Multiple sequence alignment - TraesCS5B01G483700

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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 TraesCS5B01G483700 chr5B 100.000 2555 0 0 1 2555 655321863 655324417 0.000000e+00 4719
1 TraesCS5B01G483700 chr5B 96.518 1637 36 11 106 1729 655391371 655392999 0.000000e+00 2687
2 TraesCS5B01G483700 chr5B 93.132 1456 81 10 153 1594 655278731 655280181 0.000000e+00 2117
3 TraesCS5B01G483700 chr5D 95.109 1472 64 5 106 1572 520302177 520300709 0.000000e+00 2313
4 TraesCS5B01G483700 chr5D 89.587 557 36 12 1867 2401 520300489 520299933 0.000000e+00 688
5 TraesCS5B01G483700 chr5D 87.615 218 19 4 1612 1822 520300707 520300491 1.960000e-61 246
6 TraesCS5B01G483700 chr5A 92.871 1501 90 9 106 1594 648361869 648360374 0.000000e+00 2163
7 TraesCS5B01G483700 chr5A 91.142 1287 102 7 320 1594 648228523 648227237 0.000000e+00 1735
8 TraesCS5B01G483700 chr5A 89.388 1291 108 13 315 1577 647967239 647965950 0.000000e+00 1598
9 TraesCS5B01G483700 chr5A 90.729 1111 83 10 699 1795 648175170 648174066 0.000000e+00 1463
10 TraesCS5B01G483700 chr5A 92.750 400 23 2 315 708 648176047 648175648 7.930000e-160 573
11 TraesCS5B01G483700 chr5A 87.794 467 37 5 1275 1729 647976252 647975794 1.740000e-146 529
12 TraesCS5B01G483700 chr5A 94.470 217 11 1 106 322 648238245 648238030 1.460000e-87 333
13 TraesCS5B01G483700 chr5A 92.632 190 13 1 2165 2353 647955865 647955676 3.240000e-69 272
14 TraesCS5B01G483700 chr5A 86.408 206 20 4 1619 1817 647965946 647965742 4.280000e-53 219
15 TraesCS5B01G483700 chr5A 87.407 135 9 3 1867 1993 647965735 647965601 5.700000e-32 148
16 TraesCS5B01G483700 chr5A 84.459 148 19 4 2408 2553 277535718 277535573 2.650000e-30 143
17 TraesCS5B01G483700 chr5A 86.290 124 17 0 1512 1635 648313988 648313865 4.430000e-28 135
18 TraesCS5B01G483700 chr5A 85.950 121 17 0 1515 1635 648212849 648212729 2.060000e-26 130
19 TraesCS5B01G483700 chr5A 93.939 66 4 0 1 66 647583953 647583888 1.620000e-17 100
20 TraesCS5B01G483700 chrUn 89.164 1292 101 18 317 1572 294624926 294623638 0.000000e+00 1574
21 TraesCS5B01G483700 chrUn 89.029 556 40 11 1867 2401 294623418 294622863 0.000000e+00 669
22 TraesCS5B01G483700 chrUn 84.932 219 23 6 1612 1822 294623636 294623420 1.990000e-51 213
23 TraesCS5B01G483700 chr6A 82.357 1332 207 16 315 1619 22171824 22173154 0.000000e+00 1133
24 TraesCS5B01G483700 chr7B 85.616 146 20 1 2409 2553 255946370 255946515 4.400000e-33 152
25 TraesCS5B01G483700 chr2A 85.235 149 21 1 2406 2553 150803075 150803223 4.400000e-33 152
26 TraesCS5B01G483700 chr7A 85.616 146 18 2 2406 2550 383325510 383325653 1.580000e-32 150
27 TraesCS5B01G483700 chr6D 84.967 153 18 5 2404 2553 405054952 405055102 1.580000e-32 150
28 TraesCS5B01G483700 chr1B 85.816 141 18 2 2409 2548 253759250 253759111 5.700000e-32 148
29 TraesCS5B01G483700 chr3B 84.932 146 20 2 2409 2553 597168524 597168380 2.050000e-31 147
30 TraesCS5B01G483700 chr1D 86.992 123 16 0 2406 2528 213813903 213814025 3.430000e-29 139
31 TraesCS5B01G483700 chr6B 82.877 146 25 0 2404 2549 533268914 533269059 5.740000e-27 132


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 TraesCS5B01G483700 chr5B 655321863 655324417 2554 False 4719.000000 4719 100.000000 1 2555 1 chr5B.!!$F2 2554
1 TraesCS5B01G483700 chr5B 655391371 655392999 1628 False 2687.000000 2687 96.518000 106 1729 1 chr5B.!!$F3 1623
2 TraesCS5B01G483700 chr5B 655278731 655280181 1450 False 2117.000000 2117 93.132000 153 1594 1 chr5B.!!$F1 1441
3 TraesCS5B01G483700 chr5D 520299933 520302177 2244 True 1082.333333 2313 90.770333 106 2401 3 chr5D.!!$R1 2295
4 TraesCS5B01G483700 chr5A 648360374 648361869 1495 True 2163.000000 2163 92.871000 106 1594 1 chr5A.!!$R9 1488
5 TraesCS5B01G483700 chr5A 648227237 648228523 1286 True 1735.000000 1735 91.142000 320 1594 1 chr5A.!!$R6 1274
6 TraesCS5B01G483700 chr5A 648174066 648176047 1981 True 1018.000000 1463 91.739500 315 1795 2 chr5A.!!$R11 1480
7 TraesCS5B01G483700 chr5A 647965601 647967239 1638 True 655.000000 1598 87.734333 315 1993 3 chr5A.!!$R10 1678
8 TraesCS5B01G483700 chrUn 294622863 294624926 2063 True 818.666667 1574 87.708333 317 2401 3 chrUn.!!$R1 2084
9 TraesCS5B01G483700 chr6A 22171824 22173154 1330 False 1133.000000 1133 82.357000 315 1619 1 chr6A.!!$F1 1304

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
19 20 0.382515 GTACGGTCAGGAGCAGCTAG 59.617 60.0 0.0 0.0 0.0 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 2410 0.031857 CCACATTGAAGGCAAACGCA 59.968 50.0 0.0 0.0 37.59 5.24 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
17 18 3.289525 GTACGGTCAGGAGCAGCT 58.710 61.111 0.00 0.00 0.00 4.24
18 19 2.490165 GTACGGTCAGGAGCAGCTA 58.510 57.895 0.00 0.00 0.00 3.32
