Multiple sequence alignment - TraesCS3D01G449100

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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 TraesCS3D01G449100 chr3D 100.000 3010 0 0 1 3010 557653575 557650566 0.000000e+00 5559.0
1 TraesCS3D01G449100 chr3D 95.408 392 18 0 986 1377 557699876 557699485 2.550000e-175 625.0
2 TraesCS3D01G449100 chr3D 87.919 298 36 0 1717 2014 557711771 557712068 4.770000e-93 351.0
3 TraesCS3D01G449100 chr3D 87.296 307 38 1 1719 2025 557699177 557698872 1.720000e-92 350.0
4 TraesCS3D01G449100 chr3B 91.874 1772 94 31 369 2121 739952090 739950350 0.000000e+00 2429.0
5 TraesCS3D01G449100 chr3B 91.575 1092 50 19 375 1447 739926756 739925688 0.000000e+00 1469.0
6 TraesCS3D01G449100 chr3B 87.911 761 68 13 1439 2184 739923286 739922535 0.000000e+00 874.0
7 TraesCS3D01G449100 chr3B 89.189 518 32 8 1612 2125 739948456 739947959 2.550000e-175 625.0
8 TraesCS3D01G449100 chr3B 94.987 379 19 0 986 1364 739957745 739957367 2.000000e-166 595.0
9 TraesCS3D01G449100 chr3B 94.057 387 23 0 988 1374 739932967 739932581 3.340000e-164 588.0
10 TraesCS3D01G449100 chr3B 93.434 396 23 1 988 1383 739989298 739989690 4.320000e-163 584.0
11 TraesCS3D01G449100 chr3B 87.375 301 32 2 1717 2014 739989971 739990268 1.030000e-89 340.0
12 TraesCS3D01G449100 chr3B 86.645 307 40 1 1719 2025 739932254 739931949 3.720000e-89 339.0
13 TraesCS3D01G449100 chr3B 88.129 278 33 0 85 362 739952479 739952202 6.220000e-87 331.0
14 TraesCS3D01G449100 chr3B 88.476 269 31 0 1731 1999 739957238 739956970 2.890000e-85 326.0
15 TraesCS3D01G449100 chr3B 88.636 220 25 0 143 362 739927102 739926883 4.950000e-68 268.0
16 TraesCS3D01G449100 chr3A 91.420 1387 92 11 749 2118 693444415 693443039 0.000000e+00 1877.0
17 TraesCS3D01G449100 chr3A 94.057 387 23 0 988 1374 693450426 693450040 3.340000e-164 588.0
18 TraesCS3D01G449100 chr3A 91.980 399 29 1 988 1383 693466439 693466837 9.430000e-155 556.0
19 TraesCS3D01G449100 chr3A 90.000 280 27 1 83 362 693445084 693444806 7.930000e-96 361.0
20 TraesCS3D01G449100 chr3A 92.500 80 5 1 1 80 7394325 7394247 2.450000e-21 113.0
21 TraesCS3D01G449100 chr3A 91.250 80 7 0 1 80 446583833 446583754 3.170000e-20 110.0
22 TraesCS3D01G449100 chr2B 93.045 647 33 3 2220 2866 692142705 692143339 0.000000e+00 935.0
23 TraesCS3D01G449100 chr2B 90.000 170 7 6 2850 3010 692144342 692144510 8.450000e-51 211.0
24 TraesCS3D01G449100 chr2A 91.188 261 16 1 2554 2814 605057811 605058064 6.180000e-92 348.0
25 TraesCS3D01G449100 chr2A 86.538 104 6 2 2214 2317 2737942 2738037 1.140000e-19 108.0
26 TraesCS3D01G449100 chr7A 88.621 290 21 6 2528 2814 291817709 291817989 2.870000e-90 342.0
27 TraesCS3D01G449100 chr6D 89.922 129 11 2 2220 2346 312687929 312687801 6.680000e-37 165.0
28 TraesCS3D01G449100 chr6D 92.405 79 6 0 1 79 11700238 11700316 2.450000e-21 113.0
29 TraesCS3D01G449100 chr4B 95.000 80 4 0 1 80 649699247 649699326 3.150000e-25 126.0
30 TraesCS3D01G449100 chr7B 94.937 79 4 0 2 80 11204368 11204290 1.130000e-24 124.0
31 TraesCS3D01G449100 chr2D 96.053 76 3 0 1 76 609755739 609755664 1.130000e-24 124.0
32 TraesCS3D01G449100 chr6B 93.750 80 5 0 1 80 599643643 599643722 1.470000e-23 121.0
33 TraesCS3D01G449100 chr4D 93.671 79 5 0 2 80 480100596 480100674 5.270000e-23 119.0
34 TraesCS3D01G449100 chr7D 92.500 80 6 0 1 80 581624367 581624446 6.820000e-22 115.0
35 TraesCS3D01G449100 chr5D 97.059 34 1 0 2293 2326 3608968 3609001 1.170000e-04 58.4


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 TraesCS3D01G449100 chr3D 557650566 557653575 3009 True 5559.000000 5559 100.000000 1 3010 1 chr3D.!!$R1 3009
1 TraesCS3D01G449100 chr3D 557698872 557699876 1004 True 487.500000 625 91.352000 986 2025 2 chr3D.!!$R2 1039
2 TraesCS3D01G449100 chr3B 739947959 739952479 4520 True 1128.333333 2429 89.730667 85 2125 3 chr3B.!!$R3 2040
3 TraesCS3D01G449100 chr3B 739922535 739927102 4567 True 870.333333 1469 89.374000 143 2184 3 chr3B.!!$R1 2041
4 TraesCS3D01G449100 chr3B 739931949 739932967 1018 True 463.500000 588 90.351000 988 2025 2 chr3B.!!$R2 1037
5 TraesCS3D01G449100 chr3B 739989298 739990268 970 False 462.000000 584 90.404500 988 2014 2 chr3B.!!$F1 1026
6 TraesCS3D01G449100 chr3B 739956970 739957745 775 True 460.500000 595 91.731500 986 1999 2 chr3B.!!$R4 1013
