Multiple sequence alignment - TraesCS6A01G361000

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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 TraesCS6A01G361000 chr6A 100.000 2915 0 0 829 3743 591733881 591730967 0.000000e+00 5384
1 TraesCS6A01G361000 chr6A 100.000 540 0 0 1 540 591734709 591734170 0.000000e+00 998
2 TraesCS6A01G361000 chr6D 92.726 2667 106 47 829 3456 444138283 444135666 0.000000e+00 3770
3 TraesCS6A01G361000 chr6D 74.090 1181 275 26 1568 2734 375029269 375030432 1.230000e-124 457
4 TraesCS6A01G361000 chr6D 80.255 314 25 12 218 528 444138832 444138553 6.340000e-48 202
5 TraesCS6A01G361000 chr6B 95.658 2349 63 23 829 3158 668778574 668776246 0.000000e+00 3736
6 TraesCS6A01G361000 chr6B 83.333 198 18 12 218 403 668778983 668778789 6.430000e-38 169
7 TraesCS6A01G361000 chr4A 98.433 638 10 0 2895 3532 418180225 418179588 0.000000e+00 1123
8 TraesCS6A01G361000 chr4A 93.023 129 5 2 3615 3743 418179260 418179136 6.380000e-43 185
9 TraesCS6A01G361000 chr2A 99.346 459 3 0 3074 3532 28226393 28225935 0.000000e+00 832
10 TraesCS6A01G361000 chr2A 74.979 1203 277 19 1551 2741 727957648 727958838 1.980000e-147 532
11 TraesCS6A01G361000 chr2A 95.349 129 4 2 3615 3743 28225607 28225481 1.760000e-48 204
12 TraesCS6A01G361000 chr7A 99.129 459 4 0 3074 3532 3700748 3701206 0.000000e+00 826
13 TraesCS6A01G361000 chr7A 96.124 129 4 1 3615 3743 3701495 3701622 3.790000e-50 209
14 TraesCS6A01G361000 chr2D 74.979 1183 274 19 1553 2724 593219471 593220642 3.310000e-145 525
15 TraesCS6A01G361000 chr2B 74.874 1186 274 22 1551 2724 719473162 719474335 5.540000e-143 518
16 TraesCS6A01G361000 chr7B 93.151 219 11 3 993 1210 609643669 609643884 6.030000e-83 318


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 TraesCS6A01G361000 chr6A 591730967 591734709 3742 True 3191.0 5384 100.0000 1 3743 2 chr6A.!!$R1 3742
1 TraesCS6A01G361000 chr6D 444135666 444138832 3166 True 1986.0 3770 86.4905 218 3456 2 chr6D.!!$R1 3238
2 TraesCS6A01G361000 chr6D 375029269 375030432 1163 False 457.0 457 74.0900 1568 2734 1 chr6D.!!$F1 1166
3 TraesCS6A01G361000 chr6B 668776246 668778983 2737 True 1952.5 3736 89.4955 218 3158 2 chr6B.!!$R1 2940
4 TraesCS6A01G361000 chr4A 418179136 418180225 1089 True 654.0 1123 95.7280 2895 3743 2 chr4A.!!$R1 848
5 TraesCS6A01G361000 chr2A 727957648 727958838 1190 False 532.0 532 74.9790 1551 2741 1 chr2A.!!$F1 1190
6 TraesCS6A01G361000 chr2A 28225481 28226393 912 True 518.0 832 97.3475 3074 3743 2 chr2A.!!$R1 669
7 TraesCS6A01G361000 chr7A 3700748 3701622 874 False 517.5 826 97.6265 3074 3743 2 chr7A.!!$F1 669
8 TraesCS6A01G361000 chr2D 593219471 593220642 1171 False 525.0 525 74.9790 1553 2724 1 chr2D.!!$F1 1171
9 TraesCS6A01G361000 chr2B 719473162 719474335 1173 False 518.0 518 74.8740 1551 2724 1 chr2B.!!$F1 1173

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
196 197 0.032952 TGCGGCTAACTTTGAGTCGT 59.967 50.0 0.0 0.0 43.84 4.34 F
403 449 0.102663 TATAAATCACCGCGCCGTCA 59.897 50.0 0.0 0.0 0.00 4.35 F
2163 2212 0.035056 CCATCCCCTTCTCGCTGTTT 60.035 55.0 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2212 0.689055 AGAGCAGGATCAGCACAACA 59.311 50.0 11.35 0.0 0.00 3.33 R
2256 2308 1.305930 GGATCTGGTTTGTGCGGACC 61.306 60.0 4.04 0.0 36.45 4.46 R
3569 3711 0.679505 AGTTCTGAGCAACAGCCGTA 59.320 50.0 6.13 0.0 45.38 4.02 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
18 19 3.790795 TTTTCACGCGAACGACAAG 57.209 47.368 15.93 0.00 43.93 3.16
19 20 1.000884 TTTTCACGCGAACGACAAGT 58.999 45.000 15.93 0.00 43.93 3.16
21 22 1.837648 TTCACGCGAACGACAAGTTA 58.162 45.000 15.93 0.00 44.35 2.24
22 23 1.122849 TCACGCGAACGACAAGTTAC 58.877 50.000 15.93 0.00 44.35 2.50
23 24 0.160182 CACGCGAACGACAAGTTACC 59.840 55.000 15.93 0.00 44.35 2.85
24 25 0.248990 ACGCGAACGACAAGTTACCA 60.249 50.000 15.93 0.00 44.35 3.25
25 26 1.065358 CGCGAACGACAAGTTACCAT 58.935 50.000 0.00 0.00 44.35 3.55
26 27 1.458064 CGCGAACGACAAGTTACCATT 59.542 47.619 0.00 0.00 44.35 3.16
27 28 2.096614 CGCGAACGACAAGTTACCATTT 60.097 45.455 0.00 0.00 44.35 2.32
28 29 3.476181 GCGAACGACAAGTTACCATTTC 58.524 45.455 0.00 0.00 44.35 2.17
29 30 3.717830 CGAACGACAAGTTACCATTTCG 58.282 45.455 0.00 0.00 44.35 3.46
30 31 3.426191 CGAACGACAAGTTACCATTTCGA 59.574 43.478 0.00 0.00 44.35 3.71
31 32 4.084952 CGAACGACAAGTTACCATTTCGAA 60.085 41.667 0.00 0.00 44.35 3.71
32 33 4.720530 ACGACAAGTTACCATTTCGAAC 57.279 40.909 0.00 0.00 0.00 3.95
33 34 4.121317 ACGACAAGTTACCATTTCGAACA 58.879 39.130 0.00 0.00 0.00 3.18
34 35 4.571580 ACGACAAGTTACCATTTCGAACAA 59.428 37.500 0.00 0.00 0.00 2.83
35 36 5.237779 ACGACAAGTTACCATTTCGAACAAT 59.762 36.000 0.00 0.00 0.00 2.71
36 37 6.424509 ACGACAAGTTACCATTTCGAACAATA 59.575 34.615 0.00 0.00 0.00 1.90
37 38 6.735063 CGACAAGTTACCATTTCGAACAATAC 59.265 38.462 0.00 0.00 0.00 1.89
38 39 6.905578 ACAAGTTACCATTTCGAACAATACC 58.094 36.000 0.00 0.00 0.00 2.73
39 40 5.789710 AGTTACCATTTCGAACAATACCG 57.210 39.130 0.00 0.00 0.00 4.02
40 41 5.240121 AGTTACCATTTCGAACAATACCGT 58.760 37.500 0.00 0.00 0.00 4.83
41 42 5.121142 AGTTACCATTTCGAACAATACCGTG 59.879 40.000 0.00 0.00 0.00 4.94
42 43 3.404899 ACCATTTCGAACAATACCGTGT 58.595 40.909 0.00 0.00 0.00 4.49
43 44 3.816523 ACCATTTCGAACAATACCGTGTT 59.183 39.130 0.00 0.00 44.38 3.32
