Multiple sequence alignment - TraesCS1A01G117800

Loading Multiple Alignment...

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 TraesCS1A01G117800 chr1A 100.000 3035 0 0 1 3035 125148890 125145856 0.000000e+00 5605.0
1 TraesCS1A01G117800 chr1A 76.861 497 95 17 1319 1809 545648874 545648392 2.320000e-66 263.0
2 TraesCS1A01G117800 chr1A 91.176 170 13 2 2 169 162971459 162971290 2.350000e-56 230.0
3 TraesCS1A01G117800 chr1A 90.058 171 15 2 1 169 112475006 112475176 1.420000e-53 220.0
4 TraesCS1A01G117800 chr1A 76.000 425 84 15 1400 1815 545777923 545777508 1.430000e-48 204.0
5 TraesCS1A01G117800 chr1D 93.764 1732 66 18 723 2415 114645090 114643362 0.000000e+00 2562.0
6 TraesCS1A01G117800 chr1D 92.537 201 15 0 2407 2607 114632116 114631916 3.830000e-74 289.0
7 TraesCS1A01G117800 chr1D 94.611 167 9 0 2869 3035 114631458 114631292 3.000000e-65 259.0
8 TraesCS1A01G117800 chr1D 90.643 171 14 2 1 169 121243653 121243823 3.040000e-55 226.0
9 TraesCS1A01G117800 chr1D 89.024 164 17 1 2708 2871 114631670 114631508 5.130000e-48 202.0
10 TraesCS1A01G117800 chr1D 84.158 202 22 5 250 446 463985672 463985476 1.440000e-43 187.0
11 TraesCS1A01G117800 chr1D 82.072 251 8 15 520 736 114645358 114645111 2.400000e-41 180.0
12 TraesCS1A01G117800 chr1B 93.771 1461 44 16 748 2187 175660320 175658886 0.000000e+00 2150.0
13 TraesCS1A01G117800 chr1B 90.943 265 9 11 2183 2436 175658618 175658358 2.900000e-90 342.0
14 TraesCS1A01G117800 chr1B 84.181 354 14 11 448 764 175660683 175660335 3.800000e-79 305.0
15 TraesCS1A01G117800 chr1B 95.161 186 9 0 2422 2607 175641002 175640817 8.230000e-76 294.0
16 TraesCS1A01G117800 chr1B 94.798 173 8 1 2864 3035 175640429 175640257 4.990000e-68 268.0
17 TraesCS1A01G117800 chr1B 90.000 140 10 1 2736 2871 175640612 175640473 8.650000e-41 178.0
18 TraesCS1A01G117800 chr3B 78.289 456 84 9 1352 1804 462866676 462867119 2.300000e-71 279.0
19 TraesCS1A01G117800 chr3B 86.559 186 20 3 265 448 792432757 792432939 1.850000e-47 200.0
20 TraesCS1A01G117800 chr3B 86.885 183 19 3 268 448 793397451 793397272 1.850000e-47 200.0
21 TraesCS1A01G117800 chr3B 86.932 176 19 3 275 448 76516951 76516778 8.590000e-46 195.0
22 TraesCS1A01G117800 chr7D 91.228 171 12 3 1 169 562059776 562059945 2.350000e-56 230.0
23 TraesCS1A01G117800 chr7D 89.655 58 4 2 2602 2658 13905649 13905705 4.200000e-09 73.1
24 TraesCS1A01G117800 chr7D 88.525 61 6 1 2586 2646 53485605 53485546 4.200000e-09 73.1
25 TraesCS1A01G117800 chr6A 90.643 171 14 2 1 169 17600520 17600350 3.040000e-55 226.0
26 TraesCS1A01G117800 chr5D 90.533 169 14 2 3 169 550196891 550196723 3.940000e-54 222.0
27 TraesCS1A01G117800 chr5D 82.791 215 27 8 240 448 397228880 397228670 1.860000e-42 183.0
28 TraesCS1A01G117800 chr7A 84.932 219 32 1 240 457 54820340 54820558 1.420000e-53 220.0
29 TraesCS1A01G117800 chr7A 85.784 204 23 4 1 198 589399049 589398846 8.530000e-51 211.0
30 TraesCS1A01G117800 chr7A 83.673 196 29 2 256 448 506476252 506476447 6.680000e-42 182.0
31 TraesCS1A01G117800 chr7A 86.154 65 6 3 2581 2643 30061232 30061295 1.950000e-07 67.6
32 TraesCS1A01G117800 chr4A 89.655 174 16 2 1 172 6816755 6816582 1.420000e-53 220.0
33 TraesCS1A01G117800 chr4A 90.116 172 14 3 1 169 682026217 682026388 1.420000e-53 220.0
34 TraesCS1A01G117800 chrUn 86.885 183 19 3 268 448 154950862 154950683 1.850000e-47 200.0
35 TraesCS1A01G117800 chrUn 86.885 183 19 3 268 448 155034919 155034740 1.850000e-47 200.0
36 TraesCS1A01G117800 chr6D 82.653 98 17 0 1511 1608 78490609 78490512 1.500000e-13 87.9
37 TraesCS1A01G117800 chr3D 89.552 67 4 3 2600 2664 298466302 298466367 6.970000e-12 82.4
38 TraesCS1A01G117800 chr7B 92.727 55 4 0 2603 2657 506497814 506497868 2.510000e-11 80.5
39 TraesCS1A01G117800 chr6B 92.727 55 4 0 2603 2657 7144801 7144747 2.510000e-11 80.5
40 TraesCS1A01G117800 chr5A 94.118 51 3 0 2597 2647 574401535 574401485 9.020000e-11 78.7
41 TraesCS1A01G117800 chr4B 87.097 62 8 0 2586 2647 31522745 31522684 1.510000e-08 71.3
42 TraesCS1A01G117800 chr4B 84.416 77 3 9 2574 2647 515060010 515060080 1.950000e-07 67.6


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 TraesCS1A01G117800 chr1A 125145856 125148890 3034 True 5605.000000 5605 100.000000 1 3035 1 chr1A.!!$R1 3034
1 TraesCS1A01G117800 chr1D 114643362 114645358 1996 True 1371.000000 2562 87.918000 520 2415 2 chr1D.!!$R3 1895
2 TraesCS1A01G117800 chr1D 114631292 114632116 824 True 250.000000 289 92.057333 2407 3035 3 chr1D.!!$R2 628
3 TraesCS1A01G117800 chr1B 175658358 175660683 2325 True 932.333333 2150 89.631667 448 2436 3 chr1B.!!$R2 1988
4 TraesCS1A01G117800 chr1B 175640257 175641002 745 True 246.666667 294 93.319667 2422 3035 3 chr1B.!!$R1 613

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
440 441 0.031178 GTGTTGGGCAGCTGTTGAAG 59.969 55.0 16.64 0.00 0.0 3.02 F
441 442 0.106769 TGTTGGGCAGCTGTTGAAGA 60.107 50.0 16.64 1.13 0.0 2.87 F
