Multiple sequence alignment - TraesCS3A01G070000

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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 TraesCS3A01G070000 chr3A 100.000 2818 0 0 1 2818 42205148 42207965 0.000000e+00 5204.0
1 TraesCS3A01G070000 chr3A 87.324 71 9 0 818 888 600930423 600930493 6.470000e-12 82.4
2 TraesCS3A01G070000 chr3B 89.206 1890 134 32 861 2705 52670164 52668300 0.000000e+00 2296.0
3 TraesCS3A01G070000 chr3B 95.238 189 5 1 644 832 52670347 52670163 2.120000e-76 296.0
4 TraesCS3A01G070000 chr3B 89.916 119 6 3 533 647 52670510 52670394 6.290000e-32 148.0
5 TraesCS3A01G070000 chr3D 93.434 929 50 7 1603 2525 30360036 30360959 0.000000e+00 1367.0
6 TraesCS3A01G070000 chr3D 91.744 969 46 5 644 1611 30358916 30359851 0.000000e+00 1315.0
7 TraesCS3A01G070000 chr3D 90.524 401 20 7 150 532 30358266 30358666 5.380000e-142 514.0
8 TraesCS3A01G070000 chr3D 94.737 114 5 1 534 647 30358759 30358871 2.890000e-40 176.0
9 TraesCS3A01G070000 chr7B 82.362 652 107 7 1686 2333 745160976 745160329 6.820000e-156 560.0
10 TraesCS3A01G070000 chr7B 79.915 468 59 9 1167 1607 745161564 745161105 7.580000e-81 311.0


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 TraesCS3A01G070000 chr3A 42205148 42207965 2817 False 5204.000000 5204 100.000000 1 2818 1 chr3A.!!$F1 2817
1 TraesCS3A01G070000 chr3B 52668300 52670510 2210 True 913.333333 2296 91.453333 533 2705 3 chr3B.!!$R1 2172
2 TraesCS3A01G070000 chr3D 30358266 30360959 2693 False 843.000000 1367 92.609750 150 2525 4 chr3D.!!$F1 2375
3 TraesCS3A01G070000 chr7B 745160329 745161564 1235 True 435.500000 560 81.138500 1167 2333 2 chr7B.!!$R1 1166

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
490 491 0.108138 AAGCCTAACTTCTCGCGCAT 60.108 50.0 8.75 0.0 30.77 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2605 0.178964 ACCTTTGTCACCCCATGTGG 60.179 55.0 0.0 0.0 45.48 4.17 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 5.132897 CTAACCATCTGAGCTAGGCTTAG 57.867 47.826 0.00 0.00 42.50 2.18
23 24 3.039252 ACCATCTGAGCTAGGCTTAGT 57.961 47.619 4.63 0.00 41.93 2.24
24 25 3.379452 ACCATCTGAGCTAGGCTTAGTT 58.621 45.455 4.63 0.00 41.93 2.24
25 26 3.386402 ACCATCTGAGCTAGGCTTAGTTC 59.614 47.826 12.05 12.05 41.93 3.01
26 27 3.551863 CCATCTGAGCTAGGCTTAGTTCG 60.552 52.174 13.67 9.31 41.93 3.95
27 28 2.724454 TCTGAGCTAGGCTTAGTTCGT 58.276 47.619 13.67 0.00 41.93 3.85
28 29 2.683867 TCTGAGCTAGGCTTAGTTCGTC 59.316 50.000 13.67 3.35 41.93 4.20
29 30 2.423892 CTGAGCTAGGCTTAGTTCGTCA 59.576 50.000 13.67 7.05 39.88 4.35
30 31 2.163815 TGAGCTAGGCTTAGTTCGTCAC 59.836 50.000 13.67 0.00 39.88 3.67
31 32 2.163815 GAGCTAGGCTTAGTTCGTCACA 59.836 50.000 4.00 0.00 39.88 3.58
32 33 2.094649 AGCTAGGCTTAGTTCGTCACAC 60.095 50.000 4.63 0.00 33.89 3.82
33 34 2.877335 CTAGGCTTAGTTCGTCACACC 58.123 52.381 0.00 0.00 0.00 4.16
34 35 1.339097 AGGCTTAGTTCGTCACACCT 58.661 50.000 0.00 0.00 0.00 4.00
35 36 1.272769 AGGCTTAGTTCGTCACACCTC 59.727 52.381 0.00 0.00 0.00 3.85
36 37 1.272769 GGCTTAGTTCGTCACACCTCT 59.727 52.381 0.00 0.00 0.00 3.69
37 38 2.288886 GGCTTAGTTCGTCACACCTCTT 60.289 50.000 0.00 0.00 0.00 2.85
38 39 2.987821 GCTTAGTTCGTCACACCTCTTC 59.012 50.000 0.00 0.00 0.00 2.87
39 40 2.983402 TAGTTCGTCACACCTCTTCG 57.017 50.000 0.00 0.00 0.00 3.79
40 41 1.315690 AGTTCGTCACACCTCTTCGA 58.684 50.000 0.00 0.00 0.00 3.71
41 42 1.001597 AGTTCGTCACACCTCTTCGAC 60.002 52.381 0.00 0.00 0.00 4.20
42 43 1.026584 TTCGTCACACCTCTTCGACA 58.973 50.000 0.00 0.00 0.00 4.35
43 44 1.244816 TCGTCACACCTCTTCGACAT 58.755 50.000 0.00 0.00 0.00 3.06
44 45 2.429478 TCGTCACACCTCTTCGACATA 58.571 47.619 0.00 0.00 0.00 2.29
45 46 2.161012 TCGTCACACCTCTTCGACATAC 59.839 50.000 0.00 0.00 0.00 2.39
46 47 2.095415 CGTCACACCTCTTCGACATACA 60.095 50.000 0.00 0.00 0.00 2.29
47 48 3.243336 GTCACACCTCTTCGACATACAC 58.757 50.000 0.00 0.00 0.00 2.90
48 49 2.888414 TCACACCTCTTCGACATACACA 59.112 45.455 0.00 0.00 0.00 3.72
49 50 3.509967 TCACACCTCTTCGACATACACAT 59.490 43.478 0.00 0.00 0.00 3.21
50 51 3.614176 CACACCTCTTCGACATACACATG 59.386 47.826 0.00 0.00 38.21 3.21
51 52 2.604914 CACCTCTTCGACATACACATGC 59.395 50.000 0.00 0.00 35.39 4.06
52 53 2.233676 ACCTCTTCGACATACACATGCA 59.766 45.455 0.00 0.00 35.39 3.96
53 54 3.118629 ACCTCTTCGACATACACATGCAT 60.119 43.478 0.00 0.00 35.39 3.96
54 55 3.246936 CCTCTTCGACATACACATGCATG 59.753 47.826 25.09 25.09 35.39 4.06
55 56 4.114794 CTCTTCGACATACACATGCATGA 58.885 43.478 32.75 11.53 35.39 3.07
56 57 4.696455 TCTTCGACATACACATGCATGAT 58.304 39.130 32.75 21.18 35.39 2.45
57 58 4.508861 TCTTCGACATACACATGCATGATG 59.491 41.667 32.75 25.32 35.39 3.07
58 59 3.132925 TCGACATACACATGCATGATGG 58.867 45.455 32.75 21.70 36.23 3.51
59 60 3.132925 CGACATACACATGCATGATGGA 58.867 45.455 32.75 22.24 36.23 3.41
60 61 3.560896 CGACATACACATGCATGATGGAA 59.439 43.478 32.75 17.73 36.23 3.53
61 62 4.214758 CGACATACACATGCATGATGGAAT 59.785 41.667 32.75 18.90 36.23 3.01
62 63 5.409214 CGACATACACATGCATGATGGAATA 59.591 40.000 32.75 14.63 36.23 1.75
63 64 6.093082 CGACATACACATGCATGATGGAATAT 59.907 38.462 32.75 15.95 36.23 1.28
