Multiple sequence alignment - TraesCS2D01G182600

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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 TraesCS2D01G182600 chr2D 100.000 3935 0 0 1 3935 126981767 126985701 0.000000e+00 7267
1 TraesCS2D01G182600 chr2D 84.987 373 44 6 2289 2659 103370613 103370251 6.210000e-98 368
2 TraesCS2D01G182600 chr2D 84.987 373 44 6 2289 2659 104398127 104398489 6.210000e-98 368
3 TraesCS2D01G182600 chr2B 94.441 2968 83 25 984 3935 180605291 180608192 0.000000e+00 4492
4 TraesCS2D01G182600 chr2B 88.939 669 51 14 329 984 180604600 180605258 0.000000e+00 804
5 TraesCS2D01G182600 chr2B 85.802 324 42 4 4 326 159578671 159578351 1.350000e-89 340
6 TraesCS2D01G182600 chr2A 95.002 2601 92 22 984 3575 133684703 133687274 0.000000e+00 4048
7 TraesCS2D01G182600 chr2A 86.976 668 66 11 326 986 133684020 133684673 0.000000e+00 732
8 TraesCS2D01G182600 chr2A 84.290 331 47 5 1 330 440128694 440129020 6.350000e-83 318
9 TraesCS2D01G182600 chr2A 86.824 296 8 4 3615 3908 133687271 133687537 6.390000e-78 302
10 TraesCS2D01G182600 chr2A 80.155 388 48 16 2284 2659 525822929 525822559 3.020000e-66 263
11 TraesCS2D01G182600 chr4D 89.822 786 51 11 1323 2106 236934393 236935151 0.000000e+00 981
12 TraesCS2D01G182600 chr4D 93.450 458 30 0 2105 2562 236936017 236936474 0.000000e+00 680
13 TraesCS2D01G182600 chr4D 96.059 203 8 0 2561 2763 236936594 236936796 8.150000e-87 331
14 TraesCS2D01G182600 chr4D 90.222 225 13 8 2828 3050 236939871 236940088 6.440000e-73 285
15 TraesCS2D01G182600 chr4B 88.776 784 56 10 1323 2106 338424355 338425106 0.000000e+00 931
16 TraesCS2D01G182600 chr4B 93.886 458 28 0 2105 2562 338425980 338426437 0.000000e+00 691
17 TraesCS2D01G182600 chr4B 85.933 327 43 3 1 326 416497806 416498130 2.910000e-91 346
18 TraesCS2D01G182600 chr4B 95.074 203 10 0 2561 2763 338426551 338426753 1.760000e-83 320
19 TraesCS2D01G182600 chr4B 88.889 225 16 8 2828 3050 338427912 338428129 6.480000e-68 268
20 TraesCS2D01G182600 chr4A 88.422 786 62 7 1323 2106 282080826 282081584 0.000000e+00 920
21 TraesCS2D01G182600 chr4A 94.105 458 27 0 2105 2562 282082449 282082906 0.000000e+00 697
22 TraesCS2D01G182600 chr4A 94.089 203 12 0 2561 2763 282083027 282083229 3.820000e-80 309
23 TraesCS2D01G182600 chr4A 97.590 83 2 0 2758 2840 282083305 282083387 4.100000e-30 143
24 TraesCS2D01G182600 chr7A 87.117 326 41 1 1 326 663744203 663744527 6.210000e-98 368
25 TraesCS2D01G182600 chr6B 86.850 327 40 3 1 326 227770474 227770798 2.890000e-96 363
26 TraesCS2D01G182600 chr1D 86.378 323 41 3 4 326 251939796 251940115 2.250000e-92 350
27 TraesCS2D01G182600 chr5A 85.276 326 46 2 1 326 448624034 448624357 6.300000e-88 335
28 TraesCS2D01G182600 chr7B 84.969 326 46 3 1 326 216892050 216892372 1.050000e-85 327
29 TraesCS2D01G182600 chr3D 84.709 327 44 6 1 326 168734175 168734496 4.910000e-84 322


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 TraesCS2D01G182600 chr2D 126981767 126985701 3934 False 7267.00 7267 100.000000 1 3935 1 chr2D.!!$F2 3934
1 TraesCS2D01G182600 chr2B 180604600 180608192 3592 False 2648.00 4492 91.690000 329 3935 2 chr2B.!!$F1 3606
2 TraesCS2D01G182600 chr2A 133684020 133687537 3517 False 1694.00 4048 89.600667 326 3908 3 chr2A.!!$F2 3582
3 TraesCS2D01G182600 chr4D 236934393 236940088 5695 False 569.25 981 92.388250 1323 3050 4 chr4D.!!$F1 1727
4 TraesCS2D01G182600 chr4B 338424355 338428129 3774 False 552.50 931 91.656250 1323 3050 4 chr4B.!!$F2 1727
5 TraesCS2D01G182600 chr4A 282080826 282083387 2561 False 517.25 920 93.551500 1323 2840 4 chr4A.!!$F1 1517

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
315 316 0.101759 TCGCTTACGCCTATCGCTTT 59.898 50.0 0.00 0.00 43.23 3.51 F
1275 1332 0.240411 AGGACCGACTTCGAAGTTCG 59.760 55.0 30.22 28.87 43.02 3.95 F
2154 3402 0.666913 GCATGCCACAGATAGCCAAG 59.333 55.0 6.36 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 3402 0.247460 GGCCTTTCAGGGTTGCAATC 59.753 55.0 0.59 0.0 35.37 2.67 R
2904 7374 0.320683 CCATCTCATTATCCCGCGCA 60.321 55.0 8.75 0.0 0.00 6.09 R
3908 8384 0.672401 TACGTGCTGCCAAGTTAGCC 60.672 55.0 0.00 0.0 39.15 3.93 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
18 19 2.906047 GCTTAGGTGCTAGGCGATG 58.094 57.895 0.00 0.00 30.01 3.84
19 20 0.601311 GCTTAGGTGCTAGGCGATGG 60.601 60.000 0.00 0.00 30.01 3.51
20 21 0.601311 CTTAGGTGCTAGGCGATGGC 60.601 60.000 0.00 0.00 38.90 4.40
30 31 4.559502 GCGATGGCCATACACCTT 57.440 55.556 20.84 0.00 0.00 3.50
31 32 2.024918 GCGATGGCCATACACCTTG 58.975 57.895 20.84 0.60 0.00 3.61
32 33 2.024918 CGATGGCCATACACCTTGC 58.975 57.895 20.84 2.02 0.00 4.01
33 34 1.447317 CGATGGCCATACACCTTGCC 61.447 60.000 20.84 1.20 44.27 4.52
34 35 0.106519 GATGGCCATACACCTTGCCT 60.107 55.000 20.84 0.00 44.32 4.75
