Multiple sequence alignment - TraesCS6A01G247600

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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 TraesCS6A01G247600 chr6A 100.000 2381 0 0 1 2381 459678924 459676544 0.000000e+00 4397.0
1 TraesCS6A01G247600 chr6D 95.468 1324 44 5 364 1678 322201646 322200330 0.000000e+00 2098.0
2 TraesCS6A01G247600 chr6B 94.108 1256 42 6 406 1645 501127581 501128820 0.000000e+00 1881.0
3 TraesCS6A01G247600 chr6B 92.418 699 46 6 1688 2381 574505363 574504667 0.000000e+00 990.0
4 TraesCS6A01G247600 chr6B 91.404 698 50 7 1687 2381 91144522 91145212 0.000000e+00 948.0
5 TraesCS6A01G247600 chr6B 97.561 41 1 0 289 329 501124856 501124896 1.180000e-08 71.3
6 TraesCS6A01G247600 chr6B 97.561 41 1 0 289 329 501125297 501125337 1.180000e-08 71.3
7 TraesCS6A01G247600 chr7A 94.915 708 28 6 1677 2381 49365041 49365743 0.000000e+00 1101.0
8 TraesCS6A01G247600 chr7A 90.922 705 54 9 1685 2381 577616530 577615828 0.000000e+00 939.0
9 TraesCS6A01G247600 chr4A 97.077 650 14 4 1733 2381 610257167 610257812 0.000000e+00 1090.0
10 TraesCS6A01G247600 chr1A 91.571 700 51 8 1687 2381 474167805 474167109 0.000000e+00 959.0
11 TraesCS6A01G247600 chrUn 91.261 698 51 7 1687 2381 77420745 77420055 0.000000e+00 942.0
12 TraesCS6A01G247600 chr5B 89.286 560 54 5 1693 2249 596836073 596836629 0.000000e+00 697.0
13 TraesCS6A01G247600 chr5B 89.098 532 50 5 1715 2244 502380699 502381224 0.000000e+00 654.0
14 TraesCS6A01G247600 chr5B 94.118 68 4 0 2284 2351 596836630 596836697 1.160000e-18 104.0
15 TraesCS6A01G247600 chr3A 94.326 282 16 0 1 282 150705913 150706194 1.310000e-117 433.0
16 TraesCS6A01G247600 chr4D 85.821 134 16 3 2247 2380 208900620 208900750 3.190000e-29 139.0
17 TraesCS6A01G247600 chr4D 82.781 151 20 5 1212 1359 507119778 507119925 1.920000e-26 130.0
18 TraesCS6A01G247600 chr4D 82.400 125 22 0 1235 1359 507125009 507125133 2.500000e-20 110.0
19 TraesCS6A01G247600 chr4B 86.400 125 17 0 1235 1359 654466052 654465928 1.150000e-28 137.0
20 TraesCS6A01G247600 chr5A 83.444 151 19 5 1212 1359 692062434 692062287 4.130000e-28 135.0


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 TraesCS6A01G247600 chr6A 459676544 459678924 2380 True 4397.000000 4397 100.000 1 2381 1 chr6A.!!$R1 2380
1 TraesCS6A01G247600 chr6D 322200330 322201646 1316 True 2098.000000 2098 95.468 364 1678 1 chr6D.!!$R1 1314
2 TraesCS6A01G247600 chr6B 574504667 574505363 696 True 990.000000 990 92.418 1688 2381 1 chr6B.!!$R1 693
3 TraesCS6A01G247600 chr6B 91144522 91145212 690 False 948.000000 948 91.404 1687 2381 1 chr6B.!!$F1 694
4 TraesCS6A01G247600 chr6B 501124856 501128820 3964 False 674.533333 1881 96.410 289 1645 3 chr6B.!!$F2 1356
5 TraesCS6A01G247600 chr7A 49365041 49365743 702 False 1101.000000 1101 94.915 1677 2381 1 chr7A.!!$F1 704
6 TraesCS6A01G247600 chr7A 577615828 577616530 702 True 939.000000 939 90.922 1685 2381 1 chr7A.!!$R1 696
7 TraesCS6A01G247600 chr4A 610257167 610257812 645 False 1090.000000 1090 97.077 1733 2381 1 chr4A.!!$F1 648
8 TraesCS6A01G247600 chr1A 474167109 474167805 696 True 959.000000 959 91.571 1687 2381 1 chr1A.!!$R1 694
9 TraesCS6A01G247600 chrUn 77420055 77420745 690 True 942.000000 942 91.261 1687 2381 1 chrUn.!!$R1 694
10 TraesCS6A01G247600 chr5B 502380699 502381224 525 False 654.000000 654 89.098 1715 2244 1 chr5B.!!$F1 529
11 TraesCS6A01G247600 chr5B 596836073 596836697 624 False 400.500000 697 91.702 1693 2351 2 chr5B.!!$F2 658

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
284 285 0.034574 ACGCAGGTAATTGCCCATCA 60.035 50.0 9.2 0.0 41.01 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 4304 0.943673 TGATCACAACTTGGCACACG 59.056 50.0 0.0 0.0 39.29 4.49 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
23 24 4.680237 CACAAGAGTGGGCGGCGA 62.680 66.667 12.98 0.00 42.13 5.54
24 25 3.706373 ACAAGAGTGGGCGGCGAT 61.706 61.111 12.98 0.00 0.00 4.58
25 26 2.436646 CAAGAGTGGGCGGCGATT 60.437 61.111 12.98 0.00 0.00 3.34
26 27 2.436646 AAGAGTGGGCGGCGATTG 60.437 61.111 12.98 0.00 0.00 2.67
33 34 3.799755 GGCGGCGATTGCTCGTTT 61.800 61.111 12.98 0.00 46.71 3.60
34 35 2.574212 GCGGCGATTGCTCGTTTG 60.574 61.111 12.98 0.00 46.71 2.93
35 36 3.022401 GCGGCGATTGCTCGTTTGA 62.022 57.895 12.98 0.00 46.71 2.69
36 37 1.225745 CGGCGATTGCTCGTTTGAC 60.226 57.895 0.00 0.00 46.71 3.18
37 38 1.134694 GGCGATTGCTCGTTTGACC 59.865 57.895 4.59 0.00 46.71 4.02
38 39 1.573829 GGCGATTGCTCGTTTGACCA 61.574 55.000 4.59 0.00 46.71 4.02
39 40 0.179215 GCGATTGCTCGTTTGACCAG 60.179 55.000 0.00 0.00 46.71 4.00
40 41 0.443869 CGATTGCTCGTTTGACCAGG 59.556 55.000 0.00 0.00 40.07 4.45
41 42 1.523758 GATTGCTCGTTTGACCAGGT 58.476 50.000 0.00 0.00 0.00 4.00
42 43 1.197721 GATTGCTCGTTTGACCAGGTG 59.802 52.381 0.00 0.00 0.00 4.00
43 44 0.107410 TTGCTCGTTTGACCAGGTGT 60.107 50.000 0.00 0.00 0.00 4.16
44 45 0.753867 TGCTCGTTTGACCAGGTGTA 59.246 50.000 0.00 0.00 0.00 2.90
45 46 1.346395 TGCTCGTTTGACCAGGTGTAT 59.654 47.619 0.00 0.00 0.00 2.29
46 47 2.000447 GCTCGTTTGACCAGGTGTATC 59.000 52.381 0.00 0.00 0.00 2.24
47 48 2.259618 CTCGTTTGACCAGGTGTATCG 58.740 52.381 0.00 0.00 0.00 2.92
48 49 0.719465 CGTTTGACCAGGTGTATCGC 59.281 55.000 0.00 0.00 0.00 4.58
49 50 1.084289 GTTTGACCAGGTGTATCGCC 58.916 55.000 0.00 0.00 0.00 5.54
50 51 0.981183 TTTGACCAGGTGTATCGCCT 59.019 50.000 0.00 0.00 46.26 5.52
