Multiple sequence alignment - TraesCS5D01G103600

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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 TraesCS5D01G103600 chr5D 100.000 4177 0 0 650 4826 117269417 117265241 0.000000e+00 7714.0
1 TraesCS5D01G103600 chr5D 100.000 345 0 0 1 345 117270066 117269722 5.270000e-179 638.0
2 TraesCS5D01G103600 chr5D 92.727 55 2 2 4326 4379 117265701 117265648 1.440000e-10 78.7
3 TraesCS5D01G103600 chr5D 92.727 55 2 2 4366 4419 117265741 117265688 1.440000e-10 78.7
4 TraesCS5D01G103600 chr5B 94.067 2444 98 19 1919 4339 129718096 129720515 0.000000e+00 3666.0
5 TraesCS5D01G103600 chr5B 92.971 1067 42 11 775 1840 129717012 129718046 0.000000e+00 1524.0
6 TraesCS5D01G103600 chr5B 97.608 418 9 1 4410 4826 129720505 129720922 0.000000e+00 715.0
7 TraesCS5D01G103600 chr5B 88.095 126 9 4 650 773 129716219 129716340 1.400000e-30 145.0
8 TraesCS5D01G103600 chr5B 94.737 57 3 0 1838 1894 281229336 281229280 6.650000e-14 89.8
9 TraesCS5D01G103600 chr5B 94.340 53 3 0 1 53 129715851 129715903 1.110000e-11 82.4
10 TraesCS5D01G103600 chr5A 91.153 2498 106 29 1922 4379 126275238 126272816 0.000000e+00 3282.0
11 TraesCS5D01G103600 chr5A 92.632 570 26 8 900 1458 126276343 126275779 0.000000e+00 806.0
12 TraesCS5D01G103600 chr5A 95.879 461 18 1 4366 4826 126272868 126272409 0.000000e+00 745.0
13 TraesCS5D01G103600 chr5A 89.565 345 31 4 1499 1840 126275633 126275291 2.670000e-117 433.0
14 TraesCS5D01G103600 chr5A 89.655 174 9 4 650 816 126276533 126276362 3.780000e-51 213.0
15 TraesCS5D01G103600 chr5A 97.368 38 0 1 1887 1923 126275306 126275269 4.030000e-06 63.9
16 TraesCS5D01G103600 chr7B 97.917 48 1 0 1838 1885 336591600 336591553 3.100000e-12 84.2
17 TraesCS5D01G103600 chr2A 96.000 50 2 0 1838 1887 393003344 393003295 1.110000e-11 82.4
18 TraesCS5D01G103600 chr1D 94.000 50 3 0 1837 1886 43270490 43270539 5.180000e-10 76.8


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 TraesCS5D01G103600 chr5D 117265241 117270066 4825 True 2127.350000 7714 96.363500 1 4826 4 chr5D.!!$R1 4825
1 TraesCS5D01G103600 chr5B 129715851 129720922 5071 False 1226.480000 3666 93.416200 1 4826 5 chr5B.!!$F1 4825
2 TraesCS5D01G103600 chr5A 126272409 126276533 4124 True 923.816667 3282 92.708667 650 4826 6 chr5A.!!$R1 4176

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
236 241 0.179145 AGCCATACCGAGAAACGACG 60.179 55.000 0.00 0.0 45.77 5.12 F
303 311 0.733150 TGCGTCTATCTCGTCCACTG 59.267 55.000 0.00 0.0 0.00 3.66 F
1802 2599 0.256752 TGAGGGCCATCTGGTCATTG 59.743 55.000 19.75 0.0 42.93 2.82 F
2760 3594 1.142870 TGCTTGCAGTTGACCCTACTT 59.857 47.619 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 2336 0.108186 TCTTTGATCAGCACCGCGAT 60.108 50.0 8.23 0.0 0.00 4.58 R
2099 2928 0.684479 TATCAGCACCCTCAGCTCGT 60.684 55.0 0.00 0.0 41.14 4.18 R
3538 4383 0.737715 CGCTTTCCTCCTTCTCACGG 60.738 60.0 0.00 0.0 0.00 4.94 R
3835 4682 0.111061 AGCCAAGCATCACCACTTCA 59.889 50.0 0.00 0.0 0.00 3.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.675062 CAATGATAGCTTGTCCCTTACTATCT 58.325 38.462 0.00 0.00 39.81 1.98
49 50 7.756614 TGATAGCTTGTCCCTTACTATCTCTA 58.243 38.462 0.00 0.00 39.81 2.43
50 51 8.225416 TGATAGCTTGTCCCTTACTATCTCTAA 58.775 37.037 0.00 0.00 39.81 2.10
51 52 9.080097 GATAGCTTGTCCCTTACTATCTCTAAA 57.920 37.037 0.00 0.00 37.37 1.85
52 53 7.922699 AGCTTGTCCCTTACTATCTCTAAAT 57.077 36.000 0.00 0.00 0.00 1.40
53 54 8.325477 AGCTTGTCCCTTACTATCTCTAAATT 57.675 34.615 0.00 0.00 0.00 1.82
54 55 8.425703 AGCTTGTCCCTTACTATCTCTAAATTC 58.574 37.037 0.00 0.00 0.00 2.17
55 56 7.382759 GCTTGTCCCTTACTATCTCTAAATTCG 59.617 40.741 0.00 0.00 0.00 3.34
56 57 8.529424 TTGTCCCTTACTATCTCTAAATTCGA 57.471 34.615 0.00 0.00 0.00 3.71
57 58 8.529424 TGTCCCTTACTATCTCTAAATTCGAA 57.471 34.615 0.00 0.00 0.00 3.71
58 59 8.411683 TGTCCCTTACTATCTCTAAATTCGAAC 58.588 37.037 0.00 0.00 0.00 3.95
59 60 8.411683 GTCCCTTACTATCTCTAAATTCGAACA 58.588 37.037 0.00 0.00 0.00 3.18
60 61 8.974238 TCCCTTACTATCTCTAAATTCGAACAA 58.026 33.333 0.00 0.00 0.00 2.83
61 62 9.765795 CCCTTACTATCTCTAAATTCGAACAAT 57.234 33.333 0.00 0.00 0.00 2.71
69 70 8.615878 TCTCTAAATTCGAACAATTTTCCTCA 57.384 30.769 0.00 0.00 32.64 3.86
70 71 8.504005 TCTCTAAATTCGAACAATTTTCCTCAC 58.496 33.333 0.00 0.00 32.64 3.51
71 72 7.590279 TCTAAATTCGAACAATTTTCCTCACC 58.410 34.615 0.00 0.00 32.64 4.02
72 73 5.782893 AATTCGAACAATTTTCCTCACCA 57.217 34.783 0.00 0.00 0.00 4.17
73 74 5.782893 ATTCGAACAATTTTCCTCACCAA 57.217 34.783 0.00 0.00 0.00 3.67
74 75 5.584253 TTCGAACAATTTTCCTCACCAAA 57.416 34.783 0.00 0.00 0.00 3.28
75 76 5.584253 TCGAACAATTTTCCTCACCAAAA 57.416 34.783 0.00 0.00 0.00 2.44
