Multiple sequence alignment - TraesCS2B01G130300

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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 TraesCS2B01G130300 chr2B 100.000 2472 0 0 1 2472 97440475 97442946 0.000000e+00 4566.0
1 TraesCS2B01G130300 chr2A 88.997 1645 113 35 765 2360 62397356 62398981 0.000000e+00 1973.0
2 TraesCS2B01G130300 chr2A 80.400 250 28 13 220 457 62396940 62397180 1.180000e-38 171.0
3 TraesCS2B01G130300 chr2D 88.360 1598 85 42 506 2061 62068512 62070050 0.000000e+00 1827.0
4 TraesCS2B01G130300 chr2D 87.059 255 24 7 2175 2421 62070049 62070302 1.870000e-71 279.0
5 TraesCS2B01G130300 chr2D 79.412 272 32 16 197 457 62068128 62068386 1.180000e-38 171.0
6 TraesCS2B01G130300 chr4D 87.255 204 22 4 1197 1398 293665346 293665145 1.910000e-56 230.0
7 TraesCS2B01G130300 chr4B 85.714 203 27 2 1197 1398 290913478 290913277 1.930000e-51 213.0
8 TraesCS2B01G130300 chr6D 85.577 104 15 0 2059 2162 410395586 410395483 2.600000e-20 110.0
9 TraesCS2B01G130300 chr7D 82.301 113 17 3 2057 2167 17770571 17770682 7.280000e-16 95.3
10 TraesCS2B01G130300 chr7D 92.857 42 3 0 2060 2101 608529763 608529804 7.380000e-06 62.1
11 TraesCS2B01G130300 chr5A 81.053 95 17 1 2066 2160 510278096 510278003 9.480000e-10 75.0
12 TraesCS2B01G130300 chr5A 83.582 67 4 4 2183 2242 439770144 439770210 3.430000e-04 56.5
13 TraesCS2B01G130300 chr5A 82.857 70 5 6 2183 2246 547345086 547345154 3.430000e-04 56.5
14 TraesCS2B01G130300 chr7A 97.222 36 1 0 2066 2101 613179460 613179425 7.380000e-06 62.1
15 TraesCS2B01G130300 chr7A 92.857 42 3 0 2060 2101 699801222 699801263 7.380000e-06 62.1
16 TraesCS2B01G130300 chr6B 94.872 39 2 0 2060 2098 470116225 470116263 7.380000e-06 62.1
17 TraesCS2B01G130300 chr1B 82.278 79 7 4 2186 2257 6412856 6412778 7.380000e-06 62.1
18 TraesCS2B01G130300 chr1B 84.615 65 3 4 2186 2243 23667582 23667518 9.550000e-05 58.4
19 TraesCS2B01G130300 chr7B 92.683 41 3 0 2060 2100 696788226 696788266 2.650000e-05 60.2
20 TraesCS2B01G130300 chr3A 84.615 65 3 4 2186 2243 227067796 227067732 9.550000e-05 58.4
21 TraesCS2B01G130300 chr1D 89.362 47 3 2 2212 2257 40099827 40099782 9.550000e-05 58.4
22 TraesCS2B01G130300 chr5D 84.746 59 6 2 2212 2268 432528160 432528217 3.430000e-04 56.5


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 TraesCS2B01G130300 chr2B 97440475 97442946 2471 False 4566 4566 100.000000 1 2472 1 chr2B.!!$F1 2471
1 TraesCS2B01G130300 chr2A 62396940 62398981 2041 False 1072 1973 84.698500 220 2360 2 chr2A.!!$F1 2140
2 TraesCS2B01G130300 chr2D 62068128 62070302 2174 False 759 1827 84.943667 197 2421 3 chr2D.!!$F1 2224

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
57 58 0.179073 CTCGATGGTCCCATGTCCAC 60.179 60.0 2.93 0.0 36.7 4.02 F
59 60 0.181114 CGATGGTCCCATGTCCACAT 59.819 55.0 2.93 0.0 36.7 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1005 1100 0.036858 GCGTCTCTTCTTCTTGGGCT 60.037 55.0 0.0 0.0 0.0 5.19 R
1645 1748 0.179045 CCCTTTCCCTCATACTGCCG 60.179 60.0 0.0 0.0 0.0 5.69 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 4.000620 TGAGCCCTCCCACCGGTA 62.001 66.667 6.87 0.00 0.00 4.02
18 19 2.686106 GAGCCCTCCCACCGGTAA 60.686 66.667 6.87 0.00 0.00 2.85
19 20 2.687566 AGCCCTCCCACCGGTAAG 60.688 66.667 6.87 5.19 0.00 2.34
21 22 3.087906 CCCTCCCACCGGTAAGGG 61.088 72.222 26.15 26.15 46.96 3.95
22 23 3.793888 CCTCCCACCGGTAAGGGC 61.794 72.222 22.65 0.00 46.96 5.19
23 24 3.793888 CTCCCACCGGTAAGGGCC 61.794 72.222 22.65 0.00 46.96 5.80
32 33 4.484872 GTAAGGGCCGGGCTCCAC 62.485 72.222 28.80 17.98 0.00 4.02
33 34 4.733725 TAAGGGCCGGGCTCCACT 62.734 66.667 28.80 13.59 0.00 4.00
42 43 3.695606 GGCTCCACTGTGCCTCGA 61.696 66.667 1.29 0.00 45.62 4.04
43 44 2.581354 GCTCCACTGTGCCTCGAT 59.419 61.111 1.29 0.00 0.00 3.59
44 45 1.812922 GCTCCACTGTGCCTCGATG 60.813 63.158 1.29 0.00 0.00 3.84
45 46 1.153489 CTCCACTGTGCCTCGATGG 60.153 63.158 1.29 0.00 39.35 3.51
46 47 1.892819 CTCCACTGTGCCTCGATGGT 61.893 60.000 1.29 0.00 38.35 3.55
47 48 1.448540 CCACTGTGCCTCGATGGTC 60.449 63.158 1.29 0.00 38.35 4.02
48 49 1.448540 CACTGTGCCTCGATGGTCC 60.449 63.158 0.00 0.00 38.35 4.46
49 50 2.187946 CTGTGCCTCGATGGTCCC 59.812 66.667 0.00 0.00 38.35 4.46
50 51 2.606213 TGTGCCTCGATGGTCCCA 60.606 61.111 0.00 0.00 38.35 4.37
51 52 1.976132 CTGTGCCTCGATGGTCCCAT 61.976 60.000 0.00 0.00 39.69 4.00
52 53 1.524621 GTGCCTCGATGGTCCCATG 60.525 63.158 2.93 0.00 36.70 3.66
53 54 1.995066 TGCCTCGATGGTCCCATGT 60.995 57.895 2.93 0.00 36.70 3.21
54 55 1.227674 GCCTCGATGGTCCCATGTC 60.228 63.158 2.93 0.00 36.70 3.06
55 56 1.447643 CCTCGATGGTCCCATGTCC 59.552 63.158 2.93 0.00 36.70 4.02
56 57 1.337384 CCTCGATGGTCCCATGTCCA 61.337 60.000 2.93 4.43 36.70 4.02
57 58 0.179073 CTCGATGGTCCCATGTCCAC 60.179 60.000 2.93 0.00 36.70 4.02
58 59 0.907230 TCGATGGTCCCATGTCCACA 60.907 55.000 2.93 0.00 36.70 4.17
59 60 0.181114 CGATGGTCCCATGTCCACAT 59.819 55.000 2.93 0.00 36.70 3.21
69 70 0.835941 ATGTCCACATGAGAGGAGGC 59.164 55.000 0.00 0.00 35.05 4.70
70 71 0.545071 TGTCCACATGAGAGGAGGCA 60.545 55.000 0.00 0.00 35.05 4.75
71 72 0.835941 GTCCACATGAGAGGAGGCAT 59.164 55.000 0.00 0.00 35.05 4.40
72 73 2.042464 GTCCACATGAGAGGAGGCATA 58.958 52.381 0.00 0.00 35.05 3.14