64 65 7.278424 CGACATACACATGCATGATGGAATATA 59.722 37.037 32.75 14.03 36.23 0.86
65 66 9.117183 GACATACACATGCATGATGGAATATAT 57.883 33.333 32.75 15.37 36.23 0.86
71 72 9.961265 CACATGCATGATGGAATATATATTTCC 57.039 33.333 32.75 12.09 36.23 3.13
72 73 9.703677 ACATGCATGATGGAATATATATTTCCA 57.296 29.630 32.75 21.45 36.23 3.53
108 109 9.976511 AAATAAAAACCTACAAAAGAGCTAACC 57.023 29.630 0.00 0.00 0.00 2.85
109 110 8.935614 ATAAAAACCTACAAAAGAGCTAACCT 57.064 30.769 0.00 0.00 0.00 3.50
111 112 7.981102 AAAACCTACAAAAGAGCTAACCTAG 57.019 36.000 0.00 0.00 0.00 3.02
112 113 6.683312 AACCTACAAAAGAGCTAACCTAGT 57.317 37.500 0.00 0.00 0.00 2.57
113 114 6.038997 ACCTACAAAAGAGCTAACCTAGTG 57.961 41.667 0.00 0.00 0.00 2.74
114 115 5.543020 ACCTACAAAAGAGCTAACCTAGTGT 59.457 40.000 0.00 0.00 0.00 3.55
115 116 5.869888 CCTACAAAAGAGCTAACCTAGTGTG 59.130 44.000 0.00 0.00 0.00 3.82
116 117 5.546621 ACAAAAGAGCTAACCTAGTGTGA 57.453 39.130 0.00 0.00 0.00 3.58
117 118 6.115448 ACAAAAGAGCTAACCTAGTGTGAT 57.885 37.500 0.00 0.00 0.00 3.06
118 119 6.166982 ACAAAAGAGCTAACCTAGTGTGATC 58.833 40.000 0.00 0.00 0.00 2.92
119 120 6.166279 CAAAAGAGCTAACCTAGTGTGATCA 58.834 40.000 0.00 0.00 0.00 2.92
120 121 6.360370 AAAGAGCTAACCTAGTGTGATCAA 57.640 37.500 0.00 0.00 0.00 2.57
121 122 6.360370 AAGAGCTAACCTAGTGTGATCAAA 57.640 37.500 0.00 0.00 0.00 2.69
122 123 6.552445 AGAGCTAACCTAGTGTGATCAAAT 57.448 37.500 0.00 0.00 0.00 2.32
123 124 7.661536 AGAGCTAACCTAGTGTGATCAAATA 57.338 36.000 0.00 0.00 0.00 1.40
124 125 8.256356 AGAGCTAACCTAGTGTGATCAAATAT 57.744 34.615 0.00 0.00 0.00 1.28
125 126 8.364142 AGAGCTAACCTAGTGTGATCAAATATC 58.636 37.037 0.00 0.00 0.00 1.63
126 127 8.256356 AGCTAACCTAGTGTGATCAAATATCT 57.744 34.615 0.00 0.00 0.00 1.98
127 128 8.364142 AGCTAACCTAGTGTGATCAAATATCTC 58.636 37.037 0.00 0.00 0.00 2.75
128 129 7.600752 GCTAACCTAGTGTGATCAAATATCTCC 59.399 40.741 0.00 0.00 0.00 3.71
129 130 7.682787 AACCTAGTGTGATCAAATATCTCCT 57.317 36.000 0.00 0.00 0.00 3.69
130 131 7.060383 ACCTAGTGTGATCAAATATCTCCTG 57.940 40.000 0.00 0.00 0.00 3.86
131 132 6.613271 ACCTAGTGTGATCAAATATCTCCTGT 59.387 38.462 0.00 0.00 0.00 4.00
132 133 6.927936 CCTAGTGTGATCAAATATCTCCTGTG 59.072 42.308 0.00 0.00 0.00 3.66
133 134 6.550938 AGTGTGATCAAATATCTCCTGTGA 57.449 37.500 0.00 0.00 0.00 3.58
134 135 6.580788 AGTGTGATCAAATATCTCCTGTGAG 58.419 40.000 0.00 0.00 40.17 3.51
135 136 6.155910 AGTGTGATCAAATATCTCCTGTGAGT 59.844 38.462 0.00 0.00 39.75 3.41
136 137 7.343057 AGTGTGATCAAATATCTCCTGTGAGTA 59.657 37.037 0.00 0.00 39.75 2.59
137 138 8.147058 GTGTGATCAAATATCTCCTGTGAGTAT 58.853 37.037 0.00 0.00 39.75 2.12
138 139 9.367160 TGTGATCAAATATCTCCTGTGAGTATA 57.633 33.333 0.00 0.00 39.75 1.47
141 142 9.814899 GATCAAATATCTCCTGTGAGTATATGG 57.185 37.037 0.00 0.00 39.75 2.74
142 143 8.138928 TCAAATATCTCCTGTGAGTATATGGG 57.861 38.462 0.00 0.00 39.75 4.00
143 144 7.180946 TCAAATATCTCCTGTGAGTATATGGGG 59.819 40.741 0.00 0.00 39.75 4.96
144 145 4.767000 ATCTCCTGTGAGTATATGGGGA 57.233 45.455 0.00 0.00 39.75 4.81
145 146 4.767000 TCTCCTGTGAGTATATGGGGAT 57.233 45.455 0.00 0.00 39.75 3.85
146 147 5.093236 TCTCCTGTGAGTATATGGGGATT 57.907 43.478 0.00 0.00 39.75 3.01
147 148 6.227624 TCTCCTGTGAGTATATGGGGATTA 57.772 41.667 0.00 0.00 39.75 1.75
148 149 6.630131 TCTCCTGTGAGTATATGGGGATTAA 58.370 40.000 0.00 0.00 39.75 1.40
149 150 7.256399 TCTCCTGTGAGTATATGGGGATTAAT 58.744 38.462 0.00 0.00 39.75 1.40
150 151 7.739444 TCTCCTGTGAGTATATGGGGATTAATT 59.261 37.037 0.00 0.00 39.75 1.40
151 152 7.689299 TCCTGTGAGTATATGGGGATTAATTG 58.311 38.462 0.00 0.00 0.00 2.32
173 174 2.516460 TCCTCTACTCGGCCGCTC 60.516 66.667 23.51 0.00 0.00 5.03
194 195 2.741553 CGCATGCCCATAACTACACAGA 60.742 50.000 13.15 0.00 0.00 3.41
207 208 6.946229 AACTACACAGATAAACACGCTAAG 57.054 37.500 0.00 0.00 0.00 2.18
213 214 5.230306 CACAGATAAACACGCTAAGTAGCTC 59.770 44.000 8.60 0.00 46.85 4.09
275 276 8.306680 TGTTACTACAATTTGAGAGCTGTAAC 57.693 34.615 2.79 11.55 38.25 2.50
364 365 0.460311 CGTGGCCTTCTACTCGGATT 59.540 55.000 3.32 0.00 0.00 3.01
376 377 6.480524 TCTACTCGGATTTGACATGTTTTG 57.519 37.500 0.00 0.00 0.00 2.44
384 385 6.183360 CGGATTTGACATGTTTTGTTATGCAG 60.183 38.462 0.00 0.00 39.18 4.41
394 395 5.181245 TGTTTTGTTATGCAGTTAGCTCTCC 59.819 40.000 0.00 0.00 45.94 3.71
400 401 2.813907 TGCAGTTAGCTCTCCTCTCTT 58.186 47.619 0.00 0.00 45.94 2.85
408 409 7.285401 CAGTTAGCTCTCCTCTCTTTCTAATCT 59.715 40.741 0.00 0.00 0.00 2.40
423 424 7.563188 TCTTTCTAATCTGATCCAAGAGCTACT 59.437 37.037 0.00 0.00 0.00 2.57
460 461 9.301153 GAACACAACTGAGTCAATTAAATTGTT 57.699 29.630 0.00 0.00 41.02 2.83
467 468 6.499172 TGAGTCAATTAAATTGTTTGCACGA 58.501 32.000 0.00 0.00 41.02 4.35
476 477 1.317613 TGTTTGCACGATTGAAGCCT 58.682 45.000 0.00 0.00 0.00 4.58
488 489 4.187056 AAGCCTAACTTCTCGCGC 57.813 55.556 0.00 0.00 30.77 6.86
489 490 1.292223 AAGCCTAACTTCTCGCGCA 59.708 52.632 8.75 0.00 30.77 6.09
490 491 0.108138 AAGCCTAACTTCTCGCGCAT 60.108 50.000 8.75 0.00 30.77 4.73
493 494 0.924090 CCTAACTTCTCGCGCATGTC 59.076 55.000 8.75 0.00 0.00 3.06
494 495 0.567968 CTAACTTCTCGCGCATGTCG 59.432 55.000 8.75 5.35 42.12 4.35
