Multiple sequence alignment - TraesCS4B01G167400

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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 TraesCS4B01G167400 chr4B 100.000 2480 0 0 1 2480 364486881 364489360 0.000000e+00 4580.0
1 TraesCS4B01G167400 chr4B 88.000 125 13 2 1634 1757 592702028 592702151 1.990000e-31 147.0
2 TraesCS4B01G167400 chr4B 88.235 119 13 1 1634 1751 322693058 322692940 9.250000e-30 141.0
3 TraesCS4B01G167400 chr4D 94.697 792 33 3 848 1635 295109812 295109026 0.000000e+00 1221.0
4 TraesCS4B01G167400 chr4D 80.448 670 66 14 230 863 295110471 295109831 3.760000e-123 451.0
5 TraesCS4B01G167400 chr4D 81.977 516 58 19 1001 1497 295142314 295141815 2.970000e-109 405.0
6 TraesCS4B01G167400 chr4D 94.089 203 11 1 9 211 295110752 295110551 8.620000e-80 307.0
7 TraesCS4B01G167400 chr4D 88.235 119 13 1 1633 1750 5923212 5923330 9.250000e-30 141.0
8 TraesCS4B01G167400 chr4D 87.500 80 6 2 229 306 305133617 305133694 3.400000e-14 89.8
9 TraesCS4B01G167400 chr4A 93.631 738 35 4 847 1580 198183813 198184542 0.000000e+00 1092.0
10 TraesCS4B01G167400 chr4A 81.073 671 65 22 229 863 198183151 198183795 1.730000e-131 479.0
11 TraesCS4B01G167400 chr4A 92.611 203 14 1 9 211 198182871 198183072 8.680000e-75 291.0
12 TraesCS4B01G167400 chr5B 91.449 690 46 9 1792 2480 548107334 548108011 0.000000e+00 935.0
13 TraesCS4B01G167400 chr5B 76.990 691 141 17 1799 2480 673756512 673755831 1.800000e-101 379.0
14 TraesCS4B01G167400 chr5D 90.244 123 10 2 1634 1754 352456399 352456277 2.550000e-35 159.0
15 TraesCS4B01G167400 chr7B 89.655 116 11 1 1636 1750 728628487 728628372 1.990000e-31 147.0
16 TraesCS4B01G167400 chr6A 88.333 120 13 1 1634 1752 79953883 79953764 2.570000e-30 143.0
17 TraesCS4B01G167400 chr1B 88.136 118 13 1 1633 1749 91539502 91539619 3.330000e-29 139.0
18 TraesCS4B01G167400 chr6D 85.496 131 17 2 1634 1763 137533080 137532951 4.300000e-28 135.0
19 TraesCS4B01G167400 chr1A 85.938 128 16 2 1629 1755 432987720 432987846 4.300000e-28 135.0
20 TraesCS4B01G167400 chr7A 97.917 48 1 0 229 276 40175261 40175214 1.580000e-12 84.2
21 TraesCS4B01G167400 chr5A 81.818 99 13 5 216 313 521016301 521016395 7.350000e-11 78.7
22 TraesCS4B01G167400 chr2B 86.441 59 8 0 370 428 481203753 481203695 5.730000e-07 65.8


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 TraesCS4B01G167400 chr4B 364486881 364489360 2479 False 4580.000000 4580 100.000000 1 2480 1 chr4B.!!$F1 2479
1 TraesCS4B01G167400 chr4D 295109026 295110752 1726 True 659.666667 1221 89.744667 9 1635 3 chr4D.!!$R2 1626
2 TraesCS4B01G167400 chr4A 198182871 198184542 1671 False 620.666667 1092 89.105000 9 1580 3 chr4A.!!$F1 1571
3 TraesCS4B01G167400 chr5B 548107334 548108011 677 False 935.000000 935 91.449000 1792 2480 1 chr5B.!!$F1 688
4 TraesCS4B01G167400 chr5B 673755831 673756512 681 True 379.000000 379 76.990000 1799 2480 1 chr5B.!!$R1 681

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
384 448 0.459934 ACGTTTTTGTCGGTCACGGA 60.46 50.0 0.0 0.0 41.39 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 1939 0.030807 TGAGGGAGGCATGAGATGGA 60.031 55.0 0.0 0.0 0.0 3.41 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
30 31 7.821595 ACATTAACGTAAACGATCTTGATGA 57.178 32.000 9.86 0.00 43.02 2.92
100 101 2.665165 TGGCAACATGACTTGGTCTTT 58.335 42.857 0.00 0.00 46.17 2.52
113 114 6.271391 TGACTTGGTCTTTCTAATGGTTAGGA 59.729 38.462 0.00 0.00 32.31 2.94
141 142 6.090763 GCACTAAATTTGCAACCAGTTAATCC 59.909 38.462 0.00 0.00 39.93 3.01
177 178 3.108847 ACCAAGGGGAAAAACTTCACA 57.891 42.857 0.00 0.00 38.05 3.58
211 212 1.961394 TCAAGTACCCGGCTAGCATAG 59.039 52.381 18.24 7.08 43.09 2.23
216 278 1.115930 ACCCGGCTAGCATAGTCCTG 61.116 60.000 18.24 0.00 41.16 3.86
219 281 1.467678 CGGCTAGCATAGTCCTGCCT 61.468 60.000 18.24 0.00 41.16 4.75
225 287 1.525535 CATAGTCCTGCCTGGCTGC 60.526 63.158 21.03 7.61 35.26 5.25
226 288 1.997311 ATAGTCCTGCCTGGCTGCA 60.997 57.895 21.03 1.83 39.37 4.41
227 289 1.351080 ATAGTCCTGCCTGGCTGCAT 61.351 55.000 21.03 9.95 41.16 3.96
244 306 1.026584 CATGATTGCCTTGCGATCCA 58.973 50.000 12.53 3.32 45.89 3.41
251 313 0.598065 GCCTTGCGATCCACAAAGTT 59.402 50.000 0.00 0.00 0.00 2.66
265 327 0.958822 AAAGTTGTTGGATCCCGCAC 59.041 50.000 9.90 4.03 0.00 5.34
269 331 1.822114 TTGTTGGATCCCGCACGAGA 61.822 55.000 9.90 0.00 0.00 4.04
279 341 0.647410 CCGCACGAGAGCACAATAAG 59.353 55.000 0.00 0.00 0.00 1.73
281 343 1.321743 CGCACGAGAGCACAATAAGTC 59.678 52.381 0.00 0.00 0.00 3.01