76 77 6.155475 TCGAACAATTTTCCTCACCAAAAT 57.845 33.333 0.00 0.00 35.40 1.82
77 78 6.578023 TCGAACAATTTTCCTCACCAAAATT 58.422 32.000 0.00 0.00 41.86 1.82
81 82 6.622833 CAATTTTCCTCACCAAAATTGCTT 57.377 33.333 14.42 0.00 46.41 3.91
82 83 6.432107 CAATTTTCCTCACCAAAATTGCTTG 58.568 36.000 14.42 0.00 46.41 4.01
83 84 6.513720 CAATTTTCCTCACCAAAATTGCTTGG 60.514 38.462 14.42 7.27 46.41 3.61
89 90 2.168326 CCAAAATTGCTTGGGTCCAC 57.832 50.000 1.47 0.00 41.96 4.02
90 91 1.415659 CCAAAATTGCTTGGGTCCACA 59.584 47.619 1.47 0.00 41.96 4.17
91 92 2.038820 CCAAAATTGCTTGGGTCCACAT 59.961 45.455 1.47 0.00 41.96 3.21
92 93 3.068560 CAAAATTGCTTGGGTCCACATG 58.931 45.455 0.00 0.00 0.00 3.21
93 94 2.014010 AATTGCTTGGGTCCACATGT 57.986 45.000 0.00 0.00 0.00 3.21
94 95 2.897271 ATTGCTTGGGTCCACATGTA 57.103 45.000 0.00 0.00 0.00 2.29
95 96 2.666272 TTGCTTGGGTCCACATGTAA 57.334 45.000 0.00 0.00 0.00 2.41
96 97 1.904287 TGCTTGGGTCCACATGTAAC 58.096 50.000 0.00 0.00 0.00 2.50
97 98 1.143889 TGCTTGGGTCCACATGTAACA 59.856 47.619 0.00 0.00 0.00 2.41
98 99 1.539827 GCTTGGGTCCACATGTAACAC 59.460 52.381 0.00 1.51 0.00 3.32
99 100 2.857483 CTTGGGTCCACATGTAACACA 58.143 47.619 10.58 10.58 0.00 3.72
100 101 3.218453 CTTGGGTCCACATGTAACACAA 58.782 45.455 20.83 20.83 35.19 3.33
101 102 3.298686 TGGGTCCACATGTAACACAAA 57.701 42.857 11.90 0.00 0.00 2.83
102 103 3.838565 TGGGTCCACATGTAACACAAAT 58.161 40.909 11.90 0.00 0.00 2.32
103 104 4.219115 TGGGTCCACATGTAACACAAATT 58.781 39.130 11.90 0.00 0.00 1.82
104 105 4.279671 TGGGTCCACATGTAACACAAATTC 59.720 41.667 11.90 0.00 0.00 2.17
105 106 4.279671 GGGTCCACATGTAACACAAATTCA 59.720 41.667 0.00 0.00 0.00 2.57
106 107 5.221342 GGGTCCACATGTAACACAAATTCAA 60.221 40.000 0.00 0.00 0.00 2.69
107 108 6.454795 GGTCCACATGTAACACAAATTCAAT 58.545 36.000 0.00 0.00 0.00 2.57
108 109 6.928492 GGTCCACATGTAACACAAATTCAATT 59.072 34.615 0.00 0.00 0.00 2.32
109 110 7.440856 GGTCCACATGTAACACAAATTCAATTT 59.559 33.333 0.00 0.00 0.00 1.82
110 111 8.487176 GTCCACATGTAACACAAATTCAATTTC 58.513 33.333 0.00 0.00 0.00 2.17
111 112 7.655328 TCCACATGTAACACAAATTCAATTTCC 59.345 33.333 0.00 0.00 0.00 3.13
112 113 7.440556 CCACATGTAACACAAATTCAATTTCCA 59.559 33.333 0.00 0.00 0.00 3.53
113 114 8.991026 CACATGTAACACAAATTCAATTTCCAT 58.009 29.630 0.00 0.00 0.00 3.41
114 115 9.558396 ACATGTAACACAAATTCAATTTCCATT 57.442 25.926 0.00 0.00 0.00 3.16
115 116 9.814507 CATGTAACACAAATTCAATTTCCATTG 57.185 29.630 0.00 0.00 41.25 2.82
116 117 8.375608 TGTAACACAAATTCAATTTCCATTGG 57.624 30.769 0.00 0.00 40.41 3.16
117 118 7.989741 TGTAACACAAATTCAATTTCCATTGGT 59.010 29.630 1.86 0.00 40.41 3.67
118 119 9.482627 GTAACACAAATTCAATTTCCATTGGTA 57.517 29.630 1.86 0.00 40.41 3.25
119 120 8.970859 AACACAAATTCAATTTCCATTGGTAA 57.029 26.923 1.86 0.00 40.41 2.85
120 121 9.571816 AACACAAATTCAATTTCCATTGGTAAT 57.428 25.926 1.86 1.91 40.41 1.89
121 122 9.218440 ACACAAATTCAATTTCCATTGGTAATC 57.782 29.630 7.88 0.00 40.41 1.75
156 159 7.696992 AAAAAGGACCAAATATTAAGCTCGA 57.303 32.000 0.00 0.00 0.00 4.04
160 163 5.104485 AGGACCAAATATTAAGCTCGAACCT 60.104 40.000 0.00 0.00 0.00 3.50
164 167 8.570068 ACCAAATATTAAGCTCGAACCTTAAA 57.430 30.769 16.99 10.10 38.03 1.52
194 198 6.972722 TGGTAAAGAAAAACCATAGAAACCG 58.027 36.000 0.00 0.00 40.84 4.44
215 219 4.102649 CGCCAATTTTCTATTCGAAACCC 58.897 43.478 0.00 0.00 41.13 4.11
233 238 1.269621 CCCTAGCCATACCGAGAAACG 60.270 57.143 0.00 0.00 42.18 3.60
236 241 0.179145 AGCCATACCGAGAAACGACG 60.179 55.000 0.00 0.00 45.77 5.12
244 249 1.005975 CCGAGAAACGACGATGAATGC 60.006 52.381 0.00 0.00 45.77 3.56
250 255 3.836229 AACGACGATGAATGCGATAAC 57.164 42.857 0.00 0.00 0.00 1.89
261 266 5.984627 TGAATGCGATAACGATAACATTGG 58.015 37.500 0.00 0.00 42.66 3.16
283 291 1.664956 GGGGGAAGGGGTTGGCATAT 61.665 60.000 0.00 0.00 0.00 1.78
292 300 2.504367 GGGTTGGCATATTGCGTCTAT 58.496 47.619 0.00 0.00 46.21 1.98
302 310 1.460504 TTGCGTCTATCTCGTCCACT 58.539 50.000 0.00 0.00 0.00 4.00
303 311 0.733150 TGCGTCTATCTCGTCCACTG 59.267 55.000 0.00 0.00 0.00 3.66
306 314 1.532090 CGTCTATCTCGTCCACTGTGC 60.532 57.143 1.29 0.00 0.00 4.57
334 342 2.019951 GTTCACCATCGTCGTGCGT 61.020 57.895 0.00 0.00 42.13 5.24
335 343 1.731613 TTCACCATCGTCGTGCGTC 60.732 57.895 0.00 0.00 42.13 5.19
735 743 9.367444 AGAGTACGAATTCAAGATTTATTTCGT 57.633 29.630 12.32 12.32 0.00 3.85
773 783 1.286880 CGCCTTGTTTCAGCCCAAG 59.713 57.895 0.00 0.00 38.21 3.61
823 1503 1.519455 GTCTGATTCACGAGGCCCG 60.519 63.158 11.48 11.48 45.44 6.13
890 1570 2.475187 CGCTCCTCGCATTTCTTTCTTG 60.475 50.000 0.00 0.00 39.08 3.02
898 1578 4.825085 TCGCATTTCTTTCTTGTACCCTTT 59.175 37.500 0.00 0.00 0.00 3.11
