Multiple sequence alignment - TraesCS3B01G244900

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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 TraesCS3B01G244900 chr3B 100.000 3992 0 0 1 3992 388100137 388104128 0.000000e+00 7372.0
1 TraesCS3B01G244900 chr3A 95.206 2712 84 25 500 3197 389123999 389126678 0.000000e+00 4246.0
2 TraesCS3B01G244900 chr3A 94.830 619 17 10 3385 3992 389126687 389127301 0.000000e+00 952.0
3 TraesCS3B01G244900 chr3A 95.556 135 6 0 3249 3383 434793994 434793860 2.420000e-52 217.0
4 TraesCS3B01G244900 chr3D 94.547 1944 68 9 1294 3212 294344170 294346100 0.000000e+00 2968.0
5 TraesCS3B01G244900 chr3D 95.221 837 24 8 409 1232 294343097 294343930 0.000000e+00 1310.0
6 TraesCS3B01G244900 chr3D 95.292 616 17 8 3385 3992 294346094 294346705 0.000000e+00 966.0
7 TraesCS3B01G244900 chr3D 93.583 187 9 3 3207 3391 614670376 614670561 3.930000e-70 276.0
8 TraesCS3B01G244900 chr3D 100.000 29 0 0 1274 1302 294343946 294343974 2.000000e-03 54.7
9 TraesCS3B01G244900 chr5D 93.048 187 10 3 3208 3392 255344590 255344405 1.830000e-68 270.0
10 TraesCS3B01G244900 chr5D 91.176 170 11 2 3216 3385 74150800 74150635 1.120000e-55 228.0
11 TraesCS3B01G244900 chrUn 91.935 186 14 1 3205 3389 32036955 32037140 3.960000e-65 259.0
12 TraesCS3B01G244900 chr2D 92.778 180 12 1 3205 3384 101886537 101886715 3.960000e-65 259.0
13 TraesCS3B01G244900 chr2D 85.455 55 8 0 551 605 189291474 189291528 1.550000e-04 58.4
14 TraesCS3B01G244900 chr1D 93.605 172 11 0 3213 3384 29806220 29806049 1.420000e-64 257.0
15 TraesCS3B01G244900 chr1D 89.222 167 18 0 3213 3379 170634388 170634554 4.040000e-50 209.0
16 TraesCS3B01G244900 chr5B 93.939 165 10 0 3214 3378 659417626 659417790 2.380000e-62 250.0
17 TraesCS3B01G244900 chr5B 91.781 73 6 0 3862 3934 98372858 98372930 7.060000e-18 102.0
18 TraesCS3B01G244900 chr5B 91.549 71 5 1 3607 3676 98372697 98372767 3.280000e-16 97.1
19 TraesCS3B01G244900 chr1B 91.071 112 9 1 271 381 612480093 612480204 2.490000e-32 150.0
20 TraesCS3B01G244900 chr6B 91.781 73 6 0 3862 3934 267780081 267780009 7.060000e-18 102.0
21 TraesCS3B01G244900 chr6B 91.429 70 6 0 3607 3676 92070840 92070771 3.280000e-16 97.1
22 TraesCS3B01G244900 chr6B 91.549 71 5 1 3607 3676 267780242 267780172 3.280000e-16 97.1
23 TraesCS3B01G244900 chr6B 93.878 49 3 0 557 605 693037104 693037056 1.540000e-09 75.0
24 TraesCS3B01G244900 chr4A 87.952 83 9 1 316 397 672177265 672177347 3.280000e-16 97.1
25 TraesCS3B01G244900 chr4A 86.747 83 10 1 316 397 672270924 672271006 1.530000e-14 91.6


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 TraesCS3B01G244900 chr3B 388100137 388104128 3991 False 7372.000 7372 100.000 1 3992 1 chr3B.!!$F1 3991
1 TraesCS3B01G244900 chr3A 389123999 389127301 3302 False 2599.000 4246 95.018 500 3992 2 chr3A.!!$F1 3492
2 TraesCS3B01G244900 chr3D 294343097 294346705 3608 False 1324.675 2968 96.265 409 3992 4 chr3D.!!$F2 3583

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
46 47 1.148157 CTTCTACAGCGCGGTCATGG 61.148 60.0 18.55 6.5 0.00 3.66 F
706 725 1.287041 CGCGCATCGATGACCATCAT 61.287 55.0 29.20 0.0 40.34 2.45 F
1356 1579 0.790814 GCGACAACTACTGCAAGGTC 59.209 55.0 0.00 0.0 39.30 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 1254 1.056660 GCATCGAAGGGAAGGGGATA 58.943 55.0 0.0 0.0 0.0 2.59 R
2444 2667 0.177604 CGCCTTCATCTTCTCCAGCT 59.822 55.0 0.0 0.0 0.0 4.24 R
3287 3541 0.108992 GGCGAGATGTTGTACACCGA 60.109 55.0 0.0 0.0 0.0 4.69 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
30 31 4.847444 GCTGAGGGCGAGGGCTTC 62.847 72.222 0.00 0.00 39.81 3.86
31 32 3.080121 CTGAGGGCGAGGGCTTCT 61.080 66.667 3.19 0.00 39.81 2.85
32 33 1.758514 CTGAGGGCGAGGGCTTCTA 60.759 63.158 3.19 0.00 39.81 2.10
33 34 2.022240 CTGAGGGCGAGGGCTTCTAC 62.022 65.000 3.19 0.00 39.81 2.59
34 35 2.038975 AGGGCGAGGGCTTCTACA 59.961 61.111 0.00 0.00 39.81 2.74
35 36 2.022240 GAGGGCGAGGGCTTCTACAG 62.022 65.000 0.00 0.00 39.81 2.74
43 44 2.126071 GCTTCTACAGCGCGGTCA 60.126 61.111 18.55 1.75 39.29 4.02
44 45 1.519455 GCTTCTACAGCGCGGTCAT 60.519 57.895 18.55 1.54 39.29 3.06
45 46 1.756375 GCTTCTACAGCGCGGTCATG 61.756 60.000 18.55 9.10 39.29 3.07
46 47 1.148157 CTTCTACAGCGCGGTCATGG 61.148 60.000 18.55 6.50 0.00 3.66
47 48 1.884075 TTCTACAGCGCGGTCATGGT 61.884 55.000 18.55 5.97 0.00 3.55
48 49 2.125713 TACAGCGCGGTCATGGTG 60.126 61.111 18.55 1.24 39.40 4.17
55 56 4.802051 CGGTCATGGTGCCCCCTG 62.802 72.222 0.00 0.00 0.00 4.45
57 58 4.052518 GTCATGGTGCCCCCTGCT 62.053 66.667 0.00 0.00 42.00 4.24
58 59 3.731728 TCATGGTGCCCCCTGCTC 61.732 66.667 0.00 0.00 42.00 4.26
79 80 4.785453 CCGGAGTTGCCCCTGCTC 62.785 72.222 0.00 0.00 38.71 4.26
81 82 4.021925 GGAGTTGCCCCTGCTCGT 62.022 66.667 0.00 0.00 38.71 4.18
82 83 2.743928 GAGTTGCCCCTGCTCGTG 60.744 66.667 0.00 0.00 38.71 4.35
109 110 4.135153 CCCCTGCTCACGTCGGAG 62.135 72.222 0.00 1.76 37.97 4.63
115 116 2.799371 CTCACGTCGGAGCTACCC 59.201 66.667 0.00 0.00 34.64 3.69
116 117 2.753043 TCACGTCGGAGCTACCCC 60.753 66.667 0.00 0.00 34.64 4.95
117 118 3.834799 CACGTCGGAGCTACCCCC 61.835 72.222 0.00 0.00 34.64 5.40
154 155 4.521062 CTTCTCGGGCCGGAGCTG 62.521 72.222 30.35 21.64 39.73 4.24
