Multiple sequence alignment - TraesCS6A01G132500

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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 TraesCS6A01G132500 chr6A 100.000 5811 0 0 1 5811 104449167 104443357 0.000000e+00 10695.0
1 TraesCS6A01G132500 chr6A 98.668 3379 22 9 1925 5296 104356345 104359707 0.000000e+00 5969.0
2 TraesCS6A01G132500 chr6A 99.698 1658 5 0 257 1914 104354545 104356202 0.000000e+00 3035.0
3 TraesCS6A01G132500 chr6A 84.740 308 22 9 5310 5612 104359692 104359979 9.530000e-73 285.0
4 TraesCS6A01G132500 chr6D 95.379 3376 120 13 1930 5296 86658172 86661520 0.000000e+00 5337.0
5 TraesCS6A01G132500 chr6D 91.261 595 22 12 269 853 86656343 86656917 0.000000e+00 784.0
6 TraesCS6A01G132500 chr6D 95.561 383 12 3 858 1235 86656956 86657338 4.980000e-170 608.0
7 TraesCS6A01G132500 chr6D 85.911 582 61 14 1289 1857 86657447 86658020 8.330000e-168 601.0
8 TraesCS6A01G132500 chr6D 90.728 151 10 1 5310 5460 86661505 86661651 1.280000e-46 198.0
9 TraesCS6A01G132500 chr6B 95.738 2698 84 13 2613 5296 164358108 164360788 0.000000e+00 4316.0
10 TraesCS6A01G132500 chr6B 92.970 953 30 12 257 1182 164356733 164357675 0.000000e+00 1354.0
11 TraesCS6A01G132500 chr6B 96.875 352 11 0 1925 2276 164357745 164358096 1.800000e-164 590.0
12 TraesCS6A01G132500 chr5B 85.784 612 84 3 4227 4837 684120915 684120306 0.000000e+00 645.0
13 TraesCS6A01G132500 chr5B 75.815 736 155 21 4086 4811 560442162 560441440 9.260000e-93 351.0
14 TraesCS6A01G132500 chr5B 86.822 129 13 3 2650 2776 684130820 684130694 2.180000e-29 141.0
15 TraesCS6A01G132500 chr5B 89.091 55 6 0 1127 1181 561064775 561064721 1.040000e-07 69.4
16 TraesCS6A01G132500 chr5B 89.583 48 5 0 1127 1174 560444538 560444491 1.750000e-05 62.1
17 TraesCS6A01G132500 chr4D 75.290 1036 239 17 3783 4811 15913236 15912211 4.070000e-131 479.0
18 TraesCS6A01G132500 chr4D 71.930 684 142 33 2658 3331 15914627 15913984 2.800000e-33 154.0
19 TraesCS6A01G132500 chr4A 75.024 1037 217 19 3780 4811 584679679 584680678 5.340000e-120 442.0
20 TraesCS6A01G132500 chr4A 75.048 1034 216 19 3783 4811 584735245 584734249 5.340000e-120 442.0
21 TraesCS6A01G132500 chr5A 75.549 728 165 12 4090 4812 576085595 576084876 4.310000e-91 346.0
22 TraesCS6A01G132500 chr5A 75.549 728 165 12 4090 4812 576271836 576272555 4.310000e-91 346.0
23 TraesCS6A01G132500 chr5A 96.970 33 1 0 1218 1250 558137369 558137401 8.130000e-04 56.5
24 TraesCS6A01G132500 chr4B 75.620 726 162 15 4092 4811 27519688 27518972 4.310000e-91 346.0
25 TraesCS6A01G132500 chr4B 73.139 685 134 29 2657 3331 27521791 27521147 3.550000e-47 200.0
26 TraesCS6A01G132500 chr4B 72.904 668 129 31 2657 3313 27249689 27250315 3.580000e-42 183.0
27 TraesCS6A01G132500 chr4B 78.599 257 51 4 3783 4037 27520220 27519966 3.600000e-37 167.0
28 TraesCS6A01G132500 chr4B 87.912 91 9 2 2344 2433 398567124 398567035 7.960000e-19 106.0
29 TraesCS6A01G132500 chr5D 75.370 743 160 21 4079 4811 458095519 458094790 2.590000e-88 337.0
30 TraesCS6A01G132500 chr5D 81.529 157 24 4 2657 2812 537224589 537224437 2.200000e-24 124.0
31 TraesCS6A01G132500 chr5D 89.583 48 5 0 1127 1174 458097945 458097898 1.750000e-05 62.1
32 TraesCS6A01G132500 chr7A 81.679 131 17 7 41 169 16725983 16725858 1.030000e-17 102.0
33 TraesCS6A01G132500 chr7A 88.060 67 5 3 2352 2416 539439230 539439165 6.240000e-10 76.8
34 TraesCS6A01G132500 chr2D 86.207 87 10 2 2343 2428 627330479 627330394 6.200000e-15 93.5
35 TraesCS6A01G132500 chr2D 82.828 99 16 1 2362 2459 537462948 537462850 2.880000e-13 87.9
36 TraesCS6A01G132500 chr2D 79.839 124 20 5 1550 1670 36226218 36226097 1.040000e-12 86.1
37 TraesCS6A01G132500 chr2A 77.305 141 24 7 1467 1601 39582156 39582018 6.240000e-10 76.8
38 TraesCS6A01G132500 chr2A 76.101 159 28 9 1450 1601 39945327 39945482 2.250000e-09 75.0
39 TraesCS6A01G132500 chr2B 92.453 53 1 3 1550 1600 789613068 789613119 8.080000e-09 73.1
40 TraesCS6A01G132500 chr2B 77.876 113 25 0 2344 2456 6196658 6196770 2.910000e-08 71.3
41 TraesCS6A01G132500 chr1A 88.525 61 6 1 2361 2420 480933520 480933460 8.080000e-09 73.1
42 TraesCS6A01G132500 chr7D 76.048 167 20 11 41 199 17422192 17422038 1.040000e-07 69.4
43 TraesCS6A01G132500 chr3A 90.000 50 3 2 2344 2392 423857174 423857222 4.860000e-06 63.9
44 TraesCS6A01G132500 chr7B 94.595 37 1 1 4882 4918 741949633 741949668 8.130000e-04 56.5


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 TraesCS6A01G132500 chr6A 104443357 104449167 5810 True 10695.000000 10695 100.000000 1 5811 1 chr6A.!!$R1 5810
1 TraesCS6A01G132500 chr6A 104354545 104359979 5434 False 3096.333333 5969 94.368667 257 5612 3 chr6A.!!$F1 5355
2 TraesCS6A01G132500 chr6D 86656343 86661651 5308 False 1505.600000 5337 91.768000 269 5460 5 chr6D.!!$F1 5191
