Multiple sequence alignment - TraesCS1D01G368000

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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 TraesCS1D01G368000 chr1D 100.000 2312 0 0 1 2312 447756003 447758314 0.000000e+00 4270.0
1 TraesCS1D01G368000 chr1D 95.421 546 22 1 768 1313 445367044 445366502 0.000000e+00 867.0
2 TraesCS1D01G368000 chr1D 93.773 546 31 3 768 1313 355827857 355828399 0.000000e+00 817.0
3 TraesCS1D01G368000 chr1D 96.173 392 15 0 1 392 377957971 377957580 1.940000e-180 641.0
4 TraesCS1D01G368000 chr1A 89.262 1043 58 21 651 1659 543928017 543929039 0.000000e+00 1256.0
5 TraesCS1D01G368000 chr1A 95.055 546 24 1 768 1313 541343593 541344135 0.000000e+00 856.0
6 TraesCS1D01G368000 chr1A 94.872 546 24 2 768 1313 541461014 541460473 0.000000e+00 850.0
7 TraesCS1D01G368000 chr1A 86.782 749 54 19 1587 2312 543929090 543929816 0.000000e+00 793.0
8 TraesCS1D01G368000 chr1A 96.667 390 13 0 1 390 104232103 104232492 0.000000e+00 649.0
9 TraesCS1D01G368000 chr1A 90.640 203 15 3 375 576 543927547 543927746 1.360000e-67 267.0
10 TraesCS1D01G368000 chr1B 93.673 727 34 6 609 1328 613231421 613232142 0.000000e+00 1077.0
11 TraesCS1D01G368000 chr1B 95.604 546 21 1 768 1313 610893033 610893575 0.000000e+00 872.0
12 TraesCS1D01G368000 chr1B 93.818 550 27 2 768 1313 608042989 608042443 0.000000e+00 821.0
13 TraesCS1D01G368000 chr1B 93.796 548 27 2 770 1313 608335858 608335314 0.000000e+00 817.0
14 TraesCS1D01G368000 chr1B 86.803 735 58 19 1587 2312 613232502 613233206 0.000000e+00 784.0
15 TraesCS1D01G368000 chr1B 92.381 210 12 3 368 576 613188839 613189045 1.740000e-76 296.0
16 TraesCS1D01G368000 chr1B 89.109 202 13 2 1379 1572 613232163 613232363 2.300000e-60 243.0
17 TraesCS1D01G368000 chr2D 97.716 394 9 0 1 394 26447691 26447298 0.000000e+00 678.0
18 TraesCS1D01G368000 chr2D 96.931 391 12 0 1 391 82219663 82220053 0.000000e+00 656.0
19 TraesCS1D01G368000 chr3D 96.667 390 13 0 1 390 68840109 68839720 0.000000e+00 649.0
20 TraesCS1D01G368000 chr3D 95.908 391 16 0 1 391 252333648 252334038 3.240000e-178 634.0
21 TraesCS1D01G368000 chr7D 96.164 391 15 0 1 391 604446793 604446403 6.970000e-180 640.0
22 TraesCS1D01G368000 chr5D 95.897 390 16 0 1 390 320660928 320660539 1.170000e-177 632.0
23 TraesCS1D01G368000 chr5D 95.887 389 16 0 1 389 363005808 363005420 4.190000e-177 630.0
24 TraesCS1D01G368000 chr6A 95.000 40 1 1 1622 1661 32912956 32912918 6.900000e-06 62.1


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 TraesCS1D01G368000 chr1D 447756003 447758314 2311 False 4270.000000 4270 100.000000 1 2312 1 chr1D.!!$F2 2311
1 TraesCS1D01G368000 chr1D 445366502 445367044 542 True 867.000000 867 95.421000 768 1313 1 chr1D.!!$R2 545
2 TraesCS1D01G368000 chr1D 355827857 355828399 542 False 817.000000 817 93.773000 768 1313 1 chr1D.!!$F1 545
3 TraesCS1D01G368000 chr1A 541343593 541344135 542 False 856.000000 856 95.055000 768 1313 1 chr1A.!!$F2 545
4 TraesCS1D01G368000 chr1A 541460473 541461014 541 True 850.000000 850 94.872000 768 1313 1 chr1A.!!$R1 545
5 TraesCS1D01G368000 chr1A 543927547 543929816 2269 False 772.000000 1256 88.894667 375 2312 3 chr1A.!!$F3 1937
6 TraesCS1D01G368000 chr1B 610893033 610893575 542 False 872.000000 872 95.604000 768 1313 1 chr1B.!!$F1 545
7 TraesCS1D01G368000 chr1B 608042443 608042989 546 True 821.000000 821 93.818000 768 1313 1 chr1B.!!$R1 545
8 TraesCS1D01G368000 chr1B 608335314 608335858 544 True 817.000000 817 93.796000 770 1313 1 chr1B.!!$R2 543
9 TraesCS1D01G368000 chr1B 613231421 613233206 1785 False 701.333333 1077 89.861667 609 2312 3 chr1B.!!$F3 1703

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
100 101 0.103876 AGGGAGGGGCTAAATAGGGG 60.104 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 1601 0.451783 ATGCGGCGATTTTTCAGACC 59.548 50.0 12.98 0.0 0.0 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.452733 GCTTACCTGCTCGCCGGT 62.453 66.667 1.90 9.88 37.31 5.28
18 19 3.072486 GCTTACCTGCTCGCCGGTA 62.072 63.158 1.90 7.95 34.76 4.02
19 20 1.226888 CTTACCTGCTCGCCGGTAC 60.227 63.158 11.09 0.00 35.60 3.34
20 21 2.624437 CTTACCTGCTCGCCGGTACC 62.624 65.000 11.09 0.16 35.60 3.34
23 24 3.900892 CTGCTCGCCGGTACCGAT 61.901 66.667 35.41 0.00 42.83 4.18
24 25 4.201679 TGCTCGCCGGTACCGATG 62.202 66.667 35.41 25.04 42.83 3.84
51 52 4.856607 GGGAGAGCGCGAACGGAG 62.857 72.222 12.10 0.00 40.57 4.63
52 53 4.856607 GGAGAGCGCGAACGGAGG 62.857 72.222 12.10 0.00 40.57 4.30
53 54 3.812019 GAGAGCGCGAACGGAGGA 61.812 66.667 12.10 0.00 40.57 3.71
54 55 3.338126 GAGAGCGCGAACGGAGGAA 62.338 63.158 12.10 0.00 40.57 3.36
55 56 2.881352 GAGCGCGAACGGAGGAAG 60.881 66.667 12.10 0.00 40.57 3.46
56 57 3.338126 GAGCGCGAACGGAGGAAGA 62.338 63.158 12.10 0.00 40.57 2.87
57 58 2.431942 GCGCGAACGGAGGAAGAA 60.432 61.111 12.10 0.00 40.57 2.52
58 59 1.810030 GCGCGAACGGAGGAAGAAT 60.810 57.895 12.10 0.00 40.57 2.40
59 60 1.999051 CGCGAACGGAGGAAGAATG 59.001 57.895 0.00 0.00 34.97 2.67
