Multiple sequence alignment - TraesCS3B01G180800

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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 TraesCS3B01G180800 chr3B 100.000 5973 0 0 1 5973 189148638 189154610 0.000000e+00 11031
1 TraesCS3B01G180800 chr3B 100.000 2825 0 0 6308 9132 189154945 189157769 0.000000e+00 5217
2 TraesCS3B01G180800 chr3B 83.186 226 34 4 7446 7669 189156041 189156264 4.320000e-48 204
3 TraesCS3B01G180800 chr3B 83.186 226 34 4 7404 7627 189156083 189156306 4.320000e-48 204
4 TraesCS3B01G180800 chr3D 95.926 4246 131 13 1745 5973 132599289 132603509 0.000000e+00 6844
5 TraesCS3B01G180800 chr3D 97.022 2821 76 2 6312 9132 132603569 132606381 0.000000e+00 4737
6 TraesCS3B01G180800 chr3D 96.198 1657 48 6 1 1642 132597635 132599291 0.000000e+00 2697
7 TraesCS3B01G180800 chr3D 82.743 226 35 4 7446 7669 132604661 132604884 2.010000e-46 198
8 TraesCS3B01G180800 chr3D 82.301 226 36 4 7404 7627 132604703 132604926 9.360000e-45 193
9 TraesCS3B01G180800 chr3A 96.493 3165 83 8 2808 5971 146388065 146391202 0.000000e+00 5204
10 TraesCS3B01G180800 chr3A 96.750 2831 72 6 6308 9132 146391265 146394081 0.000000e+00 4700
11 TraesCS3B01G180800 chr3A 95.831 1655 47 12 1 1642 146385579 146387224 0.000000e+00 2654
12 TraesCS3B01G180800 chr3A 93.075 852 41 9 1745 2588 146387222 146388063 0.000000e+00 1230
13 TraesCS3B01G180800 chr3A 82.743 226 35 4 7446 7669 146392359 146392582 2.010000e-46 198
14 TraesCS3B01G180800 chr3A 82.301 226 36 4 7404 7627 146392401 146392624 9.360000e-45 193
15 TraesCS3B01G180800 chr5D 99.138 116 1 0 1639 1754 257163278 257163163 9.290000e-50 209
16 TraesCS3B01G180800 chr5D 93.701 127 7 1 1622 1748 94343099 94343224 1.210000e-43 189
17 TraesCS3B01G180800 chr2D 97.436 117 2 1 1637 1752 111321518 111321402 2.010000e-46 198
18 TraesCS3B01G180800 chr2D 98.230 113 1 1 1637 1748 579421470 579421582 7.230000e-46 196
19 TraesCS3B01G180800 chr2D 97.391 115 3 0 1637 1751 617397747 617397861 7.230000e-46 196
20 TraesCS3B01G180800 chr2A 98.230 113 2 0 1638 1750 758757248 758757136 2.010000e-46 198
21 TraesCS3B01G180800 chr7A 97.391 115 3 0 1637 1751 724154860 724154974 7.230000e-46 196
22 TraesCS3B01G180800 chr4B 96.610 118 4 0 1633 1750 654206343 654206460 7.230000e-46 196
23 TraesCS3B01G180800 chr4B 82.635 167 24 4 4301 4466 311361428 311361266 9.560000e-30 143
24 TraesCS3B01G180800 chr6A 95.161 124 4 2 1627 1749 70424079 70423957 2.600000e-45 195
25 TraesCS3B01G180800 chr4D 83.133 166 22 4 4302 4466 226574172 226574332 7.390000e-31 147


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 TraesCS3B01G180800 chr3B 189148638 189157769 9131 False 4164.000000 11031 91.593000 1 9132 4 chr3B.!!$F1 9131
1 TraesCS3B01G180800 chr3D 132597635 132606381 8746 False 2933.800000 6844 90.838000 1 9132 5 chr3D.!!$F1 9131
2 TraesCS3B01G180800 chr3A 146385579 146394081 8502 False 2363.166667 5204 91.198833 1 9132 6 chr3A.!!$F1 9131

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
880 893 0.668706 CTTGAGACGTGTGCTCAGGG 60.669 60.000 12.54 0.00 42.74 4.45 F
1656 1680 0.251297 TTGTACTCCCTCCGTTCGGA 60.251 55.000 13.34 13.34 0.00 4.55 F
2454 2494 0.179100 TCATTAGGCAGCGAGTCAGC 60.179 55.000 0.00 0.00 37.41 4.26 F
2503 2543 0.179127 CGACAGACACATCAGGCGAT 60.179 55.000 0.00 0.00 45.33 4.58 F
2946 2986 0.924090 CTCTTCCACGTTCATAGCGC 59.076 55.000 0.00 0.00 0.00 5.92 F
3965 4006 0.179084 TTCGACGATGGGATTGCTCC 60.179 55.000 0.00 0.00 41.26 4.70 F
5207 5248 0.107945 AGGCGAATGGAAGCTGAGAC 60.108 55.000 0.00 0.00 0.00 3.36 F
5615 5656 3.054802 AGCACTAGGGAAGGTGATGAAAG 60.055 47.826 0.00 0.00 35.69 2.62 F
6811 6857 1.227823 TGTAGCAGCCACCACACAC 60.228 57.895 0.00 0.00 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 1968 0.252881 AGAGAGGGTTGGGATCAGCA 60.253 55.000 0.00 0.00 0.00 4.41 R
3104 3144 0.255890 TAGCCATCTGAAAGGGGTGC 59.744 55.000 7.93 0.00 33.78 5.01 R
3598 3639 1.074072 ATGCGGGGCAACTAACACA 59.926 52.632 0.00 0.00 43.62 3.72 R
3925 3966 1.079503 CTTTGCTACTGAGAACGGGC 58.920 55.000 0.00 0.00 0.00 6.13 R
4661 4702 0.682532 TGAACTGCCAACCTGTGCAA 60.683 50.000 0.00 0.00 36.98 4.08 R
5782 5823 1.133407 CCTGAGTACAGCCGTCTCTTC 59.867 57.143 0.00 0.00 42.25 2.87 R
6811 6857 1.056103 GAGCATGCGTATGAGTAGCG 58.944 55.000 18.28 0.00 36.36 4.26 R
7429 7475 0.174845 GTGCTCCATACGGTGTGCTA 59.825 55.000 0.00 0.00 0.00 3.49 R
8706 8758 1.150827 GTAAAACTACGGCGGCAGTT 58.849 50.000 19.35 19.35 36.56 3.16 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
86 88 3.055385 TCCTTTTGTACTAATCGGCTGCT 60.055 43.478 0.00 0.00 0.00 4.24
