Multiple sequence alignment - TraesCS2D01G111000

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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 TraesCS2D01G111000 chr2D 100.000 2999 0 0 1 2999 61798985 61801983 0.000000e+00 5539.0
1 TraesCS2D01G111000 chr2D 81.450 1283 185 31 724 1978 44001595 44002852 0.000000e+00 1002.0
2 TraesCS2D01G111000 chr2D 81.340 1179 176 28 818 1978 44059338 44058186 0.000000e+00 918.0
3 TraesCS2D01G111000 chr2D 81.474 502 79 10 815 1315 629058135 629058623 1.670000e-107 399.0
4 TraesCS2D01G111000 chr2D 100.000 108 0 0 2112 2219 61801042 61801149 1.820000e-47 200.0
5 TraesCS2D01G111000 chr2D 100.000 108 0 0 2058 2165 61801096 61801203 1.820000e-47 200.0
6 TraesCS2D01G111000 chr2D 100.000 54 0 0 2166 2219 61801042 61801095 1.900000e-17 100.0
7 TraesCS2D01G111000 chr2D 100.000 54 0 0 2058 2111 61801150 61801203 1.900000e-17 100.0
8 TraesCS2D01G111000 chr2D 91.667 60 5 0 2052 2111 44058142 44058083 1.920000e-12 84.2
9 TraesCS2D01G111000 chr2B 94.871 2047 99 6 69 2111 96599540 96601584 0.000000e+00 3193.0
10 TraesCS2D01G111000 chr2B 82.484 1216 179 19 818 2008 69129037 69130243 0.000000e+00 1035.0
11 TraesCS2D01G111000 chr2B 82.809 1175 175 16 818 1972 69066695 69065528 0.000000e+00 1026.0
12 TraesCS2D01G111000 chr2B 82.302 1164 176 19 836 1978 69136203 69135049 0.000000e+00 981.0
13 TraesCS2D01G111000 chr2B 80.675 1185 179 20 818 1978 69168378 69167220 0.000000e+00 874.0
14 TraesCS2D01G111000 chr2B 91.221 524 21 10 2166 2686 96601531 96602032 0.000000e+00 689.0
15 TraesCS2D01G111000 chr2B 80.198 505 82 12 819 1322 771979846 771980333 2.200000e-96 363.0
16 TraesCS2D01G111000 chr2B 91.509 106 6 2 2167 2269 69065471 69065366 3.120000e-30 143.0
17 TraesCS2D01G111000 chr2B 88.991 109 9 2 2166 2271 69167170 69167062 6.750000e-27 132.0
18 TraesCS2D01G111000 chr2B 90.323 93 8 1 2166 2257 69134999 69134907 1.460000e-23 121.0
19 TraesCS2D01G111000 chr2B 100.000 54 0 0 2112 2165 96601531 96601584 1.900000e-17 100.0
20 TraesCS2D01G111000 chr2B 95.082 61 3 0 2051 2111 69065479 69065419 2.460000e-16 97.1
21 TraesCS2D01G111000 chr2B 96.226 53 2 0 2113 2165 69065471 69065419 1.480000e-13 87.9
22 TraesCS2D01G111000 chr2A 96.670 871 28 1 1242 2111 62268292 62269162 0.000000e+00 1447.0
23 TraesCS2D01G111000 chr2A 93.632 691 28 7 2166 2856 62269109 62269783 0.000000e+00 1018.0
24 TraesCS2D01G111000 chr2A 82.333 1183 178 19 818 1978 47876640 47875467 0.000000e+00 998.0
25 TraesCS2D01G111000 chr2A 80.000 510 80 12 818 1322 758855832 758856324 1.020000e-94 357.0
26 TraesCS2D01G111000 chr2A 95.139 144 7 0 2856 2999 65696437 65696294 8.360000e-56 228.0
27 TraesCS2D01G111000 chr2A 89.908 109 8 2 2166 2271 47875417 47875309 1.450000e-28 137.0
28 TraesCS2D01G111000 chr2A 94.382 89 5 0 2166 2254 47887626 47887538 1.450000e-28 137.0
29 TraesCS2D01G111000 chr2A 93.333 60 4 0 2052 2111 47875423 47875364 4.120000e-14 89.8
30 TraesCS2D01G111000 chr2A 91.667 60 5 0 2052 2111 47858415 47858474 1.920000e-12 84.2
31 TraesCS2D01G111000 chr6D 95.946 148 6 0 2852 2999 409483054 409482907 1.070000e-59 241.0
32 TraesCS2D01G111000 chr7D 95.890 146 6 0 2854 2999 101554349 101554204 1.390000e-58 237.0
33 TraesCS2D01G111000 chr4D 96.479 142 5 0 2858 2999 15068527 15068386 5.000000e-58 235.0
34 TraesCS2D01G111000 chr4D 94.366 142 8 0 2858 2999 473164146 473164287 5.030000e-53 219.0
35 TraesCS2D01G111000 chr7A 93.919 148 8 1 2852 2999 50113341 50113195 3.890000e-54 222.0
36 TraesCS2D01G111000 chr7A 93.289 149 9 1 2852 2999 553041144 553041292 5.030000e-53 219.0
37 TraesCS2D01G111000 chr5D 93.836 146 9 0 2854 2999 513526992 513527137 1.400000e-53 220.0
38 TraesCS2D01G111000 chr4A 94.366 142 8 0 2858 2999 446954117 446953976 5.030000e-53 219.0


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 TraesCS2D01G111000 chr2D 61798985 61801983 2998 False 1227.800000 5539 100.000000 1 2999 5 chr2D.!!$F3 2998
1 TraesCS2D01G111000 chr2D 44001595 44002852 1257 False 1002.000000 1002 81.450000 724 1978 1 chr2D.!!$F1 1254
2 TraesCS2D01G111000 chr2D 44058083 44059338 1255 True 501.100000 918 86.503500 818 2111 2 chr2D.!!$R1 1293
3 TraesCS2D01G111000 chr2B 96599540 96602032 2492 False 1327.333333 3193 95.364000 69 2686 3 chr2B.!!$F3 2617
4 TraesCS2D01G111000 chr2B 69129037 69130243 1206 False 1035.000000 1035 82.484000 818 2008 1 chr2B.!!$F1 1190
5 TraesCS2D01G111000 chr2B 69134907 69136203 1296 True 551.000000 981 86.312500 836 2257 2 chr2B.!!$R2 1421
6 TraesCS2D01G111000 chr2B 69167062 69168378 1316 True 503.000000 874 84.833000 818 2271 2 chr2B.!!$R3 1453
7 TraesCS2D01G111000 chr2B 69065366 69066695 1329 True 338.500000 1026 91.406500 818 2269 4 chr2B.!!$R1 1451
