Multiple sequence alignment - TraesCS1A01G436100

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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 TraesCS1A01G436100 chr1A 100.000 2495 0 0 1 2495 586511310 586513804 0.000000e+00 4608.0
1 TraesCS1A01G436100 chr6B 95.664 2214 85 6 161 2372 393595060 393592856 0.000000e+00 3546.0
2 TraesCS1A01G436100 chr6B 80.952 105 18 2 2279 2381 269686402 269686298 5.720000e-12 82.4
3 TraesCS1A01G436100 chr4B 94.558 2113 88 11 264 2371 79526625 79524535 0.000000e+00 3240.0
4 TraesCS1A01G436100 chr4B 81.053 95 16 2 2279 2371 399948768 399948674 9.570000e-10 75.0
5 TraesCS1A01G436100 chr1B 94.792 1152 52 5 264 1413 51226531 51225386 0.000000e+00 1788.0
6 TraesCS1A01G436100 chr1B 93.936 940 36 6 1447 2382 51225386 51224464 0.000000e+00 1400.0
7 TraesCS1A01G436100 chr1B 81.481 108 16 4 2279 2382 593223872 593223979 4.420000e-13 86.1
8 TraesCS1A01G436100 chr7D 95.349 645 28 1 1558 2200 445900229 445899585 0.000000e+00 1024.0
9 TraesCS1A01G436100 chr7D 93.893 131 8 0 2242 2372 445897581 445897451 5.440000e-47 198.0
10 TraesCS1A01G436100 chr5D 83.260 454 42 15 1325 1775 39096147 39096569 1.080000e-103 387.0
11 TraesCS1A01G436100 chr3D 80.952 105 18 2 2279 2381 603163016 603163120 5.720000e-12 82.4
12 TraesCS1A01G436100 chr5A 81.000 100 17 2 2279 2376 685761334 685761235 7.400000e-11 78.7


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 TraesCS1A01G436100 chr1A 586511310 586513804 2494 False 4608 4608 100.000 1 2495 1 chr1A.!!$F1 2494
1 TraesCS1A01G436100 chr6B 393592856 393595060 2204 True 3546 3546 95.664 161 2372 1 chr6B.!!$R2 2211
2 TraesCS1A01G436100 chr4B 79524535 79526625 2090 True 3240 3240 94.558 264 2371 1 chr4B.!!$R1 2107
3 TraesCS1A01G436100 chr1B 51224464 51226531 2067 True 1594 1788 94.364 264 2382 2 chr1B.!!$R1 2118
4 TraesCS1A01G436100 chr7D 445897451 445900229 2778 True 611 1024 94.621 1558 2372 2 chr7D.!!$R1 814

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
134 135 0.035056 AGGCCTCAGATCCGTTTTGG 60.035 55.0 0.0 0.0 40.09 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1570 0.321298 TCCCGCCTAACAGAAGCAAC 60.321 55.0 0.0 0.0 0.0 4.17 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.012841 CCTTGCTCAATCTTCTCGCC 58.987 55.000 0.00 0.00 0.00 5.54
20 21 1.406614 CCTTGCTCAATCTTCTCGCCT 60.407 52.381 0.00 0.00 0.00 5.52
21 22 2.159043 CCTTGCTCAATCTTCTCGCCTA 60.159 50.000 0.00 0.00 0.00 3.93
22 23 2.586258 TGCTCAATCTTCTCGCCTAC 57.414 50.000 0.00 0.00 0.00 3.18
23 24 2.103373 TGCTCAATCTTCTCGCCTACT 58.897 47.619 0.00 0.00 0.00 2.57
24 25 2.099921 TGCTCAATCTTCTCGCCTACTC 59.900 50.000 0.00 0.00 0.00 2.59
25 26 2.544903 GCTCAATCTTCTCGCCTACTCC 60.545 54.545 0.00 0.00 0.00 3.85
26 27 2.955660 CTCAATCTTCTCGCCTACTCCT 59.044 50.000 0.00 0.00 0.00 3.69
27 28 3.366396 TCAATCTTCTCGCCTACTCCTT 58.634 45.455 0.00 0.00 0.00 3.36
28 29 3.131223 TCAATCTTCTCGCCTACTCCTTG 59.869 47.826 0.00 0.00 0.00 3.61
29 30 2.217510 TCTTCTCGCCTACTCCTTGT 57.782 50.000 0.00 0.00 0.00 3.16
30 31 2.093106 TCTTCTCGCCTACTCCTTGTC 58.907 52.381 0.00 0.00 0.00 3.18
31 32 1.819288 CTTCTCGCCTACTCCTTGTCA 59.181 52.381 0.00 0.00 0.00 3.58
32 33 1.919240 TCTCGCCTACTCCTTGTCAA 58.081 50.000 0.00 0.00 0.00 3.18
33 34 2.244695 TCTCGCCTACTCCTTGTCAAA 58.755 47.619 0.00 0.00 0.00 2.69
34 35 2.029290 TCTCGCCTACTCCTTGTCAAAC 60.029 50.000 0.00 0.00 0.00 2.93
35 36 1.001633 TCGCCTACTCCTTGTCAAACC 59.998 52.381 0.00 0.00 0.00 3.27
36 37 1.822506 GCCTACTCCTTGTCAAACCC 58.177 55.000 0.00 0.00 0.00 4.11
37 38 1.613520 GCCTACTCCTTGTCAAACCCC 60.614 57.143 0.00 0.00 0.00 4.95
38 39 1.985895 CCTACTCCTTGTCAAACCCCT 59.014 52.381 0.00 0.00 0.00 4.79
39 40 2.290323 CCTACTCCTTGTCAAACCCCTG 60.290 54.545 0.00 0.00 0.00 4.45
40 41 1.222567 ACTCCTTGTCAAACCCCTGT 58.777 50.000 0.00 0.00 0.00 4.00
41 42 2.414612 ACTCCTTGTCAAACCCCTGTA 58.585 47.619 0.00 0.00 0.00 2.74
42 43 2.372172 ACTCCTTGTCAAACCCCTGTAG 59.628 50.000 0.00 0.00 0.00 2.74
43 44 2.372172 CTCCTTGTCAAACCCCTGTAGT 59.628 50.000 0.00 0.00 0.00 2.73
44 45 2.105821 TCCTTGTCAAACCCCTGTAGTG 59.894 50.000 0.00 0.00 0.00 2.74
45 46 2.504367 CTTGTCAAACCCCTGTAGTGG 58.496 52.381 0.00 0.00 0.00 4.00
46 47 0.109723 TGTCAAACCCCTGTAGTGGC 59.890 55.000 0.00 0.00 0.00 5.01
47 48 0.953960 GTCAAACCCCTGTAGTGGCG 60.954 60.000 0.00 0.00 0.00 5.69
48 49 1.674322 CAAACCCCTGTAGTGGCGG 60.674 63.158 0.00 0.00 0.00 6.13
49 50 2.151388 AAACCCCTGTAGTGGCGGT 61.151 57.895 0.00 0.00 33.88 5.68
50 51 2.406002 AAACCCCTGTAGTGGCGGTG 62.406 60.000 0.00 0.00 33.16 4.94
51 52 3.319198 CCCCTGTAGTGGCGGTGT 61.319 66.667 0.00 0.00 0.00 4.16
52 53 1.985662 CCCCTGTAGTGGCGGTGTA 60.986 63.158 0.00 0.00 0.00 2.90
53 54 1.217244 CCCTGTAGTGGCGGTGTAC 59.783 63.158 0.00 0.00 0.00 2.90
54 55 1.537814 CCCTGTAGTGGCGGTGTACA 61.538 60.000 0.00 0.00 0.00 2.90
55 56 0.108804 CCTGTAGTGGCGGTGTACAG 60.109 60.000 0.00 7.86 42.20 2.74
56 57 0.885879 CTGTAGTGGCGGTGTACAGA 59.114 55.000 0.00 0.00 44.32 3.41
57 58 0.885879 TGTAGTGGCGGTGTACAGAG 59.114 55.000 0.00 0.00 0.00 3.35
58 59 1.171308 GTAGTGGCGGTGTACAGAGA 58.829 55.000 0.00 0.00 0.00 3.10