51 52 0.535335 TTGACCAGGTGTATCGCCTC 59.465 55.000 0.00 0.00 43.13 4.70
52 53 1.327690 TGACCAGGTGTATCGCCTCC 61.328 60.000 0.00 0.00 43.13 4.30
53 54 2.029307 GACCAGGTGTATCGCCTCCC 62.029 65.000 0.00 0.00 43.13 4.30
54 55 2.808206 CCAGGTGTATCGCCTCCCC 61.808 68.421 0.00 0.00 43.13 4.81
55 56 2.063979 CAGGTGTATCGCCTCCCCA 61.064 63.158 0.00 0.00 43.13 4.96
56 57 2.064581 AGGTGTATCGCCTCCCCAC 61.065 63.158 0.00 0.00 40.81 4.61
57 58 2.363975 GGTGTATCGCCTCCCCACA 61.364 63.158 0.00 0.00 0.00 4.17
58 59 1.600107 GTGTATCGCCTCCCCACAA 59.400 57.895 0.00 0.00 0.00 3.33
59 60 0.462047 GTGTATCGCCTCCCCACAAG 60.462 60.000 0.00 0.00 0.00 3.16
60 61 0.616395 TGTATCGCCTCCCCACAAGA 60.616 55.000 0.00 0.00 0.00 3.02
61 62 0.759346 GTATCGCCTCCCCACAAGAT 59.241 55.000 0.00 0.00 0.00 2.40
62 63 1.048601 TATCGCCTCCCCACAAGATC 58.951 55.000 0.00 0.00 0.00 2.75
63 64 2.032860 ATCGCCTCCCCACAAGATCG 62.033 60.000 0.00 0.00 0.00 3.69
64 65 2.721167 CGCCTCCCCACAAGATCGA 61.721 63.158 0.00 0.00 0.00 3.59
65 66 1.832912 GCCTCCCCACAAGATCGAT 59.167 57.895 0.00 0.00 0.00 3.59
66 67 0.250081 GCCTCCCCACAAGATCGATC 60.250 60.000 17.91 17.91 0.00 3.69
67 68 1.418334 CCTCCCCACAAGATCGATCT 58.582 55.000 22.32 22.32 39.22 2.75
68 69 1.342819 CCTCCCCACAAGATCGATCTC 59.657 57.143 27.43 2.73 35.76 2.75
69 70 1.342819 CTCCCCACAAGATCGATCTCC 59.657 57.143 27.43 0.95 35.76 3.71
70 71 1.062886 TCCCCACAAGATCGATCTCCT 60.063 52.381 27.43 11.09 35.76 3.69
71 72 1.765314 CCCCACAAGATCGATCTCCTT 59.235 52.381 27.43 10.32 35.76 3.36
72 73 2.224161 CCCCACAAGATCGATCTCCTTC 60.224 54.545 27.43 0.22 35.76 3.46
73 74 2.432146 CCCACAAGATCGATCTCCTTCA 59.568 50.000 27.43 0.00 35.76 3.02
74 75 3.118629 CCCACAAGATCGATCTCCTTCAA 60.119 47.826 27.43 0.00 35.76 2.69
75 76 4.507710 CCACAAGATCGATCTCCTTCAAA 58.492 43.478 27.43 0.00 35.76 2.69
76 77 4.331168 CCACAAGATCGATCTCCTTCAAAC 59.669 45.833 27.43 0.00 35.76 2.93
77 78 4.931601 CACAAGATCGATCTCCTTCAAACA 59.068 41.667 27.43 0.00 35.76 2.83
78 79 5.583854 CACAAGATCGATCTCCTTCAAACAT 59.416 40.000 27.43 5.76 35.76 2.71
79 80 5.583854 ACAAGATCGATCTCCTTCAAACATG 59.416 40.000 27.43 18.92 35.76 3.21
80 81 5.604758 AGATCGATCTCCTTCAAACATGA 57.395 39.130 22.32 0.00 29.30 3.07
81 82 5.599732 AGATCGATCTCCTTCAAACATGAG 58.400 41.667 22.32 0.00 29.30 2.90
82 83 4.128925 TCGATCTCCTTCAAACATGAGG 57.871 45.455 0.00 0.00 0.00 3.86
83 84 2.611292 CGATCTCCTTCAAACATGAGGC 59.389 50.000 0.00 0.00 0.00 4.70
84 85 2.099141 TCTCCTTCAAACATGAGGCG 57.901 50.000 0.00 0.00 0.00 5.52
85 86 1.347707 TCTCCTTCAAACATGAGGCGT 59.652 47.619 0.00 0.00 0.00 5.68
86 87 2.154462 CTCCTTCAAACATGAGGCGTT 58.846 47.619 0.00 0.00 0.00 4.84
87 88 2.554032 CTCCTTCAAACATGAGGCGTTT 59.446 45.455 0.00 0.00 37.04 3.60
88 89 3.745799 TCCTTCAAACATGAGGCGTTTA 58.254 40.909 0.00 0.00 34.87 2.01
89 90 3.751175 TCCTTCAAACATGAGGCGTTTAG 59.249 43.478 0.00 0.00 34.87 1.85
90 91 3.119849 CCTTCAAACATGAGGCGTTTAGG 60.120 47.826 0.00 0.00 34.87 2.69
91 92 2.432444 TCAAACATGAGGCGTTTAGGG 58.568 47.619 0.00 0.00 34.87 3.53
92 93 1.135402 CAAACATGAGGCGTTTAGGGC 60.135 52.381 0.00 0.00 34.87 5.19
100 101 4.090588 CGTTTAGGGCCTGCCGGA 62.091 66.667 18.53 0.00 36.85 5.14
101 102 2.353573 GTTTAGGGCCTGCCGGAA 59.646 61.111 18.53 0.00 36.85 4.30
102 103 1.303806 GTTTAGGGCCTGCCGGAAA 60.304 57.895 18.53 5.17 36.85 3.13
103 104 1.303806 TTTAGGGCCTGCCGGAAAC 60.304 57.895 18.53 0.00 36.85 2.78
118 119 3.145212 GGAAACGTAACATCCATTGCC 57.855 47.619 0.00 0.00 33.30 4.52
119 120 2.477189 GGAAACGTAACATCCATTGCCG 60.477 50.000 0.00 0.00 33.30 5.69
120 121 1.091537 AACGTAACATCCATTGCCGG 58.908 50.000 0.00 0.00 0.00 6.13
121 122 0.035820 ACGTAACATCCATTGCCGGT 60.036 50.000 1.90 0.00 0.00 5.28
122 123 0.655733 CGTAACATCCATTGCCGGTC 59.344 55.000 1.90 0.00 0.00 4.79
123 124 1.021968 GTAACATCCATTGCCGGTCC 58.978 55.000 1.90 0.00 0.00 4.46
124 125 0.621082 TAACATCCATTGCCGGTCCA 59.379 50.000 1.90 0.00 0.00 4.02
125 126 0.680921 AACATCCATTGCCGGTCCAG 60.681 55.000 1.90 0.00 0.00 3.86
126 127 1.224315 CATCCATTGCCGGTCCAGA 59.776 57.895 1.90 0.00 0.00 3.86
127 128 0.179009 CATCCATTGCCGGTCCAGAT 60.179 55.000 1.90 0.00 0.00 2.90
128 129 0.552848 ATCCATTGCCGGTCCAGATT 59.447 50.000 1.90 0.00 0.00 2.40
129 130 0.394216 TCCATTGCCGGTCCAGATTG 60.394 55.000 1.90 0.00 0.00 2.67
130 131 1.386525 CCATTGCCGGTCCAGATTGG 61.387 60.000 1.90 0.00 39.43 3.16
131 132 1.076777 ATTGCCGGTCCAGATTGGG 60.077 57.895 1.90 0.00 38.32 4.12
132 133 2.572333 ATTGCCGGTCCAGATTGGGG 62.572 60.000 1.90 0.00 38.32 4.96
133 134 3.728373 GCCGGTCCAGATTGGGGT 61.728 66.667 1.90 0.00 38.32 4.95
134 135 3.087065 CCGGTCCAGATTGGGGTT 58.913 61.111 0.00 0.00 38.32 4.11
135 136 1.378514 CCGGTCCAGATTGGGGTTG 60.379 63.158 0.00 0.00 38.32 3.77
136 137 1.378762 CGGTCCAGATTGGGGTTGT 59.621 57.895 0.00 0.00 38.32 3.32
137 138 0.251165 CGGTCCAGATTGGGGTTGTT 60.251 55.000 0.00 0.00 38.32 2.83
138 139 1.545841 GGTCCAGATTGGGGTTGTTC 58.454 55.000 0.00 0.00 38.32 3.18
139 140 1.075536 GGTCCAGATTGGGGTTGTTCT 59.924 52.381 0.00 0.00 38.32 3.01
140 141 2.490902 GGTCCAGATTGGGGTTGTTCTT 60.491 50.000 0.00 0.00 38.32 2.52
141 142 3.245122 GGTCCAGATTGGGGTTGTTCTTA 60.245 47.826 0.00 0.00 38.32 2.10
142 143 4.569865 GGTCCAGATTGGGGTTGTTCTTAT 60.570 45.833 0.00 0.00 38.32 1.73
143 144 4.640647 GTCCAGATTGGGGTTGTTCTTATC 59.359 45.833 0.00 0.00 38.32 1.75
144 145 3.954258 CCAGATTGGGGTTGTTCTTATCC 59.046 47.826 0.00 0.00 32.67 2.59
