Multiple sequence alignment - TraesCS7A01G214300

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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 TraesCS7A01G214300 chr7A 100.000 4015 0 0 1 4015 178298808 178294794 0.000000e+00 7415
1 TraesCS7A01G214300 chr7B 94.886 2718 100 18 367 3061 141867019 141864318 0.000000e+00 4213
2 TraesCS7A01G214300 chr7B 94.556 698 36 2 3319 4015 141856759 141856063 0.000000e+00 1077
3 TraesCS7A01G214300 chr7B 92.388 289 13 4 3057 3336 141864058 141863770 1.740000e-108 403
4 TraesCS7A01G214300 chr7B 87.500 168 15 5 146 309 557457775 557457610 5.300000e-44 189
5 TraesCS7A01G214300 chr7D 95.472 2606 82 15 593 3177 176164545 176167135 0.000000e+00 4126
6 TraesCS7A01G214300 chr7D 95.528 805 32 2 3215 4015 176167137 176167941 0.000000e+00 1284
7 TraesCS7A01G214300 chr2B 76.984 504 84 24 2431 2923 491712231 491711749 3.980000e-65 259
8 TraesCS7A01G214300 chr2B 86.550 171 18 4 145 311 43843956 43843787 2.460000e-42 183
9 TraesCS7A01G214300 chr5A 78.614 332 69 2 1974 2304 415321632 415321962 6.760000e-53 219
10 TraesCS7A01G214300 chr5D 77.711 332 72 2 1974 2304 319146508 319146178 6.800000e-48 202
11 TraesCS7A01G214300 chr5D 86.550 171 18 4 145 311 138999079 138998910 2.460000e-42 183
12 TraesCS7A01G214300 chr2D 87.135 171 17 4 145 311 415629645 415629476 5.300000e-44 189
13 TraesCS7A01G214300 chr2D 86.550 171 18 4 145 311 224161971 224162140 2.460000e-42 183
14 TraesCS7A01G214300 chr1B 86.982 169 17 3 144 308 22877376 22877209 6.850000e-43 185
15 TraesCS7A01G214300 chr1B 86.550 171 18 4 145 311 437402355 437402524 2.460000e-42 183
16 TraesCS7A01G214300 chr3D 86.550 171 17 5 145 311 534706067 534705899 2.460000e-42 183
17 TraesCS7A01G214300 chr1D 86.550 171 18 4 145 311 257560429 257560598 2.460000e-42 183


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 TraesCS7A01G214300 chr7A 178294794 178298808 4014 True 7415 7415 100.000 1 4015 1 chr7A.!!$R1 4014
1 TraesCS7A01G214300 chr7B 141863770 141867019 3249 True 2308 4213 93.637 367 3336 2 chr7B.!!$R3 2969
2 TraesCS7A01G214300 chr7B 141856063 141856759 696 True 1077 1077 94.556 3319 4015 1 chr7B.!!$R1 696
3 TraesCS7A01G214300 chr7D 176164545 176167941 3396 False 2705 4126 95.500 593 4015 2 chr7D.!!$F1 3422

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
388 389 0.038166 GCTCAACAACCATCCCTGGA 59.962 55.000 0.00 0.0 46.37 3.86 F
486 489 1.144913 TGTTCTTTCCTGTCCCTTGGG 59.855 52.381 0.00 0.0 0.00 4.12 F
1450 1471 0.172803 GCTGGCATTGCTCAAGAAGG 59.827 55.000 8.82 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1471 1.290639 GATTCCCGGAGAGATCGGC 59.709 63.158 0.73 0.0 45.60 5.54 R
1455 1476 1.828660 GAGGCGATTCCCGGAGAGA 60.829 63.158 0.73 0.0 39.04 3.10 R
3375 3685 0.042731 TGCCTAGTGTAGGGAGCCTT 59.957 55.000 2.19 0.0 46.32 4.35 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
22 23 2.619013 AAGCTGCACTATTTTGACGC 57.381 45.000 1.02 0.00 0.00 5.19
23 24 1.813513 AGCTGCACTATTTTGACGCT 58.186 45.000 1.02 0.00 0.00 5.07
24 25 2.154462 AGCTGCACTATTTTGACGCTT 58.846 42.857 1.02 0.00 0.00 4.68
25 26 2.095567 AGCTGCACTATTTTGACGCTTG 60.096 45.455 1.02 0.00 0.00 4.01
26 27 2.350772 GCTGCACTATTTTGACGCTTGT 60.351 45.455 0.00 0.00 0.00 3.16
27 28 3.853307 GCTGCACTATTTTGACGCTTGTT 60.853 43.478 0.00 0.00 0.00 2.83
28 29 4.290155 CTGCACTATTTTGACGCTTGTTT 58.710 39.130 0.00 0.00 0.00 2.83
29 30 5.425577 TGCACTATTTTGACGCTTGTTTA 57.574 34.783 0.00 0.00 0.00 2.01
30 31 6.007936 TGCACTATTTTGACGCTTGTTTAT 57.992 33.333 0.00 0.00 0.00 1.40
31 32 5.855925 TGCACTATTTTGACGCTTGTTTATG 59.144 36.000 0.00 0.00 0.00 1.90
32 33 5.220024 GCACTATTTTGACGCTTGTTTATGC 60.220 40.000 0.00 0.00 0.00 3.14
33 34 5.855925 CACTATTTTGACGCTTGTTTATGCA 59.144 36.000 0.00 0.00 0.00 3.96
34 35 6.362016 CACTATTTTGACGCTTGTTTATGCAA 59.638 34.615 0.00 0.00 0.00 4.08
35 36 6.920758 ACTATTTTGACGCTTGTTTATGCAAA 59.079 30.769 0.00 0.00 0.00 3.68
36 37 5.633996 TTTTGACGCTTGTTTATGCAAAG 57.366 34.783 0.00 0.00 0.00 2.77
37 38 3.980646 TGACGCTTGTTTATGCAAAGT 57.019 38.095 0.00 0.00 0.00 2.66
38 39 5.425577 TTGACGCTTGTTTATGCAAAGTA 57.574 34.783 0.00 0.00 0.00 2.24
39 40 5.621197 TGACGCTTGTTTATGCAAAGTAT 57.379 34.783 0.00 0.00 0.00 2.12
40 41 5.389778 TGACGCTTGTTTATGCAAAGTATG 58.610 37.500 0.00 0.00 0.00 2.39
41 42 4.732784 ACGCTTGTTTATGCAAAGTATGG 58.267 39.130 0.00 0.00 0.00 2.74
42 43 4.457603 ACGCTTGTTTATGCAAAGTATGGA 59.542 37.500 0.00 0.00 0.00 3.41
43 44 5.048364 ACGCTTGTTTATGCAAAGTATGGAA 60.048 36.000 0.00 0.00 30.96 3.53
44 45 5.512788 CGCTTGTTTATGCAAAGTATGGAAG 59.487 40.000 0.00 0.00 30.96 3.46
