Multiple sequence alignment - TraesCS2D01G297600

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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 TraesCS2D01G297600 chr2D 100.000 5884 0 0 1 5884 380087897 380082014 0.000000e+00 10866.0
1 TraesCS2D01G297600 chr2D 95.972 4667 171 11 607 5261 13211115 13215776 0.000000e+00 7561.0
2 TraesCS2D01G297600 chr2D 95.671 3188 104 15 2184 5352 46679685 46682857 0.000000e+00 5092.0
3 TraesCS2D01G297600 chr2D 93.520 1821 82 18 413 2199 46677486 46679304 0.000000e+00 2676.0
4 TraesCS2D01G297600 chr2D 93.538 619 14 3 209 801 46675258 46675876 0.000000e+00 898.0
5 TraesCS2D01G297600 chr3D 95.904 5102 167 20 209 5279 531348083 531353173 0.000000e+00 8226.0
6 TraesCS2D01G297600 chr3D 95.656 4765 168 23 615 5345 426166351 426161592 0.000000e+00 7616.0
7 TraesCS2D01G297600 chr3D 96.175 4653 130 12 209 4820 464059098 464054453 0.000000e+00 7563.0
8 TraesCS2D01G297600 chr3D 82.662 571 62 18 5345 5884 464053762 464053198 6.900000e-129 472.0
9 TraesCS2D01G297600 chr3D 90.671 343 17 8 4859 5188 464054471 464054131 5.410000e-120 442.0
10 TraesCS2D01G297600 chr3D 81.674 442 41 20 5462 5884 531363810 531364230 1.220000e-86 331.0
11 TraesCS2D01G297600 chr3D 88.235 68 6 2 5285 5352 531353221 531353286 4.890000e-11 80.5
12 TraesCS2D01G297600 chr3A 92.835 5694 279 56 275 5857 665954350 665960025 0.000000e+00 8135.0
13 TraesCS2D01G297600 chr3B 94.211 4785 194 37 244 4964 702681723 702686488 0.000000e+00 7225.0
14 TraesCS2D01G297600 chr3B 83.411 428 36 15 4944 5340 702686509 702686932 1.210000e-96 364.0
15 TraesCS2D01G297600 chr3B 88.591 149 12 4 5711 5856 702687595 702687741 6.060000e-40 176.0
16 TraesCS2D01G297600 chr6A 75.184 2587 594 42 1089 3649 169190088 169192652 0.000000e+00 1177.0
17 TraesCS2D01G297600 chr6A 91.852 135 9 2 4111 4245 456719549 456719681 2.800000e-43 187.0
18 TraesCS2D01G297600 chr6A 88.496 113 9 1 4247 4355 456719984 456720096 3.700000e-27 134.0
19 TraesCS2D01G297600 chr1B 84.030 263 36 5 345 603 120038859 120039119 1.270000e-61 248.0
20 TraesCS2D01G297600 chr1D 76.731 520 71 30 234 722 446560385 446560885 1.640000e-60 244.0
21 TraesCS2D01G297600 chr6B 85.294 238 26 4 4017 4245 504590743 504590506 2.740000e-58 237.0
22 TraesCS2D01G297600 chr6B 89.908 109 11 0 4247 4355 504590213 504590105 2.210000e-29 141.0
23 TraesCS2D01G297600 chr1A 82.375 261 41 3 348 603 542360427 542360687 7.670000e-54 222.0
24 TraesCS2D01G297600 chr1A 84.286 210 28 4 398 603 77271861 77272069 3.600000e-47 200.0
25 TraesCS2D01G297600 chr2A 97.500 40 1 0 4556 4595 735245525 735245564 1.060000e-07 69.4


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 TraesCS2D01G297600 chr2D 380082014 380087897 5883 True 10866.000000 10866 100.000000 1 5884 1 chr2D.!!$R1 5883
1 TraesCS2D01G297600 chr2D 13211115 13215776 4661 False 7561.000000 7561 95.972000 607 5261 1 chr2D.!!$F1 4654
2 TraesCS2D01G297600 chr2D 46675258 46682857 7599 False 2888.666667 5092 94.243000 209 5352 3 chr2D.!!$F2 5143
3 TraesCS2D01G297600 chr3D 426161592 426166351 4759 True 7616.000000 7616 95.656000 615 5345 1 chr3D.!!$R1 4730
4 TraesCS2D01G297600 chr3D 531348083 531353286 5203 False 4153.250000 8226 92.069500 209 5352 2 chr3D.!!$F2 5143
5 TraesCS2D01G297600 chr3D 464053198 464059098 5900 True 2825.666667 7563 89.836000 209 5884 3 chr3D.!!$R2 5675
6 TraesCS2D01G297600 chr3A 665954350 665960025 5675 False 8135.000000 8135 92.835000 275 5857 1 chr3A.!!$F1 5582
7 TraesCS2D01G297600 chr3B 702681723 702687741 6018 False 2588.333333 7225 88.737667 244 5856 3 chr3B.!!$F1 5612
8 TraesCS2D01G297600 chr6A 169190088 169192652 2564 False 1177.000000 1177 75.184000 1089 3649 1 chr6A.!!$F1 2560
9 TraesCS2D01G297600 chr1D 446560385 446560885 500 False 244.000000 244 76.731000 234 722 1 chr1D.!!$F1 488

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
73 74 0.036010 CCTGCTACCACCTGTTCTGG 60.036 60.000 0.00 0.0 34.62 3.86 F
158 159 0.179009 GCATGATTGCCCAGGCTAGA 60.179 55.000 10.58 0.0 43.38 2.43 F
1497 3609 0.675837 TGCAGCATCTCACCAAGCTC 60.676 55.000 0.00 0.0 34.61 4.09 F
1811 3923 1.335872 GGGACAAAATGCGTTCACTGG 60.336 52.381 0.00 0.0 0.00 4.00 F
3450 5966 1.133325 TCTCAGGGACCCTAGATGAGC 60.133 57.143 14.38 0.0 37.81 4.26 F
4325 6841 0.529555 GTCTCAAGATCTGCCTCGGC 60.530 60.000 0.00 0.0 42.35 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 3906 1.608590 CTCCCAGTGAACGCATTTTGT 59.391 47.619 0.00 0.00 0.00 2.83 R
1811 3923 3.766051 ACCAATTTCTTCTGGAATGCTCC 59.234 43.478 0.00 0.00 42.81 4.70 R
