545658 ACTGCACGTATAAAATTCCAGTG 57.454 39.130 0.00 0.00 31.74 3.66
2605 2642 4.394920 ACTGCACGTATAAAATTCCAGTGG 59.605 41.667 1.40 1.40 31.74 4.00
2606 2643 4.328536 TGCACGTATAAAATTCCAGTGGT 58.671 39.130 9.54 0.00 0.00 4.16
2607 2644 4.393680 TGCACGTATAAAATTCCAGTGGTC 59.606 41.667 9.54 0.00 0.00 4.02
2608 2645 4.634443 GCACGTATAAAATTCCAGTGGTCT 59.366 41.667 9.54 0.00 0.00 3.85
2609 2646 5.813672 GCACGTATAAAATTCCAGTGGTCTA 59.186 40.000 9.54 0.00 0.00 2.59
2610 2647 6.482308 GCACGTATAAAATTCCAGTGGTCTAT 59.518 38.462 9.54 0.00 0.00 1.98
2611 2648 7.307219 GCACGTATAAAATTCCAGTGGTCTATC 60.307 40.741 9.54 0.00 0.00 2.08
2612 2649 7.170998 CACGTATAAAATTCCAGTGGTCTATCC 59.829 40.741 9.54 0.00 0.00 2.59
2613 2650 6.365247 CGTATAAAATTCCAGTGGTCTATCCG 59.635 42.308 9.54 0.22 39.52 4.18
2614 2651 3.560636 AAATTCCAGTGGTCTATCCGG 57.439 47.619 9.54 0.00 39.52 5.14
2615 2652 1.424638 ATTCCAGTGGTCTATCCGGG 58.575 55.000 9.54 0.00 39.52 5.73
2616 2653 1.335132 TTCCAGTGGTCTATCCGGGC 61.335 60.000 9.54 0.00 39.52 6.13
2617 2654 1.762460 CCAGTGGTCTATCCGGGCT 60.762 63.158 0.00 0.00 39.52 5.19
2618 2655 1.742768 CAGTGGTCTATCCGGGCTC 59.257 63.158 0.00 0.00 39.52 4.70
2619 2656 0.757188 CAGTGGTCTATCCGGGCTCT 60.757 60.000 0.00 0.00 39.52 4.09
2620 2657 0.757188 AGTGGTCTATCCGGGCTCTG 60.757 60.000 0.00 0.00 39.52 3.35
2621 2658 2.134287 TGGTCTATCCGGGCTCTGC 61.134 63.158 0.00 0.00 39.52 4.26
2622 2659 2.134287 GGTCTATCCGGGCTCTGCA 61.134 63.158 0.00 0.00 0.00 4.41
2634 2671 1.677217 GGCTCTGCACAGGGTTCTTAG 60.677 57.143 0.00 0.00 0.00 2.18
2636 2673 2.093235 GCTCTGCACAGGGTTCTTAGAT 60.093 50.000 0.00 0.00 0.00 1.98
2646 2683 7.386299 GCACAGGGTTCTTAGATATATGTGAAG 59.614 40.741 16.72 0.00 38.16 3.02
2670 2707 9.725019 AAGTTAATGATGATACTTTCACTCACA 57.275 29.630 0.00 0.00 37.11 3.58
2675 2712 7.984422 TGATGATACTTTCACTCACATTTGT 57.016 32.000 0.00 0.00 37.11 2.83
2676 2713 8.394971 TGATGATACTTTCACTCACATTTGTT 57.605 30.769 0.00 0.00 37.11 2.83
2731 2768 9.790389 AACTAGCATATGTAAGAGCGATAATAC 57.210 33.333 4.29 0.00 0.00 1.89
2732 2769 8.407064 ACTAGCATATGTAAGAGCGATAATACC 58.593 37.037 4.29 0.00 0.00 2.73
2737 2774 3.633525 TGTAAGAGCGATAATACCGTGGT 59.366 43.478 0.00 0.00 0.00 4.16
2743 2780 3.192844 AGCGATAATACCGTGGTATCCTG 59.807 47.826 11.80 4.57 40.08 3.86
2745 2782 3.192844 CGATAATACCGTGGTATCCTGCT 59.807 47.826 11.80 0.00 40.08 4.24
2750 2787 1.596934 CGTGGTATCCTGCTGTGGT 59.403 57.895 0.00 0.00 0.00 4.16
2760 2797 6.437793 GGTATCCTGCTGTGGTTCTATACTAT 59.562 42.308 0.00 0.00 0.00 2.12
2764 2801 7.067421 TCCTGCTGTGGTTCTATACTATTAGT 58.933 38.462 1.30 1.30 0.00 2.24
2782 2819 9.647797 ACTATTAGTGTGACAAATCGTATTTCA 57.352 29.630 0.00 0.00 0.00 2.69
2796 2834 9.787532 AAATCGTATTTCATATTGTTTGACAGG 57.212 29.630 0.00 0.00 0.00 4.00
