Multiple sequence alignment - TraesCS2B01G272800

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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 TraesCS2B01G272800 chr2B 100.000 4532 0 0 1 4532 374204145 374208676 0.000000e+00 8370
1 TraesCS2B01G272800 chr2A 95.098 3876 107 23 198 4009 385007453 385003597 0.000000e+00 6028
2 TraesCS2B01G272800 chr2A 91.529 425 11 2 4023 4447 385003450 385003051 3.060000e-156 562
3 TraesCS2B01G272800 chr2A 90.526 190 14 3 11 200 385013114 385012929 9.740000e-62 248
4 TraesCS2B01G272800 chr2A 91.724 145 11 1 4301 4444 235712056 235712200 2.760000e-47 200
5 TraesCS2B01G272800 chr2D 95.464 3549 89 22 201 3695 306247998 306251528 0.000000e+00 5596
6 TraesCS2B01G272800 chr2D 93.642 755 21 3 3694 4447 306251643 306252371 0.000000e+00 1103
7 TraesCS2B01G272800 chr2D 88.710 186 15 5 4264 4447 553358805 553358624 5.900000e-54 222
8 TraesCS2B01G272800 chr2D 87.342 158 20 0 2 159 17617253 17617096 1.000000e-41 182
9 TraesCS2B01G272800 chr2D 86.875 160 17 3 2 159 17645037 17644880 4.660000e-40 176
10 TraesCS2B01G272800 chr5A 98.592 142 2 0 1909 2050 400867606 400867465 7.530000e-63 252
11 TraesCS2B01G272800 chr5A 86.792 159 19 2 2 159 464240639 464240796 4.660000e-40 176
12 TraesCS2B01G272800 chr5B 91.026 156 14 0 4 159 483951212 483951057 1.280000e-50 211
13 TraesCS2B01G272800 chr5D 86.364 198 14 7 4262 4447 6115877 6116073 2.140000e-48 204
14 TraesCS2B01G272800 chr7A 87.421 159 18 2 2 159 353071736 353071893 1.000000e-41 182
15 TraesCS2B01G272800 chr6A 88.667 150 16 1 11 160 557972030 557972178 1.000000e-41 182
16 TraesCS2B01G272800 chr6A 86.792 159 19 2 2 159 607089326 607089169 4.660000e-40 176
17 TraesCS2B01G272800 chr6A 86.792 159 19 2 2 159 607224512 607224355 4.660000e-40 176


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 TraesCS2B01G272800 chr2B 374204145 374208676 4531 False 8370.0 8370 100.0000 1 4532 1 chr2B.!!$F1 4531
1 TraesCS2B01G272800 chr2A 385003051 385007453 4402 True 3295.0 6028 93.3135 198 4447 2 chr2A.!!$R2 4249
2 TraesCS2B01G272800 chr2D 306247998 306252371 4373 False 3349.5 5596 94.5530 201 4447 2 chr2D.!!$F1 4246

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
104 105 0.032515 TGGATGAGGGAGACGGCTTA 60.033 55.0 0.0 0.0 0.00 3.09 F
108 109 0.106868 TGAGGGAGACGGCTTATCGA 60.107 55.0 0.0 0.0 0.00 3.59 F
1619 1704 0.105964 TCAGTCAACAAGGTGGACGG 59.894 55.0 0.0 0.0 41.05 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1081 0.038067 TCGACAGGAAATTCGCGGAA 60.038 50.0 6.13 0.0 35.15 4.30 R
1705 1790 0.105778 CCTGGATCCTCTTTCCTCGC 59.894 60.0 14.23 0.0 34.17 5.03 R
3572 3657 0.250124 TGTTGTTAGCTGGACACCCG 60.250 55.0 0.00 0.0 34.29 5.28 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
21 22 4.152284 ACTCCCCGGCTTAAAAGATAAG 57.848 45.455 0.00 0.00 0.00 1.73
22 23 2.879026 CTCCCCGGCTTAAAAGATAAGC 59.121 50.000 10.88 10.88 46.64 3.09
28 29 3.610786 GCTTAAAAGATAAGCCGCTCC 57.389 47.619 8.63 0.00 42.88 4.70
29 30 2.290916 GCTTAAAAGATAAGCCGCTCCC 59.709 50.000 8.63 0.00 42.88 4.30
30 31 3.541632 CTTAAAAGATAAGCCGCTCCCA 58.458 45.455 0.00 0.00 0.00 4.37
31 32 2.507407 AAAAGATAAGCCGCTCCCAA 57.493 45.000 0.00 0.00 0.00 4.12
32 33 2.507407 AAAGATAAGCCGCTCCCAAA 57.493 45.000 0.00 0.00 0.00 3.28
33 34 2.507407 AAGATAAGCCGCTCCCAAAA 57.493 45.000 0.00 0.00 0.00 2.44
34 35 2.736670 AGATAAGCCGCTCCCAAAAT 57.263 45.000 0.00 0.00 0.00 1.82
35 36 3.018423 AGATAAGCCGCTCCCAAAATT 57.982 42.857 0.00 0.00 0.00 1.82
36 37 2.952310 AGATAAGCCGCTCCCAAAATTC 59.048 45.455 0.00 0.00 0.00 2.17
37 38 1.091537 TAAGCCGCTCCCAAAATTCG 58.908 50.000 0.00 0.00 0.00 3.34
38 39 0.893727 AAGCCGCTCCCAAAATTCGT 60.894 50.000 0.00 0.00 0.00 3.85
39 40 0.893727 AGCCGCTCCCAAAATTCGTT 60.894 50.000 0.00 0.00 0.00 3.85
40 41 0.732538 GCCGCTCCCAAAATTCGTTG 60.733 55.000 0.00 0.00 0.00 4.10
41 42 0.878416 CCGCTCCCAAAATTCGTTGA 59.122 50.000 0.00 0.00 0.00 3.18
42 43 1.135689 CCGCTCCCAAAATTCGTTGAG 60.136 52.381 0.00 0.00 0.00 3.02
43 44 1.135689 CGCTCCCAAAATTCGTTGAGG 60.136 52.381 0.00 0.00 0.00 3.86
44 45 1.402852 GCTCCCAAAATTCGTTGAGGC 60.403 52.381 0.00 0.00 0.00 4.70
45 46 2.162681 CTCCCAAAATTCGTTGAGGCT 58.837 47.619 0.00 0.00 0.00 4.58
46 47 3.343617 CTCCCAAAATTCGTTGAGGCTA 58.656 45.455 0.00 0.00 0.00 3.93
47 48 3.078837 TCCCAAAATTCGTTGAGGCTAC 58.921 45.455 0.00 0.00 0.00 3.58
48 49 3.081804 CCCAAAATTCGTTGAGGCTACT 58.918 45.455 0.00 0.00 0.00 2.57
49 50 4.020039 TCCCAAAATTCGTTGAGGCTACTA 60.020 41.667 0.00 0.00 0.00 1.82
50 51 4.698304 CCCAAAATTCGTTGAGGCTACTAA 59.302 41.667 0.00 0.00 0.00 2.24
51 52 5.182380 CCCAAAATTCGTTGAGGCTACTAAA 59.818 40.000 0.00 0.00 0.00 1.85
52 53 6.127730 CCCAAAATTCGTTGAGGCTACTAAAT 60.128 38.462 0.00 0.00 0.00 1.40
53 54 7.312899 CCAAAATTCGTTGAGGCTACTAAATT 58.687 34.615 0.00 0.00 0.00 1.82
54 55 8.455682 CCAAAATTCGTTGAGGCTACTAAATTA 58.544 33.333 0.00 0.00 0.00 1.40
