Multiple sequence alignment - TraesCS2D01G450100

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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 TraesCS2D01G450100 chr2D 100.000 3456 0 0 1 3456 559397200 559393745 0.000000e+00 6383
1 TraesCS2D01G450100 chr2D 93.697 476 30 0 2686 3161 493170208 493170683 0.000000e+00 713
2 TraesCS2D01G450100 chr2B 86.281 2544 195 69 252 2707 668571628 668569151 0.000000e+00 2623
3 TraesCS2D01G450100 chr2B 90.868 219 18 2 3237 3454 668569156 668568939 3.370000e-75 292
4 TraesCS2D01G450100 chr2A 88.271 1637 118 31 1094 2688 699913469 699911865 0.000000e+00 1892
5 TraesCS2D01G450100 chr2A 85.127 316 14 20 691 1002 699914208 699913922 3.370000e-75 292
6 TraesCS2D01G450100 chr3A 91.107 551 49 0 2692 3242 647467415 647466865 0.000000e+00 747
7 TraesCS2D01G450100 chr3A 93.878 98 3 3 3142 3239 514054018 514054112 1.000000e-30 145
8 TraesCS2D01G450100 chr1D 94.947 475 19 2 2688 3161 10210873 10211343 0.000000e+00 739
9 TraesCS2D01G450100 chr1D 94.021 485 25 2 2686 3170 415271522 415271042 0.000000e+00 732
10 TraesCS2D01G450100 chr1D 94.681 470 25 0 2692 3161 474919400 474919869 0.000000e+00 730
11 TraesCS2D01G450100 chr1D 98.810 84 1 0 3156 3239 474919823 474919906 2.150000e-32 150
12 TraesCS2D01G450100 chr1D 86.275 102 14 0 3350 3451 479562692 479562591 1.010000e-20 111
13 TraesCS2D01G450100 chr5D 94.255 470 27 0 2692 3161 192547219 192547688 0.000000e+00 719
14 TraesCS2D01G450100 chr5D 97.701 87 2 0 3156 3242 99925807 99925721 2.150000e-32 150
15 TraesCS2D01G450100 chr5D 84.000 150 19 4 14 161 544785353 544785499 4.650000e-29 139
16 TraesCS2D01G450100 chr5D 85.577 104 15 0 3348 3451 233060899 233061002 3.650000e-20 110
17 TraesCS2D01G450100 chr5D 83.929 112 18 0 3340 3451 3969746 3969635 1.310000e-19 108
18 TraesCS2D01G450100 chr7D 93.542 480 30 1 2692 3170 423347783 423347304 0.000000e+00 713
19 TraesCS2D01G450100 chr7D 97.727 88 2 0 3155 3242 423347360 423347273 5.970000e-33 152
20 TraesCS2D01G450100 chr4D 93.542 480 29 2 2692 3170 84284264 84283786 0.000000e+00 713
21 TraesCS2D01G450100 chr4D 97.701 87 2 0 3156 3242 84283841 84283755 2.150000e-32 150
22 TraesCS2D01G450100 chr3D 92.902 479 33 1 2683 3161 426841108 426841585 0.000000e+00 695
23 TraesCS2D01G450100 chr3D 97.701 87 2 0 3156 3242 13111737 13111823 2.150000e-32 150
24 TraesCS2D01G450100 chr3D 97.701 87 2 0 3156 3242 73427801 73427715 2.150000e-32 150
25 TraesCS2D01G450100 chr3D 98.810 84 1 0 3156 3239 289837036 289837119 2.150000e-32 150
26 TraesCS2D01G450100 chr3D 86.869 99 13 0 3353 3451 105494939 105495037 1.010000e-20 111
27 TraesCS2D01G450100 chr7B 83.117 154 22 4 9 161 285337910 285337760 1.670000e-28 137
28 TraesCS2D01G450100 chr1B 88.776 98 11 0 3355 3452 642666427 642666524 1.680000e-23 121
29 TraesCS2D01G450100 chr1B 83.929 112 18 0 3340 3451 596319932 596320043 1.310000e-19 108
30 TraesCS2D01G450100 chr7A 88.000 100 12 0 3353 3452 463755236 463755137 6.060000e-23 119
31 TraesCS2D01G450100 chr6D 85.577 104 15 0 3348 3451 276018824 276018927 3.650000e-20 110


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 TraesCS2D01G450100 chr2D 559393745 559397200 3455 True 6383.0 6383 100.0000 1 3456 1 chr2D.!!$R1 3455
1 TraesCS2D01G450100 chr2B 668568939 668571628 2689 True 1457.5 2623 88.5745 252 3454 2 chr2B.!!$R1 3202
2 TraesCS2D01G450100 chr2A 699911865 699914208 2343 True 1092.0 1892 86.6990 691 2688 2 chr2A.!!$R1 1997
3 TraesCS2D01G450100 chr3A 647466865 647467415 550 True 747.0 747 91.1070 2692 3242 1 chr3A.!!$R1 550
4 TraesCS2D01G450100 chr1D 474919400 474919906 506 False 440.0 730 96.7455 2692 3239 2 chr1D.!!$F2 547
5 TraesCS2D01G450100 chr7D 423347273 423347783 510 True 432.5 713 95.6345 2692 3242 2 chr7D.!!$R1 550
6 TraesCS2D01G450100 chr4D 84283755 84284264 509 True 431.5 713 95.6215 2692 3242 2 chr4D.!!$R1 550

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
673 674 0.101579 CGTTTTGGGCGGTTTCAGTT 59.898 50.0 0.0 0.0 0.0 3.16 F
941 949 0.110192 GTGCGTTTCCTTGCTGCTAC 60.110 55.0 0.0 0.0 0.0 3.58 F
1478 1865 0.461163 GCGTGCTGGTTTTGGGTTTT 60.461 50.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2459 0.400213 GGCGTTGGGGATCCATCATA 59.600 55.0 15.23 0.41 43.63 2.15 R
2036 2502 0.526096 GCACAAGTTATGCATGGGCG 60.526 55.0 10.16 0.00 45.35 6.13 R
3265 3787 0.524816 CCGGTCACTATCCACGAACG 60.525 60.0 0.00 0.00 39.53 3.95 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
17 18 2.885861 CGGCGAGGTGCTCTAGTT 59.114 61.111 0.00 0.00 45.43 2.24
18 19 1.517257 CGGCGAGGTGCTCTAGTTG 60.517 63.158 0.00 0.00 45.43 3.16
19 20 1.890894 GGCGAGGTGCTCTAGTTGA 59.109 57.895 0.00 0.00 45.43 3.18
20 21 0.458716 GGCGAGGTGCTCTAGTTGAC 60.459 60.000 0.00 0.00 45.43 3.18
21 22 0.458716 GCGAGGTGCTCTAGTTGACC 60.459 60.000 0.00 0.00 41.73 4.02
22 23 0.173708 CGAGGTGCTCTAGTTGACCC 59.826 60.000 0.00 0.00 0.00 4.46
23 24 1.267121 GAGGTGCTCTAGTTGACCCA 58.733 55.000 0.00 0.00 0.00 4.51
24 25 1.834263 GAGGTGCTCTAGTTGACCCAT 59.166 52.381 0.00 0.00 0.00 4.00
25 26 1.834263 AGGTGCTCTAGTTGACCCATC 59.166 52.381 0.00 0.00 0.00 3.51
26 27 1.555075 GGTGCTCTAGTTGACCCATCA 59.445 52.381 0.00 0.00 0.00 3.07
27 28 2.171448 GGTGCTCTAGTTGACCCATCAT 59.829 50.000 0.00 0.00 33.85 2.45
