Multiple sequence alignment - TraesCS6A01G218800

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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 TraesCS6A01G218800 chr6A 100.000 5574 0 0 1 5574 404701439 404695866 0.000000e+00 10294.0
1 TraesCS6A01G218800 chr6D 91.631 4959 182 81 273 5133 284403030 284398207 0.000000e+00 6643.0
2 TraesCS6A01G218800 chr6D 91.353 451 24 7 5135 5574 284398063 284397617 2.220000e-168 603.0
3 TraesCS6A01G218800 chr6D 94.118 119 7 0 107 225 284403150 284403032 1.230000e-41 182.0
4 TraesCS6A01G218800 chr6D 95.890 73 3 0 53 125 284403231 284403159 9.810000e-23 119.0
5 TraesCS6A01G218800 chr6D 100.000 28 0 0 1 28 284403264 284403237 1.000000e-02 52.8
6 TraesCS6A01G218800 chr6B 91.998 2087 90 31 107 2154 445012900 445010852 0.000000e+00 2857.0
7 TraesCS6A01G218800 chr6B 90.060 1821 100 35 2149 3947 445010828 445009067 0.000000e+00 2285.0
8 TraesCS6A01G218800 chr6B 91.029 1438 67 29 4017 5444 445008675 445007290 0.000000e+00 1884.0
9 TraesCS6A01G218800 chr6B 88.966 145 15 1 5430 5574 444923234 444923091 1.600000e-40 178.0
10 TraesCS6A01G218800 chr1B 80.992 121 19 3 2894 3012 608995038 608994920 5.950000e-15 93.5


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 TraesCS6A01G218800 chr6A 404695866 404701439 5573 True 10294.00 10294 100.0000 1 5574 1 chr6A.!!$R1 5573
1 TraesCS6A01G218800 chr6D 284397617 284403264 5647 True 1519.96 6643 94.5984 1 5574 5 chr6D.!!$R1 5573
2 TraesCS6A01G218800 chr6B 445007290 445012900 5610 True 2342.00 2857 91.0290 107 5444 3 chr6B.!!$R2 5337

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
41 42 0.466124 CGAGGAAGATGAACTCCCCC 59.534 60.0 0.00 0.00 0.00 5.40 F
1566 1643 0.098025 CGGCACCGCGATAATTTTGT 59.902 50.0 8.23 0.00 0.00 2.83 F
2250 2363 0.249868 TTGACCAACGTCTGCTCTGG 60.250 55.0 0.11 0.11 39.94 3.86 F
3497 3632 0.323451 GGGAGGGCCGTTTTCATCTT 60.323 55.0 0.00 0.00 33.83 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1760 0.759346 ACTGCTCCACCGTCTTCTTT 59.241 50.0 0.00 0.00 0.00 2.52 R
2565 2680 0.871163 CAAGCGGGCACAAGTTGTTG 60.871 55.0 5.57 3.54 39.82 3.33 R
3568 3703 0.818445 ACTGCATGCTGCTAGATGGC 60.818 55.0 22.92 0.00 45.31 4.40 R
4925 5427 0.033090 GTAGTATTCCCGCCTTCCCG 59.967 60.0 0.00 0.00 0.00 5.14 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
28 29 4.283467 TCTGAAATGGAAGAAGACGAGGAA 59.717 41.667 0.00 0.00 0.00 3.36
34 35 3.832490 TGGAAGAAGACGAGGAAGATGAA 59.168 43.478 0.00 0.00 0.00 2.57
35 36 4.177783 GGAAGAAGACGAGGAAGATGAAC 58.822 47.826 0.00 0.00 0.00 3.18
36 37 4.081917 GGAAGAAGACGAGGAAGATGAACT 60.082 45.833 0.00 0.00 0.00 3.01
37 38 4.712122 AGAAGACGAGGAAGATGAACTC 57.288 45.455 0.00 0.00 0.00 3.01
38 39 3.445805 AGAAGACGAGGAAGATGAACTCC 59.554 47.826 0.00 0.00 0.00 3.85
39 40 2.104170 AGACGAGGAAGATGAACTCCC 58.896 52.381 0.00 0.00 0.00 4.30
40 41 1.137282 GACGAGGAAGATGAACTCCCC 59.863 57.143 0.00 0.00 0.00 4.81
41 42 0.466124 CGAGGAAGATGAACTCCCCC 59.534 60.000 0.00 0.00 0.00 5.40
76 77 3.507233 TGATGAACTTTCCCACATTGAGC 59.493 43.478 0.00 0.00 0.00 4.26
77 78 3.228188 TGAACTTTCCCACATTGAGCT 57.772 42.857 0.00 0.00 0.00 4.09
84 85 6.845908 ACTTTCCCACATTGAGCTATATGAT 58.154 36.000 13.00 0.00 0.00 2.45
140 168 6.388278 AGTAGTTAAGACGAACTGATGAACC 58.612 40.000 6.16 0.00 39.96 3.62
202 230 9.420551 GTTTGGTACTGCCTATCTATGTAATAC 57.579 37.037 0.00 0.00 38.35 1.89
217 245 4.940463 TGTAATACGGTAAGATCACTGCC 58.060 43.478 0.00 0.00 0.00 4.85
220 248 1.883084 CGGTAAGATCACTGCCCGC 60.883 63.158 0.00 0.00 34.92 6.13
236 264 1.218047 CGCGAGAAGGGATGACCAA 59.782 57.895 0.00 0.00 43.89 3.67
244 272 4.739793 AGAAGGGATGACCAAAACATTCA 58.260 39.130 0.00 0.00 43.89 2.57
248 276 3.165071 GGATGACCAAAACATTCACCCT 58.835 45.455 0.00 0.00 35.97 4.34
294 322 3.130869 TGCATCTTCACAACCATAATGCC 59.869 43.478 0.00 0.00 37.75 4.40
318 352 1.202867 TGCTGTCAACCAAGCACCATA 60.203 47.619 0.00 0.00 31.84 2.74
343 377 3.612423 CGAAACAATCTCGTGATGCTGTA 59.388 43.478 0.00 0.00 32.44 2.74
344 378 4.259570 CGAAACAATCTCGTGATGCTGTAG 60.260 45.833 0.00 0.00 32.44 2.74
357 391 6.049149 GTGATGCTGTAGAGTTAGCCAAATA 58.951 40.000 0.00 0.00 39.15 1.40
405 439 0.526524 GAGTCAGTCGGGCTCAATCG 60.527 60.000 0.00 0.00 0.00 3.34
432 466 4.202212 GGAAAGTAAAGGCAAAAGGAAGCA 60.202 41.667 0.00 0.00 0.00 3.91
