Multiple sequence alignment - TraesCS4B01G279900

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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 TraesCS4B01G279900 chr4B 100.000 4470 0 0 1 4470 562712705 562708236 0.000000e+00 8255.0
1 TraesCS4B01G279900 chr4B 86.850 327 25 7 2751 3077 562709835 562709527 2.560000e-92 350.0
2 TraesCS4B01G279900 chr4B 86.850 327 25 7 2871 3179 562709955 562709629 2.560000e-92 350.0
3 TraesCS4B01G279900 chr4A 92.982 4246 185 36 282 4434 16964761 16968986 0.000000e+00 6085.0
4 TraesCS4B01G279900 chr4A 89.264 326 35 0 2751 3076 16967411 16967736 4.160000e-110 409.0
5 TraesCS4B01G279900 chr4A 82.319 345 25 12 2871 3179 16967291 16967635 2.650000e-67 267.0
6 TraesCS4B01G279900 chr4A 84.000 225 18 3 2973 3179 16967291 16967515 2.730000e-47 200.0
7 TraesCS4B01G279900 chr4D 94.297 2823 104 22 282 3077 449985524 449982732 0.000000e+00 4268.0
8 TraesCS4B01G279900 chr4D 95.836 1609 55 7 2871 4470 449983040 449981435 0.000000e+00 2590.0
9 TraesCS4B01G279900 chr4D 80.631 222 25 3 2754 2975 449982935 449982732 5.990000e-34 156.0
10 TraesCS4B01G279900 chr4D 91.176 68 4 1 319 384 450017309 450017242 1.710000e-14 91.6


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 TraesCS4B01G279900 chr4B 562708236 562712705 4469 True 2985.00 8255 91.233333 1 4470 3 chr4B.!!$R1 4469
1 TraesCS4B01G279900 chr4A 16964761 16968986 4225 False 1740.25 6085 87.141250 282 4434 4 chr4A.!!$F1 4152
2 TraesCS4B01G279900 chr4D 449981435 449985524 4089 True 2338.00 4268 90.254667 282 4470 3 chr4D.!!$R2 4188

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
65 66 0.035630 GCACTGCTCAGATGGTCCTT 60.036 55.0 3.60 0.00 0.00 3.36 F
80 81 0.038166 TCCTTGTGATGGAACCAGCC 59.962 55.0 6.64 0.00 0.00 4.85 F
169 170 0.038251 GTCTGCGACACATGTGGAGA 60.038 55.0 28.64 19.48 32.09 3.71 F
1732 1786 0.038526 TCGTCAGGAGCTTCCGAAAC 60.039 55.0 0.00 0.00 42.75 2.78 F
2323 2395 0.318784 AACGGAGTGCTTCGTCTGTC 60.319 55.0 5.96 0.00 45.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1514 0.106819 ATCATTCTGAGGCCTGCCAC 60.107 55.000 12.00 4.63 38.92 5.01 R
1833 1887 0.744874 TAAATCGCCGACCTCCTCAG 59.255 55.000 0.00 0.00 0.00 3.35 R
2170 2242 4.476113 TCAGATGGTTCCAGATCAAGGAAT 59.524 41.667 18.92 6.99 46.08 3.01 R
2840 2912 2.093394 TCAAGTGTGGTTCCTCGTTCAA 60.093 45.455 0.00 0.00 0.00 2.69 R
4216 4313 1.227527 TCACCTCGGTGCAACACAG 60.228 57.895 11.21 0.00 45.04 3.66 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
17 18 4.593864 GGCTGACGATCTCGGGGC 62.594 72.222 4.44 5.11 44.95 5.80
18 19 4.933064 GCTGACGATCTCGGGGCG 62.933 72.222 4.44 0.00 44.95 6.13
19 20 4.271816 CTGACGATCTCGGGGCGG 62.272 72.222 4.44 0.00 44.95 6.13
20 21 4.807631 TGACGATCTCGGGGCGGA 62.808 66.667 4.44 0.00 44.95 5.54
21 22 3.524606 GACGATCTCGGGGCGGAA 61.525 66.667 4.44 0.00 44.95 4.30
22 23 3.769875 GACGATCTCGGGGCGGAAC 62.770 68.421 4.44 0.00 44.95 3.62
23 24 4.587189 CGATCTCGGGGCGGAACC 62.587 72.222 0.00 0.00 35.37 3.62
24 25 3.467226 GATCTCGGGGCGGAACCA 61.467 66.667 0.00 0.00 42.05 3.67
25 26 3.735037 GATCTCGGGGCGGAACCAC 62.735 68.421 0.00 0.00 42.05 4.16
27 28 2.866523 ATCTCGGGGCGGAACCACTA 62.867 60.000 0.00 0.00 41.20 2.74
28 29 3.366739 CTCGGGGCGGAACCACTAC 62.367 68.421 0.00 0.00 41.20 2.73
29 30 3.697747 CGGGGCGGAACCACTACA 61.698 66.667 0.00 0.00 41.20 2.74
30 31 2.751688 GGGGCGGAACCACTACAA 59.248 61.111 0.00 0.00 39.64 2.41
31 32 1.673337 GGGGCGGAACCACTACAAC 60.673 63.158 0.00 0.00 39.64 3.32
32 33 2.030958 GGGCGGAACCACTACAACG 61.031 63.158 0.00 0.00 42.05 4.10
33 34 1.301165 GGCGGAACCACTACAACGT 60.301 57.895 0.00 0.00 38.86 3.99
34 35 1.562575 GGCGGAACCACTACAACGTG 61.563 60.000 0.00 0.00 38.86 4.49
35 36 0.598158 GCGGAACCACTACAACGTGA 60.598 55.000 0.00 0.00 37.06 4.35
36 37 1.415374 CGGAACCACTACAACGTGAG 58.585 55.000 0.00 0.00 37.06 3.51
37 38 1.792006 GGAACCACTACAACGTGAGG 58.208 55.000 0.00 0.00 37.06 3.86
38 39 1.607251 GGAACCACTACAACGTGAGGG 60.607 57.143 0.00 0.00 37.06 4.30
39 40 1.069668 GAACCACTACAACGTGAGGGT 59.930 52.381 0.00 0.00 37.06 4.34
40 41 1.125633 ACCACTACAACGTGAGGGTT 58.874 50.000 0.00 0.00 37.06 4.11
45 46 3.030652 CAACGTGAGGGTTGTGGC 58.969 61.111 0.00 0.00 41.77 5.01
46 47 2.590575 AACGTGAGGGTTGTGGCG 60.591 61.111 0.00 0.00 0.00 5.69
