Multiple sequence alignment - TraesCS3B01G427900

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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 TraesCS3B01G427900 chr3B 100.000 5849 0 0 1 5849 666781902 666787750 0.000000e+00 10802.0
1 TraesCS3B01G427900 chr3B 87.076 619 71 6 5099 5708 561045227 561045845 0.000000e+00 691.0
2 TraesCS3B01G427900 chr3B 100.000 32 0 0 5047 5078 163684299 163684268 6.330000e-05 60.2
3 TraesCS3B01G427900 chr3D 93.444 1815 91 15 1857 3664 505049065 505050858 0.000000e+00 2667.0
4 TraesCS3B01G427900 chr3D 95.050 1414 43 13 3666 5061 505050901 505052305 0.000000e+00 2198.0
5 TraesCS3B01G427900 chr3D 87.533 1131 75 35 730 1813 505047953 505049064 0.000000e+00 1247.0
6 TraesCS3B01G427900 chr3D 91.791 670 52 3 5050 5717 505053442 505054110 0.000000e+00 929.0
7 TraesCS3B01G427900 chr3D 93.182 132 9 0 5718 5849 505054817 505054948 1.660000e-45 195.0
8 TraesCS3B01G427900 chr3D 86.047 129 17 1 5721 5849 514998253 514998126 2.840000e-28 137.0
9 TraesCS3B01G427900 chr3D 93.023 43 3 0 5050 5092 491616558 491616516 4.890000e-06 63.9
10 TraesCS3B01G427900 chr3A 90.081 1845 109 27 3666 5471 643185162 643186971 0.000000e+00 2326.0
11 TraesCS3B01G427900 chr3A 94.210 1399 61 10 1857 3250 643183219 643184602 0.000000e+00 2117.0
12 TraesCS3B01G427900 chr3A 89.009 1110 60 18 730 1813 643182145 643183218 0.000000e+00 1317.0
13 TraesCS3B01G427900 chr3A 90.144 416 38 2 3249 3664 643184707 643185119 6.670000e-149 538.0
14 TraesCS3B01G427900 chr3A 81.203 133 25 0 5717 5849 711657392 711657524 2.230000e-19 108.0
15 TraesCS3B01G427900 chr7B 94.576 719 39 0 1 719 59611203 59611921 0.000000e+00 1112.0
16 TraesCS3B01G427900 chr7B 94.093 728 40 2 1 725 474280048 474279321 0.000000e+00 1103.0
17 TraesCS3B01G427900 chr7B 94.183 722 39 3 1 719 608306688 608307409 0.000000e+00 1098.0
18 TraesCS3B01G427900 chr7B 86.907 611 71 6 5105 5708 221322062 221322670 0.000000e+00 676.0
19 TraesCS3B01G427900 chr2B 94.583 720 38 1 1 719 762460810 762461529 0.000000e+00 1112.0
20 TraesCS3B01G427900 chr1B 94.444 720 38 2 1 719 1488654 1489372 0.000000e+00 1107.0
21 TraesCS3B01G427900 chr6B 94.429 718 38 2 1 717 453116525 453117241 0.000000e+00 1103.0
22 TraesCS3B01G427900 chr6B 93.939 726 41 3 1 725 494168183 494167460 0.000000e+00 1094.0
23 TraesCS3B01G427900 chr6B 88.785 107 12 0 5741 5847 146663299 146663193 1.320000e-26 132.0
24 TraesCS3B01G427900 chr4A 94.102 729 37 5 1 725 737540794 737540068 0.000000e+00 1103.0
25 TraesCS3B01G427900 chr4A 86.822 129 13 2 5721 5849 170707594 170707470 2.200000e-29 141.0
26 TraesCS3B01G427900 chr4A 87.000 100 13 0 5717 5816 503609069 503609168 4.790000e-21 113.0
27 TraesCS3B01G427900 chr4B 93.810 727 42 3 1 725 471952045 471951320 0.000000e+00 1090.0
28 TraesCS3B01G427900 chr4B 86.893 618 77 4 5105 5720 59850962 59850347 0.000000e+00 689.0
29 TraesCS3B01G427900 chr1D 87.318 686 68 11 5050 5720 447541441 447540760 0.000000e+00 767.0
30 TraesCS3B01G427900 chr1D 88.320 625 66 7 5105 5723 60314225 60313602 0.000000e+00 743.0
31 TraesCS3B01G427900 chr6D 88.655 617 60 5 5106 5717 456515311 456514700 0.000000e+00 743.0
32 TraesCS3B01G427900 chr6D 86.517 623 77 6 5104 5720 321771801 321771180 0.000000e+00 678.0
33 TraesCS3B01G427900 chr2A 87.597 129 16 0 5721 5849 767949890 767949762 3.650000e-32 150.0
34 TraesCS3B01G427900 chr4D 87.023 131 17 0 5718 5848 483949938 483950068 1.310000e-31 148.0
35 TraesCS3B01G427900 chr5D 84.962 133 18 2 5718 5849 353649499 353649630 3.680000e-27 134.0
36 TraesCS3B01G427900 chrUn 85.246 61 9 0 3871 3931 30244952 30245012 4.890000e-06 63.9


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 TraesCS3B01G427900 chr3B 666781902 666787750 5848 False 10802.0 10802 100.000 1 5849 1 chr3B.!!$F2 5848
1 TraesCS3B01G427900 chr3B 561045227 561045845 618 False 691.0 691 87.076 5099 5708 1 chr3B.!!$F1 609
2 TraesCS3B01G427900 chr3D 505047953 505054948 6995 False 1447.2 2667 92.200 730 5849 5 chr3D.!!$F1 5119
3 TraesCS3B01G427900 chr3A 643182145 643186971 4826 False 1574.5 2326 90.861 730 5471 4 chr3A.!!$F2 4741
4 TraesCS3B01G427900 chr7B 59611203 59611921 718 False 1112.0 1112 94.576 1 719 1 chr7B.!!$F1 718
5 TraesCS3B01G427900 chr7B 474279321 474280048 727 True 1103.0 1103 94.093 1 725 1 chr7B.!!$R1 724
6 TraesCS3B01G427900 chr7B 608306688 608307409 721 False 1098.0 1098 94.183 1 719 1 chr7B.!!$F3 718
7 TraesCS3B01G427900 chr7B 221322062 221322670 608 False 676.0 676 86.907 5105 5708 1 chr7B.!!$F2 603
8 TraesCS3B01G427900 chr2B 762460810 762461529 719 False 1112.0 1112 94.583 1 719 1 chr2B.!!$F1 718
9 TraesCS3B01G427900 chr1B 1488654 1489372 718 False 1107.0 1107 94.444 1 719 1 chr1B.!!$F1 718
10 TraesCS3B01G427900 chr6B 453116525 453117241 716 False 1103.0 1103 94.429 1 717 1 chr6B.!!$F1 716
11 TraesCS3B01G427900 chr6B 494167460 494168183 723 True 1094.0 1094 93.939 1 725 1 chr6B.!!$R2 724
12 TraesCS3B01G427900 chr4A 737540068 737540794 726 True 1103.0 1103 94.102 1 725 1 chr4A.!!$R2 724
13 TraesCS3B01G427900 chr4B 471951320 471952045 725 True 1090.0 1090 93.810 1 725 1 chr4B.!!$R2 724
