Multiple sequence alignment - TraesCS5A01G056100

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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 TraesCS5A01G056100 chr5A 100.000 4592 0 0 1 4592 52340732 52345323 0.000000e+00 8480.0
1 TraesCS5A01G056100 chr5A 90.261 3481 277 40 419 3877 52418123 52414683 0.000000e+00 4494.0
2 TraesCS5A01G056100 chr5A 95.973 596 22 2 3999 4592 52350167 52350762 0.000000e+00 966.0
3 TraesCS5A01G056100 chr5D 95.800 3857 139 14 160 3999 62297440 62301290 0.000000e+00 6204.0
4 TraesCS5A01G056100 chr5D 90.221 3487 284 40 419 3877 62523207 62519750 0.000000e+00 4497.0
5 TraesCS5A01G056100 chr5D 93.846 65 4 0 3934 3998 62307818 62307882 1.050000e-16 99.0
6 TraesCS5A01G056100 chr5B 90.144 3338 269 42 599 3913 67959003 67962303 0.000000e+00 4287.0
7 TraesCS5A01G056100 chr5B 94.936 2567 100 5 1444 3984 68188441 68185879 0.000000e+00 3993.0
8 TraesCS5A01G056100 chr5B 96.429 616 21 1 835 1450 68189084 68188470 0.000000e+00 1014.0
9 TraesCS5A01G056100 chr5B 92.453 265 15 4 450 709 68189545 68189281 1.560000e-99 374.0
10 TraesCS5A01G056100 chr5B 95.000 160 6 2 1 159 525601141 525601299 2.740000e-62 250.0
11 TraesCS5A01G056100 chr5B 92.308 65 5 0 3934 3998 68176862 68176798 4.890000e-15 93.5
12 TraesCS5A01G056100 chr2B 79.721 1578 272 43 2262 3817 526379637 526381188 0.000000e+00 1098.0
13 TraesCS5A01G056100 chr2B 85.685 489 66 2 2262 2747 525826375 525826862 3.170000e-141 512.0
14 TraesCS5A01G056100 chr2B 86.325 468 61 2 2247 2714 525830108 525830572 1.470000e-139 507.0
15 TraesCS5A01G056100 chr2B 100.000 29 0 0 183 211 237176497 237176525 2.000000e-03 54.7
16 TraesCS5A01G056100 chr2D 79.410 1593 264 47 2262 3817 446603633 446605198 0.000000e+00 1066.0
17 TraesCS5A01G056100 chr2D 86.008 486 67 1 2262 2747 446318666 446319150 1.890000e-143 520.0
18 TraesCS5A01G056100 chr2D 80.534 262 48 3 1186 1446 446600185 446600444 1.010000e-46 198.0
19 TraesCS5A01G056100 chr1A 98.490 596 7 2 3999 4592 487719745 487720340 0.000000e+00 1050.0
20 TraesCS5A01G056100 chr1A 96.134 595 21 2 3999 4592 486684803 486684210 0.000000e+00 970.0
21 TraesCS5A01G056100 chr1A 94.463 596 31 2 3999 4592 565145851 565146446 0.000000e+00 917.0
22 TraesCS5A01G056100 chr4A 97.987 596 10 2 3999 4592 1734672 1735267 0.000000e+00 1033.0
23 TraesCS5A01G056100 chr7A 93.782 595 36 1 3999 4592 70194797 70194203 0.000000e+00 893.0
24 TraesCS5A01G056100 chrUn 89.244 595 63 1 3998 4591 352578046 352577452 0.000000e+00 743.0
25 TraesCS5A01G056100 chr6D 89.244 595 62 2 4000 4592 408885933 408886527 0.000000e+00 743.0
26 TraesCS5A01G056100 chr2A 83.505 776 124 4 3034 3807 590639021 590639794 0.000000e+00 721.0
27 TraesCS5A01G056100 chr2A 81.731 832 145 3 3023 3853 589792296 589793121 0.000000e+00 688.0
28 TraesCS5A01G056100 chr2A 86.965 491 63 1 2257 2747 589791523 589792012 6.710000e-153 551.0
29 TraesCS5A01G056100 chr3B 88.442 597 63 6 3999 4591 778303022 778303616 0.000000e+00 715.0
30 TraesCS5A01G056100 chr3A 95.597 159 7 0 1 159 30752708 30752866 5.900000e-64 255.0
31 TraesCS5A01G056100 chr3A 94.969 159 8 0 1 159 249855409 249855251 2.740000e-62 250.0
32 TraesCS5A01G056100 chr6B 94.969 159 8 0 1 159 718624555 718624397 2.740000e-62 250.0
33 TraesCS5A01G056100 chr6B 94.340 159 9 0 1 159 88720262 88720420 1.280000e-60 244.0
34 TraesCS5A01G056100 chr4B 94.969 159 8 0 1 159 59977991 59977833 2.740000e-62 250.0
35 TraesCS5A01G056100 chr4B 94.969 159 8 0 1 159 315477119 315477277 2.740000e-62 250.0
36 TraesCS5A01G056100 chr7B 94.340 159 9 0 1 159 521120911 521121069 1.280000e-60 244.0
37 TraesCS5A01G056100 chr4D 94.340 159 9 0 1 159 118311193 118311035 1.280000e-60 244.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G056100 chr5A 52340732 52345323 4591 False 8480.000000 8480 100.000 1 4592 1 chr5A.!!$F1 4591
1 TraesCS5A01G056100 chr5A 52414683 52418123 3440 True 4494.000000 4494 90.261 419 3877 1 chr5A.!!$R1 3458
2 TraesCS5A01G056100 chr5A 52350167 52350762 595 False 966.000000 966 95.973 3999 4592 1 chr5A.!!$F2 593
3 TraesCS5A01G056100 chr5D 62297440 62301290 3850 False 6204.000000 6204 95.800 160 3999 1 chr5D.!!$F1 3839