49 50 3.660111 GTGAGGGTTGTGGCGCAC 61.660 66.667 10.83 6.37 34.56 5.34
50 51 3.872603 TGAGGGTTGTGGCGCACT 61.873 61.111 10.83 0.00 35.11 4.40
51 52 3.357079 GAGGGTTGTGGCGCACTG 61.357 66.667 10.83 0.00 35.11 3.66
54 55 4.030452 GGTTGTGGCGCACTGCTC 62.030 66.667 10.83 0.00 45.43 4.26
55 56 3.279116 GTTGTGGCGCACTGCTCA 61.279 61.111 10.83 0.00 45.43 4.26
56 57 2.974148 TTGTGGCGCACTGCTCAG 60.974 61.111 10.83 0.00 45.43 3.35
57 58 3.459148 TTGTGGCGCACTGCTCAGA 62.459 57.895 10.83 0.00 45.43 3.27
58 59 2.435586 GTGGCGCACTGCTCAGAT 60.436 61.111 10.83 0.00 45.43 2.90
59 60 2.435410 TGGCGCACTGCTCAGATG 60.435 61.111 10.83 0.28 45.43 2.90
60 61 3.200593 GGCGCACTGCTCAGATGG 61.201 66.667 10.83 0.00 45.43 3.51
61 62 2.435586 GCGCACTGCTCAGATGGT 60.436 61.111 0.30 0.00 41.73 3.55
62 63 2.459442 GCGCACTGCTCAGATGGTC 61.459 63.158 0.30 0.00 41.73 4.02
63 64 1.812922 CGCACTGCTCAGATGGTCC 60.813 63.158 3.60 0.00 0.00 4.46
64 65 1.601171 GCACTGCTCAGATGGTCCT 59.399 57.895 3.60 0.00 0.00 3.85
65 66 0.035630 GCACTGCTCAGATGGTCCTT 60.036 55.000 3.60 0.00 0.00 3.36
66 67 1.735386 CACTGCTCAGATGGTCCTTG 58.265 55.000 3.60 0.00 0.00 3.61
67 68 1.002888 CACTGCTCAGATGGTCCTTGT 59.997 52.381 3.60 0.00 0.00 3.16
68 69 1.002888 ACTGCTCAGATGGTCCTTGTG 59.997 52.381 3.60 0.00 0.00 3.33
69 70 1.277273 CTGCTCAGATGGTCCTTGTGA 59.723 52.381 4.73 4.73 0.00 3.58
70 71 1.911357 TGCTCAGATGGTCCTTGTGAT 59.089 47.619 5.20 0.00 0.00 3.06
71 72 2.286872 GCTCAGATGGTCCTTGTGATG 58.713 52.381 5.20 2.34 0.00 3.07
72 73 2.915349 CTCAGATGGTCCTTGTGATGG 58.085 52.381 5.20 0.00 0.00 3.51
73 74 2.502947 CTCAGATGGTCCTTGTGATGGA 59.497 50.000 5.20 0.00 0.00 3.41
74 75 2.912295 TCAGATGGTCCTTGTGATGGAA 59.088 45.455 0.77 0.00 35.10 3.53
75 76 3.012518 CAGATGGTCCTTGTGATGGAAC 58.987 50.000 0.00 0.00 41.47 3.62
76 77 2.025887 AGATGGTCCTTGTGATGGAACC 60.026 50.000 0.00 0.00 40.43 3.62
77 78 1.144691 TGGTCCTTGTGATGGAACCA 58.855 50.000 0.00 0.00 40.43 3.67
78 79 1.073763 TGGTCCTTGTGATGGAACCAG 59.926 52.381 0.00 0.00 40.43 4.00
79 80 1.168714 GTCCTTGTGATGGAACCAGC 58.831 55.000 1.88 1.88 35.10 4.85
80 81 0.038166 TCCTTGTGATGGAACCAGCC 59.962 55.000 6.64 0.00 0.00 4.85
81 82 0.251297 CCTTGTGATGGAACCAGCCA 60.251 55.000 6.64 1.99 43.23 4.75
87 88 3.602104 ATGGAACCAGCCATCAAGG 57.398 52.632 0.00 0.00 45.36 3.61
88 89 0.706433 ATGGAACCAGCCATCAAGGT 59.294 50.000 0.00 0.00 45.36 3.50
89 90 1.077663 ATGGAACCAGCCATCAAGGTT 59.922 47.619 0.00 0.00 45.36 3.50
92 93 2.380064 AACCAGCCATCAAGGTTCAA 57.620 45.000 0.00 0.00 41.60 2.69
93 94 1.915141 ACCAGCCATCAAGGTTCAAG 58.085 50.000 0.00 0.00 40.61 3.02
94 95 1.145738 ACCAGCCATCAAGGTTCAAGT 59.854 47.619 0.00 0.00 40.61 3.16
95 96 2.242043 CCAGCCATCAAGGTTCAAGTT 58.758 47.619 0.00 0.00 40.61 2.66
96 97 2.229784 CCAGCCATCAAGGTTCAAGTTC 59.770 50.000 0.00 0.00 40.61 3.01
97 98 3.152341 CAGCCATCAAGGTTCAAGTTCT 58.848 45.455 0.00 0.00 40.61 3.01
98 99 4.326826 CAGCCATCAAGGTTCAAGTTCTA 58.673 43.478 0.00 0.00 40.61 2.10
99 100 4.761739 CAGCCATCAAGGTTCAAGTTCTAA 59.238 41.667 0.00 0.00 40.61 2.10
100 101 5.241506 CAGCCATCAAGGTTCAAGTTCTAAA 59.758 40.000 0.00 0.00 40.61 1.85
101 102 6.012745 AGCCATCAAGGTTCAAGTTCTAAAT 58.987 36.000 0.00 0.00 40.61 1.40
102 103 6.494835 AGCCATCAAGGTTCAAGTTCTAAATT 59.505 34.615 0.00 0.00 40.61 1.82
103 104 7.015584 AGCCATCAAGGTTCAAGTTCTAAATTT 59.984 33.333 0.00 0.00 40.61 1.82
104 105 8.303876 GCCATCAAGGTTCAAGTTCTAAATTTA 58.696 33.333 0.00 0.00 40.61 1.40
111 112 9.914131 AGGTTCAAGTTCTAAATTTATTTCAGC 57.086 29.630 0.00 0.00 0.00 4.26
112 113 9.140286 GGTTCAAGTTCTAAATTTATTTCAGCC 57.860 33.333 0.00 0.00 0.00 4.85
113 114 9.914131 GTTCAAGTTCTAAATTTATTTCAGCCT 57.086 29.630 0.00 0.00 0.00 4.58
117 118 9.929180 AAGTTCTAAATTTATTTCAGCCTTTCC 57.071 29.630 0.00 0.00 0.00 3.13
118 119 8.244113 AGTTCTAAATTTATTTCAGCCTTTCCG 58.756 33.333 0.00 0.00 0.00 4.30
119 120 7.931578 TCTAAATTTATTTCAGCCTTTCCGA 57.068 32.000 0.00 0.00 0.00 4.55
120 121 7.758495 TCTAAATTTATTTCAGCCTTTCCGAC 58.242 34.615 0.00 0.00 0.00 4.79
121 122 4.616181 ATTTATTTCAGCCTTTCCGACG 57.384 40.909 0.00 0.00 0.00 5.12
122 123 3.322211 TTATTTCAGCCTTTCCGACGA 57.678 42.857 0.00 0.00 0.00 4.20
123 124 2.403252 ATTTCAGCCTTTCCGACGAT 57.597 45.000 0.00 0.00 0.00 3.73
124 125 1.438651 TTTCAGCCTTTCCGACGATG 58.561 50.000 0.00 0.00 0.00 3.84