59 60 1.135460 GTAGTGGCGGTGTACAGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
60 61 0.826256 AGTGGCGGTGTACAGAGACA 60.826 55.000 0.00 0.00 0.00 3.41
61 62 0.246635 GTGGCGGTGTACAGAGACAT 59.753 55.000 9.02 0.00 0.00 3.06
62 63 0.530744 TGGCGGTGTACAGAGACATC 59.469 55.000 0.00 0.00 0.00 3.06
63 64 0.818296 GGCGGTGTACAGAGACATCT 59.182 55.000 0.00 0.00 35.63 2.90
64 65 1.202313 GGCGGTGTACAGAGACATCTC 60.202 57.143 0.00 0.26 43.17 2.75
76 77 4.558538 GAGACATCTCTCTCTTGCTCTC 57.441 50.000 1.44 0.00 40.09 3.20
77 78 4.202441 GAGACATCTCTCTCTTGCTCTCT 58.798 47.826 1.44 0.00 40.09 3.10
78 79 4.202441 AGACATCTCTCTCTTGCTCTCTC 58.798 47.826 0.00 0.00 0.00 3.20
79 80 4.080129 AGACATCTCTCTCTTGCTCTCTCT 60.080 45.833 0.00 0.00 0.00 3.10
80 81 4.202441 ACATCTCTCTCTTGCTCTCTCTC 58.798 47.826 0.00 0.00 0.00 3.20
81 82 4.080129 ACATCTCTCTCTTGCTCTCTCTCT 60.080 45.833 0.00 0.00 0.00 3.10
82 83 5.130975 ACATCTCTCTCTTGCTCTCTCTCTA 59.869 44.000 0.00 0.00 0.00 2.43
83 84 5.023533 TCTCTCTCTTGCTCTCTCTCTAC 57.976 47.826 0.00 0.00 0.00 2.59
84 85 4.716784 TCTCTCTCTTGCTCTCTCTCTACT 59.283 45.833 0.00 0.00 0.00 2.57
85 86 5.189736 TCTCTCTCTTGCTCTCTCTCTACTT 59.810 44.000 0.00 0.00 0.00 2.24
86 87 5.428253 TCTCTCTTGCTCTCTCTCTACTTC 58.572 45.833 0.00 0.00 0.00 3.01
87 88 4.523083 TCTCTTGCTCTCTCTCTACTTCC 58.477 47.826 0.00 0.00 0.00 3.46
88 89 4.018870 TCTCTTGCTCTCTCTCTACTTCCA 60.019 45.833 0.00 0.00 0.00 3.53
89 90 4.667573 TCTTGCTCTCTCTCTACTTCCAA 58.332 43.478 0.00 0.00 0.00 3.53
90 91 5.268387 TCTTGCTCTCTCTCTACTTCCAAT 58.732 41.667 0.00 0.00 0.00 3.16
91 92 5.359576 TCTTGCTCTCTCTCTACTTCCAATC 59.640 44.000 0.00 0.00 0.00 2.67
92 93 4.865905 TGCTCTCTCTCTACTTCCAATCT 58.134 43.478 0.00 0.00 0.00 2.40
93 94 4.644234 TGCTCTCTCTCTACTTCCAATCTG 59.356 45.833 0.00 0.00 0.00 2.90
94 95 4.887071 GCTCTCTCTCTACTTCCAATCTGA 59.113 45.833 0.00 0.00 0.00 3.27
95 96 5.221048 GCTCTCTCTCTACTTCCAATCTGAC 60.221 48.000 0.00 0.00 0.00 3.51
96 97 6.073447 TCTCTCTCTACTTCCAATCTGACT 57.927 41.667 0.00 0.00 0.00 3.41
97 98 5.885352 TCTCTCTCTACTTCCAATCTGACTG 59.115 44.000 0.00 0.00 0.00 3.51
98 99 4.400884 TCTCTCTACTTCCAATCTGACTGC 59.599 45.833 0.00 0.00 0.00 4.40
99 100 3.449018 TCTCTACTTCCAATCTGACTGCC 59.551 47.826 0.00 0.00 0.00 4.85
100 101 2.166459 TCTACTTCCAATCTGACTGCCG 59.834 50.000 0.00 0.00 0.00 5.69
101 102 0.687354 ACTTCCAATCTGACTGCCGT 59.313 50.000 0.00 0.00 0.00 5.68
102 103 1.081892 CTTCCAATCTGACTGCCGTG 58.918 55.000 0.00 0.00 0.00 4.94
103 104 0.684535 TTCCAATCTGACTGCCGTGA 59.315 50.000 0.00 0.00 0.00 4.35
104 105 0.904649 TCCAATCTGACTGCCGTGAT 59.095 50.000 0.00 0.00 0.00 3.06
105 106 1.134699 TCCAATCTGACTGCCGTGATC 60.135 52.381 0.00 0.00 0.00 2.92
106 107 1.134580 CCAATCTGACTGCCGTGATCT 60.135 52.381 0.00 0.00 0.00 2.75
107 108 2.101415 CCAATCTGACTGCCGTGATCTA 59.899 50.000 0.00 0.00 0.00 1.98
108 109 3.244009 CCAATCTGACTGCCGTGATCTAT 60.244 47.826 0.00 0.00 0.00 1.98
109 110 3.932545 ATCTGACTGCCGTGATCTATC 57.067 47.619 0.00 0.00 0.00 2.08
110 111 2.937519 TCTGACTGCCGTGATCTATCT 58.062 47.619 0.00 0.00 0.00 1.98
111 112 3.291584 TCTGACTGCCGTGATCTATCTT 58.708 45.455 0.00 0.00 0.00 2.40
112 113 3.067320 TCTGACTGCCGTGATCTATCTTG 59.933 47.826 0.00 0.00 0.00 3.02
113 114 2.760650 TGACTGCCGTGATCTATCTTGT 59.239 45.455 0.00 0.00 0.00 3.16
114 115 3.195610 TGACTGCCGTGATCTATCTTGTT 59.804 43.478 0.00 0.00 0.00 2.83
115 116 4.401202 TGACTGCCGTGATCTATCTTGTTA 59.599 41.667 0.00 0.00 0.00 2.41
116 117 4.938080 ACTGCCGTGATCTATCTTGTTAG 58.062 43.478 0.00 0.00 0.00 2.34
117 118 4.202161 ACTGCCGTGATCTATCTTGTTAGG 60.202 45.833 0.00 0.00 0.00 2.69
118 119 3.060602 GCCGTGATCTATCTTGTTAGGC 58.939 50.000 0.00 0.00 0.00 3.93
119 120 3.654414 CCGTGATCTATCTTGTTAGGCC 58.346 50.000 0.00 0.00 0.00 5.19
120 121 3.322254 CCGTGATCTATCTTGTTAGGCCT 59.678 47.826 11.78 11.78 0.00 5.19
121 122 4.551388 CGTGATCTATCTTGTTAGGCCTC 58.449 47.826 9.68 0.00 0.00 4.70
122 123 4.038042 CGTGATCTATCTTGTTAGGCCTCA 59.962 45.833 9.68 0.00 0.00 3.86
123 124 5.537188 GTGATCTATCTTGTTAGGCCTCAG 58.463 45.833 9.68 0.97 0.00 3.35
124 125 5.303078 GTGATCTATCTTGTTAGGCCTCAGA 59.697 44.000 9.68 7.50 0.00 3.27
125 126 6.014669 GTGATCTATCTTGTTAGGCCTCAGAT 60.015 42.308 9.68 14.67 0.00 2.90
126 127 6.210385 TGATCTATCTTGTTAGGCCTCAGATC 59.790 42.308 9.68 14.37 37.47 2.75
127 128 4.835615 TCTATCTTGTTAGGCCTCAGATCC 59.164 45.833 9.68 0.00 0.00 3.36
128 129 1.757118 TCTTGTTAGGCCTCAGATCCG 59.243 52.381 9.68 0.00 0.00 4.18
129 130 1.482593 CTTGTTAGGCCTCAGATCCGT 59.517 52.381 9.68 0.00 0.00 4.69
130 131 1.568504 TGTTAGGCCTCAGATCCGTT 58.431 50.000 9.68 0.00 0.00 4.44
131 132 1.906574 TGTTAGGCCTCAGATCCGTTT 59.093 47.619 9.68 0.00 0.00 3.60
132 133 2.304761 TGTTAGGCCTCAGATCCGTTTT 59.695 45.455 9.68 0.00 0.00 2.43
133 134 2.678336 GTTAGGCCTCAGATCCGTTTTG 59.322 50.000 9.68 0.00 0.00 2.44
134 135 0.035056 AGGCCTCAGATCCGTTTTGG 60.035 55.000 0.00 0.00 40.09 3.28
135 136 0.322546 GGCCTCAGATCCGTTTTGGT 60.323 55.000 0.00 0.00 39.52 3.67
136 137 1.087501 GCCTCAGATCCGTTTTGGTC 58.912 55.000 0.00 0.00 39.52 4.02
137 138 1.739067 CCTCAGATCCGTTTTGGTCC 58.261 55.000 0.00 0.00 39.52 4.46
