Multiple sequence alignment - TraesCS5A01G452200

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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 TraesCS5A01G452200 chr5A 100.000 5115 0 0 1 5115 633867380 633862266 0.000000e+00 9446
1 TraesCS5A01G452200 chr5B 93.653 3986 178 36 1181 5115 636656250 636652289 0.000000e+00 5890
2 TraesCS5A01G452200 chr5B 84.253 616 46 26 205 800 636657403 636656819 2.080000e-153 553
3 TraesCS5A01G452200 chr5D 94.955 3469 107 29 731 4162 506099373 506095936 0.000000e+00 5374
4 TraesCS5A01G452200 chr5D 90.929 904 60 7 4231 5115 506095927 506095027 0.000000e+00 1195
5 TraesCS5A01G452200 chr5D 90.604 298 27 1 1163 1460 450420929 450420633 1.330000e-105 394
6 TraesCS5A01G452200 chr5D 89.933 298 30 0 1163 1460 75600909 75600612 8.030000e-103 385
7 TraesCS5A01G452200 chr5D 84.359 390 19 15 354 731 506099759 506099400 1.360000e-90 344
8 TraesCS5A01G452200 chr5D 87.156 109 14 0 1643 1751 44708023 44707915 1.930000e-24 124
9 TraesCS5A01G452200 chr4A 87.636 461 57 0 1166 1626 658722687 658722227 2.100000e-148 536
10 TraesCS5A01G452200 chr4A 88.591 298 33 1 1163 1460 254221928 254222224 1.350000e-95 361
11 TraesCS5A01G452200 chr7B 91.346 312 26 1 1181 1492 683094670 683094360 4.730000e-115 425
12 TraesCS5A01G452200 chr2D 91.275 298 25 1 1163 1460 619986411 619986115 6.170000e-109 405
13 TraesCS5A01G452200 chr2D 96.104 77 3 0 1552 1628 415154763 415154839 5.380000e-25 126
14 TraesCS5A01G452200 chr1D 91.176 272 23 1 1184 1455 2546380 2546110 8.090000e-98 368
15 TraesCS5A01G452200 chr1D 97.297 74 2 0 1555 1628 459949152 459949079 5.380000e-25 126
16 TraesCS5A01G452200 chr2B 97.403 77 2 0 1552 1628 127018320 127018396 1.160000e-26 132
17 TraesCS5A01G452200 chr6D 96.104 77 3 0 1552 1628 434975287 434975363 5.380000e-25 126
18 TraesCS5A01G452200 chr4B 97.297 74 2 0 1555 1628 626711548 626711475 5.380000e-25 126
19 TraesCS5A01G452200 chr1B 96.104 77 3 0 1552 1628 196083347 196083423 5.380000e-25 126


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 TraesCS5A01G452200 chr5A 633862266 633867380 5114 True 9446.000000 9446 100.000 1 5115 1 chr5A.!!$R1 5114
1 TraesCS5A01G452200 chr5B 636652289 636657403 5114 True 3221.500000 5890 88.953 205 5115 2 chr5B.!!$R1 4910
2 TraesCS5A01G452200 chr5D 506095027 506099759 4732 True 2304.333333 5374 90.081 354 5115 3 chr5D.!!$R4 4761

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
93 94 0.030908 CTACGGTTCATCCCTCGCTC 59.969 60.0 0.00 0.00 0.00 5.03 F
894 965 0.109342 CCTTTCCATCCATCCCTCCG 59.891 60.0 0.00 0.00 0.00 4.63 F
1822 2081 0.954452 GCCACACCCTGTTTCTCTTG 59.046 55.0 0.00 0.00 0.00 3.02 F
2513 2778 0.324285 CTGCTGCCCAGAAGACTTCT 59.676 55.0 12.12 12.12 44.64 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2014 1.539560 ATCCATCCCTCGCATCGGAG 61.540 60.000 0.00 0.0 0.00 4.63 R
2447 2712 0.033781 GCTCTGCAAAATGGTTGCCA 59.966 50.000 8.47 0.0 44.32 4.92 R
3652 3934 1.069765 CTGTAGTATGCGGGCCAGG 59.930 63.158 4.39 0.0 0.00 4.45 R
4289 4575 0.176910 GAGTCCCTACAAGCTGCCTC 59.823 60.000 0.00 0.0 0.00 4.70 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
21 22 3.764885 ATGGCAAGACTAAATCGCAAC 57.235 42.857 0.00 0.00 0.00 4.17
22 23 2.778299 TGGCAAGACTAAATCGCAACT 58.222 42.857 0.00 0.00 0.00 3.16
23 24 2.742053 TGGCAAGACTAAATCGCAACTC 59.258 45.455 0.00 0.00 0.00 3.01
24 25 2.096013 GGCAAGACTAAATCGCAACTCC 59.904 50.000 0.00 0.00 0.00 3.85
25 26 2.742053 GCAAGACTAAATCGCAACTCCA 59.258 45.455 0.00 0.00 0.00 3.86
26 27 3.188460 GCAAGACTAAATCGCAACTCCAA 59.812 43.478 0.00 0.00 0.00 3.53
27 28 4.142600 GCAAGACTAAATCGCAACTCCAAT 60.143 41.667 0.00 0.00 0.00 3.16
28 29 5.327091 CAAGACTAAATCGCAACTCCAATG 58.673 41.667 0.00 0.00 0.00 2.82
29 30 4.579869 AGACTAAATCGCAACTCCAATGT 58.420 39.130 0.00 0.00 0.00 2.71
30 31 5.003804 AGACTAAATCGCAACTCCAATGTT 58.996 37.500 0.00 0.00 0.00 2.71
31 32 5.122396 AGACTAAATCGCAACTCCAATGTTC 59.878 40.000 0.00 0.00 0.00 3.18
32 33 3.575965 AAATCGCAACTCCAATGTTCC 57.424 42.857 0.00 0.00 0.00 3.62
33 34 2.496899 ATCGCAACTCCAATGTTCCT 57.503 45.000 0.00 0.00 0.00 3.36
34 35 1.808411 TCGCAACTCCAATGTTCCTC 58.192 50.000 0.00 0.00 0.00 3.71
35 36 1.347707 TCGCAACTCCAATGTTCCTCT 59.652 47.619 0.00 0.00 0.00 3.69
36 37 2.154462 CGCAACTCCAATGTTCCTCTT 58.846 47.619 0.00 0.00 0.00 2.85
37 38 2.160417 CGCAACTCCAATGTTCCTCTTC 59.840 50.000 0.00 0.00 0.00 2.87
38 39 2.489722 GCAACTCCAATGTTCCTCTTCC 59.510 50.000 0.00 0.00 0.00 3.46
39 40 3.812167 GCAACTCCAATGTTCCTCTTCCT 60.812 47.826 0.00 0.00 0.00 3.36
40 41 3.710209 ACTCCAATGTTCCTCTTCCTG 57.290 47.619 0.00 0.00 0.00 3.86
41 42 2.290577 ACTCCAATGTTCCTCTTCCTGC 60.291 50.000 0.00 0.00 0.00 4.85
42 43 1.089920 CCAATGTTCCTCTTCCTGCG 58.910 55.000 0.00 0.00 0.00 5.18
43 44 0.449388 CAATGTTCCTCTTCCTGCGC 59.551 55.000 0.00 0.00 0.00 6.09
44 45 0.036732 AATGTTCCTCTTCCTGCGCA 59.963 50.000 10.98 10.98 0.00 6.09
45 46 0.254178 ATGTTCCTCTTCCTGCGCAT 59.746 50.000 12.24 0.00 0.00 4.73
46 47 0.391661 TGTTCCTCTTCCTGCGCATC 60.392 55.000 12.24 0.00 0.00 3.91
47 48 0.107945 GTTCCTCTTCCTGCGCATCT 60.108 55.000 12.24 0.00 0.00 2.90
48 49 0.615331 TTCCTCTTCCTGCGCATCTT 59.385 50.000 12.24 0.00 0.00 2.40
49 50 0.176680 TCCTCTTCCTGCGCATCTTC 59.823 55.000 12.24 0.00 0.00 2.87
