Multiple sequence alignment - TraesCS7B01G293700

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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 TraesCS7B01G293700 chr7B 100.000 2504 0 0 1 2504 530435922 530433419 0.000000e+00 4625
1 TraesCS7B01G293700 chr7B 90.123 1620 89 34 140 1726 530591696 530590115 0.000000e+00 2039
2 TraesCS7B01G293700 chr7B 86.520 408 39 8 2105 2501 523602644 523603046 3.830000e-118 435
3 TraesCS7B01G293700 chr7B 81.067 375 39 12 2106 2479 388600557 388600900 1.140000e-68 270
4 TraesCS7B01G293700 chr7B 92.361 144 11 0 1 144 530592365 530592222 3.260000e-49 206
5 TraesCS7B01G293700 chr7A 86.215 2169 157 62 11 2109 567592471 567590375 0.000000e+00 2218
6 TraesCS7B01G293700 chr7D 85.268 2179 125 71 2 2109 501109469 501107416 0.000000e+00 2065
7 TraesCS7B01G293700 chr1B 89.524 420 22 10 2097 2501 50211555 50211967 1.720000e-141 512
8 TraesCS7B01G293700 chr6B 88.119 404 36 10 2108 2504 43803142 43803540 1.050000e-128 470
9 TraesCS7B01G293700 chr6B 82.283 254 31 12 1192 1439 237731240 237731485 9.080000e-50 207
10 TraesCS7B01G293700 chr4A 87.321 418 30 14 2103 2501 737637653 737638066 8.160000e-125 457
11 TraesCS7B01G293700 chr3B 89.356 357 21 8 2159 2501 132088866 132088513 1.380000e-117 433
12 TraesCS7B01G293700 chrUn 85.024 414 32 14 2105 2504 15415537 15415140 6.490000e-106 394
13 TraesCS7B01G293700 chr5B 83.210 405 54 7 2105 2501 427234403 427234801 2.370000e-95 359
14 TraesCS7B01G293700 chr5B 82.382 403 49 15 2108 2504 709167634 709167248 5.160000e-87 331
15 TraesCS7B01G293700 chr2B 82.555 407 55 8 2105 2500 737873703 737874104 6.630000e-91 344
16 TraesCS7B01G293700 chr2B 81.010 416 58 14 2106 2504 44349879 44349468 6.730000e-81 311
17 TraesCS7B01G293700 chr6A 82.143 252 36 9 1193 1439 181013368 181013615 9.080000e-50 207
18 TraesCS7B01G293700 chr6D 81.890 254 32 12 1192 1439 138384551 138384796 4.220000e-48 202


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 TraesCS7B01G293700 chr7B 530433419 530435922 2503 True 4625.0 4625 100.000 1 2504 1 chr7B.!!$R1 2503
1 TraesCS7B01G293700 chr7B 530590115 530592365 2250 True 1122.5 2039 91.242 1 1726 2 chr7B.!!$R2 1725
2 TraesCS7B01G293700 chr7A 567590375 567592471 2096 True 2218.0 2218 86.215 11 2109 1 chr7A.!!$R1 2098
3 TraesCS7B01G293700 chr7D 501107416 501109469 2053 True 2065.0 2065 85.268 2 2109 1 chr7D.!!$R1 2107

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
916 1546 1.077357 GGCCGGAGAGTGAGAGAGA 60.077 63.158 5.05 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 3071 0.031449 GAGGATGGCAGCGACTACTC 59.969 60.0 0.0 0.0 0.0 2.59 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
71 72 2.223572 CGGCACCATATTTTCTTGAGGC 60.224 50.000 0.00 0.00 0.00 4.70
94 96 5.278120 GCTGTAGGTAAAGCTAGCTCTCTAC 60.278 48.000 19.65 22.89 37.13 2.59
259 800 4.214332 GCATCTGGCCTTGTTTATACTAGC 59.786 45.833 3.32 0.00 36.11 3.42
295 838 5.566623 CACTATGCAGTGCTCTTATTGTTG 58.433 41.667 17.60 1.00 45.44 3.33
359 907 3.682885 TTGCCATGCCAGTTGCCG 61.683 61.111 0.00 0.00 40.16 5.69
389 937 4.214119 CAGAAAAGTTTGGCTGAAGATCGA 59.786 41.667 11.42 0.00 0.00 3.59
398 965 2.630580 GGCTGAAGATCGACCCTCTATT 59.369 50.000 0.00 0.00 0.00 1.73
631 1231 4.335594 CACTTCCGAAACAAGGAGAAAACT 59.664 41.667 0.00 0.00 39.22 2.66
655 1255 1.595003 GCCTATCTTGACGACGACGAG 60.595 57.143 15.32 4.85 42.66 4.18
744 1359 9.627123 CAGAAAAACCATCAGGATAGGTAATAA 57.373 33.333 0.00 0.00 38.69 1.40
835 1457 3.081554 CCAGTGGTGGGCTAAGCT 58.918 61.111 0.00 0.00 40.67 3.74
883 1513 1.548809 GCAGCCTTTTCTCCTTCCCTT 60.549 52.381 0.00 0.00 0.00 3.95
916 1546 1.077357 GGCCGGAGAGTGAGAGAGA 60.077 63.158 5.05 0.00 0.00 3.10
917 1547 1.101049 GGCCGGAGAGTGAGAGAGAG 61.101 65.000 5.05 0.00 0.00 3.20
924 1554 1.102978 GAGTGAGAGAGAGTGGCCTC 58.897 60.000 3.32 0.00 38.04 4.70
929 1559 3.073735 AGAGAGTGGCCTCCTGCG 61.074 66.667 3.32 0.00 42.61 5.18
946 1576 3.517602 CTGCGTACACTACTTGGCATAA 58.482 45.455 0.00 0.00 0.00 1.90
1056 1698 4.772687 GGTTTCGTCGGCCTCCCC 62.773 72.222 0.00 0.00 0.00 4.81
1092 1734 4.771356 CACCCGCACGACGTCGAT 62.771 66.667 41.52 23.81 43.02 3.59
1095 1737 3.238241 CCGCACGACGTCGATGTC 61.238 66.667 41.52 24.88 43.02 3.06
1542 2194 0.317103 ATGTGCTCGCGATCGTAGTC 60.317 55.000 17.81 10.89 36.96 2.59
1546 2198 2.411069 GTGCTCGCGATCGTAGTCTATA 59.589 50.000 17.81 0.00 36.96 1.31
1547 2199 3.062369 GTGCTCGCGATCGTAGTCTATAT 59.938 47.826 17.81 0.00 36.96 0.86
1548 2200 4.267214 GTGCTCGCGATCGTAGTCTATATA 59.733 45.833 17.81 0.00 36.96 0.86
1573 2226 6.183360 ACACTAGGACGATGATATATGCCATC 60.183 42.308 0.00 0.00 36.67 3.51
1590 2243 3.817647 GCCATCACCATGAGGAGATTAAC 59.182 47.826 0.00 0.00 41.73 2.01
1593 2246 6.521427 GCCATCACCATGAGGAGATTAACTAT 60.521 42.308 0.00 0.00 41.73 2.12
1618 2272 5.342525 CGGACGTGTGAATATTATGTAGCTC 59.657 44.000 0.00 0.00 0.00 4.09
1633 2290 5.940192 TGTAGCTCGATTGTGTTTTCATT 57.060 34.783 0.00 0.00 0.00 2.57