3 TraesCS6A01G132500 chr6B 164356733 164360788 4055 False 2086.666667 4316 95.194333 257 5296 3 chr6B.!!$F1 5039
4 TraesCS6A01G132500 chr5B 684120306 684120915 609 True 645.000000 645 85.784000 4227 4837 1 chr5B.!!$R2 610
5 TraesCS6A01G132500 chr5B 560441440 560444538 3098 True 206.550000 351 82.699000 1127 4811 2 chr5B.!!$R4 3684
6 TraesCS6A01G132500 chr4D 15912211 15914627 2416 True 316.500000 479 73.610000 2658 4811 2 chr4D.!!$R1 2153
7 TraesCS6A01G132500 chr4A 584679679 584680678 999 False 442.000000 442 75.024000 3780 4811 1 chr4A.!!$F1 1031
8 TraesCS6A01G132500 chr4A 584734249 584735245 996 True 442.000000 442 75.048000 3783 4811 1 chr4A.!!$R1 1028
9 TraesCS6A01G132500 chr5A 576084876 576085595 719 True 346.000000 346 75.549000 4090 4812 1 chr5A.!!$R1 722
10 TraesCS6A01G132500 chr5A 576271836 576272555 719 False 346.000000 346 75.549000 4090 4812 1 chr5A.!!$F2 722
11 TraesCS6A01G132500 chr4B 27518972 27521791 2819 True 237.666667 346 75.786000 2657 4811 3 chr4B.!!$R2 2154

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
232 233 0.031857 CATACCAGGAGCAGCTCGAG 59.968 60.0 16.47 8.45 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
5068 6269 8.902806 TGTCAAATTCAAAATCAGTAGACAAGT 58.097 29.63 0.0 0.0 30.32 3.16 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
22 23 2.557924 TCACATTTGTGGAAGTCATGGC 59.442 45.455 10.60 0.00 45.65 4.40
23 24 1.541147 ACATTTGTGGAAGTCATGGCG 59.459 47.619 0.00 0.00 0.00 5.69
24 25 1.135315 CATTTGTGGAAGTCATGGCGG 60.135 52.381 0.00 0.00 0.00 6.13
25 26 0.109532 TTTGTGGAAGTCATGGCGGA 59.890 50.000 0.00 0.00 0.00 5.54
26 27 0.109532 TTGTGGAAGTCATGGCGGAA 59.890 50.000 0.00 0.00 0.00 4.30
27 28 0.109532 TGTGGAAGTCATGGCGGAAA 59.890 50.000 0.00 0.00 0.00 3.13
28 29 1.243902 GTGGAAGTCATGGCGGAAAA 58.756 50.000 0.00 0.00 0.00 2.29
29 30 1.200020 GTGGAAGTCATGGCGGAAAAG 59.800 52.381 0.00 0.00 0.00 2.27
30 31 0.811281 GGAAGTCATGGCGGAAAAGG 59.189 55.000 0.00 0.00 0.00 3.11
31 32 0.171231 GAAGTCATGGCGGAAAAGGC 59.829 55.000 0.00 0.00 37.19 4.35
38 39 4.354155 GCGGAAAAGGCCAAAACC 57.646 55.556 5.01 1.85 0.00 3.27
39 40 1.443828 GCGGAAAAGGCCAAAACCA 59.556 52.632 5.01 0.00 0.00 3.67
40 41 0.179070 GCGGAAAAGGCCAAAACCAA 60.179 50.000 5.01 0.00 0.00 3.67
41 42 1.542328 GCGGAAAAGGCCAAAACCAAT 60.542 47.619 5.01 0.00 0.00 3.16
42 43 2.142319 CGGAAAAGGCCAAAACCAATG 58.858 47.619 5.01 0.00 0.00 2.82
43 44 2.484594 CGGAAAAGGCCAAAACCAATGT 60.485 45.455 5.01 0.00 0.00 2.71
44 45 3.550820 GGAAAAGGCCAAAACCAATGTT 58.449 40.909 5.01 0.00 35.82 2.71
45 46 3.563808 GGAAAAGGCCAAAACCAATGTTC 59.436 43.478 5.01 0.00 32.15 3.18
46 47 4.450976 GAAAAGGCCAAAACCAATGTTCT 58.549 39.130 5.01 0.00 32.15 3.01
47 48 3.473923 AAGGCCAAAACCAATGTTCTG 57.526 42.857 5.01 0.00 32.15 3.02
48 49 2.676748 AGGCCAAAACCAATGTTCTGA 58.323 42.857 5.01 0.00 32.15 3.27
49 50 3.037549 AGGCCAAAACCAATGTTCTGAA 58.962 40.909 5.01 0.00 32.15 3.02
50 51 3.454082 AGGCCAAAACCAATGTTCTGAAA 59.546 39.130 5.01 0.00 32.15 2.69
51 52 4.080638 AGGCCAAAACCAATGTTCTGAAAA 60.081 37.500 5.01 0.00 32.15 2.29
52 53 4.821260 GGCCAAAACCAATGTTCTGAAAAT 59.179 37.500 0.00 0.00 32.15 1.82
53 54 5.277925 GGCCAAAACCAATGTTCTGAAAATG 60.278 40.000 0.00 0.00 32.15 2.32
54 55 5.277925 GCCAAAACCAATGTTCTGAAAATGG 60.278 40.000 12.98 12.98 32.15 3.16
55 56 5.821995 CCAAAACCAATGTTCTGAAAATGGT 59.178 36.000 13.97 13.97 42.70 3.55
56 57 6.989169 CCAAAACCAATGTTCTGAAAATGGTA 59.011 34.615 17.90 0.00 40.13 3.25
57 58 7.042119 CCAAAACCAATGTTCTGAAAATGGTAC 60.042 37.037 17.90 0.00 40.13 3.34
58 59 6.976934 AACCAATGTTCTGAAAATGGTACT 57.023 33.333 17.90 6.30 40.13 2.73
59 60 6.976934 ACCAATGTTCTGAAAATGGTACTT 57.023 33.333 16.73 0.00 39.29 2.24
60 61 7.360113 ACCAATGTTCTGAAAATGGTACTTT 57.640 32.000 16.73 0.00 39.29 2.66
61 62 7.433680 ACCAATGTTCTGAAAATGGTACTTTC 58.566 34.615 16.73 0.00 39.29 2.62
62 63 7.069331 ACCAATGTTCTGAAAATGGTACTTTCA 59.931 33.333 16.73 8.10 39.29 2.69
63 64 7.925483 CCAATGTTCTGAAAATGGTACTTTCAA 59.075 33.333 9.31 0.00 41.10 2.69
64 65 9.311916 CAATGTTCTGAAAATGGTACTTTCAAA 57.688 29.630 9.31 5.49 41.10 2.69
65 66 8.871686 ATGTTCTGAAAATGGTACTTTCAAAC 57.128 30.769 9.31 13.67 41.10 2.93
66 67 6.970043 TGTTCTGAAAATGGTACTTTCAAACG 59.030 34.615 9.31 0.94 41.10 3.60
67 68 5.516090 TCTGAAAATGGTACTTTCAAACGC 58.484 37.500 9.31 0.00 41.10 4.84
68 69 5.066634 TCTGAAAATGGTACTTTCAAACGCA 59.933 36.000 9.31 0.00 41.10 5.24
69 70 5.837437 TGAAAATGGTACTTTCAAACGCAT 58.163 33.333 6.36 0.00 39.28 4.73
70 71 6.276847 TGAAAATGGTACTTTCAAACGCATT 58.723 32.000 6.36 0.00 39.28 3.56
71 72 6.758886 TGAAAATGGTACTTTCAAACGCATTT 59.241 30.769 6.36 0.00 39.28 2.32
72 73 7.278868 TGAAAATGGTACTTTCAAACGCATTTT 59.721 29.630 11.13 11.13 39.28 1.82
73 74 6.523676 AATGGTACTTTCAAACGCATTTTG 57.476 33.333 2.03 2.03 45.38 2.44
