Multiple sequence alignment - TraesCS7A01G221100

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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 TraesCS7A01G221100 chr7A 100.000 2414 0 0 1 2414 189349398 189351811 0.000000e+00 4458
1 TraesCS7A01G221100 chr7A 85.229 1442 208 5 1 1439 29988585 29987146 0.000000e+00 1478
2 TraesCS7A01G221100 chrUn 95.003 1441 69 2 1 1440 298402190 298403628 0.000000e+00 2259
3 TraesCS7A01G221100 chrUn 94.705 1322 67 2 120 1440 375723698 375722379 0.000000e+00 2050
4 TraesCS7A01G221100 chrUn 96.284 592 17 4 1439 2029 357191299 357191886 0.000000e+00 966
5 TraesCS7A01G221100 chrUn 95.960 99 4 0 2313 2411 333804142 333804240 6.910000e-36 161
6 TraesCS7A01G221100 chrUn 95.960 99 4 0 2313 2411 357191883 357191981 6.910000e-36 161
7 TraesCS7A01G221100 chrUn 95.960 99 4 0 2313 2411 396176291 396176389 6.910000e-36 161
8 TraesCS7A01G221100 chr4D 89.945 1442 142 3 1 1440 482768090 482769530 0.000000e+00 1857
9 TraesCS7A01G221100 chr7D 89.861 1440 139 6 1 1437 139749871 139748436 0.000000e+00 1844
10 TraesCS7A01G221100 chr3B 88.981 1443 153 6 1 1440 808034998 808036437 0.000000e+00 1779
11 TraesCS7A01G221100 chr3B 96.965 593 12 5 1439 2029 147870356 147869768 0.000000e+00 990
12 TraesCS7A01G221100 chr3B 96.115 592 18 4 1439 2029 808366814 808367401 0.000000e+00 961
13 TraesCS7A01G221100 chr3B 96.115 592 18 4 1439 2029 808439443 808440030 0.000000e+00 961
14 TraesCS7A01G221100 chr3B 95.960 99 4 0 2313 2411 808367398 808367496 6.910000e-36 161
15 TraesCS7A01G221100 chr3D 88.897 1441 143 8 1 1440 378777679 378776255 0.000000e+00 1759
16 TraesCS7A01G221100 chr3D 94.218 294 15 2 2028 2320 240482815 240482523 4.730000e-122 448
17 TraesCS7A01G221100 chr1B 87.032 1442 182 5 1 1439 41706631 41705192 0.000000e+00 1622
18 TraesCS7A01G221100 chr1B 96.791 592 13 4 1439 2029 413908297 413908883 0.000000e+00 983
19 TraesCS7A01G221100 chr1B 94.237 295 15 2 2024 2317 483743234 483742941 1.320000e-122 449
20 TraesCS7A01G221100 chr1B 95.960 99 4 0 2313 2411 413908880 413908978 6.910000e-36 161
21 TraesCS7A01G221100 chr6B 85.645 1442 198 4 1 1440 12073268 12071834 0.000000e+00 1507
22 TraesCS7A01G221100 chr6B 97.466 592 11 3 1439 2029 337732283 337732871 0.000000e+00 1007
23 TraesCS7A01G221100 chr6B 93.919 296 16 2 2024 2317 606013329 606013034 1.700000e-121 446
24 TraesCS7A01G221100 chr5A 97.475 594 10 3 1439 2029 590978139 590978730 0.000000e+00 1009
25 TraesCS7A01G221100 chr5A 96.970 99 3 0 2313 2411 590978727 590978825 1.480000e-37 167
26 TraesCS7A01G221100 chr2D 97.466 592 9 3 1439 2029 370056234 370056820 0.000000e+00 1005
27 TraesCS7A01G221100 chr2D 97.466 592 10 3 1439 2029 623755934 623756521 0.000000e+00 1005
28 TraesCS7A01G221100 chr2D 95.960 99 4 0 2313 2411 370056817 370056915 6.910000e-36 161
29 TraesCS7A01G221100 chr2B 94.881 293 14 1 2024 2315 769943035 769942743 7.870000e-125 457
30 TraesCS7A01G221100 chr5B 94.257 296 16 1 2026 2320 586857659 586857364 3.660000e-123 451
31 TraesCS7A01G221100 chr5B 95.960 99 4 0 2313 2411 166692780 166692878 6.910000e-36 161
32 TraesCS7A01G221100 chr4B 94.276 297 14 3 2028 2321 328582320 328582024 3.660000e-123 451
33 TraesCS7A01G221100 chr4B 94.521 292 15 1 2026 2316 343212573 343212282 1.320000e-122 449
34 TraesCS7A01G221100 chr1D 95.122 287 13 1 2028 2313 469385360 469385074 3.660000e-123 451
35 TraesCS7A01G221100 chr1D 94.237 295 16 1 2026 2319 142341430 142341724 1.320000e-122 449
36 TraesCS7A01G221100 chr5D 96.970 99 3 0 2313 2411 163814124 163814026 1.480000e-37 167


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 TraesCS7A01G221100 chr7A 189349398 189351811 2413 False 4458.0 4458 100.0000 1 2414 1 chr7A.!!$F1 2413
1 TraesCS7A01G221100 chr7A 29987146 29988585 1439 True 1478.0 1478 85.2290 1 1439 1 chr7A.!!$R1 1438
2 TraesCS7A01G221100 chrUn 298402190 298403628 1438 False 2259.0 2259 95.0030 1 1440 1 chrUn.!!$F1 1439
3 TraesCS7A01G221100 chrUn 375722379 375723698 1319 True 2050.0 2050 94.7050 120 1440 1 chrUn.!!$R1 1320
4 TraesCS7A01G221100 chrUn 357191299 357191981 682 False 563.5 966 96.1220 1439 2411 2 chrUn.!!$F4 972
5 TraesCS7A01G221100 chr4D 482768090 482769530 1440 False 1857.0 1857 89.9450 1 1440 1 chr4D.!!$F1 1439
6 TraesCS7A01G221100 chr7D 139748436 139749871 1435 True 1844.0 1844 89.8610 1 1437 1 chr7D.!!$R1 1436
7 TraesCS7A01G221100 chr3B 808034998 808036437 1439 False 1779.0 1779 88.9810 1 1440 1 chr3B.!!$F1 1439
8 TraesCS7A01G221100 chr3B 147869768 147870356 588 True 990.0 990 96.9650 1439 2029 1 chr3B.!!$R1 590
9 TraesCS7A01G221100 chr3B 808439443 808440030 587 False 961.0 961 96.1150 1439 2029 1 chr3B.!!$F2 590
10 TraesCS7A01G221100 chr3B 808366814 808367496 682 False 561.0 961 96.0375 1439 2411 2 chr3B.!!$F3 972
11 TraesCS7A01G221100 chr3D 378776255 378777679 1424 True 1759.0 1759 88.8970 1 1440 1 chr3D.!!$R2 1439
