Multiple sequence alignment - TraesCS7B01G418100

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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 TraesCS7B01G418100 chr7B 100.000 3059 0 0 1 3059 686527008 686530066 0.000000e+00 5650.0
1 TraesCS7B01G418100 chr7B 93.571 1991 75 12 230 2187 730873972 730875942 0.000000e+00 2918.0
2 TraesCS7B01G418100 chr7B 98.707 232 3 0 1 232 244092542 244092773 2.190000e-111 412.0
3 TraesCS7B01G418100 chr7B 97.458 236 6 0 1 236 108967665 108967430 1.320000e-108 403.0
4 TraesCS7B01G418100 chr7B 96.680 241 7 1 1 241 672720498 672720737 1.710000e-107 399.0
5 TraesCS7B01G418100 chr7B 76.517 758 109 46 1010 1744 732056180 732055469 1.750000e-92 350.0
6 TraesCS7B01G418100 chr7B 83.898 236 38 0 1509 1744 731994350 731994115 3.070000e-55 226.0
7 TraesCS7B01G418100 chr7B 77.641 407 57 22 1010 1398 732349926 732350316 1.850000e-52 217.0
8 TraesCS7B01G418100 chr7B 95.420 131 6 0 2929 3059 730876072 730876202 3.090000e-50 209.0
9 TraesCS7B01G418100 chr7D 90.898 1659 97 22 568 2190 629214075 629212435 0.000000e+00 2178.0
10 TraesCS7B01G418100 chr7D 92.283 311 22 1 2620 2928 107268378 107268688 1.010000e-119 440.0
11 TraesCS7B01G418100 chr7D 90.127 314 20 7 2305 2615 107268027 107268332 6.150000e-107 398.0
12 TraesCS7B01G418100 chr7D 92.308 130 10 0 2928 3057 629212310 629212181 5.210000e-43 185.0
13 TraesCS7B01G418100 chr7D 91.566 83 2 1 2189 2271 629212381 629212304 3.220000e-20 110.0
14 TraesCS7B01G418100 chr3B 85.362 649 51 26 2305 2925 786107515 786108147 1.550000e-177 632.0
15 TraesCS7B01G418100 chr3B 100.000 28 0 0 462 489 598191081 598191108 6.000000e-03 52.8
16 TraesCS7B01G418100 chr6A 93.226 310 20 1 2620 2928 29885347 29885656 3.600000e-124 455.0
17 TraesCS7B01G418100 chr6A 88.254 315 22 4 2305 2615 29884998 29885301 2.240000e-96 363.0
18 TraesCS7B01G418100 chr6B 92.283 311 21 3 2620 2928 33428687 33428996 3.620000e-119 438.0
19 TraesCS7B01G418100 chr6B 90.764 314 25 4 2305 2615 33428329 33428641 1.700000e-112 416.0
20 TraesCS7B01G418100 chr6B 98.690 229 3 0 1 229 499071784 499071556 1.020000e-109 407.0
21 TraesCS7B01G418100 chr4B 98.283 233 4 0 1 233 415076334 415076102 2.840000e-110 409.0
22 TraesCS7B01G418100 chr4B 98.276 232 4 0 1 232 376033486 376033255 1.020000e-109 407.0
23 TraesCS7B01G418100 chr4B 98.690 229 3 0 1 229 561311970 561311742 1.020000e-109 407.0
24 TraesCS7B01G418100 chr2B 98.696 230 3 0 1 230 688588176 688587947 2.840000e-110 409.0
25 TraesCS7B01G418100 chr2B 97.863 234 5 0 1 234 97792646 97792879 3.670000e-109 405.0
26 TraesCS7B01G418100 chr2B 86.957 115 13 2 2934 3047 84817740 84817853 8.900000e-26 128.0
27 TraesCS7B01G418100 chr2B 86.087 115 14 2 2934 3047 84970388 84970501 4.140000e-24 122.0
28 TraesCS7B01G418100 chr2B 85.088 114 17 0 2934 3047 84977003 84977116 1.930000e-22 117.0
29 TraesCS7B01G418100 chrUn 76.750 757 110 42 1010 1744 88465371 88464659 2.240000e-96 363.0
30 TraesCS7B01G418100 chrUn 76.517 758 109 46 1010 1744 160415926 160415215 1.750000e-92 350.0
31 TraesCS7B01G418100 chrUn 76.517 758 109 46 1010 1744 294252447 294251736 1.750000e-92 350.0
32 TraesCS7B01G418100 chrUn 83.898 236 38 0 1509 1744 160351178 160350943 3.070000e-55 226.0
33 TraesCS7B01G418100 chrUn 83.898 236 38 0 1509 1744 405423297 405423062 3.070000e-55 226.0
34 TraesCS7B01G418100 chrUn 83.898 236 38 0 1509 1744 417519447 417519212 3.070000e-55 226.0
35 TraesCS7B01G418100 chrUn 77.297 370 54 20 1010 1363 88413727 88413372 1.120000e-44 191.0
36 TraesCS7B01G418100 chrUn 77.297 370 54 20 1010 1363 408500728 408500373 1.120000e-44 191.0
37 TraesCS7B01G418100 chr2A 87.338 308 34 3 2304 2609 761961760 761962064 6.280000e-92 348.0
38 TraesCS7B01G418100 chr2A 85.039 127 17 2 2934 3059 54706306 54706181 8.900000e-26 128.0
39 TraesCS7B01G418100 chr2A 85.039 127 17 2 2934 3059 54817568 54817443 8.900000e-26 128.0
40 TraesCS7B01G418100 chr2A 83.333 126 21 0 2934 3059 54818635 54818510 1.930000e-22 117.0
41 TraesCS7B01G418100 chr2A 89.535 86 9 0 405 490 350738217 350738132 3.220000e-20 110.0
42 TraesCS7B01G418100 chr1D 86.667 285 21 9 2649 2928 2789253 2789525 1.780000e-77 300.0
43 TraesCS7B01G418100 chr3A 91.979 187 14 1 2745 2930 647135656 647135842 8.410000e-66 261.0
44 TraesCS7B01G418100 chr2D 85.039 127 17 2 2934 3059 54077247 54077122 8.900000e-26 128.0
45 TraesCS7B01G418100 chr2D 87.156 109 14 0 2934 3042 54103299 54103191 1.150000e-24 124.0
46 TraesCS7B01G418100 chr2D 85.470 117 17 0 2934 3050 54104320 54104204 4.140000e-24 122.0
47 TraesCS7B01G418100 chr2D 84.615 117 18 0 2934 3050 54066764 54066648 1.930000e-22 117.0
48 TraesCS7B01G418100 chr1B 85.366 82 12 0 405 486 609383325 609383406 5.430000e-13 86.1
49 TraesCS7B01G418100 chr7A 84.091 88 11 3 405 489 628704995 628705082 7.030000e-12 82.4
50 TraesCS7B01G418100 chr7A 96.970 33 0 1 463 494 8449913 8449881 2.000000e-03 54.7
51 TraesCS7B01G418100 chr7A 96.970 33 0 1 463 494 8464880 8464848 2.000000e-03 54.7
52 TraesCS7B01G418100 chr5B 83.529 85 14 0 405 489 554776747 554776663 2.530000e-11 80.5


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 TraesCS7B01G418100 chr7B 686527008 686530066 3058 False 5650.000000 5650 100.000000 1 3059 1 chr7B.!!$F3 3058
1 TraesCS7B01G418100 chr7B 730873972 730876202 2230 False 1563.500000 2918 94.495500 230 3059 2 chr7B.!!$F5 2829
