Multiple sequence alignment - TraesCS3D01G368000

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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 TraesCS3D01G368000 chr3D 100.000 2768 0 0 1 2768 481701159 481703926 0.000000e+00 5112.0
1 TraesCS3D01G368000 chr3D 85.926 135 16 3 1572 1704 474216244 474216111 1.030000e-29 141.0
2 TraesCS3D01G368000 chr3B 91.860 2371 115 29 207 2556 643255958 643258271 0.000000e+00 3238.0
3 TraesCS3D01G368000 chr3B 95.000 120 5 1 2644 2762 643258557 643258676 1.310000e-43 187.0
4 TraesCS3D01G368000 chr3A 86.798 1833 124 57 773 2549 624829147 624830917 0.000000e+00 1936.0
5 TraesCS3D01G368000 chr3A 87.333 450 33 13 291 720 624828680 624829125 6.890000e-136 494.0
6 TraesCS3D01G368000 chr3A 91.743 109 8 1 2644 2751 624831326 624831434 1.720000e-32 150.0
7 TraesCS3D01G368000 chr3A 88.000 125 13 2 1581 1704 616492648 616492525 2.220000e-31 147.0
8 TraesCS3D01G368000 chr1B 89.947 189 16 2 1583 1768 495415717 495415529 9.910000e-60 241.0
9 TraesCS3D01G368000 chr1A 80.175 343 50 14 1022 1347 470686661 470686320 9.910000e-60 241.0
10 TraesCS3D01G368000 chr1A 89.418 189 17 2 1583 1768 470686083 470685895 4.610000e-58 235.0
11 TraesCS3D01G368000 chr1A 88.095 126 13 2 1580 1704 474450730 474450606 6.180000e-32 148.0
12 TraesCS3D01G368000 chr1D 89.418 189 17 2 1583 1768 371341254 371341066 4.610000e-58 235.0
13 TraesCS3D01G368000 chr1D 87.407 135 14 3 1574 1706 375646707 375646574 4.770000e-33 152.0
14 TraesCS3D01G368000 chr2A 87.838 74 8 1 10 83 453898450 453898522 4.910000e-13 86.1


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 TraesCS3D01G368000 chr3D 481701159 481703926 2767 False 5112.0 5112 100.000000 1 2768 1 chr3D.!!$F1 2767
1 TraesCS3D01G368000 chr3B 643255958 643258676 2718 False 1712.5 3238 93.430000 207 2762 2 chr3B.!!$F1 2555
2 TraesCS3D01G368000 chr3A 624828680 624831434 2754 False 860.0 1936 88.624667 291 2751 3 chr3A.!!$F1 2460
3 TraesCS3D01G368000 chr1A 470685895 470686661 766 True 238.0 241 84.796500 1022 1768 2 chr1A.!!$R2 746

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
990 1032 0.033208 AGGAGAGCCAGAGAGACCAG 60.033 60.0 0.0 0.0 36.29 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 2368 0.451135 GACGAAACACATGTCGCAGC 60.451 55.0 0.0 0.0 40.95 5.25 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 3.400007 GGAAGATTGAGCGGTCGC 58.600 61.111 10.46 7.32 42.33 5.19
21 22 2.278596 GATTGAGCGGTCGCGCTA 60.279 61.111 18.48 12.37 46.05 4.26
22 23 2.278857 ATTGAGCGGTCGCGCTAG 60.279 61.111 18.48 0.00 46.05 3.42
23 24 2.663630 GATTGAGCGGTCGCGCTAGA 62.664 60.000 18.48 2.76 46.05 2.43
24 25 2.669808 ATTGAGCGGTCGCGCTAGAG 62.670 60.000 18.48 0.00 46.05 2.43
38 39 2.607187 GCTAGAGCGCTCTACAAAACA 58.393 47.619 37.07 21.11 40.93 2.83
39 40 2.345942 GCTAGAGCGCTCTACAAAACAC 59.654 50.000 37.07 18.86 40.93 3.32
40 41 1.797025 AGAGCGCTCTACAAAACACC 58.203 50.000 37.61 7.22 38.35 4.16
41 42 1.344763 AGAGCGCTCTACAAAACACCT 59.655 47.619 37.61 10.00 38.35 4.00
42 43 1.461127 GAGCGCTCTACAAAACACCTG 59.539 52.381 29.88 0.00 0.00 4.00
43 44 1.070134 AGCGCTCTACAAAACACCTGA 59.930 47.619 2.64 0.00 0.00 3.86
44 45 2.076863 GCGCTCTACAAAACACCTGAT 58.923 47.619 0.00 0.00 0.00 2.90
45 46 2.094417 GCGCTCTACAAAACACCTGATC 59.906 50.000 0.00 0.00 0.00 2.92
46 47 2.345641 CGCTCTACAAAACACCTGATCG 59.654 50.000 0.00 0.00 0.00 3.69
47 48 2.094417 GCTCTACAAAACACCTGATCGC 59.906 50.000 0.00 0.00 0.00 4.58
48 49 2.673368 CTCTACAAAACACCTGATCGCC 59.327 50.000 0.00 0.00 0.00 5.54
49 50 1.737793 CTACAAAACACCTGATCGCCC 59.262 52.381 0.00 0.00 0.00 6.13
50 51 0.893727 ACAAAACACCTGATCGCCCC 60.894 55.000 0.00 0.00 0.00 5.80
51 52 0.609131 CAAAACACCTGATCGCCCCT 60.609 55.000 0.00 0.00 0.00 4.79
52 53 0.322546 AAAACACCTGATCGCCCCTC 60.323 55.000 0.00 0.00 0.00 4.30
53 54 1.201429 AAACACCTGATCGCCCCTCT 61.201 55.000 0.00 0.00 0.00 3.69
54 55 0.325296 AACACCTGATCGCCCCTCTA 60.325 55.000 0.00 0.00 0.00 2.43
55 56 1.043673 ACACCTGATCGCCCCTCTAC 61.044 60.000 0.00 0.00 0.00 2.59
56 57 1.457831 ACCTGATCGCCCCTCTACC 60.458 63.158 0.00 0.00 0.00 3.18
57 58 2.565645 CCTGATCGCCCCTCTACCG 61.566 68.421 0.00 0.00 0.00 4.02
58 59 1.828660 CTGATCGCCCCTCTACCGT 60.829 63.158 0.00 0.00 0.00 4.83
59 60 0.536687 CTGATCGCCCCTCTACCGTA 60.537 60.000 0.00 0.00 0.00 4.02
60 61 0.820891 TGATCGCCCCTCTACCGTAC 60.821 60.000 0.00 0.00 0.00 3.67
