Multiple sequence alignment - TraesCS3D01G305500

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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 TraesCS3D01G305500 chr3D 100.000 3635 0 0 1 3635 419558903 419562537 0.000000e+00 6713
1 TraesCS3D01G305500 chr3D 99.219 256 2 0 1 256 419542668 419542923 2.560000e-126 462
2 TraesCS3D01G305500 chr3D 83.096 491 51 14 2024 2513 419560341 419560800 5.610000e-113 418
3 TraesCS3D01G305500 chr3D 83.130 492 49 13 1439 1898 419560926 419561415 5.610000e-113 418
4 TraesCS3D01G305500 chr3A 92.258 2299 104 30 1385 3624 531668320 531666037 0.000000e+00 3192
5 TraesCS3D01G305500 chr3A 84.114 491 46 14 2024 2513 531668266 531667807 2.580000e-121 446
6 TraesCS3D01G305500 chr3A 84.100 478 46 14 1451 1898 531667660 531667183 5.570000e-118 435
7 TraesCS3D01G305500 chr3A 91.429 245 15 4 853 1093 531669217 531668975 7.520000e-87 331
8 TraesCS3D01G305500 chr3B 95.481 1704 66 8 1938 3635 546183224 546181526 0.000000e+00 2710
9 TraesCS3D01G305500 chr3B 84.808 1514 101 52 1747 3193 545813669 545812218 0.000000e+00 1402
10 TraesCS3D01G305500 chr3B 97.053 509 15 0 1398 1906 546183731 546183223 0.000000e+00 857
11 TraesCS3D01G305500 chr3B 89.964 548 32 9 853 1377 545814585 545814038 0.000000e+00 686
12 TraesCS3D01G305500 chr3B 89.033 538 34 7 850 1376 546184309 546183786 0.000000e+00 643
13 TraesCS3D01G305500 chr3B 86.090 532 50 12 1385 1898 545813424 545812899 5.300000e-153 551
14 TraesCS3D01G305500 chr3B 94.643 336 18 0 1385 1720 545813997 545813662 4.160000e-144 521
15 TraesCS3D01G305500 chr3B 87.597 387 33 8 1527 1898 546183035 546182649 5.570000e-118 435
16 TraesCS3D01G305500 chr3B 83.061 490 51 19 2025 2513 546183689 546183231 2.020000e-112 416
17 TraesCS3D01G305500 chr3B 88.166 338 25 7 3312 3635 545811974 545811638 4.400000e-104 388
18 TraesCS3D01G305500 chr3B 78.426 394 62 11 1951 2331 545814037 545813654 6.070000e-58 235
19 TraesCS3D01G305500 chr3B 89.677 155 11 5 2362 2513 545813669 545813517 3.700000e-45 193
20 TraesCS3D01G305500 chr7D 90.925 573 48 4 265 834 242750883 242750312 0.000000e+00 767
21 TraesCS3D01G305500 chr7D 98.496 266 4 0 1 266 304634430 304634695 1.530000e-128 470
22 TraesCS3D01G305500 chr7D 98.496 266 3 1 1 266 321299895 321300159 5.500000e-128 468
23 TraesCS3D01G305500 chr7D 98.833 257 3 0 1 257 267285410 267285666 3.310000e-125 459
24 TraesCS3D01G305500 chr6B 83.042 572 84 10 270 837 664193244 664193806 1.160000e-139 507
25 TraesCS3D01G305500 chr6D 98.502 267 3 1 1 266 117275954 117276220 1.530000e-128 470
26 TraesCS3D01G305500 chr5D 98.473 262 4 0 1 262 237479124 237478863 2.560000e-126 462
27 TraesCS3D01G305500 chr5D 97.753 267 5 1 1 266 237488701 237488435 3.310000e-125 459
28 TraesCS3D01G305500 chr2D 97.368 266 7 0 1 266 254119139 254119404 1.540000e-123 453
29 TraesCS3D01G305500 chr4D 97.368 266 6 1 1 266 341488371 341488635 5.530000e-123 451


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 TraesCS3D01G305500 chr3D 419558903 419562537 3634 False 2516.333333 6713 88.742000 1 3635 3 chr3D.!!$F2 3634
1 TraesCS3D01G305500 chr3A 531666037 531669217 3180 True 1101.000000 3192 87.975250 853 3624 4 chr3A.!!$R1 2771
2 TraesCS3D01G305500 chr3B 546181526 546184309 2783 True 1012.200000 2710 90.445000 850 3635 5 chr3B.!!$R2 2785
3 TraesCS3D01G305500 chr3B 545811638 545814585 2947 True 568.000000 1402 87.396286 853 3635 7 chr3B.!!$R1 2782
4 TraesCS3D01G305500 chr7D 242750312 242750883 571 True 767.000000 767 90.925000 265 834 1 chr7D.!!$R1 569
5 TraesCS3D01G305500 chr6B 664193244 664193806 562 False 507.000000 507 83.042000 270 837 1 chr6B.!!$F1 567

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
126 127 0.035056 ATGCCTTACTTTCCGCTGCT 60.035 50.0 0.00 0.00 0.00 4.24 F
156 157 0.099259 TTGTATGCTCGCATGCTTGC 59.901 50.0 17.13 18.95 45.78 4.01 F
580 582 0.106967 GTCCTCCTTCAGGCCCAATC 60.107 60.0 0.00 0.00 43.08 2.67 F
1290 1620 0.259065 GGGATGAGGAAAAGGGGGAC 59.741 60.0 0.00 0.00 0.00 4.46 F
2244 2646 0.744874 CCAAAGGCATCATCCAGCTG 59.255 55.0 6.78 6.78 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1783 0.116541 TCCCTTCTTTCCCTCTCCGT 59.883 55.0 0.0 0.0 0.00 4.69 R
1628 2009 0.475906 GGGTAGCTGGATGATGCCTT 59.524 55.0 0.0 0.0 37.02 4.35 R
2380 2782 0.683973 CACTCCTTCAGCACCTCACT 59.316 55.0 0.0 0.0 0.00 3.41 R
2580 2982 1.334384 GCAGTTCCTCCTCCTCCTCC 61.334 65.0 0.0 0.0 0.00 4.30 R
3051 3494 2.325583 ACAAGAACAACCGCAGAGAA 57.674 45.0 0.0 0.0 0.00 2.87 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
19 20 2.882927 TGGATGTACGATAGCACCAC 57.117 50.000 0.00 0.00 42.67 4.16
20 21 1.411246 TGGATGTACGATAGCACCACC 59.589 52.381 0.00 0.00 42.67 4.61
21 22 1.687123 GGATGTACGATAGCACCACCT 59.313 52.381 0.00 0.00 42.67 4.00
22 23 2.889045 GGATGTACGATAGCACCACCTA 59.111 50.000 0.00 0.00 42.67 3.08
