Multiple sequence alignment - TraesCS2D01G447400

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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 TraesCS2D01G447400 chr2D 100.000 3943 0 0 1 3943 557256711 557260653 0.000000e+00 7282.0
1 TraesCS2D01G447400 chr2B 88.437 3788 205 101 256 3913 664931983 664935667 0.000000e+00 4353.0
2 TraesCS2D01G447400 chr2B 90.566 106 10 0 1 106 664912850 664912955 1.480000e-29 141.0
3 TraesCS2D01G447400 chr2A 88.280 3703 201 97 262 3816 697288160 697291777 0.000000e+00 4218.0
4 TraesCS2D01G447400 chr6D 93.722 223 14 0 2166 2388 354223519 354223741 6.310000e-88 335.0
5 TraesCS2D01G447400 chr6D 88.318 214 21 3 1649 1858 354223193 354223406 1.820000e-63 254.0
6 TraesCS2D01G447400 chr6A 93.722 223 14 0 2166 2388 488062703 488062481 6.310000e-88 335.0
7 TraesCS2D01G447400 chr6A 89.855 207 19 2 1654 1858 488063009 488062803 8.400000e-67 265.0
8 TraesCS2D01G447400 chr6A 83.088 272 31 12 2531 2793 488062396 488062131 2.370000e-57 233.0
9 TraesCS2D01G447400 chr6B 92.511 227 17 0 2166 2392 524064489 524064263 3.800000e-85 326.0
10 TraesCS2D01G447400 chr6B 88.732 213 20 4 1648 1858 524064817 524064607 1.410000e-64 257.0
11 TraesCS2D01G447400 chr6B 86.161 224 21 6 2579 2794 524064120 524063899 2.370000e-57 233.0
12 TraesCS2D01G447400 chr7A 82.589 224 37 2 2165 2387 573097003 573096781 3.110000e-46 196.0
13 TraesCS2D01G447400 chr7B 82.301 226 38 2 2165 2389 533570541 533570317 1.120000e-45 195.0
14 TraesCS2D01G447400 chr7B 76.423 246 35 15 2166 2389 268454509 268454753 1.160000e-20 111.0
15 TraesCS2D01G447400 chr7D 82.143 224 40 0 2166 2389 505603597 505603374 4.020000e-45 193.0
16 TraesCS2D01G447400 chr1D 80.000 115 17 5 2680 2794 275942635 275942527 3.270000e-11 80.5
17 TraesCS2D01G447400 chr1B 79.825 114 17 5 2681 2794 375257129 375257022 1.170000e-10 78.7
18 TraesCS2D01G447400 chr1A 77.536 138 21 7 2680 2817 348399217 348399090 1.520000e-09 75.0


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 TraesCS2D01G447400 chr2D 557256711 557260653 3942 False 7282.000000 7282 100.000000 1 3943 1 chr2D.!!$F1 3942
1 TraesCS2D01G447400 chr2B 664931983 664935667 3684 False 4353.000000 4353 88.437000 256 3913 1 chr2B.!!$F2 3657
2 TraesCS2D01G447400 chr2A 697288160 697291777 3617 False 4218.000000 4218 88.280000 262 3816 1 chr2A.!!$F1 3554
3 TraesCS2D01G447400 chr6D 354223193 354223741 548 False 294.500000 335 91.020000 1649 2388 2 chr6D.!!$F1 739
4 TraesCS2D01G447400 chr6A 488062131 488063009 878 True 277.666667 335 88.888333 1654 2793 3 chr6A.!!$R1 1139
5 TraesCS2D01G447400 chr6B 524063899 524064817 918 True 272.000000 326 89.134667 1648 2794 3 chr6B.!!$R1 1146

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
92 93 0.975135 CCCCAAATGTCACAATGGCA 59.025 50.0 7.36 0.0 35.91 4.92 F
1251 1326 0.111639 TCCCCTGCTGGTTTGGTTAC 59.888 55.0 9.00 0.0 0.00 2.50 F
1978 2074 0.033504 GAACTTGGAGGAGCACACGA 59.966 55.0 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1944 0.181350 CGGAGAGGGGGAAGAAATGG 59.819 60.0 0.00 0.00 0.0 3.16 R
2453 2604 0.394565 AGGCGAGCTGAACTGAACTT 59.605 50.0 0.00 0.00 0.0 2.66 R
3395 3645 0.248661 CTCACTCGCGGTCATAGGTG 60.249 60.0 6.13 4.85 0.0 4.00 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
21 22 3.971468 AAATGCATAAAGGGGGCTAGA 57.029 42.857 0.00 0.00 0.00 2.43
22 23 3.971468 AATGCATAAAGGGGGCTAGAA 57.029 42.857 0.00 0.00 0.00 2.10
23 24 2.729028 TGCATAAAGGGGGCTAGAAC 57.271 50.000 0.00 0.00 0.00 3.01
24 25 2.205342 TGCATAAAGGGGGCTAGAACT 58.795 47.619 0.00 0.00 0.00 3.01
25 26 3.389866 TGCATAAAGGGGGCTAGAACTA 58.610 45.455 0.00 0.00 0.00 2.24
26 27 3.391296 TGCATAAAGGGGGCTAGAACTAG 59.609 47.826 0.00 4.67 36.29 2.57
27 28 3.244596 GCATAAAGGGGGCTAGAACTAGG 60.245 52.174 10.30 0.00 33.87 3.02
39 40 6.836577 GCTAGAACTAGGCTAAGTCAAATG 57.163 41.667 10.30 0.00 33.87 2.32
40 41 5.235401 GCTAGAACTAGGCTAAGTCAAATGC 59.765 44.000 10.30 0.00 33.87 3.56
41 42 5.428184 AGAACTAGGCTAAGTCAAATGCT 57.572 39.130 0.00 0.00 0.00 3.79
42 43 5.810095 AGAACTAGGCTAAGTCAAATGCTT 58.190 37.500 0.00 0.00 0.00 3.91
43 44 5.645497 AGAACTAGGCTAAGTCAAATGCTTG 59.355 40.000 0.00 0.00 0.00 4.01
44 45 4.265073 ACTAGGCTAAGTCAAATGCTTGG 58.735 43.478 0.00 0.00 33.01 3.61
45 46 2.450476 AGGCTAAGTCAAATGCTTGGG 58.550 47.619 0.00 0.00 33.01 4.12
46 47 1.134995 GGCTAAGTCAAATGCTTGGGC 60.135 52.381 9.92 9.92 41.13 5.36
47 48 1.821136 GCTAAGTCAAATGCTTGGGCT 59.179 47.619 0.00 0.00 39.59 5.19
48 49 3.016736 GCTAAGTCAAATGCTTGGGCTA 58.983 45.455 0.00 0.00 39.59 3.93
49 50 3.443681 GCTAAGTCAAATGCTTGGGCTAA 59.556 43.478 0.00 0.00 39.59 3.09
50 51 4.082245 GCTAAGTCAAATGCTTGGGCTAAA 60.082 41.667 0.00 0.00 39.59 1.85
51 52 4.953940 AAGTCAAATGCTTGGGCTAAAA 57.046 36.364 0.00 0.00 39.59 1.52
52 53 5.488262 AAGTCAAATGCTTGGGCTAAAAT 57.512 34.783 0.00 0.00 39.59 1.82
53 54 5.488262 AGTCAAATGCTTGGGCTAAAATT 57.512 34.783 0.00 0.00 39.59 1.82
54 55 5.240121 AGTCAAATGCTTGGGCTAAAATTG 58.760 37.500 0.00 0.00 39.59 2.32
55 56 4.002316 TCAAATGCTTGGGCTAAAATTGC 58.998 39.130 0.00 0.00 39.59 3.56
56 57 2.298411 ATGCTTGGGCTAAAATTGCG 57.702 45.000 0.00 0.00 39.59 4.85
