Multiple sequence alignment - TraesCS1B01G203900

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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 TraesCS1B01G203900 chr1B 100.000 3350 0 0 1 3350 367889576 367886227 0.000000e+00 6187.0
1 TraesCS1B01G203900 chr1B 89.362 423 37 7 1 420 665819462 665819045 2.960000e-145 525.0
2 TraesCS1B01G203900 chr1D 96.252 2161 49 13 648 2780 233345963 233343807 0.000000e+00 3513.0
3 TraesCS1B01G203900 chr1D 93.006 529 20 7 2833 3350 233343812 233343290 0.000000e+00 756.0
4 TraesCS1B01G203900 chr1D 98.598 214 2 1 417 630 233346157 233345945 8.770000e-101 377.0
5 TraesCS1B01G203900 chr1A 95.714 2053 69 8 648 2686 314511331 314513378 0.000000e+00 3286.0
6 TraesCS1B01G203900 chr1A 91.573 534 17 10 2833 3348 314513557 314514080 0.000000e+00 712.0
7 TraesCS1B01G203900 chr1A 83.420 193 16 5 2604 2782 314513371 314513561 7.440000e-37 165.0
8 TraesCS1B01G203900 chr1A 88.571 140 7 8 493 630 314511217 314511349 9.620000e-36 161.0
9 TraesCS1B01G203900 chr5B 90.120 415 28 13 1 411 148877101 148877506 8.230000e-146 527.0
10 TraesCS1B01G203900 chr5B 88.889 54 4 1 2796 2849 398069787 398069838 7.760000e-07 65.8
11 TraesCS1B01G203900 chrUn 89.437 426 31 11 1 417 345775216 345774796 2.960000e-145 525.0
12 TraesCS1B01G203900 chr4B 89.252 428 29 13 1 417 578345992 578346413 1.380000e-143 520.0
13 TraesCS1B01G203900 chr3B 89.100 422 40 6 1 420 102472689 102473106 1.380000e-143 520.0
14 TraesCS1B01G203900 chr3B 88.599 421 35 10 1 416 762593596 762593184 1.790000e-137 499.0
15 TraesCS1B01G203900 chr3B 88.056 427 35 14 1 419 712185549 712185967 3.000000e-135 492.0
16 TraesCS1B01G203900 chr4A 88.263 426 38 10 1 416 669862484 669862061 1.790000e-137 499.0
17 TraesCS1B01G203900 chr4A 95.556 45 2 0 2792 2836 467263364 467263408 4.640000e-09 73.1
18 TraesCS1B01G203900 chr2B 88.084 428 34 12 1 416 14614381 14614803 3.000000e-135 492.0
19 TraesCS1B01G203900 chr6A 94.737 57 1 1 2777 2831 23497315 23497259 1.660000e-13 87.9
20 TraesCS1B01G203900 chr6A 94.737 57 1 1 2777 2831 112004289 112004345 1.660000e-13 87.9
21 TraesCS1B01G203900 chr6A 91.667 48 4 0 2792 2839 29544910 29544863 2.160000e-07 67.6
22 TraesCS1B01G203900 chr7B 94.444 54 1 1 2780 2831 391724098 391724045 7.700000e-12 82.4
23 TraesCS1B01G203900 chr7B 94.444 54 1 1 2780 2831 391748358 391748305 7.700000e-12 82.4
24 TraesCS1B01G203900 chr7B 100.000 28 0 0 2715 2742 531648594 531648621 6.000000e-03 52.8
25 TraesCS1B01G203900 chr6B 93.478 46 3 0 2792 2837 641887943 641887988 6.000000e-08 69.4
26 TraesCS1B01G203900 chr7A 91.667 48 4 0 2792 2839 649682363 649682410 2.160000e-07 67.6
27 TraesCS1B01G203900 chr7D 100.000 28 0 0 2715 2742 502870534 502870561 6.000000e-03 52.8
28 TraesCS1B01G203900 chr6D 100.000 28 0 0 2714 2741 273095814 273095787 6.000000e-03 52.8


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 TraesCS1B01G203900 chr1B 367886227 367889576 3349 True 6187.000000 6187 100.0000 1 3350 1 chr1B.!!$R1 3349
1 TraesCS1B01G203900 chr1D 233343290 233346157 2867 True 1548.666667 3513 95.9520 417 3350 3 chr1D.!!$R1 2933
2 TraesCS1B01G203900 chr1A 314511217 314514080 2863 False 1081.000000 3286 89.8195 493 3348 4 chr1A.!!$F1 2855

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
286 287 0.028902 AAGAAGCCGAAAACACGTGC 59.971 50.0 17.22 0.0 0.00 5.34 F
292 293 0.248134 CCGAAAACACGTGCGGAAAA 60.248 50.0 22.83 0.0 46.29 2.29 F
1818 1832 0.387929 GCCTATCCATGTTCGACGGA 59.612 55.0 0.00 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2243 0.098376 CTTTGCTCGCTGAGAATGCC 59.902 55.000 9.32 0.0 0.00 4.40 R
2250 2264 4.052229 CGCACCGTCTTCCCGACT 62.052 66.667 0.00 0.0 40.59 4.18 R
3102 3233 0.802607 GAGCGAGCGAACGGAAAGAT 60.803 55.000 0.00 0.0 0.00 2.40 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
17 18 3.181367 GCACAACCATGCCTCTCG 58.819 61.111 0.00 0.00 39.86 4.04
18 19 3.044059 GCACAACCATGCCTCTCGC 62.044 63.158 0.00 0.00 39.86 5.03
19 20 2.434884 ACAACCATGCCTCTCGCG 60.435 61.111 0.00 0.00 42.08 5.87
20 21 3.197790 CAACCATGCCTCTCGCGG 61.198 66.667 6.13 0.00 42.08 6.46
21 22 3.390521 AACCATGCCTCTCGCGGA 61.391 61.111 6.13 1.01 42.08 5.54
22 23 2.954684 AACCATGCCTCTCGCGGAA 61.955 57.895 6.13 0.00 42.08 4.30
23 24 2.587194 CCATGCCTCTCGCGGAAG 60.587 66.667 6.13 3.71 42.08 3.46
35 36 2.050442 CGGAAGCAAAACCGTGCC 60.050 61.111 0.00 0.00 46.14 5.01
36 37 2.551912 CGGAAGCAAAACCGTGCCT 61.552 57.895 0.00 0.00 46.14 4.75
37 38 1.285950 GGAAGCAAAACCGTGCCTC 59.714 57.895 0.00 0.00 46.14 4.70
38 39 1.172812 GGAAGCAAAACCGTGCCTCT 61.173 55.000 0.00 0.00 46.14 3.69
39 40 0.238553 GAAGCAAAACCGTGCCTCTC 59.761 55.000 0.00 0.00 46.14 3.20
40 41 1.507141 AAGCAAAACCGTGCCTCTCG 61.507 55.000 0.00 0.00 46.14 4.04
