Multiple sequence alignment - TraesCS1A01G323800

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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 TraesCS1A01G323800 chr1A 100.000 2905 0 0 1 2905 514548684 514551588 0.000000e+00 5365.0
1 TraesCS1A01G323800 chr1A 79.507 527 71 23 1297 1814 566590688 566590190 9.970000e-90 340.0
2 TraesCS1A01G323800 chr1B 92.238 2538 116 37 380 2904 564160743 564163212 0.000000e+00 3520.0
3 TraesCS1A01G323800 chr1B 94.017 234 13 1 1 234 144911884 144912116 1.280000e-93 353.0
4 TraesCS1A01G323800 chr1B 92.208 77 5 1 235 311 564160654 564160729 1.100000e-19 108.0
5 TraesCS1A01G323800 chr1B 95.122 41 2 0 311 351 371144332 371144372 6.720000e-07 65.8
6 TraesCS1A01G323800 chr1B 97.143 35 1 0 371 405 659980090 659980056 3.130000e-05 60.2
7 TraesCS1A01G323800 chr1D 91.304 1541 45 30 385 1901 417572192 417573667 0.000000e+00 2021.0
8 TraesCS1A01G323800 chr1D 91.390 964 47 19 1945 2904 417573674 417574605 0.000000e+00 1288.0
9 TraesCS1A01G323800 chr1D 94.118 119 6 1 234 352 417572074 417572191 2.300000e-41 180.0
10 TraesCS1A01G323800 chrUn 88.701 354 24 10 1925 2277 240128390 240128728 4.480000e-113 418.0
11 TraesCS1A01G323800 chrUn 88.857 350 24 9 1925 2274 435744592 435744926 1.610000e-112 416.0
12 TraesCS1A01G323800 chr2B 88.701 354 24 10 1925 2277 77876766 77877104 4.480000e-113 418.0
13 TraesCS1A01G323800 chr2B 93.617 235 14 1 1 235 763343699 763343932 1.660000e-92 350.0
14 TraesCS1A01G323800 chr2B 90.588 85 6 2 1670 1752 331027359 331027275 8.510000e-21 111.0
15 TraesCS1A01G323800 chr4B 88.418 354 25 10 1925 2277 517726651 517726313 2.080000e-111 412.0
16 TraesCS1A01G323800 chr3B 88.136 354 26 8 1925 2277 170507609 170507271 9.690000e-110 407.0
17 TraesCS1A01G323800 chr5B 87.853 354 27 10 1925 2277 140516962 140517300 4.510000e-108 401.0
18 TraesCS1A01G323800 chr5A 87.853 354 27 10 1925 2277 88286003 88286341 4.510000e-108 401.0
19 TraesCS1A01G323800 chr5A 95.217 230 9 2 5 234 2341282 2341055 2.130000e-96 363.0
20 TraesCS1A01G323800 chr5A 87.255 102 13 0 1646 1747 66049193 66049294 1.830000e-22 117.0
21 TraesCS1A01G323800 chr5A 87.037 54 7 0 356 409 567930757 567930810 8.690000e-06 62.1
22 TraesCS1A01G323800 chr6B 87.571 354 28 9 1925 2277 407595089 407595427 2.100000e-106 396.0
23 TraesCS1A01G323800 chr6B 87.571 354 28 10 1925 2277 418246346 418246684 2.100000e-106 396.0
24 TraesCS1A01G323800 chr6B 87.006 354 30 8 1925 2277 91905162 91904824 4.540000e-103 385.0
25 TraesCS1A01G323800 chr2A 95.763 236 9 1 1 236 38817108 38816874 2.110000e-101 379.0
26 TraesCS1A01G323800 chr2A 94.444 234 12 1 1 234 702181933 702181701 2.750000e-95 359.0
27 TraesCS1A01G323800 chr2A 92.181 243 15 4 2 242 504051425 504051185 9.970000e-90 340.0
28 TraesCS1A01G323800 chr2A 92.116 241 17 2 1 241 104403651 104403889 3.590000e-89 339.0
29 TraesCS1A01G323800 chr2A 78.867 459 59 19 2424 2856 733432049 733431603 2.850000e-70 276.0
30 TraesCS1A01G323800 chr7A 95.000 240 9 3 1 240 116531383 116531147 9.830000e-100 374.0
31 TraesCS1A01G323800 chr4A 94.468 235 12 1 1 235 715967301 715967534 7.650000e-96 361.0
32 TraesCS1A01G323800 chr2D 78.867 459 65 21 2424 2856 493194629 493195081 6.130000e-72 281.0
33 TraesCS1A01G323800 chr7D 91.139 79 7 0 1669 1747 326034627 326034705 1.100000e-19 108.0
34 TraesCS1A01G323800 chr3A 96.970 33 1 0 377 409 683539948 683539916 4.040000e-04 56.5


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 TraesCS1A01G323800 chr1A 514548684 514551588 2904 False 5365 5365 100.000000 1 2905 1 chr1A.!!$F1 2904
1 TraesCS1A01G323800 chr1B 564160654 564163212 2558 False 1814 3520 92.223000 235 2904 2 chr1B.!!$F3 2669
2 TraesCS1A01G323800 chr1D 417572074 417574605 2531 False 1163 2021 92.270667 234 2904 3 chr1D.!!$F1 2670

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
477 478 0.036875 CTGTTCTGTTGGTCCCCTCC 59.963 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2359 0.035458 CCTCGCCTCTCCTTGTTGTT 59.965 55.0 0.0 0.0 0.0 2.83 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
25 26 4.092116 GGGAGATTTTCTACCCTCATGG 57.908 50.000 0.00 0.00 41.88 3.66
26 27 3.716872 GGGAGATTTTCTACCCTCATGGA 59.283 47.826 0.00 0.00 41.88 3.41
27 28 4.352298 GGGAGATTTTCTACCCTCATGGAT 59.648 45.833 0.00 0.00 41.88 3.41
28 29 5.312079 GGAGATTTTCTACCCTCATGGATG 58.688 45.833 0.00 0.00 38.00 3.51
29 30 5.312079 GAGATTTTCTACCCTCATGGATGG 58.688 45.833 0.00 0.00 38.00 3.51
30 31 3.297134 TTTTCTACCCTCATGGATGGC 57.703 47.619 0.00 0.00 38.00 4.40
31 32 0.758734 TTCTACCCTCATGGATGGCG 59.241 55.000 0.00 0.00 38.00 5.69
32 33 1.121407 TCTACCCTCATGGATGGCGG 61.121 60.000 0.00 0.00 38.00 6.13
33 34 1.383943 TACCCTCATGGATGGCGGT 60.384 57.895 0.00 0.00 38.00 5.68
34 35 1.695114 TACCCTCATGGATGGCGGTG 61.695 60.000 0.00 0.00 38.00 4.94
35 36 2.591753 CCTCATGGATGGCGGTGT 59.408 61.111 0.00 0.00 34.57 4.16
36 37 1.820906 CCTCATGGATGGCGGTGTG 60.821 63.158 0.00 0.00 34.57 3.82
37 38 1.221566 CTCATGGATGGCGGTGTGA 59.778 57.895 0.00 0.00 0.00 3.58
38 39 0.179037 CTCATGGATGGCGGTGTGAT 60.179 55.000 0.00 0.00 0.00 3.06
39 40 0.179048 TCATGGATGGCGGTGTGATC 60.179 55.000 0.00 0.00 0.00 2.92
40 41 0.179037 CATGGATGGCGGTGTGATCT 60.179 55.000 0.00 0.00 0.00 2.75
