Multiple sequence alignment - TraesCS1B01G462100

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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 TraesCS1B01G462100 chr1B 100.000 2207 0 0 1 2207 674642629 674640423 0.000000e+00 4076
1 TraesCS1B01G462100 chr1B 98.471 327 5 0 1 327 228966625 228966299 5.280000e-161 577
2 TraesCS1B01G462100 chr1B 96.899 129 4 0 319 447 198560286 198560414 1.330000e-52 217
3 TraesCS1B01G462100 chr2B 98.004 1904 21 3 319 2207 390976002 390974101 0.000000e+00 3290
4 TraesCS1B01G462100 chr2B 97.688 1903 28 2 319 2207 10667633 10669533 0.000000e+00 3256
5 TraesCS1B01G462100 chr2B 93.033 689 46 2 630 1317 588687074 588686387 0.000000e+00 1005
6 TraesCS1B01G462100 chr2B 95.074 609 19 6 1391 1991 588686398 588685793 0.000000e+00 948
7 TraesCS1B01G462100 chr2B 93.085 564 33 5 755 1317 588685795 588685237 0.000000e+00 821
8 TraesCS1B01G462100 chr2B 93.617 141 9 0 319 459 406245778 406245638 6.170000e-51 211
9 TraesCS1B01G462100 chr2B 93.617 141 9 0 319 459 599848069 599847929 6.170000e-51 211
10 TraesCS1B01G462100 chr5A 97.802 1729 35 2 480 2207 109300410 109302136 0.000000e+00 2979
11 TraesCS1B01G462100 chr5A 97.872 141 3 0 319 459 109300110 109300250 6.090000e-61 244
12 TraesCS1B01G462100 chr2A 97.629 1729 36 3 480 2207 130179315 130177591 0.000000e+00 2961
13 TraesCS1B01G462100 chr2A 97.872 141 3 0 319 459 130179615 130179475 6.090000e-61 244
14 TraesCS1B01G462100 chr7D 91.678 1526 94 9 483 1997 301662616 301661113 0.000000e+00 2084
15 TraesCS1B01G462100 chr7D 94.192 637 25 1 927 1563 46096344 46096968 0.000000e+00 961
16 TraesCS1B01G462100 chr7D 92.508 654 37 5 1563 2207 46101977 46102627 0.000000e+00 926
17 TraesCS1B01G462100 chr7D 95.058 344 13 3 483 825 46086227 46086567 2.490000e-149 538
18 TraesCS1B01G462100 chr7D 92.958 142 8 2 319 459 559672176 559672036 2.870000e-49 206
19 TraesCS1B01G462100 chr1D 93.605 1251 49 9 967 2207 252590495 252591724 0.000000e+00 1838
20 TraesCS1B01G462100 chr1D 95.556 270 7 3 480 744 252586068 252586337 5.630000e-116 427
21 TraesCS1B01G462100 chr1D 96.169 261 7 2 480 737 252573501 252573761 7.280000e-115 424
22 TraesCS1B01G462100 chr7A 93.461 1254 50 10 967 2207 665832345 665831111 0.000000e+00 1832
23 TraesCS1B01G462100 chr7A 98.765 324 4 0 1 324 76129957 76130280 5.280000e-161 577
24 TraesCS1B01G462100 chr4A 92.149 1261 58 12 967 2207 713137572 713136333 0.000000e+00 1742
25 TraesCS1B01G462100 chr4A 91.818 440 26 6 1778 2207 504866808 504867247 2.420000e-169 604
26 TraesCS1B01G462100 chr4A 98.765 324 4 0 1 324 60696493 60696816 5.280000e-161 577
27 TraesCS1B01G462100 chr6B 95.460 815 35 2 501 1314 26562244 26563057 0.000000e+00 1299
28 TraesCS1B01G462100 chr6B 98.471 327 5 0 1 327 475242571 475242245 5.280000e-161 577
29 TraesCS1B01G462100 chr6B 98.765 324 4 0 1 324 578238950 578239273 5.280000e-161 577
30 TraesCS1B01G462100 chr6A 93.521 818 32 4 501 1317 611534867 611534070 0.000000e+00 1197
31 TraesCS1B01G462100 chr6A 94.531 256 13 1 1953 2207 611533569 611533314 5.710000e-106 394
32 TraesCS1B01G462100 chr3A 98.765 324 4 0 1 324 187768726 187769049 5.280000e-161 577
33 TraesCS1B01G462100 chr1A 98.765 324 4 0 1 324 528886979 528887302 5.280000e-161 577
34 TraesCS1B01G462100 chr1A 98.765 324 4 0 1 324 528898824 528899147 5.280000e-161 577
35 TraesCS1B01G462100 chr4B 97.345 339 6 3 1 337 563656241 563656578 6.840000e-160 573
36 TraesCS1B01G462100 chr4D 94.161 137 7 1 323 459 191268692 191268827 7.990000e-50 207


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 TraesCS1B01G462100 chr1B 674640423 674642629 2206 True 4076.000000 4076 100.000000 1 2207 1 chr1B.!!$R2 2206
1 TraesCS1B01G462100 chr2B 390974101 390976002 1901 True 3290.000000 3290 98.004000 319 2207 1 chr2B.!!$R1 1888
2 TraesCS1B01G462100 chr2B 10667633 10669533 1900 False 3256.000000 3256 97.688000 319 2207 1 chr2B.!!$F1 1888
3 TraesCS1B01G462100 chr2B 588685237 588687074 1837 True 924.666667 1005 93.730667 630 1991 3 chr2B.!!$R4 1361
4 TraesCS1B01G462100 chr5A 109300110 109302136 2026 False 1611.500000 2979 97.837000 319 2207 2 chr5A.!!$F1 1888
5 TraesCS1B01G462100 chr2A 130177591 130179615 2024 True 1602.500000 2961 97.750500 319 2207 2 chr2A.!!$R1 1888
6 TraesCS1B01G462100 chr7D 301661113 301662616 1503 True 2084.000000 2084 91.678000 483 1997 1 chr7D.!!$R1 1514
7 TraesCS1B01G462100 chr7D 46096344 46096968 624 False 961.000000 961 94.192000 927 1563 1 chr7D.!!$F2 636
8 TraesCS1B01G462100 chr7D 46101977 46102627 650 False 926.000000 926 92.508000 1563 2207 1 chr7D.!!$F3 644
9 TraesCS1B01G462100 chr1D 252590495 252591724 1229 False 1838.000000 1838 93.605000 967 2207 1 chr1D.!!$F3 1240
10 TraesCS1B01G462100 chr7A 665831111 665832345 1234 True 1832.000000 1832 93.461000 967 2207 1 chr7A.!!$R1 1240
11 TraesCS1B01G462100 chr4A 713136333 713137572 1239 True 1742.000000 1742 92.149000 967 2207 1 chr4A.!!$R1 1240
12 TraesCS1B01G462100 chr6B 26562244 26563057 813 False 1299.000000 1299 95.460000 501 1314 1 chr6B.!!$F1 813
