Multiple sequence alignment - TraesCS5B01G372600

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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 TraesCS5B01G372600 chr5B 100.000 4213 0 0 1583 5795 550558587 550562799 0.000000e+00 7781.0
1 TraesCS5B01G372600 chr5B 100.000 1243 0 0 1 1243 550557005 550558247 0.000000e+00 2296.0
2 TraesCS5B01G372600 chr5D 89.297 2504 182 47 1759 4217 450633133 450635595 0.000000e+00 3061.0
3 TraesCS5B01G372600 chr5D 86.802 1129 71 39 138 1235 450631825 450632906 0.000000e+00 1188.0
4 TraesCS5B01G372600 chr5D 90.476 651 43 7 4492 5135 450636003 450636641 0.000000e+00 841.0
5 TraesCS5B01G372600 chr5D 88.329 377 24 10 5159 5535 450636638 450636994 8.920000e-118 435.0
6 TraesCS5B01G372600 chr5D 93.704 270 13 3 4243 4511 450635721 450635987 9.040000e-108 401.0
7 TraesCS5B01G372600 chr5D 92.653 245 18 0 5551 5795 450637044 450637288 2.570000e-93 353.0
8 TraesCS5B01G372600 chr5A 91.600 1869 99 28 2400 4217 569803289 569805150 0.000000e+00 2529.0
9 TraesCS5B01G372600 chr5A 88.926 1201 87 28 4237 5412 569805281 569806460 0.000000e+00 1439.0
10 TraesCS5B01G372600 chr5A 84.456 772 69 35 480 1235 569801499 569802235 0.000000e+00 713.0
11 TraesCS5B01G372600 chr5A 80.717 669 79 28 1595 2241 569802374 569803014 5.250000e-130 475.0
12 TraesCS5B01G372600 chr5A 93.191 235 14 1 5563 5795 569806637 569806871 1.550000e-90 344.0
13 TraesCS5B01G372600 chr2A 80.190 631 81 27 1621 2237 424923979 424923379 3.210000e-117 433.0
14 TraesCS5B01G372600 chr4D 85.333 75 2 6 5413 5479 29861259 29861332 1.040000e-07 69.4
15 TraesCS5B01G372600 chr4D 100.000 33 0 0 5596 5628 123424564 123424596 1.740000e-05 62.1
16 TraesCS5B01G372600 chr1D 100.000 34 0 0 5596 5629 76449500 76449533 4.850000e-06 63.9
17 TraesCS5B01G372600 chrUn 100.000 33 0 0 5596 5628 86509162 86509130 1.740000e-05 62.1
18 TraesCS5B01G372600 chrUn 100.000 33 0 0 5596 5628 282363846 282363814 1.740000e-05 62.1
19 TraesCS5B01G372600 chrUn 100.000 33 0 0 5596 5628 397470622 397470590 1.740000e-05 62.1
20 TraesCS5B01G372600 chr6D 100.000 33 0 0 5596 5628 168767638 168767670 1.740000e-05 62.1
21 TraesCS5B01G372600 chr6D 100.000 33 0 0 5596 5628 346934787 346934819 1.740000e-05 62.1


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 TraesCS5B01G372600 chr5B 550557005 550562799 5794 False 5038.5 7781 100.000000 1 5795 2 chr5B.!!$F1 5794
1 TraesCS5B01G372600 chr5D 450631825 450637288 5463 False 1046.5 3061 90.210167 138 5795 6 chr5D.!!$F1 5657
2 TraesCS5B01G372600 chr5A 569801499 569806871 5372 False 1100.0 2529 87.778000 480 5795 5 chr5A.!!$F1 5315
3 TraesCS5B01G372600 chr2A 424923379 424923979 600 True 433.0 433 80.190000 1621 2237 1 chr2A.!!$R1 616

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
470 476 0.250234 GCTACAGTGCTGGTCCATGA 59.750 55.0 0.00 0.00 34.19 3.07 F
533 539 0.393820 TGACGGGGTTAAGTGACACC 59.606 55.0 0.84 0.00 39.83 4.16 F
745 763 0.463833 CTGCATTCTCCGGTAACCCC 60.464 60.0 0.00 0.00 0.00 4.95 F
1699 1750 0.042448 GTTTTGCTCGTGTCGGTGTC 60.042 55.0 0.00 0.00 0.00 3.67 F
1752 1804 0.105224 TCCGAACTGGCTGTTTCGAA 59.895 50.0 21.14 0.00 39.30 3.71 F
1952 2010 0.251073 GTTGGCCTTAGTTCGCCCTA 59.749 55.0 3.32 0.00 45.07 3.53 F
3053 3290 0.453282 CATGCACCTCGTTGCTTTCG 60.453 55.0 0.00 0.00 43.41 3.46 F
3265 3502 0.723414 CACTTGGCTGCGATGTAGTG 59.277 55.0 3.04 2.23 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 1632 0.179062 AATCAGACCAGCTCGATGGC 60.179 55.0 4.93 0.0 44.80 4.40 R
1611 1657 0.250467 TCAGTGGTCCAAGCAGAAGC 60.250 55.0 0.00 0.0 42.56 3.86 R
1732 1784 0.599204 TCGAAACAGCCAGTTCGGAC 60.599 55.0 11.81 0.0 40.26 4.79 R
2976 3213 0.304705 GCAACAACCACGACTGTCAG 59.695 55.0 8.73 0.0 0.00 3.51 R
3667 3904 0.439985 CACAGAATGCTTCGACGGTG 59.560 55.0 0.00 0.0 42.53 4.94 R
3668 3905 0.670546 CCACAGAATGCTTCGACGGT 60.671 55.0 0.00 0.0 42.53 4.83 R
4036 4273 0.318120 CCCATGAACCAGCAACCAAC 59.682 55.0 0.00 0.0 0.00 3.77 R
5156 5571 1.033746 CGTGGGAGGCAGCAATTCAT 61.034 55.0 0.00 0.0 0.00 2.57 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
39 40 6.443934 TTTGAAAACAAACTAGCACTAGCA 57.556 33.333 4.58 0.00 45.49 3.49
40 41 5.418310 TGAAAACAAACTAGCACTAGCAC 57.582 39.130 4.58 0.00 45.49 4.40
41 42 4.878971 TGAAAACAAACTAGCACTAGCACA 59.121 37.500 4.58 0.00 45.49 4.57
42 43 4.813296 AAACAAACTAGCACTAGCACAC 57.187 40.909 4.58 0.00 45.49 3.82
43 44 3.469008 ACAAACTAGCACTAGCACACA 57.531 42.857 4.58 0.00 45.49 3.72
44 45 4.008074 ACAAACTAGCACTAGCACACAT 57.992 40.909 4.58 0.00 45.49 3.21
45 46 4.389374 ACAAACTAGCACTAGCACACATT 58.611 39.130 4.58 0.00 45.49 2.71
46 47 5.547465 ACAAACTAGCACTAGCACACATTA 58.453 37.500 4.58 0.00 45.49 1.90
47 48 5.995282 ACAAACTAGCACTAGCACACATTAA 59.005 36.000 4.58 0.00 45.49 1.40
48 49 6.485313 ACAAACTAGCACTAGCACACATTAAA 59.515 34.615 4.58 0.00 45.49 1.52
49 50 7.012894 ACAAACTAGCACTAGCACACATTAAAA 59.987 33.333 4.58 0.00 45.49 1.52
50 51 7.504924 AACTAGCACTAGCACACATTAAAAA 57.495 32.000 4.58 0.00 45.49 1.94
