Multiple sequence alignment - TraesCS2A01G483200

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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 TraesCS2A01G483200 chr2A 100.000 1679 0 0 854 2532 719256546 719258224 0.000000e+00 3101
1 TraesCS2A01G483200 chr2A 100.000 652 0 0 1 652 719255693 719256344 0.000000e+00 1205
2 TraesCS2A01G483200 chr2A 94.224 277 16 0 370 646 12591391 12591667 8.370000e-115 424
3 TraesCS2A01G483200 chr7A 97.856 1679 36 0 854 2532 70819644 70821322 0.000000e+00 2902
4 TraesCS2A01G483200 chr6D 97.029 1683 38 7 854 2532 100359180 100360854 0.000000e+00 2820
5 TraesCS2A01G483200 chr6D 96.378 1684 47 8 854 2532 17067371 17069045 0.000000e+00 2760
6 TraesCS2A01G483200 chr6D 94.014 284 17 0 369 652 17067057 17067340 5.000000e-117 431
7 TraesCS2A01G483200 chr2D 96.679 1686 42 8 854 2532 645194966 645196644 0.000000e+00 2791
8 TraesCS2A01G483200 chr2D 92.683 287 20 1 366 652 645194644 645194929 1.810000e-111 412
9 TraesCS2A01G483200 chr2D 86.268 284 32 5 54 330 395413513 395413796 4.090000e-78 302
10 TraesCS2A01G483200 chr3D 96.617 1685 43 9 854 2532 537296661 537298337 0.000000e+00 2784
11 TraesCS2A01G483200 chr3D 95.962 1684 49 9 854 2532 45527241 45528910 0.000000e+00 2715
12 TraesCS2A01G483200 chr3D 83.422 748 73 13 854 1570 70094286 70095013 0.000000e+00 647
13 TraesCS2A01G483200 chr3D 86.942 291 27 7 60 342 599298350 599298637 1.460000e-82 316
14 TraesCS2A01G483200 chr3D 87.189 281 30 3 55 329 355714545 355714265 5.260000e-82 315
15 TraesCS2A01G483200 chr1D 96.378 1684 44 7 854 2532 490433043 490434714 0.000000e+00 2756
16 TraesCS2A01G483200 chr1D 82.533 750 75 14 854 1572 395449753 395449029 2.150000e-170 608
17 TraesCS2A01G483200 chr1D 93.972 282 17 0 369 650 490432737 490433018 6.470000e-116 427
18 TraesCS2A01G483200 chr1D 93.007 286 20 0 367 652 10554223 10554508 3.900000e-113 418
19 TraesCS2A01G483200 chr1D 87.324 284 29 2 57 333 43283307 43283024 4.060000e-83 318
20 TraesCS2A01G483200 chr1D 87.143 280 30 3 56 329 103708817 103708538 1.890000e-81 313
21 TraesCS2A01G483200 chr1A 95.463 1675 53 10 854 2518 567958914 567957253 0.000000e+00 2651
22 TraesCS2A01G483200 chr1A 93.993 283 17 0 370 652 567959234 567958952 1.800000e-116 429
23 TraesCS2A01G483200 chr5D 96.024 1635 48 8 904 2532 79126122 79124499 0.000000e+00 2643
24 TraesCS2A01G483200 chr5D 93.640 283 18 0 370 652 537774290 537774008 8.370000e-115 424
25 TraesCS2A01G483200 chr5D 93.310 284 19 0 369 652 543865237 543865520 1.080000e-113 420
26 TraesCS2A01G483200 chr5D 86.786 280 28 6 59 331 209302299 209302576 1.140000e-78 303
27 TraesCS2A01G483200 chr1B 95.339 901 34 2 854 1754 36839924 36839032 0.000000e+00 1424
28 TraesCS2A01G483200 chr1B 87.179 273 34 1 57 329 553475115 553475386 2.450000e-80 309
29 TraesCS2A01G483200 chr4D 92.958 284 20 0 369 652 36561617 36561334 5.040000e-112 414
30 TraesCS2A01G483200 chr4D 86.909 275 30 1 59 327 301644923 301644649 1.140000e-78 303
31 TraesCS2A01G483200 chr4A 86.121 281 33 3 55 329 407709973 407709693 5.300000e-77 298


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 TraesCS2A01G483200 chr2A 719255693 719258224 2531 False 2153.0 3101 100.000 1 2532 2 chr2A.!!$F2 2531
1 TraesCS2A01G483200 chr7A 70819644 70821322 1678 False 2902.0 2902 97.856 854 2532 1 chr7A.!!$F1 1678
2 TraesCS2A01G483200 chr6D 100359180 100360854 1674 False 2820.0 2820 97.029 854 2532 1 chr6D.!!$F1 1678
3 TraesCS2A01G483200 chr6D 17067057 17069045 1988 False 1595.5 2760 95.196 369 2532 2 chr6D.!!$F2 2163
4 TraesCS2A01G483200 chr2D 645194644 645196644 2000 False 1601.5 2791 94.681 366 2532 2 chr2D.!!$F2 2166
5 TraesCS2A01G483200 chr3D 537296661 537298337 1676 False 2784.0 2784 96.617 854 2532 1 chr3D.!!$F3 1678
6 TraesCS2A01G483200 chr3D 45527241 45528910 1669 False 2715.0 2715 95.962 854 2532 1 chr3D.!!$F1 1678
7 TraesCS2A01G483200 chr3D 70094286 70095013 727 False 647.0 647 83.422 854 1570 1 chr3D.!!$F2 716
8 TraesCS2A01G483200 chr1D 490432737 490434714 1977 False 1591.5 2756 95.175 369 2532 2 chr1D.!!$F2 2163
9 TraesCS2A01G483200 chr1D 395449029 395449753 724 True 608.0 608 82.533 854 1572 1 chr1D.!!$R3 718
10 TraesCS2A01G483200 chr1A 567957253 567959234 1981 True 1540.0 2651 94.728 370 2518 2 chr1A.!!$R1 2148
11 TraesCS2A01G483200 chr5D 79124499 79126122 1623 True 2643.0 2643 96.024 904 2532 1 chr5D.!!$R1 1628
12 TraesCS2A01G483200 chr1B 36839032 36839924 892 True 1424.0 1424 95.339 854 1754 1 chr1B.!!$R1 900