7 TraesCS3D01G449100 chr3A 693443039 693445084 2045 True 1119.000000 1877 90.710000 83 2118 2 chr3A.!!$R4 2035
8 TraesCS3D01G449100 chr2B 692142705 692144510 1805 False 573.000000 935 91.522500 2220 3010 2 chr2B.!!$F1 790

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
367 368 0.03779 GATCTCCTATGTGCGCTCCC 60.038 60.0 9.73 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 7229 0.035458 AAGCGTGAACTCCCTGAAGG 59.965 55.0 0.0 0.0 0.0 3.46 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
21 22 3.848726 CTTCTCTCTCTTCCAACTCAGC 58.151 50.000 0.00 0.00 0.00 4.26
22 23 2.881734 TCTCTCTCTTCCAACTCAGCA 58.118 47.619 0.00 0.00 0.00 4.41
23 24 3.234353 TCTCTCTCTTCCAACTCAGCAA 58.766 45.455 0.00 0.00 0.00 3.91
24 25 3.006323 TCTCTCTCTTCCAACTCAGCAAC 59.994 47.826 0.00 0.00 0.00 4.17
25 26 2.700371 TCTCTCTTCCAACTCAGCAACA 59.300 45.455 0.00 0.00 0.00 3.33
26 27 3.134623 TCTCTCTTCCAACTCAGCAACAA 59.865 43.478 0.00 0.00 0.00 2.83
27 28 4.070716 CTCTCTTCCAACTCAGCAACAAT 58.929 43.478 0.00 0.00 0.00 2.71
28 29 5.012046 TCTCTCTTCCAACTCAGCAACAATA 59.988 40.000 0.00 0.00 0.00 1.90
29 30 5.809001 TCTCTTCCAACTCAGCAACAATAT 58.191 37.500 0.00 0.00 0.00 1.28
30 31 6.946340 TCTCTTCCAACTCAGCAACAATATA 58.054 36.000 0.00 0.00 0.00 0.86
31 32 7.394016 TCTCTTCCAACTCAGCAACAATATAA 58.606 34.615 0.00 0.00 0.00 0.98
32 33 8.049117 TCTCTTCCAACTCAGCAACAATATAAT 58.951 33.333 0.00 0.00 0.00 1.28
33 34 9.330063 CTCTTCCAACTCAGCAACAATATAATA 57.670 33.333 0.00 0.00 0.00 0.98
34 35 9.851686 TCTTCCAACTCAGCAACAATATAATAT 57.148 29.630 0.00 0.00 0.00 1.28
55 56 8.879427 AATATTTAAATCCTTATAGCCCGCTT 57.121 30.769 3.39 0.00 0.00 4.68
56 57 9.969001 AATATTTAAATCCTTATAGCCCGCTTA 57.031 29.630 3.39 0.00 0.00 3.09
58 59 7.681939 TTTAAATCCTTATAGCCCGCTTATG 57.318 36.000 0.00 0.00 0.00 1.90
59 60 4.910458 AATCCTTATAGCCCGCTTATGT 57.090 40.909 0.00 0.00 0.00 2.29
60 61 3.955650 TCCTTATAGCCCGCTTATGTC 57.044 47.619 0.00 0.00 0.00 3.06
61 62 3.236047 TCCTTATAGCCCGCTTATGTCA 58.764 45.455 0.00 0.00 0.00 3.58
62 63 3.258372 TCCTTATAGCCCGCTTATGTCAG 59.742 47.826 0.00 0.00 0.00 3.51
63 64 2.743636 TATAGCCCGCTTATGTCAGC 57.256 50.000 0.00 0.00 36.33 4.26
64 65 1.051812 ATAGCCCGCTTATGTCAGCT 58.948 50.000 0.00 0.00 37.68 4.24
65 66 0.830648 TAGCCCGCTTATGTCAGCTT 59.169 50.000 0.00 0.00 37.68 3.74
66 67 0.830648 AGCCCGCTTATGTCAGCTTA 59.169 50.000 0.00 0.00 37.68 3.09
67 68 1.417890 AGCCCGCTTATGTCAGCTTAT 59.582 47.619 0.00 0.00 37.68 1.73
68 69 2.158755 AGCCCGCTTATGTCAGCTTATT 60.159 45.455 0.00 0.00 37.68 1.40
69 70 3.071023 AGCCCGCTTATGTCAGCTTATTA 59.929 43.478 0.00 0.00 37.68 0.98
70 71 4.003648 GCCCGCTTATGTCAGCTTATTAT 58.996 43.478 0.00 0.00 37.68 1.28
71 72 5.046591 AGCCCGCTTATGTCAGCTTATTATA 60.047 40.000 0.00 0.00 37.68 0.98
72 73 5.817816 GCCCGCTTATGTCAGCTTATTATAT 59.182 40.000 0.00 0.00 37.68 0.86
73 74 6.316390 GCCCGCTTATGTCAGCTTATTATATT 59.684 38.462 0.00 0.00 37.68 1.28
74 75 7.148239 GCCCGCTTATGTCAGCTTATTATATTT 60.148 37.037 0.00 0.00 37.68 1.40
75 76 8.177663 CCCGCTTATGTCAGCTTATTATATTTG 58.822 37.037 0.00 0.00 37.68 2.32
76 77 7.693951 CCGCTTATGTCAGCTTATTATATTTGC 59.306 37.037 0.00 0.00 37.68 3.68
77 78 8.446273 CGCTTATGTCAGCTTATTATATTTGCT 58.554 33.333 0.00 0.00 37.68 3.91
78 79 9.766277 GCTTATGTCAGCTTATTATATTTGCTC 57.234 33.333 0.00 0.00 36.79 4.26
132 133 3.645884 GCTAAGACGTATTTATCGCCCA 58.354 45.455 0.00 0.00 0.00 5.36
141 142 5.642063 ACGTATTTATCGCCCAATATGAAGG 59.358 40.000 0.00 0.00 0.00 3.46
199 200 7.950684 AGAGGAGCATAGGACTATAATAACACA 59.049 37.037 0.00 0.00 0.00 3.72
226 227 2.633657 GAGCACAACACACCTGCG 59.366 61.111 0.00 0.00 35.98 5.18
227 228 2.896801 GAGCACAACACACCTGCGG 61.897 63.158 0.00 0.00 35.98 5.69
258 259 1.231958 GGCGAAATCGTCCAACACCA 61.232 55.000 4.59 0.00 42.22 4.17
311 312 2.989909 ACAAGGCAACATCGATGATGA 58.010 42.857 32.38 0.00 42.09 2.92
362 363 2.205074 GTGGTTGATCTCCTATGTGCG 58.795 52.381 8.50 0.00 0.00 5.34
364 365 1.202580 GGTTGATCTCCTATGTGCGCT 60.203 52.381 9.73 0.00 0.00 5.92
365 366 2.131183 GTTGATCTCCTATGTGCGCTC 58.869 52.381 9.73 5.51 0.00 5.03
366 367 0.676184 TGATCTCCTATGTGCGCTCC 59.324 55.000 9.73 0.00 0.00 4.70
367 368 0.037790 GATCTCCTATGTGCGCTCCC 60.038 60.000 9.73 0.00 0.00 4.30
369 370 1.068753 CTCCTATGTGCGCTCCCTG 59.931 63.158 9.73 0.00 0.00 4.45
370 371 1.381191 TCCTATGTGCGCTCCCTGA 60.381 57.895 9.73 0.00 0.00 3.86