50 51 0.813210 CCTCTTCCTGCGCATCTTCC 60.813 60.000 12.24 0.00 0.00 3.46
51 52 0.107993 CTCTTCCTGCGCATCTTCCA 60.108 55.000 12.24 0.00 0.00 3.53
52 53 0.543277 TCTTCCTGCGCATCTTCCAT 59.457 50.000 12.24 0.00 0.00 3.41
53 54 0.661552 CTTCCTGCGCATCTTCCATG 59.338 55.000 12.24 0.00 0.00 3.66
54 55 0.252761 TTCCTGCGCATCTTCCATGA 59.747 50.000 12.24 0.00 0.00 3.07
55 56 0.471191 TCCTGCGCATCTTCCATGAT 59.529 50.000 12.24 0.00 0.00 2.45
56 57 0.873054 CCTGCGCATCTTCCATGATC 59.127 55.000 12.24 0.00 0.00 2.92
57 58 0.873054 CTGCGCATCTTCCATGATCC 59.127 55.000 12.24 0.00 0.00 3.36
58 59 0.180878 TGCGCATCTTCCATGATCCA 59.819 50.000 5.66 0.00 0.00 3.41
59 60 1.311859 GCGCATCTTCCATGATCCAA 58.688 50.000 0.30 0.00 0.00 3.53
60 61 1.002033 GCGCATCTTCCATGATCCAAC 60.002 52.381 0.30 0.00 0.00 3.77
61 62 2.569059 CGCATCTTCCATGATCCAACT 58.431 47.619 0.00 0.00 0.00 3.16
62 63 2.547211 CGCATCTTCCATGATCCAACTC 59.453 50.000 0.00 0.00 0.00 3.01
63 64 2.883386 GCATCTTCCATGATCCAACTCC 59.117 50.000 0.00 0.00 0.00 3.85
64 65 3.686405 GCATCTTCCATGATCCAACTCCA 60.686 47.826 0.00 0.00 0.00 3.86
65 66 4.726583 CATCTTCCATGATCCAACTCCAT 58.273 43.478 0.00 0.00 0.00 3.41
66 67 4.868172 TCTTCCATGATCCAACTCCATT 57.132 40.909 0.00 0.00 0.00 3.16
67 68 4.529897 TCTTCCATGATCCAACTCCATTG 58.470 43.478 0.00 0.00 38.12 2.82
68 69 2.658285 TCCATGATCCAACTCCATTGC 58.342 47.619 0.00 0.00 36.93 3.56
69 70 1.684983 CCATGATCCAACTCCATTGCC 59.315 52.381 0.00 0.00 36.93 4.52
70 71 1.335810 CATGATCCAACTCCATTGCCG 59.664 52.381 0.00 0.00 36.93 5.69
71 72 1.031571 TGATCCAACTCCATTGCCGC 61.032 55.000 0.00 0.00 36.93 6.53
72 73 1.728490 GATCCAACTCCATTGCCGCC 61.728 60.000 0.00 0.00 36.93 6.13
73 74 3.451894 CCAACTCCATTGCCGCCC 61.452 66.667 0.00 0.00 36.93 6.13
74 75 3.451894 CAACTCCATTGCCGCCCC 61.452 66.667 0.00 0.00 0.00 5.80
75 76 3.661648 AACTCCATTGCCGCCCCT 61.662 61.111 0.00 0.00 0.00 4.79
76 77 2.305607 AACTCCATTGCCGCCCCTA 61.306 57.895 0.00 0.00 0.00 3.53
77 78 2.203209 CTCCATTGCCGCCCCTAC 60.203 66.667 0.00 0.00 0.00 3.18
78 79 4.169696 TCCATTGCCGCCCCTACG 62.170 66.667 0.00 0.00 0.00 3.51
86 87 2.108362 CGCCCCTACGGTTCATCC 59.892 66.667 0.00 0.00 0.00 3.51
87 88 2.509422 GCCCCTACGGTTCATCCC 59.491 66.667 0.00 0.00 0.00 3.85
88 89 2.070650 GCCCCTACGGTTCATCCCT 61.071 63.158 0.00 0.00 0.00 4.20
89 90 2.041206 GCCCCTACGGTTCATCCCTC 62.041 65.000 0.00 0.00 0.00 4.30
90 91 1.740285 CCCTACGGTTCATCCCTCG 59.260 63.158 0.00 0.00 0.00 4.63
91 92 1.067582 CCTACGGTTCATCCCTCGC 59.932 63.158 0.00 0.00 0.00 5.03
92 93 1.392710 CCTACGGTTCATCCCTCGCT 61.393 60.000 0.00 0.00 0.00 4.93
93 94 0.030908 CTACGGTTCATCCCTCGCTC 59.969 60.000 0.00 0.00 0.00 5.03
94 95 0.395311 TACGGTTCATCCCTCGCTCT 60.395 55.000 0.00 0.00 0.00 4.09
95 96 0.395311 ACGGTTCATCCCTCGCTCTA 60.395 55.000 0.00 0.00 0.00 2.43
96 97 0.962489 CGGTTCATCCCTCGCTCTAT 59.038 55.000 0.00 0.00 0.00 1.98
97 98 1.068194 CGGTTCATCCCTCGCTCTATC 60.068 57.143 0.00 0.00 0.00 2.08
98 99 1.068194 GGTTCATCCCTCGCTCTATCG 60.068 57.143 0.00 0.00 0.00 2.92
99 100 1.068194 GTTCATCCCTCGCTCTATCGG 60.068 57.143 0.00 0.00 0.00 4.18
100 101 1.214062 CATCCCTCGCTCTATCGGC 59.786 63.158 0.00 0.00 0.00 5.54
107 108 4.014065 GCTCTATCGGCGGTGTTC 57.986 61.111 7.21 0.00 0.00 3.18
108 109 1.591863 GCTCTATCGGCGGTGTTCC 60.592 63.158 7.21 0.00 0.00 3.62
109 110 1.813859 CTCTATCGGCGGTGTTCCA 59.186 57.895 7.21 0.00 0.00 3.53
110 111 0.527817 CTCTATCGGCGGTGTTCCAC 60.528 60.000 7.21 0.00 0.00 4.02
119 120 2.851045 GTGTTCCACCACCCCCAT 59.149 61.111 0.00 0.00 0.00 4.00
120 121 1.304134 GTGTTCCACCACCCCCATC 60.304 63.158 0.00 0.00 0.00 3.51
121 122 1.776293 TGTTCCACCACCCCCATCA 60.776 57.895 0.00 0.00 0.00 3.07
122 123 1.145900 TGTTCCACCACCCCCATCAT 61.146 55.000 0.00 0.00 0.00 2.45
123 124 0.395724 GTTCCACCACCCCCATCATC 60.396 60.000 0.00 0.00 0.00 2.92
124 125 1.920734 TTCCACCACCCCCATCATCG 61.921 60.000 0.00 0.00 0.00 3.84
125 126 2.374525 CCACCACCCCCATCATCGA 61.375 63.158 0.00 0.00 0.00 3.59
126 127 1.153168 CACCACCCCCATCATCGAC 60.153 63.158 0.00 0.00 0.00 4.20
127 128 2.108976 CCACCCCCATCATCGACG 59.891 66.667 0.00 0.00 0.00 5.12
128 129 2.431454 CCACCCCCATCATCGACGA 61.431 63.158 0.00 0.00 0.00 4.20
129 130 1.227263 CACCCCCATCATCGACGAC 60.227 63.158 0.00 0.00 0.00 4.34
130 131 1.381327 ACCCCCATCATCGACGACT 60.381 57.895 0.00 0.00 0.00 4.18
131 132 1.364171 CCCCCATCATCGACGACTC 59.636 63.158 0.00 0.00 0.00 3.36
132 133 1.391933 CCCCCATCATCGACGACTCA 61.392 60.000 0.00 0.00 0.00 3.41
133 134 0.676184 CCCCATCATCGACGACTCAT 59.324 55.000 0.00 0.00 0.00 2.90
134 135 1.069204 CCCCATCATCGACGACTCATT 59.931 52.381 0.00 0.00 0.00 2.57
135 136 2.483714 CCCCATCATCGACGACTCATTT 60.484 50.000 0.00 0.00 0.00 2.32
136 137 2.797156 CCCATCATCGACGACTCATTTC 59.203 50.000 0.00 0.00 0.00 2.17
137 138 2.797156 CCATCATCGACGACTCATTTCC 59.203 50.000 0.00 0.00 0.00 3.13
138 139 3.491619 CCATCATCGACGACTCATTTCCT 60.492 47.826 0.00 0.00 0.00 3.36
139 140 3.868757 TCATCGACGACTCATTTCCTT 57.131 42.857 0.00 0.00 0.00 3.36
140 141 3.770666 TCATCGACGACTCATTTCCTTC 58.229 45.455 0.00 0.00 0.00 3.46
141 142 2.649331 TCGACGACTCATTTCCTTCC 57.351 50.000 0.00 0.00 0.00 3.46
142 143 2.168496 TCGACGACTCATTTCCTTCCT 58.832 47.619 0.00 0.00 0.00 3.36