13 TraesCS1B01G462100 chr6A 611533314 611534867 1553 True 795.500000 1197 94.026000 501 2207 2 chr6A.!!$R1 1706

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
220 221 0.030369 CGCTCGCGGTCTATAAAGGT 59.97 55.0 6.13 0.0 35.56 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 2171 0.313672 TTGTTTGGCCGAATGCACTC 59.686 50.0 9.15 0.0 43.89 3.51 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 2.358125 TCCATCAACACCACGCCG 60.358 61.111 0.00 0.00 0.00 6.46
18 19 2.668212 CCATCAACACCACGCCGT 60.668 61.111 0.00 0.00 0.00 5.68
19 20 2.677003 CCATCAACACCACGCCGTC 61.677 63.158 0.00 0.00 0.00 4.79
20 21 2.736995 ATCAACACCACGCCGTCG 60.737 61.111 0.00 0.00 42.43 5.12
34 35 3.720193 GTCGTGCTGCTGCTGGTG 61.720 66.667 17.00 4.15 40.48 4.17
38 39 4.671590 TGCTGCTGCTGGTGCCAT 62.672 61.111 17.00 0.00 40.48 4.40
39 40 3.823330 GCTGCTGCTGGTGCCATC 61.823 66.667 8.53 0.00 38.71 3.51
40 41 2.045242 CTGCTGCTGGTGCCATCT 60.045 61.111 0.00 0.00 38.71 2.90
41 42 2.045634 TGCTGCTGGTGCCATCTC 60.046 61.111 0.00 0.00 38.71 2.75
42 43 2.827642 GCTGCTGGTGCCATCTCC 60.828 66.667 0.00 0.00 38.71 3.71
43 44 2.124403 CTGCTGGTGCCATCTCCC 60.124 66.667 0.00 0.00 38.71 4.30
44 45 2.611800 TGCTGGTGCCATCTCCCT 60.612 61.111 0.00 0.00 38.71 4.20
45 46 2.191641 GCTGGTGCCATCTCCCTC 59.808 66.667 0.00 0.00 0.00 4.30
46 47 2.673200 GCTGGTGCCATCTCCCTCA 61.673 63.158 0.00 0.00 0.00 3.86
47 48 1.993653 CTGGTGCCATCTCCCTCAA 59.006 57.895 0.00 0.00 0.00 3.02
48 49 0.393537 CTGGTGCCATCTCCCTCAAC 60.394 60.000 0.00 0.00 0.00 3.18
49 50 1.077429 GGTGCCATCTCCCTCAACC 60.077 63.158 0.00 0.00 0.00 3.77
50 51 1.566298 GGTGCCATCTCCCTCAACCT 61.566 60.000 0.00 0.00 0.00 3.50
51 52 0.107459 GTGCCATCTCCCTCAACCTC 60.107 60.000 0.00 0.00 0.00 3.85
52 53 0.252881 TGCCATCTCCCTCAACCTCT 60.253 55.000 0.00 0.00 0.00 3.69
53 54 0.467804 GCCATCTCCCTCAACCTCTC 59.532 60.000 0.00 0.00 0.00 3.20
54 55 1.127343 CCATCTCCCTCAACCTCTCC 58.873 60.000 0.00 0.00 0.00 3.71
55 56 1.343884 CCATCTCCCTCAACCTCTCCT 60.344 57.143 0.00 0.00 0.00 3.69
56 57 2.038659 CATCTCCCTCAACCTCTCCTC 58.961 57.143 0.00 0.00 0.00 3.71
57 58 0.336737 TCTCCCTCAACCTCTCCTCC 59.663 60.000 0.00 0.00 0.00 4.30
58 59 0.689412 CTCCCTCAACCTCTCCTCCC 60.689 65.000 0.00 0.00 0.00 4.30
59 60 1.156322 TCCCTCAACCTCTCCTCCCT 61.156 60.000 0.00 0.00 0.00 4.20
60 61 0.689412 CCCTCAACCTCTCCTCCCTC 60.689 65.000 0.00 0.00 0.00 4.30
61 62 0.689412 CCTCAACCTCTCCTCCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
62 63 0.689412 CTCAACCTCTCCTCCCTCCC 60.689 65.000 0.00 0.00 0.00 4.30
63 64 1.156322 TCAACCTCTCCTCCCTCCCT 61.156 60.000 0.00 0.00 0.00 4.20
64 65 0.252927 CAACCTCTCCTCCCTCCCTT 60.253 60.000 0.00 0.00 0.00 3.95
65 66 0.252927 AACCTCTCCTCCCTCCCTTG 60.253 60.000 0.00 0.00 0.00 3.61
66 67 2.069430 CCTCTCCTCCCTCCCTTGC 61.069 68.421 0.00 0.00 0.00 4.01
67 68 1.002792 CTCTCCTCCCTCCCTTGCT 59.997 63.158 0.00 0.00 0.00 3.91
68 69 1.306482 TCTCCTCCCTCCCTTGCTG 60.306 63.158 0.00 0.00 0.00 4.41
69 70 2.285668 TCCTCCCTCCCTTGCTGG 60.286 66.667 0.00 0.00 0.00 4.85
70 71 2.285668 CCTCCCTCCCTTGCTGGA 60.286 66.667 0.00 0.00 38.35 3.86
71 72 1.695597 CCTCCCTCCCTTGCTGGAT 60.696 63.158 0.00 0.00 38.35 3.41
72 73 1.704007 CCTCCCTCCCTTGCTGGATC 61.704 65.000 0.00 0.00 38.35 3.36
73 74 0.984961 CTCCCTCCCTTGCTGGATCA 60.985 60.000 0.00 0.00 38.35 2.92
74 75 0.549902 TCCCTCCCTTGCTGGATCAA 60.550 55.000 0.00 0.00 38.35 2.57
75 76 0.106819 CCCTCCCTTGCTGGATCAAG 60.107 60.000 0.00 0.00 42.23 3.02
76 77 0.914644 CCTCCCTTGCTGGATCAAGA 59.085 55.000 0.00 0.00 44.61 3.02
77 78 1.283029 CCTCCCTTGCTGGATCAAGAA 59.717 52.381 0.00 0.00 44.61 2.52
78 79 2.641305 CTCCCTTGCTGGATCAAGAAG 58.359 52.381 0.00 2.15 44.61 2.85
79 80 1.283029 TCCCTTGCTGGATCAAGAAGG 59.717 52.381 16.02 16.02 44.61 3.46
80 81 1.283029 CCCTTGCTGGATCAAGAAGGA 59.717 52.381 21.16 3.00 44.61 3.36
81 82 2.641305 CCTTGCTGGATCAAGAAGGAG 58.359 52.381 17.24 0.00 44.61 3.69
82 83 2.641305 CTTGCTGGATCAAGAAGGAGG 58.359 52.381 0.00 0.00 44.61 4.30
83 84 1.956869 TGCTGGATCAAGAAGGAGGA 58.043 50.000 0.00 0.00 0.00 3.71
84 85 1.836166 TGCTGGATCAAGAAGGAGGAG 59.164 52.381 0.00 0.00 0.00 3.69
85 86 2.114616 GCTGGATCAAGAAGGAGGAGA 58.885 52.381 0.00 0.00 0.00 3.71
86 87 2.158971 GCTGGATCAAGAAGGAGGAGAC 60.159 54.545 0.00 0.00 0.00 3.36
87 88 2.100584 CTGGATCAAGAAGGAGGAGACG 59.899 54.545 0.00 0.00 0.00 4.18
88 89 2.104170 GGATCAAGAAGGAGGAGACGT 58.896 52.381 0.00 0.00 0.00 4.34
89 90 2.159170 GGATCAAGAAGGAGGAGACGTG 60.159 54.545 0.00 0.00 0.00 4.49
90 91 1.257743 TCAAGAAGGAGGAGACGTGG 58.742 55.000 0.00 0.00 0.00 4.94
91 92 0.390472 CAAGAAGGAGGAGACGTGGC 60.390 60.000 0.00 0.00 0.00 5.01
92 93 0.543174 AAGAAGGAGGAGACGTGGCT 60.543 55.000 0.00 0.00 0.00 4.75
93 94 1.216710 GAAGGAGGAGACGTGGCTG 59.783 63.158 0.00 0.00 0.00 4.85
94 95 1.534235 AAGGAGGAGACGTGGCTGT 60.534 57.895 0.00 0.00 0.00 4.40
95 96 1.122019 AAGGAGGAGACGTGGCTGTT 61.122 55.000 0.00 0.00 0.00 3.16
96 97 1.079750 GGAGGAGACGTGGCTGTTC 60.080 63.158 0.00 0.00 0.00 3.18
97 98 1.079750 GAGGAGACGTGGCTGTTCC 60.080 63.158 0.00 0.00 0.00 3.62
