Multiple sequence alignment - TraesCS2B01G486600

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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 TraesCS2B01G486600 chr2B 100.000 3128 0 0 1 3128 683147139 683144012 0.000000e+00 5777.0
1 TraesCS2B01G486600 chr2B 95.260 2658 105 14 477 3128 128272300 128274942 0.000000e+00 4191.0
2 TraesCS2B01G486600 chr2B 91.457 199 12 5 313 508 103466607 103466803 5.140000e-68 268.0
3 TraesCS2B01G486600 chr4B 95.963 2675 97 7 461 3128 515073224 515075894 0.000000e+00 4331.0
4 TraesCS2B01G486600 chr4B 94.257 2751 131 15 391 3128 593206793 593204057 0.000000e+00 4180.0
5 TraesCS2B01G486600 chr4B 98.246 228 4 0 1 228 42961294 42961521 1.750000e-107 399.0
6 TraesCS2B01G486600 chr4B 88.288 222 14 10 291 508 484763796 484763583 4.000000e-64 255.0
7 TraesCS2B01G486600 chr1D 95.507 2582 98 11 552 3128 462971779 462974347 0.000000e+00 4109.0
8 TraesCS2B01G486600 chr1D 95.038 2620 113 12 514 3128 339309446 339312053 0.000000e+00 4102.0
9 TraesCS2B01G486600 chr2D 96.064 2515 89 9 618 3128 437672490 437669982 0.000000e+00 4087.0
10 TraesCS2B01G486600 chr7D 96.168 2505 87 7 629 3128 602036205 602033705 0.000000e+00 4085.0
11 TraesCS2B01G486600 chr7D 87.273 55 2 5 203 254 189988187 189988239 1.210000e-04 58.4
12 TraesCS2B01G486600 chr6B 95.006 2583 113 9 555 3128 127034578 127032003 0.000000e+00 4041.0
13 TraesCS2B01G486600 chr6B 88.785 214 14 9 303 508 664454427 664454216 1.440000e-63 254.0
14 TraesCS2B01G486600 chr6B 89.080 174 15 4 316 486 102210626 102210454 2.440000e-51 213.0
15 TraesCS2B01G486600 chr1B 94.884 2580 113 13 555 3128 515932499 515929933 0.000000e+00 4015.0
16 TraesCS2B01G486600 chr1B 96.653 239 6 2 1 238 67469028 67468791 2.260000e-106 396.0
17 TraesCS2B01G486600 chr1B 93.536 263 9 6 1 262 225729023 225728768 4.890000e-103 385.0
18 TraesCS2B01G486600 chr1B 79.772 351 35 17 229 549 670766332 670766676 4.060000e-54 222.0
19 TraesCS2B01G486600 chr3B 97.845 232 5 0 1 232 272365961 272366192 4.860000e-108 401.0
20 TraesCS2B01G486600 chr3B 89.950 199 15 5 313 508 769411346 769411542 5.180000e-63 252.0
21 TraesCS2B01G486600 chr5B 98.246 228 4 0 1 228 587006806 587006579 1.750000e-107 399.0
22 TraesCS2B01G486600 chr5B 96.624 237 7 1 1 237 371546427 371546192 2.920000e-105 392.0
23 TraesCS2B01G486600 chr7B 98.238 227 4 0 1 227 18899586 18899360 6.290000e-107 398.0
24 TraesCS2B01G486600 chr7B 97.414 232 5 1 1 232 18891379 18891149 8.130000e-106 394.0
25 TraesCS2B01G486600 chr3A 92.193 269 15 6 1 265 629869384 629869118 2.950000e-100 375.0
26 TraesCS2B01G486600 chr5D 76.596 235 26 18 339 555 265953494 265953717 5.520000e-18 102.0


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 TraesCS2B01G486600 chr2B 683144012 683147139 3127 True 5777 5777 100.000 1 3128 1 chr2B.!!$R1 3127
1 TraesCS2B01G486600 chr2B 128272300 128274942 2642 False 4191 4191 95.260 477 3128 1 chr2B.!!$F2 2651
2 TraesCS2B01G486600 chr4B 515073224 515075894 2670 False 4331 4331 95.963 461 3128 1 chr4B.!!$F2 2667
3 TraesCS2B01G486600 chr4B 593204057 593206793 2736 True 4180 4180 94.257 391 3128 1 chr4B.!!$R2 2737
4 TraesCS2B01G486600 chr1D 462971779 462974347 2568 False 4109 4109 95.507 552 3128 1 chr1D.!!$F2 2576
5 TraesCS2B01G486600 chr1D 339309446 339312053 2607 False 4102 4102 95.038 514 3128 1 chr1D.!!$F1 2614
6 TraesCS2B01G486600 chr2D 437669982 437672490 2508 True 4087 4087 96.064 618 3128 1 chr2D.!!$R1 2510
7 TraesCS2B01G486600 chr7D 602033705 602036205 2500 True 4085 4085 96.168 629 3128 1 chr7D.!!$R1 2499
8 TraesCS2B01G486600 chr6B 127032003 127034578 2575 True 4041 4041 95.006 555 3128 1 chr6B.!!$R2 2573
9 TraesCS2B01G486600 chr1B 515929933 515932499 2566 True 4015 4015 94.884 555 3128 1 chr1B.!!$R3 2573

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
153 154 0.035056 ATTCTTTGGCTCCCCTCGTG 60.035 55.0 0.00 0.0 0.00 4.35 F
208 209 0.168128 CGAAAACTGTTGCGATCCCC 59.832 55.0 9.57 0.0 38.11 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1860 0.535102 CTTGAACCAAGGCGAGGTGT 60.535 55.000 4.67 0.0 39.86 4.16 R
2581 2611 4.585955 AAGCTCAAAAGAGTACGAGTCA 57.414 40.909 0.00 0.0 0.00 3.41 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
26 27 9.301153 CATTACTTTTGCTGTCTTTACTTTTGT 57.699 29.630 0.00 0.00 0.00 2.83
27 28 9.869757 ATTACTTTTGCTGTCTTTACTTTTGTT 57.130 25.926 0.00 0.00 0.00 2.83
29 30 8.683550 ACTTTTGCTGTCTTTACTTTTGTTAC 57.316 30.769 0.00 0.00 0.00 2.50
30 31 7.758076 ACTTTTGCTGTCTTTACTTTTGTTACC 59.242 33.333 0.00 0.00 0.00 2.85
31 32 5.412526 TGCTGTCTTTACTTTTGTTACCG 57.587 39.130 0.00 0.00 0.00 4.02
32 33 4.877251 TGCTGTCTTTACTTTTGTTACCGT 59.123 37.500 0.00 0.00 0.00 4.83
33 34 5.354792 TGCTGTCTTTACTTTTGTTACCGTT 59.645 36.000 0.00 0.00 0.00 4.44