145 146 4.325344 CCAGATTGGGGTTGTTCTTATCCT 60.325 45.833 0.00 0.00 32.67 3.24
146 147 4.884164 CAGATTGGGGTTGTTCTTATCCTC 59.116 45.833 0.00 0.00 0.00 3.71
147 148 3.732048 TTGGGGTTGTTCTTATCCTCC 57.268 47.619 0.00 0.00 0.00 4.30
148 149 1.557832 TGGGGTTGTTCTTATCCTCCG 59.442 52.381 0.00 0.00 0.00 4.63
149 150 1.664873 GGGTTGTTCTTATCCTCCGC 58.335 55.000 0.00 0.00 0.00 5.54
150 151 1.065709 GGGTTGTTCTTATCCTCCGCA 60.066 52.381 0.00 0.00 0.00 5.69
151 152 2.280628 GGTTGTTCTTATCCTCCGCAG 58.719 52.381 0.00 0.00 0.00 5.18
152 153 2.093658 GGTTGTTCTTATCCTCCGCAGA 60.094 50.000 0.00 0.00 0.00 4.26
153 154 2.930682 GTTGTTCTTATCCTCCGCAGAC 59.069 50.000 0.00 0.00 0.00 3.51
154 155 1.134367 TGTTCTTATCCTCCGCAGACG 59.866 52.381 0.00 0.00 39.67 4.18
155 156 1.134560 GTTCTTATCCTCCGCAGACGT 59.865 52.381 0.00 0.00 37.70 4.34
156 157 0.738975 TCTTATCCTCCGCAGACGTG 59.261 55.000 0.00 0.00 37.70 4.49
157 158 0.738975 CTTATCCTCCGCAGACGTGA 59.261 55.000 0.00 0.00 37.70 4.35
158 159 1.338337 CTTATCCTCCGCAGACGTGAT 59.662 52.381 0.00 0.00 37.70 3.06
159 160 2.265589 TATCCTCCGCAGACGTGATA 57.734 50.000 0.00 0.00 37.70 2.15
160 161 1.399714 ATCCTCCGCAGACGTGATAA 58.600 50.000 0.00 0.00 37.70 1.75
161 162 0.738975 TCCTCCGCAGACGTGATAAG 59.261 55.000 0.00 0.00 37.70 1.73
162 163 0.249073 CCTCCGCAGACGTGATAAGG 60.249 60.000 0.00 0.00 37.70 2.69
163 164 0.456221 CTCCGCAGACGTGATAAGGT 59.544 55.000 0.00 0.00 37.70 3.50
164 165 0.892755 TCCGCAGACGTGATAAGGTT 59.107 50.000 0.00 0.00 37.70 3.50
165 166 1.135199 TCCGCAGACGTGATAAGGTTC 60.135 52.381 0.00 0.00 37.70 3.62
166 167 1.403647 CCGCAGACGTGATAAGGTTCA 60.404 52.381 0.00 0.00 37.70 3.18
167 168 2.333926 CGCAGACGTGATAAGGTTCAA 58.666 47.619 0.00 0.00 33.53 2.69
168 169 2.734606 CGCAGACGTGATAAGGTTCAAA 59.265 45.455 0.00 0.00 33.53 2.69
169 170 3.370978 CGCAGACGTGATAAGGTTCAAAT 59.629 43.478 0.00 0.00 33.53 2.32
170 171 4.492570 CGCAGACGTGATAAGGTTCAAATC 60.493 45.833 0.00 0.00 33.53 2.17
171 172 4.391830 GCAGACGTGATAAGGTTCAAATCA 59.608 41.667 0.00 0.00 0.00 2.57
172 173 5.671329 GCAGACGTGATAAGGTTCAAATCAC 60.671 44.000 0.00 4.91 43.85 3.06
176 177 5.470845 GTGATAAGGTTCAAATCACGGAG 57.529 43.478 0.00 0.00 39.90 4.63
177 178 5.175859 GTGATAAGGTTCAAATCACGGAGA 58.824 41.667 0.00 0.00 39.90 3.71
178 179 5.642063 GTGATAAGGTTCAAATCACGGAGAA 59.358 40.000 0.00 0.00 39.90 2.87
179 180 5.642063 TGATAAGGTTCAAATCACGGAGAAC 59.358 40.000 0.00 0.00 39.59 3.01
180 181 3.485463 AGGTTCAAATCACGGAGAACA 57.515 42.857 0.00 0.00 41.49 3.18
181 182 3.815809 AGGTTCAAATCACGGAGAACAA 58.184 40.909 0.00 0.00 41.49 2.83
182 183 3.815401 AGGTTCAAATCACGGAGAACAAG 59.185 43.478 0.00 0.00 41.49 3.16
183 184 3.555518 GTTCAAATCACGGAGAACAAGC 58.444 45.455 0.00 0.00 39.95 4.01
184 185 2.151202 TCAAATCACGGAGAACAAGCC 58.849 47.619 0.00 0.00 0.00 4.35
185 186 1.879380 CAAATCACGGAGAACAAGCCA 59.121 47.619 0.00 0.00 0.00 4.75
186 187 2.489329 CAAATCACGGAGAACAAGCCAT 59.511 45.455 0.00 0.00 0.00 4.40
187 188 1.742761 ATCACGGAGAACAAGCCATG 58.257 50.000 0.00 0.00 0.00 3.66
188 189 0.321564 TCACGGAGAACAAGCCATGG 60.322 55.000 7.63 7.63 0.00 3.66
189 190 1.675641 ACGGAGAACAAGCCATGGC 60.676 57.895 30.12 30.12 42.33 4.40
195 196 2.268076 AACAAGCCATGGCGTGGTC 61.268 57.895 42.37 17.82 46.77 4.02
196 197 2.974692 AACAAGCCATGGCGTGGTCA 62.975 55.000 42.37 0.00 46.77 4.02
200 201 2.747460 CCATGGCGTGGTCACCTG 60.747 66.667 17.89 0.00 43.44 4.00
201 202 2.747460 CATGGCGTGGTCACCTGG 60.747 66.667 0.00 0.00 0.00 4.45
202 203 3.249189 ATGGCGTGGTCACCTGGT 61.249 61.111 0.00 0.00 0.00 4.00
203 204 2.829384 ATGGCGTGGTCACCTGGTT 61.829 57.895 0.00 0.00 0.00 3.67
204 205 2.978010 GGCGTGGTCACCTGGTTG 60.978 66.667 0.00 0.00 0.00 3.77
205 206 2.978010 GCGTGGTCACCTGGTTGG 60.978 66.667 0.00 0.00 42.93 3.77
206 207 2.978010 CGTGGTCACCTGGTTGGC 60.978 66.667 0.00 0.00 40.22 4.52
207 208 2.978010 GTGGTCACCTGGTTGGCG 60.978 66.667 0.00 0.00 40.22 5.69
208 209 3.164977 TGGTCACCTGGTTGGCGA 61.165 61.111 0.00 0.00 40.22 5.54
209 210 2.351276 GGTCACCTGGTTGGCGAT 59.649 61.111 0.00 0.00 40.22 4.58
210 211 1.745489 GGTCACCTGGTTGGCGATC 60.745 63.158 0.00 0.00 40.22 3.69
211 212 1.296715 GTCACCTGGTTGGCGATCT 59.703 57.895 0.00 0.00 40.22 2.75
212 213 1.021390 GTCACCTGGTTGGCGATCTG 61.021 60.000 0.00 0.00 40.22 2.90
213 214 2.045926 ACCTGGTTGGCGATCTGC 60.046 61.111 0.00 1.55 45.38 4.26
214 215 2.270205 CCTGGTTGGCGATCTGCT 59.730 61.111 8.94 0.00 45.43 4.24
215 216 2.110967 CCTGGTTGGCGATCTGCTG 61.111 63.158 8.94 0.00 45.43 4.41
216 217 2.747460 TGGTTGGCGATCTGCTGC 60.747 61.111 8.94 0.00 45.43 5.25
217 218 2.747460 GGTTGGCGATCTGCTGCA 60.747 61.111 0.88 0.88 45.43 4.41
218 219 2.758089 GGTTGGCGATCTGCTGCAG 61.758 63.158 23.31 23.31 45.43 4.41
219 220 3.129502 TTGGCGATCTGCTGCAGC 61.130 61.111 31.89 31.89 45.43 5.25
220 221 3.617143 TTGGCGATCTGCTGCAGCT 62.617 57.895 36.61 19.54 45.43 4.24
221 222 2.823147 GGCGATCTGCTGCAGCTT 60.823 61.111 36.61 22.50 45.43 3.74
222 223 2.708255 GCGATCTGCTGCAGCTTC 59.292 61.111 36.61 27.22 42.66 3.86
223 224 2.104859 GCGATCTGCTGCAGCTTCA 61.105 57.895 36.61 21.64 42.66 3.02
224 225 2.007549 CGATCTGCTGCAGCTTCAG 58.992 57.895 36.61 26.21 42.66 3.02
225 226 0.459759 CGATCTGCTGCAGCTTCAGA 60.460 55.000 36.61 30.11 42.66 3.27
226 227 1.735386 GATCTGCTGCAGCTTCAGAA 58.265 50.000 36.61 16.65 39.88 3.02
227 228 1.666700 GATCTGCTGCAGCTTCAGAAG 59.333 52.381 36.61 24.80 40.42 2.85