98 99 2.432628 GGAGACGTGGCTGTTCCG 60.433 66.667 0.00 0.00 37.80 4.30
99 100 2.338984 GAGACGTGGCTGTTCCGT 59.661 61.111 0.00 0.00 37.80 4.69
100 101 1.582968 GAGACGTGGCTGTTCCGTA 59.417 57.895 0.00 0.00 37.80 4.02
101 102 0.731855 GAGACGTGGCTGTTCCGTAC 60.732 60.000 0.00 0.00 37.80 3.67
102 103 2.049802 ACGTGGCTGTTCCGTACG 60.050 61.111 8.69 8.69 39.39 3.67
103 104 2.049802 CGTGGCTGTTCCGTACGT 60.050 61.111 15.21 0.00 37.80 3.57
104 105 2.369629 CGTGGCTGTTCCGTACGTG 61.370 63.158 15.21 5.96 37.80 4.49
105 106 1.300388 GTGGCTGTTCCGTACGTGT 60.300 57.895 15.21 0.00 37.80 4.49
106 107 1.300311 TGGCTGTTCCGTACGTGTG 60.300 57.895 15.21 0.00 37.80 3.82
107 108 1.300388 GGCTGTTCCGTACGTGTGT 60.300 57.895 15.21 0.00 0.00 3.72
108 109 0.877213 GGCTGTTCCGTACGTGTGTT 60.877 55.000 15.21 0.00 0.00 3.32
109 110 0.231279 GCTGTTCCGTACGTGTGTTG 59.769 55.000 15.21 0.00 0.00 3.33
110 111 1.842720 CTGTTCCGTACGTGTGTTGA 58.157 50.000 15.21 0.00 0.00 3.18
111 112 2.195096 CTGTTCCGTACGTGTGTTGAA 58.805 47.619 15.21 6.41 0.00 2.69
112 113 1.925847 TGTTCCGTACGTGTGTTGAAC 59.074 47.619 19.43 19.43 33.80 3.18
113 114 1.071959 GTTCCGTACGTGTGTTGAACG 60.072 52.381 15.21 0.00 46.32 3.95
114 115 1.199859 CCGTACGTGTGTTGAACGC 59.800 57.895 15.21 1.20 44.80 4.84
119 120 2.935955 GTGTGTTGAACGCGGAGG 59.064 61.111 12.47 0.00 0.00 4.30
120 121 1.885850 GTGTGTTGAACGCGGAGGT 60.886 57.895 12.47 0.00 0.00 3.85
121 122 1.885388 TGTGTTGAACGCGGAGGTG 60.885 57.895 12.47 0.00 0.00 4.00
122 123 2.970324 TGTTGAACGCGGAGGTGC 60.970 61.111 12.47 0.00 0.00 5.01
123 124 3.723348 GTTGAACGCGGAGGTGCC 61.723 66.667 12.47 0.00 0.00 5.01
144 145 3.554692 CGTTCGGCGCTGGTCATC 61.555 66.667 17.88 1.95 0.00 2.92
145 146 3.554692 GTTCGGCGCTGGTCATCG 61.555 66.667 17.88 4.84 0.00 3.84
146 147 4.812476 TTCGGCGCTGGTCATCGG 62.812 66.667 17.88 0.00 0.00 4.18
149 150 4.451150 GGCGCTGGTCATCGGTGA 62.451 66.667 7.64 0.00 34.25 4.02
150 151 2.202932 GCGCTGGTCATCGGTGAT 60.203 61.111 0.00 0.00 36.60 3.06
151 152 1.815421 GCGCTGGTCATCGGTGATT 60.815 57.895 0.00 0.00 36.60 2.57
152 153 1.369091 GCGCTGGTCATCGGTGATTT 61.369 55.000 0.00 0.00 36.60 2.17
153 154 0.374758 CGCTGGTCATCGGTGATTTG 59.625 55.000 0.00 0.00 36.60 2.32
154 155 0.734889 GCTGGTCATCGGTGATTTGG 59.265 55.000 0.00 0.00 36.60 3.28
155 156 1.678728 GCTGGTCATCGGTGATTTGGA 60.679 52.381 0.00 0.00 36.60 3.53
156 157 2.923121 CTGGTCATCGGTGATTTGGAT 58.077 47.619 0.00 0.00 36.60 3.41
157 158 2.874701 CTGGTCATCGGTGATTTGGATC 59.125 50.000 0.00 0.00 36.60 3.36
158 159 2.238395 TGGTCATCGGTGATTTGGATCA 59.762 45.455 0.00 0.00 39.92 2.92
168 169 3.766151 TGATTTGGATCACGTCGAGTAC 58.234 45.455 0.00 0.00 37.37 2.73
182 183 4.790810 TCGAGTACGACTACATCATCAC 57.209 45.455 0.00 0.00 43.81 3.06
183 184 3.558829 TCGAGTACGACTACATCATCACC 59.441 47.826 0.00 0.00 43.81 4.02
184 185 3.604085 CGAGTACGACTACATCATCACCG 60.604 52.174 0.00 0.00 42.66 4.94
185 186 3.276857 AGTACGACTACATCATCACCGT 58.723 45.455 0.00 0.00 0.00 4.83
186 187 3.693085 AGTACGACTACATCATCACCGTT 59.307 43.478 0.00 0.00 0.00 4.44
187 188 3.146618 ACGACTACATCATCACCGTTC 57.853 47.619 0.00 0.00 0.00 3.95
188 189 2.753452 ACGACTACATCATCACCGTTCT 59.247 45.455 0.00 0.00 0.00 3.01
189 190 3.943381 ACGACTACATCATCACCGTTCTA 59.057 43.478 0.00 0.00 0.00 2.10
190 191 4.579340 ACGACTACATCATCACCGTTCTAT 59.421 41.667 0.00 0.00 0.00 1.98
191 192 5.067413 ACGACTACATCATCACCGTTCTATT 59.933 40.000 0.00 0.00 0.00 1.73
192 193 5.399596 CGACTACATCATCACCGTTCTATTG 59.600 44.000 0.00 0.00 0.00 1.90
193 194 6.465439 ACTACATCATCACCGTTCTATTGA 57.535 37.500 0.00 0.00 0.00 2.57
194 195 6.873997 ACTACATCATCACCGTTCTATTGAA 58.126 36.000 0.00 0.00 0.00 2.69
195 196 6.757010 ACTACATCATCACCGTTCTATTGAAC 59.243 38.462 9.65 9.65 46.59 3.18
203 204 2.437308 GTTCTATTGAACGCTTCCGC 57.563 50.000 4.28 0.00 42.39 5.54
204 205 2.000447 GTTCTATTGAACGCTTCCGCT 59.000 47.619 4.28 0.00 42.39 5.52
205 206 1.922570 TCTATTGAACGCTTCCGCTC 58.077 50.000 0.00 0.00 38.22 5.03
206 207 0.572590 CTATTGAACGCTTCCGCTCG 59.427 55.000 0.00 0.00 38.22 5.03
207 208 1.418342 TATTGAACGCTTCCGCTCGC 61.418 55.000 0.00 0.00 38.22 5.03
219 220 2.797515 CGCTCGCGGTCTATAAAGG 58.202 57.895 6.13 0.00 35.56 3.11
220 221 0.030369 CGCTCGCGGTCTATAAAGGT 59.970 55.000 6.13 0.00 35.56 3.50
221 222 1.265095 CGCTCGCGGTCTATAAAGGTA 59.735 52.381 6.13 0.00 35.56 3.08
222 223 2.095364 CGCTCGCGGTCTATAAAGGTAT 60.095 50.000 6.13 0.00 35.56 2.73
223 224 3.243336 GCTCGCGGTCTATAAAGGTATG 58.757 50.000 6.13 0.00 0.00 2.39
224 225 3.305199 GCTCGCGGTCTATAAAGGTATGT 60.305 47.826 6.13 0.00 0.00 2.29
225 226 4.083110 GCTCGCGGTCTATAAAGGTATGTA 60.083 45.833 6.13 0.00 0.00 2.29
226 227 5.618056 TCGCGGTCTATAAAGGTATGTAG 57.382 43.478 6.13 0.00 0.00 2.74
227 228 5.308014 TCGCGGTCTATAAAGGTATGTAGA 58.692 41.667 6.13 0.00 0.00 2.59
228 229 5.942236 TCGCGGTCTATAAAGGTATGTAGAT 59.058 40.000 6.13 0.00 0.00 1.98
229 230 6.028368 CGCGGTCTATAAAGGTATGTAGATG 58.972 44.000 0.00 0.00 0.00 2.90
230 231 5.805994 GCGGTCTATAAAGGTATGTAGATGC 59.194 44.000 0.00 0.00 0.00 3.91