143 144 2.163815 TCGACGACTCATTTCCTTCCTC 59.836 50.000 0.00 0.00 0.00 3.71
144 145 2.735762 CGACGACTCATTTCCTTCCTCC 60.736 54.545 0.00 0.00 0.00 4.30
145 146 2.233922 GACGACTCATTTCCTTCCTCCA 59.766 50.000 0.00 0.00 0.00 3.86
146 147 2.234908 ACGACTCATTTCCTTCCTCCAG 59.765 50.000 0.00 0.00 0.00 3.86
147 148 2.234908 CGACTCATTTCCTTCCTCCAGT 59.765 50.000 0.00 0.00 0.00 4.00
148 149 3.447586 CGACTCATTTCCTTCCTCCAGTA 59.552 47.826 0.00 0.00 0.00 2.74
149 150 4.081642 CGACTCATTTCCTTCCTCCAGTAA 60.082 45.833 0.00 0.00 0.00 2.24
150 151 5.167303 ACTCATTTCCTTCCTCCAGTAAC 57.833 43.478 0.00 0.00 0.00 2.50
151 152 4.184629 CTCATTTCCTTCCTCCAGTAACG 58.815 47.826 0.00 0.00 0.00 3.18
152 153 2.467566 TTTCCTTCCTCCAGTAACGC 57.532 50.000 0.00 0.00 0.00 4.84
153 154 0.611714 TTCCTTCCTCCAGTAACGCC 59.388 55.000 0.00 0.00 0.00 5.68
154 155 0.252103 TCCTTCCTCCAGTAACGCCT 60.252 55.000 0.00 0.00 0.00 5.52
155 156 0.175989 CCTTCCTCCAGTAACGCCTC 59.824 60.000 0.00 0.00 0.00 4.70
156 157 1.187087 CTTCCTCCAGTAACGCCTCT 58.813 55.000 0.00 0.00 0.00 3.69
157 158 1.550976 CTTCCTCCAGTAACGCCTCTT 59.449 52.381 0.00 0.00 0.00 2.85
158 159 1.183549 TCCTCCAGTAACGCCTCTTC 58.816 55.000 0.00 0.00 0.00 2.87
159 160 0.175989 CCTCCAGTAACGCCTCTTCC 59.824 60.000 0.00 0.00 0.00 3.46
160 161 0.179134 CTCCAGTAACGCCTCTTCCG 60.179 60.000 0.00 0.00 0.00 4.30
161 162 1.810030 CCAGTAACGCCTCTTCCGC 60.810 63.158 0.00 0.00 0.00 5.54
162 163 1.810030 CAGTAACGCCTCTTCCGCC 60.810 63.158 0.00 0.00 0.00 6.13
163 164 2.510918 GTAACGCCTCTTCCGCCC 60.511 66.667 0.00 0.00 0.00 6.13
164 165 4.137872 TAACGCCTCTTCCGCCCG 62.138 66.667 0.00 0.00 0.00 6.13
167 168 4.570663 CGCCTCTTCCGCCCGTAG 62.571 72.222 0.00 0.00 0.00 3.51
179 180 2.403987 CCGTAGGCAGTCTCGACG 59.596 66.667 0.00 0.00 46.14 5.12
180 181 2.403987 CGTAGGCAGTCTCGACGG 59.596 66.667 0.00 0.00 36.20 4.79
186 187 4.498520 CAGTCTCGACGGCGCCAT 62.499 66.667 28.98 12.81 37.46 4.40
187 188 4.194720 AGTCTCGACGGCGCCATC 62.195 66.667 28.98 21.73 37.46 3.51
188 189 4.194720 GTCTCGACGGCGCCATCT 62.195 66.667 28.98 7.76 37.46 2.90
189 190 3.449227 TCTCGACGGCGCCATCTT 61.449 61.111 28.98 6.94 37.46 2.40
190 191 2.956964 CTCGACGGCGCCATCTTC 60.957 66.667 28.98 15.31 37.46 2.87
191 192 4.508128 TCGACGGCGCCATCTTCC 62.508 66.667 28.98 6.94 37.46 3.46
193 194 4.467084 GACGGCGCCATCTTCCCA 62.467 66.667 28.98 0.00 0.00 4.37
194 195 3.969250 GACGGCGCCATCTTCCCAA 62.969 63.158 28.98 0.00 0.00 4.12
195 196 3.204827 CGGCGCCATCTTCCCAAG 61.205 66.667 28.98 0.98 0.00 3.61
196 197 2.272146 GGCGCCATCTTCCCAAGA 59.728 61.111 24.80 0.00 42.69 3.02
197 198 2.115291 GGCGCCATCTTCCCAAGAC 61.115 63.158 24.80 0.00 41.01 3.01
198 199 1.078143 GCGCCATCTTCCCAAGACT 60.078 57.895 0.00 0.00 41.01 3.24
199 200 1.092345 GCGCCATCTTCCCAAGACTC 61.092 60.000 0.00 0.00 41.01 3.36
200 201 0.539051 CGCCATCTTCCCAAGACTCT 59.461 55.000 0.00 0.00 41.01 3.24
201 202 1.472376 CGCCATCTTCCCAAGACTCTC 60.472 57.143 0.00 0.00 41.01 3.20
202 203 1.134250 GCCATCTTCCCAAGACTCTCC 60.134 57.143 0.00 0.00 41.01 3.71
203 204 2.476199 CCATCTTCCCAAGACTCTCCT 58.524 52.381 0.00 0.00 41.01 3.69
210 211 1.571457 CCCAAGACTCTCCTCCTCCTA 59.429 57.143 0.00 0.00 0.00 2.94
212 213 2.424234 CCAAGACTCTCCTCCTCCTAGG 60.424 59.091 0.82 0.82 38.06 3.02
230 231 0.748450 GGACCACATTCATGCCATGG 59.252 55.000 7.63 7.63 36.46 3.66
258 259 1.079127 CGCCCGTCAAGACCAATCT 60.079 57.895 0.00 0.00 36.42 2.40
260 261 1.026718 GCCCGTCAAGACCAATCTGG 61.027 60.000 0.00 0.00 45.02 3.86
269 270 1.978580 AGACCAATCTGGGAACGTTCT 59.021 47.619 26.32 4.67 43.37 3.01
272 273 2.028020 ACCAATCTGGGAACGTTCTCTC 60.028 50.000 27.48 17.10 43.37 3.20
285 286 3.567164 ACGTTCTCTCGTTAGGTTTCTCA 59.433 43.478 0.00 0.00 41.37 3.27
286 287 4.037208 ACGTTCTCTCGTTAGGTTTCTCAA 59.963 41.667 0.00 0.00 41.37 3.02
287 288 4.980434 CGTTCTCTCGTTAGGTTTCTCAAA 59.020 41.667 0.00 0.00 0.00 2.69
326 335 1.883084 GACGGGGCGCACATAGAAG 60.883 63.158 13.89 0.00 0.00 2.85
333 342 3.941836 GCACATAGAAGCGGCCGC 61.942 66.667 42.34 42.34 42.33 6.53
355 364 3.050275 GCACGCCCCAGAGTGAAC 61.050 66.667 0.94 0.00 45.73 3.18
356 365 2.358737 CACGCCCCAGAGTGAACC 60.359 66.667 0.00 0.00 45.73 3.62
358 367 2.147387 ACGCCCCAGAGTGAACCTT 61.147 57.895 0.00 0.00 0.00 3.50
359 368 0.834687 ACGCCCCAGAGTGAACCTTA 60.835 55.000 0.00 0.00 0.00 2.69
405 422 9.981114 GGAATCATTCCGTTTGGATTTATTATT 57.019 29.630 0.00 0.00 45.91 1.40
410 427 9.594038 CATTCCGTTTGGATTTATTATTACTCG 57.406 33.333 0.00 0.00 45.91 4.18
411 428 8.721019 TTCCGTTTGGATTTATTATTACTCGT 57.279 30.769 0.00 0.00 45.91 4.18
545 573 2.432285 TTTACCCCACGCGTACGC 60.432 61.111 29.83 29.83 45.53 4.42
722 766 2.309764 ATTAGGCGCGCTGCTTTTCG 62.310 55.000 32.29 0.00 45.43 3.46
800 870 2.860735 GGAAACCGTCGATCATCTCTTG 59.139 50.000 0.00 0.00 0.00 3.02
801 871 3.512680 GAAACCGTCGATCATCTCTTGT 58.487 45.455 0.00 0.00 0.00 3.16
802 872 2.853731 ACCGTCGATCATCTCTTGTC 57.146 50.000 0.00 0.00 0.00 3.18
803 873 2.370349 ACCGTCGATCATCTCTTGTCT 58.630 47.619 0.00 0.00 0.00 3.41
809 879 5.034152 GTCGATCATCTCTTGTCTCTTCAC 58.966 45.833 0.00 0.00 0.00 3.18
814 884 5.536260 TCATCTCTTGTCTCTTCACAACAG 58.464 41.667 0.00 0.00 32.70 3.16
818 888 0.179086 TGTCTCTTCACAACAGCGCA 60.179 50.000 11.47 0.00 0.00 6.09
