Multiple sequence alignment - TraesCS1B01G187200

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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 TraesCS1B01G187200 chr1B 100.000 3923 0 0 1 3923 334546379 334550301 0.000000e+00 7245
1 TraesCS1B01G187200 chr1D 92.501 3334 163 47 131 3432 239559706 239556428 0.000000e+00 4691
2 TraesCS1B01G187200 chr1D 88.325 197 8 4 3431 3617 239556126 239555935 5.100000e-54 222
3 TraesCS1B01G187200 chr1D 86.070 201 20 3 3730 3923 239555709 239555510 3.970000e-50 209
4 TraesCS1B01G187200 chr1A 93.641 1950 83 21 1495 3432 303729513 303727593 0.000000e+00 2876
5 TraesCS1B01G187200 chr1A 94.132 1244 50 11 235 1457 303730754 303729513 0.000000e+00 1871
6 TraesCS1B01G187200 chr1A 89.560 182 12 3 3743 3923 303712484 303712309 1.420000e-54 224
7 TraesCS1B01G187200 chr1A 92.754 69 5 0 3632 3700 303712547 303712479 2.490000e-17 100


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 TraesCS1B01G187200 chr1B 334546379 334550301 3922 False 7245.000000 7245 100.000000 1 3923 1 chr1B.!!$F1 3922
1 TraesCS1B01G187200 chr1D 239555510 239559706 4196 True 1707.333333 4691 88.965333 131 3923 3 chr1D.!!$R1 3792
2 TraesCS1B01G187200 chr1A 303727593 303730754 3161 True 2373.500000 2876 93.886500 235 3432 2 chr1A.!!$R2 3197

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
229 230 1.068588 AGCTTTTTGGCTTTTCGGGAC 59.931 47.619 0.0 0.0 39.86 4.46 F
1825 1869 0.101399 CCGATCCTCGTGTCTTCCTG 59.899 60.000 0.0 0.0 38.40 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 1890 0.107017 CGCAAGGAGACATGGGGATT 60.107 55.0 0.0 0.0 38.21 3.01 R
3699 4268 0.108992 ATGGAACGCAAAGCAGCATG 60.109 50.0 0.0 0.0 40.87 4.06 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
22 23 5.814764 AGAAAAGATGCTGCAGTGAATAG 57.185 39.130 16.64 0.00 0.00 1.73
23 24 4.096081 AGAAAAGATGCTGCAGTGAATAGC 59.904 41.667 16.64 0.00 37.93 2.97
29 30 4.888038 TGCTGCAGTGAATAGCATAAAG 57.112 40.909 16.64 0.00 42.05 1.85
30 31 4.516323 TGCTGCAGTGAATAGCATAAAGA 58.484 39.130 16.64 0.00 42.05 2.52
31 32 4.943093 TGCTGCAGTGAATAGCATAAAGAA 59.057 37.500 16.64 0.00 42.05 2.52
32 33 5.065602 TGCTGCAGTGAATAGCATAAAGAAG 59.934 40.000 16.64 0.00 42.05 2.85
33 34 5.065731 GCTGCAGTGAATAGCATAAAGAAGT 59.934 40.000 16.64 0.00 40.42 3.01
34 35 6.668541 TGCAGTGAATAGCATAAAGAAGTC 57.331 37.500 0.00 0.00 35.51 3.01
35 36 6.172630 TGCAGTGAATAGCATAAAGAAGTCA 58.827 36.000 0.00 0.00 35.51 3.41
36 37 6.654582 TGCAGTGAATAGCATAAAGAAGTCAA 59.345 34.615 0.00 0.00 35.51 3.18
37 38 7.337689 TGCAGTGAATAGCATAAAGAAGTCAAT 59.662 33.333 0.00 0.00 35.51 2.57
38 39 7.642978 GCAGTGAATAGCATAAAGAAGTCAATG 59.357 37.037 0.00 0.00 34.09 2.82
39 40 7.642978 CAGTGAATAGCATAAAGAAGTCAATGC 59.357 37.037 0.00 0.00 43.97 3.56
46 47 7.019774 GCATAAAGAAGTCAATGCTGTATGA 57.980 36.000 0.00 0.00 41.16 2.15
47 48 7.475015 GCATAAAGAAGTCAATGCTGTATGAA 58.525 34.615 0.00 0.00 41.16 2.57
48 49 8.133627 GCATAAAGAAGTCAATGCTGTATGAAT 58.866 33.333 0.00 0.00 41.16 2.57
51 52 6.857777 AGAAGTCAATGCTGTATGAATAGC 57.142 37.500 0.00 0.00 40.09 2.97
59 60 4.453751 TGCTGTATGAATAGCATTGCTCA 58.546 39.130 15.81 8.01 43.99 4.26
60 61 4.883006 TGCTGTATGAATAGCATTGCTCAA 59.117 37.500 15.81 0.00 43.99 3.02
61 62 5.533528 TGCTGTATGAATAGCATTGCTCAAT 59.466 36.000 15.81 0.68 43.99 2.57
62 63 6.711645 TGCTGTATGAATAGCATTGCTCAATA 59.288 34.615 15.81 6.44 43.99 1.90
63 64 7.020010 GCTGTATGAATAGCATTGCTCAATAC 58.980 38.462 15.81 16.92 39.50 1.89
64 65 7.094890 GCTGTATGAATAGCATTGCTCAATACT 60.095 37.037 15.81 0.00 39.50 2.12
65 66 9.428097 CTGTATGAATAGCATTGCTCAATACTA 57.572 33.333 15.81 5.34 40.44 1.82
66 67 9.208022 TGTATGAATAGCATTGCTCAATACTAC 57.792 33.333 15.81 11.25 40.44 2.73
67 68 7.678947 ATGAATAGCATTGCTCAATACTACC 57.321 36.000 15.81 2.61 40.44 3.18
68 69 6.830912 TGAATAGCATTGCTCAATACTACCT 58.169 36.000 15.81 0.00 40.44 3.08
69 70 6.931281 TGAATAGCATTGCTCAATACTACCTC 59.069 38.462 15.81 0.00 40.44 3.85
70 71 4.078639 AGCATTGCTCAATACTACCTCC 57.921 45.455 5.03 0.00 30.62 4.30
71 72 2.802816 GCATTGCTCAATACTACCTCCG 59.197 50.000 0.16 0.00 0.00 4.63
72 73 3.741388 GCATTGCTCAATACTACCTCCGT 60.741 47.826 0.16 0.00 0.00 4.69
73 74 3.795623 TTGCTCAATACTACCTCCGTC 57.204 47.619 0.00 0.00 0.00 4.79
74 75 2.730382 TGCTCAATACTACCTCCGTCA 58.270 47.619 0.00 0.00 0.00 4.35
75 76 2.426024 TGCTCAATACTACCTCCGTCAC 59.574 50.000 0.00 0.00 0.00 3.67
76 77 2.426024 GCTCAATACTACCTCCGTCACA 59.574 50.000 0.00 0.00 0.00 3.58
77 78 3.734293 GCTCAATACTACCTCCGTCACAC 60.734 52.174 0.00 0.00 0.00 3.82
78 79 3.423749 TCAATACTACCTCCGTCACACA 58.576 45.455 0.00 0.00 0.00 3.72
79 80 3.827876 TCAATACTACCTCCGTCACACAA 59.172 43.478 0.00 0.00 0.00 3.33
80 81 4.464951 TCAATACTACCTCCGTCACACAAT 59.535 41.667 0.00 0.00 0.00 2.71