2619 5128 0.183492 AACCTCTGCAAGCTGGACAA 59.817 50.000 0.00 0.00 32.81 3.18 R
3664 6180 1.065926 CACCTCCTGCTGCACAATCTA 60.066 52.381 0.00 0.00 0.00 1.98 R
4526 7042 0.770499 TGGACTTCATTGTCTGGCCA 59.230 50.000 4.71 4.71 37.16 5.36 R
5827 8837 0.100325 TGCTTGTTTGTCCAACGCTG 59.900 50.000 0.00 0.00 38.36 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
25 26 8.964476 TCCAGATCAATGGAAATTCTAGTTAC 57.036 34.615 1.25 0.00 46.45 2.50
26 27 8.548025 TCCAGATCAATGGAAATTCTAGTTACA 58.452 33.333 1.25 0.00 46.45 2.41
27 28 9.347240 CCAGATCAATGGAAATTCTAGTTACAT 57.653 33.333 0.00 0.00 43.57 2.29
50 51 8.879759 ACATTTTATGTAACGTAGGAGATGTTG 58.120 33.333 0.00 0.00 42.78 3.33
51 52 9.093970 CATTTTATGTAACGTAGGAGATGTTGA 57.906 33.333 0.00 0.00 37.83 3.18
52 53 9.661563 ATTTTATGTAACGTAGGAGATGTTGAA 57.338 29.630 0.00 0.00 37.83 2.69
53 54 9.661563 TTTTATGTAACGTAGGAGATGTTGAAT 57.338 29.630 0.00 0.00 37.83 2.57
54 55 8.867112 TTATGTAACGTAGGAGATGTTGAATC 57.133 34.615 0.00 0.00 37.83 2.52
55 56 5.657474 TGTAACGTAGGAGATGTTGAATCC 58.343 41.667 0.00 0.00 37.83 3.01
56 57 5.421056 TGTAACGTAGGAGATGTTGAATCCT 59.579 40.000 0.00 0.00 45.44 3.24
57 58 4.392921 ACGTAGGAGATGTTGAATCCTG 57.607 45.455 3.24 0.00 43.36 3.86
58 59 3.126831 CGTAGGAGATGTTGAATCCTGC 58.873 50.000 3.24 1.10 43.36 4.85
59 60 3.181471 CGTAGGAGATGTTGAATCCTGCT 60.181 47.826 3.24 0.00 43.36 4.24
60 61 4.038042 CGTAGGAGATGTTGAATCCTGCTA 59.962 45.833 3.24 0.00 43.36 3.49
61 62 4.414337 AGGAGATGTTGAATCCTGCTAC 57.586 45.455 0.00 0.00 41.95 3.58
62 63 3.135530 AGGAGATGTTGAATCCTGCTACC 59.864 47.826 0.00 0.00 41.95 3.18
63 64 3.118261 GGAGATGTTGAATCCTGCTACCA 60.118 47.826 0.00 0.00 0.00 3.25
64 65 3.873952 GAGATGTTGAATCCTGCTACCAC 59.126 47.826 0.00 0.00 0.00 4.16
65 66 2.489938 TGTTGAATCCTGCTACCACC 57.510 50.000 0.00 0.00 0.00 4.61
66 67 1.985159 TGTTGAATCCTGCTACCACCT 59.015 47.619 0.00 0.00 0.00 4.00
67 68 2.290260 TGTTGAATCCTGCTACCACCTG 60.290 50.000 0.00 0.00 0.00 4.00
68 69 1.656587 TGAATCCTGCTACCACCTGT 58.343 50.000 0.00 0.00 0.00 4.00
69 70 1.985159 TGAATCCTGCTACCACCTGTT 59.015 47.619 0.00 0.00 0.00 3.16
70 71 2.027192 TGAATCCTGCTACCACCTGTTC 60.027 50.000 0.00 0.00 0.00 3.18
71 72 1.958288 ATCCTGCTACCACCTGTTCT 58.042 50.000 0.00 0.00 0.00 3.01
72 73 0.976641 TCCTGCTACCACCTGTTCTG 59.023 55.000 0.00 0.00 0.00 3.02
73 74 0.036010 CCTGCTACCACCTGTTCTGG 60.036 60.000 0.00 0.00 34.62 3.86
74 75 0.976641 CTGCTACCACCTGTTCTGGA 59.023 55.000 2.86 0.00 32.55 3.86
75 76 1.347707 CTGCTACCACCTGTTCTGGAA 59.652 52.381 2.86 0.00 32.55 3.53
76 77 1.771854 TGCTACCACCTGTTCTGGAAA 59.228 47.619 2.86 0.00 32.55 3.13
77 78 2.375174 TGCTACCACCTGTTCTGGAAAT 59.625 45.455 2.86 0.00 32.55 2.17
78 79 2.749621 GCTACCACCTGTTCTGGAAATG 59.250 50.000 2.86 0.00 32.55 2.32
79 80 1.620822 ACCACCTGTTCTGGAAATGC 58.379 50.000 2.86 0.00 32.55 3.56
80 81 0.523072 CCACCTGTTCTGGAAATGCG 59.477 55.000 2.86 0.00 0.00 4.73
81 82 1.522668 CACCTGTTCTGGAAATGCGA 58.477 50.000 2.86 0.00 0.00 5.10
82 83 1.197721 CACCTGTTCTGGAAATGCGAC 59.802 52.381 2.86 0.00 0.00 5.19
83 84 1.072331 ACCTGTTCTGGAAATGCGACT 59.928 47.619 2.86 0.00 0.00 4.18
84 85 2.154462 CCTGTTCTGGAAATGCGACTT 58.846 47.619 0.00 0.00 0.00 3.01
85 86 2.160417 CCTGTTCTGGAAATGCGACTTC 59.840 50.000 0.00 0.00 0.00 3.01
86 87 2.807967 CTGTTCTGGAAATGCGACTTCA 59.192 45.455 0.00 0.00 0.00 3.02
87 88 2.807967 TGTTCTGGAAATGCGACTTCAG 59.192 45.455 0.00 0.00 0.00 3.02
88 89 1.442769 TCTGGAAATGCGACTTCAGC 58.557 50.000 0.00 0.00 0.00 4.26
94 95 2.821685 TGCGACTTCAGCACAGGT 59.178 55.556 0.00 0.00 40.01 4.00
95 96 1.595109 TGCGACTTCAGCACAGGTG 60.595 57.895 0.00 0.00 40.01 4.00
109 110 2.771089 ACAGGTGCTGTGTGACTATTG 58.229 47.619 0.00 0.00 43.63 1.90
110 111 2.368548 ACAGGTGCTGTGTGACTATTGA 59.631 45.455 0.00 0.00 43.63 2.57
111 112 3.008375 ACAGGTGCTGTGTGACTATTGAT 59.992 43.478 0.00 0.00 43.63 2.57
112 113 4.005650 CAGGTGCTGTGTGACTATTGATT 58.994 43.478 0.00 0.00 0.00 2.57
113 114 4.093998 CAGGTGCTGTGTGACTATTGATTC 59.906 45.833 0.00 0.00 0.00 2.52
114 115 4.002982 GGTGCTGTGTGACTATTGATTCA 58.997 43.478 0.00 0.00 0.00 2.57
115 116 4.142816 GGTGCTGTGTGACTATTGATTCAC 60.143 45.833 0.00 0.00 42.18 3.18
116 117 4.002982 TGCTGTGTGACTATTGATTCACC 58.997 43.478 0.00 0.00 41.31 4.02
117 118 3.375299 GCTGTGTGACTATTGATTCACCC 59.625 47.826 0.00 0.00 41.31 4.61
118 119 3.941483 CTGTGTGACTATTGATTCACCCC 59.059 47.826 0.00 0.00 41.31 4.95
119 120 3.587061 TGTGTGACTATTGATTCACCCCT 59.413 43.478 0.00 0.00 41.31 4.79
120 121 4.192317 GTGTGACTATTGATTCACCCCTC 58.808 47.826 0.00 0.00 41.31 4.30
