Multiple sequence alignment - TraesCS4A01G076900

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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 TraesCS4A01G076900 chr4A 100.000 3231 0 0 1 3231 75844359 75841129 0.000000e+00 5967.0
1 TraesCS4A01G076900 chr4A 95.455 154 7 0 148 301 75915510 75915357 2.490000e-61 246.0
2 TraesCS4A01G076900 chr4A 83.417 199 27 5 1322 1517 75466027 75466222 2.560000e-41 180.0
3 TraesCS4A01G076900 chr4A 79.874 159 19 7 148 299 739157929 739158081 1.590000e-18 104.0
4 TraesCS4A01G076900 chr4A 96.970 33 1 0 94 126 75844079 75844047 4.500000e-04 56.5
5 TraesCS4A01G076900 chr4A 96.970 33 1 0 281 313 75844266 75844234 4.500000e-04 56.5
6 TraesCS4A01G076900 chr4D 93.468 1975 85 22 739 2694 394379682 394377733 0.000000e+00 2892.0
7 TraesCS4A01G076900 chr4D 87.315 473 47 5 148 614 394380481 394380016 2.210000e-146 529.0
8 TraesCS4A01G076900 chr4D 96.416 279 7 2 2765 3042 394377735 394377459 1.060000e-124 457.0
9 TraesCS4A01G076900 chr4D 96.795 156 5 0 3076 3231 394377466 394377311 8.890000e-66 261.0
10 TraesCS4A01G076900 chr4D 82.915 199 28 5 1322 1517 394361889 394362084 1.190000e-39 174.0
11 TraesCS4A01G076900 chr4D 83.221 149 17 6 602 747 394379864 394379721 2.620000e-26 130.0
12 TraesCS4A01G076900 chr4D 82.171 129 16 5 165 292 213419717 213419839 1.590000e-18 104.0
13 TraesCS4A01G076900 chr4D 79.032 124 25 1 170 292 410407827 410407950 2.070000e-12 84.2
14 TraesCS4A01G076900 chr4D 86.842 76 5 4 2691 2766 441079282 441079352 2.670000e-11 80.5
15 TraesCS4A01G076900 chr4D 78.512 121 23 3 174 292 71436508 71436389 3.460000e-10 76.8
16 TraesCS4A01G076900 chr4D 88.525 61 5 2 1170 1229 81666285 81666226 4.470000e-09 73.1
17 TraesCS4A01G076900 chr4B 92.344 1463 49 28 1260 2694 484105697 484104270 0.000000e+00 2023.0
18 TraesCS4A01G076900 chr4B 95.940 468 10 3 2765 3231 484104272 484103813 0.000000e+00 750.0
19 TraesCS4A01G076900 chr4B 91.304 552 26 9 739 1268 484106272 484105721 0.000000e+00 734.0
20 TraesCS4A01G076900 chr4B 82.250 569 55 17 166 727 484107705 484107176 1.770000e-122 449.0
21 TraesCS4A01G076900 chr7D 81.863 204 29 7 1318 1517 535967325 535967524 7.170000e-37 165.0
22 TraesCS4A01G076900 chr7D 92.857 98 7 0 1 98 54789720 54789817 3.360000e-30 143.0
23 TraesCS4A01G076900 chr7D 82.677 127 20 2 1369 1494 478576071 478576196 9.480000e-21 111.0
24 TraesCS4A01G076900 chr7B 81.863 204 29 7 1318 1517 578438822 578439021 7.170000e-37 165.0
25 TraesCS4A01G076900 chr7A 81.373 204 30 7 1318 1517 617385976 617385777 3.340000e-35 159.0
26 TraesCS4A01G076900 chr7A 92.857 98 7 0 1 98 622341167 622341070 3.360000e-30 143.0
27 TraesCS4A01G076900 chr7A 80.597 134 21 4 161 292 695729718 695729848 7.380000e-17 99.0
28 TraesCS4A01G076900 chr3D 92.857 98 7 0 1 98 100211034 100210937 3.360000e-30 143.0
29 TraesCS4A01G076900 chr3D 84.375 128 17 3 168 293 289686881 289687007 4.380000e-24 122.0
30 TraesCS4A01G076900 chr1D 79.803 203 35 5 1318 1517 467611815 467611616 3.360000e-30 143.0
31 TraesCS4A01G076900 chrUn 90.816 98 9 0 1 98 85687295 85687198 7.270000e-27 132.0
32 TraesCS4A01G076900 chr5B 80.488 123 23 1 171 292 488186632 488186754 3.430000e-15 93.5
33 TraesCS4A01G076900 chr5B 82.022 89 15 1 2679 2767 315165265 315165352 1.240000e-09 75.0
34 TraesCS4A01G076900 chr5B 79.381 97 16 4 1142 1236 428963236 428963142 7.480000e-07 65.8
35 TraesCS4A01G076900 chr2B 86.250 80 5 2 2692 2770 738679248 738679174 7.430000e-12 82.4
36 TraesCS4A01G076900 chr2B 84.524 84 7 3 2687 2767 647444969 647445049 9.610000e-11 78.7
37 TraesCS4A01G076900 chr2B 80.374 107 15 6 1136 1239 531053144 531053247 3.460000e-10 76.8
38 TraesCS4A01G076900 chr1B 83.158 95 8 5 2689 2779 329483602 329483512 2.670000e-11 80.5
39 TraesCS4A01G076900 chr1B 86.076 79 3 5 2692 2767 683479781 683479854 9.610000e-11 78.7
40 TraesCS4A01G076900 chr1B 83.721 86 8 2 2685 2770 67023340 67023419 3.460000e-10 76.8
41 TraesCS4A01G076900 chr3B 82.609 92 10 5 2682 2767 60865715 60865624 3.460000e-10 76.8
42 TraesCS4A01G076900 chr3A 82.418 91 13 3 2681 2770 430526514 430526426 3.460000e-10 76.8
43 TraesCS4A01G076900 chr5D 100.000 40 0 0 1 40 68214876 68214915 1.240000e-09 75.0
44 TraesCS4A01G076900 chr5D 79.381 97 16 3 1142 1236 362664865 362664771 7.480000e-07 65.8
45 TraesCS4A01G076900 chr2D 93.617 47 3 0 1183 1229 450918284 450918330 1.610000e-08 71.3
46 TraesCS4A01G076900 chr2A 93.617 47 3 0 1183 1229 598642418 598642372 1.610000e-08 71.3
47 TraesCS4A01G076900 chr5A 79.381 97 16 3 1142 1236 463765968 463765874 7.480000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G076900 chr4A 75841129 75844359 3230 True 2026.666667 5967 97.9800 1 3231 3 chr4A.!!$R2 3230
1 TraesCS4A01G076900 chr4D 394377311 394380481 3170 True 853.800000 2892 91.4430 148 3231 5 chr4D.!!$R3 3083
