Multiple sequence alignment - TraesCS3A01G397200

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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 TraesCS3A01G397200 chr3A 100.000 3302 0 0 1 3302 644696181 644699482 0.000000e+00 6098.0
1 TraesCS3A01G397200 chr3A 83.099 426 41 22 1136 1544 423497276 423497687 3.130000e-95 359.0
2 TraesCS3A01G397200 chr3A 77.138 608 102 23 1545 2121 644780175 644780776 5.320000e-83 318.0
3 TraesCS3A01G397200 chr3A 91.818 110 7 2 500 608 423497167 423497275 5.710000e-33 152.0
4 TraesCS3A01G397200 chr3A 86.842 114 15 0 331 444 644780075 644780188 9.620000e-26 128.0
5 TraesCS3A01G397200 chr3A 95.000 60 3 0 1301 1360 423497478 423497537 9.750000e-16 95.3
6 TraesCS3A01G397200 chr3A 100.000 30 0 0 3273 3302 644704096 644704125 4.600000e-04 56.5
7 TraesCS3A01G397200 chr7B 90.671 879 53 15 443 1312 746592200 746591342 0.000000e+00 1142.0
8 TraesCS3A01G397200 chr7B 91.322 242 13 5 1301 1539 746591317 746591081 1.140000e-84 324.0
9 TraesCS3A01G397200 chr7B 100.000 32 0 0 3271 3302 616511807 616511776 3.560000e-05 60.2
10 TraesCS3A01G397200 chr7B 100.000 30 0 0 3273 3302 616507149 616507120 4.600000e-04 56.5
11 TraesCS3A01G397200 chr3D 89.282 877 43 21 1545 2393 506037917 506038770 0.000000e+00 1051.0
12 TraesCS3A01G397200 chr3D 90.606 660 53 5 2613 3272 506060397 506061047 0.000000e+00 867.0
13 TraesCS3A01G397200 chr3D 88.725 612 59 6 579 1186 250021774 250022379 0.000000e+00 739.0
14 TraesCS3A01G397200 chr3D 97.306 297 7 1 151 447 506037638 506037933 1.370000e-138 503.0
15 TraesCS3A01G397200 chr3D 89.912 228 22 1 2390 2616 506059002 506059229 3.220000e-75 292.0
16 TraesCS3A01G397200 chr3D 87.379 103 12 1 343 444 506161012 506161114 2.080000e-22 117.0
17 TraesCS3A01G397200 chr3B 89.699 631 55 7 2203 2828 667772306 667772931 0.000000e+00 797.0
18 TraesCS3A01G397200 chr3B 89.071 183 16 2 3073 3251 667773177 667773359 1.190000e-54 224.0
19 TraesCS3A01G397200 chr3B 87.500 120 15 0 327 446 667855915 667856034 4.440000e-29 139.0
20 TraesCS3A01G397200 chr3B 100.000 29 0 0 3244 3272 667778483 667778511 2.000000e-03 54.7
21 TraesCS3A01G397200 chr4A 85.696 762 99 9 443 1198 34826744 34825987 0.000000e+00 795.0
22 TraesCS3A01G397200 chr2A 96.404 445 14 2 444 886 104115680 104116124 0.000000e+00 732.0
23 TraesCS3A01G397200 chr2A 92.375 459 18 10 922 1368 104116128 104116581 3.590000e-179 638.0
24 TraesCS3A01G397200 chr2A 81.607 560 85 8 443 987 677997364 677996808 6.500000e-122 448.0
25 TraesCS3A01G397200 chr2A 94.595 37 0 1 3268 3302 43207010 43207046 4.600000e-04 56.5
26 TraesCS3A01G397200 chr2A 100.000 30 0 0 3273 3302 43211660 43211689 4.600000e-04 56.5
27 TraesCS3A01G397200 chr5A 87.938 514 55 3 674 1186 77080245 77079738 1.700000e-167 599.0
28 TraesCS3A01G397200 chr2D 88.913 469 47 2 568 1036 476983153 476983616 1.030000e-159 573.0
29 TraesCS3A01G397200 chr7A 83.303 557 78 7 443 987 20399095 20398542 1.770000e-137 499.0
30 TraesCS3A01G397200 chr7A 95.506 89 4 0 1 89 126146631 126146543 3.430000e-30 143.0
31 TraesCS3A01G397200 chr7D 87.500 272 25 4 574 845 570732184 570731922 4.140000e-79 305.0
32 TraesCS3A01G397200 chr7D 84.733 262 21 7 1301 1549 570731775 570731520 9.150000e-61 244.0
33 TraesCS3A01G397200 chr2B 88.372 129 14 1 567 695 318312855 318312728 1.590000e-33 154.0
34 TraesCS3A01G397200 chr6A 92.135 89 7 0 1 89 182443696 182443784 3.460000e-25 126.0
35 TraesCS3A01G397200 chr6D 95.714 70 3 0 1 70 16247884 16247815 2.690000e-21 113.0


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 TraesCS3A01G397200 chr3A 644696181 644699482 3301 False 6098.0 6098 100.000000 1 3302 1 chr3A.!!$F1 3301
1 TraesCS3A01G397200 chr3A 644780075 644780776 701 False 223.0 318 81.990000 331 2121 2 chr3A.!!$F4 1790
2 TraesCS3A01G397200 chr3A 423497167 423497687 520 False 202.1 359 89.972333 500 1544 3 chr3A.!!$F3 1044
3 TraesCS3A01G397200 chr7B 746591081 746592200 1119 True 733.0 1142 90.996500 443 1539 2 chr7B.!!$R3 1096
4 TraesCS3A01G397200 chr3D 506037638 506038770 1132 False 777.0 1051 93.294000 151 2393 2 chr3D.!!$F3 2242
5 TraesCS3A01G397200 chr3D 250021774 250022379 605 False 739.0 739 88.725000 579 1186 1 chr3D.!!$F1 607
6 TraesCS3A01G397200 chr3D 506059002 506061047 2045 False 579.5 867 90.259000 2390 3272 2 chr3D.!!$F4 882
7 TraesCS3A01G397200 chr3B 667772306 667773359 1053 False 510.5 797 89.385000 2203 3251 2 chr3B.!!$F3 1048
8 TraesCS3A01G397200 chr4A 34825987 34826744 757 True 795.0 795 85.696000 443 1198 1 chr4A.!!$R1 755
9 TraesCS3A01G397200 chr2A 104115680 104116581 901 False 685.0 732 94.389500 444 1368 2 chr2A.!!$F3 924