74 75 4.363999 TGGTACTTTCAAACGCATTTTGG 58.636 39.130 7.70 0.00 44.30 3.28
75 76 4.098044 TGGTACTTTCAAACGCATTTTGGA 59.902 37.500 7.70 0.00 44.30 3.53
76 77 4.679654 GGTACTTTCAAACGCATTTTGGAG 59.320 41.667 7.70 8.42 44.30 3.86
77 78 3.123050 ACTTTCAAACGCATTTTGGAGC 58.877 40.909 7.70 0.00 44.30 4.70
78 79 2.147436 TTCAAACGCATTTTGGAGCC 57.853 45.000 7.70 0.00 44.30 4.70
79 80 1.327303 TCAAACGCATTTTGGAGCCT 58.673 45.000 7.70 0.00 44.30 4.58
80 81 1.686052 TCAAACGCATTTTGGAGCCTT 59.314 42.857 7.70 0.00 44.30 4.35
81 82 1.794116 CAAACGCATTTTGGAGCCTTG 59.206 47.619 0.66 0.00 40.98 3.61
82 83 1.327303 AACGCATTTTGGAGCCTTGA 58.673 45.000 0.00 0.00 0.00 3.02
83 84 1.549203 ACGCATTTTGGAGCCTTGAT 58.451 45.000 0.00 0.00 0.00 2.57
84 85 1.895131 ACGCATTTTGGAGCCTTGATT 59.105 42.857 0.00 0.00 0.00 2.57
85 86 2.299867 ACGCATTTTGGAGCCTTGATTT 59.700 40.909 0.00 0.00 0.00 2.17
86 87 3.244181 ACGCATTTTGGAGCCTTGATTTT 60.244 39.130 0.00 0.00 0.00 1.82
87 88 4.021544 ACGCATTTTGGAGCCTTGATTTTA 60.022 37.500 0.00 0.00 0.00 1.52
88 89 5.111293 CGCATTTTGGAGCCTTGATTTTAT 58.889 37.500 0.00 0.00 0.00 1.40
89 90 5.581874 CGCATTTTGGAGCCTTGATTTTATT 59.418 36.000 0.00 0.00 0.00 1.40
90 91 6.092533 CGCATTTTGGAGCCTTGATTTTATTT 59.907 34.615 0.00 0.00 0.00 1.40
91 92 7.361116 CGCATTTTGGAGCCTTGATTTTATTTT 60.361 33.333 0.00 0.00 0.00 1.82
92 93 8.945057 GCATTTTGGAGCCTTGATTTTATTTTA 58.055 29.630 0.00 0.00 0.00 1.52
98 99 8.945057 TGGAGCCTTGATTTTATTTTATTTTGC 58.055 29.630 0.00 0.00 0.00 3.68
99 100 8.397906 GGAGCCTTGATTTTATTTTATTTTGCC 58.602 33.333 0.00 0.00 0.00 4.52
100 101 8.860780 AGCCTTGATTTTATTTTATTTTGCCA 57.139 26.923 0.00 0.00 0.00 4.92
101 102 8.729756 AGCCTTGATTTTATTTTATTTTGCCAC 58.270 29.630 0.00 0.00 0.00 5.01
102 103 7.691877 GCCTTGATTTTATTTTATTTTGCCACG 59.308 33.333 0.00 0.00 0.00 4.94
103 104 8.930760 CCTTGATTTTATTTTATTTTGCCACGA 58.069 29.630 0.00 0.00 0.00 4.35
111 112 7.721286 ATTTTATTTTGCCACGATTTTCACA 57.279 28.000 0.00 0.00 0.00 3.58
112 113 7.539712 TTTTATTTTGCCACGATTTTCACAA 57.460 28.000 0.00 0.00 0.00 3.33
113 114 6.517914 TTATTTTGCCACGATTTTCACAAC 57.482 33.333 0.00 0.00 0.00 3.32
114 115 3.791973 TTTGCCACGATTTTCACAACT 57.208 38.095 0.00 0.00 0.00 3.16
115 116 2.772568 TGCCACGATTTTCACAACTG 57.227 45.000 0.00 0.00 0.00 3.16
116 117 2.020720 TGCCACGATTTTCACAACTGT 58.979 42.857 0.00 0.00 0.00 3.55
117 118 2.223456 TGCCACGATTTTCACAACTGTG 60.223 45.455 3.33 3.33 46.91 3.66
131 132 5.874895 ACAACTGTGATGTCATGATGAAG 57.125 39.130 0.00 0.00 0.00 3.02
132 133 4.155462 ACAACTGTGATGTCATGATGAAGC 59.845 41.667 0.00 0.00 0.00 3.86
133 134 4.217836 ACTGTGATGTCATGATGAAGCT 57.782 40.909 0.00 0.00 0.00 3.74
134 135 4.586884 ACTGTGATGTCATGATGAAGCTT 58.413 39.130 0.00 0.00 0.00 3.74
135 136 4.634883 ACTGTGATGTCATGATGAAGCTTC 59.365 41.667 19.89 19.89 0.00 3.86
136 137 4.840271 TGTGATGTCATGATGAAGCTTCT 58.160 39.130 26.09 12.48 0.00 2.85
137 138 4.874396 TGTGATGTCATGATGAAGCTTCTC 59.126 41.667 26.09 19.81 0.00 2.87
138 139 4.874396 GTGATGTCATGATGAAGCTTCTCA 59.126 41.667 26.09 23.96 0.00 3.27
139 140 5.353400 GTGATGTCATGATGAAGCTTCTCAA 59.647 40.000 26.09 12.23 0.00 3.02
140 141 5.585047 TGATGTCATGATGAAGCTTCTCAAG 59.415 40.000 26.09 20.97 0.00 3.02
221 222 9.189156 TCTTGAAATTTTCCTATTCATACCAGG 57.811 33.333 6.68 0.00 33.45 4.45
222 223 9.189156 CTTGAAATTTTCCTATTCATACCAGGA 57.811 33.333 6.68 0.00 36.68 3.86
223 224 8.752005 TGAAATTTTCCTATTCATACCAGGAG 57.248 34.615 6.68 0.00 39.58 3.69
224 225 7.285401 TGAAATTTTCCTATTCATACCAGGAGC 59.715 37.037 6.68 0.00 39.58 4.70
225 226 5.708736 TTTTCCTATTCATACCAGGAGCA 57.291 39.130 0.00 0.00 39.58 4.26
226 227 4.963318 TTCCTATTCATACCAGGAGCAG 57.037 45.455 0.00 0.00 39.58 4.24
227 228 2.634940 TCCTATTCATACCAGGAGCAGC 59.365 50.000 0.00 0.00 33.48 5.25
228 229 2.636893 CCTATTCATACCAGGAGCAGCT 59.363 50.000 0.00 0.00 0.00 4.24
229 230 2.926778 ATTCATACCAGGAGCAGCTC 57.073 50.000 14.69 14.69 0.00 4.09
230 231 0.461548 TTCATACCAGGAGCAGCTCG 59.538 55.000 16.47 5.30 0.00 5.03
231 232 0.395724 TCATACCAGGAGCAGCTCGA 60.396 55.000 16.47 3.13 0.00 4.04
232 233 0.031857 CATACCAGGAGCAGCTCGAG 59.968 60.000 16.47 8.45 0.00 4.04
233 234 1.743321 ATACCAGGAGCAGCTCGAGC 61.743 60.000 30.01 30.01 42.49 5.03
245 246 4.120244 TCGAGCTGAGAAAGGGCT 57.880 55.556 0.00 0.00 39.16 5.19
246 247 2.366469 TCGAGCTGAGAAAGGGCTT 58.634 52.632 0.00 0.00 36.37 4.35
247 248 0.247736 TCGAGCTGAGAAAGGGCTTC 59.752 55.000 0.00 0.00 36.37 3.86
248 249 0.036952 CGAGCTGAGAAAGGGCTTCA 60.037 55.000 0.00 0.00 36.40 3.02
249 250 1.406614 CGAGCTGAGAAAGGGCTTCAT 60.407 52.381 0.00 0.00 36.40 2.57
250 251 2.159043 CGAGCTGAGAAAGGGCTTCATA 60.159 50.000 0.00 0.00 36.40 2.15
251 252 3.494048 CGAGCTGAGAAAGGGCTTCATAT 60.494 47.826 0.00 0.00 36.40 1.78