14 TraesCS3B01G427900 chr4B 59850347 59850962 615 True 689.0 689 86.893 5105 5720 1 chr4B.!!$R1 615
15 TraesCS3B01G427900 chr1D 447540760 447541441 681 True 767.0 767 87.318 5050 5720 1 chr1D.!!$R2 670
16 TraesCS3B01G427900 chr1D 60313602 60314225 623 True 743.0 743 88.320 5105 5723 1 chr1D.!!$R1 618
17 TraesCS3B01G427900 chr6D 456514700 456515311 611 True 743.0 743 88.655 5106 5717 1 chr6D.!!$R2 611
18 TraesCS3B01G427900 chr6D 321771180 321771801 621 True 678.0 678 86.517 5104 5720 1 chr6D.!!$R1 616

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
661 668 0.248458 CGCCAACGCTGTTTTCTGTT 60.248 50.0 0.00 0.00 0.00 3.16 F
1589 1659 0.386731 GTGCAAATTCGTTGGTCCCG 60.387 55.0 0.00 0.00 37.73 5.14 F
3125 3199 0.678395 CTCCAGATATGGCTGCTCGT 59.322 55.0 0.00 0.00 34.56 4.18 F
3692 3914 0.108585 TCTGTGACTGGCCAGAAACC 59.891 55.0 39.19 22.64 34.88 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 1923 0.036388 TCCTGACCAATGAAGCCGAC 60.036 55.0 0.00 0.0 0.00 4.79 R
3548 3729 0.038166 TTGGTTGCCTCCATCTGGTC 59.962 55.0 0.00 0.0 37.33 4.02 R
4695 4926 0.314302 AAGGACGTCTCTGTGTTCCG 59.686 55.0 16.46 0.0 0.00 4.30 R
5563 6986 0.039074 GTATCGCTGGCACGCTATCT 60.039 55.0 7.22 0.0 0.00 1.98 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
38 39 3.132139 CGACCTCCTCGGCGAAGA 61.132 66.667 12.13 9.93 38.87 2.87
243 244 3.204827 GCGTTCTGCCATGGCGAT 61.205 61.111 30.87 0.00 45.51 4.58
323 324 3.744155 GCAGGGAAAGGGAGGGGG 61.744 72.222 0.00 0.00 0.00 5.40
358 362 4.329545 GGACTGGTCTGGGCGCAA 62.330 66.667 10.83 0.00 0.00 4.85
421 425 4.789075 TACGCGTGCGAGGGAAGC 62.789 66.667 24.59 0.00 42.83 3.86
598 605 2.597217 CCAAAACAGCTCGCCCCA 60.597 61.111 0.00 0.00 0.00 4.96
658 665 0.889186 ATCCGCCAACGCTGTTTTCT 60.889 50.000 0.00 0.00 38.22 2.52
660 667 1.355210 CGCCAACGCTGTTTTCTGT 59.645 52.632 0.00 0.00 0.00 3.41
661 668 0.248458 CGCCAACGCTGTTTTCTGTT 60.248 50.000 0.00 0.00 0.00 3.16
668 675 1.600413 CGCTGTTTTCTGTTCAAGCCC 60.600 52.381 0.00 0.00 0.00 5.19
687 694 0.808453 CGCGAAAATCGGGCTCCTAA 60.808 55.000 0.00 0.00 45.33 2.69
692 700 3.741388 CGAAAATCGGGCTCCTAAGATGT 60.741 47.826 0.00 0.00 36.00 3.06
749 757 0.827368 TGAACCTGCAAAACCCAACC 59.173 50.000 0.00 0.00 0.00 3.77
881 908 2.069273 CCAGCTCGAAGGTAAACACAG 58.931 52.381 0.00 0.00 0.00 3.66
882 909 2.548067 CCAGCTCGAAGGTAAACACAGT 60.548 50.000 0.00 0.00 0.00 3.55
883 910 3.305813 CCAGCTCGAAGGTAAACACAGTA 60.306 47.826 0.00 0.00 0.00 2.74
885 912 3.825014 AGCTCGAAGGTAAACACAGTAGA 59.175 43.478 0.00 0.00 0.00 2.59
886 913 3.919197 GCTCGAAGGTAAACACAGTAGAC 59.081 47.826 0.00 0.00 0.00 2.59
887 914 4.558095 GCTCGAAGGTAAACACAGTAGACA 60.558 45.833 0.00 0.00 0.00 3.41
888 915 5.518848 TCGAAGGTAAACACAGTAGACAA 57.481 39.130 0.00 0.00 0.00 3.18
889 916 5.904941 TCGAAGGTAAACACAGTAGACAAA 58.095 37.500 0.00 0.00 0.00 2.83
890 917 5.750067 TCGAAGGTAAACACAGTAGACAAAC 59.250 40.000 0.00 0.00 0.00 2.93
891 918 5.751990 CGAAGGTAAACACAGTAGACAAACT 59.248 40.000 0.00 0.00 0.00 2.66
892 919 6.074463 CGAAGGTAAACACAGTAGACAAACTC 60.074 42.308 0.00 0.00 0.00 3.01
893 920 5.608449 AGGTAAACACAGTAGACAAACTCC 58.392 41.667 0.00 0.00 0.00 3.85
894 921 4.753610 GGTAAACACAGTAGACAAACTCCC 59.246 45.833 0.00 0.00 0.00 4.30
895 922 4.497291 AAACACAGTAGACAAACTCCCA 57.503 40.909 0.00 0.00 0.00 4.37
896 923 4.497291 AACACAGTAGACAAACTCCCAA 57.503 40.909 0.00 0.00 0.00 4.12
897 924 3.805207 ACACAGTAGACAAACTCCCAAC 58.195 45.455 0.00 0.00 0.00 3.77
898 925 3.199071 ACACAGTAGACAAACTCCCAACA 59.801 43.478 0.00 0.00 0.00 3.33
899 926 3.560068 CACAGTAGACAAACTCCCAACAC 59.440 47.826 0.00 0.00 0.00 3.32
900 927 3.199071 ACAGTAGACAAACTCCCAACACA 59.801 43.478 0.00 0.00 0.00 3.72
901 928 4.196193 CAGTAGACAAACTCCCAACACAA 58.804 43.478 0.00 0.00 0.00 3.33
902 929 4.638421 CAGTAGACAAACTCCCAACACAAA 59.362 41.667 0.00 0.00 0.00 2.83
903 930 5.124776 CAGTAGACAAACTCCCAACACAAAA 59.875 40.000 0.00 0.00 0.00 2.44
1116 1156 3.379445 GCCTCCCACTCCGTTCGA 61.379 66.667 0.00 0.00 0.00 3.71
1118 1158 2.178521 CTCCCACTCCGTTCGACG 59.821 66.667 0.00 0.00 42.11 5.12
1136 1176 2.364448 GTCCCTTCCTCCTCCGCT 60.364 66.667 0.00 0.00 0.00 5.52
1140 1182 2.756283 CTTCCTCCTCCGCTCCGT 60.756 66.667 0.00 0.00 0.00 4.69
1144 1186 3.213402 CTCCTCCGCTCCGTCTCC 61.213 72.222 0.00 0.00 0.00 3.71
1162 1204 3.924065 CGGAAATGCGCGCGATCA 61.924 61.111 37.18 23.90 0.00 2.92
1177 1219 1.014352 GATCAAATCGAACCGGTGGG 58.986 55.000 8.52 2.63 40.11 4.61
1293 1340 3.009253 TGGGGAAGCGATTTGTTAGGTTA 59.991 43.478 0.00 0.00 0.00 2.85
1300 1347 3.749609 GCGATTTGTTAGGTTAGGTGTGT 59.250 43.478 0.00 0.00 0.00 3.72
1306 1353 4.857679 TGTTAGGTTAGGTGTGTGGTTTT 58.142 39.130 0.00 0.00 0.00 2.43
1307 1354 4.641094 TGTTAGGTTAGGTGTGTGGTTTTG 59.359 41.667 0.00 0.00 0.00 2.44
1308 1355 3.375647 AGGTTAGGTGTGTGGTTTTGT 57.624 42.857 0.00 0.00 0.00 2.83
1474 1544 4.946784 ATGCGAGGTGATTTTTGTAGTC 57.053 40.909 0.00 0.00 0.00 2.59
1479 1549 4.652822 GAGGTGATTTTTGTAGTCTGGGT 58.347 43.478 0.00 0.00 0.00 4.51
1497 1567 3.075882 TGGGTTGGGAATTTCTGTCAGAT 59.924 43.478 2.68 0.00 0.00 2.90
1554 1624 0.598562 CCCGCGCTGTAGTATGATCT 59.401 55.000 5.56 0.00 0.00 2.75
1589 1659 0.386731 GTGCAAATTCGTTGGTCCCG 60.387 55.000 0.00 0.00 37.73 5.14