44 45 4.276431 ACCATTTCGAACAATACCGTGTTT 59.724 37.500 0.00 0.00 41.78 2.83
45 46 4.849383 CCATTTCGAACAATACCGTGTTTC 59.151 41.667 0.00 0.00 41.78 2.78
46 47 3.774282 TTCGAACAATACCGTGTTTCG 57.226 42.857 0.00 0.00 41.78 3.46
47 48 1.456544 TCGAACAATACCGTGTTTCGC 59.543 47.619 0.00 0.00 41.78 4.70
48 49 1.462869 CGAACAATACCGTGTTTCGCC 60.463 52.381 0.00 0.00 41.78 5.54
49 50 1.532007 GAACAATACCGTGTTTCGCCA 59.468 47.619 0.00 0.00 41.78 5.69
50 51 1.816074 ACAATACCGTGTTTCGCCAT 58.184 45.000 0.00 0.00 38.35 4.40
51 52 1.466950 ACAATACCGTGTTTCGCCATG 59.533 47.619 0.00 0.00 38.35 3.66
52 53 1.091537 AATACCGTGTTTCGCCATGG 58.908 50.000 7.63 7.63 45.37 3.66
53 54 1.373590 ATACCGTGTTTCGCCATGGC 61.374 55.000 27.67 27.67 43.99 4.40
54 55 2.457743 TACCGTGTTTCGCCATGGCT 62.458 55.000 33.07 14.47 43.99 4.75
55 56 2.176546 CGTGTTTCGCCATGGCTG 59.823 61.111 33.07 25.26 39.32 4.85
56 57 2.616330 CGTGTTTCGCCATGGCTGT 61.616 57.895 33.07 0.00 39.32 4.40
57 58 1.210155 GTGTTTCGCCATGGCTGTC 59.790 57.895 33.07 20.07 39.32 3.51
58 59 1.073025 TGTTTCGCCATGGCTGTCT 59.927 52.632 33.07 0.00 39.32 3.41
59 60 1.236616 TGTTTCGCCATGGCTGTCTG 61.237 55.000 33.07 18.02 39.32 3.51
60 61 1.675310 TTTCGCCATGGCTGTCTGG 60.675 57.895 33.07 17.27 39.32 3.86
64 65 2.821366 CCATGGCTGTCTGGCGAC 60.821 66.667 0.00 3.11 45.14 5.19
65 66 2.821366 CATGGCTGTCTGGCGACC 60.821 66.667 6.94 0.00 45.14 4.79
66 67 3.321648 ATGGCTGTCTGGCGACCA 61.322 61.111 6.94 0.00 45.14 4.02
67 68 2.673200 ATGGCTGTCTGGCGACCAT 61.673 57.895 0.46 0.46 45.14 3.55
68 69 2.821366 GGCTGTCTGGCGACCATG 60.821 66.667 6.94 0.00 39.47 3.66
69 70 3.503363 GCTGTCTGGCGACCATGC 61.503 66.667 6.94 5.64 39.47 4.06
81 82 4.846551 CCATGCCGATGGTCGTAA 57.153 55.556 0.00 0.00 43.98 3.18
82 83 2.307363 CCATGCCGATGGTCGTAAC 58.693 57.895 0.00 0.00 43.98 2.50
83 84 1.487452 CCATGCCGATGGTCGTAACG 61.487 60.000 0.00 0.00 43.98 3.18
84 85 0.804544 CATGCCGATGGTCGTAACGT 60.805 55.000 0.00 0.00 38.40 3.99
85 86 0.108520 ATGCCGATGGTCGTAACGTT 60.109 50.000 5.88 5.88 38.40 3.99
86 87 1.009903 TGCCGATGGTCGTAACGTTG 61.010 55.000 11.99 0.00 38.40 4.10
87 88 1.705727 CCGATGGTCGTAACGTTGC 59.294 57.895 11.99 9.00 38.40 4.17
88 89 1.339134 CGATGGTCGTAACGTTGCG 59.661 57.895 29.32 29.32 34.72 4.85
89 90 1.058284 GATGGTCGTAACGTTGCGC 59.942 57.895 30.15 23.93 36.21 6.09
90 91 1.619526 GATGGTCGTAACGTTGCGCA 61.620 55.000 30.15 23.55 36.21 6.09
91 92 1.222766 ATGGTCGTAACGTTGCGCAA 61.223 50.000 30.15 21.02 36.21 4.85
92 93 1.276250 GGTCGTAACGTTGCGCAAA 59.724 52.632 30.15 13.61 36.21 3.68
93 94 0.110554 GGTCGTAACGTTGCGCAAAT 60.111 50.000 30.15 16.44 36.21 2.32
94 95 1.660896 GGTCGTAACGTTGCGCAAATT 60.661 47.619 30.15 23.17 36.21 1.82
95 96 1.377505 GTCGTAACGTTGCGCAAATTG 59.622 47.619 30.15 19.56 36.21 2.32
96 97 1.003759 TCGTAACGTTGCGCAAATTGT 60.004 42.857 30.15 20.24 36.21 2.71
97 98 2.220363 TCGTAACGTTGCGCAAATTGTA 59.780 40.909 30.15 11.88 36.21 2.41
98 99 2.333304 CGTAACGTTGCGCAAATTGTAC 59.667 45.455 26.87 21.01 0.00 2.90
99 100 2.766970 AACGTTGCGCAAATTGTACT 57.233 40.000 26.87 7.07 0.00 2.73
100 101 2.766970 ACGTTGCGCAAATTGTACTT 57.233 40.000 26.87 2.07 0.00 2.24
101 102 2.646250 ACGTTGCGCAAATTGTACTTC 58.354 42.857 26.87 8.01 0.00 3.01
102 103 2.032302 ACGTTGCGCAAATTGTACTTCA 59.968 40.909 26.87 0.00 0.00 3.02
103 104 3.233578 CGTTGCGCAAATTGTACTTCAT 58.766 40.909 26.87 0.00 0.00 2.57
104 105 3.297979 CGTTGCGCAAATTGTACTTCATC 59.702 43.478 26.87 6.43 0.00 2.92
105 106 4.475944 GTTGCGCAAATTGTACTTCATCT 58.524 39.130 26.87 0.00 0.00 2.90
106 107 4.082274 TGCGCAAATTGTACTTCATCTG 57.918 40.909 8.16 0.00 0.00 2.90
107 108 2.848302 GCGCAAATTGTACTTCATCTGC 59.152 45.455 0.30 0.00 0.00 4.26
108 109 3.429085 CGCAAATTGTACTTCATCTGCC 58.571 45.455 0.00 0.00 0.00 4.85
109 110 3.127548 CGCAAATTGTACTTCATCTGCCT 59.872 43.478 0.00 0.00 0.00 4.75
110 111 4.332543 CGCAAATTGTACTTCATCTGCCTA 59.667 41.667 0.00 0.00 0.00 3.93
111 112 5.503031 CGCAAATTGTACTTCATCTGCCTAG 60.503 44.000 0.00 0.00 0.00 3.02
112 113 5.586243 GCAAATTGTACTTCATCTGCCTAGA 59.414 40.000 0.00 0.00 37.35 2.43
113 114 6.094048 GCAAATTGTACTTCATCTGCCTAGAA 59.906 38.462 0.00 0.00 36.32 2.10
114 115 7.678218 GCAAATTGTACTTCATCTGCCTAGAAG 60.678 40.741 0.00 0.00 43.27 2.85
115 116 6.798427 ATTGTACTTCATCTGCCTAGAAGA 57.202 37.500 8.25 0.00 40.85 2.87
116 117 5.584253 TGTACTTCATCTGCCTAGAAGAC 57.416 43.478 8.25 3.66 40.85 3.01
117 118 5.265191 TGTACTTCATCTGCCTAGAAGACT 58.735 41.667 8.25 0.00 40.85 3.24
118 119 6.424032 TGTACTTCATCTGCCTAGAAGACTA 58.576 40.000 8.25 0.00 40.85 2.59
119 120 6.890268 TGTACTTCATCTGCCTAGAAGACTAA 59.110 38.462 8.25 0.00 40.85 2.24
120 121 7.561722 TGTACTTCATCTGCCTAGAAGACTAAT 59.438 37.037 8.25 0.00 40.85 1.73
121 122 6.815089 ACTTCATCTGCCTAGAAGACTAATG 58.185 40.000 8.25 0.00 40.85 1.90
122 123 6.609212 ACTTCATCTGCCTAGAAGACTAATGA 59.391 38.462 8.25 0.00 40.85 2.57
123 124 7.124901 ACTTCATCTGCCTAGAAGACTAATGAA 59.875 37.037 8.25 1.01 40.85 2.57
124 125 7.423844 TCATCTGCCTAGAAGACTAATGAAA 57.576 36.000 0.00 0.00 36.32 2.69
125 126 8.027524 TCATCTGCCTAGAAGACTAATGAAAT 57.972 34.615 0.00 0.00 36.32 2.17
126 127 8.489489 TCATCTGCCTAGAAGACTAATGAAATT 58.511 33.333 0.00 0.00 37.06 1.82
127 128 8.772705 CATCTGCCTAGAAGACTAATGAAATTC 58.227 37.037 0.00 0.00 35.46 2.17
