Multiple sequence alignment - TraesCS4A01G188500

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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 TraesCS4A01G188500 chr4A 100.000 3791 0 0 1 3791 467267728 467263938 0.000000e+00 7001.0
1 TraesCS4A01G188500 chr4A 96.978 695 18 3 188 880 624642012 624642705 0.000000e+00 1164.0
2 TraesCS4A01G188500 chr4A 99.479 192 0 1 1 191 19593170 19593361 7.790000e-92 348.0
3 TraesCS4A01G188500 chr4A 99.479 192 0 1 1 191 473403662 473403471 7.790000e-92 348.0
4 TraesCS4A01G188500 chr4A 96.209 211 5 3 1 211 473392466 473392259 3.630000e-90 342.0
5 TraesCS4A01G188500 chr4A 96.569 204 5 2 1 204 475681472 475681271 1.690000e-88 337.0
6 TraesCS4A01G188500 chr4D 95.236 2897 108 13 910 3789 109240320 109243203 0.000000e+00 4558.0
7 TraesCS4A01G188500 chr4D 95.556 630 25 3 191 819 304736609 304735982 0.000000e+00 1005.0
8 TraesCS4A01G188500 chr4D 95.652 69 3 0 815 883 304707102 304707034 1.110000e-20 111.0
9 TraesCS4A01G188500 chr4D 100.000 29 0 0 880 908 283854842 283854814 2.000000e-03 54.7
10 TraesCS4A01G188500 chr4B 95.413 2289 94 3 926 3214 167381253 167378976 0.000000e+00 3635.0
11 TraesCS4A01G188500 chr4B 89.341 516 34 10 3249 3750 167374576 167374068 2.490000e-176 628.0
12 TraesCS4A01G188500 chr3A 97.550 694 16 1 191 883 22234419 22233726 0.000000e+00 1186.0
13 TraesCS4A01G188500 chr3A 96.821 692 21 1 188 878 647154493 647155184 0.000000e+00 1155.0
14 TraesCS4A01G188500 chr3A 96.667 690 22 1 191 879 9865358 9864669 0.000000e+00 1146.0
15 TraesCS4A01G188500 chr3A 100.000 191 0 0 1 191 519039873 519039683 1.680000e-93 353.0
16 TraesCS4A01G188500 chr3A 100.000 189 0 0 2 190 529765759 529765947 2.170000e-92 350.0
17 TraesCS4A01G188500 chr3A 88.764 89 9 1 3592 3679 749725183 749725271 1.440000e-19 108.0
18 TraesCS4A01G188500 chr1A 96.830 694 21 1 191 883 569441694 569441001 0.000000e+00 1158.0
19 TraesCS4A01G188500 chr1A 99.476 191 1 0 1 191 507809690 507809500 7.790000e-92 348.0
20 TraesCS4A01G188500 chr1A 100.000 28 0 0 3032 3059 527955770 527955797 7.000000e-03 52.8
21 TraesCS4A01G188500 chr2B 91.511 695 41 10 188 880 72395961 72396639 0.000000e+00 941.0
22 TraesCS4A01G188500 chr1B 95.625 320 14 0 188 507 38037787 38038106 7.260000e-142 514.0
23 TraesCS4A01G188500 chr7A 95.614 228 10 0 653 880 566913481 566913708 2.150000e-97 366.0
24 TraesCS4A01G188500 chr7A 98.086 209 4 0 188 396 566913230 566913438 7.740000e-97 364.0
25 TraesCS4A01G188500 chr7A 99.476 191 1 0 1 191 136309106 136309296 7.790000e-92 348.0
26 TraesCS4A01G188500 chr6A 99.476 191 1 0 1 191 566576656 566576846 7.790000e-92 348.0
27 TraesCS4A01G188500 chr5B 83.871 186 21 6 3608 3787 533487234 533487416 6.510000e-38 169.0
28 TraesCS4A01G188500 chr1D 100.000 28 0 0 3032 3059 430415779 430415806 7.000000e-03 52.8


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 TraesCS4A01G188500 chr4A 467263938 467267728 3790 True 7001 7001 100.000 1 3791 1 chr4A.!!$R1 3790
1 TraesCS4A01G188500 chr4A 624642012 624642705 693 False 1164 1164 96.978 188 880 1 chr4A.!!$F2 692
2 TraesCS4A01G188500 chr4D 109240320 109243203 2883 False 4558 4558 95.236 910 3789 1 chr4D.!!$F1 2879
3 TraesCS4A01G188500 chr4D 304735982 304736609 627 True 1005 1005 95.556 191 819 1 chr4D.!!$R3 628
4 TraesCS4A01G188500 chr4B 167378976 167381253 2277 True 3635 3635 95.413 926 3214 1 chr4B.!!$R2 2288
5 TraesCS4A01G188500 chr4B 167374068 167374576 508 True 628 628 89.341 3249 3750 1 chr4B.!!$R1 501
6 TraesCS4A01G188500 chr3A 22233726 22234419 693 True 1186 1186 97.550 191 883 1 chr3A.!!$R2 692
7 TraesCS4A01G188500 chr3A 647154493 647155184 691 False 1155 1155 96.821 188 878 1 chr3A.!!$F2 690
8 TraesCS4A01G188500 chr3A 9864669 9865358 689 True 1146 1146 96.667 191 879 1 chr3A.!!$R1 688
9 TraesCS4A01G188500 chr1A 569441001 569441694 693 True 1158 1158 96.830 191 883 1 chr1A.!!$R2 692
10 TraesCS4A01G188500 chr2B 72395961 72396639 678 False 941 941 91.511 188 880 1 chr2B.!!$F1 692

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
84 85 0.176680 AGTCTACCTTCCGCTGCATG 59.823 55.0 0.00 0.00 0.0 4.06 F
