Multiple sequence alignment - TraesCS2B01G112000

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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 TraesCS2B01G112000 chr2B 100.000 5903 0 0 998 6900 74252166 74246264 0.000000e+00 10901.0
1 TraesCS2B01G112000 chr2B 100.000 532 0 0 1 532 74253163 74252632 0.000000e+00 983.0
2 TraesCS2B01G112000 chr2B 85.808 458 33 12 5938 6395 74022137 74022562 2.270000e-124 457.0
3 TraesCS2B01G112000 chr2B 87.775 409 18 13 6520 6900 74022763 74023167 3.800000e-122 449.0
4 TraesCS2B01G112000 chr2B 92.735 234 16 1 5580 5813 74021030 74021262 3.080000e-88 337.0
5 TraesCS2B01G112000 chr2D 93.510 3698 184 25 1124 4794 46934985 46931317 0.000000e+00 5448.0
6 TraesCS2B01G112000 chr2D 92.355 1962 86 30 4961 6900 46930995 46929076 0.000000e+00 2734.0
7 TraesCS2B01G112000 chr2D 88.493 869 58 18 5580 6445 46697502 46698331 0.000000e+00 1013.0
8 TraesCS2B01G112000 chr2D 88.147 464 26 17 6194 6655 46867727 46867291 6.130000e-145 525.0
9 TraesCS2B01G112000 chr2D 92.521 361 12 9 6548 6900 46699189 46699542 2.870000e-138 503.0
10 TraesCS2B01G112000 chr2D 89.235 353 11 6 193 522 46935809 46935461 3.850000e-112 416.0
11 TraesCS2B01G112000 chr2D 94.286 175 6 2 4793 4963 46931203 46931029 1.480000e-66 265.0
12 TraesCS2B01G112000 chr2D 95.070 142 7 0 6759 6900 46853592 46853451 2.500000e-54 224.0
13 TraesCS2B01G112000 chr2D 97.321 112 2 1 6661 6772 46867189 46867079 9.140000e-44 189.0
14 TraesCS2B01G112000 chr2D 96.512 86 3 0 998 1083 46935460 46935375 7.210000e-30 143.0
15 TraesCS2B01G112000 chr2D 91.045 67 6 0 1206 1272 469944972 469945038 2.650000e-14 91.6
16 TraesCS2B01G112000 chr2A 95.032 2778 100 15 2033 4794 50155668 50152913 0.000000e+00 4331.0
17 TraesCS2B01G112000 chr2A 93.080 1951 85 33 4961 6900 50152652 50150741 0.000000e+00 2809.0
18 TraesCS2B01G112000 chr2A 90.667 900 66 8 1095 1988 50156550 50155663 0.000000e+00 1181.0
19 TraesCS2B01G112000 chr2A 91.667 252 15 5 193 439 50157173 50156923 1.840000e-90 344.0
20 TraesCS2B01G112000 chr2A 86.245 269 19 8 6243 6510 50062844 50063095 6.820000e-70 276.0
21 TraesCS2B01G112000 chr2A 94.737 152 8 0 6749 6900 50063225 50063376 3.220000e-58 237.0
22 TraesCS2B01G112000 chr2A 84.314 204 15 7 6288 6490 50063721 50063908 4.250000e-42 183.0
23 TraesCS2B01G112000 chr2A 93.258 89 2 4 6553 6640 50063101 50063186 2.020000e-25 128.0
24 TraesCS2B01G112000 chr2A 87.037 108 10 2 1680 1787 50155909 50155806 1.220000e-22 119.0
25 TraesCS2B01G112000 chr2A 100.000 28 0 0 6659 6686 50063187 50063214 1.300000e-02 52.8
26 TraesCS2B01G112000 chr3D 88.546 454 48 3 1212 1664 396479288 396479738 1.310000e-151 547.0
27 TraesCS2B01G112000 chr5D 88.043 460 51 4 1206 1664 131503925 131503469 6.090000e-150 542.0
28 TraesCS2B01G112000 chr3B 87.174 460 55 4 1206 1664 684746187 684745731 2.850000e-143 520.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G112000 chr2B 74246264 74253163 6899 True 5942.000000 10901 100.000000 1 6900 2 chr2B.!!$R1 6899
1 TraesCS2B01G112000 chr2B 74021030 74023167 2137 False 414.333333 457 88.772667 5580 6900 3 chr2B.!!$F1 1320
2 TraesCS2B01G112000 chr2D 46929076 46935809 6733 True 1801.200000 5448 93.179600 193 6900 5 chr2D.!!$R3 6707
3 TraesCS2B01G112000 chr2D 46697502 46699542 2040 False 758.000000 1013 90.507000 5580 6900 2 chr2D.!!$F2 1320
4 TraesCS2B01G112000 chr2D 46867079 46867727 648 True 357.000000 525 92.734000 6194 6772 2 chr2D.!!$R2 578
5 TraesCS2B01G112000 chr2A 50150741 50157173 6432 True 1756.800000 4331 91.496600 193 6900 5 chr2A.!!$R1 6707

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
24 25 0.033504 TTGTCCTTGTCGAGCTCCAC 59.966 55.000 8.47 6.29 0.00 4.02 F
74 75 0.172352 CTCCGCTGTGTCTCTCTTCC 59.828 60.000 0.00 0.00 0.00 3.46 F
75 76 0.251386 TCCGCTGTGTCTCTCTTCCT 60.251 55.000 0.00 0.00 0.00 3.36 F
81 82 0.390472 GTGTCTCTCTTCCTTGCCCG 60.390 60.000 0.00 0.00 0.00 6.13 F
190 191 0.466189 CGCTGCCCTGGTGGAAATAT 60.466 55.000 0.00 0.00 35.39 1.28 F
191 192 1.035139 GCTGCCCTGGTGGAAATATG 58.965 55.000 0.00 0.00 35.39 1.78 F
1824 2197 1.073125 TCCCCAATTCACGCTTTGAGA 59.927 47.619 0.00 0.00 34.94 3.27 F
3442 3851 0.527817 CACGCCTACCGAATGAGGTC 60.528 60.000 0.00 0.00 44.68 3.85 F
5304 5876 0.343372 AGGACCTAGGGAGCCATGAA 59.657 55.000 14.81 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1089 1113 0.180406 GCGGGTACATGAAGATGGGT 59.820 55.000 0.00 0.0 33.39 4.51 R
1312 1685 0.317160 TCCGTCAAGAACTGCATCGT 59.683 50.000 0.00 0.0 0.00 3.73 R