128 129 7.851228 TCTGCCTAGAAGACTAATGAAATTCA 58.149 34.615 0.00 0.00 37.87 2.57
129 130 8.489489 TCTGCCTAGAAGACTAATGAAATTCAT 58.511 33.333 2.07 2.07 39.09 2.57
131 132 9.466497 TGCCTAGAAGACTAATGAAATTCATTT 57.534 29.630 23.98 9.31 44.03 2.32
132 133 9.943163 GCCTAGAAGACTAATGAAATTCATTTC 57.057 33.333 23.98 16.78 44.03 2.17
136 137 9.219603 AGAAGACTAATGAAATTCATTTCGTGA 57.780 29.630 23.98 7.15 44.03 4.35
137 138 9.483062 GAAGACTAATGAAATTCATTTCGTGAG 57.517 33.333 23.98 17.16 44.03 3.51
144 145 6.817396 TGAAATTCATTTCGTGAGTAGTTCG 58.183 36.000 7.59 0.00 46.92 3.95
145 146 6.422701 TGAAATTCATTTCGTGAGTAGTTCGT 59.577 34.615 7.59 0.00 46.92 3.85
146 147 6.780706 AATTCATTTCGTGAGTAGTTCGTT 57.219 33.333 0.00 0.00 38.29 3.85
147 148 5.570262 TTCATTTCGTGAGTAGTTCGTTG 57.430 39.130 0.00 0.00 38.29 4.10
148 149 4.862350 TCATTTCGTGAGTAGTTCGTTGA 58.138 39.130 0.00 0.00 31.80 3.18
149 150 5.466819 TCATTTCGTGAGTAGTTCGTTGAT 58.533 37.500 0.00 0.00 31.80 2.57
150 151 5.571741 TCATTTCGTGAGTAGTTCGTTGATC 59.428 40.000 0.00 0.00 31.80 2.92
151 152 3.482722 TCGTGAGTAGTTCGTTGATCC 57.517 47.619 0.00 0.00 0.00 3.36
152 153 2.163010 TCGTGAGTAGTTCGTTGATCCC 59.837 50.000 0.00 0.00 0.00 3.85
153 154 2.163815 CGTGAGTAGTTCGTTGATCCCT 59.836 50.000 0.00 0.00 0.00 4.20
154 155 3.376234 CGTGAGTAGTTCGTTGATCCCTA 59.624 47.826 0.00 0.00 0.00 3.53
155 156 4.036498 CGTGAGTAGTTCGTTGATCCCTAT 59.964 45.833 0.00 0.00 0.00 2.57
156 157 5.521544 GTGAGTAGTTCGTTGATCCCTATC 58.478 45.833 0.00 0.00 0.00 2.08
157 158 4.583489 TGAGTAGTTCGTTGATCCCTATCC 59.417 45.833 0.00 0.00 0.00 2.59
158 159 4.805744 AGTAGTTCGTTGATCCCTATCCT 58.194 43.478 0.00 0.00 0.00 3.24
159 160 4.828387 AGTAGTTCGTTGATCCCTATCCTC 59.172 45.833 0.00 0.00 0.00 3.71
160 161 3.643237 AGTTCGTTGATCCCTATCCTCA 58.357 45.455 0.00 0.00 0.00 3.86
161 162 3.639094 AGTTCGTTGATCCCTATCCTCAG 59.361 47.826 0.00 0.00 0.00 3.35
162 163 3.314307 TCGTTGATCCCTATCCTCAGT 57.686 47.619 0.00 0.00 0.00 3.41
163 164 3.643237 TCGTTGATCCCTATCCTCAGTT 58.357 45.455 0.00 0.00 0.00 3.16
164 165 3.384789 TCGTTGATCCCTATCCTCAGTTG 59.615 47.826 0.00 0.00 0.00 3.16
165 166 3.384789 CGTTGATCCCTATCCTCAGTTGA 59.615 47.826 0.00 0.00 0.00 3.18
166 167 4.698575 GTTGATCCCTATCCTCAGTTGAC 58.301 47.826 0.00 0.00 0.00 3.18
167 168 3.994317 TGATCCCTATCCTCAGTTGACA 58.006 45.455 0.00 0.00 0.00 3.58
168 169 3.706594 TGATCCCTATCCTCAGTTGACAC 59.293 47.826 0.00 0.00 0.00 3.67
169 170 2.100197 TCCCTATCCTCAGTTGACACG 58.900 52.381 0.00 0.00 0.00 4.49
170 171 1.825474 CCCTATCCTCAGTTGACACGT 59.175 52.381 0.00 0.00 0.00 4.49
171 172 2.417379 CCCTATCCTCAGTTGACACGTG 60.417 54.545 15.48 15.48 0.00 4.49
172 173 2.417379 CCTATCCTCAGTTGACACGTGG 60.417 54.545 21.57 0.08 0.00 4.94
173 174 1.338107 ATCCTCAGTTGACACGTGGA 58.662 50.000 21.57 4.03 0.00 4.02
174 175 0.673985 TCCTCAGTTGACACGTGGAG 59.326 55.000 21.57 14.58 0.00 3.86
175 176 0.946221 CCTCAGTTGACACGTGGAGC 60.946 60.000 21.57 9.38 0.00 4.70
191 192 3.249999 GCGTGCGGCTAACTTTGA 58.750 55.556 0.00 0.00 39.11 2.69
192 193 1.132640 GCGTGCGGCTAACTTTGAG 59.867 57.895 0.00 0.00 39.11 3.02
193 194 1.566018 GCGTGCGGCTAACTTTGAGT 61.566 55.000 0.00 0.00 39.11 3.41
194 195 0.438830 CGTGCGGCTAACTTTGAGTC 59.561 55.000 0.00 0.00 0.00 3.36
195 196 0.438830 GTGCGGCTAACTTTGAGTCG 59.561 55.000 0.00 0.00 44.76 4.18
196 197 0.032952 TGCGGCTAACTTTGAGTCGT 59.967 50.000 0.00 0.00 43.84 4.34
197 198 1.145803 GCGGCTAACTTTGAGTCGTT 58.854 50.000 0.00 0.00 43.84 3.85
198 199 1.126296 GCGGCTAACTTTGAGTCGTTC 59.874 52.381 0.00 0.00 43.84 3.95
199 200 2.673833 CGGCTAACTTTGAGTCGTTCT 58.326 47.619 0.00 0.00 37.26 3.01
200 201 2.408704 CGGCTAACTTTGAGTCGTTCTG 59.591 50.000 0.00 0.00 37.26 3.02
201 202 3.391049 GGCTAACTTTGAGTCGTTCTGT 58.609 45.455 0.00 0.00 0.00 3.41
202 203 3.808174 GGCTAACTTTGAGTCGTTCTGTT 59.192 43.478 0.00 0.00 0.00 3.16
203 204 4.272748 GGCTAACTTTGAGTCGTTCTGTTT 59.727 41.667 0.00 0.00 0.00 2.83
204 205 5.433005 GCTAACTTTGAGTCGTTCTGTTTC 58.567 41.667 0.00 0.00 0.00 2.78
205 206 4.877323 AACTTTGAGTCGTTCTGTTTCC 57.123 40.909 0.00 0.00 0.00 3.13
206 207 2.864343 ACTTTGAGTCGTTCTGTTTCCG 59.136 45.455 0.00 0.00 0.00 4.30
207 208 2.875087 TTGAGTCGTTCTGTTTCCGA 57.125 45.000 0.00 0.00 0.00 4.55
210 211 3.582743 GTCGTTCTGTTTCCGACCT 57.417 52.632 0.00 0.00 43.77 3.85
211 212 1.861971 GTCGTTCTGTTTCCGACCTT 58.138 50.000 0.00 0.00 43.77 3.50
212 213 2.207590 GTCGTTCTGTTTCCGACCTTT 58.792 47.619 0.00 0.00 43.77 3.11
213 214 3.383761 GTCGTTCTGTTTCCGACCTTTA 58.616 45.455 0.00 0.00 43.77 1.85
214 215 3.183172 GTCGTTCTGTTTCCGACCTTTAC 59.817 47.826 0.00 0.00 43.77 2.01
215 216 3.068590 TCGTTCTGTTTCCGACCTTTACT 59.931 43.478 0.00 0.00 0.00 2.24
216 217 3.805971 CGTTCTGTTTCCGACCTTTACTT 59.194 43.478 0.00 0.00 0.00 2.24
228 229 5.144359 CGACCTTTACTTCGGATTTTTGTG 58.856 41.667 0.00 0.00 0.00 3.33
259 260 0.248296 TCAAAAACTTGTGCGGCGTC 60.248 50.000 9.37 0.91 0.00 5.19
362 408 1.751927 CCATCCCCAAGCAGAGCAC 60.752 63.158 0.00 0.00 0.00 4.40
389 435 1.135024 GTCACCCTCACGCCGTATAAA 60.135 52.381 0.00 0.00 0.00 1.40
390 436 1.758280 TCACCCTCACGCCGTATAAAT 59.242 47.619 0.00 0.00 0.00 1.40
391 437 2.132762 CACCCTCACGCCGTATAAATC 58.867 52.381 0.00 0.00 0.00 2.17
