Multiple sequence alignment - TraesCS7B01G336100

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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 TraesCS7B01G336100 chr7B 100.000 4628 0 0 1 4628 591391763 591387136 0.000000e+00 8547
1 TraesCS7B01G336100 chr7B 95.880 267 9 2 1 267 591451921 591451657 9.200000e-117 431
2 TraesCS7B01G336100 chr7D 96.605 3446 86 14 302 3740 548205557 548202136 0.000000e+00 5686
3 TraesCS7B01G336100 chr7D 92.992 899 40 3 3733 4628 548202048 548201170 0.000000e+00 1290
4 TraesCS7B01G336100 chr7A 96.604 3416 86 8 333 3740 631978426 631975033 0.000000e+00 5638
5 TraesCS7B01G336100 chr7A 95.880 898 35 2 3733 4628 631974965 631974068 0.000000e+00 1452
6 TraesCS7B01G336100 chr4B 87.926 2054 248 0 1634 3687 636982762 636980709 0.000000e+00 2420
7 TraesCS7B01G336100 chr4B 87.585 2054 253 2 1634 3687 636971522 636969471 0.000000e+00 2379
8 TraesCS7B01G336100 chr4B 87.136 653 81 2 878 1527 636985426 636984774 0.000000e+00 737
9 TraesCS7B01G336100 chr4B 77.994 618 90 23 4021 4625 636980381 636979797 3.430000e-91 346
10 TraesCS7B01G336100 chr6B 95.273 275 13 0 1 275 710319871 710319597 1.980000e-118 436
11 TraesCS7B01G336100 chr6B 95.880 267 11 0 1 267 710325525 710325259 2.560000e-117 433
12 TraesCS7B01G336100 chr3D 93.478 276 17 1 1 275 445318072 445317797 4.310000e-110 409
13 TraesCS7B01G336100 chr3D 91.386 267 23 0 1 267 445334115 445333849 2.630000e-97 366


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 TraesCS7B01G336100 chr7B 591387136 591391763 4627 True 8547.000000 8547 100.0000 1 4628 1 chr7B.!!$R1 4627
1 TraesCS7B01G336100 chr7D 548201170 548205557 4387 True 3488.000000 5686 94.7985 302 4628 2 chr7D.!!$R1 4326
2 TraesCS7B01G336100 chr7A 631974068 631978426 4358 True 3545.000000 5638 96.2420 333 4628 2 chr7A.!!$R1 4295
3 TraesCS7B01G336100 chr4B 636969471 636971522 2051 True 2379.000000 2379 87.5850 1634 3687 1 chr4B.!!$R1 2053
4 TraesCS7B01G336100 chr4B 636979797 636985426 5629 True 1167.666667 2420 84.3520 878 4625 3 chr4B.!!$R2 3747

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
120 121 0.101399 CTGTGGCTGAGTAGGTAGCG 59.899 60.000 0.00 0.00 40.78 4.26 F
122 123 0.179134 GTGGCTGAGTAGGTAGCGTG 60.179 60.000 0.00 0.00 40.78 5.34 F
260 261 0.252197 GCTTAGTTGACACCCGGGAT 59.748 55.000 32.02 15.78 0.00 3.85 F
265 266 0.391263 GTTGACACCCGGGATCTGAC 60.391 60.000 32.02 20.62 0.00 3.51 F
278 279 0.617413 ATCTGACAGGGCTCCAGTTG 59.383 55.000 1.81 0.00 0.00 3.16 F
492 507 0.832135 GACCAGAGTCCAGACCACCA 60.832 60.000 0.00 0.00 37.00 4.17 F
496 511 0.902516 AGAGTCCAGACCACCAGAGC 60.903 60.000 0.00 0.00 0.00 4.09 F
1159 1193 1.063642 ACATGACGGAGGAGATGGAGA 60.064 52.381 0.00 0.00 0.00 3.71 F
2368 4310 2.549134 CCCGATGACCAATTATACGGCA 60.549 50.000 0.00 0.00 37.98 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1159 1193 2.115911 CGAGCTGCGAGTAGACCCT 61.116 63.158 0.00 0.00 44.57 4.34 R
1746 3688 2.662866 CCATCACAGAGGCCATGAATT 58.337 47.619 14.39 0.00 0.00 2.17 R
2240 4182 4.202141 CGGTATAGGTGATAACGTTGGGAA 60.202 45.833 11.99 0.00 44.70 3.97 R
2263 4205 0.032540 CACTGGCCTTGAACCAAAGC 59.967 55.000 3.32 0.00 36.56 3.51 R
2339 4281 1.275666 TTGGTCATCGGGTGTCAGAT 58.724 50.000 0.00 0.00 0.00 2.90 R
2541 4483 1.726791 GTGTACGAATCTGGTGTGCAG 59.273 52.381 0.00 0.00 0.00 4.41 R
2795 4737 0.318441 CACTCGACCTTCCTTGCAGA 59.682 55.000 0.00 0.00 0.00 4.26 R
3099 5041 5.071519 TGTGGGATTCAAACCATGTTTTGAT 59.928 36.000 17.80 9.16 43.38 2.57 R
4267 6438 2.789208 CTTGAGCAACATGTATTGGCG 58.211 47.619 0.00 0.00 0.00 5.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.681705 TTACTTACGCTGTCGACCG 57.318 52.632 14.12 12.84 39.41 4.79
19 20 0.874390 TTACTTACGCTGTCGACCGT 59.126 50.000 20.70 20.70 41.11 4.83
20 21 0.443869 TACTTACGCTGTCGACCGTC 59.556 55.000 20.54 7.13 38.75 4.79
21 22 1.862147 CTTACGCTGTCGACCGTCG 60.862 63.158 20.54 18.67 42.10 5.12
22 23 3.313007 TTACGCTGTCGACCGTCGG 62.313 63.158 20.54 10.48 40.88 4.79
24 25 4.175489 CGCTGTCGACCGTCGGAT 62.175 66.667 20.51 1.57 40.88 4.18
25 26 2.579787 GCTGTCGACCGTCGGATG 60.580 66.667 20.51 9.78 40.88 3.51
26 27 2.579787 CTGTCGACCGTCGGATGC 60.580 66.667 20.51 5.88 40.88 3.91
27 28 3.336715 CTGTCGACCGTCGGATGCA 62.337 63.158 20.51 12.85 40.88 3.96
28 29 2.104331 GTCGACCGTCGGATGCAT 59.896 61.111 20.51 0.00 40.88 3.96
29 30 1.944676 GTCGACCGTCGGATGCATC 60.945 63.158 20.51 18.81 40.88 3.91
30 31 2.119029 TCGACCGTCGGATGCATCT 61.119 57.895 25.28 5.06 40.88 2.90
31 32 0.816421 TCGACCGTCGGATGCATCTA 60.816 55.000 25.28 11.94 40.88 1.98
32 33 0.660595 CGACCGTCGGATGCATCTAC 60.661 60.000 25.28 20.84 36.00 2.59
33 34 0.669077 GACCGTCGGATGCATCTACT 59.331 55.000 25.28 9.76 0.00 2.57
34 35 0.385751 ACCGTCGGATGCATCTACTG 59.614 55.000 25.28 20.08 0.00 2.74
35 36 0.385751 CCGTCGGATGCATCTACTGT 59.614 55.000 25.28 0.00 0.00 3.55
36 37 1.202417 CCGTCGGATGCATCTACTGTT 60.202 52.381 25.28 0.00 0.00 3.16
37 38 2.540515 CGTCGGATGCATCTACTGTTT 58.459 47.619 25.28 0.00 0.00 2.83
38 39 2.930040 CGTCGGATGCATCTACTGTTTT 59.070 45.455 25.28 0.00 0.00 2.43
39 40 4.109766 CGTCGGATGCATCTACTGTTTTA 58.890 43.478 25.28 0.00 0.00 1.52
40 41 4.026804 CGTCGGATGCATCTACTGTTTTAC 60.027 45.833 25.28 4.58 0.00 2.01
41 42 5.109903 GTCGGATGCATCTACTGTTTTACT 58.890 41.667 25.28 0.00 0.00 2.24
42 43 5.581085 GTCGGATGCATCTACTGTTTTACTT 59.419 40.000 25.28 0.00 0.00 2.24
