Multiple sequence alignment - TraesCS5A01G384700

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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 TraesCS5A01G384700 chr5A 100.000 2675 0 0 1 2675 582609569 582606895 0.000000e+00 4940.0
1 TraesCS5A01G384700 chr5A 85.156 1280 96 39 411 1656 582401766 582400547 0.000000e+00 1225.0
2 TraesCS5A01G384700 chr5A 92.958 71 1 1 9 75 582551726 582551656 1.690000e-17 100.0
3 TraesCS5A01G384700 chr5A 85.333 75 7 2 1694 1767 582629851 582629780 1.030000e-09 75.0
4 TraesCS5A01G384700 chr5D 85.060 1419 109 41 308 1690 462362967 462361616 0.000000e+00 1351.0
5 TraesCS5A01G384700 chr5D 85.593 1298 103 47 411 1656 462093125 462091860 0.000000e+00 1284.0
6 TraesCS5A01G384700 chr5D 83.737 578 38 18 1814 2361 462361605 462361054 1.850000e-136 496.0
7 TraesCS5A01G384700 chr5D 94.332 247 12 2 2429 2675 462356655 462356411 6.990000e-101 377.0
8 TraesCS5A01G384700 chr5D 85.333 75 7 2 1694 1767 462454089 462454018 1.030000e-09 75.0
9 TraesCS5A01G384700 chr5D 100.000 30 0 0 2237 2266 462352850 462352821 3.720000e-04 56.5
10 TraesCS5A01G384700 chr5B 88.406 1035 77 20 639 1656 568421543 568420535 0.000000e+00 1206.0
11 TraesCS5A01G384700 chr5B 87.387 777 67 14 936 1697 568734188 568733428 0.000000e+00 863.0
12 TraesCS5A01G384700 chr5B 93.274 446 21 3 2231 2675 568732949 568732512 0.000000e+00 649.0
13 TraesCS5A01G384700 chr5B 81.481 486 35 25 353 809 568734651 568734192 5.480000e-92 348.0
14 TraesCS5A01G384700 chr5B 86.893 206 20 6 171 369 568735270 568735065 9.640000e-55 224.0
15 TraesCS5A01G384700 chr5B 81.659 229 21 12 411 623 568428279 568428056 1.270000e-38 171.0
16 TraesCS5A01G384700 chr5B 91.579 95 6 2 9 103 568515280 568515188 2.160000e-26 130.0
17 TraesCS5A01G384700 chr5B 88.000 75 5 2 1694 1767 568819265 568819194 4.740000e-13 86.1
18 TraesCS5A01G384700 chr5B 92.683 41 3 0 2227 2267 568803740 568803700 2.880000e-05 60.2
19 TraesCS5A01G384700 chr2D 100.000 31 0 0 1336 1366 623330308 623330338 1.030000e-04 58.4


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 TraesCS5A01G384700 chr5A 582606895 582609569 2674 True 4940.00 4940 100.00000 1 2675 1 chr5A.!!$R3 2674
1 TraesCS5A01G384700 chr5A 582400547 582401766 1219 True 1225.00 1225 85.15600 411 1656 1 chr5A.!!$R1 1245
2 TraesCS5A01G384700 chr5D 462091860 462093125 1265 True 1284.00 1284 85.59300 411 1656 1 chr5D.!!$R1 1245
3 TraesCS5A01G384700 chr5D 462361054 462362967 1913 True 923.50 1351 84.39850 308 2361 2 chr5D.!!$R4 2053
4 TraesCS5A01G384700 chr5D 462352821 462356655 3834 True 216.75 377 97.16600 2237 2675 2 chr5D.!!$R3 438
5 TraesCS5A01G384700 chr5B 568420535 568421543 1008 True 1206.00 1206 88.40600 639 1656 1 chr5B.!!$R1 1017
6 TraesCS5A01G384700 chr5B 568732512 568735270 2758 True 521.00 863 87.25875 171 2675 4 chr5B.!!$R6 2504

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
38 39 0.036875 AGAAGGGAGGGAAGCAAACG 59.963 55.0 0.0 0.0 0.00 3.60 F
121 122 0.039911 AGGACTTCTACTCCTGCGGT 59.960 55.0 0.0 0.0 36.73 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 1661 0.029834 CGAGCAGCAAAAGCAACAGT 59.970 50.0 0.00 0.0 0.0 3.55 R
1700 2244 0.040958 CAGCGCCAACACAGTTTCTC 60.041 55.0 2.29 0.0 0.0 2.87 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 2.283676 GTCTGGGGACGGTGGAGA 60.284 66.667 0.00 0.00 38.16 3.71
22 23 1.911766 GTCTGGGGACGGTGGAGAA 60.912 63.158 0.00 0.00 38.16 2.87
23 24 1.609501 TCTGGGGACGGTGGAGAAG 60.610 63.158 0.00 0.00 38.16 2.85
24 25 2.606519 TGGGGACGGTGGAGAAGG 60.607 66.667 0.00 0.00 0.00 3.46
25 26 3.400054 GGGGACGGTGGAGAAGGG 61.400 72.222 0.00 0.00 0.00 3.95
26 27 2.284405 GGGACGGTGGAGAAGGGA 60.284 66.667 0.00 0.00 0.00 4.20
27 28 2.359967 GGGACGGTGGAGAAGGGAG 61.360 68.421 0.00 0.00 0.00 4.30
28 29 2.359967 GGACGGTGGAGAAGGGAGG 61.360 68.421 0.00 0.00 0.00 4.30
29 30 2.284699 ACGGTGGAGAAGGGAGGG 60.285 66.667 0.00 0.00 0.00 4.30
30 31 2.038975 CGGTGGAGAAGGGAGGGA 59.961 66.667 0.00 0.00 0.00 4.20
31 32 1.612442 CGGTGGAGAAGGGAGGGAA 60.612 63.158 0.00 0.00 0.00 3.97
32 33 1.617947 CGGTGGAGAAGGGAGGGAAG 61.618 65.000 0.00 0.00 0.00 3.46
33 34 1.604915 GTGGAGAAGGGAGGGAAGC 59.395 63.158 0.00 0.00 0.00 3.86
34 35 1.160870 TGGAGAAGGGAGGGAAGCA 59.839 57.895 0.00 0.00 0.00 3.91
35 36 0.475632 TGGAGAAGGGAGGGAAGCAA 60.476 55.000 0.00 0.00 0.00 3.91
36 37 0.698818 GGAGAAGGGAGGGAAGCAAA 59.301 55.000 0.00 0.00 0.00 3.68
37 38 1.614583 GGAGAAGGGAGGGAAGCAAAC 60.615 57.143 0.00 0.00 0.00 2.93
38 39 0.036875 AGAAGGGAGGGAAGCAAACG 59.963 55.000 0.00 0.00 0.00 3.60
39 40 0.960861 GAAGGGAGGGAAGCAAACGG 60.961 60.000 0.00 0.00 0.00 4.44
40 41 1.716028 AAGGGAGGGAAGCAAACGGT 61.716 55.000 0.00 0.00 0.00 4.83
41 42 1.228459 GGGAGGGAAGCAAACGGTT 60.228 57.895 0.00 0.00 0.00 4.44
42 43 0.826256 GGGAGGGAAGCAAACGGTTT 60.826 55.000 0.00 0.00 0.00 3.27
43 44 1.037493 GGAGGGAAGCAAACGGTTTT 58.963 50.000 2.79 0.00 0.00 2.43
44 45 1.411246 GGAGGGAAGCAAACGGTTTTT 59.589 47.619 2.79 0.00 0.00 1.94
45 46 2.469826 GAGGGAAGCAAACGGTTTTTG 58.530 47.619 2.79 0.00 0.00 2.44