2 TraesCS7B01G418100 chr7B 732055469 732056180 711 True 350.000000 350 76.517000 1010 1744 1 chr7B.!!$R3 734
3 TraesCS7B01G418100 chr7D 629212181 629214075 1894 True 824.333333 2178 91.590667 568 3057 3 chr7D.!!$R1 2489
4 TraesCS7B01G418100 chr7D 107268027 107268688 661 False 419.000000 440 91.205000 2305 2928 2 chr7D.!!$F1 623
5 TraesCS7B01G418100 chr3B 786107515 786108147 632 False 632.000000 632 85.362000 2305 2925 1 chr3B.!!$F2 620
6 TraesCS7B01G418100 chr6A 29884998 29885656 658 False 409.000000 455 90.740000 2305 2928 2 chr6A.!!$F1 623
7 TraesCS7B01G418100 chr6B 33428329 33428996 667 False 427.000000 438 91.523500 2305 2928 2 chr6B.!!$F1 623
8 TraesCS7B01G418100 chrUn 88464659 88465371 712 True 363.000000 363 76.750000 1010 1744 1 chrUn.!!$R2 734
9 TraesCS7B01G418100 chrUn 160415215 160415926 711 True 350.000000 350 76.517000 1010 1744 1 chrUn.!!$R4 734
10 TraesCS7B01G418100 chrUn 294251736 294252447 711 True 350.000000 350 76.517000 1010 1744 1 chrUn.!!$R5 734

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
505 507 0.033405 CTACCCTTCACGGAGAGGGA 60.033 60.0 21.60 8.14 46.07 4.20 F
508 510 0.033405 CCCTTCACGGAGAGGGACTA 60.033 60.0 12.45 0.00 46.07 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 1491 0.105039 GACTGATAGTTCGGCAGGGG 59.895 60.0 0.00 0.00 34.05 4.79 R
2298 2431 0.107848 CTACCGGGCCTGAATTTCGT 60.108 55.0 15.09 3.32 0.00 3.85 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
24 25 7.549147 ACTAAAGCCATCCGGTTTATATAGA 57.451 36.000 0.00 0.00 42.10 1.98
25 26 7.384477 ACTAAAGCCATCCGGTTTATATAGAC 58.616 38.462 0.00 0.00 42.10 2.59
26 27 5.818678 AAGCCATCCGGTTTATATAGACA 57.181 39.130 0.00 0.00 33.26 3.41
27 28 5.148651 AGCCATCCGGTTTATATAGACAC 57.851 43.478 0.00 0.00 33.28 3.67
28 29 4.020485 AGCCATCCGGTTTATATAGACACC 60.020 45.833 0.00 2.59 33.28 4.16
34 35 5.044428 CGGTTTATATAGACACCGGAGAG 57.956 47.826 15.65 0.00 46.92 3.20
35 36 4.082895 CGGTTTATATAGACACCGGAGAGG 60.083 50.000 15.65 0.00 46.92 3.69
36 37 4.220163 GGTTTATATAGACACCGGAGAGGG 59.780 50.000 9.46 0.00 46.96 4.30
37 38 1.926108 ATATAGACACCGGAGAGGGC 58.074 55.000 9.46 0.00 46.96 5.19
38 39 0.851469 TATAGACACCGGAGAGGGCT 59.149 55.000 9.46 4.41 46.96 5.19
39 40 0.851469 ATAGACACCGGAGAGGGCTA 59.149 55.000 9.46 6.85 46.96 3.93
40 41 0.183014 TAGACACCGGAGAGGGCTAG 59.817 60.000 9.46 0.00 46.96 3.42
41 42 2.042843 ACACCGGAGAGGGCTAGG 60.043 66.667 9.46 0.00 46.96 3.02
42 43 2.840102 CACCGGAGAGGGCTAGGG 60.840 72.222 9.46 0.00 46.96 3.53
43 44 3.357082 ACCGGAGAGGGCTAGGGT 61.357 66.667 9.46 0.00 46.96 4.34
44 45 2.041819 CCGGAGAGGGCTAGGGTT 60.042 66.667 0.00 0.00 35.97 4.11
45 46 1.232216 CCGGAGAGGGCTAGGGTTA 59.768 63.158 0.00 0.00 35.97 2.85
46 47 1.114119 CCGGAGAGGGCTAGGGTTAC 61.114 65.000 0.00 0.00 35.97 2.50
47 48 0.396695 CGGAGAGGGCTAGGGTTACA 60.397 60.000 0.00 0.00 0.00 2.41
48 49 1.121378 GGAGAGGGCTAGGGTTACAC 58.879 60.000 0.00 0.00 0.00 2.90
49 50 1.621622 GGAGAGGGCTAGGGTTACACA 60.622 57.143 0.00 0.00 0.00 3.72
50 51 2.185387 GAGAGGGCTAGGGTTACACAA 58.815 52.381 0.00 0.00 0.00 3.33
51 52 2.570302 GAGAGGGCTAGGGTTACACAAA 59.430 50.000 0.00 0.00 0.00 2.83
52 53 2.572104 AGAGGGCTAGGGTTACACAAAG 59.428 50.000 0.00 0.00 0.00 2.77
53 54 2.305052 GAGGGCTAGGGTTACACAAAGT 59.695 50.000 0.00 0.00 0.00 2.66
54 55 2.305052 AGGGCTAGGGTTACACAAAGTC 59.695 50.000 0.00 0.00 0.00 3.01
55 56 2.344025 GGCTAGGGTTACACAAAGTCG 58.656 52.381 0.00 0.00 0.00 4.18
56 57 2.344025 GCTAGGGTTACACAAAGTCGG 58.656 52.381 0.00 0.00 0.00 4.79
57 58 2.289257 GCTAGGGTTACACAAAGTCGGT 60.289 50.000 0.00 0.00 0.00 4.69
58 59 3.804759 GCTAGGGTTACACAAAGTCGGTT 60.805 47.826 0.00 0.00 0.00 4.44
59 60 4.561326 GCTAGGGTTACACAAAGTCGGTTA 60.561 45.833 0.00 0.00 0.00 2.85
60 61 3.732212 AGGGTTACACAAAGTCGGTTAC 58.268 45.455 0.00 0.00 0.00 2.50
61 62 3.134442 AGGGTTACACAAAGTCGGTTACA 59.866 43.478 0.00 0.00 0.00 2.41
62 63 3.876320 GGGTTACACAAAGTCGGTTACAA 59.124 43.478 0.00 0.00 0.00 2.41
63 64 4.516321 GGGTTACACAAAGTCGGTTACAAT 59.484 41.667 0.00 0.00 0.00 2.71
64 65 5.445845 GGTTACACAAAGTCGGTTACAATG 58.554 41.667 0.00 0.00 0.00 2.82
65 66 5.445845 GTTACACAAAGTCGGTTACAATGG 58.554 41.667 0.00 0.00 0.00 3.16
66 67 3.547746 ACACAAAGTCGGTTACAATGGT 58.452 40.909 0.00 0.00 0.00 3.55
67 68 4.706035 ACACAAAGTCGGTTACAATGGTA 58.294 39.130 0.00 0.00 0.00 3.25
68 69 4.753107 ACACAAAGTCGGTTACAATGGTAG 59.247 41.667 0.00 0.00 0.00 3.18
69 70 4.153475 CACAAAGTCGGTTACAATGGTAGG 59.847 45.833 0.00 0.00 0.00 3.18
70 71 4.040706 ACAAAGTCGGTTACAATGGTAGGA 59.959 41.667 0.00 0.00 0.00 2.94
71 72 4.467198 AAGTCGGTTACAATGGTAGGAG 57.533 45.455 0.00 0.00 0.00 3.69
72 73 3.705051 AGTCGGTTACAATGGTAGGAGA 58.295 45.455 0.00 0.00 0.00 3.71
73 74 4.287552 AGTCGGTTACAATGGTAGGAGAT 58.712 43.478 0.00 0.00 0.00 2.75
74 75 4.341520 AGTCGGTTACAATGGTAGGAGATC 59.658 45.833 0.00 0.00 0.00 2.75
75 76 4.341520 GTCGGTTACAATGGTAGGAGATCT 59.658 45.833 0.00 0.00 0.00 2.75
76 77 5.533903 GTCGGTTACAATGGTAGGAGATCTA 59.466 44.000 0.00 0.00 0.00 1.98
77 78 5.533903 TCGGTTACAATGGTAGGAGATCTAC 59.466 44.000 0.00 0.00 45.78 2.59
89 90 7.410800 GTAGGAGATCTACATATCCGTATCG 57.589 44.000 7.93 0.00 44.22 2.92
90 91 4.817464 AGGAGATCTACATATCCGTATCGC 59.183 45.833 7.93 0.00 44.22 4.58
91 92 4.023878 GGAGATCTACATATCCGTATCGCC 60.024 50.000 0.00 0.00 30.60 5.54