57 58 1.252175 TGCTTGGGCTAAAATTGCGA 58.748 45.000 0.00 0.00 39.59 5.10
58 59 1.615883 TGCTTGGGCTAAAATTGCGAA 59.384 42.857 0.00 0.00 39.59 4.70
59 60 2.036475 TGCTTGGGCTAAAATTGCGAAA 59.964 40.909 0.00 0.00 39.59 3.46
60 61 3.261580 GCTTGGGCTAAAATTGCGAAAT 58.738 40.909 0.00 0.00 35.22 2.17
61 62 4.081972 TGCTTGGGCTAAAATTGCGAAATA 60.082 37.500 0.00 0.00 39.59 1.40
62 63 4.867608 GCTTGGGCTAAAATTGCGAAATAA 59.132 37.500 0.00 0.00 35.22 1.40
63 64 5.523552 GCTTGGGCTAAAATTGCGAAATAAT 59.476 36.000 0.00 0.00 35.22 1.28
64 65 6.037062 GCTTGGGCTAAAATTGCGAAATAATT 59.963 34.615 0.00 0.00 35.22 1.40
65 66 7.413988 GCTTGGGCTAAAATTGCGAAATAATTT 60.414 33.333 0.00 0.00 36.22 1.82
66 67 7.301068 TGGGCTAAAATTGCGAAATAATTTG 57.699 32.000 0.00 0.00 37.68 2.32
67 68 6.314896 TGGGCTAAAATTGCGAAATAATTTGG 59.685 34.615 0.00 0.00 37.68 3.28
68 69 6.536941 GGGCTAAAATTGCGAAATAATTTGGA 59.463 34.615 1.85 0.00 37.68 3.53
69 70 7.226523 GGGCTAAAATTGCGAAATAATTTGGAT 59.773 33.333 1.85 0.00 37.68 3.41
70 71 9.255304 GGCTAAAATTGCGAAATAATTTGGATA 57.745 29.630 1.85 0.00 37.68 2.59
75 76 8.831715 AATTGCGAAATAATTTGGATAATCCC 57.168 30.769 0.00 0.00 35.03 3.85
76 77 6.339587 TGCGAAATAATTTGGATAATCCCC 57.660 37.500 0.00 0.00 35.03 4.81
77 78 5.835819 TGCGAAATAATTTGGATAATCCCCA 59.164 36.000 0.00 0.00 35.03 4.96
78 79 6.325028 TGCGAAATAATTTGGATAATCCCCAA 59.675 34.615 0.00 0.00 41.53 4.12
85 86 5.930837 TTTGGATAATCCCCAAATGTCAC 57.069 39.130 0.00 0.00 45.64 3.67
86 87 4.599720 TGGATAATCCCCAAATGTCACA 57.400 40.909 0.00 0.00 35.03 3.58
87 88 4.940483 TGGATAATCCCCAAATGTCACAA 58.060 39.130 0.00 0.00 35.03 3.33
88 89 5.527385 TGGATAATCCCCAAATGTCACAAT 58.473 37.500 0.00 0.00 35.03 2.71
89 90 5.363292 TGGATAATCCCCAAATGTCACAATG 59.637 40.000 0.00 0.00 35.03 2.82
90 91 5.221501 GGATAATCCCCAAATGTCACAATGG 60.222 44.000 6.09 6.09 0.00 3.16
91 92 1.265236 TCCCCAAATGTCACAATGGC 58.735 50.000 7.36 0.00 0.00 4.40
92 93 0.975135 CCCCAAATGTCACAATGGCA 59.025 50.000 7.36 0.00 35.91 4.92
93 94 1.066716 CCCCAAATGTCACAATGGCAG 60.067 52.381 7.36 0.00 34.38 4.85
94 95 1.066716 CCCAAATGTCACAATGGCAGG 60.067 52.381 7.36 0.00 34.38 4.85
95 96 1.619827 CCAAATGTCACAATGGCAGGT 59.380 47.619 0.31 0.00 34.38 4.00
96 97 2.037511 CCAAATGTCACAATGGCAGGTT 59.962 45.455 0.31 0.00 34.38 3.50
97 98 3.494749 CCAAATGTCACAATGGCAGGTTT 60.495 43.478 0.31 0.00 34.38 3.27
98 99 3.389925 AATGTCACAATGGCAGGTTTG 57.610 42.857 0.00 0.00 34.38 2.93
111 112 3.896122 GCAGGTTTGCGAGTTAATTTCA 58.104 40.909 0.00 0.00 41.13 2.69
112 113 4.485163 GCAGGTTTGCGAGTTAATTTCAT 58.515 39.130 0.00 0.00 41.13 2.57
113 114 4.324402 GCAGGTTTGCGAGTTAATTTCATG 59.676 41.667 0.00 0.00 41.13 3.07
114 115 5.460646 CAGGTTTGCGAGTTAATTTCATGT 58.539 37.500 0.00 0.00 0.00 3.21
115 116 5.920273 CAGGTTTGCGAGTTAATTTCATGTT 59.080 36.000 0.00 0.00 0.00 2.71
116 117 7.081349 CAGGTTTGCGAGTTAATTTCATGTTA 58.919 34.615 0.00 0.00 0.00 2.41
117 118 7.271223 CAGGTTTGCGAGTTAATTTCATGTTAG 59.729 37.037 0.00 0.00 0.00 2.34
118 119 7.174253 AGGTTTGCGAGTTAATTTCATGTTAGA 59.826 33.333 0.00 0.00 0.00 2.10
119 120 7.806014 GGTTTGCGAGTTAATTTCATGTTAGAA 59.194 33.333 0.00 0.00 0.00 2.10
120 121 8.627428 GTTTGCGAGTTAATTTCATGTTAGAAC 58.373 33.333 0.00 0.00 0.00 3.01
121 122 7.428282 TGCGAGTTAATTTCATGTTAGAACA 57.572 32.000 0.00 0.00 44.06 3.18
123 124 8.511321 TGCGAGTTAATTTCATGTTAGAACATT 58.489 29.630 5.14 0.00 46.95 2.71
124 125 9.982291 GCGAGTTAATTTCATGTTAGAACATTA 57.018 29.630 5.14 0.00 46.95 1.90
153 154 8.635765 TTTTGGAAATATATGCTGTATCTCCC 57.364 34.615 0.00 0.00 0.00 4.30
154 155 7.574021 TTGGAAATATATGCTGTATCTCCCT 57.426 36.000 0.00 0.00 0.00 4.20
155 156 8.679344 TTGGAAATATATGCTGTATCTCCCTA 57.321 34.615 0.00 0.00 0.00 3.53
156 157 8.679344 TGGAAATATATGCTGTATCTCCCTAA 57.321 34.615 0.00 0.00 0.00 2.69
157 158 9.284131 TGGAAATATATGCTGTATCTCCCTAAT 57.716 33.333 0.00 0.00 0.00 1.73
200 201 9.601217 TTATACAGCTCTAAAGAGAACAAATCC 57.399 33.333 11.20 0.00 44.74 3.01
201 202 6.120507 ACAGCTCTAAAGAGAACAAATCCT 57.879 37.500 11.20 0.00 44.74 3.24
202 203 5.936956 ACAGCTCTAAAGAGAACAAATCCTG 59.063 40.000 11.20 7.98 44.74 3.86
203 204 5.936956 CAGCTCTAAAGAGAACAAATCCTGT 59.063 40.000 11.20 0.00 44.74 4.00
204 205 6.091986 CAGCTCTAAAGAGAACAAATCCTGTC 59.908 42.308 11.20 0.00 44.74 3.51
205 206 6.013812 AGCTCTAAAGAGAACAAATCCTGTCT 60.014 38.462 11.20 0.00 44.74 3.41
206 207 7.179338 AGCTCTAAAGAGAACAAATCCTGTCTA 59.821 37.037 11.20 0.00 44.74 2.59
207 208 7.819900 GCTCTAAAGAGAACAAATCCTGTCTAA 59.180 37.037 11.20 0.00 44.74 2.10
208 209 9.883142 CTCTAAAGAGAACAAATCCTGTCTAAT 57.117 33.333 0.38 0.00 44.74 1.73
209 210 9.877178 TCTAAAGAGAACAAATCCTGTCTAATC 57.123 33.333 0.00 0.00 37.23 1.75
210 211 7.929941 AAAGAGAACAAATCCTGTCTAATCC 57.070 36.000 0.00 0.00 37.23 3.01
211 212 6.627087 AGAGAACAAATCCTGTCTAATCCA 57.373 37.500 0.00 0.00 37.23 3.41
212 213 7.205515 AGAGAACAAATCCTGTCTAATCCAT 57.794 36.000 0.00 0.00 37.23 3.41
213 214 7.278875 AGAGAACAAATCCTGTCTAATCCATC 58.721 38.462 0.00 0.00 37.23 3.51
214 215 6.962182 AGAACAAATCCTGTCTAATCCATCA 58.038 36.000 0.00 0.00 37.23 3.07
215 216 7.405292 AGAACAAATCCTGTCTAATCCATCAA 58.595 34.615 0.00 0.00 37.23 2.57