41 42 0.548031 ATGGATGGCGGTGTGATCTT 59.452 50.000 0.00 0.00 0.00 2.40
42 43 0.107703 TGGATGGCGGTGTGATCTTC 60.108 55.000 0.00 0.00 0.00 2.87
43 44 1.154205 GGATGGCGGTGTGATCTTCG 61.154 60.000 0.00 0.00 0.00 3.79
44 45 1.153369 ATGGCGGTGTGATCTTCGG 60.153 57.895 0.00 0.00 0.00 4.30
45 46 1.613317 ATGGCGGTGTGATCTTCGGA 61.613 55.000 0.00 0.00 0.00 4.55
46 47 1.144057 GGCGGTGTGATCTTCGGAT 59.856 57.895 0.00 0.00 37.39 4.18
47 48 0.387929 GGCGGTGTGATCTTCGGATA 59.612 55.000 0.00 0.00 34.38 2.59
48 49 1.603172 GGCGGTGTGATCTTCGGATAG 60.603 57.143 0.00 0.00 34.38 2.08
49 50 1.603172 GCGGTGTGATCTTCGGATAGG 60.603 57.143 0.00 0.00 34.38 2.57
50 51 1.954382 CGGTGTGATCTTCGGATAGGA 59.046 52.381 0.00 0.00 34.38 2.94
51 52 2.558795 CGGTGTGATCTTCGGATAGGAT 59.441 50.000 0.00 0.00 34.38 3.24
52 53 3.366476 CGGTGTGATCTTCGGATAGGATC 60.366 52.174 0.00 0.00 37.11 3.36
53 54 3.574396 GGTGTGATCTTCGGATAGGATCA 59.426 47.826 11.87 11.87 42.06 2.92
54 55 4.321601 GGTGTGATCTTCGGATAGGATCAG 60.322 50.000 14.59 0.00 43.98 2.90
55 56 3.256879 TGTGATCTTCGGATAGGATCAGC 59.743 47.826 14.59 11.52 43.98 4.26
56 57 3.509575 GTGATCTTCGGATAGGATCAGCT 59.490 47.826 14.59 0.00 43.98 4.24
57 58 3.761218 TGATCTTCGGATAGGATCAGCTC 59.239 47.826 11.87 0.00 40.26 4.09
58 59 2.520069 TCTTCGGATAGGATCAGCTCC 58.480 52.381 0.00 0.00 45.33 4.70
71 72 2.557920 CAGCTCCTTTATAGGCTGGG 57.442 55.000 0.00 0.00 45.59 4.45
72 73 0.767998 AGCTCCTTTATAGGCTGGGC 59.232 55.000 0.00 0.00 41.69 5.36
73 74 0.767998 GCTCCTTTATAGGCTGGGCT 59.232 55.000 0.00 1.68 41.69 5.19
74 75 1.143889 GCTCCTTTATAGGCTGGGCTT 59.856 52.381 0.00 0.00 41.69 4.35
75 76 2.423517 GCTCCTTTATAGGCTGGGCTTT 60.424 50.000 0.00 0.00 41.69 3.51
76 77 3.181443 GCTCCTTTATAGGCTGGGCTTTA 60.181 47.826 0.00 0.00 41.69 1.85
77 78 4.507512 GCTCCTTTATAGGCTGGGCTTTAT 60.508 45.833 0.00 0.00 41.69 1.40
78 79 5.635120 CTCCTTTATAGGCTGGGCTTTATT 58.365 41.667 0.00 0.00 41.69 1.40
79 80 6.025793 TCCTTTATAGGCTGGGCTTTATTT 57.974 37.500 0.00 0.00 41.69 1.40
80 81 7.156694 TCCTTTATAGGCTGGGCTTTATTTA 57.843 36.000 0.00 0.00 41.69 1.40
81 82 7.765622 TCCTTTATAGGCTGGGCTTTATTTAT 58.234 34.615 0.00 0.00 41.69 1.40
82 83 7.888546 TCCTTTATAGGCTGGGCTTTATTTATC 59.111 37.037 0.00 0.00 41.69 1.75
83 84 7.890655 CCTTTATAGGCTGGGCTTTATTTATCT 59.109 37.037 0.00 0.00 33.99 1.98
84 85 9.301897 CTTTATAGGCTGGGCTTTATTTATCTT 57.698 33.333 0.00 0.00 0.00 2.40
85 86 9.654919 TTTATAGGCTGGGCTTTATTTATCTTT 57.345 29.630 0.00 0.00 0.00 2.52
86 87 5.859205 AGGCTGGGCTTTATTTATCTTTG 57.141 39.130 0.00 0.00 0.00 2.77
87 88 4.100035 AGGCTGGGCTTTATTTATCTTTGC 59.900 41.667 0.00 0.00 0.00 3.68
88 89 4.100035 GGCTGGGCTTTATTTATCTTTGCT 59.900 41.667 0.00 0.00 0.00 3.91
89 90 5.395657 GGCTGGGCTTTATTTATCTTTGCTT 60.396 40.000 0.00 0.00 0.00 3.91
90 91 5.750547 GCTGGGCTTTATTTATCTTTGCTTC 59.249 40.000 0.00 0.00 0.00 3.86
91 92 6.406288 GCTGGGCTTTATTTATCTTTGCTTCT 60.406 38.462 0.00 0.00 0.00 2.85
92 93 6.866480 TGGGCTTTATTTATCTTTGCTTCTG 58.134 36.000 0.00 0.00 0.00 3.02
93 94 6.127366 TGGGCTTTATTTATCTTTGCTTCTGG 60.127 38.462 0.00 0.00 0.00 3.86
94 95 5.750547 GGCTTTATTTATCTTTGCTTCTGGC 59.249 40.000 0.00 0.00 42.22 4.85
95 96 6.406288 GGCTTTATTTATCTTTGCTTCTGGCT 60.406 38.462 0.00 0.00 42.39 4.75
96 97 7.038048 GCTTTATTTATCTTTGCTTCTGGCTT 58.962 34.615 0.00 0.00 42.39 4.35
97 98 7.547019 GCTTTATTTATCTTTGCTTCTGGCTTT 59.453 33.333 0.00 0.00 42.39 3.51
98 99 9.428097 CTTTATTTATCTTTGCTTCTGGCTTTT 57.572 29.630 0.00 0.00 42.39 2.27
99 100 8.761575 TTATTTATCTTTGCTTCTGGCTTTTG 57.238 30.769 0.00 0.00 42.39 2.44
100 101 3.672767 ATCTTTGCTTCTGGCTTTTGG 57.327 42.857 0.00 0.00 42.39 3.28
101 102 1.069049 TCTTTGCTTCTGGCTTTTGGC 59.931 47.619 0.00 0.00 46.23 4.52
114 115 3.908213 GCTTTTGGCCAGTTTATTTCGA 58.092 40.909 5.11 0.00 34.27 3.71
115 116 4.494484 GCTTTTGGCCAGTTTATTTCGAT 58.506 39.130 5.11 0.00 34.27 3.59
116 117 4.562789 GCTTTTGGCCAGTTTATTTCGATC 59.437 41.667 5.11 0.00 34.27 3.69
117 118 5.622233 GCTTTTGGCCAGTTTATTTCGATCT 60.622 40.000 5.11 0.00 34.27 2.75
118 119 5.975693 TTTGGCCAGTTTATTTCGATCTT 57.024 34.783 5.11 0.00 0.00 2.40
119 120 5.975693 TTGGCCAGTTTATTTCGATCTTT 57.024 34.783 5.11 0.00 0.00 2.52
120 121 7.455641 TTTGGCCAGTTTATTTCGATCTTTA 57.544 32.000 5.11 0.00 0.00 1.85
121 122 6.431198 TGGCCAGTTTATTTCGATCTTTAC 57.569 37.500 0.00 0.00 0.00 2.01
122 123 6.177610 TGGCCAGTTTATTTCGATCTTTACT 58.822 36.000 0.00 0.00 0.00 2.24
123 124 6.657541 TGGCCAGTTTATTTCGATCTTTACTT 59.342 34.615 0.00 0.00 0.00 2.24
124 125 7.148306 TGGCCAGTTTATTTCGATCTTTACTTC 60.148 37.037 0.00 0.00 0.00 3.01
125 126 7.065923 GGCCAGTTTATTTCGATCTTTACTTCT 59.934 37.037 0.00 0.00 0.00 2.85
126 127 8.451748 GCCAGTTTATTTCGATCTTTACTTCTT 58.548 33.333 0.00 0.00 0.00 2.52
137 138 9.677567 TCGATCTTTACTTCTTTGAATTTTTGG 57.322 29.630 0.00 0.00 0.00 3.28
138 139 8.427774 CGATCTTTACTTCTTTGAATTTTTGGC 58.572 33.333 0.00 0.00 0.00 4.52
139 140 9.481340 GATCTTTACTTCTTTGAATTTTTGGCT 57.519 29.630 0.00 0.00 0.00 4.75
140 141 8.647143 TCTTTACTTCTTTGAATTTTTGGCTG 57.353 30.769 0.00 0.00 0.00 4.85
141 142 8.257306 TCTTTACTTCTTTGAATTTTTGGCTGT 58.743 29.630 0.00 0.00 0.00 4.40
142 143 7.769272 TTACTTCTTTGAATTTTTGGCTGTG 57.231 32.000 0.00 0.00 0.00 3.66
