Multiple sequence alignment - TraesCS5D01G183200

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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 TraesCS5D01G183200 chr5D 100.000 2747 0 0 1 2747 285022046 285024792 0.000000e+00 5073.0
1 TraesCS5D01G183200 chr5D 85.054 649 68 15 1 647 132930818 132931439 3.860000e-178 634.0
2 TraesCS5D01G183200 chr5D 89.655 261 25 2 2396 2656 418946192 418945934 5.670000e-87 331.0
3 TraesCS5D01G183200 chr5D 89.583 96 8 2 554 647 220079642 220079737 1.340000e-23 121.0
4 TraesCS5D01G183200 chr5B 90.873 2038 112 26 1 2027 322288283 322290257 0.000000e+00 2665.0
5 TraesCS5D01G183200 chr5B 93.796 274 12 2 2127 2397 322290286 322290557 9.160000e-110 407.0
6 TraesCS5D01G183200 chr5A 93.677 1202 57 13 875 2068 376836644 376837834 0.000000e+00 1781.0
7 TraesCS5D01G183200 chr5A 84.198 424 42 11 226 647 293861653 293862053 3.320000e-104 388.0
8 TraesCS5D01G183200 chr5A 90.747 281 18 3 2125 2397 376837837 376838117 4.320000e-98 368.0
9 TraesCS5D01G183200 chr5A 89.899 99 4 3 2655 2747 376838116 376838214 3.710000e-24 122.0
10 TraesCS5D01G183200 chr2A 88.401 569 64 2 1 568 564223540 564222973 0.000000e+00 684.0
11 TraesCS5D01G183200 chr2A 88.849 556 54 6 1 550 656830722 656831275 0.000000e+00 676.0
12 TraesCS5D01G183200 chr6D 88.266 571 64 3 1 568 48891159 48891729 0.000000e+00 680.0
13 TraesCS5D01G183200 chr2D 87.916 571 64 4 1 568 507862404 507862972 0.000000e+00 667.0
14 TraesCS5D01G183200 chr2D 87.698 569 67 3 1 567 136984289 136984856 0.000000e+00 660.0
15 TraesCS5D01G183200 chr2D 89.706 68 7 0 2068 2135 119800732 119800665 1.360000e-13 87.9
16 TraesCS5D01G183200 chr4B 84.604 695 78 17 1 691 368069369 368070038 0.000000e+00 664.0
17 TraesCS5D01G183200 chr4B 92.275 233 14 4 1059 1290 277555389 277555160 7.330000e-86 327.0
18 TraesCS5D01G183200 chr4B 91.064 235 20 1 1056 1290 215633172 215633405 1.590000e-82 316.0
19 TraesCS5D01G183200 chr3D 87.900 562 65 3 9 568 413655101 413654541 0.000000e+00 658.0
20 TraesCS5D01G183200 chr3D 89.354 263 28 0 2394 2656 151444896 151445158 5.670000e-87 331.0
21 TraesCS5D01G183200 chr3D 91.935 62 4 1 2068 2129 442391552 442391492 4.870000e-13 86.1
22 TraesCS5D01G183200 chr3D 95.918 49 2 0 2066 2114 309913833 309913881 2.270000e-11 80.5
23 TraesCS5D01G183200 chr3B 87.544 570 69 2 1 568 745520790 745521359 0.000000e+00 658.0
24 TraesCS5D01G183200 chr3B 88.136 59 6 1 2056 2114 752000061 752000118 4.910000e-08 69.4
25 TraesCS5D01G183200 chr3B 89.796 49 4 1 2059 2107 528613141 528613094 8.210000e-06 62.1
26 TraesCS5D01G183200 chrUn 84.592 649 67 20 1 647 50079225 50078608 5.030000e-172 614.0
27 TraesCS5D01G183200 chr7B 84.031 645 69 24 3 636 426522746 426523367 8.470000e-165 590.0
28 TraesCS5D01G183200 chr7B 97.059 34 1 0 2059 2092 664113527 664113494 1.060000e-04 58.4
29 TraesCS5D01G183200 chr7D 83.257 651 79 20 1 647 412099023 412099647 3.070000e-159 571.0
30 TraesCS5D01G183200 chr6A 81.911 492 54 18 158 647 569995170 569995628 1.540000e-102 383.0
31 TraesCS5D01G183200 chr6A 89.583 48 3 2 2060 2107 180891841 180891886 2.950000e-05 60.2
32 TraesCS5D01G183200 chr1D 89.773 264 27 0 2393 2656 199421566 199421303 3.390000e-89 339.0
33 TraesCS5D01G183200 chr1D 89.354 263 26 2 2396 2658 285439495 285439755 2.040000e-86 329.0
34 TraesCS5D01G183200 chr1D 95.312 64 2 1 2067 2129 491801205 491801142 1.740000e-17 100.0
35 TraesCS5D01G183200 chr1D 96.078 51 1 1 2065 2114 366680810 366680760 6.300000e-12 82.4
36 TraesCS5D01G183200 chr6B 88.679 265 29 1 2396 2659 81010512 81010776 3.410000e-84 322.0
37 TraesCS5D01G183200 chr6B 90.948 232 20 1 1059 1290 62539626 62539396 7.390000e-81 311.0
38 TraesCS5D01G183200 chr7A 88.593 263 30 0 2393 2655 665742761 665742499 1.230000e-83 320.0
39 TraesCS5D01G183200 chr7A 96.078 51 2 0 2059 2109 546707772 546707822 1.750000e-12 84.2
40 TraesCS5D01G183200 chr7A 97.872 47 1 0 2068 2114 645464650 645464604 6.300000e-12 82.4
41 TraesCS5D01G183200 chr7A 95.000 40 2 0 2067 2106 729073365 729073326 2.280000e-06 63.9
42 TraesCS5D01G183200 chr3A 88.593 263 30 0 2396 2658 670825658 670825920 1.230000e-83 320.0
43 TraesCS5D01G183200 chr1A 89.147 258 25 3 2395 2650 39361685 39361941 4.410000e-83 318.0
44 TraesCS5D01G183200 chr1A 89.105 257 27 1 2395 2651 480593696 480593951 4.410000e-83 318.0
45 TraesCS5D01G183200 chr2B 81.197 234 22 15 421 653 681347490 681347278 4.700000e-38 169.0
46 TraesCS5D01G183200 chr4A 97.872 47 1 0 2067 2113 742249110 742249064 6.300000e-12 82.4
47 TraesCS5D01G183200 chr4D 90.164 61 4 2 2068 2127 338836282 338836341 8.160000e-11 78.7
48 TraesCS5D01G183200 chr4D 92.105 38 3 0 2061 2098 31174388 31174351 1.000000e-03 54.7
49 TraesCS5D01G183200 chr1B 92.308 39 1 2 2060 2098 404965070 404965106 1.000000e-03 54.7


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 TraesCS5D01G183200 chr5D 285022046 285024792 2746 False 5073 5073 100.0000 1 2747 1 chr5D.!!$F3 2746
1 TraesCS5D01G183200 chr5D 132930818 132931439 621 False 634 634 85.0540 1 647 1 chr5D.!!$F1 646
2 TraesCS5D01G183200 chr5B 322288283 322290557 2274 False 1536 2665 92.3345 1 2397 2 chr5B.!!$F1 2396
3 TraesCS5D01G183200 chr5A 376836644 376838214 1570 False 757 1781 91.4410 875 2747 3 chr5A.!!$F2 1872