355 358 4.867086 AGAAGTGAAGAACCCCAAAGAAA 58.133 39.130 0.00 0.00 0.00 2.52
420 423 6.944234 AACAGTTAAACCTGGAAAAGAGAG 57.056 37.500 0.00 0.00 36.75 3.20
425 428 7.915923 CAGTTAAACCTGGAAAAGAGAGAAAAC 59.084 37.037 0.00 0.00 0.00 2.43
427 430 6.456795 AAACCTGGAAAAGAGAGAAAACAG 57.543 37.500 0.00 0.00 0.00 3.16
429 432 5.755849 ACCTGGAAAAGAGAGAAAACAGAA 58.244 37.500 0.00 0.00 0.00 3.02
430 433 5.825151 ACCTGGAAAAGAGAGAAAACAGAAG 59.175 40.000 0.00 0.00 0.00 2.85
454 460 2.829003 CTCGGGCGGAGTCAGCTA 60.829 66.667 15.02 0.88 38.02 3.32
455 461 3.127352 CTCGGGCGGAGTCAGCTAC 62.127 68.421 15.02 7.67 38.02 3.58
456 462 3.449227 CGGGCGGAGTCAGCTACA 61.449 66.667 15.02 0.00 34.52 2.74
457 463 2.496817 GGGCGGAGTCAGCTACAG 59.503 66.667 15.02 0.00 34.52 2.74
458 464 2.352032 GGGCGGAGTCAGCTACAGT 61.352 63.158 15.02 0.00 34.52 3.55
459 465 1.153745 GGCGGAGTCAGCTACAGTG 60.154 63.158 15.02 0.00 34.52 3.66
460 466 1.807573 GCGGAGTCAGCTACAGTGC 60.808 63.158 8.11 0.00 0.00 4.40
461 467 1.886585 CGGAGTCAGCTACAGTGCT 59.113 57.895 0.00 0.00 45.18 4.40
467 473 4.215370 AGCTACAGTGCTGGTCCA 57.785 55.556 4.11 0.00 42.33 4.02
468 474 2.689073 AGCTACAGTGCTGGTCCAT 58.311 52.632 4.11 0.00 42.33 3.41
469 475 0.251354 AGCTACAGTGCTGGTCCATG 59.749 55.000 4.11 0.00 42.33 3.66
470 476 0.250234 GCTACAGTGCTGGTCCATGA 59.750 55.000 0.00 0.00 34.19 3.07
528 534 1.528161 GAAACGTGACGGGGTTAAGTG 59.472 52.381 10.66 0.00 0.00 3.16
533 539 0.393820 TGACGGGGTTAAGTGACACC 59.606 55.000 0.84 0.00 39.83 4.16
588 598 3.547868 CGTCCTCATGATGACGTGTAAAG 59.452 47.826 32.61 13.06 46.83 1.85
625 636 2.989824 ACGACCCGTCACCCTCTG 60.990 66.667 0.00 0.00 33.69 3.35
627 638 3.311110 GACCCGTCACCCTCTGCA 61.311 66.667 0.00 0.00 0.00 4.41
629 640 3.314331 CCCGTCACCCTCTGCACT 61.314 66.667 0.00 0.00 0.00 4.40
695 713 0.673985 GGAAGAGCACAAAACCCCAC 59.326 55.000 0.00 0.00 0.00 4.61
745 763 0.463833 CTGCATTCTCCGGTAACCCC 60.464 60.000 0.00 0.00 0.00 4.95
830 857 1.759236 GAACCACTTCTCCCCCGTT 59.241 57.895 0.00 0.00 0.00 4.44
831 858 0.605589 GAACCACTTCTCCCCCGTTG 60.606 60.000 0.00 0.00 0.00 4.10
841 868 2.032528 CCCCGTTGAAGCAGAGCA 59.967 61.111 0.00 0.00 0.00 4.26
905 932 3.868200 AAGCCAGACCCAAAGCCGG 62.868 63.158 0.00 0.00 0.00 6.13
909 936 3.249189 AGACCCAAAGCCGGAGCA 61.249 61.111 5.05 0.00 43.56 4.26
945 972 1.376812 CTACCGGACCAAAGCCACC 60.377 63.158 9.46 0.00 0.00 4.61
1149 1193 2.489619 CCTCATCCCTCTCCTCTCTCTG 60.490 59.091 0.00 0.00 0.00 3.35
1200 1244 3.649986 GCGTGCCTGCGTTTGACT 61.650 61.111 0.00 0.00 0.00 3.41
1201 1245 3.022287 CGTGCCTGCGTTTGACTT 58.978 55.556 0.00 0.00 0.00 3.01
1204 1248 2.250939 TGCCTGCGTTTGACTTCGG 61.251 57.895 0.00 0.00 0.00 4.30
1210 1254 1.597027 CGTTTGACTTCGGCTGGGT 60.597 57.895 0.00 0.00 0.00 4.51
1212 1256 1.896660 TTTGACTTCGGCTGGGTGC 60.897 57.895 0.00 0.00 41.94 5.01
1213 1257 2.337879 TTTGACTTCGGCTGGGTGCT 62.338 55.000 0.00 0.00 42.39 4.40
1214 1258 2.435059 GACTTCGGCTGGGTGCTC 60.435 66.667 0.00 0.00 42.39 4.26
1215 1259 4.379243 ACTTCGGCTGGGTGCTCG 62.379 66.667 0.00 0.00 42.39 5.03
1227 1273 4.012811 TGCTCGCTCCTGCTGCTT 62.013 61.111 0.00 0.00 37.27 3.91
1611 1657 1.364626 GAGCTGGTCTGATTGTGCCG 61.365 60.000 0.00 0.00 0.00 5.69
1634 1680 1.081892 CTGCTTGGACCACTGAATCG 58.918 55.000 0.00 0.00 0.00 3.34
1639 1690 3.254060 CTTGGACCACTGAATCGTACTG 58.746 50.000 0.00 0.00 0.00 2.74
1640 1691 2.521126 TGGACCACTGAATCGTACTGA 58.479 47.619 0.00 0.00 0.00 3.41
1652 1703 7.228108 ACTGAATCGTACTGAGTAATTCGGATA 59.772 37.037 23.03 4.65 36.60 2.59
1657 1708 6.095300 TCGTACTGAGTAATTCGGATAAACCA 59.905 38.462 0.00 0.00 38.90 3.67
1662 1713 8.262227 ACTGAGTAATTCGGATAAACCATGTAA 58.738 33.333 0.00 0.00 38.90 2.41
1681 1732 5.106442 TGTAATACATGCGTTCAGAATCGT 58.894 37.500 0.00 0.00 0.00 3.73
1687 1738 1.601903 TGCGTTCAGAATCGTTTTGCT 59.398 42.857 6.90 0.00 0.00 3.91
1695 1746 0.511221 AATCGTTTTGCTCGTGTCGG 59.489 50.000 0.00 0.00 0.00 4.79
1699 1750 0.042448 GTTTTGCTCGTGTCGGTGTC 60.042 55.000 0.00 0.00 0.00 3.67
1704 1755 4.379143 TCGTGTCGGTGTCGCTCG 62.379 66.667 0.00 0.00 36.13 5.03
1714 1766 0.992802 GTGTCGCTCGAATCAGTTCC 59.007 55.000 0.00 0.00 0.00 3.62
1743 1795 3.041940 CCGTGTGTCCGAACTGGC 61.042 66.667 0.00 0.00 37.80 4.85
1750 1802 0.878523 TGTCCGAACTGGCTGTTTCG 60.879 55.000 11.21 14.28 39.30 3.46
1752 1804 0.105224 TCCGAACTGGCTGTTTCGAA 59.895 50.000 21.14 0.00 39.30 3.71
1753 1805 1.156736 CCGAACTGGCTGTTTCGAAT 58.843 50.000 21.14 0.00 39.30 3.34
1756 1808 2.480419 CGAACTGGCTGTTTCGAATCTT 59.520 45.455 11.21 0.00 39.30 2.40
1757 1809 3.058914 CGAACTGGCTGTTTCGAATCTTT 60.059 43.478 11.21 0.00 39.30 2.52
1775 1827 2.671130 TTCGATGCTGCTCATGTGTA 57.329 45.000 0.00 0.00 35.05 2.90
1776 1828 2.896745 TCGATGCTGCTCATGTGTAT 57.103 45.000 0.00 0.00 35.05 2.29
1777 1829 4.320608 TTCGATGCTGCTCATGTGTATA 57.679 40.909 0.00 0.00 35.05 1.47
1781 1833 4.385146 CGATGCTGCTCATGTGTATAAGAG 59.615 45.833 0.00 0.00 35.05 2.85
1800 1852 1.880027 AGTTGGTTGAACGAATCCTGC 59.120 47.619 0.00 0.00 39.80 4.85