371 372 1.068753 CCTATGTGCGCTCCCTGAG 59.931 63.158 9.73 0.00 0.00 3.35
451 567 7.413438 CGATCTAATGGTCAGAAAAGAAAGTGG 60.413 40.741 0.00 0.00 0.00 4.00
454 570 4.431416 TGGTCAGAAAAGAAAGTGGCTA 57.569 40.909 0.00 0.00 0.00 3.93
493 630 2.488153 GGCACCTGACAAATAACCACTC 59.512 50.000 0.00 0.00 0.00 3.51
494 631 2.488153 GCACCTGACAAATAACCACTCC 59.512 50.000 0.00 0.00 0.00 3.85
495 632 3.750371 CACCTGACAAATAACCACTCCA 58.250 45.455 0.00 0.00 0.00 3.86
571 726 5.070981 TGTTCTTTGCCATGGTTCCAAAATA 59.929 36.000 14.67 4.15 0.00 1.40
572 727 5.815233 TCTTTGCCATGGTTCCAAAATAA 57.185 34.783 14.67 1.91 0.00 1.40
575 730 7.230027 TCTTTGCCATGGTTCCAAAATAAAAT 58.770 30.769 14.67 0.00 0.00 1.82
577 732 8.924511 TTTGCCATGGTTCCAAAATAAAATAA 57.075 26.923 14.67 0.00 0.00 1.40
580 735 9.525826 TGCCATGGTTCCAAAATAAAATAAAAT 57.474 25.926 14.67 0.00 0.00 1.82
624 780 6.252967 TCATATTCGTTGCATTTGAGTTGT 57.747 33.333 0.00 0.00 0.00 3.32
676 832 8.600449 TGGTTAAAGTTGCAAAATATTCTTGG 57.400 30.769 0.00 0.00 0.00 3.61
699 855 4.142293 GGGCAAAAGATAGAAGAAGGCAAG 60.142 45.833 0.00 0.00 0.00 4.01
707 864 0.960861 GAAGAAGGCAAGAACCCCCG 60.961 60.000 0.00 0.00 0.00 5.73
755 915 4.332828 AGTGTATTCCCGAAAAAGAAGGG 58.667 43.478 0.00 0.00 46.40 3.95
781 941 8.746922 AACAACATTATCATCAATGTGTCAAC 57.253 30.769 2.48 0.00 46.00 3.18
790 950 8.806429 ATCATCAATGTGTCAACCTAATAACA 57.194 30.769 0.00 0.00 0.00 2.41
942 1111 4.512944 GCATGATTGGTATGTACTGGTGAG 59.487 45.833 0.00 0.00 0.00 3.51
957 1133 0.528684 GTGAGAAGATTCCCTCGCCG 60.529 60.000 6.14 0.00 34.74 6.46
1480 4103 4.377431 GGCTAATTTCTCGTGACTGTTGTG 60.377 45.833 0.00 0.00 0.00 3.33
1505 4129 2.534042 TCTCCAGAAGAACCCGATCT 57.466 50.000 0.00 0.00 0.00 2.75
1542 4166 1.135859 GCAAGAGCATGGTTCTGAACG 60.136 52.381 13.89 2.39 41.58 3.95
1544 4168 0.322975 AGAGCATGGTTCTGAACGCT 59.677 50.000 17.45 17.45 0.00 5.07
1553 4177 2.417719 GTTCTGAACGCTGATCAAGGT 58.582 47.619 4.57 0.00 0.00 3.50
1554 4178 2.084610 TCTGAACGCTGATCAAGGTG 57.915 50.000 0.00 0.00 0.00 4.00
1654 4281 9.565213 CCAACATAACAAAGAAAATCTCATCTC 57.435 33.333 0.00 0.00 0.00 2.75
1657 4284 8.457261 ACATAACAAAGAAAATCTCATCTCTGC 58.543 33.333 0.00 0.00 0.00 4.26
1671 4301 5.311265 TCATCTCTGCTTTTGATGTGAACT 58.689 37.500 0.00 0.00 38.78 3.01
1681 4311 6.533367 GCTTTTGATGTGAACTAACCAACAAA 59.467 34.615 0.00 0.00 0.00 2.83
1683 4313 5.163302 TGATGTGAACTAACCAACAAACG 57.837 39.130 0.00 0.00 0.00 3.60
1686 4316 5.373981 TGTGAACTAACCAACAAACGTTT 57.626 34.783 7.96 7.96 0.00 3.60
1687 4317 5.392286 TGTGAACTAACCAACAAACGTTTC 58.608 37.500 11.37 0.00 0.00 2.78
1688 4318 5.181622 TGTGAACTAACCAACAAACGTTTCT 59.818 36.000 11.37 0.00 0.00 2.52
1689 4319 6.370994 TGTGAACTAACCAACAAACGTTTCTA 59.629 34.615 11.37 0.00 0.00 2.10
1690 4320 6.903479 GTGAACTAACCAACAAACGTTTCTAG 59.097 38.462 11.37 2.71 0.00 2.43
1729 4374 1.267574 ACATGGACGCAGGACCTGAT 61.268 55.000 26.25 12.12 32.44 2.90
2121 7157 5.050490 ACACTTCGATCCGAATTAATGGAG 58.950 41.667 2.14 0.00 44.85 3.86
2125 7161 3.566742 TCGATCCGAATTAATGGAGACGA 59.433 43.478 15.86 15.86 41.27 4.20
2126 7162 4.217767 TCGATCCGAATTAATGGAGACGAT 59.782 41.667 15.86 3.25 39.88 3.73
2127 7163 4.559251 CGATCCGAATTAATGGAGACGATC 59.441 45.833 13.74 7.63 38.99 3.69
2128 7164 3.897325 TCCGAATTAATGGAGACGATCG 58.103 45.455 14.88 14.88 0.00 3.69
2129 7165 2.987149 CCGAATTAATGGAGACGATCGG 59.013 50.000 20.98 6.56 42.01 4.18
2130 7166 3.897325 CGAATTAATGGAGACGATCGGA 58.103 45.455 20.98 0.00 0.00 4.55
2131 7167 3.914966 CGAATTAATGGAGACGATCGGAG 59.085 47.826 20.98 0.00 0.00 4.63
2132 7168 3.944055 ATTAATGGAGACGATCGGAGG 57.056 47.619 20.98 0.00 0.00 4.30
2133 7169 1.617322 TAATGGAGACGATCGGAGGG 58.383 55.000 20.98 0.00 0.00 4.30
2134 7170 0.106167 AATGGAGACGATCGGAGGGA 60.106 55.000 20.98 0.13 0.00 4.20
2135 7171 0.538516 ATGGAGACGATCGGAGGGAG 60.539 60.000 20.98 0.00 0.00 4.30
2136 7172 1.152922 GGAGACGATCGGAGGGAGT 60.153 63.158 20.98 0.00 0.00 3.85
2137 7173 0.108207 GGAGACGATCGGAGGGAGTA 59.892 60.000 20.98 0.00 0.00 2.59
2138 7174 1.476471 GGAGACGATCGGAGGGAGTAA 60.476 57.143 20.98 0.00 0.00 2.24
2139 7175 2.295885 GAGACGATCGGAGGGAGTAAA 58.704 52.381 20.98 0.00 0.00 2.01
2140 7176 2.291190 GAGACGATCGGAGGGAGTAAAG 59.709 54.545 20.98 0.00 0.00 1.85
2141 7177 2.092538 AGACGATCGGAGGGAGTAAAGA 60.093 50.000 20.98 0.00 0.00 2.52
2142 7178 2.686915 GACGATCGGAGGGAGTAAAGAA 59.313 50.000 20.98 0.00 0.00 2.52
