Multiple sequence alignment - TraesCS6A01G068500

Loading Multiple Alignment...

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 TraesCS6A01G068500 chr6A 100.000 3391 0 0 374 3764 36946919 36950309 0.000000e+00 6263.0
1 TraesCS6A01G068500 chr6A 82.192 438 46 8 1151 1588 479105267 479104862 7.740000e-92 348.0
2 TraesCS6A01G068500 chr6A 86.319 307 40 2 1346 1651 479397770 479398075 2.170000e-87 333.0
3 TraesCS6A01G068500 chr6A 87.963 216 17 3 374 589 36941975 36942181 2.900000e-61 246.0
4 TraesCS6A01G068500 chr6A 78.385 384 59 9 1043 1426 577295055 577294696 1.050000e-55 228.0
5 TraesCS6A01G068500 chr6A 76.702 382 65 14 1043 1424 577497065 577496708 1.380000e-44 191.0
6 TraesCS6A01G068500 chr6A 100.000 37 0 0 1 37 36946546 36946582 6.750000e-08 69.4
7 TraesCS6A01G068500 chr6B 89.466 2003 93 43 909 2849 68292183 68294129 0.000000e+00 2422.0
8 TraesCS6A01G068500 chr6D 90.498 1526 81 30 374 1886 32458191 32459665 0.000000e+00 1956.0
9 TraesCS6A01G068500 chr6D 88.103 933 47 28 2016 2922 32459691 32460585 0.000000e+00 1050.0
10 TraesCS6A01G068500 chr6D 89.350 723 58 9 3042 3757 32460701 32461411 0.000000e+00 891.0
11 TraesCS6A01G068500 chr6D 79.651 516 68 22 1001 1514 62244510 62244030 1.670000e-88 337.0
12 TraesCS6A01G068500 chr7D 82.090 469 48 15 1122 1588 514661916 514661482 5.940000e-98 368.0
13 TraesCS6A01G068500 chr7D 80.473 169 8 9 1259 1427 430406370 430406227 5.140000e-19 106.0
14 TraesCS6A01G068500 chr7D 78.912 147 29 2 3599 3743 11680317 11680171 8.600000e-17 99.0
15 TraesCS6A01G068500 chr7D 77.711 166 28 8 3597 3756 617833807 617833969 4.000000e-15 93.5
16 TraesCS6A01G068500 chr4B 80.460 522 59 26 910 1426 580959806 580960289 3.570000e-95 359.0
17 TraesCS6A01G068500 chr1A 82.529 435 44 8 1151 1585 14356713 14357115 1.660000e-93 353.0
18 TraesCS6A01G068500 chr1A 82.099 162 19 7 3598 3755 566080290 566080135 3.050000e-26 130.0
19 TraesCS6A01G068500 chr1B 82.299 435 45 8 1151 1585 531115925 531116327 7.740000e-92 348.0
20 TraesCS6A01G068500 chr5A 80.328 427 57 15 1090 1514 155216929 155216528 7.900000e-77 298.0
21 TraesCS6A01G068500 chr2D 81.250 384 51 9 1043 1426 231721031 231721393 1.320000e-74 291.0
22 TraesCS6A01G068500 chr2D 86.594 276 22 7 1151 1426 245324922 245325182 1.320000e-74 291.0
23 TraesCS6A01G068500 chr5B 87.166 187 21 2 1700 1886 166694401 166694218 3.810000e-50 209.0
24 TraesCS6A01G068500 chr7A 86.184 152 21 0 1369 1520 95950178 95950027 8.360000e-37 165.0
25 TraesCS6A01G068500 chr5D 83.333 162 19 6 3598 3756 511950710 511950554 3.920000e-30 143.0
26 TraesCS6A01G068500 chr5D 78.616 159 31 3 3599 3755 278283938 278283781 6.650000e-18 102.0
27 TraesCS6A01G068500 chr7B 83.125 160 19 6 3598 3755 62810654 62810807 5.070000e-29 139.0
28 TraesCS6A01G068500 chr3A 81.818 165 16 7 3598 3758 427763957 427763803 3.950000e-25 126.0
29 TraesCS6A01G068500 chr3A 84.348 115 12 3 3598 3710 20350339 20350229 1.430000e-19 108.0
30 TraesCS6A01G068500 chr2A 87.654 81 10 0 1044 1124 191906007 191906087 1.110000e-15 95.3


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 TraesCS6A01G068500 chr6A 36946546 36950309 3763 False 3166.2 6263 100.000 1 3764 2 chr6A.!!$F3 3763
1 TraesCS6A01G068500 chr6B 68292183 68294129 1946 False 2422.0 2422 89.466 909 2849 1 chr6B.!!$F1 1940
2 TraesCS6A01G068500 chr6D 32458191 32461411 3220 False 1299.0 1956 89.317 374 3757 3 chr6D.!!$F1 3383

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
550 554 0.108585 ATCGGTGGCCCATCATACAC 59.891 55.0 0.0 0.0 0.0 2.90 F
1742 1790 0.179073 ATTCAGCCGTCTTGATCGGG 60.179 55.0 6.5 0.0 46.9 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2049 0.037232 CCACCTCTCTCCAAACCGAC 60.037 60.0 0.0 0.0 0.00 4.79 R
2938 3101 0.036765 CCCTTCGATCAAACGTGGGA 60.037 55.0 0.0 0.0 43.91 4.37 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
21 22 3.279434 GGTGCTTGGTTACTATGGAAGG 58.721 50.000 0.00 0.00 0.00 3.46
22 23 2.683362 GTGCTTGGTTACTATGGAAGGC 59.317 50.000 0.00 0.00 0.00 4.35
23 24 2.576191 TGCTTGGTTACTATGGAAGGCT 59.424 45.455 0.00 0.00 0.00 4.58
24 25 3.778075 TGCTTGGTTACTATGGAAGGCTA 59.222 43.478 0.00 0.00 0.00 3.93
25 26 4.141711 TGCTTGGTTACTATGGAAGGCTAG 60.142 45.833 0.00 0.00 0.00 3.42
26 27 4.743955 GCTTGGTTACTATGGAAGGCTAGG 60.744 50.000 0.00 0.00 0.00 3.02
27 28 4.274794 TGGTTACTATGGAAGGCTAGGA 57.725 45.455 0.00 0.00 0.00 2.94
