Multiple sequence alignment - TraesCS1D01G417200

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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 TraesCS1D01G417200 chr1D 100.000 3092 0 0 1 3092 475528577 475525486 0.000000e+00 5710
1 TraesCS1D01G417200 chr1D 96.082 2782 86 18 282 3048 420011140 420008367 0.000000e+00 4512
2 TraesCS1D01G417200 chr4D 98.222 2812 47 3 282 3092 507114494 507111685 0.000000e+00 4913
3 TraesCS1D01G417200 chr4D 96.569 2740 71 9 282 3008 428529859 428532588 0.000000e+00 4518
4 TraesCS1D01G417200 chr4D 95.758 2782 97 16 282 3048 502867333 502870108 0.000000e+00 4464
5 TraesCS1D01G417200 chr3D 98.356 2798 41 4 281 3075 85226133 85228928 0.000000e+00 4907
6 TraesCS1D01G417200 chr3D 96.933 2771 75 9 282 3048 359622499 359625263 0.000000e+00 4638
7 TraesCS1D01G417200 chr2D 96.140 2772 81 6 282 3048 182632456 182629706 0.000000e+00 4503
8 TraesCS1D01G417200 chr2D 95.964 2775 91 13 282 3048 382702778 382700017 0.000000e+00 4484
9 TraesCS1D01G417200 chr2D 98.295 2404 36 2 675 3073 605551640 605549237 0.000000e+00 4207
10 TraesCS1D01G417200 chr2D 95.860 1908 39 8 1188 3092 634823627 634821757 0.000000e+00 3049
11 TraesCS1D01G417200 chr6D 96.721 2714 66 16 282 2989 472510963 472513659 0.000000e+00 4497
12 TraesCS1D01G417200 chr6A 95.718 1378 43 5 1711 3088 584382527 584381166 0.000000e+00 2204
13 TraesCS1D01G417200 chr1A 95.455 264 9 1 18 281 571292087 571291827 4.770000e-113 418
14 TraesCS1D01G417200 chr1B 94.286 105 3 2 145 249 661517581 661517480 1.150000e-34 158


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 TraesCS1D01G417200 chr1D 475525486 475528577 3091 True 5710 5710 100.000 1 3092 1 chr1D.!!$R2 3091
1 TraesCS1D01G417200 chr1D 420008367 420011140 2773 True 4512 4512 96.082 282 3048 1 chr1D.!!$R1 2766
2 TraesCS1D01G417200 chr4D 507111685 507114494 2809 True 4913 4913 98.222 282 3092 1 chr4D.!!$R1 2810
3 TraesCS1D01G417200 chr4D 428529859 428532588 2729 False 4518 4518 96.569 282 3008 1 chr4D.!!$F1 2726
4 TraesCS1D01G417200 chr4D 502867333 502870108 2775 False 4464 4464 95.758 282 3048 1 chr4D.!!$F2 2766
5 TraesCS1D01G417200 chr3D 85226133 85228928 2795 False 4907 4907 98.356 281 3075 1 chr3D.!!$F1 2794
6 TraesCS1D01G417200 chr3D 359622499 359625263 2764 False 4638 4638 96.933 282 3048 1 chr3D.!!$F2 2766
7 TraesCS1D01G417200 chr2D 182629706 182632456 2750 True 4503 4503 96.140 282 3048 1 chr2D.!!$R1 2766
8 TraesCS1D01G417200 chr2D 382700017 382702778 2761 True 4484 4484 95.964 282 3048 1 chr2D.!!$R2 2766
9 TraesCS1D01G417200 chr2D 605549237 605551640 2403 True 4207 4207 98.295 675 3073 1 chr2D.!!$R3 2398
10 TraesCS1D01G417200 chr2D 634821757 634823627 1870 True 3049 3049 95.860 1188 3092 1 chr2D.!!$R4 1904
11 TraesCS1D01G417200 chr6D 472510963 472513659 2696 False 4497 4497 96.721 282 2989 1 chr6D.!!$F1 2707
12 TraesCS1D01G417200 chr6A 584381166 584382527 1361 True 2204 2204 95.718 1711 3088 1 chr6A.!!$R1 1377

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
20 21 0.102481 AGCCGTAAGATCGCGTTGAT 59.898 50.0 5.77 0.00 41.06 2.57 F
58 59 0.180406 AACAAGGTCGACAGTTGGCT 59.820 50.0 25.22 14.21 0.00 4.75 F
108 109 0.182061 ATTGACTCCGATGCCAGCAT 59.818 50.0 4.45 4.45 39.69 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1698 1.098050 CTACCCTGCCACAATTCTGC 58.902 55.000 0.0 0.0 0.00 4.26 R
1928 1991 5.048434 GCCTTCCTGGTATTCTTGATAATGC 60.048 44.000 0.0 0.0 38.35 3.56 R
2184 2250 9.190858 GACATAGACTAGATTAGCTTCACATTG 57.809 37.037 0.0 0.0 0.00 2.82 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
17 18 4.396854 GAGCCGTAAGATCGCGTT 57.603 55.556 5.77 0.00 43.02 4.84
18 19 1.917921 GAGCCGTAAGATCGCGTTG 59.082 57.895 5.77 0.00 43.02 4.10
19 20 0.524816 GAGCCGTAAGATCGCGTTGA 60.525 55.000 5.77 0.00 43.02 3.18
20 21 0.102481 AGCCGTAAGATCGCGTTGAT 59.898 50.000 5.77 0.00 41.06 2.57
21 22 1.335810 AGCCGTAAGATCGCGTTGATA 59.664 47.619 5.77 0.00 37.47 2.15
22 23 2.121786 GCCGTAAGATCGCGTTGATAA 58.878 47.619 5.77 0.00 37.47 1.75
23 24 2.729882 GCCGTAAGATCGCGTTGATAAT 59.270 45.455 5.77 0.00 37.47 1.28
24 25 3.916172 GCCGTAAGATCGCGTTGATAATA 59.084 43.478 5.77 0.00 37.47 0.98
25 26 4.561606 GCCGTAAGATCGCGTTGATAATAT 59.438 41.667 5.77 0.00 37.47 1.28
26 27 5.061808 GCCGTAAGATCGCGTTGATAATATT 59.938 40.000 5.77 0.00 37.47 1.28
27 28 6.683883 CCGTAAGATCGCGTTGATAATATTC 58.316 40.000 5.77 0.00 37.47 1.75
28 29 6.384652 CGTAAGATCGCGTTGATAATATTCG 58.615 40.000 5.77 0.00 37.47 3.34
29 30 5.763444 AAGATCGCGTTGATAATATTCGG 57.237 39.130 5.77 0.00 37.47 4.30
30 31 4.174009 AGATCGCGTTGATAATATTCGGG 58.826 43.478 5.77 0.00 37.47 5.14