231 232 6.571731 GCGGTCTATAAAGGTATGTAGATGCA 60.572 42.308 0.00 0.00 32.44 3.96
232 233 7.548097 CGGTCTATAAAGGTATGTAGATGCAT 58.452 38.462 0.00 0.00 0.00 3.96
233 234 7.702772 CGGTCTATAAAGGTATGTAGATGCATC 59.297 40.741 19.37 19.37 0.00 3.91
234 235 8.754080 GGTCTATAAAGGTATGTAGATGCATCT 58.246 37.037 30.85 30.85 40.86 2.90
240 241 8.839310 AAAGGTATGTAGATGCATCTAATCAC 57.161 34.615 32.72 26.80 40.77 3.06
241 242 7.789202 AGGTATGTAGATGCATCTAATCACT 57.211 36.000 32.72 23.61 40.77 3.41
242 243 7.835822 AGGTATGTAGATGCATCTAATCACTC 58.164 38.462 32.72 21.15 40.77 3.51
243 244 6.749578 GGTATGTAGATGCATCTAATCACTCG 59.250 42.308 32.72 0.00 40.77 4.18
244 245 5.774498 TGTAGATGCATCTAATCACTCGT 57.226 39.130 32.72 10.09 40.77 4.18
245 246 6.149129 TGTAGATGCATCTAATCACTCGTT 57.851 37.500 32.72 9.60 40.77 3.85
246 247 5.979517 TGTAGATGCATCTAATCACTCGTTG 59.020 40.000 32.72 0.00 40.77 4.10
247 248 3.806521 AGATGCATCTAATCACTCGTTGC 59.193 43.478 27.73 0.00 34.85 4.17
248 249 3.251479 TGCATCTAATCACTCGTTGCT 57.749 42.857 0.00 0.00 0.00 3.91
249 250 4.385358 TGCATCTAATCACTCGTTGCTA 57.615 40.909 0.00 0.00 0.00 3.49
250 251 4.363138 TGCATCTAATCACTCGTTGCTAG 58.637 43.478 0.00 0.00 0.00 3.42
251 252 4.097892 TGCATCTAATCACTCGTTGCTAGA 59.902 41.667 0.00 0.00 0.00 2.43
252 253 5.221322 TGCATCTAATCACTCGTTGCTAGAT 60.221 40.000 0.00 0.00 33.52 1.98
253 254 5.118357 GCATCTAATCACTCGTTGCTAGATG 59.882 44.000 19.85 19.85 43.09 2.90
254 255 6.442112 CATCTAATCACTCGTTGCTAGATGA 58.558 40.000 19.67 5.21 43.00 2.92
255 256 6.451064 TCTAATCACTCGTTGCTAGATGAA 57.549 37.500 0.00 0.00 0.00 2.57
256 257 6.266323 TCTAATCACTCGTTGCTAGATGAAC 58.734 40.000 0.00 0.00 0.00 3.18
257 258 4.727507 ATCACTCGTTGCTAGATGAACT 57.272 40.909 0.00 0.00 0.00 3.01
258 259 4.098055 TCACTCGTTGCTAGATGAACTC 57.902 45.455 0.00 0.00 0.00 3.01
259 260 3.119459 TCACTCGTTGCTAGATGAACTCC 60.119 47.826 0.00 0.00 0.00 3.85
260 261 3.093057 ACTCGTTGCTAGATGAACTCCT 58.907 45.455 0.00 0.00 0.00 3.69
261 262 4.096532 CACTCGTTGCTAGATGAACTCCTA 59.903 45.833 0.00 0.00 0.00 2.94
262 263 4.336993 ACTCGTTGCTAGATGAACTCCTAG 59.663 45.833 0.00 0.00 36.38 3.02
263 264 4.524053 TCGTTGCTAGATGAACTCCTAGA 58.476 43.478 0.00 0.00 35.55 2.43
264 265 5.133941 TCGTTGCTAGATGAACTCCTAGAT 58.866 41.667 0.00 0.00 35.55 1.98
265 266 5.009110 TCGTTGCTAGATGAACTCCTAGATG 59.991 44.000 0.00 0.00 35.55 2.90
266 267 5.009110 CGTTGCTAGATGAACTCCTAGATGA 59.991 44.000 0.00 0.00 35.55 2.92
267 268 6.294453 CGTTGCTAGATGAACTCCTAGATGAT 60.294 42.308 0.00 0.00 35.55 2.45
268 269 6.832520 TGCTAGATGAACTCCTAGATGATC 57.167 41.667 0.00 0.00 35.55 2.92
269 270 6.551085 TGCTAGATGAACTCCTAGATGATCT 58.449 40.000 0.00 0.00 35.55 2.75
270 271 7.009550 TGCTAGATGAACTCCTAGATGATCTT 58.990 38.462 0.00 0.00 35.55 2.40
271 272 7.039853 TGCTAGATGAACTCCTAGATGATCTTG 60.040 40.741 0.00 0.00 35.55 3.02
272 273 6.669125 AGATGAACTCCTAGATGATCTTGG 57.331 41.667 15.49 15.49 40.13 3.61
273 274 6.142498 AGATGAACTCCTAGATGATCTTGGT 58.858 40.000 19.73 3.88 39.80 3.67
274 275 5.604758 TGAACTCCTAGATGATCTTGGTG 57.395 43.478 19.73 19.21 39.80 4.17
275 276 5.272402 TGAACTCCTAGATGATCTTGGTGA 58.728 41.667 24.48 7.77 39.80 4.02
276 277 5.721480 TGAACTCCTAGATGATCTTGGTGAA 59.279 40.000 24.48 11.49 39.80 3.18
277 278 6.213397 TGAACTCCTAGATGATCTTGGTGAAA 59.787 38.462 24.48 11.23 39.80 2.69
278 279 5.983540 ACTCCTAGATGATCTTGGTGAAAC 58.016 41.667 24.48 0.00 39.80 2.78
279 280 5.011090 TCCTAGATGATCTTGGTGAAACG 57.989 43.478 19.73 0.00 39.80 3.60
280 281 4.709886 TCCTAGATGATCTTGGTGAAACGA 59.290 41.667 19.73 0.00 39.80 3.85
281 282 5.046529 CCTAGATGATCTTGGTGAAACGAG 58.953 45.833 13.75 0.00 38.12 4.18
282 283 4.543590 AGATGATCTTGGTGAAACGAGT 57.456 40.909 0.00 0.00 38.12 4.18
283 284 5.661056 AGATGATCTTGGTGAAACGAGTA 57.339 39.130 0.00 0.00 38.12 2.59
284 285 5.655488 AGATGATCTTGGTGAAACGAGTAG 58.345 41.667 0.00 0.00 38.12 2.57
285 286 4.188247 TGATCTTGGTGAAACGAGTAGG 57.812 45.455 0.00 0.00 38.12 3.18
286 287 3.830178 TGATCTTGGTGAAACGAGTAGGA 59.170 43.478 0.00 0.00 38.12 2.94
287 288 4.282449 TGATCTTGGTGAAACGAGTAGGAA 59.718 41.667 0.00 0.00 38.12 3.36
288 289 4.675976 TCTTGGTGAAACGAGTAGGAAA 57.324 40.909 0.00 0.00 38.12 3.13
289 290 5.026038 TCTTGGTGAAACGAGTAGGAAAA 57.974 39.130 0.00 0.00 38.12 2.29
290 291 5.617252 TCTTGGTGAAACGAGTAGGAAAAT 58.383 37.500 0.00 0.00 38.12 1.82
291 292 6.059484 TCTTGGTGAAACGAGTAGGAAAATT 58.941 36.000 0.00 0.00 38.12 1.82
292 293 6.544564 TCTTGGTGAAACGAGTAGGAAAATTT 59.455 34.615 0.00 0.00 38.12 1.82
293 294 6.702716 TGGTGAAACGAGTAGGAAAATTTT 57.297 33.333 2.28 2.28 38.12 1.82
294 295 7.102847 TGGTGAAACGAGTAGGAAAATTTTT 57.897 32.000 4.63 0.00 38.12 1.94
295 296 6.975772 TGGTGAAACGAGTAGGAAAATTTTTG 59.024 34.615 4.63 0.00 38.12 2.44
296 297 6.976349 GGTGAAACGAGTAGGAAAATTTTTGT 59.024 34.615 4.63 0.00 38.12 2.83
297 298 7.490079 GGTGAAACGAGTAGGAAAATTTTTGTT 59.510 33.333 4.63 0.00 38.12 2.83
298 299 8.865978 GTGAAACGAGTAGGAAAATTTTTGTTT 58.134 29.630 4.63 4.34 0.00 2.83
299 300 9.425577 TGAAACGAGTAGGAAAATTTTTGTTTT 57.574 25.926 4.63 0.00 34.19 2.43