169 170 4.545706 CTGCCCCCGCTCGCATAA 62.546 66.667 0.00 0.00 33.78 1.90
170 171 4.849310 TGCCCCCGCTCGCATAAC 62.849 66.667 0.00 0.00 35.36 1.89
230 231 4.436998 CGTGGCTCCACTCGGGTC 62.437 72.222 16.15 0.00 44.16 4.46
231 232 4.436998 GTGGCTCCACTCGGGTCG 62.437 72.222 11.61 0.00 43.12 4.79
235 236 3.827898 CTCCACTCGGGTCGGAGC 61.828 72.222 17.37 0.00 39.95 4.70
236 237 4.361971 TCCACTCGGGTCGGAGCT 62.362 66.667 7.19 0.00 37.57 4.09
237 238 4.135153 CCACTCGGGTCGGAGCTG 62.135 72.222 9.72 9.72 37.57 4.24
238 239 4.803426 CACTCGGGTCGGAGCTGC 62.803 72.222 11.10 0.00 37.57 5.25
245 246 4.115199 GTCGGAGCTGCCCCCATT 62.115 66.667 0.00 0.00 0.00 3.16
246 247 3.797353 TCGGAGCTGCCCCCATTC 61.797 66.667 0.00 0.00 0.00 2.67
248 249 4.115199 GGAGCTGCCCCCATTCGT 62.115 66.667 0.00 0.00 0.00 3.85
249 250 2.825836 GAGCTGCCCCCATTCGTG 60.826 66.667 0.00 0.00 0.00 4.35
252 253 4.738998 CTGCCCCCATTCGTGCCA 62.739 66.667 0.00 0.00 0.00 4.92
276 277 4.007644 CCGTGGTGCTCCTGCTCA 62.008 66.667 6.34 0.00 40.48 4.26
277 278 2.740055 CGTGGTGCTCCTGCTCAC 60.740 66.667 6.34 0.00 40.48 3.51
278 279 2.740055 GTGGTGCTCCTGCTCACG 60.740 66.667 6.34 0.00 40.48 4.35
279 280 4.687215 TGGTGCTCCTGCTCACGC 62.687 66.667 6.34 0.00 40.48 5.34
283 284 4.521062 GCTCCTGCTCACGCCGAT 62.521 66.667 0.00 0.00 36.03 4.18
284 285 2.584418 CTCCTGCTCACGCCGATG 60.584 66.667 0.00 0.00 34.43 3.84
285 286 4.819761 TCCTGCTCACGCCGATGC 62.820 66.667 0.00 0.00 34.43 3.91
306 307 4.680237 CCGACGGTGCAGCTCCAA 62.680 66.667 14.92 0.00 0.00 3.53
307 308 3.114616 CGACGGTGCAGCTCCAAG 61.115 66.667 14.92 0.00 0.00 3.61
308 309 3.426568 GACGGTGCAGCTCCAAGC 61.427 66.667 14.92 0.00 42.84 4.01
339 340 4.527583 CCTCCGCCTCAGCAGCTC 62.528 72.222 0.00 0.00 39.83 4.09
340 341 4.869440 CTCCGCCTCAGCAGCTCG 62.869 72.222 0.00 0.00 39.83 5.03
342 343 4.441695 CCGCCTCAGCAGCTCGAA 62.442 66.667 2.89 0.00 39.83 3.71
343 344 3.184683 CGCCTCAGCAGCTCGAAC 61.185 66.667 0.00 0.00 39.83 3.95
344 345 2.817396 GCCTCAGCAGCTCGAACC 60.817 66.667 0.00 0.00 39.53 3.62
345 346 2.125350 CCTCAGCAGCTCGAACCC 60.125 66.667 0.00 0.00 0.00 4.11
346 347 2.125350 CTCAGCAGCTCGAACCCC 60.125 66.667 0.00 0.00 0.00 4.95
347 348 2.922503 TCAGCAGCTCGAACCCCA 60.923 61.111 0.00 0.00 0.00 4.96
348 349 2.435586 CAGCAGCTCGAACCCCAG 60.436 66.667 0.00 0.00 0.00 4.45
349 350 4.400961 AGCAGCTCGAACCCCAGC 62.401 66.667 0.00 0.00 35.73 4.85
350 351 4.704833 GCAGCTCGAACCCCAGCA 62.705 66.667 0.00 0.00 38.18 4.41
351 352 2.435586 CAGCTCGAACCCCAGCAG 60.436 66.667 0.00 0.00 38.18 4.24
352 353 4.400961 AGCTCGAACCCCAGCAGC 62.401 66.667 0.00 0.00 38.18 5.25
377 378 4.821589 GCCTTCCCTCGCCGTCAG 62.822 72.222 0.00 0.00 0.00 3.51
378 379 4.821589 CCTTCCCTCGCCGTCAGC 62.822 72.222 0.00 0.00 38.52 4.26
379 380 4.821589 CTTCCCTCGCCGTCAGCC 62.822 72.222 0.00 0.00 38.78 4.85
384 385 4.933064 CTCGCCGTCAGCCCGATC 62.933 72.222 0.00 0.00 38.78 3.69
410 411 3.512516 GGCGCCATGCTCCTGTTC 61.513 66.667 24.80 0.00 45.43 3.18
411 412 3.869272 GCGCCATGCTCCTGTTCG 61.869 66.667 0.00 0.00 41.73 3.95
412 413 3.197790 CGCCATGCTCCTGTTCGG 61.198 66.667 0.00 0.00 0.00 4.30
413 414 2.825836 GCCATGCTCCTGTTCGGG 60.826 66.667 0.00 0.00 0.00 5.14
428 429 3.958860 GGGGGATGGCATAGCGCT 61.959 66.667 17.26 17.26 41.91 5.92
430 431 2.359230 GGGATGGCATAGCGCTCC 60.359 66.667 16.34 10.54 41.91 4.70
448 449 2.166459 CTCCAACGAGCCAGTTAGATGA 59.834 50.000 0.00 0.00 32.35 2.92
449 450 2.766263 TCCAACGAGCCAGTTAGATGAT 59.234 45.455 0.00 0.00 32.35 2.45
455 456 3.429410 CGAGCCAGTTAGATGATGTGTCA 60.429 47.826 0.00 0.00 39.04 3.58
484 485 4.101585 TCCTGCTTTAAGATCCGTGATCAT 59.898 41.667 13.95 6.72 41.12 2.45
489 490 5.698089 GCTTTAAGATCCGTGATCATCATCA 59.302 40.000 13.95 0.00 41.12 3.07
706 725 1.287041 CGCGCATCGATGACCATCAT 61.287 55.000 29.20 0.00 40.34 2.45
944 963 2.159544 AGACGAAAGAGAACGATCGACC 60.160 50.000 24.34 12.56 38.59 4.79
1218 1237 2.572284 CAGACCGACGACCCTTCC 59.428 66.667 0.00 0.00 0.00 3.46
1235 1254 4.650131 CCCTTCCGGTAACTATCTTCTTCT 59.350 45.833 0.00 0.00 0.00 2.85
1239 1258 7.309316 CCTTCCGGTAACTATCTTCTTCTATCC 60.309 44.444 0.00 0.00 0.00 2.59
1244 1263 7.309316 CGGTAACTATCTTCTTCTATCCCCTTC 60.309 44.444 0.00 0.00 0.00 3.46
1255 1274 1.709994 ATCCCCTTCCCTTCGATGCC 61.710 60.000 0.00 0.00 0.00 4.40
1256 1275 2.203070 CCCTTCCCTTCGATGCCG 60.203 66.667 0.00 0.00 37.07 5.69
1356 1579 0.790814 GCGACAACTACTGCAAGGTC 59.209 55.000 0.00 0.00 39.30 3.85
1779 2002 3.106552 CTCTCCGAGGAGACGCTG 58.893 66.667 17.24 4.90 45.26 5.18
1829 2052 2.564947 AGCACTACTCCTCCAACTTCAG 59.435 50.000 0.00 0.00 0.00 3.02
1830 2053 2.563179 GCACTACTCCTCCAACTTCAGA 59.437 50.000 0.00 0.00 0.00 3.27
1843 2066 1.265236 CTTCAGAGACCTGGAGCTGT 58.735 55.000 0.00 0.00 39.05 4.40
1845 2068 1.840737 TCAGAGACCTGGAGCTGTAC 58.159 55.000 0.00 0.00 40.76 2.90
2066 2289 2.049063 GCTGCAGGACTTCGTCGT 60.049 61.111 17.12 0.00 32.65 4.34
2367 2590 2.179517 CTGTCGACGCTGGAGGAC 59.820 66.667 11.62 0.00 0.00 3.85
2377 2600 1.267121 GCTGGAGGACTACACCAAGA 58.733 55.000 0.00 0.00 33.14 3.02
2444 2667 2.343758 GACGCAGACAGGCAAGGA 59.656 61.111 0.00 0.00 0.00 3.36
2475 2698 3.358076 GAAGGCGGACGTGGAGGAG 62.358 68.421 0.00 0.00 0.00 3.69
2517 2740 2.030805 GGTGGTACGTACTCAGTTCGTT 60.031 50.000 24.07 0.00 39.86 3.85