4 TraesCS5A01G056100 chr5D 62519750 62523207 3457 True 4497.000000 4497 90.221 419 3877 1 chr5D.!!$R1 3458
5 TraesCS5A01G056100 chr5B 67959003 67962303 3300 False 4287.000000 4287 90.144 599 3913 1 chr5B.!!$F1 3314
6 TraesCS5A01G056100 chr5B 68185879 68189545 3666 True 1793.666667 3993 94.606 450 3984 3 chr5B.!!$R2 3534
7 TraesCS5A01G056100 chr2B 526379637 526381188 1551 False 1098.000000 1098 79.721 2262 3817 1 chr2B.!!$F2 1555
8 TraesCS5A01G056100 chr2B 525826375 525830572 4197 False 509.500000 512 86.005 2247 2747 2 chr2B.!!$F3 500
9 TraesCS5A01G056100 chr2D 446600185 446605198 5013 False 632.000000 1066 79.972 1186 3817 2 chr2D.!!$F2 2631
10 TraesCS5A01G056100 chr1A 487719745 487720340 595 False 1050.000000 1050 98.490 3999 4592 1 chr1A.!!$F1 593
11 TraesCS5A01G056100 chr1A 486684210 486684803 593 True 970.000000 970 96.134 3999 4592 1 chr1A.!!$R1 593
12 TraesCS5A01G056100 chr1A 565145851 565146446 595 False 917.000000 917 94.463 3999 4592 1 chr1A.!!$F2 593
13 TraesCS5A01G056100 chr4A 1734672 1735267 595 False 1033.000000 1033 97.987 3999 4592 1 chr4A.!!$F1 593
14 TraesCS5A01G056100 chr7A 70194203 70194797 594 True 893.000000 893 93.782 3999 4592 1 chr7A.!!$R1 593
15 TraesCS5A01G056100 chrUn 352577452 352578046 594 True 743.000000 743 89.244 3998 4591 1 chrUn.!!$R1 593
16 TraesCS5A01G056100 chr6D 408885933 408886527 594 False 743.000000 743 89.244 4000 4592 1 chr6D.!!$F1 592
17 TraesCS5A01G056100 chr2A 590639021 590639794 773 False 721.000000 721 83.505 3034 3807 1 chr2A.!!$F1 773
18 TraesCS5A01G056100 chr2A 589791523 589793121 1598 False 619.500000 688 84.348 2257 3853 2 chr2A.!!$F2 1596
19 TraesCS5A01G056100 chr3B 778303022 778303616 594 False 715.000000 715 88.442 3999 4591 1 chr3B.!!$F1 592

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
240 241 0.036858 GCGGGGAGCCAGAATAGATC 60.037 60.0 0.00 0.0 40.81 2.75 F
973 1129 0.036952 GAGGCAGACAAGCAGTAGCA 60.037 55.0 7.97 0.0 45.49 3.49 F
2315 5228 0.105607 CCTACCTACCCTCCCTCCAC 60.106 65.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 4868 0.804933 AAGTCCTCGTTTATCGGCGC 60.805 55.0 0.0 0.0 40.32 6.53 R
2432 5345 0.962356 CAAGGGACGGCAAGCAAGAT 60.962 55.0 0.0 0.0 0.00 2.40 R
3746 6724 0.896226 GGTAGTTGAGGAAGCCGAGT 59.104 55.0 0.0 0.0 0.00 4.18 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
27 28 9.508642 AGAGAAATAAACCAGACTTTCCTTAAG 57.491 33.333 0.00 0.00 39.87 1.85
28 29 8.112016 AGAAATAAACCAGACTTTCCTTAAGC 57.888 34.615 0.00 0.00 37.37 3.09
29 30 7.724061 AGAAATAAACCAGACTTTCCTTAAGCA 59.276 33.333 0.00 0.00 37.37 3.91
30 31 6.819397 ATAAACCAGACTTTCCTTAAGCAC 57.181 37.500 0.00 0.00 37.37 4.40
31 32 2.767505 ACCAGACTTTCCTTAAGCACG 58.232 47.619 0.00 0.00 37.37 5.34
32 33 2.076863 CCAGACTTTCCTTAAGCACGG 58.923 52.381 0.00 0.00 37.37 4.94
33 34 2.076863 CAGACTTTCCTTAAGCACGGG 58.923 52.381 0.00 0.00 37.37 5.28
34 35 1.697982 AGACTTTCCTTAAGCACGGGT 59.302 47.619 0.00 0.00 37.37 5.28
35 36 1.804748 GACTTTCCTTAAGCACGGGTG 59.195 52.381 0.00 0.00 37.37 4.61
48 49 3.740044 CACGGGTGCTTATTTGTACAG 57.260 47.619 0.00 0.00 0.00 2.74
49 50 2.418628 CACGGGTGCTTATTTGTACAGG 59.581 50.000 0.00 0.00 0.00 4.00
50 51 2.303600 ACGGGTGCTTATTTGTACAGGA 59.696 45.455 0.00 0.00 0.00 3.86
51 52 3.054655 ACGGGTGCTTATTTGTACAGGAT 60.055 43.478 0.00 0.00 0.00 3.24
52 53 4.162698 ACGGGTGCTTATTTGTACAGGATA 59.837 41.667 0.00 0.00 0.00 2.59
53 54 4.750098 CGGGTGCTTATTTGTACAGGATAG 59.250 45.833 0.00 0.00 0.00 2.08
54 55 5.452776 CGGGTGCTTATTTGTACAGGATAGA 60.453 44.000 0.00 0.00 0.00 1.98
55 56 5.758784 GGGTGCTTATTTGTACAGGATAGAC 59.241 44.000 0.00 0.00 0.00 2.59
56 57 5.462398 GGTGCTTATTTGTACAGGATAGACG 59.538 44.000 0.00 0.00 0.00 4.18
57 58 5.047847 TGCTTATTTGTACAGGATAGACGC 58.952 41.667 0.00 4.64 0.00 5.19
58 59 5.163447 TGCTTATTTGTACAGGATAGACGCT 60.163 40.000 0.00 0.00 0.00 5.07
59 60 5.753921 GCTTATTTGTACAGGATAGACGCTT 59.246 40.000 0.00 0.00 0.00 4.68
60 61 6.921857 GCTTATTTGTACAGGATAGACGCTTA 59.078 38.462 0.00 0.00 0.00 3.09
61 62 7.437267 GCTTATTTGTACAGGATAGACGCTTAA 59.563 37.037 0.00 0.00 0.00 1.85
62 63 8.638685 TTATTTGTACAGGATAGACGCTTAAC 57.361 34.615 0.00 0.00 0.00 2.01