2 TraesCS4A01G076900 chr4B 484103813 484107705 3892 True 989.000000 2023 90.4595 166 3231 4 chr4B.!!$R1 3065

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
884 1956 0.095935 CGCTCCAAGAATCACAAGCG 59.904 55.0 0.0 0.0 45.24 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 3352 0.86988 GAACAACAAACAGCACCGGC 60.87 55.0 0.0 0.0 41.61 6.13 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
40 41 9.665719 AAGAAAAATTGTCCAACAACAATAACT 57.334 25.926 2.94 0.00 46.49 2.24
41 42 9.097257 AGAAAAATTGTCCAACAACAATAACTG 57.903 29.630 2.94 0.00 46.49 3.16
42 43 9.092876 GAAAAATTGTCCAACAACAATAACTGA 57.907 29.630 2.94 0.00 46.49 3.41
43 44 9.442047 AAAAATTGTCCAACAACAATAACTGAA 57.558 25.926 2.94 0.00 46.49 3.02
44 45 9.612066 AAAATTGTCCAACAACAATAACTGAAT 57.388 25.926 2.94 0.00 46.49 2.57
45 46 9.612066 AAATTGTCCAACAACAATAACTGAATT 57.388 25.926 2.94 0.00 46.49 2.17
46 47 9.612066 AATTGTCCAACAACAATAACTGAATTT 57.388 25.926 2.94 0.00 46.49 1.82
47 48 8.417780 TTGTCCAACAACAATAACTGAATTTG 57.582 30.769 0.00 0.00 34.31 2.32
48 49 6.983307 TGTCCAACAACAATAACTGAATTTGG 59.017 34.615 0.00 0.00 0.00 3.28
49 50 6.423604 GTCCAACAACAATAACTGAATTTGGG 59.576 38.462 0.00 0.00 0.00 4.12
50 51 6.325028 TCCAACAACAATAACTGAATTTGGGA 59.675 34.615 0.00 0.00 0.00 4.37
51 52 7.016072 TCCAACAACAATAACTGAATTTGGGAT 59.984 33.333 0.00 0.00 0.00 3.85
52 53 7.118101 CCAACAACAATAACTGAATTTGGGATG 59.882 37.037 0.00 0.00 0.00 3.51
53 54 7.301868 ACAACAATAACTGAATTTGGGATGT 57.698 32.000 0.00 0.00 0.00 3.06
54 55 7.378181 ACAACAATAACTGAATTTGGGATGTC 58.622 34.615 0.00 0.00 0.00 3.06
55 56 7.015098 ACAACAATAACTGAATTTGGGATGTCA 59.985 33.333 0.00 0.00 0.00 3.58
56 57 7.722949 ACAATAACTGAATTTGGGATGTCAT 57.277 32.000 0.00 0.00 0.00 3.06
57 58 8.137745 ACAATAACTGAATTTGGGATGTCATT 57.862 30.769 0.00 0.00 0.00 2.57
58 59 9.253832 ACAATAACTGAATTTGGGATGTCATTA 57.746 29.630 0.00 0.00 0.00 1.90
63 64 7.558604 ACTGAATTTGGGATGTCATTAATTGG 58.441 34.615 0.00 0.00 0.00 3.16
64 65 7.399765 ACTGAATTTGGGATGTCATTAATTGGA 59.600 33.333 0.00 0.00 0.00 3.53
65 66 8.321621 TGAATTTGGGATGTCATTAATTGGAT 57.678 30.769 0.00 0.00 0.00 3.41
66 67 8.205512 TGAATTTGGGATGTCATTAATTGGATG 58.794 33.333 0.00 0.00 0.00 3.51
67 68 7.679732 ATTTGGGATGTCATTAATTGGATGT 57.320 32.000 0.00 0.00 0.00 3.06
68 69 8.780616 ATTTGGGATGTCATTAATTGGATGTA 57.219 30.769 0.00 0.00 0.00 2.29
69 70 7.822161 TTGGGATGTCATTAATTGGATGTAG 57.178 36.000 0.00 0.00 0.00 2.74
70 71 7.147958 TGGGATGTCATTAATTGGATGTAGA 57.852 36.000 0.00 0.00 0.00 2.59
71 72 7.758609 TGGGATGTCATTAATTGGATGTAGAT 58.241 34.615 0.00 0.00 0.00 1.98
72 73 8.226810 TGGGATGTCATTAATTGGATGTAGATT 58.773 33.333 0.00 0.00 0.00 2.40
73 74 9.082313 GGGATGTCATTAATTGGATGTAGATTT 57.918 33.333 0.00 0.00 0.00 2.17
80 81 9.669353 CATTAATTGGATGTAGATTTACTGTGC 57.331 33.333 0.00 0.00 0.00 4.57
81 82 9.632638 ATTAATTGGATGTAGATTTACTGTGCT 57.367 29.630 0.00 0.00 0.00 4.40
82 83 6.932356 ATTGGATGTAGATTTACTGTGCTG 57.068 37.500 0.00 0.00 0.00 4.41
83 84 4.191544 TGGATGTAGATTTACTGTGCTGC 58.808 43.478 0.00 0.00 0.00 5.25
84 85 3.561725 GGATGTAGATTTACTGTGCTGCC 59.438 47.826 0.00 0.00 0.00 4.85
85 86 3.694043 TGTAGATTTACTGTGCTGCCA 57.306 42.857 0.00 0.00 0.00 4.92
86 87 4.014569 TGTAGATTTACTGTGCTGCCAA 57.985 40.909 0.00 0.00 0.00 4.52
87 88 3.751175 TGTAGATTTACTGTGCTGCCAAC 59.249 43.478 0.00 0.00 0.00 3.77
88 89 2.862541 AGATTTACTGTGCTGCCAACA 58.137 42.857 0.00 0.00 0.00 3.33
89 90 3.221771 AGATTTACTGTGCTGCCAACAA 58.778 40.909 0.00 0.00 0.00 2.83
90 91 3.828451 AGATTTACTGTGCTGCCAACAAT 59.172 39.130 0.00 0.00 0.00 2.71
91 92 5.009631 AGATTTACTGTGCTGCCAACAATA 58.990 37.500 0.00 0.00 0.00 1.90
92 93 5.476599 AGATTTACTGTGCTGCCAACAATAA 59.523 36.000 0.00 0.00 0.00 1.40
93 94 4.497473 TTACTGTGCTGCCAACAATAAC 57.503 40.909 0.00 0.00 0.00 1.89
94 95 2.586425 ACTGTGCTGCCAACAATAACT 58.414 42.857 0.00 0.00 0.00 2.24
95 96 2.958355 ACTGTGCTGCCAACAATAACTT 59.042 40.909 0.00 0.00 0.00 2.66
96 97 3.384467 ACTGTGCTGCCAACAATAACTTT 59.616 39.130 0.00 0.00 0.00 2.66
97 98 3.715495 TGTGCTGCCAACAATAACTTTG 58.285 40.909 0.00 0.00 0.00 2.77
98 99 3.131933 TGTGCTGCCAACAATAACTTTGT 59.868 39.130 0.00 0.00 0.00 2.83
99 100 3.735746 GTGCTGCCAACAATAACTTTGTC 59.264 43.478 0.00 0.00 0.00 3.18
100 101 2.979813 GCTGCCAACAATAACTTTGTCG 59.020 45.455 0.00 0.00 0.00 4.35
101 102 3.304391 GCTGCCAACAATAACTTTGTCGA 60.304 43.478 0.00 0.00 0.00 4.20
102 103 4.791411 GCTGCCAACAATAACTTTGTCGAA 60.791 41.667 0.00 0.00 0.00 3.71
103 104 5.250235 TGCCAACAATAACTTTGTCGAAA 57.750 34.783 0.00 0.00 0.00 3.46
104 105 5.651530 TGCCAACAATAACTTTGTCGAAAA 58.348 33.333 0.00 0.00 0.00 2.29
105 106 5.746245 TGCCAACAATAACTTTGTCGAAAAG 59.254 36.000 14.52 14.52 0.00 2.27
106 107 5.746721 GCCAACAATAACTTTGTCGAAAAGT 59.253 36.000 15.47 15.47 41.82 2.66
107 108 6.913673 GCCAACAATAACTTTGTCGAAAAGTA 59.086 34.615 19.19 11.82 39.36 2.24