12 TraesCS7A01G221100 chr1B 41705192 41706631 1439 True 1622.0 1622 87.0320 1 1439 1 chr1B.!!$R1 1438
13 TraesCS7A01G221100 chr1B 413908297 413908978 681 False 572.0 983 96.3755 1439 2411 2 chr1B.!!$F1 972
14 TraesCS7A01G221100 chr6B 12071834 12073268 1434 True 1507.0 1507 85.6450 1 1440 1 chr6B.!!$R1 1439
15 TraesCS7A01G221100 chr6B 337732283 337732871 588 False 1007.0 1007 97.4660 1439 2029 1 chr6B.!!$F1 590
16 TraesCS7A01G221100 chr5A 590978139 590978825 686 False 588.0 1009 97.2225 1439 2411 2 chr5A.!!$F1 972
17 TraesCS7A01G221100 chr2D 623755934 623756521 587 False 1005.0 1005 97.4660 1439 2029 1 chr2D.!!$F1 590
18 TraesCS7A01G221100 chr2D 370056234 370056915 681 False 583.0 1005 96.7130 1439 2411 2 chr2D.!!$F2 972

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
890 893 1.491668 TTGGCGGTTCCTATAGCTCA 58.508 50.0 0.0 0.0 35.26 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2152 0.034059 AACACGTGCTTGAGCTAGCT 59.966 50.0 19.45 19.45 41.76 3.32 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
129 131 2.121506 ACCCCCAAAGGCTCCTGA 60.122 61.111 0.00 0.00 0.00 3.86
186 188 4.087892 GCTTGGAGGGCAGAGCGA 62.088 66.667 0.00 0.00 0.00 4.93
224 226 3.181451 TGGGAGATGGATGTTCAGCATAC 60.181 47.826 0.00 0.00 38.06 2.39
236 238 7.148188 GGATGTTCAGCATACTCTCAAAATTCA 60.148 37.037 0.00 0.00 38.06 2.57
249 251 7.042797 TCTCAAAATTCAAACTTCTCCAAGG 57.957 36.000 0.00 0.00 33.37 3.61
315 317 7.173390 GGTGTTTTCTCAGTTAGAAGTGCTTAT 59.827 37.037 0.00 0.00 44.95 1.73
359 361 1.812571 CACGACATTTTCTGAAGGGGG 59.187 52.381 0.00 0.00 0.00 5.40
374 376 2.280592 GGGAACAAGTGCGTCGGT 60.281 61.111 0.00 0.00 0.00 4.69
382 384 2.421877 AAGTGCGTCGGTGAGTGGAG 62.422 60.000 0.00 0.00 0.00 3.86
397 399 2.111251 GAGCCCGTTCCCTATGGC 59.889 66.667 0.00 0.00 44.35 4.40
426 428 2.112198 GCAATCATCGGTCCCGCAA 61.112 57.895 0.00 0.00 39.59 4.85
442 444 4.081142 TCCCGCAAAAGATGAAGATCACTA 60.081 41.667 0.00 0.00 0.00 2.74
444 446 4.872691 CCGCAAAAGATGAAGATCACTACT 59.127 41.667 0.00 0.00 0.00 2.57
461 463 5.047164 TCACTACTTGGCAAGTTATAACGGA 60.047 40.000 35.13 19.95 42.81 4.69
483 485 2.356069 GGCTTTACCTATGCAGAAGTGC 59.644 50.000 0.00 0.00 42.56 4.40
495 497 1.531149 CAGAAGTGCAAGGTGTTACGG 59.469 52.381 0.00 0.00 0.00 4.02
544 546 2.104792 CTGTGTGGACTTGAGGAGGAAA 59.895 50.000 0.00 0.00 0.00 3.13
669 671 2.135189 AGGGAATGGCTTATGCACCTA 58.865 47.619 2.72 0.00 41.91 3.08
798 800 2.097825 GCTACGGTGGACTTCCTAGAA 58.902 52.381 0.00 0.00 36.82 2.10
829 831 2.097825 GATCCATCAAGCTTGCTGGTT 58.902 47.619 36.06 30.99 43.21 3.67
843 846 1.737793 GCTGGTTGTTATTCGGTGGAG 59.262 52.381 0.00 0.00 0.00 3.86
890 893 1.491668 TTGGCGGTTCCTATAGCTCA 58.508 50.000 0.00 0.00 35.26 4.26
893 896 1.618837 GGCGGTTCCTATAGCTCATCA 59.381 52.381 0.00 0.00 0.00 3.07
972 975 2.993937 ACTGTTGACGGTTCTTTCCAA 58.006 42.857 0.00 0.00 29.59 3.53
984 987 5.561679 GGTTCTTTCCAAGGAACAGATAGT 58.438 41.667 14.24 0.00 42.29 2.12
1037 1040 5.191426 CCATCAAGGACAGATCATCTTTGT 58.809 41.667 16.44 3.58 41.22 2.83
1072 1075 0.942410 GTTCCACTGCAACGACGCTA 60.942 55.000 0.00 0.00 0.00 4.26
1205 1208 1.600663 CGATGCTTTATCTCGCTCCGT 60.601 52.381 0.00 0.00 33.44 4.69
1301 1304 3.954258 TCTCAGAATAGAGTTGCCGATCA 59.046 43.478 0.00 0.00 36.97 2.92
1319 1322 5.056480 CGATCATTTGGCCAAGTATAGTCA 58.944 41.667 19.48 0.77 0.00 3.41
1489 1494 2.280708 GCAAAATTCTGCATGATGTCGC 59.719 45.455 0.00 0.00 42.17 5.19
1530 1535 4.059773 ACCTCCCAAAAATGGCAATCTA 57.940 40.909 0.00 0.00 0.00 1.98
1958 1969 0.324645 GGCCACCCAATCACAATCCT 60.325 55.000 0.00 0.00 0.00 3.24
2029 2041 6.025539 ACCCATATGTGAGGAGCATATAAGA 58.974 40.000 1.24 0.00 37.41 2.10
2030 2042 6.155910 ACCCATATGTGAGGAGCATATAAGAG 59.844 42.308 1.24 0.00 37.41 2.85
2031 2043 6.047870 CCATATGTGAGGAGCATATAAGAGC 58.952 44.000 1.24 0.00 37.41 4.09
2032 2044 6.351626 CCATATGTGAGGAGCATATAAGAGCA 60.352 42.308 1.24 0.00 37.41 4.26
2033 2045 5.557576 ATGTGAGGAGCATATAAGAGCAA 57.442 39.130 0.00 0.00 0.00 3.91
2034 2046 4.953667 TGTGAGGAGCATATAAGAGCAAG 58.046 43.478 0.00 0.00 0.00 4.01
2035 2047 4.406972 TGTGAGGAGCATATAAGAGCAAGT 59.593 41.667 0.00 0.00 0.00 3.16
2036 2048 5.598417 TGTGAGGAGCATATAAGAGCAAGTA 59.402 40.000 0.00 0.00 0.00 2.24
2037 2049 5.923684 GTGAGGAGCATATAAGAGCAAGTAC 59.076 44.000 0.00 0.00 0.00 2.73
2038 2050 5.598417 TGAGGAGCATATAAGAGCAAGTACA 59.402 40.000 0.00 0.00 0.00 2.90
2039 2051 6.098266 TGAGGAGCATATAAGAGCAAGTACAA 59.902 38.462 0.00 0.00 0.00 2.41
2040 2052 7.072263 AGGAGCATATAAGAGCAAGTACAAT 57.928 36.000 0.00 0.00 0.00 2.71
2041 2053 8.195165 AGGAGCATATAAGAGCAAGTACAATA 57.805 34.615 0.00 0.00 0.00 1.90
2042 2054 8.310382 AGGAGCATATAAGAGCAAGTACAATAG 58.690 37.037 0.00 0.00 0.00 1.73
2043 2055 8.307483 GGAGCATATAAGAGCAAGTACAATAGA 58.693 37.037 0.00 0.00 0.00 1.98
2044 2056 9.352784 GAGCATATAAGAGCAAGTACAATAGAG 57.647 37.037 0.00 0.00 0.00 2.43