619 670 4.033776 CCACAGCACATCGGGGGT 62.034 66.667 0.00 0.00 0.00 4.95
620 671 2.665089 CCACAGCACATCGGGGGTA 61.665 63.158 0.00 0.00 0.00 3.69
621 672 1.153369 CACAGCACATCGGGGGTAG 60.153 63.158 0.00 0.00 0.00 3.18
622 673 1.612442 ACAGCACATCGGGGGTAGT 60.612 57.895 0.00 0.00 0.00 2.73
649 700 7.371936 AGTTATAGAGAGAGAAACACACACAC 58.628 38.462 0.00 0.00 0.00 3.82
651 702 3.786635 AGAGAGAGAAACACACACACAC 58.213 45.455 0.00 0.00 0.00 3.82
653 704 3.262420 AGAGAGAAACACACACACACAC 58.738 45.455 0.00 0.00 0.00 3.82
654 705 3.000041 GAGAGAAACACACACACACACA 59.000 45.455 0.00 0.00 0.00 3.72
655 706 2.742053 AGAGAAACACACACACACACAC 59.258 45.455 0.00 0.00 0.00 3.82
674 725 1.203928 CAGAGAAAGAGGCGTATGCG 58.796 55.000 0.00 0.00 44.10 4.73
886 937 4.767892 CTGCCCCCTTCCCCTCCT 62.768 72.222 0.00 0.00 0.00 3.69
887 938 4.760220 TGCCCCCTTCCCCTCCTC 62.760 72.222 0.00 0.00 0.00 3.71
961 1022 1.611491 CGCTCCTCTAGATCAGTTCCC 59.389 57.143 0.00 0.00 0.00 3.97
962 1023 1.967779 GCTCCTCTAGATCAGTTCCCC 59.032 57.143 0.00 0.00 0.00 4.81
963 1024 2.604139 CTCCTCTAGATCAGTTCCCCC 58.396 57.143 0.00 0.00 0.00 5.40
1151 1213 3.673484 CCACACGGGTCGTACGGT 61.673 66.667 16.52 1.82 38.32 4.83
1170 1232 4.982701 GGGGTGCTGCTGTTGCCT 62.983 66.667 0.00 0.00 38.71 4.75
1280 1342 3.751049 TTCCCTAGAGCGGCCCGAT 62.751 63.158 7.68 0.00 0.00 4.18
1281 1343 3.234730 CCCTAGAGCGGCCCGATT 61.235 66.667 7.68 0.00 0.00 3.34
1439 1501 3.185797 CAGTGTAAGCACCGACTAAAACC 59.814 47.826 0.00 0.00 46.35 3.27
1446 1523 4.251268 AGCACCGACTAAAACCATAAGTC 58.749 43.478 0.00 0.00 36.99 3.01
1471 1548 5.917541 TCTTCATTTAATTCGCCGGATAC 57.082 39.130 5.05 0.00 0.00 2.24
1566 1643 0.098025 CGGCACCGCGATAATTTTGT 59.902 50.000 8.23 0.00 0.00 2.83
1567 1644 1.328069 CGGCACCGCGATAATTTTGTA 59.672 47.619 8.23 0.00 0.00 2.41
1568 1645 2.711885 GGCACCGCGATAATTTTGTAC 58.288 47.619 8.23 0.00 0.00 2.90
1575 1652 6.202188 CACCGCGATAATTTTGTACTATTCCT 59.798 38.462 8.23 0.00 0.00 3.36
1639 1716 3.191371 CCTGACCAGTGAAAATACTTGCC 59.809 47.826 0.00 0.00 0.00 4.52
1652 1729 0.598065 ACTTGCCAACTGCGAATTCC 59.402 50.000 0.00 0.00 45.60 3.01
1653 1730 0.883833 CTTGCCAACTGCGAATTCCT 59.116 50.000 0.00 0.00 45.60 3.36
1654 1731 1.270550 CTTGCCAACTGCGAATTCCTT 59.729 47.619 0.00 0.00 45.60 3.36
1655 1732 0.597568 TGCCAACTGCGAATTCCTTG 59.402 50.000 0.00 0.00 45.60 3.61
1672 1749 2.434185 GCAGGCCGACGTTCATCA 60.434 61.111 0.00 0.00 0.00 3.07
1673 1750 2.456119 GCAGGCCGACGTTCATCAG 61.456 63.158 0.00 0.00 0.00 2.90
1674 1751 1.079819 CAGGCCGACGTTCATCAGT 60.080 57.895 0.00 0.00 0.00 3.41
1683 1760 4.421058 CGACGTTCATCAGTATCTGGAAA 58.579 43.478 0.00 0.00 31.51 3.13
2057 2134 3.405592 TACGCGTCGCCATCACTCC 62.406 63.158 18.63 0.00 0.00 3.85
2077 2154 1.343465 CCACGGTCTCACCTACAAACT 59.657 52.381 0.00 0.00 35.66 2.66
2087 2164 7.338957 GGTCTCACCTACAAACTAGTACAGTAT 59.661 40.741 0.00 0.00 33.55 2.12
2105 2182 4.637534 CAGTATTGGAGTGAGATTTGGTGG 59.362 45.833 0.00 0.00 0.00 4.61
2107 2184 2.566833 TGGAGTGAGATTTGGTGGTG 57.433 50.000 0.00 0.00 0.00 4.17
2110 2192 2.304761 GGAGTGAGATTTGGTGGTGGTA 59.695 50.000 0.00 0.00 0.00 3.25
2116 2198 7.007723 AGTGAGATTTGGTGGTGGTATTTTAA 58.992 34.615 0.00 0.00 0.00 1.52
2144 2226 8.773404 ATTGATTTCAGTGTTACACTAGTACC 57.227 34.615 18.19 8.27 43.43 3.34
2145 2227 6.384224 TGATTTCAGTGTTACACTAGTACCG 58.616 40.000 18.19 4.86 43.43 4.02
2171 2282 8.847196 GGTAGGTGAGGAAATGATTAATTAACC 58.153 37.037 0.00 0.00 0.00 2.85
2175 2286 7.132863 GTGAGGAAATGATTAATTAACCGCTC 58.867 38.462 0.00 0.00 33.02 5.03
2250 2363 0.249868 TTGACCAACGTCTGCTCTGG 60.250 55.000 0.11 0.11 39.94 3.86
2251 2364 2.029844 GACCAACGTCTGCTCTGGC 61.030 63.158 1.58 0.00 35.99 4.85
2252 2365 2.743928 CCAACGTCTGCTCTGGCC 60.744 66.667 0.00 0.00 37.74 5.36
2253 2366 2.345244 CAACGTCTGCTCTGGCCT 59.655 61.111 3.32 0.00 37.74 5.19
2254 2367 1.739562 CAACGTCTGCTCTGGCCTC 60.740 63.158 3.32 0.00 37.74 4.70
2255 2368 1.910772 AACGTCTGCTCTGGCCTCT 60.911 57.895 3.32 0.00 37.74 3.69
2256 2369 2.164865 AACGTCTGCTCTGGCCTCTG 62.165 60.000 3.32 0.00 37.74 3.35
2350 2463 3.933332 GCAGTAGCTGTATTCTTTTCGGT 59.067 43.478 0.00 0.00 37.91 4.69
2353 2466 6.455246 GCAGTAGCTGTATTCTTTTCGGTTAC 60.455 42.308 0.00 0.00 37.91 2.50