392 438 1.758280 ACCCTCACGCCGTATAAATCA 59.242 47.619 0.00 0.00 0.00 2.57
393 439 2.132762 CCCTCACGCCGTATAAATCAC 58.867 52.381 0.00 0.00 0.00 3.06
394 440 2.132762 CCTCACGCCGTATAAATCACC 58.867 52.381 0.00 0.00 0.00 4.02
395 441 1.784856 CTCACGCCGTATAAATCACCG 59.215 52.381 0.00 0.00 0.00 4.94
396 442 0.231279 CACGCCGTATAAATCACCGC 59.769 55.000 0.00 0.00 0.00 5.68
397 443 1.210545 ACGCCGTATAAATCACCGCG 61.211 55.000 0.00 0.00 45.12 6.46
398 444 1.203313 GCCGTATAAATCACCGCGC 59.797 57.895 0.00 0.00 0.00 6.86
399 445 1.857364 CCGTATAAATCACCGCGCC 59.143 57.895 0.00 0.00 0.00 6.53
400 446 1.485514 CGTATAAATCACCGCGCCG 59.514 57.895 0.00 0.00 0.00 6.46
401 447 1.210545 CGTATAAATCACCGCGCCGT 61.211 55.000 0.00 0.00 0.00 5.68
402 448 0.505655 GTATAAATCACCGCGCCGTC 59.494 55.000 0.00 0.00 0.00 4.79
403 449 0.102663 TATAAATCACCGCGCCGTCA 59.897 50.000 0.00 0.00 0.00 4.35
404 450 1.426041 ATAAATCACCGCGCCGTCAC 61.426 55.000 0.00 0.00 0.00 3.67
416 462 3.740397 CGTCACCCTCACGCCGTA 61.740 66.667 0.00 0.00 0.00 4.02
417 463 2.890371 GTCACCCTCACGCCGTAT 59.110 61.111 0.00 0.00 0.00 3.06
418 464 1.717791 CGTCACCCTCACGCCGTATA 61.718 60.000 0.00 0.00 0.00 1.47
419 465 0.457035 GTCACCCTCACGCCGTATAA 59.543 55.000 0.00 0.00 0.00 0.98
420 466 1.135024 GTCACCCTCACGCCGTATAAA 60.135 52.381 0.00 0.00 0.00 1.40
421 467 1.135024 TCACCCTCACGCCGTATAAAC 60.135 52.381 0.00 0.00 0.00 2.01
422 468 0.176449 ACCCTCACGCCGTATAAACC 59.824 55.000 0.00 0.00 0.00 3.27
423 469 0.176219 CCCTCACGCCGTATAAACCA 59.824 55.000 0.00 0.00 0.00 3.67
424 470 1.283736 CCTCACGCCGTATAAACCAC 58.716 55.000 0.00 0.00 0.00 4.16
425 471 1.283736 CTCACGCCGTATAAACCACC 58.716 55.000 0.00 0.00 0.00 4.61
426 472 0.458197 TCACGCCGTATAAACCACCG 60.458 55.000 0.00 0.00 0.00 4.94
427 473 1.810853 ACGCCGTATAAACCACCGC 60.811 57.895 0.00 0.00 0.00 5.68
428 474 2.527867 CGCCGTATAAACCACCGCC 61.528 63.158 0.00 0.00 0.00 6.13
429 475 2.182181 GCCGTATAAACCACCGCCC 61.182 63.158 0.00 0.00 0.00 6.13
430 476 1.524393 CCGTATAAACCACCGCCCC 60.524 63.158 0.00 0.00 0.00 5.80
431 477 1.221293 CGTATAAACCACCGCCCCA 59.779 57.895 0.00 0.00 0.00 4.96
432 478 1.091197 CGTATAAACCACCGCCCCAC 61.091 60.000 0.00 0.00 0.00 4.61
433 479 0.749091 GTATAAACCACCGCCCCACC 60.749 60.000 0.00 0.00 0.00 4.61
434 480 1.206135 TATAAACCACCGCCCCACCA 61.206 55.000 0.00 0.00 0.00 4.17
435 481 2.082836 ATAAACCACCGCCCCACCAA 62.083 55.000 0.00 0.00 0.00 3.67
436 482 2.980105 TAAACCACCGCCCCACCAAC 62.980 60.000 0.00 0.00 0.00 3.77
987 1036 2.811317 GACAGCGCGGAGAACCTG 60.811 66.667 16.26 8.01 0.00 4.00
1476 1525 2.665777 CGTCAAGATGTACGGCAGG 58.334 57.895 0.00 0.00 35.51 4.85
1728 1777 2.583593 GTCAGGCGCGATCTCACC 60.584 66.667 12.10 0.00 0.00 4.02
2163 2212 0.035056 CCATCCCCTTCTCGCTGTTT 60.035 55.000 0.00 0.00 0.00 2.83
2226 2275 4.065281 CTCGTCGGCGGGTTCCTT 62.065 66.667 10.62 0.00 38.89 3.36
2256 2308 2.278596 CCGCACATCGAGTACCCG 60.279 66.667 0.00 0.00 41.67 5.28
2280 2332 2.746277 ACAAACCAGATCCCGCGC 60.746 61.111 0.00 0.00 0.00 6.86
2640 2692 0.183014 CCCTCTACCTCGGCTACTCA 59.817 60.000 0.00 0.00 0.00 3.41
2746 2798 3.751698 GTCTGTGAAGGCCGATTAAGTTT 59.248 43.478 0.00 0.00 0.00 2.66
2756 2811 3.000727 CCGATTAAGTTTCTCCTTGCGT 58.999 45.455 0.00 0.00 0.00 5.24
2760 2815 2.341846 AAGTTTCTCCTTGCGTGGAA 57.658 45.000 0.00 0.00 35.43 3.53
2764 2819 2.749621 GTTTCTCCTTGCGTGGAATGAT 59.250 45.455 0.00 0.00 35.43 2.45
2796 2851 3.034635 AGAGGTGAGTAAGCATAGTGGG 58.965 50.000 0.00 0.00 0.00 4.61
2797 2852 2.103263 GAGGTGAGTAAGCATAGTGGGG 59.897 54.545 0.00 0.00 0.00 4.96
2812 2868 0.189574 TGGGGAGTGGGCATTGAAAA 59.810 50.000 0.00 0.00 0.00 2.29
2839 2901 4.077108 TGTAGTCATCACAGTCGGTAGTT 58.923 43.478 0.00 0.00 0.00 2.24
2891 2953 9.712305 CTGAATAACTATTTGTATGGTCTAGGG 57.288 37.037 0.00 0.00 0.00 3.53
3041 3109 3.862845 GCAAGCTTAGTAGTGCTCTTCTC 59.137 47.826 0.00 0.00 38.75 2.87
3532 3627 5.739752 TGTTGAGAGTGTCTGACAAATTG 57.260 39.130 12.81 0.00 0.00 2.32
3533 3628 5.185454 TGTTGAGAGTGTCTGACAAATTGT 58.815 37.500 12.81 0.00 0.00 2.71
3534 3629 5.647658 TGTTGAGAGTGTCTGACAAATTGTT 59.352 36.000 12.81 0.00 0.00 2.83
3535 3630 5.739752 TGAGAGTGTCTGACAAATTGTTG 57.260 39.130 12.81 0.00 40.84 3.33
3536 3631 4.576053 TGAGAGTGTCTGACAAATTGTTGG 59.424 41.667 12.81 0.00 39.22 3.77
3537 3632 3.885297 AGAGTGTCTGACAAATTGTTGGG 59.115 43.478 12.81 0.00 39.22 4.12
3544 3686 6.071334 TGTCTGACAAATTGTTGGGTTTTGTA 60.071 34.615 8.27 0.00 42.07 2.41
3546 3688 7.169140 GTCTGACAAATTGTTGGGTTTTGTATC 59.831 37.037 0.00 0.00 42.07 2.24
3549 3691 7.708752 TGACAAATTGTTGGGTTTTGTATCTTC 59.291 33.333 0.00 0.00 42.07 2.87
3550 3692 6.989759 ACAAATTGTTGGGTTTTGTATCTTCC 59.010 34.615 0.00 0.00 40.68 3.46
3552 3694 5.782893 TTGTTGGGTTTTGTATCTTCCTG 57.217 39.130 0.00 0.00 0.00 3.86
3553 3695 4.148838 TGTTGGGTTTTGTATCTTCCTGG 58.851 43.478 0.00 0.00 0.00 4.45
3558 3700 3.010250 GGTTTTGTATCTTCCTGGGAGGT 59.990 47.826 1.19 0.00 36.53 3.85
3559 3701 4.508584 GGTTTTGTATCTTCCTGGGAGGTT 60.509 45.833 1.19 0.00 36.53 3.50
3560 3702 4.301072 TTTGTATCTTCCTGGGAGGTTG 57.699 45.455 1.19 0.00 36.53 3.77
3561 3703 2.915869 TGTATCTTCCTGGGAGGTTGT 58.084 47.619 1.19 0.00 36.53 3.32
3563 3705 2.887151 ATCTTCCTGGGAGGTTGTTG 57.113 50.000 1.19 0.00 36.53 3.33
3564 3706 1.518367 TCTTCCTGGGAGGTTGTTGT 58.482 50.000 1.19 0.00 36.53 3.32