228 229 0.683412 TCTGCTGCAGCTTCAGAAGA 59.317 50.000 36.61 26.56 44.43 2.87
229 230 1.071228 TCTGCTGCAGCTTCAGAAGAA 59.929 47.619 36.61 14.40 43.84 2.52
230 231 1.878088 CTGCTGCAGCTTCAGAAGAAA 59.122 47.619 36.61 13.65 41.36 2.52
231 232 2.292569 CTGCTGCAGCTTCAGAAGAAAA 59.707 45.455 36.61 13.13 41.36 2.29
232 233 2.033801 TGCTGCAGCTTCAGAAGAAAAC 59.966 45.455 36.61 5.77 42.66 2.43
233 234 2.292845 GCTGCAGCTTCAGAAGAAAACT 59.707 45.455 31.33 0.00 36.19 2.66
234 235 3.608941 GCTGCAGCTTCAGAAGAAAACTC 60.609 47.826 31.33 0.00 36.19 3.01
235 236 2.545526 TGCAGCTTCAGAAGAAAACTCG 59.454 45.455 14.86 0.00 32.35 4.18
236 237 2.664151 GCAGCTTCAGAAGAAAACTCGC 60.664 50.000 14.86 4.75 32.35 5.03
237 238 2.096019 CAGCTTCAGAAGAAAACTCGCC 60.096 50.000 14.86 0.00 32.35 5.54
238 239 1.197949 GCTTCAGAAGAAAACTCGCCC 59.802 52.381 14.86 0.00 32.35 6.13
239 240 2.772287 CTTCAGAAGAAAACTCGCCCT 58.228 47.619 3.82 0.00 32.35 5.19
240 241 2.457366 TCAGAAGAAAACTCGCCCTC 57.543 50.000 0.00 0.00 0.00 4.30
241 242 1.002087 TCAGAAGAAAACTCGCCCTCC 59.998 52.381 0.00 0.00 0.00 4.30
242 243 1.002544 CAGAAGAAAACTCGCCCTCCT 59.997 52.381 0.00 0.00 0.00 3.69
243 244 1.700186 AGAAGAAAACTCGCCCTCCTT 59.300 47.619 0.00 0.00 0.00 3.36
244 245 2.106684 AGAAGAAAACTCGCCCTCCTTT 59.893 45.455 0.00 0.00 0.00 3.11
245 246 1.897560 AGAAAACTCGCCCTCCTTTG 58.102 50.000 0.00 0.00 0.00 2.77
246 247 1.420138 AGAAAACTCGCCCTCCTTTGA 59.580 47.619 0.00 0.00 0.00 2.69
247 248 2.040412 AGAAAACTCGCCCTCCTTTGAT 59.960 45.455 0.00 0.00 0.00 2.57
248 249 2.115343 AAACTCGCCCTCCTTTGATC 57.885 50.000 0.00 0.00 0.00 2.92
249 250 0.984230 AACTCGCCCTCCTTTGATCA 59.016 50.000 0.00 0.00 0.00 2.92
250 251 1.207791 ACTCGCCCTCCTTTGATCAT 58.792 50.000 0.00 0.00 0.00 2.45
251 252 1.139853 ACTCGCCCTCCTTTGATCATC 59.860 52.381 0.00 0.00 0.00 2.92
252 253 1.139654 CTCGCCCTCCTTTGATCATCA 59.860 52.381 0.00 0.00 0.00 3.07
253 254 1.770658 TCGCCCTCCTTTGATCATCAT 59.229 47.619 0.00 0.00 0.00 2.45
254 255 1.878088 CGCCCTCCTTTGATCATCATG 59.122 52.381 0.00 0.00 0.00 3.07
255 256 1.612463 GCCCTCCTTTGATCATCATGC 59.388 52.381 0.00 0.00 0.00 4.06
256 257 1.878088 CCCTCCTTTGATCATCATGCG 59.122 52.381 0.00 0.00 0.00 4.73
257 258 1.878088 CCTCCTTTGATCATCATGCGG 59.122 52.381 0.00 0.00 0.00 5.69
258 259 1.266175 CTCCTTTGATCATCATGCGGC 59.734 52.381 0.00 0.00 0.00 6.53
259 260 0.313043 CCTTTGATCATCATGCGGCC 59.687 55.000 0.00 0.00 0.00 6.13
260 261 0.313043 CTTTGATCATCATGCGGCCC 59.687 55.000 0.00 0.00 0.00 5.80
261 262 0.395448 TTTGATCATCATGCGGCCCA 60.395 50.000 0.00 0.00 0.00 5.36
262 263 0.178984 TTGATCATCATGCGGCCCAT 60.179 50.000 0.00 0.00 33.39 4.00
263 264 0.691904 TGATCATCATGCGGCCCATA 59.308 50.000 0.00 0.00 31.47 2.74
264 265 1.339342 TGATCATCATGCGGCCCATAG 60.339 52.381 0.00 0.00 31.47 2.23
265 266 0.986527 ATCATCATGCGGCCCATAGA 59.013 50.000 0.00 3.38 31.47 1.98
266 267 0.035317 TCATCATGCGGCCCATAGAC 59.965 55.000 0.00 0.00 31.47 2.59
267 268 1.004560 ATCATGCGGCCCATAGACG 60.005 57.895 0.00 0.00 31.47 4.18
272 273 3.849951 CGGCCCATAGACGCAGGT 61.850 66.667 0.00 0.00 0.00 4.00
273 274 2.495409 CGGCCCATAGACGCAGGTA 61.495 63.158 0.00 0.00 0.00 3.08
274 275 1.827394 GGCCCATAGACGCAGGTAA 59.173 57.895 0.00 0.00 0.00 2.85
275 276 0.396811 GGCCCATAGACGCAGGTAAT 59.603 55.000 0.00 0.00 0.00 1.89
276 277 1.202770 GGCCCATAGACGCAGGTAATT 60.203 52.381 0.00 0.00 0.00 1.40
277 278 1.873591 GCCCATAGACGCAGGTAATTG 59.126 52.381 0.00 0.00 0.00 2.32
278 279 1.873591 CCCATAGACGCAGGTAATTGC 59.126 52.381 0.00 0.00 40.67 3.56
279 280 1.873591 CCATAGACGCAGGTAATTGCC 59.126 52.381 4.07 4.07 41.01 4.52
280 281 1.873591 CATAGACGCAGGTAATTGCCC 59.126 52.381 9.20 0.00 41.01 5.36
281 282 0.906066 TAGACGCAGGTAATTGCCCA 59.094 50.000 9.20 0.00 41.01 5.36
282 283 0.255890 AGACGCAGGTAATTGCCCAT 59.744 50.000 9.20 0.00 41.01 4.00
283 284 0.663153 GACGCAGGTAATTGCCCATC 59.337 55.000 9.20 0.00 41.01 3.51
284 285 0.034574 ACGCAGGTAATTGCCCATCA 60.035 50.000 9.20 0.00 41.01 3.07
285 286 1.102154 CGCAGGTAATTGCCCATCAA 58.898 50.000 9.20 0.00 41.01 2.57
286 287 1.202290 CGCAGGTAATTGCCCATCAAC 60.202 52.381 9.20 0.00 41.01 3.18
287 288 1.824230 GCAGGTAATTGCCCATCAACA 59.176 47.619 9.20 0.00 37.53 3.33
298 299 2.281484 ATCAACAACCGGCGCAGT 60.281 55.556 10.83 2.29 0.00 4.40
329 330 1.990327 ACCCAAAAGTCGGTATCCCTT 59.010 47.619 0.00 0.00 0.00 3.95
331 332 2.026636 CCCAAAAGTCGGTATCCCTTCA 60.027 50.000 0.00 0.00 0.00 3.02
332 333 3.560453 CCCAAAAGTCGGTATCCCTTCAA 60.560 47.826 0.00 0.00 0.00 2.69
333 334 4.076394 CCAAAAGTCGGTATCCCTTCAAA 58.924 43.478 0.00 0.00 0.00 2.69
334 335 4.521256 CCAAAAGTCGGTATCCCTTCAAAA 59.479 41.667 0.00 0.00 0.00 2.44
335 336 5.010213 CCAAAAGTCGGTATCCCTTCAAAAA 59.990 40.000 0.00 0.00 0.00 1.94
408 409 5.233988 TGTGTGACATGTGAATCGTATTCA 58.766 37.500 1.15 6.28 0.00 2.57
439 3081 1.739466 GAGCCAATGAAATGACGCTGA 59.261 47.619 0.00 0.00 0.00 4.26
440 3082 2.161855 AGCCAATGAAATGACGCTGAA 58.838 42.857 0.00 0.00 0.00 3.02
475 3117 1.447838 GGCAGAAACCGATCGAGCA 60.448 57.895 18.66 0.00 0.00 4.26
533 3175 0.943673 CAACACAGCATTGACCGTCA 59.056 50.000 0.00 0.00 0.00 4.35
549 3199 3.060615 CAGGCCCACAAGCAGAGC 61.061 66.667 0.00 0.00 0.00 4.09
602 3252 1.661341 CTGCCTCACTGCCATTCTAC 58.339 55.000 0.00 0.00 0.00 2.59
642 3292 3.173853 CATGGGTTACCGTGCACG 58.826 61.111 31.77 31.77 46.16 5.34
864 3514 9.803507 ATTATGAAAATGATGATGAAGCTAGGA 57.196 29.630 0.00 0.00 0.00 2.94