925 1605 1.846541 CGCGAGAGAGGAAAGGAATC 58.153 55.000 0.00 0.00 0.00 2.52
1030 1710 2.837291 CCAGCTCCTCCTCCTCCG 60.837 72.222 0.00 0.00 0.00 4.63
1031 1711 2.277072 CAGCTCCTCCTCCTCCGA 59.723 66.667 0.00 0.00 0.00 4.55
1248 1934 2.770475 GCTTCCCCCTCCTCCTCC 60.770 72.222 0.00 0.00 0.00 4.30
1272 1958 3.385115 CCCCCTCTCTGTGTATAGGTTT 58.615 50.000 0.00 0.00 0.00 3.27
1330 2016 2.915869 TCTAGGAGATTGGGTTGGTGT 58.084 47.619 0.00 0.00 0.00 4.16
1332 2018 1.444933 AGGAGATTGGGTTGGTGTGA 58.555 50.000 0.00 0.00 0.00 3.58
1339 2025 2.270352 TGGGTTGGTGTGATTGACTC 57.730 50.000 0.00 0.00 0.00 3.36
1379 2065 7.030165 AGAGGAAATATATGCGTAGATCAACG 58.970 38.462 0.00 0.00 45.58 4.10
1383 2069 3.620929 ATATGCGTAGATCAACGTCGT 57.379 42.857 0.00 0.00 44.64 4.34
1415 2101 4.712051 TCCAGTTGGAATCATAGGGATG 57.288 45.455 0.00 0.00 42.18 3.51
1495 2204 7.611467 TGGGTAATACTGTAAGAACTAACGAGA 59.389 37.037 0.00 0.00 37.43 4.04
1541 2336 1.367346 TGCTATTGGTGGGGACAGAA 58.633 50.000 0.00 0.00 44.46 3.02
1546 2341 2.511600 GGTGGGGACAGAATCGCG 60.512 66.667 0.00 0.00 44.46 5.87
1588 2383 2.771943 TCATGTGAGGTGATAAGGGGAC 59.228 50.000 0.00 0.00 0.00 4.46
1720 2515 7.042725 TGAGCGTGCTGACTATTTATAAATGAC 60.043 37.037 18.98 11.02 0.00 3.06
1722 2517 7.042456 AGCGTGCTGACTATTTATAAATGACTG 60.042 37.037 18.98 13.79 0.00 3.51
1749 2544 3.648009 CGCCACTTTTCTATTTGCCAAA 58.352 40.909 0.00 0.00 0.00 3.28
1772 2569 8.341903 CAAATTTTGGGGTGAAATGTCTTTTAC 58.658 33.333 0.97 0.00 31.81 2.01
1802 2599 0.256752 TGAGGGCCATCTGGTCATTG 59.743 55.000 19.75 0.00 42.93 2.82
1815 2612 2.423185 TGGTCATTGGCAATCGATGTTC 59.577 45.455 10.36 0.64 38.22 3.18
1856 2653 6.783892 TTTCTGTTTTGAAATGCATAAGGC 57.216 33.333 0.00 0.00 35.63 4.35
1876 2673 3.279853 CAGAAACTGCTCTGCCTTTTC 57.720 47.619 0.00 0.00 36.67 2.29
1877 2674 2.030451 CAGAAACTGCTCTGCCTTTTCC 60.030 50.000 8.43 0.00 36.67 3.13
1878 2675 2.158549 AGAAACTGCTCTGCCTTTTCCT 60.159 45.455 8.43 0.00 32.32 3.36
1879 2676 2.371658 AACTGCTCTGCCTTTTCCTT 57.628 45.000 0.00 0.00 0.00 3.36
1880 2677 1.902938 ACTGCTCTGCCTTTTCCTTC 58.097 50.000 0.00 0.00 0.00 3.46
1881 2678 1.143684 ACTGCTCTGCCTTTTCCTTCA 59.856 47.619 0.00 0.00 0.00 3.02
1882 2679 2.233271 CTGCTCTGCCTTTTCCTTCAA 58.767 47.619 0.00 0.00 0.00 2.69
1883 2680 2.624838 CTGCTCTGCCTTTTCCTTCAAA 59.375 45.455 0.00 0.00 0.00 2.69
1884 2681 3.030291 TGCTCTGCCTTTTCCTTCAAAA 58.970 40.909 0.00 0.00 32.77 2.44
1885 2682 3.450457 TGCTCTGCCTTTTCCTTCAAAAA 59.550 39.130 0.00 0.00 33.40 1.94
1926 2755 2.878406 AGAACCAATGTTGACAGTTCCG 59.122 45.455 9.68 0.00 38.03 4.30
2042 2871 5.523438 AATCCGGAACTTTTAACAAAGCA 57.477 34.783 9.01 0.00 43.03 3.91
2165 2994 4.165779 GGTTGTCTGGTTATTGCAAATCG 58.834 43.478 1.71 0.00 0.00 3.34
2242 3071 4.273318 ACTTTGGGCAGCTAAAGAATAGG 58.727 43.478 21.74 3.93 37.35 2.57
2244 3073 4.316025 TTGGGCAGCTAAAGAATAGGTT 57.684 40.909 0.00 0.00 0.00 3.50
2295 3124 2.549754 AGCAAACATCACGTTCCTGAAG 59.450 45.455 0.00 0.00 36.59 3.02
2335 3164 4.454504 ACCCAAACGAAGCACATACTAAAG 59.545 41.667 0.00 0.00 0.00 1.85
2403 3232 7.616313 ACTCCAGTTTTGTTTGTATTTTTGGA 58.384 30.769 0.00 0.00 0.00 3.53
2422 3251 4.054369 TGGATTGTAGGGAATTGGGATCT 58.946 43.478 0.00 0.00 0.00 2.75
2426 3255 3.469859 TGTAGGGAATTGGGATCTTCCA 58.530 45.455 12.18 0.64 42.29 3.53
2504 3333 5.833131 GGATGGGATACTCCTTTTGCAAATA 59.167 40.000 13.65 2.09 36.57 1.40
2505 3334 6.015940 GGATGGGATACTCCTTTTGCAAATAG 60.016 42.308 13.65 13.00 36.57 1.73
2506 3335 5.826643 TGGGATACTCCTTTTGCAAATAGT 58.173 37.500 13.65 17.64 36.57 2.12
2507 3336 5.652014 TGGGATACTCCTTTTGCAAATAGTG 59.348 40.000 22.67 16.07 36.57 2.74
2508 3337 5.885912 GGGATACTCCTTTTGCAAATAGTGA 59.114 40.000 22.67 15.68 36.57 3.41
2509 3338 6.547510 GGGATACTCCTTTTGCAAATAGTGAT 59.452 38.462 22.67 15.38 36.57 3.06
2510 3339 7.255277 GGGATACTCCTTTTGCAAATAGTGATC 60.255 40.741 22.67 19.62 36.57 2.92
2511 3340 7.283127 GGATACTCCTTTTGCAAATAGTGATCA 59.717 37.037 22.67 10.47 32.53 2.92
2512 3341 6.899393 ACTCCTTTTGCAAATAGTGATCAA 57.101 33.333 13.65 0.00 0.00 2.57
2513 3342 7.288810 ACTCCTTTTGCAAATAGTGATCAAA 57.711 32.000 13.65 0.00 0.00 2.69
2514 3343 7.899973 ACTCCTTTTGCAAATAGTGATCAAAT 58.100 30.769 13.65 0.00 0.00 2.32
2515 3344 9.023962 ACTCCTTTTGCAAATAGTGATCAAATA 57.976 29.630 13.65 0.00 0.00 1.40
2557 3386 3.685139 AGTCACGACTCATGATGGTTT 57.315 42.857 0.00 0.00 36.92 3.27
2691 3520 5.396101 CCTCTGTCTAAGCTTCATGGATGAA 60.396 44.000 0.00 2.19 43.94 2.57
2748 3582 6.486253 TTCAGTAGTAATTTCTGCTTGCAG 57.514 37.500 15.74 15.74 0.00 4.41
2760 3594 1.142870 TGCTTGCAGTTGACCCTACTT 59.857 47.619 0.00 0.00 0.00 2.24
2841 3675 3.020627 GCATCTGGCAGATCACGC 58.979 61.111 26.62 22.19 43.97 5.34