92 93 4.524053 AGATCTACATATCCGTATCGCCA 58.476 43.478 0.00 0.00 0.00 5.69
93 94 4.948004 AGATCTACATATCCGTATCGCCAA 59.052 41.667 0.00 0.00 0.00 4.52
94 95 4.696899 TCTACATATCCGTATCGCCAAG 57.303 45.455 0.00 0.00 0.00 3.61
95 96 2.080286 ACATATCCGTATCGCCAAGC 57.920 50.000 0.00 0.00 0.00 4.01
96 97 1.618837 ACATATCCGTATCGCCAAGCT 59.381 47.619 0.00 0.00 0.00 3.74
97 98 2.037251 ACATATCCGTATCGCCAAGCTT 59.963 45.455 0.00 0.00 0.00 3.74
98 99 2.148916 TATCCGTATCGCCAAGCTTG 57.851 50.000 19.93 19.93 0.00 4.01
99 100 1.160329 ATCCGTATCGCCAAGCTTGC 61.160 55.000 21.43 14.85 0.00 4.01
100 101 2.709475 CGTATCGCCAAGCTTGCC 59.291 61.111 21.43 9.45 0.00 4.52
101 102 1.815421 CGTATCGCCAAGCTTGCCT 60.815 57.895 21.43 7.17 0.00 4.75
102 103 1.369091 CGTATCGCCAAGCTTGCCTT 61.369 55.000 21.43 7.68 0.00 4.35
103 104 0.378610 GTATCGCCAAGCTTGCCTTC 59.621 55.000 21.43 8.32 0.00 3.46
104 105 0.748005 TATCGCCAAGCTTGCCTTCC 60.748 55.000 21.43 5.26 0.00 3.46
105 106 2.769652 ATCGCCAAGCTTGCCTTCCA 62.770 55.000 21.43 1.33 0.00 3.53
106 107 2.653115 GCCAAGCTTGCCTTCCAC 59.347 61.111 21.43 0.12 0.00 4.02
107 108 2.956987 CCAAGCTTGCCTTCCACG 59.043 61.111 21.43 0.62 0.00 4.94
108 109 2.256461 CAAGCTTGCCTTCCACGC 59.744 61.111 14.65 0.00 38.87 5.34
109 110 2.985847 AAGCTTGCCTTCCACGCC 60.986 61.111 0.00 0.00 39.36 5.68
110 111 3.790416 AAGCTTGCCTTCCACGCCA 62.790 57.895 0.00 0.00 39.36 5.69
111 112 3.294493 GCTTGCCTTCCACGCCAA 61.294 61.111 0.00 0.00 32.93 4.52
112 113 2.956987 CTTGCCTTCCACGCCAAG 59.043 61.111 0.00 0.00 0.00 3.61
113 114 2.597217 TTGCCTTCCACGCCAAGG 60.597 61.111 3.73 3.73 43.13 3.61
114 115 3.126703 TTGCCTTCCACGCCAAGGA 62.127 57.895 10.97 0.00 42.94 3.36
115 116 2.282180 GCCTTCCACGCCAAGGAA 60.282 61.111 10.97 5.63 42.94 3.36
116 117 1.901464 GCCTTCCACGCCAAGGAAA 60.901 57.895 10.97 0.00 44.07 3.13
117 118 1.866853 GCCTTCCACGCCAAGGAAAG 61.867 60.000 10.97 2.24 44.07 2.62
118 119 0.537371 CCTTCCACGCCAAGGAAAGT 60.537 55.000 2.12 0.00 44.07 2.66
119 120 0.875059 CTTCCACGCCAAGGAAAGTC 59.125 55.000 0.00 0.00 44.07 3.01
120 121 0.536460 TTCCACGCCAAGGAAAGTCC 60.536 55.000 0.00 0.00 41.94 3.85
121 122 1.971695 CCACGCCAAGGAAAGTCCC 60.972 63.158 0.00 0.00 37.19 4.46
122 123 1.228124 CACGCCAAGGAAAGTCCCA 60.228 57.895 0.00 0.00 37.19 4.37
123 124 0.609131 CACGCCAAGGAAAGTCCCAT 60.609 55.000 0.00 0.00 37.19 4.00
124 125 0.322546 ACGCCAAGGAAAGTCCCATC 60.323 55.000 0.00 0.00 37.19 3.51
125 126 1.032114 CGCCAAGGAAAGTCCCATCC 61.032 60.000 0.00 0.00 37.19 3.51
126 127 1.032114 GCCAAGGAAAGTCCCATCCG 61.032 60.000 0.00 0.00 40.78 4.18
127 128 0.394352 CCAAGGAAAGTCCCATCCGG 60.394 60.000 0.00 0.00 40.78 5.14
128 129 0.618458 CAAGGAAAGTCCCATCCGGA 59.382 55.000 6.61 6.61 40.78 5.14
159 160 7.820044 ACGAAGTCTTCAATCTTGTATCTTC 57.180 36.000 12.99 0.00 29.74 2.87
160 161 7.378966 ACGAAGTCTTCAATCTTGTATCTTCA 58.621 34.615 12.99 0.00 29.74 3.02
161 162 8.037758 ACGAAGTCTTCAATCTTGTATCTTCAT 58.962 33.333 12.99 0.00 29.74 2.57
162 163 9.521503 CGAAGTCTTCAATCTTGTATCTTCATA 57.478 33.333 12.99 0.00 32.10 2.15
173 174 9.995003 ATCTTGTATCTTCATAATCTTGGAGTC 57.005 33.333 0.00 0.00 0.00 3.36
174 175 8.424918 TCTTGTATCTTCATAATCTTGGAGTCC 58.575 37.037 0.73 0.73 0.00 3.85
175 176 6.749139 TGTATCTTCATAATCTTGGAGTCCG 58.251 40.000 4.30 0.00 0.00 4.79
176 177 4.672587 TCTTCATAATCTTGGAGTCCGG 57.327 45.455 4.30 0.00 0.00 5.14
177 178 2.910688 TCATAATCTTGGAGTCCGGC 57.089 50.000 4.30 0.00 0.00 6.13
178 179 1.416401 TCATAATCTTGGAGTCCGGCC 59.584 52.381 4.30 0.00 0.00 6.13
179 180 1.140852 CATAATCTTGGAGTCCGGCCA 59.859 52.381 2.24 0.00 0.00 5.36
180 181 1.281419 TAATCTTGGAGTCCGGCCAA 58.719 50.000 11.06 11.06 42.81 4.52
181 182 0.322546 AATCTTGGAGTCCGGCCAAC 60.323 55.000 7.84 0.00 40.32 3.77
182 183 2.198304 ATCTTGGAGTCCGGCCAACC 62.198 60.000 7.84 0.04 40.32 3.77
183 184 3.172106 TTGGAGTCCGGCCAACCA 61.172 61.111 7.84 2.78 40.32 3.67
184 185 2.484287 CTTGGAGTCCGGCCAACCAT 62.484 60.000 7.84 0.00 40.32 3.55
185 186 2.438434 GGAGTCCGGCCAACCATG 60.438 66.667 2.24 0.00 34.57 3.66
186 187 2.668632 GAGTCCGGCCAACCATGA 59.331 61.111 2.24 0.00 34.57 3.07
187 188 1.224592 GAGTCCGGCCAACCATGAT 59.775 57.895 2.24 0.00 34.57 2.45
188 189 0.468226 GAGTCCGGCCAACCATGATA 59.532 55.000 2.24 0.00 34.57 2.15
189 190 0.469917 AGTCCGGCCAACCATGATAG 59.530 55.000 2.24 0.00 34.57 2.08
190 191 0.180406 GTCCGGCCAACCATGATAGT 59.820 55.000 2.24 0.00 34.57 2.12
191 192 0.916086 TCCGGCCAACCATGATAGTT 59.084 50.000 2.24 0.00 34.57 2.24
192 193 1.134220 TCCGGCCAACCATGATAGTTC 60.134 52.381 2.24 0.00 34.57 3.01
193 194 0.937304 CGGCCAACCATGATAGTTCG 59.063 55.000 2.24 0.00 34.57 3.95
194 195 1.308998 GGCCAACCATGATAGTTCGG 58.691 55.000 0.00 0.00 35.26 4.30
195 196 0.663153 GCCAACCATGATAGTTCGGC 59.337 55.000 0.00 3.08 0.00 5.54
196 197 1.747206 GCCAACCATGATAGTTCGGCT 60.747 52.381 13.93 0.00 35.39 5.52
197 198 2.484770 GCCAACCATGATAGTTCGGCTA 60.485 50.000 13.93 0.00 35.39 3.93
198 199 3.807209 GCCAACCATGATAGTTCGGCTAT 60.807 47.826 13.93 1.08 42.75 2.97
210 211 3.069778 GGCTATCCGGACATCCCC 58.930 66.667 6.12 0.00 0.00 4.81
211 212 1.536662 GGCTATCCGGACATCCCCT 60.537 63.158 6.12 0.00 0.00 4.79
212 213 0.252103 GGCTATCCGGACATCCCCTA 60.252 60.000 6.12 0.00 0.00 3.53
213 214 1.187087 GCTATCCGGACATCCCCTAG 58.813 60.000 6.12 3.64 0.00 3.02
214 215 1.550409 GCTATCCGGACATCCCCTAGT 60.550 57.143 6.12 0.00 0.00 2.57
