Multiple sequence alignment - TraesCS5A01G349500

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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 TraesCS5A01G349500 chr5A 100.000 6388 0 0 1 6388 552521546 552527933 0.000000e+00 11797
1 TraesCS5A01G349500 chr5D 96.601 3766 111 11 2630 6388 437343301 437347056 0.000000e+00 6229
2 TraesCS5A01G349500 chr5D 88.631 2674 192 48 1 2631 437340536 437343140 0.000000e+00 3151
3 TraesCS5A01G349500 chr5B 95.667 3785 121 14 2633 6388 531539631 531543401 0.000000e+00 6041
4 TraesCS5A01G349500 chr5B 88.985 2660 181 47 1 2631 531536890 531539466 0.000000e+00 3186
5 TraesCS5A01G349500 chr5B 83.575 414 66 2 1597 2009 668828288 668827876 2.790000e-103 387
6 TraesCS5A01G349500 chr6D 84.716 229 16 9 5931 6150 63818829 63818611 1.800000e-50 211


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 TraesCS5A01G349500 chr5A 552521546 552527933 6387 False 11797.0 11797 100.000 1 6388 1 chr5A.!!$F1 6387
1 TraesCS5A01G349500 chr5D 437340536 437347056 6520 False 4690.0 6229 92.616 1 6388 2 chr5D.!!$F1 6387
2 TraesCS5A01G349500 chr5B 531536890 531543401 6511 False 4613.5 6041 92.326 1 6388 2 chr5B.!!$F1 6387

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
583 585 0.325933 TGGATTCCTGTGAGGTGCTG 59.674 55.000 3.95 0.00 36.53 4.41 F
1648 1686 0.038892 GTGATGGCAAGTTGGTGCTG 60.039 55.000 4.75 0.00 44.31 4.41 F
1649 1687 0.178995 TGATGGCAAGTTGGTGCTGA 60.179 50.000 4.75 0.00 44.31 4.26 F
3038 3263 0.179004 TTGCAGGGAAAGCCTTCGAA 60.179 50.000 0.00 0.00 31.77 3.71 F
3041 3266 0.517316 CAGGGAAAGCCTTCGAAACG 59.483 55.000 0.00 0.00 31.77 3.60 F
3227 3452 1.913262 TGAAGCCCTCGAGGAGCAA 60.913 57.895 32.83 21.19 38.24 3.91 F
4751 4981 1.467734 CCACACAAGCAGAGCAATCTC 59.532 52.381 0.00 0.00 39.65 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 1731 0.036952 CGTCCCTGAACTGCATGAGT 60.037 55.000 0.00 0.00 35.94 3.41 R
2607 2668 0.259647 CCAATGAGCCATCCCAGGAA 59.740 55.000 0.00 0.00 0.00 3.36 R
3305 3530 0.259647 CCAGCATTTCCTCATCCCCA 59.740 55.000 0.00 0.00 0.00 4.96 R
3899 4124 0.328258 TTCCCCTTCAGGCTAACAGC 59.672 55.000 0.00 0.00 41.46 4.40 R
4751 4981 0.890683 GGTGCCCCTCAAAATCAGTG 59.109 55.000 0.00 0.00 0.00 3.66 R
5386 5616 2.766263 TGATGAGGCCTACGATGTCTTT 59.234 45.455 4.42 0.00 0.00 2.52 R
6223 6482 1.895051 ATCGTTACAAAAGCGCATGC 58.105 45.000 11.47 7.91 43.24 4.06 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
103 105 4.152284 AGCCTTCCTTAGTTTATTCCCG 57.848 45.455 0.00 0.00 0.00 5.14
124 126 1.085501 CGTGTAACCGCCCATGGTAC 61.086 60.000 11.73 6.75 42.89 3.34
176 178 1.060698 GACGCAATTAGTTCCGTGAGC 59.939 52.381 0.00 0.00 33.63 4.26
185 187 0.884704 GTTCCGTGAGCAAAGGAGCA 60.885 55.000 4.05 0.00 35.68 4.26
203 205 5.930135 GGAGCATTCCTTAGTTTATCCTCA 58.070 41.667 0.00 0.00 40.58 3.86
206 208 4.511826 GCATTCCTTAGTTTATCCTCACCG 59.488 45.833 0.00 0.00 0.00 4.94
218 220 1.299620 CTCACCGTATAACCGCCCG 60.300 63.158 0.00 0.00 0.00 6.13
252 254 1.810151 GGCTTGACGCAATTAGTTCCA 59.190 47.619 0.00 0.00 41.67 3.53
300 302 3.314693 TCCTCACCATATAACCCTCCAC 58.685 50.000 0.00 0.00 0.00 4.02
326 328 7.441157 CGGTATATTGGTATTGCAAAAGAGAGA 59.559 37.037 1.71 0.00 0.00 3.10
332 334 6.205784 TGGTATTGCAAAAGAGAGAAAAACG 58.794 36.000 1.71 0.00 0.00 3.60
333 335 5.629435 GGTATTGCAAAAGAGAGAAAAACGG 59.371 40.000 1.71 0.00 0.00 4.44
343 345 5.420409 AGAGAGAAAAACGGCTTGGTATAG 58.580 41.667 0.00 0.00 0.00 1.31
374 376 7.110155 TGTTAAAATCAGGACTTATCAGGGAC 58.890 38.462 0.00 0.00 0.00 4.46
379 381 3.907474 TCAGGACTTATCAGGGACAACAA 59.093 43.478 0.00 0.00 0.00 2.83
382 384 4.351111 AGGACTTATCAGGGACAACAAGTT 59.649 41.667 0.00 0.00 0.00 2.66
391 393 1.415374 GACAACAAGTTCGAGCGCTA 58.585 50.000 11.50 0.00 0.00 4.26
398 400 3.368236 ACAAGTTCGAGCGCTATTTCTTC 59.632 43.478 11.50 0.00 0.00 2.87
443 445 5.447624 AACCCAATAAGCACAACTTACAC 57.552 39.130 0.00 0.00 43.60 2.90
491 493 4.515191 GCAACTTACACAAGTGATTGGAGA 59.485 41.667 7.28 0.00 44.41 3.71
492 494 5.560953 GCAACTTACACAAGTGATTGGAGAC 60.561 44.000 7.28 0.00 44.41 3.36
583 585 0.325933 TGGATTCCTGTGAGGTGCTG 59.674 55.000 3.95 0.00 36.53 4.41
584 586 0.393537 GGATTCCTGTGAGGTGCTGG 60.394 60.000 0.00 0.00 36.53 4.85
585 587 0.393537 GATTCCTGTGAGGTGCTGGG 60.394 60.000 0.00 0.00 36.53 4.45
586 588 1.856539 ATTCCTGTGAGGTGCTGGGG 61.857 60.000 0.00 0.00 36.53 4.96
587 589 4.729918 CCTGTGAGGTGCTGGGGC 62.730 72.222 0.00 0.00 39.26 5.80
789 796 1.369839 CCATCTCACAGCAGCAGCAG 61.370 60.000 3.17 0.00 45.49 4.24
790 797 1.745864 ATCTCACAGCAGCAGCAGC 60.746 57.895 3.17 0.46 45.49 5.25
905 912 1.456705 CGGAGGAGGAAGAGGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
1030 1064 2.691252 CCCTACCACCCTCACCCC 60.691 72.222 0.00 0.00 0.00 4.95
1068 1102 1.466167 GCGAGCACATCTGACACAAAT 59.534 47.619 0.00 0.00 0.00 2.32