252 253 4.459330 GAGCTGAGAAAGGGCTTCATATT 58.541 43.478 0.00 0.00 36.40 1.28
253 254 5.615289 GAGCTGAGAAAGGGCTTCATATTA 58.385 41.667 0.00 0.00 36.40 0.98
254 255 6.198237 AGCTGAGAAAGGGCTTCATATTAT 57.802 37.500 0.00 0.00 36.40 1.28
255 256 6.608922 AGCTGAGAAAGGGCTTCATATTATT 58.391 36.000 0.00 0.00 36.40 1.40
264 265 6.601332 AGGGCTTCATATTATTTTCCGAAGA 58.399 36.000 0.00 0.00 33.33 2.87
267 268 7.355778 GGCTTCATATTATTTTCCGAAGACAG 58.644 38.462 0.00 0.00 38.20 3.51
280 281 3.188048 CCGAAGACAGTAGTACAAGTCGT 59.812 47.826 15.79 13.90 36.18 4.34
285 286 5.001874 AGACAGTAGTACAAGTCGTGATCA 58.998 41.667 15.79 0.00 36.18 2.92
5064 6265 0.807667 AGCGAGCGTCTATTTGCCTG 60.808 55.000 0.00 0.00 0.00 4.85
5065 6266 1.084370 GCGAGCGTCTATTTGCCTGT 61.084 55.000 0.00 0.00 0.00 4.00
5066 6267 0.924090 CGAGCGTCTATTTGCCTGTC 59.076 55.000 0.00 0.00 0.00 3.51
5067 6268 1.469940 CGAGCGTCTATTTGCCTGTCT 60.470 52.381 0.00 0.00 0.00 3.41
5068 6269 2.223502 CGAGCGTCTATTTGCCTGTCTA 60.224 50.000 0.00 0.00 0.00 2.59
5069 6270 3.117046 GAGCGTCTATTTGCCTGTCTAC 58.883 50.000 0.00 0.00 0.00 2.59
5070 6271 2.761208 AGCGTCTATTTGCCTGTCTACT 59.239 45.455 0.00 0.00 0.00 2.57
5071 6272 3.195825 AGCGTCTATTTGCCTGTCTACTT 59.804 43.478 0.00 0.00 0.00 2.24
5139 6340 7.242783 TCATAACGACACATGTTGATGATTTG 58.757 34.615 6.25 0.00 33.36 2.32
5144 6345 3.056393 ACACATGTTGATGATTTGGCTGG 60.056 43.478 0.00 0.00 33.36 4.85
5166 6367 2.207590 GTCGACCACTTTTTCTTCCGT 58.792 47.619 3.51 0.00 0.00 4.69
5168 6369 3.803778 GTCGACCACTTTTTCTTCCGTAA 59.196 43.478 3.51 0.00 0.00 3.18
5169 6370 4.270808 GTCGACCACTTTTTCTTCCGTAAA 59.729 41.667 3.51 0.00 0.00 2.01
5175 6376 8.415192 ACCACTTTTTCTTCCGTAAATTTTTC 57.585 30.769 0.00 0.00 0.00 2.29
5176 6377 7.221259 ACCACTTTTTCTTCCGTAAATTTTTCG 59.779 33.333 0.00 2.31 0.00 3.46
5179 6381 9.142515 ACTTTTTCTTCCGTAAATTTTTCGTTT 57.857 25.926 0.00 0.00 0.00 3.60
5193 6395 9.899226 AAATTTTTCGTTTTCTCTTCTCTATGG 57.101 29.630 0.00 0.00 0.00 2.74
5259 6464 4.143431 CGTGGCAACCATAATTTTTGTTCG 60.143 41.667 0.00 0.00 35.28 3.95
5289 6494 9.507329 TTTCTACTGAAGATGATAACTTTTGCT 57.493 29.630 0.00 0.00 33.05 3.91
5290 6495 8.709386 TCTACTGAAGATGATAACTTTTGCTC 57.291 34.615 0.00 0.00 0.00 4.26
5294 6499 9.624373 ACTGAAGATGATAACTTTTGCTCATAT 57.376 29.630 0.00 0.00 0.00 1.78
5300 6505 9.173939 GATGATAACTTTTGCTCATATTTTCCG 57.826 33.333 0.00 0.00 0.00 4.30
5301 6506 6.972328 TGATAACTTTTGCTCATATTTTCCGC 59.028 34.615 0.00 0.00 0.00 5.54
5302 6507 4.782019 ACTTTTGCTCATATTTTCCGCA 57.218 36.364 0.00 0.00 0.00 5.69
5303 6508 5.132897 ACTTTTGCTCATATTTTCCGCAA 57.867 34.783 0.00 0.00 38.65 4.85
5304 6509 5.537188 ACTTTTGCTCATATTTTCCGCAAA 58.463 33.333 0.00 0.00 45.47 3.68
5424 6629 9.196552 AGTTGTTTCTTGCTCTATAAATTTTGC 57.803 29.630 0.00 0.00 0.00 3.68
5500 6705 6.865834 AATCTTGGCACATACCCAATTTAA 57.134 33.333 0.00 0.00 41.23 1.52
5501 6706 7.436320 AATCTTGGCACATACCCAATTTAAT 57.564 32.000 0.00 0.00 41.23 1.40
5502 6707 6.463995 TCTTGGCACATACCCAATTTAATC 57.536 37.500 0.00 0.00 41.23 1.75
5503 6708 6.194235 TCTTGGCACATACCCAATTTAATCT 58.806 36.000 0.00 0.00 41.23 2.40
5504 6709 6.667414 TCTTGGCACATACCCAATTTAATCTT 59.333 34.615 0.00 0.00 41.23 2.40
5505 6710 6.463995 TGGCACATACCCAATTTAATCTTC 57.536 37.500 0.00 0.00 0.00 2.87
5506 6711 5.362430 TGGCACATACCCAATTTAATCTTCC 59.638 40.000 0.00 0.00 0.00 3.46
5507 6712 5.221441 GGCACATACCCAATTTAATCTTCCC 60.221 44.000 0.00 0.00 0.00 3.97
5508 6713 5.362430 GCACATACCCAATTTAATCTTCCCA 59.638 40.000 0.00 0.00 0.00 4.37
5526 6731 2.480073 CCCATGCAGCGAGTTTTAATGG 60.480 50.000 0.00 0.00 34.21 3.16
5531 6736 2.162408 GCAGCGAGTTTTAATGGAGCTT 59.838 45.455 0.00 0.00 0.00 3.74
5556 6761 8.742125 TCTCCCATATAGGAACAAAGATGTAT 57.258 34.615 0.00 0.00 41.22 2.29
5566 6771 8.045720 AGGAACAAAGATGTATATATGTGGGT 57.954 34.615 0.00 0.00 39.40 4.51
5567 6772 8.502738 AGGAACAAAGATGTATATATGTGGGTT 58.497 33.333 0.00 0.00 39.40 4.11
5569 6774 9.561069 GAACAAAGATGTATATATGTGGGTTCT 57.439 33.333 12.30 0.00 39.40 3.01
5593 6802 4.986587 CCCGCGACGTGTCACGAA 62.987 66.667 30.95 0.00 46.05 3.85
5606 6815 4.614284 CGTGTCACGAAACGTAAATCTAGT 59.386 41.667 20.75 0.00 46.05 2.57
5612 6821 4.143115 ACGAAACGTAAATCTAGTCGTCGA 60.143 41.667 0.00 0.00 38.73 4.20
5613 6822 4.960354 CGAAACGTAAATCTAGTCGTCGAT 59.040 41.667 0.00 0.00 35.49 3.59
5614 6823 5.109224 CGAAACGTAAATCTAGTCGTCGATG 60.109 44.000 0.00 0.00 35.49 3.84
5615 6824 4.206698 ACGTAAATCTAGTCGTCGATGG 57.793 45.455 4.48 0.00 30.71 3.51
5616 6825 3.003068 ACGTAAATCTAGTCGTCGATGGG 59.997 47.826 4.48 0.00 30.71 4.00
5617 6826 3.003068 CGTAAATCTAGTCGTCGATGGGT 59.997 47.826 4.48 0.00 0.00 4.51
5618 6827 3.438297 AAATCTAGTCGTCGATGGGTG 57.562 47.619 4.48 0.00 0.00 4.61
5619 6828 2.343484 ATCTAGTCGTCGATGGGTGA 57.657 50.000 4.48 0.00 0.00 4.02