860 964 1.062488 ACTCTGGCCCCTTTGACACT 61.062 55.0 0.00 0.00 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1991 0.034059 AGTCTGACTCCCAAAGTGCG 59.966 55.0 4.06 0.0 38.74 5.34 R
2004 2123 0.539051 AGACTTCGATCCAGCCTTGG 59.461 55.0 0.00 0.0 46.49 3.61 R
2674 3089 0.958382 TGCATAGTTTGGTCCACGGC 60.958 55.0 0.00 0.0 0.00 5.68 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
26 27 8.295288 GCTCTAATTATCCATCACTTTCATTGG 58.705 37.037 0.00 0.00 0.00 3.16
27 28 9.347240 CTCTAATTATCCATCACTTTCATTGGT 57.653 33.333 0.00 0.00 0.00 3.67
28 29 9.699410 TCTAATTATCCATCACTTTCATTGGTT 57.301 29.630 0.00 0.00 0.00 3.67
35 36 8.642935 TCCATCACTTTCATTGGTTATAAACA 57.357 30.769 0.00 0.00 0.00 2.83
36 37 8.739039 TCCATCACTTTCATTGGTTATAAACAG 58.261 33.333 2.94 0.00 0.00 3.16
37 38 7.975616 CCATCACTTTCATTGGTTATAAACAGG 59.024 37.037 2.94 0.87 0.00 4.00
38 39 8.522830 CATCACTTTCATTGGTTATAAACAGGT 58.477 33.333 2.94 0.00 0.00 4.00
39 40 8.472007 TCACTTTCATTGGTTATAAACAGGTT 57.528 30.769 2.94 0.00 0.00 3.50
40 41 8.919145 TCACTTTCATTGGTTATAAACAGGTTT 58.081 29.630 2.94 2.66 36.63 3.27
41 42 9.541143 CACTTTCATTGGTTATAAACAGGTTTT 57.459 29.630 2.94 0.00 34.23 2.43
42 43 9.541143 ACTTTCATTGGTTATAAACAGGTTTTG 57.459 29.630 2.94 0.00 34.23 2.44
43 44 8.894768 TTTCATTGGTTATAAACAGGTTTTGG 57.105 30.769 2.94 0.00 34.23 3.28
44 45 6.459923 TCATTGGTTATAAACAGGTTTTGGC 58.540 36.000 2.94 0.00 34.23 4.52
45 46 6.268847 TCATTGGTTATAAACAGGTTTTGGCT 59.731 34.615 2.94 0.00 34.23 4.75
46 47 5.715434 TGGTTATAAACAGGTTTTGGCTC 57.285 39.130 0.00 0.00 34.23 4.70
47 48 5.141182 TGGTTATAAACAGGTTTTGGCTCA 58.859 37.500 0.00 0.00 34.23 4.26
48 49 5.598830 TGGTTATAAACAGGTTTTGGCTCAA 59.401 36.000 0.00 0.00 34.23 3.02
49 50 5.924254 GGTTATAAACAGGTTTTGGCTCAAC 59.076 40.000 2.37 0.39 34.23 3.18
50 51 2.577449 AAACAGGTTTTGGCTCAACG 57.423 45.000 0.00 0.00 0.00 4.10
51 52 0.102300 AACAGGTTTTGGCTCAACGC 59.898 50.000 0.00 0.00 38.13 4.84
52 53 0.751643 ACAGGTTTTGGCTCAACGCT 60.752 50.000 0.00 0.00 39.13 5.07
53 54 1.234821 CAGGTTTTGGCTCAACGCTA 58.765 50.000 0.00 0.00 39.13 4.26
54 55 1.812571 CAGGTTTTGGCTCAACGCTAT 59.187 47.619 0.00 0.00 39.13 2.97
55 56 2.084546 AGGTTTTGGCTCAACGCTATC 58.915 47.619 0.00 0.00 39.13 2.08
56 57 1.132453 GGTTTTGGCTCAACGCTATCC 59.868 52.381 0.00 0.00 39.13 2.59
57 58 1.132453 GTTTTGGCTCAACGCTATCCC 59.868 52.381 0.00 0.00 39.13 3.85
58 59 0.618458 TTTGGCTCAACGCTATCCCT 59.382 50.000 0.00 0.00 39.13 4.20
59 60 0.618458 TTGGCTCAACGCTATCCCTT 59.382 50.000 0.00 0.00 39.13 3.95
60 61 1.491668 TGGCTCAACGCTATCCCTTA 58.508 50.000 0.00 0.00 39.13 2.69
61 62 1.834896 TGGCTCAACGCTATCCCTTAA 59.165 47.619 0.00 0.00 39.13 1.85
62 63 2.237643 TGGCTCAACGCTATCCCTTAAA 59.762 45.455 0.00 0.00 39.13 1.52
63 64 3.118038 TGGCTCAACGCTATCCCTTAAAT 60.118 43.478 0.00 0.00 39.13 1.40
64 65 3.498777 GGCTCAACGCTATCCCTTAAATC 59.501 47.826 0.00 0.00 39.13 2.17
65 66 4.381411 GCTCAACGCTATCCCTTAAATCT 58.619 43.478 0.00 0.00 35.14 2.40
66 67 4.212214 GCTCAACGCTATCCCTTAAATCTG 59.788 45.833 0.00 0.00 35.14 2.90
67 68 4.127171 TCAACGCTATCCCTTAAATCTGC 58.873 43.478 0.00 0.00 0.00 4.26
68 69 3.127425 ACGCTATCCCTTAAATCTGCC 57.873 47.619 0.00 0.00 0.00 4.85
69 70 2.438021 ACGCTATCCCTTAAATCTGCCA 59.562 45.455 0.00 0.00 0.00 4.92
70 71 3.073062 ACGCTATCCCTTAAATCTGCCAT 59.927 43.478 0.00 0.00 0.00 4.40
71 72 3.438087 CGCTATCCCTTAAATCTGCCATG 59.562 47.826 0.00 0.00 0.00 3.66
72 73 4.401925 GCTATCCCTTAAATCTGCCATGT 58.598 43.478 0.00 0.00 0.00 3.21
73 74 5.560724 GCTATCCCTTAAATCTGCCATGTA 58.439 41.667 0.00 0.00 0.00 2.29
74 75 6.003950 GCTATCCCTTAAATCTGCCATGTAA 58.996 40.000 0.00 0.00 0.00 2.41
75 76 6.660949 GCTATCCCTTAAATCTGCCATGTAAT 59.339 38.462 0.00 0.00 0.00 1.89
76 77 7.177392 GCTATCCCTTAAATCTGCCATGTAATT 59.823 37.037 0.00 0.00 0.00 1.40
77 78 9.739276 CTATCCCTTAAATCTGCCATGTAATTA 57.261 33.333 0.00 0.00 0.00 1.40
79 80 9.605951 ATCCCTTAAATCTGCCATGTAATTAAT 57.394 29.630 0.00 0.00 0.00 1.40
96 97 9.599866 TGTAATTAATATCCTATCATTCCTGCG 57.400 33.333 0.00 0.00 0.00 5.18
97 98 9.817809 GTAATTAATATCCTATCATTCCTGCGA 57.182 33.333 0.00 0.00 0.00 5.10
99 100 9.739276 AATTAATATCCTATCATTCCTGCGAAA 57.261 29.630 0.00 0.00 0.00 3.46
100 101 9.739276 ATTAATATCCTATCATTCCTGCGAAAA 57.261 29.630 0.00 0.00 0.00 2.29
101 102 9.567776 TTAATATCCTATCATTCCTGCGAAAAA 57.432 29.630 0.00 0.00 0.00 1.94
132 133 9.825109 TTGATATCTTACCAAATATCAACGTCA 57.175 29.630 11.72 0.00 44.20 4.35
133 134 9.825109 TGATATCTTACCAAATATCAACGTCAA 57.175 29.630 3.98 0.00 40.28 3.18
135 136 7.915293 ATCTTACCAAATATCAACGTCAACA 57.085 32.000 0.00 0.00 0.00 3.33
136 137 7.359262 TCTTACCAAATATCAACGTCAACAG 57.641 36.000 0.00 0.00 0.00 3.16
137 138 7.156000 TCTTACCAAATATCAACGTCAACAGA 58.844 34.615 0.00 0.00 0.00 3.41
138 139 7.822334 TCTTACCAAATATCAACGTCAACAGAT 59.178 33.333 0.00 0.00 0.00 2.90
139 140 9.093970 CTTACCAAATATCAACGTCAACAGATA 57.906 33.333 0.00 0.00 0.00 1.98
140 141 9.607988 TTACCAAATATCAACGTCAACAGATAT 57.392 29.630 0.00 0.00 35.74 1.63
142 143 9.778741 ACCAAATATCAACGTCAACAGATATAT 57.221 29.630 0.00 0.00 33.75 0.86
