Multiple sequence alignment - TraesCS6A01G391600

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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 TraesCS6A01G391600 chr6A 100.000 1649 0 0 1 1649 606281464 606279816 0.000000e+00 3046.0
1 TraesCS6A01G391600 chr6A 100.000 388 0 0 2006 2393 606279459 606279072 0.000000e+00 717.0
2 TraesCS6A01G391600 chr6A 83.569 706 87 15 737 1428 606337000 606337690 3.360000e-178 634.0
3 TraesCS6A01G391600 chr6B 94.978 697 29 1 737 1433 700532036 700531346 0.000000e+00 1088.0
4 TraesCS6A01G391600 chr6B 79.936 628 95 17 791 1400 700906324 700906938 1.310000e-117 433.0
5 TraesCS6A01G391600 chr6B 78.509 684 106 23 740 1405 701060224 701059564 6.160000e-111 411.0
6 TraesCS6A01G391600 chr6B 86.905 252 30 2 2136 2385 700529619 700529369 1.810000e-71 279.0
7 TraesCS6A01G391600 chr6B 92.529 174 13 0 1476 1649 700530810 700530637 1.420000e-62 250.0
8 TraesCS6A01G391600 chr6B 93.827 81 5 0 2059 2139 700530431 700530351 3.230000e-24 122.0
9 TraesCS6A01G391600 chr7A 91.429 630 47 5 112 736 564263069 564263696 0.000000e+00 857.0
10 TraesCS6A01G391600 chr3A 91.626 621 43 7 117 736 706451164 706451776 0.000000e+00 850.0
11 TraesCS6A01G391600 chr1A 91.125 631 44 9 117 736 553488309 553487680 0.000000e+00 845.0
12 TraesCS6A01G391600 chr1A 90.821 621 44 5 117 736 553499502 553498894 0.000000e+00 819.0
13 TraesCS6A01G391600 chr1A 97.391 115 3 0 2 116 100245298 100245412 1.880000e-46 196.0
14 TraesCS6A01G391600 chr1A 97.391 115 3 0 2 116 471970272 471970386 1.880000e-46 196.0
15 TraesCS6A01G391600 chr1A 97.391 115 3 0 2 116 537833477 537833591 1.880000e-46 196.0
16 TraesCS6A01G391600 chr1A 96.610 118 4 0 2 119 553488258 553488141 1.880000e-46 196.0
17 TraesCS6A01G391600 chr1A 96.610 118 4 0 2 119 553493865 553493748 1.880000e-46 196.0
18 TraesCS6A01G391600 chr1A 96.610 118 4 0 2 119 553505058 553504941 1.880000e-46 196.0
19 TraesCS6A01G391600 chr1A 96.610 118 4 0 2 119 553516218 553516101 1.880000e-46 196.0
20 TraesCS6A01G391600 chr5A 91.200 625 46 9 117 736 217274667 217274047 0.000000e+00 841.0
21 TraesCS6A01G391600 chr5A 90.821 621 49 6 117 736 130260167 130260780 0.000000e+00 824.0
22 TraesCS6A01G391600 chr5A 90.690 623 51 5 117 736 563069696 563070314 0.000000e+00 822.0
23 TraesCS6A01G391600 chr4A 91.143 621 50 4 117 734 6440467 6439849 0.000000e+00 837.0
24 TraesCS6A01G391600 chr4A 90.821 621 49 6 117 736 6471001 6470388 0.000000e+00 824.0
25 TraesCS6A01G391600 chr6D 84.638 690 82 12 742 1419 460170991 460170314 0.000000e+00 665.0
26 TraesCS6A01G391600 chr6D 83.135 504 66 9 939 1428 460312264 460312762 2.180000e-120 442.0
27 TraesCS6A01G391600 chr6D 79.904 622 104 14 791 1400 460220809 460221421 1.020000e-118 436.0
28 TraesCS6A01G391600 chr6D 78.770 683 107 20 740 1405 460317113 460316452 7.910000e-115 424.0
29 TraesCS6A01G391600 chr6D 78.261 690 103 27 734 1399 460284288 460284954 1.330000e-107 399.0
30 TraesCS6A01G391600 chr5B 87.393 349 37 5 2049 2393 587065714 587065369 6.200000e-106 394.0
31 TraesCS6A01G391600 chr5D 86.782 348 44 2 2048 2393 536804742 536804395 1.040000e-103 387.0
32 TraesCS6A01G391600 chr4D 92.000 200 16 0 2047 2246 47898924 47899123 5.040000e-72 281.0
33 TraesCS6A01G391600 chr4D 86.755 151 20 0 2243 2393 47904568 47904718 4.090000e-38 169.0
34 TraesCS6A01G391600 chr7D 99.130 115 1 0 2 116 497037338 497037452 8.670000e-50 207.0
35 TraesCS6A01G391600 chr7D 96.610 118 4 0 2 119 116900725 116900608 1.880000e-46 196.0
36 TraesCS6A01G391600 chr7D 97.297 37 1 0 2164 2200 610526096 610526132 1.990000e-06 63.9


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 TraesCS6A01G391600 chr6A 606279072 606281464 2392 True 1881.50 3046 100.00000 1 2393 2 chr6A.!!$R1 2392
1 TraesCS6A01G391600 chr6A 606337000 606337690 690 False 634.00 634 83.56900 737 1428 1 chr6A.!!$F1 691
2 TraesCS6A01G391600 chr6B 700529369 700532036 2667 True 434.75 1088 92.05975 737 2385 4 chr6B.!!$R2 1648
3 TraesCS6A01G391600 chr6B 700906324 700906938 614 False 433.00 433 79.93600 791 1400 1 chr6B.!!$F1 609
4 TraesCS6A01G391600 chr6B 701059564 701060224 660 True 411.00 411 78.50900 740 1405 1 chr6B.!!$R1 665
5 TraesCS6A01G391600 chr7A 564263069 564263696 627 False 857.00 857 91.42900 112 736 1 chr7A.!!$F1 624
6 TraesCS6A01G391600 chr3A 706451164 706451776 612 False 850.00 850 91.62600 117 736 1 chr3A.!!$F1 619