215 216 2.448453 CTATCCGGACATCCCCTAGTC 58.552 57.143 6.12 0.00 0.00 2.59
246 247 3.057315 CCTCACCAACAAAGCCATGTTAG 60.057 47.826 4.57 0.99 41.44 2.34
257 258 7.398024 ACAAAGCCATGTTAGAATCTCTAAGT 58.602 34.615 0.00 0.00 39.41 2.24
297 298 7.145323 CCCACCAAACATTGACTTAGTTAAAG 58.855 38.462 0.00 0.00 41.33 1.85
337 338 4.858850 TGGATTCAGTTTATGCACCATCT 58.141 39.130 0.00 0.00 0.00 2.90
338 339 4.641541 TGGATTCAGTTTATGCACCATCTG 59.358 41.667 0.00 0.00 0.00 2.90
348 349 0.109597 GCACCATCTGCTTGGAAACG 60.110 55.000 7.74 0.00 43.33 3.60
359 360 2.494870 GCTTGGAAACGGAGGTAGTAGA 59.505 50.000 0.00 0.00 0.00 2.59
403 404 4.760715 ACAACAAGACGTAAGCTAGAGAGA 59.239 41.667 0.00 0.00 45.62 3.10
416 417 3.847780 GCTAGAGAGATACTCCCTCCCTA 59.152 52.174 0.00 0.00 45.96 3.53
417 418 4.080526 GCTAGAGAGATACTCCCTCCCTAG 60.081 54.167 0.00 0.00 45.96 3.02
427 428 5.887480 ACTCCCTCCCTAGTGTCATATAT 57.113 43.478 0.00 0.00 0.00 0.86
436 437 7.615403 TCCCTAGTGTCATATATGAGCATTTC 58.385 38.462 15.83 3.96 37.51 2.17
501 503 3.277962 GGACTACCCTTCACGGAGA 57.722 57.895 0.00 0.00 33.16 3.71
502 504 1.104630 GGACTACCCTTCACGGAGAG 58.895 60.000 0.00 0.00 33.16 3.20
503 505 1.104630 GACTACCCTTCACGGAGAGG 58.895 60.000 0.00 0.00 33.16 3.69
504 506 0.324460 ACTACCCTTCACGGAGAGGG 60.324 60.000 15.30 15.30 46.64 4.30
505 507 0.033405 CTACCCTTCACGGAGAGGGA 60.033 60.000 21.60 8.14 46.07 4.20
506 508 0.324091 TACCCTTCACGGAGAGGGAC 60.324 60.000 21.60 0.00 46.07 4.46
507 509 1.305381 CCCTTCACGGAGAGGGACT 60.305 63.158 12.45 0.00 46.07 3.85
508 510 0.033405 CCCTTCACGGAGAGGGACTA 60.033 60.000 12.45 0.00 46.07 2.59
509 511 1.104630 CCTTCACGGAGAGGGACTAC 58.895 60.000 2.65 0.00 46.07 2.73
510 512 1.104630 CTTCACGGAGAGGGACTACC 58.895 60.000 0.00 0.00 41.55 3.18
564 566 5.862924 TGGAAGAAAAGACAAATCTAGCG 57.137 39.130 0.00 0.00 33.57 4.26
573 575 6.481954 AAGACAAATCTAGCGGTAAACTTG 57.518 37.500 0.00 2.17 33.57 3.16
747 754 2.421314 CCGGCCGCATGTGAGATA 59.579 61.111 22.85 0.00 0.00 1.98
748 755 1.227527 CCGGCCGCATGTGAGATAA 60.228 57.895 22.85 0.00 0.00 1.75
792 799 7.445402 CCATGTTACCATATTCTCCTAGTTTGG 59.555 40.741 0.00 0.00 0.00 3.28
859 866 5.183228 GTTACCATACAGCCTAGCTTGAAA 58.817 41.667 0.00 0.00 36.40 2.69
879 886 5.066634 TGAAAGAGAGAGCTACGTAGATTGG 59.933 44.000 26.53 0.08 0.00 3.16
915 922 6.032094 AGTTATAAGTCAACCGTACGTGATG 58.968 40.000 15.21 10.56 0.00 3.07
979 988 6.609616 TCCTCATTGGTTCAATATAAAACCCC 59.390 38.462 13.78 0.00 43.55 4.95
1002 1011 0.401105 ATCACTCCTCCCTCCCCATG 60.401 60.000 0.00 0.00 0.00 3.66
1087 1096 2.633509 GGGTACTGCGTCACCGTCT 61.634 63.158 0.00 0.00 35.53 4.18
1678 1729 3.240134 GAGCTTCAGGACGGCACCA 62.240 63.158 0.00 0.00 0.00 4.17
1961 2030 4.695231 CGTCACGGCGAGGAACGT 62.695 66.667 16.62 0.00 45.25 3.99
2062 2131 5.756347 TCGATCTTAATTAATTGGTGACCCG 59.244 40.000 11.05 11.68 0.00 5.28
2067 2136 2.702592 TTAATTGGTGACCCGGCTAG 57.297 50.000 0.00 0.00 0.00 3.42
2087 2163 7.582679 CGGCTAGTAAATATGAAACGAAATGTG 59.417 37.037 0.00 0.00 0.00 3.21
2113 2189 2.359850 TGGGTGAAGGACATGCGC 60.360 61.111 0.00 0.00 0.00 6.09
2136 2212 3.044059 GCACCAGCATCAAGGACGC 62.044 63.158 0.00 0.00 41.58 5.19
2210 2343 4.138487 ACTCCCTAATTAGGTTTCTGCG 57.862 45.455 26.38 11.93 42.03 5.18
2271 2404 3.545481 CGGCTTGTGCGCTACGAG 61.545 66.667 9.73 15.01 42.73 4.18
2272 2405 2.126071 GGCTTGTGCGCTACGAGA 60.126 61.111 23.20 0.00 42.51 4.04
2273 2406 2.161486 GGCTTGTGCGCTACGAGAG 61.161 63.158 23.20 13.62 42.51 3.20
2274 2407 1.154016 GCTTGTGCGCTACGAGAGA 60.154 57.895 23.20 0.00 42.51 3.10
2275 2408 1.136872 GCTTGTGCGCTACGAGAGAG 61.137 60.000 23.20 10.11 42.51 3.20
2276 2409 0.169230 CTTGTGCGCTACGAGAGAGT 59.831 55.000 17.34 0.00 42.51 3.24
2277 2410 0.596577 TTGTGCGCTACGAGAGAGTT 59.403 50.000 9.73 0.00 0.00 3.01
2278 2411 0.596577 TGTGCGCTACGAGAGAGTTT 59.403 50.000 9.73 0.00 0.00 2.66
2279 2412 1.000607 TGTGCGCTACGAGAGAGTTTT 60.001 47.619 9.73 0.00 0.00 2.43
2280 2413 1.387084 GTGCGCTACGAGAGAGTTTTG 59.613 52.381 9.73 0.00 0.00 2.44
2281 2414 0.992802 GCGCTACGAGAGAGTTTTGG 59.007 55.000 0.00 0.00 0.00 3.28
2282 2415 1.402456 GCGCTACGAGAGAGTTTTGGA 60.402 52.381 0.00 0.00 0.00 3.53
2283 2416 2.735762 GCGCTACGAGAGAGTTTTGGAT 60.736 50.000 0.00 0.00 0.00 3.41
2284 2417 3.512680 CGCTACGAGAGAGTTTTGGATT 58.487 45.455 0.00 0.00 0.00 3.01
2285 2418 3.927142 CGCTACGAGAGAGTTTTGGATTT 59.073 43.478 0.00 0.00 0.00 2.17
2286 2419 4.031878 CGCTACGAGAGAGTTTTGGATTTC 59.968 45.833 0.00 0.00 0.00 2.17
2287 2420 4.031878 GCTACGAGAGAGTTTTGGATTTCG 59.968 45.833 0.00 0.00 0.00 3.46
2288 2421 3.991367 ACGAGAGAGTTTTGGATTTCGT 58.009 40.909 0.00 0.00 35.48 3.85
2289 2422 3.988517 ACGAGAGAGTTTTGGATTTCGTC 59.011 43.478 0.00 0.00 35.39 4.20
2299 2432 2.624316 GGATTTCGTCCGGGAAAAAC 57.376 50.000 9.53 7.32 39.19 2.43
2300 2433 1.135888 GGATTTCGTCCGGGAAAAACG 60.136 52.381 9.53 8.01 39.19 3.60
2301 2434 1.799994 GATTTCGTCCGGGAAAAACGA 59.200 47.619 10.91 10.91 43.06 3.85
2303 2436 3.376218 TCGTCCGGGAAAAACGAAA 57.624 47.368 12.38 0.00 41.94 3.46
2341 2474 4.810191 ATGTTAGCCGGCCAAAATTTTA 57.190 36.364 26.15 2.64 0.00 1.52
2398 2535 1.839894 CCCAGCCTGGATAACCCTC 59.160 63.158 13.74 0.00 40.96 4.30
2402 2539 1.696314 GCCTGGATAACCCTCCCCA 60.696 63.158 0.00 0.00 34.12 4.96
2403 2540 1.709994 GCCTGGATAACCCTCCCCAG 61.710 65.000 0.00 0.00 44.29 4.45