1199 1237 6.714356 GCTTTCAATTCCAAGGCTATCTATCT 59.286 38.462 0.00 0.00 0.00 1.98
1201 1239 9.956640 CTTTCAATTCCAAGGCTATCTATCTAT 57.043 33.333 0.00 0.00 0.00 1.98
1204 1242 9.997172 TCAATTCCAAGGCTATCTATCTATCTA 57.003 33.333 0.00 0.00 0.00 1.98
1331 1369 4.575973 GCATCTCCATGGGGCGCT 62.576 66.667 13.02 0.00 0.00 5.92
1429 1467 0.687354 ACACTTCTCGCTCACCCAAT 59.313 50.000 0.00 0.00 0.00 3.16
1469 1507 1.134461 CCTTCCTCTCAGATGCCACAG 60.134 57.143 0.00 0.00 0.00 3.66
1470 1508 0.251354 TTCCTCTCAGATGCCACAGC 59.749 55.000 0.00 0.00 40.48 4.40
1471 1509 1.153208 CCTCTCAGATGCCACAGCC 60.153 63.158 0.00 0.00 38.69 4.85
1518 1556 4.326255 CAGCACCCTGTGGATTCC 57.674 61.111 0.00 0.00 34.31 3.01
1520 1558 3.134127 GCACCCTGTGGATTCCGC 61.134 66.667 9.40 9.40 33.64 5.54
1524 1562 2.825836 CCTGTGGATTCCGCCAGC 60.826 66.667 13.60 0.00 38.95 4.85
1528 1566 3.797353 TGGATTCCGCCAGCCTCC 61.797 66.667 0.00 0.00 33.10 4.30
1547 1585 4.636435 CCACCGTCCGGCAAAGGT 62.636 66.667 5.47 0.00 39.32 3.50
1549 1587 2.190841 CACCGTCCGGCAAAGGTTT 61.191 57.895 5.47 0.00 39.32 3.27
1552 1590 1.574428 CGTCCGGCAAAGGTTTGAG 59.426 57.895 6.63 0.00 40.55 3.02
1563 1601 0.767375 AGGTTTGAGCAAGCTCTGGA 59.233 50.000 21.35 6.47 39.06 3.86
1570 1608 3.801698 TGAGCAAGCTCTGGATTACATC 58.198 45.455 21.35 0.00 43.12 3.06
1574 1612 3.243002 GCAAGCTCTGGATTACATCAAGC 60.243 47.826 0.00 0.00 33.63 4.01
1588 1626 3.734463 CATCAAGCAGATGCAGAGAGAT 58.266 45.455 7.68 0.41 46.90 2.75
1590 1628 1.600013 CAAGCAGATGCAGAGAGATGC 59.400 52.381 7.68 0.00 46.68 3.91
1621 1659 2.438254 CAGCTATGGGTGCCGCAA 60.438 61.111 0.00 0.00 34.11 4.85
1642 1680 2.507339 AAAACCGTGATGGCAAGTTG 57.493 45.000 0.00 0.00 43.94 3.16
1648 1686 0.038892 GTGATGGCAAGTTGGTGCTG 60.039 55.000 4.75 0.00 44.31 4.41
1649 1687 0.178995 TGATGGCAAGTTGGTGCTGA 60.179 50.000 4.75 0.00 44.31 4.26
1675 1713 1.718757 GCGGGCAGCCATTTACTCTG 61.719 60.000 15.19 0.00 40.81 3.35
1678 1716 1.383523 GGCAGCCATTTACTCTGGAC 58.616 55.000 6.55 0.00 35.70 4.02
1679 1717 1.340017 GGCAGCCATTTACTCTGGACA 60.340 52.381 6.55 0.00 35.70 4.02
1681 1719 2.162408 GCAGCCATTTACTCTGGACAAC 59.838 50.000 0.00 0.00 35.70 3.32
1690 1728 2.614259 ACTCTGGACAACACCTCAGAT 58.386 47.619 0.00 0.00 35.95 2.90
1693 1731 4.019858 CTCTGGACAACACCTCAGATAGA 58.980 47.826 0.00 0.00 35.95 1.98
1698 1736 4.404073 GGACAACACCTCAGATAGACTCAT 59.596 45.833 0.00 0.00 0.00 2.90
1699 1737 5.336150 ACAACACCTCAGATAGACTCATG 57.664 43.478 0.00 0.00 0.00 3.07
1711 1749 1.277557 AGACTCATGCAGTTCAGGGAC 59.722 52.381 0.00 0.00 34.41 4.46
1729 1767 1.700029 CGTGTCGACGCATTACCAC 59.300 57.895 27.16 8.99 39.10 4.16
1746 1784 2.082231 CCACTTCTCTGCAGATGTTGG 58.918 52.381 18.63 16.67 35.36 3.77
1753 1791 0.321564 CTGCAGATGTTGGGTCGGAA 60.322 55.000 8.42 0.00 0.00 4.30
1754 1792 0.321564 TGCAGATGTTGGGTCGGAAG 60.322 55.000 0.00 0.00 0.00 3.46
1759 1797 1.488705 ATGTTGGGTCGGAAGCCTCA 61.489 55.000 0.00 0.00 43.82 3.86
1816 1854 2.657237 CCTGAGTGGTCACCGGAC 59.343 66.667 9.46 0.00 43.55 4.79
1840 1878 1.134699 CGGCTCTTCACCAGCTATGAA 60.135 52.381 11.12 11.12 37.05 2.57
1865 1903 3.490348 CCCAGGGTAAAATATGCTCAGG 58.510 50.000 0.00 0.00 0.00 3.86
1912 1950 2.264794 CCGGTGTTCGAGAAGGGG 59.735 66.667 0.00 0.00 42.43 4.79
1940 1978 1.549203 GTGCTTGGGTGTCATGGAAT 58.451 50.000 0.00 0.00 0.00 3.01
1957 1995 3.025978 GGAATTGATCATGACCAGGCAA 58.974 45.455 0.00 0.00 0.00 4.52
1975 2013 2.358898 GCAAAAGCTCAACTTCACCTCA 59.641 45.455 0.00 0.00 37.75 3.86
1985 2023 3.584406 ACTTCACCTCAGAGATCAACG 57.416 47.619 0.00 0.00 0.00 4.10
1990 2028 3.129462 TCACCTCAGAGATCAACGACATC 59.871 47.826 0.00 0.00 0.00 3.06
1996 2034 2.159128 AGAGATCAACGACATCTGCAGG 60.159 50.000 15.13 0.36 30.30 4.85
2013 2051 1.839994 CAGGGCTCTCCAGGTATTGAA 59.160 52.381 0.00 0.00 38.24 2.69
2014 2052 1.840635 AGGGCTCTCCAGGTATTGAAC 59.159 52.381 0.00 0.00 38.24 3.18
2015 2053 1.840635 GGGCTCTCCAGGTATTGAACT 59.159 52.381 0.00 0.00 35.00 3.01
2016 2054 3.039011 GGGCTCTCCAGGTATTGAACTA 58.961 50.000 0.00 0.00 35.00 2.24
2017 2055 3.648545 GGGCTCTCCAGGTATTGAACTAT 59.351 47.826 0.00 0.00 35.00 2.12
2018 2056 4.103311 GGGCTCTCCAGGTATTGAACTATT 59.897 45.833 0.00 0.00 35.00 1.73
2019 2057 5.059833 GGCTCTCCAGGTATTGAACTATTG 58.940 45.833 0.00 0.00 0.00 1.90
2020 2058 5.163301 GGCTCTCCAGGTATTGAACTATTGA 60.163 44.000 0.00 0.00 0.00 2.57
2021 2059 6.465035 GGCTCTCCAGGTATTGAACTATTGAT 60.465 42.308 0.00 0.00 0.00 2.57
2022 2060 7.256332 GGCTCTCCAGGTATTGAACTATTGATA 60.256 40.741 0.00 0.00 0.00 2.15
2023 2061 7.600752 GCTCTCCAGGTATTGAACTATTGATAC 59.399 40.741 0.00 0.00 0.00 2.24
2024 2062 7.963532 TCTCCAGGTATTGAACTATTGATACC 58.036 38.462 3.74 3.74 42.70 2.73
2044 2082 4.962155 ACCTCAGTCACTTAACCTGAAAG 58.038 43.478 0.00 0.00 34.99 2.62