23 24 3.510360 GGATGTACGATAGCACCACCTAT 59.490 47.826 0.00 0.00 42.67 2.57
24 25 4.380655 GGATGTACGATAGCACCACCTATC 60.381 50.000 0.00 0.00 40.05 2.08
29 30 3.027974 GATAGCACCACCTATCGGAAC 57.972 52.381 0.00 0.00 35.71 3.62
30 31 1.117150 TAGCACCACCTATCGGAACC 58.883 55.000 0.00 0.00 0.00 3.62
31 32 0.907704 AGCACCACCTATCGGAACCA 60.908 55.000 0.00 0.00 0.00 3.67
32 33 0.743345 GCACCACCTATCGGAACCAC 60.743 60.000 0.00 0.00 0.00 4.16
33 34 0.459585 CACCACCTATCGGAACCACG 60.460 60.000 0.00 0.00 0.00 4.94
34 35 1.143183 CCACCTATCGGAACCACGG 59.857 63.158 0.00 0.00 0.00 4.94
35 36 1.324740 CCACCTATCGGAACCACGGA 61.325 60.000 0.00 0.00 0.00 4.69
36 37 0.750850 CACCTATCGGAACCACGGAT 59.249 55.000 0.00 0.00 40.67 4.18
37 38 1.958579 CACCTATCGGAACCACGGATA 59.041 52.381 0.00 0.00 38.95 2.59
38 39 2.363038 CACCTATCGGAACCACGGATAA 59.637 50.000 0.00 0.00 39.25 1.75
39 40 3.033184 ACCTATCGGAACCACGGATAAA 58.967 45.455 0.00 0.00 39.25 1.40
40 41 3.451902 ACCTATCGGAACCACGGATAAAA 59.548 43.478 0.00 0.00 39.25 1.52
41 42 4.080975 ACCTATCGGAACCACGGATAAAAA 60.081 41.667 0.00 0.00 39.25 1.94
61 62 5.376854 AAAATCTCCGTGTCTCCAAATTG 57.623 39.130 0.00 0.00 0.00 2.32
62 63 1.808411 TCTCCGTGTCTCCAAATTGC 58.192 50.000 0.00 0.00 0.00 3.56
63 64 0.443869 CTCCGTGTCTCCAAATTGCG 59.556 55.000 0.00 0.00 0.00 4.85
64 65 0.250124 TCCGTGTCTCCAAATTGCGT 60.250 50.000 0.00 0.00 0.00 5.24
65 66 0.591170 CCGTGTCTCCAAATTGCGTT 59.409 50.000 0.00 0.00 0.00 4.84
66 67 1.001815 CCGTGTCTCCAAATTGCGTTT 60.002 47.619 0.00 0.00 0.00 3.60
67 68 2.043411 CGTGTCTCCAAATTGCGTTTG 58.957 47.619 7.26 7.26 45.44 2.93
68 69 1.786579 GTGTCTCCAAATTGCGTTTGC 59.213 47.619 8.44 0.00 44.69 3.68
79 80 3.092081 GCGTTTGCACACTCCAATC 57.908 52.632 0.87 0.00 42.15 2.67
80 81 0.387239 GCGTTTGCACACTCCAATCC 60.387 55.000 0.87 0.00 42.15 3.01
81 82 0.240945 CGTTTGCACACTCCAATCCC 59.759 55.000 0.87 0.00 0.00 3.85
82 83 1.620822 GTTTGCACACTCCAATCCCT 58.379 50.000 0.00 0.00 0.00 4.20
83 84 1.963515 GTTTGCACACTCCAATCCCTT 59.036 47.619 0.00 0.00 0.00 3.95
84 85 1.909700 TTGCACACTCCAATCCCTTC 58.090 50.000 0.00 0.00 0.00 3.46
85 86 1.067295 TGCACACTCCAATCCCTTCT 58.933 50.000 0.00 0.00 0.00 2.85
86 87 1.003580 TGCACACTCCAATCCCTTCTC 59.996 52.381 0.00 0.00 0.00 2.87
87 88 1.280421 GCACACTCCAATCCCTTCTCT 59.720 52.381 0.00 0.00 0.00 3.10
88 89 2.290577 GCACACTCCAATCCCTTCTCTT 60.291 50.000 0.00 0.00 0.00 2.85
89 90 3.812167 GCACACTCCAATCCCTTCTCTTT 60.812 47.826 0.00 0.00 0.00 2.52
90 91 4.565652 GCACACTCCAATCCCTTCTCTTTA 60.566 45.833 0.00 0.00 0.00 1.85
91 92 4.938226 CACACTCCAATCCCTTCTCTTTAC 59.062 45.833 0.00 0.00 0.00 2.01
92 93 4.597507 ACACTCCAATCCCTTCTCTTTACA 59.402 41.667 0.00 0.00 0.00 2.41
93 94 5.251700 ACACTCCAATCCCTTCTCTTTACAT 59.748 40.000 0.00 0.00 0.00 2.29
94 95 6.183347 CACTCCAATCCCTTCTCTTTACATT 58.817 40.000 0.00 0.00 0.00 2.71
95 96 6.317391 CACTCCAATCCCTTCTCTTTACATTC 59.683 42.308 0.00 0.00 0.00 2.67
96 97 6.216456 ACTCCAATCCCTTCTCTTTACATTCT 59.784 38.462 0.00 0.00 0.00 2.40
97 98 7.032598 TCCAATCCCTTCTCTTTACATTCTT 57.967 36.000 0.00 0.00 0.00 2.52
98 99 6.886459 TCCAATCCCTTCTCTTTACATTCTTG 59.114 38.462 0.00 0.00 0.00 3.02
99 100 6.405176 CCAATCCCTTCTCTTTACATTCTTGC 60.405 42.308 0.00 0.00 0.00 4.01
100 101 5.241403 TCCCTTCTCTTTACATTCTTGCA 57.759 39.130 0.00 0.00 0.00 4.08
101 102 5.630121 TCCCTTCTCTTTACATTCTTGCAA 58.370 37.500 0.00 0.00 0.00 4.08
102 103 5.473504 TCCCTTCTCTTTACATTCTTGCAAC 59.526 40.000 0.00 0.00 0.00 4.17
103 104 5.241506 CCCTTCTCTTTACATTCTTGCAACA 59.758 40.000 0.00 0.00 0.00 3.33
104 105 6.071728 CCCTTCTCTTTACATTCTTGCAACAT 60.072 38.462 0.00 0.00 0.00 2.71
105 106 6.805271 CCTTCTCTTTACATTCTTGCAACATG 59.195 38.462 10.96 10.96 0.00 3.21
106 107 5.702865 TCTCTTTACATTCTTGCAACATGC 58.297 37.500 12.07 0.00 45.29 4.06
117 118 2.660189 GCAACATGCATGCCTTACTT 57.340 45.000 26.53 9.32 44.26 2.24
118 119 2.963432 GCAACATGCATGCCTTACTTT 58.037 42.857 26.53 8.57 44.26 2.66
119 120 2.925563 GCAACATGCATGCCTTACTTTC 59.074 45.455 26.53 3.07 44.26 2.62
120 121 3.514645 CAACATGCATGCCTTACTTTCC 58.485 45.455 26.53 0.00 0.00 3.13
121 122 1.745087 ACATGCATGCCTTACTTTCCG 59.255 47.619 26.53 0.00 0.00 4.30
122 123 0.740737 ATGCATGCCTTACTTTCCGC 59.259 50.000 16.68 0.00 0.00 5.54
123 124 0.322456 TGCATGCCTTACTTTCCGCT 60.322 50.000 16.68 0.00 0.00 5.52
124 125 0.099436 GCATGCCTTACTTTCCGCTG 59.901 55.000 6.36 0.00 0.00 5.18
125 126 0.099436 CATGCCTTACTTTCCGCTGC 59.901 55.000 0.00 0.00 0.00 5.25
126 127 0.035056 ATGCCTTACTTTCCGCTGCT 60.035 50.000 0.00 0.00 0.00 4.24
127 128 0.673644 TGCCTTACTTTCCGCTGCTC 60.674 55.000 0.00 0.00 0.00 4.26
128 129 0.673644 GCCTTACTTTCCGCTGCTCA 60.674 55.000 0.00 0.00 0.00 4.26
129 130 2.014068 GCCTTACTTTCCGCTGCTCAT 61.014 52.381 0.00 0.00 0.00 2.90