833 903 4.735132 GCAGCGGGCAGACACGTA 62.735 66.667 0.00 0.00 43.97 3.57
834 904 2.809601 CAGCGGGCAGACACGTAC 60.810 66.667 0.00 0.00 0.00 3.67
835 905 2.989824 AGCGGGCAGACACGTACT 60.990 61.111 0.00 0.00 0.00 2.73
879 949 4.513777 GGCTTTCCCGTTCCCTTT 57.486 55.556 0.00 0.00 0.00 3.11
882 952 0.538746 GCTTTCCCGTTCCCTTTCCA 60.539 55.000 0.00 0.00 0.00 3.53
890 961 1.750682 CGTTCCCTTTCCATCCATCCC 60.751 57.143 0.00 0.00 0.00 3.85
894 965 0.109342 CCTTTCCATCCATCCCTCCG 59.891 60.000 0.00 0.00 0.00 4.63
1822 2081 0.954452 GCCACACCCTGTTTCTCTTG 59.046 55.000 0.00 0.00 0.00 3.02
1831 2090 3.447229 CCCTGTTTCTCTTGGTTTGTTGT 59.553 43.478 0.00 0.00 0.00 3.32
1834 2094 4.241681 TGTTTCTCTTGGTTTGTTGTTGC 58.758 39.130 0.00 0.00 0.00 4.17
1853 2113 7.182817 TGTTGCCTGATCAAATACTACTACT 57.817 36.000 0.00 0.00 0.00 2.57
1854 2114 8.301252 TGTTGCCTGATCAAATACTACTACTA 57.699 34.615 0.00 0.00 0.00 1.82
1855 2115 8.195436 TGTTGCCTGATCAAATACTACTACTAC 58.805 37.037 0.00 0.00 0.00 2.73
1881 2141 9.509855 CTACTGTTTAGCTACTCTGTTATTGAG 57.490 37.037 0.00 0.00 37.55 3.02
1898 2158 5.796350 ATTGAGTATTTTGGCTGTACGAC 57.204 39.130 0.00 0.00 0.00 4.34
1899 2159 3.247442 TGAGTATTTTGGCTGTACGACG 58.753 45.455 0.00 0.00 0.00 5.12
1900 2160 3.057386 TGAGTATTTTGGCTGTACGACGA 60.057 43.478 0.00 0.00 0.00 4.20
1901 2161 4.110482 GAGTATTTTGGCTGTACGACGAT 58.890 43.478 0.00 0.00 0.00 3.73
1902 2162 5.163632 TGAGTATTTTGGCTGTACGACGATA 60.164 40.000 0.00 0.00 0.00 2.92
1903 2163 5.279384 AGTATTTTGGCTGTACGACGATAG 58.721 41.667 0.00 0.00 46.19 2.08
1984 2249 2.162608 CGAAGATCAGTCCAACGAGTCT 59.837 50.000 0.00 0.00 0.00 3.24
2372 2637 1.444119 TTGCACCGCAGAAACACCTC 61.444 55.000 0.00 0.00 40.61 3.85
2447 2712 1.145598 CATCGGCATCCTGTCAGCT 59.854 57.895 0.00 0.00 0.00 4.24
2513 2778 0.324285 CTGCTGCCCAGAAGACTTCT 59.676 55.000 12.12 12.12 44.64 2.85
2556 2821 4.933330 TGTTGCGCTGGTAATTTTTGTTA 58.067 34.783 9.73 0.00 0.00 2.41
2683 2949 8.375506 TCTAGAGTTGAAAAAGGAAGCAGAATA 58.624 33.333 0.00 0.00 0.00 1.75
2846 3112 1.799933 TGCCACCAATGAACCCTTTT 58.200 45.000 0.00 0.00 0.00 2.27
2860 3126 1.443802 CCTTTTTCTCTCAGGTCCGC 58.556 55.000 0.00 0.00 0.00 5.54
3054 3320 5.757850 AACTTGAAGAGTTGTGATTGTCC 57.242 39.130 0.00 0.00 46.66 4.02
3128 3402 8.947115 GTAGCAAACAGTCCAGAAGTTATTTAT 58.053 33.333 0.00 0.00 0.00 1.40
3265 3539 1.881973 TGCTTTGTTGCTTGCTAGAGG 59.118 47.619 0.00 0.00 0.00 3.69
3466 3740 1.691976 ACCCCTTTAACCAAAAGCAGC 59.308 47.619 0.00 0.00 42.85 5.25
3467 3741 1.691434 CCCCTTTAACCAAAAGCAGCA 59.309 47.619 0.00 0.00 42.85 4.41
3470 3744 4.162131 CCCCTTTAACCAAAAGCAGCATAT 59.838 41.667 0.00 0.00 42.85 1.78
3481 3755 1.168407 GCAGCATATGGTGTCCGCAT 61.168 55.000 29.91 0.00 44.70 4.73
3652 3934 7.588497 AATTAAGGGTAAGATCCAAATGCTC 57.412 36.000 0.00 0.00 0.00 4.26
3664 3946 2.283143 AAATGCTCCTGGCCCGCATA 62.283 55.000 16.12 0.00 43.02 3.14
3949 4235 2.059786 CATGGGAATGTGGGTGGGC 61.060 63.158 0.00 0.00 0.00 5.36
3959 4245 2.519780 GGGTGGGCCGTTTCAACA 60.520 61.111 0.00 0.00 34.97 3.33
4006 4292 3.627577 ACAGCGTCAAGTTCTGTCAATTT 59.372 39.130 0.00 0.00 36.42 1.82
4048 4334 1.355210 CGCGCATTACCAATCACCC 59.645 57.895 8.75 0.00 0.00 4.61
4155 4441 1.412343 CCTGACCCCTTTTTGGTGTTG 59.588 52.381 0.00 0.00 35.85 3.33
4158 4444 2.312390 GACCCCTTTTTGGTGTTGCTA 58.688 47.619 0.00 0.00 35.85 3.49
4183 4469 2.052468 TCCATATCTGCTGCTGATGGT 58.948 47.619 26.15 14.95 38.56 3.55
4195 4481 3.917760 GATGGTCCCGAGCCCGAG 61.918 72.222 0.00 0.00 38.22 4.63
4205 4491 0.249238 CGAGCCCGAGATTGAAGGAG 60.249 60.000 0.00 0.00 38.22 3.69
4206 4492 0.827368 GAGCCCGAGATTGAAGGAGT 59.173 55.000 0.00 0.00 0.00 3.85
4207 4493 2.032620 GAGCCCGAGATTGAAGGAGTA 58.967 52.381 0.00 0.00 0.00 2.59
4208 4494 1.757699 AGCCCGAGATTGAAGGAGTAC 59.242 52.381 0.00 0.00 0.00 2.73
4212 4498 4.833390 CCCGAGATTGAAGGAGTACTTTT 58.167 43.478 0.00 0.00 40.21 2.27
4289 4575 1.641577 GACCGAGGGAATGAACGAAG 58.358 55.000 0.00 0.00 0.00 3.79
4375 4665 5.469421 AGAATTTCTGACTGCTCAAGAACTG 59.531 40.000 0.00 0.00 0.00 3.16
4377 4667 0.788995 CTGACTGCTCAAGAACTGCG 59.211 55.000 0.00 0.00 0.00 5.18
4395 4685 3.348119 TGCGGCTGTAAATGTTAATGGA 58.652 40.909 0.00 0.00 0.00 3.41
4541 4834 2.821378 TCAGTCATTGTCTTTGCCATGG 59.179 45.455 7.63 7.63 0.00 3.66
4575 4872 1.595311 TGGGCCTGTCATTGTAGGAT 58.405 50.000 4.53 0.00 36.11 3.24
4608 4905 3.356290 TGTGCTGCAGTATCTGTCTCTA 58.644 45.455 16.64 0.00 33.43 2.43
4626 4923 3.028130 TCTACCGATGAACATGGCACTA 58.972 45.455 0.00 0.00 0.00 2.74
4636 4933 5.069318 TGAACATGGCACTATTTTCTGTCA 58.931 37.500 0.00 0.00 0.00 3.58
4733 5030 2.540101 CGCCGGATCTAAATTGAGTGAC 59.460 50.000 5.05 0.00 0.00 3.67
4760 5057 6.367695 CAGATCATTTTTACTGTACACGACCA 59.632 38.462 0.00 0.00 0.00 4.02
4764 5061 5.721876 TTTTTACTGTACACGACCAGTTG 57.278 39.130 0.00 0.00 41.85 3.16
4785 5082 0.034616 ACACTGCAACAGCTCTCCTC 59.965 55.000 0.00 0.00 34.37 3.71
4792 5089 0.453793 AACAGCTCTCCTCGTCATCG 59.546 55.000 0.00 0.00 38.55 3.84
4798 5095 1.331138 CTCTCCTCGTCATCGTGTACC 59.669 57.143 0.00 0.00 38.33 3.34
4799 5096 1.092348 CTCCTCGTCATCGTGTACCA 58.908 55.000 0.00 0.00 38.33 3.25
4800 5097 1.676529 CTCCTCGTCATCGTGTACCAT 59.323 52.381 0.00 0.00 38.33 3.55