1667 2324 2.290577 GGGATTGTTCACTCCTGCTTCT 60.291 50.000 8.64 0.00 0.00 2.85
1672 2329 2.224137 TGTTCACTCCTGCTTCTGTGAG 60.224 50.000 0.00 0.00 40.00 3.51
1673 2330 1.709578 TCACTCCTGCTTCTGTGAGT 58.290 50.000 0.00 0.00 38.56 3.41
1674 2331 2.042464 TCACTCCTGCTTCTGTGAGTT 58.958 47.619 0.00 0.00 35.97 3.01
1675 2332 2.141517 CACTCCTGCTTCTGTGAGTTG 58.858 52.381 0.00 0.00 35.97 3.16
1679 2336 2.568956 TCCTGCTTCTGTGAGTTGCTAT 59.431 45.455 0.00 0.00 0.00 2.97
1688 2345 4.645136 TCTGTGAGTTGCTATTCCGTATCT 59.355 41.667 0.00 0.00 0.00 1.98
1694 2351 7.438459 GTGAGTTGCTATTCCGTATCTGTTAAT 59.562 37.037 0.00 0.00 0.00 1.40
1701 2358 8.002665 GCTATTCCGTATCTGTTAATTTCGTTC 58.997 37.037 0.00 0.00 0.00 3.95
1702 2359 9.245962 CTATTCCGTATCTGTTAATTTCGTTCT 57.754 33.333 0.00 0.00 0.00 3.01
1703 2360 7.894376 TTCCGTATCTGTTAATTTCGTTCTT 57.106 32.000 0.00 0.00 0.00 2.52
1704 2361 7.894376 TCCGTATCTGTTAATTTCGTTCTTT 57.106 32.000 0.00 0.00 0.00 2.52
1708 2365 5.116069 TCTGTTAATTTCGTTCTTTGGCC 57.884 39.130 0.00 0.00 0.00 5.36
1720 2394 1.003262 CTTTGGCCGCAACATCGTTG 61.003 55.000 0.00 2.48 0.00 4.10
1721 2395 2.413437 TTTGGCCGCAACATCGTTGG 62.413 55.000 8.79 0.00 0.00 3.77
1726 2400 1.227999 CCGCAACATCGTTGGTGAGT 61.228 55.000 15.62 0.00 43.67 3.41
1727 2401 0.110688 CGCAACATCGTTGGTGAGTG 60.111 55.000 15.62 0.56 43.67 3.51
1728 2402 1.225855 GCAACATCGTTGGTGAGTGA 58.774 50.000 15.62 0.00 43.67 3.41
1729 2403 1.806542 GCAACATCGTTGGTGAGTGAT 59.193 47.619 15.62 0.00 43.67 3.06
1730 2404 3.000041 GCAACATCGTTGGTGAGTGATA 59.000 45.455 15.62 0.00 43.67 2.15
1731 2405 3.181520 GCAACATCGTTGGTGAGTGATAC 60.182 47.826 15.62 0.00 43.67 2.24
1732 2406 4.245660 CAACATCGTTGGTGAGTGATACT 58.754 43.478 5.56 0.00 43.67 2.12
1733 2407 5.407502 CAACATCGTTGGTGAGTGATACTA 58.592 41.667 5.56 0.00 43.67 1.82
1734 2408 4.995124 ACATCGTTGGTGAGTGATACTAC 58.005 43.478 0.00 0.00 0.00 2.73
1735 2409 4.142227 ACATCGTTGGTGAGTGATACTACC 60.142 45.833 0.00 0.00 0.00 3.18
1736 2410 3.423749 TCGTTGGTGAGTGATACTACCA 58.576 45.455 0.00 0.00 41.18 3.25
1737 2411 3.192001 TCGTTGGTGAGTGATACTACCAC 59.808 47.826 0.00 0.00 42.48 4.16
1738 2412 3.192844 CGTTGGTGAGTGATACTACCACT 59.807 47.826 0.00 0.00 46.51 4.00
1739 2413 4.495422 GTTGGTGAGTGATACTACCACTG 58.505 47.826 0.00 0.00 44.14 3.66
1740 2414 3.774734 TGGTGAGTGATACTACCACTGT 58.225 45.455 0.00 0.00 44.14 3.55
1741 2415 3.762288 TGGTGAGTGATACTACCACTGTC 59.238 47.826 0.00 0.00 44.14 3.51
1742 2416 3.130693 GGTGAGTGATACTACCACTGTCC 59.869 52.174 0.00 0.00 44.14 4.02
1743 2417 4.017808 GTGAGTGATACTACCACTGTCCT 58.982 47.826 0.00 0.00 44.14 3.85
1744 2418 5.191426 GTGAGTGATACTACCACTGTCCTA 58.809 45.833 0.00 0.00 44.14 2.94
1745 2419 5.066246 GTGAGTGATACTACCACTGTCCTAC 59.934 48.000 0.00 0.00 44.14 3.18
1746 2420 5.188988 AGTGATACTACCACTGTCCTACA 57.811 43.478 0.00 0.00 42.68 2.74
1758 2432 2.368875 CTGTCCTACAAGTCCCACTGTT 59.631 50.000 0.00 0.00 0.00 3.16
1769 2443 2.673368 GTCCCACTGTTGAATGATCGAC 59.327 50.000 0.00 0.00 39.97 4.20
1771 2445 2.606108 CCACTGTTGAATGATCGACGA 58.394 47.619 0.00 0.00 42.09 4.20
1785 2459 1.635663 CGACGATGGCCTTGGTGTTC 61.636 60.000 11.13 0.00 0.00 3.18
1788 2462 0.036010 CGATGGCCTTGGTGTTCTCT 60.036 55.000 3.32 0.00 0.00 3.10
1789 2463 1.207089 CGATGGCCTTGGTGTTCTCTA 59.793 52.381 3.32 0.00 0.00 2.43
1869 2543 3.397482 GCCATAGACCATCTAGTTGCTG 58.603 50.000 0.00 0.00 31.67 4.41
1876 2550 1.224075 CATCTAGTTGCTGCATCCGG 58.776 55.000 1.84 0.00 0.00 5.14
1877 2551 1.123077 ATCTAGTTGCTGCATCCGGA 58.877 50.000 6.61 6.61 0.00 5.14
1878 2552 0.461548 TCTAGTTGCTGCATCCGGAG 59.538 55.000 11.34 3.17 0.00 4.63
1886 2560 3.946604 TGCATCCGGAGCAGTAAAA 57.053 47.368 20.28 1.95 37.02 1.52
1887 2561 1.448985 TGCATCCGGAGCAGTAAAAC 58.551 50.000 20.28 0.00 37.02 2.43
1888 2562 1.003118 TGCATCCGGAGCAGTAAAACT 59.997 47.619 20.28 0.00 37.02 2.66
1889 2563 2.235155 TGCATCCGGAGCAGTAAAACTA 59.765 45.455 20.28 0.13 37.02 2.24
1890 2564 3.267483 GCATCCGGAGCAGTAAAACTAA 58.733 45.455 11.34 0.00 0.00 2.24
1891 2565 3.687698 GCATCCGGAGCAGTAAAACTAAA 59.312 43.478 11.34 0.00 0.00 1.85
1892 2566 4.155280 GCATCCGGAGCAGTAAAACTAAAA 59.845 41.667 11.34 0.00 0.00 1.52
1893 2567 5.628134 CATCCGGAGCAGTAAAACTAAAAC 58.372 41.667 11.34 0.00 0.00 2.43
1894 2568 4.067192 TCCGGAGCAGTAAAACTAAAACC 58.933 43.478 0.00 0.00 0.00 3.27
1895 2569 3.189910 CCGGAGCAGTAAAACTAAAACCC 59.810 47.826 0.00 0.00 0.00 4.11
1896 2570 3.189910 CGGAGCAGTAAAACTAAAACCCC 59.810 47.826 0.00 0.00 0.00 4.95
1897 2571 3.189910 GGAGCAGTAAAACTAAAACCCCG 59.810 47.826 0.00 0.00 0.00 5.73
1911 2585 0.840722 ACCCCGGTCAACAGGAAGAT 60.841 55.000 0.00 0.00 32.68 2.40
1917 2591 2.671396 CGGTCAACAGGAAGATTAACCG 59.329 50.000 0.00 0.00 41.90 4.44
1925 2599 2.027469 AGGAAGATTAACCGGTGTCCAC 60.027 50.000 8.52 4.35 0.00 4.02
1967 2641 1.822506 CGTCAGACACCTCCTCTGTA 58.177 55.000 0.41 0.00 37.12 2.74
1978 2652 2.494073 CCTCCTCTGTACAGGACAAGAC 59.506 54.545 22.48 0.00 37.68 3.01