1498 1871 0.374758 CCAATCCGTCACAATCTGCG 59.625 55.000 0.00 0.0 0.00 5.18 R
1645 2018 1.135575 CCCGCAAGCATTCAGAGAAAC 60.136 52.381 0.00 0.0 0.00 2.78 R
1858 2231 4.520492 CCAAGAGGTGTGAAGCACTAAATT 59.480 41.667 0.00 0.0 46.86 1.82 R
1971 2349 4.603535 GGGCATAAGGGCGGGCAT 62.604 66.667 3.27 0.0 44.56 4.40 R
3745 4155 0.032952 TACAACGTCTGTGGGACAGC 59.967 55.000 11.90 0.0 45.54 4.40 R
5365 5937 1.065272 TGGAGCACATAGAGCAATGCA 60.065 47.619 8.35 0.0 40.63 3.96 R
6346 7679 0.320683 TGGACACCGTTGATGCAGAG 60.321 55.000 0.00 0.0 0.00 3.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.771127 GCCACTTGTCCTTGTCGA 57.229 55.556 0.00 0.00 0.00 4.20
18 19 2.533318 GCCACTTGTCCTTGTCGAG 58.467 57.895 0.00 0.00 0.00 4.04
19 20 1.569479 GCCACTTGTCCTTGTCGAGC 61.569 60.000 0.00 0.00 0.00 5.03
20 21 0.034059 CCACTTGTCCTTGTCGAGCT 59.966 55.000 0.00 0.00 0.00 4.09
21 22 1.423395 CACTTGTCCTTGTCGAGCTC 58.577 55.000 2.73 2.73 0.00 4.09
22 23 0.318762 ACTTGTCCTTGTCGAGCTCC 59.681 55.000 8.47 0.00 0.00 4.70
23 24 0.318441 CTTGTCCTTGTCGAGCTCCA 59.682 55.000 8.47 0.00 0.00 3.86
24 25 0.033504 TTGTCCTTGTCGAGCTCCAC 59.966 55.000 8.47 6.29 0.00 4.02
25 26 1.079750 GTCCTTGTCGAGCTCCACC 60.080 63.158 9.11 0.00 0.00 4.61
26 27 2.125912 CCTTGTCGAGCTCCACCG 60.126 66.667 9.11 0.00 0.00 4.94
27 28 2.125912 CTTGTCGAGCTCCACCGG 60.126 66.667 9.11 0.00 0.00 5.28
28 29 4.373116 TTGTCGAGCTCCACCGGC 62.373 66.667 9.11 0.00 0.00 6.13
30 31 4.148825 GTCGAGCTCCACCGGCAT 62.149 66.667 8.47 0.00 0.00 4.40
31 32 3.838271 TCGAGCTCCACCGGCATC 61.838 66.667 8.47 0.00 0.00 3.91
32 33 4.899239 CGAGCTCCACCGGCATCC 62.899 72.222 8.47 0.00 0.00 3.51
33 34 3.474570 GAGCTCCACCGGCATCCT 61.475 66.667 0.00 0.00 0.00 3.24
34 35 3.746949 GAGCTCCACCGGCATCCTG 62.747 68.421 0.00 0.00 0.00 3.86
58 59 4.314440 TGGCACACGGACTGCTCC 62.314 66.667 1.89 0.00 34.84 4.70
66 67 2.433318 GGACTGCTCCGCTGTGTC 60.433 66.667 3.09 1.89 40.59 3.67
67 68 2.653702 GACTGCTCCGCTGTGTCT 59.346 61.111 3.09 0.00 40.59 3.41
68 69 1.445238 GACTGCTCCGCTGTGTCTC 60.445 63.158 3.09 0.00 40.59 3.36
69 70 1.872197 GACTGCTCCGCTGTGTCTCT 61.872 60.000 3.09 0.00 40.59 3.10
70 71 1.153862 CTGCTCCGCTGTGTCTCTC 60.154 63.158 0.00 0.00 0.00 3.20
71 72 1.594194 CTGCTCCGCTGTGTCTCTCT 61.594 60.000 0.00 0.00 0.00 3.10
72 73 1.181741 TGCTCCGCTGTGTCTCTCTT 61.182 55.000 0.00 0.00 0.00 2.85
73 74 0.457681 GCTCCGCTGTGTCTCTCTTC 60.458 60.000 0.00 0.00 0.00 2.87
74 75 0.172352 CTCCGCTGTGTCTCTCTTCC 59.828 60.000 0.00 0.00 0.00 3.46
75 76 0.251386 TCCGCTGTGTCTCTCTTCCT 60.251 55.000 0.00 0.00 0.00 3.36
76 77 0.605589 CCGCTGTGTCTCTCTTCCTT 59.394 55.000 0.00 0.00 0.00 3.36
77 78 1.671261 CCGCTGTGTCTCTCTTCCTTG 60.671 57.143 0.00 0.00 0.00 3.61
78 79 1.437625 GCTGTGTCTCTCTTCCTTGC 58.562 55.000 0.00 0.00 0.00 4.01
79 80 1.943507 GCTGTGTCTCTCTTCCTTGCC 60.944 57.143 0.00 0.00 0.00 4.52
80 81 0.687354 TGTGTCTCTCTTCCTTGCCC 59.313 55.000 0.00 0.00 0.00 5.36
81 82 0.390472 GTGTCTCTCTTCCTTGCCCG 60.390 60.000 0.00 0.00 0.00 6.13
82 83 1.448717 GTCTCTCTTCCTTGCCCGC 60.449 63.158 0.00 0.00 0.00 6.13
83 84 1.610673 TCTCTCTTCCTTGCCCGCT 60.611 57.895 0.00 0.00 0.00 5.52
84 85 1.449246 CTCTCTTCCTTGCCCGCTG 60.449 63.158 0.00 0.00 0.00 5.18
85 86 3.130160 CTCTTCCTTGCCCGCTGC 61.130 66.667 0.00 0.00 41.77 5.25
86 87 4.722700 TCTTCCTTGCCCGCTGCC 62.723 66.667 0.00 0.00 40.16 4.85
122 123 2.203070 GGGCACTAGCACCCATCG 60.203 66.667 14.48 0.00 46.22 3.84
123 124 2.897350 GGCACTAGCACCCATCGC 60.897 66.667 0.00 0.00 44.61 4.58
124 125 2.125147 GCACTAGCACCCATCGCA 60.125 61.111 0.00 0.00 41.58 5.10
125 126 2.176273 GCACTAGCACCCATCGCAG 61.176 63.158 0.00 0.00 41.58 5.18
126 127 2.176273 CACTAGCACCCATCGCAGC 61.176 63.158 0.00 0.00 0.00 5.25
127 128 2.590007 CTAGCACCCATCGCAGCC 60.590 66.667 0.00 0.00 0.00 4.85
128 129 4.175337 TAGCACCCATCGCAGCCC 62.175 66.667 0.00 0.00 0.00 5.19
150 151 4.363990 CAGAGCACCTGCCGACGT 62.364 66.667 0.00 0.00 43.38 4.34
151 152 4.363990 AGAGCACCTGCCGACGTG 62.364 66.667 0.00 0.00 43.38 4.49
154 155 4.980805 GCACCTGCCGACGTGGAA 62.981 66.667 0.00 0.00 42.00 3.53
155 156 2.738521 CACCTGCCGACGTGGAAG 60.739 66.667 0.00 1.97 44.16 3.46
158 159 4.760047 CTGCCGACGTGGAAGGGG 62.760 72.222 0.00 0.00 40.20 4.79
161 162 4.388499 CCGACGTGGAAGGGGTGG 62.388 72.222 0.00 0.00 42.00 4.61
162 163 3.307906 CGACGTGGAAGGGGTGGA 61.308 66.667 0.00 0.00 0.00 4.02
163 164 2.663196 GACGTGGAAGGGGTGGAG 59.337 66.667 0.00 0.00 0.00 3.86
164 165 3.607370 GACGTGGAAGGGGTGGAGC 62.607 68.421 0.00 0.00 0.00 4.70