2363 2476 3.444742 TCTTTTCGGTTACCTCGCTATCA 59.555 43.478 0.00 0.00 0.00 2.15
2392 2506 6.086222 TGAACAGCGCAAATATTCTTTTCTC 58.914 36.000 11.47 0.00 0.00 2.87
2435 2550 3.568007 ACGTACATGCAGTGTTTCCAATT 59.432 39.130 7.02 0.00 42.29 2.32
2556 2671 5.048782 TGTTCATCCTTCACTTTTTGATCCG 60.049 40.000 0.00 0.00 32.84 4.18
2563 2678 5.120830 CCTTCACTTTTTGATCCGACTGTAG 59.879 44.000 0.00 0.00 32.84 2.74
2565 2680 5.227908 TCACTTTTTGATCCGACTGTAGTC 58.772 41.667 1.92 1.92 41.47 2.59
2603 2718 5.052040 CGCTTGCACTTTTCGTTAAAATTGA 60.052 36.000 5.46 0.00 37.40 2.57
2608 2723 9.684448 TTGCACTTTTCGTTAAAATTGATCATA 57.316 25.926 0.00 0.00 37.40 2.15
2615 2730 9.988350 TTTCGTTAAAATTGATCATAGCTTCTC 57.012 29.630 0.00 0.00 0.00 2.87
2616 2731 8.948631 TCGTTAAAATTGATCATAGCTTCTCT 57.051 30.769 0.00 0.00 0.00 3.10
2617 2732 9.383519 TCGTTAAAATTGATCATAGCTTCTCTT 57.616 29.630 0.00 0.00 0.00 2.85
2643 2758 8.865590 TTTTTCCTGTTCTTTTATGCACTTAC 57.134 30.769 0.00 0.00 0.00 2.34
2660 2775 5.338463 GCACTTACTTTTAGTCCTCCCATCT 60.338 44.000 0.00 0.00 0.00 2.90
2688 2803 6.099341 ACAAAACAAAAGTTGTGTCATCTCC 58.901 36.000 0.00 0.00 44.59 3.71
2699 2814 2.969238 CATCTCCCATGCCGTCGC 60.969 66.667 0.00 0.00 0.00 5.19
2727 2842 6.640907 CCTTGGTAGTTTTTGTGCTTCATAAC 59.359 38.462 0.00 0.00 0.00 1.89
2821 2939 9.429359 ACAAACAAACAATTGTCTGTAAAATGA 57.571 25.926 17.56 0.00 46.24 2.57
2825 2943 9.814899 ACAAACAATTGTCTGTAAAATGAATGA 57.185 25.926 15.84 0.00 46.78 2.57
2866 2989 8.349983 TGTTCATCATCATCATCATGTTGATTC 58.650 33.333 15.20 0.00 42.91 2.52
3021 3145 4.251268 ACATCACCGTAAGCCTTCTAAAC 58.749 43.478 0.00 0.00 0.00 2.01
3038 3162 9.268268 CCTTCTAAACTTTCACACACAGTAATA 57.732 33.333 0.00 0.00 0.00 0.98
3040 3164 9.826574 TTCTAAACTTTCACACACAGTAATACT 57.173 29.630 0.00 0.00 0.00 2.12
3066 3190 7.887381 AGTAACCATTAGCTAGCAGTATACTG 58.113 38.462 25.68 25.68 46.40 2.74
3090 3214 1.474677 GCTGGTGTGAGATGAGGATGG 60.475 57.143 0.00 0.00 0.00 3.51
3106 3230 3.793144 GGCTTCCACTTGAGCGCG 61.793 66.667 0.00 0.00 0.00 6.86
3107 3231 4.451652 GCTTCCACTTGAGCGCGC 62.452 66.667 26.66 26.66 0.00 6.86
3178 3302 2.434185 TAAGCAGCGCCGGAAGTG 60.434 61.111 5.05 0.00 0.00 3.16
3263 3387 4.412796 TTTAGGAGGTGCATCTGATCTG 57.587 45.455 2.86 0.00 0.00 2.90
3340 3472 2.460330 CAGCCTTGCAACTAGGACG 58.540 57.895 7.13 0.00 34.56 4.79
3354 3486 0.674895 AGGACGATGTTGAGCTTGCC 60.675 55.000 0.00 0.00 0.00 4.52
3379 3511 1.588667 CAACAAGTTGCGTGCACCC 60.589 57.895 12.15 2.06 33.45 4.61
3495 3630 1.001393 TGGGAGGGCCGTTTTCATC 60.001 57.895 0.00 0.00 33.83 2.92
3496 3631 1.303282 GGGAGGGCCGTTTTCATCT 59.697 57.895 0.00 0.00 33.83 2.90
3497 3632 0.323451 GGGAGGGCCGTTTTCATCTT 60.323 55.000 0.00 0.00 33.83 2.40
3498 3633 1.545841 GGAGGGCCGTTTTCATCTTT 58.454 50.000 0.00 0.00 0.00 2.52
3499 3634 1.472878 GGAGGGCCGTTTTCATCTTTC 59.527 52.381 0.00 0.00 0.00 2.62
3500 3635 2.159382 GAGGGCCGTTTTCATCTTTCA 58.841 47.619 0.00 0.00 0.00 2.69
3501 3636 2.755103 GAGGGCCGTTTTCATCTTTCAT 59.245 45.455 0.00 0.00 0.00 2.57
3507 3642 3.679502 CCGTTTTCATCTTTCATTTGGGC 59.320 43.478 0.00 0.00 0.00 5.36
3527 3662 3.181483 GGCAAGATAAGATTGGGTTGCTG 60.181 47.826 4.99 0.00 40.11 4.41
3529 3664 2.659428 AGATAAGATTGGGTTGCTGGC 58.341 47.619 0.00 0.00 0.00 4.85
3568 3703 0.988145 TAGGACCAAGCCTCCATGGG 60.988 60.000 13.02 2.26 41.17 4.00
3729 3869 1.338020 CCAAAAGGTCAAGCCAGTGTC 59.662 52.381 0.00 0.00 40.61 3.67
3784 3927 0.314935 TGTCGGTTACCTGTTCGGAC 59.685 55.000 0.00 0.00 36.31 4.79
3789 3932 1.345415 GGTTACCTGTTCGGACTTGGA 59.655 52.381 12.35 0.00 36.31 3.53
3798 3941 2.875933 GTTCGGACTTGGAATTGTCACA 59.124 45.455 0.00 0.00 35.11 3.58
3829 3972 4.394712 CCTGTCCGCCTGTCCCAC 62.395 72.222 0.00 0.00 0.00 4.61
3914 4058 7.328277 TCGTTGAAATTCCAAGAGAGAAAAA 57.672 32.000 0.00 0.00 0.00 1.94
4013 4157 1.151668 CTGTGAGGTGTAGCTTGTGC 58.848 55.000 0.00 0.00 40.05 4.57
4051 4517 1.142465 AGGAAGACGGCGAGGTAGATA 59.858 52.381 16.62 0.00 0.00 1.98
4113 4579 0.452987 CTCCCAATCAATGCGTGTGG 59.547 55.000 0.00 0.00 0.00 4.17
4250 4721 0.443869 GCAACGCATCACCTACTGTG 59.556 55.000 0.00 0.00 46.88 3.66
4251 4722 0.443869 CAACGCATCACCTACTGTGC 59.556 55.000 0.00 0.00 45.03 4.57
4252 4723 0.321671 AACGCATCACCTACTGTGCT 59.678 50.000 0.00 0.00 45.03 4.40