130 131 2.741878 GCCTTACTTTCCGCTGCTCATA 60.742 50.000 0.00 0.00 0.00 2.15
131 132 3.733337 CCTTACTTTCCGCTGCTCATAT 58.267 45.455 0.00 0.00 0.00 1.78
132 133 4.799586 GCCTTACTTTCCGCTGCTCATATA 60.800 45.833 0.00 0.00 0.00 0.86
133 134 4.686554 CCTTACTTTCCGCTGCTCATATAC 59.313 45.833 0.00 0.00 0.00 1.47
134 135 5.509840 CCTTACTTTCCGCTGCTCATATACT 60.510 44.000 0.00 0.00 0.00 2.12
135 136 3.983741 ACTTTCCGCTGCTCATATACTC 58.016 45.455 0.00 0.00 0.00 2.59
136 137 3.639094 ACTTTCCGCTGCTCATATACTCT 59.361 43.478 0.00 0.00 0.00 3.24
137 138 4.100189 ACTTTCCGCTGCTCATATACTCTT 59.900 41.667 0.00 0.00 0.00 2.85
138 139 4.672587 TTCCGCTGCTCATATACTCTTT 57.327 40.909 0.00 0.00 0.00 2.52
139 140 3.982475 TCCGCTGCTCATATACTCTTTG 58.018 45.455 0.00 0.00 0.00 2.77
140 141 3.384789 TCCGCTGCTCATATACTCTTTGT 59.615 43.478 0.00 0.00 0.00 2.83
141 142 4.583073 TCCGCTGCTCATATACTCTTTGTA 59.417 41.667 0.00 0.00 35.37 2.41
142 143 5.243954 TCCGCTGCTCATATACTCTTTGTAT 59.756 40.000 0.00 0.00 43.62 2.29
143 144 5.347093 CCGCTGCTCATATACTCTTTGTATG 59.653 44.000 0.00 0.00 41.55 2.39
144 145 5.164012 CGCTGCTCATATACTCTTTGTATGC 60.164 44.000 0.00 0.00 41.55 3.14
145 146 5.931146 GCTGCTCATATACTCTTTGTATGCT 59.069 40.000 0.00 0.00 41.55 3.79
146 147 6.090628 GCTGCTCATATACTCTTTGTATGCTC 59.909 42.308 0.00 0.00 41.55 4.26
147 148 6.152379 TGCTCATATACTCTTTGTATGCTCG 58.848 40.000 0.00 0.00 41.55 5.03
148 149 5.061560 GCTCATATACTCTTTGTATGCTCGC 59.938 44.000 0.00 0.00 41.55 5.03
149 150 6.084326 TCATATACTCTTTGTATGCTCGCA 57.916 37.500 0.00 0.00 41.55 5.10
150 151 6.691508 TCATATACTCTTTGTATGCTCGCAT 58.308 36.000 9.57 9.57 41.55 4.73
151 152 6.587608 TCATATACTCTTTGTATGCTCGCATG 59.412 38.462 14.27 0.00 41.55 4.06
152 153 1.667724 ACTCTTTGTATGCTCGCATGC 59.332 47.619 14.27 7.91 39.07 4.06
153 154 1.938577 CTCTTTGTATGCTCGCATGCT 59.061 47.619 17.13 0.00 39.30 3.79
154 155 2.353889 CTCTTTGTATGCTCGCATGCTT 59.646 45.455 17.13 0.00 39.30 3.91
155 156 2.096335 TCTTTGTATGCTCGCATGCTTG 59.904 45.455 17.13 9.23 39.30 4.01
156 157 0.099259 TTGTATGCTCGCATGCTTGC 59.901 50.000 17.13 18.95 45.78 4.01
170 171 5.526115 GCATGCTTGCTTGATATGTATTGT 58.474 37.500 16.80 0.00 45.77 2.71
171 172 5.401376 GCATGCTTGCTTGATATGTATTGTG 59.599 40.000 16.80 0.00 45.77 3.33
172 173 6.731164 CATGCTTGCTTGATATGTATTGTGA 58.269 36.000 2.83 0.00 0.00 3.58
173 174 6.756299 TGCTTGCTTGATATGTATTGTGAA 57.244 33.333 0.00 0.00 0.00 3.18
174 175 7.337480 TGCTTGCTTGATATGTATTGTGAAT 57.663 32.000 0.00 0.00 0.00 2.57
175 176 7.197703 TGCTTGCTTGATATGTATTGTGAATG 58.802 34.615 0.00 0.00 0.00 2.67
176 177 7.148035 TGCTTGCTTGATATGTATTGTGAATGT 60.148 33.333 0.00 0.00 0.00 2.71
177 178 7.703621 GCTTGCTTGATATGTATTGTGAATGTT 59.296 33.333 0.00 0.00 0.00 2.71
178 179 9.577110 CTTGCTTGATATGTATTGTGAATGTTT 57.423 29.630 0.00 0.00 0.00 2.83
188 189 8.346476 TGTATTGTGAATGTTTAAACTTGTGC 57.654 30.769 18.72 7.62 0.00 4.57
189 190 8.194104 TGTATTGTGAATGTTTAAACTTGTGCT 58.806 29.630 18.72 0.00 0.00 4.40
190 191 9.672086 GTATTGTGAATGTTTAAACTTGTGCTA 57.328 29.630 18.72 5.05 0.00 3.49
192 193 9.762933 ATTGTGAATGTTTAAACTTGTGCTAAT 57.237 25.926 18.72 8.89 0.00 1.73
194 195 9.672086 TGTGAATGTTTAAACTTGTGCTAATAC 57.328 29.630 18.72 5.77 0.00 1.89
195 196 9.893305 GTGAATGTTTAAACTTGTGCTAATACT 57.107 29.630 18.72 0.00 0.00 2.12
197 198 9.556030 GAATGTTTAAACTTGTGCTAATACTCC 57.444 33.333 18.72 0.00 0.00 3.85
198 199 8.630054 ATGTTTAAACTTGTGCTAATACTCCA 57.370 30.769 18.72 0.00 0.00 3.86
199 200 7.867752 TGTTTAAACTTGTGCTAATACTCCAC 58.132 34.615 18.72 0.00 0.00 4.02
200 201 7.717875 TGTTTAAACTTGTGCTAATACTCCACT 59.282 33.333 18.72 0.00 0.00 4.00
201 202 8.565416 GTTTAAACTTGTGCTAATACTCCACTT 58.435 33.333 11.18 0.00 0.00 3.16
202 203 6.803154 AAACTTGTGCTAATACTCCACTTC 57.197 37.500 0.00 0.00 0.00 3.01
203 204 5.483685 ACTTGTGCTAATACTCCACTTCA 57.516 39.130 0.00 0.00 0.00 3.02
204 205 5.865085 ACTTGTGCTAATACTCCACTTCAA 58.135 37.500 0.00 0.00 0.00 2.69
205 206 5.701290 ACTTGTGCTAATACTCCACTTCAAC 59.299 40.000 0.00 0.00 0.00 3.18
206 207 5.483685 TGTGCTAATACTCCACTTCAACT 57.516 39.130 0.00 0.00 0.00 3.16
207 208 5.479306 TGTGCTAATACTCCACTTCAACTC 58.521 41.667 0.00 0.00 0.00 3.01
208 209 5.011635 TGTGCTAATACTCCACTTCAACTCA 59.988 40.000 0.00 0.00 0.00 3.41
209 210 5.932303 GTGCTAATACTCCACTTCAACTCAA 59.068 40.000 0.00 0.00 0.00 3.02
210 211 6.091441 GTGCTAATACTCCACTTCAACTCAAG 59.909 42.308 0.00 0.00 0.00 3.02
211 212 6.014584 TGCTAATACTCCACTTCAACTCAAGA 60.015 38.462 0.00 0.00 0.00 3.02
212 213 6.533367 GCTAATACTCCACTTCAACTCAAGAG 59.467 42.308 0.00 0.00 0.00 2.85
213 214 6.672266 AATACTCCACTTCAACTCAAGAGA 57.328 37.500 3.73 0.00 0.00 3.10
214 215 6.865834 ATACTCCACTTCAACTCAAGAGAT 57.134 37.500 3.73 0.00 0.00 2.75
215 216 5.559148 ACTCCACTTCAACTCAAGAGATT 57.441 39.130 3.73 0.00 0.00 2.40
