Multiple sequence alignment - TraesCS6D01G307400

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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 TraesCS6D01G307400 chr6D 100.000 2339 0 0 1 2339 418489948 418487610 0.000000e+00 4320.0
1 TraesCS6D01G307400 chr6D 93.744 1039 41 6 348 1372 418524862 418523834 0.000000e+00 1537.0
2 TraesCS6D01G307400 chr6D 88.614 404 33 4 973 1372 418530979 418530585 1.630000e-131 479.0
3 TraesCS6D01G307400 chr6D 87.980 391 36 5 976 1365 418313162 418312782 3.540000e-123 451.0
4 TraesCS6D01G307400 chr6D 78.467 274 41 12 627 896 418531413 418531154 1.860000e-36 163.0
5 TraesCS6D01G307400 chr6D 83.333 126 18 3 227 350 427577165 427577041 1.900000e-21 113.0
6 TraesCS6D01G307400 chr2D 94.342 972 43 9 1373 2338 56309768 56308803 0.000000e+00 1480.0
7 TraesCS6D01G307400 chr1D 93.973 979 48 7 1368 2339 124766411 124767385 0.000000e+00 1471.0
8 TraesCS6D01G307400 chr4D 97.532 770 19 0 1570 2339 365054029 365053260 0.000000e+00 1317.0
9 TraesCS6D01G307400 chr6A 90.171 997 52 12 386 1372 560826083 560825123 0.000000e+00 1256.0
10 TraesCS6D01G307400 chr6A 88.776 392 35 1 976 1367 560816806 560816424 2.720000e-129 472.0
11 TraesCS6D01G307400 chr6A 87.593 403 38 3 973 1372 560829435 560829042 7.620000e-125 457.0
12 TraesCS6D01G307400 chr6A 87.817 394 37 5 973 1365 560753657 560753274 3.540000e-123 451.0
13 TraesCS6D01G307400 chr6A 81.010 416 52 14 406 798 560830106 560829695 2.920000e-79 305.0
14 TraesCS6D01G307400 chr6A 83.740 123 18 2 231 352 14362818 14362939 5.280000e-22 115.0
15 TraesCS6D01G307400 chr3B 89.264 978 89 13 1367 2339 659510097 659509131 0.000000e+00 1210.0
16 TraesCS6D01G307400 chr3B 82.924 978 142 20 1370 2338 159576772 159575811 0.000000e+00 857.0
17 TraesCS6D01G307400 chr3B 79.003 381 45 11 4 354 642840613 642840238 6.500000e-56 228.0
18 TraesCS6D01G307400 chr4B 88.073 981 100 14 1373 2339 347607884 347608861 0.000000e+00 1147.0
19 TraesCS6D01G307400 chr4B 100.000 30 0 0 194 223 90168250 90168279 3.250000e-04 56.5
20 TraesCS6D01G307400 chr5A 86.448 974 115 13 1373 2337 69246077 69245112 0.000000e+00 1051.0
21 TraesCS6D01G307400 chr5A 83.065 124 18 3 236 356 169806445 169806568 2.460000e-20 110.0
22 TraesCS6D01G307400 chr7A 86.154 975 119 12 1374 2339 347109212 347108245 0.000000e+00 1038.0
23 TraesCS6D01G307400 chr7A 83.065 124 19 2 230 352 553237255 553237133 6.830000e-21 111.0
24 TraesCS6D01G307400 chr1B 88.250 800 93 1 1541 2339 439131076 439131875 0.000000e+00 955.0
25 TraesCS6D01G307400 chr1B 84.507 213 20 12 3 211 678253230 678253027 5.100000e-47 198.0
26 TraesCS6D01G307400 chr2B 83.350 979 134 21 1370 2339 426485997 426486955 0.000000e+00 878.0
27 TraesCS6D01G307400 chr2B 90.244 164 16 0 2 165 212569324 212569487 5.060000e-52 215.0
28 TraesCS6D01G307400 chr2B 89.759 166 17 0 2 167 20667556 20667391 1.820000e-51 213.0
29 TraesCS6D01G307400 chr6B 86.008 779 49 27 623 1372 630529942 630529195 0.000000e+00 780.0
30 TraesCS6D01G307400 chr6B 81.641 975 145 26 1374 2339 476837601 476836652 0.000000e+00 778.0
31 TraesCS6D01G307400 chr6B 87.069 464 35 3 920 1368 630514662 630514209 3.470000e-138 501.0
32 TraesCS6D01G307400 chr6B 87.179 390 41 3 976 1365 630465938 630465558 3.570000e-118 435.0
33 TraesCS6D01G307400 chr6B 87.121 396 32 5 976 1367 630505023 630504643 4.620000e-117 431.0
34 TraesCS6D01G307400 chr6B 79.146 609 72 29 404 961 630569444 630568840 1.020000e-98 370.0
35 TraesCS6D01G307400 chr6B 84.593 344 39 10 462 798 630532692 630532356 1.730000e-86 329.0
36 TraesCS6D01G307400 chr6B 86.129 310 22 12 623 923 630520126 630519829 4.850000e-82 315.0
37 TraesCS6D01G307400 chr6B 91.667 84 7 0 386 469 630520214 630520131 1.470000e-22 117.0
38 TraesCS6D01G307400 chr6B 83.871 124 17 3 236 356 653301497 653301374 5.280000e-22 115.0
39 TraesCS6D01G307400 chr1A 74.615 973 221 18 1373 2337 277091118 277092072 2.800000e-109 405.0
40 TraesCS6D01G307400 chr1A 74.283 976 223 20 1371 2337 277105858 277106814 1.010000e-103 387.0
41 TraesCS6D01G307400 chr1A 90.419 167 16 0 2 168 86653551 86653385 1.090000e-53 220.0
42 TraesCS6D01G307400 chr1A 83.898 118 17 2 231 346 377507572 377507689 6.830000e-21 111.0
43 TraesCS6D01G307400 chr3D 91.018 167 15 0 2 168 48818235 48818069 2.340000e-55 226.0
44 TraesCS6D01G307400 chr3D 83.200 250 23 7 2 232 427757718 427757967 6.550000e-51 211.0
45 TraesCS6D01G307400 chr4A 89.759 166 17 0 3 168 5429859 5429694 1.820000e-51 213.0
46 TraesCS6D01G307400 chr7D 90.184 163 11 4 2 164 531111925 531111768 8.470000e-50 207.0
47 TraesCS6D01G307400 chr5D 82.791 215 26 10 2 212 225833792 225833999 5.130000e-42 182.0
48 TraesCS6D01G307400 chr5D 85.586 111 15 1 236 346 56803901 56804010 5.280000e-22 115.0
49 TraesCS6D01G307400 chr7B 86.885 122 15 1 229 350 706274134 706274014 4.050000e-28 135.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G307400 chr6D 418487610 418489948 2338 True 4320.000000 4320 100.0000 1 2339 1 chr6D.!!$R2 2338
1 TraesCS6D01G307400 chr6D 418523834 418524862 1028 True 1537.000000 1537 93.7440 348 1372 1 chr6D.!!$R3 1024