108 109 7.096763 GCCAACAATAACTTTGTCGAAAAGTAC 60.097 37.037 19.19 0.00 39.36 2.73
109 110 7.911205 CCAACAATAACTTTGTCGAAAAGTACA 59.089 33.333 19.19 13.48 39.36 2.90
110 111 9.279904 CAACAATAACTTTGTCGAAAAGTACAA 57.720 29.630 19.19 12.06 39.36 2.41
112 113 9.659830 ACAATAACTTTGTCGAAAAGTACAATC 57.340 29.630 19.19 0.00 39.36 2.67
113 114 9.658475 CAATAACTTTGTCGAAAAGTACAATCA 57.342 29.630 19.19 7.48 39.36 2.57
117 118 8.560576 ACTTTGTCGAAAAGTACAATCATTTG 57.439 30.769 18.11 0.00 38.58 2.32
119 120 8.918961 TTTGTCGAAAAGTACAATCATTTGTT 57.081 26.923 0.00 0.00 43.57 2.83
120 121 7.906611 TGTCGAAAAGTACAATCATTTGTTG 57.093 32.000 0.00 0.00 43.57 3.33
121 122 7.698628 TGTCGAAAAGTACAATCATTTGTTGA 58.301 30.769 0.00 0.00 43.57 3.18
123 124 9.820229 GTCGAAAAGTACAATCATTTGTTGATA 57.180 29.630 0.00 0.00 44.51 2.15
129 130 9.912634 AAGTACAATCATTTGTTGATAACCTTG 57.087 29.630 0.00 0.00 44.51 3.61
130 131 9.077885 AGTACAATCATTTGTTGATAACCTTGT 57.922 29.630 0.00 0.00 44.51 3.16
131 132 9.341899 GTACAATCATTTGTTGATAACCTTGTC 57.658 33.333 0.00 0.00 44.51 3.18
132 133 7.950512 ACAATCATTTGTTGATAACCTTGTCA 58.049 30.769 0.00 0.00 44.51 3.58
133 134 8.587608 ACAATCATTTGTTGATAACCTTGTCAT 58.412 29.630 0.00 0.00 44.51 3.06
134 135 9.426837 CAATCATTTGTTGATAACCTTGTCATT 57.573 29.630 0.00 0.00 44.51 2.57
139 140 9.787532 ATTTGTTGATAACCTTGTCATTAATCG 57.212 29.630 0.00 0.00 0.00 3.34
140 141 7.315247 TGTTGATAACCTTGTCATTAATCGG 57.685 36.000 0.00 0.00 0.00 4.18
141 142 6.183360 TGTTGATAACCTTGTCATTAATCGGC 60.183 38.462 0.00 0.00 0.00 5.54
142 143 5.432645 TGATAACCTTGTCATTAATCGGCA 58.567 37.500 0.00 0.00 0.00 5.69
143 144 5.883115 TGATAACCTTGTCATTAATCGGCAA 59.117 36.000 5.30 5.30 0.00 4.52
144 145 6.375736 TGATAACCTTGTCATTAATCGGCAAA 59.624 34.615 6.45 0.00 0.00 3.68
145 146 5.461032 AACCTTGTCATTAATCGGCAAAA 57.539 34.783 6.45 0.00 0.00 2.44
146 147 5.461032 ACCTTGTCATTAATCGGCAAAAA 57.539 34.783 6.45 0.00 0.00 1.94
150 151 6.368516 CCTTGTCATTAATCGGCAAAAATTGT 59.631 34.615 6.45 0.00 0.00 2.71
168 169 5.799681 ATTGTTCTTTGCTGGTGTTTTTG 57.200 34.783 0.00 0.00 0.00 2.44
181 183 0.365186 GTTTTTGTGTGTGTGTGCGC 59.635 50.000 0.00 0.00 0.00 6.09
211 213 7.500892 TGTTGGTTGTGTTCATTCTAACTATGT 59.499 33.333 0.00 0.00 0.00 2.29
236 238 1.597937 GCTTGTGTGTGCTTACTGTGC 60.598 52.381 0.00 0.00 0.00 4.57
237 239 0.655208 TTGTGTGTGCTTACTGTGCG 59.345 50.000 0.00 0.00 0.00 5.34
280 282 9.936759 TTCATTTTGAGTAAATAAAATCCACCC 57.063 29.630 0.00 0.00 35.07 4.61
284 286 9.771534 TTTTGAGTAAATAAAATCCACCCTTTG 57.228 29.630 0.00 0.00 0.00 2.77
307 309 7.906611 TGTCGAAAAGTACAATCATTTGTTG 57.093 32.000 0.00 0.00 43.57 3.33
313 315 8.506140 AAAAGTACAATCATTTGTTGATCACG 57.494 30.769 0.00 0.00 44.51 4.35
340 342 2.029623 CTAACTCGATCCTCGGGGAAA 58.970 52.381 8.88 0.00 46.41 3.13
363 365 3.434319 CAGCACACGGTGATGGCC 61.434 66.667 16.29 0.00 44.80 5.36
371 373 1.452651 CGGTGATGGCCAGCTTCAT 60.453 57.895 23.69 0.00 40.94 2.57
374 376 1.135721 GGTGATGGCCAGCTTCATTTC 59.864 52.381 23.69 7.19 40.01 2.17
434 436 7.066163 TGCAGATGACATCAAACGATAGAATTT 59.934 33.333 17.57 0.00 41.38 1.82
446 448 5.989477 ACGATAGAATTTCATCCACCTGAA 58.011 37.500 0.00 0.00 41.38 3.02
448 450 6.051717 CGATAGAATTTCATCCACCTGAAGT 58.948 40.000 0.00 0.00 35.66 3.01
506 508 6.294065 CCCTCGTGGTATACAGACTAATTCTC 60.294 46.154 5.01 0.00 28.96 2.87
526 528 6.240549 TCTCTATCTGGAAAATTCACTCCC 57.759 41.667 0.00 0.00 0.00 4.30
527 529 5.966935 TCTCTATCTGGAAAATTCACTCCCT 59.033 40.000 0.00 0.00 0.00 4.20
528 530 5.994250 TCTATCTGGAAAATTCACTCCCTG 58.006 41.667 0.00 0.00 0.00 4.45
529 531 2.795329 TCTGGAAAATTCACTCCCTGC 58.205 47.619 0.00 0.00 0.00 4.85
530 532 2.108075 TCTGGAAAATTCACTCCCTGCA 59.892 45.455 0.00 0.00 0.00 4.41
531 533 3.094572 CTGGAAAATTCACTCCCTGCAT 58.905 45.455 0.00 0.00 0.00 3.96
532 534 2.827322 TGGAAAATTCACTCCCTGCATG 59.173 45.455 0.00 0.00 0.00 4.06
547 549 4.454847 CCCTGCATGCATAGACTAATTCAG 59.545 45.833 22.97 4.20 0.00 3.02
556 558 6.162777 GCATAGACTAATTCAGGAGCTAAGG 58.837 44.000 0.00 0.00 0.00 2.69
559 565 5.524535 AGACTAATTCAGGAGCTAAGGAGT 58.475 41.667 0.00 0.00 0.00 3.85
564 570 5.799827 ATTCAGGAGCTAAGGAGTATCAC 57.200 43.478 0.00 0.00 36.25 3.06
565 571 3.567397 TCAGGAGCTAAGGAGTATCACC 58.433 50.000 0.00 0.00 36.25 4.02
572 578 5.431765 AGCTAAGGAGTATCACCAACAATG 58.568 41.667 0.00 0.00 36.25 2.82
574 580 5.525378 GCTAAGGAGTATCACCAACAATGAG 59.475 44.000 0.00 0.00 36.25 2.90
599 606 0.103937 CAAAGAAAAGCACCGCCCAA 59.896 50.000 0.00 0.00 0.00 4.12
614 785 0.171007 CCCAACCGCATCATCAACAC 59.829 55.000 0.00 0.00 0.00 3.32
616 787 1.401409 CCAACCGCATCATCAACACAC 60.401 52.381 0.00 0.00 0.00 3.82
628 799 2.553086 TCAACACACAAACGTACTCCC 58.447 47.619 0.00 0.00 0.00 4.30
635 806 1.301165 AAACGTACTCCCACACGCC 60.301 57.895 0.00 0.00 41.80 5.68
638 812 1.445582 CGTACTCCCACACGCCTTC 60.446 63.158 0.00 0.00 0.00 3.46