2045 2057 7.816995 AGCATATAAGAGCAAGTACAATAGAGC 59.183 37.037 0.00 0.00 0.00 4.09
2046 2058 7.816995 GCATATAAGAGCAAGTACAATAGAGCT 59.183 37.037 0.00 0.00 34.61 4.09
2047 2059 9.138062 CATATAAGAGCAAGTACAATAGAGCTG 57.862 37.037 0.00 0.00 31.61 4.24
2048 2060 5.667539 AAGAGCAAGTACAATAGAGCTGA 57.332 39.130 0.00 0.00 31.61 4.26
2049 2061 5.261209 AGAGCAAGTACAATAGAGCTGAG 57.739 43.478 0.00 0.00 31.61 3.35
2050 2062 4.709397 AGAGCAAGTACAATAGAGCTGAGT 59.291 41.667 0.00 0.00 31.61 3.41
2051 2063 5.004922 AGCAAGTACAATAGAGCTGAGTC 57.995 43.478 0.00 0.00 0.00 3.36
2052 2064 4.464244 AGCAAGTACAATAGAGCTGAGTCA 59.536 41.667 0.00 0.00 0.00 3.41
2053 2065 4.803088 GCAAGTACAATAGAGCTGAGTCAG 59.197 45.833 16.21 16.21 34.12 3.51
2065 2077 3.383620 CTGAGTCAGCAGGCTATAAGG 57.616 52.381 7.33 0.00 32.26 2.69
2066 2078 2.961741 CTGAGTCAGCAGGCTATAAGGA 59.038 50.000 7.33 0.00 32.26 3.36
2067 2079 3.374764 TGAGTCAGCAGGCTATAAGGAA 58.625 45.455 0.00 0.00 0.00 3.36
2068 2080 3.969976 TGAGTCAGCAGGCTATAAGGAAT 59.030 43.478 0.00 0.00 0.00 3.01
2069 2081 5.147767 TGAGTCAGCAGGCTATAAGGAATA 58.852 41.667 0.00 0.00 0.00 1.75
2070 2082 5.602561 TGAGTCAGCAGGCTATAAGGAATAA 59.397 40.000 0.00 0.00 0.00 1.40
2071 2083 6.099701 TGAGTCAGCAGGCTATAAGGAATAAA 59.900 38.462 0.00 0.00 0.00 1.40
2072 2084 6.292150 AGTCAGCAGGCTATAAGGAATAAAC 58.708 40.000 0.00 0.00 0.00 2.01
2073 2085 6.100424 AGTCAGCAGGCTATAAGGAATAAACT 59.900 38.462 0.00 0.00 0.00 2.66
2074 2086 7.290248 AGTCAGCAGGCTATAAGGAATAAACTA 59.710 37.037 0.00 0.00 0.00 2.24
2075 2087 7.600752 GTCAGCAGGCTATAAGGAATAAACTAG 59.399 40.741 0.00 0.00 0.00 2.57
2076 2088 7.290248 TCAGCAGGCTATAAGGAATAAACTAGT 59.710 37.037 0.00 0.00 0.00 2.57
2077 2089 8.585881 CAGCAGGCTATAAGGAATAAACTAGTA 58.414 37.037 0.00 0.00 0.00 1.82
2078 2090 9.327731 AGCAGGCTATAAGGAATAAACTAGTAT 57.672 33.333 0.00 0.00 0.00 2.12
2097 2109 8.643324 ACTAGTATATTTCTGCTTAGTTGGAGG 58.357 37.037 0.00 0.00 0.00 4.30
2098 2110 7.676683 AGTATATTTCTGCTTAGTTGGAGGA 57.323 36.000 0.00 0.00 0.00 3.71
2099 2111 8.090788 AGTATATTTCTGCTTAGTTGGAGGAA 57.909 34.615 0.00 0.00 0.00 3.36
2100 2112 8.548877 AGTATATTTCTGCTTAGTTGGAGGAAA 58.451 33.333 0.00 0.00 0.00 3.13
2101 2113 7.872113 ATATTTCTGCTTAGTTGGAGGAAAG 57.128 36.000 0.00 0.00 0.00 2.62
2102 2114 4.974645 TTCTGCTTAGTTGGAGGAAAGA 57.025 40.909 0.00 0.00 0.00 2.52
2103 2115 4.543590 TCTGCTTAGTTGGAGGAAAGAG 57.456 45.455 0.00 0.00 0.00 2.85
2104 2116 4.160329 TCTGCTTAGTTGGAGGAAAGAGA 58.840 43.478 0.00 0.00 0.00 3.10
2105 2117 4.593206 TCTGCTTAGTTGGAGGAAAGAGAA 59.407 41.667 0.00 0.00 0.00 2.87
2106 2118 4.899502 TGCTTAGTTGGAGGAAAGAGAAG 58.100 43.478 0.00 0.00 0.00 2.85
2107 2119 4.593206 TGCTTAGTTGGAGGAAAGAGAAGA 59.407 41.667 0.00 0.00 0.00 2.87
2108 2120 5.175127 GCTTAGTTGGAGGAAAGAGAAGAG 58.825 45.833 0.00 0.00 0.00 2.85
2109 2121 5.729510 CTTAGTTGGAGGAAAGAGAAGAGG 58.270 45.833 0.00 0.00 0.00 3.69
2110 2122 3.592865 AGTTGGAGGAAAGAGAAGAGGT 58.407 45.455 0.00 0.00 0.00 3.85
2111 2123 3.326297 AGTTGGAGGAAAGAGAAGAGGTG 59.674 47.826 0.00 0.00 0.00 4.00
2112 2124 3.260269 TGGAGGAAAGAGAAGAGGTGA 57.740 47.619 0.00 0.00 0.00 4.02
2113 2125 3.169099 TGGAGGAAAGAGAAGAGGTGAG 58.831 50.000 0.00 0.00 0.00 3.51
2114 2126 3.181417 TGGAGGAAAGAGAAGAGGTGAGA 60.181 47.826 0.00 0.00 0.00 3.27
2115 2127 3.447229 GGAGGAAAGAGAAGAGGTGAGAG 59.553 52.174 0.00 0.00 0.00 3.20
2116 2128 4.340617 GAGGAAAGAGAAGAGGTGAGAGA 58.659 47.826 0.00 0.00 0.00 3.10
2117 2129 4.746466 AGGAAAGAGAAGAGGTGAGAGAA 58.254 43.478 0.00 0.00 0.00 2.87
2118 2130 4.772100 AGGAAAGAGAAGAGGTGAGAGAAG 59.228 45.833 0.00 0.00 0.00 2.85
2119 2131 4.081697 GGAAAGAGAAGAGGTGAGAGAAGG 60.082 50.000 0.00 0.00 0.00 3.46
2120 2132 3.825908 AGAGAAGAGGTGAGAGAAGGT 57.174 47.619 0.00 0.00 0.00 3.50
2121 2133 4.938575 AGAGAAGAGGTGAGAGAAGGTA 57.061 45.455 0.00 0.00 0.00 3.08
2122 2134 5.263872 AGAGAAGAGGTGAGAGAAGGTAA 57.736 43.478 0.00 0.00 0.00 2.85
2123 2135 5.261216 AGAGAAGAGGTGAGAGAAGGTAAG 58.739 45.833 0.00 0.00 0.00 2.34
2124 2136 3.767131 AGAAGAGGTGAGAGAAGGTAAGC 59.233 47.826 0.00 0.00 0.00 3.09
2125 2137 2.096248 AGAGGTGAGAGAAGGTAAGCG 58.904 52.381 0.00 0.00 0.00 4.68
2126 2138 1.135333 GAGGTGAGAGAAGGTAAGCGG 59.865 57.143 0.00 0.00 0.00 5.52
2127 2139 0.175989 GGTGAGAGAAGGTAAGCGGG 59.824 60.000 0.00 0.00 0.00 6.13
2128 2140 0.460459 GTGAGAGAAGGTAAGCGGGC 60.460 60.000 0.00 0.00 0.00 6.13
2129 2141 0.614979 TGAGAGAAGGTAAGCGGGCT 60.615 55.000 0.00 0.00 0.00 5.19
2130 2142 0.103390 GAGAGAAGGTAAGCGGGCTC 59.897 60.000 0.00 0.00 0.00 4.70
2131 2143 0.324830 AGAGAAGGTAAGCGGGCTCT 60.325 55.000 0.00 0.00 0.00 4.09
2132 2144 0.537653 GAGAAGGTAAGCGGGCTCTT 59.462 55.000 0.00 0.00 0.00 2.85
2133 2145 0.537653 AGAAGGTAAGCGGGCTCTTC 59.462 55.000 10.83 10.83 35.41 2.87
2134 2146 0.806492 GAAGGTAAGCGGGCTCTTCG 60.806 60.000 0.00 0.00 0.00 3.79
2135 2147 1.542187 AAGGTAAGCGGGCTCTTCGT 61.542 55.000 0.00 0.00 0.00 3.85
