Multiple sequence alignment - TraesCS6D01G020400

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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 TraesCS6D01G020400 chr6D 100.000 2591 0 0 1 2591 8096469 8099059 0.000000e+00 4785.0
1 TraesCS6D01G020400 chr6D 90.070 2135 124 32 485 2587 232377654 232375576 0.000000e+00 2687.0
2 TraesCS6D01G020400 chr6D 90.954 409 12 2 1692 2075 421864549 421864957 6.350000e-146 527.0
3 TraesCS6D01G020400 chr6D 92.818 181 11 2 90 269 404877861 404877682 7.110000e-66 261.0
4 TraesCS6D01G020400 chr7D 92.276 1709 90 10 401 2082 18554233 18552540 0.000000e+00 2386.0
5 TraesCS6D01G020400 chr7D 93.774 514 26 4 2079 2590 207199471 207199980 0.000000e+00 767.0
6 TraesCS6D01G020400 chr7D 93.750 512 26 6 2079 2587 175931660 175931152 0.000000e+00 763.0
7 TraesCS6D01G020400 chr7D 92.607 514 33 5 2079 2591 4824058 4823549 0.000000e+00 734.0
8 TraesCS6D01G020400 chr7D 95.882 170 7 0 90 259 517575403 517575234 2.540000e-70 276.0
9 TraesCS6D01G020400 chr7D 92.857 182 9 4 84 263 340604938 340605117 7.110000e-66 261.0
10 TraesCS6D01G020400 chr4D 92.222 1710 90 13 401 2082 84467727 84466033 0.000000e+00 2381.0
11 TraesCS6D01G020400 chr4D 91.946 1701 97 12 403 2075 481887026 481888714 0.000000e+00 2346.0
12 TraesCS6D01G020400 chr4D 91.289 1722 85 30 401 2082 486565783 486564087 0.000000e+00 2289.0
13 TraesCS6D01G020400 chr4D 90.267 1726 107 25 385 2082 502730815 502729123 0.000000e+00 2200.0
14 TraesCS6D01G020400 chr4D 92.941 510 34 2 2079 2587 84465999 84465491 0.000000e+00 741.0
15 TraesCS6D01G020400 chr4D 95.376 173 7 1 87 259 93338036 93338207 9.130000e-70 274.0
16 TraesCS6D01G020400 chr4D 94.857 175 9 0 84 258 404108568 404108742 9.130000e-70 274.0
17 TraesCS6D01G020400 chr2D 92.168 1711 94 12 401 2082 644015512 644013813 0.000000e+00 2381.0
18 TraesCS6D01G020400 chr2D 90.442 1674 99 28 449 2082 596268284 596266632 0.000000e+00 2148.0
19 TraesCS6D01G020400 chr2D 93.333 510 32 2 2079 2587 627748140 627747632 0.000000e+00 752.0
20 TraesCS6D01G020400 chr2D 94.798 173 9 0 90 262 289313261 289313089 1.180000e-68 270.0
21 TraesCS6D01G020400 chr2D 95.808 167 7 0 93 259 309971584 309971418 1.180000e-68 270.0
22 TraesCS6D01G020400 chr1D 91.993 1711 90 16 394 2075 430108481 430110173 0.000000e+00 2357.0
23 TraesCS6D01G020400 chr1D 91.876 1711 94 14 406 2082 415505717 415504018 0.000000e+00 2348.0
24 TraesCS6D01G020400 chr1D 91.350 1711 92 23 402 2082 278102468 278100784 0.000000e+00 2289.0
25 TraesCS6D01G020400 chr1D 93.191 514 33 2 2079 2591 250225089 250225601 0.000000e+00 754.0
26 TraesCS6D01G020400 chr1D 93.011 186 12 1 94 279 196817679 196817863 1.180000e-68 270.0
27 TraesCS6D01G020400 chr1D 91.667 60 4 1 1 59 462727514 462727455 5.940000e-12 82.4
28 TraesCS6D01G020400 chr3D 91.813 1710 94 14 395 2075 267288549 267290241 0.000000e+00 2340.0
29 TraesCS6D01G020400 chr3D 91.472 985 50 17 1117 2075 431337548 431338524 0.000000e+00 1323.0
30 TraesCS6D01G020400 chr5B 91.589 1712 101 13 402 2082 648784985 648783286 0.000000e+00 2324.0
31 TraesCS6D01G020400 chr5B 93.220 59 4 0 2 60 531665597 531665655 1.280000e-13 87.9
32 TraesCS6D01G020400 chr4A 91.564 1707 106 10 403 2082 669783223 669781528 0.000000e+00 2320.0
33 TraesCS6D01G020400 chr5D 90.941 1711 91 23 400 2082 495796215 495794541 0.000000e+00 2242.0
34 TraesCS6D01G020400 chr5D 96.610 59 2 0 1 59 408579283 408579225 5.900000e-17 99.0
35 TraesCS6D01G020400 chr5D 90.164 61 5 1 1 60 416792387 416792327 7.690000e-11 78.7
36 TraesCS6D01G020400 chr6B 93.969 514 27 3 2081 2591 636475900 636476412 0.000000e+00 774.0
37 TraesCS6D01G020400 chr6B 91.935 62 4 1 1 61 80680976 80680915 4.590000e-13 86.1
38 TraesCS6D01G020400 chrUn 80.146 1098 149 36 1023 2066 339325589 339326671 0.000000e+00 756.0
39 TraesCS6D01G020400 chrUn 89.918 367 12 3 1739 2082 340386244 340385880 1.410000e-122 449.0
40 TraesCS6D01G020400 chr2A 93.230 517 28 6 2079 2591 496897903 496897390 0.000000e+00 754.0
41 TraesCS6D01G020400 chr2A 92.593 513 34 3 2079 2591 549958182 549957674 0.000000e+00 734.0
42 TraesCS6D01G020400 chr2A 90.769 65 5 1 1 64 16794179 16794115 4.590000e-13 86.1
43 TraesCS6D01G020400 chr5A 95.322 171 8 0 88 258 349787522 349787352 3.290000e-69 272.0
44 TraesCS6D01G020400 chr1B 93.333 60 4 0 1 60 677912743 677912802 3.550000e-14 89.8
45 TraesCS6D01G020400 chr1B 90.164 61 5 1 1 60 564444679 564444619 7.690000e-11 78.7
46 TraesCS6D01G020400 chr4B 90.164 61 5 1 1 60 653416358 653416418 7.690000e-11 78.7


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 TraesCS6D01G020400 chr6D 8096469 8099059 2590 False 4785 4785 100.0000 1 2591 1 chr6D.!!$F1 2590
1 TraesCS6D01G020400 chr6D 232375576 232377654 2078 True 2687 2687 90.0700 485 2587 1 chr6D.!!$R1 2102
2 TraesCS6D01G020400 chr7D 18552540 18554233 1693 True 2386 2386 92.2760 401 2082 1 chr7D.!!$R2 1681
3 TraesCS6D01G020400 chr7D 207199471 207199980 509 False 767 767 93.7740 2079 2590 1 chr7D.!!$F1 511
4 TraesCS6D01G020400 chr7D 175931152 175931660 508 True 763 763 93.7500 2079 2587 1 chr7D.!!$R3 508
5 TraesCS6D01G020400 chr7D 4823549 4824058 509 True 734 734 92.6070 2079 2591 1 chr7D.!!$R1 512
6 TraesCS6D01G020400 chr4D 481887026 481888714 1688 False 2346 2346 91.9460 403 2075 1 chr4D.!!$F3 1672
