Multiple sequence alignment - TraesCS6B01G431000

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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 TraesCS6B01G431000 chr6B 100.000 7363 0 0 1 7363 699010190 699002828 0.000000e+00 13598.0
1 TraesCS6B01G431000 chr6B 89.610 154 13 3 12 162 699010077 699009924 7.540000e-45 193.0
2 TraesCS6B01G431000 chr6B 89.610 154 13 3 114 267 699010179 699010029 7.540000e-45 193.0
3 TraesCS6B01G431000 chr6A 92.244 6666 330 84 114 6664 605382458 605375865 0.000000e+00 9273.0
4 TraesCS6B01G431000 chr6A 91.228 57 4 1 5639 5695 496014557 496014502 7.920000e-10 76.8
5 TraesCS6B01G431000 chr6D 92.155 5838 303 80 205 5928 459700519 459694723 0.000000e+00 8100.0
6 TraesCS6B01G431000 chr6D 88.929 560 37 11 6112 6651 459694537 459693983 0.000000e+00 667.0
7 TraesCS6B01G431000 chr6D 91.228 57 4 1 5639 5695 152191801 152191746 7.920000e-10 76.8
8 TraesCS6B01G431000 chr5B 99.573 703 3 0 6661 7363 336222429 336223131 0.000000e+00 1282.0
9 TraesCS6B01G431000 chr5A 99.712 694 2 0 6670 7363 675491382 675492075 0.000000e+00 1271.0
10 TraesCS6B01G431000 chr5A 99.149 705 6 0 6659 7363 328702333 328703037 0.000000e+00 1269.0
11 TraesCS6B01G431000 chr5A 96.000 50 2 0 5283 5332 59629023 59629072 1.700000e-11 82.4
12 TraesCS6B01G431000 chr5A 88.889 63 6 1 5633 5695 473462551 473462612 7.920000e-10 76.8
13 TraesCS6B01G431000 chr3B 99.071 646 6 0 6665 7310 331543602 331544247 0.000000e+00 1160.0
14 TraesCS6B01G431000 chr3B 98.913 644 7 0 6670 7313 349965056 349964413 0.000000e+00 1151.0
15 TraesCS6B01G431000 chr3B 91.228 57 4 1 5639 5695 13372777 13372722 7.920000e-10 76.8
16 TraesCS6B01G431000 chr4B 98.137 644 12 0 6670 7313 88415995 88415352 0.000000e+00 1123.0
17 TraesCS6B01G431000 chr4B 95.833 48 2 0 5285 5332 79296289 79296242 2.200000e-10 78.7
18 TraesCS6B01G431000 chr2A 91.496 682 48 3 6670 7349 698149735 698149062 0.000000e+00 929.0
19 TraesCS6B01G431000 chr2A 75.373 536 101 28 4664 5182 501321176 501321697 5.750000e-56 230.0
20 TraesCS6B01G431000 chr2A 80.000 275 41 10 2865 3134 501320045 501320310 2.710000e-44 191.0
21 TraesCS6B01G431000 chr2A 94.000 50 3 0 5283 5332 112593904 112593953 7.920000e-10 76.8
22 TraesCS6B01G431000 chr5D 89.884 692 58 5 6670 7359 387815079 387815760 0.000000e+00 880.0
23 TraesCS6B01G431000 chr2B 89.665 687 60 8 6674 7359 24016924 24017600 0.000000e+00 865.0
24 TraesCS6B01G431000 chr2B 79.348 276 40 14 2865 3134 439770270 439770534 2.110000e-40 178.0
25 TraesCS6B01G431000 chr2D 72.747 910 187 50 4664 5546 370241209 370242084 4.410000e-62 250.0
26 TraesCS6B01G431000 chr2D 79.636 275 42 10 2865 3134 370240079 370240344 1.260000e-42 185.0
27 TraesCS6B01G431000 chr1B 96.000 50 2 0 5283 5332 437592527 437592576 1.700000e-11 82.4
28 TraesCS6B01G431000 chr1B 82.796 93 10 3 5639 5731 184036214 184036128 2.200000e-10 78.7
29 TraesCS6B01G431000 chr1B 91.228 57 4 1 5639 5695 488747874 488747819 7.920000e-10 76.8
30 TraesCS6B01G431000 chr1B 88.889 63 6 1 5633 5695 499502456 499502517 7.920000e-10 76.8
31 TraesCS6B01G431000 chr7A 94.000 50 3 0 5283 5332 487704539 487704490 7.920000e-10 76.8
32 TraesCS6B01G431000 chr1A 94.000 50 3 0 5283 5332 509025361 509025312 7.920000e-10 76.8
33 TraesCS6B01G431000 chr3A 92.000 50 4 0 5283 5332 25405836 25405787 3.690000e-08 71.3


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 TraesCS6B01G431000 chr6B 699002828 699010190 7362 True 4661.333333 13598 93.073333 1 7363 3 chr6B.!!$R1 7362
1 TraesCS6B01G431000 chr6A 605375865 605382458 6593 True 9273.000000 9273 92.244000 114 6664 1 chr6A.!!$R2 6550
2 TraesCS6B01G431000 chr6D 459693983 459700519 6536 True 4383.500000 8100 90.542000 205 6651 2 chr6D.!!$R2 6446
3 TraesCS6B01G431000 chr5B 336222429 336223131 702 False 1282.000000 1282 99.573000 6661 7363 1 chr5B.!!$F1 702
4 TraesCS6B01G431000 chr5A 675491382 675492075 693 False 1271.000000 1271 99.712000 6670 7363 1 chr5A.!!$F4 693
5 TraesCS6B01G431000 chr5A 328702333 328703037 704 False 1269.000000 1269 99.149000 6659 7363 1 chr5A.!!$F2 704
6 TraesCS6B01G431000 chr3B 331543602 331544247 645 False 1160.000000 1160 99.071000 6665 7310 1 chr3B.!!$F1 645
7 TraesCS6B01G431000 chr3B 349964413 349965056 643 True 1151.000000 1151 98.913000 6670 7313 1 chr3B.!!$R2 643
8 TraesCS6B01G431000 chr4B 88415352 88415995 643 True 1123.000000 1123 98.137000 6670 7313 1 chr4B.!!$R2 643
9 TraesCS6B01G431000 chr2A 698149062 698149735 673 True 929.000000 929 91.496000 6670 7349 1 chr2A.!!$R1 679
10 TraesCS6B01G431000 chr2A 501320045 501321697 1652 False 210.500000 230 77.686500 2865 5182 2 chr2A.!!$F2 2317
11 TraesCS6B01G431000 chr5D 387815079 387815760 681 False 880.000000 880 89.884000 6670 7359 1 chr5D.!!$F1 689
12 TraesCS6B01G431000 chr2B 24016924 24017600 676 False 865.000000 865 89.665000 6674 7359 1 chr2B.!!$F1 685
13 TraesCS6B01G431000 chr2D 370240079 370242084 2005 False 217.500000 250 76.191500 2865 5546 2 chr2D.!!$F1 2681

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
44 45 0.037734 CGGAGCAAAGTAACCCCCTT 59.962 55.000 0.00 0.00 0.00 3.95 F
100 101 0.250727 CCGTTGGTGTTCACCCAGAT 60.251 55.000 17.78 0.00 32.49 2.90 F
1955 2063 0.179100 ATGGGACGTCGATGCTCTTG 60.179 55.000 9.92 0.00 0.00 3.02 F