2802 2840 7.681939 TTTCATATTGTTTGACAGGTACCTC 57.318 36.000 12.84 2.30 0.00 3.85
2835 2873 6.182627 TGATGATATATGGACAATGGAAGCC 58.817 40.000 0.00 0.00 0.00 4.35
2933 2974 2.157738 AGCTCAGGCATGTTCTTGTTC 58.842 47.619 0.00 0.00 41.70 3.18
2934 2975 1.881973 GCTCAGGCATGTTCTTGTTCA 59.118 47.619 0.00 0.00 38.54 3.18
2995 3036 7.278135 TCTTGACTCAAGGAGATTATTCCATG 58.722 38.462 17.12 0.00 41.33 3.66
3038 3079 6.059787 AGATGCTTGTCCTGAGAAACTAAT 57.940 37.500 0.00 0.00 0.00 1.73
3095 3136 2.158943 GGGTTCCACTAGCCATACTGAC 60.159 54.545 0.00 0.00 35.73 3.51
3141 3182 9.942526 AATCATAAGGAGGTAAATTCAAAGGAT 57.057 29.630 0.00 0.00 0.00 3.24
3152 3193 8.321353 GGTAAATTCAAAGGATTTCTGGGAAAT 58.679 33.333 5.35 5.35 35.03 2.17
3162 3203 7.840931 AGGATTTCTGGGAAATGATACAAAAC 58.159 34.615 9.78 0.00 0.00 2.43
3198 3239 2.434336 GTTGGAAGGAAACCCTGCTTTT 59.566 45.455 0.00 0.00 35.52 2.27
3328 3369 5.699143 AGGATGATTTGGTTAAGAGATGGG 58.301 41.667 0.00 0.00 0.00 4.00
3360 3419 3.634397 TTTGTTGGCCTAGAGGAGATG 57.366 47.619 3.32 0.00 37.39 2.90
3413 3472 9.037737 CAATAAAAACATGATCCAAATAGCCAG 57.962 33.333 0.00 0.00 0.00 4.85
3538 5751 6.301169 AGGAATCCCCTATTATTCGTGATC 57.699 41.667 0.00 0.00 45.48 2.92
3539 5752 5.189934 AGGAATCCCCTATTATTCGTGATCC 59.810 44.000 0.00 0.00 45.48 3.36
3540 5753 5.045869 GGAATCCCCTATTATTCGTGATCCA 60.046 44.000 0.00 0.00 33.72 3.41
3541 5754 4.884668 TCCCCTATTATTCGTGATCCAC 57.115 45.455 0.00 0.00 0.00 4.02
3542 5755 4.228010 TCCCCTATTATTCGTGATCCACA 58.772 43.478 0.00 0.00 33.40 4.17
3543 5756 4.844085 TCCCCTATTATTCGTGATCCACAT 59.156 41.667 0.00 0.00 33.40 3.21
3548 5761 6.813649 CCTATTATTCGTGATCCACATACCAG 59.186 42.308 0.00 0.00 33.40 4.00
3553 5766 3.454447 TCGTGATCCACATACCAGGAAAT 59.546 43.478 0.00 0.00 37.48 2.17
3628 5844 0.698238 TGTGGTAGGGAGCATTGCTT 59.302 50.000 13.35 0.00 39.88 3.91
3630 5846 2.307392 TGTGGTAGGGAGCATTGCTTTA 59.693 45.455 13.35 3.73 39.88 1.85
3854 6082 8.665643 TTGCAAAAATTGAAACATCTGAAGAT 57.334 26.923 0.00 0.00 34.56 2.40
3880 6108 2.860735 GAGATCGTCGGTGGAGAAAATG 59.139 50.000 0.00 0.00 0.00 2.32
3884 6112 0.521735 GTCGGTGGAGAAAATGGTGC 59.478 55.000 0.00 0.00 0.00 5.01
3886 6114 1.176527 CGGTGGAGAAAATGGTGCAT 58.823 50.000 0.00 0.00 0.00 3.96
3887 6115 1.135315 CGGTGGAGAAAATGGTGCATG 60.135 52.381 0.00 0.00 0.00 4.06
3930 6158 3.066342 CCTCAATGTTGTGGCATCTCATC 59.934 47.826 0.00 0.00 35.36 2.92
3931 6159 3.688235 TCAATGTTGTGGCATCTCATCA 58.312 40.909 0.00 0.00 0.00 3.07
3937 6165 3.657398 TGTGGCATCTCATCATTCCTT 57.343 42.857 0.00 0.00 0.00 3.36
3938 6166 3.548770 TGTGGCATCTCATCATTCCTTC 58.451 45.455 0.00 0.00 0.00 3.46
3939 6167 3.054213 TGTGGCATCTCATCATTCCTTCA 60.054 43.478 0.00 0.00 0.00 3.02