19 20 0.382515 GTACGGTCAGGAGCAGCTAG 59.617 60.000 0.00 0.00 0.00 3.42
20 21 1.384989 TACGGTCAGGAGCAGCTAGC 61.385 60.000 6.62 6.62 46.19 3.42
30 31 2.030262 CAGCTAGCGGGAGATGCC 59.970 66.667 9.55 0.00 0.00 4.40
31 32 3.610669 AGCTAGCGGGAGATGCCG 61.611 66.667 9.55 8.58 37.63 5.69
32 33 3.917760 GCTAGCGGGAGATGCCGT 61.918 66.667 14.42 4.17 37.63 5.68
33 34 2.028190 CTAGCGGGAGATGCCGTG 59.972 66.667 14.42 1.94 37.63 4.94
34 35 3.506059 CTAGCGGGAGATGCCGTGG 62.506 68.421 14.42 1.62 37.63 4.94
40 41 4.451150 GAGATGCCGTGGCCGTCA 62.451 66.667 8.69 0.00 41.09 4.35
41 42 4.457496 AGATGCCGTGGCCGTCAG 62.457 66.667 8.69 0.00 41.09 3.51
42 43 4.451150 GATGCCGTGGCCGTCAGA 62.451 66.667 8.69 0.00 41.09 3.27
43 44 4.457496 ATGCCGTGGCCGTCAGAG 62.457 66.667 8.69 0.00 41.09 3.35
54 55 2.792599 GTCAGAGACGTCGGCGAT 59.207 61.111 20.03 3.33 42.00 4.58
55 56 1.583967 GTCAGAGACGTCGGCGATG 60.584 63.158 26.31 26.31 42.00 3.84
56 57 2.278206 CAGAGACGTCGGCGATGG 60.278 66.667 30.30 19.70 42.00 3.51
57 58 2.750637 AGAGACGTCGGCGATGGT 60.751 61.111 30.30 22.64 42.00 3.55
58 59 2.579787 GAGACGTCGGCGATGGTG 60.580 66.667 30.30 15.44 42.00 4.17
59 60 4.129737 AGACGTCGGCGATGGTGG 62.130 66.667 30.30 12.59 42.00 4.61
60 61 4.124351 GACGTCGGCGATGGTGGA 62.124 66.667 30.30 0.00 42.00 4.02
61 62 4.430765 ACGTCGGCGATGGTGGAC 62.431 66.667 30.30 8.27 42.00 4.02
66 67 4.832608 GGCGATGGTGGACGGGAC 62.833 72.222 0.00 0.00 0.00 4.46
67 68 4.077184 GCGATGGTGGACGGGACA 62.077 66.667 0.00 0.00 0.00 4.02
68 69 2.660206 CGATGGTGGACGGGACAA 59.340 61.111 0.00 0.00 0.00 3.18
69 70 1.740296 CGATGGTGGACGGGACAAC 60.740 63.158 0.00 0.00 0.00 3.32
70 71 1.677552 GATGGTGGACGGGACAACT 59.322 57.895 0.00 0.00 0.00 3.16
71 72 0.899720 GATGGTGGACGGGACAACTA 59.100 55.000 0.00 0.00 0.00 2.24
72 73 1.485066 GATGGTGGACGGGACAACTAT 59.515 52.381 0.00 0.00 0.00 2.12
73 74 2.234896 TGGTGGACGGGACAACTATA 57.765 50.000 0.00 0.00 0.00 1.31
74 75 2.754465 TGGTGGACGGGACAACTATAT 58.246 47.619 0.00 0.00 0.00 0.86
75 76 3.913509 TGGTGGACGGGACAACTATATA 58.086 45.455 0.00 0.00 0.00 0.86
76 77 3.893200 TGGTGGACGGGACAACTATATAG 59.107 47.826 8.27 8.27 0.00 1.31
77 78 4.147321 GGTGGACGGGACAACTATATAGA 58.853 47.826 16.79 0.00 0.00 1.98
78 79 4.217983 GGTGGACGGGACAACTATATAGAG 59.782 50.000 16.79 10.43 0.00 2.43
79 80 5.068636 GTGGACGGGACAACTATATAGAGA 58.931 45.833 16.79 0.00 0.00 3.10
80 81 5.181622 GTGGACGGGACAACTATATAGAGAG 59.818 48.000 16.79 7.81 0.00 3.20
81 82 5.163120 TGGACGGGACAACTATATAGAGAGT 60.163 44.000 16.79 10.72 0.00 3.24
82 83 5.412286 GGACGGGACAACTATATAGAGAGTC 59.588 48.000 16.79 17.34 0.00 3.36
83 84 5.938279 ACGGGACAACTATATAGAGAGTCA 58.062 41.667 16.79 0.00 0.00 3.41
84 85 6.363065 ACGGGACAACTATATAGAGAGTCAA 58.637 40.000 16.79 0.00 0.00 3.18
85 86 6.832384 ACGGGACAACTATATAGAGAGTCAAA 59.168 38.462 16.79 0.00 0.00 2.69
86 87 7.341256 ACGGGACAACTATATAGAGAGTCAAAA 59.659 37.037 16.79 0.00 0.00 2.44
87 88 7.648510 CGGGACAACTATATAGAGAGTCAAAAC 59.351 40.741 16.79 10.14 0.00 2.43
88 89 8.697292 GGGACAACTATATAGAGAGTCAAAACT 58.303 37.037 16.79 0.00 38.88 2.66
89 90 9.522804 GGACAACTATATAGAGAGTCAAAACTG 57.477 37.037 16.79 0.00 35.28 3.16
90 91 9.522804 GACAACTATATAGAGAGTCAAAACTGG 57.477 37.037 16.79 0.00 35.28 4.00
91 92 9.256228 ACAACTATATAGAGAGTCAAAACTGGA 57.744 33.333 16.79 0.00 35.28 3.86
1447 1985 2.750350 GTAGTGCAGCACCAGGGT 59.250 61.111 22.41 5.66 34.49 4.34
1467 2005 3.883489 GGTATGGAGTAGATTTTGTGGCC 59.117 47.826 0.00 0.00 0.00 5.36
1500 2038 3.709653 TCTTATTTGCCGTGGTAGAGGAT 59.290 43.478 0.00 0.00 0.00 3.24
1609 2153 7.221452 GGATTCCTTTGATTGTCGAATGAATTG 59.779 37.037 10.03 0.00 36.15 2.32
1635 2179 2.489971 ACATTGTTCGTCGGTCATGTT 58.510 42.857 0.00 0.00 0.00 2.71
1637 2181 3.430895 ACATTGTTCGTCGGTCATGTTAC 59.569 43.478 0.00 0.00 0.00 2.50
1643 2187 4.968812 TCGTCGGTCATGTTACTAATCA 57.031 40.909 0.00 0.00 0.00 2.57
1656 2200 2.726821 ACTAATCATGCCACCACCTTG 58.273 47.619 0.00 0.00 0.00 3.61
1730 2275 1.691434 GGCAAAAAGTGGAACCCATGA 59.309 47.619 0.00 0.00 37.80 3.07
1731 2276 2.103941 GGCAAAAAGTGGAACCCATGAA 59.896 45.455 0.00 0.00 37.80 2.57
1732 2277 3.130633 GCAAAAAGTGGAACCCATGAAC 58.869 45.455 0.00 0.00 37.80 3.18
1733 2278 3.380142 CAAAAAGTGGAACCCATGAACG 58.620 45.455 0.00 0.00 37.80 3.95
1734 2279 2.358322 AAAGTGGAACCCATGAACGT 57.642 45.000 0.00 0.00 37.80 3.99
1735 2280 1.604604 AAGTGGAACCCATGAACGTG 58.395 50.000 0.00 0.00 37.80 4.49
1737 2282 0.889186 GTGGAACCCATGAACGTGCT 60.889 55.000 0.00 0.00 35.28 4.40
1738 2283 0.179004 TGGAACCCATGAACGTGCTT 60.179 50.000 0.00 0.00 0.00 3.91
1740 2285 2.156098 GGAACCCATGAACGTGCTTTA 58.844 47.619 0.00 0.00 0.00 1.85
1741 2286 2.161609 GGAACCCATGAACGTGCTTTAG 59.838 50.000 0.00 0.00 0.00 1.85
1757 2308 3.318017 CTTTAGTATTCTCATCCGCCGG 58.682 50.000 0.00 0.00 0.00 6.13