165 166 4.760047 CGTGGAAGGGGTGGAGCG 62.760 72.222 0.00 0.00 0.00 5.03
166 167 4.410400 GTGGAAGGGGTGGAGCGG 62.410 72.222 0.00 0.00 0.00 5.52
167 168 4.649705 TGGAAGGGGTGGAGCGGA 62.650 66.667 0.00 0.00 0.00 5.54
168 169 4.097361 GGAAGGGGTGGAGCGGAC 62.097 72.222 0.00 0.00 0.00 4.79
169 170 3.003763 GAAGGGGTGGAGCGGACT 61.004 66.667 0.00 0.00 0.00 3.85
170 171 3.316573 GAAGGGGTGGAGCGGACTG 62.317 68.421 0.00 0.00 0.00 3.51
188 189 2.361610 CGCTGCCCTGGTGGAAAT 60.362 61.111 0.00 0.00 35.39 2.17
189 190 1.077787 CGCTGCCCTGGTGGAAATA 60.078 57.895 0.00 0.00 35.39 1.40
190 191 0.466189 CGCTGCCCTGGTGGAAATAT 60.466 55.000 0.00 0.00 35.39 1.28
191 192 1.035139 GCTGCCCTGGTGGAAATATG 58.965 55.000 0.00 0.00 35.39 1.78
226 228 6.741826 GAAATCGAATTTTTGGCATAGCCGG 61.742 44.000 0.00 0.00 41.52 6.13
280 283 3.251004 AGTTTCTTGACCACAAATCGCTC 59.749 43.478 0.00 0.00 35.49 5.03
477 501 3.371285 GGACGGAAAAGAGGAGAATTTCG 59.629 47.826 0.00 0.00 34.63 3.46
480 504 4.181578 CGGAAAAGAGGAGAATTTCGCTA 58.818 43.478 0.13 0.00 34.63 4.26
481 505 4.033014 CGGAAAAGAGGAGAATTTCGCTAC 59.967 45.833 0.13 0.00 34.63 3.58
482 506 4.333095 GGAAAAGAGGAGAATTTCGCTACC 59.667 45.833 0.13 0.00 34.63 3.18
1089 1113 3.012722 CCCGAGCCCCAAACCCTA 61.013 66.667 0.00 0.00 0.00 3.53
1090 1114 2.271173 CCGAGCCCCAAACCCTAC 59.729 66.667 0.00 0.00 0.00 3.18
1091 1115 2.271173 CGAGCCCCAAACCCTACC 59.729 66.667 0.00 0.00 0.00 3.18
1092 1116 2.681591 GAGCCCCAAACCCTACCC 59.318 66.667 0.00 0.00 0.00 3.69
1093 1117 2.121228 AGCCCCAAACCCTACCCA 60.121 61.111 0.00 0.00 0.00 4.51
1113 1137 3.750373 CTTCATGTACCCGCCCCCG 62.750 68.421 0.00 0.00 0.00 5.73
1221 1594 3.450115 CGGACCCACTCCCTCGTC 61.450 72.222 0.00 0.00 35.21 4.20
1266 1639 2.637947 GATTCCTCTGGTTTCTCTGCC 58.362 52.381 0.00 0.00 0.00 4.85
1275 1648 2.939261 TTTCTCTGCCGTCCCCGAC 61.939 63.158 0.00 0.00 35.63 4.79
1289 1662 1.445582 CCGACCGCCACTGAGTAAC 60.446 63.158 0.00 0.00 0.00 2.50
1299 1672 2.329379 CACTGAGTAACCTCGTGCTTC 58.671 52.381 0.00 0.00 40.85 3.86
1301 1674 1.546476 CTGAGTAACCTCGTGCTTCCT 59.454 52.381 0.00 0.00 40.85 3.36
1312 1685 1.817740 CGTGCTTCCTTTTCTTGGGGA 60.818 52.381 0.00 0.00 0.00 4.81
1313 1686 1.613925 GTGCTTCCTTTTCTTGGGGAC 59.386 52.381 0.00 0.00 0.00 4.46
1420 1793 1.152368 CTGGGGCATGGGGATTCTC 59.848 63.158 0.00 0.00 0.00 2.87
1472 1845 1.152204 TCGGGGTGGAGTTCCTGAA 60.152 57.895 0.00 0.00 35.66 3.02
1486 1859 6.039829 GGAGTTCCTGAATTCTTGTGTTTTCT 59.960 38.462 7.05 0.00 0.00 2.52
1498 1871 2.874701 TGTGTTTTCTCTGCTTGCTCTC 59.125 45.455 0.00 0.00 0.00 3.20
1529 1902 1.304134 GGATTGGGCCAAGACGGTT 60.304 57.895 25.16 6.28 36.97 4.44
1645 2018 5.657826 TTACCAAAATGATGTGGTCATGG 57.342 39.130 4.47 0.00 45.18 3.66
1759 2132 4.875536 GGTTGGATTATGCCCAATTTCAAC 59.124 41.667 0.00 13.21 44.53 3.18
1760 2133 4.383850 TGGATTATGCCCAATTTCAACG 57.616 40.909 0.00 0.00 0.00 4.10
1779 2152 9.878667 TTTCAACGTTCTATAGAATTCCATGTA 57.121 29.630 17.95 5.52 36.33 2.29
1817 2190 2.582052 TGGATTATCCCCAATTCACGC 58.418 47.619 8.98 0.00 35.03 5.34
1821 2194 4.499696 GGATTATCCCCAATTCACGCTTTG 60.500 45.833 0.00 0.00 0.00 2.77
1822 2195 2.214376 ATCCCCAATTCACGCTTTGA 57.786 45.000 0.00 0.00 0.00 2.69
1823 2196 1.533625 TCCCCAATTCACGCTTTGAG 58.466 50.000 0.00 0.00 34.94 3.02
1824 2197 1.073125 TCCCCAATTCACGCTTTGAGA 59.927 47.619 0.00 0.00 34.94 3.27
1825 2198 2.094675 CCCCAATTCACGCTTTGAGAT 58.905 47.619 0.00 0.00 34.94 2.75
1826 2199 2.493278 CCCCAATTCACGCTTTGAGATT 59.507 45.455 0.00 0.00 34.94 2.40
1918 2293 7.394816 GCCTATATTGCAAGGAAGGTAGATTA 58.605 38.462 19.34 0.00 34.58 1.75
1922 2297 8.682936 ATATTGCAAGGAAGGTAGATTACAAG 57.317 34.615 4.94 0.00 0.00 3.16
1978 2356 3.127030 GGTCTGCTATTTATAATGCCCGC 59.873 47.826 0.00 0.00 0.00 6.13
1993 2371 1.488705 CCCGCCCTTATGCCCAGATA 61.489 60.000 0.00 0.00 0.00 1.98
2013 2391 7.225538 CCAGATAATTCTCTGAGCGTTAATTGT 59.774 37.037 19.48 5.75 44.48 2.71
2076 2454 4.335594 GCACCTTCTGTTTGTTCTAGTTGT 59.664 41.667 0.00 0.00 0.00 3.32
2091 2469 3.747099 AGTTGTCGCTTATGATGCAAC 57.253 42.857 0.00 0.00 37.18 4.17
2221 2599 5.299782 GGTAACTATTGTGGTTTGTGTTCCA 59.700 40.000 0.00 0.00 0.00 3.53
2237 2615 5.163141 TGTGTTCCATCTTTCTCCACCTTTA 60.163 40.000 0.00 0.00 0.00 1.85
2238 2616 5.768164 GTGTTCCATCTTTCTCCACCTTTAA 59.232 40.000 0.00 0.00 0.00 1.52
2240 2618 7.610305 GTGTTCCATCTTTCTCCACCTTTAATA 59.390 37.037 0.00 0.00 0.00 0.98
2241 2619 8.167392 TGTTCCATCTTTCTCCACCTTTAATAA 58.833 33.333 0.00 0.00 0.00 1.40
2242 2620 8.678199 GTTCCATCTTTCTCCACCTTTAATAAG 58.322 37.037 0.00 0.00 0.00 1.73