2439 2577 7.560262 GGCCTGAATAAACTCCTAAACCTAAAT 59.440 37.037 0.00 0.00 0.00 1.40
2441 2579 8.903820 CCTGAATAAACTCCTAAACCTAAATGG 58.096 37.037 0.00 0.00 42.93 3.16
2442 2580 9.681062 CTGAATAAACTCCTAAACCTAAATGGA 57.319 33.333 0.00 0.00 39.71 3.41
2505 2644 1.439228 CCGATCCAGATGTGCTCGT 59.561 57.895 10.65 0.00 0.00 4.18
2570 2709 2.628178 CTGACCGTTCCATATGCCTCTA 59.372 50.000 0.00 0.00 0.00 2.43
2615 2754 1.416401 GTGCAAGTATGGCCCTAGCTA 59.584 52.381 0.00 0.00 39.73 3.32
2616 2755 1.416401 TGCAAGTATGGCCCTAGCTAC 59.584 52.381 0.00 0.00 39.73 3.58
2743 2936 7.163001 AGATCCTTATTTGTTTCCTTTGCTC 57.837 36.000 0.00 0.00 0.00 4.26
2794 2987 4.030366 GTCGTTTTTCGTCCAAATTTCGT 58.970 39.130 0.00 0.00 40.80 3.85
2797 2990 4.731480 CGTTTTTCGTCCAAATTTCGTTCT 59.269 37.500 0.00 0.00 34.52 3.01
2869 3065 9.996554 AATTTTCTGAAAAATCCGAAATTACCT 57.003 25.926 18.43 0.00 42.82 3.08
2888 3084 2.680841 CCTAATTTCGCCCATTTCGTCA 59.319 45.455 0.00 0.00 0.00 4.35
2892 3088 1.832719 TTCGCCCATTTCGTCAGGGA 61.833 55.000 0.00 0.00 45.80 4.20
2928 3124 4.377328 GCAAAACGAAATCCAAATCCTTGC 60.377 41.667 0.00 0.00 0.00 4.01
2929 3125 4.871933 AAACGAAATCCAAATCCTTGCT 57.128 36.364 0.00 0.00 0.00 3.91
2930 3126 5.975693 AAACGAAATCCAAATCCTTGCTA 57.024 34.783 0.00 0.00 0.00 3.49
2931 3127 6.530019 AAACGAAATCCAAATCCTTGCTAT 57.470 33.333 0.00 0.00 0.00 2.97
2932 3128 5.505173 ACGAAATCCAAATCCTTGCTATG 57.495 39.130 0.00 0.00 0.00 2.23
2933 3129 5.192927 ACGAAATCCAAATCCTTGCTATGA 58.807 37.500 0.00 0.00 0.00 2.15
2942 3138 0.541863 CCTTGCTATGACCCGGAGTT 59.458 55.000 0.73 0.00 0.00 3.01
2977 3173 3.691744 CTGTGGACGGAGAGCGAGC 62.692 68.421 0.00 0.00 0.00 5.03
2980 3176 3.749064 GGACGGAGAGCGAGCACA 61.749 66.667 0.00 0.00 0.00 4.57
2982 3178 1.153745 GACGGAGAGCGAGCACATT 60.154 57.895 0.00 0.00 0.00 2.71
2984 3180 1.153765 CGGAGAGCGAGCACATTGA 60.154 57.895 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.015877 TGTCTATATAAACCGGATGGCTTTAGT 59.984 37.037 9.46 0.00 39.70 2.24
1 2 7.331193 GTGTCTATATAAACCGGATGGCTTTAG 59.669 40.741 9.46 1.01 39.70 1.85
2 3 7.156673 GTGTCTATATAAACCGGATGGCTTTA 58.843 38.462 9.46 1.94 39.70 1.85
3 4 5.995897 GTGTCTATATAAACCGGATGGCTTT 59.004 40.000 9.46 0.00 39.70 3.51
4 5 5.512576 GGTGTCTATATAAACCGGATGGCTT 60.513 44.000 9.46 0.00 39.70 4.35
5 6 4.020485 GGTGTCTATATAAACCGGATGGCT 60.020 45.833 9.46 0.00 39.70 4.75
6 7 4.251268 GGTGTCTATATAAACCGGATGGC 58.749 47.826 9.46 0.00 39.70 4.40
13 14 4.220163 CCCTCTCCGGTGTCTATATAAACC 59.780 50.000 0.00 0.68 0.00 3.27
14 15 4.321824 GCCCTCTCCGGTGTCTATATAAAC 60.322 50.000 0.00 0.00 0.00 2.01
15 16 3.830755 GCCCTCTCCGGTGTCTATATAAA 59.169 47.826 0.00 0.00 0.00 1.40
16 17 3.075582 AGCCCTCTCCGGTGTCTATATAA 59.924 47.826 0.00 0.00 0.00 0.98
17 18 2.648304 AGCCCTCTCCGGTGTCTATATA 59.352 50.000 0.00 0.00 0.00 0.86
18 19 1.429687 AGCCCTCTCCGGTGTCTATAT 59.570 52.381 0.00 0.00 0.00 0.86
19 20 0.851469 AGCCCTCTCCGGTGTCTATA 59.149 55.000 0.00 0.00 0.00 1.31
20 21 0.851469 TAGCCCTCTCCGGTGTCTAT 59.149 55.000 0.00 0.00 0.00 1.98
21 22 0.183014 CTAGCCCTCTCCGGTGTCTA 59.817 60.000 0.00 0.05 0.00 2.59
22 23 1.076632 CTAGCCCTCTCCGGTGTCT 60.077 63.158 0.00 0.00 0.00 3.41
23 24 2.128507 CCTAGCCCTCTCCGGTGTC 61.129 68.421 0.00 0.00 0.00 3.67
24 25 2.042843 CCTAGCCCTCTCCGGTGT 60.043 66.667 0.00 0.00 0.00 4.16
25 26 2.840102 CCCTAGCCCTCTCCGGTG 60.840 72.222 0.00 0.00 0.00 4.94
26 27 1.587522 TAACCCTAGCCCTCTCCGGT 61.588 60.000 0.00 0.00 0.00 5.28
27 28 1.114119 GTAACCCTAGCCCTCTCCGG 61.114 65.000 0.00 0.00 0.00 5.14
28 29 0.396695 TGTAACCCTAGCCCTCTCCG 60.397 60.000 0.00 0.00 0.00 4.63
29 30 1.121378 GTGTAACCCTAGCCCTCTCC 58.879 60.000 0.00 0.00 0.00 3.71
30 31 1.861982 TGTGTAACCCTAGCCCTCTC 58.138 55.000 0.00 0.00 34.36 3.20
31 32 2.337359 TTGTGTAACCCTAGCCCTCT 57.663 50.000 0.00 0.00 34.36 3.69
32 33 2.305052 ACTTTGTGTAACCCTAGCCCTC 59.695 50.000 0.00 0.00 34.36 4.30
33 34 2.305052 GACTTTGTGTAACCCTAGCCCT 59.695 50.000 0.00 0.00 34.36 5.19
34 35 2.708051 GACTTTGTGTAACCCTAGCCC 58.292 52.381 0.00 0.00 34.36 5.19
35 36 2.344025 CGACTTTGTGTAACCCTAGCC 58.656 52.381 0.00 0.00 34.36 3.93
36 37 2.289257 ACCGACTTTGTGTAACCCTAGC 60.289 50.000 0.00 0.00 34.36 3.42
37 38 3.672767 ACCGACTTTGTGTAACCCTAG 57.327 47.619 0.00 0.00 34.36 3.02
38 39 4.343526 TGTAACCGACTTTGTGTAACCCTA 59.656 41.667 0.00 0.00 34.36 3.53
39 40 3.134442 TGTAACCGACTTTGTGTAACCCT 59.866 43.478 0.00 0.00 34.36 4.34
40 41 3.465871 TGTAACCGACTTTGTGTAACCC 58.534 45.455 0.00 0.00 34.36 4.11
41 42 5.445845 CATTGTAACCGACTTTGTGTAACC 58.554 41.667 0.00 0.00 34.36 2.85
42 43 5.007921 ACCATTGTAACCGACTTTGTGTAAC 59.992 40.000 0.00 0.00 37.35 2.50
43 44 5.124645 ACCATTGTAACCGACTTTGTGTAA 58.875 37.500 0.00 0.00 0.00 2.41
44 45 4.706035 ACCATTGTAACCGACTTTGTGTA 58.294 39.130 0.00 0.00 0.00 2.90
45 46 3.547746 ACCATTGTAACCGACTTTGTGT 58.452 40.909 0.00 0.00 0.00 3.72
46 47 4.153475 CCTACCATTGTAACCGACTTTGTG 59.847 45.833 0.00 0.00 0.00 3.33
47 48 4.040706 TCCTACCATTGTAACCGACTTTGT 59.959 41.667 0.00 0.00 0.00 2.83
48 49 4.571919 TCCTACCATTGTAACCGACTTTG 58.428 43.478 0.00 0.00 0.00 2.77
49 50 4.529377 TCTCCTACCATTGTAACCGACTTT 59.471 41.667 0.00 0.00 0.00 2.66
50 51 4.091549 TCTCCTACCATTGTAACCGACTT 58.908 43.478 0.00 0.00 0.00 3.01
51 52 3.705051 TCTCCTACCATTGTAACCGACT 58.295 45.455 0.00 0.00 0.00 4.18
52 53 4.341520 AGATCTCCTACCATTGTAACCGAC 59.658 45.833 0.00 0.00 0.00 4.79