28 29 4.627015 TGGTTACTATGGAAGGCTAGGAA 58.373 43.478 0.00 0.00 0.00 3.36
29 30 5.224441 TGGTTACTATGGAAGGCTAGGAAT 58.776 41.667 0.00 0.00 0.00 3.01
30 31 5.670361 TGGTTACTATGGAAGGCTAGGAATT 59.330 40.000 0.00 0.00 0.00 2.17
31 32 6.159751 TGGTTACTATGGAAGGCTAGGAATTT 59.840 38.462 0.00 0.00 0.00 1.82
32 33 7.061054 GGTTACTATGGAAGGCTAGGAATTTT 58.939 38.462 0.00 0.00 0.00 1.82
33 34 7.228906 GGTTACTATGGAAGGCTAGGAATTTTC 59.771 40.741 0.00 0.00 0.00 2.29
417 418 2.886587 AAAAACGCCTTCGGATTACG 57.113 45.000 0.00 0.00 46.11 3.18
513 516 4.778534 ATCTTGCATTTGGTGAGTCAAG 57.221 40.909 0.00 0.00 34.04 3.02
523 527 0.538287 GTGAGTCAAGCTGCCCCTTT 60.538 55.000 0.00 0.00 0.00 3.11
525 529 0.884514 GAGTCAAGCTGCCCCTTTTC 59.115 55.000 0.00 0.00 0.00 2.29
531 535 3.157087 CAAGCTGCCCCTTTTCTTAGAA 58.843 45.455 0.00 0.00 0.00 2.10
532 536 3.746792 AGCTGCCCCTTTTCTTAGAAT 57.253 42.857 0.00 0.00 0.00 2.40
536 540 2.307686 TGCCCCTTTTCTTAGAATCGGT 59.692 45.455 0.00 0.00 0.00 4.69
538 542 3.279434 CCCCTTTTCTTAGAATCGGTGG 58.721 50.000 0.00 0.56 0.00 4.61
539 543 2.683362 CCCTTTTCTTAGAATCGGTGGC 59.317 50.000 0.00 0.00 0.00 5.01
547 551 1.434188 AGAATCGGTGGCCCATCATA 58.566 50.000 0.00 0.00 0.00 2.15
550 554 0.108585 ATCGGTGGCCCATCATACAC 59.891 55.000 0.00 0.00 0.00 2.90
551 555 1.223211 CGGTGGCCCATCATACACA 59.777 57.895 0.00 0.00 35.62 3.72
552 556 1.095228 CGGTGGCCCATCATACACAC 61.095 60.000 0.00 0.00 35.62 3.82
554 558 1.615651 GGTGGCCCATCATACACACAA 60.616 52.381 0.00 0.00 35.62 3.33
558 562 3.290710 GGCCCATCATACACACAAGAAT 58.709 45.455 0.00 0.00 0.00 2.40
559 563 3.067180 GGCCCATCATACACACAAGAATG 59.933 47.826 0.00 0.00 0.00 2.67
560 564 3.696051 GCCCATCATACACACAAGAATGT 59.304 43.478 0.00 0.00 41.61 2.71
561 565 4.881273 GCCCATCATACACACAAGAATGTA 59.119 41.667 0.00 0.00 37.82 2.29
562 566 5.356751 GCCCATCATACACACAAGAATGTAA 59.643 40.000 0.00 0.00 37.82 2.41
563 567 6.127758 GCCCATCATACACACAAGAATGTAAA 60.128 38.462 0.00 0.00 37.82 2.01
564 568 7.416664 GCCCATCATACACACAAGAATGTAAAT 60.417 37.037 0.00 0.00 37.82 1.40
565 569 7.916977 CCCATCATACACACAAGAATGTAAATG 59.083 37.037 0.00 0.00 37.82 2.32
566 570 8.676401 CCATCATACACACAAGAATGTAAATGA 58.324 33.333 9.77 0.00 37.82 2.57
609 613 1.068055 CCTTGAAATGTGCACAGGAGC 60.068 52.381 25.84 14.24 0.00 4.70
611 615 0.250252 TGAAATGTGCACAGGAGCGA 60.250 50.000 25.84 3.87 37.31 4.93
612 616 0.445436 GAAATGTGCACAGGAGCGAG 59.555 55.000 25.84 0.00 37.31 5.03
613 617 0.957395 AAATGTGCACAGGAGCGAGG 60.957 55.000 25.84 0.00 37.31 4.63
614 618 1.830587 AATGTGCACAGGAGCGAGGA 61.831 55.000 25.84 0.00 37.31 3.71
615 619 2.125753 GTGCACAGGAGCGAGGAG 60.126 66.667 13.17 0.00 37.31 3.69
616 620 2.283173 TGCACAGGAGCGAGGAGA 60.283 61.111 0.00 0.00 37.31 3.71
617 621 1.908299 TGCACAGGAGCGAGGAGAA 60.908 57.895 0.00 0.00 37.31 2.87
663 670 0.736053 CGTCGAAGGAGAAGAGGAGG 59.264 60.000 0.00 0.00 0.00 4.30
665 672 2.021457 GTCGAAGGAGAAGAGGAGGAG 58.979 57.143 0.00 0.00 0.00 3.69
825 832 4.838152 CACCTGTCATCCGCCCCG 62.838 72.222 0.00 0.00 0.00 5.73
922 929 5.873179 TCCTCGCTATTAAACCAAAACAG 57.127 39.130 0.00 0.00 0.00 3.16
1452 1493 1.548973 CCGCCTCGATTCCGATTTCG 61.549 60.000 0.00 0.00 44.62 3.46
1473 1514 0.596600 GCTCCTCGTTGACGTGTTCA 60.597 55.000 0.00 0.00 40.80 3.18
1479 1520 1.068474 CGTTGACGTGTTCATCCTCC 58.932 55.000 0.00 0.00 32.84 4.30
1557 1601 1.227089 CGAGAACGCCCATCTCCTG 60.227 63.158 0.00 0.00 40.16 3.86
1571 1615 2.432628 CCTGAAGGTCCGTGACGC 60.433 66.667 0.00 0.00 32.65 5.19
1687 1734 1.271379 CATGGATTGGATTGGCCGATG 59.729 52.381 11.28 0.00 41.10 3.84
1702 1749 1.825285 CGATGAGCTCCGGCGATTTG 61.825 60.000 9.30 0.00 44.37 2.32
1742 1790 0.179073 ATTCAGCCGTCTTGATCGGG 60.179 55.000 6.50 0.00 46.90 5.14
1783 1831 1.696097 AACACTGTTCCCCGCTCACT 61.696 55.000 0.00 0.00 0.00 3.41
1784 1832 1.669115 CACTGTTCCCCGCTCACTG 60.669 63.158 0.00 0.00 0.00 3.66
1889 1937 3.077617 GAGCAAGGTGATGAGCTCC 57.922 57.895 12.15 0.00 45.79 4.70
1895 1943 1.383803 GGTGATGAGCTCCCCTCCT 60.384 63.158 12.15 0.00 39.98 3.69
1898 1946 1.841103 GATGAGCTCCCCTCCTCCC 60.841 68.421 12.15 0.00 39.98 4.30
1905 1953 0.267356 CTCCCCTCCTCCCAATCTCT 59.733 60.000 0.00 0.00 0.00 3.10
1937 1985 1.154150 GATCGGTCGGTCGTTCGTT 60.154 57.895 0.00 1.73 0.00 3.85
1954 2002 0.730494 GTTCGTTCGATCCGGTTCGT 60.730 55.000 28.80 3.13 40.03 3.85