28 29 3.201290 GTGCTCTAGTTGACCCATCATG 58.799 50.000 0.00 0.00 33.85 3.07
29 30 2.171237 TGCTCTAGTTGACCCATCATGG 59.829 50.000 0.00 0.00 33.85 3.66
30 31 2.435805 GCTCTAGTTGACCCATCATGGA 59.564 50.000 4.75 0.00 40.96 3.41
31 32 3.118261 GCTCTAGTTGACCCATCATGGAA 60.118 47.826 4.75 0.00 40.96 3.53
32 33 4.446371 CTCTAGTTGACCCATCATGGAAC 58.554 47.826 4.75 1.50 40.96 3.62
46 47 0.801872 TGGAACAAATGATGCCGTCG 59.198 50.000 0.00 0.00 31.92 5.12
47 48 1.083489 GGAACAAATGATGCCGTCGA 58.917 50.000 0.00 0.00 0.00 4.20
48 49 1.466950 GGAACAAATGATGCCGTCGAA 59.533 47.619 0.00 0.00 0.00 3.71
49 50 2.097466 GGAACAAATGATGCCGTCGAAT 59.903 45.455 0.00 0.00 0.00 3.34
50 51 3.311322 GGAACAAATGATGCCGTCGAATA 59.689 43.478 0.00 0.00 0.00 1.75
51 52 4.024048 GGAACAAATGATGCCGTCGAATAT 60.024 41.667 0.00 0.00 0.00 1.28
52 53 5.499139 AACAAATGATGCCGTCGAATATT 57.501 34.783 0.00 0.00 0.00 1.28
53 54 6.293190 GGAACAAATGATGCCGTCGAATATTA 60.293 38.462 0.00 0.00 0.00 0.98
54 55 6.801539 ACAAATGATGCCGTCGAATATTAT 57.198 33.333 0.00 0.00 0.00 1.28
55 56 6.602179 ACAAATGATGCCGTCGAATATTATG 58.398 36.000 0.00 0.00 0.00 1.90
56 57 6.204688 ACAAATGATGCCGTCGAATATTATGT 59.795 34.615 0.00 0.00 0.00 2.29
57 58 6.801539 AATGATGCCGTCGAATATTATGTT 57.198 33.333 0.00 0.00 0.00 2.71
58 59 6.801539 ATGATGCCGTCGAATATTATGTTT 57.198 33.333 0.00 0.00 0.00 2.83
59 60 5.984627 TGATGCCGTCGAATATTATGTTTG 58.015 37.500 0.00 0.00 0.00 2.93
60 61 4.804608 TGCCGTCGAATATTATGTTTGG 57.195 40.909 0.00 0.00 0.00 3.28
61 62 4.193090 TGCCGTCGAATATTATGTTTGGT 58.807 39.130 0.00 0.00 0.00 3.67
62 63 4.034626 TGCCGTCGAATATTATGTTTGGTG 59.965 41.667 0.00 0.00 0.00 4.17
63 64 4.034742 GCCGTCGAATATTATGTTTGGTGT 59.965 41.667 0.00 0.00 0.00 4.16
64 65 5.234757 GCCGTCGAATATTATGTTTGGTGTA 59.765 40.000 0.00 0.00 0.00 2.90
65 66 6.073440 GCCGTCGAATATTATGTTTGGTGTAT 60.073 38.462 0.00 0.00 0.00 2.29
66 67 7.519328 GCCGTCGAATATTATGTTTGGTGTATT 60.519 37.037 0.00 0.00 0.00 1.89
67 68 8.980610 CCGTCGAATATTATGTTTGGTGTATTA 58.019 33.333 0.00 0.00 0.00 0.98
68 69 9.787626 CGTCGAATATTATGTTTGGTGTATTAC 57.212 33.333 0.00 0.00 0.00 1.89
95 96 8.873215 AGTTATGGTATGTAGATTGACTTTCG 57.127 34.615 0.00 0.00 0.00 3.46
96 97 8.475639 AGTTATGGTATGTAGATTGACTTTCGT 58.524 33.333 0.00 0.00 0.00 3.85
97 98 9.740239 GTTATGGTATGTAGATTGACTTTCGTA 57.260 33.333 0.00 0.00 0.00 3.43
99 100 8.818141 ATGGTATGTAGATTGACTTTCGTATG 57.182 34.615 0.00 0.00 0.00 2.39
100 101 7.778083 TGGTATGTAGATTGACTTTCGTATGT 58.222 34.615 0.00 0.00 0.00 2.29
101 102 7.919091 TGGTATGTAGATTGACTTTCGTATGTC 59.081 37.037 1.72 1.72 0.00 3.06
102 103 8.136165 GGTATGTAGATTGACTTTCGTATGTCT 58.864 37.037 9.02 0.00 34.57 3.41
103 104 9.517609 GTATGTAGATTGACTTTCGTATGTCTT 57.482 33.333 9.02 0.00 34.57 3.01
104 105 7.812309 TGTAGATTGACTTTCGTATGTCTTG 57.188 36.000 9.02 0.00 34.57 3.02
105 106 7.599171 TGTAGATTGACTTTCGTATGTCTTGA 58.401 34.615 9.02 0.00 34.57 3.02
106 107 8.085909 TGTAGATTGACTTTCGTATGTCTTGAA 58.914 33.333 9.02 0.00 34.57 2.69
107 108 7.962964 AGATTGACTTTCGTATGTCTTGAAA 57.037 32.000 9.02 0.00 34.57 2.69
108 109 7.797819 AGATTGACTTTCGTATGTCTTGAAAC 58.202 34.615 9.02 0.00 34.57 2.78
109 110 7.657761 AGATTGACTTTCGTATGTCTTGAAACT 59.342 33.333 9.02 0.00 34.57 2.66
110 111 8.827177 ATTGACTTTCGTATGTCTTGAAACTA 57.173 30.769 9.02 0.00 34.57 2.24
111 112 7.869016 TGACTTTCGTATGTCTTGAAACTAG 57.131 36.000 9.02 0.00 34.57 2.57
112 113 7.654568 TGACTTTCGTATGTCTTGAAACTAGA 58.345 34.615 0.00 0.00 34.57 2.43
113 114 8.139350 TGACTTTCGTATGTCTTGAAACTAGAA 58.861 33.333 0.00 0.00 34.57 2.10
114 115 9.141400 GACTTTCGTATGTCTTGAAACTAGAAT 57.859 33.333 0.00 0.00 0.00 2.40
115 116 9.490379 ACTTTCGTATGTCTTGAAACTAGAATT 57.510 29.630 0.00 0.00 0.00 2.17
140 141 7.917730 TTTTTAGGGGTAGTTTTTAGCCTTT 57.082 32.000 2.83 0.00 35.55 3.11
142 143 8.640063 TTTTAGGGGTAGTTTTTAGCCTTTAG 57.360 34.615 2.83 0.00 35.55 1.85
143 144 5.855338 AGGGGTAGTTTTTAGCCTTTAGT 57.145 39.130 2.83 0.00 35.55 2.24
144 145 6.210172 AGGGGTAGTTTTTAGCCTTTAGTT 57.790 37.500 2.83 0.00 35.55 2.24
145 146 6.617538 AGGGGTAGTTTTTAGCCTTTAGTTT 58.382 36.000 2.83 0.00 35.55 2.66
146 147 7.071273 AGGGGTAGTTTTTAGCCTTTAGTTTT 58.929 34.615 2.83 0.00 35.55 2.43
147 148 7.566138 AGGGGTAGTTTTTAGCCTTTAGTTTTT 59.434 33.333 2.83 0.00 35.55 1.94
148 149 7.869429 GGGGTAGTTTTTAGCCTTTAGTTTTTC 59.131 37.037 2.83 0.00 35.55 2.29
149 150 7.592533 GGGTAGTTTTTAGCCTTTAGTTTTTCG 59.407 37.037 0.00 0.00 32.66 3.46
150 151 7.113965 GGTAGTTTTTAGCCTTTAGTTTTTCGC 59.886 37.037 0.00 0.00 0.00 4.70
151 152 5.981315 AGTTTTTAGCCTTTAGTTTTTCGCC 59.019 36.000 0.00 0.00 0.00 5.54
152 153 5.777850 TTTTAGCCTTTAGTTTTTCGCCT 57.222 34.783 0.00 0.00 0.00 5.52
153 154 6.880942 TTTTAGCCTTTAGTTTTTCGCCTA 57.119 33.333 0.00 0.00 0.00 3.93
154 155 6.490566 TTTAGCCTTTAGTTTTTCGCCTAG 57.509 37.500 0.00 0.00 0.00 3.02
155 156 3.344515 AGCCTTTAGTTTTTCGCCTAGG 58.655 45.455 3.67 3.67 0.00 3.02
156 157 2.422479 GCCTTTAGTTTTTCGCCTAGGG 59.578 50.000 11.72 0.44 0.00 3.53
157 158 2.422479 CCTTTAGTTTTTCGCCTAGGGC 59.578 50.000 11.72 1.76 46.75 5.19
166 167 4.228567 GCCTAGGGCGTCTGGCTC 62.229 72.222 11.72 0.00 45.00 4.70
167 168 3.541713 CCTAGGGCGTCTGGCTCC 61.542 72.222 0.00 0.00 46.23 4.70
168 169 3.905678 CTAGGGCGTCTGGCTCCG 61.906 72.222 0.00 0.00 46.23 4.63