41 42 2.556287 CAAAACCGTGCCTCTCGC 59.444 61.111 0.00 0.00 38.31 5.03
48 49 4.261888 GTGCCTCTCGCGAAAGAA 57.738 55.556 11.91 0.00 42.08 2.52
49 50 2.528797 GTGCCTCTCGCGAAAGAAA 58.471 52.632 11.91 0.00 42.08 2.52
50 51 0.440371 GTGCCTCTCGCGAAAGAAAG 59.560 55.000 11.91 3.23 42.08 2.62
51 52 0.317160 TGCCTCTCGCGAAAGAAAGA 59.683 50.000 11.91 1.76 42.08 2.52
52 53 1.270094 TGCCTCTCGCGAAAGAAAGAA 60.270 47.619 11.91 0.00 42.08 2.52
53 54 1.798813 GCCTCTCGCGAAAGAAAGAAA 59.201 47.619 11.91 0.00 0.00 2.52
54 55 2.223377 GCCTCTCGCGAAAGAAAGAAAA 59.777 45.455 11.91 0.00 0.00 2.29
55 56 3.303791 GCCTCTCGCGAAAGAAAGAAAAA 60.304 43.478 11.91 0.00 0.00 1.94
56 57 4.212150 CCTCTCGCGAAAGAAAGAAAAAC 58.788 43.478 11.91 0.00 0.00 2.43
57 58 3.857194 TCTCGCGAAAGAAAGAAAAACG 58.143 40.909 11.33 0.00 0.00 3.60
58 59 3.307782 TCTCGCGAAAGAAAGAAAAACGT 59.692 39.130 11.33 0.00 0.00 3.99
59 60 3.347443 TCGCGAAAGAAAGAAAAACGTG 58.653 40.909 6.20 0.00 0.00 4.49
60 61 3.095738 CGCGAAAGAAAGAAAAACGTGT 58.904 40.909 0.00 0.00 0.00 4.49
61 62 4.032672 TCGCGAAAGAAAGAAAAACGTGTA 59.967 37.500 6.20 0.00 0.00 2.90
62 63 4.724807 CGCGAAAGAAAGAAAAACGTGTAA 59.275 37.500 0.00 0.00 0.00 2.41
63 64 5.225538 CGCGAAAGAAAGAAAAACGTGTAAA 59.774 36.000 0.00 0.00 0.00 2.01
64 65 6.236993 CGCGAAAGAAAGAAAAACGTGTAAAA 60.237 34.615 0.00 0.00 0.00 1.52
65 66 6.885702 GCGAAAGAAAGAAAAACGTGTAAAAC 59.114 34.615 0.00 0.00 0.00 2.43
66 67 7.409555 GCGAAAGAAAGAAAAACGTGTAAAACA 60.410 33.333 0.00 0.00 0.00 2.83
67 68 7.884222 CGAAAGAAAGAAAAACGTGTAAAACAC 59.116 33.333 0.00 0.01 45.26 3.32
92 93 3.430333 TTTTTCGTTTCCAAGAGGCAC 57.570 42.857 0.00 0.00 33.74 5.01
93 94 0.941542 TTTCGTTTCCAAGAGGCACG 59.058 50.000 0.00 0.00 40.61 5.34
94 95 0.882927 TTCGTTTCCAAGAGGCACGG 60.883 55.000 0.00 0.00 40.04 4.94
95 96 2.954611 GTTTCCAAGAGGCACGGC 59.045 61.111 0.00 0.00 33.74 5.68
130 131 3.414700 CACAACCGTGCCTCTCGC 61.415 66.667 0.00 0.00 36.06 5.03
137 138 3.637714 GTGCCTCTCGCGAAAACA 58.362 55.556 11.33 3.24 42.08 2.83
138 139 1.938861 GTGCCTCTCGCGAAAACAA 59.061 52.632 11.33 0.00 42.08 2.83
139 140 0.306533 GTGCCTCTCGCGAAAACAAA 59.693 50.000 11.33 0.00 42.08 2.83
140 141 1.018148 TGCCTCTCGCGAAAACAAAA 58.982 45.000 11.33 0.00 42.08 2.44
141 142 1.268335 TGCCTCTCGCGAAAACAAAAC 60.268 47.619 11.33 0.00 42.08 2.43
142 143 1.924629 GCCTCTCGCGAAAACAAAACC 60.925 52.381 11.33 0.00 0.00 3.27
143 144 1.658968 CTCTCGCGAAAACAAAACCG 58.341 50.000 11.33 0.00 0.00 4.44
144 145 1.004292 CTCTCGCGAAAACAAAACCGT 60.004 47.619 11.33 0.00 0.00 4.83
145 146 1.109296 CTCGCGAAAACAAAACCGTG 58.891 50.000 11.33 0.00 0.00 4.94
146 147 0.725686 TCGCGAAAACAAAACCGTGA 59.274 45.000 6.20 0.00 38.89 4.35
147 148 0.835120 CGCGAAAACAAAACCGTGAC 59.165 50.000 0.00 0.00 34.86 3.67
148 149 1.530236 CGCGAAAACAAAACCGTGACT 60.530 47.619 0.00 0.00 34.86 3.41
149 150 2.106418 GCGAAAACAAAACCGTGACTC 58.894 47.619 0.00 0.00 0.00 3.36
150 151 2.223180 GCGAAAACAAAACCGTGACTCT 60.223 45.455 0.00 0.00 0.00 3.24
151 152 3.604392 CGAAAACAAAACCGTGACTCTC 58.396 45.455 0.00 0.00 0.00 3.20
152 153 3.545426 CGAAAACAAAACCGTGACTCTCC 60.545 47.826 0.00 0.00 0.00 3.71
153 154 1.963172 AACAAAACCGTGACTCTCCC 58.037 50.000 0.00 0.00 0.00 4.30
154 155 0.249741 ACAAAACCGTGACTCTCCCG 60.250 55.000 0.00 0.00 0.00 5.14
155 156 0.032952 CAAAACCGTGACTCTCCCGA 59.967 55.000 0.00 0.00 0.00 5.14
156 157 0.754472 AAAACCGTGACTCTCCCGAA 59.246 50.000 0.00 0.00 0.00 4.30
157 158 0.754472 AAACCGTGACTCTCCCGAAA 59.246 50.000 0.00 0.00 0.00 3.46
158 159 0.754472 AACCGTGACTCTCCCGAAAA 59.246 50.000 0.00 0.00 0.00 2.29
159 160 0.754472 ACCGTGACTCTCCCGAAAAA 59.246 50.000 0.00 0.00 0.00 1.94
217 218 3.495434 TTTTGGTCGAAAAGCTAGGGA 57.505 42.857 0.00 0.00 0.00 4.20
218 219 3.495434 TTTGGTCGAAAAGCTAGGGAA 57.505 42.857 0.00 0.00 0.00 3.97
219 220 2.762535 TGGTCGAAAAGCTAGGGAAG 57.237 50.000 0.00 0.00 0.00 3.46
220 221 2.253610 TGGTCGAAAAGCTAGGGAAGA 58.746 47.619 0.00 0.00 0.00 2.87
221 222 2.028385 TGGTCGAAAAGCTAGGGAAGAC 60.028 50.000 0.00 0.00 0.00 3.01
222 223 2.619147 GTCGAAAAGCTAGGGAAGACC 58.381 52.381 0.00 0.00 40.67 3.85
223 224 1.203994 TCGAAAAGCTAGGGAAGACCG 59.796 52.381 0.00 0.00 46.96 4.79
224 225 1.739371 CGAAAAGCTAGGGAAGACCGG 60.739 57.143 0.00 0.00 46.96 5.28
225 226 1.278413 GAAAAGCTAGGGAAGACCGGT 59.722 52.381 6.92 6.92 46.96 5.28
226 227 0.613777 AAAGCTAGGGAAGACCGGTG 59.386 55.000 14.63 0.00 46.96 4.94
227 228 1.265454 AAGCTAGGGAAGACCGGTGG 61.265 60.000 14.63 0.00 46.96 4.61
228 229 1.684734 GCTAGGGAAGACCGGTGGA 60.685 63.158 14.63 0.00 46.96 4.02
229 230 1.262640 GCTAGGGAAGACCGGTGGAA 61.263 60.000 14.63 0.00 46.96 3.53
230 231 1.272807 CTAGGGAAGACCGGTGGAAA 58.727 55.000 14.63 0.00 46.96 3.13
231 232 1.626825 CTAGGGAAGACCGGTGGAAAA 59.373 52.381 14.63 0.00 46.96 2.29