2 TraesCS6D01G307400 chr6D 418530585 418531413 828 True 321.000000 479 83.5405 627 1372 2 chr6D.!!$R5 745
3 TraesCS6D01G307400 chr2D 56308803 56309768 965 True 1480.000000 1480 94.3420 1373 2338 1 chr2D.!!$R1 965
4 TraesCS6D01G307400 chr1D 124766411 124767385 974 False 1471.000000 1471 93.9730 1368 2339 1 chr1D.!!$F1 971
5 TraesCS6D01G307400 chr4D 365053260 365054029 769 True 1317.000000 1317 97.5320 1570 2339 1 chr4D.!!$R1 769
6 TraesCS6D01G307400 chr6A 560825123 560830106 4983 True 672.666667 1256 86.2580 386 1372 3 chr6A.!!$R3 986
7 TraesCS6D01G307400 chr3B 659509131 659510097 966 True 1210.000000 1210 89.2640 1367 2339 1 chr3B.!!$R3 972
8 TraesCS6D01G307400 chr3B 159575811 159576772 961 True 857.000000 857 82.9240 1370 2338 1 chr3B.!!$R1 968
9 TraesCS6D01G307400 chr4B 347607884 347608861 977 False 1147.000000 1147 88.0730 1373 2339 1 chr4B.!!$F2 966
10 TraesCS6D01G307400 chr5A 69245112 69246077 965 True 1051.000000 1051 86.4480 1373 2337 1 chr5A.!!$R1 964
11 TraesCS6D01G307400 chr7A 347108245 347109212 967 True 1038.000000 1038 86.1540 1374 2339 1 chr7A.!!$R1 965
12 TraesCS6D01G307400 chr1B 439131076 439131875 799 False 955.000000 955 88.2500 1541 2339 1 chr1B.!!$F1 798
13 TraesCS6D01G307400 chr2B 426485997 426486955 958 False 878.000000 878 83.3500 1370 2339 1 chr2B.!!$F2 969
14 TraesCS6D01G307400 chr6B 476836652 476837601 949 True 778.000000 778 81.6410 1374 2339 1 chr6B.!!$R1 965
15 TraesCS6D01G307400 chr6B 630529195 630532692 3497 True 554.500000 780 85.3005 462 1372 2 chr6B.!!$R8 910
16 TraesCS6D01G307400 chr6B 630568840 630569444 604 True 370.000000 370 79.1460 404 961 1 chr6B.!!$R5 557
17 TraesCS6D01G307400 chr1A 277091118 277092072 954 False 405.000000 405 74.6150 1373 2337 1 chr1A.!!$F1 964
18 TraesCS6D01G307400 chr1A 277105858 277106814 956 False 387.000000 387 74.2830 1371 2337 1 chr1A.!!$F2 966

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
145 146 0.107456 TACCTACGGAGCCGGACTAG 59.893 60.0 5.05 6.03 44.69 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 7394 1.799258 AAGGTTTTCTGCTGGCTGCG 61.799 55.0 11.85 6.85 46.63 5.18 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 3.060866 AGAAGCGAGCCGTCCTTT 58.939 55.556 0.00 0.00 0.00 3.11
18 19 1.374758 AGAAGCGAGCCGTCCTTTG 60.375 57.895 0.00 0.00 0.00 2.77
19 20 3.028366 GAAGCGAGCCGTCCTTTGC 62.028 63.158 0.00 0.00 0.00 3.68
23 24 3.793144 GAGCCGTCCTTTGCGCTG 61.793 66.667 9.73 0.00 0.00 5.18
24 25 4.314440 AGCCGTCCTTTGCGCTGA 62.314 61.111 9.73 0.00 0.00 4.26
25 26 3.353836 GCCGTCCTTTGCGCTGAA 61.354 61.111 9.73 2.43 0.00 3.02
26 27 2.863153 CCGTCCTTTGCGCTGAAG 59.137 61.111 9.73 12.82 0.00 3.02
27 28 2.174349 CGTCCTTTGCGCTGAAGC 59.826 61.111 9.73 0.74 37.78 3.86
28 29 2.606961 CGTCCTTTGCGCTGAAGCA 61.607 57.895 9.73 0.00 46.54 3.91
36 37 2.154854 TGCGCTGAAGCATATACCTC 57.845 50.000 9.73 0.00 42.92 3.85
37 38 1.688735 TGCGCTGAAGCATATACCTCT 59.311 47.619 9.73 0.00 42.92 3.69
38 39 2.064762 GCGCTGAAGCATATACCTCTG 58.935 52.381 0.00 0.00 42.21 3.35
39 40 2.546795 GCGCTGAAGCATATACCTCTGT 60.547 50.000 0.00 0.00 42.21 3.41
40 41 3.055591 CGCTGAAGCATATACCTCTGTG 58.944 50.000 2.79 0.00 42.21 3.66
41 42 3.397482 GCTGAAGCATATACCTCTGTGG 58.603 50.000 0.00 0.00 41.59 4.17
42 43 3.397482 CTGAAGCATATACCTCTGTGGC 58.603 50.000 0.00 0.00 40.22 5.01
43 44 3.041211 TGAAGCATATACCTCTGTGGCT 58.959 45.455 0.00 0.00 40.22 4.75
44 45 3.070159 TGAAGCATATACCTCTGTGGCTC 59.930 47.826 0.00 0.00 40.22 4.70
45 46 1.974236 AGCATATACCTCTGTGGCTCC 59.026 52.381 0.00 0.00 40.22 4.70
46 47 1.002544 GCATATACCTCTGTGGCTCCC 59.997 57.143 0.00 0.00 40.22 4.30
47 48 1.273606 CATATACCTCTGTGGCTCCCG 59.726 57.143 0.00 0.00 40.22 5.14
48 49 0.554305 TATACCTCTGTGGCTCCCGA 59.446 55.000 0.00 0.00 40.22 5.14
49 50 1.043673 ATACCTCTGTGGCTCCCGAC 61.044 60.000 0.00 0.00 40.22 4.79
50 51 2.435120 TACCTCTGTGGCTCCCGACA 62.435 60.000 0.00 0.00 40.22 4.35
51 52 2.575993 CTCTGTGGCTCCCGACAG 59.424 66.667 0.00 0.00 40.89 3.51
52 53 2.203640 TCTGTGGCTCCCGACAGT 60.204 61.111 0.00 0.00 40.48 3.55
53 54 2.219325 CTCTGTGGCTCCCGACAGTC 62.219 65.000 0.00 0.00 40.48 3.51
54 55 3.302347 CTGTGGCTCCCGACAGTCC 62.302 68.421 0.00 0.00 35.78 3.85
55 56 4.436998 GTGGCTCCCGACAGTCCG 62.437 72.222 0.00 0.00 0.00 4.79
62 63 2.102357 CCGACAGTCCGGTGATCG 59.898 66.667 0.00 7.25 44.23 3.69
75 76 4.241555 GATCGGGCTGCCGGACAT 62.242 66.667 28.21 15.60 35.74 3.06
76 77 4.552365 ATCGGGCTGCCGGACATG 62.552 66.667 28.21 7.14 35.74 3.21
79 80 4.864334 GGGCTGCCGGACATGAGG 62.864 72.222 13.40 0.51 0.00 3.86
80 81 3.785859 GGCTGCCGGACATGAGGA 61.786 66.667 5.05 0.00 0.00 3.71
81 82 2.268920 GCTGCCGGACATGAGGAA 59.731 61.111 5.05 0.00 0.00 3.36
82 83 2.109126 GCTGCCGGACATGAGGAAC 61.109 63.158 5.05 0.00 0.00 3.62
83 84 1.296392 CTGCCGGACATGAGGAACA 59.704 57.895 5.05 0.00 0.00 3.18
84 85 1.003839 TGCCGGACATGAGGAACAC 60.004 57.895 5.05 0.00 0.00 3.32
85 86 1.003839 GCCGGACATGAGGAACACA 60.004 57.895 5.05 0.00 0.00 3.72
86 87 0.605319 GCCGGACATGAGGAACACAA 60.605 55.000 5.05 0.00 29.57 3.33
87 88 1.890876 CCGGACATGAGGAACACAAA 58.109 50.000 0.00 0.00 29.57 2.83
88 89 1.806542 CCGGACATGAGGAACACAAAG 59.193 52.381 0.00 0.00 29.57 2.77