2143 7179 3.094572 ACGATCGGAGGGAGTAAAGAAA 58.905 45.455 20.98 0.00 0.00 2.52
2144 7180 3.705072 ACGATCGGAGGGAGTAAAGAAAT 59.295 43.478 20.98 0.00 0.00 2.17
2145 7181 4.161754 ACGATCGGAGGGAGTAAAGAAATT 59.838 41.667 20.98 0.00 0.00 1.82
2146 7182 4.745620 CGATCGGAGGGAGTAAAGAAATTC 59.254 45.833 7.38 0.00 0.00 2.17
2147 7183 5.452077 CGATCGGAGGGAGTAAAGAAATTCT 60.452 44.000 7.38 0.00 0.00 2.40
2148 7184 5.757099 TCGGAGGGAGTAAAGAAATTCTT 57.243 39.130 1.80 1.80 38.59 2.52
2150 7186 6.540083 TCGGAGGGAGTAAAGAAATTCTTTT 58.460 36.000 23.77 9.09 43.62 2.27
2151 7187 6.653740 TCGGAGGGAGTAAAGAAATTCTTTTC 59.346 38.462 23.77 18.90 43.62 2.29
2152 7188 6.402226 CGGAGGGAGTAAAGAAATTCTTTTCG 60.402 42.308 23.77 6.92 43.62 3.46
2153 7189 6.653740 GGAGGGAGTAAAGAAATTCTTTTCGA 59.346 38.462 23.77 5.88 43.62 3.71
2154 7190 7.361031 GGAGGGAGTAAAGAAATTCTTTTCGAC 60.361 40.741 23.77 16.44 43.62 4.20
2155 7191 7.225011 AGGGAGTAAAGAAATTCTTTTCGACT 58.775 34.615 23.77 20.24 43.62 4.18
2156 7192 7.388224 AGGGAGTAAAGAAATTCTTTTCGACTC 59.612 37.037 26.30 26.30 43.62 3.36
2157 7193 7.172703 GGGAGTAAAGAAATTCTTTTCGACTCA 59.827 37.037 30.58 13.28 43.62 3.41
2158 7194 8.722394 GGAGTAAAGAAATTCTTTTCGACTCAT 58.278 33.333 30.58 13.34 43.62 2.90
2159 7195 9.535270 GAGTAAAGAAATTCTTTTCGACTCATG 57.465 33.333 27.82 0.00 43.62 3.07
2160 7196 9.057089 AGTAAAGAAATTCTTTTCGACTCATGT 57.943 29.630 23.77 0.45 43.62 3.21
2163 7199 7.962964 AGAAATTCTTTTCGACTCATGTACA 57.037 32.000 0.00 0.00 44.88 2.90
2164 7200 8.378172 AGAAATTCTTTTCGACTCATGTACAA 57.622 30.769 0.00 0.00 44.88 2.41
2165 7201 8.836413 AGAAATTCTTTTCGACTCATGTACAAA 58.164 29.630 0.00 0.00 44.88 2.83
2166 7202 9.612620 GAAATTCTTTTCGACTCATGTACAAAT 57.387 29.630 0.00 0.00 32.49 2.32
2167 7203 8.955061 AATTCTTTTCGACTCATGTACAAATG 57.045 30.769 0.00 0.00 0.00 2.32
2168 7204 5.927030 TCTTTTCGACTCATGTACAAATGC 58.073 37.500 0.00 0.00 0.00 3.56
2169 7205 4.678509 TTTCGACTCATGTACAAATGCC 57.321 40.909 0.00 0.00 0.00 4.40
2170 7206 3.326836 TCGACTCATGTACAAATGCCA 57.673 42.857 0.00 0.00 0.00 4.92
2171 7207 3.261580 TCGACTCATGTACAAATGCCAG 58.738 45.455 0.00 0.00 0.00 4.85
2172 7208 3.056179 TCGACTCATGTACAAATGCCAGA 60.056 43.478 0.00 0.00 0.00 3.86
2173 7209 3.308053 CGACTCATGTACAAATGCCAGAG 59.692 47.826 0.00 2.03 0.00 3.35
2174 7210 4.256920 GACTCATGTACAAATGCCAGAGT 58.743 43.478 0.00 5.15 37.76 3.24
2175 7211 4.005650 ACTCATGTACAAATGCCAGAGTG 58.994 43.478 0.00 0.00 34.17 3.51
2176 7212 4.256110 CTCATGTACAAATGCCAGAGTGA 58.744 43.478 0.00 0.00 0.00 3.41
2177 7213 4.650734 TCATGTACAAATGCCAGAGTGAA 58.349 39.130 0.00 0.00 0.00 3.18
2178 7214 4.696877 TCATGTACAAATGCCAGAGTGAAG 59.303 41.667 0.00 0.00 0.00 3.02
2179 7215 2.813754 TGTACAAATGCCAGAGTGAAGC 59.186 45.455 0.00 0.00 0.00 3.86
2180 7216 1.985473 ACAAATGCCAGAGTGAAGCA 58.015 45.000 0.00 0.00 41.50 3.91
2185 7221 3.920231 ATGCCAGAGTGAAGCATTAGA 57.080 42.857 0.00 0.00 44.61 2.10
2186 7222 3.701205 TGCCAGAGTGAAGCATTAGAA 57.299 42.857 0.00 0.00 0.00 2.10
2187 7223 4.226427 TGCCAGAGTGAAGCATTAGAAT 57.774 40.909 0.00 0.00 0.00 2.40
2188 7224 5.357742 TGCCAGAGTGAAGCATTAGAATA 57.642 39.130 0.00 0.00 0.00 1.75
2189 7225 5.744171 TGCCAGAGTGAAGCATTAGAATAA 58.256 37.500 0.00 0.00 0.00 1.40
2190 7226 5.819379 TGCCAGAGTGAAGCATTAGAATAAG 59.181 40.000 0.00 0.00 0.00 1.73
2191 7227 5.819901 GCCAGAGTGAAGCATTAGAATAAGT 59.180 40.000 0.00 0.00 0.00 2.24
2192 7228 6.986817 GCCAGAGTGAAGCATTAGAATAAGTA 59.013 38.462 0.00 0.00 0.00 2.24
2193 7229 7.042389 GCCAGAGTGAAGCATTAGAATAAGTAC 60.042 40.741 0.00 0.00 0.00 2.73
2194 7230 7.439655 CCAGAGTGAAGCATTAGAATAAGTACC 59.560 40.741 0.00 0.00 0.00 3.34
2195 7231 8.200792 CAGAGTGAAGCATTAGAATAAGTACCT 58.799 37.037 0.00 0.00 0.00 3.08
2196 7232 8.763601 AGAGTGAAGCATTAGAATAAGTACCTT 58.236 33.333 0.00 0.00 0.00 3.50
2197 7233 8.950208 AGTGAAGCATTAGAATAAGTACCTTC 57.050 34.615 0.00 0.00 0.00 3.46
2198 7234 8.540388 AGTGAAGCATTAGAATAAGTACCTTCA 58.460 33.333 0.00 0.00 35.26 3.02
2199 7235 8.821894 GTGAAGCATTAGAATAAGTACCTTCAG 58.178 37.037 0.00 0.00 37.44 3.02
2200 7236 7.987458 TGAAGCATTAGAATAAGTACCTTCAGG 59.013 37.037 0.00 0.00 42.17 3.86
2201 7237 6.831976 AGCATTAGAATAAGTACCTTCAGGG 58.168 40.000 0.00 0.00 40.27 4.45
2202 7238 6.615726 AGCATTAGAATAAGTACCTTCAGGGA 59.384 38.462 0.00 0.00 40.27 4.20
2203 7239 6.931840 GCATTAGAATAAGTACCTTCAGGGAG 59.068 42.308 0.00 0.00 40.27 4.30