81 82 5.653330 TCAATACTACCTCCGTCACACAATA 59.347 40.000 0.00 0.00 0.00 1.90
82 83 6.322969 TCAATACTACCTCCGTCACACAATAT 59.677 38.462 0.00 0.00 0.00 1.28
83 84 7.503230 TCAATACTACCTCCGTCACACAATATA 59.497 37.037 0.00 0.00 0.00 0.86
84 85 7.828508 ATACTACCTCCGTCACACAATATAA 57.171 36.000 0.00 0.00 0.00 0.98
85 86 6.145338 ACTACCTCCGTCACACAATATAAG 57.855 41.667 0.00 0.00 0.00 1.73
86 87 5.889853 ACTACCTCCGTCACACAATATAAGA 59.110 40.000 0.00 0.00 0.00 2.10
87 88 5.263968 ACCTCCGTCACACAATATAAGAG 57.736 43.478 0.00 0.00 0.00 2.85
88 89 4.099573 ACCTCCGTCACACAATATAAGAGG 59.900 45.833 0.00 0.00 43.24 3.69
89 90 4.099573 CCTCCGTCACACAATATAAGAGGT 59.900 45.833 0.00 0.00 34.87 3.85
90 91 5.395324 CCTCCGTCACACAATATAAGAGGTT 60.395 44.000 0.00 0.00 34.87 3.50
91 92 6.045072 TCCGTCACACAATATAAGAGGTTT 57.955 37.500 0.00 0.00 0.00 3.27
92 93 7.172868 TCCGTCACACAATATAAGAGGTTTA 57.827 36.000 0.00 0.00 0.00 2.01
93 94 7.788026 TCCGTCACACAATATAAGAGGTTTAT 58.212 34.615 0.00 0.00 0.00 1.40
94 95 8.262227 TCCGTCACACAATATAAGAGGTTTATT 58.738 33.333 0.00 0.00 0.00 1.40
95 96 9.537192 CCGTCACACAATATAAGAGGTTTATTA 57.463 33.333 0.00 0.00 0.00 0.98
107 108 7.812690 AAGAGGTTTATTACAAAAACGTCCT 57.187 32.000 14.33 3.32 45.80 3.85
108 109 8.907222 AAGAGGTTTATTACAAAAACGTCCTA 57.093 30.769 14.33 0.00 45.80 2.94
109 110 8.315391 AGAGGTTTATTACAAAAACGTCCTAC 57.685 34.615 14.33 0.00 45.80 3.18
110 111 7.933033 AGAGGTTTATTACAAAAACGTCCTACA 59.067 33.333 14.33 0.00 45.80 2.74
111 112 8.625786 AGGTTTATTACAAAAACGTCCTACAT 57.374 30.769 0.00 0.00 37.64 2.29
112 113 9.070179 AGGTTTATTACAAAAACGTCCTACATT 57.930 29.630 0.00 0.00 37.64 2.71
117 118 5.305139 ACAAAAACGTCCTACATTATGGC 57.695 39.130 0.00 0.00 0.00 4.40
118 119 5.007682 ACAAAAACGTCCTACATTATGGCT 58.992 37.500 0.00 0.00 0.00 4.75
119 120 5.475564 ACAAAAACGTCCTACATTATGGCTT 59.524 36.000 0.00 0.00 0.00 4.35
120 121 6.655848 ACAAAAACGTCCTACATTATGGCTTA 59.344 34.615 0.00 0.00 0.00 3.09
121 122 6.673154 AAAACGTCCTACATTATGGCTTAC 57.327 37.500 0.00 0.00 0.00 2.34
122 123 5.609533 AACGTCCTACATTATGGCTTACT 57.390 39.130 0.00 0.00 0.00 2.24
123 124 4.945246 ACGTCCTACATTATGGCTTACTG 58.055 43.478 0.00 0.00 0.00 2.74
124 125 3.741344 CGTCCTACATTATGGCTTACTGC 59.259 47.826 0.00 0.00 41.94 4.40
219 220 7.814587 AGATAAATGTAAGACAAGCTTTTTGGC 59.185 33.333 0.00 0.00 38.05 4.52
220 221 5.535753 AATGTAAGACAAGCTTTTTGGCT 57.464 34.783 0.00 0.00 45.30 4.75
227 228 3.986970 AGCTTTTTGGCTTTTCGGG 57.013 47.368 0.00 0.00 39.86 5.14
229 230 1.068588 AGCTTTTTGGCTTTTCGGGAC 59.931 47.619 0.00 0.00 39.86 4.46
247 261 5.424121 GGGACGGATGACATTTTGAATAG 57.576 43.478 0.00 0.00 0.00 1.73
318 332 9.740239 TTAAAACATGTCTATATACACCGACTC 57.260 33.333 0.00 0.00 30.75 3.36
319 333 5.608676 ACATGTCTATATACACCGACTCG 57.391 43.478 0.00 0.00 30.75 4.18
321 335 5.761726 ACATGTCTATATACACCGACTCGAA 59.238 40.000 0.00 0.00 30.75 3.71
403 417 4.938832 AGAGGAGATCGTTATGTAGATCGG 59.061 45.833 0.56 0.00 45.68 4.18
494 508 1.729517 GCTCTTTTGACTCGGAGAAGC 59.270 52.381 12.86 5.14 34.09 3.86
540 555 2.679837 GCACTACTGCACTGCATATGTT 59.320 45.455 3.64 0.00 43.62 2.71
638 661 6.797454 ACTCAAGCTAGGTTCTACTAAATCG 58.203 40.000 3.68 0.00 0.00 3.34
844 874 4.836255 AGCCTATATATACTCCCTCCCC 57.164 50.000 0.00 0.00 0.00 4.81
897 927 3.213402 CTCGCCTCTCGTCCTCCC 61.213 72.222 0.00 0.00 39.67 4.30
1330 1362 1.305887 CCCCGTTCCAGGTACTCCT 60.306 63.158 0.00 0.00 46.37 3.69
1333 1365 1.263356 CCGTTCCAGGTACTCCTTCA 58.737 55.000 0.00 0.00 43.07 3.02
1360 1394 2.668632 CTCTTGTTGGCCCCGCTA 59.331 61.111 0.00 0.00 0.00 4.26
1375 1409 4.443315 GCCCCGCTAGGTTAATTTACTGTA 60.443 45.833 0.00 0.00 35.12 2.74
1379 1413 7.283807 CCCCGCTAGGTTAATTTACTGTAATTT 59.716 37.037 11.18 11.18 35.12 1.82
1426 1460 1.946768 CTTCTTTGGTCTTTGCGGACA 59.053 47.619 6.62 0.00 37.91 4.02
1471 1505 0.774491 AAGGTCTAGGTGGGGGCAAA 60.774 55.000 0.00 0.00 0.00 3.68
1478 1512 1.836604 GGTGGGGGCAAAGCAAAGA 60.837 57.895 0.00 0.00 0.00 2.52
1483 1517 1.899142 GGGGGCAAAGCAAAGATACAA 59.101 47.619 0.00 0.00 0.00 2.41
1485 1519 2.825532 GGGGCAAAGCAAAGATACAAGA 59.174 45.455 0.00 0.00 0.00 3.02
1493 1527 1.983605 CAAAGATACAAGACGACGCGT 59.016 47.619 13.85 13.85 45.10 6.01
1525 1560 8.430828 GTCAAGATCTAATTGAAAAGCTTTTGC 58.569 33.333 28.42 18.75 41.02 3.68
1548 1584 5.973565 GCGAGGGAAGATCATAATTTTGTTG 59.026 40.000 0.00 0.00 0.00 3.33
1549 1585 6.498304 CGAGGGAAGATCATAATTTTGTTGG 58.502 40.000 0.00 0.00 0.00 3.77
1606 1642 1.410648 CCATGTTCCTCTCCCCATTGG 60.411 57.143 0.00 0.00 0.00 3.16
1690 1733 1.169577 ATTACGTGGCGAATTTGGCA 58.830 45.000 17.59 17.59 42.76 4.92
1733 1776 2.907910 TTCGAACGAGTGGCTAGTAC 57.092 50.000 0.00 0.00 0.00 2.73
1734 1777 2.105006 TCGAACGAGTGGCTAGTACT 57.895 50.000 0.00 0.00 0.00 2.73
1735 1778 3.251479 TCGAACGAGTGGCTAGTACTA 57.749 47.619 1.89 1.89 0.00 1.82