142 145 5.304686 TGGAGTAGGACTTGATGTTTGTT 57.695 39.130 0.00 0.00 0.00 2.83
268 274 3.299190 GGATCTCGGCGAGGAGGG 61.299 72.222 33.93 11.94 34.74 4.30
549 558 6.128007 GCACAGCTTTATTGCTTAGTTCCTTA 60.128 38.462 0.00 0.00 41.98 2.69
550 559 7.244192 CACAGCTTTATTGCTTAGTTCCTTAC 58.756 38.462 0.00 0.00 41.98 2.34
551 560 6.374613 ACAGCTTTATTGCTTAGTTCCTTACC 59.625 38.462 0.00 0.00 41.98 2.85
639 648 3.881089 TGCATGTTATCTGCTGAGGATTG 59.119 43.478 0.00 0.00 40.34 2.67
672 681 2.159198 GGCTGGGTTGCATTCATTACTG 60.159 50.000 0.00 0.00 34.04 2.74
816 829 7.359262 TGTGTTTTGTTCCTCGTCTAATATG 57.641 36.000 0.00 0.00 0.00 1.78
874 887 2.158449 CCATCTTTCTTGAGACGTGTGC 59.842 50.000 0.00 0.00 0.00 4.57
880 893 0.668706 CTTGAGACGTGTGCTCAGGG 60.669 60.000 12.54 0.00 42.74 4.45
914 927 0.845768 CCAAGCTGCGTTTTGTTTCG 59.154 50.000 0.00 0.00 0.00 3.46
1096 1109 1.462283 CAGTGGTCGCTGAAACTGATG 59.538 52.381 5.67 0.00 42.09 3.07
1211 1224 4.676924 GTCAGCTTACACTTTTGCACAATC 59.323 41.667 0.00 0.00 0.00 2.67
1233 1246 6.956299 TCCTTTGAGCTTACGTTTACATAC 57.044 37.500 0.00 0.00 0.00 2.39
1241 1254 5.122869 AGCTTACGTTTACATACTCGTCTGA 59.877 40.000 0.00 0.00 37.66 3.27
1301 1314 3.376859 ACTGTGTTTTGATGCAAGACGAA 59.623 39.130 0.00 0.00 32.21 3.85
1378 1391 8.433421 TCTGCTAACTACTTGTTATATTTGGC 57.567 34.615 0.00 0.00 40.02 4.52
1388 1401 7.826690 ACTTGTTATATTTGGCGTTTCATTCT 58.173 30.769 0.00 0.00 0.00 2.40
1463 1482 6.704937 ACATGATATCATCACTGCTACACAAG 59.295 38.462 15.49 2.25 43.01 3.16
1497 1516 2.041755 TGAGTGTCTCTTCTCCCAGCTA 59.958 50.000 0.00 0.00 0.00 3.32
1542 1566 8.964772 GCAGCCTTGAGGAATATATATTCAAAT 58.035 33.333 28.37 17.65 42.92 2.32
1642 1666 7.553881 TTTTAGCCATGCTCTAGATTTGTAC 57.446 36.000 0.00 0.00 40.44 2.90
1643 1667 6.485830 TTAGCCATGCTCTAGATTTGTACT 57.514 37.500 0.00 0.00 40.44 2.73
1644 1668 4.954875 AGCCATGCTCTAGATTTGTACTC 58.045 43.478 0.00 0.00 30.62 2.59
1645 1669 4.061596 GCCATGCTCTAGATTTGTACTCC 58.938 47.826 0.00 0.00 0.00 3.85
1646 1670 4.636249 CCATGCTCTAGATTTGTACTCCC 58.364 47.826 0.00 0.00 0.00 4.30
1647 1671 4.346418 CCATGCTCTAGATTTGTACTCCCT 59.654 45.833 0.00 0.00 0.00 4.20
1648 1672 5.510520 CCATGCTCTAGATTTGTACTCCCTC 60.511 48.000 0.00 0.00 0.00 4.30
1649 1673 3.961408 TGCTCTAGATTTGTACTCCCTCC 59.039 47.826 0.00 0.00 0.00 4.30
1650 1674 3.004944 GCTCTAGATTTGTACTCCCTCCG 59.995 52.174 0.00 0.00 0.00 4.63
1651 1675 4.208746 CTCTAGATTTGTACTCCCTCCGT 58.791 47.826 0.00 0.00 0.00 4.69
1652 1676 4.607239 TCTAGATTTGTACTCCCTCCGTT 58.393 43.478 0.00 0.00 0.00 4.44
1653 1677 3.889520 AGATTTGTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
1654 1678 2.165845 AGATTTGTACTCCCTCCGTTCG 59.834 50.000 0.00 0.00 0.00 3.95
1655 1679 0.604578 TTTGTACTCCCTCCGTTCGG 59.395 55.000 4.74 4.74 0.00 4.30
1656 1680 0.251297 TTGTACTCCCTCCGTTCGGA 60.251 55.000 13.34 13.34 0.00 4.55
1657 1681 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
1658 1682 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
1659 1683 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
1660 1684 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1661 1685 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1662 1686 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1663 1687 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1664 1688 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1665 1689 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1666 1690 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1667 1691 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
1668 1692 4.181578 CTCCGTTCGGAATTACTTGTCAT 58.818 43.478 14.79 0.00 33.41 3.06
1669 1693 5.327616 TCCGTTCGGAATTACTTGTCATA 57.672 39.130 11.66 0.00 0.00 2.15
1670 1694 5.722263 TCCGTTCGGAATTACTTGTCATAA 58.278 37.500 11.66 0.00 0.00 1.90
1671 1695 6.164876 TCCGTTCGGAATTACTTGTCATAAA 58.835 36.000 11.66 0.00 0.00 1.40
1672 1696 6.649973 TCCGTTCGGAATTACTTGTCATAAAA 59.350 34.615 11.66 0.00 0.00 1.52
1673 1697 7.172875 TCCGTTCGGAATTACTTGTCATAAAAA 59.827 33.333 11.66 0.00 0.00 1.94
1674 1698 7.966204 CCGTTCGGAATTACTTGTCATAAAAAT 59.034 33.333 5.19 0.00 0.00 1.82
1675 1699 8.785101 CGTTCGGAATTACTTGTCATAAAAATG 58.215 33.333 0.00 0.00 0.00 2.32
1676 1700 9.072294 GTTCGGAATTACTTGTCATAAAAATGG 57.928 33.333 0.00 0.00 0.00 3.16
1677 1701 8.568676 TCGGAATTACTTGTCATAAAAATGGA 57.431 30.769 0.00 0.00 0.00 3.41
1678 1702 9.184523 TCGGAATTACTTGTCATAAAAATGGAT 57.815 29.630 0.00 0.00 0.00 3.41
1679 1703 9.236691 CGGAATTACTTGTCATAAAAATGGATG 57.763 33.333 0.00 0.00 0.00 3.51
1722 1746 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
1723 1747 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