43 44 6.092259 GTCGGATGCATCTACTGTTTTACTTT 59.908 38.462 25.28 0.00 0.00 2.66
44 45 6.653320 TCGGATGCATCTACTGTTTTACTTTT 59.347 34.615 25.28 0.00 0.00 2.27
45 46 6.961554 CGGATGCATCTACTGTTTTACTTTTC 59.038 38.462 25.28 2.46 0.00 2.29
46 47 7.360861 CGGATGCATCTACTGTTTTACTTTTCA 60.361 37.037 25.28 0.00 0.00 2.69
47 48 8.462016 GGATGCATCTACTGTTTTACTTTTCAT 58.538 33.333 25.28 0.00 0.00 2.57
48 49 9.495754 GATGCATCTACTGTTTTACTTTTCATC 57.504 33.333 19.70 0.00 0.00 2.92
49 50 8.621532 TGCATCTACTGTTTTACTTTTCATCT 57.378 30.769 0.00 0.00 0.00 2.90
50 51 9.066892 TGCATCTACTGTTTTACTTTTCATCTT 57.933 29.630 0.00 0.00 0.00 2.40
59 60 9.658475 TGTTTTACTTTTCATCTTATGTTGTCG 57.342 29.630 0.00 0.00 0.00 4.35
60 61 8.627428 GTTTTACTTTTCATCTTATGTTGTCGC 58.373 33.333 0.00 0.00 0.00 5.19
61 62 7.667043 TTACTTTTCATCTTATGTTGTCGCT 57.333 32.000 0.00 0.00 0.00 4.93
62 63 8.766000 TTACTTTTCATCTTATGTTGTCGCTA 57.234 30.769 0.00 0.00 0.00 4.26
63 64 7.061752 ACTTTTCATCTTATGTTGTCGCTAC 57.938 36.000 0.00 0.00 0.00 3.58
64 65 6.649141 ACTTTTCATCTTATGTTGTCGCTACA 59.351 34.615 0.00 0.00 0.00 2.74
65 66 6.647212 TTTCATCTTATGTTGTCGCTACAG 57.353 37.500 0.00 0.00 36.83 2.74
66 67 5.324784 TCATCTTATGTTGTCGCTACAGT 57.675 39.130 0.00 0.00 36.83 3.55
67 68 5.102313 TCATCTTATGTTGTCGCTACAGTG 58.898 41.667 0.00 0.00 36.83 3.66
68 69 4.776795 TCTTATGTTGTCGCTACAGTGA 57.223 40.909 0.00 0.00 36.83 3.41
69 70 5.128992 TCTTATGTTGTCGCTACAGTGAA 57.871 39.130 0.00 0.00 36.83 3.18
70 71 4.921515 TCTTATGTTGTCGCTACAGTGAAC 59.078 41.667 0.00 0.00 36.83 3.18
71 72 2.882927 TGTTGTCGCTACAGTGAACT 57.117 45.000 0.00 0.00 36.83 3.01
84 85 4.376450 CAGTGAACTGTAACTTTCTCGC 57.624 45.455 2.14 0.00 39.09 5.03
85 86 3.184581 CAGTGAACTGTAACTTTCTCGCC 59.815 47.826 2.14 0.00 39.09 5.54
86 87 3.069729 AGTGAACTGTAACTTTCTCGCCT 59.930 43.478 0.00 0.00 0.00 5.52
87 88 4.280174 AGTGAACTGTAACTTTCTCGCCTA 59.720 41.667 0.00 0.00 0.00 3.93
88 89 5.047235 AGTGAACTGTAACTTTCTCGCCTAT 60.047 40.000 0.00 0.00 0.00 2.57
89 90 6.152323 AGTGAACTGTAACTTTCTCGCCTATA 59.848 38.462 0.00 0.00 0.00 1.31
90 91 6.810182 GTGAACTGTAACTTTCTCGCCTATAA 59.190 38.462 0.00 0.00 0.00 0.98
91 92 7.009357 GTGAACTGTAACTTTCTCGCCTATAAG 59.991 40.741 0.00 0.00 0.00 1.73
92 93 6.527057 ACTGTAACTTTCTCGCCTATAAGT 57.473 37.500 0.00 0.00 32.52 2.24
93 94 6.331061 ACTGTAACTTTCTCGCCTATAAGTG 58.669 40.000 0.00 0.00 31.64 3.16
94 95 6.152323 ACTGTAACTTTCTCGCCTATAAGTGA 59.848 38.462 0.00 0.00 31.64 3.41
95 96 6.561614 TGTAACTTTCTCGCCTATAAGTGAG 58.438 40.000 5.67 5.67 44.18 3.51
96 97 5.662674 AACTTTCTCGCCTATAAGTGAGT 57.337 39.130 10.89 0.00 43.45 3.41
97 98 5.251601 ACTTTCTCGCCTATAAGTGAGTC 57.748 43.478 10.89 0.00 43.45 3.36
98 99 3.965292 TTCTCGCCTATAAGTGAGTCG 57.035 47.619 10.89 0.00 43.45 4.18
99 100 2.219458 TCTCGCCTATAAGTGAGTCGG 58.781 52.381 10.89 0.00 43.45 4.79
100 101 1.267261 CTCGCCTATAAGTGAGTCGGG 59.733 57.143 4.06 0.00 39.14 5.14
101 102 0.318784 CGCCTATAAGTGAGTCGGGC 60.319 60.000 0.00 0.00 35.33 6.13
102 103 1.041437 GCCTATAAGTGAGTCGGGCT 58.959 55.000 0.00 0.00 35.73 5.19
103 104 1.269831 GCCTATAAGTGAGTCGGGCTG 60.270 57.143 0.00 0.00 35.73 4.85
104 105 2.032620 CCTATAAGTGAGTCGGGCTGT 58.967 52.381 0.00 0.00 0.00 4.40
105 106 2.223829 CCTATAAGTGAGTCGGGCTGTG 60.224 54.545 0.00 0.00 0.00 3.66
106 107 0.537188 ATAAGTGAGTCGGGCTGTGG 59.463 55.000 0.00 0.00 0.00 4.17
107 108 2.167398 TAAGTGAGTCGGGCTGTGGC 62.167 60.000 0.00 0.00 37.82 5.01
108 109 4.008933 GTGAGTCGGGCTGTGGCT 62.009 66.667 0.00 0.00 38.73 4.75
109 110 4.007644 TGAGTCGGGCTGTGGCTG 62.008 66.667 0.00 0.00 38.73 4.85
110 111 3.695606 GAGTCGGGCTGTGGCTGA 61.696 66.667 0.00 0.00 41.20 4.26
111 112 3.655810 GAGTCGGGCTGTGGCTGAG 62.656 68.421 2.83 0.00 44.01 3.35
112 113 4.008933 GTCGGGCTGTGGCTGAGT 62.009 66.667 2.83 0.00 44.01 3.41
113 114 2.283604 TCGGGCTGTGGCTGAGTA 60.284 61.111 0.00 0.00 38.58 2.59
114 115 2.185350 CGGGCTGTGGCTGAGTAG 59.815 66.667 0.00 0.00 36.53 2.57
115 116 2.586792 GGGCTGTGGCTGAGTAGG 59.413 66.667 0.00 0.00 38.73 3.18
116 117 2.294078 GGGCTGTGGCTGAGTAGGT 61.294 63.158 0.00 0.00 38.73 3.08
117 118 0.976073 GGGCTGTGGCTGAGTAGGTA 60.976 60.000 0.00 0.00 38.73 3.08
118 119 0.461961 GGCTGTGGCTGAGTAGGTAG 59.538 60.000 0.00 0.00 38.73 3.18
119 120 0.179097 GCTGTGGCTGAGTAGGTAGC 60.179 60.000 0.00 0.00 39.17 3.58
120 121 0.101399 CTGTGGCTGAGTAGGTAGCG 59.899 60.000 0.00 0.00 40.78 4.26
121 122 0.611062 TGTGGCTGAGTAGGTAGCGT 60.611 55.000 0.00 0.00 40.78 5.07
122 123 0.179134 GTGGCTGAGTAGGTAGCGTG 60.179 60.000 0.00 0.00 40.78 5.34
123 124 0.323087 TGGCTGAGTAGGTAGCGTGA 60.323 55.000 0.00 0.00 40.78 4.35
124 125 0.815734 GGCTGAGTAGGTAGCGTGAA 59.184 55.000 0.00 0.00 40.78 3.18
125 126 1.409427 GGCTGAGTAGGTAGCGTGAAT 59.591 52.381 0.00 0.00 40.78 2.57
126 127 2.159085 GGCTGAGTAGGTAGCGTGAATT 60.159 50.000 0.00 0.00 40.78 2.17
127 128 2.860735 GCTGAGTAGGTAGCGTGAATTG 59.139 50.000 0.00 0.00 0.00 2.32
128 129 3.428999 GCTGAGTAGGTAGCGTGAATTGA 60.429 47.826 0.00 0.00 0.00 2.57
129 130 4.737946 GCTGAGTAGGTAGCGTGAATTGAT 60.738 45.833 0.00 0.00 0.00 2.57
130 131 4.933330 TGAGTAGGTAGCGTGAATTGATC 58.067 43.478 0.00 0.00 0.00 2.92
131 132 4.202121 TGAGTAGGTAGCGTGAATTGATCC 60.202 45.833 0.00 0.00 0.00 3.36
132 133 3.961408 AGTAGGTAGCGTGAATTGATCCT 59.039 43.478 0.00 0.00 0.00 3.24