4 TraesCS5D01G183200 chr2A 564222973 564223540 567 True 684 684 88.4010 1 568 1 chr2A.!!$R1 567
5 TraesCS5D01G183200 chr2A 656830722 656831275 553 False 676 676 88.8490 1 550 1 chr2A.!!$F1 549
6 TraesCS5D01G183200 chr6D 48891159 48891729 570 False 680 680 88.2660 1 568 1 chr6D.!!$F1 567
7 TraesCS5D01G183200 chr2D 507862404 507862972 568 False 667 667 87.9160 1 568 1 chr2D.!!$F2 567
8 TraesCS5D01G183200 chr2D 136984289 136984856 567 False 660 660 87.6980 1 567 1 chr2D.!!$F1 566
9 TraesCS5D01G183200 chr4B 368069369 368070038 669 False 664 664 84.6040 1 691 1 chr4B.!!$F2 690
10 TraesCS5D01G183200 chr3D 413654541 413655101 560 True 658 658 87.9000 9 568 1 chr3D.!!$R1 559
11 TraesCS5D01G183200 chr3B 745520790 745521359 569 False 658 658 87.5440 1 568 1 chr3B.!!$F1 567
12 TraesCS5D01G183200 chrUn 50078608 50079225 617 True 614 614 84.5920 1 647 1 chrUn.!!$R1 646
13 TraesCS5D01G183200 chr7B 426522746 426523367 621 False 590 590 84.0310 3 636 1 chr7B.!!$F1 633
14 TraesCS5D01G183200 chr7D 412099023 412099647 624 False 571 571 83.2570 1 647 1 chr7D.!!$F1 646

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
781 823 0.035176 CCTTTACCCGACCCAAACGA 59.965 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2182 0.115745 TACTCCCTCCGTCCCAAAGT 59.884 55.0 0.0 0.0 0.0 2.66 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
19 20 1.073722 CTTGCAGAAGGCCACTCCA 59.926 57.895 5.01 0.00 43.89 3.86
74 75 7.442656 CATTACAACAAGGGATACTACCTAGG 58.557 42.308 7.41 7.41 37.35 3.02
100 106 4.215908 TGGTATCTATCCTCAGTGGTCAC 58.784 47.826 0.00 0.00 37.07 3.67
198 214 2.050077 GTGGAGCGTGCTTTTGGC 60.050 61.111 0.00 0.00 42.22 4.52
334 356 1.481240 CGTGCTGACATCATCTACGG 58.519 55.000 0.00 0.00 0.00 4.02
408 435 3.182967 GCAACGTTTGAACAATTCACCA 58.817 40.909 0.00 0.00 39.87 4.17
503 530 4.769688 CTCACATTGGCAACCAGTAGATA 58.230 43.478 0.00 0.00 33.81 1.98
518 545 9.635520 AACCAGTAGATATATCGGTTTATTTCG 57.364 33.333 13.87 0.00 32.96 3.46
532 563 6.905076 CGGTTTATTTCGTTCCATGTATTCAG 59.095 38.462 0.00 0.00 0.00 3.02
563 594 9.634163 ATTTCGATTGGGTTGTAAAACTATTTC 57.366 29.630 0.00 0.00 30.93 2.17
568 600 9.150348 GATTGGGTTGTAAAACTATTTCATTGG 57.850 33.333 0.00 0.00 30.93 3.16
569 601 7.841282 TGGGTTGTAAAACTATTTCATTGGA 57.159 32.000 0.00 0.00 30.93 3.53
698 731 7.814693 ATGTATACATAGGGGCTTCAACTAT 57.185 36.000 16.85 0.00 34.26 2.12
704 745 1.710809 AGGGGCTTCAACTATTGTGGT 59.289 47.619 0.00 0.00 0.00 4.16
707 748 2.890945 GGGCTTCAACTATTGTGGTTGT 59.109 45.455 6.17 0.00 42.97 3.32
712 753 4.804608 TCAACTATTGTGGTTGTGTTCG 57.195 40.909 6.17 0.00 42.97 3.95
715 756 1.199097 CTATTGTGGTTGTGTTCGCCC 59.801 52.381 0.00 0.00 0.00 6.13
720 761 2.181521 GGTTGTGTTCGCCCGTTGA 61.182 57.895 0.00 0.00 0.00 3.18
749 791 0.845768 CAGCGCAAACAGAAAAACGG 59.154 50.000 11.47 0.00 0.00 4.44
750 792 0.248866 AGCGCAAACAGAAAAACGGG 60.249 50.000 11.47 0.00 0.00 5.28
751 793 1.817217 GCGCAAACAGAAAAACGGGC 61.817 55.000 0.30 0.00 0.00 6.13
752 794 1.536462 CGCAAACAGAAAAACGGGCG 61.536 55.000 0.00 0.00 37.17 6.13
753 795 0.526739 GCAAACAGAAAAACGGGCGT 60.527 50.000 0.00 0.00 0.00 5.68
754 796 1.268640 GCAAACAGAAAAACGGGCGTA 60.269 47.619 0.00 0.00 0.00 4.42
755 797 2.606065 GCAAACAGAAAAACGGGCGTAT 60.606 45.455 0.00 0.00 0.00 3.06
756 798 2.977169 CAAACAGAAAAACGGGCGTATG 59.023 45.455 0.00 0.00 0.00 2.39
757 799 0.519961 ACAGAAAAACGGGCGTATGC 59.480 50.000 0.00 0.00 41.71 3.14
773 815 3.122971 GCCGCACCTTTACCCGAC 61.123 66.667 0.00 0.00 0.00 4.79
780 822 0.250424 ACCTTTACCCGACCCAAACG 60.250 55.000 0.00 0.00 0.00 3.60
781 823 0.035176 CCTTTACCCGACCCAAACGA 59.965 55.000 0.00 0.00 0.00 3.85
789 831 2.606065 CCCGACCCAAACGAACAAAATC 60.606 50.000 0.00 0.00 0.00 2.17
791 833 2.657184 GACCCAAACGAACAAAATCCG 58.343 47.619 0.00 0.00 0.00 4.18
813 855 1.153597 ACGGACGTTCGTTTGGGAAC 61.154 55.000 18.05 0.00 40.85 3.62
817 859 0.309612 ACGTTCGTTTGGGAACATGC 59.690 50.000 6.30 0.00 45.12 4.06
858 901 1.244697 GGAGCTCCTCTCGTGTCACA 61.245 60.000 26.25 0.00 42.82 3.58
875 918 3.879295 GTCACATGAGAGAGAGAGAGAGG 59.121 52.174 0.00 0.00 0.00 3.69
876 919 3.117926 TCACATGAGAGAGAGAGAGAGGG 60.118 52.174 0.00 0.00 0.00 4.30
877 920 2.175499 ACATGAGAGAGAGAGAGAGGGG 59.825 54.545 0.00 0.00 0.00 4.79
878 921 1.221635 TGAGAGAGAGAGAGAGGGGG 58.778 60.000 0.00 0.00 0.00 5.40
1054 1101 1.667830 CAGAAAGCCTCGCGAACCA 60.668 57.895 11.33 0.00 0.00 3.67
1071 1118 1.936631 ACCAATCTCTCTCCTCCTCCT 59.063 52.381 0.00 0.00 0.00 3.69
1074 1121 1.158007 ATCTCTCTCCTCCTCCTCCC 58.842 60.000 0.00 0.00 0.00 4.30
1291 1338 1.702957 CAAGAACCACTAACCCTCCCA 59.297 52.381 0.00 0.00 0.00 4.37
1413 1460 3.553096 GCTCGAAGGTGACTCTCAAGAAA 60.553 47.826 0.00 0.00 42.68 2.52
1449 1496 4.369182 TGAGGAAGAAGAAGAACGACAAC 58.631 43.478 0.00 0.00 0.00 3.32
1456 1503 4.458295 AGAAGAAGAACGACAACGGAGATA 59.542 41.667 0.00 0.00 44.46 1.98
1536 1586 1.027357 GCATCATCCGGCACAAGATT 58.973 50.000 0.00 0.00 0.00 2.40
1657 1709 2.053627 CTTTGCTGATGGCGTGTTTTC 58.946 47.619 0.00 0.00 45.43 2.29
1658 1710 0.040514 TTGCTGATGGCGTGTTTTCG 60.041 50.000 0.00 0.00 45.43 3.46
1669 1721 0.382873 GTGTTTTCGCCGGTTTCCTT 59.617 50.000 1.90 0.00 0.00 3.36