8 TraesCS2D01G111000 chr2A 62268292 62269783 1491 False 1232.500000 1447 95.151000 1242 2856 2 chr2A.!!$F3 1614
9 TraesCS2D01G111000 chr2A 47875309 47876640 1331 True 408.266667 998 88.524667 818 2271 3 chr2A.!!$R3 1453

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
576 580 0.099968 CACCGAATTGCTCCATGCTG 59.9 55.0 0.0 0.0 43.37 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2328 0.169672 AACGGACAGACGACATACCG 59.83 55.0 0.0 0.0 44.77 4.02 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
18 19 2.850439 CAGCATGTCACAGGGTGAG 58.150 57.895 16.49 0.00 44.64 3.51
19 20 0.322648 CAGCATGTCACAGGGTGAGA 59.677 55.000 16.49 0.00 44.64 3.27
20 21 0.322975 AGCATGTCACAGGGTGAGAC 59.677 55.000 0.00 0.00 43.57 3.36
21 22 1.016130 GCATGTCACAGGGTGAGACG 61.016 60.000 0.00 0.00 43.57 4.18
22 23 0.390340 CATGTCACAGGGTGAGACGG 60.390 60.000 0.00 0.00 43.57 4.79
23 24 2.048127 GTCACAGGGTGAGACGGC 60.048 66.667 0.00 0.00 43.57 5.68
24 25 3.311110 TCACAGGGTGAGACGGCC 61.311 66.667 0.00 0.00 37.67 6.13
25 26 3.625897 CACAGGGTGAGACGGCCA 61.626 66.667 2.24 0.00 35.23 5.36
26 27 2.847234 ACAGGGTGAGACGGCCAA 60.847 61.111 2.24 0.00 0.00 4.52
27 28 2.046892 CAGGGTGAGACGGCCAAG 60.047 66.667 2.24 0.00 0.00 3.61
28 29 3.322466 AGGGTGAGACGGCCAAGG 61.322 66.667 2.24 0.00 0.00 3.61
29 30 3.637273 GGGTGAGACGGCCAAGGT 61.637 66.667 2.24 0.00 0.00 3.50
30 31 2.288025 GGGTGAGACGGCCAAGGTA 61.288 63.158 2.24 0.00 0.00 3.08
31 32 1.079336 GGTGAGACGGCCAAGGTAC 60.079 63.158 2.24 0.00 0.00 3.34
49 50 5.694995 AGGTACTTATCATTTCATGGGTGG 58.305 41.667 0.00 0.00 27.25 4.61
50 51 5.193728 AGGTACTTATCATTTCATGGGTGGT 59.806 40.000 0.00 0.00 27.25 4.16
51 52 6.388689 AGGTACTTATCATTTCATGGGTGGTA 59.611 38.462 0.00 0.00 27.25 3.25
52 53 7.073725 AGGTACTTATCATTTCATGGGTGGTAT 59.926 37.037 0.00 0.00 27.25 2.73
53 54 7.724061 GGTACTTATCATTTCATGGGTGGTATT 59.276 37.037 0.00 0.00 0.00 1.89
54 55 7.587037 ACTTATCATTTCATGGGTGGTATTG 57.413 36.000 0.00 0.00 0.00 1.90
55 56 7.125391 ACTTATCATTTCATGGGTGGTATTGT 58.875 34.615 0.00 0.00 0.00 2.71
56 57 7.619302 ACTTATCATTTCATGGGTGGTATTGTT 59.381 33.333 0.00 0.00 0.00 2.83
57 58 5.657826 TCATTTCATGGGTGGTATTGTTG 57.342 39.130 0.00 0.00 0.00 3.33
58 59 4.465660 TCATTTCATGGGTGGTATTGTTGG 59.534 41.667 0.00 0.00 0.00 3.77
59 60 3.534357 TTCATGGGTGGTATTGTTGGT 57.466 42.857 0.00 0.00 0.00 3.67
60 61 2.801483 TCATGGGTGGTATTGTTGGTG 58.199 47.619 0.00 0.00 0.00 4.17
61 62 1.204467 CATGGGTGGTATTGTTGGTGC 59.796 52.381 0.00 0.00 0.00 5.01
62 63 0.891449 TGGGTGGTATTGTTGGTGCG 60.891 55.000 0.00 0.00 0.00 5.34
63 64 0.891904 GGGTGGTATTGTTGGTGCGT 60.892 55.000 0.00 0.00 0.00 5.24
64 65 0.519961 GGTGGTATTGTTGGTGCGTC 59.480 55.000 0.00 0.00 0.00 5.19
65 66 0.165079 GTGGTATTGTTGGTGCGTCG 59.835 55.000 0.00 0.00 0.00 5.12
66 67 1.133869 GGTATTGTTGGTGCGTCGC 59.866 57.895 11.10 11.10 0.00 5.19
67 68 1.570347 GGTATTGTTGGTGCGTCGCA 61.570 55.000 17.58 17.58 35.60 5.10
99 100 4.718774 AGCCTGGAGTTCATCTATGAAGAA 59.281 41.667 5.64 0.00 46.44 2.52
101 102 5.046529 CCTGGAGTTCATCTATGAAGAACG 58.953 45.833 5.64 0.00 46.44 3.95
102 103 5.011090 TGGAGTTCATCTATGAAGAACGG 57.989 43.478 5.64 0.00 46.44 4.44
105 106 5.520649 GGAGTTCATCTATGAAGAACGGTTC 59.479 44.000 12.91 12.91 46.44 3.62
211 213 2.360483 CTGCTCTTCTCTGAGGCGATTA 59.640 50.000 4.59 0.00 34.82 1.75
221 223 1.835483 GAGGCGATTACATGGCAGCG 61.835 60.000 0.00 0.00 35.53 5.18
253 257 0.603707 CTGCGACCAAAAGAGCCTGA 60.604 55.000 0.00 0.00 0.00 3.86
267 271 9.342308 CAAAAGAGCCTGATATAATGGAAACTA 57.658 33.333 0.00 0.00 0.00 2.24
276 280 7.977818 TGATATAATGGAAACTATGGTGAGCT 58.022 34.615 0.00 0.00 0.00 4.09
277 281 8.097038 TGATATAATGGAAACTATGGTGAGCTC 58.903 37.037 6.82 6.82 0.00 4.09
291 295 3.426695 GGTGAGCTCCGATGTTTTGATTG 60.427 47.826 12.15 0.00 0.00 2.67
325 329 5.068198 GGCTTCAGATTGCTAATTCCATCAA 59.932 40.000 0.00 0.00 0.00 2.57
351 355 0.601558 TGTAGGAGACGAACAGGTGC 59.398 55.000 0.00 0.00 0.00 5.01
355 359 0.318762 GGAGACGAACAGGTGCTCTT 59.681 55.000 0.00 0.00 0.00 2.85
364 368 3.272574 ACAGGTGCTCTTACATGATGG 57.727 47.619 0.00 0.00 36.00 3.51
402 406 2.542907 CCGTGCACAGGTTGGACAC 61.543 63.158 18.64 0.00 46.70 3.67
412 416 0.533951 GGTTGGACACGGTAGGTAGG 59.466 60.000 0.00 0.00 0.00 3.18
432 436 2.311463 GGATACAGAGGTAGCAGCTCA 58.689 52.381 0.00 0.00 44.69 4.26
453 457 0.731417 AGCTTAGCATTGCTCGCTTG 59.269 50.000 22.46 9.57 40.73 4.01
470 474 3.003480 GCTTGTACTCTGGGTGTTGATC 58.997 50.000 0.00 0.00 0.00 2.92
471 475 3.254060 CTTGTACTCTGGGTGTTGATCG 58.746 50.000 0.00 0.00 0.00 3.69
514 518 2.090760 TGCGCTTTAATGCTGGATGAA 58.909 42.857 9.73 0.00 0.00 2.57