7 TraesCS6D01G020400 chr4D 486564087 486565783 1696 True 2289 2289 91.2890 401 2082 1 chr4D.!!$R1 1681
8 TraesCS6D01G020400 chr4D 502729123 502730815 1692 True 2200 2200 90.2670 385 2082 1 chr4D.!!$R2 1697
9 TraesCS6D01G020400 chr4D 84465491 84467727 2236 True 1561 2381 92.5815 401 2587 2 chr4D.!!$R3 2186
10 TraesCS6D01G020400 chr2D 644013813 644015512 1699 True 2381 2381 92.1680 401 2082 1 chr2D.!!$R5 1681
11 TraesCS6D01G020400 chr2D 596266632 596268284 1652 True 2148 2148 90.4420 449 2082 1 chr2D.!!$R3 1633
12 TraesCS6D01G020400 chr2D 627747632 627748140 508 True 752 752 93.3330 2079 2587 1 chr2D.!!$R4 508
13 TraesCS6D01G020400 chr1D 430108481 430110173 1692 False 2357 2357 91.9930 394 2075 1 chr1D.!!$F3 1681
14 TraesCS6D01G020400 chr1D 415504018 415505717 1699 True 2348 2348 91.8760 406 2082 1 chr1D.!!$R2 1676
15 TraesCS6D01G020400 chr1D 278100784 278102468 1684 True 2289 2289 91.3500 402 2082 1 chr1D.!!$R1 1680
16 TraesCS6D01G020400 chr1D 250225089 250225601 512 False 754 754 93.1910 2079 2591 1 chr1D.!!$F2 512
17 TraesCS6D01G020400 chr3D 267288549 267290241 1692 False 2340 2340 91.8130 395 2075 1 chr3D.!!$F1 1680
18 TraesCS6D01G020400 chr3D 431337548 431338524 976 False 1323 1323 91.4720 1117 2075 1 chr3D.!!$F2 958
19 TraesCS6D01G020400 chr5B 648783286 648784985 1699 True 2324 2324 91.5890 402 2082 1 chr5B.!!$R1 1680
20 TraesCS6D01G020400 chr4A 669781528 669783223 1695 True 2320 2320 91.5640 403 2082 1 chr4A.!!$R1 1679
21 TraesCS6D01G020400 chr5D 495794541 495796215 1674 True 2242 2242 90.9410 400 2082 1 chr5D.!!$R3 1682
22 TraesCS6D01G020400 chr6B 636475900 636476412 512 False 774 774 93.9690 2081 2591 1 chr6B.!!$F1 510
23 TraesCS6D01G020400 chrUn 339325589 339326671 1082 False 756 756 80.1460 1023 2066 1 chrUn.!!$F1 1043
24 TraesCS6D01G020400 chr2A 496897390 496897903 513 True 754 754 93.2300 2079 2591 1 chr2A.!!$R2 512
25 TraesCS6D01G020400 chr2A 549957674 549958182 508 True 734 734 92.5930 2079 2591 1 chr2A.!!$R3 512

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
373 374 0.046242 AAGGACCCCCATGATCCTCA 59.954 55.0 0.0 0.0 42.23 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2167 0.106619 GGCTCGACCTCTTCCTCCTA 60.107 60.0 0.0 0.0 34.51 2.94 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
31 32 9.342308 TGTCTTCTGCCTTCTATAAAAATATGG 57.658 33.333 0.00 0.00 0.00 2.74
32 33 9.343539 GTCTTCTGCCTTCTATAAAAATATGGT 57.656 33.333 0.00 0.00 0.00 3.55
36 37 9.231297 TCTGCCTTCTATAAAAATATGGTATGC 57.769 33.333 0.00 0.00 0.00 3.14
37 38 8.348285 TGCCTTCTATAAAAATATGGTATGCC 57.652 34.615 0.00 0.00 0.00 4.40
38 39 7.120579 TGCCTTCTATAAAAATATGGTATGCCG 59.879 37.037 0.00 0.00 37.67 5.69
39 40 7.120726 GCCTTCTATAAAAATATGGTATGCCGT 59.879 37.037 0.00 0.00 37.67 5.68
40 41 8.450964 CCTTCTATAAAAATATGGTATGCCGTG 58.549 37.037 4.57 0.00 37.67 4.94
41 42 7.915293 TCTATAAAAATATGGTATGCCGTGG 57.085 36.000 4.57 0.00 37.67 4.94
42 43 3.726291 AAAAATATGGTATGCCGTGGC 57.274 42.857 4.57 3.30 42.35 5.01
43 44 1.234821 AAATATGGTATGCCGTGGCG 58.765 50.000 4.57 0.00 45.51 5.69
44 45 0.107831 AATATGGTATGCCGTGGCGT 59.892 50.000 10.93 10.93 45.51 5.68
45 46 0.970640 ATATGGTATGCCGTGGCGTA 59.029 50.000 8.73 8.73 45.51 4.42
46 47 0.970640 TATGGTATGCCGTGGCGTAT 59.029 50.000 15.43 4.32 43.39 3.06
47 48 0.107831 ATGGTATGCCGTGGCGTATT 59.892 50.000 15.43 2.41 43.39 1.89
48 49 0.107606 TGGTATGCCGTGGCGTATTT 60.108 50.000 15.43 0.00 43.39 1.40
49 50 1.018910 GGTATGCCGTGGCGTATTTT 58.981 50.000 15.43 0.00 43.39 1.82
50 51 1.003223 GGTATGCCGTGGCGTATTTTC 60.003 52.381 15.43 3.41 43.39 2.29
51 52 0.931702 TATGCCGTGGCGTATTTTCG 59.068 50.000 8.73 0.00 45.51 3.46
52 53 0.741574 ATGCCGTGGCGTATTTTCGA 60.742 50.000 3.18 0.00 45.51 3.71
53 54 0.949588 TGCCGTGGCGTATTTTCGAA 60.950 50.000 6.37 0.00 45.51 3.71
54 55 0.166379 GCCGTGGCGTATTTTCGAAA 59.834 50.000 6.47 6.47 0.00 3.46
55 56 1.399984 GCCGTGGCGTATTTTCGAAAA 60.400 47.619 24.43 24.43 0.00 2.29
56 57 2.917296 GCCGTGGCGTATTTTCGAAAAA 60.917 45.455 25.77 13.11 0.00 1.94
80 81 7.681939 AAAAGCGAAATGTATACAAGGAAGA 57.318 32.000 10.14 0.00 0.00 2.87
81 82 7.681939 AAAGCGAAATGTATACAAGGAAGAA 57.318 32.000 10.14 0.00 0.00 2.52
82 83 6.910536 AGCGAAATGTATACAAGGAAGAAG 57.089 37.500 10.14 0.00 0.00 2.85
83 84 5.294552 AGCGAAATGTATACAAGGAAGAAGC 59.705 40.000 10.14 7.81 0.00 3.86
84 85 5.064707 GCGAAATGTATACAAGGAAGAAGCA 59.935 40.000 10.14 0.00 0.00 3.91
85 86 6.478588 CGAAATGTATACAAGGAAGAAGCAC 58.521 40.000 10.14 0.00 0.00 4.40
86 87 6.092122 CGAAATGTATACAAGGAAGAAGCACA 59.908 38.462 10.14 0.00 0.00 4.57
87 88 7.360861 CGAAATGTATACAAGGAAGAAGCACAA 60.361 37.037 10.14 0.00 0.00 3.33
88 89 7.944729 AATGTATACAAGGAAGAAGCACAAT 57.055 32.000 10.14 0.00 0.00 2.71
89 90 9.461312 AAATGTATACAAGGAAGAAGCACAATA 57.539 29.630 10.14 0.00 0.00 1.90
90 91 9.632638 AATGTATACAAGGAAGAAGCACAATAT 57.367 29.630 10.14 0.00 0.00 1.28
91 92 8.437360 TGTATACAAGGAAGAAGCACAATATG 57.563 34.615 2.20 0.00 0.00 1.78
92 93 8.264347 TGTATACAAGGAAGAAGCACAATATGA 58.736 33.333 2.20 0.00 0.00 2.15
93 94 9.277783 GTATACAAGGAAGAAGCACAATATGAT 57.722 33.333 0.00 0.00 0.00 2.45
95 96 7.559590 ACAAGGAAGAAGCACAATATGATAC 57.440 36.000 0.00 0.00 0.00 2.24
96 97 7.341805 ACAAGGAAGAAGCACAATATGATACT 58.658 34.615 0.00 0.00 0.00 2.12
97 98 7.497249 ACAAGGAAGAAGCACAATATGATACTC 59.503 37.037 0.00 0.00 0.00 2.59
98 99 6.529220 AGGAAGAAGCACAATATGATACTCC 58.471 40.000 0.00 0.00 0.00 3.85