121 122 3.843619 TGTGACTATTGATTCACCCCTCA 59.156 43.478 0.00 0.00 41.31 3.86
122 123 4.288366 TGTGACTATTGATTCACCCCTCAA 59.712 41.667 0.00 0.00 41.31 3.02
123 124 4.636206 GTGACTATTGATTCACCCCTCAAC 59.364 45.833 0.00 0.00 36.85 3.18
124 125 4.536090 TGACTATTGATTCACCCCTCAACT 59.464 41.667 0.00 0.00 34.43 3.16
125 126 5.104259 ACTATTGATTCACCCCTCAACTC 57.896 43.478 0.00 0.00 34.43 3.01
126 127 2.879103 TTGATTCACCCCTCAACTCC 57.121 50.000 0.00 0.00 0.00 3.85
127 128 2.044793 TGATTCACCCCTCAACTCCT 57.955 50.000 0.00 0.00 0.00 3.69
128 129 3.199442 TGATTCACCCCTCAACTCCTA 57.801 47.619 0.00 0.00 0.00 2.94
129 130 2.838202 TGATTCACCCCTCAACTCCTAC 59.162 50.000 0.00 0.00 0.00 3.18
130 131 1.652947 TTCACCCCTCAACTCCTACC 58.347 55.000 0.00 0.00 0.00 3.18
131 132 0.490017 TCACCCCTCAACTCCTACCA 59.510 55.000 0.00 0.00 0.00 3.25
132 133 1.132657 TCACCCCTCAACTCCTACCAA 60.133 52.381 0.00 0.00 0.00 3.67
133 134 1.916181 CACCCCTCAACTCCTACCAAT 59.084 52.381 0.00 0.00 0.00 3.16
134 135 1.916181 ACCCCTCAACTCCTACCAATG 59.084 52.381 0.00 0.00 0.00 2.82
135 136 1.212935 CCCCTCAACTCCTACCAATGG 59.787 57.143 0.00 0.00 0.00 3.16
136 137 2.196595 CCCTCAACTCCTACCAATGGA 58.803 52.381 6.16 0.00 0.00 3.41
137 138 2.576191 CCCTCAACTCCTACCAATGGAA 59.424 50.000 6.16 0.00 32.61 3.53
138 139 3.370953 CCCTCAACTCCTACCAATGGAAG 60.371 52.174 6.16 0.15 32.61 3.46
139 140 3.370953 CCTCAACTCCTACCAATGGAAGG 60.371 52.174 6.16 0.00 32.61 3.46
140 141 2.026262 TCAACTCCTACCAATGGAAGGC 60.026 50.000 6.16 0.00 32.61 4.35
141 142 1.668826 ACTCCTACCAATGGAAGGCA 58.331 50.000 6.16 0.00 32.61 4.75
142 143 2.208872 ACTCCTACCAATGGAAGGCAT 58.791 47.619 6.16 0.00 32.61 4.40
143 144 2.092212 ACTCCTACCAATGGAAGGCATG 60.092 50.000 6.16 0.00 32.61 4.06
144 145 2.173356 CTCCTACCAATGGAAGGCATGA 59.827 50.000 6.16 0.00 32.61 3.07
145 146 2.785269 TCCTACCAATGGAAGGCATGAT 59.215 45.455 6.16 0.00 0.00 2.45
146 147 3.205056 TCCTACCAATGGAAGGCATGATT 59.795 43.478 6.16 0.00 0.00 2.57
147 148 3.319972 CCTACCAATGGAAGGCATGATTG 59.680 47.826 6.16 0.00 0.00 2.67
156 157 4.585070 GCATGATTGCCCAGGCTA 57.415 55.556 10.58 2.17 43.38 3.93
157 158 2.338381 GCATGATTGCCCAGGCTAG 58.662 57.895 10.58 0.00 43.38 3.42
158 159 0.179009 GCATGATTGCCCAGGCTAGA 60.179 55.000 10.58 0.00 43.38 2.43
159 160 1.547223 GCATGATTGCCCAGGCTAGAT 60.547 52.381 10.58 1.50 43.38 1.98
160 161 2.290514 GCATGATTGCCCAGGCTAGATA 60.291 50.000 10.58 0.00 43.38 1.98
161 162 3.341823 CATGATTGCCCAGGCTAGATAC 58.658 50.000 10.58 0.00 42.51 2.24
162 163 2.407562 TGATTGCCCAGGCTAGATACA 58.592 47.619 10.58 0.00 42.51 2.29
163 164 2.777114 TGATTGCCCAGGCTAGATACAA 59.223 45.455 10.58 0.00 42.51 2.41
164 165 2.710096 TTGCCCAGGCTAGATACAAC 57.290 50.000 10.58 0.00 42.51 3.32
165 166 1.879575 TGCCCAGGCTAGATACAACT 58.120 50.000 10.58 0.00 42.51 3.16
166 167 2.196595 TGCCCAGGCTAGATACAACTT 58.803 47.619 10.58 0.00 42.51 2.66
167 168 2.170607 TGCCCAGGCTAGATACAACTTC 59.829 50.000 10.58 0.00 42.51 3.01
168 169 2.170607 GCCCAGGCTAGATACAACTTCA 59.829 50.000 0.08 0.00 38.26 3.02
169 170 3.742640 GCCCAGGCTAGATACAACTTCAG 60.743 52.174 0.08 0.00 38.26 3.02
170 171 3.462021 CCAGGCTAGATACAACTTCAGC 58.538 50.000 0.00 0.00 0.00 4.26
171 172 3.118629 CCAGGCTAGATACAACTTCAGCA 60.119 47.826 0.00 0.00 0.00 4.41
172 173 4.507710 CAGGCTAGATACAACTTCAGCAA 58.492 43.478 0.00 0.00 0.00 3.91
173 174 4.569966 CAGGCTAGATACAACTTCAGCAAG 59.430 45.833 0.00 0.00 35.50 4.01
174 175 4.223923 AGGCTAGATACAACTTCAGCAAGT 59.776 41.667 0.00 0.00 45.43 3.16
175 176 4.568760 GGCTAGATACAACTTCAGCAAGTC 59.431 45.833 0.00 0.00 42.45 3.01
176 177 4.568760 GCTAGATACAACTTCAGCAAGTCC 59.431 45.833 0.00 0.00 42.45 3.85
177 178 4.899352 AGATACAACTTCAGCAAGTCCT 57.101 40.909 0.00 0.00 42.45 3.85
178 179 5.234466 AGATACAACTTCAGCAAGTCCTT 57.766 39.130 0.00 0.00 42.45 3.36
179 180 5.241662 AGATACAACTTCAGCAAGTCCTTC 58.758 41.667 0.00 0.00 42.45 3.46
180 181 3.281727 ACAACTTCAGCAAGTCCTTCA 57.718 42.857 0.00 0.00 42.45 3.02
181 182 3.825328 ACAACTTCAGCAAGTCCTTCAT 58.175 40.909 0.00 0.00 42.45 2.57
182 183 4.210331 ACAACTTCAGCAAGTCCTTCATT 58.790 39.130 0.00 0.00 42.45 2.57
183 184 4.037208 ACAACTTCAGCAAGTCCTTCATTG 59.963 41.667 0.00 0.00 42.45 2.82
184 185 4.090761 ACTTCAGCAAGTCCTTCATTGA 57.909 40.909 0.00 0.00 38.62 2.57
185 186 4.070716 ACTTCAGCAAGTCCTTCATTGAG 58.929 43.478 0.00 0.00 38.62 3.02
186 187 4.202398 ACTTCAGCAAGTCCTTCATTGAGA 60.202 41.667 0.00 0.00 38.62 3.27
187 188 3.668447 TCAGCAAGTCCTTCATTGAGAC 58.332 45.455 0.00 0.00 0.00 3.36
188 189 2.746362 CAGCAAGTCCTTCATTGAGACC 59.254 50.000 3.20 0.00 0.00 3.85