180 181 4.704833 GCTCCGCCACTGCCTTCA 62.705 66.667 0.00 0.00 0.00 3.02
181 182 2.435586 CTCCGCCACTGCCTTCAG 60.436 66.667 0.00 0.00 45.71 3.02
195 196 6.419980 CTGCCTTCAGTTATCTTTTCTCAG 57.580 41.667 0.00 0.00 35.61 3.35
196 197 5.869579 TGCCTTCAGTTATCTTTTCTCAGT 58.130 37.500 0.00 0.00 0.00 3.41
197 198 5.702670 TGCCTTCAGTTATCTTTTCTCAGTG 59.297 40.000 0.00 0.00 0.00 3.66
198 199 5.703130 GCCTTCAGTTATCTTTTCTCAGTGT 59.297 40.000 0.00 0.00 0.00 3.55
199 200 6.128418 GCCTTCAGTTATCTTTTCTCAGTGTC 60.128 42.308 0.00 0.00 0.00 3.67
200 201 6.931281 CCTTCAGTTATCTTTTCTCAGTGTCA 59.069 38.462 0.00 0.00 0.00 3.58
201 202 7.095439 CCTTCAGTTATCTTTTCTCAGTGTCAC 60.095 40.741 0.00 0.00 0.00 3.67
202 203 6.223852 TCAGTTATCTTTTCTCAGTGTCACC 58.776 40.000 0.00 0.00 0.00 4.02
203 204 5.991606 CAGTTATCTTTTCTCAGTGTCACCA 59.008 40.000 0.00 0.00 0.00 4.17
204 205 6.483307 CAGTTATCTTTTCTCAGTGTCACCAA 59.517 38.462 0.00 0.00 0.00 3.67
205 206 7.012327 CAGTTATCTTTTCTCAGTGTCACCAAA 59.988 37.037 0.00 0.00 0.00 3.28
206 207 7.556275 AGTTATCTTTTCTCAGTGTCACCAAAA 59.444 33.333 0.00 0.31 0.00 2.44
207 208 6.966534 ATCTTTTCTCAGTGTCACCAAAAT 57.033 33.333 0.00 0.00 0.00 1.82
208 209 6.377327 TCTTTTCTCAGTGTCACCAAAATC 57.623 37.500 0.00 0.00 0.00 2.17
209 210 5.885352 TCTTTTCTCAGTGTCACCAAAATCA 59.115 36.000 0.00 0.00 0.00 2.57
210 211 5.756195 TTTCTCAGTGTCACCAAAATCAG 57.244 39.130 0.00 0.00 0.00 2.90
211 212 4.687901 TCTCAGTGTCACCAAAATCAGA 57.312 40.909 0.00 0.00 0.00 3.27
212 213 5.034852 TCTCAGTGTCACCAAAATCAGAA 57.965 39.130 0.00 0.00 0.00 3.02
213 214 5.436175 TCTCAGTGTCACCAAAATCAGAAA 58.564 37.500 0.00 0.00 0.00 2.52
214 215 6.064060 TCTCAGTGTCACCAAAATCAGAAAT 58.936 36.000 0.00 0.00 0.00 2.17
215 216 6.547141 TCTCAGTGTCACCAAAATCAGAAATT 59.453 34.615 0.00 0.00 0.00 1.82
216 217 7.068593 TCTCAGTGTCACCAAAATCAGAAATTT 59.931 33.333 0.00 0.00 0.00 1.82
217 218 8.231692 TCAGTGTCACCAAAATCAGAAATTTA 57.768 30.769 0.00 0.00 0.00 1.40
218 219 8.859090 TCAGTGTCACCAAAATCAGAAATTTAT 58.141 29.630 0.00 0.00 0.00 1.40
264 265 7.645402 ACCTATTTTACGGTTTCAACTCTTTG 58.355 34.615 0.00 0.00 0.00 2.77
274 275 8.179615 ACGGTTTCAACTCTTTGTAAAACTAAG 58.820 33.333 0.00 0.00 33.31 2.18
302 303 3.699538 ACATATCTTACTCGAGTGGTGCA 59.300 43.478 28.12 10.57 0.00 4.57
339 340 5.221087 GGTTTGAAGGTACGATTTTTCACCA 60.221 40.000 0.00 0.00 33.27 4.17
395 396 3.117131 CCCATAGGTTGGCTAATTTCCCT 60.117 47.826 0.00 0.00 44.97 4.20
428 429 1.838568 CGCATCATCGGCCACATCAG 61.839 60.000 2.24 0.00 0.00 2.90
441 442 0.940126 ACATCAGCGAATTCGGATGC 59.060 50.000 30.50 17.11 39.76 3.91
444 445 1.089481 TCAGCGAATTCGGATGCCAC 61.089 55.000 27.78 10.29 40.23 5.01
459 460 1.933115 GCCACGGCATTTGAATCGGT 61.933 55.000 2.36 0.00 41.49 4.69
460 461 0.179166 CCACGGCATTTGAATCGGTG 60.179 55.000 0.00 0.00 0.00 4.94
463 464 2.160615 CACGGCATTTGAATCGGTGTAA 59.839 45.455 0.00 0.00 0.00 2.41
476 477 7.806690 TGAATCGGTGTAAATCTTTTCTTCTG 58.193 34.615 0.00 0.00 0.00 3.02
492 493 3.629855 TCTTCTGGAAACGCAAATCAACA 59.370 39.130 0.00 0.00 0.00 3.33
501 502 1.906966 CGCAAATCAACATTCTGACGC 59.093 47.619 0.00 0.00 0.00 5.19
502 503 1.906966 GCAAATCAACATTCTGACGCG 59.093 47.619 3.53 3.53 0.00 6.01
521 522 2.936993 GCGCATCCAAAGAGAAGAAGGA 60.937 50.000 0.30 0.00 0.00 3.36
522 523 3.539604 CGCATCCAAAGAGAAGAAGGAT 58.460 45.455 0.00 0.00 39.58 3.24
526 527 4.193826 TCCAAAGAGAAGAAGGATGACG 57.806 45.455 0.00 0.00 0.00 4.35
531 532 3.357203 AGAGAAGAAGGATGACGTAGCA 58.643 45.455 0.00 0.00 0.00 3.49
546 547 5.070446 TGACGTAGCATGATAAGGGATTTCT 59.930 40.000 8.74 0.00 0.00 2.52
547 548 5.300752 ACGTAGCATGATAAGGGATTTCTG 58.699 41.667 8.74 0.00 0.00 3.02
548 549 5.163301 ACGTAGCATGATAAGGGATTTCTGT 60.163 40.000 8.74 0.00 0.00 3.41
549 550 5.760253 CGTAGCATGATAAGGGATTTCTGTT 59.240 40.000 0.00 0.00 0.00 3.16
550 551 6.260936 CGTAGCATGATAAGGGATTTCTGTTT 59.739 38.462 0.00 0.00 0.00 2.83
551 552 7.201732 CGTAGCATGATAAGGGATTTCTGTTTT 60.202 37.037 0.00 0.00 0.00 2.43
670 671 2.413765 GCGTTTTGGGCGGTTTCA 59.586 55.556 0.00 0.00 0.00 2.69
671 672 1.660264 GCGTTTTGGGCGGTTTCAG 60.660 57.895 0.00 0.00 0.00 3.02
672 673 1.731093 CGTTTTGGGCGGTTTCAGT 59.269 52.632 0.00 0.00 0.00 3.41
673 674 0.101579 CGTTTTGGGCGGTTTCAGTT 59.898 50.000 0.00 0.00 0.00 3.16
674 675 1.470112 CGTTTTGGGCGGTTTCAGTTT 60.470 47.619 0.00 0.00 0.00 2.66
675 676 2.198406 GTTTTGGGCGGTTTCAGTTTC 58.802 47.619 0.00 0.00 0.00 2.78
676 677 0.747852 TTTGGGCGGTTTCAGTTTCC 59.252 50.000 0.00 0.00 0.00 3.13
685 686 1.062880 GTTTCAGTTTCCGCGTCAACA 59.937 47.619 17.12 0.00 0.00 3.33
712 713 0.110823 CGAGGCGCAGTGTTTTGTAC 60.111 55.000 10.83 0.00 0.00 2.90
713 714 0.110823 GAGGCGCAGTGTTTTGTACG 60.111 55.000 10.83 0.00 0.00 3.67
716 717 1.082366 CGCAGTGTTTTGTACGGGC 60.082 57.895 0.00 0.00 0.00 6.13
717 718 1.503818 CGCAGTGTTTTGTACGGGCT 61.504 55.000 0.00 0.00 0.00 5.19
764 767 1.405463 CACGTCGGAGATCAGATTCCA 59.595 52.381 0.00 0.00 40.67 3.53
807 811 3.444034 CGACTCCAGACTATTCTCCACAA 59.556 47.826 0.00 0.00 0.00 3.33
823 827 0.953471 ACAAGGCAAAGATACGCGCA 60.953 50.000 5.73 0.00 0.00 6.09
826 830 2.023320 GCAAAGATACGCGCAGGC 59.977 61.111 5.73 0.00 0.00 4.85
829 833 3.659089 AAAGATACGCGCAGGCCGT 62.659 57.895 5.73 11.37 39.71 5.68
830 834 4.570663 AGATACGCGCAGGCCGTC 62.571 66.667 5.73 0.00 39.71 4.79
