Multiple sequence alignment - TraesCS4D01G328500

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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 TraesCS4D01G328500 chr4D 100.000 2288 0 0 1 2288 487079625 487077338 0.000000e+00 4226
1 TraesCS4D01G328500 chr4D 95.723 1286 51 4 324 1608 39369450 39368168 0.000000e+00 2067
2 TraesCS4D01G328500 chr4D 96.765 680 22 0 1609 2288 99077735 99078414 0.000000e+00 1134
3 TraesCS4D01G328500 chr4D 93.824 340 15 6 1 337 196933095 196932759 7.290000e-140 507
4 TraesCS4D01G328500 chr4D 94.737 323 17 0 1 323 127356768 127356446 9.430000e-139 503
5 TraesCS4D01G328500 chr1A 96.361 1264 43 2 324 1587 463969626 463970886 0.000000e+00 2076
6 TraesCS4D01G328500 chr6D 95.101 1286 61 2 324 1608 446604315 446603031 0.000000e+00 2025
7 TraesCS4D01G328500 chr6D 95.016 321 14 2 3 323 36193483 36193165 9.430000e-139 503
8 TraesCS4D01G328500 chr6D 94.444 324 17 1 1 323 376375950 376375627 4.390000e-137 497
9 TraesCS4D01G328500 chr6D 94.427 323 18 0 1 323 411247455 411247777 4.390000e-137 497
10 TraesCS4D01G328500 chr2D 95.494 1265 55 2 324 1587 647090860 647089597 0.000000e+00 2019
11 TraesCS4D01G328500 chr2D 94.949 1287 62 3 324 1608 646883557 646882272 0.000000e+00 2013
12 TraesCS4D01G328500 chr2D 94.872 1287 62 4 324 1608 646799780 646798496 0.000000e+00 2008
13 TraesCS4D01G328500 chr2D 94.639 1287 66 3 324 1608 646961155 646959870 0.000000e+00 1991
14 TraesCS4D01G328500 chr2D 94.557 1286 69 1 324 1608 646928699 646927414 0.000000e+00 1986
15 TraesCS4D01G328500 chr2D 96.618 680 21 2 1609 2288 175654608 175655285 0.000000e+00 1127
16 TraesCS4D01G328500 chr2D 94.737 323 17 0 1 323 87052681 87052359 9.430000e-139 503
17 TraesCS4D01G328500 chr2A 94.639 1287 64 4 324 1608 171850235 171851518 0.000000e+00 1989
18 TraesCS4D01G328500 chr2A 95.000 320 16 0 7 326 675224843 675224524 9.430000e-139 503
19 TraesCS4D01G328500 chr3D 96.912 680 20 1 1609 2288 402019622 402020300 0.000000e+00 1138
20 TraesCS4D01G328500 chr3D 96.912 680 17 3 1609 2288 157679616 157680291 0.000000e+00 1136
21 TraesCS4D01G328500 chr3D 96.471 680 24 0 1609 2288 151813642 151812963 0.000000e+00 1123
22 TraesCS4D01G328500 chr3D 94.462 325 16 2 1 324 522504208 522504531 1.220000e-137 499
23 TraesCS4D01G328500 chr5D 96.618 680 23 0 1609 2288 391084510 391085189 0.000000e+00 1129
24 TraesCS4D01G328500 chr5D 96.476 681 24 0 1608 2288 530085142 530085822 0.000000e+00 1125
25 TraesCS4D01G328500 chr5D 96.471 680 24 0 1609 2288 108495200 108494521 0.000000e+00 1123
26 TraesCS4D01G328500 chr5D 96.476 681 22 2 1609 2288 257179437 257180116 0.000000e+00 1123
27 TraesCS4D01G328500 chr6B 95.988 324 11 2 1 323 697606577 697606899 2.010000e-145 525


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 TraesCS4D01G328500 chr4D 487077338 487079625 2287 True 4226 4226 100.000 1 2288 1 chr4D.!!$R4 2287
1 TraesCS4D01G328500 chr4D 39368168 39369450 1282 True 2067 2067 95.723 324 1608 1 chr4D.!!$R1 1284
2 TraesCS4D01G328500 chr4D 99077735 99078414 679 False 1134 1134 96.765 1609 2288 1 chr4D.!!$F1 679
3 TraesCS4D01G328500 chr1A 463969626 463970886 1260 False 2076 2076 96.361 324 1587 1 chr1A.!!$F1 1263
4 TraesCS4D01G328500 chr6D 446603031 446604315 1284 True 2025 2025 95.101 324 1608 1 chr6D.!!$R3 1284
5 TraesCS4D01G328500 chr2D 647089597 647090860 1263 True 2019 2019 95.494 324 1587 1 chr2D.!!$R6 1263
6 TraesCS4D01G328500 chr2D 646882272 646883557 1285 True 2013 2013 94.949 324 1608 1 chr2D.!!$R3 1284
7 TraesCS4D01G328500 chr2D 646798496 646799780 1284 True 2008 2008 94.872 324 1608 1 chr2D.!!$R2 1284
8 TraesCS4D01G328500 chr2D 646959870 646961155 1285 True 1991 1991 94.639 324 1608 1 chr2D.!!$R5 1284
9 TraesCS4D01G328500 chr2D 646927414 646928699 1285 True 1986 1986 94.557 324 1608 1 chr2D.!!$R4 1284
10 TraesCS4D01G328500 chr2D 175654608 175655285 677 False 1127 1127 96.618 1609 2288 1 chr2D.!!$F1 679
11 TraesCS4D01G328500 chr2A 171850235 171851518 1283 False 1989 1989 94.639 324 1608 1 chr2A.!!$F1 1284
12 TraesCS4D01G328500 chr3D 402019622 402020300 678 False 1138 1138 96.912 1609 2288 1 chr3D.!!$F2 679
13 TraesCS4D01G328500 chr3D 157679616 157680291 675 False 1136 1136 96.912 1609 2288 1 chr3D.!!$F1 679
14 TraesCS4D01G328500 chr3D 151812963 151813642 679 True 1123 1123 96.471 1609 2288 1 chr3D.!!$R1 679