2741 2858 0.478072 AGATGTTTGGTGGCAGGTGA 59.522 50.000 0.00 0.00 0.00 4.02 F
3992 4167 2.370519 TGCCAAACAGCTGGTTCTAGTA 59.629 45.455 15.77 3.06 39.29 1.82 F
4781 4969 3.312697 CCTTTTAATAGCCGGCACTTCTC 59.687 47.826 31.54 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2063 0.481128 TTCCCCAAACCTCCAAGACC 59.519 55.000 0.0 0.0 0.00 3.85 R
2032 2142 1.507141 CCTTGCCGACACCAACACTC 61.507 60.000 0.0 0.0 0.00 3.51 R
2985 3104 3.447918 ACGTGATAACAGGATAACCCG 57.552 47.619 0.0 0.0 40.87 5.28 R
4288 4466 0.319211 CTCGCTGTGGTTGTTCCGTA 60.319 55.000 0.0 0.0 39.52 4.02 R
4796 4986 0.899720 TTGGTCGCTTTATCGTCCCT 59.100 50.000 0.0 0.0 36.96 4.20 R
6478 6733 0.868406 CACCACGCTTTCAGTTCTCC 59.132 55.000 0.0 0.0 0.00 3.71 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
23 24 4.891727 CGCCCCGGATCTCCAACG 62.892 72.222 0.73 0.00 35.14 4.10
24 25 4.547367 GCCCCGGATCTCCAACGG 62.547 72.222 0.73 0.00 46.79 4.44
25 26 4.547367 CCCCGGATCTCCAACGGC 62.547 72.222 0.73 0.00 45.93 5.68
26 27 4.891727 CCCGGATCTCCAACGGCG 62.892 72.222 0.73 4.80 45.93 6.46
27 28 4.891727 CCGGATCTCCAACGGCGG 62.892 72.222 13.24 0.00 41.23 6.13
28 29 3.833645 CGGATCTCCAACGGCGGA 61.834 66.667 13.24 0.00 35.14 5.54
42 43 4.313819 CGGAGCAAAGTAACCCCC 57.686 61.111 0.00 0.00 0.00 5.40
43 44 1.683441 CGGAGCAAAGTAACCCCCT 59.317 57.895 0.00 0.00 0.00 4.79
44 45 0.037734 CGGAGCAAAGTAACCCCCTT 59.962 55.000 0.00 0.00 0.00 3.95
45 46 1.279846 CGGAGCAAAGTAACCCCCTTA 59.720 52.381 0.00 0.00 0.00 2.69
46 47 2.719739 GGAGCAAAGTAACCCCCTTAC 58.280 52.381 0.00 0.00 35.77 2.34
47 48 2.619849 GGAGCAAAGTAACCCCCTTACC 60.620 54.545 0.00 0.00 36.13 2.85
48 49 2.307980 GAGCAAAGTAACCCCCTTACCT 59.692 50.000 0.00 0.00 36.13 3.08
49 50 3.520721 GAGCAAAGTAACCCCCTTACCTA 59.479 47.826 0.00 0.00 36.13 3.08
50 51 3.522343 AGCAAAGTAACCCCCTTACCTAG 59.478 47.826 0.00 0.00 36.13 3.02
51 52 3.882444 CAAAGTAACCCCCTTACCTAGC 58.118 50.000 0.00 0.00 36.13 3.42
52 53 2.955200 AGTAACCCCCTTACCTAGCA 57.045 50.000 0.00 0.00 36.13 3.49
53 54 2.760581 AGTAACCCCCTTACCTAGCAG 58.239 52.381 0.00 0.00 36.13 4.24
54 55 1.140452 GTAACCCCCTTACCTAGCAGC 59.860 57.143 0.00 0.00 29.96 5.25
55 56 1.279749 AACCCCCTTACCTAGCAGCC 61.280 60.000 0.00 0.00 0.00 4.85
56 57 1.692749 CCCCCTTACCTAGCAGCCA 60.693 63.158 0.00 0.00 0.00 4.75
57 58 1.700042 CCCCCTTACCTAGCAGCCAG 61.700 65.000 0.00 0.00 0.00 4.85
58 59 1.147153 CCCTTACCTAGCAGCCAGC 59.853 63.158 0.00 0.00 46.19 4.85
67 68 2.721231 GCAGCCAGCAACGAAACA 59.279 55.556 0.00 0.00 44.79 2.83
68 69 1.286880 GCAGCCAGCAACGAAACAT 59.713 52.632 0.00 0.00 44.79 2.71
69 70 0.730494 GCAGCCAGCAACGAAACATC 60.730 55.000 0.00 0.00 44.79 3.06
70 71 0.592637 CAGCCAGCAACGAAACATCA 59.407 50.000 0.00 0.00 0.00 3.07
71 72 1.200716 CAGCCAGCAACGAAACATCAT 59.799 47.619 0.00 0.00 0.00 2.45
72 73 1.888512 AGCCAGCAACGAAACATCATT 59.111 42.857 0.00 0.00 0.00 2.57
73 74 1.987770 GCCAGCAACGAAACATCATTG 59.012 47.619 0.00 0.00 0.00 2.82
74 75 2.351641 GCCAGCAACGAAACATCATTGA 60.352 45.455 0.00 0.00 0.00 2.57
75 76 3.495193 CCAGCAACGAAACATCATTGAG 58.505 45.455 0.00 0.00 0.00 3.02
76 77 2.912967 CAGCAACGAAACATCATTGAGC 59.087 45.455 0.00 0.00 0.00 4.26
77 78 2.816087 AGCAACGAAACATCATTGAGCT 59.184 40.909 0.00 0.00 0.00 4.09
78 79 3.120060 AGCAACGAAACATCATTGAGCTC 60.120 43.478 6.82 6.82 0.00 4.09
79 80 3.751621 CAACGAAACATCATTGAGCTCC 58.248 45.455 12.15 0.00 0.00 4.70
80 81 2.002586 ACGAAACATCATTGAGCTCCG 58.997 47.619 12.15 5.71 0.00 4.63
81 82 1.267732 CGAAACATCATTGAGCTCCGC 60.268 52.381 12.15 0.00 0.00 5.54
82 83 1.064654 GAAACATCATTGAGCTCCGCC 59.935 52.381 12.15 0.00 0.00 6.13
83 84 1.091771 AACATCATTGAGCTCCGCCG 61.092 55.000 12.15 0.00 0.00 6.46
84 85 1.522355 CATCATTGAGCTCCGCCGT 60.522 57.895 12.15 0.00 0.00 5.68
85 86 1.091771 CATCATTGAGCTCCGCCGTT 61.092 55.000 12.15 0.00 0.00 4.44
86 87 1.091771 ATCATTGAGCTCCGCCGTTG 61.092 55.000 12.15 0.06 0.00 4.10
87 88 2.436646 ATTGAGCTCCGCCGTTGG 60.437 61.111 12.15 0.00 0.00 3.77
88 89 3.254024 ATTGAGCTCCGCCGTTGGT 62.254 57.895 12.15 0.00 0.00 3.67
89 90 4.680237 TGAGCTCCGCCGTTGGTG 62.680 66.667 12.15 0.00 0.00 4.17
90 91 4.681978 GAGCTCCGCCGTTGGTGT 62.682 66.667 0.87 0.00 0.00 4.16
91 92 4.250305 AGCTCCGCCGTTGGTGTT 62.250 61.111 0.00 0.00 0.00 3.32
92 93 3.723348 GCTCCGCCGTTGGTGTTC 61.723 66.667 0.00 0.00 0.00 3.18
93 94 2.280524 CTCCGCCGTTGGTGTTCA 60.281 61.111 0.00 0.00 0.00 3.18
94 95 2.589442 TCCGCCGTTGGTGTTCAC 60.589 61.111 0.00 0.00 0.00 3.18
95 96 3.656045 CCGCCGTTGGTGTTCACC 61.656 66.667 14.31 14.31 0.00 4.02
96 97 3.656045 CGCCGTTGGTGTTCACCC 61.656 66.667 17.78 4.22 0.00 4.61
97 98 2.517402 GCCGTTGGTGTTCACCCA 60.517 61.111 17.78 5.64 0.00 4.51
98 99 2.551912 GCCGTTGGTGTTCACCCAG 61.552 63.158 17.78 9.64 32.49 4.45
99 100 1.147376 CCGTTGGTGTTCACCCAGA 59.853 57.895 17.78 3.20 32.49 3.86
100 101 0.250727 CCGTTGGTGTTCACCCAGAT 60.251 55.000 17.78 0.00 32.49 2.90
101 102 1.002659 CCGTTGGTGTTCACCCAGATA 59.997 52.381 17.78 0.00 32.49 1.98
102 103 2.551287 CCGTTGGTGTTCACCCAGATAA 60.551 50.000 17.78 3.96 32.49 1.75
103 104 3.142951 CGTTGGTGTTCACCCAGATAAA 58.857 45.455 17.78 3.31 32.49 1.40
104 105 3.058501 CGTTGGTGTTCACCCAGATAAAC 60.059 47.826 17.78 12.93 32.49 2.01
105 106 4.142038 GTTGGTGTTCACCCAGATAAACT 58.858 43.478 17.78 0.00 32.49 2.66