63 64 5.909621 TTGTACAGGATAGACGCTTAACT 57.090 39.130 0.00 0.00 0.00 2.24
64 65 7.395190 TTTGTACAGGATAGACGCTTAACTA 57.605 36.000 0.00 0.00 0.00 2.24
65 66 7.395190 TTGTACAGGATAGACGCTTAACTAA 57.605 36.000 0.00 0.00 0.00 2.24
66 67 7.024340 TGTACAGGATAGACGCTTAACTAAG 57.976 40.000 0.00 0.00 36.40 2.18
67 68 6.600822 TGTACAGGATAGACGCTTAACTAAGT 59.399 38.462 0.00 0.00 35.75 2.24
68 69 5.892568 ACAGGATAGACGCTTAACTAAGTG 58.107 41.667 8.20 8.20 46.35 3.16
76 77 3.771798 CGCTTAACTAAGTGTCTCTCCC 58.228 50.000 2.48 0.00 38.60 4.30
77 78 3.731264 CGCTTAACTAAGTGTCTCTCCCG 60.731 52.174 2.48 0.00 38.60 5.14
78 79 3.193056 GCTTAACTAAGTGTCTCTCCCGT 59.807 47.826 0.00 0.00 35.75 5.28
79 80 4.397417 GCTTAACTAAGTGTCTCTCCCGTA 59.603 45.833 0.00 0.00 35.75 4.02
80 81 5.448904 GCTTAACTAAGTGTCTCTCCCGTAG 60.449 48.000 0.00 0.00 35.75 3.51
81 82 3.996921 ACTAAGTGTCTCTCCCGTAGA 57.003 47.619 0.00 0.00 0.00 2.59
82 83 4.298103 ACTAAGTGTCTCTCCCGTAGAA 57.702 45.455 0.00 0.00 32.46 2.10
83 84 4.660168 ACTAAGTGTCTCTCCCGTAGAAA 58.340 43.478 0.00 0.00 32.46 2.52
84 85 5.262804 ACTAAGTGTCTCTCCCGTAGAAAT 58.737 41.667 0.00 0.00 32.46 2.17
85 86 6.421485 ACTAAGTGTCTCTCCCGTAGAAATA 58.579 40.000 0.00 0.00 32.46 1.40
86 87 5.838531 AAGTGTCTCTCCCGTAGAAATAG 57.161 43.478 0.00 0.00 32.46 1.73
87 88 4.208746 AGTGTCTCTCCCGTAGAAATAGG 58.791 47.826 0.00 0.00 32.46 2.57
88 89 2.957006 TGTCTCTCCCGTAGAAATAGGC 59.043 50.000 0.00 0.00 32.46 3.93
89 90 2.957006 GTCTCTCCCGTAGAAATAGGCA 59.043 50.000 0.00 0.00 32.46 4.75
90 91 2.957006 TCTCTCCCGTAGAAATAGGCAC 59.043 50.000 0.00 0.00 32.46 5.01
91 92 2.036089 CTCTCCCGTAGAAATAGGCACC 59.964 54.545 0.00 0.00 32.46 5.01
92 93 0.748450 TCCCGTAGAAATAGGCACCG 59.252 55.000 0.00 0.00 0.00 4.94
93 94 0.249741 CCCGTAGAAATAGGCACCGG 60.250 60.000 0.00 0.00 0.00 5.28
94 95 0.462789 CCGTAGAAATAGGCACCGGT 59.537 55.000 0.00 0.00 0.00 5.28
95 96 1.567504 CGTAGAAATAGGCACCGGTG 58.432 55.000 30.66 30.66 0.00 4.94
105 106 4.473643 CACCGGTGCTTCAGGAAA 57.526 55.556 24.02 0.00 35.40 3.13
106 107 2.714259 CACCGGTGCTTCAGGAAAA 58.286 52.632 24.02 0.00 35.40 2.29
107 108 0.310854 CACCGGTGCTTCAGGAAAAC 59.689 55.000 24.02 0.00 35.40 2.43
108 109 0.182775 ACCGGTGCTTCAGGAAAACT 59.817 50.000 6.12 0.00 35.40 2.66
109 110 0.875059 CCGGTGCTTCAGGAAAACTC 59.125 55.000 0.00 0.00 33.18 3.01
110 111 0.512952 CGGTGCTTCAGGAAAACTCG 59.487 55.000 0.00 0.00 0.00 4.18
111 112 0.875059 GGTGCTTCAGGAAAACTCGG 59.125 55.000 0.00 0.00 0.00 4.63
112 113 1.594331 GTGCTTCAGGAAAACTCGGT 58.406 50.000 0.00 0.00 0.00 4.69
113 114 1.947456 GTGCTTCAGGAAAACTCGGTT 59.053 47.619 0.00 0.00 0.00 4.44
114 115 2.357952 GTGCTTCAGGAAAACTCGGTTT 59.642 45.455 0.00 0.00 37.34 3.27
115 116 3.562557 GTGCTTCAGGAAAACTCGGTTTA 59.437 43.478 3.01 0.00 34.43 2.01
116 117 4.215613 GTGCTTCAGGAAAACTCGGTTTAT 59.784 41.667 3.01 0.00 34.43 1.40
117 118 4.825085 TGCTTCAGGAAAACTCGGTTTATT 59.175 37.500 3.01 0.00 34.43 1.40
118 119 5.300792 TGCTTCAGGAAAACTCGGTTTATTT 59.699 36.000 3.01 0.00 34.43 1.40
119 120 6.183360 TGCTTCAGGAAAACTCGGTTTATTTT 60.183 34.615 3.01 0.00 34.43 1.82
120 121 6.700081 GCTTCAGGAAAACTCGGTTTATTTTT 59.300 34.615 3.01 0.00 34.43 1.94
121 122 7.096189 GCTTCAGGAAAACTCGGTTTATTTTTC 60.096 37.037 3.01 0.00 34.43 2.29
122 123 7.576861 TCAGGAAAACTCGGTTTATTTTTCT 57.423 32.000 3.01 0.00 37.84 2.52
123 124 8.680039 TCAGGAAAACTCGGTTTATTTTTCTA 57.320 30.769 3.01 0.00 37.84 2.10
124 125 9.122779 TCAGGAAAACTCGGTTTATTTTTCTAA 57.877 29.630 3.01 0.00 37.84 2.10
125 126 9.738832 CAGGAAAACTCGGTTTATTTTTCTAAA 57.261 29.630 3.01 0.00 37.84 1.85
126 127 9.740239 AGGAAAACTCGGTTTATTTTTCTAAAC 57.260 29.630 3.01 0.00 39.70 2.01
127 128 9.518906 GGAAAACTCGGTTTATTTTTCTAAACA 57.481 29.630 8.47 0.00 41.36 2.83
129 130 8.861033 AAACTCGGTTTATTTTTCTAAACACC 57.139 30.769 8.47 0.00 41.36 4.16
130 131 7.812690 ACTCGGTTTATTTTTCTAAACACCT 57.187 32.000 8.47 0.00 41.36 4.00
131 132 7.868775 ACTCGGTTTATTTTTCTAAACACCTC 58.131 34.615 8.47 0.00 41.36 3.85
132 133 7.718314 ACTCGGTTTATTTTTCTAAACACCTCT 59.282 33.333 8.47 0.00 41.36 3.69
133 134 8.091385 TCGGTTTATTTTTCTAAACACCTCTC 57.909 34.615 8.47 0.00 41.36 3.20
134 135 7.935210 TCGGTTTATTTTTCTAAACACCTCTCT 59.065 33.333 8.47 0.00 41.36 3.10