7 TraesCS6A01G391600 chr1A 553498894 553499502 608 True 819.00 819 90.82100 117 736 1 chr1A.!!$R2 619
8 TraesCS6A01G391600 chr1A 553487680 553488309 629 True 520.50 845 93.86750 2 736 2 chr1A.!!$R5 734
9 TraesCS6A01G391600 chr5A 217274047 217274667 620 True 841.00 841 91.20000 117 736 1 chr5A.!!$R1 619
10 TraesCS6A01G391600 chr5A 130260167 130260780 613 False 824.00 824 90.82100 117 736 1 chr5A.!!$F1 619
11 TraesCS6A01G391600 chr5A 563069696 563070314 618 False 822.00 822 90.69000 117 736 1 chr5A.!!$F2 619
12 TraesCS6A01G391600 chr4A 6439849 6440467 618 True 837.00 837 91.14300 117 734 1 chr4A.!!$R1 617
13 TraesCS6A01G391600 chr4A 6470388 6471001 613 True 824.00 824 90.82100 117 736 1 chr4A.!!$R2 619
14 TraesCS6A01G391600 chr6D 460170314 460170991 677 True 665.00 665 84.63800 742 1419 1 chr6D.!!$R1 677
15 TraesCS6A01G391600 chr6D 460220809 460221421 612 False 436.00 436 79.90400 791 1400 1 chr6D.!!$F1 609
16 TraesCS6A01G391600 chr6D 460316452 460317113 661 True 424.00 424 78.77000 740 1405 1 chr6D.!!$R2 665
17 TraesCS6A01G391600 chr6D 460284288 460284954 666 False 399.00 399 78.26100 734 1399 1 chr6D.!!$F2 665

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
65 66 0.174617 GTGGCGAGAGGAAGGAGAAG 59.825 60.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2629 0.107165 GAGGTGGTGGATAACTGGGC 60.107 60.0 0.0 0.0 0.0 5.36 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
18 19 3.403936 CCAAGCCGGGATTAGGAAG 57.596 57.895 2.18 0.00 0.00 3.46
19 20 0.837272 CCAAGCCGGGATTAGGAAGA 59.163 55.000 2.18 0.00 0.00 2.87
20 21 1.475213 CCAAGCCGGGATTAGGAAGAC 60.475 57.143 2.18 0.00 0.00 3.01
21 22 1.209504 CAAGCCGGGATTAGGAAGACA 59.790 52.381 2.18 0.00 0.00 3.41
22 23 1.580059 AGCCGGGATTAGGAAGACAA 58.420 50.000 2.18 0.00 0.00 3.18
23 24 1.209747 AGCCGGGATTAGGAAGACAAC 59.790 52.381 2.18 0.00 0.00 3.32
24 25 1.065709 GCCGGGATTAGGAAGACAACA 60.066 52.381 2.18 0.00 0.00 3.33
25 26 2.906354 CCGGGATTAGGAAGACAACAG 58.094 52.381 0.00 0.00 0.00 3.16
26 27 2.280628 CGGGATTAGGAAGACAACAGC 58.719 52.381 0.00 0.00 0.00 4.40
27 28 2.354704 CGGGATTAGGAAGACAACAGCA 60.355 50.000 0.00 0.00 0.00 4.41
28 29 3.274288 GGGATTAGGAAGACAACAGCAG 58.726 50.000 0.00 0.00 0.00 4.24
29 30 2.680339 GGATTAGGAAGACAACAGCAGC 59.320 50.000 0.00 0.00 0.00 5.25
30 31 3.604582 GATTAGGAAGACAACAGCAGCT 58.395 45.455 0.00 0.00 0.00 4.24
31 32 2.751166 TAGGAAGACAACAGCAGCTC 57.249 50.000 0.00 0.00 0.00 4.09
32 33 0.761187 AGGAAGACAACAGCAGCTCA 59.239 50.000 0.00 0.00 0.00 4.26
33 34 1.155042 GGAAGACAACAGCAGCTCAG 58.845 55.000 0.00 0.00 0.00 3.35
34 35 1.270518 GGAAGACAACAGCAGCTCAGA 60.271 52.381 0.00 0.00 0.00 3.27
35 36 2.067766 GAAGACAACAGCAGCTCAGAG 58.932 52.381 0.00 0.00 0.00 3.35
36 37 1.336131 AGACAACAGCAGCTCAGAGA 58.664 50.000 0.00 0.00 0.00 3.10
37 38 1.901159 AGACAACAGCAGCTCAGAGAT 59.099 47.619 0.00 0.00 0.00 2.75
38 39 2.302445 AGACAACAGCAGCTCAGAGATT 59.698 45.455 0.00 0.00 0.00 2.40
39 40 2.415857 GACAACAGCAGCTCAGAGATTG 59.584 50.000 0.00 0.00 0.00 2.67
40 41 1.738350 CAACAGCAGCTCAGAGATTGG 59.262 52.381 0.00 0.00 0.00 3.16
41 42 1.273759 ACAGCAGCTCAGAGATTGGA 58.726 50.000 0.00 0.00 0.00 3.53
42 43 1.627329 ACAGCAGCTCAGAGATTGGAA 59.373 47.619 0.00 0.00 0.00 3.53
43 44 2.008329 CAGCAGCTCAGAGATTGGAAC 58.992 52.381 0.00 0.00 0.00 3.62
44 45 1.065564 AGCAGCTCAGAGATTGGAACC 60.066 52.381 0.00 0.00 0.00 3.62
45 46 1.649664 CAGCTCAGAGATTGGAACCG 58.350 55.000 0.00 0.00 0.00 4.44
46 47 0.539051 AGCTCAGAGATTGGAACCGG 59.461 55.000 0.00 0.00 0.00 5.28
47 48 0.250513 GCTCAGAGATTGGAACCGGT 59.749 55.000 0.00 0.00 0.00 5.28
48 49 2.009042 GCTCAGAGATTGGAACCGGTG 61.009 57.143 8.52 0.00 0.00 4.94
49 50 0.613260 TCAGAGATTGGAACCGGTGG 59.387 55.000 8.52 0.00 0.00 4.61
50 51 1.026718 CAGAGATTGGAACCGGTGGC 61.027 60.000 8.52 2.88 0.00 5.01
51 52 2.046314 AGATTGGAACCGGTGGCG 60.046 61.111 8.52 0.00 0.00 5.69
52 53 2.046700 GATTGGAACCGGTGGCGA 60.047 61.111 8.52 0.00 0.00 5.54
53 54 2.046314 ATTGGAACCGGTGGCGAG 60.046 61.111 8.52 0.00 0.00 5.03
54 55 2.515996 GATTGGAACCGGTGGCGAGA 62.516 60.000 8.52 0.00 0.00 4.04
55 56 2.521958 ATTGGAACCGGTGGCGAGAG 62.522 60.000 8.52 0.00 0.00 3.20
56 57 4.452733 GGAACCGGTGGCGAGAGG 62.453 72.222 8.52 0.00 0.00 3.69
57 58 3.379445 GAACCGGTGGCGAGAGGA 61.379 66.667 8.52 0.00 0.00 3.71
58 59 2.920912 AACCGGTGGCGAGAGGAA 60.921 61.111 8.52 0.00 0.00 3.36
59 60 2.837371 GAACCGGTGGCGAGAGGAAG 62.837 65.000 8.52 0.00 0.00 3.46