941 949 0.110192 GTGCGTTTCCTTGCTGCTAC 60.110 55.000 0.00 0.00 0.00 3.58
1146 1519 2.995574 CCGGTTGGTCGGTCTCCT 60.996 66.667 0.00 0.00 44.60 3.69
1202 1575 4.785453 GCTCCCCTGTTCCCTGCG 62.785 72.222 0.00 0.00 0.00 5.18
1206 1579 4.785453 CCCTGTTCCCTGCGCCTC 62.785 72.222 4.18 0.00 0.00 4.70
1267 1640 2.594962 CGCCCCGAATCACATACGC 61.595 63.158 0.00 0.00 0.00 4.42
1339 1716 3.680786 TCTCGTGCGGGTCTGTGG 61.681 66.667 0.00 0.00 0.00 4.17
1381 1763 1.377725 GTGGATCCTGCTGTGGTGG 60.378 63.158 14.23 0.00 0.00 4.61
1440 1827 3.172339 CATGGGAGGGAGAAGATCTAGG 58.828 54.545 0.00 0.00 0.00 3.02
1476 1863 2.791868 GGCGTGCTGGTTTTGGGTT 61.792 57.895 0.00 0.00 0.00 4.11
1477 1864 1.142965 GCGTGCTGGTTTTGGGTTT 59.857 52.632 0.00 0.00 0.00 3.27
1478 1865 0.461163 GCGTGCTGGTTTTGGGTTTT 60.461 50.000 0.00 0.00 0.00 2.43
1479 1866 1.285578 CGTGCTGGTTTTGGGTTTTG 58.714 50.000 0.00 0.00 0.00 2.44
1480 1867 1.662517 GTGCTGGTTTTGGGTTTTGG 58.337 50.000 0.00 0.00 0.00 3.28
1481 1868 0.543749 TGCTGGTTTTGGGTTTTGGG 59.456 50.000 0.00 0.00 0.00 4.12
1482 1869 0.544223 GCTGGTTTTGGGTTTTGGGT 59.456 50.000 0.00 0.00 0.00 4.51
1508 1895 7.660208 TCTGGAAAGTTAGGAAAAGATGTGTAC 59.340 37.037 0.00 0.00 0.00 2.90
1524 1911 7.227156 AGATGTGTACTTCTTGGTTGAATCTT 58.773 34.615 0.00 0.00 0.00 2.40
1679 2096 4.020485 AGCTGTTACTGAAAACGGTCCTAT 60.020 41.667 0.00 0.00 37.91 2.57
1700 2117 2.143122 TGCTGTCCTTTCGTGATGAAC 58.857 47.619 0.00 0.00 35.97 3.18
1710 2130 3.034721 TCGTGATGAACCGCTTACTTT 57.965 42.857 0.00 0.00 0.00 2.66
1720 2140 4.820894 ACCGCTTACTTTTAGGAGTCAT 57.179 40.909 0.00 0.00 0.00 3.06
1723 2143 6.281405 ACCGCTTACTTTTAGGAGTCATATG 58.719 40.000 0.00 0.00 0.00 1.78
1748 2168 4.067192 GGCACCTCTTCGGTTACTTTTTA 58.933 43.478 0.00 0.00 46.37 1.52
1755 2175 5.916318 TCTTCGGTTACTTTTTACTGTCCA 58.084 37.500 0.00 0.00 0.00 4.02
1760 2180 5.050567 CGGTTACTTTTTACTGTCCAGTGAC 60.051 44.000 10.15 0.00 42.52 3.67
1770 2193 0.871057 GTCCAGTGACTGCTTTGAGC 59.129 55.000 7.16 0.00 42.82 4.26
1829 2252 7.914346 GCAATTCTTATCAGTTCTGGATGAAAG 59.086 37.037 0.00 0.00 36.30 2.62
1830 2253 8.954350 CAATTCTTATCAGTTCTGGATGAAAGT 58.046 33.333 0.00 0.00 36.30 2.66
1859 2282 0.667487 CAGTACGGAGCACTGTGTGG 60.667 60.000 9.86 0.00 38.86 4.17
1860 2283 1.374252 GTACGGAGCACTGTGTGGG 60.374 63.158 9.86 0.00 36.89 4.61
1876 2299 4.883585 TGTGTGGGATGAGAAATGAATAGC 59.116 41.667 0.00 0.00 0.00 2.97
1881 2304 4.386049 GGGATGAGAAATGAATAGCGTACG 59.614 45.833 11.84 11.84 0.00 3.67
1897 2324 2.895372 CGGCGTGGGCTGGTTATC 60.895 66.667 0.00 0.00 42.05 1.75
2014 2453 7.300304 CGAAATTTCGCTTTCTGCATTATAG 57.700 36.000 26.01 0.00 44.26 1.31
2015 2454 6.358030 CGAAATTTCGCTTTCTGCATTATAGG 59.642 38.462 26.01 0.00 44.26 2.57
2016 2455 6.942532 AATTTCGCTTTCTGCATTATAGGA 57.057 33.333 0.00 0.00 43.06 2.94
2017 2456 5.991328 TTTCGCTTTCTGCATTATAGGAG 57.009 39.130 0.00 0.00 43.06 3.69
2018 2457 4.672587 TCGCTTTCTGCATTATAGGAGT 57.327 40.909 0.00 0.00 43.06 3.85
2019 2458 5.784578 TCGCTTTCTGCATTATAGGAGTA 57.215 39.130 0.00 0.00 43.06 2.59
2020 2459 6.346477 TCGCTTTCTGCATTATAGGAGTAT 57.654 37.500 0.00 0.00 43.06 2.12
2021 2460 7.462571 TCGCTTTCTGCATTATAGGAGTATA 57.537 36.000 0.00 0.00 43.06 1.47
2022 2461 8.067751 TCGCTTTCTGCATTATAGGAGTATAT 57.932 34.615 0.00 0.00 43.06 0.86
2032 2471 8.317679 GCATTATAGGAGTATATGATGGATCCC 58.682 40.741 9.90 0.00 32.51 3.85
2046 2512 3.378472 ATCCCCAACGCCCATGCAT 62.378 57.895 0.00 0.00 37.32 3.96
2063 2529 1.201965 GCATAACTTGTGCGAGCACTC 60.202 52.381 25.74 4.39 46.30 3.51
2092 2558 1.371595 GCGTCGCCCACCTAATTTAA 58.628 50.000 5.75 0.00 0.00 1.52
2126 2592 2.047655 GTCCATGTGACCCGCGAA 60.048 61.111 8.23 0.00 38.09 4.70
2134 2600 0.386731 GTGACCCGCGAACCAAATTG 60.387 55.000 8.23 0.00 0.00 2.32
2145 2611 3.871594 CGAACCAAATTGCTACTCCCTAG 59.128 47.826 0.00 0.00 0.00 3.02
2320 2790 2.343758 GCCCTGAGCGTCAAGTCA 59.656 61.111 0.00 0.00 0.00 3.41
2329 2799 1.008194 CGTCAAGTCACCGAACGGA 60.008 57.895 20.14 0.00 38.96 4.69
2334 2804 2.430382 AAGTCACCGAACGGACGCAT 62.430 55.000 20.14 0.55 39.01 4.73
2462 2938 2.320587 AACGCCGCTTGAGCTTGAG 61.321 57.895 1.07 0.00 39.32 3.02
2491 2967 5.246429 GCCCTGTAATAGTACTGATTAGCCT 59.754 44.000 5.39 0.00 32.39 4.58
2554 3030 3.670359 CGCCCATAATAATCGCCATGTTG 60.670 47.826 0.00 0.00 0.00 3.33
2599 3075 7.833285 TGATATGCAGTGTGGAATACTACTA 57.167 36.000 0.00 0.00 35.46 1.82
2612 3088 9.837525 GTGGAATACTACTAATTACATACTCCG 57.162 37.037 0.00 0.00 30.08 4.63
2613 3089 9.578576 TGGAATACTACTAATTACATACTCCGT 57.421 33.333 0.00 0.00 0.00 4.69
2676 3155 3.754323 TGGGTGTGGAATTTTCGTGTATC 59.246 43.478 0.00 0.00 0.00 2.24
2689 3168 3.623703 TCGTGTATCTGTAGTGGCCTAA 58.376 45.455 3.32 0.00 0.00 2.69
2690 3169 4.018490 TCGTGTATCTGTAGTGGCCTAAA 58.982 43.478 3.32 0.00 0.00 1.85
2717 3196 0.605319 CTAGCAGACCCCGCAAAACA 60.605 55.000 0.00 0.00 0.00 2.83
2753 3232 4.891727 CGGCGAGTATGCGGGCTT 62.892 66.667 0.00 0.00 35.06 4.35
2770 3249 0.684535 CTTGGCCCAATTTTCCGGTT 59.315 50.000 0.00 0.00 0.00 4.44
2788 3267 2.224305 GGTTAGAACAGAGCCCGCATAT 60.224 50.000 0.00 0.00 0.00 1.78
2790 3269 2.717639 AGAACAGAGCCCGCATATTT 57.282 45.000 0.00 0.00 0.00 1.40
2923 3403 0.413434 CACCCAATTCCCCTTTCCCT 59.587 55.000 0.00 0.00 0.00 4.20