285 347 4.083802 GCACGAGAGCACAATAAGTCTTTT 60.084 41.667 0.00 0.00 0.00 2.27
288 350 6.145534 CACGAGAGCACAATAAGTCTTTTGTA 59.854 38.462 10.72 0.00 34.42 2.41
328 390 6.524101 ACAATTTTACATCTAAATGCCGGT 57.476 33.333 1.90 0.00 36.26 5.28
330 392 5.767816 ATTTTACATCTAAATGCCGGTCC 57.232 39.130 1.90 0.00 36.26 4.46
367 431 5.851177 CAGTGCTGAAAACTTTAACCATACG 59.149 40.000 0.00 0.00 0.00 3.06
375 439 9.074443 TGAAAACTTTAACCATACGTTTTTGTC 57.926 29.630 0.00 0.00 37.76 3.18
377 441 5.750650 ACTTTAACCATACGTTTTTGTCGG 58.249 37.500 0.00 0.00 35.79 4.79
384 448 0.459934 ACGTTTTTGTCGGTCACGGA 60.460 50.000 0.00 0.00 41.39 4.69
389 453 4.236935 GTTTTTGTCGGTCACGGATACTA 58.763 43.478 0.00 0.00 41.39 1.82
406 470 8.626526 ACGGATACTAAAACTTGTGATTTTGTT 58.373 29.630 0.00 0.00 31.79 2.83
422 486 3.367992 TTGTTGGTCGCTCGTACTAAA 57.632 42.857 0.00 0.00 0.00 1.85
426 490 4.751098 TGTTGGTCGCTCGTACTAAATTTT 59.249 37.500 0.00 0.00 0.00 1.82
504 568 6.941436 GGATCTTATTTGAAGGCTCTCATCAT 59.059 38.462 0.00 0.00 0.00 2.45
505 569 7.094720 GGATCTTATTTGAAGGCTCTCATCATG 60.095 40.741 0.00 0.00 0.00 3.07
528 592 9.220635 CATGAGAAACGCGAATATGAAAATAAA 57.779 29.630 15.93 0.00 0.00 1.40
603 667 5.047377 ACCAAAAGTCAAAAGAGAAAGCACA 60.047 36.000 0.00 0.00 0.00 4.57
609 673 1.295792 AAAGAGAAAGCACACGCGAA 58.704 45.000 15.93 0.00 45.49 4.70
613 677 1.959226 GAAAGCACACGCGAAGGGA 60.959 57.895 15.93 0.00 46.37 4.20
621 685 2.511600 CGCGAAGGGATGGGTGTC 60.512 66.667 0.00 0.00 46.37 3.67
634 698 4.903010 GTGTCCCCACACGTGCGT 62.903 66.667 17.22 0.00 43.63 5.24
644 708 1.299014 CACGTGCGTGCCACAAATT 60.299 52.632 11.81 0.00 44.91 1.82
649 713 0.874390 TGCGTGCCACAAATTCTCTC 59.126 50.000 0.00 0.00 0.00 3.20
652 716 1.177401 GTGCCACAAATTCTCTCCCC 58.823 55.000 0.00 0.00 0.00 4.81
662 726 5.072741 CAAATTCTCTCCCCAGAAGTTCAA 58.927 41.667 5.50 0.00 38.35 2.69
663 727 3.771577 TTCTCTCCCCAGAAGTTCAAC 57.228 47.619 5.50 0.00 0.00 3.18
675 739 4.982295 CAGAAGTTCAACGATGTGTACTCA 59.018 41.667 5.50 0.00 0.00 3.41
700 764 3.374367 TGTCATAGAAGAACTCGAGGTCG 59.626 47.826 24.17 9.50 41.45 4.79
789 873 1.198867 TGCATACATTTGCTTCGCGTT 59.801 42.857 5.77 0.00 43.18 4.84
863 975 8.949421 ACCCAAGATAACATATTCTAGGACAAT 58.051 33.333 0.00 0.00 0.00 2.71
891 1038 1.266178 GGCAGTTAGGGGCAAAATGT 58.734 50.000 0.00 0.00 0.00 2.71
991 1141 2.353889 ACCACGCACTGTACGTATAGAG 59.646 50.000 24.09 17.60 42.96 2.43
1026 1176 1.570501 AGCTCTGAGATGGAGGACTCT 59.429 52.381 9.28 0.00 34.65 3.24
1173 1323 1.380650 GCCCGTCTCTTCCTCCTCT 60.381 63.158 0.00 0.00 0.00 3.69
1185 1335 0.911769 CCTCCTCTGGTAATGTGGCA 59.088 55.000 0.00 0.00 0.00 4.92
1208 1358 1.202330 CTGAGGCTGAGGGACATCTT 58.798 55.000 0.00 0.00 0.00 2.40
1478 1628 1.402259 CGTGGTTGTGTTGCAAGGTTA 59.598 47.619 0.00 0.00 37.83 2.85
1500 1650 0.027455 CGCGTGCTTGTGTTCTCAAA 59.973 50.000 0.00 0.00 0.00 2.69
1635 1785 6.520792 TCACGCTCTTTTACACTCTTTTAC 57.479 37.500 0.00 0.00 0.00 2.01
1636 1786 6.278363 TCACGCTCTTTTACACTCTTTTACT 58.722 36.000 0.00 0.00 0.00 2.24
1637 1787 6.420008 TCACGCTCTTTTACACTCTTTTACTC 59.580 38.462 0.00 0.00 0.00 2.59
1638 1788 5.695363 ACGCTCTTTTACACTCTTTTACTCC 59.305 40.000 0.00 0.00 0.00 3.85
1639 1789 5.120363 CGCTCTTTTACACTCTTTTACTCCC 59.880 44.000 0.00 0.00 0.00 4.30
1640 1790 6.231951 GCTCTTTTACACTCTTTTACTCCCT 58.768 40.000 0.00 0.00 0.00 4.20
1641 1791 6.369340 GCTCTTTTACACTCTTTTACTCCCTC 59.631 42.308 0.00 0.00 0.00 4.30
1642 1792 6.766429 TCTTTTACACTCTTTTACTCCCTCC 58.234 40.000 0.00 0.00 0.00 4.30
1643 1793 4.796038 TTACACTCTTTTACTCCCTCCG 57.204 45.455 0.00 0.00 0.00 4.63
1644 1794 2.606378 ACACTCTTTTACTCCCTCCGT 58.394 47.619 0.00 0.00 0.00 4.69
1645 1795 2.970640 ACACTCTTTTACTCCCTCCGTT 59.029 45.455 0.00 0.00 0.00 4.44
1646 1796 3.006644 ACACTCTTTTACTCCCTCCGTTC 59.993 47.826 0.00 0.00 0.00 3.95
1647 1797 2.230750 ACTCTTTTACTCCCTCCGTTCG 59.769 50.000 0.00 0.00 0.00 3.95
1648 1798 2.490903 CTCTTTTACTCCCTCCGTTCGA 59.509 50.000 0.00 0.00 0.00 3.71
1649 1799 2.892852 TCTTTTACTCCCTCCGTTCGAA 59.107 45.455 0.00 0.00 0.00 3.71
1650 1800 3.321682 TCTTTTACTCCCTCCGTTCGAAA 59.678 43.478 0.00 0.00 0.00 3.46
1651 1801 3.967332 TTTACTCCCTCCGTTCGAAAT 57.033 42.857 0.00 0.00 0.00 2.17
1652 1802 3.967332 TTACTCCCTCCGTTCGAAATT 57.033 42.857 0.00 0.00 0.00 1.82
1653 1803 5.404466 TTTACTCCCTCCGTTCGAAATTA 57.596 39.130 0.00 0.00 0.00 1.40
1654 1804 3.242549 ACTCCCTCCGTTCGAAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
1655 1805 2.830321 ACTCCCTCCGTTCGAAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