60 61 4.148825 CCGGTGGCGAGAGGAAGG 62.149 72.222 0.00 0.00 0.00 3.46
61 62 3.068691 CGGTGGCGAGAGGAAGGA 61.069 66.667 0.00 0.00 0.00 3.36
62 63 2.896443 GGTGGCGAGAGGAAGGAG 59.104 66.667 0.00 0.00 0.00 3.69
63 64 1.682684 GGTGGCGAGAGGAAGGAGA 60.683 63.158 0.00 0.00 0.00 3.71
64 65 1.258445 GGTGGCGAGAGGAAGGAGAA 61.258 60.000 0.00 0.00 0.00 2.87
65 66 0.174617 GTGGCGAGAGGAAGGAGAAG 59.825 60.000 0.00 0.00 0.00 2.85
66 67 0.251832 TGGCGAGAGGAAGGAGAAGT 60.252 55.000 0.00 0.00 0.00 3.01
67 68 0.899019 GGCGAGAGGAAGGAGAAGTT 59.101 55.000 0.00 0.00 0.00 2.66
68 69 1.134936 GGCGAGAGGAAGGAGAAGTTC 60.135 57.143 0.00 0.00 0.00 3.01
69 70 1.822371 GCGAGAGGAAGGAGAAGTTCT 59.178 52.381 4.68 4.68 0.00 3.01
70 71 2.416701 GCGAGAGGAAGGAGAAGTTCTG 60.417 54.545 10.90 0.00 0.00 3.02
71 72 2.165437 CGAGAGGAAGGAGAAGTTCTGG 59.835 54.545 10.90 0.00 0.00 3.86
72 73 3.169908 GAGAGGAAGGAGAAGTTCTGGT 58.830 50.000 10.90 0.00 0.00 4.00
73 74 2.903135 AGAGGAAGGAGAAGTTCTGGTG 59.097 50.000 10.90 0.00 0.00 4.17
74 75 1.349357 AGGAAGGAGAAGTTCTGGTGC 59.651 52.381 10.90 0.36 0.00 5.01
75 76 1.433534 GAAGGAGAAGTTCTGGTGCG 58.566 55.000 10.90 0.00 0.00 5.34
76 77 0.759346 AAGGAGAAGTTCTGGTGCGT 59.241 50.000 10.90 0.00 0.00 5.24
77 78 0.318762 AGGAGAAGTTCTGGTGCGTC 59.681 55.000 10.90 0.00 0.00 5.19
78 79 0.318762 GGAGAAGTTCTGGTGCGTCT 59.681 55.000 10.90 0.00 0.00 4.18
79 80 1.670380 GGAGAAGTTCTGGTGCGTCTC 60.670 57.143 10.90 0.00 38.75 3.36
80 81 1.271102 GAGAAGTTCTGGTGCGTCTCT 59.729 52.381 10.90 0.00 37.30 3.10
81 82 1.271102 AGAAGTTCTGGTGCGTCTCTC 59.729 52.381 4.10 0.00 0.00 3.20
82 83 1.271102 GAAGTTCTGGTGCGTCTCTCT 59.729 52.381 0.00 0.00 0.00 3.10
83 84 0.600557 AGTTCTGGTGCGTCTCTCTG 59.399 55.000 0.00 0.00 0.00 3.35
84 85 0.389166 GTTCTGGTGCGTCTCTCTGG 60.389 60.000 0.00 0.00 0.00 3.86
85 86 1.536073 TTCTGGTGCGTCTCTCTGGG 61.536 60.000 0.00 0.00 0.00 4.45
86 87 1.979155 CTGGTGCGTCTCTCTGGGA 60.979 63.158 0.00 0.00 0.00 4.37
87 88 1.943116 CTGGTGCGTCTCTCTGGGAG 61.943 65.000 0.00 0.00 43.12 4.30
88 89 2.716017 GGTGCGTCTCTCTGGGAGG 61.716 68.421 4.41 0.00 42.10 4.30
89 90 1.679305 GTGCGTCTCTCTGGGAGGA 60.679 63.158 4.41 0.00 42.10 3.71
90 91 1.379176 TGCGTCTCTCTGGGAGGAG 60.379 63.158 4.41 0.35 42.10 3.69
91 92 2.781158 GCGTCTCTCTGGGAGGAGC 61.781 68.421 4.41 7.03 42.10 4.70
92 93 2.477176 CGTCTCTCTGGGAGGAGCG 61.477 68.421 4.41 3.92 42.10 5.03
93 94 1.077357 GTCTCTCTGGGAGGAGCGA 60.077 63.158 4.41 0.00 42.10 4.93
94 95 1.077357 TCTCTCTGGGAGGAGCGAC 60.077 63.158 4.41 0.00 42.10 5.19
95 96 2.043852 TCTCTGGGAGGAGCGACC 60.044 66.667 0.00 0.00 39.35 4.79
108 109 3.388345 GAGCGACCTCCCTTTTATAGG 57.612 52.381 0.00 0.00 44.33 2.57
109 110 1.416772 AGCGACCTCCCTTTTATAGGC 59.583 52.381 0.00 0.00 43.27 3.93
110 111 1.872653 GCGACCTCCCTTTTATAGGCG 60.873 57.143 0.00 0.00 43.27 5.52
111 112 1.872653 CGACCTCCCTTTTATAGGCGC 60.873 57.143 0.00 0.00 43.27 6.53
112 113 1.140252 GACCTCCCTTTTATAGGCGCA 59.860 52.381 10.83 0.00 43.27 6.09
113 114 1.562475 ACCTCCCTTTTATAGGCGCAA 59.438 47.619 10.83 0.00 43.27 4.85
114 115 2.222027 CCTCCCTTTTATAGGCGCAAG 58.778 52.381 10.83 2.35 43.27 4.01
115 116 2.158813 CCTCCCTTTTATAGGCGCAAGA 60.159 50.000 10.83 0.00 43.27 3.02
227 228 2.646175 CGGTGGCGAGAGGAAGGAA 61.646 63.158 0.00 0.00 0.00 3.36
241 242 0.668535 AAGGAAAAGTTCTGGTGCGC 59.331 50.000 0.00 0.00 0.00 6.09
245 246 0.465460 AAAAGTTCTGGTGCGCCTCA 60.465 50.000 18.96 1.66 35.27 3.86
285 286 3.319405 CCTTCTATAGGCGCAAGAGAAGA 59.681 47.826 31.55 16.36 42.60 2.87
340 341 1.337071 AGACAGAGACGAAGCGAACAA 59.663 47.619 0.00 0.00 0.00 2.83
455 458 5.065346 TGCGTGGCAAAAATTTAGATATCGA 59.935 36.000 0.00 0.00 34.76 3.59
474 477 2.125147 TCGGCTCATTCCCGCAAG 60.125 61.111 0.00 0.00 45.19 4.01
539 569 1.109920 AGGAGCGCACGTGGATATCT 61.110 55.000 18.88 4.99 0.00 1.98
572 602 1.141254 TGCTCGTACAAGTGGGGAAAA 59.859 47.619 0.00 0.00 0.00 2.29
713 744 6.485830 TTCTGACATAGTTATTAGGCTGCT 57.514 37.500 0.00 0.00 0.00 4.24
779 810 1.210155 GCGTGGTCTCAACAATGCC 59.790 57.895 0.00 0.00 35.59 4.40
934 988 7.069331 AGCACTAGCCTATATAATAAGCTCTGG 59.931 40.741 0.00 0.00 43.56 3.86
1023 1103 2.418060 GGAGAGCACTAGCAAGGTTCTC 60.418 54.545 8.61 8.61 45.49 2.87
1182 1262 1.965219 CGACGACCTCTTCCTGGTT 59.035 57.895 0.00 0.00 38.03 3.67
1185 1265 0.685660 ACGACCTCTTCCTGGTTTCC 59.314 55.000 0.00 0.00 38.03 3.13
1433 1527 4.437659 GCTGGTACTGTTTTCAACGTCAAA 60.438 41.667 0.00 0.00 0.00 2.69