1961 2009 1.541147 TCGATCCGGTTCGTTGTTACT 59.459 47.619 28.80 0.00 40.03 2.24
1963 2011 2.680577 GATCCGGTTCGTTGTTACTGT 58.319 47.619 0.00 0.00 0.00 3.55
1964 2012 3.670359 CGATCCGGTTCGTTGTTACTGTA 60.670 47.826 23.70 0.00 34.46 2.74
2000 2049 3.874873 TTGCGGTGCAATCTCTCG 58.125 55.556 0.00 0.00 43.99 4.04
2001 2050 1.005037 TTGCGGTGCAATCTCTCGT 60.005 52.632 0.00 0.00 43.99 4.18
2002 2051 1.014044 TTGCGGTGCAATCTCTCGTC 61.014 55.000 0.00 0.00 43.99 4.20
2003 2052 2.508891 GCGGTGCAATCTCTCGTCG 61.509 63.158 0.00 0.00 0.00 5.12
2004 2053 1.874019 CGGTGCAATCTCTCGTCGG 60.874 63.158 0.00 0.00 0.00 4.79
2005 2054 1.215647 GGTGCAATCTCTCGTCGGT 59.784 57.895 0.00 0.00 0.00 4.69
2006 2055 0.389948 GGTGCAATCTCTCGTCGGTT 60.390 55.000 0.00 0.00 0.00 4.44
2007 2056 1.429463 GTGCAATCTCTCGTCGGTTT 58.571 50.000 0.00 0.00 0.00 3.27
2008 2057 1.126846 GTGCAATCTCTCGTCGGTTTG 59.873 52.381 0.00 0.00 0.00 2.93
2009 2058 0.721718 GCAATCTCTCGTCGGTTTGG 59.278 55.000 0.00 0.00 0.00 3.28
2010 2059 1.671850 GCAATCTCTCGTCGGTTTGGA 60.672 52.381 0.00 0.00 0.00 3.53
2011 2060 2.263077 CAATCTCTCGTCGGTTTGGAG 58.737 52.381 0.00 0.00 0.00 3.86
2012 2061 1.835494 ATCTCTCGTCGGTTTGGAGA 58.165 50.000 0.00 0.00 37.44 3.71
2013 2062 3.704381 CTCTCGTCGGTTTGGAGAG 57.296 57.895 3.22 3.22 45.36 3.20
2014 2063 3.334413 TCTCGTCGGTTTGGAGAGA 57.666 52.632 0.00 0.00 35.83 3.10
2015 2064 1.166129 TCTCGTCGGTTTGGAGAGAG 58.834 55.000 0.00 0.00 33.58 3.20
2058 2107 1.238439 CATTGACCACGCCAAGTTCT 58.762 50.000 0.00 0.00 0.00 3.01
2090 2152 1.379642 GCGGCTTCCTTTCCTGGATG 61.380 60.000 0.00 0.00 35.83 3.51
2126 2189 4.729856 GTGTCGCCCGCTAACCGT 62.730 66.667 0.00 0.00 34.38 4.83
2129 2192 1.659644 GTCGCCCGCTAACCGTATC 60.660 63.158 0.00 0.00 34.38 2.24
2131 2194 2.414594 GCCCGCTAACCGTATCGT 59.585 61.111 0.00 0.00 34.38 3.73
2225 2288 3.151022 GAGGAGGACGAGGGGCAG 61.151 72.222 0.00 0.00 0.00 4.85
2240 2303 4.950479 CAGCGGAGATGGAAGCTT 57.050 55.556 0.00 0.00 42.04 3.74
2242 2305 0.107993 CAGCGGAGATGGAAGCTTCA 60.108 55.000 27.02 13.98 42.04 3.02
2490 2559 1.339151 GGCGGCAAGGATAAGGATAGG 60.339 57.143 3.07 0.00 0.00 2.57
2559 2630 2.281070 AGTTGAGGCGTGCTGGTG 60.281 61.111 0.00 0.00 0.00 4.17
2560 2631 2.280797 GTTGAGGCGTGCTGGTGA 60.281 61.111 0.00 0.00 0.00 4.02
2604 2677 1.007964 TGCGACGCCATTTTGGTTG 60.008 52.632 18.69 0.00 40.46 3.77
2669 2752 4.624882 CGCGAGGTGGTAGTATACTAGTAG 59.375 50.000 12.99 0.00 42.51 2.57
2670 2753 5.546526 GCGAGGTGGTAGTATACTAGTAGT 58.453 45.833 12.99 8.14 42.51 2.73
2671 2754 6.570571 CGCGAGGTGGTAGTATACTAGTAGTA 60.571 46.154 12.99 12.38 42.51 1.82
2672 2755 7.327214 GCGAGGTGGTAGTATACTAGTAGTAT 58.673 42.308 23.09 23.09 43.36 2.12
2673 2756 8.470805 GCGAGGTGGTAGTATACTAGTAGTATA 58.529 40.741 21.27 21.27 41.36 1.47
2788 2875 8.918202 ACATTCATGAATACCGGTATTATGTT 57.082 30.769 34.18 23.13 36.02 2.71
2789 2876 8.783093 ACATTCATGAATACCGGTATTATGTTG 58.217 33.333 34.18 29.78 36.02 3.33
2790 2877 8.998377 CATTCATGAATACCGGTATTATGTTGA 58.002 33.333 34.18 27.79 36.02 3.18
2797 2884 8.752766 AATACCGGTATTATGTTGAGTATTCG 57.247 34.615 33.45 0.00 34.27 3.34
2807 2894 3.615056 TGTTGAGTATTCGTTATGGCGTG 59.385 43.478 0.00 0.00 0.00 5.34
2819 2906 0.178068 ATGGCGTGTATGAGTGGGTC 59.822 55.000 0.00 0.00 0.00 4.46
2838 2925 3.636764 GGTCAGTGTGTTCATCCCTTTTT 59.363 43.478 0.00 0.00 0.00 1.94
2886 2976 9.405587 TGAAATCGTATTGGAAGATTGTTTTTC 57.594 29.630 0.00 0.00 36.51 2.29
2888 2978 8.970691 AATCGTATTGGAAGATTGTTTTTCTG 57.029 30.769 0.00 0.00 35.26 3.02
2889 2979 6.908825 TCGTATTGGAAGATTGTTTTTCTGG 58.091 36.000 0.00 0.00 0.00 3.86
2904 2994 5.710513 TTTTCTGGACTGATGGAATGTTG 57.289 39.130 0.00 0.00 0.00 3.33
2912 3003 0.734889 GATGGAATGTTGGCACTCCG 59.265 55.000 0.00 0.00 43.48 4.63
2922 3013 2.558313 GCACTCCGTCAGCTTTGC 59.442 61.111 0.00 0.00 0.00 3.68
2923 3014 2.856032 CACTCCGTCAGCTTTGCG 59.144 61.111 0.00 0.00 0.00 4.85
2933 3096 2.412089 GTCAGCTTTGCGTCGTTAGATT 59.588 45.455 0.00 0.00 0.00 2.40
2938 3101 3.810373 CTTTGCGTCGTTAGATTTGCTT 58.190 40.909 0.00 0.00 0.00 3.91
2939 3102 3.449322 TTGCGTCGTTAGATTTGCTTC 57.551 42.857 0.00 0.00 0.00 3.86
2952 3115 0.871722 TTGCTTCCCACGTTTGATCG 59.128 50.000 0.00 0.00 0.00 3.69
2963 3126 1.606994 CGTTTGATCGAAGGGTGGTGA 60.607 52.381 7.40 0.00 0.00 4.02
2964 3127 1.804748 GTTTGATCGAAGGGTGGTGAC 59.195 52.381 0.00 0.00 0.00 3.67
2965 3128 1.348064 TTGATCGAAGGGTGGTGACT 58.652 50.000 0.00 0.00 0.00 3.41