2063 2101 7.168135 CCTGAAAGTTTTCAAACATTAGTCTGC 59.832 37.037 8.48 0.00 45.61 4.26
2065 2103 7.701924 TGAAAGTTTTCAAACATTAGTCTGCAG 59.298 33.333 7.63 7.63 43.62 4.41
2073 2111 7.102993 TCAAACATTAGTCTGCAGCAAGTATA 58.897 34.615 9.47 0.00 0.00 1.47
2074 2112 7.278646 TCAAACATTAGTCTGCAGCAAGTATAG 59.721 37.037 9.47 0.00 0.00 1.31
2075 2113 6.227298 ACATTAGTCTGCAGCAAGTATAGT 57.773 37.500 9.47 0.00 0.00 2.12
2076 2114 6.644347 ACATTAGTCTGCAGCAAGTATAGTT 58.356 36.000 9.47 0.00 0.00 2.24
2077 2115 6.536582 ACATTAGTCTGCAGCAAGTATAGTTG 59.463 38.462 9.47 14.86 0.00 3.16
2102 2140 5.289193 CACAAAAAGAGTGTTTGGTGTCATG 59.711 40.000 8.72 0.00 37.56 3.07
2107 2145 4.380531 AGAGTGTTTGGTGTCATGTGTAG 58.619 43.478 0.00 0.00 0.00 2.74
2108 2146 3.476552 AGTGTTTGGTGTCATGTGTAGG 58.523 45.455 0.00 0.00 0.00 3.18
2109 2147 3.135712 AGTGTTTGGTGTCATGTGTAGGA 59.864 43.478 0.00 0.00 0.00 2.94
2110 2148 3.498397 GTGTTTGGTGTCATGTGTAGGAG 59.502 47.826 0.00 0.00 0.00 3.69
2111 2149 2.472695 TTGGTGTCATGTGTAGGAGC 57.527 50.000 0.00 0.00 0.00 4.70
2112 2150 1.347062 TGGTGTCATGTGTAGGAGCA 58.653 50.000 0.00 0.00 0.00 4.26
2113 2151 1.696884 TGGTGTCATGTGTAGGAGCAA 59.303 47.619 0.00 0.00 0.00 3.91
2114 2152 2.289631 TGGTGTCATGTGTAGGAGCAAG 60.290 50.000 0.00 0.00 0.00 4.01
2131 2169 3.573538 AGCAAGACACATAACAAATGCCA 59.426 39.130 0.00 0.00 33.19 4.92
2143 2181 4.584327 ACAAATGCCAACAGTAGGAAAC 57.416 40.909 0.00 0.00 0.00 2.78
2189 2227 5.045012 TGAGATCTCTTAATGGCAATGCT 57.955 39.130 22.95 0.00 0.00 3.79
2232 2270 3.065925 AGAAGCACAGAAGTTTCAAGCAC 59.934 43.478 0.00 0.00 32.00 4.40
2236 2274 2.032549 CACAGAAGTTTCAAGCACTCCG 60.033 50.000 0.00 0.00 0.00 4.63
2287 2325 7.516198 AAAACTCAAGATTTGTATCACTGCT 57.484 32.000 0.00 0.00 32.95 4.24
2296 2334 5.437289 TTTGTATCACTGCTGAGTTTTGG 57.563 39.130 0.00 0.00 0.00 3.28
2301 2339 3.351740 TCACTGCTGAGTTTTGGTTTCA 58.648 40.909 0.00 0.00 0.00 2.69
2312 2350 7.930217 TGAGTTTTGGTTTCATTAGAACTGAG 58.070 34.615 0.00 0.00 32.39 3.35
2322 2360 9.989869 GTTTCATTAGAACTGAGCCTTTAATAC 57.010 33.333 0.00 0.00 32.39 1.89
2331 2369 5.428783 ACTGAGCCTTTAATACCCACATACT 59.571 40.000 0.00 0.00 0.00 2.12
2345 2396 7.687941 ACCCACATACTAGTGAAAGAATTTG 57.312 36.000 5.39 0.00 39.27 2.32
2347 2398 6.375455 CCCACATACTAGTGAAAGAATTTGCT 59.625 38.462 5.39 0.00 39.27 3.91
2353 2404 6.169800 ACTAGTGAAAGAATTTGCTCCTCTC 58.830 40.000 0.00 0.00 39.27 3.20
2381 2436 8.958506 TGAAAGTCTAGATCTCTAGTACAAACC 58.041 37.037 12.71 1.60 44.74 3.27
2382 2437 7.885009 AAGTCTAGATCTCTAGTACAAACCC 57.115 40.000 12.71 0.00 44.74 4.11
2383 2438 6.971340 AGTCTAGATCTCTAGTACAAACCCA 58.029 40.000 12.71 0.00 44.74 4.51
2384 2439 7.057894 AGTCTAGATCTCTAGTACAAACCCAG 58.942 42.308 12.71 0.00 44.74 4.45
2385 2440 6.829811 GTCTAGATCTCTAGTACAAACCCAGT 59.170 42.308 12.71 0.00 44.74 4.00
2386 2441 7.339976 GTCTAGATCTCTAGTACAAACCCAGTT 59.660 40.741 12.71 0.00 44.74 3.16
2387 2442 8.554870 TCTAGATCTCTAGTACAAACCCAGTTA 58.445 37.037 12.71 0.00 44.74 2.24
2388 2443 9.357161 CTAGATCTCTAGTACAAACCCAGTTAT 57.643 37.037 0.00 0.00 40.72 1.89
2389 2444 8.611051 AGATCTCTAGTACAAACCCAGTTATT 57.389 34.615 0.00 0.00 0.00 1.40
2390 2445 9.047947 AGATCTCTAGTACAAACCCAGTTATTT 57.952 33.333 0.00 0.00 0.00 1.40
2393 2448 9.537852 TCTCTAGTACAAACCCAGTTATTTAGA 57.462 33.333 0.00 0.00 0.00 2.10
2394 2449 9.583765 CTCTAGTACAAACCCAGTTATTTAGAC 57.416 37.037 0.00 0.00 0.00 2.59
2395 2450 9.317827 TCTAGTACAAACCCAGTTATTTAGACT 57.682 33.333 0.00 0.00 0.00 3.24
2396 2451 9.583765 CTAGTACAAACCCAGTTATTTAGACTC 57.416 37.037 0.00 0.00 0.00 3.36
2397 2452 7.392418 AGTACAAACCCAGTTATTTAGACTCC 58.608 38.462 0.00 0.00 0.00 3.85
2398 2453 5.567430 ACAAACCCAGTTATTTAGACTCCC 58.433 41.667 0.00 0.00 0.00 4.30
2399 2454 5.073965 ACAAACCCAGTTATTTAGACTCCCA 59.926 40.000 0.00 0.00 0.00 4.37
2400 2455 5.853572 AACCCAGTTATTTAGACTCCCAA 57.146 39.130 0.00 0.00 0.00 4.12
2401 2456 5.175388 ACCCAGTTATTTAGACTCCCAAC 57.825 43.478 0.00 0.00 0.00 3.77
2406 2461 5.045869 CAGTTATTTAGACTCCCAACCCAGA 60.046 44.000 0.00 0.00 0.00 3.86
2414 2469 6.652205 AGACTCCCAACCCAGATATTTAAA 57.348 37.500 0.00 0.00 0.00 1.52
2424 2479 8.792633 CAACCCAGATATTTAAACTCTCAAACA 58.207 33.333 0.00 0.00 0.00 2.83
2426 2481 9.178758 ACCCAGATATTTAAACTCTCAAACATC 57.821 33.333 0.00 0.00 0.00 3.06
2427 2482 9.177608 CCCAGATATTTAAACTCTCAAACATCA 57.822 33.333 0.00 0.00 0.00 3.07
2441 2498 5.192927 TCAAACATCAGAAACTCAGTGGTT 58.807 37.500 0.00 0.00 0.00 3.67
2443 2500 6.998074 TCAAACATCAGAAACTCAGTGGTTAT 59.002 34.615 0.00 0.00 0.00 1.89
2445 2502 8.446273 CAAACATCAGAAACTCAGTGGTTATAG 58.554 37.037 0.00 0.00 0.00 1.31
2469 2526 2.351350 CGGTTTTACCATGTTGTCTGCC 60.351 50.000 0.00 0.00 38.47 4.85
2543 2600 4.340950 CACCAGAGAGGATAGAGGAGAAAC 59.659 50.000 0.00 0.00 41.22 2.78