1724 1748 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
1725 1749 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
1726 1750 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
1727 1751 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
1728 1752 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
1729 1753 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
1730 1754 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
1731 1755 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
1732 1756 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
1733 1757 4.868171 TCATTTCTTGGACGAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
1734 1758 4.524316 TTTCTTGGACGAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
1735 1759 4.524316 TTCTTGGACGAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
1736 1760 3.841643 TCTTGGACGAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
1737 1761 2.267188 TGGACGAGTAATTCCGAACG 57.733 50.000 0.00 0.00 0.00 3.95
1738 1762 1.135315 TGGACGAGTAATTCCGAACGG 60.135 52.381 6.94 6.94 0.00 4.44
1739 1763 1.133025 GGACGAGTAATTCCGAACGGA 59.867 52.381 12.04 12.04 43.52 4.69
1740 1764 2.448219 GACGAGTAATTCCGAACGGAG 58.552 52.381 15.34 5.60 46.06 4.63
1741 1765 1.133790 ACGAGTAATTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
1742 1766 1.535437 CGAGTAATTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
1743 1767 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
1744 1768 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1745 1769 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
1746 1770 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
1861 1886 3.641436 TCTGAGTACAACAGGCTTCTCAA 59.359 43.478 16.23 0.00 36.22 3.02
1862 1887 4.284490 TCTGAGTACAACAGGCTTCTCAAT 59.716 41.667 16.23 0.00 36.22 2.57
1938 1963 0.908198 ACATCCTCTCCTCTTGGTGC 59.092 55.000 0.00 0.00 34.23 5.01
1943 1968 1.005215 CCTCTCCTCTTGGTGCCAATT 59.995 52.381 3.91 0.00 35.20 2.32
1958 1983 1.620524 CCAATTGCTGATCCCAACCCT 60.621 52.381 0.00 0.00 0.00 4.34
2076 2102 9.571810 TGTTTGTCATATTTATCTTGTTCATGC 57.428 29.630 0.00 0.00 0.00 4.06
2110 2136 6.756074 GCATTTATTTTAGCCATGCTGTACAA 59.244 34.615 0.00 0.00 40.10 2.41
2128 2154 5.532779 TGTACAATTGCATTTGTGTACCTGA 59.467 36.000 28.50 10.77 43.63 3.86
2139 2165 7.620215 CATTTGTGTACCTGACATTTTTGTTG 58.380 34.615 0.00 0.00 41.14 3.33
2215 2241 3.376234 GCATCAACAAGCTGCTCTGAATA 59.624 43.478 1.00 0.00 36.46 1.75
2219 2245 4.214119 TCAACAAGCTGCTCTGAATACAAC 59.786 41.667 1.00 0.00 0.00 3.32
2246 2272 6.183359 GGCTTCGCAATACGTTCTACATATAC 60.183 42.308 0.00 0.00 44.19 1.47
2282 2308 5.991933 TCTACTTCTCACTTTCATCAGCT 57.008 39.130 0.00 0.00 0.00 4.24
2300 2326 1.617263 GCTCCCGCATCCTCTCCTATA 60.617 57.143 0.00 0.00 35.78 1.31
2334 2368 4.626287 GCTGATCCCAATCACCTTTGTCTA 60.626 45.833 0.00 0.00 36.98 2.59
2337 2371 2.026262 TCCCAATCACCTTTGTCTAGGC 60.026 50.000 0.00 0.00 38.99 3.93
2347 2381 5.298276 CACCTTTGTCTAGGCAGTTGTTAAA 59.702 40.000 0.00 0.00 38.99 1.52
2348 2382 6.016276 CACCTTTGTCTAGGCAGTTGTTAAAT 60.016 38.462 0.00 0.00 38.99 1.40
2403 2437 3.632189 GGAACAAGTGAACAGCAACATC 58.368 45.455 0.00 0.00 0.00 3.06
2454 2494 0.179100 TCATTAGGCAGCGAGTCAGC 60.179 55.000 0.00 0.00 37.41 4.26
2455 2495 0.460811 CATTAGGCAGCGAGTCAGCA 60.461 55.000 9.14 0.00 40.15 4.41
2503 2543 0.179127 CGACAGACACATCAGGCGAT 60.179 55.000 0.00 0.00 45.33 4.58
2553 2593 4.462483 TCAGCCTTGGATTTTTACCATCAC 59.538 41.667 0.00 0.00 37.26 3.06
2558 2598 2.675844 TGGATTTTTACCATCACGAGCG 59.324 45.455 0.00 0.00 32.03 5.03
2589 2629 1.433199 TGAGAACCTCCTCTCCCAGAA 59.567 52.381 0.00 0.00 41.09 3.02
2634 2674 0.972471 TCAGCTTCAGCCGGATCTGA 60.972 55.000 5.05 6.67 43.38 3.27
2650 2690 5.643777 CGGATCTGAAGTACCATCAGTTTTT 59.356 40.000 19.98 8.72 43.77 1.94
2682 2722 2.615869 GCTAGGAAGCTCTCTTGTGTG 58.384 52.381 0.00 0.00 45.85 3.82
2693 2733 4.084118 GCTCTCTTGTGTGTCTGACATTTC 60.084 45.833 14.37 8.09 36.78 2.17
2710 2750 6.126796 TGACATTTCCATAGAACCAGCTGATA 60.127 38.462 17.39 2.77 0.00 2.15
2765 2805 6.500589 TTCTCATTATAGCTTGGCCTAACT 57.499 37.500 3.32 0.00 0.00 2.24
2830 2870 7.878644 GGGGTGGTTAGAAGATAGAACATATTC 59.121 40.741 0.00 0.00 34.78 1.75
2853 2893 9.942526 ATTCCCTCCAAATTTACATTATCTTCT 57.057 29.630 0.00 0.00 0.00 2.85
2920 2960 1.304134 AAGTGGACCGAATTGCCCC 60.304 57.895 0.00 0.00 0.00 5.80
2945 2985 2.561733 TCTCTTCCACGTTCATAGCG 57.438 50.000 0.00 0.00 0.00 4.26
2946 2986 0.924090 CTCTTCCACGTTCATAGCGC 59.076 55.000 0.00 0.00 0.00 5.92
3004 3044 1.344763 GGCTGCGATACCAAGGAGTAT 59.655 52.381 0.00 0.00 35.63 2.12