61 62 0.820891 GATCGCCCCTCTACCGTACA 60.821 60.000 0.00 0.00 0.00 2.90
62 63 0.822532 ATCGCCCCTCTACCGTACAG 60.823 60.000 0.00 0.00 0.00 2.74
63 64 1.452651 CGCCCCTCTACCGTACAGA 60.453 63.158 0.00 0.00 0.00 3.41
64 65 1.033746 CGCCCCTCTACCGTACAGAA 61.034 60.000 0.00 0.00 0.00 3.02
65 66 1.411041 GCCCCTCTACCGTACAGAAT 58.589 55.000 0.00 0.00 0.00 2.40
66 67 1.340568 GCCCCTCTACCGTACAGAATC 59.659 57.143 0.00 0.00 0.00 2.52
67 68 2.662866 CCCCTCTACCGTACAGAATCA 58.337 52.381 0.00 0.00 0.00 2.57
68 69 2.361438 CCCCTCTACCGTACAGAATCAC 59.639 54.545 0.00 0.00 0.00 3.06
69 70 3.021695 CCCTCTACCGTACAGAATCACA 58.978 50.000 0.00 0.00 0.00 3.58
70 71 3.446161 CCCTCTACCGTACAGAATCACAA 59.554 47.826 0.00 0.00 0.00 3.33
71 72 4.440250 CCCTCTACCGTACAGAATCACAAG 60.440 50.000 0.00 0.00 0.00 3.16
72 73 4.398358 CCTCTACCGTACAGAATCACAAGA 59.602 45.833 0.00 0.00 0.00 3.02
73 74 5.449314 CCTCTACCGTACAGAATCACAAGAG 60.449 48.000 0.00 0.00 0.00 2.85
74 75 3.594603 ACCGTACAGAATCACAAGAGG 57.405 47.619 0.00 0.00 0.00 3.69
75 76 2.271800 CCGTACAGAATCACAAGAGGC 58.728 52.381 0.00 0.00 0.00 4.70
76 77 1.920574 CGTACAGAATCACAAGAGGCG 59.079 52.381 0.00 0.00 0.00 5.52
77 78 2.271800 GTACAGAATCACAAGAGGCGG 58.728 52.381 0.00 0.00 0.00 6.13
78 79 0.036010 ACAGAATCACAAGAGGCGGG 60.036 55.000 0.00 0.00 0.00 6.13
79 80 0.745845 CAGAATCACAAGAGGCGGGG 60.746 60.000 0.00 0.00 0.00 5.73
80 81 1.201429 AGAATCACAAGAGGCGGGGT 61.201 55.000 0.00 0.00 0.00 4.95
81 82 0.322546 GAATCACAAGAGGCGGGGTT 60.323 55.000 0.00 0.00 0.00 4.11
82 83 0.322546 AATCACAAGAGGCGGGGTTC 60.323 55.000 0.00 0.00 0.00 3.62
83 84 1.488705 ATCACAAGAGGCGGGGTTCA 61.489 55.000 0.00 0.00 0.00 3.18
84 85 1.966451 CACAAGAGGCGGGGTTCAC 60.966 63.158 0.00 0.00 0.00 3.18
85 86 2.147387 ACAAGAGGCGGGGTTCACT 61.147 57.895 0.00 0.00 0.00 3.41
86 87 1.672356 CAAGAGGCGGGGTTCACTG 60.672 63.158 0.00 0.00 0.00 3.66
87 88 2.147387 AAGAGGCGGGGTTCACTGT 61.147 57.895 0.00 0.00 0.00 3.55
88 89 0.834687 AAGAGGCGGGGTTCACTGTA 60.835 55.000 0.00 0.00 0.00 2.74
89 90 0.617820 AGAGGCGGGGTTCACTGTAT 60.618 55.000 0.00 0.00 0.00 2.29
90 91 0.179081 GAGGCGGGGTTCACTGTATC 60.179 60.000 0.00 0.00 0.00 2.24
91 92 0.617820 AGGCGGGGTTCACTGTATCT 60.618 55.000 0.00 0.00 0.00 1.98
92 93 1.117150 GGCGGGGTTCACTGTATCTA 58.883 55.000 0.00 0.00 0.00 1.98
93 94 1.483415 GGCGGGGTTCACTGTATCTAA 59.517 52.381 0.00 0.00 0.00 2.10
94 95 2.104281 GGCGGGGTTCACTGTATCTAAT 59.896 50.000 0.00 0.00 0.00 1.73
95 96 3.322828 GGCGGGGTTCACTGTATCTAATA 59.677 47.826 0.00 0.00 0.00 0.98
96 97 4.202284 GGCGGGGTTCACTGTATCTAATAA 60.202 45.833 0.00 0.00 0.00 1.40
97 98 5.512576 GGCGGGGTTCACTGTATCTAATAAT 60.513 44.000 0.00 0.00 0.00 1.28
98 99 5.995897 GCGGGGTTCACTGTATCTAATAATT 59.004 40.000 0.00 0.00 0.00 1.40
99 100 6.147328 GCGGGGTTCACTGTATCTAATAATTC 59.853 42.308 0.00 0.00 0.00 2.17
100 101 6.649557 CGGGGTTCACTGTATCTAATAATTCC 59.350 42.308 0.00 0.00 0.00 3.01
101 102 7.472945 CGGGGTTCACTGTATCTAATAATTCCT 60.473 40.741 0.00 0.00 0.00 3.36
102 103 8.877195 GGGGTTCACTGTATCTAATAATTCCTA 58.123 37.037 0.00 0.00 0.00 2.94
103 104 9.930693 GGGTTCACTGTATCTAATAATTCCTAG 57.069 37.037 0.00 0.00 0.00 3.02
104 105 9.930693 GGTTCACTGTATCTAATAATTCCTAGG 57.069 37.037 0.82 0.82 0.00 3.02
118 119 9.506042 AATAATTCCTAGGAAAATCCCATTGTT 57.494 29.630 27.65 15.98 37.19 2.83
119 120 6.796785 ATTCCTAGGAAAATCCCATTGTTG 57.203 37.500 27.65 0.00 37.19 3.33
120 121 4.023291 TCCTAGGAAAATCCCATTGTTGC 58.977 43.478 9.71 0.00 37.19 4.17
121 122 3.181487 CCTAGGAAAATCCCATTGTTGCG 60.181 47.826 1.05 0.00 37.19 4.85
122 123 2.524306 AGGAAAATCCCATTGTTGCGA 58.476 42.857 0.00 0.00 37.19 5.10
123 124 2.493278 AGGAAAATCCCATTGTTGCGAG 59.507 45.455 0.00 0.00 37.19 5.03
124 125 2.417243 GGAAAATCCCATTGTTGCGAGG 60.417 50.000 0.00 0.00 0.00 4.63
125 126 2.214376 AAATCCCATTGTTGCGAGGA 57.786 45.000 0.00 0.00 0.00 3.71
126 127 2.442236 AATCCCATTGTTGCGAGGAT 57.558 45.000 0.00 0.00 39.02 3.24
127 128 2.442236 ATCCCATTGTTGCGAGGATT 57.558 45.000 0.00 0.00 33.48 3.01
128 129 1.462616 TCCCATTGTTGCGAGGATTG 58.537 50.000 0.00 0.00 0.00 2.67
129 130 1.176527 CCCATTGTTGCGAGGATTGT 58.823 50.000 0.00 0.00 0.00 2.71
130 131 2.026729 TCCCATTGTTGCGAGGATTGTA 60.027 45.455 0.00 0.00 0.00 2.41
131 132 2.752354 CCCATTGTTGCGAGGATTGTAA 59.248 45.455 0.00 0.00 0.00 2.41
132 133 3.181497 CCCATTGTTGCGAGGATTGTAAG 60.181 47.826 0.00 0.00 0.00 2.34