1804 1856 1.144969 GTTGAACGAATCCTGCGACA 58.855 50.000 0.00 0.00 0.00 4.35
1822 1874 0.819582 CAGATGGTTGTGGATTGGGC 59.180 55.000 0.00 0.00 0.00 5.36
1841 1893 4.781087 TGGGCTTGGTATAAGAGTACAACT 59.219 41.667 0.00 0.00 0.00 3.16
1850 1902 6.424207 GGTATAAGAGTACAACTATTGCTGGC 59.576 42.308 0.00 0.00 31.40 4.85
1851 1903 3.981071 AGAGTACAACTATTGCTGGCA 57.019 42.857 0.00 0.00 0.00 4.92
1855 1907 0.883833 ACAACTATTGCTGGCAGTGC 59.116 50.000 17.16 6.55 0.00 4.40
1856 1908 0.883153 CAACTATTGCTGGCAGTGCA 59.117 50.000 18.61 6.87 38.80 4.57
1857 1909 1.135489 CAACTATTGCTGGCAGTGCAG 60.135 52.381 18.61 13.22 41.71 4.41
1858 1910 1.310933 ACTATTGCTGGCAGTGCAGC 61.311 55.000 24.04 24.04 41.71 5.25
1870 1928 2.025441 TGCAGCGCAAACCGAAAC 59.975 55.556 11.47 0.00 40.02 2.78
1946 2004 4.321230 CCATGACTTTGTTGGCCTTAGTTC 60.321 45.833 3.32 0.00 0.00 3.01
1951 2009 1.002502 GTTGGCCTTAGTTCGCCCT 60.003 57.895 3.32 0.00 45.07 5.19
1952 2010 0.251073 GTTGGCCTTAGTTCGCCCTA 59.749 55.000 3.32 0.00 45.07 3.53
1956 2014 1.208776 GGCCTTAGTTCGCCCTAAGAA 59.791 52.381 17.45 0.00 44.36 2.52
1974 2032 4.914177 AGAATTTTGGGGATTGCACAAT 57.086 36.364 0.00 0.00 0.00 2.71
2025 2084 4.694037 TGACATTGTCAATTCTCTGCTGAG 59.306 41.667 16.95 14.07 39.78 3.35
2041 2100 4.124970 TGCTGAGATGCACATTCAGTATC 58.875 43.478 19.27 8.50 40.29 2.24
2049 2108 4.607955 TGCACATTCAGTATCGCTACTAC 58.392 43.478 0.00 0.00 35.99 2.73
2051 2110 4.788840 GCACATTCAGTATCGCTACTACGT 60.789 45.833 0.00 0.00 35.99 3.57
2053 2112 6.600350 CACATTCAGTATCGCTACTACGTAT 58.400 40.000 0.00 0.00 35.99 3.06
2054 2113 6.520104 CACATTCAGTATCGCTACTACGTATG 59.480 42.308 0.00 1.23 35.99 2.39
2055 2114 4.658713 TCAGTATCGCTACTACGTATGC 57.341 45.455 0.00 0.45 35.99 3.14
2056 2115 4.060205 TCAGTATCGCTACTACGTATGCA 58.940 43.478 0.00 0.00 35.99 3.96
2057 2116 4.151867 TCAGTATCGCTACTACGTATGCAG 59.848 45.833 0.00 5.40 35.99 4.41
2058 2117 4.063689 AGTATCGCTACTACGTATGCAGT 58.936 43.478 13.22 5.32 36.40 4.40
2059 2118 5.119743 CAGTATCGCTACTACGTATGCAGTA 59.880 44.000 0.00 6.09 35.99 2.74
2092 2151 6.729187 AGAAAATAGCAAGTGTTTCTGTGAC 58.271 36.000 0.00 0.00 38.55 3.67
2135 2196 5.128205 TCCATCATCTGCATCTTAAACTGG 58.872 41.667 0.00 0.00 0.00 4.00
2147 2208 6.983890 GCATCTTAAACTGGTTTCCTTTGAAA 59.016 34.615 1.77 0.00 38.14 2.69
2253 2353 9.953565 AGTTTATCATAAAACTGTAGCCTACAA 57.046 29.630 5.98 0.00 45.60 2.41
2275 2375 8.319143 ACAAGATAGCTTAAAACACGTATTGT 57.681 30.769 0.00 0.00 34.26 2.71
2276 2376 8.227791 ACAAGATAGCTTAAAACACGTATTGTG 58.772 33.333 0.00 0.00 42.78 3.33
2357 2461 6.147821 CACCATAATACCAAATAGAAGCCGAG 59.852 42.308 0.00 0.00 0.00 4.63
2362 2466 4.015872 ACCAAATAGAAGCCGAGTTCAA 57.984 40.909 0.00 0.00 0.00 2.69
2375 2479 2.488153 CGAGTTCAATTTGGGAGGAACC 59.512 50.000 0.00 0.00 40.27 3.62
2433 2621 8.686334 GTTACATGTGGGATTATCTTCACAAAT 58.314 33.333 19.00 14.37 42.35 2.32
2441 2629 5.536538 GGATTATCTTCACAAATTCCCCCTC 59.463 44.000 0.00 0.00 0.00 4.30
2443 2631 1.004277 TCTTCACAAATTCCCCCTCCG 59.996 52.381 0.00 0.00 0.00 4.63
2467 2656 6.348132 CGTCTGGCTTATAGACTGATAGTGAG 60.348 46.154 0.00 0.00 41.80 3.51
2484 2673 9.770097 TGATAGTGAGAACATTCATCTTATTCC 57.230 33.333 0.00 0.00 0.00 3.01
2485 2674 9.770097 GATAGTGAGAACATTCATCTTATTCCA 57.230 33.333 0.00 0.00 0.00 3.53
2490 2679 9.246670 TGAGAACATTCATCTTATTCCAACAAT 57.753 29.630 0.00 0.00 0.00 2.71
2502 2691 8.970020 TCTTATTCCAACAATATTGCAATCTGT 58.030 29.630 16.86 17.10 0.00 3.41
2506 2695 7.643569 TCCAACAATATTGCAATCTGTACAT 57.356 32.000 16.86 0.00 0.00 2.29
2507 2696 8.065473 TCCAACAATATTGCAATCTGTACATT 57.935 30.769 16.86 6.12 0.00 2.71
2529 2730 8.389603 ACATTTTTGTGTTAAGTGAATTTGCTG 58.610 29.630 0.00 0.00 0.00 4.41
2565 2766 2.362736 GCAAGATCAATCCTGACTGCA 58.637 47.619 0.00 0.00 33.30 4.41
2569 2770 2.170187 AGATCAATCCTGACTGCAGACC 59.830 50.000 23.35 12.23 45.17 3.85
2571 2772 2.820178 TCAATCCTGACTGCAGACCTA 58.180 47.619 23.35 2.56 45.17 3.08
2583 2784 3.031736 TGCAGACCTACATTAGTCCCTC 58.968 50.000 0.00 0.00 33.29 4.30
2678 2884 4.848357 ACAGATGTGGGTTTCTGGAATAG 58.152 43.478 5.08 0.00 42.93 1.73
2699 2905 3.264964 AGCTTTTGGGGAATCATTTGCAT 59.735 39.130 0.00 0.00 0.00 3.96
2736 2942 8.517062 AAGCATGAGTTTATTTCTTCATAGCT 57.483 30.769 0.00 0.00 0.00 3.32
2771 2977 3.119029 GCACCATGTTTGCTCCAACATAT 60.119 43.478 8.88 0.47 37.00 1.78
2776 3003 7.601886 CACCATGTTTGCTCCAACATATTTTAA 59.398 33.333 8.56 0.00 0.00 1.52
2819 3047 3.412386 AGCAAACTTTTACCATCTCGCT 58.588 40.909 0.00 0.00 0.00 4.93
2837 3065 3.563808 TCGCTACAGCTTTGAACAAACAT 59.436 39.130 0.00 0.00 39.32 2.71
2864 3101 4.569719 AAATCCCATTACAAGACTCCGT 57.430 40.909 0.00 0.00 0.00 4.69
2878 3115 5.494632 AGACTCCGTTGTTTTGGTTTTAG 57.505 39.130 0.00 0.00 0.00 1.85
2886 3123 5.689961 CGTTGTTTTGGTTTTAGGATTCCAG 59.310 40.000 5.29 0.00 0.00 3.86
2900 3137 6.380079 AGGATTCCAGTTCACTAATGTTCT 57.620 37.500 5.29 0.00 0.00 3.01
2953 3190 7.778470 AATAGAAGAGCAAATTTACTCTCCG 57.222 36.000 19.08 0.00 42.41 4.63
2976 3213 4.841441 TGGGAACATTGCAGTCCC 57.159 55.556 16.16 16.16 40.90 4.46