138 139 1.279271 CCTCAGATCCGTTTTGGTCCT 59.721 52.381 0.00 0.00 39.52 3.85
139 140 2.622436 CTCAGATCCGTTTTGGTCCTC 58.378 52.381 0.00 0.00 39.52 3.71
140 141 1.974957 TCAGATCCGTTTTGGTCCTCA 59.025 47.619 0.00 0.00 39.52 3.86
141 142 2.028112 TCAGATCCGTTTTGGTCCTCAG 60.028 50.000 0.00 0.00 39.52 3.35
142 143 1.087501 GATCCGTTTTGGTCCTCAGC 58.912 55.000 0.00 0.00 39.52 4.26
143 144 0.400213 ATCCGTTTTGGTCCTCAGCA 59.600 50.000 0.00 0.00 39.52 4.41
144 145 0.181587 TCCGTTTTGGTCCTCAGCAA 59.818 50.000 0.00 0.00 38.26 3.91
145 146 1.028905 CCGTTTTGGTCCTCAGCAAA 58.971 50.000 0.00 0.00 46.01 3.68
148 149 3.511362 TTTGGTCCTCAGCAAAGCA 57.489 47.368 0.00 0.00 43.50 3.91
149 150 1.321474 TTTGGTCCTCAGCAAAGCAG 58.679 50.000 0.00 0.00 43.50 4.24
150 151 0.538057 TTGGTCCTCAGCAAAGCAGG 60.538 55.000 0.00 0.00 37.07 4.85
151 152 2.338785 GGTCCTCAGCAAAGCAGGC 61.339 63.158 0.00 0.00 0.00 4.85
152 153 2.034687 TCCTCAGCAAAGCAGGCC 59.965 61.111 0.00 0.00 0.00 5.19
153 154 2.282674 CCTCAGCAAAGCAGGCCA 60.283 61.111 5.01 0.00 0.00 5.36
154 155 1.904865 CCTCAGCAAAGCAGGCCAA 60.905 57.895 5.01 0.00 0.00 4.52
155 156 1.466025 CCTCAGCAAAGCAGGCCAAA 61.466 55.000 5.01 0.00 0.00 3.28
156 157 0.038526 CTCAGCAAAGCAGGCCAAAG 60.039 55.000 5.01 0.00 0.00 2.77
157 158 0.467844 TCAGCAAAGCAGGCCAAAGA 60.468 50.000 5.01 0.00 0.00 2.52
158 159 0.319297 CAGCAAAGCAGGCCAAAGAC 60.319 55.000 5.01 0.00 0.00 3.01
159 160 0.468771 AGCAAAGCAGGCCAAAGACT 60.469 50.000 5.01 0.00 0.00 3.24
172 173 2.093447 CCAAAGACTAATCCGAGCACCT 60.093 50.000 0.00 0.00 0.00 4.00
208 209 8.772250 TCAAGGTATATTCTTCTGTTCCAGATT 58.228 33.333 0.00 0.00 40.39 2.40
413 414 3.914094 TGCTGATGCATGCTCCAC 58.086 55.556 20.33 11.09 45.31 4.02
505 506 2.820787 CTCGGTCTTTGTCCAGTAGTCT 59.179 50.000 0.00 0.00 0.00 3.24
522 523 4.946478 AGTCTCATTCCATACTACCAGC 57.054 45.455 0.00 0.00 0.00 4.85
524 525 3.388024 GTCTCATTCCATACTACCAGCCA 59.612 47.826 0.00 0.00 0.00 4.75
539 540 3.319972 ACCAGCCAATATCATTGATGCAC 59.680 43.478 9.46 0.00 0.00 4.57
562 563 4.448210 GTGATTTACCTAGGCCATCGAAA 58.552 43.478 9.30 0.00 0.00 3.46
564 565 5.355910 GTGATTTACCTAGGCCATCGAAAAA 59.644 40.000 9.30 0.00 0.00 1.94
588 589 7.414222 AAAATTGTTCTCTCCATACATGCAT 57.586 32.000 0.00 0.00 0.00 3.96
607 608 4.662179 TGCATCCCATCTTCTTCCTAGAAT 59.338 41.667 0.00 0.00 39.58 2.40
608 609 5.846164 TGCATCCCATCTTCTTCCTAGAATA 59.154 40.000 0.00 0.00 39.58 1.75
609 610 6.329986 TGCATCCCATCTTCTTCCTAGAATAA 59.670 38.462 0.00 0.00 39.58 1.40
674 675 6.595326 AGTTTCGTTTCATCATGAGATTGCTA 59.405 34.615 0.09 0.00 30.20 3.49
675 676 6.594284 TTCGTTTCATCATGAGATTGCTAG 57.406 37.500 0.09 0.00 30.20 3.42
808 809 4.913335 CATCCTCATGGAATTGGTTGAG 57.087 45.455 0.00 0.00 46.80 3.02
822 823 1.003118 GGTTGAGCTGTCCACCACATA 59.997 52.381 0.00 0.00 38.23 2.29
883 884 3.966979 ACCAATCTACCATGTGCATTGA 58.033 40.909 0.00 0.00 0.00 2.57
1143 1145 5.370875 AGCTGCTAGAAAAATCAGAGGAT 57.629 39.130 0.00 0.00 34.43 3.24
1172 1174 3.163630 ACGCAGCAACAAAATCAAACT 57.836 38.095 0.00 0.00 0.00 2.66
1212 1214 3.002791 CAACTATGTGGATGAAGTGCGT 58.997 45.455 0.00 0.00 0.00 5.24
1234 1236 5.521010 CGTGCTGCATCAAATAAAATCCATT 59.479 36.000 5.27 0.00 0.00 3.16
1348 1350 3.128589 ACTGCAAAACACTACAACCACAG 59.871 43.478 0.00 0.00 0.00 3.66
1608 1612 3.199677 CCAGTGTGGTTCTTACGTTCAA 58.800 45.455 0.00 0.00 31.35 2.69
1712 1719 4.033990 TCGAACTGTACTCTCATCATGC 57.966 45.455 0.00 0.00 0.00 4.06
1798 1805 4.618920 TTACCCACTGAGAAACTTCCTC 57.381 45.455 0.00 0.00 0.00 3.71
1841 1848 6.749118 CACCTGCATTAACTTGCTTTATTCTC 59.251 38.462 2.92 0.00 43.18 2.87
2127 2136 4.661222 TGAGCACCTGGATGATAACAAAA 58.339 39.130 0.00 0.00 0.00 2.44
2259 4234 6.017934 AGGAGCATAGCACAAATTGTATTACG 60.018 38.462 0.00 0.00 0.00 3.18
2271 4246 8.385111 ACAAATTGTATTACGTAAGGACAATCG 58.615 33.333 31.35 27.88 46.39 3.34
2284 4260 3.000041 GGACAATCGCACATACACTCAA 59.000 45.455 0.00 0.00 0.00 3.02
2372 4348 2.464865 GCGCAACTGGTCATCTAGTAG 58.535 52.381 0.30 0.00 34.34 2.57
2373 4349 2.099263 GCGCAACTGGTCATCTAGTAGA 59.901 50.000 0.30 1.45 34.34 2.59
2376 4352 5.694816 CGCAACTGGTCATCTAGTAGATAG 58.305 45.833 12.38 8.89 34.34 2.08
2383 4359 9.482175 ACTGGTCATCTAGTAGATAGAAAAACT 57.518 33.333 12.38 0.00 43.75 2.66
2384 4360 9.743057 CTGGTCATCTAGTAGATAGAAAAACTG 57.257 37.037 12.38 0.00 43.75 3.16
2385 4361 9.475620 TGGTCATCTAGTAGATAGAAAAACTGA 57.524 33.333 12.38 1.66 43.75 3.41
2403 4379 9.471084 AAAAACTGAAACATATAAAGAAACCCG 57.529 29.630 0.00 0.00 0.00 5.28
2404 4380 6.753107 ACTGAAACATATAAAGAAACCCGG 57.247 37.500 0.00 0.00 0.00 5.73
2405 4381 6.243148 ACTGAAACATATAAAGAAACCCGGT 58.757 36.000 0.00 0.00 0.00 5.28
2406 4382 6.150474 ACTGAAACATATAAAGAAACCCGGTG 59.850 38.462 0.00 0.00 0.00 4.94
2407 4383 5.416326 TGAAACATATAAAGAAACCCGGTGG 59.584 40.000 0.00 0.00 37.80 4.61
2408 4384 3.284617 ACATATAAAGAAACCCGGTGGC 58.715 45.455 0.00 0.00 33.59 5.01
2409 4385 3.053917 ACATATAAAGAAACCCGGTGGCT 60.054 43.478 0.00 0.00 33.59 4.75
2410 4386 4.164604 ACATATAAAGAAACCCGGTGGCTA 59.835 41.667 0.00 0.00 33.59 3.93
2411 4387 3.945640 ATAAAGAAACCCGGTGGCTAT 57.054 42.857 0.00 0.00 33.59 2.97