133 134 5.138276 AGTAGGTAGCGTGAATTGATCCTA 58.862 41.667 0.00 0.00 0.00 2.94
134 135 5.775701 AGTAGGTAGCGTGAATTGATCCTAT 59.224 40.000 0.00 0.00 0.00 2.57
135 136 5.552870 AGGTAGCGTGAATTGATCCTATT 57.447 39.130 0.00 0.00 0.00 1.73
136 137 5.542779 AGGTAGCGTGAATTGATCCTATTC 58.457 41.667 9.56 9.56 33.58 1.75
137 138 5.305644 AGGTAGCGTGAATTGATCCTATTCT 59.694 40.000 14.93 2.64 34.00 2.40
138 139 5.992217 GGTAGCGTGAATTGATCCTATTCTT 59.008 40.000 14.93 5.31 34.00 2.52
139 140 5.998454 AGCGTGAATTGATCCTATTCTTG 57.002 39.130 14.93 10.12 34.00 3.02
140 141 4.274459 AGCGTGAATTGATCCTATTCTTGC 59.726 41.667 14.93 16.17 35.25 4.01
141 142 4.555511 GCGTGAATTGATCCTATTCTTGCC 60.556 45.833 14.93 4.48 34.00 4.52
142 143 4.818546 CGTGAATTGATCCTATTCTTGCCT 59.181 41.667 14.93 0.00 34.00 4.75
143 144 5.297776 CGTGAATTGATCCTATTCTTGCCTT 59.702 40.000 14.93 0.00 34.00 4.35
144 145 6.183360 CGTGAATTGATCCTATTCTTGCCTTT 60.183 38.462 14.93 0.00 34.00 3.11
145 146 6.976925 GTGAATTGATCCTATTCTTGCCTTTG 59.023 38.462 14.93 0.00 34.00 2.77
146 147 6.891361 TGAATTGATCCTATTCTTGCCTTTGA 59.109 34.615 14.93 0.00 34.00 2.69
147 148 6.956202 ATTGATCCTATTCTTGCCTTTGAG 57.044 37.500 0.00 0.00 0.00 3.02
148 149 4.202441 TGATCCTATTCTTGCCTTTGAGC 58.798 43.478 0.00 0.00 0.00 4.26
149 150 3.719268 TCCTATTCTTGCCTTTGAGCA 57.281 42.857 0.00 0.00 42.17 4.26
150 151 3.614092 TCCTATTCTTGCCTTTGAGCAG 58.386 45.455 0.00 0.00 45.13 4.24
151 152 3.264193 TCCTATTCTTGCCTTTGAGCAGA 59.736 43.478 0.00 0.00 45.13 4.26
152 153 4.012374 CCTATTCTTGCCTTTGAGCAGAA 58.988 43.478 0.00 0.00 45.13 3.02
153 154 4.096081 CCTATTCTTGCCTTTGAGCAGAAG 59.904 45.833 0.00 0.00 45.13 2.85
154 155 2.936919 TCTTGCCTTTGAGCAGAAGA 57.063 45.000 0.00 0.00 45.13 2.87
155 156 3.213206 TCTTGCCTTTGAGCAGAAGAA 57.787 42.857 0.00 0.00 45.13 2.52
156 157 3.554934 TCTTGCCTTTGAGCAGAAGAAA 58.445 40.909 0.00 0.00 45.13 2.52
157 158 4.147321 TCTTGCCTTTGAGCAGAAGAAAT 58.853 39.130 0.00 0.00 45.13 2.17
158 159 5.316167 TCTTGCCTTTGAGCAGAAGAAATA 58.684 37.500 0.00 0.00 45.13 1.40
159 160 5.182001 TCTTGCCTTTGAGCAGAAGAAATAC 59.818 40.000 0.00 0.00 45.13 1.89
160 161 3.758554 TGCCTTTGAGCAGAAGAAATACC 59.241 43.478 0.00 0.00 38.00 2.73
161 162 3.129462 GCCTTTGAGCAGAAGAAATACCC 59.871 47.826 0.00 0.00 0.00 3.69
162 163 4.593956 CCTTTGAGCAGAAGAAATACCCT 58.406 43.478 0.00 0.00 0.00 4.34
163 164 5.745227 CCTTTGAGCAGAAGAAATACCCTA 58.255 41.667 0.00 0.00 0.00 3.53
164 165 6.360618 CCTTTGAGCAGAAGAAATACCCTAT 58.639 40.000 0.00 0.00 0.00 2.57
165 166 7.509546 CCTTTGAGCAGAAGAAATACCCTATA 58.490 38.462 0.00 0.00 0.00 1.31
166 167 7.659390 CCTTTGAGCAGAAGAAATACCCTATAG 59.341 40.741 0.00 0.00 0.00 1.31
167 168 7.914427 TTGAGCAGAAGAAATACCCTATAGA 57.086 36.000 0.00 0.00 0.00 1.98
168 169 7.291411 TGAGCAGAAGAAATACCCTATAGAC 57.709 40.000 0.00 0.00 0.00 2.59
169 170 6.839134 TGAGCAGAAGAAATACCCTATAGACA 59.161 38.462 0.00 0.00 0.00 3.41
170 171 7.510685 TGAGCAGAAGAAATACCCTATAGACAT 59.489 37.037 0.00 0.00 0.00 3.06
171 172 8.958060 AGCAGAAGAAATACCCTATAGACATA 57.042 34.615 0.00 0.00 0.00 2.29
172 173 9.554053 AGCAGAAGAAATACCCTATAGACATAT 57.446 33.333 0.00 0.00 0.00 1.78
204 205 9.512588 ACAATATCCATACAAATTCTGGATCTC 57.487 33.333 6.58 0.00 44.59 2.75
205 206 9.511272 CAATATCCATACAAATTCTGGATCTCA 57.489 33.333 6.58 0.00 44.59 3.27
209 210 8.455903 TCCATACAAATTCTGGATCTCAAATC 57.544 34.615 0.00 0.00 34.17 2.17
210 211 7.503566 TCCATACAAATTCTGGATCTCAAATCC 59.496 37.037 0.00 0.00 34.17 3.01
211 212 7.255730 CCATACAAATTCTGGATCTCAAATCCC 60.256 40.741 1.76 0.00 37.40 3.85
212 213 4.958581 ACAAATTCTGGATCTCAAATCCCC 59.041 41.667 1.76 0.00 37.40 4.81
213 214 5.206587 CAAATTCTGGATCTCAAATCCCCT 58.793 41.667 1.76 0.00 37.40 4.79
214 215 5.478503 AATTCTGGATCTCAAATCCCCTT 57.521 39.130 1.76 0.00 37.40 3.95
215 216 4.510167 TTCTGGATCTCAAATCCCCTTC 57.490 45.455 1.76 0.00 37.40 3.46
216 217 2.780010 TCTGGATCTCAAATCCCCTTCC 59.220 50.000 1.76 0.00 37.40 3.46
217 218 2.782341 CTGGATCTCAAATCCCCTTCCT 59.218 50.000 1.76 0.00 37.40 3.36
218 219 2.780010 TGGATCTCAAATCCCCTTCCTC 59.220 50.000 1.76 0.00 37.40 3.71
219 220 3.052329 GGATCTCAAATCCCCTTCCTCT 58.948 50.000 0.00 0.00 32.09 3.69
220 221 4.235372 GGATCTCAAATCCCCTTCCTCTA 58.765 47.826 0.00 0.00 32.09 2.43
221 222 4.285775 GGATCTCAAATCCCCTTCCTCTAG 59.714 50.000 0.00 0.00 32.09 2.43
222 223 4.354208 TCTCAAATCCCCTTCCTCTAGT 57.646 45.455 0.00 0.00 0.00 2.57
223 224 4.699994 TCTCAAATCCCCTTCCTCTAGTT 58.300 43.478 0.00 0.00 0.00 2.24
224 225 4.717280 TCTCAAATCCCCTTCCTCTAGTTC 59.283 45.833 0.00 0.00 0.00 3.01
225 226 3.451178 TCAAATCCCCTTCCTCTAGTTCG 59.549 47.826 0.00 0.00 0.00 3.95
226 227 3.399952 AATCCCCTTCCTCTAGTTCGA 57.600 47.619 0.00 0.00 0.00 3.71
227 228 3.621682 ATCCCCTTCCTCTAGTTCGAT 57.378 47.619 0.00 0.00 0.00 3.59
228 229 2.946785 TCCCCTTCCTCTAGTTCGATC 58.053 52.381 0.00 0.00 0.00 3.69
229 230 2.514582 TCCCCTTCCTCTAGTTCGATCT 59.485 50.000 0.97 0.97 0.00 2.75
230 231 2.888414 CCCCTTCCTCTAGTTCGATCTC 59.112 54.545 0.00 0.00 0.00 2.75
231 232 3.435890 CCCCTTCCTCTAGTTCGATCTCT 60.436 52.174 0.00 0.00 0.00 3.10
232 233 3.818773 CCCTTCCTCTAGTTCGATCTCTC 59.181 52.174 0.00 0.00 0.00 3.20
233 234 4.445735 CCCTTCCTCTAGTTCGATCTCTCT 60.446 50.000 0.00 0.00 0.00 3.10
234 235 4.515191 CCTTCCTCTAGTTCGATCTCTCTG 59.485 50.000 0.00 0.00 0.00 3.35
235 236 5.360649 TTCCTCTAGTTCGATCTCTCTGA 57.639 43.478 0.00 0.00 0.00 3.27
