Multiple sequence alignment - TraesCS1D01G075500

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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 TraesCS1D01G075500 chr1D 100.000 2453 0 0 1 2453 57476073 57478525 0.000000e+00 4530.0
1 TraesCS1D01G075500 chr1A 91.434 1611 91 14 261 1866 56617143 56618711 0.000000e+00 2167.0
2 TraesCS1D01G075500 chr1A 83.966 237 30 4 1920 2155 56618727 56618956 1.140000e-53 220.0
3 TraesCS1D01G075500 chr1B 90.693 1644 85 29 261 1866 92871316 92872929 0.000000e+00 2126.0
4 TraesCS1D01G075500 chr1B 78.521 568 82 30 1903 2453 92872932 92873476 1.090000e-88 337.0
5 TraesCS1D01G075500 chr3A 86.792 53 7 0 2349 2401 568682631 568682683 2.630000e-05 60.2


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 TraesCS1D01G075500 chr1D 57476073 57478525 2452 False 4530.0 4530 100.000 1 2453 1 chr1D.!!$F1 2452
1 TraesCS1D01G075500 chr1A 56617143 56618956 1813 False 1193.5 2167 87.700 261 2155 2 chr1A.!!$F1 1894
2 TraesCS1D01G075500 chr1B 92871316 92873476 2160 False 1231.5 2126 84.607 261 2453 2 chr1B.!!$F1 2192

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
336 337 0.03601 CTCCTTTCCTGCGTGTGGAT 60.036 55.0 0.0 0.0 33.09 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1924 0.038744 CAAGCAGATTGACCCAGGGT 59.961 55.0 12.53 12.53 41.83 4.34 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
57 58 6.662414 TTTGCATACTAGTTTCTGGAATCG 57.338 37.500 0.00 0.00 0.00 3.34
58 59 5.339008 TGCATACTAGTTTCTGGAATCGT 57.661 39.130 0.00 0.00 0.00 3.73
59 60 6.459670 TGCATACTAGTTTCTGGAATCGTA 57.540 37.500 0.00 0.00 0.00 3.43
60 61 6.270815 TGCATACTAGTTTCTGGAATCGTAC 58.729 40.000 0.00 0.00 0.00 3.67
61 62 6.096423 TGCATACTAGTTTCTGGAATCGTACT 59.904 38.462 0.00 0.00 0.00 2.73
62 63 6.979238 GCATACTAGTTTCTGGAATCGTACTT 59.021 38.462 0.00 0.00 0.00 2.24
63 64 7.167801 GCATACTAGTTTCTGGAATCGTACTTC 59.832 40.741 0.00 0.00 0.00 3.01
64 65 5.963594 ACTAGTTTCTGGAATCGTACTTCC 58.036 41.667 6.89 6.89 44.23 3.46
65 66 5.715753 ACTAGTTTCTGGAATCGTACTTCCT 59.284 40.000 13.42 0.00 44.27 3.36
66 67 5.074584 AGTTTCTGGAATCGTACTTCCTC 57.925 43.478 13.42 0.00 44.27 3.71
67 68 4.081586 AGTTTCTGGAATCGTACTTCCTCC 60.082 45.833 13.42 4.79 44.27 4.30
68 69 2.385803 TCTGGAATCGTACTTCCTCCC 58.614 52.381 13.42 0.00 44.27 4.30
69 70 1.413077 CTGGAATCGTACTTCCTCCCC 59.587 57.143 13.42 0.00 44.27 4.81
70 71 0.388294 GGAATCGTACTTCCTCCCCG 59.612 60.000 6.64 0.00 41.32 5.73
71 72 1.396653 GAATCGTACTTCCTCCCCGA 58.603 55.000 0.00 0.00 0.00 5.14
72 73 1.753073 GAATCGTACTTCCTCCCCGAA 59.247 52.381 0.00 0.00 0.00 4.30
73 74 2.083628 ATCGTACTTCCTCCCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
74 75 1.856629 TCGTACTTCCTCCCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
75 76 1.753073 TCGTACTTCCTCCCCGAATTC 59.247 52.381 0.00 0.00 0.00 2.17
76 77 1.755380 CGTACTTCCTCCCCGAATTCT 59.245 52.381 3.52 0.00 0.00 2.40
77 78 2.954318 CGTACTTCCTCCCCGAATTCTA 59.046 50.000 3.52 0.00 0.00 2.10
78 79 3.004524 CGTACTTCCTCCCCGAATTCTAG 59.995 52.174 3.52 0.00 0.00 2.43
79 80 1.763545 ACTTCCTCCCCGAATTCTAGC 59.236 52.381 3.52 0.00 0.00 3.42
80 81 1.762957 CTTCCTCCCCGAATTCTAGCA 59.237 52.381 3.52 0.00 0.00 3.49
81 82 1.874129 TCCTCCCCGAATTCTAGCAA 58.126 50.000 3.52 0.00 0.00 3.91
82 83 2.193127 TCCTCCCCGAATTCTAGCAAA 58.807 47.619 3.52 0.00 0.00 3.68
83 84 2.093128 TCCTCCCCGAATTCTAGCAAAC 60.093 50.000 3.52 0.00 0.00 2.93
84 85 2.092914 CCTCCCCGAATTCTAGCAAACT 60.093 50.000 3.52 0.00 0.00 2.66
85 86 3.610911 CTCCCCGAATTCTAGCAAACTT 58.389 45.455 3.52 0.00 0.00 2.66
86 87 4.383770 CCTCCCCGAATTCTAGCAAACTTA 60.384 45.833 3.52 0.00 0.00 2.24
87 88 5.367945 TCCCCGAATTCTAGCAAACTTAT 57.632 39.130 3.52 0.00 0.00 1.73
88 89 5.751586 TCCCCGAATTCTAGCAAACTTATT 58.248 37.500 3.52 0.00 0.00 1.40
89 90 6.184789 TCCCCGAATTCTAGCAAACTTATTT 58.815 36.000 3.52 0.00 0.00 1.40
90 91 7.340256 TCCCCGAATTCTAGCAAACTTATTTA 58.660 34.615 3.52 0.00 0.00 1.40
91 92 7.281549 TCCCCGAATTCTAGCAAACTTATTTAC 59.718 37.037 3.52 0.00 0.00 2.01
92 93 7.066525 CCCCGAATTCTAGCAAACTTATTTACA 59.933 37.037 3.52 0.00 0.00 2.41
93 94 8.621286 CCCGAATTCTAGCAAACTTATTTACAT 58.379 33.333 3.52 0.00 0.00 2.29
116 117 7.858879 ACATTTTTGTACAAAGCTTAGTTACCG 59.141 33.333 19.72 1.18 0.00 4.02
117 118 7.551035 TTTTTGTACAAAGCTTAGTTACCGA 57.449 32.000 19.72 0.00 0.00 4.69
118 119 6.529463 TTTGTACAAAGCTTAGTTACCGAC 57.471 37.500 17.01 0.00 0.00 4.79
119 120 4.559153 TGTACAAAGCTTAGTTACCGACC 58.441 43.478 0.00 0.00 0.00 4.79
120 121 4.281688 TGTACAAAGCTTAGTTACCGACCT 59.718 41.667 0.00 0.00 0.00 3.85
121 122 4.347360 ACAAAGCTTAGTTACCGACCTT 57.653 40.909 0.00 0.00 0.00 3.50