133 134 3.440173 CCATTGTTGCGAGGATTGTAAGT 59.560 43.478 0.00 0.00 0.00 2.24
134 135 4.082787 CCATTGTTGCGAGGATTGTAAGTT 60.083 41.667 0.00 0.00 0.00 2.66
135 136 4.742438 TTGTTGCGAGGATTGTAAGTTC 57.258 40.909 0.00 0.00 0.00 3.01
136 137 3.071479 TGTTGCGAGGATTGTAAGTTCC 58.929 45.455 0.00 0.00 0.00 3.62
137 138 3.244422 TGTTGCGAGGATTGTAAGTTCCT 60.244 43.478 0.00 0.00 45.12 3.36
138 139 3.695830 TGCGAGGATTGTAAGTTCCTT 57.304 42.857 0.00 0.00 42.48 3.36
139 140 4.015872 TGCGAGGATTGTAAGTTCCTTT 57.984 40.909 0.00 0.00 42.48 3.11
140 141 3.751175 TGCGAGGATTGTAAGTTCCTTTG 59.249 43.478 0.00 0.00 42.48 2.77
141 142 3.751698 GCGAGGATTGTAAGTTCCTTTGT 59.248 43.478 0.00 0.00 42.48 2.83
142 143 4.378459 GCGAGGATTGTAAGTTCCTTTGTG 60.378 45.833 0.00 0.00 42.48 3.33
143 144 4.994852 CGAGGATTGTAAGTTCCTTTGTGA 59.005 41.667 0.00 0.00 42.48 3.58
144 145 5.468746 CGAGGATTGTAAGTTCCTTTGTGAA 59.531 40.000 0.00 0.00 42.48 3.18
145 146 6.347725 CGAGGATTGTAAGTTCCTTTGTGAAG 60.348 42.308 0.00 0.00 42.48 3.02
146 147 5.241728 AGGATTGTAAGTTCCTTTGTGAAGC 59.758 40.000 0.00 0.00 39.36 3.86
147 148 5.009610 GGATTGTAAGTTCCTTTGTGAAGCA 59.990 40.000 0.00 0.00 0.00 3.91
148 149 4.893424 TGTAAGTTCCTTTGTGAAGCAC 57.107 40.909 0.00 0.00 34.56 4.40
149 150 3.311322 TGTAAGTTCCTTTGTGAAGCACG 59.689 43.478 0.00 0.00 37.14 5.34
150 151 1.308998 AGTTCCTTTGTGAAGCACGG 58.691 50.000 0.00 0.00 37.14 4.94
151 152 0.317854 GTTCCTTTGTGAAGCACGGC 60.318 55.000 0.00 0.00 37.14 5.68
152 153 0.749818 TTCCTTTGTGAAGCACGGCA 60.750 50.000 0.00 0.00 37.14 5.69
153 154 0.749818 TCCTTTGTGAAGCACGGCAA 60.750 50.000 0.00 0.00 37.14 4.52
154 155 0.102120 CCTTTGTGAAGCACGGCAAA 59.898 50.000 0.00 0.00 37.14 3.68
155 156 1.269726 CCTTTGTGAAGCACGGCAAAT 60.270 47.619 0.00 0.00 37.14 2.32
156 157 2.053627 CTTTGTGAAGCACGGCAAATC 58.946 47.619 0.00 0.00 37.14 2.17
157 158 0.313672 TTGTGAAGCACGGCAAATCC 59.686 50.000 0.00 0.00 37.14 3.01
158 159 0.537143 TGTGAAGCACGGCAAATCCT 60.537 50.000 0.00 0.00 37.14 3.24
159 160 0.598065 GTGAAGCACGGCAAATCCTT 59.402 50.000 0.00 0.00 0.00 3.36
160 161 0.597568 TGAAGCACGGCAAATCCTTG 59.402 50.000 0.00 0.00 37.18 3.61
161 162 0.881118 GAAGCACGGCAAATCCTTGA 59.119 50.000 0.00 0.00 36.26 3.02
162 163 1.269448 GAAGCACGGCAAATCCTTGAA 59.731 47.619 0.00 0.00 36.26 2.69
163 164 1.327303 AGCACGGCAAATCCTTGAAA 58.673 45.000 0.00 0.00 36.26 2.69
164 165 1.686052 AGCACGGCAAATCCTTGAAAA 59.314 42.857 0.00 0.00 36.26 2.29
165 166 2.102252 AGCACGGCAAATCCTTGAAAAA 59.898 40.909 0.00 0.00 36.26 1.94
248 249 9.304731 CACAAATTACCATCAAAATCATTCGAT 57.695 29.630 0.00 0.00 0.00 3.59
332 337 5.163622 TGCGGATGAAAATCTTCAATTCTCC 60.164 40.000 0.00 0.00 44.64 3.71
379 384 1.478137 GATTCGCGCTACAGGTACAG 58.522 55.000 5.56 0.00 0.00 2.74
381 386 1.592400 TTCGCGCTACAGGTACAGCT 61.592 55.000 5.56 0.00 35.57 4.24
385 390 1.823976 GCTACAGGTACAGCTCCCC 59.176 63.158 0.00 0.00 34.86 4.81
428 436 2.288825 GCCAATCATCCATTGCATCCTG 60.289 50.000 0.00 0.00 40.75 3.86
741 778 4.047125 CCAGCCCACCACCGGATT 62.047 66.667 9.46 0.00 0.00 3.01
826 866 3.943034 CGTTCCCACGCGCAACAA 61.943 61.111 5.73 0.00 40.18 2.83
827 867 2.353030 GTTCCCACGCGCAACAAC 60.353 61.111 5.73 0.24 0.00 3.32
840 880 1.923864 GCAACAACGAACCAAACCAAG 59.076 47.619 0.00 0.00 0.00 3.61
990 1032 0.033208 AGGAGAGCCAGAGAGACCAG 60.033 60.000 0.00 0.00 36.29 4.00
991 1033 0.033601 GGAGAGCCAGAGAGACCAGA 60.034 60.000 0.00 0.00 0.00 3.86
992 1034 1.392589 GAGAGCCAGAGAGACCAGAG 58.607 60.000 0.00 0.00 0.00 3.35
994 1036 1.675720 GAGCCAGAGAGACCAGAGGC 61.676 65.000 0.00 0.00 42.31 4.70
996 1038 1.305633 CCAGAGAGACCAGAGGCCA 60.306 63.158 5.01 0.00 0.00 5.36
1101 1148 4.436998 GTGACGCTCCCGGACCAG 62.437 72.222 0.73 0.00 39.22 4.00
1257 1313 4.994201 GACGACGACGGCTGCACA 62.994 66.667 12.58 0.00 45.04 4.57
1356 1428 1.000060 GAGCACAAGTACGTGTACCCA 60.000 52.381 14.21 0.00 39.19 4.51
1357 1429 1.413445 AGCACAAGTACGTGTACCCAA 59.587 47.619 14.21 0.00 39.19 4.12
1358 1430 2.038033 AGCACAAGTACGTGTACCCAAT 59.962 45.455 14.21 0.00 39.19 3.16
1359 1431 2.809696 GCACAAGTACGTGTACCCAATT 59.190 45.455 14.21 0.00 39.19 2.32
1393 1465 5.713389 TCTCTTTTGTTCAGCCATCAATCAT 59.287 36.000 0.00 0.00 0.00 2.45
1470 1587 1.167851 CATTCAAGCGGAGAAGCCAA 58.832 50.000 0.00 0.00 38.01 4.52
1560 1699 5.065914 TGACTCTTCTTCCTTGTTGGATTG 58.934 41.667 0.00 0.00 45.68 2.67
1563 1702 2.270352 TCTTCCTTGTTGGATTGCGT 57.730 45.000 0.00 0.00 45.68 5.24