236 237 5.360649 TCCTCTAGTTCGATCTCTCTGAA 57.639 43.478 0.00 0.00 0.00 3.02
237 238 5.746284 TCCTCTAGTTCGATCTCTCTGAAA 58.254 41.667 0.00 0.00 0.00 2.69
238 239 6.361433 TCCTCTAGTTCGATCTCTCTGAAAT 58.639 40.000 0.00 0.00 0.00 2.17
239 240 6.831353 TCCTCTAGTTCGATCTCTCTGAAATT 59.169 38.462 0.00 0.00 0.00 1.82
240 241 7.012894 TCCTCTAGTTCGATCTCTCTGAAATTC 59.987 40.741 0.00 0.00 0.00 2.17
241 242 6.720343 TCTAGTTCGATCTCTCTGAAATTCG 58.280 40.000 0.00 0.00 0.00 3.34
242 243 4.109050 AGTTCGATCTCTCTGAAATTCGC 58.891 43.478 0.00 0.00 0.00 4.70
243 244 4.109050 GTTCGATCTCTCTGAAATTCGCT 58.891 43.478 0.00 0.00 0.00 4.93
244 245 4.377839 TCGATCTCTCTGAAATTCGCTT 57.622 40.909 0.00 0.00 0.00 4.68
245 246 5.500645 TCGATCTCTCTGAAATTCGCTTA 57.499 39.130 0.00 0.00 0.00 3.09
246 247 5.515184 TCGATCTCTCTGAAATTCGCTTAG 58.485 41.667 0.00 0.00 0.00 2.18
247 248 5.066634 TCGATCTCTCTGAAATTCGCTTAGT 59.933 40.000 0.00 0.00 0.00 2.24
248 249 5.746245 CGATCTCTCTGAAATTCGCTTAGTT 59.254 40.000 0.00 0.00 0.00 2.24
249 250 6.291532 CGATCTCTCTGAAATTCGCTTAGTTG 60.292 42.308 0.00 0.00 0.00 3.16
250 251 6.025749 TCTCTCTGAAATTCGCTTAGTTGA 57.974 37.500 0.00 0.00 0.00 3.18
251 252 5.864474 TCTCTCTGAAATTCGCTTAGTTGAC 59.136 40.000 0.00 0.00 0.00 3.18
252 253 5.538118 TCTCTGAAATTCGCTTAGTTGACA 58.462 37.500 0.00 0.00 0.00 3.58
253 254 5.405571 TCTCTGAAATTCGCTTAGTTGACAC 59.594 40.000 0.00 0.00 0.00 3.67
254 255 4.451096 TCTGAAATTCGCTTAGTTGACACC 59.549 41.667 0.00 0.00 0.00 4.16
255 256 3.500680 TGAAATTCGCTTAGTTGACACCC 59.499 43.478 0.00 0.00 0.00 4.61
256 257 1.722011 ATTCGCTTAGTTGACACCCG 58.278 50.000 0.00 0.00 0.00 5.28
257 258 0.320073 TTCGCTTAGTTGACACCCGG 60.320 55.000 0.00 0.00 0.00 5.73
258 259 1.740296 CGCTTAGTTGACACCCGGG 60.740 63.158 22.25 22.25 0.00 5.73
259 260 1.675219 GCTTAGTTGACACCCGGGA 59.325 57.895 32.02 0.00 0.00 5.14
260 261 0.252197 GCTTAGTTGACACCCGGGAT 59.748 55.000 32.02 15.78 0.00 3.85
261 262 1.742750 GCTTAGTTGACACCCGGGATC 60.743 57.143 32.02 24.15 0.00 3.36
262 263 1.831736 CTTAGTTGACACCCGGGATCT 59.168 52.381 32.02 16.76 0.00 2.75
263 264 1.191535 TAGTTGACACCCGGGATCTG 58.808 55.000 32.02 18.73 0.00 2.90
264 265 0.544357 AGTTGACACCCGGGATCTGA 60.544 55.000 32.02 13.86 0.00 3.27
265 266 0.391263 GTTGACACCCGGGATCTGAC 60.391 60.000 32.02 20.62 0.00 3.51
266 267 0.834261 TTGACACCCGGGATCTGACA 60.834 55.000 32.02 19.03 0.00 3.58
267 268 1.257750 TGACACCCGGGATCTGACAG 61.258 60.000 32.02 8.37 0.00 3.51
268 269 1.961180 GACACCCGGGATCTGACAGG 61.961 65.000 32.02 6.90 0.00 4.00
270 271 3.866582 CCCGGGATCTGACAGGGC 61.867 72.222 18.48 0.00 35.09 5.19
271 272 2.765807 CCGGGATCTGACAGGGCT 60.766 66.667 1.81 0.00 0.00 5.19
272 273 2.801631 CCGGGATCTGACAGGGCTC 61.802 68.421 1.81 0.00 0.00 4.70
273 274 2.801631 CGGGATCTGACAGGGCTCC 61.802 68.421 1.81 6.83 0.00 4.70
274 275 1.690633 GGGATCTGACAGGGCTCCA 60.691 63.158 16.50 0.00 0.00 3.86
275 276 1.694133 GGGATCTGACAGGGCTCCAG 61.694 65.000 16.50 0.00 0.00 3.86
276 277 0.980231 GGATCTGACAGGGCTCCAGT 60.980 60.000 1.81 0.00 0.00 4.00
277 278 0.908198 GATCTGACAGGGCTCCAGTT 59.092 55.000 1.81 0.00 0.00 3.16
278 279 0.617413 ATCTGACAGGGCTCCAGTTG 59.383 55.000 1.81 0.00 0.00 3.16
279 280 1.673665 CTGACAGGGCTCCAGTTGC 60.674 63.158 0.00 0.00 0.00 4.17
280 281 2.743928 GACAGGGCTCCAGTTGCG 60.744 66.667 0.00 0.00 0.00 4.85
281 282 4.335647 ACAGGGCTCCAGTTGCGG 62.336 66.667 0.00 0.00 0.00 5.69
282 283 4.020617 CAGGGCTCCAGTTGCGGA 62.021 66.667 0.00 0.00 0.00 5.54
283 284 3.249189 AGGGCTCCAGTTGCGGAA 61.249 61.111 0.00 0.00 33.65 4.30
284 285 2.747855 GGGCTCCAGTTGCGGAAG 60.748 66.667 0.00 0.00 33.65 3.46
285 286 2.747855 GGCTCCAGTTGCGGAAGG 60.748 66.667 0.00 0.00 33.65 3.46
286 287 3.435186 GCTCCAGTTGCGGAAGGC 61.435 66.667 0.00 0.00 43.96 4.35
295 296 4.856607 GCGGAAGGCGACTCGGAG 62.857 72.222 2.83 2.83 42.68 4.63
296 297 4.856607 CGGAAGGCGACTCGGAGC 62.857 72.222 4.58 0.00 42.68 4.70
297 298 3.453679 GGAAGGCGACTCGGAGCT 61.454 66.667 4.58 0.00 42.68 4.09
298 299 2.202676 GAAGGCGACTCGGAGCTG 60.203 66.667 4.58 0.00 42.68 4.24
299 300 3.708220 GAAGGCGACTCGGAGCTGG 62.708 68.421 4.58 0.00 42.68 4.85
300 301 4.742649 AGGCGACTCGGAGCTGGA 62.743 66.667 4.58 0.00 32.90 3.86
301 302 4.200283 GGCGACTCGGAGCTGGAG 62.200 72.222 4.58 9.31 37.54 3.86
302 303 4.863925 GCGACTCGGAGCTGGAGC 62.864 72.222 4.58 0.22 42.49 4.70
303 304 3.443925 CGACTCGGAGCTGGAGCA 61.444 66.667 4.58 0.00 45.16 4.26
304 305 2.493973 GACTCGGAGCTGGAGCAG 59.506 66.667 4.58 0.00 45.16 4.24
305 306 3.073735 ACTCGGAGCTGGAGCAGG 61.074 66.667 4.58 0.00 45.16 4.85
306 307 4.527583 CTCGGAGCTGGAGCAGGC 62.528 72.222 0.00 0.00 45.16 4.85
353 366 1.342076 GGGAAGGGAGTGGGGAATTTC 60.342 57.143 0.00 0.00 0.00 2.17
481 496 4.052229 CGCCGAACGGACCAGAGT 62.052 66.667 17.63 0.00 38.44 3.24
491 506 1.976112 GACCAGAGTCCAGACCACC 59.024 63.158 0.00 0.00 37.00 4.61
492 507 0.832135 GACCAGAGTCCAGACCACCA 60.832 60.000 0.00 0.00 37.00 4.17
496 511 0.902516 AGAGTCCAGACCACCAGAGC 60.903 60.000 0.00 0.00 0.00 4.09
1159 1193 1.063642 ACATGACGGAGGAGATGGAGA 60.064 52.381 0.00 0.00 0.00 3.71
1529 3366 4.671831 TCCCCAAATTCACACACATACAT 58.328 39.130 0.00 0.00 0.00 2.29
1650 3592 6.313658 TGACATATAATGCAATGATCGTAGGC 59.686 38.462 3.15 4.89 0.00 3.93
1746 3688 4.209307 TGATTGGACATACGGCACTTTA 57.791 40.909 0.00 0.00 0.00 1.85
