Multiple sequence alignment - TraesCS5A01G457400

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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 TraesCS5A01G457400 chr5A 100.000 2952 0 0 1 2952 637130182 637127231 0.000000e+00 5452.0
1 TraesCS5A01G457400 chr5D 93.666 2226 97 21 46 2239 509664418 509662205 0.000000e+00 3290.0
2 TraesCS5A01G457400 chr5D 90.526 380 26 5 2563 2938 509662023 509661650 7.350000e-136 494.0
3 TraesCS5A01G457400 chr5B 93.160 2266 104 22 52 2276 640545574 640543319 0.000000e+00 3278.0
4 TraesCS5A01G457400 chr5B 94.762 210 7 1 2563 2768 640543317 640543108 1.020000e-84 324.0
5 TraesCS5A01G457400 chr5B 88.966 145 16 0 2425 2569 491710509 491710365 2.340000e-41 180.0
6 TraesCS5A01G457400 chr5B 91.262 103 6 3 2320 2421 417003397 417003297 1.430000e-28 137.0
7 TraesCS5A01G457400 chr7A 91.216 148 12 1 2425 2571 648211339 648211192 1.790000e-47 200.0
8 TraesCS5A01G457400 chr4D 90.132 152 15 0 2412 2563 459687562 459687411 6.450000e-47 198.0
9 TraesCS5A01G457400 chr4D 100.000 28 0 0 2299 2326 509649096 509649123 5.000000e-03 52.8
10 TraesCS5A01G457400 chr7B 90.845 142 12 1 2425 2566 11441167 11441307 3.880000e-44 189.0
11 TraesCS5A01G457400 chr1B 90.780 141 13 0 2425 2565 149249105 149248965 3.880000e-44 189.0
12 TraesCS5A01G457400 chr1B 88.679 106 11 1 2317 2422 178262555 178262659 8.590000e-26 128.0
13 TraesCS5A01G457400 chr2B 90.647 139 13 0 2425 2563 42980084 42979946 5.020000e-43 185.0
14 TraesCS5A01G457400 chr2B 100.000 28 0 0 2299 2326 8938515 8938542 5.000000e-03 52.8
15 TraesCS5A01G457400 chr6A 90.141 142 13 1 2425 2565 42179091 42178950 1.810000e-42 183.0
16 TraesCS5A01G457400 chr6A 93.684 95 4 2 2328 2422 35178051 35178143 1.100000e-29 141.0
17 TraesCS5A01G457400 chr6A 94.444 36 1 1 2299 2334 585165268 585165302 1.000000e-03 54.7
18 TraesCS5A01G457400 chr6A 100.000 28 0 0 2299 2326 1830022 1829995 5.000000e-03 52.8
19 TraesCS5A01G457400 chr6A 100.000 28 0 0 2299 2326 20172119 20172146 5.000000e-03 52.8
20 TraesCS5A01G457400 chr2D 90.141 142 12 2 2425 2566 6671514 6671653 1.810000e-42 183.0
21 TraesCS5A01G457400 chr2D 88.393 112 10 3 2323 2434 417995836 417995728 6.640000e-27 132.0
22 TraesCS5A01G457400 chr1A 89.583 144 15 0 2425 2568 566481145 566481002 1.810000e-42 183.0
23 TraesCS5A01G457400 chr1A 100.000 28 0 0 2299 2326 541612961 541612988 5.000000e-03 52.8
24 TraesCS5A01G457400 chr4A 92.000 100 7 1 2324 2423 205500940 205500842 3.970000e-29 139.0
25 TraesCS5A01G457400 chr4A 86.957 115 11 3 2335 2449 142446906 142446796 3.090000e-25 126.0
26 TraesCS5A01G457400 chr3B 92.000 100 3 5 2324 2421 436284352 436284256 5.130000e-28 135.0
27 TraesCS5A01G457400 chr4B 89.320 103 10 1 2317 2419 439554923 439555024 8.590000e-26 128.0
28 TraesCS5A01G457400 chr4B 88.679 106 11 1 2317 2422 597764136 597764032 8.590000e-26 128.0
29 TraesCS5A01G457400 chr4B 100.000 30 0 0 2297 2326 122296457 122296428 4.110000e-04 56.5
30 TraesCS5A01G457400 chr3A 100.000 28 0 0 2299 2326 515830939 515830966 5.000000e-03 52.8
31 TraesCS5A01G457400 chr2A 100.000 28 0 0 2299 2326 632622282 632622255 5.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G457400 chr5A 637127231 637130182 2951 True 5452 5452 100.000 1 2952 1 chr5A.!!$R1 2951
1 TraesCS5A01G457400 chr5D 509661650 509664418 2768 True 1892 3290 92.096 46 2938 2 chr5D.!!$R1 2892
2 TraesCS5A01G457400 chr5B 640543108 640545574 2466 True 1801 3278 93.961 52 2768 2 chr5B.!!$R3 2716

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
636 665 0.824109 TCATCAACCCTCTGCTACCG 59.176 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2500 0.032267 GGAGTAGTAGATGGCGTGCC 59.968 60.0 3.3 3.3 0.0 5.01 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
27 28 1.971481 TGCTCAATTCAGCACACTGT 58.029 45.000 0.00 0.00 44.73 3.55
28 29 2.300433 TGCTCAATTCAGCACACTGTT 58.700 42.857 0.00 0.00 44.73 3.16
29 30 2.689471 TGCTCAATTCAGCACACTGTTT 59.311 40.909 0.00 0.00 44.73 2.83
30 31 3.882288 TGCTCAATTCAGCACACTGTTTA 59.118 39.130 0.00 0.00 44.73 2.01
31 32 4.520111 TGCTCAATTCAGCACACTGTTTAT 59.480 37.500 0.00 0.00 44.73 1.40
32 33 5.009911 TGCTCAATTCAGCACACTGTTTATT 59.990 36.000 0.00 0.00 44.73 1.40
33 34 5.922544 GCTCAATTCAGCACACTGTTTATTT 59.077 36.000 0.00 0.00 44.77 1.40
34 35 6.421801 GCTCAATTCAGCACACTGTTTATTTT 59.578 34.615 0.00 0.00 44.77 1.82
35 36 7.568134 GCTCAATTCAGCACACTGTTTATTTTG 60.568 37.037 0.00 0.00 44.77 2.44
36 37 7.264221 TCAATTCAGCACACTGTTTATTTTGT 58.736 30.769 0.00 0.00 44.77 2.83
37 38 7.434897 TCAATTCAGCACACTGTTTATTTTGTC 59.565 33.333 0.00 0.00 44.77 3.18