1434 1528 5.224562 TGGTACTGTTTTCAACGTCAAAG 57.775 39.130 0.00 0.00 0.00 2.77
1435 1529 4.696402 TGGTACTGTTTTCAACGTCAAAGT 59.304 37.500 0.00 0.00 0.00 2.66
1436 1530 5.163834 TGGTACTGTTTTCAACGTCAAAGTC 60.164 40.000 0.00 0.00 0.00 3.01
1437 1531 5.064325 GGTACTGTTTTCAACGTCAAAGTCT 59.936 40.000 0.00 0.00 0.00 3.24
1438 1532 5.622770 ACTGTTTTCAACGTCAAAGTCTT 57.377 34.783 0.00 0.00 0.00 3.01
1439 1533 6.009115 ACTGTTTTCAACGTCAAAGTCTTT 57.991 33.333 0.00 0.00 0.00 2.52
1440 1534 6.084277 ACTGTTTTCAACGTCAAAGTCTTTC 58.916 36.000 0.00 0.00 0.00 2.62
1441 1535 5.395642 TGTTTTCAACGTCAAAGTCTTTCC 58.604 37.500 0.00 0.00 0.00 3.13
1442 1536 5.182380 TGTTTTCAACGTCAAAGTCTTTCCT 59.818 36.000 0.00 0.00 0.00 3.36
1443 1537 5.479716 TTTCAACGTCAAAGTCTTTCCTC 57.520 39.130 0.00 0.00 0.00 3.71
1444 1538 3.120792 TCAACGTCAAAGTCTTTCCTCG 58.879 45.455 0.00 3.73 0.00 4.63
1445 1539 1.499049 ACGTCAAAGTCTTTCCTCGC 58.501 50.000 0.00 0.00 0.00 5.03
1446 1540 1.068741 ACGTCAAAGTCTTTCCTCGCT 59.931 47.619 0.00 0.00 0.00 4.93
1447 1541 2.295349 ACGTCAAAGTCTTTCCTCGCTA 59.705 45.455 0.00 0.00 0.00 4.26
1448 1542 3.056749 ACGTCAAAGTCTTTCCTCGCTAT 60.057 43.478 0.00 0.00 0.00 2.97
1449 1543 4.157289 ACGTCAAAGTCTTTCCTCGCTATA 59.843 41.667 0.00 0.00 0.00 1.31
1450 1544 5.163540 ACGTCAAAGTCTTTCCTCGCTATAT 60.164 40.000 0.00 0.00 0.00 0.86
1451 1545 6.039047 ACGTCAAAGTCTTTCCTCGCTATATA 59.961 38.462 0.00 0.00 0.00 0.86
1452 1546 7.085116 CGTCAAAGTCTTTCCTCGCTATATAT 58.915 38.462 0.00 0.00 0.00 0.86
1453 1547 8.235226 CGTCAAAGTCTTTCCTCGCTATATATA 58.765 37.037 0.00 0.00 0.00 0.86
1460 1554 9.900710 GTCTTTCCTCGCTATATATATATGTGG 57.099 37.037 14.42 8.73 0.00 4.17
1461 1555 8.577296 TCTTTCCTCGCTATATATATATGTGGC 58.423 37.037 15.15 15.15 0.00 5.01
1462 1556 7.833285 TTCCTCGCTATATATATATGTGGCA 57.167 36.000 21.85 11.66 0.00 4.92
1463 1557 7.454260 TCCTCGCTATATATATATGTGGCAG 57.546 40.000 21.85 17.61 0.00 4.85
1464 1558 6.071896 TCCTCGCTATATATATATGTGGCAGC 60.072 42.308 21.85 12.99 0.00 5.25
1465 1559 5.699839 TCGCTATATATATATGTGGCAGCG 58.300 41.667 26.56 26.56 41.00 5.18
1466 1560 5.240844 TCGCTATATATATATGTGGCAGCGT 59.759 40.000 28.78 4.39 40.72 5.07
1467 1561 5.569441 CGCTATATATATATGTGGCAGCGTC 59.431 44.000 25.28 3.66 37.73 5.19
1468 1562 5.569441 GCTATATATATATGTGGCAGCGTCG 59.431 44.000 18.76 0.00 0.00 5.12
1469 1563 3.868757 ATATATATGTGGCAGCGTCGT 57.131 42.857 0.00 0.00 0.00 4.34
1470 1564 2.526304 ATATATGTGGCAGCGTCGTT 57.474 45.000 0.00 0.00 0.00 3.85
1471 1565 3.653539 ATATATGTGGCAGCGTCGTTA 57.346 42.857 0.00 0.00 0.00 3.18
1472 1566 2.526304 ATATGTGGCAGCGTCGTTAT 57.474 45.000 0.00 0.00 0.00 1.89
1473 1567 2.303163 TATGTGGCAGCGTCGTTATT 57.697 45.000 0.00 0.00 0.00 1.40
1474 1568 0.726827 ATGTGGCAGCGTCGTTATTG 59.273 50.000 0.00 0.00 0.00 1.90
1484 2071 4.503007 CAGCGTCGTTATTGCTACTTACAT 59.497 41.667 0.00 0.00 37.15 2.29
1492 2079 6.487103 GTTATTGCTACTTACATGCCTTCAC 58.513 40.000 0.00 0.00 0.00 3.18
2025 2612 2.280186 CTGCCGGCGGATAACTCC 60.280 66.667 32.31 10.67 38.29 3.85
2027 2614 1.456145 TGCCGGCGGATAACTCCTA 60.456 57.895 33.44 0.00 39.65 2.94
2028 2615 1.289380 GCCGGCGGATAACTCCTAG 59.711 63.158 33.44 0.00 39.65 3.02
2030 2617 1.038280 CCGGCGGATAACTCCTAGTT 58.962 55.000 24.41 0.00 41.97 2.24
2031 2618 2.233271 CCGGCGGATAACTCCTAGTTA 58.767 52.381 24.41 2.23 43.95 2.24
2039 2626 4.868314 ATAACTCCTAGTTATCCACCGC 57.132 45.455 6.51 0.00 45.49 5.68
2040 2627 1.411041 ACTCCTAGTTATCCACCGCC 58.589 55.000 0.00 0.00 0.00 6.13
2042 2629 1.341531 CTCCTAGTTATCCACCGCCTG 59.658 57.143 0.00 0.00 0.00 4.85
2043 2630 0.249911 CCTAGTTATCCACCGCCTGC 60.250 60.000 0.00 0.00 0.00 4.85
2044 2631 0.249911 CTAGTTATCCACCGCCTGCC 60.250 60.000 0.00 0.00 0.00 4.85
2045 2632 1.692173 TAGTTATCCACCGCCTGCCC 61.692 60.000 0.00 0.00 0.00 5.36
2050 2637 4.028490 CCACCGCCTGCCCAGTTA 62.028 66.667 0.00 0.00 0.00 2.24
2051 2638 2.272146 CACCGCCTGCCCAGTTAT 59.728 61.111 0.00 0.00 0.00 1.89
2052 2639 1.819632 CACCGCCTGCCCAGTTATC 60.820 63.158 0.00 0.00 0.00 1.75
2053 2640 2.203209 CCGCCTGCCCAGTTATCC 60.203 66.667 0.00 0.00 0.00 2.59
2054 2641 2.589540 CGCCTGCCCAGTTATCCA 59.410 61.111 0.00 0.00 0.00 3.41
2056 2643 1.453928 GCCTGCCCAGTTATCCACC 60.454 63.158 0.00 0.00 0.00 4.61
2057 2644 1.998530 CCTGCCCAGTTATCCACCA 59.001 57.895 0.00 0.00 0.00 4.17
2068 2687 2.850851 TATCCACCACCTCCCCCACC 62.851 65.000 0.00 0.00 0.00 4.61