3566 3708 2.243736 TCTTCCTGGGAGGTTGTTGTTT 59.756 45.455 1.19 0.00 36.53 2.83
3567 3709 2.838637 TCCTGGGAGGTTGTTGTTTT 57.161 45.000 0.00 0.00 36.53 2.43
3586 3728 2.248280 TTTACGGCTGTTGCTCAGAA 57.752 45.000 1.99 0.00 46.27 3.02
3587 3729 1.508632 TTACGGCTGTTGCTCAGAAC 58.491 50.000 1.99 0.00 46.27 3.01
3589 3731 0.679505 ACGGCTGTTGCTCAGAACTA 59.320 50.000 12.29 0.00 46.27 2.24
3593 3735 3.932710 CGGCTGTTGCTCAGAACTATTTA 59.067 43.478 12.29 0.00 46.27 1.40
3594 3736 4.201724 CGGCTGTTGCTCAGAACTATTTAC 60.202 45.833 12.29 0.00 46.27 2.01
3595 3737 4.201724 GGCTGTTGCTCAGAACTATTTACG 60.202 45.833 12.29 0.00 46.27 3.18
3596 3738 4.201724 GCTGTTGCTCAGAACTATTTACGG 60.202 45.833 12.29 0.00 46.27 4.02
3597 3739 3.682858 TGTTGCTCAGAACTATTTACGGC 59.317 43.478 0.00 0.00 0.00 5.68
3599 3741 3.521560 TGCTCAGAACTATTTACGGCTG 58.478 45.455 0.00 0.00 0.00 4.85
3601 3743 3.933332 GCTCAGAACTATTTACGGCTGTT 59.067 43.478 1.99 0.00 0.00 3.16
3602 3744 5.107133 GCTCAGAACTATTTACGGCTGTTA 58.893 41.667 1.99 0.00 0.00 2.41
3603 3745 5.005490 GCTCAGAACTATTTACGGCTGTTAC 59.995 44.000 1.99 0.00 0.00 2.50
3604 3746 6.028146 TCAGAACTATTTACGGCTGTTACA 57.972 37.500 1.99 0.00 0.00 2.41
3605 3747 6.457355 TCAGAACTATTTACGGCTGTTACAA 58.543 36.000 1.99 0.00 0.00 2.41
3606 3748 6.930164 TCAGAACTATTTACGGCTGTTACAAA 59.070 34.615 1.99 0.00 0.00 2.83
3607 3749 7.604927 TCAGAACTATTTACGGCTGTTACAAAT 59.395 33.333 1.99 6.82 0.00 2.32
3608 3750 8.234546 CAGAACTATTTACGGCTGTTACAAATT 58.765 33.333 1.99 0.00 0.00 1.82
3611 3753 7.878036 ACTATTTACGGCTGTTACAAATTGTT 58.122 30.769 1.99 0.00 0.00 2.83
3613 3755 3.363341 ACGGCTGTTACAAATTGTTGG 57.637 42.857 3.17 0.00 39.22 3.77
3619 3958 5.220758 GGCTGTTACAAATTGTTGGGTTTTG 60.221 40.000 3.17 0.00 39.22 2.44
3622 3961 5.582665 TGTTACAAATTGTTGGGTTTTGCTC 59.417 36.000 3.17 0.00 39.22 4.26
3625 3964 4.081198 ACAAATTGTTGGGTTTTGCTCAGA 60.081 37.500 0.00 0.00 39.22 3.27
3627 3966 3.518634 TTGTTGGGTTTTGCTCAGAAC 57.481 42.857 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.000884 ACTTGTCGTTCGCGTGAAAA 58.999 45.000 13.92 3.15 42.11 2.29
1 2 1.000884 AACTTGTCGTTCGCGTGAAA 58.999 45.000 13.92 0.00 42.11 2.69
2 3 1.518102 GTAACTTGTCGTTCGCGTGAA 59.482 47.619 7.45 7.45 42.11 3.18
3 4 1.122849 GTAACTTGTCGTTCGCGTGA 58.877 50.000 5.77 0.00 42.11 4.35
4 5 0.160182 GGTAACTTGTCGTTCGCGTG 59.840 55.000 5.77 0.00 42.11 5.34
5 6 0.248990 TGGTAACTTGTCGTTCGCGT 60.249 50.000 5.77 0.00 38.78 6.01
6 7 1.065358 ATGGTAACTTGTCGTTCGCG 58.935 50.000 0.00 0.00 37.05 5.87
7 8 3.476181 GAAATGGTAACTTGTCGTTCGC 58.524 45.455 0.00 0.00 37.05 4.70
8 9 3.717830 CGAAATGGTAACTTGTCGTTCG 58.282 45.455 0.00 0.00 44.20 3.95
13 14 7.019418 GGTATTGTTCGAAATGGTAACTTGTC 58.981 38.462 0.00 0.00 37.61 3.18
14 15 6.347888 CGGTATTGTTCGAAATGGTAACTTGT 60.348 38.462 0.00 0.00 37.61 3.16
15 16 6.019152 CGGTATTGTTCGAAATGGTAACTTG 58.981 40.000 0.00 0.00 37.61 3.16
16 17 5.702209 ACGGTATTGTTCGAAATGGTAACTT 59.298 36.000 0.00 0.00 37.61 2.66
17 18 5.121142 CACGGTATTGTTCGAAATGGTAACT 59.879 40.000 0.00 0.00 37.61 2.24
18 19 5.106987 ACACGGTATTGTTCGAAATGGTAAC 60.107 40.000 0.00 0.00 0.00 2.50
19 20 4.996122 ACACGGTATTGTTCGAAATGGTAA 59.004 37.500 0.00 0.00 0.00 2.85
20 21 4.567971 ACACGGTATTGTTCGAAATGGTA 58.432 39.130 0.00 0.00 0.00 3.25
21 22 3.404899 ACACGGTATTGTTCGAAATGGT 58.595 40.909 0.00 0.00 0.00 3.55
22 23 4.413495 AACACGGTATTGTTCGAAATGG 57.587 40.909 0.00 0.00 34.48 3.16
23 24 4.548077 CGAAACACGGTATTGTTCGAAATG 59.452 41.667 0.00 0.00 38.82 2.32
24 25 4.704457 CGAAACACGGTATTGTTCGAAAT 58.296 39.130 0.00 0.00 38.82 2.17
25 26 3.604314 GCGAAACACGGTATTGTTCGAAA 60.604 43.478 0.00 0.00 38.82 3.46
26 27 2.096811 GCGAAACACGGTATTGTTCGAA 60.097 45.455 14.72 0.00 38.82 3.71
27 28 1.456544 GCGAAACACGGTATTGTTCGA 59.543 47.619 14.72 0.00 38.82 3.71
28 29 1.462869 GGCGAAACACGGTATTGTTCG 60.463 52.381 9.11 9.11 38.82 3.95
29 30 1.532007 TGGCGAAACACGGTATTGTTC 59.468 47.619 0.00 0.00 38.82 3.18
30 31 1.595466 TGGCGAAACACGGTATTGTT 58.405 45.000 0.00 0.00 41.62 2.83
31 32 1.466950 CATGGCGAAACACGGTATTGT 59.533 47.619 0.00 0.00 42.83 2.71
32 33 1.202132 CCATGGCGAAACACGGTATTG 60.202 52.381 0.00 0.00 42.83 1.90
33 34 1.091537 CCATGGCGAAACACGGTATT 58.908 50.000 0.00 0.00 42.83 1.89
34 35 1.373590 GCCATGGCGAAACACGGTAT 61.374 55.000 23.48 0.00 42.83 2.73
35 36 2.036006 GCCATGGCGAAACACGGTA 61.036 57.895 23.48 0.00 42.83 4.02
36 37 3.361977 GCCATGGCGAAACACGGT 61.362 61.111 23.48 0.00 42.83 4.83
47 48 2.821366 GTCGCCAGACAGCCATGG 60.821 66.667 7.63 7.63 46.32 3.66
65 66 0.804544 ACGTTACGACCATCGGCATG 60.805 55.000 13.03 0.00 45.59 4.06
66 67 0.108520 AACGTTACGACCATCGGCAT 60.109 50.000 13.03 0.00 45.59 4.40
67 68 1.009903 CAACGTTACGACCATCGGCA 61.010 55.000 13.03 0.00 45.59 5.69
68 69 1.705727 CAACGTTACGACCATCGGC 59.294 57.895 13.03 0.00 45.59 5.54
69 70 1.705727 GCAACGTTACGACCATCGG 59.294 57.895 13.03 0.00 45.59 4.18
70 71 1.339134 CGCAACGTTACGACCATCG 59.661 57.895 15.77 3.69 46.93 3.84
71 72 1.058284 GCGCAACGTTACGACCATC 59.942 57.895 24.35 2.47 0.00 3.51
72 73 1.222766 TTGCGCAACGTTACGACCAT 61.223 50.000 24.35 0.00 0.00 3.55
73 74 1.426816 TTTGCGCAACGTTACGACCA 61.427 50.000 24.99 10.79 0.00 4.02
74 75 0.110554 ATTTGCGCAACGTTACGACC 60.111 50.000 24.99 8.23 0.00 4.79