73 74 2.636893 GTCCACATGAGAGGAGGCATAT 59.363 50.000 0.00 0.00 35.05 1.78
74 75 2.636403 TCCACATGAGAGGAGGCATATG 59.364 50.000 0.00 0.00 30.52 1.78
75 76 2.636403 CCACATGAGAGGAGGCATATGA 59.364 50.000 6.97 0.00 0.00 2.15
76 77 3.072038 CCACATGAGAGGAGGCATATGAA 59.928 47.826 6.97 0.00 0.00 2.57
77 78 4.263374 CCACATGAGAGGAGGCATATGAAT 60.263 45.833 6.97 0.00 0.00 2.57
78 79 4.695928 CACATGAGAGGAGGCATATGAATG 59.304 45.833 6.97 0.00 36.09 2.67
79 80 4.262617 CATGAGAGGAGGCATATGAATGG 58.737 47.826 6.97 0.00 33.38 3.16
85 86 4.950744 GCATATGAATGGCGGCAC 57.049 55.556 16.34 2.51 33.38 5.01
86 87 1.286880 GCATATGAATGGCGGCACC 59.713 57.895 16.34 10.26 39.84 5.01
87 88 1.575922 CATATGAATGGCGGCACCG 59.424 57.895 16.34 4.30 43.94 4.94
104 105 2.589159 GCGAGAGGCGGGGAAATC 60.589 66.667 0.00 0.00 41.29 2.17
105 106 2.109181 CGAGAGGCGGGGAAATCC 59.891 66.667 0.00 0.00 36.03 3.01
106 107 2.435693 CGAGAGGCGGGGAAATCCT 61.436 63.158 0.00 0.00 36.03 3.24
107 108 1.113517 CGAGAGGCGGGGAAATCCTA 61.114 60.000 0.00 0.00 36.03 2.94
108 109 1.129058 GAGAGGCGGGGAAATCCTAA 58.871 55.000 0.00 0.00 35.95 2.69
109 110 1.489230 GAGAGGCGGGGAAATCCTAAA 59.511 52.381 0.00 0.00 35.95 1.85
110 111 1.212195 AGAGGCGGGGAAATCCTAAAC 59.788 52.381 0.00 0.00 35.95 2.01
111 112 0.996583 AGGCGGGGAAATCCTAAACA 59.003 50.000 0.00 0.00 35.95 2.83
112 113 1.100510 GGCGGGGAAATCCTAAACAC 58.899 55.000 0.00 0.00 35.95 3.32
113 114 1.614850 GGCGGGGAAATCCTAAACACA 60.615 52.381 0.00 0.00 35.95 3.72
114 115 2.375146 GCGGGGAAATCCTAAACACAT 58.625 47.619 0.00 0.00 35.95 3.21
115 116 2.099098 GCGGGGAAATCCTAAACACATG 59.901 50.000 0.00 0.00 35.95 3.21
116 117 2.687935 CGGGGAAATCCTAAACACATGG 59.312 50.000 0.00 0.00 35.95 3.66
117 118 3.031013 GGGGAAATCCTAAACACATGGG 58.969 50.000 0.00 0.00 35.95 4.00
118 119 3.309556 GGGGAAATCCTAAACACATGGGA 60.310 47.826 0.00 0.00 35.95 4.37
119 120 3.954258 GGGAAATCCTAAACACATGGGAG 59.046 47.826 0.00 0.00 35.95 4.30
120 121 3.381590 GGAAATCCTAAACACATGGGAGC 59.618 47.826 0.00 0.00 0.00 4.70
121 122 4.273318 GAAATCCTAAACACATGGGAGCT 58.727 43.478 0.00 0.00 0.00 4.09
122 123 4.322057 AATCCTAAACACATGGGAGCTT 57.678 40.909 0.00 0.00 0.00 3.74
123 124 3.806949 TCCTAAACACATGGGAGCTTT 57.193 42.857 0.00 0.00 0.00 3.51
124 125 4.112634 TCCTAAACACATGGGAGCTTTT 57.887 40.909 0.00 0.00 0.00 2.27
125 126 4.479158 TCCTAAACACATGGGAGCTTTTT 58.521 39.130 0.00 0.00 0.00 1.94
161 162 4.823790 AAAAACACCAATAGACGTGTCC 57.176 40.909 0.00 0.00 42.28 4.02
162 163 2.467566 AACACCAATAGACGTGTCCC 57.532 50.000 0.00 0.00 42.28 4.46
163 164 1.640917 ACACCAATAGACGTGTCCCT 58.359 50.000 0.00 0.00 38.90 4.20
164 165 1.275291 ACACCAATAGACGTGTCCCTG 59.725 52.381 0.00 0.00 38.90 4.45
165 166 1.548719 CACCAATAGACGTGTCCCTGA 59.451 52.381 0.00 0.00 0.00 3.86
166 167 1.549170 ACCAATAGACGTGTCCCTGAC 59.451 52.381 0.00 0.00 0.00 3.51
167 168 1.825474 CCAATAGACGTGTCCCTGACT 59.175 52.381 0.00 0.00 33.15 3.41
168 169 3.021695 CCAATAGACGTGTCCCTGACTA 58.978 50.000 0.00 0.00 33.15 2.59
169 170 3.637229 CCAATAGACGTGTCCCTGACTAT 59.363 47.826 0.00 0.00 33.15 2.12
170 171 4.825634 CCAATAGACGTGTCCCTGACTATA 59.174 45.833 0.00 0.00 33.15 1.31
171 172 5.301045 CCAATAGACGTGTCCCTGACTATAA 59.699 44.000 0.00 0.00 33.15 0.98
172 173 6.015350 CCAATAGACGTGTCCCTGACTATAAT 60.015 42.308 0.00 0.00 33.15 1.28
173 174 4.920640 AGACGTGTCCCTGACTATAATG 57.079 45.455 0.00 0.00 33.15 1.90
174 175 3.637229 AGACGTGTCCCTGACTATAATGG 59.363 47.826 0.00 0.00 33.15 3.16
175 176 3.371965 ACGTGTCCCTGACTATAATGGT 58.628 45.455 0.00 0.00 33.15 3.55
176 177 3.773119 ACGTGTCCCTGACTATAATGGTT 59.227 43.478 0.00 0.00 33.15 3.67
177 178 4.224370 ACGTGTCCCTGACTATAATGGTTT 59.776 41.667 0.00 0.00 33.15 3.27
178 179 4.809426 CGTGTCCCTGACTATAATGGTTTC 59.191 45.833 0.00 0.00 33.15 2.78
179 180 4.809426 GTGTCCCTGACTATAATGGTTTCG 59.191 45.833 0.00 0.00 33.15 3.46
180 181 4.712829 TGTCCCTGACTATAATGGTTTCGA 59.287 41.667 0.00 0.00 33.15 3.71
181 182 5.188163 TGTCCCTGACTATAATGGTTTCGAA 59.812 40.000 0.00 0.00 33.15 3.71
182 183 6.110707 GTCCCTGACTATAATGGTTTCGAAA 58.889 40.000 6.47 6.47 0.00 3.46
183 184 6.596497 GTCCCTGACTATAATGGTTTCGAAAA 59.404 38.462 13.10 0.00 0.00 2.29
184 185 7.282450 GTCCCTGACTATAATGGTTTCGAAAAT 59.718 37.037 13.10 4.71 0.00 1.82
185 186 7.497909 TCCCTGACTATAATGGTTTCGAAAATC 59.502 37.037 13.10 8.73 0.00 2.17
186 187 7.499232 CCCTGACTATAATGGTTTCGAAAATCT 59.501 37.037 13.10 0.38 0.00 2.40
187 188 8.893727 CCTGACTATAATGGTTTCGAAAATCTT 58.106 33.333 13.10 8.50 0.00 2.40
199 200 7.958025 GGTTTCGAAAATCTTATGTTCTCACTC 59.042 37.037 13.10 0.00 0.00 3.51
207 208 8.970859 AATCTTATGTTCTCACTCTATTTGGG 57.029 34.615 0.00 0.00 0.00 4.12
213 214 5.763204 TGTTCTCACTCTATTTGGGTTGTTC 59.237 40.000 0.00 0.00 0.00 3.18
229 230 5.877564 GGGTTGTTCAACCAATCTTTCAAAA 59.122 36.000 28.31 0.00 44.60 2.44
252 253 5.265350 CCCTCAAGGTTAGTCTAGCTTAC 57.735 47.826 0.00 0.00 34.32 2.34
286 289 4.274705 TCTTGCAAATTCTACACGCAAAGA 59.725 37.500 0.00 0.00 41.63 2.52
288 291 3.313803 TGCAAATTCTACACGCAAAGACA 59.686 39.130 0.00 0.00 0.00 3.41
291 294 5.270083 CAAATTCTACACGCAAAGACACAA 58.730 37.500 0.00 0.00 0.00 3.33
292 295 5.689383 AATTCTACACGCAAAGACACAAT 57.311 34.783 0.00 0.00 0.00 2.71
294 297 3.990092 TCTACACGCAAAGACACAATCT 58.010 40.909 0.00 0.00 40.46 2.40