46 47 1.828595 AGGGAAGCAAACGGTTTTTGT 59.171 42.857 2.79 0.00 0.00 2.83
47 48 2.235155 AGGGAAGCAAACGGTTTTTGTT 59.765 40.909 2.79 0.00 0.00 2.83
48 49 3.004171 GGGAAGCAAACGGTTTTTGTTT 58.996 40.909 2.79 0.00 40.01 2.83
49 50 3.437395 GGGAAGCAAACGGTTTTTGTTTT 59.563 39.130 2.79 0.00 37.44 2.43
50 51 4.436317 GGGAAGCAAACGGTTTTTGTTTTC 60.436 41.667 2.79 0.00 37.44 2.29
51 52 4.390603 GGAAGCAAACGGTTTTTGTTTTCT 59.609 37.500 2.79 0.00 37.44 2.52
52 53 5.106869 GGAAGCAAACGGTTTTTGTTTTCTT 60.107 36.000 2.79 3.76 42.59 2.52
53 54 5.933187 AGCAAACGGTTTTTGTTTTCTTT 57.067 30.435 2.79 0.00 37.44 2.52
54 55 5.684850 AGCAAACGGTTTTTGTTTTCTTTG 58.315 33.333 2.79 0.00 37.44 2.77
55 56 5.467063 AGCAAACGGTTTTTGTTTTCTTTGA 59.533 32.000 2.79 0.00 37.44 2.69
56 57 5.788041 GCAAACGGTTTTTGTTTTCTTTGAG 59.212 36.000 2.79 0.00 37.44 3.02
57 58 6.346999 GCAAACGGTTTTTGTTTTCTTTGAGA 60.347 34.615 2.79 0.00 37.44 3.27
58 59 7.623297 GCAAACGGTTTTTGTTTTCTTTGAGAT 60.623 33.333 2.79 0.00 37.44 2.75
59 60 6.885735 ACGGTTTTTGTTTTCTTTGAGATG 57.114 33.333 0.00 0.00 0.00 2.90
60 61 6.626302 ACGGTTTTTGTTTTCTTTGAGATGA 58.374 32.000 0.00 0.00 0.00 2.92
61 62 7.093992 ACGGTTTTTGTTTTCTTTGAGATGAA 58.906 30.769 0.00 0.00 0.00 2.57
62 63 7.763985 ACGGTTTTTGTTTTCTTTGAGATGAAT 59.236 29.630 0.00 0.00 0.00 2.57
63 64 8.603181 CGGTTTTTGTTTTCTTTGAGATGAATT 58.397 29.630 0.00 0.00 0.00 2.17
64 65 9.920826 GGTTTTTGTTTTCTTTGAGATGAATTC 57.079 29.630 0.00 0.00 0.00 2.17
69 70 9.740239 TTGTTTTCTTTGAGATGAATTCAGAAG 57.260 29.630 14.54 11.66 0.00 2.85
70 71 7.864379 TGTTTTCTTTGAGATGAATTCAGAAGC 59.136 33.333 14.54 4.14 0.00 3.86
71 72 7.514784 TTTCTTTGAGATGAATTCAGAAGCA 57.485 32.000 14.54 6.63 0.00 3.91
72 73 7.514784 TTCTTTGAGATGAATTCAGAAGCAA 57.485 32.000 14.54 11.85 0.00 3.91
73 74 7.514784 TCTTTGAGATGAATTCAGAAGCAAA 57.485 32.000 14.54 17.35 0.00 3.68
74 75 7.365741 TCTTTGAGATGAATTCAGAAGCAAAC 58.634 34.615 14.54 0.80 0.00 2.93
75 76 6.638096 TTGAGATGAATTCAGAAGCAAACA 57.362 33.333 14.54 3.18 0.00 2.83
76 77 6.638096 TGAGATGAATTCAGAAGCAAACAA 57.362 33.333 14.54 0.00 0.00 2.83
77 78 6.675026 TGAGATGAATTCAGAAGCAAACAAG 58.325 36.000 14.54 0.00 0.00 3.16
78 79 6.263842 TGAGATGAATTCAGAAGCAAACAAGT 59.736 34.615 14.54 0.00 0.00 3.16
79 80 6.444633 AGATGAATTCAGAAGCAAACAAGTG 58.555 36.000 14.54 0.00 0.00 3.16
80 81 4.362279 TGAATTCAGAAGCAAACAAGTGC 58.638 39.130 3.38 0.00 45.28 4.40
88 89 0.302589 GCAAACAAGTGCAAGCAAGC 59.697 50.000 0.00 0.00 44.29 4.01
89 90 0.573521 CAAACAAGTGCAAGCAAGCG 59.426 50.000 0.00 0.00 37.31 4.68
90 91 0.528249 AAACAAGTGCAAGCAAGCGG 60.528 50.000 0.00 0.00 37.31 5.52
91 92 1.666209 AACAAGTGCAAGCAAGCGGT 61.666 50.000 0.00 0.00 37.31 5.68
92 93 1.066257 CAAGTGCAAGCAAGCGGTT 59.934 52.632 0.00 0.00 37.31 4.44
97 98 2.597217 CAAGCAAGCGGTTGGGGA 60.597 61.111 27.01 0.00 45.01 4.81
98 99 1.978617 CAAGCAAGCGGTTGGGGAT 60.979 57.895 27.01 0.00 45.01 3.85
99 100 0.679640 CAAGCAAGCGGTTGGGGATA 60.680 55.000 27.01 0.00 45.01 2.59
100 101 0.394352 AAGCAAGCGGTTGGGGATAG 60.394 55.000 27.01 1.84 33.87 2.08
101 102 1.823899 GCAAGCGGTTGGGGATAGG 60.824 63.158 27.01 1.09 33.87 2.57
102 103 1.912220 CAAGCGGTTGGGGATAGGA 59.088 57.895 19.42 0.00 0.00 2.94
103 104 0.179045 CAAGCGGTTGGGGATAGGAG 60.179 60.000 19.42 0.00 0.00 3.69
104 105 1.345715 AAGCGGTTGGGGATAGGAGG 61.346 60.000 0.00 0.00 0.00 4.30
105 106 1.764854 GCGGTTGGGGATAGGAGGA 60.765 63.158 0.00 0.00 0.00 3.71
106 107 2.041206 GCGGTTGGGGATAGGAGGAC 62.041 65.000 0.00 0.00 0.00 3.85
107 108 0.398664 CGGTTGGGGATAGGAGGACT 60.399 60.000 0.00 0.00 0.00 3.85
108 109 1.894699 GGTTGGGGATAGGAGGACTT 58.105 55.000 0.00 0.00 0.00 3.01
109 110 1.769465 GGTTGGGGATAGGAGGACTTC 59.231 57.143 0.00 0.00 0.00 3.01
110 111 2.629909 GGTTGGGGATAGGAGGACTTCT 60.630 54.545 0.00 0.00 0.00 2.85
111 112 3.374984 GGTTGGGGATAGGAGGACTTCTA 60.375 52.174 0.00 0.00 0.00 2.10
112 113 3.614568 TGGGGATAGGAGGACTTCTAC 57.385 52.381 0.00 0.00 0.00 2.59
113 114 3.140143 TGGGGATAGGAGGACTTCTACT 58.860 50.000 0.00 0.00 40.49 2.57
114 115 3.140519 TGGGGATAGGAGGACTTCTACTC 59.859 52.174 0.00 0.00 37.87 2.59
120 121 0.741915 GAGGACTTCTACTCCTGCGG 59.258 60.000 0.00 0.00 38.35 5.69
121 122 0.039911 AGGACTTCTACTCCTGCGGT 59.960 55.000 0.00 0.00 36.73 5.68
122 123 0.456628 GGACTTCTACTCCTGCGGTC 59.543 60.000 0.00 0.00 0.00 4.79
123 124 0.456628 GACTTCTACTCCTGCGGTCC 59.543 60.000 0.00 0.00 0.00 4.46
124 125 0.039911 ACTTCTACTCCTGCGGTCCT 59.960 55.000 0.00 0.00 0.00 3.85
125 126 0.457851 CTTCTACTCCTGCGGTCCTG 59.542 60.000 0.00 0.00 0.00 3.86
126 127 1.605058 TTCTACTCCTGCGGTCCTGC 61.605 60.000 0.00 0.00 0.00 4.85
127 128 2.037367 TACTCCTGCGGTCCTGCT 59.963 61.111 7.14 0.00 35.36 4.24
128 129 2.010582 CTACTCCTGCGGTCCTGCTC 62.011 65.000 7.14 0.00 35.36 4.26
129 130 2.500815 TACTCCTGCGGTCCTGCTCT 62.501 60.000 7.14 0.00 35.36 4.09
130 131 3.071206 TCCTGCGGTCCTGCTCTC 61.071 66.667 7.14 0.00 35.36 3.20
131 132 3.073735 CCTGCGGTCCTGCTCTCT 61.074 66.667 7.14 0.00 35.36 3.10
132 133 2.654079 CCTGCGGTCCTGCTCTCTT 61.654 63.158 7.14 0.00 35.36 2.85