2062 2743 1.300542 GCCAGCTCTATCTCCACGC 60.301 63.158 0.00 0.00 0.00 5.34
2084 2765 1.670087 CGAAACACCAGCGATCAGACT 60.670 52.381 0.00 0.00 0.00 3.24
2085 2766 2.415491 CGAAACACCAGCGATCAGACTA 60.415 50.000 0.00 0.00 0.00 2.59
2090 2771 1.068281 ACCAGCGATCAGACTAGCATG 59.932 52.381 0.00 0.00 0.00 4.06
2109 2792 5.868043 CATGATGTGCACAAGAGTTTAGA 57.132 39.130 25.72 0.00 0.00 2.10
2110 2793 5.866075 CATGATGTGCACAAGAGTTTAGAG 58.134 41.667 25.72 2.08 0.00 2.43
2111 2794 3.748048 TGATGTGCACAAGAGTTTAGAGC 59.252 43.478 25.72 0.00 0.00 4.09
2112 2795 3.192541 TGTGCACAAGAGTTTAGAGCA 57.807 42.857 19.28 0.00 0.00 4.26
2113 2796 3.743521 TGTGCACAAGAGTTTAGAGCAT 58.256 40.909 19.28 0.00 32.75 3.79
2114 2797 3.748048 TGTGCACAAGAGTTTAGAGCATC 59.252 43.478 19.28 0.00 32.75 3.91
2125 2808 2.892425 GAGCATCTCCGGCCGTTG 60.892 66.667 26.12 16.29 0.00 4.10
2126 2809 4.473520 AGCATCTCCGGCCGTTGG 62.474 66.667 26.12 13.50 0.00 3.77
2148 2831 3.579232 CCCGGGGCGCGTAAAATC 61.579 66.667 22.61 0.00 0.00 2.17
2149 2832 3.932313 CCGGGGCGCGTAAAATCG 61.932 66.667 22.61 3.77 0.00 3.34
2157 2840 3.788817 CGTAAAATCGCCGCCTGA 58.211 55.556 0.00 0.00 0.00 3.86
2158 2841 1.636340 CGTAAAATCGCCGCCTGAG 59.364 57.895 0.00 0.00 0.00 3.35
2159 2842 1.762222 CGTAAAATCGCCGCCTGAGG 61.762 60.000 0.00 0.00 0.00 3.86
2160 2843 1.153249 TAAAATCGCCGCCTGAGGG 60.153 57.895 0.00 0.00 0.00 4.30
2198 2881 2.750350 CCTGAGGGCGAGTTGGTT 59.250 61.111 0.00 0.00 0.00 3.67
2199 2882 1.073199 CCTGAGGGCGAGTTGGTTT 59.927 57.895 0.00 0.00 0.00 3.27
2200 2883 0.955919 CCTGAGGGCGAGTTGGTTTC 60.956 60.000 0.00 0.00 0.00 2.78
2201 2884 0.955919 CTGAGGGCGAGTTGGTTTCC 60.956 60.000 0.00 0.00 0.00 3.13
2202 2885 1.072505 GAGGGCGAGTTGGTTTCCA 59.927 57.895 0.00 0.00 0.00 3.53
2203 2886 0.955919 GAGGGCGAGTTGGTTTCCAG 60.956 60.000 0.00 0.00 33.81 3.86
2204 2887 1.228154 GGGCGAGTTGGTTTCCAGT 60.228 57.895 0.00 0.00 33.81 4.00
2205 2888 1.235281 GGGCGAGTTGGTTTCCAGTC 61.235 60.000 0.00 0.00 33.81 3.51
2206 2889 1.566018 GGCGAGTTGGTTTCCAGTCG 61.566 60.000 14.21 14.21 41.59 4.18
2207 2890 1.860078 CGAGTTGGTTTCCAGTCGC 59.140 57.895 8.79 0.58 35.89 5.19
2208 2891 1.566018 CGAGTTGGTTTCCAGTCGCC 61.566 60.000 8.79 0.00 35.89 5.54
2209 2892 1.566018 GAGTTGGTTTCCAGTCGCCG 61.566 60.000 0.00 0.00 33.81 6.46
2210 2893 1.595929 GTTGGTTTCCAGTCGCCGA 60.596 57.895 0.00 0.00 33.81 5.54
2211 2894 1.595929 TTGGTTTCCAGTCGCCGAC 60.596 57.895 9.71 9.71 33.81 4.79
2212 2895 2.741211 GGTTTCCAGTCGCCGACC 60.741 66.667 14.60 0.00 32.18 4.79
2213 2896 2.741211 GTTTCCAGTCGCCGACCC 60.741 66.667 14.60 0.00 32.18 4.46
2214 2897 4.011517 TTTCCAGTCGCCGACCCC 62.012 66.667 14.60 0.00 32.18 4.95
2217 2900 4.838152 CCAGTCGCCGACCCCATG 62.838 72.222 14.60 5.40 32.18 3.66
2218 2901 4.838152 CAGTCGCCGACCCCATGG 62.838 72.222 14.60 4.14 32.18 3.66
2241 2924 3.446570 CCCGGACGGCGTCTAGTT 61.447 66.667 35.42 1.88 32.47 2.24
2242 2925 2.570181 CCGGACGGCGTCTAGTTT 59.430 61.111 35.42 1.00 32.47 2.66
2243 2926 1.080298 CCGGACGGCGTCTAGTTTT 60.080 57.895 35.42 0.13 32.47 2.43
2244 2927 0.668401 CCGGACGGCGTCTAGTTTTT 60.668 55.000 35.42 0.00 32.47 1.94
2267 2950 8.798748 TTTTTAATAAAAACTCATTCGGCGAA 57.201 26.923 25.88 25.88 35.57 4.70
2268 2951 8.442605 TTTTAATAAAAACTCATTCGGCGAAG 57.557 30.769 27.35 16.51 29.59 3.79
2269 2952 5.622770 AATAAAAACTCATTCGGCGAAGT 57.377 34.783 27.35 17.20 0.00 3.01
2270 2953 3.982576 AAAAACTCATTCGGCGAAGTT 57.017 38.095 27.35 21.87 0.00 2.66
2271 2954 3.982576 AAAACTCATTCGGCGAAGTTT 57.017 38.095 27.35 25.82 0.00 2.66
2272 2955 2.969443 AACTCATTCGGCGAAGTTTG 57.031 45.000 27.35 20.19 0.00 2.93
2273 2956 0.517316 ACTCATTCGGCGAAGTTTGC 59.483 50.000 27.35 6.54 0.00 3.68
2274 2957 0.516877 CTCATTCGGCGAAGTTTGCA 59.483 50.000 27.35 2.66 0.00 4.08
2275 2958 1.131126 CTCATTCGGCGAAGTTTGCAT 59.869 47.619 27.35 6.14 0.00 3.96
2276 2959 2.351418 CTCATTCGGCGAAGTTTGCATA 59.649 45.455 27.35 0.99 0.00 3.14
2277 2960 2.744741 TCATTCGGCGAAGTTTGCATAA 59.255 40.909 27.35 10.09 0.00 1.90
2278 2961 3.189495 TCATTCGGCGAAGTTTGCATAAA 59.811 39.130 27.35 7.77 0.00 1.40
2279 2962 2.604969 TCGGCGAAGTTTGCATAAAC 57.395 45.000 16.93 0.00 45.13 2.01
2291 2974 6.944557 GTTTGCATAAACTCGGCTAAAATT 57.055 33.333 0.00 0.00 42.26 1.82
2292 2975 6.978412 GTTTGCATAAACTCGGCTAAAATTC 58.022 36.000 0.00 0.00 42.26 2.17
2293 2976 4.904116 TGCATAAACTCGGCTAAAATTCG 58.096 39.130 0.00 0.00 0.00 3.34
2294 2977 4.201871 TGCATAAACTCGGCTAAAATTCGG 60.202 41.667 0.00 0.00 0.00 4.30
2295 2978 2.913777 AAACTCGGCTAAAATTCGGC 57.086 45.000 0.00 0.00 0.00 5.54
2296 2979 1.816074 AACTCGGCTAAAATTCGGCA 58.184 45.000 0.00 0.00 0.00 5.69
2297 2980 1.816074 ACTCGGCTAAAATTCGGCAA 58.184 45.000 0.00 0.00 0.00 4.52
2298 2981 2.156098 ACTCGGCTAAAATTCGGCAAA 58.844 42.857 0.00 0.00 0.00 3.68
2299 2982 2.095415 ACTCGGCTAAAATTCGGCAAAC 60.095 45.455 0.00 0.00 0.00 2.93
2300 2983 2.156098 TCGGCTAAAATTCGGCAAACT 58.844 42.857 0.00 0.00 0.00 2.66
2301 2984 2.554893 TCGGCTAAAATTCGGCAAACTT 59.445 40.909 0.00 0.00 0.00 2.66