326 330 8.409371 TGTATAGACATCAGATCACTTGACTTC 58.591 37.037 0.00 0.00 0.00 3.01
336 340 7.987458 TCAGATCACTTGACTTCTTTTTAGTGT 59.013 33.333 0.00 0.00 35.64 3.55
374 379 9.675464 TTTTAATTAATAGGGCCATATAGTCCG 57.325 33.333 10.95 0.00 0.00 4.79
378 383 2.320681 AGGGCCATATAGTCCGCTTA 57.679 50.000 6.18 0.00 0.00 3.09
382 393 4.139038 GGGCCATATAGTCCGCTTAAAAA 58.861 43.478 4.39 0.00 0.00 1.94
418 429 4.818534 CTTGCAAAGTACTGAAAGCTGA 57.181 40.909 0.00 0.00 39.70 4.26
419 430 5.173774 CTTGCAAAGTACTGAAAGCTGAA 57.826 39.130 0.00 0.00 39.70 3.02
420 431 5.574891 TTGCAAAGTACTGAAAGCTGAAA 57.425 34.783 0.00 0.00 37.60 2.69
421 432 5.173774 TGCAAAGTACTGAAAGCTGAAAG 57.826 39.130 0.00 0.00 37.60 2.62
426 437 5.757850 AGTACTGAAAGCTGAAAGTTTGG 57.242 39.130 0.00 0.00 35.87 3.28
428 439 6.064717 AGTACTGAAAGCTGAAAGTTTGGAT 58.935 36.000 0.00 0.00 35.87 3.41
440 451 5.656416 TGAAAGTTTGGATTTGTTGGACTCT 59.344 36.000 0.00 0.00 0.00 3.24
448 459 5.705441 TGGATTTGTTGGACTCTGTATGAAC 59.295 40.000 0.00 0.00 0.00 3.18
457 468 4.262894 GGACTCTGTATGAACCCAGAACAA 60.263 45.833 0.00 0.00 37.27 2.83
458 469 4.642429 ACTCTGTATGAACCCAGAACAAC 58.358 43.478 0.00 0.00 37.27 3.32
460 471 5.042463 TCTGTATGAACCCAGAACAACAA 57.958 39.130 0.00 0.00 34.88 2.83
461 472 5.441500 TCTGTATGAACCCAGAACAACAAA 58.558 37.500 0.00 0.00 34.88 2.83
462 473 5.298276 TCTGTATGAACCCAGAACAACAAAC 59.702 40.000 0.00 0.00 34.88 2.93
463 474 5.197451 TGTATGAACCCAGAACAACAAACT 58.803 37.500 0.00 0.00 0.00 2.66
466 477 6.976934 ATGAACCCAGAACAACAAACTTAT 57.023 33.333 0.00 0.00 0.00 1.73
467 478 9.005777 GTATGAACCCAGAACAACAAACTTATA 57.994 33.333 0.00 0.00 0.00 0.98
468 479 7.266922 TGAACCCAGAACAACAAACTTATAC 57.733 36.000 0.00 0.00 0.00 1.47
469 480 7.057894 TGAACCCAGAACAACAAACTTATACT 58.942 34.615 0.00 0.00 0.00 2.12
470 481 7.227910 TGAACCCAGAACAACAAACTTATACTC 59.772 37.037 0.00 0.00 0.00 2.59
471 482 6.002082 ACCCAGAACAACAAACTTATACTCC 58.998 40.000 0.00 0.00 0.00 3.85
474 485 7.827236 CCCAGAACAACAAACTTATACTCCATA 59.173 37.037 0.00 0.00 0.00 2.74
475 486 9.226606 CCAGAACAACAAACTTATACTCCATAA 57.773 33.333 0.00 0.00 0.00 1.90
477 488 9.787435 AGAACAACAAACTTATACTCCATAACA 57.213 29.630 0.00 0.00 0.00 2.41
479 490 9.569122 AACAACAAACTTATACTCCATAACAGT 57.431 29.630 0.00 0.00 0.00 3.55
480 491 8.999431 ACAACAAACTTATACTCCATAACAGTG 58.001 33.333 0.00 0.00 0.00 3.66
482 493 8.547967 ACAAACTTATACTCCATAACAGTGTG 57.452 34.615 0.00 0.00 0.00 3.82
483 494 8.154856 ACAAACTTATACTCCATAACAGTGTGT 58.845 33.333 0.00 0.00 28.14 3.72
484 495 8.443160 CAAACTTATACTCCATAACAGTGTGTG 58.557 37.037 0.00 0.00 0.00 3.82
486 497 8.079211 ACTTATACTCCATAACAGTGTGTGAT 57.921 34.615 0.00 0.00 0.00 3.06
487 498 8.540388 ACTTATACTCCATAACAGTGTGTGATT 58.460 33.333 0.00 0.00 0.00 2.57
498 515 2.026822 AGTGTGTGATTGATGGAGGGTC 60.027 50.000 0.00 0.00 0.00 4.46
499 516 1.066215 TGTGTGATTGATGGAGGGTCG 60.066 52.381 0.00 0.00 0.00 4.79
500 517 0.541392 TGTGATTGATGGAGGGTCGG 59.459 55.000 0.00 0.00 0.00 4.79
502 519 0.830648 TGATTGATGGAGGGTCGGTC 59.169 55.000 0.00 0.00 0.00 4.79
504 521 1.486726 GATTGATGGAGGGTCGGTCTT 59.513 52.381 0.00 0.00 0.00 3.01
517 605 3.120786 GGTCGGTCTTCAATGTAAACACG 60.121 47.826 0.00 0.00 0.00 4.49
532 620 4.320608 AAACACGCCAATTTTGTGAGAT 57.679 36.364 8.11 0.00 37.08 2.75
537 625 5.006552 ACACGCCAATTTTGTGAGATTTTTG 59.993 36.000 8.11 0.00 37.08 2.44
540 628 4.456914 CCAATTTTGTGAGATTTTTGCGC 58.543 39.130 0.00 0.00 0.00 6.09
548 636 2.053627 GAGATTTTTGCGCACCTTGTG 58.946 47.619 11.12 0.00 36.51 3.33
549 637 1.408702 AGATTTTTGCGCACCTTGTGT 59.591 42.857 11.12 0.00 35.75 3.72
593 681 2.435938 CGGCTGCACCCACGTATT 60.436 61.111 0.50 0.00 33.26 1.89
617 709 5.850557 TCAAAGGAGAAAATCAACTGCAA 57.149 34.783 0.00 0.00 0.00 4.08
618 710 6.219417 TCAAAGGAGAAAATCAACTGCAAA 57.781 33.333 0.00 0.00 0.00 3.68
619 711 6.819284 TCAAAGGAGAAAATCAACTGCAAAT 58.181 32.000 0.00 0.00 0.00 2.32
621 713 7.769970 TCAAAGGAGAAAATCAACTGCAAATTT 59.230 29.630 0.00 0.00 0.00 1.82
622 714 7.486802 AAGGAGAAAATCAACTGCAAATTTG 57.513 32.000 14.03 14.03 0.00 2.32
657 749 4.346734 CACTGTATGCACTGAATCCAAC 57.653 45.455 0.00 0.00 0.00 3.77
676 768 4.025563 CCAACTCAAACGTGTATGAACGAA 60.026 41.667 8.75 0.00 46.49 3.85
677 769 4.966850 ACTCAAACGTGTATGAACGAAG 57.033 40.909 8.75 3.98 46.49 3.79
683 775 5.721876 AACGTGTATGAACGAAGTGAAAA 57.278 34.783 8.75 0.00 45.00 2.29
727 819 0.794229 CAAATGCCGCGTCACATCAC 60.794 55.000 4.92 0.00 0.00 3.06
760 852 0.717224 CGTTTTCACGTATCACCCGG 59.283 55.000 0.00 0.00 41.84 5.73
763 855 2.524951 TTTCACGTATCACCCGGCCC 62.525 60.000 0.00 0.00 0.00 5.80
1005 1100 4.248842 CCCACACACCTCACGCCA 62.249 66.667 0.00 0.00 0.00 5.69
1006 1101 2.666190 CCACACACCTCACGCCAG 60.666 66.667 0.00 0.00 0.00 4.85
1007 1102 3.349006 CACACACCTCACGCCAGC 61.349 66.667 0.00 0.00 0.00 4.85
1020 1122 1.023513 CGCCAGCCCAAGAAGAAGAG 61.024 60.000 0.00 0.00 0.00 2.85
1021 1123 0.326264 GCCAGCCCAAGAAGAAGAGA 59.674 55.000 0.00 0.00 0.00 3.10
1022 1124 1.948144 GCCAGCCCAAGAAGAAGAGAC 60.948 57.143 0.00 0.00 0.00 3.36
1023 1125 1.674221 CCAGCCCAAGAAGAAGAGACG 60.674 57.143 0.00 0.00 0.00 4.18
1024 1126 0.036858 AGCCCAAGAAGAAGAGACGC 60.037 55.000 0.00 0.00 0.00 5.19