125 126 0.320374 TTCAGCCTTTCCGACGATGT 59.680 50.000 0.00 0.00 0.00 3.06
126 127 0.320374 TCAGCCTTTCCGACGATGTT 59.680 50.000 0.00 0.00 0.00 2.71
127 128 1.156736 CAGCCTTTCCGACGATGTTT 58.843 50.000 0.00 0.00 0.00 2.83
128 129 1.135972 CAGCCTTTCCGACGATGTTTG 60.136 52.381 0.00 0.00 0.00 2.93
129 130 0.872388 GCCTTTCCGACGATGTTTGT 59.128 50.000 0.00 0.00 0.00 2.83
130 131 1.265905 GCCTTTCCGACGATGTTTGTT 59.734 47.619 0.00 0.00 0.00 2.83
131 132 2.664698 GCCTTTCCGACGATGTTTGTTC 60.665 50.000 0.00 0.00 0.00 3.18
132 133 2.546368 CCTTTCCGACGATGTTTGTTCA 59.454 45.455 0.00 0.00 0.00 3.18
133 134 3.363970 CCTTTCCGACGATGTTTGTTCAG 60.364 47.826 0.00 0.00 0.00 3.02
134 135 2.519377 TCCGACGATGTTTGTTCAGT 57.481 45.000 0.00 0.00 0.00 3.41
135 136 3.646611 TCCGACGATGTTTGTTCAGTA 57.353 42.857 0.00 0.00 0.00 2.74
136 137 3.979948 TCCGACGATGTTTGTTCAGTAA 58.020 40.909 0.00 0.00 0.00 2.24
137 138 3.985279 TCCGACGATGTTTGTTCAGTAAG 59.015 43.478 0.00 0.00 0.00 2.34
138 139 3.985279 CCGACGATGTTTGTTCAGTAAGA 59.015 43.478 0.00 0.00 0.00 2.10
139 140 4.090066 CCGACGATGTTTGTTCAGTAAGAG 59.910 45.833 0.00 0.00 0.00 2.85
140 141 4.090066 CGACGATGTTTGTTCAGTAAGAGG 59.910 45.833 0.00 0.00 0.00 3.69
141 142 5.209818 ACGATGTTTGTTCAGTAAGAGGA 57.790 39.130 0.00 0.00 0.00 3.71
142 143 5.230942 ACGATGTTTGTTCAGTAAGAGGAG 58.769 41.667 0.00 0.00 0.00 3.69
143 144 5.010719 ACGATGTTTGTTCAGTAAGAGGAGA 59.989 40.000 0.00 0.00 0.00 3.71
144 145 5.346281 CGATGTTTGTTCAGTAAGAGGAGAC 59.654 44.000 0.00 0.00 0.00 3.36
146 147 6.235231 TGTTTGTTCAGTAAGAGGAGACTT 57.765 37.500 0.00 0.00 44.43 3.01
147 148 6.281405 TGTTTGTTCAGTAAGAGGAGACTTC 58.719 40.000 0.00 0.00 44.43 3.01
148 149 5.470047 TTGTTCAGTAAGAGGAGACTTCC 57.530 43.478 0.00 0.00 44.43 3.46
149 150 3.833070 TGTTCAGTAAGAGGAGACTTCCC 59.167 47.826 0.00 0.00 45.24 3.97
150 151 2.724454 TCAGTAAGAGGAGACTTCCCG 58.276 52.381 0.00 0.00 45.24 5.14
151 152 2.041350 TCAGTAAGAGGAGACTTCCCGT 59.959 50.000 0.00 0.00 45.24 5.28
152 153 2.424246 CAGTAAGAGGAGACTTCCCGTC 59.576 54.545 0.00 0.00 45.24 4.79
159 160 2.649034 GACTTCCCGTCTGCGACA 59.351 61.111 8.91 0.00 41.33 4.35
160 161 1.733399 GACTTCCCGTCTGCGACAC 60.733 63.158 8.91 0.00 41.33 3.67
161 162 2.338620 CTTCCCGTCTGCGACACA 59.661 61.111 8.91 0.00 41.33 3.72
162 163 1.079819 CTTCCCGTCTGCGACACAT 60.080 57.895 8.91 0.00 41.33 3.21
163 164 1.354337 CTTCCCGTCTGCGACACATG 61.354 60.000 8.91 0.00 41.33 3.21
164 165 2.048222 CCCGTCTGCGACACATGT 60.048 61.111 0.00 0.00 41.33 3.21
165 166 2.382746 CCCGTCTGCGACACATGTG 61.383 63.158 24.25 24.25 41.33 3.21
166 167 2.382746 CCGTCTGCGACACATGTGG 61.383 63.158 28.64 13.70 41.33 4.17
167 168 1.372872 CGTCTGCGACACATGTGGA 60.373 57.895 28.64 13.57 41.33 4.02
168 169 1.347097 CGTCTGCGACACATGTGGAG 61.347 60.000 28.64 21.58 41.33 3.86
169 170 0.038251 GTCTGCGACACATGTGGAGA 60.038 55.000 28.64 19.48 32.09 3.71
170 171 0.244721 TCTGCGACACATGTGGAGAG 59.755 55.000 28.64 17.72 34.19 3.20
171 172 0.738762 CTGCGACACATGTGGAGAGG 60.739 60.000 28.64 13.70 34.19 3.69
172 173 1.448540 GCGACACATGTGGAGAGGG 60.449 63.158 28.64 12.09 34.19 4.30
173 174 1.888436 GCGACACATGTGGAGAGGGA 61.888 60.000 28.64 0.00 34.19 4.20
174 175 0.826715 CGACACATGTGGAGAGGGAT 59.173 55.000 28.64 5.90 34.19 3.85
175 176 1.472201 CGACACATGTGGAGAGGGATG 60.472 57.143 28.64 0.85 34.19 3.51
176 177 1.833630 GACACATGTGGAGAGGGATGA 59.166 52.381 28.64 0.00 34.19 2.92
177 178 2.237143 GACACATGTGGAGAGGGATGAA 59.763 50.000 28.64 0.00 34.19 2.57
178 179 2.644299 ACACATGTGGAGAGGGATGAAA 59.356 45.455 28.64 0.00 34.19 2.69
179 180 3.276857 CACATGTGGAGAGGGATGAAAG 58.723 50.000 18.51 0.00 0.00 2.62
180 181 2.295885 CATGTGGAGAGGGATGAAAGC 58.704 52.381 0.00 0.00 0.00 3.51
181 182 0.250234 TGTGGAGAGGGATGAAAGCG 59.750 55.000 0.00 0.00 0.00 4.68
182 183 0.462759 GTGGAGAGGGATGAAAGCGG 60.463 60.000 0.00 0.00 0.00 5.52
183 184 0.617535 TGGAGAGGGATGAAAGCGGA 60.618 55.000 0.00 0.00 0.00 5.54
184 185 0.105778 GGAGAGGGATGAAAGCGGAG 59.894 60.000 0.00 0.00 0.00 4.63
197 198 4.591852 CGGAGCGTTACTAGCGAG 57.408 61.111 0.00 0.00 40.04 5.03
198 199 2.012237 CGGAGCGTTACTAGCGAGA 58.988 57.895 0.00 0.00 40.04 4.04
199 200 0.316032 CGGAGCGTTACTAGCGAGAC 60.316 60.000 0.00 0.00 40.04 3.36
200 201 0.316032 GGAGCGTTACTAGCGAGACG 60.316 60.000 0.00 2.07 40.04 4.18