45 46 6.620678 GCTTGTTTATGCAAAGTATGGAAGA 58.379 36.000 0.00 0.00 30.96 2.87
46 47 6.749118 GCTTGTTTATGCAAAGTATGGAAGAG 59.251 38.462 0.00 0.00 30.96 2.85
47 48 7.575720 GCTTGTTTATGCAAAGTATGGAAGAGT 60.576 37.037 0.00 0.00 30.96 3.24
48 49 7.144722 TGTTTATGCAAAGTATGGAAGAGTG 57.855 36.000 0.00 0.00 30.96 3.51
49 50 5.818136 TTATGCAAAGTATGGAAGAGTGC 57.182 39.130 0.00 0.00 30.96 4.40
50 51 3.138884 TGCAAAGTATGGAAGAGTGCA 57.861 42.857 0.00 0.00 38.13 4.57
51 52 3.485394 TGCAAAGTATGGAAGAGTGCAA 58.515 40.909 0.00 0.00 37.56 4.08
52 53 3.253188 TGCAAAGTATGGAAGAGTGCAAC 59.747 43.478 0.00 0.00 37.56 4.17
53 54 6.269370 ATGCAAAGTATGGAAGAGTGCAACT 61.269 40.000 0.00 0.00 41.79 3.16
54 55 7.694695 ATGCAAAGTATGGAAGAGTGCAACTT 61.695 38.462 7.05 7.05 39.70 2.66
55 56 9.598716 ATGCAAAGTATGGAAGAGTGCAACTTG 62.599 40.741 11.32 1.38 39.70 3.16
69 70 6.127498 GTGCAACTTGTGTTCAATTTATCG 57.873 37.500 0.00 0.00 33.52 2.92
70 71 5.685511 GTGCAACTTGTGTTCAATTTATCGT 59.314 36.000 0.00 0.00 33.52 3.73
71 72 6.198216 GTGCAACTTGTGTTCAATTTATCGTT 59.802 34.615 0.00 0.00 33.52 3.85
72 73 7.377397 GTGCAACTTGTGTTCAATTTATCGTTA 59.623 33.333 0.00 0.00 33.52 3.18
73 74 8.079203 TGCAACTTGTGTTCAATTTATCGTTAT 58.921 29.630 0.00 0.00 33.52 1.89
74 75 9.549509 GCAACTTGTGTTCAATTTATCGTTATA 57.450 29.630 0.00 0.00 33.52 0.98
102 103 9.905713 TCTAATTGCCACATAATAGAAAAGAGT 57.094 29.630 0.00 0.00 0.00 3.24
105 106 9.643693 AATTGCCACATAATAGAAAAGAGTTTG 57.356 29.630 0.00 0.00 0.00 2.93
106 107 7.994425 TGCCACATAATAGAAAAGAGTTTGA 57.006 32.000 0.00 0.00 0.00 2.69
107 108 7.816640 TGCCACATAATAGAAAAGAGTTTGAC 58.183 34.615 0.00 0.00 0.00 3.18
108 109 7.446931 TGCCACATAATAGAAAAGAGTTTGACA 59.553 33.333 0.00 0.00 0.00 3.58
109 110 8.296713 GCCACATAATAGAAAAGAGTTTGACAA 58.703 33.333 0.00 0.00 0.00 3.18
119 120 9.574516 AGAAAAGAGTTTGACAATAATACCACT 57.425 29.630 0.00 0.00 0.00 4.00
120 121 9.827411 GAAAAGAGTTTGACAATAATACCACTC 57.173 33.333 6.01 6.01 0.00 3.51
121 122 7.923414 AAGAGTTTGACAATAATACCACTCC 57.077 36.000 9.32 0.00 31.55 3.85
122 123 6.415573 AGAGTTTGACAATAATACCACTCCC 58.584 40.000 9.32 0.00 31.55 4.30
123 124 6.012858 AGAGTTTGACAATAATACCACTCCCA 60.013 38.462 9.32 0.00 31.55 4.37
124 125 5.944007 AGTTTGACAATAATACCACTCCCAC 59.056 40.000 0.00 0.00 0.00 4.61
125 126 5.506730 TTGACAATAATACCACTCCCACA 57.493 39.130 0.00 0.00 0.00 4.17
126 127 5.506730 TGACAATAATACCACTCCCACAA 57.493 39.130 0.00 0.00 0.00 3.33
127 128 5.496556 TGACAATAATACCACTCCCACAAG 58.503 41.667 0.00 0.00 0.00 3.16
128 129 4.270008 ACAATAATACCACTCCCACAAGC 58.730 43.478 0.00 0.00 0.00 4.01
129 130 3.577805 ATAATACCACTCCCACAAGCC 57.422 47.619 0.00 0.00 0.00 4.35
130 131 1.072266 AATACCACTCCCACAAGCCA 58.928 50.000 0.00 0.00 0.00 4.75
131 132 1.298953 ATACCACTCCCACAAGCCAT 58.701 50.000 0.00 0.00 0.00 4.40
132 133 1.072266 TACCACTCCCACAAGCCATT 58.928 50.000 0.00 0.00 0.00 3.16
133 134 0.251341 ACCACTCCCACAAGCCATTC 60.251 55.000 0.00 0.00 0.00 2.67
134 135 0.038744 CCACTCCCACAAGCCATTCT 59.961 55.000 0.00 0.00 0.00 2.40
135 136 1.548582 CCACTCCCACAAGCCATTCTT 60.549 52.381 0.00 0.00 34.78 2.52
136 137 1.815003 CACTCCCACAAGCCATTCTTC 59.185 52.381 0.00 0.00 31.27 2.87
137 138 1.272147 ACTCCCACAAGCCATTCTTCC 60.272 52.381 0.00 0.00 31.27 3.46
138 139 1.005215 CTCCCACAAGCCATTCTTCCT 59.995 52.381 0.00 0.00 31.27 3.36
139 140 2.239654 CTCCCACAAGCCATTCTTCCTA 59.760 50.000 0.00 0.00 31.27 2.94
140 141 2.647299 TCCCACAAGCCATTCTTCCTAA 59.353 45.455 0.00 0.00 31.27 2.69
141 142 3.019564 CCCACAAGCCATTCTTCCTAAG 58.980 50.000 0.00 0.00 31.27 2.18
142 143 3.308402 CCCACAAGCCATTCTTCCTAAGA 60.308 47.826 0.00 0.00 35.26 2.10
154 155 6.809976 TTCTTCCTAAGAAATACTCCCTCC 57.190 41.667 0.00 0.00 44.10 4.30
155 156 5.850278 TCTTCCTAAGAAATACTCCCTCCA 58.150 41.667 0.00 0.00 33.83 3.86
156 157 6.453476 TCTTCCTAAGAAATACTCCCTCCAT 58.547 40.000 0.00 0.00 33.83 3.41
157 158 6.909158 TCTTCCTAAGAAATACTCCCTCCATT 59.091 38.462 0.00 0.00 33.83 3.16
158 159 7.406151 TCTTCCTAAGAAATACTCCCTCCATTT 59.594 37.037 0.00 0.00 33.83 2.32
159 160 7.138054 TCCTAAGAAATACTCCCTCCATTTC 57.862 40.000 0.00 0.00 38.42 2.17
160 161 6.909158 TCCTAAGAAATACTCCCTCCATTTCT 59.091 38.462 3.56 3.56 46.06 2.52
161 162 8.071854 TCCTAAGAAATACTCCCTCCATTTCTA 58.928 37.037 8.70 0.00 44.33 2.10
162 163 8.714906 CCTAAGAAATACTCCCTCCATTTCTAA 58.285 37.037 8.70 0.00 44.33 2.10
169 170 9.799106 AATACTCCCTCCATTTCTAAATATGTG 57.201 33.333 0.00 0.00 0.00 3.21
170 171 7.213178 ACTCCCTCCATTTCTAAATATGTGT 57.787 36.000 0.00 0.00 0.00 3.72