575 579 1.660560 GCACCGAATTGCTCCATGCT 61.661 55.000 0.00 0.00 43.37 3.79
576 580 0.099968 CACCGAATTGCTCCATGCTG 59.900 55.000 0.00 0.00 43.37 4.41
591 595 1.289160 TGCTGATGGAGGGTTTAGCT 58.711 50.000 0.00 0.00 32.66 3.32
644 648 1.005289 AGGATGCAGATCTGGGGGT 59.995 57.895 23.89 0.00 0.00 4.95
696 700 1.678728 CCTTGCTGGTTCCTTGCGATA 60.679 52.381 0.00 0.00 0.00 2.92
704 708 1.013596 TTCCTTGCGATATTGTGGCG 58.986 50.000 0.00 0.00 33.75 5.69
736 740 4.125097 CGTAAACGCGGCCACGAC 62.125 66.667 22.04 6.80 44.60 4.34
750 754 0.243907 CACGACGAGGAATGGTCAGT 59.756 55.000 0.00 0.00 32.74 3.41
801 810 8.841300 AGTTTCTCCTGTTTTTCTATTTCTGAC 58.159 33.333 0.00 0.00 0.00 3.51
867 876 1.032794 TGCTCCTTGACGATATCGCT 58.967 50.000 24.59 12.03 44.43 4.93
951 960 0.107703 GGAACTGCACCGATGATCCA 60.108 55.000 0.00 0.00 0.00 3.41
1045 1064 2.470286 GCCGTCGCTTTCTCAACG 59.530 61.111 0.00 0.00 35.01 4.10
1046 1065 2.019951 GCCGTCGCTTTCTCAACGA 61.020 57.895 0.00 0.00 37.31 3.85
1169 1188 1.302033 CTGTGCGCCTCTTCAACCT 60.302 57.895 4.18 0.00 0.00 3.50
1273 1299 1.448119 CTCGGAGCGCCTCATCTACA 61.448 60.000 2.29 0.00 31.08 2.74
1275 1301 1.729470 CGGAGCGCCTCATCTACACT 61.729 60.000 2.29 0.00 31.08 3.55
1328 1360 1.293924 GTGCTCCTGATGATTGACCG 58.706 55.000 0.00 0.00 0.00 4.79
1446 1478 0.747644 TATCGTCGGCGTCAACCCTA 60.748 55.000 10.18 0.00 39.49 3.53
1524 1556 2.743928 GAGCCTCAGTTGGTGCCG 60.744 66.667 0.00 0.00 0.00 5.69
1666 1710 0.103026 TGACGAGCGGAGAATCATGG 59.897 55.000 0.00 0.00 36.25 3.66
2021 2078 1.551430 TGGTACCACCGACATAACAGG 59.449 52.381 11.60 0.00 42.58 4.00
2102 2159 1.207329 CCCTGTACCCTGCAAGAGTAC 59.793 57.143 11.69 11.69 37.47 2.73
2103 2160 1.207329 CCTGTACCCTGCAAGAGTACC 59.793 57.143 14.57 2.52 36.38 3.34
2104 2161 2.180276 CTGTACCCTGCAAGAGTACCT 58.820 52.381 14.57 0.00 36.38 3.08
2105 2162 2.166664 CTGTACCCTGCAAGAGTACCTC 59.833 54.545 14.57 0.00 36.38 3.85
2106 2163 1.134560 GTACCCTGCAAGAGTACCTCG 59.865 57.143 8.65 0.00 35.36 4.63
2107 2164 0.542232 ACCCTGCAAGAGTACCTCGT 60.542 55.000 0.00 0.00 35.36 4.18
2108 2165 0.173708 CCCTGCAAGAGTACCTCGTC 59.826 60.000 0.00 0.00 35.36 4.20
2109 2166 1.178276 CCTGCAAGAGTACCTCGTCT 58.822 55.000 0.00 0.00 35.36 4.18
2110 2167 1.135257 CCTGCAAGAGTACCTCGTCTG 60.135 57.143 0.00 0.00 35.36 3.51
2111 2168 0.888619 TGCAAGAGTACCTCGTCTGG 59.111 55.000 0.00 0.00 35.36 3.86
2112 2169 0.458716 GCAAGAGTACCTCGTCTGGC 60.459 60.000 0.00 0.00 35.36 4.85
2113 2170 1.178276 CAAGAGTACCTCGTCTGGCT 58.822 55.000 0.00 0.00 35.36 4.75
2114 2171 1.135257 CAAGAGTACCTCGTCTGGCTG 60.135 57.143 0.00 0.00 35.36 4.85
2115 2172 0.328592 AGAGTACCTCGTCTGGCTGA 59.671 55.000 0.00 0.00 35.36 4.26
2116 2173 1.174783 GAGTACCTCGTCTGGCTGAA 58.825 55.000 0.00 0.00 0.00 3.02
2117 2174 1.751924 GAGTACCTCGTCTGGCTGAAT 59.248 52.381 0.00 0.00 0.00 2.57
2118 2175 1.751924 AGTACCTCGTCTGGCTGAATC 59.248 52.381 0.00 0.00 0.00 2.52
2119 2176 1.751924 GTACCTCGTCTGGCTGAATCT 59.248 52.381 0.00 0.00 0.00 2.40
2120 2177 2.145397 ACCTCGTCTGGCTGAATCTA 57.855 50.000 0.00 0.00 0.00 1.98
2121 2178 2.028130 ACCTCGTCTGGCTGAATCTAG 58.972 52.381 0.00 0.00 0.00 2.43
2122 2179 2.028130 CCTCGTCTGGCTGAATCTAGT 58.972 52.381 0.00 0.00 0.00 2.57
2123 2180 2.223688 CCTCGTCTGGCTGAATCTAGTG 60.224 54.545 0.00 0.00 0.00 2.74
2124 2181 1.135139 TCGTCTGGCTGAATCTAGTGC 59.865 52.381 0.00 0.00 0.00 4.40
2125 2182 1.804372 CGTCTGGCTGAATCTAGTGCC 60.804 57.143 0.00 0.00 45.10 5.01
2126 2183 1.484240 GTCTGGCTGAATCTAGTGCCT 59.516 52.381 0.00 0.00 45.11 4.75
2127 2184 1.759445 TCTGGCTGAATCTAGTGCCTC 59.241 52.381 0.00 0.00 45.11 4.70
2128 2185 1.761784 CTGGCTGAATCTAGTGCCTCT 59.238 52.381 0.00 0.00 45.11 3.69
2129 2186 2.170187 CTGGCTGAATCTAGTGCCTCTT 59.830 50.000 0.00 0.00 45.11 2.85
2130 2187 2.093288 TGGCTGAATCTAGTGCCTCTTG 60.093 50.000 0.00 0.00 45.11 3.02
2131 2188 1.939255 GCTGAATCTAGTGCCTCTTGC 59.061 52.381 0.00 0.00 41.77 4.01
2132 2189 2.419851 GCTGAATCTAGTGCCTCTTGCT 60.420 50.000 0.00 0.00 42.00 3.91
2133 2190 3.456280 CTGAATCTAGTGCCTCTTGCTC 58.544 50.000 0.00 0.00 42.00 4.26
2134 2191 2.159184 TGAATCTAGTGCCTCTTGCTCG 60.159 50.000 0.00 0.00 42.00 5.03
2135 2192 0.103937 ATCTAGTGCCTCTTGCTCGC 59.896 55.000 0.00 0.00 42.00 5.03
2136 2193 1.520342 CTAGTGCCTCTTGCTCGCC 60.520 63.158 0.00 0.00 42.00 5.54
2137 2194 2.914777 CTAGTGCCTCTTGCTCGCCC 62.915 65.000 0.00 0.00 42.00 6.13
2141 2198 3.710722 CCTCTTGCTCGCCCCTGT 61.711 66.667 0.00 0.00 0.00 4.00
2142 2199 2.359169 CCTCTTGCTCGCCCCTGTA 61.359 63.158 0.00 0.00 0.00 2.74
2143 2200 1.153549 CTCTTGCTCGCCCCTGTAC 60.154 63.158 0.00 0.00 0.00 2.90
2144 2201 2.125106 CTTGCTCGCCCCTGTACC 60.125 66.667 0.00 0.00 0.00 3.34