216 217 8.057623 AGAACAAATCCTGTCTAATCCATCAAT 58.942 33.333 0.00 0.00 37.23 2.57
217 218 8.599624 AACAAATCCTGTCTAATCCATCAATT 57.400 30.769 0.00 0.00 37.23 2.32
218 219 8.599624 ACAAATCCTGTCTAATCCATCAATTT 57.400 30.769 0.00 0.00 29.87 1.82
219 220 8.472413 ACAAATCCTGTCTAATCCATCAATTTG 58.528 33.333 0.00 0.00 36.77 2.32
220 221 8.472413 CAAATCCTGTCTAATCCATCAATTTGT 58.528 33.333 0.00 0.00 0.00 2.83
221 222 9.699410 AAATCCTGTCTAATCCATCAATTTGTA 57.301 29.630 0.00 0.00 0.00 2.41
222 223 9.699410 AATCCTGTCTAATCCATCAATTTGTAA 57.301 29.630 0.00 0.00 0.00 2.41
223 224 9.699410 ATCCTGTCTAATCCATCAATTTGTAAA 57.301 29.630 0.00 0.00 0.00 2.01
224 225 9.699410 TCCTGTCTAATCCATCAATTTGTAAAT 57.301 29.630 0.00 0.00 0.00 1.40
259 260 9.654919 AATATATGCATTTTAAGTAGGGTTGGT 57.345 29.630 3.54 0.00 0.00 3.67
377 387 9.739276 TTCTAATTAGGATTCTGTCACAACATT 57.261 29.630 12.54 0.00 34.13 2.71
378 388 9.383519 TCTAATTAGGATTCTGTCACAACATTC 57.616 33.333 12.54 0.00 34.13 2.67
433 443 6.983890 TGTCCCAATCTTTTCTTAAACTTTGC 59.016 34.615 0.00 0.00 0.00 3.68
571 583 2.260434 GAGCTACGCCCGTGACAA 59.740 61.111 3.22 0.00 0.00 3.18
616 628 1.915769 CATCCGATCCCTCCCTCCC 60.916 68.421 0.00 0.00 0.00 4.30
633 645 2.347490 CCCGTCCACTGGGTTCAG 59.653 66.667 0.00 0.00 46.10 3.02
670 682 3.251729 CGCCATGGTGATTATCTTTCCTG 59.748 47.826 21.19 0.00 0.00 3.86
692 709 2.676839 CTCCTTTGATAGTGCTGTGCTG 59.323 50.000 0.00 0.00 0.00 4.41
709 726 1.421410 CTGATCGCGTGGTTAGTGGC 61.421 60.000 5.77 0.00 0.00 5.01
757 774 1.492319 TTCCGCGGAGAAAACGTGTG 61.492 55.000 29.20 0.00 39.97 3.82
904 926 4.268884 GCATAAACAAAAACAAACCGAGCA 59.731 37.500 0.00 0.00 0.00 4.26
908 930 1.854126 CAAAAACAAACCGAGCAGCAG 59.146 47.619 0.00 0.00 0.00 4.24
939 961 2.278596 CACGTAGTCGGCCGGATG 60.279 66.667 27.83 18.20 41.61 3.51
949 971 1.301479 GGCCGGATGGTTATCGGAC 60.301 63.158 5.05 0.00 36.14 4.79
1250 1325 0.404040 CTCCCCTGCTGGTTTGGTTA 59.596 55.000 9.00 0.00 0.00 2.85
1251 1326 0.111639 TCCCCTGCTGGTTTGGTTAC 59.888 55.000 9.00 0.00 0.00 2.50
1303 1378 0.318784 GTGACACTCGCGACCTTTCT 60.319 55.000 3.71 0.00 0.00 2.52
1418 1493 0.182299 CAAATCCTCTGCTCTCCCCC 59.818 60.000 0.00 0.00 0.00 5.40
1570 1645 0.538746 TTCCCCTGTTCGCCTTTTCC 60.539 55.000 0.00 0.00 0.00 3.13
1599 1675 3.062099 TGCGATTAAATGCTCTGTTCGTC 59.938 43.478 4.24 0.00 0.00 4.20
1862 1938 1.809619 CACGCCATCCAGGTACGTG 60.810 63.158 8.61 8.61 43.85 4.49
1865 1941 2.202878 CCATCCAGGTACGTGCCG 60.203 66.667 17.44 11.77 0.00 5.69
1866 1942 2.890474 CATCCAGGTACGTGCCGC 60.890 66.667 17.44 0.00 0.00 6.53
1868 1944 3.659089 ATCCAGGTACGTGCCGCAC 62.659 63.158 17.44 13.81 0.00 5.34
1870 1946 4.673298 CAGGTACGTGCCGCACCA 62.673 66.667 17.44 3.13 44.83 4.17
1901 1987 4.102561 TCCGCATTGGATTCGTCG 57.897 55.556 0.00 0.00 43.74 5.12
1902 1988 1.520564 TCCGCATTGGATTCGTCGG 60.521 57.895 0.00 0.00 43.74 4.79
1903 1989 1.520564 CCGCATTGGATTCGTCGGA 60.521 57.895 0.00 0.00 42.00 4.55
1918 2014 0.611062 TCGGAGCCGGAGAAGAAGAA 60.611 55.000 5.05 0.00 40.25 2.52
1920 2016 1.187087 GGAGCCGGAGAAGAAGAAGA 58.813 55.000 5.05 0.00 0.00 2.87
1922 2018 2.482839 GGAGCCGGAGAAGAAGAAGATG 60.483 54.545 5.05 0.00 0.00 2.90
1923 2019 1.134551 AGCCGGAGAAGAAGAAGATGC 60.135 52.381 5.05 0.00 0.00 3.91
1924 2020 1.134551 GCCGGAGAAGAAGAAGATGCT 60.135 52.381 5.05 0.00 0.00 3.79
1925 2021 2.820330 CCGGAGAAGAAGAAGATGCTC 58.180 52.381 0.00 0.00 0.00 4.26
1926 2022 2.482839 CCGGAGAAGAAGAAGATGCTCC 60.483 54.545 0.00 0.00 38.77 4.70
1927 2023 2.482839 CGGAGAAGAAGAAGATGCTCCC 60.483 54.545 0.00 0.00 38.91 4.30
1928 2024 2.771372 GGAGAAGAAGAAGATGCTCCCT 59.229 50.000 0.00 0.00 36.73 4.20
1929 2025 3.199727 GGAGAAGAAGAAGATGCTCCCTT 59.800 47.826 0.00 0.00 36.73 3.95
1933 2029 1.843206 GAAGAAGATGCTCCCTTCCCT 59.157 52.381 0.00 0.00 40.54 4.20
1935 2031 1.843206 AGAAGATGCTCCCTTCCCTTC 59.157 52.381 0.00 0.00 40.54 3.46
1961 2057 1.301423 CTGTTCCGTTTCCGTTGGAA 58.699 50.000 0.00 0.00 40.27 3.53
1963 2059 3.784642 TTCCGTTTCCGTTGGAACT 57.215 47.368 0.00 0.00 41.87 3.01
1964 2060 2.041251 TTCCGTTTCCGTTGGAACTT 57.959 45.000 0.00 0.00 41.87 2.66
1965 2061 1.301423 TCCGTTTCCGTTGGAACTTG 58.699 50.000 0.00 0.00 41.87 3.16
1966 2062 0.309612 CCGTTTCCGTTGGAACTTGG 59.690 55.000 0.00 0.00 41.87 3.61
1967 2063 1.301423 CGTTTCCGTTGGAACTTGGA 58.699 50.000 0.00 0.00 41.87 3.53
1968 2064 1.263217 CGTTTCCGTTGGAACTTGGAG 59.737 52.381 0.00 0.00 41.87 3.86
1969 2065 1.607148 GTTTCCGTTGGAACTTGGAGG 59.393 52.381 0.00 0.00 41.87 4.30
1970 2066 1.133363 TTCCGTTGGAACTTGGAGGA 58.867 50.000 0.00 0.00 36.71 3.71
1972 2068 0.955919 CCGTTGGAACTTGGAGGAGC 60.956 60.000 0.00 0.00 0.00 4.70
1974 2070 1.239347 GTTGGAACTTGGAGGAGCAC 58.761 55.000 0.00 0.00 0.00 4.40
1975 2071 0.843309 TTGGAACTTGGAGGAGCACA 59.157 50.000 0.00 0.00 0.00 4.57
1976 2072 0.108585 TGGAACTTGGAGGAGCACAC 59.891 55.000 0.00 0.00 0.00 3.82
1977 2073 0.951040 GGAACTTGGAGGAGCACACG 60.951 60.000 0.00 0.00 0.00 4.49
1978 2074 0.033504 GAACTTGGAGGAGCACACGA 59.966 55.000 0.00 0.00 0.00 4.35
1979 2075 0.249911 AACTTGGAGGAGCACACGAC 60.250 55.000 0.00 0.00 0.00 4.34