15 TraesCS4D01G328500 chr5D 391084510 391085189 679 False 1129 1129 96.618 1609 2288 1 chr5D.!!$F2 679
16 TraesCS4D01G328500 chr5D 530085142 530085822 680 False 1125 1125 96.476 1608 2288 1 chr5D.!!$F3 680
17 TraesCS4D01G328500 chr5D 108494521 108495200 679 True 1123 1123 96.471 1609 2288 1 chr5D.!!$R1 679
18 TraesCS4D01G328500 chr5D 257179437 257180116 679 False 1123 1123 96.476 1609 2288 1 chr5D.!!$F1 679

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
60 61 0.036875 CCTTCCTCGTTGCTTCCCTT 59.963 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 1595 1.54962 CATTTGGTTGCCTACATGCCA 59.45 47.619 0.0 0.0 31.74 4.92 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
44 45 4.431131 CCCCATGCCTCGTGCCTT 62.431 66.667 0.00 0.00 40.16 4.35
45 46 2.825836 CCCATGCCTCGTGCCTTC 60.826 66.667 0.00 0.00 40.16 3.46
46 47 2.825836 CCATGCCTCGTGCCTTCC 60.826 66.667 0.00 0.00 40.16 3.46
47 48 2.270205 CATGCCTCGTGCCTTCCT 59.730 61.111 0.00 0.00 40.16 3.36
48 49 1.817099 CATGCCTCGTGCCTTCCTC 60.817 63.158 0.00 0.00 40.16 3.71
49 50 3.376935 ATGCCTCGTGCCTTCCTCG 62.377 63.158 0.00 0.00 40.16 4.63
50 51 4.070552 GCCTCGTGCCTTCCTCGT 62.071 66.667 0.00 0.00 0.00 4.18
51 52 2.657237 CCTCGTGCCTTCCTCGTT 59.343 61.111 0.00 0.00 0.00 3.85
52 53 1.738099 CCTCGTGCCTTCCTCGTTG 60.738 63.158 0.00 0.00 0.00 4.10
53 54 2.357034 TCGTGCCTTCCTCGTTGC 60.357 61.111 0.00 0.00 0.00 4.17
54 55 2.357517 CGTGCCTTCCTCGTTGCT 60.358 61.111 0.00 0.00 0.00 3.91
55 56 1.961277 CGTGCCTTCCTCGTTGCTT 60.961 57.895 0.00 0.00 0.00 3.91
56 57 1.869690 GTGCCTTCCTCGTTGCTTC 59.130 57.895 0.00 0.00 0.00 3.86
57 58 1.302511 TGCCTTCCTCGTTGCTTCC 60.303 57.895 0.00 0.00 0.00 3.46
58 59 2.041115 GCCTTCCTCGTTGCTTCCC 61.041 63.158 0.00 0.00 0.00 3.97
59 60 1.679898 CCTTCCTCGTTGCTTCCCT 59.320 57.895 0.00 0.00 0.00 4.20
60 61 0.036875 CCTTCCTCGTTGCTTCCCTT 59.963 55.000 0.00 0.00 0.00 3.95
61 62 1.278127 CCTTCCTCGTTGCTTCCCTTA 59.722 52.381 0.00 0.00 0.00 2.69
62 63 2.347731 CTTCCTCGTTGCTTCCCTTAC 58.652 52.381 0.00 0.00 0.00 2.34
63 64 0.245539 TCCTCGTTGCTTCCCTTACG 59.754 55.000 0.00 0.00 35.46 3.18
64 65 0.037605 CCTCGTTGCTTCCCTTACGT 60.038 55.000 0.00 0.00 35.63 3.57
65 66 1.203052 CCTCGTTGCTTCCCTTACGTA 59.797 52.381 0.00 0.00 35.63 3.57
66 67 2.257034 CTCGTTGCTTCCCTTACGTAC 58.743 52.381 0.00 0.00 35.63 3.67
67 68 1.612950 TCGTTGCTTCCCTTACGTACA 59.387 47.619 0.00 0.00 35.63 2.90
68 69 1.723003 CGTTGCTTCCCTTACGTACAC 59.277 52.381 0.00 0.00 0.00 2.90
69 70 2.608752 CGTTGCTTCCCTTACGTACACT 60.609 50.000 0.00 0.00 0.00 3.55
70 71 2.991866 GTTGCTTCCCTTACGTACACTC 59.008 50.000 0.00 0.00 0.00 3.51
71 72 1.547372 TGCTTCCCTTACGTACACTCC 59.453 52.381 0.00 0.00 0.00 3.85
72 73 1.547372 GCTTCCCTTACGTACACTCCA 59.453 52.381 0.00 0.00 0.00 3.86
73 74 2.028748 GCTTCCCTTACGTACACTCCAA 60.029 50.000 0.00 0.00 0.00 3.53
74 75 3.846360 CTTCCCTTACGTACACTCCAAG 58.154 50.000 0.00 0.00 0.00 3.61
75 76 2.880443 TCCCTTACGTACACTCCAAGT 58.120 47.619 0.00 0.00 0.00 3.16
76 77 2.821969 TCCCTTACGTACACTCCAAGTC 59.178 50.000 0.00 0.00 0.00 3.01
77 78 2.824341 CCCTTACGTACACTCCAAGTCT 59.176 50.000 0.00 0.00 0.00 3.24
78 79 3.257624 CCCTTACGTACACTCCAAGTCTT 59.742 47.826 0.00 0.00 0.00 3.01
79 80 4.483311 CCTTACGTACACTCCAAGTCTTC 58.517 47.826 0.00 0.00 0.00 2.87
80 81 2.701073 ACGTACACTCCAAGTCTTCG 57.299 50.000 0.00 0.00 0.00 3.79
81 82 1.268899 ACGTACACTCCAAGTCTTCGG 59.731 52.381 0.00 0.00 0.00 4.30
82 83 1.402456 CGTACACTCCAAGTCTTCGGG 60.402 57.143 0.00 0.00 0.00 5.14
83 84 1.891150 GTACACTCCAAGTCTTCGGGA 59.109 52.381 0.00 0.00 0.00 5.14
84 85 1.645710 ACACTCCAAGTCTTCGGGAT 58.354 50.000 0.00 0.00 0.00 3.85
85 86 1.978580 ACACTCCAAGTCTTCGGGATT 59.021 47.619 0.00 0.00 0.00 3.01
86 87 2.289694 ACACTCCAAGTCTTCGGGATTG 60.290 50.000 7.42 7.42 37.38 2.67
87 88 1.339151 ACTCCAAGTCTTCGGGATTGC 60.339 52.381 0.00 0.00 0.00 3.56
88 89 0.984230 TCCAAGTCTTCGGGATTGCT 59.016 50.000 0.00 0.00 0.00 3.91
89 90 1.351017 TCCAAGTCTTCGGGATTGCTT 59.649 47.619 0.00 0.00 0.00 3.91
90 91 1.740025 CCAAGTCTTCGGGATTGCTTC 59.260 52.381 0.00 0.00 0.00 3.86
91 92 1.740025 CAAGTCTTCGGGATTGCTTCC 59.260 52.381 0.00 0.00 44.62 3.46
92 93 0.108138 AGTCTTCGGGATTGCTTCCG 60.108 55.000 0.00 0.00 46.52 4.30
93 94 0.391263 GTCTTCGGGATTGCTTCCGT 60.391 55.000 0.00 0.00 46.52 4.69