75 76 1.377505 CAATTTGCGCAACGTTACGAC 59.622 47.619 24.99 15.16 0.00 4.34
76 77 1.003759 ACAATTTGCGCAACGTTACGA 60.004 42.857 24.99 6.61 0.00 3.43
77 78 1.390820 ACAATTTGCGCAACGTTACG 58.609 45.000 24.99 16.46 0.00 3.18
78 79 3.547601 AGTACAATTTGCGCAACGTTAC 58.452 40.909 24.99 19.74 0.00 2.50
79 80 3.881780 AGTACAATTTGCGCAACGTTA 57.118 38.095 24.99 8.80 0.00 3.18
80 81 2.766970 AGTACAATTTGCGCAACGTT 57.233 40.000 24.99 17.75 0.00 3.99
81 82 2.032302 TGAAGTACAATTTGCGCAACGT 59.968 40.909 24.99 21.47 0.00 3.99
82 83 2.645163 TGAAGTACAATTTGCGCAACG 58.355 42.857 24.99 16.66 0.00 4.10
83 84 4.321745 CAGATGAAGTACAATTTGCGCAAC 59.678 41.667 24.99 11.35 0.00 4.17
84 85 4.475028 CAGATGAAGTACAATTTGCGCAA 58.525 39.130 21.02 21.02 0.00 4.85
85 86 3.670359 GCAGATGAAGTACAATTTGCGCA 60.670 43.478 5.66 5.66 0.00 6.09
86 87 2.848302 GCAGATGAAGTACAATTTGCGC 59.152 45.455 0.00 0.00 0.00 6.09
87 88 3.127548 AGGCAGATGAAGTACAATTTGCG 59.872 43.478 0.00 0.00 35.53 4.85
88 89 4.708726 AGGCAGATGAAGTACAATTTGC 57.291 40.909 9.07 9.07 34.66 3.68
89 90 7.550551 TCTTCTAGGCAGATGAAGTACAATTTG 59.449 37.037 0.00 0.00 38.52 2.32
90 91 7.550906 GTCTTCTAGGCAGATGAAGTACAATTT 59.449 37.037 0.00 0.00 36.88 1.82
91 92 7.044798 GTCTTCTAGGCAGATGAAGTACAATT 58.955 38.462 0.00 0.00 36.88 2.32
92 93 6.382570 AGTCTTCTAGGCAGATGAAGTACAAT 59.617 38.462 0.00 0.00 36.88 2.71
93 94 5.717178 AGTCTTCTAGGCAGATGAAGTACAA 59.283 40.000 0.00 0.00 36.88 2.41
94 95 5.265191 AGTCTTCTAGGCAGATGAAGTACA 58.735 41.667 0.00 0.00 36.88 2.90
95 96 5.845391 AGTCTTCTAGGCAGATGAAGTAC 57.155 43.478 0.00 0.00 36.88 2.73
96 97 7.780271 TCATTAGTCTTCTAGGCAGATGAAGTA 59.220 37.037 0.00 1.74 36.88 2.24
97 98 6.609212 TCATTAGTCTTCTAGGCAGATGAAGT 59.391 38.462 0.00 2.39 36.88 3.01
98 99 7.048629 TCATTAGTCTTCTAGGCAGATGAAG 57.951 40.000 0.00 0.00 36.88 3.02
99 100 7.423844 TTCATTAGTCTTCTAGGCAGATGAA 57.576 36.000 0.00 0.00 36.88 2.57
100 101 7.423844 TTTCATTAGTCTTCTAGGCAGATGA 57.576 36.000 0.00 0.00 33.73 2.92
101 102 8.674263 AATTTCATTAGTCTTCTAGGCAGATG 57.326 34.615 0.00 0.00 0.00 2.90
102 103 8.489489 TGAATTTCATTAGTCTTCTAGGCAGAT 58.511 33.333 0.00 0.00 0.00 2.90
103 104 7.851228 TGAATTTCATTAGTCTTCTAGGCAGA 58.149 34.615 0.00 0.00 0.00 4.26
104 105 8.674263 ATGAATTTCATTAGTCTTCTAGGCAG 57.326 34.615 6.06 0.00 32.13 4.85
105 106 9.466497 AAATGAATTTCATTAGTCTTCTAGGCA 57.534 29.630 21.68 0.00 45.57 4.75
106 107 9.943163 GAAATGAATTTCATTAGTCTTCTAGGC 57.057 33.333 21.68 0.00 45.57 3.93
110 111 9.219603 TCACGAAATGAATTTCATTAGTCTTCT 57.780 29.630 21.68 7.35 45.57 2.85
111 112 9.483062 CTCACGAAATGAATTTCATTAGTCTTC 57.517 33.333 21.68 14.87 45.57 2.87
112 113 9.003658 ACTCACGAAATGAATTTCATTAGTCTT 57.996 29.630 21.68 9.99 45.57 3.01
113 114 8.553459 ACTCACGAAATGAATTTCATTAGTCT 57.447 30.769 21.68 8.95 45.57 3.24
114 115 9.907576 CTACTCACGAAATGAATTTCATTAGTC 57.092 33.333 21.68 16.03 45.57 2.59
115 116 9.436957 ACTACTCACGAAATGAATTTCATTAGT 57.563 29.630 21.68 20.83 45.57 2.24
119 120 7.117812 ACGAACTACTCACGAAATGAATTTCAT 59.882 33.333 14.41 6.06 44.83 2.57
120 121 6.422701 ACGAACTACTCACGAAATGAATTTCA 59.577 34.615 14.41 0.75 44.83 2.69
121 122 6.818416 ACGAACTACTCACGAAATGAATTTC 58.182 36.000 5.81 5.81 42.00 2.17
122 123 6.780706 ACGAACTACTCACGAAATGAATTT 57.219 33.333 0.00 0.00 36.69 1.82
123 124 6.422701 TCAACGAACTACTCACGAAATGAATT 59.577 34.615 0.00 0.00 36.69 2.17
124 125 5.924254 TCAACGAACTACTCACGAAATGAAT 59.076 36.000 0.00 0.00 36.69 2.57
125 126 5.283294 TCAACGAACTACTCACGAAATGAA 58.717 37.500 0.00 0.00 36.69 2.57
126 127 4.862350 TCAACGAACTACTCACGAAATGA 58.138 39.130 0.00 0.00 35.45 2.57
127 128 5.220228 GGATCAACGAACTACTCACGAAATG 60.220 44.000 0.00 0.00 0.00 2.32
128 129 4.863131 GGATCAACGAACTACTCACGAAAT 59.137 41.667 0.00 0.00 0.00 2.17
129 130 4.232221 GGATCAACGAACTACTCACGAAA 58.768 43.478 0.00 0.00 0.00 3.46
130 131 3.366679 GGGATCAACGAACTACTCACGAA 60.367 47.826 0.00 0.00 0.00 3.85
131 132 2.163010 GGGATCAACGAACTACTCACGA 59.837 50.000 0.00 0.00 0.00 4.35
132 133 2.163815 AGGGATCAACGAACTACTCACG 59.836 50.000 0.00 0.00 0.00 4.35
133 134 3.870633 AGGGATCAACGAACTACTCAC 57.129 47.619 0.00 0.00 0.00 3.51
134 135 4.583489 GGATAGGGATCAACGAACTACTCA 59.417 45.833 0.00 0.00 33.27 3.41
135 136 4.828387 AGGATAGGGATCAACGAACTACTC 59.172 45.833 0.00 0.00 33.27 2.59
136 137 4.805744 AGGATAGGGATCAACGAACTACT 58.194 43.478 0.00 0.00 33.27 2.57
137 138 4.583489 TGAGGATAGGGATCAACGAACTAC 59.417 45.833 0.00 0.00 33.27 2.73
138 139 4.800023 TGAGGATAGGGATCAACGAACTA 58.200 43.478 0.00 0.00 33.27 2.24
139 140 3.639094 CTGAGGATAGGGATCAACGAACT 59.361 47.826 0.00 0.00 33.27 3.01
140 141 3.385111 ACTGAGGATAGGGATCAACGAAC 59.615 47.826 0.00 0.00 33.27 3.95
141 142 3.643237 ACTGAGGATAGGGATCAACGAA 58.357 45.455 0.00 0.00 33.27 3.85
142 143 3.314307 ACTGAGGATAGGGATCAACGA 57.686 47.619 0.00 0.00 33.27 3.85
143 144 3.384789 TCAACTGAGGATAGGGATCAACG 59.615 47.826 0.00 0.00 33.27 4.10
144 145 4.162320 TGTCAACTGAGGATAGGGATCAAC 59.838 45.833 0.00 0.00 33.27 3.18
145 146 4.162320 GTGTCAACTGAGGATAGGGATCAA 59.838 45.833 0.00 0.00 33.27 2.57
146 147 3.706594 GTGTCAACTGAGGATAGGGATCA 59.293 47.826 0.00 0.00 33.27 2.92
147 148 3.243569 CGTGTCAACTGAGGATAGGGATC 60.244 52.174 0.00 0.00 0.00 3.36