920 3570 1.597027 CGGGTTCTTCAGCCACGTT 60.597 57.895 0.00 0.00 44.25 3.99
1386 4037 4.414852 GCTTCATTTGCGCTTGATTAAGA 58.585 39.130 9.73 0.00 35.92 2.10
1490 4149 5.593010 GTCGATATCCTTGTCTGCTTACTT 58.407 41.667 0.00 0.00 0.00 2.24
1524 4183 7.340487 TCTGAATGTAGAACTGCTTCAGATCTA 59.660 37.037 19.13 8.98 44.03 1.98
1584 4243 1.919012 TTGCGGGGGAGATGCAATA 59.081 52.632 0.00 0.00 43.13 1.90
1645 4304 6.809196 GTCTAGCTATCCAATGCATGTAGTAC 59.191 42.308 0.00 0.00 0.00 2.73
1893 4556 8.360390 ACTTTTCCTTTGGAATGTTATTCTGAC 58.640 33.333 0.00 0.00 41.71 3.51
2158 4823 7.461182 TTGATCGAGAAACAAATTAACCCAT 57.539 32.000 0.00 0.00 0.00 4.00
2299 4967 1.372872 GAACCGCGCCAAAGCAAAT 60.373 52.632 0.00 0.00 39.83 2.32
2354 5023 3.083997 CTGGACCTAAGGGCCGCT 61.084 66.667 0.00 0.00 35.63 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.958147 ATCGCCGCCCACTCTTGTG 62.958 63.158 0.00 0.00 43.45 3.33
8 9 2.436646 AATCGCCGCCCACTCTTG 60.437 61.111 0.00 0.00 0.00 3.02
9 10 2.436646 CAATCGCCGCCCACTCTT 60.437 61.111 0.00 0.00 0.00 2.85
16 17 3.799755 AAACGAGCAATCGCCGCC 61.800 61.111 0.00 0.00 39.83 6.13
17 18 2.574212 CAAACGAGCAATCGCCGC 60.574 61.111 0.00 0.00 39.83 6.53
18 19 1.225745 GTCAAACGAGCAATCGCCG 60.226 57.895 0.00 0.00 39.83 6.46
19 20 1.134694 GGTCAAACGAGCAATCGCC 59.865 57.895 0.00 0.00 39.83 5.54
20 21 0.179215 CTGGTCAAACGAGCAATCGC 60.179 55.000 0.00 0.00 40.23 4.58
21 22 0.443869 CCTGGTCAAACGAGCAATCG 59.556 55.000 0.00 0.00 40.23 3.34
22 23 1.197721 CACCTGGTCAAACGAGCAATC 59.802 52.381 0.00 0.00 40.23 2.67
23 24 1.238439 CACCTGGTCAAACGAGCAAT 58.762 50.000 0.00 0.00 40.23 3.56
24 25 0.107410 ACACCTGGTCAAACGAGCAA 60.107 50.000 0.00 0.00 40.23 3.91
25 26 0.753867 TACACCTGGTCAAACGAGCA 59.246 50.000 0.00 0.00 38.54 4.26
26 27 2.000447 GATACACCTGGTCAAACGAGC 59.000 52.381 0.00 0.00 0.00 5.03
27 28 2.259618 CGATACACCTGGTCAAACGAG 58.740 52.381 0.00 0.00 0.00 4.18
28 29 1.670674 GCGATACACCTGGTCAAACGA 60.671 52.381 14.12 0.00 0.00 3.85
29 30 0.719465 GCGATACACCTGGTCAAACG 59.281 55.000 0.00 2.53 0.00 3.60
30 31 1.084289 GGCGATACACCTGGTCAAAC 58.916 55.000 0.00 0.00 0.00 2.93
31 32 0.981183 AGGCGATACACCTGGTCAAA 59.019 50.000 0.00 0.00 35.72 2.69
32 33 0.535335 GAGGCGATACACCTGGTCAA 59.465 55.000 0.00 0.00 37.77 3.18
33 34 1.327690 GGAGGCGATACACCTGGTCA 61.328 60.000 0.00 0.00 37.77 4.02
34 35 1.442148 GGAGGCGATACACCTGGTC 59.558 63.158 0.00 0.00 37.77 4.02
35 36 2.064581 GGGAGGCGATACACCTGGT 61.065 63.158 0.00 0.00 37.77 4.00
36 37 2.808206 GGGGAGGCGATACACCTGG 61.808 68.421 0.00 0.00 37.77 4.45
37 38 2.063979 TGGGGAGGCGATACACCTG 61.064 63.158 0.00 0.00 37.77 4.00
38 39 2.064581 GTGGGGAGGCGATACACCT 61.065 63.158 0.00 0.00 41.41 4.00
39 40 1.906105 TTGTGGGGAGGCGATACACC 61.906 60.000 0.00 0.00 0.00 4.16
40 41 0.462047 CTTGTGGGGAGGCGATACAC 60.462 60.000 0.00 0.00 0.00 2.90
41 42 0.616395 TCTTGTGGGGAGGCGATACA 60.616 55.000 0.00 0.00 0.00 2.29
42 43 0.759346 ATCTTGTGGGGAGGCGATAC 59.241 55.000 0.00 0.00 0.00 2.24
43 44 1.048601 GATCTTGTGGGGAGGCGATA 58.951 55.000 0.00 0.00 0.00 2.92
44 45 1.832912 GATCTTGTGGGGAGGCGAT 59.167 57.895 0.00 0.00 0.00 4.58
45 46 2.721167 CGATCTTGTGGGGAGGCGA 61.721 63.158 0.00 0.00 0.00 5.54
46 47 2.032860 ATCGATCTTGTGGGGAGGCG 62.033 60.000 0.00 0.00 0.00 5.52
47 48 0.250081 GATCGATCTTGTGGGGAGGC 60.250 60.000 18.29 0.00 0.00 4.70
48 49 1.342819 GAGATCGATCTTGTGGGGAGG 59.657 57.143 27.90 0.00 37.25 4.30
49 50 1.342819 GGAGATCGATCTTGTGGGGAG 59.657 57.143 27.90 0.00 37.25 4.30
50 51 1.062886 AGGAGATCGATCTTGTGGGGA 60.063 52.381 27.90 0.00 37.25 4.81
51 52 1.418334 AGGAGATCGATCTTGTGGGG 58.582 55.000 27.90 0.00 37.25 4.96
52 53 2.432146 TGAAGGAGATCGATCTTGTGGG 59.568 50.000 27.90 0.00 37.25 4.61
53 54 3.808466 TGAAGGAGATCGATCTTGTGG 57.192 47.619 27.90 0.00 37.25 4.17
54 55 4.931601 TGTTTGAAGGAGATCGATCTTGTG 59.068 41.667 27.90 0.00 37.25 3.33
55 56 5.152623 TGTTTGAAGGAGATCGATCTTGT 57.847 39.130 27.90 15.81 37.25 3.16
56 57 5.814188 TCATGTTTGAAGGAGATCGATCTTG 59.186 40.000 27.90 17.49 37.25 3.02
57 58 5.982356 TCATGTTTGAAGGAGATCGATCTT 58.018 37.500 27.90 13.44 37.25 2.40
58 59 5.453057 CCTCATGTTTGAAGGAGATCGATCT 60.453 44.000 27.63 27.63 40.50 2.75
59 60 4.749099 CCTCATGTTTGAAGGAGATCGATC 59.251 45.833 17.91 17.91 0.00 3.69
60 61 4.701765 CCTCATGTTTGAAGGAGATCGAT 58.298 43.478 0.00 0.00 0.00 3.59
61 62 3.679917 GCCTCATGTTTGAAGGAGATCGA 60.680 47.826 1.63 0.00 0.00 3.59
62 63 2.611292 GCCTCATGTTTGAAGGAGATCG 59.389 50.000 1.63 0.00 0.00 3.69
63 64 2.611292 CGCCTCATGTTTGAAGGAGATC 59.389 50.000 1.63 0.00 0.00 2.75
64 65 2.026822 ACGCCTCATGTTTGAAGGAGAT 60.027 45.455 7.92 0.00 0.00 2.75
65 66 1.347707 ACGCCTCATGTTTGAAGGAGA 59.652 47.619 7.92 0.00 0.00 3.71
66 67 1.813513 ACGCCTCATGTTTGAAGGAG 58.186 50.000 1.63 0.98 0.00 3.69
67 68 2.270352 AACGCCTCATGTTTGAAGGA 57.730 45.000 1.63 0.00 0.00 3.36
68 69 3.119849 CCTAAACGCCTCATGTTTGAAGG 60.120 47.826 1.62 0.00 39.69 3.46
69 70 3.119849 CCCTAAACGCCTCATGTTTGAAG 60.120 47.826 1.62 0.00 39.69 3.02
70 71 2.817258 CCCTAAACGCCTCATGTTTGAA 59.183 45.455 1.62 0.00 39.69 2.69
71 72 2.432444 CCCTAAACGCCTCATGTTTGA 58.568 47.619 1.62 0.00 39.69 2.69
72 73 1.135402 GCCCTAAACGCCTCATGTTTG 60.135 52.381 1.62 0.00 39.69 2.93
73 74 1.173913 GCCCTAAACGCCTCATGTTT 58.826 50.000 0.00 0.00 41.97 2.83
74 75 0.679960 GGCCCTAAACGCCTCATGTT 60.680 55.000 0.00 0.00 43.48 2.71