122 123 4.711399 ACAAAGCTTAGTTACCGACCTTT 58.289 39.130 0.00 0.00 0.00 3.11
123 124 5.128205 ACAAAGCTTAGTTACCGACCTTTT 58.872 37.500 0.00 0.00 0.00 2.27
124 125 5.237996 ACAAAGCTTAGTTACCGACCTTTTC 59.762 40.000 0.00 0.00 0.00 2.29
136 137 4.322101 CGACCTTTTCGTGGATTAGTTG 57.678 45.455 0.00 0.00 43.24 3.16
137 138 3.991773 CGACCTTTTCGTGGATTAGTTGA 59.008 43.478 0.00 0.00 43.24 3.18
138 139 4.091509 CGACCTTTTCGTGGATTAGTTGAG 59.908 45.833 0.00 0.00 43.24 3.02
139 140 5.223449 ACCTTTTCGTGGATTAGTTGAGA 57.777 39.130 0.00 0.00 0.00 3.27
140 141 5.617252 ACCTTTTCGTGGATTAGTTGAGAA 58.383 37.500 0.00 0.00 0.00 2.87
141 142 5.469084 ACCTTTTCGTGGATTAGTTGAGAAC 59.531 40.000 0.00 0.00 0.00 3.01
142 143 5.389516 CCTTTTCGTGGATTAGTTGAGAACG 60.390 44.000 0.00 0.00 36.23 3.95
143 144 3.928727 TCGTGGATTAGTTGAGAACGT 57.071 42.857 0.00 0.00 36.23 3.99
144 145 4.247267 TCGTGGATTAGTTGAGAACGTT 57.753 40.909 0.00 0.00 36.23 3.99
145 146 4.232221 TCGTGGATTAGTTGAGAACGTTC 58.768 43.478 20.71 20.71 36.23 3.95
146 147 4.022589 TCGTGGATTAGTTGAGAACGTTCT 60.023 41.667 30.12 30.12 41.00 3.01
147 148 5.181811 TCGTGGATTAGTTGAGAACGTTCTA 59.818 40.000 29.79 13.68 37.73 2.10
148 149 6.034591 CGTGGATTAGTTGAGAACGTTCTAT 58.965 40.000 29.79 18.43 37.73 1.98
149 150 6.020599 CGTGGATTAGTTGAGAACGTTCTATG 60.021 42.308 29.79 12.20 37.73 2.23
150 151 5.810587 TGGATTAGTTGAGAACGTTCTATGC 59.189 40.000 29.79 22.10 37.73 3.14
151 152 6.043411 GGATTAGTTGAGAACGTTCTATGCT 58.957 40.000 29.79 25.41 37.73 3.79
152 153 6.019479 GGATTAGTTGAGAACGTTCTATGCTG 60.019 42.308 29.79 0.00 37.73 4.41
153 154 2.996621 AGTTGAGAACGTTCTATGCTGC 59.003 45.455 29.79 16.79 37.73 5.25
154 155 2.736721 GTTGAGAACGTTCTATGCTGCA 59.263 45.455 29.79 19.11 37.73 4.41
155 156 3.251479 TGAGAACGTTCTATGCTGCAT 57.749 42.857 29.79 20.18 37.73 3.96
156 157 3.190079 TGAGAACGTTCTATGCTGCATC 58.810 45.455 29.79 14.91 37.73 3.91
157 158 3.118992 TGAGAACGTTCTATGCTGCATCT 60.119 43.478 29.79 8.17 37.73 2.90
158 159 3.193263 AGAACGTTCTATGCTGCATCTG 58.807 45.455 28.80 13.21 35.34 2.90
159 160 2.967599 ACGTTCTATGCTGCATCTGA 57.032 45.000 19.90 15.31 0.00 3.27
160 161 3.251479 ACGTTCTATGCTGCATCTGAA 57.749 42.857 19.90 19.88 0.00 3.02
161 162 3.599343 ACGTTCTATGCTGCATCTGAAA 58.401 40.909 19.90 6.61 0.00 2.69
162 163 4.194640 ACGTTCTATGCTGCATCTGAAAT 58.805 39.130 19.90 12.67 0.00 2.17
163 164 5.359756 ACGTTCTATGCTGCATCTGAAATA 58.640 37.500 19.90 0.00 0.00 1.40
164 165 5.817296 ACGTTCTATGCTGCATCTGAAATAA 59.183 36.000 19.90 0.00 0.00 1.40
165 166 6.132056 CGTTCTATGCTGCATCTGAAATAAC 58.868 40.000 19.90 11.79 0.00 1.89
166 167 5.912360 TCTATGCTGCATCTGAAATAACG 57.088 39.130 19.90 0.00 0.00 3.18
167 168 2.830772 TGCTGCATCTGAAATAACGC 57.169 45.000 0.00 0.00 0.00 4.84
168 169 2.083002 TGCTGCATCTGAAATAACGCA 58.917 42.857 0.00 0.00 0.00 5.24
169 170 2.684374 TGCTGCATCTGAAATAACGCAT 59.316 40.909 0.00 0.00 0.00 4.73
170 171 3.242837 TGCTGCATCTGAAATAACGCATC 60.243 43.478 0.00 0.00 0.00 3.91
171 172 3.003068 GCTGCATCTGAAATAACGCATCT 59.997 43.478 0.00 0.00 0.00 2.90
172 173 4.524749 CTGCATCTGAAATAACGCATCTG 58.475 43.478 0.00 0.00 0.00 2.90
173 174 3.940852 TGCATCTGAAATAACGCATCTGT 59.059 39.130 0.00 0.00 0.00 3.41
174 175 4.395854 TGCATCTGAAATAACGCATCTGTT 59.604 37.500 0.00 0.00 35.86 3.16
175 176 4.731961 GCATCTGAAATAACGCATCTGTTG 59.268 41.667 0.00 0.00 33.32 3.33
183 184 3.414272 GCATCTGTTGCCTAGCCG 58.586 61.111 0.00 0.00 46.15 5.52
184 185 2.828128 GCATCTGTTGCCTAGCCGC 61.828 63.158 0.00 0.00 46.15 6.53
185 186 1.153289 CATCTGTTGCCTAGCCGCT 60.153 57.895 0.00 0.00 0.00 5.52
186 187 1.153289 ATCTGTTGCCTAGCCGCTG 60.153 57.895 2.16 0.00 0.00 5.18
187 188 2.599645 ATCTGTTGCCTAGCCGCTGG 62.600 60.000 2.16 0.00 0.00 4.85
199 200 3.360886 CCGCTGGCAAACAAAAAGT 57.639 47.368 0.00 0.00 0.00 2.66
200 201 1.650825 CCGCTGGCAAACAAAAAGTT 58.349 45.000 0.00 0.00 43.89 2.66
201 202 1.327156 CCGCTGGCAAACAAAAAGTTG 59.673 47.619 0.00 0.00 41.19 3.16
236 237 3.414549 AAAACCGTTTACTGCTGTGTG 57.585 42.857 6.48 0.00 0.00 3.82
237 238 2.032680 AACCGTTTACTGCTGTGTGT 57.967 45.000 6.48 0.00 0.00 3.72
238 239 2.894763 ACCGTTTACTGCTGTGTGTA 57.105 45.000 6.48 0.00 0.00 2.90
239 240 3.396260 ACCGTTTACTGCTGTGTGTAT 57.604 42.857 6.48 0.00 0.00 2.29
240 241 3.735591 ACCGTTTACTGCTGTGTGTATT 58.264 40.909 6.48 0.00 0.00 1.89
241 242 3.496884 ACCGTTTACTGCTGTGTGTATTG 59.503 43.478 6.48 0.00 0.00 1.90
242 243 3.743911 CCGTTTACTGCTGTGTGTATTGA 59.256 43.478 6.48 0.00 0.00 2.57
243 244 4.377022 CCGTTTACTGCTGTGTGTATTGAC 60.377 45.833 6.48 0.00 0.00 3.18
244 245 4.377022 CGTTTACTGCTGTGTGTATTGACC 60.377 45.833 6.48 0.00 0.00 4.02
245 246 1.795768 ACTGCTGTGTGTATTGACCG 58.204 50.000 0.00 0.00 0.00 4.79