1564 1703 1.879380 TCTTCCTTGTTGGATTGCGTG 59.121 47.619 0.00 0.00 45.68 5.34
1770 1921 1.065410 ACATCACCACCCCTTGACCA 61.065 55.000 0.00 0.00 0.00 4.02
1771 1922 0.609131 CATCACCACCCCTTGACCAC 60.609 60.000 0.00 0.00 0.00 4.16
1772 1923 1.789576 ATCACCACCCCTTGACCACC 61.790 60.000 0.00 0.00 0.00 4.61
1773 1924 3.182996 ACCACCCCTTGACCACCC 61.183 66.667 0.00 0.00 0.00 4.61
1774 1925 3.182263 CCACCCCTTGACCACCCA 61.182 66.667 0.00 0.00 0.00 4.51
1775 1926 2.773527 CCACCCCTTGACCACCCAA 61.774 63.158 0.00 0.00 0.00 4.12
1776 1927 1.228552 CACCCCTTGACCACCCAAG 60.229 63.158 0.00 0.00 42.28 3.61
1777 1928 1.699930 ACCCCTTGACCACCCAAGT 60.700 57.895 0.00 0.00 41.34 3.16
1778 1929 1.074951 CCCCTTGACCACCCAAGTC 59.925 63.158 0.00 0.00 41.34 3.01
1813 1964 2.039216 TCCCTTGTTTAATCAGTCGCCA 59.961 45.455 0.00 0.00 0.00 5.69
1839 1996 6.893020 ACTCCCACAATCTTATCCTAGTTT 57.107 37.500 0.00 0.00 0.00 2.66
1840 1997 7.989947 ACTCCCACAATCTTATCCTAGTTTA 57.010 36.000 0.00 0.00 0.00 2.01
1841 1998 7.793036 ACTCCCACAATCTTATCCTAGTTTAC 58.207 38.462 0.00 0.00 0.00 2.01
1875 2040 7.875041 ACGACGTGTACATTATATCCTACTACT 59.125 37.037 0.00 0.00 0.00 2.57
1876 2041 9.358872 CGACGTGTACATTATATCCTACTACTA 57.641 37.037 0.00 0.00 0.00 1.82
1920 2088 5.157781 CCTTAAGAAGACTCTGACGAACAG 58.842 45.833 3.36 7.75 46.97 3.16
1989 2163 8.255905 TGGTTTAGTGTCTAGCTAGATTTTACC 58.744 37.037 25.74 23.72 34.39 2.85
1994 2168 7.493367 AGTGTCTAGCTAGATTTTACCATCAC 58.507 38.462 25.74 22.17 34.39 3.06
2049 2223 0.461548 ATGTCCGTGTCGATGCAGAT 59.538 50.000 0.00 0.00 0.00 2.90
2050 2224 0.458370 TGTCCGTGTCGATGCAGATG 60.458 55.000 0.00 0.00 0.00 2.90
2051 2225 1.519234 TCCGTGTCGATGCAGATGC 60.519 57.895 0.00 0.00 42.50 3.91
2079 2253 1.523095 GCGTCGCTGTTTCTATGGATC 59.477 52.381 10.68 0.00 0.00 3.36
2133 2314 5.049818 GCTGGATAATCTTGTACAGTGATGC 60.050 44.000 12.26 7.93 0.00 3.91
2159 2340 2.801111 CGCTCCATGAGATGAATGACAG 59.199 50.000 0.00 0.00 0.00 3.51
2164 2345 3.875727 CCATGAGATGAATGACAGGTGTC 59.124 47.826 2.99 2.99 44.97 3.67
2240 2422 1.086696 CTGTGTCATAAACGGCAGGG 58.913 55.000 0.00 0.00 32.87 4.45
2241 2423 0.958382 TGTGTCATAAACGGCAGGGC 60.958 55.000 0.00 0.00 0.00 5.19
2244 2426 0.733150 GTCATAAACGGCAGGGCTTC 59.267 55.000 0.00 0.00 0.00 3.86
2245 2427 0.393808 TCATAAACGGCAGGGCTTCC 60.394 55.000 0.00 0.00 0.00 3.46
2259 2441 4.178169 TTCCCGGGCACGTGTGTT 62.178 61.111 18.49 0.00 38.78 3.32
2271 2453 3.342627 TGTGTTACTGGTGCGCGC 61.343 61.111 27.26 27.26 0.00 6.86
2411 2596 3.129871 GTCTCTATGCCATTCAGCTGAC 58.870 50.000 18.03 5.40 0.00 3.51
2418 2603 0.679002 CCATTCAGCTGACCTGTGGG 60.679 60.000 18.03 7.93 42.38 4.61
2446 2631 2.097954 ACTGCACCGCATTGACAATATG 59.902 45.455 0.00 0.00 38.13 1.78
2447 2632 1.202279 TGCACCGCATTGACAATATGC 60.202 47.619 14.40 14.40 43.80 3.14
2451 2637 3.792956 CACCGCATTGACAATATGCTTTC 59.207 43.478 11.04 0.00 44.78 2.62
2455 2641 4.501559 CGCATTGACAATATGCTTTCTTGG 59.498 41.667 11.04 0.00 44.78 3.61
2472 2658 4.510038 CTTGGTCTTCCACAAGAAATGG 57.490 45.455 0.00 0.00 45.22 3.16
2475 2661 3.636300 TGGTCTTCCACAAGAAATGGTTG 59.364 43.478 0.00 0.00 40.49 3.77
2488 2674 7.603784 ACAAGAAATGGTTGCAATATTTTCTCC 59.396 33.333 22.66 11.10 0.00 3.71
2489 2675 7.486407 AGAAATGGTTGCAATATTTTCTCCT 57.514 32.000 19.41 12.54 0.00 3.69
2490 2676 7.550712 AGAAATGGTTGCAATATTTTCTCCTC 58.449 34.615 19.41 10.59 0.00 3.71
2496 2682 6.039382 GGTTGCAATATTTTCTCCTCGGTAAT 59.961 38.462 0.59 0.00 0.00 1.89
2497 2683 7.227910 GGTTGCAATATTTTCTCCTCGGTAATA 59.772 37.037 0.59 0.00 0.00 0.98
2498 2684 8.617809 GTTGCAATATTTTCTCCTCGGTAATAA 58.382 33.333 0.59 0.00 0.00 1.40
2513 2699 5.924254 TCGGTAATAAATCGATGATCCACAC 59.076 40.000 0.00 0.00 0.00 3.82
2518 2704 6.791887 ATAAATCGATGATCCACACATCAC 57.208 37.500 0.00 0.00 42.68 3.06
2520 2706 3.825143 TCGATGATCCACACATCACAT 57.175 42.857 0.00 0.00 42.68 3.21
2527 2713 1.896465 TCCACACATCACATCACGGTA 59.104 47.619 0.00 0.00 0.00 4.02
2528 2714 1.999735 CCACACATCACATCACGGTAC 59.000 52.381 0.00 0.00 0.00 3.34
2536 2722 3.386486 TCACATCACGGTACAACTTCAC 58.614 45.455 0.00 0.00 0.00 3.18
2537 2723 3.069016 TCACATCACGGTACAACTTCACT 59.931 43.478 0.00 0.00 0.00 3.41
2549 2735 4.631131 ACAACTTCACTGATCAATCGACA 58.369 39.130 0.00 0.00 0.00 4.35
2624 3202 2.906389 ACACCAGAGTTCCATAGCAAGA 59.094 45.455 0.00 0.00 0.00 3.02
2625 3203 3.265791 CACCAGAGTTCCATAGCAAGAC 58.734 50.000 0.00 0.00 0.00 3.01