2106 2725 2.203294 GTGGCCCACAACGTCCTT 60.203 61.111 9.55 0.00 34.08 3.36
2115 2734 0.468226 ACAACGTCCTTCTTGCCTCA 59.532 50.000 0.00 0.00 0.00 3.86
2158 3512 1.000060 GCATTGCAACACTGACCATGT 60.000 47.619 0.00 0.00 0.00 3.21
2161 3515 3.883830 TTGCAACACTGACCATGTTTT 57.116 38.095 0.00 0.00 38.22 2.43
2177 3531 6.072508 ACCATGTTTTAGCAACACTAGTGATG 60.073 38.462 29.30 26.68 36.58 3.07
2187 3541 4.292186 ACACTAGTGATGTTGCAATCCT 57.708 40.909 29.30 0.00 0.00 3.24
2244 3600 0.944386 TTTCAGAAACGCACCTCTGC 59.056 50.000 0.00 0.00 39.17 4.26
2250 3606 1.001378 GAAACGCACCTCTGCAACAAT 60.001 47.619 0.00 0.00 44.50 2.71
2292 3648 3.563390 TGCAACAATGTCGATGTTTCAGA 59.437 39.130 0.16 0.00 38.90 3.27
2295 3651 5.116074 GCAACAATGTCGATGTTTCAGAAAG 59.884 40.000 0.16 0.00 38.90 2.62
2298 3654 5.049405 ACAATGTCGATGTTTCAGAAAGACC 60.049 40.000 9.42 0.00 0.00 3.85
2305 3661 2.093394 TGTTTCAGAAAGACCGGTCACA 60.093 45.455 35.00 23.85 0.00 3.58
2316 3672 3.006940 GACCGGTCACATTGCAATCTAA 58.993 45.455 29.75 0.00 0.00 2.10
2319 3675 2.537529 CGGTCACATTGCAATCTAAGCG 60.538 50.000 9.53 14.14 33.85 4.68
2334 3690 3.077705 GCGCGTGCGATCTGTTTA 58.922 55.556 19.66 0.00 42.83 2.01
2339 3695 3.160545 CGCGTGCGATCTGTTTAAAAAT 58.839 40.909 8.89 0.00 42.83 1.82
2340 3696 3.003119 CGCGTGCGATCTGTTTAAAAATG 60.003 43.478 8.89 0.00 42.83 2.32
2342 3698 3.911365 CGTGCGATCTGTTTAAAAATGCA 59.089 39.130 0.00 0.00 0.00 3.96
2346 3702 6.308766 GTGCGATCTGTTTAAAAATGCATCTT 59.691 34.615 0.00 0.00 31.93 2.40
2348 3704 7.148771 TGCGATCTGTTTAAAAATGCATCTTTG 60.149 33.333 8.28 0.00 0.00 2.77
2377 3733 3.626028 ACGATGTTTCAGAAACTTGCC 57.374 42.857 23.57 10.94 41.90 4.52
2382 3738 2.951642 TGTTTCAGAAACTTGCCTCTGG 59.048 45.455 23.57 0.00 41.90 3.86
2385 3741 3.576078 TCAGAAACTTGCCTCTGGAAA 57.424 42.857 0.00 0.00 39.67 3.13
2386 3742 3.897239 TCAGAAACTTGCCTCTGGAAAA 58.103 40.909 0.00 0.00 39.67 2.29
2387 3743 4.277476 TCAGAAACTTGCCTCTGGAAAAA 58.723 39.130 0.00 0.00 39.67 1.94
2388 3744 4.895297 TCAGAAACTTGCCTCTGGAAAAAT 59.105 37.500 0.00 0.00 39.67 1.82
2389 3745 4.986659 CAGAAACTTGCCTCTGGAAAAATG 59.013 41.667 0.00 0.00 36.27 2.32
2390 3746 4.895297 AGAAACTTGCCTCTGGAAAAATGA 59.105 37.500 0.00 0.00 0.00 2.57
2391 3747 4.590850 AACTTGCCTCTGGAAAAATGAC 57.409 40.909 0.00 0.00 0.00 3.06
2392 3748 2.554032 ACTTGCCTCTGGAAAAATGACG 59.446 45.455 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.280628 GCTGTTGTCTTCCTAATCCCG 58.719 52.381 0.00 0.00 0.00 5.14
7 8 3.274288 CTGCTGTTGTCTTCCTAATCCC 58.726 50.000 0.00 0.00 0.00 3.85
8 9 2.680339 GCTGCTGTTGTCTTCCTAATCC 59.320 50.000 0.00 0.00 0.00 3.01
9 10 3.604582 AGCTGCTGTTGTCTTCCTAATC 58.395 45.455 0.00 0.00 0.00 1.75
10 11 3.008375 TGAGCTGCTGTTGTCTTCCTAAT 59.992 43.478 7.01 0.00 0.00 1.73
11 12 2.368548 TGAGCTGCTGTTGTCTTCCTAA 59.631 45.455 7.01 0.00 0.00 2.69
12 13 1.970640 TGAGCTGCTGTTGTCTTCCTA 59.029 47.619 7.01 0.00 0.00 2.94
13 14 0.761187 TGAGCTGCTGTTGTCTTCCT 59.239 50.000 7.01 0.00 0.00 3.36
14 15 1.155042 CTGAGCTGCTGTTGTCTTCC 58.845 55.000 7.01 0.00 0.00 3.46
15 16 2.067766 CTCTGAGCTGCTGTTGTCTTC 58.932 52.381 7.01 0.00 0.00 2.87
16 17 1.690893 TCTCTGAGCTGCTGTTGTCTT 59.309 47.619 7.01 0.00 0.00 3.01
17 18 1.336131 TCTCTGAGCTGCTGTTGTCT 58.664 50.000 7.01 0.00 0.00 3.41
18 19 2.383368 ATCTCTGAGCTGCTGTTGTC 57.617 50.000 7.01 0.00 0.00 3.18
19 20 2.424557 CAATCTCTGAGCTGCTGTTGT 58.575 47.619 7.01 0.00 0.00 3.32
20 21 1.738350 CCAATCTCTGAGCTGCTGTTG 59.262 52.381 7.01 2.56 0.00 3.33
21 22 1.627329 TCCAATCTCTGAGCTGCTGTT 59.373 47.619 7.01 0.00 0.00 3.16
22 23 1.273759 TCCAATCTCTGAGCTGCTGT 58.726 50.000 7.01 0.00 0.00 4.40
23 24 2.008329 GTTCCAATCTCTGAGCTGCTG 58.992 52.381 7.01 0.00 0.00 4.41
24 25 1.065564 GGTTCCAATCTCTGAGCTGCT 60.066 52.381 0.00 0.00 0.00 4.24
25 26 1.377536 GGTTCCAATCTCTGAGCTGC 58.622 55.000 0.00 0.00 0.00 5.25
26 27 1.649664 CGGTTCCAATCTCTGAGCTG 58.350 55.000 0.00 0.00 0.00 4.24
27 28 0.539051 CCGGTTCCAATCTCTGAGCT 59.461 55.000 0.00 0.00 0.00 4.09
28 29 0.250513 ACCGGTTCCAATCTCTGAGC 59.749 55.000 0.00 0.00 0.00 4.26
29 30 1.406069 CCACCGGTTCCAATCTCTGAG 60.406 57.143 2.97 0.00 0.00 3.35
30 31 0.613260 CCACCGGTTCCAATCTCTGA 59.387 55.000 2.97 0.00 0.00 3.27
31 32 1.026718 GCCACCGGTTCCAATCTCTG 61.027 60.000 2.97 0.00 0.00 3.35
32 33 1.299976 GCCACCGGTTCCAATCTCT 59.700 57.895 2.97 0.00 0.00 3.10
33 34 2.106683 CGCCACCGGTTCCAATCTC 61.107 63.158 2.97 0.00 0.00 2.75