300 301 9.895894 GAAACGAGTAGGAAAATTTTTGTTTTC 57.104 29.630 4.63 4.06 43.82 2.29
301 302 9.647797 AAACGAGTAGGAAAATTTTTGTTTTCT 57.352 25.926 4.63 0.31 43.94 2.52
302 303 8.628882 ACGAGTAGGAAAATTTTTGTTTTCTG 57.371 30.769 4.63 0.00 43.94 3.02
303 304 7.222031 ACGAGTAGGAAAATTTTTGTTTTCTGC 59.778 33.333 4.63 1.41 43.94 4.26
304 305 7.221838 CGAGTAGGAAAATTTTTGTTTTCTGCA 59.778 33.333 4.63 0.00 43.94 4.41
305 306 8.785329 AGTAGGAAAATTTTTGTTTTCTGCAA 57.215 26.923 4.63 0.00 43.94 4.08
306 307 8.664798 AGTAGGAAAATTTTTGTTTTCTGCAAC 58.335 29.630 4.63 5.77 43.94 4.17
307 308 6.541969 AGGAAAATTTTTGTTTTCTGCAACG 58.458 32.000 4.63 0.00 43.94 4.10
308 309 6.148645 AGGAAAATTTTTGTTTTCTGCAACGT 59.851 30.769 4.63 0.00 43.94 3.99
309 310 6.799441 GGAAAATTTTTGTTTTCTGCAACGTT 59.201 30.769 4.63 0.00 43.94 3.99
310 311 7.007009 GGAAAATTTTTGTTTTCTGCAACGTTC 59.993 33.333 4.63 0.00 43.94 3.95
311 312 4.912528 TTTTTGTTTTCTGCAACGTTCC 57.087 36.364 0.00 0.00 0.00 3.62
312 313 2.570442 TTGTTTTCTGCAACGTTCCC 57.430 45.000 0.00 0.00 0.00 3.97
313 314 0.741915 TGTTTTCTGCAACGTTCCCC 59.258 50.000 0.00 0.00 0.00 4.81
314 315 0.741915 GTTTTCTGCAACGTTCCCCA 59.258 50.000 0.00 0.00 0.00 4.96
315 316 1.135333 GTTTTCTGCAACGTTCCCCAA 59.865 47.619 0.00 0.00 0.00 4.12
316 317 0.741915 TTTCTGCAACGTTCCCCAAC 59.258 50.000 0.00 0.00 0.00 3.77
317 318 0.394488 TTCTGCAACGTTCCCCAACA 60.394 50.000 0.00 0.00 32.14 3.33
957 1137 8.856490 AACTGACACAATGTTTCTGATTTAAC 57.144 30.769 12.28 0.00 0.00 2.01
1302 1487 5.095145 TCATTCATTCTCTCAGGACAAGG 57.905 43.478 0.00 0.00 0.00 3.61
1425 1685 3.548745 TCTCTTGCTGTATGGTGATGG 57.451 47.619 0.00 0.00 0.00 3.51
1462 1723 4.685169 AAATCCAATACGACTGCACTTG 57.315 40.909 0.00 0.00 0.00 3.16
1686 1947 4.688413 TGCAAGTTTGTTTGTTTTCACTCC 59.312 37.500 0.00 0.00 0.00 3.85
1687 1948 4.688413 GCAAGTTTGTTTGTTTTCACTCCA 59.312 37.500 0.00 0.00 0.00 3.86
1900 2171 0.956633 AGCTTGCCTGTGTGTTGATG 59.043 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.358125 CGGCGTGGTGTTGATGGA 60.358 61.111 0.00 0.00 0.00 3.41
1 2 2.668212 ACGGCGTGGTGTTGATGG 60.668 61.111 13.76 0.00 0.00 3.51
2 3 2.860293 GACGGCGTGGTGTTGATG 59.140 61.111 21.19 0.00 0.00 3.07
3 4 2.736995 CGACGGCGTGGTGTTGAT 60.737 61.111 21.19 0.00 0.00 2.57
17 18 3.720193 CACCAGCAGCAGCACGAC 61.720 66.667 3.17 0.00 45.49 4.34
21 22 4.671590 ATGGCACCAGCAGCAGCA 62.672 61.111 3.17 0.00 45.49 4.41
22 23 3.823330 GATGGCACCAGCAGCAGC 61.823 66.667 0.00 0.00 44.61 5.25
23 24 2.045242 AGATGGCACCAGCAGCAG 60.045 61.111 7.80 0.00 44.61 4.24
24 25 2.045634 GAGATGGCACCAGCAGCA 60.046 61.111 7.80 0.00 44.61 4.41
25 26 2.827642 GGAGATGGCACCAGCAGC 60.828 66.667 7.80 0.00 44.61 5.25
26 27 2.124403 GGGAGATGGCACCAGCAG 60.124 66.667 7.80 0.00 44.61 4.24
27 28 2.611800 AGGGAGATGGCACCAGCA 60.612 61.111 7.80 0.00 44.61 4.41
28 29 2.191641 GAGGGAGATGGCACCAGC 59.808 66.667 0.00 0.00 41.10 4.85
29 30 0.393537 GTTGAGGGAGATGGCACCAG 60.394 60.000 0.00 0.00 0.00 4.00
30 31 1.685224 GTTGAGGGAGATGGCACCA 59.315 57.895 0.00 0.00 0.00 4.17
31 32 1.077429 GGTTGAGGGAGATGGCACC 60.077 63.158 0.00 0.00 0.00 5.01
32 33 0.107459 GAGGTTGAGGGAGATGGCAC 60.107 60.000 0.00 0.00 0.00 5.01
33 34 0.252881 AGAGGTTGAGGGAGATGGCA 60.253 55.000 0.00 0.00 0.00 4.92
34 35 0.467804 GAGAGGTTGAGGGAGATGGC 59.532 60.000 0.00 0.00 0.00 4.40
35 36 1.127343 GGAGAGGTTGAGGGAGATGG 58.873 60.000 0.00 0.00 0.00 3.51
36 37 2.038659 GAGGAGAGGTTGAGGGAGATG 58.961 57.143 0.00 0.00 0.00 2.90
37 38 1.062505 GGAGGAGAGGTTGAGGGAGAT 60.063 57.143 0.00 0.00 0.00 2.75
38 39 0.336737 GGAGGAGAGGTTGAGGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
39 40 0.689412 GGGAGGAGAGGTTGAGGGAG 60.689 65.000 0.00 0.00 0.00 4.30
40 41 1.156322 AGGGAGGAGAGGTTGAGGGA 61.156 60.000 0.00 0.00 0.00 4.20
41 42 0.689412 GAGGGAGGAGAGGTTGAGGG 60.689 65.000 0.00 0.00 0.00 4.30
42 43 0.689412 GGAGGGAGGAGAGGTTGAGG 60.689 65.000 0.00 0.00 0.00 3.86
43 44 0.689412 GGGAGGGAGGAGAGGTTGAG 60.689 65.000 0.00 0.00 0.00 3.02
44 45 1.156322 AGGGAGGGAGGAGAGGTTGA 61.156 60.000 0.00 0.00 0.00 3.18
45 46 0.252927 AAGGGAGGGAGGAGAGGTTG 60.253 60.000 0.00 0.00 0.00 3.77
46 47 0.252927 CAAGGGAGGGAGGAGAGGTT 60.253 60.000 0.00 0.00 0.00 3.50
47 48 1.394151 CAAGGGAGGGAGGAGAGGT 59.606 63.158 0.00 0.00 0.00 3.85
48 49 2.069430 GCAAGGGAGGGAGGAGAGG 61.069 68.421 0.00 0.00 0.00 3.69
49 50 1.002792 AGCAAGGGAGGGAGGAGAG 59.997 63.158 0.00 0.00 0.00 3.20
50 51 1.306482 CAGCAAGGGAGGGAGGAGA 60.306 63.158 0.00 0.00 0.00 3.71
51 52 2.373707 CCAGCAAGGGAGGGAGGAG 61.374 68.421 0.00 0.00 0.00 3.69
52 53 2.200373 ATCCAGCAAGGGAGGGAGGA 62.200 60.000 0.00 0.00 41.08 3.71
53 54 1.695597 ATCCAGCAAGGGAGGGAGG 60.696 63.158 0.00 0.00 41.08 4.30
54 55 0.984961 TGATCCAGCAAGGGAGGGAG 60.985 60.000 0.00 0.00 41.08 4.30
55 56 0.549902 TTGATCCAGCAAGGGAGGGA 60.550 55.000 0.00 0.00 41.08 4.20
56 57 0.106819 CTTGATCCAGCAAGGGAGGG 60.107 60.000 0.00 0.00 41.08 4.30
57 58 0.914644 TCTTGATCCAGCAAGGGAGG 59.085 55.000 4.79 0.00 44.14 4.30