1670 1722 0.382515 TGTTTTCGCCGGTTTCCTTG 59.617 50.000 1.90 0.00 0.00 3.61
1752 1821 1.474143 CCTCCCGCTTCCTGAAGAATC 60.474 57.143 11.00 0.00 40.79 2.52
1753 1822 0.541863 TCCCGCTTCCTGAAGAATCC 59.458 55.000 11.00 0.00 40.79 3.01
1754 1823 0.543749 CCCGCTTCCTGAAGAATCCT 59.456 55.000 11.00 0.00 40.79 3.24
1755 1824 1.474143 CCCGCTTCCTGAAGAATCCTC 60.474 57.143 11.00 0.00 40.79 3.71
1756 1825 1.484240 CCGCTTCCTGAAGAATCCTCT 59.516 52.381 11.00 0.00 40.79 3.69
1757 1826 2.093235 CCGCTTCCTGAAGAATCCTCTT 60.093 50.000 11.00 0.00 44.93 2.85
1758 1827 3.604582 CGCTTCCTGAAGAATCCTCTTT 58.395 45.455 11.00 0.00 42.19 2.52
1759 1828 3.620821 CGCTTCCTGAAGAATCCTCTTTC 59.379 47.826 11.00 0.00 42.19 2.62
1760 1829 4.622695 CGCTTCCTGAAGAATCCTCTTTCT 60.623 45.833 11.00 0.00 42.19 2.52
1761 1830 4.635324 GCTTCCTGAAGAATCCTCTTTCTG 59.365 45.833 11.00 0.00 42.19 3.02
1762 1831 5.570439 GCTTCCTGAAGAATCCTCTTTCTGA 60.570 44.000 11.00 0.00 42.19 3.27
1763 1832 5.413309 TCCTGAAGAATCCTCTTTCTGAC 57.587 43.478 0.00 0.00 42.19 3.51
1764 1833 5.090139 TCCTGAAGAATCCTCTTTCTGACT 58.910 41.667 0.00 0.00 42.19 3.41
1765 1834 6.256819 TCCTGAAGAATCCTCTTTCTGACTA 58.743 40.000 0.00 0.00 42.19 2.59
1766 1835 6.726299 TCCTGAAGAATCCTCTTTCTGACTAA 59.274 38.462 0.00 0.00 42.19 2.24
1767 1836 7.235606 TCCTGAAGAATCCTCTTTCTGACTAAA 59.764 37.037 0.00 0.00 42.19 1.85
1768 1837 7.880195 CCTGAAGAATCCTCTTTCTGACTAAAA 59.120 37.037 0.00 0.00 42.19 1.52
1769 1838 9.277783 CTGAAGAATCCTCTTTCTGACTAAAAA 57.722 33.333 0.00 0.00 42.19 1.94
1829 1898 2.522193 TGCCCGTTTGTTTCCCCC 60.522 61.111 0.00 0.00 0.00 5.40
1949 2018 1.064003 TAGCTGAAACTTCTGGGGCA 58.936 50.000 0.00 0.00 0.00 5.36
1961 2030 2.600470 GGGGCAGTTTGGGTCCAC 60.600 66.667 0.00 0.00 0.00 4.02
1962 2031 2.520968 GGGCAGTTTGGGTCCACT 59.479 61.111 0.00 0.00 0.00 4.00
1963 2032 1.903404 GGGCAGTTTGGGTCCACTG 60.903 63.158 3.89 3.89 42.94 3.66
2045 2114 7.363268 GGTTCATTTTGCATATCTCCTGACTTT 60.363 37.037 0.00 0.00 0.00 2.66
2079 2153 6.091718 GGATACTCAAATACTCCCTCTGTC 57.908 45.833 0.00 0.00 0.00 3.51
2080 2154 5.836358 GGATACTCAAATACTCCCTCTGTCT 59.164 44.000 0.00 0.00 0.00 3.41
2081 2155 6.015772 GGATACTCAAATACTCCCTCTGTCTC 60.016 46.154 0.00 0.00 0.00 3.36
2082 2156 4.678256 ACTCAAATACTCCCTCTGTCTCA 58.322 43.478 0.00 0.00 0.00 3.27
2083 2157 5.087323 ACTCAAATACTCCCTCTGTCTCAA 58.913 41.667 0.00 0.00 0.00 3.02
2084 2158 5.544176 ACTCAAATACTCCCTCTGTCTCAAA 59.456 40.000 0.00 0.00 0.00 2.69
2085 2159 6.043243 ACTCAAATACTCCCTCTGTCTCAAAA 59.957 38.462 0.00 0.00 0.00 2.44
2086 2160 7.020827 TCAAATACTCCCTCTGTCTCAAAAT 57.979 36.000 0.00 0.00 0.00 1.82
2087 2161 8.146053 TCAAATACTCCCTCTGTCTCAAAATA 57.854 34.615 0.00 0.00 0.00 1.40
2088 2162 8.602424 TCAAATACTCCCTCTGTCTCAAAATAA 58.398 33.333 0.00 0.00 0.00 1.40
2089 2163 8.887717 CAAATACTCCCTCTGTCTCAAAATAAG 58.112 37.037 0.00 0.00 0.00 1.73
2090 2164 7.741554 ATACTCCCTCTGTCTCAAAATAAGT 57.258 36.000 0.00 0.00 0.00 2.24
2091 2165 5.799213 ACTCCCTCTGTCTCAAAATAAGTG 58.201 41.667 0.00 0.00 0.00 3.16
2092 2166 5.308237 ACTCCCTCTGTCTCAAAATAAGTGT 59.692 40.000 0.00 0.00 0.00 3.55
2093 2167 5.794894 TCCCTCTGTCTCAAAATAAGTGTC 58.205 41.667 0.00 0.00 0.00 3.67
2094 2168 5.544176 TCCCTCTGTCTCAAAATAAGTGTCT 59.456 40.000 0.00 0.00 0.00 3.41
2095 2169 5.872070 CCCTCTGTCTCAAAATAAGTGTCTC 59.128 44.000 0.00 0.00 0.00 3.36
2096 2170 6.459066 CCTCTGTCTCAAAATAAGTGTCTCA 58.541 40.000 0.00 0.00 0.00 3.27
2097 2171 6.931281 CCTCTGTCTCAAAATAAGTGTCTCAA 59.069 38.462 0.00 0.00 0.00 3.02
2098 2172 7.442364 CCTCTGTCTCAAAATAAGTGTCTCAAA 59.558 37.037 0.00 0.00 0.00 2.69
2099 2173 8.142994 TCTGTCTCAAAATAAGTGTCTCAAAC 57.857 34.615 0.00 0.00 0.00 2.93
2100 2174 7.987458 TCTGTCTCAAAATAAGTGTCTCAAACT 59.013 33.333 0.00 0.00 0.00 2.66
2101 2175 8.506168 TGTCTCAAAATAAGTGTCTCAAACTT 57.494 30.769 0.00 0.00 40.82 2.66
2102 2176 9.607988 TGTCTCAAAATAAGTGTCTCAAACTTA 57.392 29.630 0.00 0.00 42.63 2.24
2104 2178 9.832445 TCTCAAAATAAGTGTCTCAAACTTAGT 57.168 29.630 2.85 0.00 41.95 2.24
2112 2186 8.788325 AAGTGTCTCAAACTTAGTACAACTTT 57.212 30.769 0.00 0.00 36.11 2.66
2113 2187 8.197988 AGTGTCTCAAACTTAGTACAACTTTG 57.802 34.615 0.00 0.00 0.00 2.77
2114 2188 7.280205 AGTGTCTCAAACTTAGTACAACTTTGG 59.720 37.037 0.00 0.00 0.00 3.28
2115 2189 6.540914 TGTCTCAAACTTAGTACAACTTTGGG 59.459 38.462 0.00 0.00 0.00 4.12
2116 2190 6.764560 GTCTCAAACTTAGTACAACTTTGGGA 59.235 38.462 0.00 0.04 0.00 4.37
2117 2191 6.764560 TCTCAAACTTAGTACAACTTTGGGAC 59.235 38.462 0.00 0.00 0.00 4.46
2118 2192 5.524646 TCAAACTTAGTACAACTTTGGGACG 59.475 40.000 0.00 0.00 0.00 4.79
2119 2193 3.999046 ACTTAGTACAACTTTGGGACGG 58.001 45.455 0.00 0.00 0.00 4.79
2120 2194 3.642848 ACTTAGTACAACTTTGGGACGGA 59.357 43.478 0.00 0.00 0.00 4.69
2121 2195 2.833631 AGTACAACTTTGGGACGGAG 57.166 50.000 0.00 0.00 0.00 4.63
2122 2196 1.346722 AGTACAACTTTGGGACGGAGG 59.653 52.381 0.00 0.00 0.00 4.30
2123 2197 0.688487 TACAACTTTGGGACGGAGGG 59.312 55.000 0.00 0.00 0.00 4.30
2124 2198 1.057851 ACAACTTTGGGACGGAGGGA 61.058 55.000 0.00 0.00 0.00 4.20
2125 2199 0.321653 CAACTTTGGGACGGAGGGAG 60.322 60.000 0.00 0.00 0.00 4.30
2126 2200 0.767060 AACTTTGGGACGGAGGGAGT 60.767 55.000 0.00 0.00 0.00 3.85
2127 2201 0.115745 ACTTTGGGACGGAGGGAGTA 59.884 55.000 0.00 0.00 0.00 2.59