1621 1691 6.603095 CAAAGTCTAGCTGATTTACGCTTTT 58.397 36.000 0.00 0.00 37.68 2.27
1622 1692 7.623506 GCAAAGTCTAGCTGATTTACGCTTTTA 60.624 37.037 0.00 0.00 37.68 1.52
1628 1698 8.912658 TCTAGCTGATTTACGCTTTTATAATCG 58.087 33.333 0.00 0.00 37.68 3.34
1654 1724 6.536941 GTGAGATGATTTCTGGTTCTAGGTTC 59.463 42.308 0.00 0.00 33.74 3.62
1662 1732 6.494666 TTCTGGTTCTAGGTTCTTTCAGAA 57.505 37.500 0.00 0.00 37.57 3.02
1692 1762 1.916000 GACATCGAAATGCTTTGCTGC 59.084 47.619 0.00 0.00 36.26 5.25
1735 1805 5.689514 TGTTTCAAAATGCTGACATAAACCG 59.310 36.000 0.00 0.00 34.62 4.44
1747 1817 4.510711 TGACATAAACCGCTTAAACGAACA 59.489 37.500 0.00 0.00 34.06 3.18
1783 1853 3.119316 ACTGATGCTCCTTCTGAACGTAG 60.119 47.826 0.00 0.00 0.00 3.51
1813 1883 6.265196 TGGTTCAAATGCTGTTGTTCTAGAAT 59.735 34.615 8.75 0.00 0.00 2.40
1814 1884 7.147976 GGTTCAAATGCTGTTGTTCTAGAATT 58.852 34.615 8.75 0.00 0.00 2.17
1815 1885 7.653311 GGTTCAAATGCTGTTGTTCTAGAATTT 59.347 33.333 8.75 0.00 33.43 1.82
1816 1886 9.677567 GTTCAAATGCTGTTGTTCTAGAATTTA 57.322 29.630 8.75 0.00 31.84 1.40
1818 1888 9.844790 TCAAATGCTGTTGTTCTAGAATTTATG 57.155 29.630 8.75 1.40 31.84 1.90
1819 1889 8.589629 CAAATGCTGTTGTTCTAGAATTTATGC 58.410 33.333 8.75 11.21 31.84 3.14
1820 1890 7.636150 ATGCTGTTGTTCTAGAATTTATGCT 57.364 32.000 8.75 0.28 0.00 3.79
1821 1891 7.452880 TGCTGTTGTTCTAGAATTTATGCTT 57.547 32.000 8.75 0.00 0.00 3.91
1822 1892 7.530010 TGCTGTTGTTCTAGAATTTATGCTTC 58.470 34.615 8.75 0.00 0.00 3.86
1823 1893 7.391554 TGCTGTTGTTCTAGAATTTATGCTTCT 59.608 33.333 8.75 0.00 36.87 2.85
1824 1894 7.695618 GCTGTTGTTCTAGAATTTATGCTTCTG 59.304 37.037 8.75 0.00 34.81 3.02
1825 1895 8.621532 TGTTGTTCTAGAATTTATGCTTCTGT 57.378 30.769 8.75 0.00 34.81 3.41
1826 1896 9.066892 TGTTGTTCTAGAATTTATGCTTCTGTT 57.933 29.630 8.75 0.00 34.81 3.16
1827 1897 9.334693 GTTGTTCTAGAATTTATGCTTCTGTTG 57.665 33.333 8.75 0.00 34.81 3.33
1828 1898 8.621532 TGTTCTAGAATTTATGCTTCTGTTGT 57.378 30.769 8.75 0.00 34.81 3.32
1829 1899 9.066892 TGTTCTAGAATTTATGCTTCTGTTGTT 57.933 29.630 8.75 0.00 34.81 2.83
1830 1900 9.899226 GTTCTAGAATTTATGCTTCTGTTGTTT 57.101 29.630 8.75 0.00 34.81 2.83
1831 1901 9.897744 TTCTAGAATTTATGCTTCTGTTGTTTG 57.102 29.630 0.00 0.00 34.81 2.93
1832 1902 9.066892 TCTAGAATTTATGCTTCTGTTGTTTGT 57.933 29.630 0.00 0.00 34.81 2.83
1833 1903 7.935338 AGAATTTATGCTTCTGTTGTTTGTG 57.065 32.000 0.00 0.00 31.84 3.33
1834 1904 7.715657 AGAATTTATGCTTCTGTTGTTTGTGA 58.284 30.769 0.00 0.00 31.84 3.58
1835 1905 8.196771 AGAATTTATGCTTCTGTTGTTTGTGAA 58.803 29.630 0.00 0.00 31.84 3.18
1836 1906 7.698836 ATTTATGCTTCTGTTGTTTGTGAAC 57.301 32.000 0.00 0.00 36.29 3.18
1837 1907 4.989279 ATGCTTCTGTTGTTTGTGAACT 57.011 36.364 0.00 0.00 36.70 3.01
1838 1908 4.782019 TGCTTCTGTTGTTTGTGAACTT 57.218 36.364 0.00 0.00 36.70 2.66
1839 1909 4.732784 TGCTTCTGTTGTTTGTGAACTTC 58.267 39.130 0.00 0.00 36.70 3.01
1840 1910 4.458989 TGCTTCTGTTGTTTGTGAACTTCT 59.541 37.500 0.00 0.00 36.70 2.85
1841 1911 5.645929 TGCTTCTGTTGTTTGTGAACTTCTA 59.354 36.000 0.00 0.00 36.70 2.10
1842 1912 6.318648 TGCTTCTGTTGTTTGTGAACTTCTAT 59.681 34.615 0.00 0.00 36.70 1.98
1843 1913 6.634436 GCTTCTGTTGTTTGTGAACTTCTATG 59.366 38.462 0.00 0.00 36.70 2.23
1844 1914 6.618287 TCTGTTGTTTGTGAACTTCTATGG 57.382 37.500 0.00 0.00 36.70 2.74
1845 1915 5.008613 TCTGTTGTTTGTGAACTTCTATGGC 59.991 40.000 0.00 0.00 36.70 4.40
1846 1916 4.642437 TGTTGTTTGTGAACTTCTATGGCA 59.358 37.500 0.00 0.00 36.70 4.92
1847 1917 5.301551 TGTTGTTTGTGAACTTCTATGGCAT 59.698 36.000 4.88 4.88 36.70 4.40
1848 1918 6.183360 TGTTGTTTGTGAACTTCTATGGCATT 60.183 34.615 4.78 0.00 36.70 3.56
1849 1919 6.403866 TGTTTGTGAACTTCTATGGCATTT 57.596 33.333 4.78 0.00 36.70 2.32
1850 1920 6.815089 TGTTTGTGAACTTCTATGGCATTTT 58.185 32.000 4.78 0.00 36.70 1.82
1851 1921 7.271511 TGTTTGTGAACTTCTATGGCATTTTT 58.728 30.769 4.78 0.00 36.70 1.94
1852 1922 7.224362 TGTTTGTGAACTTCTATGGCATTTTTG 59.776 33.333 4.78 0.00 36.70 2.44
1853 1923 5.782047 TGTGAACTTCTATGGCATTTTTGG 58.218 37.500 4.78 0.00 0.00 3.28
1854 1924 5.304101 TGTGAACTTCTATGGCATTTTTGGT 59.696 36.000 4.78 0.00 0.00 3.67
1855 1925 5.863935 GTGAACTTCTATGGCATTTTTGGTC 59.136 40.000 4.78 3.42 0.00 4.02
1868 1938 1.243902 TTTGGTCGGCTTCATTGGTC 58.756 50.000 0.00 0.00 0.00 4.02
1912 1986 7.119846 GTCTAAAGTTGAATATGCTCCTGTGTT 59.880 37.037 0.00 0.00 0.00 3.32
1913 1987 5.633830 AAGTTGAATATGCTCCTGTGTTG 57.366 39.130 0.00 0.00 0.00 3.33
1926 2000 5.468072 GCTCCTGTGTTGATCCTGTAATATG 59.532 44.000 0.00 0.00 0.00 1.78
1931 2005 7.302350 TGTGTTGATCCTGTAATATGTTTCG 57.698 36.000 0.00 0.00 0.00 3.46
1956 2030 9.075519 CGTGATAAAATTCATGTATGTGCTTTT 57.924 29.630 0.00 0.00 0.00 2.27
1983 2057 1.063266 AGGGGTGAAACAAGGCAAAGA 60.063 47.619 0.00 0.00 39.98 2.52
2049 2123 5.246656 AGTTTGATGAGAATGAAAATGGGCA 59.753 36.000 0.00 0.00 0.00 5.36
2051 2125 5.270893 TGATGAGAATGAAAATGGGCATG 57.729 39.130 0.00 0.00 0.00 4.06
2052 2126 3.530265 TGAGAATGAAAATGGGCATGC 57.470 42.857 9.90 9.90 0.00 4.06
2053 2127 2.168936 TGAGAATGAAAATGGGCATGCC 59.831 45.455 29.47 29.47 0.00 4.40
2054 2128 2.168936 GAGAATGAAAATGGGCATGCCA 59.831 45.455 36.56 23.14 37.98 4.92
2055 2129 2.572556 AGAATGAAAATGGGCATGCCAA 59.427 40.909 36.56 28.74 37.98 4.52