2263 4205 3.318839 TCCCAACGTTATCACCTATACCG 59.681 47.826 0.00 0.00 32.65 4.02
2339 4281 5.258841 ACTTGAAATGATGGAGCAGAATGA 58.741 37.500 0.00 0.00 39.69 2.57
2368 4310 2.549134 CCCGATGACCAATTATACGGCA 60.549 50.000 0.00 0.00 37.98 5.69
2518 4460 3.628646 GACATTGCCGCCACCCTCT 62.629 63.158 0.00 0.00 0.00 3.69
2541 4483 4.672251 AGCATGATTGGTGAGGGC 57.328 55.556 0.00 0.00 30.87 5.19
2925 4867 7.127186 TGTGGGAATATGGGATATATTGATCGT 59.873 37.037 0.00 0.00 0.00 3.73
3099 5041 5.596361 TGTTTGGCAGTTTCTTGAAAGGATA 59.404 36.000 0.00 0.00 0.00 2.59
3181 5123 1.549203 AGCCAACCGCATTGAAGAAT 58.451 45.000 0.00 0.00 41.23 2.40
3187 5129 4.096231 CCAACCGCATTGAAGAATCATGTA 59.904 41.667 0.00 0.00 41.23 2.29
3540 5482 6.828273 CCATGGAGAATAAACACTGTTCCATA 59.172 38.462 5.56 0.00 40.86 2.74
3611 5553 0.393077 AGTCTGGTTGGTGAACTCCG 59.607 55.000 0.00 0.00 32.15 4.63
3832 6001 2.722094 TCCTGATTTTCCGTTCCATGG 58.278 47.619 4.97 4.97 0.00 3.66
3892 6061 3.587061 ACAACCTGTATCATCCTTCACCA 59.413 43.478 0.00 0.00 0.00 4.17
3915 6084 6.599244 CCATAGAAACTAACCATGTCACATGT 59.401 38.462 16.74 1.52 0.00 3.21
3917 6086 5.003804 AGAAACTAACCATGTCACATGTCC 58.996 41.667 16.74 0.00 0.00 4.02
4112 6281 5.047802 ACAAAACTTCGATCAAGGCATCAAT 60.048 36.000 8.95 0.00 36.26 2.57
4267 6438 3.487544 GGATGCCGTTTGATCAGCTAAAC 60.488 47.826 6.27 2.62 34.35 2.01
4404 6581 5.366477 TGGCTTCTCCATTCTATGTGATACA 59.634 40.000 0.00 0.00 40.72 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.681705 CGGTCGACAGCGTAAGTAA 57.318 52.632 18.91 0.00 38.76 2.24
8 9 2.579787 CATCCGACGGTCGACAGC 60.580 66.667 30.33 8.80 43.74 4.40
9 10 2.579787 GCATCCGACGGTCGACAG 60.580 66.667 30.33 16.61 43.74 3.51
10 11 2.607668 GATGCATCCGACGGTCGACA 62.608 60.000 30.33 21.18 43.74 4.35
11 12 1.944676 GATGCATCCGACGGTCGAC 60.945 63.158 30.33 16.75 43.74 4.20
12 13 0.816421 TAGATGCATCCGACGGTCGA 60.816 55.000 30.33 16.97 43.74 4.20
13 14 0.660595 GTAGATGCATCCGACGGTCG 60.661 60.000 23.06 22.88 40.07 4.79
14 15 0.669077 AGTAGATGCATCCGACGGTC 59.331 55.000 23.06 3.34 0.00 4.79
15 16 0.385751 CAGTAGATGCATCCGACGGT 59.614 55.000 23.06 6.10 0.00 4.83
16 17 0.385751 ACAGTAGATGCATCCGACGG 59.614 55.000 23.06 21.58 0.00 4.79
17 18 2.209838 AACAGTAGATGCATCCGACG 57.790 50.000 23.06 17.41 0.00 5.12
18 19 5.109903 AGTAAAACAGTAGATGCATCCGAC 58.890 41.667 23.06 19.97 0.00 4.79
19 20 5.339008 AGTAAAACAGTAGATGCATCCGA 57.661 39.130 23.06 8.95 0.00 4.55
20 21 6.422776 AAAGTAAAACAGTAGATGCATCCG 57.577 37.500 23.06 11.67 0.00 4.18
21 22 7.816640 TGAAAAGTAAAACAGTAGATGCATCC 58.183 34.615 23.06 8.93 0.00 3.51
22 23 9.495754 GATGAAAAGTAAAACAGTAGATGCATC 57.504 33.333 19.37 19.37 0.00 3.91
23 24 9.236006 AGATGAAAAGTAAAACAGTAGATGCAT 57.764 29.630 0.00 0.00 0.00 3.96
24 25 8.621532 AGATGAAAAGTAAAACAGTAGATGCA 57.378 30.769 0.00 0.00 0.00 3.96
33 34 9.658475 CGACAACATAAGATGAAAAGTAAAACA 57.342 29.630 0.00 0.00 0.00 2.83
34 35 8.627428 GCGACAACATAAGATGAAAAGTAAAAC 58.373 33.333 0.00 0.00 0.00 2.43
35 36 8.564574 AGCGACAACATAAGATGAAAAGTAAAA 58.435 29.630 0.00 0.00 0.00 1.52
36 37 8.094798 AGCGACAACATAAGATGAAAAGTAAA 57.905 30.769 0.00 0.00 0.00 2.01
37 38 7.667043 AGCGACAACATAAGATGAAAAGTAA 57.333 32.000 0.00 0.00 0.00 2.24
38 39 7.815549 TGTAGCGACAACATAAGATGAAAAGTA 59.184 33.333 0.00 0.00 30.68 2.24
39 40 6.649141 TGTAGCGACAACATAAGATGAAAAGT 59.351 34.615 0.00 0.00 30.68 2.66
40 41 7.060600 TGTAGCGACAACATAAGATGAAAAG 57.939 36.000 0.00 0.00 30.68 2.27
41 42 6.649141 ACTGTAGCGACAACATAAGATGAAAA 59.351 34.615 0.14 0.00 34.35 2.29
42 43 6.090763 CACTGTAGCGACAACATAAGATGAAA 59.909 38.462 0.14 0.00 34.35 2.69
43 44 5.576774 CACTGTAGCGACAACATAAGATGAA 59.423 40.000 0.14 0.00 34.35 2.57
44 45 5.102313 CACTGTAGCGACAACATAAGATGA 58.898 41.667 0.14 0.00 34.35 2.92
45 46 5.102313 TCACTGTAGCGACAACATAAGATG 58.898 41.667 0.14 0.00 34.35 2.90
46 47 5.324784 TCACTGTAGCGACAACATAAGAT 57.675 39.130 0.14 0.00 34.35 2.40
47 48 4.776795 TCACTGTAGCGACAACATAAGA 57.223 40.909 0.14 0.00 34.35 2.10
48 49 4.923871 AGTTCACTGTAGCGACAACATAAG 59.076 41.667 0.14 0.00 34.35 1.73
49 50 4.684242 CAGTTCACTGTAGCGACAACATAA 59.316 41.667 0.14 0.00 39.09 1.90
50 51 4.234574 CAGTTCACTGTAGCGACAACATA 58.765 43.478 0.14 0.00 39.09 2.29
51 52 3.059884 CAGTTCACTGTAGCGACAACAT 58.940 45.455 0.14 0.00 39.09 2.71
52 53 2.469826 CAGTTCACTGTAGCGACAACA 58.530 47.619 0.14 0.00 39.09 3.33
64 65 3.069729 AGGCGAGAAAGTTACAGTTCACT 59.930 43.478 0.00 0.00 0.00 3.41
65 66 3.391049 AGGCGAGAAAGTTACAGTTCAC 58.609 45.455 0.00 0.00 0.00 3.18
66 67 3.746045 AGGCGAGAAAGTTACAGTTCA 57.254 42.857 0.00 0.00 0.00 3.18
67 68 7.009357 CACTTATAGGCGAGAAAGTTACAGTTC 59.991 40.741 0.00 0.00 29.93 3.01
68 69 6.812160 CACTTATAGGCGAGAAAGTTACAGTT 59.188 38.462 0.00 0.00 29.93 3.16
69 70 6.152323 TCACTTATAGGCGAGAAAGTTACAGT 59.848 38.462 0.00 0.00 29.93 3.55
70 71 6.561614 TCACTTATAGGCGAGAAAGTTACAG 58.438 40.000 0.00 0.00 29.93 2.74
71 72 6.152323 ACTCACTTATAGGCGAGAAAGTTACA 59.848 38.462 6.87 0.00 29.93 2.41
72 73 6.562518 ACTCACTTATAGGCGAGAAAGTTAC 58.437 40.000 6.87 0.00 29.93 2.50
73 74 6.770746 ACTCACTTATAGGCGAGAAAGTTA 57.229 37.500 6.87 0.00 29.93 2.24
74 75 5.652518 GACTCACTTATAGGCGAGAAAGTT 58.347 41.667 6.87 0.00 29.93 2.66
75 76 5.251601 GACTCACTTATAGGCGAGAAAGT 57.748 43.478 6.87 0.00 32.52 2.66
82 83 0.318784 GCCCGACTCACTTATAGGCG 60.319 60.000 0.00 0.00 45.26 5.52