5620 6829 1.664873 TCTAGTCGTCGATGGGTGAG 58.335 55.000 4.48 0.00 0.00 3.51
5621 6830 1.208776 TCTAGTCGTCGATGGGTGAGA 59.791 52.381 4.48 0.53 0.00 3.27
5622 6831 1.331138 CTAGTCGTCGATGGGTGAGAC 59.669 57.143 4.48 0.00 0.00 3.36
5623 6832 0.322636 AGTCGTCGATGGGTGAGACT 60.323 55.000 4.48 0.00 34.54 3.24
5624 6833 1.065636 AGTCGTCGATGGGTGAGACTA 60.066 52.381 4.48 0.00 37.21 2.59
5625 6834 1.063764 GTCGTCGATGGGTGAGACTAC 59.936 57.143 4.48 0.00 33.10 2.73
5626 6835 0.027716 CGTCGATGGGTGAGACTACG 59.972 60.000 0.00 0.00 33.10 3.51
5627 6836 1.376543 GTCGATGGGTGAGACTACGA 58.623 55.000 0.00 0.00 32.58 3.43
5628 6837 1.063764 GTCGATGGGTGAGACTACGAC 59.936 57.143 0.00 0.00 40.77 4.34
5629 6838 0.027716 CGATGGGTGAGACTACGACG 59.972 60.000 0.00 0.00 0.00 5.12
5630 6839 1.376543 GATGGGTGAGACTACGACGA 58.623 55.000 0.00 0.00 0.00 4.20
5631 6840 1.948145 GATGGGTGAGACTACGACGAT 59.052 52.381 0.00 0.00 0.00 3.73
5632 6841 1.092348 TGGGTGAGACTACGACGATG 58.908 55.000 0.00 0.00 0.00 3.84
5633 6842 0.381089 GGGTGAGACTACGACGATGG 59.619 60.000 0.00 0.00 0.00 3.51
5634 6843 1.376543 GGTGAGACTACGACGATGGA 58.623 55.000 0.00 0.00 0.00 3.41
5635 6844 1.063764 GGTGAGACTACGACGATGGAC 59.936 57.143 0.00 0.00 0.00 4.02
5637 6846 1.284657 GAGACTACGACGATGGACGA 58.715 55.000 0.00 0.00 45.77 4.20
5638 6847 1.005137 GAGACTACGACGATGGACGAC 60.005 57.143 0.00 0.00 45.77 4.34
5639 6848 1.005340 GACTACGACGATGGACGACT 58.995 55.000 0.00 0.00 45.77 4.18
5640 6849 0.725686 ACTACGACGATGGACGACTG 59.274 55.000 0.00 0.00 45.77 3.51
5641 6850 0.589229 CTACGACGATGGACGACTGC 60.589 60.000 0.00 0.00 45.77 4.40
5642 6851 2.300597 TACGACGATGGACGACTGCG 62.301 60.000 0.00 0.00 45.77 5.18
5643 6852 2.483745 GACGATGGACGACTGCGA 59.516 61.111 0.00 0.00 45.77 5.10
5644 6853 1.868251 GACGATGGACGACTGCGAC 60.868 63.158 0.00 0.00 45.77 5.19
5645 6854 2.944557 CGATGGACGACTGCGACG 60.945 66.667 0.00 0.00 45.77 5.12
5646 6855 3.248171 GATGGACGACTGCGACGC 61.248 66.667 14.19 14.19 41.64 5.19
5647 6856 4.796231 ATGGACGACTGCGACGCC 62.796 66.667 18.69 0.29 41.64 5.68
5765 6974 3.420482 GTCCCCTGGACCCCATGG 61.420 72.222 4.14 4.14 46.19 3.66
5775 6984 4.109675 CCCCATGGTCGGGTGGTC 62.110 72.222 11.73 0.00 45.80 4.02
5776 6985 3.009115 CCCATGGTCGGGTGGTCT 61.009 66.667 11.73 0.00 41.83 3.85
5777 6986 2.268920 CCATGGTCGGGTGGTCTG 59.731 66.667 2.57 0.00 0.00 3.51
5778 6987 2.268920 CATGGTCGGGTGGTCTGG 59.731 66.667 0.00 0.00 0.00 3.86
5779 6988 3.009115 ATGGTCGGGTGGTCTGGG 61.009 66.667 0.00 0.00 0.00 4.45
5786 6995 3.637273 GGTGGTCTGGGCGGACTT 61.637 66.667 8.66 0.00 36.55 3.01
5787 6996 2.358737 GTGGTCTGGGCGGACTTG 60.359 66.667 8.66 0.00 36.55 3.16
5788 6997 3.636231 TGGTCTGGGCGGACTTGG 61.636 66.667 8.66 0.00 36.55 3.61
5795 7004 4.388499 GGCGGACTTGGCGGAAGA 62.388 66.667 1.34 0.00 35.42 2.87
5796 7005 3.119096 GCGGACTTGGCGGAAGAC 61.119 66.667 1.34 0.00 42.12 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.669113 CGCCATGACTTCCACAAATGTG 60.669 50.000 6.57 6.57 45.23 3.21
3 4 1.541147 CGCCATGACTTCCACAAATGT 59.459 47.619 0.00 0.00 0.00 2.71
4 5 1.135315 CCGCCATGACTTCCACAAATG 60.135 52.381 0.00 0.00 0.00 2.32
5 6 1.176527 CCGCCATGACTTCCACAAAT 58.823 50.000 0.00 0.00 0.00 2.32
6 7 0.109532 TCCGCCATGACTTCCACAAA 59.890 50.000 0.00 0.00 0.00 2.83
7 8 0.109532 TTCCGCCATGACTTCCACAA 59.890 50.000 0.00 0.00 0.00 3.33
8 9 0.109532 TTTCCGCCATGACTTCCACA 59.890 50.000 0.00 0.00 0.00 4.17
9 10 1.200020 CTTTTCCGCCATGACTTCCAC 59.800 52.381 0.00 0.00 0.00 4.02
10 11 1.533625 CTTTTCCGCCATGACTTCCA 58.466 50.000 0.00 0.00 0.00 3.53
11 12 0.811281 CCTTTTCCGCCATGACTTCC 59.189 55.000 0.00 0.00 0.00 3.46
12 13 0.171231 GCCTTTTCCGCCATGACTTC 59.829 55.000 0.00 0.00 0.00 3.01
13 14 1.250840 GGCCTTTTCCGCCATGACTT 61.251 55.000 0.00 0.00 46.27 3.01
14 15 1.678970 GGCCTTTTCCGCCATGACT 60.679 57.895 0.00 0.00 46.27 3.41
15 16 2.885113 GGCCTTTTCCGCCATGAC 59.115 61.111 0.00 0.00 46.27 3.06
21 22 0.179070 TTGGTTTTGGCCTTTTCCGC 60.179 50.000 3.32 0.00 0.00 5.54
22 23 2.142319 CATTGGTTTTGGCCTTTTCCG 58.858 47.619 3.32 0.00 0.00 4.30
23 24 3.207265 ACATTGGTTTTGGCCTTTTCC 57.793 42.857 3.32 2.29 0.00 3.13
24 25 4.273235 CAGAACATTGGTTTTGGCCTTTTC 59.727 41.667 3.32 0.00 37.36 2.29
25 26 4.080638 TCAGAACATTGGTTTTGGCCTTTT 60.081 37.500 3.32 0.00 39.06 2.27
26 27 3.454082 TCAGAACATTGGTTTTGGCCTTT 59.546 39.130 3.32 0.00 39.06 3.11
27 28 3.037549 TCAGAACATTGGTTTTGGCCTT 58.962 40.909 3.32 0.00 39.06 4.35
28 29 2.676748 TCAGAACATTGGTTTTGGCCT 58.323 42.857 3.32 0.00 39.06 5.19
29 30 3.467374 TTCAGAACATTGGTTTTGGCC 57.533 42.857 0.00 0.00 39.06 5.36
30 31 5.277925 CCATTTTCAGAACATTGGTTTTGGC 60.278 40.000 0.00 0.00 39.06 4.52
31 32 5.821995 ACCATTTTCAGAACATTGGTTTTGG 59.178 36.000 5.39 0.00 39.06 3.28
32 33 6.923928 ACCATTTTCAGAACATTGGTTTTG 57.076 33.333 5.39 0.00 39.71 2.44