2626 3204 2.237392 ACCAGAGTTCCATAGCAAGACC 59.763 50.000 0.00 0.00 0.00 3.85
2627 3205 2.503356 CCAGAGTTCCATAGCAAGACCT 59.497 50.000 0.00 0.00 0.00 3.85
2628 3206 3.431486 CCAGAGTTCCATAGCAAGACCTC 60.431 52.174 0.00 0.00 0.00 3.85
2629 3207 2.769095 AGAGTTCCATAGCAAGACCTCC 59.231 50.000 0.00 0.00 0.00 4.30
2630 3208 1.840635 AGTTCCATAGCAAGACCTCCC 59.159 52.381 0.00 0.00 0.00 4.30
2631 3209 1.134068 GTTCCATAGCAAGACCTCCCC 60.134 57.143 0.00 0.00 0.00 4.81
2632 3210 1.048724 TCCATAGCAAGACCTCCCCG 61.049 60.000 0.00 0.00 0.00 5.73
2633 3211 1.227674 CATAGCAAGACCTCCCCGC 60.228 63.158 0.00 0.00 0.00 6.13
2634 3212 1.689233 ATAGCAAGACCTCCCCGCA 60.689 57.895 0.00 0.00 0.00 5.69
2635 3213 1.271840 ATAGCAAGACCTCCCCGCAA 61.272 55.000 0.00 0.00 0.00 4.85
2636 3214 1.485294 TAGCAAGACCTCCCCGCAAA 61.485 55.000 0.00 0.00 0.00 3.68
2637 3215 1.901464 GCAAGACCTCCCCGCAAAA 60.901 57.895 0.00 0.00 0.00 2.44
2638 3216 1.250840 GCAAGACCTCCCCGCAAAAT 61.251 55.000 0.00 0.00 0.00 1.82
2639 3217 1.953311 GCAAGACCTCCCCGCAAAATA 60.953 52.381 0.00 0.00 0.00 1.40
2640 3218 2.442413 CAAGACCTCCCCGCAAAATAA 58.558 47.619 0.00 0.00 0.00 1.40
2641 3219 2.823154 CAAGACCTCCCCGCAAAATAAA 59.177 45.455 0.00 0.00 0.00 1.40
2642 3220 3.163616 AGACCTCCCCGCAAAATAAAA 57.836 42.857 0.00 0.00 0.00 1.52
2643 3221 3.502356 AGACCTCCCCGCAAAATAAAAA 58.498 40.909 0.00 0.00 0.00 1.94
2644 3222 3.509967 AGACCTCCCCGCAAAATAAAAAG 59.490 43.478 0.00 0.00 0.00 2.27
2645 3223 3.236047 ACCTCCCCGCAAAATAAAAAGT 58.764 40.909 0.00 0.00 0.00 2.66
2646 3224 4.409187 ACCTCCCCGCAAAATAAAAAGTA 58.591 39.130 0.00 0.00 0.00 2.24
2647 3225 4.219070 ACCTCCCCGCAAAATAAAAAGTAC 59.781 41.667 0.00 0.00 0.00 2.73
2648 3226 4.381185 CCTCCCCGCAAAATAAAAAGTACC 60.381 45.833 0.00 0.00 0.00 3.34
2649 3227 4.150359 TCCCCGCAAAATAAAAAGTACCA 58.850 39.130 0.00 0.00 0.00 3.25
2650 3228 4.773149 TCCCCGCAAAATAAAAAGTACCAT 59.227 37.500 0.00 0.00 0.00 3.55
2651 3229 5.950549 TCCCCGCAAAATAAAAAGTACCATA 59.049 36.000 0.00 0.00 0.00 2.74
2652 3230 6.095720 TCCCCGCAAAATAAAAAGTACCATAG 59.904 38.462 0.00 0.00 0.00 2.23
2653 3231 5.746721 CCCGCAAAATAAAAAGTACCATAGC 59.253 40.000 0.00 0.00 0.00 2.97
2654 3232 6.326375 CCGCAAAATAAAAAGTACCATAGCA 58.674 36.000 0.00 0.00 0.00 3.49
2655 3233 6.809196 CCGCAAAATAAAAAGTACCATAGCAA 59.191 34.615 0.00 0.00 0.00 3.91
2656 3234 7.329717 CCGCAAAATAAAAAGTACCATAGCAAA 59.670 33.333 0.00 0.00 0.00 3.68
2754 3333 4.381505 CCCCCATACAGCAACAAATACAAC 60.382 45.833 0.00 0.00 0.00 3.32
2758 3337 5.858049 CCATACAGCAACAAATACAACTGTG 59.142 40.000 0.00 0.00 38.70 3.66
2762 3341 6.494842 ACAGCAACAAATACAACTGTGTAAG 58.505 36.000 0.00 0.00 43.41 2.34
2763 3342 5.399301 CAGCAACAAATACAACTGTGTAAGC 59.601 40.000 0.00 0.00 43.41 3.09
2764 3343 4.378616 GCAACAAATACAACTGTGTAAGCG 59.621 41.667 0.00 0.00 43.41 4.68
2765 3344 5.507077 CAACAAATACAACTGTGTAAGCGT 58.493 37.500 0.00 0.00 43.41 5.07
2766 3345 6.651308 CAACAAATACAACTGTGTAAGCGTA 58.349 36.000 0.00 0.00 43.41 4.42
2767 3346 7.295201 CAACAAATACAACTGTGTAAGCGTAT 58.705 34.615 0.00 0.00 43.41 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.998667 CGCGACCGCTCAATCTTC 59.001 61.111 12.69 0.00 39.32 2.87
18 19 2.345942 GTGTTTTGTAGAGCGCTCTAGC 59.654 50.000 40.20 32.30 42.31 3.42
19 20 2.924290 GGTGTTTTGTAGAGCGCTCTAG 59.076 50.000 40.20 0.00 42.31 2.43
20 21 2.561419 AGGTGTTTTGTAGAGCGCTCTA 59.439 45.455 37.07 37.07 40.93 2.43
21 22 1.344763 AGGTGTTTTGTAGAGCGCTCT 59.655 47.619 39.29 39.29 43.40 4.09
22 23 1.461127 CAGGTGTTTTGTAGAGCGCTC 59.539 52.381 30.01 30.01 0.00 5.03
23 24 1.070134 TCAGGTGTTTTGTAGAGCGCT 59.930 47.619 11.27 11.27 0.00 5.92
24 25 1.508632 TCAGGTGTTTTGTAGAGCGC 58.491 50.000 0.00 0.00 0.00 5.92
25 26 2.345641 CGATCAGGTGTTTTGTAGAGCG 59.654 50.000 0.00 0.00 0.00 5.03
26 27 2.094417 GCGATCAGGTGTTTTGTAGAGC 59.906 50.000 0.00 0.00 0.00 4.09
27 28 2.673368 GGCGATCAGGTGTTTTGTAGAG 59.327 50.000 0.00 0.00 0.00 2.43
28 29 2.614481 GGGCGATCAGGTGTTTTGTAGA 60.614 50.000 0.00 0.00 0.00 2.59
29 30 1.737793 GGGCGATCAGGTGTTTTGTAG 59.262 52.381 0.00 0.00 0.00 2.74
30 31 1.612199 GGGGCGATCAGGTGTTTTGTA 60.612 52.381 0.00 0.00 0.00 2.41
31 32 0.893727 GGGGCGATCAGGTGTTTTGT 60.894 55.000 0.00 0.00 0.00 2.83
32 33 0.609131 AGGGGCGATCAGGTGTTTTG 60.609 55.000 0.00 0.00 0.00 2.44
33 34 0.322546 GAGGGGCGATCAGGTGTTTT 60.323 55.000 0.00 0.00 0.00 2.43