2966 3129 0.608130 TGATCGAAGGGTGGTGACTG 59.392 55.000 0.00 0.00 0.00 3.51
2967 3130 0.895530 GATCGAAGGGTGGTGACTGA 59.104 55.000 0.00 0.00 0.00 3.41
2968 3131 0.898320 ATCGAAGGGTGGTGACTGAG 59.102 55.000 0.00 0.00 0.00 3.35
2969 3132 1.374758 CGAAGGGTGGTGACTGAGC 60.375 63.158 0.00 0.00 0.00 4.26
2970 3133 1.374758 GAAGGGTGGTGACTGAGCG 60.375 63.158 0.00 0.00 0.00 5.03
2971 3134 2.100879 GAAGGGTGGTGACTGAGCGT 62.101 60.000 0.00 0.00 0.00 5.07
2972 3135 1.696097 AAGGGTGGTGACTGAGCGTT 61.696 55.000 0.00 0.00 0.00 4.84
2973 3136 1.961277 GGGTGGTGACTGAGCGTTG 60.961 63.158 0.00 0.00 0.00 4.10
2974 3137 1.227556 GGTGGTGACTGAGCGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
2975 3138 0.032952 GGTGGTGACTGAGCGTTGTA 59.967 55.000 0.00 0.00 0.00 2.41
2976 3139 1.137513 GTGGTGACTGAGCGTTGTAC 58.862 55.000 0.00 0.00 0.00 2.90
2977 3140 0.032952 TGGTGACTGAGCGTTGTACC 59.967 55.000 0.00 0.00 0.00 3.34
2978 3141 1.007336 GGTGACTGAGCGTTGTACCG 61.007 60.000 0.00 0.00 0.00 4.02
2979 3142 1.007336 GTGACTGAGCGTTGTACCGG 61.007 60.000 0.00 0.00 0.00 5.28
2980 3143 1.288127 GACTGAGCGTTGTACCGGT 59.712 57.895 13.98 13.98 41.92 5.28
2981 3144 0.523072 GACTGAGCGTTGTACCGGTA 59.477 55.000 11.16 11.16 38.89 4.02
2982 3145 1.133790 GACTGAGCGTTGTACCGGTAT 59.866 52.381 19.19 0.00 38.89 2.73
2983 3146 1.133790 ACTGAGCGTTGTACCGGTATC 59.866 52.381 19.19 10.61 38.89 2.24
2984 3147 0.099259 TGAGCGTTGTACCGGTATCG 59.901 55.000 19.19 21.59 38.89 2.92
2985 3148 0.099436 GAGCGTTGTACCGGTATCGT 59.901 55.000 19.19 12.76 38.89 3.73
2986 3149 1.330521 GAGCGTTGTACCGGTATCGTA 59.669 52.381 19.19 2.10 38.89 3.43
2987 3150 1.064060 AGCGTTGTACCGGTATCGTAC 59.936 52.381 19.19 7.63 36.69 3.67
2988 3151 1.202132 GCGTTGTACCGGTATCGTACA 60.202 52.381 19.19 10.61 34.07 2.90
2989 3152 2.730715 GCGTTGTACCGGTATCGTACAA 60.731 50.000 19.19 16.46 38.82 2.41
2990 3153 3.497118 CGTTGTACCGGTATCGTACAAA 58.503 45.455 19.19 1.78 40.59 2.83
2991 3154 3.917380 CGTTGTACCGGTATCGTACAAAA 59.083 43.478 19.19 0.00 40.59 2.44
2992 3155 4.384247 CGTTGTACCGGTATCGTACAAAAA 59.616 41.667 19.19 0.00 40.59 1.94
3015 3178 6.942532 AAAAAGTTGTAGCACTTCTCATCA 57.057 33.333 0.00 0.00 35.87 3.07
3016 3179 5.931441 AAAGTTGTAGCACTTCTCATCAC 57.069 39.130 0.00 0.00 35.87 3.06
3017 3180 3.931578 AGTTGTAGCACTTCTCATCACC 58.068 45.455 0.00 0.00 0.00 4.02
3018 3181 3.324846 AGTTGTAGCACTTCTCATCACCA 59.675 43.478 0.00 0.00 0.00 4.17
3019 3182 4.019860 AGTTGTAGCACTTCTCATCACCAT 60.020 41.667 0.00 0.00 0.00 3.55
3020 3183 3.865446 TGTAGCACTTCTCATCACCATG 58.135 45.455 0.00 0.00 0.00 3.66
3021 3184 3.261643 TGTAGCACTTCTCATCACCATGT 59.738 43.478 0.00 0.00 0.00 3.21
3022 3185 2.708051 AGCACTTCTCATCACCATGTG 58.292 47.619 0.00 0.00 34.45 3.21
3023 3186 2.303890 AGCACTTCTCATCACCATGTGA 59.696 45.455 0.00 0.00 46.90 3.58
3024 3187 3.076621 GCACTTCTCATCACCATGTGAA 58.923 45.455 0.46 0.00 45.96 3.18
3025 3188 3.503363 GCACTTCTCATCACCATGTGAAA 59.497 43.478 0.46 0.00 45.96 2.69
3026 3189 4.614535 GCACTTCTCATCACCATGTGAAAC 60.615 45.833 0.46 0.00 45.96 2.78
3027 3190 4.758674 CACTTCTCATCACCATGTGAAACT 59.241 41.667 0.46 0.00 45.96 2.66
3028 3191 4.758674 ACTTCTCATCACCATGTGAAACTG 59.241 41.667 0.46 0.00 45.96 3.16
3029 3192 3.076621 TCTCATCACCATGTGAAACTGC 58.923 45.455 0.46 0.00 45.96 4.40
3030 3193 3.079578 CTCATCACCATGTGAAACTGCT 58.920 45.455 0.46 0.00 45.96 4.24
3031 3194 2.815503 TCATCACCATGTGAAACTGCTG 59.184 45.455 0.46 0.00 45.96 4.41
3032 3195 2.346766 TCACCATGTGAAACTGCTGT 57.653 45.000 0.00 0.00 39.78 4.40
3033 3196 1.948834 TCACCATGTGAAACTGCTGTG 59.051 47.619 0.00 0.00 39.78 3.66
3034 3197 0.670162 ACCATGTGAAACTGCTGTGC 59.330 50.000 0.00 0.00 38.04 4.57
3035 3198 0.669619 CCATGTGAAACTGCTGTGCA 59.330 50.000 0.00 0.00 38.04 4.57
3036 3199 1.601162 CCATGTGAAACTGCTGTGCAC 60.601 52.381 10.75 10.75 38.04 4.57
3037 3200 1.065851 CATGTGAAACTGCTGTGCACA 59.934 47.619 24.51 24.51 42.35 4.57
3038 3201 0.451383 TGTGAAACTGCTGTGCACAC 59.549 50.000 17.42 13.56 37.37 3.82
3039 3202 0.589729 GTGAAACTGCTGTGCACACG 60.590 55.000 17.42 13.34 34.50 4.49
3040 3203 1.024046 TGAAACTGCTGTGCACACGT 61.024 50.000 17.42 10.56 33.79 4.49
3046 3209 2.901840 CTGTGCACACGTTGGCCT 60.902 61.111 17.42 0.00 0.00 5.19
3081 3244 0.791422 CCGTTTTGTTGCCATGCATG 59.209 50.000 20.19 20.19 38.76 4.06
3092 3256 3.930400 CATGCATGGACGGTTGATG 57.070 52.632 19.40 0.00 0.00 3.07