3940 6168 3.564644 GTGGCATCTCATCATTCCTTCAG 59.435 47.826 0.00 0.00 0.00 3.02
3941 6169 3.457012 TGGCATCTCATCATTCCTTCAGA 59.543 43.478 0.00 0.00 0.00 3.27
3942 6170 4.104261 TGGCATCTCATCATTCCTTCAGAT 59.896 41.667 0.00 0.00 0.00 2.90
3943 6171 4.696402 GGCATCTCATCATTCCTTCAGATC 59.304 45.833 0.00 0.00 0.00 2.75
3944 6172 5.513441 GGCATCTCATCATTCCTTCAGATCT 60.513 44.000 0.00 0.00 0.00 2.75
3945 6173 5.410132 GCATCTCATCATTCCTTCAGATCTG 59.590 44.000 17.07 17.07 0.00 2.90
3946 6174 6.526526 CATCTCATCATTCCTTCAGATCTGT 58.473 40.000 21.92 0.00 0.00 3.41
3947 6175 6.159299 TCTCATCATTCCTTCAGATCTGTC 57.841 41.667 21.92 0.00 0.00 3.51
3948 6176 5.898397 TCTCATCATTCCTTCAGATCTGTCT 59.102 40.000 21.92 0.00 34.14 3.41
3949 6177 6.383436 TCTCATCATTCCTTCAGATCTGTCTT 59.617 38.462 21.92 0.74 30.42 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 1.293062 ACCACTACTAGACGAGGGGA 58.707 55.000 16.13 0.00 38.69 4.81
212 213 8.244113 ACAATGTCTCGAGAAAGTTTTTCTTTT 58.756 29.630 18.55 0.00 45.15 2.27
254 255 6.428465 TCTTGATACGGTGCTGTGAATAAAAA 59.572 34.615 0.00 0.00 0.00 1.94
271 272 5.419542 TCTGTAGTTGCACCATCTTGATAC 58.580 41.667 0.00 0.00 0.00 2.24
282 283 3.386768 TGACCTCTTCTGTAGTTGCAC 57.613 47.619 0.00 0.00 0.00 4.57
356 357 5.187576 GGGAATGAAGAAACCCATCAATCAA 59.812 40.000 0.00 0.00 41.72 2.57
462 463 5.366477 ACTCCTGGAACCAAAATCAACATTT 59.634 36.000 0.00 0.00 33.27 2.32
478 479 2.435805 GCATAATGGTCTCACTCCTGGA 59.564 50.000 0.00 0.00 0.00 3.86
599 600 1.766496 TCTTCCAACCGACTCCACTTT 59.234 47.619 0.00 0.00 0.00 2.66
813 814 1.305201 GTCAACCATGTGAACGGTGT 58.695 50.000 0.00 0.00 35.08 4.16
896 897 1.843851 GGGATGTCAAGTGGTATGGGA 59.156 52.381 0.00 0.00 0.00 4.37
949 950 7.750229 TCAAGCAATCTAAATAGCCTTATGG 57.250 36.000 0.00 0.00 0.00 2.74
963 964 4.410099 TCTTTCCCACAATCAAGCAATCT 58.590 39.130 0.00 0.00 0.00 2.40
989 990 1.259840 CCCCTCCATTTGTTGCAGGG 61.260 60.000 0.00 0.00 43.31 4.45
1085 1086 0.449388 CTTCGCATCTTTGGACAGCC 59.551 55.000 0.00 0.00 0.00 4.85
1289 1290 2.990740 TAGTTCACCCAAAAGCCCAT 57.009 45.000 0.00 0.00 0.00 4.00
1344 1345 4.077822 CCTGAGCCTTGAGTTCTTCAATT 58.922 43.478 0.00 0.00 44.48 2.32
1347 1348 2.037772 GACCTGAGCCTTGAGTTCTTCA 59.962 50.000 0.00 0.00 0.00 3.02
1356 1357 1.818642 CTTCCAAGACCTGAGCCTTG 58.181 55.000 6.03 6.03 39.43 3.61
1491 1492 3.494398 GCTTGTCCTTTGGGCGATCTATA 60.494 47.826 0.00 0.00 0.00 1.31
1517 1518 0.179089 CTCCATCCTCAGCAACTCGG 60.179 60.000 0.00 0.00 0.00 4.63
1681 1682 9.821240 AGAGAGTATATCTGACAATACCTTGAT 57.179 33.333 7.87 0.00 38.84 2.57
1941 1942 3.186001 GCATGTCTGAAGTGTCAACAGAG 59.814 47.826 0.00 0.00 40.55 3.35
2000 2023 7.532682 TGTTTTACAGAAAGGCAAAAATGAC 57.467 32.000 0.00 0.00 0.00 3.06