1788 1794 0.178301 TGAACTGTTACGTGGCCACA 59.822 50.0 34.16 14.61 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 1972 0.175760 AGCACCGTGACGCTATCAAT 59.824 50.0 1.65 0.0 39.72 2.57 R
3721 3742 0.319211 CAACCACACCTTCGCGTAGA 60.319 55.0 14.87 0.0 0.00 2.59 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
23 24 6.127810 ACATTGCTGCTATTAGTCATTGTG 57.872 37.500 0.00 0.00 0.00 3.33
24 25 4.621068 TTGCTGCTATTAGTCATTGTGC 57.379 40.909 0.00 0.00 0.00 4.57
25 26 3.877559 TGCTGCTATTAGTCATTGTGCT 58.122 40.909 0.00 0.00 0.00 4.40
26 27 4.264253 TGCTGCTATTAGTCATTGTGCTT 58.736 39.130 0.00 0.00 0.00 3.91
27 28 4.701651 TGCTGCTATTAGTCATTGTGCTTT 59.298 37.500 0.00 0.00 0.00 3.51
28 29 5.163723 TGCTGCTATTAGTCATTGTGCTTTC 60.164 40.000 0.00 0.00 0.00 2.62
29 30 5.163723 GCTGCTATTAGTCATTGTGCTTTCA 60.164 40.000 0.00 0.00 0.00 2.69
30 31 6.182039 TGCTATTAGTCATTGTGCTTTCAC 57.818 37.500 0.00 0.00 43.40 3.18
31 32 5.939883 TGCTATTAGTCATTGTGCTTTCACT 59.060 36.000 0.00 0.00 43.49 3.41
32 33 6.430925 TGCTATTAGTCATTGTGCTTTCACTT 59.569 34.615 0.00 0.00 43.49 3.16
33 34 6.963805 GCTATTAGTCATTGTGCTTTCACTTC 59.036 38.462 0.00 0.00 43.49 3.01
34 35 6.882610 ATTAGTCATTGTGCTTTCACTTCA 57.117 33.333 0.00 0.00 43.49 3.02
35 36 6.882610 TTAGTCATTGTGCTTTCACTTCAT 57.117 33.333 0.00 0.00 43.49 2.57
36 37 5.779529 AGTCATTGTGCTTTCACTTCATT 57.220 34.783 0.00 0.00 43.49 2.57
37 38 5.526115 AGTCATTGTGCTTTCACTTCATTG 58.474 37.500 0.00 0.00 43.49 2.82
38 39 5.300034 AGTCATTGTGCTTTCACTTCATTGA 59.700 36.000 0.00 0.00 43.49 2.57
39 40 5.978919 GTCATTGTGCTTTCACTTCATTGAA 59.021 36.000 0.00 0.00 43.49 2.69
40 41 6.643770 GTCATTGTGCTTTCACTTCATTGAAT 59.356 34.615 0.00 0.00 43.49 2.57
41 42 7.809331 GTCATTGTGCTTTCACTTCATTGAATA 59.191 33.333 0.00 0.00 43.49 1.75
42 43 7.809331 TCATTGTGCTTTCACTTCATTGAATAC 59.191 33.333 0.00 0.00 43.49 1.89
43 44 6.882610 TGTGCTTTCACTTCATTGAATACT 57.117 33.333 0.00 0.00 43.49 2.12
44 45 7.275888 TGTGCTTTCACTTCATTGAATACTT 57.724 32.000 0.00 0.00 43.49 2.24
45 46 7.140705 TGTGCTTTCACTTCATTGAATACTTG 58.859 34.615 0.00 0.00 43.49 3.16
46 47 7.013178 TGTGCTTTCACTTCATTGAATACTTGA 59.987 33.333 0.00 0.00 43.49 3.02
47 48 7.324616 GTGCTTTCACTTCATTGAATACTTGAC 59.675 37.037 0.00 0.00 40.03 3.18
48 49 7.229306 TGCTTTCACTTCATTGAATACTTGACT 59.771 33.333 0.00 0.00 35.42 3.41
49 50 8.721478 GCTTTCACTTCATTGAATACTTGACTA 58.279 33.333 0.00 0.00 35.42 2.59
52 53 8.722480 TCACTTCATTGAATACTTGACTATGG 57.278 34.615 0.00 0.00 0.00 2.74
53 54 8.321353 TCACTTCATTGAATACTTGACTATGGT 58.679 33.333 0.00 0.00 0.00 3.55
54 55 8.950210 CACTTCATTGAATACTTGACTATGGTT 58.050 33.333 0.00 0.00 0.00 3.67
55 56 9.520515 ACTTCATTGAATACTTGACTATGGTTT 57.479 29.630 0.00 0.00 0.00 3.27
56 57 9.778993 CTTCATTGAATACTTGACTATGGTTTG 57.221 33.333 0.00 0.00 0.00 2.93
57 58 7.761409 TCATTGAATACTTGACTATGGTTTGC 58.239 34.615 0.00 0.00 0.00 3.68
58 59 6.509418 TTGAATACTTGACTATGGTTTGCC 57.491 37.500 0.00 0.00 0.00 4.52
59 60 5.815581 TGAATACTTGACTATGGTTTGCCT 58.184 37.500 0.00 0.00 35.27 4.75
60 61 6.953101 TGAATACTTGACTATGGTTTGCCTA 58.047 36.000 0.00 0.00 35.27 3.93
61 62 7.047891 TGAATACTTGACTATGGTTTGCCTAG 58.952 38.462 0.00 0.00 35.27 3.02
62 63 4.910458 ACTTGACTATGGTTTGCCTAGT 57.090 40.909 0.00 0.00 34.04 2.57
63 64 4.579869 ACTTGACTATGGTTTGCCTAGTG 58.420 43.478 0.00 0.00 32.62 2.74
64 65 4.041691 ACTTGACTATGGTTTGCCTAGTGT 59.958 41.667 0.00 0.00 32.62 3.55
65 66 5.247564 ACTTGACTATGGTTTGCCTAGTGTA 59.752 40.000 0.00 0.00 32.62 2.90
66 67 5.339008 TGACTATGGTTTGCCTAGTGTAG 57.661 43.478 0.00 0.00 32.62 2.74
67 68 4.775780 TGACTATGGTTTGCCTAGTGTAGT 59.224 41.667 0.00 0.00 32.62 2.73
68 69 5.105473 TGACTATGGTTTGCCTAGTGTAGTC 60.105 44.000 0.00 0.00 32.62 2.59
69 70 5.024118 ACTATGGTTTGCCTAGTGTAGTCT 58.976 41.667 0.00 0.00 31.86 3.24
70 71 6.192773 ACTATGGTTTGCCTAGTGTAGTCTA 58.807 40.000 0.00 0.00 31.86 2.59
71 72 4.796038 TGGTTTGCCTAGTGTAGTCTAC 57.204 45.455 2.81 2.81 35.27 2.59
72 73 3.512724 TGGTTTGCCTAGTGTAGTCTACC 59.487 47.826 7.56 0.00 35.27 3.18
73 74 3.768215 GGTTTGCCTAGTGTAGTCTACCT 59.232 47.826 7.56 6.85 0.00 3.08
74 75 4.222366 GGTTTGCCTAGTGTAGTCTACCTT 59.778 45.833 7.56 0.00 0.00 3.50
75 76 5.409211 GTTTGCCTAGTGTAGTCTACCTTC 58.591 45.833 7.56 0.00 0.00 3.46