551 661 4.494350 ACGTAGTATTTCATACGCGGAT 57.506 40.909 12.47 3.58 46.63 4.18
665 829 8.237267 CGCTTTGGACAAGATTTTACTCTAAAT 58.763 33.333 0.00 0.00 0.00 1.40
983 1147 2.478370 GCATCCAATCACCATCAACACG 60.478 50.000 0.00 0.00 0.00 4.49
1113 1277 1.153939 CTCCTCTGAGTCGTTGCCG 60.154 63.158 3.66 0.00 33.70 5.69
1130 1297 0.661780 CCGACGAGCGATGATCTTCC 60.662 60.000 0.00 0.00 44.57 3.46
1131 1298 0.661780 CGACGAGCGATGATCTTCCC 60.662 60.000 3.19 0.00 44.57 3.97
1132 1299 0.319125 GACGAGCGATGATCTTCCCC 60.319 60.000 3.19 0.00 0.00 4.81
1133 1300 1.372251 CGAGCGATGATCTTCCCCG 60.372 63.158 3.19 1.45 0.00 5.73
1134 1301 1.742768 GAGCGATGATCTTCCCCGT 59.257 57.895 3.19 0.00 0.00 5.28
1135 1302 0.598680 GAGCGATGATCTTCCCCGTG 60.599 60.000 3.19 0.00 0.00 4.94
1197 1364 0.258484 TGATGATGGGCCGTTTCCAT 59.742 50.000 0.00 0.00 46.73 3.41
1215 1382 3.047280 GTGTGGATGACGGCGCAA 61.047 61.111 10.83 0.00 0.00 4.85
1308 1475 3.512516 GCTGTGAATGCCGAGGCC 61.513 66.667 12.05 0.00 41.09 5.19
1390 1557 3.118408 AGAGTTCATGGCGCTTTATACCA 60.118 43.478 7.64 0.00 37.99 3.25
1400 1567 3.733337 CGCTTTATACCAGGCAGATTCT 58.267 45.455 0.00 0.00 0.00 2.40
1471 1662 0.532862 GGGCACATATGAGGGTGTCG 60.533 60.000 10.38 0.00 40.43 4.35
1478 1670 1.395635 TATGAGGGTGTCGCGTGTAT 58.604 50.000 5.77 0.00 0.00 2.29
1490 1682 1.438651 GCGTGTATGCCAACTTCTCA 58.561 50.000 0.00 0.00 0.00 3.27
1530 1722 0.616111 GGACTGGAGGAAGAGAGGCA 60.616 60.000 0.00 0.00 0.00 4.75
1533 1725 0.906756 CTGGAGGAAGAGAGGCACCA 60.907 60.000 0.00 0.00 0.00 4.17
1547 1739 1.310216 GCACCATCACCCCGGTTAAC 61.310 60.000 0.00 0.00 31.41 2.01
1637 2029 3.243068 ACAATTGAGAACGACAACTTGCC 60.243 43.478 13.59 0.00 0.00 4.52
1652 2044 4.792521 ACTTGCCAACAAAGTAACAACA 57.207 36.364 0.00 0.00 34.74 3.33
1653 2045 5.140747 ACTTGCCAACAAAGTAACAACAA 57.859 34.783 0.00 0.00 34.74 2.83
1654 2046 4.926832 ACTTGCCAACAAAGTAACAACAAC 59.073 37.500 0.00 0.00 34.74 3.32
1668 2060 5.502153 AACAACAACGGCTACAAAATACA 57.498 34.783 0.00 0.00 0.00 2.29
1675 2067 8.510132 ACAACGGCTACAAAATACATTTTTAC 57.490 30.769 0.00 0.00 37.86 2.01
1680 2072 8.939926 CGGCTACAAAATACATTTTTACATACG 58.060 33.333 0.00 0.00 37.86 3.06
1681 2073 8.739461 GGCTACAAAATACATTTTTACATACGC 58.261 33.333 0.00 0.00 37.86 4.42
1775 2169 3.244078 TGCAATCGAAGGACTACACAAGT 60.244 43.478 0.00 0.00 42.80 3.16
1779 2173 4.238761 TCGAAGGACTACACAAGTTCAG 57.761 45.455 0.00 0.00 39.07 3.02
1834 2228 2.032426 GCTAGTAGACTGCGACTCCTTC 59.968 54.545 0.00 0.00 32.06 3.46
2052 2446 3.739209 GCTAACCGACCTATAGCCGTTTT 60.739 47.826 10.48 6.90 36.82 2.43
2155 2549 0.659957 CCGTCACCGTAGTAGGCTAC 59.340 60.000 16.93 16.93 43.06 3.58
2247 2641 7.611467 TGACAAAGGTTACATGCTAATGAAGAT 59.389 33.333 0.00 0.00 37.24 2.40
2316 2710 6.946009 CCAGTCTTTCCCCTTATGAAAGTAAA 59.054 38.462 11.29 0.00 45.64 2.01
2341 2735 7.649370 AGAATCGACTGATTAATATGCACAG 57.351 36.000 0.00 0.00 44.79 3.66
2342 2736 7.212976 AGAATCGACTGATTAATATGCACAGT 58.787 34.615 6.48 6.48 44.79 3.55
2367 2761 2.039746 TGTAATAGTGGCCTGCAAGTGT 59.960 45.455 3.32 0.00 0.00 3.55
2375 2769 0.385974 GCCTGCAAGTGTAAAGTGCG 60.386 55.000 0.00 0.00 41.27 5.34
2379 2773 3.424829 CCTGCAAGTGTAAAGTGCGTATG 60.425 47.826 0.00 0.00 41.27 2.39
2380 2774 3.135225 TGCAAGTGTAAAGTGCGTATGT 58.865 40.909 0.00 0.00 41.27 2.29
2381 2775 4.308265 TGCAAGTGTAAAGTGCGTATGTA 58.692 39.130 0.00 0.00 41.27 2.29
2382 2776 4.150980 TGCAAGTGTAAAGTGCGTATGTAC 59.849 41.667 0.00 0.00 41.27 2.90
2399 2795 3.798202 TGTACGTTGCATATATGTGCCA 58.202 40.909 20.22 8.01 44.43 4.92
2413 2809 8.918116 CATATATGTGCCACTATATGTCTAGGT 58.082 37.037 17.29 0.00 35.21 3.08
2421 2817 7.091443 GCCACTATATGTCTAGGTGTGTAATC 58.909 42.308 0.00 0.00 0.00 1.75
2430 2826 7.215789 TGTCTAGGTGTGTAATCCGTTTTAAA 58.784 34.615 0.00 0.00 0.00 1.52
2484 2881 8.760569 GTTGTGTTTATTGGTTTCAATGTAAGG 58.239 33.333 2.27 0.00 42.93 2.69
2548 2974 3.181475 TGCTTAGCGCATCTAGCTACTTT 60.181 43.478 11.47 0.00 45.64 2.66
2553 2979 2.734079 GCGCATCTAGCTACTTTCATCC 59.266 50.000 0.30 0.00 42.61 3.51
2554 2980 3.553922 GCGCATCTAGCTACTTTCATCCT 60.554 47.826 0.30 0.00 42.61 3.24
2557 2983 5.182190 CGCATCTAGCTACTTTCATCCTCTA 59.818 44.000 0.00 0.00 42.61 2.43
2589 3018 6.678568 ATGGAATGTATTGTGGGTCAAAAA 57.321 33.333 0.00 0.00 39.62 1.94
2624 3054 8.576442 ACCTTTTGTCTATACAGGAACAAAATG 58.424 33.333 11.34 11.13 36.76 2.32
2625 3055 8.576442 CCTTTTGTCTATACAGGAACAAAATGT 58.424 33.333 11.34 0.00 36.76 2.71
2641 3071 9.162793 GAACAAAATGTCTATAAATCATGAGCG 57.837 33.333 0.09 0.00 0.00 5.03
2642 3072 7.642669 ACAAAATGTCTATAAATCATGAGCGG 58.357 34.615 0.09 0.00 0.00 5.52
2643 3073 7.498900 ACAAAATGTCTATAAATCATGAGCGGA 59.501 33.333 0.09 0.00 0.00 5.54
2644 3074 8.509690 CAAAATGTCTATAAATCATGAGCGGAT 58.490 33.333 0.09 0.00 0.00 4.18
2645 3075 7.840342 AATGTCTATAAATCATGAGCGGATC 57.160 36.000 0.09 0.00 0.00 3.36
2649 3079 6.586463 GTCTATAAATCATGAGCGGATCGAAA 59.414 38.462 0.09 0.00 0.00 3.46
2656 3086 2.270923 TGAGCGGATCGAAACAATGAG 58.729 47.619 0.00 0.00 0.00 2.90
2657 3087 2.271800 GAGCGGATCGAAACAATGAGT 58.728 47.619 0.00 0.00 0.00 3.41
2660 3090 3.865745 AGCGGATCGAAACAATGAGTTAG 59.134 43.478 0.00 0.00 40.26 2.34