189 190 2.641815 AGCAAGTCCTTCATTGAGACCT 59.358 45.455 3.20 0.00 0.00 3.85
190 191 3.073650 AGCAAGTCCTTCATTGAGACCTT 59.926 43.478 3.20 0.00 0.00 3.50
191 192 3.438434 GCAAGTCCTTCATTGAGACCTTC 59.562 47.826 3.20 0.00 0.00 3.46
192 193 4.645535 CAAGTCCTTCATTGAGACCTTCA 58.354 43.478 3.20 0.00 0.00 3.02
202 203 1.881973 TGAGACCTTCAATGTTGCTGC 59.118 47.619 0.00 0.00 31.34 5.25
203 204 1.881973 GAGACCTTCAATGTTGCTGCA 59.118 47.619 0.00 0.00 0.00 4.41
204 205 2.490903 GAGACCTTCAATGTTGCTGCAT 59.509 45.455 1.84 0.00 0.00 3.96
205 206 2.230508 AGACCTTCAATGTTGCTGCATG 59.769 45.455 1.84 0.00 0.00 4.06
206 207 1.274167 ACCTTCAATGTTGCTGCATGG 59.726 47.619 1.84 0.00 0.00 3.66
207 208 1.546923 CCTTCAATGTTGCTGCATGGA 59.453 47.619 1.84 0.00 0.00 3.41
258 259 1.253593 CCCCTGCTTCTTGGGCTTTC 61.254 60.000 0.00 0.00 42.03 2.62
401 438 1.098050 GGCAGTGCTAAGTGGGAATG 58.902 55.000 16.11 0.00 0.00 2.67
407 444 3.821033 AGTGCTAAGTGGGAATGTTTGTC 59.179 43.478 0.00 0.00 0.00 3.18
627 706 1.648467 GGCGTCATGGTTGAGAAGGC 61.648 60.000 0.00 0.00 30.85 4.35
1374 3486 1.261619 GAACTGAACGACAACCAGCTG 59.738 52.381 6.78 6.78 0.00 4.24
1497 3609 0.675837 TGCAGCATCTCACCAAGCTC 60.676 55.000 0.00 0.00 34.61 4.09
1522 3634 1.819753 ATCCGGGAATTCCATCTCCA 58.180 50.000 25.67 3.75 37.91 3.86
1602 3714 4.780815 TGAACAGCCTAAATGGATCGATT 58.219 39.130 0.00 0.00 38.35 3.34
1671 3783 3.629398 GCCAGAATAACCTCAGTGGATTG 59.371 47.826 0.00 0.00 39.71 2.67
1680 3792 8.697507 ATAACCTCAGTGGATTGATATTTTCC 57.302 34.615 0.00 0.00 39.71 3.13
1794 3906 2.426522 CTTCGACTGCTGATTTTGGGA 58.573 47.619 0.00 0.00 0.00 4.37
1811 3923 1.335872 GGGACAAAATGCGTTCACTGG 60.336 52.381 0.00 0.00 0.00 4.00
2159 4272 5.324832 TCTCTTTTTCTGTGGAAGGGAAT 57.675 39.130 0.00 0.00 32.61 3.01
2319 4828 2.252714 GTCTCTCAGGTTCTGTCCCTT 58.747 52.381 0.00 0.00 32.61 3.95
2320 4829 2.635427 GTCTCTCAGGTTCTGTCCCTTT 59.365 50.000 0.00 0.00 32.61 3.11
2619 5128 3.060479 TCCCAGATAGCATTGGTAGGT 57.940 47.619 1.69 0.00 32.40 3.08
2726 5235 1.527034 TTCTGTCTCTGCATGGCAAC 58.473 50.000 0.00 0.00 38.41 4.17
2814 5323 2.035449 TCTAATAATCTGACCGGGCACG 59.965 50.000 5.41 0.00 40.55 5.34
2904 5413 3.069300 TGCTATTCCTGCTGAGATCTGTC 59.931 47.826 0.00 0.00 0.00 3.51
3033 5542 3.988976 AGTGTTCTATGCTGATGGTGT 57.011 42.857 0.00 0.00 0.00 4.16
3035 5544 4.005650 AGTGTTCTATGCTGATGGTGTTG 58.994 43.478 0.00 0.00 0.00 3.33
3450 5966 1.133325 TCTCAGGGACCCTAGATGAGC 60.133 57.143 14.38 0.00 37.81 4.26
3611 6127 8.177119 TCCCTTGTGGTATTTGCAATATATTC 57.823 34.615 0.00 0.00 34.77 1.75
3664 6180 3.867493 CACATCGACATGTACAGCTCATT 59.133 43.478 0.00 0.00 41.69 2.57
3710 6226 1.369091 CCACTAATGGCACTGGTCGC 61.369 60.000 0.00 0.00 39.82 5.19
3738 6254 3.494048 GGCTCATCCATCTCATCGAGTTT 60.494 47.826 0.00 0.00 34.01 2.66
3824 6340 8.443937 GTGTTTTATCTGAGACACAAACTATCC 58.556 37.037 11.82 0.00 41.42 2.59
3895 6411 1.457346 GAGCCAACCTCAAGTGATGG 58.543 55.000 0.00 0.00 40.45 3.51
3996 6512 7.308408 CCATTGATGATATACTGAAAGCCACAG 60.308 40.741 0.00 0.00 37.60 3.66
4010 6526 6.205464 TGAAAGCCACAGAGAATTTCAGTAAG 59.795 38.462 0.00 0.00 35.55 2.34
4208 6724 1.877443 GGTTACTGTGTTTGTGGCGAT 59.123 47.619 0.00 0.00 0.00 4.58
4325 6841 0.529555 GTCTCAAGATCTGCCTCGGC 60.530 60.000 0.00 0.00 42.35 5.54
4395 6911 1.094785 CCACCGGGACATGAAATCAC 58.905 55.000 6.32 0.00 35.59 3.06
4418 6934 0.615331 ACATCCTGCTGGACGTGAAT 59.385 50.000 15.36 0.00 46.51 2.57
4469 6985 1.290203 CAAGGATAATCAGCGCGTGT 58.710 50.000 8.43 0.00 0.00 4.49
4493 7009 0.667487 CTCACGTCAGCACCGACATT 60.667 55.000 0.00 0.00 35.54 2.71
4504 7020 2.013807 CCGACATTGCCGGTACATG 58.986 57.895 1.90 8.15 41.91 3.21
4601 7123 1.451028 GCTGGAGCTGCTTACAGGG 60.451 63.158 26.04 11.54 44.63 4.45
4663 7185 0.108329 CTTGTCGGCTGGGTACGATT 60.108 55.000 0.00 0.00 41.53 3.34
4680 7202 2.960957 ATTGGTGATCGCTCGCGGAG 62.961 60.000 6.13 3.47 40.25 4.63
4836 7358 2.435059 GCCTCAAGACGACCCAGC 60.435 66.667 0.00 0.00 0.00 4.85
4931 7467 7.250445 TGACAGTGATGTGATGTAATAATGC 57.750 36.000 0.00 0.00 0.00 3.56
5013 7591 3.441496 AAACCAGTGTTGCTCATGTTG 57.559 42.857 0.00 0.00 34.13 3.33
5226 7838 2.277084 ACTCTGTTGTTGTTCACGGTC 58.723 47.619 0.00 0.00 0.00 4.79
5337 7991 4.020396 TGCTCTTCTGCTCTTCATTCTTCT 60.020 41.667 0.00 0.00 0.00 2.85
5369 8295 8.244113 GGTTCTATGGAGGTTTTGAAAATACAG 58.756 37.037 0.00 0.00 0.00 2.74
5385 8311 5.587388 AATACAGCATGCAAAGCTATTGT 57.413 34.783 21.98 14.77 42.53 2.71
5434 8403 4.141959 TGCCTCCAGGAAAAGAAAACAAAG 60.142 41.667 0.00 0.00 37.39 2.77
5463 8432 3.551485 CCTGAAAACTTGCAAAACGAAGG 59.449 43.478 0.00 0.00 0.00 3.46