99 100 5.703130 GGAAGAAGCACAATATGATACTCCC 59.297 44.000 0.00 0.00 0.00 4.30
100 101 6.465035 GGAAGAAGCACAATATGATACTCCCT 60.465 42.308 0.00 0.00 0.00 4.20
101 102 6.107901 AGAAGCACAATATGATACTCCCTC 57.892 41.667 0.00 0.00 0.00 4.30
102 103 4.899352 AGCACAATATGATACTCCCTCC 57.101 45.455 0.00 0.00 0.00 4.30
103 104 3.259374 AGCACAATATGATACTCCCTCCG 59.741 47.826 0.00 0.00 0.00 4.63
104 105 3.006967 GCACAATATGATACTCCCTCCGT 59.993 47.826 0.00 0.00 0.00 4.69
105 106 4.503296 GCACAATATGATACTCCCTCCGTT 60.503 45.833 0.00 0.00 0.00 4.44
106 107 5.230942 CACAATATGATACTCCCTCCGTTC 58.769 45.833 0.00 0.00 0.00 3.95
107 108 4.283722 ACAATATGATACTCCCTCCGTTCC 59.716 45.833 0.00 0.00 0.00 3.62
108 109 2.777459 ATGATACTCCCTCCGTTCCT 57.223 50.000 0.00 0.00 0.00 3.36
109 110 3.897657 ATGATACTCCCTCCGTTCCTA 57.102 47.619 0.00 0.00 0.00 2.94
110 111 3.675348 TGATACTCCCTCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
111 112 3.985127 TGATACTCCCTCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
112 113 4.553678 TGATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
113 114 5.708544 TGATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
114 115 6.320518 TGATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
115 116 6.785963 TGATACTCCCTCCGTTCCTAAATATT 59.214 38.462 0.00 0.00 0.00 1.28
116 117 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
117 118 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
118 119 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
119 120 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
120 121 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
121 122 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
122 123 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
123 124 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
124 125 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
125 126 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
126 127 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
127 128 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
152 153 9.916397 GAGATTTTAACAAATGACTACATACGG 57.084 33.333 0.00 0.00 35.50 4.02
153 154 9.661563 AGATTTTAACAAATGACTACATACGGA 57.338 29.630 0.00 0.00 35.50 4.69
154 155 9.916397 GATTTTAACAAATGACTACATACGGAG 57.084 33.333 0.00 0.00 35.50 4.63
155 156 6.897259 TTAACAAATGACTACATACGGAGC 57.103 37.500 0.00 0.00 35.50 4.70
156 157 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
157 158 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
158 159 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
159 160 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
160 161 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
161 162 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
162 163 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
163 164 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
164 165 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
165 166 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
166 167 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
167 168 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
168 169 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
169 170 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
170 171 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
171 172 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
172 173 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
173 174 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
174 175 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
206 207 9.990360 AATATGTGTAAATACATCCGTATGTGA 57.010 29.630 3.56 0.00 45.99 3.58
209 210 9.639601 ATGTGTAAATACATCCGTATGTGATAG 57.360 33.333 3.56 0.00 45.99 2.08
210 211 8.635328 TGTGTAAATACATCCGTATGTGATAGT 58.365 33.333 3.56 0.00 45.99 2.12
211 212 9.125906 GTGTAAATACATCCGTATGTGATAGTC 57.874 37.037 3.56 0.00 45.99 2.59
212 213 9.074576 TGTAAATACATCCGTATGTGATAGTCT 57.925 33.333 3.56 0.00 45.99 3.24
218 219 8.178313 ACATCCGTATGTGATAGTCTATTTGA 57.822 34.615 0.00 0.00 44.79 2.69
219 220 8.638873 ACATCCGTATGTGATAGTCTATTTGAA 58.361 33.333 0.00 0.00 44.79 2.69
220 221 9.476202 CATCCGTATGTGATAGTCTATTTGAAA 57.524 33.333 0.00 0.00 0.00 2.69
252 253 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
253 254 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
254 255 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
255 256 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
256 257 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
257 258 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
258 259 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
259 260 1.755179 TTAGGAACGGAGGGAGTACG 58.245 55.000 0.00 0.00 0.00 3.67
260 261 0.620556 TAGGAACGGAGGGAGTACGT 59.379 55.000 0.00 0.00 43.43 3.57
261 262 0.620556 AGGAACGGAGGGAGTACGTA 59.379 55.000 0.00 0.00 40.31 3.57
262 263 1.004745 AGGAACGGAGGGAGTACGTAA 59.995 52.381 0.00 0.00 40.31 3.18
263 264 1.403323 GGAACGGAGGGAGTACGTAAG 59.597 57.143 0.00 0.00 40.31 2.34
264 265 2.359900 GAACGGAGGGAGTACGTAAGA 58.640 52.381 0.00 0.00 40.31 2.10
265 266 2.496899 ACGGAGGGAGTACGTAAGAA 57.503 50.000 0.00 0.00 39.30 2.52
266 267 2.363683 ACGGAGGGAGTACGTAAGAAG 58.636 52.381 0.00 0.00 39.30 2.85