106 107 4.447138 TGGTGTTCACCCAGATAAACTT 57.553 40.909 17.78 0.00 0.00 2.66
107 108 4.798882 TGGTGTTCACCCAGATAAACTTT 58.201 39.130 17.78 0.00 0.00 2.66
108 109 4.825085 TGGTGTTCACCCAGATAAACTTTC 59.175 41.667 17.78 0.00 0.00 2.62
109 110 4.825085 GGTGTTCACCCAGATAAACTTTCA 59.175 41.667 10.56 0.00 0.00 2.69
110 111 5.476945 GGTGTTCACCCAGATAAACTTTCAT 59.523 40.000 10.56 0.00 0.00 2.57
111 112 6.015434 GGTGTTCACCCAGATAAACTTTCATT 60.015 38.462 10.56 0.00 0.00 2.57
112 113 7.433680 GTGTTCACCCAGATAAACTTTCATTT 58.566 34.615 0.00 0.00 0.00 2.32
116 117 4.705023 ACCCAGATAAACTTTCATTTCGGG 59.295 41.667 0.00 0.00 34.84 5.14
142 143 4.416738 GGCAGGGCAGAGGGTGAC 62.417 72.222 0.00 0.00 0.00 3.67
173 174 2.953821 CGGCCAGCAACGAAACAT 59.046 55.556 2.24 0.00 0.00 2.71
174 175 1.285641 CGGCCAGCAACGAAACATT 59.714 52.632 2.24 0.00 0.00 2.71
175 176 0.519519 CGGCCAGCAACGAAACATTA 59.480 50.000 2.24 0.00 0.00 1.90
176 177 1.132262 CGGCCAGCAACGAAACATTAT 59.868 47.619 2.24 0.00 0.00 1.28
177 178 2.415357 CGGCCAGCAACGAAACATTATT 60.415 45.455 2.24 0.00 0.00 1.40
178 179 2.923020 GGCCAGCAACGAAACATTATTG 59.077 45.455 0.00 0.00 0.00 1.90
186 187 2.351726 ACGAAACATTATTGAGCTCCGC 59.648 45.455 12.15 0.00 0.00 5.54
192 193 0.742990 TTATTGAGCTCCGCCGTTGG 60.743 55.000 12.15 0.00 0.00 3.77
195 196 4.681978 GAGCTCCGCCGTTGGTGT 62.682 66.667 0.87 0.00 0.00 4.16
199 200 2.589442 TCCGCCGTTGGTGTTCAC 60.589 61.111 0.00 0.00 0.00 3.18
203 204 2.122167 GCCGTTGGTGTTCACCCAA 61.122 57.895 17.78 10.13 39.62 4.12
247 248 4.416738 GGCAGGGCAGAGGGTGAC 62.417 72.222 0.00 0.00 0.00 3.67
324 328 1.679153 CCCCGGTAAATTTCCATTCCG 59.321 52.381 0.00 3.18 38.05 4.30
336 340 3.873812 ATTCCGGGATCCGCCACC 61.874 66.667 5.45 0.00 46.86 4.61
357 361 3.231736 GGCGAGGCGAGGGGATTA 61.232 66.667 0.00 0.00 0.00 1.75
367 371 4.082125 GGCGAGGGGATTAATTCATGAAT 58.918 43.478 15.36 15.36 0.00 2.57
431 443 1.533625 TCACGGCCTGAAAAGGAATG 58.466 50.000 0.00 0.00 0.00 2.67
444 456 2.100605 AGGAATGTTTCTCGTGGAGC 57.899 50.000 0.00 0.00 0.00 4.70
445 457 1.087501 GGAATGTTTCTCGTGGAGCC 58.912 55.000 0.00 0.00 0.00 4.70
454 466 2.125552 CGTGGAGCCGCTGAATCA 60.126 61.111 0.00 0.00 0.00 2.57
463 475 2.165030 AGCCGCTGAATCAAATTCCAAG 59.835 45.455 0.00 0.00 38.50 3.61
500 512 3.367743 TCGTGGTCGCGCCTAGTT 61.368 61.111 18.14 0.00 38.35 2.24
501 513 3.179265 CGTGGTCGCGCCTAGTTG 61.179 66.667 18.14 0.00 38.35 3.16
502 514 3.488090 GTGGTCGCGCCTAGTTGC 61.488 66.667 18.14 0.00 38.35 4.17
503 515 3.997397 TGGTCGCGCCTAGTTGCA 61.997 61.111 18.14 0.00 38.35 4.08
504 516 2.740826 GGTCGCGCCTAGTTGCAA 60.741 61.111 0.00 0.00 0.00 4.08
518 530 2.048316 GCAATGCAACCCAACCCG 60.048 61.111 0.00 0.00 0.00 5.28
587 612 4.295119 GTCACGTGGAGCGGGTGT 62.295 66.667 17.00 0.00 45.75 4.16
673 698 4.827284 CCCCTACCTGCCAATATTTTACTG 59.173 45.833 0.00 0.00 0.00 2.74
674 699 4.278419 CCCTACCTGCCAATATTTTACTGC 59.722 45.833 0.00 0.00 0.00 4.40
676 701 4.989279 ACCTGCCAATATTTTACTGCTG 57.011 40.909 0.00 0.00 0.00 4.41
679 704 3.097877 GCCAATATTTTACTGCTGGCC 57.902 47.619 0.00 0.00 42.86 5.36
747 773 1.202533 AGGGAAGTCAACACACGACTG 60.203 52.381 0.00 0.00 42.90 3.51
777 812 4.527583 GCAGCCAGCGGAGGAGAG 62.528 72.222 0.00 0.00 0.00 3.20
785 820 1.076632 GCGGAGGAGAGGGAGAAGA 60.077 63.158 0.00 0.00 0.00 2.87
919 962 2.653702 GCCCGGATCTGGATCTCG 59.346 66.667 23.02 5.77 37.92 4.04
921 964 2.653702 CCGGATCTGGATCTCGCC 59.346 66.667 16.28 0.00 37.92 5.54
1107 1150 2.140792 CGGGACCATCTCCGGGATT 61.141 63.158 0.00 0.00 40.56 3.01
1285 1363 3.042887 GGCGTTTAGTTCAGCACAAAAG 58.957 45.455 0.00 0.00 0.00 2.27
1318 1396 4.386711 TGATCATGATCAAGACATGGCTC 58.613 43.478 31.46 6.55 44.14 4.70
1319 1397 3.918294 TCATGATCAAGACATGGCTCA 57.082 42.857 0.00 0.00 43.38 4.26
1337 1415 2.288666 TCATGGCGGATAAAAGTCAGC 58.711 47.619 0.00 0.00 38.38 4.26
1357 1435 2.082231 CAAGACAGGGACATTGCTGAG 58.918 52.381 0.00 0.00 0.00 3.35
1442 1532 4.853924 TTTCAGTGCTTCATTCCTTTCC 57.146 40.909 0.00 0.00 0.00 3.13
1453 1543 1.398692 TTCCTTTCCTGCTGCGTTTT 58.601 45.000 0.00 0.00 0.00 2.43
1454 1544 0.951558 TCCTTTCCTGCTGCGTTTTC 59.048 50.000 0.00 0.00 0.00 2.29
1455 1545 0.954452 CCTTTCCTGCTGCGTTTTCT 59.046 50.000 0.00 0.00 0.00 2.52
1457 1547 2.552315 CCTTTCCTGCTGCGTTTTCTTA 59.448 45.455 0.00 0.00 0.00 2.10
1458 1548 3.004315 CCTTTCCTGCTGCGTTTTCTTAA 59.996 43.478 0.00 0.00 0.00 1.85
1459 1549 4.499019 CCTTTCCTGCTGCGTTTTCTTAAA 60.499 41.667 0.00 0.00 0.00 1.52
1460 1550 3.896648 TCCTGCTGCGTTTTCTTAAAG 57.103 42.857 0.00 0.00 0.00 1.85
1461 1551 3.472652 TCCTGCTGCGTTTTCTTAAAGA 58.527 40.909 0.00 0.00 0.00 2.52
1462 1552 4.072131 TCCTGCTGCGTTTTCTTAAAGAT 58.928 39.130 0.00 0.00 0.00 2.40
1463 1553 4.083324 TCCTGCTGCGTTTTCTTAAAGATG 60.083 41.667 0.00 0.00 0.00 2.90
1464 1554 4.083324 CCTGCTGCGTTTTCTTAAAGATGA 60.083 41.667 0.00 0.00 0.00 2.92
1673 1778 2.224843 TGGTGATGGCTGTTGACTGAAT 60.225 45.455 0.00 0.00 0.00 2.57
1717 1824 5.240713 GAATCATGTGATGGTTCTTGGTC 57.759 43.478 2.85 0.00 44.90 4.02
1790 1897 2.125912 CAACGTCGAGGCTGGGAG 60.126 66.667 4.75 0.00 0.00 4.30
1821 1928 0.331278 TTGCAATGTACTGGGAGGGG 59.669 55.000 0.00 0.00 0.00 4.79
1824 1931 1.682087 GCAATGTACTGGGAGGGGAAC 60.682 57.143 0.00 0.00 0.00 3.62