2169 2248 4.137116 ACAAAAGATACGGCTAGCATCA 57.863 40.909 18.24 0.00 0.00 3.07
2181 2260 4.201950 CGGCTAGCATCAAAGCAATTAACT 60.202 41.667 18.24 0.00 40.61 2.24
2213 2292 7.941919 AGGAAAAGAGATTAACAAGAAACACC 58.058 34.615 0.00 0.00 0.00 4.16
2220 2299 7.873505 AGAGATTAACAAGAAACACCTAGACAC 59.126 37.037 0.00 0.00 0.00 3.67
2295 2377 1.673626 GGCAGCCAAATGGTCATGTTG 60.674 52.381 6.55 0.00 37.57 3.33
2328 2410 3.461061 CAGCGCCTTCAGATAAAGATGA 58.539 45.455 2.29 0.00 0.00 2.92
2329 2411 3.247173 CAGCGCCTTCAGATAAAGATGAC 59.753 47.826 2.29 0.00 0.00 3.06
2401 2485 5.010282 ACACATGAAAGTGGAAATACTCCC 58.990 41.667 0.00 0.00 44.69 4.30
2403 2487 5.355350 CACATGAAAGTGGAAATACTCCCTC 59.645 44.000 0.00 0.00 44.69 4.30
2406 2490 1.497161 AGTGGAAATACTCCCTCCGG 58.503 55.000 0.00 0.00 44.69 5.14
2407 2491 0.179054 GTGGAAATACTCCCTCCGGC 60.179 60.000 0.00 0.00 44.69 6.13
2408 2492 1.342672 TGGAAATACTCCCTCCGGCC 61.343 60.000 0.00 0.00 44.69 6.13
2409 2493 1.450642 GAAATACTCCCTCCGGCCC 59.549 63.158 0.00 0.00 0.00 5.80
2410 2494 1.004361 AAATACTCCCTCCGGCCCT 59.996 57.895 0.00 0.00 0.00 5.19
2411 2495 0.623617 AAATACTCCCTCCGGCCCTT 60.624 55.000 0.00 0.00 0.00 3.95
2412 2496 0.623617 AATACTCCCTCCGGCCCTTT 60.624 55.000 0.00 0.00 0.00 3.11
2413 2497 0.623617 ATACTCCCTCCGGCCCTTTT 60.624 55.000 0.00 0.00 0.00 2.27
2414 2498 0.843343 TACTCCCTCCGGCCCTTTTT 60.843 55.000 0.00 0.00 0.00 1.94
2415 2499 1.678970 CTCCCTCCGGCCCTTTTTG 60.679 63.158 0.00 0.00 0.00 2.44
2416 2500 2.679996 CCCTCCGGCCCTTTTTGG 60.680 66.667 0.00 0.00 0.00 3.28
2417 2501 2.117423 CCTCCGGCCCTTTTTGGT 59.883 61.111 0.00 0.00 0.00 3.67
2418 2502 1.977009 CCTCCGGCCCTTTTTGGTC 60.977 63.158 0.00 0.00 0.00 4.02
2419 2503 1.074951 CTCCGGCCCTTTTTGGTCT 59.925 57.895 0.00 0.00 0.00 3.85
2420 2504 1.228429 TCCGGCCCTTTTTGGTCTG 60.228 57.895 0.00 0.00 0.00 3.51
2421 2505 2.650778 CGGCCCTTTTTGGTCTGC 59.349 61.111 0.00 0.00 0.00 4.26
2422 2506 2.199652 CGGCCCTTTTTGGTCTGCA 61.200 57.895 0.00 0.00 0.00 4.41
2423 2507 1.535204 CGGCCCTTTTTGGTCTGCAT 61.535 55.000 0.00 0.00 0.00 3.96
2424 2508 1.555967 GGCCCTTTTTGGTCTGCATA 58.444 50.000 0.00 0.00 0.00 3.14
2425 2509 2.110578 GGCCCTTTTTGGTCTGCATAT 58.889 47.619 0.00 0.00 0.00 1.78
2426 2510 3.295973 GGCCCTTTTTGGTCTGCATATA 58.704 45.455 0.00 0.00 0.00 0.86
2427 2511 3.704061 GGCCCTTTTTGGTCTGCATATAA 59.296 43.478 0.00 0.00 0.00 0.98
2428 2512 4.202151 GGCCCTTTTTGGTCTGCATATAAG 60.202 45.833 0.00 0.00 0.00 1.73
2429 2513 4.402474 GCCCTTTTTGGTCTGCATATAAGT 59.598 41.667 0.00 0.00 0.00 2.24
2430 2514 5.105351 GCCCTTTTTGGTCTGCATATAAGTT 60.105 40.000 0.00 0.00 0.00 2.66
2431 2515 6.564328 CCCTTTTTGGTCTGCATATAAGTTC 58.436 40.000 0.00 0.00 0.00 3.01
2432 2516 6.378280 CCCTTTTTGGTCTGCATATAAGTTCT 59.622 38.462 0.00 0.00 0.00 3.01
2433 2517 7.556275 CCCTTTTTGGTCTGCATATAAGTTCTA 59.444 37.037 0.00 0.00 0.00 2.10
2434 2518 9.125026 CCTTTTTGGTCTGCATATAAGTTCTAT 57.875 33.333 0.00 0.00 0.00 1.98
2436 2520 8.677148 TTTTGGTCTGCATATAAGTTCTATCC 57.323 34.615 0.00 0.00 0.00 2.59
2437 2521 6.994421 TGGTCTGCATATAAGTTCTATCCA 57.006 37.500 0.00 0.00 0.00 3.41
2438 2522 7.373617 TGGTCTGCATATAAGTTCTATCCAA 57.626 36.000 0.00 0.00 0.00 3.53
2439 2523 7.801104 TGGTCTGCATATAAGTTCTATCCAAA 58.199 34.615 0.00 0.00 0.00 3.28
2440 2524 7.933577 TGGTCTGCATATAAGTTCTATCCAAAG 59.066 37.037 0.00 0.00 0.00 2.77
2441 2525 7.934120 GGTCTGCATATAAGTTCTATCCAAAGT 59.066 37.037 0.00 0.00 0.00 2.66
2442 2526 8.983724 GTCTGCATATAAGTTCTATCCAAAGTC 58.016 37.037 0.00 0.00 0.00 3.01
2443 2527 8.704668 TCTGCATATAAGTTCTATCCAAAGTCA 58.295 33.333 0.00 0.00 0.00 3.41
2444 2528 9.330063 CTGCATATAAGTTCTATCCAAAGTCAA 57.670 33.333 0.00 0.00 0.00 3.18
2445 2529 9.679661 TGCATATAAGTTCTATCCAAAGTCAAA 57.320 29.630 0.00 0.00 0.00 2.69
2455 2539 8.268850 TCTATCCAAAGTCAAAGTATCTTTGC 57.731 34.615 14.86 10.99 43.49 3.68
2456 2540 8.103305 TCTATCCAAAGTCAAAGTATCTTTGCT 58.897 33.333 14.86 12.56 43.49 3.91
2457 2541 6.959639 TCCAAAGTCAAAGTATCTTTGCTT 57.040 33.333 14.86 16.26 43.49 3.91
2458 2542 7.346751 TCCAAAGTCAAAGTATCTTTGCTTT 57.653 32.000 22.53 22.53 43.49 3.51
2467 2551 6.715347 AAGTATCTTTGCTTTGACCAAACT 57.285 33.333 0.00 0.00 0.00 2.66
2468 2552 6.715347 AGTATCTTTGCTTTGACCAAACTT 57.285 33.333 0.00 0.00 0.00 2.66
2469 2553 7.817418 AGTATCTTTGCTTTGACCAAACTTA 57.183 32.000 0.00 0.00 0.00 2.24
2470 2554 8.409358 AGTATCTTTGCTTTGACCAAACTTAT 57.591 30.769 0.00 0.00 0.00 1.73
2471 2555 9.515226 AGTATCTTTGCTTTGACCAAACTTATA 57.485 29.630 0.00 0.00 0.00 0.98
2472 2556 9.774742 GTATCTTTGCTTTGACCAAACTTATAG 57.225 33.333 0.00 0.00 0.00 1.31
2473 2557 8.635765 ATCTTTGCTTTGACCAAACTTATAGA 57.364 30.769 0.00 0.00 0.00 1.98
2474 2558 8.458573 TCTTTGCTTTGACCAAACTTATAGAA 57.541 30.769 0.00 0.00 0.00 2.10
2475 2559 8.908903 TCTTTGCTTTGACCAAACTTATAGAAA 58.091 29.630 0.00 0.00 0.00 2.52
2476 2560 9.528018 CTTTGCTTTGACCAAACTTATAGAAAA 57.472 29.630 0.00 0.00 0.00 2.29
2477 2561 9.877178 TTTGCTTTGACCAAACTTATAGAAAAA 57.123 25.926 0.00 0.00 0.00 1.94
2478 2562 8.865590 TGCTTTGACCAAACTTATAGAAAAAC 57.134 30.769 0.00 0.00 0.00 2.43
2479 2563 7.646130 TGCTTTGACCAAACTTATAGAAAAACG 59.354 33.333 0.00 0.00 0.00 3.60
2480 2564 7.646526 GCTTTGACCAAACTTATAGAAAAACGT 59.353 33.333 0.00 0.00 0.00 3.99