1980 2076 1.374758 CTTGGAGGAGCACACGACC 60.375 63.158 0.00 0.00 0.00 4.79
1981 2077 3.220999 TTGGAGGAGCACACGACCG 62.221 63.158 0.00 0.00 0.00 4.79
1982 2078 3.371063 GGAGGAGCACACGACCGA 61.371 66.667 0.00 0.00 0.00 4.69
1983 2079 2.649034 GAGGAGCACACGACCGAA 59.351 61.111 0.00 0.00 0.00 4.30
1984 2080 1.006571 GAGGAGCACACGACCGAAA 60.007 57.895 0.00 0.00 0.00 3.46
1985 2081 1.006102 AGGAGCACACGACCGAAAG 60.006 57.895 0.00 0.00 0.00 2.62
2107 2210 2.858476 TTCCTTGAGCTGCCCCCA 60.858 61.111 0.00 0.00 0.00 4.96
2119 2222 1.152673 GCCCCCATGTTCCATCTCC 60.153 63.158 0.00 0.00 0.00 3.71
2121 2224 1.819753 CCCCCATGTTCCATCTCCTA 58.180 55.000 0.00 0.00 0.00 2.94
2122 2225 1.701847 CCCCCATGTTCCATCTCCTAG 59.298 57.143 0.00 0.00 0.00 3.02
2126 2229 3.260380 CCCATGTTCCATCTCCTAGCTAG 59.740 52.174 14.20 14.20 0.00 3.42
2128 2231 3.320610 TGTTCCATCTCCTAGCTAGCT 57.679 47.619 23.12 23.12 0.00 3.32
2132 2238 6.552932 TGTTCCATCTCCTAGCTAGCTTATA 58.447 40.000 24.88 3.66 0.00 0.98
2398 2540 0.970640 TGCAAGGTACGTAGCTTCCA 59.029 50.000 31.42 27.53 41.62 3.53
2400 2542 1.067071 GCAAGGTACGTAGCTTCCACT 60.067 52.381 31.42 12.86 41.62 4.00
2402 2544 3.367703 GCAAGGTACGTAGCTTCCACTAA 60.368 47.826 31.42 0.00 41.62 2.24
2404 2546 4.650754 AGGTACGTAGCTTCCACTAATG 57.349 45.455 21.15 0.00 0.00 1.90
2407 2558 1.209128 CGTAGCTTCCACTAATGGCG 58.791 55.000 0.00 0.00 46.80 5.69
2448 2599 2.760581 ACGCCCCTACTAGATTCCTTT 58.239 47.619 0.00 0.00 0.00 3.11
2449 2600 2.434702 ACGCCCCTACTAGATTCCTTTG 59.565 50.000 0.00 0.00 0.00 2.77
2453 2604 4.411212 GCCCCTACTAGATTCCTTTGGTTA 59.589 45.833 0.00 0.00 0.00 2.85
2477 2633 2.811317 GTTCAGCTCGCCTGGACG 60.811 66.667 0.00 0.34 40.15 4.79
2517 2673 6.096036 CGGCATTGTGATTTGGTTGTTTATA 58.904 36.000 0.00 0.00 0.00 0.98
2521 2677 7.751348 GCATTGTGATTTGGTTGTTTATACGTA 59.249 33.333 0.00 0.00 0.00 3.57
2798 2975 3.291584 TCATCGTGGAGTTCTAGAGCAT 58.708 45.455 9.43 0.00 0.00 3.79
2799 2976 3.316588 TCATCGTGGAGTTCTAGAGCATC 59.683 47.826 9.43 3.85 0.00 3.91
2883 3072 7.420029 TCCATACCTACCTCTAGAGTTTTTCT 58.580 38.462 18.42 0.00 40.06 2.52
2884 3073 7.560626 TCCATACCTACCTCTAGAGTTTTTCTC 59.439 40.741 18.42 0.00 43.05 2.87
3004 3211 5.769367 CAATGCGGCATCTTACTACTACTA 58.231 41.667 16.98 0.00 0.00 1.82
3007 3214 3.249559 GCGGCATCTTACTACTACTACGT 59.750 47.826 0.00 0.00 0.00 3.57
3008 3215 4.449068 GCGGCATCTTACTACTACTACGTA 59.551 45.833 0.00 0.00 0.00 3.57
3009 3216 5.613577 GCGGCATCTTACTACTACTACGTAC 60.614 48.000 0.00 0.00 0.00 3.67
3010 3217 5.694006 CGGCATCTTACTACTACTACGTACT 59.306 44.000 0.00 0.00 0.00 2.73
3026 3238 8.327941 ACTACGTACTTCATAGTCACTACAAA 57.672 34.615 0.00 0.00 35.78 2.83
3027 3239 8.786898 ACTACGTACTTCATAGTCACTACAAAA 58.213 33.333 0.00 0.00 35.78 2.44
3028 3240 7.864307 ACGTACTTCATAGTCACTACAAAAC 57.136 36.000 0.00 0.00 35.78 2.43
3115 3330 6.201226 AGGTAGTAGCCGTAGTTTTTACTC 57.799 41.667 0.00 0.00 0.00 2.59
3130 3357 3.777465 TTACTCTTGTGGTAGCTAGCG 57.223 47.619 17.59 5.22 0.00 4.26
3131 3358 0.818296 ACTCTTGTGGTAGCTAGCGG 59.182 55.000 17.59 8.23 0.00 5.52
3288 3533 3.672295 CTGCTCCTGACGGCCTTCC 62.672 68.421 6.80 0.00 0.00 3.46
3322 3567 1.667212 GCTTGTTTGCTTGCTTGCTTT 59.333 42.857 3.47 0.00 0.00 3.51
3323 3568 2.538132 GCTTGTTTGCTTGCTTGCTTTG 60.538 45.455 3.47 0.00 0.00 2.77
3325 3570 2.542597 TGTTTGCTTGCTTGCTTTGAG 58.457 42.857 3.47 0.00 0.00 3.02
3328 3578 2.212869 TGCTTGCTTGCTTTGAGTTG 57.787 45.000 3.47 0.00 0.00 3.16
3338 3588 5.677091 GCTTGCTTTGAGTTGTTCTTCTTCA 60.677 40.000 0.00 0.00 0.00 3.02
3347 3597 2.567985 TGTTCTTCTTCACCGTTTCCC 58.432 47.619 0.00 0.00 0.00 3.97
3351 3601 2.037251 TCTTCTTCACCGTTTCCCTCTG 59.963 50.000 0.00 0.00 0.00 3.35
3352 3602 1.420430 TCTTCACCGTTTCCCTCTGT 58.580 50.000 0.00 0.00 0.00 3.41
3353 3603 2.600790 TCTTCACCGTTTCCCTCTGTA 58.399 47.619 0.00 0.00 0.00 2.74
3354 3604 2.298163 TCTTCACCGTTTCCCTCTGTAC 59.702 50.000 0.00 0.00 0.00 2.90
3355 3605 0.599558 TCACCGTTTCCCTCTGTACG 59.400 55.000 0.00 0.00 0.00 3.67
3408 3658 2.106332 GGGACACCTATGACCGCG 59.894 66.667 0.00 0.00 41.12 6.46
3409 3659 2.420568 GGGACACCTATGACCGCGA 61.421 63.158 8.23 0.00 41.12 5.87
3592 3859 2.879462 GACGTGGTCGCCATCGTC 60.879 66.667 23.09 23.09 43.96 4.20
3599 3867 4.829518 TCGCCATCGTCGTCGCTG 62.830 66.667 0.00 0.00 36.96 5.18
3635 3903 0.105039 CCATACGGAAGAGCCAGGAC 59.895 60.000 0.00 0.00 35.94 3.85
3726 3994 2.093500 CCTGTCTGTGGCAGTAGCAATA 60.093 50.000 0.00 0.00 44.61 1.90
3777 4049 4.094739 TGAGATCGGTCGTACGAAAATACA 59.905 41.667 21.39 11.41 46.92 2.29
3826 4104 2.801162 CACGTGCGTGGAGTCGAG 60.801 66.667 15.98 0.00 42.00 4.04
3845 4123 3.293262 GAGCGAGCTCGTAGATAACTTG 58.707 50.000 34.46 5.25 42.22 3.16
3846 4124 2.033550 AGCGAGCTCGTAGATAACTTGG 59.966 50.000 34.46 5.04 42.22 3.61
3884 4162 0.249489 CGCATCTAGGGAAAGGTCGG 60.249 60.000 0.00 0.00 0.00 4.79
3922 4200 4.875713 GGATGCGGGCCGTCCATT 62.876 66.667 28.82 7.87 46.97 3.16
3923 4201 2.828549 GATGCGGGCCGTCCATTT 60.829 61.111 28.82 3.39 34.36 2.32
3924 4202 2.362375 ATGCGGGCCGTCCATTTT 60.362 55.556 28.82 0.00 34.36 1.82
3925 4203 2.336400 GATGCGGGCCGTCCATTTTC 62.336 60.000 28.82 8.47 34.36 2.29