4253 4724 0.390340 ACGCATCACCTACTGTGCTG 60.390 55.000 0.00 0.00 45.03 4.41
4254 4725 0.108662 CGCATCACCTACTGTGCTGA 60.109 55.000 0.75 0.00 42.41 4.26
4255 4726 1.363744 GCATCACCTACTGTGCTGAC 58.636 55.000 0.75 0.00 42.41 3.51
4256 4727 1.633561 CATCACCTACTGTGCTGACG 58.366 55.000 0.00 0.00 42.41 4.35
4278 4749 0.621571 TGACCCTTGGCTCAGGCTAT 60.622 55.000 0.00 0.00 38.73 2.97
4279 4750 1.343985 TGACCCTTGGCTCAGGCTATA 60.344 52.381 0.00 0.00 38.73 1.31
4283 4754 2.565841 CCTTGGCTCAGGCTATAACAC 58.434 52.381 0.00 0.00 38.73 3.32
4284 4755 2.092968 CCTTGGCTCAGGCTATAACACA 60.093 50.000 0.00 0.00 38.73 3.72
4285 4756 3.434167 CCTTGGCTCAGGCTATAACACAT 60.434 47.826 0.00 0.00 38.73 3.21
4286 4757 3.931907 TGGCTCAGGCTATAACACATT 57.068 42.857 0.00 0.00 38.73 2.71
4287 4758 4.235079 TGGCTCAGGCTATAACACATTT 57.765 40.909 0.00 0.00 38.73 2.32
4288 4759 4.199310 TGGCTCAGGCTATAACACATTTC 58.801 43.478 0.00 0.00 38.73 2.17
4327 4798 8.930760 TGATTTGTTTTTCTGGTTACAAACTTG 58.069 29.630 0.00 0.00 41.59 3.16
4339 4810 5.294060 GGTTACAAACTTGTGTTCTCCGTTA 59.706 40.000 5.34 0.00 42.31 3.18
4342 4813 4.331717 ACAAACTTGTGTTCTCCGTTACTG 59.668 41.667 0.00 0.00 40.49 2.74
4345 4816 2.410785 TGTGTTCTCCGTTACTGTCG 57.589 50.000 0.00 0.00 0.00 4.35
4663 5137 2.933495 ATCATGTACGTACGCTGTGT 57.067 45.000 20.18 10.69 0.00 3.72
4711 5188 1.351153 GTCTTCTTGTGCGCTCTACC 58.649 55.000 9.73 0.00 0.00 3.18
4721 5198 0.741221 GCGCTCTACCACCCTTGAAG 60.741 60.000 0.00 0.00 0.00 3.02
4722 5199 0.895530 CGCTCTACCACCCTTGAAGA 59.104 55.000 0.00 0.00 0.00 2.87
4723 5200 1.482593 CGCTCTACCACCCTTGAAGAT 59.517 52.381 0.00 0.00 0.00 2.40
4724 5201 2.093447 CGCTCTACCACCCTTGAAGATT 60.093 50.000 0.00 0.00 0.00 2.40
4725 5202 3.619979 CGCTCTACCACCCTTGAAGATTT 60.620 47.826 0.00 0.00 0.00 2.17
4726 5203 3.691609 GCTCTACCACCCTTGAAGATTTG 59.308 47.826 0.00 0.00 0.00 2.32
4731 5211 3.317993 ACCACCCTTGAAGATTTGTTTCG 59.682 43.478 0.00 0.00 0.00 3.46
4742 5222 4.703897 AGATTTGTTTCGTCTTGTCTCCA 58.296 39.130 0.00 0.00 0.00 3.86
4752 5232 4.038042 TCGTCTTGTCTCCATTATGCCTAG 59.962 45.833 0.00 0.00 0.00 3.02
4754 5234 5.009710 CGTCTTGTCTCCATTATGCCTAGTA 59.990 44.000 0.00 0.00 0.00 1.82
4755 5235 6.217294 GTCTTGTCTCCATTATGCCTAGTAC 58.783 44.000 0.00 0.00 0.00 2.73
4813 5314 2.270874 GACCCTGGTTGGCGGATCAT 62.271 60.000 0.00 0.00 0.00 2.45
4903 5404 5.046910 ACATGTTGTTGTTATGCTACTGC 57.953 39.130 0.00 0.00 40.20 4.40
4905 5406 4.747540 TGTTGTTGTTATGCTACTGCTG 57.252 40.909 0.00 0.00 40.48 4.41
4908 5409 5.067153 TGTTGTTGTTATGCTACTGCTGTTT 59.933 36.000 0.09 0.00 40.48 2.83
4925 5427 4.671508 GCTGTTTCTGTTTTTGTTTTGGCC 60.672 41.667 0.00 0.00 0.00 5.36
4926 5428 3.433615 TGTTTCTGTTTTTGTTTTGGCCG 59.566 39.130 0.00 0.00 0.00 6.13
4927 5429 2.301577 TCTGTTTTTGTTTTGGCCGG 57.698 45.000 0.00 0.00 0.00 6.13
4928 5430 1.134670 TCTGTTTTTGTTTTGGCCGGG 60.135 47.619 2.18 0.00 0.00 5.73
4929 5431 0.902531 TGTTTTTGTTTTGGCCGGGA 59.097 45.000 2.18 0.00 0.00 5.14
4930 5432 1.278127 TGTTTTTGTTTTGGCCGGGAA 59.722 42.857 2.18 0.00 0.00 3.97
4931 5433 1.937223 GTTTTTGTTTTGGCCGGGAAG 59.063 47.619 2.18 0.00 0.00 3.46
4932 5434 0.466124 TTTTGTTTTGGCCGGGAAGG 59.534 50.000 2.18 0.00 44.97 3.46
5077 5579 4.722361 AGTCGACCTAGGATTGACTTTC 57.278 45.455 17.98 0.00 36.56 2.62
5078 5580 4.087182 AGTCGACCTAGGATTGACTTTCA 58.913 43.478 17.98 0.00 36.56 2.69
5079 5581 4.082136 AGTCGACCTAGGATTGACTTTCAC 60.082 45.833 17.98 1.67 36.56 3.18
5081 5583 4.527038 TCGACCTAGGATTGACTTTCACTT 59.473 41.667 17.98 0.00 0.00 3.16
5084 5586 6.531948 CGACCTAGGATTGACTTTCACTTTAG 59.468 42.308 17.98 0.00 0.00 1.85
5133 5636 3.370103 CCGCCTGGATCCTTAGTTTGTAA 60.370 47.826 14.23 0.00 37.49 2.41
5202 5847 8.804743 GCATGATTTCACAATTTATGTTCAGAG 58.195 33.333 0.00 0.00 41.46 3.35
5246 5891 9.134734 GCTAAATAAATCAATTGTGGAACGAAA 57.865 29.630 5.13 0.00 42.39 3.46
5248 5893 7.883229 AATAAATCAATTGTGGAACGAAACC 57.117 32.000 5.13 0.00 42.39 3.27
5275 5920 1.580942 CATGAACTTGTGGCACCCG 59.419 57.895 16.26 8.44 0.00 5.28
5276 5921 0.888736 CATGAACTTGTGGCACCCGA 60.889 55.000 16.26 0.00 0.00 5.14
5311 5956 1.869767 GAACACTGAGCTTCCACACAG 59.130 52.381 0.00 0.00 36.58 3.66
5334 5981 1.496060 TAGGGCATCTCCAACGTGAT 58.504 50.000 0.00 0.00 36.21 3.06
5336 5983 0.179000 GGGCATCTCCAACGTGATCT 59.821 55.000 0.00 0.00 36.21 2.75