2484 2568 9.491675 TGACCAAACTTATAGAAAAACGTATCA 57.508 29.630 0.00 0.00 0.00 2.15
2496 2580 8.506140 AGAAAAACGTATCAACAATCACAATG 57.494 30.769 0.00 0.00 0.00 2.82
2497 2581 8.134895 AGAAAAACGTATCAACAATCACAATGT 58.865 29.630 0.00 0.00 0.00 2.71
2498 2582 7.851822 AAAACGTATCAACAATCACAATGTC 57.148 32.000 0.00 0.00 0.00 3.06
2499 2583 6.552859 AACGTATCAACAATCACAATGTCA 57.447 33.333 0.00 0.00 0.00 3.58
2500 2584 6.552859 ACGTATCAACAATCACAATGTCAA 57.447 33.333 0.00 0.00 0.00 3.18
2501 2585 6.964908 ACGTATCAACAATCACAATGTCAAA 58.035 32.000 0.00 0.00 0.00 2.69
2502 2586 7.592938 ACGTATCAACAATCACAATGTCAAAT 58.407 30.769 0.00 0.00 0.00 2.32
2503 2587 7.750458 ACGTATCAACAATCACAATGTCAAATC 59.250 33.333 0.00 0.00 0.00 2.17
2504 2588 7.964559 CGTATCAACAATCACAATGTCAAATCT 59.035 33.333 0.00 0.00 0.00 2.40
2629 2713 9.878599 AGTTTGACTTGACAAAAATCTAATACG 57.121 29.630 0.00 0.00 40.62 3.06
2630 2714 8.627428 GTTTGACTTGACAAAAATCTAATACGC 58.373 33.333 0.00 0.00 40.62 4.42
2631 2715 7.428282 TGACTTGACAAAAATCTAATACGCA 57.572 32.000 0.00 0.00 0.00 5.24
2632 2716 7.518161 TGACTTGACAAAAATCTAATACGCAG 58.482 34.615 0.00 0.00 0.00 5.18
2633 2717 7.386573 TGACTTGACAAAAATCTAATACGCAGA 59.613 33.333 0.00 0.00 0.00 4.26
2634 2718 7.743104 ACTTGACAAAAATCTAATACGCAGAG 58.257 34.615 0.00 0.00 0.00 3.35
2635 2719 7.387948 ACTTGACAAAAATCTAATACGCAGAGT 59.612 33.333 0.00 0.00 0.00 3.24
2636 2720 8.766000 TTGACAAAAATCTAATACGCAGAGTA 57.234 30.769 0.00 0.00 40.03 2.59
2637 2721 8.766000 TGACAAAAATCTAATACGCAGAGTAA 57.234 30.769 0.00 0.00 39.04 2.24
2638 2722 9.210329 TGACAAAAATCTAATACGCAGAGTAAA 57.790 29.630 0.00 0.00 39.04 2.01
2643 2727 9.444600 AAAATCTAATACGCAGAGTAAAAAGGA 57.555 29.630 0.00 0.00 39.04 3.36
2644 2728 8.421673 AATCTAATACGCAGAGTAAAAAGGAC 57.578 34.615 0.00 0.00 39.04 3.85
2645 2729 6.335777 TCTAATACGCAGAGTAAAAAGGACC 58.664 40.000 0.00 0.00 39.04 4.46
2646 2730 2.922740 ACGCAGAGTAAAAAGGACCA 57.077 45.000 0.00 0.00 0.00 4.02
2647 2731 2.767505 ACGCAGAGTAAAAAGGACCAG 58.232 47.619 0.00 0.00 0.00 4.00
2648 2732 2.367567 ACGCAGAGTAAAAAGGACCAGA 59.632 45.455 0.00 0.00 0.00 3.86
2649 2733 2.996621 CGCAGAGTAAAAAGGACCAGAG 59.003 50.000 0.00 0.00 0.00 3.35
2650 2734 3.339141 GCAGAGTAAAAAGGACCAGAGG 58.661 50.000 0.00 0.00 0.00 3.69
2651 2735 3.339141 CAGAGTAAAAAGGACCAGAGGC 58.661 50.000 0.00 0.00 0.00 4.70
2652 2736 2.979678 AGAGTAAAAAGGACCAGAGGCA 59.020 45.455 0.00 0.00 0.00 4.75
2653 2737 3.008485 AGAGTAAAAAGGACCAGAGGCAG 59.992 47.826 0.00 0.00 0.00 4.85
2654 2738 2.711547 AGTAAAAAGGACCAGAGGCAGT 59.288 45.455 0.00 0.00 0.00 4.40
2655 2739 3.908103 AGTAAAAAGGACCAGAGGCAGTA 59.092 43.478 0.00 0.00 0.00 2.74
2656 2740 4.536489 AGTAAAAAGGACCAGAGGCAGTAT 59.464 41.667 0.00 0.00 0.00 2.12
2657 2741 4.388577 AAAAAGGACCAGAGGCAGTATT 57.611 40.909 0.00 0.00 0.00 1.89
2658 2742 4.388577 AAAAGGACCAGAGGCAGTATTT 57.611 40.909 0.00 0.00 0.00 1.40
2659 2743 3.636153 AAGGACCAGAGGCAGTATTTC 57.364 47.619 0.00 0.00 0.00 2.17
2660 2744 1.482593 AGGACCAGAGGCAGTATTTCG 59.517 52.381 0.00 0.00 0.00 3.46
2661 2745 1.207329 GGACCAGAGGCAGTATTTCGT 59.793 52.381 0.00 0.00 0.00 3.85
2662 2746 2.429610 GGACCAGAGGCAGTATTTCGTA 59.570 50.000 0.00 0.00 0.00 3.43
2663 2747 3.445857 GACCAGAGGCAGTATTTCGTAC 58.554 50.000 0.00 0.00 0.00 3.67
2721 2805 2.238646 AGACCAAATCTGCGGGAACATA 59.761 45.455 0.00 0.00 35.81 2.29
2734 2823 3.477530 GGGAACATATGCTAGGTCCAAC 58.522 50.000 1.58 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.477210 GGTCTCAAAGTTGACCTCTGT 57.523 47.619 5.05 0.00 46.65 3.41
74 75 4.835615 ACCACTGAGGATAGATACCATCAC 59.164 45.833 0.00 0.00 41.22 3.06
100 106 4.286297 TGGGTATTGTCTTCACAAGAGG 57.714 45.455 0.00 0.00 45.85 3.69
198 214 1.402968 CCCCATTGAGATTGAAGCACG 59.597 52.381 0.00 0.00 0.00 5.34
249 271 0.250770 ACCTCCCAAAACTTCTCGGC 60.251 55.000 0.00 0.00 0.00 5.54
298 320 2.298629 CGCTCATGCTCCACGATCG 61.299 63.158 14.88 14.88 36.97 3.69
334 356 3.326588 ACCCTAAAAATCAAACCCTTGGC 59.673 43.478 0.00 0.00 33.01 4.52
408 435 5.327616 TCACGCATTTCATGATGGAATTT 57.672 34.783 0.00 0.00 0.00 1.82
434 461 4.590222 TCTTGGAGCTGCATATGAGTATGA 59.410 41.667 9.39 0.00 40.12 2.15
475 502 2.267351 TTGCCAATGTGAGCCCACG 61.267 57.895 0.00 0.00 46.06 4.94
503 530 8.842358 ATACATGGAACGAAATAAACCGATAT 57.158 30.769 0.00 0.00 0.00 1.63
518 545 8.378172 TCGAAATTATCCTGAATACATGGAAC 57.622 34.615 0.00 0.00 33.20 3.62
532 563 8.248253 AGTTTTACAACCCAATCGAAATTATCC 58.752 33.333 0.00 0.00 32.70 2.59
698 731 2.473760 CGGGCGAACACAACCACAA 61.474 57.895 0.00 0.00 0.00 3.33
704 745 1.722677 GTTCAACGGGCGAACACAA 59.277 52.632 8.46 0.00 41.92 3.33
707 748 3.641986 GCGTTCAACGGGCGAACA 61.642 61.111 12.81 0.00 42.35 3.18
715 756 2.544359 CTGACCGTGCGTTCAACG 59.456 61.111 5.28 5.28 45.88 4.10
735 777 2.759538 TACGCCCGTTTTTCTGTTTG 57.240 45.000 0.00 0.00 0.00 2.93
752 794 1.433837 CGGGTAAAGGTGCGGCATAC 61.434 60.000 5.72 4.34 0.00 2.39
753 795 1.153329 CGGGTAAAGGTGCGGCATA 60.153 57.895 5.72 0.00 0.00 3.14
754 796 2.437716 CGGGTAAAGGTGCGGCAT 60.438 61.111 5.72 0.00 0.00 4.40
755 797 3.627952 TCGGGTAAAGGTGCGGCA 61.628 61.111 0.00 0.00 0.00 5.69
756 798 3.122971 GTCGGGTAAAGGTGCGGC 61.123 66.667 0.00 0.00 0.00 6.53