2136 2148 1.810030 GGTAAGCGGGCTCTTCGTG 60.810 63.158 0.00 0.00 0.00 4.35
2137 2149 1.214589 GTAAGCGGGCTCTTCGTGA 59.785 57.895 0.00 0.00 0.00 4.35
2138 2150 0.389426 GTAAGCGGGCTCTTCGTGAA 60.389 55.000 0.00 0.00 0.00 3.18
2139 2151 0.108804 TAAGCGGGCTCTTCGTGAAG 60.109 55.000 3.17 3.17 39.71 3.02
2140 2152 1.816863 AAGCGGGCTCTTCGTGAAGA 61.817 55.000 11.54 11.54 44.47 2.87
2149 2161 2.437413 TCTTCGTGAAGAGCTAGCTCA 58.563 47.619 38.86 21.98 44.99 4.26
2150 2162 2.820197 TCTTCGTGAAGAGCTAGCTCAA 59.180 45.455 38.86 24.70 44.99 3.02
2151 2163 2.929531 TCGTGAAGAGCTAGCTCAAG 57.070 50.000 38.86 24.52 44.99 3.02
2152 2164 1.135257 TCGTGAAGAGCTAGCTCAAGC 60.135 52.381 38.86 28.11 44.99 4.01
2153 2165 1.403382 CGTGAAGAGCTAGCTCAAGCA 60.403 52.381 38.86 29.94 45.30 3.91
2154 2166 1.999024 GTGAAGAGCTAGCTCAAGCAC 59.001 52.381 38.86 34.21 45.30 4.40
2155 2167 1.276415 GAAGAGCTAGCTCAAGCACG 58.724 55.000 38.86 0.00 45.30 5.34
2156 2168 0.605589 AAGAGCTAGCTCAAGCACGT 59.394 50.000 38.86 19.15 45.30 4.49
2157 2169 0.108898 AGAGCTAGCTCAAGCACGTG 60.109 55.000 38.86 12.28 45.30 4.49
2158 2170 0.389166 GAGCTAGCTCAAGCACGTGT 60.389 55.000 34.70 1.83 45.30 4.49
2159 2171 0.034059 AGCTAGCTCAAGCACGTGTT 59.966 50.000 18.38 8.60 45.30 3.32
2160 2172 0.440371 GCTAGCTCAAGCACGTGTTC 59.560 55.000 18.38 0.57 45.16 3.18
2161 2173 1.071605 CTAGCTCAAGCACGTGTTCC 58.928 55.000 18.38 0.00 45.16 3.62
2162 2174 0.679505 TAGCTCAAGCACGTGTTCCT 59.320 50.000 18.38 2.52 45.16 3.36
2163 2175 0.679505 AGCTCAAGCACGTGTTCCTA 59.320 50.000 18.38 0.00 45.16 2.94
2164 2176 1.071605 GCTCAAGCACGTGTTCCTAG 58.928 55.000 18.38 10.36 41.59 3.02
2165 2177 1.714794 CTCAAGCACGTGTTCCTAGG 58.285 55.000 18.38 0.82 0.00 3.02
2166 2178 0.320421 TCAAGCACGTGTTCCTAGGC 60.320 55.000 18.38 0.00 0.00 3.93
2167 2179 0.602638 CAAGCACGTGTTCCTAGGCA 60.603 55.000 18.38 0.00 0.00 4.75
2168 2180 0.602905 AAGCACGTGTTCCTAGGCAC 60.603 55.000 18.38 3.73 0.00 5.01
2169 2181 1.004918 GCACGTGTTCCTAGGCACT 60.005 57.895 18.38 0.50 46.37 4.40
2170 2182 0.602905 GCACGTGTTCCTAGGCACTT 60.603 55.000 18.38 3.13 41.75 3.16
2171 2183 1.878953 CACGTGTTCCTAGGCACTTT 58.121 50.000 12.98 0.00 41.75 2.66
2172 2184 1.531149 CACGTGTTCCTAGGCACTTTG 59.469 52.381 12.98 8.00 41.75 2.77
2173 2185 1.140252 ACGTGTTCCTAGGCACTTTGT 59.860 47.619 12.98 5.72 41.75 2.83
2174 2186 1.531149 CGTGTTCCTAGGCACTTTGTG 59.469 52.381 12.98 0.00 41.75 3.33
2175 2187 2.805295 CGTGTTCCTAGGCACTTTGTGA 60.805 50.000 12.98 0.00 41.75 3.58
2176 2188 2.808543 GTGTTCCTAGGCACTTTGTGAG 59.191 50.000 12.98 0.00 41.75 3.51
2177 2189 2.703536 TGTTCCTAGGCACTTTGTGAGA 59.296 45.455 12.98 0.00 41.75 3.27
2178 2190 3.135712 TGTTCCTAGGCACTTTGTGAGAA 59.864 43.478 12.98 0.00 41.75 2.87
2179 2191 4.202461 TGTTCCTAGGCACTTTGTGAGAAT 60.202 41.667 12.98 0.00 41.75 2.40
2180 2192 3.942829 TCCTAGGCACTTTGTGAGAATG 58.057 45.455 2.96 0.00 41.75 2.67
2181 2193 3.582647 TCCTAGGCACTTTGTGAGAATGA 59.417 43.478 2.96 0.00 41.75 2.57
2182 2194 4.041567 TCCTAGGCACTTTGTGAGAATGAA 59.958 41.667 2.96 0.00 41.75 2.57
2183 2195 4.761739 CCTAGGCACTTTGTGAGAATGAAA 59.238 41.667 0.00 0.00 41.75 2.69
2184 2196 4.843220 AGGCACTTTGTGAGAATGAAAG 57.157 40.909 1.52 0.00 35.23 2.62
2185 2197 3.571401 AGGCACTTTGTGAGAATGAAAGG 59.429 43.478 1.52 0.00 35.23 3.11
2186 2198 3.319122 GGCACTTTGTGAGAATGAAAGGT 59.681 43.478 1.52 0.00 35.23 3.50
2187 2199 4.293415 GCACTTTGTGAGAATGAAAGGTG 58.707 43.478 1.52 0.00 35.23 4.00
2188 2200 4.794003 GCACTTTGTGAGAATGAAAGGTGG 60.794 45.833 1.52 0.00 35.23 4.61
2189 2201 3.891366 ACTTTGTGAGAATGAAAGGTGGG 59.109 43.478 0.00 0.00 0.00 4.61
2190 2202 1.909700 TGTGAGAATGAAAGGTGGGC 58.090 50.000 0.00 0.00 0.00 5.36
2191 2203 1.177401 GTGAGAATGAAAGGTGGGCC 58.823 55.000 0.00 0.00 0.00 5.80
2192 2204 0.776810 TGAGAATGAAAGGTGGGCCA 59.223 50.000 0.00 0.00 37.19 5.36
2193 2205 1.177401 GAGAATGAAAGGTGGGCCAC 58.823 55.000 28.69 28.69 37.19 5.01
2194 2206 0.482446 AGAATGAAAGGTGGGCCACA 59.518 50.000 35.69 17.39 35.86 4.17
2195 2207 1.077663 AGAATGAAAGGTGGGCCACAT 59.922 47.619 35.69 28.70 35.86 3.21
2196 2208 2.311542 AGAATGAAAGGTGGGCCACATA 59.688 45.455 35.69 16.77 35.86 2.29
2197 2209 2.917713 ATGAAAGGTGGGCCACATAA 57.082 45.000 35.69 19.62 35.86 1.90
2198 2210 2.917713 TGAAAGGTGGGCCACATAAT 57.082 45.000 35.69 22.42 35.86 1.28
2199 2211 4.534647 ATGAAAGGTGGGCCACATAATA 57.465 40.909 35.69 19.38 35.86 0.98
2200 2212 4.323569 TGAAAGGTGGGCCACATAATAA 57.676 40.909 35.69 13.98 35.86 1.40
2201 2213 4.678256 TGAAAGGTGGGCCACATAATAAA 58.322 39.130 35.69 13.51 35.86 1.40
2202 2214 5.087323 TGAAAGGTGGGCCACATAATAAAA 58.913 37.500 35.69 11.39 35.86 1.52
2203 2215 5.046950 TGAAAGGTGGGCCACATAATAAAAC 60.047 40.000 35.69 16.37 35.86 2.43
2204 2216 4.054359 AGGTGGGCCACATAATAAAACA 57.946 40.909 35.69 0.00 35.86 2.83
2205 2217 4.023291 AGGTGGGCCACATAATAAAACAG 58.977 43.478 35.69 0.00 35.86 3.16