35 36 1.142870 GATGGCCATACACCTTGCCTA 59.857 52.381 20.84 0.00 44.32 3.93
36 37 0.546122 TGGCCATACACCTTGCCTAG 59.454 55.000 0.00 0.00 44.32 3.02
53 54 4.647564 CCTAGGGCATAAATGGATGTCT 57.352 45.455 0.00 0.00 31.82 3.41
54 55 5.762179 CCTAGGGCATAAATGGATGTCTA 57.238 43.478 0.00 0.00 31.82 2.59
55 56 5.738909 CCTAGGGCATAAATGGATGTCTAG 58.261 45.833 0.00 0.00 35.26 2.43
56 57 4.647564 AGGGCATAAATGGATGTCTAGG 57.352 45.455 0.00 0.00 31.82 3.02
57 58 3.084786 GGGCATAAATGGATGTCTAGGC 58.915 50.000 0.00 0.00 31.82 3.93
58 59 3.498481 GGGCATAAATGGATGTCTAGGCA 60.498 47.826 0.00 0.00 31.82 4.75
59 60 3.755378 GGCATAAATGGATGTCTAGGCAG 59.245 47.826 2.27 0.00 0.00 4.85
60 61 3.755378 GCATAAATGGATGTCTAGGCAGG 59.245 47.826 2.27 0.00 0.00 4.85
61 62 4.330250 CATAAATGGATGTCTAGGCAGGG 58.670 47.826 2.27 0.00 0.00 4.45
62 63 2.196742 AATGGATGTCTAGGCAGGGA 57.803 50.000 2.27 0.00 0.00 4.20
63 64 2.196742 ATGGATGTCTAGGCAGGGAA 57.803 50.000 2.27 0.00 0.00 3.97
64 65 1.965414 TGGATGTCTAGGCAGGGAAA 58.035 50.000 2.27 0.00 0.00 3.13
65 66 1.839994 TGGATGTCTAGGCAGGGAAAG 59.160 52.381 2.27 0.00 0.00 2.62
66 67 1.475930 GGATGTCTAGGCAGGGAAAGC 60.476 57.143 2.27 0.00 0.00 3.51
67 68 1.210478 GATGTCTAGGCAGGGAAAGCA 59.790 52.381 2.27 0.00 0.00 3.91
68 69 1.064003 TGTCTAGGCAGGGAAAGCAA 58.936 50.000 0.00 0.00 0.00 3.91
69 70 1.003580 TGTCTAGGCAGGGAAAGCAAG 59.996 52.381 0.00 0.00 0.00 4.01
70 71 1.279271 GTCTAGGCAGGGAAAGCAAGA 59.721 52.381 0.00 0.00 0.00 3.02
71 72 1.985159 TCTAGGCAGGGAAAGCAAGAA 59.015 47.619 0.00 0.00 0.00 2.52
72 73 2.375174 TCTAGGCAGGGAAAGCAAGAAA 59.625 45.455 0.00 0.00 0.00 2.52
73 74 2.315720 AGGCAGGGAAAGCAAGAAAT 57.684 45.000 0.00 0.00 0.00 2.17
74 75 2.613129 AGGCAGGGAAAGCAAGAAATT 58.387 42.857 0.00 0.00 0.00 1.82
75 76 2.301009 AGGCAGGGAAAGCAAGAAATTG 59.699 45.455 0.00 0.00 0.00 2.32
76 77 2.037641 GGCAGGGAAAGCAAGAAATTGT 59.962 45.455 0.00 0.00 0.00 2.71
77 78 3.320626 GCAGGGAAAGCAAGAAATTGTC 58.679 45.455 0.00 0.00 0.00 3.18
78 79 3.006217 GCAGGGAAAGCAAGAAATTGTCT 59.994 43.478 0.00 0.00 38.69 3.41
79 80 4.218417 GCAGGGAAAGCAAGAAATTGTCTA 59.782 41.667 0.00 0.00 34.56 2.59
80 81 5.105595 GCAGGGAAAGCAAGAAATTGTCTAT 60.106 40.000 0.00 0.00 34.56 1.98
81 82 6.558909 CAGGGAAAGCAAGAAATTGTCTATC 58.441 40.000 0.00 0.00 34.56 2.08
82 83 5.654209 AGGGAAAGCAAGAAATTGTCTATCC 59.346 40.000 0.00 0.00 34.56 2.59
83 84 5.418840 GGGAAAGCAAGAAATTGTCTATCCA 59.581 40.000 0.00 0.00 34.56 3.41
84 85 6.071391 GGGAAAGCAAGAAATTGTCTATCCAA 60.071 38.462 0.00 0.00 34.56 3.53
85 86 7.031975 GGAAAGCAAGAAATTGTCTATCCAAG 58.968 38.462 0.00 0.00 34.56 3.61
86 87 7.309438 GGAAAGCAAGAAATTGTCTATCCAAGT 60.309 37.037 0.00 0.00 34.56 3.16
87 88 8.635765 AAAGCAAGAAATTGTCTATCCAAGTA 57.364 30.769 0.00 0.00 34.56 2.24
88 89 8.635765 AAGCAAGAAATTGTCTATCCAAGTAA 57.364 30.769 0.00 0.00 34.56 2.24
89 90 8.273780 AGCAAGAAATTGTCTATCCAAGTAAG 57.726 34.615 0.00 0.00 34.56 2.34
90 91 8.103305 AGCAAGAAATTGTCTATCCAAGTAAGA 58.897 33.333 0.00 0.00 34.56 2.10
91 92 8.730680 GCAAGAAATTGTCTATCCAAGTAAGAA 58.269 33.333 0.00 0.00 34.56 2.52
99 100 8.677148 TGTCTATCCAAGTAAGAAATAATGCC 57.323 34.615 0.00 0.00 0.00 4.40
100 101 8.271458 TGTCTATCCAAGTAAGAAATAATGCCA 58.729 33.333 0.00 0.00 0.00 4.92
101 102 9.289782 GTCTATCCAAGTAAGAAATAATGCCAT 57.710 33.333 0.00 0.00 0.00 4.40
106 107 8.359642 TCCAAGTAAGAAATAATGCCATATTGC 58.640 33.333 0.00 0.00 0.00 3.56
107 108 8.143193 CCAAGTAAGAAATAATGCCATATTGCA 58.857 33.333 3.65 3.65 46.94 4.08
108 109 8.971321 CAAGTAAGAAATAATGCCATATTGCAC 58.029 33.333 3.18 0.00 45.48 4.57
109 110 8.469309 AGTAAGAAATAATGCCATATTGCACT 57.531 30.769 3.18 0.00 45.48 4.40
110 111 9.573166 AGTAAGAAATAATGCCATATTGCACTA 57.427 29.630 3.18 0.00 45.48 2.74
117 118 9.590451 AATAATGCCATATTGCACTAATATTGC 57.410 29.630 3.18 6.16 45.48 3.56
118 119 5.389859 TGCCATATTGCACTAATATTGCC 57.610 39.130 9.32 0.00 44.08 4.52
119 120 4.831710 TGCCATATTGCACTAATATTGCCA 59.168 37.500 9.32 0.00 44.08 4.92
120 121 5.303845 TGCCATATTGCACTAATATTGCCAA 59.696 36.000 9.32 0.00 44.08 4.52
121 122 6.183360 TGCCATATTGCACTAATATTGCCAAA 60.183 34.615 9.32 0.00 44.08 3.28
122 123 6.146021 GCCATATTGCACTAATATTGCCAAAC 59.854 38.462 0.00 0.00 41.26 2.93
123 124 6.363088 CCATATTGCACTAATATTGCCAAACG 59.637 38.462 0.00 0.00 39.41 3.60
124 125 3.773860 TGCACTAATATTGCCAAACGG 57.226 42.857 0.00 0.00 39.39 4.44
125 126 2.425312 TGCACTAATATTGCCAAACGGG 59.575 45.455 0.00 0.00 39.39 5.28
126 127 9.813470 ATATTGCACTAATATTGCCAAACGGGC 62.813 40.741 0.00 0.00 45.98 6.13
138 139 4.439305 CCAAACGGGCCATATATCAATG 57.561 45.455 4.39 0.00 0.00 2.82
149 150 4.880120 CCATATATCAATGGCAGTAGCTGG 59.120 45.833 0.00 0.00 40.07 4.85
156 157 4.701663 GCAGTAGCTGGCAGTTCA 57.298 55.556 17.16 0.00 37.91 3.18
157 158 2.166270 GCAGTAGCTGGCAGTTCAC 58.834 57.895 17.16 11.27 37.91 3.18