34 35 1.201429 AGAGGGGCGATCAGGTGTTT 61.201 55.000 0.00 0.00 0.00 2.83
35 36 0.325296 TAGAGGGGCGATCAGGTGTT 60.325 55.000 0.00 0.00 0.00 3.32
36 37 1.043673 GTAGAGGGGCGATCAGGTGT 61.044 60.000 0.00 0.00 0.00 4.16
37 38 1.742768 GTAGAGGGGCGATCAGGTG 59.257 63.158 0.00 0.00 0.00 4.00
38 39 1.457831 GGTAGAGGGGCGATCAGGT 60.458 63.158 0.00 0.00 0.00 4.00
39 40 2.565645 CGGTAGAGGGGCGATCAGG 61.566 68.421 0.00 0.00 0.00 3.86
40 41 0.536687 TACGGTAGAGGGGCGATCAG 60.537 60.000 0.00 0.00 0.00 2.90
41 42 0.820891 GTACGGTAGAGGGGCGATCA 60.821 60.000 0.00 0.00 0.00 2.92
42 43 0.820891 TGTACGGTAGAGGGGCGATC 60.821 60.000 0.00 0.00 0.00 3.69
43 44 0.822532 CTGTACGGTAGAGGGGCGAT 60.823 60.000 4.48 0.00 0.00 4.58
44 45 1.452651 CTGTACGGTAGAGGGGCGA 60.453 63.158 4.48 0.00 0.00 5.54
45 46 1.033746 TTCTGTACGGTAGAGGGGCG 61.034 60.000 11.86 0.00 0.00 6.13
46 47 1.340568 GATTCTGTACGGTAGAGGGGC 59.659 57.143 11.86 0.00 0.00 5.80
47 48 2.361438 GTGATTCTGTACGGTAGAGGGG 59.639 54.545 11.86 0.00 0.00 4.79
48 49 3.021695 TGTGATTCTGTACGGTAGAGGG 58.978 50.000 11.86 0.00 0.00 4.30
49 50 4.398358 TCTTGTGATTCTGTACGGTAGAGG 59.602 45.833 11.86 0.00 0.00 3.69
50 51 5.449314 CCTCTTGTGATTCTGTACGGTAGAG 60.449 48.000 5.99 5.99 0.00 2.43
51 52 4.398358 CCTCTTGTGATTCTGTACGGTAGA 59.602 45.833 0.64 0.00 0.00 2.59
52 53 4.673441 CCTCTTGTGATTCTGTACGGTAG 58.327 47.826 0.64 0.00 0.00 3.18
53 54 3.119245 GCCTCTTGTGATTCTGTACGGTA 60.119 47.826 0.64 0.00 0.00 4.02
54 55 2.353803 GCCTCTTGTGATTCTGTACGGT 60.354 50.000 0.64 0.00 0.00 4.83
55 56 2.271800 GCCTCTTGTGATTCTGTACGG 58.728 52.381 0.00 0.00 0.00 4.02
56 57 1.920574 CGCCTCTTGTGATTCTGTACG 59.079 52.381 0.00 0.00 0.00 3.67
57 58 2.271800 CCGCCTCTTGTGATTCTGTAC 58.728 52.381 0.00 0.00 0.00 2.90
58 59 1.207089 CCCGCCTCTTGTGATTCTGTA 59.793 52.381 0.00 0.00 0.00 2.74
59 60 0.036010 CCCGCCTCTTGTGATTCTGT 60.036 55.000 0.00 0.00 0.00 3.41
60 61 0.745845 CCCCGCCTCTTGTGATTCTG 60.746 60.000 0.00 0.00 0.00 3.02
61 62 1.201429 ACCCCGCCTCTTGTGATTCT 61.201 55.000 0.00 0.00 0.00 2.40
62 63 0.322546 AACCCCGCCTCTTGTGATTC 60.323 55.000 0.00 0.00 0.00 2.52
63 64 0.322546 GAACCCCGCCTCTTGTGATT 60.323 55.000 0.00 0.00 0.00 2.57
64 65 1.299976 GAACCCCGCCTCTTGTGAT 59.700 57.895 0.00 0.00 0.00 3.06
65 66 2.144078 TGAACCCCGCCTCTTGTGA 61.144 57.895 0.00 0.00 0.00 3.58
66 67 1.966451 GTGAACCCCGCCTCTTGTG 60.966 63.158 0.00 0.00 0.00 3.33
67 68 2.147387 AGTGAACCCCGCCTCTTGT 61.147 57.895 0.00 0.00 0.00 3.16
68 69 1.672356 CAGTGAACCCCGCCTCTTG 60.672 63.158 0.00 0.00 0.00 3.02
69 70 0.834687 TACAGTGAACCCCGCCTCTT 60.835 55.000 0.00 0.00 0.00 2.85
70 71 0.617820 ATACAGTGAACCCCGCCTCT 60.618 55.000 0.00 0.00 0.00 3.69
71 72 0.179081 GATACAGTGAACCCCGCCTC 60.179 60.000 0.00 0.00 0.00 4.70
72 73 0.617820 AGATACAGTGAACCCCGCCT 60.618 55.000 0.00 0.00 0.00 5.52
73 74 1.117150 TAGATACAGTGAACCCCGCC 58.883 55.000 0.00 0.00 0.00 6.13
74 75 2.973694 TTAGATACAGTGAACCCCGC 57.026 50.000 0.00 0.00 0.00 6.13
75 76 6.649557 GGAATTATTAGATACAGTGAACCCCG 59.350 42.308 0.00 0.00 0.00 5.73
76 77 7.746703 AGGAATTATTAGATACAGTGAACCCC 58.253 38.462 0.00 0.00 0.00 4.95
77 78 9.930693 CTAGGAATTATTAGATACAGTGAACCC 57.069 37.037 0.00 0.00 0.00 4.11
78 79 9.930693 CCTAGGAATTATTAGATACAGTGAACC 57.069 37.037 1.05 0.00 0.00 3.62
92 93 9.506042 AACAATGGGATTTTCCTAGGAATTATT 57.494 29.630 24.82 14.67 36.57 1.40
93 94 8.927411 CAACAATGGGATTTTCCTAGGAATTAT 58.073 33.333 24.82 19.63 36.57 1.28
94 95 7.147742 GCAACAATGGGATTTTCCTAGGAATTA 60.148 37.037 24.82 15.93 36.57 1.40
95 96 6.352137 GCAACAATGGGATTTTCCTAGGAATT 60.352 38.462 24.82 15.27 36.57 2.17
96 97 5.129320 GCAACAATGGGATTTTCCTAGGAAT 59.871 40.000 24.82 11.30 36.57 3.01
97 98 4.466015 GCAACAATGGGATTTTCCTAGGAA 59.534 41.667 20.72 20.72 36.57 3.36
98 99 4.023291 GCAACAATGGGATTTTCCTAGGA 58.977 43.478 7.62 7.62 36.57 2.94
99 100 3.181487 CGCAACAATGGGATTTTCCTAGG 60.181 47.826 0.82 0.82 41.79 3.02
100 101 3.694072 TCGCAACAATGGGATTTTCCTAG 59.306 43.478 0.00 0.00 42.90 3.02
101 102 3.691575 TCGCAACAATGGGATTTTCCTA 58.308 40.909 0.00 0.00 42.90 2.94
102 103 2.493278 CTCGCAACAATGGGATTTTCCT 59.507 45.455 0.00 0.00 46.10 3.36
103 104 2.417243 CCTCGCAACAATGGGATTTTCC 60.417 50.000 0.00 0.00 46.10 3.13
104 105 2.491693 TCCTCGCAACAATGGGATTTTC 59.508 45.455 0.00 0.00 46.10 2.29
105 106 2.524306 TCCTCGCAACAATGGGATTTT 58.476 42.857 0.00 0.00 46.10 1.82
106 107 2.214376 TCCTCGCAACAATGGGATTT 57.786 45.000 0.00 0.00 46.10 2.17