267 268 1.065251 CGGAGGGAGTACGTAAGAAGC 59.935 57.143 0.00 0.00 43.62 3.86
268 269 2.097825 GGAGGGAGTACGTAAGAAGCA 58.902 52.381 0.00 0.00 43.62 3.91
269 270 2.494870 GGAGGGAGTACGTAAGAAGCAA 59.505 50.000 0.00 0.00 43.62 3.91
270 271 3.509740 GAGGGAGTACGTAAGAAGCAAC 58.490 50.000 0.00 0.00 43.62 4.17
271 272 2.895404 AGGGAGTACGTAAGAAGCAACA 59.105 45.455 0.00 0.00 43.62 3.33
272 273 3.322828 AGGGAGTACGTAAGAAGCAACAA 59.677 43.478 0.00 0.00 43.62 2.83
273 274 4.060205 GGGAGTACGTAAGAAGCAACAAA 58.940 43.478 0.00 0.00 43.62 2.83
274 275 4.512571 GGGAGTACGTAAGAAGCAACAAAA 59.487 41.667 0.00 0.00 43.62 2.44
275 276 5.180680 GGGAGTACGTAAGAAGCAACAAAAT 59.819 40.000 0.00 0.00 43.62 1.82
276 277 6.293790 GGGAGTACGTAAGAAGCAACAAAATT 60.294 38.462 0.00 0.00 43.62 1.82
277 278 7.136772 GGAGTACGTAAGAAGCAACAAAATTT 58.863 34.615 0.00 0.00 43.62 1.82
278 279 7.112984 GGAGTACGTAAGAAGCAACAAAATTTG 59.887 37.037 3.89 3.89 43.62 2.32
279 280 7.699566 AGTACGTAAGAAGCAACAAAATTTGA 58.300 30.769 13.19 0.00 43.62 2.69
280 281 8.185505 AGTACGTAAGAAGCAACAAAATTTGAA 58.814 29.630 13.19 0.00 43.62 2.69
281 282 7.820044 ACGTAAGAAGCAACAAAATTTGAAA 57.180 28.000 13.19 0.00 43.62 2.69
282 283 7.894847 ACGTAAGAAGCAACAAAATTTGAAAG 58.105 30.769 13.19 2.96 43.62 2.62
283 284 6.840789 CGTAAGAAGCAACAAAATTTGAAAGC 59.159 34.615 13.19 12.15 43.02 3.51
284 285 6.740411 AAGAAGCAACAAAATTTGAAAGCA 57.260 29.167 13.19 0.00 0.00 3.91
285 286 6.930667 AGAAGCAACAAAATTTGAAAGCAT 57.069 29.167 13.19 6.06 0.00 3.79
286 287 8.436046 AAGAAGCAACAAAATTTGAAAGCATA 57.564 26.923 13.19 0.00 0.00 3.14
287 288 8.611654 AGAAGCAACAAAATTTGAAAGCATAT 57.388 26.923 13.19 1.29 0.00 1.78
288 289 9.709495 AGAAGCAACAAAATTTGAAAGCATATA 57.291 25.926 13.19 0.00 0.00 0.86
289 290 9.745323 GAAGCAACAAAATTTGAAAGCATATAC 57.255 29.630 13.19 2.02 0.00 1.47
290 291 9.492973 AAGCAACAAAATTTGAAAGCATATACT 57.507 25.926 13.19 0.00 0.00 2.12
291 292 9.143631 AGCAACAAAATTTGAAAGCATATACTC 57.856 29.630 13.19 0.00 0.00 2.59
292 293 8.924691 GCAACAAAATTTGAAAGCATATACTCA 58.075 29.630 13.19 0.00 0.00 3.41
301 302 9.890629 TTTGAAAGCATATACTCATACACTCTT 57.109 29.630 0.00 0.00 0.00 2.85
320 321 9.851686 ACACTCTTATAATAATTTCTGCATGGA 57.148 29.630 0.00 0.00 0.00 3.41
322 323 9.851686 ACTCTTATAATAATTTCTGCATGGACA 57.148 29.630 0.00 0.00 0.00 4.02
324 325 9.625747 TCTTATAATAATTTCTGCATGGACACA 57.374 29.630 0.00 0.00 0.00 3.72
328 329 6.778834 ATAATTTCTGCATGGACACAATGA 57.221 33.333 0.00 0.00 0.00 2.57
329 330 5.471556 AATTTCTGCATGGACACAATGAA 57.528 34.783 0.00 0.00 0.00 2.57
330 331 3.921119 TTCTGCATGGACACAATGAAC 57.079 42.857 0.00 0.00 0.00 3.18
331 332 3.144657 TCTGCATGGACACAATGAACT 57.855 42.857 0.00 0.00 0.00 3.01
332 333 3.076621 TCTGCATGGACACAATGAACTC 58.923 45.455 0.00 0.00 0.00 3.01
333 334 1.805943 TGCATGGACACAATGAACTCG 59.194 47.619 0.00 0.00 0.00 4.18
334 335 1.466360 GCATGGACACAATGAACTCGC 60.466 52.381 0.00 0.00 0.00 5.03
335 336 1.078709 ATGGACACAATGAACTCGCG 58.921 50.000 0.00 0.00 0.00 5.87
336 337 0.948623 TGGACACAATGAACTCGCGG 60.949 55.000 6.13 0.00 0.00 6.46
337 338 0.669318 GGACACAATGAACTCGCGGA 60.669 55.000 6.13 0.00 0.00 5.54
338 339 1.144969 GACACAATGAACTCGCGGAA 58.855 50.000 6.13 0.00 0.00 4.30
339 340 1.529438 GACACAATGAACTCGCGGAAA 59.471 47.619 6.13 0.00 0.00 3.13
340 341 1.944024 ACACAATGAACTCGCGGAAAA 59.056 42.857 6.13 0.00 0.00 2.29
341 342 2.356382 ACACAATGAACTCGCGGAAAAA 59.644 40.909 6.13 0.00 0.00 1.94
361 362 1.704641 AAAACAGCCAAGAAGGACCC 58.295 50.000 0.00 0.00 41.22 4.46
362 363 0.178961 AAACAGCCAAGAAGGACCCC 60.179 55.000 0.00 0.00 41.22 4.95
363 364 2.081585 AACAGCCAAGAAGGACCCCC 62.082 60.000 0.00 0.00 41.22 5.40
364 365 2.121506 AGCCAAGAAGGACCCCCA 60.122 61.111 0.00 0.00 41.22 4.96
365 366 1.544917 AGCCAAGAAGGACCCCCAT 60.545 57.895 0.00 0.00 41.22 4.00
366 367 1.380380 GCCAAGAAGGACCCCCATG 60.380 63.158 0.00 0.00 41.22 3.66
367 368 1.863155 GCCAAGAAGGACCCCCATGA 61.863 60.000 0.00 0.00 41.22 3.07
368 369 0.929244 CCAAGAAGGACCCCCATGAT 59.071 55.000 0.00 0.00 41.22 2.45
369 370 1.133668 CCAAGAAGGACCCCCATGATC 60.134 57.143 0.00 0.00 41.22 2.92
370 371 1.133668 CAAGAAGGACCCCCATGATCC 60.134 57.143 0.00 0.00 33.88 3.36
371 372 0.348370 AGAAGGACCCCCATGATCCT 59.652 55.000 0.00 0.00 45.08 3.24
372 373 0.767998 GAAGGACCCCCATGATCCTC 59.232 60.000 0.00 0.00 42.23 3.71
373 374 0.046242 AAGGACCCCCATGATCCTCA 59.954 55.000 0.00 0.00 42.23 3.86
374 375 0.273161 AGGACCCCCATGATCCTCAT 59.727 55.000 0.00 0.00 38.55 2.90
386 387 5.908562 ATGATCCTCATGGTTTCTCTGAT 57.091 39.130 0.00 0.00 35.43 2.90
387 388 5.287674 TGATCCTCATGGTTTCTCTGATC 57.712 43.478 0.00 0.00 34.23 2.92
388 389 4.102210 TGATCCTCATGGTTTCTCTGATCC 59.898 45.833 0.00 0.00 34.23 3.36
389 390 3.729108 TCCTCATGGTTTCTCTGATCCT 58.271 45.455 0.00 0.00 34.23 3.24
390 391 3.708631 TCCTCATGGTTTCTCTGATCCTC 59.291 47.826 0.00 0.00 34.23 3.71
391 392 3.181456 CCTCATGGTTTCTCTGATCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
392 393 3.710677 CTCATGGTTTCTCTGATCCTCCT 59.289 47.826 0.00 0.00 0.00 3.69
393 394 3.453717 TCATGGTTTCTCTGATCCTCCTG 59.546 47.826 0.00 0.00 0.00 3.86
469 470 1.478654 GGAAGAGGCCTGTTTGGTTGA 60.479 52.381 17.52 0.00 38.35 3.18
481 482 5.042463 TGTTTGGTTGACTGGATTCACTA 57.958 39.130 0.00 0.00 0.00 2.74
825 851 2.801631 CGGATCTGGTGCTCCCCTC 61.802 68.421 1.59 0.00 0.00 4.30