4801 5098 1.404035 TCCTCGTCATCGTGTACCATG 59.596 52.381 0.00 0.00 38.33 3.66
4845 5145 3.805971 GCATGCCCTTATCTGAAATTTGC 59.194 43.478 6.36 0.00 0.00 3.68
4852 5152 4.260375 CCTTATCTGAAATTTGCCGACTCG 60.260 45.833 0.00 0.00 0.00 4.18
4907 5231 3.099905 AGCTCATACAGGTTAGCTGACA 58.900 45.455 18.76 5.74 43.46 3.58
4914 5238 2.099921 ACAGGTTAGCTGACATAGAGCG 59.900 50.000 18.76 0.00 41.61 5.03
4959 5285 0.304705 GTGCCCGATCGCAACAATAG 59.695 55.000 10.32 0.00 41.30 1.73
4961 5287 1.014352 GCCCGATCGCAACAATAGTT 58.986 50.000 10.32 0.00 38.88 2.24
5045 5371 1.078143 GAGGCCGCTCCAATTGAGT 60.078 57.895 7.12 0.00 43.48 3.41
5060 5386 3.616956 TTGAGTCTACAAGCCTCCATG 57.383 47.619 0.00 0.00 0.00 3.66
5066 5392 2.375174 TCTACAAGCCTCCATGTTTGGT 59.625 45.455 0.00 0.00 44.06 3.67
5080 5406 0.696501 TTTGGTAGTTGGGGAGAGGC 59.303 55.000 0.00 0.00 0.00 4.70
5091 5417 1.435256 GGGAGAGGCTATTTAGGGCA 58.565 55.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.758554 AGTTGCGATTTAGTCTTGCCATT 59.241 39.130 0.00 0.00 0.00 3.16
1 2 3.347216 AGTTGCGATTTAGTCTTGCCAT 58.653 40.909 0.00 0.00 0.00 4.40
2 3 2.742053 GAGTTGCGATTTAGTCTTGCCA 59.258 45.455 0.00 0.00 0.00 4.92
3 4 2.096013 GGAGTTGCGATTTAGTCTTGCC 59.904 50.000 0.00 0.00 0.00 4.52
4 5 2.742053 TGGAGTTGCGATTTAGTCTTGC 59.258 45.455 0.00 0.00 0.00 4.01
5 6 5.106555 ACATTGGAGTTGCGATTTAGTCTTG 60.107 40.000 0.00 0.00 0.00 3.02
6 7 5.003804 ACATTGGAGTTGCGATTTAGTCTT 58.996 37.500 0.00 0.00 0.00 3.01
7 8 4.579869 ACATTGGAGTTGCGATTTAGTCT 58.420 39.130 0.00 0.00 0.00 3.24
8 9 4.946784 ACATTGGAGTTGCGATTTAGTC 57.053 40.909 0.00 0.00 0.00 2.59
9 10 4.156008 GGAACATTGGAGTTGCGATTTAGT 59.844 41.667 0.00 0.00 30.30 2.24
10 11 4.396166 AGGAACATTGGAGTTGCGATTTAG 59.604 41.667 0.00 0.00 43.54 1.85
11 12 4.331968 AGGAACATTGGAGTTGCGATTTA 58.668 39.130 0.00 0.00 43.54 1.40
12 13 3.157087 AGGAACATTGGAGTTGCGATTT 58.843 40.909 0.00 0.00 43.54 2.17
13 14 2.749621 GAGGAACATTGGAGTTGCGATT 59.250 45.455 0.00 0.00 43.54 3.34
14 15 2.026822 AGAGGAACATTGGAGTTGCGAT 60.027 45.455 0.00 0.00 43.54 4.58
15 16 1.347707 AGAGGAACATTGGAGTTGCGA 59.652 47.619 0.00 0.00 43.54 5.10
16 17 1.813513 AGAGGAACATTGGAGTTGCG 58.186 50.000 0.00 0.00 43.54 4.85
17 18 2.489722 GGAAGAGGAACATTGGAGTTGC 59.510 50.000 0.00 0.00 39.75 4.17
18 19 3.755378 CAGGAAGAGGAACATTGGAGTTG 59.245 47.826 0.00 0.00 0.00 3.16
19 20 3.812167 GCAGGAAGAGGAACATTGGAGTT 60.812 47.826 0.00 0.00 0.00 3.01
20 21 2.290577 GCAGGAAGAGGAACATTGGAGT 60.291 50.000 0.00 0.00 0.00 3.85
21 22 2.363683 GCAGGAAGAGGAACATTGGAG 58.636 52.381 0.00 0.00 0.00 3.86
22 23 1.339055 CGCAGGAAGAGGAACATTGGA 60.339 52.381 0.00 0.00 0.00 3.53
23 24 1.089920 CGCAGGAAGAGGAACATTGG 58.910 55.000 0.00 0.00 0.00 3.16
24 25 0.449388 GCGCAGGAAGAGGAACATTG 59.551 55.000 0.30 0.00 0.00 2.82
25 26 0.036732 TGCGCAGGAAGAGGAACATT 59.963 50.000 5.66 0.00 0.00 2.71
26 27 0.254178 ATGCGCAGGAAGAGGAACAT 59.746 50.000 18.32 0.00 0.00 2.71
27 28 0.391661 GATGCGCAGGAAGAGGAACA 60.392 55.000 18.32 0.00 0.00 3.18
28 29 0.107945 AGATGCGCAGGAAGAGGAAC 60.108 55.000 18.32 0.00 0.00 3.62
29 30 0.615331 AAGATGCGCAGGAAGAGGAA 59.385 50.000 18.32 0.00 0.00 3.36
30 31 0.176680 GAAGATGCGCAGGAAGAGGA 59.823 55.000 18.32 0.00 0.00 3.71
31 32 0.813210 GGAAGATGCGCAGGAAGAGG 60.813 60.000 18.32 0.00 0.00 3.69
32 33 0.107993 TGGAAGATGCGCAGGAAGAG 60.108 55.000 18.32 0.00 0.00 2.85
33 34 0.543277 ATGGAAGATGCGCAGGAAGA 59.457 50.000 18.32 0.00 0.00 2.87
34 35 0.661552 CATGGAAGATGCGCAGGAAG 59.338 55.000 18.32 0.00 0.00 3.46
35 36 0.252761 TCATGGAAGATGCGCAGGAA 59.747 50.000 18.32 0.00 0.00 3.36
36 37 0.471191 ATCATGGAAGATGCGCAGGA 59.529 50.000 18.32 0.00 0.00 3.86
37 38 0.873054 GATCATGGAAGATGCGCAGG 59.127 55.000 18.32 0.00 0.00 4.85
38 39 0.873054 GGATCATGGAAGATGCGCAG 59.127 55.000 18.32 0.00 0.00 5.18
39 40 0.180878 TGGATCATGGAAGATGCGCA 59.819 50.000 14.96 14.96 38.98 6.09
40 41 1.002033 GTTGGATCATGGAAGATGCGC 60.002 52.381 0.00 0.00 38.98 6.09
41 42 2.547211 GAGTTGGATCATGGAAGATGCG 59.453 50.000 0.00 0.00 38.98 4.73
42 43 2.883386 GGAGTTGGATCATGGAAGATGC 59.117 50.000 0.00 0.00 36.94 3.91
43 44 4.160642 TGGAGTTGGATCATGGAAGATG 57.839 45.455 0.00 0.00 0.00 2.90
44 45 5.138276 CAATGGAGTTGGATCATGGAAGAT 58.862 41.667 0.00 0.00 34.06 2.40
45 46 4.529897 CAATGGAGTTGGATCATGGAAGA 58.470 43.478 0.00 0.00 34.06 2.87
46 47 3.067742 GCAATGGAGTTGGATCATGGAAG 59.932 47.826 0.00 0.00 38.29 3.46
47 48 3.025978 GCAATGGAGTTGGATCATGGAA 58.974 45.455 0.00 0.00 38.29 3.53
48 49 2.658285 GCAATGGAGTTGGATCATGGA 58.342 47.619 0.00 0.00 38.29 3.41
49 50 1.684983 GGCAATGGAGTTGGATCATGG 59.315 52.381 0.00 0.00 38.29 3.66
50 51 1.335810 CGGCAATGGAGTTGGATCATG 59.664 52.381 0.00 0.00 38.29 3.07
51 52 1.683943 CGGCAATGGAGTTGGATCAT 58.316 50.000 0.00 0.00 38.29 2.45
52 53 1.031571 GCGGCAATGGAGTTGGATCA 61.032 55.000 0.00 0.00 38.29 2.92
53 54 1.728490 GGCGGCAATGGAGTTGGATC 61.728 60.000 3.07 0.00 38.29 3.36
54 55 1.754234 GGCGGCAATGGAGTTGGAT 60.754 57.895 3.07 0.00 38.29 3.41
55 56 2.361104 GGCGGCAATGGAGTTGGA 60.361 61.111 3.07 0.00 38.29 3.53
56 57 3.451894 GGGCGGCAATGGAGTTGG 61.452 66.667 12.47 0.00 38.29 3.77
57 58 2.550699 TAGGGGCGGCAATGGAGTTG 62.551 60.000 12.47 0.00 40.90 3.16