1794 1838 3.822192 TCCGACGCATCTGGGACG 61.822 66.667 10.98 10.98 43.10 4.79
1804 1848 0.179000 ATCTGGGACGATCTTGTGGC 59.821 55.000 0.00 0.00 0.00 5.01
1808 1852 3.554692 GACGATCTTGTGGCGCCG 61.555 66.667 23.90 9.58 0.00 6.46
1813 1857 2.650813 GATCTTGTGGCGCCGATCCT 62.651 60.000 23.83 8.54 0.00 3.24
1825 1869 0.101399 CCGATCCTCGTGTCTTCCTG 59.899 60.000 0.00 0.00 38.40 3.86
1833 1877 1.354337 CGTGTCTTCCTGTGCCGATG 61.354 60.000 0.00 0.00 0.00 3.84
1864 1908 1.396653 CAATCCCCATGTCTCCTTGC 58.603 55.000 0.00 0.00 0.00 4.01
1931 1979 4.766891 CCCTACATGTGGTTCAGAAATTGT 59.233 41.667 9.11 0.00 0.00 2.71
1937 1985 4.681744 TGTGGTTCAGAAATTGTGCTTTC 58.318 39.130 0.00 0.00 35.74 2.62
1951 2000 3.055891 TGTGCTTTCTGATCGAATCCTGA 60.056 43.478 0.00 0.00 0.00 3.86
2020 2071 4.370364 TCGGAATATGCTTGCCTTTTTC 57.630 40.909 0.00 0.00 0.00 2.29
2047 2098 5.845985 TTGCGTTAGATCTGAGAAGTTTG 57.154 39.130 5.18 0.00 0.00 2.93
2057 2108 3.117888 TCTGAGAAGTTTGTCTTGCCCTT 60.118 43.478 0.00 0.00 36.40 3.95
2058 2109 3.214328 TGAGAAGTTTGTCTTGCCCTTC 58.786 45.455 0.00 0.00 36.40 3.46
2114 2167 1.602851 GCTGATGCATGTGACTGATCC 59.397 52.381 2.46 0.00 39.41 3.36
2289 2342 4.621747 CGCTACTTCCTCAACTCCATTTCT 60.622 45.833 0.00 0.00 0.00 2.52
2472 2525 2.024871 GTCGGCGAGATCTCCACG 59.975 66.667 21.33 21.33 0.00 4.94
2646 2699 1.210538 TGCTTGAGCTGATGGAGGAT 58.789 50.000 4.44 0.00 42.66 3.24
2859 2912 2.033755 CGACGAGGAGGACGACTGT 61.034 63.158 0.00 0.00 34.70 3.55
2910 2963 1.185618 TCCTGAGGGTGTTCCGTGAG 61.186 60.000 0.00 0.00 41.52 3.51
2937 2990 2.426522 CAGTGAGGCGGAGATGAAAAA 58.573 47.619 0.00 0.00 0.00 1.94
2994 3048 3.055094 GGAGAGGATTTGCTGTTGGTAGA 60.055 47.826 0.00 0.00 0.00 2.59
2999 3053 1.234615 TTTGCTGTTGGTAGAGCGCC 61.235 55.000 2.29 0.00 43.30 6.53
3044 3098 6.513230 CGTTTCCTGTGAAATGTGATGAAGAA 60.513 38.462 0.00 0.00 42.20 2.52
3047 3101 6.479006 TCCTGTGAAATGTGATGAAGAAGAT 58.521 36.000 0.00 0.00 0.00 2.40
3055 3109 9.339492 GAAATGTGATGAAGAAGATCTGTTTTC 57.661 33.333 0.00 1.65 0.00 2.29
3145 3201 4.006319 ACCTGAAGACTTGCTTATGCTTC 58.994 43.478 0.00 0.00 36.83 3.86
3146 3202 3.063180 CCTGAAGACTTGCTTATGCTTCG 59.937 47.826 0.00 0.00 38.17 3.79
3147 3203 3.925379 TGAAGACTTGCTTATGCTTCGA 58.075 40.909 0.00 0.00 38.17 3.71
3199 3255 3.365364 GCTGTGGTACAATGCTGTTTCTC 60.365 47.826 0.00 0.00 44.16 2.87
3244 3300 8.645110 AGAGATTAGCCATCCATTTTTATTTGG 58.355 33.333 0.00 0.00 31.20 3.28
3245 3301 8.322905 AGATTAGCCATCCATTTTTATTTGGT 57.677 30.769 0.00 0.00 34.48 3.67
3246 3302 8.206189 AGATTAGCCATCCATTTTTATTTGGTG 58.794 33.333 0.00 0.00 34.48 4.17
3247 3303 4.516323 AGCCATCCATTTTTATTTGGTGC 58.484 39.130 0.00 0.00 34.48 5.01
3248 3304 4.019501 AGCCATCCATTTTTATTTGGTGCA 60.020 37.500 0.00 0.00 34.48 4.57
3249 3305 4.883006 GCCATCCATTTTTATTTGGTGCAT 59.117 37.500 0.00 0.00 34.48 3.96
3250 3306 5.357596 GCCATCCATTTTTATTTGGTGCATT 59.642 36.000 0.00 0.00 34.48 3.56
3290 3346 5.662211 TTCTACGTAGGAAAACAAACAGC 57.338 39.130 22.01 0.00 0.00 4.40
3313 3369 5.970023 GCACTAGCATTTTCTGAATCATGAC 59.030 40.000 0.00 0.00 41.58 3.06
3384 3440 4.083802 GGAGTGGCATCTATTTATTGCGAC 60.084 45.833 0.00 1.71 42.97 5.19
3400 3456 2.899900 TGCGACTGCTAGAATATCCCAT 59.100 45.455 0.00 0.00 43.34 4.00
3514 3873 5.648572 ACCTTTAGAGGAGATAAACGAACG 58.351 41.667 6.26 0.00 46.74 3.95
3532 3891 5.031578 CGAACGAAGAAACTGAGGAGATAG 58.968 45.833 0.00 0.00 0.00 2.08
3566 3933 1.451504 CAGTCCCAGTGCTTCACCA 59.548 57.895 0.00 0.00 34.49 4.17
3576 3943 2.147150 GTGCTTCACCAGTTCCTTCTC 58.853 52.381 0.00 0.00 0.00 2.87
3611 3980 0.971386 AAAGGATTTGGCCTGCACTG 59.029 50.000 3.32 0.00 36.60 3.66
3630 4199 3.203487 ACTGTCCAGGTCCTTTGGTAAAA 59.797 43.478 0.00 0.00 37.02 1.52
3631 4200 4.141018 ACTGTCCAGGTCCTTTGGTAAAAT 60.141 41.667 0.00 0.00 37.02 1.82
3632 4201 4.148838 TGTCCAGGTCCTTTGGTAAAATG 58.851 43.478 0.00 0.00 37.02 2.32
3633 4202 3.509967 GTCCAGGTCCTTTGGTAAAATGG 59.490 47.826 0.00 0.00 37.02 3.16
3634 4203 3.141272 TCCAGGTCCTTTGGTAAAATGGT 59.859 43.478 0.00 0.00 37.02 3.55
3635 4204 4.354387 TCCAGGTCCTTTGGTAAAATGGTA 59.646 41.667 0.00 0.00 37.02 3.25
3636 4205 5.081032 CCAGGTCCTTTGGTAAAATGGTAA 58.919 41.667 0.00 0.00 0.00 2.85
3637 4206 5.540719 CCAGGTCCTTTGGTAAAATGGTAAA 59.459 40.000 0.00 0.00 0.00 2.01
3649 4218 1.241315 ATGGTAAACAGCCACGCACC 61.241 55.000 0.00 0.00 39.03 5.01
3650 4219 2.554272 GTAAACAGCCACGCACCG 59.446 61.111 0.00 0.00 0.00 4.94
3651 4220 1.957186 GTAAACAGCCACGCACCGA 60.957 57.895 0.00 0.00 0.00 4.69
3652 4221 1.004320 TAAACAGCCACGCACCGAT 60.004 52.632 0.00 0.00 0.00 4.18
3653 4222 0.604243 TAAACAGCCACGCACCGATT 60.604 50.000 0.00 0.00 0.00 3.34
3654 4223 0.604243 AAACAGCCACGCACCGATTA 60.604 50.000 0.00 0.00 0.00 1.75
3655 4224 0.392461 AACAGCCACGCACCGATTAT 60.392 50.000 0.00 0.00 0.00 1.28