171 172 7.283329 ACTCCCTCCATTTCTAAATATGTGTC 58.717 38.462 0.00 0.00 0.00 3.67
172 173 7.127955 ACTCCCTCCATTTCTAAATATGTGTCT 59.872 37.037 0.00 0.00 0.00 3.41
173 174 7.872138 TCCCTCCATTTCTAAATATGTGTCTT 58.128 34.615 0.00 0.00 0.00 3.01
174 175 8.336235 TCCCTCCATTTCTAAATATGTGTCTTT 58.664 33.333 0.00 0.00 0.00 2.52
175 176 8.971073 CCCTCCATTTCTAAATATGTGTCTTTT 58.029 33.333 0.00 0.00 0.00 2.27
268 269 8.765488 ATACATTCATATGTGGTTCATTGGAA 57.235 30.769 1.90 0.00 44.56 3.53
269 270 7.479352 ACATTCATATGTGGTTCATTGGAAA 57.521 32.000 1.90 0.00 43.29 3.13
270 271 8.081517 ACATTCATATGTGGTTCATTGGAAAT 57.918 30.769 1.90 0.00 43.29 2.17
271 272 8.199449 ACATTCATATGTGGTTCATTGGAAATC 58.801 33.333 1.90 0.00 43.29 2.17
272 273 7.959658 TTCATATGTGGTTCATTGGAAATCT 57.040 32.000 1.90 0.00 37.91 2.40
273 274 7.959658 TCATATGTGGTTCATTGGAAATCTT 57.040 32.000 1.90 0.00 37.91 2.40
274 275 7.999679 TCATATGTGGTTCATTGGAAATCTTC 58.000 34.615 1.90 0.00 37.91 2.87
275 276 7.835682 TCATATGTGGTTCATTGGAAATCTTCT 59.164 33.333 1.90 0.00 37.91 2.85
276 277 9.123902 CATATGTGGTTCATTGGAAATCTTCTA 57.876 33.333 0.00 0.00 37.91 2.10
277 278 9.699410 ATATGTGGTTCATTGGAAATCTTCTAA 57.301 29.630 0.00 0.00 37.91 2.10
278 279 7.831691 TGTGGTTCATTGGAAATCTTCTAAA 57.168 32.000 0.00 0.00 33.74 1.85
279 280 8.243961 TGTGGTTCATTGGAAATCTTCTAAAA 57.756 30.769 0.00 0.00 33.74 1.52
280 281 8.359642 TGTGGTTCATTGGAAATCTTCTAAAAG 58.640 33.333 0.00 0.00 33.74 2.27
281 282 8.576442 GTGGTTCATTGGAAATCTTCTAAAAGA 58.424 33.333 0.00 0.00 45.36 2.52
282 283 9.142014 TGGTTCATTGGAAATCTTCTAAAAGAA 57.858 29.630 0.00 0.00 44.49 2.52
310 311 9.765795 AATATTTAGAAACGAAGGGAGTAGATG 57.234 33.333 0.00 0.00 0.00 2.90
311 312 6.600882 TTTAGAAACGAAGGGAGTAGATGT 57.399 37.500 0.00 0.00 0.00 3.06
312 313 4.457834 AGAAACGAAGGGAGTAGATGTG 57.542 45.455 0.00 0.00 0.00 3.21
313 314 3.833070 AGAAACGAAGGGAGTAGATGTGT 59.167 43.478 0.00 0.00 0.00 3.72
314 315 4.283722 AGAAACGAAGGGAGTAGATGTGTT 59.716 41.667 0.00 0.00 0.00 3.32
315 316 5.479375 AGAAACGAAGGGAGTAGATGTGTTA 59.521 40.000 0.00 0.00 0.00 2.41
316 317 4.715527 ACGAAGGGAGTAGATGTGTTAC 57.284 45.455 0.00 0.00 0.00 2.50
317 318 3.446516 ACGAAGGGAGTAGATGTGTTACC 59.553 47.826 0.00 0.00 0.00 2.85
318 319 3.181478 CGAAGGGAGTAGATGTGTTACCC 60.181 52.174 0.00 0.00 36.47 3.69
319 320 3.778622 AGGGAGTAGATGTGTTACCCT 57.221 47.619 0.00 0.00 40.97 4.34
320 321 3.375699 AGGGAGTAGATGTGTTACCCTG 58.624 50.000 0.00 0.00 43.61 4.45
321 322 3.012502 AGGGAGTAGATGTGTTACCCTGA 59.987 47.826 0.00 0.00 43.61 3.86
322 323 3.773119 GGGAGTAGATGTGTTACCCTGAA 59.227 47.826 0.00 0.00 33.79 3.02
323 324 4.409247 GGGAGTAGATGTGTTACCCTGAAT 59.591 45.833 0.00 0.00 33.79 2.57
324 325 5.104485 GGGAGTAGATGTGTTACCCTGAATT 60.104 44.000 0.00 0.00 33.79 2.17
325 326 6.415573 GGAGTAGATGTGTTACCCTGAATTT 58.584 40.000 0.00 0.00 0.00 1.82
326 327 6.884836 GGAGTAGATGTGTTACCCTGAATTTT 59.115 38.462 0.00 0.00 0.00 1.82
327 328 7.148239 GGAGTAGATGTGTTACCCTGAATTTTG 60.148 40.741 0.00 0.00 0.00 2.44
328 329 7.231467 AGTAGATGTGTTACCCTGAATTTTGT 58.769 34.615 0.00 0.00 0.00 2.83
329 330 8.380099 AGTAGATGTGTTACCCTGAATTTTGTA 58.620 33.333 0.00 0.00 0.00 2.41
330 331 7.448748 AGATGTGTTACCCTGAATTTTGTAC 57.551 36.000 0.00 0.00 0.00 2.90
331 332 7.231467 AGATGTGTTACCCTGAATTTTGTACT 58.769 34.615 0.00 0.00 0.00 2.73
332 333 8.380099 AGATGTGTTACCCTGAATTTTGTACTA 58.620 33.333 0.00 0.00 0.00 1.82
333 334 8.927675 ATGTGTTACCCTGAATTTTGTACTAA 57.072 30.769 0.00 0.00 0.00 2.24
334 335 8.749026 TGTGTTACCCTGAATTTTGTACTAAA 57.251 30.769 4.96 4.96 0.00 1.85
335 336 9.186837 TGTGTTACCCTGAATTTTGTACTAAAA 57.813 29.630 6.57 6.20 0.00 1.52
341 342 9.143155 ACCCTGAATTTTGTACTAAAATCAAGT 57.857 29.630 17.33 14.96 0.00 3.16
342 343 9.410556 CCCTGAATTTTGTACTAAAATCAAGTG 57.589 33.333 17.33 10.91 0.00 3.16
343 344 8.915654 CCTGAATTTTGTACTAAAATCAAGTGC 58.084 33.333 17.33 0.00 0.00 4.40
344 345 9.683069 CTGAATTTTGTACTAAAATCAAGTGCT 57.317 29.630 17.33 3.21 31.62 4.40
352 353 9.515226 TGTACTAAAATCAAGTGCTATTTTCCT 57.485 29.630 0.00 0.00 36.80 3.36
355 356 7.814587 ACTAAAATCAAGTGCTATTTTCCTTGC 59.185 33.333 0.00 0.00 36.80 4.01
356 357 3.829886 TCAAGTGCTATTTTCCTTGCG 57.170 42.857 0.00 0.00 35.42 4.85
357 358 3.407698 TCAAGTGCTATTTTCCTTGCGA 58.592 40.909 0.00 0.00 35.42 5.10
358 359 3.188460 TCAAGTGCTATTTTCCTTGCGAC 59.812 43.478 0.00 0.00 35.42 5.19
359 360 3.059352 AGTGCTATTTTCCTTGCGACT 57.941 42.857 0.00 0.00 0.00 4.18
360 361 3.412386 AGTGCTATTTTCCTTGCGACTT 58.588 40.909 0.00 0.00 0.00 3.01
361 362 3.821033 AGTGCTATTTTCCTTGCGACTTT 59.179 39.130 0.00 0.00 0.00 2.66