3158 3639 3.105852 GACGGAGGAGTACGACCGC 62.106 68.421 17.63 12.79 43.68 5.68
3159 3640 3.885521 CGGAGGAGTACGACCGCC 61.886 72.222 19.06 19.06 42.52 6.13
3160 3641 3.885521 GGAGGAGTACGACCGCCG 61.886 72.222 15.81 0.00 45.44 6.46
3161 3642 2.821366 GAGGAGTACGACCGCCGA 60.821 66.667 0.00 0.00 41.76 5.54
3162 3643 3.105852 GAGGAGTACGACCGCCGAC 62.106 68.421 0.00 0.00 41.76 4.79
3163 3644 4.527157 GGAGTACGACCGCCGACG 62.527 72.222 0.00 2.63 41.76 5.12
3164 3645 3.490759 GAGTACGACCGCCGACGA 61.491 66.667 10.09 0.00 43.93 4.20
3165 3646 3.431683 GAGTACGACCGCCGACGAG 62.432 68.421 10.09 0.00 43.93 4.18
3170 3651 4.415332 GACCGCCGACGAGCTTCA 62.415 66.667 0.00 0.00 43.93 3.02
3171 3652 3.909258 GACCGCCGACGAGCTTCAA 62.909 63.158 0.00 0.00 43.93 2.69
3172 3653 3.479269 CCGCCGACGAGCTTCAAC 61.479 66.667 0.00 0.00 43.93 3.18
3173 3654 3.479269 CGCCGACGAGCTTCAACC 61.479 66.667 0.00 0.00 43.93 3.77
3174 3655 3.479269 GCCGACGAGCTTCAACCG 61.479 66.667 0.00 0.00 0.00 4.44
3175 3656 3.479269 CCGACGAGCTTCAACCGC 61.479 66.667 0.00 0.00 0.00 5.68
3176 3657 3.479269 CGACGAGCTTCAACCGCC 61.479 66.667 0.00 0.00 0.00 6.13
3177 3658 3.479269 GACGAGCTTCAACCGCCG 61.479 66.667 0.00 0.00 0.00 6.46
3183 3664 3.479269 CTTCAACCGCCGCGAGAC 61.479 66.667 15.93 0.00 0.00 3.36
3193 3674 2.708255 CGCGAGACGGAGGAGTAC 59.292 66.667 0.00 0.00 38.44 2.73
3194 3675 2.708255 GCGAGACGGAGGAGTACG 59.292 66.667 0.00 0.00 0.00 3.67
3195 3676 1.812922 GCGAGACGGAGGAGTACGA 60.813 63.158 0.00 0.00 0.00 3.43
3196 3677 2.005220 CGAGACGGAGGAGTACGAC 58.995 63.158 0.00 0.00 0.00 4.34
3197 3678 1.427592 CGAGACGGAGGAGTACGACC 61.428 65.000 0.00 4.37 0.00 4.79
3198 3679 1.427592 GAGACGGAGGAGTACGACCG 61.428 65.000 16.65 16.65 44.72 4.79
3239 3761 2.707849 GCGAGGTCTTCCTACGCCA 61.708 63.158 14.89 0.00 45.35 5.69
3242 3764 1.183549 GAGGTCTTCCTACGCCAGAA 58.816 55.000 0.00 0.00 45.24 3.02
3252 3774 4.448210 TCCTACGCCAGAATTGGTAAATC 58.552 43.478 0.00 0.00 46.80 2.17
3253 3775 4.163458 TCCTACGCCAGAATTGGTAAATCT 59.837 41.667 0.00 0.00 46.80 2.40
3261 3783 6.131961 CCAGAATTGGTAAATCTGATCCCTT 58.868 40.000 7.92 0.00 39.79 3.95
3265 3787 9.190317 AGAATTGGTAAATCTGATCCCTTAAAC 57.810 33.333 0.00 0.00 0.00 2.01
3291 3813 2.034812 GTGGATAGTGACCGGTCATCTC 59.965 54.545 38.11 30.07 42.18 2.75
3299 3821 6.540438 AGTGACCGGTCATCTCTTAAATAA 57.460 37.500 38.11 9.52 42.18 1.40
3301 3823 7.565680 AGTGACCGGTCATCTCTTAAATAATT 58.434 34.615 38.11 6.24 42.18 1.40
3307 3829 8.507249 CCGGTCATCTCTTAAATAATTGATTCC 58.493 37.037 0.00 0.00 0.00 3.01
3361 3884 0.037447 TTCATCGTGCCCATGTCCAA 59.963 50.000 0.00 0.00 0.00 3.53
3372 3895 3.286694 ATGTCCAATGGCCGGCTGT 62.287 57.895 28.56 12.75 0.00 4.40
3392 3915 0.320508 GGTCCTCGGAGTGTTGGTTC 60.321 60.000 4.02 0.00 0.00 3.62
3396 3919 0.666577 CTCGGAGTGTTGGTTCGGTC 60.667 60.000 0.00 0.00 0.00 4.79
3426 3949 4.759782 AGGTAGAATAGCACATGTGACAC 58.240 43.478 29.80 11.82 42.67 3.67
3454 3977 1.227823 CACGGGACTCAAGGCAACA 60.228 57.895 0.00 0.00 41.41 3.33
3455 3978 1.227853 ACGGGACTCAAGGCAACAC 60.228 57.895 0.00 0.00 41.41 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.517257 CAACTAGAGCACCTCGCCG 60.517 63.158 0.00 0.00 44.04 6.46
1 2 0.458716 GTCAACTAGAGCACCTCGCC 60.459 60.000 0.00 0.00 44.04 5.54
2 3 0.458716 GGTCAACTAGAGCACCTCGC 60.459 60.000 0.00 0.00 44.14 5.03
3 4 0.173708 GGGTCAACTAGAGCACCTCG 59.826 60.000 0.00 0.00 46.51 4.63
4 5 1.267121 TGGGTCAACTAGAGCACCTC 58.733 55.000 0.00 0.00 46.51 3.85
5 6 1.834263 GATGGGTCAACTAGAGCACCT 59.166 52.381 0.00 0.00 46.51 4.00
6 7 1.555075 TGATGGGTCAACTAGAGCACC 59.445 52.381 0.00 0.00 46.51 5.01
7 8 3.201290 CATGATGGGTCAACTAGAGCAC 58.799 50.000 0.00 0.00 46.51 4.40
8 9 2.171237 CCATGATGGGTCAACTAGAGCA 59.829 50.000 2.79 0.00 46.51 4.26
9 10 2.435805 TCCATGATGGGTCAACTAGAGC 59.564 50.000 12.26 0.00 43.99 4.09
10 11 4.080919 TGTTCCATGATGGGTCAACTAGAG 60.081 45.833 12.26 0.00 38.32 2.43
11 12 3.843619 TGTTCCATGATGGGTCAACTAGA 59.156 43.478 12.26 0.00 38.32 2.43
12 13 4.220693 TGTTCCATGATGGGTCAACTAG 57.779 45.455 12.26 0.00 38.32 2.57
13 14 4.649267 TTGTTCCATGATGGGTCAACTA 57.351 40.909 12.26 3.27 38.32 2.24
14 15 3.524095 TTGTTCCATGATGGGTCAACT 57.476 42.857 12.26 0.00 38.32 3.16
15 16 4.220382 TCATTTGTTCCATGATGGGTCAAC 59.780 41.667 12.26 9.42 38.32 3.18
16 17 4.414677 TCATTTGTTCCATGATGGGTCAA 58.585 39.130 12.26 13.68 38.32 3.18
17 18 4.044946 TCATTTGTTCCATGATGGGTCA 57.955 40.909 12.26 8.39 38.32 4.02
23 24 3.025978 ACGGCATCATTTGTTCCATGAT 58.974 40.909 0.00 0.00 41.26 2.45
24 25 2.423185 GACGGCATCATTTGTTCCATGA 59.577 45.455 0.00 0.00 35.12 3.07
25 26 2.792196 CGACGGCATCATTTGTTCCATG 60.792 50.000 0.00 0.00 0.00 3.66
26 27 1.401552 CGACGGCATCATTTGTTCCAT 59.598 47.619 0.00 0.00 0.00 3.41
27 28 0.801872 CGACGGCATCATTTGTTCCA 59.198 50.000 0.00 0.00 0.00 3.53
28 29 1.083489 TCGACGGCATCATTTGTTCC 58.917 50.000 0.00 0.00 0.00 3.62
29 30 2.892373 TTCGACGGCATCATTTGTTC 57.108 45.000 0.00 0.00 0.00 3.18
30 31 5.499139 AATATTCGACGGCATCATTTGTT 57.501 34.783 0.00 0.00 0.00 2.83
31 32 6.204688 ACATAATATTCGACGGCATCATTTGT 59.795 34.615 0.00 0.00 0.00 2.83
32 33 6.602179 ACATAATATTCGACGGCATCATTTG 58.398 36.000 0.00 0.00 0.00 2.32
33 34 6.801539 ACATAATATTCGACGGCATCATTT 57.198 33.333 0.00 0.00 0.00 2.32