3100 3264 0.893727 GGACGGTTGATGGGCTTGTT 60.894 55.000 0.00 0.00 0.00 2.83
3102 3266 0.467290 ACGGTTGATGGGCTTGTTGT 60.467 50.000 0.00 0.00 0.00 3.32
3120 3284 1.234821 GTCCAAAATCGTGTGCAGGA 58.765 50.000 0.00 0.00 0.00 3.86
3126 3290 1.361668 AATCGTGTGCAGGATGTCGC 61.362 55.000 7.95 0.00 39.31 5.19
3167 3331 1.446366 GGAGACCATAAGCCGGACC 59.554 63.158 5.05 0.00 0.00 4.46
3169 3333 2.041206 GAGACCATAAGCCGGACCCC 62.041 65.000 5.05 0.00 0.00 4.95
3175 3339 0.977108 ATAAGCCGGACCCCGTTACA 60.977 55.000 5.05 0.00 46.80 2.41
3187 3351 2.322081 CGTTACACGGGGCTTGTGG 61.322 63.158 12.83 0.00 41.64 4.17
3197 3361 0.965439 GGGCTTGTGGTGCACATAAA 59.035 50.000 20.43 8.10 44.16 1.40
3267 3431 7.962964 AATATGTCAGGGATACACAATAACG 57.037 36.000 0.00 0.00 39.74 3.18
3299 3464 1.742750 GCGGGGAGATACACAAGAACC 60.743 57.143 0.00 0.00 0.00 3.62
3400 3565 1.229428 ATGACCCAATATGAAGCGCG 58.771 50.000 0.00 0.00 0.00 6.86
3422 3587 4.644954 GGCTTACATTGCGTACTGTTTAC 58.355 43.478 1.23 0.00 0.00 2.01
3490 3655 9.764363 GGATTTAGAGTATTGTGACATGATACA 57.236 33.333 0.00 0.69 0.00 2.29
3517 3684 9.926158 TGCTTGTATTATCAATGACATTTGTTT 57.074 25.926 0.00 0.00 0.00 2.83
3560 3727 1.780503 AGCATTTATGGGAGTTGGGC 58.219 50.000 0.00 0.00 0.00 5.36
3564 3731 2.143575 TTTATGGGAGTTGGGCGCCA 62.144 55.000 30.85 12.04 38.95 5.69
3582 3749 3.202001 CGCACACCATAAGCCCCG 61.202 66.667 0.00 0.00 0.00 5.73
3584 3751 2.994699 CACACCATAAGCCCCGGA 59.005 61.111 0.73 0.00 0.00 5.14
3699 3867 1.175983 TGAAACCCGTGTGCCCAATC 61.176 55.000 0.00 0.00 0.00 2.67
3718 3886 8.470002 GCCCAATCTACTTTCATGTCTAATTTT 58.530 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.279434 CCTTCCATAGTAACCAAGCACC 58.721 50.000 0.00 0.00 0.00 5.01
1 2 2.683362 GCCTTCCATAGTAACCAAGCAC 59.317 50.000 0.00 0.00 0.00 4.40
2 3 2.576191 AGCCTTCCATAGTAACCAAGCA 59.424 45.455 0.00 0.00 0.00 3.91
3 4 3.283259 AGCCTTCCATAGTAACCAAGC 57.717 47.619 0.00 0.00 0.00 4.01
4 5 4.654262 TCCTAGCCTTCCATAGTAACCAAG 59.346 45.833 0.00 0.00 0.00 3.61
5 6 4.627015 TCCTAGCCTTCCATAGTAACCAA 58.373 43.478 0.00 0.00 0.00 3.67
6 7 4.274794 TCCTAGCCTTCCATAGTAACCA 57.725 45.455 0.00 0.00 0.00 3.67
7 8 5.827326 ATTCCTAGCCTTCCATAGTAACC 57.173 43.478 0.00 0.00 0.00 2.85
8 9 7.228906 GGAAAATTCCTAGCCTTCCATAGTAAC 59.771 40.741 4.91 0.00 44.11 2.50
9 10 7.287810 GGAAAATTCCTAGCCTTCCATAGTAA 58.712 38.462 4.91 0.00 44.11 2.24
10 11 6.463897 CGGAAAATTCCTAGCCTTCCATAGTA 60.464 42.308 10.31 0.00 45.33 1.82
11 12 5.687706 CGGAAAATTCCTAGCCTTCCATAGT 60.688 44.000 10.31 0.00 45.33 2.12
12 13 4.757149 CGGAAAATTCCTAGCCTTCCATAG 59.243 45.833 10.31 0.00 45.33 2.23
13 14 4.445735 CCGGAAAATTCCTAGCCTTCCATA 60.446 45.833 10.31 0.00 45.33 2.74
14 15 3.555966 CGGAAAATTCCTAGCCTTCCAT 58.444 45.455 10.31 0.00 45.33 3.41
15 16 2.356741 CCGGAAAATTCCTAGCCTTCCA 60.357 50.000 10.31 0.00 45.33 3.53
16 17 2.298610 CCGGAAAATTCCTAGCCTTCC 58.701 52.381 10.31 0.00 45.33 3.46
492 495 3.057033 GCTTGACTCACCAAATGCAAGAT 60.057 43.478 0.00 0.00 35.89 2.40
493 496 2.294233 GCTTGACTCACCAAATGCAAGA 59.706 45.455 0.00 0.00 35.89 3.02
494 497 2.295349 AGCTTGACTCACCAAATGCAAG 59.705 45.455 0.00 0.00 36.67 4.01
495 498 2.034939 CAGCTTGACTCACCAAATGCAA 59.965 45.455 0.00 0.00 0.00 4.08
503 506 2.360475 GGGGCAGCTTGACTCACC 60.360 66.667 0.00 0.00 0.00 4.02
513 516 2.356069 CGATTCTAAGAAAAGGGGCAGC 59.644 50.000 0.00 0.00 0.00 5.25
523 527 1.281419 TGGGCCACCGATTCTAAGAA 58.719 50.000 0.00 0.00 40.75 2.52
525 529 1.140852 TGATGGGCCACCGATTCTAAG 59.859 52.381 9.28 0.00 40.75 2.18
531 535 0.108585 GTGTATGATGGGCCACCGAT 59.891 55.000 9.28 3.38 40.75 4.18
532 536 1.268283 TGTGTATGATGGGCCACCGA 61.268 55.000 9.28 0.00 40.75 4.69
536 540 1.632920 TCTTGTGTGTATGATGGGCCA 59.367 47.619 9.61 9.61 0.00 5.36
538 542 3.696051 ACATTCTTGTGTGTATGATGGGC 59.304 43.478 0.00 0.00 33.85 5.36
539 543 7.389803 TTTACATTCTTGTGTGTATGATGGG 57.610 36.000 0.00 0.00 36.53 4.00
574 578 7.913297 CACATTTCAAGGTTTTCTCTCGTTTTA 59.087 33.333 0.00 0.00 0.00 1.52
647 651 1.064314 TCCTCCTCCTCTTCTCCTTCG 60.064 57.143 0.00 0.00 0.00 3.79
652 656 2.838637 TTCCTCCTCCTCCTCTTCTC 57.161 55.000 0.00 0.00 0.00 2.87
663 670 1.219393 CCGCCTGTCTTTCCTCCTC 59.781 63.158 0.00 0.00 0.00 3.71
665 672 1.219393 CTCCGCCTGTCTTTCCTCC 59.781 63.158 0.00 0.00 0.00 4.30
719 726 0.539518 GTTTGGTGGGTTTGTTGCCT 59.460 50.000 0.00 0.00 0.00 4.75