135 136 9.211485 CGGTTTATTTTTCTAAACACCTCTCTA 57.789 33.333 8.47 0.00 41.36 2.43
139 140 9.787435 TTATTTTTCTAAACACCTCTCTAAGCA 57.213 29.630 0.00 0.00 0.00 3.91
140 141 7.492352 TTTTTCTAAACACCTCTCTAAGCAC 57.508 36.000 0.00 0.00 0.00 4.40
141 142 4.803098 TCTAAACACCTCTCTAAGCACC 57.197 45.455 0.00 0.00 0.00 5.01
142 143 4.417437 TCTAAACACCTCTCTAAGCACCT 58.583 43.478 0.00 0.00 0.00 4.00
143 144 3.686916 AAACACCTCTCTAAGCACCTC 57.313 47.619 0.00 0.00 0.00 3.85
144 145 1.562783 ACACCTCTCTAAGCACCTCC 58.437 55.000 0.00 0.00 0.00 4.30
145 146 0.827368 CACCTCTCTAAGCACCTCCC 59.173 60.000 0.00 0.00 0.00 4.30
146 147 0.413832 ACCTCTCTAAGCACCTCCCA 59.586 55.000 0.00 0.00 0.00 4.37
147 148 1.008938 ACCTCTCTAAGCACCTCCCAT 59.991 52.381 0.00 0.00 0.00 4.00
148 149 2.122768 CCTCTCTAAGCACCTCCCATT 58.877 52.381 0.00 0.00 0.00 3.16
149 150 2.158842 CCTCTCTAAGCACCTCCCATTG 60.159 54.545 0.00 0.00 0.00 2.82
150 151 2.503356 CTCTCTAAGCACCTCCCATTGT 59.497 50.000 0.00 0.00 0.00 2.71
151 152 3.706594 CTCTCTAAGCACCTCCCATTGTA 59.293 47.826 0.00 0.00 0.00 2.41
152 153 3.451178 TCTCTAAGCACCTCCCATTGTAC 59.549 47.826 0.00 0.00 0.00 2.90
153 154 3.178046 TCTAAGCACCTCCCATTGTACA 58.822 45.455 0.00 0.00 0.00 2.90
154 155 2.969821 AAGCACCTCCCATTGTACAA 57.030 45.000 11.41 11.41 0.00 2.41
155 156 2.496899 AGCACCTCCCATTGTACAAG 57.503 50.000 14.65 6.30 0.00 3.16
156 157 1.004745 AGCACCTCCCATTGTACAAGG 59.995 52.381 14.65 13.92 0.00 3.61
157 158 1.463674 CACCTCCCATTGTACAAGGC 58.536 55.000 14.66 0.00 0.00 4.35
158 159 0.331616 ACCTCCCATTGTACAAGGCC 59.668 55.000 14.66 0.00 0.00 5.19
163 164 0.610785 CCATTGTACAAGGCCGGGTT 60.611 55.000 14.66 0.00 0.00 4.11
173 174 2.717044 GGCCGGGTTGTTAATGCCC 61.717 63.158 2.18 0.00 39.03 5.36
176 177 1.190643 CCGGGTTGTTAATGCCCATT 58.809 50.000 0.00 0.00 42.44 3.16
177 178 1.552792 CCGGGTTGTTAATGCCCATTT 59.447 47.619 0.00 0.00 42.44 2.32
185 186 5.690464 TGTTAATGCCCATTTTATTGCCT 57.310 34.783 0.00 0.00 32.50 4.75
240 241 0.036858 GCGGGGAGCCAGAATAGATC 60.037 60.000 0.00 0.00 40.81 2.75
250 251 3.858868 GAATAGATCGGCGCCGGCA 62.859 63.158 44.95 30.18 42.47 5.69
273 274 1.144057 GACCGCCTCGTCATCCAAT 59.856 57.895 0.00 0.00 32.74 3.16
301 302 1.021390 AGGCATCTTGTTCGGCTTCG 61.021 55.000 0.00 0.00 30.19 3.79
348 349 2.354203 CGCAGAGACTAAGGCCTTCTTT 60.354 50.000 24.49 5.61 36.93 2.52
402 403 1.334869 CCATACAAATCAAGCTCGGCC 59.665 52.381 0.00 0.00 0.00 6.13
434 435 4.113354 CTGTCTCCGCCTAGTTATTTGTC 58.887 47.826 0.00 0.00 0.00 3.18
529 530 9.796120 TTGTTTTGTTGTAATTCTAAGTTCTGG 57.204 29.630 0.00 0.00 0.00 3.86
561 562 2.583024 TCATGTTTGTCCCAGATGCA 57.417 45.000 0.00 0.00 0.00 3.96
587 590 4.984295 TCCCACTTCATGAATCAGTCAAA 58.016 39.130 8.96 0.00 40.50 2.69
688 697 6.776116 AGGATGATGACACATTGATAGCAAAT 59.224 34.615 0.00 0.00 37.59 2.32
691 700 6.566141 TGATGACACATTGATAGCAAATTGG 58.434 36.000 0.00 0.00 37.59 3.16
692 701 4.746729 TGACACATTGATAGCAAATTGGC 58.253 39.130 0.00 0.00 37.59 4.52
703 721 2.058057 GCAAATTGGCGTTGTTGGTAG 58.942 47.619 0.00 0.00 0.00 3.18
743 766 6.269077 TCACATGTACCTCCTTTTCTACTTCA 59.731 38.462 0.00 0.00 0.00 3.02
752 775 8.877195 ACCTCCTTTTCTACTTCAATGTTAGTA 58.123 33.333 0.00 0.00 0.00 1.82
847 995 2.306219 TGGTTGTCGGTAATGATGGGAA 59.694 45.455 0.00 0.00 0.00 3.97
857 1005 7.881232 GTCGGTAATGATGGGAATAAAATAGGA 59.119 37.037 0.00 0.00 0.00 2.94
891 1039 1.839354 TGGTCCTGCTGATGCTATCAA 59.161 47.619 0.00 0.00 39.11 2.57
954 1110 0.609957 TGTTGAGGCATGCAAGAGGG 60.610 55.000 21.36 0.00 0.00 4.30
972 1128 0.742635 GGAGGCAGACAAGCAGTAGC 60.743 60.000 0.00 0.00 42.56 3.58
973 1129 0.036952 GAGGCAGACAAGCAGTAGCA 60.037 55.000 7.97 0.00 45.49 3.49
1006 1162 1.310933 AAGAAGAAGCGCCATGGCAG 61.311 55.000 34.93 26.77 42.06 4.85
1223 1382 3.194062 CGTTGTTTCCCATTTGCAGTTT 58.806 40.909 0.00 0.00 0.00 2.66
1335 1494 2.860735 CGGTGACTACAGCTGCTAATTC 59.139 50.000 15.27 4.26 41.65 2.17
1441 1600 5.720371 TTGGTCCATTTATGTTTCTGGTG 57.280 39.130 0.00 0.00 0.00 4.17
1458 2102 9.202273 GTTTCTGGTGATATACATCTTCATCTC 57.798 37.037 0.00 0.00 31.93 2.75
1747 4414 4.301628 CTCACCAAATTTGAAGGAAGTGC 58.698 43.478 19.86 0.00 0.00 4.40