94 95 0.323629 TCTTCGGGATTGCTTCCGTT 59.676 50.000 0.00 0.00 46.52 4.44
95 96 0.727398 CTTCGGGATTGCTTCCGTTC 59.273 55.000 0.00 0.00 46.52 3.95
96 97 0.675522 TTCGGGATTGCTTCCGTTCC 60.676 55.000 0.00 0.00 46.52 3.62
97 98 1.376683 CGGGATTGCTTCCGTTCCA 60.377 57.895 0.00 0.00 46.52 3.53
98 99 0.958382 CGGGATTGCTTCCGTTCCAA 60.958 55.000 0.00 0.00 46.52 3.53
99 100 1.253100 GGGATTGCTTCCGTTCCAAA 58.747 50.000 0.93 0.00 46.52 3.28
100 101 1.616374 GGGATTGCTTCCGTTCCAAAA 59.384 47.619 0.93 0.00 46.52 2.44
101 102 2.036604 GGGATTGCTTCCGTTCCAAAAA 59.963 45.455 0.93 0.00 46.52 1.94
102 103 3.306710 GGGATTGCTTCCGTTCCAAAAAT 60.307 43.478 0.93 0.00 46.52 1.82
103 104 4.081917 GGGATTGCTTCCGTTCCAAAAATA 60.082 41.667 0.93 0.00 46.52 1.40
104 105 5.474825 GGATTGCTTCCGTTCCAAAAATAA 58.525 37.500 0.00 0.00 33.93 1.40
105 106 5.347635 GGATTGCTTCCGTTCCAAAAATAAC 59.652 40.000 0.00 0.00 33.93 1.89
106 107 5.523438 TTGCTTCCGTTCCAAAAATAACT 57.477 34.783 0.00 0.00 0.00 2.24
107 108 5.116069 TGCTTCCGTTCCAAAAATAACTC 57.884 39.130 0.00 0.00 0.00 3.01
108 109 4.022676 TGCTTCCGTTCCAAAAATAACTCC 60.023 41.667 0.00 0.00 0.00 3.85
109 110 4.617530 GCTTCCGTTCCAAAAATAACTCCC 60.618 45.833 0.00 0.00 0.00 4.30
110 111 3.423749 TCCGTTCCAAAAATAACTCCCC 58.576 45.455 0.00 0.00 0.00 4.81
111 112 2.494471 CCGTTCCAAAAATAACTCCCCC 59.506 50.000 0.00 0.00 0.00 5.40
112 113 2.162809 CGTTCCAAAAATAACTCCCCCG 59.837 50.000 0.00 0.00 0.00 5.73
113 114 3.423749 GTTCCAAAAATAACTCCCCCGA 58.576 45.455 0.00 0.00 0.00 5.14
114 115 3.810721 TCCAAAAATAACTCCCCCGAA 57.189 42.857 0.00 0.00 0.00 4.30
115 116 3.692690 TCCAAAAATAACTCCCCCGAAG 58.307 45.455 0.00 0.00 0.00 3.79
131 132 2.928694 CGAAGGTTTCATTCCGTTTGG 58.071 47.619 0.00 0.00 0.00 3.28
132 133 2.550606 CGAAGGTTTCATTCCGTTTGGA 59.449 45.455 0.00 0.00 44.61 3.53
133 134 3.608474 CGAAGGTTTCATTCCGTTTGGAC 60.608 47.826 0.00 0.00 46.45 4.02
134 135 3.223674 AGGTTTCATTCCGTTTGGACT 57.776 42.857 0.00 0.00 46.45 3.85
135 136 3.146847 AGGTTTCATTCCGTTTGGACTC 58.853 45.455 0.00 0.00 46.45 3.36
136 137 2.228103 GGTTTCATTCCGTTTGGACTCC 59.772 50.000 0.00 0.00 46.45 3.85
137 138 1.803334 TTCATTCCGTTTGGACTCCG 58.197 50.000 0.00 0.00 46.45 4.63
138 139 0.682852 TCATTCCGTTTGGACTCCGT 59.317 50.000 0.00 0.00 46.45 4.69
139 140 1.071071 TCATTCCGTTTGGACTCCGTT 59.929 47.619 0.00 0.00 46.45 4.44
140 141 1.877443 CATTCCGTTTGGACTCCGTTT 59.123 47.619 0.00 0.00 46.45 3.60
141 142 1.301423 TTCCGTTTGGACTCCGTTTG 58.699 50.000 0.00 0.00 46.45 2.93
142 143 0.464870 TCCGTTTGGACTCCGTTTGA 59.535 50.000 0.00 0.00 40.17 2.69
143 144 1.071071 TCCGTTTGGACTCCGTTTGAT 59.929 47.619 0.00 0.00 40.17 2.57
144 145 2.299582 TCCGTTTGGACTCCGTTTGATA 59.700 45.455 0.00 0.00 40.17 2.15
145 146 3.055675 TCCGTTTGGACTCCGTTTGATAT 60.056 43.478 0.00 0.00 40.17 1.63
146 147 3.687698 CCGTTTGGACTCCGTTTGATATT 59.312 43.478 0.00 0.00 37.49 1.28
147 148 4.201783 CCGTTTGGACTCCGTTTGATATTC 60.202 45.833 0.00 0.00 37.49 1.75
148 149 4.201783 CGTTTGGACTCCGTTTGATATTCC 60.202 45.833 0.00 0.00 0.00 3.01
149 150 4.837093 TTGGACTCCGTTTGATATTCCT 57.163 40.909 0.00 0.00 0.00 3.36
150 151 4.837093 TGGACTCCGTTTGATATTCCTT 57.163 40.909 0.00 0.00 0.00 3.36
151 152 5.174037 TGGACTCCGTTTGATATTCCTTT 57.826 39.130 0.00 0.00 0.00 3.11
152 153 5.566469 TGGACTCCGTTTGATATTCCTTTT 58.434 37.500 0.00 0.00 0.00 2.27
153 154 5.646360 TGGACTCCGTTTGATATTCCTTTTC 59.354 40.000 0.00 0.00 0.00 2.29
154 155 5.880887 GGACTCCGTTTGATATTCCTTTTCT 59.119 40.000 0.00 0.00 0.00 2.52
155 156 6.183360 GGACTCCGTTTGATATTCCTTTTCTG 60.183 42.308 0.00 0.00 0.00 3.02
156 157 5.123979 ACTCCGTTTGATATTCCTTTTCTGC 59.876 40.000 0.00 0.00 0.00 4.26
157 158 4.094294 TCCGTTTGATATTCCTTTTCTGCG 59.906 41.667 0.00 0.00 0.00 5.18
158 159 4.094294 CCGTTTGATATTCCTTTTCTGCGA 59.906 41.667 0.00 0.00 0.00 5.10
159 160 5.391523 CCGTTTGATATTCCTTTTCTGCGAA 60.392 40.000 0.00 0.00 0.00 4.70
160 161 6.083630 CGTTTGATATTCCTTTTCTGCGAAA 58.916 36.000 0.00 0.55 0.00 3.46
161 162 6.032460 CGTTTGATATTCCTTTTCTGCGAAAC 59.968 38.462 3.71 0.00 0.00 2.78
162 163 6.567687 TTGATATTCCTTTTCTGCGAAACA 57.432 33.333 3.71 0.00 0.00 2.83
173 174 2.719798 CTGCGAAACAGTGAAACAAGG 58.280 47.619 0.00 0.00 41.86 3.61
174 175 2.354510 CTGCGAAACAGTGAAACAAGGA 59.645 45.455 0.00 0.00 41.86 3.36
175 176 2.354510 TGCGAAACAGTGAAACAAGGAG 59.645 45.455 0.00 0.00 41.43 3.69