76 77 3.629087 TGCCTAGTGTAGTCTACCTTCC 58.371 50.000 7.56 0.00 0.00 3.46
77 78 2.617774 GCCTAGTGTAGTCTACCTTCCG 59.382 54.545 7.56 0.00 0.00 4.30
78 79 2.617774 CCTAGTGTAGTCTACCTTCCGC 59.382 54.545 7.56 0.00 0.00 5.54
79 80 2.510928 AGTGTAGTCTACCTTCCGCT 57.489 50.000 7.56 0.00 0.00 5.52
80 81 2.093106 AGTGTAGTCTACCTTCCGCTG 58.907 52.381 7.56 0.00 0.00 5.18
81 82 0.815734 TGTAGTCTACCTTCCGCTGC 59.184 55.000 7.56 0.00 0.00 5.25
82 83 0.815734 GTAGTCTACCTTCCGCTGCA 59.184 55.000 0.00 0.00 0.00 4.41
83 84 1.409427 GTAGTCTACCTTCCGCTGCAT 59.591 52.381 0.00 0.00 0.00 3.96
84 85 0.176680 AGTCTACCTTCCGCTGCATG 59.823 55.000 0.00 0.00 0.00 4.06
85 86 0.811616 GTCTACCTTCCGCTGCATGG 60.812 60.000 0.00 0.00 0.00 3.66
86 87 1.221840 CTACCTTCCGCTGCATGGT 59.778 57.895 0.00 4.39 35.05 3.55
87 88 0.464036 CTACCTTCCGCTGCATGGTA 59.536 55.000 0.00 5.33 32.74 3.25
88 89 0.906066 TACCTTCCGCTGCATGGTAA 59.094 50.000 0.00 0.00 31.24 2.85
89 90 0.255890 ACCTTCCGCTGCATGGTAAT 59.744 50.000 0.00 0.00 0.00 1.89
90 91 1.488812 ACCTTCCGCTGCATGGTAATA 59.511 47.619 0.00 0.00 0.00 0.98
91 92 2.146342 CCTTCCGCTGCATGGTAATAG 58.854 52.381 0.00 0.65 0.00 1.73
92 93 2.146342 CTTCCGCTGCATGGTAATAGG 58.854 52.381 0.00 0.00 0.00 2.57
93 94 1.128200 TCCGCTGCATGGTAATAGGT 58.872 50.000 0.00 0.00 0.00 3.08
94 95 1.488812 TCCGCTGCATGGTAATAGGTT 59.511 47.619 0.00 0.00 0.00 3.50
95 96 2.092646 TCCGCTGCATGGTAATAGGTTT 60.093 45.455 0.00 0.00 0.00 3.27
96 97 3.134985 TCCGCTGCATGGTAATAGGTTTA 59.865 43.478 0.00 0.00 0.00 2.01
97 98 4.072131 CCGCTGCATGGTAATAGGTTTAT 58.928 43.478 0.00 0.00 0.00 1.40
98 99 4.518970 CCGCTGCATGGTAATAGGTTTATT 59.481 41.667 0.00 0.00 34.04 1.40
99 100 5.009610 CCGCTGCATGGTAATAGGTTTATTT 59.990 40.000 0.00 0.00 31.97 1.40
100 101 6.142817 CGCTGCATGGTAATAGGTTTATTTC 58.857 40.000 0.00 0.00 31.97 2.17
101 102 6.017109 CGCTGCATGGTAATAGGTTTATTTCT 60.017 38.462 0.00 0.00 31.97 2.52
102 103 7.172532 CGCTGCATGGTAATAGGTTTATTTCTA 59.827 37.037 0.00 0.00 31.97 2.10
103 104 9.014297 GCTGCATGGTAATAGGTTTATTTCTAT 57.986 33.333 0.00 0.00 31.97 1.98
105 106 9.214957 TGCATGGTAATAGGTTTATTTCTATCG 57.785 33.333 0.00 0.00 31.97 2.92
106 107 9.216117 GCATGGTAATAGGTTTATTTCTATCGT 57.784 33.333 0.00 0.00 31.97 3.73
115 116 7.960793 AGGTTTATTTCTATCGTTTGTCTTCG 58.039 34.615 0.00 0.00 0.00 3.79
116 117 7.816031 AGGTTTATTTCTATCGTTTGTCTTCGA 59.184 33.333 0.00 0.00 40.28 3.71
117 118 8.437742 GGTTTATTTCTATCGTTTGTCTTCGAA 58.562 33.333 0.00 0.00 39.45 3.71
118 119 9.801714 GTTTATTTCTATCGTTTGTCTTCGAAA 57.198 29.630 0.00 0.00 39.45 3.46
119 120 9.801714 TTTATTTCTATCGTTTGTCTTCGAAAC 57.198 29.630 0.00 1.53 39.45 2.78
120 121 7.653767 ATTTCTATCGTTTGTCTTCGAAACT 57.346 32.000 0.00 0.00 39.45 2.66
121 122 7.473027 TTTCTATCGTTTGTCTTCGAAACTT 57.527 32.000 0.00 0.00 39.45 2.66
122 123 6.686130 TCTATCGTTTGTCTTCGAAACTTC 57.314 37.500 0.00 0.00 39.45 3.01
123 124 4.727235 ATCGTTTGTCTTCGAAACTTCC 57.273 40.909 0.00 0.00 39.45 3.46
124 125 3.523547 TCGTTTGTCTTCGAAACTTCCA 58.476 40.909 0.00 0.00 32.17 3.53
125 126 3.307782 TCGTTTGTCTTCGAAACTTCCAC 59.692 43.478 0.00 0.00 32.17 4.02
126 127 3.604392 GTTTGTCTTCGAAACTTCCACG 58.396 45.455 0.00 0.00 31.74 4.94
127 128 2.589798 TGTCTTCGAAACTTCCACGT 57.410 45.000 0.00 0.00 0.00 4.49
128 129 2.896168 TGTCTTCGAAACTTCCACGTT 58.104 42.857 0.00 0.00 0.00 3.99
129 130 3.264104 TGTCTTCGAAACTTCCACGTTT 58.736 40.909 0.00 0.00 39.63 3.60
130 131 3.685756 TGTCTTCGAAACTTCCACGTTTT 59.314 39.130 0.00 0.00 37.24 2.43
131 132 4.026407 GTCTTCGAAACTTCCACGTTTTG 58.974 43.478 0.00 0.00 37.24 2.44
132 133 3.933955 TCTTCGAAACTTCCACGTTTTGA 59.066 39.130 0.00 3.01 42.55 2.69
133 134 4.392445 TCTTCGAAACTTCCACGTTTTGAA 59.608 37.500 14.74 14.74 46.86 2.69
134 135 4.267357 TCGAAACTTCCACGTTTTGAAG 57.733 40.909 14.50 14.50 41.77 3.02
135 136 3.933955 TCGAAACTTCCACGTTTTGAAGA 59.066 39.130 20.26 2.17 41.77 2.87
136 137 4.026407 CGAAACTTCCACGTTTTGAAGAC 58.974 43.478 20.26 12.30 40.30 3.01
137 138 4.201783 CGAAACTTCCACGTTTTGAAGACT 60.202 41.667 20.26 10.15 40.30 3.24
138 139 5.637809 GAAACTTCCACGTTTTGAAGACTT 58.362 37.500 20.26 14.20 40.30 3.01
139 140 5.638596 AACTTCCACGTTTTGAAGACTTT 57.361 34.783 20.26 6.88 40.30 2.66