3078 3118 5.624344 AATCATTTGCAGTGTCAAGAGAG 57.376 39.130 0.00 0.00 0.00 3.20
3093 3133 7.115663 GTGTCAAGAGAGTTTAGAGTTCATGTC 59.884 40.741 0.00 0.00 0.00 3.06
3104 3144 4.186926 AGAGTTCATGTCGATCAACCATG 58.813 43.478 6.62 6.62 37.82 3.66
3191 3231 8.523915 TGATATAACAGTTTTTGCCTCATCAT 57.476 30.769 0.00 0.00 0.00 2.45
3217 3257 2.284754 TTTTCCACTGTGCTGGCATA 57.715 45.000 1.29 0.00 0.00 3.14
3260 3300 9.045223 GCAACTTTTTCATTTGTTCCTTATCTT 57.955 29.630 0.00 0.00 0.00 2.40
3303 3343 5.988287 TGTCTTGGACATATTAGACATGCA 58.012 37.500 0.00 0.00 41.34 3.96
3304 3344 6.413892 TGTCTTGGACATATTAGACATGCAA 58.586 36.000 0.00 0.00 41.34 4.08
3305 3345 6.316140 TGTCTTGGACATATTAGACATGCAAC 59.684 38.462 0.00 0.00 41.34 4.17
3306 3346 5.822519 TCTTGGACATATTAGACATGCAACC 59.177 40.000 0.00 0.00 0.00 3.77
3307 3347 5.372343 TGGACATATTAGACATGCAACCT 57.628 39.130 0.00 0.00 0.00 3.50
3308 3348 5.368145 TGGACATATTAGACATGCAACCTC 58.632 41.667 0.00 0.00 0.00 3.85
3309 3349 4.757149 GGACATATTAGACATGCAACCTCC 59.243 45.833 0.00 0.00 0.00 4.30
3310 3350 5.455326 GGACATATTAGACATGCAACCTCCT 60.455 44.000 0.00 0.00 0.00 3.69
3311 3351 6.006275 ACATATTAGACATGCAACCTCCTT 57.994 37.500 0.00 0.00 0.00 3.36
3312 3352 6.426587 ACATATTAGACATGCAACCTCCTTT 58.573 36.000 0.00 0.00 0.00 3.11
3313 3353 6.891908 ACATATTAGACATGCAACCTCCTTTT 59.108 34.615 0.00 0.00 0.00 2.27
3314 3354 5.904362 ATTAGACATGCAACCTCCTTTTC 57.096 39.130 0.00 0.00 0.00 2.29
3315 3355 3.515602 AGACATGCAACCTCCTTTTCT 57.484 42.857 0.00 0.00 0.00 2.52
3316 3356 3.837355 AGACATGCAACCTCCTTTTCTT 58.163 40.909 0.00 0.00 0.00 2.52
3363 3403 5.473504 TGCAAACAGGTCCTATTTCTTTCTC 59.526 40.000 0.00 0.00 0.00 2.87
3375 3415 9.098355 TCCTATTTCTTTCTCACATGATTTACG 57.902 33.333 0.00 0.00 0.00 3.18
3494 3535 7.596248 ACAATTGTTCATGTCTATTTGCACTTC 59.404 33.333 4.92 0.00 0.00 3.01
3598 3639 9.520515 ACATCACAAGAGGTTACTAATTCAATT 57.479 29.630 0.00 0.00 34.67 2.32
3642 3683 1.439543 AAAGGCCCTCTGTCTGAACT 58.560 50.000 0.00 0.00 0.00 3.01
3677 3718 9.561069 GGTACAACCTATGAATGAATATGTCTT 57.439 33.333 0.00 0.00 34.73 3.01
3714 3755 3.129638 AGAGAGAATCCGTCTACACTTGC 59.870 47.826 0.00 0.00 36.41 4.01
3729 3770 2.024414 ACTTGCTGTTGAAGTGGGTTC 58.976 47.619 0.00 0.00 32.30 3.62
3894 3935 3.225940 TCTCAGAGTTTCAGTGCTCAGA 58.774 45.455 0.00 0.00 34.39 3.27
3929 3970 1.136565 CCATAACAGTTTGCGCCCG 59.863 57.895 4.18 0.00 0.00 6.13
3935 3976 2.110213 AGTTTGCGCCCGTTCTCA 59.890 55.556 4.18 0.00 0.00 3.27
3965 4006 0.179084 TTCGACGATGGGATTGCTCC 60.179 55.000 0.00 0.00 41.26 4.70
3981 4022 0.247460 CTCCGTGTGCTTGGATGAGA 59.753 55.000 0.00 0.00 32.83 3.27
4115 4156 6.030228 CGTTGATTTCAGAAGCTTATTTCCC 58.970 40.000 0.00 0.00 0.00 3.97
4204 4245 4.669206 ACAATTCCAAATGCAACTCACA 57.331 36.364 0.00 0.00 0.00 3.58
4247 4288 3.202151 CACCCATGAAAGGTATGGTAGGT 59.798 47.826 0.00 0.00 42.85 3.08
4279 4320 7.631717 AATTCCTAACTAGCATTTTCTGGTC 57.368 36.000 0.00 0.00 36.79 4.02
4386 4427 2.157738 GCTTCTGTGGATATCATGGCC 58.842 52.381 4.83 0.00 0.00 5.36
4593 4634 1.080298 GGTCGGTAACAGTGGTCCG 60.080 63.158 11.45 11.45 43.65 4.79
4634 4675 9.177608 TCCAAAAAGAAGTATTGGATCTACATG 57.822 33.333 2.48 0.00 45.71 3.21
4661 4702 6.770542 AGAAGAAGAAGAAAGGGAAACGTAT 58.229 36.000 0.00 0.00 0.00 3.06
4665 4706 4.394729 AGAAGAAAGGGAAACGTATTGCA 58.605 39.130 0.00 0.00 0.00 4.08
4769 4810 0.535797 GTCGGGGGTTCTAGAAGTGG 59.464 60.000 5.12 0.00 0.00 4.00
4848 4889 4.163441 TGATGTTCCTTCTGTTGACCAA 57.837 40.909 0.00 0.00 0.00 3.67
5055 5096 6.587990 CAGATGTATTTGCCTCTAAGGATACG 59.412 42.308 0.00 0.00 46.39 3.06
5056 5097 4.628074 TGTATTTGCCTCTAAGGATACGC 58.372 43.478 0.00 0.00 46.39 4.42
5057 5098 3.838244 ATTTGCCTCTAAGGATACGCA 57.162 42.857 0.00 0.00 46.39 5.24
5207 5248 0.107945 AGGCGAATGGAAGCTGAGAC 60.108 55.000 0.00 0.00 0.00 3.36
5242 5283 8.512138 AGAGGTTCTTATCAAATGTAAAAACCG 58.488 33.333 0.00 0.00 38.86 4.44
5455 5496 7.501225 AGAAATTAAGAACCGAGAAAAAGGACA 59.499 33.333 0.00 0.00 0.00 4.02
5528 5569 6.980397 ACTGTTGATAAAGTTGCTTTGAAAGG 59.020 34.615 7.09 0.00 35.21 3.11
5615 5656 3.054802 AGCACTAGGGAAGGTGATGAAAG 60.055 47.826 0.00 0.00 35.69 2.62
5782 5823 4.436451 CGGAACATGATGATGTCAACACTG 60.436 45.833 0.00 0.00 42.30 3.66
6589 6635 3.825585 TGGATATTGTTGAACTGCTTGCA 59.174 39.130 0.00 0.00 0.00 4.08
6625 6671 4.929479 AGAGACCACTGATAACTGAGACT 58.071 43.478 0.00 0.00 0.00 3.24
6811 6857 1.227823 TGTAGCAGCCACCACACAC 60.228 57.895 0.00 0.00 0.00 3.82
6817 6863 2.030562 GCCACCACACACGCTACT 59.969 61.111 0.00 0.00 0.00 2.57
6922 6968 1.394917 GTCACTATTGCTGCAACCTCG 59.605 52.381 18.51 8.63 0.00 4.63
6946 6992 5.455326 GCCACTATTATCACCAGACAAGGAT 60.455 44.000 0.00 0.00 0.00 3.24