176 177 2.612212 GCGAAACAGTGAAACAAGGAGA 59.388 45.455 0.00 0.00 41.43 3.71
177 178 3.303395 GCGAAACAGTGAAACAAGGAGAG 60.303 47.826 0.00 0.00 41.43 3.20
178 179 4.119862 CGAAACAGTGAAACAAGGAGAGA 58.880 43.478 0.00 0.00 41.43 3.10
179 180 4.570772 CGAAACAGTGAAACAAGGAGAGAA 59.429 41.667 0.00 0.00 41.43 2.87
180 181 5.064707 CGAAACAGTGAAACAAGGAGAGAAA 59.935 40.000 0.00 0.00 41.43 2.52
181 182 5.819825 AACAGTGAAACAAGGAGAGAAAC 57.180 39.130 0.00 0.00 41.43 2.78
182 183 4.843728 ACAGTGAAACAAGGAGAGAAACA 58.156 39.130 0.00 0.00 41.43 2.83
183 184 4.878397 ACAGTGAAACAAGGAGAGAAACAG 59.122 41.667 0.00 0.00 41.43 3.16
184 185 5.118990 CAGTGAAACAAGGAGAGAAACAGA 58.881 41.667 0.00 0.00 41.43 3.41
185 186 5.586243 CAGTGAAACAAGGAGAGAAACAGAA 59.414 40.000 0.00 0.00 41.43 3.02
186 187 6.094048 CAGTGAAACAAGGAGAGAAACAGAAA 59.906 38.462 0.00 0.00 41.43 2.52
187 188 6.094186 AGTGAAACAAGGAGAGAAACAGAAAC 59.906 38.462 0.00 0.00 41.43 2.78
188 189 6.094186 GTGAAACAAGGAGAGAAACAGAAACT 59.906 38.462 0.00 0.00 36.32 2.66
189 190 6.094048 TGAAACAAGGAGAGAAACAGAAACTG 59.906 38.462 0.00 0.00 37.52 3.16
190 191 4.455606 ACAAGGAGAGAAACAGAAACTGG 58.544 43.478 0.00 0.00 35.51 4.00
191 192 3.133141 AGGAGAGAAACAGAAACTGGC 57.867 47.619 0.00 0.00 35.51 4.85
192 193 1.801178 GGAGAGAAACAGAAACTGGCG 59.199 52.381 0.00 0.00 35.51 5.69
193 194 1.195674 GAGAGAAACAGAAACTGGCGC 59.804 52.381 0.00 0.00 35.51 6.53
194 195 1.202698 AGAGAAACAGAAACTGGCGCT 60.203 47.619 7.64 0.00 35.51 5.92
195 196 0.947244 AGAAACAGAAACTGGCGCTG 59.053 50.000 7.64 2.99 35.51 5.18
196 197 0.040067 GAAACAGAAACTGGCGCTGG 60.040 55.000 7.64 2.58 35.51 4.85
197 198 1.455383 AAACAGAAACTGGCGCTGGG 61.455 55.000 7.64 0.00 35.51 4.45
198 199 3.741476 CAGAAACTGGCGCTGGGC 61.741 66.667 7.64 8.35 42.51 5.36
199 200 3.958860 AGAAACTGGCGCTGGGCT 61.959 61.111 16.51 0.00 42.94 5.19
200 201 3.435186 GAAACTGGCGCTGGGCTC 61.435 66.667 16.51 7.37 42.94 4.70
201 202 3.909086 GAAACTGGCGCTGGGCTCT 62.909 63.158 16.51 0.00 42.94 4.09
202 203 4.711949 AACTGGCGCTGGGCTCTG 62.712 66.667 16.51 12.17 42.94 3.35
207 208 4.096003 GCGCTGGGCTCTGGGTTA 62.096 66.667 9.69 0.00 39.11 2.85
208 209 2.668632 CGCTGGGCTCTGGGTTAA 59.331 61.111 0.00 0.00 0.00 2.01
209 210 1.224592 CGCTGGGCTCTGGGTTAAT 59.775 57.895 0.00 0.00 0.00 1.40
210 211 0.468226 CGCTGGGCTCTGGGTTAATA 59.532 55.000 0.00 0.00 0.00 0.98
211 212 1.541233 CGCTGGGCTCTGGGTTAATAG 60.541 57.143 0.00 0.00 0.00 1.73
212 213 1.202818 GCTGGGCTCTGGGTTAATAGG 60.203 57.143 0.00 0.00 0.00 2.57
213 214 2.127708 CTGGGCTCTGGGTTAATAGGT 58.872 52.381 0.00 0.00 0.00 3.08
214 215 2.509964 CTGGGCTCTGGGTTAATAGGTT 59.490 50.000 0.00 0.00 0.00 3.50
215 216 3.714798 CTGGGCTCTGGGTTAATAGGTTA 59.285 47.826 0.00 0.00 0.00 2.85
216 217 3.714798 TGGGCTCTGGGTTAATAGGTTAG 59.285 47.826 0.00 0.00 0.00 2.34
217 218 3.715315 GGGCTCTGGGTTAATAGGTTAGT 59.285 47.826 0.00 0.00 0.00 2.24
218 219 4.202336 GGGCTCTGGGTTAATAGGTTAGTC 60.202 50.000 0.00 0.00 0.00 2.59
219 220 4.202336 GGCTCTGGGTTAATAGGTTAGTCC 60.202 50.000 0.00 0.00 0.00 3.85
220 221 4.202336 GCTCTGGGTTAATAGGTTAGTCCC 60.202 50.000 0.00 0.00 36.84 4.46
221 222 4.962839 TCTGGGTTAATAGGTTAGTCCCA 58.037 43.478 0.00 0.00 40.33 4.37
222 223 5.352264 TCTGGGTTAATAGGTTAGTCCCAA 58.648 41.667 0.00 0.00 41.14 4.12
223 224 5.791664 TCTGGGTTAATAGGTTAGTCCCAAA 59.208 40.000 0.00 0.00 41.14 3.28
224 225 6.275144 TCTGGGTTAATAGGTTAGTCCCAAAA 59.725 38.462 0.00 0.00 41.14 2.44
225 226 6.861129 TGGGTTAATAGGTTAGTCCCAAAAA 58.139 36.000 0.00 0.00 40.01 1.94
226 227 7.480437 TGGGTTAATAGGTTAGTCCCAAAAAT 58.520 34.615 0.00 0.00 40.01 1.82
227 228 8.621971 TGGGTTAATAGGTTAGTCCCAAAAATA 58.378 33.333 0.00 0.00 40.01 1.40
228 229 9.478238 GGGTTAATAGGTTAGTCCCAAAAATAA 57.522 33.333 0.00 0.00 36.57 1.40
257 258 8.578308 AAAAGTGTTTAATAAAGCCCGTAAAC 57.422 30.769 0.00 0.00 37.10 2.01
258 259 6.880942 AGTGTTTAATAAAGCCCGTAAACA 57.119 33.333 4.23 4.23 41.65 2.83
259 260 7.457024 AGTGTTTAATAAAGCCCGTAAACAT 57.543 32.000 10.11 0.19 44.09 2.71
260 261 7.532571 AGTGTTTAATAAAGCCCGTAAACATC 58.467 34.615 10.11 5.76 44.09 3.06
261 262 6.748658 GTGTTTAATAAAGCCCGTAAACATCC 59.251 38.462 10.11 0.00 44.09 3.51
262 263 6.433404 TGTTTAATAAAGCCCGTAAACATCCA 59.567 34.615 4.23 0.00 40.00 3.41
263 264 7.122948 TGTTTAATAAAGCCCGTAAACATCCAT 59.877 33.333 4.23 0.00 40.00 3.41