722 729 1.406205 GGTGGTTTGGTGGGTTTGTTG 60.406 52.381 0.00 0.00 0.00 3.33
1426 1467 4.162690 AATCGAGGCGGGCTGGAC 62.163 66.667 17.98 0.00 0.00 4.02
1452 1493 0.874607 AACACGTCAACGAGGAGCAC 60.875 55.000 9.88 0.00 43.02 4.40
1473 1514 0.105555 CAGAGGCAGAGGAGGAGGAT 60.106 60.000 0.00 0.00 0.00 3.24
1479 1520 1.067000 CACTGAACAGAGGCAGAGGAG 60.067 57.143 8.87 0.00 36.07 3.69
1557 1601 3.644399 GAGGGCGTCACGGACCTTC 62.644 68.421 0.00 0.00 32.42 3.46
1571 1615 0.888619 GGAAAAGAAAAGGCGGAGGG 59.111 55.000 0.00 0.00 0.00 4.30
1678 1725 4.161295 CCGGAGCTCATCGGCCAA 62.161 66.667 17.19 0.00 39.78 4.52
1683 1730 1.592669 AAATCGCCGGAGCTCATCG 60.593 57.895 17.19 14.79 36.60 3.84
1687 1734 0.521735 AAAACAAATCGCCGGAGCTC 59.478 50.000 5.05 4.71 36.60 4.09
1741 1789 1.305930 GGAACAGTGCCACCGATTCC 61.306 60.000 6.61 6.61 0.00 3.01
1742 1790 0.321653 AGGAACAGTGCCACCGATTC 60.322 55.000 0.00 0.00 0.00 2.52
1889 1937 0.693767 AGCAGAGATTGGGAGGAGGG 60.694 60.000 0.00 0.00 0.00 4.30
1895 1943 0.537188 GGTTCGAGCAGAGATTGGGA 59.463 55.000 0.53 0.00 0.00 4.37
1898 1946 2.266554 GACTGGTTCGAGCAGAGATTG 58.733 52.381 17.10 0.00 45.98 2.67
1928 1976 0.632241 GGATCGAACGAACGAACGAC 59.368 55.000 16.99 12.66 45.16 4.34
1929 1977 0.790495 CGGATCGAACGAACGAACGA 60.790 55.000 20.38 16.98 45.16 3.85
1930 1978 1.617179 CGGATCGAACGAACGAACG 59.383 57.895 15.45 13.98 45.16 3.95
1931 1979 0.730494 ACCGGATCGAACGAACGAAC 60.730 55.000 9.46 9.41 45.16 3.95
1937 1985 0.730155 CAACGAACCGGATCGAACGA 60.730 55.000 36.58 0.00 45.48 3.85
2000 2049 0.037232 CCACCTCTCTCCAAACCGAC 60.037 60.000 0.00 0.00 0.00 4.79
2001 2050 0.178944 TCCACCTCTCTCCAAACCGA 60.179 55.000 0.00 0.00 0.00 4.69
2002 2051 0.037232 GTCCACCTCTCTCCAAACCG 60.037 60.000 0.00 0.00 0.00 4.44
2003 2052 1.276705 GAGTCCACCTCTCTCCAAACC 59.723 57.143 0.00 0.00 37.22 3.27
2004 2053 1.276705 GGAGTCCACCTCTCTCCAAAC 59.723 57.143 3.60 0.00 44.85 2.93
2005 2054 1.645710 GGAGTCCACCTCTCTCCAAA 58.354 55.000 3.60 0.00 44.85 3.28
2006 2055 0.252284 GGGAGTCCACCTCTCTCCAA 60.252 60.000 12.30 0.00 46.61 3.53
2007 2056 1.388531 GGGAGTCCACCTCTCTCCA 59.611 63.158 12.30 0.00 46.61 3.86
2008 2057 1.382009 GGGGAGTCCACCTCTCTCC 60.382 68.421 12.30 0.00 43.98 3.71
2009 2058 1.755008 CGGGGAGTCCACCTCTCTC 60.755 68.421 12.30 0.00 40.85 3.20
2010 2059 1.585651 ATCGGGGAGTCCACCTCTCT 61.586 60.000 12.30 0.00 40.85 3.10
2011 2060 0.688087 AATCGGGGAGTCCACCTCTC 60.688 60.000 12.30 0.00 40.26 3.20
2012 2061 0.688087 GAATCGGGGAGTCCACCTCT 60.688 60.000 12.30 0.00 40.30 3.69
2013 2062 0.976073 TGAATCGGGGAGTCCACCTC 60.976 60.000 12.30 3.68 39.67 3.85
2014 2063 0.546747 TTGAATCGGGGAGTCCACCT 60.547 55.000 12.30 0.00 34.36 4.00
2015 2064 0.546598 ATTGAATCGGGGAGTCCACC 59.453 55.000 12.30 9.00 34.36 4.61
2058 2107 1.104577 AAGCCGCGGAAAACAGGAAA 61.105 50.000 33.48 0.00 0.00 3.13
2126 2189 1.075542 CTTGCCAAGTTCGCACGATA 58.924 50.000 0.00 0.00 35.56 2.92
2129 2192 2.427410 GCTTGCCAAGTTCGCACG 60.427 61.111 6.28 0.00 35.56 5.34
2131 2194 2.590291 TCGCTTGCCAAGTTCGCA 60.590 55.556 6.28 0.00 0.00 5.10
2225 2288 1.435408 GCTGAAGCTTCCATCTCCGC 61.435 60.000 23.42 10.36 38.21 5.54
2226 2289 0.813210 GGCTGAAGCTTCCATCTCCG 60.813 60.000 23.42 4.73 41.70 4.63
2367 2433 3.738246 CTGCTGCTGCTGCTGGTG 61.738 66.667 27.67 13.98 40.48 4.17
2540 2609 3.052082 CCAGCACGCCTCAACTGG 61.052 66.667 0.00 0.00 43.45 4.00
2566 2637 2.124570 CTTGATCCAGCACGGGGG 60.125 66.667 0.00 0.00 34.36 5.40
2604 2677 0.108662 CCTCGCAAAATTCCAAGCCC 60.109 55.000 0.00 0.00 0.00 5.19
2669 2752 4.202131 GCTGGAGTTCTACCACCACTATAC 60.202 50.000 0.00 0.00 33.57 1.47
2670 2753 3.958798 GCTGGAGTTCTACCACCACTATA 59.041 47.826 0.00 0.00 33.57 1.31
2671 2754 2.766828 GCTGGAGTTCTACCACCACTAT 59.233 50.000 0.00 0.00 33.57 2.12
2672 2755 2.176889 GCTGGAGTTCTACCACCACTA 58.823 52.381 0.00 0.00 33.57 2.74
2673 2756 0.977395 GCTGGAGTTCTACCACCACT 59.023 55.000 0.00 0.00 33.57 4.00
2674 2757 0.977395 AGCTGGAGTTCTACCACCAC 59.023 55.000 0.00 0.00 33.57 4.16
2675 2758 2.615986 TAGCTGGAGTTCTACCACCA 57.384 50.000 0.00 0.00 33.57 4.17
2676 2759 2.832733 ACTTAGCTGGAGTTCTACCACC 59.167 50.000 0.00 0.00 33.57 4.61
2788 2875 3.513680 ACACGCCATAACGAATACTCA 57.486 42.857 0.00 0.00 36.70 3.41
2789 2876 5.217393 TCATACACGCCATAACGAATACTC 58.783 41.667 0.00 0.00 36.70 2.59
2790 2877 5.190992 TCATACACGCCATAACGAATACT 57.809 39.130 0.00 0.00 36.70 2.12