1752 4419 4.301628 CAAATTTGAAGGAAGTGCTGTCC 58.698 43.478 13.08 0.00 35.17 4.02
1844 4511 7.765695 AAAGCAAAATAGAGACCTGATTTCA 57.234 32.000 0.00 0.00 0.00 2.69
1917 4584 1.137479 CCAACCATTTAGCCTGGCATG 59.863 52.381 22.65 15.36 37.27 4.06
1922 4593 3.458118 ACCATTTAGCCTGGCATGTACTA 59.542 43.478 22.65 0.00 37.27 1.82
1925 4596 5.643777 CCATTTAGCCTGGCATGTACTATAC 59.356 44.000 22.65 0.00 0.00 1.47
1927 4598 5.723672 TTAGCCTGGCATGTACTATACTC 57.276 43.478 22.65 0.00 0.00 2.59
1944 4615 2.423577 ACTCGACACAAACCATAAGCC 58.576 47.619 0.00 0.00 0.00 4.35
1946 4617 3.009723 CTCGACACAAACCATAAGCCAT 58.990 45.455 0.00 0.00 0.00 4.40
2128 4838 6.291637 CGAAAGATACAGTACATACTTTGGCG 60.292 42.308 0.00 0.00 33.46 5.69
2157 4868 7.393234 TCCTTGACAATGAAACCCACTTATTAG 59.607 37.037 0.00 0.00 0.00 1.73
2168 4879 3.185797 CCCACTTATTAGCGCCGATAAAC 59.814 47.826 2.29 0.00 0.00 2.01
2315 5228 0.105607 CCTACCTACCCTCCCTCCAC 60.106 65.000 0.00 0.00 0.00 4.02
2423 5336 1.475280 CTGAGTGCATTTGGTGATGGG 59.525 52.381 0.00 0.00 0.00 4.00
2432 5345 4.447290 CATTTGGTGATGGGTGTATACGA 58.553 43.478 0.00 0.00 0.00 3.43
2731 5653 3.767673 CAGGTGGTACAAGCTACTTCCTA 59.232 47.826 0.58 0.00 44.16 2.94
2988 5951 3.143211 AGAGAGTAGCGTACCCCATAG 57.857 52.381 0.00 0.00 0.00 2.23
3022 5992 4.361783 TCCATTCCCTAACTCTGTGATGA 58.638 43.478 0.00 0.00 0.00 2.92
3023 5993 4.971282 TCCATTCCCTAACTCTGTGATGAT 59.029 41.667 0.00 0.00 0.00 2.45
3024 5994 5.061853 CCATTCCCTAACTCTGTGATGATG 58.938 45.833 0.00 0.00 0.00 3.07
3111 6088 1.752198 CGTGACCAAGGTGGAGGAA 59.248 57.895 0.18 0.00 40.96 3.36
3442 6419 3.058846 GGTTGTCGAGAAAAAGAGGAAGC 60.059 47.826 0.00 0.00 0.00 3.86
3528 6505 2.981560 GACGTCGTTCACCGGGCTA 61.982 63.158 6.32 0.00 37.11 3.93
3573 6550 0.104120 CACGGGGCATGAAGTCGATA 59.896 55.000 0.00 0.00 0.00 2.92
3684 6662 4.228567 GGGTAGGCTGGCTCGAGC 62.229 72.222 29.38 29.38 38.34 5.03
3746 6724 3.537580 GGTTGTGGCTGTTATCGGATTA 58.462 45.455 0.00 0.00 0.00 1.75
3820 6798 0.859232 CAACGCGTTGCTAGAGTTGT 59.141 50.000 35.89 1.91 41.97 3.32
3836 6814 1.269448 GTTGTGCCAACGGTTGATCAT 59.731 47.619 21.88 0.00 0.00 2.45
3841 6819 2.824936 TGCCAACGGTTGATCATGATTT 59.175 40.909 21.88 0.00 0.00 2.17
3856 6834 6.628919 TCATGATTTGCCTTGACATATCAG 57.371 37.500 0.00 0.00 40.02 2.90
3863 6841 5.231702 TGCCTTGACATATCAGATATGCA 57.768 39.130 24.90 20.55 45.05 3.96
3917 6901 6.382282 AGGATGTCTGATTCACTATGTCTTGA 59.618 38.462 0.00 0.00 0.00 3.02
3943 6927 2.535984 GTCAAGTCTGTTGTCACGACTG 59.464 50.000 0.00 0.00 38.00 3.51
3966 6950 2.566279 AGATGACATATCTGCAGCGGAT 59.434 45.455 20.77 20.77 33.63 4.18
4393 9343 2.027605 CACGACAGTGGACGCACT 59.972 61.111 10.91 0.00 44.34 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.237949 GCTTAAGGAAAGTCTGGTTTATTTCTC 58.762 37.037 4.29 0.00 37.53 2.87
3 4 7.724061 TGCTTAAGGAAAGTCTGGTTTATTTCT 59.276 33.333 4.29 0.00 37.53 2.52
4 5 7.808381 GTGCTTAAGGAAAGTCTGGTTTATTTC 59.192 37.037 4.29 0.00 37.53 2.17
5 6 7.521585 CGTGCTTAAGGAAAGTCTGGTTTATTT 60.522 37.037 4.29 0.00 37.53 1.40
6 7 6.072673 CGTGCTTAAGGAAAGTCTGGTTTATT 60.073 38.462 4.29 0.00 37.53 1.40
7 8 5.411669 CGTGCTTAAGGAAAGTCTGGTTTAT 59.588 40.000 4.29 0.00 37.53 1.40
8 9 4.753107 CGTGCTTAAGGAAAGTCTGGTTTA 59.247 41.667 4.29 0.00 37.53 2.01
9 10 3.564225 CGTGCTTAAGGAAAGTCTGGTTT 59.436 43.478 4.29 0.00 37.53 3.27
10 11 3.139077 CGTGCTTAAGGAAAGTCTGGTT 58.861 45.455 4.29 0.00 37.53 3.67
11 12 2.550208 CCGTGCTTAAGGAAAGTCTGGT 60.550 50.000 4.29 0.00 37.53 4.00
12 13 2.076863 CCGTGCTTAAGGAAAGTCTGG 58.923 52.381 4.29 0.00 37.53 3.86
13 14 2.076863 CCCGTGCTTAAGGAAAGTCTG 58.923 52.381 4.29 0.00 37.53 3.51
14 15 1.697982 ACCCGTGCTTAAGGAAAGTCT 59.302 47.619 4.29 0.00 37.53 3.24
15 16 1.804748 CACCCGTGCTTAAGGAAAGTC 59.195 52.381 4.29 0.00 37.53 3.01
16 17 1.892209 CACCCGTGCTTAAGGAAAGT 58.108 50.000 4.29 0.00 37.53 2.66
28 29 2.418628 CCTGTACAAATAAGCACCCGTG 59.581 50.000 0.00 0.00 0.00 4.94
29 30 2.303600 TCCTGTACAAATAAGCACCCGT 59.696 45.455 0.00 0.00 0.00 5.28
30 31 2.980568 TCCTGTACAAATAAGCACCCG 58.019 47.619 0.00 0.00 0.00 5.28
31 32 5.758784 GTCTATCCTGTACAAATAAGCACCC 59.241 44.000 0.00 0.00 0.00 4.61