264 265 8.623030 GTTTAATAAAGCCCGTAAACATCCATA 58.377 33.333 0.00 0.00 36.75 2.74
265 266 8.749026 TTAATAAAGCCCGTAAACATCCATAA 57.251 30.769 0.00 0.00 0.00 1.90
266 267 4.976224 AAAGCCCGTAAACATCCATAAC 57.024 40.909 0.00 0.00 0.00 1.89
267 268 3.637911 AGCCCGTAAACATCCATAACA 57.362 42.857 0.00 0.00 0.00 2.41
268 269 3.541632 AGCCCGTAAACATCCATAACAG 58.458 45.455 0.00 0.00 0.00 3.16
269 270 3.199071 AGCCCGTAAACATCCATAACAGA 59.801 43.478 0.00 0.00 0.00 3.41
270 271 4.134563 GCCCGTAAACATCCATAACAGAT 58.865 43.478 0.00 0.00 0.00 2.90
271 272 5.071250 AGCCCGTAAACATCCATAACAGATA 59.929 40.000 0.00 0.00 0.00 1.98
272 273 5.761234 GCCCGTAAACATCCATAACAGATAA 59.239 40.000 0.00 0.00 0.00 1.75
273 274 6.430000 GCCCGTAAACATCCATAACAGATAAT 59.570 38.462 0.00 0.00 0.00 1.28
274 275 7.604927 GCCCGTAAACATCCATAACAGATAATA 59.395 37.037 0.00 0.00 0.00 0.98
275 276 9.667107 CCCGTAAACATCCATAACAGATAATAT 57.333 33.333 0.00 0.00 0.00 1.28
412 413 3.759618 TCATGAGCACTGCATTTGATTCA 59.240 39.130 3.30 0.00 0.00 2.57
545 547 3.680786 GGAAGGGGTTGGCGTTGC 61.681 66.667 0.00 0.00 0.00 4.17
603 607 3.838565 AGGTTGACAGTGAGAGAAGAGA 58.161 45.455 0.00 0.00 0.00 3.10
604 608 4.219115 AGGTTGACAGTGAGAGAAGAGAA 58.781 43.478 0.00 0.00 0.00 2.87
679 684 4.017958 AGGAGGAGAAGAGTGACAGTCATA 60.018 45.833 6.51 0.00 0.00 2.15
999 1005 1.699656 CGAAGCTTGAGTGCATCCCG 61.700 60.000 2.10 0.00 34.99 5.14
1309 1315 2.356667 GGGCCACCTCTTTCCAGG 59.643 66.667 4.39 0.00 39.80 4.45
1369 1375 3.226347 GCGTTGAACTGTTATGAAGTGC 58.774 45.455 0.00 0.00 0.00 4.40
1561 1567 0.754957 CAGGCAACCAAACACCAGGA 60.755 55.000 0.00 0.00 37.17 3.86
1596 1602 0.686441 ATGCAGGCAAGATGGCATGT 60.686 50.000 3.81 0.00 46.51 3.21
1736 1742 6.045106 ACAAGGTTTACATAAGGAGGGAGAAA 59.955 38.462 0.00 0.00 0.00 2.52
1834 1840 7.763356 TGAAACTCCACGAAAGTTATTTTTGA 58.237 30.769 0.00 0.00 46.40 2.69
2001 2007 7.326789 CGAAGAAAAATCATAAGCAAGCTTTCA 59.673 33.333 13.06 0.00 37.47 2.69
2075 2081 2.260869 GGCAGAGCTGTTTTGCCGA 61.261 57.895 10.15 0.00 46.82 5.54
2091 2097 1.977544 CGAGGACACTTCCCTCCGT 60.978 63.158 0.00 0.00 45.70 4.69
2125 2131 1.018752 CGCCATCGTCATCACCAACA 61.019 55.000 0.00 0.00 0.00 3.33
2225 2232 6.962182 TCTTGTATCCAATTCTTGTCTCCAT 58.038 36.000 0.00 0.00 0.00 3.41
2262 2269 5.909621 CCTGTAGGTTGCTAGTAGTGTTA 57.090 43.478 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.591254 AACGAGGAAGGCACGAGGC 62.591 63.158 0.00 0.00 43.74 4.70
34 35 1.738099 CAACGAGGAAGGCACGAGG 60.738 63.158 0.00 0.00 0.00 4.63
35 36 2.383527 GCAACGAGGAAGGCACGAG 61.384 63.158 0.00 0.00 0.00 4.18
36 37 2.357034 GCAACGAGGAAGGCACGA 60.357 61.111 0.00 0.00 0.00 4.35
37 38 1.901650 GAAGCAACGAGGAAGGCACG 61.902 60.000 0.00 0.00 0.00 5.34
38 39 1.578206 GGAAGCAACGAGGAAGGCAC 61.578 60.000 0.00 0.00 0.00 5.01
39 40 1.302511 GGAAGCAACGAGGAAGGCA 60.303 57.895 0.00 0.00 0.00 4.75
40 41 2.041115 GGGAAGCAACGAGGAAGGC 61.041 63.158 0.00 0.00 0.00 4.35
41 42 0.036875 AAGGGAAGCAACGAGGAAGG 59.963 55.000 0.00 0.00 0.00 3.46
42 43 2.347731 GTAAGGGAAGCAACGAGGAAG 58.652 52.381 0.00 0.00 0.00 3.46
43 44 1.337447 CGTAAGGGAAGCAACGAGGAA 60.337 52.381 0.00 0.00 37.53 3.36
44 45 0.245539 CGTAAGGGAAGCAACGAGGA 59.754 55.000 0.00 0.00 37.53 3.71
45 46 0.037605 ACGTAAGGGAAGCAACGAGG 60.038 55.000 0.23 0.00 46.39 4.63
46 47 2.257034 GTACGTAAGGGAAGCAACGAG 58.743 52.381 0.00 0.00 46.39 4.18
47 48 1.612950 TGTACGTAAGGGAAGCAACGA 59.387 47.619 0.00 0.00 46.39 3.85
48 49 1.723003 GTGTACGTAAGGGAAGCAACG 59.277 52.381 0.00 0.00 46.39 4.10
49 50 2.991866 GAGTGTACGTAAGGGAAGCAAC 59.008 50.000 0.00 0.00 46.39 4.17
50 51 2.028748 GGAGTGTACGTAAGGGAAGCAA 60.029 50.000 0.00 0.00 46.39 3.91
51 52 1.547372 GGAGTGTACGTAAGGGAAGCA 59.453 52.381 0.00 0.00 46.39 3.91
52 53 1.547372 TGGAGTGTACGTAAGGGAAGC 59.453 52.381 0.00 0.00 46.39 3.86
53 54 3.257624 ACTTGGAGTGTACGTAAGGGAAG 59.742 47.826 0.00 0.00 46.39 3.46
54 55 3.233507 ACTTGGAGTGTACGTAAGGGAA 58.766 45.455 0.00 0.00 46.39 3.97
55 56 2.821969 GACTTGGAGTGTACGTAAGGGA 59.178 50.000 0.00 0.00 46.39 4.20
56 57 2.824341 AGACTTGGAGTGTACGTAAGGG 59.176 50.000 0.00 0.00 46.39 3.95
57 58 4.483311 GAAGACTTGGAGTGTACGTAAGG 58.517 47.826 0.00 0.00 46.39 2.69
59 60 3.058016 CCGAAGACTTGGAGTGTACGTAA 60.058 47.826 0.00 0.00 0.00 3.18
60 61 2.485426 CCGAAGACTTGGAGTGTACGTA 59.515 50.000 0.00 0.00 0.00 3.57