2056 2130 2.702592 ATGAAAATGGGCATGCCAAG 57.297 45.000 36.56 0.00 37.98 3.61
2085 2159 2.595386 CAAGGCCTCAACAAATAACGC 58.405 47.619 5.23 0.00 0.00 4.84
2146 2220 7.102993 TGCTTGCTAGTTTACAGTTATCATGA 58.897 34.615 0.00 0.00 0.00 3.07
2152 2226 8.383619 GCTAGTTTACAGTTATCATGACACTTG 58.616 37.037 0.00 0.00 0.00 3.16
2174 2248 5.724328 TGAACTTATAGCTCTGTTCTGGTG 58.276 41.667 16.41 0.00 39.38 4.17
2175 2249 4.744795 ACTTATAGCTCTGTTCTGGTGG 57.255 45.455 0.00 0.00 0.00 4.61
2179 2253 1.972872 AGCTCTGTTCTGGTGGTTTG 58.027 50.000 0.00 0.00 0.00 2.93
2191 2265 2.948979 TGGTGGTTTGTCTGACATTCAC 59.051 45.455 11.86 17.48 0.00 3.18
2192 2266 2.293399 GGTGGTTTGTCTGACATTCACC 59.707 50.000 26.45 26.45 36.46 4.02
2193 2267 2.948979 GTGGTTTGTCTGACATTCACCA 59.051 45.455 23.09 23.09 33.34 4.17
2194 2268 3.569701 GTGGTTTGTCTGACATTCACCAT 59.430 43.478 26.71 0.00 36.25 3.55
2195 2269 4.037923 GTGGTTTGTCTGACATTCACCATT 59.962 41.667 26.71 0.00 36.25 3.16
2201 2275 3.438087 GTCTGACATTCACCATTCCACAG 59.562 47.826 2.24 0.00 0.00 3.66
2230 2304 9.783081 AATTTGATGTTATTTCCTCTGCTTTTT 57.217 25.926 0.00 0.00 0.00 1.94
2448 2522 5.796424 AATGGCAGTGAAGAAACTTGATT 57.204 34.783 0.00 0.00 0.00 2.57
2511 2585 6.377146 GGTTGGCTTACTATTGAAGATTGGAA 59.623 38.462 0.00 0.00 0.00 3.53
2629 2703 6.294010 CCATCAGCAATGATCCATACTTTCTG 60.294 42.308 0.96 0.00 37.59 3.02
2651 2725 2.500229 TGCTAGGTTTCCTTGGTTTCG 58.500 47.619 0.00 0.00 34.61 3.46
2773 2847 8.446273 GCATGATGTTCTACATGGTATGATTAC 58.554 37.037 0.00 0.00 39.27 1.89
2827 2901 6.151144 ACAAAATTTCCTATTCTCGTTGGGAG 59.849 38.462 0.00 0.00 44.58 4.30
2833 2907 0.984230 ATTCTCGTTGGGAGCTTGGA 59.016 50.000 0.00 0.00 42.82 3.53
2849 2923 1.748732 TGGAGATTGGGGTGGTACAA 58.251 50.000 0.00 0.00 44.16 2.41
2880 2954 8.178964 TGTGGATTATTTGTAAGCAATTACGTC 58.821 33.333 0.00 0.00 34.18 4.34
3026 3100 3.532542 GGTCCAGCCTTCTATTGTACAC 58.467 50.000 0.00 0.00 0.00 2.90
3044 3118 5.952347 TGTACACAGAGATGTTAGATCCAGT 59.048 40.000 0.00 0.00 33.85 4.00
3125 3199 0.678395 CTCCAGATATGGCTGCTCGT 59.322 55.000 0.00 0.00 34.56 4.18
3184 3259 1.202580 CGCCCCAGAGTAAGAATCCTG 60.203 57.143 0.00 0.00 0.00 3.86
3190 3265 5.163395 CCCCAGAGTAAGAATCCTGTACTTC 60.163 48.000 0.00 0.00 0.00 3.01
3197 3272 7.746703 AGTAAGAATCCTGTACTTCCAAACTT 58.253 34.615 0.00 0.00 0.00 2.66
3225 3300 9.236691 CAAATCCGTGATGAATTAATACTTTGG 57.763 33.333 0.00 0.00 0.00 3.28
3265 3446 8.338986 GCTAAAATATAGTTCTCTTTGGAGTGC 58.661 37.037 0.00 0.00 40.29 4.40
3279 3460 2.030185 TGGAGTGCGAACTTGTCTAGTC 60.030 50.000 0.00 0.00 35.54 2.59
3280 3461 2.243407 GAGTGCGAACTTGTCTAGTCG 58.757 52.381 0.00 0.00 35.54 4.18
3289 3470 6.312487 CGAACTTGTCTAGTCGATTCTGTAA 58.688 40.000 0.00 0.00 35.54 2.41
3292 3473 8.522178 AACTTGTCTAGTCGATTCTGTAAAAG 57.478 34.615 0.00 0.00 35.54 2.27
3295 3476 9.360093 CTTGTCTAGTCGATTCTGTAAAAGATT 57.640 33.333 0.00 0.00 33.93 2.40
3387 3568 9.827198 ATTAGAATTTAATCATTCCCTGGCATA 57.173 29.630 0.00 0.00 34.15 3.14
3441 3622 2.497107 ATGTGCTGTGAAACTTGTGC 57.503 45.000 0.00 0.00 38.04 4.57
3455 3636 1.393539 CTTGTGCCGTTGTAGAATCCG 59.606 52.381 0.00 0.00 0.00 4.18
3470 3651 2.094762 ATCCGTCAGCCTGTTGTTAC 57.905 50.000 0.00 0.00 0.00 2.50
3476 3657 3.067833 GTCAGCCTGTTGTTACTTCTCC 58.932 50.000 0.00 0.00 0.00 3.71
3483 3664 5.368989 CCTGTTGTTACTTCTCCTCTGTTT 58.631 41.667 0.00 0.00 0.00 2.83
3531 3712 8.747538 ACTGGTTTATACTCAATTACCAATCC 57.252 34.615 0.00 0.00 33.27 3.01
3532 3713 7.778382 ACTGGTTTATACTCAATTACCAATCCC 59.222 37.037 0.00 0.00 33.27 3.85
3548 3729 6.290605 ACCAATCCCAAAAAGAATCAAGTTG 58.709 36.000 0.00 0.00 0.00 3.16
3554 3735 5.068987 CCCAAAAAGAATCAAGTTGACCAGA 59.931 40.000 7.96 0.00 0.00 3.86
3566 3747 1.133181 TGACCAGATGGAGGCAACCA 61.133 55.000 5.72 5.95 44.41 3.67
3569 3750 1.318158 CCAGATGGAGGCAACCAAGC 61.318 60.000 7.45 3.88 43.47 4.01
3639 3820 3.449737 TGTTACTCCCTCCGTTCCATAAG 59.550 47.826 0.00 0.00 0.00 1.73
3641 3822 2.547990 ACTCCCTCCGTTCCATAAGTT 58.452 47.619 0.00 0.00 0.00 2.66
3653 3834 4.822036 TCCATAAGTTTTGTCGTGGTTG 57.178 40.909 0.00 0.00 0.00 3.77
3654 3835 4.200874 TCCATAAGTTTTGTCGTGGTTGT 58.799 39.130 0.00 0.00 0.00 3.32
3664 3845 5.412526 TTGTCGTGGTTGTAGTTCAAATC 57.587 39.130 0.00 0.00 37.81 2.17
3671 3893 6.347402 CGTGGTTGTAGTTCAAATCTAACCAG 60.347 42.308 0.00 0.00 37.81 4.00
3673 3895 7.012989 GTGGTTGTAGTTCAAATCTAACCAGTT 59.987 37.037 0.00 0.00 37.81 3.16
3678 3900 6.867662 AGTTCAAATCTAACCAGTTCTGTG 57.132 37.500 0.00 0.00 0.00 3.66
3692 3914 0.108585 TCTGTGACTGGCCAGAAACC 59.891 55.000 39.19 22.64 34.88 3.27
3702 3924 2.160205 GGCCAGAAACCTGTAAACTCC 58.840 52.381 0.00 0.00 0.00 3.85
3719 3942 2.969950 ACTCCACCTGCAGTAAACACTA 59.030 45.455 13.81 0.00 0.00 2.74
3720 3943 3.389983 ACTCCACCTGCAGTAAACACTAA 59.610 43.478 13.81 0.00 0.00 2.24
3721 3944 4.041691 ACTCCACCTGCAGTAAACACTAAT 59.958 41.667 13.81 0.00 0.00 1.73
3723 3946 5.484715 TCCACCTGCAGTAAACACTAATAC 58.515 41.667 13.81 0.00 0.00 1.89
3724 3947 5.247564 TCCACCTGCAGTAAACACTAATACT 59.752 40.000 13.81 0.00 32.69 2.12
4101 4324 1.470098 GTGCAGGCTACACCAAGATTG 59.530 52.381 6.60 0.00 43.14 2.67
4194 4417 2.018515 GTCTCCCTACTCCTCTTGTCG 58.981 57.143 0.00 0.00 0.00 4.35