2550 2607 5.136048 AGAGGATAGAGGAGAAACAGAGGAT 59.864 44.000 0.00 0.00 0.00 3.24
2552 2609 4.283212 GGATAGAGGAGAAACAGAGGATGG 59.717 50.000 0.00 0.00 0.00 3.51
2559 2616 5.012893 GGAGAAACAGAGGATGGAAAATGT 58.987 41.667 0.00 0.00 0.00 2.71
2562 2619 7.340487 GGAGAAACAGAGGATGGAAAATGTTAT 59.660 37.037 0.00 0.00 31.09 1.89
2564 2621 9.093458 AGAAACAGAGGATGGAAAATGTTATTT 57.907 29.630 0.00 0.00 31.09 1.40
2567 2628 9.710900 AACAGAGGATGGAAAATGTTATTTTTC 57.289 29.630 1.55 0.52 42.33 2.29
2604 2665 7.549134 CAGTTAAGTTAATCACTATGTGAGGCA 59.451 37.037 6.55 0.00 46.04 4.75
2607 2668 4.163078 AGTTAATCACTATGTGAGGCAGCT 59.837 41.667 6.55 0.00 46.04 4.24
2613 2674 0.543277 TATGTGAGGCAGCTTCCTGG 59.457 55.000 10.58 0.00 39.54 4.45
2645 2869 7.495901 TCATTGGCTTGTAAAAGAATTTGTCA 58.504 30.769 0.00 0.00 39.02 3.58
2652 2876 8.135529 GCTTGTAAAAGAATTTGTCAACCTAGT 58.864 33.333 0.00 0.00 39.02 2.57
2660 2884 5.818678 ATTTGTCAACCTAGTGTCTACCA 57.181 39.130 0.00 0.00 0.00 3.25
2673 2897 6.945938 AGTGTCTACCATATCTCACAGTAC 57.054 41.667 0.00 0.00 0.00 2.73
2810 3035 6.292923 TGCTCTACCAGAGATACTAGAAGTC 58.707 44.000 7.37 0.00 45.07 3.01
2816 3041 6.607019 ACCAGAGATACTAGAAGTCCTAAGG 58.393 44.000 0.00 0.00 0.00 2.69
2837 3062 2.672996 GCCTGCGTCACCCACAAT 60.673 61.111 0.00 0.00 0.00 2.71
2883 3108 2.624838 ACATGTGCTCAACAAGGGAAAG 59.375 45.455 0.00 0.00 43.61 2.62
2888 3113 0.777446 CTCAACAAGGGAAAGGGGGA 59.223 55.000 0.00 0.00 0.00 4.81
2912 3137 1.641577 GCCACACCGATGAGAACTAC 58.358 55.000 0.00 0.00 0.00 2.73
2914 3139 1.134788 CCACACCGATGAGAACTACCC 60.135 57.143 0.00 0.00 0.00 3.69
2916 3141 0.815734 CACCGATGAGAACTACCCGT 59.184 55.000 0.00 0.00 0.00 5.28
2937 3162 1.352017 ACTGCATCTCCACCATTGACA 59.648 47.619 0.00 0.00 0.00 3.58
2981 3206 2.681848 CCAGATGCAGAACTTCCATGAC 59.318 50.000 0.00 0.00 0.00 3.06
3036 3261 0.890996 AGTTGCAGGGAAAGCCTTCG 60.891 55.000 0.00 0.00 31.77 3.79
3037 3262 0.889186 GTTGCAGGGAAAGCCTTCGA 60.889 55.000 0.00 0.00 31.77 3.71
3038 3263 0.179004 TTGCAGGGAAAGCCTTCGAA 60.179 50.000 0.00 0.00 31.77 3.71
3041 3266 0.517316 CAGGGAAAGCCTTCGAAACG 59.483 55.000 0.00 0.00 31.77 3.60
3084 3309 6.360844 CAGACATTGGATCTTCAGCTAAAG 57.639 41.667 0.00 0.00 0.00 1.85
3085 3310 6.111382 CAGACATTGGATCTTCAGCTAAAGA 58.889 40.000 0.64 0.64 39.49 2.52
3086 3311 6.596888 CAGACATTGGATCTTCAGCTAAAGAA 59.403 38.462 2.70 0.00 38.69 2.52
3087 3312 6.597280 AGACATTGGATCTTCAGCTAAAGAAC 59.403 38.462 2.70 0.20 38.69 3.01
3089 3314 6.150140 ACATTGGATCTTCAGCTAAAGAACAC 59.850 38.462 2.70 0.00 38.69 3.32
3092 3317 7.187824 TGGATCTTCAGCTAAAGAACACTAT 57.812 36.000 2.70 0.00 38.69 2.12
3098 3323 8.758829 TCTTCAGCTAAAGAACACTATCCATTA 58.241 33.333 0.00 0.00 32.42 1.90
3131 3356 8.734386 CATGCTAAGATCTTCAACTTAAAAGGT 58.266 33.333 12.24 0.00 0.00 3.50
3134 3359 5.966742 AGATCTTCAACTTAAAAGGTGCC 57.033 39.130 2.77 0.00 43.42 5.01
3227 3452 1.913262 TGAAGCCCTCGAGGAGCAA 60.913 57.895 32.83 21.19 38.24 3.91
3263 3488 1.968017 CTTGTCAGGCACCATGCGT 60.968 57.895 0.00 0.00 46.21 5.24
3305 3530 2.635915 TGTGGTTACGGACAAGGAGATT 59.364 45.455 0.00 0.00 0.00 2.40
3383 3608 6.149640 GGAAGAATAAGGTTGAAGAGTTGTCC 59.850 42.308 0.00 0.00 0.00 4.02
3390 3615 3.951680 GGTTGAAGAGTTGTCCTTTGGAA 59.048 43.478 0.00 0.00 31.38 3.53
3438 3663 3.273434 GCATCATGGACAAGTCTAGCAA 58.727 45.455 0.00 0.00 0.00 3.91
3668 3893 4.320202 GGTTAGTAACCGTAACTCGTCACA 60.320 45.833 16.22 0.00 42.62 3.58
3808 4033 5.830912 TGTTGTCTCCACATTGTGAATTTC 58.169 37.500 18.33 5.44 35.23 2.17
3822 4047 8.755018 CATTGTGAATTTCTTTTAGTGTTGTCC 58.245 33.333 0.00 0.00 0.00 4.02
3828 4053 4.447138 TCTTTTAGTGTTGTCCCCACAT 57.553 40.909 0.00 0.00 35.24 3.21
3829 4054 4.798882 TCTTTTAGTGTTGTCCCCACATT 58.201 39.130 0.00 0.00 35.24 2.71
3867 4092 8.030692 CCACATGCACCTCATAATAAAATATGG 58.969 37.037 0.00 0.00 34.66 2.74
4751 4981 1.467734 CCACACAAGCAGAGCAATCTC 59.532 52.381 0.00 0.00 39.65 2.75
5386 5616 3.847671 TGGTCACACTGGTTTGTCATA 57.152 42.857 0.00 0.00 0.00 2.15
5809 6060 8.557592 TGATTATTGATCAACTGAGGATATGC 57.442 34.615 11.07 0.00 41.73 3.14
6059 6310 0.941542 TTTGTTGCCGTAGACAGTGC 59.058 50.000 0.00 0.00 0.00 4.40
6159 6418 8.918202 AACAACTTTGAACATGAGATAAGGTA 57.082 30.769 0.00 0.00 0.00 3.08
6197 6456 5.348451 GCCTAAAATGCAACTAACACCAATG 59.652 40.000 0.00 0.00 0.00 2.82
6212 6471 6.409524 ACACCAATGAATTTCAGTTCATGT 57.590 33.333 5.21 3.91 45.49 3.21
6228 6487 7.012327 TCAGTTCATGTTAATAGGTAAGCATGC 59.988 37.037 10.51 10.51 34.54 4.06
6311 6570 1.201647 CAGTTTGCCCTTGCTGATGAG 59.798 52.381 0.00 0.00 38.71 2.90
6312 6571 1.202976 AGTTTGCCCTTGCTGATGAGT 60.203 47.619 0.00 0.00 38.71 3.41
6313 6572 1.068055 GTTTGCCCTTGCTGATGAGTG 60.068 52.381 0.00 0.00 38.71 3.51
6314 6573 0.401356 TTGCCCTTGCTGATGAGTGA 59.599 50.000 0.00 0.00 38.71 3.41