2955 3789 2.373169 ACTTGGCCTCTCATTGACTCAA 59.627 45.455 3.32 0.00 0.00 3.02
3031 3865 5.697633 TCATAAACGGGACAAGAGTAAACAC 59.302 40.000 0.00 0.00 0.00 3.32
3146 3982 4.460263 TCTGTAAATCAGCAACTGTTGGT 58.540 39.130 18.65 18.65 43.32 3.67
3147 3983 5.616270 TCTGTAAATCAGCAACTGTTGGTA 58.384 37.500 23.06 12.94 43.32 3.25
3149 3985 7.390823 TCTGTAAATCAGCAACTGTTGGTATA 58.609 34.615 23.06 15.24 43.32 1.47
3475 4320 4.535526 AAATATTTCCTGTGCGCCTTTT 57.464 36.364 4.18 0.00 0.00 2.27
3488 4333 3.063180 TGCGCCTTTTCATTTGTTTGTTG 59.937 39.130 4.18 0.00 0.00 3.33
3541 4386 4.023726 TGTTTATTAGTTCCTTGGCCGT 57.976 40.909 0.00 0.00 0.00 5.68
3597 4442 3.326880 TCTGGTAAAAAGGTGAGGAGGAC 59.673 47.826 0.00 0.00 0.00 3.85
3618 4463 6.540189 AGGACGATTTCTCTACCATTTTGATG 59.460 38.462 0.00 0.00 0.00 3.07
3629 4474 9.512435 CTCTACCATTTTGATGCTTATCTTTTG 57.488 33.333 0.00 0.00 0.00 2.44
3669 4516 6.500684 AACAATAAGATGTTGTACCTGCTG 57.499 37.500 0.00 0.00 41.78 4.41
3835 4682 7.112122 TGCCAGTTATGATTGACAACTTATCT 58.888 34.615 0.00 0.00 30.20 1.98
3836 4683 7.066163 TGCCAGTTATGATTGACAACTTATCTG 59.934 37.037 0.00 3.45 30.20 2.90
4021 4871 5.127845 AGGTCACATGTATCACTAGGTCTTG 59.872 44.000 0.00 0.00 0.00 3.02
4022 4872 5.105310 GGTCACATGTATCACTAGGTCTTGT 60.105 44.000 0.00 0.00 0.00 3.16
4041 4891 4.864704 TGTAATTTTTGAGCTTGGGGTC 57.135 40.909 0.00 0.00 40.08 4.46
4053 4903 2.223805 GCTTGGGGTCTTTGTGTTCTTG 60.224 50.000 0.00 0.00 0.00 3.02
4125 4976 4.383770 CCGTTTAACCTGGAGATACACCAT 60.384 45.833 0.00 0.00 36.79 3.55
4128 4979 6.819649 CGTTTAACCTGGAGATACACCATTTA 59.180 38.462 0.00 0.00 36.79 1.40
4175 5029 7.220030 ACTTGATATAAGCTTGTCATACTGGG 58.780 38.462 9.86 1.52 0.00 4.45
4177 5031 6.524734 TGATATAAGCTTGTCATACTGGGTG 58.475 40.000 9.86 0.00 0.00 4.61
4305 5186 7.492352 ACAGAGTTACATGGTGAAAAGTAAC 57.508 36.000 0.00 0.00 43.95 2.50
4335 5216 3.096852 ACTGTACTCCGTTCATGATGGA 58.903 45.455 14.56 14.56 41.25 3.41
4336 5217 3.513912 ACTGTACTCCGTTCATGATGGAA 59.486 43.478 15.74 2.68 42.88 3.53
4337 5218 4.020573 ACTGTACTCCGTTCATGATGGAAA 60.021 41.667 15.74 6.82 42.88 3.13
4338 5219 4.503910 TGTACTCCGTTCATGATGGAAAG 58.496 43.478 15.74 9.39 42.88 2.62
4339 5220 3.981071 ACTCCGTTCATGATGGAAAGA 57.019 42.857 15.74 0.05 42.88 2.52
4340 5221 3.600388 ACTCCGTTCATGATGGAAAGAC 58.400 45.455 15.74 0.79 42.88 3.01
4341 5222 2.604914 CTCCGTTCATGATGGAAAGACG 59.395 50.000 15.74 11.52 42.88 4.18
4342 5223 1.062587 CCGTTCATGATGGAAAGACGC 59.937 52.381 8.48 0.00 36.44 5.19
4343 5224 1.062587 CGTTCATGATGGAAAGACGCC 59.937 52.381 0.00 0.00 0.00 5.68
4344 5225 1.401905 GTTCATGATGGAAAGACGCCC 59.598 52.381 0.00 0.00 0.00 6.13
4345 5226 0.911769 TCATGATGGAAAGACGCCCT 59.088 50.000 0.00 0.00 0.00 5.19
4346 5227 1.281867 TCATGATGGAAAGACGCCCTT 59.718 47.619 0.00 0.00 36.47 3.95
4347 5228 1.672881 CATGATGGAAAGACGCCCTTC 59.327 52.381 0.00 0.00 33.02 3.46
4348 5229 0.391130 TGATGGAAAGACGCCCTTCG 60.391 55.000 0.00 0.00 45.38 3.79
4349 5230 1.706287 GATGGAAAGACGCCCTTCGC 61.706 60.000 0.00 0.00 43.23 4.70
4350 5231 2.047179 GGAAAGACGCCCTTCGCT 60.047 61.111 0.00 0.00 43.23 4.93
4351 5232 1.217244 GGAAAGACGCCCTTCGCTA 59.783 57.895 0.00 0.00 43.23 4.26
4352 5233 0.806492 GGAAAGACGCCCTTCGCTAG 60.806 60.000 0.00 0.00 43.23 3.42
4353 5234 1.422179 GAAAGACGCCCTTCGCTAGC 61.422 60.000 4.06 4.06 43.23 3.42
4354 5235 1.889530 AAAGACGCCCTTCGCTAGCT 61.890 55.000 13.93 0.00 43.23 3.32
4355 5236 1.889530 AAGACGCCCTTCGCTAGCTT 61.890 55.000 13.93 0.00 43.23 3.74
4356 5237 1.035932 AGACGCCCTTCGCTAGCTTA 61.036 55.000 13.93 0.00 43.23 3.09
4357 5238 0.032267 GACGCCCTTCGCTAGCTTAT 59.968 55.000 13.93 0.00 43.23 1.73
4358 5239 0.032267 ACGCCCTTCGCTAGCTTATC 59.968 55.000 13.93 0.00 43.23 1.75
4359 5240 0.032130 CGCCCTTCGCTAGCTTATCA 59.968 55.000 13.93 0.00 34.21 2.15
4360 5241 1.337260 CGCCCTTCGCTAGCTTATCAT 60.337 52.381 13.93 0.00 34.21 2.45
4361 5242 2.094700 CGCCCTTCGCTAGCTTATCATA 60.095 50.000 13.93 0.00 34.21 2.15
4362 5243 3.614150 CGCCCTTCGCTAGCTTATCATAA 60.614 47.826 13.93 0.00 34.21 1.90
4363 5244 3.680458 GCCCTTCGCTAGCTTATCATAAC 59.320 47.826 13.93 0.00 0.00 1.89
4364 5245 4.561734 GCCCTTCGCTAGCTTATCATAACT 60.562 45.833 13.93 0.00 0.00 2.24
4365 5246 5.542779 CCCTTCGCTAGCTTATCATAACTT 58.457 41.667 13.93 0.00 0.00 2.66
4366 5247 5.992217 CCCTTCGCTAGCTTATCATAACTTT 59.008 40.000 13.93 0.00 0.00 2.66
4367 5248 6.146347 CCCTTCGCTAGCTTATCATAACTTTC 59.854 42.308 13.93 0.00 0.00 2.62
4368 5249 6.701841 CCTTCGCTAGCTTATCATAACTTTCA 59.298 38.462 13.93 0.00 0.00 2.69
4369 5250 7.386299 CCTTCGCTAGCTTATCATAACTTTCAT 59.614 37.037 13.93 0.00 0.00 2.57
4370 5251 7.643528 TCGCTAGCTTATCATAACTTTCATG 57.356 36.000 13.93 0.00 0.00 3.07