246 247 1.343142 ACTGCTGTGTGTATTGACCGA 59.657 47.619 0.00 0.00 0.00 4.69
247 248 2.028112 ACTGCTGTGTGTATTGACCGAT 60.028 45.455 0.00 0.00 0.00 4.18
248 249 2.604914 CTGCTGTGTGTATTGACCGATC 59.395 50.000 0.00 0.00 0.00 3.69
249 250 2.028567 TGCTGTGTGTATTGACCGATCA 60.029 45.455 0.00 0.00 0.00 2.92
282 283 1.278238 CGATGTTTGCTCGGTAGGAC 58.722 55.000 0.00 0.00 32.58 3.85
285 286 2.922740 TGTTTGCTCGGTAGGACTTT 57.077 45.000 0.00 0.00 0.00 2.66
290 291 1.590147 CTCGGTAGGACTTTGGCGT 59.410 57.895 0.00 0.00 0.00 5.68
293 294 1.826720 TCGGTAGGACTTTGGCGTAAT 59.173 47.619 0.00 0.00 0.00 1.89
304 305 5.116882 ACTTTGGCGTAATTAGATGGAGAC 58.883 41.667 0.00 0.00 0.00 3.36
336 337 0.036010 CTCCTTTCCTGCGTGTGGAT 60.036 55.000 0.00 0.00 33.09 3.41
448 458 0.474184 AATACCCAGAATGCCCTCCG 59.526 55.000 0.00 0.00 31.97 4.63
567 577 4.676849 CAGCTAAGTCCTGCTTTCTTTC 57.323 45.455 0.00 0.00 37.44 2.62
568 578 4.322567 CAGCTAAGTCCTGCTTTCTTTCT 58.677 43.478 0.00 0.00 37.44 2.52
577 587 1.271379 TGCTTTCTTTCTCCCTTCCCG 60.271 52.381 0.00 0.00 0.00 5.14
584 594 3.260128 TCTTTCTCCCTTCCCGTTCTTAC 59.740 47.826 0.00 0.00 0.00 2.34
628 638 4.628963 TTTTCCTTACAGTGTACTCCCC 57.371 45.455 1.43 0.00 0.00 4.81
646 656 1.135517 CCCGTTCCGTTGCAAATAAGG 60.136 52.381 0.00 2.76 0.00 2.69
688 698 1.183549 GCCTCGACTCCTTGGTCTTA 58.816 55.000 0.00 0.00 34.38 2.10
885 895 2.514592 CAACGCCGCATCCATCCT 60.515 61.111 0.00 0.00 0.00 3.24
909 922 4.283212 GCCTCTAGTTGATTAGATCCAGCT 59.717 45.833 0.00 0.00 0.00 4.24
910 923 5.566627 GCCTCTAGTTGATTAGATCCAGCTC 60.567 48.000 0.00 0.00 0.00 4.09
921 934 0.253327 ATCCAGCTCCGTTTCTTCCC 59.747 55.000 0.00 0.00 0.00 3.97
927 940 1.822506 CTCCGTTTCTTCCCCTTTCC 58.177 55.000 0.00 0.00 0.00 3.13
930 943 1.202891 CCGTTTCTTCCCCTTTCCTGT 60.203 52.381 0.00 0.00 0.00 4.00
965 980 4.397417 CCGCCATCAAAGAAAAGAGATCTT 59.603 41.667 0.00 0.00 38.75 2.40
984 999 4.072131 TCTTTTTCCTGGTTCTTGGATCG 58.928 43.478 0.00 0.00 31.76 3.69
1368 1383 2.217745 GGACATCCCGGAGATCCCC 61.218 68.421 0.73 3.88 30.59 4.81
1460 1475 2.421619 GTTCCAGTTCTGAGCCAAGAG 58.578 52.381 1.00 0.00 0.00 2.85
1461 1476 0.322975 TCCAGTTCTGAGCCAAGAGC 59.677 55.000 1.00 0.00 44.25 4.09
1462 1477 0.676151 CCAGTTCTGAGCCAAGAGCC 60.676 60.000 1.00 0.00 45.47 4.70
1463 1478 1.018226 CAGTTCTGAGCCAAGAGCCG 61.018 60.000 0.00 0.00 45.47 5.52
1464 1479 2.046892 TTCTGAGCCAAGAGCCGC 60.047 61.111 0.00 0.00 45.47 6.53
1465 1480 3.612247 TTCTGAGCCAAGAGCCGCC 62.612 63.158 0.00 0.00 45.47 6.13
1466 1481 4.399395 CTGAGCCAAGAGCCGCCA 62.399 66.667 0.00 0.00 45.47 5.69
1467 1482 3.907260 CTGAGCCAAGAGCCGCCAA 62.907 63.158 0.00 0.00 45.47 4.52
1468 1483 3.130160 GAGCCAAGAGCCGCCAAG 61.130 66.667 0.00 0.00 45.47 3.61
1469 1484 3.612247 GAGCCAAGAGCCGCCAAGA 62.612 63.158 0.00 0.00 45.47 3.02
1472 1487 1.377725 CCAAGAGCCGCCAAGACAT 60.378 57.895 0.00 0.00 0.00 3.06
1504 1522 2.177451 TGCATTGGACCACCATGGATAT 59.823 45.455 21.47 1.85 46.34 1.63
1517 1537 3.154710 CATGGATATGGTTGCTGCTCAT 58.845 45.455 0.00 5.20 0.00 2.90
1547 1574 6.039493 TGCTGCTGAAGAATACTAGTACTACC 59.961 42.308 4.31 0.00 0.00 3.18
1588 1615 9.921637 ATGTTTAATTATGGTTTGATTCGTGTT 57.078 25.926 0.00 0.00 0.00 3.32
1692 1731 4.219070 AGAACAATGTCATTGATGTGTGGG 59.781 41.667 28.28 2.80 42.83 4.61
1698 1737 1.077501 ATTGATGTGTGGGGGAGCG 60.078 57.895 0.00 0.00 0.00 5.03
1786 1826 7.593875 TGTTTGCATCAAATTATTTAGGCAC 57.406 32.000 8.76 2.34 35.74 5.01
1812 1852 6.019881 GTGTTACTTTGGCAAGTGTTTGATTC 60.020 38.462 11.97 1.39 43.54 2.52
1843 1883 9.699410 TTATGAAATGATCTAGGTTGATTGGTT 57.301 29.630 0.00 0.00 0.00 3.67
1866 1906 8.497554 GGTTAGTGTTGATTATGTTACGTTTGA 58.502 33.333 0.00 0.00 0.00 2.69
1870 1910 8.779303 AGTGTTGATTATGTTACGTTTGATTCA 58.221 29.630 0.00 0.00 0.00 2.57
1871 1911 9.388346 GTGTTGATTATGTTACGTTTGATTCAA 57.612 29.630 0.00 0.00 0.00 2.69
1886 1926 9.956797 CGTTTGATTCAATTTTATGAAATGACC 57.043 29.630 0.00 0.00 42.22 4.02
1889 1929 9.656040 TTGATTCAATTTTATGAAATGACCCTG 57.344 29.630 0.00 0.00 42.22 4.45
1890 1930 8.259411 TGATTCAATTTTATGAAATGACCCTGG 58.741 33.333 0.00 0.00 42.22 4.45
1891 1931 6.543430 TCAATTTTATGAAATGACCCTGGG 57.457 37.500 12.28 12.28 35.69 4.45
1892 1932 6.022315 TCAATTTTATGAAATGACCCTGGGT 58.978 36.000 20.72 20.72 35.69 4.51
1893 1933 7.310361 TTCAATTTTATGAAATGACCCTGGGTC 60.310 37.037 34.26 34.26 42.97 4.46
1901 1941 4.257890 ACCCTGGGTCAATCTGCT 57.742 55.556 14.05 0.00 0.00 4.24
1902 1942 2.479562 ACCCTGGGTCAATCTGCTT 58.520 52.632 14.05 0.00 0.00 3.91
1903 1943 0.038744 ACCCTGGGTCAATCTGCTTG 59.961 55.000 14.05 0.00 36.09 4.01
1904 1944 1.318158 CCCTGGGTCAATCTGCTTGC 61.318 60.000 3.97 0.00 34.66 4.01
1905 1945 0.609957 CCTGGGTCAATCTGCTTGCA 60.610 55.000 0.00 0.00 34.66 4.08