75 76 1.077716 GGCCCTAAACGCCTCATGT 60.078 57.895 0.00 0.00 43.48 3.21
76 77 3.827634 GGCCCTAAACGCCTCATG 58.172 61.111 0.00 0.00 43.48 3.07
83 84 3.615509 TTCCGGCAGGCCCTAAACG 62.616 63.158 0.00 0.00 37.47 3.60
84 85 1.303806 TTTCCGGCAGGCCCTAAAC 60.304 57.895 0.00 0.00 37.47 2.01
85 86 1.303806 GTTTCCGGCAGGCCCTAAA 60.304 57.895 0.00 2.84 37.47 1.85
86 87 2.353573 GTTTCCGGCAGGCCCTAA 59.646 61.111 0.00 0.00 37.47 2.69
87 88 4.090588 CGTTTCCGGCAGGCCCTA 62.091 66.667 0.00 0.00 37.47 3.53
89 90 3.905437 TTACGTTTCCGGCAGGCCC 62.905 63.158 0.00 0.00 38.78 5.80
90 91 2.358984 TTACGTTTCCGGCAGGCC 60.359 61.111 0.00 0.00 38.78 5.19
91 92 1.303091 ATGTTACGTTTCCGGCAGGC 61.303 55.000 0.00 0.00 38.78 4.85
92 93 0.725117 GATGTTACGTTTCCGGCAGG 59.275 55.000 0.00 0.00 38.78 4.85
93 94 0.725117 GGATGTTACGTTTCCGGCAG 59.275 55.000 0.00 0.00 38.78 4.85
94 95 0.035036 TGGATGTTACGTTTCCGGCA 59.965 50.000 0.00 0.00 38.78 5.69
95 96 1.375551 ATGGATGTTACGTTTCCGGC 58.624 50.000 0.00 0.00 38.78 6.13
96 97 2.477189 GCAATGGATGTTACGTTTCCGG 60.477 50.000 0.00 0.00 38.78 5.14
97 98 2.477189 GGCAATGGATGTTACGTTTCCG 60.477 50.000 0.00 0.00 40.83 4.30
98 99 2.477189 CGGCAATGGATGTTACGTTTCC 60.477 50.000 0.00 0.00 0.00 3.13
99 100 2.477189 CCGGCAATGGATGTTACGTTTC 60.477 50.000 0.00 0.00 0.00 2.78
100 101 1.470890 CCGGCAATGGATGTTACGTTT 59.529 47.619 0.00 0.00 0.00 3.60
101 102 1.091537 CCGGCAATGGATGTTACGTT 58.908 50.000 0.00 0.00 0.00 3.99
102 103 0.035820 ACCGGCAATGGATGTTACGT 60.036 50.000 0.00 0.00 0.00 3.57
103 104 0.655733 GACCGGCAATGGATGTTACG 59.344 55.000 0.00 0.00 0.00 3.18
104 105 1.021968 GGACCGGCAATGGATGTTAC 58.978 55.000 0.00 0.00 0.00 2.50
105 106 0.621082 TGGACCGGCAATGGATGTTA 59.379 50.000 0.00 0.00 0.00 2.41
106 107 0.680921 CTGGACCGGCAATGGATGTT 60.681 55.000 0.00 0.00 0.00 2.71
107 108 1.077501 CTGGACCGGCAATGGATGT 60.078 57.895 0.00 0.00 0.00 3.06
108 109 0.179009 ATCTGGACCGGCAATGGATG 60.179 55.000 0.00 0.00 0.00 3.51
109 110 0.552848 AATCTGGACCGGCAATGGAT 59.447 50.000 0.00 0.00 0.00 3.41
110 111 0.394216 CAATCTGGACCGGCAATGGA 60.394 55.000 0.00 0.00 0.00 3.41
111 112 1.386525 CCAATCTGGACCGGCAATGG 61.387 60.000 0.00 0.00 40.96 3.16
112 113 1.386525 CCCAATCTGGACCGGCAATG 61.387 60.000 0.00 0.00 40.96 2.82
113 114 1.076777 CCCAATCTGGACCGGCAAT 60.077 57.895 0.00 0.00 40.96 3.56
114 115 2.354729 CCCAATCTGGACCGGCAA 59.645 61.111 0.00 0.00 40.96 4.52
115 116 3.727258 CCCCAATCTGGACCGGCA 61.727 66.667 0.00 0.00 40.96 5.69
116 117 3.282374 AACCCCAATCTGGACCGGC 62.282 63.158 0.00 0.00 40.96 6.13
117 118 1.378514 CAACCCCAATCTGGACCGG 60.379 63.158 0.00 0.00 40.96 5.28
118 119 0.251165 AACAACCCCAATCTGGACCG 60.251 55.000 0.00 0.00 40.96 4.79
119 120 1.075536 AGAACAACCCCAATCTGGACC 59.924 52.381 0.00 0.00 40.96 4.46
120 121 2.586648 AGAACAACCCCAATCTGGAC 57.413 50.000 0.00 0.00 40.96 4.02
121 122 4.325030 GGATAAGAACAACCCCAATCTGGA 60.325 45.833 0.00 0.00 40.96 3.86
122 123 3.954258 GGATAAGAACAACCCCAATCTGG 59.046 47.826 0.00 0.00 37.25 3.86
123 124 4.860022 AGGATAAGAACAACCCCAATCTG 58.140 43.478 0.00 0.00 0.00 2.90
124 125 4.079730 GGAGGATAAGAACAACCCCAATCT 60.080 45.833 0.00 0.00 0.00 2.40
125 126 4.207955 GGAGGATAAGAACAACCCCAATC 58.792 47.826 0.00 0.00 0.00 2.67
126 127 3.371595 CGGAGGATAAGAACAACCCCAAT 60.372 47.826 0.00 0.00 0.00 3.16
127 128 2.026636 CGGAGGATAAGAACAACCCCAA 60.027 50.000 0.00 0.00 0.00 4.12
128 129 1.557832 CGGAGGATAAGAACAACCCCA 59.442 52.381 0.00 0.00 0.00 4.96
129 130 1.746171 GCGGAGGATAAGAACAACCCC 60.746 57.143 0.00 0.00 0.00 4.95
130 131 1.065709 TGCGGAGGATAAGAACAACCC 60.066 52.381 0.00 0.00 0.00 4.11
131 132 2.093658 TCTGCGGAGGATAAGAACAACC 60.094 50.000 3.37 0.00 0.00 3.77
132 133 2.930682 GTCTGCGGAGGATAAGAACAAC 59.069 50.000 3.37 0.00 0.00 3.32
133 134 2.416836 CGTCTGCGGAGGATAAGAACAA 60.417 50.000 9.71 0.00 0.00 2.83
134 135 1.134367 CGTCTGCGGAGGATAAGAACA 59.866 52.381 9.71 0.00 0.00 3.18
135 136 1.134560 ACGTCTGCGGAGGATAAGAAC 59.865 52.381 21.59 0.00 43.45 3.01
136 137 1.134367 CACGTCTGCGGAGGATAAGAA 59.866 52.381 21.59 0.00 43.45 2.52
137 138 0.738975 CACGTCTGCGGAGGATAAGA 59.261 55.000 21.59 0.00 43.45 2.10
138 139 0.738975 TCACGTCTGCGGAGGATAAG 59.261 55.000 21.59 8.44 43.45 1.73
139 140 1.399714 ATCACGTCTGCGGAGGATAA 58.600 50.000 21.59 6.80 43.45 1.75
140 141 2.265589 TATCACGTCTGCGGAGGATA 57.734 50.000 21.59 13.41 43.45 2.59
141 142 1.338337 CTTATCACGTCTGCGGAGGAT 59.662 52.381 21.59 14.34 43.45 3.24
142 143 0.738975 CTTATCACGTCTGCGGAGGA 59.261 55.000 21.59 8.01 43.45 3.71
143 144 0.249073 CCTTATCACGTCTGCGGAGG 60.249 60.000 13.62 13.62 43.45 4.30
144 145 0.456221 ACCTTATCACGTCTGCGGAG 59.544 55.000 0.00 0.00 43.45 4.63
145 146 0.892755 AACCTTATCACGTCTGCGGA 59.107 50.000 0.00 0.00 43.45 5.54
146 147 1.278238 GAACCTTATCACGTCTGCGG 58.722 55.000 0.00 0.00 43.45 5.69
147 148 1.990799 TGAACCTTATCACGTCTGCG 58.009 50.000 0.00 0.00 44.93 5.18
148 149 4.391830 TGATTTGAACCTTATCACGTCTGC 59.608 41.667 0.00 0.00 0.00 4.26
149 150 5.858475 GTGATTTGAACCTTATCACGTCTG 58.142 41.667 0.00 0.00 38.90 3.51
154 155 5.175859 TCTCCGTGATTTGAACCTTATCAC 58.824 41.667 0.00 0.00 42.86 3.06
155 156 5.414789 TCTCCGTGATTTGAACCTTATCA 57.585 39.130 0.00 0.00 0.00 2.15
156 157 5.642063 TGTTCTCCGTGATTTGAACCTTATC 59.358 40.000 0.00 0.00 38.29 1.75
157 158 5.556915 TGTTCTCCGTGATTTGAACCTTAT 58.443 37.500 0.00 0.00 38.29 1.73