143 144 5.733676 ACTTCTTTGAATTTTTGGCTGTGT 58.266 33.333 0.00 0.00 0.00 3.72
144 145 5.581874 ACTTCTTTGAATTTTTGGCTGTGTG 59.418 36.000 0.00 0.00 0.00 3.82
145 146 3.870419 TCTTTGAATTTTTGGCTGTGTGC 59.130 39.130 0.00 0.00 41.94 4.57
146 147 2.975732 TGAATTTTTGGCTGTGTGCA 57.024 40.000 0.00 0.00 45.15 4.57
147 148 3.472283 TGAATTTTTGGCTGTGTGCAT 57.528 38.095 0.00 0.00 45.15 3.96
148 149 3.391965 TGAATTTTTGGCTGTGTGCATC 58.608 40.909 0.00 0.00 45.15 3.91
149 150 3.069872 TGAATTTTTGGCTGTGTGCATCT 59.930 39.130 0.00 0.00 45.15 2.90
150 151 4.280425 TGAATTTTTGGCTGTGTGCATCTA 59.720 37.500 0.00 0.00 45.15 1.98
151 152 3.921119 TTTTTGGCTGTGTGCATCTAG 57.079 42.857 0.00 0.00 45.15 2.43
152 153 2.566833 TTTGGCTGTGTGCATCTAGT 57.433 45.000 0.00 0.00 45.15 2.57
153 154 2.566833 TTGGCTGTGTGCATCTAGTT 57.433 45.000 0.00 0.00 45.15 2.24
154 155 3.694043 TTGGCTGTGTGCATCTAGTTA 57.306 42.857 0.00 0.00 45.15 2.24
155 156 3.912496 TGGCTGTGTGCATCTAGTTAT 57.088 42.857 0.00 0.00 45.15 1.89
156 157 3.534554 TGGCTGTGTGCATCTAGTTATG 58.465 45.455 0.00 0.00 45.15 1.90
157 158 3.055167 TGGCTGTGTGCATCTAGTTATGT 60.055 43.478 0.00 0.00 45.15 2.29
158 159 4.161377 TGGCTGTGTGCATCTAGTTATGTA 59.839 41.667 0.00 0.00 45.15 2.29
159 160 4.747108 GGCTGTGTGCATCTAGTTATGTAG 59.253 45.833 0.00 0.00 45.15 2.74
160 161 5.451937 GGCTGTGTGCATCTAGTTATGTAGA 60.452 44.000 0.00 0.00 45.15 2.59
161 162 5.689514 GCTGTGTGCATCTAGTTATGTAGAG 59.310 44.000 0.00 0.00 42.31 2.43
162 163 6.149129 TGTGTGCATCTAGTTATGTAGAGG 57.851 41.667 0.00 0.00 34.58 3.69
163 164 5.656859 TGTGTGCATCTAGTTATGTAGAGGT 59.343 40.000 0.00 0.00 34.09 3.85
164 165 6.183360 TGTGTGCATCTAGTTATGTAGAGGTC 60.183 42.308 0.00 0.00 34.09 3.85
165 166 5.008712 TGTGCATCTAGTTATGTAGAGGTCG 59.991 44.000 0.00 0.00 34.09 4.79
166 167 4.519350 TGCATCTAGTTATGTAGAGGTCGG 59.481 45.833 0.00 0.00 34.09 4.79
167 168 4.082679 GCATCTAGTTATGTAGAGGTCGGG 60.083 50.000 0.00 0.00 34.09 5.14
168 169 4.785346 TCTAGTTATGTAGAGGTCGGGT 57.215 45.455 0.00 0.00 0.00 5.28
169 170 4.458397 TCTAGTTATGTAGAGGTCGGGTG 58.542 47.826 0.00 0.00 0.00 4.61
170 171 3.377253 AGTTATGTAGAGGTCGGGTGA 57.623 47.619 0.00 0.00 0.00 4.02
171 172 3.912248 AGTTATGTAGAGGTCGGGTGAT 58.088 45.455 0.00 0.00 0.00 3.06
172 173 4.287552 AGTTATGTAGAGGTCGGGTGATT 58.712 43.478 0.00 0.00 0.00 2.57
173 174 4.715297 AGTTATGTAGAGGTCGGGTGATTT 59.285 41.667 0.00 0.00 0.00 2.17
174 175 5.189145 AGTTATGTAGAGGTCGGGTGATTTT 59.811 40.000 0.00 0.00 0.00 1.82
175 176 4.569719 ATGTAGAGGTCGGGTGATTTTT 57.430 40.909 0.00 0.00 0.00 1.94
176 177 3.670625 TGTAGAGGTCGGGTGATTTTTG 58.329 45.455 0.00 0.00 0.00 2.44
177 178 3.325425 TGTAGAGGTCGGGTGATTTTTGA 59.675 43.478 0.00 0.00 0.00 2.69
178 179 3.721087 AGAGGTCGGGTGATTTTTGAT 57.279 42.857 0.00 0.00 0.00 2.57
179 180 3.347216 AGAGGTCGGGTGATTTTTGATG 58.653 45.455 0.00 0.00 0.00 3.07
180 181 1.818674 AGGTCGGGTGATTTTTGATGC 59.181 47.619 0.00 0.00 0.00 3.91
181 182 1.467374 GGTCGGGTGATTTTTGATGCG 60.467 52.381 0.00 0.00 0.00 4.73
182 183 1.466950 GTCGGGTGATTTTTGATGCGA 59.533 47.619 0.00 0.00 0.00 5.10
183 184 2.097466 GTCGGGTGATTTTTGATGCGAT 59.903 45.455 0.00 0.00 0.00 4.58
184 185 2.752354 TCGGGTGATTTTTGATGCGATT 59.248 40.909 0.00 0.00 0.00 3.34
185 186 2.853594 CGGGTGATTTTTGATGCGATTG 59.146 45.455 0.00 0.00 0.00 2.67
186 187 3.673052 CGGGTGATTTTTGATGCGATTGT 60.673 43.478 0.00 0.00 0.00 2.71
187 188 4.438065 CGGGTGATTTTTGATGCGATTGTA 60.438 41.667 0.00 0.00 0.00 2.41
188 189 5.591099 GGGTGATTTTTGATGCGATTGTAT 58.409 37.500 0.00 0.00 0.00 2.29
189 190 5.687285 GGGTGATTTTTGATGCGATTGTATC 59.313 40.000 4.16 4.16 37.68 2.24
190 191 6.264832 GGTGATTTTTGATGCGATTGTATCA 58.735 36.000 9.48 9.48 44.15 2.15
196 197 4.040445 TGATGCGATTGTATCAACTCGA 57.960 40.909 10.99 0.00 43.10 4.04
197 198 4.620982 TGATGCGATTGTATCAACTCGAT 58.379 39.130 10.99 0.00 43.10 3.59
198 199 5.768317 TGATGCGATTGTATCAACTCGATA 58.232 37.500 10.99 0.00 43.10 2.92
199 200 6.389906 TGATGCGATTGTATCAACTCGATAT 58.610 36.000 10.99 9.23 43.10 1.63
200 201 6.868339 TGATGCGATTGTATCAACTCGATATT 59.132 34.615 10.99 0.00 43.10 1.28
201 202 7.384932 TGATGCGATTGTATCAACTCGATATTT 59.615 33.333 10.99 0.00 43.10 1.40
202 203 7.105494 TGCGATTGTATCAACTCGATATTTC 57.895 36.000 13.68 0.00 38.85 2.17
203 204 6.699642 TGCGATTGTATCAACTCGATATTTCA 59.300 34.615 13.68 4.07 38.85 2.69
204 205 7.223777 TGCGATTGTATCAACTCGATATTTCAA 59.776 33.333 13.68 0.00 38.85 2.69
205 206 8.223769 GCGATTGTATCAACTCGATATTTCAAT 58.776 33.333 13.68 0.00 38.85 2.57
353 354 9.632807 AATATGAGAGCGTTTAGATCACTATTC 57.367 33.333 0.00 0.00 37.82 1.75
354 355 5.511571 TGAGAGCGTTTAGATCACTATTCG 58.488 41.667 0.00 0.00 37.82 3.34
355 356 5.066117 TGAGAGCGTTTAGATCACTATTCGT 59.934 40.000 0.00 0.00 37.82 3.85
356 357 5.892568 AGAGCGTTTAGATCACTATTCGTT 58.107 37.500 0.00 0.00 37.82 3.85
357 358 6.331061 AGAGCGTTTAGATCACTATTCGTTT 58.669 36.000 0.00 0.00 37.82 3.60
358 359 7.478322 AGAGCGTTTAGATCACTATTCGTTTA 58.522 34.615 0.00 0.00 37.82 2.01
359 360 7.644551 AGAGCGTTTAGATCACTATTCGTTTAG 59.355 37.037 0.00 0.00 37.82 1.85
360 361 7.478322 AGCGTTTAGATCACTATTCGTTTAGA 58.522 34.615 0.00 0.00 32.41 2.10