4371 5252 7.433680 TCGCTAGCTTATCATAACTTTCATGA 58.566 34.615 13.93 0.00 36.86 3.07
4372 5253 8.090831 TCGCTAGCTTATCATAACTTTCATGAT 58.909 33.333 13.93 3.55 43.72 2.45
4373 5254 8.167345 CGCTAGCTTATCATAACTTTCATGATG 58.833 37.037 13.93 0.00 41.92 3.07
4374 5255 8.449397 GCTAGCTTATCATAACTTTCATGATGG 58.551 37.037 7.70 0.00 41.92 3.51
4375 5256 9.716531 CTAGCTTATCATAACTTTCATGATGGA 57.283 33.333 0.00 0.00 41.92 3.41
4376 5257 8.985315 AGCTTATCATAACTTTCATGATGGAA 57.015 30.769 0.00 0.00 41.92 3.53
4377 5258 9.412460 AGCTTATCATAACTTTCATGATGGAAA 57.588 29.630 0.00 0.00 41.92 3.13
4384 5265 1.750193 TTCATGATGGAAAGACGCCC 58.250 50.000 0.00 0.00 0.00 6.13
4385 5266 0.911769 TCATGATGGAAAGACGCCCT 59.088 50.000 0.00 0.00 0.00 5.19
4386 5267 1.281867 TCATGATGGAAAGACGCCCTT 59.718 47.619 0.00 0.00 36.47 3.95
4387 5268 1.672881 CATGATGGAAAGACGCCCTTC 59.327 52.381 0.00 0.00 33.02 3.46
4388 5269 0.391130 TGATGGAAAGACGCCCTTCG 60.391 55.000 0.00 0.00 45.38 3.79
4389 5270 1.706287 GATGGAAAGACGCCCTTCGC 61.706 60.000 0.00 0.00 43.23 4.70
4390 5271 2.047179 GGAAAGACGCCCTTCGCT 60.047 61.111 0.00 0.00 43.23 4.93
4391 5272 1.217244 GGAAAGACGCCCTTCGCTA 59.783 57.895 0.00 0.00 43.23 4.26
4392 5273 0.806492 GGAAAGACGCCCTTCGCTAG 60.806 60.000 0.00 0.00 43.23 3.42
4393 5274 1.422179 GAAAGACGCCCTTCGCTAGC 61.422 60.000 4.06 4.06 43.23 3.42
4394 5275 1.889530 AAAGACGCCCTTCGCTAGCT 61.890 55.000 13.93 0.00 43.23 3.32
4395 5276 1.889530 AAGACGCCCTTCGCTAGCTT 61.890 55.000 13.93 0.00 43.23 3.74
4396 5277 1.035932 AGACGCCCTTCGCTAGCTTA 61.036 55.000 13.93 0.00 43.23 3.09
4397 5278 0.032267 GACGCCCTTCGCTAGCTTAT 59.968 55.000 13.93 0.00 43.23 1.73
4398 5279 0.032267 ACGCCCTTCGCTAGCTTATC 59.968 55.000 13.93 0.00 43.23 1.75
4399 5280 0.032130 CGCCCTTCGCTAGCTTATCA 59.968 55.000 13.93 0.00 34.21 2.15
4400 5281 1.337260 CGCCCTTCGCTAGCTTATCAT 60.337 52.381 13.93 0.00 34.21 2.45
4401 5282 2.094700 CGCCCTTCGCTAGCTTATCATA 60.095 50.000 13.93 0.00 34.21 2.15
4402 5283 3.614150 CGCCCTTCGCTAGCTTATCATAA 60.614 47.826 13.93 0.00 34.21 1.90
4403 5284 3.680458 GCCCTTCGCTAGCTTATCATAAC 59.320 47.826 13.93 0.00 0.00 1.89
4404 5285 4.561734 GCCCTTCGCTAGCTTATCATAACT 60.562 45.833 13.93 0.00 0.00 2.24
4405 5286 5.542779 CCCTTCGCTAGCTTATCATAACTT 58.457 41.667 13.93 0.00 0.00 2.66
4406 5287 6.688578 CCCTTCGCTAGCTTATCATAACTTA 58.311 40.000 13.93 0.00 0.00 2.24
4407 5288 6.586844 CCCTTCGCTAGCTTATCATAACTTAC 59.413 42.308 13.93 0.00 0.00 2.34
4408 5289 6.305877 CCTTCGCTAGCTTATCATAACTTACG 59.694 42.308 13.93 0.00 0.00 3.18
4409 5290 6.549912 TCGCTAGCTTATCATAACTTACGA 57.450 37.500 13.93 0.00 0.00 3.43
4410 5291 7.142306 TCGCTAGCTTATCATAACTTACGAT 57.858 36.000 13.93 0.00 0.00 3.73
4411 5292 7.021790 TCGCTAGCTTATCATAACTTACGATG 58.978 38.462 13.93 0.00 0.00 3.84
4412 5293 7.021790 CGCTAGCTTATCATAACTTACGATGA 58.978 38.462 13.93 0.00 36.54 2.92
4413 5294 7.217258 CGCTAGCTTATCATAACTTACGATGAG 59.783 40.741 13.93 0.00 35.60 2.90
4414 5295 7.008810 GCTAGCTTATCATAACTTACGATGAGC 59.991 40.741 7.70 11.67 44.66 4.26
4433 5353 2.152016 GCAAAGCTTCTAAAGACGGGT 58.848 47.619 0.00 0.00 0.00 5.28
4649 5569 1.127343 AGAGCTTGATCCTAGTGCCC 58.873 55.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.904649 GCCAAAGCTTAAAGGCCCAT 59.095 50.000 20.88 0.00 41.25 4.00
46 47 7.229707 TGGTGAGGAAAATTGTTCGAATTTAGA 59.770 33.333 0.00 0.00 30.38 2.10
49 50 6.155475 TGGTGAGGAAAATTGTTCGAATTT 57.845 33.333 0.00 0.00 0.00 1.82
50 51 5.782893 TGGTGAGGAAAATTGTTCGAATT 57.217 34.783 0.00 0.00 0.00 2.17
51 52 5.782893 TTGGTGAGGAAAATTGTTCGAAT 57.217 34.783 0.00 0.00 0.00 3.34
52 53 5.584253 TTTGGTGAGGAAAATTGTTCGAA 57.416 34.783 0.00 0.00 0.00 3.71
53 54 5.584253 TTTTGGTGAGGAAAATTGTTCGA 57.416 34.783 0.00 0.00 0.00 3.71
54 55 6.648502 CAATTTTGGTGAGGAAAATTGTTCG 58.351 36.000 16.95 0.00 46.40 3.95
59 60 5.532032 CCAAGCAATTTTGGTGAGGAAAATT 59.468 36.000 7.94 0.00 41.52 1.82
60 61 5.065235 CCAAGCAATTTTGGTGAGGAAAAT 58.935 37.500 7.94 0.00 42.16 1.82
61 62 4.450053 CCAAGCAATTTTGGTGAGGAAAA 58.550 39.130 7.94 0.00 42.16 2.29
62 63 3.181456 CCCAAGCAATTTTGGTGAGGAAA 60.181 43.478 12.95 0.00 44.98 3.13
63 64 2.368221 CCCAAGCAATTTTGGTGAGGAA 59.632 45.455 12.95 0.00 44.98 3.36
64 65 1.969923 CCCAAGCAATTTTGGTGAGGA 59.030 47.619 12.95 0.00 44.98 3.71
65 66 1.693606 ACCCAAGCAATTTTGGTGAGG 59.306 47.619 7.89 8.65 44.98 3.86
66 67 2.289010 GGACCCAAGCAATTTTGGTGAG 60.289 50.000 7.89 0.00 44.98 3.51
67 68 1.691434 GGACCCAAGCAATTTTGGTGA 59.309 47.619 7.89 0.00 44.98 4.02
68 69 1.415659 TGGACCCAAGCAATTTTGGTG 59.584 47.619 7.89 3.11 44.98 4.17
69 70 1.416030 GTGGACCCAAGCAATTTTGGT 59.584 47.619 7.89 0.00 44.98 3.67