3053 3290 0.453282 CATGCACCTCGTTGCTTTCG 60.453 55.000 0.00 0.00 43.41 3.46
3059 3296 2.022129 CTCGTTGCTTTCGTCGCCT 61.022 57.895 0.00 0.00 0.00 5.52
3223 3460 4.059511 CTGCAAAAGCCATCAAAACATCA 58.940 39.130 0.00 0.00 0.00 3.07
3265 3502 0.723414 CACTTGGCTGCGATGTAGTG 59.277 55.000 3.04 2.23 0.00 2.74
3280 3517 2.426024 TGTAGTGATACTCCTTGTCGGC 59.574 50.000 0.00 0.00 0.00 5.54
3304 3541 1.227556 CGAAGCCCTTGGTATCGGG 60.228 63.158 0.00 0.00 43.60 5.14
3328 3565 2.478134 GCTCATAGTTGTGATCGCCATC 59.522 50.000 3.31 0.00 0.00 3.51
3416 3653 2.286872 CCTCTGTCAATGGAGCACATC 58.713 52.381 0.00 0.00 39.40 3.06
3697 3934 1.730501 CATTCTGTGGCACGATGTCT 58.269 50.000 13.77 0.00 0.00 3.41
3709 3946 1.372087 CGATGTCTGGGCCAGCTTTC 61.372 60.000 29.02 20.85 0.00 2.62
3892 4129 0.831711 GGTGGGGCTTTGTCCATGTT 60.832 55.000 0.00 0.00 35.28 2.71
4168 4411 1.160137 CTCTCCGGCTGTTTTTCCTG 58.840 55.000 0.00 0.00 0.00 3.86
4192 4440 6.072728 TGTGTTTATCAGCATTAGTGACAACC 60.073 38.462 0.00 0.00 0.00 3.77
4193 4441 5.121611 TGTTTATCAGCATTAGTGACAACCG 59.878 40.000 0.00 0.00 0.00 4.44
4208 4456 1.069022 CAACCGAAGTCTGCATTGGTG 60.069 52.381 0.00 0.00 0.00 4.17
4217 4465 3.636300 AGTCTGCATTGGTGTTTTGCTAA 59.364 39.130 0.00 0.00 37.28 3.09
4221 4490 5.523188 TCTGCATTGGTGTTTTGCTAAAAAG 59.477 36.000 0.00 0.00 35.96 2.27
4234 4503 5.717038 TGCTAAAAAGAAAAGCAAACTGC 57.283 34.783 0.00 0.00 42.96 4.40
4295 4654 7.116233 CCTGTTTAGTTCAACATTTTGCATACC 59.884 37.037 0.00 0.00 36.08 2.73
4402 4765 8.087750 TCCTTTACATTGCCTTTAGTGAAATTG 58.912 33.333 0.00 0.00 0.00 2.32
4403 4766 7.872483 CCTTTACATTGCCTTTAGTGAAATTGT 59.128 33.333 0.00 0.00 0.00 2.71
4522 4921 1.405105 TGCTTGTCCACTGAAAACTGC 59.595 47.619 0.00 0.00 0.00 4.40
4562 4961 4.399934 TGTTATTTATCCACCGAAAAGGGC 59.600 41.667 0.00 0.00 46.96 5.19
4575 4974 2.920076 AAAGGGCAGCGGTCCAACAA 62.920 55.000 10.95 0.00 43.06 2.83
4616 5019 4.777896 TGTCCCTTACTGTTCTATGCTTCT 59.222 41.667 0.00 0.00 0.00 2.85
4624 5027 9.817809 CTTACTGTTCTATGCTTCTGGTTTATA 57.182 33.333 0.00 0.00 0.00 0.98
4636 5039 9.705290 TGCTTCTGGTTTATAATTTTCTTTTCC 57.295 29.630 0.00 0.00 0.00 3.13
4734 5137 0.179000 CAGAGAACCCCCAGAATCCG 59.821 60.000 0.00 0.00 0.00 4.18
4767 5170 1.521681 GATACCAGACCACCTGCGC 60.522 63.158 0.00 0.00 41.57 6.09
4809 5212 3.184783 CAGATTGATCTCTTGCTCATCGC 59.815 47.826 0.00 0.00 34.22 4.58
4826 5229 2.191375 CCCATGTGCGATCCTGCT 59.809 61.111 0.00 0.00 35.36 4.24
5012 5419 2.416027 GCTTGTGTAGAGCGAGATGTCA 60.416 50.000 0.00 0.00 0.00 3.58
5036 5443 2.529632 AGTCACCTGTGCAGATACTGA 58.470 47.619 0.02 0.00 32.44 3.41
5063 5470 7.940137 GGTCAGTAAAGGAGAGTAGATGATCTA 59.060 40.741 0.00 0.00 0.00 1.98
5071 5478 6.998074 AGGAGAGTAGATGATCTAAGACAGTG 59.002 42.308 3.31 0.00 29.58 3.66
5074 5481 5.204292 AGTAGATGATCTAAGACAGTGGCA 58.796 41.667 3.31 0.00 29.58 4.92
5084 5498 6.401394 TCTAAGACAGTGGCATGCATATATC 58.599 40.000 21.36 10.95 0.00 1.63
5102 5516 2.743636 TCTGCAGCTGTACCTGTAAC 57.256 50.000 16.64 0.00 35.28 2.50
5104 5518 0.963225 TGCAGCTGTACCTGTAACGA 59.037 50.000 16.64 0.00 35.28 3.85
5109 5523 5.561773 GCAGCTGTACCTGTAACGAAAGTT 61.562 45.833 16.64 0.00 44.08 2.66
5126 5541 7.651788 ACGAAAGTTTTGTGCATGAACACATC 61.652 38.462 5.84 0.00 46.59 3.06
5156 5571 4.354208 AGAAGATACTCCCTTTCCTGGA 57.646 45.455 0.00 0.00 0.00 3.86
5226 5641 5.691305 TCAAAATTCAGCCATTTTCTTGTCG 59.309 36.000 0.00 0.00 34.70 4.35
5358 5778 3.378112 CCACAATTATGAAGCGTCATGGT 59.622 43.478 23.20 13.39 44.49 3.55
5428 5848 0.178932 TATGGACGAGGATCCCCTGG 60.179 60.000 8.55 0.00 44.53 4.45
5432 5852 4.050313 CGAGGATCCCCTGGTGAA 57.950 61.111 8.55 0.00 44.53 3.18
5433 5853 1.522569 CGAGGATCCCCTGGTGAAC 59.477 63.158 8.55 0.00 44.53 3.18
5434 5854 1.522569 GAGGATCCCCTGGTGAACG 59.477 63.158 8.55 0.00 44.53 3.95
5435 5855 1.972660 GAGGATCCCCTGGTGAACGG 61.973 65.000 8.55 0.00 44.53 4.44
5436 5856 2.124695 GATCCCCTGGTGAACGGC 60.125 66.667 0.00 0.00 0.00 5.68
5437 5857 2.933287 ATCCCCTGGTGAACGGCA 60.933 61.111 0.00 0.00 0.00 5.69
5438 5858 3.268103 ATCCCCTGGTGAACGGCAC 62.268 63.158 2.44 2.44 46.98 5.01
5453 5873 0.671781 GGCACTTCGCTGACTGACAT 60.672 55.000 0.00 0.00 41.91 3.06
5461 5881 1.681666 CTGACTGACATGTGGGCCT 59.318 57.895 1.15 0.00 0.00 5.19
5497 5917 3.112075 CGGCACTGGCTGTACGTG 61.112 66.667 0.00 0.00 41.67 4.49
5498 5918 2.342279 GGCACTGGCTGTACGTGA 59.658 61.111 0.00 0.00 40.87 4.35
5499 5919 1.738099 GGCACTGGCTGTACGTGAG 60.738 63.158 0.00 0.00 40.87 3.51
5500 5920 1.289066 GCACTGGCTGTACGTGAGA 59.711 57.895 0.00 0.00 36.96 3.27
5501 5921 0.734253 GCACTGGCTGTACGTGAGAG 60.734 60.000 0.00 0.00 36.96 3.20
5502 5922 0.109086 CACTGGCTGTACGTGAGAGG 60.109 60.000 0.00 0.00 0.00 3.69
5503 5923 0.251209 ACTGGCTGTACGTGAGAGGA 60.251 55.000 0.00 0.00 0.00 3.71
5504 5924 0.453793 CTGGCTGTACGTGAGAGGAG 59.546 60.000 0.00 0.00 0.00 3.69
5505 5925 1.139947 GGCTGTACGTGAGAGGAGC 59.860 63.158 0.00 0.00 0.00 4.70
5535 5955 2.236146 TGACCTTATTCCGTGTGCATCT 59.764 45.455 0.00 0.00 0.00 2.90