34 35 6.538021 TGCTGTCTTTACTTTTGTTACCGTTA 59.462 34.615 0.00 0.00 0.00 3.18
35 36 6.847792 GCTGTCTTTACTTTTGTTACCGTTAC 59.152 38.462 0.00 0.00 0.00 2.50
36 37 7.245419 TGTCTTTACTTTTGTTACCGTTACC 57.755 36.000 0.00 0.00 0.00 2.85
37 38 6.820656 TGTCTTTACTTTTGTTACCGTTACCA 59.179 34.615 0.00 0.00 0.00 3.25
38 39 7.125755 GTCTTTACTTTTGTTACCGTTACCAC 58.874 38.462 0.00 0.00 0.00 4.16
39 40 6.259829 TCTTTACTTTTGTTACCGTTACCACC 59.740 38.462 0.00 0.00 0.00 4.61
40 41 3.883669 ACTTTTGTTACCGTTACCACCA 58.116 40.909 0.00 0.00 0.00 4.17
41 42 3.627123 ACTTTTGTTACCGTTACCACCAC 59.373 43.478 0.00 0.00 0.00 4.16
42 43 3.557228 TTTGTTACCGTTACCACCACT 57.443 42.857 0.00 0.00 0.00 4.00
43 44 4.679373 TTTGTTACCGTTACCACCACTA 57.321 40.909 0.00 0.00 0.00 2.74
44 45 4.888326 TTGTTACCGTTACCACCACTAT 57.112 40.909 0.00 0.00 0.00 2.12
45 46 4.454728 TGTTACCGTTACCACCACTATC 57.545 45.455 0.00 0.00 0.00 2.08
46 47 3.831333 TGTTACCGTTACCACCACTATCA 59.169 43.478 0.00 0.00 0.00 2.15
47 48 4.467082 TGTTACCGTTACCACCACTATCAT 59.533 41.667 0.00 0.00 0.00 2.45
48 49 5.655974 TGTTACCGTTACCACCACTATCATA 59.344 40.000 0.00 0.00 0.00 2.15
49 50 6.324512 TGTTACCGTTACCACCACTATCATAT 59.675 38.462 0.00 0.00 0.00 1.78
50 51 5.881923 ACCGTTACCACCACTATCATATT 57.118 39.130 0.00 0.00 0.00 1.28
51 52 6.982160 ACCGTTACCACCACTATCATATTA 57.018 37.500 0.00 0.00 0.00 0.98
52 53 6.752168 ACCGTTACCACCACTATCATATTAC 58.248 40.000 0.00 0.00 0.00 1.89
53 54 6.552350 ACCGTTACCACCACTATCATATTACT 59.448 38.462 0.00 0.00 0.00 2.24
54 55 7.070322 ACCGTTACCACCACTATCATATTACTT 59.930 37.037 0.00 0.00 0.00 2.24
55 56 7.929785 CCGTTACCACCACTATCATATTACTTT 59.070 37.037 0.00 0.00 0.00 2.66
56 57 8.761497 CGTTACCACCACTATCATATTACTTTG 58.239 37.037 0.00 0.00 0.00 2.77
57 58 8.557029 GTTACCACCACTATCATATTACTTTGC 58.443 37.037 0.00 0.00 0.00 3.68
58 59 6.900194 ACCACCACTATCATATTACTTTGCT 58.100 36.000 0.00 0.00 0.00 3.91
59 60 8.029782 ACCACCACTATCATATTACTTTGCTA 57.970 34.615 0.00 0.00 0.00 3.49
60 61 7.931948 ACCACCACTATCATATTACTTTGCTAC 59.068 37.037 0.00 0.00 0.00 3.58
61 62 8.150945 CCACCACTATCATATTACTTTGCTACT 58.849 37.037 0.00 0.00 0.00 2.57
73 74 7.562454 TTACTTTGCTACTAAACACTTTGCT 57.438 32.000 0.00 0.00 0.00 3.91
74 75 5.821204 ACTTTGCTACTAAACACTTTGCTG 58.179 37.500 0.00 0.00 0.00 4.41
75 76 3.896648 TGCTACTAAACACTTTGCTGC 57.103 42.857 0.00 0.00 0.00 5.25
76 77 3.210227 TGCTACTAAACACTTTGCTGCA 58.790 40.909 0.00 0.00 0.00 4.41
77 78 3.629855 TGCTACTAAACACTTTGCTGCAA 59.370 39.130 11.69 11.69 0.00 4.08
78 79 4.097135 TGCTACTAAACACTTTGCTGCAAA 59.903 37.500 24.68 24.68 0.00 3.68
79 80 5.221224 TGCTACTAAACACTTTGCTGCAAAT 60.221 36.000 26.18 14.60 32.70 2.32
80 81 6.016693 TGCTACTAAACACTTTGCTGCAAATA 60.017 34.615 26.18 14.93 32.70 1.40
81 82 6.305638 GCTACTAAACACTTTGCTGCAAATAC 59.694 38.462 26.18 6.60 32.70 1.89
82 83 6.391227 ACTAAACACTTTGCTGCAAATACT 57.609 33.333 26.18 10.59 32.70 2.12
83 84 7.504924 ACTAAACACTTTGCTGCAAATACTA 57.495 32.000 26.18 13.07 32.70 1.82
84 85 7.936584 ACTAAACACTTTGCTGCAAATACTAA 58.063 30.769 26.18 10.99 32.70 2.24
85 86 8.076178 ACTAAACACTTTGCTGCAAATACTAAG 58.924 33.333 26.18 19.80 32.70 2.18
86 87 6.391227 AACACTTTGCTGCAAATACTAAGT 57.609 33.333 26.18 17.07 32.70 2.24
87 88 6.391227 ACACTTTGCTGCAAATACTAAGTT 57.609 33.333 26.18 9.10 32.70 2.66
88 89 6.805713 ACACTTTGCTGCAAATACTAAGTTT 58.194 32.000 26.18 11.13 32.70 2.66
89 90 6.918022 ACACTTTGCTGCAAATACTAAGTTTC 59.082 34.615 26.18 0.00 32.70 2.78
90 91 6.363357 CACTTTGCTGCAAATACTAAGTTTCC 59.637 38.462 26.18 0.00 32.70 3.13
91 92 6.040391 ACTTTGCTGCAAATACTAAGTTTCCA 59.960 34.615 26.18 1.11 32.70 3.53
92 93 5.627499 TGCTGCAAATACTAAGTTTCCAG 57.373 39.130 0.00 0.00 0.00 3.86
93 94 4.458989 TGCTGCAAATACTAAGTTTCCAGG 59.541 41.667 0.00 0.00 0.00 4.45
94 95 4.459337 GCTGCAAATACTAAGTTTCCAGGT 59.541 41.667 0.00 0.00 0.00 4.00
95 96 5.619981 GCTGCAAATACTAAGTTTCCAGGTG 60.620 44.000 0.00 0.00 0.00 4.00
96 97 5.381757 TGCAAATACTAAGTTTCCAGGTGT 58.618 37.500 0.00 0.00 0.00 4.16
97 98 5.240623 TGCAAATACTAAGTTTCCAGGTGTG 59.759 40.000 0.00 0.00 0.00 3.82
98 99 5.335661 GCAAATACTAAGTTTCCAGGTGTGG 60.336 44.000 0.00 0.00 46.63 4.17
99 100 5.578157 AATACTAAGTTTCCAGGTGTGGT 57.422 39.130 0.00 0.00 45.28 4.16
100 101 3.945640 ACTAAGTTTCCAGGTGTGGTT 57.054 42.857 0.00 0.00 45.28 3.67
101 102 3.551846 ACTAAGTTTCCAGGTGTGGTTG 58.448 45.455 0.00 0.00 45.28 3.77
102 103 2.818751 AAGTTTCCAGGTGTGGTTGA 57.181 45.000 0.00 0.00 45.28 3.18
103 104 2.818751 AGTTTCCAGGTGTGGTTGAA 57.181 45.000 0.00 0.00 45.28 2.69
104 105 3.312736 AGTTTCCAGGTGTGGTTGAAT 57.687 42.857 0.00 0.00 45.28 2.57
105 106 3.642141 AGTTTCCAGGTGTGGTTGAATT 58.358 40.909 0.00 0.00 45.28 2.17
106 107 3.384467 AGTTTCCAGGTGTGGTTGAATTG 59.616 43.478 0.00 0.00 45.28 2.32
