Multiple sequence alignment - TraesCS3A01G126600

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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 TraesCS3A01G126600 chr3A 100.000 3398 0 0 1 3398 102117978 102114581 0.000000e+00 6276.0
1 TraesCS3A01G126600 chr3A 90.608 724 51 5 2634 3356 290434649 290435356 0.000000e+00 944.0
2 TraesCS3A01G126600 chr3A 96.618 414 14 0 2638 3051 102110502 102110089 0.000000e+00 688.0
3 TraesCS3A01G126600 chr3A 94.521 73 4 0 270 342 32884125 32884053 2.770000e-21 113.0
4 TraesCS3A01G126600 chr3A 94.828 58 2 1 16 73 729789717 729789661 4.670000e-14 89.8
5 TraesCS3A01G126600 chr3D 95.069 2170 101 5 469 2637 85063053 85060889 0.000000e+00 3410.0
6 TraesCS3A01G126600 chr3D 94.861 467 23 1 2637 3102 260990331 260989865 0.000000e+00 728.0
7 TraesCS3A01G126600 chr3D 93.478 414 27 0 2638 3051 260985542 260985129 1.730000e-172 616.0
8 TraesCS3A01G126600 chr3D 93.532 201 10 1 3156 3356 260989854 260989657 2.560000e-76 296.0
9 TraesCS3A01G126600 chr3D 91.584 202 5 5 72 269 85063241 85063048 5.590000e-68 268.0
10 TraesCS3A01G126600 chr3B 94.621 2175 83 8 469 2634 130648647 130646498 0.000000e+00 3338.0
11 TraesCS3A01G126600 chr3B 95.397 2042 73 6 599 2637 134276187 134274164 0.000000e+00 3230.0
12 TraesCS3A01G126600 chr3B 93.012 415 23 2 2637 3051 327054747 327054339 4.850000e-168 601.0
13 TraesCS3A01G126600 chr3B 92.857 196 9 3 72 264 134305030 134304837 2.580000e-71 279.0
14 TraesCS3A01G126600 chr3B 92.216 167 7 4 88 251 130648882 130648719 7.330000e-57 231.0
15 TraesCS3A01G126600 chr3B 93.333 75 5 0 268 342 250979870 250979796 9.970000e-21 111.0
16 TraesCS3A01G126600 chr6B 85.365 2125 233 40 469 2576 89694993 89697056 0.000000e+00 2130.0
17 TraesCS3A01G126600 chr6B 92.405 79 6 0 264 342 462907046 462907124 2.770000e-21 113.0
18 TraesCS3A01G126600 chrUn 88.831 1352 119 14 813 2153 114263530 114262200 0.000000e+00 1631.0
19 TraesCS3A01G126600 chrUn 83.371 445 65 7 2151 2591 114253139 114252700 1.470000e-108 403.0
20 TraesCS3A01G126600 chrUn 94.521 73 4 0 270 342 70790856 70790784 2.770000e-21 113.0
21 TraesCS3A01G126600 chrUn 93.151 73 5 0 270 342 70839776 70839704 1.290000e-19 108.0
22 TraesCS3A01G126600 chr6D 88.138 1214 130 12 1368 2576 38582618 38583822 0.000000e+00 1432.0
23 TraesCS3A01G126600 chr6D 82.965 904 103 25 485 1372 38576520 38577388 0.000000e+00 769.0
24 TraesCS3A01G126600 chr6D 88.596 228 25 1 2647 2873 194243783 194243556 3.340000e-70 276.0
25 TraesCS3A01G126600 chr6D 82.418 91 11 4 348 434 427749737 427749648 1.310000e-09 75.0
26 TraesCS3A01G126600 chr1B 89.281 765 78 2 2638 3398 464115138 464114374 0.000000e+00 955.0
27 TraesCS3A01G126600 chr1B 93.299 388 26 0 2638 3025 464110284 464109897 1.060000e-159 573.0
28 TraesCS3A01G126600 chr1B 86.802 197 23 1 3202 3398 207269279 207269472 2.050000e-52 217.0
29 TraesCS3A01G126600 chr2B 77.693 1309 253 30 1088 2372 760829824 760828531 0.000000e+00 763.0
30 TraesCS3A01G126600 chr2B 88.095 420 45 4 2636 3053 312197075 312196659 8.470000e-136 494.0
31 TraesCS3A01G126600 chr2B 94.667 75 4 0 268 342 676340084 676340010 2.140000e-22 117.0
32 TraesCS3A01G126600 chr2D 82.625 777 90 18 2636 3398 275944856 275945601 0.000000e+00 645.0
33 TraesCS3A01G126600 chr2D 78.444 951 176 22 1064 1998 620399297 620398360 8.120000e-166 593.0
34 TraesCS3A01G126600 chr1D 86.802 197 26 0 3202 3398 130610953 130611149 1.590000e-53 220.0
35 TraesCS3A01G126600 chr6A 94.521 73 4 0 270 342 578608531 578608459 2.770000e-21 113.0
36 TraesCS3A01G126600 chr2A 93.333 75 5 0 268 342 618983154 618983080 9.970000e-21 111.0
37 TraesCS3A01G126600 chr1A 89.286 84 7 2 270 352 556444459 556444541 1.670000e-18 104.0


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 TraesCS3A01G126600 chr3A 102114581 102117978 3397 True 6276.0 6276 100.0000 1 3398 1 chr3A.!!$R3 3397
1 TraesCS3A01G126600 chr3A 290434649 290435356 707 False 944.0 944 90.6080 2634 3356 1 chr3A.!!$F1 722
2 TraesCS3A01G126600 chr3D 85060889 85063241 2352 True 1839.0 3410 93.3265 72 2637 2 chr3D.!!$R2 2565
3 TraesCS3A01G126600 chr3D 260989657 260990331 674 True 512.0 728 94.1965 2637 3356 2 chr3D.!!$R3 719
4 TraesCS3A01G126600 chr3B 134274164 134276187 2023 True 3230.0 3230 95.3970 599 2637 1 chr3B.!!$R1 2038
5 TraesCS3A01G126600 chr3B 130646498 130648882 2384 True 1784.5 3338 93.4185 88 2634 2 chr3B.!!$R5 2546
6 TraesCS3A01G126600 chr6B 89694993 89697056 2063 False 2130.0 2130 85.3650 469 2576 1 chr6B.!!$F1 2107
7 TraesCS3A01G126600 chrUn 114262200 114263530 1330 True 1631.0 1631 88.8310 813 2153 1 chrUn.!!$R4 1340
8 TraesCS3A01G126600 chr6D 38582618 38583822 1204 False 1432.0 1432 88.1380 1368 2576 1 chr6D.!!$F2 1208
9 TraesCS3A01G126600 chr6D 38576520 38577388 868 False 769.0 769 82.9650 485 1372 1 chr6D.!!$F1 887