639 813 1.874345 CGTACTCCCACACGCCTTCT 61.874 60.000 0.00 0.00 0.00 2.85
642 816 1.079543 CTCCCACACGCCTTCTGAG 60.080 63.158 0.00 0.00 0.00 3.35
648 822 2.451132 CACACGCCTTCTGAGTATACG 58.549 52.381 0.00 0.00 0.00 3.06
650 824 1.065701 CACGCCTTCTGAGTATACGCT 59.934 52.381 8.14 0.00 0.00 5.07
655 829 4.492570 CGCCTTCTGAGTATACGCTTTTTG 60.493 45.833 8.14 0.00 0.00 2.44
656 830 4.201822 GCCTTCTGAGTATACGCTTTTTGG 60.202 45.833 8.14 5.35 0.00 3.28
659 833 6.316390 CCTTCTGAGTATACGCTTTTTGGAAT 59.684 38.462 8.14 0.00 0.00 3.01
662 836 8.780846 TCTGAGTATACGCTTTTTGGAATAAA 57.219 30.769 8.14 0.00 0.00 1.40
663 837 9.391006 TCTGAGTATACGCTTTTTGGAATAAAT 57.609 29.630 8.14 0.00 0.00 1.40
737 1756 7.067532 TCAGCACATAGTTTATGGTTTTACG 57.932 36.000 1.61 0.00 40.47 3.18
814 1886 3.561143 AGAGCGAGTCCACTCATATTCT 58.439 45.455 7.48 1.62 43.00 2.40
884 1956 0.095935 CGCTCCAAGAATCACAAGCG 59.904 55.000 0.00 0.00 45.24 4.68
949 2025 1.851666 GAGCAAGCGAAAGAGAGATCG 59.148 52.381 0.00 0.00 41.81 3.69
1006 2090 1.268743 GGTAGCAAATCAAGATGGCGC 60.269 52.381 0.00 0.00 0.00 6.53
1018 2102 4.722535 TGGCGCCTCCTTCTCCCT 62.723 66.667 29.70 0.00 35.26 4.20
1115 2199 2.825836 CCCGGCCTACTACGACGT 60.826 66.667 5.52 5.52 0.00 4.34
1146 2230 3.170585 GTCTACGACACGGTGCGC 61.171 66.667 19.59 0.00 32.09 6.09
1234 2318 1.401530 CGACTGCTTCGTCAACGTAA 58.598 50.000 2.09 0.00 43.24 3.18
1236 2320 1.124477 GACTGCTTCGTCAACGTAAGC 59.876 52.381 21.73 21.73 44.58 3.09
1518 2635 3.749064 GTCTCCGTCGAGCTGGCA 61.749 66.667 0.00 0.00 35.94 4.92
1624 2741 0.320508 GGACACCCTCAACGTCCTTC 60.321 60.000 0.00 0.00 44.82 3.46
1683 2800 2.582978 GTCGCCCTCCAAGGTACC 59.417 66.667 2.73 2.73 31.93 3.34
1699 2816 0.389296 TACCACGACGCACTCCATTG 60.389 55.000 0.00 0.00 0.00 2.82
1804 2921 1.150567 CGCTTCATCTTCCAGGAGCG 61.151 60.000 0.35 0.35 38.15 5.03
1843 2960 0.689623 AGTGCAGGTTCTTCCAGGAG 59.310 55.000 0.00 0.00 39.02 3.69
2011 3128 3.067106 CAACAGCTACTACCACAACCTG 58.933 50.000 0.00 0.00 0.00 4.00
2235 3352 0.368227 GTGAACAGAAGCTGATCGCG 59.632 55.000 0.00 0.00 45.59 5.87
2263 3380 3.859386 GCTGTTTGTTGTTCAAAGGAGTG 59.141 43.478 0.00 0.00 45.15 3.51
2330 3461 5.063204 TCACGAATGGTCATTGAAGAGTTT 58.937 37.500 0.43 0.00 0.00 2.66
2472 3616 7.407393 AAGACAATAACTAGTCACCTAGGAC 57.593 40.000 17.98 3.77 44.25 3.85
2536 3680 3.499918 GCTAAGCAAGAGAAACTCAAGCA 59.500 43.478 14.20 0.00 35.85 3.91
2537 3681 4.155644 GCTAAGCAAGAGAAACTCAAGCAT 59.844 41.667 14.20 7.76 35.85 3.79
2538 3682 4.500603 AAGCAAGAGAAACTCAAGCATG 57.499 40.909 14.20 0.00 35.85 4.06
2539 3683 2.228343 AGCAAGAGAAACTCAAGCATGC 59.772 45.455 10.51 10.51 35.85 4.06
2540 3684 2.228343 GCAAGAGAAACTCAAGCATGCT 59.772 45.455 16.30 16.30 34.38 3.79
2541 3685 3.305199 GCAAGAGAAACTCAAGCATGCTT 60.305 43.478 27.21 27.21 34.38 3.91
2542 3686 4.474113 CAAGAGAAACTCAAGCATGCTTC 58.526 43.478 29.81 17.62 33.42 3.86
2543 3687 2.740981 AGAGAAACTCAAGCATGCTTCG 59.259 45.455 29.81 23.83 33.42 3.79
2544 3688 2.738846 GAGAAACTCAAGCATGCTTCGA 59.261 45.455 29.81 25.42 33.42 3.71
2545 3689 2.740981 AGAAACTCAAGCATGCTTCGAG 59.259 45.455 34.07 34.07 33.42 4.04
2546 3690 2.175878 AACTCAAGCATGCTTCGAGT 57.824 45.000 34.92 34.92 38.55 4.18
2548 3692 1.274728 ACTCAAGCATGCTTCGAGTCT 59.725 47.619 34.92 24.38 31.39 3.24
2549 3693 2.493675 ACTCAAGCATGCTTCGAGTCTA 59.506 45.455 34.92 17.32 31.39 2.59
2550 3694 3.056536 ACTCAAGCATGCTTCGAGTCTAA 60.057 43.478 34.92 16.52 31.39 2.10
2551 3695 3.925379 TCAAGCATGCTTCGAGTCTAAA 58.075 40.909 29.81 5.69 33.42 1.85
2552 3696 4.507710 TCAAGCATGCTTCGAGTCTAAAT 58.492 39.130 29.81 1.69 33.42 1.40
2553 3697 4.568359 TCAAGCATGCTTCGAGTCTAAATC 59.432 41.667 29.81 0.00 33.42 2.17
2554 3698 4.399004 AGCATGCTTCGAGTCTAAATCT 57.601 40.909 16.30 0.00 0.00 2.40
2555 3699 4.764172 AGCATGCTTCGAGTCTAAATCTT 58.236 39.130 16.30 0.00 0.00 2.40
2556 3700 4.808364 AGCATGCTTCGAGTCTAAATCTTC 59.192 41.667 16.30 0.00 0.00 2.87
2557 3701 4.568359 GCATGCTTCGAGTCTAAATCTTCA 59.432 41.667 11.37 0.00 0.00 3.02
2558 3702 5.501574 GCATGCTTCGAGTCTAAATCTTCAC 60.502 44.000 11.37 0.00 0.00 3.18
2559 3703 4.166523 TGCTTCGAGTCTAAATCTTCACG 58.833 43.478 0.00 0.00 0.00 4.35
2560 3704 4.167268 GCTTCGAGTCTAAATCTTCACGT 58.833 43.478 0.00 0.00 0.00 4.49
2561 3705 4.621886 GCTTCGAGTCTAAATCTTCACGTT 59.378 41.667 0.00 0.00 0.00 3.99
2562 3706 5.798934 GCTTCGAGTCTAAATCTTCACGTTA 59.201 40.000 0.00 0.00 0.00 3.18
2563 3707 6.472808 GCTTCGAGTCTAAATCTTCACGTTAT 59.527 38.462 0.00 0.00 0.00 1.89
2621 3765 7.818493 TCGAGTCTAAATCTTCATGTTTCTG 57.182 36.000 0.00 0.00 0.00 3.02
2642 3786 6.228995 TCTGATGGCTGATAACATCTCAATC 58.771 40.000 0.00 0.00 42.96 2.67
2649 3793 5.464722 GCTGATAACATCTCAATCGTCACAT 59.535 40.000 0.00 0.00 0.00 3.21
2683 3829 7.413438 GGTTAATTAGCTGACAGATGACAACTG 60.413 40.741 6.65 10.91 40.68 3.16
2691 3837 6.591834 GCTGACAGATGACAACTGTAATAACT 59.408 38.462 17.34 0.00 46.57 2.24