1782 2333 7.207383 GTCAGTGGTTTAGGCAAAAAGTTTAT 58.793 34.615 0.00 0.00 0.00 1.40
1822 2373 5.957910 TGCCAAACAAAATTGTAAACTCG 57.042 34.783 0.00 0.00 41.31 4.18
1823 2374 5.651530 TGCCAAACAAAATTGTAAACTCGA 58.348 33.333 0.00 0.00 41.31 4.04
1824 2375 5.517054 TGCCAAACAAAATTGTAAACTCGAC 59.483 36.000 0.00 0.00 41.31 4.20
1825 2376 5.331235 GCCAAACAAAATTGTAAACTCGACG 60.331 40.000 0.00 0.00 41.31 5.12
1826 2377 5.966503 CCAAACAAAATTGTAAACTCGACGA 59.033 36.000 0.00 0.00 41.31 4.20
1827 2378 6.140108 CCAAACAAAATTGTAAACTCGACGAG 59.860 38.462 22.97 22.97 41.31 4.18
1828 2379 5.338614 ACAAAATTGTAAACTCGACGAGG 57.661 39.130 27.39 10.77 40.16 4.63
1829 2380 5.051816 ACAAAATTGTAAACTCGACGAGGA 58.948 37.500 27.39 10.66 40.16 3.71
1830 2381 5.050567 ACAAAATTGTAAACTCGACGAGGAC 60.051 40.000 27.39 20.84 40.16 3.85
1831 2382 3.928727 ATTGTAAACTCGACGAGGACA 57.071 42.857 27.39 22.86 33.35 4.02
1832 2383 3.713858 TTGTAAACTCGACGAGGACAA 57.286 42.857 27.39 26.31 32.58 3.18
1833 2384 3.713858 TGTAAACTCGACGAGGACAAA 57.286 42.857 27.39 8.55 33.35 2.83
1834 2385 4.044336 TGTAAACTCGACGAGGACAAAA 57.956 40.909 27.39 7.02 33.35 2.44
1835 2386 4.624015 TGTAAACTCGACGAGGACAAAAT 58.376 39.130 27.39 2.91 33.35 1.82
1836 2387 5.051816 TGTAAACTCGACGAGGACAAAATT 58.948 37.500 27.39 9.09 33.35 1.82
1837 2388 4.468095 AAACTCGACGAGGACAAAATTG 57.532 40.909 27.39 0.90 33.35 2.32
1838 2389 3.107642 ACTCGACGAGGACAAAATTGT 57.892 42.857 27.39 0.00 37.32 2.71
1839 2390 4.247267 ACTCGACGAGGACAAAATTGTA 57.753 40.909 27.39 0.00 35.84 2.41
1840 2391 4.624015 ACTCGACGAGGACAAAATTGTAA 58.376 39.130 27.39 0.00 35.84 2.41
1841 2392 5.051816 ACTCGACGAGGACAAAATTGTAAA 58.948 37.500 27.39 0.00 35.84 2.01
1842 2393 5.050567 ACTCGACGAGGACAAAATTGTAAAC 60.051 40.000 27.39 0.00 35.84 2.01
1843 2394 4.809958 TCGACGAGGACAAAATTGTAAACA 59.190 37.500 0.00 0.00 42.43 2.83
1844 2395 5.293814 TCGACGAGGACAAAATTGTAAACAA 59.706 36.000 0.00 0.00 42.43 2.83
1845 2396 5.966503 CGACGAGGACAAAATTGTAAACAAA 59.033 36.000 0.00 0.00 42.43 2.83
1846 2397 6.469595 CGACGAGGACAAAATTGTAAACAAAA 59.530 34.615 0.00 0.00 42.43 2.44
1847 2398 7.166804 CGACGAGGACAAAATTGTAAACAAAAT 59.833 33.333 0.00 0.00 42.43 1.82
1848 2399 8.710835 ACGAGGACAAAATTGTAAACAAAATT 57.289 26.923 0.00 0.00 42.43 1.82
1849 2400 9.804758 ACGAGGACAAAATTGTAAACAAAATTA 57.195 25.926 0.00 0.00 42.43 1.40
1928 2479 2.795175 AACGTCGTCACTGAGATGTT 57.205 45.000 0.00 8.89 40.54 2.71
1935 2486 5.164177 CGTCGTCACTGAGATGTTAACTTTC 60.164 44.000 7.22 4.26 34.73 2.62
1936 2487 5.921408 GTCGTCACTGAGATGTTAACTTTCT 59.079 40.000 7.22 9.02 34.73 2.52
1937 2488 6.088350 GTCGTCACTGAGATGTTAACTTTCTC 59.912 42.308 22.14 22.14 34.73 2.87
1938 2489 5.920840 CGTCACTGAGATGTTAACTTTCTCA 59.079 40.000 26.30 26.30 36.24 3.27
1939 2490 6.587990 CGTCACTGAGATGTTAACTTTCTCAT 59.412 38.462 27.32 19.47 36.92 2.90
1940 2491 7.755373 CGTCACTGAGATGTTAACTTTCTCATA 59.245 37.037 27.32 18.75 36.92 2.15
1941 2492 9.081997 GTCACTGAGATGTTAACTTTCTCATAG 57.918 37.037 27.32 23.41 36.92 2.23
1942 2493 9.025041 TCACTGAGATGTTAACTTTCTCATAGA 57.975 33.333 27.32 24.51 36.92 1.98
1943 2494 9.814899 CACTGAGATGTTAACTTTCTCATAGAT 57.185 33.333 27.32 17.28 36.92 1.98
2002 2561 6.922247 TGTTATGTGTTGTTTCTCGGTTAA 57.078 33.333 0.00 0.00 0.00 2.01
2035 2601 8.383374 ACCCCATTAAAGATGTGTTACTAGTA 57.617 34.615 0.00 0.00 0.00 1.82
2037 2603 9.847224 CCCCATTAAAGATGTGTTACTAGTATT 57.153 33.333 2.79 0.00 0.00 1.89
2068 2634 9.981114 AATAATTAATATCCTTCCCAAAAAGCG 57.019 29.630 0.00 0.00 0.00 4.68
2079 2645 2.223572 CCCAAAAAGCGGTATCATGAGC 60.224 50.000 0.09 0.00 0.00 4.26
2096 2662 4.365899 TGAGCTTATTGATGCAAAGCAG 57.634 40.909 19.34 0.60 46.35 4.24
2100 2666 3.444916 CTTATTGATGCAAAGCAGCCAG 58.555 45.455 4.70 0.00 44.94 4.85
2103 2669 0.537828 TGATGCAAAGCAGCCAGTCA 60.538 50.000 4.70 0.00 44.94 3.41
2105 2671 1.203994 GATGCAAAGCAGCCAGTCATT 59.796 47.619 0.00 0.00 43.65 2.57
2107 2673 1.814394 TGCAAAGCAGCCAGTCATTAG 59.186 47.619 0.00 0.00 33.32 1.73
2141 2712 8.547967 TTAAAAATTAGTCGCTCAAGACATCT 57.452 30.769 0.00 0.00 43.24 2.90
2167 2738 6.897259 TCGTACTTTGTATACAAGCCAATC 57.103 37.500 17.36 7.63 37.15 2.67
2225 2796 5.760253 AGGGATTTGATTCGTAGTATTGCAG 59.240 40.000 0.00 0.00 0.00 4.41
2232 2803 6.504398 TGATTCGTAGTATTGCAGTCCTAAG 58.496 40.000 0.00 0.00 0.00 2.18
2311 2883 9.886132 TCCATCTACTCAAACCTCTTATAAAAC 57.114 33.333 0.00 0.00 0.00 2.43
2394 2968 7.805083 AATCCTATAGAATACAGCAGGACAT 57.195 36.000 0.00 0.00 35.12 3.06
2397 2971 6.209589 TCCTATAGAATACAGCAGGACATGTC 59.790 42.308 17.91 17.91 0.00 3.06
2401 2975 3.533606 ATACAGCAGGACATGTCACTC 57.466 47.619 26.47 13.99 0.00 3.51
2402 2976 1.346062 ACAGCAGGACATGTCACTCT 58.654 50.000 26.47 15.88 0.00 3.24
2403 2977 1.001746 ACAGCAGGACATGTCACTCTG 59.998 52.381 26.47 25.94 0.00 3.35