10 TraesCS3A01G126600 chr1B 464114374 464115138 764 True 955.0 955 89.2810 2638 3398 1 chr1B.!!$R2 760
11 TraesCS3A01G126600 chr2B 760828531 760829824 1293 True 763.0 763 77.6930 1088 2372 1 chr2B.!!$R3 1284
12 TraesCS3A01G126600 chr2D 275944856 275945601 745 False 645.0 645 82.6250 2636 3398 1 chr2D.!!$F1 762
13 TraesCS3A01G126600 chr2D 620398360 620399297 937 True 593.0 593 78.4440 1064 1998 1 chr2D.!!$R1 934

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
306 370 0.033366 ATGCGCTACGGTGATATGCA 59.967 50.0 9.73 0.0 35.10 3.96 F
439 503 0.099436 GAATTCAGGCCGCATGTCAC 59.901 55.0 4.73 0.0 0.00 3.67 F
448 512 0.249280 CCGCATGTCACCATAGCGTA 60.249 55.0 0.00 0.0 42.12 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 1261 0.323302 TGGCAGCACTGGTAATTCGA 59.677 50.0 0.00 0.0 0.00 3.71 R
2215 2315 0.885879 TACTCGTGGTCGTCAGCAAT 59.114 50.0 0.00 0.0 38.33 3.56 R
2517 2630 0.608130 CAGCTGGCTTTTAAACCCCC 59.392 55.0 5.57 0.0 0.00 5.40 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
20 21 3.110447 CCAACCCCAATCAAACAAGTG 57.890 47.619 0.00 0.00 0.00 3.16
21 22 2.224257 CCAACCCCAATCAAACAAGTGG 60.224 50.000 0.00 0.00 34.18 4.00
22 23 2.433970 CAACCCCAATCAAACAAGTGGT 59.566 45.455 0.00 0.00 32.49 4.16
23 24 2.038659 ACCCCAATCAAACAAGTGGTG 58.961 47.619 0.00 0.00 32.49 4.17
24 25 2.315176 CCCCAATCAAACAAGTGGTGA 58.685 47.619 0.00 0.00 32.49 4.02
25 26 2.697751 CCCCAATCAAACAAGTGGTGAA 59.302 45.455 0.00 0.00 32.49 3.18
26 27 3.133721 CCCCAATCAAACAAGTGGTGAAA 59.866 43.478 0.00 0.00 32.49 2.69
27 28 4.119136 CCCAATCAAACAAGTGGTGAAAC 58.881 43.478 0.00 0.00 32.49 2.78
28 29 3.796178 CCAATCAAACAAGTGGTGAAACG 59.204 43.478 0.00 0.00 38.12 3.60
29 30 4.420168 CAATCAAACAAGTGGTGAAACGT 58.580 39.130 0.00 0.00 38.12 3.99
30 31 3.479505 TCAAACAAGTGGTGAAACGTG 57.520 42.857 0.00 0.00 38.12 4.49
31 32 2.162608 TCAAACAAGTGGTGAAACGTGG 59.837 45.455 0.00 0.00 38.12 4.94
32 33 1.828979 AACAAGTGGTGAAACGTGGT 58.171 45.000 0.00 0.00 38.12 4.16
33 34 1.091537 ACAAGTGGTGAAACGTGGTG 58.908 50.000 0.00 0.00 38.12 4.17
34 35 0.380378 CAAGTGGTGAAACGTGGTGG 59.620 55.000 0.00 0.00 38.12 4.61
35 36 1.381165 AAGTGGTGAAACGTGGTGGC 61.381 55.000 0.00 0.00 38.12 5.01
36 37 2.897846 TGGTGAAACGTGGTGGCG 60.898 61.111 0.00 0.00 38.12 5.69
38 39 1.594836 GGTGAAACGTGGTGGCGTA 60.595 57.895 0.00 0.00 45.00 4.42
39 40 1.159098 GGTGAAACGTGGTGGCGTAA 61.159 55.000 0.00 0.00 45.00 3.18
40 41 0.656785 GTGAAACGTGGTGGCGTAAA 59.343 50.000 0.00 0.00 45.00 2.01
41 42 0.656785 TGAAACGTGGTGGCGTAAAC 59.343 50.000 0.00 0.00 45.00 2.01
42 43 0.939419 GAAACGTGGTGGCGTAAACT 59.061 50.000 0.00 0.00 45.00 2.66
43 44 1.331447 GAAACGTGGTGGCGTAAACTT 59.669 47.619 0.00 0.00 45.00 2.66
44 45 0.939419 AACGTGGTGGCGTAAACTTC 59.061 50.000 0.00 0.00 45.00 3.01
45 46 0.881600 ACGTGGTGGCGTAAACTTCC 60.882 55.000 0.00 0.00 43.83 3.46
46 47 1.571215 CGTGGTGGCGTAAACTTCCC 61.571 60.000 0.00 0.00 0.00 3.97
47 48 1.073548 TGGTGGCGTAAACTTCCCC 59.926 57.895 0.00 0.00 0.00 4.81
48 49 2.036571 GGTGGCGTAAACTTCCCCG 61.037 63.158 0.00 0.00 0.00 5.73
49 50 2.036571 GTGGCGTAAACTTCCCCGG 61.037 63.158 0.00 0.00 0.00 5.73
50 51 2.215625 TGGCGTAAACTTCCCCGGA 61.216 57.895 0.73 0.00 0.00 5.14
51 52 1.222661 GGCGTAAACTTCCCCGGAT 59.777 57.895 0.73 0.00 0.00 4.18
52 53 0.465287 GGCGTAAACTTCCCCGGATA 59.535 55.000 0.73 0.00 0.00 2.59
53 54 1.071228 GGCGTAAACTTCCCCGGATAT 59.929 52.381 0.73 0.00 0.00 1.63
54 55 2.299867 GGCGTAAACTTCCCCGGATATA 59.700 50.000 0.73 0.00 0.00 0.86
55 56 3.582780 GCGTAAACTTCCCCGGATATAG 58.417 50.000 0.73 0.00 0.00 1.31
56 57 3.615834 GCGTAAACTTCCCCGGATATAGG 60.616 52.174 0.73 0.00 0.00 2.57
63 64 1.991230 CCCGGATATAGGGGCTTGG 59.009 63.158 0.73 0.00 45.14 3.61
64 65 1.562672 CCCGGATATAGGGGCTTGGG 61.563 65.000 0.73 0.00 45.14 4.12
65 66 0.840722 CCGGATATAGGGGCTTGGGT 60.841 60.000 0.00 0.00 0.00 4.51
66 67 1.553884 CCGGATATAGGGGCTTGGGTA 60.554 57.143 0.00 0.00 0.00 3.69
67 68 2.478292 CGGATATAGGGGCTTGGGTAT 58.522 52.381 0.00 0.00 0.00 2.73
68 69 2.844348 CGGATATAGGGGCTTGGGTATT 59.156 50.000 0.00 0.00 0.00 1.89
69 70 3.370527 CGGATATAGGGGCTTGGGTATTG 60.371 52.174 0.00 0.00 0.00 1.90
70 71 3.053619 GGATATAGGGGCTTGGGTATTGG 60.054 52.174 0.00 0.00 0.00 3.16
207 212 7.094118 GGCACTAAAGAAAACCCAACATGTATA 60.094 37.037 0.00 0.00 0.00 1.47
265 329 2.640316 CCTGTCCCAGGCCTATTAAC 57.360 55.000 3.98 1.99 45.13 2.01
266 330 1.143073 CCTGTCCCAGGCCTATTAACC 59.857 57.143 3.98 0.00 45.13 2.85
267 331 1.843851 CTGTCCCAGGCCTATTAACCA 59.156 52.381 3.98 0.00 0.00 3.67
268 332 2.241176 CTGTCCCAGGCCTATTAACCAA 59.759 50.000 3.98 0.00 0.00 3.67
269 333 2.241176 TGTCCCAGGCCTATTAACCAAG 59.759 50.000 3.98 0.00 0.00 3.61
270 334 1.850345 TCCCAGGCCTATTAACCAAGG 59.150 52.381 3.98 0.00 35.86 3.61