10 TraesCS3A01G397200 chr2A 677996808 677997364 556 True 448.0 448 81.607000 443 987 1 chr2A.!!$R1 544
11 TraesCS3A01G397200 chr5A 77079738 77080245 507 True 599.0 599 87.938000 674 1186 1 chr5A.!!$R1 512
12 TraesCS3A01G397200 chr7A 20398542 20399095 553 True 499.0 499 83.303000 443 987 1 chr7A.!!$R1 544
13 TraesCS3A01G397200 chr7D 570731520 570732184 664 True 274.5 305 86.116500 574 1549 2 chr7D.!!$R1 975

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
88 89 0.032615 TGCCAAACCAAACACCTCCT 60.033 50.0 0.00 0.0 0.0 3.69 F
1969 2128 0.032678 CTCGTATTGCCGCTGAGGAT 59.967 55.0 0.09 0.0 45.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2214 1.008194 TCGTTGAACTCCACCGTCG 60.008 57.895 0.0 0.0 32.20 5.12 R
3128 4552 0.185901 GCCATTGATAGGGGCAAGGA 59.814 55.000 0.0 0.0 46.92 3.36 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
21 22 3.756933 ACGGAGCTACCTAAACAAACA 57.243 42.857 0.00 0.00 36.31 2.83
22 23 3.660865 ACGGAGCTACCTAAACAAACAG 58.339 45.455 0.00 0.00 36.31 3.16
23 24 2.415512 CGGAGCTACCTAAACAAACAGC 59.584 50.000 0.00 0.00 36.31 4.40
24 25 3.676093 GGAGCTACCTAAACAAACAGCT 58.324 45.455 0.00 0.00 41.82 4.24
25 26 4.619863 CGGAGCTACCTAAACAAACAGCTA 60.620 45.833 0.00 0.00 39.36 3.32
26 27 5.429130 GGAGCTACCTAAACAAACAGCTAT 58.571 41.667 0.00 0.00 39.36 2.97
27 28 5.880887 GGAGCTACCTAAACAAACAGCTATT 59.119 40.000 0.00 0.00 39.36 1.73
28 29 7.046033 GGAGCTACCTAAACAAACAGCTATTA 58.954 38.462 0.00 0.00 39.36 0.98
29 30 7.551617 GGAGCTACCTAAACAAACAGCTATTAA 59.448 37.037 0.00 0.00 39.36 1.40
30 31 8.265165 AGCTACCTAAACAAACAGCTATTAAC 57.735 34.615 0.00 0.00 37.58 2.01
31 32 7.064253 AGCTACCTAAACAAACAGCTATTAACG 59.936 37.037 0.00 0.00 37.58 3.18
32 33 5.934921 ACCTAAACAAACAGCTATTAACGC 58.065 37.500 0.00 0.00 0.00 4.84
33 34 5.470777 ACCTAAACAAACAGCTATTAACGCA 59.529 36.000 0.00 0.00 0.00 5.24
34 35 6.016943 ACCTAAACAAACAGCTATTAACGCAA 60.017 34.615 0.00 0.00 0.00 4.85
35 36 7.027161 CCTAAACAAACAGCTATTAACGCAAT 58.973 34.615 0.00 0.00 0.00 3.56
36 37 6.927933 AAACAAACAGCTATTAACGCAATC 57.072 33.333 0.00 0.00 0.00 2.67
37 38 4.981794 ACAAACAGCTATTAACGCAATCC 58.018 39.130 0.00 0.00 0.00 3.01
38 39 3.944422 AACAGCTATTAACGCAATCCG 57.056 42.857 0.00 0.00 44.21 4.18
47 48 2.992313 CGCAATCCGTTACCGTCG 59.008 61.111 0.00 0.00 0.00 5.12
48 49 1.802715 CGCAATCCGTTACCGTCGT 60.803 57.895 0.00 0.00 0.00 4.34
49 50 1.346378 CGCAATCCGTTACCGTCGTT 61.346 55.000 0.00 0.00 0.00 3.85
50 51 1.627879 GCAATCCGTTACCGTCGTTA 58.372 50.000 0.00 0.00 0.00 3.18
51 52 1.991965 GCAATCCGTTACCGTCGTTAA 59.008 47.619 0.00 0.00 0.00 2.01
52 53 2.222574 GCAATCCGTTACCGTCGTTAAC 60.223 50.000 2.81 2.81 0.00 2.01
53 54 2.985809 CAATCCGTTACCGTCGTTAACA 59.014 45.455 12.38 0.00 0.00 2.41
54 55 2.330231 TCCGTTACCGTCGTTAACAG 57.670 50.000 12.38 2.03 0.00 3.16
55 56 1.068610 TCCGTTACCGTCGTTAACAGG 60.069 52.381 12.38 12.95 0.00 4.00
56 57 1.335872 CCGTTACCGTCGTTAACAGGT 60.336 52.381 17.72 17.72 38.06 4.00
57 58 2.393764 CGTTACCGTCGTTAACAGGTT 58.606 47.619 18.51 7.15 36.56 3.50
58 59 2.153627 CGTTACCGTCGTTAACAGGTTG 59.846 50.000 18.51 8.84 36.56 3.77
59 60 1.782044 TACCGTCGTTAACAGGTTGC 58.218 50.000 18.51 0.00 36.56 4.17
60 61 1.216941 ACCGTCGTTAACAGGTTGCG 61.217 55.000 6.39 0.38 32.99 4.85
61 62 1.216941 CCGTCGTTAACAGGTTGCGT 61.217 55.000 6.39 0.00 0.00 5.24
62 63 0.578211 CGTCGTTAACAGGTTGCGTT 59.422 50.000 6.39 0.00 0.00 4.84
63 64 1.786004 CGTCGTTAACAGGTTGCGTTA 59.214 47.619 6.39 0.00 0.00 3.18
64 65 2.408865 CGTCGTTAACAGGTTGCGTTAC 60.409 50.000 6.39 3.45 0.00 2.50
65 66 2.539274 GTCGTTAACAGGTTGCGTTACA 59.461 45.455 6.39 0.00 0.00 2.41
66 67 3.001127 GTCGTTAACAGGTTGCGTTACAA 59.999 43.478 6.39 0.00 35.33 2.41
67 68 3.808726 TCGTTAACAGGTTGCGTTACAAT 59.191 39.130 6.39 0.00 41.27 2.71
68 69 4.272991 TCGTTAACAGGTTGCGTTACAATT 59.727 37.500 6.39 0.00 41.27 2.32
69 70 4.971220 CGTTAACAGGTTGCGTTACAATTT 59.029 37.500 6.39 0.00 41.27 1.82
70 71 5.108555 CGTTAACAGGTTGCGTTACAATTTG 60.109 40.000 6.39 0.00 41.27 2.32
71 72 2.738135 ACAGGTTGCGTTACAATTTGC 58.262 42.857 0.00 0.00 41.27 3.68
72 73 2.058057 CAGGTTGCGTTACAATTTGCC 58.942 47.619 0.00 0.00 41.27 4.52
73 74 1.683917 AGGTTGCGTTACAATTTGCCA 59.316 42.857 0.00 0.00 41.27 4.92
74 75 2.101582 AGGTTGCGTTACAATTTGCCAA 59.898 40.909 0.00 0.00 41.27 4.52
75 76 2.866762 GGTTGCGTTACAATTTGCCAAA 59.133 40.909 0.00 0.00 41.27 3.28
76 77 3.302805 GGTTGCGTTACAATTTGCCAAAC 60.303 43.478 0.00 0.00 41.27 2.93
77 78 2.474816 TGCGTTACAATTTGCCAAACC 58.525 42.857 0.00 0.00 0.00 3.27
78 79 2.159099 TGCGTTACAATTTGCCAAACCA 60.159 40.909 0.00 0.00 0.00 3.67
79 80 2.866762 GCGTTACAATTTGCCAAACCAA 59.133 40.909 0.00 0.00 0.00 3.67
80 81 3.309954 GCGTTACAATTTGCCAAACCAAA 59.690 39.130 0.00 0.00 38.87 3.28