1906 1946 0.809385 CTGGGTCAATCTGCTTGCAG 59.191 55.000 15.74 15.74 34.66 4.41
1907 1947 0.401356 TGGGTCAATCTGCTTGCAGA 59.599 50.000 24.76 24.76 34.66 4.26
1908 1948 1.202915 TGGGTCAATCTGCTTGCAGAA 60.203 47.619 26.00 9.97 34.56 3.02
1912 1952 3.057033 GGTCAATCTGCTTGCAGAAATGT 60.057 43.478 26.00 9.63 34.56 2.71
1934 1980 6.279882 TGTTAGTCTCCTTTTGCCAAAATTG 58.720 36.000 2.58 0.00 0.00 2.32
1954 2000 4.927267 TGGATTACTCACAGGGATTGTT 57.073 40.909 0.00 0.00 38.16 2.83
1962 2008 5.388654 ACTCACAGGGATTGTTTCTGAAAT 58.611 37.500 6.06 0.00 38.16 2.17
1973 2019 9.321562 GGATTGTTTCTGAAATTATCAATGCAT 57.678 29.630 20.46 0.00 37.67 3.96
2017 2063 0.034896 GTGAACCTGTGATGACCGGT 59.965 55.000 6.92 6.92 41.19 5.28
2073 2119 4.098501 GCTCTAGCATTTGCCCTTTTATGT 59.901 41.667 0.00 0.00 43.38 2.29
2105 2152 2.888834 AAAAATTGCAAGCGTCCACT 57.111 40.000 4.94 0.00 0.00 4.00
2116 2163 5.007626 TGCAAGCGTCCACTGATATTTTATC 59.992 40.000 0.00 0.00 0.00 1.75
2155 2202 6.463995 TTGTGACTGGCTTTTGTTTAGAAT 57.536 33.333 0.00 0.00 0.00 2.40
2163 2210 6.945218 TGGCTTTTGTTTAGAATATTGGCAT 58.055 32.000 0.00 0.00 0.00 4.40
2164 2211 7.041107 TGGCTTTTGTTTAGAATATTGGCATC 58.959 34.615 0.00 0.00 0.00 3.91
2165 2212 7.041107 GGCTTTTGTTTAGAATATTGGCATCA 58.959 34.615 0.00 0.00 0.00 3.07
2166 2213 7.712205 GGCTTTTGTTTAGAATATTGGCATCAT 59.288 33.333 0.00 0.00 0.00 2.45
2167 2214 8.758715 GCTTTTGTTTAGAATATTGGCATCATC 58.241 33.333 0.00 0.00 0.00 2.92
2168 2215 9.806203 CTTTTGTTTAGAATATTGGCATCATCA 57.194 29.630 0.00 0.00 0.00 3.07
2179 2226 2.091775 TGGCATCATCATCCACCAATGA 60.092 45.455 0.00 0.00 39.85 2.57
2187 2234 4.305539 TCATCCACCAATGATGTTCAGT 57.694 40.909 0.00 0.00 40.38 3.41
2190 2237 4.852134 TCCACCAATGATGTTCAGTTTG 57.148 40.909 0.00 0.00 0.00 2.93
2191 2238 4.214310 TCCACCAATGATGTTCAGTTTGT 58.786 39.130 0.00 0.00 0.00 2.83
2192 2239 4.037803 TCCACCAATGATGTTCAGTTTGTG 59.962 41.667 0.00 0.00 0.00 3.33
2193 2240 4.202141 CCACCAATGATGTTCAGTTTGTGT 60.202 41.667 0.00 0.00 0.00 3.72
2194 2241 4.741185 CACCAATGATGTTCAGTTTGTGTG 59.259 41.667 0.00 0.00 0.00 3.82
2233 2281 6.261381 TGGTAACACTAAAAAGTGATGTCCAC 59.739 38.462 12.23 0.00 46.17 4.02
2248 2296 2.493675 TGTCCACTGTATCTGCTCTGTC 59.506 50.000 0.00 0.00 0.00 3.51
2251 2299 2.223456 CCACTGTATCTGCTCTGTCTCG 60.223 54.545 0.00 0.00 0.00 4.04
2252 2300 2.421775 CACTGTATCTGCTCTGTCTCGT 59.578 50.000 0.00 0.00 0.00 4.18
2253 2301 3.085533 ACTGTATCTGCTCTGTCTCGTT 58.914 45.455 0.00 0.00 0.00 3.85
2254 2302 3.508012 ACTGTATCTGCTCTGTCTCGTTT 59.492 43.478 0.00 0.00 0.00 3.60
2255 2303 4.021894 ACTGTATCTGCTCTGTCTCGTTTT 60.022 41.667 0.00 0.00 0.00 2.43
2256 2304 4.237724 TGTATCTGCTCTGTCTCGTTTTG 58.762 43.478 0.00 0.00 0.00 2.44
2257 2305 2.154854 TCTGCTCTGTCTCGTTTTGG 57.845 50.000 0.00 0.00 0.00 3.28
2258 2306 1.412710 TCTGCTCTGTCTCGTTTTGGT 59.587 47.619 0.00 0.00 0.00 3.67
2259 2307 2.626266 TCTGCTCTGTCTCGTTTTGGTA 59.374 45.455 0.00 0.00 0.00 3.25
2260 2308 2.989840 CTGCTCTGTCTCGTTTTGGTAG 59.010 50.000 0.00 0.00 0.00 3.18
2261 2309 2.364324 TGCTCTGTCTCGTTTTGGTAGT 59.636 45.455 0.00 0.00 0.00 2.73
2263 2311 3.318017 CTCTGTCTCGTTTTGGTAGTGG 58.682 50.000 0.00 0.00 0.00 4.00
2264 2312 2.036733 TCTGTCTCGTTTTGGTAGTGGG 59.963 50.000 0.00 0.00 0.00 4.61
2265 2313 2.036733 CTGTCTCGTTTTGGTAGTGGGA 59.963 50.000 0.00 0.00 0.00 4.37
2277 2332 5.765576 TGGTAGTGGGAGTATTTGCTAAA 57.234 39.130 0.00 0.00 0.00 1.85
2284 2339 7.454225 AGTGGGAGTATTTGCTAAATATCCTC 58.546 38.462 17.18 13.40 35.92 3.71
2296 2351 8.732746 TGCTAAATATCCTCCAAGTAGTTTTC 57.267 34.615 0.00 0.00 0.00 2.29
2301 2356 9.753674 AAATATCCTCCAAGTAGTTTTCATTCA 57.246 29.630 0.00 0.00 0.00 2.57
2302 2357 9.927081 AATATCCTCCAAGTAGTTTTCATTCAT 57.073 29.630 0.00 0.00 0.00 2.57
2305 2360 9.753674 ATCCTCCAAGTAGTTTTCATTCATAAA 57.246 29.630 0.00 0.00 0.00 1.40
2346 2401 8.086851 TGGTTCGTTAAAGTGTTAATCTTACC 57.913 34.615 0.00 0.00 31.94 2.85
2347 2402 7.714377 TGGTTCGTTAAAGTGTTAATCTTACCA 59.286 33.333 0.00 0.00 32.64 3.25
2369 2443 6.095377 CCAAGTCAATCATTGGTTTTAGCTC 58.905 40.000 0.00 0.00 40.93 4.09
2370 2444 6.294675 CCAAGTCAATCATTGGTTTTAGCTCA 60.295 38.462 0.00 0.00 40.93 4.26
2371 2445 7.318141 CAAGTCAATCATTGGTTTTAGCTCAT 58.682 34.615 0.00 0.00 0.00 2.90
2372 2446 7.472334 AGTCAATCATTGGTTTTAGCTCATT 57.528 32.000 0.00 0.00 0.00 2.57
2373 2447 8.579850 AGTCAATCATTGGTTTTAGCTCATTA 57.420 30.769 0.00 0.00 0.00 1.90
2374 2448 9.023962 AGTCAATCATTGGTTTTAGCTCATTAA 57.976 29.630 0.00 0.00 0.00 1.40
2375 2449 9.638239 GTCAATCATTGGTTTTAGCTCATTAAA 57.362 29.630 0.00 0.00 0.00 1.52
2376 2450 9.638239 TCAATCATTGGTTTTAGCTCATTAAAC 57.362 29.630 0.00 0.00 0.00 2.01