133 134 1.294780 CTGCGGTCCTGCTCTCTTT 59.705 57.895 7.14 0.00 35.36 2.52
134 135 1.004560 TGCGGTCCTGCTCTCTTTG 60.005 57.895 7.14 0.00 35.36 2.77
135 136 1.743252 GCGGTCCTGCTCTCTTTGG 60.743 63.158 0.00 0.00 0.00 3.28
136 137 1.674057 CGGTCCTGCTCTCTTTGGT 59.326 57.895 0.00 0.00 0.00 3.67
137 138 0.895530 CGGTCCTGCTCTCTTTGGTA 59.104 55.000 0.00 0.00 0.00 3.25
138 139 1.275291 CGGTCCTGCTCTCTTTGGTAA 59.725 52.381 0.00 0.00 0.00 2.85
139 140 2.289444 CGGTCCTGCTCTCTTTGGTAAA 60.289 50.000 0.00 0.00 0.00 2.01
140 141 3.075148 GGTCCTGCTCTCTTTGGTAAAC 58.925 50.000 0.00 0.00 0.00 2.01
141 142 3.496160 GGTCCTGCTCTCTTTGGTAAACA 60.496 47.826 0.00 0.00 0.00 2.83
142 143 4.134563 GTCCTGCTCTCTTTGGTAAACAA 58.865 43.478 0.00 0.00 37.28 2.83
143 144 4.578928 GTCCTGCTCTCTTTGGTAAACAAA 59.421 41.667 0.00 0.00 46.34 2.83
177 178 8.876275 ATACGTTGTAAGTCACTTAGTTTTCA 57.124 30.769 0.00 0.00 0.00 2.69
192 193 3.803778 AGTTTTCATTTTCAAGCAAGCCG 59.196 39.130 0.00 0.00 0.00 5.52
207 208 4.867599 CCGCGCCGTCCTTAGTCC 62.868 72.222 0.00 0.00 0.00 3.85
214 215 1.474077 GCCGTCCTTAGTCCGAAGTAA 59.526 52.381 0.00 0.00 0.00 2.24
220 221 5.515626 CGTCCTTAGTCCGAAGTAATTTCAG 59.484 44.000 0.00 0.00 35.43 3.02
227 228 5.940470 AGTCCGAAGTAATTTCAGAATTGCT 59.060 36.000 0.00 0.00 46.07 3.91
229 230 5.937540 TCCGAAGTAATTTCAGAATTGCTCA 59.062 36.000 3.56 0.00 44.22 4.26
231 232 6.024049 CGAAGTAATTTCAGAATTGCTCACC 58.976 40.000 3.56 0.00 44.22 4.02
241 242 5.130975 TCAGAATTGCTCACCCATATACTGT 59.869 40.000 0.00 0.00 0.00 3.55
245 246 1.867233 GCTCACCCATATACTGTTGCG 59.133 52.381 0.00 0.00 0.00 4.85
249 250 2.612212 CACCCATATACTGTTGCGTTCC 59.388 50.000 0.00 0.00 0.00 3.62
254 255 2.831685 ATACTGTTGCGTTCCTGACA 57.168 45.000 0.00 0.00 0.00 3.58
257 263 2.297701 ACTGTTGCGTTCCTGACATTT 58.702 42.857 0.00 0.00 0.00 2.32
302 310 3.411415 ACTTATTTCTGCGCAATGCTC 57.589 42.857 13.05 0.00 46.63 4.26
325 333 1.738700 GCGAGCAGAGAAAAGGGAGAG 60.739 57.143 0.00 0.00 0.00 3.20
361 369 3.806625 AATGGGCCAATCAAAGAATCG 57.193 42.857 11.89 0.00 0.00 3.34
369 377 5.460091 GGCCAATCAAAGAATCGCTTATTTC 59.540 40.000 0.00 0.00 35.24 2.17
370 378 6.268566 GCCAATCAAAGAATCGCTTATTTCT 58.731 36.000 0.00 0.00 35.24 2.52
380 818 8.190888 AGAATCGCTTATTTCTAAAGTCTGTG 57.809 34.615 0.00 0.00 0.00 3.66
427 870 2.300433 TGGCGGGATCAATGATTGAAG 58.700 47.619 12.36 5.60 43.95 3.02
428 871 2.092484 TGGCGGGATCAATGATTGAAGA 60.092 45.455 12.36 0.00 43.95 2.87
430 873 3.190118 GGCGGGATCAATGATTGAAGATC 59.810 47.826 12.36 5.40 43.95 2.75
466 909 1.738346 GCGAATTGGGGGATTCTGCC 61.738 60.000 0.00 0.00 34.58 4.85
538 1001 0.740868 TCCTTGTGTGCATAGCGCTC 60.741 55.000 16.34 0.00 43.06 5.03
539 1002 1.346197 CTTGTGTGCATAGCGCTCG 59.654 57.895 16.34 8.01 43.06 5.03
540 1003 2.622722 CTTGTGTGCATAGCGCTCGC 62.623 60.000 16.34 19.63 43.33 5.03
582 1063 1.355210 CACACACAACAAGACGCCC 59.645 57.895 0.00 0.00 0.00 6.13
585 1066 2.186826 ACACAACAAGACGCCCAGC 61.187 57.895 0.00 0.00 0.00 4.85
587 1068 3.365265 CAACAAGACGCCCAGCCC 61.365 66.667 0.00 0.00 0.00 5.19
588 1069 3.884774 AACAAGACGCCCAGCCCA 61.885 61.111 0.00 0.00 0.00 5.36
589 1070 3.850098 AACAAGACGCCCAGCCCAG 62.850 63.158 0.00 0.00 0.00 4.45
676 1168 4.829064 TTGCAGTGGTGATAAAACTGAC 57.171 40.909 6.24 0.00 43.22 3.51
727 1224 1.476488 GAGCACACACAAACCAAACCT 59.524 47.619 0.00 0.00 0.00 3.50
747 1244 2.949451 ACGATGACATCAGTGGAGTC 57.051 50.000 15.58 8.40 0.00 3.36
836 1339 3.323403 CCTCTCTCTCTCTCTCTCTCTCC 59.677 56.522 0.00 0.00 0.00 3.71
879 1386 2.701780 CCCGGTGACACTCGAGAGG 61.702 68.421 21.68 13.24 0.00 3.69
880 1387 2.701780 CCGGTGACACTCGAGAGGG 61.702 68.421 21.68 10.58 37.98 4.30
887 1394 1.202817 GACACTCGAGAGGGAAGGAAC 59.797 57.143 21.68 0.00 35.36 3.62
906 1413 1.815003 ACAATTCACCAGCTAGCTTGC 59.185 47.619 16.46 12.54 0.00 4.01
916 1423 2.165380 CTAGCTTGCGCTTGCTTGA 58.835 52.632 26.67 13.19 46.47 3.02
977 1491 4.699522 AGCGTCGGGGTTTGGCTC 62.700 66.667 0.00 0.00 0.00 4.70
1133 1665 1.673665 GCAAGGCTGCTGCTACTGT 60.674 57.895 15.64 0.00 45.74 3.55
1134 1666 1.239968 GCAAGGCTGCTGCTACTGTT 61.240 55.000 15.64 0.00 45.74 3.16
1135 1667 0.520404 CAAGGCTGCTGCTACTGTTG 59.480 55.000 15.64 7.85 39.59 3.33
1136 1668 1.239968 AAGGCTGCTGCTACTGTTGC 61.240 55.000 15.64 7.29 39.59 4.17
1137 1669 1.673665 GGCTGCTGCTACTGTTGCT 60.674 57.895 15.64 0.00 39.59 3.91
1138 1670 1.239968 GGCTGCTGCTACTGTTGCTT 61.240 55.000 15.64 0.00 39.59 3.91
1197 1729 3.432588 CACTCGTCGTCGCTCCCT 61.433 66.667 0.00 0.00 36.96 4.20
1432 1976 2.754658 GGAAGAGCGTCCTCCGGA 60.755 66.667 2.93 2.93 38.96 5.14
1435 1979 4.742649 AGAGCGTCCTCCGGAGCA 62.743 66.667 26.87 9.03 38.96 4.26
1518 2062 1.502231 GCGTCAAGAACAAGAGCTCA 58.498 50.000 17.77 0.00 0.00 4.26
1698 2242 0.179161 CACGGAGAAGAGCTACACGG 60.179 60.000 0.00 0.00 0.00 4.94
1699 2243 1.313812 ACGGAGAAGAGCTACACGGG 61.314 60.000 0.00 0.00 0.00 5.28
1700 2244 1.817209 GGAGAAGAGCTACACGGGG 59.183 63.158 0.00 0.00 0.00 5.73
1702 2246 0.741915 GAGAAGAGCTACACGGGGAG 59.258 60.000 0.00 0.00 0.00 4.30