2302 2985 2.661195 CGGCTAAAATTCGGCAAACTTG 59.339 45.455 0.00 0.00 0.00 3.16
2303 2986 2.993220 GGCTAAAATTCGGCAAACTTGG 59.007 45.455 0.00 0.00 0.00 3.61
2319 3002 7.651808 GCAAACTTGGCATATATTAGACATGT 58.348 34.615 0.00 0.00 0.00 3.21
2320 3003 8.137437 GCAAACTTGGCATATATTAGACATGTT 58.863 33.333 0.00 7.82 0.00 2.71
2321 3004 9.669353 CAAACTTGGCATATATTAGACATGTTC 57.331 33.333 0.00 0.00 0.00 3.18
2322 3005 7.658179 ACTTGGCATATATTAGACATGTTCG 57.342 36.000 0.00 0.00 0.00 3.95
2323 3006 6.147821 ACTTGGCATATATTAGACATGTTCGC 59.852 38.462 0.00 0.00 0.00 4.70
2324 3007 4.625311 TGGCATATATTAGACATGTTCGCG 59.375 41.667 0.00 0.00 0.00 5.87
2325 3008 4.032900 GGCATATATTAGACATGTTCGCGG 59.967 45.833 6.13 0.00 0.00 6.46
2326 3009 4.625742 GCATATATTAGACATGTTCGCGGT 59.374 41.667 6.13 0.00 0.00 5.68
2327 3010 5.120208 GCATATATTAGACATGTTCGCGGTT 59.880 40.000 6.13 0.00 0.00 4.44
2328 3011 6.347402 GCATATATTAGACATGTTCGCGGTTT 60.347 38.462 6.13 0.00 0.00 3.27
2329 3012 7.148705 GCATATATTAGACATGTTCGCGGTTTA 60.149 37.037 6.13 0.00 0.00 2.01
2330 3013 4.852609 ATTAGACATGTTCGCGGTTTAC 57.147 40.909 6.13 0.09 0.00 2.01
2331 3014 2.157834 AGACATGTTCGCGGTTTACA 57.842 45.000 6.13 6.50 0.00 2.41
2332 3015 2.695359 AGACATGTTCGCGGTTTACAT 58.305 42.857 6.13 8.67 32.98 2.29
2333 3016 3.852286 AGACATGTTCGCGGTTTACATA 58.148 40.909 6.13 0.00 31.64 2.29
2334 3017 3.863424 AGACATGTTCGCGGTTTACATAG 59.137 43.478 6.13 8.73 31.64 2.23
2335 3018 2.350498 ACATGTTCGCGGTTTACATAGC 59.650 45.455 6.13 0.00 31.64 2.97
2336 3019 2.081725 TGTTCGCGGTTTACATAGCA 57.918 45.000 6.13 0.00 0.00 3.49
2337 3020 2.414806 TGTTCGCGGTTTACATAGCAA 58.585 42.857 6.13 0.00 0.00 3.91
2338 3021 2.806818 TGTTCGCGGTTTACATAGCAAA 59.193 40.909 6.13 0.00 0.00 3.68
2339 3022 3.437395 TGTTCGCGGTTTACATAGCAAAT 59.563 39.130 6.13 0.00 0.00 2.32
2340 3023 4.083217 TGTTCGCGGTTTACATAGCAAATT 60.083 37.500 6.13 0.00 0.00 1.82
2341 3024 4.688511 TCGCGGTTTACATAGCAAATTT 57.311 36.364 6.13 0.00 0.00 1.82
2342 3025 5.798015 TCGCGGTTTACATAGCAAATTTA 57.202 34.783 6.13 0.00 0.00 1.40
2343 3026 6.366315 TCGCGGTTTACATAGCAAATTTAT 57.634 33.333 6.13 0.00 0.00 1.40
2344 3027 7.479897 TCGCGGTTTACATAGCAAATTTATA 57.520 32.000 6.13 0.00 0.00 0.98
2345 3028 8.090250 TCGCGGTTTACATAGCAAATTTATAT 57.910 30.769 6.13 0.00 0.00 0.86
2346 3029 8.561212 TCGCGGTTTACATAGCAAATTTATATT 58.439 29.630 6.13 0.00 0.00 1.28
2347 3030 9.814507 CGCGGTTTACATAGCAAATTTATATTA 57.185 29.630 0.00 0.00 0.00 0.98
2370 3053 4.579647 AAAAATCCTAACTAAGGGGCGA 57.420 40.909 0.00 0.00 46.55 5.54
2371 3054 4.579647 AAAATCCTAACTAAGGGGCGAA 57.420 40.909 0.00 0.00 46.55 4.70
2372 3055 3.840124 AATCCTAACTAAGGGGCGAAG 57.160 47.619 0.00 0.00 46.55 3.79
2373 3056 2.537633 TCCTAACTAAGGGGCGAAGA 57.462 50.000 0.00 0.00 46.55 2.87
2374 3057 2.823959 TCCTAACTAAGGGGCGAAGAA 58.176 47.619 0.00 0.00 46.55 2.52
2375 3058 2.764572 TCCTAACTAAGGGGCGAAGAAG 59.235 50.000 0.00 0.00 46.55 2.85
2376 3059 2.500504 CCTAACTAAGGGGCGAAGAAGT 59.499 50.000 0.00 0.00 42.32 3.01
2377 3060 2.764439 AACTAAGGGGCGAAGAAGTC 57.236 50.000 0.00 0.00 0.00 3.01
2378 3061 6.746565 CCTAACTAAGGGGCGAAGAAGTCG 62.747 54.167 0.00 0.00 46.55 4.18
2386 3069 3.615763 CGAAGAAGTCGTTGAACGC 57.384 52.632 13.62 8.38 45.09 4.84
2387 3070 0.179307 CGAAGAAGTCGTTGAACGCG 60.179 55.000 13.62 3.53 45.09 6.01
2388 3071 0.161024 GAAGAAGTCGTTGAACGCGG 59.839 55.000 13.62 0.00 42.21 6.46
2389 3072 0.249155 AAGAAGTCGTTGAACGCGGA 60.249 50.000 13.62 0.00 42.21 5.54
2390 3073 0.663568 AGAAGTCGTTGAACGCGGAG 60.664 55.000 13.62 0.00 42.21 4.63
2391 3074 0.938168 GAAGTCGTTGAACGCGGAGT 60.938 55.000 13.62 0.00 42.21 3.85
2392 3075 0.311790 AAGTCGTTGAACGCGGAGTA 59.688 50.000 13.62 0.00 42.21 2.59
2393 3076 0.109873 AGTCGTTGAACGCGGAGTAG 60.110 55.000 13.62 0.00 42.21 2.57
2394 3077 0.386478 GTCGTTGAACGCGGAGTAGT 60.386 55.000 13.62 0.00 42.21 2.73
2395 3078 0.110056 TCGTTGAACGCGGAGTAGTC 60.110 55.000 13.62 0.00 42.21 2.59
2396 3079 1.393597 CGTTGAACGCGGAGTAGTCG 61.394 60.000 12.47 2.43 33.65 4.18
2403 3086 2.808315 CGGAGTAGTCGCTGCCAT 59.192 61.111 0.00 0.00 0.00 4.40
2404 3087 1.299468 CGGAGTAGTCGCTGCCATC 60.299 63.158 0.00 0.00 0.00 3.51
2405 3088 1.068250 GGAGTAGTCGCTGCCATCC 59.932 63.158 0.00 0.00 0.00 3.51
2406 3089 1.395826 GGAGTAGTCGCTGCCATCCT 61.396 60.000 0.00 0.00 0.00 3.24
2407 3090 0.031449 GAGTAGTCGCTGCCATCCTC 59.969 60.000 0.00 0.00 0.00 3.71
2408 3091 1.299468 GTAGTCGCTGCCATCCTCG 60.299 63.158 0.00 0.00 0.00 4.63
2409 3092 3.138930 TAGTCGCTGCCATCCTCGC 62.139 63.158 0.00 0.00 0.00 5.03
2438 3121 4.475135 GCGGTGGCCTTCTCCTCC 62.475 72.222 3.32 0.00 36.63 4.30
2439 3122 2.685380 CGGTGGCCTTCTCCTCCT 60.685 66.667 3.32 0.00 37.57 3.69
2440 3123 2.294078 CGGTGGCCTTCTCCTCCTT 61.294 63.158 3.32 0.00 37.57 3.36
2441 3124 1.301293 GGTGGCCTTCTCCTCCTTG 59.699 63.158 3.32 0.00 36.94 3.61
2442 3125 1.201429 GGTGGCCTTCTCCTCCTTGA 61.201 60.000 3.32 0.00 36.94 3.02