3656 4225 1.089481 ACAGCCACGCACCGATTATG 61.089 55.000 0.00 0.00 0.00 1.90
3657 4226 0.809636 CAGCCACGCACCGATTATGA 60.810 55.000 0.00 0.00 0.00 2.15
3658 4227 0.107897 AGCCACGCACCGATTATGAA 60.108 50.000 0.00 0.00 0.00 2.57
3659 4228 0.944386 GCCACGCACCGATTATGAAT 59.056 50.000 0.00 0.00 0.00 2.57
3660 4229 1.069906 GCCACGCACCGATTATGAATC 60.070 52.381 0.00 0.00 34.52 2.52
3661 4230 2.483876 CCACGCACCGATTATGAATCT 58.516 47.619 0.00 0.00 35.73 2.40
3662 4231 3.649073 CCACGCACCGATTATGAATCTA 58.351 45.455 0.00 0.00 35.73 1.98
3663 4232 3.428870 CCACGCACCGATTATGAATCTAC 59.571 47.826 0.00 0.00 35.73 2.59
3664 4233 4.299155 CACGCACCGATTATGAATCTACT 58.701 43.478 0.00 0.00 35.73 2.57
3665 4234 5.458015 CACGCACCGATTATGAATCTACTA 58.542 41.667 0.00 0.00 35.73 1.82
3666 4235 5.569441 CACGCACCGATTATGAATCTACTAG 59.431 44.000 0.00 0.00 35.73 2.57
3667 4236 5.241064 ACGCACCGATTATGAATCTACTAGT 59.759 40.000 0.00 0.00 35.73 2.57
3668 4237 5.569441 CGCACCGATTATGAATCTACTAGTG 59.431 44.000 5.39 0.00 35.73 2.74
3669 4238 5.346281 GCACCGATTATGAATCTACTAGTGC 59.654 44.000 5.39 0.00 35.09 4.40
3670 4239 6.682746 CACCGATTATGAATCTACTAGTGCT 58.317 40.000 5.39 0.00 35.73 4.40
3671 4240 7.575155 GCACCGATTATGAATCTACTAGTGCTA 60.575 40.741 5.39 0.00 37.04 3.49
3672 4241 8.297426 CACCGATTATGAATCTACTAGTGCTAA 58.703 37.037 5.39 0.00 35.73 3.09
3673 4242 8.516234 ACCGATTATGAATCTACTAGTGCTAAG 58.484 37.037 5.39 0.00 35.73 2.18
3674 4243 8.516234 CCGATTATGAATCTACTAGTGCTAAGT 58.484 37.037 5.39 0.00 35.73 2.24
3675 4244 9.900710 CGATTATGAATCTACTAGTGCTAAGTT 57.099 33.333 5.39 0.00 35.73 2.66
3679 4248 7.101652 TGAATCTACTAGTGCTAAGTTCTGG 57.898 40.000 5.39 0.00 0.00 3.86
3680 4249 6.890268 TGAATCTACTAGTGCTAAGTTCTGGA 59.110 38.462 5.39 0.00 0.00 3.86
3681 4250 7.561722 TGAATCTACTAGTGCTAAGTTCTGGAT 59.438 37.037 5.39 0.00 0.00 3.41
3682 4251 6.701145 TCTACTAGTGCTAAGTTCTGGATG 57.299 41.667 5.39 0.00 0.00 3.51
3683 4252 6.188407 TCTACTAGTGCTAAGTTCTGGATGT 58.812 40.000 5.39 0.00 0.00 3.06
3684 4253 5.331876 ACTAGTGCTAAGTTCTGGATGTC 57.668 43.478 0.00 0.00 0.00 3.06
3685 4254 3.618690 AGTGCTAAGTTCTGGATGTCC 57.381 47.619 0.00 0.00 0.00 4.02
3686 4255 2.906389 AGTGCTAAGTTCTGGATGTCCA 59.094 45.455 1.17 1.17 45.30 4.02
3687 4256 3.327757 AGTGCTAAGTTCTGGATGTCCAA 59.672 43.478 2.97 0.00 46.97 3.53
3688 4257 3.437049 GTGCTAAGTTCTGGATGTCCAAC 59.563 47.826 2.97 0.00 46.97 3.77
3689 4258 3.072330 TGCTAAGTTCTGGATGTCCAACA 59.928 43.478 2.97 0.00 46.97 3.33
3690 4259 3.437049 GCTAAGTTCTGGATGTCCAACAC 59.563 47.826 2.97 3.10 46.97 3.32
3691 4260 3.864789 AAGTTCTGGATGTCCAACACT 57.135 42.857 2.97 5.27 46.97 3.55
3692 4261 4.974645 AAGTTCTGGATGTCCAACACTA 57.025 40.909 11.34 0.00 46.97 2.74
3693 4262 4.974645 AGTTCTGGATGTCCAACACTAA 57.025 40.909 9.86 0.00 46.97 2.24
3694 4263 5.304686 AGTTCTGGATGTCCAACACTAAA 57.695 39.130 9.86 0.00 46.97 1.85
3695 4264 5.308825 AGTTCTGGATGTCCAACACTAAAG 58.691 41.667 9.86 0.00 46.97 1.85
3696 4265 5.071788 AGTTCTGGATGTCCAACACTAAAGA 59.928 40.000 9.86 0.00 46.97 2.52
3697 4266 5.560722 TCTGGATGTCCAACACTAAAGAA 57.439 39.130 2.97 0.00 46.97 2.52
3698 4267 5.935945 TCTGGATGTCCAACACTAAAGAAA 58.064 37.500 2.97 0.00 46.97 2.52
3699 4268 5.763204 TCTGGATGTCCAACACTAAAGAAAC 59.237 40.000 2.97 0.00 46.97 2.78
3700 4269 5.441500 TGGATGTCCAACACTAAAGAAACA 58.558 37.500 0.00 0.00 44.35 2.83
3701 4270 6.068010 TGGATGTCCAACACTAAAGAAACAT 58.932 36.000 0.00 0.00 44.35 2.71
3702 4271 6.016360 TGGATGTCCAACACTAAAGAAACATG 60.016 38.462 0.00 0.00 44.35 3.21
3703 4272 5.181690 TGTCCAACACTAAAGAAACATGC 57.818 39.130 0.00 0.00 0.00 4.06
3704 4273 4.887071 TGTCCAACACTAAAGAAACATGCT 59.113 37.500 0.00 0.00 0.00 3.79
3705 4274 5.215160 GTCCAACACTAAAGAAACATGCTG 58.785 41.667 0.00 0.00 0.00 4.41
3706 4275 3.983344 CCAACACTAAAGAAACATGCTGC 59.017 43.478 0.00 0.00 0.00 5.25
3707 4276 4.261741 CCAACACTAAAGAAACATGCTGCT 60.262 41.667 0.00 0.00 0.00 4.24
3708 4277 5.284079 CAACACTAAAGAAACATGCTGCTT 58.716 37.500 0.00 0.00 0.00 3.91
3709 4278 5.520376 ACACTAAAGAAACATGCTGCTTT 57.480 34.783 7.25 7.25 35.09 3.51
3710 4279 5.284079 ACACTAAAGAAACATGCTGCTTTG 58.716 37.500 11.69 5.28 33.16 2.77
3711 4280 4.149396 CACTAAAGAAACATGCTGCTTTGC 59.851 41.667 11.69 0.00 33.16 3.68
3712 4281 1.774639 AAGAAACATGCTGCTTTGCG 58.225 45.000 0.00 0.00 35.36 4.85
3713 4282 0.670162 AGAAACATGCTGCTTTGCGT 59.330 45.000 0.00 0.00 35.36 5.24
3714 4283 1.067516 AGAAACATGCTGCTTTGCGTT 59.932 42.857 0.00 0.00 35.36 4.84
3715 4284 1.453148 GAAACATGCTGCTTTGCGTTC 59.547 47.619 0.00 3.42 35.36 3.95
3716 4285 0.318955 AACATGCTGCTTTGCGTTCC 60.319 50.000 0.00 0.00 35.36 3.62
3717 4286 1.286570 CATGCTGCTTTGCGTTCCA 59.713 52.632 0.00 0.00 35.36 3.53
3718 4287 0.108992 CATGCTGCTTTGCGTTCCAT 60.109 50.000 0.00 0.00 35.36 3.41