5536 5956 2.609459 GACCTTATTCCGTGTGCATCTG 59.391 50.000 0.00 0.00 0.00 2.90
5537 5957 2.236146 ACCTTATTCCGTGTGCATCTGA 59.764 45.455 0.00 0.00 0.00 3.27
5543 5963 0.319813 CCGTGTGCATCTGACAGTCA 60.320 55.000 2.48 2.48 0.00 3.41
5544 5964 1.673923 CCGTGTGCATCTGACAGTCAT 60.674 52.381 2.97 0.00 0.00 3.06
5545 5965 1.392510 CGTGTGCATCTGACAGTCATG 59.607 52.381 2.97 1.45 0.00 3.07
5547 5967 2.810274 GTGTGCATCTGACAGTCATGTT 59.190 45.455 2.97 0.00 40.68 2.71
5548 5968 2.809696 TGTGCATCTGACAGTCATGTTG 59.190 45.455 2.97 3.65 40.68 3.33
5549 5969 2.161012 GTGCATCTGACAGTCATGTTGG 59.839 50.000 2.97 0.00 40.68 3.77
5550 5970 1.131883 GCATCTGACAGTCATGTTGGC 59.868 52.381 2.97 0.69 40.68 4.52
5551 5971 2.708051 CATCTGACAGTCATGTTGGCT 58.292 47.619 2.97 0.00 40.68 4.75
5552 5972 2.936919 TCTGACAGTCATGTTGGCTT 57.063 45.000 2.97 0.00 40.68 4.35
5553 5973 3.213206 TCTGACAGTCATGTTGGCTTT 57.787 42.857 2.97 0.00 40.68 3.51
5554 5974 3.141398 TCTGACAGTCATGTTGGCTTTC 58.859 45.455 2.97 0.00 40.68 2.62
5555 5975 1.872952 TGACAGTCATGTTGGCTTTCG 59.127 47.619 0.00 0.00 40.68 3.46
5590 6149 8.789767 ATAAGGTTTCTCTAGATCATCCTTCA 57.210 34.615 16.96 8.95 35.91 3.02
5593 6152 6.052360 GGTTTCTCTAGATCATCCTTCAACC 58.948 44.000 0.00 0.00 0.00 3.77
5681 6242 4.401202 TGTCTGCATCGTATGGACTCTTTA 59.599 41.667 0.00 0.00 0.00 1.85
5699 6260 1.567504 TAAAATCTAGGTGAGCGCGC 58.432 50.000 26.66 26.66 0.00 6.86
5730 6291 1.341383 GGCATCAAGGTCCCTGTTGAT 60.341 52.381 3.12 1.57 42.84 2.57
5743 6304 3.244911 CCCTGTTGATGAAGGTGGTAGTT 60.245 47.826 0.00 0.00 0.00 2.24
5757 6318 3.678548 GTGGTAGTTGTCTTCGTCATTCC 59.321 47.826 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.792633 TGCTAGTGCTAGTTTGTTTTCAAATAT 58.207 29.630 7.90 0.00 44.20 1.28
14 15 8.073768 GTGCTAGTGCTAGTTTGTTTTCAAATA 58.926 33.333 7.90 0.00 44.20 1.40
15 16 6.918022 GTGCTAGTGCTAGTTTGTTTTCAAAT 59.082 34.615 7.90 0.00 44.20 2.32
16 17 6.127869 TGTGCTAGTGCTAGTTTGTTTTCAAA 60.128 34.615 7.90 0.00 42.34 2.69
17 18 5.355630 TGTGCTAGTGCTAGTTTGTTTTCAA 59.644 36.000 7.90 0.00 40.48 2.69
18 19 4.878971 TGTGCTAGTGCTAGTTTGTTTTCA 59.121 37.500 7.90 0.00 40.48 2.69
19 20 5.205565 GTGTGCTAGTGCTAGTTTGTTTTC 58.794 41.667 7.90 0.00 40.48 2.29
20 21 4.638421 TGTGTGCTAGTGCTAGTTTGTTTT 59.362 37.500 7.90 0.00 40.48 2.43
21 22 4.196193 TGTGTGCTAGTGCTAGTTTGTTT 58.804 39.130 7.90 0.00 40.48 2.83
22 23 3.804036 TGTGTGCTAGTGCTAGTTTGTT 58.196 40.909 7.90 0.00 40.48 2.83
23 24 3.469008 TGTGTGCTAGTGCTAGTTTGT 57.531 42.857 7.90 0.00 40.48 2.83
24 25 6.480524 TTAATGTGTGCTAGTGCTAGTTTG 57.519 37.500 7.90 0.00 40.48 2.93
25 26 7.504924 TTTTAATGTGTGCTAGTGCTAGTTT 57.495 32.000 7.90 0.00 40.48 2.66
26 27 7.504924 TTTTTAATGTGTGCTAGTGCTAGTT 57.495 32.000 7.90 0.00 40.48 2.24
311 314 9.670719 CTTCTCCTTGTTTATTTCTTCAGTTTC 57.329 33.333 0.00 0.00 0.00 2.78
377 380 0.684805 TGCACCGGTTTTCCTTGGTT 60.685 50.000 2.97 0.00 32.57 3.67
378 381 0.684805 TTGCACCGGTTTTCCTTGGT 60.685 50.000 2.97 0.00 34.70 3.67
383 386 0.458260 ACTGTTTGCACCGGTTTTCC 59.542 50.000 2.97 0.00 0.00 3.13
420 423 4.607955 CCCGAGTTTTTCCTTCTGTTTTC 58.392 43.478 0.00 0.00 0.00 2.29
425 428 0.517316 CGCCCGAGTTTTTCCTTCTG 59.483 55.000 0.00 0.00 0.00 3.02
427 430 0.604511 TCCGCCCGAGTTTTTCCTTC 60.605 55.000 0.00 0.00 0.00 3.46
429 432 1.003718 CTCCGCCCGAGTTTTTCCT 60.004 57.895 0.00 0.00 33.51 3.36
430 433 3.574780 CTCCGCCCGAGTTTTTCC 58.425 61.111 0.00 0.00 33.51 3.13
451 457 0.250234 TCATGGACCAGCACTGTAGC 59.750 55.000 0.00 0.00 0.00 3.58
452 458 2.768253 TTCATGGACCAGCACTGTAG 57.232 50.000 0.00 0.00 0.00 2.74
453 459 3.500448 TTTTCATGGACCAGCACTGTA 57.500 42.857 0.00 0.00 0.00 2.74
454 460 2.363306 TTTTCATGGACCAGCACTGT 57.637 45.000 0.00 0.00 0.00 3.55
475 481 1.027357 CTGTCCAGCACTGCAGTTTT 58.973 50.000 18.94 5.19 0.00 2.43
481 487 2.745492 GAGCCTGTCCAGCACTGC 60.745 66.667 0.00 0.00 0.00 4.40
528 534 0.179000 ATCTCTCGCCCATTGGTGTC 59.821 55.000 1.20 0.00 43.03 3.67
533 539 2.077413 GAGCTATCTCTCGCCCATTG 57.923 55.000 0.00 0.00 36.42 2.82
588 598 4.011517 TCGGGTTTGGACCTCGGC 62.012 66.667 0.00 0.00 45.75 5.54
625 636 1.416813 CGAGCGATGACTTGGAGTGC 61.417 60.000 0.00 0.00 0.00 4.40
627 638 1.153745 GCGAGCGATGACTTGGAGT 60.154 57.895 0.00 0.00 0.00 3.85
629 640 2.184322 GGCGAGCGATGACTTGGA 59.816 61.111 0.00 0.00 0.00 3.53
707 725 0.765510 GGTGGTTTGGGTCTCTGACT 59.234 55.000 0.00 0.00 32.47 3.41
830 857 1.375140 CTTCGCCTGCTCTGCTTCA 60.375 57.895 0.00 0.00 0.00 3.02
831 858 2.748843 GCTTCGCCTGCTCTGCTTC 61.749 63.158 0.00 0.00 0.00 3.86
841 868 0.040067 CTTTTTCGCTTGCTTCGCCT 60.040 50.000 0.00 0.00 0.00 5.52
893 920 3.056328 GTGCTCCGGCTTTGGGTC 61.056 66.667 0.00 0.00 39.59 4.46
894 921 3.210012 ATGTGCTCCGGCTTTGGGT 62.210 57.895 0.00 0.00 39.59 4.51
905 932 8.024285 GGTAGTAGTAGTGATAATCATGTGCTC 58.976 40.741 0.00 0.00 0.00 4.26
909 936 7.174599 GTCCGGTAGTAGTAGTGATAATCATGT 59.825 40.741 0.00 0.00 0.00 3.21
945 972 4.065088 CTCTCTCTCTCTCTAATCCGTGG 58.935 52.174 0.00 0.00 0.00 4.94
1215 1259 0.666577 CAAGCAAAAGCAGCAGGAGC 60.667 55.000 0.00 0.00 42.56 4.70