31 32 3.646611 TCGCGTTGATAATATTCGGGA 57.353 42.857 5.77 8.53 40.08 5.14
32 33 3.571571 TCGCGTTGATAATATTCGGGAG 58.428 45.455 5.77 0.00 38.22 4.30
33 34 2.666508 CGCGTTGATAATATTCGGGAGG 59.333 50.000 0.00 0.00 36.78 4.30
34 35 3.660865 GCGTTGATAATATTCGGGAGGT 58.339 45.455 0.00 0.00 0.00 3.85
35 36 4.062991 GCGTTGATAATATTCGGGAGGTT 58.937 43.478 0.00 0.00 0.00 3.50
36 37 5.232463 GCGTTGATAATATTCGGGAGGTTA 58.768 41.667 0.00 0.00 0.00 2.85
37 38 5.119743 GCGTTGATAATATTCGGGAGGTTAC 59.880 44.000 0.00 0.00 0.00 2.50
38 39 5.636543 CGTTGATAATATTCGGGAGGTTACC 59.363 44.000 0.00 0.00 0.00 2.85
39 40 6.527423 GTTGATAATATTCGGGAGGTTACCA 58.473 40.000 3.51 0.00 0.00 3.25
40 41 6.750660 TGATAATATTCGGGAGGTTACCAA 57.249 37.500 3.51 0.00 0.00 3.67
41 42 6.527423 TGATAATATTCGGGAGGTTACCAAC 58.473 40.000 3.51 0.00 0.00 3.77
42 43 4.847990 AATATTCGGGAGGTTACCAACA 57.152 40.909 3.51 0.00 0.00 3.33
43 44 4.847990 ATATTCGGGAGGTTACCAACAA 57.152 40.909 3.51 0.00 0.00 2.83
44 45 2.554370 TTCGGGAGGTTACCAACAAG 57.446 50.000 3.51 0.00 0.00 3.16
45 46 0.688487 TCGGGAGGTTACCAACAAGG 59.312 55.000 3.51 0.00 45.67 3.61
57 58 0.307760 CAACAAGGTCGACAGTTGGC 59.692 55.000 26.66 8.90 38.09 4.52
58 59 0.180406 AACAAGGTCGACAGTTGGCT 59.820 50.000 25.22 14.21 0.00 4.75
59 60 0.249911 ACAAGGTCGACAGTTGGCTC 60.250 55.000 25.22 5.65 0.00 4.70
60 61 0.249868 CAAGGTCGACAGTTGGCTCA 60.250 55.000 18.91 0.00 0.00 4.26
61 62 0.468226 AAGGTCGACAGTTGGCTCAA 59.532 50.000 18.91 0.00 0.00 3.02
62 63 0.249911 AGGTCGACAGTTGGCTCAAC 60.250 55.000 18.91 9.31 43.83 3.18
63 64 1.228657 GGTCGACAGTTGGCTCAACC 61.229 60.000 18.91 0.00 44.49 3.77
64 65 0.249911 GTCGACAGTTGGCTCAACCT 60.250 55.000 11.55 1.46 44.49 3.50
65 66 0.468226 TCGACAGTTGGCTCAACCTT 59.532 50.000 12.63 2.71 44.49 3.50
66 67 0.868406 CGACAGTTGGCTCAACCTTC 59.132 55.000 12.63 9.24 44.49 3.46
67 68 1.810031 CGACAGTTGGCTCAACCTTCA 60.810 52.381 12.63 0.00 44.49 3.02
68 69 2.508526 GACAGTTGGCTCAACCTTCAT 58.491 47.619 12.63 0.00 44.49 2.57
69 70 2.887152 GACAGTTGGCTCAACCTTCATT 59.113 45.455 12.63 0.00 44.49 2.57
70 71 4.072131 GACAGTTGGCTCAACCTTCATTA 58.928 43.478 12.63 0.00 44.49 1.90
71 72 3.821033 ACAGTTGGCTCAACCTTCATTAC 59.179 43.478 12.63 0.00 44.49 1.89
72 73 3.820467 CAGTTGGCTCAACCTTCATTACA 59.180 43.478 12.63 0.00 44.49 2.41
73 74 4.278170 CAGTTGGCTCAACCTTCATTACAA 59.722 41.667 12.63 0.00 44.49 2.41
74 75 4.278419 AGTTGGCTCAACCTTCATTACAAC 59.722 41.667 12.63 0.00 44.49 3.32
75 76 4.098914 TGGCTCAACCTTCATTACAACT 57.901 40.909 0.00 0.00 40.22 3.16
76 77 4.469657 TGGCTCAACCTTCATTACAACTT 58.530 39.130 0.00 0.00 40.22 2.66
77 78 4.518970 TGGCTCAACCTTCATTACAACTTC 59.481 41.667 0.00 0.00 40.22 3.01
78 79 4.518970 GGCTCAACCTTCATTACAACTTCA 59.481 41.667 0.00 0.00 34.51 3.02
79 80 5.452777 GCTCAACCTTCATTACAACTTCAC 58.547 41.667 0.00 0.00 0.00 3.18
80 81 5.008613 GCTCAACCTTCATTACAACTTCACA 59.991 40.000 0.00 0.00 0.00 3.58
81 82 6.459573 GCTCAACCTTCATTACAACTTCACAA 60.460 38.462 0.00 0.00 0.00 3.33
82 83 7.026631 TCAACCTTCATTACAACTTCACAAG 57.973 36.000 0.00 0.00 0.00 3.16
83 84 5.438761 ACCTTCATTACAACTTCACAAGC 57.561 39.130 0.00 0.00 0.00 4.01
84 85 4.887071 ACCTTCATTACAACTTCACAAGCA 59.113 37.500 0.00 0.00 0.00 3.91
85 86 5.536161 ACCTTCATTACAACTTCACAAGCAT 59.464 36.000 0.00 0.00 0.00 3.79
86 87 6.714810 ACCTTCATTACAACTTCACAAGCATA 59.285 34.615 0.00 0.00 0.00 3.14
87 88 7.394359 ACCTTCATTACAACTTCACAAGCATAT 59.606 33.333 0.00 0.00 0.00 1.78
88 89 7.912250 CCTTCATTACAACTTCACAAGCATATC 59.088 37.037 0.00 0.00 0.00 1.63
89 90 7.920160 TCATTACAACTTCACAAGCATATCA 57.080 32.000 0.00 0.00 0.00 2.15
90 91 8.510243 TCATTACAACTTCACAAGCATATCAT 57.490 30.769 0.00 0.00 0.00 2.45
91 92 8.959548 TCATTACAACTTCACAAGCATATCATT 58.040 29.630 0.00 0.00 0.00 2.57
92 93 9.016623 CATTACAACTTCACAAGCATATCATTG 57.983 33.333 0.00 0.00 0.00 2.82
93 94 6.822667 ACAACTTCACAAGCATATCATTGA 57.177 33.333 3.92 0.00 0.00 2.57
94 95 6.615088 ACAACTTCACAAGCATATCATTGAC 58.385 36.000 3.92 0.00 0.00 3.18
95 96 6.432162 ACAACTTCACAAGCATATCATTGACT 59.568 34.615 3.92 0.00 0.00 3.41
96 97 6.674694 ACTTCACAAGCATATCATTGACTC 57.325 37.500 3.92 0.00 0.00 3.36
97 98 5.587844 ACTTCACAAGCATATCATTGACTCC 59.412 40.000 3.92 0.00 0.00 3.85
98 99 4.122046 TCACAAGCATATCATTGACTCCG 58.878 43.478 3.92 0.00 0.00 4.63
99 100 4.122046 CACAAGCATATCATTGACTCCGA 58.878 43.478 3.92 0.00 0.00 4.55
100 101 4.753610 CACAAGCATATCATTGACTCCGAT 59.246 41.667 3.92 0.00 0.00 4.18
101 102 4.753610 ACAAGCATATCATTGACTCCGATG 59.246 41.667 3.92 0.00 35.85 3.84
102 103 3.332919 AGCATATCATTGACTCCGATGC 58.667 45.455 9.54 9.54 38.75 3.91