362 363 4.278419 AGTGCTATTTTCCTTGCGACTTTT 59.722 37.500 0.00 0.00 0.00 2.27
363 364 4.982295 GTGCTATTTTCCTTGCGACTTTTT 59.018 37.500 0.00 0.00 0.00 1.94
364 365 5.117135 GTGCTATTTTCCTTGCGACTTTTTC 59.883 40.000 0.00 0.00 0.00 2.29
365 366 4.621460 GCTATTTTCCTTGCGACTTTTTCC 59.379 41.667 0.00 0.00 0.00 3.13
369 370 1.804151 TCCTTGCGACTTTTTCCATCG 59.196 47.619 0.00 0.00 38.87 3.84
379 380 3.243401 ACTTTTTCCATCGCTCAACAACC 60.243 43.478 0.00 0.00 0.00 3.77
388 389 0.038166 GCTCAACAACCATCCCTGGA 59.962 55.000 0.00 0.00 46.37 3.86
479 482 6.372937 CCTTTCCTCTTATGTTCTTTCCTGTC 59.627 42.308 0.00 0.00 0.00 3.51
486 489 1.144913 TGTTCTTTCCTGTCCCTTGGG 59.855 52.381 0.00 0.00 0.00 4.12
495 498 1.352352 CTGTCCCTTGGGTGTTCATCT 59.648 52.381 5.51 0.00 0.00 2.90
509 512 5.238214 GGTGTTCATCTGATGCCTTAGAATC 59.762 44.000 12.78 0.26 0.00 2.52
541 544 4.325741 TGAAGCAACACAAAATTTCACGTG 59.674 37.500 9.94 9.94 35.48 4.49
547 550 3.119316 ACACAAAATTTCACGTGCCTGAA 60.119 39.130 11.67 3.36 32.53 3.02
571 574 1.207089 CAGGTGCTCCCGAACAAGATA 59.793 52.381 0.00 0.00 38.74 1.98
605 608 1.221414 CAACGCCTTGGAGCTATAGC 58.779 55.000 17.33 17.33 42.49 2.97
752 757 2.369860 CAGCTGCTGGAGTAATATGGGA 59.630 50.000 21.71 0.00 0.00 4.37
754 759 3.072184 AGCTGCTGGAGTAATATGGGAAG 59.928 47.826 0.00 0.00 0.00 3.46
755 760 3.808618 GCTGCTGGAGTAATATGGGAAGG 60.809 52.174 0.00 0.00 0.00 3.46
756 761 3.648067 CTGCTGGAGTAATATGGGAAGGA 59.352 47.826 0.00 0.00 0.00 3.36
757 762 4.044308 TGCTGGAGTAATATGGGAAGGAA 58.956 43.478 0.00 0.00 0.00 3.36
758 763 4.665009 TGCTGGAGTAATATGGGAAGGAAT 59.335 41.667 0.00 0.00 0.00 3.01
797 802 2.572290 GCGCCCTATTTAATCACAGGT 58.428 47.619 0.00 0.00 0.00 4.00
957 972 1.689984 GTCCCTTCCTCTACCTACCG 58.310 60.000 0.00 0.00 0.00 4.02
970 988 3.166560 ACCTACCGTCTTCTTGGTACT 57.833 47.619 0.00 0.00 39.70 2.73
973 991 3.119566 CCTACCGTCTTCTTGGTACTGTC 60.120 52.174 0.00 0.00 39.70 3.51
979 997 4.142359 CGTCTTCTTGGTACTGTCAGCTAT 60.142 45.833 0.00 0.00 0.00 2.97
980 998 5.066117 CGTCTTCTTGGTACTGTCAGCTATA 59.934 44.000 0.00 0.00 0.00 1.31
981 999 6.404403 CGTCTTCTTGGTACTGTCAGCTATAA 60.404 42.308 0.00 0.00 0.00 0.98
983 1001 5.263968 TCTTGGTACTGTCAGCTATAAGC 57.736 43.478 0.00 0.00 42.84 3.09
995 1016 1.268896 GCTATAAGCTGTACCGCGTCA 60.269 52.381 4.92 0.12 38.45 4.35
1149 1170 1.811266 CGCCGTGGGAAGTCATCTG 60.811 63.158 0.00 0.00 0.00 2.90
1160 1181 2.334006 AGTCATCTGAAGTGGGACCT 57.666 50.000 0.00 0.00 0.00 3.85
1299 1320 3.712907 GGCAACCTCACCGCCCTA 61.713 66.667 0.00 0.00 40.07 3.53
1450 1471 0.172803 GCTGGCATTGCTCAAGAAGG 59.827 55.000 8.82 0.00 0.00 3.46
1455 1476 1.386533 CATTGCTCAAGAAGGCCGAT 58.613 50.000 0.00 0.00 0.00 4.18
1795 1816 1.006825 TGCGTTGGTCGTTCTCATCG 61.007 55.000 0.00 0.00 42.13 3.84
2154 2175 3.461773 CGCGATGTCCACCTCCCT 61.462 66.667 0.00 0.00 0.00 4.20
2338 2359 3.782244 CGCACCTCAGCTTCGCAC 61.782 66.667 0.00 0.00 0.00 5.34
2386 2416 5.805728 TGTTTAGATTCCCTTCTTGTCTCC 58.194 41.667 0.00 0.00 0.00 3.71
2423 2453 2.870161 CGCCTCGACTTCACGACG 60.870 66.667 0.00 0.00 37.37 5.12
2522 2552 0.669318 TCAAGGCGTCCAACATCGTC 60.669 55.000 0.00 0.00 0.00 4.20
2678 2708 1.081641 CGACGTGTACAGCTTCGGT 60.082 57.895 11.21 0.00 0.00 4.69
3144 3441 5.634896 CGCTTTCATTTGACTCATAAGCTT 58.365 37.500 3.48 3.48 33.22 3.74
3217 3523 7.872483 CCCCCATAATCACAAGTTTATATTTGC 59.128 37.037 0.00 0.00 0.00 3.68
3312 3618 4.421948 CCTTGCTGAGCATTCAAATTCTC 58.578 43.478 8.44 0.00 38.76 2.87
3341 3651 6.182627 TCTCAGTGGATGAAATAAATGCAGT 58.817 36.000 0.00 0.00 37.52 4.40
3449 3759 4.202461 TGCTACAATTCCTCAACTTGGAGT 60.202 41.667 0.00 0.00 34.05 3.85
3473 3783 3.591835 CCACACGGGCAGCGTTTT 61.592 61.111 0.00 0.00 0.00 2.43
3506 3816 1.465387 GTCTCTTCGTCGAAGCTCTGA 59.535 52.381 26.65 18.41 39.29 3.27
3513 3823 1.133216 CGTCGAAGCTCTGATCTTCCA 59.867 52.381 13.83 0.71 37.29 3.53
3515 3825 1.133216 TCGAAGCTCTGATCTTCCACG 59.867 52.381 13.83 5.40 37.29 4.94
3589 3899 1.418342 GCGCGTGTACGATGATTGGT 61.418 55.000 8.43 0.00 43.02 3.67
3652 3962 5.428457 TCTGGGGATTATCAACTTTAGCTGA 59.572 40.000 0.00 0.00 0.00 4.26
3861 4172 5.470098 ACAAACATGTCACATCACCTTAGTC 59.530 40.000 0.00 0.00 0.00 2.59
3902 4213 5.366829 TTTCTCACTACGATGACGAAAGA 57.633 39.130 0.00 0.00 42.66 2.52
3912 4223 0.179059 TGACGAAAGAGCACTGCCAA 60.179 50.000 0.00 0.00 0.00 4.52
3938 4249 8.974060 TTCACCAAAATACTATCCTTCATACC 57.026 34.615 0.00 0.00 0.00 2.73
3964 4275 7.301054 GCTACATTTGTATGCCAATACATCTC 58.699 38.462 0.00 0.00 46.23 2.75
3993 4304 5.885352 ACATGCTACACAATTTATGCTGGTA 59.115 36.000 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.215399 AGCGTCAAAATAGTGCAGCTTTAA 59.785 37.500 0.00 0.00 30.39 1.52