140 141 5.231265 ACTTCCACGTTTTGAAGACTTTC 57.769 39.130 20.26 0.00 40.30 2.62
141 142 4.698304 ACTTCCACGTTTTGAAGACTTTCA 59.302 37.500 20.26 0.00 40.30 2.69
142 143 5.357032 ACTTCCACGTTTTGAAGACTTTCAT 59.643 36.000 20.26 0.46 42.60 2.57
143 144 6.540914 ACTTCCACGTTTTGAAGACTTTCATA 59.459 34.615 20.26 0.00 42.60 2.15
144 145 6.928979 TCCACGTTTTGAAGACTTTCATAA 57.071 33.333 0.00 0.00 42.60 1.90
145 146 7.323049 TCCACGTTTTGAAGACTTTCATAAA 57.677 32.000 0.00 0.00 42.60 1.40
146 147 7.763356 TCCACGTTTTGAAGACTTTCATAAAA 58.237 30.769 0.00 0.00 42.60 1.52
147 148 8.244802 TCCACGTTTTGAAGACTTTCATAAAAA 58.755 29.630 0.00 0.00 42.60 1.94
148 149 9.030301 CCACGTTTTGAAGACTTTCATAAAAAT 57.970 29.630 0.00 0.00 42.60 1.82
150 151 8.953990 ACGTTTTGAAGACTTTCATAAAAATCG 58.046 29.630 0.00 0.00 42.60 3.34
151 152 7.939386 CGTTTTGAAGACTTTCATAAAAATCGC 59.061 33.333 0.00 0.00 42.60 4.58
152 153 7.867445 TTTGAAGACTTTCATAAAAATCGCC 57.133 32.000 0.00 0.00 42.60 5.54
153 154 6.817765 TGAAGACTTTCATAAAAATCGCCT 57.182 33.333 0.00 0.00 38.37 5.52
154 155 7.915293 TGAAGACTTTCATAAAAATCGCCTA 57.085 32.000 0.00 0.00 38.37 3.93
155 156 8.506168 TGAAGACTTTCATAAAAATCGCCTAT 57.494 30.769 0.00 0.00 38.37 2.57
156 157 8.956426 TGAAGACTTTCATAAAAATCGCCTATT 58.044 29.630 0.00 0.00 38.37 1.73
157 158 9.439537 GAAGACTTTCATAAAAATCGCCTATTC 57.560 33.333 0.00 0.00 33.38 1.75
158 159 8.506168 AGACTTTCATAAAAATCGCCTATTCA 57.494 30.769 0.00 0.00 0.00 2.57
159 160 8.398665 AGACTTTCATAAAAATCGCCTATTCAC 58.601 33.333 0.00 0.00 0.00 3.18
160 161 7.480810 ACTTTCATAAAAATCGCCTATTCACC 58.519 34.615 0.00 0.00 0.00 4.02
161 162 6.385649 TTCATAAAAATCGCCTATTCACCC 57.614 37.500 0.00 0.00 0.00 4.61
162 163 4.825085 TCATAAAAATCGCCTATTCACCCC 59.175 41.667 0.00 0.00 0.00 4.95
163 164 2.067365 AAAATCGCCTATTCACCCCC 57.933 50.000 0.00 0.00 0.00 5.40
182 183 2.422832 CCCCCTCTAGTCGATATAACGC 59.577 54.545 0.00 0.00 0.00 4.84
183 184 3.079578 CCCCTCTAGTCGATATAACGCA 58.920 50.000 0.00 0.00 0.00 5.24
184 185 3.119919 CCCCTCTAGTCGATATAACGCAC 60.120 52.174 0.00 0.00 0.00 5.34
185 186 3.752222 CCCTCTAGTCGATATAACGCACT 59.248 47.826 0.00 5.39 0.00 4.40
186 187 4.215827 CCCTCTAGTCGATATAACGCACTT 59.784 45.833 10.84 0.00 0.00 3.16
187 188 5.278364 CCCTCTAGTCGATATAACGCACTTT 60.278 44.000 10.84 0.00 0.00 2.66
188 189 5.852229 CCTCTAGTCGATATAACGCACTTTC 59.148 44.000 10.84 0.00 0.00 2.62
189 190 6.367686 TCTAGTCGATATAACGCACTTTCA 57.632 37.500 10.84 0.00 0.00 2.69
274 275 2.925170 AGCTCGCACCAGGAACCT 60.925 61.111 0.00 0.00 0.00 3.50
301 302 2.558359 GTTGCTGGTTTATGCAGTCCTT 59.442 45.455 0.00 0.00 40.46 3.36
396 397 3.313012 TTCCGTCTTGTGTACCAGATG 57.687 47.619 0.00 0.00 0.00 2.90
455 456 1.800805 CTCAACGACTCCTGCATGTT 58.199 50.000 0.00 0.00 0.00 2.71
509 510 1.146930 CTCCCATACGCTGCACCAT 59.853 57.895 0.00 0.00 0.00 3.55
647 650 2.831685 TTAGCACATCTGTTGTCGGT 57.168 45.000 0.00 0.00 36.00 4.69
674 677 3.051210 CGTGCCAGTCTCCACAGA 58.949 61.111 0.00 0.00 32.37 3.41
790 793 0.449388 CAGTCTTCCCGCTGCATTTC 59.551 55.000 0.00 0.00 0.00 2.17
856 859 1.825474 CTTCCTATCTGGGTGTCACGT 59.175 52.381 0.00 0.00 36.20 4.49
880 883 4.499696 CCAAAAATCCTCCATATTCCGTGC 60.500 45.833 0.00 0.00 0.00 5.34
883 886 1.069765 CCTCCATATTCCGTGCGCT 59.930 57.895 9.73 0.00 0.00 5.92
884 887 0.946221 CCTCCATATTCCGTGCGCTC 60.946 60.000 9.73 3.51 0.00 5.03
885 888 1.278172 CTCCATATTCCGTGCGCTCG 61.278 60.000 23.83 23.83 0.00 5.03
886 889 1.591594 CCATATTCCGTGCGCTCGT 60.592 57.895 27.51 13.92 0.00 4.18
887 890 1.151777 CCATATTCCGTGCGCTCGTT 61.152 55.000 27.51 15.62 0.00 3.85
888 891 1.483316 CATATTCCGTGCGCTCGTTA 58.517 50.000 27.51 16.50 0.00 3.18
889 892 1.855978 CATATTCCGTGCGCTCGTTAA 59.144 47.619 27.51 21.23 0.00 2.01
890 893 1.270971 TATTCCGTGCGCTCGTTAAC 58.729 50.000 27.51 7.17 0.00 2.01
891 894 0.389426 ATTCCGTGCGCTCGTTAACT 60.389 50.000 27.51 7.06 0.00 2.24
892 895 0.240678 TTCCGTGCGCTCGTTAACTA 59.759 50.000 27.51 5.79 0.00 2.24
893 896 0.179181 TCCGTGCGCTCGTTAACTAG 60.179 55.000 27.51 12.45 0.00 2.57
894 897 0.455633 CCGTGCGCTCGTTAACTAGT 60.456 55.000 27.51 0.00 0.00 2.57
895 898 1.334054 CGTGCGCTCGTTAACTAGTT 58.666 50.000 22.65 13.68 0.00 2.24
896 899 1.057285 CGTGCGCTCGTTAACTAGTTG 59.943 52.381 22.65 1.62 0.00 3.16