2014 2037 8.626526 GGATTTAAGTGGACTTTGTTTTACAGA 58.373 33.333 0.00 0.00 37.40 3.41
2102 2126 5.477291 AGTCTAGTTGGATACGTCATATGGG 59.523 44.000 2.13 0.00 42.51 4.00
2109 2133 6.696148 CCACATTTAGTCTAGTTGGATACGTC 59.304 42.308 0.00 0.00 42.51 4.34
2201 2235 2.170397 TGTGCTCAAAGTCTCAGACCAA 59.830 45.455 0.00 0.00 32.18 3.67
2230 2264 5.422650 AGTTTAGGCCTCCACTTCTAAGTAG 59.577 44.000 9.68 0.00 37.08 2.57
2238 2273 2.711547 AGTGAAGTTTAGGCCTCCACTT 59.288 45.455 23.51 23.51 30.19 3.16
2247 2282 9.612620 GAAACATAAATGACAGTGAAGTTTAGG 57.387 33.333 0.00 3.47 0.00 2.69
2257 2292 7.961351 TCCAATTTGGAAACATAAATGACAGT 58.039 30.769 15.83 0.00 45.00 3.55
2324 2360 6.857437 TCCACTTGAGTAATTCTGATCAGA 57.143 37.500 21.67 21.67 35.27 3.27
2326 2362 8.868522 AAATTCCACTTGAGTAATTCTGATCA 57.131 30.769 0.00 0.00 0.00 2.92
2354 2390 8.239998 GCAGCTTAGTTTGAATCTTGATTACTT 58.760 33.333 3.54 0.00 0.00 2.24
2364 2401 8.970691 TTTCTAATTGCAGCTTAGTTTGAATC 57.029 30.769 14.34 0.00 0.00 2.52
2405 2442 9.817809 AGAAATATACAGATAAAAGACTCGCAA 57.182 29.630 0.00 0.00 0.00 4.85
2440 2477 0.697854 AGGGTCTGACCACTTTGGGT 60.698 55.000 26.94 0.00 43.37 4.51
2442 2479 1.545651 GGAAGGGTCTGACCACTTTGG 60.546 57.143 26.94 0.00 41.02 3.28
2443 2480 1.545651 GGGAAGGGTCTGACCACTTTG 60.546 57.143 26.94 0.00 41.02 2.77
2446 2483 0.838122 CAGGGAAGGGTCTGACCACT 60.838 60.000 26.94 18.28 41.02 4.00
2447 2484 1.679898 CAGGGAAGGGTCTGACCAC 59.320 63.158 26.94 16.44 41.02 4.16
2448 2485 1.538876 CCAGGGAAGGGTCTGACCA 60.539 63.158 26.94 0.00 41.02 4.02
2449 2486 1.229529 TCCAGGGAAGGGTCTGACC 60.230 63.158 18.65 18.65 37.60 4.02
2450 2487 1.554583 GGTCCAGGGAAGGGTCTGAC 61.555 65.000 0.00 0.00 33.11 3.51
2451 2488 1.229529 GGTCCAGGGAAGGGTCTGA 60.230 63.158 0.00 0.00 33.11 3.27
2452 2489 1.229658 AGGTCCAGGGAAGGGTCTG 60.230 63.158 0.00 0.00 0.00 3.51
2453 2490 1.229658 CAGGTCCAGGGAAGGGTCT 60.230 63.158 0.00 0.00 0.00 3.85
2454 2491 2.972819 GCAGGTCCAGGGAAGGGTC 61.973 68.421 0.00 0.00 0.00 4.46
2455 2492 2.936032 GCAGGTCCAGGGAAGGGT 60.936 66.667 0.00 0.00 0.00 4.34
2456 2493 4.101448 CGCAGGTCCAGGGAAGGG 62.101 72.222 0.00 0.00 0.00 3.95
2457 2494 4.785453 GCGCAGGTCCAGGGAAGG 62.785 72.222 0.30 0.00 0.00 3.46
2458 2495 2.303549 CTAGCGCAGGTCCAGGGAAG 62.304 65.000 11.47 0.00 40.68 3.46
2459 2496 2.284331 TAGCGCAGGTCCAGGGAA 60.284 61.111 11.47 0.00 40.68 3.97
2460 2497 2.759973 CTAGCGCAGGTCCAGGGA 60.760 66.667 11.47 0.00 40.68 4.20
2461 2498 2.759973 TCTAGCGCAGGTCCAGGG 60.760 66.667 11.47 0.00 40.68 4.45
2462 2499 2.790791 CCTCTAGCGCAGGTCCAGG 61.791 68.421 11.47 4.20 40.68 4.45
2463 2500 2.790791 CCCTCTAGCGCAGGTCCAG 61.791 68.421 11.47 0.00 40.68 3.86
2464 2501 2.759973 CCCTCTAGCGCAGGTCCA 60.760 66.667 11.47 0.00 40.68 4.02