2412 4388 2.124277 AAAGAAACCCGGTGGCTATC 57.876 50.000 0.00 0.00 33.59 2.08
2413 4389 0.988832 AAGAAACCCGGTGGCTATCA 59.011 50.000 0.00 0.00 33.59 2.15
2414 4390 1.213296 AGAAACCCGGTGGCTATCAT 58.787 50.000 0.00 0.00 33.59 2.45
2415 4391 1.564348 AGAAACCCGGTGGCTATCATT 59.436 47.619 0.00 0.00 33.59 2.57
2416 4392 1.947456 GAAACCCGGTGGCTATCATTC 59.053 52.381 0.00 0.00 33.59 2.67
2417 4393 0.916086 AACCCGGTGGCTATCATTCA 59.084 50.000 0.00 0.00 33.59 2.57
2418 4394 0.916086 ACCCGGTGGCTATCATTCAA 59.084 50.000 0.00 0.00 33.59 2.69
2419 4395 1.134098 ACCCGGTGGCTATCATTCAAG 60.134 52.381 0.00 0.00 33.59 3.02
2420 4396 1.597742 CCGGTGGCTATCATTCAAGG 58.402 55.000 0.00 0.00 0.00 3.61
2421 4397 0.947244 CGGTGGCTATCATTCAAGGC 59.053 55.000 0.00 0.00 38.68 4.35
2422 4398 1.746861 CGGTGGCTATCATTCAAGGCA 60.747 52.381 0.00 0.00 45.01 4.75
2425 4401 2.378038 TGGCTATCATTCAAGGCAACC 58.622 47.619 0.00 0.00 44.34 3.77
2426 4402 2.025037 TGGCTATCATTCAAGGCAACCT 60.025 45.455 0.00 0.00 44.34 3.50
2427 4403 2.620585 GGCTATCATTCAAGGCAACCTC 59.379 50.000 0.00 0.00 38.14 3.85
2428 4404 3.549794 GCTATCATTCAAGGCAACCTCT 58.450 45.455 0.00 0.00 30.89 3.69
2429 4405 3.563390 GCTATCATTCAAGGCAACCTCTC 59.437 47.826 0.00 0.00 30.89 3.20
2430 4406 3.726557 ATCATTCAAGGCAACCTCTCA 57.273 42.857 0.00 0.00 30.89 3.27
2431 4407 3.507162 TCATTCAAGGCAACCTCTCAA 57.493 42.857 0.00 0.00 30.89 3.02
2432 4408 3.149196 TCATTCAAGGCAACCTCTCAAC 58.851 45.455 0.00 0.00 30.89 3.18
2433 4409 2.727123 TTCAAGGCAACCTCTCAACA 57.273 45.000 0.00 0.00 30.89 3.33
2434 4410 2.957402 TCAAGGCAACCTCTCAACAT 57.043 45.000 0.00 0.00 30.89 2.71
2435 4411 2.507484 TCAAGGCAACCTCTCAACATG 58.493 47.619 0.00 0.00 30.89 3.21
2436 4412 2.158623 TCAAGGCAACCTCTCAACATGT 60.159 45.455 0.00 0.00 30.89 3.21
2437 4413 1.901591 AGGCAACCTCTCAACATGTG 58.098 50.000 0.00 0.00 37.17 3.21
2438 4414 0.242017 GGCAACCTCTCAACATGTGC 59.758 55.000 0.00 0.00 0.00 4.57
2439 4415 0.953727 GCAACCTCTCAACATGTGCA 59.046 50.000 0.00 0.00 0.00 4.57
2440 4416 1.068748 GCAACCTCTCAACATGTGCAG 60.069 52.381 0.00 0.00 0.00 4.41
2441 4417 2.497138 CAACCTCTCAACATGTGCAGA 58.503 47.619 0.00 2.79 0.00 4.26
2442 4418 3.079578 CAACCTCTCAACATGTGCAGAT 58.920 45.455 0.00 0.00 0.00 2.90
2443 4419 4.256110 CAACCTCTCAACATGTGCAGATA 58.744 43.478 0.00 0.00 0.00 1.98
2444 4420 4.134379 ACCTCTCAACATGTGCAGATAG 57.866 45.455 0.00 0.69 0.00 2.08
2445 4421 3.771479 ACCTCTCAACATGTGCAGATAGA 59.229 43.478 0.00 0.00 0.00 1.98
2446 4422 4.408270 ACCTCTCAACATGTGCAGATAGAT 59.592 41.667 0.00 0.00 0.00 1.98
2447 4423 4.750598 CCTCTCAACATGTGCAGATAGATG 59.249 45.833 0.00 0.00 0.00 2.90
2448 4424 4.124970 TCTCAACATGTGCAGATAGATGC 58.875 43.478 0.00 0.00 46.68 3.91
2461 4437 7.012959 GCAGATAGATGCACCAACATATATG 57.987 40.000 11.29 11.29 45.77 1.78
2462 4438 6.457934 GCAGATAGATGCACCAACATATATGC 60.458 42.308 12.79 0.00 45.77 3.14
2467 4443 4.044336 TGCACCAACATATATGCAAAGC 57.956 40.909 12.79 10.81 44.72 3.51
2468 4444 3.044986 GCACCAACATATATGCAAAGCG 58.955 45.455 12.79 0.00 38.00 4.68
2469 4445 3.243035 GCACCAACATATATGCAAAGCGA 60.243 43.478 12.79 0.00 38.00 4.93
2470 4446 4.530388 CACCAACATATATGCAAAGCGAG 58.470 43.478 12.79 0.00 0.00 5.03
2471 4447 3.003689 ACCAACATATATGCAAAGCGAGC 59.996 43.478 12.79 0.00 0.00 5.03
2472 4448 3.558505 CAACATATATGCAAAGCGAGCC 58.441 45.455 12.79 0.00 0.00 4.70
2473 4449 3.131709 ACATATATGCAAAGCGAGCCT 57.868 42.857 12.79 0.00 0.00 4.58
2474 4450 2.810274 ACATATATGCAAAGCGAGCCTG 59.190 45.455 12.79 0.00 0.00 4.85
2475 4451 2.620251 TATATGCAAAGCGAGCCTGT 57.380 45.000 0.00 0.00 0.00 4.00
2476 4452 1.303309 ATATGCAAAGCGAGCCTGTC 58.697 50.000 0.00 0.00 0.00 3.51
2477 4453 0.250234 TATGCAAAGCGAGCCTGTCT 59.750 50.000 0.00 0.00 0.00 3.41
2478 4454 0.607489 ATGCAAAGCGAGCCTGTCTT 60.607 50.000 0.00 0.00 0.00 3.01
2479 4455 0.819259 TGCAAAGCGAGCCTGTCTTT 60.819 50.000 0.00 0.00 0.00 2.52
2480 4456 1.156736 GCAAAGCGAGCCTGTCTTTA 58.843 50.000 0.00 0.00 0.00 1.85
2481 4457 1.740025 GCAAAGCGAGCCTGTCTTTAT 59.260 47.619 0.00 0.00 0.00 1.40
2482 4458 2.936498 GCAAAGCGAGCCTGTCTTTATA 59.064 45.455 0.00 0.00 0.00 0.98
2483 4459 3.242446 GCAAAGCGAGCCTGTCTTTATAC 60.242 47.826 0.00 0.00 0.00 1.47
2484 4460 2.493713 AGCGAGCCTGTCTTTATACG 57.506 50.000 0.00 0.00 0.00 3.06
2485 4461 0.853419 GCGAGCCTGTCTTTATACGC 59.147 55.000 0.00 0.00 38.23 4.42
2486 4462 1.536284 GCGAGCCTGTCTTTATACGCT 60.536 52.381 0.00 0.00 41.25 5.07
2487 4463 2.120232 CGAGCCTGTCTTTATACGCTG 58.880 52.381 0.00 0.00 0.00 5.18
2488 4464 2.474816 GAGCCTGTCTTTATACGCTGG 58.525 52.381 0.00 0.00 0.00 4.85
2489 4465 2.100916 GAGCCTGTCTTTATACGCTGGA 59.899 50.000 0.00 0.00 0.00 3.86
2490 4466 2.700897 AGCCTGTCTTTATACGCTGGAT 59.299 45.455 0.00 0.00 0.00 3.41
2491 4467 3.134804 AGCCTGTCTTTATACGCTGGATT 59.865 43.478 0.00 0.00 0.00 3.01
2492 4468 3.495001 GCCTGTCTTTATACGCTGGATTC 59.505 47.826 0.00 0.00 0.00 2.52
2493 4469 4.058817 CCTGTCTTTATACGCTGGATTCC 58.941 47.826 0.00 0.00 0.00 3.01
2494 4470 4.202264 CCTGTCTTTATACGCTGGATTCCT 60.202 45.833 3.95 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.021355 AGGCGAGAAGATTGAGCAAG 57.979 50.000 0.00 0.00 0.00 4.01