81 82 4.783764 GCGTTACAATTTGCCAAACCAAAC 60.784 41.667 0.00 0.00 37.51 2.93
82 83 4.330074 CGTTACAATTTGCCAAACCAAACA 59.670 37.500 0.00 0.00 37.51 2.83
83 84 5.564768 GTTACAATTTGCCAAACCAAACAC 58.435 37.500 0.00 0.00 37.51 3.32
84 85 3.013219 ACAATTTGCCAAACCAAACACC 58.987 40.909 0.00 0.00 37.51 4.16
85 86 3.277715 CAATTTGCCAAACCAAACACCT 58.722 40.909 0.00 0.00 37.51 4.00
86 87 2.682155 TTTGCCAAACCAAACACCTC 57.318 45.000 0.00 0.00 30.28 3.85
87 88 0.827368 TTGCCAAACCAAACACCTCC 59.173 50.000 0.00 0.00 0.00 4.30
88 89 0.032615 TGCCAAACCAAACACCTCCT 60.033 50.000 0.00 0.00 0.00 3.69
89 90 0.389025 GCCAAACCAAACACCTCCTG 59.611 55.000 0.00 0.00 0.00 3.86
90 91 2.026905 GCCAAACCAAACACCTCCTGA 61.027 52.381 0.00 0.00 0.00 3.86
91 92 1.956477 CCAAACCAAACACCTCCTGAG 59.044 52.381 0.00 0.00 0.00 3.35
92 93 2.422803 CCAAACCAAACACCTCCTGAGA 60.423 50.000 0.00 0.00 0.00 3.27
93 94 2.880890 CAAACCAAACACCTCCTGAGAG 59.119 50.000 0.00 0.00 40.09 3.20
94 95 1.807814 ACCAAACACCTCCTGAGAGT 58.192 50.000 0.00 0.00 38.58 3.24
95 96 2.127708 ACCAAACACCTCCTGAGAGTT 58.872 47.619 0.00 0.00 38.58 3.01
96 97 2.509964 ACCAAACACCTCCTGAGAGTTT 59.490 45.455 10.10 10.10 38.58 2.66
97 98 3.714798 ACCAAACACCTCCTGAGAGTTTA 59.285 43.478 13.52 0.00 38.58 2.01
98 99 4.065789 CCAAACACCTCCTGAGAGTTTAC 58.934 47.826 13.52 0.00 38.58 2.01
99 100 4.444306 CCAAACACCTCCTGAGAGTTTACA 60.444 45.833 13.52 0.00 38.58 2.41
100 101 4.338379 AACACCTCCTGAGAGTTTACAC 57.662 45.455 0.00 0.00 38.58 2.90
101 102 2.296471 ACACCTCCTGAGAGTTTACACG 59.704 50.000 0.00 0.00 38.58 4.49
102 103 2.557056 CACCTCCTGAGAGTTTACACGA 59.443 50.000 0.00 0.00 38.58 4.35
103 104 3.193691 CACCTCCTGAGAGTTTACACGAT 59.806 47.826 0.00 0.00 38.58 3.73
104 105 3.444388 ACCTCCTGAGAGTTTACACGATC 59.556 47.826 0.00 0.00 38.58 3.69
105 106 3.697045 CCTCCTGAGAGTTTACACGATCT 59.303 47.826 0.00 0.00 38.58 2.75
106 107 4.882427 CCTCCTGAGAGTTTACACGATCTA 59.118 45.833 0.00 0.00 38.58 1.98
107 108 5.220892 CCTCCTGAGAGTTTACACGATCTAC 60.221 48.000 0.00 0.00 38.58 2.59
108 109 5.502706 CTCCTGAGAGTTTACACGATCTACG 60.503 48.000 0.00 0.00 40.54 3.51
109 110 4.331992 CCTGAGAGTTTACACGATCTACGA 59.668 45.833 0.00 0.00 45.77 3.43
110 111 5.163784 CCTGAGAGTTTACACGATCTACGAA 60.164 44.000 0.00 0.00 45.77 3.85
111 112 6.432607 TGAGAGTTTACACGATCTACGAAT 57.567 37.500 0.00 0.00 45.77 3.34
112 113 7.254692 CCTGAGAGTTTACACGATCTACGAATA 60.255 40.741 0.00 0.00 45.77 1.75
113 114 8.151141 TGAGAGTTTACACGATCTACGAATAT 57.849 34.615 0.00 0.00 45.77 1.28
114 115 9.264719 TGAGAGTTTACACGATCTACGAATATA 57.735 33.333 0.00 0.00 45.77 0.86
128 129 3.511699 CGAATATATCGCAGCTAAGCCA 58.488 45.455 0.00 0.00 45.89 4.75
129 130 3.926527 CGAATATATCGCAGCTAAGCCAA 59.073 43.478 0.00 0.00 45.89 4.52
130 131 4.032217 CGAATATATCGCAGCTAAGCCAAG 59.968 45.833 0.00 0.00 45.89 3.61
131 132 1.517242 ATATCGCAGCTAAGCCAAGC 58.483 50.000 0.00 0.00 43.11 4.01
132 133 0.532862 TATCGCAGCTAAGCCAAGCC 60.533 55.000 4.35 0.00 43.86 4.35
133 134 3.869272 CGCAGCTAAGCCAAGCCG 61.869 66.667 4.35 0.00 43.86 5.52
134 135 2.747855 GCAGCTAAGCCAAGCCGT 60.748 61.111 4.35 0.00 43.86 5.68
135 136 1.449601 GCAGCTAAGCCAAGCCGTA 60.450 57.895 4.35 0.00 43.86 4.02
136 137 1.706287 GCAGCTAAGCCAAGCCGTAC 61.706 60.000 4.35 0.00 43.86 3.67
137 138 1.090052 CAGCTAAGCCAAGCCGTACC 61.090 60.000 4.35 0.00 43.86 3.34
138 139 2.171725 GCTAAGCCAAGCCGTACCG 61.172 63.158 0.00 0.00 36.45 4.02
159 160 1.498176 AACTTACCAGGTCCAGGCCC 61.498 60.000 0.00 0.00 0.00 5.80
201 202 1.070601 ACCGCTACAACGTAAACCCTT 59.929 47.619 0.00 0.00 0.00 3.95
232 233 1.746220 ACTCGGACTTGAATCCTCTCG 59.254 52.381 0.00 0.00 36.52 4.04
441 442 3.843240 CGGAGCTTGCGCGTTCTC 61.843 66.667 8.43 8.48 42.32 2.87
445 446 4.451652 GCTTGCGCGTTCTCCAGC 62.452 66.667 8.43 0.00 0.00 4.85
647 658 2.875933 CCACTTAAACGCCAAGAAGACA 59.124 45.455 0.00 0.00 0.00 3.41
683 694 6.811665 TCAAACTACTCTGAAATACGACATGG 59.188 38.462 0.00 0.00 0.00 3.66
730 741 9.884636 TGTCATATGGGAATTTAAGATATACGG 57.115 33.333 2.13 0.00 0.00 4.02
927 955 2.418197 GCCGCTAGGTTCAAGTACATCA 60.418 50.000 0.00 0.00 40.50 3.07
975 1003 5.983118 TGCGACAACCATAACTGTATATGAG 59.017 40.000 9.88 0.00 35.69 2.90
1008 1036 3.733337 ACATTGACGAGTCTGAGCTTTT 58.267 40.909 4.78 0.00 0.00 2.27
1218 1254 5.706833 TGCATTGCCGTATGAATCAGATTAT 59.293 36.000 6.12 0.00 0.00 1.28
1221 1257 9.045223 GCATTGCCGTATGAATCAGATTATATA 57.955 33.333 0.00 0.00 0.00 0.86
1407 1511 2.325484 GGGCCTTTTTCCTTTCTCCAA 58.675 47.619 0.84 0.00 0.00 3.53
1473 1577 8.396272 ACCTGCAAATCTTATCGCTAATTAAT 57.604 30.769 0.00 0.00 0.00 1.40
1754 1868 3.175240 CAGTCAGCGGCGTCGAAG 61.175 66.667 16.53 3.92 39.00 3.79