158 159 0.321122 GCAGTAGCTGGCAGTTCACT 60.321 55.000 17.16 13.32 37.91 3.41
159 160 1.879796 GCAGTAGCTGGCAGTTCACTT 60.880 52.381 17.16 0.00 37.91 3.16
160 161 2.612972 GCAGTAGCTGGCAGTTCACTTA 60.613 50.000 17.16 0.00 37.91 2.24
161 162 3.866651 CAGTAGCTGGCAGTTCACTTAT 58.133 45.455 17.16 0.00 0.00 1.73
162 163 4.256920 CAGTAGCTGGCAGTTCACTTATT 58.743 43.478 17.16 0.00 0.00 1.40
163 164 4.697352 CAGTAGCTGGCAGTTCACTTATTT 59.303 41.667 17.16 0.00 0.00 1.40
164 165 5.874810 CAGTAGCTGGCAGTTCACTTATTTA 59.125 40.000 17.16 0.00 0.00 1.40
165 166 6.540189 CAGTAGCTGGCAGTTCACTTATTTAT 59.460 38.462 17.16 0.00 0.00 1.40
166 167 6.763610 AGTAGCTGGCAGTTCACTTATTTATC 59.236 38.462 17.16 0.00 0.00 1.75
167 168 5.500234 AGCTGGCAGTTCACTTATTTATCA 58.500 37.500 17.16 0.00 0.00 2.15
168 169 5.587844 AGCTGGCAGTTCACTTATTTATCAG 59.412 40.000 17.16 0.00 0.00 2.90
169 170 5.586243 GCTGGCAGTTCACTTATTTATCAGA 59.414 40.000 17.16 0.00 0.00 3.27
170 171 6.457528 GCTGGCAGTTCACTTATTTATCAGAC 60.458 42.308 17.16 0.00 0.00 3.51
171 172 5.880332 TGGCAGTTCACTTATTTATCAGACC 59.120 40.000 0.00 0.00 0.00 3.85
172 173 6.116126 GGCAGTTCACTTATTTATCAGACCT 58.884 40.000 0.00 0.00 0.00 3.85
173 174 7.093068 TGGCAGTTCACTTATTTATCAGACCTA 60.093 37.037 0.00 0.00 0.00 3.08
174 175 7.769044 GGCAGTTCACTTATTTATCAGACCTAA 59.231 37.037 0.00 0.00 0.00 2.69
175 176 9.162764 GCAGTTCACTTATTTATCAGACCTAAA 57.837 33.333 0.00 0.00 0.00 1.85
213 214 9.127277 ACACATATAATAACCACAAATACACCC 57.873 33.333 0.00 0.00 0.00 4.61
214 215 9.349713 CACATATAATAACCACAAATACACCCT 57.650 33.333 0.00 0.00 0.00 4.34
215 216 9.349713 ACATATAATAACCACAAATACACCCTG 57.650 33.333 0.00 0.00 0.00 4.45
216 217 9.567776 CATATAATAACCACAAATACACCCTGA 57.432 33.333 0.00 0.00 0.00 3.86
219 220 9.793259 ATAATAACCACAAATACACCCTGATAG 57.207 33.333 0.00 0.00 0.00 2.08
220 221 5.514500 AACCACAAATACACCCTGATAGT 57.486 39.130 0.00 0.00 0.00 2.12
221 222 4.843728 ACCACAAATACACCCTGATAGTG 58.156 43.478 0.00 0.00 41.15 2.74
222 223 4.534500 ACCACAAATACACCCTGATAGTGA 59.466 41.667 0.00 0.00 38.63 3.41
223 224 5.013704 ACCACAAATACACCCTGATAGTGAA 59.986 40.000 0.00 0.00 38.63 3.18
224 225 5.943416 CCACAAATACACCCTGATAGTGAAA 59.057 40.000 0.00 0.00 38.63 2.69
225 226 6.432783 CCACAAATACACCCTGATAGTGAAAA 59.567 38.462 0.00 0.00 38.63 2.29
226 227 7.122650 CCACAAATACACCCTGATAGTGAAAAT 59.877 37.037 0.00 0.00 38.63 1.82
227 228 8.522830 CACAAATACACCCTGATAGTGAAAATT 58.477 33.333 0.00 0.00 38.63 1.82
228 229 9.747898 ACAAATACACCCTGATAGTGAAAATTA 57.252 29.630 0.00 0.00 38.63 1.40
245 246 9.659830 GTGAAAATTATATTACTGTTTAGGCCG 57.340 33.333 0.00 0.00 0.00 6.13
246 247 8.347035 TGAAAATTATATTACTGTTTAGGCCGC 58.653 33.333 0.00 0.00 0.00 6.53
247 248 6.476243 AATTATATTACTGTTTAGGCCGCG 57.524 37.500 0.00 0.00 0.00 6.46
248 249 1.574134 TATTACTGTTTAGGCCGCGC 58.426 50.000 0.00 0.00 0.00 6.86
259 260 4.918201 GCCGCGCCTAGGATGCTT 62.918 66.667 14.75 0.00 0.00 3.91
260 261 2.734591 CCGCGCCTAGGATGCTTA 59.265 61.111 14.75 0.00 0.00 3.09
261 262 1.069090 CCGCGCCTAGGATGCTTAA 59.931 57.895 14.75 0.00 0.00 1.85
262 263 0.946221 CCGCGCCTAGGATGCTTAAG 60.946 60.000 14.75 0.00 0.00 1.85
263 264 1.560860 CGCGCCTAGGATGCTTAAGC 61.561 60.000 20.84 20.84 42.50 3.09
264 265 1.560860 GCGCCTAGGATGCTTAAGCG 61.561 60.000 21.97 16.96 45.83 4.68
265 266 1.560860 CGCCTAGGATGCTTAAGCGC 61.561 60.000 21.97 15.93 45.83 5.92
266 267 1.231296 GCCTAGGATGCTTAAGCGCC 61.231 60.000 24.19 24.19 45.83 6.53
267 268 0.946221 CCTAGGATGCTTAAGCGCCG 60.946 60.000 24.81 15.81 45.83 6.46
268 269 0.249489 CTAGGATGCTTAAGCGCCGT 60.249 55.000 24.81 19.99 45.83 5.68
269 270 0.249322 TAGGATGCTTAAGCGCCGTC 60.249 55.000 24.81 18.16 45.83 4.79
270 271 1.521681 GGATGCTTAAGCGCCGTCT 60.522 57.895 21.97 2.91 45.83 4.18
271 272 0.249322 GGATGCTTAAGCGCCGTCTA 60.249 55.000 21.97 3.38 45.83 2.59
272 273 1.132588 GATGCTTAAGCGCCGTCTAG 58.867 55.000 21.97 0.00 45.83 2.43
273 274 0.249489 ATGCTTAAGCGCCGTCTAGG 60.249 55.000 21.97 0.00 45.83 3.02
282 283 4.635925 CCGTCTAGGCACTATGCG 57.364 61.111 0.00 0.00 46.21 4.73
283 284 2.030551 CCGTCTAGGCACTATGCGA 58.969 57.895 0.00 0.00 46.21 5.10
284 285 0.384309 CCGTCTAGGCACTATGCGAA 59.616 55.000 0.00 0.00 46.21 4.70
285 286 1.600663 CCGTCTAGGCACTATGCGAAG 60.601 57.143 0.00 0.00 46.21 3.79
286 287 1.600663 CGTCTAGGCACTATGCGAAGG 60.601 57.143 0.00 0.00 46.21 3.46
287 288 0.389391 TCTAGGCACTATGCGAAGGC 59.611 55.000 0.00 0.00 46.21 4.35
288 289 0.601311 CTAGGCACTATGCGAAGGCC 60.601 60.000 0.00 0.00 46.21 5.19
289 290 1.334384 TAGGCACTATGCGAAGGCCA 61.334 55.000 5.01 0.00 46.21 5.36
290 291 1.748879 GGCACTATGCGAAGGCCAA 60.749 57.895 5.01 0.00 46.21 4.52
291 292 1.429423 GCACTATGCGAAGGCCAAC 59.571 57.895 5.01 0.00 38.85 3.77
292 293 1.993369 GCACTATGCGAAGGCCAACC 61.993 60.000 5.01 0.00 38.85 3.77
293 294 1.449601 ACTATGCGAAGGCCAACCG 60.450 57.895 5.01 6.27 42.76 4.44