89 90 1.806542 CGGACATGAGGAACACAAAGG 59.193 52.381 0.00 0.00 29.57 3.11
90 91 2.162681 GGACATGAGGAACACAAAGGG 58.837 52.381 0.00 0.00 29.57 3.95
91 92 2.224769 GGACATGAGGAACACAAAGGGA 60.225 50.000 0.00 0.00 29.57 4.20
92 93 3.562176 GGACATGAGGAACACAAAGGGAT 60.562 47.826 0.00 0.00 29.57 3.85
93 94 3.690460 ACATGAGGAACACAAAGGGATC 58.310 45.455 0.00 0.00 29.57 3.36
94 95 2.879103 TGAGGAACACAAAGGGATCC 57.121 50.000 1.92 1.92 0.00 3.36
95 96 1.003118 TGAGGAACACAAAGGGATCCG 59.997 52.381 5.45 0.00 35.31 4.18
96 97 0.322546 AGGAACACAAAGGGATCCGC 60.323 55.000 5.45 0.00 35.31 5.54
97 98 1.644786 GGAACACAAAGGGATCCGCG 61.645 60.000 5.45 0.00 0.00 6.46
98 99 1.644786 GAACACAAAGGGATCCGCGG 61.645 60.000 22.12 22.12 0.00 6.46
99 100 2.824041 CACAAAGGGATCCGCGGG 60.824 66.667 27.83 8.96 0.00 6.13
100 101 4.796495 ACAAAGGGATCCGCGGGC 62.796 66.667 27.83 17.86 0.00 6.13
112 113 2.594592 GCGGGCGGCCATTTAGAT 60.595 61.111 29.19 0.00 34.80 1.98
113 114 2.193536 GCGGGCGGCCATTTAGATT 61.194 57.895 29.19 0.00 34.80 2.40
114 115 0.887387 GCGGGCGGCCATTTAGATTA 60.887 55.000 29.19 0.00 34.80 1.75
115 116 1.156736 CGGGCGGCCATTTAGATTAG 58.843 55.000 29.19 3.06 0.00 1.73
116 117 1.534729 GGGCGGCCATTTAGATTAGG 58.465 55.000 25.33 0.00 0.00 2.69
117 118 1.202891 GGGCGGCCATTTAGATTAGGT 60.203 52.381 25.33 0.00 0.00 3.08
118 119 2.039348 GGGCGGCCATTTAGATTAGGTA 59.961 50.000 25.33 0.00 0.00 3.08
119 120 3.308188 GGGCGGCCATTTAGATTAGGTAT 60.308 47.826 25.33 0.00 0.00 2.73
120 121 4.332828 GGCGGCCATTTAGATTAGGTATT 58.667 43.478 15.62 0.00 0.00 1.89
121 122 5.493809 GGCGGCCATTTAGATTAGGTATTA 58.506 41.667 15.62 0.00 0.00 0.98
122 123 5.585047 GGCGGCCATTTAGATTAGGTATTAG 59.415 44.000 15.62 0.00 0.00 1.73
123 124 6.171213 GCGGCCATTTAGATTAGGTATTAGT 58.829 40.000 2.24 0.00 0.00 2.24
124 125 6.653740 GCGGCCATTTAGATTAGGTATTAGTT 59.346 38.462 2.24 0.00 0.00 2.24
125 126 7.820872 GCGGCCATTTAGATTAGGTATTAGTTA 59.179 37.037 2.24 0.00 0.00 2.24
126 127 9.886132 CGGCCATTTAGATTAGGTATTAGTTAT 57.114 33.333 2.24 0.00 0.00 1.89
139 140 5.873732 GTATTAGTTATACCTACGGAGCCG 58.126 45.833 7.48 7.48 38.27 5.52
140 141 1.613836 AGTTATACCTACGGAGCCGG 58.386 55.000 14.07 0.00 44.69 6.13
141 142 1.143684 AGTTATACCTACGGAGCCGGA 59.856 52.381 5.05 3.33 44.69 5.14
142 143 1.268079 GTTATACCTACGGAGCCGGAC 59.732 57.143 5.05 0.00 44.69 4.79
143 144 0.767375 TATACCTACGGAGCCGGACT 59.233 55.000 5.05 0.50 44.69 3.85
144 145 0.767375 ATACCTACGGAGCCGGACTA 59.233 55.000 5.05 0.00 44.69 2.59
145 146 0.107456 TACCTACGGAGCCGGACTAG 59.893 60.000 5.05 6.03 44.69 2.57
146 147 2.553727 CCTACGGAGCCGGACTAGC 61.554 68.421 5.05 0.00 44.69 3.42
147 148 2.894565 CTACGGAGCCGGACTAGCG 61.895 68.421 5.05 0.00 44.69 4.26
148 149 3.687321 TACGGAGCCGGACTAGCGT 62.687 63.158 5.05 6.38 44.69 5.07
149 150 4.253257 CGGAGCCGGACTAGCGTC 62.253 72.222 5.05 0.00 39.49 5.19
150 151 4.253257 GGAGCCGGACTAGCGTCG 62.253 72.222 5.05 0.00 41.16 5.12
151 152 3.507009 GAGCCGGACTAGCGTCGT 61.507 66.667 5.05 0.00 41.16 4.34
152 153 3.048941 GAGCCGGACTAGCGTCGTT 62.049 63.158 5.05 0.00 41.16 3.85
153 154 2.879462 GCCGGACTAGCGTCGTTG 60.879 66.667 5.05 0.00 41.16 4.10
154 155 2.872557 CCGGACTAGCGTCGTTGA 59.127 61.111 0.00 0.00 41.16 3.18
155 156 1.432251 CCGGACTAGCGTCGTTGAT 59.568 57.895 0.00 0.00 41.16 2.57
156 157 0.866061 CCGGACTAGCGTCGTTGATG 60.866 60.000 0.00 0.00 41.16 3.07
157 158 0.179171 CGGACTAGCGTCGTTGATGT 60.179 55.000 0.00 0.00 41.16 3.06
158 159 1.063027 CGGACTAGCGTCGTTGATGTA 59.937 52.381 0.00 0.00 41.16 2.29
159 160 2.476686 CGGACTAGCGTCGTTGATGTAA 60.477 50.000 0.00 0.00 41.16 2.41
160 161 3.504863 GGACTAGCGTCGTTGATGTAAA 58.495 45.455 0.00 0.00 41.16 2.01
161 162 4.110482 GGACTAGCGTCGTTGATGTAAAT 58.890 43.478 0.00 0.00 41.16 1.40
162 163 4.026804 GGACTAGCGTCGTTGATGTAAATG 60.027 45.833 0.00 0.00 41.16 2.32
163 164 4.491676 ACTAGCGTCGTTGATGTAAATGT 58.508 39.130 0.00 0.00 0.00 2.71
164 165 5.643664 ACTAGCGTCGTTGATGTAAATGTA 58.356 37.500 0.00 0.00 0.00 2.29
165 166 4.835199 AGCGTCGTTGATGTAAATGTAC 57.165 40.909 0.00 0.00 0.00 2.90
166 167 4.491676 AGCGTCGTTGATGTAAATGTACT 58.508 39.130 0.00 0.00 0.00 2.73
167 168 4.326278 AGCGTCGTTGATGTAAATGTACTG 59.674 41.667 0.00 0.00 0.00 2.74
168 169 4.090930 GCGTCGTTGATGTAAATGTACTGT 59.909 41.667 0.00 0.00 0.00 3.55
169 170 5.389098 GCGTCGTTGATGTAAATGTACTGTT 60.389 40.000 0.00 0.00 0.00 3.16
170 171 6.586751 CGTCGTTGATGTAAATGTACTGTTT 58.413 36.000 0.00 0.00 0.00 2.83
171 172 7.619776 GCGTCGTTGATGTAAATGTACTGTTTA 60.620 37.037 0.00 0.00 0.00 2.01
172 173 8.377681 CGTCGTTGATGTAAATGTACTGTTTAT 58.622 33.333 0.00 0.00 0.00 1.40
186 187 8.967664 TGTACTGTTTATATAAAAATCCGCCT 57.032 30.769 9.48 0.00 0.00 5.52
187 188 9.398538 TGTACTGTTTATATAAAAATCCGCCTT 57.601 29.630 9.48 0.00 0.00 4.35
201 202 8.887036 AAAATCCGCCTTTTTATATGAAATCC 57.113 30.769 0.00 0.00 0.00 3.01
202 203 5.682943 TCCGCCTTTTTATATGAAATCCG 57.317 39.130 0.00 0.00 0.00 4.18
203 204 4.517453 TCCGCCTTTTTATATGAAATCCGG 59.483 41.667 14.69 14.69 34.05 5.14
204 205 4.226761 CGCCTTTTTATATGAAATCCGGC 58.773 43.478 0.00 13.72 0.00 6.13
205 206 4.556233 GCCTTTTTATATGAAATCCGGCC 58.444 43.478 0.00 0.00 0.00 6.13