273 274 9.941325 AAAATATCTATGCAATCTAGTCCAGAG 57.059 33.333 0.00 0.00 36.48 3.35
274 275 8.663209 AATATCTATGCAATCTAGTCCAGAGT 57.337 34.615 0.00 0.00 36.48 3.24
280 281 4.442375 CAATCTAGTCCAGAGTGTTCGT 57.558 45.455 0.00 0.00 42.99 3.85
281 282 4.169508 CAATCTAGTCCAGAGTGTTCGTG 58.830 47.826 0.00 0.00 42.99 4.35
282 283 1.540267 TCTAGTCCAGAGTGTTCGTGC 59.460 52.381 0.00 0.00 0.00 5.34
283 284 0.240145 TAGTCCAGAGTGTTCGTGCG 59.760 55.000 0.00 0.00 0.00 5.34
284 285 1.007734 GTCCAGAGTGTTCGTGCGA 60.008 57.895 0.00 0.00 0.00 5.10
285 286 1.004277 GTCCAGAGTGTTCGTGCGAG 61.004 60.000 0.00 0.00 0.00 5.03
286 287 1.170290 TCCAGAGTGTTCGTGCGAGA 61.170 55.000 0.00 0.00 0.00 4.04
287 288 0.730834 CCAGAGTGTTCGTGCGAGAG 60.731 60.000 0.00 0.00 0.00 3.20
312 313 2.951227 GCTGCATTTTAGCGCGCC 60.951 61.111 30.33 11.28 37.31 6.53
313 314 2.793946 CTGCATTTTAGCGCGCCT 59.206 55.556 30.33 17.79 37.31 5.52
314 315 1.584483 CTGCATTTTAGCGCGCCTG 60.584 57.895 30.33 18.07 37.31 4.85
315 316 2.951227 GCATTTTAGCGCGCCTGC 60.951 61.111 30.33 23.55 37.91 4.85
317 318 1.584483 CATTTTAGCGCGCCTGCTG 60.584 57.895 30.33 15.41 46.70 4.41
318 319 2.764314 ATTTTAGCGCGCCTGCTGG 61.764 57.895 30.33 5.03 46.70 4.85
319 320 3.892740 TTTTAGCGCGCCTGCTGGA 62.893 57.895 30.33 4.58 46.70 3.86
320 321 4.819761 TTAGCGCGCCTGCTGGAG 62.820 66.667 30.33 11.77 46.70 3.86
324 325 3.188786 CGCGCCTGCTGGAGTTAC 61.189 66.667 14.77 0.00 39.65 2.50
325 326 3.188786 GCGCCTGCTGGAGTTACG 61.189 66.667 14.77 7.98 38.39 3.18
326 327 2.261671 CGCCTGCTGGAGTTACGT 59.738 61.111 14.77 0.00 34.57 3.57
327 328 2.094659 CGCCTGCTGGAGTTACGTG 61.095 63.158 14.77 0.00 34.57 4.49
328 329 2.391389 GCCTGCTGGAGTTACGTGC 61.391 63.158 14.77 0.00 34.57 5.34
329 330 2.094659 CCTGCTGGAGTTACGTGCG 61.095 63.158 2.92 0.00 34.57 5.34
330 331 1.372997 CTGCTGGAGTTACGTGCGT 60.373 57.895 0.00 2.05 0.00 5.24
331 332 1.617755 CTGCTGGAGTTACGTGCGTG 61.618 60.000 7.55 0.00 0.00 5.34
332 333 3.011760 GCTGGAGTTACGTGCGTGC 62.012 63.158 7.55 0.69 0.00 5.34
333 334 1.372997 CTGGAGTTACGTGCGTGCT 60.373 57.895 7.55 5.53 0.00 4.40
334 335 0.109458 CTGGAGTTACGTGCGTGCTA 60.109 55.000 7.55 0.00 0.00 3.49
335 336 0.314618 TGGAGTTACGTGCGTGCTAA 59.685 50.000 7.55 0.00 0.00 3.09
336 337 1.269673 TGGAGTTACGTGCGTGCTAAA 60.270 47.619 7.55 0.00 0.00 1.85
337 338 1.997606 GGAGTTACGTGCGTGCTAAAT 59.002 47.619 7.55 0.00 0.00 1.40
338 339 2.414138 GGAGTTACGTGCGTGCTAAATT 59.586 45.455 7.55 0.00 0.00 1.82
339 340 3.120442 GGAGTTACGTGCGTGCTAAATTT 60.120 43.478 7.55 0.00 0.00 1.82
340 341 4.091800 GGAGTTACGTGCGTGCTAAATTTA 59.908 41.667 7.55 0.00 0.00 1.40
341 342 5.220529 GGAGTTACGTGCGTGCTAAATTTAT 60.221 40.000 7.55 0.00 0.00 1.40
342 343 5.792631 AGTTACGTGCGTGCTAAATTTATC 58.207 37.500 7.55 0.00 0.00 1.75
343 344 3.298489 ACGTGCGTGCTAAATTTATCG 57.702 42.857 0.00 5.92 0.00 2.92
344 345 2.026990 CGTGCGTGCTAAATTTATCGC 58.973 47.619 23.10 23.10 43.14 4.58
345 346 2.026990 GTGCGTGCTAAATTTATCGCG 58.973 47.619 23.58 23.58 45.23 5.87
346 347 1.927838 TGCGTGCTAAATTTATCGCGA 59.072 42.857 29.09 13.09 45.23 5.87
347 348 2.285371 TGCGTGCTAAATTTATCGCGAC 60.285 45.455 29.09 21.82 45.23 5.19
348 349 2.887733 CGTGCTAAATTTATCGCGACC 58.112 47.619 23.56 6.41 35.52 4.79
349 350 2.655577 CGTGCTAAATTTATCGCGACCG 60.656 50.000 23.56 12.63 35.52 4.79
350 351 1.259507 TGCTAAATTTATCGCGACCGC 59.740 47.619 12.93 4.06 37.85 5.68
351 352 1.525619 GCTAAATTTATCGCGACCGCT 59.474 47.619 12.93 0.00 39.32 5.52
352 353 2.727798 GCTAAATTTATCGCGACCGCTA 59.272 45.455 12.93 0.00 39.32 4.26
353 354 3.181543 GCTAAATTTATCGCGACCGCTAG 60.182 47.826 12.93 9.05 39.32 3.42
354 355 2.787601 AATTTATCGCGACCGCTAGA 57.212 45.000 12.93 0.00 39.32 2.43
355 356 2.333389 ATTTATCGCGACCGCTAGAG 57.667 50.000 12.93 0.00 39.32 2.43
356 357 1.019673 TTTATCGCGACCGCTAGAGT 58.980 50.000 12.93 0.00 39.32 3.24
357 358 0.585357 TTATCGCGACCGCTAGAGTC 59.415 55.000 12.93 0.00 39.32 3.36
358 359 0.531311 TATCGCGACCGCTAGAGTCA 60.531 55.000 12.93 0.00 39.32 3.41
359 360 1.777030 ATCGCGACCGCTAGAGTCAG 61.777 60.000 12.93 6.76 39.32 3.51
360 361 2.278271 GCGACCGCTAGAGTCAGC 60.278 66.667 7.19 11.77 38.26 4.26
366 367 2.415426 GCTAGAGTCAGCGCTCCC 59.585 66.667 7.13 0.00 36.20 4.30
367 368 3.124686 CTAGAGTCAGCGCTCCCC 58.875 66.667 7.13 0.00 36.20 4.81
368 369 2.829003 TAGAGTCAGCGCTCCCCG 60.829 66.667 7.13 0.00 36.20 5.73
390 391 2.819595 GCCAAAGCAGGCGATCGA 60.820 61.111 21.57 0.00 46.12 3.59
391 392 3.093278 CCAAAGCAGGCGATCGAC 58.907 61.111 21.57 18.32 0.00 4.20
392 393 2.697425 CAAAGCAGGCGATCGACG 59.303 61.111 21.57 13.88 45.66 5.12
401 402 3.837687 CGATCGACGCGCTGCAAA 61.838 61.111 10.26 0.00 34.51 3.68
402 403 2.276058 GATCGACGCGCTGCAAAC 60.276 61.111 5.73 0.00 0.00 2.93
403 404 2.730672 GATCGACGCGCTGCAAACT 61.731 57.895 5.73 0.00 0.00 2.66
404 405 2.227968 GATCGACGCGCTGCAAACTT 62.228 55.000 5.73 0.00 0.00 2.66
405 406 1.011968 ATCGACGCGCTGCAAACTTA 61.012 50.000 5.73 0.00 0.00 2.24