60 61 1.421410 CGCGAACGGAGGAAGAATGG 61.421 60.000 0.00 0.00 34.97 3.16
61 62 0.391263 GCGAACGGAGGAAGAATGGT 60.391 55.000 0.00 0.00 0.00 3.55
62 63 1.359848 CGAACGGAGGAAGAATGGTG 58.640 55.000 0.00 0.00 0.00 4.17
63 64 1.739067 GAACGGAGGAAGAATGGTGG 58.261 55.000 0.00 0.00 0.00 4.61
64 65 0.322546 AACGGAGGAAGAATGGTGGC 60.323 55.000 0.00 0.00 0.00 5.01
65 66 1.815421 CGGAGGAAGAATGGTGGCG 60.815 63.158 0.00 0.00 0.00 5.69
66 67 1.452108 GGAGGAAGAATGGTGGCGG 60.452 63.158 0.00 0.00 0.00 6.13
67 68 1.452108 GAGGAAGAATGGTGGCGGG 60.452 63.158 0.00 0.00 0.00 6.13
68 69 1.910580 GAGGAAGAATGGTGGCGGGA 61.911 60.000 0.00 0.00 0.00 5.14
69 70 1.452108 GGAAGAATGGTGGCGGGAG 60.452 63.158 0.00 0.00 0.00 4.30
70 71 1.299976 GAAGAATGGTGGCGGGAGT 59.700 57.895 0.00 0.00 0.00 3.85
71 72 0.322546 GAAGAATGGTGGCGGGAGTT 60.323 55.000 0.00 0.00 0.00 3.01
72 73 0.609131 AAGAATGGTGGCGGGAGTTG 60.609 55.000 0.00 0.00 0.00 3.16
73 74 2.035626 AATGGTGGCGGGAGTTGG 59.964 61.111 0.00 0.00 0.00 3.77
74 75 3.583882 AATGGTGGCGGGAGTTGGG 62.584 63.158 0.00 0.00 0.00 4.12
82 83 4.410400 GGGAGTTGGGGCGGTGAG 62.410 72.222 0.00 0.00 0.00 3.51
83 84 4.410400 GGAGTTGGGGCGGTGAGG 62.410 72.222 0.00 0.00 0.00 3.86
84 85 4.410400 GAGTTGGGGCGGTGAGGG 62.410 72.222 0.00 0.00 0.00 4.30
85 86 4.974438 AGTTGGGGCGGTGAGGGA 62.974 66.667 0.00 0.00 0.00 4.20
86 87 4.410400 GTTGGGGCGGTGAGGGAG 62.410 72.222 0.00 0.00 0.00 4.30
93 94 2.365105 CGGTGAGGGAGGGGCTAA 60.365 66.667 0.00 0.00 0.00 3.09
94 95 1.993391 CGGTGAGGGAGGGGCTAAA 60.993 63.158 0.00 0.00 0.00 1.85
95 96 1.345715 CGGTGAGGGAGGGGCTAAAT 61.346 60.000 0.00 0.00 0.00 1.40
96 97 1.815757 GGTGAGGGAGGGGCTAAATA 58.184 55.000 0.00 0.00 0.00 1.40
97 98 1.700186 GGTGAGGGAGGGGCTAAATAG 59.300 57.143 0.00 0.00 0.00 1.73
98 99 1.700186 GTGAGGGAGGGGCTAAATAGG 59.300 57.143 0.00 0.00 0.00 2.57
99 100 1.363246 GAGGGAGGGGCTAAATAGGG 58.637 60.000 0.00 0.00 0.00 3.53
100 101 0.103876 AGGGAGGGGCTAAATAGGGG 60.104 60.000 0.00 0.00 0.00 4.79
101 102 1.140772 GGGAGGGGCTAAATAGGGGG 61.141 65.000 0.00 0.00 0.00 5.40
102 103 0.403008 GGAGGGGCTAAATAGGGGGT 60.403 60.000 0.00 0.00 0.00 4.95
103 104 0.771755 GAGGGGCTAAATAGGGGGTG 59.228 60.000 0.00 0.00 0.00 4.61
104 105 0.701310 AGGGGCTAAATAGGGGGTGG 60.701 60.000 0.00 0.00 0.00 4.61
105 106 0.699922 GGGGCTAAATAGGGGGTGGA 60.700 60.000 0.00 0.00 0.00 4.02
106 107 0.771755 GGGCTAAATAGGGGGTGGAG 59.228 60.000 0.00 0.00 0.00 3.86
107 108 0.110678 GGCTAAATAGGGGGTGGAGC 59.889 60.000 0.00 0.00 0.00 4.70
108 109 0.250338 GCTAAATAGGGGGTGGAGCG 60.250 60.000 0.00 0.00 0.00 5.03
109 110 0.396811 CTAAATAGGGGGTGGAGCGG 59.603 60.000 0.00 0.00 0.00 5.52
110 111 1.702022 TAAATAGGGGGTGGAGCGGC 61.702 60.000 0.00 0.00 0.00 6.53
126 127 4.388499 GCGGGAGGTGAGCCGAAA 62.388 66.667 0.00 0.00 40.50 3.46
127 128 2.584608 CGGGAGGTGAGCCGAAAT 59.415 61.111 0.00 0.00 40.50 2.17
128 129 1.521681 CGGGAGGTGAGCCGAAATC 60.522 63.158 0.00 0.00 40.50 2.17
129 130 1.153147 GGGAGGTGAGCCGAAATCC 60.153 63.158 0.00 0.00 40.50 3.01
130 131 1.627297 GGGAGGTGAGCCGAAATCCT 61.627 60.000 0.00 0.00 40.50 3.24
131 132 0.179070 GGAGGTGAGCCGAAATCCTC 60.179 60.000 0.00 0.00 42.53 3.71
132 133 0.179070 GAGGTGAGCCGAAATCCTCC 60.179 60.000 0.00 0.00 38.81 4.30
133 134 1.153147 GGTGAGCCGAAATCCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
134 135 1.521681 GTGAGCCGAAATCCTCCCG 60.522 63.158 0.00 0.00 0.00 5.14
135 136 2.589159 GAGCCGAAATCCTCCCGC 60.589 66.667 0.00 0.00 0.00 6.13
136 137 4.176752 AGCCGAAATCCTCCCGCC 62.177 66.667 0.00 0.00 0.00 6.13
138 139 3.845259 CCGAAATCCTCCCGCCGA 61.845 66.667 0.00 0.00 0.00 5.54
139 140 2.421739 CGAAATCCTCCCGCCGAT 59.578 61.111 0.00 0.00 0.00 4.18
140 141 1.227556 CGAAATCCTCCCGCCGATT 60.228 57.895 0.00 0.00 0.00 3.34
141 142 0.814010 CGAAATCCTCCCGCCGATTT 60.814 55.000 0.00 0.00 40.52 2.17
142 143 1.389555 GAAATCCTCCCGCCGATTTT 58.610 50.000 0.00 0.00 38.50 1.82
143 144 1.749063 GAAATCCTCCCGCCGATTTTT 59.251 47.619 0.00 0.00 38.50 1.94
144 145 1.389555 AATCCTCCCGCCGATTTTTC 58.610 50.000 0.00 0.00 0.00 2.29
145 146 0.814010 ATCCTCCCGCCGATTTTTCG 60.814 55.000 0.00 0.00 0.00 3.46
173 174 2.279120 CGAGCTCGCACCATCTCC 60.279 66.667 25.07 0.00 0.00 3.71
174 175 2.107953 GAGCTCGCACCATCTCCC 59.892 66.667 0.00 0.00 0.00 4.30
175 176 3.453070 GAGCTCGCACCATCTCCCC 62.453 68.421 0.00 0.00 0.00 4.81
176 177 3.474570 GCTCGCACCATCTCCCCT 61.475 66.667 0.00 0.00 0.00 4.79
177 178 2.503061 CTCGCACCATCTCCCCTG 59.497 66.667 0.00 0.00 0.00 4.45
178 179 3.746949 CTCGCACCATCTCCCCTGC 62.747 68.421 0.00 0.00 0.00 4.85
179 180 3.790437 CGCACCATCTCCCCTGCT 61.790 66.667 0.00 0.00 0.00 4.24
180 181 2.191641 GCACCATCTCCCCTGCTC 59.808 66.667 0.00 0.00 0.00 4.26
181 182 2.503061 CACCATCTCCCCTGCTCG 59.497 66.667 0.00 0.00 0.00 5.03
182 183 3.474570 ACCATCTCCCCTGCTCGC 61.475 66.667 0.00 0.00 0.00 5.03
183 184 3.473647 CCATCTCCCCTGCTCGCA 61.474 66.667 0.00 0.00 0.00 5.10
184 185 2.202987 CATCTCCCCTGCTCGCAC 60.203 66.667 0.00 0.00 0.00 5.34