232 233 0.109913 AGGGAAGACCGGTGGAAAAC 59.890 55.000 14.63 0.00 46.96 2.43
233 234 0.892358 GGGAAGACCGGTGGAAAACC 60.892 60.000 14.63 6.56 46.60 3.27
275 276 3.358707 AAAAACCCGTTTAAGAAGCCG 57.641 42.857 0.00 0.00 31.63 5.52
276 277 2.259266 AAACCCGTTTAAGAAGCCGA 57.741 45.000 0.00 0.00 0.00 5.54
277 278 2.259266 AACCCGTTTAAGAAGCCGAA 57.741 45.000 0.00 0.00 0.00 4.30
278 279 2.259266 ACCCGTTTAAGAAGCCGAAA 57.741 45.000 0.00 0.00 0.00 3.46
279 280 2.574450 ACCCGTTTAAGAAGCCGAAAA 58.426 42.857 0.00 0.00 0.00 2.29
280 281 2.291465 ACCCGTTTAAGAAGCCGAAAAC 59.709 45.455 0.00 0.00 0.00 2.43
281 282 2.291190 CCCGTTTAAGAAGCCGAAAACA 59.709 45.455 0.00 0.00 32.61 2.83
282 283 3.294102 CCGTTTAAGAAGCCGAAAACAC 58.706 45.455 0.00 0.00 32.61 3.32
283 284 2.962191 CGTTTAAGAAGCCGAAAACACG 59.038 45.455 0.00 0.00 32.61 4.49
284 285 3.544637 CGTTTAAGAAGCCGAAAACACGT 60.545 43.478 0.00 0.00 32.61 4.49
285 286 3.595709 TTAAGAAGCCGAAAACACGTG 57.404 42.857 15.48 15.48 0.00 4.49
286 287 0.028902 AAGAAGCCGAAAACACGTGC 59.971 50.000 17.22 0.00 0.00 5.34
287 288 1.721133 GAAGCCGAAAACACGTGCG 60.721 57.895 17.22 10.98 35.71 5.34
288 289 3.175976 AAGCCGAAAACACGTGCGG 62.176 57.895 22.90 22.90 46.14 5.69
289 290 3.641986 GCCGAAAACACGTGCGGA 61.642 61.111 28.86 0.00 46.29 5.54
290 291 3.015677 CCGAAAACACGTGCGGAA 58.984 55.556 22.83 0.00 46.29 4.30
291 292 1.352404 CCGAAAACACGTGCGGAAA 59.648 52.632 22.83 0.00 46.29 3.13
292 293 0.248134 CCGAAAACACGTGCGGAAAA 60.248 50.000 22.83 0.00 46.29 2.29
293 294 1.598430 CCGAAAACACGTGCGGAAAAT 60.598 47.619 22.83 0.00 46.29 1.82
294 295 2.349627 CCGAAAACACGTGCGGAAAATA 60.350 45.455 22.83 0.00 46.29 1.40
295 296 3.289911 CGAAAACACGTGCGGAAAATAA 58.710 40.909 17.22 0.00 0.00 1.40
296 297 3.724751 CGAAAACACGTGCGGAAAATAAA 59.275 39.130 17.22 0.00 0.00 1.40
297 298 4.204573 CGAAAACACGTGCGGAAAATAAAA 59.795 37.500 17.22 0.00 0.00 1.52
298 299 5.275788 CGAAAACACGTGCGGAAAATAAAAA 60.276 36.000 17.22 0.00 0.00 1.94
337 338 4.368808 CCCAAAGCGCGACACGTG 62.369 66.667 15.48 15.48 46.11 4.49
338 339 4.368808 CCAAAGCGCGACACGTGG 62.369 66.667 21.57 5.21 46.11 4.94
362 363 4.427661 GCTGAGAGCGCGTCAGGT 62.428 66.667 31.39 4.67 41.60 4.00
363 364 2.505777 CTGAGAGCGCGTCAGGTG 60.506 66.667 26.43 9.62 38.24 4.00
364 365 2.982744 CTGAGAGCGCGTCAGGTGA 61.983 63.158 26.43 3.09 38.24 4.02
365 366 2.505118 GAGAGCGCGTCAGGTGAC 60.505 66.667 8.43 0.00 41.47 3.67
373 374 4.079090 GTCAGGTGACGCTGATCG 57.921 61.111 6.97 0.00 45.38 3.69
383 384 2.510238 GCTGATCGTTGCGAGGCT 60.510 61.111 0.00 0.00 39.91 4.58
384 385 2.103042 GCTGATCGTTGCGAGGCTT 61.103 57.895 0.00 0.00 39.91 4.35
385 386 2.002127 CTGATCGTTGCGAGGCTTC 58.998 57.895 0.00 0.00 39.91 3.86
386 387 1.424493 CTGATCGTTGCGAGGCTTCC 61.424 60.000 0.00 0.00 39.91 3.46
387 388 2.509336 ATCGTTGCGAGGCTTCCG 60.509 61.111 0.00 0.00 39.91 4.30
388 389 2.884087 GATCGTTGCGAGGCTTCCGA 62.884 60.000 0.00 0.00 39.91 4.55
389 390 2.501223 ATCGTTGCGAGGCTTCCGAA 62.501 55.000 0.00 0.00 39.91 4.30
390 391 2.730672 CGTTGCGAGGCTTCCGAAG 61.731 63.158 3.56 3.56 0.00 3.79
407 408 4.418572 CGAAGGAACGCTCGTTAATTAG 57.581 45.455 7.70 3.29 38.60 1.73
408 409 3.855950 CGAAGGAACGCTCGTTAATTAGT 59.144 43.478 7.70 0.00 38.60 2.24
409 410 4.325472 CGAAGGAACGCTCGTTAATTAGTT 59.675 41.667 7.70 0.00 38.60 2.24
410 411 5.526010 AAGGAACGCTCGTTAATTAGTTG 57.474 39.130 7.70 0.00 38.60 3.16
411 412 4.563061 AGGAACGCTCGTTAATTAGTTGT 58.437 39.130 7.70 0.00 38.60 3.32
412 413 4.992951 AGGAACGCTCGTTAATTAGTTGTT 59.007 37.500 7.70 0.00 38.60 2.83
413 414 5.119743 AGGAACGCTCGTTAATTAGTTGTTC 59.880 40.000 7.70 13.08 38.60 3.18
414 415 4.916099 ACGCTCGTTAATTAGTTGTTCC 57.084 40.909 0.00 0.00 0.00 3.62
415 416 3.681417 ACGCTCGTTAATTAGTTGTTCCC 59.319 43.478 0.00 0.00 0.00 3.97
589 590 3.690139 TGGCAGTCAACGAGTTTTTACAA 59.310 39.130 0.00 0.00 0.00 2.41
630 631 7.822822 ACCGTGAGCAAACTATAACTATTCTTT 59.177 33.333 0.00 0.00 0.00 2.52
631 632 8.665685 CCGTGAGCAAACTATAACTATTCTTTT 58.334 33.333 0.00 0.00 0.00 2.27
844 850 1.604378 CCCAACTCCGCTCCATTCT 59.396 57.895 0.00 0.00 0.00 2.40
1147 1161 4.760047 CCGACCCGCAGAACCCTG 62.760 72.222 0.00 0.00 43.22 4.45
1818 1832 0.387929 GCCTATCCATGTTCGACGGA 59.612 55.000 0.00 0.00 0.00 4.69
2037 2051 3.841643 CATTGAGTCCTCATTGTTTGGC 58.158 45.455 9.84 0.00 39.64 4.52
2053 2067 1.001641 GGCAATCCAGACTGCAGGT 60.002 57.895 19.93 3.31 40.46 4.00
2115 2129 0.807275 TCATCACGATGGCAAGCTCG 60.807 55.000 7.39 7.39 39.24 5.03
2190 2204 2.590092 GTTAGCCGGGGCACAGAT 59.410 61.111 12.97 0.00 44.88 2.90
2220 2234 2.679837 GGTGTACATGGAGAGCATTGTG 59.320 50.000 0.00 0.00 0.00 3.33
2250 2264 1.466167 GCATTCTCAGCGAGCAAAGAA 59.534 47.619 12.32 12.32 32.69 2.52
2355 2369 3.781407 TGTACCTAGAGTCCTAGACTGCT 59.219 47.826 1.16 2.59 43.53 4.24