406 407 1.011968 TCGACGCGCTGCAAACTTAT 61.012 50.000 5.73 0.00 0.00 1.73
407 408 0.179225 CGACGCGCTGCAAACTTATT 60.179 50.000 5.73 0.00 0.00 1.40
408 409 1.724654 CGACGCGCTGCAAACTTATTT 60.725 47.619 5.73 0.00 0.00 1.40
409 410 2.315901 GACGCGCTGCAAACTTATTTT 58.684 42.857 5.73 0.00 0.00 1.82
410 411 2.724174 GACGCGCTGCAAACTTATTTTT 59.276 40.909 5.73 0.00 0.00 1.94
411 412 3.891324 ACGCGCTGCAAACTTATTTTTA 58.109 36.364 5.73 0.00 0.00 1.52
412 413 4.291783 ACGCGCTGCAAACTTATTTTTAA 58.708 34.783 5.73 0.00 0.00 1.52
413 414 4.147479 ACGCGCTGCAAACTTATTTTTAAC 59.853 37.500 5.73 0.00 0.00 2.01
414 415 4.614417 GCGCTGCAAACTTATTTTTAACG 58.386 39.130 0.00 0.00 0.00 3.18
415 416 4.614417 CGCTGCAAACTTATTTTTAACGC 58.386 39.130 0.00 0.00 0.00 4.84
416 417 4.614417 GCTGCAAACTTATTTTTAACGCG 58.386 39.130 3.53 3.53 0.00 6.01
417 418 4.147479 GCTGCAAACTTATTTTTAACGCGT 59.853 37.500 5.58 5.58 0.00 6.01
418 419 5.662099 GCTGCAAACTTATTTTTAACGCGTC 60.662 40.000 14.44 0.00 0.00 5.19
419 420 5.271625 TGCAAACTTATTTTTAACGCGTCA 58.728 33.333 14.44 0.00 0.00 4.35
420 421 5.171695 TGCAAACTTATTTTTAACGCGTCAC 59.828 36.000 14.44 0.00 0.00 3.67
431 432 4.012895 GCGTCACGTGTTGGGCAG 62.013 66.667 16.51 1.81 0.00 4.85
432 433 4.012895 CGTCACGTGTTGGGCAGC 62.013 66.667 16.51 0.00 0.00 5.25
433 434 2.591715 GTCACGTGTTGGGCAGCT 60.592 61.111 16.51 0.00 0.00 4.24
434 435 2.591429 TCACGTGTTGGGCAGCTG 60.591 61.111 16.51 10.11 0.00 4.24
435 436 2.901840 CACGTGTTGGGCAGCTGT 60.902 61.111 16.64 0.00 0.00 4.40
436 437 2.124320 ACGTGTTGGGCAGCTGTT 60.124 55.556 16.64 0.00 0.00 3.16
437 438 2.332514 CGTGTTGGGCAGCTGTTG 59.667 61.111 16.64 0.00 0.00 3.33
438 439 2.186160 CGTGTTGGGCAGCTGTTGA 61.186 57.895 16.64 0.00 0.00 3.18
439 440 1.723608 CGTGTTGGGCAGCTGTTGAA 61.724 55.000 16.64 2.41 0.00 2.69
440 441 0.031178 GTGTTGGGCAGCTGTTGAAG 59.969 55.000 16.64 0.00 0.00 3.02
441 442 0.106769 TGTTGGGCAGCTGTTGAAGA 60.107 50.000 16.64 1.13 0.00 2.87
442 443 1.251251 GTTGGGCAGCTGTTGAAGAT 58.749 50.000 16.64 0.00 0.00 2.40
443 444 1.068055 GTTGGGCAGCTGTTGAAGATG 60.068 52.381 16.64 0.00 45.49 2.90
469 470 1.523154 GGATGCAAAGTGACCGGCAA 61.523 55.000 0.00 0.00 40.02 4.52
516 517 3.255725 TGTTGTTCATTATCCCGTCGTC 58.744 45.455 0.00 0.00 0.00 4.20
583 604 3.955650 TTCTCCCTTCTACTTTCACCG 57.044 47.619 0.00 0.00 0.00 4.94
624 650 6.148976 GGTGGATGACTAACCAAAACTCTAAC 59.851 42.308 0.00 0.00 37.94 2.34
625 651 6.708949 GTGGATGACTAACCAAAACTCTAACA 59.291 38.462 0.00 0.00 37.94 2.41
631 659 7.494625 TGACTAACCAAAACTCTAACAGTTCTG 59.505 37.037 0.00 0.00 45.32 3.02
679 719 6.973006 TTAAACTCGAAAATAAAACACGCC 57.027 33.333 0.00 0.00 0.00 5.68
689 729 7.201316 CGAAAATAAAACACGCCTTCCATTTAG 60.201 37.037 0.00 0.00 0.00 1.85
736 808 7.980662 CACAACATGCATATATGGAAGGAAAAA 59.019 33.333 11.23 0.00 32.32 1.94
847 951 1.064296 CACGCGCTACCTACTCTGG 59.936 63.158 5.73 0.00 0.00 3.86
855 959 1.486726 CTACCTACTCTGGCCCCTTTG 59.513 57.143 0.00 0.00 0.00 2.77
860 964 1.062488 ACTCTGGCCCCTTTGACACT 61.062 55.000 0.00 0.00 0.00 3.55
883 987 2.361992 CAGATTGCCTGCCTGCCA 60.362 61.111 0.00 0.00 35.89 4.92
925 1029 1.623542 ATACCTTCCGCACCAGACCC 61.624 60.000 0.00 0.00 0.00 4.46
1338 1442 4.129737 CGCGGGCTCGAGGAAGAA 62.130 66.667 12.03 0.00 39.00 2.52
1502 1606 1.743623 CGGCGGGTCATACAAAGCA 60.744 57.895 0.00 0.00 0.00 3.91
1695 1799 3.293714 TTCACCGACGCCGTACCA 61.294 61.111 0.00 0.00 0.00 3.25
2385 2800 5.030147 TCTCCTGAATCTTTTGCCTACCTA 58.970 41.667 0.00 0.00 0.00 3.08
2404 2819 4.347453 GCCACCAAGTTGCAGCCG 62.347 66.667 0.00 0.00 0.00 5.52
2405 2820 2.594303 CCACCAAGTTGCAGCCGA 60.594 61.111 0.00 0.00 0.00 5.54
2464 2879 1.067846 TGTTCCACCTCAAGTCGATCG 60.068 52.381 9.36 9.36 0.00 3.69
2468 2883 0.179134 CACCTCAAGTCGATCGGTCC 60.179 60.000 16.41 3.74 0.00 4.46
2469 2884 1.321074 ACCTCAAGTCGATCGGTCCC 61.321 60.000 16.41 1.10 0.00 4.46
2471 2886 0.101399 CTCAAGTCGATCGGTCCCAG 59.899 60.000 16.41 2.68 0.00 4.45
2500 2915 5.606505 TGGATTCATCGGACGATTTTCATA 58.393 37.500 4.20 0.00 31.62 2.15
2608 3023 9.555727 TCTTATTTGTGCAAGAAGTAAAGTACT 57.444 29.630 0.00 0.00 41.73 2.73
2609 3024 9.813080 CTTATTTGTGCAAGAAGTAAAGTACTC 57.187 33.333 0.00 0.00 38.26 2.59
2610 3025 6.613755 TTTGTGCAAGAAGTAAAGTACTCC 57.386 37.500 0.00 0.00 38.26 3.85
2611 3026 5.546621 TGTGCAAGAAGTAAAGTACTCCT 57.453 39.130 0.00 0.00 38.26 3.69
2612 3027 5.925509 TGTGCAAGAAGTAAAGTACTCCTT 58.074 37.500 0.00 0.00 38.26 3.36
2613 3028 5.989777 TGTGCAAGAAGTAAAGTACTCCTTC 59.010 40.000 16.40 16.40 38.26 3.46
2614 3029 6.183360 TGTGCAAGAAGTAAAGTACTCCTTCT 60.183 38.462 19.17 19.17 44.05 2.85
2615 3030 6.146347 GTGCAAGAAGTAAAGTACTCCTTCTG 59.854 42.308 22.81 18.71 41.99 3.02
2616 3031 6.183360 TGCAAGAAGTAAAGTACTCCTTCTGT 60.183 38.462 22.81 14.74 41.99 3.41
2617 3032 7.014905 TGCAAGAAGTAAAGTACTCCTTCTGTA 59.985 37.037 22.81 16.44 41.99 2.74
2618 3033 7.871463 GCAAGAAGTAAAGTACTCCTTCTGTAA 59.129 37.037 22.81 0.00 41.99 2.41
2619 3034 9.760077 CAAGAAGTAAAGTACTCCTTCTGTAAA 57.240 33.333 22.81 0.00 41.99 2.01