4212 4435 1.667722 GCTTGCCCCCTCTTTTGTG 59.332 57.895 0.00 0.00 0.00 3.33
4215 4438 2.807676 CTTGCCCCCTCTTTTGTGTAT 58.192 47.619 0.00 0.00 0.00 2.29
4288 4513 2.866762 CCTTCGCACCTTAATACAGCTC 59.133 50.000 0.00 0.00 0.00 4.09
4324 4549 3.678289 TCTGTGTGTGCAATATGAAGCT 58.322 40.909 0.00 0.00 0.00 3.74
4569 4794 0.175760 GCCTGCACGAAGATAGTCCA 59.824 55.000 0.00 0.00 0.00 4.02
4594 4819 1.874231 CTTGCCTCATGCTGCTATCTG 59.126 52.381 0.00 0.00 42.00 2.90
4606 4831 4.941263 TGCTGCTATCTGTTTTACCGAAAT 59.059 37.500 0.00 0.00 0.00 2.17
4664 4895 6.100279 TGGAGCCTTGTCAGATCACTTTATAT 59.900 38.462 0.00 0.00 0.00 0.86
4665 4896 7.290014 TGGAGCCTTGTCAGATCACTTTATATA 59.710 37.037 0.00 0.00 0.00 0.86
4695 4926 0.948678 TTAAGACGTGTGGCTTTGGC 59.051 50.000 0.00 0.00 37.82 4.52
4716 4947 2.405172 GGAACACAGAGACGTCCTTTC 58.595 52.381 13.01 3.27 0.00 2.62
4726 4957 5.524646 CAGAGACGTCCTTTCCTAGTAGTAG 59.475 48.000 13.01 0.00 0.00 2.57
4727 4958 5.189539 AGAGACGTCCTTTCCTAGTAGTAGT 59.810 44.000 13.01 0.00 0.00 2.73
4728 4959 5.184711 AGACGTCCTTTCCTAGTAGTAGTG 58.815 45.833 13.01 0.00 0.00 2.74
4867 5122 4.227134 CGATCCTCCTGGCCGTGG 62.227 72.222 8.19 8.19 0.00 4.94
4868 5123 3.866582 GATCCTCCTGGCCGTGGG 61.867 72.222 13.76 8.60 0.00 4.61
5009 5268 4.286297 TCAACTGGTTTATAGTGCTGCT 57.714 40.909 0.00 0.00 0.00 4.24
5020 5279 3.393106 TGCTGCTCCCTCGCATCA 61.393 61.111 0.00 0.00 39.52 3.07
5072 6479 1.971167 GCATCTCCAACGGCAACCA 60.971 57.895 0.00 0.00 0.00 3.67
5073 6480 1.523154 GCATCTCCAACGGCAACCAA 61.523 55.000 0.00 0.00 0.00 3.67
5142 6557 4.155826 ACGCTAGCTGCATACATTTCAAAA 59.844 37.500 13.93 0.00 43.06 2.44
5228 6645 2.949177 TAGCACAAACCATCCACACT 57.051 45.000 0.00 0.00 0.00 3.55
5232 6649 3.146066 GCACAAACCATCCACACTTAGA 58.854 45.455 0.00 0.00 0.00 2.10
5260 6677 7.650104 TGCAAATTAAGTTTAGTACAACAAGGC 59.350 33.333 0.00 0.00 0.00 4.35
5288 6705 0.517755 CGACTAGATCCCGGATGTCG 59.482 60.000 18.91 18.91 40.55 4.35
5371 6794 1.262151 GTGTGCACGTAAATGACCGTT 59.738 47.619 13.13 0.00 34.59 4.44
5396 6819 1.412079 TACCTGTGGTACAACACGGT 58.588 50.000 21.12 21.12 44.38 4.83
5521 6944 0.041535 TGCAATGGCCATCTTCCCTT 59.958 50.000 21.08 0.00 40.13 3.95
5563 6986 2.826128 AGAACTTGATGACGCTGACCTA 59.174 45.455 0.00 0.00 0.00 3.08
5612 7036 2.523179 CACGTTGTGTGGTCGCATA 58.477 52.632 0.00 0.00 45.21 3.14
5711 7137 2.421952 GGTCCTGCCTATGAAATCTGCA 60.422 50.000 0.00 0.00 32.87 4.41
5720 7146 5.303165 CCTATGAAATCTGCAGATACAGCA 58.697 41.667 28.92 22.06 40.19 4.41
5731 7863 5.463286 TGCAGATACAGCAGTTCAAATTTG 58.537 37.500 12.15 12.15 37.02 2.32
5776 7908 4.461431 CCTACATTGTTGTCCCCTTTAACC 59.539 45.833 0.00 0.00 37.28 2.85
5783 7915 2.154747 TCCCCTTTAACCGCCCACA 61.155 57.895 0.00 0.00 0.00 4.17
5784 7916 1.677633 CCCCTTTAACCGCCCACAG 60.678 63.158 0.00 0.00 0.00 3.66
5802 7934 5.768662 CCCACAGATGCTCAATCAGATATTT 59.231 40.000 0.00 0.00 37.81 1.40
5808 7940 8.927721 CAGATGCTCAATCAGATATTTAGTCAG 58.072 37.037 0.00 0.00 37.81 3.51
5814 7946 6.927936 TCAATCAGATATTTAGTCAGCTGCTC 59.072 38.462 9.47 4.66 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.396911 GAGGTCGAGATCGTGCGCA 62.397 63.158 5.66 5.66 40.80 6.09
639 646 0.889186 AGAAAACAGCGTTGGCGGAT 60.889 50.000 3.74 0.00 46.35 4.18
658 665 0.239879 GATTTTCGCGGGCTTGAACA 59.760 50.000 6.13 0.00 0.00 3.18
660 667 1.499949 CGATTTTCGCGGGCTTGAA 59.500 52.632 6.13 0.00 31.14 2.69
661 668 2.395360 CCGATTTTCGCGGGCTTGA 61.395 57.895 6.13 0.00 44.87 3.02
668 675 0.808453 TTAGGAGCCCGATTTTCGCG 60.808 55.000 0.00 0.00 38.82 5.87
687 694 0.110486 AAAACGGCCCAGTCACATCT 59.890 50.000 0.00 0.00 0.00 2.90
719 727 0.899717 GCAGGTTCAGGGCATTTCCA 60.900 55.000 0.00 0.00 36.21 3.53
720 728 0.899717 TGCAGGTTCAGGGCATTTCC 60.900 55.000 0.00 0.00 31.58 3.13
725 733 1.398958 GGTTTTGCAGGTTCAGGGCA 61.399 55.000 0.00 0.00 35.41 5.36
726 734 1.367471 GGTTTTGCAGGTTCAGGGC 59.633 57.895 0.00 0.00 0.00 5.19
727 735 0.758685 TGGGTTTTGCAGGTTCAGGG 60.759 55.000 0.00 0.00 0.00 4.45
728 736 1.118838 TTGGGTTTTGCAGGTTCAGG 58.881 50.000 0.00 0.00 0.00 3.86
749 757 2.556287 GTGAGTGCCGGCTTTTCG 59.444 61.111 29.70 0.00 0.00 3.46
828 855 3.127533 GCCGGATGTGTCACTGCC 61.128 66.667 5.05 4.71 0.00 4.85
833 860 2.047655 GAACGGCCGGATGTGTCA 60.048 61.111 31.76 0.00 0.00 3.58
881 908 5.570234 TTTTGTGTTGGGAGTTTGTCTAC 57.430 39.130 0.00 0.00 0.00 2.59
882 909 5.477291 TGTTTTTGTGTTGGGAGTTTGTCTA 59.523 36.000 0.00 0.00 0.00 2.59
883 910 4.282195 TGTTTTTGTGTTGGGAGTTTGTCT 59.718 37.500 0.00 0.00 0.00 3.41
885 912 4.608948 TGTTTTTGTGTTGGGAGTTTGT 57.391 36.364 0.00 0.00 0.00 2.83
886 913 5.931441 TTTGTTTTTGTGTTGGGAGTTTG 57.069 34.783 0.00 0.00 0.00 2.93
887 914 6.318900 TGTTTTTGTTTTTGTGTTGGGAGTTT 59.681 30.769 0.00 0.00 0.00 2.66
888 915 5.823045 TGTTTTTGTTTTTGTGTTGGGAGTT 59.177 32.000 0.00 0.00 0.00 3.01
889 916 5.368989 TGTTTTTGTTTTTGTGTTGGGAGT 58.631 33.333 0.00 0.00 0.00 3.85
890 917 5.931441 TGTTTTTGTTTTTGTGTTGGGAG 57.069 34.783 0.00 0.00 0.00 4.30
891 918 6.693315 TTTGTTTTTGTTTTTGTGTTGGGA 57.307 29.167 0.00 0.00 0.00 4.37
892 919 7.702348 TCTTTTTGTTTTTGTTTTTGTGTTGGG 59.298 29.630 0.00 0.00 0.00 4.12