148 149 2.695666 CGTGTCAACTGAGGATAGGGAT 59.304 50.000 0.00 0.00 0.00 3.85
149 150 2.100197 CGTGTCAACTGAGGATAGGGA 58.900 52.381 0.00 0.00 0.00 4.20
150 151 1.825474 ACGTGTCAACTGAGGATAGGG 59.175 52.381 0.00 0.00 0.00 3.53
151 152 2.417379 CCACGTGTCAACTGAGGATAGG 60.417 54.545 15.65 0.00 0.00 2.57
152 153 2.492088 TCCACGTGTCAACTGAGGATAG 59.508 50.000 15.65 0.00 0.00 2.08
153 154 2.492088 CTCCACGTGTCAACTGAGGATA 59.508 50.000 15.65 0.00 0.00 2.59
154 155 1.273606 CTCCACGTGTCAACTGAGGAT 59.726 52.381 15.65 0.00 0.00 3.24
155 156 0.673985 CTCCACGTGTCAACTGAGGA 59.326 55.000 15.65 0.00 0.00 3.71
156 157 0.946221 GCTCCACGTGTCAACTGAGG 60.946 60.000 15.65 0.00 0.00 3.86
157 158 1.278172 CGCTCCACGTGTCAACTGAG 61.278 60.000 15.65 13.21 36.87 3.35
158 159 1.299850 CGCTCCACGTGTCAACTGA 60.300 57.895 15.65 2.15 36.87 3.41
159 160 3.234390 CGCTCCACGTGTCAACTG 58.766 61.111 15.65 0.00 36.87 3.16
174 175 1.132640 CTCAAAGTTAGCCGCACGC 59.867 57.895 0.00 0.00 37.98 5.34
175 176 0.438830 GACTCAAAGTTAGCCGCACG 59.561 55.000 0.00 0.00 0.00 5.34
176 177 0.438830 CGACTCAAAGTTAGCCGCAC 59.561 55.000 0.00 0.00 0.00 5.34
177 178 0.032952 ACGACTCAAAGTTAGCCGCA 59.967 50.000 0.00 0.00 0.00 5.69
178 179 1.126296 GAACGACTCAAAGTTAGCCGC 59.874 52.381 0.00 0.00 0.00 6.53
179 180 2.408704 CAGAACGACTCAAAGTTAGCCG 59.591 50.000 0.00 0.00 0.00 5.52
180 181 3.391049 ACAGAACGACTCAAAGTTAGCC 58.609 45.455 0.00 0.00 0.00 3.93
181 182 5.405331 AAACAGAACGACTCAAAGTTAGC 57.595 39.130 0.00 0.00 0.00 3.09
182 183 5.332355 CGGAAACAGAACGACTCAAAGTTAG 60.332 44.000 0.00 0.00 0.00 2.34
183 184 4.505191 CGGAAACAGAACGACTCAAAGTTA 59.495 41.667 0.00 0.00 0.00 2.24
184 185 3.308866 CGGAAACAGAACGACTCAAAGTT 59.691 43.478 0.00 0.00 0.00 2.66
185 186 2.864343 CGGAAACAGAACGACTCAAAGT 59.136 45.455 0.00 0.00 0.00 2.66
186 187 3.120792 TCGGAAACAGAACGACTCAAAG 58.879 45.455 0.00 0.00 0.00 2.77
187 188 3.167921 TCGGAAACAGAACGACTCAAA 57.832 42.857 0.00 0.00 0.00 2.69
188 189 2.875087 TCGGAAACAGAACGACTCAA 57.125 45.000 0.00 0.00 0.00 3.02
193 194 2.607631 AAAGGTCGGAAACAGAACGA 57.392 45.000 0.00 0.00 0.00 3.85
194 195 3.387397 AGTAAAGGTCGGAAACAGAACG 58.613 45.455 0.00 0.00 0.00 3.95
195 196 4.084693 CGAAGTAAAGGTCGGAAACAGAAC 60.085 45.833 0.00 0.00 33.62 3.01
196 197 4.053295 CGAAGTAAAGGTCGGAAACAGAA 58.947 43.478 0.00 0.00 33.62 3.02
197 198 3.645884 CGAAGTAAAGGTCGGAAACAGA 58.354 45.455 0.00 0.00 33.62 3.41
205 206 5.144359 CACAAAAATCCGAAGTAAAGGTCG 58.856 41.667 0.00 0.00 37.01 4.79
206 207 6.068473 ACACAAAAATCCGAAGTAAAGGTC 57.932 37.500 0.00 0.00 0.00 3.85
207 208 6.993902 TCTACACAAAAATCCGAAGTAAAGGT 59.006 34.615 0.00 0.00 0.00 3.50
208 209 7.429636 TCTACACAAAAATCCGAAGTAAAGG 57.570 36.000 0.00 0.00 0.00 3.11
209 210 9.166126 GTTTCTACACAAAAATCCGAAGTAAAG 57.834 33.333 0.00 0.00 0.00 1.85
210 211 7.851963 CGTTTCTACACAAAAATCCGAAGTAAA 59.148 33.333 0.00 0.00 0.00 2.01
211 212 7.011295 ACGTTTCTACACAAAAATCCGAAGTAA 59.989 33.333 0.00 0.00 0.00 2.24
212 213 6.479660 ACGTTTCTACACAAAAATCCGAAGTA 59.520 34.615 0.00 0.00 0.00 2.24
213 214 5.295045 ACGTTTCTACACAAAAATCCGAAGT 59.705 36.000 0.00 0.00 0.00 3.01
214 215 5.619607 CACGTTTCTACACAAAAATCCGAAG 59.380 40.000 0.00 0.00 0.00 3.79
215 216 5.293814 TCACGTTTCTACACAAAAATCCGAA 59.706 36.000 0.00 0.00 0.00 4.30
216 217 4.809958 TCACGTTTCTACACAAAAATCCGA 59.190 37.500 0.00 0.00 0.00 4.55
228 229 6.075572 GCACAAGTTTTTGATCACGTTTCTAC 60.076 38.462 0.00 0.00 37.73 2.59
259 260 4.881019 TCTTCACCCTTCTTCTTCTCTG 57.119 45.455 0.00 0.00 0.00 3.35
317 319 2.897350 GGAGGAATTCGGCCTGCG 60.897 66.667 0.00 0.00 35.44 5.18
318 320 2.115291 GTGGAGGAATTCGGCCTGC 61.115 63.158 14.13 6.52 43.42 4.85
319 321 1.815421 CGTGGAGGAATTCGGCCTG 60.815 63.158 14.13 0.00 35.44 4.85
320 322 1.838073 AACGTGGAGGAATTCGGCCT 61.838 55.000 14.13 0.78 38.81 5.19
321 323 1.366854 GAACGTGGAGGAATTCGGCC 61.367 60.000 7.96 7.96 0.00 6.13
322 324 0.391263 AGAACGTGGAGGAATTCGGC 60.391 55.000 0.00 0.00 0.00 5.54
323 325 1.204941 AGAGAACGTGGAGGAATTCGG 59.795 52.381 0.00 0.00 0.00 4.30
324 326 2.531206 GAGAGAACGTGGAGGAATTCG 58.469 52.381 0.00 0.00 0.00 3.34
325 327 2.233922 TGGAGAGAACGTGGAGGAATTC 59.766 50.000 0.00 0.00 0.00 2.17
374 420 2.132762 GGTGATTTATACGGCGTGAGG 58.867 52.381 24.86 0.00 0.00 3.86
399 445 1.717791 TATACGGCGTGAGGGTGACG 61.718 60.000 24.86 0.00 39.87 4.35
400 446 0.457035 TTATACGGCGTGAGGGTGAC 59.543 55.000 24.86 0.00 0.00 3.67
401 447 1.135024 GTTTATACGGCGTGAGGGTGA 60.135 52.381 24.86 0.00 0.00 4.02
402 448 1.283736 GTTTATACGGCGTGAGGGTG 58.716 55.000 24.86 0.00 0.00 4.61
403 449 0.176449 GGTTTATACGGCGTGAGGGT 59.824 55.000 24.86 5.89 0.00 4.34
404 450 0.176219 TGGTTTATACGGCGTGAGGG 59.824 55.000 24.86 0.00 0.00 4.30
405 451 1.283736 GTGGTTTATACGGCGTGAGG 58.716 55.000 24.86 0.00 0.00 3.86
406 452 1.283736 GGTGGTTTATACGGCGTGAG 58.716 55.000 24.86 0.00 0.00 3.51
407 453 0.458197 CGGTGGTTTATACGGCGTGA 60.458 55.000 24.86 7.69 0.00 4.35
408 454 2.000587 CGGTGGTTTATACGGCGTG 58.999 57.895 24.86 0.00 0.00 5.34
409 455 1.810853 GCGGTGGTTTATACGGCGT 60.811 57.895 19.64 19.64 35.25 5.68
410 456 2.527867 GGCGGTGGTTTATACGGCG 61.528 63.158 4.80 4.80 42.96 6.46
411 457 3.413166 GGCGGTGGTTTATACGGC 58.587 61.111 0.00 0.00 44.25 5.68
412 458 1.524393 GGGGCGGTGGTTTATACGG 60.524 63.158 0.00 0.00 0.00 4.02