2363 2377 1.754621 CCTAGACTGCTGAGGGCGA 60.755 63.158 0.00 0.00 45.43 5.54
2364 2378 1.112315 CCTAGACTGCTGAGGGCGAT 61.112 60.000 0.00 0.00 45.43 4.58
2584 2601 4.149598 GTGTAAAAGGGGGTGTTCTTGAT 58.850 43.478 0.00 0.00 0.00 2.57
2613 2631 3.184581 CGTTGTACAAAGGTTCAGAGAGC 59.815 47.826 10.51 0.00 0.00 4.09
2632 2650 4.993584 AGAGCTGTGTTCTAACATTGTCAG 59.006 41.667 0.00 3.31 41.59 3.51
2645 2733 8.731605 TCTAACATTGTCAGAGAGTTACTACTG 58.268 37.037 11.04 11.04 33.84 2.74
2648 2736 5.378292 TTGTCAGAGAGTTACTACTGCTG 57.622 43.478 12.01 5.82 35.92 4.41
2714 2813 6.493189 TTCCTTGTGCTGATATATACACCA 57.507 37.500 9.37 0.79 31.98 4.17
2721 2834 7.312899 TGTGCTGATATATACACCATAAGACG 58.687 38.462 9.37 0.00 31.98 4.18
2743 2856 7.704472 AGACGTTTTTGCAGTTCAAATTGATTA 59.296 29.630 0.00 0.00 43.53 1.75
2775 2891 3.690139 TGAACTGCAAAAACGTCTGGTAA 59.310 39.130 0.00 0.00 0.00 2.85
2780 2896 6.225318 ACTGCAAAAACGTCTGGTAATACTA 58.775 36.000 0.00 0.00 0.00 1.82
2781 2897 6.146673 ACTGCAAAAACGTCTGGTAATACTAC 59.853 38.462 0.00 0.00 0.00 2.73
2783 2899 5.640783 GCAAAAACGTCTGGTAATACTACCT 59.359 40.000 1.49 0.00 46.97 3.08
2784 2900 6.183360 GCAAAAACGTCTGGTAATACTACCTC 60.183 42.308 1.49 0.00 46.97 3.85
2785 2901 6.847421 AAAACGTCTGGTAATACTACCTCT 57.153 37.500 1.49 0.00 46.97 3.69
2786 2902 5.831702 AACGTCTGGTAATACTACCTCTG 57.168 43.478 1.49 0.00 46.97 3.35
2787 2903 4.853007 ACGTCTGGTAATACTACCTCTGT 58.147 43.478 1.49 0.00 46.97 3.41
2788 2904 5.994250 ACGTCTGGTAATACTACCTCTGTA 58.006 41.667 1.49 0.00 46.97 2.74
2789 2905 5.819901 ACGTCTGGTAATACTACCTCTGTAC 59.180 44.000 1.49 0.00 46.97 2.90
2790 2906 5.238214 CGTCTGGTAATACTACCTCTGTACC 59.762 48.000 1.49 0.00 46.97 3.34
2791 2907 6.125029 GTCTGGTAATACTACCTCTGTACCA 58.875 44.000 1.49 0.00 46.97 3.25
2792 2908 6.604795 GTCTGGTAATACTACCTCTGTACCAA 59.395 42.308 1.49 0.00 46.97 3.67
2793 2909 7.123247 GTCTGGTAATACTACCTCTGTACCAAA 59.877 40.741 1.49 0.00 46.97 3.28
2794 2910 7.675195 TCTGGTAATACTACCTCTGTACCAAAA 59.325 37.037 1.49 0.00 46.97 2.44
2795 2911 8.383374 TGGTAATACTACCTCTGTACCAAAAT 57.617 34.615 1.49 0.00 46.97 1.82
2796 2912 9.491406 TGGTAATACTACCTCTGTACCAAAATA 57.509 33.333 1.49 0.00 46.97 1.40
2797 2913 9.978044 GGTAATACTACCTCTGTACCAAAATAG 57.022 37.037 0.00 0.00 43.92 1.73
2798 2914 9.473640 GTAATACTACCTCTGTACCAAAATAGC 57.526 37.037 0.00 0.00 0.00 2.97
2799 2915 5.354842 ACTACCTCTGTACCAAAATAGCC 57.645 43.478 0.00 0.00 0.00 3.93
2800 2916 5.030820 ACTACCTCTGTACCAAAATAGCCT 58.969 41.667 0.00 0.00 0.00 4.58
2801 2917 6.200114 ACTACCTCTGTACCAAAATAGCCTA 58.800 40.000 0.00 0.00 0.00 3.93
2802 2918 5.354842 ACCTCTGTACCAAAATAGCCTAC 57.645 43.478 0.00 0.00 0.00 3.18
2803 2919 4.781087 ACCTCTGTACCAAAATAGCCTACA 59.219 41.667 0.00 0.00 0.00 2.74
2804 2920 5.249852 ACCTCTGTACCAAAATAGCCTACAA 59.750 40.000 0.00 0.00 0.00 2.41
2805 2921 6.177610 CCTCTGTACCAAAATAGCCTACAAA 58.822 40.000 0.00 0.00 0.00 2.83
2806 2922 6.657541 CCTCTGTACCAAAATAGCCTACAAAA 59.342 38.462 0.00 0.00 0.00 2.44
2807 2923 7.175990 CCTCTGTACCAAAATAGCCTACAAAAA 59.824 37.037 0.00 0.00 0.00 1.94
2808 2924 8.644374 TCTGTACCAAAATAGCCTACAAAAAT 57.356 30.769 0.00 0.00 0.00 1.82
2809 2925 8.519526 TCTGTACCAAAATAGCCTACAAAAATG 58.480 33.333 0.00 0.00 0.00 2.32
2810 2926 8.184304 TGTACCAAAATAGCCTACAAAAATGT 57.816 30.769 0.00 0.00 0.00 2.71
2811 2927 8.301002 TGTACCAAAATAGCCTACAAAAATGTC 58.699 33.333 0.00 0.00 0.00 3.06
2812 2928 7.539034 ACCAAAATAGCCTACAAAAATGTCT 57.461 32.000 0.00 0.00 0.00 3.41
2813 2929 7.962441 ACCAAAATAGCCTACAAAAATGTCTT 58.038 30.769 0.00 0.00 0.00 3.01
2814 2930 9.084533 ACCAAAATAGCCTACAAAAATGTCTTA 57.915 29.630 0.00 0.00 0.00 2.10
2834 2950 9.213777 TGTCTTATATTTTGATACAGAGGGAGT 57.786 33.333 0.00 0.00 0.00 3.85
2882 2998 8.029782 TGTGTAAATCTACAGGCTGGTAATAT 57.970 34.615 20.34 3.46 38.73 1.28
2906 3022 4.216902 TGCATTCTGTCTTGTCTGAAATGG 59.783 41.667 0.00 0.00 0.00 3.16
2908 3024 5.278660 GCATTCTGTCTTGTCTGAAATGGTT 60.279 40.000 0.00 0.00 0.00 3.67
2959 3076 2.115291 GGCGTCTTGATTGAGGGCC 61.115 63.158 0.00 0.00 40.13 5.80
3037 3160 6.314784 GTTAATGGATGTGTGTGCTTAAGAC 58.685 40.000 6.67 2.51 0.00 3.01
3068 3199 1.679139 TCCATGATTGATTCGGGCAC 58.321 50.000 0.00 0.00 0.00 5.01
3094 3225 0.603707 CGCACTTTCTGCCTTGAGGA 60.604 55.000 0.06 0.00 43.84 3.71
3102 3233 2.908015 GCCTTGAGGACGGGCATA 59.092 61.111 0.06 0.00 44.69 3.14
3104 3235 0.603975 GCCTTGAGGACGGGCATATC 60.604 60.000 0.06 0.00 44.69 1.63
3106 3237 1.417890 CCTTGAGGACGGGCATATCTT 59.582 52.381 0.00 0.00 37.39 2.40
3107 3238 2.158755 CCTTGAGGACGGGCATATCTTT 60.159 50.000 0.00 0.00 37.39 2.52
3108 3239 2.910688 TGAGGACGGGCATATCTTTC 57.089 50.000 0.00 0.00 0.00 2.62