103 104 2.417933 GCATATCATTGACTCCGATGCC 59.582 50.000 0.00 0.00 34.77 4.40
104 105 3.667360 CATATCATTGACTCCGATGCCA 58.333 45.455 0.00 0.00 34.77 4.92
105 106 2.251409 ATCATTGACTCCGATGCCAG 57.749 50.000 0.00 0.00 34.77 4.85
106 107 0.462581 TCATTGACTCCGATGCCAGC 60.463 55.000 0.00 0.00 34.77 4.85
107 108 0.745486 CATTGACTCCGATGCCAGCA 60.745 55.000 0.00 0.00 0.00 4.41
108 109 0.182061 ATTGACTCCGATGCCAGCAT 59.818 50.000 4.45 4.45 39.69 3.79
109 110 0.462581 TTGACTCCGATGCCAGCATC 60.463 55.000 20.31 20.31 46.71 3.91
118 119 0.742505 ATGCCAGCATCACGAAATGG 59.257 50.000 0.00 0.00 29.42 3.16
119 120 1.314534 TGCCAGCATCACGAAATGGG 61.315 55.000 0.00 0.00 0.00 4.00
120 121 2.008268 GCCAGCATCACGAAATGGGG 62.008 60.000 0.00 0.00 0.00 4.96
121 122 1.434696 CAGCATCACGAAATGGGGC 59.565 57.895 0.00 0.00 0.00 5.80
122 123 2.114670 AGCATCACGAAATGGGGCG 61.115 57.895 0.00 0.00 34.25 6.13
123 124 2.408835 CATCACGAAATGGGGCGC 59.591 61.111 0.00 0.00 0.00 6.53
124 125 2.828549 ATCACGAAATGGGGCGCC 60.829 61.111 21.18 21.18 0.00 6.53
125 126 3.344137 ATCACGAAATGGGGCGCCT 62.344 57.895 28.56 5.35 0.00 5.52
126 127 2.837031 ATCACGAAATGGGGCGCCTT 62.837 55.000 28.56 13.14 0.00 4.35
127 128 3.061848 ACGAAATGGGGCGCCTTG 61.062 61.111 28.56 12.61 0.00 3.61
128 129 4.496927 CGAAATGGGGCGCCTTGC 62.497 66.667 28.56 10.90 45.38 4.01
137 138 2.672996 GCGCCTTGCCCTCTGAAA 60.673 61.111 0.00 0.00 37.76 2.69
138 139 2.694760 GCGCCTTGCCCTCTGAAAG 61.695 63.158 0.00 0.00 37.76 2.62
139 140 1.003355 CGCCTTGCCCTCTGAAAGA 60.003 57.895 0.00 0.00 43.69 2.52
140 141 0.393537 CGCCTTGCCCTCTGAAAGAT 60.394 55.000 0.00 0.00 45.62 2.40
141 142 1.101331 GCCTTGCCCTCTGAAAGATG 58.899 55.000 0.00 0.00 45.62 2.90
142 143 1.615384 GCCTTGCCCTCTGAAAGATGT 60.615 52.381 0.00 0.00 45.62 3.06
143 144 2.089980 CCTTGCCCTCTGAAAGATGTG 58.910 52.381 0.00 0.00 45.62 3.21
144 145 2.089980 CTTGCCCTCTGAAAGATGTGG 58.910 52.381 0.00 0.00 45.62 4.17
145 146 1.067295 TGCCCTCTGAAAGATGTGGT 58.933 50.000 0.00 0.00 45.62 4.16
146 147 1.271543 TGCCCTCTGAAAGATGTGGTG 60.272 52.381 0.00 0.00 45.62 4.17
147 148 1.952367 GCCCTCTGAAAGATGTGGTGG 60.952 57.143 0.00 0.00 45.62 4.61
148 149 1.457346 CCTCTGAAAGATGTGGTGGC 58.543 55.000 0.00 0.00 45.62 5.01
149 150 1.081892 CTCTGAAAGATGTGGTGGCG 58.918 55.000 0.00 0.00 45.62 5.69
150 151 0.955428 TCTGAAAGATGTGGTGGCGC 60.955 55.000 0.00 0.00 38.67 6.53
151 152 1.926511 CTGAAAGATGTGGTGGCGCC 61.927 60.000 22.73 22.73 34.07 6.53
152 153 1.675641 GAAAGATGTGGTGGCGCCT 60.676 57.895 29.70 5.42 38.35 5.52
153 154 1.228552 AAAGATGTGGTGGCGCCTT 60.229 52.632 29.70 7.86 38.35 4.35
154 155 1.526575 AAAGATGTGGTGGCGCCTTG 61.527 55.000 29.70 0.00 38.35 3.61
155 156 4.120331 GATGTGGTGGCGCCTTGC 62.120 66.667 29.70 17.30 45.38 4.01
164 165 2.672996 GCGCCTTGCCCTCTGAAA 60.673 61.111 0.00 0.00 37.76 2.69
165 166 2.694760 GCGCCTTGCCCTCTGAAAG 61.695 63.158 0.00 0.00 37.76 2.62
166 167 1.003355 CGCCTTGCCCTCTGAAAGA 60.003 57.895 0.00 0.00 43.69 2.52
167 168 0.393537 CGCCTTGCCCTCTGAAAGAT 60.394 55.000 0.00 0.00 45.62 2.40
168 169 1.844687 GCCTTGCCCTCTGAAAGATT 58.155 50.000 0.00 0.00 45.62 2.40
169 170 2.174360 GCCTTGCCCTCTGAAAGATTT 58.826 47.619 0.00 0.00 45.62 2.17
170 171 2.094338 GCCTTGCCCTCTGAAAGATTTG 60.094 50.000 0.00 0.00 45.62 2.32
171 172 2.494870 CCTTGCCCTCTGAAAGATTTGG 59.505 50.000 0.00 0.00 45.62 3.28
172 173 2.220653 TGCCCTCTGAAAGATTTGGG 57.779 50.000 0.00 0.00 45.62 4.12
173 174 1.710244 TGCCCTCTGAAAGATTTGGGA 59.290 47.619 0.00 0.00 46.20 4.37
174 175 2.312741 TGCCCTCTGAAAGATTTGGGAT 59.687 45.455 0.00 0.00 46.20 3.85
175 176 2.692041 GCCCTCTGAAAGATTTGGGATG 59.308 50.000 0.00 0.00 46.20 3.51
176 177 2.692041 CCCTCTGAAAGATTTGGGATGC 59.308 50.000 0.00 0.00 46.20 3.91
177 178 2.692041 CCTCTGAAAGATTTGGGATGCC 59.308 50.000 0.00 0.00 45.62 4.40
178 179 2.357009 CTCTGAAAGATTTGGGATGCCG 59.643 50.000 0.00 0.00 45.62 5.69
179 180 1.406539 CTGAAAGATTTGGGATGCCGG 59.593 52.381 0.00 0.00 34.07 6.13
180 181 0.746659 GAAAGATTTGGGATGCCGGG 59.253 55.000 2.18 0.00 0.00 5.73
181 182 0.334676 AAAGATTTGGGATGCCGGGA 59.665 50.000 2.18 0.00 0.00 5.14
182 183 0.334676 AAGATTTGGGATGCCGGGAA 59.665 50.000 0.00 0.00 0.00 3.97
183 184 0.557729 AGATTTGGGATGCCGGGAAT 59.442 50.000 0.00 0.00 0.00 3.01
184 185 0.675633 GATTTGGGATGCCGGGAATG 59.324 55.000 0.00 0.00 0.00 2.67
185 186 1.402107 ATTTGGGATGCCGGGAATGC 61.402 55.000 0.00 0.00 0.00 3.56
186 187 2.795024 TTTGGGATGCCGGGAATGCA 62.795 55.000 8.95 0.00 43.97 3.96
187 188 2.441901 GGGATGCCGGGAATGCAA 60.442 61.111 8.95 0.00 42.92 4.08
188 189 2.785425 GGGATGCCGGGAATGCAAC 61.785 63.158 8.95 0.00 42.92 4.17