55 56 9.490663 CAAAATTCGTTGAGGCTACTAAATTAG 57.509 33.333 0.00 0.00 0.00 1.73
56 57 8.788325 AAATTCGTTGAGGCTACTAAATTAGT 57.212 30.769 10.75 10.75 42.68 2.24
57 58 9.880157 AAATTCGTTGAGGCTACTAAATTAGTA 57.120 29.630 11.85 11.85 40.14 1.82
58 59 9.880157 AATTCGTTGAGGCTACTAAATTAGTAA 57.120 29.630 13.20 0.00 40.49 2.24
60 61 9.525409 TTCGTTGAGGCTACTAAATTAGTAATC 57.475 33.333 13.20 11.57 40.49 1.75
61 62 8.139989 TCGTTGAGGCTACTAAATTAGTAATCC 58.860 37.037 13.20 15.26 40.49 3.01
62 63 7.384387 CGTTGAGGCTACTAAATTAGTAATCCC 59.616 40.741 19.04 15.83 40.49 3.85
63 64 7.924358 TGAGGCTACTAAATTAGTAATCCCA 57.076 36.000 19.04 15.54 40.49 4.37
64 65 8.506196 TGAGGCTACTAAATTAGTAATCCCAT 57.494 34.615 19.04 8.77 40.49 4.00
65 66 9.610104 TGAGGCTACTAAATTAGTAATCCCATA 57.390 33.333 19.04 9.69 40.49 2.74
79 80 7.501844 AGTAATCCCATAACTAGTTCAGAAGC 58.498 38.462 12.39 0.00 0.00 3.86
80 81 6.567602 AATCCCATAACTAGTTCAGAAGCT 57.432 37.500 12.39 0.00 0.00 3.74
81 82 5.599999 TCCCATAACTAGTTCAGAAGCTC 57.400 43.478 12.39 0.00 0.00 4.09
82 83 4.406003 TCCCATAACTAGTTCAGAAGCTCC 59.594 45.833 12.39 0.00 0.00 4.70
83 84 4.162320 CCCATAACTAGTTCAGAAGCTCCA 59.838 45.833 12.39 0.00 0.00 3.86
84 85 5.338381 CCCATAACTAGTTCAGAAGCTCCAA 60.338 44.000 12.39 0.00 0.00 3.53
85 86 6.352516 CCATAACTAGTTCAGAAGCTCCAAT 58.647 40.000 12.39 0.00 0.00 3.16
86 87 6.259608 CCATAACTAGTTCAGAAGCTCCAATG 59.740 42.308 12.39 5.59 0.00 2.82
87 88 4.213564 ACTAGTTCAGAAGCTCCAATGG 57.786 45.455 0.00 0.00 0.00 3.16
88 89 3.840666 ACTAGTTCAGAAGCTCCAATGGA 59.159 43.478 0.48 0.48 0.00 3.41
89 90 4.472833 ACTAGTTCAGAAGCTCCAATGGAT 59.527 41.667 0.87 0.00 0.00 3.41
90 91 3.618351 AGTTCAGAAGCTCCAATGGATG 58.382 45.455 0.87 0.00 0.00 3.51
91 92 3.265221 AGTTCAGAAGCTCCAATGGATGA 59.735 43.478 0.87 0.00 0.00 2.92
92 93 3.555527 TCAGAAGCTCCAATGGATGAG 57.444 47.619 0.87 0.00 0.00 2.90
93 94 2.172082 TCAGAAGCTCCAATGGATGAGG 59.828 50.000 0.87 0.00 0.00 3.86
94 95 1.493871 AGAAGCTCCAATGGATGAGGG 59.506 52.381 0.87 0.00 0.00 4.30
95 96 1.492176 GAAGCTCCAATGGATGAGGGA 59.508 52.381 0.87 0.00 0.00 4.20
99 100 1.123077 TCCAATGGATGAGGGAGACG 58.877 55.000 0.00 0.00 0.00 4.18
100 101 0.107456 CCAATGGATGAGGGAGACGG 59.893 60.000 0.00 0.00 0.00 4.79
101 102 0.533755 CAATGGATGAGGGAGACGGC 60.534 60.000 0.00 0.00 0.00 5.68
102 103 0.692419 AATGGATGAGGGAGACGGCT 60.692 55.000 0.00 0.00 0.00 5.52
103 104 0.692419 ATGGATGAGGGAGACGGCTT 60.692 55.000 0.00 0.00 0.00 4.35
104 105 0.032515 TGGATGAGGGAGACGGCTTA 60.033 55.000 0.00 0.00 0.00 3.09
105 106 1.343069 GGATGAGGGAGACGGCTTAT 58.657 55.000 0.00 0.00 0.00 1.73
106 107 1.273886 GGATGAGGGAGACGGCTTATC 59.726 57.143 0.00 0.00 0.00 1.75
107 108 0.962489 ATGAGGGAGACGGCTTATCG 59.038 55.000 0.00 0.00 0.00 2.92
108 109 0.106868 TGAGGGAGACGGCTTATCGA 60.107 55.000 0.00 0.00 0.00 3.59
109 110 1.030457 GAGGGAGACGGCTTATCGAA 58.970 55.000 0.00 0.00 0.00 3.71
110 111 1.407979 GAGGGAGACGGCTTATCGAAA 59.592 52.381 0.00 0.00 0.00 3.46
111 112 1.829222 AGGGAGACGGCTTATCGAAAA 59.171 47.619 0.00 0.00 0.00 2.29
112 113 2.235402 AGGGAGACGGCTTATCGAAAAA 59.765 45.455 0.00 0.00 0.00 1.94
113 114 3.118371 AGGGAGACGGCTTATCGAAAAAT 60.118 43.478 0.00 0.00 0.00 1.82
114 115 3.247886 GGGAGACGGCTTATCGAAAAATC 59.752 47.826 0.00 0.00 0.00 2.17
115 116 4.120589 GGAGACGGCTTATCGAAAAATCT 58.879 43.478 0.00 0.00 0.00 2.40
116 117 4.025647 GGAGACGGCTTATCGAAAAATCTG 60.026 45.833 0.00 0.00 0.00 2.90
117 118 4.755411 AGACGGCTTATCGAAAAATCTGA 58.245 39.130 0.00 0.00 0.00 3.27
118 119 5.175859 AGACGGCTTATCGAAAAATCTGAA 58.824 37.500 0.00 0.00 0.00 3.02
119 120 5.292101 AGACGGCTTATCGAAAAATCTGAAG 59.708 40.000 0.00 0.00 0.00 3.02
120 121 5.175859 ACGGCTTATCGAAAAATCTGAAGA 58.824 37.500 0.00 0.00 0.00 2.87
121 122 5.292101 ACGGCTTATCGAAAAATCTGAAGAG 59.708 40.000 0.00 0.00 0.00 2.85
122 123 5.277058 CGGCTTATCGAAAAATCTGAAGAGG 60.277 44.000 0.00 0.00 0.00 3.69
123 124 5.817816 GGCTTATCGAAAAATCTGAAGAGGA 59.182 40.000 0.00 0.00 0.00 3.71
124 125 6.018343 GGCTTATCGAAAAATCTGAAGAGGAG 60.018 42.308 0.00 0.00 0.00 3.69
125 126 6.018343 GCTTATCGAAAAATCTGAAGAGGAGG 60.018 42.308 0.00 0.00 0.00 4.30
126 127 3.600388 TCGAAAAATCTGAAGAGGAGGC 58.400 45.455 0.00 0.00 0.00 4.70
127 128 2.349886 CGAAAAATCTGAAGAGGAGGCG 59.650 50.000 0.00 0.00 0.00 5.52
128 129 2.409948 AAAATCTGAAGAGGAGGCGG 57.590 50.000 0.00 0.00 0.00 6.13
129 130 0.107459 AAATCTGAAGAGGAGGCGGC 60.107 55.000 0.00 0.00 0.00 6.53
130 131 0.980231 AATCTGAAGAGGAGGCGGCT 60.980 55.000 13.09 13.09 0.00 5.52
131 132 0.980231 ATCTGAAGAGGAGGCGGCTT 60.980 55.000 14.76 0.00 0.00 4.35
132 133 0.324368 TCTGAAGAGGAGGCGGCTTA 60.324 55.000 14.76 0.00 0.00 3.09
133 134 0.755686 CTGAAGAGGAGGCGGCTTAT 59.244 55.000 14.76 4.47 0.00 1.73
134 135 1.139853 CTGAAGAGGAGGCGGCTTATT 59.860 52.381 14.76 0.59 0.00 1.40
135 136 1.559682 TGAAGAGGAGGCGGCTTATTT 59.440 47.619 14.76 5.80 0.00 1.40
136 137 2.026262 TGAAGAGGAGGCGGCTTATTTT 60.026 45.455 14.76 6.40 0.00 1.82