107 108 3.304911 TTCCAGGTGTGGTTGAATTGA 57.695 42.857 0.00 0.00 45.28 2.57
108 109 2.582052 TCCAGGTGTGGTTGAATTGAC 58.418 47.619 0.00 0.00 45.28 3.18
109 110 2.092158 TCCAGGTGTGGTTGAATTGACA 60.092 45.455 0.00 0.00 45.28 3.58
110 111 2.692557 CCAGGTGTGGTTGAATTGACAA 59.307 45.455 0.00 0.00 39.30 3.18
111 112 3.490761 CCAGGTGTGGTTGAATTGACAAC 60.491 47.826 0.00 0.00 46.20 3.32
112 113 3.381272 CAGGTGTGGTTGAATTGACAACT 59.619 43.478 9.21 0.00 46.17 3.16
113 114 3.632145 AGGTGTGGTTGAATTGACAACTC 59.368 43.478 9.21 0.00 46.17 3.01
114 115 3.380004 GGTGTGGTTGAATTGACAACTCA 59.620 43.478 9.21 0.00 46.17 3.41
115 116 4.498009 GGTGTGGTTGAATTGACAACTCAG 60.498 45.833 0.00 0.00 46.17 3.35
116 117 3.066621 TGTGGTTGAATTGACAACTCAGC 59.933 43.478 5.07 5.07 46.17 4.26
117 118 3.316308 GTGGTTGAATTGACAACTCAGCT 59.684 43.478 12.25 0.00 46.17 4.24
118 119 3.565482 TGGTTGAATTGACAACTCAGCTC 59.435 43.478 12.25 4.78 46.17 4.09
119 120 3.057946 GGTTGAATTGACAACTCAGCTCC 60.058 47.826 12.25 7.39 46.17 4.70
120 121 3.777106 TGAATTGACAACTCAGCTCCT 57.223 42.857 0.00 0.00 0.00 3.69
121 122 4.890158 TGAATTGACAACTCAGCTCCTA 57.110 40.909 0.00 0.00 0.00 2.94
122 123 4.825422 TGAATTGACAACTCAGCTCCTAG 58.175 43.478 0.00 0.00 0.00 3.02
123 124 4.284490 TGAATTGACAACTCAGCTCCTAGT 59.716 41.667 0.00 0.00 0.00 2.57
124 125 5.480422 TGAATTGACAACTCAGCTCCTAGTA 59.520 40.000 0.00 0.00 0.00 1.82
125 126 4.785511 TTGACAACTCAGCTCCTAGTAC 57.214 45.455 0.00 0.00 0.00 2.73
126 127 4.035612 TGACAACTCAGCTCCTAGTACT 57.964 45.455 0.00 0.00 0.00 2.73
127 128 4.408276 TGACAACTCAGCTCCTAGTACTT 58.592 43.478 0.00 0.00 0.00 2.24
128 129 4.218635 TGACAACTCAGCTCCTAGTACTTG 59.781 45.833 0.00 0.00 0.00 3.16
129 130 4.408276 ACAACTCAGCTCCTAGTACTTGA 58.592 43.478 0.00 0.00 0.00 3.02
130 131 4.461081 ACAACTCAGCTCCTAGTACTTGAG 59.539 45.833 15.36 15.36 0.00 3.02
131 132 4.577988 ACTCAGCTCCTAGTACTTGAGA 57.422 45.455 21.31 9.96 0.00 3.27
132 133 4.924625 ACTCAGCTCCTAGTACTTGAGAA 58.075 43.478 21.31 8.58 0.00 2.87
133 134 5.515106 ACTCAGCTCCTAGTACTTGAGAAT 58.485 41.667 21.31 9.50 0.00 2.40
134 135 6.664714 ACTCAGCTCCTAGTACTTGAGAATA 58.335 40.000 21.31 8.06 0.00 1.75
135 136 7.294584 ACTCAGCTCCTAGTACTTGAGAATAT 58.705 38.462 21.31 2.26 0.00 1.28
136 137 7.782644 ACTCAGCTCCTAGTACTTGAGAATATT 59.217 37.037 21.31 0.00 0.00 1.28
137 138 8.172352 TCAGCTCCTAGTACTTGAGAATATTC 57.828 38.462 20.44 7.41 0.00 1.75
138 139 8.001875 TCAGCTCCTAGTACTTGAGAATATTCT 58.998 37.037 17.96 17.96 41.00 2.40
139 140 8.637986 CAGCTCCTAGTACTTGAGAATATTCTT 58.362 37.037 18.88 6.06 37.73 2.52
140 141 9.207868 AGCTCCTAGTACTTGAGAATATTCTTT 57.792 33.333 18.88 7.13 37.73 2.52
141 142 9.255304 GCTCCTAGTACTTGAGAATATTCTTTG 57.745 37.037 18.88 13.63 37.73 2.77
142 143 9.757227 CTCCTAGTACTTGAGAATATTCTTTGG 57.243 37.037 18.88 11.22 37.73 3.28
143 144 8.204836 TCCTAGTACTTGAGAATATTCTTTGGC 58.795 37.037 18.88 7.13 37.73 4.52
144 145 8.207545 CCTAGTACTTGAGAATATTCTTTGGCT 58.792 37.037 18.88 13.80 37.73 4.75
145 146 9.255304 CTAGTACTTGAGAATATTCTTTGGCTC 57.745 37.037 18.88 6.34 37.73 4.70
146 147 7.051000 AGTACTTGAGAATATTCTTTGGCTCC 58.949 38.462 18.88 5.41 37.73 4.70
147 148 5.196695 ACTTGAGAATATTCTTTGGCTCCC 58.803 41.667 18.88 4.72 37.73 4.30
148 149 4.170468 TGAGAATATTCTTTGGCTCCCC 57.830 45.455 18.88 4.05 37.73 4.81
149 150 3.788142 TGAGAATATTCTTTGGCTCCCCT 59.212 43.478 18.88 0.00 37.73 4.79
150 151 4.141390 TGAGAATATTCTTTGGCTCCCCTC 60.141 45.833 18.88 3.15 37.73 4.30
151 152 2.938956 ATATTCTTTGGCTCCCCTCG 57.061 50.000 0.00 0.00 0.00 4.63
152 153 1.580059 TATTCTTTGGCTCCCCTCGT 58.420 50.000 0.00 0.00 0.00 4.18
153 154 0.035056 ATTCTTTGGCTCCCCTCGTG 60.035 55.000 0.00 0.00 0.00 4.35
154 155 1.415672 TTCTTTGGCTCCCCTCGTGT 61.416 55.000 0.00 0.00 0.00 4.49
155 156 1.376037 CTTTGGCTCCCCTCGTGTC 60.376 63.158 0.00 0.00 0.00 3.67
156 157 3.234630 TTTGGCTCCCCTCGTGTCG 62.235 63.158 0.00 0.00 0.00 4.35
157 158 4.671590 TGGCTCCCCTCGTGTCGA 62.672 66.667 0.00 0.00 0.00 4.20
158 159 3.379445 GGCTCCCCTCGTGTCGAA 61.379 66.667 0.00 0.00 34.74 3.71
159 160 2.722201 GGCTCCCCTCGTGTCGAAT 61.722 63.158 0.00 0.00 34.74 3.34
160 161 1.227002 GCTCCCCTCGTGTCGAATC 60.227 63.158 0.00 0.00 34.74 2.52
161 162 1.945354 GCTCCCCTCGTGTCGAATCA 61.945 60.000 0.00 0.00 34.74 2.57
162 163 0.530744 CTCCCCTCGTGTCGAATCAA 59.469 55.000 0.00 0.00 34.74 2.57
163 164 1.137086 CTCCCCTCGTGTCGAATCAAT 59.863 52.381 0.00 0.00 34.74 2.57
164 165 2.361119 CTCCCCTCGTGTCGAATCAATA 59.639 50.000 0.00 0.00 34.74 1.90
165 166 2.761767 TCCCCTCGTGTCGAATCAATAA 59.238 45.455 0.00 0.00 34.74 1.40
166 167 3.196039 TCCCCTCGTGTCGAATCAATAAA 59.804 43.478 0.00 0.00 34.74 1.40
167 168 4.127171 CCCCTCGTGTCGAATCAATAAAT 58.873 43.478 0.00 0.00 34.74 1.40
168 169 4.574828 CCCCTCGTGTCGAATCAATAAATT 59.425 41.667 0.00 0.00 34.74 1.82