189 190 2.408835 GATGCCGGGAATGCAACG 59.591 61.111 0.00 0.00 42.92 4.10
193 194 2.046314 CCGGGAATGCAACGGTCT 60.046 61.111 12.53 0.00 42.53 3.85
194 195 1.674322 CCGGGAATGCAACGGTCTT 60.674 57.895 12.53 0.00 42.53 3.01
195 196 1.644786 CCGGGAATGCAACGGTCTTC 61.645 60.000 12.53 1.30 42.53 2.87
196 197 1.644786 CGGGAATGCAACGGTCTTCC 61.645 60.000 6.03 6.03 37.11 3.46
197 198 2.180674 GGAATGCAACGGTCTTCCC 58.819 57.895 3.52 0.00 32.67 3.97
198 199 1.313091 GGAATGCAACGGTCTTCCCC 61.313 60.000 3.52 0.00 32.67 4.81
199 200 1.304134 AATGCAACGGTCTTCCCCC 60.304 57.895 0.00 0.00 0.00 5.40
200 201 2.075355 AATGCAACGGTCTTCCCCCA 62.075 55.000 0.00 0.00 0.00 4.96
201 202 1.863155 ATGCAACGGTCTTCCCCCAT 61.863 55.000 0.00 0.00 0.00 4.00
202 203 1.202099 TGCAACGGTCTTCCCCCATA 61.202 55.000 0.00 0.00 0.00 2.74
203 204 0.182775 GCAACGGTCTTCCCCCATAT 59.817 55.000 0.00 0.00 0.00 1.78
204 205 1.409661 GCAACGGTCTTCCCCCATATT 60.410 52.381 0.00 0.00 0.00 1.28
205 206 2.297701 CAACGGTCTTCCCCCATATTG 58.702 52.381 0.00 0.00 0.00 1.90
206 207 1.887797 ACGGTCTTCCCCCATATTGA 58.112 50.000 0.00 0.00 0.00 2.57
207 208 1.489230 ACGGTCTTCCCCCATATTGAC 59.511 52.381 0.00 0.00 0.00 3.18
208 209 1.202770 CGGTCTTCCCCCATATTGACC 60.203 57.143 0.00 0.00 40.16 4.02
209 210 1.850345 GGTCTTCCCCCATATTGACCA 59.150 52.381 0.00 0.00 42.32 4.02
210 211 2.158608 GGTCTTCCCCCATATTGACCAG 60.159 54.545 0.00 0.00 42.32 4.00
211 212 1.494721 TCTTCCCCCATATTGACCAGC 59.505 52.381 0.00 0.00 0.00 4.85
212 213 1.215173 CTTCCCCCATATTGACCAGCA 59.785 52.381 0.00 0.00 0.00 4.41
213 214 1.533187 TCCCCCATATTGACCAGCAT 58.467 50.000 0.00 0.00 0.00 3.79
214 215 2.712384 TCCCCCATATTGACCAGCATA 58.288 47.619 0.00 0.00 0.00 3.14
215 216 2.644299 TCCCCCATATTGACCAGCATAG 59.356 50.000 0.00 0.00 0.00 2.23
216 217 2.440409 CCCCATATTGACCAGCATAGC 58.560 52.381 0.00 0.00 0.00 2.97
217 218 2.040813 CCCCATATTGACCAGCATAGCT 59.959 50.000 0.00 0.00 40.77 3.32
218 219 3.341823 CCCATATTGACCAGCATAGCTC 58.658 50.000 0.00 0.00 36.40 4.09
219 220 3.341823 CCATATTGACCAGCATAGCTCC 58.658 50.000 0.00 0.00 36.40 4.70
220 221 3.244665 CCATATTGACCAGCATAGCTCCA 60.245 47.826 0.00 0.00 36.40 3.86
221 222 4.567116 CCATATTGACCAGCATAGCTCCAT 60.567 45.833 0.00 0.00 36.40 3.41
222 223 2.627515 TTGACCAGCATAGCTCCATC 57.372 50.000 0.00 0.00 36.40 3.51
223 224 1.499368 TGACCAGCATAGCTCCATCA 58.501 50.000 0.00 0.00 36.40 3.07
224 225 2.052468 TGACCAGCATAGCTCCATCAT 58.948 47.619 0.00 0.00 36.40 2.45
225 226 2.224450 TGACCAGCATAGCTCCATCATG 60.224 50.000 0.00 0.00 36.40 3.07
226 227 2.038164 GACCAGCATAGCTCCATCATGA 59.962 50.000 0.00 0.00 36.40 3.07
227 228 2.643304 ACCAGCATAGCTCCATCATGAT 59.357 45.455 1.18 1.18 36.40 2.45
228 229 3.271729 CCAGCATAGCTCCATCATGATC 58.728 50.000 4.86 0.00 36.40 2.92
229 230 3.307480 CCAGCATAGCTCCATCATGATCA 60.307 47.826 4.86 0.00 36.40 2.92
230 231 3.935828 CAGCATAGCTCCATCATGATCAG 59.064 47.826 4.86 6.04 36.40 2.90
231 232 3.055021 AGCATAGCTCCATCATGATCAGG 60.055 47.826 4.86 5.43 30.62 3.86
232 233 3.055312 GCATAGCTCCATCATGATCAGGA 60.055 47.826 13.16 13.16 0.00 3.86
233 234 4.565028 GCATAGCTCCATCATGATCAGGAA 60.565 45.833 14.88 0.00 0.00 3.36
234 235 5.746284 CATAGCTCCATCATGATCAGGAAT 58.254 41.667 14.88 9.34 0.00 3.01
235 236 6.631992 GCATAGCTCCATCATGATCAGGAATA 60.632 42.308 14.88 10.79 0.00 1.75
236 237 5.423704 AGCTCCATCATGATCAGGAATAG 57.576 43.478 14.88 12.37 0.00 1.73
237 238 4.845225 AGCTCCATCATGATCAGGAATAGT 59.155 41.667 14.88 0.00 0.00 2.12
238 239 6.021672 AGCTCCATCATGATCAGGAATAGTA 58.978 40.000 14.88 0.00 0.00 1.82
239 240 6.673097 AGCTCCATCATGATCAGGAATAGTAT 59.327 38.462 14.88 0.00 0.00 2.12
240 241 6.985645 GCTCCATCATGATCAGGAATAGTATC 59.014 42.308 14.88 0.00 0.00 2.24
241 242 7.364497 GCTCCATCATGATCAGGAATAGTATCA 60.364 40.741 14.88 0.00 33.20 2.15
242 243 8.619683 TCCATCATGATCAGGAATAGTATCAT 57.380 34.615 14.88 0.00 39.14 2.45
243 244 9.719433 TCCATCATGATCAGGAATAGTATCATA 57.281 33.333 14.88 0.00 37.04 2.15
244 245 9.984190 CCATCATGATCAGGAATAGTATCATAG 57.016 37.037 14.88 0.00 37.04 2.23
247 248 8.897752 TCATGATCAGGAATAGTATCATAGACG 58.102 37.037 7.78 0.00 37.04 4.18
248 249 8.897752 CATGATCAGGAATAGTATCATAGACGA 58.102 37.037 0.00 0.00 37.04 4.20
249 250 8.270080 TGATCAGGAATAGTATCATAGACGAC 57.730 38.462 0.00 0.00 0.00 4.34
250 251 8.103935 TGATCAGGAATAGTATCATAGACGACT 58.896 37.037 0.00 0.00 0.00 4.18
251 252 8.871629 ATCAGGAATAGTATCATAGACGACTT 57.128 34.615 0.00 0.00 0.00 3.01
252 253 9.961264 ATCAGGAATAGTATCATAGACGACTTA 57.039 33.333 0.00 0.00 0.00 2.24
253 254 9.788889 TCAGGAATAGTATCATAGACGACTTAA 57.211 33.333 0.00 0.00 0.00 1.85