1656 1806 3.260128 ACTCCCTCCGTTCGAAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
1657 1807 3.592059 TCCCTCCGTTCGAAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
1658 1808 3.007182 TCCCTCCGTTCGAAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
1659 1809 3.370061 CCCTCCGTTCGAAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
1660 1810 3.060363 CCTCCGTTCGAAATTACTTGTCG 59.940 47.826 0.00 0.00 36.12 4.35
1661 1811 2.409378 TCCGTTCGAAATTACTTGTCGC 59.591 45.455 0.00 0.00 34.80 5.19
1662 1812 2.473376 CCGTTCGAAATTACTTGTCGCC 60.473 50.000 0.00 0.00 34.80 5.54
1663 1813 2.754478 GTTCGAAATTACTTGTCGCCG 58.246 47.619 0.00 0.00 34.80 6.46
1664 1814 2.350899 TCGAAATTACTTGTCGCCGA 57.649 45.000 0.00 0.00 34.80 5.54
1665 1815 2.674954 TCGAAATTACTTGTCGCCGAA 58.325 42.857 0.00 0.00 34.80 4.30
1666 1816 3.058450 TCGAAATTACTTGTCGCCGAAA 58.942 40.909 0.00 0.00 34.80 3.46
1667 1817 3.680937 TCGAAATTACTTGTCGCCGAAAT 59.319 39.130 0.00 0.00 34.80 2.17
1668 1818 4.019867 CGAAATTACTTGTCGCCGAAATC 58.980 43.478 0.00 0.00 0.00 2.17
1669 1819 3.651562 AATTACTTGTCGCCGAAATCG 57.348 42.857 0.00 0.00 39.44 3.34
1670 1820 2.350899 TTACTTGTCGCCGAAATCGA 57.649 45.000 4.04 0.00 43.02 3.59
1671 1821 2.572191 TACTTGTCGCCGAAATCGAT 57.428 45.000 4.04 0.00 43.02 3.59
1672 1822 2.572191 ACTTGTCGCCGAAATCGATA 57.428 45.000 0.00 0.00 43.02 2.92
1673 1823 2.883574 ACTTGTCGCCGAAATCGATAA 58.116 42.857 0.00 0.00 43.02 1.75
1674 1824 3.255725 ACTTGTCGCCGAAATCGATAAA 58.744 40.909 0.00 0.00 43.02 1.40
1675 1825 3.680937 ACTTGTCGCCGAAATCGATAAAA 59.319 39.130 0.00 0.00 43.02 1.52
1676 1826 4.152759 ACTTGTCGCCGAAATCGATAAAAA 59.847 37.500 0.00 0.00 43.02 1.94
1677 1827 4.868450 TGTCGCCGAAATCGATAAAAAT 57.132 36.364 0.00 0.00 43.02 1.82
1678 1828 5.970140 TGTCGCCGAAATCGATAAAAATA 57.030 34.783 0.00 0.00 43.02 1.40
1679 1829 6.347270 TGTCGCCGAAATCGATAAAAATAA 57.653 33.333 0.00 0.00 43.02 1.40
1680 1830 6.773080 TGTCGCCGAAATCGATAAAAATAAA 58.227 32.000 0.00 0.00 43.02 1.40
1681 1831 7.411274 TGTCGCCGAAATCGATAAAAATAAAT 58.589 30.769 0.00 0.00 43.02 1.40
1682 1832 8.549548 TGTCGCCGAAATCGATAAAAATAAATA 58.450 29.630 0.00 0.00 43.02 1.40
1683 1833 9.537848 GTCGCCGAAATCGATAAAAATAAATAT 57.462 29.630 0.00 0.00 43.02 1.28
1726 1876 7.841915 TTTAGATACATGCATTTCTTCGACA 57.158 32.000 0.00 0.00 0.00 4.35
1727 1877 7.841915 TTAGATACATGCATTTCTTCGACAA 57.158 32.000 0.00 0.00 0.00 3.18
1728 1878 6.355397 AGATACATGCATTTCTTCGACAAG 57.645 37.500 0.00 0.00 0.00 3.16
1729 1879 5.877012 AGATACATGCATTTCTTCGACAAGT 59.123 36.000 0.00 0.00 0.00 3.16
1730 1880 7.041721 AGATACATGCATTTCTTCGACAAGTA 58.958 34.615 0.00 0.00 0.00 2.24
1731 1881 7.712639 AGATACATGCATTTCTTCGACAAGTAT 59.287 33.333 0.00 0.00 30.37 2.12
1732 1882 6.500684 ACATGCATTTCTTCGACAAGTATT 57.499 33.333 0.00 0.00 0.00 1.89
1733 1883 6.913170 ACATGCATTTCTTCGACAAGTATTT 58.087 32.000 0.00 0.00 0.00 1.40
1734 1884 7.023575 ACATGCATTTCTTCGACAAGTATTTC 58.976 34.615 0.00 0.00 0.00 2.17
1735 1885 5.938322 TGCATTTCTTCGACAAGTATTTCC 58.062 37.500 0.00 0.00 0.00 3.13
1736 1886 5.022021 GCATTTCTTCGACAAGTATTTCCG 58.978 41.667 0.00 0.00 0.00 4.30
1737 1887 5.560148 CATTTCTTCGACAAGTATTTCCGG 58.440 41.667 0.00 0.00 0.00 5.14
1738 1888 4.524316 TTCTTCGACAAGTATTTCCGGA 57.476 40.909 0.00 0.00 0.00 5.14
1739 1889 3.841643 TCTTCGACAAGTATTTCCGGAC 58.158 45.455 1.83 0.00 0.00 4.79
1740 1890 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
1741 1891 1.135315 TCGACAAGTATTTCCGGACGG 60.135 52.381 1.83 3.96 0.00 4.79
1742 1892 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
1743 1893 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
1744 1894 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1745 1895 1.479323 CAAGTATTTCCGGACGGAGGA 59.521 52.381 13.64 7.39 46.06 3.71
1746 1896 1.400737 AGTATTTCCGGACGGAGGAG 58.599 55.000 13.64 0.00 46.06 3.69
1747 1897 1.109609 GTATTTCCGGACGGAGGAGT 58.890 55.000 13.64 0.00 46.06 3.85
1748 1898 2.092212 AGTATTTCCGGACGGAGGAGTA 60.092 50.000 13.64 0.00 46.06 2.59
1749 1899 2.083628 ATTTCCGGACGGAGGAGTAT 57.916 50.000 13.64 1.87 46.06 2.12
1750 1900 1.856629 TTTCCGGACGGAGGAGTATT 58.143 50.000 13.64 0.00 46.06 1.89
1751 1901 1.856629 TTCCGGACGGAGGAGTATTT 58.143 50.000 13.64 0.00 46.06 1.40
1752 1902 2.734755 TCCGGACGGAGGAGTATTTA 57.265 50.000 9.76 0.00 39.76 1.40
1753 1903 3.234234 TCCGGACGGAGGAGTATTTAT 57.766 47.619 9.76 0.00 39.76 1.40
1754 1904 2.889045 TCCGGACGGAGGAGTATTTATG 59.111 50.000 9.76 0.00 39.76 1.90