33 34 7.791029 AGTACCATTTTCAGAACATTGGTTTT 58.209 30.769 13.50 3.69 38.39 2.43
34 35 7.360113 AGTACCATTTTCAGAACATTGGTTT 57.640 32.000 13.50 3.95 38.39 3.27
35 36 6.976934 AGTACCATTTTCAGAACATTGGTT 57.023 33.333 13.50 0.00 38.39 3.67
36 37 6.976934 AAGTACCATTTTCAGAACATTGGT 57.023 33.333 13.03 13.03 40.42 3.67
37 38 7.432869 TGAAAGTACCATTTTCAGAACATTGG 58.567 34.615 5.02 4.36 39.05 3.16
38 39 8.870160 TTGAAAGTACCATTTTCAGAACATTG 57.130 30.769 8.30 0.00 43.22 2.82
39 40 9.313118 GTTTGAAAGTACCATTTTCAGAACATT 57.687 29.630 17.35 0.00 43.22 2.71
40 41 7.647715 CGTTTGAAAGTACCATTTTCAGAACAT 59.352 33.333 19.43 0.00 43.22 2.71
41 42 6.970043 CGTTTGAAAGTACCATTTTCAGAACA 59.030 34.615 19.43 5.38 43.22 3.18
42 43 6.075046 GCGTTTGAAAGTACCATTTTCAGAAC 60.075 38.462 8.30 12.40 43.22 3.01
43 44 5.974751 GCGTTTGAAAGTACCATTTTCAGAA 59.025 36.000 8.30 5.05 43.22 3.02
44 45 5.066634 TGCGTTTGAAAGTACCATTTTCAGA 59.933 36.000 8.30 3.08 43.22 3.27
45 46 5.277825 TGCGTTTGAAAGTACCATTTTCAG 58.722 37.500 8.30 1.21 43.22 3.02
46 47 5.250235 TGCGTTTGAAAGTACCATTTTCA 57.750 34.783 5.02 5.02 41.40 2.69
47 48 6.763303 AATGCGTTTGAAAGTACCATTTTC 57.237 33.333 0.00 0.00 35.59 2.29
48 49 7.546778 AAAATGCGTTTGAAAGTACCATTTT 57.453 28.000 4.29 0.00 36.89 1.82
61 62 1.794116 CAAGGCTCCAAAATGCGTTTG 59.206 47.619 4.29 5.20 45.36 2.93
62 63 1.686052 TCAAGGCTCCAAAATGCGTTT 59.314 42.857 0.00 0.00 35.50 3.60
63 64 1.327303 TCAAGGCTCCAAAATGCGTT 58.673 45.000 0.00 0.00 37.70 4.84
64 65 1.549203 ATCAAGGCTCCAAAATGCGT 58.451 45.000 0.00 0.00 0.00 5.24
65 66 2.660189 AATCAAGGCTCCAAAATGCG 57.340 45.000 0.00 0.00 0.00 4.73
66 67 6.990341 AATAAAATCAAGGCTCCAAAATGC 57.010 33.333 0.00 0.00 0.00 3.56
72 73 8.945057 GCAAAATAAAATAAAATCAAGGCTCCA 58.055 29.630 0.00 0.00 0.00 3.86
73 74 8.397906 GGCAAAATAAAATAAAATCAAGGCTCC 58.602 33.333 0.00 0.00 0.00 4.70
74 75 8.945057 TGGCAAAATAAAATAAAATCAAGGCTC 58.055 29.630 0.00 0.00 0.00 4.70
75 76 8.729756 GTGGCAAAATAAAATAAAATCAAGGCT 58.270 29.630 0.00 0.00 0.00 4.58
76 77 7.691877 CGTGGCAAAATAAAATAAAATCAAGGC 59.308 33.333 0.00 0.00 0.00 4.35
77 78 8.930760 TCGTGGCAAAATAAAATAAAATCAAGG 58.069 29.630 0.00 0.00 0.00 3.61
85 86 9.261180 TGTGAAAATCGTGGCAAAATAAAATAA 57.739 25.926 0.00 0.00 0.00 1.40
86 87 8.818141 TGTGAAAATCGTGGCAAAATAAAATA 57.182 26.923 0.00 0.00 0.00 1.40
87 88 7.721286 TGTGAAAATCGTGGCAAAATAAAAT 57.279 28.000 0.00 0.00 0.00 1.82
88 89 7.278868 AGTTGTGAAAATCGTGGCAAAATAAAA 59.721 29.630 0.00 0.00 0.00 1.52
89 90 6.758886 AGTTGTGAAAATCGTGGCAAAATAAA 59.241 30.769 0.00 0.00 0.00 1.40
90 91 6.199908 CAGTTGTGAAAATCGTGGCAAAATAA 59.800 34.615 0.00 0.00 0.00 1.40
91 92 5.689514 CAGTTGTGAAAATCGTGGCAAAATA 59.310 36.000 0.00 0.00 0.00 1.40
92 93 4.507388 CAGTTGTGAAAATCGTGGCAAAAT 59.493 37.500 0.00 0.00 0.00 1.82
93 94 3.862267 CAGTTGTGAAAATCGTGGCAAAA 59.138 39.130 0.00 0.00 0.00 2.44
94 95 3.119316 ACAGTTGTGAAAATCGTGGCAAA 60.119 39.130 0.00 0.00 0.00 3.68
95 96 2.425312 ACAGTTGTGAAAATCGTGGCAA 59.575 40.909 0.00 0.00 0.00 4.52
96 97 2.020720 ACAGTTGTGAAAATCGTGGCA 58.979 42.857 0.00 0.00 0.00 4.92
97 98 2.774439 ACAGTTGTGAAAATCGTGGC 57.226 45.000 0.00 0.00 0.00 5.01
108 109 5.616488 TTCATCATGACATCACAGTTGTG 57.384 39.130 0.00 5.91 46.91 3.33
109 110 4.155462 GCTTCATCATGACATCACAGTTGT 59.845 41.667 0.00 0.00 0.00 3.32
110 111 4.395231 AGCTTCATCATGACATCACAGTTG 59.605 41.667 0.00 0.00 0.00 3.16
111 112 4.586884 AGCTTCATCATGACATCACAGTT 58.413 39.130 0.00 0.00 0.00 3.16
112 113 4.217836 AGCTTCATCATGACATCACAGT 57.782 40.909 0.00 0.00 0.00 3.55
113 114 4.876679 AGAAGCTTCATCATGACATCACAG 59.123 41.667 27.57 0.00 0.00 3.66
114 115 4.840271 AGAAGCTTCATCATGACATCACA 58.160 39.130 27.57 0.00 0.00 3.58
115 116 4.874396 TGAGAAGCTTCATCATGACATCAC 59.126 41.667 27.57 0.00 0.00 3.06
116 117 5.093849 TGAGAAGCTTCATCATGACATCA 57.906 39.130 27.57 15.71 0.00 3.07
117 118 6.050454 CTTGAGAAGCTTCATCATGACATC 57.950 41.667 27.57 13.39 0.00 3.06
195 196 9.189156 CCTGGTATGAATAGGAAAATTTCAAGA 57.811 33.333 8.09 0.00 33.45 3.02
196 197 9.189156 TCCTGGTATGAATAGGAAAATTTCAAG 57.811 33.333 8.09 0.00 37.66 3.02
197 198 9.189156 CTCCTGGTATGAATAGGAAAATTTCAA 57.811 33.333 8.09 0.00 39.93 2.69
198 199 7.285401 GCTCCTGGTATGAATAGGAAAATTTCA 59.715 37.037 8.09 0.00 39.93 2.69
199 200 7.285401 TGCTCCTGGTATGAATAGGAAAATTTC 59.715 37.037 0.00 0.00 39.93 2.17
200 201 7.125391 TGCTCCTGGTATGAATAGGAAAATTT 58.875 34.615 0.00 0.00 39.93 1.82
201 202 6.672593 TGCTCCTGGTATGAATAGGAAAATT 58.327 36.000 0.00 0.00 39.93 1.82
202 203 6.266131 TGCTCCTGGTATGAATAGGAAAAT 57.734 37.500 0.00 0.00 39.93 1.82
203 204 5.684704 CTGCTCCTGGTATGAATAGGAAAA 58.315 41.667 0.00 0.00 39.93 2.29
204 205 4.444876 GCTGCTCCTGGTATGAATAGGAAA 60.445 45.833 0.00 0.00 39.93 3.13
205 206 3.071602 GCTGCTCCTGGTATGAATAGGAA 59.928 47.826 0.00 0.00 39.93 3.36