169 170 5.065988 CCCCTCGTGTCGAATCAATAAATTT 59.934 40.000 0.00 0.00 34.74 1.82
170 171 5.965334 CCCTCGTGTCGAATCAATAAATTTG 59.035 40.000 0.00 0.00 34.74 2.32
171 172 5.965334 CCTCGTGTCGAATCAATAAATTTGG 59.035 40.000 0.00 0.00 34.74 3.28
172 173 5.874831 TCGTGTCGAATCAATAAATTTGGG 58.125 37.500 0.00 0.00 31.06 4.12
173 174 5.413213 TCGTGTCGAATCAATAAATTTGGGT 59.587 36.000 0.00 0.00 31.06 4.51
174 175 6.072397 TCGTGTCGAATCAATAAATTTGGGTT 60.072 34.615 0.00 0.00 31.06 4.11
175 176 6.033407 CGTGTCGAATCAATAAATTTGGGTTG 59.967 38.462 0.00 3.99 0.00 3.77
176 177 7.087639 GTGTCGAATCAATAAATTTGGGTTGA 58.912 34.615 14.00 14.00 35.33 3.18
177 178 7.596995 GTGTCGAATCAATAAATTTGGGTTGAA 59.403 33.333 15.01 2.31 34.62 2.69
178 179 8.310382 TGTCGAATCAATAAATTTGGGTTGAAT 58.690 29.630 15.01 9.74 34.62 2.57
179 180 9.796120 GTCGAATCAATAAATTTGGGTTGAATA 57.204 29.630 15.01 4.16 34.62 1.75
180 181 9.796120 TCGAATCAATAAATTTGGGTTGAATAC 57.204 29.630 15.01 10.41 34.62 1.89
181 182 9.801873 CGAATCAATAAATTTGGGTTGAATACT 57.198 29.630 15.01 5.42 34.62 2.12
192 193 4.996788 GGTTGAATACTCTACCCTCGAA 57.003 45.455 0.00 0.00 40.45 3.71
193 194 5.334724 GGTTGAATACTCTACCCTCGAAA 57.665 43.478 0.00 0.00 40.45 3.46
194 195 5.727434 GGTTGAATACTCTACCCTCGAAAA 58.273 41.667 0.00 0.00 40.45 2.29
195 196 5.579904 GGTTGAATACTCTACCCTCGAAAAC 59.420 44.000 0.00 0.00 40.45 2.43
196 197 6.396450 GTTGAATACTCTACCCTCGAAAACT 58.604 40.000 0.00 0.00 0.00 2.66
197 198 5.962433 TGAATACTCTACCCTCGAAAACTG 58.038 41.667 0.00 0.00 0.00 3.16
198 199 5.479375 TGAATACTCTACCCTCGAAAACTGT 59.521 40.000 0.00 0.00 0.00 3.55
199 200 5.997384 ATACTCTACCCTCGAAAACTGTT 57.003 39.130 0.00 0.00 0.00 3.16
200 201 3.991367 ACTCTACCCTCGAAAACTGTTG 58.009 45.455 0.00 0.00 0.00 3.33
201 202 2.737252 CTCTACCCTCGAAAACTGTTGC 59.263 50.000 0.00 0.00 0.00 4.17
202 203 1.459592 CTACCCTCGAAAACTGTTGCG 59.540 52.381 9.05 9.05 37.10 4.85
203 204 0.179067 ACCCTCGAAAACTGTTGCGA 60.179 50.000 14.99 14.99 42.74 5.10
204 205 1.156736 CCCTCGAAAACTGTTGCGAT 58.843 50.000 15.79 0.00 43.94 4.58
205 206 1.128692 CCCTCGAAAACTGTTGCGATC 59.871 52.381 15.79 3.49 43.94 3.69
206 207 1.128692 CCTCGAAAACTGTTGCGATCC 59.871 52.381 15.79 0.00 43.94 3.36
207 208 1.128692 CTCGAAAACTGTTGCGATCCC 59.871 52.381 15.79 0.00 43.94 3.85
208 209 0.168128 CGAAAACTGTTGCGATCCCC 59.832 55.000 9.57 0.00 38.11 4.81
209 210 1.534729 GAAAACTGTTGCGATCCCCT 58.465 50.000 0.00 0.00 0.00 4.79
210 211 2.706890 GAAAACTGTTGCGATCCCCTA 58.293 47.619 0.00 0.00 0.00 3.53
211 212 3.279434 GAAAACTGTTGCGATCCCCTAT 58.721 45.455 0.00 0.00 0.00 2.57
212 213 4.448210 GAAAACTGTTGCGATCCCCTATA 58.552 43.478 0.00 0.00 0.00 1.31
213 214 3.470645 AACTGTTGCGATCCCCTATAC 57.529 47.619 0.00 0.00 0.00 1.47
214 215 2.679082 ACTGTTGCGATCCCCTATACT 58.321 47.619 0.00 0.00 0.00 2.12
215 216 3.039011 ACTGTTGCGATCCCCTATACTT 58.961 45.455 0.00 0.00 0.00 2.24
216 217 3.181465 ACTGTTGCGATCCCCTATACTTG 60.181 47.826 0.00 0.00 0.00 3.16
217 218 2.769663 TGTTGCGATCCCCTATACTTGT 59.230 45.455 0.00 0.00 0.00 3.16
218 219 3.131396 GTTGCGATCCCCTATACTTGTG 58.869 50.000 0.00 0.00 0.00 3.33
219 220 1.691976 TGCGATCCCCTATACTTGTGG 59.308 52.381 0.00 0.00 0.00 4.17
220 221 1.002087 GCGATCCCCTATACTTGTGGG 59.998 57.143 0.00 0.00 40.59 4.61
221 222 2.326428 CGATCCCCTATACTTGTGGGT 58.674 52.381 0.00 0.00 39.31 4.51
222 223 2.704065 CGATCCCCTATACTTGTGGGTT 59.296 50.000 0.00 0.00 39.31 4.11
223 224 3.899360 CGATCCCCTATACTTGTGGGTTA 59.101 47.826 0.00 0.00 39.31 2.85
224 225 4.530946 CGATCCCCTATACTTGTGGGTTAT 59.469 45.833 0.00 0.00 39.31 1.89
225 226 5.337330 CGATCCCCTATACTTGTGGGTTATC 60.337 48.000 0.00 0.00 39.31 1.75
226 227 4.898268 TCCCCTATACTTGTGGGTTATCA 58.102 43.478 0.00 0.00 39.31 2.15
227 228 5.482580 TCCCCTATACTTGTGGGTTATCAT 58.517 41.667 0.00 0.00 39.31 2.45
228 229 5.546499 TCCCCTATACTTGTGGGTTATCATC 59.454 44.000 0.00 0.00 39.31 2.92
229 230 5.280521 CCCCTATACTTGTGGGTTATCATCC 60.281 48.000 0.00 0.00 39.31 3.51
230 231 5.479306 CCTATACTTGTGGGTTATCATCCG 58.521 45.833 0.00 0.00 0.00 4.18
231 232 2.038387 ACTTGTGGGTTATCATCCGC 57.962 50.000 0.00 0.00 0.00 5.54
232 233 0.937304 CTTGTGGGTTATCATCCGCG 59.063 55.000 0.00 0.00 36.41 6.46
233 234 1.092921 TTGTGGGTTATCATCCGCGC 61.093 55.000 0.00 0.00 36.41 6.86
234 235 2.279851 TGGGTTATCATCCGCGCG 60.280 61.111 25.67 25.67 0.00 6.86
235 236 3.712881 GGGTTATCATCCGCGCGC 61.713 66.667 27.36 23.91 0.00 6.86
236 237 3.712881 GGTTATCATCCGCGCGCC 61.713 66.667 27.36 14.12 0.00 6.53
237 238 4.059459 GTTATCATCCGCGCGCCG 62.059 66.667 27.36 20.35 0.00 6.46
238 239 4.578898 TTATCATCCGCGCGCCGT 62.579 61.111 27.36 9.37 34.38 5.68
239 240 3.196913 TTATCATCCGCGCGCCGTA 62.197 57.895 27.36 11.70 34.38 4.02
240 241 3.604494 TATCATCCGCGCGCCGTAG 62.604 63.158 27.36 15.54 34.38 3.51