61 62 1.268899 CCGAAGACTTGGAGTGTACGT 59.731 52.381 0.00 0.00 0.00 3.57
62 63 1.402456 CCCGAAGACTTGGAGTGTACG 60.402 57.143 0.00 0.00 0.00 3.67
63 64 1.891150 TCCCGAAGACTTGGAGTGTAC 59.109 52.381 0.00 0.00 0.00 2.90
64 65 2.297698 TCCCGAAGACTTGGAGTGTA 57.702 50.000 0.00 0.00 0.00 2.90
65 66 1.645710 ATCCCGAAGACTTGGAGTGT 58.354 50.000 0.00 0.00 0.00 3.55
66 67 2.350522 CAATCCCGAAGACTTGGAGTG 58.649 52.381 7.40 7.40 37.83 3.51
67 68 1.339151 GCAATCCCGAAGACTTGGAGT 60.339 52.381 0.00 0.00 0.00 3.85
68 69 1.065854 AGCAATCCCGAAGACTTGGAG 60.066 52.381 0.00 0.00 0.00 3.86
69 70 0.984230 AGCAATCCCGAAGACTTGGA 59.016 50.000 0.00 0.00 0.00 3.53
70 71 1.740025 GAAGCAATCCCGAAGACTTGG 59.260 52.381 0.00 0.00 0.00 3.61
71 72 1.740025 GGAAGCAATCCCGAAGACTTG 59.260 52.381 0.00 0.00 43.00 3.16
72 73 2.115343 GGAAGCAATCCCGAAGACTT 57.885 50.000 0.00 0.00 43.00 3.01
73 74 3.863407 GGAAGCAATCCCGAAGACT 57.137 52.632 0.00 0.00 43.00 3.24
79 80 0.958382 TTGGAACGGAAGCAATCCCG 60.958 55.000 0.00 0.00 46.39 5.14
80 81 1.253100 TTTGGAACGGAAGCAATCCC 58.747 50.000 3.23 0.00 46.39 3.85
81 82 3.378911 TTTTTGGAACGGAAGCAATCC 57.621 42.857 0.00 0.00 45.57 3.01
82 83 6.156519 AGTTATTTTTGGAACGGAAGCAATC 58.843 36.000 0.00 0.00 0.00 2.67
83 84 6.096673 AGTTATTTTTGGAACGGAAGCAAT 57.903 33.333 0.00 0.00 0.00 3.56
84 85 5.508320 GGAGTTATTTTTGGAACGGAAGCAA 60.508 40.000 0.00 0.00 0.00 3.91
85 86 4.022676 GGAGTTATTTTTGGAACGGAAGCA 60.023 41.667 0.00 0.00 0.00 3.91
86 87 4.482386 GGAGTTATTTTTGGAACGGAAGC 58.518 43.478 0.00 0.00 0.00 3.86
87 88 4.082408 GGGGAGTTATTTTTGGAACGGAAG 60.082 45.833 0.00 0.00 0.00 3.46
88 89 3.827876 GGGGAGTTATTTTTGGAACGGAA 59.172 43.478 0.00 0.00 0.00 4.30
89 90 3.423749 GGGGAGTTATTTTTGGAACGGA 58.576 45.455 0.00 0.00 0.00 4.69
90 91 2.494471 GGGGGAGTTATTTTTGGAACGG 59.506 50.000 0.00 0.00 0.00 4.44
91 92 2.162809 CGGGGGAGTTATTTTTGGAACG 59.837 50.000 0.00 0.00 0.00 3.95
92 93 3.423749 TCGGGGGAGTTATTTTTGGAAC 58.576 45.455 0.00 0.00 0.00 3.62
93 94 3.810721 TCGGGGGAGTTATTTTTGGAA 57.189 42.857 0.00 0.00 0.00 3.53
94 95 3.562609 CCTTCGGGGGAGTTATTTTTGGA 60.563 47.826 0.00 0.00 0.00 3.53
95 96 2.758423 CCTTCGGGGGAGTTATTTTTGG 59.242 50.000 0.00 0.00 0.00 3.28
96 97 3.427573 ACCTTCGGGGGAGTTATTTTTG 58.572 45.455 1.80 0.00 40.03 2.44
97 98 3.820195 ACCTTCGGGGGAGTTATTTTT 57.180 42.857 1.80 0.00 40.03 1.94
98 99 3.820195 AACCTTCGGGGGAGTTATTTT 57.180 42.857 1.80 0.00 40.03 1.82
99 100 3.074836 TGAAACCTTCGGGGGAGTTATTT 59.925 43.478 1.80 0.00 40.03 1.40
100 101 2.645797 TGAAACCTTCGGGGGAGTTATT 59.354 45.455 1.80 0.00 40.03 1.40
101 102 2.271777 TGAAACCTTCGGGGGAGTTAT 58.728 47.619 1.80 0.00 40.03 1.89
102 103 1.732117 TGAAACCTTCGGGGGAGTTA 58.268 50.000 1.80 0.00 40.03 2.24
103 104 1.073098 ATGAAACCTTCGGGGGAGTT 58.927 50.000 1.80 0.00 40.03 3.01
104 105 1.004394 GAATGAAACCTTCGGGGGAGT 59.996 52.381 1.80 0.00 40.03 3.85
105 106 1.682087 GGAATGAAACCTTCGGGGGAG 60.682 57.143 1.80 0.00 40.03 4.30
106 107 0.330267 GGAATGAAACCTTCGGGGGA 59.670 55.000 1.80 0.00 40.03 4.81
107 108 1.029947 CGGAATGAAACCTTCGGGGG 61.030 60.000 0.89 0.00 40.03 5.40
108 109 0.322187 ACGGAATGAAACCTTCGGGG 60.322 55.000 0.00 0.00 40.03 5.73
109 110 1.530323 AACGGAATGAAACCTTCGGG 58.470 50.000 0.00 0.00 41.87 5.14
110 111 2.351350 CCAAACGGAATGAAACCTTCGG 60.351 50.000 0.00 0.00 0.00 4.30
111 112 2.550606 TCCAAACGGAATGAAACCTTCG 59.449 45.455 0.00 0.00 0.00 3.79
112 113 3.568430 AGTCCAAACGGAATGAAACCTTC 59.432 43.478 0.00 0.00 33.16 3.46
113 114 3.562182 AGTCCAAACGGAATGAAACCTT 58.438 40.909 0.00 0.00 33.16 3.50
114 115 3.146847 GAGTCCAAACGGAATGAAACCT 58.853 45.455 0.00 0.00 33.16 3.50
115 116 2.228103 GGAGTCCAAACGGAATGAAACC 59.772 50.000 3.60 0.00 33.16 3.27
116 117 2.095919 CGGAGTCCAAACGGAATGAAAC 60.096 50.000 10.49 0.00 33.16 2.78
117 118 2.147958 CGGAGTCCAAACGGAATGAAA 58.852 47.619 10.49 0.00 33.16 2.69
118 119 1.071071 ACGGAGTCCAAACGGAATGAA 59.929 47.619 10.49 0.00 29.74 2.57
119 120 0.682852 ACGGAGTCCAAACGGAATGA 59.317 50.000 10.49 0.00 29.74 2.57
120 121 1.519408 AACGGAGTCCAAACGGAATG 58.481 50.000 10.49 0.00 45.00 2.67
121 122 1.877443 CAAACGGAGTCCAAACGGAAT 59.123 47.619 10.49 0.00 45.00 3.01
122 123 1.134461 TCAAACGGAGTCCAAACGGAA 60.134 47.619 10.49 0.00 45.00 4.30
123 124 0.464870 TCAAACGGAGTCCAAACGGA 59.535 50.000 10.49 0.00 45.00 4.69