216 217 6.672266 ACTCCACTTCAACTCAAGAGATTA 57.328 37.500 3.73 0.00 0.00 1.75
217 218 7.067496 ACTCCACTTCAACTCAAGAGATTAA 57.933 36.000 3.73 0.00 0.00 1.40
218 219 7.509546 ACTCCACTTCAACTCAAGAGATTAAA 58.490 34.615 3.73 0.00 0.00 1.52
219 220 7.993183 ACTCCACTTCAACTCAAGAGATTAAAA 59.007 33.333 3.73 0.00 0.00 1.52
220 221 8.746052 TCCACTTCAACTCAAGAGATTAAAAA 57.254 30.769 3.73 0.00 0.00 1.94
221 222 8.621286 TCCACTTCAACTCAAGAGATTAAAAAC 58.379 33.333 3.73 0.00 0.00 2.43
222 223 8.624776 CCACTTCAACTCAAGAGATTAAAAACT 58.375 33.333 3.73 0.00 0.00 2.66
223 224 9.443283 CACTTCAACTCAAGAGATTAAAAACTG 57.557 33.333 3.73 0.00 0.00 3.16
224 225 8.131731 ACTTCAACTCAAGAGATTAAAAACTGC 58.868 33.333 3.73 0.00 0.00 4.40
225 226 7.566760 TCAACTCAAGAGATTAAAAACTGCA 57.433 32.000 3.73 0.00 0.00 4.41
226 227 7.995289 TCAACTCAAGAGATTAAAAACTGCAA 58.005 30.769 3.73 0.00 0.00 4.08
227 228 7.915397 TCAACTCAAGAGATTAAAAACTGCAAC 59.085 33.333 3.73 0.00 0.00 4.17
228 229 7.573968 ACTCAAGAGATTAAAAACTGCAACT 57.426 32.000 3.73 0.00 0.00 3.16
229 230 8.000780 ACTCAAGAGATTAAAAACTGCAACTT 57.999 30.769 3.73 0.00 0.00 2.66
230 231 8.470002 ACTCAAGAGATTAAAAACTGCAACTTT 58.530 29.630 3.73 0.00 0.00 2.66
231 232 9.305925 CTCAAGAGATTAAAAACTGCAACTTTT 57.694 29.630 9.61 9.61 0.00 2.27
232 233 9.301153 TCAAGAGATTAAAAACTGCAACTTTTC 57.699 29.630 8.31 0.00 0.00 2.29
233 234 9.305925 CAAGAGATTAAAAACTGCAACTTTTCT 57.694 29.630 8.31 1.94 0.00 2.52
234 235 9.875691 AAGAGATTAAAAACTGCAACTTTTCTT 57.124 25.926 8.31 4.32 0.00 2.52
235 236 9.305925 AGAGATTAAAAACTGCAACTTTTCTTG 57.694 29.630 8.31 0.00 0.00 3.02
236 237 9.301153 GAGATTAAAAACTGCAACTTTTCTTGA 57.699 29.630 8.31 0.00 0.00 3.02
237 238 9.822185 AGATTAAAAACTGCAACTTTTCTTGAT 57.178 25.926 8.31 1.78 0.00 2.57
242 243 8.862550 AAAACTGCAACTTTTCTTGATTAGAG 57.137 30.769 0.00 0.00 33.51 2.43
243 244 7.573968 AACTGCAACTTTTCTTGATTAGAGT 57.426 32.000 0.00 0.00 33.51 3.24
244 245 7.195839 ACTGCAACTTTTCTTGATTAGAGTC 57.804 36.000 0.00 0.00 33.51 3.36
245 246 6.995091 ACTGCAACTTTTCTTGATTAGAGTCT 59.005 34.615 0.00 0.00 33.51 3.24
246 247 8.150945 ACTGCAACTTTTCTTGATTAGAGTCTA 58.849 33.333 0.00 0.00 33.51 2.59
247 248 9.160496 CTGCAACTTTTCTTGATTAGAGTCTAT 57.840 33.333 0.00 0.00 33.51 1.98
248 249 9.507329 TGCAACTTTTCTTGATTAGAGTCTATT 57.493 29.630 0.00 0.00 33.51 1.73
249 250 9.980780 GCAACTTTTCTTGATTAGAGTCTATTC 57.019 33.333 13.04 13.04 33.51 1.75
252 253 9.660180 ACTTTTCTTGATTAGAGTCTATTCACC 57.340 33.333 19.58 2.38 33.51 4.02
253 254 9.103861 CTTTTCTTGATTAGAGTCTATTCACCC 57.896 37.037 19.58 0.00 33.51 4.61
254 255 6.732896 TCTTGATTAGAGTCTATTCACCCC 57.267 41.667 19.58 0.00 0.00 4.95
255 256 5.602978 TCTTGATTAGAGTCTATTCACCCCC 59.397 44.000 19.58 0.00 0.00 5.40
288 289 2.227865 GCGAAGGTTTTGTGAAGCCATA 59.772 45.455 0.00 0.00 38.50 2.74
289 290 3.119495 GCGAAGGTTTTGTGAAGCCATAT 60.119 43.478 0.00 0.00 38.50 1.78
304 305 5.242795 AGCCATATTACTGGGTAATCACC 57.757 43.478 6.25 0.00 44.97 4.02
330 331 3.636764 TCTTTTCCTTTGAAGGTCCAAGC 59.363 43.478 9.48 0.00 46.54 4.01
358 360 2.304470 TCCATCACTCGTTCCCAATCAA 59.696 45.455 0.00 0.00 0.00 2.57
422 424 1.479709 CGGATCTTCACCTCCTGAGT 58.520 55.000 0.00 0.00 0.00 3.41
533 535 1.047596 GCCTCCTCCATCAGCTCAGA 61.048 60.000 0.00 0.00 0.00 3.27
557 559 1.374125 CGATCACCACGTCCTGCAA 60.374 57.895 0.00 0.00 0.00 4.08
580 582 0.106967 GTCCTCCTTCAGGCCCAATC 60.107 60.000 0.00 0.00 43.08 2.67
614 616 1.605753 TCGAGATCGGATGTACCAGG 58.394 55.000 1.91 0.00 40.29 4.45
677 679 3.936203 TTGCTTCTGTCCGCGGGT 61.936 61.111 27.83 0.00 0.00 5.28
711 713 2.530661 ATCCCGTTCCCCACACCA 60.531 61.111 0.00 0.00 0.00 4.17
745 747 3.469863 GACCCAACAGTCACCGGCA 62.470 63.158 0.00 0.00 36.73 5.69
790 793 1.067915 GCAGATCTCTACGATGGGAGC 60.068 57.143 0.00 0.00 30.84 4.70
828 832 2.166050 GGAGAGGAAACCCTAACGAGAC 59.834 54.545 0.00 0.00 33.25 3.36
837 841 1.015868 CCTAACGAGACGGGAGACTC 58.984 60.000 0.00 0.00 45.88 3.36
842 846 1.424635 GAGACGGGAGACTCGTTCG 59.575 63.158 0.00 9.07 41.34 3.95
843 847 2.202453 GACGGGAGACTCGTTCGC 60.202 66.667 10.14 2.58 41.22 4.70
844 848 2.672307 ACGGGAGACTCGTTCGCT 60.672 61.111 10.14 0.00 37.61 4.93
845 849 1.364626 GACGGGAGACTCGTTCGCTA 61.365 60.000 10.14 0.00 41.22 4.26
846 850 1.062206 CGGGAGACTCGTTCGCTAC 59.938 63.158 0.00 0.00 0.00 3.58
847 851 1.432657 GGGAGACTCGTTCGCTACC 59.567 63.158 0.00 0.00 0.00 3.18
848 852 1.062206 GGAGACTCGTTCGCTACCG 59.938 63.158 0.00 0.00 0.00 4.02
849 853 1.062206 GAGACTCGTTCGCTACCGG 59.938 63.158 0.00 0.00 34.56 5.28
850 854 1.364626 GAGACTCGTTCGCTACCGGA 61.365 60.000 9.46 0.00 34.56 5.14
851 855 0.747283 AGACTCGTTCGCTACCGGAT 60.747 55.000 9.46 0.00 34.56 4.18
883 889 6.403866 AGTGTAGCTATCTCCTTCATGAAG 57.596 41.667 25.75 25.75 38.14 3.02