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
553 554 0.107066 TATGACACGCGGGACCTAGA 60.107 55.0 19.19 0.0 0.00 2.43 F
1259 1297 0.178967 TGGGCATTTTGAGTGGCTCA 60.179 50.0 0.00 0.0 41.43 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1453 2.160219 TCAGATGCTTTAGTTGCTTGCG 59.840 45.455 0.00 0.00 0.0 4.85 R
2416 2466 7.546778 TCTAGCTTGCTATAGATCTATCGTG 57.453 40.000 18.59 11.22 0.0 4.35 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
22 23 5.779529 CAAGCCATGGTTCTAAGCATTAT 57.220 39.130 14.67 0.00 44.02 1.28
23 24 6.882610 CAAGCCATGGTTCTAAGCATTATA 57.117 37.500 14.67 0.00 44.02 0.98
24 25 6.906659 CAAGCCATGGTTCTAAGCATTATAG 58.093 40.000 14.67 0.00 44.02 1.31
25 26 6.192970 AGCCATGGTTCTAAGCATTATAGT 57.807 37.500 14.67 0.00 44.02 2.12
26 27 6.234177 AGCCATGGTTCTAAGCATTATAGTC 58.766 40.000 14.67 0.00 44.02 2.59
27 28 5.120830 GCCATGGTTCTAAGCATTATAGTCG 59.879 44.000 14.67 0.00 44.02 4.18
28 29 5.120830 CCATGGTTCTAAGCATTATAGTCGC 59.879 44.000 2.57 0.00 44.02 5.19
29 30 4.628074 TGGTTCTAAGCATTATAGTCGCC 58.372 43.478 0.00 0.00 0.00 5.54
30 31 4.100344 TGGTTCTAAGCATTATAGTCGCCA 59.900 41.667 0.00 0.00 0.00 5.69
31 32 4.686554 GGTTCTAAGCATTATAGTCGCCAG 59.313 45.833 0.00 0.00 0.00 4.85
32 33 5.509163 GGTTCTAAGCATTATAGTCGCCAGA 60.509 44.000 0.00 0.00 0.00 3.86
41 42 3.117171 GTCGCCAGACAGCTGCTG 61.117 66.667 27.02 27.02 46.32 4.41
44 45 2.750637 GCCAGACAGCTGCTGCAT 60.751 61.111 28.39 14.98 40.91 3.96
45 46 3.052620 GCCAGACAGCTGCTGCATG 62.053 63.158 28.39 24.37 40.91 4.06
46 47 2.485582 CAGACAGCTGCTGCATGC 59.514 61.111 28.39 11.82 42.74 4.06
58 59 3.424300 GCATGCATGCGCTCCTAA 58.576 55.556 33.99 0.00 44.67 2.69
59 60 1.281960 GCATGCATGCGCTCCTAAG 59.718 57.895 33.99 2.26 44.67 2.18
60 61 1.947013 CATGCATGCGCTCCTAAGG 59.053 57.895 14.93 0.00 39.64 2.69
61 62 1.895707 ATGCATGCGCTCCTAAGGC 60.896 57.895 14.09 0.69 39.64 4.35
62 63 2.203126 GCATGCGCTCCTAAGGCT 60.203 61.111 9.73 0.00 34.30 4.58
63 64 1.069765 GCATGCGCTCCTAAGGCTA 59.930 57.895 9.73 0.00 34.30 3.93
64 65 0.948141 GCATGCGCTCCTAAGGCTAG 60.948 60.000 9.73 0.00 34.30 3.42
65 66 0.390860 CATGCGCTCCTAAGGCTAGT 59.609 55.000 9.73 0.00 0.00 2.57
66 67 0.676736 ATGCGCTCCTAAGGCTAGTC 59.323 55.000 9.73 0.00 0.00 2.59
67 68 0.683179 TGCGCTCCTAAGGCTAGTCA 60.683 55.000 9.73 0.00 0.00 3.41
68 69 0.676736 GCGCTCCTAAGGCTAGTCAT 59.323 55.000 0.00 0.00 0.00 3.06
69 70 1.887198 GCGCTCCTAAGGCTAGTCATA 59.113 52.381 0.00 0.00 0.00 2.15
70 71 2.094957 GCGCTCCTAAGGCTAGTCATAG 60.095 54.545 0.00 0.00 0.00 2.23
71 72 3.150767 CGCTCCTAAGGCTAGTCATAGT 58.849 50.000 5.92 0.00 0.00 2.12
72 73 3.057876 CGCTCCTAAGGCTAGTCATAGTG 60.058 52.174 5.92 0.39 0.00 2.74
73 74 3.257127 GCTCCTAAGGCTAGTCATAGTGG 59.743 52.174 5.92 0.10 0.00 4.00
74 75 3.829601 CTCCTAAGGCTAGTCATAGTGGG 59.170 52.174 5.92 0.00 0.00 4.61
75 76 3.465966 TCCTAAGGCTAGTCATAGTGGGA 59.534 47.826 5.92 0.00 0.00 4.37
76 77 3.829601 CCTAAGGCTAGTCATAGTGGGAG 59.170 52.174 5.92 0.00 0.00 4.30
77 78 3.406512 AAGGCTAGTCATAGTGGGAGT 57.593 47.619 0.00 0.00 0.00 3.85
78 79 4.537945 AAGGCTAGTCATAGTGGGAGTA 57.462 45.455 0.00 0.00 0.00 2.59
79 80 4.537945 AGGCTAGTCATAGTGGGAGTAA 57.462 45.455 0.00 0.00 0.00 2.24
80 81 4.216708 AGGCTAGTCATAGTGGGAGTAAC 58.783 47.826 0.00 0.00 0.00 2.50
81 82 4.079096 AGGCTAGTCATAGTGGGAGTAACT 60.079 45.833 0.00 0.00 0.00 2.24
82 83 4.650131 GGCTAGTCATAGTGGGAGTAACTT 59.350 45.833 0.00 0.00 0.00 2.66
83 84 5.832060 GGCTAGTCATAGTGGGAGTAACTTA 59.168 44.000 0.00 0.00 0.00 2.24
84 85 6.016108 GGCTAGTCATAGTGGGAGTAACTTAG 60.016 46.154 0.00 0.00 0.00 2.18
85 86 5.855740 AGTCATAGTGGGAGTAACTTAGC 57.144 43.478 0.00 0.00 0.00 3.09
86 87 5.520751 AGTCATAGTGGGAGTAACTTAGCT 58.479 41.667 0.00 0.00 0.00 3.32
87 88 6.670617 AGTCATAGTGGGAGTAACTTAGCTA 58.329 40.000 0.00 0.00 0.00 3.32
88 89 7.124052 AGTCATAGTGGGAGTAACTTAGCTAA 58.876 38.462 5.94 5.94 0.00 3.09
89 90 7.785506 AGTCATAGTGGGAGTAACTTAGCTAAT 59.214 37.037 6.64 0.00 0.00 1.73
90 91 9.075678 GTCATAGTGGGAGTAACTTAGCTAATA 57.924 37.037 6.64 0.00 0.00 0.98
91 92 9.298250 TCATAGTGGGAGTAACTTAGCTAATAG 57.702 37.037 6.64 0.00 0.00 1.73
92 93 6.408107 AGTGGGAGTAACTTAGCTAATAGC 57.592 41.667 6.64 3.66 42.84 2.97
93 94 5.897824 AGTGGGAGTAACTTAGCTAATAGCA 59.102 40.000 15.28 0.00 45.56 3.49
94 95 6.555360 AGTGGGAGTAACTTAGCTAATAGCAT 59.445 38.462 15.28 2.50 45.56 3.79
95 96 7.728981 AGTGGGAGTAACTTAGCTAATAGCATA 59.271 37.037 15.28 0.72 45.56 3.14