137 138 2.808906 AGAGGAGGCGGCTTATTTTT 57.191 45.000 14.76 0.00 0.00 1.94
158 159 4.492791 TTAAGCCGTAAAAAGAACTGGC 57.507 40.909 0.00 0.00 42.76 4.85
162 163 3.818387 GCCGTAAAAAGAACTGGCTAAC 58.182 45.455 0.00 0.00 39.38 2.34
163 164 3.501062 GCCGTAAAAAGAACTGGCTAACT 59.499 43.478 0.00 0.00 39.38 2.24
164 165 4.692155 GCCGTAAAAAGAACTGGCTAACTA 59.308 41.667 0.00 0.00 39.38 2.24
165 166 5.179929 GCCGTAAAAAGAACTGGCTAACTAA 59.820 40.000 0.00 0.00 39.38 2.24
166 167 6.293571 GCCGTAAAAAGAACTGGCTAACTAAA 60.294 38.462 0.00 0.00 39.38 1.85
167 168 7.641760 CCGTAAAAAGAACTGGCTAACTAAAA 58.358 34.615 0.00 0.00 0.00 1.52
168 169 8.130469 CCGTAAAAAGAACTGGCTAACTAAAAA 58.870 33.333 0.00 0.00 0.00 1.94
169 170 8.950961 CGTAAAAAGAACTGGCTAACTAAAAAC 58.049 33.333 0.00 0.00 0.00 2.43
170 171 9.791820 GTAAAAAGAACTGGCTAACTAAAAACA 57.208 29.630 0.00 0.00 0.00 2.83
171 172 8.926715 AAAAAGAACTGGCTAACTAAAAACAG 57.073 30.769 0.00 0.00 0.00 3.16
172 173 7.875327 AAAGAACTGGCTAACTAAAAACAGA 57.125 32.000 0.00 0.00 0.00 3.41
173 174 7.875327 AAGAACTGGCTAACTAAAAACAGAA 57.125 32.000 0.00 0.00 0.00 3.02
174 175 7.875327 AGAACTGGCTAACTAAAAACAGAAA 57.125 32.000 0.00 0.00 0.00 2.52
175 176 8.288689 AGAACTGGCTAACTAAAAACAGAAAA 57.711 30.769 0.00 0.00 0.00 2.29
176 177 8.406297 AGAACTGGCTAACTAAAAACAGAAAAG 58.594 33.333 0.00 0.00 0.00 2.27
177 178 7.875327 ACTGGCTAACTAAAAACAGAAAAGA 57.125 32.000 0.00 0.00 0.00 2.52
178 179 7.931275 ACTGGCTAACTAAAAACAGAAAAGAG 58.069 34.615 0.00 0.00 0.00 2.85
179 180 7.773690 ACTGGCTAACTAAAAACAGAAAAGAGA 59.226 33.333 0.00 0.00 0.00 3.10
180 181 8.514330 TGGCTAACTAAAAACAGAAAAGAGAA 57.486 30.769 0.00 0.00 0.00 2.87
181 182 8.403236 TGGCTAACTAAAAACAGAAAAGAGAAC 58.597 33.333 0.00 0.00 0.00 3.01
182 183 7.861372 GGCTAACTAAAAACAGAAAAGAGAACC 59.139 37.037 0.00 0.00 0.00 3.62
183 184 7.861372 GCTAACTAAAAACAGAAAAGAGAACCC 59.139 37.037 0.00 0.00 0.00 4.11
184 185 7.956328 AACTAAAAACAGAAAAGAGAACCCT 57.044 32.000 0.00 0.00 0.00 4.34
185 186 7.956328 ACTAAAAACAGAAAAGAGAACCCTT 57.044 32.000 0.00 0.00 0.00 3.95
186 187 9.470399 AACTAAAAACAGAAAAGAGAACCCTTA 57.530 29.630 0.00 0.00 0.00 2.69
187 188 9.470399 ACTAAAAACAGAAAAGAGAACCCTTAA 57.530 29.630 0.00 0.00 0.00 1.85
304 305 1.352083 GGTATGGATCCCAGCTAGCA 58.648 55.000 18.83 0.00 36.75 3.49
305 306 1.912043 GGTATGGATCCCAGCTAGCAT 59.088 52.381 18.83 0.38 36.75 3.79
308 317 0.761187 TGGATCCCAGCTAGCATCAC 59.239 55.000 18.83 6.01 0.00 3.06
320 335 2.338577 AGCATCACCATCCAGCTAAC 57.661 50.000 0.00 0.00 33.06 2.34
322 337 1.945394 GCATCACCATCCAGCTAACAG 59.055 52.381 0.00 0.00 0.00 3.16
344 366 3.108144 CAACTTTGTTTTGGTGAGCTCG 58.892 45.455 9.64 0.00 0.00 5.03
426 448 1.001503 CCACCTCCTCCTGAGAGCT 59.998 63.158 0.00 0.00 44.42 4.09
437 459 3.680490 TCCTGAGAGCTGATAGATACCG 58.320 50.000 0.00 0.00 0.00 4.02
448 470 0.554305 TAGATACCGCTCCCTGTCCA 59.446 55.000 0.00 0.00 0.00 4.02
526 552 5.122396 GCGCCTGATTTCCCAATTATACTAG 59.878 44.000 0.00 0.00 0.00 2.57
529 555 7.331193 CGCCTGATTTCCCAATTATACTAGTAC 59.669 40.741 4.31 0.00 0.00 2.73
627 661 1.610038 TGCCATTTGTTGCTCTCTGTG 59.390 47.619 0.00 0.00 0.00 3.66
659 697 4.437682 TGGAGCTTTCTTTCTTCTTCCA 57.562 40.909 0.00 0.00 0.00 3.53
677 715 3.571588 GCGCTAGCTGCTCTTGCC 61.572 66.667 19.70 0.82 39.83 4.52
678 716 2.186384 CGCTAGCTGCTCTTGCCT 59.814 61.111 13.93 0.00 39.83 4.75
679 717 1.449246 CGCTAGCTGCTCTTGCCTT 60.449 57.895 13.93 0.00 39.83 4.35
680 718 1.703438 CGCTAGCTGCTCTTGCCTTG 61.703 60.000 13.93 0.00 39.83 3.61
681 719 0.392193 GCTAGCTGCTCTTGCCTTGA 60.392 55.000 4.91 0.00 37.54 3.02
682 720 1.746516 GCTAGCTGCTCTTGCCTTGAT 60.747 52.381 4.91 0.00 37.54 2.57
683 721 2.641305 CTAGCTGCTCTTGCCTTGATT 58.359 47.619 4.91 0.00 38.71 2.57
684 722 1.920610 AGCTGCTCTTGCCTTGATTT 58.079 45.000 0.00 0.00 38.71 2.17
685 723 1.544691 AGCTGCTCTTGCCTTGATTTG 59.455 47.619 0.00 0.00 38.71 2.32
686 724 1.992170 CTGCTCTTGCCTTGATTTGC 58.008 50.000 0.00 0.00 38.71 3.68
687 725 1.544691 CTGCTCTTGCCTTGATTTGCT 59.455 47.619 0.00 0.00 38.71 3.91
688 726 1.965643 TGCTCTTGCCTTGATTTGCTT 59.034 42.857 0.00 0.00 38.71 3.91
691 729 2.735134 CTCTTGCCTTGATTTGCTTTGC 59.265 45.455 0.00 0.00 0.00 3.68
724 778 1.068434 GGGGAGAGAAGATCGAGCAAG 59.932 57.143 2.38 0.00 0.00 4.01
787 849 1.545706 GCCTTCCGGTTCCTGAGAGT 61.546 60.000 0.00 0.00 0.00 3.24
857 923 8.452534 CGTAGCCTTATTATCACTCTAGGTTAG 58.547 40.741 0.00 0.00 0.00 2.34
1182 1255 2.048222 TTCACGCTCAGCTTCCCG 60.048 61.111 0.00 0.00 0.00 5.14
1230 1315 1.406069 CCGGGAGTTGATGGAGAACAG 60.406 57.143 0.00 0.00 0.00 3.16
1376 1461 2.001803 CCCAGGAGCCCATCTTCAA 58.998 57.895 0.00 0.00 0.00 2.69
1461 1546 4.540715 GGGATTCCCAGATCAATTCAACT 58.459 43.478 17.36 0.00 44.65 3.16
1539 1624 0.546747 AGTTCACCCCCGATGAAGGA 60.547 55.000 0.00 0.00 36.76 3.36
1617 1702 3.476552 TGATTCAGTCAACAAGGTGGAC 58.523 45.455 0.00 0.00 36.79 4.02