2377 2451 9.643693 CAATCATTGGTTTTAGCTCATTAAACT 57.356 29.630 0.00 0.00 33.44 2.66
2407 2481 0.677842 ACCGAACAAGCTACCGAGTT 59.322 50.000 0.00 0.00 0.00 3.01
2436 2511 8.204836 ACGATCAACTTGTTAAGCTCCTAATAT 58.795 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.826710 CGATTCCAGAAACTAGTATGCAAATTA 58.173 33.333 0.00 0.00 0.00 1.40
32 33 7.336931 ACGATTCCAGAAACTAGTATGCAAATT 59.663 33.333 0.00 0.00 0.00 1.82
33 34 6.823689 ACGATTCCAGAAACTAGTATGCAAAT 59.176 34.615 0.00 0.00 0.00 2.32
34 35 6.170506 ACGATTCCAGAAACTAGTATGCAAA 58.829 36.000 0.00 0.00 0.00 3.68
35 36 5.730550 ACGATTCCAGAAACTAGTATGCAA 58.269 37.500 0.00 0.00 0.00 4.08
36 37 5.339008 ACGATTCCAGAAACTAGTATGCA 57.661 39.130 0.00 0.00 0.00 3.96
37 38 6.505272 AGTACGATTCCAGAAACTAGTATGC 58.495 40.000 0.00 0.00 0.00 3.14
38 39 7.648510 GGAAGTACGATTCCAGAAACTAGTATG 59.351 40.741 8.63 0.00 46.77 2.39
39 40 7.714703 GGAAGTACGATTCCAGAAACTAGTAT 58.285 38.462 8.63 0.00 46.77 2.12
40 41 7.093322 GGAAGTACGATTCCAGAAACTAGTA 57.907 40.000 8.63 0.00 46.77 1.82
41 42 5.963594 GGAAGTACGATTCCAGAAACTAGT 58.036 41.667 8.63 0.00 46.77 2.57
52 53 1.396653 TCGGGGAGGAAGTACGATTC 58.603 55.000 0.00 0.00 0.00 2.52
53 54 1.856629 TTCGGGGAGGAAGTACGATT 58.143 50.000 0.00 0.00 33.26 3.34
54 55 2.083628 ATTCGGGGAGGAAGTACGAT 57.916 50.000 0.00 0.00 33.26 3.73
55 56 1.753073 GAATTCGGGGAGGAAGTACGA 59.247 52.381 0.00 0.00 0.00 3.43
56 57 1.755380 AGAATTCGGGGAGGAAGTACG 59.245 52.381 0.00 0.00 0.00 3.67
57 58 3.243805 GCTAGAATTCGGGGAGGAAGTAC 60.244 52.174 0.00 0.00 0.00 2.73
58 59 2.963782 GCTAGAATTCGGGGAGGAAGTA 59.036 50.000 0.00 0.00 0.00 2.24
59 60 1.763545 GCTAGAATTCGGGGAGGAAGT 59.236 52.381 0.00 0.00 0.00 3.01
60 61 1.762957 TGCTAGAATTCGGGGAGGAAG 59.237 52.381 0.00 0.00 0.00 3.46
61 62 1.874129 TGCTAGAATTCGGGGAGGAA 58.126 50.000 0.00 0.00 0.00 3.36
62 63 1.874129 TTGCTAGAATTCGGGGAGGA 58.126 50.000 0.00 0.00 0.00 3.71
63 64 2.092914 AGTTTGCTAGAATTCGGGGAGG 60.093 50.000 0.00 0.00 0.00 4.30
64 65 3.268023 AGTTTGCTAGAATTCGGGGAG 57.732 47.619 0.00 0.00 0.00 4.30
65 66 3.713826 AAGTTTGCTAGAATTCGGGGA 57.286 42.857 0.00 0.00 0.00 4.81
66 67 6.451064 AAATAAGTTTGCTAGAATTCGGGG 57.549 37.500 0.00 0.00 0.00 5.73
67 68 7.981142 TGTAAATAAGTTTGCTAGAATTCGGG 58.019 34.615 0.00 0.00 32.02 5.14
90 91 7.858879 CGGTAACTAAGCTTTGTACAAAAATGT 59.141 33.333 20.89 12.53 0.00 2.71
91 92 8.071368 TCGGTAACTAAGCTTTGTACAAAAATG 58.929 33.333 20.89 11.35 0.00 2.32
92 93 8.071967 GTCGGTAACTAAGCTTTGTACAAAAAT 58.928 33.333 20.89 12.49 0.00 1.82
93 94 7.408910 GTCGGTAACTAAGCTTTGTACAAAAA 58.591 34.615 20.89 7.20 0.00 1.94
94 95 6.018016 GGTCGGTAACTAAGCTTTGTACAAAA 60.018 38.462 20.89 6.40 0.00 2.44
95 96 5.466393 GGTCGGTAACTAAGCTTTGTACAAA 59.534 40.000 19.53 19.53 0.00 2.83
96 97 4.990426 GGTCGGTAACTAAGCTTTGTACAA 59.010 41.667 13.95 3.59 0.00 2.41
97 98 4.281688 AGGTCGGTAACTAAGCTTTGTACA 59.718 41.667 13.95 2.87 0.00 2.90
98 99 4.814147 AGGTCGGTAACTAAGCTTTGTAC 58.186 43.478 13.95 11.56 0.00 2.90
99 100 5.473066 AAGGTCGGTAACTAAGCTTTGTA 57.527 39.130 13.95 0.77 35.14 2.41
100 101 4.347360 AAGGTCGGTAACTAAGCTTTGT 57.653 40.909 3.20 5.86 35.14 2.83
101 102 5.614013 CGAAAAGGTCGGTAACTAAGCTTTG 60.614 44.000 3.20 5.03 46.45 2.77
102 103 4.450080 CGAAAAGGTCGGTAACTAAGCTTT 59.550 41.667 3.20 2.44 46.45 3.51
103 104 3.992427 CGAAAAGGTCGGTAACTAAGCTT 59.008 43.478 3.48 3.48 46.45 3.74
104 105 3.582780 CGAAAAGGTCGGTAACTAAGCT 58.417 45.455 0.00 0.00 46.45 3.74
105 106 3.985912 CGAAAAGGTCGGTAACTAAGC 57.014 47.619 0.00 0.00 46.45 3.09
116 117 5.235516 TCTCAACTAATCCACGAAAAGGTC 58.764 41.667 0.00 0.00 0.00 3.85
117 118 5.223449 TCTCAACTAATCCACGAAAAGGT 57.777 39.130 0.00 0.00 0.00 3.50
118 119 5.389516 CGTTCTCAACTAATCCACGAAAAGG 60.390 44.000 0.00 0.00 0.00 3.11
119 120 5.176958 ACGTTCTCAACTAATCCACGAAAAG 59.823 40.000 0.00 0.00 0.00 2.27
120 121 5.051816 ACGTTCTCAACTAATCCACGAAAA 58.948 37.500 0.00 0.00 0.00 2.29
121 122 4.624015 ACGTTCTCAACTAATCCACGAAA 58.376 39.130 0.00 0.00 0.00 3.46
122 123 4.247267 ACGTTCTCAACTAATCCACGAA 57.753 40.909 0.00 0.00 0.00 3.85
123 124 3.928727 ACGTTCTCAACTAATCCACGA 57.071 42.857 0.00 0.00 0.00 4.35
124 125 4.235360 AGAACGTTCTCAACTAATCCACG 58.765 43.478 24.93 0.00 29.94 4.94
125 126 6.237861 GCATAGAACGTTCTCAACTAATCCAC 60.238 42.308 32.86 8.96 38.70 4.02
126 127 5.810587 GCATAGAACGTTCTCAACTAATCCA 59.189 40.000 32.86 12.93 38.70 3.41
127 128 6.019479 CAGCATAGAACGTTCTCAACTAATCC 60.019 42.308 32.86 11.35 38.70 3.01
128 129 6.508721 GCAGCATAGAACGTTCTCAACTAATC 60.509 42.308 32.86 15.69 38.70 1.75
129 130 5.292101 GCAGCATAGAACGTTCTCAACTAAT 59.708 40.000 32.86 17.47 38.70 1.73
130 131 4.625742 GCAGCATAGAACGTTCTCAACTAA 59.374 41.667 32.86 15.91 38.70 2.24