423 424 2.656069 AACGATGCGGCACTAGGGT 61.656 57.895 4.03 0.00 0.00 4.34
424 425 2.180159 AACGATGCGGCACTAGGGTT 62.180 55.000 4.03 2.50 0.00 4.11
425 426 1.449601 CGATGCGGCACTAGGGTTT 60.450 57.895 4.03 0.00 0.00 3.27
426 427 1.024579 CGATGCGGCACTAGGGTTTT 61.025 55.000 4.03 0.00 0.00 2.43
440 441 1.439679 GGTTTTCCCTAGCGTCACTG 58.560 55.000 0.00 0.00 0.00 3.66
443 444 1.812686 TTTCCCTAGCGTCACTGCGT 61.813 55.000 0.00 0.00 40.67 5.24
444 445 2.486636 TTCCCTAGCGTCACTGCGTG 62.487 60.000 2.79 2.79 40.67 5.34
445 446 2.258591 CCTAGCGTCACTGCGTGT 59.741 61.111 8.22 0.00 40.67 4.49
451 452 4.961511 GTCACTGCGTGTGGCCGA 62.962 66.667 0.00 0.00 44.95 5.54
452 453 4.662961 TCACTGCGTGTGGCCGAG 62.663 66.667 0.00 0.00 46.20 4.63
615 628 2.580867 CGAGCTAGACTGCACGCC 60.581 66.667 0.00 0.00 39.71 5.68
679 694 8.270080 TGTTTTTACGTGCATTATATTCCTGA 57.730 30.769 0.00 0.00 0.00 3.86
969 987 4.619973 CTTTGTGCAAAAGATTACCTGCA 58.380 39.130 13.03 0.00 42.28 4.41
1255 1274 1.228675 AGTGCTTCTGGCCTTTGGG 60.229 57.895 3.32 0.00 40.92 4.12
1395 1414 2.159338 GCACCGGATTTGTACGACTCTA 60.159 50.000 9.46 0.00 0.00 2.43
1507 1526 2.436115 GCCAGGGGAACTACACGC 60.436 66.667 0.00 0.00 0.00 5.34
1526 1545 2.285220 CGCGGTATTCAGAGTTGATTGG 59.715 50.000 0.00 0.00 32.27 3.16
1644 1663 0.465460 AAGTCCGCAAGCCTCAACAA 60.465 50.000 0.00 0.00 0.00 2.83
1701 1725 3.171388 CCTCCTGCCCCGGCTAAT 61.171 66.667 7.35 0.00 42.51 1.73
1836 1860 4.717629 CGGAAGGCGCGTGAGACA 62.718 66.667 8.43 0.00 0.00 3.41
1854 1878 0.817634 CACACCTCGCCTTGGTTCAA 60.818 55.000 0.00 0.00 35.28 2.69
1910 1934 3.537874 GATCGCTACGCCCCCTGT 61.538 66.667 0.00 0.00 0.00 4.00
2012 2036 2.665000 CCACATGGTCGCCTCTGT 59.335 61.111 0.00 0.00 0.00 3.41
2013 2037 1.897423 CCACATGGTCGCCTCTGTA 59.103 57.895 0.00 0.00 0.00 2.74
2581 2611 0.881600 GCGTTGTTGTACCCGGAGTT 60.882 55.000 0.73 0.00 0.00 3.01
2616 2646 1.824852 TGAGCTTTAGAGACATCCGCA 59.175 47.619 0.00 0.00 0.00 5.69
2680 2710 2.038952 AGTGCCTACTCATCACAAAGCA 59.961 45.455 0.00 0.00 33.44 3.91
2712 2742 5.644636 GGTGGTAAACATGTTATCGAAAGGA 59.355 40.000 12.39 0.00 0.00 3.36
2740 2770 3.259876 TCGTTTGACACAGGGCTATACTT 59.740 43.478 0.00 0.00 0.00 2.24
2760 2790 8.754991 ATACTTCACTAAGATAGTAGCACTGT 57.245 34.615 0.00 0.00 37.23 3.55
2773 2803 2.168496 AGCACTGTCCGTGTACACTAT 58.832 47.619 23.01 0.15 45.57 2.12
2904 2935 8.960591 CCATAATGTTAACATGAAGAACTTCCT 58.039 33.333 21.46 4.26 38.77 3.36
3099 3130 4.166725 TGATGCTTCCTCTAAATGGTCCAT 59.833 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.869757 AACAAAAGTAAAGACAGCAAAAGTAAT 57.130 25.926 0.00 0.00 0.00 1.89
3 4 9.777575 GTAACAAAAGTAAAGACAGCAAAAGTA 57.222 29.630 0.00 0.00 0.00 2.24
4 5 7.758076 GGTAACAAAAGTAAAGACAGCAAAAGT 59.242 33.333 0.00 0.00 0.00 2.66
5 6 7.044314 CGGTAACAAAAGTAAAGACAGCAAAAG 60.044 37.037 0.00 0.00 0.00 2.27
6 7 6.748198 CGGTAACAAAAGTAAAGACAGCAAAA 59.252 34.615 0.00 0.00 0.00 2.44
7 8 6.127952 ACGGTAACAAAAGTAAAGACAGCAAA 60.128 34.615 0.00 0.00 0.00 3.68
10 11 5.413969 ACGGTAACAAAAGTAAAGACAGC 57.586 39.130 0.00 0.00 0.00 4.40
11 12 7.011295 TGGTAACGGTAACAAAAGTAAAGACAG 59.989 37.037 0.00 0.00 42.51 3.51
12 13 6.820656 TGGTAACGGTAACAAAAGTAAAGACA 59.179 34.615 0.00 0.00 42.51 3.41
13 14 7.125755 GTGGTAACGGTAACAAAAGTAAAGAC 58.874 38.462 0.00 0.00 42.51 3.01
14 15 6.259829 GGTGGTAACGGTAACAAAAGTAAAGA 59.740 38.462 0.00 0.00 42.51 2.52
15 16 6.038050 TGGTGGTAACGGTAACAAAAGTAAAG 59.962 38.462 0.00 0.00 42.51 1.85
16 17 5.882557 TGGTGGTAACGGTAACAAAAGTAAA 59.117 36.000 0.00 0.00 42.51 2.01
17 18 5.295540 GTGGTGGTAACGGTAACAAAAGTAA 59.704 40.000 0.00 0.00 42.51 2.24
18 19 4.813697 GTGGTGGTAACGGTAACAAAAGTA 59.186 41.667 0.00 0.00 42.51 2.24
19 20 3.627123 GTGGTGGTAACGGTAACAAAAGT 59.373 43.478 0.00 0.00 42.51 2.66
20 21 3.878699 AGTGGTGGTAACGGTAACAAAAG 59.121 43.478 0.00 0.00 42.51 2.27
21 22 3.883669 AGTGGTGGTAACGGTAACAAAA 58.116 40.909 0.00 0.00 42.51 2.44
22 23 3.557228 AGTGGTGGTAACGGTAACAAA 57.443 42.857 0.00 0.00 42.51 2.83
23 24 4.282957 TGATAGTGGTGGTAACGGTAACAA 59.717 41.667 0.00 0.00 42.51 2.83
24 25 3.831333 TGATAGTGGTGGTAACGGTAACA 59.169 43.478 0.00 0.00 42.51 2.41
25 26 4.454728 TGATAGTGGTGGTAACGGTAAC 57.545 45.455 0.00 0.00 42.51 2.50
26 27 6.982160 ATATGATAGTGGTGGTAACGGTAA 57.018 37.500 0.00 0.00 42.51 2.85
27 28 6.982160 AATATGATAGTGGTGGTAACGGTA 57.018 37.500 0.00 0.00 42.51 4.02
28 29 5.881923 AATATGATAGTGGTGGTAACGGT 57.118 39.130 0.00 0.00 42.51 4.83
29 30 6.989659 AGTAATATGATAGTGGTGGTAACGG 58.010 40.000 0.00 0.00 42.51 4.44
30 31 8.761497 CAAAGTAATATGATAGTGGTGGTAACG 58.239 37.037 0.00 0.00 42.51 3.18
31 32 8.557029 GCAAAGTAATATGATAGTGGTGGTAAC 58.443 37.037 0.00 0.00 0.00 2.50
32 33 8.491134 AGCAAAGTAATATGATAGTGGTGGTAA 58.509 33.333 0.00 0.00 0.00 2.85