2518 2741 3.229552 GTGGTACGTACTCAGTTCGTTC 58.770 50.000 24.07 9.78 39.86 3.95
2519 2742 2.096268 TGGTACGTACTCAGTTCGTTCG 60.096 50.000 24.07 0.21 39.86 3.95
2566 2790 2.430332 CTGAAAGGGCAAGTGGTTTGAA 59.570 45.455 0.00 0.00 39.21 2.69
2642 2868 1.272490 ACTGGAAATCAAGCGTCTCGA 59.728 47.619 0.00 0.00 0.00 4.04
2729 2962 3.551915 GCGACGAGGTAAAGCGGC 61.552 66.667 0.00 0.00 0.00 6.53
2733 2966 4.137872 CGAGGTAAAGCGGCCGGA 62.138 66.667 29.38 0.00 0.00 5.14
2821 3066 1.875576 CGCTTCAGAACAAGGAGCTGT 60.876 52.381 0.00 0.00 0.00 4.40
3005 3259 4.708726 ACAGCTGAATGATTTGTTAGGC 57.291 40.909 23.35 0.00 0.00 3.93
3009 3263 6.548622 ACAGCTGAATGATTTGTTAGGCATAT 59.451 34.615 23.35 0.00 0.00 1.78
3011 3265 8.235226 CAGCTGAATGATTTGTTAGGCATATAG 58.765 37.037 8.42 0.00 0.00 1.31
3060 3314 4.158209 GCTAGACCTCGTTACCTTCTTTCT 59.842 45.833 0.00 0.00 0.00 2.52
3120 3374 0.608640 CTCCCCTCGTTTAGCACAGT 59.391 55.000 0.00 0.00 0.00 3.55
3173 3427 4.701956 AGAAAAATGGGAATACTGTGCG 57.298 40.909 0.00 0.00 0.00 5.34
3176 3430 1.750193 AATGGGAATACTGTGCGGTG 58.250 50.000 0.00 0.00 0.00 4.94
3197 3451 1.202710 TGTTAGCGAGGCTTTCAACCA 60.203 47.619 0.00 0.00 40.44 3.67
3201 3455 0.169009 GCGAGGCTTTCAACCATCAC 59.831 55.000 0.00 0.00 0.00 3.06
3203 3457 1.466167 CGAGGCTTTCAACCATCACTG 59.534 52.381 0.00 0.00 0.00 3.66
3212 3466 5.689383 TTCAACCATCACTGCTTAAACTC 57.311 39.130 0.00 0.00 0.00 3.01
3213 3467 4.713553 TCAACCATCACTGCTTAAACTCA 58.286 39.130 0.00 0.00 0.00 3.41
3214 3468 4.515191 TCAACCATCACTGCTTAAACTCAC 59.485 41.667 0.00 0.00 0.00 3.51
3215 3469 4.357918 ACCATCACTGCTTAAACTCACT 57.642 40.909 0.00 0.00 0.00 3.41
3218 3472 4.756642 CCATCACTGCTTAAACTCACTGAA 59.243 41.667 0.00 0.00 0.00 3.02
3219 3473 5.239306 CCATCACTGCTTAAACTCACTGAAA 59.761 40.000 0.00 0.00 0.00 2.69
3220 3474 6.238731 CCATCACTGCTTAAACTCACTGAAAA 60.239 38.462 0.00 0.00 0.00 2.29
3221 3475 6.751514 TCACTGCTTAAACTCACTGAAAAA 57.248 33.333 0.00 0.00 0.00 1.94
3250 3504 3.132629 GCTATAGCGTCGCTAATAGCA 57.867 47.619 34.13 19.54 44.62 3.49
3251 3505 2.847133 GCTATAGCGTCGCTAATAGCAC 59.153 50.000 34.13 20.55 44.62 4.40
3252 3506 1.965083 ATAGCGTCGCTAATAGCACG 58.035 50.000 29.13 22.97 44.62 5.34
3254 3508 4.303853 CGTCGCTAATAGCACGCT 57.696 55.556 18.51 0.00 42.58 5.07
3255 3509 3.449789 CGTCGCTAATAGCACGCTA 57.550 52.632 18.51 0.39 42.58 4.26
3256 3510 1.965083 CGTCGCTAATAGCACGCTAT 58.035 50.000 18.51 5.72 42.58 2.97
3257 3511 3.113325 CGTCGCTAATAGCACGCTATA 57.887 47.619 18.51 1.16 42.58 1.31
3258 3512 3.092135 CGTCGCTAATAGCACGCTATAG 58.908 50.000 18.51 10.32 42.58 1.31
3259 3513 2.847133 GTCGCTAATAGCACGCTATAGC 59.153 50.000 15.09 15.09 42.58 2.97
3260 3514 2.486592 TCGCTAATAGCACGCTATAGCA 59.513 45.455 23.99 4.83 42.58 3.49
3261 3515 3.128764 TCGCTAATAGCACGCTATAGCAT 59.871 43.478 23.99 6.50 42.58 3.79
3262 3516 4.334481 TCGCTAATAGCACGCTATAGCATA 59.666 41.667 23.99 11.14 42.58 3.14
3263 3517 5.008712 TCGCTAATAGCACGCTATAGCATAT 59.991 40.000 23.99 12.75 42.58 1.78
3264 3518 5.687730 CGCTAATAGCACGCTATAGCATATT 59.312 40.000 23.99 20.32 42.58 1.28
3265 3519 6.345329 CGCTAATAGCACGCTATAGCATATTG 60.345 42.308 23.99 14.98 42.58 1.90
3266 3520 6.697455 GCTAATAGCACGCTATAGCATATTGA 59.303 38.462 23.99 5.24 41.89 2.57
3267 3521 7.096271 GCTAATAGCACGCTATAGCATATTGAG 60.096 40.741 23.99 16.63 41.89 3.02
3268 3522 4.790765 AGCACGCTATAGCATATTGAGA 57.209 40.909 23.99 0.00 42.21 3.27
3269 3523 5.139435 AGCACGCTATAGCATATTGAGAA 57.861 39.130 23.99 0.00 42.21 2.87
3270 3524 5.728471 AGCACGCTATAGCATATTGAGAAT 58.272 37.500 23.99 1.38 42.21 2.40
3271 3525 6.169094 AGCACGCTATAGCATATTGAGAATT 58.831 36.000 23.99 0.00 42.21 2.17
3272 3526 6.091849 AGCACGCTATAGCATATTGAGAATTG 59.908 38.462 23.99 5.79 42.21 2.32
3273 3527 6.246449 CACGCTATAGCATATTGAGAATTGC 58.754 40.000 23.99 0.00 42.21 3.56
3274 3528 5.352569 ACGCTATAGCATATTGAGAATTGCC 59.647 40.000 23.99 0.00 42.21 4.52
3275 3529 5.583854 CGCTATAGCATATTGAGAATTGCCT 59.416 40.000 23.99 0.00 42.21 4.75
3276 3530 6.238049 CGCTATAGCATATTGAGAATTGCCTC 60.238 42.308 23.99 0.00 42.21 4.70
3277 3531 6.238049 GCTATAGCATATTGAGAATTGCCTCG 60.238 42.308 20.01 0.00 41.59 4.63
3278 3532 2.551459 AGCATATTGAGAATTGCCTCGC 59.449 45.455 0.00 0.00 35.71 5.03
3279 3533 2.551459 GCATATTGAGAATTGCCTCGCT 59.449 45.455 0.00 0.00 35.99 4.93
3280 3534 3.748048 GCATATTGAGAATTGCCTCGCTA 59.252 43.478 0.00 0.00 35.99 4.26
3281 3535 4.214119 GCATATTGAGAATTGCCTCGCTAA 59.786 41.667 0.00 0.00 35.99 3.09
3282 3536 5.277974 GCATATTGAGAATTGCCTCGCTAAA 60.278 40.000 0.00 0.00 35.99 1.85
3283 3537 6.569226 GCATATTGAGAATTGCCTCGCTAAAT 60.569 38.462 0.00 0.00 35.99 1.40
3284 3538 7.361201 GCATATTGAGAATTGCCTCGCTAAATA 60.361 37.037 0.00 0.00 35.99 1.40
3285 3539 8.671921 CATATTGAGAATTGCCTCGCTAAATAT 58.328 33.333 0.00 0.00 35.99 1.28
3286 3540 9.890629 ATATTGAGAATTGCCTCGCTAAATATA 57.109 29.630 0.00 0.00 35.99 0.86
3287 3541 8.798859 ATTGAGAATTGCCTCGCTAAATATAT 57.201 30.769 0.00 0.00 35.99 0.86
3288 3542 7.834068 TGAGAATTGCCTCGCTAAATATATC 57.166 36.000 0.00 0.00 35.99 1.63
3289 3543 6.531594 TGAGAATTGCCTCGCTAAATATATCG 59.468 38.462 0.00 0.00 35.99 2.92
3290 3544 5.812642 AGAATTGCCTCGCTAAATATATCGG 59.187 40.000 0.00 0.00 0.00 4.18