3719 4288 0.604578 ATGCTGCTTTGCGTTCCATT 59.395 45.000 0.00 0.00 35.36 3.16
3720 4289 1.242989 TGCTGCTTTGCGTTCCATTA 58.757 45.000 0.00 0.00 35.36 1.90
3721 4290 1.199789 TGCTGCTTTGCGTTCCATTAG 59.800 47.619 0.00 0.00 35.36 1.73
3722 4291 1.900237 CTGCTTTGCGTTCCATTAGC 58.100 50.000 0.00 0.00 34.10 3.09
3723 4292 0.167908 TGCTTTGCGTTCCATTAGCG 59.832 50.000 0.00 0.00 35.43 4.26
3728 4297 2.890474 CGTTCCATTAGCGCCGCT 60.890 61.111 18.67 18.67 43.41 5.52
3736 4305 2.813226 ATTAGCGCCGCTGGTTTGGA 62.813 55.000 23.97 0.00 40.10 3.53
3754 4323 5.549742 TTGGAAAATCAGAAACCAAGCAT 57.450 34.783 0.00 0.00 36.00 3.79
3756 4325 4.588106 TGGAAAATCAGAAACCAAGCATCA 59.412 37.500 0.00 0.00 0.00 3.07
3779 4348 5.993106 AGCAGTCTTTAACACTTCTTGTC 57.007 39.130 0.00 0.00 37.51 3.18
3784 4353 6.477688 CAGTCTTTAACACTTCTTGTCGGTTA 59.522 38.462 0.00 0.00 37.51 2.85
3816 4392 3.136809 TGGCGGTTAATCCTTATAGGCAA 59.863 43.478 0.00 0.00 34.61 4.52
3817 4393 3.501062 GGCGGTTAATCCTTATAGGCAAC 59.499 47.826 0.00 0.00 34.61 4.17
3822 4398 0.756903 ATCCTTATAGGCAACCGCGT 59.243 50.000 4.92 0.00 39.92 6.01
3913 4489 1.692148 TTGTTATTCTCGCGCGCCTG 61.692 55.000 27.95 18.52 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.096081 GCTATTCACTGCAGCATCTTTTCT 59.904 41.667 15.27 0.00 35.35 2.52
1 2 4.142534 TGCTATTCACTGCAGCATCTTTTC 60.143 41.667 15.27 0.00 40.26 2.29
2 3 3.760151 TGCTATTCACTGCAGCATCTTTT 59.240 39.130 15.27 0.00 40.26 2.27
3 4 3.349927 TGCTATTCACTGCAGCATCTTT 58.650 40.909 15.27 0.00 40.26 2.52
4 5 2.995283 TGCTATTCACTGCAGCATCTT 58.005 42.857 15.27 0.00 40.26 2.40
5 6 2.704464 TGCTATTCACTGCAGCATCT 57.296 45.000 15.27 0.00 40.26 2.90
9 10 5.065731 ACTTCTTTATGCTATTCACTGCAGC 59.934 40.000 15.27 0.00 42.74 5.25
10 11 6.314648 TGACTTCTTTATGCTATTCACTGCAG 59.685 38.462 13.48 13.48 42.74 4.41
11 12 6.172630 TGACTTCTTTATGCTATTCACTGCA 58.827 36.000 0.00 0.00 43.67 4.41
12 13 6.668541 TGACTTCTTTATGCTATTCACTGC 57.331 37.500 0.00 0.00 0.00 4.40
13 14 7.642978 GCATTGACTTCTTTATGCTATTCACTG 59.357 37.037 0.00 0.00 40.08 3.66
14 15 7.701445 GCATTGACTTCTTTATGCTATTCACT 58.299 34.615 0.00 0.00 40.08 3.41
15 16 7.905031 GCATTGACTTCTTTATGCTATTCAC 57.095 36.000 0.00 0.00 40.08 3.18
22 23 7.019774 TCATACAGCATTGACTTCTTTATGC 57.980 36.000 0.00 0.00 42.76 3.14
25 26 8.830580 GCTATTCATACAGCATTGACTTCTTTA 58.169 33.333 0.00 0.00 37.73 1.85
26 27 7.337689 TGCTATTCATACAGCATTGACTTCTTT 59.662 33.333 0.00 0.00 42.68 2.52
27 28 6.825213 TGCTATTCATACAGCATTGACTTCTT 59.175 34.615 0.00 0.00 42.68 2.52
28 29 6.351711 TGCTATTCATACAGCATTGACTTCT 58.648 36.000 0.00 0.00 42.68 2.85
29 30 6.609237 TGCTATTCATACAGCATTGACTTC 57.391 37.500 0.00 0.00 42.68 3.01
38 39 5.428496 TTGAGCAATGCTATTCATACAGC 57.572 39.130 8.12 0.00 39.88 4.40
39 40 8.320396 AGTATTGAGCAATGCTATTCATACAG 57.680 34.615 8.12 0.00 41.00 2.74
40 41 9.208022 GTAGTATTGAGCAATGCTATTCATACA 57.792 33.333 19.17 0.00 44.01 2.29
41 42 8.660373 GGTAGTATTGAGCAATGCTATTCATAC 58.340 37.037 19.17 11.74 44.01 2.39
42 43 8.597167 AGGTAGTATTGAGCAATGCTATTCATA 58.403 33.333 19.17 0.00 44.01 2.15
43 44 7.456725 AGGTAGTATTGAGCAATGCTATTCAT 58.543 34.615 19.17 0.39 44.01 2.57
44 45 6.830912 AGGTAGTATTGAGCAATGCTATTCA 58.169 36.000 19.17 0.00 44.01 2.57
45 46 6.370166 GGAGGTAGTATTGAGCAATGCTATTC 59.630 42.308 19.17 18.10 44.01 1.75
46 47 6.234177 GGAGGTAGTATTGAGCAATGCTATT 58.766 40.000 19.17 12.96 44.01 1.73
47 48 5.567623 CGGAGGTAGTATTGAGCAATGCTAT 60.568 44.000 19.17 1.06 44.01 2.97
48 49 4.262036 CGGAGGTAGTATTGAGCAATGCTA 60.262 45.833 8.12 14.37 42.40 3.49
49 50 3.493350 CGGAGGTAGTATTGAGCAATGCT 60.493 47.826 7.79 7.79 44.15 3.79
50 51 2.802816 CGGAGGTAGTATTGAGCAATGC 59.197 50.000 0.00 0.00 34.26 3.56
51 52 4.051922 GACGGAGGTAGTATTGAGCAATG 58.948 47.826 5.99 0.00 32.50 2.82
52 53 3.704566 TGACGGAGGTAGTATTGAGCAAT 59.295 43.478 0.97 0.97 34.93 3.56
53 54 3.093814 TGACGGAGGTAGTATTGAGCAA 58.906 45.455 0.00 0.00 0.00 3.91
54 55 2.426024 GTGACGGAGGTAGTATTGAGCA 59.574 50.000 0.00 0.00 0.00 4.26
55 56 2.426024 TGTGACGGAGGTAGTATTGAGC 59.574 50.000 0.00 0.00 0.00 4.26
56 57 3.442625 TGTGTGACGGAGGTAGTATTGAG 59.557 47.826 0.00 0.00 0.00 3.02
57 58 3.423749 TGTGTGACGGAGGTAGTATTGA 58.576 45.455 0.00 0.00 0.00 2.57
58 59 3.861276 TGTGTGACGGAGGTAGTATTG 57.139 47.619 0.00 0.00 0.00 1.90
59 60 6.726490 ATATTGTGTGACGGAGGTAGTATT 57.274 37.500 0.00 0.00 0.00 1.89
60 61 7.722728 TCTTATATTGTGTGACGGAGGTAGTAT 59.277 37.037 0.00 0.00 0.00 2.12
61 62 7.056006 TCTTATATTGTGTGACGGAGGTAGTA 58.944 38.462 0.00 0.00 0.00 1.82
62 63 5.889853 TCTTATATTGTGTGACGGAGGTAGT 59.110 40.000 0.00 0.00 0.00 2.73
63 64 6.387041 TCTTATATTGTGTGACGGAGGTAG 57.613 41.667 0.00 0.00 0.00 3.18
64 65 5.301045 CCTCTTATATTGTGTGACGGAGGTA 59.699 44.000 0.00 0.00 34.77 3.08