6315 6574 0.622136 TGCCCTTGCTGATGAGTGAT 59.378 50.000 0.00 0.00 38.71 3.06
6316 6575 1.022735 GCCCTTGCTGATGAGTGATG 58.977 55.000 0.00 0.00 33.53 3.07
6317 6576 1.407851 GCCCTTGCTGATGAGTGATGA 60.408 52.381 0.00 0.00 33.53 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 6.319152 GGAATAAACTAAGGAAGGCTTTCTCC 59.681 42.308 8.88 1.44 33.68 3.71
83 85 2.617308 GCGGGAATAAACTAAGGAAGGC 59.383 50.000 0.00 0.00 0.00 4.35
140 142 0.456995 CGTCAAGCCGTCTTCCTCTC 60.457 60.000 0.00 0.00 0.00 3.20
185 187 5.952347 ACGGTGAGGATAAACTAAGGAAT 57.048 39.130 0.00 0.00 0.00 3.01
203 205 2.495866 CACGGGCGGTTATACGGT 59.504 61.111 0.00 0.00 0.00 4.83
206 208 3.874392 ATATACCACGGGCGGTTATAC 57.126 47.619 0.00 0.00 40.67 1.47
218 220 2.870411 GTCAAGCCGTCCAATATACCAC 59.130 50.000 0.00 0.00 0.00 4.16
252 254 6.133253 ACTAAGGAAGGCTTCTTTTCTCAT 57.867 37.500 26.58 7.03 31.03 2.90
300 302 7.441157 TCTCTCTTTTGCAATACCAATATACCG 59.559 37.037 0.00 0.00 0.00 4.02
326 328 7.438564 ACAAAAATCTATACCAAGCCGTTTTT 58.561 30.769 0.00 0.00 0.00 1.94
358 360 3.981071 TGTTGTCCCTGATAAGTCCTG 57.019 47.619 0.00 0.00 0.00 3.86
364 366 4.566004 CTCGAACTTGTTGTCCCTGATAA 58.434 43.478 0.00 0.00 0.00 1.75
374 376 3.123621 AGAAATAGCGCTCGAACTTGTTG 59.876 43.478 16.34 0.00 0.00 3.33
379 381 3.182967 CTGAAGAAATAGCGCTCGAACT 58.817 45.455 16.34 7.28 0.00 3.01
382 384 1.135139 AGCTGAAGAAATAGCGCTCGA 59.865 47.619 16.34 0.00 44.43 4.04
461 463 2.680841 ACTTGTGTAAGTTGCGCTTCAA 59.319 40.909 9.73 0.00 44.57 2.69
466 468 2.969443 ATCACTTGTGTAAGTTGCGC 57.031 45.000 0.00 0.00 44.57 6.09
479 481 0.687354 ACCAGCGTCTCCAATCACTT 59.313 50.000 0.00 0.00 0.00 3.16
480 482 1.557099 TACCAGCGTCTCCAATCACT 58.443 50.000 0.00 0.00 0.00 3.41
491 493 2.699954 CTTGACAAGGATTACCAGCGT 58.300 47.619 7.35 0.00 38.94 5.07
492 494 1.398390 GCTTGACAAGGATTACCAGCG 59.602 52.381 16.80 0.00 38.94 5.18
643 650 3.670377 GGCCCACCACTGCGTTTC 61.670 66.667 0.00 0.00 35.26 2.78
791 798 3.591835 CTCTCTCCGCTCTCCGCC 61.592 72.222 0.00 0.00 35.03 6.13
803 810 3.073735 CGCCCCTGTCTGCTCTCT 61.074 66.667 0.00 0.00 0.00 3.10
896 903 2.652113 CCCTCCCTCCCTCCCTCTT 61.652 68.421 0.00 0.00 0.00 2.85
897 904 3.039526 CCCTCCCTCCCTCCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
898 905 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
899 906 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
900 907 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
902 909 4.179599 CCCCTCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
905 912 4.179599 CCTCCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
939 963 1.135315 TCACTGGTAATCGTACGGTGC 60.135 52.381 16.52 7.39 35.96 5.01
944 968 2.165845 AGGTGCTCACTGGTAATCGTAC 59.834 50.000 0.00 0.00 0.00 3.67
1030 1064 0.502275 GCGTTTGTGTTTGGATTGCG 59.498 50.000 0.00 0.00 0.00 4.85
1068 1102 1.793902 GGAGGGGGTCTAGGGAAGATA 59.206 57.143 0.00 0.00 36.36 1.98
1210 1248 4.336993 TCAGTTTTAGCGCCTGAAAGAAAA 59.663 37.500 2.29 0.00 34.07 2.29
1223 1261 5.106157 ACCATAACACTGCATCAGTTTTAGC 60.106 40.000 10.19 0.00 42.59 3.09
1331 1369 2.721167 CGCCTTCCGAGGACATGGA 61.721 63.158 0.00 0.00 46.74 3.41
1435 1473 1.201429 GGAAGGTGGAGGGAGAAGCA 61.201 60.000 0.00 0.00 0.00 3.91
1496 1534 1.181098 ATCCACAGGGTGCTGTTTGC 61.181 55.000 0.00 0.00 43.25 3.68
1503 1541 3.134127 GCGGAATCCACAGGGTGC 61.134 66.667 0.00 0.00 34.93 5.01
1505 1543 2.933287 TGGCGGAATCCACAGGGT 60.933 61.111 0.00 0.00 34.93 4.34
1520 1558 3.775654 GACGGTGGAGGAGGCTGG 61.776 72.222 0.00 0.00 0.00 4.85
1528 1566 2.742372 CTTTGCCGGACGGTGGAG 60.742 66.667 5.05 4.10 37.65 3.86
1547 1585 4.019792 TGTAATCCAGAGCTTGCTCAAA 57.980 40.909 22.44 9.18 0.00 2.69
1549 1587 3.198417 TGATGTAATCCAGAGCTTGCTCA 59.802 43.478 22.44 4.67 44.73 4.26
1552 1590 3.243002 GCTTGATGTAATCCAGAGCTTGC 60.243 47.826 0.00 0.00 44.73 4.01
1570 1608 1.600013 GCATCTCTCTGCATCTGCTTG 59.400 52.381 3.53 0.00 41.87 4.01
1574 1612 0.600518 CCGGCATCTCTCTGCATCTG 60.601 60.000 0.00 0.00 44.12 2.90
1626 1664 1.150536 ACCAACTTGCCATCACGGT 59.849 52.632 0.00 0.00 36.97 4.83
1628 1666 1.081242 GCACCAACTTGCCATCACG 60.081 57.895 0.00 0.00 36.42 4.35
1633 1671 0.682532 TTGTCAGCACCAACTTGCCA 60.683 50.000 0.00 0.00 44.14 4.92
1636 1674 1.003545 CTCGTTGTCAGCACCAACTTG 60.004 52.381 10.22 1.81 39.98 3.16
1637 1675 1.299541 CTCGTTGTCAGCACCAACTT 58.700 50.000 10.22 0.00 39.98 2.66
1642 1680 3.414700 CCGCTCGTTGTCAGCACC 61.415 66.667 0.00 0.00 36.61 5.01
1669 1707 3.238788 TCTGAGGTGTTGTCCAGAGTA 57.761 47.619 0.00 0.00 32.51 2.59
1675 1713 3.764434 TGAGTCTATCTGAGGTGTTGTCC 59.236 47.826 0.00 0.00 0.00 4.02
1678 1716 4.118410 GCATGAGTCTATCTGAGGTGTTG 58.882 47.826 0.00 0.00 0.00 3.33
1679 1717 3.771479 TGCATGAGTCTATCTGAGGTGTT 59.229 43.478 0.00 0.00 0.00 3.32
1681 1719 3.384146 ACTGCATGAGTCTATCTGAGGTG 59.616 47.826 0.00 0.00 0.00 4.00