33 34 8.029782 AGCAAAGTAATATGATAGTGGTGGTA 57.970 34.615 0.00 0.00 0.00 3.25
34 35 6.900194 AGCAAAGTAATATGATAGTGGTGGT 58.100 36.000 0.00 0.00 0.00 4.16
35 36 8.150945 AGTAGCAAAGTAATATGATAGTGGTGG 58.849 37.037 0.00 0.00 0.00 4.61
47 48 9.280174 AGCAAAGTGTTTAGTAGCAAAGTAATA 57.720 29.630 0.00 0.00 0.00 0.98
48 49 8.076178 CAGCAAAGTGTTTAGTAGCAAAGTAAT 58.924 33.333 0.00 0.00 0.00 1.89
49 50 7.414436 CAGCAAAGTGTTTAGTAGCAAAGTAA 58.586 34.615 0.00 0.00 0.00 2.24
50 51 6.512741 GCAGCAAAGTGTTTAGTAGCAAAGTA 60.513 38.462 0.00 0.00 0.00 2.24
51 52 5.733373 GCAGCAAAGTGTTTAGTAGCAAAGT 60.733 40.000 0.00 0.00 0.00 2.66
52 53 4.676924 GCAGCAAAGTGTTTAGTAGCAAAG 59.323 41.667 0.00 0.00 0.00 2.77
53 54 4.097135 TGCAGCAAAGTGTTTAGTAGCAAA 59.903 37.500 0.00 0.00 0.00 3.68
54 55 3.629855 TGCAGCAAAGTGTTTAGTAGCAA 59.370 39.130 0.00 0.00 0.00 3.91
55 56 3.210227 TGCAGCAAAGTGTTTAGTAGCA 58.790 40.909 0.00 0.00 0.00 3.49
56 57 3.896648 TGCAGCAAAGTGTTTAGTAGC 57.103 42.857 0.00 0.00 0.00 3.58
57 58 7.584987 AGTATTTGCAGCAAAGTGTTTAGTAG 58.415 34.615 24.39 0.00 36.76 2.57
58 59 7.504924 AGTATTTGCAGCAAAGTGTTTAGTA 57.495 32.000 24.39 7.91 36.76 1.82
59 60 6.391227 AGTATTTGCAGCAAAGTGTTTAGT 57.609 33.333 24.39 12.17 36.76 2.24
60 61 8.076178 ACTTAGTATTTGCAGCAAAGTGTTTAG 58.924 33.333 24.39 17.75 36.76 1.85
61 62 7.936584 ACTTAGTATTTGCAGCAAAGTGTTTA 58.063 30.769 24.39 9.96 36.76 2.01
62 63 6.805713 ACTTAGTATTTGCAGCAAAGTGTTT 58.194 32.000 24.39 10.93 36.76 2.83
63 64 6.391227 ACTTAGTATTTGCAGCAAAGTGTT 57.609 33.333 24.39 11.29 36.76 3.32
64 65 6.391227 AACTTAGTATTTGCAGCAAAGTGT 57.609 33.333 24.39 11.63 36.76 3.55
65 66 6.363357 GGAAACTTAGTATTTGCAGCAAAGTG 59.637 38.462 24.39 12.83 36.76 3.16
66 67 6.040391 TGGAAACTTAGTATTTGCAGCAAAGT 59.960 34.615 24.39 13.51 36.76 2.66
67 68 6.446318 TGGAAACTTAGTATTTGCAGCAAAG 58.554 36.000 24.39 12.89 36.76 2.77
68 69 6.398234 TGGAAACTTAGTATTTGCAGCAAA 57.602 33.333 22.71 22.71 37.75 3.68
69 70 6.012658 CTGGAAACTTAGTATTTGCAGCAA 57.987 37.500 2.83 2.83 44.85 3.91
70 71 5.627499 CTGGAAACTTAGTATTTGCAGCA 57.373 39.130 5.60 0.00 44.85 4.41
73 74 5.240623 CACACCTGGAAACTTAGTATTTGCA 59.759 40.000 0.00 0.00 36.20 4.08
74 75 5.335661 CCACACCTGGAAACTTAGTATTTGC 60.336 44.000 0.00 0.00 40.55 3.68
75 76 5.768164 ACCACACCTGGAAACTTAGTATTTG 59.232 40.000 0.00 0.00 40.55 2.32
76 77 5.948842 ACCACACCTGGAAACTTAGTATTT 58.051 37.500 0.00 0.00 40.55 1.40
77 78 5.578157 ACCACACCTGGAAACTTAGTATT 57.422 39.130 0.00 0.00 40.55 1.89
78 79 5.072600 TCAACCACACCTGGAAACTTAGTAT 59.927 40.000 0.00 0.00 40.55 2.12
79 80 4.409574 TCAACCACACCTGGAAACTTAGTA 59.590 41.667 0.00 0.00 40.55 1.82
80 81 3.201266 TCAACCACACCTGGAAACTTAGT 59.799 43.478 0.00 0.00 40.55 2.24
81 82 3.815809 TCAACCACACCTGGAAACTTAG 58.184 45.455 0.00 0.00 40.55 2.18
82 83 3.935818 TCAACCACACCTGGAAACTTA 57.064 42.857 0.00 0.00 40.55 2.24
83 84 2.818751 TCAACCACACCTGGAAACTT 57.181 45.000 0.00 0.00 40.55 2.66
84 85 2.818751 TTCAACCACACCTGGAAACT 57.181 45.000 0.00 0.00 40.55 2.66
85 86 3.383185 TCAATTCAACCACACCTGGAAAC 59.617 43.478 0.00 0.00 40.55 2.78
86 87 3.383185 GTCAATTCAACCACACCTGGAAA 59.617 43.478 0.00 0.00 40.55 3.13
87 88 2.955660 GTCAATTCAACCACACCTGGAA 59.044 45.455 0.00 0.00 40.55 3.53
88 89 2.092158 TGTCAATTCAACCACACCTGGA 60.092 45.455 0.00 0.00 40.55 3.86
89 90 2.305928 TGTCAATTCAACCACACCTGG 58.694 47.619 0.00 0.00 44.26 4.45
90 91 3.381272 AGTTGTCAATTCAACCACACCTG 59.619 43.478 6.44 0.00 45.90 4.00
91 92 3.631250 AGTTGTCAATTCAACCACACCT 58.369 40.909 6.44 0.00 45.90 4.00
92 93 3.380004 TGAGTTGTCAATTCAACCACACC 59.620 43.478 8.22 0.00 45.90 4.16
93 94 4.601019 CTGAGTTGTCAATTCAACCACAC 58.399 43.478 11.44 0.00 45.90 3.82
94 95 3.066621 GCTGAGTTGTCAATTCAACCACA 59.933 43.478 11.44 6.79 45.90 4.17
95 96 3.316308 AGCTGAGTTGTCAATTCAACCAC 59.684 43.478 11.44 3.11 45.90 4.16
96 97 3.554934 AGCTGAGTTGTCAATTCAACCA 58.445 40.909 11.44 4.56 45.90 3.67
97 98 3.057946 GGAGCTGAGTTGTCAATTCAACC 60.058 47.826 11.44 10.87 45.90 3.77
98 99 3.817647 AGGAGCTGAGTTGTCAATTCAAC 59.182 43.478 11.44 7.62 45.33 3.18
99 100 4.090761 AGGAGCTGAGTTGTCAATTCAA 57.909 40.909 11.44 0.00 30.14 2.69
100 101 3.777106 AGGAGCTGAGTTGTCAATTCA 57.223 42.857 10.07 10.07 30.14 2.57
101 102 4.826556 ACTAGGAGCTGAGTTGTCAATTC 58.173 43.478 0.00 1.25 30.14 2.17
102 103 4.899352 ACTAGGAGCTGAGTTGTCAATT 57.101 40.909 0.00 0.00 30.14 2.32
103 104 5.020132 AGTACTAGGAGCTGAGTTGTCAAT 58.980 41.667 0.00 0.00 30.14 2.57
104 105 4.408276 AGTACTAGGAGCTGAGTTGTCAA 58.592 43.478 0.00 0.00 30.14 3.18
105 106 4.035612 AGTACTAGGAGCTGAGTTGTCA 57.964 45.455 0.00 0.00 0.00 3.58
106 107 4.459685 TCAAGTACTAGGAGCTGAGTTGTC 59.540 45.833 0.00 0.00 0.00 3.18
107 108 4.408276 TCAAGTACTAGGAGCTGAGTTGT 58.592 43.478 0.00 0.00 0.00 3.32