303 304 3.497031 GCCAACCGCCTCGCTTAC 61.497 66.667 0.00 0.00 0.00 2.34
304 305 3.186047 CCAACCGCCTCGCTTACG 61.186 66.667 0.00 0.00 42.01 3.18
305 306 3.849953 CAACCGCCTCGCTTACGC 61.850 66.667 0.00 0.00 39.84 4.42
308 309 3.896133 CCGCCTCGCTTACGCCTA 61.896 66.667 0.00 0.00 39.84 3.93
309 310 2.335369 CGCCTCGCTTACGCCTAT 59.665 61.111 0.00 0.00 39.84 2.57
310 311 1.729838 CGCCTCGCTTACGCCTATC 60.730 63.158 0.00 0.00 39.84 2.08
311 312 1.729838 GCCTCGCTTACGCCTATCG 60.730 63.158 0.00 0.00 45.38 2.92
312 313 1.729838 CCTCGCTTACGCCTATCGC 60.730 63.158 0.00 0.00 43.23 4.58
313 314 1.283181 CTCGCTTACGCCTATCGCT 59.717 57.895 0.00 0.00 43.23 4.93
314 315 0.317938 CTCGCTTACGCCTATCGCTT 60.318 55.000 0.00 0.00 43.23 4.68
315 316 0.101759 TCGCTTACGCCTATCGCTTT 59.898 50.000 0.00 0.00 43.23 3.51
316 317 0.928229 CGCTTACGCCTATCGCTTTT 59.072 50.000 0.00 0.00 43.23 2.27
317 318 1.326548 CGCTTACGCCTATCGCTTTTT 59.673 47.619 0.00 0.00 43.23 1.94
318 319 2.596807 CGCTTACGCCTATCGCTTTTTC 60.597 50.000 0.00 0.00 43.23 2.29
319 320 2.286242 GCTTACGCCTATCGCTTTTTCC 60.286 50.000 0.00 0.00 43.23 3.13
320 321 2.676632 TACGCCTATCGCTTTTTCCA 57.323 45.000 0.00 0.00 43.23 3.53
321 322 1.816074 ACGCCTATCGCTTTTTCCAA 58.184 45.000 0.00 0.00 43.23 3.53
322 323 1.467342 ACGCCTATCGCTTTTTCCAAC 59.533 47.619 0.00 0.00 43.23 3.77
323 324 1.202143 CGCCTATCGCTTTTTCCAACC 60.202 52.381 0.00 0.00 34.21 3.77
324 325 2.092323 GCCTATCGCTTTTTCCAACCT 58.908 47.619 0.00 0.00 0.00 3.50
373 375 9.525409 GGTATGAGTTAAAGAATTTAGCGACTA 57.475 33.333 0.00 0.00 44.99 2.59
402 404 9.449719 CTTTACTATTAGTTGGTGAAAGGACAT 57.550 33.333 0.85 0.00 0.00 3.06
407 409 2.559668 AGTTGGTGAAAGGACATGCATG 59.440 45.455 25.09 25.09 0.00 4.06
408 410 0.889994 TGGTGAAAGGACATGCATGC 59.110 50.000 26.53 18.01 0.00 4.06
412 414 1.270274 TGAAAGGACATGCATGCACAC 59.730 47.619 25.37 16.49 0.00 3.82
428 430 3.001406 ACTGGCCGGTCCACTACC 61.001 66.667 12.85 0.00 45.77 3.18
472 474 7.330946 CCAGTACATAGATCGACTGAAACAAAA 59.669 37.037 13.06 0.00 41.51 2.44
510 512 6.007936 TGACCCAAATATTGTTTTCAGTCG 57.992 37.500 0.00 0.00 0.00 4.18
529 531 1.028905 GACTGTCATCTAGCCGCTCT 58.971 55.000 2.24 0.00 0.00 4.09
550 552 3.777522 CTCAAGAAACATACCTCCTCCCT 59.222 47.826 0.00 0.00 0.00 4.20
557 559 0.644937 ATACCTCCTCCCTTGCCTCT 59.355 55.000 0.00 0.00 0.00 3.69
579 588 1.834540 GTCCCCTTCCCCTTCCATAT 58.165 55.000 0.00 0.00 0.00 1.78
602 611 2.101575 TAGCGTCGATGGTCGTGC 59.898 61.111 13.51 9.90 41.35 5.34
604 613 1.929806 TAGCGTCGATGGTCGTGCTT 61.930 55.000 13.51 9.84 44.96 3.91
675 684 1.208293 CCCTCCTCTACCAAGTTGCTC 59.792 57.143 0.00 0.00 0.00 4.26
698 707 2.755469 GCCAATGCCACCGTCCAT 60.755 61.111 0.00 0.00 0.00 3.41
709 718 1.762957 CACCGTCCATCTCCACCTATT 59.237 52.381 0.00 0.00 0.00 1.73
721 730 1.626686 CACCTATTGCCCAACACCAA 58.373 50.000 0.00 0.00 0.00 3.67
734 743 0.532862 ACACCAACGCTCTTCACTGG 60.533 55.000 0.00 0.00 0.00 4.00
770 779 3.211045 TCTGATCCATATGTCGACGACA 58.789 45.455 30.90 30.90 46.90 4.35
793 802 1.298602 CATCATTCGGATGCGTTCCA 58.701 50.000 6.49 0.00 46.35 3.53
798 807 1.822114 TTCGGATGCGTTCCAGGTCA 61.822 55.000 6.49 0.00 45.78 4.02
825 834 0.874390 CAACACCAATGACCACGAGG 59.126 55.000 0.00 0.00 42.21 4.63
838 847 3.213402 CGAGGTCGAGCTCCCTCC 61.213 72.222 32.56 17.10 43.65 4.30
993 1041 2.693864 CCCCTCCTGCACATCCCT 60.694 66.667 0.00 0.00 0.00 4.20
1060 1108 3.898509 CAGCGGCCGAGAGAGAGG 61.899 72.222 33.48 3.73 0.00 3.69
1064 1112 1.452289 CGGCCGAGAGAGAGGAGAA 60.452 63.158 24.07 0.00 0.00 2.87
1099 1147 1.218844 GGGATTGTGGCCTAGGGTTA 58.781 55.000 11.72 0.00 0.00 2.85
1105 1157 1.282382 GTGGCCTAGGGTTAAGTGGA 58.718 55.000 11.72 0.00 0.00 4.02
1106 1158 1.065636 GTGGCCTAGGGTTAAGTGGAC 60.066 57.143 11.72 0.00 0.00 4.02
1123 1176 3.924686 GTGGACGTGAGGTTACTTATGTG 59.075 47.826 0.00 0.00 33.12 3.21
1145 1201 1.550327 TTTTGTGTGTGTGGGCTTGA 58.450 45.000 0.00 0.00 0.00 3.02
1148 1204 1.152963 GTGTGTGTGGGCTTGAGGT 60.153 57.895 0.00 0.00 0.00 3.85
1149 1205 0.751643 GTGTGTGTGGGCTTGAGGTT 60.752 55.000 0.00 0.00 0.00 3.50
1150 1206 0.751277 TGTGTGTGGGCTTGAGGTTG 60.751 55.000 0.00 0.00 0.00 3.77
1151 1207 1.827789 TGTGTGGGCTTGAGGTTGC 60.828 57.895 0.00 0.00 0.00 4.17
1152 1208 1.529244 GTGTGGGCTTGAGGTTGCT 60.529 57.895 0.00 0.00 0.00 3.91
1163 1219 4.787598 CTTGAGGTTGCTTATGTGTGTTC 58.212 43.478 0.00 0.00 0.00 3.18
1213 1269 3.351740 TCAAATGCAGGCCGAATCTTTA 58.648 40.909 0.00 0.00 0.00 1.85
1271 1328 0.314302 ACACAGGACCGACTTCGAAG 59.686 55.000 23.43 23.43 43.02 3.79
1273 1330 1.038280 ACAGGACCGACTTCGAAGTT 58.962 50.000 30.22 16.11 43.02 2.66
1274 1331 1.000496 ACAGGACCGACTTCGAAGTTC 60.000 52.381 30.22 22.80 43.02 3.01
1275 1332 0.240411 AGGACCGACTTCGAAGTTCG 59.760 55.000 30.22 28.87 43.02 3.95