83 84 1.041437 AGCCCGACTCACTTATAGGC 58.959 55.000 0.00 0.00 39.25 3.93
84 85 2.032620 ACAGCCCGACTCACTTATAGG 58.967 52.381 0.00 0.00 0.00 2.57
85 86 2.223829 CCACAGCCCGACTCACTTATAG 60.224 54.545 0.00 0.00 0.00 1.31
86 87 1.754803 CCACAGCCCGACTCACTTATA 59.245 52.381 0.00 0.00 0.00 0.98
87 88 0.537188 CCACAGCCCGACTCACTTAT 59.463 55.000 0.00 0.00 0.00 1.73
88 89 1.972198 CCACAGCCCGACTCACTTA 59.028 57.895 0.00 0.00 0.00 2.24
89 90 2.743718 CCACAGCCCGACTCACTT 59.256 61.111 0.00 0.00 0.00 3.16
90 91 4.008933 GCCACAGCCCGACTCACT 62.009 66.667 0.00 0.00 0.00 3.41
91 92 4.008933 AGCCACAGCCCGACTCAC 62.009 66.667 0.00 0.00 41.25 3.51
92 93 4.007644 CAGCCACAGCCCGACTCA 62.008 66.667 0.00 0.00 41.25 3.41
93 94 3.655810 CTCAGCCACAGCCCGACTC 62.656 68.421 0.00 0.00 41.25 3.36
94 95 3.699894 CTCAGCCACAGCCCGACT 61.700 66.667 0.00 0.00 41.25 4.18
95 96 2.564553 CTACTCAGCCACAGCCCGAC 62.565 65.000 0.00 0.00 41.25 4.79
96 97 2.283604 TACTCAGCCACAGCCCGA 60.284 61.111 0.00 0.00 41.25 5.14
97 98 2.185350 CTACTCAGCCACAGCCCG 59.815 66.667 0.00 0.00 41.25 6.13
98 99 0.976073 TACCTACTCAGCCACAGCCC 60.976 60.000 0.00 0.00 41.25 5.19
99 100 0.461961 CTACCTACTCAGCCACAGCC 59.538 60.000 0.00 0.00 41.25 4.85
100 101 0.179097 GCTACCTACTCAGCCACAGC 60.179 60.000 0.00 0.00 40.32 4.40
101 102 0.101399 CGCTACCTACTCAGCCACAG 59.899 60.000 0.00 0.00 34.15 3.66
102 103 0.611062 ACGCTACCTACTCAGCCACA 60.611 55.000 0.00 0.00 34.15 4.17
103 104 0.179134 CACGCTACCTACTCAGCCAC 60.179 60.000 0.00 0.00 34.15 5.01
104 105 0.323087 TCACGCTACCTACTCAGCCA 60.323 55.000 0.00 0.00 34.15 4.75
105 106 0.815734 TTCACGCTACCTACTCAGCC 59.184 55.000 0.00 0.00 34.15 4.85
106 107 2.860735 CAATTCACGCTACCTACTCAGC 59.139 50.000 0.00 0.00 0.00 4.26
107 108 4.371855 TCAATTCACGCTACCTACTCAG 57.628 45.455 0.00 0.00 0.00 3.35
108 109 4.202121 GGATCAATTCACGCTACCTACTCA 60.202 45.833 0.00 0.00 0.00 3.41
109 110 4.038162 AGGATCAATTCACGCTACCTACTC 59.962 45.833 0.00 0.00 0.00 2.59
110 111 3.961408 AGGATCAATTCACGCTACCTACT 59.039 43.478 0.00 0.00 0.00 2.57
111 112 4.323553 AGGATCAATTCACGCTACCTAC 57.676 45.455 0.00 0.00 0.00 3.18
112 113 6.493802 AGAATAGGATCAATTCACGCTACCTA 59.506 38.462 17.50 0.00 36.09 3.08
113 114 5.305644 AGAATAGGATCAATTCACGCTACCT 59.694 40.000 17.50 0.00 36.09 3.08
114 115 5.542779 AGAATAGGATCAATTCACGCTACC 58.457 41.667 17.50 0.00 36.09 3.18
115 116 6.564873 GCAAGAATAGGATCAATTCACGCTAC 60.565 42.308 17.50 3.12 36.09 3.58
116 117 5.466728 GCAAGAATAGGATCAATTCACGCTA 59.533 40.000 17.50 0.00 36.09 4.26
117 118 4.274459 GCAAGAATAGGATCAATTCACGCT 59.726 41.667 17.50 0.00 36.09 5.07
118 119 4.531332 GCAAGAATAGGATCAATTCACGC 58.469 43.478 17.50 15.19 36.09 5.34
119 120 4.818546 AGGCAAGAATAGGATCAATTCACG 59.181 41.667 17.50 11.08 36.09 4.35
120 121 6.705863 AAGGCAAGAATAGGATCAATTCAC 57.294 37.500 17.50 9.42 36.09 3.18
121 122 6.891361 TCAAAGGCAAGAATAGGATCAATTCA 59.109 34.615 17.50 0.00 36.09 2.57
122 123 7.338800 TCAAAGGCAAGAATAGGATCAATTC 57.661 36.000 10.55 10.55 34.23 2.17
123 124 6.183360 GCTCAAAGGCAAGAATAGGATCAATT 60.183 38.462 0.00 0.00 0.00 2.32
124 125 5.301298 GCTCAAAGGCAAGAATAGGATCAAT 59.699 40.000 0.00 0.00 0.00 2.57
125 126 4.641989 GCTCAAAGGCAAGAATAGGATCAA 59.358 41.667 0.00 0.00 0.00 2.57
126 127 4.202441 GCTCAAAGGCAAGAATAGGATCA 58.798 43.478 0.00 0.00 0.00 2.92
127 128 4.202441 TGCTCAAAGGCAAGAATAGGATC 58.798 43.478 0.00 0.00 39.43 3.36
128 129 4.080129 TCTGCTCAAAGGCAAGAATAGGAT 60.080 41.667 0.00 0.00 41.94 3.24
129 130 3.264193 TCTGCTCAAAGGCAAGAATAGGA 59.736 43.478 0.00 0.00 41.94 2.94
130 131 3.614092 TCTGCTCAAAGGCAAGAATAGG 58.386 45.455 0.00 0.00 41.94 2.57
131 132 4.940046 TCTTCTGCTCAAAGGCAAGAATAG 59.060 41.667 0.00 0.00 41.94 1.73
132 133 4.910195 TCTTCTGCTCAAAGGCAAGAATA 58.090 39.130 0.00 0.00 41.94 1.75
133 134 3.759581 TCTTCTGCTCAAAGGCAAGAAT 58.240 40.909 0.00 0.00 41.94 2.40
134 135 3.213206 TCTTCTGCTCAAAGGCAAGAA 57.787 42.857 0.00 0.00 41.94 2.52
135 136 2.936919 TCTTCTGCTCAAAGGCAAGA 57.063 45.000 0.00 0.00 41.94 3.02
136 137 3.996150 TTTCTTCTGCTCAAAGGCAAG 57.004 42.857 0.00 0.00 41.94 4.01
137 138 4.218417 GGTATTTCTTCTGCTCAAAGGCAA 59.782 41.667 0.00 0.00 41.94 4.52
138 139 3.758554 GGTATTTCTTCTGCTCAAAGGCA 59.241 43.478 0.00 0.00 40.15 4.75
139 140 3.129462 GGGTATTTCTTCTGCTCAAAGGC 59.871 47.826 0.00 0.00 0.00 4.35
140 141 4.593956 AGGGTATTTCTTCTGCTCAAAGG 58.406 43.478 0.00 0.00 0.00 3.11
141 142 8.424918 TCTATAGGGTATTTCTTCTGCTCAAAG 58.575 37.037 0.00 0.00 0.00 2.77
142 143 8.204836 GTCTATAGGGTATTTCTTCTGCTCAAA 58.795 37.037 0.00 0.00 0.00 2.69
143 144 7.344612 TGTCTATAGGGTATTTCTTCTGCTCAA 59.655 37.037 0.00 0.00 0.00 3.02
144 145 6.839134 TGTCTATAGGGTATTTCTTCTGCTCA 59.161 38.462 0.00 0.00 0.00 4.26
145 146 7.291411 TGTCTATAGGGTATTTCTTCTGCTC 57.709 40.000 0.00 0.00 0.00 4.26
146 147 7.863901 ATGTCTATAGGGTATTTCTTCTGCT 57.136 36.000 0.00 0.00 0.00 4.24
185 186 7.255730 GGGATTTGAGATCCAGAATTTGTATGG 60.256 40.741 4.27 0.00 40.26 2.74
186 187 7.255730 GGGGATTTGAGATCCAGAATTTGTATG 60.256 40.741 4.27 0.00 39.93 2.39
187 188 6.779539 GGGGATTTGAGATCCAGAATTTGTAT 59.220 38.462 4.27 0.00 39.93 2.29
188 189 6.068853 AGGGGATTTGAGATCCAGAATTTGTA 60.069 38.462 4.27 0.00 39.93 2.41
189 190 4.958581 GGGGATTTGAGATCCAGAATTTGT 59.041 41.667 4.27 0.00 39.93 2.83
190 191 5.206587 AGGGGATTTGAGATCCAGAATTTG 58.793 41.667 4.27 0.00 39.93 2.32