757 799 2.435410 GGTCGGGTAAAGGTGCGG 60.435 66.667 0.00 0.00 0.00 5.69
758 800 2.435410 GGGTCGGGTAAAGGTGCG 60.435 66.667 0.00 0.00 0.00 5.34
759 801 0.537828 TTTGGGTCGGGTAAAGGTGC 60.538 55.000 0.00 0.00 0.00 5.01
767 809 0.394080 TTTGTTCGTTTGGGTCGGGT 60.394 50.000 0.00 0.00 0.00 5.28
768 810 0.739561 TTTTGTTCGTTTGGGTCGGG 59.260 50.000 0.00 0.00 0.00 5.14
773 815 3.357166 TTCGGATTTTGTTCGTTTGGG 57.643 42.857 0.00 0.00 0.00 4.12
802 844 0.309302 CAACGCATGTTCCCAAACGA 59.691 50.000 0.00 0.00 38.28 3.85
803 845 0.662970 CCAACGCATGTTCCCAAACG 60.663 55.000 0.00 0.00 38.28 3.60
809 851 0.240945 CCAACTCCAACGCATGTTCC 59.759 55.000 0.00 0.00 35.72 3.62
813 855 0.676466 TAGGCCAACTCCAACGCATG 60.676 55.000 5.01 0.00 0.00 4.06
817 859 2.432444 TGAATTAGGCCAACTCCAACG 58.568 47.619 5.01 0.00 0.00 4.10
858 901 1.782752 CCCCCTCTCTCTCTCTCTCAT 59.217 57.143 0.00 0.00 0.00 2.90
876 919 2.423538 CGATGAAACAATGAACTCCCCC 59.576 50.000 0.00 0.00 0.00 5.40
877 920 3.081804 ACGATGAAACAATGAACTCCCC 58.918 45.455 0.00 0.00 0.00 4.81
878 921 4.475944 CAACGATGAAACAATGAACTCCC 58.524 43.478 0.00 0.00 0.00 4.30
879 922 4.215399 TCCAACGATGAAACAATGAACTCC 59.785 41.667 0.00 0.00 0.00 3.85
880 923 5.356882 TCCAACGATGAAACAATGAACTC 57.643 39.130 0.00 0.00 0.00 3.01
881 924 4.320494 GCTCCAACGATGAAACAATGAACT 60.320 41.667 0.00 0.00 0.00 3.01
882 925 3.914364 GCTCCAACGATGAAACAATGAAC 59.086 43.478 0.00 0.00 0.00 3.18
883 926 3.567585 TGCTCCAACGATGAAACAATGAA 59.432 39.130 0.00 0.00 0.00 2.57
884 927 3.145286 TGCTCCAACGATGAAACAATGA 58.855 40.909 0.00 0.00 0.00 2.57
945 989 2.106338 CCCCCAATTGTTTTTGCTTCCT 59.894 45.455 4.43 0.00 0.00 3.36
1049 1093 2.698274 GGAGGAGGAGAGAGATTGGTTC 59.302 54.545 0.00 0.00 0.00 3.62
1054 1101 1.503347 GGGAGGAGGAGGAGAGAGATT 59.497 57.143 0.00 0.00 0.00 2.40
1071 1118 1.685765 CGGATGTGGAGACAGGGGA 60.686 63.158 0.00 0.00 44.46 4.81
1074 1121 0.390860 GGATCGGATGTGGAGACAGG 59.609 60.000 0.00 0.00 44.46 4.00
1291 1338 7.008021 ACCAAATCAAGAAACCAAATATGCT 57.992 32.000 0.00 0.00 0.00 3.79
1413 1460 2.433446 CTCAGCACAAGCAGGGGT 59.567 61.111 0.00 0.00 45.49 4.95
1536 1586 2.291043 GGGGCGGTCCTTGAAGAGA 61.291 63.158 0.00 0.00 35.33 3.10
1560 1610 5.010112 GGATCGGTGATTACTTGAGATGAGA 59.990 44.000 0.00 0.00 0.00 3.27
1617 1667 1.011968 TTTCTGCCGAATCACCGACG 61.012 55.000 0.00 0.00 0.00 5.12
1657 1709 3.254014 CTGCACAAGGAAACCGGCG 62.254 63.158 0.00 0.00 0.00 6.46
1658 1710 1.856265 CTCTGCACAAGGAAACCGGC 61.856 60.000 0.00 0.00 0.00 6.13
1768 1837 8.465273 AGCTACAGATCCTTAACAAACTTTTT 57.535 30.769 0.00 0.00 0.00 1.94
1769 1838 7.175119 GGAGCTACAGATCCTTAACAAACTTTT 59.825 37.037 6.27 0.00 46.53 2.27
1770 1839 6.655425 GGAGCTACAGATCCTTAACAAACTTT 59.345 38.462 6.27 0.00 46.53 2.66
1829 1898 4.966965 AGATGTGACCACTAACTAGACG 57.033 45.455 0.00 0.00 0.00 4.18
1929 1998 1.635487 TGCCCCAGAAGTTTCAGCTAT 59.365 47.619 0.00 0.00 0.00 2.97
1934 2003 2.031120 CAAACTGCCCCAGAAGTTTCA 58.969 47.619 0.00 0.00 43.09 2.69
1935 2004 1.341209 CCAAACTGCCCCAGAAGTTTC 59.659 52.381 0.00 0.00 43.09 2.78
1949 2018 1.529244 GCAGCAGTGGACCCAAACT 60.529 57.895 0.00 0.00 0.00 2.66
1961 2030 1.838112 TTTGGTTCCCATAGCAGCAG 58.162 50.000 0.00 0.00 31.53 4.24
1962 2031 2.530460 ATTTGGTTCCCATAGCAGCA 57.470 45.000 0.00 0.00 31.53 4.41
1963 2032 2.623416 GGTATTTGGTTCCCATAGCAGC 59.377 50.000 0.00 0.00 31.53 5.25
2045 2114 8.484214 AGTATTTGAGTATCCTCTAGATGCAA 57.516 34.615 0.00 0.00 39.87 4.08
2069 2143 5.799213 ACACTTATTTTGAGACAGAGGGAG 58.201 41.667 0.00 0.00 0.00 4.30
2070 2144 5.544176 AGACACTTATTTTGAGACAGAGGGA 59.456 40.000 0.00 0.00 0.00 4.20
2071 2145 5.799213 AGACACTTATTTTGAGACAGAGGG 58.201 41.667 0.00 0.00 0.00 4.30
2072 2146 6.459066 TGAGACACTTATTTTGAGACAGAGG 58.541 40.000 0.00 0.00 0.00 3.69
2073 2147 7.953158 TTGAGACACTTATTTTGAGACAGAG 57.047 36.000 0.00 0.00 0.00 3.35
2074 2148 7.987458 AGTTTGAGACACTTATTTTGAGACAGA 59.013 33.333 0.00 0.00 0.00 3.41
2075 2149 8.147642 AGTTTGAGACACTTATTTTGAGACAG 57.852 34.615 0.00 0.00 0.00 3.51
2076 2150 8.506168 AAGTTTGAGACACTTATTTTGAGACA 57.494 30.769 0.00 0.00 32.48 3.41
2078 2152 9.832445 ACTAAGTTTGAGACACTTATTTTGAGA 57.168 29.630 0.00 0.00 36.39 3.27
2086 2160 9.880157 AAAGTTGTACTAAGTTTGAGACACTTA 57.120 29.630 8.92 0.00 35.95 2.24
2087 2161 8.665685 CAAAGTTGTACTAAGTTTGAGACACTT 58.334 33.333 21.39 0.00 40.96 3.16
2088 2162 7.280205 CCAAAGTTGTACTAAGTTTGAGACACT 59.720 37.037 24.53 0.00 40.96 3.55
2089 2163 7.407337 CCAAAGTTGTACTAAGTTTGAGACAC 58.593 38.462 24.53 0.00 40.96 3.67
2090 2164 6.540914 CCCAAAGTTGTACTAAGTTTGAGACA 59.459 38.462 24.53 0.00 40.96 3.41
2091 2165 6.764560 TCCCAAAGTTGTACTAAGTTTGAGAC 59.235 38.462 24.53 0.00 40.96 3.36
2092 2166 6.764560 GTCCCAAAGTTGTACTAAGTTTGAGA 59.235 38.462 24.53 19.14 40.96 3.27
2093 2167 6.292703 CGTCCCAAAGTTGTACTAAGTTTGAG 60.293 42.308 24.53 17.91 40.96 3.02
2094 2168 5.524646 CGTCCCAAAGTTGTACTAAGTTTGA 59.475 40.000 24.53 12.91 40.96 2.69
2095 2169 5.277634 CCGTCCCAAAGTTGTACTAAGTTTG 60.278 44.000 20.17 20.17 39.21 2.93
2096 2170 4.818005 CCGTCCCAAAGTTGTACTAAGTTT 59.182 41.667 0.00 0.28 0.00 2.66
2097 2171 4.101430 TCCGTCCCAAAGTTGTACTAAGTT 59.899 41.667 0.00 0.00 0.00 2.66
2098 2172 3.642848 TCCGTCCCAAAGTTGTACTAAGT 59.357 43.478 0.00 0.00 0.00 2.24