1366 1426 2.156102 AACCCTAGTCCTAGTTCCCG 57.844 55.000 0.96 0.00 0.00 5.14
1810 1873 4.698625 AGGACGAACGGGGAGCCT 62.699 66.667 0.00 0.00 0.00 4.58
2091 2157 3.154473 TTCTCCCGGGATGCCTCG 61.154 66.667 27.07 11.74 0.00 4.63
2106 3354 1.446792 CTCGATGCTCGCCACAAGT 60.447 57.895 0.00 0.00 40.21 3.16
2154 3402 0.666913 GCATGCCACAGATAGCCAAG 59.333 55.000 6.36 0.00 0.00 3.61
2548 3796 5.487488 AGATTGTACTGTACCCTCATTGGAA 59.513 40.000 14.91 0.45 38.35 3.53
2703 4073 4.569966 AGTCTCATCTCGCATGTGAAATTC 59.430 41.667 10.71 0.00 0.00 2.17
2995 7467 2.746362 CTGTCCTTTTGCTGATCTGTCC 59.254 50.000 1.27 0.00 0.00 4.02
3012 7484 4.287067 TCTGTCCTTCCAAGCTCTTTACAT 59.713 41.667 0.00 0.00 0.00 2.29
3282 7756 6.127083 TGCTTTGAAAAGGATGGTCTTTCTTT 60.127 34.615 5.02 0.00 36.09 2.52
3307 7781 5.462530 AACATTAGGTTTTAGCAACCACC 57.537 39.130 7.15 0.00 42.69 4.61
3397 7871 1.727535 CGTGCGCAATTTGGAATCGAA 60.728 47.619 14.00 0.00 0.00 3.71
3426 7900 5.004361 TGGAAACATGGGGTTGAAATAGA 57.996 39.130 0.00 0.00 40.35 1.98
3551 8025 9.643693 AACATAGAGCCAACAAAATATTTCTTG 57.356 29.630 0.10 6.40 0.00 3.02
3658 8132 8.090214 ACATCTTTGGTATTGGAAAATGAAGTG 58.910 33.333 0.00 0.00 0.00 3.16
3742 8216 4.985413 ACGATGCCACTAATTGTTCATTG 58.015 39.130 0.00 0.00 31.77 2.82
3748 8222 4.220602 GCCACTAATTGTTCATTGGGTTCT 59.779 41.667 0.00 0.00 0.00 3.01
3826 8300 3.834231 ACAAGCAGTCCATAAGCCAAATT 59.166 39.130 0.00 0.00 0.00 1.82
3828 8302 5.126061 ACAAGCAGTCCATAAGCCAAATTAG 59.874 40.000 0.00 0.00 0.00 1.73
3856 8330 5.876691 AATGGCCCATCCCACTATAAATA 57.123 39.130 0.00 0.00 37.79 1.40
3857 8331 4.927267 TGGCCCATCCCACTATAAATAG 57.073 45.455 0.00 0.00 36.46 1.73
3908 8384 3.067106 AGGCTAACACATGTTCTTCACG 58.933 45.455 0.00 0.00 39.31 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.601311 CCATCGCCTAGCACCTAAGC 60.601 60.000 0.00 0.00 0.00 3.09
1 2 0.601311 GCCATCGCCTAGCACCTAAG 60.601 60.000 0.00 0.00 0.00 2.18
2 3 1.445942 GCCATCGCCTAGCACCTAA 59.554 57.895 0.00 0.00 0.00 2.69
3 4 3.138625 GCCATCGCCTAGCACCTA 58.861 61.111 0.00 0.00 0.00 3.08
13 14 2.024918 CAAGGTGTATGGCCATCGC 58.975 57.895 24.80 19.22 0.00 4.58
14 15 1.447317 GGCAAGGTGTATGGCCATCG 61.447 60.000 24.80 4.33 45.70 3.84
15 16 2.419057 GGCAAGGTGTATGGCCATC 58.581 57.895 24.80 14.58 45.70 3.51
16 17 4.684623 GGCAAGGTGTATGGCCAT 57.315 55.556 24.45 24.45 45.70 4.40
18 19 0.179018 CCTAGGCAAGGTGTATGGCC 60.179 60.000 0.00 0.00 46.77 5.36
19 20 0.179018 CCCTAGGCAAGGTGTATGGC 60.179 60.000 2.05 0.00 44.90 4.40
32 33 4.647564 AGACATCCATTTATGCCCTAGG 57.352 45.455 0.06 0.06 0.00 3.02
33 34 5.738909 CCTAGACATCCATTTATGCCCTAG 58.261 45.833 0.00 0.00 35.44 3.02
34 35 4.019321 GCCTAGACATCCATTTATGCCCTA 60.019 45.833 0.00 0.00 0.00 3.53
35 36 3.245052 GCCTAGACATCCATTTATGCCCT 60.245 47.826 0.00 0.00 0.00 5.19
36 37 3.084786 GCCTAGACATCCATTTATGCCC 58.915 50.000 0.00 0.00 0.00 5.36
37 38 3.754965 TGCCTAGACATCCATTTATGCC 58.245 45.455 0.00 0.00 0.00 4.40
38 39 3.755378 CCTGCCTAGACATCCATTTATGC 59.245 47.826 0.00 0.00 0.00 3.14
39 40 4.042062 TCCCTGCCTAGACATCCATTTATG 59.958 45.833 0.00 0.00 0.00 1.90
40 41 4.242811 TCCCTGCCTAGACATCCATTTAT 58.757 43.478 0.00 0.00 0.00 1.40
41 42 3.664320 TCCCTGCCTAGACATCCATTTA 58.336 45.455 0.00 0.00 0.00 1.40
42 43 2.492025 TCCCTGCCTAGACATCCATTT 58.508 47.619 0.00 0.00 0.00 2.32
43 44 2.196742 TCCCTGCCTAGACATCCATT 57.803 50.000 0.00 0.00 0.00 3.16
44 45 2.196742 TTCCCTGCCTAGACATCCAT 57.803 50.000 0.00 0.00 0.00 3.41
45 46 1.839994 CTTTCCCTGCCTAGACATCCA 59.160 52.381 0.00 0.00 0.00 3.41
46 47 1.475930 GCTTTCCCTGCCTAGACATCC 60.476 57.143 0.00 0.00 0.00 3.51
47 48 1.210478 TGCTTTCCCTGCCTAGACATC 59.790 52.381 0.00 0.00 0.00 3.06
48 49 1.289160 TGCTTTCCCTGCCTAGACAT 58.711 50.000 0.00 0.00 0.00 3.06
49 50 1.003580 CTTGCTTTCCCTGCCTAGACA 59.996 52.381 0.00 0.00 0.00 3.41
50 51 1.279271 TCTTGCTTTCCCTGCCTAGAC 59.721 52.381 0.00 0.00 0.00 2.59
51 52 1.656587 TCTTGCTTTCCCTGCCTAGA 58.343 50.000 0.00 0.00 0.00 2.43
52 53 2.496899 TTCTTGCTTTCCCTGCCTAG 57.503 50.000 0.00 0.00 0.00 3.02
53 54 2.969821 TTTCTTGCTTTCCCTGCCTA 57.030 45.000 0.00 0.00 0.00 3.93
54 55 2.301009 CAATTTCTTGCTTTCCCTGCCT 59.699 45.455 0.00 0.00 0.00 4.75
55 56 2.037641 ACAATTTCTTGCTTTCCCTGCC 59.962 45.455 0.00 0.00 35.69 4.85
56 57 3.006217 AGACAATTTCTTGCTTTCCCTGC 59.994 43.478 0.00 0.00 35.69 4.85
57 58 4.861102 AGACAATTTCTTGCTTTCCCTG 57.139 40.909 0.00 0.00 35.69 4.45
58 59 5.654209 GGATAGACAATTTCTTGCTTTCCCT 59.346 40.000 0.00 0.00 34.49 4.20
59 60 5.418840 TGGATAGACAATTTCTTGCTTTCCC 59.581 40.000 0.00 0.00 36.71 3.97
60 61 6.515272 TGGATAGACAATTTCTTGCTTTCC 57.485 37.500 0.00 0.00 37.27 3.13
61 62 7.597386 ACTTGGATAGACAATTTCTTGCTTTC 58.403 34.615 0.00 0.00 35.69 2.62
62 63 7.530426 ACTTGGATAGACAATTTCTTGCTTT 57.470 32.000 0.00 0.00 35.69 3.51
63 64 8.635765 TTACTTGGATAGACAATTTCTTGCTT 57.364 30.769 0.00 0.00 35.69 3.91