58 59 2.305607 TAGGGGCGGCAATGGAGTT 61.306 57.895 12.47 0.00 0.00 3.01
59 60 2.690881 TAGGGGCGGCAATGGAGT 60.691 61.111 12.47 0.00 0.00 3.85
60 61 2.203209 GTAGGGGCGGCAATGGAG 60.203 66.667 12.47 0.00 0.00 3.86
61 62 4.169696 CGTAGGGGCGGCAATGGA 62.170 66.667 12.47 0.00 0.00 3.41
74 75 0.030908 GAGCGAGGGATGAACCGTAG 59.969 60.000 0.00 0.00 40.11 3.51
75 76 0.395311 AGAGCGAGGGATGAACCGTA 60.395 55.000 0.00 0.00 40.11 4.02
76 77 0.395311 TAGAGCGAGGGATGAACCGT 60.395 55.000 0.00 0.00 40.11 4.83
77 78 0.962489 ATAGAGCGAGGGATGAACCG 59.038 55.000 0.00 0.00 40.11 4.44
78 79 1.068194 CGATAGAGCGAGGGATGAACC 60.068 57.143 0.00 0.00 39.76 3.62
79 80 1.068194 CCGATAGAGCGAGGGATGAAC 60.068 57.143 0.00 0.00 39.76 3.18
80 81 1.248486 CCGATAGAGCGAGGGATGAA 58.752 55.000 0.00 0.00 39.76 2.57
81 82 1.244697 GCCGATAGAGCGAGGGATGA 61.245 60.000 0.00 0.00 39.76 2.92
82 83 1.214062 GCCGATAGAGCGAGGGATG 59.786 63.158 0.00 0.00 39.76 3.51
83 84 3.688086 GCCGATAGAGCGAGGGAT 58.312 61.111 0.00 0.00 39.76 3.85
90 91 1.591863 GGAACACCGCCGATAGAGC 60.592 63.158 0.00 0.00 39.76 4.09
91 92 1.813859 TGGAACACCGCCGATAGAG 59.186 57.895 0.00 0.00 39.76 2.43
92 93 4.021559 TGGAACACCGCCGATAGA 57.978 55.556 0.00 0.00 39.76 1.98
103 104 1.145900 ATGATGGGGGTGGTGGAACA 61.146 55.000 0.00 0.00 39.98 3.18
104 105 0.395724 GATGATGGGGGTGGTGGAAC 60.396 60.000 0.00 0.00 0.00 3.62
105 106 1.920734 CGATGATGGGGGTGGTGGAA 61.921 60.000 0.00 0.00 0.00 3.53
106 107 2.374525 CGATGATGGGGGTGGTGGA 61.375 63.158 0.00 0.00 0.00 4.02
107 108 2.192979 CGATGATGGGGGTGGTGG 59.807 66.667 0.00 0.00 0.00 4.61
108 109 1.153168 GTCGATGATGGGGGTGGTG 60.153 63.158 0.00 0.00 0.00 4.17
109 110 2.731571 CGTCGATGATGGGGGTGGT 61.732 63.158 0.00 0.00 0.00 4.16
110 111 2.108976 CGTCGATGATGGGGGTGG 59.891 66.667 0.00 0.00 0.00 4.61
111 112 1.227263 GTCGTCGATGATGGGGGTG 60.227 63.158 11.16 0.00 0.00 4.61
112 113 1.381327 AGTCGTCGATGATGGGGGT 60.381 57.895 11.16 0.00 0.00 4.95
113 114 1.364171 GAGTCGTCGATGATGGGGG 59.636 63.158 11.16 0.00 0.00 5.40
114 115 0.676184 ATGAGTCGTCGATGATGGGG 59.324 55.000 11.16 0.00 0.00 4.96
115 116 2.515926 AATGAGTCGTCGATGATGGG 57.484 50.000 11.16 0.00 0.00 4.00
116 117 2.797156 GGAAATGAGTCGTCGATGATGG 59.203 50.000 11.16 0.00 0.00 3.51
117 118 3.711086 AGGAAATGAGTCGTCGATGATG 58.289 45.455 11.16 0.00 0.00 3.07
118 119 4.363999 GAAGGAAATGAGTCGTCGATGAT 58.636 43.478 11.16 0.00 0.00 2.45
119 120 3.428999 GGAAGGAAATGAGTCGTCGATGA 60.429 47.826 2.39 2.39 0.00 2.92
120 121 2.860735 GGAAGGAAATGAGTCGTCGATG 59.139 50.000 0.00 0.00 0.00 3.84
121 122 2.761208 AGGAAGGAAATGAGTCGTCGAT 59.239 45.455 0.00 0.00 0.00 3.59
122 123 2.163815 GAGGAAGGAAATGAGTCGTCGA 59.836 50.000 0.00 0.00 0.00 4.20
123 124 2.531206 GAGGAAGGAAATGAGTCGTCG 58.469 52.381 0.00 0.00 0.00 5.12
124 125 2.233922 TGGAGGAAGGAAATGAGTCGTC 59.766 50.000 0.00 0.00 0.00 4.20
125 126 2.234908 CTGGAGGAAGGAAATGAGTCGT 59.765 50.000 0.00 0.00 0.00 4.34
126 127 2.234908 ACTGGAGGAAGGAAATGAGTCG 59.765 50.000 0.00 0.00 0.00 4.18
127 128 3.990959 ACTGGAGGAAGGAAATGAGTC 57.009 47.619 0.00 0.00 0.00 3.36
128 129 4.322801 CGTTACTGGAGGAAGGAAATGAGT 60.323 45.833 0.00 0.00 0.00 3.41
129 130 4.184629 CGTTACTGGAGGAAGGAAATGAG 58.815 47.826 0.00 0.00 0.00 2.90
130 131 3.618997 GCGTTACTGGAGGAAGGAAATGA 60.619 47.826 0.00 0.00 0.00 2.57
131 132 2.678336 GCGTTACTGGAGGAAGGAAATG 59.322 50.000 0.00 0.00 0.00 2.32
132 133 2.355818 GGCGTTACTGGAGGAAGGAAAT 60.356 50.000 0.00 0.00 0.00 2.17
133 134 1.002773 GGCGTTACTGGAGGAAGGAAA 59.997 52.381 0.00 0.00 0.00 3.13
134 135 0.611714 GGCGTTACTGGAGGAAGGAA 59.388 55.000 0.00 0.00 0.00 3.36
135 136 0.252103 AGGCGTTACTGGAGGAAGGA 60.252 55.000 0.00 0.00 0.00 3.36
136 137 0.175989 GAGGCGTTACTGGAGGAAGG 59.824 60.000 0.00 0.00 0.00 3.46
137 138 1.187087 AGAGGCGTTACTGGAGGAAG 58.813 55.000 0.00 0.00 0.00 3.46
138 139 1.549170 GAAGAGGCGTTACTGGAGGAA 59.451 52.381 0.00 0.00 0.00 3.36
139 140 1.183549 GAAGAGGCGTTACTGGAGGA 58.816 55.000 0.00 0.00 0.00 3.71
140 141 0.175989 GGAAGAGGCGTTACTGGAGG 59.824 60.000 0.00 0.00 0.00 4.30
141 142 0.179134 CGGAAGAGGCGTTACTGGAG 60.179 60.000 0.00 0.00 0.00 3.86
142 143 1.888018 CGGAAGAGGCGTTACTGGA 59.112 57.895 0.00 0.00 0.00 3.86
143 144 1.810030 GCGGAAGAGGCGTTACTGG 60.810 63.158 0.00 0.00 0.00 4.00
144 145 1.810030 GGCGGAAGAGGCGTTACTG 60.810 63.158 0.00 0.00 0.00 2.74
145 146 2.577593 GGCGGAAGAGGCGTTACT 59.422 61.111 0.00 0.00 0.00 2.24
146 147 2.510918 GGGCGGAAGAGGCGTTAC 60.511 66.667 0.00 0.00 37.59 2.50
147 148 4.137872 CGGGCGGAAGAGGCGTTA 62.138 66.667 0.00 0.00 37.59 3.18
150 151 4.570663 CTACGGGCGGAAGAGGCG 62.571 72.222 0.00 0.00 37.59 5.52
151 152 4.222847 CCTACGGGCGGAAGAGGC 62.223 72.222 0.00 0.00 0.00 4.70
161 162 2.799371 GTCGAGACTGCCTACGGG 59.201 66.667 0.00 0.00 0.00 5.28
162 163 2.403987 CGTCGAGACTGCCTACGG 59.596 66.667 1.56 0.00 0.00 4.02
163 164 2.403987 CCGTCGAGACTGCCTACG 59.596 66.667 0.00 0.00 0.00 3.51
164 165 2.102553 GCCGTCGAGACTGCCTAC 59.897 66.667 8.19 0.00 35.84 3.18
165 166 3.506096 CGCCGTCGAGACTGCCTA 61.506 66.667 12.71 0.00 38.14 3.93
169 170 4.498520 ATGGCGCCGTCGAGACTG 62.499 66.667 23.90 0.00 38.10 3.51
170 171 4.194720 GATGGCGCCGTCGAGACT 62.195 66.667 31.62 3.61 38.10 3.24
171 172 3.701604 AAGATGGCGCCGTCGAGAC 62.702 63.158 36.35 18.40 38.10 3.36