2465 2502 2.058595 TTCCCTCTAGCGCAGGTCC 61.059 63.158 11.47 0.00 40.68 4.46
2466 2503 1.142097 GTTCCCTCTAGCGCAGGTC 59.858 63.158 11.47 0.00 40.68 3.85
2467 2504 0.033405 TAGTTCCCTCTAGCGCAGGT 60.033 55.000 11.47 0.00 44.89 4.00
2468 2505 0.386113 GTAGTTCCCTCTAGCGCAGG 59.614 60.000 11.47 7.90 0.00 4.85
2469 2506 0.386113 GGTAGTTCCCTCTAGCGCAG 59.614 60.000 11.47 5.22 0.00 5.18
2470 2507 0.033405 AGGTAGTTCCCTCTAGCGCA 60.033 55.000 11.47 0.00 41.48 6.09
2471 2508 0.386113 CAGGTAGTTCCCTCTAGCGC 59.614 60.000 0.00 0.00 41.48 5.92
2472 2509 0.386113 GCAGGTAGTTCCCTCTAGCG 59.614 60.000 0.00 0.00 41.48 4.26
2473 2510 1.486211 TGCAGGTAGTTCCCTCTAGC 58.514 55.000 0.00 0.00 38.30 3.42
2474 2511 2.294791 CGATGCAGGTAGTTCCCTCTAG 59.705 54.545 0.00 0.00 36.75 2.43
2475 2512 2.307768 CGATGCAGGTAGTTCCCTCTA 58.692 52.381 0.00 0.00 36.75 2.43
2476 2513 1.115467 CGATGCAGGTAGTTCCCTCT 58.885 55.000 0.00 0.00 36.75 3.69
2477 2514 0.105039 CCGATGCAGGTAGTTCCCTC 59.895 60.000 0.00 0.00 36.75 4.30
2478 2515 1.338136 CCCGATGCAGGTAGTTCCCT 61.338 60.000 0.00 0.00 36.75 4.20
2479 2516 1.146263 CCCGATGCAGGTAGTTCCC 59.854 63.158 0.00 0.00 36.75 3.97
2480 2517 1.523938 GCCCGATGCAGGTAGTTCC 60.524 63.158 0.00 0.00 40.77 3.62
2481 2518 1.523938 GGCCCGATGCAGGTAGTTC 60.524 63.158 0.00 0.00 43.89 3.01
2482 2519 2.590092 GGCCCGATGCAGGTAGTT 59.410 61.111 0.00 0.00 43.89 2.24
2483 2520 3.849951 CGGCCCGATGCAGGTAGT 61.850 66.667 0.00 0.00 43.89 2.73
2488 2525 2.561549 AAAAATGCGGCCCGATGCAG 62.562 55.000 7.68 0.00 45.52 4.41
2489 2526 2.644212 AAAAATGCGGCCCGATGCA 61.644 52.632 7.68 5.46 46.51 3.96
2490 2527 2.184066 AAAAATGCGGCCCGATGC 59.816 55.556 7.68 0.00 40.16 3.91
2510 2547 9.419297 GCATGCATGATTGAGAAATATACAAAT 57.581 29.630 30.64 0.00 0.00 2.32
2511 2548 8.635328 AGCATGCATGATTGAGAAATATACAAA 58.365 29.630 30.64 0.00 0.00 2.83
2512 2549 8.079809 CAGCATGCATGATTGAGAAATATACAA 58.920 33.333 30.64 0.00 0.00 2.41
2513 2550 7.308951 CCAGCATGCATGATTGAGAAATATACA 60.309 37.037 30.64 0.00 31.97 2.29
2514 2551 7.027760 CCAGCATGCATGATTGAGAAATATAC 58.972 38.462 30.64 6.96 31.97 1.47
2515 2552 6.943718 TCCAGCATGCATGATTGAGAAATATA 59.056 34.615 30.64 0.00 31.97 0.86
2516 2553 5.773176 TCCAGCATGCATGATTGAGAAATAT 59.227 36.000 30.64 0.00 31.97 1.28
2517 2554 5.134661 TCCAGCATGCATGATTGAGAAATA 58.865 37.500 30.64 0.00 31.97 1.40
2518 2555 3.958147 TCCAGCATGCATGATTGAGAAAT 59.042 39.130 30.64 0.88 31.97 2.17
2519 2556 3.358118 TCCAGCATGCATGATTGAGAAA 58.642 40.909 30.64 10.29 31.97 2.52
2520 2557 3.007473 TCCAGCATGCATGATTGAGAA 57.993 42.857 30.64 12.39 31.97 2.87
2521 2558 2.721425 TCCAGCATGCATGATTGAGA 57.279 45.000 30.64 16.82 31.97 3.27
2522 2559 3.793797 TTTCCAGCATGCATGATTGAG 57.206 42.857 30.64 14.75 31.97 3.02