96 97 8.030106 GTGGGAGTAACTTAGCTAATAGCATAG 58.970 40.741 15.28 12.61 45.56 2.23
97 98 7.036829 GGGAGTAACTTAGCTAATAGCATAGC 58.963 42.308 15.28 7.81 45.56 2.97
104 105 2.347731 GCTAATAGCATAGCGGGTTCC 58.652 52.381 7.49 0.00 41.89 3.62
105 106 2.289444 GCTAATAGCATAGCGGGTTCCA 60.289 50.000 7.49 0.00 41.89 3.53
106 107 3.805807 GCTAATAGCATAGCGGGTTCCAA 60.806 47.826 7.49 0.00 41.89 3.53
107 108 2.256117 ATAGCATAGCGGGTTCCAAC 57.744 50.000 0.00 0.00 0.00 3.77
108 109 0.906066 TAGCATAGCGGGTTCCAACA 59.094 50.000 0.00 0.00 0.00 3.33
109 110 0.676782 AGCATAGCGGGTTCCAACAC 60.677 55.000 0.00 0.00 0.00 3.32
110 111 0.958382 GCATAGCGGGTTCCAACACA 60.958 55.000 0.00 0.00 31.01 3.72
111 112 1.529226 CATAGCGGGTTCCAACACAA 58.471 50.000 0.00 0.00 31.01 3.33
112 113 1.883275 CATAGCGGGTTCCAACACAAA 59.117 47.619 0.00 0.00 31.01 2.83
113 114 2.279935 TAGCGGGTTCCAACACAAAT 57.720 45.000 0.00 0.00 31.01 2.32
114 115 1.408969 AGCGGGTTCCAACACAAATT 58.591 45.000 0.00 0.00 31.01 1.82
115 116 1.760029 AGCGGGTTCCAACACAAATTT 59.240 42.857 0.00 0.00 31.01 1.82
116 117 1.864082 GCGGGTTCCAACACAAATTTG 59.136 47.619 16.67 16.67 31.01 2.32
117 118 1.864082 CGGGTTCCAACACAAATTTGC 59.136 47.619 18.12 0.00 31.01 3.68
118 119 2.482839 CGGGTTCCAACACAAATTTGCT 60.483 45.455 18.12 2.95 31.01 3.91
119 120 3.540617 GGGTTCCAACACAAATTTGCTT 58.459 40.909 18.12 6.96 31.01 3.91
120 121 4.698575 GGGTTCCAACACAAATTTGCTTA 58.301 39.130 18.12 0.00 31.01 3.09
121 122 5.304778 GGGTTCCAACACAAATTTGCTTAT 58.695 37.500 18.12 0.00 31.01 1.73
122 123 5.179182 GGGTTCCAACACAAATTTGCTTATG 59.821 40.000 18.12 11.03 31.01 1.90
123 124 5.757808 GGTTCCAACACAAATTTGCTTATGT 59.242 36.000 18.12 11.66 0.00 2.29
124 125 6.292811 GGTTCCAACACAAATTTGCTTATGTG 60.293 38.462 18.12 10.75 46.52 3.21
125 126 6.154203 TCCAACACAAATTTGCTTATGTGA 57.846 33.333 18.12 6.80 44.52 3.58
126 127 6.757237 TCCAACACAAATTTGCTTATGTGAT 58.243 32.000 18.12 0.52 44.52 3.06
127 128 7.890515 TCCAACACAAATTTGCTTATGTGATA 58.109 30.769 18.12 2.06 44.52 2.15
128 129 8.530311 TCCAACACAAATTTGCTTATGTGATAT 58.470 29.630 18.12 0.00 44.52 1.63
129 130 8.597227 CCAACACAAATTTGCTTATGTGATATG 58.403 33.333 18.12 9.33 44.52 1.78
130 131 9.142515 CAACACAAATTTGCTTATGTGATATGT 57.857 29.630 18.12 7.37 44.52 2.29
132 133 9.787532 ACACAAATTTGCTTATGTGATATGTAC 57.212 29.630 18.12 0.00 44.52 2.90
153 154 9.950496 ATGTACTTAATGAGAAGAGATGTGTTT 57.050 29.630 0.00 0.00 0.00 2.83
157 158 9.868277 ACTTAATGAGAAGAGATGTGTTTAGAG 57.132 33.333 0.00 0.00 0.00 2.43
158 159 9.868277 CTTAATGAGAAGAGATGTGTTTAGAGT 57.132 33.333 0.00 0.00 0.00 3.24
204 205 9.868277 ACATAACACTTTCTAAGAGAAGATGAG 57.132 33.333 8.13 0.00 35.37 2.90
205 206 9.868277 CATAACACTTTCTAAGAGAAGATGAGT 57.132 33.333 8.13 0.00 35.37 3.41
209 210 9.699703 ACACTTTCTAAGAGAAGATGAGTTTAC 57.300 33.333 8.13 0.00 35.37 2.01
210 211 9.698309 CACTTTCTAAGAGAAGATGAGTTTACA 57.302 33.333 0.00 0.00 35.37 2.41
213 214 8.764524 TTCTAAGAGAAGATGAGTTTACAAGC 57.235 34.615 0.00 0.00 29.50 4.01
214 215 8.128322 TCTAAGAGAAGATGAGTTTACAAGCT 57.872 34.615 0.00 0.00 0.00 3.74
215 216 9.244292 TCTAAGAGAAGATGAGTTTACAAGCTA 57.756 33.333 0.00 0.00 0.00 3.32
216 217 9.862371 CTAAGAGAAGATGAGTTTACAAGCTAA 57.138 33.333 0.00 0.00 0.00 3.09
257 258 8.928270 ATGACACTACTACTATGTTACTTTGC 57.072 34.615 0.00 0.00 0.00 3.68
258 259 7.888424 TGACACTACTACTATGTTACTTTGCA 58.112 34.615 0.00 0.00 0.00 4.08
259 260 8.361889 TGACACTACTACTATGTTACTTTGCAA 58.638 33.333 0.00 0.00 0.00 4.08
260 261 8.758633 ACACTACTACTATGTTACTTTGCAAG 57.241 34.615 0.00 0.00 0.00 4.01
261 262 8.582437 ACACTACTACTATGTTACTTTGCAAGA 58.418 33.333 0.00 0.00 0.00 3.02
262 263 9.587772 CACTACTACTATGTTACTTTGCAAGAT 57.412 33.333 0.00 0.00 0.00 2.40
266 267 9.587772 ACTACTATGTTACTTTGCAAGATAGTG 57.412 33.333 11.67 6.55 40.61 2.74
267 268 9.803315 CTACTATGTTACTTTGCAAGATAGTGA 57.197 33.333 11.67 1.82 40.61 3.41
268 269 8.480643 ACTATGTTACTTTGCAAGATAGTGAC 57.519 34.615 14.52 14.52 39.60 3.67
269 270 8.314751 ACTATGTTACTTTGCAAGATAGTGACT 58.685 33.333 19.42 11.23 39.60 3.41
270 271 7.986085 ATGTTACTTTGCAAGATAGTGACTT 57.014 32.000 19.42 13.38 31.78 3.01
272 273 8.534333 TGTTACTTTGCAAGATAGTGACTTAG 57.466 34.615 19.42 5.76 31.78 2.18
273 274 8.364894 TGTTACTTTGCAAGATAGTGACTTAGA 58.635 33.333 19.42 3.51 31.78 2.10
274 275 8.648968 GTTACTTTGCAAGATAGTGACTTAGAC 58.351 37.037 14.25 0.89 0.00 2.59
275 276 6.998802 ACTTTGCAAGATAGTGACTTAGACT 58.001 36.000 0.00 0.00 0.00 3.24