2 3 2.497675 AGTAGGCGAGAAGATTGAGCAA 59.502 45.455 0.00 0.00 0.00 3.91
3 4 2.099921 GAGTAGGCGAGAAGATTGAGCA 59.900 50.000 0.00 0.00 0.00 4.26
4 5 2.544903 GGAGTAGGCGAGAAGATTGAGC 60.545 54.545 0.00 0.00 0.00 4.26
5 6 2.955660 AGGAGTAGGCGAGAAGATTGAG 59.044 50.000 0.00 0.00 0.00 3.02
6 7 3.019799 AGGAGTAGGCGAGAAGATTGA 57.980 47.619 0.00 0.00 0.00 2.57
7 8 3.118956 ACAAGGAGTAGGCGAGAAGATTG 60.119 47.826 0.00 0.00 0.00 2.67
8 9 3.100671 ACAAGGAGTAGGCGAGAAGATT 58.899 45.455 0.00 0.00 0.00 2.40
9 10 2.691011 GACAAGGAGTAGGCGAGAAGAT 59.309 50.000 0.00 0.00 0.00 2.40
10 11 2.093106 GACAAGGAGTAGGCGAGAAGA 58.907 52.381 0.00 0.00 0.00 2.87
11 12 1.819288 TGACAAGGAGTAGGCGAGAAG 59.181 52.381 0.00 0.00 0.00 2.85
12 13 1.919240 TGACAAGGAGTAGGCGAGAA 58.081 50.000 0.00 0.00 0.00 2.87
13 14 1.919240 TTGACAAGGAGTAGGCGAGA 58.081 50.000 0.00 0.00 0.00 4.04
14 15 2.338500 GTTTGACAAGGAGTAGGCGAG 58.662 52.381 0.00 0.00 0.00 5.03
15 16 1.001633 GGTTTGACAAGGAGTAGGCGA 59.998 52.381 0.00 0.00 0.00 5.54
16 17 1.439679 GGTTTGACAAGGAGTAGGCG 58.560 55.000 0.00 0.00 0.00 5.52
17 18 1.613520 GGGGTTTGACAAGGAGTAGGC 60.614 57.143 0.00 0.00 0.00 3.93
18 19 1.985895 AGGGGTTTGACAAGGAGTAGG 59.014 52.381 0.00 0.00 0.00 3.18
19 20 2.372172 ACAGGGGTTTGACAAGGAGTAG 59.628 50.000 0.00 0.00 0.00 2.57
20 21 2.414612 ACAGGGGTTTGACAAGGAGTA 58.585 47.619 0.00 0.00 0.00 2.59
21 22 1.222567 ACAGGGGTTTGACAAGGAGT 58.777 50.000 0.00 0.00 0.00 3.85
22 23 2.372172 ACTACAGGGGTTTGACAAGGAG 59.628 50.000 0.00 0.00 0.00 3.69
23 24 2.105821 CACTACAGGGGTTTGACAAGGA 59.894 50.000 0.00 0.00 0.00 3.36
24 25 2.504367 CACTACAGGGGTTTGACAAGG 58.496 52.381 0.00 0.00 0.00 3.61
25 26 2.504367 CCACTACAGGGGTTTGACAAG 58.496 52.381 0.00 0.00 0.00 3.16
26 27 1.477923 GCCACTACAGGGGTTTGACAA 60.478 52.381 0.00 0.00 0.00 3.18
27 28 0.109723 GCCACTACAGGGGTTTGACA 59.890 55.000 0.00 0.00 0.00 3.58
28 29 0.953960 CGCCACTACAGGGGTTTGAC 60.954 60.000 0.00 0.00 36.89 3.18
29 30 1.373435 CGCCACTACAGGGGTTTGA 59.627 57.895 0.00 0.00 36.89 2.69
30 31 1.674322 CCGCCACTACAGGGGTTTG 60.674 63.158 0.00 0.00 39.79 2.93
31 32 2.754375 CCGCCACTACAGGGGTTT 59.246 61.111 0.00 0.00 39.79 3.27
34 35 1.985662 TACACCGCCACTACAGGGG 60.986 63.158 0.00 0.00 42.80 4.79
35 36 1.217244 GTACACCGCCACTACAGGG 59.783 63.158 0.00 0.00 0.00 4.45
36 37 0.108804 CTGTACACCGCCACTACAGG 60.109 60.000 0.00 0.00 35.63 4.00
37 38 0.885879 TCTGTACACCGCCACTACAG 59.114 55.000 0.00 0.00 39.09 2.74
38 39 0.885879 CTCTGTACACCGCCACTACA 59.114 55.000 0.00 0.00 0.00 2.74
39 40 1.135460 GTCTCTGTACACCGCCACTAC 60.135 57.143 0.00 0.00 0.00 2.73
40 41 1.171308 GTCTCTGTACACCGCCACTA 58.829 55.000 0.00 0.00 0.00 2.74
41 42 0.826256 TGTCTCTGTACACCGCCACT 60.826 55.000 0.00 0.00 0.00 4.00
42 43 0.246635 ATGTCTCTGTACACCGCCAC 59.753 55.000 0.00 0.00 30.75 5.01
43 44 0.530744 GATGTCTCTGTACACCGCCA 59.469 55.000 0.00 0.00 30.75 5.69
44 45 0.818296 AGATGTCTCTGTACACCGCC 59.182 55.000 0.00 0.00 30.75 6.13
45 46 2.196295 GAGATGTCTCTGTACACCGC 57.804 55.000 2.80 0.00 39.81 5.68
56 57 4.080129 AGAGAGAGCAAGAGAGAGATGTCT 60.080 45.833 0.00 0.00 34.86 3.41
57 58 4.202441 AGAGAGAGCAAGAGAGAGATGTC 58.798 47.826 0.00 0.00 0.00 3.06
58 59 4.080129 AGAGAGAGAGCAAGAGAGAGATGT 60.080 45.833 0.00 0.00 0.00 3.06
59 60 4.458397 AGAGAGAGAGCAAGAGAGAGATG 58.542 47.826 0.00 0.00 0.00 2.90
60 61 4.785346 AGAGAGAGAGCAAGAGAGAGAT 57.215 45.455 0.00 0.00 0.00 2.75
61 62 4.716784 AGTAGAGAGAGAGCAAGAGAGAGA 59.283 45.833 0.00 0.00 0.00 3.10
62 63 5.028549 AGTAGAGAGAGAGCAAGAGAGAG 57.971 47.826 0.00 0.00 0.00 3.20
63 64 5.428253 GAAGTAGAGAGAGAGCAAGAGAGA 58.572 45.833 0.00 0.00 0.00 3.10
64 65 4.576463 GGAAGTAGAGAGAGAGCAAGAGAG 59.424 50.000 0.00 0.00 0.00 3.20
65 66 4.018870 TGGAAGTAGAGAGAGAGCAAGAGA 60.019 45.833 0.00 0.00 0.00 3.10
66 67 4.269183 TGGAAGTAGAGAGAGAGCAAGAG 58.731 47.826 0.00 0.00 0.00 2.85
67 68 4.308526 TGGAAGTAGAGAGAGAGCAAGA 57.691 45.455 0.00 0.00 0.00 3.02
68 69 5.360714 AGATTGGAAGTAGAGAGAGAGCAAG 59.639 44.000 0.00 0.00 0.00 4.01
69 70 5.126869 CAGATTGGAAGTAGAGAGAGAGCAA 59.873 44.000 0.00 0.00 0.00 3.91
70 71 4.644234 CAGATTGGAAGTAGAGAGAGAGCA 59.356 45.833 0.00 0.00 0.00 4.26
71 72 4.887071 TCAGATTGGAAGTAGAGAGAGAGC 59.113 45.833 0.00 0.00 0.00 4.09
72 73 6.038603 CAGTCAGATTGGAAGTAGAGAGAGAG 59.961 46.154 0.00 0.00 0.00 3.20
73 74 5.885352 CAGTCAGATTGGAAGTAGAGAGAGA 59.115 44.000 0.00 0.00 0.00 3.10
74 75 5.450412 GCAGTCAGATTGGAAGTAGAGAGAG 60.450 48.000 0.00 0.00 0.00 3.20
75 76 4.400884 GCAGTCAGATTGGAAGTAGAGAGA 59.599 45.833 0.00 0.00 0.00 3.10
76 77 4.441356 GGCAGTCAGATTGGAAGTAGAGAG 60.441 50.000 0.00 0.00 0.00 3.20
77 78 3.449018 GGCAGTCAGATTGGAAGTAGAGA 59.551 47.826 0.00 0.00 0.00 3.10
78 79 3.736433 CGGCAGTCAGATTGGAAGTAGAG 60.736 52.174 0.00 0.00 0.00 2.43
79 80 2.166459 CGGCAGTCAGATTGGAAGTAGA 59.834 50.000 0.00 0.00 0.00 2.59
80 81 2.093973 ACGGCAGTCAGATTGGAAGTAG 60.094 50.000 0.00 0.00 0.00 2.57
81 82 1.899814 ACGGCAGTCAGATTGGAAGTA 59.100 47.619 0.00 0.00 0.00 2.24
82 83 0.687354 ACGGCAGTCAGATTGGAAGT 59.313 50.000 0.00 0.00 0.00 3.01