34 35 2.046314 CGCCACCGGTTCCAATCT 60.046 61.111 2.97 0.00 0.00 2.40
35 36 2.046700 TCGCCACCGGTTCCAATC 60.047 61.111 2.97 0.00 34.56 2.67
36 37 2.046314 CTCGCCACCGGTTCCAAT 60.046 61.111 2.97 0.00 34.56 3.16
37 38 3.234630 CTCTCGCCACCGGTTCCAA 62.235 63.158 2.97 0.00 34.56 3.53
38 39 3.691342 CTCTCGCCACCGGTTCCA 61.691 66.667 2.97 0.00 34.56 3.53
39 40 4.452733 CCTCTCGCCACCGGTTCC 62.453 72.222 2.97 0.00 34.56 3.62
40 41 2.837371 CTTCCTCTCGCCACCGGTTC 62.837 65.000 2.97 0.00 34.56 3.62
41 42 2.920912 TTCCTCTCGCCACCGGTT 60.921 61.111 2.97 0.00 34.56 4.44
42 43 3.382832 CTTCCTCTCGCCACCGGT 61.383 66.667 0.00 0.00 34.56 5.28
43 44 4.148825 CCTTCCTCTCGCCACCGG 62.149 72.222 0.00 0.00 34.56 5.28
44 45 3.068691 TCCTTCCTCTCGCCACCG 61.069 66.667 0.00 0.00 0.00 4.94
45 46 1.258445 TTCTCCTTCCTCTCGCCACC 61.258 60.000 0.00 0.00 0.00 4.61
46 47 0.174617 CTTCTCCTTCCTCTCGCCAC 59.825 60.000 0.00 0.00 0.00 5.01
47 48 0.251832 ACTTCTCCTTCCTCTCGCCA 60.252 55.000 0.00 0.00 0.00 5.69
48 49 0.899019 AACTTCTCCTTCCTCTCGCC 59.101 55.000 0.00 0.00 0.00 5.54
49 50 1.822371 AGAACTTCTCCTTCCTCTCGC 59.178 52.381 0.00 0.00 0.00 5.03
50 51 2.165437 CCAGAACTTCTCCTTCCTCTCG 59.835 54.545 0.00 0.00 0.00 4.04
51 52 3.056179 CACCAGAACTTCTCCTTCCTCTC 60.056 52.174 0.00 0.00 0.00 3.20
52 53 2.903135 CACCAGAACTTCTCCTTCCTCT 59.097 50.000 0.00 0.00 0.00 3.69
53 54 2.614229 GCACCAGAACTTCTCCTTCCTC 60.614 54.545 0.00 0.00 0.00 3.71
54 55 1.349357 GCACCAGAACTTCTCCTTCCT 59.651 52.381 0.00 0.00 0.00 3.36
55 56 1.814793 GCACCAGAACTTCTCCTTCC 58.185 55.000 0.00 0.00 0.00 3.46
56 57 1.270358 ACGCACCAGAACTTCTCCTTC 60.270 52.381 0.00 0.00 0.00 3.46
57 58 0.759346 ACGCACCAGAACTTCTCCTT 59.241 50.000 0.00 0.00 0.00 3.36
58 59 0.318762 GACGCACCAGAACTTCTCCT 59.681 55.000 0.00 0.00 0.00 3.69
59 60 0.318762 AGACGCACCAGAACTTCTCC 59.681 55.000 0.00 0.00 0.00 3.71
60 61 1.271102 AGAGACGCACCAGAACTTCTC 59.729 52.381 0.00 0.00 0.00 2.87
61 62 1.271102 GAGAGACGCACCAGAACTTCT 59.729 52.381 0.00 0.00 0.00 2.85
62 63 1.271102 AGAGAGACGCACCAGAACTTC 59.729 52.381 0.00 0.00 0.00 3.01
63 64 1.000283 CAGAGAGACGCACCAGAACTT 60.000 52.381 0.00 0.00 0.00 2.66
64 65 0.600557 CAGAGAGACGCACCAGAACT 59.399 55.000 0.00 0.00 0.00 3.01
65 66 0.389166 CCAGAGAGACGCACCAGAAC 60.389 60.000 0.00 0.00 0.00 3.01
66 67 1.536073 CCCAGAGAGACGCACCAGAA 61.536 60.000 0.00 0.00 0.00 3.02
67 68 1.979155 CCCAGAGAGACGCACCAGA 60.979 63.158 0.00 0.00 0.00 3.86
68 69 1.943116 CTCCCAGAGAGACGCACCAG 61.943 65.000 0.00 0.00 46.50 4.00
69 70 1.979155 CTCCCAGAGAGACGCACCA 60.979 63.158 0.00 0.00 46.50 4.17
70 71 2.716017 CCTCCCAGAGAGACGCACC 61.716 68.421 0.00 0.00 46.50 5.01
71 72 1.662438 CTCCTCCCAGAGAGACGCAC 61.662 65.000 0.00 0.00 46.50 5.34
72 73 1.379176 CTCCTCCCAGAGAGACGCA 60.379 63.158 0.00 0.00 46.50 5.24
73 74 2.781158 GCTCCTCCCAGAGAGACGC 61.781 68.421 0.00 0.00 46.50 5.19
74 75 2.477176 CGCTCCTCCCAGAGAGACG 61.477 68.421 0.00 0.00 46.50 4.18
75 76 1.077357 TCGCTCCTCCCAGAGAGAC 60.077 63.158 0.00 0.00 46.50 3.36
76 77 1.077357 GTCGCTCCTCCCAGAGAGA 60.077 63.158 0.00 0.00 46.50 3.10
77 78 2.124693 GGTCGCTCCTCCCAGAGAG 61.125 68.421 0.00 0.00 42.83 3.20
78 79 2.043852 GGTCGCTCCTCCCAGAGA 60.044 66.667 0.00 0.00 35.82 3.10
79 80 2.043450 AGGTCGCTCCTCCCAGAG 60.043 66.667 0.00 0.00 44.42 3.35
86 87 4.262446 CCTATAAAAGGGAGGTCGCTCCT 61.262 52.174 8.72 4.07 42.62 3.69
87 88 2.037381 CCTATAAAAGGGAGGTCGCTCC 59.963 54.545 0.68 0.68 42.32 4.70
88 89 2.548280 GCCTATAAAAGGGAGGTCGCTC 60.548 54.545 0.00 0.00 46.65 5.03
89 90 1.416772 GCCTATAAAAGGGAGGTCGCT 59.583 52.381 0.00 0.00 46.65 4.93
90 91 1.872653 CGCCTATAAAAGGGAGGTCGC 60.873 57.143 0.00 0.00 46.65 5.19
91 92 1.872653 GCGCCTATAAAAGGGAGGTCG 60.873 57.143 0.00 0.00 46.65 4.79
92 93 1.140252 TGCGCCTATAAAAGGGAGGTC 59.860 52.381 4.18 0.00 46.65 3.85
93 94 1.209621 TGCGCCTATAAAAGGGAGGT 58.790 50.000 4.18 0.00 46.65 3.85
94 95 2.158813 TCTTGCGCCTATAAAAGGGAGG 60.159 50.000 4.18 0.00 46.65 4.30
95 96 2.872858 GTCTTGCGCCTATAAAAGGGAG 59.127 50.000 4.18 0.00 46.65 4.30
96 97 2.237643 TGTCTTGCGCCTATAAAAGGGA 59.762 45.455 4.18 0.00 46.65 4.20
97 98 2.639065 TGTCTTGCGCCTATAAAAGGG 58.361 47.619 4.18 0.00 46.65 3.95
99 100 6.033831 CACATTTTGTCTTGCGCCTATAAAAG 59.966 38.462 4.18 0.00 0.00 2.27
100 101 5.861251 CACATTTTGTCTTGCGCCTATAAAA 59.139 36.000 4.18 7.82 0.00 1.52
101 102 5.398169 CACATTTTGTCTTGCGCCTATAAA 58.602 37.500 4.18 0.00 0.00 1.40