276 277 8.123639 ACTTTGCAAGATAGTGACTTAGACTA 57.876 34.615 0.00 0.00 0.00 2.59
277 278 8.247562 ACTTTGCAAGATAGTGACTTAGACTAG 58.752 37.037 0.00 0.00 29.52 2.57
278 279 7.704578 TTGCAAGATAGTGACTTAGACTAGT 57.295 36.000 0.00 0.00 29.52 2.57
279 280 7.089770 TGCAAGATAGTGACTTAGACTAGTG 57.910 40.000 0.00 0.00 29.52 2.74
280 281 6.659668 TGCAAGATAGTGACTTAGACTAGTGT 59.340 38.462 0.00 0.00 29.52 3.55
281 282 7.148222 TGCAAGATAGTGACTTAGACTAGTGTC 60.148 40.741 0.00 1.69 43.22 3.67
282 283 7.148222 GCAAGATAGTGACTTAGACTAGTGTCA 60.148 40.741 0.00 4.75 45.20 3.58
283 284 8.898761 CAAGATAGTGACTTAGACTAGTGTCAT 58.101 37.037 14.69 8.32 45.20 3.06
287 288 7.033530 AGTGACTTAGACTAGTGTCATATGC 57.966 40.000 14.69 4.79 45.20 3.14
288 289 6.603599 AGTGACTTAGACTAGTGTCATATGCA 59.396 38.462 14.69 0.00 45.20 3.96
289 290 7.286546 AGTGACTTAGACTAGTGTCATATGCAT 59.713 37.037 14.69 3.79 45.20 3.96
290 291 7.380870 GTGACTTAGACTAGTGTCATATGCATG 59.619 40.741 10.16 0.00 45.20 4.06
291 292 7.285401 TGACTTAGACTAGTGTCATATGCATGA 59.715 37.037 10.16 0.00 45.20 3.07
292 293 8.011844 ACTTAGACTAGTGTCATATGCATGAA 57.988 34.615 10.16 0.00 42.79 2.57
293 294 8.478066 ACTTAGACTAGTGTCATATGCATGAAA 58.522 33.333 10.16 0.00 42.79 2.69
294 295 8.648557 TTAGACTAGTGTCATATGCATGAAAC 57.351 34.615 10.16 5.95 46.12 2.78
304 305 9.783081 TGTCATATGCATGAAACTGATATAAGT 57.217 29.630 10.16 0.00 42.79 2.24
310 311 8.662781 TGCATGAAACTGATATAAGTTACTCC 57.337 34.615 5.86 0.00 39.48 3.85
311 312 7.715249 TGCATGAAACTGATATAAGTTACTCCC 59.285 37.037 5.86 0.00 39.48 4.30
312 313 7.173390 GCATGAAACTGATATAAGTTACTCCCC 59.827 40.741 5.86 0.00 39.48 4.81
313 314 7.743116 TGAAACTGATATAAGTTACTCCCCA 57.257 36.000 5.86 0.00 39.48 4.96
314 315 7.562135 TGAAACTGATATAAGTTACTCCCCAC 58.438 38.462 5.86 0.00 39.48 4.61
315 316 7.402071 TGAAACTGATATAAGTTACTCCCCACT 59.598 37.037 5.86 0.00 39.48 4.00
316 317 7.750947 AACTGATATAAGTTACTCCCCACTT 57.249 36.000 3.38 0.00 38.62 3.16
317 318 7.750947 ACTGATATAAGTTACTCCCCACTTT 57.249 36.000 0.00 0.00 34.92 2.66
318 319 7.565680 ACTGATATAAGTTACTCCCCACTTTG 58.434 38.462 0.00 0.00 34.92 2.77
319 320 7.402071 ACTGATATAAGTTACTCCCCACTTTGA 59.598 37.037 0.00 0.00 34.92 2.69
320 321 7.562135 TGATATAAGTTACTCCCCACTTTGAC 58.438 38.462 0.00 0.00 34.92 3.18
321 322 3.503800 AAGTTACTCCCCACTTTGACC 57.496 47.619 0.00 0.00 28.27 4.02
322 323 2.414612 AGTTACTCCCCACTTTGACCA 58.585 47.619 0.00 0.00 0.00 4.02
323 324 2.372172 AGTTACTCCCCACTTTGACCAG 59.628 50.000 0.00 0.00 0.00 4.00
324 325 0.690762 TACTCCCCACTTTGACCAGC 59.309 55.000 0.00 0.00 0.00 4.85
325 326 1.303643 CTCCCCACTTTGACCAGCC 60.304 63.158 0.00 0.00 0.00 4.85
326 327 1.774217 TCCCCACTTTGACCAGCCT 60.774 57.895 0.00 0.00 0.00 4.58
327 328 0.474854 TCCCCACTTTGACCAGCCTA 60.475 55.000 0.00 0.00 0.00 3.93
328 329 0.404040 CCCCACTTTGACCAGCCTAA 59.596 55.000 0.00 0.00 0.00 2.69
329 330 1.005924 CCCCACTTTGACCAGCCTAAT 59.994 52.381 0.00 0.00 0.00 1.73
330 331 2.241176 CCCCACTTTGACCAGCCTAATA 59.759 50.000 0.00 0.00 0.00 0.98
331 332 3.545703 CCCACTTTGACCAGCCTAATAG 58.454 50.000 0.00 0.00 0.00 1.73
332 333 3.545703 CCACTTTGACCAGCCTAATAGG 58.454 50.000 0.99 0.99 38.80 2.57
346 347 5.596836 CCTAATAGGCCAAAGCATGAAAA 57.403 39.130 5.01 0.00 42.56 2.29
347 348 6.165700 CCTAATAGGCCAAAGCATGAAAAT 57.834 37.500 5.01 0.00 42.56 1.82
348 349 7.288810 CCTAATAGGCCAAAGCATGAAAATA 57.711 36.000 5.01 0.00 42.56 1.40
349 350 7.147976 CCTAATAGGCCAAAGCATGAAAATAC 58.852 38.462 5.01 0.00 42.56 1.89
350 351 6.543430 AATAGGCCAAAGCATGAAAATACA 57.457 33.333 5.01 0.00 42.56 2.29
351 352 6.736110 ATAGGCCAAAGCATGAAAATACAT 57.264 33.333 5.01 0.00 42.56 2.29
352 353 4.761975 AGGCCAAAGCATGAAAATACATG 58.238 39.130 5.01 0.00 46.96 3.21
353 354 4.223477 AGGCCAAAGCATGAAAATACATGT 59.777 37.500 5.01 2.69 46.25 3.21
354 355 5.421693 AGGCCAAAGCATGAAAATACATGTA 59.578 36.000 8.27 8.27 46.25 2.29
355 356 5.750067 GGCCAAAGCATGAAAATACATGTAG 59.250 40.000 11.91 0.00 46.25 2.74
356 357 6.332630 GCCAAAGCATGAAAATACATGTAGT 58.667 36.000 11.91 5.77 46.25 2.73
357 358 6.813152 GCCAAAGCATGAAAATACATGTAGTT 59.187 34.615 12.58 12.58 46.25 2.24
358 359 7.973388 GCCAAAGCATGAAAATACATGTAGTTA 59.027 33.333 18.08 5.09 46.25 2.24
401 402 4.478699 CTCATGTGCGATGTTTTTCATGT 58.521 39.130 0.00 0.00 36.83 3.21
418 419 2.655090 TGTGAATTGGAAGGAGTGCA 57.345 45.000 0.00 0.00 0.00 4.57
450 451 2.436469 AATGGCTGCGATGCGACA 60.436 55.556 0.00 0.00 0.00 4.35