1 2 3.751175 AGCGTCAAAATAGTGCAGCTTTA 59.249 39.130 0.00 0.00 30.39 1.85
2 3 2.554032 AGCGTCAAAATAGTGCAGCTTT 59.446 40.909 0.00 0.00 30.39 3.51
3 4 2.154462 AGCGTCAAAATAGTGCAGCTT 58.846 42.857 0.00 0.00 30.39 3.74
4 5 1.813513 AGCGTCAAAATAGTGCAGCT 58.186 45.000 0.00 0.00 0.00 4.24
5 6 2.245096 CAAGCGTCAAAATAGTGCAGC 58.755 47.619 0.00 0.00 0.00 5.25
6 7 3.542712 ACAAGCGTCAAAATAGTGCAG 57.457 42.857 0.00 0.00 0.00 4.41
7 8 3.980646 AACAAGCGTCAAAATAGTGCA 57.019 38.095 0.00 0.00 0.00 4.57
8 9 5.220024 GCATAAACAAGCGTCAAAATAGTGC 60.220 40.000 0.00 0.00 0.00 4.40
9 10 5.855925 TGCATAAACAAGCGTCAAAATAGTG 59.144 36.000 0.00 0.00 0.00 2.74
10 11 6.007936 TGCATAAACAAGCGTCAAAATAGT 57.992 33.333 0.00 0.00 0.00 2.12
11 12 6.926280 TTGCATAAACAAGCGTCAAAATAG 57.074 33.333 0.00 0.00 0.00 1.73
12 13 6.920758 ACTTTGCATAAACAAGCGTCAAAATA 59.079 30.769 0.00 0.00 0.00 1.40
13 14 5.752955 ACTTTGCATAAACAAGCGTCAAAAT 59.247 32.000 0.00 0.00 0.00 1.82
14 15 5.105752 ACTTTGCATAAACAAGCGTCAAAA 58.894 33.333 0.00 0.00 0.00 2.44
15 16 4.677584 ACTTTGCATAAACAAGCGTCAAA 58.322 34.783 0.00 0.00 0.00 2.69
16 17 4.300189 ACTTTGCATAAACAAGCGTCAA 57.700 36.364 0.00 0.00 0.00 3.18
17 18 3.980646 ACTTTGCATAAACAAGCGTCA 57.019 38.095 0.00 0.00 0.00 4.35
18 19 4.793216 CCATACTTTGCATAAACAAGCGTC 59.207 41.667 0.00 0.00 0.00 5.19
19 20 4.457603 TCCATACTTTGCATAAACAAGCGT 59.542 37.500 0.00 0.00 0.00 5.07
20 21 4.980590 TCCATACTTTGCATAAACAAGCG 58.019 39.130 0.00 0.00 0.00 4.68
21 22 6.620678 TCTTCCATACTTTGCATAAACAAGC 58.379 36.000 0.00 0.00 0.00 4.01
22 23 7.752239 CACTCTTCCATACTTTGCATAAACAAG 59.248 37.037 0.00 0.00 0.00 3.16
23 24 7.592938 CACTCTTCCATACTTTGCATAAACAA 58.407 34.615 0.00 0.00 0.00 2.83
24 25 6.349280 GCACTCTTCCATACTTTGCATAAACA 60.349 38.462 0.00 0.00 0.00 2.83
25 26 6.030228 GCACTCTTCCATACTTTGCATAAAC 58.970 40.000 0.00 0.00 0.00 2.01
26 27 5.709631 TGCACTCTTCCATACTTTGCATAAA 59.290 36.000 0.00 0.00 33.72 1.40
27 28 5.252547 TGCACTCTTCCATACTTTGCATAA 58.747 37.500 0.00 0.00 33.72 1.90
28 29 4.842574 TGCACTCTTCCATACTTTGCATA 58.157 39.130 0.00 0.00 33.72 3.14
29 30 3.689347 TGCACTCTTCCATACTTTGCAT 58.311 40.909 0.00 0.00 33.72 3.96
30 31 3.138884 TGCACTCTTCCATACTTTGCA 57.861 42.857 0.00 0.00 36.20 4.08
31 32 3.503748 AGTTGCACTCTTCCATACTTTGC 59.496 43.478 0.00 0.00 0.00 3.68
32 33 5.009010 ACAAGTTGCACTCTTCCATACTTTG 59.991 40.000 1.81 0.00 0.00 2.77
33 34 5.009010 CACAAGTTGCACTCTTCCATACTTT 59.991 40.000 1.81 0.00 0.00 2.66
34 35 4.516698 CACAAGTTGCACTCTTCCATACTT 59.483 41.667 1.81 0.00 0.00 2.24
35 36 4.067896 CACAAGTTGCACTCTTCCATACT 58.932 43.478 1.81 0.00 0.00 2.12
36 37 3.815401 ACACAAGTTGCACTCTTCCATAC 59.185 43.478 1.81 0.00 0.00 2.39
37 38 4.085357 ACACAAGTTGCACTCTTCCATA 57.915 40.909 1.81 0.00 0.00 2.74
38 39 2.936202 ACACAAGTTGCACTCTTCCAT 58.064 42.857 1.81 0.00 0.00 3.41
39 40 2.418368 ACACAAGTTGCACTCTTCCA 57.582 45.000 1.81 0.00 0.00 3.53
40 41 2.682856 TGAACACAAGTTGCACTCTTCC 59.317 45.455 1.81 0.00 38.30 3.46
41 42 4.355543 TTGAACACAAGTTGCACTCTTC 57.644 40.909 1.81 0.00 38.30 2.87
42 43 4.989279 ATTGAACACAAGTTGCACTCTT 57.011 36.364 1.81 0.00 38.30 2.85
43 44 4.989279 AATTGAACACAAGTTGCACTCT 57.011 36.364 1.81 0.00 38.30 3.24
44 45 6.086765 CGATAAATTGAACACAAGTTGCACTC 59.913 38.462 1.81 0.00 38.30 3.51
45 46 5.914635 CGATAAATTGAACACAAGTTGCACT 59.085 36.000 1.81 0.00 38.30 4.40
46 47 5.685511 ACGATAAATTGAACACAAGTTGCAC 59.314 36.000 1.81 0.00 38.30 4.57
47 48 5.826586 ACGATAAATTGAACACAAGTTGCA 58.173 33.333 1.81 0.00 38.30 4.08
48 49 6.747659 AACGATAAATTGAACACAAGTTGC 57.252 33.333 1.81 0.00 38.30 4.17
76 77 9.905713 ACTCTTTTCTATTATGTGGCAATTAGA 57.094 29.630 0.00 0.00 0.00 2.10
79 80 9.643693 CAAACTCTTTTCTATTATGTGGCAATT 57.356 29.630 0.00 0.00 0.00 2.32
80 81 9.023962 TCAAACTCTTTTCTATTATGTGGCAAT 57.976 29.630 0.00 0.00 0.00 3.56
81 82 8.296713 GTCAAACTCTTTTCTATTATGTGGCAA 58.703 33.333 0.00 0.00 0.00 4.52
82 83 7.446931 TGTCAAACTCTTTTCTATTATGTGGCA 59.553 33.333 0.00 0.00 0.00 4.92
83 84 7.816640 TGTCAAACTCTTTTCTATTATGTGGC 58.183 34.615 0.00 0.00 0.00 5.01
93 94 9.574516 AGTGGTATTATTGTCAAACTCTTTTCT 57.425 29.630 0.00 0.00 0.00 2.52
94 95 9.827411 GAGTGGTATTATTGTCAAACTCTTTTC 57.173 33.333 4.70 0.00 32.09 2.29
95 96 8.793592 GGAGTGGTATTATTGTCAAACTCTTTT 58.206 33.333 9.88 0.00 34.58 2.27
96 97 7.393515 GGGAGTGGTATTATTGTCAAACTCTTT 59.606 37.037 9.88 0.00 34.58 2.52
97 98 6.884836 GGGAGTGGTATTATTGTCAAACTCTT 59.115 38.462 9.88 0.00 34.58 2.85