842 868 2.672651 CGCTGTTGGCCACCATCA 60.673 61.111 3.88 1.56 37.74 3.07
988 1019 2.159156 CCCACTGAATGAACCGTCGATA 60.159 50.000 0.00 0.00 0.00 2.92
1087 1126 1.901833 TGTTCATGCACCAGAGAGCTA 59.098 47.619 0.00 0.00 0.00 3.32
1134 1173 5.554437 TCCGCTATGGTCCATTGTTTATA 57.446 39.130 10.33 0.00 39.52 0.98
1135 1174 6.121776 TCCGCTATGGTCCATTGTTTATAT 57.878 37.500 10.33 0.00 39.52 0.86
1179 1219 8.993121 CAAAATCTGAACTACATCTACAACTGT 58.007 33.333 0.00 0.00 0.00 3.55
1324 1367 3.088532 GCCATGTTCCTCCATGTTGTTA 58.911 45.455 0.00 0.00 40.50 2.41
1338 1381 4.901197 TGTTGTTAGCCATAACCAGAGA 57.099 40.909 0.00 0.00 40.57 3.10
1339 1382 5.435686 TGTTGTTAGCCATAACCAGAGAT 57.564 39.130 0.00 0.00 40.57 2.75
1340 1383 5.815581 TGTTGTTAGCCATAACCAGAGATT 58.184 37.500 0.00 0.00 40.57 2.40
1341 1384 5.880332 TGTTGTTAGCCATAACCAGAGATTC 59.120 40.000 0.00 0.00 40.57 2.52
1342 1385 5.692115 TGTTAGCCATAACCAGAGATTCA 57.308 39.130 0.00 0.00 40.57 2.57
1343 1386 5.674525 TGTTAGCCATAACCAGAGATTCAG 58.325 41.667 0.00 0.00 40.57 3.02
1344 1387 3.853355 AGCCATAACCAGAGATTCAGG 57.147 47.619 0.00 0.00 0.00 3.86
1345 1388 3.387962 AGCCATAACCAGAGATTCAGGA 58.612 45.455 0.00 0.00 0.00 3.86
1357 1400 4.347583 AGAGATTCAGGATTCAGGGTCATC 59.652 45.833 0.00 0.00 0.00 2.92
1366 1409 1.135960 TCAGGGTCATCCACAACACA 58.864 50.000 0.00 0.00 38.24 3.72
1520 1564 3.616956 TCCATACTTCAAGGTGAGCAG 57.383 47.619 0.00 0.00 0.00 4.24
1531 1575 6.048732 TCAAGGTGAGCAGTGACAATATAA 57.951 37.500 0.00 0.00 0.00 0.98
1555 1599 7.408756 AACTTTTCATGGCTTGATATGCTTA 57.591 32.000 3.72 0.00 33.34 3.09
1752 1819 3.054434 AGTTCATATGTGTTGGCTGGCTA 60.054 43.478 1.90 0.00 0.00 3.93
1855 1922 0.543749 ACCTTGGAGATGCTGGCTAC 59.456 55.000 0.00 0.00 0.00 3.58
1897 1987 3.157881 ACCATCTCAACGAGTTCTCTGA 58.842 45.455 0.00 0.00 0.00 3.27
1937 2027 3.754965 TGCACAGGAGCTGTTTAATCTT 58.245 40.909 0.00 0.00 42.59 2.40
1941 2031 5.643777 GCACAGGAGCTGTTTAATCTTAGAA 59.356 40.000 0.00 0.00 42.59 2.10
1945 2035 7.939588 ACAGGAGCTGTTTAATCTTAGAAACTT 59.060 33.333 0.00 0.00 42.59 2.66
2241 2367 6.173427 AGAAGAAGAAGAAGAAGCAGAAGT 57.827 37.500 0.00 0.00 0.00 3.01
2417 2552 8.924303 ACTATCTGGCACTACATGTTTAGATTA 58.076 33.333 2.30 0.00 31.37 1.75
2533 2668 0.383949 CAACCAAACACCGGGTCAAG 59.616 55.000 6.32 0.00 36.05 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.343539 ACCATATTTTTATAGAAGGCAGAAGAC 57.656 33.333 0.00 0.00 0.00 3.01
10 11 9.231297 GCATACCATATTTTTATAGAAGGCAGA 57.769 33.333 0.00 0.00 0.00 4.26
11 12 8.462016 GGCATACCATATTTTTATAGAAGGCAG 58.538 37.037 0.00 0.00 35.26 4.85
12 13 7.120579 CGGCATACCATATTTTTATAGAAGGCA 59.879 37.037 0.00 0.00 34.57 4.75
14 15 8.450964 CACGGCATACCATATTTTTATAGAAGG 58.549 37.037 0.00 0.00 34.57 3.46
15 16 8.450964 CCACGGCATACCATATTTTTATAGAAG 58.549 37.037 0.00 0.00 34.57 2.85
16 17 7.094549 GCCACGGCATACCATATTTTTATAGAA 60.095 37.037 2.36 0.00 41.49 2.10
17 18 6.373216 GCCACGGCATACCATATTTTTATAGA 59.627 38.462 2.36 0.00 41.49 1.98
18 19 6.551736 GCCACGGCATACCATATTTTTATAG 58.448 40.000 2.36 0.00 41.49 1.31
19 20 5.122554 CGCCACGGCATACCATATTTTTATA 59.877 40.000 9.11 0.00 42.06 0.98
20 21 4.083003 CGCCACGGCATACCATATTTTTAT 60.083 41.667 9.11 0.00 42.06 1.40
21 22 3.251245 CGCCACGGCATACCATATTTTTA 59.749 43.478 9.11 0.00 42.06 1.52
22 23 2.034053 CGCCACGGCATACCATATTTTT 59.966 45.455 9.11 0.00 42.06 1.94
23 24 1.606668 CGCCACGGCATACCATATTTT 59.393 47.619 9.11 0.00 42.06 1.82
24 25 1.234821 CGCCACGGCATACCATATTT 58.765 50.000 9.11 0.00 42.06 1.40
25 26 0.107831 ACGCCACGGCATACCATATT 59.892 50.000 9.11 0.00 42.06 1.28
26 27 0.970640 TACGCCACGGCATACCATAT 59.029 50.000 9.11 0.00 42.06 1.78
27 28 0.970640 ATACGCCACGGCATACCATA 59.029 50.000 9.11 0.00 42.06 2.74
28 29 0.107831 AATACGCCACGGCATACCAT 59.892 50.000 9.11 0.00 42.06 3.55
29 30 0.107606 AAATACGCCACGGCATACCA 60.108 50.000 9.11 0.00 42.06 3.25
30 31 1.003223 GAAAATACGCCACGGCATACC 60.003 52.381 9.11 0.00 42.06 2.73
31 32 1.332552 CGAAAATACGCCACGGCATAC 60.333 52.381 9.11 0.00 42.06 2.39
32 33 0.931702 CGAAAATACGCCACGGCATA 59.068 50.000 9.11 0.00 42.06 3.14
33 34 0.741574 TCGAAAATACGCCACGGCAT 60.742 50.000 9.11 0.00 42.06 4.40
34 35 0.949588 TTCGAAAATACGCCACGGCA 60.950 50.000 9.11 0.00 42.06 5.69
35 36 0.166379 TTTCGAAAATACGCCACGGC 59.834 50.000 8.44 0.00 37.85 5.68
36 37 2.598000 TTTTCGAAAATACGCCACGG 57.402 45.000 19.08 0.00 0.00 4.94
55 56 8.106247 TCTTCCTTGTATACATTTCGCTTTTT 57.894 30.769 6.36 0.00 0.00 1.94
56 57 7.681939 TCTTCCTTGTATACATTTCGCTTTT 57.318 32.000 6.36 0.00 0.00 2.27
57 58 7.626452 GCTTCTTCCTTGTATACATTTCGCTTT 60.626 37.037 6.36 0.00 0.00 3.51
58 59 6.183360 GCTTCTTCCTTGTATACATTTCGCTT 60.183 38.462 6.36 0.00 0.00 4.68
59 60 5.294552 GCTTCTTCCTTGTATACATTTCGCT 59.705 40.000 6.36 0.00 0.00 4.93
60 61 5.064707 TGCTTCTTCCTTGTATACATTTCGC 59.935 40.000 6.36 3.08 0.00 4.70
61 62 6.092122 TGTGCTTCTTCCTTGTATACATTTCG 59.908 38.462 6.36 0.00 0.00 3.46
62 63 7.377766 TGTGCTTCTTCCTTGTATACATTTC 57.622 36.000 6.36 0.00 0.00 2.17
63 64 7.759489 TTGTGCTTCTTCCTTGTATACATTT 57.241 32.000 6.36 0.00 0.00 2.32
64 65 7.944729 ATTGTGCTTCTTCCTTGTATACATT 57.055 32.000 6.36 0.00 0.00 2.71
65 66 9.060347 CATATTGTGCTTCTTCCTTGTATACAT 57.940 33.333 6.36 0.00 0.00 2.29
66 67 8.264347 TCATATTGTGCTTCTTCCTTGTATACA 58.736 33.333 0.08 0.08 0.00 2.29
67 68 8.662781 TCATATTGTGCTTCTTCCTTGTATAC 57.337 34.615 0.00 0.00 0.00 1.47