361 362 8.136165 AGCGTTTAGATCACTATTCGTTTAGAT 58.864 33.333 0.00 0.00 32.41 1.98
362 363 8.753175 GCGTTTAGATCACTATTCGTTTAGATT 58.247 33.333 0.00 0.00 32.41 2.40
409 410 8.701540 GCTTTTATATTAGTTTACGGAGAGAGC 58.298 37.037 0.00 0.00 0.00 4.09
425 426 5.105716 GGAGAGAGCATTACAGTGTAGACAA 60.106 44.000 2.68 0.00 0.00 3.18
433 434 6.924060 GCATTACAGTGTAGACAATAGTAGGG 59.076 42.308 2.68 0.00 0.00 3.53
449 450 5.731957 AGTAGGGAAAAGAGACTCTGAAC 57.268 43.478 5.55 0.42 0.00 3.18
477 478 0.036875 CTGTTCTGTTGGTCCCCTCC 59.963 60.000 0.00 0.00 0.00 4.30
478 479 1.379146 GTTCTGTTGGTCCCCTCCC 59.621 63.158 0.00 0.00 0.00 4.30
479 480 1.850755 TTCTGTTGGTCCCCTCCCC 60.851 63.158 0.00 0.00 0.00 4.81
480 481 3.339093 CTGTTGGTCCCCTCCCCC 61.339 72.222 0.00 0.00 0.00 5.40
535 543 1.600957 CAGCATGCATGGTACTACAGC 59.399 52.381 29.48 11.21 36.64 4.40
695 704 3.117888 GGAAGGTGAATTGATGAGCCCTA 60.118 47.826 0.00 0.00 0.00 3.53
706 715 5.028549 TGATGAGCCCTATGACTTTTCTC 57.971 43.478 0.00 0.00 0.00 2.87
794 809 6.655930 TCATTTTCATCTCATCTCATCCACA 58.344 36.000 0.00 0.00 0.00 4.17
806 821 3.248446 ATCCACACCAACGGACGGG 62.248 63.158 0.00 0.00 33.05 5.28
849 864 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
908 924 8.367156 ACCATTGCTGCTTATTTCTTTCTTTAA 58.633 29.630 0.00 0.00 0.00 1.52
924 940 8.721478 TCTTTCTTTAATTCTTTCTGGTCATCG 58.279 33.333 0.00 0.00 0.00 3.84
940 956 7.347485 TCTGGTCATCGATCTACCTATCCTATA 59.653 40.741 21.40 4.24 34.23 1.31
952 968 9.243762 TCTACCTATCCTATATATCTGCTTCCT 57.756 37.037 0.00 0.00 0.00 3.36
953 969 9.515226 CTACCTATCCTATATATCTGCTTCCTC 57.485 40.741 0.00 0.00 0.00 3.71
954 970 8.125042 ACCTATCCTATATATCTGCTTCCTCT 57.875 38.462 0.00 0.00 0.00 3.69
955 971 8.573975 ACCTATCCTATATATCTGCTTCCTCTT 58.426 37.037 0.00 0.00 0.00 2.85
956 972 9.077885 CCTATCCTATATATCTGCTTCCTCTTC 57.922 40.741 0.00 0.00 0.00 2.87
957 973 9.866655 CTATCCTATATATCTGCTTCCTCTTCT 57.133 37.037 0.00 0.00 0.00 2.85
959 975 8.588290 TCCTATATATCTGCTTCCTCTTCTTC 57.412 38.462 0.00 0.00 0.00 2.87
960 976 8.397957 TCCTATATATCTGCTTCCTCTTCTTCT 58.602 37.037 0.00 0.00 0.00 2.85
1033 1049 3.077484 TCTCCAATTCCAAGCAAGGAG 57.923 47.619 0.00 0.00 43.05 3.69
1072 1106 3.515286 CCATGCTTGGCCTCTGCG 61.515 66.667 3.32 0.00 38.85 5.18
1125 1159 1.449601 CGCACCTACCATCCACCAC 60.450 63.158 0.00 0.00 0.00 4.16
1126 1160 1.449601 GCACCTACCATCCACCACG 60.450 63.158 0.00 0.00 0.00 4.94
1127 1161 1.220749 CACCTACCATCCACCACGG 59.779 63.158 0.00 0.00 0.00 4.94
1128 1162 1.229400 ACCTACCATCCACCACGGT 60.229 57.895 0.00 0.00 36.79 4.83
1129 1163 0.041535 ACCTACCATCCACCACGGTA 59.958 55.000 0.00 0.00 34.12 4.02
1179 1218 1.962807 CGATGCATCTTCTCCTCCTCT 59.037 52.381 23.73 0.00 0.00 3.69
1180 1219 2.030007 CGATGCATCTTCTCCTCCTCTC 60.030 54.545 23.73 0.00 0.00 3.20
1181 1220 2.844654 TGCATCTTCTCCTCCTCTCT 57.155 50.000 0.00 0.00 0.00 3.10
1182 1221 2.665165 TGCATCTTCTCCTCCTCTCTC 58.335 52.381 0.00 0.00 0.00 3.20
1183 1222 2.244510 TGCATCTTCTCCTCCTCTCTCT 59.755 50.000 0.00 0.00 0.00 3.10
1184 1223 2.887152 GCATCTTCTCCTCCTCTCTCTC 59.113 54.545 0.00 0.00 0.00 3.20
1185 1224 3.435601 GCATCTTCTCCTCCTCTCTCTCT 60.436 52.174 0.00 0.00 0.00 3.10
1186 1225 4.392940 CATCTTCTCCTCCTCTCTCTCTC 58.607 52.174 0.00 0.00 0.00 3.20
1187 1226 3.736094 TCTTCTCCTCCTCTCTCTCTCT 58.264 50.000 0.00 0.00 0.00 3.10
1231 1274 0.245266 TGCATGTGCTTGGCTCATTG 59.755 50.000 6.55 3.28 40.13 2.82
1511 1554 2.499685 GAGGTCTACGCCGCCAAT 59.500 61.111 0.00 0.00 0.00 3.16
1833 1876 1.366366 CACCAAACCGGACGACTCT 59.634 57.895 9.46 0.00 38.63 3.24
1861 1904 1.145738 AGACACATCCTTTGCCTTGGT 59.854 47.619 0.00 0.00 0.00 3.67
1880 1923 2.101415 GGTTGCTTCCACTCTGCTTTTT 59.899 45.455 0.00 0.00 0.00 1.94
1892 1935 2.039084 TCTGCTTTTTCTCCTCCAGTCC 59.961 50.000 0.00 0.00 0.00 3.85
1911 1954 6.278363 CAGTCCAGTCTAGTCTAGTCTAGTC 58.722 48.000 19.35 15.30 38.66 2.59
1912 1955 6.097839 CAGTCCAGTCTAGTCTAGTCTAGTCT 59.902 46.154 19.35 16.89 38.66 3.24
1913 1956 7.286087 CAGTCCAGTCTAGTCTAGTCTAGTCTA 59.714 44.444 19.35 11.76 38.66 2.59
1915 1958 7.286316 GTCCAGTCTAGTCTAGTCTAGTCTAGT 59.714 44.444 26.77 14.87 41.87 2.57
1916 1959 7.503566 TCCAGTCTAGTCTAGTCTAGTCTAGTC 59.496 44.444 26.77 23.47 41.87 2.59
1919 1962 9.790344 AGTCTAGTCTAGTCTAGTCTAGTCTAG 57.210 40.741 29.89 29.89 46.00 2.43
1920 1963 9.566432 GTCTAGTCTAGTCTAGTCTAGTCTAGT 57.434 40.741 31.66 18.46 45.51 2.57
1948 1991 6.710744 AGTCTGTACCAACTGAATTGTTAAGG 59.289 38.462 0.00 0.00 36.47 2.69
1964 2007 1.258445 AAGGTAGCAGAGACACCCCG 61.258 60.000 0.00 0.00 32.43 5.73
1971 2014 0.905357 CAGAGACACCCCGGAAGATT 59.095 55.000 0.73 0.00 0.00 2.40
1984 2027 5.773680 CCCCGGAAGATTCTAGTATTACTCA 59.226 44.000 0.73 0.00 0.00 3.41
2013 2056 9.462174 CTTGTAATTTTGCTATTCAAACAGTCA 57.538 29.630 0.00 0.00 43.76 3.41
2036 2079 4.282957 AGTCAGTCAGTGATGAGTGTGATT 59.717 41.667 11.67 0.00 39.55 2.57
2056 2099 8.844244 TGTGATTATTTTTCAAAACATTTGGGG 58.156 29.630 3.25 0.00 0.00 4.96
2157 2202 5.283457 AGTACTAGGATTGGATTGAGCAC 57.717 43.478 0.00 0.00 0.00 4.40
2172 2217 1.929836 GAGCACTCCATGTTCATCGTC 59.070 52.381 0.00 0.00 38.38 4.20
2173 2218 1.009829 GCACTCCATGTTCATCGTCC 58.990 55.000 0.00 0.00 0.00 4.79
2175 2220 2.002586 CACTCCATGTTCATCGTCCAC 58.997 52.381 0.00 0.00 0.00 4.02