34 35 6.801539 AACATAATATTCGACGGCATCATT 57.198 33.333 0.00 0.00 0.00 2.57
35 36 6.348458 CCAAACATAATATTCGACGGCATCAT 60.348 38.462 0.00 0.00 0.00 2.45
36 37 5.049749 CCAAACATAATATTCGACGGCATCA 60.050 40.000 0.00 0.00 0.00 3.07
37 38 5.049680 ACCAAACATAATATTCGACGGCATC 60.050 40.000 0.00 0.00 0.00 3.91
38 39 4.819630 ACCAAACATAATATTCGACGGCAT 59.180 37.500 0.00 0.00 0.00 4.40
39 40 4.034626 CACCAAACATAATATTCGACGGCA 59.965 41.667 0.00 0.00 0.00 5.69
40 41 4.034742 ACACCAAACATAATATTCGACGGC 59.965 41.667 0.00 0.00 0.00 5.68
41 42 5.728351 ACACCAAACATAATATTCGACGG 57.272 39.130 0.00 0.00 0.00 4.79
42 43 9.787626 GTAATACACCAAACATAATATTCGACG 57.212 33.333 0.00 0.00 0.00 5.12
69 70 9.961265 CGAAAGTCAATCTACATACCATAACTA 57.039 33.333 0.00 0.00 0.00 2.24
70 71 8.475639 ACGAAAGTCAATCTACATACCATAACT 58.524 33.333 0.00 0.00 44.19 2.24
71 72 8.644318 ACGAAAGTCAATCTACATACCATAAC 57.356 34.615 0.00 0.00 44.19 1.89
116 117 7.917730 AAAGGCTAAAAACTACCCCTAAAAA 57.082 32.000 0.00 0.00 0.00 1.94
117 118 8.226810 ACTAAAGGCTAAAAACTACCCCTAAAA 58.773 33.333 0.00 0.00 0.00 1.52
118 119 7.758609 ACTAAAGGCTAAAAACTACCCCTAAA 58.241 34.615 0.00 0.00 0.00 1.85
119 120 7.333779 ACTAAAGGCTAAAAACTACCCCTAA 57.666 36.000 0.00 0.00 0.00 2.69
120 121 6.957853 ACTAAAGGCTAAAAACTACCCCTA 57.042 37.500 0.00 0.00 0.00 3.53
121 122 5.855338 ACTAAAGGCTAAAAACTACCCCT 57.145 39.130 0.00 0.00 0.00 4.79
122 123 6.906157 AAACTAAAGGCTAAAAACTACCCC 57.094 37.500 0.00 0.00 0.00 4.95
123 124 7.592533 CGAAAAACTAAAGGCTAAAAACTACCC 59.407 37.037 0.00 0.00 0.00 3.69
124 125 7.113965 GCGAAAAACTAAAGGCTAAAAACTACC 59.886 37.037 0.00 0.00 0.00 3.18
125 126 7.113965 GGCGAAAAACTAAAGGCTAAAAACTAC 59.886 37.037 0.00 0.00 0.00 2.73
126 127 7.013559 AGGCGAAAAACTAAAGGCTAAAAACTA 59.986 33.333 0.00 0.00 35.93 2.24
127 128 5.981315 GGCGAAAAACTAAAGGCTAAAAACT 59.019 36.000 0.00 0.00 0.00 2.66
128 129 5.981315 AGGCGAAAAACTAAAGGCTAAAAAC 59.019 36.000 0.00 0.00 35.93 2.43
129 130 6.151663 AGGCGAAAAACTAAAGGCTAAAAA 57.848 33.333 0.00 0.00 35.93 1.94
130 131 5.777850 AGGCGAAAAACTAAAGGCTAAAA 57.222 34.783 0.00 0.00 35.93 1.52
131 132 5.413523 CCTAGGCGAAAAACTAAAGGCTAAA 59.586 40.000 0.00 0.00 39.03 1.85
132 133 4.939439 CCTAGGCGAAAAACTAAAGGCTAA 59.061 41.667 0.00 0.00 39.03 3.09
133 134 4.510571 CCTAGGCGAAAAACTAAAGGCTA 58.489 43.478 0.00 0.00 38.64 3.93
134 135 3.344515 CCTAGGCGAAAAACTAAAGGCT 58.655 45.455 0.00 0.00 40.78 4.58
135 136 2.422479 CCCTAGGCGAAAAACTAAAGGC 59.578 50.000 2.05 0.00 0.00 4.35
136 137 2.422479 GCCCTAGGCGAAAAACTAAAGG 59.578 50.000 2.05 0.00 39.62 3.11
137 138 3.759527 GCCCTAGGCGAAAAACTAAAG 57.240 47.619 2.05 0.00 39.62 1.85
150 151 3.541713 GGAGCCAGACGCCCTAGG 61.542 72.222 0.06 0.06 38.78 3.02
151 152 3.905678 CGGAGCCAGACGCCCTAG 61.906 72.222 0.00 0.00 38.78 3.02
164 165 2.435586 CTGAAGGCAGTGGCGGAG 60.436 66.667 11.51 4.74 42.47 4.63
173 174 5.702670 CACTGAGAAAAGATAACTGAAGGCA 59.297 40.000 0.00 0.00 0.00 4.75
174 175 5.703130 ACACTGAGAAAAGATAACTGAAGGC 59.297 40.000 0.00 0.00 0.00 4.35
175 176 6.931281 TGACACTGAGAAAAGATAACTGAAGG 59.069 38.462 0.00 0.00 0.00 3.46
176 177 7.095439 GGTGACACTGAGAAAAGATAACTGAAG 60.095 40.741 5.39 0.00 0.00 3.02
177 178 6.706270 GGTGACACTGAGAAAAGATAACTGAA 59.294 38.462 5.39 0.00 0.00 3.02
178 179 6.183360 TGGTGACACTGAGAAAAGATAACTGA 60.183 38.462 5.39 0.00 33.40 3.41
179 180 5.991606 TGGTGACACTGAGAAAAGATAACTG 59.008 40.000 5.39 0.00 33.40 3.16
180 181 6.174720 TGGTGACACTGAGAAAAGATAACT 57.825 37.500 5.39 0.00 33.40 2.24
181 182 6.861065 TTGGTGACACTGAGAAAAGATAAC 57.139 37.500 5.39 0.00 42.67 1.89
182 183 7.873719 TTTTGGTGACACTGAGAAAAGATAA 57.126 32.000 5.39 0.00 42.67 1.75
183 184 7.719193 TGATTTTGGTGACACTGAGAAAAGATA 59.281 33.333 5.39 0.00 42.67 1.98
184 185 6.547141 TGATTTTGGTGACACTGAGAAAAGAT 59.453 34.615 5.39 0.00 42.67 2.40
185 186 5.885352 TGATTTTGGTGACACTGAGAAAAGA 59.115 36.000 5.39 0.00 42.67 2.52
186 187 6.038603 TCTGATTTTGGTGACACTGAGAAAAG 59.961 38.462 5.39 0.00 42.67 2.27
187 188 5.885352 TCTGATTTTGGTGACACTGAGAAAA 59.115 36.000 5.39 6.67 42.67 2.29
188 189 5.436175 TCTGATTTTGGTGACACTGAGAAA 58.564 37.500 5.39 2.71 42.67 2.52
189 190 5.034852 TCTGATTTTGGTGACACTGAGAA 57.965 39.130 5.39 0.00 42.67 2.87
190 191 4.687901 TCTGATTTTGGTGACACTGAGA 57.312 40.909 5.39 0.00 42.67 3.27
191 192 5.756195 TTTCTGATTTTGGTGACACTGAG 57.244 39.130 5.39 0.00 42.67 3.35
192 193 6.713762 AATTTCTGATTTTGGTGACACTGA 57.286 33.333 5.39 0.00 42.67 3.41
239 240 7.283807 ACAAAGAGTTGAAACCGTAAAATAGGT 59.716 33.333 0.00 0.00 39.17 3.08
240 241 7.645402 ACAAAGAGTTGAAACCGTAAAATAGG 58.355 34.615 0.00 0.00 38.20 2.57
243 244 9.857957 TTTTACAAAGAGTTGAAACCGTAAAAT 57.142 25.926 0.00 0.00 38.20 1.82
244 245 9.127006 GTTTTACAAAGAGTTGAAACCGTAAAA 57.873 29.630 0.00 0.00 38.20 1.52
245 246 8.513774 AGTTTTACAAAGAGTTGAAACCGTAAA 58.486 29.630 0.00 0.00 36.50 2.01
246 247 8.042944 AGTTTTACAAAGAGTTGAAACCGTAA 57.957 30.769 0.00 0.00 36.50 3.18
247 248 7.614124 AGTTTTACAAAGAGTTGAAACCGTA 57.386 32.000 0.00 0.00 36.50 4.02
248 249 6.505044 AGTTTTACAAAGAGTTGAAACCGT 57.495 33.333 0.00 0.00 36.50 4.83
249 250 8.392612 TCTTAGTTTTACAAAGAGTTGAAACCG 58.607 33.333 0.00 0.00 36.50 4.44
274 275 7.221067 CACCACTCGAGTAAGATATGTTTCTTC 59.779 40.741 19.57 0.00 37.20 2.87