3926 4204 2.750237 GCGGGCCGTCCATTTTCT 60.750 61.111 28.82 0.00 34.36 2.52
3927 4205 2.761195 GCGGGCCGTCCATTTTCTC 61.761 63.158 28.82 1.99 34.36 2.87
3928 4206 2.112815 CGGGCCGTCCATTTTCTCC 61.113 63.158 19.97 0.00 34.36 3.71
3929 4207 1.303282 GGGCCGTCCATTTTCTCCT 59.697 57.895 0.00 0.00 35.00 3.69
3930 4208 1.032114 GGGCCGTCCATTTTCTCCTG 61.032 60.000 0.00 0.00 35.00 3.86
3931 4209 1.032114 GGCCGTCCATTTTCTCCTGG 61.032 60.000 0.00 0.00 0.00 4.45
3932 4210 1.657751 GCCGTCCATTTTCTCCTGGC 61.658 60.000 0.00 0.00 32.30 4.85
3933 4211 0.322456 CCGTCCATTTTCTCCTGGCA 60.322 55.000 0.00 0.00 32.30 4.92
3934 4212 1.683011 CCGTCCATTTTCTCCTGGCAT 60.683 52.381 0.00 0.00 32.30 4.40
3935 4213 1.402968 CGTCCATTTTCTCCTGGCATG 59.597 52.381 0.00 0.00 32.30 4.06
3936 4214 2.450476 GTCCATTTTCTCCTGGCATGT 58.550 47.619 0.00 0.00 32.30 3.21
3937 4215 2.165030 GTCCATTTTCTCCTGGCATGTG 59.835 50.000 0.00 0.00 32.30 3.21
3938 4216 2.173519 CCATTTTCTCCTGGCATGTGT 58.826 47.619 0.00 0.00 0.00 3.72
3939 4217 2.094390 CCATTTTCTCCTGGCATGTGTG 60.094 50.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.264373 TCTAGCCCCCTTTATGCATTTT 57.736 40.909 3.54 0.00 0.00 1.82
1 2 3.960755 GTTCTAGCCCCCTTTATGCATTT 59.039 43.478 3.54 0.00 0.00 2.32
2 3 3.205282 AGTTCTAGCCCCCTTTATGCATT 59.795 43.478 3.54 0.00 0.00 3.56
4 5 2.205342 AGTTCTAGCCCCCTTTATGCA 58.795 47.619 0.00 0.00 0.00 3.96
5 6 3.244596 CCTAGTTCTAGCCCCCTTTATGC 60.245 52.174 1.68 0.00 0.00 3.14
6 7 3.244596 GCCTAGTTCTAGCCCCCTTTATG 60.245 52.174 1.68 0.00 0.00 1.90
7 8 2.980379 GCCTAGTTCTAGCCCCCTTTAT 59.020 50.000 1.68 0.00 0.00 1.40
8 9 2.022330 AGCCTAGTTCTAGCCCCCTTTA 60.022 50.000 1.68 0.00 0.00 1.85
9 10 1.214217 GCCTAGTTCTAGCCCCCTTT 58.786 55.000 1.68 0.00 0.00 3.11
11 12 1.242444 TAGCCTAGTTCTAGCCCCCT 58.758 55.000 1.68 0.00 0.00 4.79
13 14 2.629137 GACTTAGCCTAGTTCTAGCCCC 59.371 54.545 1.68 0.00 0.00 5.80
15 16 5.340439 TTTGACTTAGCCTAGTTCTAGCC 57.660 43.478 1.68 0.00 0.00 3.93
17 18 6.578023 AGCATTTGACTTAGCCTAGTTCTAG 58.422 40.000 0.31 0.31 0.00 2.43
18 19 6.546428 AGCATTTGACTTAGCCTAGTTCTA 57.454 37.500 0.00 0.00 0.00 2.10
19 20 5.428184 AGCATTTGACTTAGCCTAGTTCT 57.572 39.130 0.00 0.00 0.00 3.01
20 21 5.163713 CCAAGCATTTGACTTAGCCTAGTTC 60.164 44.000 0.00 0.00 36.36 3.01
21 22 4.702131 CCAAGCATTTGACTTAGCCTAGTT 59.298 41.667 0.00 0.00 36.36 2.24
22 23 4.265073 CCAAGCATTTGACTTAGCCTAGT 58.735 43.478 0.00 0.00 36.36 2.57
23 24 3.629398 CCCAAGCATTTGACTTAGCCTAG 59.371 47.826 0.00 0.00 36.36 3.02
24 25 3.620488 CCCAAGCATTTGACTTAGCCTA 58.380 45.455 0.00 0.00 36.36 3.93
25 26 2.450476 CCCAAGCATTTGACTTAGCCT 58.550 47.619 0.00 0.00 36.36 4.58
26 27 1.134995 GCCCAAGCATTTGACTTAGCC 60.135 52.381 0.00 0.00 39.53 3.93
27 28 1.821136 AGCCCAAGCATTTGACTTAGC 59.179 47.619 0.00 0.00 43.56 3.09
28 29 5.643379 TTTAGCCCAAGCATTTGACTTAG 57.357 39.130 0.00 0.00 43.56 2.18
29 30 6.603940 ATTTTAGCCCAAGCATTTGACTTA 57.396 33.333 0.00 0.00 43.56 2.24
30 31 4.953940 TTTTAGCCCAAGCATTTGACTT 57.046 36.364 0.00 0.00 43.56 3.01
31 32 5.240121 CAATTTTAGCCCAAGCATTTGACT 58.760 37.500 0.00 0.00 43.56 3.41
32 33 4.142838 GCAATTTTAGCCCAAGCATTTGAC 60.143 41.667 0.00 0.00 43.56 3.18
33 34 4.002316 GCAATTTTAGCCCAAGCATTTGA 58.998 39.130 0.00 0.00 43.56 2.69
34 35 3.181518 CGCAATTTTAGCCCAAGCATTTG 60.182 43.478 0.00 0.00 43.56 2.32
35 36 3.002102 CGCAATTTTAGCCCAAGCATTT 58.998 40.909 0.00 0.00 43.56 2.32
36 37 2.233431 TCGCAATTTTAGCCCAAGCATT 59.767 40.909 0.00 0.00 43.56 3.56
37 38 1.824230 TCGCAATTTTAGCCCAAGCAT 59.176 42.857 0.00 0.00 43.56 3.79
38 39 1.252175 TCGCAATTTTAGCCCAAGCA 58.748 45.000 0.00 0.00 43.56 3.91
39 40 2.362169 TTCGCAATTTTAGCCCAAGC 57.638 45.000 0.00 0.00 40.32 4.01
40 41 7.538303 AATTATTTCGCAATTTTAGCCCAAG 57.462 32.000 0.00 0.00 0.00 3.61
41 42 7.148340 CCAAATTATTTCGCAATTTTAGCCCAA 60.148 33.333 0.00 0.00 34.22 4.12
42 43 6.314896 CCAAATTATTTCGCAATTTTAGCCCA 59.685 34.615 0.00 0.00 34.22 5.36
43 44 6.536941 TCCAAATTATTTCGCAATTTTAGCCC 59.463 34.615 0.00 0.00 34.22 5.19
44 45 7.532682 TCCAAATTATTTCGCAATTTTAGCC 57.467 32.000 0.00 0.00 34.22 3.93
49 50 9.271828 GGGATTATCCAAATTATTTCGCAATTT 57.728 29.630 13.78 0.00 38.64 1.82
50 51 7.877612 GGGGATTATCCAAATTATTTCGCAATT 59.122 33.333 13.78 0.00 38.64 2.32
51 52 7.016072 TGGGGATTATCCAAATTATTTCGCAAT 59.984 33.333 13.78 0.00 38.64 3.56
52 53 6.325028 TGGGGATTATCCAAATTATTTCGCAA 59.675 34.615 13.78 0.00 38.64 4.85
53 54 5.835819 TGGGGATTATCCAAATTATTTCGCA 59.164 36.000 13.78 0.00 38.64 5.10
54 55 6.339587 TGGGGATTATCCAAATTATTTCGC 57.660 37.500 13.78 0.00 38.64 4.70
64 65 4.940483 TGTGACATTTGGGGATTATCCAA 58.060 39.130 13.78 0.00 41.97 3.53
65 66 4.599720 TGTGACATTTGGGGATTATCCA 57.400 40.909 13.78 0.00 38.64 3.41
66 67 5.221501 CCATTGTGACATTTGGGGATTATCC 60.222 44.000 1.91 1.91 35.23 2.59
67 68 5.739935 GCCATTGTGACATTTGGGGATTATC 60.740 44.000 14.52 0.00 0.00 1.75
68 69 4.101430 GCCATTGTGACATTTGGGGATTAT 59.899 41.667 14.52 0.00 0.00 1.28
69 70 3.450457 GCCATTGTGACATTTGGGGATTA 59.550 43.478 14.52 0.00 0.00 1.75
70 71 2.236893 GCCATTGTGACATTTGGGGATT 59.763 45.455 14.52 0.00 0.00 3.01
71 72 1.832998 GCCATTGTGACATTTGGGGAT 59.167 47.619 14.52 0.00 0.00 3.85