2620 3035 9.761504 AAGAAGTAAAGTACTCCTTCTGTAAAC 57.238 33.333 22.81 2.01 41.99 2.01
2621 3036 9.145442 AGAAGTAAAGTACTCCTTCTGTAAACT 57.855 33.333 22.03 3.23 41.45 2.66
2633 3048 9.400638 CTCCTTCTGTAAACTAATATAAGAGCG 57.599 37.037 0.00 0.00 0.00 5.03
2634 3049 8.910944 TCCTTCTGTAAACTAATATAAGAGCGT 58.089 33.333 0.00 0.00 0.00 5.07
2635 3050 9.530633 CCTTCTGTAAACTAATATAAGAGCGTT 57.469 33.333 0.00 0.00 0.00 4.84
2651 3066 9.930693 ATAAGAGCGTTTAGATTATTAAGGAGG 57.069 33.333 0.00 0.00 0.00 4.30
2652 3067 6.760291 AGAGCGTTTAGATTATTAAGGAGGG 58.240 40.000 0.00 0.00 0.00 4.30
2653 3068 6.553852 AGAGCGTTTAGATTATTAAGGAGGGA 59.446 38.462 0.00 0.00 0.00 4.20
2654 3069 6.760291 AGCGTTTAGATTATTAAGGAGGGAG 58.240 40.000 0.00 0.00 0.00 4.30
2655 3070 6.326843 AGCGTTTAGATTATTAAGGAGGGAGT 59.673 38.462 0.00 0.00 0.00 3.85
2656 3071 7.508296 AGCGTTTAGATTATTAAGGAGGGAGTA 59.492 37.037 0.00 0.00 0.00 2.59
2669 3084 3.054361 GGAGGGAGTATTTCTTGAAGCCA 60.054 47.826 0.00 0.00 0.00 4.75
2674 3089 4.098501 GGAGTATTTCTTGAAGCCAATGGG 59.901 45.833 0.00 0.00 37.18 4.00
2704 3119 5.142639 ACCAAACTATGCATGCTTCCATAT 58.857 37.500 20.33 5.16 0.00 1.78
2712 3322 3.566742 TGCATGCTTCCATATTGTAGCAG 59.433 43.478 20.33 7.15 45.72 4.24
2717 3327 4.199310 GCTTCCATATTGTAGCAGTTCCA 58.801 43.478 1.15 0.00 33.88 3.53
2734 3344 2.368655 CCAACAATTGGCTTGGCTAC 57.631 50.000 13.23 0.00 45.17 3.58
2740 3476 4.860022 ACAATTGGCTTGGCTACTAGAAT 58.140 39.130 10.83 0.00 39.30 2.40
2813 3549 0.958091 TCATTTTGTGGGTCGCCTTG 59.042 50.000 0.00 0.00 0.00 3.61
2838 3574 2.368439 GCATGTTCATGAAGGGCTACA 58.632 47.619 8.80 2.99 0.00 2.74
2845 3581 1.066858 CATGAAGGGCTACACAGACGT 60.067 52.381 0.00 0.00 0.00 4.34
2917 3709 1.140452 GCTGGATCATCTCTTGGCTCA 59.860 52.381 0.00 0.00 0.00 4.26
2921 3713 3.201487 TGGATCATCTCTTGGCTCAATGT 59.799 43.478 0.00 0.00 0.00 2.71
2932 3724 0.106819 GCTCAATGTGAGGCCTCCAT 60.107 55.000 29.95 26.18 44.43 3.41
2949 3741 2.833943 TCCATGATATGTGCTCGCCTAT 59.166 45.455 0.00 0.00 0.00 2.57
2982 3774 3.495629 GGCAGATCATTGAGCTCACCATA 60.496 47.826 18.03 1.16 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.295288 CCAATGAAAGTGATGGATAATTAGAGC 58.705 37.037 0.00 0.00 30.28 4.09
1 2 9.347240 ACCAATGAAAGTGATGGATAATTAGAG 57.653 33.333 0.00 0.00 30.28 2.43
2 3 9.699410 AACCAATGAAAGTGATGGATAATTAGA 57.301 29.630 0.00 0.00 30.28 2.10
9 10 9.253832 TGTTTATAACCAATGAAAGTGATGGAT 57.746 29.630 0.00 0.00 30.28 3.41
10 11 8.642935 TGTTTATAACCAATGAAAGTGATGGA 57.357 30.769 0.00 0.00 30.28 3.41
11 12 7.975616 CCTGTTTATAACCAATGAAAGTGATGG 59.024 37.037 0.00 0.00 30.28 3.51
12 13 8.522830 ACCTGTTTATAACCAATGAAAGTGATG 58.477 33.333 0.00 0.00 30.28 3.07
13 14 8.650143 ACCTGTTTATAACCAATGAAAGTGAT 57.350 30.769 0.00 0.00 30.28 3.06
14 15 8.472007 AACCTGTTTATAACCAATGAAAGTGA 57.528 30.769 0.00 0.00 30.28 3.41
15 16 9.541143 AAAACCTGTTTATAACCAATGAAAGTG 57.459 29.630 0.00 0.00 31.63 3.16
16 17 9.541143 CAAAACCTGTTTATAACCAATGAAAGT 57.459 29.630 0.00 0.00 31.63 2.66
17 18 8.987890 CCAAAACCTGTTTATAACCAATGAAAG 58.012 33.333 0.00 0.00 31.63 2.62
18 19 7.442666 GCCAAAACCTGTTTATAACCAATGAAA 59.557 33.333 0.00 0.00 31.63 2.69
19 20 6.931840 GCCAAAACCTGTTTATAACCAATGAA 59.068 34.615 0.00 0.00 31.63 2.57
20 21 6.268847 AGCCAAAACCTGTTTATAACCAATGA 59.731 34.615 0.00 0.00 31.63 2.57
21 22 6.463360 AGCCAAAACCTGTTTATAACCAATG 58.537 36.000 0.00 0.00 31.63 2.82
22 23 6.268847 TGAGCCAAAACCTGTTTATAACCAAT 59.731 34.615 0.00 0.00 31.63 3.16
23 24 5.598830 TGAGCCAAAACCTGTTTATAACCAA 59.401 36.000 0.00 0.00 31.63 3.67
24 25 5.141182 TGAGCCAAAACCTGTTTATAACCA 58.859 37.500 0.00 0.00 31.63 3.67
25 26 5.715434 TGAGCCAAAACCTGTTTATAACC 57.285 39.130 0.00 0.00 31.63 2.85
26 27 5.627780 CGTTGAGCCAAAACCTGTTTATAAC 59.372 40.000 0.00 0.00 31.63 1.89
27 28 5.764131 CGTTGAGCCAAAACCTGTTTATAA 58.236 37.500 0.00 0.00 31.63 0.98
28 29 4.320641 GCGTTGAGCCAAAACCTGTTTATA 60.321 41.667 0.00 0.00 40.81 0.98
29 30 3.552068 GCGTTGAGCCAAAACCTGTTTAT 60.552 43.478 0.00 0.00 40.81 1.40
30 31 2.223618 GCGTTGAGCCAAAACCTGTTTA 60.224 45.455 0.00 0.00 40.81 2.01
31 32 1.470805 GCGTTGAGCCAAAACCTGTTT 60.471 47.619 0.00 0.00 40.81 2.83
32 33 0.102300 GCGTTGAGCCAAAACCTGTT 59.898 50.000 0.00 0.00 40.81 3.16
33 34 1.733526 GCGTTGAGCCAAAACCTGT 59.266 52.632 0.00 0.00 40.81 4.00
34 35 4.633980 GCGTTGAGCCAAAACCTG 57.366 55.556 0.00 0.00 40.81 4.00
44 45 4.212214 GCAGATTTAAGGGATAGCGTTGAG 59.788 45.833 0.00 0.00 0.00 3.02
45 46 4.127171 GCAGATTTAAGGGATAGCGTTGA 58.873 43.478 0.00 0.00 0.00 3.18
46 47 3.251004 GGCAGATTTAAGGGATAGCGTTG 59.749 47.826 0.00 0.00 0.00 4.10
47 48 3.118038 TGGCAGATTTAAGGGATAGCGTT 60.118 43.478 0.00 0.00 0.00 4.84
48 49 2.438021 TGGCAGATTTAAGGGATAGCGT 59.562 45.455 0.00 0.00 0.00 5.07
49 50 3.126001 TGGCAGATTTAAGGGATAGCG 57.874 47.619 0.00 0.00 0.00 4.26
50 51 4.401925 ACATGGCAGATTTAAGGGATAGC 58.598 43.478 0.00 0.00 0.00 2.97
51 52 8.641498 AATTACATGGCAGATTTAAGGGATAG 57.359 34.615 0.00 0.00 0.00 2.08