893 920 8.620533 TCTTTTTGTTTTTGTTTTTGTGTTGG 57.379 26.923 0.00 0.00 0.00 3.77
1051 1091 2.202756 GCGCGGAGACCTTACCTG 60.203 66.667 8.83 0.00 0.00 4.00
1073 1113 1.655114 ATTCCGGGGAGGGGGATTTG 61.655 60.000 0.00 0.00 41.52 2.32
1116 1156 2.039137 GGAGGAGGAAGGGACCGT 59.961 66.667 0.00 0.00 34.73 4.83
1118 1158 3.471806 GCGGAGGAGGAAGGGACC 61.472 72.222 0.00 0.00 0.00 4.46
1124 1164 2.754658 GACGGAGCGGAGGAGGAA 60.755 66.667 0.00 0.00 0.00 3.36
1144 1186 4.649954 GATCGCGCGCATTTCCGG 62.650 66.667 32.61 13.04 0.00 5.14
1162 1204 2.071636 AACCCCCACCGGTTCGATTT 62.072 55.000 2.97 0.00 42.71 2.17
1293 1340 1.822371 GAACCACAAAACCACACACCT 59.178 47.619 0.00 0.00 0.00 4.00
1300 1347 1.021202 CGCAGAGAACCACAAAACCA 58.979 50.000 0.00 0.00 0.00 3.67
1306 1353 1.405933 CCATGATCGCAGAGAACCACA 60.406 52.381 0.00 0.00 43.63 4.17
1307 1354 1.293924 CCATGATCGCAGAGAACCAC 58.706 55.000 0.00 0.00 43.63 4.16
1308 1355 0.904649 ACCATGATCGCAGAGAACCA 59.095 50.000 0.00 0.00 43.63 3.67
1453 1523 4.393062 CAGACTACAAAAATCACCTCGCAT 59.607 41.667 0.00 0.00 0.00 4.73
1454 1524 3.745975 CAGACTACAAAAATCACCTCGCA 59.254 43.478 0.00 0.00 0.00 5.10
1474 1544 2.821969 CTGACAGAAATTCCCAACCCAG 59.178 50.000 0.00 0.00 0.00 4.45
1479 1549 3.091545 GCCATCTGACAGAAATTCCCAA 58.908 45.455 9.70 0.00 0.00 4.12
1497 1567 3.316588 TCAACTGAAAATAAACTGCGCCA 59.683 39.130 4.18 0.00 0.00 5.69
1589 1659 4.927978 TCAGCTAGACTTTGCTCTATCC 57.072 45.455 0.00 0.00 37.44 2.59
1621 1691 7.303182 ACCAGAAATCATCTCACCGATTATA 57.697 36.000 0.00 0.00 35.73 0.98
1622 1692 6.179906 ACCAGAAATCATCTCACCGATTAT 57.820 37.500 0.00 0.00 35.73 1.28
1628 1698 5.104735 ACCTAGAACCAGAAATCATCTCACC 60.105 44.000 0.00 0.00 35.73 4.02
1662 1732 6.017400 AGCATTTCGATGTCAGAAACAAAT 57.983 33.333 0.00 0.00 42.37 2.32
1692 1762 2.819608 ACATCAAAGTTGTTCCCGATGG 59.180 45.455 0.00 0.00 35.64 3.51
1720 1790 4.436852 CGTTTAAGCGGTTTATGTCAGCAT 60.437 41.667 4.64 0.00 39.03 3.79
1783 1853 3.243839 ACAACAGCATTTGAACCACCATC 60.244 43.478 4.45 0.00 0.00 3.51
1813 1883 6.862209 AGTTCACAAACAACAGAAGCATAAA 58.138 32.000 0.00 0.00 37.88 1.40
1814 1884 6.449635 AGTTCACAAACAACAGAAGCATAA 57.550 33.333 0.00 0.00 37.88 1.90
1815 1885 6.318648 AGAAGTTCACAAACAACAGAAGCATA 59.681 34.615 5.50 0.00 37.88 3.14
1816 1886 4.989279 AGTTCACAAACAACAGAAGCAT 57.011 36.364 0.00 0.00 37.88 3.79
1817 1887 4.458989 AGAAGTTCACAAACAACAGAAGCA 59.541 37.500 5.50 0.00 37.88 3.91
1818 1888 4.986622 AGAAGTTCACAAACAACAGAAGC 58.013 39.130 5.50 0.00 37.88 3.86
1819 1889 7.134815 CCATAGAAGTTCACAAACAACAGAAG 58.865 38.462 5.50 0.00 37.88 2.85
1820 1890 6.459573 GCCATAGAAGTTCACAAACAACAGAA 60.460 38.462 5.50 0.00 37.88 3.02
1821 1891 5.008613 GCCATAGAAGTTCACAAACAACAGA 59.991 40.000 5.50 0.00 37.88 3.41
1822 1892 5.215160 GCCATAGAAGTTCACAAACAACAG 58.785 41.667 5.50 0.00 37.88 3.16
1823 1893 4.642437 TGCCATAGAAGTTCACAAACAACA 59.358 37.500 5.50 0.00 37.88 3.33
1824 1894 5.181690 TGCCATAGAAGTTCACAAACAAC 57.818 39.130 5.50 0.00 37.88 3.32
1825 1895 6.403866 AATGCCATAGAAGTTCACAAACAA 57.596 33.333 5.50 0.00 37.88 2.83
1826 1896 6.403866 AAATGCCATAGAAGTTCACAAACA 57.596 33.333 5.50 0.00 37.88 2.83
1827 1897 7.307337 CCAAAAATGCCATAGAAGTTCACAAAC 60.307 37.037 5.50 0.00 35.50 2.93
1828 1898 6.705381 CCAAAAATGCCATAGAAGTTCACAAA 59.295 34.615 5.50 0.00 0.00 2.83
1829 1899 6.183360 ACCAAAAATGCCATAGAAGTTCACAA 60.183 34.615 5.50 0.00 0.00 3.33
1830 1900 5.304101 ACCAAAAATGCCATAGAAGTTCACA 59.696 36.000 5.50 0.00 0.00 3.58
1831 1901 5.783111 ACCAAAAATGCCATAGAAGTTCAC 58.217 37.500 5.50 0.00 0.00 3.18
1832 1902 5.335583 CGACCAAAAATGCCATAGAAGTTCA 60.336 40.000 5.50 0.00 0.00 3.18
1833 1903 5.095490 CGACCAAAAATGCCATAGAAGTTC 58.905 41.667 0.00 0.00 0.00 3.01
1834 1904 4.082245 CCGACCAAAAATGCCATAGAAGTT 60.082 41.667 0.00 0.00 0.00 2.66
1835 1905 3.443681 CCGACCAAAAATGCCATAGAAGT 59.556 43.478 0.00 0.00 0.00 3.01
1836 1906 3.734902 GCCGACCAAAAATGCCATAGAAG 60.735 47.826 0.00 0.00 0.00 2.85
1837 1907 2.165437 GCCGACCAAAAATGCCATAGAA 59.835 45.455 0.00 0.00 0.00 2.10
1838 1908 1.748493 GCCGACCAAAAATGCCATAGA 59.252 47.619 0.00 0.00 0.00 1.98
1839 1909 1.750778 AGCCGACCAAAAATGCCATAG 59.249 47.619 0.00 0.00 0.00 2.23
1840 1910 1.846007 AGCCGACCAAAAATGCCATA 58.154 45.000 0.00 0.00 0.00 2.74
1841 1911 0.975887 AAGCCGACCAAAAATGCCAT 59.024 45.000 0.00 0.00 0.00 4.40
1842 1912 0.316841 GAAGCCGACCAAAAATGCCA 59.683 50.000 0.00 0.00 0.00 4.92
1843 1913 0.316841 TGAAGCCGACCAAAAATGCC 59.683 50.000 0.00 0.00 0.00 4.40
1844 1914 2.368655 ATGAAGCCGACCAAAAATGC 57.631 45.000 0.00 0.00 0.00 3.56
1845 1915 2.995258 CCAATGAAGCCGACCAAAAATG 59.005 45.455 0.00 0.00 0.00 2.32
1846 1916 2.632512 ACCAATGAAGCCGACCAAAAAT 59.367 40.909 0.00 0.00 0.00 1.82
1847 1917 2.035321 GACCAATGAAGCCGACCAAAAA 59.965 45.455 0.00 0.00 0.00 1.94
1848 1918 1.611491 GACCAATGAAGCCGACCAAAA 59.389 47.619 0.00 0.00 0.00 2.44
1849 1919 1.243902 GACCAATGAAGCCGACCAAA 58.756 50.000 0.00 0.00 0.00 3.28
1850 1920 0.109532 TGACCAATGAAGCCGACCAA 59.890 50.000 0.00 0.00 0.00 3.67
1851 1921 0.321564 CTGACCAATGAAGCCGACCA 60.322 55.000 0.00 0.00 0.00 4.02
1852 1922 1.026718 CCTGACCAATGAAGCCGACC 61.027 60.000 0.00 0.00 0.00 4.79