2145 2202 3.682292 CTTGCTCGCCCCTGTACCC 62.682 68.421 0.00 0.00 0.00 3.69
2146 2203 4.715130 TGCTCGCCCCTGTACCCT 62.715 66.667 0.00 0.00 0.00 4.34
2147 2204 4.162690 GCTCGCCCCTGTACCCTG 62.163 72.222 0.00 0.00 0.00 4.45
2148 2205 4.162690 CTCGCCCCTGTACCCTGC 62.163 72.222 0.00 0.00 0.00 4.85
2150 2207 4.028490 CGCCCCTGTACCCTGCAA 62.028 66.667 0.00 0.00 0.00 4.08
2151 2208 2.044946 GCCCCTGTACCCTGCAAG 60.045 66.667 0.00 0.00 0.00 4.01
2152 2209 2.602676 GCCCCTGTACCCTGCAAGA 61.603 63.158 0.00 0.00 34.07 3.02
2153 2210 1.604378 CCCCTGTACCCTGCAAGAG 59.396 63.158 0.00 0.00 34.07 2.85
2154 2211 1.201429 CCCCTGTACCCTGCAAGAGT 61.201 60.000 0.00 0.00 34.07 3.24
2155 2212 1.568504 CCCTGTACCCTGCAAGAGTA 58.431 55.000 0.00 0.00 34.07 2.59
2156 2213 1.207329 CCCTGTACCCTGCAAGAGTAC 59.793 57.143 11.69 11.69 37.47 2.73
2157 2214 1.207329 CCTGTACCCTGCAAGAGTACC 59.793 57.143 14.57 2.52 36.38 3.34
2158 2215 2.180276 CTGTACCCTGCAAGAGTACCT 58.820 52.381 14.57 0.00 36.38 3.08
2159 2216 2.166664 CTGTACCCTGCAAGAGTACCTC 59.833 54.545 14.57 0.00 36.38 3.85
2160 2217 1.134560 GTACCCTGCAAGAGTACCTCG 59.865 57.143 8.65 0.00 35.36 4.63
2161 2218 0.542232 ACCCTGCAAGAGTACCTCGT 60.542 55.000 0.00 0.00 35.36 4.18
2162 2219 0.173708 CCCTGCAAGAGTACCTCGTC 59.826 60.000 0.00 0.00 35.36 4.20
2163 2220 1.178276 CCTGCAAGAGTACCTCGTCT 58.822 55.000 0.00 0.00 35.36 4.18
2164 2221 1.135257 CCTGCAAGAGTACCTCGTCTG 60.135 57.143 0.00 0.00 35.36 3.51
2165 2222 0.888619 TGCAAGAGTACCTCGTCTGG 59.111 55.000 0.00 0.00 35.36 3.86
2166 2223 0.458716 GCAAGAGTACCTCGTCTGGC 60.459 60.000 0.00 0.00 35.36 4.85
2167 2224 1.178276 CAAGAGTACCTCGTCTGGCT 58.822 55.000 0.00 0.00 35.36 4.75
2168 2225 1.135257 CAAGAGTACCTCGTCTGGCTG 60.135 57.143 0.00 0.00 35.36 4.85
2169 2226 0.328592 AGAGTACCTCGTCTGGCTGA 59.671 55.000 0.00 0.00 35.36 4.26
2170 2227 1.174783 GAGTACCTCGTCTGGCTGAA 58.825 55.000 0.00 0.00 0.00 3.02
2171 2228 1.751924 GAGTACCTCGTCTGGCTGAAT 59.248 52.381 0.00 0.00 0.00 2.57
2172 2229 1.751924 AGTACCTCGTCTGGCTGAATC 59.248 52.381 0.00 0.00 0.00 2.52
2173 2230 1.751924 GTACCTCGTCTGGCTGAATCT 59.248 52.381 0.00 0.00 0.00 2.40
2174 2231 2.145397 ACCTCGTCTGGCTGAATCTA 57.855 50.000 0.00 0.00 0.00 1.98
2175 2232 2.028130 ACCTCGTCTGGCTGAATCTAG 58.972 52.381 0.00 0.00 0.00 2.43
2176 2233 2.028130 CCTCGTCTGGCTGAATCTAGT 58.972 52.381 0.00 0.00 0.00 2.57
2177 2234 2.223688 CCTCGTCTGGCTGAATCTAGTG 60.224 54.545 0.00 0.00 0.00 2.74
2178 2235 1.135139 TCGTCTGGCTGAATCTAGTGC 59.865 52.381 0.00 0.00 0.00 4.40
2179 2236 1.804372 CGTCTGGCTGAATCTAGTGCC 60.804 57.143 0.00 0.00 45.10 5.01
2180 2237 1.484240 GTCTGGCTGAATCTAGTGCCT 59.516 52.381 0.00 0.00 45.11 4.75
2181 2238 1.759445 TCTGGCTGAATCTAGTGCCTC 59.241 52.381 0.00 0.00 45.11 4.70
2182 2239 1.761784 CTGGCTGAATCTAGTGCCTCT 59.238 52.381 0.00 0.00 45.11 3.69
2183 2240 2.170187 CTGGCTGAATCTAGTGCCTCTT 59.830 50.000 0.00 0.00 45.11 2.85
2184 2241 2.093288 TGGCTGAATCTAGTGCCTCTTG 60.093 50.000 0.00 0.00 45.11 3.02
2185 2242 1.939255 GCTGAATCTAGTGCCTCTTGC 59.061 52.381 0.00 0.00 41.77 4.01
2186 2243 2.419851 GCTGAATCTAGTGCCTCTTGCT 60.420 50.000 0.00 0.00 42.00 3.91
2187 2244 3.456280 CTGAATCTAGTGCCTCTTGCTC 58.544 50.000 0.00 0.00 42.00 4.26
2188 2245 2.159184 TGAATCTAGTGCCTCTTGCTCG 60.159 50.000 0.00 0.00 42.00 5.03
2189 2246 0.103937 ATCTAGTGCCTCTTGCTCGC 59.896 55.000 0.00 0.00 42.00 5.03
2190 2247 1.520342 CTAGTGCCTCTTGCTCGCC 60.520 63.158 0.00 0.00 42.00 5.54
2191 2248 2.914777 CTAGTGCCTCTTGCTCGCCC 62.915 65.000 0.00 0.00 42.00 6.13
2195 2252 3.710722 CCTCTTGCTCGCCCCTGT 61.711 66.667 0.00 0.00 0.00 4.00
2196 2253 2.359169 CCTCTTGCTCGCCCCTGTA 61.359 63.158 0.00 0.00 0.00 2.74
2197 2254 1.153549 CTCTTGCTCGCCCCTGTAC 60.154 63.158 0.00 0.00 0.00 2.90
2198 2255 2.125106 CTTGCTCGCCCCTGTACC 60.125 66.667 0.00 0.00 0.00 3.34
2199 2256 3.682292 CTTGCTCGCCCCTGTACCC 62.682 68.421 0.00 0.00 0.00 3.69
2200 2257 4.715130 TGCTCGCCCCTGTACCCT 62.715 66.667 0.00 0.00 0.00 4.34
2201 2258 4.162690 GCTCGCCCCTGTACCCTG 62.163 72.222 0.00 0.00 0.00 4.45
2202 2259 4.162690 CTCGCCCCTGTACCCTGC 62.163 72.222 0.00 0.00 0.00 4.85
2204 2261 4.028490 CGCCCCTGTACCCTGCAA 62.028 66.667 0.00 0.00 0.00 4.08
2205 2262 2.044946 GCCCCTGTACCCTGCAAG 60.045 66.667 0.00 0.00 0.00 4.01
2206 2263 2.602676 GCCCCTGTACCCTGCAAGA 61.603 63.158 0.00 0.00 34.07 3.02
2207 2264 1.604378 CCCCTGTACCCTGCAAGAG 59.396 63.158 0.00 0.00 34.07 2.85
2208 2265 1.201429 CCCCTGTACCCTGCAAGAGT 61.201 60.000 0.00 0.00 34.07 3.24
2209 2266 1.568504 CCCTGTACCCTGCAAGAGTA 58.431 55.000 0.00 0.00 34.07 2.59
2271 2328 6.183360 GGACTAATCAAATCCTCAGCAAGTTC 60.183 42.308 0.00 0.00 0.00 3.01
2319 2376 7.502226 TGGATTGTGTGTTCTTGAGAAGTTTAT 59.498 33.333 0.00 0.00 34.27 1.40