3115 3248 0.586802 GGGCATATCTTTCCGTTCGC 59.413 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.044059 GCGAGAGGCATGGTTGTGC 62.044 63.158 0.00 0.00 44.31 4.57
1 2 2.743752 CGCGAGAGGCATGGTTGTG 61.744 63.158 0.00 0.00 43.84 3.33
3 4 3.197790 CCGCGAGAGGCATGGTTG 61.198 66.667 8.23 0.00 43.84 3.77
6 7 2.587194 CTTCCGCGAGAGGCATGG 60.587 66.667 8.23 0.00 43.84 3.66
7 8 3.267860 GCTTCCGCGAGAGGCATG 61.268 66.667 20.89 0.00 46.54 4.06
11 12 1.497722 GTTTTGCTTCCGCGAGAGG 59.502 57.895 8.23 4.88 39.65 3.69
12 13 1.497722 GGTTTTGCTTCCGCGAGAG 59.502 57.895 8.23 5.93 39.65 3.20
13 14 2.314647 CGGTTTTGCTTCCGCGAGA 61.315 57.895 8.23 0.00 40.28 4.04
14 15 2.173382 CGGTTTTGCTTCCGCGAG 59.827 61.111 8.23 0.00 40.28 5.03
19 20 1.172812 AGAGGCACGGTTTTGCTTCC 61.173 55.000 4.54 0.00 46.96 3.46
20 21 0.238553 GAGAGGCACGGTTTTGCTTC 59.761 55.000 0.28 0.28 46.31 3.86
21 22 1.507141 CGAGAGGCACGGTTTTGCTT 61.507 55.000 0.00 0.00 42.56 3.91
22 23 1.961277 CGAGAGGCACGGTTTTGCT 60.961 57.895 0.00 0.00 42.56 3.91
23 24 2.556287 CGAGAGGCACGGTTTTGC 59.444 61.111 0.00 0.00 42.18 3.68
24 25 2.556287 GCGAGAGGCACGGTTTTG 59.444 61.111 0.00 0.00 42.87 2.44
25 26 2.981977 TTCGCGAGAGGCACGGTTTT 62.982 55.000 9.59 0.00 43.84 2.43
26 27 2.981977 TTTCGCGAGAGGCACGGTTT 62.982 55.000 9.59 0.00 43.84 3.27
27 28 3.509137 TTTCGCGAGAGGCACGGTT 62.509 57.895 9.59 0.00 43.84 4.44
28 29 3.916392 CTTTCGCGAGAGGCACGGT 62.916 63.158 18.35 0.00 43.84 4.83
29 30 3.181967 CTTTCGCGAGAGGCACGG 61.182 66.667 18.35 0.00 43.84 4.94
30 31 1.282248 TTTCTTTCGCGAGAGGCACG 61.282 55.000 24.53 1.69 43.84 5.34
31 32 0.440371 CTTTCTTTCGCGAGAGGCAC 59.560 55.000 24.53 0.00 43.84 5.01
32 33 0.317160 TCTTTCTTTCGCGAGAGGCA 59.683 50.000 24.53 10.58 43.84 4.75
33 34 1.429463 TTCTTTCTTTCGCGAGAGGC 58.571 50.000 24.53 0.00 43.69 4.70
34 35 4.212150 GTTTTTCTTTCTTTCGCGAGAGG 58.788 43.478 24.53 10.46 43.69 3.69
35 36 3.894868 CGTTTTTCTTTCTTTCGCGAGAG 59.105 43.478 19.89 19.89 43.69 3.20
36 37 3.307782 ACGTTTTTCTTTCTTTCGCGAGA 59.692 39.130 9.59 3.35 39.20 4.04
37 38 3.414422 CACGTTTTTCTTTCTTTCGCGAG 59.586 43.478 9.59 0.00 0.00 5.03
38 39 3.181518 ACACGTTTTTCTTTCTTTCGCGA 60.182 39.130 3.71 3.71 0.00 5.87
39 40 3.095738 ACACGTTTTTCTTTCTTTCGCG 58.904 40.909 0.00 0.00 0.00 5.87
40 41 6.543187 TTTACACGTTTTTCTTTCTTTCGC 57.457 33.333 0.00 0.00 0.00 4.70
41 42 7.884222 GTGTTTTACACGTTTTTCTTTCTTTCG 59.116 33.333 0.00 0.00 39.53 3.46
72 73 2.223386 CGTGCCTCTTGGAAACGAAAAA 60.223 45.455 0.00 0.00 43.27 1.94
73 74 1.332375 CGTGCCTCTTGGAAACGAAAA 59.668 47.619 0.00 0.00 43.27 2.29
74 75 0.941542 CGTGCCTCTTGGAAACGAAA 59.058 50.000 0.00 0.00 43.27 3.46
75 76 0.882927 CCGTGCCTCTTGGAAACGAA 60.883 55.000 10.74 0.00 43.27 3.85
76 77 1.301401 CCGTGCCTCTTGGAAACGA 60.301 57.895 10.74 0.00 43.27 3.85
77 78 2.966309 GCCGTGCCTCTTGGAAACG 61.966 63.158 0.00 0.00 41.54 3.60
78 79 2.626780 GGCCGTGCCTCTTGGAAAC 61.627 63.158 7.58 0.00 46.69 2.78
79 80 2.282180 GGCCGTGCCTCTTGGAAA 60.282 61.111 7.58 0.00 46.69 3.13
95 96 3.181967 CTTTCGCGAGAGGCACGG 61.182 66.667 18.35 0.00 43.84 4.94
96 97 3.843240 GCTTTCGCGAGAGGCACG 61.843 66.667 25.84 3.72 43.84 5.34
97 98 2.738521 TGCTTTCGCGAGAGGCAC 60.739 61.111 25.84 11.56 42.51 5.01
98 99 2.738521 GTGCTTTCGCGAGAGGCA 60.739 61.111 25.84 23.78 44.13 4.75
99 100 2.317609 TTGTGCTTTCGCGAGAGGC 61.318 57.895 25.84 21.76 43.69 4.70
100 101 1.493311 GTTGTGCTTTCGCGAGAGG 59.507 57.895 25.84 13.55 43.69 3.69
101 102 1.493311 GGTTGTGCTTTCGCGAGAG 59.507 57.895 21.42 21.42 43.69 3.20
102 103 2.307309 CGGTTGTGCTTTCGCGAGA 61.307 57.895 9.59 3.35 39.65 4.04
103 104 2.170985 CGGTTGTGCTTTCGCGAG 59.829 61.111 9.59 0.00 39.65 5.03
104 105 2.586635 ACGGTTGTGCTTTCGCGA 60.587 55.556 3.71 3.71 39.65 5.87
105 106 2.425124 CACGGTTGTGCTTTCGCG 60.425 61.111 0.00 0.00 39.67 5.87
115 116 4.717629 TCGCGAGAGGCACGGTTG 62.718 66.667 3.71 0.00 43.84 3.77
116 117 2.981977 TTTTCGCGAGAGGCACGGTT 62.982 55.000 9.59 0.00 43.84 4.44
117 118 3.509137 TTTTCGCGAGAGGCACGGT 62.509 57.895 9.59 0.00 43.84 4.83
118 119 2.736995 TTTTCGCGAGAGGCACGG 60.737 61.111 9.59 0.00 43.84 4.94
119 120 1.827315 TTGTTTTCGCGAGAGGCACG 61.827 55.000 9.59 0.00 43.84 5.34
120 121 0.306533 TTTGTTTTCGCGAGAGGCAC 59.693 50.000 9.59 0.37 43.84 5.01
121 122 1.018148 TTTTGTTTTCGCGAGAGGCA 58.982 45.000 9.59 5.38 43.84 4.75
122 123 1.395670 GTTTTGTTTTCGCGAGAGGC 58.604 50.000 9.59 2.53 43.69 4.70
123 124 1.659211 CGGTTTTGTTTTCGCGAGAGG 60.659 52.381 9.59 0.00 43.69 3.69
124 125 1.004292 ACGGTTTTGTTTTCGCGAGAG 60.004 47.619 9.59 0.00 43.69 3.20
125 126 1.008329 ACGGTTTTGTTTTCGCGAGA 58.992 45.000 9.59 0.43 39.20 4.04
126 127 1.109296 CACGGTTTTGTTTTCGCGAG 58.891 50.000 9.59 0.00 0.00 5.03
127 128 0.725686 TCACGGTTTTGTTTTCGCGA 59.274 45.000 3.71 3.71 0.00 5.87