1875 2028 2.035442 GCCTTGCCGAGAACCAGAC 61.035 63.158 0.00 0.00 0.00 3.51
1965 2124 2.202878 GGCTCGTATTGCCGCTGA 60.203 61.111 0.00 0.00 41.03 4.26
1966 2125 2.240500 GGCTCGTATTGCCGCTGAG 61.241 63.158 0.00 0.00 41.03 3.35
1967 2126 2.240500 GCTCGTATTGCCGCTGAGG 61.241 63.158 0.00 0.00 44.97 3.86
1968 2127 1.437573 CTCGTATTGCCGCTGAGGA 59.562 57.895 0.09 0.00 45.00 3.71
1969 2128 0.032678 CTCGTATTGCCGCTGAGGAT 59.967 55.000 0.09 0.00 45.00 3.24
1970 2129 0.249447 TCGTATTGCCGCTGAGGATG 60.249 55.000 0.09 0.00 45.00 3.51
1971 2130 1.835483 CGTATTGCCGCTGAGGATGC 61.835 60.000 0.09 0.00 45.00 3.91
1972 2131 1.227943 TATTGCCGCTGAGGATGCC 60.228 57.895 0.09 0.00 45.00 4.40
2140 2300 0.521291 CTCGGAGCAGAGGATCGATC 59.479 60.000 17.36 17.36 42.67 3.69
2156 2320 5.751028 GGATCGATCCAAGAAGTGAAGTTAG 59.249 44.000 34.65 0.00 46.38 2.34
2159 2323 4.579869 GATCCAAGAAGTGAAGTTAGGCA 58.420 43.478 0.00 0.00 0.00 4.75
2164 2328 5.065731 CCAAGAAGTGAAGTTAGGCATGATC 59.934 44.000 0.00 0.00 0.00 2.92
2176 2340 6.989169 AGTTAGGCATGATCAATTAGTCTGAC 59.011 38.462 0.00 0.00 0.00 3.51
2177 2341 4.712476 AGGCATGATCAATTAGTCTGACC 58.288 43.478 0.00 0.00 0.00 4.02
2178 2342 4.164796 AGGCATGATCAATTAGTCTGACCA 59.835 41.667 0.00 0.00 0.00 4.02
2179 2343 5.068636 GGCATGATCAATTAGTCTGACCAT 58.931 41.667 0.00 0.00 25.97 3.55
2180 2344 6.043590 AGGCATGATCAATTAGTCTGACCATA 59.956 38.462 0.00 0.00 25.33 2.74
2181 2345 6.148480 GGCATGATCAATTAGTCTGACCATAC 59.852 42.308 0.00 0.00 25.33 2.39
2182 2346 6.933521 GCATGATCAATTAGTCTGACCATACT 59.066 38.462 0.00 0.00 25.33 2.12
2183 2347 7.095313 GCATGATCAATTAGTCTGACCATACTG 60.095 40.741 0.00 0.00 25.33 2.74
2184 2348 7.423844 TGATCAATTAGTCTGACCATACTGT 57.576 36.000 3.76 0.00 0.00 3.55
2210 2374 0.991920 AGGTGTGGGTGATTACAGGG 59.008 55.000 0.00 0.00 0.00 4.45
2410 2579 4.388773 TCGATGATGTCCTTTTCGTTCTTG 59.611 41.667 0.00 0.00 0.00 3.02
2455 2624 0.512952 GCGGCTACAACAGTCAACAG 59.487 55.000 0.00 0.00 0.00 3.16
2463 2632 5.696724 GCTACAACAGTCAACAGTAGTCAAT 59.303 40.000 0.00 0.00 35.71 2.57
2476 2645 4.386049 CAGTAGTCAATTGAAGGACACGAC 59.614 45.833 10.35 3.94 36.50 4.34
2508 2677 5.175856 CGAGTTTTCTTACTGAACAGAGTGG 59.824 44.000 8.87 0.00 33.88 4.00
2510 2679 6.831976 AGTTTTCTTACTGAACAGAGTGGAT 58.168 36.000 8.87 0.00 33.88 3.41
2517 2686 9.793259 TCTTACTGAACAGAGTGGATTTTATTT 57.207 29.630 8.87 0.00 0.00 1.40
2523 2692 6.840780 ACAGAGTGGATTTTATTTTGGAGG 57.159 37.500 0.00 0.00 0.00 4.30
2583 2753 8.846943 TTTATGAGTGAACTGCAATTCTTCTA 57.153 30.769 9.58 0.00 0.00 2.10
2602 2772 9.925268 TTCTTCTAAAACAACAATCTAACGAAC 57.075 29.630 0.00 0.00 0.00 3.95
2606 2776 8.332464 TCTAAAACAACAATCTAACGAACACTG 58.668 33.333 0.00 0.00 0.00 3.66
2609 2779 4.510340 ACAACAATCTAACGAACACTGGTC 59.490 41.667 0.00 0.00 0.00 4.02
2616 2786 0.319297 ACGAACACTGGTCGCCTAAC 60.319 55.000 16.50 0.00 0.00 2.34
2655 3995 0.391661 ACGGTGCATTTGCTCGAGAT 60.392 50.000 18.75 0.00 42.66 2.75
2657 3997 1.524355 CGGTGCATTTGCTCGAGATAG 59.476 52.381 18.75 1.40 42.66 2.08
2672 4012 7.093992 GCTCGAGATAGCAGTTATATTTTCCT 58.906 38.462 18.75 0.00 42.30 3.36
2701 4041 5.809001 TCTGAAAATATGACAGAAGTGCCT 58.191 37.500 0.00 0.00 37.66 4.75
2702 4042 6.946340 TCTGAAAATATGACAGAAGTGCCTA 58.054 36.000 0.00 0.00 37.66 3.93
2707 4047 9.508567 GAAAATATGACAGAAGTGCCTAAATTC 57.491 33.333 0.00 0.00 0.00 2.17
2754 4094 9.486497 AATATGCACACAAATAACAATCAAACA 57.514 25.926 0.00 0.00 0.00 2.83
2772 4112 6.653020 TCAAACACTATGAGCCTTGTATGAT 58.347 36.000 0.00 0.00 0.00 2.45
2796 4136 1.270252 GGGTTGTTTGCTGTCATTGGG 60.270 52.381 0.00 0.00 0.00 4.12
2802 4142 1.794151 TTGCTGTCATTGGGTGTGCG 61.794 55.000 0.00 0.00 0.00 5.34
2826 4166 4.431131 CCATTGGCCGCCACCTCT 62.431 66.667 13.00 0.00 30.78 3.69
2827 4167 2.361610 CATTGGCCGCCACCTCTT 60.362 61.111 13.00 0.00 30.78 2.85
2828 4168 1.077787 CATTGGCCGCCACCTCTTA 60.078 57.895 13.00 0.00 30.78 2.10
2829 4169 1.097547 CATTGGCCGCCACCTCTTAG 61.098 60.000 13.00 0.00 30.78 2.18
2830 4170 1.562672 ATTGGCCGCCACCTCTTAGT 61.563 55.000 13.00 0.00 30.78 2.24
2831 4171 2.180159 TTGGCCGCCACCTCTTAGTC 62.180 60.000 13.00 0.00 30.78 2.59
2832 4172 2.187163 GCCGCCACCTCTTAGTCC 59.813 66.667 0.00 0.00 0.00 3.85
2833 4173 2.359967 GCCGCCACCTCTTAGTCCT 61.360 63.158 0.00 0.00 0.00 3.85
2834 4174 1.041447 GCCGCCACCTCTTAGTCCTA 61.041 60.000 0.00 0.00 0.00 2.94
2835 4175 1.705873 CCGCCACCTCTTAGTCCTAT 58.294 55.000 0.00 0.00 0.00 2.57
2836 4176 1.341531 CCGCCACCTCTTAGTCCTATG 59.658 57.143 0.00 0.00 0.00 2.23
2837 4177 2.032620 CGCCACCTCTTAGTCCTATGT 58.967 52.381 0.00 0.00 0.00 2.29
2838 4178 3.220110 CGCCACCTCTTAGTCCTATGTA 58.780 50.000 0.00 0.00 0.00 2.29