2320 2377 8.352942 GGATTGTGTGTTCTTGAGAAGTTTATT 58.647 33.333 0.00 0.00 34.27 1.40
2321 2378 9.736023 GATTGTGTGTTCTTGAGAAGTTTATTT 57.264 29.630 0.00 0.00 34.27 1.40
2377 2438 3.005791 GGTTCATTTCTCCCTTGTGTTGG 59.994 47.826 0.00 0.00 0.00 3.77
2407 2468 8.496707 AAAAATTATGAAAGATGGGCAATGAC 57.503 30.769 0.00 0.00 0.00 3.06
2426 2487 8.446273 GCAATGACGTCTAGAATTATGCAATAT 58.554 33.333 17.92 0.00 0.00 1.28
2490 2551 4.287766 ACTTGCCTCGGTTAATTTCTCT 57.712 40.909 0.00 0.00 0.00 3.10
2502 2563 3.885484 AATTTCTCTCGTGTGTTGCTG 57.115 42.857 0.00 0.00 0.00 4.41
2597 2658 9.150348 CCCTCCAAATTTTAAATGATGTGTTAC 57.850 33.333 0.00 0.00 0.00 2.50
2600 2662 9.703892 TCCAAATTTTAAATGATGTGTTACTGG 57.296 29.630 0.00 0.00 0.00 4.00
2733 2797 3.448301 TGAATTCCATGCCCATCTTTGTC 59.552 43.478 2.27 0.00 0.00 3.18
2742 2806 2.162408 GCCCATCTTTGTCTGTAAGCAC 59.838 50.000 0.00 0.00 0.00 4.40
2789 2853 2.346099 TGCGTGCAATCTTTTTAGCC 57.654 45.000 0.00 0.00 0.00 3.93
2808 2872 2.429930 CTCGGGGGCAACTGTTGA 59.570 61.111 23.81 1.08 0.00 3.18
2836 2900 5.104360 AGGCATGAACATGTAGGAACATACT 60.104 40.000 14.82 0.94 44.70 2.12
2837 2901 5.237344 GGCATGAACATGTAGGAACATACTC 59.763 44.000 14.82 0.00 44.70 2.59
2838 2902 5.817296 GCATGAACATGTAGGAACATACTCA 59.183 40.000 14.82 0.00 44.70 3.41
2839 2903 6.238211 GCATGAACATGTAGGAACATACTCAC 60.238 42.308 14.82 0.00 44.70 3.51
2856 2920 9.841295 ACATACTCACAAAACTTAAGAAACCTA 57.159 29.630 10.09 0.00 0.00 3.08
2860 2924 9.110502 ACTCACAAAACTTAAGAAACCTAAGAG 57.889 33.333 10.09 8.77 0.00 2.85
2861 2925 7.927048 TCACAAAACTTAAGAAACCTAAGAGC 58.073 34.615 10.09 0.00 0.00 4.09
2862 2926 7.554835 TCACAAAACTTAAGAAACCTAAGAGCA 59.445 33.333 10.09 0.00 0.00 4.26
2863 2927 8.352942 CACAAAACTTAAGAAACCTAAGAGCAT 58.647 33.333 10.09 0.00 0.00 3.79
2864 2928 8.568794 ACAAAACTTAAGAAACCTAAGAGCATC 58.431 33.333 10.09 0.00 0.00 3.91
2875 2939 3.805267 GAGCATCTCCAACAGGCG 58.195 61.111 0.00 0.00 0.00 5.52
2876 2940 2.437359 AGCATCTCCAACAGGCGC 60.437 61.111 0.00 0.00 0.00 6.53
2877 2941 3.869272 GCATCTCCAACAGGCGCG 61.869 66.667 0.00 0.00 0.00 6.86
2878 2942 3.197790 CATCTCCAACAGGCGCGG 61.198 66.667 8.83 0.00 0.00 6.46
2883 2947 4.277593 CCAACAGGCGCGGCAAAA 62.278 61.111 34.94 0.00 0.00 2.44
2884 2948 2.730604 CAACAGGCGCGGCAAAAG 60.731 61.111 34.94 22.03 0.00 2.27
2885 2949 3.977244 AACAGGCGCGGCAAAAGG 61.977 61.111 34.94 19.28 0.00 3.11
2905 2969 3.045492 CGCCCGCGTGGTAAAGTT 61.045 61.111 15.14 0.00 36.04 2.66
2906 2970 2.609759 CGCCCGCGTGGTAAAGTTT 61.610 57.895 15.14 0.00 36.04 2.66
2907 2971 1.081708 GCCCGCGTGGTAAAGTTTG 60.082 57.895 15.14 0.00 36.04 2.93
2908 2972 1.577421 CCCGCGTGGTAAAGTTTGG 59.423 57.895 15.14 0.00 0.00 3.28
2909 2973 1.167781 CCCGCGTGGTAAAGTTTGGT 61.168 55.000 15.14 0.00 0.00 3.67
2910 2974 0.664224 CCGCGTGGTAAAGTTTGGTT 59.336 50.000 6.91 0.00 0.00 3.67
2911 2975 1.065851 CCGCGTGGTAAAGTTTGGTTT 59.934 47.619 6.91 0.00 0.00 3.27
2912 2976 2.479901 CCGCGTGGTAAAGTTTGGTTTT 60.480 45.455 6.91 0.00 0.00 2.43
2913 2977 3.243002 CCGCGTGGTAAAGTTTGGTTTTA 60.243 43.478 6.91 0.00 0.00 1.52
2914 2978 3.969981 CGCGTGGTAAAGTTTGGTTTTAG 59.030 43.478 0.00 0.00 0.00 1.85
2915 2979 3.732219 GCGTGGTAAAGTTTGGTTTTAGC 59.268 43.478 0.00 1.26 38.39 3.09
2916 2980 3.969981 CGTGGTAAAGTTTGGTTTTAGCG 59.030 43.478 0.00 0.00 39.89 4.26
2917 2981 3.732219 GTGGTAAAGTTTGGTTTTAGCGC 59.268 43.478 0.00 0.00 39.89 5.92
2918 2982 2.975193 GGTAAAGTTTGGTTTTAGCGCG 59.025 45.455 0.00 0.00 31.42 6.86
2919 2983 1.483316 AAAGTTTGGTTTTAGCGCGC 58.517 45.000 26.66 26.66 0.00 6.86
2920 2984 0.659123 AAGTTTGGTTTTAGCGCGCG 60.659 50.000 28.44 28.44 0.00 6.86
2921 2985 2.427740 TTTGGTTTTAGCGCGCGC 60.428 55.556 45.10 45.10 42.33 6.86
2922 2986 3.882835 TTTGGTTTTAGCGCGCGCC 62.883 57.895 46.98 32.13 43.17 6.53
2959 3023 3.315949 AGCGGTGGCGGGAACTTA 61.316 61.111 0.00 0.00 46.35 2.24
2960 3024 3.122971 GCGGTGGCGGGAACTTAC 61.123 66.667 0.00 0.00 0.00 2.34
2961 3025 2.435410 CGGTGGCGGGAACTTACC 60.435 66.667 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.322648 TCTCACCCTGTGACATGCTG 59.677 55.000 0.00 0.00 37.67 4.41
1 2 0.322975 GTCTCACCCTGTGACATGCT 59.677 55.000 0.00 0.00 39.78 3.79
2 3 1.016130 CGTCTCACCCTGTGACATGC 61.016 60.000 0.00 0.00 39.94 4.06
3 4 0.390340 CCGTCTCACCCTGTGACATG 60.390 60.000 0.00 0.00 39.94 3.21
4 5 1.975327 CCGTCTCACCCTGTGACAT 59.025 57.895 5.55 0.00 39.94 3.06
5 6 2.867855 GCCGTCTCACCCTGTGACA 61.868 63.158 5.55 0.00 39.94 3.58
6 7 2.048127 GCCGTCTCACCCTGTGAC 60.048 66.667 0.00 0.00 37.67 3.67
7 8 3.311110 GGCCGTCTCACCCTGTGA 61.311 66.667 0.00 0.00 40.50 3.58
8 9 3.177194 TTGGCCGTCTCACCCTGTG 62.177 63.158 0.00 0.00 34.45 3.66