1619 1704 0.105964 TCAGTCAACAAGGTGGACGG 59.894 55.000 0.00 0.00 41.05 4.79
1705 1790 1.070601 TGGGATGCATCGATGTACTGG 59.929 52.381 25.47 0.30 0.00 4.00
1781 1866 2.529005 TTCTCTCTCAACGCCGCGAG 62.529 60.000 21.79 11.63 0.00 5.03
2181 2266 1.429927 CGGCTGCTGATGCTCTTCTG 61.430 60.000 1.17 0.00 40.48 3.02
2355 2440 4.328169 GCAATTGCTGGTGCTCTTTATTTC 59.672 41.667 23.21 0.00 40.48 2.17
2369 2454 7.086376 GCTCTTTATTTCTGTTTCAATCTGCA 58.914 34.615 0.00 0.00 0.00 4.41
2371 2456 9.467258 CTCTTTATTTCTGTTTCAATCTGCAAA 57.533 29.630 0.00 0.00 0.00 3.68
2388 2473 6.668323 TCTGCAAAGGAAGAAAAATAGTTCG 58.332 36.000 0.00 0.00 32.50 3.95
2393 2478 4.403734 AGGAAGAAAAATAGTTCGGCCAA 58.596 39.130 2.24 0.00 31.76 4.52
2420 2505 3.077484 CAAGGACAATCTCCATGGTGT 57.923 47.619 12.58 8.67 42.46 4.16
3263 3348 2.909006 ACACACTGGAGTCCATCAAGAT 59.091 45.455 13.56 0.00 32.65 2.40
3546 3631 2.360165 GCCATGATACAGAAGGGCTTTG 59.640 50.000 0.00 0.00 38.37 2.77
3572 3657 5.482006 AGTTTCAAGCAAAATGAATAGGGC 58.518 37.500 0.00 0.00 36.72 5.19
3634 3719 6.211587 TGTAGTACTGTAACGCCATATGTT 57.788 37.500 5.39 0.00 0.00 2.71
3856 4062 7.443879 TCAGTTGTGTCATGTTCAGCTATTTTA 59.556 33.333 0.00 0.00 0.00 1.52
3867 4073 8.044060 TGTTCAGCTATTTTATTCAAGTCAGG 57.956 34.615 0.00 0.00 0.00 3.86
3884 4090 3.068732 GTCAGGCTCTGTGCACTCATATA 59.931 47.826 19.41 0.00 45.15 0.86
3885 4091 3.899980 TCAGGCTCTGTGCACTCATATAT 59.100 43.478 19.41 0.00 45.15 0.86
3901 4107 6.327626 ACTCATATATCCACTGCCTTGTTAGT 59.672 38.462 0.00 0.00 0.00 2.24
3908 4114 3.214328 CACTGCCTTGTTAGTTGAAGGT 58.786 45.455 0.00 0.00 40.89 3.50
4029 4368 6.797707 AGTATAGGGATATAGGTGTCCGAAA 58.202 40.000 0.00 0.00 36.54 3.46
4176 4515 1.152777 CCACCCAGAGCAACAACCA 60.153 57.895 0.00 0.00 0.00 3.67
4214 4553 9.814899 CATAAACCAAGGCATGAATGTTATTTA 57.185 29.630 0.00 0.00 0.00 1.40
4241 4580 9.154264 TTTCCCAAAGAAAAGAGGCAACTGAAA 62.154 37.037 0.00 0.00 44.94 2.69
4252 4591 4.632538 GGCAACTGAAACGCCTATTTAT 57.367 40.909 0.00 0.00 42.78 1.40
4253 4592 4.993905 GGCAACTGAAACGCCTATTTATT 58.006 39.130 0.00 0.00 42.78 1.40
4254 4593 5.407502 GGCAACTGAAACGCCTATTTATTT 58.592 37.500 0.00 0.00 42.78 1.40
4255 4594 6.557110 GGCAACTGAAACGCCTATTTATTTA 58.443 36.000 0.00 0.00 42.78 1.40
4256 4595 7.030768 GGCAACTGAAACGCCTATTTATTTAA 58.969 34.615 0.00 0.00 42.78 1.52
4257 4596 7.542824 GGCAACTGAAACGCCTATTTATTTAAA 59.457 33.333 0.00 0.00 42.78 1.52
4258 4597 9.083080 GCAACTGAAACGCCTATTTATTTAAAT 57.917 29.630 5.89 5.89 39.14 1.40
4263 4602 9.724839 TGAAACGCCTATTTATTTAAATGTAGC 57.275 29.630 11.05 4.60 36.62 3.58
4264 4603 8.776680 AAACGCCTATTTATTTAAATGTAGCG 57.223 30.769 21.41 21.41 45.02 4.26
4369 4708 7.461043 TCTTCTGGGTTATATATTGGGCTACAT 59.539 37.037 0.00 0.00 0.00 2.29
4380 4719 7.672983 ATATTGGGCTACATTAAAGACATCG 57.327 36.000 0.00 0.00 0.00 3.84
4448 4787 7.031226 TCTGAATGCTATTATTTTCACTGGC 57.969 36.000 0.00 0.00 0.00 4.85
4449 4788 6.602803 TCTGAATGCTATTATTTTCACTGGCA 59.397 34.615 0.00 0.00 0.00 4.92
4450 4789 7.286087 TCTGAATGCTATTATTTTCACTGGCAT 59.714 33.333 0.00 0.00 40.24 4.40
4451 4790 7.428020 TGAATGCTATTATTTTCACTGGCATC 58.572 34.615 0.00 0.00 38.05 3.91
4452 4791 7.286087 TGAATGCTATTATTTTCACTGGCATCT 59.714 33.333 0.00 0.00 38.05 2.90
4453 4792 7.592885 ATGCTATTATTTTCACTGGCATCTT 57.407 32.000 0.00 0.00 34.68 2.40
4454 4793 7.031226 TGCTATTATTTTCACTGGCATCTTC 57.969 36.000 0.00 0.00 0.00 2.87
4455 4794 6.830324 TGCTATTATTTTCACTGGCATCTTCT 59.170 34.615 0.00 0.00 0.00 2.85
4456 4795 7.340232 TGCTATTATTTTCACTGGCATCTTCTT 59.660 33.333 0.00 0.00 0.00 2.52
4457 4796 7.646922 GCTATTATTTTCACTGGCATCTTCTTG 59.353 37.037 0.00 0.00 0.00 3.02
4458 4797 7.707624 ATTATTTTCACTGGCATCTTCTTGA 57.292 32.000 0.00 0.00 0.00 3.02
4459 4798 7.523293 TTATTTTCACTGGCATCTTCTTGAA 57.477 32.000 0.00 0.00 0.00 2.69
4460 4799 4.836125 TTTCACTGGCATCTTCTTGAAC 57.164 40.909 0.00 0.00 0.00 3.18
4461 4800 3.490439 TCACTGGCATCTTCTTGAACA 57.510 42.857 0.00 0.00 0.00 3.18
4462 4801 4.025040 TCACTGGCATCTTCTTGAACAT 57.975 40.909 0.00 0.00 0.00 2.71
4463 4802 4.401022 TCACTGGCATCTTCTTGAACATT 58.599 39.130 0.00 0.00 0.00 2.71
4464 4803 4.828939 TCACTGGCATCTTCTTGAACATTT 59.171 37.500 0.00 0.00 0.00 2.32
4465 4804 5.302568 TCACTGGCATCTTCTTGAACATTTT 59.697 36.000 0.00 0.00 0.00 1.82
4466 4805 5.987347 CACTGGCATCTTCTTGAACATTTTT 59.013 36.000 0.00 0.00 0.00 1.94
4467 4806 7.014134 TCACTGGCATCTTCTTGAACATTTTTA 59.986 33.333 0.00 0.00 0.00 1.52
4468 4807 7.816031 CACTGGCATCTTCTTGAACATTTTTAT 59.184 33.333 0.00 0.00 0.00 1.40
4469 4808 8.031277 ACTGGCATCTTCTTGAACATTTTTATC 58.969 33.333 0.00 0.00 0.00 1.75
4470 4809 7.894708 TGGCATCTTCTTGAACATTTTTATCA 58.105 30.769 0.00 0.00 0.00 2.15
4471 4810 8.533657 TGGCATCTTCTTGAACATTTTTATCAT 58.466 29.630 0.00 0.00 0.00 2.45
4472 4811 9.028185 GGCATCTTCTTGAACATTTTTATCATC 57.972 33.333 0.00 0.00 0.00 2.92
4473 4812 9.798994 GCATCTTCTTGAACATTTTTATCATCT 57.201 29.630 0.00 0.00 0.00 2.90