271 335 1.850345 CCCAGGCCTATTAACCAAGGA 59.150 52.381 3.98 0.00 34.58 3.36
272 336 2.422945 CCCAGGCCTATTAACCAAGGAC 60.423 54.545 3.98 1.96 41.70 3.85
283 347 2.702093 CCAAGGACTGGGATCAGGT 58.298 57.895 0.00 0.00 44.99 4.00
284 348 0.254178 CCAAGGACTGGGATCAGGTG 59.746 60.000 0.00 0.00 44.99 4.00
285 349 1.279496 CAAGGACTGGGATCAGGTGA 58.721 55.000 0.00 0.00 44.99 4.02
286 350 1.065854 CAAGGACTGGGATCAGGTGAC 60.066 57.143 0.00 0.00 44.99 3.67
287 351 0.117140 AGGACTGGGATCAGGTGACA 59.883 55.000 0.00 0.00 44.99 3.58
288 352 1.207791 GGACTGGGATCAGGTGACAT 58.792 55.000 0.00 0.00 44.99 3.06
289 353 1.134280 GGACTGGGATCAGGTGACATG 60.134 57.143 0.00 0.00 44.99 3.21
290 354 0.254178 ACTGGGATCAGGTGACATGC 59.746 55.000 0.00 0.00 44.99 4.06
291 355 0.812811 CTGGGATCAGGTGACATGCG 60.813 60.000 0.00 0.00 37.36 4.73
292 356 2.182842 GGGATCAGGTGACATGCGC 61.183 63.158 0.00 0.00 0.00 6.09
293 357 1.153289 GGATCAGGTGACATGCGCT 60.153 57.895 9.73 0.00 0.00 5.92
294 358 0.104855 GGATCAGGTGACATGCGCTA 59.895 55.000 9.73 0.00 0.00 4.26
295 359 1.212616 GATCAGGTGACATGCGCTAC 58.787 55.000 9.73 0.00 0.00 3.58
296 360 0.528466 ATCAGGTGACATGCGCTACG 60.528 55.000 9.73 0.00 0.00 3.51
297 361 2.167219 CAGGTGACATGCGCTACGG 61.167 63.158 9.73 0.00 0.00 4.02
298 362 2.125673 GGTGACATGCGCTACGGT 60.126 61.111 9.73 0.57 0.00 4.83
299 363 2.452813 GGTGACATGCGCTACGGTG 61.453 63.158 9.73 2.33 0.00 4.94
300 364 1.445410 GTGACATGCGCTACGGTGA 60.445 57.895 9.73 0.00 0.00 4.02
301 365 0.806102 GTGACATGCGCTACGGTGAT 60.806 55.000 9.73 0.00 0.00 3.06
302 366 0.741915 TGACATGCGCTACGGTGATA 59.258 50.000 9.73 0.00 0.00 2.15
303 367 1.339929 TGACATGCGCTACGGTGATAT 59.660 47.619 9.73 0.00 0.00 1.63
304 368 1.721389 GACATGCGCTACGGTGATATG 59.279 52.381 9.73 2.68 0.00 1.78
305 369 0.439985 CATGCGCTACGGTGATATGC 59.560 55.000 9.73 0.00 0.00 3.14
306 370 0.033366 ATGCGCTACGGTGATATGCA 59.967 50.000 9.73 0.00 35.10 3.96
307 371 0.874175 TGCGCTACGGTGATATGCAC 60.874 55.000 9.73 0.00 46.98 4.57
317 381 1.003545 GTGATATGCACGGTGACATGC 60.004 52.381 20.67 15.09 42.40 4.06
318 382 0.233074 GATATGCACGGTGACATGCG 59.767 55.000 20.67 0.00 45.13 4.73
319 383 1.159713 ATATGCACGGTGACATGCGG 61.160 55.000 20.67 0.00 45.13 5.69
323 387 3.387091 ACGGTGACATGCGGCCTA 61.387 61.111 0.00 0.00 0.00 3.93
324 388 2.125310 CGGTGACATGCGGCCTAA 60.125 61.111 0.00 0.00 0.00 2.69
325 389 1.743623 CGGTGACATGCGGCCTAAA 60.744 57.895 0.00 0.00 0.00 1.85
326 390 1.095228 CGGTGACATGCGGCCTAAAT 61.095 55.000 0.00 0.00 0.00 1.40
327 391 1.102978 GGTGACATGCGGCCTAAATT 58.897 50.000 0.00 0.00 0.00 1.82
328 392 1.065551 GGTGACATGCGGCCTAAATTC 59.934 52.381 0.00 0.00 0.00 2.17
329 393 1.742831 GTGACATGCGGCCTAAATTCA 59.257 47.619 0.00 0.00 0.00 2.57
330 394 2.358898 GTGACATGCGGCCTAAATTCAT 59.641 45.455 0.00 0.00 0.00 2.57
331 395 3.563808 GTGACATGCGGCCTAAATTCATA 59.436 43.478 0.00 0.00 0.00 2.15
332 396 4.216257 GTGACATGCGGCCTAAATTCATAT 59.784 41.667 0.00 0.00 0.00 1.78
333 397 4.826733 TGACATGCGGCCTAAATTCATATT 59.173 37.500 0.00 0.00 0.00 1.28
334 398 5.301551 TGACATGCGGCCTAAATTCATATTT 59.698 36.000 0.00 0.00 37.68 1.40
335 399 6.488344 TGACATGCGGCCTAAATTCATATTTA 59.512 34.615 0.00 0.00 35.61 1.40
336 400 7.013750 TGACATGCGGCCTAAATTCATATTTAA 59.986 33.333 0.00 0.00 36.16 1.52
337 401 7.721402 ACATGCGGCCTAAATTCATATTTAAA 58.279 30.769 0.00 0.00 36.16 1.52
338 402 8.367156 ACATGCGGCCTAAATTCATATTTAAAT 58.633 29.630 5.89 5.89 36.16 1.40
339 403 9.853555 CATGCGGCCTAAATTCATATTTAAATA 57.146 29.630 10.27 10.27 36.16 1.40
373 437 8.958119 TTTTAGGGTTATCTTACTATGTGCTG 57.042 34.615 0.00 0.00 0.00 4.41
374 438 7.670605 TTAGGGTTATCTTACTATGTGCTGT 57.329 36.000 0.00 0.00 0.00 4.40
375 439 5.918608 AGGGTTATCTTACTATGTGCTGTG 58.081 41.667 0.00 0.00 0.00 3.66
376 440 5.661312 AGGGTTATCTTACTATGTGCTGTGA 59.339 40.000 0.00 0.00 0.00 3.58
377 441 6.156256 AGGGTTATCTTACTATGTGCTGTGAA 59.844 38.462 0.00 0.00 0.00 3.18
378 442 6.992715 GGGTTATCTTACTATGTGCTGTGAAT 59.007 38.462 0.00 0.00 0.00 2.57
379 443 8.148351 GGGTTATCTTACTATGTGCTGTGAATA 58.852 37.037 0.00 0.00 0.00 1.75
380 444 9.712305 GGTTATCTTACTATGTGCTGTGAATAT 57.288 33.333 0.00 0.00 0.00 1.28
382 446 7.664082 ATCTTACTATGTGCTGTGAATATGC 57.336 36.000 0.00 0.00 0.00 3.14
383 447 6.581712 TCTTACTATGTGCTGTGAATATGCA 58.418 36.000 0.00 0.00 0.00 3.96
384 448 7.219322 TCTTACTATGTGCTGTGAATATGCAT 58.781 34.615 3.79 3.79 39.00 3.96
385 449 5.684550 ACTATGTGCTGTGAATATGCATG 57.315 39.130 10.16 0.00 39.00 4.06
386 450 5.370679 ACTATGTGCTGTGAATATGCATGA 58.629 37.500 10.16 0.00 39.00 3.07
387 451 6.002082 ACTATGTGCTGTGAATATGCATGAT 58.998 36.000 10.16 0.00 39.00 2.45
388 452 5.784578 ATGTGCTGTGAATATGCATGATT 57.215 34.783 10.16 5.33 39.00 2.57
389 453 5.585820 TGTGCTGTGAATATGCATGATTT 57.414 34.783 10.16 0.00 39.00 2.17
390 454 5.968254 TGTGCTGTGAATATGCATGATTTT 58.032 33.333 10.16 0.00 39.00 1.82