897 900 1.065358 TGCGCTCGTTAACTAGTTGC 58.935 50.000 18.56 11.18 0.00 4.17
898 901 1.336517 TGCGCTCGTTAACTAGTTGCT 60.337 47.619 18.56 0.00 0.00 3.91
899 902 1.725164 GCGCTCGTTAACTAGTTGCTT 59.275 47.619 18.56 0.00 0.00 3.91
900 903 2.222530 GCGCTCGTTAACTAGTTGCTTC 60.223 50.000 18.56 5.01 0.00 3.86
901 904 2.344741 CGCTCGTTAACTAGTTGCTTCC 59.655 50.000 18.56 1.78 0.00 3.46
902 905 3.323243 GCTCGTTAACTAGTTGCTTCCA 58.677 45.455 18.56 0.00 0.00 3.53
903 906 3.368236 GCTCGTTAACTAGTTGCTTCCAG 59.632 47.826 18.56 7.41 0.00 3.86
904 907 4.806330 CTCGTTAACTAGTTGCTTCCAGA 58.194 43.478 18.56 6.91 0.00 3.86
905 908 5.204409 TCGTTAACTAGTTGCTTCCAGAA 57.796 39.130 18.56 0.00 0.00 3.02
906 909 5.603596 TCGTTAACTAGTTGCTTCCAGAAA 58.396 37.500 18.56 0.00 0.00 2.52
907 910 6.228258 TCGTTAACTAGTTGCTTCCAGAAAT 58.772 36.000 18.56 0.00 0.00 2.17
908 911 6.708949 TCGTTAACTAGTTGCTTCCAGAAATT 59.291 34.615 18.56 0.00 0.00 1.82
918 921 3.002759 GCTTCCAGAAATTAGGTCGCATC 59.997 47.826 0.00 0.00 0.00 3.91
924 927 4.336433 CAGAAATTAGGTCGCATCAACCAT 59.664 41.667 0.00 0.00 39.39 3.55
1575 1581 2.187946 GCGCTGCTCACCACCTAT 59.812 61.111 0.00 0.00 0.00 2.57
1605 1611 3.760035 AGGGATTCGTCGTGCGCT 61.760 61.111 9.73 0.00 41.07 5.92
1752 1758 2.654085 GCGCACGCGTATGCTCTA 60.654 61.111 22.97 0.00 43.80 2.43
1757 1763 0.527600 CACGCGTATGCTCTAAGGCA 60.528 55.000 13.44 0.00 46.63 4.75
1765 1771 1.451028 GCTCTAAGGCACAGGCTGG 60.451 63.158 20.34 9.00 38.81 4.85
1788 1794 0.178301 TGAACTGTTACGTGGCCACA 59.822 50.000 34.16 14.61 0.00 4.17
1869 1875 1.680105 GCGTTACGGACATGGACACG 61.680 60.000 6.94 0.00 0.00 4.49
2046 2052 4.162690 GGGCGGTGGCTCTTCGAT 62.163 66.667 0.00 0.00 36.44 3.59
2140 2146 0.178995 TGGTCAGCTTGATGTTGCCA 60.179 50.000 0.00 0.00 33.49 4.92
2312 2318 1.000955 CCTGCTGTCCAACTTCTACGT 59.999 52.381 0.00 0.00 0.00 3.57
2385 2391 4.751431 GGCATTGACAAGAGCCCT 57.249 55.556 18.91 0.00 41.25 5.19
2409 2415 3.842869 AAGCCTCCTTGACATCGAC 57.157 52.632 0.00 0.00 0.00 4.20
2433 2439 5.006386 GGTGTTCTCCATGAGTTCTTGATT 58.994 41.667 0.00 0.00 0.00 2.57
2506 2512 1.628340 TCGAGGCCAGATTGAAGGAAA 59.372 47.619 5.01 0.00 0.00 3.13
2564 2570 1.682684 TCGAGGAGGAGGACAAGGC 60.683 63.158 0.00 0.00 0.00 4.35
2583 2589 1.415659 GCAGATGCTCTGTCCTACCAT 59.584 52.381 12.71 0.00 45.94 3.55
2880 2886 2.644676 CTACTCCAGACTGGACGATGA 58.355 52.381 20.74 0.00 42.67 2.92
2910 2916 1.298859 GAACACGAAGCAGCCGGAAT 61.299 55.000 5.05 0.00 0.00 3.01
3078 3084 1.351017 GCTGGGGCCTTATGCAGTATA 59.649 52.381 0.84 0.00 43.89 1.47
3163 3170 2.369203 TGGGACACGGAGTTTGATTACA 59.631 45.455 0.00 0.00 41.61 2.41
3178 3185 9.569122 AGTTTGATTACACAATAGTTGTAACCT 57.431 29.630 0.00 0.00 43.23 3.50
3195 3202 3.487120 ACCTAGCGAAGTGAGGTTTTT 57.513 42.857 0.00 0.00 40.90 1.94
3227 3234 3.951563 ACTGTATGGGTATGCCATGTT 57.048 42.857 1.04 0.00 36.17 2.71
3240 3247 1.202336 GCCATGTTAGCATTCAGTGGC 60.202 52.381 5.52 5.52 33.82 5.01
3262 3269 3.149981 GGAGCTACCAAAGAAAAGCTGT 58.850 45.455 0.00 0.00 45.04 4.40
3284 3291 1.270625 CGGGCCACAGAGTAGAAACAA 60.271 52.381 4.39 0.00 0.00 2.83
3317 3333 1.740905 CATTGTTGTGTGCTGGGCA 59.259 52.632 0.00 0.00 35.60 5.36
3322 3338 0.108992 GTTGTGTGCTGGGCATCATG 60.109 55.000 0.00 0.00 41.91 3.07
3324 3340 3.135457 TGTGCTGGGCATCATGCG 61.135 61.111 2.82 0.00 46.21 4.73
3385 3401 2.269241 GGCCTTGCCGTAGCTTCT 59.731 61.111 0.00 0.00 39.62 2.85
3399 3415 1.009829 GCTTCTCCGGTGTTAGCATG 58.990 55.000 20.54 0.00 0.00 4.06
3408 3424 2.350388 CGGTGTTAGCATGACAACAACC 60.350 50.000 17.36 15.74 38.81 3.77
3413 3429 1.696063 AGCATGACAACAACCTGCTT 58.304 45.000 0.00 0.00 36.78 3.91
3485 3502 4.022849 GCTGTGCCTTGTTCTGAATTTAGT 60.023 41.667 0.00 0.00 0.00 2.24
3486 3503 5.181245 GCTGTGCCTTGTTCTGAATTTAGTA 59.819 40.000 0.00 0.00 0.00 1.82
3487 3504 6.293955 GCTGTGCCTTGTTCTGAATTTAGTAA 60.294 38.462 0.00 0.00 0.00 2.24
3559 3576 4.806247 TCCAAAGGTTTAATGTTGTTTGCG 59.194 37.500 0.00 0.00 0.00 4.85
3721 3742 5.303971 CAGGAAGACTCAGTTTCAGTCATT 58.696 41.667 2.84 0.00 42.51 2.57
3736 3757 1.654105 GTCATTCTACGCGAAGGTGTG 59.346 52.381 15.93 4.39 37.48 3.82
3765 3786 5.574188 AGCAAGATCAAGTTTTAGTGGGAT 58.426 37.500 0.00 0.00 0.00 3.85