5464 8433 2.926838 TGAAAACTTGCAAAACGAAGGC 59.073 40.909 0.00 0.00 0.00 4.35
5465 8434 2.663826 AAACTTGCAAAACGAAGGCA 57.336 40.000 0.00 0.00 35.41 4.75
5466 8435 2.663826 AACTTGCAAAACGAAGGCAA 57.336 40.000 0.00 0.00 44.50 4.52
5469 8438 2.159114 ACTTGCAAAACGAAGGCAATGT 60.159 40.909 0.00 0.00 45.43 2.71
5470 8439 2.593346 TGCAAAACGAAGGCAATGTT 57.407 40.000 0.00 0.00 34.05 2.71
5471 8440 2.468831 TGCAAAACGAAGGCAATGTTC 58.531 42.857 0.00 0.00 34.05 3.18
5473 8442 2.050691 CAAAACGAAGGCAATGTTCCG 58.949 47.619 0.00 0.00 0.00 4.30
5474 8443 0.596082 AAACGAAGGCAATGTTCCGG 59.404 50.000 0.00 0.00 0.00 5.14
5475 8444 1.241315 AACGAAGGCAATGTTCCGGG 61.241 55.000 0.00 0.00 0.00 5.73
5477 8446 2.679996 AAGGCAATGTTCCGGGCC 60.680 61.111 8.95 8.95 46.77 5.80
5479 8448 2.679996 GGCAATGTTCCGGGCCTT 60.680 61.111 9.65 0.00 43.09 4.35
5480 8449 2.573340 GCAATGTTCCGGGCCTTG 59.427 61.111 0.84 6.13 0.00 3.61
5481 8450 3.005540 GCAATGTTCCGGGCCTTGG 62.006 63.158 0.84 5.29 0.00 3.61
5492 8461 3.458653 GCCTTGGGCTTTTGAGCA 58.541 55.556 0.80 0.00 46.69 4.26
5539 8510 8.597662 ACCTATTGCAATTATGAAAATGATGC 57.402 30.769 18.75 0.00 0.00 3.91
5544 8515 7.297229 TGCAATTATGAAAATGATGCAGTTG 57.703 32.000 0.00 0.00 0.00 3.16
5557 8528 1.644786 GCAGTTGTACCGGTGCCATC 61.645 60.000 19.93 12.66 0.00 3.51
5629 8600 6.004574 AGGTGACTCCTGTTTATTTTCCTTC 58.995 40.000 0.00 0.00 46.19 3.46
5688 8670 8.717717 TCTAATGTTCATTTCATAGGGACATCT 58.282 33.333 3.36 0.00 0.00 2.90
5697 8679 2.254152 TAGGGACATCTTGGAGCACT 57.746 50.000 0.00 0.00 0.00 4.40
5704 8686 1.998315 CATCTTGGAGCACTTCGTGAG 59.002 52.381 0.00 0.00 35.23 3.51
5759 8766 3.181507 CGGCCTTTAACACACATGATGAG 60.182 47.826 0.00 0.00 0.00 2.90
5775 8785 7.166638 CACATGATGAGACAAAGTACTCGTATC 59.833 40.741 0.00 11.28 36.11 2.24
5804 8814 9.947433 TCTTCGTCTCCTTATTTGGTTATTTAA 57.053 29.630 0.00 0.00 0.00 1.52
5831 8841 9.031360 ACTGATTATTACAAACACTATACAGCG 57.969 33.333 0.00 0.00 0.00 5.18
5844 8854 3.896648 ATACAGCGTTGGACAAACAAG 57.103 42.857 3.74 0.00 38.84 3.16
5848 8858 1.199852 GCGTTGGACAAACAAGCACG 61.200 55.000 0.00 0.00 38.84 5.34
5869 8879 3.119463 CGAATGACACAACGGCATTTTTC 59.881 43.478 0.00 0.00 32.80 2.29
5871 8881 5.446143 AATGACACAACGGCATTTTTCTA 57.554 34.783 0.00 0.00 0.00 2.10
5876 8886 4.165779 CACAACGGCATTTTTCTATCACC 58.834 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.879759 CAACATCTCCTACGTTACATAAAATGT 58.120 33.333 0.00 0.00 46.92 2.71
25 26 9.093970 TCAACATCTCCTACGTTACATAAAATG 57.906 33.333 0.00 0.00 0.00 2.32
26 27 9.661563 TTCAACATCTCCTACGTTACATAAAAT 57.338 29.630 0.00 0.00 0.00 1.82
27 28 9.661563 ATTCAACATCTCCTACGTTACATAAAA 57.338 29.630 0.00 0.00 0.00 1.52
28 29 9.309516 GATTCAACATCTCCTACGTTACATAAA 57.690 33.333 0.00 0.00 0.00 1.40
29 30 7.924412 GGATTCAACATCTCCTACGTTACATAA 59.076 37.037 0.00 0.00 0.00 1.90
30 31 7.287005 AGGATTCAACATCTCCTACGTTACATA 59.713 37.037 0.00 0.00 37.64 2.29
31 32 6.098409 AGGATTCAACATCTCCTACGTTACAT 59.902 38.462 0.00 0.00 37.64 2.29
32 33 5.421056 AGGATTCAACATCTCCTACGTTACA 59.579 40.000 0.00 0.00 37.64 2.41
33 34 5.749109 CAGGATTCAACATCTCCTACGTTAC 59.251 44.000 0.00 0.00 37.30 2.50
34 35 5.681437 GCAGGATTCAACATCTCCTACGTTA 60.681 44.000 0.00 0.00 37.30 3.18
35 36 4.759782 CAGGATTCAACATCTCCTACGTT 58.240 43.478 0.00 0.00 37.30 3.99
36 37 3.430929 GCAGGATTCAACATCTCCTACGT 60.431 47.826 0.00 0.00 37.30 3.57
37 38 3.126831 GCAGGATTCAACATCTCCTACG 58.873 50.000 0.00 0.00 37.30 3.51
38 39 4.414337 AGCAGGATTCAACATCTCCTAC 57.586 45.455 0.00 0.00 37.30 3.18
39 40 4.345257 GGTAGCAGGATTCAACATCTCCTA 59.655 45.833 0.00 0.00 37.30 2.94
40 41 3.135530 GGTAGCAGGATTCAACATCTCCT 59.864 47.826 0.00 0.00 40.05 3.69
41 42 3.118261 TGGTAGCAGGATTCAACATCTCC 60.118 47.826 0.00 0.00 0.00 3.71
42 43 3.873952 GTGGTAGCAGGATTCAACATCTC 59.126 47.826 0.00 0.00 0.00 2.75
43 44 3.370953 GGTGGTAGCAGGATTCAACATCT 60.371 47.826 0.00 0.00 0.00 2.90
44 45 2.945668 GGTGGTAGCAGGATTCAACATC 59.054 50.000 0.00 0.00 0.00 3.06
45 46 2.578021 AGGTGGTAGCAGGATTCAACAT 59.422 45.455 0.00 0.00 0.00 2.71
46 47 1.985159 AGGTGGTAGCAGGATTCAACA 59.015 47.619 0.00 0.00 0.00 3.33
47 48 2.290323 ACAGGTGGTAGCAGGATTCAAC 60.290 50.000 0.00 0.00 0.00 3.18
48 49 1.985159 ACAGGTGGTAGCAGGATTCAA 59.015 47.619 0.00 0.00 0.00 2.69
49 50 1.656587 ACAGGTGGTAGCAGGATTCA 58.343 50.000 0.00 0.00 0.00 2.57
50 51 2.237392 AGAACAGGTGGTAGCAGGATTC 59.763 50.000 0.00 0.00 0.00 2.52
51 52 2.026822 CAGAACAGGTGGTAGCAGGATT 60.027 50.000 0.00 0.00 0.00 3.01
52 53 1.556911 CAGAACAGGTGGTAGCAGGAT 59.443 52.381 0.00 0.00 0.00 3.24