83 84 1.081892 CACGGCAGTCAGATTGGAAG 58.918 55.000 0.00 0.00 0.00 3.46
84 85 0.684535 TCACGGCAGTCAGATTGGAA 59.315 50.000 0.00 0.00 0.00 3.53
85 86 0.904649 ATCACGGCAGTCAGATTGGA 59.095 50.000 0.00 0.00 0.00 3.53
86 87 1.134580 AGATCACGGCAGTCAGATTGG 60.135 52.381 0.00 0.00 0.00 3.16
87 88 2.306341 AGATCACGGCAGTCAGATTG 57.694 50.000 0.00 0.00 0.00 2.67
88 89 3.894427 AGATAGATCACGGCAGTCAGATT 59.106 43.478 0.00 0.00 0.00 2.40
89 90 3.495331 AGATAGATCACGGCAGTCAGAT 58.505 45.455 0.00 0.00 0.00 2.90
90 91 2.937519 AGATAGATCACGGCAGTCAGA 58.062 47.619 0.00 0.00 0.00 3.27
91 92 3.181482 ACAAGATAGATCACGGCAGTCAG 60.181 47.826 0.00 0.00 0.00 3.51
92 93 2.760650 ACAAGATAGATCACGGCAGTCA 59.239 45.455 0.00 0.00 0.00 3.41
93 94 3.444703 ACAAGATAGATCACGGCAGTC 57.555 47.619 0.00 0.00 0.00 3.51
94 95 3.895232 AACAAGATAGATCACGGCAGT 57.105 42.857 0.00 0.00 0.00 4.40
95 96 4.302455 CCTAACAAGATAGATCACGGCAG 58.698 47.826 0.00 0.00 0.00 4.85
96 97 3.492656 GCCTAACAAGATAGATCACGGCA 60.493 47.826 0.00 0.00 34.16 5.69
97 98 3.060602 GCCTAACAAGATAGATCACGGC 58.939 50.000 0.00 0.00 0.00 5.68
98 99 3.322254 AGGCCTAACAAGATAGATCACGG 59.678 47.826 1.29 0.00 0.00 4.94
99 100 4.038042 TGAGGCCTAACAAGATAGATCACG 59.962 45.833 4.42 0.00 0.00 4.35
100 101 5.303078 TCTGAGGCCTAACAAGATAGATCAC 59.697 44.000 4.42 0.00 0.00 3.06
101 102 5.458595 TCTGAGGCCTAACAAGATAGATCA 58.541 41.667 4.42 0.00 0.00 2.92
102 103 6.350949 GGATCTGAGGCCTAACAAGATAGATC 60.351 46.154 4.42 13.28 38.04 2.75
103 104 5.483583 GGATCTGAGGCCTAACAAGATAGAT 59.516 44.000 4.42 5.17 0.00 1.98
104 105 4.835615 GGATCTGAGGCCTAACAAGATAGA 59.164 45.833 4.42 0.00 0.00 1.98
105 106 4.321601 CGGATCTGAGGCCTAACAAGATAG 60.322 50.000 4.42 6.53 0.00 2.08
106 107 3.574396 CGGATCTGAGGCCTAACAAGATA 59.426 47.826 4.42 0.00 0.00 1.98
107 108 2.366916 CGGATCTGAGGCCTAACAAGAT 59.633 50.000 4.42 12.33 0.00 2.40
108 109 1.757118 CGGATCTGAGGCCTAACAAGA 59.243 52.381 4.42 7.36 0.00 3.02
109 110 1.482593 ACGGATCTGAGGCCTAACAAG 59.517 52.381 4.42 0.91 0.00 3.16
110 111 1.568504 ACGGATCTGAGGCCTAACAA 58.431 50.000 4.42 0.00 0.00 2.83
111 112 1.568504 AACGGATCTGAGGCCTAACA 58.431 50.000 4.42 0.00 0.00 2.41
112 113 2.678336 CAAAACGGATCTGAGGCCTAAC 59.322 50.000 4.42 0.00 0.00 2.34
113 114 2.355716 CCAAAACGGATCTGAGGCCTAA 60.356 50.000 4.42 0.00 36.56 2.69
114 115 1.209504 CCAAAACGGATCTGAGGCCTA 59.790 52.381 4.42 0.00 36.56 3.93
115 116 0.035056 CCAAAACGGATCTGAGGCCT 60.035 55.000 3.86 3.86 36.56 5.19
116 117 0.322546 ACCAAAACGGATCTGAGGCC 60.323 55.000 9.00 0.00 38.63 5.19
117 118 1.087501 GACCAAAACGGATCTGAGGC 58.912 55.000 9.00 0.00 38.63 4.70
118 119 1.279271 AGGACCAAAACGGATCTGAGG 59.721 52.381 9.00 7.01 38.63 3.86
119 120 2.028112 TGAGGACCAAAACGGATCTGAG 60.028 50.000 9.00 0.00 38.63 3.35
120 121 1.974957 TGAGGACCAAAACGGATCTGA 59.025 47.619 9.00 0.00 38.63 3.27
121 122 2.350522 CTGAGGACCAAAACGGATCTG 58.649 52.381 0.00 0.00 38.63 2.90
122 123 1.339151 GCTGAGGACCAAAACGGATCT 60.339 52.381 0.00 0.00 38.63 2.75
123 124 1.087501 GCTGAGGACCAAAACGGATC 58.912 55.000 0.00 0.00 38.63 3.36
124 125 0.400213 TGCTGAGGACCAAAACGGAT 59.600 50.000 0.00 0.00 38.63 4.18
125 126 0.181587 TTGCTGAGGACCAAAACGGA 59.818 50.000 0.00 0.00 38.63 4.69
126 127 1.001378 CTTTGCTGAGGACCAAAACGG 60.001 52.381 0.00 0.00 42.50 4.44
127 128 1.600413 GCTTTGCTGAGGACCAAAACG 60.600 52.381 0.00 0.00 31.29 3.60
128 129 1.408702 TGCTTTGCTGAGGACCAAAAC 59.591 47.619 0.00 0.00 31.29 2.43
129 130 1.682854 CTGCTTTGCTGAGGACCAAAA 59.317 47.619 0.00 0.00 31.29 2.44
130 131 1.321474 CTGCTTTGCTGAGGACCAAA 58.679 50.000 0.00 0.00 0.00 3.28
131 132 0.538057 CCTGCTTTGCTGAGGACCAA 60.538 55.000 0.00 0.00 0.00 3.67
132 133 1.073722 CCTGCTTTGCTGAGGACCA 59.926 57.895 0.00 0.00 0.00 4.02
133 134 2.338785 GCCTGCTTTGCTGAGGACC 61.339 63.158 0.00 0.00 0.00 4.46
134 135 2.338785 GGCCTGCTTTGCTGAGGAC 61.339 63.158 0.00 0.00 0.00 3.85
135 136 2.034687 GGCCTGCTTTGCTGAGGA 59.965 61.111 0.00 0.00 0.00 3.71
136 137 1.466025 TTTGGCCTGCTTTGCTGAGG 61.466 55.000 3.32 0.00 0.00 3.86
137 138 0.038526 CTTTGGCCTGCTTTGCTGAG 60.039 55.000 3.32 0.00 0.00 3.35
138 139 0.467844 TCTTTGGCCTGCTTTGCTGA 60.468 50.000 3.32 0.00 0.00 4.26
139 140 0.319297 GTCTTTGGCCTGCTTTGCTG 60.319 55.000 3.32 0.00 0.00 4.41
140 141 0.468771 AGTCTTTGGCCTGCTTTGCT 60.469 50.000 3.32 0.00 0.00 3.91
141 142 1.247567 TAGTCTTTGGCCTGCTTTGC 58.752 50.000 3.32 0.00 0.00 3.68
142 143 3.119352 GGATTAGTCTTTGGCCTGCTTTG 60.119 47.826 3.32 0.00 0.00 2.77
143 144 3.092301 GGATTAGTCTTTGGCCTGCTTT 58.908 45.455 3.32 0.00 0.00 3.51
144 145 2.728007 GGATTAGTCTTTGGCCTGCTT 58.272 47.619 3.32 0.00 0.00 3.91
145 146 1.407437 CGGATTAGTCTTTGGCCTGCT 60.407 52.381 3.32 0.00 0.00 4.24
146 147 1.017387 CGGATTAGTCTTTGGCCTGC 58.983 55.000 3.32 0.00 0.00 4.85
147 148 2.555199 CTCGGATTAGTCTTTGGCCTG 58.445 52.381 3.32 0.00 0.00 4.85
148 149 1.134371 GCTCGGATTAGTCTTTGGCCT 60.134 52.381 3.32 0.00 0.00 5.19
149 150 1.300481 GCTCGGATTAGTCTTTGGCC 58.700 55.000 0.00 0.00 0.00 5.36
150 151 1.666189 GTGCTCGGATTAGTCTTTGGC 59.334 52.381 0.00 0.00 0.00 4.52
151 152 2.093447 AGGTGCTCGGATTAGTCTTTGG 60.093 50.000 0.00 0.00 0.00 3.28