70 71 1.415659 TGTGGACCCAAGCAATTTTGG 59.584 47.619 2.36 2.36 45.83 3.28
71 72 2.906691 TGTGGACCCAAGCAATTTTG 57.093 45.000 0.00 0.00 0.00 2.44
72 73 2.705127 ACATGTGGACCCAAGCAATTTT 59.295 40.909 0.00 0.00 0.00 1.82
73 74 2.328319 ACATGTGGACCCAAGCAATTT 58.672 42.857 0.00 0.00 0.00 1.82
74 75 2.014010 ACATGTGGACCCAAGCAATT 57.986 45.000 0.00 0.00 0.00 2.32
75 76 2.825532 GTTACATGTGGACCCAAGCAAT 59.174 45.455 9.11 0.00 0.00 3.56
76 77 2.235016 GTTACATGTGGACCCAAGCAA 58.765 47.619 9.11 0.00 0.00 3.91
77 78 1.143889 TGTTACATGTGGACCCAAGCA 59.856 47.619 9.11 0.00 0.00 3.91
78 79 1.539827 GTGTTACATGTGGACCCAAGC 59.460 52.381 9.11 0.00 0.00 4.01
79 80 2.857483 TGTGTTACATGTGGACCCAAG 58.143 47.619 9.11 0.00 0.00 3.61
80 81 3.298686 TTGTGTTACATGTGGACCCAA 57.701 42.857 9.11 8.15 0.00 4.12
81 82 3.298686 TTTGTGTTACATGTGGACCCA 57.701 42.857 9.11 1.93 0.00 4.51
82 83 4.279671 TGAATTTGTGTTACATGTGGACCC 59.720 41.667 9.11 0.00 0.00 4.46
83 84 5.446143 TGAATTTGTGTTACATGTGGACC 57.554 39.130 9.11 2.80 0.00 4.46
84 85 7.945033 AATTGAATTTGTGTTACATGTGGAC 57.055 32.000 9.11 7.89 0.00 4.02
85 86 7.655328 GGAAATTGAATTTGTGTTACATGTGGA 59.345 33.333 9.11 0.00 31.47 4.02
86 87 7.440556 TGGAAATTGAATTTGTGTTACATGTGG 59.559 33.333 9.11 0.00 31.47 4.17
87 88 8.362860 TGGAAATTGAATTTGTGTTACATGTG 57.637 30.769 9.11 0.00 31.47 3.21
88 89 9.558396 AATGGAAATTGAATTTGTGTTACATGT 57.442 25.926 8.03 2.69 31.47 3.21
89 90 9.814507 CAATGGAAATTGAATTTGTGTTACATG 57.185 29.630 8.03 0.00 33.55 3.21
90 91 9.001542 CCAATGGAAATTGAATTTGTGTTACAT 57.998 29.630 8.03 0.00 33.55 2.29
91 92 7.989741 ACCAATGGAAATTGAATTTGTGTTACA 59.010 29.630 6.16 0.00 33.55 2.41
92 93 8.376889 ACCAATGGAAATTGAATTTGTGTTAC 57.623 30.769 6.16 0.00 33.55 2.50
94 95 8.970859 TTACCAATGGAAATTGAATTTGTGTT 57.029 26.923 6.16 0.00 33.55 3.32
95 96 9.218440 GATTACCAATGGAAATTGAATTTGTGT 57.782 29.630 6.16 0.00 33.55 3.72
96 97 8.667463 GGATTACCAATGGAAATTGAATTTGTG 58.333 33.333 6.16 1.37 33.55 3.33
97 98 8.381636 TGGATTACCAATGGAAATTGAATTTGT 58.618 29.630 6.16 1.48 43.91 2.83
98 99 8.789825 TGGATTACCAATGGAAATTGAATTTG 57.210 30.769 6.16 0.00 43.91 2.32
132 133 7.696992 TCGAGCTTAATATTTGGTCCTTTTT 57.303 32.000 11.90 0.00 0.00 1.94
177 180 3.926821 TGGCGGTTTCTATGGTTTTTC 57.073 42.857 0.00 0.00 0.00 2.29
178 181 4.882842 ATTGGCGGTTTCTATGGTTTTT 57.117 36.364 0.00 0.00 0.00 1.94
183 186 4.718940 AGAAAATTGGCGGTTTCTATGG 57.281 40.909 7.78 0.00 41.23 2.74
215 219 2.728922 GTCGTTTCTCGGTATGGCTAG 58.271 52.381 0.00 0.00 40.32 3.42
233 238 5.116528 TGTTATCGTTATCGCATTCATCGTC 59.883 40.000 0.00 0.00 36.96 4.20
236 241 6.738200 CCAATGTTATCGTTATCGCATTCATC 59.262 38.462 0.00 0.00 36.96 2.92
244 249 3.994392 CCCTCCCAATGTTATCGTTATCG 59.006 47.826 0.00 0.00 38.55 2.92
250 255 1.136828 TCCCCCTCCCAATGTTATCG 58.863 55.000 0.00 0.00 0.00 2.92
261 266 3.347590 CCAACCCCTTCCCCCTCC 61.348 72.222 0.00 0.00 0.00 4.30
283 291 1.132453 CAGTGGACGAGATAGACGCAA 59.868 52.381 0.00 0.00 0.00 4.85
292 300 3.680786 CGGGCACAGTGGACGAGA 61.681 66.667 1.84 0.00 0.00 4.04
310 318 4.752879 ACGATGGTGAACGGCGGG 62.753 66.667 13.24 0.00 0.00 6.13
696 704 9.537192 TGAATTCGTACTCTTAAGTCTGAAAAA 57.463 29.630 1.63 0.00 36.92 1.94
753 763 1.040339 TTGGGCTGAAACAAGGCGTT 61.040 50.000 0.00 0.00 43.45 4.84
890 1570 0.800631 CGCGGAAAAGGAAAGGGTAC 59.199 55.000 0.00 0.00 0.00 3.34
898 1578 0.611062 TCCTCTCTCGCGGAAAAGGA 60.611 55.000 6.13 13.86 0.00 3.36
925 1605 0.511221 ACGAAAAATCTCACGCACGG 59.489 50.000 0.00 0.00 0.00 4.94
1030 1710 4.736896 GGTGGAGTCCGTGCCGTC 62.737 72.222 4.30 0.00 0.00 4.79
1272 1958 2.029623 CTAACCCTAGCTAGCAACGGA 58.970 52.381 18.83 0.00 0.00 4.69
1330 2016 1.186200 CGACCCTCCAGAGTCAATCA 58.814 55.000 0.00 0.00 33.08 2.57
1332 2018 0.978146 CCCGACCCTCCAGAGTCAAT 60.978 60.000 0.00 0.00 33.08 2.57
1339 2025 1.454847 CTCTCTCCCGACCCTCCAG 60.455 68.421 0.00 0.00 0.00 3.86
1379 2065 2.673833 ACTGGAAATCGAGACAACGAC 58.326 47.619 0.00 0.00 44.84 4.34
1383 2069 3.762407 TCCAACTGGAAATCGAGACAA 57.238 42.857 0.00 0.00 42.18 3.18
1415 2101 3.104843 AGAAGGAAGCTGCGTATCATC 57.895 47.619 0.00 0.00 0.00 2.92
1495 2204 5.977635 TGAAGTGCAGCATATACTACTGTT 58.022 37.500 0.00 0.00 33.87 3.16
1541 2336 0.108186 TCTTTGATCAGCACCGCGAT 60.108 50.000 8.23 0.00 0.00 4.58
1546 2341 4.397103 TGATTCATGTCTTTGATCAGCACC 59.603 41.667 0.00 0.00 0.00 5.01
1588 2383 3.485216 GGTCTAAATCGCAACCATTGTCG 60.485 47.826 0.00 0.00 0.00 4.35
1749 2544 6.041069 TCGTAAAAGACATTTCACCCCAAAAT 59.959 34.615 0.00 0.00 32.27 1.82
1772 2569 2.266055 GCCCTCACCTCCACTTCG 59.734 66.667 0.00 0.00 0.00 3.79
1802 2599 7.547019 TCATCATAGAATAGAACATCGATTGCC 59.453 37.037 0.00 0.00 0.00 4.52