4486 4825 9.722056 CATTTTTATCATCTAAACAGTACAGCC 57.278 33.333 0.00 0.00 0.00 4.85
4487 4826 9.686683 ATTTTTATCATCTAAACAGTACAGCCT 57.313 29.630 0.00 0.00 0.00 4.58
4488 4827 8.492673 TTTTATCATCTAAACAGTACAGCCTG 57.507 34.615 0.00 0.00 38.45 4.85
4489 4828 3.861840 TCATCTAAACAGTACAGCCTGC 58.138 45.455 0.00 0.00 35.83 4.85
4490 4829 3.515502 TCATCTAAACAGTACAGCCTGCT 59.484 43.478 0.00 0.00 35.83 4.24
4491 4830 4.020218 TCATCTAAACAGTACAGCCTGCTT 60.020 41.667 0.00 0.00 35.83 3.91
4492 4831 5.186992 TCATCTAAACAGTACAGCCTGCTTA 59.813 40.000 0.00 0.00 35.83 3.09
4493 4832 5.677319 TCTAAACAGTACAGCCTGCTTAT 57.323 39.130 0.00 0.00 35.83 1.73
4494 4833 6.785337 TCTAAACAGTACAGCCTGCTTATA 57.215 37.500 0.00 0.00 35.83 0.98
4495 4834 7.361457 TCTAAACAGTACAGCCTGCTTATAT 57.639 36.000 0.00 0.00 35.83 0.86
4496 4835 8.473358 TCTAAACAGTACAGCCTGCTTATATA 57.527 34.615 0.00 0.00 35.83 0.86
4497 4836 9.090103 TCTAAACAGTACAGCCTGCTTATATAT 57.910 33.333 0.00 0.00 35.83 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.684697 GCTTATCTTTTAAGCCGGGGAGT 60.685 47.826 2.18 0.00 42.88 3.85
1 2 2.879026 GCTTATCTTTTAAGCCGGGGAG 59.121 50.000 2.18 0.00 42.88 4.30
2 3 2.927028 GCTTATCTTTTAAGCCGGGGA 58.073 47.619 2.18 0.00 42.88 4.81
8 9 2.290916 GGGAGCGGCTTATCTTTTAAGC 59.709 50.000 2.97 8.49 46.64 3.09
9 10 3.541632 TGGGAGCGGCTTATCTTTTAAG 58.458 45.455 2.97 0.00 0.00 1.85
10 11 3.637911 TGGGAGCGGCTTATCTTTTAA 57.362 42.857 2.97 0.00 0.00 1.52
11 12 3.637911 TTGGGAGCGGCTTATCTTTTA 57.362 42.857 2.97 0.00 0.00 1.52
12 13 2.507407 TTGGGAGCGGCTTATCTTTT 57.493 45.000 2.97 0.00 0.00 2.27
13 14 2.507407 TTTGGGAGCGGCTTATCTTT 57.493 45.000 2.97 0.00 0.00 2.52
14 15 2.507407 TTTTGGGAGCGGCTTATCTT 57.493 45.000 2.97 0.00 0.00 2.40
15 16 2.736670 ATTTTGGGAGCGGCTTATCT 57.263 45.000 2.97 0.00 0.00 1.98
16 17 2.287009 CGAATTTTGGGAGCGGCTTATC 60.287 50.000 2.97 0.00 0.00 1.75
17 18 1.676006 CGAATTTTGGGAGCGGCTTAT 59.324 47.619 2.97 0.00 0.00 1.73
18 19 1.091537 CGAATTTTGGGAGCGGCTTA 58.908 50.000 2.97 0.00 0.00 3.09
19 20 0.893727 ACGAATTTTGGGAGCGGCTT 60.894 50.000 2.97 0.00 0.00 4.35
20 21 0.893727 AACGAATTTTGGGAGCGGCT 60.894 50.000 0.00 0.00 0.00 5.52
21 22 0.732538 CAACGAATTTTGGGAGCGGC 60.733 55.000 0.00 0.00 0.00 6.53
22 23 0.878416 TCAACGAATTTTGGGAGCGG 59.122 50.000 0.00 0.00 0.00 5.52
23 24 1.135689 CCTCAACGAATTTTGGGAGCG 60.136 52.381 0.00 0.00 0.00 5.03
24 25 1.402852 GCCTCAACGAATTTTGGGAGC 60.403 52.381 0.00 0.00 0.00 4.70
25 26 2.162681 AGCCTCAACGAATTTTGGGAG 58.837 47.619 0.00 0.00 0.00 4.30
26 27 2.286365 AGCCTCAACGAATTTTGGGA 57.714 45.000 0.00 0.00 0.00 4.37
27 28 3.081804 AGTAGCCTCAACGAATTTTGGG 58.918 45.455 0.00 0.00 0.00 4.12
28 29 5.873179 TTAGTAGCCTCAACGAATTTTGG 57.127 39.130 0.00 0.00 0.00 3.28
29 30 9.490663 CTAATTTAGTAGCCTCAACGAATTTTG 57.509 33.333 0.00 0.00 0.00 2.44
30 31 9.227777 ACTAATTTAGTAGCCTCAACGAATTTT 57.772 29.630 7.31 0.00 37.23 1.82
31 32 8.788325 ACTAATTTAGTAGCCTCAACGAATTT 57.212 30.769 7.31 0.00 37.23 1.82
32 33 9.880157 TTACTAATTTAGTAGCCTCAACGAATT 57.120 29.630 14.29 0.00 41.84 2.17
34 35 9.525409 GATTACTAATTTAGTAGCCTCAACGAA 57.475 33.333 14.29 1.32 41.84 3.85
35 36 8.139989 GGATTACTAATTTAGTAGCCTCAACGA 58.860 37.037 19.88 6.08 41.84 3.85
36 37 7.384387 GGGATTACTAATTTAGTAGCCTCAACG 59.616 40.741 23.06 0.00 41.84 4.10
37 38 8.208903 TGGGATTACTAATTTAGTAGCCTCAAC 58.791 37.037 23.06 14.32 41.84 3.18
38 39 8.326765 TGGGATTACTAATTTAGTAGCCTCAA 57.673 34.615 23.06 11.13 41.84 3.02
39 40 7.924358 TGGGATTACTAATTTAGTAGCCTCA 57.076 36.000 23.06 18.01 41.84 3.86
53 54 8.639761 GCTTCTGAACTAGTTATGGGATTACTA 58.360 37.037 8.42 0.00 0.00 1.82
54 55 7.345914 AGCTTCTGAACTAGTTATGGGATTACT 59.654 37.037 8.42 0.00 0.00 2.24
55 56 7.501844 AGCTTCTGAACTAGTTATGGGATTAC 58.498 38.462 8.42 0.00 0.00 1.89
56 57 7.202011 GGAGCTTCTGAACTAGTTATGGGATTA 60.202 40.741 8.42 0.00 0.00 1.75
57 58 6.408662 GGAGCTTCTGAACTAGTTATGGGATT 60.409 42.308 8.42 0.00 0.00 3.01
58 59 5.071115 GGAGCTTCTGAACTAGTTATGGGAT 59.929 44.000 8.42 0.00 0.00 3.85
59 60 4.406003 GGAGCTTCTGAACTAGTTATGGGA 59.594 45.833 8.42 1.98 0.00 4.37
60 61 4.162320 TGGAGCTTCTGAACTAGTTATGGG 59.838 45.833 8.42 0.00 0.00 4.00
61 62 5.344743 TGGAGCTTCTGAACTAGTTATGG 57.655 43.478 8.42 2.04 0.00 2.74
62 63 6.259608 CCATTGGAGCTTCTGAACTAGTTATG 59.740 42.308 8.42 4.60 0.00 1.90
63 64 6.156949 TCCATTGGAGCTTCTGAACTAGTTAT 59.843 38.462 8.42 0.00 0.00 1.89
64 65 5.483937 TCCATTGGAGCTTCTGAACTAGTTA 59.516 40.000 8.42 0.00 0.00 2.24
65 66 4.287067 TCCATTGGAGCTTCTGAACTAGTT 59.713 41.667 8.13 8.13 0.00 2.24
66 67 3.840666 TCCATTGGAGCTTCTGAACTAGT 59.159 43.478 0.00 0.00 0.00 2.57
67 68 4.478206 TCCATTGGAGCTTCTGAACTAG 57.522 45.455 0.00 0.00 0.00 2.57
68 69 4.471025 TCATCCATTGGAGCTTCTGAACTA 59.529 41.667 11.78 0.00 34.05 2.24
69 70 3.265221 TCATCCATTGGAGCTTCTGAACT 59.735 43.478 11.78 0.00 34.05 3.01