2204 7240 7.419172 GCATTAGAATAAGTACCTTCAGGGAGT 60.419 40.741 0.00 0.00 40.27 3.85
2205 7241 8.487028 CATTAGAATAAGTACCTTCAGGGAGTT 58.513 37.037 3.52 3.52 43.87 3.01
2206 7242 6.547930 AGAATAAGTACCTTCAGGGAGTTC 57.452 41.667 0.94 0.00 40.78 3.01
2207 7243 6.023603 AGAATAAGTACCTTCAGGGAGTTCA 58.976 40.000 0.94 0.00 40.78 3.18
2208 7244 5.678955 ATAAGTACCTTCAGGGAGTTCAC 57.321 43.478 0.94 0.00 40.78 3.18
2209 7245 1.893801 AGTACCTTCAGGGAGTTCACG 59.106 52.381 0.00 0.00 40.27 4.35
2210 7246 0.606604 TACCTTCAGGGAGTTCACGC 59.393 55.000 0.00 0.00 40.27 5.34
2211 7247 1.122019 ACCTTCAGGGAGTTCACGCT 61.122 55.000 0.00 0.00 40.27 5.07
2212 7248 0.035458 CCTTCAGGGAGTTCACGCTT 59.965 55.000 0.00 0.00 37.23 4.68
2213 7249 1.275291 CCTTCAGGGAGTTCACGCTTA 59.725 52.381 0.00 0.00 37.23 3.09
2214 7250 2.289444 CCTTCAGGGAGTTCACGCTTAA 60.289 50.000 0.00 0.00 37.23 1.85
2215 7251 3.399330 CTTCAGGGAGTTCACGCTTAAA 58.601 45.455 0.00 0.00 0.00 1.52
2216 7252 2.762745 TCAGGGAGTTCACGCTTAAAC 58.237 47.619 0.00 0.00 0.00 2.01
2217 7253 2.367567 TCAGGGAGTTCACGCTTAAACT 59.632 45.455 0.00 0.00 38.40 2.66
2218 7254 2.480419 CAGGGAGTTCACGCTTAAACTG 59.520 50.000 0.00 0.00 35.90 3.16
2262 7298 9.079833 CAAAGCTTTATTATGAAGACATGTTGG 57.920 33.333 12.25 0.00 37.87 3.77
2269 7305 3.940209 TGAAGACATGTTGGGCATTTC 57.060 42.857 0.00 0.00 35.19 2.17
2284 7320 2.602217 GCATTTCGCCCATTACGATGAC 60.602 50.000 0.00 0.00 39.65 3.06
2285 7321 2.388310 TTTCGCCCATTACGATGACA 57.612 45.000 0.00 0.00 39.65 3.58
2346 7382 5.628193 GCTTCATCAACATTACATGCATAGC 59.372 40.000 0.00 0.00 0.00 2.97
2347 7383 5.694231 TCATCAACATTACATGCATAGCC 57.306 39.130 0.00 0.00 0.00 3.93
2352 7388 5.066375 TCAACATTACATGCATAGCCAAGTC 59.934 40.000 0.00 0.00 0.00 3.01
2363 7399 4.450419 GCATAGCCAAGTCTAGCAATAGTG 59.550 45.833 0.00 0.00 0.00 2.74
2364 7400 5.605534 CATAGCCAAGTCTAGCAATAGTGT 58.394 41.667 0.00 0.00 0.00 3.55
2417 7453 3.423539 TGGACAGTGCAGCTAGAAAAT 57.576 42.857 0.00 0.00 0.00 1.82
2461 7497 0.831711 TCCTCCAGCGGCATAGCATA 60.832 55.000 1.45 0.00 40.15 3.14
2463 7499 0.671781 CTCCAGCGGCATAGCATACC 60.672 60.000 1.45 0.00 40.15 2.73
2464 7500 1.121407 TCCAGCGGCATAGCATACCT 61.121 55.000 1.45 0.00 40.15 3.08
2465 7501 0.952497 CCAGCGGCATAGCATACCTG 60.952 60.000 1.45 0.00 40.15 4.00
2466 7502 0.952497 CAGCGGCATAGCATACCTGG 60.952 60.000 1.45 0.00 40.15 4.45
2467 7503 1.121407 AGCGGCATAGCATACCTGGA 61.121 55.000 0.00 0.00 40.15 3.86
2618 7654 2.357009 GTGAATGCATCAGGGACATGAC 59.643 50.000 0.00 0.00 39.19 3.06
2619 7655 2.026075 TGAATGCATCAGGGACATGACA 60.026 45.455 0.00 0.00 33.04 3.58
2620 7656 2.048444 ATGCATCAGGGACATGACAC 57.952 50.000 0.00 0.00 30.46 3.67
2621 7657 0.691904 TGCATCAGGGACATGACACA 59.308 50.000 0.00 0.00 30.46 3.72
2622 7658 1.282738 TGCATCAGGGACATGACACAT 59.717 47.619 0.00 0.00 30.46 3.21
2623 7659 1.674441 GCATCAGGGACATGACACATG 59.326 52.381 0.00 9.72 30.46 3.21
2624 7660 2.681682 GCATCAGGGACATGACACATGA 60.682 50.000 16.86 2.71 30.46 3.07
2665 7701 1.606885 GCCACCACATCCCCAACATG 61.607 60.000 0.00 0.00 0.00 3.21
2666 7702 0.039472 CCACCACATCCCCAACATGA 59.961 55.000 0.00 0.00 0.00 3.07
2675 7711 0.751643 CCCCAACATGATCCCGAACC 60.752 60.000 0.00 0.00 0.00 3.62
2687 7723 2.281484 CGAACCACCACACCCCAG 60.281 66.667 0.00 0.00 0.00 4.45
2695 7731 2.676608 CACACCCCAGGCTGCATA 59.323 61.111 9.56 0.00 0.00 3.14
2702 7738 1.410648 CCCCAGGCTGCATAATCTTGT 60.411 52.381 9.56 0.00 0.00 3.16
2716 7752 4.525912 AATCTTGTCCTGGAACAAATGC 57.474 40.909 0.00 0.00 38.60 3.56
2718 7754 0.313672 TTGTCCTGGAACAAATGCGC 59.686 50.000 0.00 0.00 38.70 6.09
2737 7773 4.220572 GCGCCGTCAGTGTTAAATTTTAA 58.779 39.130 0.00 0.00 0.00 1.52
2743 7779 6.791775 CCGTCAGTGTTAAATTTTAACGTACC 59.208 38.462 21.15 12.21 0.00 3.34
2746 7782 6.703607 TCAGTGTTAAATTTTAACGTACCGGA 59.296 34.615 21.15 14.18 0.00 5.14
2752 7788 1.357907 TTTAACGTACCGGATTGCGG 58.642 50.000 15.64 15.64 0.00 5.69
2796 7832 1.762370 TCTGCACACTCTCCTTGTTCA 59.238 47.619 0.00 0.00 0.00 3.18
2799 7835 2.369860 TGCACACTCTCCTTGTTCAGAT 59.630 45.455 0.00 0.00 0.00 2.90
2802 7838 4.561530 GCACACTCTCCTTGTTCAGATACA 60.562 45.833 0.00 0.00 0.00 2.29
2834 7870 7.012610 TCCATATATTCAGCATTGTCAACAGTG 59.987 37.037 1.61 1.61 36.76 3.66
2838 7874 1.338973 CAGCATTGTCAACAGTGGCTT 59.661 47.619 7.61 0.00 34.62 4.35