5349 5996 2.289444 ACGTGATCTCCAAAACGGACAT 60.289 45.455 6.06 0.00 39.64 3.06
5359 6006 6.432783 TCTCCAAAACGGACATCATATTTGTT 59.567 34.615 0.00 0.00 39.64 2.83
5360 6007 6.987386 TCCAAAACGGACATCATATTTGTTT 58.013 32.000 0.00 0.00 39.64 2.83
5405 6060 4.317671 CGGACACCGGATTCTATACTTT 57.682 45.455 9.46 0.00 44.15 2.66
5464 6119 1.928868 AGACTCCCAAGGCATTTTGG 58.071 50.000 6.84 6.84 45.83 3.28
5482 6137 1.314730 GGACTTGGCCAAAACTCGAA 58.685 50.000 20.91 0.00 0.00 3.71
5483 6138 1.001706 GGACTTGGCCAAAACTCGAAC 60.002 52.381 20.91 7.24 0.00 3.95
5484 6139 1.001706 GACTTGGCCAAAACTCGAACC 60.002 52.381 20.91 0.00 0.00 3.62
5534 6189 7.950236 TCGTGAATTTCTCTACTCGAAAATTC 58.050 34.615 17.73 17.73 34.42 2.17
5563 6218 4.935808 ACTTACTTAGGACATTGGCTTTCG 59.064 41.667 0.00 0.00 0.00 3.46
5566 6221 3.260884 ACTTAGGACATTGGCTTTCGAGA 59.739 43.478 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.107017 ATCAATGTCGAGCAAGGGGG 60.107 55.000 0.00 0.00 0.00 5.40
39 40 1.019673 CATCAATGTCGAGCAAGGGG 58.980 55.000 0.00 0.00 0.00 4.79
40 41 2.028420 TCATCAATGTCGAGCAAGGG 57.972 50.000 0.00 0.00 0.00 3.95
41 42 3.005554 AGTTCATCAATGTCGAGCAAGG 58.994 45.455 0.00 0.00 0.00 3.61
42 43 4.675190 AAGTTCATCAATGTCGAGCAAG 57.325 40.909 0.00 0.00 0.00 4.01
43 44 4.083324 GGAAAGTTCATCAATGTCGAGCAA 60.083 41.667 0.00 0.00 0.00 3.91
44 45 3.436704 GGAAAGTTCATCAATGTCGAGCA 59.563 43.478 0.00 0.00 0.00 4.26
45 46 3.181506 GGGAAAGTTCATCAATGTCGAGC 60.182 47.826 0.00 0.00 0.00 5.03
46 47 4.002982 TGGGAAAGTTCATCAATGTCGAG 58.997 43.478 0.00 0.00 0.00 4.04
47 48 3.751175 GTGGGAAAGTTCATCAATGTCGA 59.249 43.478 0.00 0.00 0.00 4.20
48 49 3.501828 TGTGGGAAAGTTCATCAATGTCG 59.498 43.478 0.00 0.00 0.00 4.35
49 50 5.649782 ATGTGGGAAAGTTCATCAATGTC 57.350 39.130 0.00 0.00 0.00 3.06
50 51 5.539574 TCAATGTGGGAAAGTTCATCAATGT 59.460 36.000 0.00 0.00 0.00 2.71
51 52 6.028146 TCAATGTGGGAAAGTTCATCAATG 57.972 37.500 0.00 0.00 0.00 2.82
52 53 5.337009 GCTCAATGTGGGAAAGTTCATCAAT 60.337 40.000 0.00 0.00 0.00 2.57
140 168 6.978659 TCAATCCTAGCTACTAACAAATGACG 59.021 38.462 0.00 0.00 0.00 4.35
202 230 1.883084 GCGGGCAGTGATCTTACCG 60.883 63.158 0.00 0.00 40.82 4.02
217 245 2.107141 GGTCATCCCTTCTCGCGG 59.893 66.667 6.13 0.00 0.00 6.46
220 248 2.778299 TGTTTTGGTCATCCCTTCTCG 58.222 47.619 0.00 0.00 0.00 4.04
236 264 1.963515 GTTGCTCCAGGGTGAATGTTT 59.036 47.619 0.00 0.00 0.00 2.83
244 272 1.282157 GATGTTAGGTTGCTCCAGGGT 59.718 52.381 1.79 0.00 39.02 4.34
248 276 1.346395 ACACGATGTTAGGTTGCTCCA 59.654 47.619 0.00 0.00 39.02 3.86
294 322 1.102809 TGCTTGGTTGACAGCACTGG 61.103 55.000 2.21 0.00 31.40 4.00
343 377 7.466746 TCTGCATTTTTATTTGGCTAACTCT 57.533 32.000 0.00 0.00 0.00 3.24
344 378 8.707938 ATTCTGCATTTTTATTTGGCTAACTC 57.292 30.769 0.00 0.00 0.00 3.01
386 420 0.526524 CGATTGAGCCCGACTGACTC 60.527 60.000 0.00 0.00 0.00 3.36
405 439 3.305131 CCTTTTGCCTTTACTTTCCGTCC 60.305 47.826 0.00 0.00 0.00 4.79
565 616 3.499745 GGGTGGGTTGGTCATACTTTTCT 60.500 47.826 0.00 0.00 0.00 2.52
570 621 1.559065 CCGGGTGGGTTGGTCATACT 61.559 60.000 0.00 0.00 0.00 2.12
620 671 9.298250 TGTGTGTTTCTCTCTCTATAACTAACT 57.702 33.333 0.00 0.00 0.00 2.24
621 672 9.344309 GTGTGTGTTTCTCTCTCTATAACTAAC 57.656 37.037 0.00 0.00 0.00 2.34
622 673 9.074576 TGTGTGTGTTTCTCTCTCTATAACTAA 57.925 33.333 0.00 0.00 0.00 2.24
649 700 1.143305 CGCCTCTTTCTCTGTGTGTG 58.857 55.000 0.00 0.00 0.00 3.82
651 702 2.724977 TACGCCTCTTTCTCTGTGTG 57.275 50.000 0.00 0.00 0.00 3.82
653 704 1.929836 GCATACGCCTCTTTCTCTGTG 59.070 52.381 0.00 0.00 0.00 3.66
654 705 1.469940 CGCATACGCCTCTTTCTCTGT 60.470 52.381 0.00 0.00 33.11 3.41
655 706 1.202302 TCGCATACGCCTCTTTCTCTG 60.202 52.381 0.00 0.00 39.84 3.35
886 937 1.916181 GATTTCTGGACTTGGAGGGGA 59.084 52.381 0.00 0.00 0.00 4.81
887 938 1.064389 GGATTTCTGGACTTGGAGGGG 60.064 57.143 0.00 0.00 0.00 4.79
888 939 1.407437 CGGATTTCTGGACTTGGAGGG 60.407 57.143 0.00 0.00 0.00 4.30
961 1022 3.366739 GAGGTAACCGCACCGAGGG 62.367 68.421 0.00 0.00 43.84 4.30
962 1023 2.183555 GAGGTAACCGCACCGAGG 59.816 66.667 0.00 0.00 43.84 4.63
963 1024 1.139095 GAGAGGTAACCGCACCGAG 59.861 63.158 0.00 0.00 43.84 4.63
1105 1167 1.005294 CACATGGTTTTCGCTGCAGC 61.005 55.000 29.12 29.12 37.78 5.25