2797 2884 2.210116 CCCACTCATACACGCCATAAC 58.790 52.381 0.00 0.00 0.00 1.89
2807 2894 3.244078 TGAACACACTGACCCACTCATAC 60.244 47.826 0.00 0.00 0.00 2.39
2853 2943 9.956720 AATCTTCCAATACGATTTCATCAAATC 57.043 29.630 0.00 0.00 43.21 2.17
2855 2945 8.739039 ACAATCTTCCAATACGATTTCATCAAA 58.261 29.630 0.00 0.00 0.00 2.69
2858 2948 9.573133 AAAACAATCTTCCAATACGATTTCATC 57.427 29.630 0.00 0.00 0.00 2.92
2859 2949 9.927668 AAAAACAATCTTCCAATACGATTTCAT 57.072 25.926 0.00 0.00 0.00 2.57
2861 2951 9.626045 AGAAAAACAATCTTCCAATACGATTTC 57.374 29.630 0.00 0.00 0.00 2.17
2867 2957 7.809806 CAGTCCAGAAAAACAATCTTCCAATAC 59.190 37.037 0.00 0.00 0.00 1.89
2876 2966 5.964958 TCCATCAGTCCAGAAAAACAATC 57.035 39.130 0.00 0.00 0.00 2.67
2879 2969 5.139727 ACATTCCATCAGTCCAGAAAAACA 58.860 37.500 0.00 0.00 0.00 2.83
2886 2976 1.747355 GCCAACATTCCATCAGTCCAG 59.253 52.381 0.00 0.00 0.00 3.86
2888 2978 1.474077 GTGCCAACATTCCATCAGTCC 59.526 52.381 0.00 0.00 0.00 3.85
2889 2979 2.421424 GAGTGCCAACATTCCATCAGTC 59.579 50.000 0.00 0.00 0.00 3.51
2912 3003 1.415374 TCTAACGACGCAAAGCTGAC 58.585 50.000 0.00 0.00 0.00 3.51
2922 3013 2.093783 GTGGGAAGCAAATCTAACGACG 59.906 50.000 0.00 0.00 0.00 5.12
2923 3014 2.093783 CGTGGGAAGCAAATCTAACGAC 59.906 50.000 0.00 0.00 33.17 4.34
2933 3096 0.871722 CGATCAAACGTGGGAAGCAA 59.128 50.000 0.00 0.00 0.00 3.91
2938 3101 0.036765 CCCTTCGATCAAACGTGGGA 60.037 55.000 0.00 0.00 43.91 4.37
2939 3102 0.321298 ACCCTTCGATCAAACGTGGG 60.321 55.000 1.22 1.22 45.23 4.61
2952 3115 1.374758 CGCTCAGTCACCACCCTTC 60.375 63.158 0.00 0.00 0.00 3.46
2963 3126 1.133790 GATACCGGTACAACGCTCAGT 59.866 52.381 18.55 0.00 0.00 3.41
2964 3127 1.836383 GATACCGGTACAACGCTCAG 58.164 55.000 18.55 0.00 0.00 3.35
2965 3128 0.099259 CGATACCGGTACAACGCTCA 59.901 55.000 18.55 0.00 0.00 4.26
2966 3129 0.099436 ACGATACCGGTACAACGCTC 59.901 55.000 26.27 15.83 40.78 5.03
2967 3130 1.064060 GTACGATACCGGTACAACGCT 59.936 52.381 26.27 18.99 40.78 5.07
2968 3131 1.202132 TGTACGATACCGGTACAACGC 60.202 52.381 26.27 16.81 40.78 4.84
2969 3132 2.823196 TGTACGATACCGGTACAACG 57.177 50.000 25.35 25.35 40.78 4.10
2970 3133 5.837586 TTTTTGTACGATACCGGTACAAC 57.162 39.130 18.55 12.82 39.49 3.32
2992 3155 6.238759 GGTGATGAGAAGTGCTACAACTTTTT 60.239 38.462 0.00 0.00 40.48 1.94
2993 3156 5.239525 GGTGATGAGAAGTGCTACAACTTTT 59.760 40.000 0.00 0.00 40.48 2.27
2994 3157 4.757149 GGTGATGAGAAGTGCTACAACTTT 59.243 41.667 0.00 0.00 40.48 2.66
2995 3158 4.202357 TGGTGATGAGAAGTGCTACAACTT 60.202 41.667 0.00 0.00 43.08 2.66
2996 3159 3.324846 TGGTGATGAGAAGTGCTACAACT 59.675 43.478 0.00 0.00 0.00 3.16
2997 3160 3.664107 TGGTGATGAGAAGTGCTACAAC 58.336 45.455 0.00 0.00 0.00 3.32
2998 3161 4.256110 CATGGTGATGAGAAGTGCTACAA 58.744 43.478 0.00 0.00 0.00 2.41
2999 3162 3.261643 ACATGGTGATGAGAAGTGCTACA 59.738 43.478 0.00 0.00 33.36 2.74
3000 3163 3.620374 CACATGGTGATGAGAAGTGCTAC 59.380 47.826 0.00 0.00 35.23 3.58
3001 3164 3.515104 TCACATGGTGATGAGAAGTGCTA 59.485 43.478 0.00 0.00 37.67 3.49
3002 3165 2.303890 TCACATGGTGATGAGAAGTGCT 59.696 45.455 0.00 0.00 37.67 4.40
3003 3166 2.703416 TCACATGGTGATGAGAAGTGC 58.297 47.619 0.00 0.00 37.67 4.40
3004 3167 4.758674 AGTTTCACATGGTGATGAGAAGTG 59.241 41.667 0.00 0.00 42.40 3.16
3005 3168 4.758674 CAGTTTCACATGGTGATGAGAAGT 59.241 41.667 0.00 0.00 42.40 3.01
3006 3169 4.379186 GCAGTTTCACATGGTGATGAGAAG 60.379 45.833 0.00 0.00 42.40 2.85
3007 3170 3.503363 GCAGTTTCACATGGTGATGAGAA 59.497 43.478 0.00 0.00 42.40 2.87
3008 3171 3.076621 GCAGTTTCACATGGTGATGAGA 58.923 45.455 0.00 0.00 42.40 3.27
3009 3172 3.079578 AGCAGTTTCACATGGTGATGAG 58.920 45.455 0.00 0.00 42.40 2.90
3010 3173 2.815503 CAGCAGTTTCACATGGTGATGA 59.184 45.455 0.00 0.00 45.46 2.92
3011 3174 2.555325 ACAGCAGTTTCACATGGTGATG 59.445 45.455 10.95 0.00 45.46 3.07
3012 3175 2.555325 CACAGCAGTTTCACATGGTGAT 59.445 45.455 10.95 0.00 45.46 3.06
3013 3176 1.948834 CACAGCAGTTTCACATGGTGA 59.051 47.619 10.95 0.00 45.46 4.02
3015 3178 0.670162 GCACAGCAGTTTCACATGGT 59.330 50.000 0.00 0.00 0.00 3.55
3016 3179 0.669619 TGCACAGCAGTTTCACATGG 59.330 50.000 0.00 0.00 33.32 3.66
3017 3180 1.065851 TGTGCACAGCAGTTTCACATG 59.934 47.619 17.42 0.00 40.08 3.21
3018 3181 1.066002 GTGTGCACAGCAGTTTCACAT 59.934 47.619 22.40 0.00 40.08 3.21
3019 3182 0.451383 GTGTGCACAGCAGTTTCACA 59.549 50.000 22.40 9.18 40.08 3.58