9 10 2.847234 TTGGCCGTCTCACCCTGT 60.847 61.111 0.00 0.00 0.00 4.00
10 11 2.046892 CTTGGCCGTCTCACCCTG 60.047 66.667 0.00 0.00 0.00 4.45
11 12 2.741878 TACCTTGGCCGTCTCACCCT 62.742 60.000 0.00 0.00 0.00 4.34
12 13 2.288025 TACCTTGGCCGTCTCACCC 61.288 63.158 0.00 0.00 0.00 4.61
13 14 1.079336 GTACCTTGGCCGTCTCACC 60.079 63.158 0.00 0.00 0.00 4.02
14 15 0.320697 AAGTACCTTGGCCGTCTCAC 59.679 55.000 0.00 0.00 0.00 3.51
15 16 1.927487 TAAGTACCTTGGCCGTCTCA 58.073 50.000 0.00 0.00 0.00 3.27
16 17 2.429610 TGATAAGTACCTTGGCCGTCTC 59.570 50.000 0.00 0.00 0.00 3.36
17 18 2.463752 TGATAAGTACCTTGGCCGTCT 58.536 47.619 0.00 0.00 0.00 4.18
18 19 2.973694 TGATAAGTACCTTGGCCGTC 57.026 50.000 0.00 0.00 0.00 4.79
19 20 3.926058 AATGATAAGTACCTTGGCCGT 57.074 42.857 0.00 0.00 0.00 5.68
20 21 4.196193 TGAAATGATAAGTACCTTGGCCG 58.804 43.478 0.00 0.00 0.00 6.13
36 37 4.222588 ACCAACAATACCACCCATGAAATG 59.777 41.667 0.00 0.00 46.21 2.32
37 38 4.222588 CACCAACAATACCACCCATGAAAT 59.777 41.667 0.00 0.00 0.00 2.17
38 39 3.576118 CACCAACAATACCACCCATGAAA 59.424 43.478 0.00 0.00 0.00 2.69
39 40 3.161067 CACCAACAATACCACCCATGAA 58.839 45.455 0.00 0.00 0.00 2.57
40 41 2.801483 CACCAACAATACCACCCATGA 58.199 47.619 0.00 0.00 0.00 3.07
41 42 1.204467 GCACCAACAATACCACCCATG 59.796 52.381 0.00 0.00 0.00 3.66
42 43 1.555967 GCACCAACAATACCACCCAT 58.444 50.000 0.00 0.00 0.00 4.00
43 44 0.891449 CGCACCAACAATACCACCCA 60.891 55.000 0.00 0.00 0.00 4.51
44 45 0.891904 ACGCACCAACAATACCACCC 60.892 55.000 0.00 0.00 0.00 4.61
45 46 0.519961 GACGCACCAACAATACCACC 59.480 55.000 0.00 0.00 0.00 4.61
46 47 0.165079 CGACGCACCAACAATACCAC 59.835 55.000 0.00 0.00 0.00 4.16
47 48 1.570347 GCGACGCACCAACAATACCA 61.570 55.000 16.42 0.00 0.00 3.25
48 49 1.133869 GCGACGCACCAACAATACC 59.866 57.895 16.42 0.00 0.00 2.73
49 50 0.236187 TTGCGACGCACCAACAATAC 59.764 50.000 24.42 0.00 38.71 1.89
50 51 1.135831 CATTGCGACGCACCAACAATA 60.136 47.619 24.42 5.40 38.71 1.90
51 52 0.387112 CATTGCGACGCACCAACAAT 60.387 50.000 24.42 9.49 38.71 2.71
52 53 1.009108 CATTGCGACGCACCAACAA 60.009 52.632 24.42 7.12 38.71 2.83
53 54 2.636462 CATTGCGACGCACCAACA 59.364 55.556 24.42 7.99 38.71 3.33
54 55 2.800746 GCATTGCGACGCACCAAC 60.801 61.111 24.42 8.81 38.71 3.77
55 56 2.977456 AGCATTGCGACGCACCAA 60.977 55.556 24.42 8.87 38.71 3.67
56 57 3.725459 CAGCATTGCGACGCACCA 61.725 61.111 24.42 9.74 38.71 4.17
66 67 0.107312 ACTCCAGGCTAGCAGCATTG 60.107 55.000 18.24 6.28 44.75 2.82
67 68 0.622665 AACTCCAGGCTAGCAGCATT 59.377 50.000 18.24 0.00 44.75 3.56
99 100 0.670546 CATCACCAGAAGCGAACCGT 60.671 55.000 0.00 0.00 0.00 4.83
101 102 1.648467 GCCATCACCAGAAGCGAACC 61.648 60.000 0.00 0.00 0.00 3.62
102 103 1.796796 GCCATCACCAGAAGCGAAC 59.203 57.895 0.00 0.00 0.00 3.95
105 106 3.197790 CCGCCATCACCAGAAGCG 61.198 66.667 0.00 0.00 45.04 4.68
253 257 7.398024 GGAGCTCACCATAGTTTCCATTATAT 58.602 38.462 17.19 0.00 0.00 0.86
267 271 2.086869 CAAAACATCGGAGCTCACCAT 58.913 47.619 17.19 0.42 0.00 3.55
276 280 6.317642 CACCCTAATACAATCAAAACATCGGA 59.682 38.462 0.00 0.00 0.00 4.55
277 281 6.459573 CCACCCTAATACAATCAAAACATCGG 60.460 42.308 0.00 0.00 0.00 4.18
291 295 3.565902 GCAATCTGAAGCCACCCTAATAC 59.434 47.826 0.00 0.00 0.00 1.89
325 329 4.369182 CTGTTCGTCTCCTACAAAGTTGT 58.631 43.478 1.75 1.75 44.86 3.32
351 355 5.757320 GTCTTGGATCACCATCATGTAAGAG 59.243 44.000 0.00 0.00 46.34 2.85
355 359 5.130809 TCATGTCTTGGATCACCATCATGTA 59.869 40.000 18.39 10.15 46.34 2.29
364 368 3.372206 CGGTTCTTCATGTCTTGGATCAC 59.628 47.826 0.00 0.00 0.00 3.06
402 406 2.107901 ACCTCTGTATCCCTACCTACCG 59.892 54.545 0.00 0.00 0.00 4.02
412 416 2.035321 GTGAGCTGCTACCTCTGTATCC 59.965 54.545 0.15 0.00 0.00 2.59
432 436 0.392193 AGCGAGCAATGCTAAGCTGT 60.392 50.000 28.24 12.27 45.75 4.40
453 457 1.641577 GCGATCAACACCCAGAGTAC 58.358 55.000 0.00 0.00 0.00 2.73
496 500 5.065218 AGTTACTTCATCCAGCATTAAAGCG 59.935 40.000 0.00 0.00 40.15 4.68
536 540 9.391006 TCGGTGCCTATATATATTTTCCATTTC 57.609 33.333 0.00 0.00 0.00 2.17
575 579 0.255890 GGCAGCTAAACCCTCCATCA 59.744 55.000 0.00 0.00 0.00 3.07
576 580 0.815615 CGGCAGCTAAACCCTCCATC 60.816 60.000 0.00 0.00 0.00 3.51
591 595 3.845259 GGATGACGGGTAGCGGCA 61.845 66.667 1.45 0.00 0.00 5.69
597 601 0.752658 CTGATGCTGGATGACGGGTA 59.247 55.000 0.00 0.00 0.00 3.69
600 604 0.873312 CGACTGATGCTGGATGACGG 60.873 60.000 0.00 0.00 0.00 4.79
602 606 0.461548 TCCGACTGATGCTGGATGAC 59.538 55.000 0.00 0.00 0.00 3.06
644 648 1.742880 GCTTGCTCATGCGACCTGA 60.743 57.895 0.00 0.00 43.34 3.86
696 700 3.713902 GGATGATCTCCGCCACAAT 57.286 52.632 0.00 0.00 33.29 2.71
704 708 3.001330 CGTTTACGCAAAGGATGATCTCC 59.999 47.826 0.00 0.00 45.33 3.71