2443 3126 0.035915 GTGGCCTTCTCCTCCTTGAC 60.036 60.000 3.32 0.00 0.00 3.18
2444 3127 1.219393 GGCCTTCTCCTCCTTGACG 59.781 63.158 0.00 0.00 0.00 4.35
2445 3128 1.545706 GGCCTTCTCCTCCTTGACGT 61.546 60.000 0.00 0.00 0.00 4.34
2446 3129 0.390472 GCCTTCTCCTCCTTGACGTG 60.390 60.000 0.00 0.00 0.00 4.49
2447 3130 0.247736 CCTTCTCCTCCTTGACGTGG 59.752 60.000 0.00 0.00 0.00 4.94
2448 3131 0.390472 CTTCTCCTCCTTGACGTGGC 60.390 60.000 0.00 0.00 0.00 5.01
2449 3132 1.827399 TTCTCCTCCTTGACGTGGCC 61.827 60.000 0.00 0.00 0.00 5.36
2450 3133 3.649277 CTCCTCCTTGACGTGGCCG 62.649 68.421 0.00 0.00 40.83 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.911514 AAATATGGTGCCGGTTTATGTC 57.088 40.909 1.90 0.00 0.00 3.06
71 72 5.049954 CGTAGAGAGCTAGCTTTACCTACAG 60.050 48.000 27.12 20.90 0.00 2.74
168 706 1.429148 CGGCGTCAGAGGTTTATGGC 61.429 60.000 0.00 0.00 0.00 4.40
259 800 1.070821 CATAGTGACGCCACACAGTG 58.929 55.000 4.23 0.00 45.54 3.66
295 838 5.346822 CCTTTGTCTTTGTGCAAGATATTGC 59.653 40.000 18.03 18.03 43.72 3.56
359 907 1.852280 GCCAAACTTTTCTGTTGTCGC 59.148 47.619 0.00 0.00 0.00 5.19
389 937 7.773099 AGGAAATTTTCTCCTAATAGAGGGT 57.227 36.000 8.93 0.00 46.70 4.34
398 965 7.038231 GGCTATAGGCTAGGAAATTTTCTCCTA 60.038 40.741 18.61 13.73 42.20 2.94
582 1182 3.248171 GTGCGGTGTCGATCGAGC 61.248 66.667 20.09 18.48 39.00 5.03
631 1231 3.486375 CGTCGTCGTCAAGATAGGCTTAA 60.486 47.826 0.00 0.00 34.31 1.85
831 1453 1.376037 CCGCGAAAAGGGAGAGCTT 60.376 57.895 8.23 0.00 34.27 3.74
832 1454 2.113243 AACCGCGAAAAGGGAGAGCT 62.113 55.000 8.23 0.00 34.27 4.09
833 1455 1.235281 AAACCGCGAAAAGGGAGAGC 61.235 55.000 8.23 0.00 34.27 4.09
834 1456 2.088950 TAAACCGCGAAAAGGGAGAG 57.911 50.000 8.23 0.00 34.27 3.20
835 1457 2.547299 TTAAACCGCGAAAAGGGAGA 57.453 45.000 8.23 0.00 34.27 3.71
861 1487 0.321653 GGAAGGAGAAAAGGCTGCGA 60.322 55.000 0.00 0.00 0.00 5.10
862 1488 1.308783 GGGAAGGAGAAAAGGCTGCG 61.309 60.000 0.00 0.00 0.00 5.18
863 1489 0.038890 AGGGAAGGAGAAAAGGCTGC 59.961 55.000 0.00 0.00 0.00 5.25
864 1490 2.224867 TGAAGGGAAGGAGAAAAGGCTG 60.225 50.000 0.00 0.00 0.00 4.85
868 1494 4.307032 TGGATGAAGGGAAGGAGAAAAG 57.693 45.455 0.00 0.00 0.00 2.27
872 1502 2.435805 CGAATGGATGAAGGGAAGGAGA 59.564 50.000 0.00 0.00 0.00 3.71
883 1513 2.584970 GCCGCGTCGAATGGATGA 60.585 61.111 4.92 0.00 33.19 2.92
916 1546 2.603473 TGTACGCAGGAGGCCACT 60.603 61.111 5.01 0.00 40.31 4.00
917 1547 1.601419 TAGTGTACGCAGGAGGCCAC 61.601 60.000 5.01 0.00 40.31 5.01
924 1554 0.037697 TGCCAAGTAGTGTACGCAGG 60.038 55.000 9.48 3.66 0.00 4.85
929 1559 4.998672 TGGTTGTTATGCCAAGTAGTGTAC 59.001 41.667 0.00 0.00 0.00 2.90
946 1576 1.901591 CTGCTGTGGAGATTGGTTGT 58.098 50.000 0.00 0.00 0.00 3.32
1056 1698 4.814294 GGCGGCAGGTAGGACGTG 62.814 72.222 3.07 0.00 42.62 4.49
1546 2198 6.833933 TGGCATATATCATCGTCCTAGTGTAT 59.166 38.462 0.00 0.00 0.00 2.29
1547 2199 6.184789 TGGCATATATCATCGTCCTAGTGTA 58.815 40.000 0.00 0.00 0.00 2.90
1548 2200 5.016831 TGGCATATATCATCGTCCTAGTGT 58.983 41.667 0.00 0.00 0.00 3.55
1573 2226 5.243954 TCCGATAGTTAATCTCCTCATGGTG 59.756 44.000 0.00 0.00 31.87 4.17
1590 2243 7.218393 GCTACATAATATTCACACGTCCGATAG 59.782 40.741 0.00 0.00 0.00 2.08
1593 2246 5.009310 AGCTACATAATATTCACACGTCCGA 59.991 40.000 0.00 0.00 0.00 4.55
1618 2272 4.097714 CCCGATCAATGAAAACACAATCG 58.902 43.478 0.00 0.00 35.53 3.34
1633 2290 0.181114 CAATCCCAAGAGCCCGATCA 59.819 55.000 0.00 0.00 0.00 2.92
1667 2324 4.159693 ACAGATACGGAATAGCAACTCACA 59.840 41.667 0.00 0.00 0.00 3.58
1672 2329 7.792508 CGAAATTAACAGATACGGAATAGCAAC 59.207 37.037 0.00 0.00 0.00 4.17
1673 2330 7.493320 ACGAAATTAACAGATACGGAATAGCAA 59.507 33.333 0.00 0.00 0.00 3.91
1674 2331 6.982141 ACGAAATTAACAGATACGGAATAGCA 59.018 34.615 0.00 0.00 0.00 3.49
1675 2332 7.404139 ACGAAATTAACAGATACGGAATAGC 57.596 36.000 0.00 0.00 0.00 2.97
1679 2336 7.894376 AAGAACGAAATTAACAGATACGGAA 57.106 32.000 0.00 0.00 0.00 4.30
1688 2345 3.854045 GCGGCCAAAGAACGAAATTAACA 60.854 43.478 2.24 0.00 0.00 2.41
1694 2351 0.248702 GTTGCGGCCAAAGAACGAAA 60.249 50.000 2.24 0.00 31.68 3.46
1701 2358 1.003262 CAACGATGTTGCGGCCAAAG 61.003 55.000 2.24 0.00 35.12 2.77
1702 2359 1.007964 CAACGATGTTGCGGCCAAA 60.008 52.632 2.24 0.00 35.12 3.28
1703 2360 2.642129 CAACGATGTTGCGGCCAA 59.358 55.556 2.24 0.00 35.12 4.52
1704 2361 3.361158 CCAACGATGTTGCGGCCA 61.361 61.111 2.24 0.00 35.12 5.36
1708 2365 0.110688 CACTCACCAACGATGTTGCG 60.111 55.000 4.18 1.30 37.29 4.85
1720 2394 3.130693 GGACAGTGGTAGTATCACTCACC 59.869 52.174 13.34 14.62 42.87 4.02
1721 2395 4.017808 AGGACAGTGGTAGTATCACTCAC 58.982 47.826 13.34 9.91 42.87 3.51
1726 2400 5.577100 ACTTGTAGGACAGTGGTAGTATCA 58.423 41.667 0.00 0.00 0.00 2.15
1727 2401 5.067544 GGACTTGTAGGACAGTGGTAGTATC 59.932 48.000 0.00 0.00 0.00 2.24
1728 2402 4.954826 GGACTTGTAGGACAGTGGTAGTAT 59.045 45.833 0.00 0.00 0.00 2.12
1729 2403 4.338879 GGACTTGTAGGACAGTGGTAGTA 58.661 47.826 0.00 0.00 0.00 1.82
1730 2404 3.163467 GGACTTGTAGGACAGTGGTAGT 58.837 50.000 0.00 0.00 0.00 2.73