107 108 2.428171 CAATCCTCGCAACAATGGGATT 59.572 45.455 0.00 0.00 46.10 3.01
108 109 2.026641 CAATCCTCGCAACAATGGGAT 58.973 47.619 0.00 0.00 46.10 3.85
109 110 1.271871 ACAATCCTCGCAACAATGGGA 60.272 47.619 0.00 0.00 45.25 4.37
110 111 1.176527 ACAATCCTCGCAACAATGGG 58.823 50.000 0.00 0.00 40.66 4.00
111 112 3.440173 ACTTACAATCCTCGCAACAATGG 59.560 43.478 0.00 0.00 0.00 3.16
112 113 4.685169 ACTTACAATCCTCGCAACAATG 57.315 40.909 0.00 0.00 0.00 2.82
113 114 4.156008 GGAACTTACAATCCTCGCAACAAT 59.844 41.667 0.00 0.00 32.75 2.71
114 115 3.500680 GGAACTTACAATCCTCGCAACAA 59.499 43.478 0.00 0.00 32.75 2.83
115 116 3.071479 GGAACTTACAATCCTCGCAACA 58.929 45.455 0.00 0.00 32.75 3.33
116 117 3.335579 AGGAACTTACAATCCTCGCAAC 58.664 45.455 0.00 0.00 42.44 4.17
117 118 3.695830 AGGAACTTACAATCCTCGCAA 57.304 42.857 0.00 0.00 42.44 4.85
131 132 1.308998 CCGTGCTTCACAAAGGAACT 58.691 50.000 0.00 0.00 34.32 3.01
132 133 0.317854 GCCGTGCTTCACAAAGGAAC 60.318 55.000 0.00 0.00 34.32 3.62
133 134 0.749818 TGCCGTGCTTCACAAAGGAA 60.750 50.000 0.00 0.00 34.32 3.36
134 135 0.749818 TTGCCGTGCTTCACAAAGGA 60.750 50.000 0.00 0.00 33.40 3.36
135 136 0.102120 TTTGCCGTGCTTCACAAAGG 59.898 50.000 0.00 0.00 33.40 3.11
136 137 2.053627 GATTTGCCGTGCTTCACAAAG 58.946 47.619 0.00 0.00 35.65 2.77
137 138 1.269517 GGATTTGCCGTGCTTCACAAA 60.270 47.619 0.00 0.00 36.53 2.83
138 139 0.313672 GGATTTGCCGTGCTTCACAA 59.686 50.000 0.00 0.00 33.40 3.33
139 140 0.537143 AGGATTTGCCGTGCTTCACA 60.537 50.000 0.00 0.00 43.43 3.58
140 141 0.598065 AAGGATTTGCCGTGCTTCAC 59.402 50.000 0.00 0.00 43.43 3.18
141 142 0.597568 CAAGGATTTGCCGTGCTTCA 59.402 50.000 0.00 0.00 43.43 3.02
142 143 0.881118 TCAAGGATTTGCCGTGCTTC 59.119 50.000 0.00 0.00 44.67 3.86
143 144 1.327303 TTCAAGGATTTGCCGTGCTT 58.673 45.000 0.00 0.00 44.67 3.91
144 145 1.327303 TTTCAAGGATTTGCCGTGCT 58.673 45.000 0.00 0.00 44.67 4.40
145 146 2.147436 TTTTCAAGGATTTGCCGTGC 57.853 45.000 0.00 0.00 44.67 5.34
201 202 5.529430 TGTGTACTCGTGGATGACAATTTTT 59.471 36.000 0.00 0.00 0.00 1.94
202 203 5.060506 TGTGTACTCGTGGATGACAATTTT 58.939 37.500 0.00 0.00 0.00 1.82
203 204 4.637276 TGTGTACTCGTGGATGACAATTT 58.363 39.130 0.00 0.00 0.00 1.82
204 205 4.265904 TGTGTACTCGTGGATGACAATT 57.734 40.909 0.00 0.00 0.00 2.32
205 206 3.953712 TGTGTACTCGTGGATGACAAT 57.046 42.857 0.00 0.00 0.00 2.71
248 249 0.913934 TGCTGGGAGGGCATGTCTAA 60.914 55.000 0.00 0.00 34.56 2.10
250 251 1.792757 TTTGCTGGGAGGGCATGTCT 61.793 55.000 0.00 0.00 39.54 3.41
253 254 2.703798 CGTTTGCTGGGAGGGCATG 61.704 63.158 0.00 0.00 39.54 4.06
305 310 6.320672 AGAATTGAAGATTTTCATCCGCATCT 59.679 34.615 0.00 0.00 42.60 2.90
311 316 6.683974 TCGGAGAATTGAAGATTTTCATCC 57.316 37.500 0.00 3.28 42.60 3.51
317 322 6.889722 TGGGTTTATCGGAGAATTGAAGATTT 59.110 34.615 0.00 0.00 43.58 2.17
332 337 4.389374 AGATTGCTGGTATGGGTTTATCG 58.611 43.478 0.00 0.00 0.00 2.92
379 384 0.321298 TAAGTTCGCTGTTGGGGAGC 60.321 55.000 0.00 0.00 38.14 4.70
381 386 2.617021 GGAATAAGTTCGCTGTTGGGGA 60.617 50.000 0.00 0.00 35.10 4.81
385 390 2.073816 ACGGGAATAAGTTCGCTGTTG 58.926 47.619 4.17 0.00 43.09 3.33
428 436 3.141398 TGAACAGACAGAAAGATGTGCC 58.859 45.455 0.00 0.00 32.25 5.01
825 865 0.102300 GCTGCTTGGTTTGGTTCGTT 59.898 50.000 0.00 0.00 0.00 3.85
826 866 1.733526 GCTGCTTGGTTTGGTTCGT 59.266 52.632 0.00 0.00 0.00 3.85
827 867 1.007387 GGCTGCTTGGTTTGGTTCG 60.007 57.895 0.00 0.00 0.00 3.95
990 1032 1.751927 CAAGTCCATGGCTGGCCTC 60.752 63.158 6.96 0.00 42.80 4.70
991 1033 1.207488 TACAAGTCCATGGCTGGCCT 61.207 55.000 6.96 0.00 42.80 5.19
992 1034 1.032114 GTACAAGTCCATGGCTGGCC 61.032 60.000 6.96 4.43 42.80 5.36
994 1036 2.420129 GGTAGTACAAGTCCATGGCTGG 60.420 54.545 6.96 7.94 44.64 4.85
996 1038 2.501723 CTGGTAGTACAAGTCCATGGCT 59.498 50.000 6.96 4.72 0.00 4.75
1356 1428 7.791029 TGAACAAAAGAGAAGGGCTTTTAATT 58.209 30.769 0.00 0.00 42.03 1.40
1357 1429 7.360113 TGAACAAAAGAGAAGGGCTTTTAAT 57.640 32.000 0.00 0.00 42.03 1.40
1358 1430 6.682861 GCTGAACAAAAGAGAAGGGCTTTTAA 60.683 38.462 0.00 0.00 42.03 1.52
1359 1431 5.221244 GCTGAACAAAAGAGAAGGGCTTTTA 60.221 40.000 0.00 0.00 42.03 1.52
1470 1587 2.123640 GGCCTAGGAGGAGCTCGT 60.124 66.667 14.75 9.04 37.67 4.18
1534 1651 3.817647 CCAACAAGGAAGAAGAGTCAAGG 59.182 47.826 0.00 0.00 41.22 3.61
1573 1712 4.374702 GAACAGCCTGCGCACACG 62.375 66.667 5.66 0.00 44.07 4.49