131 132 4.174009 GCAGCATAGAACGTTCTCAACTA 58.826 43.478 32.86 16.66 38.70 2.24
132 133 2.996621 GCAGCATAGAACGTTCTCAACT 59.003 45.455 32.86 23.56 38.70 3.16
133 134 2.736721 TGCAGCATAGAACGTTCTCAAC 59.263 45.455 32.86 21.87 38.70 3.18
134 135 3.038788 TGCAGCATAGAACGTTCTCAA 57.961 42.857 32.86 18.18 38.70 3.02
135 136 2.741759 TGCAGCATAGAACGTTCTCA 57.258 45.000 32.86 20.53 38.70 3.27
136 137 3.244814 CAGATGCAGCATAGAACGTTCTC 59.755 47.826 32.86 19.30 38.70 2.87
137 138 3.118992 TCAGATGCAGCATAGAACGTTCT 60.119 43.478 31.70 31.70 41.24 3.01
138 139 3.190079 TCAGATGCAGCATAGAACGTTC 58.810 45.455 20.71 20.71 0.00 3.95
139 140 3.251479 TCAGATGCAGCATAGAACGTT 57.749 42.857 8.22 0.00 0.00 3.99
140 141 2.967599 TCAGATGCAGCATAGAACGT 57.032 45.000 8.22 0.00 0.00 3.99
141 142 4.808077 ATTTCAGATGCAGCATAGAACG 57.192 40.909 17.94 3.31 0.00 3.95
142 143 6.132056 CGTTATTTCAGATGCAGCATAGAAC 58.868 40.000 17.94 10.93 0.00 3.01
143 144 5.277490 GCGTTATTTCAGATGCAGCATAGAA 60.277 40.000 8.22 12.79 0.00 2.10
144 145 4.212004 GCGTTATTTCAGATGCAGCATAGA 59.788 41.667 8.22 6.90 0.00 1.98
145 146 4.024641 TGCGTTATTTCAGATGCAGCATAG 60.025 41.667 8.22 4.33 33.17 2.23
146 147 3.876320 TGCGTTATTTCAGATGCAGCATA 59.124 39.130 8.22 0.00 33.17 3.14
147 148 2.684374 TGCGTTATTTCAGATGCAGCAT 59.316 40.909 7.91 7.91 33.17 3.79
148 149 2.083002 TGCGTTATTTCAGATGCAGCA 58.917 42.857 4.07 0.00 33.17 4.41
149 150 2.830772 TGCGTTATTTCAGATGCAGC 57.169 45.000 0.00 0.00 33.17 5.25
150 151 4.034858 ACAGATGCGTTATTTCAGATGCAG 59.965 41.667 0.00 0.00 40.72 4.41
151 152 3.940852 ACAGATGCGTTATTTCAGATGCA 59.059 39.130 0.00 0.00 41.53 3.96
152 153 4.542662 ACAGATGCGTTATTTCAGATGC 57.457 40.909 0.00 0.00 0.00 3.91
153 154 4.731961 GCAACAGATGCGTTATTTCAGATG 59.268 41.667 0.00 0.00 46.87 2.90
154 155 4.913376 GCAACAGATGCGTTATTTCAGAT 58.087 39.130 0.00 0.00 46.87 2.90
155 156 4.340894 GCAACAGATGCGTTATTTCAGA 57.659 40.909 0.00 0.00 46.87 3.27
167 168 1.153289 AGCGGCTAGGCAACAGATG 60.153 57.895 17.45 0.00 41.41 2.90
168 169 1.153289 CAGCGGCTAGGCAACAGAT 60.153 57.895 17.45 0.00 41.41 2.90
169 170 2.265739 CAGCGGCTAGGCAACAGA 59.734 61.111 17.45 0.00 41.41 3.41
170 171 2.821366 CCAGCGGCTAGGCAACAG 60.821 66.667 17.45 4.52 41.41 3.16
180 181 4.428514 CAACTTTTTGTTTGCCAGCGGC 62.429 50.000 11.92 11.92 42.56 6.53
181 182 1.327156 CAACTTTTTGTTTGCCAGCGG 59.673 47.619 0.00 0.00 36.63 5.52
182 183 1.999024 ACAACTTTTTGTTTGCCAGCG 59.001 42.857 0.00 0.00 43.89 5.18
183 184 5.733226 ATTACAACTTTTTGTTTGCCAGC 57.267 34.783 0.00 0.00 43.89 4.85
184 185 8.586570 TCATATTACAACTTTTTGTTTGCCAG 57.413 30.769 0.00 0.00 43.89 4.85
185 186 8.948631 TTCATATTACAACTTTTTGTTTGCCA 57.051 26.923 0.00 0.00 43.89 4.92
186 187 9.255304 TCTTCATATTACAACTTTTTGTTTGCC 57.745 29.630 0.00 0.00 43.89 4.52
215 216 3.191791 ACACACAGCAGTAAACGGTTTTT 59.808 39.130 11.87 0.00 0.00 1.94
216 217 2.750712 ACACACAGCAGTAAACGGTTTT 59.249 40.909 11.87 0.00 0.00 2.43
217 218 2.361789 ACACACAGCAGTAAACGGTTT 58.638 42.857 11.33 11.33 0.00 3.27
218 219 2.032680 ACACACAGCAGTAAACGGTT 57.967 45.000 0.00 0.00 0.00 4.44
219 220 2.894763 TACACACAGCAGTAAACGGT 57.105 45.000 0.00 0.00 0.00 4.83
220 221 3.743911 TCAATACACACAGCAGTAAACGG 59.256 43.478 0.00 0.00 0.00 4.44
221 222 4.377022 GGTCAATACACACAGCAGTAAACG 60.377 45.833 0.00 0.00 0.00 3.60
222 223 4.377022 CGGTCAATACACACAGCAGTAAAC 60.377 45.833 0.00 0.00 0.00 2.01
223 224 3.743911 CGGTCAATACACACAGCAGTAAA 59.256 43.478 0.00 0.00 0.00 2.01
224 225 3.006003 TCGGTCAATACACACAGCAGTAA 59.994 43.478 0.00 0.00 0.00 2.24
225 226 2.559231 TCGGTCAATACACACAGCAGTA 59.441 45.455 0.00 0.00 0.00 2.74
226 227 1.343142 TCGGTCAATACACACAGCAGT 59.657 47.619 0.00 0.00 0.00 4.40
227 228 2.078849 TCGGTCAATACACACAGCAG 57.921 50.000 0.00 0.00 0.00 4.24
228 229 2.028567 TGATCGGTCAATACACACAGCA 60.029 45.455 0.00 0.00 0.00 4.41
229 230 2.616960 TGATCGGTCAATACACACAGC 58.383 47.619 0.00 0.00 0.00 4.40
230 231 5.605564 TTTTGATCGGTCAATACACACAG 57.394 39.130 12.77 0.00 43.49 3.66
254 255 3.628017 CGAGCAAACATCGGTTCTTTTT 58.372 40.909 0.00 0.00 35.82 1.94
255 256 3.268013 CGAGCAAACATCGGTTCTTTT 57.732 42.857 0.00 0.00 35.82 2.27
256 257 2.969443 CGAGCAAACATCGGTTCTTT 57.031 45.000 0.00 0.00 35.82 2.52
274 275 2.304751 ATTACGCCAAAGTCCTACCG 57.695 50.000 0.00 0.00 0.00 4.02
282 283 5.116180 TGTCTCCATCTAATTACGCCAAAG 58.884 41.667 0.00 0.00 0.00 2.77
285 286 4.955811 ATGTCTCCATCTAATTACGCCA 57.044 40.909 0.00 0.00 0.00 5.69
293 294 6.892456 AGGATATTCGCTATGTCTCCATCTAA 59.108 38.462 0.00 0.00 32.29 2.10
304 305 5.174395 CAGGAAAGGAGGATATTCGCTATG 58.826 45.833 0.00 0.00 0.00 2.23
319 320 1.068333 CAAATCCACACGCAGGAAAGG 60.068 52.381 0.00 0.00 38.93 3.11