172 173 3.411418 GAAGATGGCGCCGTCGAGA 62.411 63.158 36.35 13.84 38.10 4.04
173 174 2.956964 GAAGATGGCGCCGTCGAG 60.957 66.667 36.35 0.00 38.10 4.04
174 175 4.508128 GGAAGATGGCGCCGTCGA 62.508 66.667 36.35 15.06 38.10 4.20
176 177 3.969250 TTGGGAAGATGGCGCCGTC 62.969 63.158 36.49 36.49 0.00 4.79
177 178 3.976701 CTTGGGAAGATGGCGCCGT 62.977 63.158 24.16 24.16 0.00 5.68
178 179 3.204827 CTTGGGAAGATGGCGCCG 61.205 66.667 23.90 0.00 0.00 6.46
179 180 2.115291 GTCTTGGGAAGATGGCGCC 61.115 63.158 22.73 22.73 40.18 6.53
180 181 1.078143 AGTCTTGGGAAGATGGCGC 60.078 57.895 0.00 0.00 40.18 6.53
181 182 0.539051 AGAGTCTTGGGAAGATGGCG 59.461 55.000 0.00 0.00 40.18 5.69
182 183 1.134250 GGAGAGTCTTGGGAAGATGGC 60.134 57.143 0.00 0.00 40.18 4.40
183 184 2.433970 GAGGAGAGTCTTGGGAAGATGG 59.566 54.545 0.00 0.00 40.18 3.51
184 185 2.433970 GGAGGAGAGTCTTGGGAAGATG 59.566 54.545 0.00 0.00 40.18 2.90
185 186 2.317594 AGGAGGAGAGTCTTGGGAAGAT 59.682 50.000 0.00 0.00 40.18 2.40
186 187 1.719378 AGGAGGAGAGTCTTGGGAAGA 59.281 52.381 0.00 0.00 34.51 2.87
187 188 2.107366 GAGGAGGAGAGTCTTGGGAAG 58.893 57.143 0.00 0.00 0.00 3.46
188 189 1.273324 GGAGGAGGAGAGTCTTGGGAA 60.273 57.143 0.00 0.00 0.00 3.97
189 190 0.336737 GGAGGAGGAGAGTCTTGGGA 59.663 60.000 0.00 0.00 0.00 4.37
190 191 0.338120 AGGAGGAGGAGAGTCTTGGG 59.662 60.000 0.00 0.00 0.00 4.12
191 192 2.424234 CCTAGGAGGAGGAGAGTCTTGG 60.424 59.091 1.05 0.00 37.67 3.61
192 193 2.512056 TCCTAGGAGGAGGAGAGTCTTG 59.488 54.545 7.62 0.00 40.06 3.02
193 194 2.512476 GTCCTAGGAGGAGGAGAGTCTT 59.488 54.545 13.15 0.00 46.90 3.01
194 195 2.132686 GTCCTAGGAGGAGGAGAGTCT 58.867 57.143 13.15 0.00 46.90 3.24
195 196 1.144298 GGTCCTAGGAGGAGGAGAGTC 59.856 61.905 13.15 0.00 46.90 3.36
196 197 1.228190 GGTCCTAGGAGGAGGAGAGT 58.772 60.000 13.15 0.00 46.90 3.24
197 198 1.133606 GTGGTCCTAGGAGGAGGAGAG 60.134 61.905 13.15 0.00 46.90 3.20
198 199 0.927767 GTGGTCCTAGGAGGAGGAGA 59.072 60.000 13.15 0.00 46.90 3.71
199 200 0.631753 TGTGGTCCTAGGAGGAGGAG 59.368 60.000 13.15 0.00 46.90 3.69
200 201 1.319947 ATGTGGTCCTAGGAGGAGGA 58.680 55.000 13.15 0.00 46.90 3.71
201 202 2.043227 GAATGTGGTCCTAGGAGGAGG 58.957 57.143 13.15 0.00 46.90 4.30
202 203 2.752030 TGAATGTGGTCCTAGGAGGAG 58.248 52.381 13.15 0.00 46.90 3.69
203 204 2.940514 TGAATGTGGTCCTAGGAGGA 57.059 50.000 13.15 0.00 43.43 3.71
210 211 1.687054 CCATGGCATGAATGTGGTCCT 60.687 52.381 28.43 0.00 0.00 3.85
212 213 0.103572 GCCATGGCATGAATGTGGTC 59.896 55.000 32.08 5.28 41.49 4.02
235 236 2.049802 GTCTTGACGGGCGAACGA 60.050 61.111 6.19 0.00 37.61 3.85
243 244 0.613260 TCCCAGATTGGTCTTGACGG 59.387 55.000 0.00 0.00 35.17 4.79
286 287 6.237097 CGTCTTTGTTTGTTCGTTCGATTTTT 60.237 34.615 0.00 0.00 0.00 1.94
287 288 5.226360 CGTCTTTGTTTGTTCGTTCGATTTT 59.774 36.000 0.00 0.00 0.00 1.82
293 294 2.540157 CCCCGTCTTTGTTTGTTCGTTC 60.540 50.000 0.00 0.00 0.00 3.95
298 299 1.731093 CGCCCCGTCTTTGTTTGTT 59.269 52.632 0.00 0.00 0.00 2.83
304 305 1.705337 CTATGTGCGCCCCGTCTTTG 61.705 60.000 4.18 0.00 0.00 2.77
305 306 1.449601 CTATGTGCGCCCCGTCTTT 60.450 57.895 4.18 0.00 0.00 2.52
306 307 1.895020 TTCTATGTGCGCCCCGTCTT 61.895 55.000 4.18 0.00 0.00 3.01
308 309 1.883084 CTTCTATGTGCGCCCCGTC 60.883 63.158 4.18 0.00 0.00 4.79
338 347 3.050275 GTTCACTCTGGGGCGTGC 61.050 66.667 0.00 0.00 0.00 5.34
342 351 0.391263 CGTAAGGTTCACTCTGGGGC 60.391 60.000 0.00 0.00 0.00 5.80
401 418 5.443562 CGTTGAACATTCGCACGAGTAATAA 60.444 40.000 9.46 0.00 38.20 1.40
404 421 2.154198 CGTTGAACATTCGCACGAGTAA 59.846 45.455 9.46 0.00 38.20 2.24
405 422 1.717113 CGTTGAACATTCGCACGAGTA 59.283 47.619 9.46 0.00 38.20 2.59
407 424 3.258498 CGTTGAACATTCGCACGAG 57.742 52.632 9.46 0.00 38.20 4.18
555 583 3.695606 TGGAGCCGTGGACTGAGC 61.696 66.667 0.00 0.00 0.00 4.26
592 620 4.752879 CCGTGTACGTGGGGGCAG 62.753 72.222 0.00 0.00 37.74 4.85
690 734 2.481795 GCGCCTAATTTACTCCGTACCA 60.482 50.000 0.00 0.00 0.00 3.25
691 735 2.130395 GCGCCTAATTTACTCCGTACC 58.870 52.381 0.00 0.00 0.00 3.34
692 736 1.783140 CGCGCCTAATTTACTCCGTAC 59.217 52.381 0.00 0.00 0.00 3.67
693 737 1.865248 GCGCGCCTAATTTACTCCGTA 60.865 52.381 23.24 0.00 0.00 4.02
722 766 7.132213 TCTAGCGCTATTTTTATTGTGATTGC 58.868 34.615 19.19 0.00 0.00 3.56
800 870 0.510359 CTGCGCTGTTGTGAAGAGAC 59.490 55.000 9.73 0.00 30.94 3.36
801 871 1.224069 GCTGCGCTGTTGTGAAGAGA 61.224 55.000 16.05 0.00 30.94 3.10
802 872 1.206072 GCTGCGCTGTTGTGAAGAG 59.794 57.895 16.05 0.00 30.94 2.85
803 873 2.597713 CGCTGCGCTGTTGTGAAGA 61.598 57.895 9.88 0.00 30.94 2.87
818 888 1.676635 TAGTACGTGTCTGCCCGCT 60.677 57.895 0.00 0.00 0.00 5.52
832 902 1.366111 GACGGGCGTGGTACGTAGTA 61.366 60.000 0.00 0.00 44.73 1.82
833 903 2.672996 ACGGGCGTGGTACGTAGT 60.673 61.111 0.00 0.00 44.73 2.73
834 904 2.100991 GACGGGCGTGGTACGTAG 59.899 66.667 0.00 0.00 44.73 3.51
835 905 3.439540 GGACGGGCGTGGTACGTA 61.440 66.667 3.19 0.00 44.73 3.57
873 943 1.522900 GAGGGATGGATGGAAAGGGA 58.477 55.000 0.00 0.00 0.00 4.20
878 948 1.054406 GGACGGAGGGATGGATGGAA 61.054 60.000 0.00 0.00 0.00 3.53
879 949 1.459539 GGACGGAGGGATGGATGGA 60.460 63.158 0.00 0.00 0.00 3.41
882 952 2.134287 CACGGACGGAGGGATGGAT 61.134 63.158 0.00 0.00 0.00 3.41
966 1043 2.632602 CTAGCTGGGAGGAGGCGAGA 62.633 65.000 0.00 0.00 32.01 4.04