339 340 2.693074 GTGGTTTTGATGGTTGGTCAGT 59.307 45.455 0.00 0.00 0.00 3.41
385 386 3.772619 TTCCGCCGAGGGAAATTAG 57.227 52.632 4.87 0.00 42.94 1.73
412 413 1.596203 CGCTGATGTGGCCGATGAT 60.596 57.895 0.00 0.00 0.00 2.45
414 415 1.162181 ATTCGCTGATGTGGCCGATG 61.162 55.000 0.00 0.00 0.00 3.84
428 429 2.324477 CGTGGCATCCGAATTCGC 59.676 61.111 22.36 8.37 38.18 4.70
441 442 0.179166 CACCGATTCAAATGCCGTGG 60.179 55.000 0.00 0.00 0.00 4.94
444 445 3.479505 TTTACACCGATTCAAATGCCG 57.520 42.857 0.00 0.00 0.00 5.69
459 460 6.038825 TGCGTTTCCAGAAGAAAAGATTTACA 59.961 34.615 5.47 0.00 45.93 2.41
460 461 6.435428 TGCGTTTCCAGAAGAAAAGATTTAC 58.565 36.000 5.47 0.00 45.93 2.01
463 464 5.514274 TTGCGTTTCCAGAAGAAAAGATT 57.486 34.783 5.47 0.00 45.93 2.40
476 477 4.382754 GTCAGAATGTTGATTTGCGTTTCC 59.617 41.667 0.00 0.00 37.40 3.13
492 493 0.729116 CTTTGGATGCGCGTCAGAAT 59.271 50.000 29.46 3.31 0.00 2.40
501 502 2.977914 TCCTTCTTCTCTTTGGATGCG 58.022 47.619 0.00 0.00 0.00 4.73
502 503 4.897025 CATCCTTCTTCTCTTTGGATGC 57.103 45.455 7.27 0.00 44.78 3.91
521 522 5.489792 AATCCCTTATCATGCTACGTCAT 57.510 39.130 0.00 0.00 0.00 3.06
522 523 4.955811 AATCCCTTATCATGCTACGTCA 57.044 40.909 0.00 0.00 0.00 4.35
526 527 7.573968 AAACAGAAATCCCTTATCATGCTAC 57.426 36.000 0.00 0.00 0.00 3.58
567 568 1.865865 GTCGGCATCCAATATCACGT 58.134 50.000 0.00 0.00 0.00 4.49
569 570 2.061773 CTCGTCGGCATCCAATATCAC 58.938 52.381 0.00 0.00 0.00 3.06
670 671 1.088306 TTGTTGTTGACGCGGAAACT 58.912 45.000 21.67 0.00 0.00 2.66
671 672 1.185189 GTTGTTGTTGACGCGGAAAC 58.815 50.000 12.47 15.00 0.00 2.78
672 673 0.099082 GGTTGTTGTTGACGCGGAAA 59.901 50.000 12.47 0.28 0.00 3.13
673 674 1.722677 GGTTGTTGTTGACGCGGAA 59.277 52.632 12.47 0.00 0.00 4.30
674 675 2.526993 CGGTTGTTGTTGACGCGGA 61.527 57.895 12.47 0.00 0.00 5.54
675 676 2.052590 CGGTTGTTGTTGACGCGG 60.053 61.111 12.47 0.00 0.00 6.46
676 677 2.720750 GCGGTTGTTGTTGACGCG 60.721 61.111 3.53 3.53 40.84 6.01
712 713 2.801631 CCTGCCTCTCCTAAGCCCG 61.802 68.421 0.00 0.00 0.00 6.13
713 714 3.113514 GCCTGCCTCTCCTAAGCCC 62.114 68.421 0.00 0.00 0.00 5.19
716 717 1.070445 CTCATGCCTGCCTCTCCTAAG 59.930 57.143 0.00 0.00 0.00 2.18
717 718 1.126488 CTCATGCCTGCCTCTCCTAA 58.874 55.000 0.00 0.00 0.00 2.69
807 811 1.815421 CCTGCGCGTATCTTTGCCT 60.815 57.895 8.43 0.00 0.00 4.75
833 837 1.595093 GAATTCTTGGTGCCGTGGGG 61.595 60.000 0.00 0.00 0.00 4.96
941 949 0.389166 GGACGTGAGCTGGAGTCAAG 60.389 60.000 0.00 0.00 35.49 3.02
1146 1519 0.187851 GACGATAGGGAGGGAGGGAA 59.812 60.000 0.00 0.00 43.77 3.97
1202 1575 4.851214 AGGAGAGGCGGAGGAGGC 62.851 72.222 0.00 0.00 0.00 4.70
1206 1579 3.213402 GACGAGGAGAGGCGGAGG 61.213 72.222 0.00 0.00 0.00 4.30
1240 1613 2.306255 GATTCGGGGCGCTTACCAGA 62.306 60.000 7.64 3.26 0.00 3.86
1241 1614 1.887707 GATTCGGGGCGCTTACCAG 60.888 63.158 7.64 0.32 0.00 4.00
1242 1615 2.188469 GATTCGGGGCGCTTACCA 59.812 61.111 7.64 0.00 0.00 3.25
1243 1616 2.178235 GTGATTCGGGGCGCTTACC 61.178 63.158 7.64 6.82 0.00 2.85
1267 1640 1.222113 GGCGAAGAAAGGAGGGAGG 59.778 63.158 0.00 0.00 0.00 4.30
1339 1716 1.278637 CACGGGAACAAGCAACGAC 59.721 57.895 0.00 0.00 0.00 4.34
1440 1827 1.685180 GCCTCTAAACCCCATGAACCC 60.685 57.143 0.00 0.00 0.00 4.11
1476 1863 4.799715 TTCCTAACTTTCCAGACCCAAA 57.200 40.909 0.00 0.00 0.00 3.28
1477 1864 4.799715 TTTCCTAACTTTCCAGACCCAA 57.200 40.909 0.00 0.00 0.00 4.12
1478 1865 4.414182 TCTTTTCCTAACTTTCCAGACCCA 59.586 41.667 0.00 0.00 0.00 4.51
1479 1866 4.981812 TCTTTTCCTAACTTTCCAGACCC 58.018 43.478 0.00 0.00 0.00 4.46
1480 1867 6.004574 ACATCTTTTCCTAACTTTCCAGACC 58.995 40.000 0.00 0.00 0.00 3.85
1481 1868 6.486993 ACACATCTTTTCCTAACTTTCCAGAC 59.513 38.462 0.00 0.00 0.00 3.51
1482 1869 6.601332 ACACATCTTTTCCTAACTTTCCAGA 58.399 36.000 0.00 0.00 0.00 3.86
1508 1895 2.095059 CGGCCAAGATTCAACCAAGAAG 60.095 50.000 2.24 0.00 0.00 2.85
1679 2096 2.542020 TCATCACGAAAGGACAGCAA 57.458 45.000 0.00 0.00 0.00 3.91
1700 2117 5.696724 CCATATGACTCCTAAAAGTAAGCGG 59.303 44.000 3.65 0.00 0.00 5.52
1710 2130 2.054799 GTGCCCCCATATGACTCCTAA 58.945 52.381 3.65 0.00 0.00 2.69
1720 2140 2.070039 CCGAAGAGGTGCCCCCATA 61.070 63.158 0.00 0.00 34.66 2.74
1737 2157 6.018180 CAGTCACTGGACAGTAAAAAGTAACC 60.018 42.308 4.41 0.00 46.80 2.85
1742 2162 4.130118 AGCAGTCACTGGACAGTAAAAAG 58.870 43.478 7.00 0.00 46.80 2.27
1748 2168 1.486310 TCAAAGCAGTCACTGGACAGT 59.514 47.619 7.00 0.00 46.80 3.55
1755 2175 2.772287 GGTTAGCTCAAAGCAGTCACT 58.228 47.619 0.00 0.00 45.56 3.41
1760 2180 1.512926 ACACGGTTAGCTCAAAGCAG 58.487 50.000 0.00 0.00 45.56 4.24
1770 2193 5.515797 TCTCATGAATCCTACACGGTTAG 57.484 43.478 0.00 0.00 0.00 2.34
1859 2282 4.386049 CCGTACGCTATTCATTTCTCATCC 59.614 45.833 10.49 0.00 0.00 3.51
1860 2283 4.143305 GCCGTACGCTATTCATTTCTCATC 60.143 45.833 10.49 0.00 0.00 2.92
1881 2304 2.112815 GTGATAACCAGCCCACGCC 61.113 63.158 0.00 0.00 34.57 5.68
1884 2307 2.902705 TATCGTGATAACCAGCCCAC 57.097 50.000 0.00 0.00 0.00 4.61
1897 2324 5.678483 GCATAATTGCTGACACTTTATCGTG 59.322 40.000 0.00 0.00 45.77 4.35
1922 2356 4.937620 AGAAAGAAAGCGAAGTGATGCATA 59.062 37.500 0.00 0.00 0.00 3.14
1923 2357 3.755378 AGAAAGAAAGCGAAGTGATGCAT 59.245 39.130 0.00 0.00 0.00 3.96
1924 2358 3.141398 AGAAAGAAAGCGAAGTGATGCA 58.859 40.909 0.00 0.00 0.00 3.96