98 99 6.012858 TGGGAGTGGTATTATTGTCAAACTCT 60.013 38.462 9.88 0.00 34.58 3.24
99 100 6.093633 GTGGGAGTGGTATTATTGTCAAACTC 59.906 42.308 3.65 3.65 33.63 3.01
100 101 5.944007 GTGGGAGTGGTATTATTGTCAAACT 59.056 40.000 0.00 0.00 0.00 2.66
101 102 5.708230 TGTGGGAGTGGTATTATTGTCAAAC 59.292 40.000 0.00 0.00 0.00 2.93
102 103 5.882040 TGTGGGAGTGGTATTATTGTCAAA 58.118 37.500 0.00 0.00 0.00 2.69
103 104 5.506730 TGTGGGAGTGGTATTATTGTCAA 57.493 39.130 0.00 0.00 0.00 3.18
104 105 5.496556 CTTGTGGGAGTGGTATTATTGTCA 58.503 41.667 0.00 0.00 0.00 3.58
105 106 4.335594 GCTTGTGGGAGTGGTATTATTGTC 59.664 45.833 0.00 0.00 0.00 3.18
106 107 4.270008 GCTTGTGGGAGTGGTATTATTGT 58.730 43.478 0.00 0.00 0.00 2.71
107 108 3.632145 GGCTTGTGGGAGTGGTATTATTG 59.368 47.826 0.00 0.00 0.00 1.90
108 109 3.268334 TGGCTTGTGGGAGTGGTATTATT 59.732 43.478 0.00 0.00 0.00 1.40
109 110 2.849943 TGGCTTGTGGGAGTGGTATTAT 59.150 45.455 0.00 0.00 0.00 1.28
110 111 2.270858 TGGCTTGTGGGAGTGGTATTA 58.729 47.619 0.00 0.00 0.00 0.98
111 112 1.072266 TGGCTTGTGGGAGTGGTATT 58.928 50.000 0.00 0.00 0.00 1.89
112 113 1.298953 ATGGCTTGTGGGAGTGGTAT 58.701 50.000 0.00 0.00 0.00 2.73
113 114 1.004277 GAATGGCTTGTGGGAGTGGTA 59.996 52.381 0.00 0.00 0.00 3.25
114 115 0.251341 GAATGGCTTGTGGGAGTGGT 60.251 55.000 0.00 0.00 0.00 4.16
115 116 0.038744 AGAATGGCTTGTGGGAGTGG 59.961 55.000 0.00 0.00 0.00 4.00
116 117 1.815003 GAAGAATGGCTTGTGGGAGTG 59.185 52.381 0.00 0.00 36.83 3.51
117 118 1.272147 GGAAGAATGGCTTGTGGGAGT 60.272 52.381 0.00 0.00 36.83 3.85
118 119 1.005215 AGGAAGAATGGCTTGTGGGAG 59.995 52.381 0.00 0.00 36.83 4.30
119 120 1.075601 AGGAAGAATGGCTTGTGGGA 58.924 50.000 0.00 0.00 36.83 4.37
120 121 2.806945 TAGGAAGAATGGCTTGTGGG 57.193 50.000 0.00 0.00 36.83 4.61
121 122 3.955471 TCTTAGGAAGAATGGCTTGTGG 58.045 45.455 0.00 0.00 36.83 4.17
122 123 5.964958 TTTCTTAGGAAGAATGGCTTGTG 57.035 39.130 2.65 0.00 46.15 3.33
123 124 7.406104 AGTATTTCTTAGGAAGAATGGCTTGT 58.594 34.615 2.65 0.00 46.15 3.16
124 125 7.012799 GGAGTATTTCTTAGGAAGAATGGCTTG 59.987 40.741 2.65 0.00 46.15 4.01
125 126 7.057264 GGAGTATTTCTTAGGAAGAATGGCTT 58.943 38.462 2.65 0.00 46.15 4.35
126 127 6.409810 GGGAGTATTTCTTAGGAAGAATGGCT 60.410 42.308 2.65 2.14 46.15 4.75
127 128 5.765677 GGGAGTATTTCTTAGGAAGAATGGC 59.234 44.000 2.65 0.00 46.15 4.40
128 129 7.142995 AGGGAGTATTTCTTAGGAAGAATGG 57.857 40.000 2.65 0.00 46.15 3.16
129 130 7.147479 TGGAGGGAGTATTTCTTAGGAAGAATG 60.147 40.741 2.65 0.00 46.15 2.67
130 131 6.909158 TGGAGGGAGTATTTCTTAGGAAGAAT 59.091 38.462 2.65 0.00 46.15 2.40
131 132 6.269194 TGGAGGGAGTATTTCTTAGGAAGAA 58.731 40.000 0.00 0.00 45.30 2.52
132 133 5.850278 TGGAGGGAGTATTTCTTAGGAAGA 58.150 41.667 0.00 0.00 35.26 2.87
133 134 6.755542 ATGGAGGGAGTATTTCTTAGGAAG 57.244 41.667 0.00 0.00 32.61 3.46
134 135 7.406151 AGAAATGGAGGGAGTATTTCTTAGGAA 59.594 37.037 0.00 0.00 44.42 3.36
135 136 6.909158 AGAAATGGAGGGAGTATTTCTTAGGA 59.091 38.462 0.00 0.00 44.42 2.94
136 137 7.142995 AGAAATGGAGGGAGTATTTCTTAGG 57.857 40.000 0.00 0.00 44.42 2.69
143 144 9.799106 CACATATTTAGAAATGGAGGGAGTATT 57.201 33.333 0.00 0.00 0.00 1.89
144 145 8.949421 ACACATATTTAGAAATGGAGGGAGTAT 58.051 33.333 0.00 0.00 0.00 2.12
145 146 8.331931 ACACATATTTAGAAATGGAGGGAGTA 57.668 34.615 0.00 0.00 0.00 2.59
146 147 7.127955 AGACACATATTTAGAAATGGAGGGAGT 59.872 37.037 0.00 0.00 0.00 3.85
147 148 7.512992 AGACACATATTTAGAAATGGAGGGAG 58.487 38.462 0.00 0.00 0.00 4.30
148 149 7.451731 AGACACATATTTAGAAATGGAGGGA 57.548 36.000 0.00 0.00 0.00 4.20
149 150 8.525290 AAAGACACATATTTAGAAATGGAGGG 57.475 34.615 0.00 0.00 0.00 4.30
242 243 9.859152 TTCCAATGAACCACATATGAATGTATA 57.141 29.630 10.38 0.00 44.70 1.47
243 244 8.765488 TTCCAATGAACCACATATGAATGTAT 57.235 30.769 10.38 0.00 44.70 2.29
244 245 8.586879 TTTCCAATGAACCACATATGAATGTA 57.413 30.769 10.38 0.00 44.70 2.29
246 247 8.418662 AGATTTCCAATGAACCACATATGAATG 58.581 33.333 10.38 0.00 38.38 2.67
247 248 8.543293 AGATTTCCAATGAACCACATATGAAT 57.457 30.769 10.38 0.00 38.38 2.57
248 249 7.959658 AGATTTCCAATGAACCACATATGAA 57.040 32.000 10.38 0.00 38.38 2.57
249 250 7.835682 AGAAGATTTCCAATGAACCACATATGA 59.164 33.333 10.38 0.00 38.38 2.15
250 251 8.004087 AGAAGATTTCCAATGAACCACATATG 57.996 34.615 0.00 0.00 38.38 1.78
251 252 9.699410 TTAGAAGATTTCCAATGAACCACATAT 57.301 29.630 0.00 0.00 38.38 1.78
252 253 9.527157 TTTAGAAGATTTCCAATGAACCACATA 57.473 29.630 0.00 0.00 38.38 2.29
253 254 8.421249 TTTAGAAGATTTCCAATGAACCACAT 57.579 30.769 0.00 0.00 41.45 3.21
254 255 7.831691 TTTAGAAGATTTCCAATGAACCACA 57.168 32.000 0.00 0.00 0.00 4.17
255 256 8.576442 TCTTTTAGAAGATTTCCAATGAACCAC 58.424 33.333 0.00 0.00 36.99 4.16