206 207 2.634940 GCTGCTCCTGGTATGAATAGGA 59.365 50.000 0.00 0.00 38.25 2.94
207 208 2.636893 AGCTGCTCCTGGTATGAATAGG 59.363 50.000 0.00 0.00 0.00 2.57
208 209 3.613671 CGAGCTGCTCCTGGTATGAATAG 60.614 52.174 22.97 1.28 0.00 1.73
209 210 2.297315 CGAGCTGCTCCTGGTATGAATA 59.703 50.000 22.97 0.00 0.00 1.75
210 211 1.069823 CGAGCTGCTCCTGGTATGAAT 59.930 52.381 22.97 0.00 0.00 2.57
211 212 0.461548 CGAGCTGCTCCTGGTATGAA 59.538 55.000 22.97 0.00 0.00 2.57
212 213 0.395724 TCGAGCTGCTCCTGGTATGA 60.396 55.000 22.97 10.19 0.00 2.15
213 214 0.031857 CTCGAGCTGCTCCTGGTATG 59.968 60.000 22.97 7.98 0.00 2.39
214 215 1.743321 GCTCGAGCTGCTCCTGGTAT 61.743 60.000 29.88 0.00 38.21 2.73
215 216 2.418910 GCTCGAGCTGCTCCTGGTA 61.419 63.158 29.88 3.97 38.21 3.25
216 217 3.768922 GCTCGAGCTGCTCCTGGT 61.769 66.667 29.88 0.00 38.21 4.00
226 227 1.813337 GCCCTTTCTCAGCTCGAGC 60.813 63.158 30.01 30.01 41.98 5.03
227 228 0.248843 AAGCCCTTTCTCAGCTCGAG 59.751 55.000 8.45 8.45 43.80 4.04
228 229 0.247736 GAAGCCCTTTCTCAGCTCGA 59.752 55.000 0.00 0.00 35.30 4.04
229 230 0.036952 TGAAGCCCTTTCTCAGCTCG 60.037 55.000 0.00 0.00 35.30 5.03
230 231 2.416680 ATGAAGCCCTTTCTCAGCTC 57.583 50.000 0.00 0.00 35.30 4.09
231 232 4.516652 AATATGAAGCCCTTTCTCAGCT 57.483 40.909 0.00 0.00 38.88 4.24
232 233 6.890979 AATAATATGAAGCCCTTTCTCAGC 57.109 37.500 0.00 0.00 36.71 4.26
233 234 8.355913 GGAAAATAATATGAAGCCCTTTCTCAG 58.644 37.037 0.00 0.00 36.71 3.35
234 235 7.013274 CGGAAAATAATATGAAGCCCTTTCTCA 59.987 37.037 0.00 0.00 36.71 3.27
235 236 7.228706 TCGGAAAATAATATGAAGCCCTTTCTC 59.771 37.037 0.00 0.00 36.71 2.87
236 237 7.060421 TCGGAAAATAATATGAAGCCCTTTCT 58.940 34.615 0.00 0.00 36.71 2.52
237 238 7.272037 TCGGAAAATAATATGAAGCCCTTTC 57.728 36.000 0.00 0.00 36.29 2.62
238 239 7.559897 TCTTCGGAAAATAATATGAAGCCCTTT 59.440 33.333 0.00 0.00 34.35 3.11
239 240 7.013369 GTCTTCGGAAAATAATATGAAGCCCTT 59.987 37.037 0.00 0.00 34.35 3.95
240 241 6.486993 GTCTTCGGAAAATAATATGAAGCCCT 59.513 38.462 0.00 0.00 34.35 5.19
241 242 6.262273 TGTCTTCGGAAAATAATATGAAGCCC 59.738 38.462 0.00 0.00 34.35 5.19
242 243 7.012421 ACTGTCTTCGGAAAATAATATGAAGCC 59.988 37.037 0.00 0.00 34.35 4.35
243 244 7.920738 ACTGTCTTCGGAAAATAATATGAAGC 58.079 34.615 0.00 0.00 34.35 3.86
250 251 9.367444 CTTGTACTACTGTCTTCGGAAAATAAT 57.633 33.333 0.00 0.00 0.00 1.28
251 252 8.362639 ACTTGTACTACTGTCTTCGGAAAATAA 58.637 33.333 0.00 0.00 0.00 1.40
252 253 7.889469 ACTTGTACTACTGTCTTCGGAAAATA 58.111 34.615 0.00 0.00 0.00 1.40
253 254 6.756221 ACTTGTACTACTGTCTTCGGAAAAT 58.244 36.000 0.00 0.00 0.00 1.82
254 255 6.152932 ACTTGTACTACTGTCTTCGGAAAA 57.847 37.500 0.00 0.00 0.00 2.29
255 256 5.561532 CGACTTGTACTACTGTCTTCGGAAA 60.562 44.000 0.00 0.00 0.00 3.13
264 265 5.001874 TCTGATCACGACTTGTACTACTGT 58.998 41.667 0.00 0.00 0.00 3.55
267 268 4.344448 GCTCTGATCACGACTTGTACTAC 58.656 47.826 0.00 0.00 0.00 2.73
5068 6269 8.902806 TGTCAAATTCAAAATCAGTAGACAAGT 58.097 29.630 0.00 0.00 30.32 3.16
5069 6270 9.903682 ATGTCAAATTCAAAATCAGTAGACAAG 57.096 29.630 0.00 0.00 36.11 3.16
5098 6299 9.653287 TGTCGTTATGAAGAAAATCTGACTAAT 57.347 29.630 0.00 0.00 0.00 1.73
5099 6300 8.922676 GTGTCGTTATGAAGAAAATCTGACTAA 58.077 33.333 0.00 0.00 0.00 2.24
5100 6301 8.085909 TGTGTCGTTATGAAGAAAATCTGACTA 58.914 33.333 0.00 0.00 0.00 2.59
5101 6302 6.929049 TGTGTCGTTATGAAGAAAATCTGACT 59.071 34.615 0.00 0.00 0.00 3.41
5161 6362 8.400186 AGAAGAGAAAACGAAAAATTTACGGAA 58.600 29.630 17.48 0.00 0.00 4.30
5168 6369 9.067986 ACCATAGAGAAGAGAAAACGAAAAATT 57.932 29.630 0.00 0.00 0.00 1.82
5169 6370 8.622948 ACCATAGAGAAGAGAAAACGAAAAAT 57.377 30.769 0.00 0.00 0.00 1.82
5175 6376 8.758633 TCTAAAACCATAGAGAAGAGAAAACG 57.241 34.615 0.00 0.00 0.00 3.60
5233 6435 5.119694 ACAAAAATTATGGTTGCCACGTTT 58.880 33.333 0.00 0.00 35.80 3.60
5234 6436 4.698575 ACAAAAATTATGGTTGCCACGTT 58.301 34.783 0.00 0.00 35.80 3.99
5235 6437 4.329462 ACAAAAATTATGGTTGCCACGT 57.671 36.364 0.00 0.00 35.80 4.49
5268 6473 7.934855 ATGAGCAAAAGTTATCATCTTCAGT 57.065 32.000 0.00 0.00 0.00 3.41
5278 6483 6.862209 TGCGGAAAATATGAGCAAAAGTTAT 58.138 32.000 0.00 0.00 34.66 1.89
5280 6485 5.132897 TGCGGAAAATATGAGCAAAAGTT 57.867 34.783 0.00 0.00 34.66 2.66
5281 6486 4.782019 TGCGGAAAATATGAGCAAAAGT 57.218 36.364 0.00 0.00 34.66 2.66
5308 6513 9.914131 GAAGGAAAGTAATATGAGCAAAAGTTT 57.086 29.630 0.00 0.00 0.00 2.66
5337 6542 1.748493 GAACAAAGCAGTGGTGAACCA 59.252 47.619 0.00 0.00 45.30 3.67
5348 6553 9.585099 GAAAATCATAATACCATGAACAAAGCA 57.415 29.630 0.00 0.00 38.39 3.91
5424 6629 6.149973 TGAACCAAAATCATCACAGCTCTTAG 59.850 38.462 0.00 0.00 0.00 2.18
5426 6631 4.828939 TGAACCAAAATCATCACAGCTCTT 59.171 37.500 0.00 0.00 0.00 2.85
5428 6633 4.771590 TGAACCAAAATCATCACAGCTC 57.228 40.909 0.00 0.00 0.00 4.09