206 207 4.038642 GCCTTTTTATATGAAATCCGGCCA 59.961 41.667 2.24 0.00 0.00 5.36
207 208 5.279456 GCCTTTTTATATGAAATCCGGCCAT 60.279 40.000 2.24 0.00 0.00 4.40
208 209 6.741240 GCCTTTTTATATGAAATCCGGCCATT 60.741 38.462 2.24 0.00 0.00 3.16
209 210 7.216494 CCTTTTTATATGAAATCCGGCCATTT 58.784 34.615 2.24 1.38 0.00 2.32
210 211 7.714813 CCTTTTTATATGAAATCCGGCCATTTT 59.285 33.333 2.24 0.00 0.00 1.82
211 212 9.108284 CTTTTTATATGAAATCCGGCCATTTTT 57.892 29.630 2.24 0.00 0.00 1.94
212 213 8.430801 TTTTATATGAAATCCGGCCATTTTTG 57.569 30.769 2.24 0.00 0.00 2.44
213 214 2.091852 TGAAATCCGGCCATTTTTGC 57.908 45.000 2.24 0.00 0.00 3.68
214 215 1.345741 TGAAATCCGGCCATTTTTGCA 59.654 42.857 2.24 0.00 0.00 4.08
215 216 1.731709 GAAATCCGGCCATTTTTGCAC 59.268 47.619 2.24 0.00 0.00 4.57
216 217 0.389687 AATCCGGCCATTTTTGCACG 60.390 50.000 2.24 0.00 0.00 5.34
217 218 1.247419 ATCCGGCCATTTTTGCACGA 61.247 50.000 2.24 0.00 0.00 4.35
218 219 1.006805 CCGGCCATTTTTGCACGAA 60.007 52.632 2.24 0.00 0.00 3.85
219 220 0.389687 CCGGCCATTTTTGCACGAAT 60.390 50.000 2.24 0.00 0.00 3.34
220 221 1.427435 CGGCCATTTTTGCACGAATT 58.573 45.000 2.24 0.00 0.00 2.17
221 222 1.797635 CGGCCATTTTTGCACGAATTT 59.202 42.857 2.24 0.00 0.00 1.82
222 223 2.159854 CGGCCATTTTTGCACGAATTTC 60.160 45.455 2.24 0.00 0.00 2.17
223 224 2.159854 GGCCATTTTTGCACGAATTTCG 60.160 45.455 16.84 16.84 46.93 3.46
240 241 7.790861 GAATTTCGTTCGGTTGAAAATGTAT 57.209 32.000 2.01 0.00 37.60 2.29
241 242 7.561237 AATTTCGTTCGGTTGAAAATGTATG 57.439 32.000 2.01 0.00 37.60 2.39
242 243 4.073169 TCGTTCGGTTGAAAATGTATGC 57.927 40.909 0.00 0.00 35.46 3.14
243 244 2.837878 CGTTCGGTTGAAAATGTATGCG 59.162 45.455 0.00 0.00 35.46 4.73
244 245 3.168193 GTTCGGTTGAAAATGTATGCGG 58.832 45.455 0.00 0.00 35.46 5.69
245 246 1.131504 TCGGTTGAAAATGTATGCGGC 59.868 47.619 0.00 0.00 0.00 6.53
246 247 1.132262 CGGTTGAAAATGTATGCGGCT 59.868 47.619 0.00 0.00 0.00 5.52
247 248 2.529151 GGTTGAAAATGTATGCGGCTG 58.471 47.619 0.00 0.00 0.00 4.85
248 249 2.529151 GTTGAAAATGTATGCGGCTGG 58.471 47.619 0.00 0.00 0.00 4.85
249 250 0.455410 TGAAAATGTATGCGGCTGGC 59.545 50.000 0.00 0.00 43.96 4.85
258 259 3.941836 GCGGCTGGCGTTAGATGC 61.942 66.667 24.53 2.28 0.00 3.91
264 265 2.499685 GGCGTTAGATGCCGTCCT 59.500 61.111 0.00 0.00 40.96 3.85
265 266 1.591863 GGCGTTAGATGCCGTCCTC 60.592 63.158 0.00 0.00 40.96 3.71
266 267 1.591863 GCGTTAGATGCCGTCCTCC 60.592 63.158 0.00 0.00 0.00 4.30
267 268 1.067582 CGTTAGATGCCGTCCTCCC 59.932 63.158 0.00 0.00 0.00 4.30
268 269 1.067582 GTTAGATGCCGTCCTCCCG 59.932 63.158 0.00 0.00 0.00 5.14
269 270 2.792947 TTAGATGCCGTCCTCCCGC 61.793 63.158 0.00 0.00 0.00 6.13
271 272 4.241555 GATGCCGTCCTCCCGCAT 62.242 66.667 0.00 0.00 0.00 4.73
272 273 4.241555 ATGCCGTCCTCCCGCATC 62.242 66.667 0.00 0.00 0.00 3.91
276 277 4.873129 CGTCCTCCCGCATCCGTG 62.873 72.222 0.00 0.00 0.00 4.94
277 278 3.771160 GTCCTCCCGCATCCGTGT 61.771 66.667 0.00 0.00 0.00 4.49
278 279 3.458163 TCCTCCCGCATCCGTGTC 61.458 66.667 0.00 0.00 0.00 3.67
279 280 4.530857 CCTCCCGCATCCGTGTCC 62.531 72.222 0.00 0.00 0.00 4.02
280 281 4.873129 CTCCCGCATCCGTGTCCG 62.873 72.222 0.00 0.00 0.00 4.79
291 292 4.736896 GTGTCCGCGGACTGGTCC 62.737 72.222 46.72 29.41 44.80 4.46
296 297 2.439701 CGCGGACTGGTCCCTCTA 60.440 66.667 13.41 0.00 46.96 2.43
297 298 1.828660 CGCGGACTGGTCCCTCTAT 60.829 63.158 13.41 0.00 46.96 1.98
298 299 1.797211 CGCGGACTGGTCCCTCTATC 61.797 65.000 13.41 0.00 46.96 2.08
299 300 0.468400 GCGGACTGGTCCCTCTATCT 60.468 60.000 13.41 0.00 46.96 1.98
300 301 1.202903 GCGGACTGGTCCCTCTATCTA 60.203 57.143 13.41 0.00 46.96 1.98
301 302 2.555670 GCGGACTGGTCCCTCTATCTAT 60.556 54.545 13.41 0.00 46.96 1.98
302 303 3.085533 CGGACTGGTCCCTCTATCTATG 58.914 54.545 13.41 0.00 46.96 2.23
303 304 3.436243 GGACTGGTCCCTCTATCTATGG 58.564 54.545 8.48 0.00 43.94 2.74
304 305 3.076182 GGACTGGTCCCTCTATCTATGGA 59.924 52.174 8.48 0.00 43.94 3.41
305 306 4.083565 GACTGGTCCCTCTATCTATGGAC 58.916 52.174 0.00 0.00 45.25 4.02
306 307 3.085533 CTGGTCCCTCTATCTATGGACG 58.914 54.545 0.00 0.00 46.60 4.79
307 308 2.225041 TGGTCCCTCTATCTATGGACGG 60.225 54.545 0.00 0.00 46.60 4.79
308 309 2.041350 GGTCCCTCTATCTATGGACGGA 59.959 54.545 0.00 0.00 46.60 4.69
309 310 3.309265 GGTCCCTCTATCTATGGACGGAT 60.309 52.174 0.00 0.00 46.60 4.18
310 311 3.697045 GTCCCTCTATCTATGGACGGATG 59.303 52.174 0.00 0.00 38.07 3.51
311 312 2.428890 CCCTCTATCTATGGACGGATGC 59.571 54.545 0.00 0.00 0.00 3.91
312 313 2.098280 CCTCTATCTATGGACGGATGCG 59.902 54.545 4.58 4.58 0.00 4.73
313 314 2.092323 TCTATCTATGGACGGATGCGG 58.908 52.381 12.44 0.00 0.00 5.69
314 315 2.092323 CTATCTATGGACGGATGCGGA 58.908 52.381 12.44 0.00 0.00 5.54
315 316 1.338107 ATCTATGGACGGATGCGGAA 58.662 50.000 12.44 0.00 0.00 4.30
316 317 0.673985 TCTATGGACGGATGCGGAAG 59.326 55.000 12.44 0.72 0.00 3.46
317 318 0.673985 CTATGGACGGATGCGGAAGA 59.326 55.000 12.44 0.00 0.00 2.87
318 319 0.387929 TATGGACGGATGCGGAAGAC 59.612 55.000 12.44 0.00 0.00 3.01
319 320 1.613317 ATGGACGGATGCGGAAGACA 61.613 55.000 12.44 2.53 0.00 3.41
320 321 1.144057 GGACGGATGCGGAAGACAT 59.856 57.895 12.44 0.00 0.00 3.06