256 257 8.704849 TCTTTTAGAAGATTTCCAATGAACCA 57.295 30.769 0.00 0.00 36.99 3.67
284 285 9.765795 CATCTACTCCCTTCGTTTCTAAATATT 57.234 33.333 0.00 0.00 0.00 1.28
285 286 8.925338 ACATCTACTCCCTTCGTTTCTAAATAT 58.075 33.333 0.00 0.00 0.00 1.28
286 287 8.195436 CACATCTACTCCCTTCGTTTCTAAATA 58.805 37.037 0.00 0.00 0.00 1.40
287 288 7.042335 CACATCTACTCCCTTCGTTTCTAAAT 58.958 38.462 0.00 0.00 0.00 1.40
288 289 6.014840 ACACATCTACTCCCTTCGTTTCTAAA 60.015 38.462 0.00 0.00 0.00 1.85
289 290 5.479375 ACACATCTACTCCCTTCGTTTCTAA 59.521 40.000 0.00 0.00 0.00 2.10
290 291 5.014858 ACACATCTACTCCCTTCGTTTCTA 58.985 41.667 0.00 0.00 0.00 2.10
291 292 3.833070 ACACATCTACTCCCTTCGTTTCT 59.167 43.478 0.00 0.00 0.00 2.52
292 293 4.189639 ACACATCTACTCCCTTCGTTTC 57.810 45.455 0.00 0.00 0.00 2.78
293 294 4.618920 AACACATCTACTCCCTTCGTTT 57.381 40.909 0.00 0.00 0.00 3.60
294 295 4.081807 GGTAACACATCTACTCCCTTCGTT 60.082 45.833 0.00 0.00 0.00 3.85
295 296 3.446516 GGTAACACATCTACTCCCTTCGT 59.553 47.826 0.00 0.00 0.00 3.85
296 297 3.181478 GGGTAACACATCTACTCCCTTCG 60.181 52.174 0.00 0.00 39.74 3.79
297 298 4.031611 AGGGTAACACATCTACTCCCTTC 58.968 47.826 0.00 0.00 40.56 3.46
298 299 3.775316 CAGGGTAACACATCTACTCCCTT 59.225 47.826 0.00 0.00 41.37 3.95
299 300 3.012502 TCAGGGTAACACATCTACTCCCT 59.987 47.826 0.00 0.00 43.70 4.20
300 301 3.371965 TCAGGGTAACACATCTACTCCC 58.628 50.000 0.00 0.00 39.74 4.30
301 302 5.615925 ATTCAGGGTAACACATCTACTCC 57.384 43.478 0.00 0.00 39.74 3.85
302 303 7.390718 ACAAAATTCAGGGTAACACATCTACTC 59.609 37.037 0.00 0.00 39.74 2.59
303 304 7.231467 ACAAAATTCAGGGTAACACATCTACT 58.769 34.615 0.00 0.00 39.74 2.57
304 305 7.448748 ACAAAATTCAGGGTAACACATCTAC 57.551 36.000 0.00 0.00 39.74 2.59
305 306 8.380099 AGTACAAAATTCAGGGTAACACATCTA 58.620 33.333 0.00 0.00 39.74 1.98
306 307 7.231467 AGTACAAAATTCAGGGTAACACATCT 58.769 34.615 0.00 0.00 39.74 2.90
307 308 7.448748 AGTACAAAATTCAGGGTAACACATC 57.551 36.000 0.00 0.00 39.74 3.06
308 309 8.927675 TTAGTACAAAATTCAGGGTAACACAT 57.072 30.769 0.00 0.00 39.74 3.21
309 310 8.749026 TTTAGTACAAAATTCAGGGTAACACA 57.251 30.769 0.00 0.00 39.74 3.72
315 316 9.143155 ACTTGATTTTAGTACAAAATTCAGGGT 57.857 29.630 13.58 12.04 33.57 4.34
316 317 9.410556 CACTTGATTTTAGTACAAAATTCAGGG 57.589 33.333 13.58 10.93 33.57 4.45
317 318 8.915654 GCACTTGATTTTAGTACAAAATTCAGG 58.084 33.333 13.58 13.91 34.56 3.86
318 319 9.683069 AGCACTTGATTTTAGTACAAAATTCAG 57.317 29.630 13.58 13.68 33.02 3.02
326 327 9.515226 AGGAAAATAGCACTTGATTTTAGTACA 57.485 29.630 0.00 0.00 35.82 2.90
329 330 7.814587 GCAAGGAAAATAGCACTTGATTTTAGT 59.185 33.333 7.38 0.00 42.07 2.24
330 331 7.008628 CGCAAGGAAAATAGCACTTGATTTTAG 59.991 37.037 7.38 0.00 42.07 1.85
331 332 6.806249 CGCAAGGAAAATAGCACTTGATTTTA 59.194 34.615 7.38 0.00 42.07 1.52
332 333 5.634859 CGCAAGGAAAATAGCACTTGATTTT 59.365 36.000 7.38 0.00 42.07 1.82
333 334 5.048083 TCGCAAGGAAAATAGCACTTGATTT 60.048 36.000 7.38 0.00 42.07 2.17
334 335 4.458989 TCGCAAGGAAAATAGCACTTGATT 59.541 37.500 7.38 0.00 42.07 2.57
335 336 4.009675 TCGCAAGGAAAATAGCACTTGAT 58.990 39.130 7.38 0.00 42.07 2.57
336 337 3.188460 GTCGCAAGGAAAATAGCACTTGA 59.812 43.478 7.38 0.00 42.07 3.02
337 338 3.189287 AGTCGCAAGGAAAATAGCACTTG 59.811 43.478 0.00 0.00 42.31 3.16
338 339 3.412386 AGTCGCAAGGAAAATAGCACTT 58.588 40.909 0.00 0.00 38.47 3.16
339 340 3.059352 AGTCGCAAGGAAAATAGCACT 57.941 42.857 0.00 0.00 38.47 4.40
340 341 3.831715 AAGTCGCAAGGAAAATAGCAC 57.168 42.857 0.00 0.00 38.47 4.40
341 342 4.846779 AAAAGTCGCAAGGAAAATAGCA 57.153 36.364 0.00 0.00 38.47 3.49
342 343 4.621460 GGAAAAAGTCGCAAGGAAAATAGC 59.379 41.667 0.00 0.00 38.47 2.97
343 344 5.768317 TGGAAAAAGTCGCAAGGAAAATAG 58.232 37.500 0.00 0.00 38.47 1.73
344 345 5.776173 TGGAAAAAGTCGCAAGGAAAATA 57.224 34.783 0.00 0.00 38.47 1.40
345 346 4.664150 TGGAAAAAGTCGCAAGGAAAAT 57.336 36.364 0.00 0.00 38.47 1.82
346 347 4.616953 GATGGAAAAAGTCGCAAGGAAAA 58.383 39.130 0.00 0.00 38.47 2.29
347 348 3.304391 CGATGGAAAAAGTCGCAAGGAAA 60.304 43.478 0.00 0.00 38.47 3.13
348 349 2.225491 CGATGGAAAAAGTCGCAAGGAA 59.775 45.455 0.00 0.00 38.47 3.36
349 350 1.804151 CGATGGAAAAAGTCGCAAGGA 59.196 47.619 0.00 0.00 38.47 3.36
350 351 2.247311 CGATGGAAAAAGTCGCAAGG 57.753 50.000 0.00 0.00 38.47 3.61
355 356 2.223144 TGTTGAGCGATGGAAAAAGTCG 59.777 45.455 0.00 0.00 38.34 4.18
356 357 3.896648 TGTTGAGCGATGGAAAAAGTC 57.103 42.857 0.00 0.00 0.00 3.01
357 358 3.243401 GGTTGTTGAGCGATGGAAAAAGT 60.243 43.478 0.00 0.00 0.00 2.66
358 359 3.243367 TGGTTGTTGAGCGATGGAAAAAG 60.243 43.478 0.00 0.00 0.00 2.27