2932 8994 1.902938 AAACAGCTCCAGCCTCTTTC 58.097 50.000 0.00 0.00 43.38 2.62
2935 8997 0.107752 CAGCTCCAGCCTCTTTCTCC 60.108 60.000 0.00 0.00 43.38 3.71
2962 9024 6.451340 TGGGATTAGCCATAGGATATCCATTT 59.549 38.462 23.81 5.88 38.95 2.32
2965 9027 8.907885 GGATTAGCCATAGGATATCCATTTTTC 58.092 37.037 23.81 7.97 35.87 2.29
2978 9041 5.766150 TCCATTTTTCCTGTACTGTTGTG 57.234 39.130 0.00 0.00 0.00 3.33
2983 9046 3.275617 TTCCTGTACTGTTGTGCAACT 57.724 42.857 14.97 0.25 41.67 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.257873 TGCTGAGTTGGAAGAGAGAGAAG 59.742 47.826 0.00 0.00 0.00 2.85
1 2 3.234353 TGCTGAGTTGGAAGAGAGAGAA 58.766 45.455 0.00 0.00 0.00 2.87
2 3 2.881734 TGCTGAGTTGGAAGAGAGAGA 58.118 47.619 0.00 0.00 0.00 3.10
3 4 3.244009 TGTTGCTGAGTTGGAAGAGAGAG 60.244 47.826 0.00 0.00 0.00 3.20
4 5 2.700371 TGTTGCTGAGTTGGAAGAGAGA 59.300 45.455 0.00 0.00 0.00 3.10
5 6 3.117491 TGTTGCTGAGTTGGAAGAGAG 57.883 47.619 0.00 0.00 0.00 3.20
6 7 3.558931 TTGTTGCTGAGTTGGAAGAGA 57.441 42.857 0.00 0.00 0.00 3.10
7 8 7.615582 TTATATTGTTGCTGAGTTGGAAGAG 57.384 36.000 0.00 0.00 0.00 2.85
8 9 9.851686 ATATTATATTGTTGCTGAGTTGGAAGA 57.148 29.630 0.00 0.00 0.00 2.87
29 30 9.969001 AAGCGGGCTATAAGGATTTAAATATTA 57.031 29.630 0.00 4.48 0.00 0.98
30 31 8.879427 AAGCGGGCTATAAGGATTTAAATATT 57.121 30.769 0.00 2.34 0.00 1.28
32 33 9.391006 CATAAGCGGGCTATAAGGATTTAAATA 57.609 33.333 0.00 0.00 0.00 1.40
33 34 7.888546 ACATAAGCGGGCTATAAGGATTTAAAT 59.111 33.333 0.00 0.00 0.00 1.40
34 35 7.228590 ACATAAGCGGGCTATAAGGATTTAAA 58.771 34.615 0.00 0.00 0.00 1.52
35 36 6.775708 ACATAAGCGGGCTATAAGGATTTAA 58.224 36.000 0.00 0.00 0.00 1.52
36 37 6.014070 TGACATAAGCGGGCTATAAGGATTTA 60.014 38.462 0.00 0.00 0.00 1.40
37 38 5.221843 TGACATAAGCGGGCTATAAGGATTT 60.222 40.000 0.00 0.00 0.00 2.17
38 39 4.286032 TGACATAAGCGGGCTATAAGGATT 59.714 41.667 0.00 0.00 0.00 3.01
39 40 3.838317 TGACATAAGCGGGCTATAAGGAT 59.162 43.478 0.00 0.00 0.00 3.24
40 41 3.236047 TGACATAAGCGGGCTATAAGGA 58.764 45.455 0.00 0.00 0.00 3.36
41 42 3.589988 CTGACATAAGCGGGCTATAAGG 58.410 50.000 0.00 0.00 0.00 2.69
42 43 2.996621 GCTGACATAAGCGGGCTATAAG 59.003 50.000 0.00 0.00 32.56 1.73
43 44 3.040147 GCTGACATAAGCGGGCTATAA 57.960 47.619 0.00 0.00 32.56 0.98
44 45 2.743636 GCTGACATAAGCGGGCTATA 57.256 50.000 0.00 0.00 32.56 1.31
45 46 3.614399 GCTGACATAAGCGGGCTAT 57.386 52.632 0.00 0.00 32.56 2.97
52 53 9.766277 GAGCAAATATAATAAGCTGACATAAGC 57.234 33.333 0.00 0.00 43.88 3.09
56 57 8.997323 GTGAGAGCAAATATAATAAGCTGACAT 58.003 33.333 0.00 0.00 35.36 3.06
57 58 7.986889 TGTGAGAGCAAATATAATAAGCTGACA 59.013 33.333 0.00 0.00 35.36 3.58
58 59 8.370493 TGTGAGAGCAAATATAATAAGCTGAC 57.630 34.615 0.00 0.00 35.36 3.51
59 60 8.206867 ACTGTGAGAGCAAATATAATAAGCTGA 58.793 33.333 0.00 0.00 35.36 4.26
60 61 8.281194 CACTGTGAGAGCAAATATAATAAGCTG 58.719 37.037 0.32 0.00 35.36 4.24
61 62 7.041508 GCACTGTGAGAGCAAATATAATAAGCT 60.042 37.037 12.86 0.00 38.43 3.74
62 63 7.074502 GCACTGTGAGAGCAAATATAATAAGC 58.925 38.462 12.86 0.00 31.92 3.09
63 64 8.146479 TGCACTGTGAGAGCAAATATAATAAG 57.854 34.615 12.86 0.00 38.82 1.73
64 65 8.504812 TTGCACTGTGAGAGCAAATATAATAA 57.495 30.769 12.86 0.00 46.03 1.40
74 75 2.837532 TACATTGCACTGTGAGAGCA 57.162 45.000 19.05 0.00 39.97 4.26
75 76 2.159599 GCTTACATTGCACTGTGAGAGC 60.160 50.000 26.55 22.27 35.39 4.09
76 77 3.069289 TGCTTACATTGCACTGTGAGAG 58.931 45.455 26.55 18.03 35.39 3.20
77 78 3.124578 TGCTTACATTGCACTGTGAGA 57.875 42.857 26.55 12.77 35.39 3.27
78 79 3.003585 TGTTGCTTACATTGCACTGTGAG 59.996 43.478 20.47 20.47 40.40 3.51
79 80 2.948315 TGTTGCTTACATTGCACTGTGA 59.052 40.909 19.05 10.49 40.40 3.58
80 81 3.352554 TGTTGCTTACATTGCACTGTG 57.647 42.857 19.05 2.76 40.40 3.66
81 82 3.858129 GCATGTTGCTTACATTGCACTGT 60.858 43.478 14.59 14.59 45.19 3.55
111 112 3.645884 TGGGCGATAAATACGTCTTAGC 58.354 45.455 0.00 0.00 35.64 3.09
132 133 7.922699 AAACTCTACTCTAGCCCTTCATATT 57.077 36.000 0.00 0.00 0.00 1.28
141 142 4.803098 TGGTGAAAACTCTACTCTAGCC 57.197 45.455 0.00 0.00 0.00 3.93
199 200 4.278419 GGTGTGTTGTGCTCCTTTCTAAAT 59.722 41.667 0.00 0.00 0.00 1.40
237 238 2.097728 GTTGGACGATTTCGCCGC 59.902 61.111 0.00 0.00 44.43 6.53
317 318 1.228831 CATGCCCCAACCCAACTCA 60.229 57.895 0.00 0.00 0.00 3.41
362 363 0.253044 TAACATGCCACTCAGGGAGC 59.747 55.000 0.00 0.00 43.00 4.70
364 365 2.171237 CTCATAACATGCCACTCAGGGA 59.829 50.000 0.00 0.00 44.34 4.20