2177 2222 2.038426 ACTCCATGTTCATCGTCCACAA 59.962 45.455 0.00 0.00 0.00 3.33
2179 2224 3.481453 TCCATGTTCATCGTCCACAAAA 58.519 40.909 0.00 0.00 0.00 2.44
2180 2225 4.078537 TCCATGTTCATCGTCCACAAAAT 58.921 39.130 0.00 0.00 0.00 1.82
2181 2226 5.249420 TCCATGTTCATCGTCCACAAAATA 58.751 37.500 0.00 0.00 0.00 1.40
2183 2228 5.123820 CCATGTTCATCGTCCACAAAATACT 59.876 40.000 0.00 0.00 0.00 2.12
2184 2229 6.315144 CCATGTTCATCGTCCACAAAATACTA 59.685 38.462 0.00 0.00 0.00 1.82
2185 2230 6.715344 TGTTCATCGTCCACAAAATACTAC 57.285 37.500 0.00 0.00 0.00 2.73
2190 2235 6.379133 TCATCGTCCACAAAATACTACCTACT 59.621 38.462 0.00 0.00 0.00 2.57
2192 2237 7.088589 TCGTCCACAAAATACTACCTACTAC 57.911 40.000 0.00 0.00 0.00 2.73
2193 2238 6.658816 TCGTCCACAAAATACTACCTACTACA 59.341 38.462 0.00 0.00 0.00 2.74
2194 2239 7.340232 TCGTCCACAAAATACTACCTACTACAT 59.660 37.037 0.00 0.00 0.00 2.29
2289 2343 9.685828 TCAAGCCAAACTAAATTATACAACAAC 57.314 29.630 0.00 0.00 0.00 3.32
2290 2344 9.469807 CAAGCCAAACTAAATTATACAACAACA 57.530 29.630 0.00 0.00 0.00 3.33
2292 2346 9.471084 AGCCAAACTAAATTATACAACAACAAC 57.529 29.630 0.00 0.00 0.00 3.32
2293 2347 9.250624 GCCAAACTAAATTATACAACAACAACA 57.749 29.630 0.00 0.00 0.00 3.33
2302 2356 8.988064 ATTATACAACAACAACAACAACAACA 57.012 26.923 0.00 0.00 0.00 3.33
2303 2357 8.812147 TTATACAACAACAACAACAACAACAA 57.188 26.923 0.00 0.00 0.00 2.83
2304 2358 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2305 2359 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2306 2360 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2307 2361 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2308 2362 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2309 2363 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2310 2364 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2311 2365 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2312 2366 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2347 2401 3.254166 CGAGGCAATTATGATCCCTTTGG 59.746 47.826 0.00 0.00 0.00 3.28
2521 2575 1.503542 GCCTTGATGTTCTGCACCG 59.496 57.895 0.00 0.00 0.00 4.94
2578 2632 4.098807 GCCTTCTTCTTCACTACTAGGAGG 59.901 50.000 6.98 0.00 0.00 4.30
2625 2679 1.924320 GAGCTGCACTCGACGTAGGT 61.924 60.000 1.02 0.39 35.18 3.08
2703 2757 7.098477 AGATGAGATCACTATCTTATGCAAGC 58.902 38.462 0.00 0.00 42.73 4.01
2720 2774 3.550639 GCAAGCAAGCAACAGAACATACA 60.551 43.478 0.00 0.00 0.00 2.29
2796 2851 1.679032 GCGGTGGAAATAGGAACAGCT 60.679 52.381 0.00 0.00 32.07 4.24
2847 2902 5.349817 GTCATCCCGCAGATCTATTAACATG 59.650 44.000 0.00 0.00 30.59 3.21
2894 2949 4.725556 TTTCTTACAGCAACAAGTAGCG 57.274 40.909 0.00 0.00 35.48 4.26
2904 2959 2.802816 CAACAAGTAGCGAGAAAGCAGT 59.197 45.455 0.00 0.00 40.15 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.847088 AGGGTAGAAAATCTCCCAGGC 59.153 52.381 13.69 0.00 36.74 4.85
1 2 3.115390 TGAGGGTAGAAAATCTCCCAGG 58.885 50.000 13.69 0.00 36.74 4.45
2 3 4.445448 CCATGAGGGTAGAAAATCTCCCAG 60.445 50.000 13.69 4.84 36.74 4.45
3 4 3.459598 CCATGAGGGTAGAAAATCTCCCA 59.540 47.826 13.69 0.00 36.74 4.37
4 5 3.716872 TCCATGAGGGTAGAAAATCTCCC 59.283 47.826 0.00 6.73 35.44 4.30
5 6 5.312079 CATCCATGAGGGTAGAAAATCTCC 58.688 45.833 0.00 0.00 38.11 3.71
6 7 5.312079 CCATCCATGAGGGTAGAAAATCTC 58.688 45.833 0.00 0.00 38.11 2.75
7 8 4.446889 GCCATCCATGAGGGTAGAAAATCT 60.447 45.833 0.00 0.00 35.75 2.40
8 9 3.823304 GCCATCCATGAGGGTAGAAAATC 59.177 47.826 0.00 0.00 35.75 2.17
9 10 3.748668 CGCCATCCATGAGGGTAGAAAAT 60.749 47.826 0.00 0.00 35.75 1.82
10 11 2.421388 CGCCATCCATGAGGGTAGAAAA 60.421 50.000 0.00 0.00 35.75 2.29
11 12 1.140852 CGCCATCCATGAGGGTAGAAA 59.859 52.381 0.00 0.00 35.75 2.52
12 13 0.758734 CGCCATCCATGAGGGTAGAA 59.241 55.000 0.00 0.00 35.75 2.10
13 14 1.121407 CCGCCATCCATGAGGGTAGA 61.121 60.000 0.00 0.00 35.75 2.59
14 15 1.372683 CCGCCATCCATGAGGGTAG 59.627 63.158 0.00 0.00 35.75 3.18
15 16 1.383943 ACCGCCATCCATGAGGGTA 60.384 57.895 0.00 0.00 35.75 3.69
16 17 2.692368 ACCGCCATCCATGAGGGT 60.692 61.111 0.00 2.18 35.75 4.34
17 18 2.203252 CACCGCCATCCATGAGGG 60.203 66.667 0.00 0.00 36.49 4.30
18 19 1.820906 CACACCGCCATCCATGAGG 60.821 63.158 0.00 0.00 0.00 3.86
19 20 0.179037 ATCACACCGCCATCCATGAG 60.179 55.000 0.00 0.00 0.00 2.90
20 21 0.179048 GATCACACCGCCATCCATGA 60.179 55.000 0.00 0.00 0.00 3.07
21 22 0.179037 AGATCACACCGCCATCCATG 60.179 55.000 0.00 0.00 0.00 3.66
22 23 0.548031 AAGATCACACCGCCATCCAT 59.452 50.000 0.00 0.00 0.00 3.41
23 24 0.107703 GAAGATCACACCGCCATCCA 60.108 55.000 0.00 0.00 0.00 3.41
24 25 1.154205 CGAAGATCACACCGCCATCC 61.154 60.000 0.00 0.00 0.00 3.51
25 26 1.154205 CCGAAGATCACACCGCCATC 61.154 60.000 0.00 0.00 0.00 3.51
26 27 1.153369 CCGAAGATCACACCGCCAT 60.153 57.895 0.00 0.00 0.00 4.40
27 28 1.613317 ATCCGAAGATCACACCGCCA 61.613 55.000 0.00 0.00 0.00 5.69
28 29 0.387929 TATCCGAAGATCACACCGCC 59.612 55.000 0.00 0.00 33.67 6.13
29 30 1.603172 CCTATCCGAAGATCACACCGC 60.603 57.143 0.00 0.00 33.67 5.68
30 31 1.954382 TCCTATCCGAAGATCACACCG 59.046 52.381 0.00 0.00 33.67 4.94
31 32 3.574396 TGATCCTATCCGAAGATCACACC 59.426 47.826 0.00 0.00 41.03 4.16
32 33 4.804108 CTGATCCTATCCGAAGATCACAC 58.196 47.826 0.00 0.00 41.03 3.82