254 255 9.828852 CAGGAATAGTATCATAGACGACTTAAC 57.171 37.037 0.00 0.00 0.00 2.01
255 256 8.719648 AGGAATAGTATCATAGACGACTTAACG 58.280 37.037 0.00 0.00 39.31 3.18
256 257 7.961827 GGAATAGTATCATAGACGACTTAACGG 59.038 40.741 0.00 0.00 37.61 4.44
257 258 7.976135 ATAGTATCATAGACGACTTAACGGT 57.024 36.000 0.00 0.00 37.61 4.83
258 259 6.057627 AGTATCATAGACGACTTAACGGTG 57.942 41.667 0.00 0.00 37.61 4.94
259 260 4.978083 ATCATAGACGACTTAACGGTGT 57.022 40.909 0.00 0.00 37.61 4.16
260 261 4.346734 TCATAGACGACTTAACGGTGTC 57.653 45.455 0.00 0.00 37.61 3.67
261 262 3.752747 TCATAGACGACTTAACGGTGTCA 59.247 43.478 0.00 0.00 37.61 3.58
262 263 2.412421 AGACGACTTAACGGTGTCAC 57.588 50.000 0.00 0.00 37.61 3.67
263 264 1.000938 AGACGACTTAACGGTGTCACC 60.001 52.381 12.40 12.40 37.61 4.02
275 276 3.614159 GGTGTCACCGGTTAAAGAAAC 57.386 47.619 2.97 4.09 37.36 2.78
903 954 6.866010 TGAGCTATGTTTATGTATGCTTGG 57.134 37.500 0.00 0.00 0.00 3.61
1281 1338 4.833380 AGTTGCTCTTCTGAACCTACACTA 59.167 41.667 0.00 0.00 0.00 2.74
1342 1399 7.793948 AGGTATTGAGGGATATGGTTACTAC 57.206 40.000 0.00 0.00 0.00 2.73
1928 1991 3.503363 TGCATTTTACAGAGTCAAGCTGG 59.497 43.478 0.00 0.00 37.69 4.85
2184 2250 1.567357 ATGGGGTGTACATTTTGGGC 58.433 50.000 0.00 0.00 0.00 5.36
2485 2561 4.810790 CTCATAAATAGCCTACTCCACCG 58.189 47.826 0.00 0.00 0.00 4.94
2487 2563 4.897076 TCATAAATAGCCTACTCCACCGAA 59.103 41.667 0.00 0.00 0.00 4.30
2660 2736 1.573108 CTTGGGAGCTAGAGTGGGAA 58.427 55.000 0.00 0.00 0.00 3.97
2818 2894 1.717077 TCCTCACCCTTCTACCAGAGT 59.283 52.381 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.524816 TCAACGCGATCTTACGGCTC 60.525 55.000 15.93 0.00 0.00 4.70
1 2 0.102481 ATCAACGCGATCTTACGGCT 59.898 50.000 15.93 0.00 0.00 5.52
2 3 1.762419 TATCAACGCGATCTTACGGC 58.238 50.000 15.93 0.00 35.39 5.68
3 4 6.504335 CGAATATTATCAACGCGATCTTACGG 60.504 42.308 15.93 0.00 35.39 4.02
4 5 6.384652 CGAATATTATCAACGCGATCTTACG 58.615 40.000 15.93 0.60 35.39 3.18
5 6 6.237490 CCCGAATATTATCAACGCGATCTTAC 60.237 42.308 15.93 0.00 35.39 2.34
6 7 5.803461 CCCGAATATTATCAACGCGATCTTA 59.197 40.000 15.93 0.00 35.39 2.10
7 8 4.625742 CCCGAATATTATCAACGCGATCTT 59.374 41.667 15.93 0.00 35.39 2.40
8 9 4.082408 TCCCGAATATTATCAACGCGATCT 60.082 41.667 15.93 0.00 35.39 2.75
9 10 4.171005 TCCCGAATATTATCAACGCGATC 58.829 43.478 15.93 0.00 35.39 3.69
10 11 4.174009 CTCCCGAATATTATCAACGCGAT 58.826 43.478 15.93 0.00 38.21 4.58
11 12 3.571571 CTCCCGAATATTATCAACGCGA 58.428 45.455 15.93 0.00 0.00 5.87
12 13 2.666508 CCTCCCGAATATTATCAACGCG 59.333 50.000 3.53 3.53 0.00 6.01
13 14 3.660865 ACCTCCCGAATATTATCAACGC 58.339 45.455 0.00 0.00 0.00 4.84
14 15 5.636543 GGTAACCTCCCGAATATTATCAACG 59.363 44.000 0.00 0.00 0.00 4.10
15 16 6.527423 TGGTAACCTCCCGAATATTATCAAC 58.473 40.000 0.00 0.00 0.00 3.18
16 17 6.750660 TGGTAACCTCCCGAATATTATCAA 57.249 37.500 0.00 0.00 0.00 2.57
17 18 6.099990 TGTTGGTAACCTCCCGAATATTATCA 59.900 38.462 0.00 0.00 0.00 2.15
18 19 6.527423 TGTTGGTAACCTCCCGAATATTATC 58.473 40.000 0.00 0.00 0.00 1.75
19 20 6.503560 TGTTGGTAACCTCCCGAATATTAT 57.496 37.500 0.00 0.00 0.00 1.28
20 21 5.954153 TGTTGGTAACCTCCCGAATATTA 57.046 39.130 0.00 0.00 0.00 0.98
21 22 4.847990 TGTTGGTAACCTCCCGAATATT 57.152 40.909 0.00 0.00 0.00 1.28
22 23 4.384868 CCTTGTTGGTAACCTCCCGAATAT 60.385 45.833 0.00 0.00 0.00 1.28
23 24 3.054948 CCTTGTTGGTAACCTCCCGAATA 60.055 47.826 0.00 0.00 0.00 1.75
24 25 2.290705 CCTTGTTGGTAACCTCCCGAAT 60.291 50.000 0.00 0.00 0.00 3.34
25 26 1.072648 CCTTGTTGGTAACCTCCCGAA 59.927 52.381 0.00 0.00 0.00 4.30
26 27 0.688487 CCTTGTTGGTAACCTCCCGA 59.312 55.000 0.00 0.00 0.00 5.14
27 28 3.243128 CCTTGTTGGTAACCTCCCG 57.757 57.895 0.00 0.00 0.00 5.14
38 39 0.307760 GCCAACTGTCGACCTTGTTG 59.692 55.000 25.67 25.67 39.35 3.33
39 40 0.180406 AGCCAACTGTCGACCTTGTT 59.820 50.000 14.12 12.38 0.00 2.83
40 41 0.249911 GAGCCAACTGTCGACCTTGT 60.250 55.000 14.12 6.62 0.00 3.16
41 42 0.249868 TGAGCCAACTGTCGACCTTG 60.250 55.000 14.12 13.80 0.00 3.61
42 43 0.468226 TTGAGCCAACTGTCGACCTT 59.532 50.000 14.12 1.03 0.00 3.50
43 44 0.249911 GTTGAGCCAACTGTCGACCT 60.250 55.000 14.12 0.65 40.73 3.85
44 45 1.228657 GGTTGAGCCAACTGTCGACC 61.229 60.000 14.12 5.30 43.14 4.79
45 46 0.249911 AGGTTGAGCCAACTGTCGAC 60.250 55.000 9.11 9.11 43.14 4.20
46 47 0.468226 AAGGTTGAGCCAACTGTCGA 59.532 50.000 14.91 0.00 43.14 4.20
47 48 0.868406 GAAGGTTGAGCCAACTGTCG 59.132 55.000 14.91 0.00 43.14 4.35
48 49 1.967319 TGAAGGTTGAGCCAACTGTC 58.033 50.000 14.91 12.78 43.14 3.51
49 50 2.664402 ATGAAGGTTGAGCCAACTGT 57.336 45.000 14.91 6.08 43.14 3.55
50 51 3.820467 TGTAATGAAGGTTGAGCCAACTG 59.180 43.478 14.91 0.00 43.14 3.16