391 455 6.399743 TGTGCTGTGAATATGCATGATTTTT 58.600 32.000 10.16 0.00 39.00 1.94
428 492 8.016497 TCGCAATGTTTAAATTTGAATTCAGG 57.984 30.769 8.41 0.00 0.00 3.86
429 493 6.737750 CGCAATGTTTAAATTTGAATTCAGGC 59.262 34.615 8.41 2.74 0.00 4.85
430 494 7.022979 GCAATGTTTAAATTTGAATTCAGGCC 58.977 34.615 8.41 0.00 0.00 5.19
431 495 6.966435 ATGTTTAAATTTGAATTCAGGCCG 57.034 33.333 8.41 0.00 0.00 6.13
432 496 4.688413 TGTTTAAATTTGAATTCAGGCCGC 59.312 37.500 8.41 0.00 0.00 6.53
433 497 4.527509 TTAAATTTGAATTCAGGCCGCA 57.472 36.364 8.41 0.00 0.00 5.69
434 498 3.615224 AAATTTGAATTCAGGCCGCAT 57.385 38.095 8.41 0.00 0.00 4.73
435 499 2.589798 ATTTGAATTCAGGCCGCATG 57.410 45.000 8.41 0.00 0.00 4.06
436 500 1.255882 TTTGAATTCAGGCCGCATGT 58.744 45.000 8.41 0.00 0.00 3.21
437 501 0.810648 TTGAATTCAGGCCGCATGTC 59.189 50.000 8.41 0.00 0.00 3.06
438 502 0.322366 TGAATTCAGGCCGCATGTCA 60.322 50.000 3.38 0.00 0.00 3.58
439 503 0.099436 GAATTCAGGCCGCATGTCAC 59.901 55.000 4.73 0.00 0.00 3.67
440 504 1.315257 AATTCAGGCCGCATGTCACC 61.315 55.000 4.73 0.00 0.00 4.02
441 505 2.482796 ATTCAGGCCGCATGTCACCA 62.483 55.000 4.73 0.00 0.00 4.17
442 506 2.438975 CAGGCCGCATGTCACCAT 60.439 61.111 0.00 0.00 0.00 3.55
443 507 1.153188 CAGGCCGCATGTCACCATA 60.153 57.895 0.00 0.00 0.00 2.74
444 508 1.146930 AGGCCGCATGTCACCATAG 59.853 57.895 0.00 0.00 0.00 2.23
445 509 2.546494 GGCCGCATGTCACCATAGC 61.546 63.158 0.00 0.00 0.00 2.97
446 510 2.885676 GCCGCATGTCACCATAGCG 61.886 63.158 0.00 0.00 42.70 4.26
447 511 1.521457 CCGCATGTCACCATAGCGT 60.521 57.895 0.00 0.00 42.12 5.07
448 512 0.249280 CCGCATGTCACCATAGCGTA 60.249 55.000 0.00 0.00 42.12 4.42
449 513 1.605457 CCGCATGTCACCATAGCGTAT 60.605 52.381 0.00 0.00 42.12 3.06
450 514 1.456923 CGCATGTCACCATAGCGTATG 59.543 52.381 0.00 0.00 40.48 2.39
451 515 2.483876 GCATGTCACCATAGCGTATGT 58.516 47.619 0.00 0.00 34.36 2.29
452 516 2.476619 GCATGTCACCATAGCGTATGTC 59.523 50.000 0.00 0.00 34.36 3.06
453 517 3.716601 CATGTCACCATAGCGTATGTCA 58.283 45.455 4.91 0.00 34.36 3.58
454 518 3.159353 TGTCACCATAGCGTATGTCAC 57.841 47.619 4.91 0.00 34.36 3.67
455 519 2.159156 TGTCACCATAGCGTATGTCACC 60.159 50.000 4.91 0.00 34.36 4.02
456 520 2.100916 GTCACCATAGCGTATGTCACCT 59.899 50.000 4.91 0.00 34.36 4.00
457 521 2.100749 TCACCATAGCGTATGTCACCTG 59.899 50.000 4.91 0.00 34.36 4.00
458 522 2.100749 CACCATAGCGTATGTCACCTGA 59.899 50.000 4.91 0.00 34.36 3.86
459 523 2.965831 ACCATAGCGTATGTCACCTGAT 59.034 45.455 4.91 0.00 34.36 2.90
460 524 3.005897 ACCATAGCGTATGTCACCTGATC 59.994 47.826 0.00 0.00 34.36 2.92
461 525 3.579709 CATAGCGTATGTCACCTGATCC 58.420 50.000 0.00 0.00 0.00 3.36
462 526 0.753262 AGCGTATGTCACCTGATCCC 59.247 55.000 0.00 0.00 0.00 3.85
463 527 0.464036 GCGTATGTCACCTGATCCCA 59.536 55.000 0.00 0.00 0.00 4.37
464 528 1.539065 GCGTATGTCACCTGATCCCAG 60.539 57.143 0.00 0.00 40.09 4.45
465 529 1.757118 CGTATGTCACCTGATCCCAGT 59.243 52.381 0.00 0.00 38.74 4.00
466 530 2.223829 CGTATGTCACCTGATCCCAGTC 60.224 54.545 0.00 0.00 38.74 3.51
467 531 1.207791 ATGTCACCTGATCCCAGTCC 58.792 55.000 0.00 0.00 38.74 3.85
476 540 1.496857 TGATCCCAGTCCAACCAAACA 59.503 47.619 0.00 0.00 0.00 2.83
562 629 1.344438 TCCTGCTGCTATACAATCCCG 59.656 52.381 0.00 0.00 0.00 5.14
585 652 4.415150 ACATGCCCTCCAGCCACG 62.415 66.667 0.00 0.00 0.00 4.94
607 674 2.470821 CTGTATCATTCCCGGTTCGTC 58.529 52.381 0.00 0.00 0.00 4.20
648 724 2.285368 AGCGAATCCCCACCTCCA 60.285 61.111 0.00 0.00 0.00 3.86
697 773 2.320781 GGAGCTGGATTACTGAGCCTA 58.679 52.381 0.00 0.00 33.94 3.93
707 783 6.066032 GGATTACTGAGCCTACTACTCTCTT 58.934 44.000 0.00 0.00 35.12 2.85
719 795 6.825721 CCTACTACTCTCTTTCGGGTTAGTTA 59.174 42.308 0.00 0.00 0.00 2.24
736 812 4.722361 AGTTATGTTCTTCGGTCTCTCC 57.278 45.455 0.00 0.00 0.00 3.71
841 917 1.591863 GGAGTGGCGTAATCGGAGC 60.592 63.158 0.00 0.00 37.56 4.70
884 966 2.364842 GCAGCAGAGGAGGGGAGA 60.365 66.667 0.00 0.00 0.00 3.71
965 1047 1.412079 TGCAACCTTCCAACAAGCAT 58.588 45.000 0.00 0.00 0.00 3.79
990 1073 7.769272 TTGTTGTTCTAAAAGAGCCAATTTG 57.231 32.000 0.00 0.00 0.00 2.32
1172 1261 0.606401 CCGATGGAGGTTGCAGTTGT 60.606 55.000 0.00 0.00 0.00 3.32
1254 1343 3.561213 CTGATGCGTGCCAGCTCG 61.561 66.667 9.56 9.56 38.13 5.03
1362 1451 4.259356 CATCTGAATCTGCTGGTGAAAGA 58.741 43.478 0.00 0.00 0.00 2.52
1498 1587 4.338879 TGATGAGAGATCCGAGATGCATA 58.661 43.478 0.00 0.00 0.00 3.14
1499 1588 4.954826 TGATGAGAGATCCGAGATGCATAT 59.045 41.667 0.00 0.00 0.00 1.78
1559 1648 2.703409 GTGATCACCATCGCGCAC 59.297 61.111 15.31 0.00 29.89 5.34
1600 1689 4.759693 TGAAACAGGTGCCTTATGTAAGTG 59.240 41.667 0.00 0.00 0.00 3.16
1612 1701 6.538742 GCCTTATGTAAGTGCATTTACTCTCA 59.461 38.462 26.37 11.70 35.16 3.27
1690 1788 2.103432 TGCGACACTACCTCCAGAAAAA 59.897 45.455 0.00 0.00 0.00 1.94