33 34 3.256879 GCTGATCCTATCCGAAGATCACA 59.743 47.826 0.00 0.00 41.03 3.58
34 35 3.509575 AGCTGATCCTATCCGAAGATCAC 59.490 47.826 0.00 0.00 41.03 3.06
35 36 3.761218 GAGCTGATCCTATCCGAAGATCA 59.239 47.826 0.00 0.00 43.06 2.92
36 37 3.130340 GGAGCTGATCCTATCCGAAGATC 59.870 52.174 4.35 0.00 45.64 2.75
37 38 3.096092 GGAGCTGATCCTATCCGAAGAT 58.904 50.000 4.35 0.00 45.64 2.40
38 39 2.520069 GGAGCTGATCCTATCCGAAGA 58.480 52.381 4.35 0.00 45.64 2.87
57 58 7.890655 AGATAAATAAAGCCCAGCCTATAAAGG 59.109 37.037 0.00 0.00 46.76 3.11
58 59 8.870075 AGATAAATAAAGCCCAGCCTATAAAG 57.130 34.615 0.00 0.00 0.00 1.85
59 60 9.654919 AAAGATAAATAAAGCCCAGCCTATAAA 57.345 29.630 0.00 0.00 0.00 1.40
60 61 9.077885 CAAAGATAAATAAAGCCCAGCCTATAA 57.922 33.333 0.00 0.00 0.00 0.98
61 62 7.176690 GCAAAGATAAATAAAGCCCAGCCTATA 59.823 37.037 0.00 0.00 0.00 1.31
62 63 6.015095 GCAAAGATAAATAAAGCCCAGCCTAT 60.015 38.462 0.00 0.00 0.00 2.57
63 64 5.301805 GCAAAGATAAATAAAGCCCAGCCTA 59.698 40.000 0.00 0.00 0.00 3.93
64 65 4.100035 GCAAAGATAAATAAAGCCCAGCCT 59.900 41.667 0.00 0.00 0.00 4.58
65 66 4.100035 AGCAAAGATAAATAAAGCCCAGCC 59.900 41.667 0.00 0.00 0.00 4.85
66 67 5.268118 AGCAAAGATAAATAAAGCCCAGC 57.732 39.130 0.00 0.00 0.00 4.85
67 68 6.976925 CAGAAGCAAAGATAAATAAAGCCCAG 59.023 38.462 0.00 0.00 0.00 4.45
68 69 6.127366 CCAGAAGCAAAGATAAATAAAGCCCA 60.127 38.462 0.00 0.00 0.00 5.36
69 70 6.276091 CCAGAAGCAAAGATAAATAAAGCCC 58.724 40.000 0.00 0.00 0.00 5.19
70 71 5.750547 GCCAGAAGCAAAGATAAATAAAGCC 59.249 40.000 0.00 0.00 42.97 4.35
71 72 6.818869 GCCAGAAGCAAAGATAAATAAAGC 57.181 37.500 0.00 0.00 42.97 3.51
93 94 3.908213 TCGAAATAAACTGGCCAAAAGC 58.092 40.909 7.01 0.00 42.60 3.51
94 95 5.954335 AGATCGAAATAAACTGGCCAAAAG 58.046 37.500 7.01 0.00 0.00 2.27
95 96 5.975693 AGATCGAAATAAACTGGCCAAAA 57.024 34.783 7.01 0.00 0.00 2.44
96 97 5.975693 AAGATCGAAATAAACTGGCCAAA 57.024 34.783 7.01 0.00 0.00 3.28
97 98 5.975693 AAAGATCGAAATAAACTGGCCAA 57.024 34.783 7.01 0.00 0.00 4.52
98 99 6.177610 AGTAAAGATCGAAATAAACTGGCCA 58.822 36.000 4.71 4.71 0.00 5.36
99 100 6.679327 AGTAAAGATCGAAATAAACTGGCC 57.321 37.500 0.00 0.00 0.00 5.36
100 101 7.975750 AGAAGTAAAGATCGAAATAAACTGGC 58.024 34.615 0.00 0.00 0.00 4.85
111 112 9.677567 CCAAAAATTCAAAGAAGTAAAGATCGA 57.322 29.630 0.00 0.00 0.00 3.59
112 113 8.427774 GCCAAAAATTCAAAGAAGTAAAGATCG 58.572 33.333 0.00 0.00 0.00 3.69
113 114 9.481340 AGCCAAAAATTCAAAGAAGTAAAGATC 57.519 29.630 0.00 0.00 0.00 2.75
114 115 9.264719 CAGCCAAAAATTCAAAGAAGTAAAGAT 57.735 29.630 0.00 0.00 0.00 2.40
115 116 8.257306 ACAGCCAAAAATTCAAAGAAGTAAAGA 58.743 29.630 0.00 0.00 0.00 2.52
116 117 8.330302 CACAGCCAAAAATTCAAAGAAGTAAAG 58.670 33.333 0.00 0.00 0.00 1.85
117 118 7.821846 ACACAGCCAAAAATTCAAAGAAGTAAA 59.178 29.630 0.00 0.00 0.00 2.01
118 119 7.277539 CACACAGCCAAAAATTCAAAGAAGTAA 59.722 33.333 0.00 0.00 0.00 2.24
119 120 6.756074 CACACAGCCAAAAATTCAAAGAAGTA 59.244 34.615 0.00 0.00 0.00 2.24
120 121 5.581874 CACACAGCCAAAAATTCAAAGAAGT 59.418 36.000 0.00 0.00 0.00 3.01
121 122 5.502869 GCACACAGCCAAAAATTCAAAGAAG 60.503 40.000 0.00 0.00 37.23 2.85
122 123 4.332268 GCACACAGCCAAAAATTCAAAGAA 59.668 37.500 0.00 0.00 37.23 2.52
123 124 3.870419 GCACACAGCCAAAAATTCAAAGA 59.130 39.130 0.00 0.00 37.23 2.52
124 125 3.622163 TGCACACAGCCAAAAATTCAAAG 59.378 39.130 0.00 0.00 44.83 2.77
125 126 3.603532 TGCACACAGCCAAAAATTCAAA 58.396 36.364 0.00 0.00 44.83 2.69
126 127 3.257469 TGCACACAGCCAAAAATTCAA 57.743 38.095 0.00 0.00 44.83 2.69
127 128 2.975732 TGCACACAGCCAAAAATTCA 57.024 40.000 0.00 0.00 44.83 2.57
128 129 3.656559 AGATGCACACAGCCAAAAATTC 58.343 40.909 0.00 0.00 44.83 2.17
129 130 3.756933 AGATGCACACAGCCAAAAATT 57.243 38.095 0.00 0.00 44.83 1.82
130 131 3.828451 ACTAGATGCACACAGCCAAAAAT 59.172 39.130 0.00 0.00 44.83 1.82
131 132 3.221771 ACTAGATGCACACAGCCAAAAA 58.778 40.909 0.00 0.00 44.83 1.94
132 133 2.862541 ACTAGATGCACACAGCCAAAA 58.137 42.857 0.00 0.00 44.83 2.44
133 134 2.566833 ACTAGATGCACACAGCCAAA 57.433 45.000 0.00 0.00 44.83 3.28
134 135 2.566833 AACTAGATGCACACAGCCAA 57.433 45.000 0.00 0.00 44.83 4.52
135 136 3.055167 ACATAACTAGATGCACACAGCCA 60.055 43.478 0.00 0.00 44.83 4.75
136 137 3.535561 ACATAACTAGATGCACACAGCC 58.464 45.455 0.00 0.00 44.83 4.85
137 138 5.592054 TCTACATAACTAGATGCACACAGC 58.408 41.667 0.00 0.00 45.96 4.40
138 139 6.183360 ACCTCTACATAACTAGATGCACACAG 60.183 42.308 0.00 0.00 0.00 3.66
139 140 5.656859 ACCTCTACATAACTAGATGCACACA 59.343 40.000 0.00 0.00 0.00 3.72
140 141 6.150396 ACCTCTACATAACTAGATGCACAC 57.850 41.667 0.00 0.00 0.00 3.82
141 142 5.008712 CGACCTCTACATAACTAGATGCACA 59.991 44.000 0.00 0.00 0.00 4.57
142 143 5.453648 CGACCTCTACATAACTAGATGCAC 58.546 45.833 0.00 0.00 0.00 4.57
143 144 4.519350 CCGACCTCTACATAACTAGATGCA 59.481 45.833 0.00 0.00 0.00 3.96
144 145 4.082679 CCCGACCTCTACATAACTAGATGC 60.083 50.000 0.00 0.00 0.00 3.91
145 146 5.048643 CACCCGACCTCTACATAACTAGATG 60.049 48.000 0.00 0.00 0.00 2.90
146 147 5.071370 CACCCGACCTCTACATAACTAGAT 58.929 45.833 0.00 0.00 0.00 1.98
147 148 4.164796 TCACCCGACCTCTACATAACTAGA 59.835 45.833 0.00 0.00 0.00 2.43
148 149 4.458397 TCACCCGACCTCTACATAACTAG 58.542 47.826 0.00 0.00 0.00 2.57
149 150 4.508551 TCACCCGACCTCTACATAACTA 57.491 45.455 0.00 0.00 0.00 2.24