222 223 1.279496 GGGGGTAGGGAACTTTACGT 58.721 55.000 0.00 0.00 43.67 3.57
223 224 1.630369 GGGGGTAGGGAACTTTACGTT 59.370 52.381 0.00 0.00 43.67 3.99
224 225 2.040278 GGGGGTAGGGAACTTTACGTTT 59.960 50.000 0.00 0.00 43.67 3.60
225 226 3.498481 GGGGGTAGGGAACTTTACGTTTT 60.498 47.826 0.00 0.00 43.67 2.43
226 227 4.144297 GGGGTAGGGAACTTTACGTTTTT 58.856 43.478 0.00 0.00 43.67 1.94
307 308 3.369366 CCCTTTTTCATGGCCATGGTAAC 60.369 47.826 38.81 4.92 39.24 2.50
308 309 3.515104 CCTTTTTCATGGCCATGGTAACT 59.485 43.478 38.81 6.39 39.24 2.24
332 333 6.239217 TGAGGCTATGCTTAAATCTCTCAA 57.761 37.500 0.00 0.00 0.00 3.02
407 410 0.907230 GCACCCTGTTCCCTCTCTCT 60.907 60.000 0.00 0.00 0.00 3.10
408 411 1.190643 CACCCTGTTCCCTCTCTCTC 58.809 60.000 0.00 0.00 0.00 3.20
490 493 2.503765 ACCAAAACTTCCCCCAAACTTG 59.496 45.455 0.00 0.00 0.00 3.16
537 540 3.036429 GCCTCCTGCCAGATTCCGT 62.036 63.158 0.00 0.00 0.00 4.69
567 596 0.176680 TCTGGAGAATCGCAGCTTCC 59.823 55.000 0.00 0.00 34.65 3.46
591 620 2.125391 GAGATCCGCAGCAGCACA 60.125 61.111 0.82 0.00 42.27 4.57
616 645 1.338674 TGTTCCGCTTTCCGATCACAT 60.339 47.619 0.00 0.00 40.02 3.21
617 646 2.093921 TGTTCCGCTTTCCGATCACATA 60.094 45.455 0.00 0.00 40.02 2.29
722 759 3.486383 TCAAAAATCGAGGGTTCTTGCT 58.514 40.909 0.00 0.00 0.00 3.91
732 769 1.745653 GGGTTCTTGCTACCAATCTGC 59.254 52.381 0.00 0.00 37.40 4.26
734 771 2.162408 GGTTCTTGCTACCAATCTGCAC 59.838 50.000 0.00 0.00 36.37 4.57
812 849 0.734889 AGAAATTTGGCTCATCGGCG 59.265 50.000 0.00 0.00 42.02 6.46
818 855 1.019278 TTGGCTCATCGGCGAAGTTC 61.019 55.000 15.93 5.77 42.02 3.01
824 861 1.011968 CATCGGCGAAGTTCCGTTGA 61.012 55.000 15.93 0.00 44.95 3.18
825 862 0.320073 ATCGGCGAAGTTCCGTTGAA 60.320 50.000 15.93 0.00 46.49 2.69
865 910 2.747446 GACGTTGGCATGAGTAACCAAT 59.253 45.455 0.00 0.00 44.79 3.16
982 1027 5.309323 TGAGCAACCTACATGCAAATTAC 57.691 39.130 0.00 0.00 46.22 1.89
1158 1203 3.344215 CGCATCTGCAGGATCCGC 61.344 66.667 15.13 18.08 42.21 5.54
1202 1247 2.655090 TTGGACAAGGTTCTGCATGA 57.345 45.000 0.00 0.00 0.00 3.07
1266 1311 0.299300 TGGAAATCGCGCGTTTATCG 59.701 50.000 30.98 1.58 43.12 2.92
1401 1446 4.514585 AAGGCGGGGCACACACAA 62.515 61.111 0.00 0.00 0.00 3.33
1469 1514 4.154918 GCACAAGTTATTTGAGGAGGTGAG 59.845 45.833 0.00 0.00 39.21 3.51
1477 1522 3.322318 GAGGAGGTGAGTGGCAGGC 62.322 68.421 0.00 0.00 0.00 4.85
1636 1690 3.054948 TGTCTCAGATGATGATGTTGGCA 60.055 43.478 0.00 0.00 37.28 4.92
1680 1734 3.662247 AAACGTCGAACCAGAGATCTT 57.338 42.857 0.00 0.00 0.00 2.40
1732 1786 0.038526 TCGTCAGGAGCTTCCGAAAC 60.039 55.000 0.00 0.00 42.75 2.78
1833 1887 5.959618 AATGTAGCTTTTCTGGTTGGTAC 57.040 39.130 0.00 0.00 34.98 3.34
2071 2143 0.836606 TGTCCCAGTTGTCTTCTGCA 59.163 50.000 0.00 0.00 0.00 4.41
2224 2296 2.149578 CCAACTGAAGCTGAAGGTGAG 58.850 52.381 14.11 2.78 32.60 3.51
2323 2395 0.318784 AACGGAGTGCTTCGTCTGTC 60.319 55.000 5.96 0.00 45.00 3.51
2344 2416 2.042831 AGCAAGTGAAGCGATGGCC 61.043 57.895 0.00 0.00 41.24 5.36
2486 2558 7.936301 ACTTGCTTACAGAAAGAGAGAAAGAAT 59.064 33.333 0.00 0.00 34.38 2.40
2536 2608 0.463295 ATGAGAGCAGGTTCCGCATG 60.463 55.000 0.00 0.00 0.00 4.06
2757 2829 2.248248 CCTACAGAGTGGGTCACTGAA 58.752 52.381 5.20 0.00 45.44 3.02
2808 2880 5.948992 AGTGTAGAAAACTCAGAATTGGC 57.051 39.130 0.00 0.00 0.00 4.52
2840 2912 1.209019 CACTATTGCCTCAGGAGCACT 59.791 52.381 0.00 0.00 40.69 4.40
2848 2920 1.671261 CCTCAGGAGCACTTGAACGAG 60.671 57.143 0.00 0.00 32.00 4.18
2852 2924 1.149148 GGAGCACTTGAACGAGGAAC 58.851 55.000 0.00 0.00 0.00 3.62
2924 2996 4.293415 CCAACATGCAGAAAACTCAGAAC 58.707 43.478 0.00 0.00 0.00 3.01
2934 3006 4.752101 AGAAAACTCAGAACTGGAATGTCG 59.248 41.667 1.93 0.00 0.00 4.35
2945 3017 3.576982 ACTGGAATGTCGGAGTTCACTAA 59.423 43.478 5.69 0.00 0.00 2.24
2951 3023 3.093814 TGTCGGAGTTCACTAATGCCTA 58.906 45.455 0.00 0.00 0.00 3.93
2957 3029 5.119694 GGAGTTCACTAATGCCTAAGGAAG 58.880 45.833 0.00 0.00 0.00 3.46
2960 3032 5.485708 AGTTCACTAATGCCTAAGGAAGACT 59.514 40.000 0.00 0.00 0.00 3.24
2966 3038 4.640771 ATGCCTAAGGAAGACTTGAACA 57.359 40.909 0.00 0.00 40.37 3.18
3088 3178 4.930963 ACGATGAATCACTGAGAGATCAC 58.069 43.478 0.00 0.00 31.33 3.06
3567 3657 7.271511 AGAACATGCTGTGGAAAAACAAAATA 58.728 30.769 0.00 0.00 0.00 1.40
3614 3705 4.142609 TCAGGATAGGTTGATGTTCAGC 57.857 45.455 0.00 0.00 0.00 4.26