2839 4179 3.253677 CGCCACCTCTTAGTCCTATGTAG 59.746 52.174 0.00 0.00 0.00 2.74
2840 4180 4.471548 GCCACCTCTTAGTCCTATGTAGA 58.528 47.826 0.00 0.00 0.00 2.59
2841 4181 5.081032 GCCACCTCTTAGTCCTATGTAGAT 58.919 45.833 0.00 0.00 0.00 1.98
2842 4182 6.246919 GCCACCTCTTAGTCCTATGTAGATA 58.753 44.000 0.00 0.00 0.00 1.98
2843 4183 6.376018 GCCACCTCTTAGTCCTATGTAGATAG 59.624 46.154 0.00 0.00 32.55 2.08
2844 4184 7.691213 CCACCTCTTAGTCCTATGTAGATAGA 58.309 42.308 8.44 0.00 34.44 1.98
2845 4185 8.333235 CCACCTCTTAGTCCTATGTAGATAGAT 58.667 40.741 8.44 0.00 34.44 1.98
2846 4186 9.391006 CACCTCTTAGTCCTATGTAGATAGATC 57.609 40.741 8.44 1.73 34.44 2.75
2847 4187 9.118367 ACCTCTTAGTCCTATGTAGATAGATCA 57.882 37.037 8.44 0.00 34.44 2.92
2848 4188 9.967451 CCTCTTAGTCCTATGTAGATAGATCAA 57.033 37.037 8.44 0.00 34.44 2.57
2850 4190 9.742144 TCTTAGTCCTATGTAGATAGATCAACC 57.258 37.037 8.44 0.00 34.44 3.77
2851 4191 9.747898 CTTAGTCCTATGTAGATAGATCAACCT 57.252 37.037 8.44 0.00 34.44 3.50
2921 4299 3.132925 GCACCTTTGTGTACTCCGTTTA 58.867 45.455 0.00 0.00 44.65 2.01
2987 4365 7.552687 TGCTTCTACCATATTCTTGATCGTTTT 59.447 33.333 0.00 0.00 0.00 2.43
3028 4406 2.427506 CTTCTTGGTCAGGCTAACCAC 58.572 52.381 9.67 0.00 46.27 4.16
3034 4412 0.108138 GTCAGGCTAACCACGCATCT 60.108 55.000 0.00 0.00 39.06 2.90
3035 4413 0.108186 TCAGGCTAACCACGCATCTG 60.108 55.000 0.00 0.00 39.06 2.90
3036 4414 1.091771 CAGGCTAACCACGCATCTGG 61.092 60.000 0.00 0.00 39.06 3.86
3037 4415 2.472909 GGCTAACCACGCATCTGGC 61.473 63.158 0.00 0.00 34.20 4.85
3038 4416 1.745115 GCTAACCACGCATCTGGCA 60.745 57.895 0.00 0.00 45.17 4.92
3039 4417 1.982073 GCTAACCACGCATCTGGCAC 61.982 60.000 0.00 0.00 45.17 5.01
3040 4418 1.369091 CTAACCACGCATCTGGCACC 61.369 60.000 0.00 0.00 45.17 5.01
3079 4503 3.411446 TCATGAGATTGGCGTCAAAGTT 58.589 40.909 6.51 0.00 36.36 2.66
3145 4569 3.152341 GACATCCTTGCCCCTATCAATG 58.848 50.000 0.00 0.00 0.00 2.82
3146 4570 2.158415 ACATCCTTGCCCCTATCAATGG 60.158 50.000 0.00 0.00 0.00 3.16
3272 4700 1.480545 GGTTGTGAGGTGCTTTGGTTT 59.519 47.619 0.00 0.00 0.00 3.27
3273 4701 2.539476 GTTGTGAGGTGCTTTGGTTTG 58.461 47.619 0.00 0.00 0.00 2.93
3274 4702 1.846007 TGTGAGGTGCTTTGGTTTGT 58.154 45.000 0.00 0.00 0.00 2.83
3275 4703 2.175202 TGTGAGGTGCTTTGGTTTGTT 58.825 42.857 0.00 0.00 0.00 2.83
3276 4704 3.357203 TGTGAGGTGCTTTGGTTTGTTA 58.643 40.909 0.00 0.00 0.00 2.41
3277 4705 3.764434 TGTGAGGTGCTTTGGTTTGTTAA 59.236 39.130 0.00 0.00 0.00 2.01
3278 4706 4.109766 GTGAGGTGCTTTGGTTTGTTAAC 58.890 43.478 0.00 0.00 0.00 2.01
3279 4707 3.764434 TGAGGTGCTTTGGTTTGTTAACA 59.236 39.130 3.59 3.59 35.92 2.41
3280 4708 4.220821 TGAGGTGCTTTGGTTTGTTAACAA 59.779 37.500 17.01 17.01 35.92 2.83
3281 4709 5.105146 TGAGGTGCTTTGGTTTGTTAACAAT 60.105 36.000 21.17 2.26 35.92 2.71
3282 4710 5.356426 AGGTGCTTTGGTTTGTTAACAATC 58.644 37.500 21.17 19.11 35.92 2.67
3283 4711 4.208253 GGTGCTTTGGTTTGTTAACAATCG 59.792 41.667 21.17 9.15 35.92 3.34
3284 4712 4.801516 GTGCTTTGGTTTGTTAACAATCGT 59.198 37.500 21.17 0.00 35.92 3.73
3285 4713 5.972382 GTGCTTTGGTTTGTTAACAATCGTA 59.028 36.000 21.17 10.45 35.92 3.43
3286 4714 6.639279 GTGCTTTGGTTTGTTAACAATCGTAT 59.361 34.615 21.17 0.00 35.92 3.06
3287 4715 7.804129 GTGCTTTGGTTTGTTAACAATCGTATA 59.196 33.333 21.17 3.00 35.92 1.47
3288 4716 8.516234 TGCTTTGGTTTGTTAACAATCGTATAT 58.484 29.630 21.17 0.00 35.92 0.86
3289 4717 9.349145 GCTTTGGTTTGTTAACAATCGTATATT 57.651 29.630 21.17 0.00 35.92 1.28
3291 4719 8.676454 TTGGTTTGTTAACAATCGTATATTGC 57.324 30.769 21.17 6.50 35.92 3.56
3292 4720 8.046294 TGGTTTGTTAACAATCGTATATTGCT 57.954 30.769 21.17 0.00 35.92 3.91
3293 4721 7.965655 TGGTTTGTTAACAATCGTATATTGCTG 59.034 33.333 21.17 0.00 35.92 4.41
3294 4722 7.966204 GGTTTGTTAACAATCGTATATTGCTGT 59.034 33.333 21.17 0.00 35.92 4.40
3295 4723 8.785101 GTTTGTTAACAATCGTATATTGCTGTG 58.215 33.333 21.17 0.00 35.55 3.66
3296 4724 7.603963 TGTTAACAATCGTATATTGCTGTGT 57.396 32.000 5.64 0.00 32.55 3.72
3297 4725 8.035165 TGTTAACAATCGTATATTGCTGTGTT 57.965 30.769 5.64 0.00 32.55 3.32
3298 4726 9.152595 TGTTAACAATCGTATATTGCTGTGTTA 57.847 29.630 5.64 0.00 32.55 2.41
3299 4727 9.632969 GTTAACAATCGTATATTGCTGTGTTAG 57.367 33.333 0.00 0.00 33.25 2.34
3300 4728 7.843490 AACAATCGTATATTGCTGTGTTAGT 57.157 32.000 0.00 0.00 32.55 2.24
3301 4729 7.843490 ACAATCGTATATTGCTGTGTTAGTT 57.157 32.000 0.00 0.00 32.55 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.062991 CTGTTTGTTTAGGTAGCTCCGTT 58.937 43.478 0.00 0.00 41.99 4.44
2 3 2.415512 GCTGTTTGTTTAGGTAGCTCCG 59.584 50.000 0.00 0.00 41.99 4.63
5 6 7.064253 CGTTAATAGCTGTTTGTTTAGGTAGCT 59.936 37.037 0.00 0.00 43.27 3.32
6 7 7.178074 CGTTAATAGCTGTTTGTTTAGGTAGC 58.822 38.462 0.00 0.00 31.29 3.58