2206 2218 3.767131 GGTGGGCCACATAATAAAACAGT 59.233 43.478 35.69 0.00 35.86 3.55
2207 2219 4.951094 GGTGGGCCACATAATAAAACAGTA 59.049 41.667 35.69 0.00 35.86 2.74
2208 2220 5.067283 GGTGGGCCACATAATAAAACAGTAG 59.933 44.000 35.69 0.00 35.86 2.57
2209 2221 5.650703 GTGGGCCACATAATAAAACAGTAGT 59.349 40.000 31.26 0.00 34.08 2.73
2210 2222 6.824704 GTGGGCCACATAATAAAACAGTAGTA 59.175 38.462 31.26 0.00 34.08 1.82
2211 2223 6.824704 TGGGCCACATAATAAAACAGTAGTAC 59.175 38.462 0.00 0.00 0.00 2.73
2212 2224 6.824704 GGGCCACATAATAAAACAGTAGTACA 59.175 38.462 4.39 0.00 0.00 2.90
2213 2225 7.201670 GGGCCACATAATAAAACAGTAGTACAC 60.202 40.741 4.39 0.00 0.00 2.90
2214 2226 7.551617 GGCCACATAATAAAACAGTAGTACACT 59.448 37.037 0.00 0.00 38.32 3.55
2215 2227 8.943002 GCCACATAATAAAACAGTAGTACACTT 58.057 33.333 2.52 0.00 34.26 3.16
2254 2266 9.448438 TTGTACATGTTGACTATAAAATGAGCT 57.552 29.630 2.30 0.00 0.00 4.09
2269 2281 6.964807 AAATGAGCTATAAATGACATGGCA 57.035 33.333 2.18 2.18 32.72 4.92
2270 2282 5.954296 ATGAGCTATAAATGACATGGCAC 57.046 39.130 1.45 0.00 32.72 5.01
2271 2283 5.039920 TGAGCTATAAATGACATGGCACT 57.960 39.130 1.45 0.00 32.72 4.40
2272 2284 4.818005 TGAGCTATAAATGACATGGCACTG 59.182 41.667 1.45 0.00 32.72 3.66
2273 2285 4.139786 AGCTATAAATGACATGGCACTGG 58.860 43.478 1.45 0.00 32.72 4.00
2274 2286 3.304928 GCTATAAATGACATGGCACTGGC 60.305 47.826 1.45 0.00 40.13 4.85
2275 2287 2.512692 TAAATGACATGGCACTGGCT 57.487 45.000 1.45 0.00 40.87 4.75
2276 2288 1.636148 AAATGACATGGCACTGGCTT 58.364 45.000 1.45 0.00 40.87 4.35
2277 2289 2.512692 AATGACATGGCACTGGCTTA 57.487 45.000 1.45 0.00 40.87 3.09
2278 2290 2.742428 ATGACATGGCACTGGCTTAT 57.258 45.000 1.45 0.00 40.87 1.73
2279 2291 3.862877 ATGACATGGCACTGGCTTATA 57.137 42.857 1.45 0.00 40.87 0.98
2280 2292 3.198409 TGACATGGCACTGGCTTATAG 57.802 47.619 0.00 0.00 40.87 1.31
2281 2293 1.876156 GACATGGCACTGGCTTATAGC 59.124 52.381 3.97 0.00 41.46 2.97
2304 2316 6.787085 CCAACAGCTGGCTATACTATTAAC 57.213 41.667 19.93 0.00 38.76 2.01
2305 2317 5.701290 CCAACAGCTGGCTATACTATTAACC 59.299 44.000 19.93 0.00 38.76 2.85
2306 2318 6.288294 CAACAGCTGGCTATACTATTAACCA 58.712 40.000 19.93 0.00 0.00 3.67
2307 2319 6.688073 ACAGCTGGCTATACTATTAACCAT 57.312 37.500 19.93 0.00 0.00 3.55
2308 2320 6.467677 ACAGCTGGCTATACTATTAACCATG 58.532 40.000 19.93 0.00 0.00 3.66
2309 2321 5.352569 CAGCTGGCTATACTATTAACCATGC 59.647 44.000 5.57 0.00 0.00 4.06
2310 2322 5.249393 AGCTGGCTATACTATTAACCATGCT 59.751 40.000 0.00 0.00 31.38 3.79
2311 2323 5.582665 GCTGGCTATACTATTAACCATGCTC 59.417 44.000 0.00 0.00 0.00 4.26
2312 2324 6.575254 GCTGGCTATACTATTAACCATGCTCT 60.575 42.308 0.00 0.00 0.00 4.09
2313 2325 7.363880 GCTGGCTATACTATTAACCATGCTCTA 60.364 40.741 0.00 0.00 0.00 2.43
2314 2326 8.430573 TGGCTATACTATTAACCATGCTCTAA 57.569 34.615 0.00 0.00 0.00 2.10
2315 2327 8.531982 TGGCTATACTATTAACCATGCTCTAAG 58.468 37.037 0.00 0.00 0.00 2.18
2330 2342 1.751351 TCTAAGGATGTCCGAGCTGTG 59.249 52.381 0.00 0.00 42.08 3.66
2353 2365 1.684248 GGCATGTTCTCCAAGGAGCAT 60.684 52.381 11.31 7.24 41.71 3.79
2377 2389 6.141083 TCCAGGTAATAGGCTAGCTCTTTTA 58.859 40.000 15.72 12.11 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 131 1.792949 GCTGAAACACGATTGAGACGT 59.207 47.619 0.00 0.00 44.83 4.34
224 226 7.144000 CCTTGGAGAAGTTTGAATTTTGAGAG 58.856 38.462 0.00 0.00 0.00 3.20
236 238 0.179018 ACGCTGCCTTGGAGAAGTTT 60.179 50.000 0.00 0.00 0.00 2.66
249 251 1.658095 GAGATGAAGTCAGAACGCTGC 59.342 52.381 0.00 0.00 42.01 5.25
315 317 8.664798 GTGTTGTGATCACATGTAGCTAATTTA 58.335 33.333 28.32 6.65 41.52 1.40
359 361 0.874607 ACTCACCGACGCACTTGTTC 60.875 55.000 0.00 0.00 0.00 3.18
374 376 2.449967 TAGGGAACGGGCTCCACTCA 62.450 60.000 3.28 0.00 37.20 3.41
382 384 2.516225 GTGCCATAGGGAACGGGC 60.516 66.667 0.00 0.00 44.05 6.13
426 428 5.809001 TGCCAAGTAGTGATCTTCATCTTT 58.191 37.500 0.00 0.00 0.00 2.52
442 444 3.606687 CCTCCGTTATAACTTGCCAAGT 58.393 45.455 13.56 3.74 45.46 3.16
444 446 2.026636 AGCCTCCGTTATAACTTGCCAA 60.027 45.455 13.56 0.00 0.00 4.52
461 463 3.933061 GCACTTCTGCATAGGTAAAGCCT 60.933 47.826 0.00 0.00 46.15 4.58
483 485 1.735571 GGTATGTGCCGTAACACCTTG 59.264 52.381 0.00 0.00 39.93 3.61
495 497 1.472480 GTGGATGTTGTGGGTATGTGC 59.528 52.381 0.00 0.00 0.00 4.57
544 546 4.428845 CAAGGCATGGAAGGTGCT 57.571 55.556 0.00 0.00 42.16 4.40
603 605 0.980231 GTGGGAGAGGCCATCTGTCT 60.980 60.000 5.01 0.00 38.84 3.41
720 722 0.322456 TCCTTAGCTGCCAAATGCGT 60.322 50.000 0.00 0.00 45.60 5.24
798 800 6.552445 AGCTTGATGGATCTGTAGTAACTT 57.448 37.500 0.00 0.00 0.00 2.66
829 831 4.941263 CAGAATTTCCTCCACCGAATAACA 59.059 41.667 0.00 0.00 0.00 2.41
843 846 5.997129 TGGCATTTTTCCTTTCAGAATTTCC 59.003 36.000 0.00 0.00 0.00 3.13
890 893 5.251700 AGTGGTATGTTTTCCTTCTCCTGAT 59.748 40.000 0.00 0.00 0.00 2.90
893 896 5.045797 GGTAGTGGTATGTTTTCCTTCTCCT 60.046 44.000 0.00 0.00 0.00 3.69