3708 3799 1.623311 TCTTCCATCGAAGTGCCTCAA 59.377 47.619 0.00 0.00 45.02 3.02
3724 3815 4.937620 TGCCTCAAGTCAATAATCTCACAC 59.062 41.667 0.00 0.00 0.00 3.82
3725 3816 4.937620 GCCTCAAGTCAATAATCTCACACA 59.062 41.667 0.00 0.00 0.00 3.72
3745 3838 4.393062 CACAGGACACATCTCACCAATTAC 59.607 45.833 0.00 0.00 0.00 1.89
3825 3918 7.783042 TCCCTAGCATTACTCTACTCTTTTTC 58.217 38.462 0.00 0.00 0.00 2.29
3848 3941 4.578928 CCTTGTAACCTACAGCAACAACTT 59.421 41.667 0.00 0.00 40.24 2.66
3889 3982 5.578005 TTAGATCTTACACAGTTCCTCCG 57.422 43.478 0.00 0.00 0.00 4.63
3960 4053 8.175716 GGAACATATAGCACAAGTTACTGTTTC 58.824 37.037 0.00 0.00 0.00 2.78
3968 4061 5.163652 GCACAAGTTACTGTTTCTTGGACTT 60.164 40.000 20.27 0.00 41.64 3.01
4150 4247 1.380246 TTCATGATGCCCAGTGCCC 60.380 57.895 0.00 0.00 40.16 5.36
4216 4313 1.802960 CTGGGATACGATGCATGCTTC 59.197 52.381 20.33 20.52 37.60 3.86
4222 4319 1.527034 ACGATGCATGCTTCTGTGTT 58.473 45.000 25.72 7.17 0.00 3.32
4293 4397 3.452627 GCTGGAGGAGAAGTGGAATTCTA 59.547 47.826 5.23 0.00 39.63 2.10
4419 4523 4.100279 TGTAGAGAAGATCGCCATCCTA 57.900 45.455 0.00 0.00 0.00 2.94
4435 4539 2.320781 TCCTAGGAGCTGAGGTAATGC 58.679 52.381 7.62 0.00 34.20 3.56
4445 4549 1.134367 TGAGGTAATGCGGAGACTTCG 59.866 52.381 0.00 0.00 0.00 3.79
4460 4564 2.196382 CTTCGGAAGAGTCGACCGCA 62.196 60.000 20.53 12.59 45.25 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.593864 GCCCCGAGATCGTCAGCC 62.594 72.222 1.09 0.00 37.74 4.85
1 2 4.933064 CGCCCCGAGATCGTCAGC 62.933 72.222 1.09 0.48 37.74 4.26
2 3 4.271816 CCGCCCCGAGATCGTCAG 62.272 72.222 1.09 0.00 37.74 3.51
3 4 4.807631 TCCGCCCCGAGATCGTCA 62.808 66.667 1.09 0.00 37.74 4.35
4 5 3.524606 TTCCGCCCCGAGATCGTC 61.525 66.667 1.09 0.00 37.74 4.20
5 6 3.834799 GTTCCGCCCCGAGATCGT 61.835 66.667 1.09 0.00 37.74 3.73
6 7 4.587189 GGTTCCGCCCCGAGATCG 62.587 72.222 0.00 0.00 39.44 3.69
7 8 3.467226 TGGTTCCGCCCCGAGATC 61.467 66.667 0.00 0.00 36.04 2.75
8 9 2.866523 TAGTGGTTCCGCCCCGAGAT 62.867 60.000 0.00 0.00 36.04 2.75
9 10 3.588817 TAGTGGTTCCGCCCCGAGA 62.589 63.158 0.00 0.00 36.04 4.04
10 11 3.072468 TAGTGGTTCCGCCCCGAG 61.072 66.667 0.00 0.00 36.04 4.63
11 12 3.384532 GTAGTGGTTCCGCCCCGA 61.385 66.667 0.00 0.00 36.04 5.14
12 13 3.242897 TTGTAGTGGTTCCGCCCCG 62.243 63.158 0.00 0.00 36.04 5.73
13 14 1.673337 GTTGTAGTGGTTCCGCCCC 60.673 63.158 0.00 0.00 36.04 5.80
14 15 2.030958 CGTTGTAGTGGTTCCGCCC 61.031 63.158 0.00 0.00 36.04 6.13
15 16 1.301165 ACGTTGTAGTGGTTCCGCC 60.301 57.895 0.00 0.00 37.90 6.13
16 17 0.598158 TCACGTTGTAGTGGTTCCGC 60.598 55.000 0.00 0.00 42.10 5.54
17 18 1.415374 CTCACGTTGTAGTGGTTCCG 58.585 55.000 0.00 0.00 42.10 4.30
18 19 1.607251 CCCTCACGTTGTAGTGGTTCC 60.607 57.143 0.00 0.00 42.10 3.62
19 20 1.069668 ACCCTCACGTTGTAGTGGTTC 59.930 52.381 0.00 0.00 42.10 3.62
20 21 1.125633 ACCCTCACGTTGTAGTGGTT 58.874 50.000 0.00 0.00 42.10 3.67
21 22 1.125633 AACCCTCACGTTGTAGTGGT 58.874 50.000 0.00 0.00 42.10 4.16
22 23 1.508632 CAACCCTCACGTTGTAGTGG 58.491 55.000 0.00 0.00 42.10 4.00
28 29 2.892334 CGCCACAACCCTCACGTTG 61.892 63.158 0.09 0.09 46.94 4.10
29 30 2.590575 CGCCACAACCCTCACGTT 60.591 61.111 0.00 0.00 0.00 3.99
32 33 3.660111 GTGCGCCACAACCCTCAC 61.660 66.667 4.18 0.00 34.08 3.51
33 34 3.872603 AGTGCGCCACAACCCTCA 61.873 61.111 4.18 0.00 36.74 3.86
34 35 3.357079 CAGTGCGCCACAACCCTC 61.357 66.667 4.18 0.00 36.74 4.30
37 38 4.030452 GAGCAGTGCGCCACAACC 62.030 66.667 10.00 0.00 44.04 3.77
38 39 3.245948 CTGAGCAGTGCGCCACAAC 62.246 63.158 16.63 0.00 44.04 3.32
39 40 2.736579 ATCTGAGCAGTGCGCCACAA 62.737 55.000 16.63 5.14 44.04 3.33
40 41 3.244281 ATCTGAGCAGTGCGCCACA 62.244 57.895 16.63 10.99 44.04 4.17
41 42 2.435586 ATCTGAGCAGTGCGCCAC 60.436 61.111 16.63 3.02 44.04 5.01
42 43 2.435410 CATCTGAGCAGTGCGCCA 60.435 61.111 16.63 13.84 44.04 5.69
43 44 3.200593 CCATCTGAGCAGTGCGCC 61.201 66.667 16.63 9.82 44.04 6.53
44 45 2.435586 ACCATCTGAGCAGTGCGC 60.436 61.111 12.40 12.40 42.91 6.09
45 46 1.812922 GGACCATCTGAGCAGTGCG 60.813 63.158 10.00 0.00 0.00 5.34
46 47 0.035630 AAGGACCATCTGAGCAGTGC 60.036 55.000 7.13 7.13 0.00 4.40
47 48 1.002888 ACAAGGACCATCTGAGCAGTG 59.997 52.381 0.00 0.00 0.00 3.66
48 49 1.002888 CACAAGGACCATCTGAGCAGT 59.997 52.381 0.00 0.00 0.00 4.40
49 50 1.277273 TCACAAGGACCATCTGAGCAG 59.723 52.381 0.00 0.00 0.00 4.24