158 159 4.963373 TGTTCTCCGTGATTTGAACCTTA 58.037 39.130 0.00 0.00 38.29 2.69
159 160 3.815809 TGTTCTCCGTGATTTGAACCTT 58.184 40.909 0.00 0.00 38.29 3.50
160 161 3.485463 TGTTCTCCGTGATTTGAACCT 57.515 42.857 0.00 0.00 38.29 3.50
161 162 3.609409 GCTTGTTCTCCGTGATTTGAACC 60.609 47.826 0.00 0.00 38.29 3.62
162 163 3.555518 GCTTGTTCTCCGTGATTTGAAC 58.444 45.455 0.00 0.00 39.18 3.18
163 164 2.552315 GGCTTGTTCTCCGTGATTTGAA 59.448 45.455 0.00 0.00 0.00 2.69
164 165 2.151202 GGCTTGTTCTCCGTGATTTGA 58.849 47.619 0.00 0.00 0.00 2.69
165 166 1.879380 TGGCTTGTTCTCCGTGATTTG 59.121 47.619 0.00 0.00 0.00 2.32
166 167 2.270352 TGGCTTGTTCTCCGTGATTT 57.730 45.000 0.00 0.00 0.00 2.17
167 168 2.086869 CATGGCTTGTTCTCCGTGATT 58.913 47.619 0.00 0.00 40.86 2.57
168 169 1.679944 CCATGGCTTGTTCTCCGTGAT 60.680 52.381 0.00 0.00 40.86 3.06
169 170 0.321564 CCATGGCTTGTTCTCCGTGA 60.322 55.000 0.00 0.00 40.86 4.35
170 171 1.926511 GCCATGGCTTGTTCTCCGTG 61.927 60.000 29.98 0.00 38.71 4.94
171 172 1.675641 GCCATGGCTTGTTCTCCGT 60.676 57.895 29.98 0.00 38.26 4.69
172 173 2.753966 CGCCATGGCTTGTTCTCCG 61.754 63.158 33.07 11.50 39.32 4.63
173 174 1.675641 ACGCCATGGCTTGTTCTCC 60.676 57.895 33.07 2.52 39.32 3.71
174 175 1.503542 CACGCCATGGCTTGTTCTC 59.496 57.895 33.07 3.30 39.32 2.87
175 176 1.973281 CCACGCCATGGCTTGTTCT 60.973 57.895 33.72 9.68 43.24 3.01
176 177 2.568090 CCACGCCATGGCTTGTTC 59.432 61.111 33.72 8.44 43.24 3.18
187 188 2.978010 CAACCAGGTGACCACGCC 60.978 66.667 3.63 0.00 46.05 5.68
188 189 2.978010 CCAACCAGGTGACCACGC 60.978 66.667 3.63 0.00 0.00 5.34
189 190 2.978010 GCCAACCAGGTGACCACG 60.978 66.667 3.63 0.00 40.61 4.94
196 197 2.045926 GCAGATCGCCAACCAGGT 60.046 61.111 0.00 0.00 40.61 4.00
197 198 2.110967 CAGCAGATCGCCAACCAGG 61.111 63.158 6.02 0.00 44.04 4.45
198 199 2.758089 GCAGCAGATCGCCAACCAG 61.758 63.158 6.02 0.00 44.04 4.00
199 200 2.747460 GCAGCAGATCGCCAACCA 60.747 61.111 6.02 0.00 44.04 3.67
200 201 2.747460 TGCAGCAGATCGCCAACC 60.747 61.111 0.00 0.00 44.04 3.77
201 202 2.789917 CTGCAGCAGATCGCCAAC 59.210 61.111 18.42 0.00 44.04 3.77
202 203 3.129502 GCTGCAGCAGATCGCCAA 61.130 61.111 33.36 0.00 44.04 4.52
203 204 3.617143 AAGCTGCAGCAGATCGCCA 62.617 57.895 38.24 0.00 45.16 5.69
204 205 2.821688 GAAGCTGCAGCAGATCGCC 61.822 63.158 38.24 15.67 45.16 5.54
205 206 2.037913 CTGAAGCTGCAGCAGATCGC 62.038 60.000 38.24 20.39 45.16 4.58
206 207 0.459759 TCTGAAGCTGCAGCAGATCG 60.460 55.000 38.24 24.93 45.16 3.69
207 208 1.666700 CTTCTGAAGCTGCAGCAGATC 59.333 52.381 38.24 30.16 45.16 2.75
208 209 1.278413 TCTTCTGAAGCTGCAGCAGAT 59.722 47.619 38.24 24.53 45.16 2.90
209 210 0.683412 TCTTCTGAAGCTGCAGCAGA 59.317 50.000 38.24 28.66 45.16 4.26
210 211 1.520494 TTCTTCTGAAGCTGCAGCAG 58.480 50.000 38.24 26.91 45.16 4.24
211 212 1.971481 TTTCTTCTGAAGCTGCAGCA 58.029 45.000 38.24 18.87 45.16 4.41
212 213 2.292845 AGTTTTCTTCTGAAGCTGCAGC 59.707 45.455 31.53 31.53 42.49 5.25
213 214 3.363772 CGAGTTTTCTTCTGAAGCTGCAG 60.364 47.826 16.43 16.43 37.24 4.41
214 215 2.545526 CGAGTTTTCTTCTGAAGCTGCA 59.454 45.455 12.54 0.00 33.28 4.41
215 216 2.664151 GCGAGTTTTCTTCTGAAGCTGC 60.664 50.000 12.54 6.89 33.28 5.25
216 217 2.096019 GGCGAGTTTTCTTCTGAAGCTG 60.096 50.000 12.54 1.64 33.28 4.24
217 218 2.147150 GGCGAGTTTTCTTCTGAAGCT 58.853 47.619 12.54 3.91 33.28 3.74
218 219 1.197949 GGGCGAGTTTTCTTCTGAAGC 59.802 52.381 12.54 0.00 33.28 3.86
219 220 2.739379 GAGGGCGAGTTTTCTTCTGAAG 59.261 50.000 11.18 11.18 33.28 3.02
220 221 2.550208 GGAGGGCGAGTTTTCTTCTGAA 60.550 50.000 0.00 0.00 0.00 3.02
221 222 1.002087 GGAGGGCGAGTTTTCTTCTGA 59.998 52.381 0.00 0.00 0.00 3.27
222 223 1.002544 AGGAGGGCGAGTTTTCTTCTG 59.997 52.381 0.00 0.00 0.00 3.02
223 224 1.353091 AGGAGGGCGAGTTTTCTTCT 58.647 50.000 0.00 0.00 0.00 2.85
224 225 2.186532 AAGGAGGGCGAGTTTTCTTC 57.813 50.000 0.00 0.00 0.00 2.87
225 226 2.158667 TCAAAGGAGGGCGAGTTTTCTT 60.159 45.455 0.00 0.00 0.00 2.52
226 227 1.420138 TCAAAGGAGGGCGAGTTTTCT 59.580 47.619 0.00 0.00 0.00 2.52
227 228 1.892209 TCAAAGGAGGGCGAGTTTTC 58.108 50.000 0.00 0.00 0.00 2.29
228 229 2.224769 TGATCAAAGGAGGGCGAGTTTT 60.225 45.455 0.00 0.00 0.00 2.43
229 230 1.351017 TGATCAAAGGAGGGCGAGTTT 59.649 47.619 0.00 0.00 0.00 2.66
230 231 0.984230 TGATCAAAGGAGGGCGAGTT 59.016 50.000 0.00 0.00 0.00 3.01
231 232 1.139853 GATGATCAAAGGAGGGCGAGT 59.860 52.381 0.00 0.00 0.00 4.18
232 233 1.139654 TGATGATCAAAGGAGGGCGAG 59.860 52.381 0.00 0.00 0.00 5.03
233 234 1.203237 TGATGATCAAAGGAGGGCGA 58.797 50.000 0.00 0.00 0.00 5.54
234 235 1.878088 CATGATGATCAAAGGAGGGCG 59.122 52.381 0.00 0.00 0.00 6.13
235 236 1.612463 GCATGATGATCAAAGGAGGGC 59.388 52.381 0.00 0.00 0.00 5.19
236 237 1.878088 CGCATGATGATCAAAGGAGGG 59.122 52.381 0.00 0.00 0.00 4.30
237 238 1.878088 CCGCATGATGATCAAAGGAGG 59.122 52.381 0.00 0.31 0.00 4.30
238 239 1.266175 GCCGCATGATGATCAAAGGAG 59.734 52.381 15.22 0.00 0.00 3.69
239 240 1.311859 GCCGCATGATGATCAAAGGA 58.688 50.000 15.22 0.00 0.00 3.36
240 241 0.313043 GGCCGCATGATGATCAAAGG 59.687 55.000 0.00 4.59 0.00 3.11
241 242 0.313043 GGGCCGCATGATGATCAAAG 59.687 55.000 0.00 0.00 0.00 2.77
242 243 0.395448 TGGGCCGCATGATGATCAAA 60.395 50.000 0.00 0.00 0.00 2.69
243 244 0.178984 ATGGGCCGCATGATGATCAA 60.179 50.000 0.00 0.00 0.00 2.57
244 245 0.691904 TATGGGCCGCATGATGATCA 59.308 50.000 14.84 0.00 0.00 2.92
245 246 1.065926 TCTATGGGCCGCATGATGATC 60.066 52.381 14.84 0.00 0.00 2.92