3020 3183 0.589729 CGTGTGCACAGCAGTTTCAC 60.590 55.000 22.40 3.83 40.08 3.18
3021 3184 1.024046 ACGTGTGCACAGCAGTTTCA 61.024 50.000 22.40 0.00 40.08 2.69
3022 3185 0.098728 AACGTGTGCACAGCAGTTTC 59.901 50.000 22.40 5.45 40.08 2.78
3023 3186 0.179166 CAACGTGTGCACAGCAGTTT 60.179 50.000 22.40 6.15 40.08 2.66
3024 3187 1.429021 CAACGTGTGCACAGCAGTT 59.571 52.632 22.40 22.21 40.08 3.16
3025 3188 2.472059 CCAACGTGTGCACAGCAGT 61.472 57.895 22.40 17.61 40.08 4.40
3026 3189 2.328989 CCAACGTGTGCACAGCAG 59.671 61.111 22.40 16.93 40.08 4.24
3027 3190 3.886694 GCCAACGTGTGCACAGCA 61.887 61.111 22.40 0.00 35.60 4.41
3028 3191 4.629115 GGCCAACGTGTGCACAGC 62.629 66.667 22.40 19.30 0.00 4.40
3029 3192 0.955428 ATAGGCCAACGTGTGCACAG 60.955 55.000 22.40 16.54 0.00 3.66
3030 3193 0.953471 GATAGGCCAACGTGTGCACA 60.953 55.000 17.42 17.42 0.00 4.57
3031 3194 1.794222 GATAGGCCAACGTGTGCAC 59.206 57.895 10.75 10.75 0.00 4.57
3032 3195 1.739929 CGATAGGCCAACGTGTGCA 60.740 57.895 5.01 0.00 0.00 4.57
3033 3196 1.740296 ACGATAGGCCAACGTGTGC 60.740 57.895 18.05 0.00 38.79 4.57
3034 3197 4.590487 ACGATAGGCCAACGTGTG 57.410 55.556 18.05 0.00 38.79 3.82
3037 3200 1.079405 CCACACGATAGGCCAACGT 60.079 57.895 5.01 10.97 43.77 3.99
3038 3201 1.079405 ACCACACGATAGGCCAACG 60.079 57.895 5.01 10.24 43.77 4.10
3039 3202 0.743345 GGACCACACGATAGGCCAAC 60.743 60.000 5.01 0.00 43.77 3.77
3040 3203 1.600107 GGACCACACGATAGGCCAA 59.400 57.895 5.01 0.00 43.77 4.52
3046 3209 3.463585 GGCCCGGACCACACGATA 61.464 66.667 0.73 0.00 0.00 2.92
3081 3244 0.893727 AACAAGCCCATCAACCGTCC 60.894 55.000 0.00 0.00 0.00 4.79
3087 3250 2.079170 TTGGACAACAAGCCCATCAA 57.921 45.000 0.00 0.00 33.18 2.57
3092 3256 1.339929 ACGATTTTGGACAACAAGCCC 59.660 47.619 0.00 0.00 40.82 5.19
3100 3264 0.950836 CCTGCACACGATTTTGGACA 59.049 50.000 0.00 0.00 0.00 4.02
3102 3266 1.811965 CATCCTGCACACGATTTTGGA 59.188 47.619 0.00 0.00 0.00 3.53
3149 3313 1.446366 GGTCCGGCTTATGGTCTCC 59.554 63.158 0.00 0.00 0.00 3.71
3151 3315 2.070650 GGGGTCCGGCTTATGGTCT 61.071 63.158 0.00 0.00 0.00 3.85
3170 3334 1.228033 ACCACAAGCCCCGTGTAAC 60.228 57.895 0.00 0.00 32.26 2.50
3187 3351 7.611213 AACTATCTACAGGTTTTATGTGCAC 57.389 36.000 10.75 10.75 32.02 4.57
3235 3399 9.913310 TGTGTATCCCTGACATATTTTTGATAA 57.087 29.630 0.00 0.00 0.00 1.75
3249 3413 6.469410 AGAAAACGTTATTGTGTATCCCTGA 58.531 36.000 0.00 0.00 0.00 3.86
3322 3487 9.912634 TTTCTCTAGCTATGTTTCAAATTTTGG 57.087 29.630 9.18 0.00 0.00 3.28
3362 3527 9.397280 TGGGTCATTATCGATATTGTTAACAAA 57.603 29.630 23.97 13.85 39.55 2.83
3377 3542 4.436050 CGCGCTTCATATTGGGTCATTATC 60.436 45.833 5.56 0.00 0.00 1.75
3378 3543 3.436704 CGCGCTTCATATTGGGTCATTAT 59.563 43.478 5.56 0.00 0.00 1.28
3379 3544 2.805671 CGCGCTTCATATTGGGTCATTA 59.194 45.455 5.56 0.00 0.00 1.90
3380 3545 1.603802 CGCGCTTCATATTGGGTCATT 59.396 47.619 5.56 0.00 0.00 2.57
3381 3546 1.229428 CGCGCTTCATATTGGGTCAT 58.771 50.000 5.56 0.00 0.00 3.06
3382 3547 0.813610 CCGCGCTTCATATTGGGTCA 60.814 55.000 5.56 0.00 0.00 4.02
3383 3548 1.941812 CCGCGCTTCATATTGGGTC 59.058 57.895 5.56 0.00 0.00 4.46
3384 3549 2.186826 GCCGCGCTTCATATTGGGT 61.187 57.895 5.56 0.00 0.00 4.51
3385 3550 1.447317 AAGCCGCGCTTCATATTGGG 61.447 55.000 5.56 0.00 46.77 4.12
3400 3565 3.824414 AAACAGTACGCAATGTAAGCC 57.176 42.857 0.00 0.00 34.07 4.35
3410 3575 6.196571 ACAAAATCAACAGTAAACAGTACGC 58.803 36.000 0.00 0.00 0.00 4.42
3449 3614 8.918202 ACTCTAAATCCAAATTGTAACACAGA 57.082 30.769 0.00 0.00 0.00 3.41
3463 3628 9.764363 GTATCATGTCACAATACTCTAAATCCA 57.236 33.333 0.00 0.00 0.00 3.41
3532 3699 9.230122 CCAACTCCCATAAATGCTTTTAATTTT 57.770 29.630 8.67 0.00 31.33 1.82
3534 3701 7.337938 CCCAACTCCCATAAATGCTTTTAATT 58.662 34.615 8.67 0.00 31.33 1.40
3535 3702 6.632445 GCCCAACTCCCATAAATGCTTTTAAT 60.632 38.462 8.67 0.00 31.33 1.40
3543 3710 0.385390 GCGCCCAACTCCCATAAATG 59.615 55.000 0.00 0.00 0.00 2.32
3560 3727 2.784596 CTTATGGTGTGCGTGGCG 59.215 61.111 0.00 0.00 0.00 5.69
3564 3731 2.045340 GGGGCTTATGGTGTGCGT 60.045 61.111 0.00 0.00 0.00 5.24
3582 3749 1.966451 CCCACCTCTTGCGTGTTCC 60.966 63.158 0.00 0.00 0.00 3.62
3584 3751 1.525995 CACCCACCTCTTGCGTGTT 60.526 57.895 0.00 0.00 30.45 3.32
3663 3830 4.403734 GTTTCATGTCCCAAAACCCTAGA 58.596 43.478 0.00 0.00 0.00 2.43
3687 3855 2.422597 TGAAAGTAGATTGGGCACACG 58.577 47.619 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.