65 66 4.099573 CCTCTTATATTGTGTGACGGAGGT 59.900 45.833 0.00 0.00 34.77 3.85
66 67 4.099573 ACCTCTTATATTGTGTGACGGAGG 59.900 45.833 0.00 0.00 42.23 4.30
67 68 5.263968 ACCTCTTATATTGTGTGACGGAG 57.736 43.478 0.00 0.00 0.00 4.63
68 69 5.670792 AACCTCTTATATTGTGTGACGGA 57.329 39.130 0.00 0.00 0.00 4.69
69 70 8.433421 AATAAACCTCTTATATTGTGTGACGG 57.567 34.615 0.00 0.00 0.00 4.79
81 82 9.511272 AGGACGTTTTTGTAATAAACCTCTTAT 57.489 29.630 0.00 0.00 33.07 1.73
82 83 8.907222 AGGACGTTTTTGTAATAAACCTCTTA 57.093 30.769 0.00 0.00 33.07 2.10
83 84 7.812690 AGGACGTTTTTGTAATAAACCTCTT 57.187 32.000 0.00 0.00 33.07 2.85
84 85 7.933033 TGTAGGACGTTTTTGTAATAAACCTCT 59.067 33.333 0.00 0.00 33.07 3.69
85 86 8.086851 TGTAGGACGTTTTTGTAATAAACCTC 57.913 34.615 0.00 0.00 33.07 3.85
86 87 8.625786 ATGTAGGACGTTTTTGTAATAAACCT 57.374 30.769 0.00 0.00 33.07 3.50
91 92 8.614346 GCCATAATGTAGGACGTTTTTGTAATA 58.386 33.333 0.00 0.00 0.00 0.98
92 93 7.338449 AGCCATAATGTAGGACGTTTTTGTAAT 59.662 33.333 0.00 0.00 0.00 1.89
93 94 6.655848 AGCCATAATGTAGGACGTTTTTGTAA 59.344 34.615 0.00 0.00 0.00 2.41
94 95 6.174760 AGCCATAATGTAGGACGTTTTTGTA 58.825 36.000 0.00 0.00 0.00 2.41
95 96 5.007682 AGCCATAATGTAGGACGTTTTTGT 58.992 37.500 0.00 0.00 0.00 2.83
96 97 5.560966 AGCCATAATGTAGGACGTTTTTG 57.439 39.130 0.00 0.00 0.00 2.44
97 98 6.882678 AGTAAGCCATAATGTAGGACGTTTTT 59.117 34.615 0.00 0.00 0.00 1.94
98 99 6.315393 CAGTAAGCCATAATGTAGGACGTTTT 59.685 38.462 0.00 0.00 0.00 2.43
99 100 5.815740 CAGTAAGCCATAATGTAGGACGTTT 59.184 40.000 0.00 0.00 0.00 3.60
100 101 5.357257 CAGTAAGCCATAATGTAGGACGTT 58.643 41.667 0.00 0.00 0.00 3.99
101 102 4.739735 GCAGTAAGCCATAATGTAGGACGT 60.740 45.833 0.00 0.00 37.23 4.34
102 103 3.741344 GCAGTAAGCCATAATGTAGGACG 59.259 47.826 0.00 0.00 37.23 4.79
116 117 0.392461 TTGGGATGTCGGCAGTAAGC 60.392 55.000 0.00 0.00 44.65 3.09
117 118 2.107950 TTTGGGATGTCGGCAGTAAG 57.892 50.000 0.00 0.00 0.00 2.34
118 119 2.570415 TTTTGGGATGTCGGCAGTAA 57.430 45.000 0.00 0.00 0.00 2.24
119 120 2.570415 TTTTTGGGATGTCGGCAGTA 57.430 45.000 0.00 0.00 0.00 2.74
120 121 3.430473 TTTTTGGGATGTCGGCAGT 57.570 47.368 0.00 0.00 0.00 4.40
210 211 1.497991 GTCCCGAAAAGCCAAAAAGC 58.502 50.000 0.00 0.00 0.00 3.51
219 220 2.024176 ATGTCATCCGTCCCGAAAAG 57.976 50.000 0.00 0.00 0.00 2.27
220 221 2.483014 AATGTCATCCGTCCCGAAAA 57.517 45.000 0.00 0.00 0.00 2.29
221 222 2.483014 AAATGTCATCCGTCCCGAAA 57.517 45.000 0.00 0.00 0.00 3.46
222 223 2.080693 CAAAATGTCATCCGTCCCGAA 58.919 47.619 0.00 0.00 0.00 4.30
223 224 1.276705 TCAAAATGTCATCCGTCCCGA 59.723 47.619 0.00 0.00 0.00 5.14
224 225 1.732941 TCAAAATGTCATCCGTCCCG 58.267 50.000 0.00 0.00 0.00 5.14
226 227 6.436843 AACTATTCAAAATGTCATCCGTCC 57.563 37.500 0.00 0.00 0.00 4.79
292 306 9.740239 GAGTCGGTGTATATAGACATGTTTTAA 57.260 33.333 11.75 0.00 36.18 1.52
300 314 6.682423 TTTTCGAGTCGGTGTATATAGACA 57.318 37.500 13.54 0.00 36.18 3.41
329 343 5.065218 CGTTCCTATTTTTGAGATGTCCTGG 59.935 44.000 0.00 0.00 0.00 4.45
330 344 5.065218 CCGTTCCTATTTTTGAGATGTCCTG 59.935 44.000 0.00 0.00 0.00 3.86
332 346 4.335594 CCCGTTCCTATTTTTGAGATGTCC 59.664 45.833 0.00 0.00 0.00 4.02
340 354 6.812879 AGTACTTTCCCGTTCCTATTTTTG 57.187 37.500 0.00 0.00 0.00 2.44
447 461 6.149129 AGTTCAAGATTTTCTGGGTTTGTC 57.851 37.500 0.00 0.00 0.00 3.18
540 555 1.409241 GCATCTTGCCCAGATTCCAGA 60.409 52.381 0.00 0.00 40.67 3.86
638 661 1.300233 CTGTATTCGGCTCGGCTCC 60.300 63.158 0.00 0.00 0.00 4.70
897 927 4.150454 AGGAGAGAGAGGCCGGGG 62.150 72.222 2.18 0.00 0.00 5.73
1330 1362 0.772124 ACAAGAGGGGAAGGGCTGAA 60.772 55.000 0.00 0.00 0.00 3.02
1333 1365 1.770324 CAACAAGAGGGGAAGGGCT 59.230 57.895 0.00 0.00 0.00 5.19
1407 1441 1.673920 GTGTCCGCAAAGACCAAAGAA 59.326 47.619 0.00 0.00 35.83 2.52
1426 1460 4.202151 GCAAAACTCCAATCTTGAACAGGT 60.202 41.667 0.00 0.00 0.00 4.00
1471 1505 1.993370 GCGTCGTCTTGTATCTTTGCT 59.007 47.619 0.00 0.00 0.00 3.91
1478 1512 2.054687 TGAAACGCGTCGTCTTGTAT 57.945 45.000 14.44 0.00 39.99 2.29
1483 1517 0.248743 TGACTTGAAACGCGTCGTCT 60.249 50.000 14.44 0.00 39.99 4.18
1485 1519 0.575390 CTTGACTTGAAACGCGTCGT 59.425 50.000 14.44 2.88 43.97 4.34
1493 1527 9.683069 GCTTTTCAATTAGATCTTGACTTGAAA 57.317 29.630 19.57 19.57 39.49 2.69
1525 1560 6.318648 TCCAACAAAATTATGATCTTCCCTCG 59.681 38.462 0.00 0.00 0.00 4.63
1561 1597 9.846248 GGCATATCTCCAACATCAAAATATTAC 57.154 33.333 0.00 0.00 0.00 1.89
1680 1723 4.916983 TTCCAATCCTATGCCAAATTCG 57.083 40.909 0.00 0.00 0.00 3.34
1690 1733 3.347216 GCCACGCATATTCCAATCCTAT 58.653 45.455 0.00 0.00 0.00 2.57
1751 1794 1.213430 TGACACGAGTTTCCCCCTTTT 59.787 47.619 0.00 0.00 0.00 2.27
1760 1803 1.790623 CGGACGATTTGACACGAGTTT 59.209 47.619 0.00 0.00 0.00 2.66
1794 1838 2.247437 GGATCGGCGCCACAAGATC 61.247 63.158 28.98 26.78 38.88 2.75