1731 2405 2.496470 GGGACTTGTAGGACAGTGGTAG 59.504 54.545 0.00 0.00 0.00 3.18
1732 2406 2.158279 TGGGACTTGTAGGACAGTGGTA 60.158 50.000 0.00 0.00 0.00 3.25
1733 2407 1.349067 GGGACTTGTAGGACAGTGGT 58.651 55.000 0.00 0.00 0.00 4.16
1734 2408 1.002087 GTGGGACTTGTAGGACAGTGG 59.998 57.143 0.00 0.00 0.00 4.00
1735 2409 1.971357 AGTGGGACTTGTAGGACAGTG 59.029 52.381 0.00 0.00 0.00 3.66
1736 2410 1.971357 CAGTGGGACTTGTAGGACAGT 59.029 52.381 0.00 0.00 0.00 3.55
1737 2411 1.971357 ACAGTGGGACTTGTAGGACAG 59.029 52.381 0.00 0.00 0.00 3.51
1738 2412 2.097110 ACAGTGGGACTTGTAGGACA 57.903 50.000 0.00 0.00 0.00 4.02
1739 2413 2.367567 TCAACAGTGGGACTTGTAGGAC 59.632 50.000 0.00 0.00 0.00 3.85
1740 2414 2.684943 TCAACAGTGGGACTTGTAGGA 58.315 47.619 0.00 0.00 0.00 2.94
1741 2415 3.485463 TTCAACAGTGGGACTTGTAGG 57.515 47.619 0.00 0.00 0.00 3.18
1742 2416 4.641396 TCATTCAACAGTGGGACTTGTAG 58.359 43.478 0.00 0.00 0.00 2.74
1743 2417 4.698201 TCATTCAACAGTGGGACTTGTA 57.302 40.909 0.00 0.00 0.00 2.41
1744 2418 3.576078 TCATTCAACAGTGGGACTTGT 57.424 42.857 0.00 0.00 0.00 3.16
1745 2419 3.125829 CGATCATTCAACAGTGGGACTTG 59.874 47.826 0.00 0.00 0.00 3.16
1746 2420 3.007940 TCGATCATTCAACAGTGGGACTT 59.992 43.478 0.00 0.00 0.00 3.01
1758 2432 0.752658 AGGCCATCGTCGATCATTCA 59.247 50.000 5.01 0.00 0.00 2.57
1769 2443 0.036010 AGAGAACACCAAGGCCATCG 60.036 55.000 5.01 0.00 0.00 3.84
1771 2445 1.065126 GCTAGAGAACACCAAGGCCAT 60.065 52.381 5.01 0.00 0.00 4.40
1785 2459 3.764810 CTGTCGCCGGCAGCTAGAG 62.765 68.421 28.98 12.30 40.39 2.43
1869 2543 1.739067 AGTTTTACTGCTCCGGATGC 58.261 50.000 3.57 11.93 0.00 3.91
1876 2550 3.189910 CCGGGGTTTTAGTTTTACTGCTC 59.810 47.826 0.00 0.00 0.00 4.26
1877 2551 3.151554 CCGGGGTTTTAGTTTTACTGCT 58.848 45.455 0.00 0.00 0.00 4.24
1878 2552 2.886523 ACCGGGGTTTTAGTTTTACTGC 59.113 45.455 6.32 0.00 0.00 4.40
1879 2553 4.136051 TGACCGGGGTTTTAGTTTTACTG 58.864 43.478 6.32 0.00 0.00 2.74
1880 2554 4.436113 TGACCGGGGTTTTAGTTTTACT 57.564 40.909 6.32 0.00 0.00 2.24
1881 2555 4.337836 TGTTGACCGGGGTTTTAGTTTTAC 59.662 41.667 6.32 0.00 0.00 2.01
1882 2556 4.530875 TGTTGACCGGGGTTTTAGTTTTA 58.469 39.130 6.32 0.00 0.00 1.52
1883 2557 3.363627 TGTTGACCGGGGTTTTAGTTTT 58.636 40.909 6.32 0.00 0.00 2.43
1884 2558 2.953648 CTGTTGACCGGGGTTTTAGTTT 59.046 45.455 6.32 0.00 0.00 2.66
1885 2559 2.578786 CTGTTGACCGGGGTTTTAGTT 58.421 47.619 6.32 0.00 0.00 2.24
1886 2560 1.202842 CCTGTTGACCGGGGTTTTAGT 60.203 52.381 6.32 0.00 35.76 2.24
1887 2561 1.072648 TCCTGTTGACCGGGGTTTTAG 59.927 52.381 6.32 0.00 40.38 1.85
1888 2562 1.138568 TCCTGTTGACCGGGGTTTTA 58.861 50.000 6.32 0.00 40.38 1.52
1889 2563 0.259356 TTCCTGTTGACCGGGGTTTT 59.741 50.000 6.32 0.00 40.38 2.43
1890 2564 0.179001 CTTCCTGTTGACCGGGGTTT 60.179 55.000 6.32 0.00 40.38 3.27
1891 2565 1.057851 TCTTCCTGTTGACCGGGGTT 61.058 55.000 6.32 0.00 40.38 4.11
1892 2566 0.840722 ATCTTCCTGTTGACCGGGGT 60.841 55.000 6.32 0.00 40.38 4.95
1893 2567 0.328258 AATCTTCCTGTTGACCGGGG 59.672 55.000 6.32 0.00 40.38 5.73
1894 2568 3.007635 GTTAATCTTCCTGTTGACCGGG 58.992 50.000 6.32 0.00 41.48 5.73
1895 2569 3.007635 GGTTAATCTTCCTGTTGACCGG 58.992 50.000 0.00 0.00 0.00 5.28
1896 2570 2.671396 CGGTTAATCTTCCTGTTGACCG 59.329 50.000 6.99 6.99 46.21 4.79
1897 2571 3.007635 CCGGTTAATCTTCCTGTTGACC 58.992 50.000 0.00 0.00 32.40 4.02
1911 2585 0.599558 CTCTCGTGGACACCGGTTAA 59.400 55.000 2.97 0.00 0.00 2.01
1917 2591 1.819288 TCTGAATCTCTCGTGGACACC 59.181 52.381 0.00 0.00 0.00 4.16
1925 2599 3.242480 CGCAACATCTTCTGAATCTCTCG 59.758 47.826 0.00 0.00 0.00 4.04
1967 2641 4.681978 GCCGCCGTCTTGTCCTGT 62.682 66.667 0.00 0.00 0.00 4.00
2048 2729 2.663630 TTCGCGCGTGGAGATAGAGC 62.664 60.000 30.98 0.00 0.00 4.09
2049 2730 0.248498 TTTCGCGCGTGGAGATAGAG 60.248 55.000 30.98 0.00 0.00 2.43
2090 2771 3.748048 TGCTCTAAACTCTTGTGCACATC 59.252 43.478 22.39 0.00 0.00 3.06
2097 2778 3.118956 CCGGAGATGCTCTAAACTCTTGT 60.119 47.826 0.00 0.00 0.00 3.16
2109 2792 4.473520 CCAACGGCCGGAGATGCT 62.474 66.667 31.76 2.42 0.00 3.79
2131 2814 3.579232 GATTTTACGCGCCCCGGG 61.579 66.667 15.80 15.80 45.13 5.73
2132 2815 3.932313 CGATTTTACGCGCCCCGG 61.932 66.667 5.73 0.00 42.52 5.73
2140 2823 1.636340 CTCAGGCGGCGATTTTACG 59.364 57.895 12.98 0.00 0.00 3.18
2141 2824 1.436983 CCCTCAGGCGGCGATTTTAC 61.437 60.000 12.98 0.00 0.00 2.01
2142 2825 1.153249 CCCTCAGGCGGCGATTTTA 60.153 57.895 12.98 0.00 0.00 1.52
2143 2826 2.438434 CCCTCAGGCGGCGATTTT 60.438 61.111 12.98 0.00 0.00 1.82
2181 2864 0.955919 GAAACCAACTCGCCCTCAGG 60.956 60.000 0.00 0.00 0.00 3.86
2182 2865 0.955919 GGAAACCAACTCGCCCTCAG 60.956 60.000 0.00 0.00 0.00 3.35
2183 2866 1.072505 GGAAACCAACTCGCCCTCA 59.927 57.895 0.00 0.00 0.00 3.86
2184 2867 0.955919 CTGGAAACCAACTCGCCCTC 60.956 60.000 0.00 0.00 30.80 4.30
2185 2868 1.073199 CTGGAAACCAACTCGCCCT 59.927 57.895 0.00 0.00 30.80 5.19
2186 2869 1.228154 ACTGGAAACCAACTCGCCC 60.228 57.895 0.00 0.00 30.80 6.13
2187 2870 1.566018 CGACTGGAAACCAACTCGCC 61.566 60.000 0.00 0.00 30.56 5.54