69 70 9.277783 GTATCATATTGTGCTTCTTCCTTGTAT 57.722 33.333 0.00 0.00 0.00 2.29
70 71 8.486210 AGTATCATATTGTGCTTCTTCCTTGTA 58.514 33.333 0.00 0.00 0.00 2.41
71 72 7.341805 AGTATCATATTGTGCTTCTTCCTTGT 58.658 34.615 0.00 0.00 0.00 3.16
72 73 7.041508 GGAGTATCATATTGTGCTTCTTCCTTG 60.042 40.741 0.00 0.00 36.25 3.61
73 74 6.995091 GGAGTATCATATTGTGCTTCTTCCTT 59.005 38.462 0.00 0.00 36.25 3.36
74 75 6.465035 GGGAGTATCATATTGTGCTTCTTCCT 60.465 42.308 0.00 0.00 36.25 3.36
75 76 5.703130 GGGAGTATCATATTGTGCTTCTTCC 59.297 44.000 0.00 0.00 36.25 3.46
76 77 6.529220 AGGGAGTATCATATTGTGCTTCTTC 58.471 40.000 0.00 0.00 36.25 2.87
77 78 6.465035 GGAGGGAGTATCATATTGTGCTTCTT 60.465 42.308 0.00 0.00 36.25 2.52
78 79 5.012561 GGAGGGAGTATCATATTGTGCTTCT 59.987 44.000 0.00 0.00 36.25 2.85
79 80 5.241662 GGAGGGAGTATCATATTGTGCTTC 58.758 45.833 0.00 0.00 36.25 3.86
80 81 4.262635 CGGAGGGAGTATCATATTGTGCTT 60.263 45.833 0.00 0.00 36.25 3.91
81 82 3.259374 CGGAGGGAGTATCATATTGTGCT 59.741 47.826 0.00 0.00 36.25 4.40
82 83 3.006967 ACGGAGGGAGTATCATATTGTGC 59.993 47.826 0.00 0.00 36.25 4.57
83 84 4.873746 ACGGAGGGAGTATCATATTGTG 57.126 45.455 0.00 0.00 36.25 3.33
84 85 4.283722 GGAACGGAGGGAGTATCATATTGT 59.716 45.833 0.00 0.00 36.25 2.71
85 86 4.528596 AGGAACGGAGGGAGTATCATATTG 59.471 45.833 0.00 0.00 36.25 1.90
86 87 4.753186 AGGAACGGAGGGAGTATCATATT 58.247 43.478 0.00 0.00 36.25 1.28
87 88 4.405756 AGGAACGGAGGGAGTATCATAT 57.594 45.455 0.00 0.00 36.25 1.78
88 89 3.897657 AGGAACGGAGGGAGTATCATA 57.102 47.619 0.00 0.00 36.25 2.15
89 90 2.777459 AGGAACGGAGGGAGTATCAT 57.223 50.000 0.00 0.00 36.25 2.45
90 91 3.675348 TTAGGAACGGAGGGAGTATCA 57.325 47.619 0.00 0.00 36.25 2.15
91 92 6.854091 ATATTTAGGAACGGAGGGAGTATC 57.146 41.667 0.00 0.00 0.00 2.24
92 93 7.072076 ACAAATATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
93 94 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
94 95 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
95 96 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
96 97 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
97 98 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
98 99 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
99 100 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
100 101 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
101 102 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
126 127 9.916397 CCGTATGTAGTCATTTGTTAAAATCTC 57.084 33.333 0.00 0.00 33.59 2.75
127 128 9.661563 TCCGTATGTAGTCATTTGTTAAAATCT 57.338 29.630 0.00 0.00 33.59 2.40
128 129 9.916397 CTCCGTATGTAGTCATTTGTTAAAATC 57.084 33.333 0.00 0.00 33.59 2.17
129 130 8.395633 GCTCCGTATGTAGTCATTTGTTAAAAT 58.604 33.333 0.00 0.00 36.39 1.82
130 131 7.388224 TGCTCCGTATGTAGTCATTTGTTAAAA 59.612 33.333 0.00 0.00 35.70 1.52
131 132 6.874664 TGCTCCGTATGTAGTCATTTGTTAAA 59.125 34.615 0.00 0.00 35.70 1.52
132 133 6.399743 TGCTCCGTATGTAGTCATTTGTTAA 58.600 36.000 0.00 0.00 35.70 2.01
133 134 5.968254 TGCTCCGTATGTAGTCATTTGTTA 58.032 37.500 0.00 0.00 35.70 2.41
134 135 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
135 136 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
136 137 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
137 138 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
138 139 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
139 140 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
140 141 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
141 142 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
142 143 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
143 144 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
144 145 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
145 146 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
146 147 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
147 148 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
148 149 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
149 150 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
150 151 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
151 152 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
152 153 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
180 181 9.990360 TCACATACGGATGTATTTACACATATT 57.010 29.630 14.23 0.00 44.82 1.28
183 184 9.639601 CTATCACATACGGATGTATTTACACAT 57.360 33.333 14.23 0.00 44.82 3.21
184 185 8.635328 ACTATCACATACGGATGTATTTACACA 58.365 33.333 14.23 0.00 44.82 3.72
185 186 9.125906 GACTATCACATACGGATGTATTTACAC 57.874 37.037 14.23 0.00 44.82 2.90
186 187 9.074576 AGACTATCACATACGGATGTATTTACA 57.925 33.333 14.23 0.00 44.82 2.41
192 193 9.292195 TCAAATAGACTATCACATACGGATGTA 57.708 33.333 14.23 2.61 44.82 2.29
194 195 9.476202 TTTCAAATAGACTATCACATACGGATG 57.524 33.333 5.94 5.94 39.16 3.51
226 227 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
227 228 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
228 229 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
229 230 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
230 231 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
231 232 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
232 233 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
233 234 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