448 458 5.088026 AGAGGGTCTATTTATAGGTGGAGC 58.912 45.833 0.00 0.00 0.00 4.70
567 577 3.735181 CGTAAGAACGGGAAGGGAG 57.265 57.895 0.00 0.00 45.50 4.30
646 656 0.035630 AATGTGACAGAGCTCAGGGC 60.036 55.000 17.77 10.55 42.19 5.19
688 698 0.681564 ATCTGCGACGAACTCCTCCT 60.682 55.000 0.00 0.00 0.00 3.69
885 895 4.039730 GCTGGATCTAATCAACTAGAGGCA 59.960 45.833 0.00 0.00 31.51 4.75
909 922 1.073284 CAGGAAAGGGGAAGAAACGGA 59.927 52.381 0.00 0.00 0.00 4.69
910 923 1.202891 ACAGGAAAGGGGAAGAAACGG 60.203 52.381 0.00 0.00 0.00 4.44
921 934 3.560239 GGGAAGGAAGAAGACAGGAAAGG 60.560 52.174 0.00 0.00 0.00 3.11
927 940 0.391793 GGCGGGAAGGAAGAAGACAG 60.392 60.000 0.00 0.00 0.00 3.51
930 943 0.541863 GATGGCGGGAAGGAAGAAGA 59.458 55.000 0.00 0.00 0.00 2.87
965 980 3.326588 TCTCGATCCAAGAACCAGGAAAA 59.673 43.478 0.00 0.00 37.48 2.29
969 984 2.622436 GTTCTCGATCCAAGAACCAGG 58.378 52.381 18.51 0.00 44.41 4.45
984 999 1.153628 CATGGTCGGTCGGGTTCTC 60.154 63.158 0.00 0.00 0.00 2.87
1029 1044 1.511305 GTCGATGTTGCTCTCGGGA 59.489 57.895 0.00 0.00 35.64 5.14
1344 1359 4.385740 TCCGGGATGTCCACGGGA 62.386 66.667 21.06 12.81 44.56 5.14
1434 1449 1.337817 CTCAGAACTGGAACGCGTCG 61.338 60.000 14.44 4.06 0.00 5.12
1460 1475 1.430632 CATGACATGTCTTGGCGGC 59.569 57.895 26.37 0.00 35.37 6.53
1461 1476 1.430632 GCATGACATGTCTTGGCGG 59.569 57.895 31.51 15.05 35.37 6.13
1462 1477 1.430632 GGCATGACATGTCTTGGCG 59.569 57.895 36.12 18.25 45.31 5.69
1464 1479 1.471287 CAGTGGCATGACATGTCTTGG 59.529 52.381 31.51 20.19 35.48 3.61
1465 1480 1.135489 GCAGTGGCATGACATGTCTTG 60.135 52.381 28.56 28.56 40.72 3.02
1466 1481 1.171308 GCAGTGGCATGACATGTCTT 58.829 50.000 25.55 17.25 40.72 3.01
1467 1482 2.864114 GCAGTGGCATGACATGTCT 58.136 52.632 25.55 11.59 40.72 3.41
1504 1522 1.676916 GCAGTAGATGAGCAGCAACCA 60.677 52.381 0.00 0.00 0.00 3.67
1513 1533 3.797451 TCTTCAGCAGCAGTAGATGAG 57.203 47.619 0.00 0.00 31.30 2.90
1515 1535 5.599732 AGTATTCTTCAGCAGCAGTAGATG 58.400 41.667 0.00 0.00 0.00 2.90
1517 1537 5.888724 ACTAGTATTCTTCAGCAGCAGTAGA 59.111 40.000 0.00 0.00 0.00 2.59
1643 1682 2.405618 TATCCACTGGCTAGGAGCAT 57.594 50.000 0.85 0.00 44.75 3.79
1692 1731 0.179129 CACAATCCATTTGCGCTCCC 60.179 55.000 9.73 0.00 39.03 4.30
1698 1737 4.660789 AAGATAGGCACAATCCATTTGC 57.339 40.909 0.00 0.00 39.03 3.68
1761 1801 7.010367 CGTGCCTAAATAATTTGATGCAAACAT 59.990 33.333 0.00 0.00 36.13 2.71
1762 1802 6.309980 CGTGCCTAAATAATTTGATGCAAACA 59.690 34.615 0.00 0.00 36.13 2.83
1783 1823 1.064952 ACTTGCCAAAGTAACACGTGC 59.935 47.619 17.22 0.00 45.01 5.34
1784 1824 2.096819 ACACTTGCCAAAGTAACACGTG 59.903 45.455 15.48 15.48 45.07 4.49
1786 1826 3.414549 AACACTTGCCAAAGTAACACG 57.585 42.857 0.00 0.00 45.07 4.49
1830 1870 9.173021 CATAATCAACACTAACCAATCAACCTA 57.827 33.333 0.00 0.00 0.00 3.08
1866 1906 7.182568 ACCCAGGGTCATTTCATAAAATTGAAT 59.817 33.333 4.76 0.00 35.64 2.57
1867 1907 6.500049 ACCCAGGGTCATTTCATAAAATTGAA 59.500 34.615 4.76 0.00 32.69 2.69
1869 1909 6.298441 ACCCAGGGTCATTTCATAAAATTG 57.702 37.500 4.76 0.00 32.69 2.32
1884 1924 0.038744 CAAGCAGATTGACCCAGGGT 59.961 55.000 12.53 12.53 41.83 4.34
1885 1925 1.318158 GCAAGCAGATTGACCCAGGG 61.318 60.000 2.85 2.85 41.83 4.45
1886 1926 0.609957 TGCAAGCAGATTGACCCAGG 60.610 55.000 1.54 0.00 41.83 4.45
1887 1927 0.809385 CTGCAAGCAGATTGACCCAG 59.191 55.000 16.75 0.00 46.30 4.45
1888 1928 0.401356 TCTGCAAGCAGATTGACCCA 59.599 50.000 20.00 0.00 46.80 4.51
1889 1929 3.254629 TCTGCAAGCAGATTGACCC 57.745 52.632 20.00 0.00 46.80 4.46
1895 1935 9.639937 AGGAGACTAACATTTCTGCAAGCAGAT 62.640 40.741 23.80 12.13 45.86 2.90
1896 1936 8.427274 AGGAGACTAACATTTCTGCAAGCAGA 62.427 42.308 20.00 20.00 45.29 4.26
1897 1937 4.142730 GGAGACTAACATTTCTGCAAGCAG 60.143 45.833 15.67 15.67 44.86 4.24
1898 1938 3.753272 GGAGACTAACATTTCTGCAAGCA 59.247 43.478 0.00 0.00 30.91 3.91
1899 1939 4.006319 AGGAGACTAACATTTCTGCAAGC 58.994 43.478 0.00 0.00 40.61 4.01
1900 1940 6.566197 AAAGGAGACTAACATTTCTGCAAG 57.434 37.500 0.00 0.00 42.68 4.01
1901 1941 6.735694 GCAAAAGGAGACTAACATTTCTGCAA 60.736 38.462 0.00 0.00 42.68 4.08
1902 1942 5.278463 GCAAAAGGAGACTAACATTTCTGCA 60.278 40.000 0.00 0.00 42.68 4.41
1903 1943 5.157067 GCAAAAGGAGACTAACATTTCTGC 58.843 41.667 0.00 0.00 42.68 4.26
1904 1944 5.241506 TGGCAAAAGGAGACTAACATTTCTG 59.758 40.000 0.00 0.00 42.68 3.02
1905 1945 5.385198 TGGCAAAAGGAGACTAACATTTCT 58.615 37.500 0.00 0.00 42.68 2.52
1906 1946 5.705609 TGGCAAAAGGAGACTAACATTTC 57.294 39.130 0.00 0.00 42.68 2.17
1907 1947 6.478512 TTTGGCAAAAGGAGACTAACATTT 57.521 33.333 10.83 0.00 42.68 2.32
1908 1948 6.478512 TTTTGGCAAAAGGAGACTAACATT 57.521 33.333 20.81 0.00 42.68 2.71
1912 1952 5.852827 CCAATTTTGGCAAAAGGAGACTAA 58.147 37.500 27.21 4.71 40.36 2.24