3789 3810 2.918712 AATAGAGTGAATGGCTCCGG 57.081 50.000 0.00 0.00 33.69 5.14
3790 3811 0.394565 ATAGAGTGAATGGCTCCGGC 59.605 55.000 0.00 0.00 33.69 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.449588 GCACAATGACTAATAGCAGCAATGT 60.450 40.000 0.00 0.00 0.00 2.71
2 3 4.885907 AGCACAATGACTAATAGCAGCAAT 59.114 37.500 0.00 0.00 0.00 3.56
3 4 4.264253 AGCACAATGACTAATAGCAGCAA 58.736 39.130 0.00 0.00 0.00 3.91
4 5 3.877559 AGCACAATGACTAATAGCAGCA 58.122 40.909 0.00 0.00 0.00 4.41
5 6 4.889832 AAGCACAATGACTAATAGCAGC 57.110 40.909 0.00 0.00 0.00 5.25
6 7 6.253746 GTGAAAGCACAATGACTAATAGCAG 58.746 40.000 0.00 0.00 44.51 4.24
7 8 6.182039 GTGAAAGCACAATGACTAATAGCA 57.818 37.500 0.00 0.00 44.51 3.49
21 22 7.324616 GTCAAGTATTCAATGAAGTGAAAGCAC 59.675 37.037 1.10 0.00 45.49 4.40
22 23 7.229306 AGTCAAGTATTCAATGAAGTGAAAGCA 59.771 33.333 1.10 0.00 40.76 3.91
23 24 7.588512 AGTCAAGTATTCAATGAAGTGAAAGC 58.411 34.615 1.10 0.00 40.76 3.51
26 27 9.166173 CCATAGTCAAGTATTCAATGAAGTGAA 57.834 33.333 1.10 0.00 41.59 3.18
27 28 8.321353 ACCATAGTCAAGTATTCAATGAAGTGA 58.679 33.333 1.10 0.17 0.00 3.41
28 29 8.498054 ACCATAGTCAAGTATTCAATGAAGTG 57.502 34.615 1.10 0.00 0.00 3.16
29 30 9.520515 AAACCATAGTCAAGTATTCAATGAAGT 57.479 29.630 1.10 0.00 0.00 3.01
30 31 9.778993 CAAACCATAGTCAAGTATTCAATGAAG 57.221 33.333 1.10 0.00 0.00 3.02
31 32 8.243426 GCAAACCATAGTCAAGTATTCAATGAA 58.757 33.333 0.00 0.00 0.00 2.57
32 33 7.148086 GGCAAACCATAGTCAAGTATTCAATGA 60.148 37.037 0.00 0.00 35.26 2.57
33 34 6.974622 GGCAAACCATAGTCAAGTATTCAATG 59.025 38.462 0.00 0.00 35.26 2.82
34 35 6.891908 AGGCAAACCATAGTCAAGTATTCAAT 59.108 34.615 0.00 0.00 39.06 2.57
35 36 6.245408 AGGCAAACCATAGTCAAGTATTCAA 58.755 36.000 0.00 0.00 39.06 2.69
36 37 5.815581 AGGCAAACCATAGTCAAGTATTCA 58.184 37.500 0.00 0.00 39.06 2.57
37 38 7.011482 CACTAGGCAAACCATAGTCAAGTATTC 59.989 40.741 0.00 0.00 39.06 1.75
38 39 6.823689 CACTAGGCAAACCATAGTCAAGTATT 59.176 38.462 0.00 0.00 39.06 1.89
39 40 6.070194 ACACTAGGCAAACCATAGTCAAGTAT 60.070 38.462 0.00 0.00 39.06 2.12
40 41 5.247564 ACACTAGGCAAACCATAGTCAAGTA 59.752 40.000 0.00 0.00 39.06 2.24
41 42 4.041691 ACACTAGGCAAACCATAGTCAAGT 59.958 41.667 0.00 0.00 39.06 3.16
42 43 4.579869 ACACTAGGCAAACCATAGTCAAG 58.420 43.478 0.00 0.00 39.06 3.02
43 44 4.634012 ACACTAGGCAAACCATAGTCAA 57.366 40.909 0.00 0.00 39.06 3.18
44 45 4.775780 ACTACACTAGGCAAACCATAGTCA 59.224 41.667 0.00 0.00 39.06 3.41
45 46 5.127356 AGACTACACTAGGCAAACCATAGTC 59.873 44.000 0.00 0.00 38.26 2.59
46 47 5.024118 AGACTACACTAGGCAAACCATAGT 58.976 41.667 0.00 0.00 35.81 2.12
47 48 5.599999 AGACTACACTAGGCAAACCATAG 57.400 43.478 0.00 0.00 35.81 2.23
48 49 5.361857 GGTAGACTACACTAGGCAAACCATA 59.638 44.000 14.48 0.00 40.18 2.74
49 50 4.161754 GGTAGACTACACTAGGCAAACCAT 59.838 45.833 14.48 0.00 40.18 3.55
50 51 3.512724 GGTAGACTACACTAGGCAAACCA 59.487 47.826 14.48 0.00 40.18 3.67
51 52 3.768215 AGGTAGACTACACTAGGCAAACC 59.232 47.826 14.48 0.00 40.53 3.27
52 53 5.402997 AAGGTAGACTACACTAGGCAAAC 57.597 43.478 14.48 0.00 35.81 2.93
53 54 4.465305 GGAAGGTAGACTACACTAGGCAAA 59.535 45.833 14.48 0.00 35.81 3.68
54 55 4.021916 GGAAGGTAGACTACACTAGGCAA 58.978 47.826 14.48 0.00 35.81 4.52
55 56 3.629087 GGAAGGTAGACTACACTAGGCA 58.371 50.000 14.48 0.00 35.81 4.75
56 57 2.617774 CGGAAGGTAGACTACACTAGGC 59.382 54.545 14.48 0.00 0.00 3.93
57 58 2.617774 GCGGAAGGTAGACTACACTAGG 59.382 54.545 14.48 2.10 0.00 3.02
58 59 3.312973 CAGCGGAAGGTAGACTACACTAG 59.687 52.174 14.48 3.11 41.81 2.57
59 60 3.276857 CAGCGGAAGGTAGACTACACTA 58.723 50.000 14.48 0.00 41.81 2.74
60 61 2.093106 CAGCGGAAGGTAGACTACACT 58.907 52.381 14.48 6.41 41.81 3.55
61 62 1.469423 GCAGCGGAAGGTAGACTACAC 60.469 57.143 14.48 4.28 41.81 2.90
62 63 0.815734 GCAGCGGAAGGTAGACTACA 59.184 55.000 14.48 0.00 41.81 2.74
63 64 0.815734 TGCAGCGGAAGGTAGACTAC 59.184 55.000 3.86 3.86 41.81 2.73
64 65 1.409064 CATGCAGCGGAAGGTAGACTA 59.591 52.381 0.00 0.00 41.81 2.59
65 66 0.176680 CATGCAGCGGAAGGTAGACT 59.823 55.000 0.00 0.00 41.81 3.24
66 67 0.811616 CCATGCAGCGGAAGGTAGAC 60.812 60.000 0.00 0.00 41.81 2.59
67 68 1.264749 ACCATGCAGCGGAAGGTAGA 61.265 55.000 11.77 0.00 41.81 2.59