185 186 3.842923 ATCTCCCCTGCTCGCACG 61.843 66.667 0.00 0.00 0.00 5.34
187 188 4.504916 CTCCCCTGCTCGCACGAG 62.505 72.222 15.50 15.50 44.56 4.18
196 197 3.760035 TCGCACGAGGGGAGAAGC 61.760 66.667 0.00 0.00 33.99 3.86
201 202 4.856607 CGAGGGGAGAAGCGCGTC 62.857 72.222 15.94 15.94 39.93 5.19
202 203 4.856607 GAGGGGAGAAGCGCGTCG 62.857 72.222 17.57 0.00 35.19 5.12
246 247 3.877357 CTCGCGAGCTACTGCCGA 61.877 66.667 25.07 0.00 40.80 5.54
247 248 3.396911 CTCGCGAGCTACTGCCGAA 62.397 63.158 25.07 0.00 40.80 4.30
248 249 2.278857 CGCGAGCTACTGCCGAAT 60.279 61.111 0.00 0.00 40.80 3.34
249 250 2.296480 CGCGAGCTACTGCCGAATC 61.296 63.158 0.00 0.00 40.80 2.52
250 251 2.296480 GCGAGCTACTGCCGAATCG 61.296 63.158 0.00 0.00 40.80 3.34
251 252 1.064296 CGAGCTACTGCCGAATCGT 59.936 57.895 0.82 0.00 40.80 3.73
252 253 1.202973 CGAGCTACTGCCGAATCGTG 61.203 60.000 0.82 0.00 40.80 4.35
253 254 1.483424 GAGCTACTGCCGAATCGTGC 61.483 60.000 0.82 5.55 40.80 5.34
254 255 2.860628 GCTACTGCCGAATCGTGCG 61.861 63.158 0.82 4.56 0.00 5.34
255 256 1.516386 CTACTGCCGAATCGTGCGT 60.516 57.895 0.82 9.55 0.00 5.24
256 257 1.076533 CTACTGCCGAATCGTGCGTT 61.077 55.000 0.82 0.00 0.00 4.84
257 258 1.348538 TACTGCCGAATCGTGCGTTG 61.349 55.000 0.82 2.72 0.00 4.10
258 259 3.982424 CTGCCGAATCGTGCGTTGC 62.982 63.158 0.82 0.00 0.00 4.17
259 260 4.811761 GCCGAATCGTGCGTTGCC 62.812 66.667 0.82 0.00 0.00 4.52
260 261 4.160635 CCGAATCGTGCGTTGCCC 62.161 66.667 0.82 0.00 0.00 5.36
261 262 4.160635 CGAATCGTGCGTTGCCCC 62.161 66.667 0.00 0.00 0.00 5.80
262 263 2.746277 GAATCGTGCGTTGCCCCT 60.746 61.111 0.00 0.00 0.00 4.79
263 264 3.039202 GAATCGTGCGTTGCCCCTG 62.039 63.158 0.00 0.00 0.00 4.45
283 284 4.335647 CCTGGGCTGGACGTGCTT 62.336 66.667 8.99 0.00 0.00 3.91
284 285 2.281761 CTGGGCTGGACGTGCTTT 60.282 61.111 8.99 0.00 0.00 3.51
285 286 1.003839 CTGGGCTGGACGTGCTTTA 60.004 57.895 8.99 0.00 0.00 1.85
286 287 0.605319 CTGGGCTGGACGTGCTTTAA 60.605 55.000 8.99 0.00 0.00 1.52
287 288 0.605319 TGGGCTGGACGTGCTTTAAG 60.605 55.000 8.99 0.00 0.00 1.85
288 289 1.502190 GGCTGGACGTGCTTTAAGC 59.498 57.895 10.38 10.38 42.82 3.09
289 290 0.955919 GGCTGGACGTGCTTTAAGCT 60.956 55.000 18.20 0.00 42.97 3.74
290 291 0.875059 GCTGGACGTGCTTTAAGCTT 59.125 50.000 18.20 3.48 42.97 3.74
291 292 1.135944 GCTGGACGTGCTTTAAGCTTC 60.136 52.381 18.20 11.05 42.97 3.86
292 293 1.126846 CTGGACGTGCTTTAAGCTTCG 59.873 52.381 23.59 23.59 42.97 3.79
294 295 1.136336 GGACGTGCTTTAAGCTTCGTG 60.136 52.381 30.55 15.22 45.68 4.35
295 296 0.234884 ACGTGCTTTAAGCTTCGTGC 59.765 50.000 27.32 6.38 44.76 5.34
296 297 3.355006 ACGTGCTTTAAGCTTCGTGCG 62.355 52.381 27.32 18.95 44.76 5.34
317 318 4.910722 CGGGCCGCGCAATGAATG 62.911 66.667 15.42 0.00 0.00 2.67
330 331 4.996062 CAATGAATGCAGGAAACCAAAC 57.004 40.909 0.00 0.00 0.00 2.93
331 332 2.791383 TGAATGCAGGAAACCAAACG 57.209 45.000 0.00 0.00 0.00 3.60
332 333 1.339610 TGAATGCAGGAAACCAAACGG 59.660 47.619 0.00 0.00 0.00 4.44
333 334 0.678950 AATGCAGGAAACCAAACGGG 59.321 50.000 0.00 0.00 44.81 5.28
334 335 1.815817 ATGCAGGAAACCAAACGGGC 61.816 55.000 0.00 0.00 42.05 6.13
335 336 3.047735 CAGGAAACCAAACGGGCC 58.952 61.111 0.00 0.00 42.05 5.80
336 337 1.830408 CAGGAAACCAAACGGGCCA 60.830 57.895 4.39 0.00 42.05 5.36
337 338 1.075896 AGGAAACCAAACGGGCCAA 60.076 52.632 4.39 0.00 42.05 4.52
338 339 0.688087 AGGAAACCAAACGGGCCAAA 60.688 50.000 4.39 0.00 42.05 3.28
339 340 0.394938 GGAAACCAAACGGGCCAAAT 59.605 50.000 4.39 0.00 42.05 2.32
340 341 1.202710 GGAAACCAAACGGGCCAAATT 60.203 47.619 4.39 0.00 42.05 1.82
341 342 2.139917 GAAACCAAACGGGCCAAATTC 58.860 47.619 4.39 0.00 42.05 2.17
342 343 1.419381 AACCAAACGGGCCAAATTCT 58.581 45.000 4.39 0.00 42.05 2.40
343 344 1.419381 ACCAAACGGGCCAAATTCTT 58.581 45.000 4.39 0.00 42.05 2.52
344 345 1.765904 ACCAAACGGGCCAAATTCTTT 59.234 42.857 4.39 0.00 42.05 2.52
345 346 2.224185 ACCAAACGGGCCAAATTCTTTC 60.224 45.455 4.39 0.00 42.05 2.62
346 347 2.412870 CAAACGGGCCAAATTCTTTCC 58.587 47.619 4.39 0.00 0.00 3.13
347 348 0.601057 AACGGGCCAAATTCTTTCCG 59.399 50.000 4.39 0.00 42.69 4.30
348 349 1.153842 CGGGCCAAATTCTTTCCGC 60.154 57.895 4.39 0.00 0.00 5.54
349 350 1.218047 GGGCCAAATTCTTTCCGCC 59.782 57.895 4.39 0.00 35.39 6.13
350 351 1.218047 GGCCAAATTCTTTCCGCCC 59.782 57.895 0.00 0.00 31.80 6.13
351 352 1.153842 GCCAAATTCTTTCCGCCCG 60.154 57.895 0.00 0.00 0.00 6.13
352 353 1.510844 CCAAATTCTTTCCGCCCGG 59.489 57.895 0.00 0.00 0.00 5.73
353 354 1.510844 CAAATTCTTTCCGCCCGGG 59.489 57.895 19.09 19.09 35.59 5.73
354 355 2.348104 AAATTCTTTCCGCCCGGGC 61.348 57.895 36.69 36.69 34.94 6.13
355 356 4.815108 ATTCTTTCCGCCCGGGCC 62.815 66.667 39.24 21.72 37.98 5.80
378 379 3.134127 GGACCTCATGCGGGCAAC 61.134 66.667 10.40 0.00 31.91 4.17
416 417 4.593864 GGGGGATGAGAGCGCGAC 62.594 72.222 12.10 2.22 0.00 5.19
454 455 4.217767 GGACCAAACCATAGACAAAAGTCC 59.782 45.833 0.00 0.00 33.90 3.85
461 462 4.003648 CCATAGACAAAAGTCCTTTCGCT 58.996 43.478 0.00 0.00 31.45 4.93