3291 3545 4.530710 TTGCCTCGCTAAATATATCGGT 57.469 40.909 0.00 0.00 0.00 4.69
3292 3546 3.845178 TGCCTCGCTAAATATATCGGTG 58.155 45.455 0.00 0.00 0.00 4.94
3293 3547 3.257375 TGCCTCGCTAAATATATCGGTGT 59.743 43.478 0.00 0.00 0.00 4.16
3294 3548 4.460034 TGCCTCGCTAAATATATCGGTGTA 59.540 41.667 0.00 0.00 0.00 2.90
3295 3549 4.797349 GCCTCGCTAAATATATCGGTGTAC 59.203 45.833 0.00 0.00 0.00 2.90
3296 3550 5.620654 GCCTCGCTAAATATATCGGTGTACA 60.621 44.000 0.00 0.00 0.00 2.90
3297 3551 6.384224 CCTCGCTAAATATATCGGTGTACAA 58.616 40.000 0.00 0.00 0.00 2.41
3298 3552 6.307318 CCTCGCTAAATATATCGGTGTACAAC 59.693 42.308 0.00 0.00 0.00 3.32
3299 3553 6.737118 TCGCTAAATATATCGGTGTACAACA 58.263 36.000 12.27 0.00 0.00 3.33
3300 3554 7.372714 TCGCTAAATATATCGGTGTACAACAT 58.627 34.615 12.27 6.41 0.00 2.71
3301 3555 7.539710 TCGCTAAATATATCGGTGTACAACATC 59.460 37.037 12.27 0.00 0.00 3.06
3302 3556 7.541091 CGCTAAATATATCGGTGTACAACATCT 59.459 37.037 12.27 0.00 0.00 2.90
3303 3557 8.861101 GCTAAATATATCGGTGTACAACATCTC 58.139 37.037 12.27 0.00 0.00 2.75
3304 3558 7.869016 AAATATATCGGTGTACAACATCTCG 57.131 36.000 12.27 3.10 0.00 4.04
3305 3559 1.922570 ATCGGTGTACAACATCTCGC 58.077 50.000 12.27 0.00 0.00 5.03
3306 3560 0.108992 TCGGTGTACAACATCTCGCC 60.109 55.000 12.27 0.00 0.00 5.54
3307 3561 0.389296 CGGTGTACAACATCTCGCCA 60.389 55.000 12.27 0.00 0.00 5.69
3308 3562 1.803334 GGTGTACAACATCTCGCCAA 58.197 50.000 5.89 0.00 0.00 4.52
3309 3563 2.356135 GGTGTACAACATCTCGCCAAT 58.644 47.619 5.89 0.00 0.00 3.16
3310 3564 3.527533 GGTGTACAACATCTCGCCAATA 58.472 45.455 5.89 0.00 0.00 1.90
3311 3565 3.555956 GGTGTACAACATCTCGCCAATAG 59.444 47.826 5.89 0.00 0.00 1.73
3312 3566 3.001330 GTGTACAACATCTCGCCAATAGC 59.999 47.826 0.00 0.00 38.52 2.97
3313 3567 2.401583 ACAACATCTCGCCAATAGCA 57.598 45.000 0.00 0.00 44.04 3.49
3314 3568 2.009774 ACAACATCTCGCCAATAGCAC 58.990 47.619 0.00 0.00 44.04 4.40
3315 3569 1.004610 CAACATCTCGCCAATAGCACG 60.005 52.381 0.00 0.00 44.04 5.34
3316 3570 1.154205 ACATCTCGCCAATAGCACGC 61.154 55.000 0.00 0.00 44.04 5.34
3317 3571 0.877649 CATCTCGCCAATAGCACGCT 60.878 55.000 0.00 0.00 44.04 5.07
3318 3572 0.673985 ATCTCGCCAATAGCACGCTA 59.326 50.000 0.39 0.39 44.04 4.26
3319 3573 0.673985 TCTCGCCAATAGCACGCTAT 59.326 50.000 5.72 5.72 44.04 2.97
3320 3574 1.883926 TCTCGCCAATAGCACGCTATA 59.116 47.619 11.80 0.00 44.04 1.31
3321 3575 2.095212 TCTCGCCAATAGCACGCTATAG 60.095 50.000 11.80 8.03 44.04 1.31
3322 3576 0.716108 CGCCAATAGCACGCTATAGC 59.284 55.000 15.09 15.09 44.04 2.97
3323 3577 1.795768 GCCAATAGCACGCTATAGCA 58.204 50.000 23.99 4.83 42.97 3.49
3324 3578 2.350522 GCCAATAGCACGCTATAGCAT 58.649 47.619 23.99 6.50 42.97 3.79
3325 3579 2.094894 GCCAATAGCACGCTATAGCATG 59.905 50.000 23.99 20.27 42.97 4.06
3333 3587 4.768659 CACGCTATAGCATGCTAATAGC 57.231 45.455 32.63 32.63 40.83 2.97
3334 3588 4.176271 CACGCTATAGCATGCTAATAGCA 58.824 43.478 35.99 17.97 45.30 3.49
3349 3603 6.543736 GCTAATAGCATATTTTTAGGTCGCC 58.456 40.000 7.49 0.00 41.89 5.54
3350 3604 5.607119 AATAGCATATTTTTAGGTCGCCG 57.393 39.130 0.00 0.00 0.00 6.46
3351 3605 1.602377 AGCATATTTTTAGGTCGCCGC 59.398 47.619 0.00 0.00 0.00 6.53
3352 3606 1.602377 GCATATTTTTAGGTCGCCGCT 59.398 47.619 0.00 0.00 0.00 5.52
3353 3607 2.803956 GCATATTTTTAGGTCGCCGCTA 59.196 45.455 0.00 0.00 0.00 4.26
3354 3608 3.435671 GCATATTTTTAGGTCGCCGCTAT 59.564 43.478 0.00 0.00 0.00 2.97
3355 3609 4.083484 GCATATTTTTAGGTCGCCGCTATT 60.083 41.667 0.00 0.00 0.00 1.73
3356 3610 5.562113 GCATATTTTTAGGTCGCCGCTATTT 60.562 40.000 0.00 0.00 0.00 1.40
3357 3611 4.976224 ATTTTTAGGTCGCCGCTATTTT 57.024 36.364 0.00 0.00 0.00 1.82
3358 3612 3.750639 TTTTAGGTCGCCGCTATTTTG 57.249 42.857 0.00 0.00 0.00 2.44
3359 3613 1.011333 TTAGGTCGCCGCTATTTTGC 58.989 50.000 0.00 0.00 0.00 3.68
3360 3614 0.177141 TAGGTCGCCGCTATTTTGCT 59.823 50.000 0.00 0.00 0.00 3.91
3361 3615 1.062525 GGTCGCCGCTATTTTGCTG 59.937 57.895 0.00 0.00 0.00 4.41
3362 3616 1.644786 GGTCGCCGCTATTTTGCTGT 61.645 55.000 0.00 0.00 0.00 4.40
3363 3617 1.003851 GTCGCCGCTATTTTGCTGTA 58.996 50.000 0.00 0.00 0.00 2.74
3364 3618 1.004927 GTCGCCGCTATTTTGCTGTAG 60.005 52.381 0.00 0.00 0.00 2.74
3365 3619 0.316196 CGCCGCTATTTTGCTGTAGC 60.316 55.000 0.00 0.00 39.86 3.58
3368 3622 3.133814 GCTATTTTGCTGTAGCGCG 57.866 52.632 0.00 0.00 45.83 6.86
3369 3623 0.925721 GCTATTTTGCTGTAGCGCGC 60.926 55.000 26.66 26.66 45.83 6.86
3370 3624 0.652592 CTATTTTGCTGTAGCGCGCT 59.347 50.000 38.01 38.01 45.83 5.92
3371 3625 1.858458 CTATTTTGCTGTAGCGCGCTA 59.142 47.619 35.48 35.48 45.83 4.26
3372 3626 1.299541 ATTTTGCTGTAGCGCGCTAT 58.700 45.000 39.99 22.30 45.83 2.97
3373 3627 1.083489 TTTTGCTGTAGCGCGCTATT 58.917 45.000 39.99 20.35 45.83 1.73
3374 3628 1.083489 TTTGCTGTAGCGCGCTATTT 58.917 45.000 39.99 19.95 45.83 1.40
3375 3629 1.083489 TTGCTGTAGCGCGCTATTTT 58.917 45.000 39.99 19.54 45.83 1.82
3376 3630 1.083489 TGCTGTAGCGCGCTATTTTT 58.917 45.000 39.99 18.75 45.83 1.94
3407 3661 4.546829 AAACTACAAGACCGCTATGGAA 57.453 40.909 0.00 0.00 42.00 3.53
3411 3665 1.899814 ACAAGACCGCTATGGAAGACA 59.100 47.619 0.00 0.00 42.00 3.41
3426 3680 4.019681 TGGAAGACATAACGAGGAACCAAT 60.020 41.667 0.00 0.00 0.00 3.16