68 69 0.464036 TACCATGCAGCGGAAGGTAG 59.536 55.000 11.77 0.00 41.81 3.18
69 70 0.906066 TTACCATGCAGCGGAAGGTA 59.094 50.000 11.77 4.71 41.81 3.08
70 71 0.255890 ATTACCATGCAGCGGAAGGT 59.744 50.000 11.77 5.62 46.81 3.50
71 72 2.146342 CTATTACCATGCAGCGGAAGG 58.854 52.381 11.77 0.00 0.00 3.46
72 73 2.146342 CCTATTACCATGCAGCGGAAG 58.854 52.381 11.77 3.93 0.00 3.46
73 74 1.488812 ACCTATTACCATGCAGCGGAA 59.511 47.619 11.77 0.00 0.00 4.30
74 75 1.128200 ACCTATTACCATGCAGCGGA 58.872 50.000 11.77 0.00 0.00 5.54
75 76 1.967319 AACCTATTACCATGCAGCGG 58.033 50.000 3.41 3.41 0.00 5.52
76 77 5.689383 AATAAACCTATTACCATGCAGCG 57.311 39.130 0.00 0.00 0.00 5.18
77 78 7.277174 AGAAATAAACCTATTACCATGCAGC 57.723 36.000 0.00 0.00 0.00 5.25
79 80 9.214957 CGATAGAAATAAACCTATTACCATGCA 57.785 33.333 0.00 0.00 39.76 3.96
80 81 9.216117 ACGATAGAAATAAACCTATTACCATGC 57.784 33.333 0.00 0.00 41.38 4.06
89 90 9.079833 CGAAGACAAACGATAGAAATAAACCTA 57.920 33.333 0.00 0.00 41.38 3.08
90 91 7.816031 TCGAAGACAAACGATAGAAATAAACCT 59.184 33.333 0.00 0.00 41.38 3.50
91 92 7.956558 TCGAAGACAAACGATAGAAATAAACC 58.043 34.615 0.00 0.00 41.38 3.27
92 93 9.801714 TTTCGAAGACAAACGATAGAAATAAAC 57.198 29.630 0.00 0.00 38.30 2.01
93 94 9.801714 GTTTCGAAGACAAACGATAGAAATAAA 57.198 29.630 0.00 0.00 38.30 1.40
94 95 9.199982 AGTTTCGAAGACAAACGATAGAAATAA 57.800 29.630 0.00 0.00 38.54 1.40
95 96 8.752766 AGTTTCGAAGACAAACGATAGAAATA 57.247 30.769 0.00 0.00 38.54 1.40
96 97 7.653767 AGTTTCGAAGACAAACGATAGAAAT 57.346 32.000 0.00 0.00 38.54 2.17
97 98 7.306983 GGAAGTTTCGAAGACAAACGATAGAAA 60.307 37.037 0.00 0.00 38.54 2.52
98 99 6.145048 GGAAGTTTCGAAGACAAACGATAGAA 59.855 38.462 0.00 0.00 38.54 2.10
99 100 5.632347 GGAAGTTTCGAAGACAAACGATAGA 59.368 40.000 0.00 0.00 38.54 1.98
100 101 5.404366 TGGAAGTTTCGAAGACAAACGATAG 59.596 40.000 0.00 0.00 38.54 2.08
101 102 5.176223 GTGGAAGTTTCGAAGACAAACGATA 59.824 40.000 0.00 0.00 38.54 2.92
102 103 4.025145 GTGGAAGTTTCGAAGACAAACGAT 60.025 41.667 0.00 0.00 38.54 3.73
103 104 3.307782 GTGGAAGTTTCGAAGACAAACGA 59.692 43.478 0.00 0.00 38.54 3.85
104 105 3.604392 GTGGAAGTTTCGAAGACAAACG 58.396 45.455 0.00 0.00 38.54 3.60
105 106 3.063045 ACGTGGAAGTTTCGAAGACAAAC 59.937 43.478 0.00 0.00 34.32 2.93
106 107 3.264104 ACGTGGAAGTTTCGAAGACAAA 58.736 40.909 0.00 0.00 34.32 2.83
107 108 2.896168 ACGTGGAAGTTTCGAAGACAA 58.104 42.857 0.00 0.00 34.32 3.18
108 109 2.589798 ACGTGGAAGTTTCGAAGACA 57.410 45.000 0.00 0.00 34.32 3.41
109 110 3.938778 AAACGTGGAAGTTTCGAAGAC 57.061 42.857 0.00 0.18 39.90 3.01
110 111 3.933955 TCAAAACGTGGAAGTTTCGAAGA 59.066 39.130 0.00 0.00 42.81 2.87
111 112 4.267357 TCAAAACGTGGAAGTTTCGAAG 57.733 40.909 0.00 0.00 42.81 3.79
112 113 4.392445 TCTTCAAAACGTGGAAGTTTCGAA 59.608 37.500 18.59 0.00 42.81 3.71
113 114 3.933955 TCTTCAAAACGTGGAAGTTTCGA 59.066 39.130 18.59 0.00 42.81 3.71
114 115 4.026407 GTCTTCAAAACGTGGAAGTTTCG 58.974 43.478 18.59 0.00 42.81 3.46
115 116 5.231265 AGTCTTCAAAACGTGGAAGTTTC 57.769 39.130 18.59 12.78 42.81 2.78
116 117 5.638596 AAGTCTTCAAAACGTGGAAGTTT 57.361 34.783 18.59 13.58 45.21 2.66
117 118 5.182380 TGAAAGTCTTCAAAACGTGGAAGTT 59.818 36.000 18.59 10.09 38.65 2.66
118 119 4.698304 TGAAAGTCTTCAAAACGTGGAAGT 59.302 37.500 18.59 5.54 38.65 3.01
119 120 5.229921 TGAAAGTCTTCAAAACGTGGAAG 57.770 39.130 15.10 15.10 38.65 3.46
120 121 5.828299 ATGAAAGTCTTCAAAACGTGGAA 57.172 34.783 0.00 0.00 44.64 3.53
121 122 6.928979 TTATGAAAGTCTTCAAAACGTGGA 57.071 33.333 0.00 0.00 44.64 4.02
122 123 7.979115 TTTTATGAAAGTCTTCAAAACGTGG 57.021 32.000 0.00 0.00 44.64 4.94
124 125 8.953990 CGATTTTTATGAAAGTCTTCAAAACGT 58.046 29.630 4.37 0.00 44.64 3.99
125 126 7.939386 GCGATTTTTATGAAAGTCTTCAAAACG 59.061 33.333 4.37 0.00 44.64 3.60
126 127 8.214472 GGCGATTTTTATGAAAGTCTTCAAAAC 58.786 33.333 4.37 0.00 44.64 2.43
127 128 8.141268 AGGCGATTTTTATGAAAGTCTTCAAAA 58.859 29.630 4.37 0.00 44.64 2.44
128 129 7.657336 AGGCGATTTTTATGAAAGTCTTCAAA 58.343 30.769 4.37 0.00 44.64 2.69
129 130 7.214467 AGGCGATTTTTATGAAAGTCTTCAA 57.786 32.000 4.37 0.00 44.64 2.69
130 131 6.817765 AGGCGATTTTTATGAAAGTCTTCA 57.182 33.333 4.37 0.00 45.53 3.02
131 132 9.439537 GAATAGGCGATTTTTATGAAAGTCTTC 57.560 33.333 4.37 0.00 31.44 2.87