234 235 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
235 236 5.010415 CGTACTCCCTCCGTTCCTAAATATT 59.990 44.000 0.00 0.00 0.00 1.28
236 237 4.522022 CGTACTCCCTCCGTTCCTAAATAT 59.478 45.833 0.00 0.00 0.00 1.28
237 238 3.885297 CGTACTCCCTCCGTTCCTAAATA 59.115 47.826 0.00 0.00 0.00 1.40
238 239 2.692041 CGTACTCCCTCCGTTCCTAAAT 59.308 50.000 0.00 0.00 0.00 1.40
239 240 2.094675 CGTACTCCCTCCGTTCCTAAA 58.905 52.381 0.00 0.00 0.00 1.85
240 241 1.004745 ACGTACTCCCTCCGTTCCTAA 59.995 52.381 0.00 0.00 0.00 2.69
241 242 0.620556 ACGTACTCCCTCCGTTCCTA 59.379 55.000 0.00 0.00 0.00 2.94
242 243 0.620556 TACGTACTCCCTCCGTTCCT 59.379 55.000 0.00 0.00 36.12 3.36
243 244 1.403323 CTTACGTACTCCCTCCGTTCC 59.597 57.143 0.00 0.00 36.12 3.62
244 245 2.359900 TCTTACGTACTCCCTCCGTTC 58.640 52.381 0.00 0.00 36.12 3.95
245 246 2.496899 TCTTACGTACTCCCTCCGTT 57.503 50.000 0.00 0.00 36.12 4.44
246 247 2.363683 CTTCTTACGTACTCCCTCCGT 58.636 52.381 0.00 0.00 38.53 4.69
247 248 1.065251 GCTTCTTACGTACTCCCTCCG 59.935 57.143 0.00 0.00 0.00 4.63
248 249 2.097825 TGCTTCTTACGTACTCCCTCC 58.902 52.381 0.00 0.00 0.00 4.30
249 250 3.057033 TGTTGCTTCTTACGTACTCCCTC 60.057 47.826 0.00 0.00 0.00 4.30
250 251 2.895404 TGTTGCTTCTTACGTACTCCCT 59.105 45.455 0.00 0.00 0.00 4.20
251 252 3.308438 TGTTGCTTCTTACGTACTCCC 57.692 47.619 0.00 0.00 0.00 4.30
252 253 5.662211 TTTTGTTGCTTCTTACGTACTCC 57.338 39.130 0.00 0.00 0.00 3.85
253 254 7.853929 TCAAATTTTGTTGCTTCTTACGTACTC 59.146 33.333 8.89 0.00 0.00 2.59
254 255 7.699566 TCAAATTTTGTTGCTTCTTACGTACT 58.300 30.769 8.89 0.00 0.00 2.73
255 256 7.901874 TCAAATTTTGTTGCTTCTTACGTAC 57.098 32.000 8.89 0.00 0.00 3.67
256 257 8.912787 TTTCAAATTTTGTTGCTTCTTACGTA 57.087 26.923 8.89 0.00 0.00 3.57
257 258 7.464045 GCTTTCAAATTTTGTTGCTTCTTACGT 60.464 33.333 8.89 0.00 0.00 3.57
258 259 6.840789 GCTTTCAAATTTTGTTGCTTCTTACG 59.159 34.615 8.89 0.00 0.00 3.18
259 260 7.683746 TGCTTTCAAATTTTGTTGCTTCTTAC 58.316 30.769 8.89 0.00 0.00 2.34
260 261 7.840342 TGCTTTCAAATTTTGTTGCTTCTTA 57.160 28.000 8.89 0.00 0.00 2.10
261 262 6.740411 TGCTTTCAAATTTTGTTGCTTCTT 57.260 29.167 8.89 0.00 0.00 2.52
262 263 6.930667 ATGCTTTCAAATTTTGTTGCTTCT 57.069 29.167 8.89 0.98 0.00 2.85
263 264 9.745323 GTATATGCTTTCAAATTTTGTTGCTTC 57.255 29.630 8.89 0.00 0.00 3.86
264 265 9.492973 AGTATATGCTTTCAAATTTTGTTGCTT 57.507 25.926 8.89 11.13 0.00 3.91
265 266 9.143631 GAGTATATGCTTTCAAATTTTGTTGCT 57.856 29.630 8.89 5.52 0.00 3.91
266 267 8.924691 TGAGTATATGCTTTCAAATTTTGTTGC 58.075 29.630 8.89 11.30 0.00 4.17
275 276 9.890629 AAGAGTGTATGAGTATATGCTTTCAAA 57.109 29.630 0.00 0.00 0.00 2.69
294 295 9.851686 TCCATGCAGAAATTATTATAAGAGTGT 57.148 29.630 0.00 0.00 0.00 3.55
296 297 9.851686 TGTCCATGCAGAAATTATTATAAGAGT 57.148 29.630 0.00 0.00 0.00 3.24
298 299 9.625747 TGTGTCCATGCAGAAATTATTATAAGA 57.374 29.630 0.00 0.00 0.00 2.10
302 303 8.916062 TCATTGTGTCCATGCAGAAATTATTAT 58.084 29.630 0.00 0.00 0.00 1.28
303 304 8.291191 TCATTGTGTCCATGCAGAAATTATTA 57.709 30.769 0.00 0.00 0.00 0.98
304 305 7.172868 TCATTGTGTCCATGCAGAAATTATT 57.827 32.000 0.00 0.00 0.00 1.40
305 306 6.778834 TCATTGTGTCCATGCAGAAATTAT 57.221 33.333 0.00 0.00 0.00 1.28
306 307 6.209192 AGTTCATTGTGTCCATGCAGAAATTA 59.791 34.615 0.00 0.00 0.00 1.40
307 308 5.011329 AGTTCATTGTGTCCATGCAGAAATT 59.989 36.000 0.00 0.00 0.00 1.82
308 309 4.525487 AGTTCATTGTGTCCATGCAGAAAT 59.475 37.500 0.00 0.00 0.00 2.17
309 310 3.890756 AGTTCATTGTGTCCATGCAGAAA 59.109 39.130 0.00 0.00 0.00 2.52
310 311 3.489355 AGTTCATTGTGTCCATGCAGAA 58.511 40.909 0.00 0.00 0.00 3.02
311 312 3.076621 GAGTTCATTGTGTCCATGCAGA 58.923 45.455 0.00 0.00 0.00 4.26
312 313 2.159612 CGAGTTCATTGTGTCCATGCAG 60.160 50.000 0.00 0.00 0.00 4.41
313 314 1.805943 CGAGTTCATTGTGTCCATGCA 59.194 47.619 0.00 0.00 0.00 3.96
314 315 1.466360 GCGAGTTCATTGTGTCCATGC 60.466 52.381 0.00 0.00 0.00 4.06
315 316 1.201954 CGCGAGTTCATTGTGTCCATG 60.202 52.381 0.00 0.00 0.00 3.66
316 317 1.078709 CGCGAGTTCATTGTGTCCAT 58.921 50.000 0.00 0.00 0.00 3.41
317 318 0.948623 CCGCGAGTTCATTGTGTCCA 60.949 55.000 8.23 0.00 0.00 4.02
318 319 0.669318 TCCGCGAGTTCATTGTGTCC 60.669 55.000 8.23 0.00 0.00 4.02
319 320 1.144969 TTCCGCGAGTTCATTGTGTC 58.855 50.000 8.23 0.00 0.00 3.67
320 321 1.588674 TTTCCGCGAGTTCATTGTGT 58.411 45.000 8.23 0.00 0.00 3.72
321 322 2.679355 TTTTCCGCGAGTTCATTGTG 57.321 45.000 8.23 0.00 0.00 3.33
341 342 2.039418 GGGTCCTTCTTGGCTGTTTTT 58.961 47.619 0.00 0.00 35.26 1.94
342 343 1.704641 GGGTCCTTCTTGGCTGTTTT 58.295 50.000 0.00 0.00 35.26 2.43
343 344 0.178961 GGGGTCCTTCTTGGCTGTTT 60.179 55.000 0.00 0.00 35.26 2.83
344 345 1.460699 GGGGTCCTTCTTGGCTGTT 59.539 57.895 0.00 0.00 35.26 3.16
345 346 2.539081 GGGGGTCCTTCTTGGCTGT 61.539 63.158 0.00 0.00 35.26 4.40
346 347 1.867595 ATGGGGGTCCTTCTTGGCTG 61.868 60.000 0.00 0.00 35.26 4.85
347 348 1.544917 ATGGGGGTCCTTCTTGGCT 60.545 57.895 0.00 0.00 35.26 4.75
348 349 1.380380 CATGGGGGTCCTTCTTGGC 60.380 63.158 0.00 0.00 35.26 4.52
349 350 0.929244 ATCATGGGGGTCCTTCTTGG 59.071 55.000 0.00 0.00 37.10 3.61
350 351 1.133668 GGATCATGGGGGTCCTTCTTG 60.134 57.143 0.00 0.00 0.00 3.02
351 352 1.226311 GGATCATGGGGGTCCTTCTT 58.774 55.000 0.00 0.00 0.00 2.52
352 353 0.348370 AGGATCATGGGGGTCCTTCT 59.652 55.000 0.00 0.00 39.28 2.85
353 354 0.767998 GAGGATCATGGGGGTCCTTC 59.232 60.000 9.99 3.08 42.27 3.46