3432 3686 6.488683 AGACATAACGAGGAACCAATGAAAAA 59.511 34.615 0.00 0.00 0.00 1.94
3434 3688 4.584327 AACGAGGAACCAATGAAAAAGG 57.416 40.909 0.00 0.00 0.00 3.11
3436 3690 3.568430 ACGAGGAACCAATGAAAAAGGTC 59.432 43.478 0.00 0.00 33.74 3.85
3437 3691 3.568007 CGAGGAACCAATGAAAAAGGTCA 59.432 43.478 0.00 0.00 33.74 4.02
3438 3692 4.218417 CGAGGAACCAATGAAAAAGGTCAT 59.782 41.667 0.00 0.00 40.01 3.06
3439 3693 5.473039 GAGGAACCAATGAAAAAGGTCATG 58.527 41.667 0.00 0.00 38.28 3.07
3440 3694 3.996363 GGAACCAATGAAAAAGGTCATGC 59.004 43.478 0.00 0.00 38.28 4.06
3442 3696 4.686191 ACCAATGAAAAAGGTCATGCAA 57.314 36.364 0.00 0.00 38.28 4.08
3450 3709 6.148948 TGAAAAAGGTCATGCAATACTTTCG 58.851 36.000 0.00 0.00 31.56 3.46
3537 3797 5.010933 TGGAACAAGTTACAGACCACAAAA 58.989 37.500 0.00 0.00 31.92 2.44
3758 4020 0.250209 CTGCCTGCAATCTCGCCTAT 60.250 55.000 0.00 0.00 0.00 2.57
3831 4093 0.325671 CCACCCTGAGCTCCTTCCTA 60.326 60.000 12.15 0.00 0.00 2.94
3980 4244 7.594758 GCTTAAGCACAATAGAAAACATTCACA 59.405 33.333 22.59 0.00 41.59 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.847444 GAAGCCCTCGCCCTCAGC 62.847 72.222 0.00 0.00 34.57 4.26
14 15 1.758514 TAGAAGCCCTCGCCCTCAG 60.759 63.158 0.00 0.00 34.57 3.35
15 16 2.058595 GTAGAAGCCCTCGCCCTCA 61.059 63.158 0.00 0.00 34.57 3.86
16 17 2.022240 CTGTAGAAGCCCTCGCCCTC 62.022 65.000 0.00 0.00 34.57 4.30
17 18 2.038975 TGTAGAAGCCCTCGCCCT 59.961 61.111 0.00 0.00 34.57 5.19
18 19 2.501610 CTGTAGAAGCCCTCGCCC 59.498 66.667 0.00 0.00 34.57 6.13
27 28 1.148157 CCATGACCGCGCTGTAGAAG 61.148 60.000 3.84 0.00 0.00 2.85
28 29 1.153647 CCATGACCGCGCTGTAGAA 60.154 57.895 3.84 0.00 0.00 2.10
29 30 2.348104 ACCATGACCGCGCTGTAGA 61.348 57.895 3.84 0.00 0.00 2.59
30 31 2.167219 CACCATGACCGCGCTGTAG 61.167 63.158 3.84 0.00 0.00 2.74
31 32 2.125713 CACCATGACCGCGCTGTA 60.126 61.111 3.84 0.00 0.00 2.74
62 63 4.785453 GAGCAGGGGCAACTCCGG 62.785 72.222 0.00 0.00 44.61 5.14
64 65 4.021925 ACGAGCAGGGGCAACTCC 62.022 66.667 0.00 0.00 44.61 3.85
65 66 2.743928 CACGAGCAGGGGCAACTC 60.744 66.667 0.00 0.00 44.61 3.01
92 93 4.135153 CTCCGACGTGAGCAGGGG 62.135 72.222 0.00 0.00 0.00 4.79
98 99 2.772691 GGGGTAGCTCCGACGTGAG 61.773 68.421 0.00 0.00 37.00 3.51
99 100 2.753043 GGGGTAGCTCCGACGTGA 60.753 66.667 0.00 0.00 37.00 4.35
100 101 3.834799 GGGGGTAGCTCCGACGTG 61.835 72.222 0.00 0.00 37.00 4.49
137 138 4.521062 CAGCTCCGGCCCGAGAAG 62.521 72.222 23.37 11.21 39.73 2.85
152 153 4.545706 TTATGCGAGCGGGGGCAG 62.546 66.667 0.00 0.00 43.27 4.85
153 154 4.849310 GTTATGCGAGCGGGGGCA 62.849 66.667 0.00 0.00 44.29 5.36
214 215 4.436998 CGACCCGAGTGGAGCCAC 62.437 72.222 11.67 11.67 46.50 5.01
217 218 3.827898 CTCCGACCCGAGTGGAGC 61.828 72.222 3.40 0.00 42.53 4.70
219 220 4.361971 AGCTCCGACCCGAGTGGA 62.362 66.667 0.00 0.00 37.49 4.02
220 221 4.135153 CAGCTCCGACCCGAGTGG 62.135 72.222 0.00 0.00 41.37 4.00
221 222 4.803426 GCAGCTCCGACCCGAGTG 62.803 72.222 0.00 0.00 32.11 3.51
228 229 4.115199 AATGGGGGCAGCTCCGAC 62.115 66.667 4.81 0.00 34.94 4.79
229 230 3.797353 GAATGGGGGCAGCTCCGA 61.797 66.667 4.81 0.12 34.94 4.55
231 232 4.115199 ACGAATGGGGGCAGCTCC 62.115 66.667 0.96 0.96 0.00 4.70
232 233 2.825836 CACGAATGGGGGCAGCTC 60.826 66.667 0.00 0.00 0.00 4.09
235 236 4.738998 TGGCACGAATGGGGGCAG 62.739 66.667 0.00 0.00 32.91 4.85
259 260 4.007644 TGAGCAGGAGCACCACGG 62.008 66.667 2.07 0.00 45.49 4.94
260 261 2.740055 GTGAGCAGGAGCACCACG 60.740 66.667 2.07 0.00 45.49 4.94
261 262 2.740055 CGTGAGCAGGAGCACCAC 60.740 66.667 2.07 0.00 45.49 4.16
289 290 4.680237 TTGGAGCTGCACCGTCGG 62.680 66.667 7.72 10.48 0.00 4.79
290 291 3.114616 CTTGGAGCTGCACCGTCG 61.115 66.667 7.72 0.00 0.00 5.12
291 292 3.426568 GCTTGGAGCTGCACCGTC 61.427 66.667 7.72 0.00 38.45 4.79
325 326 4.441695 TTCGAGCTGCTGAGGCGG 62.442 66.667 7.01 0.00 46.87 6.13
326 327 3.184683 GTTCGAGCTGCTGAGGCG 61.185 66.667 7.01 4.24 42.25 5.52
327 328 2.817396 GGTTCGAGCTGCTGAGGC 60.817 66.667 7.01 2.66 39.26 4.70
328 329 2.125350 GGGTTCGAGCTGCTGAGG 60.125 66.667 7.01 0.00 0.00 3.86
329 330 2.125350 GGGGTTCGAGCTGCTGAG 60.125 66.667 7.01 0.37 0.00 3.35
330 331 2.922503 TGGGGTTCGAGCTGCTGA 60.923 61.111 7.01 1.94 0.00 4.26
331 332 2.435586 CTGGGGTTCGAGCTGCTG 60.436 66.667 7.01 0.00 0.00 4.41
332 333 4.400961 GCTGGGGTTCGAGCTGCT 62.401 66.667 0.00 0.00 40.84 4.24
333 334 4.704833 TGCTGGGGTTCGAGCTGC 62.705 66.667 0.00 0.00 43.78 5.25
334 335 2.435586 CTGCTGGGGTTCGAGCTG 60.436 66.667 0.00 0.00 43.78 4.24
335 336 4.400961 GCTGCTGGGGTTCGAGCT 62.401 66.667 0.00 0.00 43.78 4.09
360 361 4.821589 CTGACGGCGAGGGAAGGC 62.822 72.222 16.62 0.00 0.00 4.35
361 362 4.821589 GCTGACGGCGAGGGAAGG 62.822 72.222 16.62 0.00 0.00 3.46
362 363 4.821589 GGCTGACGGCGAGGGAAG 62.822 72.222 16.62 4.27 42.94 3.46
367 368 4.933064 GATCGGGCTGACGGCGAG 62.933 72.222 16.62 1.58 42.94 5.03
394 395 3.869272 CGAACAGGAGCATGGCGC 61.869 66.667 0.00 0.00 42.91 6.53
395 396 3.197790 CCGAACAGGAGCATGGCG 61.198 66.667 0.00 0.00 45.00 5.69
396 397 2.825836 CCCGAACAGGAGCATGGC 60.826 66.667 0.00 0.00 45.00 4.40
397 398 2.124570 CCCCGAACAGGAGCATGG 60.125 66.667 0.00 0.00 45.00 3.66
398 399 1.987807 ATCCCCCGAACAGGAGCATG 61.988 60.000 0.00 0.00 45.00 4.06
399 400 1.694169 ATCCCCCGAACAGGAGCAT 60.694 57.895 0.00 0.00 45.00 3.79