887 893 3.710677 AGCTATCTCCTTCATGAAGCACT 59.289 43.478 27.01 14.38 37.11 4.40
968 974 2.419990 GCCCAAAACTCCAGCTTGTTTT 60.420 45.455 13.16 13.16 44.18 2.43
1081 1087 1.498176 GCAGTTCCCCACCTAACCCT 61.498 60.000 0.00 0.00 0.00 4.34
1199 1529 2.519780 GGGAGCGACGGAGGAGAT 60.520 66.667 0.00 0.00 0.00 2.75
1282 1612 3.792736 CGGCCGGGGATGAGGAAA 61.793 66.667 20.10 0.00 0.00 3.13
1290 1620 0.259065 GGGATGAGGAAAAGGGGGAC 59.741 60.000 0.00 0.00 0.00 4.46
1325 1673 2.355108 CGGAGCAAAAGGGAGAGAATCA 60.355 50.000 0.00 0.00 37.82 2.57
1332 1680 1.066587 GGGAGAGAATCAGTCGGCG 59.933 63.158 0.00 0.00 37.82 6.46
1429 1810 1.544759 GGGAAAGAAGGGAGCGACAAA 60.545 52.381 0.00 0.00 0.00 2.83
1856 2237 2.351336 ATCGCCGCTAAGTTCCTCCG 62.351 60.000 0.00 0.00 0.00 4.63
1916 2297 1.393539 CGTCGTGGACATGGTCAATTC 59.606 52.381 0.00 0.00 33.68 2.17
2072 2474 1.680522 GGAGCGATGGCAGAGGAGAA 61.681 60.000 1.50 0.00 43.41 2.87
2244 2646 0.744874 CCAAAGGCATCATCCAGCTG 59.255 55.000 6.78 6.78 0.00 4.24
2280 2682 4.778143 GCCCTCGCCACGGTGATT 62.778 66.667 10.28 0.00 33.90 2.57
2380 2782 2.268920 GCAACTCCGAGGCATCCA 59.731 61.111 0.00 0.00 0.00 3.41
2387 2789 2.362369 CCGAGGCATCCAGTGAGGT 61.362 63.158 0.00 0.00 39.02 3.85
2580 2982 2.432628 GCCACCGACTTCACCGAG 60.433 66.667 0.00 0.00 0.00 4.63
2581 2983 2.261671 CCACCGACTTCACCGAGG 59.738 66.667 0.00 0.00 0.00 4.63
2582 2984 2.273179 CCACCGACTTCACCGAGGA 61.273 63.158 0.00 0.00 0.00 3.71
2628 3036 0.539986 GTCCATGGGCCTTCGAGTAA 59.460 55.000 13.02 0.00 0.00 2.24
2639 3058 4.189231 GCCTTCGAGTAAGAGCCATTTAA 58.811 43.478 0.00 0.00 37.38 1.52
2644 3063 7.926555 CCTTCGAGTAAGAGCCATTTAATTCTA 59.073 37.037 0.00 0.00 37.38 2.10
2904 3342 0.630673 ACCAGCCCCATGAATTGCTA 59.369 50.000 0.00 0.00 31.69 3.49
2942 3380 2.028930 ACTCTTGATCGAAGGTGGTGTC 60.029 50.000 0.00 0.00 31.85 3.67
3051 3494 5.184479 GCAATACCATACCATGATTGCTCAT 59.816 40.000 15.15 0.00 42.51 2.90
3059 3502 2.031944 CCATGATTGCTCATTCTCTGCG 60.032 50.000 0.00 0.00 40.20 5.18
3065 3508 1.160137 GCTCATTCTCTGCGGTTGTT 58.840 50.000 0.00 0.00 0.00 2.83
3278 3784 5.960113 TGTGTGTTTTGCTTGACTACATTT 58.040 33.333 0.00 0.00 0.00 2.32
3415 4039 5.599242 TGTCACCATGTAACGGATAAGGATA 59.401 40.000 0.00 0.00 0.00 2.59
3474 4099 7.498900 TCATACTATGCTTGGTTTTCAGTATGG 59.501 37.037 15.17 2.38 42.05 2.74
3593 4220 2.093638 CATTTGCGATGCGTAAACTCG 58.906 47.619 5.30 0.00 43.10 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.411246 GGTGGTGCTATCGTACATCCA 59.589 52.381 0.00 0.00 0.00 3.41
1 2 1.687123 AGGTGGTGCTATCGTACATCC 59.313 52.381 0.00 0.00 0.00 3.51
2 3 4.672024 CGATAGGTGGTGCTATCGTACATC 60.672 50.000 3.96 0.00 45.51 3.06
4 5 2.551032 CGATAGGTGGTGCTATCGTACA 59.449 50.000 3.96 0.00 45.51 2.90
5 6 3.198863 CGATAGGTGGTGCTATCGTAC 57.801 52.381 3.96 0.00 45.51 3.67
38 39 5.772521 CAATTTGGAGACACGGAGATTTTT 58.227 37.500 0.00 0.00 42.67 1.94
39 40 4.321230 GCAATTTGGAGACACGGAGATTTT 60.321 41.667 0.00 0.00 42.67 1.82
40 41 3.191371 GCAATTTGGAGACACGGAGATTT 59.809 43.478 0.00 0.00 42.67 2.17
41 42 2.749621 GCAATTTGGAGACACGGAGATT 59.250 45.455 0.00 0.00 42.67 2.40
42 43 2.359900 GCAATTTGGAGACACGGAGAT 58.640 47.619 0.00 0.00 42.67 2.75
43 44 1.808411 GCAATTTGGAGACACGGAGA 58.192 50.000 0.00 0.00 42.67 3.71
44 45 0.443869 CGCAATTTGGAGACACGGAG 59.556 55.000 0.00 0.00 42.67 4.63
45 46 0.250124 ACGCAATTTGGAGACACGGA 60.250 50.000 0.00 0.00 42.67 4.69
46 47 0.591170 AACGCAATTTGGAGACACGG 59.409 50.000 0.00 0.00 42.67 4.94
47 48 2.043411 CAAACGCAATTTGGAGACACG 58.957 47.619 0.00 0.00 43.52 4.49
48 49 1.786579 GCAAACGCAATTTGGAGACAC 59.213 47.619 11.31 0.00 46.73 3.67
49 50 1.406898 TGCAAACGCAATTTGGAGACA 59.593 42.857 11.31 0.23 46.73 3.41
50 51 2.132740 TGCAAACGCAATTTGGAGAC 57.867 45.000 11.31 0.00 46.73 3.36
53 54 1.135915 AGTGTGCAAACGCAATTTGGA 59.864 42.857 0.16 6.56 46.73 3.53
54 55 1.522258 GAGTGTGCAAACGCAATTTGG 59.478 47.619 5.81 0.00 46.73 3.28
56 57 1.135915 TGGAGTGTGCAAACGCAATTT 59.864 42.857 13.11 0.00 42.17 1.82
57 58 0.743688 TGGAGTGTGCAAACGCAATT 59.256 45.000 13.11 0.00 42.17 2.32
58 59 0.743688 TTGGAGTGTGCAAACGCAAT 59.256 45.000 13.11 0.00 42.17 3.56
59 60 0.743688 ATTGGAGTGTGCAAACGCAA 59.256 45.000 13.11 0.00 42.17 4.85
60 61 0.310543 GATTGGAGTGTGCAAACGCA 59.689 50.000 13.11 0.00 36.95 5.24
61 62 0.387239 GGATTGGAGTGTGCAAACGC 60.387 55.000 1.48 1.48 29.75 4.84
62 63 0.240945 GGGATTGGAGTGTGCAAACG 59.759 55.000 0.16 0.00 29.75 3.60
63 64 1.620822 AGGGATTGGAGTGTGCAAAC 58.379 50.000 0.00 0.00 29.75 2.93
64 65 2.158475 AGAAGGGATTGGAGTGTGCAAA 60.158 45.455 0.00 0.00 29.75 3.68
65 66 1.425066 AGAAGGGATTGGAGTGTGCAA 59.575 47.619 0.00 0.00 30.73 4.08
66 67 1.003580 GAGAAGGGATTGGAGTGTGCA 59.996 52.381 0.00 0.00 0.00 4.57
67 68 1.280421 AGAGAAGGGATTGGAGTGTGC 59.720 52.381 0.00 0.00 0.00 4.57
68 69 3.710209 AAGAGAAGGGATTGGAGTGTG 57.290 47.619 0.00 0.00 0.00 3.82