108 109 4.702612 TCTCAAGTACTAGGAGCTGAGTTG 59.297 45.833 16.01 0.00 0.00 3.16
109 110 4.924625 TCTCAAGTACTAGGAGCTGAGTT 58.075 43.478 16.01 0.00 0.00 3.01
110 111 4.577988 TCTCAAGTACTAGGAGCTGAGT 57.422 45.455 16.01 0.00 0.00 3.41
111 112 7.759489 ATATTCTCAAGTACTAGGAGCTGAG 57.241 40.000 16.05 14.09 0.00 3.35
112 113 8.001875 AGAATATTCTCAAGTACTAGGAGCTGA 58.998 37.037 12.37 6.16 29.94 4.26
113 114 8.177119 AGAATATTCTCAAGTACTAGGAGCTG 57.823 38.462 12.37 2.28 29.94 4.24
114 115 8.776061 AAGAATATTCTCAAGTACTAGGAGCT 57.224 34.615 18.19 10.25 36.28 4.09
115 116 9.255304 CAAAGAATATTCTCAAGTACTAGGAGC 57.745 37.037 18.19 5.12 36.28 4.70
116 117 9.757227 CCAAAGAATATTCTCAAGTACTAGGAG 57.243 37.037 18.19 15.12 36.28 3.69
117 118 8.204836 GCCAAAGAATATTCTCAAGTACTAGGA 58.795 37.037 18.19 0.00 36.28 2.94
118 119 8.207545 AGCCAAAGAATATTCTCAAGTACTAGG 58.792 37.037 18.19 10.30 36.28 3.02
119 120 9.255304 GAGCCAAAGAATATTCTCAAGTACTAG 57.745 37.037 18.19 0.00 36.28 2.57
120 121 8.204836 GGAGCCAAAGAATATTCTCAAGTACTA 58.795 37.037 18.19 0.00 36.28 1.82
121 122 7.051000 GGAGCCAAAGAATATTCTCAAGTACT 58.949 38.462 18.19 10.93 36.28 2.73
122 123 6.261158 GGGAGCCAAAGAATATTCTCAAGTAC 59.739 42.308 18.19 9.09 36.28 2.73
123 124 6.357367 GGGAGCCAAAGAATATTCTCAAGTA 58.643 40.000 18.19 0.00 36.28 2.24
124 125 5.196695 GGGAGCCAAAGAATATTCTCAAGT 58.803 41.667 18.19 0.00 36.28 3.16
125 126 4.582240 GGGGAGCCAAAGAATATTCTCAAG 59.418 45.833 18.19 10.54 36.28 3.02
126 127 4.230502 AGGGGAGCCAAAGAATATTCTCAA 59.769 41.667 18.19 0.00 36.28 3.02
127 128 3.788142 AGGGGAGCCAAAGAATATTCTCA 59.212 43.478 18.19 0.00 36.28 3.27
128 129 4.393834 GAGGGGAGCCAAAGAATATTCTC 58.606 47.826 18.19 6.14 36.28 2.87
129 130 3.181450 CGAGGGGAGCCAAAGAATATTCT 60.181 47.826 12.37 12.37 39.74 2.40
130 131 3.142174 CGAGGGGAGCCAAAGAATATTC 58.858 50.000 7.41 7.41 0.00 1.75
131 132 2.509964 ACGAGGGGAGCCAAAGAATATT 59.490 45.455 0.00 0.00 0.00 1.28
132 133 2.127708 ACGAGGGGAGCCAAAGAATAT 58.872 47.619 0.00 0.00 0.00 1.28
133 134 1.209504 CACGAGGGGAGCCAAAGAATA 59.790 52.381 0.00 0.00 0.00 1.75
134 135 0.035056 CACGAGGGGAGCCAAAGAAT 60.035 55.000 0.00 0.00 0.00 2.40
135 136 1.374947 CACGAGGGGAGCCAAAGAA 59.625 57.895 0.00 0.00 0.00 2.52
136 137 1.827399 GACACGAGGGGAGCCAAAGA 61.827 60.000 0.00 0.00 0.00 2.52
137 138 1.376037 GACACGAGGGGAGCCAAAG 60.376 63.158 0.00 0.00 0.00 2.77
138 139 2.747686 GACACGAGGGGAGCCAAA 59.252 61.111 0.00 0.00 0.00 3.28
139 140 3.691342 CGACACGAGGGGAGCCAA 61.691 66.667 0.00 0.00 0.00 4.52
140 141 4.671590 TCGACACGAGGGGAGCCA 62.672 66.667 0.00 0.00 0.00 4.75
141 142 2.630592 GATTCGACACGAGGGGAGCC 62.631 65.000 0.00 0.00 37.14 4.70
142 143 1.227002 GATTCGACACGAGGGGAGC 60.227 63.158 0.00 0.00 37.14 4.70
143 144 0.530744 TTGATTCGACACGAGGGGAG 59.469 55.000 0.00 0.00 37.14 4.30
144 145 1.191535 ATTGATTCGACACGAGGGGA 58.808 50.000 0.00 0.00 37.14 4.81
145 146 2.882927 TATTGATTCGACACGAGGGG 57.117 50.000 0.00 0.00 37.14 4.79
146 147 5.734855 AATTTATTGATTCGACACGAGGG 57.265 39.130 0.00 0.00 37.14 4.30
147 148 5.965334 CCAAATTTATTGATTCGACACGAGG 59.035 40.000 0.00 0.00 37.14 4.63
148 149 5.965334 CCCAAATTTATTGATTCGACACGAG 59.035 40.000 0.00 0.00 37.14 4.18
149 150 5.413213 ACCCAAATTTATTGATTCGACACGA 59.587 36.000 0.00 0.00 0.00 4.35
150 151 5.636837 ACCCAAATTTATTGATTCGACACG 58.363 37.500 0.00 0.00 0.00 4.49
151 152 7.087639 TCAACCCAAATTTATTGATTCGACAC 58.912 34.615 7.33 0.00 0.00 3.67
152 153 7.220741 TCAACCCAAATTTATTGATTCGACA 57.779 32.000 7.33 0.00 0.00 4.35
153 154 8.702163 ATTCAACCCAAATTTATTGATTCGAC 57.298 30.769 10.73 0.00 31.45 4.20
154 155 9.796120 GTATTCAACCCAAATTTATTGATTCGA 57.204 29.630 10.73 0.00 31.45 3.71
155 156 9.801873 AGTATTCAACCCAAATTTATTGATTCG 57.198 29.630 10.73 0.00 31.45 3.34
171 172 4.996788 TTCGAGGGTAGAGTATTCAACC 57.003 45.455 0.00 0.00 0.00 3.77
172 173 6.310711 CAGTTTTCGAGGGTAGAGTATTCAAC 59.689 42.308 0.00 0.00 0.00 3.18
173 174 6.014840 ACAGTTTTCGAGGGTAGAGTATTCAA 60.015 38.462 0.00 0.00 0.00 2.69
174 175 5.479375 ACAGTTTTCGAGGGTAGAGTATTCA 59.521 40.000 0.00 0.00 0.00 2.57
175 176 5.963594 ACAGTTTTCGAGGGTAGAGTATTC 58.036 41.667 0.00 0.00 0.00 1.75
176 177 5.997384 ACAGTTTTCGAGGGTAGAGTATT 57.003 39.130 0.00 0.00 0.00 1.89
177 178 5.721232 CAACAGTTTTCGAGGGTAGAGTAT 58.279 41.667 0.00 0.00 0.00 2.12
178 179 4.560108 GCAACAGTTTTCGAGGGTAGAGTA 60.560 45.833 0.00 0.00 0.00 2.59
179 180 3.802675 GCAACAGTTTTCGAGGGTAGAGT 60.803 47.826 0.00 0.00 0.00 3.24
180 181 2.737252 GCAACAGTTTTCGAGGGTAGAG 59.263 50.000 0.00 0.00 0.00 2.43
181 182 2.762745 GCAACAGTTTTCGAGGGTAGA 58.237 47.619 0.00 0.00 0.00 2.59
182 183 1.459592 CGCAACAGTTTTCGAGGGTAG 59.540 52.381 0.00 0.00 0.00 3.18
183 184 1.068895 TCGCAACAGTTTTCGAGGGTA 59.931 47.619 3.87 0.00 0.00 3.69