1690 1728 2.497675 GTCCCTGAACTGCATGAGTCTA 59.502 50.000 0.00 0.00 31.73 2.59
1693 1731 0.036952 CGTCCCTGAACTGCATGAGT 60.037 55.000 0.00 0.00 35.94 3.41
1698 1736 1.069090 GACACGTCCCTGAACTGCA 59.931 57.895 0.00 0.00 0.00 4.41
1699 1737 2.022129 CGACACGTCCCTGAACTGC 61.022 63.158 0.00 0.00 0.00 4.40
1723 1761 4.318332 CAACATCTGCAGAGAAGTGGTAA 58.682 43.478 22.96 0.00 30.52 2.85
1729 1767 2.354259 GACCCAACATCTGCAGAGAAG 58.646 52.381 22.96 16.16 0.00 2.85
1774 1812 2.046285 GCCAATGAACACCCTCCCG 61.046 63.158 0.00 0.00 0.00 5.14
1816 1854 2.383527 GCTGGTGAAGAGCCGAACG 61.384 63.158 0.00 0.00 0.00 3.95
1822 1860 4.061596 GGTATTCATAGCTGGTGAAGAGC 58.938 47.826 18.22 18.22 38.81 4.09
1823 1861 4.503991 GGGGTATTCATAGCTGGTGAAGAG 60.504 50.000 17.66 0.00 38.81 2.85
1824 1862 3.391296 GGGGTATTCATAGCTGGTGAAGA 59.609 47.826 17.66 12.56 38.81 2.87
1855 1893 3.495100 GGACGTCCAAATCCTGAGCATAT 60.495 47.826 29.75 0.00 35.64 1.78
1856 1894 2.158957 GGACGTCCAAATCCTGAGCATA 60.159 50.000 29.75 0.00 35.64 3.14
1885 1923 4.299796 AACACCGGCAGCCCCATT 62.300 61.111 5.63 0.00 0.00 3.16
1912 1950 1.270147 ACACCCAAGCACGAGTAACTC 60.270 52.381 0.00 0.00 0.00 3.01
1940 1978 2.231964 GCTTTTGCCTGGTCATGATCAA 59.768 45.455 10.49 2.21 40.15 2.57
1957 1995 3.389329 TCTCTGAGGTGAAGTTGAGCTTT 59.611 43.478 4.59 0.00 37.59 3.51
1975 2013 2.159128 CCTGCAGATGTCGTTGATCTCT 60.159 50.000 17.39 0.00 0.00 3.10
1985 2023 1.145819 GGAGAGCCCTGCAGATGTC 59.854 63.158 17.39 8.62 0.00 3.06
1996 2034 4.965200 ATAGTTCAATACCTGGAGAGCC 57.035 45.455 0.00 0.00 0.00 4.70
2013 2051 7.620094 AGGTTAAGTGACTGAGGTATCAATAGT 59.380 37.037 0.00 0.00 34.23 2.12
2014 2052 7.923344 CAGGTTAAGTGACTGAGGTATCAATAG 59.077 40.741 0.00 0.00 34.23 1.73
2015 2053 7.618117 TCAGGTTAAGTGACTGAGGTATCAATA 59.382 37.037 0.00 0.00 36.41 1.90
2016 2054 6.440647 TCAGGTTAAGTGACTGAGGTATCAAT 59.559 38.462 0.00 0.00 36.41 2.57
2017 2055 5.778241 TCAGGTTAAGTGACTGAGGTATCAA 59.222 40.000 0.00 0.00 36.41 2.57
2018 2056 5.330233 TCAGGTTAAGTGACTGAGGTATCA 58.670 41.667 0.00 0.00 36.41 2.15
2019 2057 5.916661 TCAGGTTAAGTGACTGAGGTATC 57.083 43.478 0.00 0.00 36.41 2.24
2020 2058 6.270231 ACTTTCAGGTTAAGTGACTGAGGTAT 59.730 38.462 0.00 0.00 41.71 2.73
2021 2059 5.601313 ACTTTCAGGTTAAGTGACTGAGGTA 59.399 40.000 0.00 0.00 41.71 3.08
2022 2060 4.409247 ACTTTCAGGTTAAGTGACTGAGGT 59.591 41.667 0.00 0.00 41.71 3.85
2023 2061 4.962155 ACTTTCAGGTTAAGTGACTGAGG 58.038 43.478 0.00 0.00 41.71 3.86
2024 2062 6.927294 AAACTTTCAGGTTAAGTGACTGAG 57.073 37.500 0.00 0.00 41.71 3.35
2025 2063 6.882140 TGAAAACTTTCAGGTTAAGTGACTGA 59.118 34.615 0.69 0.00 41.88 3.41
2026 2064 7.083875 TGAAAACTTTCAGGTTAAGTGACTG 57.916 36.000 0.69 0.00 41.88 3.51
2027 2065 7.696992 TTGAAAACTTTCAGGTTAAGTGACT 57.303 32.000 5.13 0.00 46.68 3.41
2028 2066 7.810759 TGTTTGAAAACTTTCAGGTTAAGTGAC 59.189 33.333 7.39 0.00 46.68 3.67
2044 2082 5.280945 TGCTGCAGACTAATGTTTGAAAAC 58.719 37.500 20.43 0.00 39.33 2.43
2057 2095 3.265791 GCAACTATACTTGCTGCAGACT 58.734 45.455 20.43 0.00 42.84 3.24
2063 2101 6.437928 TCTTTTTGTGCAACTATACTTGCTG 58.562 36.000 15.33 2.09 45.79 4.41
2065 2103 6.360681 CACTCTTTTTGTGCAACTATACTTGC 59.639 38.462 9.43 9.43 45.80 4.01
2073 2111 4.244862 CCAAACACTCTTTTTGTGCAACT 58.755 39.130 0.00 0.00 38.86 3.16
2074 2112 3.993736 ACCAAACACTCTTTTTGTGCAAC 59.006 39.130 0.00 0.00 38.86 4.17
2075 2113 3.993081 CACCAAACACTCTTTTTGTGCAA 59.007 39.130 0.00 0.00 38.86 4.08
2076 2114 3.006323 ACACCAAACACTCTTTTTGTGCA 59.994 39.130 0.00 0.00 38.86 4.57
2077 2115 3.584834 ACACCAAACACTCTTTTTGTGC 58.415 40.909 0.00 0.00 38.86 4.57
2078 2116 4.804108 TGACACCAAACACTCTTTTTGTG 58.196 39.130 0.00 0.00 40.87 3.33
2079 2117 5.047377 ACATGACACCAAACACTCTTTTTGT 60.047 36.000 0.00 0.00 32.92 2.83
2080 2118 5.289193 CACATGACACCAAACACTCTTTTTG 59.711 40.000 0.00 0.00 34.31 2.44
2081 2119 5.047377 ACACATGACACCAAACACTCTTTTT 60.047 36.000 0.00 0.00 0.00 1.94
2082 2120 4.462483 ACACATGACACCAAACACTCTTTT 59.538 37.500 0.00 0.00 0.00 2.27
2089 2127 3.738982 CTCCTACACATGACACCAAACA 58.261 45.455 0.00 0.00 0.00 2.83
2102 2140 4.566004 TGTTATGTGTCTTGCTCCTACAC 58.434 43.478 0.00 0.00 43.00 2.90
2107 2145 4.168760 GCATTTGTTATGTGTCTTGCTCC 58.831 43.478 0.00 0.00 0.00 4.70
2108 2146 4.168760 GGCATTTGTTATGTGTCTTGCTC 58.831 43.478 0.00 0.00 0.00 4.26
2109 2147 3.573538 TGGCATTTGTTATGTGTCTTGCT 59.426 39.130 0.00 0.00 0.00 3.91
2110 2148 3.911868 TGGCATTTGTTATGTGTCTTGC 58.088 40.909 0.00 0.00 0.00 4.01
2111 2149 5.288015 TGTTGGCATTTGTTATGTGTCTTG 58.712 37.500 0.00 0.00 0.00 3.02
2112 2150 5.068987 ACTGTTGGCATTTGTTATGTGTCTT 59.931 36.000 0.00 0.00 0.00 3.01
2113 2151 4.584325 ACTGTTGGCATTTGTTATGTGTCT 59.416 37.500 0.00 0.00 0.00 3.41
2114 2152 4.870363 ACTGTTGGCATTTGTTATGTGTC 58.130 39.130 0.00 0.00 0.00 3.67