69 70 4.597507 TGTAAAGAGAAGGGATTGGAGTGT 59.402 41.667 0.00 0.00 0.00 3.55
70 71 5.165961 TGTAAAGAGAAGGGATTGGAGTG 57.834 43.478 0.00 0.00 0.00 3.51
71 72 6.216456 AGAATGTAAAGAGAAGGGATTGGAGT 59.784 38.462 0.00 0.00 0.00 3.85
72 73 6.657875 AGAATGTAAAGAGAAGGGATTGGAG 58.342 40.000 0.00 0.00 0.00 3.86
73 74 6.642733 AGAATGTAAAGAGAAGGGATTGGA 57.357 37.500 0.00 0.00 0.00 3.53
74 75 6.405176 GCAAGAATGTAAAGAGAAGGGATTGG 60.405 42.308 0.00 0.00 0.00 3.16
75 76 6.151648 TGCAAGAATGTAAAGAGAAGGGATTG 59.848 38.462 0.00 0.00 0.00 2.67
76 77 6.248433 TGCAAGAATGTAAAGAGAAGGGATT 58.752 36.000 0.00 0.00 0.00 3.01
77 78 5.819991 TGCAAGAATGTAAAGAGAAGGGAT 58.180 37.500 0.00 0.00 0.00 3.85
78 79 5.241403 TGCAAGAATGTAAAGAGAAGGGA 57.759 39.130 0.00 0.00 0.00 4.20
79 80 5.241506 TGTTGCAAGAATGTAAAGAGAAGGG 59.758 40.000 0.00 0.00 32.75 3.95
80 81 6.317789 TGTTGCAAGAATGTAAAGAGAAGG 57.682 37.500 0.00 0.00 32.75 3.46
81 82 6.307318 GCATGTTGCAAGAATGTAAAGAGAAG 59.693 38.462 18.54 0.00 44.26 2.85
82 83 6.151691 GCATGTTGCAAGAATGTAAAGAGAA 58.848 36.000 18.54 0.00 44.26 2.87
83 84 5.702865 GCATGTTGCAAGAATGTAAAGAGA 58.297 37.500 18.54 0.00 44.26 3.10
98 99 2.660189 AAGTAAGGCATGCATGTTGC 57.340 45.000 26.79 17.29 45.29 4.17
99 100 3.514645 GGAAAGTAAGGCATGCATGTTG 58.485 45.455 26.79 4.87 0.00 3.33
100 101 2.164219 CGGAAAGTAAGGCATGCATGTT 59.836 45.455 26.79 16.76 0.00 2.71
101 102 1.745087 CGGAAAGTAAGGCATGCATGT 59.255 47.619 26.79 10.85 0.00 3.21
102 103 1.534595 GCGGAAAGTAAGGCATGCATG 60.535 52.381 22.70 22.70 0.00 4.06
103 104 0.740737 GCGGAAAGTAAGGCATGCAT 59.259 50.000 21.36 10.32 0.00 3.96
104 105 0.322456 AGCGGAAAGTAAGGCATGCA 60.322 50.000 21.36 0.00 0.00 3.96
105 106 0.099436 CAGCGGAAAGTAAGGCATGC 59.901 55.000 9.90 9.90 0.00 4.06
106 107 0.099436 GCAGCGGAAAGTAAGGCATG 59.901 55.000 0.00 0.00 0.00 4.06
107 108 0.035056 AGCAGCGGAAAGTAAGGCAT 60.035 50.000 0.00 0.00 0.00 4.40
108 109 0.673644 GAGCAGCGGAAAGTAAGGCA 60.674 55.000 0.00 0.00 0.00 4.75
109 110 0.673644 TGAGCAGCGGAAAGTAAGGC 60.674 55.000 0.00 0.00 0.00 4.35
110 111 2.029838 ATGAGCAGCGGAAAGTAAGG 57.970 50.000 0.00 0.00 0.00 2.69
111 112 5.533482 AGTATATGAGCAGCGGAAAGTAAG 58.467 41.667 0.00 0.00 0.00 2.34
112 113 5.302059 AGAGTATATGAGCAGCGGAAAGTAA 59.698 40.000 0.00 0.00 0.00 2.24
113 114 4.827835 AGAGTATATGAGCAGCGGAAAGTA 59.172 41.667 0.00 0.00 0.00 2.24
114 115 3.639094 AGAGTATATGAGCAGCGGAAAGT 59.361 43.478 0.00 0.00 0.00 2.66
115 116 4.250116 AGAGTATATGAGCAGCGGAAAG 57.750 45.455 0.00 0.00 0.00 2.62
116 117 4.672587 AAGAGTATATGAGCAGCGGAAA 57.327 40.909 0.00 0.00 0.00 3.13
117 118 4.141937 ACAAAGAGTATATGAGCAGCGGAA 60.142 41.667 0.00 0.00 0.00 4.30
118 119 3.384789 ACAAAGAGTATATGAGCAGCGGA 59.615 43.478 0.00 0.00 0.00 5.54
119 120 3.722147 ACAAAGAGTATATGAGCAGCGG 58.278 45.455 0.00 0.00 0.00 5.52
120 121 5.164012 GCATACAAAGAGTATATGAGCAGCG 60.164 44.000 0.00 0.00 41.47 5.18
121 122 5.931146 AGCATACAAAGAGTATATGAGCAGC 59.069 40.000 0.00 0.00 41.47 5.25
122 123 6.307558 CGAGCATACAAAGAGTATATGAGCAG 59.692 42.308 0.00 0.00 41.47 4.24
123 124 6.152379 CGAGCATACAAAGAGTATATGAGCA 58.848 40.000 0.00 0.00 41.47 4.26
124 125 5.061560 GCGAGCATACAAAGAGTATATGAGC 59.938 44.000 0.00 0.00 41.47 4.26
125 126 6.152379 TGCGAGCATACAAAGAGTATATGAG 58.848 40.000 0.00 0.00 41.47 2.90
126 127 6.084326 TGCGAGCATACAAAGAGTATATGA 57.916 37.500 0.00 0.00 41.47 2.15
127 128 6.671641 GCATGCGAGCATACAAAGAGTATATG 60.672 42.308 10.48 0.00 41.47 1.78
128 129 5.349817 GCATGCGAGCATACAAAGAGTATAT 59.650 40.000 10.48 0.00 41.47 0.86
129 130 4.686091 GCATGCGAGCATACAAAGAGTATA 59.314 41.667 10.48 0.00 41.47 1.47
130 131 3.496130 GCATGCGAGCATACAAAGAGTAT 59.504 43.478 10.48 0.00 44.20 2.12
131 132 2.866156 GCATGCGAGCATACAAAGAGTA 59.134 45.455 10.48 0.00 34.91 2.59
132 133 1.667724 GCATGCGAGCATACAAAGAGT 59.332 47.619 10.48 0.00 34.91 3.24
133 134 1.938577 AGCATGCGAGCATACAAAGAG 59.061 47.619 13.01 0.00 34.91 2.85
134 135 2.028420 AGCATGCGAGCATACAAAGA 57.972 45.000 13.01 0.00 34.91 2.52
135 136 2.447250 CAAGCATGCGAGCATACAAAG 58.553 47.619 13.01 0.00 34.91 2.77
136 137 1.467883 GCAAGCATGCGAGCATACAAA 60.468 47.619 25.74 0.00 43.83 2.83
137 138 0.099259 GCAAGCATGCGAGCATACAA 59.901 50.000 25.74 0.00 43.83 2.41
138 139 1.723273 GCAAGCATGCGAGCATACA 59.277 52.632 25.74 0.00 43.83 2.29
139 140 4.603216 GCAAGCATGCGAGCATAC 57.397 55.556 25.74 5.18 43.83 2.39
148 149 6.731164 TCACAATACATATCAAGCAAGCATG 58.269 36.000 0.00 0.00 0.00 4.06
149 150 6.947644 TCACAATACATATCAAGCAAGCAT 57.052 33.333 0.00 0.00 0.00 3.79
150 151 6.756299 TTCACAATACATATCAAGCAAGCA 57.244 33.333 0.00 0.00 0.00 3.91
151 152 7.198390 ACATTCACAATACATATCAAGCAAGC 58.802 34.615 0.00 0.00 0.00 4.01
152 153 9.577110 AAACATTCACAATACATATCAAGCAAG 57.423 29.630 0.00 0.00 0.00 4.01