2404 2978 2.464682 GCAGGACATGTCACTCTGC 58.535 57.895 28.20 28.20 42.89 4.26
2405 2979 1.023513 GCAGGACATGTCACTCTGCC 61.024 60.000 30.16 19.04 43.36 4.85
2406 2980 0.738762 CAGGACATGTCACTCTGCCG 60.739 60.000 26.47 6.28 0.00 5.69
2407 2981 1.448540 GGACATGTCACTCTGCCGG 60.449 63.158 26.47 0.00 0.00 6.13
2408 2982 2.046892 ACATGTCACTCTGCCGGC 60.047 61.111 22.73 22.73 0.00 6.13
2409 2983 2.046988 CATGTCACTCTGCCGGCA 60.047 61.111 30.59 30.59 0.00 5.69
2410 2984 2.046892 ATGTCACTCTGCCGGCAC 60.047 61.111 29.03 15.92 0.00 5.01
2411 2985 2.587247 ATGTCACTCTGCCGGCACT 61.587 57.895 29.03 8.03 0.00 4.40
2412 2986 2.433318 GTCACTCTGCCGGCACTC 60.433 66.667 29.03 8.47 0.00 3.51
2413 2987 3.695606 TCACTCTGCCGGCACTCC 61.696 66.667 29.03 0.00 0.00 3.85
2414 2988 4.767255 CACTCTGCCGGCACTCCC 62.767 72.222 29.03 0.00 0.00 4.30
2416 2990 2.759973 CTCTGCCGGCACTCCCTA 60.760 66.667 29.03 1.63 0.00 3.53
2417 2991 2.759973 TCTGCCGGCACTCCCTAG 60.760 66.667 29.03 14.79 0.00 3.02
2418 2992 3.077556 CTGCCGGCACTCCCTAGT 61.078 66.667 29.03 0.00 35.91 2.57
2426 3000 4.977810 ACTCCCTAGTGGTGTGCT 57.022 55.556 4.72 0.00 39.36 4.40
2427 3001 3.165657 ACTCCCTAGTGGTGTGCTT 57.834 52.632 4.72 0.00 39.36 3.91
2428 3002 0.687354 ACTCCCTAGTGGTGTGCTTG 59.313 55.000 4.72 0.00 39.36 4.01
2429 3003 0.036010 CTCCCTAGTGGTGTGCTTGG 60.036 60.000 0.00 0.00 34.77 3.61
2430 3004 1.002134 CCCTAGTGGTGTGCTTGGG 60.002 63.158 0.00 0.00 41.24 4.12
2431 3005 1.675641 CCTAGTGGTGTGCTTGGGC 60.676 63.158 0.00 0.00 39.26 5.36
2452 3026 5.038247 GCAAAATCAAATTGCCCTTCTTG 57.962 39.130 0.00 0.00 45.73 3.02
2453 3027 4.516321 GCAAAATCAAATTGCCCTTCTTGT 59.484 37.500 0.00 0.00 45.73 3.16
2454 3028 5.334337 GCAAAATCAAATTGCCCTTCTTGTC 60.334 40.000 0.00 0.00 45.73 3.18
2455 3029 5.813513 AAATCAAATTGCCCTTCTTGTCT 57.186 34.783 0.00 0.00 0.00 3.41
2456 3030 5.813513 AATCAAATTGCCCTTCTTGTCTT 57.186 34.783 0.00 0.00 0.00 3.01
2457 3031 5.813513 ATCAAATTGCCCTTCTTGTCTTT 57.186 34.783 0.00 0.00 0.00 2.52
2458 3032 5.612725 TCAAATTGCCCTTCTTGTCTTTT 57.387 34.783 0.00 0.00 0.00 2.27
2459 3033 5.988287 TCAAATTGCCCTTCTTGTCTTTTT 58.012 33.333 0.00 0.00 0.00 1.94
2479 3053 4.897509 TTTCATGTGGATCAGACAGAGT 57.102 40.909 0.00 0.00 0.00 3.24
2480 3054 4.897509 TTCATGTGGATCAGACAGAGTT 57.102 40.909 0.00 0.00 0.00 3.01
2481 3055 4.198028 TCATGTGGATCAGACAGAGTTG 57.802 45.455 0.00 0.00 0.00 3.16
2482 3056 3.055602 TCATGTGGATCAGACAGAGTTGG 60.056 47.826 0.00 0.00 0.00 3.77
2483 3057 2.329267 TGTGGATCAGACAGAGTTGGT 58.671 47.619 0.00 0.00 0.00 3.67
2484 3058 2.300152 TGTGGATCAGACAGAGTTGGTC 59.700 50.000 0.00 0.00 35.50 4.02
2485 3059 1.546029 TGGATCAGACAGAGTTGGTCG 59.454 52.381 0.00 0.00 40.20 4.79
2486 3060 1.819288 GGATCAGACAGAGTTGGTCGA 59.181 52.381 0.00 0.00 40.20 4.20
2487 3061 2.159310 GGATCAGACAGAGTTGGTCGAG 60.159 54.545 0.00 0.00 40.20 4.04
2488 3062 1.248486 TCAGACAGAGTTGGTCGAGG 58.752 55.000 0.00 0.00 40.20 4.63
2489 3063 1.202891 TCAGACAGAGTTGGTCGAGGA 60.203 52.381 0.00 0.00 40.20 3.71
2490 3064 1.821753 CAGACAGAGTTGGTCGAGGAT 59.178 52.381 0.00 0.00 40.20 3.24
2491 3065 1.821753 AGACAGAGTTGGTCGAGGATG 59.178 52.381 0.00 0.00 40.20 3.51
2492 3066 1.546476 GACAGAGTTGGTCGAGGATGT 59.454 52.381 0.00 0.00 0.00 3.06
2493 3067 1.546476 ACAGAGTTGGTCGAGGATGTC 59.454 52.381 0.00 0.00 0.00 3.06
2502 3076 3.955291 CGAGGATGTCGCTCTTCAT 57.045 52.632 0.00 0.00 43.03 2.57
2503 3077 1.485397 CGAGGATGTCGCTCTTCATG 58.515 55.000 0.00 0.00 43.03 3.07
2504 3078 1.863267 GAGGATGTCGCTCTTCATGG 58.137 55.000 0.00 0.00 0.00 3.66
2505 3079 1.137872 GAGGATGTCGCTCTTCATGGT 59.862 52.381 0.00 0.00 0.00 3.55
2506 3080 1.134580 AGGATGTCGCTCTTCATGGTG 60.135 52.381 0.00 0.00 0.00 4.17
2507 3081 1.134699 GGATGTCGCTCTTCATGGTGA 60.135 52.381 0.00 0.00 0.00 4.02
2508 3082 1.929836 GATGTCGCTCTTCATGGTGAC 59.070 52.381 6.47 6.47 41.58 3.67
2509 3083 0.969149 TGTCGCTCTTCATGGTGACT 59.031 50.000 12.56 0.00 41.70 3.41
2510 3084 1.344438 TGTCGCTCTTCATGGTGACTT 59.656 47.619 12.56 0.00 41.70 3.01
2511 3085 1.728971 GTCGCTCTTCATGGTGACTTG 59.271 52.381 6.24 0.00 39.15 3.16
2512 3086 0.445436 CGCTCTTCATGGTGACTTGC 59.555 55.000 0.00 0.00 35.57 4.01
2513 3087 0.807496 GCTCTTCATGGTGACTTGCC 59.193 55.000 0.00 0.00 35.57 4.52
2514 3088 1.612726 GCTCTTCATGGTGACTTGCCT 60.613 52.381 0.00 0.00 35.57 4.75
2515 3089 2.787994 CTCTTCATGGTGACTTGCCTT 58.212 47.619 0.00 0.00 35.57 4.35
2516 3090 3.152341 CTCTTCATGGTGACTTGCCTTT 58.848 45.455 0.00 0.00 35.57 3.11
2517 3091 3.565307 TCTTCATGGTGACTTGCCTTTT 58.435 40.909 0.00 0.00 35.57 2.27
2518 3092 3.569701 TCTTCATGGTGACTTGCCTTTTC 59.430 43.478 0.00 0.00 35.57 2.29
2519 3093 2.238521 TCATGGTGACTTGCCTTTTCC 58.761 47.619 0.00 0.00 35.57 3.13
2520 3094 1.273327 CATGGTGACTTGCCTTTTCCC 59.727 52.381 0.00 0.00 0.00 3.97