191 192 5.478503 AGGGGATTTGAGATCCAGAATTT 57.521 39.130 4.27 0.00 39.93 1.82
192 193 5.453158 GAAGGGGATTTGAGATCCAGAATT 58.547 41.667 4.27 0.00 39.93 2.17
193 194 4.141065 GGAAGGGGATTTGAGATCCAGAAT 60.141 45.833 4.27 0.00 39.93 2.40
194 195 3.203040 GGAAGGGGATTTGAGATCCAGAA 59.797 47.826 4.27 0.00 39.93 3.02
195 196 2.780010 GGAAGGGGATTTGAGATCCAGA 59.220 50.000 4.27 0.00 39.93 3.86
196 197 2.782341 AGGAAGGGGATTTGAGATCCAG 59.218 50.000 4.27 0.00 39.93 3.86
197 198 2.780010 GAGGAAGGGGATTTGAGATCCA 59.220 50.000 4.27 0.00 39.93 3.41
198 199 3.052329 AGAGGAAGGGGATTTGAGATCC 58.948 50.000 0.00 0.00 37.47 3.36
199 200 4.904853 ACTAGAGGAAGGGGATTTGAGATC 59.095 45.833 0.00 0.00 0.00 2.75
200 201 4.901927 ACTAGAGGAAGGGGATTTGAGAT 58.098 43.478 0.00 0.00 0.00 2.75
201 202 4.354208 ACTAGAGGAAGGGGATTTGAGA 57.646 45.455 0.00 0.00 0.00 3.27
202 203 4.442192 CGAACTAGAGGAAGGGGATTTGAG 60.442 50.000 0.00 0.00 0.00 3.02
203 204 3.451178 CGAACTAGAGGAAGGGGATTTGA 59.549 47.826 0.00 0.00 0.00 2.69
204 205 3.451178 TCGAACTAGAGGAAGGGGATTTG 59.549 47.826 0.00 0.00 0.00 2.32
205 206 3.721021 TCGAACTAGAGGAAGGGGATTT 58.279 45.455 0.00 0.00 0.00 2.17
206 207 3.399952 TCGAACTAGAGGAAGGGGATT 57.600 47.619 0.00 0.00 0.00 3.01
207 208 3.141272 AGATCGAACTAGAGGAAGGGGAT 59.859 47.826 0.00 0.00 0.00 3.85
208 209 2.514582 AGATCGAACTAGAGGAAGGGGA 59.485 50.000 0.00 0.00 0.00 4.81
209 210 2.888414 GAGATCGAACTAGAGGAAGGGG 59.112 54.545 0.00 0.00 0.00 4.79
210 211 3.818773 GAGAGATCGAACTAGAGGAAGGG 59.181 52.174 0.00 0.00 0.00 3.95
211 212 4.515191 CAGAGAGATCGAACTAGAGGAAGG 59.485 50.000 0.00 0.00 0.00 3.46
212 213 5.364778 TCAGAGAGATCGAACTAGAGGAAG 58.635 45.833 0.00 0.00 0.00 3.46
213 214 5.360649 TCAGAGAGATCGAACTAGAGGAA 57.639 43.478 0.00 0.00 0.00 3.36
214 215 5.360649 TTCAGAGAGATCGAACTAGAGGA 57.639 43.478 0.00 0.00 0.00 3.71
215 216 6.633500 ATTTCAGAGAGATCGAACTAGAGG 57.367 41.667 0.00 0.00 0.00 3.69
216 217 6.850823 CGAATTTCAGAGAGATCGAACTAGAG 59.149 42.308 0.00 0.00 0.00 2.43
217 218 6.720343 CGAATTTCAGAGAGATCGAACTAGA 58.280 40.000 0.00 0.00 0.00 2.43
218 219 5.398122 GCGAATTTCAGAGAGATCGAACTAG 59.602 44.000 0.00 0.00 0.00 2.57
219 220 5.066634 AGCGAATTTCAGAGAGATCGAACTA 59.933 40.000 0.00 0.00 0.00 2.24
220 221 4.109050 GCGAATTTCAGAGAGATCGAACT 58.891 43.478 0.00 0.00 0.00 3.01
221 222 4.109050 AGCGAATTTCAGAGAGATCGAAC 58.891 43.478 0.00 0.00 0.00 3.95
222 223 4.377839 AGCGAATTTCAGAGAGATCGAA 57.622 40.909 0.00 0.00 0.00 3.71
223 224 4.377839 AAGCGAATTTCAGAGAGATCGA 57.622 40.909 0.00 0.00 0.00 3.59
224 225 5.277825 ACTAAGCGAATTTCAGAGAGATCG 58.722 41.667 0.00 0.00 0.00 3.69
225 226 6.754209 TCAACTAAGCGAATTTCAGAGAGATC 59.246 38.462 0.00 0.00 0.00 2.75
226 227 6.533367 GTCAACTAAGCGAATTTCAGAGAGAT 59.467 38.462 0.00 0.00 0.00 2.75
227 228 5.864474 GTCAACTAAGCGAATTTCAGAGAGA 59.136 40.000 0.00 0.00 0.00 3.10
228 229 5.635280 TGTCAACTAAGCGAATTTCAGAGAG 59.365 40.000 0.00 0.00 0.00 3.20
229 230 5.405571 GTGTCAACTAAGCGAATTTCAGAGA 59.594 40.000 0.00 0.00 0.00 3.10
230 231 5.389935 GGTGTCAACTAAGCGAATTTCAGAG 60.390 44.000 0.00 0.00 0.00 3.35
231 232 4.451096 GGTGTCAACTAAGCGAATTTCAGA 59.549 41.667 0.00 0.00 0.00 3.27
232 233 4.378459 GGGTGTCAACTAAGCGAATTTCAG 60.378 45.833 0.00 0.00 0.00 3.02
233 234 3.500680 GGGTGTCAACTAAGCGAATTTCA 59.499 43.478 0.00 0.00 0.00 2.69
234 235 3.424433 CGGGTGTCAACTAAGCGAATTTC 60.424 47.826 0.00 0.00 0.00 2.17
235 236 2.482721 CGGGTGTCAACTAAGCGAATTT 59.517 45.455 0.00 0.00 0.00 1.82
236 237 2.073816 CGGGTGTCAACTAAGCGAATT 58.926 47.619 0.00 0.00 0.00 2.17
237 238 1.674817 CCGGGTGTCAACTAAGCGAAT 60.675 52.381 0.00 0.00 0.00 3.34
238 239 0.320073 CCGGGTGTCAACTAAGCGAA 60.320 55.000 0.00 0.00 0.00 4.70
239 240 1.290955 CCGGGTGTCAACTAAGCGA 59.709 57.895 0.00 0.00 0.00 4.93
240 241 1.740296 CCCGGGTGTCAACTAAGCG 60.740 63.158 14.18 0.00 0.00 4.68
241 242 0.252197 ATCCCGGGTGTCAACTAAGC 59.748 55.000 22.86 0.00 0.00 3.09
242 243 1.831736 AGATCCCGGGTGTCAACTAAG 59.168 52.381 22.86 0.00 0.00 2.18
243 244 1.553248 CAGATCCCGGGTGTCAACTAA 59.447 52.381 22.86 0.00 0.00 2.24
244 245 1.191535 CAGATCCCGGGTGTCAACTA 58.808 55.000 22.86 0.00 0.00 2.24
245 246 0.544357 TCAGATCCCGGGTGTCAACT 60.544 55.000 22.86 1.41 0.00 3.16
246 247 0.391263 GTCAGATCCCGGGTGTCAAC 60.391 60.000 22.86 16.88 0.00 3.18
247 248 0.834261 TGTCAGATCCCGGGTGTCAA 60.834 55.000 22.86 9.65 0.00 3.18
248 249 1.229051 TGTCAGATCCCGGGTGTCA 60.229 57.895 22.86 12.87 0.00 3.58
249 250 1.517832 CTGTCAGATCCCGGGTGTC 59.482 63.158 22.86 19.61 0.00 3.67
250 251 1.990060 CCTGTCAGATCCCGGGTGT 60.990 63.158 22.86 11.05 0.00 4.16
251 252 2.735772 CCCTGTCAGATCCCGGGTG 61.736 68.421 22.86 12.35 0.00 4.61
252 253 2.365635 CCCTGTCAGATCCCGGGT 60.366 66.667 22.86 8.01 0.00 5.28
253 254 3.866582 GCCCTGTCAGATCCCGGG 61.867 72.222 16.85 16.85 37.97 5.73
254 255 2.765807 AGCCCTGTCAGATCCCGG 60.766 66.667 0.00 0.00 0.00 5.73
255 256 2.801631 GGAGCCCTGTCAGATCCCG 61.802 68.421 0.00 0.00 0.00 5.14
256 257 1.690633 TGGAGCCCTGTCAGATCCC 60.691 63.158 0.00 0.00 0.00 3.85
257 258 0.980231 ACTGGAGCCCTGTCAGATCC 60.980 60.000 0.00 6.59 29.71 3.36
258 259 0.908198 AACTGGAGCCCTGTCAGATC 59.092 55.000 0.00 0.00 34.63 2.75
259 260 0.617413 CAACTGGAGCCCTGTCAGAT 59.383 55.000 0.00 0.00 34.63 2.90
260 261 2.061220 CAACTGGAGCCCTGTCAGA 58.939 57.895 0.00 0.00 34.63 3.27