475 476 3.806521 CCTTTCGCTCCTGAGACATATTG 59.193 47.826 0.00 0.00 0.00 1.90
510 511 1.349026 TGCTTTCCAACTGGAGAGGAG 59.651 52.381 15.92 7.11 46.36 3.69
535 536 3.046374 TCTAACCAAATAGGAGAGGCCC 58.954 50.000 0.00 0.00 41.22 5.80
536 537 0.546598 AACCAAATAGGAGAGGCCCG 59.453 55.000 0.00 0.00 41.22 6.13
576 578 5.989777 TGACAACTAGCTACTTTGAAGGAAC 59.010 40.000 14.60 3.33 0.00 3.62
636 638 6.128090 TGCTATCTGCTTCTTCACAGAAATTG 60.128 38.462 0.00 0.00 45.49 2.32
648 864 6.844696 TCACAGAAATTGATAGGCGAATAC 57.155 37.500 0.00 0.00 0.00 1.89
649 865 5.758296 TCACAGAAATTGATAGGCGAATACC 59.242 40.000 0.00 0.00 0.00 2.73
889 1107 4.778415 CACACGCCTCCTCCGACG 62.778 72.222 0.00 0.00 0.00 5.12
938 1156 1.651240 CTCCCCGCAAATCACAGCAG 61.651 60.000 0.00 0.00 0.00 4.24
965 1183 0.739813 CACCACCGTTCCTCCGATTC 60.740 60.000 0.00 0.00 0.00 2.52
966 1184 1.153429 CCACCGTTCCTCCGATTCC 60.153 63.158 0.00 0.00 0.00 3.01
967 1185 1.594833 CACCGTTCCTCCGATTCCA 59.405 57.895 0.00 0.00 0.00 3.53
1325 1547 2.138179 GCTAGGCCACCACCGGATA 61.138 63.158 9.46 0.00 33.69 2.59
1339 1573 2.562298 ACCGGATAGTCGTTGTTTGGTA 59.438 45.455 9.46 0.00 0.00 3.25
1340 1574 2.925563 CCGGATAGTCGTTGTTTGGTAC 59.074 50.000 0.00 0.00 0.00 3.34
1346 1580 4.660789 AGTCGTTGTTTGGTACAGTACT 57.339 40.909 10.62 0.00 42.39 2.73
1354 1588 4.342951 TGTTTGGTACAGTACTAGCAGTGT 59.657 41.667 10.62 8.49 42.39 3.55
1366 1600 2.022129 GCAGTGTTCGTGGTCCTCG 61.022 63.158 7.02 7.02 0.00 4.63
1367 1601 1.372997 CAGTGTTCGTGGTCCTCGG 60.373 63.158 13.11 0.00 0.00 4.63
1370 1604 2.260743 GTTCGTGGTCCTCGGGTC 59.739 66.667 13.11 1.48 0.00 4.46
1372 1606 2.273179 TTCGTGGTCCTCGGGTCTG 61.273 63.158 13.11 0.00 0.00 3.51
1373 1607 2.675423 CGTGGTCCTCGGGTCTGA 60.675 66.667 5.40 0.00 0.00 3.27
1374 1608 2.273179 CGTGGTCCTCGGGTCTGAA 61.273 63.158 5.40 0.00 0.00 3.02
1375 1609 1.812686 CGTGGTCCTCGGGTCTGAAA 61.813 60.000 5.40 0.00 0.00 2.69
1382 1616 0.727398 CTCGGGTCTGAAAAATCGCC 59.273 55.000 0.00 0.00 0.00 5.54
1406 1640 4.047059 CGCTGCTGTTTGCCCTGG 62.047 66.667 0.00 0.00 42.00 4.45
1472 1714 3.751698 AGCAGTTTACCCTTGAATTCGTC 59.248 43.478 0.04 0.00 0.00 4.20
1473 1715 3.119955 GCAGTTTACCCTTGAATTCGTCC 60.120 47.826 0.04 0.00 0.00 4.79
1475 1717 3.329814 AGTTTACCCTTGAATTCGTCCCT 59.670 43.478 0.04 0.00 0.00 4.20
1476 1718 3.343941 TTACCCTTGAATTCGTCCCTG 57.656 47.619 0.04 0.00 0.00 4.45
1479 1721 3.112263 ACCCTTGAATTCGTCCCTGATA 58.888 45.455 0.04 0.00 0.00 2.15
1485 1728 3.709141 TGAATTCGTCCCTGATATGTGGA 59.291 43.478 0.04 0.00 0.00 4.02
1503 1746 4.886489 TGTGGATCTGTTGATGTTTGTTCA 59.114 37.500 0.00 0.00 32.19 3.18
1515 1758 1.163420 TTTGTTCATGCGCGTGGTCT 61.163 50.000 28.29 0.00 0.00 3.85
1564 1807 4.457257 GTCTTGCTCTGTAAATTTCAGCCT 59.543 41.667 0.00 0.00 33.48 4.58
1572 1815 6.009589 TCTGTAAATTTCAGCCTCCAAATCA 58.990 36.000 0.00 0.00 33.48 2.57
1574 1817 3.881937 AATTTCAGCCTCCAAATCAGC 57.118 42.857 0.00 0.00 0.00 4.26
1577 1820 2.119801 TCAGCCTCCAAATCAGCTTC 57.880 50.000 0.00 0.00 31.93 3.86
1578 1821 0.731417 CAGCCTCCAAATCAGCTTCG 59.269 55.000 0.00 0.00 31.93 3.79
1580 1823 0.392998 GCCTCCAAATCAGCTTCGGA 60.393 55.000 0.00 0.00 0.00 4.55
1602 1856 3.981071 TTGGATCCTACTCTGTGTTGG 57.019 47.619 14.23 4.32 41.83 3.77
1605 1859 2.237392 GGATCCTACTCTGTGTTGGCTT 59.763 50.000 3.84 0.00 40.58 4.35
1612 1866 2.292267 CTCTGTGTTGGCTTCAGTGTT 58.708 47.619 0.00 0.00 0.00 3.32
1613 1867 2.016318 TCTGTGTTGGCTTCAGTGTTG 58.984 47.619 0.00 0.00 0.00 3.33
1615 1869 1.340502 TGTGTTGGCTTCAGTGTTGGA 60.341 47.619 0.00 0.00 0.00 3.53
1616 1870 1.065551 GTGTTGGCTTCAGTGTTGGAC 59.934 52.381 0.00 0.00 0.00 4.02
1617 1871 1.064758 TGTTGGCTTCAGTGTTGGACT 60.065 47.619 0.00 0.00 34.02 3.85
1618 1872 1.604278 GTTGGCTTCAGTGTTGGACTC 59.396 52.381 0.00 0.00 29.75 3.36
1620 1874 1.211703 TGGCTTCAGTGTTGGACTCAA 59.788 47.619 0.00 0.00 29.75 3.02
1641 1944 5.988561 TCAACAAATCCTATTTTGTGTTGGC 59.011 36.000 12.80 0.00 46.33 4.52
1689 2077 2.125592 GCGCTCTTCTGCTGCTCT 60.126 61.111 0.00 0.00 32.72 4.09
1732 2122 8.315482 TGTAGTGCTGGAATGTGTTTAACTATA 58.685 33.333 0.00 0.00 0.00 1.31
1739 2129 8.500753 TGGAATGTGTTTAACTATATGTGACC 57.499 34.615 0.00 0.00 0.00 4.02
1743 2133 8.718102 ATGTGTTTAACTATATGTGACCTCAC 57.282 34.615 0.00 0.00 46.59 3.51
1898 2302 4.820716 GCATTGCTTGTGAAGGAGATCTAT 59.179 41.667 0.16 0.00 0.00 1.98
1917 2321 6.126863 TCTATTTTCTCTGGTGATTGGTGT 57.873 37.500 0.00 0.00 0.00 4.16
1925 2329 2.226330 TGGTGATTGGTGTAGTGTTGC 58.774 47.619 0.00 0.00 0.00 4.17
1936 2340 4.562757 GGTGTAGTGTTGCTGTTCATCCTA 60.563 45.833 0.00 0.00 0.00 2.94
1940 2344 6.816640 TGTAGTGTTGCTGTTCATCCTATTAC 59.183 38.462 0.00 0.00 0.00 1.89
1945 2349 3.199727 TGCTGTTCATCCTATTACTGCCA 59.800 43.478 0.00 0.00 35.43 4.92
1951 2355 7.398829 TGTTCATCCTATTACTGCCAGTTTAA 58.601 34.615 1.02 0.00 0.00 1.52
2046 2450 1.083806 GGCAATTTTTAGCAGCGGGC 61.084 55.000 0.00 0.00 45.30 6.13
2125 2531 2.256174 CCACGCAGCAATTTCAGAATG 58.744 47.619 0.00 0.00 37.54 2.67