72 73 1.265236 GCCATTGTGACATTTGGGGA 58.735 50.000 14.52 0.00 0.00 4.81
73 74 0.975135 TGCCATTGTGACATTTGGGG 59.025 50.000 14.52 1.80 0.00 4.96
74 75 1.066716 CCTGCCATTGTGACATTTGGG 60.067 52.381 14.52 3.33 0.00 4.12
75 76 1.619827 ACCTGCCATTGTGACATTTGG 59.380 47.619 9.90 9.90 0.00 3.28
76 77 3.389925 AACCTGCCATTGTGACATTTG 57.610 42.857 0.00 0.00 0.00 2.32
77 78 3.731089 CAAACCTGCCATTGTGACATTT 58.269 40.909 0.00 0.00 0.00 2.32
78 79 2.548493 GCAAACCTGCCATTGTGACATT 60.548 45.455 0.00 0.00 43.26 2.71
79 80 1.001181 GCAAACCTGCCATTGTGACAT 59.999 47.619 0.00 0.00 43.26 3.06
80 81 0.388659 GCAAACCTGCCATTGTGACA 59.611 50.000 0.00 0.00 43.26 3.58
81 82 0.664166 CGCAAACCTGCCATTGTGAC 60.664 55.000 0.00 0.00 46.56 3.67
82 83 0.821301 TCGCAAACCTGCCATTGTGA 60.821 50.000 0.00 0.00 46.56 3.58
83 84 0.387622 CTCGCAAACCTGCCATTGTG 60.388 55.000 0.00 0.00 46.56 3.33
84 85 0.823356 ACTCGCAAACCTGCCATTGT 60.823 50.000 0.00 0.00 46.56 2.71
85 86 0.314935 AACTCGCAAACCTGCCATTG 59.685 50.000 0.00 0.00 46.56 2.82
86 87 1.904287 TAACTCGCAAACCTGCCATT 58.096 45.000 0.00 0.00 46.56 3.16
87 88 1.904287 TTAACTCGCAAACCTGCCAT 58.096 45.000 0.00 0.00 46.56 4.40
88 89 1.904287 ATTAACTCGCAAACCTGCCA 58.096 45.000 0.00 0.00 46.56 4.92
89 90 3.242518 GAAATTAACTCGCAAACCTGCC 58.757 45.455 0.00 0.00 46.56 4.85
90 91 3.896122 TGAAATTAACTCGCAAACCTGC 58.104 40.909 0.00 0.00 45.75 4.85
91 92 5.460646 ACATGAAATTAACTCGCAAACCTG 58.539 37.500 0.00 0.00 0.00 4.00
92 93 5.705609 ACATGAAATTAACTCGCAAACCT 57.294 34.783 0.00 0.00 0.00 3.50
93 94 7.302524 TCTAACATGAAATTAACTCGCAAACC 58.697 34.615 0.00 0.00 0.00 3.27
94 95 8.627428 GTTCTAACATGAAATTAACTCGCAAAC 58.373 33.333 0.00 0.00 0.00 2.93
95 96 8.346300 TGTTCTAACATGAAATTAACTCGCAAA 58.654 29.630 0.00 0.00 33.17 3.68
96 97 7.866729 TGTTCTAACATGAAATTAACTCGCAA 58.133 30.769 0.00 0.00 33.17 4.85
97 98 7.428282 TGTTCTAACATGAAATTAACTCGCA 57.572 32.000 0.00 0.00 33.17 5.10
127 128 9.247861 GGGAGATACAGCATATATTTCCAAAAT 57.752 33.333 11.28 0.00 35.79 1.82
128 129 8.448008 AGGGAGATACAGCATATATTTCCAAAA 58.552 33.333 11.28 0.00 35.79 2.44
129 130 7.988937 AGGGAGATACAGCATATATTTCCAAA 58.011 34.615 11.28 0.00 35.79 3.28
130 131 7.574021 AGGGAGATACAGCATATATTTCCAA 57.426 36.000 11.28 0.00 35.79 3.53
131 132 8.679344 TTAGGGAGATACAGCATATATTTCCA 57.321 34.615 11.28 0.00 35.79 3.53
174 175 9.601217 GGATTTGTTCTCTTTAGAGCTGTATAA 57.399 33.333 0.00 0.00 41.80 0.98
175 176 8.982723 AGGATTTGTTCTCTTTAGAGCTGTATA 58.017 33.333 0.00 0.00 41.80 1.47
176 177 7.768120 CAGGATTTGTTCTCTTTAGAGCTGTAT 59.232 37.037 0.00 0.00 41.80 2.29
177 178 7.099764 CAGGATTTGTTCTCTTTAGAGCTGTA 58.900 38.462 0.00 0.00 41.80 2.74
178 179 5.936956 CAGGATTTGTTCTCTTTAGAGCTGT 59.063 40.000 0.00 0.00 41.80 4.40
179 180 5.936956 ACAGGATTTGTTCTCTTTAGAGCTG 59.063 40.000 0.00 4.15 36.31 4.24
180 181 6.013812 AGACAGGATTTGTTCTCTTTAGAGCT 60.014 38.462 1.79 0.00 41.05 4.09
181 182 6.169800 AGACAGGATTTGTTCTCTTTAGAGC 58.830 40.000 1.79 0.00 41.05 4.09
182 183 9.883142 ATTAGACAGGATTTGTTCTCTTTAGAG 57.117 33.333 0.15 0.15 41.05 2.43
183 184 9.877178 GATTAGACAGGATTTGTTCTCTTTAGA 57.123 33.333 0.00 0.00 41.05 2.10
184 185 9.103861 GGATTAGACAGGATTTGTTCTCTTTAG 57.896 37.037 0.00 0.00 41.05 1.85
185 186 8.602424 TGGATTAGACAGGATTTGTTCTCTTTA 58.398 33.333 0.00 0.00 41.05 1.85
186 187 7.461749 TGGATTAGACAGGATTTGTTCTCTTT 58.538 34.615 0.00 0.00 41.05 2.52
187 188 7.020827 TGGATTAGACAGGATTTGTTCTCTT 57.979 36.000 0.00 0.00 41.05 2.85
188 189 6.627087 TGGATTAGACAGGATTTGTTCTCT 57.373 37.500 0.00 0.00 41.05 3.10
189 190 7.050377 TGATGGATTAGACAGGATTTGTTCTC 58.950 38.462 0.00 0.00 41.05 2.87
190 191 6.962182 TGATGGATTAGACAGGATTTGTTCT 58.038 36.000 0.00 0.00 41.05 3.01
191 192 7.630242 TTGATGGATTAGACAGGATTTGTTC 57.370 36.000 0.00 0.00 41.05 3.18
192 193 8.599624 AATTGATGGATTAGACAGGATTTGTT 57.400 30.769 0.00 0.00 41.05 2.83
193 194 8.472413 CAAATTGATGGATTAGACAGGATTTGT 58.528 33.333 0.00 0.00 44.55 2.83
194 195 8.472413 ACAAATTGATGGATTAGACAGGATTTG 58.528 33.333 0.00 0.00 0.00 2.32
195 196 8.599624 ACAAATTGATGGATTAGACAGGATTT 57.400 30.769 0.00 0.00 0.00 2.17
196 197 9.699410 TTACAAATTGATGGATTAGACAGGATT 57.301 29.630 0.00 0.00 0.00 3.01
197 198 9.699410 TTTACAAATTGATGGATTAGACAGGAT 57.301 29.630 0.00 0.00 0.00 3.24
198 199 9.699410 ATTTACAAATTGATGGATTAGACAGGA 57.301 29.630 0.00 0.00 0.00 3.86
233 234 9.654919 ACCAACCCTACTTAAAATGCATATATT 57.345 29.630 0.00 0.00 0.00 1.28
236 237 9.654919 AATACCAACCCTACTTAAAATGCATAT 57.345 29.630 0.00 0.00 0.00 1.78
237 238 9.482175 AAATACCAACCCTACTTAAAATGCATA 57.518 29.630 0.00 0.00 0.00 3.14
238 239 7.971368 AATACCAACCCTACTTAAAATGCAT 57.029 32.000 0.00 0.00 0.00 3.96
239 240 7.784470 AAATACCAACCCTACTTAAAATGCA 57.216 32.000 0.00 0.00 0.00 3.96
247 248 8.809066 GGTTGAATTAAAATACCAACCCTACTT 58.191 33.333 19.20 0.00 46.59 2.24
248 249 8.357290 GGTTGAATTAAAATACCAACCCTACT 57.643 34.615 19.20 0.00 46.59 2.57
352 353 9.383519 GAATGTTGTGACAGAATCCTAATTAGA 57.616 33.333 14.28 0.88 39.58 2.10
353 354 9.388506 AGAATGTTGTGACAGAATCCTAATTAG 57.611 33.333 5.43 5.43 39.58 1.73