1216 1260 0.038526 CCAAGCAAAAGCAGCAGGAG 60.039 55.000 0.00 0.00 33.07 3.69
1217 1261 1.466025 CCCAAGCAAAAGCAGCAGGA 61.466 55.000 0.00 0.00 33.07 3.86
1582 1628 2.437359 ACCAGCTCGATGGCAAGC 60.437 61.111 4.93 1.37 44.80 4.01
1583 1629 1.088340 CAGACCAGCTCGATGGCAAG 61.088 60.000 4.93 0.00 44.80 4.01
1584 1630 1.078918 CAGACCAGCTCGATGGCAA 60.079 57.895 4.93 0.00 44.80 4.52
1585 1631 1.332889 ATCAGACCAGCTCGATGGCA 61.333 55.000 4.93 0.00 44.80 4.92
1586 1632 0.179062 AATCAGACCAGCTCGATGGC 60.179 55.000 4.93 0.00 44.80 4.40
1587 1633 1.134580 ACAATCAGACCAGCTCGATGG 60.135 52.381 3.43 3.43 46.47 3.51
1588 1634 1.931841 CACAATCAGACCAGCTCGATG 59.068 52.381 0.00 0.00 0.00 3.84
1589 1635 1.741732 GCACAATCAGACCAGCTCGAT 60.742 52.381 0.00 0.00 0.00 3.59
1590 1636 0.390340 GCACAATCAGACCAGCTCGA 60.390 55.000 0.00 0.00 0.00 4.04
1591 1637 1.364626 GGCACAATCAGACCAGCTCG 61.365 60.000 0.00 0.00 0.00 5.03
1592 1638 1.364626 CGGCACAATCAGACCAGCTC 61.365 60.000 0.00 0.00 0.00 4.09
1593 1639 1.376424 CGGCACAATCAGACCAGCT 60.376 57.895 0.00 0.00 0.00 4.24
1611 1657 0.250467 TCAGTGGTCCAAGCAGAAGC 60.250 55.000 0.00 0.00 42.56 3.86
1634 1680 7.709613 ACATGGTTTATCCGAATTACTCAGTAC 59.290 37.037 0.00 0.00 39.52 2.73
1657 1708 5.753438 ACGATTCTGAACGCATGTATTACAT 59.247 36.000 3.40 3.40 39.91 2.29
1662 1713 5.323900 CAAAACGATTCTGAACGCATGTAT 58.676 37.500 10.70 0.00 0.00 2.29
1664 1715 3.554524 CAAAACGATTCTGAACGCATGT 58.445 40.909 10.70 0.00 0.00 3.21
1665 1716 2.339400 GCAAAACGATTCTGAACGCATG 59.661 45.455 10.70 0.00 0.00 4.06
1666 1717 2.226437 AGCAAAACGATTCTGAACGCAT 59.774 40.909 10.70 1.08 0.00 4.73
1667 1718 1.601903 AGCAAAACGATTCTGAACGCA 59.398 42.857 10.70 0.00 0.00 5.24
1668 1719 2.234187 GAGCAAAACGATTCTGAACGC 58.766 47.619 10.70 0.00 0.00 4.84
1669 1720 2.096909 ACGAGCAAAACGATTCTGAACG 60.097 45.455 9.66 9.66 34.70 3.95
1674 1725 1.455786 CGACACGAGCAAAACGATTCT 59.544 47.619 0.00 0.00 34.70 2.40
1681 1732 1.484227 CGACACCGACACGAGCAAAA 61.484 55.000 0.00 0.00 38.22 2.44
1687 1738 4.379143 CGAGCGACACCGACACGA 62.379 66.667 0.00 0.00 38.22 4.35
1695 1746 0.992802 GGAACTGATTCGAGCGACAC 59.007 55.000 0.00 0.00 35.48 3.67
1732 1784 0.599204 TCGAAACAGCCAGTTCGGAC 60.599 55.000 11.81 0.00 40.26 4.79
1734 1786 1.128692 GATTCGAAACAGCCAGTTCGG 59.871 52.381 0.00 0.26 40.26 4.30
1756 1808 2.671130 TACACATGAGCAGCATCGAA 57.329 45.000 0.00 0.00 34.15 3.71
1757 1809 2.896745 ATACACATGAGCAGCATCGA 57.103 45.000 0.00 0.00 34.15 3.59
1775 1827 5.643777 CAGGATTCGTTCAACCAACTCTTAT 59.356 40.000 0.00 0.00 32.09 1.73
1776 1828 4.994852 CAGGATTCGTTCAACCAACTCTTA 59.005 41.667 0.00 0.00 32.09 2.10
1777 1829 3.815401 CAGGATTCGTTCAACCAACTCTT 59.185 43.478 0.00 0.00 32.09 2.85
1781 1833 1.399727 CGCAGGATTCGTTCAACCAAC 60.400 52.381 0.00 0.00 0.00 3.77
1800 1852 1.739466 CCAATCCACAACCATCTGTCG 59.261 52.381 0.00 0.00 0.00 4.35
1804 1856 0.706433 AGCCCAATCCACAACCATCT 59.294 50.000 0.00 0.00 0.00 2.90
1822 1874 9.035607 CAGCAATAGTTGTACTCTTATACCAAG 57.964 37.037 0.00 0.00 0.00 3.61
1850 1902 2.660553 TTTCGGTTTGCGCTGCACTG 62.661 55.000 9.73 7.82 38.71 3.66
1851 1903 2.477176 TTTCGGTTTGCGCTGCACT 61.477 52.632 9.73 0.00 38.71 4.40
1855 1907 1.438710 CTCGTTTCGGTTTGCGCTG 60.439 57.895 9.73 0.00 0.00 5.18
1856 1908 2.604174 CCTCGTTTCGGTTTGCGCT 61.604 57.895 9.73 0.00 0.00 5.92
1857 1909 2.127383 CCTCGTTTCGGTTTGCGC 60.127 61.111 0.00 0.00 0.00 6.09
1858 1910 2.127383 GCCTCGTTTCGGTTTGCG 60.127 61.111 0.00 0.00 0.00 4.85
1862 1920 2.251642 GCACTGCCTCGTTTCGGTT 61.252 57.895 0.00 0.00 0.00 4.44
1893 1951 3.577334 TAGGCCGCCAAACCCCAAG 62.577 63.158 13.15 0.00 0.00 3.61
1946 2004 2.137810 TCCCCAAAATTCTTAGGGCG 57.862 50.000 0.00 0.00 40.07 6.13
1951 2009 5.815233 TTGTGCAATCCCCAAAATTCTTA 57.185 34.783 0.00 0.00 0.00 2.10
1952 2010 4.703379 TTGTGCAATCCCCAAAATTCTT 57.297 36.364 0.00 0.00 0.00 2.52
1956 2014 5.832060 TCAAAAATTGTGCAATCCCCAAAAT 59.168 32.000 0.00 0.00 0.00 1.82
2021 2080 3.183976 GCGATACTGAATGTGCATCTCAG 59.816 47.826 16.69 16.69 41.93 3.35
2025 2084 4.302455 AGTAGCGATACTGAATGTGCATC 58.698 43.478 13.47 0.00 0.00 3.91
2106 2165 3.542648 AGATGCAGATGATGGAGTTGTG 58.457 45.455 0.00 0.00 30.11 3.33
2114 2173 6.446781 AACCAGTTTAAGATGCAGATGATG 57.553 37.500 0.00 0.00 0.00 3.07
2135 2196 8.887036 AATTGTACCAGAATTTCAAAGGAAAC 57.113 30.769 8.86 7.32 45.22 2.78
2147 2208 7.560991 TGGCAATCAGAATAATTGTACCAGAAT 59.439 33.333 0.00 0.00 36.65 2.40
2222 2322 8.336080 GGCTACAGTTTTATGATAAACTAGCAC 58.664 37.037 18.29 6.88 44.21 4.40
2253 2353 6.183360 GCCACAATACGTGTTTTAAGCTATCT 60.183 38.462 0.00 0.00 44.78 1.98
2287 2387 7.690952 TGCAACGAGTTATTTATTTTACCCT 57.309 32.000 0.00 0.00 0.00 4.34
2296 2396 9.263538 TCTTAGAAACTTGCAACGAGTTATTTA 57.736 29.630 2.78 0.00 36.38 1.40
2336 2440 7.506114 TGAACTCGGCTTCTATTTGGTATTAT 58.494 34.615 0.00 0.00 0.00 1.28
2337 2441 6.880484 TGAACTCGGCTTCTATTTGGTATTA 58.120 36.000 0.00 0.00 0.00 0.98
2346 2450 3.947834 CCCAAATTGAACTCGGCTTCTAT 59.052 43.478 0.00 0.00 0.00 1.98