38 39 5.826601 TCAGCACACTGTTTATTTTGTCA 57.173 34.783 0.00 0.00 44.77 3.58
39 40 6.389830 TCAGCACACTGTTTATTTTGTCAT 57.610 33.333 0.00 0.00 44.77 3.06
40 41 6.207928 TCAGCACACTGTTTATTTTGTCATG 58.792 36.000 0.00 0.00 44.77 3.07
41 42 5.978919 CAGCACACTGTTTATTTTGTCATGT 59.021 36.000 0.00 0.00 39.22 3.21
42 43 6.476380 CAGCACACTGTTTATTTTGTCATGTT 59.524 34.615 0.00 0.00 39.22 2.71
43 44 6.476380 AGCACACTGTTTATTTTGTCATGTTG 59.524 34.615 0.00 0.00 0.00 3.33
44 45 6.255453 GCACACTGTTTATTTTGTCATGTTGT 59.745 34.615 0.00 0.00 0.00 3.32
128 129 2.805897 CAACTTCTGCAACCCACCA 58.194 52.632 0.00 0.00 0.00 4.17
568 597 2.470821 CGGAAACCTTATCTGCTACCG 58.529 52.381 0.00 0.00 0.00 4.02
620 649 2.584608 CTCCCCGCCGAACTTCAT 59.415 61.111 0.00 0.00 0.00 2.57
636 665 0.824109 TCATCAACCCTCTGCTACCG 59.176 55.000 0.00 0.00 0.00 4.02
637 666 0.824109 CATCAACCCTCTGCTACCGA 59.176 55.000 0.00 0.00 0.00 4.69
860 902 3.568007 TGCTACTTTGCAACGGAAGATTT 59.432 39.130 7.92 0.00 40.29 2.17
897 939 1.009829 CGTTGGATCTACAGCTTGCC 58.990 55.000 0.00 0.00 0.00 4.52
925 967 2.740981 CTCTGCTGCTAACTCTGTTTGG 59.259 50.000 0.00 0.00 0.00 3.28
1098 1140 3.649277 CTGCGTCAAGTCCCGGGAG 62.649 68.421 27.72 13.49 0.00 4.30
1161 1203 1.070786 CATACCCCGGGTGAATCGG 59.929 63.158 21.85 4.12 46.43 4.18
1255 1297 1.692519 AGTATTGCATCCGTAGACCCC 59.307 52.381 0.00 0.00 0.00 4.95
1262 1310 0.342313 ATCCGTAGACCCCTTTCCCT 59.658 55.000 0.00 0.00 0.00 4.20
1266 1314 1.626825 CGTAGACCCCTTTCCCTTTGA 59.373 52.381 0.00 0.00 0.00 2.69
1267 1315 2.614734 CGTAGACCCCTTTCCCTTTGAC 60.615 54.545 0.00 0.00 0.00 3.18
1268 1316 0.778083 AGACCCCTTTCCCTTTGACC 59.222 55.000 0.00 0.00 0.00 4.02
1269 1317 0.251653 GACCCCTTTCCCTTTGACCC 60.252 60.000 0.00 0.00 0.00 4.46
1270 1318 0.704813 ACCCCTTTCCCTTTGACCCT 60.705 55.000 0.00 0.00 0.00 4.34
1271 1319 0.487325 CCCCTTTCCCTTTGACCCTT 59.513 55.000 0.00 0.00 0.00 3.95
1317 1365 1.075374 TGACCCTGGTATTTGCTTGCT 59.925 47.619 0.00 0.00 0.00 3.91
1446 1494 0.532115 ATGGGTTTGATTTCAGCGGC 59.468 50.000 0.00 0.00 0.00 6.53
1580 1628 0.037447 AAGAAGAGGCCCAAGCTGAC 59.963 55.000 0.00 0.00 39.73 3.51
1587 1635 2.260869 GCCCAAGCTGACGCAGAAA 61.261 57.895 10.46 0.00 39.10 2.52
1607 1655 6.643770 CAGAAATGCTTGCTTGTAATGTTCTT 59.356 34.615 0.00 0.00 0.00 2.52
1622 1670 9.950680 TGTAATGTTCTTTTTCATCTCAGAAAC 57.049 29.630 0.00 0.00 37.24 2.78
1644 1692 9.278734 GAAACTAAACTGTCAAGTTCTTTTCTG 57.721 33.333 7.83 0.00 46.15 3.02
1652 1700 6.842163 TGTCAAGTTCTTTTCTGTCAAAGAC 58.158 36.000 4.86 0.00 41.52 3.01
1653 1701 6.429692 TGTCAAGTTCTTTTCTGTCAAAGACA 59.570 34.615 0.00 0.00 41.52 3.41
1658 1706 7.475840 AGTTCTTTTCTGTCAAAGACATGTTC 58.524 34.615 0.00 0.00 41.52 3.18
1668 1716 5.798934 GTCAAAGACATGTTCATGCTCATTC 59.201 40.000 12.00 3.20 32.09 2.67
1669 1717 5.708697 TCAAAGACATGTTCATGCTCATTCT 59.291 36.000 12.00 5.20 0.00 2.40
1742 1791 0.540923 AGGAGCTTGGCTGTCAGATC 59.459 55.000 3.32 0.00 39.88 2.75
1744 1793 1.473080 GGAGCTTGGCTGTCAGATCTC 60.473 57.143 3.32 1.95 39.88 2.75
1750 1799 0.388659 GGCTGTCAGATCTCTCGCAT 59.611 55.000 3.32 0.00 0.00 4.73
1766 1815 4.046938 TCGCATGAGAGGTATGAAGTTC 57.953 45.455 0.00 0.00 0.00 3.01
1798 1847 1.501604 AGCTCCAAAAAGGTACCCCAA 59.498 47.619 8.74 0.00 39.02 4.12
1804 1853 5.220521 TCCAAAAAGGTACCCCAAATCTTT 58.779 37.500 8.74 0.00 39.02 2.52
1807 1856 6.239858 CCAAAAAGGTACCCCAAATCTTTGAT 60.240 38.462 8.74 0.00 40.55 2.57
1818 1867 6.383726 CCCCAAATCTTTGATTCATTTCCCTA 59.616 38.462 4.25 0.00 40.55 3.53
1861 1914 4.563184 GTGGAGCTGTTAGTTCAATCTACG 59.437 45.833 0.00 0.00 0.00 3.51
1868 1921 7.491696 AGCTGTTAGTTCAATCTACGTTTATCC 59.508 37.037 0.00 0.00 0.00 2.59
1972 2025 1.287146 AGGCAGAAGCAGGATGGATTT 59.713 47.619 0.00 0.00 44.61 2.17
2020 2073 1.146263 GCCGCACCTAGGTAGCAAT 59.854 57.895 25.89 0.00 0.00 3.56
2085 2141 1.377333 GCCCGTTTCCCTTCTCCTG 60.377 63.158 0.00 0.00 0.00 3.86
2194 2256 6.823689 ACCATGAAGCAAAATAGTGGTAGTAG 59.176 38.462 0.00 0.00 36.77 2.57
2239 2449 5.512942 TCCTCTGTGGAAAATGTTATGGA 57.487 39.130 0.00 0.00 42.94 3.41
2259 2469 3.056458 TGGAATCGCCACAGTCGT 58.944 55.556 0.00 0.00 43.33 4.34
2276 2486 1.156736 CGTTGTGGATGAGTTGGGAC 58.843 55.000 0.00 0.00 0.00 4.46
2277 2487 1.534729 GTTGTGGATGAGTTGGGACC 58.465 55.000 0.00 0.00 0.00 4.46
2278 2488 0.036164 TTGTGGATGAGTTGGGACCG 59.964 55.000 0.00 0.00 0.00 4.79
2279 2489 1.745489 GTGGATGAGTTGGGACCGC 60.745 63.158 0.00 0.00 0.00 5.68
2280 2490 2.220586 TGGATGAGTTGGGACCGCA 61.221 57.895 0.00 0.00 0.00 5.69
2281 2491 1.002624 GGATGAGTTGGGACCGCAA 60.003 57.895 0.00 0.00 0.00 4.85