321 322 0.462047 GGACGGATGCGGAAGACATT 60.462 55.000 12.44 0.00 0.00 2.71
322 323 1.369625 GACGGATGCGGAAGACATTT 58.630 50.000 12.44 0.00 0.00 2.32
323 324 1.737793 GACGGATGCGGAAGACATTTT 59.262 47.619 12.44 0.00 0.00 1.82
324 325 2.933906 GACGGATGCGGAAGACATTTTA 59.066 45.455 12.44 0.00 0.00 1.52
325 326 2.676342 ACGGATGCGGAAGACATTTTAC 59.324 45.455 12.44 0.00 0.00 2.01
326 327 2.285602 CGGATGCGGAAGACATTTTACG 60.286 50.000 0.00 0.00 0.00 3.18
327 328 2.031683 GGATGCGGAAGACATTTTACGG 59.968 50.000 0.00 0.00 0.00 4.02
328 329 1.444836 TGCGGAAGACATTTTACGGG 58.555 50.000 0.00 0.00 0.00 5.28
329 330 1.270947 TGCGGAAGACATTTTACGGGT 60.271 47.619 0.00 0.00 0.00 5.28
330 331 1.808343 GCGGAAGACATTTTACGGGTT 59.192 47.619 0.00 0.00 0.00 4.11
331 332 2.413634 GCGGAAGACATTTTACGGGTTG 60.414 50.000 0.00 0.00 0.00 3.77
332 333 2.413634 CGGAAGACATTTTACGGGTTGC 60.414 50.000 0.00 0.00 0.00 4.17
333 334 2.094906 GGAAGACATTTTACGGGTTGCC 60.095 50.000 0.00 0.00 0.00 4.52
334 335 2.279935 AGACATTTTACGGGTTGCCA 57.720 45.000 0.00 0.00 0.00 4.92
335 336 2.802719 AGACATTTTACGGGTTGCCAT 58.197 42.857 0.00 0.00 0.00 4.40
336 337 3.161866 AGACATTTTACGGGTTGCCATT 58.838 40.909 0.00 0.00 0.00 3.16
337 338 3.056891 AGACATTTTACGGGTTGCCATTG 60.057 43.478 0.00 0.00 0.00 2.82
338 339 2.894126 ACATTTTACGGGTTGCCATTGA 59.106 40.909 0.00 0.00 0.00 2.57
339 340 3.322254 ACATTTTACGGGTTGCCATTGAA 59.678 39.130 0.00 0.00 0.00 2.69
340 341 3.651803 TTTTACGGGTTGCCATTGAAG 57.348 42.857 0.00 0.00 0.00 3.02
341 342 2.570415 TTACGGGTTGCCATTGAAGA 57.430 45.000 0.00 0.00 0.00 2.87
342 343 2.799126 TACGGGTTGCCATTGAAGAT 57.201 45.000 0.00 0.00 0.00 2.40
343 344 1.176527 ACGGGTTGCCATTGAAGATG 58.823 50.000 0.00 0.00 0.00 2.90
344 345 0.179129 CGGGTTGCCATTGAAGATGC 60.179 55.000 0.00 0.00 0.00 3.91
345 346 0.176449 GGGTTGCCATTGAAGATGCC 59.824 55.000 0.00 0.00 0.00 4.40
346 347 1.188863 GGTTGCCATTGAAGATGCCT 58.811 50.000 0.00 0.00 0.00 4.75
351 352 3.700538 TGCCATTGAAGATGCCTTTAGT 58.299 40.909 0.00 0.00 31.62 2.24
360 361 3.615155 AGATGCCTTTAGTCAAAGCCTC 58.385 45.455 0.00 0.00 39.95 4.70
416 420 2.093341 AGCGGTACCCATTAATCAACGT 60.093 45.455 6.25 0.00 0.00 3.99
446 450 0.394352 CCAGTAGGCAATGACCCCAC 60.394 60.000 0.00 0.00 0.00 4.61
504 517 3.364549 CACTTGGGGAATTTAGGATGCA 58.635 45.455 0.00 0.00 0.00 3.96
512 525 2.645838 ATTTAGGATGCAGTGGCGAT 57.354 45.000 0.00 0.00 45.35 4.58
605 632 1.009222 CTGTCCGCGACGTATACCC 60.009 63.158 8.23 0.00 34.95 3.69
668 696 2.957402 AGAATGCAGAGGACAAACCA 57.043 45.000 0.00 0.00 42.04 3.67
670 698 4.574674 AGAATGCAGAGGACAAACCATA 57.425 40.909 0.00 0.00 42.04 2.74
676 705 3.624777 CAGAGGACAAACCATATGCCTT 58.375 45.455 0.00 0.00 42.04 4.35
686 715 2.153645 CCATATGCCTTGCTGCGAATA 58.846 47.619 0.00 0.00 0.00 1.75
711 740 1.153628 GTAGCGTGGAGACGGCAAT 60.154 57.895 0.00 0.00 46.20 3.56
850 6170 1.904032 GGCTACTCTCCAAGCTGCT 59.096 57.895 0.00 0.00 38.80 4.24
858 6178 3.699038 ACTCTCCAAGCTGCTAGACTAAG 59.301 47.826 0.90 0.00 0.00 2.18
870 6190 1.144936 GACTAAGCGAGCCCAGCAT 59.855 57.895 0.00 0.00 37.01 3.79
933 6254 0.831288 CCACTGGCACCCATCCAAAA 60.831 55.000 0.00 0.00 32.41 2.44
1012 6343 4.776322 TGAAGATGGTGGCGCCCG 62.776 66.667 26.77 0.00 36.04 6.13
1013 6344 4.467084 GAAGATGGTGGCGCCCGA 62.467 66.667 26.77 13.24 36.04 5.14
1443 6790 3.817084 CAGAGAGCATGTGGAAAAACAGA 59.183 43.478 0.00 0.00 32.52 3.41
1498 6880 8.642935 AAAGATAAAGAAAAAGGAGGAAGGAG 57.357 34.615 0.00 0.00 0.00 3.69
1526 6909 4.407296 AGATTACAAGCCCACTAGGAGAAG 59.593 45.833 0.00 0.00 38.24 2.85
1995 7394 1.212935 ACCACAACCTATCCAGCATCC 59.787 52.381 0.00 0.00 0.00 3.51
2296 7695 2.632996 CGGCCATACTCCTATTCTTCCA 59.367 50.000 2.24 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.028366 GCAAAGGACGGCTCGCTTC 62.028 63.158 0.00 0.00 0.00 3.86
6 7 3.793144 CAGCGCAAAGGACGGCTC 61.793 66.667 11.47 0.00 32.46 4.70
7 8 3.825160 TTCAGCGCAAAGGACGGCT 62.825 57.895 11.47 0.00 35.84 5.52
8 9 3.314388 CTTCAGCGCAAAGGACGGC 62.314 63.158 11.47 0.00 0.00 5.68
9 10 2.863153 CTTCAGCGCAAAGGACGG 59.137 61.111 11.47 0.00 0.00 4.79
10 11 1.915614 ATGCTTCAGCGCAAAGGACG 61.916 55.000 20.00 7.39 44.06 4.79
11 12 1.086696 TATGCTTCAGCGCAAAGGAC 58.913 50.000 20.00 8.36 44.06 3.85
12 13 2.042686 ATATGCTTCAGCGCAAAGGA 57.957 45.000 20.00 18.41 44.06 3.36
13 14 2.031682 GGTATATGCTTCAGCGCAAAGG 60.032 50.000 20.00 5.85 44.06 3.11
14 15 2.874701 AGGTATATGCTTCAGCGCAAAG 59.125 45.455 11.47 14.23 44.06 2.77
15 16 2.872245 GAGGTATATGCTTCAGCGCAAA 59.128 45.455 11.47 2.02 44.06 3.68
16 17 2.103094 AGAGGTATATGCTTCAGCGCAA 59.897 45.455 11.47 0.00 44.06 4.85
17 18 1.688735 AGAGGTATATGCTTCAGCGCA 59.311 47.619 11.47 0.00 45.83 6.09
18 19 2.064762 CAGAGGTATATGCTTCAGCGC 58.935 52.381 0.00 0.00 45.83 5.92
19 20 3.055591 CACAGAGGTATATGCTTCAGCG 58.944 50.000 5.75 0.00 45.83 5.18
20 21 3.397482 CCACAGAGGTATATGCTTCAGC 58.603 50.000 5.75 0.00 42.50 4.26
21 22 3.070734 AGCCACAGAGGTATATGCTTCAG 59.929 47.826 5.75 0.10 40.61 3.02
22 23 3.041211 AGCCACAGAGGTATATGCTTCA 58.959 45.455 5.75 0.00 40.61 3.02
23 24 3.556004 GGAGCCACAGAGGTATATGCTTC 60.556 52.174 0.00 0.00 40.61 3.86
24 25 2.370189 GGAGCCACAGAGGTATATGCTT 59.630 50.000 0.00 0.00 40.61 3.91