7240 7286 2.488153 GTCAACCATGGAAGCTGGTAAC 59.512 50.000 21.47 0.00 46.29 2.50
7290 7336 9.093458 ACATTCAGGTTTTTATCCAAGAGAAAT 57.907 29.630 0.00 0.00 0.00 2.17
7429 7475 1.617850 GATCAGTCCATCGGATCAGCT 59.382 52.381 0.00 0.00 43.68 4.24
7450 7496 1.361668 GCACACCGTATGGAGCACAG 61.362 60.000 8.33 0.00 39.21 3.66
7563 7609 2.238144 ACATTGGATCAGCTAGCACACT 59.762 45.455 18.83 0.00 0.00 3.55
7638 7684 2.158415 ACCTAAATGGCATGGGATCAGG 60.158 50.000 17.40 12.23 40.22 3.86
7651 7697 3.177228 GGGATCAGGTAGCACATCCTAT 58.823 50.000 17.21 0.00 35.93 2.57
7904 7950 0.743097 GGCATTGAACTCAGGGATGC 59.257 55.000 6.38 6.38 41.67 3.91
7969 8015 4.006319 CCAGTCCAGGATTTTCTTCAGTC 58.994 47.826 0.00 0.00 0.00 3.51
8266 8318 0.237235 CACCGTGGTGGAAATGAACG 59.763 55.000 11.29 0.00 42.00 3.95
8319 8371 6.075315 TGCAGGCTCCTTAGTAAGATATGTA 58.925 40.000 11.66 0.50 0.00 2.29
8342 8394 3.245730 TGCTCCCTTTTCTGGATGGAAAT 60.246 43.478 0.00 0.00 35.51 2.17
8346 8398 6.462067 GCTCCCTTTTCTGGATGGAAATATTG 60.462 42.308 0.00 0.00 35.51 1.90
8356 8408 5.593909 TGGATGGAAATATTGCAGTTACCAG 59.406 40.000 0.00 0.00 33.40 4.00
8469 8521 9.821240 ATGAACTATCCTCATATCTAGTTGTCT 57.179 33.333 0.00 0.00 35.22 3.41
8473 8525 9.953565 ACTATCCTCATATCTAGTTGTCTAGTC 57.046 37.037 2.84 0.00 42.88 2.59
8474 8526 9.952030 CTATCCTCATATCTAGTTGTCTAGTCA 57.048 37.037 2.84 0.00 42.88 3.41
8485 8537 6.716934 AGTTGTCTAGTCAAGAGAAAGTGA 57.283 37.500 2.46 0.00 39.06 3.41
8596 8648 4.345547 TGGTGGTAATATCGGCAGATTACA 59.654 41.667 4.22 0.00 39.34 2.41
8635 8687 6.827641 GTTGTAAACTATCGAATTGCAGTCA 58.172 36.000 0.00 0.00 45.32 3.41
8654 8706 6.109359 CAGTCACTTACTTCTAAAGGATGGG 58.891 44.000 0.00 0.00 35.76 4.00
8672 8724 3.218453 TGGGTTGTCAGTGGTAATGTTG 58.782 45.455 0.00 0.00 0.00 3.33
8803 8855 9.494479 GTGTGACTCATTAATCATACAATTGTG 57.506 33.333 21.42 5.51 37.04 3.33
8819 8871 1.832883 TGTGTTGTTGCTTGTCCTGT 58.167 45.000 0.00 0.00 0.00 4.00
8927 8979 3.118261 ACCACTGATTTGGATATCACGCT 60.118 43.478 4.83 0.00 39.24 5.07
8936 8988 3.234353 TGGATATCACGCTGAGAAGGAT 58.766 45.455 4.83 0.00 0.00 3.24
8945 8997 3.387374 ACGCTGAGAAGGATGATGATTCT 59.613 43.478 0.00 0.00 36.02 2.40
8946 8998 3.741856 CGCTGAGAAGGATGATGATTCTG 59.258 47.826 0.00 0.00 33.53 3.02
8960 9012 6.710278 TGATGATTCTGCCGGATATGATTTA 58.290 36.000 5.05 0.00 0.00 1.40
9038 9090 5.949735 TGTTCCAGTTGTGTTTTTCTCTTC 58.050 37.500 0.00 0.00 0.00 2.87
9050 9102 8.188139 TGTGTTTTTCTCTTCATTTAGGTTGAC 58.812 33.333 0.00 0.00 0.00 3.18
9051 9103 8.406297 GTGTTTTTCTCTTCATTTAGGTTGACT 58.594 33.333 0.00 0.00 0.00 3.41
9052 9104 8.966868 TGTTTTTCTCTTCATTTAGGTTGACTT 58.033 29.630 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.202382 GCCAGACGTAAATCTACCGCT 60.202 52.381 0.00 0.00 0.00 5.52
86 88 2.922955 TCCAAAATGGGGTGGAGATGTA 59.077 45.455 0.00 0.00 39.04 2.29
142 145 2.027073 CACGCAAGCTACGCAAGGA 61.027 57.895 8.84 0.00 43.11 3.36
268 274 1.745489 CTCTTGGCCTGGCGGTTAC 60.745 63.158 13.40 0.00 0.00 2.50
403 409 2.928396 ACGGAGTTGGGAGGTGGG 60.928 66.667 0.00 0.00 37.78 4.61
549 558 1.548719 TGTAGACACGCAGCTAATGGT 59.451 47.619 0.00 0.00 0.00 3.55
550 559 1.927174 GTGTAGACACGCAGCTAATGG 59.073 52.381 0.00 0.00 37.10 3.16
639 648 1.379044 CCCAGCCACATCTCCAACC 60.379 63.158 0.00 0.00 0.00 3.77
672 681 2.618709 ACACAGCAAACCAAGCTAAGAC 59.381 45.455 0.00 0.00 41.14 3.01
816 829 2.735823 CCTGAAACAAGAAGCAAGCAC 58.264 47.619 0.00 0.00 0.00 4.40
874 887 2.704464 TCATCATGCAGAACCCTGAG 57.296 50.000 0.00 0.00 43.02 3.35
880 893 2.950309 AGCTTGGATCATCATGCAGAAC 59.050 45.455 10.86 0.00 39.39 3.01
914 927 2.175322 GAAGCAGCACGCAGAAGC 59.825 61.111 0.00 0.00 46.13 3.86
1096 1109 0.873743 GGCTGCTCTGCTGACGTATC 60.874 60.000 0.00 0.00 0.00 2.24
1211 1224 6.237490 CGAGTATGTAAACGTAAGCTCAAAGG 60.237 42.308 0.00 0.00 45.62 3.11
1233 1246 2.995939 TGCATGCTTAAACTCAGACGAG 59.004 45.455 20.33 0.00 45.49 4.18
1388 1401 9.213777 ACTATGGTGGATATGAAGTAGAAAAGA 57.786 33.333 0.00 0.00 0.00 2.52
1463 1482 4.035792 AGAGACACTCATATAGACACGCAC 59.964 45.833 0.00 0.00 32.06 5.34
1497 1516 3.804638 AAAGCAGCAGCAGCCAGGT 62.805 57.895 6.10 0.00 45.49 4.00
1550 1574 9.950680 ACACAATAATTACTCAACAAAAGACAG 57.049 29.630 0.00 0.00 0.00 3.51
1600 1624 6.582295 GGCTAAAATAAATGCATGTATCCACG 59.418 38.462 9.89 1.76 0.00 4.94
1642 1666 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1643 1667 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1644 1668 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1645 1669 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1646 1670 3.581755 TGACAAGTAATTCCGAACGGAG 58.418 45.455 15.34 5.60 46.06 4.63