1842 1949 2.764128 GAGCCCGGTCAGGATGGA 60.764 66.667 0.00 0.00 45.00 3.41
1946 2054 0.461163 TAATGTGCCATGGGACGTCG 60.461 55.000 28.91 0.00 39.39 5.12
1955 2063 0.179100 ATGGGACGTCGATGCTCTTG 60.179 55.000 9.92 0.00 0.00 3.02
1987 2095 1.965414 TGGGGAAGGTGCTGAATCTA 58.035 50.000 0.00 0.00 0.00 1.98
2032 2142 4.156556 TGCTAGCTTGCCAATTACTTGAAG 59.843 41.667 17.57 0.00 34.04 3.02
2062 2172 3.006677 GGCAAGGGGGATGCTGTA 58.993 61.111 0.00 0.00 43.34 2.74
2116 2226 2.510691 GCCATGCTTGCATGTGCC 60.511 61.111 27.11 15.14 41.18 5.01
2125 2235 3.649986 GCATGTGCCCGTATCGGC 61.650 66.667 2.41 0.00 46.86 5.54
2408 2518 9.523168 GATTCTCTGTAGGTATGTACTAGGATT 57.477 37.037 0.00 0.00 0.00 3.01
2497 2612 6.072064 CCATTACGGGGTTTAATGTTGTGTTA 60.072 38.462 0.00 0.00 35.84 2.41
2498 2613 7.363094 CCATTACGGGGTTTAATGTTGTGTTAT 60.363 37.037 0.00 0.00 35.84 1.89
2499 2614 7.521871 TTACGGGGTTTAATGTTGTGTTATT 57.478 32.000 0.00 0.00 0.00 1.40
2584 2700 8.262933 TGATGACTTACAGATCATTGACAGATT 58.737 33.333 0.00 0.00 35.67 2.40
2586 2702 6.753744 TGACTTACAGATCATTGACAGATTCG 59.246 38.462 0.00 0.00 0.00 3.34
2671 2788 6.183360 GCTGAGCAGGTATTTGTTTGACATAT 60.183 38.462 0.00 0.00 0.00 1.78
2683 2800 7.581213 TTGTTTGACATATGAAAACCAGTCT 57.419 32.000 23.58 0.00 33.76 3.24
2715 2832 2.483538 GGCAAGACACAAAATGGCAAGT 60.484 45.455 0.00 0.00 39.81 3.16
2722 2839 2.364970 CACAAAATGGCAAGTGGGAAGA 59.635 45.455 0.00 0.00 0.00 2.87
2741 2858 0.478072 AGATGTTTGGTGGCAGGTGA 59.522 50.000 0.00 0.00 0.00 4.02
2776 2895 5.070770 TCAACAGCAACTTGTCAACATTT 57.929 34.783 0.00 0.00 0.00 2.32
2807 2926 3.890527 CTGTATTTCAGGGCAGGCT 57.109 52.632 0.00 0.00 40.23 4.58
2988 3107 2.498885 AGGTACTTTAAGCTACACCGGG 59.501 50.000 6.32 0.00 27.25 5.73
2999 3118 2.431782 GCTACACCGGGTTATCCTGTTA 59.568 50.000 6.32 0.00 38.38 2.41
3100 3219 6.331369 ACTGCAACAACATTTAAGTATGCT 57.669 33.333 0.00 0.00 33.87 3.79
3459 3630 4.696402 GGGGTTGTCATTATGTTTGACGTA 59.304 41.667 0.00 0.00 45.14 3.57
3468 3639 7.218204 GTCATTATGTTTGACGTATCCTTTTGC 59.782 37.037 0.00 0.00 34.67 3.68
3564 3738 8.702438 ACTCAATTTGTTTGCTTCGATAATTTG 58.298 29.630 0.00 0.00 35.16 2.32
3975 4150 5.164620 TCACTAGATCTCAACATTTGCCA 57.835 39.130 0.00 0.00 0.00 4.92
3992 4167 2.370519 TGCCAAACAGCTGGTTCTAGTA 59.629 45.455 15.77 3.06 39.29 1.82
4175 4350 3.966154 AGCTCGTATGACTTATCAACCG 58.034 45.455 0.00 0.00 38.69 4.44
4384 4568 7.820044 TGAAACACTGAAAATAAAACACACC 57.180 32.000 0.00 0.00 0.00 4.16
4767 4955 5.105351 GGCTTCATGGTAAGTGCCTTTTAAT 60.105 40.000 0.00 0.00 37.58 1.40
4771 4959 5.592688 TCATGGTAAGTGCCTTTTAATAGCC 59.407 40.000 0.00 0.00 0.00 3.93
4773 4961 3.314357 GGTAAGTGCCTTTTAATAGCCGG 59.686 47.826 0.00 0.00 0.00 6.13
4781 4969 3.312697 CCTTTTAATAGCCGGCACTTCTC 59.687 47.826 31.54 0.00 0.00 2.87
4782 4970 3.620427 TTTAATAGCCGGCACTTCTCA 57.380 42.857 31.54 3.27 0.00 3.27
4790 4980 3.388024 AGCCGGCACTTCTCATATTTCTA 59.612 43.478 31.54 0.00 0.00 2.10
4796 4986 7.012327 CCGGCACTTCTCATATTTCTATTTCAA 59.988 37.037 0.00 0.00 0.00 2.69
4809 4999 6.920569 TTCTATTTCAAGGGACGATAAAGC 57.079 37.500 0.00 0.00 0.00 3.51
4813 5003 1.134907 TCAAGGGACGATAAAGCGACC 60.135 52.381 0.53 0.53 43.60 4.79
4814 5004 0.899720 AAGGGACGATAAAGCGACCA 59.100 50.000 10.90 0.00 45.56 4.02
5362 5577 6.552629 GTTAGGTAAGCTGCTTATTTGGTTC 58.447 40.000 23.51 9.84 0.00 3.62
5363 5578 4.662278 AGGTAAGCTGCTTATTTGGTTCA 58.338 39.130 23.51 0.00 0.00 3.18
5368 5583 5.473066 AGCTGCTTATTTGGTTCATTTGT 57.527 34.783 0.00 0.00 0.00 2.83
5381 5596 6.634805 TGGTTCATTTGTTGTTTGCTAGAAA 58.365 32.000 0.00 0.00 0.00 2.52
5384 5599 8.275632 GGTTCATTTGTTGTTTGCTAGAAATTC 58.724 33.333 0.00 0.00 0.00 2.17
5563 5778 1.270678 GGTATGGCCCACCGATACTTC 60.271 57.143 7.81 0.00 39.70 3.01
5813 6029 5.885230 TCACATCTTCATTCAAAAGCGAT 57.115 34.783 0.00 0.00 0.00 4.58
5820 6036 6.077197 TCTTCATTCAAAAGCGATTTACACG 58.923 36.000 0.00 0.00 0.00 4.49
5842 6058 4.976116 CGATCAGAAAATAAAATTCCGCCC 59.024 41.667 0.00 0.00 0.00 6.13
5859 6075 2.744823 CGCCCTTACATGGAAGTATGCA 60.745 50.000 16.61 0.00 0.00 3.96
5928 6144 2.887152 ACAAAGTGAGTTCTGGCCAATC 59.113 45.455 7.01 3.28 0.00 2.67
5935 6151 1.970640 AGTTCTGGCCAATCCCAAAAC 59.029 47.619 7.01 3.10 33.73 2.43
5936 6152 1.691434 GTTCTGGCCAATCCCAAAACA 59.309 47.619 7.01 0.00 33.73 2.83
5938 6154 2.402564 TCTGGCCAATCCCAAAACAAA 58.597 42.857 7.01 0.00 33.73 2.83
5939 6155 2.978278 TCTGGCCAATCCCAAAACAAAT 59.022 40.909 7.01 0.00 33.73 2.32
5940 6156 3.393941 TCTGGCCAATCCCAAAACAAATT 59.606 39.130 7.01 0.00 33.73 1.82
5941 6157 3.484407 TGGCCAATCCCAAAACAAATTG 58.516 40.909 0.61 0.00 30.32 2.32
5942 6158 2.228582 GGCCAATCCCAAAACAAATTGC 59.771 45.455 0.00 0.00 0.00 3.56
5943 6159 2.095819 GCCAATCCCAAAACAAATTGCG 60.096 45.455 0.00 0.00 0.00 4.85
5944 6160 3.397482 CCAATCCCAAAACAAATTGCGA 58.603 40.909 0.00 0.00 0.00 5.10
5945 6161 3.812053 CCAATCCCAAAACAAATTGCGAA 59.188 39.130 0.00 0.00 0.00 4.70
5946 6162 4.083908 CCAATCCCAAAACAAATTGCGAAG 60.084 41.667 0.00 0.00 0.00 3.79
5947 6163 3.104843 TCCCAAAACAAATTGCGAAGG 57.895 42.857 0.00 0.00 0.00 3.46
5948 6164 2.432510 TCCCAAAACAAATTGCGAAGGT 59.567 40.909 0.00 0.00 0.00 3.50
5949 6165 2.543430 CCCAAAACAAATTGCGAAGGTG 59.457 45.455 0.00 0.00 0.00 4.00
5950 6166 2.032979 CCAAAACAAATTGCGAAGGTGC 60.033 45.455 0.00 0.00 0.00 5.01