102 103 4.674101 GCACATTTTGTCTTGCGCCTATAA 60.674 41.667 4.18 0.00 0.00 0.98
103 104 3.181501 GCACATTTTGTCTTGCGCCTATA 60.182 43.478 4.18 0.00 0.00 1.31
104 105 2.415893 GCACATTTTGTCTTGCGCCTAT 60.416 45.455 4.18 0.00 0.00 2.57
105 106 1.068610 GCACATTTTGTCTTGCGCCTA 60.069 47.619 4.18 0.00 0.00 3.93
106 107 0.318955 GCACATTTTGTCTTGCGCCT 60.319 50.000 4.18 0.00 0.00 5.52
107 108 2.144362 GCACATTTTGTCTTGCGCC 58.856 52.632 4.18 0.00 0.00 6.53
110 111 1.851658 AACCGCACATTTTGTCTTGC 58.148 45.000 0.00 0.00 0.00 4.01
111 112 2.467305 CGAAACCGCACATTTTGTCTTG 59.533 45.455 0.00 0.00 0.00 3.02
112 113 2.542824 CCGAAACCGCACATTTTGTCTT 60.543 45.455 0.00 0.00 0.00 3.01
113 114 1.001815 CCGAAACCGCACATTTTGTCT 60.002 47.619 0.00 0.00 0.00 3.41
114 115 1.002251 TCCGAAACCGCACATTTTGTC 60.002 47.619 0.00 0.00 0.00 3.18
115 116 1.001815 CTCCGAAACCGCACATTTTGT 60.002 47.619 0.00 0.00 0.00 2.83
227 228 1.148273 TGAGGCGCACCAGAACTTT 59.852 52.632 10.83 0.00 39.06 2.66
267 268 3.648009 CCTTCTTCTCTTGCGCCTATAG 58.352 50.000 4.18 0.00 0.00 1.31
285 286 3.311110 TCGTTGCCCTCTCGCCTT 61.311 61.111 0.00 0.00 0.00 4.35
455 458 2.859273 CTTGCGGGAATGAGCCGAGT 62.859 60.000 0.00 0.00 0.00 4.18
474 477 4.383861 GCCTTGCCTTGCCTTGCC 62.384 66.667 0.00 0.00 0.00 4.52
539 569 3.506067 TGTACGAGCATGAGAACAAGAGA 59.494 43.478 0.00 0.00 0.00 3.10
600 630 4.286032 AGTCCCACATTGCTAGTTTAGTGA 59.714 41.667 8.45 0.00 0.00 3.41
706 737 7.039082 TGGAATTTAGTTTATTTTGAGCAGCCT 60.039 33.333 0.00 0.00 0.00 4.58
864 917 3.518590 GAGGGACCTACGTACAAATGTG 58.481 50.000 0.00 0.00 0.00 3.21
934 988 1.239968 CCTGGCTGTGTGCTTTCTCC 61.240 60.000 0.00 0.00 42.39 3.71
1023 1103 0.593128 CCAGAAGGCCAAAGAACACG 59.407 55.000 5.01 0.00 0.00 4.49
1182 1262 3.613193 CGTACCACTTCGAAGTCATGGAA 60.613 47.826 29.87 12.31 37.08 3.53
1185 1265 2.259618 CCGTACCACTTCGAAGTCATG 58.740 52.381 27.54 19.86 37.08 3.07
1333 1422 4.097361 GTCGAGCCCCAAGACCCC 62.097 72.222 0.00 0.00 0.00 4.95
1434 1528 9.900710 CCACATATATATATAGCGAGGAAAGAC 57.099 37.037 4.90 0.00 0.00 3.01
1435 1529 8.577296 GCCACATATATATATAGCGAGGAAAGA 58.423 37.037 16.30 0.00 0.00 2.52
1436 1530 8.360390 TGCCACATATATATATAGCGAGGAAAG 58.640 37.037 16.30 0.00 0.00 2.62
1437 1531 8.245195 TGCCACATATATATATAGCGAGGAAA 57.755 34.615 16.30 6.47 0.00 3.13
1438 1532 7.523873 GCTGCCACATATATATATAGCGAGGAA 60.524 40.741 16.30 9.25 0.00 3.36
1439 1533 6.071896 GCTGCCACATATATATATAGCGAGGA 60.072 42.308 16.30 5.32 0.00 3.71
1440 1534 6.096036 GCTGCCACATATATATATAGCGAGG 58.904 44.000 4.90 10.06 0.00 4.63
1443 1537 5.999483 CGCTGCCACATATATATATAGCG 57.001 43.478 22.69 22.69 44.04 4.26
1444 1538 5.569441 CGACGCTGCCACATATATATATAGC 59.431 44.000 4.90 9.08 0.00 2.97
1445 1539 6.669278 ACGACGCTGCCACATATATATATAG 58.331 40.000 4.90 0.78 0.00 1.31
1446 1540 6.628919 ACGACGCTGCCACATATATATATA 57.371 37.500 4.90 4.92 0.00 0.86
1447 1541 5.515797 ACGACGCTGCCACATATATATAT 57.484 39.130 0.00 0.00 0.00 0.86
1448 1542 4.976224 ACGACGCTGCCACATATATATA 57.024 40.909 0.00 0.00 0.00 0.86
1449 1543 3.868757 ACGACGCTGCCACATATATAT 57.131 42.857 0.00 0.00 0.00 0.86
1450 1544 3.653539 AACGACGCTGCCACATATATA 57.346 42.857 0.00 0.00 0.00 0.86
1451 1545 2.526304 AACGACGCTGCCACATATAT 57.474 45.000 0.00 0.00 0.00 0.86
1452 1546 3.653539 ATAACGACGCTGCCACATATA 57.346 42.857 0.00 0.00 0.00 0.86
1453 1547 2.526304 ATAACGACGCTGCCACATAT 57.474 45.000 0.00 0.00 0.00 1.78
1454 1548 1.930503 CAATAACGACGCTGCCACATA 59.069 47.619 0.00 0.00 0.00 2.29
1455 1549 0.726827 CAATAACGACGCTGCCACAT 59.273 50.000 0.00 0.00 0.00 3.21
1456 1550 1.906994 GCAATAACGACGCTGCCACA 61.907 55.000 0.00 0.00 0.00 4.17
1457 1551 1.226018 GCAATAACGACGCTGCCAC 60.226 57.895 0.00 0.00 0.00 5.01
1458 1552 0.108567 TAGCAATAACGACGCTGCCA 60.109 50.000 0.00 0.00 37.20 4.92
1459 1553 0.300789 GTAGCAATAACGACGCTGCC 59.699 55.000 0.00 0.00 37.20 4.85
1460 1554 1.278238 AGTAGCAATAACGACGCTGC 58.722 50.000 0.00 0.00 38.49 5.25
1461 1555 3.855379 TGTAAGTAGCAATAACGACGCTG 59.145 43.478 0.00 0.00 37.20 5.18
1462 1556 4.100707 TGTAAGTAGCAATAACGACGCT 57.899 40.909 0.00 0.00 39.80 5.07
1463 1557 4.748023 CATGTAAGTAGCAATAACGACGC 58.252 43.478 0.00 0.00 0.00 5.19
1464 1558 4.317839 GGCATGTAAGTAGCAATAACGACG 60.318 45.833 0.00 0.00 0.00 5.12
1465 1559 4.809426 AGGCATGTAAGTAGCAATAACGAC 59.191 41.667 0.00 0.00 0.00 4.34
1466 1560 5.018539 AGGCATGTAAGTAGCAATAACGA 57.981 39.130 0.00 0.00 0.00 3.85