53 54 9.605951 ATTAATTACATGGCAGATTTAAGGGAT 57.394 29.630 0.00 0.00 0.00 3.85
70 71 9.599866 CGCAGGAATGATAGGATATTAATTACA 57.400 33.333 0.00 0.00 0.00 2.41
71 72 9.817809 TCGCAGGAATGATAGGATATTAATTAC 57.182 33.333 0.00 0.00 0.00 1.89
73 74 9.739276 TTTCGCAGGAATGATAGGATATTAATT 57.261 29.630 0.00 0.00 30.88 1.40
74 75 9.739276 TTTTCGCAGGAATGATAGGATATTAAT 57.261 29.630 0.00 0.00 30.88 1.40
75 76 9.567776 TTTTTCGCAGGAATGATAGGATATTAA 57.432 29.630 0.00 0.00 30.88 1.40
106 107 9.825109 TGACGTTGATATTTGGTAAGATATCAA 57.175 29.630 5.32 12.34 45.70 2.57
107 108 9.825109 TTGACGTTGATATTTGGTAAGATATCA 57.175 29.630 5.32 2.78 41.21 2.15
109 110 9.607988 TGTTGACGTTGATATTTGGTAAGATAT 57.392 29.630 0.00 0.00 0.00 1.63
110 111 9.093970 CTGTTGACGTTGATATTTGGTAAGATA 57.906 33.333 0.00 0.00 0.00 1.98
111 112 7.822334 TCTGTTGACGTTGATATTTGGTAAGAT 59.178 33.333 0.00 0.00 0.00 2.40
112 113 7.156000 TCTGTTGACGTTGATATTTGGTAAGA 58.844 34.615 0.00 0.00 0.00 2.10
113 114 7.359262 TCTGTTGACGTTGATATTTGGTAAG 57.641 36.000 0.00 0.00 0.00 2.34
114 115 7.915293 ATCTGTTGACGTTGATATTTGGTAA 57.085 32.000 0.00 0.00 0.00 2.85
116 117 9.778741 ATATATCTGTTGACGTTGATATTTGGT 57.221 29.630 0.00 0.00 34.91 3.67
247 248 9.941325 CTCTGGACTAGATTGCATAGATATTTT 57.059 33.333 0.00 0.00 34.21 1.82
248 249 9.099071 ACTCTGGACTAGATTGCATAGATATTT 57.901 33.333 0.00 0.00 34.21 1.40
249 250 8.530311 CACTCTGGACTAGATTGCATAGATATT 58.470 37.037 0.00 0.00 34.21 1.28
250 251 7.673504 ACACTCTGGACTAGATTGCATAGATAT 59.326 37.037 6.15 0.00 39.10 1.63
251 252 7.007116 ACACTCTGGACTAGATTGCATAGATA 58.993 38.462 6.15 0.00 39.10 1.98
252 253 5.837979 ACACTCTGGACTAGATTGCATAGAT 59.162 40.000 6.15 0.00 39.10 1.98
253 254 5.204292 ACACTCTGGACTAGATTGCATAGA 58.796 41.667 6.15 0.00 39.10 1.98
254 255 5.528043 ACACTCTGGACTAGATTGCATAG 57.472 43.478 6.15 0.00 39.10 2.23
255 256 5.450550 CGAACACTCTGGACTAGATTGCATA 60.451 44.000 6.15 0.00 39.10 3.14
256 257 4.679106 CGAACACTCTGGACTAGATTGCAT 60.679 45.833 6.15 0.00 39.10 3.96
257 258 3.367395 CGAACACTCTGGACTAGATTGCA 60.367 47.826 6.15 0.00 39.10 4.08
258 259 3.182967 CGAACACTCTGGACTAGATTGC 58.817 50.000 6.15 0.00 39.10 3.56
259 260 4.169508 CACGAACACTCTGGACTAGATTG 58.830 47.826 0.00 4.85 40.75 2.67
260 261 3.367498 GCACGAACACTCTGGACTAGATT 60.367 47.826 0.00 0.00 34.21 2.40
261 262 2.164624 GCACGAACACTCTGGACTAGAT 59.835 50.000 0.00 0.00 34.21 1.98
262 263 1.540267 GCACGAACACTCTGGACTAGA 59.460 52.381 0.00 0.00 0.00 2.43
263 264 1.729472 CGCACGAACACTCTGGACTAG 60.729 57.143 0.00 0.00 0.00 2.57
264 265 0.240145 CGCACGAACACTCTGGACTA 59.760 55.000 0.00 0.00 0.00 2.59
265 266 1.007271 CGCACGAACACTCTGGACT 60.007 57.895 0.00 0.00 0.00 3.85
266 267 1.004277 CTCGCACGAACACTCTGGAC 61.004 60.000 0.00 0.00 0.00 4.02
267 268 1.170290 TCTCGCACGAACACTCTGGA 61.170 55.000 0.00 0.00 0.00 3.86
268 269 0.730834 CTCTCGCACGAACACTCTGG 60.731 60.000 0.00 0.00 0.00 3.86
269 270 1.340657 GCTCTCGCACGAACACTCTG 61.341 60.000 0.00 0.00 35.78 3.35
270 271 1.081108 GCTCTCGCACGAACACTCT 60.081 57.895 0.00 0.00 35.78 3.24
271 272 2.429351 CGCTCTCGCACGAACACTC 61.429 63.158 0.00 0.00 35.30 3.51
272 273 2.429236 CGCTCTCGCACGAACACT 60.429 61.111 0.00 0.00 35.30 3.55
273 274 2.729862 ACGCTCTCGCACGAACAC 60.730 61.111 0.00 0.00 39.84 3.32
274 275 2.729491 CACGCTCTCGCACGAACA 60.729 61.111 0.00 0.00 39.84 3.18
275 276 4.122515 GCACGCTCTCGCACGAAC 62.123 66.667 0.00 0.00 39.84 3.95
295 296 2.951227 GGCGCGCTAAAATGCAGC 60.951 61.111 32.29 5.91 36.17 5.25
296 297 1.584483 CAGGCGCGCTAAAATGCAG 60.584 57.895 32.29 5.05 0.00 4.41
297 298 2.484662 CAGGCGCGCTAAAATGCA 59.515 55.556 32.29 0.00 0.00 3.96
298 299 2.951227 GCAGGCGCGCTAAAATGC 60.951 61.111 32.29 26.05 0.00 3.56
299 300 1.584483 CAGCAGGCGCGCTAAAATG 60.584 57.895 32.29 21.08 45.49 2.32
300 301 2.764314 CCAGCAGGCGCGCTAAAAT 61.764 57.895 32.29 10.84 45.49 1.82
301 302 3.430862 CCAGCAGGCGCGCTAAAA 61.431 61.111 32.29 0.00 45.49 1.52
302 303 4.386951 TCCAGCAGGCGCGCTAAA 62.387 61.111 32.29 6.90 45.49 1.85
303 304 4.819761 CTCCAGCAGGCGCGCTAA 62.820 66.667 32.29 7.65 45.49 3.09
307 308 3.188786 GTAACTCCAGCAGGCGCG 61.189 66.667 0.00 0.00 45.49 6.86
308 309 3.188786 CGTAACTCCAGCAGGCGC 61.189 66.667 0.00 0.00 38.99 6.53
309 310 2.094659 CACGTAACTCCAGCAGGCG 61.095 63.158 0.00 0.00 33.74 5.52
310 311 2.391389 GCACGTAACTCCAGCAGGC 61.391 63.158 0.00 0.00 33.74 4.85
311 312 2.094659 CGCACGTAACTCCAGCAGG 61.095 63.158 0.00 0.00 0.00 4.85
312 313 1.372997 ACGCACGTAACTCCAGCAG 60.373 57.895 0.00 0.00 0.00 4.24
313 314 1.663388 CACGCACGTAACTCCAGCA 60.663 57.895 0.00 0.00 0.00 4.41
314 315 3.011760 GCACGCACGTAACTCCAGC 62.012 63.158 0.00 0.00 0.00 4.85
315 316 0.109458 TAGCACGCACGTAACTCCAG 60.109 55.000 0.00 0.00 0.00 3.86
316 317 0.314618 TTAGCACGCACGTAACTCCA 59.685 50.000 0.00 0.00 0.00 3.86
317 318 1.421382 TTTAGCACGCACGTAACTCC 58.579 50.000 0.00 0.00 0.00 3.85
318 319 3.717350 AATTTAGCACGCACGTAACTC 57.283 42.857 0.00 0.00 0.00 3.01
319 320 5.499652 CGATAAATTTAGCACGCACGTAACT 60.500 40.000 13.48 0.00 0.00 2.24