2121 2159 4.404073 TGTTTCCTACTGTTGGCATTTGTT 59.596 37.500 3.24 0.00 0.00 2.83
2131 2169 7.823745 AAGAACATGATTGTTTCCTACTGTT 57.176 32.000 0.00 0.00 46.01 3.16
2189 2227 2.229792 CAGGTTAACTGCCTGCAAAGA 58.770 47.619 5.42 0.00 45.72 2.52
2236 2274 3.799755 CCTACCTTTGTGGCGCGC 61.800 66.667 25.94 25.94 40.22 6.86
2275 2313 4.460263 ACCAAAACTCAGCAGTGATACAA 58.540 39.130 0.00 0.00 31.06 2.41
2276 2314 4.085357 ACCAAAACTCAGCAGTGATACA 57.915 40.909 0.00 0.00 31.06 2.29
2277 2315 5.008613 TGAAACCAAAACTCAGCAGTGATAC 59.991 40.000 0.00 0.00 31.06 2.24
2278 2316 5.129634 TGAAACCAAAACTCAGCAGTGATA 58.870 37.500 0.00 0.00 31.06 2.15
2279 2317 3.953612 TGAAACCAAAACTCAGCAGTGAT 59.046 39.130 0.00 0.00 31.06 3.06
2280 2318 3.351740 TGAAACCAAAACTCAGCAGTGA 58.648 40.909 0.00 0.00 31.06 3.41
2282 2320 5.827797 TCTAATGAAACCAAAACTCAGCAGT 59.172 36.000 0.00 0.00 0.00 4.40
2283 2321 6.317789 TCTAATGAAACCAAAACTCAGCAG 57.682 37.500 0.00 0.00 0.00 4.24
2284 2322 6.321181 AGTTCTAATGAAACCAAAACTCAGCA 59.679 34.615 0.00 0.00 33.52 4.41
2285 2323 6.638468 CAGTTCTAATGAAACCAAAACTCAGC 59.362 38.462 0.00 0.00 33.52 4.26
2286 2324 7.930217 TCAGTTCTAATGAAACCAAAACTCAG 58.070 34.615 0.00 0.00 33.52 3.35
2287 2325 7.468631 GCTCAGTTCTAATGAAACCAAAACTCA 60.469 37.037 0.00 0.00 33.52 3.41
2296 2334 9.989869 GTATTAAAGGCTCAGTTCTAATGAAAC 57.010 33.333 0.00 0.00 33.52 2.78
2301 2339 7.054751 GTGGGTATTAAAGGCTCAGTTCTAAT 58.945 38.462 0.00 0.00 0.00 1.73
2312 2350 6.823497 TCACTAGTATGTGGGTATTAAAGGC 58.177 40.000 0.00 0.00 38.40 4.35
2322 2360 6.375455 AGCAAATTCTTTCACTAGTATGTGGG 59.625 38.462 0.00 0.00 38.40 4.61
2331 2369 6.114187 TGAGAGGAGCAAATTCTTTCACTA 57.886 37.500 0.00 0.00 0.00 2.74
2340 2391 5.568392 AGACTTTCATGAGAGGAGCAAATT 58.432 37.500 16.92 0.00 0.00 1.82
2345 2396 5.536161 AGATCTAGACTTTCATGAGAGGAGC 59.464 44.000 16.92 7.59 0.00 4.70
2347 2398 6.910191 AGAGATCTAGACTTTCATGAGAGGA 58.090 40.000 16.92 5.47 0.00 3.71
2380 2435 4.524053 GGTTGGGAGTCTAAATAACTGGG 58.476 47.826 0.00 0.00 0.00 4.45
2381 2436 4.018779 TGGGTTGGGAGTCTAAATAACTGG 60.019 45.833 0.00 0.00 0.00 4.00
2382 2437 5.045869 TCTGGGTTGGGAGTCTAAATAACTG 60.046 44.000 0.00 0.00 0.00 3.16
2383 2438 5.098663 TCTGGGTTGGGAGTCTAAATAACT 58.901 41.667 0.00 0.00 0.00 2.24
2384 2439 5.431179 TCTGGGTTGGGAGTCTAAATAAC 57.569 43.478 0.00 0.00 0.00 1.89
2385 2440 7.947782 ATATCTGGGTTGGGAGTCTAAATAA 57.052 36.000 0.00 0.00 0.00 1.40
2386 2441 7.947782 AATATCTGGGTTGGGAGTCTAAATA 57.052 36.000 0.00 0.00 0.00 1.40
2387 2442 6.848562 AATATCTGGGTTGGGAGTCTAAAT 57.151 37.500 0.00 0.00 0.00 1.40
2388 2443 6.652205 AAATATCTGGGTTGGGAGTCTAAA 57.348 37.500 0.00 0.00 0.00 1.85
2389 2444 7.758820 TTAAATATCTGGGTTGGGAGTCTAA 57.241 36.000 0.00 0.00 0.00 2.10
2390 2445 7.404980 AGTTTAAATATCTGGGTTGGGAGTCTA 59.595 37.037 0.00 0.00 0.00 2.59
2391 2446 6.217693 AGTTTAAATATCTGGGTTGGGAGTCT 59.782 38.462 0.00 0.00 0.00 3.24
2392 2447 6.424032 AGTTTAAATATCTGGGTTGGGAGTC 58.576 40.000 0.00 0.00 0.00 3.36
2393 2448 6.217693 AGAGTTTAAATATCTGGGTTGGGAGT 59.782 38.462 5.39 0.00 0.00 3.85
2394 2449 6.663734 AGAGTTTAAATATCTGGGTTGGGAG 58.336 40.000 5.39 0.00 0.00 4.30
2395 2450 6.216662 TGAGAGTTTAAATATCTGGGTTGGGA 59.783 38.462 9.82 0.00 0.00 4.37
2396 2451 6.423182 TGAGAGTTTAAATATCTGGGTTGGG 58.577 40.000 9.82 0.00 0.00 4.12
2397 2452 7.938140 TTGAGAGTTTAAATATCTGGGTTGG 57.062 36.000 9.82 0.00 0.00 3.77
2398 2453 8.792633 TGTTTGAGAGTTTAAATATCTGGGTTG 58.207 33.333 9.82 0.00 0.00 3.77
2399 2454 8.934023 TGTTTGAGAGTTTAAATATCTGGGTT 57.066 30.769 9.82 0.00 0.00 4.11
2400 2455 9.178758 GATGTTTGAGAGTTTAAATATCTGGGT 57.821 33.333 9.82 0.00 33.96 4.51
2401 2456 9.177608 TGATGTTTGAGAGTTTAAATATCTGGG 57.822 33.333 9.82 0.00 36.20 4.45
2414 2469 5.757320 CACTGAGTTTCTGATGTTTGAGAGT 59.243 40.000 0.00 0.00 0.00 3.24
2424 2479 6.578023 GCTCTATAACCACTGAGTTTCTGAT 58.422 40.000 0.00 0.00 0.00 2.90
2426 2481 4.800993 CGCTCTATAACCACTGAGTTTCTG 59.199 45.833 0.00 0.00 0.00 3.02
2427 2482 4.142138 CCGCTCTATAACCACTGAGTTTCT 60.142 45.833 0.00 0.00 0.00 2.52
2441 2498 5.736813 ACAACATGGTAAAACCGCTCTATA 58.263 37.500 0.00 0.00 42.58 1.31
2443 2500 3.998341 GACAACATGGTAAAACCGCTCTA 59.002 43.478 0.00 0.00 42.58 2.43
2445 2502 2.812011 AGACAACATGGTAAAACCGCTC 59.188 45.455 0.00 0.00 42.58 5.03
2469 2526 4.146564 TGATTGGAATGGATGCCATGTAG 58.853 43.478 0.00 0.00 44.40 2.74
2507 2564 1.198759 TCTGGTGGGTCCTGCCTTAC 61.199 60.000 4.36 0.00 37.43 2.34
2511 2568 2.607750 TCTCTGGTGGGTCCTGCC 60.608 66.667 0.00 0.00 37.07 4.85
2514 2571 1.219213 CTATCCTCTCTGGTGGGTCCT 59.781 57.143 0.00 0.00 37.07 3.85
2578 2639 7.549134 TGCCTCACATAGTGATTAACTTAACTG 59.451 37.037 0.00 0.00 41.94 3.16
2604 2665 0.992431 ATGAGCCATCCCAGGAAGCT 60.992 55.000 12.92 12.92 39.47 3.74