150 151 3.377253 TCACCCGACCTCTACATAACT 57.623 47.619 0.00 0.00 0.00 2.24
151 152 4.667519 AATCACCCGACCTCTACATAAC 57.332 45.455 0.00 0.00 0.00 1.89
152 153 5.687166 AAAATCACCCGACCTCTACATAA 57.313 39.130 0.00 0.00 0.00 1.90
153 154 5.188163 TCAAAAATCACCCGACCTCTACATA 59.812 40.000 0.00 0.00 0.00 2.29
154 155 4.019681 TCAAAAATCACCCGACCTCTACAT 60.020 41.667 0.00 0.00 0.00 2.29
155 156 3.325425 TCAAAAATCACCCGACCTCTACA 59.675 43.478 0.00 0.00 0.00 2.74
156 157 3.934068 TCAAAAATCACCCGACCTCTAC 58.066 45.455 0.00 0.00 0.00 2.59
157 158 4.513442 CATCAAAAATCACCCGACCTCTA 58.487 43.478 0.00 0.00 0.00 2.43
158 159 3.347216 CATCAAAAATCACCCGACCTCT 58.653 45.455 0.00 0.00 0.00 3.69
159 160 2.159379 GCATCAAAAATCACCCGACCTC 60.159 50.000 0.00 0.00 0.00 3.85
160 161 1.818674 GCATCAAAAATCACCCGACCT 59.181 47.619 0.00 0.00 0.00 3.85
161 162 1.467374 CGCATCAAAAATCACCCGACC 60.467 52.381 0.00 0.00 0.00 4.79
162 163 1.466950 TCGCATCAAAAATCACCCGAC 59.533 47.619 0.00 0.00 0.00 4.79
163 164 1.814793 TCGCATCAAAAATCACCCGA 58.185 45.000 0.00 0.00 0.00 5.14
164 165 2.849880 ATCGCATCAAAAATCACCCG 57.150 45.000 0.00 0.00 0.00 5.28
165 166 3.848726 ACAATCGCATCAAAAATCACCC 58.151 40.909 0.00 0.00 0.00 4.61
166 167 6.264832 TGATACAATCGCATCAAAAATCACC 58.735 36.000 0.00 0.00 0.00 4.02
167 168 7.485913 AGTTGATACAATCGCATCAAAAATCAC 59.514 33.333 0.00 0.00 41.50 3.06
168 169 7.537715 AGTTGATACAATCGCATCAAAAATCA 58.462 30.769 0.00 0.00 41.50 2.57
169 170 7.097289 CGAGTTGATACAATCGCATCAAAAATC 60.097 37.037 0.00 0.00 41.50 2.17
170 171 6.688385 CGAGTTGATACAATCGCATCAAAAAT 59.312 34.615 0.00 0.00 41.50 1.82
171 172 6.020984 CGAGTTGATACAATCGCATCAAAAA 58.979 36.000 0.00 0.00 41.50 1.94
172 173 5.350091 TCGAGTTGATACAATCGCATCAAAA 59.650 36.000 0.00 0.00 41.50 2.44
173 174 4.867608 TCGAGTTGATACAATCGCATCAAA 59.132 37.500 0.00 0.00 41.50 2.69
174 175 4.429108 TCGAGTTGATACAATCGCATCAA 58.571 39.130 0.00 0.00 38.50 2.57
175 176 4.040445 TCGAGTTGATACAATCGCATCA 57.960 40.909 0.00 0.00 35.23 3.07
176 177 6.877556 ATATCGAGTTGATACAATCGCATC 57.122 37.500 1.96 0.00 42.24 3.91
177 178 7.384932 TGAAATATCGAGTTGATACAATCGCAT 59.615 33.333 1.96 0.00 42.24 4.73
178 179 6.699642 TGAAATATCGAGTTGATACAATCGCA 59.300 34.615 1.96 0.00 42.24 5.10
179 180 7.105494 TGAAATATCGAGTTGATACAATCGC 57.895 36.000 1.96 0.00 42.24 4.58
193 194 9.748708 GGGATTTTCATTGAATTGAAATATCGA 57.251 29.630 0.00 0.00 43.20 3.59
194 195 9.754382 AGGGATTTTCATTGAATTGAAATATCG 57.246 29.630 0.00 0.00 43.20 2.92
231 232 4.206200 CACGCATACGCTTGTTTTCTTTTT 59.794 37.500 0.00 0.00 45.53 1.94
232 233 3.728718 CACGCATACGCTTGTTTTCTTTT 59.271 39.130 0.00 0.00 45.53 2.27
246 247 1.073177 ACCGCTAAACACACGCATAC 58.927 50.000 0.00 0.00 0.00 2.39
271 272 1.271656 GCCATGCTTCAACTTGCTTCT 59.728 47.619 0.00 0.00 0.00 2.85
332 333 5.512473 ACGAATAGTGATCTAAACGCTCTC 58.488 41.667 0.00 0.00 34.71 3.20
382 383 9.968870 CTCTCTCCGTAAACTAATATAAAAGCT 57.031 33.333 0.00 0.00 0.00 3.74
409 410 8.234136 TCCCTACTATTGTCTACACTGTAATG 57.766 38.462 0.00 0.00 0.00 1.90
425 426 6.095720 CGTTCAGAGTCTCTTTTCCCTACTAT 59.904 42.308 0.00 0.00 0.00 2.12
433 434 4.861210 TCTGTCGTTCAGAGTCTCTTTTC 58.139 43.478 0.00 0.00 46.77 2.29
479 480 2.883316 AAATGAGGGGAGGGGGAGGG 62.883 65.000 0.00 0.00 0.00 4.30
480 481 1.309102 AAATGAGGGGAGGGGGAGG 60.309 63.158 0.00 0.00 0.00 4.30
481 482 0.624500 TGAAATGAGGGGAGGGGGAG 60.625 60.000 0.00 0.00 0.00 4.30
482 483 0.047802 ATGAAATGAGGGGAGGGGGA 59.952 55.000 0.00 0.00 0.00 4.81
535 543 1.821753 CCTCCACTACCACTGTCTCTG 59.178 57.143 0.00 0.00 0.00 3.35
695 704 4.519350 GGAAAGGAAACGGAGAAAAGTCAT 59.481 41.667 0.00 0.00 0.00 3.06
706 715 0.589708 GTTCCACGGAAAGGAAACGG 59.410 55.000 0.00 0.00 46.03 4.44
749 759 0.608640 ATCGGAGAAAGTGAAGGCGT 59.391 50.000 0.00 0.00 43.58 5.68
806 821 2.506472 GGGAAGAGATGGGTCCGC 59.494 66.667 0.00 0.00 0.00 5.54
849 864 7.385478 ACACGGAAAGAAGAAGAATAAGAAGAC 59.615 37.037 0.00 0.00 0.00 3.01
908 924 5.600484 AGGTAGATCGATGACCAGAAAGAAT 59.400 40.000 22.21 2.80 35.56 2.40
940 956 7.345392 AGAAGAAGAAGAAGAGGAAGCAGATAT 59.655 37.037 0.00 0.00 0.00 1.63
951 967 9.196552 GAAGAAGAAGAAGAAGAAGAAGAAGAG 57.803 37.037 0.00 0.00 0.00 2.85
952 968 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
953 969 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
954 970 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
955 971 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
956 972 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
957 973 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
958 974 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
959 975 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1020 1036 1.774254 TGTCCTTCTCCTTGCTTGGAA 59.226 47.619 0.36 0.00 35.43 3.53
1033 1049 0.398318 ACCACTGCTCCTTGTCCTTC 59.602 55.000 0.00 0.00 0.00 3.46
1072 1106 4.406648 TCGACATGGATATGGATATGGC 57.593 45.455 0.00 0.00 38.66 4.40
1113 1147 1.321805 CCGTACCGTGGTGGATGGTA 61.322 60.000 0.72 0.00 42.77 3.25
1125 1159 4.818534 ATGTATGTACTGTACCGTACCG 57.181 45.455 20.66 2.51 39.14 4.02
1126 1160 8.103948 AGAATATGTATGTACTGTACCGTACC 57.896 38.462 20.66 9.35 39.14 3.34