720 724 4.125097 CGTCGTGGCCGCGTTTAC 62.125 66.667 35.52 25.57 0.00 2.01
736 740 5.376854 AATTTTGAACTGACCATTCCTCG 57.623 39.130 0.00 0.00 0.00 4.63
750 754 4.384868 GGATAGAGGACGGGGAATTTTGAA 60.385 45.833 0.00 0.00 0.00 2.69
801 810 0.813610 TGCCGGCACAAGGATAATCG 60.814 55.000 29.03 0.00 0.00 3.34
867 876 1.030488 CGTAGAGGAGAAGCCGACCA 61.030 60.000 0.00 0.00 43.43 4.02
990 1009 1.153289 GGACAGCATGATCCAGCGT 60.153 57.895 0.00 0.00 39.69 5.07
1169 1188 2.853542 TGAAGGCCCTGGTGAGCA 60.854 61.111 0.00 0.00 0.00 4.26
1209 1228 3.506096 TACGCTCTGCCGAGGTCG 61.506 66.667 7.30 5.55 37.75 4.79
1221 1240 0.108804 CCGTCCAGACAATGTACGCT 60.109 55.000 1.29 0.00 32.43 5.07
1308 1334 1.405933 CGGTCAATCATCAGGAGCACA 60.406 52.381 0.00 0.00 0.00 4.57
1446 1478 0.321653 CAAAGTAGAAGCGCCCCTGT 60.322 55.000 2.29 0.00 0.00 4.00
1524 1556 0.535335 TGGGCTGGTTCACGACTATC 59.465 55.000 0.00 0.00 0.00 2.08
1691 1735 1.352352 ACCTGTTCTCCACCCTGATTG 59.648 52.381 0.00 0.00 0.00 2.67
1692 1736 1.747444 ACCTGTTCTCCACCCTGATT 58.253 50.000 0.00 0.00 0.00 2.57
1802 1856 3.818121 CTCCCCGACAAACACCGCA 62.818 63.158 0.00 0.00 0.00 5.69
2021 2078 4.217118 TCAAGAAAAAGATTCAGCTCTGGC 59.783 41.667 0.00 0.00 39.06 4.85
2102 2159 2.028130 ACTAGATTCAGCCAGACGAGG 58.972 52.381 0.00 0.00 0.00 4.63
2103 2160 2.797792 GCACTAGATTCAGCCAGACGAG 60.798 54.545 0.00 0.00 0.00 4.18
2104 2161 1.135139 GCACTAGATTCAGCCAGACGA 59.865 52.381 0.00 0.00 0.00 4.20
2105 2162 1.565305 GCACTAGATTCAGCCAGACG 58.435 55.000 0.00 0.00 0.00 4.18
2106 2163 1.946745 GGCACTAGATTCAGCCAGAC 58.053 55.000 0.00 0.00 46.26 3.51
2111 2168 1.939255 GCAAGAGGCACTAGATTCAGC 59.061 52.381 0.00 0.00 41.55 4.26
2124 2181 2.359169 TACAGGGGCGAGCAAGAGG 61.359 63.158 0.00 0.00 0.00 3.69
2125 2182 1.153549 GTACAGGGGCGAGCAAGAG 60.154 63.158 0.00 0.00 0.00 2.85
2126 2183 2.656069 GGTACAGGGGCGAGCAAGA 61.656 63.158 0.00 0.00 0.00 3.02
2127 2184 2.125106 GGTACAGGGGCGAGCAAG 60.125 66.667 0.00 0.00 0.00 4.01
2128 2185 3.712907 GGGTACAGGGGCGAGCAA 61.713 66.667 0.00 0.00 0.00 3.91
2129 2186 4.715130 AGGGTACAGGGGCGAGCA 62.715 66.667 0.00 0.00 0.00 4.26
2130 2187 4.162690 CAGGGTACAGGGGCGAGC 62.163 72.222 0.00 0.00 0.00 5.03
2131 2188 4.162690 GCAGGGTACAGGGGCGAG 62.163 72.222 0.00 0.00 0.00 5.03
2133 2190 3.976701 CTTGCAGGGTACAGGGGCG 62.977 68.421 0.00 0.00 0.00 6.13
2134 2191 2.044946 CTTGCAGGGTACAGGGGC 60.045 66.667 0.00 0.00 0.00 5.80
2135 2192 1.201429 ACTCTTGCAGGGTACAGGGG 61.201 60.000 0.00 0.00 0.00 4.79
2136 2193 1.207329 GTACTCTTGCAGGGTACAGGG 59.793 57.143 16.67 1.02 36.71 4.45
2137 2194 1.207329 GGTACTCTTGCAGGGTACAGG 59.793 57.143 20.67 0.27 37.95 4.00
2138 2195 2.180276 AGGTACTCTTGCAGGGTACAG 58.820 52.381 20.67 5.06 37.95 2.74
2139 2196 2.320681 AGGTACTCTTGCAGGGTACA 57.679 50.000 20.67 0.00 37.95 2.90
2153 2210 1.751924 AGATTCAGCCAGACGAGGTAC 59.248 52.381 0.00 0.00 0.00 3.34
2154 2211 2.145397 AGATTCAGCCAGACGAGGTA 57.855 50.000 0.00 0.00 0.00 3.08
2155 2212 2.028130 CTAGATTCAGCCAGACGAGGT 58.972 52.381 0.00 0.00 0.00 3.85
2156 2213 2.028130 ACTAGATTCAGCCAGACGAGG 58.972 52.381 0.00 0.00 0.00 4.63
2157 2214 2.797792 GCACTAGATTCAGCCAGACGAG 60.798 54.545 0.00 0.00 0.00 4.18
2158 2215 1.135139 GCACTAGATTCAGCCAGACGA 59.865 52.381 0.00 0.00 0.00 4.20
2159 2216 1.565305 GCACTAGATTCAGCCAGACG 58.435 55.000 0.00 0.00 0.00 4.18
2160 2217 1.946745 GGCACTAGATTCAGCCAGAC 58.053 55.000 0.00 0.00 46.26 3.51
2165 2222 1.939255 GCAAGAGGCACTAGATTCAGC 59.061 52.381 0.00 0.00 41.55 4.26
2178 2235 2.359169 TACAGGGGCGAGCAAGAGG 61.359 63.158 0.00 0.00 0.00 3.69
2179 2236 1.153549 GTACAGGGGCGAGCAAGAG 60.154 63.158 0.00 0.00 0.00 2.85
2180 2237 2.656069 GGTACAGGGGCGAGCAAGA 61.656 63.158 0.00 0.00 0.00 3.02
2181 2238 2.125106 GGTACAGGGGCGAGCAAG 60.125 66.667 0.00 0.00 0.00 4.01
2182 2239 3.712907 GGGTACAGGGGCGAGCAA 61.713 66.667 0.00 0.00 0.00 3.91
2183 2240 4.715130 AGGGTACAGGGGCGAGCA 62.715 66.667 0.00 0.00 0.00 4.26
2184 2241 4.162690 CAGGGTACAGGGGCGAGC 62.163 72.222 0.00 0.00 0.00 5.03
2185 2242 4.162690 GCAGGGTACAGGGGCGAG 62.163 72.222 0.00 0.00 0.00 5.03
2187 2244 3.976701 CTTGCAGGGTACAGGGGCG 62.977 68.421 0.00 0.00 0.00 6.13
2188 2245 2.044946 CTTGCAGGGTACAGGGGC 60.045 66.667 0.00 0.00 0.00 5.80
2189 2246 1.201429 ACTCTTGCAGGGTACAGGGG 61.201 60.000 0.00 0.00 0.00 4.79
2190 2247 1.207329 GTACTCTTGCAGGGTACAGGG 59.793 57.143 16.67 1.02 36.71 4.45
2191 2248 1.207329 GGTACTCTTGCAGGGTACAGG 59.793 57.143 20.67 0.27 37.95 4.00
2192 2249 2.180276 AGGTACTCTTGCAGGGTACAG 58.820 52.381 20.67 5.06 37.95 2.74
2193 2250 2.320681 AGGTACTCTTGCAGGGTACA 57.679 50.000 20.67 0.00 37.95 2.90
2207 2264 1.372499 TGCGCAACAGACGAGGTAC 60.372 57.895 8.16 0.00 0.00 3.34