162 163 8.977505 GCACAAGTTTAAACATTCACAATACAT 58.022 29.630 20.06 0.00 0.00 2.29
163 164 8.194104 AGCACAAGTTTAAACATTCACAATACA 58.806 29.630 20.06 0.00 0.00 2.29
164 165 8.574196 AGCACAAGTTTAAACATTCACAATAC 57.426 30.769 20.06 0.00 0.00 1.89
166 167 9.762933 ATTAGCACAAGTTTAAACATTCACAAT 57.237 25.926 20.06 8.20 0.00 2.71
168 169 9.672086 GTATTAGCACAAGTTTAAACATTCACA 57.328 29.630 20.06 0.00 0.00 3.58
169 170 9.893305 AGTATTAGCACAAGTTTAAACATTCAC 57.107 29.630 20.06 6.81 0.00 3.18
171 172 9.556030 GGAGTATTAGCACAAGTTTAAACATTC 57.444 33.333 20.06 4.87 0.00 2.67
172 173 9.073475 TGGAGTATTAGCACAAGTTTAAACATT 57.927 29.630 20.06 8.77 0.00 2.71
173 174 8.512138 GTGGAGTATTAGCACAAGTTTAAACAT 58.488 33.333 20.06 5.63 0.00 2.71
174 175 7.717875 AGTGGAGTATTAGCACAAGTTTAAACA 59.282 33.333 20.06 0.00 0.00 2.83
175 176 8.095937 AGTGGAGTATTAGCACAAGTTTAAAC 57.904 34.615 10.47 10.47 0.00 2.01
176 177 8.685838 AAGTGGAGTATTAGCACAAGTTTAAA 57.314 30.769 0.00 0.00 0.00 1.52
177 178 7.934665 TGAAGTGGAGTATTAGCACAAGTTTAA 59.065 33.333 0.00 0.00 0.00 1.52
178 179 7.446769 TGAAGTGGAGTATTAGCACAAGTTTA 58.553 34.615 0.00 0.00 0.00 2.01
179 180 6.296026 TGAAGTGGAGTATTAGCACAAGTTT 58.704 36.000 0.00 0.00 0.00 2.66
180 181 5.865085 TGAAGTGGAGTATTAGCACAAGTT 58.135 37.500 0.00 0.00 0.00 2.66
181 182 5.483685 TGAAGTGGAGTATTAGCACAAGT 57.516 39.130 0.00 0.00 0.00 3.16
182 183 5.934625 AGTTGAAGTGGAGTATTAGCACAAG 59.065 40.000 0.00 0.00 0.00 3.16
183 184 5.865085 AGTTGAAGTGGAGTATTAGCACAA 58.135 37.500 0.00 0.00 0.00 3.33
184 185 5.011635 TGAGTTGAAGTGGAGTATTAGCACA 59.988 40.000 0.00 0.00 0.00 4.57
185 186 5.479306 TGAGTTGAAGTGGAGTATTAGCAC 58.521 41.667 0.00 0.00 0.00 4.40
186 187 5.738619 TGAGTTGAAGTGGAGTATTAGCA 57.261 39.130 0.00 0.00 0.00 3.49
187 188 6.398918 TCTTGAGTTGAAGTGGAGTATTAGC 58.601 40.000 0.00 0.00 0.00 3.09
188 189 7.831753 TCTCTTGAGTTGAAGTGGAGTATTAG 58.168 38.462 0.00 0.00 0.00 1.73
189 190 7.776618 TCTCTTGAGTTGAAGTGGAGTATTA 57.223 36.000 0.00 0.00 0.00 0.98
190 191 6.672266 TCTCTTGAGTTGAAGTGGAGTATT 57.328 37.500 0.00 0.00 0.00 1.89
191 192 6.865834 ATCTCTTGAGTTGAAGTGGAGTAT 57.134 37.500 0.00 0.00 0.00 2.12
192 193 6.672266 AATCTCTTGAGTTGAAGTGGAGTA 57.328 37.500 0.00 0.00 0.00 2.59
193 194 5.559148 AATCTCTTGAGTTGAAGTGGAGT 57.441 39.130 0.00 0.00 0.00 3.85
194 195 7.969536 TTTAATCTCTTGAGTTGAAGTGGAG 57.030 36.000 0.00 0.00 0.00 3.86
195 196 8.621286 GTTTTTAATCTCTTGAGTTGAAGTGGA 58.379 33.333 0.00 0.00 0.00 4.02
196 197 8.624776 AGTTTTTAATCTCTTGAGTTGAAGTGG 58.375 33.333 0.00 0.00 0.00 4.00
197 198 9.443283 CAGTTTTTAATCTCTTGAGTTGAAGTG 57.557 33.333 0.00 0.00 0.00 3.16
198 199 8.131731 GCAGTTTTTAATCTCTTGAGTTGAAGT 58.868 33.333 0.00 0.00 0.00 3.01
199 200 8.131100 TGCAGTTTTTAATCTCTTGAGTTGAAG 58.869 33.333 0.00 0.00 0.00 3.02
200 201 7.995289 TGCAGTTTTTAATCTCTTGAGTTGAA 58.005 30.769 0.00 0.00 0.00 2.69
201 202 7.566760 TGCAGTTTTTAATCTCTTGAGTTGA 57.433 32.000 0.00 0.00 0.00 3.18
202 203 7.917505 AGTTGCAGTTTTTAATCTCTTGAGTTG 59.082 33.333 0.00 0.00 0.00 3.16
203 204 8.000780 AGTTGCAGTTTTTAATCTCTTGAGTT 57.999 30.769 0.00 0.00 0.00 3.01
204 205 7.573968 AGTTGCAGTTTTTAATCTCTTGAGT 57.426 32.000 0.00 0.00 0.00 3.41
205 206 8.862550 AAAGTTGCAGTTTTTAATCTCTTGAG 57.137 30.769 0.00 0.00 0.00 3.02
206 207 9.301153 GAAAAGTTGCAGTTTTTAATCTCTTGA 57.699 29.630 9.50 0.00 31.40 3.02
207 208 9.305925 AGAAAAGTTGCAGTTTTTAATCTCTTG 57.694 29.630 9.50 0.00 31.40 3.02
208 209 9.875691 AAGAAAAGTTGCAGTTTTTAATCTCTT 57.124 25.926 9.50 6.66 31.40 2.85
209 210 9.305925 CAAGAAAAGTTGCAGTTTTTAATCTCT 57.694 29.630 9.50 1.95 31.40 3.10
210 211 9.301153 TCAAGAAAAGTTGCAGTTTTTAATCTC 57.699 29.630 9.50 0.07 31.40 2.75
211 212 9.822185 ATCAAGAAAAGTTGCAGTTTTTAATCT 57.178 25.926 9.50 2.51 31.40 2.40
216 217 9.305925 CTCTAATCAAGAAAAGTTGCAGTTTTT 57.694 29.630 9.50 9.37 31.40 1.94
217 218 8.470002 ACTCTAATCAAGAAAAGTTGCAGTTTT 58.530 29.630 8.23 8.23 33.74 2.43
218 219 8.000780 ACTCTAATCAAGAAAAGTTGCAGTTT 57.999 30.769 0.00 0.00 32.46 2.66
219 220 7.500559 AGACTCTAATCAAGAAAAGTTGCAGTT 59.499 33.333 0.00 0.00 32.46 3.16
220 221 6.995091 AGACTCTAATCAAGAAAAGTTGCAGT 59.005 34.615 0.00 0.00 32.46 4.40
221 222 7.432350 AGACTCTAATCAAGAAAAGTTGCAG 57.568 36.000 0.00 0.00 32.46 4.41
222 223 9.507329 AATAGACTCTAATCAAGAAAAGTTGCA 57.493 29.630 0.00 0.00 32.46 4.08
223 224 9.980780 GAATAGACTCTAATCAAGAAAAGTTGC 57.019 33.333 0.00 0.00 32.46 4.17
226 227 9.660180 GGTGAATAGACTCTAATCAAGAAAAGT 57.340 33.333 5.54 0.00 32.46 2.66
227 228 9.103861 GGGTGAATAGACTCTAATCAAGAAAAG 57.896 37.037 5.54 0.00 32.46 2.27
228 229 8.047310 GGGGTGAATAGACTCTAATCAAGAAAA 58.953 37.037 5.54 0.00 32.46 2.29
229 230 7.365652 GGGGGTGAATAGACTCTAATCAAGAAA 60.366 40.741 5.54 0.00 32.46 2.52
230 231 6.099845 GGGGGTGAATAGACTCTAATCAAGAA 59.900 42.308 5.54 0.00 32.46 2.52