320 321 4.658723 CGATAAATTTAGCACGCACGTAAC 59.341 41.667 13.48 0.00 0.00 2.50
321 322 4.779702 GCGATAAATTTAGCACGCACGTAA 60.780 41.667 26.58 0.00 44.29 3.18
322 323 3.301963 GCGATAAATTTAGCACGCACGTA 60.302 43.478 26.58 0.00 44.29 3.57
323 324 2.536130 GCGATAAATTTAGCACGCACGT 60.536 45.455 26.58 0.00 44.29 4.49
324 325 2.026990 GCGATAAATTTAGCACGCACG 58.973 47.619 26.58 15.01 44.29 5.34
325 326 2.026990 CGCGATAAATTTAGCACGCAC 58.973 47.619 28.52 13.61 44.96 5.34
326 327 1.927838 TCGCGATAAATTTAGCACGCA 59.072 42.857 28.52 19.82 44.96 5.24
327 328 2.287079 GTCGCGATAAATTTAGCACGC 58.713 47.619 24.05 24.05 42.07 5.34
328 329 2.655577 CGGTCGCGATAAATTTAGCACG 60.656 50.000 14.06 15.65 0.00 5.34
329 330 2.887733 CGGTCGCGATAAATTTAGCAC 58.112 47.619 14.06 3.01 0.00 4.40
330 331 1.259507 GCGGTCGCGATAAATTTAGCA 59.740 47.619 14.06 0.00 0.00 3.49
331 332 1.933457 GCGGTCGCGATAAATTTAGC 58.067 50.000 14.06 3.31 0.00 3.09
343 344 2.278271 GCTGACTCTAGCGGTCGC 60.278 66.667 7.32 7.32 42.33 5.19
349 350 2.415426 GGGAGCGCTGACTCTAGC 59.585 66.667 18.48 0.00 40.29 3.42
350 351 2.840066 CGGGGAGCGCTGACTCTAG 61.840 68.421 18.48 0.00 36.87 2.43
351 352 2.829003 CGGGGAGCGCTGACTCTA 60.829 66.667 18.48 0.00 36.87 2.43
374 375 2.802667 CGTCGATCGCCTGCTTTGG 61.803 63.158 11.09 0.00 0.00 3.28
375 376 2.697425 CGTCGATCGCCTGCTTTG 59.303 61.111 11.09 0.00 0.00 2.77
384 385 3.837687 TTTGCAGCGCGTCGATCG 61.838 61.111 9.36 9.36 43.12 3.69
385 386 2.227968 AAGTTTGCAGCGCGTCGATC 62.228 55.000 8.43 0.00 0.00 3.69
386 387 1.011968 TAAGTTTGCAGCGCGTCGAT 61.012 50.000 8.43 0.00 0.00 3.59
387 388 1.011968 ATAAGTTTGCAGCGCGTCGA 61.012 50.000 8.43 0.00 0.00 4.20
388 389 0.179225 AATAAGTTTGCAGCGCGTCG 60.179 50.000 8.43 0.00 0.00 5.12
389 390 1.963747 AAATAAGTTTGCAGCGCGTC 58.036 45.000 8.43 0.00 0.00 5.19
390 391 2.415697 AAAATAAGTTTGCAGCGCGT 57.584 40.000 8.43 0.00 0.00 6.01
391 392 4.614417 GTTAAAAATAAGTTTGCAGCGCG 58.386 39.130 0.00 0.00 0.00 6.86
392 393 4.614417 CGTTAAAAATAAGTTTGCAGCGC 58.386 39.130 0.00 0.00 0.00 5.92
393 394 4.614417 GCGTTAAAAATAAGTTTGCAGCG 58.386 39.130 0.00 0.00 0.00 5.18
394 395 4.147479 ACGCGTTAAAAATAAGTTTGCAGC 59.853 37.500 5.58 0.00 0.00 5.25
395 396 5.396947 TGACGCGTTAAAAATAAGTTTGCAG 59.603 36.000 15.53 0.00 0.00 4.41
396 397 5.171695 GTGACGCGTTAAAAATAAGTTTGCA 59.828 36.000 15.53 0.00 0.00 4.08
397 398 5.583087 GTGACGCGTTAAAAATAAGTTTGC 58.417 37.500 15.53 0.00 0.00 3.68
398 399 5.803734 CGTGACGCGTTAAAAATAAGTTTG 58.196 37.500 15.53 0.00 35.54 2.93
414 415 4.012895 CTGCCCAACACGTGACGC 62.013 66.667 25.01 16.92 0.00 5.19
415 416 4.012895 GCTGCCCAACACGTGACG 62.013 66.667 25.01 12.26 0.00 4.35
416 417 2.591715 AGCTGCCCAACACGTGAC 60.592 61.111 25.01 6.45 0.00 3.67
417 418 2.591429 CAGCTGCCCAACACGTGA 60.591 61.111 25.01 0.00 0.00 4.35
418 419 2.480610 AACAGCTGCCCAACACGTG 61.481 57.895 15.27 15.48 0.00 4.49
419 420 2.124320 AACAGCTGCCCAACACGT 60.124 55.556 15.27 0.00 0.00 4.49
420 421 1.723608 TTCAACAGCTGCCCAACACG 61.724 55.000 15.27 0.00 0.00 4.49
421 422 0.031178 CTTCAACAGCTGCCCAACAC 59.969 55.000 15.27 0.00 0.00 3.32
422 423 0.106769 TCTTCAACAGCTGCCCAACA 60.107 50.000 15.27 0.00 0.00 3.33
423 424 1.068055 CATCTTCAACAGCTGCCCAAC 60.068 52.381 15.27 0.00 0.00 3.77
424 425 1.250328 CATCTTCAACAGCTGCCCAA 58.750 50.000 15.27 2.47 0.00 4.12
425 426 1.246056 GCATCTTCAACAGCTGCCCA 61.246 55.000 15.27 0.00 38.51 5.36
426 427 0.964358 AGCATCTTCAACAGCTGCCC 60.964 55.000 15.27 0.00 44.51 5.36
427 428 0.450983 GAGCATCTTCAACAGCTGCC 59.549 55.000 15.27 0.00 44.51 4.85
428 429 3.992636 GAGCATCTTCAACAGCTGC 57.007 52.632 15.27 0.00 43.88 5.25
440 441 2.355132 CACTTTGCATCCTGAGAGCATC 59.645 50.000 0.00 0.00 38.19 3.91
441 442 2.026542 TCACTTTGCATCCTGAGAGCAT 60.027 45.455 0.00 0.00 38.19 3.79
442 443 1.348696 TCACTTTGCATCCTGAGAGCA 59.651 47.619 0.00 0.00 36.32 4.26
443 444 1.736681 GTCACTTTGCATCCTGAGAGC 59.263 52.381 0.00 0.00 0.00 4.09
444 445 2.354259 GGTCACTTTGCATCCTGAGAG 58.646 52.381 0.00 0.00 0.00 3.20
445 446 1.338105 CGGTCACTTTGCATCCTGAGA 60.338 52.381 0.00 0.00 0.00 3.27
446 447 1.081892 CGGTCACTTTGCATCCTGAG 58.918 55.000 0.00 0.00 0.00 3.35
469 470 0.179100 TAGTACCGACTAGCGAGCGT 60.179 55.000 7.94 1.57 44.57 5.07
471 472 2.095819 GGAATAGTACCGACTAGCGAGC 60.096 54.545 7.94 0.00 41.50 5.03
516 517 5.658190 ACCACATTATTCCTCCTTTCAATGG 59.342 40.000 0.00 0.00 0.00 3.16
583 604 7.231722 AGTCATCCACCTGTTGAGTCTATATAC 59.768 40.741 0.00 0.00 0.00 1.47
624 650 1.774639 GTGCCAAATGTGCAGAACTG 58.225 50.000 0.00 0.00 39.87 3.16
625 651 0.311790 CGTGCCAAATGTGCAGAACT 59.688 50.000 0.00 0.00 39.87 3.01
631 659 1.782044 ATCAAACGTGCCAAATGTGC 58.218 45.000 0.00 0.00 0.00 4.57
679 719 4.201920 GGAAAACTAGCGGCTAAATGGAAG 60.202 45.833 11.39 1.59 0.00 3.46
689 729 2.407428 GGCAGGGAAAACTAGCGGC 61.407 63.158 0.00 0.00 0.00 6.53
736 808 3.320826 GGGAACACATGTTTTAGCCAGTT 59.679 43.478 0.00 0.00 38.56 3.16
737 809 2.890945 GGGAACACATGTTTTAGCCAGT 59.109 45.455 0.00 0.00 38.56 4.00