465 466 3.550561 TGCGACATTTTAGAAGCAAACG 58.449 40.909 0.00 0.00 0.00 3.60
474 475 1.927895 AGAAGCAAACGATAGCTCCG 58.072 50.000 6.86 6.86 40.90 4.63
524 525 3.564053 TGAAAAACACGAGGGGTTAGT 57.436 42.857 0.00 0.00 0.00 2.24
527 528 2.538512 AAACACGAGGGGTTAGTGAC 57.461 50.000 1.63 0.00 39.04 3.67
530 531 1.254026 CACGAGGGGTTAGTGACTCA 58.746 55.000 0.00 0.00 38.06 3.41
553 554 0.107066 TATGACACGCGGGACCTAGA 60.107 55.000 19.19 0.00 0.00 2.43
568 569 2.496070 ACCTAGAAGTTACTCGCATGCA 59.504 45.455 19.57 4.02 0.00 3.96
638 639 4.473520 CCGACCCGAGCAAGCCAT 62.474 66.667 0.00 0.00 0.00 4.40
1011 1038 3.916544 CCGCGCATGGAGCCTCTA 61.917 66.667 8.75 0.00 41.38 2.43
1107 1134 1.446366 GGGGCAGGTTAGATCCGTC 59.554 63.158 0.00 0.00 0.00 4.79
1259 1297 0.178967 TGGGCATTTTGAGTGGCTCA 60.179 50.000 0.00 0.00 41.43 4.26
1415 1453 8.862550 ACTGAAGTGTGAATTGAAGAAAATTC 57.137 30.769 3.29 3.29 43.76 2.17
1454 1492 3.125829 TCTGATCGATTTGAAGCAGCAAC 59.874 43.478 0.00 0.00 34.71 4.17
1688 1728 0.625849 AGGGGCCCTATTCAGTGTTG 59.374 55.000 27.62 0.00 28.47 3.33
1726 1766 8.026607 CCTCTGTTTTTGTTCTTCAGTTAACAA 58.973 33.333 8.61 0.00 42.27 2.83
1819 1865 5.423290 AGAAAATGGGCCCTGAGAAAATAAG 59.577 40.000 25.70 0.00 0.00 1.73
2259 2309 7.492524 TCCACAAATAATAGCACAAAACACAA 58.507 30.769 0.00 0.00 0.00 3.33
2494 2548 3.565670 GGTTCTTCTTCTCCTCCTCCTCT 60.566 52.174 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.779529 ATAATGCTTAGAACCATGGCTTG 57.220 39.130 13.04 0.10 0.00 4.01
1 2 6.605119 ACTATAATGCTTAGAACCATGGCTT 58.395 36.000 13.04 5.39 0.00 4.35
4 5 5.120830 GCGACTATAATGCTTAGAACCATGG 59.879 44.000 11.19 11.19 0.00 3.66
5 6 5.120830 GGCGACTATAATGCTTAGAACCATG 59.879 44.000 0.00 0.00 0.00 3.66
6 7 5.221641 TGGCGACTATAATGCTTAGAACCAT 60.222 40.000 0.00 0.00 0.00 3.55
7 8 4.100344 TGGCGACTATAATGCTTAGAACCA 59.900 41.667 0.00 0.00 0.00 3.67
8 9 4.628074 TGGCGACTATAATGCTTAGAACC 58.372 43.478 0.00 0.00 0.00 3.62
9 10 5.402867 GTCTGGCGACTATAATGCTTAGAAC 59.597 44.000 0.00 0.00 37.19 3.01
10 11 5.068591 TGTCTGGCGACTATAATGCTTAGAA 59.931 40.000 10.03 0.00 40.86 2.10
11 12 4.583073 TGTCTGGCGACTATAATGCTTAGA 59.417 41.667 10.03 0.00 40.86 2.10
12 13 4.871513 TGTCTGGCGACTATAATGCTTAG 58.128 43.478 10.03 0.00 40.86 2.18
13 14 4.796290 GCTGTCTGGCGACTATAATGCTTA 60.796 45.833 10.03 0.00 40.86 3.09
14 15 3.722147 CTGTCTGGCGACTATAATGCTT 58.278 45.455 10.03 0.00 40.86 3.91
15 16 2.546795 GCTGTCTGGCGACTATAATGCT 60.547 50.000 10.03 0.00 40.86 3.79
16 17 1.795286 GCTGTCTGGCGACTATAATGC 59.205 52.381 10.03 0.00 40.86 3.56
17 18 3.055591 CAGCTGTCTGGCGACTATAATG 58.944 50.000 5.25 1.12 40.86 1.90
18 19 2.546795 GCAGCTGTCTGGCGACTATAAT 60.547 50.000 16.64 0.00 40.86 1.28
19 20 1.202417 GCAGCTGTCTGGCGACTATAA 60.202 52.381 16.64 0.00 40.86 0.98
20 21 0.385751 GCAGCTGTCTGGCGACTATA 59.614 55.000 16.64 0.00 40.86 1.31
21 22 1.142748 GCAGCTGTCTGGCGACTAT 59.857 57.895 16.64 0.00 40.86 2.12
22 23 1.979155 AGCAGCTGTCTGGCGACTA 60.979 57.895 16.64 0.00 40.86 2.59
23 24 3.309506 AGCAGCTGTCTGGCGACT 61.310 61.111 16.64 0.00 40.86 4.18
24 25 3.117171 CAGCAGCTGTCTGGCGAC 61.117 66.667 22.77 3.44 40.65 5.19
27 28 2.750637 ATGCAGCAGCTGTCTGGC 60.751 61.111 27.90 22.16 42.74 4.85
28 29 3.052620 GCATGCAGCAGCTGTCTGG 62.053 63.158 27.90 17.88 44.79 3.86
29 30 2.485582 GCATGCAGCAGCTGTCTG 59.514 61.111 23.60 24.89 44.79 3.51
42 43 1.947013 CCTTAGGAGCGCATGCATG 59.053 57.895 22.70 22.70 46.23 4.06
43 44 1.895707 GCCTTAGGAGCGCATGCAT 60.896 57.895 19.57 5.12 46.23 3.96
44 45 1.685355 TAGCCTTAGGAGCGCATGCA 61.685 55.000 19.57 0.00 46.23 3.96
45 46 0.948141 CTAGCCTTAGGAGCGCATGC 60.948 60.000 11.47 7.91 43.24 4.06
46 47 0.390860 ACTAGCCTTAGGAGCGCATG 59.609 55.000 11.47 0.00 34.64 4.06
47 48 0.676736 GACTAGCCTTAGGAGCGCAT 59.323 55.000 11.47 0.00 34.64 4.73
48 49 0.683179 TGACTAGCCTTAGGAGCGCA 60.683 55.000 11.47 0.00 34.64 6.09
49 50 0.676736 ATGACTAGCCTTAGGAGCGC 59.323 55.000 0.69 0.00 34.64 5.92
50 51 3.057876 CACTATGACTAGCCTTAGGAGCG 60.058 52.174 0.69 0.00 34.64 5.03
51 52 3.257127 CCACTATGACTAGCCTTAGGAGC 59.743 52.174 0.69 0.00 0.00 4.70
52 53 3.829601 CCCACTATGACTAGCCTTAGGAG 59.170 52.174 0.69 0.00 0.00 3.69
53 54 3.465966 TCCCACTATGACTAGCCTTAGGA 59.534 47.826 0.69 0.00 0.00 2.94
54 55 3.829601 CTCCCACTATGACTAGCCTTAGG 59.170 52.174 0.00 0.00 0.00 2.69
55 56 4.475345 ACTCCCACTATGACTAGCCTTAG 58.525 47.826 0.00 0.00 0.00 2.18
56 57 4.537945 ACTCCCACTATGACTAGCCTTA 57.462 45.455 0.00 0.00 0.00 2.69