231 232 5.602978 GGGGGTGAATAGACTCTAATCAAGA 59.397 44.000 5.54 0.00 0.00 3.02
232 233 5.859495 GGGGGTGAATAGACTCTAATCAAG 58.141 45.833 5.54 0.00 0.00 3.02
233 234 5.888982 GGGGGTGAATAGACTCTAATCAA 57.111 43.478 5.54 0.00 0.00 2.57
256 257 1.265454 AACCTTCGCAGTCTAGGGGG 61.265 60.000 0.00 0.00 33.22 5.40
257 258 0.613777 AAACCTTCGCAGTCTAGGGG 59.386 55.000 0.00 0.00 33.22 4.79
258 259 2.076863 CAAAACCTTCGCAGTCTAGGG 58.923 52.381 0.00 0.00 33.22 3.53
259 260 2.480419 CACAAAACCTTCGCAGTCTAGG 59.520 50.000 0.00 0.00 35.14 3.02
260 261 3.390135 TCACAAAACCTTCGCAGTCTAG 58.610 45.455 0.00 0.00 0.00 2.43
261 262 3.462483 TCACAAAACCTTCGCAGTCTA 57.538 42.857 0.00 0.00 0.00 2.59
262 263 2.325583 TCACAAAACCTTCGCAGTCT 57.674 45.000 0.00 0.00 0.00 3.24
263 264 2.854805 GCTTCACAAAACCTTCGCAGTC 60.855 50.000 0.00 0.00 0.00 3.51
264 265 1.065551 GCTTCACAAAACCTTCGCAGT 59.934 47.619 0.00 0.00 0.00 4.40
265 266 1.600413 GGCTTCACAAAACCTTCGCAG 60.600 52.381 0.00 0.00 0.00 5.18
266 267 0.383949 GGCTTCACAAAACCTTCGCA 59.616 50.000 0.00 0.00 0.00 5.10
267 268 0.383949 TGGCTTCACAAAACCTTCGC 59.616 50.000 0.00 0.00 0.00 4.70
268 269 4.701956 ATATGGCTTCACAAAACCTTCG 57.298 40.909 0.00 0.00 0.00 3.79
288 289 6.388619 AAGAAGTGGTGATTACCCAGTAAT 57.611 37.500 3.88 0.00 46.96 1.89
289 290 5.836024 AAGAAGTGGTGATTACCCAGTAA 57.164 39.130 3.88 0.00 46.96 2.24
358 360 1.609208 ATGCAGTTTTCTTGCCTCGT 58.391 45.000 0.00 0.00 0.00 4.18
474 476 3.067180 TCGCTAGGGTTTACACCGATAAG 59.933 47.826 6.70 0.00 45.39 1.73
533 535 1.757118 AGGACGTGGTGATCGATGATT 59.243 47.619 0.54 0.00 0.00 2.57
557 559 1.985116 GGCCTGAAGGAGGACGACT 60.985 63.158 0.00 0.00 46.33 4.18
580 582 1.139654 TCTCGAAGCAATGATGGAGGG 59.860 52.381 1.06 0.00 0.00 4.30
677 679 3.954740 ATCGTTGGGGCCCCTACCA 62.955 63.158 39.41 32.29 38.33 3.25
720 722 3.584868 GACTGTTGGGTCGTCGGGG 62.585 68.421 0.00 0.00 0.00 5.73
728 730 2.829384 ATGCCGGTGACTGTTGGGT 61.829 57.895 1.90 0.00 0.00 4.51
733 735 2.665000 CTCCATGCCGGTGACTGT 59.335 61.111 1.90 0.00 35.57 3.55
734 736 2.124983 CCTCCATGCCGGTGACTG 60.125 66.667 1.90 0.00 35.57 3.51
781 784 2.464459 GGCGACTTTGCTCCCATCG 61.464 63.158 0.00 0.00 35.91 3.84
790 793 3.181967 CTCTCGGCGGCGACTTTG 61.182 66.667 31.46 20.54 0.00 2.77
828 832 1.062206 GTAGCGAACGAGTCTCCCG 59.938 63.158 0.00 0.00 0.00 5.14
865 869 3.710677 AGTGCTTCATGAAGGAGATAGCT 59.289 43.478 31.41 20.53 39.44 3.32
899 905 6.931281 TGTAATATTATGCTTGAGCCAGTCTC 59.069 38.462 0.00 0.00 42.23 3.36
968 974 1.481871 CCTACTTCTGGGCCGAACTA 58.518 55.000 0.00 0.00 0.00 2.24
1081 1087 1.227350 CCGCCATTGCTCTCGATGA 60.227 57.895 0.00 0.00 36.40 2.92
1198 1528 4.162690 GGCCGCGTCTCCCTTCAT 62.163 66.667 4.92 0.00 0.00 2.57
1221 1551 1.601419 CCGTCGACCCCTTCTGCTTA 61.601 60.000 10.58 0.00 0.00 3.09
1225 1555 4.796231 CGCCGTCGACCCCTTCTG 62.796 72.222 10.58 0.00 38.10 3.02
1282 1612 2.364961 CTCCTCCTCGTCCCCCTT 59.635 66.667 0.00 0.00 0.00 3.95
1290 1620 4.507916 TCCGCCTCCTCCTCCTCG 62.508 72.222 0.00 0.00 0.00 4.63
1320 1668 3.255379 GCCGACGCCGACTGATTC 61.255 66.667 0.00 0.00 38.22 2.52
1402 1783 0.116541 TCCCTTCTTTCCCTCTCCGT 59.883 55.000 0.00 0.00 0.00 4.69
1429 1810 3.181458 TGTCCCTTCGTTCTGCTAAAACT 60.181 43.478 0.00 0.00 0.00 2.66
1628 2009 0.475906 GGGTAGCTGGATGATGCCTT 59.524 55.000 0.00 0.00 37.02 4.35
1856 2237 1.092345 GTCGAAGAGCCCCTTGATGC 61.092 60.000 0.00 0.00 36.95 3.91
2194 2596 1.658717 CGATCATGTCGGCGAGGAC 60.659 63.158 11.20 0.00 46.47 3.85
2244 2646 3.443045 CTGGCGTCCACATTGGGC 61.443 66.667 0.00 0.00 39.19 5.36
2380 2782 0.683973 CACTCCTTCAGCACCTCACT 59.316 55.000 0.00 0.00 0.00 3.41
2387 2789 2.583441 CGGTCCCACTCCTTCAGCA 61.583 63.158 0.00 0.00 0.00 4.41
2580 2982 1.334384 GCAGTTCCTCCTCCTCCTCC 61.334 65.000 0.00 0.00 0.00 4.30
2581 2983 1.671901 CGCAGTTCCTCCTCCTCCTC 61.672 65.000 0.00 0.00 0.00 3.71
2582 2984 1.684049 CGCAGTTCCTCCTCCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
2639 3058 9.988815 GATACAGTGAGATGTTACCATTAGAAT 57.011 33.333 0.00 0.00 34.56 2.40
2644 3063 6.156949 ACCAGATACAGTGAGATGTTACCATT 59.843 38.462 0.00 0.00 34.56 3.16
2801 3236 7.772757 AGCTTTAAACACAAATTTGATCCCAAA 59.227 29.630 24.64 15.42 45.28 3.28
2835 3270 4.338012 TCATTCATCCACTTGAAGCATGT 58.662 39.130 0.00 0.00 38.90 3.21
2904 3342 8.804912 ATCAAGAGTAGCTGAAGAAATTCAAT 57.195 30.769 0.00 0.00 0.00 2.57
2968 3411 9.316730 CATTTTGAGGAAACTTTCAAATTCAGA 57.683 29.630 3.93 0.00 44.43 3.27
3051 3494 2.325583 ACAAGAACAACCGCAGAGAA 57.674 45.000 0.00 0.00 0.00 2.87
3059 3502 6.636850 CACTGCAACTTTATACAAGAACAACC 59.363 38.462 0.00 0.00 0.00 3.77
3125 3576 9.367160 TCATGGTATCTCTAATCAGTGACATAA 57.633 33.333 0.00 0.00 0.00 1.90
3278 3784 4.298626 ACTGGACCTATATTCTTCAGCCA 58.701 43.478 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.