1025 1127 1.021920 GCCCAAGAAGAAGAGACGCC 61.022 60.000 0.00 0.00 0.00 5.68
1026 1128 0.737715 CCCAAGAAGAAGAGACGCCG 60.738 60.000 0.00 0.00 0.00 6.46
1027 1129 1.355066 CCAAGAAGAAGAGACGCCGC 61.355 60.000 0.00 0.00 0.00 6.53
1028 1130 0.389166 CAAGAAGAAGAGACGCCGCT 60.389 55.000 0.00 0.00 0.00 5.52
1029 1131 1.135373 CAAGAAGAAGAGACGCCGCTA 60.135 52.381 0.00 0.00 0.00 4.26
1409 1511 0.101399 CCGTCAAGAGGACCTGATCG 59.899 60.000 0.00 0.00 43.95 3.69
1410 1512 0.526524 CGTCAAGAGGACCTGATCGC 60.527 60.000 0.00 0.00 43.95 4.58
1416 1518 4.593864 GGACCTGATCGCCTCGCC 62.594 72.222 0.00 0.00 0.00 5.54
1431 1533 2.514824 GCCGGATTCTCAGGGCAC 60.515 66.667 5.05 0.00 44.91 5.01
1452 1554 0.102481 TCGCCTCGCTTTGTATCTCC 59.898 55.000 0.00 0.00 0.00 3.71
1465 1567 8.616076 CGCTTTGTATCTCCATAAATCTCTTTT 58.384 33.333 0.00 0.00 0.00 2.27
1623 1726 2.632537 TCTGAAGCTACTTCCCCCTTT 58.367 47.619 4.96 0.00 39.51 3.11
1635 1738 6.222227 ACTTCCCCCTTTCCAAATTACTTA 57.778 37.500 0.00 0.00 0.00 2.24
1643 1746 4.413495 TTCCAAATTACTTACAGCGTGC 57.587 40.909 0.00 0.00 0.00 5.34
1644 1747 3.670625 TCCAAATTACTTACAGCGTGCT 58.329 40.909 0.00 0.00 0.00 4.40
1645 1748 3.682858 TCCAAATTACTTACAGCGTGCTC 59.317 43.478 0.00 0.00 0.00 4.26
1673 1776 1.640670 TGAGGGAAAGGGAATGGAAGG 59.359 52.381 0.00 0.00 0.00 3.46
1697 1803 6.778559 GGTTACAAGAGGGAGTATGTCTAGAT 59.221 42.308 0.00 0.00 0.00 1.98
1753 1859 5.183713 TCAATCTCCATTTTGATGTGTGGTC 59.816 40.000 0.00 0.00 33.47 4.02
1769 1878 2.104967 TGGTCGGAATTATCGGTGAGT 58.895 47.619 1.63 0.00 0.00 3.41
1780 1914 8.122952 GGAATTATCGGTGAGTTGAATTAACAG 58.877 37.037 0.00 0.00 41.88 3.16
1787 1921 3.181423 TGAGTTGAATTAACAGGGGGCTT 60.181 43.478 0.00 0.00 41.88 4.35
1798 1932 1.616628 GGGGGCTTGGGAAGAGAGA 60.617 63.158 0.00 0.00 0.00 3.10
1800 1934 1.604915 GGGCTTGGGAAGAGAGACC 59.395 63.158 0.00 0.00 0.00 3.85
1801 1935 1.201429 GGGCTTGGGAAGAGAGACCA 61.201 60.000 0.00 0.00 38.52 4.02
1802 1936 0.915364 GGCTTGGGAAGAGAGACCAT 59.085 55.000 0.00 0.00 33.63 3.55
1818 1952 6.310149 AGAGACCATGAAATTGACCTCTTTT 58.690 36.000 0.00 0.00 0.00 2.27
1822 1956 9.093458 AGACCATGAAATTGACCTCTTTTATTT 57.907 29.630 0.00 0.00 0.00 1.40
1844 1978 2.849318 CCTTTCCCCTTCTCTCCTCAAT 59.151 50.000 0.00 0.00 0.00 2.57
1851 1985 3.371380 CCCTTCTCTCCTCAATTCCCTTG 60.371 52.174 0.00 0.00 36.09 3.61
1869 2003 0.407528 TGCCCCTAGCCAAACAATGA 59.592 50.000 0.00 0.00 42.71 2.57
1874 2008 4.344968 GCCCCTAGCCAAACAATGAATAAT 59.655 41.667 0.00 0.00 34.35 1.28
1876 2010 6.211384 GCCCCTAGCCAAACAATGAATAATAT 59.789 38.462 0.00 0.00 34.35 1.28
1903 2038 7.119407 GTCTTGTATCCTTAAACTCTTGTTCCC 59.881 40.741 0.00 0.00 34.96 3.97
1908 2043 6.945636 TCCTTAAACTCTTGTTCCCTATCA 57.054 37.500 0.00 0.00 34.96 2.15
1915 2050 6.824305 ACTCTTGTTCCCTATCACAAATTG 57.176 37.500 0.00 0.00 32.53 2.32
1930 2065 3.136260 ACAAATTGCCTCCAACCAAACAT 59.864 39.130 0.00 0.00 32.95 2.71
1931 2066 3.405823 AATTGCCTCCAACCAAACATG 57.594 42.857 0.00 0.00 32.95 3.21
1932 2067 0.392336 TTGCCTCCAACCAAACATGC 59.608 50.000 0.00 0.00 0.00 4.06
1967 2102 6.712276 AGGTTGATCCTAAATCGAACTTCTT 58.288 36.000 0.00 0.00 46.10 2.52
1983 2119 9.458374 TCGAACTTCTTTAAATTTGACCAAATC 57.542 29.630 8.26 0.00 39.88 2.17
2068 2209 5.840940 ACTTTTATTCATATACGCGCTCC 57.159 39.130 5.73 0.00 0.00 4.70
2084 2225 1.405121 GCTCCGTCCCGAATTACTTGT 60.405 52.381 0.00 0.00 0.00 3.16
2088 2229 0.643820 GTCCCGAATTACTTGTCGCG 59.356 55.000 0.00 0.00 35.93 5.87
2089 2230 0.458889 TCCCGAATTACTTGTCGCGG 60.459 55.000 6.13 0.00 35.93 6.46
2099 2240 3.194005 ACTTGTCGCGGAAATGGATAT 57.806 42.857 6.13 0.00 0.00 1.63
2109 2250 8.234546 GTCGCGGAAATGGATATAAATTAATGT 58.765 33.333 6.13 0.00 0.00 2.71
2165 2306 7.898725 CACTTCTGTGACAAGTAATTCAAAC 57.101 36.000 0.00 0.00 46.55 2.93
2166 2307 6.628856 CACTTCTGTGACAAGTAATTCAAACG 59.371 38.462 0.00 0.00 46.55 3.60
2167 2308 6.537301 ACTTCTGTGACAAGTAATTCAAACGA 59.463 34.615 0.00 0.00 32.08 3.85
2170 2311 7.753659 TCTGTGACAAGTAATTCAAACGAAAA 58.246 30.769 0.00 0.00 0.00 2.29
2171 2312 8.237949 TCTGTGACAAGTAATTCAAACGAAAAA 58.762 29.630 0.00 0.00 0.00 1.94
2258 2406 7.636326 ACTTAGACAAAACCATAACTTCAACG 58.364 34.615 0.00 0.00 0.00 4.10
2343 2494 7.605410 ATTGAATCCAATGTTTGATTCTTGC 57.395 32.000 16.00 0.00 41.18 4.01
2377 2529 0.729116 GTCTGTTGCCATCCGATGTG 59.271 55.000 7.60 0.77 0.00 3.21
2390 2542 2.841266 TCCGATGTGGGAGGATAAACAA 59.159 45.455 0.00 0.00 38.76 2.83
2391 2543 3.458118 TCCGATGTGGGAGGATAAACAAT 59.542 43.478 0.00 0.00 38.76 2.71
2439 2591 3.499737 GCCGACTGCCGTTCATGG 61.500 66.667 0.00 0.00 36.31 3.66
2440 2592 2.264480 CCGACTGCCGTTCATGGA 59.736 61.111 0.00 0.00 36.31 3.41
2441 2593 2.100631 CCGACTGCCGTTCATGGAC 61.101 63.158 0.00 0.00 36.31 4.02
2442 2594 1.374125 CGACTGCCGTTCATGGACA 60.374 57.895 4.68 0.00 0.00 4.02
2443 2595 0.948623 CGACTGCCGTTCATGGACAA 60.949 55.000 4.68 0.00 0.00 3.18
2444 2596 1.234821 GACTGCCGTTCATGGACAAA 58.765 50.000 4.68 0.00 0.00 2.83
2445 2597 1.606668 GACTGCCGTTCATGGACAAAA 59.393 47.619 4.68 0.00 0.00 2.44
2446 2598 1.608590 ACTGCCGTTCATGGACAAAAG 59.391 47.619 4.68 0.30 0.00 2.27
2447 2599 1.608590 CTGCCGTTCATGGACAAAAGT 59.391 47.619 4.68 0.00 0.00 2.66
2448 2600 1.336440 TGCCGTTCATGGACAAAAGTG 59.664 47.619 4.68 0.00 0.00 3.16