128 129 0.835120 GTCACGGTTTTGTTTTCGCG 59.165 50.000 0.00 0.00 0.00 5.87
129 130 2.106418 GAGTCACGGTTTTGTTTTCGC 58.894 47.619 0.00 0.00 0.00 4.70
130 131 3.545426 GGAGAGTCACGGTTTTGTTTTCG 60.545 47.826 0.00 0.00 0.00 3.46
131 132 3.242969 GGGAGAGTCACGGTTTTGTTTTC 60.243 47.826 0.00 0.00 0.00 2.29
132 133 2.686405 GGGAGAGTCACGGTTTTGTTTT 59.314 45.455 0.00 0.00 0.00 2.43
133 134 2.294979 GGGAGAGTCACGGTTTTGTTT 58.705 47.619 0.00 0.00 0.00 2.83
134 135 1.808891 CGGGAGAGTCACGGTTTTGTT 60.809 52.381 0.00 0.00 40.12 2.83
135 136 0.249741 CGGGAGAGTCACGGTTTTGT 60.250 55.000 0.00 0.00 40.12 2.83
136 137 0.032952 TCGGGAGAGTCACGGTTTTG 59.967 55.000 0.00 0.00 44.75 2.44
137 138 0.754472 TTCGGGAGAGTCACGGTTTT 59.246 50.000 0.00 0.00 44.75 2.43
138 139 0.754472 TTTCGGGAGAGTCACGGTTT 59.246 50.000 0.00 0.00 44.75 3.27
139 140 0.754472 TTTTCGGGAGAGTCACGGTT 59.246 50.000 0.00 0.00 44.75 4.44
140 141 0.754472 TTTTTCGGGAGAGTCACGGT 59.246 50.000 0.00 0.00 44.75 4.83
141 142 3.599412 TTTTTCGGGAGAGTCACGG 57.401 52.632 0.00 0.00 44.75 4.94
196 197 3.822940 TCCCTAGCTTTTCGACCAAAAA 58.177 40.909 0.00 0.00 33.40 1.94
197 198 3.495434 TCCCTAGCTTTTCGACCAAAA 57.505 42.857 0.00 0.00 32.77 2.44
198 199 3.071892 TCTTCCCTAGCTTTTCGACCAAA 59.928 43.478 0.00 0.00 0.00 3.28
199 200 2.635915 TCTTCCCTAGCTTTTCGACCAA 59.364 45.455 0.00 0.00 0.00 3.67
200 201 2.028385 GTCTTCCCTAGCTTTTCGACCA 60.028 50.000 0.00 0.00 0.00 4.02
201 202 2.619147 GTCTTCCCTAGCTTTTCGACC 58.381 52.381 0.00 0.00 0.00 4.79
202 203 2.619147 GGTCTTCCCTAGCTTTTCGAC 58.381 52.381 0.00 0.00 0.00 4.20
203 204 1.203994 CGGTCTTCCCTAGCTTTTCGA 59.796 52.381 0.00 0.00 0.00 3.71
204 205 1.641577 CGGTCTTCCCTAGCTTTTCG 58.358 55.000 0.00 0.00 0.00 3.46
205 206 1.278413 ACCGGTCTTCCCTAGCTTTTC 59.722 52.381 0.00 0.00 0.00 2.29
206 207 1.003233 CACCGGTCTTCCCTAGCTTTT 59.997 52.381 2.59 0.00 0.00 2.27
207 208 0.613777 CACCGGTCTTCCCTAGCTTT 59.386 55.000 2.59 0.00 0.00 3.51
208 209 1.265454 CCACCGGTCTTCCCTAGCTT 61.265 60.000 2.59 0.00 0.00 3.74
209 210 1.686110 CCACCGGTCTTCCCTAGCT 60.686 63.158 2.59 0.00 0.00 3.32
210 211 1.262640 TTCCACCGGTCTTCCCTAGC 61.263 60.000 2.59 0.00 0.00 3.42
211 212 1.272807 TTTCCACCGGTCTTCCCTAG 58.727 55.000 2.59 0.00 0.00 3.02
212 213 1.348696 GTTTTCCACCGGTCTTCCCTA 59.651 52.381 2.59 0.00 0.00 3.53
213 214 0.109913 GTTTTCCACCGGTCTTCCCT 59.890 55.000 2.59 0.00 0.00 4.20
214 215 0.892358 GGTTTTCCACCGGTCTTCCC 60.892 60.000 2.59 0.00 40.31 3.97
215 216 2.637521 GGTTTTCCACCGGTCTTCC 58.362 57.895 2.59 0.00 40.31 3.46
255 256 2.950975 TCGGCTTCTTAAACGGGTTTTT 59.049 40.909 1.70 0.00 34.23 1.94
256 257 2.574450 TCGGCTTCTTAAACGGGTTTT 58.426 42.857 1.70 0.00 34.23 2.43
257 258 2.259266 TCGGCTTCTTAAACGGGTTT 57.741 45.000 2.05 2.05 36.63 3.27
258 259 2.259266 TTCGGCTTCTTAAACGGGTT 57.741 45.000 0.00 0.00 0.00 4.11
259 260 2.259266 TTTCGGCTTCTTAAACGGGT 57.741 45.000 0.00 0.00 0.00 5.28
260 261 2.291190 TGTTTTCGGCTTCTTAAACGGG 59.709 45.455 0.00 0.00 34.16 5.28
261 262 3.294102 GTGTTTTCGGCTTCTTAAACGG 58.706 45.455 0.00 0.00 34.16 4.44
262 263 2.962191 CGTGTTTTCGGCTTCTTAAACG 59.038 45.455 0.00 0.00 34.16 3.60
263 264 3.722289 CACGTGTTTTCGGCTTCTTAAAC 59.278 43.478 7.58 0.00 34.94 2.01
264 265 3.789459 GCACGTGTTTTCGGCTTCTTAAA 60.789 43.478 18.38 0.00 34.94 1.52
265 266 2.286536 GCACGTGTTTTCGGCTTCTTAA 60.287 45.455 18.38 0.00 34.94 1.85
266 267 1.262151 GCACGTGTTTTCGGCTTCTTA 59.738 47.619 18.38 0.00 34.94 2.10
267 268 0.028902 GCACGTGTTTTCGGCTTCTT 59.971 50.000 18.38 0.00 34.94 2.52
268 269 1.647084 GCACGTGTTTTCGGCTTCT 59.353 52.632 18.38 0.00 34.94 2.85
269 270 1.721133 CGCACGTGTTTTCGGCTTC 60.721 57.895 18.38 0.00 34.94 3.86
270 271 2.326550 CGCACGTGTTTTCGGCTT 59.673 55.556 18.38 0.00 34.94 4.35
271 272 3.645975 CCGCACGTGTTTTCGGCT 61.646 61.111 18.38 0.00 35.20 5.52
272 273 2.649843 TTTCCGCACGTGTTTTCGGC 62.650 55.000 22.57 4.73 41.49 5.54
273 274 0.248134 TTTTCCGCACGTGTTTTCGG 60.248 50.000 21.70 21.70 42.96 4.30
274 275 1.749153 ATTTTCCGCACGTGTTTTCG 58.251 45.000 18.38 11.76 0.00 3.46
275 276 5.623174 TTTTATTTTCCGCACGTGTTTTC 57.377 34.783 18.38 0.00 0.00 2.29
296 297 3.244078 GCTCCCTCCGGATTTTTGTTTTT 60.244 43.478 3.57 0.00 37.60 1.94
297 298 2.299013 GCTCCCTCCGGATTTTTGTTTT 59.701 45.455 3.57 0.00 37.60 2.43
298 299 1.893137 GCTCCCTCCGGATTTTTGTTT 59.107 47.619 3.57 0.00 37.60 2.83
299 300 1.545841 GCTCCCTCCGGATTTTTGTT 58.454 50.000 3.57 0.00 37.60 2.83
300 301 0.676782 CGCTCCCTCCGGATTTTTGT 60.677 55.000 3.57 0.00 37.60 2.83
301 302 1.993369 GCGCTCCCTCCGGATTTTTG 61.993 60.000 3.57 0.00 37.60 2.44
302 303 1.749258 GCGCTCCCTCCGGATTTTT 60.749 57.895 3.57 0.00 37.60 1.94
303 304 2.124695 GCGCTCCCTCCGGATTTT 60.125 61.111 3.57 0.00 37.60 1.82
304 305 4.176752 GGCGCTCCCTCCGGATTT 62.177 66.667 3.57 0.00 37.60 2.17