1647 1671 3.663995 TGACAAGTAATTCCGAACGGA 57.336 42.857 12.04 12.04 43.52 4.69
1648 1672 6.411630 TTTATGACAAGTAATTCCGAACGG 57.588 37.500 6.94 6.94 0.00 4.44
1649 1673 8.785101 CATTTTTATGACAAGTAATTCCGAACG 58.215 33.333 0.00 0.00 0.00 3.95
1650 1674 9.072294 CCATTTTTATGACAAGTAATTCCGAAC 57.928 33.333 0.00 0.00 0.00 3.95
1651 1675 9.015367 TCCATTTTTATGACAAGTAATTCCGAA 57.985 29.630 0.00 0.00 0.00 4.30
1652 1676 8.568676 TCCATTTTTATGACAAGTAATTCCGA 57.431 30.769 0.00 0.00 0.00 4.55
1653 1677 9.236691 CATCCATTTTTATGACAAGTAATTCCG 57.763 33.333 0.00 0.00 0.00 4.30
1696 1720 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
1697 1721 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
1698 1722 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
1699 1723 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
1700 1724 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
1701 1725 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
1702 1726 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
1703 1727 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
1704 1728 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
1705 1729 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
1706 1730 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
1707 1731 7.189512 GGAATTACTCGTCCAAGAAATGAATG 58.810 38.462 0.00 0.00 33.79 2.67
1708 1732 6.037172 CGGAATTACTCGTCCAAGAAATGAAT 59.963 38.462 0.00 0.00 33.10 2.57
1709 1733 5.350365 CGGAATTACTCGTCCAAGAAATGAA 59.650 40.000 0.00 0.00 33.10 2.57
1710 1734 4.868171 CGGAATTACTCGTCCAAGAAATGA 59.132 41.667 0.00 0.00 33.10 2.57
1711 1735 4.868171 TCGGAATTACTCGTCCAAGAAATG 59.132 41.667 0.00 0.00 33.10 2.32
1712 1736 5.080969 TCGGAATTACTCGTCCAAGAAAT 57.919 39.130 0.00 0.00 33.10 2.17
1713 1737 4.524316 TCGGAATTACTCGTCCAAGAAA 57.476 40.909 0.00 0.00 33.10 2.52
1714 1738 4.240096 GTTCGGAATTACTCGTCCAAGAA 58.760 43.478 0.00 0.00 33.10 2.52
1715 1739 3.671433 CGTTCGGAATTACTCGTCCAAGA 60.671 47.826 0.00 0.00 33.10 3.02
1716 1740 2.597305 CGTTCGGAATTACTCGTCCAAG 59.403 50.000 0.00 0.00 33.10 3.61
1717 1741 2.598589 CGTTCGGAATTACTCGTCCAA 58.401 47.619 0.00 0.00 33.10 3.53
1718 1742 1.135315 CCGTTCGGAATTACTCGTCCA 60.135 52.381 5.19 0.00 33.10 4.02
1719 1743 1.133025 TCCGTTCGGAATTACTCGTCC 59.867 52.381 11.66 0.00 0.00 4.79
1720 1744 2.448219 CTCCGTTCGGAATTACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
1721 1745 1.133790 CCTCCGTTCGGAATTACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
1722 1746 1.535437 CCCTCCGTTCGGAATTACTCG 60.535 57.143 14.79 1.97 33.41 4.18
1723 1747 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
1724 1748 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1725 1749 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1726 1750 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1727 1751 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
1728 1752 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
1729 1753 1.856629 AATACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.00 33.41 4.30
1730 1754 1.479323 CAAATACTCCCTCCGTTCGGA 59.521 52.381 13.34 13.34 0.00 4.55
1731 1755 1.206371 ACAAATACTCCCTCCGTTCGG 59.794 52.381 4.74 4.74 0.00 4.30
1732 1756 2.268298 CACAAATACTCCCTCCGTTCG 58.732 52.381 0.00 0.00 0.00 3.95
1733 1757 3.329929 ACACAAATACTCCCTCCGTTC 57.670 47.619 0.00 0.00 0.00 3.95
1734 1758 3.055602 GGTACACAAATACTCCCTCCGTT 60.056 47.826 0.00 0.00 0.00 4.44
1735 1759 2.498885 GGTACACAAATACTCCCTCCGT 59.501 50.000 0.00 0.00 0.00 4.69
1736 1760 2.764572 AGGTACACAAATACTCCCTCCG 59.235 50.000 0.00 0.00 0.00 4.63
1737 1761 3.773119 TCAGGTACACAAATACTCCCTCC 59.227 47.826 0.00 0.00 0.00 4.30
1738 1762 4.222145 TGTCAGGTACACAAATACTCCCTC 59.778 45.833 0.00 0.00 31.43 4.30
1739 1763 4.164981 TGTCAGGTACACAAATACTCCCT 58.835 43.478 0.00 0.00 31.43 4.20
1740 1764 4.546829 TGTCAGGTACACAAATACTCCC 57.453 45.455 0.00 0.00 31.43 4.30
1741 1765 7.448748 AAAATGTCAGGTACACAAATACTCC 57.551 36.000 0.00 0.00 42.09 3.85
1938 1963 0.826062 GGGTTGGGATCAGCAATTGG 59.174 55.000 7.72 0.00 0.00 3.16
1943 1968 0.252881 AGAGAGGGTTGGGATCAGCA 60.253 55.000 0.00 0.00 0.00 4.41
1958 1983 1.131638 AACAACTGCCCAGACAGAGA 58.868 50.000 1.69 0.00 40.25 3.10
2076 2102 4.386652 GGCTAAAATAAATGCATGCATCCG 59.613 41.667 32.25 15.01 35.31 4.18
2110 2136 5.726980 AATGTCAGGTACACAAATGCAAT 57.273 34.783 0.00 0.00 42.09 3.56
2128 2154 5.229052 CGATGAAACACGTCAACAAAAATGT 59.771 36.000 0.00 0.00 34.46 2.71
2139 2165 0.513717 CGCGTTCGATGAAACACGTC 60.514 55.000 0.00 0.00 38.10 4.34
2219 2245 8.258083 TATATGTAGAACGTATTGCGAAGCCTG 61.258 40.741 0.00 0.00 41.08 4.85