58 59 2.641305 CTTCTTGATCCAGCAAGGGAG 58.359 52.381 4.79 0.74 44.14 4.30
59 60 1.283029 CCTTCTTGATCCAGCAAGGGA 59.717 52.381 4.79 0.00 44.14 4.20
60 61 1.283029 TCCTTCTTGATCCAGCAAGGG 59.717 52.381 17.39 0.00 44.14 3.95
61 62 2.641305 CTCCTTCTTGATCCAGCAAGG 58.359 52.381 14.03 14.03 44.14 3.61
62 63 2.238144 TCCTCCTTCTTGATCCAGCAAG 59.762 50.000 0.00 0.00 45.10 4.01
63 64 2.238144 CTCCTCCTTCTTGATCCAGCAA 59.762 50.000 0.00 0.00 0.00 3.91
64 65 1.836166 CTCCTCCTTCTTGATCCAGCA 59.164 52.381 0.00 0.00 0.00 4.41
65 66 2.114616 TCTCCTCCTTCTTGATCCAGC 58.885 52.381 0.00 0.00 0.00 4.85
66 67 2.100584 CGTCTCCTCCTTCTTGATCCAG 59.899 54.545 0.00 0.00 0.00 3.86
67 68 2.103373 CGTCTCCTCCTTCTTGATCCA 58.897 52.381 0.00 0.00 0.00 3.41
68 69 2.104170 ACGTCTCCTCCTTCTTGATCC 58.896 52.381 0.00 0.00 0.00 3.36
69 70 2.159170 CCACGTCTCCTCCTTCTTGATC 60.159 54.545 0.00 0.00 0.00 2.92
70 71 1.827969 CCACGTCTCCTCCTTCTTGAT 59.172 52.381 0.00 0.00 0.00 2.57
71 72 1.257743 CCACGTCTCCTCCTTCTTGA 58.742 55.000 0.00 0.00 0.00 3.02
72 73 0.390472 GCCACGTCTCCTCCTTCTTG 60.390 60.000 0.00 0.00 0.00 3.02
73 74 0.543174 AGCCACGTCTCCTCCTTCTT 60.543 55.000 0.00 0.00 0.00 2.52
74 75 1.077625 AGCCACGTCTCCTCCTTCT 59.922 57.895 0.00 0.00 0.00 2.85
75 76 1.216710 CAGCCACGTCTCCTCCTTC 59.783 63.158 0.00 0.00 0.00 3.46
76 77 1.122019 AACAGCCACGTCTCCTCCTT 61.122 55.000 0.00 0.00 0.00 3.36
77 78 1.534235 AACAGCCACGTCTCCTCCT 60.534 57.895 0.00 0.00 0.00 3.69
78 79 1.079750 GAACAGCCACGTCTCCTCC 60.080 63.158 0.00 0.00 0.00 4.30
79 80 1.079750 GGAACAGCCACGTCTCCTC 60.080 63.158 0.00 0.00 36.34 3.71
80 81 2.932234 CGGAACAGCCACGTCTCCT 61.932 63.158 0.00 0.00 35.94 3.69
81 82 1.870055 TACGGAACAGCCACGTCTCC 61.870 60.000 0.00 0.00 41.53 3.71
82 83 0.731855 GTACGGAACAGCCACGTCTC 60.732 60.000 0.00 0.00 41.53 3.36
83 84 1.288127 GTACGGAACAGCCACGTCT 59.712 57.895 0.00 0.00 41.53 4.18
84 85 2.084681 CGTACGGAACAGCCACGTC 61.085 63.158 7.57 0.00 41.53 4.34
85 86 2.049802 CGTACGGAACAGCCACGT 60.050 61.111 7.57 0.00 43.88 4.49
86 87 2.049802 ACGTACGGAACAGCCACG 60.050 61.111 21.06 0.00 40.72 4.94
87 88 1.300388 ACACGTACGGAACAGCCAC 60.300 57.895 21.06 0.00 35.94 5.01
88 89 1.300311 CACACGTACGGAACAGCCA 60.300 57.895 21.06 0.00 35.94 4.75
89 90 0.877213 AACACACGTACGGAACAGCC 60.877 55.000 21.06 0.00 0.00 4.85
90 91 0.231279 CAACACACGTACGGAACAGC 59.769 55.000 21.06 0.00 0.00 4.40
91 92 1.842720 TCAACACACGTACGGAACAG 58.157 50.000 21.06 7.04 0.00 3.16
92 93 1.925847 GTTCAACACACGTACGGAACA 59.074 47.619 21.06 0.00 33.96 3.18
93 94 1.071959 CGTTCAACACACGTACGGAAC 60.072 52.381 21.06 18.86 32.80 3.62
94 95 1.198767 CGTTCAACACACGTACGGAA 58.801 50.000 21.06 9.16 32.80 4.30
95 96 1.208009 GCGTTCAACACACGTACGGA 61.208 55.000 21.06 2.65 39.92 4.69
96 97 1.199859 GCGTTCAACACACGTACGG 59.800 57.895 21.06 11.05 39.92 4.02
97 98 1.155158 CGCGTTCAACACACGTACG 60.155 57.895 15.01 15.01 39.92 3.67
98 99 1.199859 CCGCGTTCAACACACGTAC 59.800 57.895 4.92 0.00 39.92 3.67
99 100 0.935831 CTCCGCGTTCAACACACGTA 60.936 55.000 4.92 0.00 39.92 3.57
100 101 2.202770 TCCGCGTTCAACACACGT 60.203 55.556 4.92 0.00 39.92 4.49
101 102 2.544359 CTCCGCGTTCAACACACG 59.456 61.111 4.92 0.00 40.75 4.49
102 103 1.885850 ACCTCCGCGTTCAACACAC 60.886 57.895 4.92 0.00 0.00 3.82
103 104 1.885388 CACCTCCGCGTTCAACACA 60.885 57.895 4.92 0.00 0.00 3.72
104 105 2.935955 CACCTCCGCGTTCAACAC 59.064 61.111 4.92 0.00 0.00 3.32
105 106 2.970324 GCACCTCCGCGTTCAACA 60.970 61.111 4.92 0.00 0.00 3.33
106 107 3.723348 GGCACCTCCGCGTTCAAC 61.723 66.667 4.92 0.00 0.00 3.18
128 129 3.554692 CGATGACCAGCGCCGAAC 61.555 66.667 2.29 0.00 32.02 3.95
129 130 4.812476 CCGATGACCAGCGCCGAA 62.812 66.667 2.29 0.00 39.12 4.30
132 133 3.740128 ATCACCGATGACCAGCGCC 62.740 63.158 2.29 0.00 39.12 6.53
133 134 1.369091 AAATCACCGATGACCAGCGC 61.369 55.000 0.00 0.00 39.12 5.92
134 135 0.374758 CAAATCACCGATGACCAGCG 59.625 55.000 0.18 0.18 37.79 5.18
135 136 0.734889 CCAAATCACCGATGACCAGC 59.265 55.000 0.00 0.00 37.79 4.85
136 137 2.401583 TCCAAATCACCGATGACCAG 57.598 50.000 0.00 0.00 37.79 4.00
137 138 2.238395 TGATCCAAATCACCGATGACCA 59.762 45.455 0.00 0.00 37.79 4.02
138 139 2.917933 TGATCCAAATCACCGATGACC 58.082 47.619 0.00 0.00 37.79 4.02
146 147 5.760783 CGTACTCGACGTGATCCAAATCAC 61.761 50.000 3.58 8.20 46.68 3.06
147 148 3.729762 CGTACTCGACGTGATCCAAATCA 60.730 47.826 3.58 0.00 46.86 2.57
148 149 2.782192 CGTACTCGACGTGATCCAAATC 59.218 50.000 3.58 0.00 46.86 2.17
149 150 2.793933 CGTACTCGACGTGATCCAAAT 58.206 47.619 3.58 0.00 46.86 2.32
150 151 2.251869 CGTACTCGACGTGATCCAAA 57.748 50.000 3.58 0.00 46.86 3.28
151 152 3.982213 CGTACTCGACGTGATCCAA 57.018 52.632 3.58 0.00 46.86 3.53
161 162 3.558829 GGTGATGATGTAGTCGTACTCGA 59.441 47.826 0.00 0.00 44.12 4.04
162 163 3.604085 CGGTGATGATGTAGTCGTACTCG 60.604 52.174 0.00 0.00 38.55 4.18
163 164 3.311871 ACGGTGATGATGTAGTCGTACTC 59.688 47.826 0.00 0.00 0.00 2.59
164 165 3.276857 ACGGTGATGATGTAGTCGTACT 58.723 45.455 0.00 0.00 0.00 2.73
165 166 3.687572 ACGGTGATGATGTAGTCGTAC 57.312 47.619 0.00 0.00 0.00 3.67