1072 1075 0.674895 GCGTGAAGTTCAGCCTCCAT 60.675 55.000 5.62 0.00 0.00 3.41
1205 1208 5.258841 TCTCTAGAACCAAATGACCGTAGA 58.741 41.667 0.00 0.00 0.00 2.59
1301 1304 4.821805 CGGAATGACTATACTTGGCCAAAT 59.178 41.667 20.91 13.08 0.00 2.32
1311 1314 4.564940 AGTCCGTTCGGAATGACTATAC 57.435 45.455 15.59 1.08 36.36 1.47
1319 1322 0.892755 TGCTGTAGTCCGTTCGGAAT 59.107 50.000 17.58 17.58 35.89 3.01
1489 1494 6.038714 GGAGGTTAGTTCCATCAAGCTTAATG 59.961 42.308 2.22 2.22 34.74 1.90
1548 1554 9.381033 CTGAGATCAAAACTTATCAACAGAGAT 57.619 33.333 0.00 0.00 34.12 2.75
1796 1806 9.423061 GCAAATGAATATTTTTCTACAGTTGGT 57.577 29.630 12.01 0.00 34.34 3.67
1958 1969 2.107378 TGGACATGCCCAGACAAAGTAA 59.893 45.455 0.00 0.00 34.97 2.24
2029 2041 4.464244 TGACTCAGCTCTATTGTACTTGCT 59.536 41.667 0.00 0.00 0.00 3.91
2030 2042 4.748892 TGACTCAGCTCTATTGTACTTGC 58.251 43.478 0.00 0.00 0.00 4.01
2045 2057 2.961741 TCCTTATAGCCTGCTGACTCAG 59.038 50.000 0.97 1.21 34.12 3.35
2046 2058 3.032265 TCCTTATAGCCTGCTGACTCA 57.968 47.619 0.97 0.00 0.00 3.41
2047 2059 4.615588 ATTCCTTATAGCCTGCTGACTC 57.384 45.455 0.97 0.00 0.00 3.36
2048 2060 6.100424 AGTTTATTCCTTATAGCCTGCTGACT 59.900 38.462 0.97 0.00 0.00 3.41
2049 2061 6.292150 AGTTTATTCCTTATAGCCTGCTGAC 58.708 40.000 0.97 0.00 0.00 3.51
2050 2062 6.500589 AGTTTATTCCTTATAGCCTGCTGA 57.499 37.500 0.97 0.00 0.00 4.26
2051 2063 7.445945 ACTAGTTTATTCCTTATAGCCTGCTG 58.554 38.462 0.97 0.00 0.00 4.41
2052 2064 7.619512 ACTAGTTTATTCCTTATAGCCTGCT 57.380 36.000 0.00 0.00 0.00 4.24
2071 2083 8.643324 CCTCCAACTAAGCAGAAATATACTAGT 58.357 37.037 0.00 0.00 0.00 2.57
2072 2084 8.861086 TCCTCCAACTAAGCAGAAATATACTAG 58.139 37.037 0.00 0.00 0.00 2.57
2073 2085 8.777578 TCCTCCAACTAAGCAGAAATATACTA 57.222 34.615 0.00 0.00 0.00 1.82
2074 2086 7.676683 TCCTCCAACTAAGCAGAAATATACT 57.323 36.000 0.00 0.00 0.00 2.12
2075 2087 8.732746 TTTCCTCCAACTAAGCAGAAATATAC 57.267 34.615 0.00 0.00 0.00 1.47
2076 2088 8.768397 TCTTTCCTCCAACTAAGCAGAAATATA 58.232 33.333 0.00 0.00 0.00 0.86
2077 2089 7.633789 TCTTTCCTCCAACTAAGCAGAAATAT 58.366 34.615 0.00 0.00 0.00 1.28
2078 2090 7.016153 TCTTTCCTCCAACTAAGCAGAAATA 57.984 36.000 0.00 0.00 0.00 1.40
2079 2091 5.880901 TCTTTCCTCCAACTAAGCAGAAAT 58.119 37.500 0.00 0.00 0.00 2.17
2080 2092 5.071788 TCTCTTTCCTCCAACTAAGCAGAAA 59.928 40.000 0.00 0.00 0.00 2.52
2081 2093 4.593206 TCTCTTTCCTCCAACTAAGCAGAA 59.407 41.667 0.00 0.00 0.00 3.02
2082 2094 4.160329 TCTCTTTCCTCCAACTAAGCAGA 58.840 43.478 0.00 0.00 0.00 4.26
2083 2095 4.543590 TCTCTTTCCTCCAACTAAGCAG 57.456 45.455 0.00 0.00 0.00 4.24
2084 2096 4.593206 TCTTCTCTTTCCTCCAACTAAGCA 59.407 41.667 0.00 0.00 0.00 3.91
2085 2097 5.153950 TCTTCTCTTTCCTCCAACTAAGC 57.846 43.478 0.00 0.00 0.00 3.09
2086 2098 5.247337 ACCTCTTCTCTTTCCTCCAACTAAG 59.753 44.000 0.00 0.00 0.00 2.18
2087 2099 5.012148 CACCTCTTCTCTTTCCTCCAACTAA 59.988 44.000 0.00 0.00 0.00 2.24
2088 2100 4.528596 CACCTCTTCTCTTTCCTCCAACTA 59.471 45.833 0.00 0.00 0.00 2.24
2089 2101 3.326297 CACCTCTTCTCTTTCCTCCAACT 59.674 47.826 0.00 0.00 0.00 3.16
2090 2102 3.325135 TCACCTCTTCTCTTTCCTCCAAC 59.675 47.826 0.00 0.00 0.00 3.77
2091 2103 3.580458 CTCACCTCTTCTCTTTCCTCCAA 59.420 47.826 0.00 0.00 0.00 3.53
2092 2104 3.169099 CTCACCTCTTCTCTTTCCTCCA 58.831 50.000 0.00 0.00 0.00 3.86
2093 2105 3.436243 TCTCACCTCTTCTCTTTCCTCC 58.564 50.000 0.00 0.00 0.00 4.30
2094 2106 4.340617 TCTCTCACCTCTTCTCTTTCCTC 58.659 47.826 0.00 0.00 0.00 3.71
2095 2107 4.396357 TCTCTCACCTCTTCTCTTTCCT 57.604 45.455 0.00 0.00 0.00 3.36
2096 2108 4.081697 CCTTCTCTCACCTCTTCTCTTTCC 60.082 50.000 0.00 0.00 0.00 3.13
2097 2109 4.526650 ACCTTCTCTCACCTCTTCTCTTTC 59.473 45.833 0.00 0.00 0.00 2.62
2098 2110 4.488770 ACCTTCTCTCACCTCTTCTCTTT 58.511 43.478 0.00 0.00 0.00 2.52
2099 2111 4.126520 ACCTTCTCTCACCTCTTCTCTT 57.873 45.455 0.00 0.00 0.00 2.85
2100 2112 3.825908 ACCTTCTCTCACCTCTTCTCT 57.174 47.619 0.00 0.00 0.00 3.10
2101 2113 4.142249 GCTTACCTTCTCTCACCTCTTCTC 60.142 50.000 0.00 0.00 0.00 2.87
2102 2114 3.767131 GCTTACCTTCTCTCACCTCTTCT 59.233 47.826 0.00 0.00 0.00 2.85
2103 2115 3.428316 CGCTTACCTTCTCTCACCTCTTC 60.428 52.174 0.00 0.00 0.00 2.87
2104 2116 2.494073 CGCTTACCTTCTCTCACCTCTT 59.506 50.000 0.00 0.00 0.00 2.85
2105 2117 2.096248 CGCTTACCTTCTCTCACCTCT 58.904 52.381 0.00 0.00 0.00 3.69
2106 2118 1.135333 CCGCTTACCTTCTCTCACCTC 59.865 57.143 0.00 0.00 0.00 3.85
2107 2119 1.187087 CCGCTTACCTTCTCTCACCT 58.813 55.000 0.00 0.00 0.00 4.00
2108 2120 0.175989 CCCGCTTACCTTCTCTCACC 59.824 60.000 0.00 0.00 0.00 4.02
2109 2121 0.460459 GCCCGCTTACCTTCTCTCAC 60.460 60.000 0.00 0.00 0.00 3.51
2110 2122 0.614979 AGCCCGCTTACCTTCTCTCA 60.615 55.000 0.00 0.00 0.00 3.27
2111 2123 0.103390 GAGCCCGCTTACCTTCTCTC 59.897 60.000 0.00 0.00 0.00 3.20
2112 2124 0.324830 AGAGCCCGCTTACCTTCTCT 60.325 55.000 0.00 0.00 0.00 3.10
2113 2125 0.537653 AAGAGCCCGCTTACCTTCTC 59.462 55.000 0.00 0.00 0.00 2.87