53 54 4.543689 AGATCTCCTACCATTGTAACCGA 58.456 43.478 0.00 0.00 0.00 4.69
54 55 4.939052 AGATCTCCTACCATTGTAACCG 57.061 45.455 0.00 0.00 0.00 4.44
55 56 6.726490 TGTAGATCTCCTACCATTGTAACC 57.274 41.667 0.00 0.00 45.60 2.85
57 58 9.256228 GGATATGTAGATCTCCTACCATTGTAA 57.744 37.037 0.00 0.00 45.60 2.41
58 59 7.556635 CGGATATGTAGATCTCCTACCATTGTA 59.443 40.741 0.00 0.00 45.60 2.41
59 60 6.378564 CGGATATGTAGATCTCCTACCATTGT 59.621 42.308 0.00 0.00 45.60 2.71
60 61 6.378564 ACGGATATGTAGATCTCCTACCATTG 59.621 42.308 0.00 0.00 45.60 2.82
61 62 6.494952 ACGGATATGTAGATCTCCTACCATT 58.505 40.000 0.00 0.00 45.60 3.16
62 63 6.080969 ACGGATATGTAGATCTCCTACCAT 57.919 41.667 0.00 0.00 45.60 3.55
63 64 5.516059 ACGGATATGTAGATCTCCTACCA 57.484 43.478 0.00 0.00 45.60 3.25
64 65 6.424509 CGATACGGATATGTAGATCTCCTACC 59.575 46.154 0.00 0.00 45.60 3.18
65 66 6.073657 GCGATACGGATATGTAGATCTCCTAC 60.074 46.154 0.00 0.00 46.21 3.18
66 67 5.990386 GCGATACGGATATGTAGATCTCCTA 59.010 44.000 0.00 0.00 0.00 2.94
67 68 4.817464 GCGATACGGATATGTAGATCTCCT 59.183 45.833 0.00 0.00 0.00 3.69
68 69 4.023878 GGCGATACGGATATGTAGATCTCC 60.024 50.000 0.00 0.00 0.00 3.71
69 70 4.575236 TGGCGATACGGATATGTAGATCTC 59.425 45.833 0.00 0.00 0.00 2.75
70 71 4.524053 TGGCGATACGGATATGTAGATCT 58.476 43.478 0.00 0.00 0.00 2.75
71 72 4.895224 TGGCGATACGGATATGTAGATC 57.105 45.455 0.00 0.00 0.00 2.75
72 73 4.440250 GCTTGGCGATACGGATATGTAGAT 60.440 45.833 0.00 0.00 0.00 1.98
73 74 3.119602 GCTTGGCGATACGGATATGTAGA 60.120 47.826 0.00 0.00 0.00 2.59
74 75 3.119459 AGCTTGGCGATACGGATATGTAG 60.119 47.826 0.00 0.00 0.00 2.74
75 76 2.823747 AGCTTGGCGATACGGATATGTA 59.176 45.455 0.00 0.00 0.00 2.29
76 77 1.618837 AGCTTGGCGATACGGATATGT 59.381 47.619 0.00 0.00 0.00 2.29
77 78 2.370281 AGCTTGGCGATACGGATATG 57.630 50.000 0.00 0.00 0.00 1.78
78 79 2.688507 CAAGCTTGGCGATACGGATAT 58.311 47.619 19.14 0.00 0.00 1.63
79 80 1.872237 GCAAGCTTGGCGATACGGATA 60.872 52.381 27.10 0.00 0.00 2.59
80 81 1.160329 GCAAGCTTGGCGATACGGAT 61.160 55.000 27.10 0.00 0.00 4.18
81 82 1.813753 GCAAGCTTGGCGATACGGA 60.814 57.895 27.10 0.00 0.00 4.69
82 83 2.709475 GCAAGCTTGGCGATACGG 59.291 61.111 27.10 0.00 0.00 4.02
83 84 2.709475 GGCAAGCTTGGCGATACG 59.291 61.111 33.68 4.49 43.97 3.06
90 91 2.956987 CGTGGAAGGCAAGCTTGG 59.043 61.111 27.10 9.80 0.00 3.61
99 100 0.537371 ACTTTCCTTGGCGTGGAAGG 60.537 55.000 15.33 15.33 43.48 3.46
100 101 0.875059 GACTTTCCTTGGCGTGGAAG 59.125 55.000 10.20 8.04 43.48 3.46
101 102 0.536460 GGACTTTCCTTGGCGTGGAA 60.536 55.000 6.88 6.88 41.33 3.53
102 103 1.072505 GGACTTTCCTTGGCGTGGA 59.927 57.895 0.00 0.00 32.53 4.02
103 104 1.971695 GGGACTTTCCTTGGCGTGG 60.972 63.158 0.00 0.00 36.57 4.94
104 105 0.609131 ATGGGACTTTCCTTGGCGTG 60.609 55.000 0.00 0.00 36.57 5.34
105 106 0.322546 GATGGGACTTTCCTTGGCGT 60.323 55.000 0.00 0.00 36.57 5.68
106 107 1.032114 GGATGGGACTTTCCTTGGCG 61.032 60.000 0.00 0.00 36.57 5.69
107 108 1.032114 CGGATGGGACTTTCCTTGGC 61.032 60.000 0.00 0.00 36.57 4.52
108 109 0.394352 CCGGATGGGACTTTCCTTGG 60.394 60.000 0.00 0.00 38.47 3.61
109 110 0.618458 TCCGGATGGGACTTTCCTTG 59.382 55.000 0.00 0.00 40.94 3.61
110 111 3.098445 TCCGGATGGGACTTTCCTT 57.902 52.632 0.00 0.00 40.94 3.36
111 112 4.910613 TCCGGATGGGACTTTCCT 57.089 55.556 0.00 0.00 40.94 3.36
125 126 2.126580 GACTTCGTCCCGTGTCCG 60.127 66.667 0.00 0.00 0.00 4.79
126 127 0.388263 GAAGACTTCGTCCCGTGTCC 60.388 60.000 0.00 0.00 34.39 4.02
127 128 0.313043 TGAAGACTTCGTCCCGTGTC 59.687 55.000 10.56 0.00 32.18 3.67
128 129 0.748450 TTGAAGACTTCGTCCCGTGT 59.252 50.000 10.56 0.00 32.18 4.49
129 130 1.993370 GATTGAAGACTTCGTCCCGTG 59.007 52.381 10.56 0.00 32.18 4.94
130 131 1.893801 AGATTGAAGACTTCGTCCCGT 59.106 47.619 10.56 0.00 32.18 5.28
131 132 2.656560 AGATTGAAGACTTCGTCCCG 57.343 50.000 10.56 0.00 32.18 5.14
132 133 3.665190 ACAAGATTGAAGACTTCGTCCC 58.335 45.455 10.56 0.53 32.18 4.46
133 134 6.334202 AGATACAAGATTGAAGACTTCGTCC 58.666 40.000 10.56 2.18 32.18 4.79
134 135 7.542477 TGAAGATACAAGATTGAAGACTTCGTC 59.458 37.037 10.56 10.67 34.37 4.20
135 136 7.378966 TGAAGATACAAGATTGAAGACTTCGT 58.621 34.615 10.56 1.87 34.37 3.85
136 137 7.818493 TGAAGATACAAGATTGAAGACTTCG 57.182 36.000 10.56 0.00 34.37 3.79
147 148 9.995003 GACTCCAAGATTATGAAGATACAAGAT 57.005 33.333 0.00 0.00 0.00 2.40
148 149 8.424918 GGACTCCAAGATTATGAAGATACAAGA 58.575 37.037 0.00 0.00 0.00 3.02
149 150 7.383572 CGGACTCCAAGATTATGAAGATACAAG 59.616 40.741 0.00 0.00 0.00 3.16
150 151 7.210174 CGGACTCCAAGATTATGAAGATACAA 58.790 38.462 0.00 0.00 0.00 2.41
151 152 6.239317 CCGGACTCCAAGATTATGAAGATACA 60.239 42.308 0.00 0.00 0.00 2.29
152 153 6.159988 CCGGACTCCAAGATTATGAAGATAC 58.840 44.000 0.00 0.00 0.00 2.24
153 154 5.279506 GCCGGACTCCAAGATTATGAAGATA 60.280 44.000 5.05 0.00 0.00 1.98
154 155 4.503991 GCCGGACTCCAAGATTATGAAGAT 60.504 45.833 5.05 0.00 0.00 2.40
155 156 3.181465 GCCGGACTCCAAGATTATGAAGA 60.181 47.826 5.05 0.00 0.00 2.87
156 157 3.134458 GCCGGACTCCAAGATTATGAAG 58.866 50.000 5.05 0.00 0.00 3.02
157 158 2.158813 GGCCGGACTCCAAGATTATGAA 60.159 50.000 5.05 0.00 0.00 2.57
158 159 1.416401 GGCCGGACTCCAAGATTATGA 59.584 52.381 5.05 0.00 0.00 2.15
159 160 1.140852 TGGCCGGACTCCAAGATTATG 59.859 52.381 9.82 0.00 0.00 1.90
160 161 1.507140 TGGCCGGACTCCAAGATTAT 58.493 50.000 9.82 0.00 0.00 1.28