2692 3838 7.759886 GCTGACAGATGACAACTGTAATAACTA 59.240 37.037 17.34 0.21 46.57 2.24
2693 3839 8.981724 TGACAGATGACAACTGTAATAACTAC 57.018 34.615 17.34 4.55 46.57 2.73
2694 3840 8.803235 TGACAGATGACAACTGTAATAACTACT 58.197 33.333 17.34 0.00 46.57 2.57
2695 3841 9.291664 GACAGATGACAACTGTAATAACTACTC 57.708 37.037 17.34 0.00 46.57 2.59
2696 3842 8.251721 ACAGATGACAACTGTAATAACTACTCC 58.748 37.037 16.01 0.00 45.10 3.85
2697 3843 7.707035 CAGATGACAACTGTAATAACTACTCCC 59.293 40.741 4.61 0.00 0.00 4.30
2698 3844 7.620094 AGATGACAACTGTAATAACTACTCCCT 59.380 37.037 0.00 0.00 0.00 4.20
2699 3845 7.166691 TGACAACTGTAATAACTACTCCCTC 57.833 40.000 0.00 0.00 0.00 4.30
2700 3846 6.154021 TGACAACTGTAATAACTACTCCCTCC 59.846 42.308 0.00 0.00 0.00 4.30
2701 3847 5.126707 ACAACTGTAATAACTACTCCCTCCG 59.873 44.000 0.00 0.00 0.00 4.63
2702 3848 4.864726 ACTGTAATAACTACTCCCTCCGT 58.135 43.478 0.00 0.00 0.00 4.69
2703 3849 6.006275 ACTGTAATAACTACTCCCTCCGTA 57.994 41.667 0.00 0.00 0.00 4.02
2704 3850 6.426587 ACTGTAATAACTACTCCCTCCGTAA 58.573 40.000 0.00 0.00 0.00 3.18
2705 3851 6.891908 ACTGTAATAACTACTCCCTCCGTAAA 59.108 38.462 0.00 0.00 0.00 2.01
2706 3852 7.067981 ACTGTAATAACTACTCCCTCCGTAAAG 59.932 40.741 0.00 0.00 0.00 1.85
2707 3853 7.118723 TGTAATAACTACTCCCTCCGTAAAGA 58.881 38.462 0.00 0.00 0.00 2.52
2708 3854 7.615365 TGTAATAACTACTCCCTCCGTAAAGAA 59.385 37.037 0.00 0.00 0.00 2.52
2709 3855 7.486407 AATAACTACTCCCTCCGTAAAGAAA 57.514 36.000 0.00 0.00 0.00 2.52
2710 3856 7.672122 ATAACTACTCCCTCCGTAAAGAAAT 57.328 36.000 0.00 0.00 0.00 2.17
2711 3857 8.773033 ATAACTACTCCCTCCGTAAAGAAATA 57.227 34.615 0.00 0.00 0.00 1.40
2712 3858 7.672122 AACTACTCCCTCCGTAAAGAAATAT 57.328 36.000 0.00 0.00 0.00 1.28
2713 3859 8.773033 AACTACTCCCTCCGTAAAGAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
2714 3860 8.773033 ACTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
2715 3861 9.205513 ACTACTCCCTCCGTAAAGAAATATAAA 57.794 33.333 0.00 0.00 0.00 1.40
2716 3862 9.694137 CTACTCCCTCCGTAAAGAAATATAAAG 57.306 37.037 0.00 0.00 0.00 1.85
2717 3863 7.506971 ACTCCCTCCGTAAAGAAATATAAAGG 58.493 38.462 0.00 0.00 0.00 3.11
2718 3864 6.293698 TCCCTCCGTAAAGAAATATAAAGGC 58.706 40.000 0.00 0.00 0.00 4.35
2719 3865 6.059484 CCCTCCGTAAAGAAATATAAAGGCA 58.941 40.000 0.00 0.00 0.00 4.75
2720 3866 6.715264 CCCTCCGTAAAGAAATATAAAGGCAT 59.285 38.462 0.00 0.00 0.00 4.40
2721 3867 7.230712 CCCTCCGTAAAGAAATATAAAGGCATT 59.769 37.037 0.00 0.00 0.00 3.56
2722 3868 8.630037 CCTCCGTAAAGAAATATAAAGGCATTT 58.370 33.333 0.53 0.53 0.00 2.32
2738 3884 7.772332 AAGGCATTTAGTTTAGATCACTACG 57.228 36.000 0.00 0.00 0.00 3.51
2739 3885 5.753921 AGGCATTTAGTTTAGATCACTACGC 59.246 40.000 0.00 0.00 0.00 4.42
2740 3886 5.753921 GGCATTTAGTTTAGATCACTACGCT 59.246 40.000 0.00 0.00 0.00 5.07
2741 3887 6.074249 GGCATTTAGTTTAGATCACTACGCTC 60.074 42.308 0.00 0.00 0.00 5.03
2742 3888 6.697892 GCATTTAGTTTAGATCACTACGCTCT 59.302 38.462 0.00 0.00 0.00 4.09
2743 3889 7.222999 GCATTTAGTTTAGATCACTACGCTCTT 59.777 37.037 0.00 0.00 0.00 2.85
2744 3890 9.731819 CATTTAGTTTAGATCACTACGCTCTTA 57.268 33.333 0.00 0.00 0.00 2.10
2760 3906 9.828852 CTACGCTCTTATATTAGTTTACAGAGG 57.171 37.037 0.00 0.00 0.00 3.69
2761 3907 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2762 3908 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2763 3909 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2796 3942 7.385267 AGAGCAGAAATTATACCATGCTAGAG 58.615 38.462 0.00 0.00 43.61 2.43
2797 3943 7.234371 AGAGCAGAAATTATACCATGCTAGAGA 59.766 37.037 0.00 0.00 43.61 3.10
2942 4089 2.665165 TGATTATTTGGCGGCTGGAAT 58.335 42.857 11.43 10.39 0.00 3.01
2988 4135 2.679837 CAACATCTGGAATTGTCTCCGG 59.320 50.000 0.00 0.00 42.51 5.14
3148 4295 0.179100 GGCGCTGCTTGTATCTCTCA 60.179 55.000 7.64 0.00 0.00 3.27
3192 4339 4.666402 GCGCAATCTGCCAAACAAAATTAC 60.666 41.667 0.30 0.00 41.12 1.89
3228 4375 4.985538 ACTAACTCAAAATCCAGCCAAGA 58.014 39.130 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.665719 AGTTATTGTTGTTGGACAATTTTTCTT 57.334 25.926 8.35 0.00 45.38 2.52
15 16 9.097257 CAGTTATTGTTGTTGGACAATTTTTCT 57.903 29.630 8.35 1.58 45.38 2.52
16 17 9.092876 TCAGTTATTGTTGTTGGACAATTTTTC 57.907 29.630 8.35 0.00 45.38 2.29
17 18 9.442047 TTCAGTTATTGTTGTTGGACAATTTTT 57.558 25.926 8.35 0.00 45.38 1.94
18 19 9.612066 ATTCAGTTATTGTTGTTGGACAATTTT 57.388 25.926 8.35 0.00 45.38 1.82
19 20 9.612066 AATTCAGTTATTGTTGTTGGACAATTT 57.388 25.926 8.35 0.00 45.38 1.82
20 21 9.612066 AAATTCAGTTATTGTTGTTGGACAATT 57.388 25.926 8.35 0.00 45.38 2.32
22 23 7.493971 CCAAATTCAGTTATTGTTGTTGGACAA 59.506 33.333 0.00 0.00 43.08 3.18
23 24 6.983307 CCAAATTCAGTTATTGTTGTTGGACA 59.017 34.615 0.00 0.00 35.60 4.02
24 25 6.423604 CCCAAATTCAGTTATTGTTGTTGGAC 59.576 38.462 0.00 0.00 35.60 4.02
25 26 6.325028 TCCCAAATTCAGTTATTGTTGTTGGA 59.675 34.615 0.00 0.00 35.60 3.53