2114 2126 0.537653 GAAGAGCCCGCTTACCTTCT 59.462 55.000 8.59 0.00 32.72 2.85
2115 2127 0.806492 CGAAGAGCCCGCTTACCTTC 60.806 60.000 6.57 6.57 0.00 3.46
2116 2128 1.218316 CGAAGAGCCCGCTTACCTT 59.782 57.895 0.00 0.00 0.00 3.50
2117 2129 1.982938 ACGAAGAGCCCGCTTACCT 60.983 57.895 0.00 0.00 0.00 3.08
2118 2130 1.810030 CACGAAGAGCCCGCTTACC 60.810 63.158 0.00 0.00 0.00 2.85
2119 2131 0.389426 TTCACGAAGAGCCCGCTTAC 60.389 55.000 0.00 0.00 0.00 2.34
2120 2132 0.108804 CTTCACGAAGAGCCCGCTTA 60.109 55.000 0.20 0.00 40.79 3.09
2121 2133 1.374758 CTTCACGAAGAGCCCGCTT 60.375 57.895 0.20 0.00 40.79 4.68
2122 2134 2.262915 CTTCACGAAGAGCCCGCT 59.737 61.111 0.20 0.00 40.79 5.52
2123 2135 2.261671 TCTTCACGAAGAGCCCGC 59.738 61.111 5.38 0.00 42.06 6.13
2129 2141 2.437413 TGAGCTAGCTCTTCACGAAGA 58.563 47.619 37.42 17.15 44.47 2.87
2130 2142 2.929531 TGAGCTAGCTCTTCACGAAG 57.070 50.000 37.42 0.08 43.12 3.79
2131 2143 2.672478 GCTTGAGCTAGCTCTTCACGAA 60.672 50.000 37.42 24.10 43.12 3.85
2132 2144 1.135257 GCTTGAGCTAGCTCTTCACGA 60.135 52.381 37.42 19.20 43.12 4.35
2133 2145 1.276415 GCTTGAGCTAGCTCTTCACG 58.724 55.000 37.42 21.36 43.12 4.35
2134 2146 1.999024 GTGCTTGAGCTAGCTCTTCAC 59.001 52.381 37.42 32.98 43.12 3.18
2135 2147 1.403382 CGTGCTTGAGCTAGCTCTTCA 60.403 52.381 37.42 28.74 43.12 3.02
2136 2148 1.276415 CGTGCTTGAGCTAGCTCTTC 58.724 55.000 37.42 26.96 43.12 2.87
2137 2149 0.605589 ACGTGCTTGAGCTAGCTCTT 59.394 50.000 37.42 10.60 43.12 2.85
2138 2150 0.108898 CACGTGCTTGAGCTAGCTCT 60.109 55.000 37.42 18.52 43.12 4.09
2139 2151 0.389166 ACACGTGCTTGAGCTAGCTC 60.389 55.000 33.47 33.47 41.76 4.09
2140 2152 0.034059 AACACGTGCTTGAGCTAGCT 59.966 50.000 19.45 19.45 41.76 3.32
2141 2153 0.440371 GAACACGTGCTTGAGCTAGC 59.560 55.000 17.22 6.62 42.66 3.42
2142 2154 1.071605 GGAACACGTGCTTGAGCTAG 58.928 55.000 17.22 1.14 42.66 3.42
2143 2155 0.679505 AGGAACACGTGCTTGAGCTA 59.320 50.000 17.22 0.00 42.66 3.32
2144 2156 0.679505 TAGGAACACGTGCTTGAGCT 59.320 50.000 17.22 0.00 42.66 4.09
2145 2157 1.071605 CTAGGAACACGTGCTTGAGC 58.928 55.000 17.22 0.00 42.50 4.26
2146 2158 1.714794 CCTAGGAACACGTGCTTGAG 58.285 55.000 17.22 6.78 0.00 3.02
2147 2159 0.320421 GCCTAGGAACACGTGCTTGA 60.320 55.000 17.22 0.00 0.00 3.02
2148 2160 0.602638 TGCCTAGGAACACGTGCTTG 60.603 55.000 17.22 5.82 0.00 4.01
2149 2161 0.602905 GTGCCTAGGAACACGTGCTT 60.603 55.000 15.80 9.30 0.00 3.91
2150 2162 1.004918 GTGCCTAGGAACACGTGCT 60.005 57.895 15.80 2.15 0.00 4.40
2151 2163 0.602905 AAGTGCCTAGGAACACGTGC 60.603 55.000 22.67 0.00 41.72 5.34
2152 2164 1.531149 CAAAGTGCCTAGGAACACGTG 59.469 52.381 22.67 15.48 41.72 4.49
2153 2165 1.140252 ACAAAGTGCCTAGGAACACGT 59.860 47.619 22.67 12.35 41.72 4.49
2154 2166 1.531149 CACAAAGTGCCTAGGAACACG 59.469 52.381 22.67 11.70 41.72 4.49
2155 2167 2.808543 CTCACAAAGTGCCTAGGAACAC 59.191 50.000 22.67 16.13 37.05 3.32
2156 2168 2.703536 TCTCACAAAGTGCCTAGGAACA 59.296 45.455 22.67 3.61 32.98 3.18
2157 2169 3.402628 TCTCACAAAGTGCCTAGGAAC 57.597 47.619 14.75 13.64 32.98 3.62
2158 2170 4.041567 TCATTCTCACAAAGTGCCTAGGAA 59.958 41.667 14.75 0.00 32.98 3.36
2159 2171 3.582647 TCATTCTCACAAAGTGCCTAGGA 59.417 43.478 14.75 0.00 32.98 2.94
2160 2172 3.942829 TCATTCTCACAAAGTGCCTAGG 58.057 45.455 3.67 3.67 32.98 3.02
2161 2173 5.106396 CCTTTCATTCTCACAAAGTGCCTAG 60.106 44.000 0.00 0.00 32.98 3.02
2162 2174 4.761739 CCTTTCATTCTCACAAAGTGCCTA 59.238 41.667 0.00 0.00 32.98 3.93
2163 2175 3.571401 CCTTTCATTCTCACAAAGTGCCT 59.429 43.478 0.00 0.00 32.98 4.75
2164 2176 3.319122 ACCTTTCATTCTCACAAAGTGCC 59.681 43.478 0.00 0.00 32.98 5.01
2165 2177 4.293415 CACCTTTCATTCTCACAAAGTGC 58.707 43.478 0.00 0.00 32.98 4.40
2166 2178 4.261741 CCCACCTTTCATTCTCACAAAGTG 60.262 45.833 0.00 0.00 34.45 3.16
2167 2179 3.891366 CCCACCTTTCATTCTCACAAAGT 59.109 43.478 0.00 0.00 0.00 2.66
2168 2180 3.305608 GCCCACCTTTCATTCTCACAAAG 60.306 47.826 0.00 0.00 0.00 2.77
2169 2181 2.627699 GCCCACCTTTCATTCTCACAAA 59.372 45.455 0.00 0.00 0.00 2.83
2170 2182 2.238521 GCCCACCTTTCATTCTCACAA 58.761 47.619 0.00 0.00 0.00 3.33
2171 2183 1.547675 GGCCCACCTTTCATTCTCACA 60.548 52.381 0.00 0.00 0.00 3.58
2172 2184 1.177401 GGCCCACCTTTCATTCTCAC 58.823 55.000 0.00 0.00 0.00 3.51
2173 2185 0.776810 TGGCCCACCTTTCATTCTCA 59.223 50.000 0.00 0.00 36.63 3.27
2174 2186 1.177401 GTGGCCCACCTTTCATTCTC 58.823 55.000 1.17 0.00 36.63 2.87
2175 2187 0.482446 TGTGGCCCACCTTTCATTCT 59.518 50.000 12.25 0.00 36.63 2.40
2176 2188 1.560505 ATGTGGCCCACCTTTCATTC 58.439 50.000 12.25 0.00 36.63 2.67
2177 2189 2.917713 TATGTGGCCCACCTTTCATT 57.082 45.000 12.25 0.00 36.63 2.57
2178 2190 2.917713 TTATGTGGCCCACCTTTCAT 57.082 45.000 12.25 0.00 36.63 2.57
2179 2191 2.917713 ATTATGTGGCCCACCTTTCA 57.082 45.000 12.25 0.00 36.63 2.69
2180 2192 5.046950 TGTTTTATTATGTGGCCCACCTTTC 60.047 40.000 12.25 0.00 36.63 2.62
2181 2193 4.841246 TGTTTTATTATGTGGCCCACCTTT 59.159 37.500 12.25 0.00 36.63 3.11