32 33 5.462398 CGTCTATCCTGTACAAATAAGCACC 59.538 44.000 0.00 0.00 0.00 5.01
33 34 5.050972 GCGTCTATCCTGTACAAATAAGCAC 60.051 44.000 0.00 0.00 0.00 4.40
34 35 5.047847 GCGTCTATCCTGTACAAATAAGCA 58.952 41.667 0.00 0.00 0.00 3.91
35 36 5.290386 AGCGTCTATCCTGTACAAATAAGC 58.710 41.667 0.00 4.79 0.00 3.09
36 37 8.753175 GTTAAGCGTCTATCCTGTACAAATAAG 58.247 37.037 0.00 0.00 0.00 1.73
37 38 8.472413 AGTTAAGCGTCTATCCTGTACAAATAA 58.528 33.333 0.00 0.00 0.00 1.40
38 39 8.004087 AGTTAAGCGTCTATCCTGTACAAATA 57.996 34.615 0.00 0.00 0.00 1.40
39 40 6.875076 AGTTAAGCGTCTATCCTGTACAAAT 58.125 36.000 0.00 0.00 0.00 2.32
40 41 6.276832 AGTTAAGCGTCTATCCTGTACAAA 57.723 37.500 0.00 0.00 0.00 2.83
41 42 5.909621 AGTTAAGCGTCTATCCTGTACAA 57.090 39.130 0.00 0.00 0.00 2.41
42 43 6.600822 ACTTAGTTAAGCGTCTATCCTGTACA 59.399 38.462 0.00 0.00 36.79 2.90
43 44 6.911511 CACTTAGTTAAGCGTCTATCCTGTAC 59.088 42.308 0.00 0.00 36.79 2.90
44 45 6.600822 ACACTTAGTTAAGCGTCTATCCTGTA 59.399 38.462 0.00 0.00 36.79 2.74
45 46 5.418209 ACACTTAGTTAAGCGTCTATCCTGT 59.582 40.000 0.00 0.00 36.79 4.00
46 47 5.892568 ACACTTAGTTAAGCGTCTATCCTG 58.107 41.667 0.00 0.00 36.79 3.86
47 48 6.134040 GACACTTAGTTAAGCGTCTATCCT 57.866 41.667 11.07 0.00 40.42 3.24
53 54 4.413969 GGAGAGACACTTAGTTAAGCGTC 58.586 47.826 10.57 10.57 42.62 5.19
54 55 3.193056 GGGAGAGACACTTAGTTAAGCGT 59.807 47.826 0.00 0.00 36.79 5.07
55 56 3.731264 CGGGAGAGACACTTAGTTAAGCG 60.731 52.174 0.00 0.00 36.79 4.68
56 57 3.193056 ACGGGAGAGACACTTAGTTAAGC 59.807 47.826 0.00 0.00 36.79 3.09
57 58 5.879223 TCTACGGGAGAGACACTTAGTTAAG 59.121 44.000 0.00 0.00 39.18 1.85
58 59 5.809001 TCTACGGGAGAGACACTTAGTTAA 58.191 41.667 0.00 0.00 0.00 2.01
59 60 5.426689 TCTACGGGAGAGACACTTAGTTA 57.573 43.478 0.00 0.00 0.00 2.24
60 61 4.298103 TCTACGGGAGAGACACTTAGTT 57.702 45.455 0.00 0.00 0.00 2.24
61 62 3.996921 TCTACGGGAGAGACACTTAGT 57.003 47.619 0.00 0.00 0.00 2.24
62 63 5.838531 ATTTCTACGGGAGAGACACTTAG 57.161 43.478 0.00 0.00 34.93 2.18
63 64 5.826737 CCTATTTCTACGGGAGAGACACTTA 59.173 44.000 0.00 0.00 34.93 2.24
64 65 4.645588 CCTATTTCTACGGGAGAGACACTT 59.354 45.833 0.00 0.00 34.93 3.16
65 66 4.208746 CCTATTTCTACGGGAGAGACACT 58.791 47.826 0.00 0.00 34.93 3.55
66 67 3.243468 GCCTATTTCTACGGGAGAGACAC 60.243 52.174 0.00 0.00 34.93 3.67
67 68 2.957006 GCCTATTTCTACGGGAGAGACA 59.043 50.000 0.00 0.00 34.93 3.41
68 69 2.957006 TGCCTATTTCTACGGGAGAGAC 59.043 50.000 0.00 0.00 34.93 3.36
69 70 2.957006 GTGCCTATTTCTACGGGAGAGA 59.043 50.000 0.00 0.00 34.93 3.10
70 71 2.036089 GGTGCCTATTTCTACGGGAGAG 59.964 54.545 0.00 0.00 34.93 3.20
71 72 2.037144 GGTGCCTATTTCTACGGGAGA 58.963 52.381 0.00 0.00 0.00 3.71
72 73 1.269621 CGGTGCCTATTTCTACGGGAG 60.270 57.143 0.00 0.00 0.00 4.30
73 74 0.748450 CGGTGCCTATTTCTACGGGA 59.252 55.000 0.00 0.00 0.00 5.14
74 75 0.249741 CCGGTGCCTATTTCTACGGG 60.250 60.000 0.00 0.00 36.45 5.28
75 76 0.462789 ACCGGTGCCTATTTCTACGG 59.537 55.000 6.12 0.00 44.86 4.02
76 77 1.567504 CACCGGTGCCTATTTCTACG 58.432 55.000 24.02 0.00 0.00 3.51
88 89 0.310854 GTTTTCCTGAAGCACCGGTG 59.689 55.000 30.66 30.66 0.00 4.94
89 90 0.182775 AGTTTTCCTGAAGCACCGGT 59.817 50.000 0.00 0.00 0.00 5.28
90 91 0.875059 GAGTTTTCCTGAAGCACCGG 59.125 55.000 0.00 0.00 0.00 5.28
91 92 0.512952 CGAGTTTTCCTGAAGCACCG 59.487 55.000 0.00 0.00 0.00 4.94
92 93 0.875059 CCGAGTTTTCCTGAAGCACC 59.125 55.000 0.00 0.00 0.00 5.01
93 94 1.594331 ACCGAGTTTTCCTGAAGCAC 58.406 50.000 0.00 0.00 0.00 4.40
94 95 2.341846 AACCGAGTTTTCCTGAAGCA 57.658 45.000 0.00 0.00 0.00 3.91
95 96 5.372547 AATAAACCGAGTTTTCCTGAAGC 57.627 39.130 7.22 0.00 37.01 3.86
96 97 8.135529 AGAAAAATAAACCGAGTTTTCCTGAAG 58.864 33.333 7.22 0.00 41.85 3.02
97 98 8.002984 AGAAAAATAAACCGAGTTTTCCTGAA 57.997 30.769 7.22 0.00 41.85 3.02
98 99 7.576861 AGAAAAATAAACCGAGTTTTCCTGA 57.423 32.000 7.22 0.00 41.85 3.86
99 100 9.738832 TTTAGAAAAATAAACCGAGTTTTCCTG 57.261 29.630 7.22 0.00 41.85 3.86
100 101 9.740239 GTTTAGAAAAATAAACCGAGTTTTCCT 57.260 29.630 7.22 0.00 41.85 3.36
101 102 9.518906 TGTTTAGAAAAATAAACCGAGTTTTCC 57.481 29.630 7.22 0.00 41.85 3.13
103 104 9.304731 GGTGTTTAGAAAAATAAACCGAGTTTT 57.695 29.630 7.22 0.00 42.45 2.43
104 105 8.689061 AGGTGTTTAGAAAAATAAACCGAGTTT 58.311 29.630 6.84 7.11 42.45 2.66