1856 1956 9.362539 CTTGTACAAAGACGGTAAGTTATATGT 57.637 33.333 10.03 0.00 0.00 2.29
1881 1981 6.421485 AGTGACATTGCTAGGAGAAATTCAT 58.579 36.000 0.00 0.00 0.00 2.57
1929 2029 6.002082 GGTCACAACAAAGGTAATTAGAGGT 58.998 40.000 0.00 0.00 0.00 3.85
1989 2089 0.625683 AGGCTCCATGTGGGGATCTT 60.626 55.000 2.32 0.00 38.16 2.40
2067 2167 4.436050 GCAACACATGTGCACTATACTGAC 60.436 45.833 25.68 0.00 0.00 3.51
2106 2206 6.959639 AAAGTTGAGACTATGGCTGAAAAA 57.040 33.333 0.00 0.00 34.21 1.94
2186 2286 5.008415 CACTTTGTCTCAGTGCTGAAGAATT 59.992 40.000 3.36 0.00 39.39 2.17
2215 2315 1.139256 TGAAGGCAAACACCGTCTACA 59.861 47.619 0.00 0.00 38.81 2.74
2378 2481 3.074412 CCAGTCTTACAAAACCGCATCT 58.926 45.455 0.00 0.00 0.00 2.90
2468 2580 9.541143 GAAAATGTTTTGTATGGAAGGAAAAGA 57.459 29.630 0.00 0.00 0.00 2.52
2510 2623 5.860941 TTTTGAGGAAATTACAGTTGGCA 57.139 34.783 0.00 0.00 0.00 4.92
2517 2630 4.378459 GGAAATTACAGTTGGCAAGAGTCG 60.378 45.833 0.00 0.00 0.00 4.18
2584 2698 4.519540 TCCTTTGTTGCTTAAGATTGGC 57.480 40.909 6.67 0.00 0.00 4.52
2661 2775 1.694856 GGACAGGTATTGGGGGCAA 59.305 57.895 0.00 0.00 0.00 4.52
2775 2890 4.336280 GCCAAGAAGTCCAAGTTTATCCT 58.664 43.478 0.00 0.00 0.00 3.24
2779 2894 7.394816 CCAAGAAGTCCAAGTTTATCCTTAGA 58.605 38.462 0.00 0.00 0.00 2.10
2854 2969 4.875536 GGTTTGCTTTCCAAGTTTTGTGAT 59.124 37.500 0.00 0.00 34.34 3.06
2855 2970 6.045955 GGTTTGCTTTCCAAGTTTTGTGATA 58.954 36.000 0.00 0.00 34.34 2.15
3070 3189 4.877773 ACATCTTGGTATCAGAGAGGACT 58.122 43.478 6.78 0.00 0.00 3.85
3093 3212 2.124507 CTCGACCACCCACCACCAAT 62.125 60.000 0.00 0.00 0.00 3.16
3150 3273 7.781324 ACCTAGAATCAATGTTGTCCAATTT 57.219 32.000 0.00 0.00 0.00 1.82
3151 3274 8.193953 ACCTAGAATCAATGTTGTCCAATTTT 57.806 30.769 0.00 0.00 0.00 1.82
3152 3275 8.650490 ACCTAGAATCAATGTTGTCCAATTTTT 58.350 29.630 0.00 0.00 0.00 1.94
3186 3310 1.625818 CCTGACCTCAAAGCACTACCT 59.374 52.381 0.00 0.00 0.00 3.08
3190 3314 2.300437 GACCTCAAAGCACTACCTGAGT 59.700 50.000 0.00 0.00 39.82 3.41
3317 3448 3.198409 TGAGATTGACAACACAGCTGT 57.802 42.857 15.25 15.25 0.00 4.40
3342 3473 4.332637 GCACTGGCTGCACCGTTG 62.333 66.667 0.50 0.00 46.29 4.10
3361 3492 2.901042 CCTACAGGGAGGAACGGC 59.099 66.667 0.00 0.00 39.15 5.68
3385 3516 2.301346 CTGCTCCAAAGTTCCACAAGT 58.699 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.433970 CACCACTTGTTTGATTGGGGTT 59.566 45.455 0.00 0.00 33.00 4.11
3 4 2.038659 CACCACTTGTTTGATTGGGGT 58.961 47.619 0.00 0.00 33.00 4.95
4 5 2.315176 TCACCACTTGTTTGATTGGGG 58.685 47.619 0.00 0.00 33.40 4.96
5 6 4.119136 GTTTCACCACTTGTTTGATTGGG 58.881 43.478 0.00 0.00 33.00 4.12
6 7 3.796178 CGTTTCACCACTTGTTTGATTGG 59.204 43.478 0.00 0.00 35.06 3.16
7 8 4.265085 CACGTTTCACCACTTGTTTGATTG 59.735 41.667 0.00 0.00 0.00 2.67
8 9 4.420168 CACGTTTCACCACTTGTTTGATT 58.580 39.130 0.00 0.00 0.00 2.57
9 10 3.181491 CCACGTTTCACCACTTGTTTGAT 60.181 43.478 0.00 0.00 0.00 2.57
10 11 2.162608 CCACGTTTCACCACTTGTTTGA 59.837 45.455 0.00 0.00 0.00 2.69
11 12 2.094957 ACCACGTTTCACCACTTGTTTG 60.095 45.455 0.00 0.00 0.00 2.93
12 13 2.094957 CACCACGTTTCACCACTTGTTT 60.095 45.455 0.00 0.00 0.00 2.83
13 14 1.470890 CACCACGTTTCACCACTTGTT 59.529 47.619 0.00 0.00 0.00 2.83
14 15 1.091537 CACCACGTTTCACCACTTGT 58.908 50.000 0.00 0.00 0.00 3.16
15 16 0.380378 CCACCACGTTTCACCACTTG 59.620 55.000 0.00 0.00 0.00 3.16
16 17 1.381165 GCCACCACGTTTCACCACTT 61.381 55.000 0.00 0.00 0.00 3.16
17 18 1.822186 GCCACCACGTTTCACCACT 60.822 57.895 0.00 0.00 0.00 4.00
18 19 2.719354 GCCACCACGTTTCACCAC 59.281 61.111 0.00 0.00 0.00 4.16
19 20 2.307611 TACGCCACCACGTTTCACCA 62.308 55.000 0.00 0.00 45.75 4.17
20 21 1.159098 TTACGCCACCACGTTTCACC 61.159 55.000 0.00 0.00 45.75 4.02
21 22 0.656785 TTTACGCCACCACGTTTCAC 59.343 50.000 0.00 0.00 45.75 3.18
22 23 0.656785 GTTTACGCCACCACGTTTCA 59.343 50.000 0.00 0.00 45.75 2.69
23 24 0.939419 AGTTTACGCCACCACGTTTC 59.061 50.000 0.00 0.00 45.75 2.78
24 25 1.331447 GAAGTTTACGCCACCACGTTT 59.669 47.619 0.00 0.00 45.75 3.60
25 26 0.939419 GAAGTTTACGCCACCACGTT 59.061 50.000 0.00 0.00 45.75 3.99
27 28 1.571215 GGGAAGTTTACGCCACCACG 61.571 60.000 0.00 0.00 39.50 4.94
28 29 1.239296 GGGGAAGTTTACGCCACCAC 61.239 60.000 0.00 0.00 39.61 4.16
29 30 1.073548 GGGGAAGTTTACGCCACCA 59.926 57.895 0.00 0.00 39.61 4.17
30 31 2.036571 CGGGGAAGTTTACGCCACC 61.037 63.158 0.00 0.00 39.78 4.61
31 32 2.036571 CCGGGGAAGTTTACGCCAC 61.037 63.158 0.00 0.00 39.78 5.01
32 33 1.555477 ATCCGGGGAAGTTTACGCCA 61.555 55.000 0.00 0.00 39.78 5.69
33 34 0.465287 TATCCGGGGAAGTTTACGCC 59.535 55.000 0.00 0.00 37.07 5.68
34 35 2.538512 ATATCCGGGGAAGTTTACGC 57.461 50.000 0.00 0.00 0.00 4.42
35 36 3.056322 CCCTATATCCGGGGAAGTTTACG 60.056 52.174 0.00 0.00 45.18 3.18
36 37 4.548451 CCCTATATCCGGGGAAGTTTAC 57.452 50.000 0.00 0.00 45.18 2.01