2282 2492 0.394352 GGATGAGTTGGGACCGCAAT 60.394 55.000 2.89 0.00 0.00 3.56
2283 2493 0.734889 GATGAGTTGGGACCGCAATG 59.265 55.000 2.89 0.00 0.00 2.82
2284 2494 0.680921 ATGAGTTGGGACCGCAATGG 60.681 55.000 2.89 0.00 46.41 3.16
2285 2495 1.002624 GAGTTGGGACCGCAATGGA 60.003 57.895 2.89 0.00 42.00 3.41
2286 2496 1.303317 AGTTGGGACCGCAATGGAC 60.303 57.895 2.89 0.00 42.00 4.02
2287 2497 1.602323 GTTGGGACCGCAATGGACA 60.602 57.895 2.89 0.00 42.00 4.02
2288 2498 1.151679 TTGGGACCGCAATGGACAA 59.848 52.632 0.00 0.00 42.00 3.18
2289 2499 0.251564 TTGGGACCGCAATGGACAAT 60.252 50.000 0.00 0.00 42.00 2.71
2290 2500 0.964860 TGGGACCGCAATGGACAATG 60.965 55.000 0.00 0.00 42.00 2.82
2291 2501 1.666209 GGGACCGCAATGGACAATGG 61.666 60.000 0.00 0.00 42.00 3.16
2292 2502 1.139520 GACCGCAATGGACAATGGC 59.860 57.895 0.00 0.00 42.00 4.40
2293 2503 1.594194 GACCGCAATGGACAATGGCA 61.594 55.000 0.00 0.00 42.00 4.92
2294 2504 1.153784 CCGCAATGGACAATGGCAC 60.154 57.895 0.00 0.00 42.00 5.01
2295 2505 1.514657 CGCAATGGACAATGGCACG 60.515 57.895 0.00 0.00 34.48 5.34
2296 2506 1.806758 GCAATGGACAATGGCACGC 60.807 57.895 0.00 0.00 35.01 5.34
2297 2507 1.153784 CAATGGACAATGGCACGCC 60.154 57.895 0.00 0.00 0.00 5.68
2307 2517 2.896278 TGGCACGCCATCTACTACT 58.104 52.632 6.67 0.00 41.89 2.57
2308 2518 0.744874 TGGCACGCCATCTACTACTC 59.255 55.000 6.67 0.00 41.89 2.59
2309 2519 0.032267 GGCACGCCATCTACTACTCC 59.968 60.000 2.36 0.00 35.81 3.85
2310 2520 0.032267 GCACGCCATCTACTACTCCC 59.968 60.000 0.00 0.00 0.00 4.30
2311 2521 1.693627 CACGCCATCTACTACTCCCT 58.306 55.000 0.00 0.00 0.00 4.20
2312 2522 1.609555 CACGCCATCTACTACTCCCTC 59.390 57.143 0.00 0.00 0.00 4.30
2313 2523 1.249407 CGCCATCTACTACTCCCTCC 58.751 60.000 0.00 0.00 0.00 4.30
2314 2524 1.249407 GCCATCTACTACTCCCTCCG 58.751 60.000 0.00 0.00 0.00 4.63
2315 2525 1.479021 GCCATCTACTACTCCCTCCGT 60.479 57.143 0.00 0.00 0.00 4.69
2316 2526 2.946785 CCATCTACTACTCCCTCCGTT 58.053 52.381 0.00 0.00 0.00 4.44
2317 2527 2.885894 CCATCTACTACTCCCTCCGTTC 59.114 54.545 0.00 0.00 0.00 3.95
2318 2528 2.725221 TCTACTACTCCCTCCGTTCC 57.275 55.000 0.00 0.00 0.00 3.62
2319 2529 2.203584 TCTACTACTCCCTCCGTTCCT 58.796 52.381 0.00 0.00 0.00 3.36
2320 2530 3.387962 TCTACTACTCCCTCCGTTCCTA 58.612 50.000 0.00 0.00 0.00 2.94
2321 2531 3.782523 TCTACTACTCCCTCCGTTCCTAA 59.217 47.826 0.00 0.00 0.00 2.69
2322 2532 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2323 2533 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2324 2534 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2325 2535 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
2326 2536 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
2327 2537 3.450096 ACTCCCTCCGTTCCTAAATACAC 59.550 47.826 0.00 0.00 0.00 2.90
2328 2538 2.767960 TCCCTCCGTTCCTAAATACACC 59.232 50.000 0.00 0.00 0.00 4.16
2329 2539 2.770232 CCCTCCGTTCCTAAATACACCT 59.230 50.000 0.00 0.00 0.00 4.00
2330 2540 3.199289 CCCTCCGTTCCTAAATACACCTT 59.801 47.826 0.00 0.00 0.00 3.50
2331 2541 4.439968 CCTCCGTTCCTAAATACACCTTC 58.560 47.826 0.00 0.00 0.00 3.46
2332 2542 4.161754 CCTCCGTTCCTAAATACACCTTCT 59.838 45.833 0.00 0.00 0.00 2.85
2333 2543 5.080969 TCCGTTCCTAAATACACCTTCTG 57.919 43.478 0.00 0.00 0.00 3.02
2334 2544 4.529377 TCCGTTCCTAAATACACCTTCTGT 59.471 41.667 0.00 0.00 36.82 3.41
2335 2545 5.012354 TCCGTTCCTAAATACACCTTCTGTT 59.988 40.000 0.00 0.00 33.91 3.16
2336 2546 5.350640 CCGTTCCTAAATACACCTTCTGTTC 59.649 44.000 0.00 0.00 33.91 3.18
2337 2547 6.164176 CGTTCCTAAATACACCTTCTGTTCT 58.836 40.000 0.00 0.00 33.91 3.01
2338 2548 7.318141 CGTTCCTAAATACACCTTCTGTTCTA 58.682 38.462 0.00 0.00 33.91 2.10
2339 2549 7.816031 CGTTCCTAAATACACCTTCTGTTCTAA 59.184 37.037 0.00 0.00 33.91 2.10
2340 2550 9.498176 GTTCCTAAATACACCTTCTGTTCTAAA 57.502 33.333 0.00 0.00 33.91 1.85
2411 2621 9.918630 AAAGTTTGAGTCATCTATTTTGGAATG 57.081 29.630 0.00 0.00 0.00 2.67
2412 2622 8.059798 AGTTTGAGTCATCTATTTTGGAATGG 57.940 34.615 0.00 0.00 0.00 3.16
2413 2623 7.890127 AGTTTGAGTCATCTATTTTGGAATGGA 59.110 33.333 0.00 0.00 37.20 3.41
2414 2624 7.870509 TTGAGTCATCTATTTTGGAATGGAG 57.129 36.000 0.00 0.00 36.39 3.86
2415 2625 6.359804 TGAGTCATCTATTTTGGAATGGAGG 58.640 40.000 0.00 0.00 36.39 4.30
2416 2626 5.699143 AGTCATCTATTTTGGAATGGAGGG 58.301 41.667 0.00 0.00 36.39 4.30
2417 2627 5.433051 AGTCATCTATTTTGGAATGGAGGGA 59.567 40.000 0.00 0.00 36.39 4.20
2418 2628 5.767168 GTCATCTATTTTGGAATGGAGGGAG 59.233 44.000 0.00 0.00 36.39 4.30
2419 2629 5.433051 TCATCTATTTTGGAATGGAGGGAGT 59.567 40.000 0.00 0.00 36.39 3.85