1934 1980 5.355350 CAGAAACAATCCCTGTGAGTAATCC 59.645 44.000 0.00 0.00 38.67 3.01
1954 2000 7.664552 AAGGGATGCATTGATAATTTCAGAA 57.335 32.000 0.00 0.00 35.27 3.02
1962 2008 8.830915 TTAGGTAAAAAGGGATGCATTGATAA 57.169 30.769 0.00 0.00 0.00 1.75
1973 2019 8.499406 ACAGCACATATATTAGGTAAAAAGGGA 58.501 33.333 0.00 0.00 0.00 4.20
1974 2020 8.567948 CACAGCACATATATTAGGTAAAAAGGG 58.432 37.037 0.00 0.00 0.00 3.95
2017 2063 4.402155 CCACTATGGCCTTTTAGCAATTCA 59.598 41.667 3.32 0.00 0.00 2.57
2095 2142 5.597806 TCGATAAAATATCAGTGGACGCTT 58.402 37.500 0.00 0.00 0.00 4.68
2116 2163 7.411804 GCCAGTCACAATAAATGGAAATTTTCG 60.412 37.037 3.17 0.00 32.55 3.46
2125 2172 5.540911 ACAAAAGCCAGTCACAATAAATGG 58.459 37.500 0.00 0.00 0.00 3.16
2127 2174 8.637986 TCTAAACAAAAGCCAGTCACAATAAAT 58.362 29.630 0.00 0.00 0.00 1.40
2138 2185 6.397272 TGCCAATATTCTAAACAAAAGCCAG 58.603 36.000 0.00 0.00 0.00 4.85
2155 2202 3.880168 TGGTGGATGATGATGCCAATA 57.120 42.857 0.00 0.00 32.68 1.90
2165 2212 4.863548 ACTGAACATCATTGGTGGATGAT 58.136 39.130 9.18 0.00 45.25 2.45
2166 2213 4.305539 ACTGAACATCATTGGTGGATGA 57.694 40.909 9.18 0.00 43.80 2.92
2167 2214 5.165676 CAAACTGAACATCATTGGTGGATG 58.834 41.667 1.31 0.00 45.93 3.51
2168 2215 4.834496 ACAAACTGAACATCATTGGTGGAT 59.166 37.500 1.31 0.00 0.00 3.41
2169 2216 4.037803 CACAAACTGAACATCATTGGTGGA 59.962 41.667 1.31 0.00 0.00 4.02
2179 2226 7.038587 TCCTATACCTACACACAAACTGAACAT 60.039 37.037 0.00 0.00 0.00 2.71
2186 2233 7.732996 ACCATATCCTATACCTACACACAAAC 58.267 38.462 0.00 0.00 0.00 2.93
2187 2234 7.924358 ACCATATCCTATACCTACACACAAA 57.076 36.000 0.00 0.00 0.00 2.83
2190 2237 8.302438 GTGTTACCATATCCTATACCTACACAC 58.698 40.741 0.00 0.00 33.24 3.82
2191 2238 8.229605 AGTGTTACCATATCCTATACCTACACA 58.770 37.037 0.00 0.00 34.90 3.72
2192 2239 8.647256 AGTGTTACCATATCCTATACCTACAC 57.353 38.462 0.00 0.00 33.19 2.90
2228 2276 2.757868 AGACAGAGCAGATACAGTGGAC 59.242 50.000 0.00 0.00 0.00 4.02
2233 2281 3.773860 AACGAGACAGAGCAGATACAG 57.226 47.619 0.00 0.00 0.00 2.74
2248 2296 2.833631 ACTCCCACTACCAAAACGAG 57.166 50.000 0.00 0.00 0.00 4.18
2251 2299 4.765339 AGCAAATACTCCCACTACCAAAAC 59.235 41.667 0.00 0.00 0.00 2.43
2252 2300 4.993028 AGCAAATACTCCCACTACCAAAA 58.007 39.130 0.00 0.00 0.00 2.44
2253 2301 4.650972 AGCAAATACTCCCACTACCAAA 57.349 40.909 0.00 0.00 0.00 3.28
2254 2302 5.765576 TTAGCAAATACTCCCACTACCAA 57.234 39.130 0.00 0.00 0.00 3.67
2255 2303 5.765576 TTTAGCAAATACTCCCACTACCA 57.234 39.130 0.00 0.00 0.00 3.25
2256 2304 7.606839 GGATATTTAGCAAATACTCCCACTACC 59.393 40.741 4.23 0.00 36.27 3.18
2257 2305 8.376270 AGGATATTTAGCAAATACTCCCACTAC 58.624 37.037 15.87 0.00 36.27 2.73
2258 2306 8.506196 AGGATATTTAGCAAATACTCCCACTA 57.494 34.615 15.87 0.00 36.27 2.74
2259 2307 7.394144 AGGATATTTAGCAAATACTCCCACT 57.606 36.000 15.87 0.00 36.27 4.00
2260 2308 6.655425 GGAGGATATTTAGCAAATACTCCCAC 59.345 42.308 16.90 11.44 38.95 4.61
2261 2309 6.331572 TGGAGGATATTTAGCAAATACTCCCA 59.668 38.462 20.52 14.62 41.44 4.37
2263 2311 7.939588 ACTTGGAGGATATTTAGCAAATACTCC 59.060 37.037 18.75 18.75 41.93 3.85
2264 2312 8.910351 ACTTGGAGGATATTTAGCAAATACTC 57.090 34.615 4.23 6.92 36.27 2.59
2322 2377 8.086851 TGGTAAGATTAACACTTTAACGAACC 57.913 34.615 0.00 4.31 29.77 3.62
2325 2380 8.891671 ACTTGGTAAGATTAACACTTTAACGA 57.108 30.769 0.00 0.00 28.35 3.85
2332 2387 9.520515 AATGATTGACTTGGTAAGATTAACACT 57.479 29.630 0.00 0.00 28.35 3.55
2345 2400 6.029346 AGCTAAAACCAATGATTGACTTGG 57.971 37.500 6.76 0.00 46.03 3.61
2346 2401 6.680810 TGAGCTAAAACCAATGATTGACTTG 58.319 36.000 6.76 0.00 0.00 3.16
2347 2402 6.899393 TGAGCTAAAACCAATGATTGACTT 57.101 33.333 6.76 0.00 0.00 3.01
2370 2444 8.556213 TGTTCGGTAAGCTCATTAAGTTTAAT 57.444 30.769 0.00 0.00 33.14 1.40
2371 2445 7.966246 TGTTCGGTAAGCTCATTAAGTTTAA 57.034 32.000 0.00 0.00 33.14 1.52
2372 2446 7.360607 GCTTGTTCGGTAAGCTCATTAAGTTTA 60.361 37.037 10.54 0.00 45.34 2.01
2373 2447 6.567891 GCTTGTTCGGTAAGCTCATTAAGTTT 60.568 38.462 10.54 0.00 45.34 2.66
2374 2448 5.106673 GCTTGTTCGGTAAGCTCATTAAGTT 60.107 40.000 10.54 0.00 45.34 2.66
2375 2449 4.392138 GCTTGTTCGGTAAGCTCATTAAGT 59.608 41.667 10.54 0.00 45.34 2.24
2376 2450 4.898370 GCTTGTTCGGTAAGCTCATTAAG 58.102 43.478 10.54 0.00 45.34 1.85
2377 2451 4.939509 GCTTGTTCGGTAAGCTCATTAA 57.060 40.909 10.54 0.00 45.34 1.40
2385 2459 2.094854 ACTCGGTAGCTTGTTCGGTAAG 60.095 50.000 0.00 0.00 0.00 2.34
2386 2460 1.888512 ACTCGGTAGCTTGTTCGGTAA 59.111 47.619 0.00 0.00 0.00 2.85
2391 2465 1.194772 GTGCAACTCGGTAGCTTGTTC 59.805 52.381 0.00 0.00 0.00 3.18
2407 2481 3.138304 AGCTTAACAAGTTGATCGTGCA 58.862 40.909 10.54 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.