1853 1923 0.036388 TCCTGACCAATGAAGCCGAC 60.036 55.000 0.00 0.00 0.00 4.79
1854 1924 0.250234 CTCCTGACCAATGAAGCCGA 59.750 55.000 0.00 0.00 0.00 5.54
1855 1925 0.250234 TCTCCTGACCAATGAAGCCG 59.750 55.000 0.00 0.00 0.00 5.52
1868 1938 6.968263 TTAGACCTAAGATGTCATCTCCTG 57.032 41.667 15.75 9.30 39.08 3.86
1882 1952 7.987458 CAGGAGCATATTCAACTTTAGACCTAA 59.013 37.037 0.00 0.00 0.00 2.69
1883 1953 7.125811 ACAGGAGCATATTCAACTTTAGACCTA 59.874 37.037 0.00 0.00 0.00 3.08
1884 1954 6.069963 ACAGGAGCATATTCAACTTTAGACCT 60.070 38.462 0.00 0.00 0.00 3.85
1886 1956 6.595716 ACACAGGAGCATATTCAACTTTAGAC 59.404 38.462 0.00 0.00 0.00 2.59
1912 1986 9.825109 TTTATCACGAAACATATTACAGGATCA 57.175 29.630 0.00 0.00 0.00 2.92
1926 2000 8.523464 GCACATACATGAATTTTATCACGAAAC 58.477 33.333 0.00 0.00 30.82 2.78
1945 2019 5.527582 CACCCCTACTATGAAAAGCACATAC 59.472 44.000 0.00 0.00 0.00 2.39
1956 2030 3.054655 GCCTTGTTTCACCCCTACTATGA 60.055 47.826 0.00 0.00 0.00 2.15
1957 2031 3.279434 GCCTTGTTTCACCCCTACTATG 58.721 50.000 0.00 0.00 0.00 2.23
1958 2032 2.916934 TGCCTTGTTTCACCCCTACTAT 59.083 45.455 0.00 0.00 0.00 2.12
1983 2057 0.179134 GCGACGCCACATTACTCTCT 60.179 55.000 9.14 0.00 0.00 3.10
2052 2126 2.999063 CCTTGGCCTTGGCCTTGG 60.999 66.667 28.37 24.23 0.00 3.61
2053 2127 3.698820 GCCTTGGCCTTGGCCTTG 61.699 66.667 28.37 20.23 43.11 3.61
2072 2146 4.998033 TGTACCATCTGCGTTATTTGTTGA 59.002 37.500 0.00 0.00 0.00 3.18
2098 2172 8.627403 AGCAAATGATACAATCAAGGTAAGATG 58.373 33.333 0.00 0.00 43.50 2.90
2101 2175 7.221452 GCAAGCAAATGATACAATCAAGGTAAG 59.779 37.037 0.00 0.00 43.50 2.34
2146 2220 6.870965 CAGAACAGAGCTATAAGTTCAAGTGT 59.129 38.462 12.46 0.00 42.01 3.55
2152 2226 5.112686 CCACCAGAACAGAGCTATAAGTTC 58.887 45.833 3.93 3.93 40.37 3.01
2159 2233 2.438021 ACAAACCACCAGAACAGAGCTA 59.562 45.455 0.00 0.00 0.00 3.32
2161 2235 1.604278 GACAAACCACCAGAACAGAGC 59.396 52.381 0.00 0.00 0.00 4.09
2174 2248 4.321230 GGAATGGTGAATGTCAGACAAACC 60.321 45.833 19.64 19.64 33.40 3.27
2175 2249 4.278170 TGGAATGGTGAATGTCAGACAAAC 59.722 41.667 7.50 6.60 0.00 2.93
2179 2253 3.411446 TGTGGAATGGTGAATGTCAGAC 58.589 45.455 0.00 0.00 0.00 3.51
2191 2265 5.909621 ACATCAAATTCTCTGTGGAATGG 57.090 39.130 0.00 0.00 36.24 3.16
2192 2266 9.865321 AAATAACATCAAATTCTCTGTGGAATG 57.135 29.630 0.00 0.00 36.24 2.67
2194 2268 8.522830 GGAAATAACATCAAATTCTCTGTGGAA 58.477 33.333 0.00 0.00 0.00 3.53
2195 2269 7.890127 AGGAAATAACATCAAATTCTCTGTGGA 59.110 33.333 0.00 0.00 0.00 4.02
2201 2275 7.994194 AGCAGAGGAAATAACATCAAATTCTC 58.006 34.615 0.00 0.00 0.00 2.87
2230 2304 5.454062 TCAAACCCTTTCTCATTCCTTGAA 58.546 37.500 0.00 0.00 32.78 2.69
2242 2316 5.459536 AGCAGAATCTTTCAAACCCTTTC 57.540 39.130 0.00 0.00 0.00 2.62
2339 2413 4.270245 TGCCCCAAAATCATCAGTTTTC 57.730 40.909 0.00 0.00 0.00 2.29
2342 2416 3.008266 CCTTTGCCCCAAAATCATCAGTT 59.992 43.478 0.00 0.00 32.75 3.16
2448 2522 6.327365 TCTGATATGGGCTCATTTTCAGTAGA 59.673 38.462 26.23 13.54 40.06 2.59
2531 2605 6.492007 CTTCATGCATTAAGAAGTGTCAGT 57.508 37.500 14.29 0.00 35.28 3.41
2596 2670 3.986996 TCATTGCTGATGGACTCTTCA 57.013 42.857 1.67 0.00 36.37 3.02
2598 2672 3.201487 TGGATCATTGCTGATGGACTCTT 59.799 43.478 0.00 0.00 42.27 2.85
2629 2703 3.127030 CGAAACCAAGGAAACCTAGCATC 59.873 47.826 0.00 0.00 31.13 3.91
2651 2725 6.473397 ACGAAGTTCTCATGTTTCAATCTC 57.527 37.500 0.56 0.00 37.78 2.75
2666 2740 9.790389 CAGTATCCCAATATATCTACGAAGTTC 57.210 37.037 0.00 0.00 37.78 3.01
2773 2847 5.714047 ACTGTGTAGTATGATGGATATGCG 58.286 41.667 0.00 0.00 34.74 4.73
2827 2901 0.623723 TACCACCCCAATCTCCAAGC 59.376 55.000 0.00 0.00 0.00 4.01
2833 2907 4.291249 ACAATAGTTGTACCACCCCAATCT 59.709 41.667 0.00 0.00 43.27 2.40
2874 2948 6.201425 CCTGTTAGCACAAGTTAAAGACGTAA 59.799 38.462 0.00 0.00 30.36 3.18
2877 2951 4.748102 TCCTGTTAGCACAAGTTAAAGACG 59.252 41.667 0.00 0.00 30.36 4.18
2880 2954 6.861065 TCTTCCTGTTAGCACAAGTTAAAG 57.139 37.500 0.00 0.00 30.36 1.85
3125 3199 3.249799 CCAACACACGAGTAGAATGCAAA 59.750 43.478 0.00 0.00 0.00 3.68
3164 3238 1.123928 AGGATTCTTACTCTGGGGCG 58.876 55.000 0.00 0.00 0.00 6.13
3184 3259 4.517832 ACGGATTTGGAAGTTTGGAAGTAC 59.482 41.667 0.00 0.00 0.00 2.73
3190 3265 3.505680 TCATCACGGATTTGGAAGTTTGG 59.494 43.478 0.00 0.00 0.00 3.28
3197 3272 8.746052 AAGTATTAATTCATCACGGATTTGGA 57.254 30.769 0.00 0.00 0.00 3.53
3265 3446 4.724303 ACAGAATCGACTAGACAAGTTCG 58.276 43.478 0.00 0.00 39.07 3.95
3279 3460 8.529102 CAATGCAATCAATCTTTTACAGAATCG 58.471 33.333 0.00 0.00 34.16 3.34
3280 3461 8.325997 GCAATGCAATCAATCTTTTACAGAATC 58.674 33.333 0.00 0.00 34.16 2.52
3289 3470 5.992829 TGAACAAGCAATGCAATCAATCTTT 59.007 32.000 8.35 0.00 0.00 2.52
3292 3473 5.849357 TTGAACAAGCAATGCAATCAATC 57.151 34.783 8.35 0.00 29.62 2.67
3295 3476 3.495377 GCTTTGAACAAGCAATGCAATCA 59.505 39.130 8.35 3.10 44.00 2.57
3333 3514 9.836864 TTGTTGATAGATGTGCTTATCTGTTAT 57.163 29.630 11.87 0.67 37.91 1.89
3334 3515 9.098355 GTTGTTGATAGATGTGCTTATCTGTTA 57.902 33.333 11.87 2.06 37.91 2.41
3424 3605 0.592247 CGGCACAAGTTTCACAGCAC 60.592 55.000 0.00 0.00 0.00 4.40
3430 3611 2.907634 TCTACAACGGCACAAGTTTCA 58.092 42.857 0.00 0.00 0.00 2.69
3441 3622 1.278238 GCTGACGGATTCTACAACGG 58.722 55.000 0.00 0.00 0.00 4.44