2188 2871 1.860078 CGACTGGAAACCAACTCGC 59.140 57.895 0.00 0.00 30.56 5.03
2189 2872 1.566018 GGCGACTGGAAACCAACTCG 61.566 60.000 11.01 11.01 37.05 4.18
2190 2873 1.566018 CGGCGACTGGAAACCAACTC 61.566 60.000 0.00 0.00 30.80 3.01
2191 2874 1.597027 CGGCGACTGGAAACCAACT 60.597 57.895 0.00 0.00 30.80 3.16
2192 2875 1.595929 TCGGCGACTGGAAACCAAC 60.596 57.895 4.99 0.00 30.80 3.77
2193 2876 1.595929 GTCGGCGACTGGAAACCAA 60.596 57.895 31.15 0.00 30.80 3.67
2194 2877 2.029964 GTCGGCGACTGGAAACCA 59.970 61.111 31.15 0.00 0.00 3.67
2195 2878 2.741211 GGTCGGCGACTGGAAACC 60.741 66.667 35.42 17.28 32.47 3.27
2196 2879 2.741211 GGGTCGGCGACTGGAAAC 60.741 66.667 35.42 19.68 32.47 2.78
2197 2880 4.011517 GGGGTCGGCGACTGGAAA 62.012 66.667 35.42 0.00 32.47 3.13
2200 2883 4.838152 CATGGGGTCGGCGACTGG 62.838 72.222 35.42 18.37 32.47 4.00
2201 2884 4.838152 CCATGGGGTCGGCGACTG 62.838 72.222 35.42 25.81 32.47 3.51
2224 2907 2.496828 AAAACTAGACGCCGTCCGGG 62.497 60.000 14.60 6.88 42.52 5.73
2225 2908 0.668401 AAAAACTAGACGCCGTCCGG 60.668 55.000 14.60 9.47 42.52 5.14
2226 2909 2.818350 AAAAACTAGACGCCGTCCG 58.182 52.632 14.60 8.12 44.21 4.79
2242 2925 8.798748 TTCGCCGAATGAGTTTTTATTAAAAA 57.201 26.923 9.69 9.69 37.99 1.94
2243 2926 8.077386 ACTTCGCCGAATGAGTTTTTATTAAAA 58.923 29.630 0.00 0.00 0.00 1.52
2244 2927 7.586747 ACTTCGCCGAATGAGTTTTTATTAAA 58.413 30.769 0.00 0.00 0.00 1.52
2245 2928 7.136289 ACTTCGCCGAATGAGTTTTTATTAA 57.864 32.000 0.00 0.00 0.00 1.40
2246 2929 6.730960 ACTTCGCCGAATGAGTTTTTATTA 57.269 33.333 0.00 0.00 0.00 0.98
2247 2930 5.622770 ACTTCGCCGAATGAGTTTTTATT 57.377 34.783 0.00 0.00 0.00 1.40
2248 2931 5.622770 AACTTCGCCGAATGAGTTTTTAT 57.377 34.783 0.00 0.00 0.00 1.40
2249 2932 5.209240 CAAACTTCGCCGAATGAGTTTTTA 58.791 37.500 11.55 0.00 0.00 1.52
2250 2933 3.982576 AACTTCGCCGAATGAGTTTTT 57.017 38.095 0.00 0.00 0.00 1.94
2251 2934 3.628017 CAAACTTCGCCGAATGAGTTTT 58.372 40.909 11.55 0.29 0.00 2.43
2252 2935 2.604614 GCAAACTTCGCCGAATGAGTTT 60.605 45.455 9.05 9.05 0.00 2.66
2253 2936 1.069227 GCAAACTTCGCCGAATGAGTT 60.069 47.619 0.00 0.00 0.00 3.01
2254 2937 0.517316 GCAAACTTCGCCGAATGAGT 59.483 50.000 0.00 0.00 0.00 3.41
2255 2938 0.516877 TGCAAACTTCGCCGAATGAG 59.483 50.000 0.00 0.00 0.00 2.90
2256 2939 1.164411 ATGCAAACTTCGCCGAATGA 58.836 45.000 0.00 0.00 0.00 2.57
2257 2940 2.823196 TATGCAAACTTCGCCGAATG 57.177 45.000 0.00 0.00 0.00 2.67
2258 2941 3.498082 GTTTATGCAAACTTCGCCGAAT 58.502 40.909 0.00 0.00 40.78 3.34
2259 2942 2.923643 GTTTATGCAAACTTCGCCGAA 58.076 42.857 0.00 0.00 40.78 4.30
2260 2943 2.604969 GTTTATGCAAACTTCGCCGA 57.395 45.000 0.00 0.00 40.78 5.54
2268 2951 6.237201 CGAATTTTAGCCGAGTTTATGCAAAC 60.237 38.462 0.00 0.00 43.71 2.93
2269 2952 5.797934 CGAATTTTAGCCGAGTTTATGCAAA 59.202 36.000 0.00 0.00 0.00 3.68
2270 2953 5.328691 CGAATTTTAGCCGAGTTTATGCAA 58.671 37.500 0.00 0.00 0.00 4.08
2271 2954 4.201871 CCGAATTTTAGCCGAGTTTATGCA 60.202 41.667 0.00 0.00 0.00 3.96
2272 2955 4.279659 CCGAATTTTAGCCGAGTTTATGC 58.720 43.478 0.00 0.00 0.00 3.14
2273 2956 4.201871 TGCCGAATTTTAGCCGAGTTTATG 60.202 41.667 0.00 0.00 0.00 1.90
2274 2957 3.942748 TGCCGAATTTTAGCCGAGTTTAT 59.057 39.130 0.00 0.00 0.00 1.40
2275 2958 3.336468 TGCCGAATTTTAGCCGAGTTTA 58.664 40.909 0.00 0.00 0.00 2.01
2276 2959 2.156098 TGCCGAATTTTAGCCGAGTTT 58.844 42.857 0.00 0.00 0.00 2.66
2277 2960 1.816074 TGCCGAATTTTAGCCGAGTT 58.184 45.000 0.00 0.00 0.00 3.01
2278 2961 1.816074 TTGCCGAATTTTAGCCGAGT 58.184 45.000 0.00 0.00 0.00 4.18
2279 2962 2.161609 AGTTTGCCGAATTTTAGCCGAG 59.838 45.455 0.00 0.00 0.00 4.63
2280 2963 2.156098 AGTTTGCCGAATTTTAGCCGA 58.844 42.857 0.00 0.00 0.00 5.54
2281 2964 2.629639 AGTTTGCCGAATTTTAGCCG 57.370 45.000 0.00 0.00 0.00 5.52
2282 2965 2.993220 CCAAGTTTGCCGAATTTTAGCC 59.007 45.455 0.00 0.00 0.00 3.93
2283 2966 2.411748 GCCAAGTTTGCCGAATTTTAGC 59.588 45.455 0.00 0.00 0.00 3.09
2284 2967 3.648009 TGCCAAGTTTGCCGAATTTTAG 58.352 40.909 0.00 0.00 0.00 1.85
2285 2968 3.735237 TGCCAAGTTTGCCGAATTTTA 57.265 38.095 0.00 0.00 0.00 1.52
2286 2969 2.611225 TGCCAAGTTTGCCGAATTTT 57.389 40.000 0.00 0.00 0.00 1.82
2287 2970 2.837532 ATGCCAAGTTTGCCGAATTT 57.162 40.000 0.00 0.00 0.00 1.82
2288 2971 5.789643 ATATATGCCAAGTTTGCCGAATT 57.210 34.783 0.00 0.00 0.00 2.17
2289 2972 5.789643 AATATATGCCAAGTTTGCCGAAT 57.210 34.783 0.00 0.00 0.00 3.34
2290 2973 6.017440 GTCTAATATATGCCAAGTTTGCCGAA 60.017 38.462 0.00 0.00 0.00 4.30
2291 2974 5.468746 GTCTAATATATGCCAAGTTTGCCGA 59.531 40.000 0.00 0.00 0.00 5.54
2292 2975 5.238432 TGTCTAATATATGCCAAGTTTGCCG 59.762 40.000 0.00 0.00 0.00 5.69
2293 2976 6.633500 TGTCTAATATATGCCAAGTTTGCC 57.367 37.500 0.00 0.00 0.00 4.52
2294 2977 7.651808 ACATGTCTAATATATGCCAAGTTTGC 58.348 34.615 0.00 0.00 30.12 3.68
2295 2978 9.669353 GAACATGTCTAATATATGCCAAGTTTG 57.331 33.333 0.00 0.00 30.12 2.93
2296 2979 8.559536 CGAACATGTCTAATATATGCCAAGTTT 58.440 33.333 0.00 0.00 30.12 2.66