2523 2560 4.538746 TTTTTCCAGCATGCATGATTGA 57.461 36.364 30.64 22.17 31.97 2.57
2524 2561 5.584649 AGAATTTTTCCAGCATGCATGATTG 59.415 36.000 30.64 23.94 31.97 2.67
2525 2562 5.741011 AGAATTTTTCCAGCATGCATGATT 58.259 33.333 30.64 16.99 31.97 2.57
2560 2597 5.833131 AGTTCTCCTGCATGGTTAAGAAAAA 59.167 36.000 0.00 0.00 37.07 1.94
2562 2599 4.761739 CAGTTCTCCTGCATGGTTAAGAAA 59.238 41.667 0.00 0.00 33.59 2.52
2575 2612 6.422776 AATTTTATACGTGCAGTTCTCCTG 57.577 37.500 0.00 0.00 44.53 3.86
2576 2613 5.585047 GGAATTTTATACGTGCAGTTCTCCT 59.415 40.000 0.00 0.00 0.00 3.69
2577 2614 5.353123 TGGAATTTTATACGTGCAGTTCTCC 59.647 40.000 0.00 0.00 0.00 3.71
2578 2615 6.092259 ACTGGAATTTTATACGTGCAGTTCTC 59.908 38.462 0.00 0.00 39.30 2.87
2579 2616 5.938125 ACTGGAATTTTATACGTGCAGTTCT 59.062 36.000 0.00 0.00 39.30 3.01
2580 2617 6.021596 CACTGGAATTTTATACGTGCAGTTC 58.978 40.000 0.00 0.00 40.21 3.01
2581 2618 5.106317 CCACTGGAATTTTATACGTGCAGTT 60.106 40.000 0.00 0.00 40.21 3.16
2582 2619 4.394920 CCACTGGAATTTTATACGTGCAGT 59.605 41.667 0.00 0.00 42.54 4.40
2583 2620 4.394920 ACCACTGGAATTTTATACGTGCAG 59.605 41.667 0.71 0.00 35.74 4.41
2584 2621 4.328536 ACCACTGGAATTTTATACGTGCA 58.671 39.130 0.71 0.00 0.00 4.57
2585 2622 4.634443 AGACCACTGGAATTTTATACGTGC 59.366 41.667 0.71 0.00 0.00 5.34
2586 2623 7.170998 GGATAGACCACTGGAATTTTATACGTG 59.829 40.741 0.71 0.00 38.79 4.49
2587 2624 7.215085 GGATAGACCACTGGAATTTTATACGT 58.785 38.462 0.71 0.00 38.79 3.57
2588 2625 6.365247 CGGATAGACCACTGGAATTTTATACG 59.635 42.308 0.71 1.57 38.90 3.06
2589 2626 6.649557 CCGGATAGACCACTGGAATTTTATAC 59.350 42.308 0.71 0.00 38.90 1.47
2590 2627 6.239772 CCCGGATAGACCACTGGAATTTTATA 60.240 42.308 0.73 0.00 38.90 0.98
2591 2628 5.456186 CCCGGATAGACCACTGGAATTTTAT 60.456 44.000 0.73 0.00 38.90 1.40
2592 2629 4.141574 CCCGGATAGACCACTGGAATTTTA 60.142 45.833 0.73 0.00 38.90 1.52
2593 2630 3.371595 CCCGGATAGACCACTGGAATTTT 60.372 47.826 0.73 0.00 38.90 1.82
2594 2631 2.172717 CCCGGATAGACCACTGGAATTT 59.827 50.000 0.73 0.00 38.90 1.82
2595 2632 1.768870 CCCGGATAGACCACTGGAATT 59.231 52.381 0.73 0.00 38.90 2.17
2596 2633 1.424638 CCCGGATAGACCACTGGAAT 58.575 55.000 0.73 0.00 38.90 3.01
2597 2634 1.335132 GCCCGGATAGACCACTGGAA 61.335 60.000 0.73 0.00 38.90 3.53
2598 2635 1.760875 GCCCGGATAGACCACTGGA 60.761 63.158 0.73 0.00 38.90 3.86
2599 2636 1.749334 GAGCCCGGATAGACCACTGG 61.749 65.000 0.73 0.00 38.90 4.00
2600 2637 0.757188 AGAGCCCGGATAGACCACTG 60.757 60.000 0.73 0.00 38.90 3.66
2601 2638 0.757188 CAGAGCCCGGATAGACCACT 60.757 60.000 0.73 0.00 38.90 4.00
2602 2639 1.742768 CAGAGCCCGGATAGACCAC 59.257 63.158 0.73 0.00 38.90 4.16
2603 2640 2.134287 GCAGAGCCCGGATAGACCA 61.134 63.158 0.73 0.00 38.90 4.02