5951 6167 1.864565 AAACAAATTGCGAAGGTGCC 58.135 45.000 0.00 0.00 0.00 5.01
5952 6168 0.033366 AACAAATTGCGAAGGTGCCC 59.967 50.000 0.00 0.00 0.00 5.36
5953 6169 1.444212 CAAATTGCGAAGGTGCCCG 60.444 57.895 0.00 0.00 0.00 6.13
5954 6170 1.602323 AAATTGCGAAGGTGCCCGA 60.602 52.632 0.00 0.00 0.00 5.14
5955 6171 0.965363 AAATTGCGAAGGTGCCCGAT 60.965 50.000 0.00 0.00 0.00 4.18
5956 6172 0.965363 AATTGCGAAGGTGCCCGATT 60.965 50.000 0.00 0.00 0.00 3.34
5957 6173 1.376609 ATTGCGAAGGTGCCCGATTC 61.377 55.000 0.00 0.00 0.00 2.52
5958 6174 2.125106 GCGAAGGTGCCCGATTCT 60.125 61.111 0.00 0.00 0.00 2.40
5959 6175 1.143183 GCGAAGGTGCCCGATTCTA 59.857 57.895 0.00 0.00 0.00 2.10
5960 6176 1.152383 GCGAAGGTGCCCGATTCTAC 61.152 60.000 0.00 0.00 0.00 2.59
5961 6177 0.174845 CGAAGGTGCCCGATTCTACA 59.825 55.000 0.00 0.00 0.00 2.74
5962 6178 1.404986 CGAAGGTGCCCGATTCTACAA 60.405 52.381 0.00 0.00 0.00 2.41
5963 6179 2.741878 CGAAGGTGCCCGATTCTACAAT 60.742 50.000 0.00 0.00 0.00 2.71
5964 6180 3.491964 CGAAGGTGCCCGATTCTACAATA 60.492 47.826 0.00 0.00 0.00 1.90
5965 6181 4.448210 GAAGGTGCCCGATTCTACAATAA 58.552 43.478 0.00 0.00 0.00 1.40
5966 6182 4.497291 AGGTGCCCGATTCTACAATAAA 57.503 40.909 0.00 0.00 0.00 1.40
5993 6209 3.895656 TCACCAGCTATTATAACGAGGCT 59.104 43.478 0.00 0.00 0.00 4.58
6014 6231 6.013842 GCTTGTAGTTCAGGCAAATTAGTT 57.986 37.500 0.00 0.00 46.35 2.24
6015 6232 7.141100 GCTTGTAGTTCAGGCAAATTAGTTA 57.859 36.000 0.00 0.00 46.35 2.24
6016 6233 7.244192 GCTTGTAGTTCAGGCAAATTAGTTAG 58.756 38.462 0.00 0.00 46.35 2.34
6057 6279 3.387374 AGATGAACATGCTCCAGACTAGG 59.613 47.826 0.00 0.00 0.00 3.02
6089 6311 5.086104 TCTTATGTTGGCTAGGAAGACAC 57.914 43.478 0.00 0.00 41.83 3.67
6091 6313 5.189736 TCTTATGTTGGCTAGGAAGACACAT 59.810 40.000 0.00 0.00 41.83 3.21
6107 6329 8.968242 GGAAGACACATCAAAGAATTAAAACAC 58.032 33.333 0.00 0.00 0.00 3.32
6194 6448 3.474230 GATCGGGGCATTTGCAGCG 62.474 63.158 4.74 0.00 44.36 5.18
6311 6565 2.526120 GCTCGGCGACATAAGCACC 61.526 63.158 4.99 0.00 34.86 5.01
6317 6571 1.883084 CGACATAAGCACCCTCGCC 60.883 63.158 0.00 0.00 0.00 5.54
6373 6627 5.294306 TCAAAGATTGCTAGGATGTAAAGCG 59.706 40.000 0.00 0.00 39.14 4.68
6389 6643 2.373540 AGCGGTTATGCGACTGTTTA 57.626 45.000 0.00 0.00 40.67 2.01
6392 6646 3.687698 AGCGGTTATGCGACTGTTTATTT 59.312 39.130 0.00 0.00 40.67 1.40
6396 6650 4.201980 GGTTATGCGACTGTTTATTTCCCC 60.202 45.833 0.00 0.00 0.00 4.81
6397 6651 1.828979 TGCGACTGTTTATTTCCCCC 58.171 50.000 0.00 0.00 0.00 5.40
6398 6652 0.730840 GCGACTGTTTATTTCCCCCG 59.269 55.000 0.00 0.00 0.00 5.73
6409 6663 0.609681 TTTCCCCCGTGTGGTTATGC 60.610 55.000 0.00 0.00 0.00 3.14
6458 6713 4.579869 TCACTGGTCTCCTTTTAATCAGC 58.420 43.478 0.00 0.00 0.00 4.26
6478 6733 1.131883 CGCAATTTTCTCCTGAGGCTG 59.868 52.381 0.00 0.00 0.00 4.85
6480 6735 2.881403 GCAATTTTCTCCTGAGGCTGGA 60.881 50.000 0.00 0.00 0.00 3.86
6487 6742 0.115152 TCCTGAGGCTGGAGAACTGA 59.885 55.000 0.00 0.00 0.00 3.41
6557 6825 3.564644 ACATATCCGTAGAGTTCCGTGAG 59.435 47.826 0.00 0.00 0.00 3.51
6562 6830 2.681848 CCGTAGAGTTCCGTGAGTGTAT 59.318 50.000 0.00 0.00 0.00 2.29
6579 6847 6.038161 TGAGTGTATTTGATTGGCCGAATAAG 59.962 38.462 0.00 0.00 0.00 1.73
6609 6877 7.442969 ACGTCAATAAAGGAAATGTCAACTGTA 59.557 33.333 0.00 0.00 0.00 2.74
6610 6878 8.286800 CGTCAATAAAGGAAATGTCAACTGTAA 58.713 33.333 0.00 0.00 0.00 2.41
6654 6927 1.067060 GGTGTTTTGTCAAGGCTGGTC 59.933 52.381 0.00 0.00 0.00 4.02
6659 6932 4.338118 TGTTTTGTCAAGGCTGGTCTAAAG 59.662 41.667 0.00 0.00 0.00 1.85
7214 7487 3.307242 GCAGCTCGAATCTCGTACATTTT 59.693 43.478 0.00 0.00 41.35 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.891727 CGTTGGAGATCCGGGGCG 62.892 72.222 0.00 0.00 39.43 6.13
7 8 4.547367 CCGTTGGAGATCCGGGGC 62.547 72.222 0.00 0.00 38.09 5.80
8 9 4.547367 GCCGTTGGAGATCCGGGG 62.547 72.222 0.00 0.00 41.96 5.73
9 10 4.891727 CGCCGTTGGAGATCCGGG 62.892 72.222 0.00 0.00 41.96 5.73
10 11 4.891727 CCGCCGTTGGAGATCCGG 62.892 72.222 0.00 0.00 44.46 5.14
11 12 3.833645 TCCGCCGTTGGAGATCCG 61.834 66.667 0.00 0.00 39.43 4.18
17 18 2.102109 TACTTTGCTCCGCCGTTGGA 62.102 55.000 0.00 0.00 36.37 3.53
18 19 1.231958 TTACTTTGCTCCGCCGTTGG 61.232 55.000 0.00 0.00 0.00 3.77
19 20 0.110373 GTTACTTTGCTCCGCCGTTG 60.110 55.000 0.00 0.00 0.00 4.10
20 21 1.232621 GGTTACTTTGCTCCGCCGTT 61.233 55.000 0.00 0.00 0.00 4.44
21 22 1.670083 GGTTACTTTGCTCCGCCGT 60.670 57.895 0.00 0.00 0.00 5.68
22 23 2.396157 GGGTTACTTTGCTCCGCCG 61.396 63.158 0.00 0.00 0.00 6.46
23 24 2.044555 GGGGTTACTTTGCTCCGCC 61.045 63.158 0.00 0.00 0.00 6.13
24 25 2.044555 GGGGGTTACTTTGCTCCGC 61.045 63.158 0.00 0.00 0.00 5.54
25 26 0.037734 AAGGGGGTTACTTTGCTCCG 59.962 55.000 0.00 0.00 0.00 4.63
26 27 2.619849 GGTAAGGGGGTTACTTTGCTCC 60.620 54.545 0.00 0.00 40.93 4.70
27 28 2.307980 AGGTAAGGGGGTTACTTTGCTC 59.692 50.000 0.00 0.00 40.93 4.26
28 29 2.355309 AGGTAAGGGGGTTACTTTGCT 58.645 47.619 0.00 0.00 40.93 3.91
29 30 2.893215 AGGTAAGGGGGTTACTTTGC 57.107 50.000 0.00 0.00 40.93 3.68
30 31 3.264964 TGCTAGGTAAGGGGGTTACTTTG 59.735 47.826 0.00 0.00 40.93 2.77
31 32 3.522343 CTGCTAGGTAAGGGGGTTACTTT 59.478 47.826 0.00 0.00 40.93 2.66
32 33 3.113043 CTGCTAGGTAAGGGGGTTACTT 58.887 50.000 0.00 0.00 40.93 2.24
33 34 2.760581 CTGCTAGGTAAGGGGGTTACT 58.239 52.381 0.00 0.00 40.93 2.24