1155 1217 3.368571 GGAGGCAACAGCAGCACC 61.369 66.667 0.00 0.00 41.41 5.01
1156 1218 2.282040 AGGAGGCAACAGCAGCAC 60.282 61.111 0.00 0.00 41.41 4.40
1170 1232 4.214119 CGAGAAACAAAAAGAGCATCAGGA 59.786 41.667 0.00 0.00 37.82 3.86
1280 1342 0.881159 ACCGCCGAACAAATCACGAA 60.881 50.000 0.00 0.00 30.89 3.85
1281 1343 0.881159 AACCGCCGAACAAATCACGA 60.881 50.000 0.00 0.00 30.89 4.35
1446 1523 6.727824 ATCCGGCGAATTAAATGAAGATAG 57.272 37.500 9.30 0.00 0.00 2.08
1471 1548 6.018832 GCACAATTAATTCCGGAATCCATTTG 60.019 38.462 29.32 27.14 0.00 2.32
1542 1619 0.885879 ATTATCGCGGTGCCGATCTA 59.114 50.000 15.45 0.00 43.91 1.98
1639 1716 1.973138 CTGCAAGGAATTCGCAGTTG 58.027 50.000 19.75 12.41 46.36 3.16
1652 1729 1.970917 GATGAACGTCGGCCTGCAAG 61.971 60.000 0.00 0.00 0.00 4.01
1653 1730 2.031919 ATGAACGTCGGCCTGCAA 59.968 55.556 0.00 0.00 0.00 4.08
1654 1731 2.434185 GATGAACGTCGGCCTGCA 60.434 61.111 0.00 0.00 0.00 4.41
1655 1732 2.434185 TGATGAACGTCGGCCTGC 60.434 61.111 0.00 0.00 0.00 4.85
1672 1749 5.238583 CACCGTCTTCTTTTTCCAGATACT 58.761 41.667 0.00 0.00 0.00 2.12
1673 1750 4.392138 CCACCGTCTTCTTTTTCCAGATAC 59.608 45.833 0.00 0.00 0.00 2.24
1674 1751 4.285003 TCCACCGTCTTCTTTTTCCAGATA 59.715 41.667 0.00 0.00 0.00 1.98
1683 1760 0.759346 ACTGCTCCACCGTCTTCTTT 59.241 50.000 0.00 0.00 0.00 2.52
1837 1914 1.608717 AAGGTGAGGAAGAGCGCGAT 61.609 55.000 12.10 1.23 0.00 4.58
2057 2134 1.343465 AGTTTGTAGGTGAGACCGTGG 59.657 52.381 0.00 0.00 44.90 4.94
2077 2154 7.399191 ACCAAATCTCACTCCAATACTGTACTA 59.601 37.037 0.00 0.00 0.00 1.82
2087 2164 2.488891 CCACCACCAAATCTCACTCCAA 60.489 50.000 0.00 0.00 0.00 3.53
2144 2226 8.557029 GTTAATTAATCATTTCCTCACCTACCG 58.443 37.037 0.31 0.00 0.00 4.02
2145 2227 8.847196 GGTTAATTAATCATTTCCTCACCTACC 58.153 37.037 3.49 0.00 0.00 3.18
2151 2262 7.054124 AGAGCGGTTAATTAATCATTTCCTCA 58.946 34.615 9.11 0.00 0.00 3.86
2171 2282 4.112634 TGGTTATTCTCATTCGAAGAGCG 58.887 43.478 15.56 2.83 38.43 5.03
2175 2286 8.662781 TTTCCTATGGTTATTCTCATTCGAAG 57.337 34.615 3.35 0.00 0.00 3.79
2250 2363 1.218316 CCAGAACGTACCCAGAGGC 59.782 63.158 0.00 0.00 36.11 4.70
2251 2364 0.903454 ACCCAGAACGTACCCAGAGG 60.903 60.000 0.00 0.00 40.04 3.69
2252 2365 0.246635 CACCCAGAACGTACCCAGAG 59.753 60.000 0.00 0.00 0.00 3.35
2253 2366 1.189524 CCACCCAGAACGTACCCAGA 61.190 60.000 0.00 0.00 0.00 3.86
2254 2367 1.189524 TCCACCCAGAACGTACCCAG 61.190 60.000 0.00 0.00 0.00 4.45
2255 2368 1.152290 TCCACCCAGAACGTACCCA 60.152 57.895 0.00 0.00 0.00 4.51
2256 2369 0.901580 TCTCCACCCAGAACGTACCC 60.902 60.000 0.00 0.00 0.00 3.69
2297 2410 2.993899 AGAAAACGACAGGATTACGCAG 59.006 45.455 0.00 0.00 0.00 5.18
2350 2463 5.543714 TGTTCAAAGTTGATAGCGAGGTAA 58.456 37.500 0.00 0.00 37.00 2.85
2353 2466 3.181516 GCTGTTCAAAGTTGATAGCGAGG 60.182 47.826 12.26 0.00 37.72 4.63
2363 2476 5.772521 AGAATATTTGCGCTGTTCAAAGTT 58.227 33.333 9.73 0.00 36.93 2.66
2406 2520 8.273109 TGGAAACACTGCATGTACGTAATACAT 61.273 37.037 0.00 0.00 45.26 2.29
2407 2521 7.015030 TGGAAACACTGCATGTACGTAATACA 61.015 38.462 0.00 0.00 42.31 2.29
2435 2550 3.270027 CAGGAGTTGATTTGACGCCATA 58.730 45.455 0.16 0.00 39.16 2.74
2556 2671 3.002348 GGCACAAGTTGTTGACTACAGTC 59.998 47.826 5.57 2.29 44.97 3.51
2563 2678 1.299089 GCGGGCACAAGTTGTTGAC 60.299 57.895 5.57 4.30 37.10 3.18
2565 2680 0.871163 CAAGCGGGCACAAGTTGTTG 60.871 55.000 5.57 3.54 39.82 3.33
2619 2734 8.232913 AGTAAGTGCATAAAAGAACAGGAAAA 57.767 30.769 0.00 0.00 0.00 2.29
2622 2737 7.817418 AAAGTAAGTGCATAAAAGAACAGGA 57.183 32.000 0.00 0.00 0.00 3.86
2623 2738 9.612620 CTAAAAGTAAGTGCATAAAAGAACAGG 57.387 33.333 0.00 0.00 0.00 4.00
2627 2742 9.569122 AGGACTAAAAGTAAGTGCATAAAAGAA 57.431 29.630 0.00 0.00 37.73 2.52
2628 2743 9.216117 GAGGACTAAAAGTAAGTGCATAAAAGA 57.784 33.333 0.00 0.00 37.73 2.52
2629 2744 8.451748 GGAGGACTAAAAGTAAGTGCATAAAAG 58.548 37.037 0.00 0.00 37.73 2.27
2630 2745 7.392393 GGGAGGACTAAAAGTAAGTGCATAAAA 59.608 37.037 0.00 0.00 37.73 1.52
2631 2746 6.882678 GGGAGGACTAAAAGTAAGTGCATAAA 59.117 38.462 0.00 0.00 37.73 1.40
2632 2747 6.013206 TGGGAGGACTAAAAGTAAGTGCATAA 60.013 38.462 0.00 0.00 37.73 1.90
2633 2748 5.486063 TGGGAGGACTAAAAGTAAGTGCATA 59.514 40.000 0.00 0.00 37.73 3.14
2634 2749 4.288626 TGGGAGGACTAAAAGTAAGTGCAT 59.711 41.667 0.00 0.00 37.73 3.96