400 401 2.285368 ATCCCCCGAACAGGAGCA 60.285 61.111 0.00 0.00 45.00 4.26
401 402 2.190578 CATCCCCCGAACAGGAGC 59.809 66.667 0.00 0.00 45.00 4.70
402 403 2.911143 CCATCCCCCGAACAGGAG 59.089 66.667 0.00 0.00 45.00 3.69
403 404 3.407967 GCCATCCCCCGAACAGGA 61.408 66.667 0.00 0.00 45.00 3.86
404 405 1.705002 TATGCCATCCCCCGAACAGG 61.705 60.000 0.00 0.00 40.63 4.00
405 406 0.250467 CTATGCCATCCCCCGAACAG 60.250 60.000 0.00 0.00 0.00 3.16
406 407 1.836391 CTATGCCATCCCCCGAACA 59.164 57.895 0.00 0.00 0.00 3.18
407 408 1.600916 GCTATGCCATCCCCCGAAC 60.601 63.158 0.00 0.00 0.00 3.95
408 409 2.836154 GCTATGCCATCCCCCGAA 59.164 61.111 0.00 0.00 0.00 4.30
409 410 3.625897 CGCTATGCCATCCCCCGA 61.626 66.667 0.00 0.00 0.00 5.14
428 429 2.176045 TCATCTAACTGGCTCGTTGGA 58.824 47.619 8.23 8.23 38.48 3.53
430 431 3.308053 CACATCATCTAACTGGCTCGTTG 59.692 47.826 3.55 0.00 0.00 4.10
448 449 1.302511 GCAGGACCGGTTGACACAT 60.303 57.895 9.42 0.00 0.00 3.21
449 450 1.978455 AAGCAGGACCGGTTGACACA 61.978 55.000 9.42 0.00 0.00 3.72
455 456 2.355818 GGATCTTAAAGCAGGACCGGTT 60.356 50.000 9.42 0.00 0.00 4.44
484 485 6.162777 TGACGTTGTTGTAATCATCTGATGA 58.837 36.000 21.55 21.55 44.55 2.92
489 490 4.929808 GTCCTGACGTTGTTGTAATCATCT 59.070 41.667 0.00 0.00 0.00 2.90
505 506 1.687628 CGAAGACACTTCGTCCTGAC 58.312 55.000 20.79 0.00 46.69 3.51
561 563 6.149308 CCTGATTTTTAAATTTGGGCAAGTCC 59.851 38.462 0.00 0.00 0.00 3.85
1218 1237 6.011481 AGGGGATAGAAGAAGATAGTTACCG 58.989 44.000 0.00 0.00 0.00 4.02
1235 1254 1.056660 GCATCGAAGGGAAGGGGATA 58.943 55.000 0.00 0.00 0.00 2.59
1239 1258 2.203070 CGGCATCGAAGGGAAGGG 60.203 66.667 0.00 0.00 39.00 3.95
1244 1263 3.341043 CATCGCGGCATCGAAGGG 61.341 66.667 6.13 0.00 42.15 3.95
1255 1274 4.630785 AGACGGATCGGCATCGCG 62.631 66.667 0.00 0.00 37.34 5.87
1256 1275 2.731348 GAGACGGATCGGCATCGC 60.731 66.667 0.00 0.00 37.34 4.58
1438 1661 3.188786 CGGTGGTAGCGCTTCAGC 61.189 66.667 18.68 22.08 37.78 4.26
1439 1662 1.805945 GACGGTGGTAGCGCTTCAG 60.806 63.158 18.68 7.66 43.79 3.02
1440 1663 2.260434 GACGGTGGTAGCGCTTCA 59.740 61.111 18.68 12.57 43.79 3.02
1497 1720 1.666011 GAACTCGTCCAGCTCCACA 59.334 57.895 0.00 0.00 0.00 4.17
1684 1907 2.488355 GCCGTCGAGGATGTTCGA 59.512 61.111 6.70 0.00 46.41 3.71
1829 2052 1.810532 CCGTACAGCTCCAGGTCTC 59.189 63.158 0.00 0.00 0.00 3.36
1830 2053 2.352032 GCCGTACAGCTCCAGGTCT 61.352 63.158 0.00 0.00 0.00 3.85
2155 2378 4.335647 CTCCACCTGCCTGGCGTT 62.336 66.667 14.98 0.00 40.22 4.84
2367 2590 3.005554 CTGGTTCAGCATCTTGGTGTAG 58.994 50.000 6.59 0.00 45.34 2.74
2377 2600 0.537188 CCGTACCTCTGGTTCAGCAT 59.463 55.000 0.00 0.00 37.09 3.79
2428 2651 2.345244 CTCCTTGCCTGTCTGCGT 59.655 61.111 0.00 0.00 0.00 5.24
2444 2667 0.177604 CGCCTTCATCTTCTCCAGCT 59.822 55.000 0.00 0.00 0.00 4.24
2475 2698 1.003233 GTCCTTCCACTCCACCAGC 60.003 63.158 0.00 0.00 0.00 4.85
2517 2740 2.063015 ATCACACAAGGTTGGGGCGA 62.063 55.000 0.00 0.00 35.39 5.54
2518 2741 1.603455 ATCACACAAGGTTGGGGCG 60.603 57.895 0.00 0.00 35.39 6.13
2519 2742 1.966762 CATCACACAAGGTTGGGGC 59.033 57.895 0.00 0.00 35.39 5.80
2566 2790 6.751888 CCAAAACGAGAGACAACAAAAGAAAT 59.248 34.615 0.00 0.00 0.00 2.17
2733 2966 1.810151 CCACGTCAAAACAATCCCGAT 59.190 47.619 0.00 0.00 0.00 4.18
2821 3066 1.377202 GGCTGATGGAAAGCACCGA 60.377 57.895 0.00 0.00 42.69 4.69
3014 3268 7.217200 AGCTCGCAAAGGAGTCATTATTATTA 58.783 34.615 0.00 0.00 36.41 0.98
3015 3269 6.058183 AGCTCGCAAAGGAGTCATTATTATT 58.942 36.000 0.00 0.00 36.41 1.40
3017 3271 5.023533 AGCTCGCAAAGGAGTCATTATTA 57.976 39.130 0.00 0.00 36.41 0.98
3018 3272 3.878778 AGCTCGCAAAGGAGTCATTATT 58.121 40.909 0.00 0.00 36.41 1.40
3019 3273 3.550437 AGCTCGCAAAGGAGTCATTAT 57.450 42.857 0.00 0.00 36.41 1.28
3020 3274 3.699538 TCTAGCTCGCAAAGGAGTCATTA 59.300 43.478 0.00 0.00 36.41 1.90
3021 3275 2.497675 TCTAGCTCGCAAAGGAGTCATT 59.502 45.455 0.00 0.00 36.41 2.57
3022 3276 2.103373 TCTAGCTCGCAAAGGAGTCAT 58.897 47.619 0.00 0.00 36.41 3.06
3023 3277 1.202582 GTCTAGCTCGCAAAGGAGTCA 59.797 52.381 0.00 0.00 36.41 3.41
3024 3278 1.470112 GGTCTAGCTCGCAAAGGAGTC 60.470 57.143 0.00 0.00 36.41 3.36
3025 3279 0.533032 GGTCTAGCTCGCAAAGGAGT 59.467 55.000 0.00 0.00 36.41 3.85
3026 3280 0.820871 AGGTCTAGCTCGCAAAGGAG 59.179 55.000 0.00 0.00 37.11 3.69
3027 3281 0.818296 GAGGTCTAGCTCGCAAAGGA 59.182 55.000 0.00 0.00 0.00 3.36
3028 3282 0.526524 CGAGGTCTAGCTCGCAAAGG 60.527 60.000 17.38 0.00 36.29 3.11
3163 3417 2.073816 GCTAACACACCGCACAGTATT 58.926 47.619 0.00 0.00 0.00 1.89
3173 3427 0.796927 GAAAGCCTCGCTAACACACC 59.203 55.000 0.00 0.00 38.25 4.16
3176 3430 1.197036 GGTTGAAAGCCTCGCTAACAC 59.803 52.381 0.00 0.00 38.25 3.32
3197 3451 6.942532 TTTTCAGTGAGTTTAAGCAGTGAT 57.057 33.333 11.13 0.00 42.25 3.06
3230 3484 2.847133 GTGCTATTAGCGACGCTATAGC 59.153 50.000 34.54 34.54 46.26 2.97
3231 3485 3.092135 CGTGCTATTAGCGACGCTATAG 58.908 50.000 28.67 26.76 46.26 1.31
3232 3486 3.113325 CGTGCTATTAGCGACGCTATA 57.887 47.619 28.67 19.32 46.26 1.31
3233 3487 1.965083 CGTGCTATTAGCGACGCTAT 58.035 50.000 28.67 19.98 46.26 2.97
3234 3488 3.449789 CGTGCTATTAGCGACGCTA 57.550 52.632 25.04 25.04 46.26 4.26
3235 3489 4.303853 CGTGCTATTAGCGACGCT 57.696 55.556 27.45 27.45 46.26 5.07