1703 2247 0.331954 AGAAGAGCTACACGGGGAGA 59.668 55.000 0.00 0.00 0.00 3.71
1705 2249 1.549170 GAAGAGCTACACGGGGAGAAA 59.451 52.381 0.00 0.00 0.00 2.52
1707 2251 0.896226 GAGCTACACGGGGAGAAACT 59.104 55.000 0.00 0.00 0.00 2.66
1708 2252 0.608640 AGCTACACGGGGAGAAACTG 59.391 55.000 0.00 0.00 0.00 3.16
1709 2253 0.320697 GCTACACGGGGAGAAACTGT 59.679 55.000 0.00 0.00 0.00 3.55
1712 2256 3.396951 CACGGGGAGAAACTGTGTT 57.603 52.632 0.00 0.00 39.72 3.32
1713 2257 0.944386 CACGGGGAGAAACTGTGTTG 59.056 55.000 0.00 0.00 39.72 3.33
1714 2258 0.179029 ACGGGGAGAAACTGTGTTGG 60.179 55.000 0.00 0.00 0.00 3.77
1716 2260 1.515521 GGGGAGAAACTGTGTTGGCG 61.516 60.000 0.00 0.00 0.00 5.69
1717 2261 1.282875 GGAGAAACTGTGTTGGCGC 59.717 57.895 0.00 0.00 0.00 6.53
1718 2262 1.166531 GGAGAAACTGTGTTGGCGCT 61.167 55.000 7.64 0.00 0.00 5.92
1719 2263 0.040958 GAGAAACTGTGTTGGCGCTG 60.041 55.000 7.64 0.00 0.00 5.18
1722 2266 2.340453 AAACTGTGTTGGCGCTGCAG 62.340 55.000 10.11 10.11 0.00 4.41
1723 2267 4.034258 CTGTGTTGGCGCTGCAGG 62.034 66.667 17.12 6.85 0.00 4.85
1733 2277 4.400961 GCTGCAGGGACGAAGCCT 62.401 66.667 17.12 0.00 0.00 4.58
1744 2288 2.261671 GAAGCCTCGACGCCTCAA 59.738 61.111 2.59 0.00 0.00 3.02
1745 2289 1.374252 GAAGCCTCGACGCCTCAAA 60.374 57.895 2.59 0.00 0.00 2.69
1746 2290 1.355066 GAAGCCTCGACGCCTCAAAG 61.355 60.000 2.59 0.00 0.00 2.77
1747 2291 3.491652 GCCTCGACGCCTCAAAGC 61.492 66.667 0.00 0.00 0.00 3.51
1748 2292 2.048222 CCTCGACGCCTCAAAGCA 60.048 61.111 0.00 0.00 0.00 3.91
1751 2295 2.048222 CGACGCCTCAAAGCAGGA 60.048 61.111 0.00 0.00 35.20 3.86
1752 2296 2.097038 CGACGCCTCAAAGCAGGAG 61.097 63.158 0.00 0.00 39.20 3.69
1759 2303 0.676151 CTCAAAGCAGGAGGAGGTGC 60.676 60.000 0.00 0.00 40.17 5.01
1763 2307 4.792804 GCAGGAGGAGGTGCTGGC 62.793 72.222 0.00 0.00 44.68 4.85
1764 2308 4.106925 CAGGAGGAGGTGCTGGCC 62.107 72.222 0.00 0.00 40.89 5.36
1776 2320 3.058160 CTGGCCGCCCTCAAAGTG 61.058 66.667 7.03 0.00 0.00 3.16
1777 2321 3.850098 CTGGCCGCCCTCAAAGTGT 62.850 63.158 7.03 0.00 0.00 3.55
1779 2323 3.423154 GCCGCCCTCAAAGTGTCG 61.423 66.667 0.00 0.00 0.00 4.35
1781 2325 2.027625 CCGCCCTCAAAGTGTCGAC 61.028 63.158 9.11 9.11 0.00 4.20
1782 2326 2.027625 CGCCCTCAAAGTGTCGACC 61.028 63.158 14.12 4.42 0.00 4.79
1783 2327 1.371558 GCCCTCAAAGTGTCGACCT 59.628 57.895 14.12 6.92 0.00 3.85
1784 2328 0.951040 GCCCTCAAAGTGTCGACCTG 60.951 60.000 14.12 5.45 0.00 4.00
1785 2329 0.393077 CCCTCAAAGTGTCGACCTGT 59.607 55.000 14.12 1.81 0.00 4.00
1786 2330 1.605712 CCCTCAAAGTGTCGACCTGTC 60.606 57.143 14.12 1.12 0.00 3.51
1799 2367 0.885879 ACCTGTCGACGCACAAGATA 59.114 50.000 11.62 0.00 0.00 1.98
1808 2376 0.999406 CGCACAAGATACCGGTGAAG 59.001 55.000 19.93 5.04 34.52 3.02
1810 2378 2.738643 CGCACAAGATACCGGTGAAGAT 60.739 50.000 19.93 1.19 34.52 2.40
1811 2379 2.866762 GCACAAGATACCGGTGAAGATC 59.133 50.000 19.93 12.44 34.52 2.75
1831 2399 6.980593 AGATCAGGAACGATAAGAAGATCAG 58.019 40.000 0.00 0.00 34.58 2.90
1836 2404 4.747605 GGAACGATAAGAAGATCAGGAAGC 59.252 45.833 0.00 0.00 0.00 3.86
1839 2407 3.740321 CGATAAGAAGATCAGGAAGCAGC 59.260 47.826 0.00 0.00 0.00 5.25
1894 2462 1.002087 GGTCCTAGTCCCTGTGTTGTG 59.998 57.143 0.00 0.00 0.00 3.33
1900 2468 0.537143 GTCCCTGTGTTGTGCCATGA 60.537 55.000 0.00 0.00 0.00 3.07
1906 2474 0.953727 GTGTTGTGCCATGAGAAGCA 59.046 50.000 0.00 0.00 36.44 3.91
1928 2496 2.746362 GAGAGCACAAGGAAGGAATGTG 59.254 50.000 0.97 0.97 45.54 3.21
1930 2498 2.485814 GAGCACAAGGAAGGAATGTGTC 59.514 50.000 6.95 0.63 44.79 3.67
1937 2505 3.403038 AGGAAGGAATGTGTCGACAAAG 58.597 45.455 21.95 0.00 35.11 2.77
1967 2535 4.007659 AGTAGGTTCGGCTACCATTTTTG 58.992 43.478 8.16 0.00 40.82 2.44
1968 2536 3.149005 AGGTTCGGCTACCATTTTTGA 57.851 42.857 8.16 0.00 40.82 2.69
1969 2537 2.817844 AGGTTCGGCTACCATTTTTGAC 59.182 45.455 8.16 0.00 40.82 3.18
1970 2538 2.094906 GGTTCGGCTACCATTTTTGACC 60.095 50.000 1.26 0.00 38.12 4.02
1973 2541 4.497291 TCGGCTACCATTTTTGACCTAT 57.503 40.909 0.00 0.00 0.00 2.57
1975 2543 5.607477 TCGGCTACCATTTTTGACCTATAG 58.393 41.667 0.00 0.00 0.00 1.31
2018 2592 1.425428 CTTCAGTCGAAATGCCGCC 59.575 57.895 0.00 0.00 0.00 6.13
2021 2595 1.089481 TCAGTCGAAATGCCGCCATC 61.089 55.000 0.00 0.00 0.00 3.51
2027 2601 1.655099 CGAAATGCCGCCATCTTTTTG 59.345 47.619 0.00 0.00 0.00 2.44
2030 2604 3.951775 AATGCCGCCATCTTTTTGTTA 57.048 38.095 0.00 0.00 0.00 2.41
2031 2605 3.508744 ATGCCGCCATCTTTTTGTTAG 57.491 42.857 0.00 0.00 0.00 2.34
2053 2632 5.368145 AGTAATTTGTGAGCTGTGACTTGA 58.632 37.500 0.00 0.00 0.00 3.02
2093 2672 9.093970 TCCTATACAAATTGTTGTTGATCTACG 57.906 33.333 3.17 0.00 46.01 3.51
2099 2678 1.804151 TGTTGTTGATCTACGCCAAGC 59.196 47.619 2.86 0.00 0.00 4.01
2129 2708 5.205056 AGTTGGGTTGAATCTACACCAAAA 58.795 37.500 14.91 1.87 39.43 2.44
2131 2710 6.326323 AGTTGGGTTGAATCTACACCAAAATT 59.674 34.615 14.91 6.09 39.43 1.82
2132 2711 6.095432 TGGGTTGAATCTACACCAAAATTG 57.905 37.500 0.00 0.00 0.00 2.32
2134 2713 6.098982 TGGGTTGAATCTACACCAAAATTGTT 59.901 34.615 0.00 0.00 0.00 2.83
2153 2732 2.472695 TGTGTCACAGGATGGCTTAC 57.527 50.000 0.18 0.00 43.62 2.34