7 8 7.148540 TGCGTTAATAGCTGTTTGTTTAGGTAG 60.149 37.037 0.00 0.00 35.28 3.18
8 9 6.649973 TGCGTTAATAGCTGTTTGTTTAGGTA 59.350 34.615 0.00 0.00 35.28 3.08
9 10 5.470777 TGCGTTAATAGCTGTTTGTTTAGGT 59.529 36.000 0.00 0.00 35.28 3.08
10 11 5.933790 TGCGTTAATAGCTGTTTGTTTAGG 58.066 37.500 0.00 0.00 35.28 2.69
11 12 7.218204 GGATTGCGTTAATAGCTGTTTGTTTAG 59.782 37.037 0.00 0.00 35.28 1.85
12 13 7.024768 GGATTGCGTTAATAGCTGTTTGTTTA 58.975 34.615 0.00 0.00 35.28 2.01
13 14 5.861787 GGATTGCGTTAATAGCTGTTTGTTT 59.138 36.000 0.00 0.00 35.28 2.83
14 15 5.399013 GGATTGCGTTAATAGCTGTTTGTT 58.601 37.500 0.00 0.00 35.28 2.83
15 16 4.436852 CGGATTGCGTTAATAGCTGTTTGT 60.437 41.667 0.00 0.00 35.28 2.83
16 17 4.028383 CGGATTGCGTTAATAGCTGTTTG 58.972 43.478 0.00 0.00 35.28 2.93
17 18 3.687698 ACGGATTGCGTTAATAGCTGTTT 59.312 39.130 0.00 0.00 35.28 2.83
18 19 3.267483 ACGGATTGCGTTAATAGCTGTT 58.733 40.909 0.04 0.04 35.28 3.16
19 20 2.901249 ACGGATTGCGTTAATAGCTGT 58.099 42.857 0.00 0.00 35.28 4.40
20 21 3.944422 AACGGATTGCGTTAATAGCTG 57.056 42.857 14.53 0.00 35.28 4.24
21 22 3.805971 GGTAACGGATTGCGTTAATAGCT 59.194 43.478 22.09 0.00 34.27 3.32
22 23 4.124594 GGTAACGGATTGCGTTAATAGC 57.875 45.455 22.09 10.68 34.27 2.97
38 39 2.096762 GCAACCTGTTAACGACGGTAAC 60.097 50.000 25.30 25.30 35.21 2.50
39 40 2.134346 GCAACCTGTTAACGACGGTAA 58.866 47.619 12.61 0.07 35.21 2.85
40 41 1.782044 GCAACCTGTTAACGACGGTA 58.218 50.000 12.61 0.00 35.21 4.02
41 42 1.216941 CGCAACCTGTTAACGACGGT 61.217 55.000 0.00 7.89 36.95 4.83
42 43 1.216941 ACGCAACCTGTTAACGACGG 61.217 55.000 0.00 4.15 0.00 4.79
43 44 0.578211 AACGCAACCTGTTAACGACG 59.422 50.000 10.43 0.00 0.00 5.12
44 45 2.539274 TGTAACGCAACCTGTTAACGAC 59.461 45.455 10.43 2.27 33.89 4.34
45 46 2.819115 TGTAACGCAACCTGTTAACGA 58.181 42.857 10.43 0.00 33.89 3.85
46 47 3.589061 TTGTAACGCAACCTGTTAACG 57.411 42.857 0.26 3.85 33.89 3.18
47 48 5.331980 GCAAATTGTAACGCAACCTGTTAAC 60.332 40.000 0.00 0.00 40.28 2.01
48 49 4.740695 GCAAATTGTAACGCAACCTGTTAA 59.259 37.500 0.00 0.00 40.28 2.01
49 50 4.291783 GCAAATTGTAACGCAACCTGTTA 58.708 39.130 0.00 0.00 40.28 2.41
50 51 3.120041 GCAAATTGTAACGCAACCTGTT 58.880 40.909 0.00 0.00 40.28 3.16
51 52 2.544903 GGCAAATTGTAACGCAACCTGT 60.545 45.455 0.00 0.00 40.28 4.00
52 53 2.058057 GGCAAATTGTAACGCAACCTG 58.942 47.619 0.00 0.00 40.28 4.00
53 54 1.683917 TGGCAAATTGTAACGCAACCT 59.316 42.857 0.00 0.00 40.28 3.50
54 55 2.141535 TGGCAAATTGTAACGCAACC 57.858 45.000 0.00 0.00 40.28 3.77
55 56 3.302805 GGTTTGGCAAATTGTAACGCAAC 60.303 43.478 16.74 0.00 40.28 4.17
56 57 2.866762 GGTTTGGCAAATTGTAACGCAA 59.133 40.909 16.74 0.00 41.89 4.85
57 58 2.159099 TGGTTTGGCAAATTGTAACGCA 60.159 40.909 16.74 0.90 0.00 5.24
58 59 2.474816 TGGTTTGGCAAATTGTAACGC 58.525 42.857 16.74 0.06 0.00 4.84
59 60 4.330074 TGTTTGGTTTGGCAAATTGTAACG 59.670 37.500 16.74 0.00 0.00 3.18
60 61 5.447954 GGTGTTTGGTTTGGCAAATTGTAAC 60.448 40.000 16.74 16.52 0.00 2.50
61 62 4.636206 GGTGTTTGGTTTGGCAAATTGTAA 59.364 37.500 16.74 6.51 0.00 2.41
62 63 4.080863 AGGTGTTTGGTTTGGCAAATTGTA 60.081 37.500 16.74 0.36 0.00 2.41
63 64 3.013219 GGTGTTTGGTTTGGCAAATTGT 58.987 40.909 16.74 0.00 0.00 2.71
64 65 3.277715 AGGTGTTTGGTTTGGCAAATTG 58.722 40.909 16.74 0.00 0.00 2.32
65 66 3.540617 GAGGTGTTTGGTTTGGCAAATT 58.459 40.909 16.74 0.00 0.00 1.82
66 67 2.158827 GGAGGTGTTTGGTTTGGCAAAT 60.159 45.455 16.74 0.00 0.00 2.32
67 68 1.208293 GGAGGTGTTTGGTTTGGCAAA 59.792 47.619 8.93 8.93 0.00 3.68
68 69 0.827368 GGAGGTGTTTGGTTTGGCAA 59.173 50.000 0.00 0.00 0.00 4.52
69 70 0.032615 AGGAGGTGTTTGGTTTGGCA 60.033 50.000 0.00 0.00 0.00 4.92
70 71 0.389025 CAGGAGGTGTTTGGTTTGGC 59.611 55.000 0.00 0.00 0.00 4.52
71 72 1.956477 CTCAGGAGGTGTTTGGTTTGG 59.044 52.381 0.00 0.00 0.00 3.28
72 73 2.880890 CTCTCAGGAGGTGTTTGGTTTG 59.119 50.000 0.00 0.00 36.03 2.93
73 74 2.509964 ACTCTCAGGAGGTGTTTGGTTT 59.490 45.455 0.00 0.00 43.46 3.27
74 75 2.127708 ACTCTCAGGAGGTGTTTGGTT 58.872 47.619 0.00 0.00 43.46 3.67
75 76 1.807814 ACTCTCAGGAGGTGTTTGGT 58.192 50.000 0.00 0.00 43.46 3.67
76 77 2.938956 AACTCTCAGGAGGTGTTTGG 57.061 50.000 0.00 0.00 43.46 3.28
77 78 4.511826 GTGTAAACTCTCAGGAGGTGTTTG 59.488 45.833 20.56 2.44 38.79 2.93
78 79 4.704965 GTGTAAACTCTCAGGAGGTGTTT 58.295 43.478 17.95 17.95 38.79 2.83
79 80 3.243771 CGTGTAAACTCTCAGGAGGTGTT 60.244 47.826 0.00 0.46 38.79 3.32
80 81 2.296471 CGTGTAAACTCTCAGGAGGTGT 59.704 50.000 0.00 0.00 38.79 4.16
81 82 2.557056 TCGTGTAAACTCTCAGGAGGTG 59.443 50.000 0.00 0.00 38.79 4.00
82 83 2.872732 TCGTGTAAACTCTCAGGAGGT 58.127 47.619 0.00 0.00 42.01 3.85
83 84 3.697045 AGATCGTGTAAACTCTCAGGAGG 59.303 47.826 0.00 0.00 43.46 4.30