70 71 3.614092 TCATCCATTGGAGCTTCTGAAC 58.386 45.455 11.78 0.00 34.05 3.18
71 72 3.371273 CCTCATCCATTGGAGCTTCTGAA 60.371 47.826 11.78 0.00 34.05 3.02
72 73 2.172082 CCTCATCCATTGGAGCTTCTGA 59.828 50.000 11.78 8.46 34.05 3.27
73 74 2.573369 CCTCATCCATTGGAGCTTCTG 58.427 52.381 11.78 4.29 34.05 3.02
74 75 1.493871 CCCTCATCCATTGGAGCTTCT 59.506 52.381 11.78 0.00 34.05 2.85
75 76 1.492176 TCCCTCATCCATTGGAGCTTC 59.508 52.381 11.78 0.00 34.05 3.86
76 77 1.493871 CTCCCTCATCCATTGGAGCTT 59.506 52.381 11.78 0.00 38.12 3.74
77 78 1.138568 CTCCCTCATCCATTGGAGCT 58.861 55.000 11.78 0.00 38.12 4.09
78 79 1.135094 TCTCCCTCATCCATTGGAGC 58.865 55.000 11.78 0.00 43.33 4.70
79 80 1.069823 CGTCTCCCTCATCCATTGGAG 59.930 57.143 11.78 3.92 44.69 3.86
80 81 1.123077 CGTCTCCCTCATCCATTGGA 58.877 55.000 8.08 8.08 35.55 3.53
81 82 0.107456 CCGTCTCCCTCATCCATTGG 59.893 60.000 0.00 0.00 0.00 3.16
82 83 0.533755 GCCGTCTCCCTCATCCATTG 60.534 60.000 0.00 0.00 0.00 2.82
83 84 0.692419 AGCCGTCTCCCTCATCCATT 60.692 55.000 0.00 0.00 0.00 3.16
84 85 0.692419 AAGCCGTCTCCCTCATCCAT 60.692 55.000 0.00 0.00 0.00 3.41
85 86 0.032515 TAAGCCGTCTCCCTCATCCA 60.033 55.000 0.00 0.00 0.00 3.41
86 87 1.273886 GATAAGCCGTCTCCCTCATCC 59.726 57.143 0.00 0.00 0.00 3.51
87 88 1.068194 CGATAAGCCGTCTCCCTCATC 60.068 57.143 0.00 0.00 0.00 2.92
88 89 0.962489 CGATAAGCCGTCTCCCTCAT 59.038 55.000 0.00 0.00 0.00 2.90
89 90 0.106868 TCGATAAGCCGTCTCCCTCA 60.107 55.000 0.00 0.00 0.00 3.86
90 91 1.030457 TTCGATAAGCCGTCTCCCTC 58.970 55.000 0.00 0.00 0.00 4.30
91 92 1.481871 TTTCGATAAGCCGTCTCCCT 58.518 50.000 0.00 0.00 0.00 4.20
92 93 2.304751 TTTTCGATAAGCCGTCTCCC 57.695 50.000 0.00 0.00 0.00 4.30
93 94 4.025647 CAGATTTTTCGATAAGCCGTCTCC 60.026 45.833 0.00 0.00 0.00 3.71
94 95 4.804139 TCAGATTTTTCGATAAGCCGTCTC 59.196 41.667 0.00 0.00 0.00 3.36
95 96 4.755411 TCAGATTTTTCGATAAGCCGTCT 58.245 39.130 0.00 0.00 0.00 4.18
96 97 5.291128 TCTTCAGATTTTTCGATAAGCCGTC 59.709 40.000 0.00 0.00 0.00 4.79
97 98 5.175859 TCTTCAGATTTTTCGATAAGCCGT 58.824 37.500 0.00 0.00 0.00 5.68
98 99 5.277058 CCTCTTCAGATTTTTCGATAAGCCG 60.277 44.000 0.00 0.00 0.00 5.52
99 100 5.817816 TCCTCTTCAGATTTTTCGATAAGCC 59.182 40.000 0.00 0.00 0.00 4.35
100 101 6.018343 CCTCCTCTTCAGATTTTTCGATAAGC 60.018 42.308 0.00 0.00 0.00 3.09
101 102 6.018343 GCCTCCTCTTCAGATTTTTCGATAAG 60.018 42.308 0.00 0.00 0.00 1.73
102 103 5.817816 GCCTCCTCTTCAGATTTTTCGATAA 59.182 40.000 0.00 0.00 0.00 1.75
103 104 5.360591 GCCTCCTCTTCAGATTTTTCGATA 58.639 41.667 0.00 0.00 0.00 2.92
104 105 4.195416 GCCTCCTCTTCAGATTTTTCGAT 58.805 43.478 0.00 0.00 0.00 3.59
105 106 3.600388 GCCTCCTCTTCAGATTTTTCGA 58.400 45.455 0.00 0.00 0.00 3.71
106 107 2.349886 CGCCTCCTCTTCAGATTTTTCG 59.650 50.000 0.00 0.00 0.00 3.46
107 108 2.680339 CCGCCTCCTCTTCAGATTTTTC 59.320 50.000 0.00 0.00 0.00 2.29
108 109 2.716217 CCGCCTCCTCTTCAGATTTTT 58.284 47.619 0.00 0.00 0.00 1.94
109 110 1.680249 GCCGCCTCCTCTTCAGATTTT 60.680 52.381 0.00 0.00 0.00 1.82
110 111 0.107459 GCCGCCTCCTCTTCAGATTT 60.107 55.000 0.00 0.00 0.00 2.17
111 112 0.980231 AGCCGCCTCCTCTTCAGATT 60.980 55.000 0.00 0.00 0.00 2.40
112 113 0.980231 AAGCCGCCTCCTCTTCAGAT 60.980 55.000 0.00 0.00 0.00 2.90
113 114 0.324368 TAAGCCGCCTCCTCTTCAGA 60.324 55.000 0.00 0.00 0.00 3.27
114 115 0.755686 ATAAGCCGCCTCCTCTTCAG 59.244 55.000 0.00 0.00 0.00 3.02
115 116 1.204146 AATAAGCCGCCTCCTCTTCA 58.796 50.000 0.00 0.00 0.00 3.02
116 117 2.333688 AAATAAGCCGCCTCCTCTTC 57.666 50.000 0.00 0.00 0.00 2.87
117 118 2.808906 AAAATAAGCCGCCTCCTCTT 57.191 45.000 0.00 0.00 0.00 2.85
118 119 2.808906 AAAAATAAGCCGCCTCCTCT 57.191 45.000 0.00 0.00 0.00 3.69
134 135 5.749588 GCCAGTTCTTTTTACGGCTTAAAAA 59.250 36.000 17.37 17.37 44.10 1.94
135 136 5.068067 AGCCAGTTCTTTTTACGGCTTAAAA 59.932 36.000 4.95 4.95 40.23 1.52
136 137 4.581409 AGCCAGTTCTTTTTACGGCTTAAA 59.419 37.500 0.00 0.00 40.23 1.52
137 138 4.139038 AGCCAGTTCTTTTTACGGCTTAA 58.861 39.130 0.00 0.00 40.23 1.85
138 139 3.746940 AGCCAGTTCTTTTTACGGCTTA 58.253 40.909 0.00 0.00 40.23 3.09
139 140 2.583143 AGCCAGTTCTTTTTACGGCTT 58.417 42.857 0.00 0.00 40.23 4.35
140 141 2.271944 AGCCAGTTCTTTTTACGGCT 57.728 45.000 0.00 0.00 39.19 5.52
141 142 3.501062 AGTTAGCCAGTTCTTTTTACGGC 59.499 43.478 0.00 0.00 36.28 5.68
142 143 6.790285 TTAGTTAGCCAGTTCTTTTTACGG 57.210 37.500 0.00 0.00 0.00 4.02
143 144 8.950961 GTTTTTAGTTAGCCAGTTCTTTTTACG 58.049 33.333 0.00 0.00 0.00 3.18
144 145 9.791820 TGTTTTTAGTTAGCCAGTTCTTTTTAC 57.208 29.630 0.00 0.00 0.00 2.01
146 147 8.745590 TCTGTTTTTAGTTAGCCAGTTCTTTTT 58.254 29.630 0.00 0.00 0.00 1.94
147 148 8.288689 TCTGTTTTTAGTTAGCCAGTTCTTTT 57.711 30.769 0.00 0.00 0.00 2.27
148 149 7.875327 TCTGTTTTTAGTTAGCCAGTTCTTT 57.125 32.000 0.00 0.00 0.00 2.52
149 150 7.875327 TTCTGTTTTTAGTTAGCCAGTTCTT 57.125 32.000 0.00 0.00 0.00 2.52
150 151 7.875327 TTTCTGTTTTTAGTTAGCCAGTTCT 57.125 32.000 0.00 0.00 0.00 3.01
151 152 8.403236 TCTTTTCTGTTTTTAGTTAGCCAGTTC 58.597 33.333 0.00 0.00 0.00 3.01