25 26 1.974236 GGAGCCACAGAGGTATATGCT 59.026 52.381 0.00 0.00 40.61 3.79
26 27 1.002544 GGGAGCCACAGAGGTATATGC 59.997 57.143 0.00 0.00 40.61 3.14
27 28 1.273606 CGGGAGCCACAGAGGTATATG 59.726 57.143 0.00 0.00 40.61 1.78
28 29 1.147191 TCGGGAGCCACAGAGGTATAT 59.853 52.381 0.00 0.00 40.61 0.86
29 30 0.554305 TCGGGAGCCACAGAGGTATA 59.446 55.000 0.00 0.00 40.61 1.47
30 31 1.043673 GTCGGGAGCCACAGAGGTAT 61.044 60.000 0.00 0.00 40.61 2.73
31 32 1.681327 GTCGGGAGCCACAGAGGTA 60.681 63.158 0.00 0.00 40.61 3.08
32 33 2.997897 GTCGGGAGCCACAGAGGT 60.998 66.667 0.00 0.00 40.61 3.85
33 34 2.997315 TGTCGGGAGCCACAGAGG 60.997 66.667 0.00 0.00 41.84 3.69
34 35 2.219325 GACTGTCGGGAGCCACAGAG 62.219 65.000 12.39 0.00 42.37 3.35
35 36 2.203640 ACTGTCGGGAGCCACAGA 60.204 61.111 12.39 0.00 42.37 3.41
36 37 2.262915 GACTGTCGGGAGCCACAG 59.737 66.667 5.68 5.68 44.83 3.66
37 38 3.311110 GGACTGTCGGGAGCCACA 61.311 66.667 1.07 0.00 0.00 4.17
38 39 4.436998 CGGACTGTCGGGAGCCAC 62.437 72.222 7.42 0.00 0.00 5.01
62 63 4.864334 CCTCATGTCCGGCAGCCC 62.864 72.222 5.63 0.00 0.00 5.19
63 64 3.329542 TTCCTCATGTCCGGCAGCC 62.330 63.158 0.00 0.00 0.00 4.85
64 65 2.109126 GTTCCTCATGTCCGGCAGC 61.109 63.158 0.00 0.00 0.00 5.25
65 66 1.021390 GTGTTCCTCATGTCCGGCAG 61.021 60.000 0.00 0.00 0.00 4.85
66 67 1.003839 GTGTTCCTCATGTCCGGCA 60.004 57.895 0.00 0.00 0.00 5.69
67 68 0.605319 TTGTGTTCCTCATGTCCGGC 60.605 55.000 0.00 0.00 0.00 6.13
68 69 1.806542 CTTTGTGTTCCTCATGTCCGG 59.193 52.381 0.00 0.00 0.00 5.14
69 70 1.806542 CCTTTGTGTTCCTCATGTCCG 59.193 52.381 0.00 0.00 0.00 4.79
70 71 2.162681 CCCTTTGTGTTCCTCATGTCC 58.837 52.381 0.00 0.00 0.00 4.02
71 72 3.140325 TCCCTTTGTGTTCCTCATGTC 57.860 47.619 0.00 0.00 0.00 3.06
72 73 3.562176 GGATCCCTTTGTGTTCCTCATGT 60.562 47.826 0.00 0.00 0.00 3.21
73 74 3.019564 GGATCCCTTTGTGTTCCTCATG 58.980 50.000 0.00 0.00 0.00 3.07
74 75 2.356125 CGGATCCCTTTGTGTTCCTCAT 60.356 50.000 6.06 0.00 0.00 2.90
75 76 1.003118 CGGATCCCTTTGTGTTCCTCA 59.997 52.381 6.06 0.00 0.00 3.86
76 77 1.739067 CGGATCCCTTTGTGTTCCTC 58.261 55.000 6.06 0.00 0.00 3.71
77 78 0.322546 GCGGATCCCTTTGTGTTCCT 60.323 55.000 6.06 0.00 0.00 3.36
78 79 1.644786 CGCGGATCCCTTTGTGTTCC 61.645 60.000 6.06 0.00 0.00 3.62
79 80 1.644786 CCGCGGATCCCTTTGTGTTC 61.645 60.000 24.07 0.00 0.00 3.18
80 81 1.674322 CCGCGGATCCCTTTGTGTT 60.674 57.895 24.07 0.00 0.00 3.32
81 82 2.046314 CCGCGGATCCCTTTGTGT 60.046 61.111 24.07 0.00 0.00 3.72
82 83 2.824041 CCCGCGGATCCCTTTGTG 60.824 66.667 30.73 0.44 0.00 3.33
83 84 4.796495 GCCCGCGGATCCCTTTGT 62.796 66.667 30.73 0.00 0.00 2.83
95 96 0.887387 TAATCTAAATGGCCGCCCGC 60.887 55.000 7.03 0.00 0.00 6.13
96 97 1.156736 CTAATCTAAATGGCCGCCCG 58.843 55.000 7.03 0.00 0.00 6.13
97 98 1.202891 ACCTAATCTAAATGGCCGCCC 60.203 52.381 7.03 0.00 0.00 6.13
98 99 2.271944 ACCTAATCTAAATGGCCGCC 57.728 50.000 1.04 1.04 0.00 6.13
99 100 6.171213 ACTAATACCTAATCTAAATGGCCGC 58.829 40.000 0.00 0.00 0.00 6.53
100 101 9.886132 ATAACTAATACCTAATCTAAATGGCCG 57.114 33.333 0.00 0.00 0.00 6.13
129 130 2.894565 CGCTAGTCCGGCTCCGTAG 61.895 68.421 7.59 4.13 37.81 3.51
130 131 2.898840 CGCTAGTCCGGCTCCGTA 60.899 66.667 7.59 0.00 37.81 4.02
132 133 4.253257 GACGCTAGTCCGGCTCCG 62.253 72.222 0.00 6.92 41.41 4.63
133 134 4.253257 CGACGCTAGTCCGGCTCC 62.253 72.222 0.00 0.00 44.28 4.70
134 135 3.048941 AACGACGCTAGTCCGGCTC 62.049 63.158 0.00 0.00 44.28 4.70
135 136 3.060615 AACGACGCTAGTCCGGCT 61.061 61.111 0.00 0.00 44.28 5.52
136 137 2.609183 ATCAACGACGCTAGTCCGGC 62.609 60.000 0.00 0.00 44.28 6.13
137 138 0.866061 CATCAACGACGCTAGTCCGG 60.866 60.000 0.00 0.00 44.28 5.14
138 139 0.179171 ACATCAACGACGCTAGTCCG 60.179 55.000 0.00 0.00 44.28 4.79
139 140 2.838386 TACATCAACGACGCTAGTCC 57.162 50.000 0.00 0.00 44.28 3.85
140 141 4.561606 ACATTTACATCAACGACGCTAGTC 59.438 41.667 0.00 0.00 43.72 2.59
141 142 4.491676 ACATTTACATCAACGACGCTAGT 58.508 39.130 0.00 0.00 0.00 2.57
142 143 5.742453 AGTACATTTACATCAACGACGCTAG 59.258 40.000 0.00 0.00 0.00 3.42
143 144 5.513849 CAGTACATTTACATCAACGACGCTA 59.486 40.000 0.00 0.00 0.00 4.26
144 145 4.326278 CAGTACATTTACATCAACGACGCT 59.674 41.667 0.00 0.00 0.00 5.07
145 146 4.090930 ACAGTACATTTACATCAACGACGC 59.909 41.667 0.00 0.00 0.00 5.19
146 147 5.756950 ACAGTACATTTACATCAACGACG 57.243 39.130 0.00 0.00 0.00 5.12
160 161 9.569122 AGGCGGATTTTTATATAAACAGTACAT 57.431 29.630 7.43 0.00 0.00 2.29
161 162 8.967664 AGGCGGATTTTTATATAAACAGTACA 57.032 30.769 7.43 0.00 0.00 2.90
175 176 9.325198 GGATTTCATATAAAAAGGCGGATTTTT 57.675 29.630 9.62 9.62 43.10 1.94
176 177 7.651704 CGGATTTCATATAAAAAGGCGGATTTT 59.348 33.333 4.59 4.59 33.86 1.82
177 178 7.145323 CGGATTTCATATAAAAAGGCGGATTT 58.855 34.615 0.00 0.00 0.00 2.17
178 179 6.294508 CCGGATTTCATATAAAAAGGCGGATT 60.295 38.462 0.00 0.00 0.00 3.01
179 180 5.183140 CCGGATTTCATATAAAAAGGCGGAT 59.817 40.000 0.00 0.00 0.00 4.18
180 181 4.517453 CCGGATTTCATATAAAAAGGCGGA 59.483 41.667 0.00 0.00 0.00 5.54
181 182 4.794169 CCGGATTTCATATAAAAAGGCGG 58.206 43.478 0.00 0.00 0.00 6.13
182 183 4.226761 GCCGGATTTCATATAAAAAGGCG 58.773 43.478 5.05 0.00 32.05 5.52