2690 3120 9.965902 ACTATGATCATATCCCTACAAAAATCC 57.034 33.333 15.71 0.00 0.00 3.01
2707 3137 9.118300 ACAAAAATCCACAAGAATAAAAATGCA 57.882 25.926 0.00 0.00 0.00 3.96
2708 3138 9.947669 CAAAAATCCACAAGAATAAAAATGCAA 57.052 25.926 0.00 0.00 0.00 4.08
2721 3151 9.862585 GAATAAAAATGCAATATTTTTAGGCCG 57.137 29.630 17.04 0.00 42.82 6.13
2722 3152 9.606631 AATAAAAATGCAATATTTTTAGGCCGA 57.393 25.926 17.04 0.00 42.82 5.54
2723 3153 7.913674 AAAAATGCAATATTTTTAGGCCGAA 57.086 28.000 7.33 0.00 38.84 4.30
2724 3154 8.504812 AAAAATGCAATATTTTTAGGCCGAAT 57.495 26.923 7.33 0.69 38.84 3.34
2725 3155 9.606631 AAAAATGCAATATTTTTAGGCCGAATA 57.393 25.926 7.33 2.99 38.84 1.75
2726 3156 8.816640 AAATGCAATATTTTTAGGCCGAATAG 57.183 30.769 0.00 0.00 0.00 1.73
2727 3157 5.768317 TGCAATATTTTTAGGCCGAATAGC 58.232 37.500 0.00 4.36 0.00 2.97
2728 3158 5.534654 TGCAATATTTTTAGGCCGAATAGCT 59.465 36.000 0.00 0.00 0.00 3.32
2729 3159 6.086871 GCAATATTTTTAGGCCGAATAGCTC 58.913 40.000 0.00 0.00 0.00 4.09
2739 3169 1.858091 CGAATAGCTCGGCAATCACT 58.142 50.000 0.00 0.00 44.20 3.41
2740 3170 1.524355 CGAATAGCTCGGCAATCACTG 59.476 52.381 0.00 0.00 44.20 3.66
2741 3171 2.555199 GAATAGCTCGGCAATCACTGT 58.445 47.619 0.00 0.00 0.00 3.55
2742 3172 3.717707 GAATAGCTCGGCAATCACTGTA 58.282 45.455 0.00 0.00 0.00 2.74
2743 3173 4.310769 GAATAGCTCGGCAATCACTGTAT 58.689 43.478 0.00 0.00 0.00 2.29
2744 3174 1.945387 AGCTCGGCAATCACTGTATG 58.055 50.000 0.00 0.00 0.00 2.39
2745 3175 1.208052 AGCTCGGCAATCACTGTATGT 59.792 47.619 0.00 0.00 0.00 2.29
2746 3176 1.594862 GCTCGGCAATCACTGTATGTC 59.405 52.381 0.00 0.00 0.00 3.06
2747 3177 1.854743 CTCGGCAATCACTGTATGTCG 59.145 52.381 7.74 7.74 43.07 4.35
2748 3178 0.301687 CGGCAATCACTGTATGTCGC 59.698 55.000 2.34 0.00 35.26 5.19
2749 3179 1.656652 GGCAATCACTGTATGTCGCT 58.343 50.000 0.00 0.00 0.00 4.93
2750 3180 1.594862 GGCAATCACTGTATGTCGCTC 59.405 52.381 0.00 0.00 0.00 5.03
2751 3181 1.594862 GCAATCACTGTATGTCGCTCC 59.405 52.381 0.00 0.00 0.00 4.70
2752 3182 1.854743 CAATCACTGTATGTCGCTCCG 59.145 52.381 0.00 0.00 0.00 4.63
2753 3183 0.249073 ATCACTGTATGTCGCTCCGC 60.249 55.000 0.00 0.00 0.00 5.54
2754 3184 1.139734 CACTGTATGTCGCTCCGCT 59.860 57.895 0.00 0.00 0.00 5.52
2755 3185 0.458543 CACTGTATGTCGCTCCGCTT 60.459 55.000 0.00 0.00 0.00 4.68
2756 3186 1.100510 ACTGTATGTCGCTCCGCTTA 58.899 50.000 0.00 0.00 0.00 3.09
2757 3187 1.202268 ACTGTATGTCGCTCCGCTTAC 60.202 52.381 0.00 0.00 0.00 2.34
2758 3188 0.101759 TGTATGTCGCTCCGCTTACC 59.898 55.000 0.00 0.00 0.00 2.85
2759 3189 0.101759 GTATGTCGCTCCGCTTACCA 59.898 55.000 0.00 0.00 0.00 3.25
2760 3190 1.037493 TATGTCGCTCCGCTTACCAT 58.963 50.000 0.00 0.00 0.00 3.55
2761 3191 0.530650 ATGTCGCTCCGCTTACCATG 60.531 55.000 0.00 0.00 0.00 3.66
2762 3192 1.153628 GTCGCTCCGCTTACCATGT 60.154 57.895 0.00 0.00 0.00 3.21
2763 3193 1.153647 TCGCTCCGCTTACCATGTG 60.154 57.895 0.00 0.00 0.00 3.21
2764 3194 2.813179 CGCTCCGCTTACCATGTGC 61.813 63.158 0.00 0.00 0.00 4.57
2765 3195 1.745115 GCTCCGCTTACCATGTGCA 60.745 57.895 0.00 0.00 0.00 4.57
2766 3196 1.709147 GCTCCGCTTACCATGTGCAG 61.709 60.000 0.00 0.00 0.00 4.41
2767 3197 0.108186 CTCCGCTTACCATGTGCAGA 60.108 55.000 0.00 0.00 0.00 4.26
2768 3198 0.108186 TCCGCTTACCATGTGCAGAG 60.108 55.000 0.00 0.00 0.00 3.35
2769 3199 1.709147 CCGCTTACCATGTGCAGAGC 61.709 60.000 0.00 0.00 0.00 4.09
2770 3200 1.709147 CGCTTACCATGTGCAGAGCC 61.709 60.000 0.00 0.00 0.00 4.70
2771 3201 0.677731 GCTTACCATGTGCAGAGCCA 60.678 55.000 0.00 0.00 0.00 4.75
2772 3202 2.020694 GCTTACCATGTGCAGAGCCAT 61.021 52.381 0.00 0.00 0.00 4.40
2773 3203 1.945394 CTTACCATGTGCAGAGCCATC 59.055 52.381 0.00 0.00 0.00 3.51
2774 3204 0.911053 TACCATGTGCAGAGCCATCA 59.089 50.000 0.00 0.00 0.00 3.07
2775 3205 0.679002 ACCATGTGCAGAGCCATCAC 60.679 55.000 0.00 0.00 0.00 3.06
2776 3206 1.381928 CCATGTGCAGAGCCATCACC 61.382 60.000 0.00 0.00 0.00 4.02
2777 3207 1.077212 ATGTGCAGAGCCATCACCC 60.077 57.895 0.00 0.00 0.00 4.61
2778 3208 2.439156 GTGCAGAGCCATCACCCC 60.439 66.667 0.00 0.00 0.00 4.95
2779 3209 2.934932 TGCAGAGCCATCACCCCA 60.935 61.111 0.00 0.00 0.00 4.96
2780 3210 2.356278 GCAGAGCCATCACCCCAA 59.644 61.111 0.00 0.00 0.00 4.12
2781 3211 1.304381 GCAGAGCCATCACCCCAAA 60.304 57.895 0.00 0.00 0.00 3.28
2782 3212 1.598701 GCAGAGCCATCACCCCAAAC 61.599 60.000 0.00 0.00 0.00 2.93
2783 3213 0.251297 CAGAGCCATCACCCCAAACA 60.251 55.000 0.00 0.00 0.00 2.83
2784 3214 0.706433 AGAGCCATCACCCCAAACAT 59.294 50.000 0.00 0.00 0.00 2.71
2785 3215 1.106285 GAGCCATCACCCCAAACATC 58.894 55.000 0.00 0.00 0.00 3.06
2786 3216 0.409092 AGCCATCACCCCAAACATCA 59.591 50.000 0.00 0.00 0.00 3.07
2787 3217 1.203162 AGCCATCACCCCAAACATCAA 60.203 47.619 0.00 0.00 0.00 2.57
2788 3218 1.832998 GCCATCACCCCAAACATCAAT 59.167 47.619 0.00 0.00 0.00 2.57
2789 3219 2.419021 GCCATCACCCCAAACATCAATG 60.419 50.000 0.00 0.00 0.00 2.82
2790 3220 3.098377 CCATCACCCCAAACATCAATGA 58.902 45.455 0.00 0.00 0.00 2.57
2791 3221 3.119029 CCATCACCCCAAACATCAATGAC 60.119 47.826 0.00 0.00 0.00 3.06
2792 3222 3.235750 TCACCCCAAACATCAATGACA 57.764 42.857 0.00 0.00 0.00 3.58