1788 1939 3.125316 CGACTGATTAAACAAGGGAGTGC 59.875 47.826 0.00 0.00 0.00 4.40
1813 1964 6.684538 ACTAGGATAAGATTGTGGGAGTAGT 58.315 40.000 0.00 0.00 0.00 2.73
1839 1996 5.550232 ATGTACACGTCGTCATGTAAGTA 57.450 39.130 0.00 0.00 33.23 2.24
1840 1997 3.902261 TGTACACGTCGTCATGTAAGT 57.098 42.857 0.00 0.00 33.23 2.24
1841 1998 8.723777 ATATAATGTACACGTCGTCATGTAAG 57.276 34.615 0.00 0.00 33.23 2.34
1850 2007 8.249327 AGTAGTAGGATATAATGTACACGTCG 57.751 38.462 0.00 0.00 0.00 5.12
1875 2040 7.205515 AGGCTAAGTCTAAGTACTAGTGGTA 57.794 40.000 5.39 0.00 0.00 3.25
1876 2041 6.077202 AGGCTAAGTCTAAGTACTAGTGGT 57.923 41.667 5.39 0.00 0.00 4.16
1877 2042 8.517062 TTAAGGCTAAGTCTAAGTACTAGTGG 57.483 38.462 5.39 0.00 0.00 4.00
1948 2116 3.142838 CCATTTGCTGGCCGGGAG 61.143 66.667 15.02 0.00 38.47 4.30
1989 2163 3.126858 CCATTAGTTGTTCCACCGTGATG 59.873 47.826 0.00 0.00 0.00 3.07
1992 2166 1.810151 CCCATTAGTTGTTCCACCGTG 59.190 52.381 0.00 0.00 0.00 4.94
1994 2168 1.271707 ACCCCATTAGTTGTTCCACCG 60.272 52.381 0.00 0.00 0.00 4.94
2031 2205 0.458370 CATCTGCATCGACACGGACA 60.458 55.000 0.34 0.00 0.00 4.02
2052 2226 4.609018 AACAGCGACGCCTGCACT 62.609 61.111 17.79 0.00 36.29 4.40
2053 2227 3.579626 GAAACAGCGACGCCTGCAC 62.580 63.158 17.79 2.09 36.29 4.57
2140 2321 4.127907 CACCTGTCATTCATCTCATGGAG 58.872 47.826 0.00 0.00 0.00 3.86
2159 2340 4.077184 TCCATCACCGGCGACACC 62.077 66.667 9.30 0.00 0.00 4.16
2187 2368 0.451135 GACGAAACACATGTCGCAGC 60.451 55.000 0.00 0.00 40.95 5.25
2193 2374 1.554042 GCCGACGACGAAACACATGT 61.554 55.000 9.28 0.00 42.66 3.21
2241 2423 2.718747 TAACACACGTGCCCGGGAAG 62.719 60.000 29.31 17.06 41.01 3.46
2244 2426 3.045492 GTAACACACGTGCCCGGG 61.045 66.667 19.09 19.09 45.16 5.73
2245 2427 2.029964 AGTAACACACGTGCCCGG 59.970 61.111 17.22 5.49 38.78 5.73
2259 2441 4.308458 AAGTGGCGCGCACCAGTA 62.308 61.111 34.42 8.38 42.77 2.74
2339 2521 4.323180 GGTGGGGTTTCTTTTGTTTTGAGT 60.323 41.667 0.00 0.00 0.00 3.41
2411 2596 4.704833 CAGTCCACGCCCCACAGG 62.705 72.222 0.00 0.00 39.47 4.00
2455 2641 3.068024 TGCAACCATTTCTTGTGGAAGAC 59.932 43.478 0.00 0.00 37.97 3.01
2472 2658 4.965119 ACCGAGGAGAAAATATTGCAAC 57.035 40.909 0.00 0.00 0.00 4.17
2475 2661 9.827411 GATTTATTACCGAGGAGAAAATATTGC 57.173 33.333 0.00 0.00 0.00 3.56
2488 2674 6.089551 GTGTGGATCATCGATTTATTACCGAG 59.910 42.308 0.00 0.00 35.70 4.63
2489 2675 5.924254 GTGTGGATCATCGATTTATTACCGA 59.076 40.000 0.00 0.00 36.72 4.69
2490 2676 5.694458 TGTGTGGATCATCGATTTATTACCG 59.306 40.000 0.00 0.00 0.00 4.02
2496 2682 5.669477 TGTGATGTGTGGATCATCGATTTA 58.331 37.500 0.00 0.00 42.96 1.40
2497 2683 4.516323 TGTGATGTGTGGATCATCGATTT 58.484 39.130 0.00 0.00 42.96 2.17
2498 2684 4.141233 TGTGATGTGTGGATCATCGATT 57.859 40.909 0.00 0.00 42.96 3.34
2513 2699 3.993736 TGAAGTTGTACCGTGATGTGATG 59.006 43.478 0.00 0.00 0.00 3.07
2518 2704 3.649073 TCAGTGAAGTTGTACCGTGATG 58.351 45.455 0.00 0.00 0.00 3.07
2520 2706 3.319689 TGATCAGTGAAGTTGTACCGTGA 59.680 43.478 0.00 0.00 0.00 4.35
2527 2713 4.449068 GTGTCGATTGATCAGTGAAGTTGT 59.551 41.667 0.00 0.00 0.00 3.32
2528 2714 4.143030 GGTGTCGATTGATCAGTGAAGTTG 60.143 45.833 0.00 0.00 0.00 3.16
2536 2722 2.158914 TGATGGGGTGTCGATTGATCAG 60.159 50.000 0.00 0.00 0.00 2.90
2537 2723 1.836802 TGATGGGGTGTCGATTGATCA 59.163 47.619 0.00 0.00 0.00 2.92
2549 2735 7.454380 TGAATTTTGATTTACTTCTGATGGGGT 59.546 33.333 0.00 0.00 0.00 4.95
2596 3174 6.116126 GCTATGGAACTCTGGTGTCTATTTT 58.884 40.000 0.00 0.00 0.00 1.82
2606 3184 2.503356 AGGTCTTGCTATGGAACTCTGG 59.497 50.000 0.00 0.00 0.00 3.86
2613 3191 1.048724 CGGGGAGGTCTTGCTATGGA 61.049 60.000 0.00 0.00 0.00 3.41
2624 3202 3.236047 ACTTTTTATTTTGCGGGGAGGT 58.764 40.909 0.00 0.00 0.00 3.85
2625 3203 3.953712 ACTTTTTATTTTGCGGGGAGG 57.046 42.857 0.00 0.00 0.00 4.30
2626 3204 4.218852 TGGTACTTTTTATTTTGCGGGGAG 59.781 41.667 0.00 0.00 0.00 4.30
2627 3205 4.150359 TGGTACTTTTTATTTTGCGGGGA 58.850 39.130 0.00 0.00 0.00 4.81
2628 3206 4.522722 TGGTACTTTTTATTTTGCGGGG 57.477 40.909 0.00 0.00 0.00 5.73
2629 3207 5.746721 GCTATGGTACTTTTTATTTTGCGGG 59.253 40.000 0.00 0.00 0.00 6.13
2630 3208 6.326375 TGCTATGGTACTTTTTATTTTGCGG 58.674 36.000 0.00 0.00 0.00 5.69
2631 3209 7.804614 TTGCTATGGTACTTTTTATTTTGCG 57.195 32.000 0.00 0.00 0.00 4.85
2677 3255 3.813166 TCGCCCAGAAAACTTCTAAACAG 59.187 43.478 0.00 0.00 38.11 3.16


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

AutoCloner maintained by Alex Coulton.