2099 2173 4.243270 CTCCGTCCCAAAGTTGTACTAAG 58.757 47.826 0.00 0.00 0.00 2.18
2100 2174 3.007182 CCTCCGTCCCAAAGTTGTACTAA 59.993 47.826 0.00 0.00 0.00 2.24
2101 2175 2.564062 CCTCCGTCCCAAAGTTGTACTA 59.436 50.000 0.00 0.00 0.00 1.82
2102 2176 1.346722 CCTCCGTCCCAAAGTTGTACT 59.653 52.381 0.00 0.00 0.00 2.73
2103 2177 1.609841 CCCTCCGTCCCAAAGTTGTAC 60.610 57.143 0.00 0.00 0.00 2.90
2104 2178 0.688487 CCCTCCGTCCCAAAGTTGTA 59.312 55.000 0.00 0.00 0.00 2.41
2105 2179 1.057851 TCCCTCCGTCCCAAAGTTGT 61.058 55.000 0.00 0.00 0.00 3.32
2106 2180 0.321653 CTCCCTCCGTCCCAAAGTTG 60.322 60.000 0.00 0.00 0.00 3.16
2107 2181 0.767060 ACTCCCTCCGTCCCAAAGTT 60.767 55.000 0.00 0.00 0.00 2.66
2108 2182 0.115745 TACTCCCTCCGTCCCAAAGT 59.884 55.000 0.00 0.00 0.00 2.66
2109 2183 1.497161 ATACTCCCTCCGTCCCAAAG 58.503 55.000 0.00 0.00 0.00 2.77
2110 2184 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2111 2185 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2112 2186 3.339713 AATTATACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
2113 2187 5.393896 CGATAAATTATACTCCCTCCGTCCC 60.394 48.000 0.00 0.00 0.00 4.46
2114 2188 5.184671 ACGATAAATTATACTCCCTCCGTCC 59.815 44.000 0.00 0.00 0.00 4.79
2115 2189 6.091437 CACGATAAATTATACTCCCTCCGTC 58.909 44.000 0.00 0.00 0.00 4.79
2116 2190 5.537674 ACACGATAAATTATACTCCCTCCGT 59.462 40.000 0.00 0.00 0.00 4.69
2117 2191 6.022163 ACACGATAAATTATACTCCCTCCG 57.978 41.667 0.00 0.00 0.00 4.63
2118 2192 7.929785 TCAAACACGATAAATTATACTCCCTCC 59.070 37.037 0.00 0.00 0.00 4.30
2119 2193 8.882415 TCAAACACGATAAATTATACTCCCTC 57.118 34.615 0.00 0.00 0.00 4.30
2120 2194 9.326413 CTTCAAACACGATAAATTATACTCCCT 57.674 33.333 0.00 0.00 0.00 4.20
2121 2195 9.106070 ACTTCAAACACGATAAATTATACTCCC 57.894 33.333 0.00 0.00 0.00 4.30
2169 2248 7.817418 TTTCCTAGTCACAGTTAATTGCTTT 57.183 32.000 0.00 0.00 0.00 3.51
2181 2260 8.647796 TCTTGTTAATCTCTTTTCCTAGTCACA 58.352 33.333 0.00 0.00 0.00 3.58
2213 2292 9.705471 CTTTCGTTCTTACATACTAGTGTCTAG 57.295 37.037 5.39 2.71 33.62 2.43
2220 2299 6.906143 CGAGGACTTTCGTTCTTACATACTAG 59.094 42.308 0.00 0.00 35.91 2.57
2295 2377 1.023513 AGGCGCTGCTCTGAAACATC 61.024 55.000 7.64 0.00 0.00 3.06
2328 2410 3.190535 GGATAGAAAACATTGGCGTGTGT 59.809 43.478 0.00 0.00 31.49 3.72
2329 2411 3.190327 TGGATAGAAAACATTGGCGTGTG 59.810 43.478 0.00 0.00 31.49 3.82
2399 2483 3.523374 ACCAAAAAGGGCCGGAGGG 62.523 63.158 5.05 0.00 46.23 4.30
2401 2485 3.681473 GACCAAAAAGGGCCGGAG 58.319 61.111 5.05 0.00 40.85 4.63
2407 2491 6.378280 AGAACTTATATGCAGACCAAAAAGGG 59.622 38.462 0.00 0.00 43.89 3.95
2408 2492 7.396540 AGAACTTATATGCAGACCAAAAAGG 57.603 36.000 0.00 0.00 45.67 3.11
2410 2494 9.120538 GGATAGAACTTATATGCAGACCAAAAA 57.879 33.333 0.00 0.00 0.00 1.94
2411 2495 8.271458 TGGATAGAACTTATATGCAGACCAAAA 58.729 33.333 0.00 0.00 0.00 2.44
2412 2496 7.801104 TGGATAGAACTTATATGCAGACCAAA 58.199 34.615 0.00 0.00 0.00 3.28
2413 2497 7.373617 TGGATAGAACTTATATGCAGACCAA 57.626 36.000 0.00 0.00 0.00 3.67
2414 2498 6.994421 TGGATAGAACTTATATGCAGACCA 57.006 37.500 0.00 0.00 0.00 4.02
2415 2499 7.934120 ACTTTGGATAGAACTTATATGCAGACC 59.066 37.037 0.00 0.00 33.31 3.85
2416 2500 8.894768 ACTTTGGATAGAACTTATATGCAGAC 57.105 34.615 0.00 0.00 33.31 3.51
2417 2501 8.704668 TGACTTTGGATAGAACTTATATGCAGA 58.295 33.333 0.00 0.00 33.31 4.26
2418 2502 8.893219 TGACTTTGGATAGAACTTATATGCAG 57.107 34.615 0.00 0.00 33.31 4.41
2419 2503 9.679661 TTTGACTTTGGATAGAACTTATATGCA 57.320 29.630 0.00 0.00 0.00 3.96
2429 2513 8.730680 GCAAAGATACTTTGACTTTGGATAGAA 58.269 33.333 22.74 0.00 45.69 2.10
2430 2514 8.103305 AGCAAAGATACTTTGACTTTGGATAGA 58.897 33.333 22.74 0.00 45.69 1.98
2431 2515 8.273780 AGCAAAGATACTTTGACTTTGGATAG 57.726 34.615 22.74 0.00 45.69 2.08
2432 2516 8.635765 AAGCAAAGATACTTTGACTTTGGATA 57.364 30.769 22.74 0.00 45.69 2.59
2433 2517 7.530426 AAGCAAAGATACTTTGACTTTGGAT 57.470 32.000 22.74 6.34 45.69 3.41
2434 2518 6.959639 AAGCAAAGATACTTTGACTTTGGA 57.040 33.333 22.74 0.00 45.69 3.53
2443 2527 7.112452 AGTTTGGTCAAAGCAAAGATACTTT 57.888 32.000 4.68 0.00 44.89 2.66
2444 2528 6.715347 AGTTTGGTCAAAGCAAAGATACTT 57.285 33.333 4.68 0.00 44.89 2.24
2445 2529 6.715347 AAGTTTGGTCAAAGCAAAGATACT 57.285 33.333 4.68 0.00 44.89 2.12
2446 2530 9.774742 CTATAAGTTTGGTCAAAGCAAAGATAC 57.225 33.333 4.68 0.00 44.89 2.24
2447 2531 9.733556 TCTATAAGTTTGGTCAAAGCAAAGATA 57.266 29.630 4.68 2.72 44.89 1.98
2448 2532 8.635765 TCTATAAGTTTGGTCAAAGCAAAGAT 57.364 30.769 4.68 2.88 44.89 2.40
2449 2533 8.458573 TTCTATAAGTTTGGTCAAAGCAAAGA 57.541 30.769 4.68 0.00 44.89 2.52
2450 2534 9.528018 TTTTCTATAAGTTTGGTCAAAGCAAAG 57.472 29.630 4.68 0.00 44.89 2.77
2451 2535 9.877178 TTTTTCTATAAGTTTGGTCAAAGCAAA 57.123 25.926 0.50 0.50 42.49 3.68
2452 2536 9.308318 GTTTTTCTATAAGTTTGGTCAAAGCAA 57.692 29.630 0.00 0.00 33.27 3.91
2453 2537 7.646130 CGTTTTTCTATAAGTTTGGTCAAAGCA 59.354 33.333 0.00 0.00 0.00 3.91
2454 2538 7.646526 ACGTTTTTCTATAAGTTTGGTCAAAGC 59.353 33.333 0.00 0.00 0.00 3.51
2458 2542 9.491675 TGATACGTTTTTCTATAAGTTTGGTCA 57.508 29.630 0.00 0.00 0.00 4.02
2470 2554 9.605955 CATTGTGATTGTTGATACGTTTTTCTA 57.394 29.630 0.00 0.00 0.00 2.10
2471 2555 8.134895 ACATTGTGATTGTTGATACGTTTTTCT 58.865 29.630 0.00 0.00 0.00 2.52