354 355 0.046242 TGAGGATCATGGGGGTCCTT 59.954 55.000 9.99 0.00 42.56 3.36
355 356 1.718611 TGAGGATCATGGGGGTCCT 59.281 57.895 8.85 8.85 42.56 3.85
356 357 4.418820 TGAGGATCATGGGGGTCC 57.581 61.111 0.00 0.00 42.56 4.46
365 366 7.873692 GAGGATCAGAGAAACCATGAGGATCA 61.874 46.154 0.00 0.00 43.50 2.92
366 367 4.347583 AGGATCAGAGAAACCATGAGGATC 59.652 45.833 0.00 0.00 38.69 3.36
367 368 4.305524 AGGATCAGAGAAACCATGAGGAT 58.694 43.478 0.00 0.00 38.69 3.24
368 369 3.708631 GAGGATCAGAGAAACCATGAGGA 59.291 47.826 0.00 0.00 34.73 3.71
369 370 3.181456 GGAGGATCAGAGAAACCATGAGG 60.181 52.174 0.00 0.00 37.76 3.86
370 371 3.710677 AGGAGGATCAGAGAAACCATGAG 59.289 47.826 0.00 0.00 36.25 2.90
371 372 3.453717 CAGGAGGATCAGAGAAACCATGA 59.546 47.826 0.00 0.00 36.25 3.07
372 373 3.199508 ACAGGAGGATCAGAGAAACCATG 59.800 47.826 0.00 0.00 36.25 3.66
373 374 3.454082 GACAGGAGGATCAGAGAAACCAT 59.546 47.826 0.00 0.00 36.25 3.55
374 375 2.834549 GACAGGAGGATCAGAGAAACCA 59.165 50.000 0.00 0.00 36.25 3.67
375 376 2.834549 TGACAGGAGGATCAGAGAAACC 59.165 50.000 0.00 0.00 36.25 3.27
376 377 4.405358 AGATGACAGGAGGATCAGAGAAAC 59.595 45.833 0.00 0.00 36.25 2.78
377 378 4.618635 AGATGACAGGAGGATCAGAGAAA 58.381 43.478 0.00 0.00 36.25 2.52
378 379 4.262891 AGATGACAGGAGGATCAGAGAA 57.737 45.455 0.00 0.00 36.25 2.87
379 380 3.969466 AGATGACAGGAGGATCAGAGA 57.031 47.619 0.00 0.00 36.25 3.10
380 381 4.081406 CCTAGATGACAGGAGGATCAGAG 58.919 52.174 0.00 0.00 36.25 3.35
381 382 3.181424 CCCTAGATGACAGGAGGATCAGA 60.181 52.174 0.00 0.00 36.25 3.27
382 383 3.164268 CCCTAGATGACAGGAGGATCAG 58.836 54.545 0.00 0.00 36.25 2.90
383 384 2.757950 GCCCTAGATGACAGGAGGATCA 60.758 54.545 0.00 0.00 36.25 2.92
384 385 1.899142 GCCCTAGATGACAGGAGGATC 59.101 57.143 0.00 0.00 34.91 3.36
385 386 1.825242 CGCCCTAGATGACAGGAGGAT 60.825 57.143 0.00 0.00 34.91 3.24
386 387 0.468214 CGCCCTAGATGACAGGAGGA 60.468 60.000 0.00 0.00 34.91 3.71
387 388 0.757188 ACGCCCTAGATGACAGGAGG 60.757 60.000 0.00 0.00 34.91 4.30
388 389 0.387202 CACGCCCTAGATGACAGGAG 59.613 60.000 0.00 0.00 34.91 3.69
389 390 0.324368 ACACGCCCTAGATGACAGGA 60.324 55.000 0.00 0.00 34.91 3.86
390 391 0.537188 AACACGCCCTAGATGACAGG 59.463 55.000 0.00 0.00 0.00 4.00
391 392 2.002586 CAAACACGCCCTAGATGACAG 58.997 52.381 0.00 0.00 0.00 3.51
392 393 1.338674 CCAAACACGCCCTAGATGACA 60.339 52.381 0.00 0.00 0.00 3.58
393 394 1.338769 ACCAAACACGCCCTAGATGAC 60.339 52.381 0.00 0.00 0.00 3.06
469 470 2.092212 CAGGCCCAATAGTGAATCCAGT 60.092 50.000 0.00 0.00 0.00 4.00
481 482 2.123597 ATGCGATGCAGGCCCAAT 60.124 55.556 0.00 0.00 43.65 3.16
842 868 0.247736 GGCACAGACAAGGTCGATCT 59.752 55.000 0.00 0.00 37.67 2.75
844 870 2.057830 TGGCACAGACAAGGTCGAT 58.942 52.632 0.00 0.00 37.67 3.59
988 1019 4.380531 CATGCGTCCATAACCTAGTCAAT 58.619 43.478 0.00 0.00 0.00 2.57
1047 1086 0.034186 TGACCCATGCCTGAATCACC 60.034 55.000 0.00 0.00 0.00 4.02
1087 1126 1.215647 GTCTCCCAGCACGACGAAT 59.784 57.895 0.00 0.00 0.00 3.34
1134 1173 2.780414 TGGATCATCTCCTGTTCCCAT 58.220 47.619 0.00 0.00 45.21 4.00
1135 1174 2.268796 TGGATCATCTCCTGTTCCCA 57.731 50.000 0.00 0.00 45.21 4.37
1179 1219 1.132453 CACAGAGCCTCGACGTCATTA 59.868 52.381 17.16 0.00 0.00 1.90
1324 1367 3.387962 TCCTGAATCTCTGGTTATGGCT 58.612 45.455 0.23 0.00 36.89 4.75
1338 1381 3.117738 GTGGATGACCCTGAATCCTGAAT 60.118 47.826 3.54 0.00 42.51 2.57
1339 1382 2.239654 GTGGATGACCCTGAATCCTGAA 59.760 50.000 3.54 0.00 42.51 3.02
1340 1383 1.839994 GTGGATGACCCTGAATCCTGA 59.160 52.381 3.54 0.00 42.51 3.86
1341 1384 1.561076 TGTGGATGACCCTGAATCCTG 59.439 52.381 3.54 0.00 42.51 3.86
1342 1385 1.971149 TGTGGATGACCCTGAATCCT 58.029 50.000 3.54 0.00 42.51 3.24
1343 1386 2.290896 TGTTGTGGATGACCCTGAATCC 60.291 50.000 0.00 0.00 42.40 3.01
1344 1387 2.749621 GTGTTGTGGATGACCCTGAATC 59.250 50.000 0.00 0.00 35.38 2.52
1345 1388 2.108075 TGTGTTGTGGATGACCCTGAAT 59.892 45.455 0.00 0.00 35.38 2.57
1357 1400 3.678289 TGATCTCCTGAATGTGTTGTGG 58.322 45.455 0.00 0.00 0.00 4.17
1366 1409 4.042884 TGGTCTCCATTGATCTCCTGAAT 58.957 43.478 0.00 0.00 0.00 2.57
1520 1564 8.863049 CAAGCCATGAAAAGTTTATATTGTCAC 58.137 33.333 0.00 0.00 0.00 3.67
1531 1575 5.927281 AGCATATCAAGCCATGAAAAGTT 57.073 34.783 0.00 0.00 42.54 2.66
1555 1599 7.228507 TGTGTTAGTGCTCAACTTGAACAATAT 59.771 33.333 3.81 0.00 38.48 1.28
1752 1819 3.790437 CATGCGCTGACCCCTCCT 61.790 66.667 9.73 0.00 0.00 3.69
1855 1922 4.602259 ATACCCGGCCGACATGCG 62.602 66.667 30.73 8.54 40.47 4.73
1937 2027 7.232941 ACAGTTACTCTAAGGCTGAAGTTTCTA 59.767 37.037 0.00 0.00 0.00 2.10
1941 2031 5.810080 ACAGTTACTCTAAGGCTGAAGTT 57.190 39.130 0.00 0.00 0.00 2.66
1945 2035 5.077564 TCTCAACAGTTACTCTAAGGCTGA 58.922 41.667 0.00 0.00 0.00 4.26
2075 2165 1.409101 GCTCGACCTCTTCCTCCTAGT 60.409 57.143 0.00 0.00 0.00 2.57
2076 2166 1.314730 GCTCGACCTCTTCCTCCTAG 58.685 60.000 0.00 0.00 0.00 3.02
2077 2167 0.106619 GGCTCGACCTCTTCCTCCTA 60.107 60.000 0.00 0.00 34.51 2.94
2241 2367 5.955355 CCTCTTCCTCTTCCTCTTCTTTCTA 59.045 44.000 0.00 0.00 0.00 2.10
2379 2514 9.542462 GTAGTGCCAGATAGTTAAACATATGAA 57.458 33.333 10.38 0.00 0.00 2.57
2384 2519 7.338710 ACATGTAGTGCCAGATAGTTAAACAT 58.661 34.615 0.00 0.00 0.00 2.71
2533 2668 4.095483 CCTAGTTGCATGAGACAACCATTC 59.905 45.833 10.06 0.00 46.85 2.67


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

AutoCloner maintained by Alex Coulton.