354 355 9.739276 AAGAATGTTGTGACAGAATCCTAATTA 57.261 29.630 0.00 0.00 39.58 1.40
356 357 9.167311 GTAAGAATGTTGTGACAGAATCCTAAT 57.833 33.333 0.00 0.00 39.58 1.73
358 359 7.602644 GTGTAAGAATGTTGTGACAGAATCCTA 59.397 37.037 0.00 0.00 39.58 2.94
359 360 6.428159 GTGTAAGAATGTTGTGACAGAATCCT 59.572 38.462 0.00 0.00 39.58 3.24
362 363 5.334105 GCGTGTAAGAATGTTGTGACAGAAT 60.334 40.000 0.00 0.00 39.58 2.40
363 364 4.025229 GCGTGTAAGAATGTTGTGACAGAA 60.025 41.667 0.00 0.00 39.58 3.02
364 365 3.493129 GCGTGTAAGAATGTTGTGACAGA 59.507 43.478 0.00 0.00 39.58 3.41
369 379 3.247411 TGTGAGCGTGTAAGAATGTTGTG 59.753 43.478 0.00 0.00 0.00 3.33
377 387 6.163476 ACAATCTAAATGTGAGCGTGTAAGA 58.837 36.000 0.00 0.00 0.00 2.10
378 388 6.408858 ACAATCTAAATGTGAGCGTGTAAG 57.591 37.500 0.00 0.00 0.00 2.34
433 443 1.095807 GCGGAAAATTCTCTCCCCCG 61.096 60.000 0.00 0.00 38.58 5.73
571 583 2.044946 GCATTCTGAAGGGGGCGT 60.045 61.111 4.09 0.00 0.00 5.68
574 586 0.179062 CTCTCGCATTCTGAAGGGGG 60.179 60.000 17.14 10.06 0.00 5.40
577 589 1.288350 CTGCTCTCGCATTCTGAAGG 58.712 55.000 0.00 0.00 46.74 3.46
596 608 2.527875 AGGGAGGGATCGGATGCC 60.528 66.667 19.77 19.77 41.75 4.40
670 682 1.399791 GCACAGCACTATCAAAGGAGC 59.600 52.381 0.00 0.00 0.00 4.70
692 709 1.421410 CTGCCACTAACCACGCGATC 61.421 60.000 15.93 0.00 0.00 3.69
709 726 1.227999 CCACTAACCACGCCACACTG 61.228 60.000 0.00 0.00 0.00 3.66
904 926 3.079478 TCCTCGCTGATGCCTGCT 61.079 61.111 0.00 0.00 35.41 4.24
908 930 2.279502 TACGTGTCCTCGCTGATGCC 62.280 60.000 0.00 0.00 35.36 4.40
939 961 2.805807 GCGTTGCCGTCCGATAACC 61.806 63.158 0.00 0.00 36.15 2.85
1175 1241 3.546543 CTTATCCGCTCCCGCCCA 61.547 66.667 0.00 0.00 0.00 5.36
1250 1325 1.943730 AATGGTGGTGGTGGTGGTGT 61.944 55.000 0.00 0.00 0.00 4.16
1251 1326 1.152567 AATGGTGGTGGTGGTGGTG 60.153 57.895 0.00 0.00 0.00 4.17
1418 1493 3.157949 GGAAGGAGGAGGAGGCGG 61.158 72.222 0.00 0.00 0.00 6.13
1570 1645 4.025896 CAGAGCATTTAATCGCACAGAGAG 60.026 45.833 0.00 0.00 0.00 3.20
1599 1675 4.475944 CAGAGAACCAAGCAATAAAACCG 58.524 43.478 0.00 0.00 0.00 4.44
1862 1938 2.710902 GGGGAAGAAATGGTGCGGC 61.711 63.158 0.00 0.00 0.00 6.53
1865 1941 0.332972 AGAGGGGGAAGAAATGGTGC 59.667 55.000 0.00 0.00 0.00 5.01
1866 1942 1.064389 GGAGAGGGGGAAGAAATGGTG 60.064 57.143 0.00 0.00 0.00 4.17
1868 1944 0.181350 CGGAGAGGGGGAAGAAATGG 59.819 60.000 0.00 0.00 0.00 3.16
1870 1946 0.914417 TGCGGAGAGGGGGAAGAAAT 60.914 55.000 0.00 0.00 0.00 2.17
1898 1984 1.139947 CTTCTTCTCCGGCTCCGAC 59.860 63.158 10.28 0.00 42.83 4.79
1901 1987 1.187087 TCTTCTTCTTCTCCGGCTCC 58.813 55.000 0.00 0.00 0.00 4.70
1902 1988 2.820330 CATCTTCTTCTTCTCCGGCTC 58.180 52.381 0.00 0.00 0.00 4.70
1903 1989 1.134551 GCATCTTCTTCTTCTCCGGCT 60.135 52.381 0.00 0.00 0.00 5.52
1918 2014 0.990818 GGGAAGGGAAGGGAGCATCT 60.991 60.000 0.00 0.00 33.73 2.90
1920 2016 0.990818 GAGGGAAGGGAAGGGAGCAT 60.991 60.000 0.00 0.00 0.00 3.79
1922 2018 2.379459 GGAGGGAAGGGAAGGGAGC 61.379 68.421 0.00 0.00 0.00 4.70
1923 2019 1.694525 GGGAGGGAAGGGAAGGGAG 60.695 68.421 0.00 0.00 0.00 4.30
1924 2020 2.459710 GGGAGGGAAGGGAAGGGA 59.540 66.667 0.00 0.00 0.00 4.20
1925 2021 2.696504 GGGGAGGGAAGGGAAGGG 60.697 72.222 0.00 0.00 0.00 3.95
1926 2022 2.003548 CAGGGGAGGGAAGGGAAGG 61.004 68.421 0.00 0.00 0.00 3.46
1927 2023 0.846870 AACAGGGGAGGGAAGGGAAG 60.847 60.000 0.00 0.00 0.00 3.46
1928 2024 0.845102 GAACAGGGGAGGGAAGGGAA 60.845 60.000 0.00 0.00 0.00 3.97
1929 2025 1.229853 GAACAGGGGAGGGAAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
1933 2029 1.063654 AAACGGAACAGGGGAGGGAA 61.064 55.000 0.00 0.00 0.00 3.97
1935 2031 1.002502 GAAACGGAACAGGGGAGGG 60.003 63.158 0.00 0.00 0.00 4.30
1961 2057 1.367840 GTCGTGTGCTCCTCCAAGT 59.632 57.895 0.00 0.00 0.00 3.16
1963 2059 2.741092 GGTCGTGTGCTCCTCCAA 59.259 61.111 0.00 0.00 0.00 3.53
1964 2060 3.680786 CGGTCGTGTGCTCCTCCA 61.681 66.667 0.00 0.00 0.00 3.86
1965 2061 2.430382 TTTCGGTCGTGTGCTCCTCC 62.430 60.000 0.00 0.00 0.00 4.30
1966 2062 1.006571 TTTCGGTCGTGTGCTCCTC 60.007 57.895 0.00 0.00 0.00 3.71
1967 2063 1.006102 CTTTCGGTCGTGTGCTCCT 60.006 57.895 0.00 0.00 0.00 3.69
1968 2064 1.006571 TCTTTCGGTCGTGTGCTCC 60.007 57.895 0.00 0.00 0.00 4.70
1969 2065 0.318784 ACTCTTTCGGTCGTGTGCTC 60.319 55.000 0.00 0.00 0.00 4.26
1970 2066 0.318784 GACTCTTTCGGTCGTGTGCT 60.319 55.000 0.00 0.00 0.00 4.40
1972 2068 0.666577 GGGACTCTTTCGGTCGTGTG 60.667 60.000 0.00 0.00 34.82 3.82
1974 2070 1.965219 AGGGACTCTTTCGGTCGTG 59.035 57.895 0.00 0.00 34.82 4.35
1975 2071 4.515718 AGGGACTCTTTCGGTCGT 57.484 55.556 0.00 0.00 34.82 4.34
2021 2123 3.721706 GGGGGCTGGAGGACACAG 61.722 72.222 0.00 0.00 38.95 3.66
2022 2124 4.590553 TGGGGGCTGGAGGACACA 62.591 66.667 0.00 0.00 0.00 3.72
2023 2125 3.256960 TTGGGGGCTGGAGGACAC 61.257 66.667 0.00 0.00 0.00 3.67
2119 2222 8.067784 GCATCGTTAGAGATATAAGCTAGCTAG 58.932 40.741 19.70 16.84 0.00 3.42
2121 2224 6.601613 AGCATCGTTAGAGATATAAGCTAGCT 59.398 38.462 12.68 12.68 28.49 3.32
2122 2225 6.791303 AGCATCGTTAGAGATATAAGCTAGC 58.209 40.000 6.62 6.62 28.49 3.42
2398 2540 2.819595 CGGTGCAGCGCCATTAGT 60.820 61.111 26.59 0.00 32.88 2.24
2433 2584 8.319146 TGAACTTAACCAAAGGAATCTAGTAGG 58.681 37.037 0.00 0.00 39.73 3.18