57 58 3.406512 ACTCCCACTATGACTAGCCTT 57.593 47.619 0.00 0.00 0.00 4.35
58 59 4.079096 AGTTACTCCCACTATGACTAGCCT 60.079 45.833 0.00 0.00 0.00 4.58
59 60 4.216708 AGTTACTCCCACTATGACTAGCC 58.783 47.826 0.00 0.00 0.00 3.93
60 61 5.855740 AAGTTACTCCCACTATGACTAGC 57.144 43.478 0.00 0.00 0.00 3.42
61 62 6.773685 AGCTAAGTTACTCCCACTATGACTAG 59.226 42.308 0.00 0.00 0.00 2.57
62 63 6.670617 AGCTAAGTTACTCCCACTATGACTA 58.329 40.000 0.00 0.00 0.00 2.59
63 64 5.520751 AGCTAAGTTACTCCCACTATGACT 58.479 41.667 0.00 0.00 0.00 3.41
64 65 5.855740 AGCTAAGTTACTCCCACTATGAC 57.144 43.478 0.00 0.00 0.00 3.06
65 66 9.298250 CTATTAGCTAAGTTACTCCCACTATGA 57.702 37.037 12.54 0.00 0.00 2.15
66 67 8.030106 GCTATTAGCTAAGTTACTCCCACTATG 58.970 40.741 12.54 0.00 38.45 2.23
67 68 7.728981 TGCTATTAGCTAAGTTACTCCCACTAT 59.271 37.037 16.29 0.00 42.97 2.12
68 69 7.064866 TGCTATTAGCTAAGTTACTCCCACTA 58.935 38.462 16.29 0.00 42.97 2.74
69 70 5.897824 TGCTATTAGCTAAGTTACTCCCACT 59.102 40.000 16.29 0.00 42.97 4.00
70 71 6.158023 TGCTATTAGCTAAGTTACTCCCAC 57.842 41.667 16.29 0.00 42.97 4.61
71 72 6.996180 ATGCTATTAGCTAAGTTACTCCCA 57.004 37.500 16.29 1.44 42.97 4.37
72 73 7.036829 GCTATGCTATTAGCTAAGTTACTCCC 58.963 42.308 16.29 0.00 42.97 4.30
73 74 6.748198 CGCTATGCTATTAGCTAAGTTACTCC 59.252 42.308 16.29 0.00 42.97 3.85
74 75 6.748198 CCGCTATGCTATTAGCTAAGTTACTC 59.252 42.308 16.29 0.00 42.97 2.59
75 76 6.350277 CCCGCTATGCTATTAGCTAAGTTACT 60.350 42.308 16.29 0.00 42.97 2.24
76 77 5.805994 CCCGCTATGCTATTAGCTAAGTTAC 59.194 44.000 16.29 2.35 42.97 2.50
77 78 5.479375 ACCCGCTATGCTATTAGCTAAGTTA 59.521 40.000 16.29 0.00 42.97 2.24
78 79 4.283722 ACCCGCTATGCTATTAGCTAAGTT 59.716 41.667 16.29 0.00 42.97 2.66
79 80 3.833070 ACCCGCTATGCTATTAGCTAAGT 59.167 43.478 16.29 3.33 42.97 2.24
80 81 4.457834 ACCCGCTATGCTATTAGCTAAG 57.542 45.455 16.29 13.46 42.97 2.18
81 82 4.322499 GGAACCCGCTATGCTATTAGCTAA 60.322 45.833 16.29 8.99 42.97 3.09
82 83 3.194968 GGAACCCGCTATGCTATTAGCTA 59.805 47.826 16.29 4.09 42.97 3.32
83 84 2.028020 GGAACCCGCTATGCTATTAGCT 60.028 50.000 16.29 0.00 42.97 3.32
84 85 2.289444 TGGAACCCGCTATGCTATTAGC 60.289 50.000 8.80 8.80 42.82 3.09
85 86 3.678056 TGGAACCCGCTATGCTATTAG 57.322 47.619 0.00 0.00 0.00 1.73
86 87 3.134985 TGTTGGAACCCGCTATGCTATTA 59.865 43.478 0.00 0.00 0.00 0.98
87 88 2.092646 TGTTGGAACCCGCTATGCTATT 60.093 45.455 0.00 0.00 0.00 1.73
88 89 1.488812 TGTTGGAACCCGCTATGCTAT 59.511 47.619 0.00 0.00 0.00 2.97
89 90 0.906066 TGTTGGAACCCGCTATGCTA 59.094 50.000 0.00 0.00 0.00 3.49
90 91 0.676782 GTGTTGGAACCCGCTATGCT 60.677 55.000 0.00 0.00 0.00 3.79
91 92 0.958382 TGTGTTGGAACCCGCTATGC 60.958 55.000 0.00 0.00 0.00 3.14
92 93 1.529226 TTGTGTTGGAACCCGCTATG 58.471 50.000 0.00 0.00 0.00 2.23
93 94 2.279935 TTTGTGTTGGAACCCGCTAT 57.720 45.000 0.00 0.00 0.00 2.97
94 95 2.279935 ATTTGTGTTGGAACCCGCTA 57.720 45.000 0.00 0.00 0.00 4.26
95 96 1.408969 AATTTGTGTTGGAACCCGCT 58.591 45.000 0.00 0.00 0.00 5.52
96 97 1.864082 CAAATTTGTGTTGGAACCCGC 59.136 47.619 10.15 0.00 0.00 6.13
97 98 1.864082 GCAAATTTGTGTTGGAACCCG 59.136 47.619 19.03 0.00 0.00 5.28
98 99 3.192541 AGCAAATTTGTGTTGGAACCC 57.807 42.857 19.03 0.00 0.00 4.11
99 100 5.757808 ACATAAGCAAATTTGTGTTGGAACC 59.242 36.000 19.03 0.00 29.51 3.62
100 101 6.478344 TCACATAAGCAAATTTGTGTTGGAAC 59.522 34.615 19.03 0.45 40.22 3.62
101 102 6.577103 TCACATAAGCAAATTTGTGTTGGAA 58.423 32.000 19.03 0.54 40.22 3.53
102 103 6.154203 TCACATAAGCAAATTTGTGTTGGA 57.846 33.333 19.03 7.57 40.22 3.53
103 104 8.597227 CATATCACATAAGCAAATTTGTGTTGG 58.403 33.333 19.03 11.68 40.22 3.77
104 105 9.142515 ACATATCACATAAGCAAATTTGTGTTG 57.857 29.630 19.03 13.45 40.22 3.33
106 107 9.787532 GTACATATCACATAAGCAAATTTGTGT 57.212 29.630 19.03 12.32 40.22 3.72
127 128 9.950496 AAACACATCTCTTCTCATTAAGTACAT 57.050 29.630 0.00 0.00 0.00 2.29
131 132 9.868277 CTCTAAACACATCTCTTCTCATTAAGT 57.132 33.333 0.00 0.00 0.00 2.24
132 133 9.868277 ACTCTAAACACATCTCTTCTCATTAAG 57.132 33.333 0.00 0.00 0.00 1.85
178 179 9.868277 CTCATCTTCTCTTAGAAAGTGTTATGT 57.132 33.333 0.00 0.00 33.19 2.29
179 180 9.868277 ACTCATCTTCTCTTAGAAAGTGTTATG 57.132 33.333 0.00 0.00 33.19 1.90
183 184 9.699703 GTAAACTCATCTTCTCTTAGAAAGTGT 57.300 33.333 0.00 0.00 33.19 3.55
184 185 9.698309 TGTAAACTCATCTTCTCTTAGAAAGTG 57.302 33.333 0.00 0.00 33.19 3.16
187 188 9.209175 GCTTGTAAACTCATCTTCTCTTAGAAA 57.791 33.333 0.00 0.00 33.19 2.52
188 189 8.589338 AGCTTGTAAACTCATCTTCTCTTAGAA 58.411 33.333 0.00 0.00 32.50 2.10