34 35 1.140452 GCTGCTAGGTAAGGGGGTTAC 59.860 57.143 0.00 0.00 40.48 2.50
35 36 1.503800 GCTGCTAGGTAAGGGGGTTA 58.496 55.000 0.00 0.00 0.00 2.85
36 37 1.279749 GGCTGCTAGGTAAGGGGGTT 61.280 60.000 0.00 0.00 0.00 4.11
37 38 1.693103 GGCTGCTAGGTAAGGGGGT 60.693 63.158 0.00 0.00 0.00 4.95
38 39 1.692749 TGGCTGCTAGGTAAGGGGG 60.693 63.158 0.00 0.00 0.00 5.40
39 40 1.832912 CTGGCTGCTAGGTAAGGGG 59.167 63.158 4.94 0.00 0.00 4.79
40 41 1.147153 GCTGGCTGCTAGGTAAGGG 59.853 63.158 15.05 0.00 38.95 3.95
41 42 0.253044 TTGCTGGCTGCTAGGTAAGG 59.747 55.000 17.45 0.00 43.37 2.69
42 43 1.373570 GTTGCTGGCTGCTAGGTAAG 58.626 55.000 17.45 0.00 43.37 2.34
43 44 0.391130 CGTTGCTGGCTGCTAGGTAA 60.391 55.000 17.45 0.00 43.37 2.85
44 45 1.218047 CGTTGCTGGCTGCTAGGTA 59.782 57.895 17.45 0.00 43.37 3.08
45 46 2.046892 CGTTGCTGGCTGCTAGGT 60.047 61.111 17.45 0.00 43.37 3.08
46 47 0.955428 TTTCGTTGCTGGCTGCTAGG 60.955 55.000 17.45 14.80 43.37 3.02
47 48 0.166814 GTTTCGTTGCTGGCTGCTAG 59.833 55.000 17.45 8.84 43.37 3.42
48 49 0.533978 TGTTTCGTTGCTGGCTGCTA 60.534 50.000 17.45 7.18 43.37 3.49
49 50 1.174712 ATGTTTCGTTGCTGGCTGCT 61.175 50.000 17.45 0.00 43.37 4.24
50 51 0.730494 GATGTTTCGTTGCTGGCTGC 60.730 55.000 9.67 9.67 43.25 5.25
51 52 0.592637 TGATGTTTCGTTGCTGGCTG 59.407 50.000 0.00 0.00 0.00 4.85
52 53 1.538047 ATGATGTTTCGTTGCTGGCT 58.462 45.000 0.00 0.00 0.00 4.75
53 54 1.987770 CAATGATGTTTCGTTGCTGGC 59.012 47.619 0.00 0.00 40.85 4.85
54 55 3.495193 CTCAATGATGTTTCGTTGCTGG 58.505 45.455 3.58 0.00 44.92 4.85
55 56 2.912967 GCTCAATGATGTTTCGTTGCTG 59.087 45.455 3.58 1.54 44.92 4.41
56 57 2.816087 AGCTCAATGATGTTTCGTTGCT 59.184 40.909 3.58 0.00 44.92 3.91
57 58 3.166657 GAGCTCAATGATGTTTCGTTGC 58.833 45.455 9.40 0.00 44.92 4.17
58 59 3.725895 CGGAGCTCAATGATGTTTCGTTG 60.726 47.826 17.19 2.26 46.10 4.10
59 60 2.416547 CGGAGCTCAATGATGTTTCGTT 59.583 45.455 17.19 0.00 0.00 3.85
60 61 2.002586 CGGAGCTCAATGATGTTTCGT 58.997 47.619 17.19 0.00 0.00 3.85
61 62 2.726555 CGGAGCTCAATGATGTTTCG 57.273 50.000 17.19 1.45 0.00 3.46
76 77 2.280524 TGAACACCAACGGCGGAG 60.281 61.111 13.24 2.29 0.00 4.63
77 78 2.589442 GTGAACACCAACGGCGGA 60.589 61.111 13.24 0.00 0.00 5.54
87 88 6.575162 ATGAAAGTTTATCTGGGTGAACAC 57.425 37.500 0.00 0.00 0.00 3.32
88 89 7.521423 CGAAATGAAAGTTTATCTGGGTGAACA 60.521 37.037 0.00 0.00 0.00 3.18
89 90 6.801862 CGAAATGAAAGTTTATCTGGGTGAAC 59.198 38.462 0.00 0.00 0.00 3.18
90 91 6.072175 CCGAAATGAAAGTTTATCTGGGTGAA 60.072 38.462 0.00 0.00 0.00 3.18
91 92 5.414454 CCGAAATGAAAGTTTATCTGGGTGA 59.586 40.000 0.00 0.00 0.00 4.02
92 93 5.393027 CCCGAAATGAAAGTTTATCTGGGTG 60.393 44.000 0.00 0.00 0.00 4.61
93 94 4.705023 CCCGAAATGAAAGTTTATCTGGGT 59.295 41.667 0.00 0.00 0.00 4.51
94 95 4.705023 ACCCGAAATGAAAGTTTATCTGGG 59.295 41.667 8.00 8.00 37.77 4.45
95 96 5.648092 AGACCCGAAATGAAAGTTTATCTGG 59.352 40.000 0.00 0.00 0.00 3.86
96 97 6.183360 GGAGACCCGAAATGAAAGTTTATCTG 60.183 42.308 0.00 0.00 0.00 2.90
97 98 5.880887 GGAGACCCGAAATGAAAGTTTATCT 59.119 40.000 0.00 0.00 0.00 1.98
98 99 6.120378 GGAGACCCGAAATGAAAGTTTATC 57.880 41.667 0.00 0.00 0.00 1.75
126 127 4.416738 GGTCACCCTCTGCCCTGC 62.417 72.222 0.00 0.00 0.00 4.85
137 138 1.121378 GCTAGGTAAGGGAGGTCACC 58.879 60.000 0.00 0.00 0.00 4.02
138 139 0.745468 CGCTAGGTAAGGGAGGTCAC 59.255 60.000 0.00 0.00 40.56 3.67
139 140 0.396695 CCGCTAGGTAAGGGAGGTCA 60.397 60.000 0.00 0.00 40.56 4.02
140 141 1.746322 GCCGCTAGGTAAGGGAGGTC 61.746 65.000 0.00 0.00 40.56 3.85
141 142 1.761271 GCCGCTAGGTAAGGGAGGT 60.761 63.158 0.00 0.00 40.56 3.85
142 143 2.508751 GGCCGCTAGGTAAGGGAGG 61.509 68.421 0.00 0.00 40.56 4.30
143 144 1.749334 CTGGCCGCTAGGTAAGGGAG 61.749 65.000 0.00 0.00 40.56 4.30
144 145 1.760875 CTGGCCGCTAGGTAAGGGA 60.761 63.158 0.00 0.00 40.56 4.20
155 156 2.747507 AATGTTTCGTTGCTGGCCGC 62.748 55.000 11.92 11.92 39.77 6.53
163 164 4.334443 CGGAGCTCAATAATGTTTCGTTG 58.666 43.478 17.19 0.00 0.00 4.10
192 193 5.523438 TGGAAGTTTATTTGGGTGAACAC 57.477 39.130 0.00 0.00 0.00 3.32
195 196 6.451393 CGAAATGGAAGTTTATTTGGGTGAA 58.549 36.000 4.39 0.00 0.00 3.18
199 200 4.221924 ACCCGAAATGGAAGTTTATTTGGG 59.778 41.667 18.97 18.97 42.00 4.12
203 204 4.948004 GGAGACCCGAAATGGAAGTTTATT 59.052 41.667 0.00 0.00 42.00 1.40
231 232 4.416738 GGTCACCCTCTGCCCTGC 62.417 72.222 0.00 0.00 0.00 4.85
271 272 2.281484 GAGCTTTGGGGTGCGACA 60.281 61.111 0.00 0.00 0.00 4.35
367 371 8.827832 ATTGGTCATTTCTTCCTTGATATTGA 57.172 30.769 0.00 0.00 0.00 2.57
431 443 2.048127 AGCGGCTCCACGAGAAAC 60.048 61.111 0.00 0.00 35.47 2.78
444 456 2.094597 TGCTTGGAATTTGATTCAGCGG 60.095 45.455 3.39 0.00 39.69 5.52
445 457 2.919229 GTGCTTGGAATTTGATTCAGCG 59.081 45.455 3.39 0.00 39.69 5.18
454 466 1.270550 CTTCAGGCGTGCTTGGAATTT 59.729 47.619 0.35 0.00 0.00 1.82
500 512 2.865598 CGGGTTGGGTTGCATTGCA 61.866 57.895 7.38 7.38 36.47 4.08
501 513 2.048316 CGGGTTGGGTTGCATTGC 60.048 61.111 0.46 0.46 0.00 3.56
502 514 1.288752 GTCGGGTTGGGTTGCATTG 59.711 57.895 0.00 0.00 0.00 2.82
503 515 1.906333 GGTCGGGTTGGGTTGCATT 60.906 57.895 0.00 0.00 0.00 3.56
504 516 2.282887 GGTCGGGTTGGGTTGCAT 60.283 61.111 0.00 0.00 0.00 3.96
518 530 2.109126 GTGATGAGCGGCTTGGGTC 61.109 63.158 2.97 1.08 35.07 4.46
530 542 2.358125 CGCGGGTTGGTGTGATGA 60.358 61.111 0.00 0.00 0.00 2.92