53 54 0.976641 CAGAACAGGTGGTAGCAGGA 59.023 55.000 0.00 0.00 0.00 3.86
54 55 0.036010 CCAGAACAGGTGGTAGCAGG 60.036 60.000 0.00 0.00 0.00 4.85
55 56 0.976641 TCCAGAACAGGTGGTAGCAG 59.023 55.000 0.00 0.00 36.37 4.24
56 57 1.429930 TTCCAGAACAGGTGGTAGCA 58.570 50.000 0.00 0.00 36.37 3.49
57 58 2.561478 TTTCCAGAACAGGTGGTAGC 57.439 50.000 0.00 0.00 36.37 3.58
58 59 2.749621 GCATTTCCAGAACAGGTGGTAG 59.250 50.000 0.00 0.00 36.37 3.18
59 60 2.790433 GCATTTCCAGAACAGGTGGTA 58.210 47.619 0.00 0.00 36.37 3.25
60 61 1.620822 GCATTTCCAGAACAGGTGGT 58.379 50.000 0.00 0.00 36.37 4.16
61 62 0.523072 CGCATTTCCAGAACAGGTGG 59.477 55.000 0.00 0.00 36.28 4.61
62 63 1.197721 GTCGCATTTCCAGAACAGGTG 59.802 52.381 0.00 0.00 0.00 4.00
63 64 1.072331 AGTCGCATTTCCAGAACAGGT 59.928 47.619 0.00 0.00 0.00 4.00
64 65 1.813513 AGTCGCATTTCCAGAACAGG 58.186 50.000 0.00 0.00 0.00 4.00
65 66 2.807967 TGAAGTCGCATTTCCAGAACAG 59.192 45.455 0.00 0.00 0.00 3.16
66 67 2.807967 CTGAAGTCGCATTTCCAGAACA 59.192 45.455 0.00 0.00 0.00 3.18
67 68 2.413371 GCTGAAGTCGCATTTCCAGAAC 60.413 50.000 0.00 0.00 0.00 3.01
68 69 1.806542 GCTGAAGTCGCATTTCCAGAA 59.193 47.619 0.00 0.00 0.00 3.02
69 70 1.270785 TGCTGAAGTCGCATTTCCAGA 60.271 47.619 0.00 0.00 31.40 3.86
70 71 1.135859 GTGCTGAAGTCGCATTTCCAG 60.136 52.381 0.00 0.00 39.89 3.86
71 72 0.874390 GTGCTGAAGTCGCATTTCCA 59.126 50.000 0.00 0.00 39.89 3.53
72 73 0.874390 TGTGCTGAAGTCGCATTTCC 59.126 50.000 0.00 0.00 39.89 3.13
73 74 1.135859 CCTGTGCTGAAGTCGCATTTC 60.136 52.381 0.00 0.00 39.89 2.17
74 75 0.877071 CCTGTGCTGAAGTCGCATTT 59.123 50.000 0.00 0.00 39.89 2.32
75 76 0.250467 ACCTGTGCTGAAGTCGCATT 60.250 50.000 0.00 0.00 39.89 3.56
76 77 0.952497 CACCTGTGCTGAAGTCGCAT 60.952 55.000 0.00 0.00 39.89 4.73
77 78 1.595109 CACCTGTGCTGAAGTCGCA 60.595 57.895 0.00 0.00 34.52 5.10
78 79 3.248029 CACCTGTGCTGAAGTCGC 58.752 61.111 0.00 0.00 0.00 5.19
89 90 2.368548 TCAATAGTCACACAGCACCTGT 59.631 45.455 0.00 0.00 46.51 4.00
90 91 3.044235 TCAATAGTCACACAGCACCTG 57.956 47.619 0.00 0.00 37.52 4.00
91 92 3.988976 ATCAATAGTCACACAGCACCT 57.011 42.857 0.00 0.00 0.00 4.00
92 93 4.002982 TGAATCAATAGTCACACAGCACC 58.997 43.478 0.00 0.00 0.00 5.01
101 102 4.536090 AGTTGAGGGGTGAATCAATAGTCA 59.464 41.667 0.00 0.00 37.72 3.41
102 103 5.104259 AGTTGAGGGGTGAATCAATAGTC 57.896 43.478 0.00 0.00 37.72 2.59
103 104 4.080299 GGAGTTGAGGGGTGAATCAATAGT 60.080 45.833 0.00 0.00 37.72 2.12
104 105 4.164988 AGGAGTTGAGGGGTGAATCAATAG 59.835 45.833 0.00 0.00 37.72 1.73
105 106 4.111577 AGGAGTTGAGGGGTGAATCAATA 58.888 43.478 0.00 0.00 37.72 1.90
106 107 2.922283 AGGAGTTGAGGGGTGAATCAAT 59.078 45.455 0.00 0.00 37.72 2.57
107 108 2.348472 AGGAGTTGAGGGGTGAATCAA 58.652 47.619 0.00 0.00 33.16 2.57
108 109 2.044793 AGGAGTTGAGGGGTGAATCA 57.955 50.000 0.00 0.00 0.00 2.57
109 110 2.170817 GGTAGGAGTTGAGGGGTGAATC 59.829 54.545 0.00 0.00 0.00 2.52
110 111 2.197465 GGTAGGAGTTGAGGGGTGAAT 58.803 52.381 0.00 0.00 0.00 2.57
111 112 1.132657 TGGTAGGAGTTGAGGGGTGAA 60.133 52.381 0.00 0.00 0.00 3.18
112 113 0.490017 TGGTAGGAGTTGAGGGGTGA 59.510 55.000 0.00 0.00 0.00 4.02
113 114 1.358152 TTGGTAGGAGTTGAGGGGTG 58.642 55.000 0.00 0.00 0.00 4.61
114 115 1.916181 CATTGGTAGGAGTTGAGGGGT 59.084 52.381 0.00 0.00 0.00 4.95
115 116 1.212935 CCATTGGTAGGAGTTGAGGGG 59.787 57.143 0.00 0.00 0.00 4.79
116 117 2.196595 TCCATTGGTAGGAGTTGAGGG 58.803 52.381 1.86 0.00 0.00 4.30
117 118 3.370953 CCTTCCATTGGTAGGAGTTGAGG 60.371 52.174 20.76 4.20 41.95 3.86
118 119 3.878778 CCTTCCATTGGTAGGAGTTGAG 58.121 50.000 20.76 0.00 41.95 3.02
119 120 2.026262 GCCTTCCATTGGTAGGAGTTGA 60.026 50.000 27.48 0.00 41.95 3.18
120 121 2.290896 TGCCTTCCATTGGTAGGAGTTG 60.291 50.000 27.48 5.56 41.95 3.16
121 122 1.992557 TGCCTTCCATTGGTAGGAGTT 59.007 47.619 27.48 0.00 41.95 3.01
122 123 1.668826 TGCCTTCCATTGGTAGGAGT 58.331 50.000 27.48 0.00 41.95 3.85
123 124 2.173356 TCATGCCTTCCATTGGTAGGAG 59.827 50.000 27.48 17.19 41.95 3.69
124 125 2.204463 TCATGCCTTCCATTGGTAGGA 58.796 47.619 27.48 15.05 41.95 2.94
125 126 2.734755 TCATGCCTTCCATTGGTAGG 57.265 50.000 20.98 20.98 42.23 3.18
126 127 4.579454 CAATCATGCCTTCCATTGGTAG 57.421 45.455 1.86 2.19 29.71 3.18
140 141 2.581216 ATCTAGCCTGGGCAATCATG 57.419 50.000 14.39 0.00 44.88 3.07
141 142 2.981784 TGTATCTAGCCTGGGCAATCAT 59.018 45.455 14.39 3.04 44.88 2.45
142 143 2.407562 TGTATCTAGCCTGGGCAATCA 58.592 47.619 14.39 1.93 44.88 2.57
143 144 3.142174 GTTGTATCTAGCCTGGGCAATC 58.858 50.000 14.39 0.00 44.88 2.67
144 145 2.780010 AGTTGTATCTAGCCTGGGCAAT 59.220 45.455 14.39 6.85 44.88 3.56