320 321 4.368808 CACGTGTCGCGCTTTGGG 62.369 66.667 7.58 0.00 46.11 4.12
321 322 4.368808 CCACGTGTCGCGCTTTGG 62.369 66.667 15.65 2.50 46.11 3.28
328 329 2.995482 CTATTCGCCACGTGTCGC 59.005 61.111 15.09 10.47 0.00 5.19
329 330 1.516386 AGCTATTCGCCACGTGTCG 60.516 57.895 13.61 13.61 40.39 4.35
330 331 0.457853 TCAGCTATTCGCCACGTGTC 60.458 55.000 15.65 0.00 40.39 3.67
331 332 0.458543 CTCAGCTATTCGCCACGTGT 60.459 55.000 15.65 0.00 40.39 4.49
332 333 0.179137 TCTCAGCTATTCGCCACGTG 60.179 55.000 9.08 9.08 40.39 4.49
333 334 0.101399 CTCTCAGCTATTCGCCACGT 59.899 55.000 0.00 0.00 40.39 4.49
334 335 1.211818 GCTCTCAGCTATTCGCCACG 61.212 60.000 0.00 0.00 38.45 4.94
335 336 1.211818 CGCTCTCAGCTATTCGCCAC 61.212 60.000 0.00 0.00 39.60 5.01
336 337 1.066422 CGCTCTCAGCTATTCGCCA 59.934 57.895 0.00 0.00 39.60 5.69
337 338 2.306581 GCGCTCTCAGCTATTCGCC 61.307 63.158 0.00 0.00 39.60 5.54
338 339 2.643644 CGCGCTCTCAGCTATTCGC 61.644 63.158 5.56 7.61 39.60 4.70
339 340 1.265462 GACGCGCTCTCAGCTATTCG 61.265 60.000 5.73 0.00 39.60 3.34
340 341 0.248661 TGACGCGCTCTCAGCTATTC 60.249 55.000 5.73 0.00 39.60 1.75
341 342 0.248825 CTGACGCGCTCTCAGCTATT 60.249 55.000 16.31 0.00 39.60 1.73
342 343 1.358402 CTGACGCGCTCTCAGCTAT 59.642 57.895 16.31 0.00 39.60 2.97
343 344 2.765356 CCTGACGCGCTCTCAGCTA 61.765 63.158 20.91 0.00 39.60 3.32
344 345 4.127040 CCTGACGCGCTCTCAGCT 62.127 66.667 20.91 0.00 39.60 4.24
345 346 4.427661 ACCTGACGCGCTCTCAGC 62.428 66.667 20.91 0.00 34.84 4.26
346 347 2.505777 CACCTGACGCGCTCTCAG 60.506 66.667 19.87 19.87 35.78 3.35
347 348 2.983592 TCACCTGACGCGCTCTCA 60.984 61.111 5.73 0.90 0.00 3.27
348 349 2.505118 GTCACCTGACGCGCTCTC 60.505 66.667 5.73 0.00 35.12 3.20
356 357 4.079090 CGATCAGCGTCACCTGAC 57.921 61.111 0.00 0.00 44.00 3.51
366 367 2.029904 GAAGCCTCGCAACGATCAGC 62.030 60.000 0.00 0.00 34.61 4.26
367 368 1.424493 GGAAGCCTCGCAACGATCAG 61.424 60.000 0.00 0.00 34.61 2.90
368 369 1.447838 GGAAGCCTCGCAACGATCA 60.448 57.895 0.00 0.00 34.61 2.92
369 370 2.517450 CGGAAGCCTCGCAACGATC 61.517 63.158 0.00 0.00 34.61 3.69
370 371 2.501223 TTCGGAAGCCTCGCAACGAT 62.501 55.000 0.00 0.00 34.61 3.73
371 372 3.215597 TTCGGAAGCCTCGCAACGA 62.216 57.895 0.00 0.00 0.00 3.85
372 373 2.730672 CTTCGGAAGCCTCGCAACG 61.731 63.158 4.57 0.00 0.00 4.10
373 374 2.391389 CCTTCGGAAGCCTCGCAAC 61.391 63.158 12.29 0.00 0.00 4.17
374 375 2.047274 CCTTCGGAAGCCTCGCAA 60.047 61.111 12.29 0.00 0.00 4.85
375 376 2.579657 TTCCTTCGGAAGCCTCGCA 61.580 57.895 12.29 0.00 36.71 5.10
376 377 2.101233 GTTCCTTCGGAAGCCTCGC 61.101 63.158 12.29 0.00 42.88 5.03
377 378 1.805945 CGTTCCTTCGGAAGCCTCG 60.806 63.158 12.29 11.13 42.88 4.63
378 379 2.101233 GCGTTCCTTCGGAAGCCTC 61.101 63.158 12.29 3.74 42.88 4.70
379 380 2.047179 GCGTTCCTTCGGAAGCCT 60.047 61.111 12.29 0.00 42.88 4.58
380 381 2.047179 AGCGTTCCTTCGGAAGCC 60.047 61.111 12.29 1.82 42.88 4.35
381 382 2.445438 CGAGCGTTCCTTCGGAAGC 61.445 63.158 12.29 1.57 42.88 3.86
382 383 0.666577 AACGAGCGTTCCTTCGGAAG 60.667 55.000 10.82 10.82 42.88 3.46
383 384 0.597568 TAACGAGCGTTCCTTCGGAA 59.402 50.000 11.89 0.00 39.66 4.30
384 385 0.597568 TTAACGAGCGTTCCTTCGGA 59.402 50.000 11.89 0.00 39.31 4.55
385 386 1.636988 ATTAACGAGCGTTCCTTCGG 58.363 50.000 11.89 0.00 39.31 4.30
386 387 3.855950 ACTAATTAACGAGCGTTCCTTCG 59.144 43.478 11.89 6.01 39.31 3.79
387 388 5.119743 ACAACTAATTAACGAGCGTTCCTTC 59.880 40.000 11.89 0.00 39.31 3.46
388 389 4.992951 ACAACTAATTAACGAGCGTTCCTT 59.007 37.500 11.89 9.23 39.31 3.36
389 390 4.563061 ACAACTAATTAACGAGCGTTCCT 58.437 39.130 11.89 1.03 39.31 3.36
390 391 4.916099 ACAACTAATTAACGAGCGTTCC 57.084 40.909 11.89 0.00 39.31 3.62
391 392 5.311271 GGAACAACTAATTAACGAGCGTTC 58.689 41.667 11.89 10.23 39.31 3.95
392 393 4.152938 GGGAACAACTAATTAACGAGCGTT 59.847 41.667 13.11 13.11 41.65 4.84
393 394 3.681417 GGGAACAACTAATTAACGAGCGT 59.319 43.478 0.00 0.00 0.00 5.07
394 395 3.241868 CGGGAACAACTAATTAACGAGCG 60.242 47.826 0.00 0.00 0.00 5.03
395 396 3.928375 TCGGGAACAACTAATTAACGAGC 59.072 43.478 0.00 0.00 0.00 5.03
396 397 6.475207 CATTCGGGAACAACTAATTAACGAG 58.525 40.000 0.00 0.00 0.00 4.18
397 398 5.163834 GCATTCGGGAACAACTAATTAACGA 60.164 40.000 0.00 0.00 0.00 3.85
398 399 5.025826 GCATTCGGGAACAACTAATTAACG 58.974 41.667 0.00 0.00 0.00 3.18
399 400 5.945155 TGCATTCGGGAACAACTAATTAAC 58.055 37.500 0.00 0.00 0.00 2.01
400 401 6.576662 TTGCATTCGGGAACAACTAATTAA 57.423 33.333 0.00 0.00 0.00 1.40
401 402 6.767524 ATTGCATTCGGGAACAACTAATTA 57.232 33.333 0.00 0.00 0.00 1.40
402 403 5.659440 ATTGCATTCGGGAACAACTAATT 57.341 34.783 0.00 0.00 0.00 1.40
403 404 5.394115 GGAATTGCATTCGGGAACAACTAAT 60.394 40.000 0.00 0.00 40.17 1.73
404 405 4.082463 GGAATTGCATTCGGGAACAACTAA 60.082 41.667 0.00 0.00 40.17 2.24