124 125 1.519408 ATCAAACGGAGTCCAAACGG 58.481 50.000 10.49 0.00 45.00 4.44
125 126 4.201783 GGAATATCAAACGGAGTCCAAACG 60.202 45.833 10.49 0.00 45.00 3.60
126 127 4.941873 AGGAATATCAAACGGAGTCCAAAC 59.058 41.667 10.49 0.00 45.00 2.93
127 128 5.174037 AGGAATATCAAACGGAGTCCAAA 57.826 39.130 10.49 0.00 45.00 3.28
128 129 4.837093 AGGAATATCAAACGGAGTCCAA 57.163 40.909 10.49 0.00 45.00 3.53
129 130 4.837093 AAGGAATATCAAACGGAGTCCA 57.163 40.909 10.49 0.00 45.00 4.02
130 131 5.880887 AGAAAAGGAATATCAAACGGAGTCC 59.119 40.000 0.00 0.00 45.00 3.85
131 132 6.675728 GCAGAAAAGGAATATCAAACGGAGTC 60.676 42.308 0.00 0.00 45.00 3.36
133 134 5.573146 GCAGAAAAGGAATATCAAACGGAG 58.427 41.667 0.00 0.00 0.00 4.63
134 135 4.094294 CGCAGAAAAGGAATATCAAACGGA 59.906 41.667 0.00 0.00 0.00 4.69
135 136 4.094294 TCGCAGAAAAGGAATATCAAACGG 59.906 41.667 0.00 0.00 0.00 4.44
136 137 5.216566 TCGCAGAAAAGGAATATCAAACG 57.783 39.130 0.00 0.00 0.00 3.60
137 138 6.861055 TGTTTCGCAGAAAAGGAATATCAAAC 59.139 34.615 5.51 0.00 45.90 2.93
138 139 6.976088 TGTTTCGCAGAAAAGGAATATCAAA 58.024 32.000 5.51 0.00 45.90 2.69
139 140 6.567687 TGTTTCGCAGAAAAGGAATATCAA 57.432 33.333 5.51 0.00 45.90 2.57
154 155 2.354510 CTCCTTGTTTCACTGTTTCGCA 59.645 45.455 0.00 0.00 0.00 5.10
155 156 2.612212 TCTCCTTGTTTCACTGTTTCGC 59.388 45.455 0.00 0.00 0.00 4.70
156 157 4.119862 TCTCTCCTTGTTTCACTGTTTCG 58.880 43.478 0.00 0.00 0.00 3.46
157 158 6.128007 TGTTTCTCTCCTTGTTTCACTGTTTC 60.128 38.462 0.00 0.00 0.00 2.78
158 159 5.710099 TGTTTCTCTCCTTGTTTCACTGTTT 59.290 36.000 0.00 0.00 0.00 2.83
159 160 5.253330 TGTTTCTCTCCTTGTTTCACTGTT 58.747 37.500 0.00 0.00 0.00 3.16
160 161 4.843728 TGTTTCTCTCCTTGTTTCACTGT 58.156 39.130 0.00 0.00 0.00 3.55
161 162 5.118990 TCTGTTTCTCTCCTTGTTTCACTG 58.881 41.667 0.00 0.00 0.00 3.66
162 163 5.359194 TCTGTTTCTCTCCTTGTTTCACT 57.641 39.130 0.00 0.00 0.00 3.41
163 164 6.094186 AGTTTCTGTTTCTCTCCTTGTTTCAC 59.906 38.462 0.00 0.00 0.00 3.18
164 165 6.094048 CAGTTTCTGTTTCTCTCCTTGTTTCA 59.906 38.462 0.00 0.00 0.00 2.69
165 166 6.458888 CCAGTTTCTGTTTCTCTCCTTGTTTC 60.459 42.308 0.00 0.00 0.00 2.78
166 167 5.358160 CCAGTTTCTGTTTCTCTCCTTGTTT 59.642 40.000 0.00 0.00 0.00 2.83
167 168 4.884164 CCAGTTTCTGTTTCTCTCCTTGTT 59.116 41.667 0.00 0.00 0.00 2.83
168 169 4.455606 CCAGTTTCTGTTTCTCTCCTTGT 58.544 43.478 0.00 0.00 0.00 3.16
169 170 3.251972 GCCAGTTTCTGTTTCTCTCCTTG 59.748 47.826 0.00 0.00 0.00 3.61
170 171 3.481453 GCCAGTTTCTGTTTCTCTCCTT 58.519 45.455 0.00 0.00 0.00 3.36
171 172 2.548920 CGCCAGTTTCTGTTTCTCTCCT 60.549 50.000 0.00 0.00 0.00 3.69
172 173 1.801178 CGCCAGTTTCTGTTTCTCTCC 59.199 52.381 0.00 0.00 0.00 3.71
173 174 1.195674 GCGCCAGTTTCTGTTTCTCTC 59.804 52.381 0.00 0.00 0.00 3.20
174 175 1.202698 AGCGCCAGTTTCTGTTTCTCT 60.203 47.619 2.29 0.00 0.00 3.10
175 176 1.069636 CAGCGCCAGTTTCTGTTTCTC 60.070 52.381 2.29 0.00 0.00 2.87
176 177 0.947244 CAGCGCCAGTTTCTGTTTCT 59.053 50.000 2.29 0.00 0.00 2.52
177 178 0.040067 CCAGCGCCAGTTTCTGTTTC 60.040 55.000 2.29 0.00 0.00 2.78
178 179 1.455383 CCCAGCGCCAGTTTCTGTTT 61.455 55.000 2.29 0.00 0.00 2.83
179 180 1.898574 CCCAGCGCCAGTTTCTGTT 60.899 57.895 2.29 0.00 0.00 3.16
180 181 2.281761 CCCAGCGCCAGTTTCTGT 60.282 61.111 2.29 0.00 0.00 3.41
181 182 3.741476 GCCCAGCGCCAGTTTCTG 61.741 66.667 2.29 0.00 0.00 3.02
182 183 3.909086 GAGCCCAGCGCCAGTTTCT 62.909 63.158 2.29 0.00 38.78 2.52
183 184 3.435186 GAGCCCAGCGCCAGTTTC 61.435 66.667 2.29 0.00 38.78 2.78
184 185 3.958860 AGAGCCCAGCGCCAGTTT 61.959 61.111 2.29 0.00 38.78 2.66
185 186 4.711949 CAGAGCCCAGCGCCAGTT 62.712 66.667 2.29 0.00 38.78 3.16
190 191 2.893682 ATTAACCCAGAGCCCAGCGC 62.894 60.000 0.00 0.00 37.98 5.92
191 192 0.468226 TATTAACCCAGAGCCCAGCG 59.532 55.000 0.00 0.00 0.00 5.18
192 193 1.202818 CCTATTAACCCAGAGCCCAGC 60.203 57.143 0.00 0.00 0.00 4.85
193 194 2.127708 ACCTATTAACCCAGAGCCCAG 58.872 52.381 0.00 0.00 0.00 4.45
194 195 2.280308 ACCTATTAACCCAGAGCCCA 57.720 50.000 0.00 0.00 0.00 5.36
195 196 3.715315 ACTAACCTATTAACCCAGAGCCC 59.285 47.826 0.00 0.00 0.00 5.19
196 197 4.202336 GGACTAACCTATTAACCCAGAGCC 60.202 50.000 0.00 0.00 35.41 4.70
197 198 4.202336 GGGACTAACCTATTAACCCAGAGC 60.202 50.000 0.00 0.00 37.14 4.09
198 199 4.966805 TGGGACTAACCTATTAACCCAGAG 59.033 45.833 0.00 0.00 39.77 3.35
199 200 4.962839 TGGGACTAACCTATTAACCCAGA 58.037 43.478 0.00 0.00 39.77 3.86