2449 2601 1.335872 GCCGTTCATGGACAAAAGTGG 60.336 52.381 4.68 0.00 0.00 4.00
2450 2602 1.269448 CCGTTCATGGACAAAAGTGGG 59.731 52.381 4.68 0.00 0.00 4.61
2451 2603 1.335872 CGTTCATGGACAAAAGTGGGC 60.336 52.381 4.68 0.00 0.00 5.36
2452 2604 0.958091 TTCATGGACAAAAGTGGGCG 59.042 50.000 0.00 0.00 0.00 6.13
2453 2605 1.080569 CATGGACAAAAGTGGGCGC 60.081 57.895 0.00 0.00 0.00 6.53
2454 2606 2.275380 ATGGACAAAAGTGGGCGCC 61.275 57.895 21.18 21.18 0.00 6.53
2455 2607 4.038080 GGACAAAAGTGGGCGCCG 62.038 66.667 22.54 7.07 0.00 6.46
2456 2608 4.700365 GACAAAAGTGGGCGCCGC 62.700 66.667 22.54 16.19 0.00 6.53
2458 2610 3.053291 CAAAAGTGGGCGCCGCTA 61.053 61.111 22.54 6.44 44.35 4.26
2459 2611 3.053896 AAAAGTGGGCGCCGCTAC 61.054 61.111 22.54 18.97 44.35 3.58
2466 2618 4.547367 GGCGCCGCTACCTCCAAT 62.547 66.667 12.58 0.00 0.00 3.16
2467 2619 2.513897 GCGCCGCTACCTCCAATT 60.514 61.111 0.00 0.00 0.00 2.32
2468 2620 1.227438 GCGCCGCTACCTCCAATTA 60.227 57.895 0.00 0.00 0.00 1.40
2469 2621 0.602905 GCGCCGCTACCTCCAATTAT 60.603 55.000 0.00 0.00 0.00 1.28
2470 2622 1.429463 CGCCGCTACCTCCAATTATC 58.571 55.000 0.00 0.00 0.00 1.75
2471 2623 1.270094 CGCCGCTACCTCCAATTATCA 60.270 52.381 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.549433 TTACCGGTGGGAGGGCTCA 62.549 63.158 19.93 0.00 36.97 4.26
1 2 2.686106 TTACCGGTGGGAGGGCTC 60.686 66.667 19.93 0.00 36.97 4.70
2 3 2.687566 CTTACCGGTGGGAGGGCT 60.688 66.667 19.93 0.00 36.97 5.19
3 4 3.793888 CCTTACCGGTGGGAGGGC 61.794 72.222 19.93 0.00 36.97 5.19
4 5 3.087906 CCCTTACCGGTGGGAGGG 61.088 72.222 27.77 27.77 46.15 4.30
5 6 3.793888 GCCCTTACCGGTGGGAGG 61.794 72.222 29.75 24.77 46.15 4.30
6 7 3.793888 GGCCCTTACCGGTGGGAG 61.794 72.222 29.75 18.27 46.15 4.30
15 16 4.484872 GTGGAGCCCGGCCCTTAC 62.485 72.222 5.55 0.00 0.00 2.34
16 17 4.733725 AGTGGAGCCCGGCCCTTA 62.734 66.667 5.55 0.00 0.00 2.69
26 27 1.812922 CATCGAGGCACAGTGGAGC 60.813 63.158 1.84 0.00 0.00 4.70
27 28 1.153489 CCATCGAGGCACAGTGGAG 60.153 63.158 1.84 0.00 31.59 3.86
28 29 1.888436 GACCATCGAGGCACAGTGGA 61.888 60.000 5.99 0.00 43.14 4.02
29 30 1.448540 GACCATCGAGGCACAGTGG 60.449 63.158 1.84 0.00 43.14 4.00
30 31 1.448540 GGACCATCGAGGCACAGTG 60.449 63.158 0.00 0.00 43.14 3.66
31 32 2.660064 GGGACCATCGAGGCACAGT 61.660 63.158 0.00 0.00 43.14 3.55
32 33 1.976132 ATGGGACCATCGAGGCACAG 61.976 60.000 0.00 0.00 43.14 3.66
33 34 1.995066 ATGGGACCATCGAGGCACA 60.995 57.895 0.00 0.00 43.14 4.57
34 35 1.524621 CATGGGACCATCGAGGCAC 60.525 63.158 0.00 0.00 43.14 5.01
35 36 1.971505 GACATGGGACCATCGAGGCA 61.972 60.000 0.00 0.00 43.14 4.75
36 37 1.227674 GACATGGGACCATCGAGGC 60.228 63.158 0.00 0.00 43.14 4.70
37 38 1.337384 TGGACATGGGACCATCGAGG 61.337 60.000 0.00 0.00 45.67 4.63
38 39 0.179073 GTGGACATGGGACCATCGAG 60.179 60.000 0.00 0.00 40.86 4.04
39 40 0.907230 TGTGGACATGGGACCATCGA 60.907 55.000 0.00 0.00 40.86 3.59
40 41 0.181114 ATGTGGACATGGGACCATCG 59.819 55.000 0.00 0.53 40.86 3.84
50 51 0.835941 GCCTCCTCTCATGTGGACAT 59.164 55.000 0.00 0.00 36.96 3.06
51 52 0.545071 TGCCTCCTCTCATGTGGACA 60.545 55.000 0.00 0.00 32.96 4.02
52 53 0.835941 ATGCCTCCTCTCATGTGGAC 59.164 55.000 0.00 0.00 32.96 4.02
53 54 2.477104 TATGCCTCCTCTCATGTGGA 57.523 50.000 0.00 0.00 34.96 4.02
54 55 2.636403 TCATATGCCTCCTCTCATGTGG 59.364 50.000 0.00 0.00 34.11 4.17
55 56 4.347360 TTCATATGCCTCCTCTCATGTG 57.653 45.455 0.00 0.00 34.46 3.21
56 57 4.263374 CCATTCATATGCCTCCTCTCATGT 60.263 45.833 0.00 0.00 0.00 3.21
57 58 4.262617 CCATTCATATGCCTCCTCTCATG 58.737 47.826 0.00 0.00 0.00 3.07
58 59 3.308259 GCCATTCATATGCCTCCTCTCAT 60.308 47.826 0.00 0.00 0.00 2.90
59 60 2.039480 GCCATTCATATGCCTCCTCTCA 59.961 50.000 0.00 0.00 0.00 3.27
60 61 2.709213 GCCATTCATATGCCTCCTCTC 58.291 52.381 0.00 0.00 0.00 3.20
61 62 1.002888 CGCCATTCATATGCCTCCTCT 59.997 52.381 0.00 0.00 0.00 3.69
62 63 1.446907 CGCCATTCATATGCCTCCTC 58.553 55.000 0.00 0.00 0.00 3.71
63 64 0.037303 CCGCCATTCATATGCCTCCT 59.963 55.000 0.00 0.00 0.00 3.69
64 65 1.589716 GCCGCCATTCATATGCCTCC 61.590 60.000 0.00 0.00 0.00 4.30
65 66 0.890542 TGCCGCCATTCATATGCCTC 60.891 55.000 0.00 0.00 0.00 4.70
66 67 1.151221 TGCCGCCATTCATATGCCT 59.849 52.632 0.00 0.00 0.00 4.75
67 68 1.286880 GTGCCGCCATTCATATGCC 59.713 57.895 0.00 0.00 0.00 4.40
68 69 1.286880 GGTGCCGCCATTCATATGC 59.713 57.895 0.00 0.00 37.17 3.14
69 70 1.575922 CGGTGCCGCCATTCATATG 59.424 57.895 0.00 0.00 36.97 1.78
70 71 4.063529 CGGTGCCGCCATTCATAT 57.936 55.556 0.00 0.00 36.97 1.78
87 88 2.589159 GATTTCCCCGCCTCTCGC 60.589 66.667 0.00 0.00 36.73 5.03
88 89 1.113517 TAGGATTTCCCCGCCTCTCG 61.114 60.000 0.00 0.00 36.42 4.04
89 90 1.129058 TTAGGATTTCCCCGCCTCTC 58.871 55.000 0.00 0.00 36.42 3.20
90 91 1.212195 GTTTAGGATTTCCCCGCCTCT 59.788 52.381 0.00 0.00 36.42 3.69
91 92 1.064979 TGTTTAGGATTTCCCCGCCTC 60.065 52.381 0.00 0.00 36.42 4.70
92 93 0.996583 TGTTTAGGATTTCCCCGCCT 59.003 50.000 0.00 0.00 36.42 5.52
93 94 1.100510 GTGTTTAGGATTTCCCCGCC 58.899 55.000 0.00 0.00 36.42 6.13
94 95 1.828979 TGTGTTTAGGATTTCCCCGC 58.171 50.000 0.00 0.00 36.42 6.13
95 96 2.687935 CCATGTGTTTAGGATTTCCCCG 59.312 50.000 0.00 0.00 36.42 5.73
96 97 3.031013 CCCATGTGTTTAGGATTTCCCC 58.969 50.000 0.00 0.00 36.42 4.81
97 98 3.954258 CTCCCATGTGTTTAGGATTTCCC 59.046 47.826 0.00 0.00 36.42 3.97