1832 2629 7.188468 GCCTTATGCATTTCAAAACAGAAAA 57.812 32.000 3.54 0.00 40.54 2.29
1833 2630 6.783892 GCCTTATGCATTTCAAAACAGAAA 57.216 33.333 3.54 0.00 41.31 2.52
1856 2653 2.030451 GGAAAAGGCAGAGCAGTTTCTG 60.030 50.000 12.98 0.00 45.85 3.02
1857 2654 2.158549 AGGAAAAGGCAGAGCAGTTTCT 60.159 45.455 12.98 0.00 35.04 2.52
1858 2655 2.234143 AGGAAAAGGCAGAGCAGTTTC 58.766 47.619 7.63 7.63 34.40 2.78
1859 2656 2.371658 AGGAAAAGGCAGAGCAGTTT 57.628 45.000 0.00 0.00 0.00 2.66
1860 2657 2.234143 GAAGGAAAAGGCAGAGCAGTT 58.766 47.619 0.00 0.00 0.00 3.16
1861 2658 1.143684 TGAAGGAAAAGGCAGAGCAGT 59.856 47.619 0.00 0.00 0.00 4.40
1862 2659 1.901591 TGAAGGAAAAGGCAGAGCAG 58.098 50.000 0.00 0.00 0.00 4.24
1863 2660 2.363306 TTGAAGGAAAAGGCAGAGCA 57.637 45.000 0.00 0.00 0.00 4.26
1864 2661 3.733443 TTTTGAAGGAAAAGGCAGAGC 57.267 42.857 0.00 0.00 0.00 4.09
1926 2755 2.163010 CCCATCAATAGCAATCCGATGC 59.837 50.000 0.00 0.29 46.78 3.91
2042 2871 8.682936 ATTAACTGATGAAAGAACAGAACACT 57.317 30.769 0.00 0.00 35.85 3.55
2076 2905 9.121658 TCGTATCTAAGAAGCTCTTATCTTGAA 57.878 33.333 8.37 0.00 38.20 2.69
2099 2928 0.684479 TATCAGCACCCTCAGCTCGT 60.684 55.000 0.00 0.00 41.14 4.18
2182 3011 6.376978 AGCTCAAATCACAGAGAAAAATTCG 58.623 36.000 0.00 0.00 33.74 3.34
2195 3024 9.443283 GTTTGACATCATAATAGCTCAAATCAC 57.557 33.333 0.00 0.00 32.03 3.06
2242 3071 9.722184 AAACATTCTCTAGAACCTAAGGTTAAC 57.278 33.333 0.00 0.00 46.95 2.01
2276 3105 4.811555 TTCTTCAGGAACGTGATGTTTG 57.188 40.909 0.00 0.00 42.09 2.93
2285 3114 5.288472 CCAAAACAACTTTTCTTCAGGAACG 59.712 40.000 0.00 0.00 33.13 3.95
2295 3124 4.209307 TGGGTTCCCAAAACAACTTTTC 57.791 40.909 8.26 0.00 32.48 2.29
2323 3152 8.383619 CAGATACAAACTCACTTTAGTATGTGC 58.616 37.037 0.00 0.00 34.49 4.57
2335 3164 4.455877 CCCCTTGAACAGATACAAACTCAC 59.544 45.833 0.00 0.00 0.00 3.51
2403 3232 4.482025 TGGAAGATCCCAATTCCCTACAAT 59.518 41.667 8.55 0.00 43.68 2.71
2516 3345 9.677567 GTGACTAAAAAGATCACAGCAATTAAA 57.322 29.630 0.00 0.00 41.94 1.52
2517 3346 8.015087 CGTGACTAAAAAGATCACAGCAATTAA 58.985 33.333 0.00 0.00 42.37 1.40
2518 3347 7.386573 TCGTGACTAAAAAGATCACAGCAATTA 59.613 33.333 0.00 0.00 42.37 1.40
2519 3348 6.204688 TCGTGACTAAAAAGATCACAGCAATT 59.795 34.615 0.00 0.00 42.37 2.32
2520 3349 5.700832 TCGTGACTAAAAAGATCACAGCAAT 59.299 36.000 0.00 0.00 42.37 3.56
2521 3350 5.050363 GTCGTGACTAAAAAGATCACAGCAA 60.050 40.000 0.00 0.00 42.37 3.91
2557 3386 7.178628 CCTGGCCTTTATCTAGCTAATACACTA 59.821 40.741 3.32 0.00 0.00 2.74
2648 3477 6.774656 ACAGAGGATTAATGGCTGGAAATTAG 59.225 38.462 0.00 0.00 0.00 1.73
2732 3563 4.229876 GGTCAACTGCAAGCAGAAATTAC 58.770 43.478 27.17 15.93 46.30 1.89
2736 3567 1.032014 GGGTCAACTGCAAGCAGAAA 58.968 50.000 27.17 9.86 46.30 2.52
2748 3582 4.947388 TCAATATGCCAAAGTAGGGTCAAC 59.053 41.667 0.00 0.00 0.00 3.18
2760 3594 6.182627 AGAATCAGACACTTCAATATGCCAA 58.817 36.000 0.00 0.00 0.00 4.52
2841 3675 6.279123 TGATCTACTGCTCTTCTTATGCTTG 58.721 40.000 0.00 0.00 0.00 4.01
2924 3758 3.258372 TGAGAGGCCAAGTACTAAGTGTG 59.742 47.826 5.01 0.00 0.00 3.82
2929 3763 4.777896 AGTCAATGAGAGGCCAAGTACTAA 59.222 41.667 5.01 0.00 0.00 2.24
2955 3789 3.972638 AGACTGCCAGAATGAGGATACAT 59.027 43.478 0.00 0.00 39.69 2.29
3401 4245 3.385577 ACGTTCACTCTCTTTCTTCTGC 58.614 45.455 0.00 0.00 0.00 4.26
3521 4366 4.004982 TCACGGCCAAGGAACTAATAAAC 58.995 43.478 2.24 0.00 38.49 2.01
3538 4383 0.737715 CGCTTTCCTCCTTCTCACGG 60.738 60.000 0.00 0.00 0.00 4.94
3541 4386 1.296715 GCCGCTTTCCTCCTTCTCA 59.703 57.895 0.00 0.00 0.00 3.27
3597 4442 6.369059 AGCATCAAAATGGTAGAGAAATCG 57.631 37.500 0.00 0.00 41.71 3.34
3618 4463 7.335924 TGTGAGTATACAACCCAAAAGATAAGC 59.664 37.037 5.50 0.00 0.00 3.09
3650 4495 5.435686 TTCCAGCAGGTACAACATCTTAT 57.564 39.130 0.00 0.00 35.89 1.73
3653 4498 3.264193 TCATTCCAGCAGGTACAACATCT 59.736 43.478 0.00 0.00 35.89 2.90
3835 4682 0.111061 AGCCAAGCATCACCACTTCA 59.889 50.000 0.00 0.00 0.00 3.02
3836 4683 0.524862 CAGCCAAGCATCACCACTTC 59.475 55.000 0.00 0.00 0.00 3.01
4021 4871 5.468540 AAGACCCCAAGCTCAAAAATTAC 57.531 39.130 0.00 0.00 0.00 1.89
4022 4872 5.365314 ACAAAGACCCCAAGCTCAAAAATTA 59.635 36.000 0.00 0.00 0.00 1.40
4041 4891 7.684062 ACGATCAAATTTCAAGAACACAAAG 57.316 32.000 0.00 0.00 0.00 2.77
4053 4903 8.287503 AGTACAAACTGGTAACGATCAAATTTC 58.712 33.333 0.00 0.00 42.51 2.17
4157 5010 3.523564 ACCACCCAGTATGACAAGCTTAT 59.476 43.478 0.00 0.00 39.69 1.73
4175 5029 7.875971 ACAAAGAAACAAGATGAGAATACCAC 58.124 34.615 0.00 0.00 0.00 4.16
4177 5031 8.567948 TCAACAAAGAAACAAGATGAGAATACC 58.432 33.333 0.00 0.00 0.00 2.73
4305 5186 2.942710 ACGGAGTACAGTTCATGAACG 58.057 47.619 28.18 24.23 42.85 3.95