64 65 8.103305 TCTTACTTGGATAGACAATTTCTTGCT 58.897 33.333 0.00 0.00 35.69 3.91
65 66 8.268850 TCTTACTTGGATAGACAATTTCTTGC 57.731 34.615 0.00 0.00 35.69 4.01
73 74 9.120538 GGCATTATTTCTTACTTGGATAGACAA 57.879 33.333 0.00 0.00 0.00 3.18
74 75 8.271458 TGGCATTATTTCTTACTTGGATAGACA 58.729 33.333 0.00 0.00 0.00 3.41
75 76 8.677148 TGGCATTATTTCTTACTTGGATAGAC 57.323 34.615 0.00 0.00 0.00 2.59
80 81 8.359642 GCAATATGGCATTATTTCTTACTTGGA 58.640 33.333 4.78 0.00 0.00 3.53
81 82 8.143193 TGCAATATGGCATTATTTCTTACTTGG 58.857 33.333 4.78 0.00 39.25 3.61
82 83 8.971321 GTGCAATATGGCATTATTTCTTACTTG 58.029 33.333 8.32 0.00 46.92 3.16
83 84 8.917088 AGTGCAATATGGCATTATTTCTTACTT 58.083 29.630 8.32 0.00 46.92 2.24
84 85 8.469309 AGTGCAATATGGCATTATTTCTTACT 57.531 30.769 8.32 0.00 46.92 2.24
98 99 6.363088 CGTTTGGCAATATTAGTGCAATATGG 59.637 38.462 16.95 0.00 44.07 2.74
99 100 6.363088 CCGTTTGGCAATATTAGTGCAATATG 59.637 38.462 16.95 7.19 44.07 1.78
100 101 6.446318 CCGTTTGGCAATATTAGTGCAATAT 58.554 36.000 16.95 0.00 44.07 1.28
101 102 5.221145 CCCGTTTGGCAATATTAGTGCAATA 60.221 40.000 16.95 0.00 44.07 1.90
102 103 4.441356 CCCGTTTGGCAATATTAGTGCAAT 60.441 41.667 16.95 0.00 44.07 3.56
103 104 3.119316 CCCGTTTGGCAATATTAGTGCAA 60.119 43.478 16.95 3.72 44.07 4.08
104 105 2.425312 CCCGTTTGGCAATATTAGTGCA 59.575 45.455 16.95 2.01 44.07 4.57
105 106 3.078594 CCCGTTTGGCAATATTAGTGC 57.921 47.619 7.56 7.56 41.45 4.40
117 118 3.193267 CCATTGATATATGGCCCGTTTGG 59.807 47.826 0.00 0.00 38.75 3.28
118 119 4.439305 CCATTGATATATGGCCCGTTTG 57.561 45.455 0.00 0.00 38.75 2.93
126 127 4.880120 CCAGCTACTGCCATTGATATATGG 59.120 45.833 0.66 0.66 46.46 2.74
127 128 4.334759 GCCAGCTACTGCCATTGATATATG 59.665 45.833 0.00 0.00 40.80 1.78
128 129 4.019051 TGCCAGCTACTGCCATTGATATAT 60.019 41.667 0.00 0.00 40.80 0.86
129 130 3.327464 TGCCAGCTACTGCCATTGATATA 59.673 43.478 0.00 0.00 40.80 0.86
130 131 2.107031 TGCCAGCTACTGCCATTGATAT 59.893 45.455 0.00 0.00 40.80 1.63
131 132 1.490069 TGCCAGCTACTGCCATTGATA 59.510 47.619 0.00 0.00 40.80 2.15
132 133 0.256752 TGCCAGCTACTGCCATTGAT 59.743 50.000 0.00 0.00 40.80 2.57
133 134 0.393402 CTGCCAGCTACTGCCATTGA 60.393 55.000 0.00 0.00 40.80 2.57
134 135 0.679002 ACTGCCAGCTACTGCCATTG 60.679 55.000 0.00 0.00 40.80 2.82
135 136 0.038744 AACTGCCAGCTACTGCCATT 59.961 50.000 0.00 0.00 40.80 3.16
136 137 0.393537 GAACTGCCAGCTACTGCCAT 60.394 55.000 0.00 0.00 40.80 4.40
137 138 1.003355 GAACTGCCAGCTACTGCCA 60.003 57.895 0.00 0.00 40.80 4.92
138 139 1.003355 TGAACTGCCAGCTACTGCC 60.003 57.895 0.00 0.00 40.80 4.85
139 140 0.321122 AGTGAACTGCCAGCTACTGC 60.321 55.000 0.00 0.00 40.05 4.40
140 141 2.175878 AAGTGAACTGCCAGCTACTG 57.824 50.000 0.00 0.00 0.00 2.74
141 142 4.559862 AATAAGTGAACTGCCAGCTACT 57.440 40.909 0.00 0.00 0.00 2.57
142 143 6.538742 TGATAAATAAGTGAACTGCCAGCTAC 59.461 38.462 0.00 0.00 0.00 3.58
143 144 6.649155 TGATAAATAAGTGAACTGCCAGCTA 58.351 36.000 0.00 0.00 0.00 3.32
144 145 5.500234 TGATAAATAAGTGAACTGCCAGCT 58.500 37.500 0.00 0.00 0.00 4.24
145 146 5.586243 TCTGATAAATAAGTGAACTGCCAGC 59.414 40.000 0.00 0.00 0.00 4.85
146 147 6.037610 GGTCTGATAAATAAGTGAACTGCCAG 59.962 42.308 0.00 0.00 0.00 4.85
147 148 5.880332 GGTCTGATAAATAAGTGAACTGCCA 59.120 40.000 0.00 0.00 0.00 4.92
148 149 6.116126 AGGTCTGATAAATAAGTGAACTGCC 58.884 40.000 0.00 0.00 0.00 4.85
149 150 8.718102 TTAGGTCTGATAAATAAGTGAACTGC 57.282 34.615 0.00 0.00 0.00 4.40
187 188 9.127277 GGGTGTATTTGTGGTTATTATATGTGT 57.873 33.333 0.00 0.00 0.00 3.72
188 189 9.349713 AGGGTGTATTTGTGGTTATTATATGTG 57.650 33.333 0.00 0.00 0.00 3.21
189 190 9.349713 CAGGGTGTATTTGTGGTTATTATATGT 57.650 33.333 0.00 0.00 0.00 2.29
190 191 9.567776 TCAGGGTGTATTTGTGGTTATTATATG 57.432 33.333 0.00 0.00 0.00 1.78
193 194 9.793259 CTATCAGGGTGTATTTGTGGTTATTAT 57.207 33.333 0.00 0.00 0.00 1.28
194 195 8.774183 ACTATCAGGGTGTATTTGTGGTTATTA 58.226 33.333 0.00 0.00 0.00 0.98
195 196 7.556275 CACTATCAGGGTGTATTTGTGGTTATT 59.444 37.037 0.00 0.00 0.00 1.40
196 197 7.054124 CACTATCAGGGTGTATTTGTGGTTAT 58.946 38.462 0.00 0.00 0.00 1.89
197 198 6.213802 TCACTATCAGGGTGTATTTGTGGTTA 59.786 38.462 0.00 0.00 36.25 2.85
198 199 5.013704 TCACTATCAGGGTGTATTTGTGGTT 59.986 40.000 0.00 0.00 36.25 3.67
199 200 4.534500 TCACTATCAGGGTGTATTTGTGGT 59.466 41.667 0.00 0.00 36.25 4.16
200 201 5.097742 TCACTATCAGGGTGTATTTGTGG 57.902 43.478 0.00 0.00 36.25 4.17
201 202 7.447374 TTTTCACTATCAGGGTGTATTTGTG 57.553 36.000 0.00 0.00 36.25 3.33
202 203 8.650143 AATTTTCACTATCAGGGTGTATTTGT 57.350 30.769 0.00 0.00 36.25 2.83
219 220 9.659830 CGGCCTAAACAGTAATATAATTTTCAC 57.340 33.333 0.00 0.00 0.00 3.18
220 221 8.347035 GCGGCCTAAACAGTAATATAATTTTCA 58.653 33.333 0.00 0.00 0.00 2.69
221 222 7.532884 CGCGGCCTAAACAGTAATATAATTTTC 59.467 37.037 0.00 0.00 0.00 2.29