200 201 5.703730 TTGGGACTAACCTATTAACCCAG 57.296 43.478 0.00 0.00 42.67 4.45
201 202 6.466009 TTTTGGGACTAACCTATTAACCCA 57.534 37.500 0.00 0.00 41.38 4.51
202 203 7.966339 ATTTTTGGGACTAACCTATTAACCC 57.034 36.000 0.00 0.00 37.43 4.11
231 232 9.676195 GTTTACGGGCTTTATTAAACACTTTTA 57.324 29.630 0.00 0.00 35.43 1.52
232 233 8.196103 TGTTTACGGGCTTTATTAAACACTTTT 58.804 29.630 2.44 0.00 38.75 2.27
233 234 7.714703 TGTTTACGGGCTTTATTAAACACTTT 58.285 30.769 2.44 0.00 38.75 2.66
234 235 7.274603 TGTTTACGGGCTTTATTAAACACTT 57.725 32.000 2.44 0.00 38.75 3.16
235 236 6.880942 TGTTTACGGGCTTTATTAAACACT 57.119 33.333 2.44 0.00 38.75 3.55
236 237 6.748658 GGATGTTTACGGGCTTTATTAAACAC 59.251 38.462 7.68 3.74 43.57 3.32
237 238 6.433404 TGGATGTTTACGGGCTTTATTAAACA 59.567 34.615 7.90 7.90 44.39 2.83
238 239 6.854778 TGGATGTTTACGGGCTTTATTAAAC 58.145 36.000 0.00 0.00 35.75 2.01
239 240 7.648039 ATGGATGTTTACGGGCTTTATTAAA 57.352 32.000 0.00 0.00 0.00 1.52
240 241 8.623030 GTTATGGATGTTTACGGGCTTTATTAA 58.377 33.333 0.00 0.00 0.00 1.40
241 242 7.774157 TGTTATGGATGTTTACGGGCTTTATTA 59.226 33.333 0.00 0.00 0.00 0.98
242 243 6.603997 TGTTATGGATGTTTACGGGCTTTATT 59.396 34.615 0.00 0.00 0.00 1.40
243 244 6.123651 TGTTATGGATGTTTACGGGCTTTAT 58.876 36.000 0.00 0.00 0.00 1.40
244 245 5.498393 TGTTATGGATGTTTACGGGCTTTA 58.502 37.500 0.00 0.00 0.00 1.85
245 246 4.337145 TGTTATGGATGTTTACGGGCTTT 58.663 39.130 0.00 0.00 0.00 3.51
246 247 3.945285 CTGTTATGGATGTTTACGGGCTT 59.055 43.478 0.00 0.00 0.00 4.35
247 248 3.199071 TCTGTTATGGATGTTTACGGGCT 59.801 43.478 0.00 0.00 0.00 5.19
248 249 3.537580 TCTGTTATGGATGTTTACGGGC 58.462 45.455 0.00 0.00 0.00 6.13
249 250 7.979444 ATTATCTGTTATGGATGTTTACGGG 57.021 36.000 0.00 0.00 0.00 5.28
308 309 4.929808 AGTTGACATTGATACGTCTCCAAC 59.070 41.667 0.00 1.57 33.18 3.77
309 310 4.929211 CAGTTGACATTGATACGTCTCCAA 59.071 41.667 0.00 0.00 33.18 3.53
310 311 4.494484 CAGTTGACATTGATACGTCTCCA 58.506 43.478 0.00 0.00 33.18 3.86
311 312 3.307242 GCAGTTGACATTGATACGTCTCC 59.693 47.826 0.00 0.00 33.18 3.71
312 313 3.307242 GGCAGTTGACATTGATACGTCTC 59.693 47.826 0.00 0.00 33.18 3.36
313 314 3.262420 GGCAGTTGACATTGATACGTCT 58.738 45.455 0.00 0.00 33.18 4.18
314 315 3.000041 TGGCAGTTGACATTGATACGTC 59.000 45.455 0.00 0.00 0.00 4.34
315 316 3.052455 TGGCAGTTGACATTGATACGT 57.948 42.857 0.00 0.00 0.00 3.57
316 317 3.302675 CGATGGCAGTTGACATTGATACG 60.303 47.826 9.23 1.00 45.42 3.06
317 318 3.546815 GCGATGGCAGTTGACATTGATAC 60.547 47.826 17.56 0.00 45.42 2.24
318 319 2.613595 GCGATGGCAGTTGACATTGATA 59.386 45.455 17.56 0.00 45.42 2.15
319 320 1.402968 GCGATGGCAGTTGACATTGAT 59.597 47.619 17.56 0.00 45.42 2.57
320 321 0.804364 GCGATGGCAGTTGACATTGA 59.196 50.000 17.56 0.00 45.42 2.57
321 322 0.521867 CGCGATGGCAGTTGACATTG 60.522 55.000 0.00 10.34 45.42 2.82
322 323 1.796151 CGCGATGGCAGTTGACATT 59.204 52.632 0.00 0.00 45.42 2.71
555 557 1.147824 CCCATCGCCATGAGCTCTT 59.852 57.895 16.19 5.66 40.39 2.85
603 607 1.132299 ACCACTACTTACCCACCCCTT 60.132 52.381 0.00 0.00 0.00 3.95
604 608 0.495008 ACCACTACTTACCCACCCCT 59.505 55.000 0.00 0.00 0.00 4.79
679 684 5.865085 TGAAGAGCTTGTAGTTACAATGGT 58.135 37.500 5.27 5.78 44.34 3.55
999 1005 1.077429 GGTGAAGTCCAGGGGCATC 60.077 63.158 0.00 0.00 0.00 3.91
1152 1158 3.895041 TCACCATGTAGCCGATCTTGATA 59.105 43.478 0.00 0.00 0.00 2.15
1276 1282 2.365105 CCGGCCCTACTCCTTGGA 60.365 66.667 0.00 0.00 0.00 3.53
1309 1315 6.266323 TGTTCAAAGCAGACTCGATAGTATC 58.734 40.000 0.00 0.00 35.56 2.24
1369 1375 7.761704 AGCATAATTCAGATATAAGCAGTACCG 59.238 37.037 0.00 0.00 0.00 4.02
1471 1477 2.240160 TGGTGTGTGGTAACCTCTTTGT 59.760 45.455 0.00 0.00 37.36 2.83
1561 1567 1.795170 GCATGGCACGAACCACACTT 61.795 55.000 3.30 0.00 44.17 3.16
1589 1595 1.549620 CATTTGGTTGCCTACATGCCA 59.450 47.619 0.00 0.00 31.74 4.92
1596 1602 3.055021 TGGACGTATCATTTGGTTGCCTA 60.055 43.478 0.00 0.00 0.00 3.93
2075 2081 0.900647 CTCACGGAGGGAAGTGTCCT 60.901 60.000 0.00 0.00 44.28 3.85
2091 2097 1.278302 TGGCGATGATTTCCCCCTCA 61.278 55.000 0.00 0.00 0.00 3.86
2144 2151 3.947612 AGATGTTGATGGAGATTGGCT 57.052 42.857 0.00 0.00 0.00 4.75
2262 2269 7.852263 ACTAGCATCAACTACAAGGAGTAATT 58.148 34.615 0.00 0.00 30.92 1.40


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

AutoCloner maintained by Alex Coulton.