5429 6634 5.534207 TTTGAACCAAAATCATCACAGCT 57.466 34.783 0.00 0.00 29.89 4.24
5469 6674 6.667414 TGGGTATGTGCCAAGATTAGATTTTT 59.333 34.615 0.00 0.00 0.00 1.94
5470 6675 6.194235 TGGGTATGTGCCAAGATTAGATTTT 58.806 36.000 0.00 0.00 0.00 1.82
5471 6676 5.765510 TGGGTATGTGCCAAGATTAGATTT 58.234 37.500 0.00 0.00 0.00 2.17
5472 6677 5.387113 TGGGTATGTGCCAAGATTAGATT 57.613 39.130 0.00 0.00 0.00 2.40
5473 6678 5.387113 TTGGGTATGTGCCAAGATTAGAT 57.613 39.130 0.00 0.00 0.00 1.98
5474 6679 4.853468 TTGGGTATGTGCCAAGATTAGA 57.147 40.909 0.00 0.00 0.00 2.10
5475 6680 6.469782 AAATTGGGTATGTGCCAAGATTAG 57.530 37.500 0.00 0.00 0.00 1.73
5476 6681 7.962995 TTAAATTGGGTATGTGCCAAGATTA 57.037 32.000 0.00 0.00 0.00 1.75
5490 6695 4.360889 TGCATGGGAAGATTAAATTGGGT 58.639 39.130 0.00 0.00 0.00 4.51
5500 6705 0.254178 AACTCGCTGCATGGGAAGAT 59.746 50.000 0.00 0.00 37.18 2.40
5501 6706 0.036732 AAACTCGCTGCATGGGAAGA 59.963 50.000 0.00 0.00 37.18 2.87
5502 6707 0.883833 AAAACTCGCTGCATGGGAAG 59.116 50.000 0.00 0.00 37.18 3.46
5503 6708 2.192664 TAAAACTCGCTGCATGGGAA 57.807 45.000 0.00 0.00 37.18 3.97
5504 6709 2.192664 TTAAAACTCGCTGCATGGGA 57.807 45.000 0.00 0.00 36.19 4.37
5505 6710 2.480073 CCATTAAAACTCGCTGCATGGG 60.480 50.000 0.00 0.00 0.00 4.00
5506 6711 2.423185 TCCATTAAAACTCGCTGCATGG 59.577 45.455 0.00 2.72 0.00 3.66
5507 6712 3.688272 CTCCATTAAAACTCGCTGCATG 58.312 45.455 0.00 0.00 0.00 4.06
5508 6713 2.098117 GCTCCATTAAAACTCGCTGCAT 59.902 45.455 0.00 0.00 0.00 3.96
5526 6731 5.552870 TTGTTCCTATATGGGAGAAGCTC 57.447 43.478 7.97 0.00 36.66 4.09
5531 6736 8.742125 ATACATCTTTGTTCCTATATGGGAGA 57.258 34.615 7.97 2.41 37.28 3.71
5556 6761 4.417437 GGGAGCTAGAGAACCCACATATA 58.583 47.826 1.03 0.00 41.72 0.86
5592 6801 5.032863 CCATCGACGACTAGATTTACGTTT 58.967 41.667 0.00 0.00 39.04 3.60
5593 6802 4.497006 CCCATCGACGACTAGATTTACGTT 60.497 45.833 0.00 0.00 39.04 3.99
5601 6810 1.208776 TCTCACCCATCGACGACTAGA 59.791 52.381 0.00 0.00 0.00 2.43
5606 6815 1.376543 GTAGTCTCACCCATCGACGA 58.623 55.000 0.00 0.00 33.10 4.20
5612 6821 1.676529 CATCGTCGTAGTCTCACCCAT 59.323 52.381 0.00 0.00 0.00 4.00
5613 6822 1.092348 CATCGTCGTAGTCTCACCCA 58.908 55.000 0.00 0.00 0.00 4.51
5614 6823 0.381089 CCATCGTCGTAGTCTCACCC 59.619 60.000 0.00 0.00 0.00 4.61
5615 6824 1.063764 GTCCATCGTCGTAGTCTCACC 59.936 57.143 0.00 0.00 0.00 4.02
5616 6825 1.267433 CGTCCATCGTCGTAGTCTCAC 60.267 57.143 0.00 0.00 34.52 3.51
5617 6826 1.004595 CGTCCATCGTCGTAGTCTCA 58.995 55.000 0.00 0.00 34.52 3.27
5618 6827 1.005137 GTCGTCCATCGTCGTAGTCTC 60.005 57.143 0.00 0.00 40.80 3.36
5619 6828 1.005340 GTCGTCCATCGTCGTAGTCT 58.995 55.000 0.00 0.00 40.80 3.24
5620 6829 1.005340 AGTCGTCCATCGTCGTAGTC 58.995 55.000 0.00 0.00 40.80 2.59
5621 6830 0.725686 CAGTCGTCCATCGTCGTAGT 59.274 55.000 0.00 0.00 40.80 2.73
5622 6831 0.589229 GCAGTCGTCCATCGTCGTAG 60.589 60.000 0.00 0.00 40.80 3.51
5623 6832 1.426621 GCAGTCGTCCATCGTCGTA 59.573 57.895 0.00 0.00 40.80 3.43
5624 6833 2.178521 GCAGTCGTCCATCGTCGT 59.821 61.111 0.00 0.00 40.80 4.34
5625 6834 2.944557 CGCAGTCGTCCATCGTCG 60.945 66.667 0.00 0.00 40.80 5.12
5626 6835 1.868251 GTCGCAGTCGTCCATCGTC 60.868 63.158 0.00 0.00 40.80 4.20
5627 6836 2.178521 GTCGCAGTCGTCCATCGT 59.821 61.111 0.00 0.00 40.80 3.73
5628 6837 2.944557 CGTCGCAGTCGTCCATCG 60.945 66.667 0.00 0.00 41.41 3.84
5629 6838 3.248171 GCGTCGCAGTCGTCCATC 61.248 66.667 13.44 0.00 41.79 3.51
5630 6839 4.796231 GGCGTCGCAGTCGTCCAT 62.796 66.667 20.50 0.00 41.79 3.41
5760 6969 2.268920 CAGACCACCCGACCATGG 59.731 66.667 11.19 11.19 42.13 3.66
5761 6970 2.268920 CCAGACCACCCGACCATG 59.731 66.667 0.00 0.00 0.00 3.66
5762 6971 3.009115 CCCAGACCACCCGACCAT 61.009 66.667 0.00 0.00 0.00 3.55
5769 6978 3.637273 AAGTCCGCCCAGACCACC 61.637 66.667 0.00 0.00 37.49 4.61
5770 6979 2.358737 CAAGTCCGCCCAGACCAC 60.359 66.667 0.00 0.00 37.49 4.16
5771 6980 3.636231 CCAAGTCCGCCCAGACCA 61.636 66.667 0.00 0.00 37.49 4.02
5778 6987 4.388499 TCTTCCGCCAAGTCCGCC 62.388 66.667 0.00 0.00 33.27 6.13
5779 6988 3.119096 GTCTTCCGCCAAGTCCGC 61.119 66.667 0.00 0.00 33.27 5.54
5780 6989 2.558554 ATCGTCTTCCGCCAAGTCCG 62.559 60.000 0.00 0.00 36.19 4.79
5781 6990 1.084370 CATCGTCTTCCGCCAAGTCC 61.084 60.000 0.00 0.00 36.19 3.85
5782 6991 0.108804 TCATCGTCTTCCGCCAAGTC 60.109 55.000 0.00 0.00 36.19 3.01
5783 6992 0.389948 GTCATCGTCTTCCGCCAAGT 60.390 55.000 0.00 0.00 36.19 3.16
5784 6993 1.084370 GGTCATCGTCTTCCGCCAAG 61.084 60.000 0.00 0.00 36.19 3.61
5785 6994 1.079405 GGTCATCGTCTTCCGCCAA 60.079 57.895 0.00 0.00 36.19 4.52
5786 6995 2.577059 GGTCATCGTCTTCCGCCA 59.423 61.111 0.00 0.00 36.19 5.69
5787 6996 2.582498 CGGTCATCGTCTTCCGCC 60.582 66.667 0.00 0.00 36.68 6.13


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

AutoCloner maintained by Alex Coulton.