2448 2599 3.390135 CGAGCTGAACTGAACTTAACCA 58.610 45.455 0.00 0.00 0.00 3.67
2449 2600 2.157863 GCGAGCTGAACTGAACTTAACC 59.842 50.000 0.00 0.00 0.00 2.85
2453 2604 0.394565 AGGCGAGCTGAACTGAACTT 59.605 50.000 0.00 0.00 0.00 2.66
2521 2677 1.008424 CTACGATCTGCGCGTCCAT 60.008 57.895 8.43 0.00 46.04 3.41
2818 2999 4.371417 TACCGGCGAGGGAGGTGT 62.371 66.667 9.30 0.00 46.96 4.16
2883 3072 6.719829 TGTATAGAACAGGACAGAACAGAAGA 59.280 38.462 0.00 0.00 33.01 2.87
2884 3073 6.809196 GTGTATAGAACAGGACAGAACAGAAG 59.191 42.308 0.00 0.00 39.29 2.85
2885 3074 6.295123 GGTGTATAGAACAGGACAGAACAGAA 60.295 42.308 0.00 0.00 39.29 3.02
2886 3075 5.185249 GGTGTATAGAACAGGACAGAACAGA 59.815 44.000 0.00 0.00 39.29 3.41
2887 3076 5.047306 TGGTGTATAGAACAGGACAGAACAG 60.047 44.000 0.00 0.00 39.29 3.16
2893 3082 4.422057 TCCTTGGTGTATAGAACAGGACA 58.578 43.478 0.00 0.00 39.29 4.02
2896 3085 5.395768 CCTTCTCCTTGGTGTATAGAACAGG 60.396 48.000 0.00 0.00 39.29 4.00
3004 3211 7.380602 GTGTTTTGTAGTGACTATGAAGTACGT 59.619 37.037 0.00 0.00 35.56 3.57
3007 3214 8.418662 ACTGTGTTTTGTAGTGACTATGAAGTA 58.581 33.333 0.00 0.00 35.56 2.24
3008 3215 7.272978 ACTGTGTTTTGTAGTGACTATGAAGT 58.727 34.615 0.00 0.00 39.21 3.01
3009 3216 7.715265 ACTGTGTTTTGTAGTGACTATGAAG 57.285 36.000 0.00 0.00 0.00 3.02
3010 3217 9.037737 GTAACTGTGTTTTGTAGTGACTATGAA 57.962 33.333 0.00 0.00 0.00 2.57
3115 3330 1.749634 AGTACCGCTAGCTACCACAAG 59.250 52.381 13.93 0.00 0.00 3.16
3130 3357 6.809689 ACAACAAAGTTGCAAAACTTAGTACC 59.190 34.615 0.00 0.00 41.76 3.34
3131 3358 7.806149 ACAACAAAGTTGCAAAACTTAGTAC 57.194 32.000 0.00 0.00 41.76 2.73
3154 3381 9.174166 ACCATATCAAACACACCTAATAAGAAC 57.826 33.333 0.00 0.00 0.00 3.01
3159 3386 9.996554 CATCTACCATATCAAACACACCTAATA 57.003 33.333 0.00 0.00 0.00 0.98
3160 3387 8.494433 ACATCTACCATATCAAACACACCTAAT 58.506 33.333 0.00 0.00 0.00 1.73
3322 3567 3.536956 ACGGTGAAGAAGAACAACTCA 57.463 42.857 0.00 0.00 0.00 3.41
3323 3568 4.260661 GGAAACGGTGAAGAAGAACAACTC 60.261 45.833 0.00 0.00 0.00 3.01
3325 3570 3.242969 GGGAAACGGTGAAGAAGAACAAC 60.243 47.826 0.00 0.00 0.00 3.32
3328 3578 2.806818 GAGGGAAACGGTGAAGAAGAAC 59.193 50.000 0.00 0.00 0.00 3.01
3338 3588 1.909700 TACGTACAGAGGGAAACGGT 58.090 50.000 0.00 0.00 39.57 4.83
3347 3597 5.332883 GCATTTGCTGATGATACGTACAGAG 60.333 44.000 13.44 8.16 38.21 3.35
3395 3645 0.248661 CTCACTCGCGGTCATAGGTG 60.249 60.000 6.13 4.85 0.00 4.00
3400 3650 3.071206 AGGCTCACTCGCGGTCAT 61.071 61.111 6.13 0.00 0.00 3.06
3401 3651 4.056125 CAGGCTCACTCGCGGTCA 62.056 66.667 6.13 0.00 0.00 4.02
3402 3652 3.691744 CTCAGGCTCACTCGCGGTC 62.692 68.421 6.13 0.00 0.00 4.79
3403 3653 3.753434 CTCAGGCTCACTCGCGGT 61.753 66.667 6.13 0.00 0.00 5.68
3404 3654 3.408501 CTCTCAGGCTCACTCGCGG 62.409 68.421 6.13 0.00 0.00 6.46
3405 3655 2.101965 CTCTCAGGCTCACTCGCG 59.898 66.667 0.00 0.00 0.00 5.87
3406 3656 2.493973 CCTCTCAGGCTCACTCGC 59.506 66.667 0.00 0.00 0.00 5.03
3407 3657 1.680651 ACCCTCTCAGGCTCACTCG 60.681 63.158 0.00 0.00 32.73 4.18
3408 3658 1.896694 CACCCTCTCAGGCTCACTC 59.103 63.158 0.00 0.00 32.73 3.51
3409 3659 2.289532 GCACCCTCTCAGGCTCACT 61.290 63.158 0.00 0.00 32.73 3.41
3529 3796 1.502190 GCGGGTCAAGCAAGTTAGC 59.498 57.895 0.00 0.00 34.19 3.09
3587 3854 4.175489 CGGTCCAGCGACGACGAT 62.175 66.667 12.29 0.40 40.17 3.73
3589 3856 4.695231 AACGGTCCAGCGACGACG 62.695 66.667 4.96 2.12 40.17 5.12
3590 3857 3.103911 CAACGGTCCAGCGACGAC 61.104 66.667 4.96 0.00 40.17 4.34
3690 3958 3.325753 AGGGGCACACAGAGGAGC 61.326 66.667 0.00 0.00 0.00 4.70
3692 3960 2.122413 ACAGGGGCACACAGAGGA 60.122 61.111 0.00 0.00 0.00 3.71
3726 3994 5.667539 AGATCGATCCATCCATCGTATTT 57.332 39.130 21.66 0.00 44.99 1.40
3824 4102 3.293262 CAAGTTATCTACGAGCTCGCTC 58.707 50.000 34.83 16.61 44.43 5.03
3825 4103 2.033550 CCAAGTTATCTACGAGCTCGCT 59.966 50.000 34.83 23.28 44.43 4.93
3826 4104 2.223525 ACCAAGTTATCTACGAGCTCGC 60.224 50.000 34.83 17.10 44.43 5.03
3841 4119 0.898320 CATGGGAGACGAGACCAAGT 59.102 55.000 0.00 0.00 37.89 3.16
3845 4123 1.040646 TATGCATGGGAGACGAGACC 58.959 55.000 10.16 0.00 0.00 3.85
3846 4124 1.600663 CGTATGCATGGGAGACGAGAC 60.601 57.143 10.16 0.00 35.59 3.36
3913 4191 1.657751 GCCAGGAGAAAATGGACGGC 61.658 60.000 0.00 0.00 39.02 5.68
3914 4192 0.322456 TGCCAGGAGAAAATGGACGG 60.322 55.000 0.00 0.00 39.02 4.79
3915 4193 1.402968 CATGCCAGGAGAAAATGGACG 59.597 52.381 0.00 0.00 39.02 4.79
3916 4194 2.165030 CACATGCCAGGAGAAAATGGAC 59.835 50.000 0.00 0.00 39.02 4.02
3917 4195 2.225091 ACACATGCCAGGAGAAAATGGA 60.225 45.455 0.00 0.00 39.02 3.41
3918 4196 2.094390 CACACATGCCAGGAGAAAATGG 60.094 50.000 0.00 0.00 39.73 3.16
3919 4197 2.673043 GCACACATGCCAGGAGAAAATG 60.673 50.000 0.00 0.00 46.97 2.32
3920 4198 1.547372 GCACACATGCCAGGAGAAAAT 59.453 47.619 0.00 0.00 46.97 1.82
3921 4199 0.961019 GCACACATGCCAGGAGAAAA 59.039 50.000 0.00 0.00 46.97 2.29
3922 4200 2.644887 GCACACATGCCAGGAGAAA 58.355 52.632 0.00 0.00 46.97 2.52
3923 4201 4.402851 GCACACATGCCAGGAGAA 57.597 55.556 0.00 0.00 46.97 2.87


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

AutoCloner maintained by Alex Coulton.