145 146 2.196595 AGTTGTATCTAGCCTGGGCAA 58.803 47.619 14.39 0.00 44.88 4.52
146 147 1.879575 AGTTGTATCTAGCCTGGGCA 58.120 50.000 14.39 0.00 44.88 5.36
147 148 2.170607 TGAAGTTGTATCTAGCCTGGGC 59.829 50.000 3.00 3.00 42.33 5.36
148 149 3.742640 GCTGAAGTTGTATCTAGCCTGGG 60.743 52.174 0.00 0.00 0.00 4.45
149 150 3.118629 TGCTGAAGTTGTATCTAGCCTGG 60.119 47.826 0.00 0.00 0.00 4.45
150 151 4.128925 TGCTGAAGTTGTATCTAGCCTG 57.871 45.455 0.00 0.00 0.00 4.85
151 152 4.223923 ACTTGCTGAAGTTGTATCTAGCCT 59.776 41.667 0.00 0.00 39.56 4.58
152 153 4.508662 ACTTGCTGAAGTTGTATCTAGCC 58.491 43.478 0.00 0.00 39.56 3.93
153 154 4.568760 GGACTTGCTGAAGTTGTATCTAGC 59.431 45.833 0.00 0.00 42.80 3.42
154 155 5.971763 AGGACTTGCTGAAGTTGTATCTAG 58.028 41.667 0.00 0.00 42.80 2.43
155 156 6.014584 TGAAGGACTTGCTGAAGTTGTATCTA 60.015 38.462 0.00 0.00 42.80 1.98
156 157 4.899352 AGGACTTGCTGAAGTTGTATCT 57.101 40.909 0.00 0.00 42.80 1.98
157 158 4.997395 TGAAGGACTTGCTGAAGTTGTATC 59.003 41.667 0.00 0.00 42.80 2.24
158 159 4.973168 TGAAGGACTTGCTGAAGTTGTAT 58.027 39.130 0.00 0.00 42.80 2.29
159 160 4.415881 TGAAGGACTTGCTGAAGTTGTA 57.584 40.909 0.00 0.00 42.80 2.41
160 161 3.281727 TGAAGGACTTGCTGAAGTTGT 57.718 42.857 0.00 0.00 42.80 3.32
161 162 4.276678 TCAATGAAGGACTTGCTGAAGTTG 59.723 41.667 0.00 0.00 42.80 3.16
162 163 4.464008 TCAATGAAGGACTTGCTGAAGTT 58.536 39.130 0.00 0.00 42.80 2.66
163 164 4.070716 CTCAATGAAGGACTTGCTGAAGT 58.929 43.478 0.00 0.00 45.59 3.01
164 165 4.153835 GTCTCAATGAAGGACTTGCTGAAG 59.846 45.833 0.00 0.00 35.07 3.02
165 166 4.067896 GTCTCAATGAAGGACTTGCTGAA 58.932 43.478 0.00 0.00 0.00 3.02
166 167 3.557898 GGTCTCAATGAAGGACTTGCTGA 60.558 47.826 3.24 0.00 0.00 4.26
167 168 2.746362 GGTCTCAATGAAGGACTTGCTG 59.254 50.000 3.24 0.00 0.00 4.41
168 169 2.641815 AGGTCTCAATGAAGGACTTGCT 59.358 45.455 3.24 0.00 0.00 3.91
169 170 3.064900 AGGTCTCAATGAAGGACTTGC 57.935 47.619 3.24 0.00 0.00 4.01
170 171 4.645535 TGAAGGTCTCAATGAAGGACTTG 58.354 43.478 3.24 0.00 0.00 3.16
171 172 4.982241 TGAAGGTCTCAATGAAGGACTT 57.018 40.909 3.24 0.00 0.00 3.01
172 173 4.982241 TTGAAGGTCTCAATGAAGGACT 57.018 40.909 3.24 0.00 39.20 3.85
182 183 1.881973 GCAGCAACATTGAAGGTCTCA 59.118 47.619 0.00 0.00 0.00 3.27
183 184 1.881973 TGCAGCAACATTGAAGGTCTC 59.118 47.619 0.00 0.00 0.00 3.36
184 185 1.985473 TGCAGCAACATTGAAGGTCT 58.015 45.000 0.00 0.00 0.00 3.85
185 186 2.602878 CATGCAGCAACATTGAAGGTC 58.397 47.619 0.00 0.00 0.00 3.85
186 187 1.274167 CCATGCAGCAACATTGAAGGT 59.726 47.619 0.00 0.00 0.00 3.50
187 188 1.546923 TCCATGCAGCAACATTGAAGG 59.453 47.619 0.00 0.00 0.00 3.46
188 189 3.119280 TGATCCATGCAGCAACATTGAAG 60.119 43.478 0.00 0.00 0.00 3.02
189 190 2.826725 TGATCCATGCAGCAACATTGAA 59.173 40.909 0.00 0.00 0.00 2.69
190 191 2.448453 TGATCCATGCAGCAACATTGA 58.552 42.857 0.00 0.00 0.00 2.57
191 192 2.951457 TGATCCATGCAGCAACATTG 57.049 45.000 0.00 0.00 0.00 2.82
192 193 2.102420 CCATGATCCATGCAGCAACATT 59.898 45.455 0.00 0.00 40.20 2.71
193 194 1.686587 CCATGATCCATGCAGCAACAT 59.313 47.619 0.00 0.00 40.20 2.71
194 195 1.107945 CCATGATCCATGCAGCAACA 58.892 50.000 0.00 0.00 40.20 3.33
195 196 0.387929 CCCATGATCCATGCAGCAAC 59.612 55.000 0.00 0.00 40.20 4.17
196 197 1.396607 GCCCATGATCCATGCAGCAA 61.397 55.000 0.00 0.00 40.20 3.91
197 198 1.830847 GCCCATGATCCATGCAGCA 60.831 57.895 0.00 0.00 40.20 4.41
198 199 1.185618 ATGCCCATGATCCATGCAGC 61.186 55.000 0.00 11.02 40.20 5.25
199 200 0.888619 GATGCCCATGATCCATGCAG 59.111 55.000 0.00 0.00 40.20 4.41
200 201 0.541063 GGATGCCCATGATCCATGCA 60.541 55.000 6.97 0.00 40.20 3.96
201 202 0.251653 AGGATGCCCATGATCCATGC 60.252 55.000 12.98 8.53 41.82 4.06
202 203 1.203013 ACAGGATGCCCATGATCCATG 60.203 52.381 12.98 10.44 41.82 3.66
203 204 1.155323 ACAGGATGCCCATGATCCAT 58.845 50.000 12.98 4.05 41.82 3.41
204 205 0.184211 CACAGGATGCCCATGATCCA 59.816 55.000 12.98 0.00 41.82 3.41
205 206 0.184451 ACACAGGATGCCCATGATCC 59.816 55.000 4.12 4.12 42.53 3.36
206 207 1.602311 GACACAGGATGCCCATGATC 58.398 55.000 0.00 0.00 42.53 2.92
207 208 0.184451 GGACACAGGATGCCCATGAT 59.816 55.000 0.00 0.00 42.53 2.45
401 438 2.933906 TGAAGAACCACGAGTGACAAAC 59.066 45.455 4.59 0.00 0.00 2.93
407 444 2.285220 CACAACTGAAGAACCACGAGTG 59.715 50.000 0.00 0.00 0.00 3.51
1391 3503 8.874156 TCAGCATCTTCAAGGTATATAATGAGT 58.126 33.333 0.00 0.00 0.00 3.41
1497 3609 3.521126 AGATGGAATTCCCGGATATGGAG 59.479 47.826 21.90 0.00 37.93 3.86
1522 3634 2.026822 CCAACTCTGTAGGAATGCCACT 60.027 50.000 0.00 0.00 36.29 4.00
1602 3714 3.002791 CAGATTACGAAAAGCTGCTGGA 58.997 45.455 1.35 0.00 0.00 3.86