3455 3636 3.067833 GGAGAAGTAACAACAGGCTGAC 58.932 50.000 23.66 8.44 0.00 3.51
3470 3651 6.396829 AACAAAATCCAAACAGAGGAGAAG 57.603 37.500 0.00 0.00 38.83 2.85
3476 3657 5.659463 TGGTCAAACAAAATCCAAACAGAG 58.341 37.500 0.00 0.00 0.00 3.35
3483 3664 7.925483 CAGTTTTATCTGGTCAAACAAAATCCA 59.075 33.333 1.06 0.00 33.58 3.41
3522 3703 7.610580 ACTTGATTCTTTTTGGGATTGGTAA 57.389 32.000 0.00 0.00 0.00 2.85
3531 3712 6.147864 TCTGGTCAACTTGATTCTTTTTGG 57.852 37.500 0.00 0.00 0.00 3.28
3532 3713 6.643770 CCATCTGGTCAACTTGATTCTTTTTG 59.356 38.462 0.00 0.00 0.00 2.44
3548 3729 0.038166 TTGGTTGCCTCCATCTGGTC 59.962 55.000 0.00 0.00 37.33 4.02
3554 3735 0.613012 GGAAGCTTGGTTGCCTCCAT 60.613 55.000 2.10 0.00 41.78 3.41
3566 3747 2.972713 TCTGACCAAGTACAGGAAGCTT 59.027 45.455 0.00 0.00 35.20 3.74
3569 3750 5.152623 TGATTCTGACCAAGTACAGGAAG 57.847 43.478 10.94 7.99 35.20 3.46
3583 3764 8.523915 ACATAAATATTTGTGGCTGATTCTGA 57.476 30.769 23.67 0.00 34.12 3.27
3618 3799 3.450096 ACTTATGGAACGGAGGGAGTAAC 59.550 47.826 0.00 0.00 0.00 2.50
3619 3800 3.716431 ACTTATGGAACGGAGGGAGTAA 58.284 45.455 0.00 0.00 0.00 2.24
3628 3809 3.364565 CCACGACAAAACTTATGGAACGG 60.365 47.826 0.00 0.00 0.00 4.44
3629 3810 3.249080 ACCACGACAAAACTTATGGAACG 59.751 43.478 0.00 0.00 0.00 3.95
3639 3820 4.603231 TGAACTACAACCACGACAAAAC 57.397 40.909 0.00 0.00 0.00 2.43
3641 3822 5.587043 AGATTTGAACTACAACCACGACAAA 59.413 36.000 0.00 0.00 38.29 2.83
3653 3834 7.656137 TCACAGAACTGGTTAGATTTGAACTAC 59.344 37.037 6.76 0.00 34.19 2.73
3654 3835 7.656137 GTCACAGAACTGGTTAGATTTGAACTA 59.344 37.037 6.76 0.00 34.19 2.24
3671 3893 3.706055 TTCTGGCCAGTCACAGAAC 57.294 52.632 31.58 0.00 45.76 3.01
3673 3895 0.108585 GGTTTCTGGCCAGTCACAGA 59.891 55.000 31.58 9.51 41.63 3.41
3678 3900 2.552743 GTTTACAGGTTTCTGGCCAGTC 59.447 50.000 31.58 21.37 44.99 3.51
3692 3914 2.550830 ACTGCAGGTGGAGTTTACAG 57.449 50.000 19.93 0.00 44.54 2.74
3702 3924 5.351465 CCAGTATTAGTGTTTACTGCAGGTG 59.649 44.000 19.93 0.00 42.49 4.00
3828 4051 9.494271 TCATTGCATACCTAGAAAGTTCATATC 57.506 33.333 0.00 0.00 0.00 1.63
3833 4056 6.037610 CCAGTCATTGCATACCTAGAAAGTTC 59.962 42.308 0.00 0.00 0.00 3.01
3847 4070 0.397564 TCAGCTGACCAGTCATTGCA 59.602 50.000 13.74 0.00 39.13 4.08
3874 4097 5.887754 ACCCCAAAACTATACACATCACTT 58.112 37.500 0.00 0.00 0.00 3.16
4017 4240 0.541392 TGAAGGATGGGGATGTGTCG 59.459 55.000 0.00 0.00 0.00 4.35
4101 4324 1.608283 CCCTTCACCTTGTCTTCGGTC 60.608 57.143 0.00 0.00 0.00 4.79
4194 4417 1.115326 ACACAAAAGAGGGGGCAAGC 61.115 55.000 0.00 0.00 0.00 4.01
4212 4435 5.238583 ACAAGTTGTCAAGCTAGTGGATAC 58.761 41.667 1.64 0.00 0.00 2.24
4215 4438 3.838244 ACAAGTTGTCAAGCTAGTGGA 57.162 42.857 1.64 0.00 0.00 4.02
4324 4549 0.684535 TCATGCTTGGACGGAACTCA 59.315 50.000 0.00 0.00 0.00 3.41
4387 4612 2.359230 GCTGGTGCAGGTGGAGTC 60.359 66.667 0.00 0.00 39.41 3.36
4594 4819 7.639039 TGCATATCATCAGATTTCGGTAAAAC 58.361 34.615 0.00 0.00 35.67 2.43
4606 4831 8.591072 TCATATCTTGACTTGCATATCATCAGA 58.409 33.333 1.55 3.62 0.00 3.27
4664 4895 8.090214 AGCCACACGTCTTAATTTAGTTAGTTA 58.910 33.333 0.00 0.00 0.00 2.24
4665 4896 6.932960 AGCCACACGTCTTAATTTAGTTAGTT 59.067 34.615 0.00 0.00 0.00 2.24
4695 4926 0.314302 AAGGACGTCTCTGTGTTCCG 59.686 55.000 16.46 0.00 0.00 4.30
4867 5122 2.191128 ACATTGTTCCTCAGCTGACC 57.809 50.000 13.74 1.62 0.00 4.02
4868 5123 3.057946 GGAAACATTGTTCCTCAGCTGAC 60.058 47.826 13.74 4.09 43.32 3.51
4899 5154 4.946160 AGAAATCATAACCCCAAGGACA 57.054 40.909 0.00 0.00 36.73 4.02
5009 5268 0.609151 TAACCGTTTGATGCGAGGGA 59.391 50.000 0.00 0.00 0.00 4.20
5020 5279 3.067684 ACTGCAATAGGCTAACCGTTT 57.932 42.857 0.00 0.00 45.15 3.60
5085 6492 1.522668 CAGTCCGAGGACAAATGCAA 58.477 50.000 22.66 0.00 46.76 4.08
5160 6575 4.142116 TGGCTGATTCGCATGAATTTCATT 60.142 37.500 9.19 0.00 44.79 2.57
5174 6589 9.132521 CCGAATTATGATAAAATTGGCTGATTC 57.867 33.333 0.00 0.00 0.00 2.52
5260 6677 3.553096 CCGGGATCTAGTCGAATTTGAGG 60.553 52.174 0.00 0.00 0.00 3.86
5288 6705 6.438763 ACATGATTCGTTCCTGAAAAACTTC 58.561 36.000 0.00 0.00 0.00 3.01
5371 6794 3.322828 GTGTTGTACCACAGGTAAGAGGA 59.677 47.826 0.00 0.00 40.12 3.71
5402 6825 3.664107 ACACATTATATGTAGCCCGCAG 58.336 45.455 0.00 0.00 42.70 5.18
5513 6936 1.620819 GTCAGTCAGCTCAAGGGAAGA 59.379 52.381 0.00 0.00 0.00 2.87
5521 6944 1.811558 GCAACTTGGTCAGTCAGCTCA 60.812 52.381 0.00 0.00 32.94 4.26
5563 6986 0.039074 GTATCGCTGGCACGCTATCT 60.039 55.000 7.22 0.00 0.00 1.98
5612 7036 2.158827 TGCGCCCTATGACATGTACATT 60.159 45.455 5.37 0.00 0.00 2.71
5711 7137 7.869429 CCTTTTCAAATTTGAACTGCTGTATCT 59.131 33.333 28.78 0.00 45.99 1.98
5766 7898 1.677633 CTGTGGGCGGTTAAAGGGG 60.678 63.158 0.00 0.00 0.00 4.79
5776 7908 0.745486 TGATTGAGCATCTGTGGGCG 60.745 55.000 0.00 0.00 34.92 6.13
5783 7915 7.603404 GCTGACTAAATATCTGATTGAGCATCT 59.397 37.037 0.00 0.00 34.92 2.90
5784 7916 7.603404 AGCTGACTAAATATCTGATTGAGCATC 59.397 37.037 0.00 0.00 0.00 3.91
5802 7934 1.068264 CAACTCACGAGCAGCTGACTA 60.068 52.381 20.43 0.00 0.00 2.59
5808 7940 2.375766 CGACCAACTCACGAGCAGC 61.376 63.158 0.00 0.00 0.00 5.25
5814 7946 2.444624 CCGCATCGACCAACTCACG 61.445 63.158 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.