1755 1905 2.626743 CCGGACGGAGGAGTATTTATGT 59.373 50.000 4.40 0.00 37.50 2.29
1756 1906 3.069158 CCGGACGGAGGAGTATTTATGTT 59.931 47.826 4.40 0.00 37.50 2.71
1757 1907 4.049186 CGGACGGAGGAGTATTTATGTTG 58.951 47.826 0.00 0.00 0.00 3.33
1758 1908 4.377897 GGACGGAGGAGTATTTATGTTGG 58.622 47.826 0.00 0.00 0.00 3.77
1759 1909 4.377897 GACGGAGGAGTATTTATGTTGGG 58.622 47.826 0.00 0.00 0.00 4.12
1760 1910 4.035112 ACGGAGGAGTATTTATGTTGGGA 58.965 43.478 0.00 0.00 0.00 4.37
1761 1911 4.658901 ACGGAGGAGTATTTATGTTGGGAT 59.341 41.667 0.00 0.00 0.00 3.85
1762 1912 4.997395 CGGAGGAGTATTTATGTTGGGATG 59.003 45.833 0.00 0.00 0.00 3.51
1763 1913 5.454755 CGGAGGAGTATTTATGTTGGGATGT 60.455 44.000 0.00 0.00 0.00 3.06
1764 1914 6.365520 GGAGGAGTATTTATGTTGGGATGTT 58.634 40.000 0.00 0.00 0.00 2.71
1765 1915 6.263168 GGAGGAGTATTTATGTTGGGATGTTG 59.737 42.308 0.00 0.00 0.00 3.33
1766 1916 6.731467 AGGAGTATTTATGTTGGGATGTTGT 58.269 36.000 0.00 0.00 0.00 3.32
1767 1917 7.867921 AGGAGTATTTATGTTGGGATGTTGTA 58.132 34.615 0.00 0.00 0.00 2.41
1768 1918 7.993183 AGGAGTATTTATGTTGGGATGTTGTAG 59.007 37.037 0.00 0.00 0.00 2.74
1769 1919 7.773690 GGAGTATTTATGTTGGGATGTTGTAGT 59.226 37.037 0.00 0.00 0.00 2.73
1770 1920 8.732746 AGTATTTATGTTGGGATGTTGTAGTC 57.267 34.615 0.00 0.00 0.00 2.59
1771 1921 8.548877 AGTATTTATGTTGGGATGTTGTAGTCT 58.451 33.333 0.00 0.00 0.00 3.24
1772 1922 7.865706 ATTTATGTTGGGATGTTGTAGTCTC 57.134 36.000 0.00 0.00 0.00 3.36
1773 1923 4.908601 ATGTTGGGATGTTGTAGTCTCA 57.091 40.909 0.00 0.00 0.00 3.27
1774 1924 4.908601 TGTTGGGATGTTGTAGTCTCAT 57.091 40.909 0.00 0.00 0.00 2.90
1775 1925 4.832248 TGTTGGGATGTTGTAGTCTCATC 58.168 43.478 0.00 0.00 37.72 2.92
1776 1926 4.285775 TGTTGGGATGTTGTAGTCTCATCA 59.714 41.667 0.00 0.00 39.47 3.07
1777 1927 5.045651 TGTTGGGATGTTGTAGTCTCATCAT 60.046 40.000 0.00 0.00 39.47 2.45
1778 1928 5.027293 TGGGATGTTGTAGTCTCATCATG 57.973 43.478 0.00 0.00 39.47 3.07
1779 1929 4.471025 TGGGATGTTGTAGTCTCATCATGT 59.529 41.667 0.00 0.00 39.47 3.21
1780 1930 5.660864 TGGGATGTTGTAGTCTCATCATGTA 59.339 40.000 0.00 0.00 39.47 2.29
1781 1931 5.986135 GGGATGTTGTAGTCTCATCATGTAC 59.014 44.000 0.00 0.00 39.47 2.90
1782 1932 6.183360 GGGATGTTGTAGTCTCATCATGTACT 60.183 42.308 0.00 1.80 39.47 2.73
1783 1933 6.920758 GGATGTTGTAGTCTCATCATGTACTC 59.079 42.308 0.00 0.00 39.47 2.59
1784 1934 6.834168 TGTTGTAGTCTCATCATGTACTCA 57.166 37.500 0.00 0.00 0.00 3.41
1785 1935 7.227049 TGTTGTAGTCTCATCATGTACTCAA 57.773 36.000 0.00 2.84 0.00 3.02
1786 1936 7.315890 TGTTGTAGTCTCATCATGTACTCAAG 58.684 38.462 0.00 0.00 0.00 3.02
1787 1937 7.039714 TGTTGTAGTCTCATCATGTACTCAAGT 60.040 37.037 0.00 0.00 0.00 3.16
1788 1938 8.459635 GTTGTAGTCTCATCATGTACTCAAGTA 58.540 37.037 0.00 0.00 0.00 2.24
1789 1939 8.753497 TGTAGTCTCATCATGTACTCAAGTAT 57.247 34.615 0.00 0.00 32.54 2.12
1790 1940 8.841300 TGTAGTCTCATCATGTACTCAAGTATC 58.159 37.037 0.00 0.00 32.54 2.24
1791 1941 7.283625 AGTCTCATCATGTACTCAAGTATCC 57.716 40.000 0.00 0.00 32.54 2.59
1792 1942 6.836007 AGTCTCATCATGTACTCAAGTATCCA 59.164 38.462 0.00 0.00 32.54 3.41
1793 1943 7.508636 AGTCTCATCATGTACTCAAGTATCCAT 59.491 37.037 0.00 0.00 32.54 3.41
1794 1944 7.812191 GTCTCATCATGTACTCAAGTATCCATC 59.188 40.741 0.00 0.00 32.54 3.51
1795 1945 7.727634 TCTCATCATGTACTCAAGTATCCATCT 59.272 37.037 0.00 0.00 32.54 2.90
1796 1946 7.890515 TCATCATGTACTCAAGTATCCATCTC 58.109 38.462 0.00 0.00 32.54 2.75
1797 1947 7.506938 TCATCATGTACTCAAGTATCCATCTCA 59.493 37.037 0.00 0.00 32.54 3.27
1807 1957 1.360185 ATCCATCTCATGCCTCCCTC 58.640 55.000 0.00 0.00 0.00 4.30
1824 1974 1.099689 CTCAGAACTCTCTCGTCCCC 58.900 60.000 0.00 0.00 0.00 4.81
1837 1987 1.606889 GTCCCCTCCAGTGACGAGT 60.607 63.158 0.00 0.00 0.00 4.18
1841 1991 1.067071 CCCCTCCAGTGACGAGTAAAC 60.067 57.143 0.00 0.00 0.00 2.01
1903 2054 2.025981 TGCATCCATCCTAGTGTGCTTT 60.026 45.455 0.00 0.00 33.95 3.51
1909 2060 4.041567 TCCATCCTAGTGTGCTTTCAAAGA 59.958 41.667 0.00 0.00 0.00 2.52
1914 2065 5.527582 TCCTAGTGTGCTTTCAAAGAAAGAC 59.472 40.000 20.30 15.26 0.00 3.01
1917 2068 4.034510 AGTGTGCTTTCAAAGAAAGACTCG 59.965 41.667 20.30 0.00 0.00 4.18
1918 2069 3.312421 TGTGCTTTCAAAGAAAGACTCGG 59.688 43.478 20.30 0.00 0.00 4.63
1933 2084 0.244994 CTCGGTCTCCTCAACACCAG 59.755 60.000 0.00 0.00 0.00 4.00
1938 2089 0.105194 TCTCCTCAACACCAGGACCA 60.105 55.000 0.00 0.00 34.91 4.02
1939 2090 0.764890 CTCCTCAACACCAGGACCAA 59.235 55.000 0.00 0.00 34.91 3.67
1961 2112 1.595357 CCGTACCCCCAGTTCTCAC 59.405 63.158 0.00 0.00 0.00 3.51