98 99 3.381590 GCTCCCATGTGTTTAGGATTTCC 59.618 47.826 0.00 0.00 0.00 3.13
99 100 4.273318 AGCTCCCATGTGTTTAGGATTTC 58.727 43.478 0.00 0.00 0.00 2.17
100 101 4.322057 AGCTCCCATGTGTTTAGGATTT 57.678 40.909 0.00 0.00 0.00 2.17
101 102 4.322057 AAGCTCCCATGTGTTTAGGATT 57.678 40.909 0.00 0.00 0.00 3.01
102 103 4.322057 AAAGCTCCCATGTGTTTAGGAT 57.678 40.909 0.00 0.00 0.00 3.24
103 104 3.806949 AAAGCTCCCATGTGTTTAGGA 57.193 42.857 0.00 0.00 0.00 2.94
104 105 4.871933 AAAAAGCTCCCATGTGTTTAGG 57.128 40.909 0.00 0.00 0.00 2.69
140 141 3.566742 GGGACACGTCTATTGGTGTTTTT 59.433 43.478 0.00 0.00 46.64 1.94
141 142 3.143728 GGGACACGTCTATTGGTGTTTT 58.856 45.455 0.00 0.00 46.64 2.43
142 143 2.370849 AGGGACACGTCTATTGGTGTTT 59.629 45.455 0.00 0.00 46.64 2.83
143 144 1.975680 AGGGACACGTCTATTGGTGTT 59.024 47.619 0.00 0.00 46.64 3.32
145 146 1.548719 TCAGGGACACGTCTATTGGTG 59.451 52.381 0.00 0.00 39.98 4.17
146 147 1.549170 GTCAGGGACACGTCTATTGGT 59.451 52.381 0.00 0.00 32.09 3.67
147 148 1.825474 AGTCAGGGACACGTCTATTGG 59.175 52.381 0.00 0.00 34.60 3.16
148 149 4.920640 ATAGTCAGGGACACGTCTATTG 57.079 45.455 0.00 0.00 34.60 1.90
149 150 6.015350 CCATTATAGTCAGGGACACGTCTATT 60.015 42.308 0.00 0.00 34.60 1.73
150 151 5.477291 CCATTATAGTCAGGGACACGTCTAT 59.523 44.000 0.00 0.00 34.60 1.98
151 152 4.825634 CCATTATAGTCAGGGACACGTCTA 59.174 45.833 0.00 0.00 34.60 2.59
152 153 3.637229 CCATTATAGTCAGGGACACGTCT 59.363 47.826 0.00 0.00 34.60 4.18
153 154 3.383825 ACCATTATAGTCAGGGACACGTC 59.616 47.826 0.00 0.00 34.60 4.34
154 155 3.371965 ACCATTATAGTCAGGGACACGT 58.628 45.455 0.00 0.00 34.60 4.49
155 156 4.402056 AACCATTATAGTCAGGGACACG 57.598 45.455 0.00 0.00 34.60 4.49
156 157 4.809426 CGAAACCATTATAGTCAGGGACAC 59.191 45.833 0.00 0.00 34.60 3.67
157 158 4.712829 TCGAAACCATTATAGTCAGGGACA 59.287 41.667 0.00 0.00 34.60 4.02
158 159 5.272283 TCGAAACCATTATAGTCAGGGAC 57.728 43.478 0.00 0.00 0.00 4.46
159 160 5.943349 TTCGAAACCATTATAGTCAGGGA 57.057 39.130 0.00 0.00 0.00 4.20
160 161 6.995511 TTTTCGAAACCATTATAGTCAGGG 57.004 37.500 10.79 0.00 0.00 4.45
161 162 8.438676 AGATTTTCGAAACCATTATAGTCAGG 57.561 34.615 10.79 0.00 0.00 3.86
170 171 8.792633 TGAGAACATAAGATTTTCGAAACCATT 58.207 29.630 10.79 7.86 0.00 3.16
171 172 8.237267 GTGAGAACATAAGATTTTCGAAACCAT 58.763 33.333 10.79 2.00 0.00 3.55
172 173 7.444183 AGTGAGAACATAAGATTTTCGAAACCA 59.556 33.333 10.79 0.00 0.00 3.67
173 174 7.807680 AGTGAGAACATAAGATTTTCGAAACC 58.192 34.615 10.79 5.74 0.00 3.27
174 175 8.713271 AGAGTGAGAACATAAGATTTTCGAAAC 58.287 33.333 10.79 0.00 0.00 2.78
175 176 8.833231 AGAGTGAGAACATAAGATTTTCGAAA 57.167 30.769 6.47 6.47 0.00 3.46
181 182 9.401058 CCCAAATAGAGTGAGAACATAAGATTT 57.599 33.333 0.00 0.00 0.00 2.17
182 183 8.552296 ACCCAAATAGAGTGAGAACATAAGATT 58.448 33.333 0.00 0.00 0.00 2.40
183 184 8.095452 ACCCAAATAGAGTGAGAACATAAGAT 57.905 34.615 0.00 0.00 0.00 2.40
184 185 7.496346 ACCCAAATAGAGTGAGAACATAAGA 57.504 36.000 0.00 0.00 0.00 2.10
185 186 7.607991 ACAACCCAAATAGAGTGAGAACATAAG 59.392 37.037 0.00 0.00 0.00 1.73
186 187 7.458397 ACAACCCAAATAGAGTGAGAACATAA 58.542 34.615 0.00 0.00 0.00 1.90
187 188 7.016153 ACAACCCAAATAGAGTGAGAACATA 57.984 36.000 0.00 0.00 0.00 2.29
188 189 5.880901 ACAACCCAAATAGAGTGAGAACAT 58.119 37.500 0.00 0.00 0.00 2.71
189 190 5.304686 ACAACCCAAATAGAGTGAGAACA 57.695 39.130 0.00 0.00 0.00 3.18
190 191 5.763204 TGAACAACCCAAATAGAGTGAGAAC 59.237 40.000 0.00 0.00 0.00 3.01
191 192 5.935945 TGAACAACCCAAATAGAGTGAGAA 58.064 37.500 0.00 0.00 0.00 2.87
192 193 5.560722 TGAACAACCCAAATAGAGTGAGA 57.439 39.130 0.00 0.00 0.00 3.27
193 194 6.002062 GTTGAACAACCCAAATAGAGTGAG 57.998 41.667 6.43 0.00 35.36 3.51
207 208 6.183360 GGGTTTTGAAAGATTGGTTGAACAAC 60.183 38.462 8.91 8.91 40.45 3.32
213 214 5.275067 TGAGGGTTTTGAAAGATTGGTTG 57.725 39.130 0.00 0.00 0.00 3.77
248 249 4.371855 TGCAAGAGACCATCTACGTAAG 57.628 45.455 0.00 0.00 37.23 2.34
251 252 3.678056 TTTGCAAGAGACCATCTACGT 57.322 42.857 0.00 0.00 37.23 3.57
252 253 4.872691 AGAATTTGCAAGAGACCATCTACG 59.127 41.667 0.00 0.00 37.23 3.51
298 301 9.579932 AGTCAAGTGATCTGATGTCTATACATA 57.420 33.333 0.00 0.00 46.49 2.29
301 304 8.629158 AGAAGTCAAGTGATCTGATGTCTATAC 58.371 37.037 0.00 0.00 0.00 1.47
302 305 8.759481 AGAAGTCAAGTGATCTGATGTCTATA 57.241 34.615 0.00 0.00 0.00 1.31
303 306 7.658525 AGAAGTCAAGTGATCTGATGTCTAT 57.341 36.000 0.00 0.00 0.00 1.98
317 321 9.614792 ACATAAGACACTAAAAAGAAGTCAAGT 57.385 29.630 0.00 0.00 0.00 3.16
352 357 5.428783 AGCGGACTATATGGCCCTATTAATT 59.571 40.000 5.81 0.00 42.31 1.40
354 359 4.359105 AGCGGACTATATGGCCCTATTAA 58.641 43.478 5.81 0.00 42.31 1.40
355 360 3.990369 AGCGGACTATATGGCCCTATTA 58.010 45.455 5.81 0.00 42.31 0.98
357 362 2.552093 AGCGGACTATATGGCCCTAT 57.448 50.000 0.00 2.32 42.31 2.57
360 365 3.412237 TTTAAGCGGACTATATGGCCC 57.588 47.619 0.00 0.00 42.31 5.80
398 409 5.125417 ACTTTCAGCTTTCAGTACTTTGCAA 59.875 36.000 0.00 0.00 0.00 4.08
400 411 5.175090 ACTTTCAGCTTTCAGTACTTTGC 57.825 39.130 0.00 0.00 0.00 3.68
410 421 6.238184 CCAACAAATCCAAACTTTCAGCTTTC 60.238 38.462 0.00 0.00 0.00 2.62
415 426 5.906073 AGTCCAACAAATCCAAACTTTCAG 58.094 37.500 0.00 0.00 0.00 3.02
416 427 5.656416 AGAGTCCAACAAATCCAAACTTTCA 59.344 36.000 0.00 0.00 0.00 2.69