359 360 2.690497 TGGTTGTTGAGCGATGGAAAAA 59.310 40.909 0.00 0.00 0.00 1.94
360 361 2.302260 TGGTTGTTGAGCGATGGAAAA 58.698 42.857 0.00 0.00 0.00 2.29
361 362 1.974265 TGGTTGTTGAGCGATGGAAA 58.026 45.000 0.00 0.00 0.00 3.13
362 363 2.083774 GATGGTTGTTGAGCGATGGAA 58.916 47.619 0.00 0.00 0.00 3.53
363 364 1.678728 GGATGGTTGTTGAGCGATGGA 60.679 52.381 0.00 0.00 0.00 3.41
364 365 0.734889 GGATGGTTGTTGAGCGATGG 59.265 55.000 0.00 0.00 0.00 3.51
365 366 0.734889 GGGATGGTTGTTGAGCGATG 59.265 55.000 0.00 0.00 0.00 3.84
369 370 0.038166 TCCAGGGATGGTTGTTGAGC 59.962 55.000 0.00 0.00 0.00 4.26
403 405 3.117512 AGTTTCAGTCATTTGTGGAGGGT 60.118 43.478 0.00 0.00 0.00 4.34
408 410 7.759433 ACTTGTTTTAGTTTCAGTCATTTGTGG 59.241 33.333 0.00 0.00 0.00 4.17
452 455 6.150140 CAGGAAAGAACATAAGAGGAAAGGTG 59.850 42.308 0.00 0.00 0.00 4.00
465 468 2.225117 CCCAAGGGACAGGAAAGAACAT 60.225 50.000 0.00 0.00 37.50 2.71
479 482 2.372264 CATCAGATGAACACCCAAGGG 58.628 52.381 4.11 2.91 42.03 3.95
486 489 5.050499 CGATTCTAAGGCATCAGATGAACAC 60.050 44.000 15.12 1.04 0.00 3.32
495 498 4.160439 AGTCACTTCGATTCTAAGGCATCA 59.840 41.667 3.33 0.00 0.00 3.07
509 512 1.933181 TGTGTTGCTTCAGTCACTTCG 59.067 47.619 0.00 0.00 0.00 3.79
571 574 2.618053 GCGTTGGTAACTACTGCATCT 58.382 47.619 0.00 0.00 40.40 2.90
752 757 4.204799 GGCCGGAAATTACTACATTCCTT 58.795 43.478 5.05 0.00 40.37 3.36
754 759 3.314357 GTGGCCGGAAATTACTACATTCC 59.686 47.826 5.05 0.00 39.38 3.01
755 760 3.001939 CGTGGCCGGAAATTACTACATTC 59.998 47.826 5.05 0.00 0.00 2.67
756 761 2.940410 CGTGGCCGGAAATTACTACATT 59.060 45.455 5.05 0.00 0.00 2.71
757 762 2.557317 CGTGGCCGGAAATTACTACAT 58.443 47.619 5.05 0.00 0.00 2.29
758 763 2.008045 GCGTGGCCGGAAATTACTACA 61.008 52.381 5.05 0.00 33.68 2.74
957 972 3.669251 AGCTGACAGTACCAAGAAGAC 57.331 47.619 3.99 0.00 0.00 3.01
979 997 0.109458 CTGTGACGCGGTACAGCTTA 60.109 55.000 24.97 0.00 38.01 3.09
980 998 1.372997 CTGTGACGCGGTACAGCTT 60.373 57.895 24.97 6.56 38.01 3.74
981 999 2.258591 CTGTGACGCGGTACAGCT 59.741 61.111 24.97 3.22 38.01 4.24
983 1001 1.446099 ATGCTGTGACGCGGTACAG 60.446 57.895 29.23 29.23 45.40 2.74
984 1002 1.736282 CATGCTGTGACGCGGTACA 60.736 57.895 12.47 14.24 0.00 2.90
985 1003 2.452813 CCATGCTGTGACGCGGTAC 61.453 63.158 12.47 9.75 0.00 3.34
986 1004 2.125713 CCATGCTGTGACGCGGTA 60.126 61.111 12.47 0.00 0.00 4.02
1065 1086 3.848301 AACATGGCGAGGCAGCACA 62.848 57.895 5.43 3.59 39.27 4.57
1142 1163 2.167487 GAGAGGTCCCACTTCAGATGAC 59.833 54.545 0.00 0.00 0.00 3.06
1143 1164 2.461695 GAGAGGTCCCACTTCAGATGA 58.538 52.381 0.00 0.00 0.00 2.92
1227 1248 2.820037 GCAACTAGCCGCACCTCC 60.820 66.667 0.00 0.00 37.23 4.30
1450 1471 1.290639 GATTCCCGGAGAGATCGGC 59.709 63.158 0.73 0.00 45.60 5.54
1455 1476 1.828660 GAGGCGATTCCCGGAGAGA 60.829 63.158 0.73 0.00 39.04 3.10
1795 1816 3.686726 AGAACGCAGATTGAAAGGATGAC 59.313 43.478 0.00 0.00 0.00 3.06
2338 2359 2.202932 CATGGACGCGGGGAAGAG 60.203 66.667 12.47 0.00 0.00 2.85
2678 2708 3.170672 AGCTCCAGCACCACCACA 61.171 61.111 0.48 0.00 45.16 4.17
2915 2945 4.554036 GCCTCCACCTCGGCCATC 62.554 72.222 2.24 0.00 40.43 3.51
3192 3496 7.872483 GGCAAATATAAACTTGTGATTATGGGG 59.128 37.037 0.00 0.00 0.00 4.96
3194 3498 9.985730 ATGGCAAATATAAACTTGTGATTATGG 57.014 29.630 0.00 0.00 0.00 2.74
3217 3523 5.531634 AGTAGCATCAACAACAACAAATGG 58.468 37.500 0.00 0.00 0.00 3.16
3312 3618 7.914346 GCATTTATTTCATCCACTGAGAAAGAG 59.086 37.037 0.00 0.00 35.05 2.85
3375 3685 0.042731 TGCCTAGTGTAGGGAGCCTT 59.957 55.000 2.19 0.00 46.32 4.35
3449 3759 2.010582 GCTGCCCGTGTGGTTTTTCA 62.011 55.000 0.00 0.00 36.04 2.69
3473 3783 2.143122 GAAGAGACATTTGTGCGGACA 58.857 47.619 5.33 5.33 0.00 4.02
3485 3795 1.197949 CAGAGCTTCGACGAAGAGACA 59.802 52.381 35.39 3.05 41.71 3.41
3506 3816 2.941415 GCATGAGTTTCCCGTGGAAGAT 60.941 50.000 0.00 0.13 43.06 2.40
3513 3823 1.679944 CCATGAGCATGAGTTTCCCGT 60.680 52.381 11.84 0.00 41.20 5.28
3515 3825 2.019984 GACCATGAGCATGAGTTTCCC 58.980 52.381 11.84 0.00 41.20 3.97
3609 3919 2.040278 AGAAAAGCACCAGTGATAGCCA 59.960 45.455 0.99 0.00 0.00 4.75
3611 3921 2.421424 CCAGAAAAGCACCAGTGATAGC 59.579 50.000 0.99 0.00 0.00 2.97
3652 3962 2.202851 CGCTTGCGCCAGAGAGAT 60.203 61.111 13.50 0.00 0.00 2.75
3902 4213 1.412079 TTTGGTGAATTGGCAGTGCT 58.588 45.000 16.11 0.00 0.00 4.40
3912 4223 9.574516 GGTATGAAGGATAGTATTTTGGTGAAT 57.425 33.333 0.00 0.00 0.00 2.57
3938 4249 5.416862 TGTATTGGCATACAAATGTAGCG 57.583 39.130 7.14 0.00 42.01 4.26
3964 4275 7.008901 CAGCATAAATTGTGTAGCATGTTTCAG 59.991 37.037 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.