166 167 3.943381 AGAACGGTGATGATGTAGTCGTA 59.057 43.478 0.00 0.00 0.00 3.43
167 168 2.753452 AGAACGGTGATGATGTAGTCGT 59.247 45.455 0.00 0.00 0.00 4.34
168 169 3.422417 AGAACGGTGATGATGTAGTCG 57.578 47.619 0.00 0.00 0.00 4.18
169 170 6.504398 TCAATAGAACGGTGATGATGTAGTC 58.496 40.000 0.00 0.00 0.00 2.59
170 171 6.465439 TCAATAGAACGGTGATGATGTAGT 57.535 37.500 0.00 0.00 0.00 2.73
171 172 7.166628 GTTCAATAGAACGGTGATGATGTAG 57.833 40.000 0.00 0.00 44.11 2.74
201 202 0.030369 ACCTTTATAGACCGCGAGCG 59.970 55.000 8.23 10.86 39.44 5.03
202 203 3.243336 CATACCTTTATAGACCGCGAGC 58.757 50.000 8.23 0.00 0.00 5.03
203 204 4.500603 ACATACCTTTATAGACCGCGAG 57.499 45.455 8.23 0.00 0.00 5.03
204 205 5.308014 TCTACATACCTTTATAGACCGCGA 58.692 41.667 8.23 0.00 0.00 5.87
205 206 5.618056 TCTACATACCTTTATAGACCGCG 57.382 43.478 0.00 0.00 0.00 6.46
206 207 5.805994 GCATCTACATACCTTTATAGACCGC 59.194 44.000 0.00 0.00 0.00 5.68
207 208 6.920817 TGCATCTACATACCTTTATAGACCG 58.079 40.000 0.00 0.00 0.00 4.79
208 209 8.754080 AGATGCATCTACATACCTTTATAGACC 58.246 37.037 27.73 0.00 34.85 3.85
214 215 9.929180 GTGATTAGATGCATCTACATACCTTTA 57.071 33.333 31.46 16.62 39.00 1.85
215 216 8.654997 AGTGATTAGATGCATCTACATACCTTT 58.345 33.333 31.46 13.95 39.00 3.11
216 217 8.200024 AGTGATTAGATGCATCTACATACCTT 57.800 34.615 31.46 14.50 39.00 3.50
217 218 7.362487 CGAGTGATTAGATGCATCTACATACCT 60.362 40.741 31.46 22.68 39.00 3.08
218 219 6.749578 CGAGTGATTAGATGCATCTACATACC 59.250 42.308 31.46 19.20 39.00 2.73
219 220 7.309177 ACGAGTGATTAGATGCATCTACATAC 58.691 38.462 31.46 26.53 39.00 2.39
220 221 7.454260 ACGAGTGATTAGATGCATCTACATA 57.546 36.000 31.46 19.94 39.00 2.29
221 222 6.338214 ACGAGTGATTAGATGCATCTACAT 57.662 37.500 31.46 25.56 39.00 2.29
222 223 5.774498 ACGAGTGATTAGATGCATCTACA 57.226 39.130 31.46 24.38 39.00 2.74
223 224 5.107683 GCAACGAGTGATTAGATGCATCTAC 60.108 44.000 31.46 23.57 39.00 2.59
224 225 4.984785 GCAACGAGTGATTAGATGCATCTA 59.015 41.667 28.69 28.69 38.32 1.98
225 226 3.806521 GCAACGAGTGATTAGATGCATCT 59.193 43.478 30.85 30.85 40.86 2.90
226 227 3.806521 AGCAACGAGTGATTAGATGCATC 59.193 43.478 19.37 19.37 34.89 3.91
227 228 3.801698 AGCAACGAGTGATTAGATGCAT 58.198 40.909 0.00 0.00 34.89 3.96
228 229 3.251479 AGCAACGAGTGATTAGATGCA 57.749 42.857 0.00 0.00 34.89 3.96
229 230 4.611943 TCTAGCAACGAGTGATTAGATGC 58.388 43.478 0.00 0.00 0.00 3.91
230 231 6.442112 TCATCTAGCAACGAGTGATTAGATG 58.558 40.000 22.09 22.09 44.66 2.90
231 232 6.641169 TCATCTAGCAACGAGTGATTAGAT 57.359 37.500 0.00 1.59 36.70 1.98
232 233 6.095580 AGTTCATCTAGCAACGAGTGATTAGA 59.904 38.462 0.00 0.00 32.67 2.10
233 234 6.269315 AGTTCATCTAGCAACGAGTGATTAG 58.731 40.000 0.00 0.00 0.00 1.73
234 235 6.208988 AGTTCATCTAGCAACGAGTGATTA 57.791 37.500 0.00 0.00 0.00 1.75
235 236 5.078411 AGTTCATCTAGCAACGAGTGATT 57.922 39.130 0.00 0.00 0.00 2.57
236 237 4.440802 GGAGTTCATCTAGCAACGAGTGAT 60.441 45.833 0.00 0.00 0.00 3.06
237 238 3.119459 GGAGTTCATCTAGCAACGAGTGA 60.119 47.826 0.00 0.00 0.00 3.41
238 239 3.119316 AGGAGTTCATCTAGCAACGAGTG 60.119 47.826 0.00 0.00 0.00 3.51
239 240 3.093057 AGGAGTTCATCTAGCAACGAGT 58.907 45.455 0.00 0.00 0.00 4.18
240 241 3.791973 AGGAGTTCATCTAGCAACGAG 57.208 47.619 0.00 0.00 0.00 4.18
241 242 4.524053 TCTAGGAGTTCATCTAGCAACGA 58.476 43.478 0.00 0.00 34.52 3.85
242 243 4.902443 TCTAGGAGTTCATCTAGCAACG 57.098 45.455 0.00 0.00 34.52 4.10
243 244 6.398234 TCATCTAGGAGTTCATCTAGCAAC 57.602 41.667 0.00 0.00 34.52 4.17
244 245 7.009550 AGATCATCTAGGAGTTCATCTAGCAA 58.990 38.462 0.00 0.00 34.52 3.91
245 246 6.551085 AGATCATCTAGGAGTTCATCTAGCA 58.449 40.000 0.00 0.00 34.52 3.49
246 247 7.315142 CAAGATCATCTAGGAGTTCATCTAGC 58.685 42.308 0.00 0.00 34.52 3.42
247 248 7.451255 ACCAAGATCATCTAGGAGTTCATCTAG 59.549 40.741 0.00 0.00 35.52 2.43
248 249 7.232330 CACCAAGATCATCTAGGAGTTCATCTA 59.768 40.741 0.00 0.00 0.00 1.98
249 250 6.041865 CACCAAGATCATCTAGGAGTTCATCT 59.958 42.308 0.00 0.00 0.00 2.90
250 251 6.041409 TCACCAAGATCATCTAGGAGTTCATC 59.959 42.308 0.00 0.00 0.00 2.92
251 252 5.901853 TCACCAAGATCATCTAGGAGTTCAT 59.098 40.000 0.00 0.00 0.00 2.57
252 253 5.272402 TCACCAAGATCATCTAGGAGTTCA 58.728 41.667 0.00 0.00 0.00 3.18
253 254 5.860941 TCACCAAGATCATCTAGGAGTTC 57.139 43.478 0.00 0.00 0.00 3.01
254 255 6.410540 GTTTCACCAAGATCATCTAGGAGTT 58.589 40.000 0.00 0.00 0.00 3.01
255 256 5.394663 CGTTTCACCAAGATCATCTAGGAGT 60.395 44.000 0.00 0.00 0.00 3.85
256 257 5.046529 CGTTTCACCAAGATCATCTAGGAG 58.953 45.833 0.00 0.00 0.00 3.69
257 258 4.709886 TCGTTTCACCAAGATCATCTAGGA 59.290 41.667 0.00 0.00 0.00 2.94
258 259 5.011090 TCGTTTCACCAAGATCATCTAGG 57.989 43.478 0.00 0.00 0.00 3.02
259 260 5.655488 ACTCGTTTCACCAAGATCATCTAG 58.345 41.667 0.00 0.00 0.00 2.43
260 261 5.661056 ACTCGTTTCACCAAGATCATCTA 57.339 39.130 0.00 0.00 0.00 1.98
261 262 4.543590 ACTCGTTTCACCAAGATCATCT 57.456 40.909 0.00 0.00 0.00 2.90
262 263 4.806247 CCTACTCGTTTCACCAAGATCATC 59.194 45.833 0.00 0.00 0.00 2.92
263 264 4.466370 TCCTACTCGTTTCACCAAGATCAT 59.534 41.667 0.00 0.00 0.00 2.45
264 265 3.830178 TCCTACTCGTTTCACCAAGATCA 59.170 43.478 0.00 0.00 0.00 2.92