417 428 5.979517 CAGAGTCCAACAAATCCAAACTTTC 59.020 40.000 0.00 0.00 0.00 2.62
418 429 5.422012 ACAGAGTCCAACAAATCCAAACTTT 59.578 36.000 0.00 0.00 0.00 2.66
419 430 4.956075 ACAGAGTCCAACAAATCCAAACTT 59.044 37.500 0.00 0.00 0.00 2.66
420 431 4.536765 ACAGAGTCCAACAAATCCAAACT 58.463 39.130 0.00 0.00 0.00 2.66
421 432 4.918810 ACAGAGTCCAACAAATCCAAAC 57.081 40.909 0.00 0.00 0.00 2.93
426 437 5.123979 GGGTTCATACAGAGTCCAACAAATC 59.876 44.000 0.00 0.00 0.00 2.17
428 439 4.141367 TGGGTTCATACAGAGTCCAACAAA 60.141 41.667 0.00 0.00 30.53 2.83
440 451 5.197451 AGTTTGTTGTTCTGGGTTCATACA 58.803 37.500 0.00 0.00 0.00 2.29
448 459 6.001460 TGGAGTATAAGTTTGTTGTTCTGGG 58.999 40.000 0.00 0.00 0.00 4.45
457 468 8.154856 ACACACTGTTATGGAGTATAAGTTTGT 58.845 33.333 0.00 0.00 32.07 2.83
458 469 8.443160 CACACACTGTTATGGAGTATAAGTTTG 58.557 37.037 0.00 0.00 32.07 2.93
460 471 7.903145 TCACACACTGTTATGGAGTATAAGTT 58.097 34.615 0.00 0.00 32.07 2.66
461 472 7.476540 TCACACACTGTTATGGAGTATAAGT 57.523 36.000 0.00 0.00 32.07 2.24
462 473 8.820933 CAATCACACACTGTTATGGAGTATAAG 58.179 37.037 0.00 0.00 32.07 1.73
463 474 8.536175 TCAATCACACACTGTTATGGAGTATAA 58.464 33.333 0.00 0.00 0.00 0.98
466 477 6.353404 TCAATCACACACTGTTATGGAGTA 57.647 37.500 0.00 0.00 0.00 2.59
467 478 5.227569 TCAATCACACACTGTTATGGAGT 57.772 39.130 0.00 0.00 0.00 3.85
468 479 5.065602 CCATCAATCACACACTGTTATGGAG 59.934 44.000 0.00 0.00 34.57 3.86
469 480 4.943093 CCATCAATCACACACTGTTATGGA 59.057 41.667 0.00 0.00 34.57 3.41
470 481 4.943093 TCCATCAATCACACACTGTTATGG 59.057 41.667 0.00 0.00 34.07 2.74
471 482 5.065602 CCTCCATCAATCACACACTGTTATG 59.934 44.000 0.00 0.00 0.00 1.90
474 485 3.415212 CCTCCATCAATCACACACTGTT 58.585 45.455 0.00 0.00 0.00 3.16
475 486 2.290514 CCCTCCATCAATCACACACTGT 60.291 50.000 0.00 0.00 0.00 3.55
476 487 2.290514 ACCCTCCATCAATCACACACTG 60.291 50.000 0.00 0.00 0.00 3.66
477 488 1.988107 ACCCTCCATCAATCACACACT 59.012 47.619 0.00 0.00 0.00 3.55
479 490 1.066215 CGACCCTCCATCAATCACACA 60.066 52.381 0.00 0.00 0.00 3.72
480 491 1.656652 CGACCCTCCATCAATCACAC 58.343 55.000 0.00 0.00 0.00 3.82
482 493 0.541863 ACCGACCCTCCATCAATCAC 59.458 55.000 0.00 0.00 0.00 3.06
483 494 0.830648 GACCGACCCTCCATCAATCA 59.169 55.000 0.00 0.00 0.00 2.57
484 495 1.123928 AGACCGACCCTCCATCAATC 58.876 55.000 0.00 0.00 0.00 2.67
486 497 0.902531 GAAGACCGACCCTCCATCAA 59.097 55.000 0.00 0.00 0.00 2.57
487 498 0.252057 TGAAGACCGACCCTCCATCA 60.252 55.000 0.00 0.00 0.00 3.07
498 515 2.412325 GGCGTGTTTACATTGAAGACCG 60.412 50.000 0.00 0.00 0.00 4.79
499 516 2.550606 TGGCGTGTTTACATTGAAGACC 59.449 45.455 0.00 0.00 0.00 3.85
500 517 3.889196 TGGCGTGTTTACATTGAAGAC 57.111 42.857 0.00 0.00 0.00 3.01
502 519 6.019156 ACAAAATTGGCGTGTTTACATTGAAG 60.019 34.615 0.00 0.00 0.00 3.02
504 521 5.233050 CACAAAATTGGCGTGTTTACATTGA 59.767 36.000 0.00 0.00 0.00 2.57
517 605 4.456914 CGCAAAAATCTCACAAAATTGGC 58.543 39.130 0.00 0.00 0.00 4.52
532 620 3.041874 CACACAAGGTGCGCAAAAA 57.958 47.368 14.00 0.00 41.36 1.94
548 636 4.445385 CGTGTGGGTTTAACTACACTACAC 59.555 45.833 22.63 15.99 40.81 2.90
549 637 4.501229 CCGTGTGGGTTTAACTACACTACA 60.501 45.833 22.63 8.56 40.81 2.74
550 638 3.989817 CCGTGTGGGTTTAACTACACTAC 59.010 47.826 22.63 16.75 40.81 2.73
551 639 4.255833 CCGTGTGGGTTTAACTACACTA 57.744 45.455 22.63 10.48 40.81 2.74
552 640 3.116079 CCGTGTGGGTTTAACTACACT 57.884 47.619 22.63 0.00 40.81 3.55
579 667 3.564511 CTTTGAAAATACGTGGGTGCAG 58.435 45.455 0.00 0.00 0.00 4.41
593 681 6.219417 TGCAGTTGATTTTCTCCTTTGAAA 57.781 33.333 0.00 0.00 34.55 2.69
636 728 4.005650 AGTTGGATTCAGTGCATACAGTG 58.994 43.478 0.00 0.00 46.81 3.66
637 729 4.256920 GAGTTGGATTCAGTGCATACAGT 58.743 43.478 0.00 0.00 0.00 3.55
638 730 4.256110 TGAGTTGGATTCAGTGCATACAG 58.744 43.478 0.00 0.00 0.00 2.74
639 731 4.284829 TGAGTTGGATTCAGTGCATACA 57.715 40.909 0.00 0.00 0.00 2.29
640 732 5.393962 GTTTGAGTTGGATTCAGTGCATAC 58.606 41.667 0.00 0.00 0.00 2.39
641 733 4.154015 CGTTTGAGTTGGATTCAGTGCATA 59.846 41.667 0.00 0.00 0.00 3.14
642 734 3.058016 CGTTTGAGTTGGATTCAGTGCAT 60.058 43.478 0.00 0.00 0.00 3.96
653 745 3.491639 TCGTTCATACACGTTTGAGTTGG 59.508 43.478 0.00 0.00 41.16 3.77
657 749 4.443063 TCACTTCGTTCATACACGTTTGAG 59.557 41.667 0.00 0.00 41.16 3.02
683 775 4.586841 AGCAGAGCGAGAGGATAATACTTT 59.413 41.667 0.00 0.00 0.00 2.66
727 819 4.027458 CGTGAAAACGTATGTATGTACCGG 60.027 45.833 0.00 0.00 0.00 5.28
884 979 4.135153 CCGACGTGGGGAGCTCTG 62.135 72.222 14.64 1.50 0.00 3.35
939 1034 4.814294 GTAGGGCGTGTGGAGGCG 62.814 72.222 0.00 0.00 33.56 5.52
940 1035 1.610554 TTAGTAGGGCGTGTGGAGGC 61.611 60.000 0.00 0.00 0.00 4.70
941 1036 0.899720 TTTAGTAGGGCGTGTGGAGG 59.100 55.000 0.00 0.00 0.00 4.30
1005 1100 0.036858 GCGTCTCTTCTTCTTGGGCT 60.037 55.000 0.00 0.00 0.00 5.19
1006 1101 1.021920 GGCGTCTCTTCTTCTTGGGC 61.022 60.000 0.00 0.00 0.00 5.36
1007 1102 0.737715 CGGCGTCTCTTCTTCTTGGG 60.738 60.000 0.00 0.00 0.00 4.12
1028 1130 2.259204 GTACTGCGTGGGTGCGTA 59.741 61.111 0.00 0.00 37.81 4.42
1409 1511 2.279784 CTGAGAATCCGGCGAGGC 60.280 66.667 9.30 0.00 40.77 4.70
1410 1512 2.419198 CCTGAGAATCCGGCGAGG 59.581 66.667 9.30 0.17 42.97 4.63
1416 1518 1.519455 GACGTGCCCTGAGAATCCG 60.519 63.158 0.00 0.00 0.00 4.18