4341 5222 2.464157 ATGATAAGCTAGCGAAGGGC 57.536 50.000 9.55 0.00 44.05 5.19
4342 5223 5.140747 AGTTATGATAAGCTAGCGAAGGG 57.859 43.478 9.55 0.00 0.00 3.95
4343 5224 6.701841 TGAAAGTTATGATAAGCTAGCGAAGG 59.298 38.462 9.55 0.00 0.00 3.46
4344 5225 7.700322 TGAAAGTTATGATAAGCTAGCGAAG 57.300 36.000 9.55 0.00 0.00 3.79
4345 5226 7.926018 TCATGAAAGTTATGATAAGCTAGCGAA 59.074 33.333 9.55 1.26 30.03 4.70
4346 5227 7.433680 TCATGAAAGTTATGATAAGCTAGCGA 58.566 34.615 9.55 1.39 30.03 4.93
4347 5228 7.643528 TCATGAAAGTTATGATAAGCTAGCG 57.356 36.000 9.55 0.00 30.03 4.26
4348 5229 8.449397 CCATCATGAAAGTTATGATAAGCTAGC 58.551 37.037 6.62 6.62 41.91 3.42
4349 5230 9.716531 TCCATCATGAAAGTTATGATAAGCTAG 57.283 33.333 0.00 0.00 41.91 3.42
4351 5232 8.985315 TTCCATCATGAAAGTTATGATAAGCT 57.015 30.769 0.00 0.00 41.91 3.74
4352 5233 9.674824 CTTTCCATCATGAAAGTTATGATAAGC 57.325 33.333 0.00 0.00 43.95 3.09
4364 5245 2.091541 GGGCGTCTTTCCATCATGAAA 58.908 47.619 0.00 0.00 33.42 2.69
4365 5246 1.281867 AGGGCGTCTTTCCATCATGAA 59.718 47.619 0.00 0.00 0.00 2.57
4366 5247 0.911769 AGGGCGTCTTTCCATCATGA 59.088 50.000 0.00 0.00 0.00 3.07
4367 5248 1.672881 GAAGGGCGTCTTTCCATCATG 59.327 52.381 0.00 0.00 35.50 3.07
4368 5249 1.743772 CGAAGGGCGTCTTTCCATCAT 60.744 52.381 6.27 0.00 35.50 2.45
4369 5250 0.391130 CGAAGGGCGTCTTTCCATCA 60.391 55.000 6.27 0.00 35.50 3.07
4370 5251 1.706287 GCGAAGGGCGTCTTTCCATC 61.706 60.000 6.27 0.00 43.41 3.51
4371 5252 1.745489 GCGAAGGGCGTCTTTCCAT 60.745 57.895 6.27 0.00 43.41 3.41
4372 5253 2.358247 GCGAAGGGCGTCTTTCCA 60.358 61.111 6.27 0.00 43.41 3.53
4381 5262 2.464157 ATGATAAGCTAGCGAAGGGC 57.536 50.000 9.55 0.00 44.05 5.19
4382 5263 5.140747 AGTTATGATAAGCTAGCGAAGGG 57.859 43.478 9.55 0.00 0.00 3.95
4383 5264 6.305877 CGTAAGTTATGATAAGCTAGCGAAGG 59.694 42.308 9.55 0.00 0.00 3.46
4384 5265 7.076362 TCGTAAGTTATGATAAGCTAGCGAAG 58.924 38.462 9.55 0.00 39.48 3.79
4385 5266 6.962686 TCGTAAGTTATGATAAGCTAGCGAA 58.037 36.000 9.55 1.26 39.48 4.70
4386 5267 6.549912 TCGTAAGTTATGATAAGCTAGCGA 57.450 37.500 9.55 1.39 39.48 4.93
4387 5268 7.021790 TCATCGTAAGTTATGATAAGCTAGCG 58.978 38.462 15.66 3.64 33.28 4.26
4388 5269 7.008810 GCTCATCGTAAGTTATGATAAGCTAGC 59.991 40.741 24.46 18.52 40.68 3.42
4389 5270 8.023706 TGCTCATCGTAAGTTATGATAAGCTAG 58.976 37.037 28.67 17.00 43.10 3.42
4390 5271 7.882179 TGCTCATCGTAAGTTATGATAAGCTA 58.118 34.615 28.67 18.15 43.10 3.32
4391 5272 6.749139 TGCTCATCGTAAGTTATGATAAGCT 58.251 36.000 28.67 5.78 43.10 3.74
4392 5273 7.408132 TTGCTCATCGTAAGTTATGATAAGC 57.592 36.000 24.79 24.79 43.02 3.09
4393 5274 8.006590 GCTTTGCTCATCGTAAGTTATGATAAG 58.993 37.037 15.66 12.75 33.28 1.73
4394 5275 7.710907 AGCTTTGCTCATCGTAAGTTATGATAA 59.289 33.333 15.66 2.87 30.62 1.75
4395 5276 7.210174 AGCTTTGCTCATCGTAAGTTATGATA 58.790 34.615 15.66 0.16 30.62 2.15
4396 5277 6.051717 AGCTTTGCTCATCGTAAGTTATGAT 58.948 36.000 11.19 11.19 30.62 2.45
4397 5278 5.419542 AGCTTTGCTCATCGTAAGTTATGA 58.580 37.500 7.26 7.26 30.62 2.15
4398 5279 5.725110 AGCTTTGCTCATCGTAAGTTATG 57.275 39.130 0.00 0.00 30.62 1.90
4399 5280 6.109359 AGAAGCTTTGCTCATCGTAAGTTAT 58.891 36.000 0.00 0.00 38.25 1.89
4400 5281 5.479306 AGAAGCTTTGCTCATCGTAAGTTA 58.521 37.500 0.00 0.00 38.25 2.24
4401 5282 4.319177 AGAAGCTTTGCTCATCGTAAGTT 58.681 39.130 0.00 0.00 38.25 2.66
4402 5283 3.931578 AGAAGCTTTGCTCATCGTAAGT 58.068 40.909 0.00 0.00 38.25 2.24
4403 5284 6.311445 TCTTTAGAAGCTTTGCTCATCGTAAG 59.689 38.462 0.00 0.00 38.25 2.34
4404 5285 6.090898 GTCTTTAGAAGCTTTGCTCATCGTAA 59.909 38.462 0.00 0.00 38.25 3.18
4405 5286 5.577164 GTCTTTAGAAGCTTTGCTCATCGTA 59.423 40.000 0.00 0.00 38.25 3.43
4406 5287 4.390297 GTCTTTAGAAGCTTTGCTCATCGT 59.610 41.667 0.00 0.00 38.25 3.73
4407 5288 4.491602 CGTCTTTAGAAGCTTTGCTCATCG 60.492 45.833 0.00 0.00 38.25 3.84
4408 5289 4.201763 CCGTCTTTAGAAGCTTTGCTCATC 60.202 45.833 0.00 0.00 38.25 2.92
4409 5290 3.686726 CCGTCTTTAGAAGCTTTGCTCAT 59.313 43.478 0.00 0.00 38.25 2.90
4410 5291 3.067106 CCGTCTTTAGAAGCTTTGCTCA 58.933 45.455 0.00 0.00 38.25 4.26
4411 5292 2.416893 CCCGTCTTTAGAAGCTTTGCTC 59.583 50.000 0.00 0.00 38.25 4.26
4412 5293 2.224548 ACCCGTCTTTAGAAGCTTTGCT 60.225 45.455 0.00 0.00 42.56 3.91
4413 5294 2.152016 ACCCGTCTTTAGAAGCTTTGC 58.848 47.619 0.00 0.00 0.00 3.68
4414 5295 5.699458 TCTTAACCCGTCTTTAGAAGCTTTG 59.301 40.000 0.00 0.00 0.00 2.77
4433 5353 8.938883 AGGCTCAGAGGTTTATATTCATCTTAA 58.061 33.333 0.00 0.00 0.00 1.85
4649 5569 4.821589 GGCGAGGGAGCGGTCAAG 62.822 72.222 17.59 5.30 38.18 3.02
4694 5614 0.476023 TGGCCAAGGGTAACAGGGTA 60.476 55.000 0.61 0.00 39.74 3.69


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

AutoCloner maintained by Alex Coulton.