2420 2630 6.619437 TCATCTATTTTGGAATGGAGGGAGTA 59.381 38.462 0.00 0.00 36.39 2.59
2421 2631 7.295672 TCATCTATTTTGGAATGGAGGGAGTAT 59.704 37.037 0.00 0.00 36.39 2.12
2422 2632 7.079451 TCTATTTTGGAATGGAGGGAGTATC 57.921 40.000 0.00 0.00 30.37 2.24
2423 2633 3.838244 TTTGGAATGGAGGGAGTATCG 57.162 47.619 0.00 0.00 34.37 2.92
2424 2634 1.717032 TGGAATGGAGGGAGTATCGG 58.283 55.000 0.00 0.00 34.37 4.18
2425 2635 1.062428 TGGAATGGAGGGAGTATCGGT 60.062 52.381 0.00 0.00 34.37 4.69
2426 2636 1.619332 GGAATGGAGGGAGTATCGGTC 59.381 57.143 0.00 0.00 34.37 4.79
2427 2637 2.599677 GAATGGAGGGAGTATCGGTCT 58.400 52.381 0.00 0.00 34.37 3.85
2428 2638 2.777459 ATGGAGGGAGTATCGGTCTT 57.223 50.000 0.00 0.00 34.37 3.01
2429 2639 2.544844 TGGAGGGAGTATCGGTCTTT 57.455 50.000 0.00 0.00 34.37 2.52
2430 2640 2.829023 TGGAGGGAGTATCGGTCTTTT 58.171 47.619 0.00 0.00 34.37 2.27
2431 2641 3.178865 TGGAGGGAGTATCGGTCTTTTT 58.821 45.455 0.00 0.00 34.37 1.94
2432 2642 4.355549 TGGAGGGAGTATCGGTCTTTTTA 58.644 43.478 0.00 0.00 34.37 1.52
2433 2643 4.404715 TGGAGGGAGTATCGGTCTTTTTAG 59.595 45.833 0.00 0.00 34.37 1.85
2434 2644 4.648307 GGAGGGAGTATCGGTCTTTTTAGA 59.352 45.833 0.00 0.00 34.37 2.10
2435 2645 5.221283 GGAGGGAGTATCGGTCTTTTTAGAG 60.221 48.000 0.00 0.00 34.37 2.43
2436 2646 5.516984 AGGGAGTATCGGTCTTTTTAGAGA 58.483 41.667 0.00 0.00 34.37 3.10
2437 2647 6.137559 AGGGAGTATCGGTCTTTTTAGAGAT 58.862 40.000 0.00 0.00 34.37 2.75
2438 2648 6.612049 AGGGAGTATCGGTCTTTTTAGAGATT 59.388 38.462 0.00 0.00 34.37 2.40
2439 2649 7.125963 AGGGAGTATCGGTCTTTTTAGAGATTT 59.874 37.037 0.00 0.00 34.37 2.17
2440 2650 7.438757 GGGAGTATCGGTCTTTTTAGAGATTTC 59.561 40.741 0.00 0.00 34.37 2.17
2441 2651 7.980099 GGAGTATCGGTCTTTTTAGAGATTTCA 59.020 37.037 0.00 0.00 34.37 2.69
2442 2652 8.705048 AGTATCGGTCTTTTTAGAGATTTCAC 57.295 34.615 0.00 0.00 0.00 3.18
2443 2653 8.532819 AGTATCGGTCTTTTTAGAGATTTCACT 58.467 33.333 0.00 0.00 0.00 3.41
2444 2654 9.798994 GTATCGGTCTTTTTAGAGATTTCACTA 57.201 33.333 0.00 0.00 0.00 2.74
2445 2655 8.705048 ATCGGTCTTTTTAGAGATTTCACTAC 57.295 34.615 0.00 0.00 0.00 2.73
2446 2656 7.663827 TCGGTCTTTTTAGAGATTTCACTACA 58.336 34.615 0.00 0.00 0.00 2.74
2447 2657 8.145767 TCGGTCTTTTTAGAGATTTCACTACAA 58.854 33.333 0.00 0.00 0.00 2.41
2448 2658 8.770828 CGGTCTTTTTAGAGATTTCACTACAAA 58.229 33.333 0.00 0.00 0.00 2.83
2449 2659 9.880064 GGTCTTTTTAGAGATTTCACTACAAAC 57.120 33.333 0.00 0.00 0.00 2.93
2458 2668 9.862371 AGAGATTTCACTACAAACTACATACAG 57.138 33.333 0.00 0.00 0.00 2.74
2459 2669 9.856488 GAGATTTCACTACAAACTACATACAGA 57.144 33.333 0.00 0.00 0.00 3.41
2504 2714 9.384764 AGAGTGTAGATTTACTTATTTTGCTCC 57.615 33.333 0.00 0.00 0.00 4.70
2505 2715 8.197988 AGTGTAGATTTACTTATTTTGCTCCG 57.802 34.615 0.00 0.00 0.00 4.63
2506 2716 7.822822 AGTGTAGATTTACTTATTTTGCTCCGT 59.177 33.333 0.00 0.00 0.00 4.69
2507 2717 9.090692 GTGTAGATTTACTTATTTTGCTCCGTA 57.909 33.333 0.00 0.00 0.00 4.02
2508 2718 9.826574 TGTAGATTTACTTATTTTGCTCCGTAT 57.173 29.630 0.00 0.00 0.00 3.06
2510 2720 8.732746 AGATTTACTTATTTTGCTCCGTATGT 57.267 30.769 0.00 0.00 0.00 2.29
2511 2721 9.826574 AGATTTACTTATTTTGCTCCGTATGTA 57.173 29.630 0.00 0.00 0.00 2.29
2513 2723 9.609346 ATTTACTTATTTTGCTCCGTATGTAGT 57.391 29.630 0.00 0.00 0.00 2.73
2514 2724 9.439500 TTTACTTATTTTGCTCCGTATGTAGTT 57.561 29.630 0.00 0.00 0.00 2.24
2515 2725 7.535489 ACTTATTTTGCTCCGTATGTAGTTC 57.465 36.000 0.00 0.00 0.00 3.01
2516 2726 7.101054 ACTTATTTTGCTCCGTATGTAGTTCA 58.899 34.615 0.00 0.00 0.00 3.18
2517 2727 7.769044 ACTTATTTTGCTCCGTATGTAGTTCAT 59.231 33.333 0.00 0.00 40.25 2.57
2518 2728 5.794687 TTTTGCTCCGTATGTAGTTCATG 57.205 39.130 0.00 0.00 37.91 3.07
2519 2729 3.452755 TGCTCCGTATGTAGTTCATGG 57.547 47.619 0.00 0.00 37.91 3.66
2520 2730 2.764010 TGCTCCGTATGTAGTTCATGGT 59.236 45.455 0.00 0.00 37.91 3.55
2521 2731 3.123804 GCTCCGTATGTAGTTCATGGTG 58.876 50.000 0.00 0.00 37.91 4.17
2522 2732 3.181479 GCTCCGTATGTAGTTCATGGTGA 60.181 47.826 0.00 0.00 37.91 4.02
2523 2733 4.679639 GCTCCGTATGTAGTTCATGGTGAA 60.680 45.833 0.00 0.00 37.91 3.18
2524 2734 5.408880 TCCGTATGTAGTTCATGGTGAAA 57.591 39.130 0.00 0.00 38.22 2.69
2525 2735 5.984725 TCCGTATGTAGTTCATGGTGAAAT 58.015 37.500 0.00 0.00 38.22 2.17
2526 2736 6.411376 TCCGTATGTAGTTCATGGTGAAATT 58.589 36.000 0.00 0.00 38.22 1.82
2527 2737 6.882140 TCCGTATGTAGTTCATGGTGAAATTT 59.118 34.615 0.00 0.00 38.22 1.82
2528 2738 7.065324 TCCGTATGTAGTTCATGGTGAAATTTC 59.935 37.037 11.41 11.41 38.22 2.17
2529 2739 7.065803 CCGTATGTAGTTCATGGTGAAATTTCT 59.934 37.037 18.64 0.00 38.22 2.52
2530 2740 9.093970 CGTATGTAGTTCATGGTGAAATTTCTA 57.906 33.333 18.64 6.33 38.22 2.10