2246 2272 7.223582 AGTGAGAAGTAGATTATGCAAATGTCG 59.776 37.037 0.00 0.00 0.00 4.35
2282 2308 1.006043 CCTATAGGAGAGGATGCGGGA 59.994 57.143 14.11 0.00 35.99 5.14
2300 2326 1.076485 GGATCAGCCATTGCCACCT 60.076 57.895 0.00 0.00 38.69 4.00
2334 2368 6.127730 CCGGATAGAAAATTTAACAACTGCCT 60.128 38.462 0.00 0.00 0.00 4.75
2337 2371 6.852664 AGCCGGATAGAAAATTTAACAACTG 58.147 36.000 5.05 0.00 0.00 3.16
2347 2381 3.213206 TGCATGAGCCGGATAGAAAAT 57.787 42.857 5.05 0.00 41.13 1.82
2348 2382 2.708216 TGCATGAGCCGGATAGAAAA 57.292 45.000 5.05 0.00 41.13 2.29
2403 2437 3.102052 AGTGTGCAAAAATGGAAGCAG 57.898 42.857 0.00 0.00 37.72 4.24
2454 2494 1.140589 CCTGTCAGCGCTCCTAGTG 59.859 63.158 7.13 0.00 0.00 2.74
2455 2495 2.716017 GCCTGTCAGCGCTCCTAGT 61.716 63.158 7.13 0.00 0.00 2.57
2553 2593 2.328473 TCTCAACACTGAAATCGCTCG 58.672 47.619 0.00 0.00 0.00 5.03
2558 2598 4.646572 AGGAGGTTCTCAACACTGAAATC 58.353 43.478 0.00 0.00 31.08 2.17
2589 2629 2.636830 CAACTGATGAATCTCCCGCTT 58.363 47.619 0.00 0.00 0.00 4.68
2634 2674 4.729868 AGGAGCAAAAACTGATGGTACTT 58.270 39.130 0.00 0.00 34.66 2.24
2682 2722 4.333926 GCTGGTTCTATGGAAATGTCAGAC 59.666 45.833 13.10 0.00 32.81 3.51
2747 2787 5.896073 ACAGAGTTAGGCCAAGCTATAAT 57.104 39.130 5.01 0.00 0.00 1.28
2754 2794 1.351017 TGGGAACAGAGTTAGGCCAAG 59.649 52.381 5.01 0.00 35.01 3.61
2755 2795 1.440618 TGGGAACAGAGTTAGGCCAA 58.559 50.000 5.01 0.00 35.01 4.52
2853 2893 7.014711 TGCAAATGACTAAACATGGAAACCTTA 59.985 33.333 0.00 0.00 0.00 2.69
2920 2960 5.006165 GCTATGAACGTGGAAGAGAATTCTG 59.994 44.000 14.00 0.00 32.79 3.02
2945 2985 2.300996 TCCTGGATGGAAGGAGTGC 58.699 57.895 0.00 0.00 42.94 4.40
2966 3006 2.504175 AGCCTTGGATCTAACGCCTAAA 59.496 45.455 8.73 0.00 0.00 1.85
3004 3044 4.627284 TGTAAGTTTGGATCTTTCCCGA 57.373 40.909 0.00 0.00 41.83 5.14
3078 3118 5.637810 TGGTTGATCGACATGAACTCTAAAC 59.362 40.000 15.11 0.00 0.00 2.01
3093 3133 0.680921 AAGGGGTGCATGGTTGATCG 60.681 55.000 0.00 0.00 0.00 3.69
3104 3144 0.255890 TAGCCATCTGAAAGGGGTGC 59.744 55.000 7.93 0.00 33.78 5.01
3191 3231 6.125719 TGCCAGCACAGTGGAAAATATATAA 58.874 36.000 1.84 0.00 40.44 0.98
3217 3257 5.343307 AGTTGCCTTTTCAGAAAACACAT 57.657 34.783 4.06 0.00 0.00 3.21
3260 3300 5.656416 AGACATCTGGTTTTCTCACCAAAAA 59.344 36.000 0.00 0.00 46.60 1.94
3303 3343 7.780271 AGATACACAAAGAAAGAAAAGGAGGTT 59.220 33.333 0.00 0.00 0.00 3.50
3304 3344 7.290813 AGATACACAAAGAAAGAAAAGGAGGT 58.709 34.615 0.00 0.00 0.00 3.85
3305 3345 7.751768 AGATACACAAAGAAAGAAAAGGAGG 57.248 36.000 0.00 0.00 0.00 4.30
3312 3352 9.772973 TGCTAGTTAAGATACACAAAGAAAGAA 57.227 29.630 0.00 0.00 0.00 2.52
3313 3353 9.944376 ATGCTAGTTAAGATACACAAAGAAAGA 57.056 29.630 0.00 0.00 0.00 2.52
3314 3354 9.979270 CATGCTAGTTAAGATACACAAAGAAAG 57.021 33.333 0.00 0.00 0.00 2.62
3315 3355 8.450964 GCATGCTAGTTAAGATACACAAAGAAA 58.549 33.333 11.37 0.00 0.00 2.52
3316 3356 7.606073 TGCATGCTAGTTAAGATACACAAAGAA 59.394 33.333 20.33 0.00 0.00 2.52
3467 3508 8.109705 AGTGCAAATAGACATGAACAATTGTA 57.890 30.769 12.39 0.00 0.00 2.41
3598 3639 1.074072 ATGCGGGGCAACTAACACA 59.926 52.632 0.00 0.00 43.62 3.72
3894 3935 1.686355 TGGCGTTCATCCAGTTGTTT 58.314 45.000 0.00 0.00 0.00 2.83
3900 3941 2.632377 ACTGTTATGGCGTTCATCCAG 58.368 47.619 13.49 13.49 39.19 3.86
3925 3966 1.079503 CTTTGCTACTGAGAACGGGC 58.920 55.000 0.00 0.00 0.00 6.13
3929 3970 4.375105 CGTCGAAACTTTGCTACTGAGAAC 60.375 45.833 0.00 0.00 0.00 3.01
3935 3976 2.993899 CCATCGTCGAAACTTTGCTACT 59.006 45.455 0.00 0.00 0.00 2.57
3965 4006 2.014335 TCATCTCATCCAAGCACACG 57.986 50.000 0.00 0.00 0.00 4.49
3981 4022 9.288576 TGTTGTTCTGTCATCTAAGATTTTCAT 57.711 29.630 0.00 0.00 0.00 2.57
4115 4156 2.212652 TGAGCTAACAGTTGTGTGCAG 58.787 47.619 0.00 0.00 36.84 4.41
4178 4219 6.258507 GTGAGTTGCATTTGGAATTGTTTTCT 59.741 34.615 0.00 0.00 0.00 2.52
4204 4245 5.482908 GTGGATCAGTATTCGCCTCATAAT 58.517 41.667 0.00 0.00 0.00 1.28
4217 4258 3.189606 ACCTTTCATGGGTGGATCAGTA 58.810 45.455 0.00 0.00 35.51 2.74
4305 4346 1.777272 GGCCCCTGTAAATCTGAGGAT 59.223 52.381 0.00 0.00 0.00 3.24
4386 4427 7.070571 ACTCTAATCTGGGAATCTTCAGGTAAG 59.929 40.741 4.87 0.00 36.45 2.34
4483 4524 5.237127 CCTTGTTTTTCCCATTTTCTTCTGC 59.763 40.000 0.00 0.00 0.00 4.26
4593 4634 1.597742 TTGGAGCTGCTTCTTCACAC 58.402 50.000 9.76 0.00 0.00 3.82
4634 4675 6.482641 ACGTTTCCCTTTCTTCTTCTTCTTAC 59.517 38.462 0.00 0.00 0.00 2.34
4661 4702 0.682532 TGAACTGCCAACCTGTGCAA 60.683 50.000 0.00 0.00 36.98 4.08
4665 4706 1.143684 ACATCTGAACTGCCAACCTGT 59.856 47.619 0.00 0.00 0.00 4.00
4769 4810 6.617879 ACCTTTTCGCCATTAACTTCAATAC 58.382 36.000 0.00 0.00 0.00 1.89