405 406 3.442273 GGAATTGCATTCGGGAACAACTA 59.558 43.478 0.00 0.00 40.17 2.24
406 407 2.231235 GGAATTGCATTCGGGAACAACT 59.769 45.455 0.00 0.00 40.17 3.16
407 408 2.029470 TGGAATTGCATTCGGGAACAAC 60.029 45.455 0.00 0.00 40.17 3.32
408 409 2.029470 GTGGAATTGCATTCGGGAACAA 60.029 45.455 1.94 0.00 40.17 2.83
409 410 1.543802 GTGGAATTGCATTCGGGAACA 59.456 47.619 1.94 0.00 40.17 3.18
410 411 1.543802 TGTGGAATTGCATTCGGGAAC 59.456 47.619 1.94 0.00 40.17 3.62
411 412 1.916506 TGTGGAATTGCATTCGGGAA 58.083 45.000 1.94 0.00 40.17 3.97
412 413 1.543802 GTTGTGGAATTGCATTCGGGA 59.456 47.619 1.94 0.00 40.17 5.14
413 414 1.545582 AGTTGTGGAATTGCATTCGGG 59.454 47.619 1.94 0.00 40.17 5.14
414 415 3.689161 TCTAGTTGTGGAATTGCATTCGG 59.311 43.478 1.94 0.00 40.17 4.30
415 416 4.944962 TCTAGTTGTGGAATTGCATTCG 57.055 40.909 1.94 0.00 40.17 3.34
589 590 4.156008 GCTCACGGTACCTTGATGATTTTT 59.844 41.667 20.41 0.00 0.00 1.94
641 642 9.135189 AGAAGAATATTTATAGTTTGCCATGCA 57.865 29.630 0.00 0.00 36.47 3.96
642 643 9.617975 GAGAAGAATATTTATAGTTTGCCATGC 57.382 33.333 0.00 0.00 0.00 4.06
643 644 9.817365 CGAGAAGAATATTTATAGTTTGCCATG 57.183 33.333 0.00 0.00 0.00 3.66
644 645 9.561069 ACGAGAAGAATATTTATAGTTTGCCAT 57.439 29.630 0.00 0.00 0.00 4.40
645 646 8.826710 CACGAGAAGAATATTTATAGTTTGCCA 58.173 33.333 0.00 0.00 0.00 4.92
646 647 8.283291 CCACGAGAAGAATATTTATAGTTTGCC 58.717 37.037 0.00 0.00 0.00 4.52
647 648 8.827677 ACCACGAGAAGAATATTTATAGTTTGC 58.172 33.333 0.00 0.00 0.00 3.68
1333 1347 1.740296 GCCGCTTTAGCTCCGACAA 60.740 57.895 0.00 0.00 39.32 3.18
1818 1832 3.611766 CCGAACTGGTAGGAGTCAAAT 57.388 47.619 0.00 0.00 0.00 2.32
2037 2051 2.414994 ATGACCTGCAGTCTGGATTG 57.585 50.000 13.81 0.00 46.46 2.67
2115 2129 4.274459 GCCAATCTGTGAAGTGTCCATATC 59.726 45.833 0.00 0.00 0.00 1.63
2190 2204 4.274978 TCTCCATGTACACCGATGAGTAA 58.725 43.478 0.00 0.00 0.00 2.24
2229 2243 0.098376 CTTTGCTCGCTGAGAATGCC 59.902 55.000 9.32 0.00 0.00 4.40
2250 2264 4.052229 CGCACCGTCTTCCCGACT 62.052 66.667 0.00 0.00 40.59 4.18
2355 2369 1.801242 TAATTCCTCCATCGCCCTCA 58.199 50.000 0.00 0.00 0.00 3.86
2440 2454 5.000591 TCATCTTTGATCGCCTTTACACAA 58.999 37.500 0.00 0.00 0.00 3.33
2584 2601 4.634883 TGAACCTTTGTACAACGCTACAAA 59.365 37.500 8.07 8.28 41.97 2.83
2613 2631 6.219473 ACTCTCTGACAATGTTAGAACACAG 58.781 40.000 9.16 5.70 42.51 3.66
2632 2650 2.165437 AGCAGCAGCAGTAGTAACTCTC 59.835 50.000 3.17 0.00 45.49 3.20
2645 2733 3.256558 CCAAAATTAGGAAAGCAGCAGC 58.743 45.455 0.00 0.00 42.56 5.25
2648 2736 3.961480 ACCCAAAATTAGGAAAGCAGC 57.039 42.857 0.00 0.00 0.00 5.25
2692 2783 6.686484 ATGGTGTATATATCAGCACAAGGA 57.314 37.500 14.87 0.00 44.09 3.36
2694 2785 9.144747 GTCTTATGGTGTATATATCAGCACAAG 57.855 37.037 18.84 18.84 44.10 3.16
2743 2856 7.033185 ACGTTTTTGCAGTTCAAATTAGTTCT 58.967 30.769 0.00 0.00 43.53 3.01
2775 2891 6.844917 AGGCTATTTTGGTACAGAGGTAGTAT 59.155 38.462 0.00 0.00 42.39 2.12
2780 2896 4.781087 TGTAGGCTATTTTGGTACAGAGGT 59.219 41.667 0.00 0.00 42.39 3.85
2781 2897 5.353394 TGTAGGCTATTTTGGTACAGAGG 57.647 43.478 0.00 0.00 42.39 3.69
2782 2898 7.681939 TTTTGTAGGCTATTTTGGTACAGAG 57.318 36.000 0.00 0.00 42.39 3.35
2783 2899 8.519526 CATTTTTGTAGGCTATTTTGGTACAGA 58.480 33.333 0.00 0.00 42.39 3.41
2784 2900 8.303876 ACATTTTTGTAGGCTATTTTGGTACAG 58.696 33.333 0.00 0.00 42.39 2.74
2785 2901 8.184304 ACATTTTTGTAGGCTATTTTGGTACA 57.816 30.769 0.00 0.00 0.00 2.90
2786 2902 8.520351 AGACATTTTTGTAGGCTATTTTGGTAC 58.480 33.333 0.00 0.00 0.00 3.34
2787 2903 8.644374 AGACATTTTTGTAGGCTATTTTGGTA 57.356 30.769 0.00 0.00 0.00 3.25
2788 2904 7.539034 AGACATTTTTGTAGGCTATTTTGGT 57.461 32.000 0.00 0.00 0.00 3.67
2808 2924 9.213777 ACTCCCTCTGTATCAAAATATAAGACA 57.786 33.333 0.00 0.00 0.00 3.41
2852 2968 5.423015 CAGCCTGTAGATTTACACAGACAT 58.577 41.667 3.37 0.00 43.99 3.06
2882 2998 5.278610 CCATTTCAGACAAGACAGAATGCAA 60.279 40.000 0.00 0.00 42.53 4.08
2906 3022 4.462483 TGGCAGGAGTTAATGGAAATCAAC 59.538 41.667 0.00 0.00 33.68 3.18
2908 3024 4.263905 ACTGGCAGGAGTTAATGGAAATCA 60.264 41.667 20.34 0.00 33.68 2.57
2959 3076 1.299316 CAAACCAACCTGCACTGCG 60.299 57.895 0.00 0.00 0.00 5.18
2982 3099 3.059597 CAGGAGAAACACAGTAAACAGCG 60.060 47.826 0.00 0.00 0.00 5.18
3037 3160 4.196971 TCAATCATGGATCTCAGCAACTG 58.803 43.478 0.00 0.00 0.00 3.16
3102 3233 0.802607 GAGCGAGCGAACGGAAAGAT 60.803 55.000 0.00 0.00 0.00 2.40
3104 3235 1.733041 TGAGCGAGCGAACGGAAAG 60.733 57.895 0.00 0.00 0.00 2.62
3106 3237 2.430244 GTGAGCGAGCGAACGGAA 60.430 61.111 0.00 0.00 0.00 4.30
3107 3238 4.753877 CGTGAGCGAGCGAACGGA 62.754 66.667 14.62 0.00 41.33 4.69
3108 3239 4.753877 TCGTGAGCGAGCGAACGG 62.754 66.667 19.57 7.02 42.81 4.44


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

AutoCloner maintained by Alex Coulton.