26 27 6.520272 TCCCAAATTCAGTTATTGTTGTTGG 58.480 36.000 0.00 0.00 34.48 3.77
27 28 7.656948 ACATCCCAAATTCAGTTATTGTTGTTG 59.343 33.333 0.00 0.00 0.00 3.33
28 29 7.734942 ACATCCCAAATTCAGTTATTGTTGTT 58.265 30.769 0.00 0.00 0.00 2.83
29 30 7.015098 TGACATCCCAAATTCAGTTATTGTTGT 59.985 33.333 0.00 0.00 0.00 3.32
30 31 7.377398 TGACATCCCAAATTCAGTTATTGTTG 58.623 34.615 0.00 0.00 0.00 3.33
31 32 7.537596 TGACATCCCAAATTCAGTTATTGTT 57.462 32.000 0.00 0.00 0.00 2.83
32 33 7.722949 ATGACATCCCAAATTCAGTTATTGT 57.277 32.000 0.00 0.00 0.00 2.71
37 38 8.042515 CCAATTAATGACATCCCAAATTCAGTT 58.957 33.333 0.00 0.00 0.00 3.16
38 39 7.399765 TCCAATTAATGACATCCCAAATTCAGT 59.600 33.333 0.00 0.00 0.00 3.41
39 40 7.784037 TCCAATTAATGACATCCCAAATTCAG 58.216 34.615 0.00 0.00 0.00 3.02
40 41 7.730672 TCCAATTAATGACATCCCAAATTCA 57.269 32.000 0.00 0.00 0.00 2.57
41 42 8.206189 ACATCCAATTAATGACATCCCAAATTC 58.794 33.333 6.93 0.00 0.00 2.17
42 43 8.093118 ACATCCAATTAATGACATCCCAAATT 57.907 30.769 6.93 0.00 0.00 1.82
43 44 7.679732 ACATCCAATTAATGACATCCCAAAT 57.320 32.000 6.93 0.00 0.00 2.32
44 45 8.058235 TCTACATCCAATTAATGACATCCCAAA 58.942 33.333 6.93 0.00 0.00 3.28
45 46 7.581814 TCTACATCCAATTAATGACATCCCAA 58.418 34.615 6.93 0.00 0.00 4.12
46 47 7.147958 TCTACATCCAATTAATGACATCCCA 57.852 36.000 6.93 0.00 0.00 4.37
47 48 8.641498 AATCTACATCCAATTAATGACATCCC 57.359 34.615 6.93 0.00 0.00 3.85
54 55 9.669353 GCACAGTAAATCTACATCCAATTAATG 57.331 33.333 0.00 0.00 0.00 1.90
55 56 9.632638 AGCACAGTAAATCTACATCCAATTAAT 57.367 29.630 0.00 0.00 0.00 1.40
56 57 8.892723 CAGCACAGTAAATCTACATCCAATTAA 58.107 33.333 0.00 0.00 0.00 1.40
57 58 7.012327 GCAGCACAGTAAATCTACATCCAATTA 59.988 37.037 0.00 0.00 0.00 1.40
58 59 6.183360 GCAGCACAGTAAATCTACATCCAATT 60.183 38.462 0.00 0.00 0.00 2.32
59 60 5.297776 GCAGCACAGTAAATCTACATCCAAT 59.702 40.000 0.00 0.00 0.00 3.16
60 61 4.635765 GCAGCACAGTAAATCTACATCCAA 59.364 41.667 0.00 0.00 0.00 3.53
61 62 4.191544 GCAGCACAGTAAATCTACATCCA 58.808 43.478 0.00 0.00 0.00 3.41
62 63 3.561725 GGCAGCACAGTAAATCTACATCC 59.438 47.826 0.00 0.00 0.00 3.51
63 64 4.191544 TGGCAGCACAGTAAATCTACATC 58.808 43.478 0.00 0.00 0.00 3.06
64 65 4.220693 TGGCAGCACAGTAAATCTACAT 57.779 40.909 0.00 0.00 0.00 2.29
65 66 3.694043 TGGCAGCACAGTAAATCTACA 57.306 42.857 0.00 0.00 0.00 2.74
66 67 3.751175 TGTTGGCAGCACAGTAAATCTAC 59.249 43.478 0.00 0.00 0.00 2.59
67 68 4.014569 TGTTGGCAGCACAGTAAATCTA 57.985 40.909 0.00 0.00 0.00 1.98
68 69 2.862541 TGTTGGCAGCACAGTAAATCT 58.137 42.857 0.00 0.00 0.00 2.40
69 70 3.641437 TTGTTGGCAGCACAGTAAATC 57.359 42.857 2.60 0.00 0.00 2.17
70 71 5.243730 AGTTATTGTTGGCAGCACAGTAAAT 59.756 36.000 2.60 2.77 30.70 1.40
71 72 4.582656 AGTTATTGTTGGCAGCACAGTAAA 59.417 37.500 2.60 0.00 30.70 2.01
72 73 4.141287 AGTTATTGTTGGCAGCACAGTAA 58.859 39.130 2.60 3.41 0.00 2.24
73 74 3.750371 AGTTATTGTTGGCAGCACAGTA 58.250 40.909 2.60 0.00 0.00 2.74
74 75 2.586425 AGTTATTGTTGGCAGCACAGT 58.414 42.857 2.60 0.00 0.00 3.55
75 76 3.648339 AAGTTATTGTTGGCAGCACAG 57.352 42.857 2.60 0.00 0.00 3.66
76 77 3.131933 ACAAAGTTATTGTTGGCAGCACA 59.868 39.130 2.60 0.00 0.00 4.57
77 78 3.716601 ACAAAGTTATTGTTGGCAGCAC 58.283 40.909 2.60 0.00 0.00 4.40
78 79 3.549827 CGACAAAGTTATTGTTGGCAGCA 60.550 43.478 0.00 0.00 31.83 4.41
79 80 2.979813 CGACAAAGTTATTGTTGGCAGC 59.020 45.455 0.00 0.00 31.83 5.25
80 81 4.481930 TCGACAAAGTTATTGTTGGCAG 57.518 40.909 8.32 0.00 35.15 4.85
81 82 4.902443 TTCGACAAAGTTATTGTTGGCA 57.098 36.364 8.32 0.00 35.15 4.92
82 83 5.746721 ACTTTTCGACAAAGTTATTGTTGGC 59.253 36.000 15.47 0.00 37.18 4.52
83 84 7.911205 TGTACTTTTCGACAAAGTTATTGTTGG 59.089 33.333 22.06 0.00 40.58 3.77
84 85 8.829514 TGTACTTTTCGACAAAGTTATTGTTG 57.170 30.769 22.06 2.77 40.58 3.33
86 87 9.659830 GATTGTACTTTTCGACAAAGTTATTGT 57.340 29.630 22.06 11.13 40.58 2.71
87 88 9.658475 TGATTGTACTTTTCGACAAAGTTATTG 57.342 29.630 22.06 0.00 40.58 1.90
91 92 9.019764 CAAATGATTGTACTTTTCGACAAAGTT 57.980 29.630 22.06 10.73 40.58 2.66
92 93 8.560576 CAAATGATTGTACTTTTCGACAAAGT 57.439 30.769 21.19 21.19 42.53 2.66
108 109 8.991243 ATGACAAGGTTATCAACAAATGATTG 57.009 30.769 0.00 0.00 46.85 2.67
113 114 9.787532 CGATTAATGACAAGGTTATCAACAAAT 57.212 29.630 0.00 0.00 0.00 2.32
114 115 8.240682 CCGATTAATGACAAGGTTATCAACAAA 58.759 33.333 0.00 0.00 0.00 2.83
115 116 7.627513 GCCGATTAATGACAAGGTTATCAACAA 60.628 37.037 0.00 0.00 0.00 2.83
116 117 6.183360 GCCGATTAATGACAAGGTTATCAACA 60.183 38.462 0.00 0.00 0.00 3.33
117 118 6.183360 TGCCGATTAATGACAAGGTTATCAAC 60.183 38.462 0.00 0.00 0.00 3.18
118 119 5.883115 TGCCGATTAATGACAAGGTTATCAA 59.117 36.000 0.00 0.00 0.00 2.57
119 120 5.432645 TGCCGATTAATGACAAGGTTATCA 58.567 37.500 0.00 0.00 0.00 2.15
120 121 6.371809 TTGCCGATTAATGACAAGGTTATC 57.628 37.500 0.00 0.00 0.00 1.75
121 122 6.767524 TTTGCCGATTAATGACAAGGTTAT 57.232 33.333 0.00 0.00 0.00 1.89