1671 3783 7.040409 ACCAATGAGCTTATTCCGGAAAATATC 60.040 37.037 23.08 15.55 0.00 1.63
1680 3792 3.065371 GGTTCACCAATGAGCTTATTCCG 59.935 47.826 0.00 0.00 36.37 4.30
1749 3861 3.370840 TCCAATTGACCAATCTCCCTG 57.629 47.619 7.12 0.00 0.00 4.45
1794 3906 1.608590 CTCCCAGTGAACGCATTTTGT 59.391 47.619 0.00 0.00 0.00 2.83
1811 3923 3.766051 ACCAATTTCTTCTGGAATGCTCC 59.234 43.478 0.00 0.00 42.81 4.70
2036 4149 8.142994 TCTTCTTGCAGTTACTTAGTTCTTTG 57.857 34.615 0.00 0.00 0.00 2.77
2159 4272 9.288576 CAATCTGGAATATTGCCTGATAGTTTA 57.711 33.333 18.05 0.00 41.46 2.01
2294 4803 2.818432 GACAGAACCTGAGAGACGGTTA 59.182 50.000 0.45 0.00 43.23 2.85
2319 4828 4.816385 GGAGTTGTCTTGACACATCTCAAA 59.184 41.667 20.16 0.25 41.81 2.69
2320 4829 4.380531 GGAGTTGTCTTGACACATCTCAA 58.619 43.478 20.16 0.00 41.81 3.02
2619 5128 0.183492 AACCTCTGCAAGCTGGACAA 59.817 50.000 0.00 0.00 32.81 3.18
2726 5235 2.572290 GGAATGTTCCCAGATAACCCG 58.428 52.381 0.09 0.00 41.62 5.28
2814 5323 1.275573 GTTAGATATGGCCCTCGGGAC 59.724 57.143 6.08 2.74 45.60 4.46
2904 5413 3.640967 TGAACCTCATTTTCAAACCCCAG 59.359 43.478 0.00 0.00 29.89 4.45
3033 5542 1.136695 CAAGTTGCCTTGCAGGTTCAA 59.863 47.619 0.00 0.00 41.51 2.69
3035 5544 3.575399 CAAGTTGCCTTGCAGGTTC 57.425 52.632 0.00 0.00 41.51 3.62
3450 5966 4.623167 CAGTTGTGTGAAGTTCGAGATAGG 59.377 45.833 0.00 0.00 0.00 2.57
3664 6180 1.065926 CACCTCCTGCTGCACAATCTA 60.066 52.381 0.00 0.00 0.00 1.98
3738 6254 8.280258 AGGATACAAATGATCCCTAATCTTCA 57.720 34.615 0.00 0.00 43.52 3.02
3824 6340 5.163513 GCAATAACCAATGAACTGTTCCTG 58.836 41.667 17.26 13.71 0.00 3.86
3869 6385 0.106918 TTGAGGTTGGCTCAACGGTT 60.107 50.000 10.63 0.00 44.36 4.44
3996 6512 7.672983 TGATGTGTTCCTTACTGAAATTCTC 57.327 36.000 0.00 0.00 0.00 2.87
4010 6526 2.146342 CCATCGCCTATGATGTGTTCC 58.854 52.381 3.36 0.00 43.39 3.62
4208 6724 2.422479 CTCGTAGATCAGGAACCGTTCA 59.578 50.000 13.23 0.00 33.89 3.18
4395 6911 2.743752 CGTCCAGCAGGATGTTGCG 61.744 63.158 9.16 0.01 46.73 4.85
4418 6934 1.304217 AGAGACCCTCGGCTCGAAA 60.304 57.895 0.00 0.00 34.74 3.46
4493 7009 1.196012 TGTATCCACATGTACCGGCA 58.804 50.000 0.00 0.00 0.00 5.69
4526 7042 0.770499 TGGACTTCATTGTCTGGCCA 59.230 50.000 4.71 4.71 37.16 5.36
4663 7185 4.193334 CTCCGCGAGCGATCACCA 62.193 66.667 19.72 0.00 42.83 4.17
4680 7202 0.944311 TCAAACAGCTCGTTCCTCGC 60.944 55.000 2.65 0.00 36.59 5.03
4836 7358 4.431131 AGGCCCGCACTCCATTGG 62.431 66.667 0.00 0.00 0.00 3.16
4931 7467 3.055094 ACAAGTTACCTACCATCAGCCTG 60.055 47.826 0.00 0.00 0.00 4.85
5013 7591 2.561478 TTTGTCCCAACTACAGCCTC 57.439 50.000 0.00 0.00 0.00 4.70
5226 7838 2.427232 TAAAGCAAAAGCAGCAGCAG 57.573 45.000 3.17 0.00 45.49 4.24
5251 7863 5.177696 GCACTACGACACAGAAGAAGAAAAT 59.822 40.000 0.00 0.00 0.00 1.82
5256 7868 2.726760 GTGCACTACGACACAGAAGAAG 59.273 50.000 10.32 0.00 36.77 2.85
5337 7991 4.376225 AAACCTCCATAGAACCCGAAAA 57.624 40.909 0.00 0.00 0.00 2.29
5369 8295 3.979495 GCAGATACAATAGCTTTGCATGC 59.021 43.478 11.82 11.82 0.00 4.06
5399 8325 1.751927 GGAGGCAGTCCATTGCAGG 60.752 63.158 0.00 0.00 46.10 4.85
5434 8403 1.215014 GCAAGTTTTCAGGCCGCAAC 61.215 55.000 0.00 0.00 0.00 4.17
5463 8432 2.573340 CAAGGCCCGGAACATTGC 59.427 61.111 0.73 0.00 0.00 3.56
5464 8433 2.350458 CCCAAGGCCCGGAACATTG 61.350 63.158 0.73 9.06 0.00 2.82
5465 8434 2.037208 CCCAAGGCCCGGAACATT 59.963 61.111 0.73 0.00 0.00 2.71
5466 8435 4.759205 GCCCAAGGCCCGGAACAT 62.759 66.667 0.73 0.00 44.06 2.71
5516 8485 9.256477 ACTGCATCATTTTCATAATTGCAATAG 57.744 29.630 13.39 6.25 38.07 1.73
5539 8510 1.358725 CGATGGCACCGGTACAACTG 61.359 60.000 6.87 0.00 0.00 3.16
5544 8515 4.460683 TGGCGATGGCACCGGTAC 62.461 66.667 6.87 0.00 42.47 3.34
5557 8528 2.032528 TCAGCTGGGAAAGTGGCG 59.967 61.111 15.13 0.00 0.00 5.69
5629 8600 5.856126 TCAACACGCTATAAAGGAAAGTG 57.144 39.130 0.00 0.00 0.00 3.16
5704 8686 1.657751 GCTTTGCTCGGGGTGATTCC 61.658 60.000 0.00 0.00 0.00 3.01
5759 8766 6.746364 ACGAAGAATGATACGAGTACTTTGTC 59.254 38.462 0.00 0.00 0.00 3.18
5775 8785 6.743575 AACCAAATAAGGAGACGAAGAATG 57.256 37.500 0.00 0.00 0.00 2.67
5827 8837 0.100325 TGCTTGTTTGTCCAACGCTG 59.900 50.000 0.00 0.00 38.36 5.18
5830 8840 0.375454 TCGTGCTTGTTTGTCCAACG 59.625 50.000 0.00 0.00 38.36 4.10
5831 8841 2.553079 TTCGTGCTTGTTTGTCCAAC 57.447 45.000 0.00 0.00 35.71 3.77
5844 8854 1.440353 GCCGTTGTGTCATTCGTGC 60.440 57.895 0.00 0.00 0.00 5.34
5848 8858 4.298332 AGAAAAATGCCGTTGTGTCATTC 58.702 39.130 0.00 0.00 30.84 2.67


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

AutoCloner maintained by Alex Coulton.