365 366 2.092753 ACTCATAACATGCCACTCAGGG 60.093 50.000 0.00 0.00 38.09 4.45
366 367 2.941064 CACTCATAACATGCCACTCAGG 59.059 50.000 0.00 0.00 41.84 3.86
367 368 2.941064 CCACTCATAACATGCCACTCAG 59.059 50.000 0.00 0.00 0.00 3.35
369 370 1.672881 GCCACTCATAACATGCCACTC 59.327 52.381 0.00 0.00 0.00 3.51
370 371 1.283029 AGCCACTCATAACATGCCACT 59.717 47.619 0.00 0.00 0.00 4.00
371 372 1.672881 GAGCCACTCATAACATGCCAC 59.327 52.381 0.00 0.00 0.00 5.01
502 645 3.071479 TCTTTCGAAACGAAGGAATGGG 58.929 45.455 6.47 0.00 45.88 4.00
577 732 8.729756 TGAATGTGTGACTTTATCGATTGATTT 58.270 29.630 1.71 0.00 35.99 2.17
580 735 7.848223 ATGAATGTGTGACTTTATCGATTGA 57.152 32.000 1.71 0.00 0.00 2.57
584 739 7.704899 ACGAATATGAATGTGTGACTTTATCGA 59.295 33.333 0.00 0.00 0.00 3.59
653 809 7.360861 GCCCCAAGAATATTTTGCAACTTTAAC 60.361 37.037 0.00 0.00 0.00 2.01
675 831 2.690497 GCCTTCTTCTATCTTTTGCCCC 59.310 50.000 0.00 0.00 0.00 5.80
676 832 3.356290 TGCCTTCTTCTATCTTTTGCCC 58.644 45.455 0.00 0.00 0.00 5.36
699 855 4.204012 TCATTTCATTGATACGGGGGTTC 58.796 43.478 0.00 0.00 0.00 3.62
727 884 1.946984 TTCGGGAATACACTCAGGGT 58.053 50.000 0.00 0.00 0.00 4.34
755 915 8.853345 GTTGACACATTGATGATAATGTTGTTC 58.147 33.333 1.68 1.21 46.18 3.18
818 978 1.341976 ACCCATGCCCACCTTACAATC 60.342 52.381 0.00 0.00 0.00 2.67
942 1111 0.460311 TCTTCGGCGAGGGAATCTTC 59.540 55.000 19.22 0.00 0.00 2.87
980 1156 0.385029 CGGATCTCACCTCAGCTCAG 59.615 60.000 0.00 0.00 0.00 3.35
981 1157 0.034089 TCGGATCTCACCTCAGCTCA 60.034 55.000 0.00 0.00 0.00 4.26
1520 4144 3.338249 GTTCAGAACCATGCTCTTGCTA 58.662 45.455 1.29 0.00 40.48 3.49
1542 4166 2.467826 GCCGAGCACCTTGATCAGC 61.468 63.158 0.00 0.00 31.10 4.26
1544 4168 2.268920 GGCCGAGCACCTTGATCA 59.731 61.111 0.00 0.00 31.10 2.92
1654 4281 5.437289 TGGTTAGTTCACATCAAAAGCAG 57.563 39.130 0.00 0.00 0.00 4.24
1656 4283 5.587289 TGTTGGTTAGTTCACATCAAAAGC 58.413 37.500 0.00 0.00 0.00 3.51
1657 4284 7.253618 CGTTTGTTGGTTAGTTCACATCAAAAG 60.254 37.037 0.00 0.00 36.29 2.27
1671 4301 8.413229 AGTACTACTAGAAACGTTTGTTGGTTA 58.587 33.333 20.10 5.77 38.62 2.85
1689 4319 8.851145 CCATGTTGTGAGTATGATAGTACTACT 58.149 37.037 4.31 0.00 35.14 2.57
1690 4320 8.847196 TCCATGTTGTGAGTATGATAGTACTAC 58.153 37.037 4.31 0.35 35.14 2.73
1729 4374 2.358615 CCAGCAACGTAGCCAGCA 60.359 61.111 0.00 0.00 34.23 4.41
1754 4399 3.241530 TCCACGAACTGGCAGCCT 61.242 61.111 15.89 1.04 40.39 4.58
2121 7157 2.295885 TCTTTACTCCCTCCGATCGTC 58.704 52.381 15.09 0.00 0.00 4.20
2125 7161 5.959583 AGAATTTCTTTACTCCCTCCGAT 57.040 39.130 0.00 0.00 0.00 4.18
2126 7162 5.757099 AAGAATTTCTTTACTCCCTCCGA 57.243 39.130 5.82 0.00 31.57 4.55
2127 7163 6.402226 CGAAAAGAATTTCTTTACTCCCTCCG 60.402 42.308 21.47 12.19 45.19 4.63
2128 7164 6.653740 TCGAAAAGAATTTCTTTACTCCCTCC 59.346 38.462 21.47 6.26 45.19 4.30
2129 7165 7.388224 AGTCGAAAAGAATTTCTTTACTCCCTC 59.612 37.037 21.47 14.12 45.19 4.30
2130 7166 7.225011 AGTCGAAAAGAATTTCTTTACTCCCT 58.775 34.615 21.47 12.50 45.19 4.20
2131 7167 7.172703 TGAGTCGAAAAGAATTTCTTTACTCCC 59.827 37.037 29.22 18.19 45.19 4.30
2132 7168 8.084590 TGAGTCGAAAAGAATTTCTTTACTCC 57.915 34.615 29.22 20.10 45.19 3.85
2133 7169 9.535270 CATGAGTCGAAAAGAATTTCTTTACTC 57.465 33.333 27.60 27.60 45.19 2.59
2134 7170 9.057089 ACATGAGTCGAAAAGAATTTCTTTACT 57.943 29.630 21.47 20.04 45.19 2.24
2138 7174 8.378172 TGTACATGAGTCGAAAAGAATTTCTT 57.622 30.769 5.82 5.82 42.29 2.52
2139 7175 7.962964 TGTACATGAGTCGAAAAGAATTTCT 57.037 32.000 0.00 0.00 42.29 2.52
2140 7176 9.612620 ATTTGTACATGAGTCGAAAAGAATTTC 57.387 29.630 0.00 0.00 37.28 2.17
2141 7177 9.398170 CATTTGTACATGAGTCGAAAAGAATTT 57.602 29.630 0.00 0.00 42.41 1.82
2142 7178 7.538678 GCATTTGTACATGAGTCGAAAAGAATT 59.461 33.333 0.00 0.00 0.00 2.17
2143 7179 7.023575 GCATTTGTACATGAGTCGAAAAGAAT 58.976 34.615 0.00 0.00 0.00 2.40
2144 7180 6.370593 GCATTTGTACATGAGTCGAAAAGAA 58.629 36.000 0.00 0.00 0.00 2.52
2145 7181 5.106712 GGCATTTGTACATGAGTCGAAAAGA 60.107 40.000 0.00 0.00 0.00 2.52
2146 7182 5.088739 GGCATTTGTACATGAGTCGAAAAG 58.911 41.667 0.00 0.00 0.00 2.27
2147 7183 4.517075 TGGCATTTGTACATGAGTCGAAAA 59.483 37.500 0.00 0.00 0.00 2.29
2148 7184 4.068599 TGGCATTTGTACATGAGTCGAAA 58.931 39.130 0.00 0.00 0.00 3.46
2149 7185 3.669536 TGGCATTTGTACATGAGTCGAA 58.330 40.909 0.00 0.00 0.00 3.71
2150 7186 3.056179 TCTGGCATTTGTACATGAGTCGA 60.056 43.478 0.00 0.00 0.00 4.20