1808 1852 1.737363 GCACAGGAAGACACGAGGATC 60.737 57.143 0.00 0.00 0.00 3.36
1813 1857 1.532604 ATCGGCACAGGAAGACACGA 61.533 55.000 0.00 0.00 0.00 4.35
1840 1884 0.475906 GAGACATGGGGATTGGGGAG 59.524 60.000 0.00 0.00 0.00 4.30
1841 1885 0.993509 GGAGACATGGGGATTGGGGA 60.994 60.000 0.00 0.00 0.00 4.81
1842 1886 0.995675 AGGAGACATGGGGATTGGGG 60.996 60.000 0.00 0.00 0.00 4.96
1843 1887 0.929244 AAGGAGACATGGGGATTGGG 59.071 55.000 0.00 0.00 0.00 4.12
1844 1888 2.025863 GCAAGGAGACATGGGGATTGG 61.026 57.143 0.00 0.00 0.00 3.16
1845 1889 1.396653 GCAAGGAGACATGGGGATTG 58.603 55.000 0.00 0.00 0.00 2.67
1846 1890 0.107017 CGCAAGGAGACATGGGGATT 60.107 55.000 0.00 0.00 38.21 3.01
1847 1891 0.982852 TCGCAAGGAGACATGGGGAT 60.983 55.000 0.00 0.00 41.68 3.85
1931 1979 3.893326 TCAGGATTCGATCAGAAAGCA 57.107 42.857 4.52 0.00 42.91 3.91
2026 2077 4.883083 ACAAACTTCTCAGATCTAACGCA 58.117 39.130 0.00 0.00 0.00 5.24
2043 2094 7.448748 TTTATTAGAGAAGGGCAAGACAAAC 57.551 36.000 0.00 0.00 0.00 2.93
2047 2098 7.716998 TCATGATTTATTAGAGAAGGGCAAGAC 59.283 37.037 0.00 0.00 0.00 3.01
2114 2167 2.149578 CTTCCAAGACACTGCAGGAAG 58.850 52.381 19.93 15.65 46.39 3.46
2232 2285 1.005748 CGTGAGCCAGCAGAAGTCA 60.006 57.895 0.00 0.00 0.00 3.41
2289 2342 0.738975 CGGCGACATGGTAGAAGAGA 59.261 55.000 0.00 0.00 0.00 3.10
2937 2990 1.413812 CTGCAAAAACTCCAAGCCCTT 59.586 47.619 0.00 0.00 0.00 3.95
2939 2992 0.752658 ACTGCAAAAACTCCAAGCCC 59.247 50.000 0.00 0.00 0.00 5.19
2999 3053 4.093952 CAAGGCAGGCGCAACTCG 62.094 66.667 10.83 0.00 41.24 4.18
3055 3109 9.520204 AACATGTCTCAACAAAGAACAAATTAG 57.480 29.630 0.00 0.00 39.30 1.73
3146 3202 5.084722 GCACGATGCTGCTTTATTATCATC 58.915 41.667 0.00 0.00 40.96 2.92
3147 3203 4.516321 TGCACGATGCTGCTTTATTATCAT 59.484 37.500 0.00 0.00 45.31 2.45
3199 3255 5.582550 TCTCTACGTTGTCATCATAAGCTG 58.417 41.667 0.00 0.00 0.00 4.24
3204 3260 6.264518 TGGCTAATCTCTACGTTGTCATCATA 59.735 38.462 0.00 0.00 0.00 2.15
3205 3261 5.069119 TGGCTAATCTCTACGTTGTCATCAT 59.931 40.000 0.00 0.00 0.00 2.45
3206 3262 4.401202 TGGCTAATCTCTACGTTGTCATCA 59.599 41.667 0.00 0.00 0.00 3.07
3207 3263 4.933330 TGGCTAATCTCTACGTTGTCATC 58.067 43.478 0.00 0.00 0.00 2.92
3208 3264 5.509840 GGATGGCTAATCTCTACGTTGTCAT 60.510 44.000 0.00 0.00 35.43 3.06
3209 3265 4.202121 GGATGGCTAATCTCTACGTTGTCA 60.202 45.833 0.00 0.00 35.43 3.58
3213 3269 5.552870 AATGGATGGCTAATCTCTACGTT 57.447 39.130 0.00 0.00 35.43 3.99
3274 3330 4.274950 TGCTAGTGCTGTTTGTTTTCCTAC 59.725 41.667 0.00 0.00 40.48 3.18
3290 3346 7.317842 AGTCATGATTCAGAAAATGCTAGTG 57.682 36.000 0.00 0.00 0.00 2.74
3338 3394 2.802816 GTGTGTCAGTCCAGATGTTCAC 59.197 50.000 0.00 0.00 0.00 3.18
3384 3440 7.619050 ACATCACTTATGGGATATTCTAGCAG 58.381 38.462 0.00 0.00 40.16 4.24
3400 3456 9.474920 GTTGAAAAATCCAATGAACATCACTTA 57.525 29.630 0.00 0.00 0.00 2.24
3475 3834 9.968870 CCTCTAAAGGTTATGTCTAGTGATTAC 57.031 37.037 0.00 0.00 37.94 1.89
3486 3845 8.302515 TCGTTTATCTCCTCTAAAGGTTATGT 57.697 34.615 0.00 0.00 43.82 2.29
3496 3855 6.748333 TTCTTCGTTCGTTTATCTCCTCTA 57.252 37.500 0.00 0.00 0.00 2.43
3514 3873 4.981674 CGATGCTATCTCCTCAGTTTCTTC 59.018 45.833 0.00 0.00 0.00 2.87
3532 3891 1.365633 CTGGGTAGAGCCTCGATGC 59.634 63.158 4.31 4.31 37.43 3.91
3576 3943 7.697691 CAAATCCTTTTGGCTACATACAGTAG 58.302 38.462 0.00 0.00 41.81 2.57
3611 3980 3.509967 CCATTTTACCAAAGGACCTGGAC 59.490 47.826 6.77 0.00 37.40 4.02
3630 4199 1.241315 GGTGCGTGGCTGTTTACCAT 61.241 55.000 0.00 0.00 39.95 3.55
3631 4200 1.894756 GGTGCGTGGCTGTTTACCA 60.895 57.895 0.00 0.00 33.84 3.25
3632 4201 2.951458 GGTGCGTGGCTGTTTACC 59.049 61.111 0.00 0.00 0.00 2.85
3633 4202 1.296056 ATCGGTGCGTGGCTGTTTAC 61.296 55.000 0.00 0.00 0.00 2.01
3634 4203 0.604243 AATCGGTGCGTGGCTGTTTA 60.604 50.000 0.00 0.00 0.00 2.01
3635 4204 0.604243 TAATCGGTGCGTGGCTGTTT 60.604 50.000 0.00 0.00 0.00 2.83
3636 4205 0.392461 ATAATCGGTGCGTGGCTGTT 60.392 50.000 0.00 0.00 0.00 3.16
3637 4206 1.089481 CATAATCGGTGCGTGGCTGT 61.089 55.000 0.00 0.00 0.00 4.40
3649 4218 9.900710 AACTTAGCACTAGTAGATTCATAATCG 57.099 33.333 3.59 0.00 42.75 3.34
3653 4222 8.851145 CCAGAACTTAGCACTAGTAGATTCATA 58.149 37.037 3.59 0.00 0.00 2.15
3654 4223 7.561722 TCCAGAACTTAGCACTAGTAGATTCAT 59.438 37.037 3.59 0.00 0.00 2.57
3655 4224 6.890268 TCCAGAACTTAGCACTAGTAGATTCA 59.110 38.462 3.59 0.00 0.00 2.57
3656 4225 7.336161 TCCAGAACTTAGCACTAGTAGATTC 57.664 40.000 3.59 0.00 0.00 2.52
3657 4226 7.343316 ACATCCAGAACTTAGCACTAGTAGATT 59.657 37.037 3.59 0.00 0.00 2.40
3658 4227 6.836527 ACATCCAGAACTTAGCACTAGTAGAT 59.163 38.462 3.59 0.00 0.00 1.98
3659 4228 6.188407 ACATCCAGAACTTAGCACTAGTAGA 58.812 40.000 3.59 0.00 0.00 2.59
3660 4229 6.458232 ACATCCAGAACTTAGCACTAGTAG 57.542 41.667 0.00 0.00 0.00 2.57
3661 4230 5.360144 GGACATCCAGAACTTAGCACTAGTA 59.640 44.000 0.00 0.00 35.64 1.82