1962 2113 0.903454 CCGTACCCCCAGTTCTCACT 60.903 60.000 0.00 0.00 0.00 3.41
1992 2143 0.122435 AGGTAGGGGTGATTTGGGGA 59.878 55.000 0.00 0.00 0.00 4.81
1993 2144 1.004436 GGTAGGGGTGATTTGGGGAA 58.996 55.000 0.00 0.00 0.00 3.97
2009 2161 5.109500 TGGGGAAAATTCTTGTTTGCTTT 57.891 34.783 0.00 0.00 0.00 3.51
2036 2188 1.875813 GGCTGTGCGTCAGATCTCG 60.876 63.158 11.97 0.00 46.27 4.04
2042 2194 2.425668 TGTGCGTCAGATCTCGGAAATA 59.574 45.455 6.02 0.00 0.00 1.40
2059 2211 3.959495 AATATGAGGGTGTGAATGGCT 57.041 42.857 0.00 0.00 0.00 4.75
2096 2248 4.166888 TGGAGGCGGAGATGCAGC 62.167 66.667 0.00 0.00 36.28 5.25
2127 2279 3.955471 ACACGGATTTGACAATGGAGAT 58.045 40.909 0.00 0.00 0.00 2.75
2254 2406 0.181114 CGGATGCCCTCATCTTGGAA 59.819 55.000 5.41 0.00 46.41 3.53
2255 2407 1.202855 CGGATGCCCTCATCTTGGAAT 60.203 52.381 5.41 0.00 46.41 3.01
2321 2473 5.576563 TGGTAAGGTATTATCCCCACATG 57.423 43.478 0.00 0.00 0.00 3.21
2326 2478 4.763355 AGGTATTATCCCCACATGCTCTA 58.237 43.478 0.00 0.00 0.00 2.43
2350 2502 3.560902 ATACAGACTATCATGTCGGCG 57.439 47.619 0.00 0.00 41.47 6.46
2383 2535 2.877866 TGGGCGAATCCAAAAGGTTTA 58.122 42.857 0.00 0.00 36.21 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.377681 TCAAGATCGTTTACGTTAATGTTGATC 58.622 33.333 5.48 12.82 40.80 2.92
3 4 7.640616 TCAAGATCGTTTACGTTAATGTTGA 57.359 32.000 5.48 6.66 40.80 3.18
5 6 8.166706 GTCATCAAGATCGTTTACGTTAATGTT 58.833 33.333 5.48 0.00 40.80 2.71
6 7 7.544566 AGTCATCAAGATCGTTTACGTTAATGT 59.455 33.333 5.50 5.50 40.80 2.71
7 8 7.895870 AGTCATCAAGATCGTTTACGTTAATG 58.104 34.615 0.00 0.00 40.80 1.90
8 9 7.758076 TGAGTCATCAAGATCGTTTACGTTAAT 59.242 33.333 0.00 0.00 34.89 1.40
9 10 7.085746 TGAGTCATCAAGATCGTTTACGTTAA 58.914 34.615 0.00 0.00 34.89 2.01
10 11 6.614160 TGAGTCATCAAGATCGTTTACGTTA 58.386 36.000 0.00 0.00 34.89 3.18
11 12 5.466819 TGAGTCATCAAGATCGTTTACGTT 58.533 37.500 0.00 0.00 34.89 3.99
12 13 5.055642 TGAGTCATCAAGATCGTTTACGT 57.944 39.130 1.88 0.00 34.89 3.57
30 31 7.992754 AGAGCATAAAAGACTTGAATTGAGT 57.007 32.000 0.00 0.00 0.00 3.41
100 101 9.474313 AAATTTAGTGCATTCCTAACCATTAGA 57.526 29.630 0.00 0.00 35.20 2.10
131 132 1.656652 CAGCGGTCTGGATTAACTGG 58.343 55.000 0.00 0.00 36.68 4.00
177 178 6.109359 CGGGTACTTGATCATTCTTCTCTTT 58.891 40.000 0.00 0.00 0.00 2.52
225 287 1.026584 TGGATCGCAAGGCAATCATG 58.973 50.000 0.00 0.00 38.47 3.07
226 288 1.027357 GTGGATCGCAAGGCAATCAT 58.973 50.000 0.00 0.00 38.47 2.45
227 289 0.322366 TGTGGATCGCAAGGCAATCA 60.322 50.000 0.00 0.00 38.47 2.57
244 306 0.958822 GCGGGATCCAACAACTTTGT 59.041 50.000 15.23 0.00 44.72 2.83
251 313 2.225791 CTCTCGTGCGGGATCCAACA 62.226 60.000 15.23 8.04 0.00 3.33
265 327 5.597813 ACAAAAGACTTATTGTGCTCTCG 57.402 39.130 12.16 0.00 38.29 4.04
307 369 5.891551 AGGACCGGCATTTAGATGTAAAATT 59.108 36.000 0.00 0.00 35.63 1.82
313 375 2.238646 TGAAGGACCGGCATTTAGATGT 59.761 45.455 0.00 0.00 35.63 3.06
319 381 4.706842 ACTATATGAAGGACCGGCATTT 57.293 40.909 0.00 0.00 0.00 2.32
324 386 5.050490 CACTGAAACTATATGAAGGACCGG 58.950 45.833 0.00 0.00 0.00 5.28
328 390 6.544928 TCAGCACTGAAACTATATGAAGGA 57.455 37.500 0.00 0.00 36.53 3.36
354 418 5.296531 ACCGACAAAAACGTATGGTTAAAGT 59.703 36.000 0.00 0.00 38.08 2.66
355 419 5.750650 ACCGACAAAAACGTATGGTTAAAG 58.249 37.500 0.00 0.00 38.08 1.85
361 425 2.410517 CGTGACCGACAAAAACGTATGG 60.411 50.000 0.00 0.00 35.63 2.74
367 431 3.062042 AGTATCCGTGACCGACAAAAAC 58.938 45.455 0.00 0.00 35.63 2.43
375 439 4.090930 CACAAGTTTTAGTATCCGTGACCG 59.909 45.833 0.00 0.00 0.00 4.79
377 441 6.963049 ATCACAAGTTTTAGTATCCGTGAC 57.037 37.500 0.00 0.00 35.20 3.67
384 448 9.744468 GACCAACAAAATCACAAGTTTTAGTAT 57.256 29.630 0.00 0.00 0.00 2.12
389 453 4.328712 GCGACCAACAAAATCACAAGTTTT 59.671 37.500 0.00 0.00 0.00 2.43
406 470 7.171337 ACTTTTAAAATTTAGTACGAGCGACCA 59.829 33.333 0.09 0.00 0.00 4.02
504 568 9.057365 GTTTTATTTTCATATTCGCGTTTCTCA 57.943 29.630 5.77 0.00 0.00 3.27
505 569 9.274065 AGTTTTATTTTCATATTCGCGTTTCTC 57.726 29.630 5.77 0.00 0.00 2.87
571 635 9.500785 TTCTCTTTTGACTTTTGGTTTTCAATT 57.499 25.926 0.00 0.00 34.98 2.32
593 657 1.493311 CCTTCGCGTGTGCTTTCTC 59.507 57.895 5.77 0.00 39.65 2.87
603 667 3.310860 GACACCCATCCCTTCGCGT 62.311 63.158 5.77 0.00 0.00 6.01
631 695 0.169009 GGAGAGAATTTGTGGCACGC 59.831 55.000 13.77 0.00 40.62 5.34
632 696 0.804989 GGGAGAGAATTTGTGGCACG 59.195 55.000 13.77 0.00 0.00 5.34
633 697 1.177401 GGGGAGAGAATTTGTGGCAC 58.823 55.000 11.55 11.55 0.00 5.01