184 185 0.179067 TCGCAACAGTTTTCGAGGGT 60.179 50.000 3.87 0.00 0.00 4.34
185 186 1.128692 GATCGCAACAGTTTTCGAGGG 59.871 52.381 11.65 0.00 34.30 4.30
186 187 1.128692 GGATCGCAACAGTTTTCGAGG 59.871 52.381 11.65 0.00 34.30 4.63
187 188 1.128692 GGGATCGCAACAGTTTTCGAG 59.871 52.381 4.64 0.00 34.30 4.04
188 189 1.153353 GGGATCGCAACAGTTTTCGA 58.847 50.000 4.64 9.18 35.34 3.71
189 190 0.168128 GGGGATCGCAACAGTTTTCG 59.832 55.000 12.32 0.00 0.00 3.46
190 191 1.534729 AGGGGATCGCAACAGTTTTC 58.465 50.000 12.32 0.00 0.00 2.29
191 192 2.871096 TAGGGGATCGCAACAGTTTT 57.129 45.000 12.32 0.00 0.00 2.43
192 193 3.454812 AGTATAGGGGATCGCAACAGTTT 59.545 43.478 12.32 0.00 0.00 2.66
193 194 3.039011 AGTATAGGGGATCGCAACAGTT 58.961 45.455 12.32 0.00 0.00 3.16
194 195 2.679082 AGTATAGGGGATCGCAACAGT 58.321 47.619 12.32 0.00 0.00 3.55
195 196 3.181465 ACAAGTATAGGGGATCGCAACAG 60.181 47.826 12.32 4.14 0.00 3.16
196 197 2.769663 ACAAGTATAGGGGATCGCAACA 59.230 45.455 12.32 0.00 0.00 3.33
197 198 3.131396 CACAAGTATAGGGGATCGCAAC 58.869 50.000 12.32 4.19 0.00 4.17
198 199 2.104111 CCACAAGTATAGGGGATCGCAA 59.896 50.000 12.32 0.00 0.00 4.85
199 200 1.691976 CCACAAGTATAGGGGATCGCA 59.308 52.381 12.32 0.00 0.00 5.10
200 201 1.002087 CCCACAAGTATAGGGGATCGC 59.998 57.143 0.06 0.06 43.57 4.58
207 208 5.479306 CGGATGATAACCCACAAGTATAGG 58.521 45.833 0.00 0.00 0.00 2.57
208 209 4.929808 GCGGATGATAACCCACAAGTATAG 59.070 45.833 0.00 0.00 0.00 1.31
209 210 4.559906 CGCGGATGATAACCCACAAGTATA 60.560 45.833 0.00 0.00 0.00 1.47
210 211 3.740115 GCGGATGATAACCCACAAGTAT 58.260 45.455 0.00 0.00 0.00 2.12
211 212 2.482316 CGCGGATGATAACCCACAAGTA 60.482 50.000 0.00 0.00 0.00 2.24
212 213 1.742411 CGCGGATGATAACCCACAAGT 60.742 52.381 0.00 0.00 0.00 3.16
213 214 0.937304 CGCGGATGATAACCCACAAG 59.063 55.000 0.00 0.00 0.00 3.16
214 215 1.092921 GCGCGGATGATAACCCACAA 61.093 55.000 8.83 0.00 0.00 3.33
215 216 1.522806 GCGCGGATGATAACCCACA 60.523 57.895 8.83 0.00 0.00 4.17
216 217 2.594962 CGCGCGGATGATAACCCAC 61.595 63.158 24.84 0.00 0.00 4.61
217 218 2.279851 CGCGCGGATGATAACCCA 60.280 61.111 24.84 0.00 0.00 4.51
218 219 3.712881 GCGCGCGGATGATAACCC 61.713 66.667 33.06 6.44 0.00 4.11
219 220 3.712881 GGCGCGCGGATGATAACC 61.713 66.667 33.06 17.57 0.00 2.85
220 221 4.059459 CGGCGCGCGGATGATAAC 62.059 66.667 32.05 11.83 0.00 1.89
221 222 3.196913 TACGGCGCGCGGATGATAA 62.197 57.895 39.84 17.25 0.00 1.75
222 223 3.604494 CTACGGCGCGCGGATGATA 62.604 63.158 39.84 22.56 0.00 2.15
405 406 2.180159 AACCCTAGTGCCGCATCGTT 62.180 55.000 0.00 0.00 0.00 3.85
406 407 2.180159 AAACCCTAGTGCCGCATCGT 62.180 55.000 0.00 0.00 0.00 3.73
407 408 1.024579 AAAACCCTAGTGCCGCATCG 61.025 55.000 0.00 0.00 0.00 3.84
408 409 0.733150 GAAAACCCTAGTGCCGCATC 59.267 55.000 0.00 0.00 0.00 3.91
409 410 0.679960 GGAAAACCCTAGTGCCGCAT 60.680 55.000 0.00 0.00 0.00 4.73
410 411 1.302993 GGAAAACCCTAGTGCCGCA 60.303 57.895 0.00 0.00 0.00 5.69
412 413 0.906775 TAGGGAAAACCCTAGTGCCG 59.093 55.000 10.55 0.00 41.63 5.69
423 424 0.669318 CGCAGTGACGCTAGGGAAAA 60.669 55.000 14.59 0.00 0.00 2.29
424 425 1.080093 CGCAGTGACGCTAGGGAAA 60.080 57.895 14.59 0.00 0.00 3.13
425 426 2.273179 ACGCAGTGACGCTAGGGAA 61.273 57.895 14.59 0.00 42.51 3.97
426 427 2.675423 ACGCAGTGACGCTAGGGA 60.675 61.111 14.59 0.00 42.51 4.20
443 444 4.334118 ATGTGCTGCTCGGCCACA 62.334 61.111 2.24 0.00 0.00 4.17
444 445 3.807538 CATGTGCTGCTCGGCCAC 61.808 66.667 2.24 0.00 0.00 5.01
615 628 4.404654 GCAAAGAACCCCGCGCAG 62.405 66.667 8.75 0.00 0.00 5.18
679 694 7.667219 CAGGGGCTTCTACATGAAATATTACAT 59.333 37.037 0.00 0.00 33.79 2.29
692 708 0.984230 CAGTTCCAGGGGCTTCTACA 59.016 55.000 0.00 0.00 0.00 2.74
1395 1414 1.405872 TCTCAGTACCACACAACCGT 58.594 50.000 0.00 0.00 0.00 4.83
1507 1526 2.285220 CGCCAATCAACTCTGAATACCG 59.715 50.000 0.00 0.00 34.49 4.02
1644 1663 1.303643 CTTGCGGCCCCTCTTCTTT 60.304 57.895 0.00 0.00 0.00 2.52
1701 1725 1.600636 CTTGCCCGGCTTGTTCTGA 60.601 57.895 11.61 0.00 0.00 3.27
1836 1860 0.535102 CTTGAACCAAGGCGAGGTGT 60.535 55.000 4.67 0.00 39.86 4.16
2581 2611 4.585955 AAGCTCAAAAGAGTACGAGTCA 57.414 40.909 0.00 0.00 0.00 3.41
2616 2646 4.265073 GTCTCAGCATGGAAACCATTAGT 58.735 43.478 0.11 0.00 42.23 2.24
2680 2710 0.623723 ATGTTTACCACCGGCATCCT 59.376 50.000 0.00 0.00 0.00 3.24
2712 2742 2.504367 CCCTGTGTCAAACGAAGGAAT 58.496 47.619 0.00 0.00 0.00 3.01
2740 2770 4.575236 CGGACAGTGCTACTATCTTAGTGA 59.425 45.833 0.00 0.00 39.81 3.41
2760 2790 3.693085 GTCTTGAGGATAGTGTACACGGA 59.307 47.826 19.93 12.72 36.20 4.69
2773 2803 3.056749 GCTTCTAAAGACGGTCTTGAGGA 60.057 47.826 27.42 21.35 35.95 3.71
3051 3082 2.147958 GCACCATGAAGTACCGAAACA 58.852 47.619 0.00 0.00 0.00 2.83
3099 3130 1.135141 GTGTTGACAGCAGGCAAACAA 60.135 47.619 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.