570 595 4.295119 ACACCCGCTCCACGTGAC 62.295 66.667 19.30 5.06 41.42 3.67
642 667 2.768344 CAGGTAGGGGGTGGCGAT 60.768 66.667 0.00 0.00 0.00 4.58
653 678 5.009010 CCAGCAGTAAAATATTGGCAGGTAG 59.991 44.000 0.00 0.00 0.00 3.18
776 811 0.252467 CACCACCCTCTCTTCTCCCT 60.252 60.000 0.00 0.00 0.00 4.20
777 812 1.268283 CCACCACCCTCTCTTCTCCC 61.268 65.000 0.00 0.00 0.00 4.30
848 883 7.847487 TGTATAAATAAACGATCTTTGAGCGG 58.153 34.615 9.89 0.00 46.07 5.52
919 962 4.554036 GGAGGTGGGAGATGCGGC 62.554 72.222 0.00 0.00 0.00 6.53
921 964 2.187946 GTGGAGGTGGGAGATGCG 59.812 66.667 0.00 0.00 0.00 4.73
1156 1199 3.854669 CTCGGCGCTGGGGAAGAT 61.855 66.667 17.88 0.00 0.00 2.40
1188 1231 2.683933 TTGGGGGAGGAGACGAGC 60.684 66.667 0.00 0.00 0.00 5.03
1285 1363 4.763073 TGATCATGATCAGGACAAGACAC 58.237 43.478 30.27 4.93 42.42 3.67
1318 1396 2.016318 TGCTGACTTTTATCCGCCATG 58.984 47.619 0.00 0.00 0.00 3.66
1319 1397 2.418368 TGCTGACTTTTATCCGCCAT 57.582 45.000 0.00 0.00 0.00 4.40
1337 1415 2.082231 CTCAGCAATGTCCCTGTCTTG 58.918 52.381 0.00 0.00 0.00 3.02
1357 1435 5.868177 CGATCTGTCGGTAGAACATAAAC 57.132 43.478 0.00 0.00 44.00 2.01
1411 1500 7.406031 AATGAAGCACTGAAATCAAGATGAT 57.594 32.000 0.00 0.00 39.09 2.45
1442 1532 5.034554 TCATCTTTAAGAAAACGCAGCAG 57.965 39.130 0.00 0.00 0.00 4.24
1453 1543 9.597170 CAAGAGAGATCACAATCATCTTTAAGA 57.403 33.333 0.00 0.00 37.76 2.10
1454 1544 8.828644 CCAAGAGAGATCACAATCATCTTTAAG 58.171 37.037 0.00 0.00 37.76 1.85
1455 1545 8.324306 ACCAAGAGAGATCACAATCATCTTTAA 58.676 33.333 0.00 0.00 37.76 1.52
1457 1547 6.598457 CACCAAGAGAGATCACAATCATCTTT 59.402 38.462 0.00 0.00 37.76 2.52
1458 1548 6.114089 CACCAAGAGAGATCACAATCATCTT 58.886 40.000 0.00 0.00 39.17 2.40
1459 1549 5.189342 ACACCAAGAGAGATCACAATCATCT 59.811 40.000 0.00 0.00 33.82 2.90
1460 1550 5.293814 CACACCAAGAGAGATCACAATCATC 59.706 44.000 0.00 0.00 34.07 2.92
1461 1551 5.183969 CACACCAAGAGAGATCACAATCAT 58.816 41.667 0.00 0.00 34.07 2.45
1462 1552 4.040829 ACACACCAAGAGAGATCACAATCA 59.959 41.667 0.00 0.00 34.07 2.57
1463 1553 4.391216 CACACACCAAGAGAGATCACAATC 59.609 45.833 0.00 0.00 0.00 2.67
1464 1554 4.321718 CACACACCAAGAGAGATCACAAT 58.678 43.478 0.00 0.00 0.00 2.71
1543 1648 4.208686 AAGGCGTCGGCGATCTCC 62.209 66.667 16.53 14.56 41.24 3.71
1673 1778 5.620206 TCACAGTCTCCAGAAATGCTAAAA 58.380 37.500 0.00 0.00 0.00 1.52
1717 1824 0.675633 CCTTTGAACCACTGGCCAAG 59.324 55.000 7.01 1.66 0.00 3.61
1790 1897 1.895131 ACATTGCAATCTTGTCCCCAC 59.105 47.619 9.53 0.00 0.00 4.61
1821 1928 2.722201 ATCCTGACCGGGCTCGTTC 61.722 63.158 9.82 0.00 33.95 3.95
1824 1931 4.227134 CCATCCTGACCGGGCTCG 62.227 72.222 9.82 0.00 0.00 5.03
1946 2054 1.280421 ACCTCCAAGACCAAGAGCATC 59.720 52.381 0.00 0.00 0.00 3.91
1955 2063 0.481128 TTCCCCAAACCTCCAAGACC 59.519 55.000 0.00 0.00 0.00 3.85
2032 2142 1.507141 CCTTGCCGACACCAACACTC 61.507 60.000 0.00 0.00 0.00 3.51
2062 2172 4.039730 AGCAGCATCGGTAAGTAGATGATT 59.960 41.667 9.32 0.00 45.08 2.57
2125 2235 0.739462 TGCTTACCGAATGGACAGCG 60.739 55.000 0.00 0.00 42.97 5.18
2408 2518 5.722021 TTGTCTATGCAGTACAGAAGTCA 57.278 39.130 0.00 0.00 0.00 3.41
2510 2625 7.730332 ACCACTGACAATATATAGATCTGACCA 59.270 37.037 5.18 0.00 0.00 4.02
2512 2627 8.031864 CCACCACTGACAATATATAGATCTGAC 58.968 40.741 5.18 0.00 0.00 3.51
2671 2788 5.997746 CCTCTTCATTACAGACTGGTTTTCA 59.002 40.000 7.51 0.00 0.00 2.69
2683 2800 4.350368 TGTGTCTTGCCTCTTCATTACA 57.650 40.909 0.00 0.00 0.00 2.41
2715 2832 1.547675 GCCACCAAACATCTCTTCCCA 60.548 52.381 0.00 0.00 0.00 4.37
2722 2839 0.478072 TCACCTGCCACCAAACATCT 59.522 50.000 0.00 0.00 0.00 2.90
2807 2926 5.465532 TTTGCTGTTATTTGAGGATGCAA 57.534 34.783 0.00 0.00 37.39 4.08
2985 3104 3.447918 ACGTGATAACAGGATAACCCG 57.552 47.619 0.00 0.00 40.87 5.28
2988 3107 6.489675 TCGAGTAACGTGATAACAGGATAAC 58.510 40.000 0.00 0.00 43.13 1.89
2999 3118 8.283992 CAGAGATTAATACTCGAGTAACGTGAT 58.716 37.037 27.90 17.38 43.13 3.06
3100 3219 5.843673 TGTCTGTTGGCTTGTAATCAAAA 57.156 34.783 0.00 0.00 32.87 2.44
3379 3550 5.381174 TCAAATTTGGATTGAGCTGACAG 57.619 39.130 17.90 0.00 33.15 3.51
3459 3630 6.211184 TGTTATGAATTGTCAGGCAAAAGGAT 59.789 34.615 0.00 0.00 40.91 3.24
3468 3639 6.764308 AGTGGATTGTTATGAATTGTCAGG 57.236 37.500 0.00 0.00 37.14 3.86
3564 3738 4.893608 ACAATTAAAATCAAGCCCCACAC 58.106 39.130 0.00 0.00 0.00 3.82
3950 4125 5.163713 GGCAAATGTTGAGATCTAGTGAACC 60.164 44.000 0.00 0.00 0.00 3.62
3975 4150 4.510340 CGTGTTTACTAGAACCAGCTGTTT 59.490 41.667 13.81 4.06 37.29 2.83
3992 4167 2.940410 ACGGACAGTTCAATTCGTGTTT 59.060 40.909 0.00 0.00 0.00 2.83
4132 4307 6.899114 GCTTCTTAGCAACTTAAGCAACTAA 58.101 36.000 1.29 6.90 46.95 2.24
4169 4344 1.135083 GCTCGAGAATCTTCCGGTTGA 60.135 52.381 18.75 0.81 0.00 3.18
4175 4350 3.855858 AGAAACAGCTCGAGAATCTTCC 58.144 45.455 18.75 0.00 0.00 3.46
4288 4466 0.319211 CTCGCTGTGGTTGTTCCGTA 60.319 55.000 0.00 0.00 39.52 4.02
4299 4477 2.613595 TGGCAATAAATAGCTCGCTGTG 59.386 45.455 0.85 0.00 0.00 3.66
4340 4518 7.606456 TGTTTCATATTTGTAGTCTCCTGGTTC 59.394 37.037 0.00 0.00 0.00 3.62
4384 4568 5.643348 TGCTATCCAAATCATATTACAGCCG 59.357 40.000 0.00 0.00 0.00 5.52
4489 4676 8.131100 GTGTAACATACTGCAAAAGCATATCAT 58.869 33.333 0.00 0.00 36.32 2.45