2168 2747 2.417586 GGCTTACCGTGTGACAATTACC 59.582 50.000 0.00 0.00 0.00 2.85
2198 2777 6.648725 CGAGTTCGTTTCTTGGAGAATTAT 57.351 37.500 0.00 0.00 33.67 1.28
2224 2803 1.373570 GTCTTCCCTGATTGCTTCGG 58.626 55.000 0.00 0.00 0.00 4.30
2228 2807 2.753966 CCCTGATTGCTTCGGCGTG 61.754 63.158 6.85 2.20 45.37 5.34
2229 2808 1.741401 CCTGATTGCTTCGGCGTGA 60.741 57.895 6.85 0.00 45.37 4.35
2288 2913 1.737838 TTCCGTGCAATGATGGTCTC 58.262 50.000 0.00 0.00 0.00 3.36
2289 2914 0.612744 TCCGTGCAATGATGGTCTCA 59.387 50.000 0.00 0.00 38.53 3.27
2290 2915 1.003003 TCCGTGCAATGATGGTCTCAA 59.997 47.619 0.00 0.00 37.44 3.02
2347 2972 3.941657 AAGAGCTGGAACGAGCGGC 62.942 63.158 0.00 0.00 44.24 6.53
2406 3031 1.148310 ATATTTTCCAGCGATCGCCG 58.852 50.000 34.89 25.92 43.17 6.46
2415 3040 2.388232 GCGATCGCCGGTTTGTCTT 61.388 57.895 29.48 0.00 39.04 3.01
2426 3051 3.422603 CCGGTTTGTCTTCATTTCGTACG 60.423 47.826 9.53 9.53 0.00 3.67
2435 3060 4.915667 TCTTCATTTCGTACGTCAGAGTTG 59.084 41.667 16.05 5.18 0.00 3.16
2593 3219 4.696402 TGACCCATGTGTTTCGGTTAATAC 59.304 41.667 0.00 0.00 0.00 1.89
2630 3256 8.407832 TGGTTACATGATTGAAATATCTTGCAG 58.592 33.333 0.00 0.00 34.66 4.41
2635 3261 9.932207 ACATGATTGAAATATCTTGCAGAAAAA 57.068 25.926 0.00 0.00 34.66 1.94
2663 3289 4.328983 GGAAGAATAAAGCGAATGACGACA 59.671 41.667 0.00 0.00 45.77 4.35
2666 3292 3.520290 ATAAAGCGAATGACGACAGGA 57.480 42.857 0.00 0.00 45.77 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.660064 CCTTCTCCACCGTCCCCAG 61.660 68.421 0.00 0.00 0.00 4.45
7 8 2.606519 CCTTCTCCACCGTCCCCA 60.607 66.667 0.00 0.00 0.00 4.96
8 9 3.400054 CCCTTCTCCACCGTCCCC 61.400 72.222 0.00 0.00 0.00 4.81
9 10 2.284405 TCCCTTCTCCACCGTCCC 60.284 66.667 0.00 0.00 0.00 4.46
10 11 2.359967 CCTCCCTTCTCCACCGTCC 61.360 68.421 0.00 0.00 0.00 4.79
11 12 2.359967 CCCTCCCTTCTCCACCGTC 61.360 68.421 0.00 0.00 0.00 4.79
12 13 2.284699 CCCTCCCTTCTCCACCGT 60.285 66.667 0.00 0.00 0.00 4.83
13 14 1.612442 TTCCCTCCCTTCTCCACCG 60.612 63.158 0.00 0.00 0.00 4.94
14 15 1.916206 GCTTCCCTCCCTTCTCCACC 61.916 65.000 0.00 0.00 0.00 4.61
15 16 1.201429 TGCTTCCCTCCCTTCTCCAC 61.201 60.000 0.00 0.00 0.00 4.02
16 17 0.475632 TTGCTTCCCTCCCTTCTCCA 60.476 55.000 0.00 0.00 0.00 3.86
17 18 0.698818 TTTGCTTCCCTCCCTTCTCC 59.301 55.000 0.00 0.00 0.00 3.71
18 19 1.827681 GTTTGCTTCCCTCCCTTCTC 58.172 55.000 0.00 0.00 0.00 2.87
19 20 0.036875 CGTTTGCTTCCCTCCCTTCT 59.963 55.000 0.00 0.00 0.00 2.85
20 21 0.960861 CCGTTTGCTTCCCTCCCTTC 60.961 60.000 0.00 0.00 0.00 3.46
21 22 1.074951 CCGTTTGCTTCCCTCCCTT 59.925 57.895 0.00 0.00 0.00 3.95
22 23 1.716028 AACCGTTTGCTTCCCTCCCT 61.716 55.000 0.00 0.00 0.00 4.20
23 24 0.826256 AAACCGTTTGCTTCCCTCCC 60.826 55.000 0.00 0.00 0.00 4.30
24 25 1.037493 AAAACCGTTTGCTTCCCTCC 58.963 50.000 0.00 0.00 0.00 4.30
25 26 2.159156 ACAAAAACCGTTTGCTTCCCTC 60.159 45.455 0.00 0.00 32.93 4.30
26 27 1.828595 ACAAAAACCGTTTGCTTCCCT 59.171 42.857 0.00 0.00 32.93 4.20
27 28 2.303163 ACAAAAACCGTTTGCTTCCC 57.697 45.000 0.00 0.00 32.93 3.97
28 29 4.390603 AGAAAACAAAAACCGTTTGCTTCC 59.609 37.500 0.00 0.00 38.82 3.46
29 30 5.524511 AGAAAACAAAAACCGTTTGCTTC 57.475 34.783 0.00 3.33 38.82 3.86
30 31 5.933187 AAGAAAACAAAAACCGTTTGCTT 57.067 30.435 3.65 3.65 44.09 3.91
31 32 5.467063 TCAAAGAAAACAAAAACCGTTTGCT 59.533 32.000 0.00 0.00 42.85 3.91
32 33 5.680893 TCAAAGAAAACAAAAACCGTTTGC 58.319 33.333 0.00 0.00 36.71 3.68
33 34 7.111353 TCTCAAAGAAAACAAAAACCGTTTG 57.889 32.000 0.00 0.00 36.71 2.93
34 35 7.600752 TCATCTCAAAGAAAACAAAAACCGTTT 59.399 29.630 0.00 0.00 38.19 3.60
35 36 7.093992 TCATCTCAAAGAAAACAAAAACCGTT 58.906 30.769 0.00 0.00 0.00 4.44
36 37 6.626302 TCATCTCAAAGAAAACAAAAACCGT 58.374 32.000 0.00 0.00 0.00 4.83
37 38 7.518731 TTCATCTCAAAGAAAACAAAAACCG 57.481 32.000 0.00 0.00 0.00 4.44
38 39 9.920826 GAATTCATCTCAAAGAAAACAAAAACC 57.079 29.630 0.00 0.00 0.00 3.27
43 44 9.740239 CTTCTGAATTCATCTCAAAGAAAACAA 57.260 29.630 8.96 0.00 0.00 2.83
44 45 7.864379 GCTTCTGAATTCATCTCAAAGAAAACA 59.136 33.333 8.96 0.00 0.00 2.83
45 46 7.864379 TGCTTCTGAATTCATCTCAAAGAAAAC 59.136 33.333 8.96 3.53 0.00 2.43
46 47 7.944061 TGCTTCTGAATTCATCTCAAAGAAAA 58.056 30.769 8.96 0.00 0.00 2.29
47 48 7.514784 TGCTTCTGAATTCATCTCAAAGAAA 57.485 32.000 8.96 0.00 0.00 2.52
48 49 7.514784 TTGCTTCTGAATTCATCTCAAAGAA 57.485 32.000 8.96 6.27 0.00 2.52
49 50 7.013559 TGTTTGCTTCTGAATTCATCTCAAAGA 59.986 33.333 8.96 11.91 0.00 2.52
50 51 7.143340 TGTTTGCTTCTGAATTCATCTCAAAG 58.857 34.615 8.96 8.91 0.00 2.77
51 52 7.041635 TGTTTGCTTCTGAATTCATCTCAAA 57.958 32.000 8.96 13.16 0.00 2.69
52 53 6.638096 TGTTTGCTTCTGAATTCATCTCAA 57.362 33.333 8.96 8.25 0.00 3.02
53 54 6.263842 ACTTGTTTGCTTCTGAATTCATCTCA 59.736 34.615 8.96 2.47 0.00 3.27
54 55 6.581542 CACTTGTTTGCTTCTGAATTCATCTC 59.418 38.462 8.96 0.00 0.00 2.75
55 56 6.444633 CACTTGTTTGCTTCTGAATTCATCT 58.555 36.000 8.96 0.00 0.00 2.90
56 57 5.118203 GCACTTGTTTGCTTCTGAATTCATC 59.882 40.000 8.96 0.00 39.59 2.92
57 58 4.986659 GCACTTGTTTGCTTCTGAATTCAT 59.013 37.500 8.96 0.00 39.59 2.57