84 85 4.974368 AGATCGTGTAAACTCTCAGGAG 57.026 45.455 0.00 0.00 44.62 3.69
85 86 4.331992 CGTAGATCGTGTAAACTCTCAGGA 59.668 45.833 0.00 0.00 33.99 3.86
86 87 4.331992 TCGTAGATCGTGTAAACTCTCAGG 59.668 45.833 0.00 0.00 40.80 3.86
87 88 5.466432 TCGTAGATCGTGTAAACTCTCAG 57.534 43.478 0.00 0.00 40.80 3.35
88 89 5.868043 TTCGTAGATCGTGTAAACTCTCA 57.132 39.130 0.00 0.00 40.80 3.27
91 92 9.196948 CGATATATTCGTAGATCGTGTAAACTC 57.803 37.037 4.76 0.00 43.01 3.01
107 108 7.404516 GCTTGGCTTAGCTGCGATATATTCG 62.405 48.000 3.59 3.78 43.07 3.34
108 109 4.201763 GCTTGGCTTAGCTGCGATATATTC 60.202 45.833 3.59 0.00 38.15 1.75
109 110 3.686726 GCTTGGCTTAGCTGCGATATATT 59.313 43.478 3.59 0.00 38.15 1.28
110 111 3.265791 GCTTGGCTTAGCTGCGATATAT 58.734 45.455 3.59 0.00 38.15 0.86
111 112 2.612972 GGCTTGGCTTAGCTGCGATATA 60.613 50.000 3.59 0.00 40.99 0.86
112 113 1.517242 GCTTGGCTTAGCTGCGATAT 58.483 50.000 3.59 0.00 38.15 1.63
113 114 0.532862 GGCTTGGCTTAGCTGCGATA 60.533 55.000 3.59 0.00 40.99 2.92
114 115 1.821332 GGCTTGGCTTAGCTGCGAT 60.821 57.895 3.59 0.00 40.99 4.58
115 116 2.436646 GGCTTGGCTTAGCTGCGA 60.437 61.111 3.59 0.00 40.99 5.10
116 117 3.869272 CGGCTTGGCTTAGCTGCG 61.869 66.667 3.59 4.83 40.38 5.18
119 120 1.221021 GGTACGGCTTGGCTTAGCT 59.779 57.895 3.59 0.00 40.99 3.32
120 121 3.809423 GGTACGGCTTGGCTTAGC 58.191 61.111 0.00 0.00 40.48 3.09
133 134 1.205655 GGACCTGGTAAGTTCCGGTAC 59.794 57.143 2.44 2.44 35.65 3.34
134 135 1.203162 TGGACCTGGTAAGTTCCGGTA 60.203 52.381 0.00 0.00 35.65 4.02
135 136 0.472352 TGGACCTGGTAAGTTCCGGT 60.472 55.000 0.00 0.00 37.20 5.28
136 137 0.249398 CTGGACCTGGTAAGTTCCGG 59.751 60.000 0.00 0.00 0.00 5.14
137 138 0.249398 CCTGGACCTGGTAAGTTCCG 59.751 60.000 9.26 0.00 0.00 4.30
138 139 0.035343 GCCTGGACCTGGTAAGTTCC 60.035 60.000 17.97 0.00 0.00 3.62
139 140 0.035343 GGCCTGGACCTGGTAAGTTC 60.035 60.000 17.97 1.12 0.00 3.01
140 141 1.498176 GGGCCTGGACCTGGTAAGTT 61.498 60.000 12.69 0.00 0.00 2.66
141 142 1.923909 GGGCCTGGACCTGGTAAGT 60.924 63.158 12.69 0.00 0.00 2.24
142 143 2.998949 GGGCCTGGACCTGGTAAG 59.001 66.667 12.69 0.13 0.00 2.34
143 144 3.006728 CGGGCCTGGACCTGGTAA 61.007 66.667 18.47 0.00 31.89 2.85
201 202 4.373527 TCAAGTCCGAGTTCGAAATGAAA 58.626 39.130 1.32 0.00 43.02 2.69
615 626 5.708230 TGGCGTTTAAGTGGAATTATTGACT 59.292 36.000 0.00 0.00 0.00 3.41
683 694 4.202010 ACAATGTTTAATAGCACGGCATCC 60.202 41.667 0.00 0.00 0.00 3.51
829 841 8.349983 ACGTTGATCTGTTTTTGCTAACTAAAT 58.650 29.630 0.00 0.00 0.00 1.40
927 955 0.456221 CCTGCCAACGACGACTATCT 59.544 55.000 0.00 0.00 0.00 1.98
975 1003 2.032799 TCGTCAATGTTTGGTTGAGCAC 59.967 45.455 0.00 0.00 36.35 4.40
1008 1036 6.303839 AGGTTAAAGCACCTGAAATAGTTCA 58.696 36.000 5.38 5.38 46.22 3.18
1231 1267 3.787577 TCCAATCTGATTCATCCCCTCAA 59.212 43.478 0.00 0.00 0.00 3.02
1232 1268 3.396565 TCCAATCTGATTCATCCCCTCA 58.603 45.455 0.00 0.00 0.00 3.86
1233 1269 4.333690 CATCCAATCTGATTCATCCCCTC 58.666 47.826 0.00 0.00 0.00 4.30
1237 1273 5.628130 TCTTCCATCCAATCTGATTCATCC 58.372 41.667 0.00 0.00 0.00 3.51
1407 1511 5.163683 CCCCTATCGATCGTTACGTGAATAT 60.164 44.000 15.94 0.00 0.00 1.28
1473 1577 1.536072 GCGGACATCTCGTATCAGCAA 60.536 52.381 0.00 0.00 0.00 3.91
1551 1656 4.807631 TGATCCGGACGCGGGAGA 62.808 66.667 6.12 1.34 36.35 3.71
1667 1775 4.373116 GACCTCGCCGGAAGCACA 62.373 66.667 5.05 0.00 44.04 4.57
1705 1813 2.863153 CGCTTCTTGTTCCTGGCG 59.137 61.111 0.00 0.00 36.89 5.69
1852 2005 4.002506 TTCTCGGCAAGGCGAGCA 62.003 61.111 32.76 24.03 32.48 4.26
2055 2214 1.008194 TCGTTGAACTCCACCGTCG 60.008 57.895 0.00 0.00 32.20 5.12
2140 2300 4.326826 TCATGCCTAACTTCACTTCTTGG 58.673 43.478 0.00 0.00 0.00 3.61
2142 2302 5.809001 TGATCATGCCTAACTTCACTTCTT 58.191 37.500 0.00 0.00 0.00 2.52
2143 2303 5.426689 TGATCATGCCTAACTTCACTTCT 57.573 39.130 0.00 0.00 0.00 2.85
2144 2304 6.690194 ATTGATCATGCCTAACTTCACTTC 57.310 37.500 0.00 0.00 0.00 3.01
2145 2305 7.831193 ACTAATTGATCATGCCTAACTTCACTT 59.169 33.333 0.00 0.00 0.00 3.16
2146 2306 7.341805 ACTAATTGATCATGCCTAACTTCACT 58.658 34.615 0.00 0.00 0.00 3.41
2147 2307 7.497249 AGACTAATTGATCATGCCTAACTTCAC 59.503 37.037 0.00 0.00 0.00 3.18
2148 2308 7.496920 CAGACTAATTGATCATGCCTAACTTCA 59.503 37.037 0.00 0.00 0.00 3.02
2156 2320 4.454678 TGGTCAGACTAATTGATCATGCC 58.545 43.478 0.00 0.00 31.03 4.40
2159 2323 8.027524 ACAGTATGGTCAGACTAATTGATCAT 57.972 34.615 0.00 6.29 45.65 2.45
2164 2328 5.977635 TGGACAGTATGGTCAGACTAATTG 58.022 41.667 0.00 0.00 43.62 2.32
2182 2346 0.690192 CACCCACACCTGTATGGACA 59.310 55.000 0.00 0.00 38.34 4.02
2183 2347 0.981183 TCACCCACACCTGTATGGAC 59.019 55.000 0.00 0.00 38.34 4.02
2184 2348 1.965414 ATCACCCACACCTGTATGGA 58.035 50.000 0.00 0.00 38.34 3.41