222 223 7.357303 CGCGGCCTAAACAGTAATATAATTTT 58.643 34.615 0.00 0.00 0.00 1.82
223 224 6.567132 GCGCGGCCTAAACAGTAATATAATTT 60.567 38.462 8.83 0.00 0.00 1.82
224 225 5.106830 GCGCGGCCTAAACAGTAATATAATT 60.107 40.000 8.83 0.00 0.00 1.40
225 226 4.390909 GCGCGGCCTAAACAGTAATATAAT 59.609 41.667 8.83 0.00 0.00 1.28
226 227 3.742369 GCGCGGCCTAAACAGTAATATAA 59.258 43.478 8.83 0.00 0.00 0.98
227 228 3.319755 GCGCGGCCTAAACAGTAATATA 58.680 45.455 8.83 0.00 0.00 0.86
228 229 2.140717 GCGCGGCCTAAACAGTAATAT 58.859 47.619 8.83 0.00 0.00 1.28
229 230 1.574134 GCGCGGCCTAAACAGTAATA 58.426 50.000 8.83 0.00 0.00 0.98
230 231 1.093496 GGCGCGGCCTAAACAGTAAT 61.093 55.000 23.89 0.00 46.69 1.89
231 232 1.742510 GGCGCGGCCTAAACAGTAA 60.743 57.895 23.89 0.00 46.69 2.24
232 233 2.125431 GGCGCGGCCTAAACAGTA 60.125 61.111 23.89 0.00 46.69 2.74
242 243 2.989055 TTAAGCATCCTAGGCGCGGC 62.989 60.000 27.06 27.06 36.08 6.53
243 244 0.946221 CTTAAGCATCCTAGGCGCGG 60.946 60.000 8.83 0.00 36.08 6.46
244 245 1.560860 GCTTAAGCATCCTAGGCGCG 61.561 60.000 22.59 0.00 41.59 6.86
245 246 1.560860 CGCTTAAGCATCCTAGGCGC 61.561 60.000 26.29 13.57 42.21 6.53
246 247 1.560860 GCGCTTAAGCATCCTAGGCG 61.561 60.000 26.29 11.46 42.21 5.52
247 248 1.231296 GGCGCTTAAGCATCCTAGGC 61.231 60.000 26.29 18.31 42.21 3.93
248 249 0.946221 CGGCGCTTAAGCATCCTAGG 60.946 60.000 26.29 0.82 42.21 3.02
249 250 0.249489 ACGGCGCTTAAGCATCCTAG 60.249 55.000 26.29 15.79 42.21 3.02
250 251 0.249322 GACGGCGCTTAAGCATCCTA 60.249 55.000 26.29 0.00 42.21 2.94
251 252 1.521681 GACGGCGCTTAAGCATCCT 60.522 57.895 26.29 15.09 42.21 3.24
252 253 0.249322 TAGACGGCGCTTAAGCATCC 60.249 55.000 26.29 22.89 42.21 3.51
253 254 1.132588 CTAGACGGCGCTTAAGCATC 58.867 55.000 26.29 16.62 42.21 3.91
254 255 0.249489 CCTAGACGGCGCTTAAGCAT 60.249 55.000 26.29 9.08 42.21 3.79
255 256 1.141019 CCTAGACGGCGCTTAAGCA 59.859 57.895 26.29 4.80 42.21 3.91
256 257 4.014065 CCTAGACGGCGCTTAAGC 57.986 61.111 17.83 17.83 37.78 3.09
265 266 0.384309 TTCGCATAGTGCCTAGACGG 59.616 55.000 0.00 0.00 41.12 4.79
266 267 1.600663 CCTTCGCATAGTGCCTAGACG 60.601 57.143 0.00 0.00 41.12 4.18
267 268 1.870167 GCCTTCGCATAGTGCCTAGAC 60.870 57.143 0.00 0.00 41.12 2.59
268 269 0.389391 GCCTTCGCATAGTGCCTAGA 59.611 55.000 0.00 0.00 41.12 2.43
269 270 0.601311 GGCCTTCGCATAGTGCCTAG 60.601 60.000 0.00 0.00 41.12 3.02
270 271 1.334384 TGGCCTTCGCATAGTGCCTA 61.334 55.000 3.32 0.00 41.12 3.93
271 272 2.190578 GGCCTTCGCATAGTGCCT 59.809 61.111 0.00 0.00 41.12 4.75
272 273 1.748879 TTGGCCTTCGCATAGTGCC 60.749 57.895 3.32 0.00 41.12 5.01
273 274 1.429423 GTTGGCCTTCGCATAGTGC 59.571 57.895 3.32 0.00 40.69 4.40
274 275 1.705337 CGGTTGGCCTTCGCATAGTG 61.705 60.000 3.32 0.00 36.38 2.74
275 276 1.449601 CGGTTGGCCTTCGCATAGT 60.450 57.895 3.32 0.00 36.38 2.12
276 277 3.409856 CGGTTGGCCTTCGCATAG 58.590 61.111 3.32 0.00 36.38 2.23
286 287 3.497031 GTAAGCGAGGCGGTTGGC 61.497 66.667 13.64 4.02 46.80 4.52
287 288 3.186047 CGTAAGCGAGGCGGTTGG 61.186 66.667 13.64 3.06 46.80 3.77
304 305 2.092323 AGGTTGGAAAAAGCGATAGGC 58.908 47.619 0.00 0.00 44.05 3.93
305 306 4.201920 GCTAAGGTTGGAAAAAGCGATAGG 60.202 45.833 0.00 0.00 0.00 2.57
306 307 4.394920 TGCTAAGGTTGGAAAAAGCGATAG 59.605 41.667 0.00 0.00 32.67 2.08
307 308 4.155280 GTGCTAAGGTTGGAAAAAGCGATA 59.845 41.667 0.00 0.00 32.67 2.92
308 309 3.057526 GTGCTAAGGTTGGAAAAAGCGAT 60.058 43.478 0.00 0.00 32.67 4.58
309 310 2.292292 GTGCTAAGGTTGGAAAAAGCGA 59.708 45.455 0.00 0.00 32.67 4.93
310 311 2.607038 GGTGCTAAGGTTGGAAAAAGCG 60.607 50.000 0.00 0.00 32.67 4.68
311 312 2.607038 CGGTGCTAAGGTTGGAAAAAGC 60.607 50.000 0.00 0.00 0.00 3.51
312 313 2.607038 GCGGTGCTAAGGTTGGAAAAAG 60.607 50.000 0.00 0.00 0.00 2.27
313 314 1.338655 GCGGTGCTAAGGTTGGAAAAA 59.661 47.619 0.00 0.00 0.00 1.94
314 315 0.955905 GCGGTGCTAAGGTTGGAAAA 59.044 50.000 0.00 0.00 0.00 2.29
315 316 0.109723 AGCGGTGCTAAGGTTGGAAA 59.890 50.000 0.00 0.00 36.99 3.13
316 317 0.109723 AAGCGGTGCTAAGGTTGGAA 59.890 50.000 0.00 0.00 38.25 3.53
317 318 0.605319 CAAGCGGTGCTAAGGTTGGA 60.605 55.000 8.98 0.00 38.25 3.53
318 319 1.875963 CAAGCGGTGCTAAGGTTGG 59.124 57.895 8.98 0.00 38.25 3.77
346 347 8.038944 AGTCGCTAAATTCTTTAACTCATACCA 58.961 33.333 0.00 0.00 0.00 3.25
347 348 8.421673 AGTCGCTAAATTCTTTAACTCATACC 57.578 34.615 0.00 0.00 0.00 2.73
365 367 7.255381 CCAACTAATAGTAAAGCCTAGTCGCTA 60.255 40.741 0.00 0.00 38.44 4.26
373 375 6.884836 CCTTTCACCAACTAATAGTAAAGCCT 59.115 38.462 6.96 0.00 0.00 4.58
374 376 6.882678 TCCTTTCACCAACTAATAGTAAAGCC 59.117 38.462 6.96 0.00 0.00 4.35
428 430 4.101448 CGAGGCTTCCCCTGGGTG 62.101 72.222 12.71 3.30 46.60 4.61
434 436 3.081409 TACTGGCGAGGCTTCCCC 61.081 66.667 0.00 0.00 0.00 4.81
447 449 7.812309 TTTGTTTCAGTCGATCTATGTACTG 57.188 36.000 0.00 0.00 40.54 2.74
472 474 3.791640 TCAGTCGGCTGACCACAT 58.208 55.556 17.42 0.09 45.94 3.21