1925 2359 3.820777 AGAAAGAAAGCGAAGTGATGC 57.179 42.857 0.00 0.00 0.00 3.91
1926 2360 7.095439 ACTCTTAAGAAAGAAAGCGAAGTGATG 60.095 37.037 6.63 0.00 41.19 3.07
1927 2361 6.931840 ACTCTTAAGAAAGAAAGCGAAGTGAT 59.068 34.615 6.63 0.00 41.19 3.06
1928 2362 6.281405 ACTCTTAAGAAAGAAAGCGAAGTGA 58.719 36.000 6.63 0.00 41.19 3.41
1929 2363 6.201044 TGACTCTTAAGAAAGAAAGCGAAGTG 59.799 38.462 6.63 0.00 41.19 3.16
1930 2364 6.201234 GTGACTCTTAAGAAAGAAAGCGAAGT 59.799 38.462 6.63 0.00 41.19 3.01
1931 2365 6.346999 GGTGACTCTTAAGAAAGAAAGCGAAG 60.347 42.308 6.63 0.00 41.19 3.79
1932 2366 5.465724 GGTGACTCTTAAGAAAGAAAGCGAA 59.534 40.000 6.63 0.00 41.19 4.70
1999 2433 9.829507 ATCATATACTCCTATAATGCAGAAAGC 57.170 33.333 0.00 0.00 45.96 3.51
2013 2452 4.717328 TGGGGATCCATCATATACTCCT 57.283 45.455 15.23 0.00 38.32 3.69
2014 2453 4.383118 CGTTGGGGATCCATCATATACTCC 60.383 50.000 15.23 1.53 43.63 3.85
2015 2454 4.759782 CGTTGGGGATCCATCATATACTC 58.240 47.826 15.23 0.00 43.63 2.59
2016 2455 3.055094 GCGTTGGGGATCCATCATATACT 60.055 47.826 15.23 0.00 43.63 2.12
2017 2456 3.270877 GCGTTGGGGATCCATCATATAC 58.729 50.000 15.23 5.92 43.63 1.47
2018 2457 2.238646 GGCGTTGGGGATCCATCATATA 59.761 50.000 15.23 0.00 43.63 0.86
2019 2458 1.004745 GGCGTTGGGGATCCATCATAT 59.995 52.381 15.23 0.00 43.63 1.78
2020 2459 0.400213 GGCGTTGGGGATCCATCATA 59.600 55.000 15.23 0.41 43.63 2.15
2021 2460 1.151450 GGCGTTGGGGATCCATCAT 59.849 57.895 15.23 0.00 43.63 2.45
2022 2461 2.595095 GGCGTTGGGGATCCATCA 59.405 61.111 15.23 8.55 43.63 3.07
2032 2471 0.817013 AAGTTATGCATGGGCGTTGG 59.183 50.000 10.16 0.00 45.35 3.77
2036 2502 0.526096 GCACAAGTTATGCATGGGCG 60.526 55.000 10.16 0.00 45.35 6.13
2039 2505 1.532505 GCTCGCACAAGTTATGCATGG 60.533 52.381 10.16 0.00 43.57 3.66
2078 2544 2.688446 GAGTGGCTTAAATTAGGTGGGC 59.312 50.000 0.00 0.00 0.00 5.36
2110 2576 2.047655 GTTCGCGGGTCACATGGA 60.048 61.111 6.13 0.00 0.00 3.41
2126 2592 4.042934 ACAACTAGGGAGTAGCAATTTGGT 59.957 41.667 6.33 6.33 33.58 3.67
2134 2600 2.427812 GGTGAGACAACTAGGGAGTAGC 59.572 54.545 0.00 0.00 33.58 3.58
2211 2677 2.910479 TGGACTGTGTCGGCGTCT 60.910 61.111 6.85 0.00 32.65 4.18
2302 2772 2.210013 TGACTTGACGCTCAGGGCT 61.210 57.895 0.00 0.00 31.97 5.19
2320 2790 3.229156 TTCCATGCGTCCGTTCGGT 62.229 57.895 11.04 0.00 0.00 4.69
2329 2799 4.634703 TGCCCGTGTTCCATGCGT 62.635 61.111 0.00 0.00 0.00 5.24
2334 2804 4.308458 CGTCCTGCCCGTGTTCCA 62.308 66.667 0.00 0.00 0.00 3.53
2462 2938 5.786264 TCAGTACTATTACAGGGCTAAGC 57.214 43.478 0.00 0.00 0.00 3.09
2537 3013 3.507233 CCCAGCAACATGGCGATTATTAT 59.493 43.478 0.00 0.00 39.17 1.28
2554 3030 1.243902 TTCATCACCGAAAACCCAGC 58.756 50.000 0.00 0.00 0.00 4.85
2676 3155 3.412386 AGTTGCTTTTAGGCCACTACAG 58.588 45.455 5.01 0.00 36.62 2.74
2689 3168 1.003696 GGGGTCTGCTAGAGTTGCTTT 59.996 52.381 0.00 0.00 0.00 3.51
2690 3169 0.615850 GGGGTCTGCTAGAGTTGCTT 59.384 55.000 0.00 0.00 0.00 3.91
2717 3196 2.920384 AATTTTTGCGGGCCGGGT 60.920 55.556 29.48 0.00 0.00 5.28
2753 3232 1.075698 TCTAACCGGAAAATTGGGCCA 59.924 47.619 9.46 0.00 0.00 5.36
2770 3249 3.466836 CAAATATGCGGGCTCTGTTCTA 58.533 45.455 0.00 0.00 0.00 2.10
2873 3352 1.497161 CGGGGGATAGAGTTTGGACT 58.503 55.000 0.00 0.00 39.32 3.85
2909 3389 1.646447 GGGAGAAGGGAAAGGGGAATT 59.354 52.381 0.00 0.00 0.00 2.17
2923 3403 1.024579 GCGGCGAGAAATTGGGAGAA 61.025 55.000 12.98 0.00 0.00 2.87
3158 3639 3.479269 GCGGTTGAAGCTCGTCGG 61.479 66.667 0.00 0.00 0.00 4.79
3159 3640 3.479269 GGCGGTTGAAGCTCGTCG 61.479 66.667 0.00 0.00 34.52 5.12
3160 3641 3.479269 CGGCGGTTGAAGCTCGTC 61.479 66.667 0.00 0.00 34.52 4.20
3166 3647 3.479269 GTCTCGCGGCGGTTGAAG 61.479 66.667 23.46 12.07 0.00 3.02
3176 3657 2.708255 GTACTCCTCCGTCTCGCG 59.292 66.667 0.00 0.00 40.95 5.87
3177 3658 1.812922 TCGTACTCCTCCGTCTCGC 60.813 63.158 0.00 0.00 0.00 5.03
3178 3659 1.427592 GGTCGTACTCCTCCGTCTCG 61.428 65.000 0.00 0.00 0.00 4.04
3179 3660 1.427592 CGGTCGTACTCCTCCGTCTC 61.428 65.000 0.00 0.00 38.45 3.36
3180 3661 1.449246 CGGTCGTACTCCTCCGTCT 60.449 63.158 0.00 0.00 38.45 4.18
3181 3662 3.096791 CGGTCGTACTCCTCCGTC 58.903 66.667 0.00 0.00 38.45 4.79
3182 3663 3.130160 GCGGTCGTACTCCTCCGT 61.130 66.667 13.30 0.00 44.07 4.69
3183 3664 3.885521 GGCGGTCGTACTCCTCCG 61.886 72.222 9.40 9.40 44.86 4.63
3184 3665 3.885521 CGGCGGTCGTACTCCTCC 61.886 72.222 0.00 3.76 0.00 4.30
3185 3666 3.885521 CCGGCGGTCGTACTCCTC 61.886 72.222 19.97 0.00 37.11 3.71
3239 3761 9.190317 GTTTAAGGGATCAGATTTACCAATTCT 57.810 33.333 0.00 0.00 0.00 2.40
3242 3764 7.116736 ACGTTTAAGGGATCAGATTTACCAAT 58.883 34.615 0.00 0.00 0.00 3.16
3252 3774 2.671396 CCACGAACGTTTAAGGGATCAG 59.329 50.000 0.46 0.00 0.00 2.90
3253 3775 2.299582 TCCACGAACGTTTAAGGGATCA 59.700 45.455 0.46 0.00 0.00 2.92
3261 3783 3.670359 CGGTCACTATCCACGAACGTTTA 60.670 47.826 0.46 0.00 35.19 2.01
3265 3787 0.524816 CCGGTCACTATCCACGAACG 60.525 60.000 0.00 0.00 39.53 3.95
3372 3895 1.052124 AACCAACACTCCGAGGACCA 61.052 55.000 0.00 0.00 0.00 4.02
3375 3898 1.663739 CGAACCAACACTCCGAGGA 59.336 57.895 0.00 0.00 0.00 3.71
3380 3903 2.315386 GCGACCGAACCAACACTCC 61.315 63.158 0.00 0.00 0.00 3.85
3396 3919 1.081376 CTATTCTACCTCGCCGGCG 60.081 63.158 42.13 42.13 41.35 6.46


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

AutoCloner maintained by Alex Coulton.