3237 3491 1.965083 ATAGCGTGCTATTAGCGACG 58.035 50.000 23.96 23.96 46.26 5.12
3238 3492 2.847133 GCTATAGCGTGCTATTAGCGAC 59.153 50.000 18.62 9.06 46.26 5.19
3239 3493 2.486592 TGCTATAGCGTGCTATTAGCGA 59.513 45.455 18.62 12.37 44.30 4.93
3240 3494 2.863739 TGCTATAGCGTGCTATTAGCG 58.136 47.619 18.62 7.48 44.30 4.26
3241 3495 6.697455 TCAATATGCTATAGCGTGCTATTAGC 59.303 38.462 26.43 21.07 45.83 3.09
3242 3496 8.131731 TCTCAATATGCTATAGCGTGCTATTAG 58.868 37.037 26.43 16.02 45.83 1.73
3243 3497 7.996385 TCTCAATATGCTATAGCGTGCTATTA 58.004 34.615 26.43 8.34 45.83 0.98
3244 3498 6.867550 TCTCAATATGCTATAGCGTGCTATT 58.132 36.000 26.43 16.34 45.83 1.73
3245 3499 6.456795 TCTCAATATGCTATAGCGTGCTAT 57.543 37.500 26.43 17.65 45.83 2.97
3246 3500 5.897377 TCTCAATATGCTATAGCGTGCTA 57.103 39.130 26.43 9.76 45.83 3.49
3247 3501 4.790765 TCTCAATATGCTATAGCGTGCT 57.209 40.909 26.43 12.72 45.83 4.40
3248 3502 6.246449 CAATTCTCAATATGCTATAGCGTGC 58.754 40.000 26.43 2.18 45.83 5.34
3249 3503 6.246449 GCAATTCTCAATATGCTATAGCGTG 58.754 40.000 26.43 17.43 45.83 5.34
3250 3504 5.352569 GGCAATTCTCAATATGCTATAGCGT 59.647 40.000 22.53 22.53 45.83 5.07
3251 3505 5.583854 AGGCAATTCTCAATATGCTATAGCG 59.416 40.000 19.55 5.29 45.83 4.26
3252 3506 6.238049 CGAGGCAATTCTCAATATGCTATAGC 60.238 42.308 18.18 18.18 38.79 2.97
3253 3507 6.238049 GCGAGGCAATTCTCAATATGCTATAG 60.238 42.308 0.00 0.00 38.79 1.31
3254 3508 5.582269 GCGAGGCAATTCTCAATATGCTATA 59.418 40.000 0.00 0.00 38.79 1.31
3255 3509 4.394300 GCGAGGCAATTCTCAATATGCTAT 59.606 41.667 0.00 0.00 38.79 2.97
3256 3510 3.748048 GCGAGGCAATTCTCAATATGCTA 59.252 43.478 0.00 0.00 38.79 3.49
3257 3511 2.551459 GCGAGGCAATTCTCAATATGCT 59.449 45.455 0.00 0.00 38.79 3.79
3258 3512 2.551459 AGCGAGGCAATTCTCAATATGC 59.449 45.455 0.00 0.00 38.06 3.14
3259 3513 5.929697 TTAGCGAGGCAATTCTCAATATG 57.070 39.130 0.00 0.00 33.59 1.78
3260 3514 8.798859 ATATTTAGCGAGGCAATTCTCAATAT 57.201 30.769 0.00 0.00 33.59 1.28
3261 3515 9.890629 ATATATTTAGCGAGGCAATTCTCAATA 57.109 29.630 0.00 0.00 33.59 1.90
3262 3516 8.798859 ATATATTTAGCGAGGCAATTCTCAAT 57.201 30.769 0.00 0.00 33.59 2.57
3263 3517 7.063426 CGATATATTTAGCGAGGCAATTCTCAA 59.937 37.037 0.00 0.00 39.53 3.02
3264 3518 6.531594 CGATATATTTAGCGAGGCAATTCTCA 59.468 38.462 0.00 0.00 39.53 3.27
3265 3519 6.019479 CCGATATATTTAGCGAGGCAATTCTC 60.019 42.308 2.29 0.00 39.53 2.87
3266 3520 5.812642 CCGATATATTTAGCGAGGCAATTCT 59.187 40.000 2.29 0.00 39.53 2.40
3267 3521 5.581085 ACCGATATATTTAGCGAGGCAATTC 59.419 40.000 2.29 0.00 39.53 2.17
3268 3522 5.351465 CACCGATATATTTAGCGAGGCAATT 59.649 40.000 2.29 0.00 39.53 2.32
3269 3523 4.870426 CACCGATATATTTAGCGAGGCAAT 59.130 41.667 2.29 0.00 39.53 3.56
3270 3524 4.242475 CACCGATATATTTAGCGAGGCAA 58.758 43.478 2.29 0.00 39.53 4.52
3271 3525 3.257375 ACACCGATATATTTAGCGAGGCA 59.743 43.478 2.29 0.00 39.53 4.75
3272 3526 3.846360 ACACCGATATATTTAGCGAGGC 58.154 45.455 2.29 0.00 39.53 4.70
3273 3527 5.946298 TGTACACCGATATATTTAGCGAGG 58.054 41.667 2.29 0.00 39.53 4.63
3274 3528 6.859508 TGTTGTACACCGATATATTTAGCGAG 59.140 38.462 2.29 0.00 39.53 5.03
3275 3529 6.737118 TGTTGTACACCGATATATTTAGCGA 58.263 36.000 2.29 0.00 39.53 4.93
3276 3530 6.996562 TGTTGTACACCGATATATTTAGCG 57.003 37.500 0.00 0.00 36.99 4.26
3277 3531 8.758633 AGATGTTGTACACCGATATATTTAGC 57.241 34.615 0.00 0.00 0.00 3.09
3278 3532 9.062674 CGAGATGTTGTACACCGATATATTTAG 57.937 37.037 0.00 0.00 0.00 1.85
3279 3533 7.539710 GCGAGATGTTGTACACCGATATATTTA 59.460 37.037 0.00 0.00 0.00 1.40
3280 3534 6.365247 GCGAGATGTTGTACACCGATATATTT 59.635 38.462 0.00 0.00 0.00 1.40
3281 3535 5.862323 GCGAGATGTTGTACACCGATATATT 59.138 40.000 0.00 0.00 0.00 1.28
3282 3536 5.399858 GCGAGATGTTGTACACCGATATAT 58.600 41.667 0.00 0.00 0.00 0.86
3283 3537 4.320714 GGCGAGATGTTGTACACCGATATA 60.321 45.833 0.00 0.00 0.00 0.86
3284 3538 3.552273 GGCGAGATGTTGTACACCGATAT 60.552 47.826 0.00 0.00 0.00 1.63
3285 3539 2.223641 GGCGAGATGTTGTACACCGATA 60.224 50.000 0.00 0.00 0.00 2.92
3286 3540 1.470979 GGCGAGATGTTGTACACCGAT 60.471 52.381 0.00 0.00 0.00 4.18
3287 3541 0.108992 GGCGAGATGTTGTACACCGA 60.109 55.000 0.00 0.00 0.00 4.69
3288 3542 0.389296 TGGCGAGATGTTGTACACCG 60.389 55.000 0.00 0.00 0.00 4.94
3289 3543 1.803334 TTGGCGAGATGTTGTACACC 58.197 50.000 0.00 0.00 0.00 4.16
3290 3544 3.001330 GCTATTGGCGAGATGTTGTACAC 59.999 47.826 0.00 0.00 0.00 2.90
3291 3545 3.194861 GCTATTGGCGAGATGTTGTACA 58.805 45.455 0.00 0.00 0.00 2.90
3292 3546 3.001330 GTGCTATTGGCGAGATGTTGTAC 59.999 47.826 0.00 0.00 45.43 2.90
3293 3547 3.194861 GTGCTATTGGCGAGATGTTGTA 58.805 45.455 0.00 0.00 45.43 2.41
3294 3548 2.009774 GTGCTATTGGCGAGATGTTGT 58.990 47.619 0.00 0.00 45.43 3.32
3295 3549 1.004610 CGTGCTATTGGCGAGATGTTG 60.005 52.381 0.00 0.00 45.43 3.33
3296 3550 1.290203 CGTGCTATTGGCGAGATGTT 58.710 50.000 0.00 0.00 45.43 2.71
3297 3551 1.154205 GCGTGCTATTGGCGAGATGT 61.154 55.000 0.00 0.00 45.43 3.06
3298 3552 0.877649 AGCGTGCTATTGGCGAGATG 60.878 55.000 0.00 0.00 45.43 2.90
3299 3553 0.673985 TAGCGTGCTATTGGCGAGAT 59.326 50.000 0.00 0.00 45.43 2.75
3300 3554 0.673985 ATAGCGTGCTATTGGCGAGA 59.326 50.000 8.54 0.00 45.43 4.04
3301 3555 2.254459 CTATAGCGTGCTATTGGCGAG 58.746 52.381 18.62 6.90 45.43 5.03