2357 2461 3.230976 ACTGGTTCCTCCCAAATTGAAC 58.769 45.455 0.00 0.00 37.08 3.18
2362 2466 2.965147 CAACAACTGGTTCCTCCCAAAT 59.035 45.455 0.00 0.00 37.72 2.32
2414 2602 5.069119 GGGGAATTTGTGAAGATAATCCCAC 59.931 44.000 9.53 0.00 35.51 4.61
2433 2621 2.465010 TAAGCCAGACGGAGGGGGAA 62.465 60.000 0.00 0.00 0.00 3.97
2441 2629 4.762765 ACTATCAGTCTATAAGCCAGACGG 59.237 45.833 0.00 0.00 45.76 4.79
2443 2631 6.712998 TCTCACTATCAGTCTATAAGCCAGAC 59.287 42.308 0.00 0.00 42.30 3.51
2493 2682 8.194104 ACTTAACACAAAAATGTACAGATTGCA 58.806 29.630 14.50 0.00 30.75 4.08
2494 2683 8.479280 CACTTAACACAAAAATGTACAGATTGC 58.521 33.333 14.50 0.00 30.75 3.56
2502 2691 9.593134 AGCAAATTCACTTAACACAAAAATGTA 57.407 25.926 0.00 0.00 30.75 2.29
2503 2692 8.389603 CAGCAAATTCACTTAACACAAAAATGT 58.610 29.630 0.00 0.00 0.00 2.71
2506 2695 7.897575 ACAGCAAATTCACTTAACACAAAAA 57.102 28.000 0.00 0.00 0.00 1.94
2507 2696 7.897575 AACAGCAAATTCACTTAACACAAAA 57.102 28.000 0.00 0.00 0.00 2.44
2511 2700 8.289618 TCTGATAACAGCAAATTCACTTAACAC 58.710 33.333 0.00 0.00 43.17 3.32
2529 2730 5.819379 TGATCTTGCCATCTTGTCTGATAAC 59.181 40.000 0.00 0.00 0.00 1.89
2565 2766 6.042208 GCAAATAGAGGGACTAATGTAGGTCT 59.958 42.308 0.00 0.00 41.55 3.85
2651 2857 3.556213 CCAGAAACCCACATCTGTAACGA 60.556 47.826 0.00 0.00 41.16 3.85
2652 2858 2.742053 CCAGAAACCCACATCTGTAACG 59.258 50.000 2.51 0.00 41.16 3.18
2662 2868 4.321974 CCAAAAGCTATTCCAGAAACCCAC 60.322 45.833 0.00 0.00 0.00 4.61
2678 2884 3.056588 TGCAAATGATTCCCCAAAAGC 57.943 42.857 0.00 0.00 0.00 3.51
2699 2905 4.694760 ACTCATGCTTATAGTGATGCCA 57.305 40.909 0.00 0.00 0.00 4.92
2736 2942 5.888691 AACATGGTGCATTAATCGTACAA 57.111 34.783 0.00 0.00 0.00 2.41
2776 3003 8.537728 TGCTATCCTTTGAATGTTATGGAAAT 57.462 30.769 0.00 0.00 0.00 2.17
2780 3007 7.775120 AGTTTGCTATCCTTTGAATGTTATGG 58.225 34.615 0.00 0.00 0.00 2.74
2790 3017 7.830739 AGATGGTAAAAGTTTGCTATCCTTTG 58.169 34.615 12.38 0.00 40.04 2.77
2837 3065 7.713507 CGGAGTCTTGTAATGGGATTTTGTATA 59.286 37.037 0.00 0.00 0.00 1.47
2855 3092 4.794278 AAAACCAAAACAACGGAGTCTT 57.206 36.364 0.00 0.00 45.00 3.01
2856 3093 4.337274 CCTAAAACCAAAACAACGGAGTCT 59.663 41.667 0.00 0.00 45.00 3.24
2857 3094 4.336153 TCCTAAAACCAAAACAACGGAGTC 59.664 41.667 0.00 0.00 45.00 3.36
2859 3096 4.904253 TCCTAAAACCAAAACAACGGAG 57.096 40.909 0.00 0.00 0.00 4.63
2861 3098 4.986034 GGAATCCTAAAACCAAAACAACGG 59.014 41.667 0.00 0.00 0.00 4.44
2864 3101 6.800072 ACTGGAATCCTAAAACCAAAACAA 57.200 33.333 0.00 0.00 31.85 2.83
2878 3115 7.065923 GGTTAGAACATTAGTGAACTGGAATCC 59.934 40.741 0.00 0.00 0.00 3.01
2886 3123 8.828688 AAGTAGTGGTTAGAACATTAGTGAAC 57.171 34.615 0.00 0.00 0.00 3.18
2900 3137 3.007614 GGCACCTGAAGAAGTAGTGGTTA 59.992 47.826 0.00 0.00 0.00 2.85
2953 3190 2.945668 GACTGCAATGTTCCCATAGACC 59.054 50.000 0.00 0.00 0.00 3.85
2976 3213 0.304705 GCAACAACCACGACTGTCAG 59.695 55.000 8.73 0.00 0.00 3.51
3014 3251 5.798934 GCATGATGAACAGAATCTTTGTGAC 59.201 40.000 0.00 0.00 0.00 3.67
3053 3290 3.365364 CCAAGAAAGATTGTGAAGGCGAC 60.365 47.826 0.00 0.00 0.00 5.19
3059 3296 5.047566 TGGACTCCAAGAAAGATTGTGAA 57.952 39.130 0.00 0.00 0.00 3.18
3223 3460 1.346068 GAAACAGGAGCTGTCCAGAGT 59.654 52.381 0.00 0.00 44.62 3.24
3265 3502 1.603172 CCATCGCCGACAAGGAGTATC 60.603 57.143 0.00 0.00 45.00 2.24
3298 3535 2.102420 CACAACTATGAGCACCCCGATA 59.898 50.000 0.00 0.00 0.00 2.92
3304 3541 1.594862 GCGATCACAACTATGAGCACC 59.405 52.381 0.00 0.00 34.60 5.01
3472 3709 1.340017 GCAACTGTCCAGAAGGCCATA 60.340 52.381 5.01 0.00 33.74 2.74
3514 3751 2.149973 AATCCATGAAGTGCCCTTCC 57.850 50.000 6.47 0.00 45.45 3.46
3664 3901 3.083600 GAATGCTTCGACGGTGCCG 62.084 63.158 9.29 9.29 46.03 5.69
3667 3904 0.439985 CACAGAATGCTTCGACGGTG 59.560 55.000 0.00 0.00 42.53 4.94
3668 3905 0.670546 CCACAGAATGCTTCGACGGT 60.671 55.000 0.00 0.00 42.53 4.83
3697 3934 3.565214 TCACCGAAAGCTGGCCCA 61.565 61.111 0.00 0.00 0.00 5.36
3709 3946 0.890542 CCCCCATGCATATGTCACCG 60.891 60.000 0.00 0.00 32.21 4.94
3898 4135 4.016706 CAGAACGCCTTCCCCCGT 62.017 66.667 0.00 0.00 39.70 5.28
3946 4183 4.467084 GCCATCCCGCGGAGAACA 62.467 66.667 30.73 4.78 34.05 3.18
4033 4270 1.336440 CATGAACCAGCAACCAACGAA 59.664 47.619 0.00 0.00 0.00 3.85
4036 4273 0.318120 CCCATGAACCAGCAACCAAC 59.682 55.000 0.00 0.00 0.00 3.77
4168 4411 6.314784 GGTTGTCACTAATGCTGATAAACAC 58.685 40.000 0.00 0.00 29.39 3.32
4192 4440 3.044986 CAAAACACCAATGCAGACTTCG 58.955 45.455 0.00 0.00 0.00 3.79
4193 4441 2.796593 GCAAAACACCAATGCAGACTTC 59.203 45.455 0.00 0.00 39.81 3.01
4217 4465 5.759763 CCAATAGGCAGTTTGCTTTTCTTTT 59.240 36.000 0.67 0.00 44.28 2.27
4221 4490 3.989817 CACCAATAGGCAGTTTGCTTTTC 59.010 43.478 0.67 0.00 44.28 2.29
4229 4498 5.361285 TGTAAACAAACACCAATAGGCAGTT 59.639 36.000 0.00 0.00 37.87 3.16
4234 4503 8.194769 ACTTCTTTGTAAACAAACACCAATAGG 58.805 33.333 4.19 0.00 40.55 2.57
4295 4654 6.823689 ACTACCTAAAATGTCAAGTGGCATAG 59.176 38.462 0.00 0.00 39.84 2.23
4376 4739 7.775053 ATTTCACTAAAGGCAATGTAAAGGA 57.225 32.000 0.00 0.00 0.00 3.36