2297 2980 7.307989 GCGAACATGTCTAATATATGCCAAGTT 60.308 37.037 0.00 0.00 30.12 2.66
2298 2981 6.147821 GCGAACATGTCTAATATATGCCAAGT 59.852 38.462 0.00 0.00 30.12 3.16
2299 2982 6.537566 GCGAACATGTCTAATATATGCCAAG 58.462 40.000 0.00 0.00 30.12 3.61
2300 2983 5.120053 CGCGAACATGTCTAATATATGCCAA 59.880 40.000 0.00 0.00 30.12 4.52
2301 2984 4.625311 CGCGAACATGTCTAATATATGCCA 59.375 41.667 0.00 0.00 30.12 4.92
2302 2985 4.032900 CCGCGAACATGTCTAATATATGCC 59.967 45.833 8.23 0.00 30.12 4.40
2303 2986 4.625742 ACCGCGAACATGTCTAATATATGC 59.374 41.667 8.23 0.00 30.12 3.14
2304 2987 6.706055 AACCGCGAACATGTCTAATATATG 57.294 37.500 8.23 0.00 33.16 1.78
2305 2988 7.868922 TGTAAACCGCGAACATGTCTAATATAT 59.131 33.333 8.23 0.00 0.00 0.86
2306 2989 7.201835 TGTAAACCGCGAACATGTCTAATATA 58.798 34.615 8.23 0.00 0.00 0.86
2307 2990 6.044046 TGTAAACCGCGAACATGTCTAATAT 58.956 36.000 8.23 0.00 0.00 1.28
2308 2991 5.409211 TGTAAACCGCGAACATGTCTAATA 58.591 37.500 8.23 0.00 0.00 0.98
2309 2992 4.247258 TGTAAACCGCGAACATGTCTAAT 58.753 39.130 8.23 0.00 0.00 1.73
2310 2993 3.651206 TGTAAACCGCGAACATGTCTAA 58.349 40.909 8.23 0.00 0.00 2.10
2311 2994 3.300852 TGTAAACCGCGAACATGTCTA 57.699 42.857 8.23 0.00 0.00 2.59
2312 2995 2.157834 TGTAAACCGCGAACATGTCT 57.842 45.000 8.23 0.00 0.00 3.41
2313 2996 3.543460 GCTATGTAAACCGCGAACATGTC 60.543 47.826 8.23 4.87 35.54 3.06
2314 2997 2.350498 GCTATGTAAACCGCGAACATGT 59.650 45.455 8.23 0.00 35.54 3.21
2315 2998 2.350192 TGCTATGTAAACCGCGAACATG 59.650 45.455 8.23 7.97 35.54 3.21
2316 2999 2.623535 TGCTATGTAAACCGCGAACAT 58.376 42.857 8.23 14.00 37.58 2.71
2317 3000 2.081725 TGCTATGTAAACCGCGAACA 57.918 45.000 8.23 6.86 0.00 3.18
2318 3001 3.458779 TTTGCTATGTAAACCGCGAAC 57.541 42.857 8.23 0.16 0.00 3.95
2319 3002 4.688511 AATTTGCTATGTAAACCGCGAA 57.311 36.364 8.23 0.00 0.00 4.70
2320 3003 4.688511 AAATTTGCTATGTAAACCGCGA 57.311 36.364 8.23 0.00 0.00 5.87
2321 3004 8.722342 AATATAAATTTGCTATGTAAACCGCG 57.278 30.769 0.00 0.00 0.00 6.46
2355 3038 2.500504 ACTTCTTCGCCCCTTAGTTAGG 59.499 50.000 0.00 0.00 44.33 2.69
2356 3039 3.734293 CGACTTCTTCGCCCCTTAGTTAG 60.734 52.174 0.00 0.00 41.87 2.34
2357 3040 2.165030 CGACTTCTTCGCCCCTTAGTTA 59.835 50.000 0.00 0.00 41.87 2.24
2358 3041 1.067071 CGACTTCTTCGCCCCTTAGTT 60.067 52.381 0.00 0.00 41.87 2.24
2359 3042 0.531200 CGACTTCTTCGCCCCTTAGT 59.469 55.000 0.00 0.00 41.87 2.24
2360 3043 3.347411 CGACTTCTTCGCCCCTTAG 57.653 57.895 0.00 0.00 41.87 2.18
2369 3052 0.161024 CCGCGTTCAACGACTTCTTC 59.839 55.000 15.79 0.00 46.05 2.87
2370 3053 0.249155 TCCGCGTTCAACGACTTCTT 60.249 50.000 15.79 0.00 46.05 2.52
2371 3054 0.663568 CTCCGCGTTCAACGACTTCT 60.664 55.000 15.79 0.00 46.05 2.85
2372 3055 0.938168 ACTCCGCGTTCAACGACTTC 60.938 55.000 15.79 0.00 46.05 3.01
2373 3056 0.311790 TACTCCGCGTTCAACGACTT 59.688 50.000 15.79 0.00 46.05 3.01
2374 3057 0.109873 CTACTCCGCGTTCAACGACT 60.110 55.000 15.79 0.00 46.05 4.18
2375 3058 0.386478 ACTACTCCGCGTTCAACGAC 60.386 55.000 15.79 4.09 46.05 4.34
2376 3059 0.110056 GACTACTCCGCGTTCAACGA 60.110 55.000 15.79 0.00 46.05 3.85
2377 3060 1.393597 CGACTACTCCGCGTTCAACG 61.394 60.000 5.28 5.28 45.88 4.10
2378 3061 1.671880 GCGACTACTCCGCGTTCAAC 61.672 60.000 4.92 0.00 43.28 3.18
2379 3062 1.443194 GCGACTACTCCGCGTTCAA 60.443 57.895 4.92 0.00 43.28 2.69
2380 3063 2.177531 GCGACTACTCCGCGTTCA 59.822 61.111 4.92 0.00 43.28 3.18
2386 3069 1.299468 GATGGCAGCGACTACTCCG 60.299 63.158 0.00 0.00 0.00 4.63
2387 3070 1.068250 GGATGGCAGCGACTACTCC 59.932 63.158 0.00 0.00 0.00 3.85
2388 3071 0.031449 GAGGATGGCAGCGACTACTC 59.969 60.000 0.00 0.00 0.00 2.59
2389 3072 1.729470 CGAGGATGGCAGCGACTACT 61.729 60.000 0.00 0.00 0.00 2.57
2390 3073 1.299468 CGAGGATGGCAGCGACTAC 60.299 63.158 0.00 0.00 0.00 2.73
2391 3074 3.120105 CGAGGATGGCAGCGACTA 58.880 61.111 0.00 0.00 0.00 2.59
2392 3075 4.521062 GCGAGGATGGCAGCGACT 62.521 66.667 0.00 0.00 40.68 4.18
2421 3104 4.475135 GGAGGAGAAGGCCACCGC 62.475 72.222 5.01 4.45 0.00 5.68
2422 3105 2.294078 AAGGAGGAGAAGGCCACCG 61.294 63.158 5.01 0.00 42.74 4.94
2423 3106 1.201429 TCAAGGAGGAGAAGGCCACC 61.201 60.000 5.01 2.48 38.78 4.61
2424 3107 0.035915 GTCAAGGAGGAGAAGGCCAC 60.036 60.000 5.01 0.00 0.00 5.01
2425 3108 1.544825 CGTCAAGGAGGAGAAGGCCA 61.545 60.000 5.01 0.00 0.00 5.36
2426 3109 1.219393 CGTCAAGGAGGAGAAGGCC 59.781 63.158 0.00 0.00 0.00 5.19
2427 3110 0.390472 CACGTCAAGGAGGAGAAGGC 60.390 60.000 0.00 0.00 0.00 4.35
2428 3111 0.247736 CCACGTCAAGGAGGAGAAGG 59.752 60.000 0.00 0.00 0.00 3.46
2429 3112 0.390472 GCCACGTCAAGGAGGAGAAG 60.390 60.000 0.00 0.00 0.00 2.85
2430 3113 1.671742 GCCACGTCAAGGAGGAGAA 59.328 57.895 0.00 0.00 0.00 2.87
2431 3114 2.283529 GGCCACGTCAAGGAGGAGA 61.284 63.158 0.00 0.00 0.00 3.71
2432 3115 2.266055 GGCCACGTCAAGGAGGAG 59.734 66.667 0.00 0.00 0.00 3.69
2433 3116 3.691342 CGGCCACGTCAAGGAGGA 61.691 66.667 2.24 0.00 34.81 3.71


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

AutoCloner maintained by Alex Coulton.