45 46 1.562672 CCCAAGCCCCTATATCCGGG 61.563 65.000 0.00 3.08 42.82 5.73
46 47 0.840722 ACCCAAGCCCCTATATCCGG 60.841 60.000 0.00 0.00 0.00 5.14
47 48 1.946984 TACCCAAGCCCCTATATCCG 58.053 55.000 0.00 0.00 0.00 4.18
48 49 3.053619 CCAATACCCAAGCCCCTATATCC 60.054 52.174 0.00 0.00 0.00 2.59
49 50 3.591977 ACCAATACCCAAGCCCCTATATC 59.408 47.826 0.00 0.00 0.00 1.63
50 51 3.620195 ACCAATACCCAAGCCCCTATAT 58.380 45.455 0.00 0.00 0.00 0.86
51 52 3.083573 ACCAATACCCAAGCCCCTATA 57.916 47.619 0.00 0.00 0.00 1.31
52 53 1.921352 ACCAATACCCAAGCCCCTAT 58.079 50.000 0.00 0.00 0.00 2.57
53 54 1.286553 CAACCAATACCCAAGCCCCTA 59.713 52.381 0.00 0.00 0.00 3.53
54 55 0.041090 CAACCAATACCCAAGCCCCT 59.959 55.000 0.00 0.00 0.00 4.79
55 56 0.975556 CCAACCAATACCCAAGCCCC 60.976 60.000 0.00 0.00 0.00 5.80
56 57 0.040499 TCCAACCAATACCCAAGCCC 59.960 55.000 0.00 0.00 0.00 5.19
57 58 1.272480 ACTCCAACCAATACCCAAGCC 60.272 52.381 0.00 0.00 0.00 4.35
58 59 2.215942 ACTCCAACCAATACCCAAGC 57.784 50.000 0.00 0.00 0.00 4.01
59 60 3.761897 TCAACTCCAACCAATACCCAAG 58.238 45.455 0.00 0.00 0.00 3.61
60 61 3.885976 TCAACTCCAACCAATACCCAA 57.114 42.857 0.00 0.00 0.00 4.12
61 62 3.492337 GTTCAACTCCAACCAATACCCA 58.508 45.455 0.00 0.00 0.00 4.51
62 63 2.486592 CGTTCAACTCCAACCAATACCC 59.513 50.000 0.00 0.00 0.00 3.69
63 64 3.143728 ACGTTCAACTCCAACCAATACC 58.856 45.455 0.00 0.00 0.00 2.73
64 65 4.823790 AACGTTCAACTCCAACCAATAC 57.176 40.909 0.00 0.00 0.00 1.89
65 66 5.127491 AGAAACGTTCAACTCCAACCAATA 58.873 37.500 0.00 0.00 0.00 1.90
66 67 3.951680 AGAAACGTTCAACTCCAACCAAT 59.048 39.130 0.00 0.00 0.00 3.16
67 68 3.349022 AGAAACGTTCAACTCCAACCAA 58.651 40.909 0.00 0.00 0.00 3.67
68 69 2.993937 AGAAACGTTCAACTCCAACCA 58.006 42.857 0.00 0.00 0.00 3.67
69 70 4.025145 CACTAGAAACGTTCAACTCCAACC 60.025 45.833 0.00 0.00 0.00 3.77
70 71 4.807304 TCACTAGAAACGTTCAACTCCAAC 59.193 41.667 0.00 0.00 0.00 3.77
214 219 2.672195 GCCCTTGCCGAAATGAAAGAAG 60.672 50.000 0.00 0.00 0.00 2.85
215 220 1.272212 GCCCTTGCCGAAATGAAAGAA 59.728 47.619 0.00 0.00 0.00 2.52
263 327 0.995024 CCTGATCCCAGTCCTTGGTT 59.005 55.000 0.00 0.00 46.25 3.67
264 328 0.178861 ACCTGATCCCAGTCCTTGGT 60.179 55.000 0.00 0.00 46.25 3.67
266 330 1.065854 GTCACCTGATCCCAGTCCTTG 60.066 57.143 0.00 0.00 38.74 3.61
267 331 1.280457 GTCACCTGATCCCAGTCCTT 58.720 55.000 0.00 0.00 38.74 3.36
268 332 0.117140 TGTCACCTGATCCCAGTCCT 59.883 55.000 0.00 0.00 38.74 3.85
269 333 1.134280 CATGTCACCTGATCCCAGTCC 60.134 57.143 0.00 0.00 38.74 3.85
270 334 1.745141 GCATGTCACCTGATCCCAGTC 60.745 57.143 0.00 0.00 38.74 3.51
271 335 0.254178 GCATGTCACCTGATCCCAGT 59.746 55.000 0.00 0.00 38.74 4.00
272 336 0.812811 CGCATGTCACCTGATCCCAG 60.813 60.000 0.00 0.00 40.09 4.45
273 337 1.221566 CGCATGTCACCTGATCCCA 59.778 57.895 0.00 0.00 0.00 4.37
274 338 2.182842 GCGCATGTCACCTGATCCC 61.183 63.158 0.30 0.00 0.00 3.85
275 339 0.104855 TAGCGCATGTCACCTGATCC 59.895 55.000 11.47 0.00 0.00 3.36
276 340 1.212616 GTAGCGCATGTCACCTGATC 58.787 55.000 11.47 0.00 0.00 2.92
277 341 0.528466 CGTAGCGCATGTCACCTGAT 60.528 55.000 11.47 0.00 0.00 2.90
278 342 1.153842 CGTAGCGCATGTCACCTGA 60.154 57.895 11.47 0.00 0.00 3.86
279 343 2.167219 CCGTAGCGCATGTCACCTG 61.167 63.158 11.47 0.00 0.00 4.00
280 344 2.184322 CCGTAGCGCATGTCACCT 59.816 61.111 11.47 0.00 0.00 4.00
281 345 2.125673 ACCGTAGCGCATGTCACC 60.126 61.111 11.47 0.00 0.00 4.02
282 346 0.806102 ATCACCGTAGCGCATGTCAC 60.806 55.000 11.47 0.00 0.00 3.67
283 347 0.741915 TATCACCGTAGCGCATGTCA 59.258 50.000 11.47 0.00 0.00 3.58
284 348 1.721389 CATATCACCGTAGCGCATGTC 59.279 52.381 11.47 0.00 0.00 3.06
285 349 1.783284 CATATCACCGTAGCGCATGT 58.217 50.000 11.47 0.00 0.00 3.21
286 350 0.439985 GCATATCACCGTAGCGCATG 59.560 55.000 11.47 1.68 0.00 4.06
287 351 0.033366 TGCATATCACCGTAGCGCAT 59.967 50.000 11.47 0.00 0.00 4.73
288 352 0.874175 GTGCATATCACCGTAGCGCA 60.874 55.000 11.47 0.00 39.79 6.09
289 353 1.853319 GTGCATATCACCGTAGCGC 59.147 57.895 0.00 0.00 39.79 5.92
290 354 1.275471 CCGTGCATATCACCGTAGCG 61.275 60.000 0.00 0.00 42.69 4.26
291 355 0.249322 ACCGTGCATATCACCGTAGC 60.249 55.000 0.00 0.00 42.69 3.58
292 356 1.066454 TCACCGTGCATATCACCGTAG 59.934 52.381 0.00 0.00 42.69 3.51
293 357 1.104630 TCACCGTGCATATCACCGTA 58.895 50.000 0.00 0.00 42.69 4.02
294 358 0.459585 GTCACCGTGCATATCACCGT 60.460 55.000 0.00 0.00 42.69 4.83
295 359 0.459411 TGTCACCGTGCATATCACCG 60.459 55.000 0.00 0.00 42.69 4.94
296 360 1.599071 CATGTCACCGTGCATATCACC 59.401 52.381 7.75 0.00 42.69 4.02
305 369 3.657448 TAGGCCGCATGTCACCGTG 62.657 63.158 0.00 0.00 0.00 4.94
306 370 2.457743 TTTAGGCCGCATGTCACCGT 62.458 55.000 0.00 0.00 0.00 4.83
307 371 1.095228 ATTTAGGCCGCATGTCACCG 61.095 55.000 0.00 0.00 0.00 4.94
308 372 1.065551 GAATTTAGGCCGCATGTCACC 59.934 52.381 0.00 0.00 0.00 4.02