2156 2562 2.941720 CTGAGCATTTACAGAAGCCTCC 59.058 50.000 0.00 0.00 36.38 4.30
2209 2615 2.667536 AGCTGGCAAGTGTCGCTG 60.668 61.111 0.00 0.00 30.88 5.18
2219 2625 3.000322 GCAAGTGTCGCTGTACATCATAC 60.000 47.826 0.00 0.00 0.00 2.39
2226 2632 3.116300 CGCTGTACATCATACTCCACAC 58.884 50.000 0.00 0.00 0.00 3.82
2227 2633 3.428862 CGCTGTACATCATACTCCACACA 60.429 47.826 0.00 0.00 0.00 3.72
2308 2714 5.234466 AGTACAATATGAAGAGGATGGCC 57.766 43.478 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.072486 TACCGGCGAGCAGGTAAGC 62.072 63.158 21.43 0.00 42.22 3.09
1 2 1.226888 GTACCGGCGAGCAGGTAAG 60.227 63.158 24.35 0.00 45.49 2.34
2 3 2.713967 GGTACCGGCGAGCAGGTAA 61.714 63.158 24.35 9.71 45.49 2.85
3 4 3.142838 GGTACCGGCGAGCAGGTA 61.143 66.667 20.20 20.20 42.48 3.08
6 7 3.900892 ATCGGTACCGGCGAGCAG 61.901 66.667 32.80 3.50 40.25 4.24
7 8 4.201679 CATCGGTACCGGCGAGCA 62.202 66.667 32.80 14.07 40.25 4.26
34 35 4.856607 CTCCGTTCGCGCTCTCCC 62.857 72.222 5.56 0.00 39.70 4.30
35 36 4.856607 CCTCCGTTCGCGCTCTCC 62.857 72.222 5.56 0.00 39.70 3.71
36 37 3.338126 TTCCTCCGTTCGCGCTCTC 62.338 63.158 5.56 0.00 39.70 3.20
37 38 3.343788 CTTCCTCCGTTCGCGCTCT 62.344 63.158 5.56 0.00 39.70 4.09
38 39 2.814183 TTCTTCCTCCGTTCGCGCTC 62.814 60.000 5.56 0.00 39.70 5.03
39 40 2.227089 ATTCTTCCTCCGTTCGCGCT 62.227 55.000 5.56 0.00 39.70 5.92
40 41 1.810030 ATTCTTCCTCCGTTCGCGC 60.810 57.895 0.00 0.00 39.70 6.86
41 42 1.421410 CCATTCTTCCTCCGTTCGCG 61.421 60.000 0.00 0.00 40.93 5.87
42 43 0.391263 ACCATTCTTCCTCCGTTCGC 60.391 55.000 0.00 0.00 0.00 4.70
43 44 1.359848 CACCATTCTTCCTCCGTTCG 58.640 55.000 0.00 0.00 0.00 3.95
44 45 1.739067 CCACCATTCTTCCTCCGTTC 58.261 55.000 0.00 0.00 0.00 3.95
45 46 0.322546 GCCACCATTCTTCCTCCGTT 60.323 55.000 0.00 0.00 0.00 4.44
46 47 1.299976 GCCACCATTCTTCCTCCGT 59.700 57.895 0.00 0.00 0.00 4.69
47 48 1.815421 CGCCACCATTCTTCCTCCG 60.815 63.158 0.00 0.00 0.00 4.63
48 49 1.452108 CCGCCACCATTCTTCCTCC 60.452 63.158 0.00 0.00 0.00 4.30
49 50 1.452108 CCCGCCACCATTCTTCCTC 60.452 63.158 0.00 0.00 0.00 3.71
50 51 1.915078 CTCCCGCCACCATTCTTCCT 61.915 60.000 0.00 0.00 0.00 3.36
51 52 1.452108 CTCCCGCCACCATTCTTCC 60.452 63.158 0.00 0.00 0.00 3.46
52 53 0.322546 AACTCCCGCCACCATTCTTC 60.323 55.000 0.00 0.00 0.00 2.87
53 54 0.609131 CAACTCCCGCCACCATTCTT 60.609 55.000 0.00 0.00 0.00 2.52
54 55 1.002134 CAACTCCCGCCACCATTCT 60.002 57.895 0.00 0.00 0.00 2.40
55 56 2.046285 CCAACTCCCGCCACCATTC 61.046 63.158 0.00 0.00 0.00 2.67
56 57 2.035626 CCAACTCCCGCCACCATT 59.964 61.111 0.00 0.00 0.00 3.16
57 58 4.047125 CCCAACTCCCGCCACCAT 62.047 66.667 0.00 0.00 0.00 3.55
65 66 4.410400 CTCACCGCCCCAACTCCC 62.410 72.222 0.00 0.00 0.00 4.30
66 67 4.410400 CCTCACCGCCCCAACTCC 62.410 72.222 0.00 0.00 0.00 3.85
67 68 4.410400 CCCTCACCGCCCCAACTC 62.410 72.222 0.00 0.00 0.00 3.01
68 69 4.974438 TCCCTCACCGCCCCAACT 62.974 66.667 0.00 0.00 0.00 3.16
69 70 4.410400 CTCCCTCACCGCCCCAAC 62.410 72.222 0.00 0.00 0.00 3.77
76 77 1.345715 ATTTAGCCCCTCCCTCACCG 61.346 60.000 0.00 0.00 0.00 4.94
77 78 1.700186 CTATTTAGCCCCTCCCTCACC 59.300 57.143 0.00 0.00 0.00 4.02
78 79 1.700186 CCTATTTAGCCCCTCCCTCAC 59.300 57.143 0.00 0.00 0.00 3.51
79 80 1.416013 CCCTATTTAGCCCCTCCCTCA 60.416 57.143 0.00 0.00 0.00 3.86
80 81 1.363246 CCCTATTTAGCCCCTCCCTC 58.637 60.000 0.00 0.00 0.00 4.30
81 82 0.103876 CCCCTATTTAGCCCCTCCCT 60.104 60.000 0.00 0.00 0.00 4.20
82 83 1.140772 CCCCCTATTTAGCCCCTCCC 61.141 65.000 0.00 0.00 0.00 4.30
83 84 0.403008 ACCCCCTATTTAGCCCCTCC 60.403 60.000 0.00 0.00 0.00 4.30
84 85 0.771755 CACCCCCTATTTAGCCCCTC 59.228 60.000 0.00 0.00 0.00 4.30
85 86 0.701310 CCACCCCCTATTTAGCCCCT 60.701 60.000 0.00 0.00 0.00 4.79
86 87 0.699922 TCCACCCCCTATTTAGCCCC 60.700 60.000 0.00 0.00 0.00 5.80
87 88 0.771755 CTCCACCCCCTATTTAGCCC 59.228 60.000 0.00 0.00 0.00 5.19
88 89 0.110678 GCTCCACCCCCTATTTAGCC 59.889 60.000 0.00 0.00 0.00 3.93
89 90 0.250338 CGCTCCACCCCCTATTTAGC 60.250 60.000 0.00 0.00 0.00 3.09
90 91 0.396811 CCGCTCCACCCCCTATTTAG 59.603 60.000 0.00 0.00 0.00 1.85
91 92 1.702022 GCCGCTCCACCCCCTATTTA 61.702 60.000 0.00 0.00 0.00 1.40
92 93 3.056754 GCCGCTCCACCCCCTATTT 62.057 63.158 0.00 0.00 0.00 1.40
93 94 3.489513 GCCGCTCCACCCCCTATT 61.490 66.667 0.00 0.00 0.00 1.73
109 110 3.682292 ATTTCGGCTCACCTCCCGC 62.682 63.158 0.00 0.00 44.01 6.13
110 111 1.521681 GATTTCGGCTCACCTCCCG 60.522 63.158 0.00 0.00 45.64 5.14
111 112 1.153147 GGATTTCGGCTCACCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
112 113 0.179070 GAGGATTTCGGCTCACCTCC 60.179 60.000 0.00 0.00 40.58 4.30
113 114 0.179070 GGAGGATTTCGGCTCACCTC 60.179 60.000 0.00 0.00 44.21 3.85
114 115 1.627297 GGGAGGATTTCGGCTCACCT 61.627 60.000 0.00 0.00 0.00 4.00
115 116 1.153147 GGGAGGATTTCGGCTCACC 60.153 63.158 0.00 0.00 0.00 4.02
116 117 1.521681 CGGGAGGATTTCGGCTCAC 60.522 63.158 0.00 0.00 0.00 3.51
117 118 2.900273 CGGGAGGATTTCGGCTCA 59.100 61.111 0.00 0.00 0.00 4.26