152 153 2.932614 CAGGTGCTCGGATTAGTCTTTG 59.067 50.000 0.00 0.00 0.00 2.77
153 154 2.678190 GCAGGTGCTCGGATTAGTCTTT 60.678 50.000 0.00 0.00 38.21 2.52
154 155 1.134670 GCAGGTGCTCGGATTAGTCTT 60.135 52.381 0.00 0.00 38.21 3.01
155 156 0.461961 GCAGGTGCTCGGATTAGTCT 59.538 55.000 0.00 0.00 38.21 3.24
156 157 0.530870 GGCAGGTGCTCGGATTAGTC 60.531 60.000 1.26 0.00 41.70 2.59
157 158 0.978146 AGGCAGGTGCTCGGATTAGT 60.978 55.000 1.26 0.00 41.70 2.24
158 159 1.040646 TAGGCAGGTGCTCGGATTAG 58.959 55.000 1.26 0.00 41.70 1.73
159 160 1.491668 TTAGGCAGGTGCTCGGATTA 58.508 50.000 1.26 0.00 41.70 1.75
172 173 7.514127 AGAAGAATATACCTTGAGGATTAGGCA 59.486 37.037 3.59 0.00 38.94 4.75
261 262 9.625747 TTATGCAAATATACAACATTCTGAGGA 57.374 29.630 0.00 0.00 0.00 3.71
308 309 4.133820 TCAAACGTGGACATTGAACAGAT 58.866 39.130 0.00 0.00 30.60 2.90
312 313 3.365969 GGGATCAAACGTGGACATTGAAC 60.366 47.826 3.90 1.87 36.72 3.18
406 407 4.081917 TGCGGATATAATATTCGTGGAGCA 60.082 41.667 0.00 0.00 0.00 4.26
413 414 5.118664 CGGCCTTATGCGGATATAATATTCG 59.881 44.000 0.00 0.00 42.55 3.34
505 506 6.272090 TGATATTGGCTGGTAGTATGGAATGA 59.728 38.462 0.00 0.00 0.00 2.57
522 523 4.816786 TCACGTGCATCAATGATATTGG 57.183 40.909 11.67 0.00 0.00 3.16
524 525 7.229306 AGGTAAATCACGTGCATCAATGATATT 59.771 33.333 11.67 0.00 31.56 1.28
539 540 2.035449 TCGATGGCCTAGGTAAATCACG 59.965 50.000 11.31 7.86 0.00 4.35
564 565 6.839124 TGCATGTATGGAGAGAACAATTTT 57.161 33.333 0.00 0.00 0.00 1.82
565 566 6.040166 GGATGCATGTATGGAGAGAACAATTT 59.960 38.462 2.46 0.00 0.00 1.82
566 567 5.533903 GGATGCATGTATGGAGAGAACAATT 59.466 40.000 2.46 0.00 0.00 2.32
567 568 5.068636 GGATGCATGTATGGAGAGAACAAT 58.931 41.667 2.46 0.00 0.00 2.71
582 583 3.225177 AGGAAGAAGATGGGATGCATG 57.775 47.619 2.46 0.00 0.00 4.06
588 589 8.654997 CAGAATTATTCTAGGAAGAAGATGGGA 58.345 37.037 7.18 0.00 44.79 4.37
608 609 9.574516 AAATTCACAGAGGTAAGTAACAGAATT 57.425 29.630 0.00 0.00 34.54 2.17
609 610 9.220767 GAAATTCACAGAGGTAAGTAACAGAAT 57.779 33.333 0.00 0.00 0.00 2.40
674 675 4.381079 GCATACAGAACCGAAGAACTCTCT 60.381 45.833 0.00 0.00 0.00 3.10
675 676 3.860536 GCATACAGAACCGAAGAACTCTC 59.139 47.826 0.00 0.00 0.00 3.20
705 706 0.251474 TGAGCAGCCAAGCCTTTGAT 60.251 50.000 0.00 0.00 36.36 2.57
808 809 1.134946 GCCAAATATGTGGTGGACAGC 59.865 52.381 13.70 0.00 41.12 4.40
822 823 4.039488 TCTCAAACATTGCTTCAGCCAAAT 59.961 37.500 0.00 0.00 41.18 2.32
883 884 3.503748 GCTTTACATCACCTTGCTCAAGT 59.496 43.478 8.60 0.00 36.72 3.16
1143 1145 1.598882 TGTTGCTGCGTTGGTTGATA 58.401 45.000 0.00 0.00 0.00 2.15
1172 1174 5.500234 AGTTGCATGCCTCTTTAGTTATCA 58.500 37.500 16.68 0.00 0.00 2.15
1212 1214 6.408035 ACAATGGATTTTATTTGATGCAGCA 58.592 32.000 0.00 0.00 0.00 4.41
1234 1236 2.571212 CAAGGCAACACCAGTAAGACA 58.429 47.619 0.00 0.00 43.14 3.41
1423 1425 5.505985 GGCAATCTTCAGCAGAATCTTCATC 60.506 44.000 0.00 0.00 34.16 2.92
1566 1570 0.321298 TCCCGCCTAACAGAAGCAAC 60.321 55.000 0.00 0.00 0.00 4.17
1608 1612 4.780021 ACACAGGAGACTAAACATGGAGAT 59.220 41.667 0.00 0.00 40.21 2.75
1712 1719 7.585210 CACAGCACGATGAATTCAATACTTATG 59.415 37.037 13.09 8.87 0.00 1.90
1798 1805 2.398498 GTGCATAGCGATGGTACTGAG 58.602 52.381 8.97 0.00 33.26 3.35
1841 1848 1.560923 CGCACTGATTTAGTCTCGGG 58.439 55.000 0.00 0.00 37.60 5.14
2085 2094 5.339008 TCAACTGATCGGCTGTAGTAAAT 57.661 39.130 0.00 0.00 0.00 1.40
2127 2136 3.004752 AGGTCAGTGAACAAGCACTTT 57.995 42.857 11.57 0.00 46.42 2.66
2259 4234 4.181578 AGTGTATGTGCGATTGTCCTTAC 58.818 43.478 0.00 0.00 0.00 2.34
2271 4246 5.467735 TCATGCATAGATTGAGTGTATGTGC 59.532 40.000 0.00 0.00 36.65 4.57
2359 4335 9.475620 TCAGTTTTTCTATCTACTAGATGACCA 57.524 33.333 8.62 0.00 35.37 4.02
2382 4358 6.404293 CCACCGGGTTTCTTTATATGTTTCAG 60.404 42.308 6.32 0.00 0.00 3.02
2383 4359 5.416326 CCACCGGGTTTCTTTATATGTTTCA 59.584 40.000 6.32 0.00 0.00 2.69
2384 4360 5.677852 GCCACCGGGTTTCTTTATATGTTTC 60.678 44.000 6.32 0.00 36.17 2.78
2385 4361 4.158949 GCCACCGGGTTTCTTTATATGTTT 59.841 41.667 6.32 0.00 36.17 2.83
2386 4362 3.697542 GCCACCGGGTTTCTTTATATGTT 59.302 43.478 6.32 0.00 36.17 2.71
2387 4363 3.053917 AGCCACCGGGTTTCTTTATATGT 60.054 43.478 6.32 0.00 36.17 2.29
2388 4364 3.551846 AGCCACCGGGTTTCTTTATATG 58.448 45.455 6.32 0.00 36.17 1.78
2389 4365 3.945640 AGCCACCGGGTTTCTTTATAT 57.054 42.857 6.32 0.00 36.17 0.86
2390 4366 4.409574 TGATAGCCACCGGGTTTCTTTATA 59.590 41.667 6.32 0.00 33.52 0.98
2391 4367 3.201266 TGATAGCCACCGGGTTTCTTTAT 59.799 43.478 6.32 0.00 33.52 1.40
2392 4368 2.572556 TGATAGCCACCGGGTTTCTTTA 59.427 45.455 6.32 0.00 33.52 1.85
2393 4369 1.353022 TGATAGCCACCGGGTTTCTTT 59.647 47.619 6.32 0.00 33.52 2.52
2394 4370 0.988832 TGATAGCCACCGGGTTTCTT 59.011 50.000 6.32 0.00 33.52 2.52
2395 4371 1.213296 ATGATAGCCACCGGGTTTCT 58.787 50.000 6.32 0.00 33.52 2.52
2396 4372 1.947456 GAATGATAGCCACCGGGTTTC 59.053 52.381 6.32 0.00 34.28 2.78
2397 4373 1.283613 TGAATGATAGCCACCGGGTTT 59.716 47.619 6.32 0.00 34.28 3.27
2398 4374 0.916086 TGAATGATAGCCACCGGGTT 59.084 50.000 6.32 0.00 34.28 4.11
2399 4375 0.916086 TTGAATGATAGCCACCGGGT 59.084 50.000 6.32 0.00 37.19 5.28