2793 3223 3.777087 TCACCCCAAACATCAATGACAT 58.223 40.909 0.00 0.00 0.00 3.06
2794 3224 3.510753 TCACCCCAAACATCAATGACATG 59.489 43.478 0.00 0.00 0.00 3.21
2795 3225 3.510753 CACCCCAAACATCAATGACATGA 59.489 43.478 0.00 0.00 0.00 3.07
2796 3226 4.160814 CACCCCAAACATCAATGACATGAT 59.839 41.667 0.00 0.00 40.64 2.45
2797 3227 4.403432 ACCCCAAACATCAATGACATGATC 59.597 41.667 0.00 0.00 37.96 2.92
2798 3228 4.202182 CCCCAAACATCAATGACATGATCC 60.202 45.833 0.00 0.00 37.96 3.36
2799 3229 4.498513 CCCAAACATCAATGACATGATCCG 60.499 45.833 0.00 0.00 37.96 4.18
2800 3230 4.498513 CCAAACATCAATGACATGATCCGG 60.499 45.833 0.00 0.00 37.96 5.14
2801 3231 2.224606 ACATCAATGACATGATCCGGC 58.775 47.619 0.00 0.00 37.96 6.13
2802 3232 1.538512 CATCAATGACATGATCCGGCC 59.461 52.381 0.00 0.00 37.96 6.13
2803 3233 0.179020 TCAATGACATGATCCGGCCC 60.179 55.000 0.00 0.00 0.00 5.80
2804 3234 0.466007 CAATGACATGATCCGGCCCA 60.466 55.000 0.00 0.00 0.00 5.36
2805 3235 0.258484 AATGACATGATCCGGCCCAA 59.742 50.000 0.00 0.00 0.00 4.12
2806 3236 0.479815 ATGACATGATCCGGCCCAAT 59.520 50.000 0.00 0.00 0.00 3.16
2807 3237 0.258484 TGACATGATCCGGCCCAATT 59.742 50.000 0.00 0.00 0.00 2.32
2808 3238 1.492599 TGACATGATCCGGCCCAATTA 59.507 47.619 0.00 0.00 0.00 1.40
2809 3239 2.108075 TGACATGATCCGGCCCAATTAT 59.892 45.455 0.00 0.00 0.00 1.28
2810 3240 3.157087 GACATGATCCGGCCCAATTATT 58.843 45.455 0.00 0.00 0.00 1.40
2811 3241 2.892852 ACATGATCCGGCCCAATTATTG 59.107 45.455 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.586841 ACTAAGCCTAGCTCAGATGGTTAG 59.413 45.833 13.59 13.59 38.25 2.34
4 5 3.551863 CGAACTAAGCCTAGCTCAGATGG 60.552 52.174 0.00 0.00 38.25 3.51
5 6 3.067461 ACGAACTAAGCCTAGCTCAGATG 59.933 47.826 0.00 0.00 38.25 2.90
6 7 3.292460 ACGAACTAAGCCTAGCTCAGAT 58.708 45.455 0.00 0.00 38.25 2.90
7 8 2.683867 GACGAACTAAGCCTAGCTCAGA 59.316 50.000 0.00 0.00 38.25 3.27
8 9 2.423892 TGACGAACTAAGCCTAGCTCAG 59.576 50.000 0.00 0.00 38.25 3.35
9 10 2.163815 GTGACGAACTAAGCCTAGCTCA 59.836 50.000 0.00 0.00 38.25 4.26
10 11 2.163815 TGTGACGAACTAAGCCTAGCTC 59.836 50.000 0.00 0.00 38.25 4.09
11 12 2.094649 GTGTGACGAACTAAGCCTAGCT 60.095 50.000 0.00 0.00 42.56 3.32
12 13 2.260481 GTGTGACGAACTAAGCCTAGC 58.740 52.381 0.00 0.00 0.00 3.42
13 14 2.492484 AGGTGTGACGAACTAAGCCTAG 59.508 50.000 0.00 0.00 0.00 3.02
14 15 2.490903 GAGGTGTGACGAACTAAGCCTA 59.509 50.000 0.00 0.00 0.00 3.93
15 16 1.272769 GAGGTGTGACGAACTAAGCCT 59.727 52.381 0.00 0.00 0.00 4.58
16 17 1.272769 AGAGGTGTGACGAACTAAGCC 59.727 52.381 0.00 0.00 0.00 4.35
17 18 2.726832 AGAGGTGTGACGAACTAAGC 57.273 50.000 0.00 0.00 0.00 3.09
18 19 3.058432 TCGAAGAGGTGTGACGAACTAAG 60.058 47.826 0.00 0.00 0.00 2.18
19 20 2.880268 TCGAAGAGGTGTGACGAACTAA 59.120 45.455 0.00 0.00 0.00 2.24
20 21 2.225019 GTCGAAGAGGTGTGACGAACTA 59.775 50.000 0.00 0.00 36.95 2.24
21 22 1.001597 GTCGAAGAGGTGTGACGAACT 60.002 52.381 0.00 0.00 36.95 3.01
22 23 1.268896 TGTCGAAGAGGTGTGACGAAC 60.269 52.381 0.00 0.00 36.95 3.95
23 24 1.026584 TGTCGAAGAGGTGTGACGAA 58.973 50.000 0.00 0.00 36.95 3.85
24 25 1.244816 ATGTCGAAGAGGTGTGACGA 58.755 50.000 0.00 0.00 36.95 4.20
25 26 2.095415 TGTATGTCGAAGAGGTGTGACG 60.095 50.000 0.00 0.00 36.95 4.35
26 27 3.243336 GTGTATGTCGAAGAGGTGTGAC 58.757 50.000 0.00 0.00 36.95 3.67
27 28 2.888414 TGTGTATGTCGAAGAGGTGTGA 59.112 45.455 0.00 0.00 36.95 3.58
28 29 3.297830 TGTGTATGTCGAAGAGGTGTG 57.702 47.619 0.00 0.00 36.95 3.82
29 30 3.849911 CATGTGTATGTCGAAGAGGTGT 58.150 45.455 0.00 0.00 36.95 4.16
30 31 2.604914 GCATGTGTATGTCGAAGAGGTG 59.395 50.000 0.00 0.00 36.95 4.00
31 32 2.233676 TGCATGTGTATGTCGAAGAGGT 59.766 45.455 0.00 0.00 36.95 3.85
32 33 2.892374 TGCATGTGTATGTCGAAGAGG 58.108 47.619 0.00 0.00 36.95 3.69
33 34 4.114794 TCATGCATGTGTATGTCGAAGAG 58.885 43.478 25.43 0.00 38.89 2.85
34 35 4.122143 TCATGCATGTGTATGTCGAAGA 57.878 40.909 25.43 0.00 38.89 2.87
35 36 4.319261 CCATCATGCATGTGTATGTCGAAG 60.319 45.833 25.43 6.21 38.89 3.79
36 37 3.560896 CCATCATGCATGTGTATGTCGAA 59.439 43.478 25.43 3.20 38.89 3.71
37 38 3.132925 CCATCATGCATGTGTATGTCGA 58.867 45.455 25.43 3.97 38.89 4.20
38 39 3.132925 TCCATCATGCATGTGTATGTCG 58.867 45.455 25.43 10.66 38.89 4.35
39 40 5.700722 ATTCCATCATGCATGTGTATGTC 57.299 39.130 25.43 0.00 38.89 3.06
45 46 9.961265 GGAAATATATATTCCATCATGCATGTG 57.039 33.333 25.43 20.71 44.70 3.21
82 83 9.976511 GGTTAGCTCTTTTGTAGGTTTTTATTT 57.023 29.630 0.00 0.00 0.00 1.40
83 84 9.363401 AGGTTAGCTCTTTTGTAGGTTTTTATT 57.637 29.630 0.00 0.00 0.00 1.40
84 85 8.935614 AGGTTAGCTCTTTTGTAGGTTTTTAT 57.064 30.769 0.00 0.00 0.00 1.40
85 86 9.498176 CTAGGTTAGCTCTTTTGTAGGTTTTTA 57.502 33.333 0.00 0.00 0.00 1.52
86 87 7.997223 ACTAGGTTAGCTCTTTTGTAGGTTTTT 59.003 33.333 0.00 0.00 0.00 1.94
87 88 7.444487 CACTAGGTTAGCTCTTTTGTAGGTTTT 59.556 37.037 0.00 0.00 0.00 2.43
88 89 6.935208 CACTAGGTTAGCTCTTTTGTAGGTTT 59.065 38.462 0.00 0.00 0.00 3.27
89 90 6.042897 ACACTAGGTTAGCTCTTTTGTAGGTT 59.957 38.462 0.00 0.00 0.00 3.50
90 91 5.543020 ACACTAGGTTAGCTCTTTTGTAGGT 59.457 40.000 0.00 0.00 0.00 3.08
91 92 5.869888 CACACTAGGTTAGCTCTTTTGTAGG 59.130 44.000 0.00 0.00 0.00 3.18