4848 4889 1.366319 AGATTTCTCCCACTGCCTGT 58.634 50.000 0.00 0.00 0.00 4.00
4941 4982 5.656859 TCTCTTCGGTATTCTCTTCATCCAA 59.343 40.000 0.00 0.00 0.00 3.53
5055 5096 4.037684 CCTGAGGATGGAAAATCTTGATGC 59.962 45.833 0.00 0.00 0.00 3.91
5056 5097 5.198965 ACCTGAGGATGGAAAATCTTGATG 58.801 41.667 4.99 0.00 0.00 3.07
5057 5098 5.463051 ACCTGAGGATGGAAAATCTTGAT 57.537 39.130 4.99 0.00 0.00 2.57
5157 5198 4.524328 TCTGTGCTCTGTGTATTTCTCTCA 59.476 41.667 0.00 0.00 0.00 3.27
5242 5283 7.175119 AGGCATTTTCCTCTTACTCAAACTAAC 59.825 37.037 0.00 0.00 0.00 2.34
5455 5496 8.432805 AGAAGAATCATTATCCTTGTATTCCGT 58.567 33.333 0.00 0.00 0.00 4.69
5615 5656 7.877003 TCTCTCCAGATTATCGTTCTGAATAC 58.123 38.462 2.36 0.00 42.63 1.89
5757 5798 2.399916 TGACATCATCATGTTCCGCA 57.600 45.000 0.00 0.00 43.79 5.69
5782 5823 1.133407 CCTGAGTACAGCCGTCTCTTC 59.867 57.143 0.00 0.00 42.25 2.87
6348 6394 8.787852 TCATTGTGTTAACACTAATATTGCACA 58.212 29.630 32.58 10.89 46.55 4.57
6589 6635 5.128499 CAGTGGTCTCTTATCCTGACATCTT 59.872 44.000 0.00 0.00 32.84 2.40
6625 6671 9.082313 TGAGTATGACTAATATCAGCAGAATCA 57.918 33.333 0.00 0.00 30.46 2.57
6811 6857 1.056103 GAGCATGCGTATGAGTAGCG 58.944 55.000 18.28 0.00 36.36 4.26
6817 6863 5.115480 TGTAATTTGAGAGCATGCGTATGA 58.885 37.500 18.28 0.00 36.36 2.15
6922 6968 4.130118 CCTTGTCTGGTGATAATAGTGGC 58.870 47.826 0.00 0.00 0.00 5.01
6958 7004 2.856032 CGCTCAGGTGTTGCTTCG 59.144 61.111 0.00 0.00 0.00 3.79
7240 7286 4.321452 CCAACATTTCTTCCATCACACAGG 60.321 45.833 0.00 0.00 0.00 4.00
7290 7336 0.761187 GGGATGAGTAGCAGGCATGA 59.239 55.000 0.62 0.00 0.00 3.07
7429 7475 0.174845 GTGCTCCATACGGTGTGCTA 59.825 55.000 0.00 0.00 0.00 3.49
7450 7496 6.071672 TGCTAGCTGATCCTATGTACTGATTC 60.072 42.308 17.23 0.00 0.00 2.52
7504 7550 3.624861 CACACAATGAGCTAGTTGATCCC 59.375 47.826 15.30 0.00 0.00 3.85
7563 7609 6.068461 TGCCATTTAGGTTACTTCCATACA 57.932 37.500 0.00 0.00 40.61 2.29
7638 7684 5.070580 AGGTTACTTCCATAGGATGTGCTAC 59.929 44.000 13.11 8.93 39.80 3.58
7651 7697 6.652205 ATCCTTCCATTTAGGTTACTTCCA 57.348 37.500 0.00 0.00 39.02 3.53
7969 8015 2.499289 AGACTGAGCAGTACCATTCCTG 59.501 50.000 2.65 0.00 42.66 3.86
8143 8195 6.783892 AATGTTTTGGAAATGTATGCACAC 57.216 33.333 0.00 0.00 37.54 3.82
8185 8237 5.796350 ATAGAGCGTTTGACACCATAAAC 57.204 39.130 0.00 0.00 34.35 2.01
8266 8318 7.907214 ACATCAATGACTAAAGTAAGTGACC 57.093 36.000 0.00 0.00 36.45 4.02
8319 8371 1.925255 TCCATCCAGAAAAGGGAGCAT 59.075 47.619 0.00 0.00 37.96 3.79
8342 8394 1.211949 GAGCCCCTGGTAACTGCAATA 59.788 52.381 0.00 0.00 37.61 1.90
8346 8398 1.222113 GAGAGCCCCTGGTAACTGC 59.778 63.158 0.00 0.00 37.61 4.40
8356 8408 1.514553 GCTGCAATTTGAGAGCCCC 59.485 57.895 0.00 0.00 0.00 5.80
8469 8521 6.902771 AGCTTACTCACTTTCTCTTGACTA 57.097 37.500 0.00 0.00 0.00 2.59
8470 8522 5.799827 AGCTTACTCACTTTCTCTTGACT 57.200 39.130 0.00 0.00 0.00 3.41
8471 8523 6.852858 AAAGCTTACTCACTTTCTCTTGAC 57.147 37.500 0.00 0.00 30.35 3.18
8472 8524 7.047891 TCAAAAGCTTACTCACTTTCTCTTGA 58.952 34.615 0.00 0.00 35.10 3.02
8473 8525 7.251704 TCAAAAGCTTACTCACTTTCTCTTG 57.748 36.000 0.00 0.00 35.10 3.02
8474 8526 8.457238 AATCAAAAGCTTACTCACTTTCTCTT 57.543 30.769 0.00 0.00 35.10 2.85
8485 8537 6.691508 CAAGCCCTAAAATCAAAAGCTTACT 58.308 36.000 0.00 0.00 37.00 2.24
8544 8596 1.682854 CCTTTGCACCAGTCACAACAT 59.317 47.619 0.00 0.00 0.00 2.71
8596 8648 4.760530 TTACAACATCTGGCAGCTAGAT 57.239 40.909 15.33 15.33 35.34 1.98
8635 8687 6.043938 TGACAACCCATCCTTTAGAAGTAAGT 59.956 38.462 0.00 0.00 0.00 2.24
8654 8706 2.884639 AGCCAACATTACCACTGACAAC 59.115 45.455 0.00 0.00 0.00 3.32
8672 8724 5.611374 TCTTACAGCTATAACCATTCAGCC 58.389 41.667 0.00 0.00 34.49 4.85
8706 8758 1.150827 GTAAAACTACGGCGGCAGTT 58.849 50.000 19.35 19.35 36.56 3.16
8803 8855 1.476488 ACCAACAGGACAAGCAACAAC 59.524 47.619 0.00 0.00 0.00 3.32
8819 8871 5.109500 TCATCAGTATAACATGCCACCAA 57.891 39.130 0.00 0.00 0.00 3.67
8894 8946 4.109766 CAAATCAGTGGTATGCATGCTTG 58.890 43.478 20.33 10.58 0.00 4.01
8927 8979 3.493873 CGGCAGAATCATCATCCTTCTCA 60.494 47.826 0.00 0.00 0.00 3.27
8936 8988 4.831674 ATCATATCCGGCAGAATCATCA 57.168 40.909 0.00 0.00 0.00 3.07
8945 8997 3.054166 CGAACGTAAATCATATCCGGCA 58.946 45.455 0.00 0.00 0.00 5.69
8946 8998 3.054878 ACGAACGTAAATCATATCCGGC 58.945 45.455 0.00 0.00 0.00 6.13
8960 9012 5.978934 ACTCTATTCAACAAAACGAACGT 57.021 34.783 0.00 0.00 0.00 3.99
9052 9104 8.823818 GCACAACTTAGTCTTTCTAGTACAAAA 58.176 33.333 0.00 0.00 0.00 2.44
9066 9118 3.467803 ACAAGTCCAGCACAACTTAGTC 58.532 45.455 0.00 0.00 34.05 2.59


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

AutoCloner maintained by Alex Coulton.