2278 2658 2.486592 TGTCATGTCAATCTTGCAGCAG 59.513 45.455 0.00 0.00 0.00 4.24
2496 2876 7.376615 ACTATACCTGTATTTACGAATCCTGC 58.623 38.462 0.00 0.00 0.00 4.85
2527 2913 7.067494 GCAATTACCTTAACTCATGGAGTGAAT 59.933 37.037 0.00 0.00 42.59 2.57
2546 2948 5.007136 GTGAATCTGTTAGTGAGCATTAGGC 59.993 44.000 0.00 0.00 45.30 3.93
2567 2975 7.304497 AGGCCGATATTGTTCTAGATAGTTT 57.696 36.000 0.00 0.00 0.00 2.66
2664 3072 1.133199 TCAAACATGGCCCTGAACCTT 60.133 47.619 15.66 0.00 0.00 3.50
2679 3087 5.068215 TGAACCTTGGATACCTTTTTCCA 57.932 39.130 0.00 0.00 40.24 3.53
2712 3120 5.464722 CCTGACTGATTCATAACCGAATGAG 59.535 44.000 0.00 0.00 40.97 2.90
2730 3138 3.728845 TGAGGTTCTAGAAGTGCACAAC 58.271 45.455 21.04 12.95 0.00 3.32
3201 3609 4.702612 TGTACTTGGTTCTTTTGCTCACAA 59.297 37.500 0.00 0.00 0.00 3.33
3373 3781 9.728100 TCCCCTTTGAATCTTATGGATTTATTT 57.272 29.630 0.00 0.00 43.90 1.40
3442 3851 0.527817 CACGCCTACCGAATGAGGTC 60.528 60.000 0.00 0.00 44.68 3.85
3515 3924 2.486191 CCAAGCAGTCAGTCAAGGAGTT 60.486 50.000 0.00 0.00 0.00 3.01
3561 3970 3.466836 CACATATTCCCATGTACGCACT 58.533 45.455 0.00 0.00 37.02 4.40
3575 3984 2.874849 ACGCACTGACTTTTTGTTTGG 58.125 42.857 0.00 0.00 0.00 3.28
3595 4004 4.180057 TGGTCAACACATTTGCAAAGAAC 58.820 39.130 18.19 11.03 0.00 3.01
3673 4083 4.882671 TCTGCAGTTTTTCTGAGTTCAC 57.117 40.909 14.67 0.00 46.27 3.18
3687 4097 5.014123 TCTGAGTTCACCACCCTAAATGATT 59.986 40.000 0.00 0.00 0.00 2.57
3688 4098 5.640147 TGAGTTCACCACCCTAAATGATTT 58.360 37.500 0.00 0.00 0.00 2.17
3745 4155 8.890410 ATCCCTCCAAATTATCTTTATCATGG 57.110 34.615 0.00 0.00 0.00 3.66
3761 4171 2.426023 GGCTGTCCCACAGACGTT 59.574 61.111 7.87 0.00 45.42 3.99
3966 4376 7.994425 TTCTAATTTAATTCACCAGCACTCA 57.006 32.000 0.00 0.00 0.00 3.41
4002 4412 6.613679 TGTCCCCTACATAATTGTACATGAGA 59.386 38.462 0.00 0.00 37.28 3.27
4004 4414 8.157476 GTCCCCTACATAATTGTACATGAGAAT 58.843 37.037 0.00 0.00 37.28 2.40
4029 4440 6.811665 TCCAAGTAGTCATGTTTGAATCTACG 59.188 38.462 0.00 0.00 36.91 3.51
4036 4447 5.578727 GTCATGTTTGAATCTACGCTTCTCT 59.421 40.000 0.00 0.00 32.48 3.10
4164 4575 8.684386 TTGTTTCCATTGATTTACTGTGACTA 57.316 30.769 0.00 0.00 0.00 2.59
4257 4668 9.809096 TCTGTTTGTTAACAATTTATGCAGAAA 57.191 25.926 21.17 9.24 43.33 2.52
4302 4713 0.398664 AACTATGGGCTAGGAGGCGT 60.399 55.000 0.00 0.00 42.43 5.68
4372 4784 5.658634 TGTTCAGCTATATTCTGGTCTGACT 59.341 40.000 7.85 0.00 31.24 3.41
4465 4877 4.761227 TCTTGCAGCATATGTTTGTCAGAA 59.239 37.500 4.29 0.00 0.00 3.02
4619 5031 3.370846 CCATAGTGATGCCTTGTTCTCCA 60.371 47.826 0.00 0.00 0.00 3.86
4646 5058 3.706698 GCTCTGTGCGTCTAATATGACA 58.293 45.455 0.00 0.00 36.82 3.58
4729 5141 7.598118 GGTCAGTAAGTTAGGTAGTTTCACTTC 59.402 40.741 0.00 0.00 0.00 3.01
4730 5142 7.598118 GTCAGTAAGTTAGGTAGTTTCACTTCC 59.402 40.741 0.00 0.00 36.08 3.46
4741 5153 4.331968 AGTTTCACTTCCAGTTGTGTTCA 58.668 39.130 0.00 0.00 35.82 3.18
4759 5171 2.699954 TCATCCTGCTTTTCGAAGTCC 58.300 47.619 0.00 0.00 0.00 3.85
4760 5172 2.038426 TCATCCTGCTTTTCGAAGTCCA 59.962 45.455 0.00 0.00 0.00 4.02
4851 5379 3.445096 AGATTGGTCAACTTGCTTATGCC 59.555 43.478 0.00 0.00 38.71 4.40
4867 5395 5.357032 GCTTATGCCTACATAAACCAACACT 59.643 40.000 0.69 0.00 45.73 3.55
4882 5410 5.308825 ACCAACACTTTCTGACATTCCTAG 58.691 41.667 0.00 0.00 0.00 3.02
4991 5562 9.053840 CAAAATGATCTAGCTTGACACATAGAT 57.946 33.333 15.56 5.79 37.62 1.98
4994 5565 7.823745 TGATCTAGCTTGACACATAGATACA 57.176 36.000 0.00 0.00 35.61 2.29
5134 5706 5.193679 AGTATACATTTTCCCCTTGTCTGC 58.806 41.667 5.50 0.00 0.00 4.26
5159 5731 7.309194 GCCCTCTTAACAAAACTGTACATGATT 60.309 37.037 0.00 0.00 0.00 2.57
5184 5756 7.491682 TCAGCTTATCTTGGAATATTTTTGCC 58.508 34.615 0.00 0.00 0.00 4.52
5237 5809 4.681025 CGCATATGTTTGCTTGAACACTTT 59.319 37.500 4.29 0.00 41.86 2.66
5304 5876 0.343372 AGGACCTAGGGAGCCATGAA 59.657 55.000 14.81 0.00 0.00 2.57
5365 5937 9.912634 ATTCGACAACATATGAACAATTTCTTT 57.087 25.926 10.38 0.00 32.36 2.52
5410 5982 3.349927 TCTGAAGAACTGCATGATTGGG 58.650 45.455 0.00 0.00 0.00 4.12
5510 6082 3.192633 TCATACTCACGCAGCTCAACTAA 59.807 43.478 0.00 0.00 0.00 2.24
5530 6102 7.325660 ACTAATCATTTAGTGCAAGGATGTG 57.674 36.000 0.00 0.00 44.99 3.21
5531 6103 7.112122 ACTAATCATTTAGTGCAAGGATGTGA 58.888 34.615 0.00 0.00 44.99 3.58
5532 6104 6.839124 AATCATTTAGTGCAAGGATGTGAA 57.161 33.333 0.00 0.00 0.00 3.18
5533 6105 6.839124 ATCATTTAGTGCAAGGATGTGAAA 57.161 33.333 0.00 0.00 0.00 2.69
5534 6106 6.012658 TCATTTAGTGCAAGGATGTGAAAC 57.987 37.500 0.00 0.00 37.35 2.78