2210 2374 3.887716 TCAGTAGATTAGGGCTAACCGAC 59.112 47.826 0.00 0.00 46.96 4.79
2265 2432 4.104383 TGCATAATCAGAAGGGGGAATC 57.896 45.455 0.00 0.00 0.00 2.52
2410 2579 2.047179 GGACTGAAGACACCCCGC 60.047 66.667 0.00 0.00 0.00 6.13
2455 2624 3.364023 CGTCGTGTCCTTCAATTGACTAC 59.636 47.826 7.89 7.29 32.67 2.73
2463 2632 2.355363 CGCCGTCGTGTCCTTCAA 60.355 61.111 0.00 0.00 0.00 2.69
2476 2645 1.623081 TAAGAAAACTCGCTGCGCCG 61.623 55.000 18.65 13.10 0.00 6.46
2486 2655 6.235231 TCCACTCTGTTCAGTAAGAAAACT 57.765 37.500 0.00 0.00 38.13 2.66
2508 2677 9.448438 AAATTTACCTGCCTCCAAAATAAAATC 57.552 29.630 0.00 0.00 0.00 2.17
2510 2679 7.880713 GGAAATTTACCTGCCTCCAAAATAAAA 59.119 33.333 0.00 0.00 0.00 1.52
2517 2686 3.430453 CTGGAAATTTACCTGCCTCCAA 58.570 45.455 0.00 0.00 32.74 3.53
2583 2753 6.127842 ACCAGTGTTCGTTAGATTGTTGTTTT 60.128 34.615 0.00 0.00 0.00 2.43
2599 2769 1.873698 TTGTTAGGCGACCAGTGTTC 58.126 50.000 0.00 0.00 0.00 3.18
2602 2772 6.671614 TTTTATATTGTTAGGCGACCAGTG 57.328 37.500 0.00 0.00 0.00 3.66
2606 2776 4.965762 GCGTTTTTATATTGTTAGGCGACC 59.034 41.667 0.00 0.00 0.00 4.79
2609 2779 5.164606 AGGCGTTTTTATATTGTTAGGCG 57.835 39.130 0.00 0.00 0.00 5.52
2616 2786 7.121272 CACCGTAGTTAGGCGTTTTTATATTG 58.879 38.462 0.00 0.00 0.00 1.90
2690 4030 6.485171 AGTAATGGAATTTAGGCACTTCTGT 58.515 36.000 0.00 0.00 37.61 3.41
2754 4094 6.330250 ACCCTAAATCATACAAGGCTCATAGT 59.670 38.462 0.00 0.00 0.00 2.12
2772 4112 4.202202 CCAATGACAGCAAACAACCCTAAA 60.202 41.667 0.00 0.00 0.00 1.85
2796 4136 1.285641 CAATGGGGTTGACGCACAC 59.714 57.895 0.58 0.00 45.46 3.82
2802 4142 3.758931 GCGGCCAATGGGGTTGAC 61.759 66.667 2.24 0.00 40.37 3.18
2824 4164 9.742144 GGTTGATCTATCTACATAGGACTAAGA 57.258 37.037 6.83 0.00 34.85 2.10
2825 4165 9.747898 AGGTTGATCTATCTACATAGGACTAAG 57.252 37.037 6.83 0.00 34.85 2.18
2837 4177 9.982651 GCAAACACTATAAGGTTGATCTATCTA 57.017 33.333 6.77 0.00 0.00 1.98
2838 4178 8.709308 AGCAAACACTATAAGGTTGATCTATCT 58.291 33.333 6.77 0.00 0.00 1.98
2839 4179 8.894768 AGCAAACACTATAAGGTTGATCTATC 57.105 34.615 6.77 0.00 0.00 2.08
2840 4180 9.686683 AAAGCAAACACTATAAGGTTGATCTAT 57.313 29.630 6.77 0.00 0.00 1.98
2841 4181 8.946085 CAAAGCAAACACTATAAGGTTGATCTA 58.054 33.333 6.77 0.00 0.00 1.98
2842 4182 7.094205 CCAAAGCAAACACTATAAGGTTGATCT 60.094 37.037 6.77 0.00 0.00 2.75
2843 4183 7.029563 CCAAAGCAAACACTATAAGGTTGATC 58.970 38.462 6.77 0.00 0.00 2.92
2844 4184 6.719370 TCCAAAGCAAACACTATAAGGTTGAT 59.281 34.615 6.77 0.00 0.00 2.57
2845 4185 6.065374 TCCAAAGCAAACACTATAAGGTTGA 58.935 36.000 6.77 0.00 0.00 3.18
2846 4186 6.325919 TCCAAAGCAAACACTATAAGGTTG 57.674 37.500 0.00 0.00 0.00 3.77
2847 4187 7.539034 AATCCAAAGCAAACACTATAAGGTT 57.461 32.000 0.00 0.00 0.00 3.50
2848 4188 7.539034 AAATCCAAAGCAAACACTATAAGGT 57.461 32.000 0.00 0.00 0.00 3.50
2854 4194 9.418045 GCTAAATAAAATCCAAAGCAAACACTA 57.582 29.630 0.00 0.00 0.00 2.74
2855 4195 7.387673 GGCTAAATAAAATCCAAAGCAAACACT 59.612 33.333 0.00 0.00 0.00 3.55
2856 4196 7.172361 TGGCTAAATAAAATCCAAAGCAAACAC 59.828 33.333 0.00 0.00 0.00 3.32
2857 4197 7.220030 TGGCTAAATAAAATCCAAAGCAAACA 58.780 30.769 0.00 0.00 0.00 2.83
2858 4198 7.665561 TGGCTAAATAAAATCCAAAGCAAAC 57.334 32.000 0.00 0.00 0.00 2.93
2859 4199 8.682936 TTTGGCTAAATAAAATCCAAAGCAAA 57.317 26.923 0.00 0.00 40.60 3.68
2860 4200 8.682936 TTTTGGCTAAATAAAATCCAAAGCAA 57.317 26.923 0.00 0.00 44.51 3.91
2861 4201 8.682936 TTTTTGGCTAAATAAAATCCAAAGCA 57.317 26.923 0.00 0.00 44.51 3.91
2862 4202 8.783093 ACTTTTTGGCTAAATAAAATCCAAAGC 58.217 29.630 0.00 0.00 44.51 3.51
2987 4365 5.514500 AGGTCTACCTGGAAGCAATAAAA 57.486 39.130 0.00 0.00 46.55 1.52
3040 4418 1.735018 TGAATGTTACCGTCAATGCCG 59.265 47.619 0.00 0.00 0.00 5.69
3041 4419 3.376859 TCATGAATGTTACCGTCAATGCC 59.623 43.478 0.00 0.00 0.00 4.40
3042 4420 4.332543 TCTCATGAATGTTACCGTCAATGC 59.667 41.667 0.00 0.00 0.00 3.56
3079 4503 3.694043 TGTCGATTTGGATGGAGAACA 57.306 42.857 0.00 0.00 0.00 3.18
3128 4552 0.185901 GCCATTGATAGGGGCAAGGA 59.814 55.000 0.00 0.00 46.92 3.36
3145 4569 5.660460 CATAAATCCACACTTTTTAGGGCC 58.340 41.667 0.00 0.00 0.00 5.80
3146 4570 5.105351 AGCATAAATCCACACTTTTTAGGGC 60.105 40.000 0.00 0.00 0.00 5.19
3272 4700 7.603963 ACACAGCAATATACGATTGTTAACA 57.396 32.000 3.59 3.59 0.00 2.41
3273 4701 9.632969 CTAACACAGCAATATACGATTGTTAAC 57.367 33.333 0.00 0.00 30.13 2.01
3274 4702 9.373603 ACTAACACAGCAATATACGATTGTTAA 57.626 29.630 0.00 0.00 30.13 2.01
3275 4703 8.936070 ACTAACACAGCAATATACGATTGTTA 57.064 30.769 0.00 0.00 0.00 2.41
3276 4704 7.843490 ACTAACACAGCAATATACGATTGTT 57.157 32.000 0.00 0.00 0.00 2.83
3277 4705 7.843490 AACTAACACAGCAATATACGATTGT 57.157 32.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.