105 106 8.229253 AGGTGTTTAGAAAAATAAACCGAGTT 57.771 30.769 6.84 0.00 42.45 3.01
106 107 7.718314 AGAGGTGTTTAGAAAAATAAACCGAGT 59.282 33.333 6.84 0.00 42.45 4.18
107 108 8.095937 AGAGGTGTTTAGAAAAATAAACCGAG 57.904 34.615 6.84 0.00 42.45 4.63
108 109 7.935210 AGAGAGGTGTTTAGAAAAATAAACCGA 59.065 33.333 6.84 0.00 42.45 4.69
109 110 8.095937 AGAGAGGTGTTTAGAAAAATAAACCG 57.904 34.615 6.84 0.00 42.45 4.44
113 114 9.787435 TGCTTAGAGAGGTGTTTAGAAAAATAA 57.213 29.630 0.00 0.00 0.00 1.40
114 115 9.216117 GTGCTTAGAGAGGTGTTTAGAAAAATA 57.784 33.333 0.00 0.00 0.00 1.40
115 116 7.175119 GGTGCTTAGAGAGGTGTTTAGAAAAAT 59.825 37.037 0.00 0.00 0.00 1.82
116 117 6.485648 GGTGCTTAGAGAGGTGTTTAGAAAAA 59.514 38.462 0.00 0.00 0.00 1.94
117 118 5.995897 GGTGCTTAGAGAGGTGTTTAGAAAA 59.004 40.000 0.00 0.00 0.00 2.29
118 119 5.307196 AGGTGCTTAGAGAGGTGTTTAGAAA 59.693 40.000 0.00 0.00 0.00 2.52
119 120 4.838986 AGGTGCTTAGAGAGGTGTTTAGAA 59.161 41.667 0.00 0.00 0.00 2.10
120 121 4.417437 AGGTGCTTAGAGAGGTGTTTAGA 58.583 43.478 0.00 0.00 0.00 2.10
121 122 4.382147 GGAGGTGCTTAGAGAGGTGTTTAG 60.382 50.000 0.00 0.00 0.00 1.85
122 123 3.514309 GGAGGTGCTTAGAGAGGTGTTTA 59.486 47.826 0.00 0.00 0.00 2.01
123 124 2.303311 GGAGGTGCTTAGAGAGGTGTTT 59.697 50.000 0.00 0.00 0.00 2.83
124 125 1.903183 GGAGGTGCTTAGAGAGGTGTT 59.097 52.381 0.00 0.00 0.00 3.32
125 126 1.562783 GGAGGTGCTTAGAGAGGTGT 58.437 55.000 0.00 0.00 0.00 4.16
126 127 0.827368 GGGAGGTGCTTAGAGAGGTG 59.173 60.000 0.00 0.00 0.00 4.00
127 128 0.413832 TGGGAGGTGCTTAGAGAGGT 59.586 55.000 0.00 0.00 0.00 3.85
128 129 1.799933 ATGGGAGGTGCTTAGAGAGG 58.200 55.000 0.00 0.00 0.00 3.69
129 130 2.503356 ACAATGGGAGGTGCTTAGAGAG 59.497 50.000 0.00 0.00 0.00 3.20
130 131 2.551270 ACAATGGGAGGTGCTTAGAGA 58.449 47.619 0.00 0.00 0.00 3.10
131 132 3.197766 TGTACAATGGGAGGTGCTTAGAG 59.802 47.826 0.00 0.00 0.00 2.43
132 133 3.178046 TGTACAATGGGAGGTGCTTAGA 58.822 45.455 0.00 0.00 0.00 2.10
133 134 3.627395 TGTACAATGGGAGGTGCTTAG 57.373 47.619 0.00 0.00 0.00 2.18
134 135 3.308117 CCTTGTACAATGGGAGGTGCTTA 60.308 47.826 9.13 0.00 0.00 3.09
135 136 2.555227 CCTTGTACAATGGGAGGTGCTT 60.555 50.000 9.13 0.00 0.00 3.91
136 137 1.004745 CCTTGTACAATGGGAGGTGCT 59.995 52.381 9.13 0.00 0.00 4.40
137 138 1.463674 CCTTGTACAATGGGAGGTGC 58.536 55.000 9.13 0.00 0.00 5.01
138 139 1.463674 GCCTTGTACAATGGGAGGTG 58.536 55.000 16.08 0.00 0.00 4.00
139 140 0.331616 GGCCTTGTACAATGGGAGGT 59.668 55.000 16.08 0.00 0.00 3.85
140 141 0.748005 CGGCCTTGTACAATGGGAGG 60.748 60.000 16.08 11.34 0.00 4.30
141 142 0.748005 CCGGCCTTGTACAATGGGAG 60.748 60.000 16.08 9.45 0.00 4.30
142 143 1.301623 CCGGCCTTGTACAATGGGA 59.698 57.895 16.08 0.00 0.00 4.37
143 144 1.752694 CCCGGCCTTGTACAATGGG 60.753 63.158 19.36 17.88 0.00 4.00
144 145 0.610785 AACCCGGCCTTGTACAATGG 60.611 55.000 9.13 13.26 0.00 3.16
145 146 0.525761 CAACCCGGCCTTGTACAATG 59.474 55.000 9.13 7.68 0.00 2.82
146 147 0.111639 ACAACCCGGCCTTGTACAAT 59.888 50.000 9.13 0.00 29.81 2.71
147 148 0.106619 AACAACCCGGCCTTGTACAA 60.107 50.000 14.27 8.28 31.43 2.41
148 149 0.763652 TAACAACCCGGCCTTGTACA 59.236 50.000 14.27 0.00 31.43 2.90
149 150 1.894881 TTAACAACCCGGCCTTGTAC 58.105 50.000 14.27 0.00 31.43 2.90
150 151 2.438411 CATTAACAACCCGGCCTTGTA 58.562 47.619 14.27 3.01 31.43 2.41
151 152 1.253100 CATTAACAACCCGGCCTTGT 58.747 50.000 9.38 9.38 33.09 3.16
152 153 0.108851 GCATTAACAACCCGGCCTTG 60.109 55.000 0.00 0.55 0.00 3.61
153 154 1.254975 GGCATTAACAACCCGGCCTT 61.255 55.000 0.00 0.00 38.37 4.35
154 155 1.680989 GGCATTAACAACCCGGCCT 60.681 57.895 0.00 0.00 38.37 5.19
155 156 2.717044 GGGCATTAACAACCCGGCC 61.717 63.158 0.00 0.00 40.63 6.13
156 157 2.889617 GGGCATTAACAACCCGGC 59.110 61.111 0.00 0.00 32.92 6.13
163 164 5.188555 TGAGGCAATAAAATGGGCATTAACA 59.811 36.000 0.00 0.00 0.00 2.41
185 186 1.403814 CTCCTCGTATCCCTGCTTGA 58.596 55.000 0.00 0.00 0.00 3.02
259 260 0.462581 TGCTCATTGGATGACGAGGC 60.463 55.000 0.00 0.00 35.06 4.70
273 274 0.251033 ACAAGATGCCTGCTTGCTCA 60.251 50.000 9.40 0.00 45.00 4.26
382 383 1.334869 GGCCGAGCTTGATTTGTATGG 59.665 52.381 1.22 0.00 0.00 2.74