5535 6107 5.769662 TCATTTAGTGCAAGGATGTGAAACT 59.230 36.000 0.00 0.00 38.04 2.66
5536 6108 5.437289 TTTAGTGCAAGGATGTGAAACTG 57.563 39.130 0.00 0.00 38.04 3.16
5537 6109 2.936202 AGTGCAAGGATGTGAAACTGT 58.064 42.857 0.00 0.00 38.04 3.55
5629 6201 5.482006 TCACAGGAAGTTGATCATACAGTG 58.518 41.667 0.00 0.00 0.00 3.66
5694 6266 9.599056 TCAATCAGATACTCTTCTTGATCCTAT 57.401 33.333 0.00 0.00 0.00 2.57
5764 6336 4.389077 GGAAAGGTGAAATGTACAGACTCG 59.611 45.833 0.33 0.00 0.00 4.18
5907 6875 5.940470 GGAGTACAATTGGCTAGGATATTGG 59.060 44.000 10.83 0.00 33.41 3.16
5936 7262 3.550820 TCTGGCACTTACTCTTTTGCAA 58.449 40.909 0.00 0.00 36.66 4.08
5937 7263 3.565482 TCTGGCACTTACTCTTTTGCAAG 59.435 43.478 0.00 0.00 37.37 4.01
5938 7264 2.034558 TGGCACTTACTCTTTTGCAAGC 59.965 45.455 0.00 0.00 36.66 4.01
5939 7265 2.034558 GGCACTTACTCTTTTGCAAGCA 59.965 45.455 0.00 0.00 36.66 3.91
5991 7317 4.520111 TCAATCATGTCTGTGGGTTTCTTG 59.480 41.667 0.00 0.00 0.00 3.02
6081 7408 4.937620 TGCACTAAGATCATGAAACTGACC 59.062 41.667 0.00 0.00 0.00 4.02
6143 7470 2.496070 TGGTCAGTATATCGGCATAGCC 59.504 50.000 0.00 0.00 46.75 3.93
6288 7620 4.778143 CGGAAGCCGGTGGAAGGG 62.778 72.222 1.90 0.00 44.15 3.95
6297 7629 0.321298 CGGTGGAAGGGGTTACTGTG 60.321 60.000 0.00 0.00 0.00 3.66
6324 7656 0.776810 TGAAGATGGGGAGGCAAACA 59.223 50.000 0.00 0.00 0.00 2.83
6354 7687 4.260170 AGAAGGTGAAATGTCTCTGCATC 58.740 43.478 0.00 0.00 0.00 3.91
6475 7822 6.511416 AGTATGTGCTGTTACATTTTGCAAA 58.489 32.000 8.05 8.05 41.31 3.68
6490 7837 1.109323 GCAAACAGGACAGCCCTTGT 61.109 55.000 0.00 0.00 44.85 3.16
6594 8683 6.866248 AACTGTAAAGTGAAAAACACCAGTTG 59.134 34.615 15.57 0.00 46.14 3.16
6618 8707 3.740115 ACTGTATGTGGTCTTGTGTTCC 58.260 45.455 0.00 0.00 0.00 3.62
6651 8740 5.590259 GGTGGATGATGTTTGCTAGTAATGT 59.410 40.000 0.00 0.00 0.00 2.71
6658 8747 9.840427 ATGATGTTTGCTAGTAATGTTTTGTAC 57.160 29.630 0.00 0.00 0.00 2.90
6695 8896 2.578786 TGATGATGATGGTGATGGTGC 58.421 47.619 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.569479 GCTCGACAAGGACAAGTGGC 61.569 60.000 0.00 0.00 0.00 5.01
1 2 0.034059 AGCTCGACAAGGACAAGTGG 59.966 55.000 0.00 0.00 0.00 4.00
2 3 1.423395 GAGCTCGACAAGGACAAGTG 58.577 55.000 0.00 0.00 0.00 3.16
3 4 0.318762 GGAGCTCGACAAGGACAAGT 59.681 55.000 7.83 0.00 0.00 3.16
4 5 0.318441 TGGAGCTCGACAAGGACAAG 59.682 55.000 7.83 0.00 0.00 3.16
5 6 0.033504 GTGGAGCTCGACAAGGACAA 59.966 55.000 22.40 0.00 0.00 3.18
6 7 1.666011 GTGGAGCTCGACAAGGACA 59.334 57.895 22.40 2.50 0.00 4.02
7 8 1.079750 GGTGGAGCTCGACAAGGAC 60.080 63.158 27.22 8.52 0.00 3.85
8 9 2.636412 CGGTGGAGCTCGACAAGGA 61.636 63.158 27.22 0.00 0.00 3.36
9 10 2.125912 CGGTGGAGCTCGACAAGG 60.126 66.667 27.22 13.75 0.00 3.61
10 11 2.125912 CCGGTGGAGCTCGACAAG 60.126 66.667 27.22 20.04 0.00 3.16
11 12 4.373116 GCCGGTGGAGCTCGACAA 62.373 66.667 27.22 2.21 0.00 3.18
13 14 4.148825 ATGCCGGTGGAGCTCGAC 62.149 66.667 19.63 19.63 0.00 4.20
14 15 3.838271 GATGCCGGTGGAGCTCGA 61.838 66.667 7.83 0.00 0.00 4.04
15 16 4.899239 GGATGCCGGTGGAGCTCG 62.899 72.222 7.83 0.00 0.00 5.03
16 17 3.474570 AGGATGCCGGTGGAGCTC 61.475 66.667 4.71 4.71 0.00 4.09
17 18 3.790437 CAGGATGCCGGTGGAGCT 61.790 66.667 1.90 0.00 0.00 4.09
39 40 4.626081 AGCAGTCCGTGTGCCACC 62.626 66.667 0.00 0.00 42.24 4.61
40 41 3.044305 GAGCAGTCCGTGTGCCAC 61.044 66.667 0.00 0.00 42.24 5.01
41 42 4.314440 GGAGCAGTCCGTGTGCCA 62.314 66.667 0.00 0.00 42.24 4.92
55 56 0.172352 GGAAGAGAGACACAGCGGAG 59.828 60.000 0.00 0.00 0.00 4.63
56 57 0.251386 AGGAAGAGAGACACAGCGGA 60.251 55.000 0.00 0.00 0.00 5.54
57 58 0.605589 AAGGAAGAGAGACACAGCGG 59.394 55.000 0.00 0.00 0.00 5.52
58 59 1.707632 CAAGGAAGAGAGACACAGCG 58.292 55.000 0.00 0.00 0.00 5.18
59 60 1.437625 GCAAGGAAGAGAGACACAGC 58.562 55.000 0.00 0.00 0.00 4.40
60 61 1.338579 GGGCAAGGAAGAGAGACACAG 60.339 57.143 0.00 0.00 0.00 3.66
61 62 0.687354 GGGCAAGGAAGAGAGACACA 59.313 55.000 0.00 0.00 0.00 3.72
62 63 0.390472 CGGGCAAGGAAGAGAGACAC 60.390 60.000 0.00 0.00 0.00 3.67
63 64 1.975327 CGGGCAAGGAAGAGAGACA 59.025 57.895 0.00 0.00 0.00 3.41
64 65 1.448717 GCGGGCAAGGAAGAGAGAC 60.449 63.158 0.00 0.00 0.00 3.36
65 66 1.610673 AGCGGGCAAGGAAGAGAGA 60.611 57.895 0.00 0.00 0.00 3.10
66 67 1.449246 CAGCGGGCAAGGAAGAGAG 60.449 63.158 0.00 0.00 0.00 3.20
67 68 2.665000 CAGCGGGCAAGGAAGAGA 59.335 61.111 0.00 0.00 0.00 3.10
68 69 3.130160 GCAGCGGGCAAGGAAGAG 61.130 66.667 0.00 0.00 43.97 2.85
105 106 2.203070 CGATGGGTGCTAGTGCCC 60.203 66.667 14.48 14.48 45.04 5.36