3662 4231 4.160626 GGACATCCAGAACTTAGCACTAGT 59.839 45.833 0.00 0.00 35.64 2.57
3663 4232 4.160439 TGGACATCCAGAACTTAGCACTAG 59.840 45.833 0.00 0.00 42.01 2.57
3664 4233 4.093743 TGGACATCCAGAACTTAGCACTA 58.906 43.478 0.00 0.00 42.01 2.74
3665 4234 2.906389 TGGACATCCAGAACTTAGCACT 59.094 45.455 0.00 0.00 42.01 4.40
3666 4235 3.334583 TGGACATCCAGAACTTAGCAC 57.665 47.619 0.00 0.00 42.01 4.40
3677 4246 5.441500 TGTTTCTTTAGTGTTGGACATCCA 58.558 37.500 0.00 0.00 45.94 3.41
3678 4247 6.381801 CATGTTTCTTTAGTGTTGGACATCC 58.618 40.000 0.00 0.00 0.00 3.51
3679 4248 5.858581 GCATGTTTCTTTAGTGTTGGACATC 59.141 40.000 0.00 0.00 0.00 3.06
3680 4249 5.536161 AGCATGTTTCTTTAGTGTTGGACAT 59.464 36.000 0.00 0.00 0.00 3.06
3681 4250 4.887071 AGCATGTTTCTTTAGTGTTGGACA 59.113 37.500 0.00 0.00 0.00 4.02
3682 4251 5.215160 CAGCATGTTTCTTTAGTGTTGGAC 58.785 41.667 0.00 0.00 0.00 4.02
3683 4252 4.261572 GCAGCATGTTTCTTTAGTGTTGGA 60.262 41.667 0.00 0.00 39.31 3.53
3684 4253 3.983344 GCAGCATGTTTCTTTAGTGTTGG 59.017 43.478 0.00 0.00 39.31 3.77
3685 4254 4.863491 AGCAGCATGTTTCTTTAGTGTTG 58.137 39.130 0.00 0.00 39.31 3.33
3686 4255 5.520376 AAGCAGCATGTTTCTTTAGTGTT 57.480 34.783 0.00 0.00 32.65 3.32
3687 4256 5.284079 CAAAGCAGCATGTTTCTTTAGTGT 58.716 37.500 6.85 0.00 39.13 3.55
3688 4257 4.149396 GCAAAGCAGCATGTTTCTTTAGTG 59.851 41.667 6.85 0.00 39.13 2.74
3689 4258 4.301628 GCAAAGCAGCATGTTTCTTTAGT 58.698 39.130 6.85 0.00 39.13 2.24
3690 4259 3.362831 CGCAAAGCAGCATGTTTCTTTAG 59.637 43.478 6.85 4.07 39.13 1.85
3691 4260 3.243367 ACGCAAAGCAGCATGTTTCTTTA 60.243 39.130 6.85 0.00 39.13 1.85
3692 4261 2.129607 CGCAAAGCAGCATGTTTCTTT 58.870 42.857 1.54 1.54 39.13 2.52
3693 4262 1.067516 ACGCAAAGCAGCATGTTTCTT 59.932 42.857 0.00 0.00 39.13 2.52
3694 4263 0.670162 ACGCAAAGCAGCATGTTTCT 59.330 45.000 0.00 0.00 39.13 2.52
3695 4264 1.453148 GAACGCAAAGCAGCATGTTTC 59.547 47.619 0.00 0.00 39.13 2.78
3696 4265 1.490621 GAACGCAAAGCAGCATGTTT 58.509 45.000 0.00 0.00 43.07 2.83
3697 4266 0.318955 GGAACGCAAAGCAGCATGTT 60.319 50.000 0.00 0.00 39.31 2.71
3698 4267 1.286880 GGAACGCAAAGCAGCATGT 59.713 52.632 0.00 0.00 39.31 3.21
3699 4268 0.108992 ATGGAACGCAAAGCAGCATG 60.109 50.000 0.00 0.00 40.87 4.06
3700 4269 0.604578 AATGGAACGCAAAGCAGCAT 59.395 45.000 0.00 0.00 0.00 3.79
3701 4270 1.199789 CTAATGGAACGCAAAGCAGCA 59.800 47.619 0.00 0.00 0.00 4.41
3702 4271 1.900237 CTAATGGAACGCAAAGCAGC 58.100 50.000 0.00 0.00 0.00 5.25
3703 4272 1.791555 CGCTAATGGAACGCAAAGCAG 60.792 52.381 0.00 0.00 0.00 4.24
3704 4273 0.167908 CGCTAATGGAACGCAAAGCA 59.832 50.000 0.00 0.00 0.00 3.91
3705 4274 2.930168 CGCTAATGGAACGCAAAGC 58.070 52.632 0.00 0.00 0.00 3.51
3711 4280 2.890474 AGCGGCGCTAATGGAACG 60.890 61.111 35.68 0.00 36.99 3.95
3712 4281 2.709475 CAGCGGCGCTAATGGAAC 59.291 61.111 35.90 0.00 36.40 3.62
3713 4282 2.513666 CCAGCGGCGCTAATGGAA 60.514 61.111 35.90 0.00 36.40 3.53
3714 4283 2.813226 AAACCAGCGGCGCTAATGGA 62.813 55.000 35.64 0.00 36.40 3.41
3715 4284 2.406616 AAACCAGCGGCGCTAATGG 61.407 57.895 35.90 32.38 36.40 3.16
3716 4285 1.226379 CAAACCAGCGGCGCTAATG 60.226 57.895 35.90 26.26 36.40 1.90
3717 4286 2.406616 CCAAACCAGCGGCGCTAAT 61.407 57.895 35.90 22.57 36.40 1.73
3718 4287 3.053291 CCAAACCAGCGGCGCTAA 61.053 61.111 35.90 0.00 36.40 3.09
3719 4288 3.538785 TTCCAAACCAGCGGCGCTA 62.539 57.895 35.90 14.89 36.40 4.26
3720 4289 4.947147 TTCCAAACCAGCGGCGCT 62.947 61.111 31.35 31.35 40.77 5.92
3721 4290 2.763627 ATTTTCCAAACCAGCGGCGC 62.764 55.000 26.86 26.86 0.00 6.53
3722 4291 0.732538 GATTTTCCAAACCAGCGGCG 60.733 55.000 0.51 0.51 0.00 6.46
3723 4292 0.316841 TGATTTTCCAAACCAGCGGC 59.683 50.000 0.00 0.00 0.00 6.53
3724 4293 1.885887 TCTGATTTTCCAAACCAGCGG 59.114 47.619 0.00 0.00 0.00 5.52
3725 4294 3.641437 TTCTGATTTTCCAAACCAGCG 57.359 42.857 0.00 0.00 0.00 5.18
3726 4295 4.058124 GGTTTCTGATTTTCCAAACCAGC 58.942 43.478 7.41 0.00 44.90 4.85
3736 4305 4.992951 GCTTGATGCTTGGTTTCTGATTTT 59.007 37.500 0.00 0.00 38.95 1.82
3756 4325 5.006746 CGACAAGAAGTGTTAAAGACTGCTT 59.993 40.000 4.02 4.02 41.96 3.91
3779 4348 1.864711 CCGCCATACATTGTCTAACCG 59.135 52.381 0.00 0.00 0.00 4.44
3784 4353 4.134563 GGATTAACCGCCATACATTGTCT 58.865 43.478 0.00 0.00 0.00 3.41
3816 4392 0.381445 GGTTAAACCACAAACGCGGT 59.619 50.000 12.47 0.00 38.42 5.68
3817 4393 0.381089 TGGTTAAACCACAAACGCGG 59.619 50.000 12.47 0.00 44.79 6.46
3822 4398 2.683867 CGGTGTCTGGTTAAACCACAAA 59.316 45.455 0.00 0.00 44.79 2.83
3828 4404 1.589803 AGTGCGGTGTCTGGTTAAAC 58.410 50.000 0.00 0.00 0.00 2.01
3829 4405 2.335316 AAGTGCGGTGTCTGGTTAAA 57.665 45.000 0.00 0.00 0.00 1.52
3896 4472 2.165301 ACAGGCGCGCGAGAATAAC 61.165 57.895 37.18 13.98 0.00 1.89


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

AutoCloner maintained by Alex Coulton.