265 266 4.451629 TCCTACTCGTTTCACCAAGATC 57.548 45.455 0.00 0.00 0.00 2.75
266 267 4.884668 TTCCTACTCGTTTCACCAAGAT 57.115 40.909 0.00 0.00 0.00 2.40
267 268 4.675976 TTTCCTACTCGTTTCACCAAGA 57.324 40.909 0.00 0.00 0.00 3.02
268 269 5.941948 ATTTTCCTACTCGTTTCACCAAG 57.058 39.130 0.00 0.00 0.00 3.61
269 270 6.702716 AAATTTTCCTACTCGTTTCACCAA 57.297 33.333 0.00 0.00 0.00 3.67
270 271 6.702716 AAAATTTTCCTACTCGTTTCACCA 57.297 33.333 0.00 0.00 0.00 4.17
271 272 6.976349 ACAAAAATTTTCCTACTCGTTTCACC 59.024 34.615 3.41 0.00 0.00 4.02
272 273 7.980742 ACAAAAATTTTCCTACTCGTTTCAC 57.019 32.000 3.41 0.00 0.00 3.18
273 274 8.989653 AAACAAAAATTTTCCTACTCGTTTCA 57.010 26.923 3.41 0.00 0.00 2.69
274 275 9.895894 GAAAACAAAAATTTTCCTACTCGTTTC 57.104 29.630 3.41 3.36 40.99 2.78
275 276 9.647797 AGAAAACAAAAATTTTCCTACTCGTTT 57.352 25.926 3.41 3.66 45.72 3.60
276 277 9.083080 CAGAAAACAAAAATTTTCCTACTCGTT 57.917 29.630 3.41 0.00 45.72 3.85
277 278 7.222031 GCAGAAAACAAAAATTTTCCTACTCGT 59.778 33.333 3.41 0.00 45.72 4.18
278 279 7.221838 TGCAGAAAACAAAAATTTTCCTACTCG 59.778 33.333 3.41 0.00 45.72 4.18
279 280 8.419076 TGCAGAAAACAAAAATTTTCCTACTC 57.581 30.769 3.41 0.00 45.72 2.59
280 281 8.664798 GTTGCAGAAAACAAAAATTTTCCTACT 58.335 29.630 3.41 0.00 45.72 2.57
281 282 7.634432 CGTTGCAGAAAACAAAAATTTTCCTAC 59.366 33.333 3.41 0.00 45.72 3.18
282 283 7.332182 ACGTTGCAGAAAACAAAAATTTTCCTA 59.668 29.630 3.41 0.00 45.72 2.94
283 284 6.148645 ACGTTGCAGAAAACAAAAATTTTCCT 59.851 30.769 3.41 0.00 45.72 3.36
284 285 6.310960 ACGTTGCAGAAAACAAAAATTTTCC 58.689 32.000 3.41 0.00 45.72 3.13
285 286 7.007009 GGAACGTTGCAGAAAACAAAAATTTTC 59.993 33.333 15.52 3.34 45.18 2.29
286 287 6.799441 GGAACGTTGCAGAAAACAAAAATTTT 59.201 30.769 15.52 0.00 34.46 1.82
287 288 6.310960 GGAACGTTGCAGAAAACAAAAATTT 58.689 32.000 15.52 0.00 0.00 1.82
288 289 5.163804 GGGAACGTTGCAGAAAACAAAAATT 60.164 36.000 21.74 0.00 0.00 1.82
289 290 4.331443 GGGAACGTTGCAGAAAACAAAAAT 59.669 37.500 21.74 0.00 0.00 1.82
290 291 3.680458 GGGAACGTTGCAGAAAACAAAAA 59.320 39.130 21.74 0.00 0.00 1.94
291 292 3.254892 GGGAACGTTGCAGAAAACAAAA 58.745 40.909 21.74 0.00 0.00 2.44
292 293 2.417515 GGGGAACGTTGCAGAAAACAAA 60.418 45.455 21.74 0.00 0.00 2.83
293 294 1.135333 GGGGAACGTTGCAGAAAACAA 59.865 47.619 21.74 0.00 0.00 2.83
294 295 0.741915 GGGGAACGTTGCAGAAAACA 59.258 50.000 21.74 0.00 0.00 2.83
295 296 0.741915 TGGGGAACGTTGCAGAAAAC 59.258 50.000 21.74 2.56 0.00 2.43
296 297 1.135333 GTTGGGGAACGTTGCAGAAAA 59.865 47.619 21.74 6.84 0.00 2.29
297 298 0.741915 GTTGGGGAACGTTGCAGAAA 59.258 50.000 21.74 9.26 0.00 2.52
298 299 0.394488 TGTTGGGGAACGTTGCAGAA 60.394 50.000 21.74 10.10 0.00 3.02
299 300 0.394488 TTGTTGGGGAACGTTGCAGA 60.394 50.000 21.74 3.97 0.00 4.26
300 301 0.673437 ATTGTTGGGGAACGTTGCAG 59.327 50.000 21.74 0.00 0.00 4.41
301 302 1.883275 CTATTGTTGGGGAACGTTGCA 59.117 47.619 21.74 0.00 0.00 4.08
302 303 1.402325 GCTATTGTTGGGGAACGTTGC 60.402 52.381 11.85 11.85 0.00 4.17
303 304 1.883275 TGCTATTGTTGGGGAACGTTG 59.117 47.619 5.00 0.00 0.00 4.10
304 305 2.279935 TGCTATTGTTGGGGAACGTT 57.720 45.000 0.00 0.00 0.00 3.99
305 306 2.091541 CATGCTATTGTTGGGGAACGT 58.908 47.619 0.00 0.00 0.00 3.99
306 307 1.405105 CCATGCTATTGTTGGGGAACG 59.595 52.381 0.00 0.00 0.00 3.95
307 308 2.456577 ACCATGCTATTGTTGGGGAAC 58.543 47.619 0.00 0.00 34.72 3.62
308 309 2.917713 ACCATGCTATTGTTGGGGAA 57.082 45.000 0.00 0.00 34.72 3.97
309 310 2.917713 AACCATGCTATTGTTGGGGA 57.082 45.000 0.00 0.00 34.72 4.81
310 311 3.099141 AGAAACCATGCTATTGTTGGGG 58.901 45.455 0.00 0.00 34.72 4.96
311 312 5.829924 AGATAGAAACCATGCTATTGTTGGG 59.170 40.000 0.00 0.00 34.72 4.12
312 313 6.949352 AGATAGAAACCATGCTATTGTTGG 57.051 37.500 0.00 0.00 36.56 3.77
313 314 7.716998 AGGTAGATAGAAACCATGCTATTGTTG 59.283 37.037 0.00 0.00 38.30 3.33
314 315 7.716998 CAGGTAGATAGAAACCATGCTATTGTT 59.283 37.037 0.00 0.00 38.30 2.83
315 316 7.071196 TCAGGTAGATAGAAACCATGCTATTGT 59.929 37.037 0.00 0.00 38.30 2.71
316 317 7.445121 TCAGGTAGATAGAAACCATGCTATTG 58.555 38.462 0.00 0.00 38.30 1.90
317 318 7.291182 ACTCAGGTAGATAGAAACCATGCTATT 59.709 37.037 0.00 0.00 38.30 1.73
537 677 3.756933 AATTTGCAGTGACCATTGCTT 57.243 38.095 16.43 2.74 43.39 3.91
957 1137 1.970917 GAACGCATGGTTGGCTCTCG 61.971 60.000 4.55 0.00 39.50 4.04
1108 1288 1.656818 ATTTGCATTCCGAGGTGCCG 61.657 55.000 0.00 0.00 40.56 5.69
1302 1487 7.013178 ACACAAAATTTGAATCAATTTGGTCCC 59.987 33.333 19.82 0.00 31.56 4.46
1387 1573 1.135699 GATGCAAGCAATTGGTCGCG 61.136 55.000 15.23 0.00 0.00 5.87
1425 1685 2.007608 GATTTAACAGGAGCCGGTCAC 58.992 52.381 1.90 0.00 0.00 3.67
1462 1723 3.423154 CGGCCACCTGAAGCGAAC 61.423 66.667 2.24 0.00 0.00 3.95
1686 1947 9.738832 TCATGTATCATAAAAATCATGCTTGTG 57.261 29.630 0.00 0.00 34.56 3.33
1687 1948 9.740239 GTCATGTATCATAAAAATCATGCTTGT 57.260 29.630 0.00 0.00 34.56 3.16
1900 2171 0.313672 TTGTTTGGCCGAATGCACTC 59.686 50.000 9.15 0.00 43.89 3.51


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

AutoCloner maintained by Alex Coulton.