161 162 1.065709 GTTGGCCGGACTCCAAGATTA 60.066 52.381 9.82 0.00 43.57 1.75
162 163 0.322546 GTTGGCCGGACTCCAAGATT 60.323 55.000 9.82 0.00 43.57 2.40
163 164 1.299976 GTTGGCCGGACTCCAAGAT 59.700 57.895 9.82 0.00 43.57 2.40
164 165 2.747686 GTTGGCCGGACTCCAAGA 59.252 61.111 9.82 0.00 43.57 3.02
165 166 2.359975 GGTTGGCCGGACTCCAAG 60.360 66.667 9.82 0.00 43.57 3.61
166 167 2.534396 ATGGTTGGCCGGACTCCAA 61.534 57.895 24.17 16.71 40.98 3.53
167 168 2.933287 ATGGTTGGCCGGACTCCA 60.933 61.111 23.01 23.01 37.67 3.86
168 169 2.270874 ATCATGGTTGGCCGGACTCC 62.271 60.000 9.82 12.37 37.67 3.85
169 170 0.468226 TATCATGGTTGGCCGGACTC 59.532 55.000 9.82 0.73 37.67 3.36
170 171 0.469917 CTATCATGGTTGGCCGGACT 59.530 55.000 9.82 0.00 37.67 3.85
171 172 0.180406 ACTATCATGGTTGGCCGGAC 59.820 55.000 5.05 0.56 37.67 4.79
172 173 0.916086 AACTATCATGGTTGGCCGGA 59.084 50.000 5.05 0.00 37.67 5.14
173 174 1.308998 GAACTATCATGGTTGGCCGG 58.691 55.000 0.00 0.00 37.67 6.13
174 175 0.937304 CGAACTATCATGGTTGGCCG 59.063 55.000 0.00 0.00 37.67 6.13
175 176 1.308998 CCGAACTATCATGGTTGGCC 58.691 55.000 0.00 0.00 0.00 5.36
176 177 0.663153 GCCGAACTATCATGGTTGGC 59.337 55.000 10.19 10.19 35.52 4.52
177 178 2.332063 AGCCGAACTATCATGGTTGG 57.668 50.000 0.00 0.00 0.00 3.77
193 194 0.252103 TAGGGGATGTCCGGATAGCC 60.252 60.000 25.90 25.90 36.71 3.93
194 195 1.187087 CTAGGGGATGTCCGGATAGC 58.813 60.000 7.81 7.97 36.71 2.97
195 196 2.448453 GACTAGGGGATGTCCGGATAG 58.552 57.143 7.81 5.89 36.71 2.08
196 197 1.076677 GGACTAGGGGATGTCCGGATA 59.923 57.143 7.81 4.93 42.51 2.59
197 198 0.178929 GGACTAGGGGATGTCCGGAT 60.179 60.000 7.81 0.00 42.51 4.18
198 199 1.232216 GGACTAGGGGATGTCCGGA 59.768 63.158 0.00 0.00 42.51 5.14
199 200 3.872431 GGACTAGGGGATGTCCGG 58.128 66.667 0.00 0.00 42.51 5.14
209 210 0.631753 TGAGGGAGTCCTGGACTAGG 59.368 60.000 28.41 0.00 43.53 3.02
210 211 1.686741 GGTGAGGGAGTCCTGGACTAG 60.687 61.905 28.41 0.00 43.53 2.57
211 212 0.335361 GGTGAGGGAGTCCTGGACTA 59.665 60.000 28.41 10.70 43.53 2.59
212 213 1.079438 GGTGAGGGAGTCCTGGACT 59.921 63.158 28.70 28.70 46.42 3.85
213 214 0.836400 TTGGTGAGGGAGTCCTGGAC 60.836 60.000 19.20 19.20 45.05 4.02
214 215 0.836400 GTTGGTGAGGGAGTCCTGGA 60.836 60.000 9.58 0.00 45.05 3.86
215 216 1.127567 TGTTGGTGAGGGAGTCCTGG 61.128 60.000 9.58 0.00 45.05 4.45
216 217 0.764890 TTGTTGGTGAGGGAGTCCTG 59.235 55.000 9.58 0.00 45.05 3.86
218 219 1.897560 CTTTGTTGGTGAGGGAGTCC 58.102 55.000 0.00 0.00 0.00 3.85
219 220 1.239347 GCTTTGTTGGTGAGGGAGTC 58.761 55.000 0.00 0.00 0.00 3.36
220 221 0.178990 GGCTTTGTTGGTGAGGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
221 222 0.178992 TGGCTTTGTTGGTGAGGGAG 60.179 55.000 0.00 0.00 0.00 4.30
222 223 0.482446 ATGGCTTTGTTGGTGAGGGA 59.518 50.000 0.00 0.00 0.00 4.20
223 224 0.604578 CATGGCTTTGTTGGTGAGGG 59.395 55.000 0.00 0.00 0.00 4.30
224 225 1.331214 ACATGGCTTTGTTGGTGAGG 58.669 50.000 0.00 0.00 0.00 3.86
225 226 3.820467 TCTAACATGGCTTTGTTGGTGAG 59.180 43.478 14.09 6.07 40.00 3.51
226 227 3.826524 TCTAACATGGCTTTGTTGGTGA 58.173 40.909 14.09 8.39 40.00 4.02
227 228 4.582701 TTCTAACATGGCTTTGTTGGTG 57.417 40.909 14.09 6.76 40.00 4.17
228 229 5.079643 AGATTCTAACATGGCTTTGTTGGT 58.920 37.500 14.09 0.29 40.00 3.67
246 247 6.231211 TGAGTGTTCCCAAACTTAGAGATTC 58.769 40.000 0.00 0.00 36.30 2.52
297 298 8.099364 TGAATCCAAAAGTCAATGTCTCTAAC 57.901 34.615 0.00 0.00 0.00 2.34
303 304 9.132521 CATAAACTGAATCCAAAAGTCAATGTC 57.867 33.333 0.00 0.00 0.00 3.06
337 338 1.053424 ACTACCTCCGTTTCCAAGCA 58.947 50.000 0.00 0.00 0.00 3.91
338 339 2.494870 TCTACTACCTCCGTTTCCAAGC 59.505 50.000 0.00 0.00 0.00 4.01
339 340 4.796038 TTCTACTACCTCCGTTTCCAAG 57.204 45.455 0.00 0.00 0.00 3.61
403 404 5.887480 ATATGACACTAGGGAGGGAGTAT 57.113 43.478 0.00 0.00 0.00 2.12
416 417 7.330454 GTGATCGAAATGCTCATATATGACACT 59.670 37.037 11.49 2.89 32.50 3.55
417 418 7.330454 AGTGATCGAAATGCTCATATATGACAC 59.670 37.037 11.49 12.84 32.50 3.67
461 462 9.495382 AGTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
503 505 5.136105 TCTATTCTCCGTAAAGGGTAGTCC 58.864 45.833 0.00 0.00 41.52 3.85
504 506 5.241285 CCTCTATTCTCCGTAAAGGGTAGTC 59.759 48.000 0.00 0.00 41.52 2.59
505 507 5.139001 CCTCTATTCTCCGTAAAGGGTAGT 58.861 45.833 0.00 0.00 41.52 2.73
506 508 4.523558 CCCTCTATTCTCCGTAAAGGGTAG 59.476 50.000 0.00 0.00 41.52 3.18
507 509 4.477249 CCCTCTATTCTCCGTAAAGGGTA 58.523 47.826 0.00 0.00 41.52 3.69
508 510 3.306613 CCCTCTATTCTCCGTAAAGGGT 58.693 50.000 0.00 0.00 41.52 4.34
509 511 2.633481 CCCCTCTATTCTCCGTAAAGGG 59.367 54.545 0.00 0.00 41.41 3.95
510 512 3.321396 GTCCCCTCTATTCTCCGTAAAGG 59.679 52.174 0.00 0.00 42.97 3.11
511 513 4.038162 CAGTCCCCTCTATTCTCCGTAAAG 59.962 50.000 0.00 0.00 0.00 1.85
512 514 3.958798 CAGTCCCCTCTATTCTCCGTAAA 59.041 47.826 0.00 0.00 0.00 2.01
513 515 3.563223 CAGTCCCCTCTATTCTCCGTAA 58.437 50.000 0.00 0.00 0.00 3.18
514 516 2.752154 GCAGTCCCCTCTATTCTCCGTA 60.752 54.545 0.00 0.00 0.00 4.02
515 517 2.030045 GCAGTCCCCTCTATTCTCCGT 61.030 57.143 0.00 0.00 0.00 4.69
516 518 0.676736 GCAGTCCCCTCTATTCTCCG 59.323 60.000 0.00 0.00 0.00 4.63
517 519 1.794714 TGCAGTCCCCTCTATTCTCC 58.205 55.000 0.00 0.00 0.00 3.71
518 520 2.501723 TGTTGCAGTCCCCTCTATTCTC 59.498 50.000 0.00 0.00 0.00 2.87
519 521 2.237392 GTGTTGCAGTCCCCTCTATTCT 59.763 50.000 0.00 0.00 0.00 2.40