2521 3095 0.469144 TGGTGACTTGCCTTTTCCCC 60.469 55.000 0.00 0.00 0.00 4.81
2522 3096 0.178961 GGTGACTTGCCTTTTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
2523 3097 1.704641 GTGACTTGCCTTTTCCCCTT 58.295 50.000 0.00 0.00 0.00 3.95
2524 3098 2.039418 GTGACTTGCCTTTTCCCCTTT 58.961 47.619 0.00 0.00 0.00 3.11
2525 3099 2.035961 GTGACTTGCCTTTTCCCCTTTC 59.964 50.000 0.00 0.00 0.00 2.62
2526 3100 2.316108 GACTTGCCTTTTCCCCTTTCA 58.684 47.619 0.00 0.00 0.00 2.69
2527 3101 2.698274 GACTTGCCTTTTCCCCTTTCAA 59.302 45.455 0.00 0.00 0.00 2.69
2528 3102 3.111484 ACTTGCCTTTTCCCCTTTCAAA 58.889 40.909 0.00 0.00 0.00 2.69
2529 3103 3.521531 ACTTGCCTTTTCCCCTTTCAAAA 59.478 39.130 0.00 0.00 0.00 2.44
2530 3104 4.165950 ACTTGCCTTTTCCCCTTTCAAAAT 59.834 37.500 0.00 0.00 0.00 1.82
2531 3105 4.787135 TGCCTTTTCCCCTTTCAAAATT 57.213 36.364 0.00 0.00 0.00 1.82
2532 3106 5.122707 TGCCTTTTCCCCTTTCAAAATTT 57.877 34.783 0.00 0.00 0.00 1.82
2533 3107 5.129634 TGCCTTTTCCCCTTTCAAAATTTC 58.870 37.500 0.00 0.00 0.00 2.17
2534 3108 5.104151 TGCCTTTTCCCCTTTCAAAATTTCT 60.104 36.000 0.00 0.00 0.00 2.52
2535 3109 5.827797 GCCTTTTCCCCTTTCAAAATTTCTT 59.172 36.000 0.00 0.00 0.00 2.52
2536 3110 6.321181 GCCTTTTCCCCTTTCAAAATTTCTTT 59.679 34.615 0.00 0.00 0.00 2.52
2537 3111 7.147915 GCCTTTTCCCCTTTCAAAATTTCTTTT 60.148 33.333 0.00 0.00 34.90 2.27
2549 3123 5.756195 AAATTTCTTTTGCTTTTGGGAGC 57.244 34.783 0.00 0.00 43.00 4.70
2550 3124 2.908688 TTCTTTTGCTTTTGGGAGCC 57.091 45.000 0.00 0.00 42.01 4.70
2551 3125 2.086610 TCTTTTGCTTTTGGGAGCCT 57.913 45.000 0.00 0.00 42.01 4.58
2552 3126 2.397597 TCTTTTGCTTTTGGGAGCCTT 58.602 42.857 0.00 0.00 42.01 4.35
2553 3127 2.102925 TCTTTTGCTTTTGGGAGCCTTG 59.897 45.455 0.00 0.00 42.01 3.61
2554 3128 0.758123 TTTGCTTTTGGGAGCCTTGG 59.242 50.000 0.00 0.00 42.01 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.384989 GCTAGCTGCTCCTGACCGTA 61.385 60.000 4.91 0.00 38.95 4.02
2 3 2.716017 GCTAGCTGCTCCTGACCGT 61.716 63.158 4.91 0.00 38.95 4.83
3 4 2.105930 GCTAGCTGCTCCTGACCG 59.894 66.667 4.91 0.00 38.95 4.79
4 5 2.105930 CGCTAGCTGCTCCTGACC 59.894 66.667 13.93 0.00 40.11 4.02
5 6 2.105930 CCGCTAGCTGCTCCTGAC 59.894 66.667 13.93 0.00 40.11 3.51
6 7 3.150335 CCCGCTAGCTGCTCCTGA 61.150 66.667 13.93 0.00 40.11 3.86
7 8 3.149338 CTCCCGCTAGCTGCTCCTG 62.149 68.421 13.93 0.00 40.11 3.86
8 9 2.655077 ATCTCCCGCTAGCTGCTCCT 62.655 60.000 13.93 0.00 40.11 3.69
9 10 2.206536 ATCTCCCGCTAGCTGCTCC 61.207 63.158 13.93 0.00 40.11 4.70
10 11 1.006337 CATCTCCCGCTAGCTGCTC 60.006 63.158 13.93 0.00 40.11 4.26
11 12 3.136750 CATCTCCCGCTAGCTGCT 58.863 61.111 13.93 7.57 40.11 4.24
12 13 2.664518 GCATCTCCCGCTAGCTGC 60.665 66.667 13.93 10.86 32.11 5.25
13 14 2.030262 GGCATCTCCCGCTAGCTG 59.970 66.667 13.93 6.10 0.00 4.24
14 15 3.610669 CGGCATCTCCCGCTAGCT 61.611 66.667 13.93 0.00 42.03 3.32
37 38 1.583967 CATCGCCGACGTCTCTGAC 60.584 63.158 14.70 0.00 41.18 3.51
38 39 2.761195 CCATCGCCGACGTCTCTGA 61.761 63.158 14.70 8.39 41.18 3.27
39 40 2.278206 CCATCGCCGACGTCTCTG 60.278 66.667 14.70 3.10 41.18 3.35
40 41 2.750637 ACCATCGCCGACGTCTCT 60.751 61.111 14.70 0.00 41.18 3.10
41 42 2.579787 CACCATCGCCGACGTCTC 60.580 66.667 14.70 4.31 41.18 3.36
42 43 4.129737 CCACCATCGCCGACGTCT 62.130 66.667 14.70 0.00 41.18 4.18
43 44 4.124351 TCCACCATCGCCGACGTC 62.124 66.667 5.18 5.18 41.18 4.34
44 45 4.430765 GTCCACCATCGCCGACGT 62.431 66.667 0.00 0.00 41.18 4.34
49 50 4.832608 GTCCCGTCCACCATCGCC 62.833 72.222 0.00 0.00 0.00 5.54
50 51 3.599285 TTGTCCCGTCCACCATCGC 62.599 63.158 0.00 0.00 0.00 4.58
51 52 1.740296 GTTGTCCCGTCCACCATCG 60.740 63.158 0.00 0.00 0.00 3.84
52 53 0.899720 TAGTTGTCCCGTCCACCATC 59.100 55.000 0.00 0.00 0.00 3.51
53 54 1.580059 ATAGTTGTCCCGTCCACCAT 58.420 50.000 0.00 0.00 0.00 3.55
54 55 2.234896 TATAGTTGTCCCGTCCACCA 57.765 50.000 0.00 0.00 0.00 4.17
55 56 4.147321 TCTATATAGTTGTCCCGTCCACC 58.853 47.826 9.58 0.00 0.00 4.61
56 57 5.068636 TCTCTATATAGTTGTCCCGTCCAC 58.931 45.833 9.58 0.00 0.00 4.02
57 58 5.163120 ACTCTCTATATAGTTGTCCCGTCCA 60.163 44.000 9.58 0.00 0.00 4.02
58 59 5.315348 ACTCTCTATATAGTTGTCCCGTCC 58.685 45.833 9.58 0.00 0.00 4.79
59 60 5.996513 TGACTCTCTATATAGTTGTCCCGTC 59.003 44.000 19.41 13.55 0.00 4.79
60 61 5.938279 TGACTCTCTATATAGTTGTCCCGT 58.062 41.667 19.41 7.89 0.00 5.28
61 62 6.879276 TTGACTCTCTATATAGTTGTCCCG 57.121 41.667 19.41 5.76 0.00 5.14
62 63 8.697292 AGTTTTGACTCTCTATATAGTTGTCCC 58.303 37.037 19.41 11.12 0.00 4.46
63 64 9.522804 CAGTTTTGACTCTCTATATAGTTGTCC 57.477 37.037 19.41 10.78 0.00 4.02
64 65 9.522804 CCAGTTTTGACTCTCTATATAGTTGTC 57.477 37.037 9.58 14.49 0.00 3.18
65 66 9.256228 TCCAGTTTTGACTCTCTATATAGTTGT 57.744 33.333 9.58 7.09 0.00 3.32
72 73 9.823647 GATCAAATCCAGTTTTGACTCTCTATA 57.176 33.333 6.13 0.00 45.55 1.31