2557 2767 9.579932 AAAAGAATTATATTTAGGAGCAGAGGG 57.420 33.333 0.00 0.00 0.00 4.30
2558 2768 8.511748 AAGAATTATATTTAGGAGCAGAGGGA 57.488 34.615 0.00 0.00 0.00 4.20
2559 2769 8.144862 AGAATTATATTTAGGAGCAGAGGGAG 57.855 38.462 0.00 0.00 0.00 4.30
2560 2770 7.737149 AGAATTATATTTAGGAGCAGAGGGAGT 59.263 37.037 0.00 0.00 0.00 3.85
2561 2771 8.974292 AATTATATTTAGGAGCAGAGGGAGTA 57.026 34.615 0.00 0.00 0.00 2.59
2571 2781 5.775701 GGAGCAGAGGGAGTAGTATTTATGA 59.224 44.000 0.00 0.00 0.00 2.15
2599 2809 2.115427 TCTTGGGCGTGATCCTGAATA 58.885 47.619 0.00 0.00 0.00 1.75
2746 2961 2.857489 GCTTCAGAGCTGCAACTTGTTG 60.857 50.000 8.95 8.95 45.65 3.33
2754 2969 1.406539 CTGCAACTTGTTGAACCTGCT 59.593 47.619 16.57 0.00 0.00 4.24
2768 2983 7.706179 TGTTGAACCTGCTTTCAAAAGAAATAG 59.294 33.333 6.67 0.00 44.96 1.73
2769 2984 6.748132 TGAACCTGCTTTCAAAAGAAATAGG 58.252 36.000 6.67 14.57 38.28 2.57
2770 2985 6.549364 TGAACCTGCTTTCAAAAGAAATAGGA 59.451 34.615 19.45 1.54 38.28 2.94
2771 2986 6.581171 ACCTGCTTTCAAAAGAAATAGGAG 57.419 37.500 19.45 8.85 38.28 3.69
2772 2987 6.071320 ACCTGCTTTCAAAAGAAATAGGAGT 58.929 36.000 19.45 4.69 38.28 3.85
2773 2988 7.231467 ACCTGCTTTCAAAAGAAATAGGAGTA 58.769 34.615 19.45 0.00 38.28 2.59
2774 2989 7.890655 ACCTGCTTTCAAAAGAAATAGGAGTAT 59.109 33.333 19.45 3.98 38.28 2.12
2775 2990 9.396022 CCTGCTTTCAAAAGAAATAGGAGTATA 57.604 33.333 6.67 0.00 38.28 1.47
2818 3035 2.743664 TGAAATGACTGAGCATGGAACG 59.256 45.455 0.00 0.00 0.00 3.95
2825 3042 2.154462 CTGAGCATGGAACGGTTTTCT 58.846 47.619 0.00 0.00 0.00 2.52
2827 3044 2.955660 TGAGCATGGAACGGTTTTCTTT 59.044 40.909 0.00 0.00 0.00 2.52
2836 3053 1.967779 ACGGTTTTCTTTGGGGAATGG 59.032 47.619 0.00 0.00 0.00 3.16
2841 3058 5.419471 CGGTTTTCTTTGGGGAATGGTATAA 59.581 40.000 0.00 0.00 0.00 0.98
2867 3084 2.884639 GCAACAACAGTCAGGTAATGGT 59.115 45.455 0.00 0.00 0.00 3.55
2871 3088 5.755409 ACAACAGTCAGGTAATGGTATGA 57.245 39.130 0.00 0.00 0.00 2.15
2898 3115 5.582269 ACATTTCACTCACTCACGGATATTG 59.418 40.000 0.00 0.00 0.00 1.90
2901 3118 3.195610 TCACTCACTCACGGATATTGCTT 59.804 43.478 0.00 0.00 0.00 3.91
2922 3139 5.695816 GCTTGCACAAGGATTTGTTATTTCA 59.304 36.000 12.09 0.00 45.01 2.69
2923 3140 6.128742 GCTTGCACAAGGATTTGTTATTTCAG 60.129 38.462 12.09 0.00 45.01 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.971481 ACAGTGTGCTGAATTGAGCA 58.029 45.000 16.06 16.06 46.87 4.26
9 10 3.360249 AAACAGTGTGCTGAATTGAGC 57.640 42.857 10.25 10.25 45.28 4.26
10 11 7.436080 ACAAAATAAACAGTGTGCTGAATTGAG 59.564 33.333 0.00 0.00 45.28 3.02
11 12 7.264221 ACAAAATAAACAGTGTGCTGAATTGA 58.736 30.769 0.00 0.00 45.28 2.57
12 13 7.222417 TGACAAAATAAACAGTGTGCTGAATTG 59.778 33.333 0.00 1.72 45.28 2.32
13 14 7.264221 TGACAAAATAAACAGTGTGCTGAATT 58.736 30.769 0.00 0.00 45.28 2.17
14 15 6.804677 TGACAAAATAAACAGTGTGCTGAAT 58.195 32.000 0.00 0.00 45.28 2.57
15 16 6.201226 TGACAAAATAAACAGTGTGCTGAA 57.799 33.333 0.00 0.00 45.28 3.02
16 17 5.826601 TGACAAAATAAACAGTGTGCTGA 57.173 34.783 0.00 0.00 45.28 4.26
18 19 6.147864 ACATGACAAAATAAACAGTGTGCT 57.852 33.333 0.00 0.00 0.00 4.40
19 20 6.255453 ACAACATGACAAAATAAACAGTGTGC 59.745 34.615 0.00 0.00 0.00 4.57
20 21 7.487509 TCACAACATGACAAAATAAACAGTGTG 59.512 33.333 0.00 0.00 29.99 3.82
21 22 7.542890 TCACAACATGACAAAATAAACAGTGT 58.457 30.769 0.00 0.00 29.99 3.55
22 23 7.984002 TCACAACATGACAAAATAAACAGTG 57.016 32.000 0.00 0.00 29.99 3.66
33 34 9.978044 TCATCAAATTTATTCACAACATGACAA 57.022 25.926 0.00 0.00 36.92 3.18
34 35 9.409312 GTCATCAAATTTATTCACAACATGACA 57.591 29.630 0.00 0.00 36.92 3.58
35 36 9.409312 TGTCATCAAATTTATTCACAACATGAC 57.591 29.630 0.00 0.00 36.92 3.06
36 37 9.978044 TTGTCATCAAATTTATTCACAACATGA 57.022 25.926 0.00 0.00 34.65 3.07
56 57 7.872113 TTGCAAGGGTTTTAAATTTTGTCAT 57.128 28.000 0.00 0.00 0.00 3.06
119 120 3.936585 CACGACTTTTGGTGGGTTG 57.063 52.632 0.00 0.00 0.00 3.77
128 129 1.202651 ACTACTGCTGCCACGACTTTT 60.203 47.619 0.00 0.00 0.00 2.27
219 227 2.595655 GGGAGAATGGGAACGGGG 59.404 66.667 0.00 0.00 0.00 5.73
220 228 2.595655 GGGGAGAATGGGAACGGG 59.404 66.667 0.00 0.00 0.00 5.28
417 446 4.379243 CAGGCGGACGCAGGAAGT 62.379 66.667 18.95 0.00 44.11 3.01
620 649 0.895530 CTTCGGTAGCAGAGGGTTGA 59.104 55.000 0.00 0.00 0.00 3.18
897 939 1.824230 AGTTAGCAGCAGAGGAGACAG 59.176 52.381 0.00 0.00 0.00 3.51
899 941 2.099405 AGAGTTAGCAGCAGAGGAGAC 58.901 52.381 0.00 0.00 0.00 3.36
925 967 1.064654 GCAGATCGGGATGAACTTTGC 59.935 52.381 0.00 0.00 0.00 3.68
1177 1219 1.937223 TGAACGAAACTGTGCGACATT 59.063 42.857 9.79 0.00 0.00 2.71
1209 1251 1.216710 CCTCCGGTGAAGAGTGCTC 59.783 63.158 4.76 0.00 0.00 4.26