309 373 1.742831 TGAATTTAGGCCGCATGTCAC 59.257 47.619 0.00 0.00 0.00 3.67
310 374 2.121291 TGAATTTAGGCCGCATGTCA 57.879 45.000 0.00 0.00 0.00 3.58
311 375 5.376854 AATATGAATTTAGGCCGCATGTC 57.623 39.130 0.00 0.00 0.00 3.06
312 376 5.789643 AAATATGAATTTAGGCCGCATGT 57.210 34.783 0.00 0.00 33.45 3.21
313 377 8.761575 ATTTAAATATGAATTTAGGCCGCATG 57.238 30.769 0.00 0.00 38.48 4.06
347 411 9.391006 CAGCACATAGTAAGATAACCCTAAAAA 57.609 33.333 0.00 0.00 0.00 1.94
348 412 8.545472 ACAGCACATAGTAAGATAACCCTAAAA 58.455 33.333 0.00 0.00 0.00 1.52
349 413 7.985184 CACAGCACATAGTAAGATAACCCTAAA 59.015 37.037 0.00 0.00 0.00 1.85
350 414 7.343574 TCACAGCACATAGTAAGATAACCCTAA 59.656 37.037 0.00 0.00 0.00 2.69
351 415 6.837048 TCACAGCACATAGTAAGATAACCCTA 59.163 38.462 0.00 0.00 0.00 3.53
352 416 5.661312 TCACAGCACATAGTAAGATAACCCT 59.339 40.000 0.00 0.00 0.00 4.34
353 417 5.914033 TCACAGCACATAGTAAGATAACCC 58.086 41.667 0.00 0.00 0.00 4.11
354 418 9.712305 ATATTCACAGCACATAGTAAGATAACC 57.288 33.333 0.00 0.00 0.00 2.85
356 420 9.208022 GCATATTCACAGCACATAGTAAGATAA 57.792 33.333 0.00 0.00 0.00 1.75
357 421 8.367156 TGCATATTCACAGCACATAGTAAGATA 58.633 33.333 0.00 0.00 32.55 1.98
358 422 7.219322 TGCATATTCACAGCACATAGTAAGAT 58.781 34.615 0.00 0.00 32.55 2.40
359 423 6.581712 TGCATATTCACAGCACATAGTAAGA 58.418 36.000 0.00 0.00 32.55 2.10
360 424 6.849588 TGCATATTCACAGCACATAGTAAG 57.150 37.500 0.00 0.00 32.55 2.34
361 425 6.991531 TCATGCATATTCACAGCACATAGTAA 59.008 34.615 0.00 0.00 41.60 2.24
362 426 6.523840 TCATGCATATTCACAGCACATAGTA 58.476 36.000 0.00 0.00 41.60 1.82
363 427 5.370679 TCATGCATATTCACAGCACATAGT 58.629 37.500 0.00 0.00 41.60 2.12
364 428 5.934935 TCATGCATATTCACAGCACATAG 57.065 39.130 0.00 0.00 41.60 2.23
365 429 6.887626 AATCATGCATATTCACAGCACATA 57.112 33.333 0.00 0.00 41.60 2.29
366 430 5.784578 AATCATGCATATTCACAGCACAT 57.215 34.783 0.00 0.00 41.60 3.21
367 431 5.585820 AAATCATGCATATTCACAGCACA 57.414 34.783 0.00 0.00 41.60 4.57
368 432 6.897259 AAAAATCATGCATATTCACAGCAC 57.103 33.333 0.00 0.00 41.60 4.40
402 466 8.658609 CCTGAATTCAAATTTAAACATTGCGAT 58.341 29.630 9.88 5.26 0.00 4.58
403 467 7.359933 GCCTGAATTCAAATTTAAACATTGCGA 60.360 33.333 9.88 3.66 0.00 5.10
404 468 6.737750 GCCTGAATTCAAATTTAAACATTGCG 59.262 34.615 9.88 0.00 0.00 4.85
405 469 7.022979 GGCCTGAATTCAAATTTAAACATTGC 58.977 34.615 9.88 0.00 0.00 3.56
406 470 7.235777 CGGCCTGAATTCAAATTTAAACATTG 58.764 34.615 9.88 8.56 0.00 2.82
407 471 6.128309 GCGGCCTGAATTCAAATTTAAACATT 60.128 34.615 9.88 0.00 0.00 2.71
408 472 5.351189 GCGGCCTGAATTCAAATTTAAACAT 59.649 36.000 9.88 0.00 0.00 2.71
409 473 4.688413 GCGGCCTGAATTCAAATTTAAACA 59.312 37.500 9.88 0.00 0.00 2.83
410 474 4.688413 TGCGGCCTGAATTCAAATTTAAAC 59.312 37.500 9.88 0.00 0.00 2.01
411 475 4.887748 TGCGGCCTGAATTCAAATTTAAA 58.112 34.783 9.88 0.00 0.00 1.52
412 476 4.527509 TGCGGCCTGAATTCAAATTTAA 57.472 36.364 9.88 0.00 0.00 1.52
413 477 4.081752 ACATGCGGCCTGAATTCAAATTTA 60.082 37.500 12.29 0.00 0.00 1.40
414 478 3.264104 CATGCGGCCTGAATTCAAATTT 58.736 40.909 9.88 0.00 0.00 1.82
415 479 2.234414 ACATGCGGCCTGAATTCAAATT 59.766 40.909 12.29 0.00 0.00 1.82
416 480 1.826720 ACATGCGGCCTGAATTCAAAT 59.173 42.857 12.29 0.00 0.00 2.32
417 481 1.202114 GACATGCGGCCTGAATTCAAA 59.798 47.619 12.29 0.00 0.00 2.69
418 482 0.810648 GACATGCGGCCTGAATTCAA 59.189 50.000 12.29 0.00 0.00 2.69
419 483 0.322366 TGACATGCGGCCTGAATTCA 60.322 50.000 12.29 8.12 0.00 2.57
420 484 0.099436 GTGACATGCGGCCTGAATTC 59.901 55.000 12.29 0.00 0.00 2.17
421 485 1.315257 GGTGACATGCGGCCTGAATT 61.315 55.000 12.29 0.00 0.00 2.17
422 486 1.750399 GGTGACATGCGGCCTGAAT 60.750 57.895 12.29 0.00 0.00 2.57
423 487 2.359850 GGTGACATGCGGCCTGAA 60.360 61.111 12.29 0.00 0.00 3.02
424 488 3.635191 TGGTGACATGCGGCCTGA 61.635 61.111 12.29 0.00 33.40 3.86
435 499 2.100916 AGGTGACATACGCTATGGTGAC 59.899 50.000 0.00 0.00 40.47 3.67
436 500 2.100749 CAGGTGACATACGCTATGGTGA 59.899 50.000 0.00 0.00 40.47 4.02
437 501 2.100749 TCAGGTGACATACGCTATGGTG 59.899 50.000 9.00 0.00 40.47 4.17
438 502 2.384828 TCAGGTGACATACGCTATGGT 58.615 47.619 9.00 0.00 40.47 3.55
439 503 3.579709 GATCAGGTGACATACGCTATGG 58.420 50.000 9.00 0.00 40.47 2.74
440 504 3.579709 GGATCAGGTGACATACGCTATG 58.420 50.000 0.00 4.20 41.88 2.23
441 505 2.563179 GGGATCAGGTGACATACGCTAT 59.437 50.000 0.00 0.00 0.00 2.97
442 506 1.961394 GGGATCAGGTGACATACGCTA 59.039 52.381 0.00 0.00 0.00 4.26
443 507 0.753262 GGGATCAGGTGACATACGCT 59.247 55.000 0.00 0.00 0.00 5.07
444 508 0.464036 TGGGATCAGGTGACATACGC 59.536 55.000 0.00 0.00 0.00 4.42
445 509 1.757118 ACTGGGATCAGGTGACATACG 59.243 52.381 0.00 0.00 44.99 3.06
446 510 2.103263 GGACTGGGATCAGGTGACATAC 59.897 54.545 0.00 0.00 44.99 2.39
447 511 2.292851 TGGACTGGGATCAGGTGACATA 60.293 50.000 0.00 0.00 44.99 2.29