183 184 4.038642 TGGCCGGATTTCATATAAAAAGGC 59.961 41.667 5.05 7.10 36.94 4.35
184 185 5.782893 TGGCCGGATTTCATATAAAAAGG 57.217 39.130 5.05 0.00 0.00 3.11
185 186 8.661352 AAAATGGCCGGATTTCATATAAAAAG 57.339 30.769 5.05 0.00 0.00 2.27
186 187 8.887717 CAAAAATGGCCGGATTTCATATAAAAA 58.112 29.630 5.05 0.00 0.00 1.94
187 188 7.011857 GCAAAAATGGCCGGATTTCATATAAAA 59.988 33.333 5.05 0.00 0.00 1.52
188 189 6.481644 GCAAAAATGGCCGGATTTCATATAAA 59.518 34.615 5.05 0.00 0.00 1.40
189 190 5.988561 GCAAAAATGGCCGGATTTCATATAA 59.011 36.000 5.05 0.00 0.00 0.98
190 191 5.069648 TGCAAAAATGGCCGGATTTCATATA 59.930 36.000 5.05 0.00 0.00 0.86
191 192 4.141756 TGCAAAAATGGCCGGATTTCATAT 60.142 37.500 5.05 0.00 0.00 1.78
192 193 3.196469 TGCAAAAATGGCCGGATTTCATA 59.804 39.130 5.05 0.00 0.00 2.15
193 194 2.027377 TGCAAAAATGGCCGGATTTCAT 60.027 40.909 5.05 0.00 0.00 2.57
194 195 1.345741 TGCAAAAATGGCCGGATTTCA 59.654 42.857 5.05 0.00 0.00 2.69
195 196 1.731709 GTGCAAAAATGGCCGGATTTC 59.268 47.619 5.05 0.00 0.00 2.17
196 197 1.807139 GTGCAAAAATGGCCGGATTT 58.193 45.000 5.05 0.00 0.00 2.17
197 198 0.389687 CGTGCAAAAATGGCCGGATT 60.390 50.000 5.05 0.00 0.00 3.01
198 199 1.215117 CGTGCAAAAATGGCCGGAT 59.785 52.632 5.05 0.00 0.00 4.18
199 200 1.456196 TTCGTGCAAAAATGGCCGGA 61.456 50.000 5.05 0.00 0.00 5.14
200 201 0.389687 ATTCGTGCAAAAATGGCCGG 60.390 50.000 0.00 0.00 0.00 6.13
201 202 1.427435 AATTCGTGCAAAAATGGCCG 58.573 45.000 0.00 0.00 0.00 6.13
202 203 2.159854 CGAAATTCGTGCAAAAATGGCC 60.160 45.455 7.29 0.00 34.72 5.36
203 204 3.088972 CGAAATTCGTGCAAAAATGGC 57.911 42.857 7.29 0.00 34.72 4.40
216 217 7.653783 CATACATTTTCAACCGAACGAAATTC 58.346 34.615 0.00 0.00 31.54 2.17
217 218 6.088883 GCATACATTTTCAACCGAACGAAATT 59.911 34.615 0.00 0.00 31.54 1.82
218 219 5.571357 GCATACATTTTCAACCGAACGAAAT 59.429 36.000 0.00 0.00 31.54 2.17
219 220 4.912766 GCATACATTTTCAACCGAACGAAA 59.087 37.500 0.00 0.00 0.00 3.46
220 221 4.468643 GCATACATTTTCAACCGAACGAA 58.531 39.130 0.00 0.00 0.00 3.85
221 222 3.423776 CGCATACATTTTCAACCGAACGA 60.424 43.478 0.00 0.00 0.00 3.85
222 223 2.837878 CGCATACATTTTCAACCGAACG 59.162 45.455 0.00 0.00 0.00 3.95
223 224 3.168193 CCGCATACATTTTCAACCGAAC 58.832 45.455 0.00 0.00 0.00 3.95
224 225 2.414824 GCCGCATACATTTTCAACCGAA 60.415 45.455 0.00 0.00 0.00 4.30
225 226 1.131504 GCCGCATACATTTTCAACCGA 59.868 47.619 0.00 0.00 0.00 4.69
226 227 1.132262 AGCCGCATACATTTTCAACCG 59.868 47.619 0.00 0.00 0.00 4.44
227 228 2.529151 CAGCCGCATACATTTTCAACC 58.471 47.619 0.00 0.00 0.00 3.77
228 229 2.529151 CCAGCCGCATACATTTTCAAC 58.471 47.619 0.00 0.00 0.00 3.18
229 230 1.135141 GCCAGCCGCATACATTTTCAA 60.135 47.619 0.00 0.00 37.47 2.69
230 231 0.455410 GCCAGCCGCATACATTTTCA 59.545 50.000 0.00 0.00 37.47 2.69
231 232 0.592247 CGCCAGCCGCATACATTTTC 60.592 55.000 0.00 0.00 37.30 2.29
232 233 1.312371 ACGCCAGCCGCATACATTTT 61.312 50.000 0.00 0.00 41.76 1.82
233 234 1.312371 AACGCCAGCCGCATACATTT 61.312 50.000 0.00 0.00 41.76 2.32
234 235 0.462937 TAACGCCAGCCGCATACATT 60.463 50.000 0.00 0.00 41.76 2.71
235 236 0.880278 CTAACGCCAGCCGCATACAT 60.880 55.000 0.00 0.00 41.76 2.29
236 237 1.520564 CTAACGCCAGCCGCATACA 60.521 57.895 0.00 0.00 41.76 2.29
237 238 0.600255 ATCTAACGCCAGCCGCATAC 60.600 55.000 0.00 0.00 41.76 2.39
238 239 0.599991 CATCTAACGCCAGCCGCATA 60.600 55.000 0.00 0.00 41.76 3.14
239 240 1.889105 CATCTAACGCCAGCCGCAT 60.889 57.895 0.00 0.00 41.76 4.73
240 241 2.511373 CATCTAACGCCAGCCGCA 60.511 61.111 0.00 0.00 41.76 5.69
241 242 3.941836 GCATCTAACGCCAGCCGC 61.942 66.667 0.00 0.00 41.76 6.53
247 248 1.591863 GAGGACGGCATCTAACGCC 60.592 63.158 0.00 0.00 46.62 5.68
248 249 1.591863 GGAGGACGGCATCTAACGC 60.592 63.158 1.57 0.00 0.00 4.84
249 250 1.067582 GGGAGGACGGCATCTAACG 59.932 63.158 1.57 0.00 0.00 3.18
250 251 1.067582 CGGGAGGACGGCATCTAAC 59.932 63.158 1.57 0.00 0.00 2.34
251 252 2.792947 GCGGGAGGACGGCATCTAA 61.793 63.158 1.57 0.00 44.12 2.10
252 253 3.224324 GCGGGAGGACGGCATCTA 61.224 66.667 1.57 0.00 44.12 1.98
259 260 4.873129 CACGGATGCGGGAGGACG 62.873 72.222 12.44 0.00 0.00 4.79
260 261 3.718210 GACACGGATGCGGGAGGAC 62.718 68.421 18.37 0.00 0.00 3.85
261 262 3.458163 GACACGGATGCGGGAGGA 61.458 66.667 18.37 0.00 0.00 3.71
262 263 4.530857 GGACACGGATGCGGGAGG 62.531 72.222 18.37 1.75 0.00 4.30
263 264 4.873129 CGGACACGGATGCGGGAG 62.873 72.222 18.37 5.04 36.18 4.30
283 284 4.083565 GTCCATAGATAGAGGGACCAGTC 58.916 52.174 0.00 0.00 43.14 3.51
284 285 3.498841 CGTCCATAGATAGAGGGACCAGT 60.499 52.174 0.00 0.00 45.51 4.00
285 286 3.085533 CGTCCATAGATAGAGGGACCAG 58.914 54.545 0.00 0.00 45.51 4.00
286 287 2.225041 CCGTCCATAGATAGAGGGACCA 60.225 54.545 0.00 0.00 45.51 4.02
287 288 2.041350 TCCGTCCATAGATAGAGGGACC 59.959 54.545 0.00 0.00 45.51 4.46
288 289 3.436577 TCCGTCCATAGATAGAGGGAC 57.563 52.381 0.00 0.00 41.01 4.46
290 291 2.428890 GCATCCGTCCATAGATAGAGGG 59.571 54.545 0.00 0.00 39.00 4.30
291 292 2.098280 CGCATCCGTCCATAGATAGAGG 59.902 54.545 0.00 0.00 0.00 3.69
292 293 2.098280 CCGCATCCGTCCATAGATAGAG 59.902 54.545 0.00 0.00 0.00 2.43
293 294 2.092323 CCGCATCCGTCCATAGATAGA 58.908 52.381 0.00 0.00 0.00 1.98