634 698 0.776810 TGGGGAGAGAATTTGTGGCA 59.223 50.000 0.00 0.00 0.00 4.92
637 701 4.026356 ACTTCTGGGGAGAGAATTTGTG 57.974 45.455 0.00 0.00 31.51 3.33
644 708 1.618837 CGTTGAACTTCTGGGGAGAGA 59.381 52.381 0.00 0.00 0.00 3.10
649 713 1.806542 CACATCGTTGAACTTCTGGGG 59.193 52.381 0.00 0.00 0.00 4.96
652 716 4.982295 TGAGTACACATCGTTGAACTTCTG 59.018 41.667 0.00 0.00 0.00 3.02
662 726 7.745620 TCTATGACATATGAGTACACATCGT 57.254 36.000 10.38 8.29 0.00 3.73
663 727 8.507249 TCTTCTATGACATATGAGTACACATCG 58.493 37.037 10.38 5.25 0.00 3.84
675 739 6.072948 CGACCTCGAGTTCTTCTATGACATAT 60.073 42.308 12.31 0.00 43.02 1.78
700 764 1.279840 GTCCACGTTGAGCAAGTGC 59.720 57.895 0.00 0.00 42.49 4.40
789 873 1.801983 CACATGCTGCGGTTATGCA 59.198 52.632 10.61 0.00 43.95 3.96
835 947 8.429641 TGTCCTAGAATATGTTATCTTGGGTTC 58.570 37.037 0.00 0.00 38.57 3.62
863 975 1.003839 CCTAACTGCCCGTGCTCAA 60.004 57.895 0.00 0.00 38.71 3.02
891 1038 6.703165 GCGATGGTGCATGATATATAAGATGA 59.297 38.462 0.00 0.00 34.15 2.92
911 1058 1.805261 CTGCTCGACGATGTGCGATG 61.805 60.000 0.00 0.00 44.57 3.84
1173 1323 2.039974 CAGCGCTGCCACATTACCA 61.040 57.895 26.68 0.00 0.00 3.25
1251 1401 3.625897 CACTCCACGCCCACAGGA 61.626 66.667 0.00 0.00 33.47 3.86
1518 1668 5.220796 CCATGAACAGCACAGACAATCATAG 60.221 44.000 0.00 0.00 0.00 2.23
1635 1785 3.521947 AGTAATTTCGAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
1636 1786 3.007182 ACAAGTAATTTCGAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
1637 1787 3.332034 ACAAGTAATTTCGAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
1638 1788 3.060363 CGACAAGTAATTTCGAACGGAGG 59.940 47.826 0.00 0.00 34.62 4.30
1639 1789 3.481467 GCGACAAGTAATTTCGAACGGAG 60.481 47.826 0.00 0.00 34.62 4.63
1640 1790 2.409378 GCGACAAGTAATTTCGAACGGA 59.591 45.455 0.00 0.00 34.62 4.69
1641 1791 2.473376 GGCGACAAGTAATTTCGAACGG 60.473 50.000 0.00 0.00 34.62 4.44
1642 1792 2.754478 GGCGACAAGTAATTTCGAACG 58.246 47.619 0.00 0.00 34.62 3.95
1643 1793 2.409378 TCGGCGACAAGTAATTTCGAAC 59.591 45.455 4.99 0.00 34.62 3.95
1644 1794 2.674954 TCGGCGACAAGTAATTTCGAA 58.325 42.857 4.99 0.00 34.62 3.71
1645 1795 2.350899 TCGGCGACAAGTAATTTCGA 57.649 45.000 4.99 0.00 34.62 3.71
1646 1796 3.443054 TTTCGGCGACAAGTAATTTCG 57.557 42.857 10.16 4.05 35.82 3.46
1647 1797 4.019867 CGATTTCGGCGACAAGTAATTTC 58.980 43.478 10.16 0.00 35.37 2.17
1648 1798 3.680937 TCGATTTCGGCGACAAGTAATTT 59.319 39.130 10.16 0.00 40.29 1.82
1649 1799 3.255725 TCGATTTCGGCGACAAGTAATT 58.744 40.909 10.16 0.00 40.29 1.40
1650 1800 2.883574 TCGATTTCGGCGACAAGTAAT 58.116 42.857 10.16 6.23 40.29 1.89
1651 1801 2.350899 TCGATTTCGGCGACAAGTAA 57.649 45.000 10.16 0.01 40.29 2.24
1652 1802 2.572191 ATCGATTTCGGCGACAAGTA 57.428 45.000 10.16 0.00 40.94 2.24
1653 1803 2.572191 TATCGATTTCGGCGACAAGT 57.428 45.000 10.16 0.00 40.94 3.16
1654 1804 3.918258 TTTATCGATTTCGGCGACAAG 57.082 42.857 10.16 1.93 40.94 3.16
1655 1805 4.665281 TTTTTATCGATTTCGGCGACAA 57.335 36.364 10.16 8.07 40.94 3.18
1656 1806 4.868450 ATTTTTATCGATTTCGGCGACA 57.132 36.364 10.16 2.52 40.94 4.35
1657 1807 7.831750 ATTTATTTTTATCGATTTCGGCGAC 57.168 32.000 10.16 0.00 40.94 5.19
1700 1850 9.541143 TGTCGAAGAAATGCATGTATCTAAATA 57.459 29.630 0.00 0.00 39.69 1.40
1701 1851 8.437360 TGTCGAAGAAATGCATGTATCTAAAT 57.563 30.769 0.00 0.00 39.69 1.40
1702 1852 7.841915 TGTCGAAGAAATGCATGTATCTAAA 57.158 32.000 0.00 0.00 39.69 1.85
1703 1853 7.549134 ACTTGTCGAAGAAATGCATGTATCTAA 59.451 33.333 0.00 0.00 39.69 2.10
1704 1854 7.041721 ACTTGTCGAAGAAATGCATGTATCTA 58.958 34.615 0.00 0.00 39.69 1.98
1705 1855 5.877012 ACTTGTCGAAGAAATGCATGTATCT 59.123 36.000 0.00 1.70 39.69 1.98
1706 1856 6.111768 ACTTGTCGAAGAAATGCATGTATC 57.888 37.500 0.00 0.00 39.69 2.24
1707 1857 7.792374 ATACTTGTCGAAGAAATGCATGTAT 57.208 32.000 0.00 0.00 39.69 2.29
1708 1858 7.609760 AATACTTGTCGAAGAAATGCATGTA 57.390 32.000 0.00 0.00 39.69 2.29
1709 1859 6.500684 AATACTTGTCGAAGAAATGCATGT 57.499 33.333 0.00 0.00 39.69 3.21
1710 1860 6.470235 GGAAATACTTGTCGAAGAAATGCATG 59.530 38.462 0.00 0.00 39.69 4.06
1711 1861 6.555315 GGAAATACTTGTCGAAGAAATGCAT 58.445 36.000 0.00 0.00 39.69 3.96
1712 1862 5.390461 CGGAAATACTTGTCGAAGAAATGCA 60.390 40.000 0.00 0.00 39.69 3.96
1713 1863 5.022021 CGGAAATACTTGTCGAAGAAATGC 58.978 41.667 0.00 0.00 39.69 3.56
1714 1864 5.350365 TCCGGAAATACTTGTCGAAGAAATG 59.650 40.000 0.00 0.00 39.69 2.32
1715 1865 5.350640 GTCCGGAAATACTTGTCGAAGAAAT 59.649 40.000 5.23 0.00 39.69 2.17
1716 1866 4.687483 GTCCGGAAATACTTGTCGAAGAAA 59.313 41.667 5.23 0.00 39.69 2.52