1127 1161 9.604626 GAAGAATATGTATGTACTGTACCGTAC 57.395 37.037 17.79 17.79 40.06 3.67
1128 1162 8.786898 GGAAGAATATGTATGTACTGTACCGTA 58.213 37.037 14.91 6.35 0.00 4.02
1129 1163 7.255730 GGGAAGAATATGTATGTACTGTACCGT 60.256 40.741 14.91 6.81 0.00 4.83
1179 1218 6.210385 AGCACATAACAAGAAGAAGAGAGAGA 59.790 38.462 0.00 0.00 0.00 3.10
1180 1219 6.310956 CAGCACATAACAAGAAGAAGAGAGAG 59.689 42.308 0.00 0.00 0.00 3.20
1181 1220 6.162079 CAGCACATAACAAGAAGAAGAGAGA 58.838 40.000 0.00 0.00 0.00 3.10
1182 1221 5.931146 ACAGCACATAACAAGAAGAAGAGAG 59.069 40.000 0.00 0.00 0.00 3.20
1183 1222 5.698089 CACAGCACATAACAAGAAGAAGAGA 59.302 40.000 0.00 0.00 0.00 3.10
1184 1223 5.616424 GCACAGCACATAACAAGAAGAAGAG 60.616 44.000 0.00 0.00 0.00 2.85
1185 1224 4.214119 GCACAGCACATAACAAGAAGAAGA 59.786 41.667 0.00 0.00 0.00 2.87
1186 1225 4.023792 TGCACAGCACATAACAAGAAGAAG 60.024 41.667 0.00 0.00 31.71 2.85
1187 1226 3.882288 TGCACAGCACATAACAAGAAGAA 59.118 39.130 0.00 0.00 31.71 2.52
1215 1258 3.362706 AGAATCAATGAGCCAAGCACAT 58.637 40.909 0.00 0.00 41.19 3.21
1253 1296 1.300963 GCCTCCTTCTGCACATCCA 59.699 57.895 0.00 0.00 0.00 3.41
1833 1876 3.458163 GGATGTGTCTCCGGCGGA 61.458 66.667 29.14 29.14 0.00 5.54
1861 1904 3.290710 AGAAAAAGCAGAGTGGAAGCAA 58.709 40.909 0.00 0.00 0.00 3.91
1880 1923 2.240160 GACTAGACTGGACTGGAGGAGA 59.760 54.545 0.00 0.00 0.00 3.71
1892 1935 8.461249 AGACTAGACTAGACTAGACTAGACTG 57.539 42.308 35.34 23.24 46.78 3.51
1911 1954 7.493320 CAGTTGGTACAGACTAGACTAGACTAG 59.507 44.444 22.54 22.54 42.39 2.57
1912 1955 7.179872 TCAGTTGGTACAGACTAGACTAGACTA 59.820 40.741 16.55 0.00 42.39 2.59
1913 1956 6.013553 TCAGTTGGTACAGACTAGACTAGACT 60.014 42.308 16.55 12.27 42.39 3.24
1915 1958 6.370186 TCAGTTGGTACAGACTAGACTAGA 57.630 41.667 16.55 0.00 42.39 2.43
1916 1959 7.633193 ATTCAGTTGGTACAGACTAGACTAG 57.367 40.000 8.00 8.00 42.39 2.57
1919 1962 6.456501 ACAATTCAGTTGGTACAGACTAGAC 58.543 40.000 0.00 0.00 42.39 2.59
1920 1963 6.665992 ACAATTCAGTTGGTACAGACTAGA 57.334 37.500 0.00 0.00 42.39 2.43
1923 1966 6.710744 CCTTAACAATTCAGTTGGTACAGACT 59.289 38.462 0.00 0.00 39.64 3.24
1948 1991 1.255667 TTCCGGGGTGTCTCTGCTAC 61.256 60.000 0.00 0.00 0.00 3.58
1964 2007 9.959749 CAAGTCTGAGTAATACTAGAATCTTCC 57.040 37.037 0.00 0.00 0.00 3.46
2013 2056 3.225940 TCACACTCATCACTGACTGACT 58.774 45.455 0.00 0.00 0.00 3.41
2036 2079 7.048512 ACGAACCCCAAATGTTTTGAAAAATA 58.951 30.769 1.65 0.00 0.00 1.40
2056 2099 3.234386 GCAGTGGCAAATTTAGACGAAC 58.766 45.455 0.00 0.00 40.72 3.95
2157 2202 2.385013 TGTGGACGATGAACATGGAG 57.615 50.000 0.00 0.00 0.00 3.86
2245 2290 5.877564 GGCTTGATAAGGAAGATATGTAGGC 59.122 44.000 0.00 0.00 0.00 3.93
2289 2343 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2290 2344 5.007136 CCTTGTTGTTGTTGTTGTTGTTGTT 59.993 36.000 0.00 0.00 0.00 2.83
2291 2345 4.509600 CCTTGTTGTTGTTGTTGTTGTTGT 59.490 37.500 0.00 0.00 0.00 3.32
2292 2346 4.747108 TCCTTGTTGTTGTTGTTGTTGTTG 59.253 37.500 0.00 0.00 0.00 3.33
2293 2347 4.950050 TCCTTGTTGTTGTTGTTGTTGTT 58.050 34.783 0.00 0.00 0.00 2.83
2294 2348 4.279671 TCTCCTTGTTGTTGTTGTTGTTGT 59.720 37.500 0.00 0.00 0.00 3.32
2295 2349 4.804108 TCTCCTTGTTGTTGTTGTTGTTG 58.196 39.130 0.00 0.00 0.00 3.33
2296 2350 4.082245 CCTCTCCTTGTTGTTGTTGTTGTT 60.082 41.667 0.00 0.00 0.00 2.83
2297 2351 3.443681 CCTCTCCTTGTTGTTGTTGTTGT 59.556 43.478 0.00 0.00 0.00 3.32
2298 2352 3.734902 GCCTCTCCTTGTTGTTGTTGTTG 60.735 47.826 0.00 0.00 0.00 3.33
2299 2353 2.427095 GCCTCTCCTTGTTGTTGTTGTT 59.573 45.455 0.00 0.00 0.00 2.83
2300 2354 2.024414 GCCTCTCCTTGTTGTTGTTGT 58.976 47.619 0.00 0.00 0.00 3.32
2301 2355 1.002468 CGCCTCTCCTTGTTGTTGTTG 60.002 52.381 0.00 0.00 0.00 3.33
2302 2356 1.134220 TCGCCTCTCCTTGTTGTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
2303 2357 0.468226 TCGCCTCTCCTTGTTGTTGT 59.532 50.000 0.00 0.00 0.00 3.32
2304 2358 1.151668 CTCGCCTCTCCTTGTTGTTG 58.848 55.000 0.00 0.00 0.00 3.33
2305 2359 0.035458 CCTCGCCTCTCCTTGTTGTT 59.965 55.000 0.00 0.00 0.00 2.83
2306 2360 1.674057 CCTCGCCTCTCCTTGTTGT 59.326 57.895 0.00 0.00 0.00 3.32
2307 2361 1.743252 GCCTCGCCTCTCCTTGTTG 60.743 63.158 0.00 0.00 0.00 3.33
2308 2362 2.665603 GCCTCGCCTCTCCTTGTT 59.334 61.111 0.00 0.00 0.00 2.83
2309 2363 3.764466 CGCCTCGCCTCTCCTTGT 61.764 66.667 0.00 0.00 0.00 3.16
2310 2364 3.423162 CTCGCCTCGCCTCTCCTTG 62.423 68.421 0.00 0.00 0.00 3.61
2311 2365 3.144193 CTCGCCTCGCCTCTCCTT 61.144 66.667 0.00 0.00 0.00 3.36
2347 2401 0.939577 TTGCAGTGTCTCGCTTCGAC 60.940 55.000 0.00 0.00 0.00 4.20
2394 2448 7.648142 TCTTGTAAAACTAGCTCAAAATGGTG 58.352 34.615 0.00 0.00 0.00 4.17
2521 2575 2.625790 TGGGTTAGTGATTTGGTTGCAC 59.374 45.455 0.00 0.00 0.00 4.57
2578 2632 2.554032 ACAGCAGGTAAAATGAGTGCAC 59.446 45.455 9.40 9.40 36.57 4.57
2625 2679 1.079681 AAGGTAATTGGCGCGACGA 60.080 52.632 12.10 7.68 0.00 4.20
2703 2757 5.740569 GCATATGTGTATGTTCTGTTGCTTG 59.259 40.000 4.29 0.00 39.90 4.01
2746 2800 6.242508 ACTCGGAAGCTTTATCTGTTTTTC 57.757 37.500 0.00 0.00 0.00 2.29
2796 2851 1.060729 TTTTCGTGGATCACCCTGGA 58.939 50.000 0.00 0.00 35.38 3.86
2847 2902 8.251750 TGTTGTATAACTCAGCAACTATGTTC 57.748 34.615 3.89 0.00 41.04 3.18


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

AutoCloner maintained by Alex Coulton.