106 107 2.897350 GCGATGGGTGCTAGTGCC 60.897 66.667 0.00 0.00 38.71 5.01
107 108 2.125147 TGCGATGGGTGCTAGTGC 60.125 61.111 0.00 0.00 40.20 4.40
108 109 2.176273 GCTGCGATGGGTGCTAGTG 61.176 63.158 0.00 0.00 0.00 2.74
109 110 2.187946 GCTGCGATGGGTGCTAGT 59.812 61.111 0.00 0.00 0.00 2.57
110 111 2.590007 GGCTGCGATGGGTGCTAG 60.590 66.667 0.00 0.00 0.00 3.42
111 112 4.175337 GGGCTGCGATGGGTGCTA 62.175 66.667 0.00 0.00 0.00 3.49
133 134 4.363990 ACGTCGGCAGGTGCTCTG 62.364 66.667 1.26 3.74 46.03 3.35
134 135 4.363990 CACGTCGGCAGGTGCTCT 62.364 66.667 1.26 0.00 41.70 4.09
137 138 4.980805 TTCCACGTCGGCAGGTGC 62.981 66.667 0.00 0.00 37.12 5.01
138 139 2.738521 CTTCCACGTCGGCAGGTG 60.739 66.667 0.00 0.00 38.02 4.00
139 140 4.003788 CCTTCCACGTCGGCAGGT 62.004 66.667 12.31 0.00 42.93 4.00
141 142 4.760047 CCCCTTCCACGTCGGCAG 62.760 72.222 0.00 0.00 33.14 4.85
144 145 4.388499 CCACCCCTTCCACGTCGG 62.388 72.222 0.00 0.00 0.00 4.79
145 146 3.296709 CTCCACCCCTTCCACGTCG 62.297 68.421 0.00 0.00 0.00 5.12
146 147 2.663196 CTCCACCCCTTCCACGTC 59.337 66.667 0.00 0.00 0.00 4.34
147 148 3.637273 GCTCCACCCCTTCCACGT 61.637 66.667 0.00 0.00 0.00 4.49
148 149 4.760047 CGCTCCACCCCTTCCACG 62.760 72.222 0.00 0.00 0.00 4.94
149 150 4.410400 CCGCTCCACCCCTTCCAC 62.410 72.222 0.00 0.00 0.00 4.02
150 151 4.649705 TCCGCTCCACCCCTTCCA 62.650 66.667 0.00 0.00 0.00 3.53
151 152 4.097361 GTCCGCTCCACCCCTTCC 62.097 72.222 0.00 0.00 0.00 3.46
152 153 3.003763 AGTCCGCTCCACCCCTTC 61.004 66.667 0.00 0.00 0.00 3.46
153 154 3.322466 CAGTCCGCTCCACCCCTT 61.322 66.667 0.00 0.00 0.00 3.95
171 172 0.466189 ATATTTCCACCAGGGCAGCG 60.466 55.000 0.00 0.00 36.21 5.18
172 173 1.035139 CATATTTCCACCAGGGCAGC 58.965 55.000 0.00 0.00 36.21 5.25
173 174 1.035139 GCATATTTCCACCAGGGCAG 58.965 55.000 0.00 0.00 36.21 4.85
174 175 0.630673 AGCATATTTCCACCAGGGCA 59.369 50.000 0.00 0.00 36.21 5.36
175 176 2.656947 TAGCATATTTCCACCAGGGC 57.343 50.000 0.00 0.00 36.21 5.19
176 177 5.835280 AGAAATTAGCATATTTCCACCAGGG 59.165 40.000 15.73 0.00 42.72 4.45
177 178 6.966534 AGAAATTAGCATATTTCCACCAGG 57.033 37.500 15.73 0.00 42.72 4.45
178 179 8.908786 TCTAGAAATTAGCATATTTCCACCAG 57.091 34.615 15.73 10.39 42.72 4.00
179 180 9.693739 TTTCTAGAAATTAGCATATTTCCACCA 57.306 29.630 13.99 3.77 42.72 4.17
226 228 0.303493 TTTTGTGACGCGTCAAGAGC 59.697 50.000 40.60 28.34 41.85 4.09
248 250 0.323629 TCAAGAAACTAGGGCGTGGG 59.676 55.000 0.00 0.00 0.00 4.61
280 283 0.109226 GAAGGTTCGGTCCTGTCTCG 60.109 60.000 0.46 0.00 37.93 4.04
408 432 3.190738 TTCTGGGGTTCTGTGCCGG 62.191 63.158 0.00 0.00 0.00 6.13
410 434 1.603739 GGTTCTGGGGTTCTGTGCC 60.604 63.158 0.00 0.00 0.00 5.01
413 437 1.386772 TGGGGTTCTGGGGTTCTGT 60.387 57.895 0.00 0.00 0.00 3.41
445 469 4.986587 TTCCGTCCGACGCGTGTG 62.987 66.667 20.70 9.15 40.91 3.82
1083 1107 3.458487 GGTACATGAAGATGGGTAGGGTT 59.542 47.826 0.00 0.00 33.39 4.11
1084 1108 3.046374 GGTACATGAAGATGGGTAGGGT 58.954 50.000 0.00 0.00 33.39 4.34
1086 1110 2.037251 CGGGTACATGAAGATGGGTAGG 59.963 54.545 0.00 0.00 33.39 3.18
1087 1111 2.548067 GCGGGTACATGAAGATGGGTAG 60.548 54.545 0.00 0.00 33.39 3.18
1088 1112 1.414919 GCGGGTACATGAAGATGGGTA 59.585 52.381 0.00 0.00 33.39 3.69
1089 1113 0.180406 GCGGGTACATGAAGATGGGT 59.820 55.000 0.00 0.00 33.39 4.51
1090 1114 0.535102 GGCGGGTACATGAAGATGGG 60.535 60.000 0.00 0.00 33.39 4.00
1091 1115 0.535102 GGGCGGGTACATGAAGATGG 60.535 60.000 0.00 0.00 33.39 3.51
1092 1116 0.535102 GGGGCGGGTACATGAAGATG 60.535 60.000 0.00 0.00 35.49 2.90
1093 1117 1.705997 GGGGGCGGGTACATGAAGAT 61.706 60.000 0.00 0.00 0.00 2.40
1239 1612 4.918201 CCAGAGGAATCGGCGGCC 62.918 72.222 9.54 9.54 0.00 6.13
1243 1616 1.208293 AGAGAAACCAGAGGAATCGGC 59.792 52.381 0.00 0.00 0.00 5.54
1275 1648 1.153823 CGAGGTTACTCAGTGGCGG 60.154 63.158 0.00 0.00 44.17 6.13
1276 1649 0.732880 CACGAGGTTACTCAGTGGCG 60.733 60.000 0.00 0.00 44.17 5.69
1277 1650 1.014564 GCACGAGGTTACTCAGTGGC 61.015 60.000 15.72 8.64 44.17 5.01
1278 1651 0.603569 AGCACGAGGTTACTCAGTGG 59.396 55.000 15.72 0.00 44.17 4.00
1280 1653 1.272769 GGAAGCACGAGGTTACTCAGT 59.727 52.381 0.00 0.00 44.17 3.41
1289 1662 1.537202 CCAAGAAAAGGAAGCACGAGG 59.463 52.381 0.00 0.00 0.00 4.63
1299 1672 0.811281 GCATCGTCCCCAAGAAAAGG 59.189 55.000 0.00 0.00 0.00 3.11
1301 1674 1.202879 ACTGCATCGTCCCCAAGAAAA 60.203 47.619 0.00 0.00 0.00 2.29
1312 1685 0.317160 TCCGTCAAGAACTGCATCGT 59.683 50.000 0.00 0.00 0.00 3.73
1313 1686 0.716108 GTCCGTCAAGAACTGCATCG 59.284 55.000 0.00 0.00 0.00 3.84