1717 1867 4.240096 GTCCGGAAATACTTGTCGAAGAA 58.760 43.478 5.23 0.00 39.69 2.52
1718 1868 3.671433 CGTCCGGAAATACTTGTCGAAGA 60.671 47.826 5.23 0.00 32.98 2.87
1719 1869 2.597305 CGTCCGGAAATACTTGTCGAAG 59.403 50.000 5.23 0.00 35.07 3.79
1720 1870 2.598589 CGTCCGGAAATACTTGTCGAA 58.401 47.619 5.23 0.00 0.00 3.71
1721 1871 1.135315 CCGTCCGGAAATACTTGTCGA 60.135 52.381 5.23 0.00 37.50 4.20
1722 1872 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1723 1873 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1724 1874 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1725 1875 1.479323 TCCTCCGTCCGGAAATACTTG 59.521 52.381 5.23 0.00 44.66 3.16
1726 1876 1.755380 CTCCTCCGTCCGGAAATACTT 59.245 52.381 5.23 0.00 44.66 2.24
1727 1877 1.341778 ACTCCTCCGTCCGGAAATACT 60.342 52.381 5.23 0.00 44.66 2.12
1728 1878 1.109609 ACTCCTCCGTCCGGAAATAC 58.890 55.000 5.23 0.00 44.66 1.89
1729 1879 2.734755 TACTCCTCCGTCCGGAAATA 57.265 50.000 5.23 0.00 44.66 1.40
1730 1880 2.083628 ATACTCCTCCGTCCGGAAAT 57.916 50.000 5.23 0.00 44.66 2.17
1731 1881 1.856629 AATACTCCTCCGTCCGGAAA 58.143 50.000 5.23 0.00 44.66 3.13
1732 1882 1.856629 AAATACTCCTCCGTCCGGAA 58.143 50.000 5.23 0.00 44.66 4.30
1733 1883 2.734755 TAAATACTCCTCCGTCCGGA 57.265 50.000 0.00 0.00 42.90 5.14
1734 1884 2.626743 ACATAAATACTCCTCCGTCCGG 59.373 50.000 0.00 0.00 0.00 5.14
1735 1885 4.049186 CAACATAAATACTCCTCCGTCCG 58.951 47.826 0.00 0.00 0.00 4.79
1736 1886 4.377897 CCAACATAAATACTCCTCCGTCC 58.622 47.826 0.00 0.00 0.00 4.79
1737 1887 4.100498 TCCCAACATAAATACTCCTCCGTC 59.900 45.833 0.00 0.00 0.00 4.79
1738 1888 4.035112 TCCCAACATAAATACTCCTCCGT 58.965 43.478 0.00 0.00 0.00 4.69
1739 1889 4.682778 TCCCAACATAAATACTCCTCCG 57.317 45.455 0.00 0.00 0.00 4.63
1740 1890 5.941788 ACATCCCAACATAAATACTCCTCC 58.058 41.667 0.00 0.00 0.00 4.30
1741 1891 6.828785 ACAACATCCCAACATAAATACTCCTC 59.171 38.462 0.00 0.00 0.00 3.71
1742 1892 6.731467 ACAACATCCCAACATAAATACTCCT 58.269 36.000 0.00 0.00 0.00 3.69
1743 1893 7.773690 ACTACAACATCCCAACATAAATACTCC 59.226 37.037 0.00 0.00 0.00 3.85
1744 1894 8.732746 ACTACAACATCCCAACATAAATACTC 57.267 34.615 0.00 0.00 0.00 2.59
1745 1895 8.548877 AGACTACAACATCCCAACATAAATACT 58.451 33.333 0.00 0.00 0.00 2.12
1746 1896 8.732746 AGACTACAACATCCCAACATAAATAC 57.267 34.615 0.00 0.00 0.00 1.89
1747 1897 8.544622 TGAGACTACAACATCCCAACATAAATA 58.455 33.333 0.00 0.00 0.00 1.40
1748 1898 7.402054 TGAGACTACAACATCCCAACATAAAT 58.598 34.615 0.00 0.00 0.00 1.40
1749 1899 6.774673 TGAGACTACAACATCCCAACATAAA 58.225 36.000 0.00 0.00 0.00 1.40
1750 1900 6.367374 TGAGACTACAACATCCCAACATAA 57.633 37.500 0.00 0.00 0.00 1.90
1751 1901 6.156083 TGATGAGACTACAACATCCCAACATA 59.844 38.462 0.00 0.00 39.41 2.29
1752 1902 4.908601 TGAGACTACAACATCCCAACAT 57.091 40.909 0.00 0.00 0.00 2.71
1753 1903 4.285775 TGATGAGACTACAACATCCCAACA 59.714 41.667 0.00 0.00 39.41 3.33
1754 1904 4.832248 TGATGAGACTACAACATCCCAAC 58.168 43.478 0.00 0.00 39.41 3.77
1755 1905 5.045651 ACATGATGAGACTACAACATCCCAA 60.046 40.000 0.00 0.00 39.41 4.12
1756 1906 4.471025 ACATGATGAGACTACAACATCCCA 59.529 41.667 0.00 0.00 39.41 4.37
1757 1907 5.028549 ACATGATGAGACTACAACATCCC 57.971 43.478 0.00 0.00 39.41 3.85
1758 1908 6.810911 AGTACATGATGAGACTACAACATCC 58.189 40.000 0.00 0.00 39.41 3.51
1759 1909 7.484140 TGAGTACATGATGAGACTACAACATC 58.516 38.462 0.00 0.00 40.22 3.06
1760 1910 7.410120 TGAGTACATGATGAGACTACAACAT 57.590 36.000 0.00 0.00 34.51 2.71
1761 1911 6.834168 TGAGTACATGATGAGACTACAACA 57.166 37.500 0.00 0.00 0.00 3.33
1762 1912 7.316640 ACTTGAGTACATGATGAGACTACAAC 58.683 38.462 0.00 0.00 0.00 3.32
1763 1913 7.468141 ACTTGAGTACATGATGAGACTACAA 57.532 36.000 0.00 7.79 0.00 2.41
1764 1914 8.753497 ATACTTGAGTACATGATGAGACTACA 57.247 34.615 0.00 0.95 32.72 2.74
1765 1915 8.293867 GGATACTTGAGTACATGATGAGACTAC 58.706 40.741 0.00 0.00 32.72 2.73
1766 1916 7.998964 TGGATACTTGAGTACATGATGAGACTA 59.001 37.037 0.00 0.00 32.72 2.59
1767 1917 6.836007 TGGATACTTGAGTACATGATGAGACT 59.164 38.462 0.00 1.69 32.72 3.24
1768 1918 7.043961 TGGATACTTGAGTACATGATGAGAC 57.956 40.000 0.00 0.00 32.72 3.36
1769 1919 7.727634 AGATGGATACTTGAGTACATGATGAGA 59.272 37.037 0.00 0.00 32.72 3.27
1770 1920 7.894708 AGATGGATACTTGAGTACATGATGAG 58.105 38.462 0.00 0.00 32.72 2.90
1771 1921 7.506938 TGAGATGGATACTTGAGTACATGATGA 59.493 37.037 0.00 0.00 32.72 2.92
1772 1922 7.664758 TGAGATGGATACTTGAGTACATGATG 58.335 38.462 0.00 0.00 32.72 3.07
1773 1923 7.846101 TGAGATGGATACTTGAGTACATGAT 57.154 36.000 0.00 0.00 32.72 2.45