51 52 4.098914 TGTAATGAAGGTTGAGCCAACT 57.901 40.909 14.91 0.36 43.14 3.16
52 53 4.278419 AGTTGTAATGAAGGTTGAGCCAAC 59.722 41.667 8.94 8.94 42.89 3.77
53 54 4.469657 AGTTGTAATGAAGGTTGAGCCAA 58.530 39.130 0.00 0.00 40.61 4.52
54 55 4.098914 AGTTGTAATGAAGGTTGAGCCA 57.901 40.909 0.00 0.00 40.61 4.75
55 56 4.518970 TGAAGTTGTAATGAAGGTTGAGCC 59.481 41.667 0.00 0.00 37.58 4.70
56 57 5.008613 TGTGAAGTTGTAATGAAGGTTGAGC 59.991 40.000 0.00 0.00 0.00 4.26
57 58 6.618287 TGTGAAGTTGTAATGAAGGTTGAG 57.382 37.500 0.00 0.00 0.00 3.02
58 59 6.459573 GCTTGTGAAGTTGTAATGAAGGTTGA 60.460 38.462 0.00 0.00 0.00 3.18
59 60 5.687285 GCTTGTGAAGTTGTAATGAAGGTTG 59.313 40.000 0.00 0.00 0.00 3.77
60 61 5.359576 TGCTTGTGAAGTTGTAATGAAGGTT 59.640 36.000 0.00 0.00 0.00 3.50
61 62 4.887071 TGCTTGTGAAGTTGTAATGAAGGT 59.113 37.500 0.00 0.00 0.00 3.50
62 63 5.437289 TGCTTGTGAAGTTGTAATGAAGG 57.563 39.130 0.00 0.00 0.00 3.46
63 64 8.453320 TGATATGCTTGTGAAGTTGTAATGAAG 58.547 33.333 0.00 0.00 0.00 3.02
64 65 8.334263 TGATATGCTTGTGAAGTTGTAATGAA 57.666 30.769 0.00 0.00 0.00 2.57
65 66 7.920160 TGATATGCTTGTGAAGTTGTAATGA 57.080 32.000 0.00 0.00 0.00 2.57
66 67 9.016623 CAATGATATGCTTGTGAAGTTGTAATG 57.983 33.333 0.00 0.00 0.00 1.90
67 68 8.959548 TCAATGATATGCTTGTGAAGTTGTAAT 58.040 29.630 0.00 0.00 0.00 1.89
68 69 8.236586 GTCAATGATATGCTTGTGAAGTTGTAA 58.763 33.333 0.00 0.00 0.00 2.41
69 70 7.607607 AGTCAATGATATGCTTGTGAAGTTGTA 59.392 33.333 0.00 0.00 0.00 2.41
70 71 6.432162 AGTCAATGATATGCTTGTGAAGTTGT 59.568 34.615 0.00 0.00 0.00 3.32
71 72 6.849502 AGTCAATGATATGCTTGTGAAGTTG 58.150 36.000 0.00 0.00 0.00 3.16
72 73 6.094603 GGAGTCAATGATATGCTTGTGAAGTT 59.905 38.462 0.00 0.00 0.00 2.66
73 74 5.587844 GGAGTCAATGATATGCTTGTGAAGT 59.412 40.000 0.00 0.00 0.00 3.01
74 75 5.277202 CGGAGTCAATGATATGCTTGTGAAG 60.277 44.000 0.00 0.00 0.00 3.02
75 76 4.571984 CGGAGTCAATGATATGCTTGTGAA 59.428 41.667 0.00 0.00 0.00 3.18
76 77 4.122046 CGGAGTCAATGATATGCTTGTGA 58.878 43.478 0.00 0.00 0.00 3.58
77 78 4.122046 TCGGAGTCAATGATATGCTTGTG 58.878 43.478 0.00 0.00 0.00 3.33
78 79 4.406648 TCGGAGTCAATGATATGCTTGT 57.593 40.909 0.00 0.00 0.00 3.16
79 80 4.378149 GCATCGGAGTCAATGATATGCTTG 60.378 45.833 8.50 0.00 36.27 4.01
80 81 3.750130 GCATCGGAGTCAATGATATGCTT 59.250 43.478 8.50 0.00 36.27 3.91
81 82 3.332919 GCATCGGAGTCAATGATATGCT 58.667 45.455 8.50 0.00 36.27 3.79
82 83 2.417933 GGCATCGGAGTCAATGATATGC 59.582 50.000 8.50 0.00 37.97 3.14
83 84 3.667360 TGGCATCGGAGTCAATGATATG 58.333 45.455 8.50 0.00 0.00 1.78
84 85 3.867600 GCTGGCATCGGAGTCAATGATAT 60.868 47.826 8.50 0.00 0.00 1.63
85 86 2.548707 GCTGGCATCGGAGTCAATGATA 60.549 50.000 8.50 0.00 0.00 2.15
86 87 1.813092 GCTGGCATCGGAGTCAATGAT 60.813 52.381 8.50 0.00 0.00 2.45
87 88 0.462581 GCTGGCATCGGAGTCAATGA 60.463 55.000 8.50 0.00 0.00 2.57
88 89 0.745486 TGCTGGCATCGGAGTCAATG 60.745 55.000 0.00 0.00 0.00 2.82
89 90 0.182061 ATGCTGGCATCGGAGTCAAT 59.818 50.000 1.86 0.00 29.42 2.57
90 91 0.462581 GATGCTGGCATCGGAGTCAA 60.463 55.000 17.89 0.00 42.55 3.18
91 92 1.144716 GATGCTGGCATCGGAGTCA 59.855 57.895 17.89 0.00 42.55 3.41
92 93 4.040068 GATGCTGGCATCGGAGTC 57.960 61.111 17.89 0.00 42.55 3.36
99 100 0.742505 CCATTTCGTGATGCTGGCAT 59.257 50.000 7.86 7.86 39.69 4.40
100 101 1.314534 CCCATTTCGTGATGCTGGCA 61.315 55.000 0.00 0.00 0.00 4.92
101 102 1.434696 CCCATTTCGTGATGCTGGC 59.565 57.895 0.00 0.00 0.00 4.85
102 103 2.008268 GCCCCATTTCGTGATGCTGG 62.008 60.000 0.00 0.00 0.00 4.85
103 104 1.434696 GCCCCATTTCGTGATGCTG 59.565 57.895 0.00 0.00 0.00 4.41
104 105 2.114670 CGCCCCATTTCGTGATGCT 61.115 57.895 0.00 0.00 0.00 3.79
105 106 2.408835 CGCCCCATTTCGTGATGC 59.591 61.111 0.00 0.00 0.00 3.91
106 107 2.408835 GCGCCCCATTTCGTGATG 59.591 61.111 0.00 0.00 0.00 3.07
107 108 2.828549 GGCGCCCCATTTCGTGAT 60.829 61.111 18.11 0.00 0.00 3.06
108 109 3.561120 AAGGCGCCCCATTTCGTGA 62.561 57.895 26.15 0.00 0.00 4.35
109 110 3.061848 AAGGCGCCCCATTTCGTG 61.062 61.111 26.15 0.00 0.00 4.35
110 111 3.061848 CAAGGCGCCCCATTTCGT 61.062 61.111 26.15 0.00 0.00 3.85
111 112 4.496927 GCAAGGCGCCCCATTTCG 62.497 66.667 26.15 6.99 32.94 3.46
120 121 2.672996 TTTCAGAGGGCAAGGCGC 60.673 61.111 0.00 0.00 41.91 6.53
121 122 0.393537 ATCTTTCAGAGGGCAAGGCG 60.394 55.000 0.00 0.00 0.00 5.52
122 123 1.101331 CATCTTTCAGAGGGCAAGGC 58.899 55.000 0.00 0.00 0.00 4.35
123 124 2.089980 CACATCTTTCAGAGGGCAAGG 58.910 52.381 0.00 0.00 28.79 3.61
124 125 2.089980 CCACATCTTTCAGAGGGCAAG 58.910 52.381 0.00 0.00 28.79 4.01
125 126 1.425066 ACCACATCTTTCAGAGGGCAA 59.575 47.619 0.00 0.00 28.79 4.52
126 127 1.067295 ACCACATCTTTCAGAGGGCA 58.933 50.000 0.00 0.00 28.79 5.36