1467 1561 5.293324 TGAAGGCATGTAAGTAGCAATAACG 59.707 40.000 0.00 0.00 0.00 3.18
1468 1562 6.487103 GTGAAGGCATGTAAGTAGCAATAAC 58.513 40.000 0.00 0.00 0.00 1.89
1469 1563 5.293324 CGTGAAGGCATGTAAGTAGCAATAA 59.707 40.000 0.00 0.00 0.00 1.40
1470 1564 4.808895 CGTGAAGGCATGTAAGTAGCAATA 59.191 41.667 0.00 0.00 0.00 1.90
1471 1565 3.623060 CGTGAAGGCATGTAAGTAGCAAT 59.377 43.478 0.00 0.00 0.00 3.56
1472 1566 3.000041 CGTGAAGGCATGTAAGTAGCAA 59.000 45.455 0.00 0.00 0.00 3.91
1473 1567 2.616960 CGTGAAGGCATGTAAGTAGCA 58.383 47.619 0.00 0.00 0.00 3.49
1474 1568 1.933853 CCGTGAAGGCATGTAAGTAGC 59.066 52.381 0.00 0.00 0.00 3.58
1492 2079 8.658499 ATTTTATTAAGTTACCTACTCAGCCG 57.342 34.615 0.00 0.00 35.54 5.52
1542 2129 7.093354 ACACTAACATATAAGCAGATCATCCG 58.907 38.462 0.00 0.00 0.00 4.18
1546 2133 9.481340 GATTGACACTAACATATAAGCAGATCA 57.519 33.333 0.00 0.00 0.00 2.92
1604 2191 3.643792 GCCTCCTTATCAGTGACCTACAT 59.356 47.826 0.00 0.00 0.00 2.29
2005 2592 2.280186 GTTATCCGCCGGCAGAGG 60.280 66.667 28.98 20.14 0.00 3.69
2006 2593 1.300233 GAGTTATCCGCCGGCAGAG 60.300 63.158 28.98 14.85 0.00 3.35
2008 2595 2.280186 GGAGTTATCCGCCGGCAG 60.280 66.667 28.98 16.96 35.37 4.85
2025 2612 0.249911 GGCAGGCGGTGGATAACTAG 60.250 60.000 0.00 0.00 0.00 2.57
2027 2614 2.590092 GGCAGGCGGTGGATAACT 59.410 61.111 0.00 0.00 0.00 2.24
2028 2615 2.516225 GGGCAGGCGGTGGATAAC 60.516 66.667 0.00 0.00 0.00 1.89
2030 2617 3.479203 CTGGGCAGGCGGTGGATA 61.479 66.667 0.00 0.00 0.00 2.59
2033 2620 3.344137 ATAACTGGGCAGGCGGTGG 62.344 63.158 0.00 0.00 0.00 4.61
2035 2622 2.590092 GATAACTGGGCAGGCGGT 59.410 61.111 0.00 0.00 0.00 5.68
2036 2623 2.203209 GGATAACTGGGCAGGCGG 60.203 66.667 0.00 0.00 0.00 6.13
2039 2626 0.394352 GTGGTGGATAACTGGGCAGG 60.394 60.000 0.00 0.00 0.00 4.85
2040 2627 0.394352 GGTGGTGGATAACTGGGCAG 60.394 60.000 0.00 0.00 0.00 4.85
2042 2629 0.107165 GAGGTGGTGGATAACTGGGC 60.107 60.000 0.00 0.00 0.00 5.36
2043 2630 0.546598 GGAGGTGGTGGATAACTGGG 59.453 60.000 0.00 0.00 0.00 4.45
2044 2631 0.546598 GGGAGGTGGTGGATAACTGG 59.453 60.000 0.00 0.00 0.00 4.00
2045 2632 0.546598 GGGGAGGTGGTGGATAACTG 59.453 60.000 0.00 0.00 0.00 3.16
2049 2636 1.307517 GTGGGGGAGGTGGTGGATA 60.308 63.158 0.00 0.00 0.00 2.59
2050 2637 2.614013 GTGGGGGAGGTGGTGGAT 60.614 66.667 0.00 0.00 0.00 3.41
2051 2638 4.995058 GGTGGGGGAGGTGGTGGA 62.995 72.222 0.00 0.00 0.00 4.02
2056 2643 3.706373 CTGACGGTGGGGGAGGTG 61.706 72.222 0.00 0.00 0.00 4.00
2057 2644 3.254035 ATCTGACGGTGGGGGAGGT 62.254 63.158 0.00 0.00 0.00 3.85
2068 2687 5.063944 CCACTTGATTAAGGTTGATCTGACG 59.936 44.000 1.95 0.00 38.26 4.35
2115 2734 1.009078 CAACGTCACCGATGATGCAT 58.991 50.000 0.00 0.00 44.55 3.96
2125 2744 1.265635 TGCAATGCTTACAACGTCACC 59.734 47.619 6.82 0.00 0.00 4.02
2132 2751 3.243367 GGTCAGTGTTGCAATGCTTACAA 60.243 43.478 13.48 0.00 29.02 2.41
2151 3505 5.468746 TCACTAGTGTTGCTAAAACATGGTC 59.531 40.000 21.99 0.00 32.23 4.02
2177 3531 0.445436 CGAGCTCACAGGATTGCAAC 59.555 55.000 15.40 0.00 0.00 4.17
2187 3541 2.343426 ACGGATCTGCGAGCTCACA 61.343 57.895 15.40 9.67 0.00 3.58
2203 3557 4.669318 ACATCGTCCTTGTTATAGACACG 58.331 43.478 0.00 0.00 38.18 4.49
2264 3620 4.681744 ACATCGACATTGTTGCAAAAGTT 58.318 34.783 0.00 0.00 0.00 2.66
2265 3621 4.305989 ACATCGACATTGTTGCAAAAGT 57.694 36.364 0.00 0.00 0.00 2.66
2269 3625 4.036144 TCTGAAACATCGACATTGTTGCAA 59.964 37.500 11.29 0.00 41.07 4.08
2278 3634 3.057019 CGGTCTTTCTGAAACATCGACA 58.943 45.455 16.91 0.00 0.00 4.35
2292 3648 1.686355 TTGCAATGTGACCGGTCTTT 58.314 45.000 33.39 21.15 0.00 2.52
2295 3651 1.453155 AGATTGCAATGTGACCGGTC 58.547 50.000 28.17 28.17 0.00 4.79
2298 3654 2.537529 CGCTTAGATTGCAATGTGACCG 60.538 50.000 18.59 9.14 0.00 4.79
2305 3661 0.248215 GCACGCGCTTAGATTGCAAT 60.248 50.000 12.83 12.83 33.24 3.56
2316 3672 1.011968 TTAAACAGATCGCACGCGCT 61.012 50.000 5.73 0.00 39.59 5.92
2319 3675 3.241333 GCATTTTTAAACAGATCGCACGC 60.241 43.478 0.00 0.00 0.00 5.34
2342 3698 4.305989 ACATCGTTGTTGTTGCAAAGAT 57.694 36.364 0.00 0.00 44.24 2.40
2346 3702 3.838120 TGAAACATCGTTGTTGTTGCAA 58.162 36.364 12.39 0.00 45.30 4.08
2348 3704 3.690422 TCTGAAACATCGTTGTTGTTGC 58.310 40.909 12.39 3.96 45.30 4.17
2351 3707 5.560966 AGTTTCTGAAACATCGTTGTTGT 57.439 34.783 28.99 7.17 45.30 3.32
2358 3714 3.499918 AGAGGCAAGTTTCTGAAACATCG 59.500 43.478 28.99 19.18 43.79 3.84


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

AutoCloner maintained by Alex Coulton.