1774 1924 7.664758 CATGAGATGGATACTTGAGTACATGA 58.335 38.462 0.00 0.00 31.94 3.07
1775 1925 6.368243 GCATGAGATGGATACTTGAGTACATG 59.632 42.308 0.00 0.00 32.70 3.21
1776 1926 6.462500 GCATGAGATGGATACTTGAGTACAT 58.538 40.000 0.00 0.00 32.72 2.29
1777 1927 5.221521 GGCATGAGATGGATACTTGAGTACA 60.222 44.000 0.00 0.00 32.72 2.90
1778 1928 5.011533 AGGCATGAGATGGATACTTGAGTAC 59.988 44.000 0.00 0.00 32.72 2.73
1779 1929 5.150715 AGGCATGAGATGGATACTTGAGTA 58.849 41.667 0.00 0.00 37.61 2.59
1780 1930 3.972638 AGGCATGAGATGGATACTTGAGT 59.027 43.478 0.00 0.00 37.61 3.41
1781 1931 4.563168 GGAGGCATGAGATGGATACTTGAG 60.563 50.000 0.00 0.00 37.61 3.02
1782 1932 3.326006 GGAGGCATGAGATGGATACTTGA 59.674 47.826 0.00 0.00 37.61 3.02
1783 1933 3.558746 GGGAGGCATGAGATGGATACTTG 60.559 52.174 0.00 0.00 37.61 3.16
1784 1934 2.641815 GGGAGGCATGAGATGGATACTT 59.358 50.000 0.00 0.00 37.61 2.24
1785 1935 2.158035 AGGGAGGCATGAGATGGATACT 60.158 50.000 0.00 0.00 37.61 2.12
1786 1936 2.235898 GAGGGAGGCATGAGATGGATAC 59.764 54.545 0.00 0.00 0.00 2.24
1787 1937 2.158112 TGAGGGAGGCATGAGATGGATA 60.158 50.000 0.00 0.00 0.00 2.59
1788 1938 1.360185 GAGGGAGGCATGAGATGGAT 58.640 55.000 0.00 0.00 0.00 3.41
1789 1939 0.030807 TGAGGGAGGCATGAGATGGA 60.031 55.000 0.00 0.00 0.00 3.41
1790 1940 0.397187 CTGAGGGAGGCATGAGATGG 59.603 60.000 0.00 0.00 0.00 3.51
1791 1941 1.421480 TCTGAGGGAGGCATGAGATG 58.579 55.000 0.00 0.00 0.00 2.90
1792 1942 1.767681 GTTCTGAGGGAGGCATGAGAT 59.232 52.381 0.00 0.00 0.00 2.75
1793 1943 1.198713 GTTCTGAGGGAGGCATGAGA 58.801 55.000 0.00 0.00 0.00 3.27
1794 1944 1.138661 GAGTTCTGAGGGAGGCATGAG 59.861 57.143 0.00 0.00 0.00 2.90
1795 1945 1.198713 GAGTTCTGAGGGAGGCATGA 58.801 55.000 0.00 0.00 0.00 3.07
1796 1946 1.138661 GAGAGTTCTGAGGGAGGCATG 59.861 57.143 0.00 0.00 0.00 4.06
1797 1947 1.008206 AGAGAGTTCTGAGGGAGGCAT 59.992 52.381 0.00 0.00 30.72 4.40
1807 1957 1.099689 GAGGGGACGAGAGAGTTCTG 58.900 60.000 0.00 0.00 32.53 3.02
1824 1974 1.616865 TGGGTTTACTCGTCACTGGAG 59.383 52.381 0.00 0.00 37.54 3.86
1837 1987 2.228480 AAGCCTCGCCCTGGGTTTA 61.228 57.895 15.56 0.00 41.86 2.01
1903 2054 3.231818 AGGAGACCGAGTCTTTCTTTGA 58.768 45.455 7.80 0.00 43.53 2.69
1909 2060 2.036089 GTGTTGAGGAGACCGAGTCTTT 59.964 50.000 7.80 1.30 43.53 2.52
1914 2065 0.244994 CTGGTGTTGAGGAGACCGAG 59.755 60.000 0.00 0.00 44.54 4.63
1917 2068 0.321996 GTCCTGGTGTTGAGGAGACC 59.678 60.000 0.00 0.00 40.42 3.85
1918 2069 0.321996 GGTCCTGGTGTTGAGGAGAC 59.678 60.000 0.00 0.00 40.42 3.36
1933 2084 2.663075 GGGGTACGGGAGTTGGTCC 61.663 68.421 0.00 0.00 43.33 4.46
1938 2089 1.151965 AACTGGGGGTACGGGAGTT 60.152 57.895 0.00 0.00 43.33 3.01
1961 2112 1.477558 CCCCTACCTGCAGCCAAATAG 60.478 57.143 8.66 4.42 0.00 1.73
1962 2113 0.550914 CCCCTACCTGCAGCCAAATA 59.449 55.000 8.66 0.00 0.00 1.40
1992 2143 4.881273 GGGTGGAAAGCAAACAAGAATTTT 59.119 37.500 0.00 0.00 0.00 1.82
1993 2144 4.450976 GGGTGGAAAGCAAACAAGAATTT 58.549 39.130 0.00 0.00 0.00 1.82
2036 2188 3.319122 GCCATTCACACCCTCATATTTCC 59.681 47.826 0.00 0.00 0.00 3.13
2042 2194 0.994247 TCAGCCATTCACACCCTCAT 59.006 50.000 0.00 0.00 0.00 2.90
2059 2211 0.740868 CTTCGCCGCTCCTCAAATCA 60.741 55.000 0.00 0.00 0.00 2.57
2110 2262 3.382546 CCACCATCTCCATTGTCAAATCC 59.617 47.826 0.00 0.00 0.00 3.01
2127 2279 2.890258 TTCCCCTTGGAATCCACCA 58.110 52.632 0.00 0.00 45.88 4.17
2146 2298 3.909086 GACCAGCTTTCCTGCGGCT 62.909 63.158 0.00 0.00 40.36 5.52
2147 2299 3.435186 GACCAGCTTTCCTGCGGC 61.435 66.667 0.00 0.00 40.36 6.53
2152 2304 2.879233 TTCGCCGACCAGCTTTCCT 61.879 57.895 0.00 0.00 0.00 3.36
2176 2328 3.412624 GACCTGGCCCTCTGCATCC 62.413 68.421 0.00 0.00 43.89 3.51
2189 2341 1.693062 CTCCATCATCTCCCTGACCTG 59.307 57.143 0.00 0.00 0.00 4.00
2239 2391 4.362470 CTCATATTCCAAGATGAGGGCA 57.638 45.455 13.85 0.00 46.01 5.36
2254 2406 7.058525 TCACCAAATCAGCTTCATTCTCATAT 58.941 34.615 0.00 0.00 0.00 1.78
2255 2407 6.417258 TCACCAAATCAGCTTCATTCTCATA 58.583 36.000 0.00 0.00 0.00 2.15
2321 2473 8.119845 CGACATGATAGTCTGTATATGTAGAGC 58.880 40.741 0.00 0.00 36.38 4.09
2326 2478 5.392057 CGCCGACATGATAGTCTGTATATGT 60.392 44.000 0.00 0.00 36.38 2.29
2350 2502 2.109126 CGCCCAAGCTGGTCTAAGC 61.109 63.158 0.00 0.00 43.88 3.09
2367 2519 4.865776 TGCAACTAAACCTTTTGGATTCG 58.134 39.130 0.00 0.00 44.07 3.34
2383 2535 3.006323 TGTTTGACACTGGTTTTGCAACT 59.994 39.130 0.00 0.00 32.90 3.16


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

AutoCloner maintained by Alex Coulton.