2604 2641 2.134287 TGCAGAGCCCGGATAGACC 61.134 63.158 0.73 0.00 0.00 3.85
2605 2642 1.068250 GTGCAGAGCCCGGATAGAC 59.932 63.158 0.73 0.00 0.00 2.59
2606 2643 1.381191 TGTGCAGAGCCCGGATAGA 60.381 57.895 0.73 0.00 0.00 1.98
2607 2644 1.068753 CTGTGCAGAGCCCGGATAG 59.931 63.158 0.73 0.00 0.00 2.08
2608 2645 2.434843 CCTGTGCAGAGCCCGGATA 61.435 63.158 0.73 0.00 0.00 2.59
2609 2646 3.790437 CCTGTGCAGAGCCCGGAT 61.790 66.667 0.73 0.00 0.00 4.18
2612 2649 4.335647 AACCCTGTGCAGAGCCCG 62.336 66.667 5.08 0.00 0.00 6.13
2613 2650 2.360475 GAACCCTGTGCAGAGCCC 60.360 66.667 5.08 0.00 0.00 5.19
2614 2651 0.324943 TAAGAACCCTGTGCAGAGCC 59.675 55.000 5.08 0.00 0.00 4.70
2615 2652 1.276421 TCTAAGAACCCTGTGCAGAGC 59.724 52.381 5.08 0.00 0.00 4.09
2616 2653 3.902881 ATCTAAGAACCCTGTGCAGAG 57.097 47.619 3.32 3.32 0.00 3.35
2617 2654 6.554982 ACATATATCTAAGAACCCTGTGCAGA 59.445 38.462 0.02 0.00 0.00 4.26
2618 2655 6.648310 CACATATATCTAAGAACCCTGTGCAG 59.352 42.308 0.00 0.00 0.00 4.41
2619 2656 6.326323 TCACATATATCTAAGAACCCTGTGCA 59.674 38.462 0.00 0.00 33.34 4.57
2620 2657 6.759272 TCACATATATCTAAGAACCCTGTGC 58.241 40.000 0.00 0.00 33.34 4.57
2621 2658 8.424918 ACTTCACATATATCTAAGAACCCTGTG 58.575 37.037 0.00 0.00 34.31 3.66
2622 2659 8.554490 ACTTCACATATATCTAAGAACCCTGT 57.446 34.615 5.61 0.00 0.00 4.00
2698 2735 9.586150 CGCTCTTACATATGCTAGTTAAATTTG 57.414 33.333 1.58 0.00 0.00 2.32
2699 2736 9.542462 TCGCTCTTACATATGCTAGTTAAATTT 57.458 29.630 1.58 0.00 0.00 1.82
2700 2737 9.712305 ATCGCTCTTACATATGCTAGTTAAATT 57.288 29.630 1.58 0.00 0.00 1.82
2731 2768 1.153369 CCACAGCAGGATACCACGG 60.153 63.158 0.00 0.00 37.17 4.94
2732 2769 0.036388 AACCACAGCAGGATACCACG 60.036 55.000 0.00 0.00 37.17 4.94
2737 2774 9.244292 CTAATAGTATAGAACCACAGCAGGATA 57.756 37.037 0.00 0.00 0.00 2.59
2743 2780 7.648510 GTCACACTAATAGTATAGAACCACAGC 59.351 40.741 0.00 0.00 0.00 4.40
2745 2782 8.584063 TGTCACACTAATAGTATAGAACCACA 57.416 34.615 0.00 0.00 0.00 4.17
2774 2811 8.120465 GGTACCTGTCAAACAATATGAAATACG 58.880 37.037 4.06 0.00 0.00 3.06
2777 2814 7.888021 TGAGGTACCTGTCAAACAATATGAAAT 59.112 33.333 22.10 0.00 0.00 2.17
2778 2815 7.227873 TGAGGTACCTGTCAAACAATATGAAA 58.772 34.615 22.10 0.00 0.00 2.69
2779 2816 6.774673 TGAGGTACCTGTCAAACAATATGAA 58.225 36.000 22.10 0.00 0.00 2.57
2780 2817 6.367374 TGAGGTACCTGTCAAACAATATGA 57.633 37.500 22.10 0.00 0.00 2.15
2781 2818 6.018751 CGATGAGGTACCTGTCAAACAATATG 60.019 42.308 22.10 0.00 0.00 1.78
2782 2819 6.049149 CGATGAGGTACCTGTCAAACAATAT 58.951 40.000 22.10 0.00 0.00 1.28
2802 2840 8.483307 TTGTCCATATATCATCAATGACGATG 57.517 34.615 1.69 0.00 43.50 3.84
2859 2897 8.317679 ACTCTACTGCCATTATTATTCTCCATC 58.682 37.037 0.00 0.00 0.00 3.51
2872 2910 8.537016 TGTAGTTGTTATAACTCTACTGCCATT 58.463 33.333 29.01 11.71 37.62 3.16