127 128 1.457346 CACCACATCTTTCAGAGGGC 58.543 55.000 0.00 0.00 28.79 5.19
128 129 1.952367 GCCACCACATCTTTCAGAGGG 60.952 57.143 0.00 0.00 28.79 4.30
129 130 1.457346 GCCACCACATCTTTCAGAGG 58.543 55.000 0.00 0.00 31.33 3.69
130 131 1.081892 CGCCACCACATCTTTCAGAG 58.918 55.000 0.00 0.00 0.00 3.35
131 132 0.955428 GCGCCACCACATCTTTCAGA 60.955 55.000 0.00 0.00 0.00 3.27
132 133 1.503542 GCGCCACCACATCTTTCAG 59.496 57.895 0.00 0.00 0.00 3.02
133 134 1.971167 GGCGCCACCACATCTTTCA 60.971 57.895 24.80 0.00 38.86 2.69
134 135 1.244019 AAGGCGCCACCACATCTTTC 61.244 55.000 31.54 0.00 43.14 2.62
135 136 1.228552 AAGGCGCCACCACATCTTT 60.229 52.632 31.54 7.70 43.14 2.52
136 137 1.973281 CAAGGCGCCACCACATCTT 60.973 57.895 31.54 8.56 43.14 2.40
137 138 2.360350 CAAGGCGCCACCACATCT 60.360 61.111 31.54 0.76 43.14 2.90
138 139 4.120331 GCAAGGCGCCACCACATC 62.120 66.667 31.54 6.14 43.14 3.06
147 148 2.672996 TTTCAGAGGGCAAGGCGC 60.673 61.111 0.00 0.00 41.91 6.53
148 149 0.393537 ATCTTTCAGAGGGCAAGGCG 60.394 55.000 0.00 0.00 0.00 5.52
149 150 1.844687 AATCTTTCAGAGGGCAAGGC 58.155 50.000 0.00 0.00 0.00 4.35
150 151 2.494870 CCAAATCTTTCAGAGGGCAAGG 59.505 50.000 0.00 0.00 0.00 3.61
151 152 2.494870 CCCAAATCTTTCAGAGGGCAAG 59.505 50.000 0.00 0.00 0.00 4.01
152 153 2.109834 TCCCAAATCTTTCAGAGGGCAA 59.890 45.455 0.00 0.00 36.24 4.52
153 154 1.710244 TCCCAAATCTTTCAGAGGGCA 59.290 47.619 0.00 0.00 36.24 5.36
154 155 2.514458 TCCCAAATCTTTCAGAGGGC 57.486 50.000 0.00 0.00 36.24 5.19
155 156 2.692041 GCATCCCAAATCTTTCAGAGGG 59.308 50.000 0.00 0.00 37.65 4.30
156 157 2.692041 GGCATCCCAAATCTTTCAGAGG 59.308 50.000 0.00 0.00 0.00 3.69
157 158 2.357009 CGGCATCCCAAATCTTTCAGAG 59.643 50.000 0.00 0.00 0.00 3.35
158 159 2.368439 CGGCATCCCAAATCTTTCAGA 58.632 47.619 0.00 0.00 0.00 3.27
159 160 1.406539 CCGGCATCCCAAATCTTTCAG 59.593 52.381 0.00 0.00 0.00 3.02
160 161 1.473258 CCGGCATCCCAAATCTTTCA 58.527 50.000 0.00 0.00 0.00 2.69
161 162 0.746659 CCCGGCATCCCAAATCTTTC 59.253 55.000 0.00 0.00 0.00 2.62
162 163 0.334676 TCCCGGCATCCCAAATCTTT 59.665 50.000 0.00 0.00 0.00 2.52
163 164 0.334676 TTCCCGGCATCCCAAATCTT 59.665 50.000 0.00 0.00 0.00 2.40
164 165 0.557729 ATTCCCGGCATCCCAAATCT 59.442 50.000 0.00 0.00 0.00 2.40
165 166 0.675633 CATTCCCGGCATCCCAAATC 59.324 55.000 0.00 0.00 0.00 2.17
166 167 1.402107 GCATTCCCGGCATCCCAAAT 61.402 55.000 0.00 0.00 0.00 2.32
167 168 2.057408 GCATTCCCGGCATCCCAAA 61.057 57.895 0.00 0.00 0.00 3.28
168 169 2.441901 GCATTCCCGGCATCCCAA 60.442 61.111 0.00 0.00 0.00 4.12
169 170 3.293933 TTGCATTCCCGGCATCCCA 62.294 57.895 0.00 0.00 41.58 4.37
170 171 2.441901 TTGCATTCCCGGCATCCC 60.442 61.111 0.00 0.00 41.58 3.85
171 172 2.807622 GTTGCATTCCCGGCATCC 59.192 61.111 0.00 0.00 41.58 3.51
172 173 2.408835 CGTTGCATTCCCGGCATC 59.591 61.111 0.00 0.00 41.58 3.91
173 174 3.140141 CCGTTGCATTCCCGGCAT 61.140 61.111 0.00 0.00 41.58 4.40
174 175 4.652131 ACCGTTGCATTCCCGGCA 62.652 61.111 12.72 0.00 45.49 5.69
175 176 3.810896 GACCGTTGCATTCCCGGC 61.811 66.667 12.72 4.67 45.49 6.13
176 177 1.644786 GAAGACCGTTGCATTCCCGG 61.645 60.000 11.60 11.60 46.93 5.73
177 178 1.644786 GGAAGACCGTTGCATTCCCG 61.645 60.000 3.52 0.00 36.08 5.14
178 179 2.180674 GGAAGACCGTTGCATTCCC 58.819 57.895 3.52 0.00 36.08 3.97
179 180 1.313091 GGGGAAGACCGTTGCATTCC 61.313 60.000 6.03 6.03 41.60 3.01
180 181 1.313091 GGGGGAAGACCGTTGCATTC 61.313 60.000 0.00 0.00 41.60 2.67
181 182 1.304134 GGGGGAAGACCGTTGCATT 60.304 57.895 0.00 0.00 41.60 3.56
182 183 1.863155 ATGGGGGAAGACCGTTGCAT 61.863 55.000 0.00 0.00 41.60 3.96
183 184 1.202099 TATGGGGGAAGACCGTTGCA 61.202 55.000 0.00 0.00 41.60 4.08
184 185 0.182775 ATATGGGGGAAGACCGTTGC 59.817 55.000 0.00 0.00 41.60 4.17
185 186 2.092646 TCAATATGGGGGAAGACCGTTG 60.093 50.000 0.00 0.00 41.60 4.10
186 187 2.092592 GTCAATATGGGGGAAGACCGTT 60.093 50.000 0.00 0.00 41.60 4.44
187 188 1.489230 GTCAATATGGGGGAAGACCGT 59.511 52.381 0.00 0.00 41.60 4.83
188 189 1.202770 GGTCAATATGGGGGAAGACCG 60.203 57.143 0.00 0.00 41.60 4.79
189 190 1.850345 TGGTCAATATGGGGGAAGACC 59.150 52.381 0.00 0.00 44.37 3.85
190 191 2.749800 GCTGGTCAATATGGGGGAAGAC 60.750 54.545 0.00 0.00 0.00 3.01
191 192 1.494721 GCTGGTCAATATGGGGGAAGA 59.505 52.381 0.00 0.00 0.00 2.87
192 193 1.215173 TGCTGGTCAATATGGGGGAAG 59.785 52.381 0.00 0.00 0.00 3.46
193 194 1.303898 TGCTGGTCAATATGGGGGAA 58.696 50.000 0.00 0.00 0.00 3.97
194 195 1.533187 ATGCTGGTCAATATGGGGGA 58.467 50.000 0.00 0.00 0.00 4.81
195 196 2.881403 GCTATGCTGGTCAATATGGGGG 60.881 54.545 0.00 0.00 0.00 5.40
196 197 2.040813 AGCTATGCTGGTCAATATGGGG 59.959 50.000 0.00 0.00 37.57 4.96