2208 2265 3.044280 TGCGCAACAGACGAGGTA 58.956 55.556 8.16 0.00 0.00 3.08
2271 2328 0.169672 AACGGACAGACGACATACCG 59.830 55.000 0.00 0.00 44.77 4.02
2325 2382 9.770503 GAGCTATAGCATTGAACATAATTGATG 57.229 33.333 26.07 0.00 45.16 3.07
2326 2383 8.954350 GGAGCTATAGCATTGAACATAATTGAT 58.046 33.333 26.07 0.00 45.16 2.57
2327 2384 8.159447 AGGAGCTATAGCATTGAACATAATTGA 58.841 33.333 26.07 0.00 45.16 2.57
2328 2385 8.332996 AGGAGCTATAGCATTGAACATAATTG 57.667 34.615 26.07 0.00 45.16 2.32
2329 2386 7.332926 CGAGGAGCTATAGCATTGAACATAATT 59.667 37.037 26.07 0.58 45.16 1.40
2330 2387 6.815641 CGAGGAGCTATAGCATTGAACATAAT 59.184 38.462 26.07 0.80 45.16 1.28
2331 2388 6.159293 CGAGGAGCTATAGCATTGAACATAA 58.841 40.000 26.07 0.00 45.16 1.90
2332 2389 5.336770 CCGAGGAGCTATAGCATTGAACATA 60.337 44.000 26.07 0.00 45.16 2.29
2333 2390 4.562347 CCGAGGAGCTATAGCATTGAACAT 60.562 45.833 26.07 2.90 45.16 2.71
2334 2391 3.243873 CCGAGGAGCTATAGCATTGAACA 60.244 47.826 26.07 0.00 45.16 3.18
2335 2392 3.243907 ACCGAGGAGCTATAGCATTGAAC 60.244 47.826 26.07 11.03 45.16 3.18
2336 2393 2.965831 ACCGAGGAGCTATAGCATTGAA 59.034 45.455 26.07 0.00 45.16 2.69
2407 2468 8.982685 ACAACTGATATTGCATAATTCTAGACG 58.017 33.333 0.00 0.00 32.47 4.18
2426 2487 6.482308 GCTTGAACTTTAGAGGTAACAACTGA 59.518 38.462 0.00 0.00 41.41 3.41
2490 2551 0.746204 TTTCCTGCAGCAACACACGA 60.746 50.000 8.66 0.00 0.00 4.35
2502 2563 6.506500 TTCTCATCTTTCAGAATTTCCTGC 57.493 37.500 0.00 0.00 34.28 4.85
2597 2658 7.782897 TCCTCAGAACCATATAGTATTCCAG 57.217 40.000 0.00 0.00 0.00 3.86
2653 2715 3.780294 TGGTTCCTGCTGTATGGATTAGT 59.220 43.478 0.00 0.00 31.76 2.24
2715 2779 2.225091 ACAGACAAAGATGGGCATGGAA 60.225 45.455 0.00 0.00 0.00 3.53
2742 2806 4.860907 GCTCTTTAGTCATTGCACAATTGG 59.139 41.667 10.83 0.00 0.00 3.16
2808 2872 2.840038 TCCTACATGTTCATGCCTCACT 59.160 45.455 2.30 0.00 0.00 3.41
2836 2900 7.554835 TGCTCTTAGGTTTCTTAAGTTTTGTGA 59.445 33.333 1.63 0.00 0.00 3.58
2837 2901 7.703328 TGCTCTTAGGTTTCTTAAGTTTTGTG 58.297 34.615 1.63 0.00 0.00 3.33
2838 2902 7.875327 TGCTCTTAGGTTTCTTAAGTTTTGT 57.125 32.000 1.63 0.00 0.00 2.83
2839 2903 8.787852 AGATGCTCTTAGGTTTCTTAAGTTTTG 58.212 33.333 1.63 0.00 0.00 2.44
2856 2920 0.392193 CGCCTGTTGGAGATGCTCTT 60.392 55.000 0.00 0.00 34.95 2.85
2857 2921 1.220206 CGCCTGTTGGAGATGCTCT 59.780 57.895 0.00 0.00 34.95 4.09
2858 2922 2.467826 GCGCCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 34.95 4.26
2859 2923 2.437359 GCGCCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 34.95 3.79
2860 2924 3.869272 CGCGCCTGTTGGAGATGC 61.869 66.667 0.00 0.00 34.95 3.91
2861 2925 3.197790 CCGCGCCTGTTGGAGATG 61.198 66.667 0.00 0.00 34.95 2.90
2866 2930 4.277593 TTTTGCCGCGCCTGTTGG 62.278 61.111 0.00 0.00 0.00 3.77
2867 2931 2.730604 CTTTTGCCGCGCCTGTTG 60.731 61.111 0.00 0.00 0.00 3.33
2868 2932 3.977244 CCTTTTGCCGCGCCTGTT 61.977 61.111 0.00 0.00 0.00 3.16
2888 2952 2.609759 AAACTTTACCACGCGGGCG 61.610 57.895 12.47 12.04 42.05 6.13
2889 2953 1.081708 CAAACTTTACCACGCGGGC 60.082 57.895 12.47 0.00 42.05 6.13
2890 2954 1.167781 ACCAAACTTTACCACGCGGG 61.168 55.000 12.47 6.05 44.81 6.13
2891 2955 0.664224 AACCAAACTTTACCACGCGG 59.336 50.000 12.47 0.00 38.77 6.46
2892 2956 2.478547 AAACCAAACTTTACCACGCG 57.521 45.000 3.53 3.53 0.00 6.01
2893 2957 3.732219 GCTAAAACCAAACTTTACCACGC 59.268 43.478 0.00 0.00 0.00 5.34
2894 2958 3.969981 CGCTAAAACCAAACTTTACCACG 59.030 43.478 0.00 0.00 0.00 4.94
2895 2959 3.732219 GCGCTAAAACCAAACTTTACCAC 59.268 43.478 0.00 0.00 0.00 4.16
2896 2960 3.548415 CGCGCTAAAACCAAACTTTACCA 60.548 43.478 5.56 0.00 0.00 3.25
2897 2961 2.975193 CGCGCTAAAACCAAACTTTACC 59.025 45.455 5.56 0.00 0.00 2.85
2898 2962 2.402707 GCGCGCTAAAACCAAACTTTAC 59.597 45.455 26.67 0.00 0.00 2.01
2899 2963 2.652795 GCGCGCTAAAACCAAACTTTA 58.347 42.857 26.67 0.00 0.00 1.85
2900 2964 1.483316 GCGCGCTAAAACCAAACTTT 58.517 45.000 26.67 0.00 0.00 2.66
2901 2965 0.659123 CGCGCGCTAAAACCAAACTT 60.659 50.000 30.48 0.00 0.00 2.66
2902 2966 1.082366 CGCGCGCTAAAACCAAACT 60.082 52.632 30.48 0.00 0.00 2.66
2903 2967 2.703230 GCGCGCGCTAAAACCAAAC 61.703 57.895 44.38 13.88 38.26 2.93
2904 2968 2.427740 GCGCGCGCTAAAACCAAA 60.428 55.556 44.38 0.00 38.26 3.28
2941 3005 3.599285 TAAGTTCCCGCCACCGCTG 62.599 63.158 0.00 0.00 0.00 5.18
2942 3006 3.315949 TAAGTTCCCGCCACCGCT 61.316 61.111 0.00 0.00 0.00 5.52
2943 3007 3.122971 GTAAGTTCCCGCCACCGC 61.123 66.667 0.00 0.00 0.00 5.68
2944 3008 2.435410 GGTAAGTTCCCGCCACCG 60.435 66.667 0.00 0.00 0.00 4.94
2945 3009 2.435410 CGGTAAGTTCCCGCCACC 60.435 66.667 0.00 0.00 38.85 4.61


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

AutoCloner maintained by Alex Coulton.