58 59 4.142204 TGCACTTGTTTGCTTCTGAATTCA 60.142 37.500 8.12 8.12 43.41 2.57
59 60 4.362279 TGCACTTGTTTGCTTCTGAATTC 58.638 39.130 0.00 0.00 43.41 2.17
60 61 4.389890 TGCACTTGTTTGCTTCTGAATT 57.610 36.364 0.00 0.00 43.41 2.17
61 62 4.365723 CTTGCACTTGTTTGCTTCTGAAT 58.634 39.130 0.00 0.00 43.41 2.57
62 63 3.772932 CTTGCACTTGTTTGCTTCTGAA 58.227 40.909 0.00 0.00 43.41 3.02
63 64 2.480073 GCTTGCACTTGTTTGCTTCTGA 60.480 45.455 0.00 0.00 43.41 3.27
64 65 1.856597 GCTTGCACTTGTTTGCTTCTG 59.143 47.619 0.00 0.00 43.41 3.02
65 66 1.477700 TGCTTGCACTTGTTTGCTTCT 59.522 42.857 0.00 0.00 43.41 2.85
66 67 1.925229 TGCTTGCACTTGTTTGCTTC 58.075 45.000 0.00 0.00 43.41 3.86
67 68 2.273557 CTTGCTTGCACTTGTTTGCTT 58.726 42.857 0.00 0.00 43.41 3.91
68 69 1.930567 CTTGCTTGCACTTGTTTGCT 58.069 45.000 0.00 0.00 43.41 3.91
69 70 0.302589 GCTTGCTTGCACTTGTTTGC 59.697 50.000 0.00 0.00 43.31 3.68
70 71 0.573521 CGCTTGCTTGCACTTGTTTG 59.426 50.000 0.00 0.00 0.00 2.93
71 72 0.528249 CCGCTTGCTTGCACTTGTTT 60.528 50.000 0.00 0.00 0.00 2.83
72 73 1.066257 CCGCTTGCTTGCACTTGTT 59.934 52.632 0.00 0.00 0.00 2.83
73 74 1.666209 AACCGCTTGCTTGCACTTGT 61.666 50.000 0.00 0.00 0.00 3.16
74 75 1.066257 AACCGCTTGCTTGCACTTG 59.934 52.632 0.00 0.00 0.00 3.16
75 76 1.066257 CAACCGCTTGCTTGCACTT 59.934 52.632 0.00 0.00 0.00 3.16
76 77 2.723746 CAACCGCTTGCTTGCACT 59.276 55.556 0.00 0.00 0.00 4.40
77 78 2.355009 CCAACCGCTTGCTTGCAC 60.355 61.111 0.00 0.00 0.00 4.57
78 79 3.604667 CCCAACCGCTTGCTTGCA 61.605 61.111 0.00 0.00 0.00 4.08
79 80 4.362476 CCCCAACCGCTTGCTTGC 62.362 66.667 0.00 0.00 0.00 4.01
80 81 0.679640 TATCCCCAACCGCTTGCTTG 60.680 55.000 0.00 0.00 0.00 4.01
81 82 0.394352 CTATCCCCAACCGCTTGCTT 60.394 55.000 0.00 0.00 0.00 3.91
82 83 1.224592 CTATCCCCAACCGCTTGCT 59.775 57.895 0.00 0.00 0.00 3.91
83 84 1.823899 CCTATCCCCAACCGCTTGC 60.824 63.158 0.00 0.00 0.00 4.01
84 85 0.179045 CTCCTATCCCCAACCGCTTG 60.179 60.000 0.00 0.00 0.00 4.01
85 86 1.345715 CCTCCTATCCCCAACCGCTT 61.346 60.000 0.00 0.00 0.00 4.68
86 87 1.766461 CCTCCTATCCCCAACCGCT 60.766 63.158 0.00 0.00 0.00 5.52
87 88 1.764854 TCCTCCTATCCCCAACCGC 60.765 63.158 0.00 0.00 0.00 5.68
88 89 0.398664 AGTCCTCCTATCCCCAACCG 60.399 60.000 0.00 0.00 0.00 4.44
89 90 1.769465 GAAGTCCTCCTATCCCCAACC 59.231 57.143 0.00 0.00 0.00 3.77
90 91 2.765502 AGAAGTCCTCCTATCCCCAAC 58.234 52.381 0.00 0.00 0.00 3.77
91 92 3.536434 AGTAGAAGTCCTCCTATCCCCAA 59.464 47.826 0.00 0.00 0.00 4.12
92 93 3.140143 AGTAGAAGTCCTCCTATCCCCA 58.860 50.000 0.00 0.00 0.00 4.96
93 94 3.500836 GGAGTAGAAGTCCTCCTATCCCC 60.501 56.522 0.00 0.00 43.29 4.81
94 95 3.770046 GGAGTAGAAGTCCTCCTATCCC 58.230 54.545 0.00 0.00 43.29 3.85
100 101 0.741915 CGCAGGAGTAGAAGTCCTCC 59.258 60.000 0.10 0.00 44.63 4.30
115 116 1.018226 CAAAGAGAGCAGGACCGCAG 61.018 60.000 10.28 0.00 0.00 5.18
116 117 1.004560 CAAAGAGAGCAGGACCGCA 60.005 57.895 10.28 0.00 0.00 5.69
117 118 1.743252 CCAAAGAGAGCAGGACCGC 60.743 63.158 0.68 0.68 0.00 5.68
118 119 0.895530 TACCAAAGAGAGCAGGACCG 59.104 55.000 0.00 0.00 0.00 4.79
119 120 3.075148 GTTTACCAAAGAGAGCAGGACC 58.925 50.000 0.00 0.00 0.00 4.46
120 121 3.740115 TGTTTACCAAAGAGAGCAGGAC 58.260 45.455 0.00 0.00 0.00 3.85
121 122 4.431416 TTGTTTACCAAAGAGAGCAGGA 57.569 40.909 0.00 0.00 0.00 3.86
122 123 5.514274 TTTTGTTTACCAAAGAGAGCAGG 57.486 39.130 0.00 0.00 43.63 4.85
151 152 9.316730 TGAAAACTAAGTGACTTACAACGTATT 57.683 29.630 0.00 0.00 0.00 1.89
152 153 8.876275 TGAAAACTAAGTGACTTACAACGTAT 57.124 30.769 0.00 0.00 0.00 3.06
153 154 8.876275 ATGAAAACTAAGTGACTTACAACGTA 57.124 30.769 0.00 0.00 0.00 3.57
154 155 7.781548 ATGAAAACTAAGTGACTTACAACGT 57.218 32.000 0.00 0.00 0.00 3.99
155 156 9.498307 AAAATGAAAACTAAGTGACTTACAACG 57.502 29.630 0.00 0.00 0.00 4.10
160 161 9.730420 GCTTGAAAATGAAAACTAAGTGACTTA 57.270 29.630 4.81 4.81 0.00 2.24
161 162 8.250332 TGCTTGAAAATGAAAACTAAGTGACTT 58.750 29.630 2.37 2.37 0.00 3.01
162 163 7.771183 TGCTTGAAAATGAAAACTAAGTGACT 58.229 30.769 0.00 0.00 0.00 3.41
163 164 7.985634 TGCTTGAAAATGAAAACTAAGTGAC 57.014 32.000 0.00 0.00 0.00 3.67
164 165 7.222611 GCTTGCTTGAAAATGAAAACTAAGTGA 59.777 33.333 0.00 0.00 0.00 3.41
165 166 7.339953 GCTTGCTTGAAAATGAAAACTAAGTG 58.660 34.615 0.00 0.00 0.00 3.16
166 167 6.479990 GGCTTGCTTGAAAATGAAAACTAAGT 59.520 34.615 0.00 0.00 0.00 2.24
167 168 6.346040 CGGCTTGCTTGAAAATGAAAACTAAG 60.346 38.462 0.00 0.00 0.00 2.18
168 169 5.461737 CGGCTTGCTTGAAAATGAAAACTAA 59.538 36.000 0.00 0.00 0.00 2.24
169 170 4.981674 CGGCTTGCTTGAAAATGAAAACTA 59.018 37.500 0.00 0.00 0.00 2.24
177 178 1.734117 GCGCGGCTTGCTTGAAAAT 60.734 52.632 8.83 0.00 43.27 1.82
192 193 3.346631 TTCGGACTAAGGACGGCGC 62.347 63.158 6.90 0.00 0.00 6.53
205 206 5.937540 TGAGCAATTCTGAAATTACTTCGGA 59.062 36.000 0.00 0.00 45.90 4.55
207 208 6.024049 GGTGAGCAATTCTGAAATTACTTCG 58.976 40.000 0.00 0.00 36.78 3.79
214 215 7.230108 CAGTATATGGGTGAGCAATTCTGAAAT 59.770 37.037 0.00 0.00 0.00 2.17
220 221 5.506317 GCAACAGTATATGGGTGAGCAATTC 60.506 44.000 0.00 0.00 0.00 2.17
227 228 3.527533 GAACGCAACAGTATATGGGTGA 58.472 45.455 0.00 0.00 41.22 4.02