1431 1533 0.525668 AGATACAAAGCGAGGCGACG 60.526 55.000 0.00 0.00 0.00 5.12
1465 1567 5.010719 ACAGAGTCTCCGAATAAAACACAGA 59.989 40.000 0.00 0.00 0.00 3.41
1605 1707 1.633945 GGAAAGGGGGAAGTAGCTTCA 59.366 52.381 10.51 0.00 41.77 3.02
1609 1711 2.597578 TTTGGAAAGGGGGAAGTAGC 57.402 50.000 0.00 0.00 0.00 3.58
1623 1726 3.670625 AGCACGCTGTAAGTAATTTGGA 58.329 40.909 0.00 0.00 35.30 3.53
1635 1738 3.006756 ATACTGCCGAGCACGCTGT 62.007 57.895 0.00 6.84 38.29 4.40
1643 1746 1.202580 CCTTTCCCTCATACTGCCGAG 60.203 57.143 0.00 0.00 0.00 4.63
1644 1747 0.830648 CCTTTCCCTCATACTGCCGA 59.169 55.000 0.00 0.00 0.00 5.54
1645 1748 0.179045 CCCTTTCCCTCATACTGCCG 60.179 60.000 0.00 0.00 0.00 5.69
1673 1776 7.826918 ATCTAGACATACTCCCTCTTGTAAC 57.173 40.000 0.00 0.00 0.00 2.50
1732 1838 3.691118 CGACCACACATCAAAATGGAGAT 59.309 43.478 0.00 0.00 37.19 2.75
1738 1844 6.458206 CGATAATTCCGACCACACATCAAAAT 60.458 38.462 0.00 0.00 0.00 1.82
1753 1859 5.734855 AATTCAACTCACCGATAATTCCG 57.265 39.130 0.00 0.00 0.00 4.30
1769 1878 2.534990 CCAAGCCCCCTGTTAATTCAA 58.465 47.619 0.00 0.00 0.00 2.69
1780 1914 1.616628 TCTCTCTTCCCAAGCCCCC 60.617 63.158 0.00 0.00 0.00 5.40
1787 1921 4.289410 TCAATTTCATGGTCTCTCTTCCCA 59.711 41.667 0.00 0.00 0.00 4.37
1798 1932 8.314021 GGAAATAAAAGAGGTCAATTTCATGGT 58.686 33.333 8.00 0.00 37.97 3.55
1800 1934 9.933723 AAGGAAATAAAAGAGGTCAATTTCATG 57.066 29.630 8.00 0.00 37.97 3.07
1802 1936 9.981114 GAAAGGAAATAAAAGAGGTCAATTTCA 57.019 29.630 8.00 0.00 37.97 2.69
1818 1952 4.711055 AGGAGAGAAGGGGAAAGGAAATA 58.289 43.478 0.00 0.00 0.00 1.40
1822 1956 1.437149 TGAGGAGAGAAGGGGAAAGGA 59.563 52.381 0.00 0.00 0.00 3.36
1844 1978 2.204228 TGGCTAGGGGCAAGGGAA 60.204 61.111 0.00 0.00 45.10 3.97
1851 1985 1.555967 TTCATTGTTTGGCTAGGGGC 58.444 50.000 0.00 0.00 40.90 5.80
1876 2010 7.660208 GGAACAAGAGTTTAAGGATACAAGACA 59.340 37.037 0.00 0.00 38.30 3.41
1897 2032 4.016444 GAGGCAATTTGTGATAGGGAACA 58.984 43.478 0.00 0.00 0.00 3.18
1903 2038 3.763360 TGGTTGGAGGCAATTTGTGATAG 59.237 43.478 0.00 0.00 0.00 2.08
1908 2043 2.503356 TGTTTGGTTGGAGGCAATTTGT 59.497 40.909 0.00 0.00 0.00 2.83
1915 2050 0.681175 AAGCATGTTTGGTTGGAGGC 59.319 50.000 0.00 0.00 41.81 4.70
1955 2090 9.810545 TTTGGTCAAATTTAAAGAAGTTCGATT 57.189 25.926 0.00 0.00 0.00 3.34
2039 2178 9.245962 GCGCGTATATGAATAAAAGTATATCCT 57.754 33.333 8.43 0.00 0.00 3.24
2040 2179 9.245962 AGCGCGTATATGAATAAAAGTATATCC 57.754 33.333 8.43 0.00 0.00 2.59
2073 2214 3.342269 CATTTCCGCGACAAGTAATTCG 58.658 45.455 8.23 0.00 38.31 3.34
2074 2215 3.372822 TCCATTTCCGCGACAAGTAATTC 59.627 43.478 8.23 0.00 0.00 2.17
2084 2225 8.330466 ACATTAATTTATATCCATTTCCGCGA 57.670 30.769 8.23 0.00 0.00 5.87
2143 2284 6.943981 TCGTTTGAATTACTTGTCACAGAAG 58.056 36.000 0.00 0.00 0.00 2.85
2146 2287 7.962934 TTTTCGTTTGAATTACTTGTCACAG 57.037 32.000 0.00 0.00 33.20 3.66
2179 2321 9.739276 AAAAGTCCAATATCTACAACATCAGAA 57.261 29.630 0.00 0.00 0.00 3.02
2258 2406 4.226620 TGGTACTACCTCCCTTCCAAATTC 59.773 45.833 6.79 0.00 39.58 2.17
2363 2515 1.224315 CTCCCACATCGGATGGCAA 59.776 57.895 21.19 4.12 36.56 4.52
2377 2529 4.372656 CTCGTCTCATTGTTTATCCTCCC 58.627 47.826 0.00 0.00 0.00 4.30
2390 2542 1.067821 GCCGATTCTTCCTCGTCTCAT 59.932 52.381 0.00 0.00 34.36 2.90
2391 2543 0.456221 GCCGATTCTTCCTCGTCTCA 59.544 55.000 0.00 0.00 34.36 3.27
2422 2574 3.499737 CCATGAACGGCAGTCGGC 61.500 66.667 0.00 0.00 44.45 5.54
2423 2575 2.100631 GTCCATGAACGGCAGTCGG 61.101 63.158 0.00 0.00 44.45 4.79
2424 2576 0.948623 TTGTCCATGAACGGCAGTCG 60.949 55.000 0.00 0.00 45.88 4.18
2425 2577 1.234821 TTTGTCCATGAACGGCAGTC 58.765 50.000 0.00 0.00 0.00 3.51
2426 2578 1.608590 CTTTTGTCCATGAACGGCAGT 59.391 47.619 0.00 0.00 0.00 4.40
2427 2579 1.608590 ACTTTTGTCCATGAACGGCAG 59.391 47.619 0.00 0.00 0.00 4.85
2428 2580 1.336440 CACTTTTGTCCATGAACGGCA 59.664 47.619 0.00 0.00 0.00 5.69
2429 2581 1.335872 CCACTTTTGTCCATGAACGGC 60.336 52.381 0.00 0.00 0.00 5.68
2430 2582 1.269448 CCCACTTTTGTCCATGAACGG 59.731 52.381 0.00 0.00 0.00 4.44
2431 2583 1.335872 GCCCACTTTTGTCCATGAACG 60.336 52.381 0.00 0.00 0.00 3.95
2432 2584 1.335872 CGCCCACTTTTGTCCATGAAC 60.336 52.381 0.00 0.00 0.00 3.18
2433 2585 0.958091 CGCCCACTTTTGTCCATGAA 59.042 50.000 0.00 0.00 0.00 2.57
2434 2586 1.523154 GCGCCCACTTTTGTCCATGA 61.523 55.000 0.00 0.00 0.00 3.07
2435 2587 1.080569 GCGCCCACTTTTGTCCATG 60.081 57.895 0.00 0.00 0.00 3.66
2436 2588 2.275380 GGCGCCCACTTTTGTCCAT 61.275 57.895 18.11 0.00 0.00 3.41
2437 2589 2.909965 GGCGCCCACTTTTGTCCA 60.910 61.111 18.11 0.00 0.00 4.02
2438 2590 4.038080 CGGCGCCCACTTTTGTCC 62.038 66.667 23.46 0.00 0.00 4.02
2439 2591 4.700365 GCGGCGCCCACTTTTGTC 62.700 66.667 23.58 0.00 0.00 3.18
2440 2592 3.835790 TAGCGGCGCCCACTTTTGT 62.836 57.895 30.40 9.19 0.00 2.83
2441 2593 3.053291 TAGCGGCGCCCACTTTTG 61.053 61.111 30.40 5.76 0.00 2.44
2442 2594 3.053896 GTAGCGGCGCCCACTTTT 61.054 61.111 30.40 10.88 0.00 2.27
2449 2601 2.653953 TAATTGGAGGTAGCGGCGCC 62.654 60.000 30.40 19.07 0.00 6.53
2450 2602 0.602905 ATAATTGGAGGTAGCGGCGC 60.603 55.000 26.86 26.86 0.00 6.53
2451 2603 1.270094 TGATAATTGGAGGTAGCGGCG 60.270 52.381 0.51 0.51 0.00 6.46
2452 2604 2.543777 TGATAATTGGAGGTAGCGGC 57.456 50.000 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.