413 459 1.091197 GTGGGGCGGTGGTTTATACG 61.091 60.000 0.00 0.00 0.00 3.06
414 460 0.749091 GGTGGGGCGGTGGTTTATAC 60.749 60.000 0.00 0.00 0.00 1.47
415 461 1.206135 TGGTGGGGCGGTGGTTTATA 61.206 55.000 0.00 0.00 0.00 0.98
416 462 2.082836 TTGGTGGGGCGGTGGTTTAT 62.083 55.000 0.00 0.00 0.00 1.40
417 463 2.764737 TTGGTGGGGCGGTGGTTTA 61.765 57.895 0.00 0.00 0.00 2.01
418 464 4.144727 TTGGTGGGGCGGTGGTTT 62.145 61.111 0.00 0.00 0.00 3.27
419 465 4.906537 GTTGGTGGGGCGGTGGTT 62.907 66.667 0.00 0.00 0.00 3.67
990 1039 4.519437 TCGCCCATGAGCAGCTCG 62.519 66.667 17.81 5.26 32.35 5.03
1104 1153 4.845580 ATGCGGCGCTTGAGGAGG 62.846 66.667 33.26 0.00 0.00 4.30
1476 1525 1.815003 CACTTGATCTTGCTGGGGAAC 59.185 52.381 0.00 0.00 0.00 3.62
2163 2212 0.689055 AGAGCAGGATCAGCACAACA 59.311 50.000 11.35 0.00 0.00 3.33
2256 2308 1.305930 GGATCTGGTTTGTGCGGACC 61.306 60.000 4.04 0.00 36.45 4.46
2280 2332 3.154473 TTCTGGGCGGGGATCTCG 61.154 66.667 0.00 0.00 0.00 4.04
2289 2341 2.183555 GACGGGTACTTCTGGGCG 59.816 66.667 0.00 0.00 0.00 6.13
2640 2692 0.904649 TGGCGATGACCATGAAGAGT 59.095 50.000 0.00 0.00 33.75 3.24
2746 2798 1.554617 TGATCATTCCACGCAAGGAGA 59.445 47.619 0.00 0.00 46.39 3.71
2756 2811 6.320418 CACCTCTCAATTCAATGATCATTCCA 59.680 38.462 18.16 8.14 0.00 3.53
2760 2815 6.660800 ACTCACCTCTCAATTCAATGATCAT 58.339 36.000 1.18 1.18 0.00 2.45
2764 2819 5.877012 GCTTACTCACCTCTCAATTCAATGA 59.123 40.000 0.00 0.00 0.00 2.57
2796 2851 3.751479 AACTTTTTCAATGCCCACTCC 57.249 42.857 0.00 0.00 0.00 3.85
2797 2852 4.441792 ACAAACTTTTTCAATGCCCACTC 58.558 39.130 0.00 0.00 0.00 3.51
2812 2868 4.202223 ACCGACTGTGATGACTACAAACTT 60.202 41.667 0.00 0.00 0.00 2.66
3308 3387 2.224793 ACTGGAGTTTTCCCCTTGTAGC 60.225 50.000 0.00 0.00 43.33 3.58
3532 3627 3.509967 CCCAGGAAGATACAAAACCCAAC 59.490 47.826 0.00 0.00 0.00 3.77
3533 3628 3.399644 TCCCAGGAAGATACAAAACCCAA 59.600 43.478 0.00 0.00 0.00 4.12
3534 3629 2.990284 TCCCAGGAAGATACAAAACCCA 59.010 45.455 0.00 0.00 0.00 4.51
3535 3630 3.621558 CTCCCAGGAAGATACAAAACCC 58.378 50.000 0.00 0.00 0.00 4.11
3536 3631 3.010250 ACCTCCCAGGAAGATACAAAACC 59.990 47.826 0.00 0.00 37.67 3.27
3537 3632 4.302559 ACCTCCCAGGAAGATACAAAAC 57.697 45.455 0.00 0.00 37.67 2.43
3544 3686 2.065799 ACAACAACCTCCCAGGAAGAT 58.934 47.619 0.00 0.00 37.67 2.40
3546 3688 2.364972 AACAACAACCTCCCAGGAAG 57.635 50.000 0.00 0.00 37.67 3.46
3566 3708 2.248280 TCTGAGCAACAGCCGTAAAA 57.752 45.000 6.13 0.00 45.38 1.52
3567 3709 1.871039 GTTCTGAGCAACAGCCGTAAA 59.129 47.619 6.13 0.00 45.38 2.01
3569 3711 0.679505 AGTTCTGAGCAACAGCCGTA 59.320 50.000 6.13 0.00 45.38 4.02
3570 3712 0.679505 TAGTTCTGAGCAACAGCCGT 59.320 50.000 6.13 0.00 45.38 5.68
3571 3713 2.015736 ATAGTTCTGAGCAACAGCCG 57.984 50.000 6.13 0.00 45.38 5.52
3572 3714 4.201724 CGTAAATAGTTCTGAGCAACAGCC 60.202 45.833 6.13 0.85 45.38 4.85
3573 3715 4.201724 CCGTAAATAGTTCTGAGCAACAGC 60.202 45.833 6.13 0.00 45.38 4.40
3574 3716 4.201724 GCCGTAAATAGTTCTGAGCAACAG 60.202 45.833 4.84 4.84 46.97 3.16
3576 3718 3.933332 AGCCGTAAATAGTTCTGAGCAAC 59.067 43.478 0.00 0.00 0.00 4.17
3577 3719 3.932710 CAGCCGTAAATAGTTCTGAGCAA 59.067 43.478 0.00 0.00 0.00 3.91
3578 3720 3.056107 ACAGCCGTAAATAGTTCTGAGCA 60.056 43.478 0.00 0.00 0.00 4.26
3579 3721 3.522553 ACAGCCGTAAATAGTTCTGAGC 58.477 45.455 0.00 0.00 0.00 4.26
3581 3723 6.028146 TGTAACAGCCGTAAATAGTTCTGA 57.972 37.500 0.00 0.00 0.00 3.27
3582 3724 6.715344 TTGTAACAGCCGTAAATAGTTCTG 57.285 37.500 0.00 0.00 0.00 3.02
3583 3725 7.916914 ATTTGTAACAGCCGTAAATAGTTCT 57.083 32.000 0.00 0.00 0.00 3.01
3584 3726 8.019094 ACAATTTGTAACAGCCGTAAATAGTTC 58.981 33.333 0.00 0.00 0.00 3.01
3586 3728 7.443259 ACAATTTGTAACAGCCGTAAATAGT 57.557 32.000 0.00 0.00 0.00 2.12
3587 3729 7.272515 CCAACAATTTGTAACAGCCGTAAATAG 59.727 37.037 1.76 0.00 0.00 1.73
3589 3731 5.923684 CCAACAATTTGTAACAGCCGTAAAT 59.076 36.000 1.76 0.00 0.00 1.40
3593 3735 2.035321 CCCAACAATTTGTAACAGCCGT 59.965 45.455 1.76 0.00 0.00 5.68
3594 3736 2.035321 ACCCAACAATTTGTAACAGCCG 59.965 45.455 1.76 0.00 0.00 5.52
3595 3737 3.744238 ACCCAACAATTTGTAACAGCC 57.256 42.857 1.76 0.00 0.00 4.85
3596 3738 5.729176 GCAAAACCCAACAATTTGTAACAGC 60.729 40.000 1.76 0.00 36.63 4.40
3597 3739 5.584251 AGCAAAACCCAACAATTTGTAACAG 59.416 36.000 1.76 0.00 36.63 3.16
3599 3741 5.582665 TGAGCAAAACCCAACAATTTGTAAC 59.417 36.000 1.76 0.00 36.63 2.50
3601 3743 5.127845 TCTGAGCAAAACCCAACAATTTGTA 59.872 36.000 1.76 0.00 36.63 2.41
3602 3744 4.081198 TCTGAGCAAAACCCAACAATTTGT 60.081 37.500 0.00 0.00 36.63 2.83
3603 3745 4.440880 TCTGAGCAAAACCCAACAATTTG 58.559 39.130 0.00 0.00 37.17 2.32
3604 3746 4.751767 TCTGAGCAAAACCCAACAATTT 57.248 36.364 0.00 0.00 0.00 1.82
3605 3747 4.162131 AGTTCTGAGCAAAACCCAACAATT 59.838 37.500 0.00 0.00 0.00 2.32
3606 3748 3.706086 AGTTCTGAGCAAAACCCAACAAT 59.294 39.130 0.00 0.00 0.00 2.71
3607 3749 3.096092 AGTTCTGAGCAAAACCCAACAA 58.904 40.909 0.00 0.00 0.00 2.83
3608 3750 2.733956 AGTTCTGAGCAAAACCCAACA 58.266 42.857 0.00 0.00 0.00 3.33
3611 3753 6.065374 TGTAAATAGTTCTGAGCAAAACCCA 58.935 36.000 0.00 0.00 0.00 4.51
3613 3755 6.577427 CGTTGTAAATAGTTCTGAGCAAAACC 59.423 38.462 0.00 0.00 0.00 3.27
3619 3958 5.840940 ACACGTTGTAAATAGTTCTGAGC 57.159 39.130 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.