229 230 2.504175 AGGAACGCAACAGTATATGGGT 59.496 45.455 0.00 0.00 43.55 4.51
231 232 3.555956 GTCAGGAACGCAACAGTATATGG 59.444 47.826 0.00 0.00 0.00 2.74
262 268 8.789767 ATAAGTTATCAAGATCCTCTCTCCAA 57.210 34.615 0.00 0.00 31.03 3.53
264 270 9.705290 GAAATAAGTTATCAAGATCCTCTCTCC 57.295 37.037 0.00 0.00 31.03 3.71
272 278 6.948353 TGCGCAGAAATAAGTTATCAAGATC 58.052 36.000 5.66 0.00 0.00 2.75
280 286 4.635765 AGAGCATTGCGCAGAAATAAGTTA 59.364 37.500 11.31 0.00 46.13 2.24
302 310 1.080995 CCCTTTTCTCTGCTCGCGAG 61.081 60.000 31.37 31.37 0.00 5.03
316 324 3.790089 AATTTCGGTGTCTCTCCCTTT 57.210 42.857 0.00 0.00 0.00 3.11
325 333 4.421058 GCCCATTTCTTAATTTCGGTGTC 58.579 43.478 0.00 0.00 0.00 3.67
380 818 8.029642 TGTTCGAATTGAAAGATTTAGAGTCC 57.970 34.615 0.00 0.00 38.60 3.85
384 822 7.754924 GCCATTGTTCGAATTGAAAGATTTAGA 59.245 33.333 0.00 0.00 38.60 2.10
387 825 5.345741 CGCCATTGTTCGAATTGAAAGATTT 59.654 36.000 0.00 0.00 38.60 2.17
427 870 1.741770 GGTGCTGGGTCACACGATC 60.742 63.158 0.00 0.00 38.66 3.69
428 871 2.347490 GGTGCTGGGTCACACGAT 59.653 61.111 0.00 0.00 38.66 3.73
456 899 2.514824 GAGGTGCGGCAGAATCCC 60.515 66.667 1.18 0.00 0.00 3.85
538 1001 1.427819 GAACCGTGCCCAATTAGCG 59.572 57.895 0.00 0.00 0.00 4.26
539 1002 1.303091 ACGAACCGTGCCCAATTAGC 61.303 55.000 0.00 0.00 39.18 3.09
540 1003 0.725117 GACGAACCGTGCCCAATTAG 59.275 55.000 0.00 0.00 41.37 1.73
541 1004 1.015085 CGACGAACCGTGCCCAATTA 61.015 55.000 0.00 0.00 41.37 1.40
591 1072 3.512154 TTTCACTGGCCTGGGCTGG 62.512 63.158 26.60 18.65 41.60 4.85
592 1073 1.531365 TTTTCACTGGCCTGGGCTG 60.531 57.895 22.70 22.70 41.60 4.85
593 1074 1.531602 GTTTTCACTGGCCTGGGCT 60.532 57.895 21.72 0.00 41.60 5.19
594 1075 1.531602 AGTTTTCACTGGCCTGGGC 60.532 57.895 14.23 14.23 41.06 5.36
595 1076 2.344535 CAGTTTTCACTGGCCTGGG 58.655 57.895 14.82 10.46 46.10 4.45
676 1168 2.355756 CCAAAACTGCATGTCCCTATCG 59.644 50.000 0.00 0.00 0.00 2.92
727 1224 2.688446 GGACTCCACTGATGTCATCGTA 59.312 50.000 8.29 0.00 32.84 3.43
804 1307 1.929494 AGAGAGAGAGGTGTGGGAGAT 59.071 52.381 0.00 0.00 0.00 2.75
836 1339 3.127895 AGAAGAAGACGAAGATGACGAGG 59.872 47.826 0.00 0.00 34.70 4.63
879 1386 2.519013 AGCTGGTGAATTGTTCCTTCC 58.481 47.619 0.00 0.00 0.00 3.46
880 1387 3.127721 GCTAGCTGGTGAATTGTTCCTTC 59.872 47.826 7.70 0.00 0.00 3.46
887 1394 1.202110 CGCAAGCTAGCTGGTGAATTG 60.202 52.381 25.78 15.46 29.30 2.32
906 1413 1.062294 GCAGAGAAGATCAAGCAAGCG 59.938 52.381 0.00 0.00 33.02 4.68
916 1423 0.743701 CGGCTTGCAGCAGAGAAGAT 60.744 55.000 9.78 0.00 44.75 2.40
969 1483 0.877743 GCCTGACAGAAGAGCCAAAC 59.122 55.000 3.32 0.00 0.00 2.93
977 1491 0.324285 AAGAGCCAGCCTGACAGAAG 59.676 55.000 3.32 0.00 0.00 2.85
1121 1653 2.658285 CAAAAGCAACAGTAGCAGCAG 58.342 47.619 0.00 0.00 0.00 4.24
1129 1661 0.029834 CGAGCAGCAAAAGCAACAGT 59.970 50.000 0.00 0.00 0.00 3.55
1179 1711 3.429141 GGGAGCGACGACGAGTGA 61.429 66.667 12.29 0.00 42.66 3.41
1432 1976 4.731612 CTGCGCTCTGACGGTGCT 62.732 66.667 9.73 0.00 40.39 4.40
1458 2002 1.666011 GGAGCACGACCTGACAAGA 59.334 57.895 0.00 0.00 0.00 3.02
1461 2005 2.203640 AGGGAGCACGACCTGACA 60.204 61.111 0.00 0.00 35.30 3.58
1465 2009 2.997897 GTCCAGGGAGCACGACCT 60.998 66.667 0.00 0.00 37.66 3.85
1554 2098 3.203412 CCGTCCTCCGACTCCTCG 61.203 72.222 0.00 0.00 39.56 4.63
1621 2165 2.444624 CGAAGATGTGCACCGTCCG 61.445 63.158 15.69 7.81 0.00 4.79
1656 2200 2.418368 ATCACCTGCAAGCGGATAAA 57.582 45.000 1.69 0.00 0.00 1.40
1658 2202 2.484770 GGTAATCACCTGCAAGCGGATA 60.485 50.000 1.69 0.00 42.11 2.59
1698 2242 1.949257 CGCCAACACAGTTTCTCCC 59.051 57.895 0.00 0.00 0.00 4.30
1699 2243 1.166531 AGCGCCAACACAGTTTCTCC 61.167 55.000 2.29 0.00 0.00 3.71
1700 2244 0.040958 CAGCGCCAACACAGTTTCTC 60.041 55.000 2.29 0.00 0.00 2.87
1702 2246 1.658409 GCAGCGCCAACACAGTTTC 60.658 57.895 2.29 0.00 0.00 2.78
1703 2247 2.340453 CTGCAGCGCCAACACAGTTT 62.340 55.000 2.29 0.00 0.00 2.66
1705 2249 3.282157 CTGCAGCGCCAACACAGT 61.282 61.111 2.29 0.00 0.00 3.55
1716 2260 4.400961 AGGCTTCGTCCCTGCAGC 62.401 66.667 8.66 0.00 0.00 5.25
1717 2261 2.125350 GAGGCTTCGTCCCTGCAG 60.125 66.667 6.78 6.78 31.41 4.41
1718 2262 4.069232 CGAGGCTTCGTCCCTGCA 62.069 66.667 10.50 0.00 41.84 4.41
1719 2263 3.760035 TCGAGGCTTCGTCCCTGC 61.760 66.667 18.33 0.00 46.72 4.85
1732 2276 2.097038 CCTGCTTTGAGGCGTCGAG 61.097 63.158 0.00 3.80 34.52 4.04
1733 2277 2.048222 CCTGCTTTGAGGCGTCGA 60.048 61.111 0.00 0.00 34.52 4.20
1735 2279 1.743252 CCTCCTGCTTTGAGGCGTC 60.743 63.158 0.00 0.00 42.75 5.19
1736 2280 2.348998 CCTCCTGCTTTGAGGCGT 59.651 61.111 4.22 0.00 42.75 5.68
1740 2284 0.676151 GCACCTCCTCCTGCTTTGAG 60.676 60.000 0.00 0.00 0.00 3.02
1741 2285 1.130054 AGCACCTCCTCCTGCTTTGA 61.130 55.000 0.00 0.00 41.04 2.69
1742 2286 0.959372 CAGCACCTCCTCCTGCTTTG 60.959 60.000 0.00 0.00 41.97 2.77
1743 2287 1.377994 CAGCACCTCCTCCTGCTTT 59.622 57.895 0.00 0.00 41.97 3.51
1744 2288 2.600729 CCAGCACCTCCTCCTGCTT 61.601 63.158 0.00 0.00 41.97 3.91
1745 2289 3.007920 CCAGCACCTCCTCCTGCT 61.008 66.667 0.00 0.00 44.82 4.24