73 74 8.729805 GATCAAATCCAGTTTTGACTCTCTAT 57.270 34.615 6.13 0.00 45.55 1.98
90 91 2.484889 GCGTCTACCAGGGATCAAATC 58.515 52.381 0.00 0.00 0.00 2.17
91 92 1.202533 CGCGTCTACCAGGGATCAAAT 60.203 52.381 0.00 0.00 0.00 2.32
92 93 0.174845 CGCGTCTACCAGGGATCAAA 59.825 55.000 0.00 0.00 0.00 2.69
93 94 0.681887 TCGCGTCTACCAGGGATCAA 60.682 55.000 5.77 0.00 0.00 2.57
94 95 1.077285 TCGCGTCTACCAGGGATCA 60.077 57.895 5.77 0.00 0.00 2.92
95 96 0.818445 TCTCGCGTCTACCAGGGATC 60.818 60.000 5.77 0.00 0.00 3.36
96 97 0.178987 ATCTCGCGTCTACCAGGGAT 60.179 55.000 5.77 0.00 0.00 3.85
97 98 0.471191 TATCTCGCGTCTACCAGGGA 59.529 55.000 5.77 0.00 0.00 4.20
98 99 0.875728 CTATCTCGCGTCTACCAGGG 59.124 60.000 5.77 0.00 0.00 4.45
99 100 0.875728 CCTATCTCGCGTCTACCAGG 59.124 60.000 5.77 2.90 0.00 4.45
100 101 1.801771 CTCCTATCTCGCGTCTACCAG 59.198 57.143 5.77 0.00 0.00 4.00
101 102 1.415289 TCTCCTATCTCGCGTCTACCA 59.585 52.381 5.77 0.00 0.00 3.25
102 103 2.070783 CTCTCCTATCTCGCGTCTACC 58.929 57.143 5.77 0.00 0.00 3.18
103 104 2.070783 CCTCTCCTATCTCGCGTCTAC 58.929 57.143 5.77 0.00 0.00 2.59
104 105 1.693062 ACCTCTCCTATCTCGCGTCTA 59.307 52.381 5.77 0.00 0.00 2.59
1447 1985 3.452990 TCGGCCACAAAATCTACTCCATA 59.547 43.478 2.24 0.00 0.00 2.74
1467 2005 2.287009 GGCAAATAAGAAAGGCCGATCG 60.287 50.000 8.51 8.51 34.56 3.69
1500 2038 1.227527 CAACACTGCGTCTGTCCCA 60.228 57.895 0.00 0.00 0.00 4.37
1577 2121 5.123820 TCGACAATCAAAGGAATCCACATTC 59.876 40.000 0.61 0.00 38.19 2.67
1586 2130 6.980593 ACAATTCATTCGACAATCAAAGGAA 58.019 32.000 0.00 0.00 0.00 3.36
1609 2153 3.245754 TGACCGACGAACAATGTTACAAC 59.754 43.478 0.00 0.00 0.00 3.32
1635 2179 3.371487 CCAAGGTGGTGGCATGATTAGTA 60.371 47.826 0.00 0.00 31.35 1.82
1637 2181 2.026641 CCAAGGTGGTGGCATGATTAG 58.973 52.381 0.00 0.00 31.35 1.73
1656 2200 3.104766 CATGTCCTGCGCATCACC 58.895 61.111 12.24 0.00 0.00 4.02
1730 2275 4.804139 CGGATGAGAATACTAAAGCACGTT 59.196 41.667 0.00 0.00 0.00 3.99
1731 2276 4.360563 CGGATGAGAATACTAAAGCACGT 58.639 43.478 0.00 0.00 0.00 4.49
1732 2277 3.182572 GCGGATGAGAATACTAAAGCACG 59.817 47.826 0.00 0.00 0.00 5.34
1733 2278 3.495001 GGCGGATGAGAATACTAAAGCAC 59.505 47.826 0.00 0.00 0.00 4.40
1734 2279 3.728845 GGCGGATGAGAATACTAAAGCA 58.271 45.455 0.00 0.00 0.00 3.91
1735 2280 2.731976 CGGCGGATGAGAATACTAAAGC 59.268 50.000 0.00 0.00 0.00 3.51
1737 2282 2.696707 ACCGGCGGATGAGAATACTAAA 59.303 45.455 35.78 0.00 0.00 1.85
1738 2283 2.295349 GACCGGCGGATGAGAATACTAA 59.705 50.000 35.78 0.00 0.00 2.24
1740 2285 0.674534 GACCGGCGGATGAGAATACT 59.325 55.000 35.78 5.26 0.00 2.12
1741 2286 0.387929 TGACCGGCGGATGAGAATAC 59.612 55.000 35.78 11.59 0.00 1.89
1757 2308 4.649088 ACTTTTTGCCTAAACCACTGAC 57.351 40.909 0.00 0.00 0.00 3.51
1797 2348 6.680758 CGAGTTTACAATTTTGTTTGGCAAAC 59.319 34.615 30.99 30.99 45.70 2.93
1813 2364 3.713858 TTTGTCCTCGTCGAGTTTACA 57.286 42.857 20.37 17.12 0.00 2.41
1819 2370 5.050634 TGTTTACAATTTTGTCCTCGTCGAG 60.051 40.000 15.53 15.53 42.35 4.04
1822 2373 7.743520 TTTTGTTTACAATTTTGTCCTCGTC 57.256 32.000 0.00 0.00 42.35 4.20
1823 2374 8.710835 AATTTTGTTTACAATTTTGTCCTCGT 57.289 26.923 0.00 0.00 42.35 4.18
1841 2392 8.643752 GCAAACGCACTATGTTTATAATTTTGT 58.356 29.630 0.00 0.00 37.44 2.83
1842 2393 8.107564 GGCAAACGCACTATGTTTATAATTTTG 58.892 33.333 0.00 0.00 37.44 2.44
1843 2394 8.032451 AGGCAAACGCACTATGTTTATAATTTT 58.968 29.630 0.00 0.00 37.44 1.82
1844 2395 7.543756 AGGCAAACGCACTATGTTTATAATTT 58.456 30.769 0.00 0.00 37.44 1.82
1845 2396 7.095695 AGGCAAACGCACTATGTTTATAATT 57.904 32.000 0.00 0.00 37.44 1.40
1846 2397 6.693315 AGGCAAACGCACTATGTTTATAAT 57.307 33.333 0.00 0.00 37.44 1.28
1847 2398 6.149640 TGAAGGCAAACGCACTATGTTTATAA 59.850 34.615 0.00 0.00 37.44 0.98
1848 2399 5.644206 TGAAGGCAAACGCACTATGTTTATA 59.356 36.000 0.00 0.00 37.44 0.98
1849 2400 4.457603 TGAAGGCAAACGCACTATGTTTAT 59.542 37.500 0.00 0.00 37.44 1.40
1850 2401 3.815962 TGAAGGCAAACGCACTATGTTTA 59.184 39.130 0.00 0.00 37.44 2.01
1851 2402 2.621055 TGAAGGCAAACGCACTATGTTT 59.379 40.909 0.00 0.00 40.01 2.83
1852 2403 2.226330 TGAAGGCAAACGCACTATGTT 58.774 42.857 0.00 0.00 0.00 2.71
1853 2404 1.890876 TGAAGGCAAACGCACTATGT 58.109 45.000 0.00 0.00 0.00 2.29
1854 2405 2.987413 TTGAAGGCAAACGCACTATG 57.013 45.000 0.00 0.00 0.00 2.23
1855 2406 2.819608 ACATTGAAGGCAAACGCACTAT 59.180 40.909 0.00 0.00 37.59 2.12
1856 2407 2.031245 CACATTGAAGGCAAACGCACTA 60.031 45.455 0.00 0.00 37.59 2.74
1857 2408 1.032014 ACATTGAAGGCAAACGCACT 58.968 45.000 0.00 0.00 37.59 4.40
1858 2409 1.130955 CACATTGAAGGCAAACGCAC 58.869 50.000 0.00 0.00 37.59 5.34
1859 2410 0.031857 CCACATTGAAGGCAAACGCA 59.968 50.000 0.00 0.00 37.59 5.24
1860 2411 0.031994 ACCACATTGAAGGCAAACGC 59.968 50.000 0.00 0.00 37.59 4.84
1861 2412 1.602668 CCACCACATTGAAGGCAAACG 60.603 52.381 0.00 0.00 37.59 3.60