1459 1832 4.137543 ACACAAGAATTCAGGAACTCCAC 58.862 43.478 8.44 0.00 34.60 4.02
1472 1845 4.340381 AGCAAGCAGAGAAAACACAAGAAT 59.660 37.500 0.00 0.00 0.00 2.40
1498 1871 0.374758 CCAATCCGTCACAATCTGCG 59.625 55.000 0.00 0.00 0.00 5.18
1529 1902 1.152030 AACCCTCTCCTCACAGGCA 60.152 57.895 0.00 0.00 34.61 4.75
1553 1926 4.078516 GTAGCCGTCACCCGCCTT 62.079 66.667 0.00 0.00 34.38 4.35
1645 2018 1.135575 CCCGCAAGCATTCAGAGAAAC 60.136 52.381 0.00 0.00 0.00 2.78
1715 2088 7.356540 CAACCAATTTACTACGACAAACATGA 58.643 34.615 0.00 0.00 0.00 3.07
1725 2098 6.435428 GGCATAATCCAACCAATTTACTACG 58.565 40.000 0.00 0.00 0.00 3.51
1784 2157 7.064229 TGGGGATAATCCAACCAATTTACTAC 58.936 38.462 0.00 0.00 38.64 2.73
1858 2231 4.520492 CCAAGAGGTGTGAAGCACTAAATT 59.480 41.667 0.00 0.00 46.86 1.82
1918 2293 9.988815 CTGTATTGTCTCTAATAATAGGCTTGT 57.011 33.333 0.00 0.00 0.00 3.16
1922 2297 7.762159 GCTCCTGTATTGTCTCTAATAATAGGC 59.238 40.741 0.00 0.00 33.49 3.93
1962 2340 5.221048 GCATAAGGGCGGGCATTATAAATAG 60.221 44.000 18.95 9.31 0.00 1.73
1971 2349 4.603535 GGGCATAAGGGCGGGCAT 62.604 66.667 3.27 0.00 44.56 4.40
1978 2356 5.013495 TCAGAGAATTATCTGGGCATAAGGG 59.987 44.000 25.64 1.03 45.60 3.95
1993 2371 7.677276 GCACATACAATTAACGCTCAGAGAATT 60.677 37.037 0.00 0.00 0.00 2.17
2076 2454 4.961435 TGATTTGTTGCATCATAAGCGA 57.039 36.364 0.00 0.00 33.85 4.93
2221 2599 8.393959 TCCTCTTATTAAAGGTGGAGAAAGAT 57.606 34.615 0.00 0.00 33.71 2.40
2237 2615 7.050970 TGACATGCGTTAGTATCCTCTTATT 57.949 36.000 0.00 0.00 0.00 1.40
2238 2616 6.650427 TGACATGCGTTAGTATCCTCTTAT 57.350 37.500 0.00 0.00 0.00 1.73
2240 2618 5.163405 ACATGACATGCGTTAGTATCCTCTT 60.163 40.000 15.49 0.00 0.00 2.85
2241 2619 4.342378 ACATGACATGCGTTAGTATCCTCT 59.658 41.667 15.49 0.00 0.00 3.69
2242 2620 4.621991 ACATGACATGCGTTAGTATCCTC 58.378 43.478 15.49 0.00 0.00 3.71
2289 2669 4.335315 ACTTGAGAATTTGTCGCAGAACAA 59.665 37.500 1.03 0.00 39.69 2.83
2496 2876 5.163622 CCATGAGTTAAGGTAATTGCACAGG 60.164 44.000 0.00 0.00 0.00 4.00
2527 2913 2.159099 CGGCCTAATGCTCACTAACAGA 60.159 50.000 0.00 0.00 40.92 3.41
2664 3072 4.715534 TGACACTGGAAAAAGGTATCCA 57.284 40.909 0.00 0.00 43.32 3.41
2701 3109 5.623824 GCACTTCTAGAACCTCATTCGGTTA 60.624 44.000 0.00 0.00 46.85 2.85
2712 3120 3.673809 CGTAGTTGTGCACTTCTAGAACC 59.326 47.826 19.41 7.53 36.88 3.62
2730 3138 3.190874 GCAAGGAAAGTCAGGATCGTAG 58.809 50.000 0.00 0.00 0.00 3.51
2971 3379 4.525874 AGTGAGATCTTGTCACACAGATCA 59.474 41.667 21.88 9.40 46.81 2.92
3046 3454 5.871396 AATGACATTAGACGTCCCATAGT 57.129 39.130 13.01 4.92 32.15 2.12
3201 3609 3.955551 TGGCTTCATCATGCACATATTGT 59.044 39.130 0.00 0.00 0.00 2.71
3373 3781 4.646945 GGTCACTATCTGATCCAACTCTCA 59.353 45.833 0.00 0.00 0.00 3.27
3414 3823 2.216046 TCGGTAGGCGTGTGATAGTAG 58.784 52.381 0.00 0.00 0.00 2.57
3415 3824 2.330440 TCGGTAGGCGTGTGATAGTA 57.670 50.000 0.00 0.00 0.00 1.82
3416 3825 1.466856 TTCGGTAGGCGTGTGATAGT 58.533 50.000 0.00 0.00 0.00 2.12
3531 3940 2.733956 TGGGAATATGTGGTGGCTTTC 58.266 47.619 0.00 0.00 0.00 2.62
3575 3984 6.019881 GGTAAGTTCTTTGCAAATGTGTTGAC 60.020 38.462 13.23 6.05 0.00 3.18
3595 4004 7.496529 TGTGAGTTCTTTTGATCAAGGTAAG 57.503 36.000 8.41 9.81 0.00 2.34
3650 4059 5.221126 GGTGAACTCAGAAAAACTGCAGAAT 60.221 40.000 23.35 5.76 45.38 2.40
3745 4155 0.032952 TACAACGTCTGTGGGACAGC 59.967 55.000 11.90 0.00 45.54 4.40
3966 4376 4.447138 TGTAGGGGACAAAAATGTGACT 57.553 40.909 0.00 0.00 34.15 3.41
4002 4412 9.167311 GTAGATTCAAACATGACTACTTGGATT 57.833 33.333 0.00 0.00 0.00 3.01
4004 4414 6.811665 CGTAGATTCAAACATGACTACTTGGA 59.188 38.462 0.00 0.00 0.00 3.53
4029 4440 9.980780 GAGTAAGTAAATGAATTGAAGAGAAGC 57.019 33.333 0.00 0.00 0.00 3.86
4117 4528 8.123639 ACAAGAGCACTGATAAGAGTAAGTAA 57.876 34.615 0.00 0.00 0.00 2.24
4119 4530 6.597832 ACAAGAGCACTGATAAGAGTAAGT 57.402 37.500 0.00 0.00 0.00 2.24
4120 4531 7.064016 GGAAACAAGAGCACTGATAAGAGTAAG 59.936 40.741 0.00 0.00 0.00 2.34
4121 4532 6.874134 GGAAACAAGAGCACTGATAAGAGTAA 59.126 38.462 0.00 0.00 0.00 2.24
4122 4533 6.014584 TGGAAACAAGAGCACTGATAAGAGTA 60.015 38.462 0.00 0.00 37.44 2.59
4123 4534 5.221722 TGGAAACAAGAGCACTGATAAGAGT 60.222 40.000 0.00 0.00 37.44 3.24
4257 4668 2.095059 GCATCGCAACAGAACTTGGAAT 60.095 45.455 0.00 0.00 0.00 3.01
4302 4713 3.966979 ACATACATGGCAATGAAGTCCA 58.033 40.909 8.45 0.00 37.24 4.02
4465 4877 1.698532 TGGCAGTGGCATTTGGAAATT 59.301 42.857 16.56 0.00 43.71 1.82
4619 5031 4.057428 GACGCACAGAGCTCCGGT 62.057 66.667 10.93 6.45 42.61 5.28
4729 5141 1.901591 AGCAGGATGAACACAACTGG 58.098 50.000 0.00 0.00 39.69 4.00