118 119 2.589159 GCGGGAGGATTTCGGCTC 60.589 66.667 0.00 0.00 0.00 4.70
119 120 4.176752 GGCGGGAGGATTTCGGCT 62.177 66.667 0.00 0.00 44.29 5.52
121 122 2.660258 AATCGGCGGGAGGATTTCGG 62.660 60.000 7.21 0.00 28.81 4.30
122 123 0.814010 AAATCGGCGGGAGGATTTCG 60.814 55.000 7.21 0.00 38.18 3.46
123 124 1.389555 AAAATCGGCGGGAGGATTTC 58.610 50.000 7.21 0.00 40.85 2.17
124 125 1.749063 GAAAAATCGGCGGGAGGATTT 59.251 47.619 7.21 1.98 42.87 2.17
125 126 1.389555 GAAAAATCGGCGGGAGGATT 58.610 50.000 7.21 0.00 34.48 3.01
126 127 0.814010 CGAAAAATCGGCGGGAGGAT 60.814 55.000 7.21 0.00 0.00 3.24
127 128 1.448893 CGAAAAATCGGCGGGAGGA 60.449 57.895 7.21 0.00 0.00 3.71
128 129 2.469516 CCGAAAAATCGGCGGGAGG 61.470 63.158 7.21 0.00 46.76 4.30
129 130 3.098555 CCGAAAAATCGGCGGGAG 58.901 61.111 7.21 0.00 46.76 4.30
136 137 2.640457 CGCGTCGCCGAAAAATCG 60.640 61.111 12.44 0.00 35.63 3.34
137 138 2.276430 CCGCGTCGCCGAAAAATC 60.276 61.111 12.44 0.00 35.63 2.17
138 139 3.795342 CCCGCGTCGCCGAAAAAT 61.795 61.111 12.44 0.00 35.63 1.82
156 157 2.279120 GGAGATGGTGCGAGCTCG 60.279 66.667 31.37 31.37 43.27 5.03
157 158 2.107953 GGGAGATGGTGCGAGCTC 59.892 66.667 2.73 2.73 0.00 4.09
158 159 3.474570 GGGGAGATGGTGCGAGCT 61.475 66.667 0.00 0.00 0.00 4.09
159 160 3.474570 AGGGGAGATGGTGCGAGC 61.475 66.667 0.00 0.00 0.00 5.03
160 161 2.503061 CAGGGGAGATGGTGCGAG 59.497 66.667 0.00 0.00 0.00 5.03
161 162 3.785859 GCAGGGGAGATGGTGCGA 61.786 66.667 0.00 0.00 0.00 5.10
162 163 3.746949 GAGCAGGGGAGATGGTGCG 62.747 68.421 0.00 0.00 40.97 5.34
163 164 2.191641 GAGCAGGGGAGATGGTGC 59.808 66.667 0.00 0.00 36.10 5.01
164 165 2.503061 CGAGCAGGGGAGATGGTG 59.497 66.667 0.00 0.00 0.00 4.17
165 166 3.474570 GCGAGCAGGGGAGATGGT 61.475 66.667 0.00 0.00 0.00 3.55
166 167 3.473647 TGCGAGCAGGGGAGATGG 61.474 66.667 0.00 0.00 0.00 3.51
167 168 2.202987 GTGCGAGCAGGGGAGATG 60.203 66.667 0.00 0.00 0.00 2.90
168 169 3.842923 CGTGCGAGCAGGGGAGAT 61.843 66.667 9.63 0.00 0.00 2.75
170 171 4.504916 CTCGTGCGAGCAGGGGAG 62.505 72.222 11.78 8.68 34.53 4.30
175 176 4.504916 CTCCCCTCGTGCGAGCAG 62.505 72.222 15.32 8.95 40.69 4.24
177 178 3.708220 CTTCTCCCCTCGTGCGAGC 62.708 68.421 15.32 0.00 40.69 5.03
178 179 2.492090 CTTCTCCCCTCGTGCGAG 59.508 66.667 13.99 13.99 41.63 5.03
179 180 3.760035 GCTTCTCCCCTCGTGCGA 61.760 66.667 0.00 0.00 0.00 5.10
184 185 4.856607 GACGCGCTTCTCCCCTCG 62.857 72.222 5.73 0.00 0.00 4.63
185 186 4.856607 CGACGCGCTTCTCCCCTC 62.857 72.222 12.41 0.00 0.00 4.30
229 230 2.669808 ATTCGGCAGTAGCTCGCGAG 62.670 60.000 31.37 31.37 41.70 5.03
230 231 2.663630 GATTCGGCAGTAGCTCGCGA 62.664 60.000 9.26 9.26 41.70 5.87
231 232 2.278857 ATTCGGCAGTAGCTCGCG 60.279 61.111 0.00 0.00 41.70 5.87
232 233 2.296480 CGATTCGGCAGTAGCTCGC 61.296 63.158 0.00 0.00 41.70 5.03
233 234 1.064296 ACGATTCGGCAGTAGCTCG 59.936 57.895 11.29 0.00 39.65 5.03
234 235 1.483424 GCACGATTCGGCAGTAGCTC 61.483 60.000 11.29 0.00 41.70 4.09
235 236 1.519455 GCACGATTCGGCAGTAGCT 60.519 57.895 11.29 0.00 41.70 3.32
236 237 2.860628 CGCACGATTCGGCAGTAGC 61.861 63.158 11.29 3.85 41.10 3.58
237 238 1.076533 AACGCACGATTCGGCAGTAG 61.077 55.000 11.29 1.73 0.00 2.57
238 239 1.080366 AACGCACGATTCGGCAGTA 60.080 52.632 11.29 0.00 0.00 2.74
239 240 2.357034 AACGCACGATTCGGCAGT 60.357 55.556 11.29 10.04 0.00 4.40
240 241 2.096406 CAACGCACGATTCGGCAG 59.904 61.111 11.29 9.51 0.00 4.85
241 242 4.083600 GCAACGCACGATTCGGCA 62.084 61.111 11.29 0.00 0.00 5.69
242 243 4.811761 GGCAACGCACGATTCGGC 62.812 66.667 11.29 9.85 0.00 5.54
243 244 4.160635 GGGCAACGCACGATTCGG 62.161 66.667 11.29 0.73 37.60 4.30
266 267 2.463589 TAAAGCACGTCCAGCCCAGG 62.464 60.000 0.00 0.00 0.00 4.45
267 268 0.605319 TTAAAGCACGTCCAGCCCAG 60.605 55.000 0.00 0.00 0.00 4.45
268 269 0.605319 CTTAAAGCACGTCCAGCCCA 60.605 55.000 0.00 0.00 0.00 5.36
269 270 1.923227 GCTTAAAGCACGTCCAGCCC 61.923 60.000 0.00 0.00 41.89 5.19
270 271 0.955919 AGCTTAAAGCACGTCCAGCC 60.956 55.000 0.00 0.00 45.56 4.85
271 272 0.875059 AAGCTTAAAGCACGTCCAGC 59.125 50.000 0.00 0.00 45.56 4.85
272 273 1.126846 CGAAGCTTAAAGCACGTCCAG 59.873 52.381 0.00 0.00 45.56 3.86
273 274 1.144969 CGAAGCTTAAAGCACGTCCA 58.855 50.000 0.00 0.00 45.56 4.02
274 275 1.136336 CACGAAGCTTAAAGCACGTCC 60.136 52.381 0.00 0.00 46.66 4.79
275 276 1.721804 GCACGAAGCTTAAAGCACGTC 60.722 52.381 0.00 0.00 46.66 4.34
277 278 0.785708 CGCACGAAGCTTAAAGCACG 60.786 55.000 0.00 0.00 45.56 5.34
278 279 0.511221 TCGCACGAAGCTTAAAGCAC 59.489 50.000 0.00 0.00 45.56 4.40
279 280 1.128507 CATCGCACGAAGCTTAAAGCA 59.871 47.619 0.00 0.00 45.56 3.91
280 281 1.802839 CATCGCACGAAGCTTAAAGC 58.197 50.000 0.00 2.41 42.84 3.51
281 282 1.802839 GCATCGCACGAAGCTTAAAG 58.197 50.000 12.51 0.00 42.61 1.85
282 283 0.094558 CGCATCGCACGAAGCTTAAA 59.905 50.000 16.80 0.00 42.61 1.52
283 284 1.692148 CCGCATCGCACGAAGCTTAA 61.692 55.000 16.80 0.00 42.61 1.85
284 285 2.164663 CCGCATCGCACGAAGCTTA 61.165 57.895 16.80 0.00 42.61 3.09
285 286 3.490759 CCGCATCGCACGAAGCTT 61.491 61.111 16.80 0.00 42.61 3.74