261 262 1.673665 GCAACTGGAGCCCTGTCAG 60.674 63.158 4.63 0.00 34.63 3.51
262 263 2.431683 GCAACTGGAGCCCTGTCA 59.568 61.111 4.63 0.00 34.63 3.58
263 264 2.743928 CGCAACTGGAGCCCTGTC 60.744 66.667 4.63 0.00 34.63 3.51
264 265 4.335647 CCGCAACTGGAGCCCTGT 62.336 66.667 0.00 0.00 37.28 4.00
265 266 3.551496 TTCCGCAACTGGAGCCCTG 62.551 63.158 0.00 0.00 39.72 4.45
266 267 3.249189 TTCCGCAACTGGAGCCCT 61.249 61.111 0.00 0.00 39.72 5.19
267 268 2.747855 CTTCCGCAACTGGAGCCC 60.748 66.667 0.00 0.00 39.72 5.19
268 269 2.747855 CCTTCCGCAACTGGAGCC 60.748 66.667 0.00 0.00 39.72 4.70
269 270 3.435186 GCCTTCCGCAACTGGAGC 61.435 66.667 0.00 0.00 39.72 4.70
270 271 3.121030 CGCCTTCCGCAACTGGAG 61.121 66.667 0.00 0.00 39.72 3.86
271 272 3.621805 TCGCCTTCCGCAACTGGA 61.622 61.111 0.00 0.00 37.30 3.86
272 273 3.423154 GTCGCCTTCCGCAACTGG 61.423 66.667 0.00 0.00 37.30 4.00
273 274 2.357517 AGTCGCCTTCCGCAACTG 60.358 61.111 0.00 0.00 37.30 3.16
274 275 2.048127 GAGTCGCCTTCCGCAACT 60.048 61.111 0.00 0.00 37.30 3.16
275 276 3.479269 CGAGTCGCCTTCCGCAAC 61.479 66.667 0.00 0.00 37.30 4.17
276 277 4.735132 CCGAGTCGCCTTCCGCAA 62.735 66.667 7.12 0.00 37.30 4.85
278 279 4.856607 CTCCGAGTCGCCTTCCGC 62.857 72.222 7.12 0.00 36.73 5.54
279 280 4.856607 GCTCCGAGTCGCCTTCCG 62.857 72.222 7.12 0.00 38.61 4.30
280 281 3.453679 AGCTCCGAGTCGCCTTCC 61.454 66.667 7.12 0.00 0.00 3.46
281 282 2.202676 CAGCTCCGAGTCGCCTTC 60.203 66.667 7.12 0.00 0.00 3.46
282 283 3.764466 CCAGCTCCGAGTCGCCTT 61.764 66.667 7.12 0.00 0.00 4.35
283 284 4.742649 TCCAGCTCCGAGTCGCCT 62.743 66.667 7.12 0.00 0.00 5.52
284 285 4.200283 CTCCAGCTCCGAGTCGCC 62.200 72.222 7.12 0.00 0.00 5.54
285 286 4.863925 GCTCCAGCTCCGAGTCGC 62.864 72.222 7.12 0.00 38.21 5.19
286 287 3.408501 CTGCTCCAGCTCCGAGTCG 62.409 68.421 5.29 5.29 42.66 4.18
287 288 2.493973 CTGCTCCAGCTCCGAGTC 59.506 66.667 8.72 3.16 42.66 3.36
288 289 3.073735 CCTGCTCCAGCTCCGAGT 61.074 66.667 8.72 0.00 42.66 4.18
289 290 4.527583 GCCTGCTCCAGCTCCGAG 62.528 72.222 0.00 3.36 42.66 4.63
336 349 1.359130 CCAGAAATTCCCCACTCCCTT 59.641 52.381 0.00 0.00 0.00 3.95
424 438 1.746615 CCCGCTTACTGCACAGCAT 60.747 57.895 8.20 0.00 43.06 3.79
428 442 4.715523 GGCCCCGCTTACTGCACA 62.716 66.667 0.00 0.00 43.06 4.57
429 443 4.410400 AGGCCCCGCTTACTGCAC 62.410 66.667 0.00 0.00 43.06 4.57
480 495 2.262915 CGCTCTGGTGGTCTGGAC 59.737 66.667 0.00 0.00 0.00 4.02
481 496 2.805313 ATCCGCTCTGGTGGTCTGGA 62.805 60.000 0.00 0.00 43.20 3.86
490 505 0.323360 TTTTCCCCAATCCGCTCTGG 60.323 55.000 0.00 0.00 40.09 3.86
491 506 1.474077 CTTTTTCCCCAATCCGCTCTG 59.526 52.381 0.00 0.00 0.00 3.35
492 507 1.354368 TCTTTTTCCCCAATCCGCTCT 59.646 47.619 0.00 0.00 0.00 4.09
496 511 4.864704 TTCTTTCTTTTTCCCCAATCCG 57.135 40.909 0.00 0.00 0.00 4.18
689 723 3.574074 GATGGGGATGGGGATGCGG 62.574 68.421 0.00 0.00 0.00 5.69
690 724 2.034687 GATGGGGATGGGGATGCG 59.965 66.667 0.00 0.00 0.00 4.73
691 725 2.442413 GGATGGGGATGGGGATGC 59.558 66.667 0.00 0.00 0.00 3.91
692 726 2.551413 GGGGATGGGGATGGGGATG 61.551 68.421 0.00 0.00 0.00 3.51
693 727 2.120854 GGGGATGGGGATGGGGAT 60.121 66.667 0.00 0.00 0.00 3.85
694 728 3.078909 ATGGGGATGGGGATGGGGA 62.079 63.158 0.00 0.00 0.00 4.81
1159 1193 2.115911 CGAGCTGCGAGTAGACCCT 61.116 63.158 0.00 0.00 44.57 4.34
1473 1510 3.495193 CCTCATCATCAAAAACAGCACG 58.505 45.455 0.00 0.00 0.00 5.34
1512 1549 6.489700 TCAGGAACATGTATGTGTGTGAATTT 59.510 34.615 0.00 0.00 41.61 1.82
1529 3366 4.467084 GGCCGCCGATCAGGAACA 62.467 66.667 7.64 0.00 45.00 3.18
1650 3592 3.742640 GCATCCTTCCTGCCTTACAGTAG 60.743 52.174 0.00 0.00 45.68 2.57
1746 3688 2.662866 CCATCACAGAGGCCATGAATT 58.337 47.619 14.39 0.00 0.00 2.17
2239 4181 5.295152 GGTATAGGTGATAACGTTGGGAAG 58.705 45.833 11.99 0.00 0.00 3.46
2240 4182 4.202141 CGGTATAGGTGATAACGTTGGGAA 60.202 45.833 11.99 0.00 44.70 3.97
2263 4205 0.032540 CACTGGCCTTGAACCAAAGC 59.967 55.000 3.32 0.00 36.56 3.51
2339 4281 1.275666 TTGGTCATCGGGTGTCAGAT 58.724 50.000 0.00 0.00 0.00 2.90
2368 4310 2.154462 GCACAGTGCACCAGTTAAGAT 58.846 47.619 21.22 0.00 44.26 2.40
2518 4460 3.370846 CCCTCACCAATCATGCTGTCTAA 60.371 47.826 0.00 0.00 0.00 2.10
2541 4483 1.726791 GTGTACGAATCTGGTGTGCAG 59.273 52.381 0.00 0.00 0.00 4.41
2795 4737 0.318441 CACTCGACCTTCCTTGCAGA 59.682 55.000 0.00 0.00 0.00 4.26
3099 5041 5.071519 TGTGGGATTCAAACCATGTTTTGAT 59.928 36.000 17.80 9.16 43.38 2.57
3181 5123 9.955208 GCACATATGATCAAAAAGAATACATGA 57.045 29.630 10.38 0.00 0.00 3.07
3540 5482 4.019860 ACCATAGCATGTGTCTGAGAACTT 60.020 41.667 0.00 0.00 0.00 2.66
3611 5553 3.848726 CTGACTCAAAGAGCTTCTCCTC 58.151 50.000 0.00 0.00 32.04 3.71
3832 6001 5.569059 CGTGACAATTTGTAGGCAAGATTTC 59.431 40.000 1.15 0.00 35.82 2.17
3892 6061 6.823689 GGACATGTGACATGGTTAGTTTCTAT 59.176 38.462 27.23 3.71 0.00 1.98
3915 6084 6.064060 CAGCAGATTCAAAACCATATAGGGA 58.936 40.000 11.11 0.00 43.89 4.20
3917 6086 7.572523 TTCAGCAGATTCAAAACCATATAGG 57.427 36.000 0.00 0.00 45.67 2.57
4044 6213 8.322091 ACAAAGTATCTGCTTTATTGGACTACT 58.678 33.333 0.00 0.00 36.64 2.57
4207 6378 6.475076 GCTCATCTCAAGTCAGTTATGTACAG 59.525 42.308 0.33 0.00 0.00 2.74
4267 6438 2.789208 CTTGAGCAACATGTATTGGCG 58.211 47.619 0.00 0.00 0.00 5.69
4404 6581 9.533253 GATAACCAAATGCATAGTAAAGCAAAT 57.467 29.630 0.00 0.00 44.88 2.32


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

AutoCloner maintained by Alex Coulton.