189 190 8.128322 AGCTTGTAAACTCATCTTCTCTTAGA 57.872 34.615 0.00 0.00 0.00 2.10
190 191 9.862371 TTAGCTTGTAAACTCATCTTCTCTTAG 57.138 33.333 0.00 0.00 0.00 2.18
232 233 8.528643 TGCAAAGTAACATAGTAGTAGTGTCAT 58.471 33.333 0.00 0.00 0.00 3.06
233 234 7.888424 TGCAAAGTAACATAGTAGTAGTGTCA 58.112 34.615 0.00 0.00 0.00 3.58
234 235 8.752766 TTGCAAAGTAACATAGTAGTAGTGTC 57.247 34.615 0.00 0.00 0.00 3.67
235 236 8.582437 TCTTGCAAAGTAACATAGTAGTAGTGT 58.418 33.333 0.00 0.00 46.34 3.55
236 237 8.981724 TCTTGCAAAGTAACATAGTAGTAGTG 57.018 34.615 0.00 0.00 46.34 2.74
240 241 9.587772 CACTATCTTGCAAAGTAACATAGTAGT 57.412 33.333 0.00 0.00 46.34 2.73
241 242 9.803315 TCACTATCTTGCAAAGTAACATAGTAG 57.197 33.333 0.00 2.57 46.34 2.57
242 243 9.582431 GTCACTATCTTGCAAAGTAACATAGTA 57.418 33.333 0.00 0.00 46.34 1.82
243 244 8.314751 AGTCACTATCTTGCAAAGTAACATAGT 58.685 33.333 0.00 3.32 46.34 2.12
244 245 8.709386 AGTCACTATCTTGCAAAGTAACATAG 57.291 34.615 0.00 2.74 46.34 2.23
246 247 7.986085 AAGTCACTATCTTGCAAAGTAACAT 57.014 32.000 0.00 0.00 46.34 2.71
247 248 8.364894 TCTAAGTCACTATCTTGCAAAGTAACA 58.635 33.333 0.00 0.00 46.34 2.41
248 249 8.648968 GTCTAAGTCACTATCTTGCAAAGTAAC 58.351 37.037 0.00 0.00 46.34 2.50
249 250 8.585881 AGTCTAAGTCACTATCTTGCAAAGTAA 58.414 33.333 0.00 0.00 46.34 2.24
250 251 8.123639 AGTCTAAGTCACTATCTTGCAAAGTA 57.876 34.615 0.00 0.00 46.34 2.24
251 252 6.998802 AGTCTAAGTCACTATCTTGCAAAGT 58.001 36.000 0.00 0.00 46.34 2.66
253 254 8.029522 CACTAGTCTAAGTCACTATCTTGCAAA 58.970 37.037 0.00 0.00 0.00 3.68
254 255 7.176865 ACACTAGTCTAAGTCACTATCTTGCAA 59.823 37.037 0.00 0.00 0.00 4.08
255 256 6.659668 ACACTAGTCTAAGTCACTATCTTGCA 59.340 38.462 0.00 0.00 0.00 4.08
256 257 7.090953 ACACTAGTCTAAGTCACTATCTTGC 57.909 40.000 0.00 0.00 0.00 4.01
257 258 8.270080 TGACACTAGTCTAAGTCACTATCTTG 57.730 38.462 9.13 0.00 45.20 3.02
261 262 8.788806 GCATATGACACTAGTCTAAGTCACTAT 58.211 37.037 14.09 10.76 45.20 2.12
262 263 7.773690 TGCATATGACACTAGTCTAAGTCACTA 59.226 37.037 14.09 9.41 45.20 2.74
263 264 6.603599 TGCATATGACACTAGTCTAAGTCACT 59.396 38.462 14.09 7.96 45.20 3.41
264 265 6.796426 TGCATATGACACTAGTCTAAGTCAC 58.204 40.000 14.09 4.79 45.20 3.67
265 266 7.285401 TCATGCATATGACACTAGTCTAAGTCA 59.715 37.037 14.14 14.14 45.20 3.41
266 267 7.652727 TCATGCATATGACACTAGTCTAAGTC 58.347 38.462 6.97 0.00 45.20 3.01
267 268 7.588497 TCATGCATATGACACTAGTCTAAGT 57.412 36.000 6.97 0.00 45.20 2.24
268 269 8.759641 GTTTCATGCATATGACACTAGTCTAAG 58.240 37.037 6.97 0.00 42.79 2.18
269 270 8.478066 AGTTTCATGCATATGACACTAGTCTAA 58.522 33.333 6.97 0.00 46.92 2.10
270 271 8.011844 AGTTTCATGCATATGACACTAGTCTA 57.988 34.615 6.97 0.00 46.92 2.59
271 272 6.882656 AGTTTCATGCATATGACACTAGTCT 58.117 36.000 6.97 0.00 46.92 3.24
278 279 9.783081 ACTTATATCAGTTTCATGCATATGACA 57.217 29.630 6.97 4.57 42.79 3.58
284 285 9.277783 GGAGTAACTTATATCAGTTTCATGCAT 57.722 33.333 7.57 0.00 38.07 3.96
285 286 7.715249 GGGAGTAACTTATATCAGTTTCATGCA 59.285 37.037 7.57 0.00 38.07 3.96
286 287 7.173390 GGGGAGTAACTTATATCAGTTTCATGC 59.827 40.741 7.57 0.99 38.07 4.06
287 288 8.210946 TGGGGAGTAACTTATATCAGTTTCATG 58.789 37.037 7.57 0.00 38.07 3.07
288 289 8.211629 GTGGGGAGTAACTTATATCAGTTTCAT 58.788 37.037 7.57 0.00 38.07 2.57
289 290 7.402071 AGTGGGGAGTAACTTATATCAGTTTCA 59.598 37.037 7.57 0.00 38.07 2.69
290 291 7.793036 AGTGGGGAGTAACTTATATCAGTTTC 58.207 38.462 7.57 3.33 38.07 2.78
291 292 7.750947 AGTGGGGAGTAACTTATATCAGTTT 57.249 36.000 7.57 0.00 38.07 2.66
292 293 7.750947 AAGTGGGGAGTAACTTATATCAGTT 57.249 36.000 7.42 7.42 40.28 3.16
293 294 7.402071 TCAAAGTGGGGAGTAACTTATATCAGT 59.598 37.037 0.00 0.00 35.60 3.41
294 295 7.711339 GTCAAAGTGGGGAGTAACTTATATCAG 59.289 40.741 0.00 0.00 35.60 2.90
295 296 7.365295 GGTCAAAGTGGGGAGTAACTTATATCA 60.365 40.741 0.00 0.00 35.60 2.15
296 297 6.990939 GGTCAAAGTGGGGAGTAACTTATATC 59.009 42.308 0.00 0.00 35.60 1.63
297 298 6.445786 TGGTCAAAGTGGGGAGTAACTTATAT 59.554 38.462 0.00 0.00 35.60 0.86
298 299 5.786457 TGGTCAAAGTGGGGAGTAACTTATA 59.214 40.000 0.00 0.00 35.60 0.98
299 300 4.600111 TGGTCAAAGTGGGGAGTAACTTAT 59.400 41.667 0.00 0.00 35.60 1.73
300 301 3.975312 TGGTCAAAGTGGGGAGTAACTTA 59.025 43.478 0.00 0.00 35.60 2.24
301 302 2.781174 TGGTCAAAGTGGGGAGTAACTT 59.219 45.455 0.00 0.00 38.25 2.66
302 303 2.372172 CTGGTCAAAGTGGGGAGTAACT 59.628 50.000 0.00 0.00 0.00 2.24
303 304 2.779506 CTGGTCAAAGTGGGGAGTAAC 58.220 52.381 0.00 0.00 0.00 2.50
304 305 1.073284 GCTGGTCAAAGTGGGGAGTAA 59.927 52.381 0.00 0.00 0.00 2.24