92 93 6.688578 TCACACTAGGTTAGCTCTTTTGTAG 58.311 40.000 0.00 0.00 0.00 2.74
93 94 6.659745 TCACACTAGGTTAGCTCTTTTGTA 57.340 37.500 0.00 0.00 0.00 2.41
94 95 5.546621 TCACACTAGGTTAGCTCTTTTGT 57.453 39.130 0.00 0.00 0.00 2.83
95 96 6.166279 TGATCACACTAGGTTAGCTCTTTTG 58.834 40.000 0.00 0.00 0.00 2.44
96 97 6.360370 TGATCACACTAGGTTAGCTCTTTT 57.640 37.500 0.00 0.00 0.00 2.27
97 98 6.360370 TTGATCACACTAGGTTAGCTCTTT 57.640 37.500 0.00 0.00 0.00 2.52
98 99 6.360370 TTTGATCACACTAGGTTAGCTCTT 57.640 37.500 0.00 0.00 0.00 2.85
99 100 6.552445 ATTTGATCACACTAGGTTAGCTCT 57.448 37.500 0.00 0.00 0.00 4.09
100 101 8.364142 AGATATTTGATCACACTAGGTTAGCTC 58.636 37.037 0.00 0.00 0.00 4.09
101 102 8.256356 AGATATTTGATCACACTAGGTTAGCT 57.744 34.615 0.00 0.00 0.00 3.32
102 103 7.600752 GGAGATATTTGATCACACTAGGTTAGC 59.399 40.741 0.00 0.00 0.00 3.09
103 104 8.865090 AGGAGATATTTGATCACACTAGGTTAG 58.135 37.037 0.00 0.00 0.00 2.34
104 105 8.642432 CAGGAGATATTTGATCACACTAGGTTA 58.358 37.037 0.00 0.00 0.00 2.85
105 106 7.126421 ACAGGAGATATTTGATCACACTAGGTT 59.874 37.037 0.00 0.00 0.00 3.50
106 107 6.613271 ACAGGAGATATTTGATCACACTAGGT 59.387 38.462 0.00 0.00 0.00 3.08
107 108 6.927936 CACAGGAGATATTTGATCACACTAGG 59.072 42.308 0.00 0.00 0.00 3.02
108 109 7.720442 TCACAGGAGATATTTGATCACACTAG 58.280 38.462 0.00 0.00 0.00 2.57
109 110 7.343057 ACTCACAGGAGATATTTGATCACACTA 59.657 37.037 0.00 0.00 44.26 2.74
110 111 6.155910 ACTCACAGGAGATATTTGATCACACT 59.844 38.462 0.00 0.00 44.26 3.55
111 112 6.344500 ACTCACAGGAGATATTTGATCACAC 58.656 40.000 0.00 0.00 44.26 3.82
112 113 6.550938 ACTCACAGGAGATATTTGATCACA 57.449 37.500 0.00 0.00 44.26 3.58
115 116 9.814899 CCATATACTCACAGGAGATATTTGATC 57.185 37.037 0.00 0.00 44.26 2.92
116 117 8.766476 CCCATATACTCACAGGAGATATTTGAT 58.234 37.037 0.00 0.00 44.26 2.57
117 118 7.180946 CCCCATATACTCACAGGAGATATTTGA 59.819 40.741 0.00 0.00 44.26 2.69
118 119 7.180946 TCCCCATATACTCACAGGAGATATTTG 59.819 40.741 0.00 0.35 44.26 2.32
119 120 7.256399 TCCCCATATACTCACAGGAGATATTT 58.744 38.462 0.00 0.00 44.26 1.40
120 121 6.815880 TCCCCATATACTCACAGGAGATATT 58.184 40.000 0.00 0.00 44.26 1.28
121 122 6.423358 TCCCCATATACTCACAGGAGATAT 57.577 41.667 0.00 0.00 44.26 1.63
122 123 5.878484 TCCCCATATACTCACAGGAGATA 57.122 43.478 0.00 0.00 44.26 1.98
123 124 4.767000 TCCCCATATACTCACAGGAGAT 57.233 45.455 0.00 0.00 44.26 2.75
124 125 4.767000 ATCCCCATATACTCACAGGAGA 57.233 45.455 0.00 0.00 44.26 3.71
125 126 6.935240 TTAATCCCCATATACTCACAGGAG 57.065 41.667 0.00 0.00 46.96 3.69
126 127 7.257016 CCAATTAATCCCCATATACTCACAGGA 60.257 40.741 0.00 0.00 0.00 3.86
127 128 6.886459 CCAATTAATCCCCATATACTCACAGG 59.114 42.308 0.00 0.00 0.00 4.00
128 129 7.461749 ACCAATTAATCCCCATATACTCACAG 58.538 38.462 0.00 0.00 0.00 3.66
129 130 7.401060 ACCAATTAATCCCCATATACTCACA 57.599 36.000 0.00 0.00 0.00 3.58
130 131 8.603304 AGTACCAATTAATCCCCATATACTCAC 58.397 37.037 0.00 0.00 0.00 3.51
131 132 8.751215 AGTACCAATTAATCCCCATATACTCA 57.249 34.615 0.00 0.00 0.00 3.41
132 133 8.265764 GGAGTACCAATTAATCCCCATATACTC 58.734 40.741 0.00 0.00 38.79 2.59
133 134 7.967747 AGGAGTACCAATTAATCCCCATATACT 59.032 37.037 0.00 0.00 44.82 2.12
134 135 8.159229 AGGAGTACCAATTAATCCCCATATAC 57.841 38.462 0.00 0.00 44.82 1.47
135 136 8.191110 AGAGGAGTACCAATTAATCCCCATATA 58.809 37.037 0.00 0.00 44.82 0.86
136 137 7.031917 AGAGGAGTACCAATTAATCCCCATAT 58.968 38.462 0.00 0.00 44.82 1.78
137 138 6.399013 AGAGGAGTACCAATTAATCCCCATA 58.601 40.000 0.00 0.00 44.82 2.74
138 139 5.235534 AGAGGAGTACCAATTAATCCCCAT 58.764 41.667 0.00 0.00 44.82 4.00
139 140 4.641868 AGAGGAGTACCAATTAATCCCCA 58.358 43.478 0.00 0.00 44.82 4.96
140 141 5.845065 AGTAGAGGAGTACCAATTAATCCCC 59.155 44.000 0.00 0.00 44.82 4.81
141 142 6.294620 CGAGTAGAGGAGTACCAATTAATCCC 60.295 46.154 0.00 0.00 44.82 3.85
142 143 6.294620 CCGAGTAGAGGAGTACCAATTAATCC 60.295 46.154 0.00 0.00 44.17 3.01
143 144 6.679843 CCGAGTAGAGGAGTACCAATTAATC 58.320 44.000 0.00 0.00 38.94 1.75
144 145 5.010820 GCCGAGTAGAGGAGTACCAATTAAT 59.989 44.000 0.00 0.00 38.94 1.40
145 146 4.340381 GCCGAGTAGAGGAGTACCAATTAA 59.660 45.833 0.00 0.00 38.94 1.40
146 147 3.887716 GCCGAGTAGAGGAGTACCAATTA 59.112 47.826 0.00 0.00 38.94 1.40
147 148 2.694109 GCCGAGTAGAGGAGTACCAATT 59.306 50.000 0.00 0.00 38.94 2.32
148 149 2.308690 GCCGAGTAGAGGAGTACCAAT 58.691 52.381 0.00 0.00 38.94 3.16
149 150 1.684248 GGCCGAGTAGAGGAGTACCAA 60.684 57.143 0.00 0.00 38.94 3.67
150 151 0.106819 GGCCGAGTAGAGGAGTACCA 60.107 60.000 0.00 0.00 38.94 3.25
151 152 1.165284 CGGCCGAGTAGAGGAGTACC 61.165 65.000 24.07 0.00 0.00 3.34
173 174 1.599071 CTGTGTAGTTATGGGCATGCG 59.401 52.381 12.44 0.00 0.00 4.73
313 314 9.263538 GCATTGGCATATTTCAATTTTATCAGA 57.736 29.630 0.00 0.00 40.72 3.27
364 365 6.640499 GCTAACTGCATAACAAAACATGTCAA 59.360 34.615 0.00 0.00 40.94 3.18
376 377 4.340950 AGAGAGGAGAGCTAACTGCATAAC 59.659 45.833 0.00 0.00 45.94 1.89
384 385 7.284489 TCAGATTAGAAAGAGAGGAGAGCTAAC 59.716 40.741 0.00 0.00 0.00 2.34
394 395 6.925165 GCTCTTGGATCAGATTAGAAAGAGAG 59.075 42.308 19.56 11.59 40.92 3.20
400 401 7.201956 GGAAGTAGCTCTTGGATCAGATTAGAA 60.202 40.741 0.00 0.00 36.40 2.10