1255 1297 0.969149 GGCAAGGGTCAAAGGGAAAG 59.031 55.000 0.00 0.00 0.00 2.62
1262 1310 1.754621 TTGCACGGCAAGGGTCAAA 60.755 52.632 7.15 0.00 43.99 2.69
1271 1319 1.028130 TCTTGACATTTTGCACGGCA 58.972 45.000 0.00 0.00 36.47 5.69
1317 1365 1.277842 TGTGCCTCGGATTTTCTGCTA 59.722 47.619 0.00 0.00 0.00 3.49
1323 1371 2.040544 CGCCTGTGCCTCGGATTTT 61.041 57.895 0.00 0.00 0.00 1.82
1446 1494 2.990479 CCCTTCTCTTCCACCCCG 59.010 66.667 0.00 0.00 0.00 5.73
1551 1599 1.893919 GCCTCTTCTTCGGCCTCTGT 61.894 60.000 0.00 0.00 40.43 3.41
1587 1635 6.985645 TGAAAAAGAACATTACAAGCAAGCAT 59.014 30.769 0.00 0.00 0.00 3.79
1607 1655 8.731275 TGACAGTTTAGTTTCTGAGATGAAAA 57.269 30.769 0.00 0.00 37.63 2.29
1622 1670 7.974675 TGACAGAAAAGAACTTGACAGTTTAG 58.025 34.615 0.00 0.00 43.79 1.85
1644 1692 4.754372 TGAGCATGAACATGTCTTTGAC 57.246 40.909 14.82 0.00 40.80 3.18
1652 1700 5.359009 AGGGTTAAGAATGAGCATGAACATG 59.641 40.000 10.04 10.04 41.60 3.21
1653 1701 5.513233 AGGGTTAAGAATGAGCATGAACAT 58.487 37.500 0.00 0.00 0.00 2.71
1658 1706 6.949352 ACATTAGGGTTAAGAATGAGCATG 57.051 37.500 1.10 0.00 35.12 4.06
1668 1716 6.146898 CGACCAACAAAACATTAGGGTTAAG 58.853 40.000 0.00 0.00 0.00 1.85
1669 1717 5.593502 ACGACCAACAAAACATTAGGGTTAA 59.406 36.000 0.00 0.00 0.00 2.01
1729 1778 0.174389 GCGAGAGATCTGACAGCCAA 59.826 55.000 0.00 0.00 0.00 4.52
1744 1793 3.724508 ACTTCATACCTCTCATGCGAG 57.275 47.619 5.69 5.69 40.98 5.03
1750 1799 4.844884 TCTCTCGAACTTCATACCTCTCA 58.155 43.478 0.00 0.00 0.00 3.27
1766 1815 3.584406 TTTGGAGCTCTTCTTCTCTCG 57.416 47.619 14.64 0.00 0.00 4.04
1798 1847 8.480501 CAACCATAGGGAAATGAATCAAAGATT 58.519 33.333 0.00 0.00 38.05 2.40
1804 1853 4.608269 TGCAACCATAGGGAAATGAATCA 58.392 39.130 0.00 0.00 38.05 2.57
1807 1856 4.415596 ACTTGCAACCATAGGGAAATGAA 58.584 39.130 0.00 0.00 38.05 2.57
1838 1891 4.563184 CGTAGATTGAACTAACAGCTCCAC 59.437 45.833 0.00 0.00 0.00 4.02
1854 1907 8.255206 TCAGTAACACATGGATAAACGTAGATT 58.745 33.333 0.00 0.00 0.00 2.40
1861 1914 8.916654 CGAGATATCAGTAACACATGGATAAAC 58.083 37.037 5.32 0.00 0.00 2.01
1868 1921 6.588348 TTTGCGAGATATCAGTAACACATG 57.412 37.500 5.32 0.00 0.00 3.21
2020 2073 1.206371 GCCTAGTTAGAAGAACCGCCA 59.794 52.381 0.00 0.00 0.00 5.69
2085 2141 6.488344 GGAGATTAAACAGGGGATGAAGAATC 59.512 42.308 0.00 0.00 34.19 2.52
2144 2206 3.611986 CAGACGAACAATCTCTTCAGAGC 59.388 47.826 0.00 0.00 41.80 4.09
2259 2469 0.036164 CGGTCCCAACTCATCCACAA 59.964 55.000 0.00 0.00 0.00 3.33
2269 2479 1.175983 TTGTCCATTGCGGTCCCAAC 61.176 55.000 0.00 0.00 35.57 3.77
2276 2486 1.153784 GTGCCATTGTCCATTGCGG 60.154 57.895 0.00 0.00 0.00 5.69
2277 2487 1.514657 CGTGCCATTGTCCATTGCG 60.515 57.895 0.00 0.00 0.00 4.85
2278 2488 1.806758 GCGTGCCATTGTCCATTGC 60.807 57.895 0.00 0.00 0.00 3.56
2279 2489 1.153784 GGCGTGCCATTGTCCATTG 60.154 57.895 5.89 0.00 35.81 2.82
2280 2490 1.606025 TGGCGTGCCATTGTCCATT 60.606 52.632 10.06 0.00 41.89 3.16
2281 2491 2.035469 TGGCGTGCCATTGTCCAT 59.965 55.556 10.06 0.00 41.89 3.41
2290 2500 0.032267 GGAGTAGTAGATGGCGTGCC 59.968 60.000 3.30 3.30 0.00 5.01
2291 2501 0.032267 GGGAGTAGTAGATGGCGTGC 59.968 60.000 0.00 0.00 0.00 5.34
2292 2502 1.609555 GAGGGAGTAGTAGATGGCGTG 59.390 57.143 0.00 0.00 0.00 5.34
2293 2503 1.479021 GGAGGGAGTAGTAGATGGCGT 60.479 57.143 0.00 0.00 0.00 5.68
2294 2504 1.249407 GGAGGGAGTAGTAGATGGCG 58.751 60.000 0.00 0.00 0.00 5.69
2295 2505 1.249407 CGGAGGGAGTAGTAGATGGC 58.751 60.000 0.00 0.00 0.00 4.40
2296 2506 2.660670 ACGGAGGGAGTAGTAGATGG 57.339 55.000 0.00 0.00 0.00 3.51
2297 2507 2.885894 GGAACGGAGGGAGTAGTAGATG 59.114 54.545 0.00 0.00 0.00 2.90
2298 2508 2.784682 AGGAACGGAGGGAGTAGTAGAT 59.215 50.000 0.00 0.00 0.00 1.98
2299 2509 2.203584 AGGAACGGAGGGAGTAGTAGA 58.796 52.381 0.00 0.00 0.00 2.59
2300 2510 2.732844 AGGAACGGAGGGAGTAGTAG 57.267 55.000 0.00 0.00 0.00 2.57
2301 2511 4.591321 TTTAGGAACGGAGGGAGTAGTA 57.409 45.455 0.00 0.00 0.00 1.82
2302 2512 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
2303 2513 4.891756 TGTATTTAGGAACGGAGGGAGTAG 59.108 45.833 0.00 0.00 0.00 2.57
2304 2514 4.646492 GTGTATTTAGGAACGGAGGGAGTA 59.354 45.833 0.00 0.00 0.00 2.59
2305 2515 3.450096 GTGTATTTAGGAACGGAGGGAGT 59.550 47.826 0.00 0.00 0.00 3.85
2306 2516 3.181468 GGTGTATTTAGGAACGGAGGGAG 60.181 52.174 0.00 0.00 0.00 4.30
2307 2517 2.767960 GGTGTATTTAGGAACGGAGGGA 59.232 50.000 0.00 0.00 0.00 4.20
2308 2518 2.770232 AGGTGTATTTAGGAACGGAGGG 59.230 50.000 0.00 0.00 0.00 4.30
2309 2519 4.161754 AGAAGGTGTATTTAGGAACGGAGG 59.838 45.833 0.00 0.00 0.00 4.30
2310 2520 5.109903 CAGAAGGTGTATTTAGGAACGGAG 58.890 45.833 0.00 0.00 0.00 4.63