1862 2413 1.412343 ACCACCACATTGAAGGCAAAC 59.588 47.619 0.00 0.00 37.59 2.93
1863 2414 1.786937 ACCACCACATTGAAGGCAAA 58.213 45.000 0.00 0.00 37.59 3.68
1864 2415 1.786937 AACCACCACATTGAAGGCAA 58.213 45.000 0.00 0.00 38.60 4.52
1865 2416 1.786937 AAACCACCACATTGAAGGCA 58.213 45.000 0.00 0.00 0.00 4.75
1971 2530 7.007367 CGAGAAACAACACATAACATTGCATAC 59.993 37.037 0.00 0.00 0.00 2.39
2002 2561 9.487442 AACACATCTTTAATGGGGTTTGTATAT 57.513 29.630 0.00 0.00 0.00 0.86
2055 2621 3.694072 TCATGATACCGCTTTTTGGGAAG 59.306 43.478 0.00 0.00 0.00 3.46
2068 2634 6.564709 TTGCATCAATAAGCTCATGATACC 57.435 37.500 0.00 4.74 32.73 2.73
2079 2645 3.119245 ACTGGCTGCTTTGCATCAATAAG 60.119 43.478 0.00 0.00 38.13 1.73
2082 2648 1.203994 GACTGGCTGCTTTGCATCAAT 59.796 47.619 0.00 0.00 38.13 2.57
2133 2704 8.683615 TGTATACAAAGTACGATCAGATGTCTT 58.316 33.333 2.20 0.00 0.00 3.01
2141 2712 5.968254 TGGCTTGTATACAAAGTACGATCA 58.032 37.500 18.55 6.88 35.15 2.92
2214 2785 7.683437 AAAAACCTTAGGACTGCAATACTAC 57.317 36.000 4.77 0.00 0.00 2.73
2249 2821 9.667107 CCCTCAAAATAGAGTACAAATGAAGTA 57.333 33.333 0.00 0.00 33.75 2.24
2273 2845 5.755849 TGAGTAGATGGAATTCTTTTCCCC 58.244 41.667 5.23 0.00 37.79 4.81
2311 2883 7.974675 TGATACCGCAGAGAAAAGAAATAAAG 58.025 34.615 0.00 0.00 0.00 1.85
2319 2891 6.910536 AGTATTTGATACCGCAGAGAAAAG 57.089 37.500 0.00 0.00 36.40 2.27
2368 2941 8.123639 TGTCCTGCTGTATTCTATAGGATTAC 57.876 38.462 0.00 0.53 36.77 1.89
2379 2952 3.866651 AGTGACATGTCCTGCTGTATTC 58.133 45.455 22.85 0.00 0.00 1.75
2387 2961 0.738762 CGGCAGAGTGACATGTCCTG 60.739 60.000 22.85 21.30 0.00 3.86
2394 2968 3.226429 GAGTGCCGGCAGAGTGACA 62.226 63.158 33.73 0.61 0.00 3.58
2397 2971 4.767255 GGGAGTGCCGGCAGAGTG 62.767 72.222 33.73 0.00 33.83 3.51
2401 2975 3.077556 ACTAGGGAGTGCCGGCAG 61.078 66.667 33.73 19.26 33.41 4.85
2402 2976 3.390521 CACTAGGGAGTGCCGGCA 61.391 66.667 29.03 29.03 46.41 5.69
2409 2983 0.687354 CAAGCACACCACTAGGGAGT 59.313 55.000 0.00 0.00 41.61 3.85
2410 2984 0.036010 CCAAGCACACCACTAGGGAG 60.036 60.000 0.00 0.00 41.15 4.30
2411 2985 1.488705 CCCAAGCACACCACTAGGGA 61.489 60.000 0.00 0.00 41.15 4.20
2412 2986 1.002134 CCCAAGCACACCACTAGGG 60.002 63.158 0.00 0.00 44.81 3.53
2413 2987 1.675641 GCCCAAGCACACCACTAGG 60.676 63.158 0.00 0.00 39.53 3.02
2414 2988 1.073025 TGCCCAAGCACACCACTAG 59.927 57.895 0.00 0.00 46.52 2.57
2415 2989 3.245650 TGCCCAAGCACACCACTA 58.754 55.556 0.00 0.00 46.52 2.74
2424 2998 3.206034 GCAATTTGATTTTGCCCAAGC 57.794 42.857 0.00 0.00 42.84 4.01
2430 3004 4.516321 ACAAGAAGGGCAATTTGATTTTGC 59.484 37.500 0.00 0.00 46.82 3.68
2431 3005 5.993441 AGACAAGAAGGGCAATTTGATTTTG 59.007 36.000 0.00 0.00 0.00 2.44
2432 3006 6.178607 AGACAAGAAGGGCAATTTGATTTT 57.821 33.333 0.00 0.00 0.00 1.82
2433 3007 5.813513 AGACAAGAAGGGCAATTTGATTT 57.186 34.783 0.00 0.00 0.00 2.17
2434 3008 5.813513 AAGACAAGAAGGGCAATTTGATT 57.186 34.783 0.00 0.00 0.00 2.57
2435 3009 5.813513 AAAGACAAGAAGGGCAATTTGAT 57.186 34.783 0.00 0.00 0.00 2.57
2436 3010 5.612725 AAAAGACAAGAAGGGCAATTTGA 57.387 34.783 0.00 0.00 0.00 2.69
2456 3030 5.624159 ACTCTGTCTGATCCACATGAAAAA 58.376 37.500 0.00 0.00 0.00 1.94
2457 3031 5.233083 ACTCTGTCTGATCCACATGAAAA 57.767 39.130 0.00 0.00 0.00 2.29
2458 3032 4.897509 ACTCTGTCTGATCCACATGAAA 57.102 40.909 0.00 0.00 0.00 2.69
2459 3033 4.564199 CCAACTCTGTCTGATCCACATGAA 60.564 45.833 0.00 0.00 0.00 2.57
2460 3034 3.055602 CCAACTCTGTCTGATCCACATGA 60.056 47.826 0.00 0.00 0.00 3.07
2461 3035 3.268330 CCAACTCTGTCTGATCCACATG 58.732 50.000 0.00 0.00 0.00 3.21
2462 3036 2.909006 ACCAACTCTGTCTGATCCACAT 59.091 45.455 0.00 0.00 0.00 3.21
2463 3037 2.300152 GACCAACTCTGTCTGATCCACA 59.700 50.000 0.00 0.00 0.00 4.17
2464 3038 2.672478 CGACCAACTCTGTCTGATCCAC 60.672 54.545 0.00 0.00 0.00 4.02
2465 3039 1.546029 CGACCAACTCTGTCTGATCCA 59.454 52.381 0.00 0.00 0.00 3.41
2466 3040 1.819288 TCGACCAACTCTGTCTGATCC 59.181 52.381 0.00 0.00 0.00 3.36
2467 3041 2.159310 CCTCGACCAACTCTGTCTGATC 60.159 54.545 0.00 0.00 0.00 2.92
2468 3042 1.821753 CCTCGACCAACTCTGTCTGAT 59.178 52.381 0.00 0.00 0.00 2.90
2469 3043 1.202891 TCCTCGACCAACTCTGTCTGA 60.203 52.381 0.00 0.00 0.00 3.27
2470 3044 1.248486 TCCTCGACCAACTCTGTCTG 58.752 55.000 0.00 0.00 0.00 3.51
2471 3045 1.821753 CATCCTCGACCAACTCTGTCT 59.178 52.381 0.00 0.00 0.00 3.41
2472 3046 1.546476 ACATCCTCGACCAACTCTGTC 59.454 52.381 0.00 0.00 0.00 3.51
2473 3047 1.546476 GACATCCTCGACCAACTCTGT 59.454 52.381 0.00 0.00 0.00 3.41
2474 3048 1.468224 CGACATCCTCGACCAACTCTG 60.468 57.143 0.00 0.00 46.14 3.35
2475 3049 0.811915 CGACATCCTCGACCAACTCT 59.188 55.000 0.00 0.00 46.14 3.24
2476 3050 0.802607 GCGACATCCTCGACCAACTC 60.803 60.000 0.00 0.00 46.14 3.01
2477 3051 1.215647 GCGACATCCTCGACCAACT 59.784 57.895 0.00 0.00 46.14 3.16