50 51 1.351076 TCACAAGGACCATCTGAGCA 58.649 50.000 0.00 0.00 0.00 4.26
51 52 2.286872 CATCACAAGGACCATCTGAGC 58.713 52.381 0.00 0.00 0.00 4.26
52 53 2.502947 TCCATCACAAGGACCATCTGAG 59.497 50.000 0.00 0.00 0.00 3.35
53 54 2.550175 TCCATCACAAGGACCATCTGA 58.450 47.619 0.00 0.00 0.00 3.27
54 55 3.012518 GTTCCATCACAAGGACCATCTG 58.987 50.000 0.00 0.00 34.19 2.90
55 56 2.025887 GGTTCCATCACAAGGACCATCT 60.026 50.000 0.00 0.00 34.19 2.90
56 57 2.290896 TGGTTCCATCACAAGGACCATC 60.291 50.000 0.00 0.00 33.98 3.51
57 58 1.710244 TGGTTCCATCACAAGGACCAT 59.290 47.619 0.00 0.00 33.98 3.55
58 59 1.073763 CTGGTTCCATCACAAGGACCA 59.926 52.381 0.00 0.00 36.02 4.02
59 60 1.826385 CTGGTTCCATCACAAGGACC 58.174 55.000 0.00 0.00 34.19 4.46
60 61 1.168714 GCTGGTTCCATCACAAGGAC 58.831 55.000 0.00 0.00 34.19 3.85
61 62 0.038166 GGCTGGTTCCATCACAAGGA 59.962 55.000 0.00 0.00 0.00 3.36
62 63 0.251297 TGGCTGGTTCCATCACAAGG 60.251 55.000 0.00 0.00 0.00 3.61
63 64 1.843368 ATGGCTGGTTCCATCACAAG 58.157 50.000 0.00 0.00 43.00 3.16
70 71 0.482446 AACCTTGATGGCTGGTTCCA 59.518 50.000 0.00 0.00 39.61 3.53
71 72 3.363787 AACCTTGATGGCTGGTTCC 57.636 52.632 0.00 0.00 39.61 3.62
73 74 2.242043 CTTGAACCTTGATGGCTGGTT 58.758 47.619 0.00 0.00 45.57 3.67
74 75 1.145738 ACTTGAACCTTGATGGCTGGT 59.854 47.619 0.00 0.00 40.22 4.00
75 76 1.915141 ACTTGAACCTTGATGGCTGG 58.085 50.000 0.00 0.00 40.22 4.85
76 77 3.152341 AGAACTTGAACCTTGATGGCTG 58.848 45.455 0.00 0.00 40.22 4.85
77 78 3.515602 AGAACTTGAACCTTGATGGCT 57.484 42.857 0.00 0.00 40.22 4.75
78 79 5.705609 TTTAGAACTTGAACCTTGATGGC 57.294 39.130 0.00 0.00 40.22 4.40
85 86 9.914131 GCTGAAATAAATTTAGAACTTGAACCT 57.086 29.630 3.94 0.00 0.00 3.50
86 87 9.140286 GGCTGAAATAAATTTAGAACTTGAACC 57.860 33.333 3.94 0.00 0.00 3.62
87 88 9.914131 AGGCTGAAATAAATTTAGAACTTGAAC 57.086 29.630 3.94 0.00 0.00 3.18
91 92 9.929180 GGAAAGGCTGAAATAAATTTAGAACTT 57.071 29.630 3.94 0.00 0.00 2.66
92 93 8.244113 CGGAAAGGCTGAAATAAATTTAGAACT 58.756 33.333 3.94 0.00 0.00 3.01
93 94 8.241367 TCGGAAAGGCTGAAATAAATTTAGAAC 58.759 33.333 3.94 0.00 0.00 3.01
94 95 8.241367 GTCGGAAAGGCTGAAATAAATTTAGAA 58.759 33.333 3.94 0.00 32.59 2.10
95 96 7.413657 CGTCGGAAAGGCTGAAATAAATTTAGA 60.414 37.037 3.94 0.00 32.59 2.10
96 97 6.687105 CGTCGGAAAGGCTGAAATAAATTTAG 59.313 38.462 3.94 0.00 32.59 1.85
97 98 6.372103 TCGTCGGAAAGGCTGAAATAAATTTA 59.628 34.615 0.00 0.00 32.59 1.40
98 99 5.182380 TCGTCGGAAAGGCTGAAATAAATTT 59.818 36.000 0.00 0.00 32.59 1.82
99 100 4.698304 TCGTCGGAAAGGCTGAAATAAATT 59.302 37.500 0.00 0.00 32.59 1.82
100 101 4.258543 TCGTCGGAAAGGCTGAAATAAAT 58.741 39.130 0.00 0.00 32.59 1.40
101 102 3.666274 TCGTCGGAAAGGCTGAAATAAA 58.334 40.909 0.00 0.00 32.59 1.40
102 103 3.322211 TCGTCGGAAAGGCTGAAATAA 57.678 42.857 0.00 0.00 32.59 1.40
103 104 3.194861 CATCGTCGGAAAGGCTGAAATA 58.805 45.455 0.00 0.00 32.59 1.40
104 105 2.009774 CATCGTCGGAAAGGCTGAAAT 58.990 47.619 0.00 0.00 32.59 2.17
105 106 1.270625 ACATCGTCGGAAAGGCTGAAA 60.271 47.619 0.00 0.00 32.59 2.69
106 107 0.320374 ACATCGTCGGAAAGGCTGAA 59.680 50.000 0.00 0.00 32.59 3.02
107 108 0.320374 AACATCGTCGGAAAGGCTGA 59.680 50.000 0.00 0.00 0.00 4.26
108 109 1.135972 CAAACATCGTCGGAAAGGCTG 60.136 52.381 0.00 0.00 0.00 4.85
109 110 1.156736 CAAACATCGTCGGAAAGGCT 58.843 50.000 0.00 0.00 0.00 4.58
110 111 0.872388 ACAAACATCGTCGGAAAGGC 59.128 50.000 0.00 0.00 0.00 4.35
111 112 2.546368 TGAACAAACATCGTCGGAAAGG 59.454 45.455 0.00 0.00 0.00 3.11
112 113 3.247648 ACTGAACAAACATCGTCGGAAAG 59.752 43.478 0.00 0.00 0.00 2.62
113 114 3.199677 ACTGAACAAACATCGTCGGAAA 58.800 40.909 0.00 0.00 0.00 3.13
114 115 2.828877 ACTGAACAAACATCGTCGGAA 58.171 42.857 0.00 0.00 0.00 4.30
115 116 2.519377 ACTGAACAAACATCGTCGGA 57.481 45.000 0.00 0.00 0.00 4.55
116 117 3.985279 TCTTACTGAACAAACATCGTCGG 59.015 43.478 0.00 0.00 0.00 4.79
117 118 4.090066 CCTCTTACTGAACAAACATCGTCG 59.910 45.833 0.00 0.00 0.00 5.12
118 119 5.227908 TCCTCTTACTGAACAAACATCGTC 58.772 41.667 0.00 0.00 0.00 4.20
119 120 5.010719 TCTCCTCTTACTGAACAAACATCGT 59.989 40.000 0.00 0.00 0.00 3.73
120 121 5.346281 GTCTCCTCTTACTGAACAAACATCG 59.654 44.000 0.00 0.00 0.00 3.84
121 122 6.459923 AGTCTCCTCTTACTGAACAAACATC 58.540 40.000 0.00 0.00 0.00 3.06
122 123 6.426646 AGTCTCCTCTTACTGAACAAACAT 57.573 37.500 0.00 0.00 0.00 2.71