738 810 3.157087 AGGGAACACATGTTTTAGCCAG 58.843 45.455 0.00 0.00 38.56 4.85
739 811 3.237268 AGGGAACACATGTTTTAGCCA 57.763 42.857 0.00 0.00 38.56 4.75
741 813 3.826729 AGGAAGGGAACACATGTTTTAGC 59.173 43.478 0.00 0.00 38.56 3.09
742 814 7.519032 TTTAGGAAGGGAACACATGTTTTAG 57.481 36.000 0.00 0.00 38.56 1.85
743 815 9.589461 TTATTTAGGAAGGGAACACATGTTTTA 57.411 29.630 0.00 0.00 38.56 1.52
744 816 6.994421 ATTTAGGAAGGGAACACATGTTTT 57.006 33.333 0.00 0.00 38.56 2.43
806 910 2.222678 CGATAGCTCATTGACATGTGGC 59.777 50.000 1.15 0.00 33.51 5.01
843 947 1.455849 CAGTGTCAAAGGGGCCAGA 59.544 57.895 4.39 0.00 0.00 3.86
847 951 1.588082 CATGCAGTGTCAAAGGGGC 59.412 57.895 0.00 0.00 0.00 5.80
855 959 3.324170 GCAATCTGCATGCAGTGTC 57.676 52.632 39.08 24.52 44.26 3.67
925 1029 0.457853 CACCCAGTGGTACGTCGATG 60.458 60.000 8.74 2.26 45.57 3.84
953 1057 3.434637 GTGTGGTTCATGTTTGTGTGTC 58.565 45.455 0.00 0.00 0.00 3.67
1101 1205 3.441290 ACGACGAAGAGCTCCCCG 61.441 66.667 19.70 19.70 0.00 5.73
1368 1472 2.634100 GAGGTAATCCAGCCCCCTT 58.366 57.895 0.00 0.00 35.89 3.95
1492 1596 0.096976 CCGAACGGCTGCTTTGTATG 59.903 55.000 0.00 0.00 0.00 2.39
1635 1739 1.143373 GCACGTTATCATCGGCGTCA 61.143 55.000 6.85 0.00 35.25 4.35
1641 1745 1.846648 GGCGAGCACGTTATCATCG 59.153 57.895 5.23 0.00 41.98 3.84
1887 1991 0.034059 AGTCTGACTCCCAAAGTGCG 59.966 55.000 4.06 0.00 38.74 5.34
2004 2123 0.539051 AGACTTCGATCCAGCCTTGG 59.461 55.000 0.00 0.00 46.49 3.61
2333 2739 6.040391 TCTGAGGGGAACAACAACTATTTTTG 59.960 38.462 0.00 0.00 0.00 2.44
2349 2755 3.205519 TCAGGAGAAAATCTGAGGGGA 57.794 47.619 0.00 0.00 35.37 4.81
2350 2756 4.165758 AGATTCAGGAGAAAATCTGAGGGG 59.834 45.833 0.00 0.00 39.99 4.79
2385 2800 3.595758 GCTGCAACTTGGTGGCGT 61.596 61.111 0.00 0.00 34.77 5.68
2438 2853 0.995024 CTTGAGGTGGAACAGGGGAT 59.005 55.000 0.00 0.00 41.80 3.85
2464 2879 1.025041 GAATCCATTTCGCTGGGACC 58.975 55.000 0.00 0.00 36.89 4.46
2468 2883 1.265095 CCGATGAATCCATTTCGCTGG 59.735 52.381 0.00 0.00 37.13 4.85
2469 2884 2.032549 GTCCGATGAATCCATTTCGCTG 60.033 50.000 0.00 0.00 37.13 5.18
2471 2886 1.070577 CGTCCGATGAATCCATTTCGC 60.071 52.381 0.00 0.00 37.13 4.70
2607 3022 9.400638 CGCTCTTATATTAGTTTACAGAAGGAG 57.599 37.037 0.00 0.00 0.00 3.69
2608 3023 8.910944 ACGCTCTTATATTAGTTTACAGAAGGA 58.089 33.333 0.00 0.00 0.00 3.36
2609 3024 9.530633 AACGCTCTTATATTAGTTTACAGAAGG 57.469 33.333 0.00 0.00 0.00 3.46
2625 3040 9.930693 CCTCCTTAATAATCTAAACGCTCTTAT 57.069 33.333 0.00 0.00 0.00 1.73
2626 3041 8.365647 CCCTCCTTAATAATCTAAACGCTCTTA 58.634 37.037 0.00 0.00 0.00 2.10
2627 3042 7.070821 TCCCTCCTTAATAATCTAAACGCTCTT 59.929 37.037 0.00 0.00 0.00 2.85
2628 3043 6.553852 TCCCTCCTTAATAATCTAAACGCTCT 59.446 38.462 0.00 0.00 0.00 4.09
2629 3044 6.756221 TCCCTCCTTAATAATCTAAACGCTC 58.244 40.000 0.00 0.00 0.00 5.03
2630 3045 6.326843 ACTCCCTCCTTAATAATCTAAACGCT 59.673 38.462 0.00 0.00 0.00 5.07
2631 3046 6.522946 ACTCCCTCCTTAATAATCTAAACGC 58.477 40.000 0.00 0.00 0.00 4.84
2641 3056 8.211629 GCTTCAAGAAATACTCCCTCCTTAATA 58.788 37.037 0.00 0.00 0.00 0.98
2642 3057 7.057264 GCTTCAAGAAATACTCCCTCCTTAAT 58.943 38.462 0.00 0.00 0.00 1.40
2643 3058 6.415573 GCTTCAAGAAATACTCCCTCCTTAA 58.584 40.000 0.00 0.00 0.00 1.85
2644 3059 5.104485 GGCTTCAAGAAATACTCCCTCCTTA 60.104 44.000 0.00 0.00 0.00 2.69
2645 3060 4.324641 GGCTTCAAGAAATACTCCCTCCTT 60.325 45.833 0.00 0.00 0.00 3.36
2646 3061 3.201045 GGCTTCAAGAAATACTCCCTCCT 59.799 47.826 0.00 0.00 0.00 3.69
2647 3062 3.054361 TGGCTTCAAGAAATACTCCCTCC 60.054 47.826 0.00 0.00 0.00 4.30
2648 3063 4.222124 TGGCTTCAAGAAATACTCCCTC 57.778 45.455 0.00 0.00 0.00 4.30
2649 3064 4.657814 TTGGCTTCAAGAAATACTCCCT 57.342 40.909 0.00 0.00 0.00 4.20
2650 3065 4.098501 CCATTGGCTTCAAGAAATACTCCC 59.901 45.833 0.00 0.00 33.43 4.30
2651 3066 4.098501 CCCATTGGCTTCAAGAAATACTCC 59.901 45.833 0.00 0.00 33.43 3.85
2652 3067 5.254339 CCCATTGGCTTCAAGAAATACTC 57.746 43.478 0.00 0.00 33.43 2.59
2669 3084 1.906333 GTTTGGTCCACGGCCCATT 60.906 57.895 0.00 0.00 0.00 3.16
2674 3089 0.958382 TGCATAGTTTGGTCCACGGC 60.958 55.000 0.00 0.00 0.00 5.68
2686 3101 5.413833 GCTACAATATGGAAGCATGCATAGT 59.586 40.000 21.98 5.15 42.23 2.12
2717 3327 4.301072 TCTAGTAGCCAAGCCAATTGTT 57.699 40.909 4.43 0.00 37.17 2.83
2734 3344 3.064545 GCAAGGCTGTGCTACAATTCTAG 59.935 47.826 12.44 0.00 41.51 2.43
2740 3476 1.603455 GGGCAAGGCTGTGCTACAA 60.603 57.895 17.11 0.00 44.31 2.41
2813 3549 2.417787 GCCCTTCATGAACATGCCTTTC 60.418 50.000 3.38 0.00 38.65 2.62
2821 3557 2.637382 TCTGTGTAGCCCTTCATGAACA 59.363 45.455 3.38 0.00 0.00 3.18
2838 3574 4.406173 CGAGCCGAGCACGTCTGT 62.406 66.667 2.18 0.00 37.80 3.41
2917 3709 3.396946 ACATATCATGGAGGCCTCACATT 59.603 43.478 33.29 20.06 33.60 2.71
2921 3713 1.072806 GCACATATCATGGAGGCCTCA 59.927 52.381 33.29 19.80 33.60 3.86
2932 3724 4.071961 ACAAATAGGCGAGCACATATCA 57.928 40.909 0.00 0.00 0.00 2.15
2949 3741 2.552599 TGATCTGCCACGGTAACAAA 57.447 45.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.