4730 5142 3.996150 AAAGCAGGATGAACACAACTG 57.004 42.857 0.00 0.00 39.69 3.16
4741 5153 2.039084 ACTGGACTTCGAAAAGCAGGAT 59.961 45.455 0.00 0.00 35.81 3.24
4759 5171 3.374745 GTGCATTTCACAAACTCCACTG 58.625 45.455 0.00 0.00 44.98 3.66
4760 5172 3.715628 GTGCATTTCACAAACTCCACT 57.284 42.857 0.00 0.00 44.98 4.00
4851 5379 7.490962 TGTCAGAAAGTGTTGGTTTATGTAG 57.509 36.000 0.00 0.00 29.98 2.74
4867 5395 2.912956 AGTGGCCTAGGAATGTCAGAAA 59.087 45.455 14.75 0.00 0.00 2.52
4882 5410 2.295885 CATGGAAGATCTGAAGTGGCC 58.704 52.381 0.00 0.00 0.00 5.36
4912 5443 1.531578 GAACAGGAAAGAGTGCCGAAC 59.468 52.381 0.00 0.00 0.00 3.95
4991 5562 7.450074 AGTGAACAAGGAACACAAGATATGTA 58.550 34.615 0.00 0.00 41.46 2.29
4994 5565 6.998074 TGAAGTGAACAAGGAACACAAGATAT 59.002 34.615 0.00 0.00 37.05 1.63
5000 5571 4.331968 ACTTGAAGTGAACAAGGAACACA 58.668 39.130 0.00 0.00 45.92 3.72
5134 5706 7.687941 ATCATGTACAGTTTTGTTAAGAGGG 57.312 36.000 0.33 0.00 38.76 4.30
5159 5731 7.491682 GGCAAAAATATTCCAAGATAAGCTGA 58.508 34.615 0.00 0.00 0.00 4.26
5184 5756 7.094890 TGGTCTAGTACTAGAGAAAACTGAACG 60.095 40.741 29.00 1.69 42.31 3.95
5304 5876 4.286549 TCAAAAATCCATGCCCACTCAAAT 59.713 37.500 0.00 0.00 0.00 2.32
5365 5937 1.065272 TGGAGCACATAGAGCAATGCA 60.065 47.619 8.35 0.00 40.63 3.96
5510 6082 6.435277 AGTTTCACATCCTTGCACTAAATGAT 59.565 34.615 0.00 0.00 0.00 2.45
5629 6201 8.131100 CAGTGATATACAATGTTGGGTTTGATC 58.869 37.037 0.00 0.00 39.36 2.92
5694 6266 6.864151 TCATGAAATCTTCCTTCAGAGAGA 57.136 37.500 0.00 0.00 36.30 3.10
5764 6336 1.079750 GAGGGACAACGTCAGCTCC 60.080 63.158 0.00 0.00 33.68 4.70
5859 6827 2.124819 CAGCTGCTGCCTGGTAGG 60.125 66.667 17.73 0.00 40.80 3.18
5907 6875 3.133721 AGAGTAAGTGCCAGATGATCCAC 59.866 47.826 0.00 0.00 0.00 4.02
5936 7262 6.522946 CCCGATGATCATCATATAAGATGCT 58.477 40.000 30.13 3.80 43.94 3.79
5937 7263 5.178996 GCCCGATGATCATCATATAAGATGC 59.821 44.000 30.13 16.27 43.94 3.91
5938 7264 5.699915 GGCCCGATGATCATCATATAAGATG 59.300 44.000 30.13 10.99 45.28 2.90
5939 7265 5.510349 CGGCCCGATGATCATCATATAAGAT 60.510 44.000 30.13 0.00 37.20 2.40
5991 7317 3.558109 GCTAGGGGCAATAAGGAGATGAC 60.558 52.174 0.00 0.00 41.35 3.06
6081 7408 2.486472 AACCATCAGAGCAGAACCAG 57.514 50.000 0.00 0.00 0.00 4.00
6166 7495 2.912771 CCACTATGCCGACAATACCAA 58.087 47.619 0.00 0.00 0.00 3.67
6172 7501 3.802329 GCTATAAGCCACTATGCCGACAA 60.802 47.826 0.00 0.00 34.48 3.18
6270 7600 4.016706 CCTTCCACCGGCTTCCGT 62.017 66.667 0.00 0.00 46.80 4.69
6288 7620 4.394729 TCTTCAATGGGTTCACAGTAACC 58.605 43.478 0.00 0.00 46.90 2.85
6330 7663 4.067896 TGCAGAGACATTTCACCTTCTTC 58.932 43.478 0.00 0.00 0.00 2.87
6331 7664 4.090761 TGCAGAGACATTTCACCTTCTT 57.909 40.909 0.00 0.00 0.00 2.52
6333 7666 4.005650 TGATGCAGAGACATTTCACCTTC 58.994 43.478 0.00 0.00 0.00 3.46
6336 7669 3.425359 CGTTGATGCAGAGACATTTCACC 60.425 47.826 0.00 0.00 0.00 4.02
6338 7671 2.743664 CCGTTGATGCAGAGACATTTCA 59.256 45.455 0.00 0.00 0.00 2.69
6340 7673 2.485426 CACCGTTGATGCAGAGACATTT 59.515 45.455 0.00 0.00 0.00 2.32
6343 7676 0.392706 ACACCGTTGATGCAGAGACA 59.607 50.000 0.00 0.00 0.00 3.41
6344 7677 1.071605 GACACCGTTGATGCAGAGAC 58.928 55.000 0.00 0.00 0.00 3.36
6346 7679 0.320683 TGGACACCGTTGATGCAGAG 60.321 55.000 0.00 0.00 0.00 3.35
6354 7687 1.648720 CAGCACTTGGACACCGTTG 59.351 57.895 0.00 0.00 0.00 4.10
6404 7737 3.532501 ACCTTGGGTGGTTTTGCG 58.467 55.556 0.00 0.00 36.89 4.85
6490 7837 6.601613 AGTTACACAAAAGAATGGTTCAGTGA 59.398 34.615 0.00 0.00 0.00 3.41
6590 8679 5.296780 CACAAGACCACATACAGTTTCAACT 59.703 40.000 0.00 0.00 40.60 3.16
6591 8680 5.065988 ACACAAGACCACATACAGTTTCAAC 59.934 40.000 0.00 0.00 0.00 3.18
6592 8681 5.189928 ACACAAGACCACATACAGTTTCAA 58.810 37.500 0.00 0.00 0.00 2.69
6593 8682 4.776349 ACACAAGACCACATACAGTTTCA 58.224 39.130 0.00 0.00 0.00 2.69
6594 8683 5.277828 GGAACACAAGACCACATACAGTTTC 60.278 44.000 0.00 0.00 0.00 2.78
6597 8686 3.740115 GGAACACAAGACCACATACAGT 58.260 45.455 0.00 0.00 0.00 3.55
6618 8707 0.812811 CATCATCCACCTCTGCACCG 60.813 60.000 0.00 0.00 0.00 4.94
6651 8740 9.486497 TCAATACCAAATACGTACAGTACAAAA 57.514 29.630 11.37 0.00 38.29 2.44
6658 8747 8.587952 TCATCATCAATACCAAATACGTACAG 57.412 34.615 0.00 0.00 0.00 2.74
6695 8896 9.454585 CAAAATACCATCATGCTAAACAGTATG 57.545 33.333 0.00 0.00 46.00 2.39
6840 9052 2.060980 AAGAGCTAGCCCGGGTCAG 61.061 63.158 24.63 20.00 34.14 3.51
6847 9059 1.063183 ATGATCCCAAGAGCTAGCCC 58.937 55.000 12.13 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.