4767 4955 3.388024 AGAAATATGAGAAGTGCCGGCTA 59.612 43.478 29.70 11.59 0.00 3.93
4771 4959 7.482654 TGAAATAGAAATATGAGAAGTGCCG 57.517 36.000 0.00 0.00 0.00 5.69
4773 4961 8.348507 CCCTTGAAATAGAAATATGAGAAGTGC 58.651 37.037 0.00 0.00 0.00 4.40
4790 4980 3.621715 GTCGCTTTATCGTCCCTTGAAAT 59.378 43.478 0.00 0.00 0.00 2.17
4796 4986 0.899720 TTGGTCGCTTTATCGTCCCT 59.100 50.000 0.00 0.00 36.96 4.20
4813 5003 9.514822 CATTTACAACAGTTAATTTTGCGATTG 57.485 29.630 0.00 0.00 0.00 2.67
4814 5004 8.220434 GCATTTACAACAGTTAATTTTGCGATT 58.780 29.630 0.00 0.00 0.00 3.34
4818 5008 8.298030 AGAGCATTTACAACAGTTAATTTTGC 57.702 30.769 0.00 0.00 0.00 3.68
4819 5009 9.683069 AGAGAGCATTTACAACAGTTAATTTTG 57.317 29.630 0.00 0.00 0.00 2.44
4820 5010 9.683069 CAGAGAGCATTTACAACAGTTAATTTT 57.317 29.630 0.00 0.00 0.00 1.82
5257 5468 6.757947 ACATGAAAATATTATTTGCTGCGCTT 59.242 30.769 9.73 0.00 0.00 4.68
5362 5577 8.356533 ACTGAATTTCTAGCAAACAACAAATG 57.643 30.769 0.00 0.00 0.00 2.32
5363 5578 8.947055 AACTGAATTTCTAGCAAACAACAAAT 57.053 26.923 0.00 0.00 0.00 2.32
5368 5583 7.333528 ACTGAACTGAATTTCTAGCAAACAA 57.666 32.000 0.00 0.00 0.00 2.83
5381 5596 4.292186 ACAGCCACATACTGAACTGAAT 57.708 40.909 0.00 0.00 38.55 2.57
5384 5599 2.095567 GCAACAGCCACATACTGAACTG 60.096 50.000 0.00 0.00 38.55 3.16
5563 5778 3.054802 AGAAGTGCAGGGAAGGTTAGATG 60.055 47.826 0.00 0.00 0.00 2.90
5644 5859 9.720769 TTGACCTGAAGTACTTCTTTTATTAGG 57.279 33.333 30.47 26.94 40.14 2.69
5805 6021 5.856126 TTCTGATCGTGTAAATCGCTTTT 57.144 34.783 0.00 0.00 0.00 2.27
5813 6029 9.549509 CGGAATTTTATTTTCTGATCGTGTAAA 57.450 29.630 0.00 0.00 32.28 2.01
5820 6036 6.149129 AGGGCGGAATTTTATTTTCTGATC 57.851 37.500 0.00 0.00 32.28 2.92
5842 6058 5.056480 TCGGATTGCATACTTCCATGTAAG 58.944 41.667 0.00 0.00 34.61 2.34
5859 6075 9.736023 GAATAGACAAATTTTAAGCATCGGATT 57.264 29.630 0.00 0.00 0.00 3.01
5922 6138 2.095819 CGCAATTTGTTTTGGGATTGGC 60.096 45.455 0.00 0.00 40.81 4.52
5928 6144 2.543430 CACCTTCGCAATTTGTTTTGGG 59.457 45.455 0.00 0.00 39.98 4.12
5947 6163 4.634443 AGTGTTTATTGTAGAATCGGGCAC 59.366 41.667 0.00 0.00 0.00 5.01
5948 6164 4.839121 AGTGTTTATTGTAGAATCGGGCA 58.161 39.130 0.00 0.00 0.00 5.36
5949 6165 5.353123 TGAAGTGTTTATTGTAGAATCGGGC 59.647 40.000 0.00 0.00 0.00 6.13
5950 6166 6.183360 GGTGAAGTGTTTATTGTAGAATCGGG 60.183 42.308 0.00 0.00 0.00 5.14
5951 6167 6.370442 TGGTGAAGTGTTTATTGTAGAATCGG 59.630 38.462 0.00 0.00 0.00 4.18
5952 6168 7.359262 TGGTGAAGTGTTTATTGTAGAATCG 57.641 36.000 0.00 0.00 0.00 3.34
5953 6169 7.119846 AGCTGGTGAAGTGTTTATTGTAGAATC 59.880 37.037 0.00 0.00 0.00 2.52
5954 6170 6.942576 AGCTGGTGAAGTGTTTATTGTAGAAT 59.057 34.615 0.00 0.00 0.00 2.40
5955 6171 6.296026 AGCTGGTGAAGTGTTTATTGTAGAA 58.704 36.000 0.00 0.00 0.00 2.10
5956 6172 5.865085 AGCTGGTGAAGTGTTTATTGTAGA 58.135 37.500 0.00 0.00 0.00 2.59
5957 6173 7.849804 ATAGCTGGTGAAGTGTTTATTGTAG 57.150 36.000 0.00 0.00 0.00 2.74
5958 6174 9.899661 ATAATAGCTGGTGAAGTGTTTATTGTA 57.100 29.630 0.00 0.00 0.00 2.41
5959 6175 8.807948 ATAATAGCTGGTGAAGTGTTTATTGT 57.192 30.769 0.00 0.00 0.00 2.71
5962 6178 9.042008 CGTTATAATAGCTGGTGAAGTGTTTAT 57.958 33.333 0.00 0.00 0.00 1.40
5963 6179 8.252417 TCGTTATAATAGCTGGTGAAGTGTTTA 58.748 33.333 0.00 0.00 0.00 2.01
5964 6180 7.101054 TCGTTATAATAGCTGGTGAAGTGTTT 58.899 34.615 0.00 0.00 0.00 2.83
5965 6181 6.636705 TCGTTATAATAGCTGGTGAAGTGTT 58.363 36.000 0.00 0.00 0.00 3.32
5966 6182 6.216801 TCGTTATAATAGCTGGTGAAGTGT 57.783 37.500 0.00 0.00 0.00 3.55
5993 6209 6.712998 TGCTAACTAATTTGCCTGAACTACAA 59.287 34.615 0.00 0.00 35.92 2.41
6057 6279 6.480320 CCTAGCCAACATAAGATTGACAGTAC 59.520 42.308 0.00 0.00 0.00 2.73
6089 6311 5.226396 TGCCCGTGTTTTAATTCTTTGATG 58.774 37.500 0.00 0.00 0.00 3.07
6091 6313 4.920640 TGCCCGTGTTTTAATTCTTTGA 57.079 36.364 0.00 0.00 0.00 2.69
6107 6329 1.743252 GAAGGAGCTCAGTTGCCCG 60.743 63.158 17.19 0.00 0.00 6.13
6194 6448 1.222936 CCAGTGGATCCTGTCTGGC 59.777 63.158 25.98 6.66 40.43 4.85
6373 6627 4.201980 GGGGAAATAAACAGTCGCATAACC 60.202 45.833 0.00 0.00 0.00 2.85
6389 6643 1.958069 GCATAACCACACGGGGGAAAT 60.958 52.381 0.00 0.00 42.91 2.17
6392 6646 2.672295 GCATAACCACACGGGGGA 59.328 61.111 0.00 0.00 42.91 4.81
6397 6651 1.231958 ACCAACCGCATAACCACACG 61.232 55.000 0.00 0.00 0.00 4.49
6398 6652 1.735571 CTACCAACCGCATAACCACAC 59.264 52.381 0.00 0.00 0.00 3.82
6409 6663 5.704053 ACTAAAATCAACCTTCTACCAACCG 59.296 40.000 0.00 0.00 0.00 4.44
6458 6713 1.131883 CAGCCTCAGGAGAAAATTGCG 59.868 52.381 0.00 0.00 0.00 4.85
6478 6733 0.868406 CACCACGCTTTCAGTTCTCC 59.132 55.000 0.00 0.00 0.00 3.71
6480 6735 2.902705 TACACCACGCTTTCAGTTCT 57.097 45.000 0.00 0.00 0.00 3.01
6487 6742 5.472137 AGAACATTACATTACACCACGCTTT 59.528 36.000 0.00 0.00 0.00 3.51
6557 6825 6.371809 TCTTATTCGGCCAATCAAATACAC 57.628 37.500 2.24 0.00 0.00 2.90
6562 6830 5.587043 ACGTATTCTTATTCGGCCAATCAAA 59.413 36.000 2.24 0.00 0.00 2.69
6579 6847 9.274065 GTTGACATTTCCTTTATTGACGTATTC 57.726 33.333 0.00 0.00 0.00 1.75
6631 6904 2.288395 CCAGCCTTGACAAAACACCATC 60.288 50.000 0.00 0.00 0.00 3.51
6665 6938 3.053619 CCTGGGGTGCTATTACCTCTTTT 60.054 47.826 0.00 0.00 41.99 2.27
7214 7487 2.183300 CGACCCCGATTCGAGCAA 59.817 61.111 7.83 0.00 38.85 3.91


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

AutoCloner maintained by Alex Coulton.