2311 2521 4.529377 ACAGAAGGTGTATTTAGGAACGGA 59.471 41.667 0.00 0.00 37.75 4.69
2312 2522 4.828829 ACAGAAGGTGTATTTAGGAACGG 58.171 43.478 0.00 0.00 37.75 4.44
2313 2523 6.164176 AGAACAGAAGGTGTATTTAGGAACG 58.836 40.000 0.00 0.00 39.03 3.95
2314 2524 9.498176 TTTAGAACAGAAGGTGTATTTAGGAAC 57.502 33.333 0.00 0.00 39.03 3.62
2385 2595 9.918630 CATTCCAAAATAGATGACTCAAACTTT 57.081 29.630 0.00 0.00 0.00 2.66
2386 2596 8.526147 CCATTCCAAAATAGATGACTCAAACTT 58.474 33.333 0.00 0.00 0.00 2.66
2387 2597 7.890127 TCCATTCCAAAATAGATGACTCAAACT 59.110 33.333 0.00 0.00 0.00 2.66
2388 2598 8.055279 TCCATTCCAAAATAGATGACTCAAAC 57.945 34.615 0.00 0.00 0.00 2.93
2389 2599 7.340232 CCTCCATTCCAAAATAGATGACTCAAA 59.660 37.037 0.00 0.00 0.00 2.69
2390 2600 6.830324 CCTCCATTCCAAAATAGATGACTCAA 59.170 38.462 0.00 0.00 0.00 3.02
2391 2601 6.359804 CCTCCATTCCAAAATAGATGACTCA 58.640 40.000 0.00 0.00 0.00 3.41
2392 2602 5.767168 CCCTCCATTCCAAAATAGATGACTC 59.233 44.000 0.00 0.00 0.00 3.36
2393 2603 5.433051 TCCCTCCATTCCAAAATAGATGACT 59.567 40.000 0.00 0.00 0.00 3.41
2394 2604 5.694995 TCCCTCCATTCCAAAATAGATGAC 58.305 41.667 0.00 0.00 0.00 3.06
2395 2605 5.433051 ACTCCCTCCATTCCAAAATAGATGA 59.567 40.000 0.00 0.00 0.00 2.92
2396 2606 5.699143 ACTCCCTCCATTCCAAAATAGATG 58.301 41.667 0.00 0.00 0.00 2.90
2397 2607 7.527868 CGATACTCCCTCCATTCCAAAATAGAT 60.528 40.741 0.00 0.00 0.00 1.98
2398 2608 6.239600 CGATACTCCCTCCATTCCAAAATAGA 60.240 42.308 0.00 0.00 0.00 1.98
2399 2609 5.934625 CGATACTCCCTCCATTCCAAAATAG 59.065 44.000 0.00 0.00 0.00 1.73
2400 2610 5.221843 CCGATACTCCCTCCATTCCAAAATA 60.222 44.000 0.00 0.00 0.00 1.40
2401 2611 4.446311 CCGATACTCCCTCCATTCCAAAAT 60.446 45.833 0.00 0.00 0.00 1.82
2402 2612 3.118038 CCGATACTCCCTCCATTCCAAAA 60.118 47.826 0.00 0.00 0.00 2.44
2403 2613 2.438021 CCGATACTCCCTCCATTCCAAA 59.562 50.000 0.00 0.00 0.00 3.28
2404 2614 2.047061 CCGATACTCCCTCCATTCCAA 58.953 52.381 0.00 0.00 0.00 3.53
2405 2615 1.062428 ACCGATACTCCCTCCATTCCA 60.062 52.381 0.00 0.00 0.00 3.53
2406 2616 1.619332 GACCGATACTCCCTCCATTCC 59.381 57.143 0.00 0.00 0.00 3.01
2407 2617 2.599677 AGACCGATACTCCCTCCATTC 58.400 52.381 0.00 0.00 0.00 2.67
2408 2618 2.777459 AGACCGATACTCCCTCCATT 57.223 50.000 0.00 0.00 0.00 3.16
2409 2619 2.777459 AAGACCGATACTCCCTCCAT 57.223 50.000 0.00 0.00 0.00 3.41
2410 2620 2.544844 AAAGACCGATACTCCCTCCA 57.455 50.000 0.00 0.00 0.00 3.86
2411 2621 3.908643 AAAAAGACCGATACTCCCTCC 57.091 47.619 0.00 0.00 0.00 4.30
2412 2622 5.593502 TCTCTAAAAAGACCGATACTCCCTC 59.406 44.000 0.00 0.00 0.00 4.30
2413 2623 5.516984 TCTCTAAAAAGACCGATACTCCCT 58.483 41.667 0.00 0.00 0.00 4.20
2414 2624 5.848833 TCTCTAAAAAGACCGATACTCCC 57.151 43.478 0.00 0.00 0.00 4.30
2415 2625 7.980099 TGAAATCTCTAAAAAGACCGATACTCC 59.020 37.037 0.00 0.00 0.00 3.85
2416 2626 8.809478 GTGAAATCTCTAAAAAGACCGATACTC 58.191 37.037 0.00 0.00 0.00 2.59
2417 2627 8.532819 AGTGAAATCTCTAAAAAGACCGATACT 58.467 33.333 0.00 0.00 0.00 2.12
2418 2628 8.705048 AGTGAAATCTCTAAAAAGACCGATAC 57.295 34.615 0.00 0.00 0.00 2.24
2419 2629 9.798994 GTAGTGAAATCTCTAAAAAGACCGATA 57.201 33.333 0.00 0.00 0.00 2.92
2420 2630 8.311836 TGTAGTGAAATCTCTAAAAAGACCGAT 58.688 33.333 0.00 0.00 0.00 4.18
2421 2631 7.663827 TGTAGTGAAATCTCTAAAAAGACCGA 58.336 34.615 0.00 0.00 0.00 4.69
2422 2632 7.884816 TGTAGTGAAATCTCTAAAAAGACCG 57.115 36.000 0.00 0.00 0.00 4.79
2423 2633 9.880064 GTTTGTAGTGAAATCTCTAAAAAGACC 57.120 33.333 7.69 0.00 32.80 3.85
2432 2642 9.862371 CTGTATGTAGTTTGTAGTGAAATCTCT 57.138 33.333 0.00 0.00 0.00 3.10
2433 2643 9.856488 TCTGTATGTAGTTTGTAGTGAAATCTC 57.144 33.333 0.00 0.00 0.00 2.75
2436 2646 9.944376 ACATCTGTATGTAGTTTGTAGTGAAAT 57.056 29.630 0.00 0.00 44.66 2.17
2478 2688 9.384764 GGAGCAAAATAAGTAAATCTACACTCT 57.615 33.333 0.00 0.00 0.00 3.24
2479 2689 8.328864 CGGAGCAAAATAAGTAAATCTACACTC 58.671 37.037 0.00 0.00 0.00 3.51
2480 2690 7.822822 ACGGAGCAAAATAAGTAAATCTACACT 59.177 33.333 0.00 0.00 0.00 3.55
2481 2691 7.971455 ACGGAGCAAAATAAGTAAATCTACAC 58.029 34.615 0.00 0.00 0.00 2.90
2482 2692 9.826574 ATACGGAGCAAAATAAGTAAATCTACA 57.173 29.630 0.00 0.00 0.00 2.74
2484 2694 9.826574 ACATACGGAGCAAAATAAGTAAATCTA 57.173 29.630 0.00 0.00 0.00 1.98
2485 2695 8.732746 ACATACGGAGCAAAATAAGTAAATCT 57.267 30.769 0.00 0.00 0.00 2.40
2487 2697 9.609346 ACTACATACGGAGCAAAATAAGTAAAT 57.391 29.630 0.00 0.00 0.00 1.40
2488 2698 9.439500 AACTACATACGGAGCAAAATAAGTAAA 57.561 29.630 0.00 0.00 0.00 2.01
2489 2699 9.090692 GAACTACATACGGAGCAAAATAAGTAA 57.909 33.333 0.00 0.00 0.00 2.24