402 403 2.055042 CGGAGACAGTGAGGGAGGG 61.055 68.421 0.00 0.00 0.00 4.30
434 435 1.585006 CTGCAGGCAGCTGGAAAAG 59.415 57.895 17.12 0.00 45.94 2.27
529 530 8.452534 TGGGACAAACATGATAAAAACGTATAC 58.547 33.333 0.00 0.00 31.92 1.47
537 538 5.479724 TGCATCTGGGACAAACATGATAAAA 59.520 36.000 0.00 0.00 38.70 1.52
538 539 5.015515 TGCATCTGGGACAAACATGATAAA 58.984 37.500 0.00 0.00 38.70 1.40
561 562 3.784763 ACTGATTCATGAAGTGGGATCCT 59.215 43.478 14.54 0.00 0.00 3.24
688 697 1.402259 CACAACTACCAACAACGCCAA 59.598 47.619 0.00 0.00 0.00 4.52
691 700 1.018910 ACCACAACTACCAACAACGC 58.981 50.000 0.00 0.00 0.00 4.84
692 701 3.768468 AAACCACAACTACCAACAACG 57.232 42.857 0.00 0.00 0.00 4.10
743 766 7.981225 ACGGTACAAAACGGATATACTAACATT 59.019 33.333 0.00 0.00 32.91 2.71
752 775 3.781079 TCGACGGTACAAAACGGATAT 57.219 42.857 0.00 0.00 32.91 1.63
830 978 7.663905 CCTATTTTATTCCCATCATTACCGACA 59.336 37.037 0.00 0.00 0.00 4.35
833 981 7.663905 TGTCCTATTTTATTCCCATCATTACCG 59.336 37.037 0.00 0.00 0.00 4.02
857 1005 3.760684 GCAGGACCAATCAAAGATTCTGT 59.239 43.478 0.00 0.00 0.00 3.41
891 1039 8.460317 AAGGTGGATATTCATATTCAGAGGAT 57.540 34.615 0.00 0.00 29.13 3.24
954 1110 0.036952 TGCTACTGCTTGTCTGCCTC 60.037 55.000 0.00 0.00 40.48 4.70
972 1128 4.244425 TCTTCTTCGTCCTTCTGACTTG 57.756 45.455 0.00 0.00 42.13 3.16
973 1129 4.797933 GCTTCTTCTTCGTCCTTCTGACTT 60.798 45.833 0.00 0.00 42.13 3.01
1006 1162 4.022849 CCTCCAATTCACAAAGACTCCAAC 60.023 45.833 0.00 0.00 0.00 3.77
1223 1382 2.678836 CCACGTTTGTTACCACAGTCAA 59.321 45.455 0.00 0.00 33.22 3.18
1335 1494 3.814268 CGGATGTGGCGCCAAAGG 61.814 66.667 34.66 15.93 0.00 3.11
1572 3853 7.138081 TGATAAAGCCGCATATGTTTAACATG 58.862 34.615 19.55 7.51 39.53 3.21
1747 4414 4.944962 TTTACATCAGAATTGCGGACAG 57.055 40.909 0.00 0.00 0.00 3.51
1752 4419 7.579589 TTTGGAAATTTACATCAGAATTGCG 57.420 32.000 3.35 0.00 0.00 4.85
1917 4584 7.167136 GCTTATGGTTTGTGTCGAGTATAGTAC 59.833 40.741 0.00 0.00 0.00 2.73
1922 4593 4.189231 GGCTTATGGTTTGTGTCGAGTAT 58.811 43.478 0.00 0.00 0.00 2.12
1925 4596 2.422597 TGGCTTATGGTTTGTGTCGAG 58.577 47.619 0.00 0.00 0.00 4.04
1927 4598 4.955925 TTATGGCTTATGGTTTGTGTCG 57.044 40.909 0.00 0.00 0.00 4.35
1944 4615 8.925161 ATTTCGTACACCCAAAATTGATTATG 57.075 30.769 0.00 0.00 0.00 1.90
1946 4617 8.361139 ACAATTTCGTACACCCAAAATTGATTA 58.639 29.630 20.21 0.00 45.39 1.75
2011 4682 3.809279 GCTAAAGGCACATTGCTGTTTTT 59.191 39.130 0.00 0.00 44.28 1.94
2039 4710 4.517453 AGTTTTAAGTTTCAGCATACCGCA 59.483 37.500 0.00 0.00 46.13 5.69
2099 4771 5.589192 AGTATGTACTGTATCTTTCGCACC 58.411 41.667 0.00 0.00 34.72 5.01
2128 4838 5.010282 AGTGGGTTTCATTGTCAAGGATAC 58.990 41.667 11.04 11.04 0.00 2.24
2157 4868 0.804933 AAGTCCTCGTTTATCGGCGC 60.805 55.000 0.00 0.00 40.32 6.53
2315 5228 1.122227 CAATATTGCAAGGGGGTGGG 58.878 55.000 4.94 0.00 0.00 4.61
2423 5336 2.218759 CGGCAAGCAAGATCGTATACAC 59.781 50.000 3.32 0.00 0.00 2.90
2432 5345 0.962356 CAAGGGACGGCAAGCAAGAT 60.962 55.000 0.00 0.00 0.00 2.40
2988 5951 6.434340 AGTTAGGGAATGGATTCTCAAAACAC 59.566 38.462 14.82 1.69 39.75 3.32
3024 5994 0.379669 CGAGAAATCTGGCACCATGC 59.620 55.000 0.00 0.00 44.08 4.06
3442 6419 2.513204 CATCTGCACCTCAGCCCG 60.513 66.667 0.00 0.00 42.56 6.13
3528 6505 3.243569 CCTCACTGTTGAAGAACTCGAGT 60.244 47.826 13.58 13.58 32.79 4.18
3573 6550 3.649277 CTAGAACAGCGCCGTGGCT 62.649 63.158 2.29 4.05 46.13 4.75
3590 6567 3.023949 GCGAGCCCCAGATCACACT 62.024 63.158 0.00 0.00 0.00 3.55
3684 6662 1.867233 ACTAGTGTTCAAGCTTGCACG 59.133 47.619 21.99 14.06 36.99 5.34
3746 6724 0.896226 GGTAGTTGAGGAAGCCGAGT 59.104 55.000 0.00 0.00 0.00 4.18
3820 6798 2.127271 ATCATGATCAACCGTTGGCA 57.873 45.000 11.35 10.14 0.00 4.92
3836 6814 7.094506 GCATATCTGATATGTCAAGGCAAATCA 60.095 37.037 28.87 0.00 43.52 2.57
3841 6819 5.231702 TGCATATCTGATATGTCAAGGCA 57.768 39.130 28.87 20.39 43.52 4.75
3888 6872 7.782168 AGACATAGTGAATCAGACATCCTTCTA 59.218 37.037 0.00 0.00 0.00 2.10
3917 6901 5.462398 GTCGTGACAACAGACTTGACTAATT 59.538 40.000 0.00 0.00 31.43 1.40
3932 6916 1.068434 TGTCATCTGCAGTCGTGACAA 59.932 47.619 30.91 21.45 45.50 3.18
4393 9343 4.289672 AGAAGCAGGAGGGTATTTTTCTCA 59.710 41.667 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.