122 123 6.576662 TTTTGCCGATTAATGACAAGGTTA 57.423 33.333 0.00 0.00 0.00 2.85
123 124 5.461032 TTTTGCCGATTAATGACAAGGTT 57.539 34.783 0.00 0.00 0.00 3.50
124 125 5.461032 TTTTTGCCGATTAATGACAAGGT 57.539 34.783 0.00 0.00 0.00 3.50
125 126 6.368516 ACAATTTTTGCCGATTAATGACAAGG 59.631 34.615 0.00 0.00 0.00 3.61
126 127 7.350110 ACAATTTTTGCCGATTAATGACAAG 57.650 32.000 0.00 0.00 0.00 3.16
127 128 7.655328 AGAACAATTTTTGCCGATTAATGACAA 59.345 29.630 0.00 0.00 0.00 3.18
128 129 7.151308 AGAACAATTTTTGCCGATTAATGACA 58.849 30.769 0.00 0.00 0.00 3.58
129 130 7.581011 AGAACAATTTTTGCCGATTAATGAC 57.419 32.000 0.00 0.00 0.00 3.06
130 131 8.494347 CAAAGAACAATTTTTGCCGATTAATGA 58.506 29.630 0.00 0.00 0.00 2.57
131 132 8.644264 CAAAGAACAATTTTTGCCGATTAATG 57.356 30.769 0.00 0.00 0.00 1.90
141 142 5.799681 ACACCAGCAAAGAACAATTTTTG 57.200 34.783 0.00 0.00 37.35 2.44
142 143 6.816134 AAACACCAGCAAAGAACAATTTTT 57.184 29.167 0.00 0.00 0.00 1.94
143 144 6.816134 AAAACACCAGCAAAGAACAATTTT 57.184 29.167 0.00 0.00 0.00 1.82
144 145 6.206438 ACAAAAACACCAGCAAAGAACAATTT 59.794 30.769 0.00 0.00 0.00 1.82
145 146 5.704978 ACAAAAACACCAGCAAAGAACAATT 59.295 32.000 0.00 0.00 0.00 2.32
146 147 5.122082 CACAAAAACACCAGCAAAGAACAAT 59.878 36.000 0.00 0.00 0.00 2.71
150 151 3.993081 CACACAAAAACACCAGCAAAGAA 59.007 39.130 0.00 0.00 0.00 2.52
158 159 2.864097 GCACACACACACAAAAACACCA 60.864 45.455 0.00 0.00 0.00 4.17
168 169 1.151777 ACACTAGCGCACACACACAC 61.152 55.000 11.47 0.00 0.00 3.82
181 183 7.226720 AGTTAGAATGAACACAACCAACACTAG 59.773 37.037 0.00 0.00 0.00 2.57
307 309 1.281899 GAGTTAGTGCAGGCGTGATC 58.718 55.000 11.29 1.89 0.00 2.92
313 315 0.461961 AGGATCGAGTTAGTGCAGGC 59.538 55.000 0.00 0.00 0.00 4.85
340 342 0.038166 ATCACCGTGTGCTGGGAAAT 59.962 50.000 0.00 0.00 32.98 2.17
363 365 2.413112 ACACGTGATCGAAATGAAGCTG 59.587 45.455 25.01 0.00 40.62 4.24
403 405 3.425359 CGTTTGATGTCATCTGCAAGGAC 60.425 47.826 13.90 6.70 0.00 3.85
446 448 4.163078 AGGCAACAGATAGAAGTATGCACT 59.837 41.667 0.00 0.00 41.41 4.40
448 450 4.445453 CAGGCAACAGATAGAAGTATGCA 58.555 43.478 0.00 0.00 41.41 3.96
480 482 2.068834 AGTCTGTATACCACGAGGGG 57.931 55.000 3.29 0.00 42.91 4.79
506 508 4.578105 GCAGGGAGTGAATTTTCCAGATAG 59.422 45.833 6.84 0.00 35.09 2.08
526 528 5.303165 TCCTGAATTAGTCTATGCATGCAG 58.697 41.667 26.69 13.62 0.00 4.41
527 529 5.294734 TCCTGAATTAGTCTATGCATGCA 57.705 39.130 25.04 25.04 0.00 3.96
528 530 4.153835 GCTCCTGAATTAGTCTATGCATGC 59.846 45.833 11.82 11.82 0.00 4.06
529 531 5.549347 AGCTCCTGAATTAGTCTATGCATG 58.451 41.667 10.16 0.00 0.00 4.06
530 532 5.822132 AGCTCCTGAATTAGTCTATGCAT 57.178 39.130 3.79 3.79 0.00 3.96
531 533 6.239430 CCTTAGCTCCTGAATTAGTCTATGCA 60.239 42.308 0.00 0.00 0.00 3.96
532 534 6.015010 TCCTTAGCTCCTGAATTAGTCTATGC 60.015 42.308 0.00 0.00 0.00 3.14
547 549 3.451178 TGTTGGTGATACTCCTTAGCTCC 59.549 47.826 0.00 0.00 31.49 4.70
556 558 3.062639 CACGCTCATTGTTGGTGATACTC 59.937 47.826 0.00 0.00 0.00 2.59
559 565 3.000041 GACACGCTCATTGTTGGTGATA 59.000 45.455 9.50 0.00 33.08 2.15
564 570 2.290367 TCTTTGACACGCTCATTGTTGG 59.710 45.455 0.00 0.00 0.00 3.77
565 571 3.607422 TCTTTGACACGCTCATTGTTG 57.393 42.857 0.00 0.00 0.00 3.33
572 578 2.376032 GTGCTTTTCTTTGACACGCTC 58.624 47.619 0.00 0.00 0.00 5.03
574 580 1.477105 GGTGCTTTTCTTTGACACGC 58.523 50.000 0.00 0.00 32.00 5.34
599 606 1.603456 TTGTGTGTTGATGATGCGGT 58.397 45.000 0.00 0.00 0.00 5.68
607 614 3.135994 GGGAGTACGTTTGTGTGTTGAT 58.864 45.455 0.00 0.00 0.00 2.57
614 785 0.856641 CGTGTGGGAGTACGTTTGTG 59.143 55.000 0.00 0.00 35.70 3.33
616 787 1.562575 GGCGTGTGGGAGTACGTTTG 61.563 60.000 0.00 0.00 41.98 2.93
628 799 2.451132 CGTATACTCAGAAGGCGTGTG 58.549 52.381 0.56 0.00 0.00 3.82
635 806 6.721571 TTCCAAAAAGCGTATACTCAGAAG 57.278 37.500 0.56 0.00 0.00 2.85
669 843 9.220906 TCCACACTCAACTAATAACCCTATAAT 57.779 33.333 0.00 0.00 0.00 1.28
670 844 8.480501 GTCCACACTCAACTAATAACCCTATAA 58.519 37.037 0.00 0.00 0.00 0.98
671 845 7.070322 GGTCCACACTCAACTAATAACCCTATA 59.930 40.741 0.00 0.00 0.00 1.31
672 846 6.126854 GGTCCACACTCAACTAATAACCCTAT 60.127 42.308 0.00 0.00 0.00 2.57
673 847 5.188359 GGTCCACACTCAACTAATAACCCTA 59.812 44.000 0.00 0.00 0.00 3.53
674 848 4.019591 GGTCCACACTCAACTAATAACCCT 60.020 45.833 0.00 0.00 0.00 4.34
676 850 4.259356 GGGTCCACACTCAACTAATAACC 58.741 47.826 0.00 0.00 0.00 2.85
677 851 4.901868 TGGGTCCACACTCAACTAATAAC 58.098 43.478 0.00 0.00 26.01 1.89
678 852 4.595781 ACTGGGTCCACACTCAACTAATAA 59.404 41.667 0.00 0.00 30.29 1.40
679 853 4.020573 CACTGGGTCCACACTCAACTAATA 60.021 45.833 0.00 0.00 30.29 0.98
680 854 2.979678 ACTGGGTCCACACTCAACTAAT 59.020 45.455 0.00 0.00 30.29 1.73
737 1756 1.318576 CACTGTGGTTGAAAGGGTCC 58.681 55.000 0.00 0.00 0.00 4.46
790 1861 4.900154 GAGTGGACTCGCTCTTGG 57.100 61.111 0.00 0.00 44.69 3.61