2873 2911 7.980099 GTGTAGTTGTTATAACTCTACTGCCAT 59.020 37.037 29.01 12.14 37.62 4.40
2949 2990 7.335422 TCAAGATCATTAAGAGGTTTGAGCTTC 59.665 37.037 2.80 0.00 41.42 3.86
2953 2994 7.821359 TGAGTCAAGATCATTAAGAGGTTTGAG 59.179 37.037 0.00 0.00 29.85 3.02
2995 3036 3.267031 TCTTCAGAGGGGAAAATCCTTCC 59.733 47.826 0.00 0.00 36.57 3.46
3198 3239 4.849813 AAGGACATGTCTCATCCATTGA 57.150 40.909 24.50 0.00 34.73 2.57
3233 3274 8.646900 AGGTCTTGAGATCCAGAGATAAATAAC 58.353 37.037 0.00 0.00 30.90 1.89
3252 3293 4.454847 CCAAGATATAGCATGCAGGTCTTG 59.545 45.833 28.91 28.91 40.23 3.02
3328 3369 1.281656 CAACAAAACCCTCGGCGAC 59.718 57.895 4.99 0.00 0.00 5.19
3360 3419 6.149474 TGAGCTCACTAAAATAACTTTCTGCC 59.851 38.462 13.74 0.00 0.00 4.85
3413 3472 3.057315 CACATTCCCACAGTCATCAAACC 60.057 47.826 0.00 0.00 0.00 3.27
3528 5729 4.219919 TCCTGGTATGTGGATCACGAATA 58.780 43.478 0.00 0.00 37.14 1.75
3532 5745 2.979814 TTCCTGGTATGTGGATCACG 57.020 50.000 0.00 0.00 37.14 4.35
3533 5746 3.316308 GCATTTCCTGGTATGTGGATCAC 59.684 47.826 11.31 0.00 34.56 3.06
3534 5747 3.202818 AGCATTTCCTGGTATGTGGATCA 59.797 43.478 11.31 0.00 32.64 2.92
3535 5748 3.817647 GAGCATTTCCTGGTATGTGGATC 59.182 47.826 11.31 0.00 35.19 3.36
3536 5749 3.435601 GGAGCATTTCCTGGTATGTGGAT 60.436 47.826 11.31 0.00 43.16 3.41
3537 5750 2.092429 GGAGCATTTCCTGGTATGTGGA 60.092 50.000 11.31 0.00 43.16 4.02
3538 5751 2.301346 GGAGCATTTCCTGGTATGTGG 58.699 52.381 11.31 0.00 43.16 4.17
3539 5752 3.003394 TGGAGCATTTCCTGGTATGTG 57.997 47.619 11.31 1.70 46.92 3.21
3540 5753 3.559069 CATGGAGCATTTCCTGGTATGT 58.441 45.455 11.31 2.02 46.92 2.29
3541 5754 2.889045 CCATGGAGCATTTCCTGGTATG 59.111 50.000 5.56 0.49 46.92 2.39
3542 5755 2.785269 TCCATGGAGCATTTCCTGGTAT 59.215 45.455 11.44 0.00 46.92 2.73
3543 5756 2.204463 TCCATGGAGCATTTCCTGGTA 58.796 47.619 11.44 0.00 46.92 3.25
3548 5761 2.098117 CGAACTTCCATGGAGCATTTCC 59.902 50.000 15.53 1.47 46.98 3.13
3553 5766 1.377202 GGCGAACTTCCATGGAGCA 60.377 57.895 20.79 5.68 0.00 4.26
3628 5844 6.786122 AGTTAAATGACCTAACTTGGGCTAA 58.214 36.000 0.00 0.00 36.42 3.09
3630 5846 5.256806 AGTTAAATGACCTAACTTGGGCT 57.743 39.130 0.00 0.00 36.42 5.19
3730 5958 4.036518 AGATCATACTGCTCTTCCTTGGT 58.963 43.478 0.00 0.00 0.00 3.67
3854 6082 1.954382 CTCCACCGACGATCTCCAATA 59.046 52.381 0.00 0.00 0.00 1.90
3880 6108 1.811860 GAACATCCAGCCATGCACC 59.188 57.895 0.00 0.00 0.00 5.01
3884 6112 0.940126 GTAGCGAACATCCAGCCATG 59.060 55.000 0.00 0.00 0.00 3.66
3886 6114 0.613260 AAGTAGCGAACATCCAGCCA 59.387 50.000 0.00 0.00 0.00 4.75
3887 6115 2.202566 GTAAGTAGCGAACATCCAGCC 58.797 52.381 0.00 0.00 0.00 4.85



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

AutoCloner maintained by Alex Coulton.