4522 4921 5.896073 ATAACAGTATCTCCCTCCCTTTG 57.104 43.478 0.00 0.00 0.00 2.77
4562 4961 3.848272 ATAATTGTTGTTGGACCGCTG 57.152 42.857 0.00 0.00 0.00 5.18
4628 5031 8.537049 CAACATTGCAATATGAAGGAAAAGAA 57.463 30.769 12.53 0.00 0.00 2.52
4662 5065 1.729276 CGGCCACGCAATCATCATT 59.271 52.632 2.24 0.00 0.00 2.57
4734 5137 1.679032 GGTATCAGTGTTCCCAGGTGC 60.679 57.143 0.00 0.00 0.00 5.01
4767 5170 4.100981 GCTAGTGCTTGGAGCTCG 57.899 61.111 7.83 0.00 42.97 5.03
4809 5212 1.890979 GAGCAGGATCGCACATGGG 60.891 63.158 0.00 0.00 0.00 4.00
4824 5227 2.563179 TGAAGAATCTATAGCCCCGAGC 59.437 50.000 0.00 0.00 44.25 5.03
4826 5229 4.114015 TCTGAAGAATCTATAGCCCCGA 57.886 45.455 0.00 0.00 0.00 5.14
4919 5325 1.228583 ACCTCGACTCTGACTGGCA 60.229 57.895 0.00 0.00 0.00 4.92
4920 5326 1.214062 CACCTCGACTCTGACTGGC 59.786 63.158 0.00 0.00 0.00 4.85
4921 5327 1.214062 GCACCTCGACTCTGACTGG 59.786 63.158 0.00 0.00 0.00 4.00
5012 5419 4.026744 AGTATCTGCACAGGTGACTATGT 58.973 43.478 3.10 0.00 37.14 2.29
5036 5443 6.080969 TCATCTACTCTCCTTTACTGACCT 57.919 41.667 0.00 0.00 0.00 3.85
5044 5451 8.058847 ACTGTCTTAGATCATCTACTCTCCTTT 58.941 37.037 0.00 0.00 0.00 3.11
5052 5459 5.521906 TGCCACTGTCTTAGATCATCTAC 57.478 43.478 0.00 0.00 0.00 2.59
5063 5470 5.001874 CAGATATATGCATGCCACTGTCTT 58.998 41.667 16.68 0.00 0.00 3.01
5084 5498 1.067846 TCGTTACAGGTACAGCTGCAG 60.068 52.381 15.27 10.11 0.00 4.41
5102 5516 3.856521 TGTGTTCATGCACAAAACTTTCG 59.143 39.130 0.00 0.00 45.17 3.46
5129 5544 7.730784 CCAGGAAAGGGAGTATCTTCTATTCTA 59.269 40.741 0.00 0.00 33.73 2.10
5135 5550 4.354208 TCCAGGAAAGGGAGTATCTTCT 57.646 45.455 0.00 0.00 33.73 2.85
5142 5557 3.879321 GCAATTCATCCAGGAAAGGGAGT 60.879 47.826 0.00 0.00 37.96 3.85
5143 5558 2.692041 GCAATTCATCCAGGAAAGGGAG 59.308 50.000 0.00 0.00 37.96 4.30
5156 5571 1.033746 CGTGGGAGGCAGCAATTCAT 61.034 55.000 0.00 0.00 0.00 2.57
5242 5657 3.969976 AGGCATCCTCTTTGAGCTGTATA 59.030 43.478 0.00 0.00 0.00 1.47
5318 5738 6.502136 TTGTGGCAATCGTAATAATTGTCA 57.498 33.333 0.00 0.00 44.17 3.58
5435 5855 0.441533 CATGTCAGTCAGCGAAGTGC 59.558 55.000 0.00 0.00 46.98 4.40
5436 5856 1.458445 CACATGTCAGTCAGCGAAGTG 59.542 52.381 0.00 0.00 0.00 3.16
5437 5857 1.606480 CCACATGTCAGTCAGCGAAGT 60.606 52.381 0.00 0.00 0.00 3.01
5438 5858 1.073964 CCACATGTCAGTCAGCGAAG 58.926 55.000 0.00 0.00 0.00 3.79
5446 5866 2.034687 GCAGGCCCACATGTCAGT 59.965 61.111 0.00 0.00 0.00 3.41
5479 5899 3.612681 ACGTACAGCCAGTGCCGT 61.613 61.111 0.00 0.00 38.69 5.68
5480 5900 3.112075 CACGTACAGCCAGTGCCG 61.112 66.667 0.00 0.00 38.69 5.69
5481 5901 1.738099 CTCACGTACAGCCAGTGCC 60.738 63.158 0.00 0.00 38.69 5.01
5483 5903 0.109086 CCTCTCACGTACAGCCAGTG 60.109 60.000 0.00 0.00 37.24 3.66
5484 5904 0.251209 TCCTCTCACGTACAGCCAGT 60.251 55.000 0.00 0.00 0.00 4.00
5485 5905 0.453793 CTCCTCTCACGTACAGCCAG 59.546 60.000 0.00 0.00 0.00 4.85
5486 5906 1.595993 GCTCCTCTCACGTACAGCCA 61.596 60.000 0.00 0.00 0.00 4.75
5487 5907 1.139947 GCTCCTCTCACGTACAGCC 59.860 63.158 0.00 0.00 0.00 4.85
5489 5909 1.429825 CGGCTCCTCTCACGTACAG 59.570 63.158 0.00 0.00 0.00 2.74
5490 5910 2.044555 CCGGCTCCTCTCACGTACA 61.045 63.158 0.00 0.00 0.00 2.90
5491 5911 1.102222 ATCCGGCTCCTCTCACGTAC 61.102 60.000 0.00 0.00 0.00 3.67
5492 5912 0.818445 GATCCGGCTCCTCTCACGTA 60.818 60.000 0.00 0.00 0.00 3.57
5494 5914 2.725008 GATCCGGCTCCTCTCACG 59.275 66.667 0.00 0.00 0.00 4.35
5495 5915 2.851071 CGGATCCGGCTCCTCTCAC 61.851 68.421 26.95 0.00 35.56 3.51
5496 5916 2.519541 CGGATCCGGCTCCTCTCA 60.520 66.667 26.95 0.00 35.56 3.27
5497 5917 2.519780 ACGGATCCGGCTCCTCTC 60.520 66.667 35.87 0.00 44.69 3.20
5498 5918 2.835431 CACGGATCCGGCTCCTCT 60.835 66.667 35.87 12.31 44.69 3.69
5499 5919 2.833582 TCACGGATCCGGCTCCTC 60.834 66.667 35.87 3.88 44.69 3.71
5500 5920 3.148279 GTCACGGATCCGGCTCCT 61.148 66.667 35.87 13.89 44.69 3.69
5501 5921 4.222847 GGTCACGGATCCGGCTCC 62.223 72.222 35.87 27.68 44.69 4.70
5502 5922 1.389609 TAAGGTCACGGATCCGGCTC 61.390 60.000 35.87 23.60 44.69 4.70
5503 5923 0.759436 ATAAGGTCACGGATCCGGCT 60.759 55.000 35.87 15.50 44.69 5.52
5504 5924 0.106149 AATAAGGTCACGGATCCGGC 59.894 55.000 35.87 24.31 44.69 6.13
5505 5925 1.270147 GGAATAAGGTCACGGATCCGG 60.270 57.143 35.87 24.50 44.69 5.14
5535 5955 1.872952 CGAAAGCCAACATGACTGTCA 59.127 47.619 13.60 13.60 33.36 3.58
5536 5956 2.601481 CGAAAGCCAACATGACTGTC 57.399 50.000 0.00 0.00 33.36 3.51
5553 5973 0.244450 AACCTTATTCGTCACCGCGA 59.756 50.000 8.23 0.00 39.28 5.87
5554 5974 1.060122 GAAACCTTATTCGTCACCGCG 59.940 52.381 0.00 0.00 0.00 6.46
5555 5975 2.344025 AGAAACCTTATTCGTCACCGC 58.656 47.619 0.00 0.00 34.46 5.68
5681 6242 1.090052 GGCGCGCTCACCTAGATTTT 61.090 55.000 32.29 0.00 0.00 1.82
5713 6274 3.308688 CCTTCATCAACAGGGACCTTGAT 60.309 47.826 11.16 6.13 36.89 2.57
5730 6291 2.696707 ACGAAGACAACTACCACCTTCA 59.303 45.455 0.00 0.00 34.51 3.02
5743 6304 1.480954 GGGCTAGGAATGACGAAGACA 59.519 52.381 0.00 0.00 36.25 3.41
5757 6318 1.760029 GAGGACAAGGAGAAGGGCTAG 59.240 57.143 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.