123 124 5.871396 AGTCTCCTCTTACTGAACAAACA 57.129 39.130 0.00 0.00 0.00 2.83
124 125 5.697178 GGAAGTCTCCTCTTACTGAACAAAC 59.303 44.000 0.00 0.00 38.88 2.93
125 126 5.221661 GGGAAGTCTCCTCTTACTGAACAAA 60.222 44.000 0.00 0.00 42.05 2.83
126 127 4.283722 GGGAAGTCTCCTCTTACTGAACAA 59.716 45.833 0.00 0.00 42.05 2.83
127 128 3.833070 GGGAAGTCTCCTCTTACTGAACA 59.167 47.826 0.00 0.00 42.05 3.18
128 129 3.119424 CGGGAAGTCTCCTCTTACTGAAC 60.119 52.174 0.00 0.00 42.05 3.18
129 130 3.090037 CGGGAAGTCTCCTCTTACTGAA 58.910 50.000 0.00 0.00 42.05 3.02
130 131 2.041350 ACGGGAAGTCTCCTCTTACTGA 59.959 50.000 4.74 0.00 42.05 3.41
131 132 2.424246 GACGGGAAGTCTCCTCTTACTG 59.576 54.545 0.00 0.00 46.13 2.74
132 133 2.725637 GACGGGAAGTCTCCTCTTACT 58.274 52.381 0.00 0.00 46.13 2.24
151 152 0.244721 CTCTCCACATGTGTCGCAGA 59.755 55.000 23.79 16.59 0.00 4.26
152 153 0.738762 CCTCTCCACATGTGTCGCAG 60.739 60.000 23.79 13.57 0.00 5.18
153 154 1.293179 CCTCTCCACATGTGTCGCA 59.707 57.895 23.79 4.67 0.00 5.10
154 155 1.448540 CCCTCTCCACATGTGTCGC 60.449 63.158 23.79 0.00 0.00 5.19
155 156 0.826715 ATCCCTCTCCACATGTGTCG 59.173 55.000 23.79 14.11 0.00 4.35
156 157 1.833630 TCATCCCTCTCCACATGTGTC 59.166 52.381 23.79 0.00 0.00 3.67
157 158 1.956869 TCATCCCTCTCCACATGTGT 58.043 50.000 23.79 0.07 0.00 3.72
158 159 3.276857 CTTTCATCCCTCTCCACATGTG 58.723 50.000 19.31 19.31 0.00 3.21
159 160 2.356535 GCTTTCATCCCTCTCCACATGT 60.357 50.000 0.00 0.00 0.00 3.21
160 161 2.295885 GCTTTCATCCCTCTCCACATG 58.704 52.381 0.00 0.00 0.00 3.21
161 162 1.134280 CGCTTTCATCCCTCTCCACAT 60.134 52.381 0.00 0.00 0.00 3.21
162 163 0.250234 CGCTTTCATCCCTCTCCACA 59.750 55.000 0.00 0.00 0.00 4.17
163 164 0.462759 CCGCTTTCATCCCTCTCCAC 60.463 60.000 0.00 0.00 0.00 4.02
164 165 0.617535 TCCGCTTTCATCCCTCTCCA 60.618 55.000 0.00 0.00 0.00 3.86
165 166 0.105778 CTCCGCTTTCATCCCTCTCC 59.894 60.000 0.00 0.00 0.00 3.71
166 167 0.531753 GCTCCGCTTTCATCCCTCTC 60.532 60.000 0.00 0.00 0.00 3.20
167 168 1.524482 GCTCCGCTTTCATCCCTCT 59.476 57.895 0.00 0.00 0.00 3.69
168 169 1.884926 CGCTCCGCTTTCATCCCTC 60.885 63.158 0.00 0.00 0.00 4.30
169 170 2.185310 AACGCTCCGCTTTCATCCCT 62.185 55.000 0.00 0.00 0.00 4.20
170 171 0.461339 TAACGCTCCGCTTTCATCCC 60.461 55.000 0.00 0.00 0.00 3.85
171 172 0.651031 GTAACGCTCCGCTTTCATCC 59.349 55.000 0.00 0.00 0.00 3.51
172 173 1.641577 AGTAACGCTCCGCTTTCATC 58.358 50.000 0.00 0.00 0.00 2.92
173 174 2.810650 CTAGTAACGCTCCGCTTTCAT 58.189 47.619 0.00 0.00 0.00 2.57
174 175 1.734707 GCTAGTAACGCTCCGCTTTCA 60.735 52.381 0.00 0.00 0.00 2.69
175 176 0.922032 GCTAGTAACGCTCCGCTTTC 59.078 55.000 0.00 0.00 0.00 2.62
176 177 0.801067 CGCTAGTAACGCTCCGCTTT 60.801 55.000 0.00 0.00 0.00 3.51
177 178 1.226603 CGCTAGTAACGCTCCGCTT 60.227 57.895 0.00 0.00 0.00 4.68
178 179 2.049475 CTCGCTAGTAACGCTCCGCT 62.049 60.000 0.00 0.00 0.00 5.52
179 180 1.654743 CTCGCTAGTAACGCTCCGC 60.655 63.158 0.00 0.00 0.00 5.54
180 181 0.316032 GTCTCGCTAGTAACGCTCCG 60.316 60.000 0.00 0.00 0.00 4.63
181 182 0.316032 CGTCTCGCTAGTAACGCTCC 60.316 60.000 0.00 0.00 0.00 4.70
182 183 3.130835 CGTCTCGCTAGTAACGCTC 57.869 57.895 0.00 0.00 0.00 5.03
203 204 1.279496 ACGTAAAGTTCCCTACCCCC 58.721 55.000 0.00 0.00 0.00 5.40
204 205 3.423539 AAACGTAAAGTTCCCTACCCC 57.576 47.619 0.00 0.00 43.37 4.95
285 286 1.278537 ACCATGGCCATGAAAAAGGG 58.721 50.000 41.32 27.06 41.20 3.95
286 287 3.515104 AGTTACCATGGCCATGAAAAAGG 59.485 43.478 41.32 27.75 41.20 3.11
287 288 4.806640 AGTTACCATGGCCATGAAAAAG 57.193 40.909 41.32 27.66 41.20 2.27
288 289 4.590647 TCAAGTTACCATGGCCATGAAAAA 59.409 37.500 41.32 28.39 41.20 1.94
294 295 1.686115 GCCTCAAGTTACCATGGCCAT 60.686 52.381 14.09 14.09 34.81 4.40
307 308 6.286758 TGAGAGATTTAAGCATAGCCTCAAG 58.713 40.000 0.00 0.00 0.00 3.02
308 309 6.239217 TGAGAGATTTAAGCATAGCCTCAA 57.761 37.500 0.00 0.00 0.00 3.02
332 333 0.185901 ACCTTTGCATGTGGTGAGGT 59.814 50.000 5.20 0.00 32.16 3.85
396 399 0.930726 GAGAGGGGAGAGAGAGGGAA 59.069 60.000 0.00 0.00 0.00 3.97
407 410 3.533697 CGTAGGATTGGAGAGGGGA 57.466 57.895 0.00 0.00 0.00 4.81
529 532 2.499289 AGATCAACAGCTGACGGAATCT 59.501 45.455 23.35 16.38 36.69 2.40
537 540 3.429960 CGATTCTCCAGATCAACAGCTGA 60.430 47.826 23.35 0.00 38.41 4.26
567 596 1.598132 CTGCTGCGGATCTCAAATCAG 59.402 52.381 1.17 0.00 0.00 2.90
591 620 0.899720 TCGGAAAGCGGAACATACCT 59.100 50.000 0.00 0.00 0.00 3.08