2400 4376 1.597742 CTTGAATGATAGCCACCGGG 58.402 55.000 6.32 0.00 37.18 5.73
2401 4377 1.597742 CCTTGAATGATAGCCACCGG 58.402 55.000 0.00 0.00 0.00 5.28
2402 4378 0.947244 GCCTTGAATGATAGCCACCG 59.053 55.000 0.00 0.00 0.00 4.94
2403 4379 2.057137 TGCCTTGAATGATAGCCACC 57.943 50.000 0.00 0.00 0.00 4.61
2404 4380 2.099756 GGTTGCCTTGAATGATAGCCAC 59.900 50.000 0.00 0.00 0.00 5.01
2405 4381 2.025037 AGGTTGCCTTGAATGATAGCCA 60.025 45.455 0.00 0.00 0.00 4.75
2406 4382 2.620585 GAGGTTGCCTTGAATGATAGCC 59.379 50.000 0.00 0.00 31.76 3.93
2407 4383 3.549794 AGAGGTTGCCTTGAATGATAGC 58.450 45.455 0.00 0.00 31.76 2.97
2408 4384 4.774124 TGAGAGGTTGCCTTGAATGATAG 58.226 43.478 0.00 0.00 31.76 2.08
2409 4385 4.842531 TGAGAGGTTGCCTTGAATGATA 57.157 40.909 0.00 0.00 31.76 2.15
2410 4386 3.726557 TGAGAGGTTGCCTTGAATGAT 57.273 42.857 0.00 0.00 31.76 2.45
2411 4387 3.149196 GTTGAGAGGTTGCCTTGAATGA 58.851 45.455 0.00 0.00 31.76 2.57
2412 4388 2.886523 TGTTGAGAGGTTGCCTTGAATG 59.113 45.455 0.00 0.00 31.76 2.67
2413 4389 3.228188 TGTTGAGAGGTTGCCTTGAAT 57.772 42.857 0.00 0.00 31.76 2.57
2414 4390 2.727123 TGTTGAGAGGTTGCCTTGAA 57.273 45.000 0.00 0.00 31.76 2.69
2415 4391 2.158623 ACATGTTGAGAGGTTGCCTTGA 60.159 45.455 0.00 0.00 31.76 3.02
2416 4392 2.030540 CACATGTTGAGAGGTTGCCTTG 60.031 50.000 0.00 0.00 31.76 3.61
2417 4393 2.233271 CACATGTTGAGAGGTTGCCTT 58.767 47.619 0.00 0.00 31.76 4.35
2418 4394 1.901591 CACATGTTGAGAGGTTGCCT 58.098 50.000 0.00 0.00 36.03 4.75
2419 4395 0.242017 GCACATGTTGAGAGGTTGCC 59.758 55.000 0.00 0.00 0.00 4.52
2420 4396 0.953727 TGCACATGTTGAGAGGTTGC 59.046 50.000 0.00 0.00 0.00 4.17
2421 4397 2.497138 TCTGCACATGTTGAGAGGTTG 58.503 47.619 0.00 0.00 0.00 3.77
2422 4398 2.936919 TCTGCACATGTTGAGAGGTT 57.063 45.000 0.00 0.00 0.00 3.50
2423 4399 3.771479 TCTATCTGCACATGTTGAGAGGT 59.229 43.478 0.00 0.00 0.00 3.85
2424 4400 4.397481 TCTATCTGCACATGTTGAGAGG 57.603 45.455 0.00 0.00 0.00 3.69
2425 4401 4.211584 GCATCTATCTGCACATGTTGAGAG 59.788 45.833 0.00 2.17 41.87 3.20
2426 4402 4.124970 GCATCTATCTGCACATGTTGAGA 58.875 43.478 0.00 0.15 41.87 3.27
2427 4403 3.875134 TGCATCTATCTGCACATGTTGAG 59.125 43.478 0.00 0.00 46.76 3.02
2428 4404 3.876341 TGCATCTATCTGCACATGTTGA 58.124 40.909 0.00 0.00 46.76 3.18
2437 4413 6.457934 GCATATATGTTGGTGCATCTATCTGC 60.458 42.308 14.14 0.00 42.62 4.26
2438 4414 6.596497 TGCATATATGTTGGTGCATCTATCTG 59.404 38.462 14.14 0.00 42.13 2.90
2439 4415 6.714278 TGCATATATGTTGGTGCATCTATCT 58.286 36.000 14.14 0.00 42.13 1.98
2440 4416 6.990341 TGCATATATGTTGGTGCATCTATC 57.010 37.500 14.14 0.00 42.13 2.08
2441 4417 7.576287 GCTTTGCATATATGTTGGTGCATCTAT 60.576 37.037 14.14 0.00 45.80 1.98
2442 4418 6.294120 GCTTTGCATATATGTTGGTGCATCTA 60.294 38.462 14.14 0.00 45.80 1.98
2443 4419 5.508489 GCTTTGCATATATGTTGGTGCATCT 60.508 40.000 14.14 0.00 45.80 2.90
2444 4420 4.682860 GCTTTGCATATATGTTGGTGCATC 59.317 41.667 14.14 0.00 45.80 3.91
2445 4421 4.624015 GCTTTGCATATATGTTGGTGCAT 58.376 39.130 14.14 0.00 45.80 3.96
2446 4422 3.488890 CGCTTTGCATATATGTTGGTGCA 60.489 43.478 14.14 3.53 44.97 4.57
2447 4423 3.044986 CGCTTTGCATATATGTTGGTGC 58.955 45.455 14.14 10.85 38.05 5.01
2448 4424 4.530388 CTCGCTTTGCATATATGTTGGTG 58.470 43.478 14.14 8.78 0.00 4.17
2449 4425 3.003689 GCTCGCTTTGCATATATGTTGGT 59.996 43.478 14.14 0.00 0.00 3.67
2450 4426 3.558505 GCTCGCTTTGCATATATGTTGG 58.441 45.455 14.14 4.20 0.00 3.77
2451 4427 3.251729 AGGCTCGCTTTGCATATATGTTG 59.748 43.478 14.14 3.89 0.00 3.33
2452 4428 3.251729 CAGGCTCGCTTTGCATATATGTT 59.748 43.478 14.14 0.00 0.00 2.71
2453 4429 2.810274 CAGGCTCGCTTTGCATATATGT 59.190 45.455 14.14 0.00 0.00 2.29
2454 4430 2.810274 ACAGGCTCGCTTTGCATATATG 59.190 45.455 8.45 8.45 0.00 1.78
2455 4431 3.070018 GACAGGCTCGCTTTGCATATAT 58.930 45.455 0.00 0.00 0.00 0.86
2456 4432 2.103094 AGACAGGCTCGCTTTGCATATA 59.897 45.455 0.00 0.00 0.00 0.86
2457 4433 1.134280 AGACAGGCTCGCTTTGCATAT 60.134 47.619 0.00 0.00 0.00 1.78
2458 4434 0.250234 AGACAGGCTCGCTTTGCATA 59.750 50.000 0.00 0.00 0.00 3.14
2459 4435 0.607489 AAGACAGGCTCGCTTTGCAT 60.607 50.000 0.00 0.00 0.00 3.96
2460 4436 0.819259 AAAGACAGGCTCGCTTTGCA 60.819 50.000 9.58 0.00 31.21 4.08
2461 4437 1.156736 TAAAGACAGGCTCGCTTTGC 58.843 50.000 17.01 0.00 34.12 3.68
2462 4438 3.000322 CGTATAAAGACAGGCTCGCTTTG 60.000 47.826 17.01 2.01 34.12 2.77
2463 4439 3.187700 CGTATAAAGACAGGCTCGCTTT 58.812 45.455 13.62 13.62 36.06 3.51
2464 4440 2.810650 CGTATAAAGACAGGCTCGCTT 58.189 47.619 0.00 0.00 0.00 4.68
2465 4441 1.536284 GCGTATAAAGACAGGCTCGCT 60.536 52.381 0.00 0.00 39.43 4.93
2466 4442 0.853419 GCGTATAAAGACAGGCTCGC 59.147 55.000 0.00 0.00 36.06 5.03
2467 4443 2.120232 CAGCGTATAAAGACAGGCTCG 58.880 52.381 0.00 0.00 33.86 5.03
2468 4444 2.100916 TCCAGCGTATAAAGACAGGCTC 59.899 50.000 0.00 0.00 33.86 4.70
2469 4445 2.108168 TCCAGCGTATAAAGACAGGCT 58.892 47.619 0.00 0.00 36.38 4.58
2470 4446 2.596904 TCCAGCGTATAAAGACAGGC 57.403 50.000 0.00 0.00 0.00 4.85
2471 4447 4.058817 GGAATCCAGCGTATAAAGACAGG 58.941 47.826 0.00 0.00 0.00 4.00
2472 4448 4.950050 AGGAATCCAGCGTATAAAGACAG 58.050 43.478 0.61 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.