2607 2668 0.259647 CCAATGAGCCATCCCAGGAA 59.740 55.000 0.00 0.00 0.00 3.36
2613 2674 2.057137 TACAAGCCAATGAGCCATCC 57.943 50.000 0.00 0.00 0.00 3.51
2645 2869 6.432581 TGTGAGATATGGTAGACACTAGGTT 58.567 40.000 0.00 0.00 0.00 3.50
2652 2876 6.890268 ACTTGTACTGTGAGATATGGTAGACA 59.110 38.462 0.00 0.00 0.00 3.41
2731 2956 0.885879 CAGCAAGAGCAGCCATGAAA 59.114 50.000 0.00 0.00 45.49 2.69
2810 3035 4.101448 ACGCAGGCTGCCCTTAGG 62.101 66.667 32.08 19.62 41.12 2.69
2837 3062 2.392662 CAGGTCTGAGCTAATGGGAGA 58.607 52.381 9.32 0.00 0.00 3.71
2888 3113 3.958147 CTCATCGGTGTGGCGGCTT 62.958 63.158 11.43 0.00 0.00 4.35
2898 3123 2.019984 GTACGGGTAGTTCTCATCGGT 58.980 52.381 0.00 0.00 0.00 4.69
2912 3137 1.144057 GGTGGAGATGCAGTACGGG 59.856 63.158 0.00 0.00 0.00 5.28
2914 3139 1.935873 CAATGGTGGAGATGCAGTACG 59.064 52.381 0.00 0.00 0.00 3.67
2916 3141 2.571202 TGTCAATGGTGGAGATGCAGTA 59.429 45.455 0.00 0.00 0.00 2.74
2937 3162 2.385013 TCATTGACGTAGCATGCTGT 57.615 45.000 30.42 20.16 0.00 4.40
2981 3206 1.294780 GTGGTGGTCAGAGCAGGAG 59.705 63.158 1.45 0.00 0.00 3.69
3017 3242 0.890996 CGAAGGCTTTCCCTGCAACT 60.891 55.000 0.00 0.00 45.62 3.16
3036 3261 0.598065 AAGCATGGCTGGTTCGTTTC 59.402 50.000 0.00 0.00 38.72 2.78
3037 3262 0.598065 GAAGCATGGCTGGTTCGTTT 59.402 50.000 11.22 0.00 46.44 3.60
3038 3263 2.257353 GAAGCATGGCTGGTTCGTT 58.743 52.632 11.22 0.00 46.44 3.85
3071 3296 7.187824 TGGATAGTGTTCTTTAGCTGAAGAT 57.812 36.000 20.40 9.17 35.70 2.40
3078 3303 7.173390 GTGGGATAATGGATAGTGTTCTTTAGC 59.827 40.741 0.00 0.00 0.00 3.09
3084 3309 5.304686 TGGTGGGATAATGGATAGTGTTC 57.695 43.478 0.00 0.00 0.00 3.18
3085 3310 5.634118 CATGGTGGGATAATGGATAGTGTT 58.366 41.667 0.00 0.00 0.00 3.32
3086 3311 4.507335 GCATGGTGGGATAATGGATAGTGT 60.507 45.833 0.00 0.00 0.00 3.55
3087 3312 4.012374 GCATGGTGGGATAATGGATAGTG 58.988 47.826 0.00 0.00 0.00 2.74
3089 3314 4.581309 AGCATGGTGGGATAATGGATAG 57.419 45.455 0.00 0.00 0.00 2.08
3092 3317 3.980022 TCTTAGCATGGTGGGATAATGGA 59.020 43.478 7.89 0.00 0.00 3.41
3098 3323 3.718434 TGAAGATCTTAGCATGGTGGGAT 59.282 43.478 8.25 10.53 0.00 3.85
3134 3359 2.398554 CCTCAACCGGATTGCCACG 61.399 63.158 9.46 0.00 38.29 4.94
3227 3452 2.070639 GGAGTCCAGGACTGCCTTT 58.929 57.895 27.94 0.87 43.90 3.11
3263 3488 1.135489 CGTAGAGTTCGGCAAGCACTA 60.135 52.381 0.00 0.00 0.00 2.74
3293 3518 1.846439 TCATCCCCAATCTCCTTGTCC 59.154 52.381 0.00 0.00 32.61 4.02
3305 3530 0.259647 CCAGCATTTCCTCATCCCCA 59.740 55.000 0.00 0.00 0.00 4.96
3368 3593 3.551846 TCCAAAGGACAACTCTTCAACC 58.448 45.455 0.00 0.00 0.00 3.77
3383 3608 3.799281 TCTGTTGCTTGGTTTCCAAAG 57.201 42.857 2.85 0.00 43.44 2.77
3390 3615 4.973168 TCTCTATGTTCTGTTGCTTGGTT 58.027 39.130 0.00 0.00 0.00 3.67
3438 3663 7.887495 AGCTAAATCTGATTCTTTTGAAGTCCT 59.113 33.333 2.92 0.00 42.30 3.85
3476 3701 7.026429 TCCTACAGGTGATAGCATACCATGC 62.026 48.000 2.89 2.89 45.65 4.06
3808 4033 6.642707 TTAATGTGGGGACAACACTAAAAG 57.357 37.500 0.00 0.00 46.06 2.27
3822 4047 3.506067 GTGGAGGTTGACTTTAATGTGGG 59.494 47.826 0.00 0.00 0.00 4.61
3828 4053 3.568007 GTGCATGTGGAGGTTGACTTTAA 59.432 43.478 0.00 0.00 0.00 1.52
3829 4054 3.146066 GTGCATGTGGAGGTTGACTTTA 58.854 45.455 0.00 0.00 0.00 1.85
3887 4112 3.194542 AGGCTAACAGCACAAAACACAAA 59.805 39.130 0.00 0.00 44.75 2.83
3899 4124 0.328258 TTCCCCTTCAGGCTAACAGC 59.672 55.000 0.00 0.00 41.46 4.40
3941 4166 5.559227 TCTCATCGTGTTCAATTTATTGCG 58.441 37.500 0.00 0.00 37.68 4.85
3950 4175 6.018262 CCTGTTTTAGTTCTCATCGTGTTCAA 60.018 38.462 0.00 0.00 0.00 2.69
3986 4211 4.381079 GGCAGTTCTTGAGAGTCGACTATT 60.381 45.833 20.09 10.11 0.00 1.73
4104 4332 6.344500 TGTTTTGTCATGTAAATTTGCCAGT 58.656 32.000 0.00 0.00 0.00 4.00
4358 4586 4.520492 GTGATCACACCTTGGAGACAAAAT 59.480 41.667 21.07 0.00 43.25 1.82
4751 4981 0.890683 GGTGCCCCTCAAAATCAGTG 59.109 55.000 0.00 0.00 0.00 3.66
5386 5616 2.766263 TGATGAGGCCTACGATGTCTTT 59.234 45.455 4.42 0.00 0.00 2.52
6059 6310 9.750125 ACCAAACTGAAAGCTTCTTAAATAAAG 57.250 29.630 0.00 0.00 37.60 1.85
6223 6482 1.895051 ATCGTTACAAAAGCGCATGC 58.105 45.000 11.47 7.91 43.24 4.06
6228 6487 4.957971 ACTCATCAATCGTTACAAAAGCG 58.042 39.130 0.00 0.00 0.00 4.68
6281 6540 4.021981 GCAAGGGCAAACTGAAAAGTATCT 60.022 41.667 0.00 0.00 40.72 1.98
6311 6570 4.368315 TGTTGTGTAGTCTGTGTCATCAC 58.632 43.478 0.00 0.00 44.08 3.06
6312 6571 4.664150 TGTTGTGTAGTCTGTGTCATCA 57.336 40.909 0.00 0.00 0.00 3.07
6313 6572 4.211374 GGTTGTTGTGTAGTCTGTGTCATC 59.789 45.833 0.00 0.00 0.00 2.92
6314 6573 4.127171 GGTTGTTGTGTAGTCTGTGTCAT 58.873 43.478 0.00 0.00 0.00 3.06
6315 6574 3.055747 TGGTTGTTGTGTAGTCTGTGTCA 60.056 43.478 0.00 0.00 0.00 3.58
6316 6575 3.527533 TGGTTGTTGTGTAGTCTGTGTC 58.472 45.455 0.00 0.00 0.00 3.67
6317 6576 3.531538 CTGGTTGTTGTGTAGTCTGTGT 58.468 45.455 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.