2490 2700 8.252417 TGAACTACATACGGAGCAAAATAAGTA 58.748 33.333 0.00 0.00 0.00 2.24
2491 2701 7.101054 TGAACTACATACGGAGCAAAATAAGT 58.899 34.615 0.00 0.00 0.00 2.24
2492 2702 7.534085 TGAACTACATACGGAGCAAAATAAG 57.466 36.000 0.00 0.00 0.00 1.73
2493 2703 7.011950 CCATGAACTACATACGGAGCAAAATAA 59.988 37.037 0.00 0.00 37.46 1.40
2494 2704 6.481976 CCATGAACTACATACGGAGCAAAATA 59.518 38.462 0.00 0.00 37.46 1.40
2495 2705 5.296780 CCATGAACTACATACGGAGCAAAAT 59.703 40.000 0.00 0.00 37.46 1.82
2496 2706 4.634004 CCATGAACTACATACGGAGCAAAA 59.366 41.667 0.00 0.00 37.46 2.44
2497 2707 4.188462 CCATGAACTACATACGGAGCAAA 58.812 43.478 0.00 0.00 37.46 3.68
2498 2708 3.196901 ACCATGAACTACATACGGAGCAA 59.803 43.478 0.00 0.00 37.46 3.91
2499 2709 2.764010 ACCATGAACTACATACGGAGCA 59.236 45.455 0.00 0.00 37.46 4.26
2500 2710 3.123804 CACCATGAACTACATACGGAGC 58.876 50.000 0.00 0.00 37.46 4.70
2501 2711 4.649088 TCACCATGAACTACATACGGAG 57.351 45.455 0.00 0.00 37.46 4.63
2502 2712 5.408880 TTTCACCATGAACTACATACGGA 57.591 39.130 0.00 0.00 35.89 4.69
2503 2713 6.677781 AATTTCACCATGAACTACATACGG 57.322 37.500 0.00 0.00 35.89 4.02
2504 2714 7.974675 AGAAATTTCACCATGAACTACATACG 58.025 34.615 19.99 0.00 35.89 3.06
2531 2741 9.579932 CCCTCTGCTCCTAAATATAATTCTTTT 57.420 33.333 0.00 0.00 0.00 2.27
2532 2742 8.949421 TCCCTCTGCTCCTAAATATAATTCTTT 58.051 33.333 0.00 0.00 0.00 2.52
2533 2743 8.511748 TCCCTCTGCTCCTAAATATAATTCTT 57.488 34.615 0.00 0.00 0.00 2.52
2534 2744 7.737149 ACTCCCTCTGCTCCTAAATATAATTCT 59.263 37.037 0.00 0.00 0.00 2.40
2535 2745 7.912719 ACTCCCTCTGCTCCTAAATATAATTC 58.087 38.462 0.00 0.00 0.00 2.17
2536 2746 7.880265 ACTCCCTCTGCTCCTAAATATAATT 57.120 36.000 0.00 0.00 0.00 1.40
2537 2747 8.180844 ACTACTCCCTCTGCTCCTAAATATAAT 58.819 37.037 0.00 0.00 0.00 1.28
2538 2748 7.536625 ACTACTCCCTCTGCTCCTAAATATAA 58.463 38.462 0.00 0.00 0.00 0.98
2539 2749 7.104974 ACTACTCCCTCTGCTCCTAAATATA 57.895 40.000 0.00 0.00 0.00 0.86
2540 2750 5.971493 ACTACTCCCTCTGCTCCTAAATAT 58.029 41.667 0.00 0.00 0.00 1.28
2541 2751 5.405063 ACTACTCCCTCTGCTCCTAAATA 57.595 43.478 0.00 0.00 0.00 1.40
2542 2752 4.273300 ACTACTCCCTCTGCTCCTAAAT 57.727 45.455 0.00 0.00 0.00 1.40
2543 2753 3.759815 ACTACTCCCTCTGCTCCTAAA 57.240 47.619 0.00 0.00 0.00 1.85
2544 2754 5.405063 AATACTACTCCCTCTGCTCCTAA 57.595 43.478 0.00 0.00 0.00 2.69
2545 2755 5.405063 AAATACTACTCCCTCTGCTCCTA 57.595 43.478 0.00 0.00 0.00 2.94
2546 2756 3.983533 AATACTACTCCCTCTGCTCCT 57.016 47.619 0.00 0.00 0.00 3.69
2547 2757 5.775701 TCATAAATACTACTCCCTCTGCTCC 59.224 44.000 0.00 0.00 0.00 4.70
2548 2758 6.294843 GGTCATAAATACTACTCCCTCTGCTC 60.295 46.154 0.00 0.00 0.00 4.26
2549 2759 5.540719 GGTCATAAATACTACTCCCTCTGCT 59.459 44.000 0.00 0.00 0.00 4.24
2550 2760 5.279556 GGGTCATAAATACTACTCCCTCTGC 60.280 48.000 0.00 0.00 0.00 4.26
2551 2761 5.246429 GGGGTCATAAATACTACTCCCTCTG 59.754 48.000 0.00 0.00 34.63 3.35
2552 2762 5.102783 TGGGGTCATAAATACTACTCCCTCT 60.103 44.000 0.00 0.00 30.96 3.69
2553 2763 5.152934 TGGGGTCATAAATACTACTCCCTC 58.847 45.833 0.00 0.00 30.96 4.30
2554 2764 5.166013 TGGGGTCATAAATACTACTCCCT 57.834 43.478 0.00 0.00 30.96 4.20
2555 2765 5.309806 ACATGGGGTCATAAATACTACTCCC 59.690 44.000 0.00 0.00 30.96 4.30
2556 2766 6.435292 ACATGGGGTCATAAATACTACTCC 57.565 41.667 0.00 0.00 32.78 3.85
2737 2952 4.108699 TGAAAGCAGGTTCAACAAGTTG 57.891 40.909 6.60 6.60 41.71 3.16
2793 3008 4.401022 TCCATGCTCAGTCATTTCAAGTT 58.599 39.130 0.00 0.00 0.00 2.66
2795 3010 4.670992 CGTTCCATGCTCAGTCATTTCAAG 60.671 45.833 0.00 0.00 0.00 3.02
2804 3019 1.880027 GAAAACCGTTCCATGCTCAGT 59.120 47.619 0.00 0.00 0.00 3.41
2818 3035 6.860790 TTATACCATTCCCCAAAGAAAACC 57.139 37.500 0.00 0.00 0.00 3.27
2825 3042 7.400339 TGTTGCTAAATTATACCATTCCCCAAA 59.600 33.333 0.00 0.00 0.00 3.28
2827 3044 6.436027 TGTTGCTAAATTATACCATTCCCCA 58.564 36.000 0.00 0.00 0.00 4.96
2836 3053 8.040716 ACCTGACTGTTGTTGCTAAATTATAC 57.959 34.615 0.00 0.00 0.00 1.47
2841 3058 6.071952 CCATTACCTGACTGTTGTTGCTAAAT 60.072 38.462 0.00 0.00 0.00 1.40
2867 3084 6.322491 CGTGAGTGAGTGAAATGTAGTCATA 58.678 40.000 0.00 0.00 33.49 2.15
2871 3088 3.572682 TCCGTGAGTGAGTGAAATGTAGT 59.427 43.478 0.00 0.00 0.00 2.73
2874 3091 3.685139 ATCCGTGAGTGAGTGAAATGT 57.315 42.857 0.00 0.00 0.00 2.71
2875 3092 5.503031 GCAATATCCGTGAGTGAGTGAAATG 60.503 44.000 0.00 0.00 0.00 2.32
2898 3115 5.695816 TGAAATAACAAATCCTTGTGCAAGC 59.304 36.000 6.42 0.00 45.25 4.01
2901 3118 5.229423 GCTGAAATAACAAATCCTTGTGCA 58.771 37.500 0.00 0.00 45.25 4.57


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

AutoCloner maintained by Alex Coulton.