300 301 4.910722 CATTCATTGCGCGGCCCG 62.911 66.667 8.83 0.00 40.75 6.13
309 310 3.429543 CGTTTGGTTTCCTGCATTCATTG 59.570 43.478 0.00 0.00 0.00 2.82
310 311 3.554752 CCGTTTGGTTTCCTGCATTCATT 60.555 43.478 0.00 0.00 0.00 2.57
311 312 2.029110 CCGTTTGGTTTCCTGCATTCAT 60.029 45.455 0.00 0.00 0.00 2.57
312 313 1.339610 CCGTTTGGTTTCCTGCATTCA 59.660 47.619 0.00 0.00 0.00 2.57
313 314 1.336795 CCCGTTTGGTTTCCTGCATTC 60.337 52.381 0.00 0.00 0.00 2.67
314 315 0.678950 CCCGTTTGGTTTCCTGCATT 59.321 50.000 0.00 0.00 0.00 3.56
315 316 1.815817 GCCCGTTTGGTTTCCTGCAT 61.816 55.000 0.00 0.00 36.04 3.96
316 317 2.494530 GCCCGTTTGGTTTCCTGCA 61.495 57.895 0.00 0.00 36.04 4.41
317 318 2.338620 GCCCGTTTGGTTTCCTGC 59.661 61.111 0.00 0.00 36.04 4.85
318 319 1.395826 TTGGCCCGTTTGGTTTCCTG 61.396 55.000 0.00 0.00 36.04 3.86
319 320 0.688087 TTTGGCCCGTTTGGTTTCCT 60.688 50.000 0.00 0.00 36.04 3.36
320 321 0.394938 ATTTGGCCCGTTTGGTTTCC 59.605 50.000 0.00 0.00 36.04 3.13
321 322 2.139917 GAATTTGGCCCGTTTGGTTTC 58.860 47.619 0.00 0.00 36.04 2.78
322 323 1.765904 AGAATTTGGCCCGTTTGGTTT 59.234 42.857 0.00 0.00 36.04 3.27
323 324 1.419381 AGAATTTGGCCCGTTTGGTT 58.581 45.000 0.00 0.00 36.04 3.67
324 325 1.419381 AAGAATTTGGCCCGTTTGGT 58.581 45.000 0.00 0.00 36.04 3.67
325 326 2.412870 GAAAGAATTTGGCCCGTTTGG 58.587 47.619 0.00 0.00 39.27 3.28
326 327 2.412870 GGAAAGAATTTGGCCCGTTTG 58.587 47.619 0.00 0.00 39.27 2.93
327 328 1.000394 CGGAAAGAATTTGGCCCGTTT 60.000 47.619 0.00 0.00 39.27 3.60
328 329 0.601057 CGGAAAGAATTTGGCCCGTT 59.399 50.000 0.00 0.00 39.27 4.44
329 330 1.873270 GCGGAAAGAATTTGGCCCGT 61.873 55.000 0.00 0.00 42.73 5.28
330 331 1.153842 GCGGAAAGAATTTGGCCCG 60.154 57.895 0.00 0.00 43.37 6.13
331 332 1.218047 GGCGGAAAGAATTTGGCCC 59.782 57.895 0.00 0.00 44.25 5.80
332 333 4.910956 GGCGGAAAGAATTTGGCC 57.089 55.556 0.00 0.00 43.91 5.36
333 334 1.153842 CGGGCGGAAAGAATTTGGC 60.154 57.895 0.00 0.00 39.27 4.52
334 335 1.510844 CCGGGCGGAAAGAATTTGG 59.489 57.895 0.00 0.00 39.27 3.28
335 336 1.510844 CCCGGGCGGAAAGAATTTG 59.489 57.895 8.08 0.00 39.27 2.32
336 337 2.348104 GCCCGGGCGGAAAGAATTT 61.348 57.895 33.60 0.00 43.98 1.82
337 338 2.754254 GCCCGGGCGGAAAGAATT 60.754 61.111 33.60 0.00 37.50 2.17
338 339 4.815108 GGCCCGGGCGGAAAGAAT 62.815 66.667 38.22 0.00 43.06 2.40
357 358 4.864334 CCCGCATGAGGTCCAGCC 62.864 72.222 14.88 0.00 37.58 4.85
359 360 3.626996 TTGCCCGCATGAGGTCCAG 62.627 63.158 14.88 0.00 0.00 3.86
360 361 3.645660 TTGCCCGCATGAGGTCCA 61.646 61.111 14.88 8.24 0.00 4.02
361 362 3.134127 GTTGCCCGCATGAGGTCC 61.134 66.667 14.88 5.64 0.00 4.46
362 363 3.134127 GGTTGCCCGCATGAGGTC 61.134 66.667 14.88 1.40 0.00 3.85
363 364 2.992817 TTTGGTTGCCCGCATGAGGT 62.993 55.000 14.88 0.00 0.00 3.85
364 365 2.274645 TTTGGTTGCCCGCATGAGG 61.275 57.895 8.78 8.78 0.00 3.86
365 366 1.080569 GTTTGGTTGCCCGCATGAG 60.081 57.895 0.00 0.00 0.00 2.90
366 367 1.829970 TGTTTGGTTGCCCGCATGA 60.830 52.632 0.00 0.00 0.00 3.07
367 368 1.664333 GTGTTTGGTTGCCCGCATG 60.664 57.895 0.00 0.00 0.00 4.06
368 369 2.733945 GTGTTTGGTTGCCCGCAT 59.266 55.556 0.00 0.00 0.00 4.73
369 370 3.893763 CGTGTTTGGTTGCCCGCA 61.894 61.111 0.00 0.00 0.00 5.69
370 371 3.817274 GACGTGTTTGGTTGCCCGC 62.817 63.158 0.00 0.00 0.00 6.13
371 372 2.330041 GACGTGTTTGGTTGCCCG 59.670 61.111 0.00 0.00 0.00 6.13
372 373 0.535553 TAGGACGTGTTTGGTTGCCC 60.536 55.000 0.00 0.00 0.00 5.36
373 374 1.265905 CTTAGGACGTGTTTGGTTGCC 59.734 52.381 0.00 0.00 0.00 4.52
378 379 2.095263 CCATTGCTTAGGACGTGTTTGG 60.095 50.000 0.00 0.00 0.00 3.28
403 404 2.202663 TGCAGTCGCGCTCTCATC 60.203 61.111 5.56 0.00 42.97 2.92
404 405 2.507992 GTGCAGTCGCGCTCTCAT 60.508 61.111 5.56 0.00 45.49 2.90
426 427 2.224917 TGTCTATGGTTTGGTCCAACCC 60.225 50.000 11.25 11.25 41.09 4.11
427 428 3.149005 TGTCTATGGTTTGGTCCAACC 57.851 47.619 2.98 9.75 41.09 3.77
428 429 5.068591 ACTTTTGTCTATGGTTTGGTCCAAC 59.931 40.000 2.98 0.00 41.09 3.77
454 455 4.437239 ACAATATGTCTCAGGAGCGAAAG 58.563 43.478 0.00 0.00 0.00 2.62
475 476 6.234723 TGGAAAGCAAACTTTTGTTCAAAC 57.765 33.333 3.74 0.00 46.20 2.93
510 511 5.301555 GCCTCTCCTATTTGGTTAGATGTC 58.698 45.833 0.00 0.00 37.07 3.06
552 554 5.801531 TCCTTCAAAGTAGCTAGTTGTCA 57.198 39.130 14.55 0.00 0.00 3.58
585 587 9.832445 ATTTGGATGTACGTAGATCAAACTAAT 57.168 29.630 27.88 17.66 0.00 1.73
586 588 9.093970 CATTTGGATGTACGTAGATCAAACTAA 57.906 33.333 27.88 16.53 0.00 2.24
587 589 7.223971 GCATTTGGATGTACGTAGATCAAACTA 59.776 37.037 27.88 13.81 35.63 2.24
588 590 6.037172 GCATTTGGATGTACGTAGATCAAACT 59.963 38.462 27.88 17.66 35.63 2.66
589 591 6.037172 AGCATTTGGATGTACGTAGATCAAAC 59.963 38.462 27.88 14.95 35.63 2.93
590 592 6.112734 AGCATTTGGATGTACGTAGATCAAA 58.887 36.000 27.88 22.46 35.63 2.69
591 593 5.670485 AGCATTTGGATGTACGTAGATCAA 58.330 37.500 27.88 18.34 35.63 2.57
592 594 5.276461 AGCATTTGGATGTACGTAGATCA 57.724 39.130 27.88 15.00 35.63 2.92
593 595 7.274468 CAGATAGCATTTGGATGTACGTAGATC 59.726 40.741 21.28 21.28 35.63 2.75