1746 2290 4.792804 GCCAGCACCTCCTCCTGC 62.793 72.222 0.00 0.00 0.00 4.85
1747 2291 4.106925 GGCCAGCACCTCCTCCTG 62.107 72.222 0.00 0.00 0.00 3.86
1759 2303 3.058160 CACTTTGAGGGCGGCCAG 61.058 66.667 31.59 20.64 0.00 4.85
1762 2306 3.423154 CGACACTTTGAGGGCGGC 61.423 66.667 0.00 0.00 0.00 6.53
1763 2307 2.027625 GTCGACACTTTGAGGGCGG 61.028 63.158 11.55 0.00 0.00 6.13
1764 2308 2.027625 GGTCGACACTTTGAGGGCG 61.028 63.158 18.91 0.00 0.00 6.13
1765 2309 0.951040 CAGGTCGACACTTTGAGGGC 60.951 60.000 18.91 0.00 0.00 5.19
1766 2310 0.393077 ACAGGTCGACACTTTGAGGG 59.607 55.000 18.91 2.15 0.00 4.30
1767 2311 1.784525 GACAGGTCGACACTTTGAGG 58.215 55.000 18.91 2.81 0.00 3.86
1779 2323 0.388649 ATCTTGTGCGTCGACAGGTC 60.389 55.000 17.16 3.38 0.00 3.85
1781 2325 1.269166 GTATCTTGTGCGTCGACAGG 58.731 55.000 17.16 0.67 0.00 4.00
1782 2326 1.269166 GGTATCTTGTGCGTCGACAG 58.731 55.000 17.16 9.59 0.00 3.51
1783 2327 0.455464 CGGTATCTTGTGCGTCGACA 60.455 55.000 17.16 0.00 0.00 4.35
1784 2328 1.138047 CCGGTATCTTGTGCGTCGAC 61.138 60.000 5.18 5.18 0.00 4.20
1785 2329 1.138036 CCGGTATCTTGTGCGTCGA 59.862 57.895 0.00 0.00 0.00 4.20
1786 2330 1.153901 ACCGGTATCTTGTGCGTCG 60.154 57.895 4.49 0.00 0.00 5.12
1787 2331 0.108992 TCACCGGTATCTTGTGCGTC 60.109 55.000 6.87 0.00 0.00 5.19
1788 2332 0.319083 TTCACCGGTATCTTGTGCGT 59.681 50.000 6.87 0.00 0.00 5.24
1799 2367 0.246635 CGTTCCTGATCTTCACCGGT 59.753 55.000 0.00 0.00 0.00 5.28
1808 2376 6.015856 TCCTGATCTTCTTATCGTTCCTGATC 60.016 42.308 0.00 0.00 0.00 2.92
1810 2378 5.201243 TCCTGATCTTCTTATCGTTCCTGA 58.799 41.667 0.00 0.00 0.00 3.86
1811 2379 5.521906 TCCTGATCTTCTTATCGTTCCTG 57.478 43.478 0.00 0.00 0.00 3.86
1839 2407 1.904865 TTGCAGGCCAAGCAAGAGG 60.905 57.895 25.99 0.00 46.13 3.69
1859 2427 0.957395 GGACCTGTGATGTGGCACTG 60.957 60.000 19.83 2.26 39.49 3.66
1894 2462 0.107800 TGCTCTCTGCTTCTCATGGC 60.108 55.000 0.00 0.00 43.37 4.40
1900 2468 1.346062 TCCTTGTGCTCTCTGCTTCT 58.654 50.000 0.00 0.00 43.37 2.85
1906 2474 2.641815 ACATTCCTTCCTTGTGCTCTCT 59.358 45.455 0.00 0.00 0.00 3.10
1937 2505 0.735287 GCCGAACCTACTCCGACAAC 60.735 60.000 0.00 0.00 0.00 3.32
1943 2511 1.411041 ATGGTAGCCGAACCTACTCC 58.589 55.000 2.54 0.00 40.44 3.85
1967 2535 2.478831 GCAGCTTCTGTGCTATAGGTC 58.521 52.381 1.04 0.00 41.98 3.85
1968 2536 2.611225 GCAGCTTCTGTGCTATAGGT 57.389 50.000 1.04 0.00 41.98 3.08
1975 2543 3.691110 GCTTAAGCAGCTTCTGTGC 57.309 52.632 22.59 8.26 46.27 4.57
2018 2592 9.683069 AGCTCACAAATTACTAACAAAAAGATG 57.317 29.630 0.00 0.00 0.00 2.90
2021 2595 8.745837 CACAGCTCACAAATTACTAACAAAAAG 58.254 33.333 0.00 0.00 0.00 2.27
2027 2601 6.787085 AGTCACAGCTCACAAATTACTAAC 57.213 37.500 0.00 0.00 0.00 2.34
2030 2604 5.368145 TCAAGTCACAGCTCACAAATTACT 58.632 37.500 0.00 0.00 0.00 2.24
2031 2605 5.673337 TCAAGTCACAGCTCACAAATTAC 57.327 39.130 0.00 0.00 0.00 1.89
2079 2658 1.804151 GCTTGGCGTAGATCAACAACA 59.196 47.619 0.00 0.00 0.00 3.33
2093 2672 2.639286 CAACTCACACCGCTTGGC 59.361 61.111 0.00 0.00 35.53 4.52
2099 2678 1.535462 GATTCAACCCAACTCACACCG 59.465 52.381 0.00 0.00 0.00 4.94
2129 2708 1.888512 GCCATCCTGTGACACAACAAT 59.111 47.619 10.02 0.77 0.00 2.71
2131 2710 0.473755 AGCCATCCTGTGACACAACA 59.526 50.000 10.02 0.00 0.00 3.33
2132 2711 1.609208 AAGCCATCCTGTGACACAAC 58.391 50.000 10.02 0.00 0.00 3.32
2134 2713 1.003118 GGTAAGCCATCCTGTGACACA 59.997 52.381 8.26 8.26 34.09 3.72
2153 2732 3.370978 GTCTGATGGTAATTGTCACACGG 59.629 47.826 0.00 0.00 0.00 4.94
2197 2776 0.254178 ATCAGGGAAGACGCAGCAAT 59.746 50.000 0.00 0.00 0.00 3.56
2198 2777 0.036732 AATCAGGGAAGACGCAGCAA 59.963 50.000 0.00 0.00 0.00 3.91
2224 2803 0.306840 TATCGGAGATCACGTCACGC 59.693 55.000 0.00 0.00 45.12 5.34
2228 2807 2.840673 CGTCATATCGGAGATCACGTC 58.159 52.381 0.71 0.00 45.12 4.34
2229 2808 2.971430 CGTCATATCGGAGATCACGT 57.029 50.000 0.71 0.00 45.12 4.49
2288 2913 1.482955 CGCGTCACGTTGAGACTTG 59.517 57.895 0.00 0.00 36.87 3.16
2289 2914 2.300787 GCGCGTCACGTTGAGACTT 61.301 57.895 8.43 0.00 46.11 3.01
2290 2915 2.729862 GCGCGTCACGTTGAGACT 60.730 61.111 8.43 0.00 46.11 3.24
2323 2948 0.891373 TCGTTCCAGCTCTTCAGAGG 59.109 55.000 5.97 0.00 42.29 3.69
2347 2972 2.865308 CACGACATGTGCTGCAGG 59.135 61.111 17.12 0.00 42.70 4.85
2369 2994 8.672815 GGAAAATATTCTTCTCTGTTTGAGAGG 58.327 37.037 0.00 0.00 46.50 3.69
2406 3031 4.209703 TGACGTACGAAATGAAGACAAACC 59.790 41.667 24.41 0.00 0.00 3.27
2415 3040 4.214758 TCTCAACTCTGACGTACGAAATGA 59.785 41.667 24.41 13.75 0.00 2.57
2426 3051 5.702670 TGGATGACAATTTCTCAACTCTGAC 59.297 40.000 0.00 0.00 0.00 3.51
2435 3060 2.027385 GGCCCTGGATGACAATTTCTC 58.973 52.381 0.00 0.00 0.00 2.87
2494 3120 9.713713 GGGTTCTTATCTTATGTAAGAAGGATC 57.286 37.037 6.57 0.00 44.41 3.36
2593 3219 9.949174 TTCAATCATGTAACCATTTTATGATCG 57.051 29.630 0.00 0.00 37.47 3.69
2630 3256 8.742554 TTCGCTTTATTCTTCCTTGATTTTTC 57.257 30.769 0.00 0.00 0.00 2.29
2635 3261 6.238211 CGTCATTCGCTTTATTCTTCCTTGAT 60.238 38.462 0.00 0.00 0.00 2.57
2636 3262 5.063438 CGTCATTCGCTTTATTCTTCCTTGA 59.937 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.