448 512 1.207791 GGACTGGGATCAGGTGACAT 58.792 55.000 0.00 0.00 44.99 3.06
449 513 0.178906 TGGACTGGGATCAGGTGACA 60.179 55.000 0.00 0.00 44.99 3.58
450 514 0.984230 TTGGACTGGGATCAGGTGAC 59.016 55.000 0.00 0.00 44.99 3.67
451 515 0.984230 GTTGGACTGGGATCAGGTGA 59.016 55.000 0.00 0.00 44.99 4.02
452 516 0.035056 GGTTGGACTGGGATCAGGTG 60.035 60.000 0.00 0.00 44.99 4.00
453 517 0.475632 TGGTTGGACTGGGATCAGGT 60.476 55.000 0.00 0.00 44.99 4.00
454 518 0.698238 TTGGTTGGACTGGGATCAGG 59.302 55.000 0.00 0.00 44.99 3.86
455 519 2.162681 GTTTGGTTGGACTGGGATCAG 58.837 52.381 0.00 0.00 46.10 2.90
456 520 1.496857 TGTTTGGTTGGACTGGGATCA 59.503 47.619 0.00 0.00 0.00 2.92
457 521 2.286365 TGTTTGGTTGGACTGGGATC 57.714 50.000 0.00 0.00 0.00 3.36
458 522 2.316108 GTTGTTTGGTTGGACTGGGAT 58.684 47.619 0.00 0.00 0.00 3.85
459 523 1.686741 GGTTGTTTGGTTGGACTGGGA 60.687 52.381 0.00 0.00 0.00 4.37
460 524 0.750249 GGTTGTTTGGTTGGACTGGG 59.250 55.000 0.00 0.00 0.00 4.45
461 525 0.750249 GGGTTGTTTGGTTGGACTGG 59.250 55.000 0.00 0.00 0.00 4.00
462 526 1.408702 CTGGGTTGTTTGGTTGGACTG 59.591 52.381 0.00 0.00 0.00 3.51
463 527 1.775385 CTGGGTTGTTTGGTTGGACT 58.225 50.000 0.00 0.00 0.00 3.85
464 528 0.104120 GCTGGGTTGTTTGGTTGGAC 59.896 55.000 0.00 0.00 0.00 4.02
465 529 0.324738 TGCTGGGTTGTTTGGTTGGA 60.325 50.000 0.00 0.00 0.00 3.53
466 530 0.104671 CTGCTGGGTTGTTTGGTTGG 59.895 55.000 0.00 0.00 0.00 3.77
467 531 0.530431 GCTGCTGGGTTGTTTGGTTG 60.530 55.000 0.00 0.00 0.00 3.77
562 629 3.711059 CTGGAGGGCATGTGGAGGC 62.711 68.421 0.00 0.00 0.00 4.70
585 652 1.594331 GAACCGGGAATGATACAGCC 58.406 55.000 6.32 0.00 0.00 4.85
607 674 1.406219 CTTCGTCGTCAGATGCGGTG 61.406 60.000 6.62 0.00 33.49 4.94
648 724 3.148279 GGAGACGGAGGATGGCGT 61.148 66.667 0.00 0.00 0.00 5.68
685 761 6.261381 CGAAAGAGAGTAGTAGGCTCAGTAAT 59.739 42.308 0.00 0.00 35.55 1.89
688 764 3.942748 CGAAAGAGAGTAGTAGGCTCAGT 59.057 47.826 0.00 0.00 35.55 3.41
697 773 6.662663 ACATAACTAACCCGAAAGAGAGTAGT 59.337 38.462 0.00 0.00 0.00 2.73
707 783 4.021192 ACCGAAGAACATAACTAACCCGAA 60.021 41.667 0.00 0.00 0.00 4.30
736 812 1.857217 CTGCAGGACTGAATCGAATCG 59.143 52.381 5.57 0.00 0.00 3.34
884 966 0.910566 TGGGCGTACTTATGGGTGGT 60.911 55.000 0.00 0.00 0.00 4.16
929 1011 1.825191 CAATCCTGGATGGGCCACG 60.825 63.158 9.28 0.00 43.33 4.94
965 1047 7.821846 ACAAATTGGCTCTTTTAGAACAACAAA 59.178 29.630 0.00 0.00 28.39 2.83
976 1059 6.916360 TGGAGATAACAAATTGGCTCTTTT 57.084 33.333 0.00 0.00 0.00 2.27
1172 1261 0.323302 TGGCAGCACTGGTAATTCGA 59.677 50.000 0.00 0.00 0.00 3.71
1254 1343 3.827898 CGCCACGAGGAGGAGACC 61.828 72.222 1.86 0.00 36.89 3.85
1362 1451 1.374758 GCTGTAGAGGCACGCAACT 60.375 57.895 0.00 0.00 0.00 3.16
1498 1587 6.844829 TCACATGTGATGGGATTGAGAATAT 58.155 36.000 24.56 0.00 37.88 1.28
1499 1588 6.251255 TCACATGTGATGGGATTGAGAATA 57.749 37.500 24.56 0.00 37.88 1.75
1559 1648 4.811555 TTCATCAAAAACAGGAGTCACG 57.188 40.909 0.00 0.00 0.00 4.35
1600 1689 3.242220 CGCTGTGTCATGAGAGTAAATGC 60.242 47.826 0.00 0.00 0.00 3.56
1612 1701 2.046892 GGTGCTCCGCTGTGTCAT 60.047 61.111 0.00 0.00 0.00 3.06
1690 1788 8.426489 AGATGCATCATAAAATACAAATGCCTT 58.574 29.630 27.81 0.00 38.92 4.35
1856 1956 6.946340 TGAATTTCTCCTAGCAATGTCACTA 58.054 36.000 0.00 0.00 0.00 2.74
1881 1981 1.107114 GGCCTCTGAGATCGAAGACA 58.893 55.000 6.17 0.00 42.51 3.41
1929 2029 4.201676 CGACAACTGTAATTATCTGCGCAA 60.202 41.667 13.05 2.72 0.00 4.85
1989 2089 7.615365 ACATCTTGGGATCTAAAAACTTGCATA 59.385 33.333 0.00 0.00 0.00 3.14
2106 2206 9.866655 TCCATCAAGCTATTTATTTCCATAACT 57.133 29.630 0.00 0.00 0.00 2.24
2186 2286 2.165437 GTGTTTGCCTTCAACTGTGGAA 59.835 45.455 0.00 0.00 30.75 3.53
2215 2315 0.885879 TACTCGTGGTCGTCAGCAAT 59.114 50.000 0.00 0.00 38.33 3.56
2510 2623 2.511659 GCTTTTAAACCCCCGACTCTT 58.488 47.619 0.00 0.00 0.00 2.85
2517 2630 0.608130 CAGCTGGCTTTTAAACCCCC 59.392 55.000 5.57 0.00 0.00 5.40
2584 2698 3.811497 TCGCATTTATCTTCTCCATGCAG 59.189 43.478 0.00 0.00 40.28 4.41
2634 2748 3.370103 CCCAATACCTGTCCGTAACATGT 60.370 47.826 0.00 0.00 39.64 3.21
2912 3029 3.966665 TCTCAGTTTGGGGCAATTTTCTT 59.033 39.130 0.00 0.00 0.00 2.52
3070 3189 1.766864 TGGTGGGTGGTCGAGGAAA 60.767 57.895 0.00 0.00 0.00 3.13
3078 3197 1.382629 GCTATTGGTGGTGGGTGGT 59.617 57.895 0.00 0.00 0.00 4.16
3150 3273 2.698274 GTCAGGCAGAAAAGGGGAAAAA 59.302 45.455 0.00 0.00 0.00 1.94
3151 3274 2.316108 GTCAGGCAGAAAAGGGGAAAA 58.684 47.619 0.00 0.00 0.00 2.29
3152 3275 1.480498 GGTCAGGCAGAAAAGGGGAAA 60.480 52.381 0.00 0.00 0.00 3.13
3153 3276 0.112412 GGTCAGGCAGAAAAGGGGAA 59.888 55.000 0.00 0.00 0.00 3.97
3186 3310 0.388520 CGACATCAGACCGCAACTCA 60.389 55.000 0.00 0.00 0.00 3.41
3317 3448 2.908428 CAGCCAGTGCAGCACCAA 60.908 61.111 22.41 0.00 41.13 3.67
3361 3492 1.165907 TGGAACTTTGGAGCAGCACG 61.166 55.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.