408 409 3.389329 GGATGGAAGTAGCTCTTGGATCA 59.611 47.826 0.00 0.00 36.40 2.92
435 436 9.651913 AAACAATTTAATTGACTCAGTTGTGTT 57.348 25.926 22.53 1.64 42.83 3.32
439 440 8.057742 GTGCAAACAATTTAATTGACTCAGTTG 58.942 33.333 22.53 15.29 42.83 3.16
460 461 2.778299 AGTTAGGCTTCAATCGTGCAA 58.222 42.857 0.00 0.00 0.00 4.08
476 477 0.169451 TCGACATGCGCGAGAAGTTA 59.831 50.000 12.10 0.00 40.61 2.24
486 487 0.384230 AAACAAAGCGTCGACATGCG 60.384 50.000 17.16 2.14 39.81 4.73
487 488 2.587612 TAAACAAAGCGTCGACATGC 57.412 45.000 17.16 11.87 34.33 4.06
488 489 4.088648 GGATTAAACAAAGCGTCGACATG 58.911 43.478 17.16 10.80 0.00 3.21
489 490 3.181524 CGGATTAAACAAAGCGTCGACAT 60.182 43.478 17.16 0.00 0.00 3.06
490 491 2.156117 CGGATTAAACAAAGCGTCGACA 59.844 45.455 17.16 0.00 0.00 4.35
493 494 1.789054 GCCGGATTAAACAAAGCGTCG 60.789 52.381 5.05 0.00 0.00 5.12
494 495 1.466866 GGCCGGATTAAACAAAGCGTC 60.467 52.381 5.05 0.00 0.00 5.19
541 651 2.151202 AGGCCAAAATATCCGCGTATG 58.849 47.619 5.01 0.00 0.00 2.39
547 657 6.430925 TGAAATCATAGAGGCCAAAATATCCG 59.569 38.462 5.01 0.00 0.00 4.18
665 829 8.145767 CACGTCTAGTCCACCCATATTTATTTA 58.854 37.037 0.00 0.00 0.00 1.40
666 830 6.990349 CACGTCTAGTCCACCCATATTTATTT 59.010 38.462 0.00 0.00 0.00 1.40
667 831 6.463897 CCACGTCTAGTCCACCCATATTTATT 60.464 42.308 0.00 0.00 0.00 1.40
668 832 5.011738 CCACGTCTAGTCCACCCATATTTAT 59.988 44.000 0.00 0.00 0.00 1.40
887 1051 7.496529 TGCTATATGAAAGAAGTAACATGCC 57.503 36.000 0.00 0.00 0.00 4.40
943 1107 1.955157 CGCTCATGCTCAGCTAGGC 60.955 63.158 0.00 3.48 36.97 3.93
960 1124 1.066002 GTTGATGGTGATTGGATGCCG 59.934 52.381 0.00 0.00 0.00 5.69
961 1125 2.101783 TGTTGATGGTGATTGGATGCC 58.898 47.619 0.00 0.00 0.00 4.40
996 1160 1.877637 TCGTGTGACCAGTCATTTGG 58.122 50.000 3.41 0.00 42.18 3.28
1031 1195 2.196295 CGCTACTGAAGAGCACCTAC 57.804 55.000 0.00 0.00 40.09 3.18
1113 1277 0.319125 GGGGAAGATCATCGCTCGTC 60.319 60.000 13.75 0.00 33.16 4.20
1197 1364 3.816367 TTGCGCCGTCATCCACACA 62.816 57.895 4.18 0.00 0.00 3.72
1215 1382 3.108376 GGAGGTGGAGTAGGATCTGTTT 58.892 50.000 0.00 0.00 0.00 2.83
1308 1475 2.348998 GTGAGCCCAGAGGTGGTG 59.651 66.667 0.00 0.00 43.23 4.17
1390 1557 2.158986 CGTCATCTTCCAGAATCTGCCT 60.159 50.000 4.40 0.00 0.00 4.75
1400 1567 4.342092 TGATAATCTGCTCGTCATCTTCCA 59.658 41.667 0.00 0.00 0.00 3.53
1404 1571 3.638627 TGGTGATAATCTGCTCGTCATCT 59.361 43.478 0.00 0.00 0.00 2.90
1471 1662 1.394917 CTGAGAAGTTGGCATACACGC 59.605 52.381 0.00 0.00 0.00 5.34
1478 1670 1.073722 CCTGGCTGAGAAGTTGGCA 59.926 57.895 0.00 0.00 35.07 4.92
1530 1722 1.193462 TCGTTAACCGGGGTGATGGT 61.193 55.000 6.32 0.00 41.20 3.55
1533 1725 1.598517 GGTCGTTAACCGGGGTGAT 59.401 57.895 6.32 0.00 38.58 3.06
1547 1739 0.391927 TACCGCATTTCCCTTGGTCG 60.392 55.000 0.00 0.00 34.18 4.79
1557 1749 0.878416 ATGTTGCACGTACCGCATTT 59.122 45.000 5.52 0.00 39.58 2.32
1637 2029 3.765026 AGCCGTTGTTGTTACTTTGTTG 58.235 40.909 0.00 0.00 0.00 3.33
1653 2045 9.777575 GTATGTAAAAATGTATTTTGTAGCCGT 57.222 29.630 3.56 0.00 39.70 5.68
1654 2046 8.939926 CGTATGTAAAAATGTATTTTGTAGCCG 58.060 33.333 3.56 0.58 39.70 5.52
1680 2072 5.747951 AACTTAATCATTGAGCTAGCTGC 57.252 39.130 24.99 14.20 43.29 5.25
1681 2073 7.011763 TGCTTAACTTAATCATTGAGCTAGCTG 59.988 37.037 24.99 8.86 38.06 4.24
1779 2173 1.990614 GACACCAGGGTCCCTCTCC 60.991 68.421 7.76 0.00 0.00 3.71
1834 2228 4.459331 CCATTGCAACCGCCGTCG 62.459 66.667 0.00 0.00 37.32 5.12
1874 2268 3.455910 CCTCCATTCTGTTGGATCCACTA 59.544 47.826 15.91 5.37 44.66 2.74
2052 2446 1.737735 CTGCCACTTGACGCGATCA 60.738 57.895 15.93 10.48 34.65 2.92
2155 2549 3.958147 ATCTTGTGCCTGTCGCCCG 62.958 63.158 0.00 0.00 36.24 6.13
2211 2605 0.178964 ACCTTTGTCACCCCATGTGG 60.179 55.000 0.00 0.00 45.48 4.17
2247 2641 2.449464 CTGATGGATTCTTTGTGCCCA 58.551 47.619 0.00 0.00 0.00 5.36
2316 2710 7.712639 ACTGTGCATATTAATCAGTCGATTCTT 59.287 33.333 0.00 0.00 41.09 2.52
2335 2729 3.252215 GCCACTATTACAAACACTGTGCA 59.748 43.478 7.90 0.00 39.20 4.57
2341 2735 2.817258 TGCAGGCCACTATTACAAACAC 59.183 45.455 5.01 0.00 0.00 3.32
2342 2736 3.147553 TGCAGGCCACTATTACAAACA 57.852 42.857 5.01 0.00 0.00 2.83
2353 2747 1.001378 CACTTTACACTTGCAGGCCAC 60.001 52.381 5.01 0.00 0.00 5.01
2394 2790 4.099573 ACACACCTAGACATATAGTGGCAC 59.900 45.833 10.29 10.29 38.81 5.01
2399 2795 7.002879 ACGGATTACACACCTAGACATATAGT 58.997 38.462 0.00 0.00 0.00 2.12
2430 2826 6.766467 ACAAAGTTCGTACAGATCCTTCTTTT 59.234 34.615 0.00 0.00 0.00 2.27
2433 2829 5.470047 ACAAAGTTCGTACAGATCCTTCT 57.530 39.130 0.00 0.00 0.00 2.85
2461 2857 7.923878 ACACCTTACATTGAAACCAATAAACAC 59.076 33.333 0.00 0.00 33.27 3.32
2484 2881 8.712285 TGATAGTGCTACCAATAAGTTAACAC 57.288 34.615 8.61 0.00 0.00 3.32
2589 3018 9.449719 CCTGTATAGACAAAAGGTTTATCACTT 57.550 33.333 0.00 0.00 34.35 3.16
2593 3022 9.444600 TGTTCCTGTATAGACAAAAGGTTTATC 57.555 33.333 0.00 0.00 34.35 1.75
2594 3023 9.802039 TTGTTCCTGTATAGACAAAAGGTTTAT 57.198 29.630 0.00 0.00 34.35 1.40
2624 3054 5.641709 TCGATCCGCTCATGATTTATAGAC 58.358 41.667 0.00 0.00 0.00 2.59
2625 3055 5.897377 TCGATCCGCTCATGATTTATAGA 57.103 39.130 0.00 0.00 0.00 1.98