294 295 2.092323 TCCGCATCCGTCCATAGATAG 58.908 52.381 0.00 0.00 0.00 2.08
295 296 2.209690 TCCGCATCCGTCCATAGATA 57.790 50.000 0.00 0.00 0.00 1.98
296 297 1.273606 CTTCCGCATCCGTCCATAGAT 59.726 52.381 0.00 0.00 0.00 1.98
297 298 0.673985 CTTCCGCATCCGTCCATAGA 59.326 55.000 0.00 0.00 0.00 1.98
298 299 0.673985 TCTTCCGCATCCGTCCATAG 59.326 55.000 0.00 0.00 0.00 2.23
299 300 0.387929 GTCTTCCGCATCCGTCCATA 59.612 55.000 0.00 0.00 0.00 2.74
300 301 1.144057 GTCTTCCGCATCCGTCCAT 59.856 57.895 0.00 0.00 0.00 3.41
301 302 1.613317 ATGTCTTCCGCATCCGTCCA 61.613 55.000 0.00 0.00 0.00 4.02
302 303 0.462047 AATGTCTTCCGCATCCGTCC 60.462 55.000 0.00 0.00 0.00 4.79
303 304 1.369625 AAATGTCTTCCGCATCCGTC 58.630 50.000 0.00 0.00 0.00 4.79
304 305 1.821216 AAAATGTCTTCCGCATCCGT 58.179 45.000 0.00 0.00 0.00 4.69
305 306 2.285602 CGTAAAATGTCTTCCGCATCCG 60.286 50.000 0.00 0.00 0.00 4.18
306 307 2.031683 CCGTAAAATGTCTTCCGCATCC 59.968 50.000 0.00 0.00 0.00 3.51
307 308 2.031683 CCCGTAAAATGTCTTCCGCATC 59.968 50.000 0.00 0.00 0.00 3.91
308 309 2.014128 CCCGTAAAATGTCTTCCGCAT 58.986 47.619 0.00 0.00 0.00 4.73
309 310 1.270947 ACCCGTAAAATGTCTTCCGCA 60.271 47.619 0.00 0.00 0.00 5.69
310 311 1.445871 ACCCGTAAAATGTCTTCCGC 58.554 50.000 0.00 0.00 0.00 5.54
311 312 2.413634 GCAACCCGTAAAATGTCTTCCG 60.414 50.000 0.00 0.00 0.00 4.30
312 313 2.094906 GGCAACCCGTAAAATGTCTTCC 60.095 50.000 0.00 0.00 0.00 3.46
313 314 2.554893 TGGCAACCCGTAAAATGTCTTC 59.445 45.455 0.00 0.00 0.00 2.87
314 315 2.588620 TGGCAACCCGTAAAATGTCTT 58.411 42.857 0.00 0.00 0.00 3.01
315 316 2.279935 TGGCAACCCGTAAAATGTCT 57.720 45.000 0.00 0.00 0.00 3.41
316 317 3.057174 TCAATGGCAACCCGTAAAATGTC 60.057 43.478 0.00 0.00 0.00 3.06
317 318 2.894126 TCAATGGCAACCCGTAAAATGT 59.106 40.909 0.00 0.00 0.00 2.71
318 319 3.584406 TCAATGGCAACCCGTAAAATG 57.416 42.857 0.00 0.00 0.00 2.32
319 320 3.829601 TCTTCAATGGCAACCCGTAAAAT 59.170 39.130 0.00 0.00 0.00 1.82
320 321 3.223435 TCTTCAATGGCAACCCGTAAAA 58.777 40.909 0.00 0.00 0.00 1.52
321 322 2.865079 TCTTCAATGGCAACCCGTAAA 58.135 42.857 0.00 0.00 0.00 2.01
322 323 2.570415 TCTTCAATGGCAACCCGTAA 57.430 45.000 0.00 0.00 0.00 3.18
323 324 2.364632 CATCTTCAATGGCAACCCGTA 58.635 47.619 0.00 0.00 0.00 4.02
324 325 1.176527 CATCTTCAATGGCAACCCGT 58.823 50.000 0.00 0.00 0.00 5.28
325 326 0.179129 GCATCTTCAATGGCAACCCG 60.179 55.000 0.00 0.00 0.00 5.28
326 327 0.176449 GGCATCTTCAATGGCAACCC 59.824 55.000 6.70 0.00 43.15 4.11
327 328 1.188863 AGGCATCTTCAATGGCAACC 58.811 50.000 13.17 0.00 45.66 3.77
328 329 3.323751 AAAGGCATCTTCAATGGCAAC 57.676 42.857 13.17 0.00 45.66 4.17
329 330 4.088634 ACTAAAGGCATCTTCAATGGCAA 58.911 39.130 13.17 0.00 45.66 4.52
330 331 3.696051 GACTAAAGGCATCTTCAATGGCA 59.304 43.478 13.17 0.00 45.66 4.92
331 332 3.696051 TGACTAAAGGCATCTTCAATGGC 59.304 43.478 3.60 3.60 43.88 4.40
332 333 5.902613 TTGACTAAAGGCATCTTCAATGG 57.097 39.130 0.00 0.00 31.82 3.16
333 334 5.803967 GCTTTGACTAAAGGCATCTTCAATG 59.196 40.000 0.00 0.00 42.81 2.82
334 335 5.958955 GCTTTGACTAAAGGCATCTTCAAT 58.041 37.500 0.00 0.00 42.81 2.57
335 336 5.376854 GCTTTGACTAAAGGCATCTTCAA 57.623 39.130 0.00 0.00 42.81 2.69
344 345 3.604582 CAGGAGAGGCTTTGACTAAAGG 58.395 50.000 0.00 0.00 42.81 3.11
345 346 3.006247 GCAGGAGAGGCTTTGACTAAAG 58.994 50.000 0.00 0.00 44.86 1.85
346 347 2.371841 TGCAGGAGAGGCTTTGACTAAA 59.628 45.455 0.00 0.00 0.00 1.85
351 352 1.059098 TTCTGCAGGAGAGGCTTTGA 58.941 50.000 15.13 0.00 30.18 2.69
360 361 4.937620 TGCTATTGTAGTTTTCTGCAGGAG 59.062 41.667 15.13 0.00 42.88 3.69
422 426 1.369625 GTCATTGCCTACTGGGTTCG 58.630 55.000 0.00 0.00 37.43 3.95
446 450 6.198029 GCTGTCGTATATGCATTGAGCTATAG 59.802 42.308 3.54 0.00 45.94 1.31
504 517 2.281484 AAACGCCACATCGCCACT 60.281 55.556 0.00 0.00 0.00 4.00
512 525 2.465860 ACTATAGCACAAACGCCACA 57.534 45.000 0.00 0.00 0.00 4.17
631 659 6.092944 TGCATTCTTATGAATTCCGTTAACGT 59.907 34.615 25.15 7.90 40.61 3.99
668 696 1.800586 CGTATTCGCAGCAAGGCATAT 59.199 47.619 0.00 0.00 0.00 1.78
670 698 0.744414 ACGTATTCGCAGCAAGGCAT 60.744 50.000 0.00 0.00 41.18 4.40
711 740 3.131326 CGTGGATTTACGTGCTCCA 57.869 52.632 10.46 10.46 39.13 3.86
838 6158 2.428890 GCTTAGTCTAGCAGCTTGGAGA 59.571 50.000 0.00 0.00 40.89 3.71
850 6170 0.683179 TGCTGGGCTCGCTTAGTCTA 60.683 55.000 2.27 0.00 0.00 2.59
870 6190 0.179012 GGACTTTTTCCGGTGGTGGA 60.179 55.000 0.00 0.00 33.46 4.02
879 6199 7.470079 GTCGGTTGATTTATAGGACTTTTTCC 58.530 38.462 0.00 0.00 46.33 3.13
913 6234 2.017668 TTTGGATGGGTGCCAGTGGT 62.018 55.000 11.74 0.00 36.75 4.16
918 6239 2.323999 AAGATTTTGGATGGGTGCCA 57.676 45.000 0.00 0.00 38.19 4.92
933 6254 4.323868 GCTGGTAGGAGTGGAAGAAAAGAT 60.324 45.833 0.00 0.00 0.00 2.40
1443 6790 3.112205 GCGGATCAGCCCCATGTCT 62.112 63.158 6.57 0.00 0.00 3.41
1498 6880 4.640647 CCTAGTGGGCTTGTAATCTTTTCC 59.359 45.833 0.00 0.00 0.00 3.13
1526 6909 3.485877 GCTGATCGTTTTGCCACTGTATC 60.486 47.826 0.00 0.00 0.00 2.24
1995 7394 1.799258 AAGGTTTTCTGCTGGCTGCG 61.799 55.000 11.85 6.85 46.63 5.18
2296 7695 3.058570 CGCTCTATATCAGCACTCGAAGT 60.059 47.826 7.24 0.00 36.61 3.01


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

AutoCloner maintained by Alex Coulton.