2478 3052 0.802607 GAGCGACATCCTCGACCAAC 60.803 60.000 0.00 0.00 46.14 3.77
2479 3053 0.965866 AGAGCGACATCCTCGACCAA 60.966 55.000 0.00 0.00 46.14 3.67
2480 3054 0.965866 AAGAGCGACATCCTCGACCA 60.966 55.000 0.00 0.00 46.14 4.02
2481 3055 0.248702 GAAGAGCGACATCCTCGACC 60.249 60.000 0.00 0.00 46.14 4.79
2482 3056 0.452184 TGAAGAGCGACATCCTCGAC 59.548 55.000 0.00 0.00 46.14 4.20
2483 3057 1.066152 CATGAAGAGCGACATCCTCGA 59.934 52.381 0.00 0.00 46.14 4.04
2484 3058 1.485397 CATGAAGAGCGACATCCTCG 58.515 55.000 0.00 0.00 45.97 4.63
2485 3059 1.137872 ACCATGAAGAGCGACATCCTC 59.862 52.381 0.00 0.00 0.00 3.71
2486 3060 1.134580 CACCATGAAGAGCGACATCCT 60.135 52.381 0.00 0.00 0.00 3.24
2487 3061 1.134699 TCACCATGAAGAGCGACATCC 60.135 52.381 0.00 0.00 0.00 3.51
2488 3062 1.929836 GTCACCATGAAGAGCGACATC 59.070 52.381 0.00 0.00 0.00 3.06
2489 3063 1.552337 AGTCACCATGAAGAGCGACAT 59.448 47.619 0.00 0.00 0.00 3.06
2490 3064 0.969149 AGTCACCATGAAGAGCGACA 59.031 50.000 0.00 0.00 0.00 4.35
2491 3065 1.728971 CAAGTCACCATGAAGAGCGAC 59.271 52.381 0.00 0.00 0.00 5.19
2492 3066 1.941209 GCAAGTCACCATGAAGAGCGA 60.941 52.381 0.00 0.00 0.00 4.93
2493 3067 0.445436 GCAAGTCACCATGAAGAGCG 59.555 55.000 0.00 0.00 0.00 5.03
2494 3068 0.807496 GGCAAGTCACCATGAAGAGC 59.193 55.000 0.00 0.00 0.00 4.09
2495 3069 2.486472 AGGCAAGTCACCATGAAGAG 57.514 50.000 0.00 0.00 0.00 2.85
2496 3070 2.957402 AAGGCAAGTCACCATGAAGA 57.043 45.000 0.00 0.00 0.00 2.87
2497 3071 3.305608 GGAAAAGGCAAGTCACCATGAAG 60.306 47.826 0.00 0.00 0.00 3.02
2498 3072 2.627699 GGAAAAGGCAAGTCACCATGAA 59.372 45.455 0.00 0.00 0.00 2.57
2499 3073 2.238521 GGAAAAGGCAAGTCACCATGA 58.761 47.619 0.00 0.00 0.00 3.07
2500 3074 1.273327 GGGAAAAGGCAAGTCACCATG 59.727 52.381 0.00 0.00 0.00 3.66
2501 3075 1.632589 GGGAAAAGGCAAGTCACCAT 58.367 50.000 0.00 0.00 0.00 3.55
2502 3076 0.469144 GGGGAAAAGGCAAGTCACCA 60.469 55.000 0.00 0.00 34.75 4.17
2503 3077 0.178961 AGGGGAAAAGGCAAGTCACC 60.179 55.000 0.00 0.00 34.84 4.02
2504 3078 1.704641 AAGGGGAAAAGGCAAGTCAC 58.295 50.000 0.00 0.00 0.00 3.67
2505 3079 2.316108 GAAAGGGGAAAAGGCAAGTCA 58.684 47.619 0.00 0.00 0.00 3.41
2506 3080 2.316108 TGAAAGGGGAAAAGGCAAGTC 58.684 47.619 0.00 0.00 0.00 3.01
2507 3081 2.470057 TGAAAGGGGAAAAGGCAAGT 57.530 45.000 0.00 0.00 0.00 3.16
2508 3082 3.836365 TTTGAAAGGGGAAAAGGCAAG 57.164 42.857 0.00 0.00 0.00 4.01
2509 3083 4.787135 ATTTTGAAAGGGGAAAAGGCAA 57.213 36.364 0.00 0.00 0.00 4.52
2510 3084 4.787135 AATTTTGAAAGGGGAAAAGGCA 57.213 36.364 0.00 0.00 0.00 4.75
2511 3085 5.376625 AGAAATTTTGAAAGGGGAAAAGGC 58.623 37.500 0.00 0.00 0.00 4.35
2512 3086 7.880160 AAAGAAATTTTGAAAGGGGAAAAGG 57.120 32.000 0.00 0.00 0.00 3.11
2513 3087 7.701924 GCAAAAGAAATTTTGAAAGGGGAAAAG 59.298 33.333 15.60 0.00 42.79 2.27
2514 3088 7.395772 AGCAAAAGAAATTTTGAAAGGGGAAAA 59.604 29.630 15.60 0.00 42.79 2.29
2515 3089 6.889177 AGCAAAAGAAATTTTGAAAGGGGAAA 59.111 30.769 15.60 0.00 42.79 3.13
2516 3090 6.422333 AGCAAAAGAAATTTTGAAAGGGGAA 58.578 32.000 15.60 0.00 42.79 3.97
2517 3091 6.000246 AGCAAAAGAAATTTTGAAAGGGGA 58.000 33.333 15.60 0.00 42.79 4.81
2518 3092 6.698008 AAGCAAAAGAAATTTTGAAAGGGG 57.302 33.333 15.60 0.00 42.79 4.79
2519 3093 7.488792 CCAAAAGCAAAAGAAATTTTGAAAGGG 59.511 33.333 15.60 7.19 42.48 3.95
2520 3094 7.488792 CCCAAAAGCAAAAGAAATTTTGAAAGG 59.511 33.333 15.60 9.45 42.48 3.11
2521 3095 8.242739 TCCCAAAAGCAAAAGAAATTTTGAAAG 58.757 29.630 15.60 2.70 42.48 2.62
2522 3096 8.115490 TCCCAAAAGCAAAAGAAATTTTGAAA 57.885 26.923 15.60 0.00 42.48 2.69
2523 3097 7.628153 GCTCCCAAAAGCAAAAGAAATTTTGAA 60.628 33.333 15.60 0.00 42.48 2.69
2524 3098 6.183360 GCTCCCAAAAGCAAAAGAAATTTTGA 60.183 34.615 15.60 0.00 42.48 2.69
2525 3099 5.972973 GCTCCCAAAAGCAAAAGAAATTTTG 59.027 36.000 8.69 8.69 42.05 2.44
2526 3100 5.067674 GGCTCCCAAAAGCAAAAGAAATTTT 59.932 36.000 0.00 0.00 44.35 1.82
2527 3101 4.580167 GGCTCCCAAAAGCAAAAGAAATTT 59.420 37.500 0.00 0.00 44.35 1.82
2528 3102 4.136796 GGCTCCCAAAAGCAAAAGAAATT 58.863 39.130 0.00 0.00 44.35 1.82
2529 3103 3.392285 AGGCTCCCAAAAGCAAAAGAAAT 59.608 39.130 0.00 0.00 44.35 2.17
2530 3104 2.771372 AGGCTCCCAAAAGCAAAAGAAA 59.229 40.909 0.00 0.00 44.35 2.52
2531 3105 2.397597 AGGCTCCCAAAAGCAAAAGAA 58.602 42.857 0.00 0.00 44.35 2.52
2532 3106 2.086610 AGGCTCCCAAAAGCAAAAGA 57.913 45.000 0.00 0.00 44.35 2.52
2533 3107 2.486918 CAAGGCTCCCAAAAGCAAAAG 58.513 47.619 0.00 0.00 44.35 2.27
2534 3108 1.140652 CCAAGGCTCCCAAAAGCAAAA 59.859 47.619 0.00 0.00 44.35 2.44
2535 3109 0.758123 CCAAGGCTCCCAAAAGCAAA 59.242 50.000 0.00 0.00 44.35 3.68
2536 3110 2.439837 CCAAGGCTCCCAAAAGCAA 58.560 52.632 0.00 0.00 44.35 3.91
2537 3111 4.196372 CCAAGGCTCCCAAAAGCA 57.804 55.556 0.00 0.00 44.35 3.91


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

AutoCloner maintained by Alex Coulton.