3302 3556 1.668919 GCTATAGCGTGCTATTGGCGA 60.669 52.381 18.62 0.92 45.43 5.54
3303 3557 0.716108 GCTATAGCGTGCTATTGGCG 59.284 55.000 18.62 7.48 45.43 5.69
3304 3558 1.795768 TGCTATAGCGTGCTATTGGC 58.204 50.000 18.62 20.45 45.83 4.52
3325 3579 6.543736 GGCGACCTAAAAATATGCTATTAGC 58.456 40.000 8.80 8.80 42.82 3.09
3326 3580 6.672357 GCGGCGACCTAAAAATATGCTATTAG 60.672 42.308 12.98 0.00 0.00 1.73
3327 3581 5.121142 GCGGCGACCTAAAAATATGCTATTA 59.879 40.000 12.98 0.00 0.00 0.98
3328 3582 4.083484 GCGGCGACCTAAAAATATGCTATT 60.083 41.667 12.98 0.00 0.00 1.73
3329 3583 3.435671 GCGGCGACCTAAAAATATGCTAT 59.564 43.478 12.98 0.00 0.00 2.97
3330 3584 2.803956 GCGGCGACCTAAAAATATGCTA 59.196 45.455 12.98 0.00 0.00 3.49
3331 3585 1.602377 GCGGCGACCTAAAAATATGCT 59.398 47.619 12.98 0.00 0.00 3.79
3332 3586 1.602377 AGCGGCGACCTAAAAATATGC 59.398 47.619 12.98 0.00 0.00 3.14
3333 3587 5.607119 AATAGCGGCGACCTAAAAATATG 57.393 39.130 12.98 0.00 0.00 1.78
3334 3588 6.435428 CAAAATAGCGGCGACCTAAAAATAT 58.565 36.000 12.98 0.00 0.00 1.28
3335 3589 5.731126 GCAAAATAGCGGCGACCTAAAAATA 60.731 40.000 12.98 0.00 0.00 1.40
3336 3590 4.668289 CAAAATAGCGGCGACCTAAAAAT 58.332 39.130 12.98 0.00 0.00 1.82
3337 3591 3.671164 GCAAAATAGCGGCGACCTAAAAA 60.671 43.478 12.98 0.00 0.00 1.94
3338 3592 2.159490 GCAAAATAGCGGCGACCTAAAA 60.159 45.455 12.98 0.00 0.00 1.52
3339 3593 1.399089 GCAAAATAGCGGCGACCTAAA 59.601 47.619 12.98 0.00 0.00 1.85
3340 3594 1.011333 GCAAAATAGCGGCGACCTAA 58.989 50.000 12.98 0.00 0.00 2.69
3341 3595 0.177141 AGCAAAATAGCGGCGACCTA 59.823 50.000 12.98 3.44 40.15 3.08
3342 3596 1.078426 AGCAAAATAGCGGCGACCT 60.078 52.632 12.98 0.56 40.15 3.85
3343 3597 1.062525 CAGCAAAATAGCGGCGACC 59.937 57.895 12.98 0.00 40.15 4.79
3344 3598 1.003851 TACAGCAAAATAGCGGCGAC 58.996 50.000 12.98 1.23 40.15 5.19
3345 3599 1.286501 CTACAGCAAAATAGCGGCGA 58.713 50.000 12.98 0.00 40.15 5.54
3346 3600 0.316196 GCTACAGCAAAATAGCGGCG 60.316 55.000 0.51 0.51 41.59 6.46
3347 3601 3.533913 GCTACAGCAAAATAGCGGC 57.466 52.632 0.00 0.00 41.59 6.53
3350 3604 0.925721 GCGCGCTACAGCAAAATAGC 60.926 55.000 26.67 0.00 42.21 2.97
3351 3605 0.652592 AGCGCGCTACAGCAAAATAG 59.347 50.000 35.79 0.00 42.21 1.73
3352 3606 1.929230 TAGCGCGCTACAGCAAAATA 58.071 45.000 35.48 13.06 42.21 1.40
3353 3607 1.299541 ATAGCGCGCTACAGCAAAAT 58.700 45.000 40.42 22.12 42.21 1.82
3354 3608 1.083489 AATAGCGCGCTACAGCAAAA 58.917 45.000 40.42 20.74 42.21 2.44
3355 3609 1.083489 AAATAGCGCGCTACAGCAAA 58.917 45.000 40.42 21.55 42.21 3.68
3356 3610 1.083489 AAAATAGCGCGCTACAGCAA 58.917 45.000 40.42 22.36 42.21 3.91
3357 3611 1.083489 AAAAATAGCGCGCTACAGCA 58.917 45.000 40.42 23.17 42.21 4.41
3358 3612 3.897819 AAAAATAGCGCGCTACAGC 57.102 47.368 40.42 6.98 37.78 4.40
3374 3628 7.432838 GCGGTCTTGTAGTTTAACAATGAAAAA 59.567 33.333 0.00 0.00 38.61 1.94
3375 3629 6.913673 GCGGTCTTGTAGTTTAACAATGAAAA 59.086 34.615 0.00 0.00 38.61 2.29
3376 3630 6.261381 AGCGGTCTTGTAGTTTAACAATGAAA 59.739 34.615 0.00 0.00 38.61 2.69
3377 3631 5.761234 AGCGGTCTTGTAGTTTAACAATGAA 59.239 36.000 0.00 0.00 38.61 2.57
3378 3632 5.302360 AGCGGTCTTGTAGTTTAACAATGA 58.698 37.500 0.00 0.00 38.61 2.57
3379 3633 5.607119 AGCGGTCTTGTAGTTTAACAATG 57.393 39.130 0.00 0.00 38.61 2.82
3380 3634 6.315393 CCATAGCGGTCTTGTAGTTTAACAAT 59.685 38.462 0.00 0.00 38.61 2.71
3381 3635 5.640357 CCATAGCGGTCTTGTAGTTTAACAA 59.360 40.000 0.00 0.00 37.75 2.83
3382 3636 5.047164 TCCATAGCGGTCTTGTAGTTTAACA 60.047 40.000 0.00 0.00 35.57 2.41
3383 3637 5.413499 TCCATAGCGGTCTTGTAGTTTAAC 58.587 41.667 0.00 0.00 35.57 2.01
3384 3638 5.664294 TCCATAGCGGTCTTGTAGTTTAA 57.336 39.130 0.00 0.00 35.57 1.52
3385 3639 5.419788 TCTTCCATAGCGGTCTTGTAGTTTA 59.580 40.000 0.00 0.00 35.57 2.01
3386 3640 4.222145 TCTTCCATAGCGGTCTTGTAGTTT 59.778 41.667 0.00 0.00 35.57 2.66
3387 3641 3.767673 TCTTCCATAGCGGTCTTGTAGTT 59.232 43.478 0.00 0.00 35.57 2.24
3388 3642 3.130693 GTCTTCCATAGCGGTCTTGTAGT 59.869 47.826 0.00 0.00 35.57 2.73
3389 3643 3.130516 TGTCTTCCATAGCGGTCTTGTAG 59.869 47.826 0.00 0.00 35.57 2.74
3390 3644 3.093814 TGTCTTCCATAGCGGTCTTGTA 58.906 45.455 0.00 0.00 35.57 2.41
3391 3645 1.899814 TGTCTTCCATAGCGGTCTTGT 59.100 47.619 0.00 0.00 35.57 3.16
3392 3646 2.672961 TGTCTTCCATAGCGGTCTTG 57.327 50.000 0.00 0.00 35.57 3.02
3393 3647 4.694339 GTTATGTCTTCCATAGCGGTCTT 58.306 43.478 0.00 0.00 37.34 3.01
3394 3648 4.323553 GTTATGTCTTCCATAGCGGTCT 57.676 45.455 0.00 0.00 37.34 3.85
3407 3661 4.819105 TCATTGGTTCCTCGTTATGTCT 57.181 40.909 0.00 0.00 0.00 3.41
3411 3665 5.773176 ACCTTTTTCATTGGTTCCTCGTTAT 59.227 36.000 0.00 0.00 0.00 1.89
3426 3680 6.148948 CGAAAGTATTGCATGACCTTTTTCA 58.851 36.000 0.00 0.00 0.00 2.69
3450 3709 1.523758 ACCCATTTCTCGTTGCAGAC 58.476 50.000 0.00 0.00 0.00 3.51
3537 3797 5.807011 GCTCGCTCAATTGTCCATTATTTTT 59.193 36.000 5.13 0.00 0.00 1.94
3676 3937 2.413837 AGGCGCGCCTTATAAATACTG 58.586 47.619 45.60 0.00 45.70 2.74
3699 3961 5.578727 CGGCTATAAGGTCTGAATTAGATGC 59.421 44.000 0.00 0.00 37.83 3.91
3817 4079 3.708631 TGGAAGAATAGGAAGGAGCTCAG 59.291 47.826 17.19 0.00 0.00 3.35
3831 4093 3.005155 GTGTCAAGCAGCTTTGGAAGAAT 59.995 43.478 4.38 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.