1277 1535 3.787001 GGGAGGAGTTGAGGCGGG 61.787 72.222 0.00 0.00 0.00 6.13
1756 2014 1.539560 ATCCATCCCTCGCATCGGAG 61.540 60.000 0.00 0.00 0.00 4.63
1805 2063 2.348411 ACCAAGAGAAACAGGGTGTG 57.652 50.000 0.00 0.00 0.00 3.82
1822 2081 3.451141 TTGATCAGGCAACAACAAACC 57.549 42.857 0.00 0.00 41.41 3.27
1831 2090 8.534954 AGTAGTAGTAGTATTTGATCAGGCAA 57.465 34.615 0.00 0.00 0.00 4.52
1854 2114 9.021807 TCAATAACAGAGTAGCTAAACAGTAGT 57.978 33.333 0.00 0.00 0.00 2.73
1855 2115 9.509855 CTCAATAACAGAGTAGCTAAACAGTAG 57.490 37.037 0.00 0.00 0.00 2.57
1881 2141 5.276270 TCTATCGTCGTACAGCCAAAATAC 58.724 41.667 0.00 0.00 0.00 1.89
1898 2158 9.558648 TGAACAACAATTCAATCAATTCTATCG 57.441 29.630 0.00 0.00 35.65 2.92
1901 2161 9.681692 CACTGAACAACAATTCAATCAATTCTA 57.318 29.630 0.00 0.00 38.12 2.10
1902 2162 7.654520 CCACTGAACAACAATTCAATCAATTCT 59.345 33.333 0.00 0.00 38.12 2.40
1903 2163 7.652909 TCCACTGAACAACAATTCAATCAATTC 59.347 33.333 0.00 0.00 38.12 2.17
1984 2249 3.755112 TTCAACCACCATGTCGTCTTA 57.245 42.857 0.00 0.00 0.00 2.10
2074 2339 1.618861 CAGCGGTGAGAGTAAGAACG 58.381 55.000 9.50 0.00 0.00 3.95
2372 2637 0.449388 GCCAAGCTGGAAACATCTCG 59.551 55.000 6.40 0.00 40.96 4.04
2407 2672 4.162320 TGAATATCTCGGCTGGTTCTTCTT 59.838 41.667 0.00 0.00 0.00 2.52
2447 2712 0.033781 GCTCTGCAAAATGGTTGCCA 59.966 50.000 8.47 0.00 44.32 4.92
2556 2821 9.440761 AGGAATTACTAACCATAGATTGAGTCT 57.559 33.333 0.00 0.00 41.11 3.24
2683 2949 4.803588 GCACAATGACAATGTCCCCAAAAT 60.804 41.667 11.24 0.00 0.00 1.82
2846 3112 3.760035 GGCGCGGACCTGAGAGAA 61.760 66.667 8.83 0.00 0.00 2.87
2860 3126 5.839262 TTATATATTTTGCAGAGACGGCG 57.161 39.130 4.80 4.80 0.00 6.46
2915 3181 5.945784 TCTTAACTTCAGCCATTACTGCATT 59.054 36.000 0.00 0.00 37.59 3.56
3069 3343 9.211485 GTAGTGAAGCACTAACTTAATAAACCA 57.789 33.333 8.70 0.00 46.55 3.67
3265 3539 7.012704 TGCATTCTTCCTACAGATTTATTCAGC 59.987 37.037 0.00 0.00 0.00 4.26
3652 3934 1.069765 CTGTAGTATGCGGGCCAGG 59.930 63.158 4.39 0.00 0.00 4.45
3664 3946 8.629158 TGCAAATTGTTGACTAATTTCTGTAGT 58.371 29.630 0.00 0.00 36.02 2.73
3693 3975 5.241506 GTGAAATTCTGGTTCATTCTGGTGA 59.758 40.000 0.00 0.00 37.34 4.02
3771 4053 2.555325 TCTTGTGCTTGGAAATCTGCAG 59.445 45.455 7.63 7.63 36.03 4.41
3873 4159 7.692460 AGCAAAATGTGAATTAGTCATCTGA 57.308 32.000 0.00 0.00 38.90 3.27
3874 4160 7.201410 GCAAGCAAAATGTGAATTAGTCATCTG 60.201 37.037 0.00 0.00 38.90 2.90
3949 4235 1.064952 GGTCTGGTGTTGTTGAAACGG 59.935 52.381 0.00 0.00 0.00 4.44
3959 4245 1.067354 GTATTCGACGGGTCTGGTGTT 60.067 52.381 0.00 0.00 0.00 3.32
4006 4292 4.275196 GTGTAGTAGTCGTCTATGCATCCA 59.725 45.833 0.19 0.00 0.00 3.41
4048 4334 0.956633 ACAAACACAGCATCTGCCTG 59.043 50.000 0.00 0.00 43.38 4.85
4155 4441 4.333095 CAGCAGCAGATATGGATGATTAGC 59.667 45.833 0.00 0.00 0.00 3.09
4158 4444 4.635699 TCAGCAGCAGATATGGATGATT 57.364 40.909 0.00 0.00 0.00 2.57
4195 4481 5.564848 GCCACCAAAAAGTACTCCTTCAATC 60.565 44.000 0.00 0.00 31.27 2.67
4205 4491 7.541122 TGTAAAATTTGCCACCAAAAAGTAC 57.459 32.000 0.00 0.00 43.58 2.73
4206 4492 8.738645 AATGTAAAATTTGCCACCAAAAAGTA 57.261 26.923 0.00 0.00 43.58 2.24
4207 4493 7.637631 AATGTAAAATTTGCCACCAAAAAGT 57.362 28.000 0.00 0.00 43.58 2.66
4208 4494 8.805688 CAAAATGTAAAATTTGCCACCAAAAAG 58.194 29.630 0.00 0.00 43.58 2.27
4212 4498 7.396540 AACAAAATGTAAAATTTGCCACCAA 57.603 28.000 0.00 0.00 39.55 3.67
4289 4575 0.176910 GAGTCCCTACAAGCTGCCTC 59.823 60.000 0.00 0.00 0.00 4.70
4375 4665 4.095782 TCTTCCATTAACATTTACAGCCGC 59.904 41.667 0.00 0.00 0.00 6.53
4377 4667 7.063426 GCTTTTCTTCCATTAACATTTACAGCC 59.937 37.037 0.00 0.00 0.00 4.85
4413 4703 6.942576 AGCCACTCAAAAAGTAACAGTATCAT 59.057 34.615 0.00 0.00 36.07 2.45
4421 4711 5.687285 CACAATCAGCCACTCAAAAAGTAAC 59.313 40.000 0.00 0.00 36.07 2.50
4541 4834 2.495866 CCATGTGCGGGCCAAATC 59.504 61.111 4.39 0.00 0.00 2.17
4551 4844 1.252904 ACAATGACAGGCCCATGTGC 61.253 55.000 1.69 0.00 32.25 4.57
4608 4905 3.281727 AATAGTGCCATGTTCATCGGT 57.718 42.857 0.00 0.00 0.00 4.69
4626 4923 5.047021 TGCTAGACTAGTGCTGACAGAAAAT 60.047 40.000 6.65 0.00 0.00 1.82
4636 4933 1.668101 GGCCGTGCTAGACTAGTGCT 61.668 60.000 11.15 0.00 0.00 4.40
4733 5030 5.872617 TCGTGTACAGTAAAAATGATCTGGG 59.127 40.000 0.00 0.00 32.92 4.45
4760 5057 1.672881 GAGCTGTTGCAGTGTTCAACT 59.327 47.619 12.84 2.36 43.00 3.16
4764 5061 0.871057 GGAGAGCTGTTGCAGTGTTC 59.129 55.000 0.00 0.00 42.74 3.18
4828 5128 3.947834 AGTCGGCAAATTTCAGATAAGGG 59.052 43.478 0.00 0.00 0.00 3.95
4845 5145 2.865551 GACTTACCTCTCTACGAGTCGG 59.134 54.545 18.30 0.00 38.11 4.79
4852 5152 1.760192 TGGCCGACTTACCTCTCTAC 58.240 55.000 0.00 0.00 0.00 2.59
4907 5231 4.963373 TCTACTAGAGTTGCTCGCTCTAT 58.037 43.478 0.00 6.51 42.54 1.98
4959 5285 3.485877 GCCAGAATTATCGTGCTGACAAC 60.486 47.826 0.00 0.00 0.00 3.32
4961 5287 2.093500 AGCCAGAATTATCGTGCTGACA 60.093 45.455 0.00 0.00 36.40 3.58
5045 5371 2.375174 ACCAAACATGGAGGCTTGTAGA 59.625 45.455 1.10 0.00 0.00 2.59
5060 5386 1.613520 GCCTCTCCCCAACTACCAAAC 60.614 57.143 0.00 0.00 0.00 2.93
5066 5392 4.232091 CCTAAATAGCCTCTCCCCAACTA 58.768 47.826 0.00 0.00 0.00 2.24
5080 5406 6.455647 TCGAGATGTAATGTGCCCTAAATAG 58.544 40.000 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.