510 512 1.001815 GAGAGCGGCTAGATGACAGTC 60.002 57.143 0.60 0.00 0.00 3.51
529 531 3.803340 AGGGAGGAGGTATGTTTCTTGA 58.197 45.455 0.00 0.00 0.00 3.02
550 552 3.249189 AAGGGGACGCAGAGGCAA 61.249 61.111 0.00 0.00 41.24 4.52
557 559 3.327404 GAAGGGGAAGGGGACGCA 61.327 66.667 0.00 0.00 0.00 5.24
579 588 1.940883 GACCATCGACGCTACCACCA 61.941 60.000 0.00 0.00 0.00 4.17
602 611 3.238108 ACAGAGGCTCAATACGTGAAG 57.762 47.619 18.26 0.00 35.22 3.02
604 613 2.930887 GCAACAGAGGCTCAATACGTGA 60.931 50.000 18.26 0.00 34.17 4.35
649 658 0.909610 TTGGTAGAGGAGGGCAGTGG 60.910 60.000 0.00 0.00 0.00 4.00
655 664 1.208293 GAGCAACTTGGTAGAGGAGGG 59.792 57.143 0.00 0.00 0.00 4.30
698 707 1.004277 GTGTTGGGCAATAGGTGGAGA 59.996 52.381 0.00 0.00 0.00 3.71
709 718 2.902423 AAGAGCGTTGGTGTTGGGCA 62.902 55.000 0.00 0.00 0.00 5.36
721 730 0.247736 GTGGATCCAGTGAAGAGCGT 59.752 55.000 16.81 0.00 0.00 5.07
734 743 1.768077 CAGAGGGAGGGGGTGGATC 60.768 68.421 0.00 0.00 0.00 3.36
790 799 1.152419 TTGTCTCCGGTGACCTGGA 60.152 57.895 28.70 11.53 36.21 3.86
792 801 0.600255 GTGTTGTCTCCGGTGACCTG 60.600 60.000 28.70 0.00 36.21 4.00
793 802 1.746517 GTGTTGTCTCCGGTGACCT 59.253 57.895 28.70 0.00 36.21 3.85
798 807 0.762418 TCATTGGTGTTGTCTCCGGT 59.238 50.000 0.00 0.00 0.00 5.28
989 1037 1.078214 CGCTGCATCCTTTCAGGGA 60.078 57.895 0.00 0.00 43.35 4.20
1060 1108 1.355005 GCGCCACTCTCTTTCTTCTC 58.645 55.000 0.00 0.00 0.00 2.87
1064 1112 2.262915 CCGCGCCACTCTCTTTCT 59.737 61.111 0.00 0.00 0.00 2.52
1099 1147 4.282703 ACATAAGTAACCTCACGTCCACTT 59.717 41.667 0.00 0.00 35.17 3.16
1105 1157 6.930667 AAAAACACATAAGTAACCTCACGT 57.069 33.333 0.00 0.00 0.00 4.49
1140 1196 2.554032 ACACACATAAGCAACCTCAAGC 59.446 45.455 0.00 0.00 0.00 4.01
1141 1197 4.516698 AGAACACACATAAGCAACCTCAAG 59.483 41.667 0.00 0.00 0.00 3.02
1142 1198 4.275689 CAGAACACACATAAGCAACCTCAA 59.724 41.667 0.00 0.00 0.00 3.02
1143 1199 3.814842 CAGAACACACATAAGCAACCTCA 59.185 43.478 0.00 0.00 0.00 3.86
1145 1201 2.554032 GCAGAACACACATAAGCAACCT 59.446 45.455 0.00 0.00 0.00 3.50
1148 1204 1.535028 CCGCAGAACACACATAAGCAA 59.465 47.619 0.00 0.00 0.00 3.91
1149 1205 1.155889 CCGCAGAACACACATAAGCA 58.844 50.000 0.00 0.00 0.00 3.91
1150 1206 1.128692 GTCCGCAGAACACACATAAGC 59.871 52.381 0.00 0.00 0.00 3.09
1151 1207 1.390123 CGTCCGCAGAACACACATAAG 59.610 52.381 0.00 0.00 0.00 1.73
1152 1208 1.424403 CGTCCGCAGAACACACATAA 58.576 50.000 0.00 0.00 0.00 1.90
1213 1269 0.974010 TTCAGAATACCGACCGCCCT 60.974 55.000 0.00 0.00 0.00 5.19
1253 1309 0.314302 ACTTCGAAGTCGGTCCTGTG 59.686 55.000 24.93 0.00 40.29 3.66
1275 1332 7.085052 AGGTTTTATTGCCGAAATAGAGTTC 57.915 36.000 0.00 0.00 32.30 3.01
1276 1333 7.312899 CAAGGTTTTATTGCCGAAATAGAGTT 58.687 34.615 0.00 0.00 32.30 3.01
1277 1334 6.127730 CCAAGGTTTTATTGCCGAAATAGAGT 60.128 38.462 0.00 0.00 32.30 3.24
1282 1339 4.282195 TGACCAAGGTTTTATTGCCGAAAT 59.718 37.500 0.00 0.00 0.00 2.17
1366 1426 4.525949 GGACGCTAGCCGGGGTTC 62.526 72.222 9.66 0.00 42.52 3.62
1894 1960 3.118629 AGTGAGTACATGGCGATGTCAAT 60.119 43.478 18.26 6.87 42.14 2.57
2091 2157 0.674895 AGGAACTTGTGGCGAGCATC 60.675 55.000 0.00 0.00 27.25 3.91
2106 3354 0.252057 TGACGATCCCACTCCAGGAA 60.252 55.000 0.00 0.00 36.85 3.36
2149 3397 0.968405 TTCAGGGTTGCAATCTTGGC 59.032 50.000 20.40 0.00 0.00 4.52
2154 3402 0.247460 GGCCTTTCAGGGTTGCAATC 59.753 55.000 0.59 0.00 35.37 2.67
2271 3519 5.704515 ACCATCAAAAGACATCAGAAGTGAG 59.295 40.000 0.00 0.00 35.66 3.51
2548 3796 3.910627 ACTCCTAGGACAGGTTTCACATT 59.089 43.478 7.62 0.00 45.71 2.71
2904 7374 0.320683 CCATCTCATTATCCCGCGCA 60.321 55.000 8.75 0.00 0.00 6.09
2995 7467 7.596494 TCATCAAAATGTAAAGAGCTTGGAAG 58.404 34.615 0.00 0.00 34.32 3.46
3042 7514 5.005628 AGTATTTCAAAGGCCAAGGGTTA 57.994 39.130 5.01 0.00 0.00 2.85
3043 7515 3.856900 AGTATTTCAAAGGCCAAGGGTT 58.143 40.909 5.01 0.00 0.00 4.11
3282 7756 6.016108 GGTGGTTGCTAAAACCTAATGTTACA 60.016 38.462 8.60 0.00 40.88 2.41
3307 7781 3.635591 AGGGTTTCAATTGATGCCCTAG 58.364 45.455 32.38 0.00 42.77 3.02
3397 7871 2.688477 ACCCCATGTTTCCAAATGTGT 58.312 42.857 0.00 0.00 0.00 3.72
3551 8025 4.557496 GCAAATCAAAGACACTTCCTGGTC 60.557 45.833 0.00 0.00 0.00 4.02
3658 8132 2.290323 ACCACCAGCTGAAGTAATGTCC 60.290 50.000 17.39 0.00 0.00 4.02
3718 8192 3.669536 TGAACAATTAGTGGCATCGTCA 58.330 40.909 0.00 0.00 0.00 4.35
3826 8300 2.043664 TGGGATGGGCCATTTGTTTCTA 59.956 45.455 22.20 0.00 38.95 2.10
3828 8302 1.066215 GTGGGATGGGCCATTTGTTTC 60.066 52.381 22.20 7.30 38.95 2.78
3856 8330 4.037803 TCAATAAGTTGTGCACATTGTGCT 59.962 37.500 34.44 20.07 45.11 4.40
3857 8331 4.297510 TCAATAAGTTGTGCACATTGTGC 58.702 39.130 30.28 30.28 45.11 4.57
3908 8384 0.672401 TACGTGCTGCCAAGTTAGCC 60.672 55.000 0.00 0.00 39.15 3.93


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

AutoCloner maintained by Alex Coulton.