594 596 7.093354 CAGATAGCATTTGGATGTACGTAGAT 58.907 38.462 4.66 4.66 35.63 1.98
595 597 6.447162 CAGATAGCATTTGGATGTACGTAGA 58.553 40.000 0.00 0.00 35.63 2.59
596 598 5.119279 GCAGATAGCATTTGGATGTACGTAG 59.881 44.000 0.00 0.00 44.79 3.51
597 599 4.988540 GCAGATAGCATTTGGATGTACGTA 59.011 41.667 0.00 0.00 44.79 3.57
598 600 3.809832 GCAGATAGCATTTGGATGTACGT 59.190 43.478 0.00 0.00 44.79 3.57
599 601 4.395581 GCAGATAGCATTTGGATGTACG 57.604 45.455 0.00 0.00 44.79 3.67
636 638 3.367025 GCAACATACGGTATTCGCCTATC 59.633 47.826 0.00 0.00 43.89 2.08
965 1183 4.758251 TGCGAGCGGATGTGGTGG 62.758 66.667 0.00 0.00 0.00 4.61
966 1184 3.190849 CTGCGAGCGGATGTGGTG 61.191 66.667 0.00 0.00 0.00 4.17
1321 1543 4.563061 ACTGTACCAAACAACGACTATCC 58.437 43.478 0.00 0.00 37.74 2.59
1325 1547 4.660789 AGTACTGTACCAAACAACGACT 57.339 40.909 14.05 0.00 37.74 4.18
1339 1573 2.030185 CCACGAACACTGCTAGTACTGT 60.030 50.000 5.39 0.00 0.00 3.55
1340 1574 2.030185 ACCACGAACACTGCTAGTACTG 60.030 50.000 5.39 0.00 0.00 2.74
1346 1580 0.601558 GAGGACCACGAACACTGCTA 59.398 55.000 0.00 0.00 0.00 3.49
1354 1588 2.116772 AGACCCGAGGACCACGAA 59.883 61.111 13.31 0.00 0.00 3.85
1366 1600 1.136774 GCGGCGATTTTTCAGACCC 59.863 57.895 12.98 0.00 0.00 4.46
1367 1601 0.451783 ATGCGGCGATTTTTCAGACC 59.548 50.000 12.98 0.00 0.00 3.85
1370 1604 1.593070 CGAGATGCGGCGATTTTTCAG 60.593 52.381 12.98 0.00 36.03 3.02
1372 1606 0.925721 GCGAGATGCGGCGATTTTTC 60.926 55.000 12.98 0.00 41.29 2.29
1373 1607 1.062525 GCGAGATGCGGCGATTTTT 59.937 52.632 12.98 0.00 41.29 1.94
1374 1608 2.709475 GCGAGATGCGGCGATTTT 59.291 55.556 12.98 0.00 41.29 1.82
1406 1640 1.270550 CATCCAGACAACAAACAGGGC 59.729 52.381 0.00 0.00 0.00 5.19
1409 1643 5.639506 CCTAGTACATCCAGACAACAAACAG 59.360 44.000 0.00 0.00 0.00 3.16
1472 1714 4.694760 TCAACAGATCCACATATCAGGG 57.305 45.455 0.00 0.00 0.00 4.45
1473 1715 5.618236 ACATCAACAGATCCACATATCAGG 58.382 41.667 0.00 0.00 0.00 3.86
1475 1717 6.885918 ACAAACATCAACAGATCCACATATCA 59.114 34.615 0.00 0.00 0.00 2.15
1476 1718 7.325660 ACAAACATCAACAGATCCACATATC 57.674 36.000 0.00 0.00 0.00 1.63
1479 1721 5.535783 TGAACAAACATCAACAGATCCACAT 59.464 36.000 0.00 0.00 0.00 3.21
1485 1728 4.478699 CGCATGAACAAACATCAACAGAT 58.521 39.130 0.00 0.00 0.00 2.90
1503 1746 2.404215 GTAATATCAGACCACGCGCAT 58.596 47.619 5.73 0.00 0.00 4.73
1515 1758 5.079689 TGAAGAACGCACTGGTAATATCA 57.920 39.130 0.00 0.00 0.00 2.15
1580 1823 4.848357 CCAACACAGAGTAGGATCCAAAT 58.152 43.478 15.82 0.00 0.00 2.32
1592 1846 1.959042 ACACTGAAGCCAACACAGAG 58.041 50.000 0.00 0.00 35.85 3.35
1594 1848 1.066002 CCAACACTGAAGCCAACACAG 59.934 52.381 0.00 0.00 37.62 3.66
1641 1944 3.057736 CCTGAATCCAGCAAACACTGAAG 60.058 47.826 0.00 0.00 40.25 3.02
1689 2077 7.062956 CAGCACTACAAGTTTAACATCACGATA 59.937 37.037 0.00 0.00 0.00 2.92
1862 2266 7.252708 TCACAAGCAATGCTAATAACTTGATG 58.747 34.615 8.68 1.05 38.25 3.07
1876 2280 6.939132 AATAGATCTCCTTCACAAGCAATG 57.061 37.500 0.00 0.00 0.00 2.82
1898 2302 5.063204 CACTACACCAATCACCAGAGAAAA 58.937 41.667 0.00 0.00 0.00 2.29
1917 2321 7.041721 CAGTAATAGGATGAACAGCAACACTA 58.958 38.462 0.00 0.00 0.00 2.74
1925 2329 5.028549 ACTGGCAGTAATAGGATGAACAG 57.971 43.478 20.61 0.00 0.00 3.16
1936 2340 3.428413 ACGGGTTAAACTGGCAGTAAT 57.572 42.857 22.37 15.36 0.00 1.89
1940 2344 3.672241 GCAATTACGGGTTAAACTGGCAG 60.672 47.826 14.16 14.16 0.00 4.85
1945 2349 4.822896 TCAACAGCAATTACGGGTTAAACT 59.177 37.500 0.00 0.00 0.00 2.66
1951 2355 2.561478 AGTCAACAGCAATTACGGGT 57.439 45.000 0.00 0.00 0.00 5.28
1983 2387 9.387123 GCAAAACAAACTTAAACAAAATTCACA 57.613 25.926 0.00 0.00 0.00 3.58
2062 2466 2.514458 ATTTACCTGTTCTGGCCCAG 57.486 50.000 3.69 3.69 0.00 4.45
2064 2468 3.323691 ACAAAATTTACCTGTTCTGGCCC 59.676 43.478 0.00 0.00 0.00 5.80
2065 2469 4.306600 CACAAAATTTACCTGTTCTGGCC 58.693 43.478 0.00 0.00 0.00 5.36
2099 2503 4.332543 TCTGAAATTGCTGCGTGGTATTAG 59.667 41.667 0.00 0.00 0.00 1.73
2100 2504 4.257731 TCTGAAATTGCTGCGTGGTATTA 58.742 39.130 0.00 0.00 0.00 0.98
2101 2505 3.081061 TCTGAAATTGCTGCGTGGTATT 58.919 40.909 0.00 0.00 0.00 1.89
2102 2506 2.710377 TCTGAAATTGCTGCGTGGTAT 58.290 42.857 0.00 0.00 0.00 2.73
2103 2507 2.177394 TCTGAAATTGCTGCGTGGTA 57.823 45.000 0.00 0.00 0.00 3.25
2105 2509 2.256174 CATTCTGAAATTGCTGCGTGG 58.744 47.619 0.00 0.00 0.00 4.94
2106 2510 1.652124 GCATTCTGAAATTGCTGCGTG 59.348 47.619 8.37 0.00 0.00 5.34
2125 2531 2.496828 AAATGCTCAGCGCCTTTGGC 62.497 55.000 2.29 2.32 46.75 4.52
2193 2599 1.667830 TACAGCGACACTTGCCAGC 60.668 57.895 0.00 0.00 0.00 4.85
2209 2615 4.625742 GTGTGTGTGTGGAGTATGATGTAC 59.374 45.833 0.00 0.00 0.00 2.90
2219 2625 3.378112 AGAATGTTTGTGTGTGTGTGGAG 59.622 43.478 0.00 0.00 0.00 3.86
2226 2632 5.688621 CCTGAATTCAGAATGTTTGTGTGTG 59.311 40.000 32.49 10.02 46.59 3.82
2227 2633 5.737063 GCCTGAATTCAGAATGTTTGTGTGT 60.737 40.000 32.49 0.00 46.59 3.72


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

AutoCloner maintained by Alex Coulton.