2636 2751 4.281898 TGGGAGGACTAAAAGTAAGTGC 57.718 45.455 0.00 0.00 35.71 4.40
2637 2752 6.070767 TGAGATGGGAGGACTAAAAGTAAGTG 60.071 42.308 0.00 0.00 0.00 3.16
2638 2753 6.023603 TGAGATGGGAGGACTAAAAGTAAGT 58.976 40.000 0.00 0.00 0.00 2.24
2639 2754 6.546428 TGAGATGGGAGGACTAAAAGTAAG 57.454 41.667 0.00 0.00 0.00 2.34
2640 2755 6.945636 TTGAGATGGGAGGACTAAAAGTAA 57.054 37.500 0.00 0.00 0.00 2.24
2641 2756 6.271391 TGTTTGAGATGGGAGGACTAAAAGTA 59.729 38.462 0.00 0.00 0.00 2.24
2642 2757 5.073144 TGTTTGAGATGGGAGGACTAAAAGT 59.927 40.000 0.00 0.00 0.00 2.66
2643 2758 5.560724 TGTTTGAGATGGGAGGACTAAAAG 58.439 41.667 0.00 0.00 0.00 2.27
2688 2803 2.436646 AAGGAAGCGACGGCATGG 60.437 61.111 0.00 0.00 43.41 3.66
2699 2814 4.918810 AGCACAAAAACTACCAAGGAAG 57.081 40.909 0.00 0.00 0.00 3.46
2727 2842 3.956199 TCCCTCTACACGTATTAACCAGG 59.044 47.826 0.00 0.00 0.00 4.45
2768 2883 4.262164 GCACAATTCATCCAAAGAACAGGT 60.262 41.667 0.00 0.00 0.00 4.00
2853 2976 5.300969 ACACGGAAAGAATCAACATGATG 57.699 39.130 0.00 0.00 37.15 3.07
2854 2977 4.396166 GGACACGGAAAGAATCAACATGAT 59.604 41.667 0.00 0.00 39.09 2.45
2855 2978 3.751175 GGACACGGAAAGAATCAACATGA 59.249 43.478 0.00 0.00 0.00 3.07
2866 2989 1.260561 CTGAAACACGGACACGGAAAG 59.739 52.381 0.00 0.00 46.48 2.62
3021 3145 9.136952 GGTTACTAGTATTACTGTGTGTGAAAG 57.863 37.037 2.79 0.00 0.00 2.62
3038 3162 9.012161 GTATACTGCTAGCTAATGGTTACTAGT 57.988 37.037 17.23 8.59 35.58 2.57
3039 3163 9.233649 AGTATACTGCTAGCTAATGGTTACTAG 57.766 37.037 17.23 2.46 36.11 2.57
3040 3164 9.011095 CAGTATACTGCTAGCTAATGGTTACTA 57.989 37.037 19.55 0.00 37.15 1.82
3066 3190 2.093288 TCCTCATCTCACACCAGCAATC 60.093 50.000 0.00 0.00 0.00 2.67
3090 3214 4.451652 GCGCGCTCAAGTGGAAGC 62.452 66.667 26.67 0.00 0.00 3.86
3178 3302 3.412386 ACTTAGCAAGTCACCCATGTTC 58.588 45.455 0.00 0.00 37.02 3.18
3340 3472 2.161211 GTGAGAAGGCAAGCTCAACATC 59.839 50.000 5.70 0.00 42.27 3.06
3354 3486 2.708514 CACGCAACTTGTTGTGAGAAG 58.291 47.619 26.99 13.42 36.38 2.85
3379 3511 2.030958 GTTACTTGTGTCCGCGGGG 61.031 63.158 27.83 13.31 0.00 5.73
3390 3522 0.963856 GAAAGGGCCCCGGTTACTTG 60.964 60.000 21.43 0.00 0.00 3.16
3495 3630 6.759827 CCAATCTTATCTTGCCCAAATGAAAG 59.240 38.462 0.00 0.00 0.00 2.62
3496 3631 6.352051 CCCAATCTTATCTTGCCCAAATGAAA 60.352 38.462 0.00 0.00 0.00 2.69
3497 3632 5.129155 CCCAATCTTATCTTGCCCAAATGAA 59.871 40.000 0.00 0.00 0.00 2.57
3498 3633 4.650588 CCCAATCTTATCTTGCCCAAATGA 59.349 41.667 0.00 0.00 0.00 2.57
3499 3634 4.406649 ACCCAATCTTATCTTGCCCAAATG 59.593 41.667 0.00 0.00 0.00 2.32
3500 3635 4.623863 ACCCAATCTTATCTTGCCCAAAT 58.376 39.130 0.00 0.00 0.00 2.32
3501 3636 4.059773 ACCCAATCTTATCTTGCCCAAA 57.940 40.909 0.00 0.00 0.00 3.28
3507 3642 3.181483 GCCAGCAACCCAATCTTATCTTG 60.181 47.826 0.00 0.00 0.00 3.02
3527 3662 2.418983 AATAACGACGCTAGCTAGCC 57.581 50.000 34.27 22.49 46.34 3.93
3529 3664 5.636965 TCCTACTAATAACGACGCTAGCTAG 59.363 44.000 16.84 16.84 0.00 3.42
3533 3668 4.512944 TGGTCCTACTAATAACGACGCTAG 59.487 45.833 0.00 0.00 0.00 3.42
3537 3672 4.040376 GCTTGGTCCTACTAATAACGACG 58.960 47.826 0.00 0.00 0.00 5.12
3568 3703 0.818445 ACTGCATGCTGCTAGATGGC 60.818 55.000 22.92 0.00 45.31 4.40
3588 3723 2.438434 CCCGTGGCCAGCCTAAAG 60.438 66.667 5.11 0.00 36.94 1.85
3622 3757 1.668151 GCCGCCTGGTCCGATATTC 60.668 63.158 0.00 0.00 37.67 1.75
3711 3851 1.308998 CGACACTGGCTTGACCTTTT 58.691 50.000 0.00 0.00 40.22 2.27
3729 3869 3.414700 GCAAGGCCAGTCGTGACG 61.415 66.667 5.01 0.00 36.20 4.35
3771 3914 4.069304 CAATTCCAAGTCCGAACAGGTAA 58.931 43.478 0.00 0.00 41.99 2.85
3780 3923 2.494059 AGTGTGACAATTCCAAGTCCG 58.506 47.619 0.00 0.00 33.89 4.79
3784 3927 4.275689 TGCTGTTAGTGTGACAATTCCAAG 59.724 41.667 0.00 0.00 0.00 3.61
3789 3932 3.944650 TGTGTGCTGTTAGTGTGACAATT 59.055 39.130 0.00 0.00 0.00 2.32
3798 3941 1.202651 GGACAGGTGTGTGCTGTTAGT 60.203 52.381 0.00 0.00 41.64 2.24
3829 3972 5.333339 CGCCAACAGTAATTATTCATCGGAG 60.333 44.000 0.00 0.00 0.00 4.63
3914 4058 4.221041 TCCCTTTGAACGAAAACCTGTTTT 59.779 37.500 7.68 7.68 44.59 2.43
3915 4059 3.764972 TCCCTTTGAACGAAAACCTGTTT 59.235 39.130 0.00 0.00 0.00 2.83
3916 4060 3.358118 TCCCTTTGAACGAAAACCTGTT 58.642 40.909 0.00 0.00 0.00 3.16
3935 4079 1.217882 CAGTTGACAACACGACCTCC 58.782 55.000 20.08 0.00 0.00 4.30