152 153 8.288689 TCTTTTCTGTTTTTAGTTAGCCAGTT 57.711 30.769 0.00 0.00 0.00 3.16
153 154 7.773690 TCTCTTTTCTGTTTTTAGTTAGCCAGT 59.226 33.333 0.00 0.00 0.00 4.00
154 155 8.154649 TCTCTTTTCTGTTTTTAGTTAGCCAG 57.845 34.615 0.00 0.00 0.00 4.85
155 156 8.403236 GTTCTCTTTTCTGTTTTTAGTTAGCCA 58.597 33.333 0.00 0.00 0.00 4.75
156 157 7.861372 GGTTCTCTTTTCTGTTTTTAGTTAGCC 59.139 37.037 0.00 0.00 0.00 3.93
157 158 7.861372 GGGTTCTCTTTTCTGTTTTTAGTTAGC 59.139 37.037 0.00 0.00 0.00 3.09
158 159 9.121658 AGGGTTCTCTTTTCTGTTTTTAGTTAG 57.878 33.333 0.00 0.00 0.00 2.34
159 160 9.470399 AAGGGTTCTCTTTTCTGTTTTTAGTTA 57.530 29.630 0.00 0.00 0.00 2.24
160 161 7.956328 AGGGTTCTCTTTTCTGTTTTTAGTT 57.044 32.000 0.00 0.00 0.00 2.24
161 162 7.956328 AAGGGTTCTCTTTTCTGTTTTTAGT 57.044 32.000 0.00 0.00 0.00 2.24
188 189 3.414759 AACTCCTTTCCCCCTGTTTTT 57.585 42.857 0.00 0.00 0.00 1.94
189 190 3.038280 CAAACTCCTTTCCCCCTGTTTT 58.962 45.455 0.00 0.00 0.00 2.43
190 191 2.023404 ACAAACTCCTTTCCCCCTGTTT 60.023 45.455 0.00 0.00 0.00 2.83
191 192 1.573857 ACAAACTCCTTTCCCCCTGTT 59.426 47.619 0.00 0.00 0.00 3.16
192 193 1.231963 ACAAACTCCTTTCCCCCTGT 58.768 50.000 0.00 0.00 0.00 4.00
193 194 2.365293 CAAACAAACTCCTTTCCCCCTG 59.635 50.000 0.00 0.00 0.00 4.45
194 195 2.023404 ACAAACAAACTCCTTTCCCCCT 60.023 45.455 0.00 0.00 0.00 4.79
195 196 2.102420 CACAAACAAACTCCTTTCCCCC 59.898 50.000 0.00 0.00 0.00 5.40
196 197 2.483013 GCACAAACAAACTCCTTTCCCC 60.483 50.000 0.00 0.00 0.00 4.81
292 293 1.350351 GATGGTGATGCTAGCTGGGAT 59.650 52.381 17.23 3.07 0.00 3.85
304 305 1.561076 TGCTGTTAGCTGGATGGTGAT 59.439 47.619 0.00 0.00 42.97 3.06
305 306 0.983467 TGCTGTTAGCTGGATGGTGA 59.017 50.000 0.00 0.00 42.97 4.02
308 317 2.119801 AGTTGCTGTTAGCTGGATGG 57.880 50.000 0.00 0.00 42.97 3.51
320 335 2.604462 GCTCACCAAAACAAAGTTGCTG 59.396 45.455 0.00 0.00 0.00 4.41
322 337 2.860136 GAGCTCACCAAAACAAAGTTGC 59.140 45.455 9.40 0.00 0.00 4.17
344 366 3.306710 CCTGTGGGGCTATTTTTGAAACC 60.307 47.826 0.00 0.00 0.00 3.27
426 448 2.515854 GACAGGGAGCGGTATCTATCA 58.484 52.381 0.00 0.00 0.00 2.15
437 459 0.980231 AGGAGACATGGACAGGGAGC 60.980 60.000 0.00 0.00 0.00 4.70
448 470 0.712979 TGGACCTGGAGAGGAGACAT 59.287 55.000 0.00 0.00 42.93 3.06
627 661 0.037447 AAAGCTCCAAGCCCAGAGAC 59.963 55.000 0.00 0.00 43.77 3.36
674 712 2.873472 CAAAGCAAAGCAAATCAAGGCA 59.127 40.909 0.00 0.00 0.00 4.75
675 713 2.350102 GCAAAGCAAAGCAAATCAAGGC 60.350 45.455 0.00 0.00 0.00 4.35
676 714 3.135994 AGCAAAGCAAAGCAAATCAAGG 58.864 40.909 0.00 0.00 0.00 3.61
677 715 4.806342 AAGCAAAGCAAAGCAAATCAAG 57.194 36.364 0.00 0.00 0.00 3.02
678 716 4.731193 GCAAAGCAAAGCAAAGCAAATCAA 60.731 37.500 0.00 0.00 0.00 2.57
679 717 3.242804 GCAAAGCAAAGCAAAGCAAATCA 60.243 39.130 0.00 0.00 0.00 2.57
680 718 3.002965 AGCAAAGCAAAGCAAAGCAAATC 59.997 39.130 0.00 0.00 0.00 2.17
681 719 2.946990 AGCAAAGCAAAGCAAAGCAAAT 59.053 36.364 0.00 0.00 0.00 2.32
682 720 2.096174 CAGCAAAGCAAAGCAAAGCAAA 59.904 40.909 0.00 0.00 0.00 3.68
683 721 1.666700 CAGCAAAGCAAAGCAAAGCAA 59.333 42.857 0.00 0.00 0.00 3.91
684 722 1.292061 CAGCAAAGCAAAGCAAAGCA 58.708 45.000 0.00 0.00 0.00 3.91
685 723 0.584876 CCAGCAAAGCAAAGCAAAGC 59.415 50.000 0.00 0.00 0.00 3.51
686 724 1.223187 CCCAGCAAAGCAAAGCAAAG 58.777 50.000 0.00 0.00 0.00 2.77
687 725 0.179051 CCCCAGCAAAGCAAAGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
688 726 1.446791 CCCCAGCAAAGCAAAGCAA 59.553 52.632 0.00 0.00 0.00 3.91
691 729 0.540365 TCTCCCCCAGCAAAGCAAAG 60.540 55.000 0.00 0.00 0.00 2.77
724 778 1.186267 ACCTGAGGAGTCGTGGGTTC 61.186 60.000 4.99 0.00 0.00 3.62
787 849 4.755411 AGAGAACAAGAACAAGAACACGA 58.245 39.130 0.00 0.00 0.00 4.35
1008 1081 0.038067 TCGACAGGAAATTCGCGGAA 60.038 50.000 6.13 0.00 35.15 4.30
1014 1087 2.939103 CACCAGGATCGACAGGAAATTC 59.061 50.000 0.00 0.00 0.00 2.17
1230 1315 0.533951 ACAAATCTCCGTACGGGTCC 59.466 55.000 32.80 0.00 37.00 4.46
1455 1540 1.067846 ACGATGACGCTGCTAGTTGAA 60.068 47.619 0.00 0.00 43.96 2.69
1461 1546 0.179137 CCTTGACGATGACGCTGCTA 60.179 55.000 0.00 0.00 43.96 3.49
1539 1624 1.952296 GCATTGATGAAGGCGAAGGAT 59.048 47.619 0.00 0.00 0.00 3.24
1617 1702 1.595093 GGCCTTTCAACCCATGACCG 61.595 60.000 0.00 0.00 37.92 4.79
1619 1704 2.276869 GGGCCTTTCAACCCATGAC 58.723 57.895 0.84 0.00 46.22 3.06
1654 1739 0.467474 TACATGGTCTCGATCCCGCT 60.467 55.000 0.00 0.00 35.37 5.52
1705 1790 0.105778 CCTGGATCCTCTTTCCTCGC 59.894 60.000 14.23 0.00 34.17 5.03
1781 1866 4.821805 TGTTGGAAGAGTTGAAGATGGAAC 59.178 41.667 0.00 0.00 0.00 3.62
2061 2146 2.775490 AAAAGGCCTTGTTCTTCCCT 57.225 45.000 21.33 0.00 0.00 4.20
2064 2149 6.207614 AGTCTTCATAAAAGGCCTTGTTCTTC 59.792 38.462 21.33 4.84 0.00 2.87
2181 2266 5.136105 ACCTTAAAGATCTCCATGCCATTC 58.864 41.667 0.00 0.00 0.00 2.67
2259 2344 1.066587 TTTTGGTTTCCTTGCGCCG 59.933 52.632 4.18 0.00 0.00 6.46
2268 2353 1.110518 TGGGGCTCCGTTTTGGTTTC 61.111 55.000 0.00 0.00 39.52 2.78