197 198 3.341823 GAGCTATGCTGGTCAATATGGG 58.658 50.000 0.00 0.00 39.88 4.00
198 199 3.244665 TGGAGCTATGCTGGTCAATATGG 60.245 47.826 0.00 0.00 39.88 2.74
199 200 4.011966 TGGAGCTATGCTGGTCAATATG 57.988 45.455 0.00 0.00 39.88 1.78
200 201 4.287845 TGATGGAGCTATGCTGGTCAATAT 59.712 41.667 0.00 0.00 39.88 1.28
201 202 3.647590 TGATGGAGCTATGCTGGTCAATA 59.352 43.478 0.00 0.00 39.88 1.90
202 203 2.440627 TGATGGAGCTATGCTGGTCAAT 59.559 45.455 0.00 0.00 39.88 2.57
203 204 1.839354 TGATGGAGCTATGCTGGTCAA 59.161 47.619 0.00 0.00 39.88 3.18
204 205 1.499368 TGATGGAGCTATGCTGGTCA 58.501 50.000 0.00 0.00 39.88 4.02
205 206 2.038164 TCATGATGGAGCTATGCTGGTC 59.962 50.000 0.00 0.00 39.88 4.02
206 207 2.052468 TCATGATGGAGCTATGCTGGT 58.948 47.619 0.00 0.00 39.88 4.00
207 208 2.853235 TCATGATGGAGCTATGCTGG 57.147 50.000 0.00 0.00 39.88 4.85
208 209 3.935828 CTGATCATGATGGAGCTATGCTG 59.064 47.826 14.30 0.00 39.88 4.41
209 210 3.055021 CCTGATCATGATGGAGCTATGCT 60.055 47.826 14.30 0.00 43.88 3.79
210 211 3.055312 TCCTGATCATGATGGAGCTATGC 60.055 47.826 14.30 0.00 0.00 3.14
211 212 4.820894 TCCTGATCATGATGGAGCTATG 57.179 45.455 14.30 0.00 0.00 2.23
212 213 6.673097 ACTATTCCTGATCATGATGGAGCTAT 59.327 38.462 14.30 7.77 0.00 2.97
213 214 6.021672 ACTATTCCTGATCATGATGGAGCTA 58.978 40.000 14.30 8.98 0.00 3.32
214 215 4.845225 ACTATTCCTGATCATGATGGAGCT 59.155 41.667 14.30 8.35 0.00 4.09
215 216 5.163281 ACTATTCCTGATCATGATGGAGC 57.837 43.478 14.30 0.00 0.00 4.70
216 217 8.075761 TGATACTATTCCTGATCATGATGGAG 57.924 38.462 14.30 8.55 0.00 3.86
217 218 8.619683 ATGATACTATTCCTGATCATGATGGA 57.380 34.615 14.30 11.81 37.58 3.41
218 219 9.984190 CTATGATACTATTCCTGATCATGATGG 57.016 37.037 14.30 9.40 38.98 3.51
221 222 8.897752 CGTCTATGATACTATTCCTGATCATGA 58.102 37.037 0.00 0.00 38.98 3.07
222 223 8.897752 TCGTCTATGATACTATTCCTGATCATG 58.102 37.037 0.00 0.00 38.98 3.07
223 224 8.898761 GTCGTCTATGATACTATTCCTGATCAT 58.101 37.037 0.00 0.00 40.99 2.45
224 225 8.103935 AGTCGTCTATGATACTATTCCTGATCA 58.896 37.037 0.00 0.00 33.09 2.92
225 226 8.500753 AGTCGTCTATGATACTATTCCTGATC 57.499 38.462 0.00 0.00 0.00 2.92
226 227 8.871629 AAGTCGTCTATGATACTATTCCTGAT 57.128 34.615 0.00 0.00 0.00 2.90
227 228 9.788889 TTAAGTCGTCTATGATACTATTCCTGA 57.211 33.333 0.00 0.00 0.00 3.86
228 229 9.828852 GTTAAGTCGTCTATGATACTATTCCTG 57.171 37.037 0.00 0.00 0.00 3.86
229 230 8.719648 CGTTAAGTCGTCTATGATACTATTCCT 58.280 37.037 0.00 0.00 0.00 3.36
230 231 7.961827 CCGTTAAGTCGTCTATGATACTATTCC 59.038 40.741 0.00 0.00 0.00 3.01
231 232 8.502387 ACCGTTAAGTCGTCTATGATACTATTC 58.498 37.037 0.00 0.00 0.00 1.75
232 233 8.288208 CACCGTTAAGTCGTCTATGATACTATT 58.712 37.037 0.00 0.00 0.00 1.73
233 234 7.443575 ACACCGTTAAGTCGTCTATGATACTAT 59.556 37.037 0.00 0.00 0.00 2.12
234 235 6.763135 ACACCGTTAAGTCGTCTATGATACTA 59.237 38.462 0.00 0.00 0.00 1.82
235 236 5.587844 ACACCGTTAAGTCGTCTATGATACT 59.412 40.000 0.00 0.00 0.00 2.12
236 237 5.814783 ACACCGTTAAGTCGTCTATGATAC 58.185 41.667 0.00 0.00 0.00 2.24
237 238 5.585844 TGACACCGTTAAGTCGTCTATGATA 59.414 40.000 0.00 0.00 37.58 2.15
238 239 4.397103 TGACACCGTTAAGTCGTCTATGAT 59.603 41.667 0.00 0.00 37.58 2.45
239 240 3.752747 TGACACCGTTAAGTCGTCTATGA 59.247 43.478 0.00 0.00 37.58 2.15
240 241 3.850273 GTGACACCGTTAAGTCGTCTATG 59.150 47.826 0.00 0.00 37.58 2.23
241 242 3.119708 GGTGACACCGTTAAGTCGTCTAT 60.120 47.826 9.33 0.00 37.58 1.98
242 243 2.226437 GGTGACACCGTTAAGTCGTCTA 59.774 50.000 9.33 0.00 37.58 2.59
243 244 1.000938 GGTGACACCGTTAAGTCGTCT 60.001 52.381 9.33 0.00 37.58 4.18
244 245 1.412387 GGTGACACCGTTAAGTCGTC 58.588 55.000 9.33 0.00 37.58 4.20
245 246 3.575399 GGTGACACCGTTAAGTCGT 57.425 52.632 9.33 0.00 37.58 4.34
255 256 2.291465 GGTTTCTTTAACCGGTGACACC 59.709 50.000 15.13 15.13 46.48 4.16
256 257 3.614159 GGTTTCTTTAACCGGTGACAC 57.386 47.619 8.52 3.91 46.48 3.67
670 720 4.431131 CCAGGAAGGCATGGCGGT 62.431 66.667 14.30 5.87 39.36 5.68
903 954 4.107072 ACCCTAACCCTAACCCTAGTTTC 58.893 47.826 0.00 0.00 37.42 2.78
1342 1399 6.218746 GCTTCCTATCCATAAGCATTTTTGG 58.781 40.000 0.00 0.00 43.98 3.28
1638 1698 1.098050 CTACCCTGCCACAATTCTGC 58.902 55.000 0.00 0.00 0.00 4.26
1928 1991 5.048434 GCCTTCCTGGTATTCTTGATAATGC 60.048 44.000 0.00 0.00 38.35 3.56
2184 2250 9.190858 GACATAGACTAGATTAGCTTCACATTG 57.809 37.037 0.00 0.00 0.00 2.82
2485 2561 0.906066 GTTCTGGAGGGAGGAGGTTC 59.094 60.000 0.00 0.00 0.00 3.62
2487 2563 0.545548 GTGTTCTGGAGGGAGGAGGT 60.546 60.000 0.00 0.00 0.00 3.85
2660 2736 0.980423 GCCTCCTCTTGAACTCCAGT 59.020 55.000 0.00 0.00 0.00 4.00
2818 2894 0.869730 GAAGAAACGGCGCCACTTTA 59.130 50.000 28.98 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.