520 522 2.237392 AGTGTTGCAGTCCCCTCTATTC 59.763 50.000 0.00 0.00 0.00 1.75
625 628 4.057406 TGTCTTTCTTGTTTGCAATGGG 57.943 40.909 0.00 0.00 33.65 4.00
701 708 1.907255 GGAACCAGGTAAGTAGCCAGT 59.093 52.381 0.00 0.00 0.00 4.00
859 866 2.882137 GCCAATCTACGTAGCTCTCTCT 59.118 50.000 18.00 0.00 0.00 3.10
879 886 6.241207 TGACTTATAACTTCACAAAGCTGC 57.759 37.500 0.00 0.00 35.81 5.25
915 922 2.079925 AGCTCTCTCAAAATTGCGGTC 58.920 47.619 0.00 0.00 0.00 4.79
979 988 1.694133 GGGAGGGAGGAGTGATGCTG 61.694 65.000 0.00 0.00 0.00 4.41
1165 1174 5.672421 ATTAGCTAACTAACGAACAGGGT 57.328 39.130 8.70 0.00 41.12 4.34
1465 1491 0.105039 GACTGATAGTTCGGCAGGGG 59.895 60.000 0.00 0.00 34.05 4.79
1678 1729 3.461773 CTCCCACAGCCCGACGAT 61.462 66.667 0.00 0.00 0.00 3.73
1761 1812 1.509463 GCCATACTGGTCGTCGTCA 59.491 57.895 0.00 0.00 40.46 4.35
1948 2017 2.259511 GGTAACGTTCCTCGCCGT 59.740 61.111 2.82 0.00 44.19 5.68
2001 2070 6.545666 TGTTTTGATTATCTGTTGTCACCTGT 59.454 34.615 0.00 0.00 0.00 4.00
2062 2131 8.395633 ACACATTTCGTTTCATATTTACTAGCC 58.604 33.333 0.00 0.00 0.00 3.93
2067 2136 8.995906 GCTACACACATTTCGTTTCATATTTAC 58.004 33.333 0.00 0.00 0.00 2.01
2087 2163 0.685097 TCCTTCACCCAGTGCTACAC 59.315 55.000 0.00 0.00 32.98 2.90
2113 2189 3.047718 CTTGATGCTGGTGCTGCGG 62.048 63.158 0.00 0.00 40.48 5.69
2187 2264 7.612560 GTCGCAGAAACCTAATTAGGGAGTTC 61.613 46.154 30.61 26.78 43.66 3.01
2225 2358 9.303116 CCTGAGGTACAGTATATATTCTCAGTT 57.697 37.037 14.97 0.00 42.96 3.16
2236 2369 2.954318 GCCGAACCTGAGGTACAGTATA 59.046 50.000 3.68 0.00 44.40 1.47
2237 2370 1.755380 GCCGAACCTGAGGTACAGTAT 59.245 52.381 3.68 0.00 44.40 2.12
2238 2371 1.180029 GCCGAACCTGAGGTACAGTA 58.820 55.000 3.68 0.00 44.40 2.74
2239 2372 0.542232 AGCCGAACCTGAGGTACAGT 60.542 55.000 3.68 0.00 44.40 3.55
2240 2373 0.608640 AAGCCGAACCTGAGGTACAG 59.391 55.000 3.68 0.00 45.36 2.74
2280 2413 1.135888 CGTTTTTCCCGGACGAAATCC 60.136 52.381 0.73 0.00 45.20 3.01
2281 2414 1.799994 TCGTTTTTCCCGGACGAAATC 59.200 47.619 12.38 6.03 42.14 2.17
2282 2415 1.881591 TCGTTTTTCCCGGACGAAAT 58.118 45.000 12.38 0.00 42.14 2.17
2283 2416 3.376218 TCGTTTTTCCCGGACGAAA 57.624 47.368 12.38 7.27 42.14 3.46
2285 2418 1.881591 ATTTCGTTTTTCCCGGACGA 58.118 45.000 10.91 10.91 43.22 4.20
2286 2419 2.031857 TGAATTTCGTTTTTCCCGGACG 60.032 45.455 0.73 4.23 38.09 4.79
2287 2420 3.561503 CTGAATTTCGTTTTTCCCGGAC 58.438 45.455 0.73 0.00 0.00 4.79
2288 2421 2.554893 CCTGAATTTCGTTTTTCCCGGA 59.445 45.455 0.73 0.00 0.00 5.14
2289 2422 2.924880 GCCTGAATTTCGTTTTTCCCGG 60.925 50.000 0.00 0.00 0.00 5.73
2290 2423 2.324860 GCCTGAATTTCGTTTTTCCCG 58.675 47.619 0.00 0.00 0.00 5.14
2291 2424 2.611971 GGGCCTGAATTTCGTTTTTCCC 60.612 50.000 0.84 0.00 0.00 3.97
2292 2425 2.683968 GGGCCTGAATTTCGTTTTTCC 58.316 47.619 0.84 0.00 0.00 3.13
2293 2426 2.324860 CGGGCCTGAATTTCGTTTTTC 58.675 47.619 5.28 0.00 0.00 2.29
2294 2427 1.000394 CCGGGCCTGAATTTCGTTTTT 60.000 47.619 15.09 0.00 0.00 1.94
2295 2428 0.601057 CCGGGCCTGAATTTCGTTTT 59.399 50.000 15.09 0.00 0.00 2.43
2296 2429 0.538746 ACCGGGCCTGAATTTCGTTT 60.539 50.000 15.09 0.00 0.00 3.60
2297 2430 0.325602 TACCGGGCCTGAATTTCGTT 59.674 50.000 15.09 0.00 0.00 3.85
2298 2431 0.107848 CTACCGGGCCTGAATTTCGT 60.108 55.000 15.09 3.32 0.00 3.85
2299 2432 0.177141 TCTACCGGGCCTGAATTTCG 59.823 55.000 15.09 0.00 0.00 3.46
2300 2433 2.640316 ATCTACCGGGCCTGAATTTC 57.360 50.000 15.09 0.00 0.00 2.17
2301 2434 3.394606 ACATATCTACCGGGCCTGAATTT 59.605 43.478 15.09 0.00 0.00 1.82
2302 2435 2.979678 ACATATCTACCGGGCCTGAATT 59.020 45.455 15.09 0.00 0.00 2.17
2303 2436 2.621070 ACATATCTACCGGGCCTGAAT 58.379 47.619 15.09 2.90 0.00 2.57
2393 2530 1.993301 CTTTTACTTCCTGGGGAGGGT 59.007 52.381 0.00 0.00 32.76 4.34
2398 2535 0.704664 AGGCCTTTTACTTCCTGGGG 59.295 55.000 0.00 0.00 0.00 4.96
2402 2539 6.552932 AGTTTATTCAGGCCTTTTACTTCCT 58.447 36.000 0.00 0.00 0.00 3.36
2403 2540 6.127703 GGAGTTTATTCAGGCCTTTTACTTCC 60.128 42.308 0.00 0.00 0.00 3.46
2439 2577 3.075882 AGAGATGTGGGGAATTTGTTCCA 59.924 43.478 9.22 0.00 42.89 3.53
2441 2579 5.012893 AGAAGAGATGTGGGGAATTTGTTC 58.987 41.667 0.00 0.00 0.00 3.18
2442 2580 5.003096 AGAAGAGATGTGGGGAATTTGTT 57.997 39.130 0.00 0.00 0.00 2.83
2484 2623 0.249657 GAGCACATCTGGATCGGGAC 60.250 60.000 0.00 0.00 0.00 4.46
2543 2682 0.750850 TATGGAACGGTCAGCTAGCC 59.249 55.000 12.13 0.00 0.00 3.93
2570 2709 4.349503 TGCACCAAGCTGCCGGAT 62.350 61.111 5.05 0.00 45.94 4.18
2590 2729 0.676782 GGGCCATACTTGCACTCGTT 60.677 55.000 4.39 0.00 0.00 3.85
2743 2936 9.506018 AAATTCTACCAAAAATTGAAATCCTGG 57.494 29.630 0.00 0.00 0.00 4.45
2818 3012 6.073440 TCCGGACGAAAAGACTGAATTAAAAG 60.073 38.462 0.00 0.00 0.00 2.27
2823 3017 3.396260 TCCGGACGAAAAGACTGAATT 57.604 42.857 0.00 0.00 0.00 2.17
2869 3065 2.680841 CCTGACGAAATGGGCGAAATTA 59.319 45.455 0.00 0.00 0.00 1.40
2888 3084 4.674281 TTTGCAAATTTTACCGTTCCCT 57.326 36.364 8.05 0.00 0.00 4.20
2892 3088 6.404712 TTTCGTTTTGCAAATTTTACCGTT 57.595 29.167 13.65 0.00 0.00 4.44
2928 3124 0.753262 CCAGGAACTCCGGGTCATAG 59.247 60.000 0.00 0.00 44.92 2.23
2929 3125 2.910579 CCAGGAACTCCGGGTCATA 58.089 57.895 0.00 0.00 44.92 2.15
2930 3126 3.727387 CCAGGAACTCCGGGTCAT 58.273 61.111 0.00 0.00 44.92 3.06
2942 3138 3.371063 GCACCGACTCGTCCAGGA 61.371 66.667 0.00 0.00 0.00 3.86
2977 3173 1.787847 GGAAGCCGTCGTCAATGTG 59.212 57.895 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.