2355 2440 5.443185 TCTTCCTTTGCAGATTGAAACAG 57.557 39.130 0.00 0.00 0.00 3.16
2369 2454 4.830600 TGGCCGAACTATTTTTCTTCCTTT 59.169 37.500 0.00 0.00 0.00 3.11
2371 2456 4.028993 TGGCCGAACTATTTTTCTTCCT 57.971 40.909 0.00 0.00 0.00 3.36
2393 2478 2.519013 GGAGATTGTCCTTGGCTTTGT 58.481 47.619 0.00 0.00 42.99 2.83
2420 2505 3.579586 AGTTGGAGAACGGGTATGTGTAA 59.420 43.478 0.00 0.00 37.15 2.41
2928 3013 1.652563 GGCAACAAGGTTGTCGTCC 59.347 57.895 10.44 0.33 41.31 4.79
3263 3348 6.293081 GCATTTTTCTGCTATCTCGCTGAATA 60.293 38.462 6.05 0.22 43.93 1.75
3291 3376 1.450312 GTTCACCCCCTCATCTGCG 60.450 63.158 0.00 0.00 0.00 5.18
3399 3484 1.338579 GGCTTCAGTTGAGGGTCTGAG 60.339 57.143 0.00 0.00 40.91 3.35
3546 3631 6.591448 CCCTATTCATTTTGCTTGAAACTTCC 59.409 38.462 0.00 0.00 36.72 3.46
3572 3657 0.250124 TGTTGTTAGCTGGACACCCG 60.250 55.000 0.00 0.00 34.29 5.28
3634 3719 7.931015 ATTTCAGTATATTGTAGGGACCTCA 57.069 36.000 0.00 0.00 0.00 3.86
3724 3930 4.565166 CCAGCGTGTTACGAAGAATCAATA 59.435 41.667 5.44 0.00 46.05 1.90
3735 3941 0.938713 TTTGGTTCCAGCGTGTTACG 59.061 50.000 0.00 0.00 45.88 3.18
3856 4062 1.072806 TGCACAGAGCCTGACTTGAAT 59.927 47.619 8.91 0.00 44.83 2.57
3867 4073 3.993081 GTGGATATATGAGTGCACAGAGC 59.007 47.826 21.04 5.85 45.96 4.09
3884 4090 3.788227 TCAACTAACAAGGCAGTGGAT 57.212 42.857 0.00 0.00 0.00 3.41
3885 4091 3.476552 CTTCAACTAACAAGGCAGTGGA 58.523 45.455 0.00 0.00 0.00 4.02
4019 4225 3.703052 TCTAGGGTAGATTTTCGGACACC 59.297 47.826 0.00 0.00 0.00 4.16
4029 4368 8.980832 AGGATTTACATCATCTAGGGTAGATT 57.019 34.615 0.00 0.00 42.70 2.40
4077 4416 2.555199 CTTCTTGAAGCCTGGTATCGG 58.445 52.381 0.00 0.00 0.00 4.18
4176 4515 4.463891 CCTTGGTTTATGCAGGAAAGACAT 59.536 41.667 0.00 0.00 0.00 3.06
4214 4553 4.655649 AGTTGCCTCTTTTCTTTGGGAAAT 59.344 37.500 0.00 0.00 42.63 2.17
4241 4580 6.567132 GCCGCTACATTTAAATAAATAGGCGT 60.567 38.462 22.23 11.61 40.70 5.68
4242 4581 5.793457 GCCGCTACATTTAAATAAATAGGCG 59.207 40.000 19.91 19.91 41.22 5.52
4243 4582 5.793457 CGCCGCTACATTTAAATAAATAGGC 59.207 40.000 18.46 18.46 34.36 3.93
4244 4583 7.117236 TCTCGCCGCTACATTTAAATAAATAGG 59.883 37.037 0.00 3.96 34.36 2.57
4245 4584 8.014322 TCTCGCCGCTACATTTAAATAAATAG 57.986 34.615 0.00 4.95 34.36 1.73
4246 4585 7.359765 GCTCTCGCCGCTACATTTAAATAAATA 60.360 37.037 0.00 0.00 34.36 1.40
4247 4586 6.565999 GCTCTCGCCGCTACATTTAAATAAAT 60.566 38.462 0.00 0.00 36.39 1.40
4248 4587 5.277154 GCTCTCGCCGCTACATTTAAATAAA 60.277 40.000 0.00 0.00 0.00 1.40
4249 4588 4.210537 GCTCTCGCCGCTACATTTAAATAA 59.789 41.667 0.00 0.00 0.00 1.40
4250 4589 3.739300 GCTCTCGCCGCTACATTTAAATA 59.261 43.478 0.00 0.00 0.00 1.40
4251 4590 2.544267 GCTCTCGCCGCTACATTTAAAT 59.456 45.455 0.00 0.00 0.00 1.40
4252 4591 1.931172 GCTCTCGCCGCTACATTTAAA 59.069 47.619 0.00 0.00 0.00 1.52
4253 4592 1.136305 AGCTCTCGCCGCTACATTTAA 59.864 47.619 0.00 0.00 35.63 1.52
4254 4593 0.744874 AGCTCTCGCCGCTACATTTA 59.255 50.000 0.00 0.00 35.63 1.40
4255 4594 0.108138 AAGCTCTCGCCGCTACATTT 60.108 50.000 0.00 0.00 36.56 2.32
4256 4595 0.108138 AAAGCTCTCGCCGCTACATT 60.108 50.000 0.00 0.00 36.56 2.71
4257 4596 0.744874 TAAAGCTCTCGCCGCTACAT 59.255 50.000 0.00 0.00 36.56 2.29
4258 4597 0.528924 TTAAAGCTCTCGCCGCTACA 59.471 50.000 0.00 0.00 36.56 2.74
4259 4598 1.201343 CTTAAAGCTCTCGCCGCTAC 58.799 55.000 0.00 0.00 36.56 3.58
4260 4599 1.100510 TCTTAAAGCTCTCGCCGCTA 58.899 50.000 0.00 0.00 36.56 4.26
4261 4600 0.461961 ATCTTAAAGCTCTCGCCGCT 59.538 50.000 0.00 0.00 39.94 5.52
4262 4601 0.855995 GATCTTAAAGCTCTCGCCGC 59.144 55.000 0.00 0.00 36.60 6.53
4263 4602 2.209838 TGATCTTAAAGCTCTCGCCG 57.790 50.000 0.00 0.00 36.60 6.46
4264 4603 3.873952 ACAATGATCTTAAAGCTCTCGCC 59.126 43.478 0.00 0.00 36.60 5.54
4447 4786 9.798994 AGATGATAAAAATGTTCAAGAAGATGC 57.201 29.630 0.00 0.00 0.00 3.91
4460 4799 9.722056 GGCTGTACTGTTTAGATGATAAAAATG 57.278 33.333 1.46 0.00 0.00 2.32
4461 4800 9.686683 AGGCTGTACTGTTTAGATGATAAAAAT 57.313 29.630 1.46 0.00 0.00 1.82
4462 4801 8.946085 CAGGCTGTACTGTTTAGATGATAAAAA 58.054 33.333 6.28 0.00 33.81 1.94
4463 4802 7.065803 GCAGGCTGTACTGTTTAGATGATAAAA 59.934 37.037 17.16 0.00 40.59 1.52
4464 4803 6.538742 GCAGGCTGTACTGTTTAGATGATAAA 59.461 38.462 17.16 0.00 40.59 1.40
4465 4804 6.049149 GCAGGCTGTACTGTTTAGATGATAA 58.951 40.000 17.16 0.00 40.59 1.75
4466 4805 5.363868 AGCAGGCTGTACTGTTTAGATGATA 59.636 40.000 17.16 0.00 40.59 2.15
4467 4806 4.163078 AGCAGGCTGTACTGTTTAGATGAT 59.837 41.667 17.16 0.00 40.59 2.45
4468 4807 3.515502 AGCAGGCTGTACTGTTTAGATGA 59.484 43.478 17.16 0.00 40.59 2.92
4469 4808 3.866651 AGCAGGCTGTACTGTTTAGATG 58.133 45.455 17.16 0.00 40.59 2.90
4470 4809 4.559862 AAGCAGGCTGTACTGTTTAGAT 57.440 40.909 17.16 0.00 39.63 1.98
4471 4810 5.677319 ATAAGCAGGCTGTACTGTTTAGA 57.323 39.130 17.16 0.00 43.90 2.10


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

AutoCloner maintained by Alex Coulton.