2472 2556 8.280909 ACATTGTGATTGTTGATACGTTTTTC 57.719 30.769 0.00 0.00 0.00 2.29
2473 2557 7.918033 TGACATTGTGATTGTTGATACGTTTTT 59.082 29.630 0.00 0.00 0.00 1.94
2474 2558 7.421599 TGACATTGTGATTGTTGATACGTTTT 58.578 30.769 0.00 0.00 0.00 2.43
2475 2559 6.964908 TGACATTGTGATTGTTGATACGTTT 58.035 32.000 0.00 0.00 0.00 3.60
2476 2560 6.552859 TGACATTGTGATTGTTGATACGTT 57.447 33.333 0.00 0.00 0.00 3.99
2477 2561 6.552859 TTGACATTGTGATTGTTGATACGT 57.447 33.333 0.00 0.00 0.00 3.57
2478 2562 7.964559 AGATTTGACATTGTGATTGTTGATACG 59.035 33.333 0.00 0.00 0.00 3.06
2597 2681 9.921637 AGATTTTTGTCAAGTCAAACTTTACAA 57.078 25.926 12.97 12.97 45.26 2.41
2603 2687 9.878599 CGTATTAGATTTTTGTCAAGTCAAACT 57.121 29.630 0.00 0.00 37.10 2.66
2604 2688 8.627428 GCGTATTAGATTTTTGTCAAGTCAAAC 58.373 33.333 0.00 0.00 37.10 2.93
2605 2689 8.346300 TGCGTATTAGATTTTTGTCAAGTCAAA 58.654 29.630 0.00 0.00 35.83 2.69
2606 2690 7.866729 TGCGTATTAGATTTTTGTCAAGTCAA 58.133 30.769 0.00 0.00 0.00 3.18
2607 2691 7.386573 TCTGCGTATTAGATTTTTGTCAAGTCA 59.613 33.333 0.00 0.00 0.00 3.41
2608 2692 7.739295 TCTGCGTATTAGATTTTTGTCAAGTC 58.261 34.615 0.00 0.00 0.00 3.01
2609 2693 7.387948 ACTCTGCGTATTAGATTTTTGTCAAGT 59.612 33.333 0.00 0.00 0.00 3.16
2610 2694 7.743104 ACTCTGCGTATTAGATTTTTGTCAAG 58.257 34.615 0.00 0.00 0.00 3.02
2611 2695 7.667043 ACTCTGCGTATTAGATTTTTGTCAA 57.333 32.000 0.00 0.00 0.00 3.18
2612 2696 8.766000 TTACTCTGCGTATTAGATTTTTGTCA 57.234 30.769 0.00 0.00 0.00 3.58
2617 2701 9.444600 TCCTTTTTACTCTGCGTATTAGATTTT 57.555 29.630 0.00 0.00 0.00 1.82
2618 2702 8.880750 GTCCTTTTTACTCTGCGTATTAGATTT 58.119 33.333 0.00 0.00 0.00 2.17
2619 2703 7.494952 GGTCCTTTTTACTCTGCGTATTAGATT 59.505 37.037 0.00 0.00 0.00 2.40
2620 2704 6.985059 GGTCCTTTTTACTCTGCGTATTAGAT 59.015 38.462 0.00 0.00 0.00 1.98
2621 2705 6.071221 TGGTCCTTTTTACTCTGCGTATTAGA 60.071 38.462 0.00 0.00 0.00 2.10
2622 2706 6.103997 TGGTCCTTTTTACTCTGCGTATTAG 58.896 40.000 0.00 0.00 0.00 1.73
2623 2707 6.040209 TGGTCCTTTTTACTCTGCGTATTA 57.960 37.500 0.00 0.00 0.00 0.98
2624 2708 4.901868 TGGTCCTTTTTACTCTGCGTATT 58.098 39.130 0.00 0.00 0.00 1.89
2625 2709 4.222145 TCTGGTCCTTTTTACTCTGCGTAT 59.778 41.667 0.00 0.00 0.00 3.06
2626 2710 3.575256 TCTGGTCCTTTTTACTCTGCGTA 59.425 43.478 0.00 0.00 0.00 4.42
2627 2711 2.367567 TCTGGTCCTTTTTACTCTGCGT 59.632 45.455 0.00 0.00 0.00 5.24
2628 2712 2.996621 CTCTGGTCCTTTTTACTCTGCG 59.003 50.000 0.00 0.00 0.00 5.18
2629 2713 3.339141 CCTCTGGTCCTTTTTACTCTGC 58.661 50.000 0.00 0.00 0.00 4.26
2630 2714 3.244561 TGCCTCTGGTCCTTTTTACTCTG 60.245 47.826 0.00 0.00 0.00 3.35
2631 2715 2.979678 TGCCTCTGGTCCTTTTTACTCT 59.020 45.455 0.00 0.00 0.00 3.24
2632 2716 3.244596 ACTGCCTCTGGTCCTTTTTACTC 60.245 47.826 0.00 0.00 0.00 2.59
2633 2717 2.711547 ACTGCCTCTGGTCCTTTTTACT 59.288 45.455 0.00 0.00 0.00 2.24
2634 2718 3.141767 ACTGCCTCTGGTCCTTTTTAC 57.858 47.619 0.00 0.00 0.00 2.01
2635 2719 5.514500 AATACTGCCTCTGGTCCTTTTTA 57.486 39.130 0.00 0.00 0.00 1.52
2636 2720 4.388577 AATACTGCCTCTGGTCCTTTTT 57.611 40.909 0.00 0.00 0.00 1.94
2637 2721 4.336280 GAAATACTGCCTCTGGTCCTTTT 58.664 43.478 0.00 0.00 0.00 2.27
2638 2722 3.619979 CGAAATACTGCCTCTGGTCCTTT 60.620 47.826 0.00 0.00 0.00 3.11
2639 2723 2.093447 CGAAATACTGCCTCTGGTCCTT 60.093 50.000 0.00 0.00 0.00 3.36
2640 2724 1.482593 CGAAATACTGCCTCTGGTCCT 59.517 52.381 0.00 0.00 0.00 3.85
2641 2725 1.207329 ACGAAATACTGCCTCTGGTCC 59.793 52.381 0.00 0.00 0.00 4.46
2642 2726 2.674796 ACGAAATACTGCCTCTGGTC 57.325 50.000 0.00 0.00 0.00 4.02
2643 2727 3.097614 AGTACGAAATACTGCCTCTGGT 58.902 45.455 0.00 0.00 42.90 4.00
2644 2728 3.802948 AGTACGAAATACTGCCTCTGG 57.197 47.619 0.00 0.00 42.90 3.86
2645 2729 5.502153 AGTAGTACGAAATACTGCCTCTG 57.498 43.478 0.00 0.00 45.11 3.35
2646 2730 5.239087 GCTAGTAGTACGAAATACTGCCTCT 59.761 44.000 0.00 0.00 45.11 3.69
2647 2731 5.451039 GCTAGTAGTACGAAATACTGCCTC 58.549 45.833 0.00 0.00 45.11 4.70
2648 2732 4.024218 CGCTAGTAGTACGAAATACTGCCT 60.024 45.833 0.00 0.00 45.11 4.75
2649 2733 4.024556 TCGCTAGTAGTACGAAATACTGCC 60.025 45.833 0.00 0.00 45.11 4.85
2650 2734 5.088141 TCGCTAGTAGTACGAAATACTGC 57.912 43.478 0.00 0.00 44.30 4.40
2651 2735 5.564504 GCATCGCTAGTAGTACGAAATACTG 59.435 44.000 4.34 0.51 44.30 2.74
2652 2736 5.334724 GGCATCGCTAGTAGTACGAAATACT 60.335 44.000 4.34 0.00 46.39 2.12
2653 2737 4.850470 GGCATCGCTAGTAGTACGAAATAC 59.150 45.833 4.34 0.00 39.56 1.89
2654 2738 4.516321 TGGCATCGCTAGTAGTACGAAATA 59.484 41.667 4.34 0.00 39.56 1.40
2655 2739 3.317149 TGGCATCGCTAGTAGTACGAAAT 59.683 43.478 4.34 0.00 39.56 2.17
2656 2740 2.684374 TGGCATCGCTAGTAGTACGAAA 59.316 45.455 4.34 0.00 39.56 3.46
2657 2741 2.032550 GTGGCATCGCTAGTAGTACGAA 59.967 50.000 4.34 0.00 39.56 3.85
2658 2742 1.600957 GTGGCATCGCTAGTAGTACGA 59.399 52.381 0.00 0.72 40.53 3.43
2659 2743 1.659491 CGTGGCATCGCTAGTAGTACG 60.659 57.143 0.00 0.00 0.00 3.67
2660 2744 2.033793 CGTGGCATCGCTAGTAGTAC 57.966 55.000 0.00 0.00 0.00 2.73
2681 2765 0.388134 TTCCTAGTCGCGTCAACTGC 60.388 55.000 5.77 0.00 0.00 4.40
2686 2770 0.607217 TGGTCTTCCTAGTCGCGTCA 60.607 55.000 5.77 0.00 34.23 4.35


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

AutoCloner maintained by Alex Coulton.