2151 7187 3.261580 TCTGGCATTTGTACATGAGTCG 58.738 45.455 0.00 0.00 0.00 4.18
2152 7188 4.093998 CACTCTGGCATTTGTACATGAGTC 59.906 45.833 0.00 0.00 32.13 3.36
2153 7189 4.005650 CACTCTGGCATTTGTACATGAGT 58.994 43.478 0.00 0.17 34.38 3.41
2154 7190 4.256110 TCACTCTGGCATTTGTACATGAG 58.744 43.478 0.00 0.00 0.00 2.90
2155 7191 4.284829 TCACTCTGGCATTTGTACATGA 57.715 40.909 0.00 0.00 0.00 3.07
2156 7192 4.673580 GCTTCACTCTGGCATTTGTACATG 60.674 45.833 0.00 0.00 0.00 3.21
2157 7193 3.441572 GCTTCACTCTGGCATTTGTACAT 59.558 43.478 0.00 0.00 0.00 2.29
2158 7194 2.813754 GCTTCACTCTGGCATTTGTACA 59.186 45.455 0.00 0.00 0.00 2.90
2159 7195 2.813754 TGCTTCACTCTGGCATTTGTAC 59.186 45.455 0.00 0.00 0.00 2.90
2160 7196 3.138884 TGCTTCACTCTGGCATTTGTA 57.861 42.857 0.00 0.00 0.00 2.41
2161 7197 1.985473 TGCTTCACTCTGGCATTTGT 58.015 45.000 0.00 0.00 0.00 2.83
2165 7201 3.920231 TCTAATGCTTCACTCTGGCAT 57.080 42.857 0.00 0.00 46.79 4.40
2166 7202 3.701205 TTCTAATGCTTCACTCTGGCA 57.299 42.857 0.00 0.00 40.32 4.92
2167 7203 5.819901 ACTTATTCTAATGCTTCACTCTGGC 59.180 40.000 0.00 0.00 0.00 4.85
2168 7204 7.439655 GGTACTTATTCTAATGCTTCACTCTGG 59.560 40.741 0.00 0.00 0.00 3.86
2169 7205 8.200792 AGGTACTTATTCTAATGCTTCACTCTG 58.799 37.037 0.00 0.00 27.25 3.35
2170 7206 8.312669 AGGTACTTATTCTAATGCTTCACTCT 57.687 34.615 0.00 0.00 27.25 3.24
2190 7226 1.672145 GCGTGAACTCCCTGAAGGTAC 60.672 57.143 0.00 0.00 36.75 3.34
2191 7227 0.606604 GCGTGAACTCCCTGAAGGTA 59.393 55.000 0.00 0.00 36.75 3.08
2192 7228 1.122019 AGCGTGAACTCCCTGAAGGT 61.122 55.000 0.00 0.00 36.75 3.50
2193 7229 0.035458 AAGCGTGAACTCCCTGAAGG 59.965 55.000 0.00 0.00 0.00 3.46
2194 7230 2.743636 TAAGCGTGAACTCCCTGAAG 57.256 50.000 0.00 0.00 0.00 3.02
2195 7231 3.135994 GTTTAAGCGTGAACTCCCTGAA 58.864 45.455 0.05 0.00 0.00 3.02
2196 7232 2.367567 AGTTTAAGCGTGAACTCCCTGA 59.632 45.455 3.99 0.00 27.68 3.86
2197 7233 2.480419 CAGTTTAAGCGTGAACTCCCTG 59.520 50.000 6.83 0.00 31.52 4.45
2198 7234 2.104281 ACAGTTTAAGCGTGAACTCCCT 59.896 45.455 6.83 0.00 31.52 4.20
2199 7235 2.490991 ACAGTTTAAGCGTGAACTCCC 58.509 47.619 6.83 0.00 31.52 4.30
2200 7236 4.547406 AAACAGTTTAAGCGTGAACTCC 57.453 40.909 6.83 0.00 31.52 3.85
2249 7285 2.228582 CGAAATGCCCAACATGTCTTCA 59.771 45.455 0.00 0.00 40.44 3.02
2250 7286 2.867429 CGAAATGCCCAACATGTCTTC 58.133 47.619 0.00 0.00 40.44 2.87
2269 7305 0.809636 TGCTGTCATCGTAATGGGCG 60.810 55.000 0.00 0.00 33.42 6.13
2279 7315 2.894387 GCCGAGGCTGCTGTCATC 60.894 66.667 6.90 0.00 38.26 2.92
2346 7382 3.372206 GCACACACTATTGCTAGACTTGG 59.628 47.826 0.00 0.00 35.74 3.61
2347 7383 3.996363 TGCACACACTATTGCTAGACTTG 59.004 43.478 0.00 0.00 39.62 3.16
2352 7388 2.349590 TGCTGCACACACTATTGCTAG 58.650 47.619 0.00 0.00 39.62 3.42
2417 7453 4.329392 TGAAGATGCAGATGAAGCTTTGA 58.671 39.130 0.00 0.00 0.00 2.69
2467 7503 0.680061 GTGAACCGGACTTCTCCAGT 59.320 55.000 9.46 0.00 39.07 4.00
2665 7701 1.376812 GGTGTGGTGGTTCGGGATC 60.377 63.158 0.00 0.00 0.00 3.36
2666 7702 2.754375 GGTGTGGTGGTTCGGGAT 59.246 61.111 0.00 0.00 0.00 3.85
2687 7723 1.952296 CCAGGACAAGATTATGCAGCC 59.048 52.381 0.00 0.00 0.00 4.85
2690 7726 4.299586 TGTTCCAGGACAAGATTATGCA 57.700 40.909 0.00 0.00 0.00 3.96
2695 7731 3.057315 CGCATTTGTTCCAGGACAAGATT 60.057 43.478 0.00 0.00 40.33 2.40
2702 7738 2.331893 CGGCGCATTTGTTCCAGGA 61.332 57.895 10.83 0.00 0.00 3.86
2716 7752 4.316254 CGTTAAAATTTAACACTGACGGCG 59.684 41.667 23.28 4.80 0.00 6.46
2718 7754 6.791775 GGTACGTTAAAATTTAACACTGACGG 59.208 38.462 23.28 11.01 32.81 4.79
2834 7870 4.184629 CGCAGAATATAGGATACCAAGCC 58.815 47.826 0.00 0.00 37.17 4.35
2838 7874 2.416836 GCGCGCAGAATATAGGATACCA 60.417 50.000 29.10 0.00 37.17 3.25
2885 8940 0.451783 GTGGCATTGGTGGAATCGAC 59.548 55.000 0.00 0.00 0.00 4.20
2889 8944 1.196911 CATGGTGGCATTGGTGGAAT 58.803 50.000 0.00 0.00 0.00 3.01
2932 8994 1.276421 CCTATGGCTAATCCCACGGAG 59.724 57.143 0.00 0.00 37.79 4.63
2935 8997 4.202264 GGATATCCTATGGCTAATCCCACG 60.202 50.000 14.97 0.00 37.79 4.94
2962 9024 3.616219 AGTTGCACAACAGTACAGGAAA 58.384 40.909 15.40 0.00 43.47 3.13
2965 9027 2.545526 CAGAGTTGCACAACAGTACAGG 59.454 50.000 15.40 0.00 43.47 4.00
2978 9041 2.219674 CAGACGTTCAGTTCAGAGTTGC 59.780 50.000 0.00 0.00 0.00 4.17
2983 9046 3.305403 GGATGTCAGACGTTCAGTTCAGA 60.305 47.826 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.