2641 3071 7.807680 AGTTTTCTAACTCATTGTTTCGATCC 58.192 34.615 0.00 0.00 40.60 3.36
2644 3074 9.483916 TCATAGTTTTCTAACTCATTGTTTCGA 57.516 29.630 0.00 0.00 43.45 3.71
2671 3101 7.638444 TCTTGTGGATTTTTGTAGGGATATGA 58.362 34.615 0.00 0.00 0.00 2.15
2675 3105 8.893563 TTATTCTTGTGGATTTTTGTAGGGAT 57.106 30.769 0.00 0.00 0.00 3.85
2682 3112 9.947669 TTGCATTTTTATTCTTGTGGATTTTTG 57.052 25.926 0.00 0.00 0.00 2.44
2705 3135 6.013842 AGCTATTCGGCCTAAAAATATTGC 57.986 37.500 0.00 1.48 0.00 3.56
2706 3136 6.307155 CGAGCTATTCGGCCTAAAAATATTG 58.693 40.000 0.00 0.00 45.54 1.90
2707 3137 6.481954 CGAGCTATTCGGCCTAAAAATATT 57.518 37.500 0.00 0.00 45.54 1.28
2721 3151 2.555199 ACAGTGATTGCCGAGCTATTC 58.445 47.619 0.00 0.00 0.00 1.75
2722 3152 2.698855 ACAGTGATTGCCGAGCTATT 57.301 45.000 0.00 0.00 0.00 1.73
2723 3153 3.070159 ACATACAGTGATTGCCGAGCTAT 59.930 43.478 0.00 0.00 0.00 2.97
2724 3154 2.430694 ACATACAGTGATTGCCGAGCTA 59.569 45.455 0.00 0.00 0.00 3.32
2725 3155 1.208052 ACATACAGTGATTGCCGAGCT 59.792 47.619 0.00 0.00 0.00 4.09
2726 3156 1.594862 GACATACAGTGATTGCCGAGC 59.405 52.381 0.00 0.00 0.00 5.03
2727 3157 1.854743 CGACATACAGTGATTGCCGAG 59.145 52.381 0.00 0.00 0.00 4.63
2728 3158 1.921243 CGACATACAGTGATTGCCGA 58.079 50.000 0.00 0.00 0.00 5.54
2729 3159 0.301687 GCGACATACAGTGATTGCCG 59.698 55.000 0.00 0.00 0.00 5.69
2730 3160 1.594862 GAGCGACATACAGTGATTGCC 59.405 52.381 0.00 0.00 0.00 4.52
2731 3161 1.594862 GGAGCGACATACAGTGATTGC 59.405 52.381 0.00 0.00 0.00 3.56
2732 3162 1.854743 CGGAGCGACATACAGTGATTG 59.145 52.381 0.00 0.00 0.00 2.67
2733 3163 2.209838 CGGAGCGACATACAGTGATT 57.790 50.000 0.00 0.00 0.00 2.57
2734 3164 3.946950 CGGAGCGACATACAGTGAT 57.053 52.632 0.00 0.00 0.00 3.06
2748 3178 0.108186 TCTGCACATGGTAAGCGGAG 60.108 55.000 8.53 0.00 38.64 4.63
2749 3179 0.108186 CTCTGCACATGGTAAGCGGA 60.108 55.000 11.14 11.14 41.05 5.54
2750 3180 1.709147 GCTCTGCACATGGTAAGCGG 61.709 60.000 0.00 0.85 36.00 5.52
2751 3181 1.709147 GGCTCTGCACATGGTAAGCG 61.709 60.000 0.00 0.00 0.00 4.68
2752 3182 0.677731 TGGCTCTGCACATGGTAAGC 60.678 55.000 0.00 0.00 0.00 3.09
2753 3183 1.945394 GATGGCTCTGCACATGGTAAG 59.055 52.381 0.00 0.00 0.00 2.34
2754 3184 1.281577 TGATGGCTCTGCACATGGTAA 59.718 47.619 0.00 0.00 0.00 2.85
2755 3185 0.911053 TGATGGCTCTGCACATGGTA 59.089 50.000 0.00 0.00 0.00 3.25
2756 3186 0.679002 GTGATGGCTCTGCACATGGT 60.679 55.000 0.00 0.00 32.96 3.55
2757 3187 1.381928 GGTGATGGCTCTGCACATGG 61.382 60.000 0.00 0.00 34.33 3.66
2758 3188 1.381928 GGGTGATGGCTCTGCACATG 61.382 60.000 0.00 0.00 34.33 3.21
2759 3189 1.077212 GGGTGATGGCTCTGCACAT 60.077 57.895 0.00 0.00 34.33 3.21
2760 3190 2.352422 GGGTGATGGCTCTGCACA 59.648 61.111 0.00 0.00 34.33 4.57
2761 3191 2.439156 GGGGTGATGGCTCTGCAC 60.439 66.667 0.00 0.00 0.00 4.57
2762 3192 2.079088 TTTGGGGTGATGGCTCTGCA 62.079 55.000 0.00 0.00 0.00 4.41
2763 3193 1.304381 TTTGGGGTGATGGCTCTGC 60.304 57.895 0.00 0.00 0.00 4.26
2764 3194 0.251297 TGTTTGGGGTGATGGCTCTG 60.251 55.000 0.00 0.00 0.00 3.35
2765 3195 0.706433 ATGTTTGGGGTGATGGCTCT 59.294 50.000 0.00 0.00 0.00 4.09
2766 3196 1.106285 GATGTTTGGGGTGATGGCTC 58.894 55.000 0.00 0.00 0.00 4.70
2767 3197 0.409092 TGATGTTTGGGGTGATGGCT 59.591 50.000 0.00 0.00 0.00 4.75
2768 3198 1.265236 TTGATGTTTGGGGTGATGGC 58.735 50.000 0.00 0.00 0.00 4.40
2769 3199 3.098377 TCATTGATGTTTGGGGTGATGG 58.902 45.455 0.00 0.00 0.00 3.51
2770 3200 3.510753 TGTCATTGATGTTTGGGGTGATG 59.489 43.478 0.00 0.00 0.00 3.07
2771 3201 3.777087 TGTCATTGATGTTTGGGGTGAT 58.223 40.909 0.00 0.00 0.00 3.06
2772 3202 3.235750 TGTCATTGATGTTTGGGGTGA 57.764 42.857 0.00 0.00 0.00 4.02
2773 3203 3.510753 TCATGTCATTGATGTTTGGGGTG 59.489 43.478 0.00 0.00 0.00 4.61
2774 3204 3.777087 TCATGTCATTGATGTTTGGGGT 58.223 40.909 0.00 0.00 0.00 4.95
2775 3205 4.202182 GGATCATGTCATTGATGTTTGGGG 60.202 45.833 0.00 0.00 36.48 4.96
2776 3206 4.498513 CGGATCATGTCATTGATGTTTGGG 60.499 45.833 0.00 0.00 36.48 4.12
2777 3207 4.498513 CCGGATCATGTCATTGATGTTTGG 60.499 45.833 0.00 0.00 36.48 3.28
2778 3208 4.603985 CCGGATCATGTCATTGATGTTTG 58.396 43.478 0.00 0.00 36.48 2.93
2779 3209 3.067180 GCCGGATCATGTCATTGATGTTT 59.933 43.478 5.05 0.00 36.48 2.83
2780 3210 2.620115 GCCGGATCATGTCATTGATGTT 59.380 45.455 5.05 0.00 36.48 2.71
2781 3211 2.224606 GCCGGATCATGTCATTGATGT 58.775 47.619 5.05 0.00 36.48 3.06
2782 3212 1.538512 GGCCGGATCATGTCATTGATG 59.461 52.381 5.05 0.00 36.48 3.07
2783 3213 1.546323 GGGCCGGATCATGTCATTGAT 60.546 52.381 5.05 0.00 39.04 2.57
2784 3214 0.179020 GGGCCGGATCATGTCATTGA 60.179 55.000 5.05 0.00 0.00 2.57
2785 3215 0.466007 TGGGCCGGATCATGTCATTG 60.466 55.000 5.05 0.00 0.00 2.82
2786 3216 0.258484 TTGGGCCGGATCATGTCATT 59.742 50.000 5.05 0.00 0.00 2.57
2787 3217 0.479815 ATTGGGCCGGATCATGTCAT 59.520 50.000 5.05 0.00 0.00 3.06
2788 3218 0.258484 AATTGGGCCGGATCATGTCA 59.742 50.000 5.05 0.00 0.00 3.58
2789 3219 2.270352 TAATTGGGCCGGATCATGTC 57.730 50.000 5.05 0.00 0.00 3.06
2790 3220 2.892852 CAATAATTGGGCCGGATCATGT 59.107 45.455 5.05 0.00 0.00 3.21
2791 3221 3.581024 CAATAATTGGGCCGGATCATG 57.419 47.619 5.05 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.