2182 2194 4.421131 TGTTTTATTATGTGGCCCACCTT 58.579 39.130 12.25 1.15 36.63 3.50
2183 2195 4.023291 CTGTTTTATTATGTGGCCCACCT 58.977 43.478 12.25 3.78 36.63 4.00
2184 2196 3.767131 ACTGTTTTATTATGTGGCCCACC 59.233 43.478 12.25 0.00 32.73 4.61
2185 2197 5.650703 ACTACTGTTTTATTATGTGGCCCAC 59.349 40.000 7.01 7.01 34.56 4.61
2186 2198 5.822204 ACTACTGTTTTATTATGTGGCCCA 58.178 37.500 0.00 0.00 0.00 5.36
2187 2199 6.824704 TGTACTACTGTTTTATTATGTGGCCC 59.175 38.462 0.00 0.00 0.00 5.80
2188 2200 7.551617 AGTGTACTACTGTTTTATTATGTGGCC 59.448 37.037 0.00 0.00 38.49 5.36
2189 2201 8.488651 AGTGTACTACTGTTTTATTATGTGGC 57.511 34.615 0.00 0.00 38.49 5.01
2228 2240 9.448438 AGCTCATTTTATAGTCAACATGTACAA 57.552 29.630 0.00 0.00 0.00 2.41
2243 2255 9.081204 TGCCATGTCATTTATAGCTCATTTTAT 57.919 29.630 0.00 0.00 0.00 1.40
2244 2256 8.352201 GTGCCATGTCATTTATAGCTCATTTTA 58.648 33.333 0.00 0.00 0.00 1.52
2245 2257 7.069085 AGTGCCATGTCATTTATAGCTCATTTT 59.931 33.333 0.00 0.00 0.00 1.82
2246 2258 6.548622 AGTGCCATGTCATTTATAGCTCATTT 59.451 34.615 0.00 0.00 0.00 2.32
2247 2259 6.016527 CAGTGCCATGTCATTTATAGCTCATT 60.017 38.462 0.00 0.00 0.00 2.57
2248 2260 5.472478 CAGTGCCATGTCATTTATAGCTCAT 59.528 40.000 0.00 0.00 0.00 2.90
2249 2261 4.818005 CAGTGCCATGTCATTTATAGCTCA 59.182 41.667 0.00 0.00 0.00 4.26
2250 2262 4.214971 CCAGTGCCATGTCATTTATAGCTC 59.785 45.833 0.00 0.00 0.00 4.09
2251 2263 4.139786 CCAGTGCCATGTCATTTATAGCT 58.860 43.478 0.00 0.00 0.00 3.32
2252 2264 3.304928 GCCAGTGCCATGTCATTTATAGC 60.305 47.826 0.00 0.00 0.00 2.97
2253 2265 4.139786 AGCCAGTGCCATGTCATTTATAG 58.860 43.478 0.00 0.00 38.69 1.31
2254 2266 4.169059 AGCCAGTGCCATGTCATTTATA 57.831 40.909 0.00 0.00 38.69 0.98
2255 2267 3.022557 AGCCAGTGCCATGTCATTTAT 57.977 42.857 0.00 0.00 38.69 1.40
2256 2268 2.512692 AGCCAGTGCCATGTCATTTA 57.487 45.000 0.00 0.00 38.69 1.40
2257 2269 1.636148 AAGCCAGTGCCATGTCATTT 58.364 45.000 0.00 0.00 38.69 2.32
2258 2270 2.512692 TAAGCCAGTGCCATGTCATT 57.487 45.000 0.00 0.00 38.69 2.57
2259 2271 2.742428 ATAAGCCAGTGCCATGTCAT 57.258 45.000 0.00 0.00 38.69 3.06
2260 2272 2.746142 GCTATAAGCCAGTGCCATGTCA 60.746 50.000 0.00 0.00 38.69 3.58
2261 2273 1.876156 GCTATAAGCCAGTGCCATGTC 59.124 52.381 0.00 0.00 38.69 3.06
2262 2274 1.972872 GCTATAAGCCAGTGCCATGT 58.027 50.000 0.00 0.00 38.69 3.21
2282 2294 6.288294 TGGTTAATAGTATAGCCAGCTGTTG 58.712 40.000 13.81 0.00 32.02 3.33
2283 2295 6.494666 TGGTTAATAGTATAGCCAGCTGTT 57.505 37.500 13.81 2.90 32.02 3.16
2284 2296 6.467677 CATGGTTAATAGTATAGCCAGCTGT 58.532 40.000 13.81 0.00 39.18 4.40
2285 2297 5.352569 GCATGGTTAATAGTATAGCCAGCTG 59.647 44.000 6.78 6.78 39.18 4.24
2286 2298 5.249393 AGCATGGTTAATAGTATAGCCAGCT 59.751 40.000 0.00 0.00 39.18 4.24
2287 2299 5.491982 AGCATGGTTAATAGTATAGCCAGC 58.508 41.667 0.00 8.73 39.18 4.85
2288 2300 6.940739 AGAGCATGGTTAATAGTATAGCCAG 58.059 40.000 0.00 2.11 39.18 4.85
2289 2301 6.935240 AGAGCATGGTTAATAGTATAGCCA 57.065 37.500 0.00 3.65 39.96 4.75
2290 2302 7.982354 CCTTAGAGCATGGTTAATAGTATAGCC 59.018 40.741 0.00 0.00 0.00 3.93
2291 2303 8.750298 TCCTTAGAGCATGGTTAATAGTATAGC 58.250 37.037 0.00 0.00 0.00 2.97
2294 2306 9.105844 ACATCCTTAGAGCATGGTTAATAGTAT 57.894 33.333 0.00 0.00 0.00 2.12
2295 2307 8.492415 ACATCCTTAGAGCATGGTTAATAGTA 57.508 34.615 0.00 0.00 0.00 1.82
2296 2308 7.380423 ACATCCTTAGAGCATGGTTAATAGT 57.620 36.000 0.00 0.00 0.00 2.12
2297 2309 6.876257 GGACATCCTTAGAGCATGGTTAATAG 59.124 42.308 0.00 0.00 0.00 1.73
2298 2310 6.518369 CGGACATCCTTAGAGCATGGTTAATA 60.518 42.308 0.00 0.00 0.00 0.98
2299 2311 5.625150 GGACATCCTTAGAGCATGGTTAAT 58.375 41.667 0.00 0.00 0.00 1.40
2300 2312 4.442893 CGGACATCCTTAGAGCATGGTTAA 60.443 45.833 0.00 0.00 0.00 2.01
2301 2313 3.069586 CGGACATCCTTAGAGCATGGTTA 59.930 47.826 0.00 0.00 0.00 2.85
2302 2314 2.158900 CGGACATCCTTAGAGCATGGTT 60.159 50.000 0.00 0.00 0.00 3.67
2303 2315 1.414181 CGGACATCCTTAGAGCATGGT 59.586 52.381 0.00 0.00 0.00 3.55
2304 2316 1.688735 TCGGACATCCTTAGAGCATGG 59.311 52.381 0.00 0.00 0.00 3.66
2305 2317 3.023946 CTCGGACATCCTTAGAGCATG 57.976 52.381 0.00 0.00 0.00 4.06
2308 2320 3.579066 GCTCGGACATCCTTAGAGC 57.421 57.895 9.61 9.61 45.74 4.09
2309 2321 2.028130 ACAGCTCGGACATCCTTAGAG 58.972 52.381 0.00 0.00 0.00 2.43
2310 2322 1.751351 CACAGCTCGGACATCCTTAGA 59.249 52.381 0.00 0.00 0.00 2.10
2311 2323 1.804372 GCACAGCTCGGACATCCTTAG 60.804 57.143 0.00 0.00 0.00 2.18
2312 2324 0.175760 GCACAGCTCGGACATCCTTA 59.824 55.000 0.00 0.00 0.00 2.69
2313 2325 1.078848 GCACAGCTCGGACATCCTT 60.079 57.895 0.00 0.00 0.00 3.36
2314 2326 2.581354 GCACAGCTCGGACATCCT 59.419 61.111 0.00 0.00 0.00 3.24
2315 2327 2.887568 CGCACAGCTCGGACATCC 60.888 66.667 0.00 0.00 0.00 3.51
2330 2342 2.409870 CCTTGGAGAACATGCCCGC 61.410 63.158 0.00 0.00 0.00 6.13
2353 2365 3.905493 AGAGCTAGCCTATTACCTGGA 57.095 47.619 12.13 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.