305 306 0.690762 GCTGGTCAAAGTGGGGAGTA 59.309 55.000 0.00 0.00 0.00 2.59
306 307 1.456287 GCTGGTCAAAGTGGGGAGT 59.544 57.895 0.00 0.00 0.00 3.85
307 308 1.303643 GGCTGGTCAAAGTGGGGAG 60.304 63.158 0.00 0.00 0.00 4.30
308 309 0.474854 TAGGCTGGTCAAAGTGGGGA 60.475 55.000 0.00 0.00 0.00 4.81
309 310 0.404040 TTAGGCTGGTCAAAGTGGGG 59.596 55.000 0.00 0.00 0.00 4.96
310 311 2.514458 ATTAGGCTGGTCAAAGTGGG 57.486 50.000 0.00 0.00 0.00 4.61
311 312 3.545703 CCTATTAGGCTGGTCAAAGTGG 58.454 50.000 0.00 0.00 0.00 4.00
324 325 5.596836 TTTTCATGCTTTGGCCTATTAGG 57.403 39.130 3.32 5.28 38.80 2.69
325 326 7.715657 TGTATTTTCATGCTTTGGCCTATTAG 58.284 34.615 3.32 0.00 37.74 1.73
326 327 7.652524 TGTATTTTCATGCTTTGGCCTATTA 57.347 32.000 3.32 0.00 37.74 0.98
327 328 6.543430 TGTATTTTCATGCTTTGGCCTATT 57.457 33.333 3.32 0.00 37.74 1.73
328 329 6.098695 ACATGTATTTTCATGCTTTGGCCTAT 59.901 34.615 3.32 0.00 46.15 2.57
329 330 5.421693 ACATGTATTTTCATGCTTTGGCCTA 59.578 36.000 3.32 0.00 46.15 3.93
330 331 4.223477 ACATGTATTTTCATGCTTTGGCCT 59.777 37.500 3.32 0.00 46.15 5.19
331 332 4.506758 ACATGTATTTTCATGCTTTGGCC 58.493 39.130 0.00 0.00 46.15 5.36
332 333 6.332630 ACTACATGTATTTTCATGCTTTGGC 58.667 36.000 5.91 0.00 46.15 4.52
347 348 8.984855 GGCCCCTGTAATATATAACTACATGTA 58.015 37.037 5.25 5.25 0.00 2.29
348 349 7.459763 TGGCCCCTGTAATATATAACTACATGT 59.540 37.037 2.69 2.69 0.00 3.21
349 350 7.857456 TGGCCCCTGTAATATATAACTACATG 58.143 38.462 0.00 0.00 0.00 3.21
350 351 8.457585 TTGGCCCCTGTAATATATAACTACAT 57.542 34.615 0.00 0.00 0.00 2.29
351 352 7.875338 TTGGCCCCTGTAATATATAACTACA 57.125 36.000 0.00 7.47 0.00 2.74
353 354 8.711170 GCTATTGGCCCCTGTAATATATAACTA 58.289 37.037 0.00 0.00 34.27 2.24
354 355 7.406151 AGCTATTGGCCCCTGTAATATATAACT 59.594 37.037 0.00 0.00 43.05 2.24
355 356 7.574607 AGCTATTGGCCCCTGTAATATATAAC 58.425 38.462 0.00 0.00 43.05 1.89
356 357 7.404688 TGAGCTATTGGCCCCTGTAATATATAA 59.595 37.037 0.00 0.00 43.05 0.98
357 358 6.906339 TGAGCTATTGGCCCCTGTAATATATA 59.094 38.462 0.00 0.00 43.05 0.86
358 359 5.731187 TGAGCTATTGGCCCCTGTAATATAT 59.269 40.000 0.00 0.00 43.05 0.86
359 360 5.097948 TGAGCTATTGGCCCCTGTAATATA 58.902 41.667 0.00 0.00 43.05 0.86
360 361 3.916349 TGAGCTATTGGCCCCTGTAATAT 59.084 43.478 0.00 0.00 43.05 1.28
361 362 3.322862 TGAGCTATTGGCCCCTGTAATA 58.677 45.455 0.00 0.00 43.05 0.98
362 363 2.135189 TGAGCTATTGGCCCCTGTAAT 58.865 47.619 0.00 0.00 43.05 1.89
363 364 1.590591 TGAGCTATTGGCCCCTGTAA 58.409 50.000 0.00 0.00 43.05 2.41
364 365 1.421268 CATGAGCTATTGGCCCCTGTA 59.579 52.381 0.00 0.00 43.05 2.74
365 366 0.184451 CATGAGCTATTGGCCCCTGT 59.816 55.000 0.00 0.00 43.05 4.00
366 367 0.184451 ACATGAGCTATTGGCCCCTG 59.816 55.000 0.00 0.00 43.05 4.45
367 368 0.184451 CACATGAGCTATTGGCCCCT 59.816 55.000 0.00 0.00 43.05 4.79
382 383 4.502171 TCACATGAAAAACATCGCACAT 57.498 36.364 0.00 0.00 37.07 3.21
401 402 1.879380 CGTTGCACTCCTTCCAATTCA 59.121 47.619 0.00 0.00 0.00 2.57
418 419 2.627699 AGCCATTCATTCCAACAACGTT 59.372 40.909 0.00 0.00 0.00 3.99
450 451 5.006746 CGGAGCTATCGTTTGCTTCTAAAAT 59.993 40.000 3.98 0.00 39.91 1.82
465 466 1.344458 CATGTCGCATCGGAGCTATC 58.656 55.000 0.00 0.00 0.00 2.08
474 475 1.089920 AAACAGAGCCATGTCGCATC 58.910 50.000 0.00 0.00 31.50 3.91
524 525 2.324860 CGCGTGTCATAACTTGAGTCA 58.675 47.619 0.00 0.00 34.17 3.41
527 528 0.999406 CCCGCGTGTCATAACTTGAG 59.001 55.000 4.92 0.00 34.17 3.02
530 531 0.390735 GGTCCCGCGTGTCATAACTT 60.391 55.000 4.92 0.00 0.00 2.66
553 554 1.442769 CACCTGCATGCGAGTAACTT 58.557 50.000 14.09 0.00 0.00 2.66
632 633 4.496336 GGCTCGGGCTCATGGCTT 62.496 66.667 7.48 0.00 41.46 4.35
1011 1038 2.097466 CCTCACACAAGTCAAACGCTTT 59.903 45.455 0.00 0.00 0.00 3.51
1259 1297 9.480053 CAATTTCAACCTTTCAACATAGTCATT 57.520 29.630 0.00 0.00 0.00 2.57
1415 1453 2.160219 TCAGATGCTTTAGTTGCTTGCG 59.840 45.455 0.00 0.00 0.00 4.85
1454 1492 2.589720 TGCTCCAGCCATCATATTTGG 58.410 47.619 0.00 0.00 41.18 3.28
1688 1728 5.218139 CAAAAACAGAGGAAACAGAGCATC 58.782 41.667 0.00 0.00 0.00 3.91
1726 1766 5.891551 AGAAACTGAATTTGGGTGTGTACTT 59.108 36.000 0.00 0.00 0.00 2.24
1819 1865 3.455469 GGCTGGTCTTGGGCATGC 61.455 66.667 9.90 9.90 0.00 4.06
2002 2048 5.534278 TGCAACTCATTTAGTTCATGGAACA 59.466 36.000 11.28 0.00 45.64 3.18
2416 2466 7.546778 TCTAGCTTGCTATAGATCTATCGTG 57.453 40.000 18.59 11.22 0.00 4.35


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

AutoCloner maintained by Alex Coulton.