616 645 2.156891 GTCGCGCAGATTCAAACAAGTA 59.843 45.455 8.75 0.00 0.00 2.24
617 646 1.069906 GTCGCGCAGATTCAAACAAGT 60.070 47.619 8.75 0.00 0.00 3.16
812 849 5.629079 AAGATGGAATTCAACGGAACTTC 57.371 39.130 7.93 0.00 35.46 3.01
865 910 3.499338 AGGAAACATCAATCCTGCAACA 58.501 40.909 0.00 0.00 44.38 3.33
1158 1203 2.865308 CACAGCATGCACGGTGAG 59.135 61.111 19.93 7.03 42.53 3.51
1202 1247 1.831652 CTCCGAGAACCAGGCCTTGT 61.832 60.000 0.00 1.62 0.00 3.16
1266 1311 3.733077 GCTTGCTGTGAATCTGGCAATAC 60.733 47.826 0.00 0.00 42.51 1.89
1350 1395 2.830651 TGTTTGTTGGGTTACCTGGT 57.169 45.000 4.05 4.05 37.76 4.00
1401 1446 2.800544 CTCCGAACAACAAGAACATCGT 59.199 45.455 0.00 0.00 0.00 3.73
1419 1464 1.478510 TCTCTCTTCGTGAATGGCTCC 59.521 52.381 0.00 0.00 0.00 4.70
1469 1514 0.106819 ATCATTCTGAGGCCTGCCAC 60.107 55.000 12.00 4.63 38.92 5.01
1477 1522 1.880675 GCTCATGCCATCATTCTGAGG 59.119 52.381 0.00 0.00 0.00 3.86
1636 1690 2.042686 TCATAAGGCTTTGCATCGCT 57.957 45.000 4.45 0.00 0.00 4.93
1732 1786 9.672086 TTTTGGAAAACGATACATACTTTTCTG 57.328 29.630 0.00 0.00 34.44 3.02
1833 1887 0.744874 TAAATCGCCGACCTCCTCAG 59.255 55.000 0.00 0.00 0.00 3.35
2170 2242 4.476113 TCAGATGGTTCCAGATCAAGGAAT 59.524 41.667 18.92 6.99 46.08 3.01
2200 2272 2.092429 ACCTTCAGCTTCAGTTGGAACA 60.092 45.455 0.00 0.00 0.00 3.18
2224 2296 2.166907 TCAGGGACTCAAGGGAGATC 57.833 55.000 0.00 0.00 44.26 2.75
2344 2416 4.641541 TCCACTTGCAACCTATTGATCATG 59.358 41.667 0.00 0.00 38.15 3.07
2536 2608 5.582689 ATTTTCCGAGATCAAATGGTTCC 57.417 39.130 0.00 0.00 0.00 3.62
2730 2802 2.625790 GACCCACTCTGTAGGCTATCAG 59.374 54.545 14.25 14.25 0.00 2.90
2808 2880 2.609459 GGCAATAGTGAACTCCGACATG 59.391 50.000 0.00 0.00 0.00 3.21
2840 2912 2.093394 TCAAGTGTGGTTCCTCGTTCAA 60.093 45.455 0.00 0.00 0.00 2.69
2848 2920 2.223377 GTCATCGTTCAAGTGTGGTTCC 59.777 50.000 0.00 0.00 0.00 3.62
2852 2924 2.476619 GTGAGTCATCGTTCAAGTGTGG 59.523 50.000 0.00 0.00 0.00 4.17
2906 2978 3.817084 TCCAGTTCTGAGTTTTCTGCATG 59.183 43.478 1.00 0.00 0.00 4.06
2909 2981 4.276926 ACATTCCAGTTCTGAGTTTTCTGC 59.723 41.667 1.00 0.00 0.00 4.26
2910 2982 5.333645 CGACATTCCAGTTCTGAGTTTTCTG 60.334 44.000 1.00 0.00 0.00 3.02
2924 2996 2.751166 AGTGAACTCCGACATTCCAG 57.249 50.000 0.00 0.00 0.00 3.86
2934 3006 4.755266 TCCTTAGGCATTAGTGAACTCC 57.245 45.455 0.00 0.00 0.00 3.85
2945 3017 4.640771 TGTTCAAGTCTTCCTTAGGCAT 57.359 40.909 0.00 0.00 0.00 4.40
2951 3023 6.774656 AGTGATTCATTGTTCAAGTCTTCCTT 59.225 34.615 0.00 0.00 0.00 3.36
2957 3029 6.648310 TCTCTCAGTGATTCATTGTTCAAGTC 59.352 38.462 8.77 0.00 0.00 3.01
2960 3032 7.163441 TGATCTCTCAGTGATTCATTGTTCAA 58.837 34.615 8.77 0.00 0.00 2.69
2966 3038 6.496144 TGGATGATCTCTCAGTGATTCATT 57.504 37.500 0.00 0.00 34.12 2.57
3480 3570 8.778358 CCTATTATTACCTTCTGAATGCTGAAC 58.222 37.037 0.00 0.00 0.00 3.18
3614 3705 5.371526 ACCTCATACAATGCATAAGGTCTG 58.628 41.667 0.00 2.59 30.49 3.51
3708 3799 5.012046 TGTGTCCTGTGTGAGATTATTGACT 59.988 40.000 0.00 0.00 0.00 3.41
3724 3815 3.941483 GGTAATTGGTGAGATGTGTCCTG 59.059 47.826 0.00 0.00 0.00 3.86
3725 3816 3.587061 TGGTAATTGGTGAGATGTGTCCT 59.413 43.478 0.00 0.00 0.00 3.85
3745 3838 5.047306 TCTGGAAGTTCATACACTACACTGG 60.047 44.000 5.01 0.00 33.76 4.00
3825 3918 4.134563 AGTTGTTGCTGTAGGTTACAAGG 58.865 43.478 0.00 0.00 38.38 3.61
3848 3941 6.312141 TCTAATGATCACCCTGATTCAACA 57.688 37.500 0.00 0.00 37.20 3.33
3889 3982 7.544915 GTCAGAGGTTACTTAAGGATACACAAC 59.455 40.741 7.53 0.00 41.41 3.32
3960 4053 5.582689 ACTTGTTTCTTTCCAAGTCCAAG 57.417 39.130 0.00 0.00 46.15 3.61
3990 4084 2.029739 TCGGTTATTTCGACACTGCTGA 60.030 45.455 0.00 0.00 0.00 4.26
4022 4116 4.142708 TGTCAATAAACATCATGACACGCC 60.143 41.667 0.00 0.00 45.14 5.68
4120 4217 2.093625 GCATCATGAAGTTCGCGTGTTA 59.906 45.455 5.77 0.00 0.00 2.41
4216 4313 1.227527 TCACCTCGGTGCAACACAG 60.228 57.895 11.21 0.00 45.04 3.66
4222 4319 3.625897 CCCAGTCACCTCGGTGCA 61.626 66.667 11.21 0.00 45.04 4.57
4293 4397 2.160417 GCTCGTGCTATTTTCTGCTTGT 59.840 45.455 1.41 0.00 36.03 3.16
4419 4523 0.687757 TCCGCATTACCTCAGCTCCT 60.688 55.000 0.00 0.00 0.00 3.69
4435 4539 0.097325 CGACTCTTCCGAAGTCTCCG 59.903 60.000 8.01 4.77 0.00 4.63
4445 4549 1.444553 CTGTGCGGTCGACTCTTCC 60.445 63.158 16.46 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.