884 1956 1.025113 TGCTGATCTGCTCTGCTTGC 61.025 55.000 23.02 0.00 46.04 4.01
949 2025 7.130917 CCAACAAGATCAATCAATTCGATCTC 58.869 38.462 13.32 0.21 43.92 2.75
1006 2090 1.606531 CTGGCAAGGGAGAAGGAGG 59.393 63.158 0.00 0.00 0.00 4.30
1234 2318 1.982938 GGTGGAGGTAGACGGTGCT 60.983 63.158 0.00 0.00 0.00 4.40
1236 2320 1.975407 ACGGTGGAGGTAGACGGTG 60.975 63.158 0.00 0.00 0.00 4.94
1683 2800 2.476051 GCAATGGAGTGCGTCGTG 59.524 61.111 0.00 0.00 34.21 4.35
2235 3352 0.869880 GAACAACAAACAGCACCGGC 60.870 55.000 0.00 0.00 41.61 6.13
2342 3473 9.573133 GGACATTTATTCAGAACATTTCGAATT 57.427 29.630 0.00 0.00 35.81 2.17
2413 3556 8.428186 TTCACTGACTACACGTAAGAAAATTT 57.572 30.769 4.23 0.00 43.62 1.82
2416 3559 6.256321 GGTTTCACTGACTACACGTAAGAAAA 59.744 38.462 4.23 0.00 43.62 2.29
2421 3564 3.550639 CGGGTTTCACTGACTACACGTAA 60.551 47.826 6.88 0.00 33.04 3.18
2423 3566 1.269413 CGGGTTTCACTGACTACACGT 60.269 52.381 6.88 0.00 33.04 4.49
2424 3567 1.415374 CGGGTTTCACTGACTACACG 58.585 55.000 1.84 1.84 0.00 4.49
2536 3680 4.800993 CGTGAAGATTTAGACTCGAAGCAT 59.199 41.667 0.00 0.00 0.00 3.79
2537 3681 4.166523 CGTGAAGATTTAGACTCGAAGCA 58.833 43.478 0.00 0.00 0.00 3.91
2538 3682 4.167268 ACGTGAAGATTTAGACTCGAAGC 58.833 43.478 0.00 0.00 0.00 3.86
2539 3683 7.972623 ATAACGTGAAGATTTAGACTCGAAG 57.027 36.000 0.00 0.00 0.00 3.79
2540 3684 8.752766 AAATAACGTGAAGATTTAGACTCGAA 57.247 30.769 0.00 0.00 0.00 3.71
2541 3685 9.282247 GTAAATAACGTGAAGATTTAGACTCGA 57.718 33.333 0.00 0.00 0.00 4.04
2542 3686 8.251114 CGTAAATAACGTGAAGATTTAGACTCG 58.749 37.037 0.00 0.00 46.72 4.18
2559 3703 4.274214 GGGTATGGGCTCAACGTAAATAAC 59.726 45.833 0.00 0.00 0.00 1.89
2560 3704 4.164604 AGGGTATGGGCTCAACGTAAATAA 59.835 41.667 0.00 0.00 0.00 1.40
2561 3705 3.712733 AGGGTATGGGCTCAACGTAAATA 59.287 43.478 0.00 0.00 0.00 1.40
2562 3706 2.508300 AGGGTATGGGCTCAACGTAAAT 59.492 45.455 0.00 0.00 0.00 1.40
2563 3707 1.910671 AGGGTATGGGCTCAACGTAAA 59.089 47.619 0.00 0.00 0.00 2.01
2575 3719 1.065854 GCATGCCTAGCTAGGGTATGG 60.066 57.143 35.44 15.10 43.76 2.74
2621 3765 4.993584 ACGATTGAGATGTTATCAGCCATC 59.006 41.667 0.00 0.00 38.17 3.51
2642 3786 8.234546 AGCTAATTAACCTGTTTTTATGTGACG 58.765 33.333 0.00 0.00 0.00 4.35
2649 3793 8.911918 TCTGTCAGCTAATTAACCTGTTTTTA 57.088 30.769 10.79 0.00 0.00 1.52
2683 3829 7.573968 TCTTTACGGAGGGAGTAGTTATTAC 57.426 40.000 0.00 0.00 0.00 1.89
2691 3837 8.645110 CCTTTATATTTCTTTACGGAGGGAGTA 58.355 37.037 0.00 0.00 0.00 2.59
2692 3838 7.506971 CCTTTATATTTCTTTACGGAGGGAGT 58.493 38.462 0.00 0.00 0.00 3.85
2693 3839 6.427242 GCCTTTATATTTCTTTACGGAGGGAG 59.573 42.308 0.00 0.00 0.00 4.30
2694 3840 6.126710 TGCCTTTATATTTCTTTACGGAGGGA 60.127 38.462 0.00 0.00 0.00 4.20
2695 3841 6.059484 TGCCTTTATATTTCTTTACGGAGGG 58.941 40.000 0.00 0.00 0.00 4.30
2696 3842 7.745620 ATGCCTTTATATTTCTTTACGGAGG 57.254 36.000 0.00 0.00 0.00 4.30
2712 3858 9.309516 CGTAGTGATCTAAACTAAATGCCTTTA 57.690 33.333 0.00 0.00 32.10 1.85
2713 3859 7.201617 GCGTAGTGATCTAAACTAAATGCCTTT 60.202 37.037 0.00 0.00 32.10 3.11
2714 3860 6.258068 GCGTAGTGATCTAAACTAAATGCCTT 59.742 38.462 0.00 0.00 32.10 4.35
2715 3861 5.753921 GCGTAGTGATCTAAACTAAATGCCT 59.246 40.000 0.00 0.00 32.10 4.75
2716 3862 5.753921 AGCGTAGTGATCTAAACTAAATGCC 59.246 40.000 0.00 0.00 32.10 4.40
2717 3863 6.697892 AGAGCGTAGTGATCTAAACTAAATGC 59.302 38.462 0.00 0.00 42.79 3.56
2718 3864 8.635877 AAGAGCGTAGTGATCTAAACTAAATG 57.364 34.615 0.00 0.00 44.14 2.32
2734 3880 9.828852 CCTCTGTAAACTAATATAAGAGCGTAG 57.171 37.037 0.00 0.00 0.00 3.51
2735 3881 8.790718 CCCTCTGTAAACTAATATAAGAGCGTA 58.209 37.037 0.00 0.00 0.00 4.42
2736 3882 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2737 3883 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2738 3884 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2747 3893 9.537852 TCTTTATGTACTCCCTCTGTAAACTAA 57.462 33.333 0.00 0.00 0.00 2.24
2748 3894 9.186837 CTCTTTATGTACTCCCTCTGTAAACTA 57.813 37.037 0.00 0.00 0.00 2.24
2749 3895 7.363968 GCTCTTTATGTACTCCCTCTGTAAACT 60.364 40.741 0.00 0.00 0.00 2.66
2750 3896 6.757478 GCTCTTTATGTACTCCCTCTGTAAAC 59.243 42.308 0.00 0.00 0.00 2.01
2751 3897 6.439375 TGCTCTTTATGTACTCCCTCTGTAAA 59.561 38.462 0.00 0.00 0.00 2.01
2752 3898 5.955959 TGCTCTTTATGTACTCCCTCTGTAA 59.044 40.000 0.00 0.00 0.00 2.41
2753 3899 5.516044 TGCTCTTTATGTACTCCCTCTGTA 58.484 41.667 0.00 0.00 0.00 2.74
2754 3900 4.353777 TGCTCTTTATGTACTCCCTCTGT 58.646 43.478 0.00 0.00 0.00 3.41
2755 3901 4.646945 TCTGCTCTTTATGTACTCCCTCTG 59.353 45.833 0.00 0.00 0.00 3.35
2756 3902 4.873010 TCTGCTCTTTATGTACTCCCTCT 58.127 43.478 0.00 0.00 0.00 3.69
2757 3903 5.599999 TTCTGCTCTTTATGTACTCCCTC 57.400 43.478 0.00 0.00 0.00 4.30
2758 3904 6.567602 ATTTCTGCTCTTTATGTACTCCCT 57.432 37.500 0.00 0.00 0.00 4.20
2759 3905 8.910351 ATAATTTCTGCTCTTTATGTACTCCC 57.090 34.615 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.