246 247 0.986527 TCTATGGGCCGCATGATGAT 59.013 50.000 14.84 0.00 0.00 2.45
247 248 0.035317 GTCTATGGGCCGCATGATGA 59.965 55.000 14.84 8.72 0.00 2.92
248 249 1.293963 CGTCTATGGGCCGCATGATG 61.294 60.000 14.84 11.60 0.00 3.07
249 250 1.004560 CGTCTATGGGCCGCATGAT 60.005 57.895 14.84 0.00 0.00 2.45
250 251 2.421314 CGTCTATGGGCCGCATGA 59.579 61.111 14.84 8.74 0.00 3.07
251 252 3.349006 GCGTCTATGGGCCGCATG 61.349 66.667 14.84 6.99 46.26 4.06
255 256 2.023414 TTACCTGCGTCTATGGGCCG 62.023 60.000 0.00 0.00 0.00 6.13
256 257 0.396811 ATTACCTGCGTCTATGGGCC 59.603 55.000 0.00 0.00 0.00 5.80
257 258 1.873591 CAATTACCTGCGTCTATGGGC 59.126 52.381 0.00 0.00 0.00 5.36
258 259 1.873591 GCAATTACCTGCGTCTATGGG 59.126 52.381 0.00 0.00 31.50 4.00
259 260 1.873591 GGCAATTACCTGCGTCTATGG 59.126 52.381 0.00 0.00 43.60 2.74
260 261 1.873591 GGGCAATTACCTGCGTCTATG 59.126 52.381 0.00 0.00 43.60 2.23
261 262 1.488812 TGGGCAATTACCTGCGTCTAT 59.511 47.619 0.00 0.00 43.60 1.98
262 263 0.906066 TGGGCAATTACCTGCGTCTA 59.094 50.000 0.00 0.00 43.60 2.59
263 264 0.255890 ATGGGCAATTACCTGCGTCT 59.744 50.000 0.00 0.00 43.60 4.18
264 265 0.663153 GATGGGCAATTACCTGCGTC 59.337 55.000 0.00 0.00 43.60 5.19
265 266 0.034574 TGATGGGCAATTACCTGCGT 60.035 50.000 0.00 0.00 43.60 5.24
266 267 1.102154 TTGATGGGCAATTACCTGCG 58.898 50.000 0.00 0.00 43.60 5.18
267 268 1.824230 TGTTGATGGGCAATTACCTGC 59.176 47.619 0.00 0.00 39.03 4.85
268 269 3.368323 GGTTGTTGATGGGCAATTACCTG 60.368 47.826 0.00 0.00 38.62 4.00
269 270 2.831526 GGTTGTTGATGGGCAATTACCT 59.168 45.455 0.00 0.00 38.62 3.08
270 271 2.416701 CGGTTGTTGATGGGCAATTACC 60.417 50.000 0.00 0.00 39.03 2.85
271 272 2.416701 CCGGTTGTTGATGGGCAATTAC 60.417 50.000 0.00 0.00 39.03 1.89
272 273 1.821753 CCGGTTGTTGATGGGCAATTA 59.178 47.619 0.00 0.00 39.03 1.40
273 274 0.607620 CCGGTTGTTGATGGGCAATT 59.392 50.000 0.00 0.00 39.03 2.32
274 275 1.887344 GCCGGTTGTTGATGGGCAAT 61.887 55.000 1.90 0.00 43.23 3.56
275 276 2.569354 GCCGGTTGTTGATGGGCAA 61.569 57.895 1.90 0.00 43.23 4.52
276 277 2.988684 GCCGGTTGTTGATGGGCA 60.989 61.111 1.90 0.00 43.23 5.36
277 278 4.114997 CGCCGGTTGTTGATGGGC 62.115 66.667 1.90 0.00 40.36 5.36
278 279 4.114997 GCGCCGGTTGTTGATGGG 62.115 66.667 1.90 0.00 0.00 4.00
279 280 3.326889 CTGCGCCGGTTGTTGATGG 62.327 63.158 4.18 0.00 0.00 3.51
280 281 2.176546 CTGCGCCGGTTGTTGATG 59.823 61.111 4.18 0.00 0.00 3.07
281 282 2.281484 ACTGCGCCGGTTGTTGAT 60.281 55.556 4.18 0.00 0.00 2.57
282 283 3.276091 CACTGCGCCGGTTGTTGA 61.276 61.111 4.18 0.00 0.00 3.18
283 284 3.582120 ACACTGCGCCGGTTGTTG 61.582 61.111 4.18 0.00 0.00 3.33
284 285 3.582120 CACACTGCGCCGGTTGTT 61.582 61.111 4.18 0.00 0.00 2.83
298 299 3.686098 TTTTGGGTGGGGCAGCACA 62.686 57.895 0.00 0.00 33.07 4.57
344 345 2.036089 GAGATCCACCGTGAAGGGATAC 59.964 54.545 0.00 0.00 46.96 2.24
345 346 2.317040 GAGATCCACCGTGAAGGGATA 58.683 52.381 0.00 0.00 46.96 2.59
346 347 1.123928 GAGATCCACCGTGAAGGGAT 58.876 55.000 0.00 0.00 46.96 3.85
347 348 0.976073 GGAGATCCACCGTGAAGGGA 60.976 60.000 0.00 0.00 46.96 4.20
348 349 0.978146 AGGAGATCCACCGTGAAGGG 60.978 60.000 0.00 0.00 46.96 3.95
350 351 0.176680 CCAGGAGATCCACCGTGAAG 59.823 60.000 0.00 0.00 38.89 3.02
351 352 0.544357 ACCAGGAGATCCACCGTGAA 60.544 55.000 0.00 0.00 38.89 3.18
352 353 0.970937 GACCAGGAGATCCACCGTGA 60.971 60.000 0.00 0.00 38.89 4.35
353 354 0.972983 AGACCAGGAGATCCACCGTG 60.973 60.000 0.92 0.00 38.89 4.94
354 355 0.684805 GAGACCAGGAGATCCACCGT 60.685 60.000 0.92 0.00 38.89 4.83
421 3063 2.095059 ACTTCAGCGTCATTTCATTGGC 60.095 45.455 0.00 0.00 0.00 4.52
475 3117 4.021925 GCTCCCTGGCTGGTTCGT 62.022 66.667 9.73 0.00 0.00 3.85
496 3138 2.672996 CCGTTGGCACCCTCTTGG 60.673 66.667 0.00 0.00 41.37 3.61
509 3151 0.030638 GTCAATGCTGTGTTGCCGTT 59.969 50.000 0.00 0.00 0.00 4.44
516 3158 0.603707 CCTGACGGTCAATGCTGTGT 60.604 55.000 12.54 0.00 0.00 3.72
533 3175 3.137385 TTGCTCTGCTTGTGGGCCT 62.137 57.895 4.53 0.00 0.00 5.19
602 3252 3.060615 GCAGTGGAGCTGGCAAGG 61.061 66.667 0.00 0.00 45.14 3.61
642 3292 0.249238 CATGTCTCGGACTGCTAGCC 60.249 60.000 13.29 0.00 33.15 3.93
751 3401 2.407428 TAGCTCGGTCCTGCGAGTG 61.407 63.158 0.00 0.00 34.98 3.51
864 3514 6.346896 GGTATTTGTAGAGGAGAACCGAAAT 58.653 40.000 0.00 0.00 41.83 2.17
920 3570 0.875908 GAGTGCTTGTGCGACTGTGA 60.876 55.000 0.00 0.00 43.34 3.58
1183 3834 4.135153 CTGGTCGACCTGGGCGAG 62.135 72.222 33.39 18.45 38.59 5.03
1386 4037 6.569780 TGCAAGTACATGATGAACTACGTAT 58.430 36.000 0.00 0.00 0.00 3.06
1584 4243 3.375647 ACAACCCCAAGTACAAACACT 57.624 42.857 0.00 0.00 0.00 3.55
1645 4304 0.943673 TGATCACAACTTGGCACACG 59.056 50.000 0.00 0.00 39.29 4.49
1682 4341 9.687210 CACGGACATTTATGCTAGTAATACTTA 57.313 33.333 0.00 0.00 0.00 2.24
1683 4342 7.170998 GCACGGACATTTATGCTAGTAATACTT 59.829 37.037 0.00 0.00 35.16 2.24
1684 4343 6.645415 GCACGGACATTTATGCTAGTAATACT 59.355 38.462 0.00 0.00 35.16 2.12
1685 4344 6.399669 CGCACGGACATTTATGCTAGTAATAC 60.400 42.308 0.00 0.00 35.88 1.89
1918 4581 1.541147 CGTGAACCAGATGTTGCCAAT 59.459 47.619 0.00 0.00 37.29 3.16
2082 4747 8.076178 CCTTTTCACGTATTTTCTCTTGACATT 58.924 33.333 0.00 0.00 0.00 2.71
2158 4823 4.570772 GCTAATTGGAGCAGTCGAATAACA 59.429 41.667 0.00 0.00 42.36 2.41
2205 4870 2.524306 CACTTGTGGGCCCTAAATTCA 58.476 47.619 25.70 9.58 0.00 2.57
2239 4905 2.213310 TGGCCAAGATCAAAGGGGATA 58.787 47.619 0.61 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.