4113 4579 1.270893 GGACGGATAGATCCCAAAGGC 60.271 57.143 2.89 0.00 44.24 4.35
4250 4721 2.743928 CAAGGGTCAGCCGTCAGC 60.744 66.667 0.00 0.00 44.25 4.26
4251 4722 2.046892 CCAAGGGTCAGCCGTCAG 60.047 66.667 0.00 0.00 34.97 3.51
4252 4723 4.329545 GCCAAGGGTCAGCCGTCA 62.330 66.667 0.00 0.00 34.97 4.35
4253 4724 3.959991 GAGCCAAGGGTCAGCCGTC 62.960 68.421 13.12 0.00 41.72 4.79
4254 4725 4.021925 GAGCCAAGGGTCAGCCGT 62.022 66.667 13.12 0.00 41.72 5.68
4255 4726 4.020617 TGAGCCAAGGGTCAGCCG 62.021 66.667 16.43 0.00 46.01 5.52
4339 4810 0.470766 TTTAACCCACAGCCGACAGT 59.529 50.000 0.00 0.00 0.00 3.55
4342 4813 1.201414 CCAATTTAACCCACAGCCGAC 59.799 52.381 0.00 0.00 0.00 4.79
4345 4816 4.709886 AGAATACCAATTTAACCCACAGCC 59.290 41.667 0.00 0.00 0.00 4.85
4673 5150 2.666190 CGACAGTGGTGCACAGGG 60.666 66.667 20.43 7.32 36.74 4.45
4680 5157 0.597637 AAGAAGACGCGACAGTGGTG 60.598 55.000 15.93 0.00 0.00 4.17
4681 5158 0.597637 CAAGAAGACGCGACAGTGGT 60.598 55.000 15.93 0.00 0.00 4.16
4682 5159 0.597637 ACAAGAAGACGCGACAGTGG 60.598 55.000 15.93 0.00 0.00 4.00
4711 5188 4.275936 AGACGAAACAAATCTTCAAGGGTG 59.724 41.667 0.00 0.00 0.00 4.61
4813 5314 3.702792 TCCAGAAAACCAAGAACACCAA 58.297 40.909 0.00 0.00 0.00 3.67
4894 5395 5.163519 ACAAAAACAGAAACAGCAGTAGCAT 60.164 36.000 0.00 0.00 45.49 3.79
4896 5397 4.672409 ACAAAAACAGAAACAGCAGTAGC 58.328 39.130 0.00 0.00 42.56 3.58
4903 5404 4.435386 CGGCCAAAACAAAAACAGAAACAG 60.435 41.667 2.24 0.00 0.00 3.16
4905 5406 3.181515 CCGGCCAAAACAAAAACAGAAAC 60.182 43.478 2.24 0.00 0.00 2.78
4908 5409 1.134670 CCCGGCCAAAACAAAAACAGA 60.135 47.619 2.24 0.00 0.00 3.41
4925 5427 0.033090 GTAGTATTCCCGCCTTCCCG 59.967 60.000 0.00 0.00 0.00 5.14
4926 5428 1.421480 AGTAGTATTCCCGCCTTCCC 58.579 55.000 0.00 0.00 0.00 3.97
4927 5429 3.005578 CAGTAGTAGTATTCCCGCCTTCC 59.994 52.174 0.00 0.00 0.00 3.46
4928 5430 3.635836 ACAGTAGTAGTATTCCCGCCTTC 59.364 47.826 0.00 0.00 0.00 3.46
4929 5431 3.639952 ACAGTAGTAGTATTCCCGCCTT 58.360 45.455 0.00 0.00 0.00 4.35
4930 5432 3.309600 ACAGTAGTAGTATTCCCGCCT 57.690 47.619 0.00 0.00 0.00 5.52
4931 5433 4.397481 AAACAGTAGTAGTATTCCCGCC 57.603 45.455 0.00 0.00 0.00 6.13
4932 5434 5.173664 ACAAAACAGTAGTAGTATTCCCGC 58.826 41.667 0.00 0.00 0.00 6.13
4990 5492 2.046892 CGGTTGCACCCCTCTGAG 60.047 66.667 0.00 0.00 33.75 3.35
5077 5579 4.009675 ACCCACATGCATGTACTAAAGTG 58.990 43.478 30.92 16.11 39.39 3.16
5078 5580 4.301072 ACCCACATGCATGTACTAAAGT 57.699 40.909 30.92 18.00 39.39 2.66
5079 5581 4.699735 TGAACCCACATGCATGTACTAAAG 59.300 41.667 30.92 17.47 39.39 1.85
5081 5583 4.006989 GTGAACCCACATGCATGTACTAA 58.993 43.478 30.92 12.62 42.72 2.24
5084 5586 2.919666 GTGAACCCACATGCATGTAC 57.080 50.000 30.92 20.31 42.72 2.90
5133 5636 6.717540 TGGGTACATTTAGCACACTGTTATTT 59.282 34.615 0.00 0.00 0.00 1.40
5246 5891 3.826157 CACAAGTTCATGGTTATGGTGGT 59.174 43.478 0.00 0.00 34.97 4.16
5247 5892 3.193267 CCACAAGTTCATGGTTATGGTGG 59.807 47.826 0.00 0.00 36.20 4.61
5248 5893 3.367292 GCCACAAGTTCATGGTTATGGTG 60.367 47.826 4.89 0.00 38.34 4.17
5275 5920 5.241506 TCAGTGTTCCTCCACAATCAAATTC 59.758 40.000 0.00 0.00 37.82 2.17
5276 5921 5.139727 TCAGTGTTCCTCCACAATCAAATT 58.860 37.500 0.00 0.00 37.82 1.82
5311 5956 1.429148 CGTTGGAGATGCCCTAACGC 61.429 60.000 0.00 0.00 35.60 4.84
5349 5996 8.408043 AAGACTGATTCCACAAACAAATATGA 57.592 30.769 0.00 0.00 0.00 2.15
5359 6006 6.647334 TTTGCATAAAGACTGATTCCACAA 57.353 33.333 0.00 0.00 0.00 3.33
5360 6007 6.446318 GTTTTGCATAAAGACTGATTCCACA 58.554 36.000 0.00 0.00 0.00 4.17
5405 6060 7.868906 TGCATAAAGACTGATTTCATCATCA 57.131 32.000 0.00 0.00 38.85 3.07
5464 6119 1.001706 GGTTCGAGTTTTGGCCAAGTC 60.002 52.381 19.48 15.25 0.00 3.01
5466 6121 1.028905 TGGTTCGAGTTTTGGCCAAG 58.971 50.000 19.48 6.82 0.00 3.61
5482 6137 5.334879 CGCAAAAGCTAATAGTGTTCTTGGT 60.335 40.000 0.00 0.00 0.00 3.67
5483 6138 5.088739 CGCAAAAGCTAATAGTGTTCTTGG 58.911 41.667 0.00 0.00 0.00 3.61
5484 6139 4.554973 GCGCAAAAGCTAATAGTGTTCTTG 59.445 41.667 0.30 0.00 0.00 3.02
5506 6161 4.352039 TCGAGTAGAGAAATTCACGATGC 58.648 43.478 0.00 0.00 0.00 3.91
5534 6189 5.589192 CCAATGTCCTAAGTAAGTACTCGG 58.411 45.833 0.00 0.00 34.99 4.63
5543 6198 4.464951 TCTCGAAAGCCAATGTCCTAAGTA 59.535 41.667 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.