132 133 8.956426 TGAATAGGCGATTTTTATGAAAGTCTT 58.044 29.630 4.37 0.00 31.44 3.01
133 134 8.398665 GTGAATAGGCGATTTTTATGAAAGTCT 58.601 33.333 4.37 0.00 31.44 3.24
134 135 7.644157 GGTGAATAGGCGATTTTTATGAAAGTC 59.356 37.037 0.00 0.00 0.00 3.01
135 136 7.416326 GGGTGAATAGGCGATTTTTATGAAAGT 60.416 37.037 0.00 0.00 0.00 2.66
136 137 6.918022 GGGTGAATAGGCGATTTTTATGAAAG 59.082 38.462 0.00 0.00 0.00 2.62
137 138 6.183360 GGGGTGAATAGGCGATTTTTATGAAA 60.183 38.462 0.00 0.00 0.00 2.69
138 139 5.300792 GGGGTGAATAGGCGATTTTTATGAA 59.699 40.000 0.00 0.00 0.00 2.57
139 140 4.825085 GGGGTGAATAGGCGATTTTTATGA 59.175 41.667 0.00 0.00 0.00 2.15
140 141 4.022329 GGGGGTGAATAGGCGATTTTTATG 60.022 45.833 0.00 0.00 0.00 1.90
141 142 4.149598 GGGGGTGAATAGGCGATTTTTAT 58.850 43.478 0.00 0.00 0.00 1.40
142 143 3.558033 GGGGGTGAATAGGCGATTTTTA 58.442 45.455 0.00 0.00 0.00 1.52
143 144 2.384828 GGGGGTGAATAGGCGATTTTT 58.615 47.619 0.00 0.00 0.00 1.94
144 145 2.067365 GGGGGTGAATAGGCGATTTT 57.933 50.000 0.00 0.00 0.00 1.82
145 146 3.821306 GGGGGTGAATAGGCGATTT 57.179 52.632 0.00 0.00 0.00 2.17
161 162 2.422832 GCGTTATATCGACTAGAGGGGG 59.577 54.545 7.38 0.00 0.00 5.40
162 163 3.079578 TGCGTTATATCGACTAGAGGGG 58.920 50.000 7.38 0.00 0.00 4.79
163 164 3.752222 AGTGCGTTATATCGACTAGAGGG 59.248 47.826 7.38 0.00 0.00 4.30
164 165 5.359716 AAGTGCGTTATATCGACTAGAGG 57.640 43.478 7.38 0.00 0.00 3.69
165 166 6.427974 TGAAAGTGCGTTATATCGACTAGAG 58.572 40.000 7.38 0.00 0.00 2.43
166 167 6.367686 TGAAAGTGCGTTATATCGACTAGA 57.632 37.500 7.38 0.00 0.00 2.43
167 168 6.471198 TGTTGAAAGTGCGTTATATCGACTAG 59.529 38.462 7.38 0.00 0.00 2.57
168 169 6.324042 TGTTGAAAGTGCGTTATATCGACTA 58.676 36.000 7.38 0.00 0.00 2.59
169 170 5.165676 TGTTGAAAGTGCGTTATATCGACT 58.834 37.500 7.38 5.26 0.00 4.18
170 171 5.444586 TGTTGAAAGTGCGTTATATCGAC 57.555 39.130 7.38 3.28 0.00 4.20
171 172 6.311690 TCAATGTTGAAAGTGCGTTATATCGA 59.688 34.615 7.38 0.00 33.55 3.59
172 173 6.474364 TCAATGTTGAAAGTGCGTTATATCG 58.526 36.000 0.00 0.00 33.55 2.92
173 174 8.338259 AGATCAATGTTGAAAGTGCGTTATATC 58.662 33.333 0.00 0.00 41.13 1.63
174 175 8.213518 AGATCAATGTTGAAAGTGCGTTATAT 57.786 30.769 0.00 0.00 41.13 0.86
175 176 7.609760 AGATCAATGTTGAAAGTGCGTTATA 57.390 32.000 0.00 0.00 41.13 0.98
176 177 6.500684 AGATCAATGTTGAAAGTGCGTTAT 57.499 33.333 0.00 0.00 41.13 1.89
177 178 5.940192 AGATCAATGTTGAAAGTGCGTTA 57.060 34.783 0.00 0.00 41.13 3.18
178 179 4.836125 AGATCAATGTTGAAAGTGCGTT 57.164 36.364 0.00 0.00 41.13 4.84
179 180 4.836125 AAGATCAATGTTGAAAGTGCGT 57.164 36.364 0.00 0.00 41.13 5.24
180 181 4.143473 GCAAAGATCAATGTTGAAAGTGCG 60.143 41.667 0.00 0.00 41.13 5.34
181 182 4.986659 AGCAAAGATCAATGTTGAAAGTGC 59.013 37.500 0.00 7.50 41.13 4.40
182 183 7.010738 ACAAAGCAAAGATCAATGTTGAAAGTG 59.989 33.333 0.00 0.00 41.13 3.16
183 184 7.043565 ACAAAGCAAAGATCAATGTTGAAAGT 58.956 30.769 0.00 0.00 41.13 2.66
184 185 7.306983 GGACAAAGCAAAGATCAATGTTGAAAG 60.307 37.037 0.00 0.00 41.13 2.62
185 186 6.479660 GGACAAAGCAAAGATCAATGTTGAAA 59.520 34.615 0.00 0.00 41.13 2.69
186 187 5.984926 GGACAAAGCAAAGATCAATGTTGAA 59.015 36.000 0.00 0.00 41.13 2.69
187 188 5.509501 GGGACAAAGCAAAGATCAATGTTGA 60.510 40.000 0.00 0.00 42.14 3.18
188 189 4.687483 GGGACAAAGCAAAGATCAATGTTG 59.313 41.667 0.00 0.00 0.00 3.33
189 190 4.262592 GGGGACAAAGCAAAGATCAATGTT 60.263 41.667 0.00 0.00 0.00 2.71
301 302 9.752961 CATTAACTCATATTTGATGGATTTGCA 57.247 29.630 0.00 0.00 0.00 4.08
396 397 3.945640 ATGGTTGTTACCCTATGGTCC 57.054 47.619 0.00 0.00 43.06 4.46
455 456 3.214328 GGTGCCAAGAACTTTCTCTTCA 58.786 45.455 0.00 0.00 36.28 3.02
509 510 1.556911 GGGCCTTGTCAGATTCAGAGA 59.443 52.381 0.84 0.00 0.00 3.10
647 650 2.154798 GACTGGCACGCCACTCACTA 62.155 60.000 6.67 0.00 41.89 2.74
674 677 9.238368 TCGGTTCCATCTAAAGTGAAAATATTT 57.762 29.630 0.00 0.00 0.00 1.40
790 793 8.404889 TGCATACAAATTCATTATCAAAACCG 57.595 30.769 0.00 0.00 0.00 4.44
851 854 2.940994 TGGAGGATTTTTGGACGTGA 57.059 45.000 0.00 0.00 0.00 4.35
856 859 4.887071 CACGGAATATGGAGGATTTTTGGA 59.113 41.667 0.00 0.00 0.00 3.53
880 883 2.344741 GGAAGCAACTAGTTAACGAGCG 59.655 50.000 14.82 8.20 0.00 5.03
883 886 4.859304 TCTGGAAGCAACTAGTTAACGA 57.141 40.909 8.04 0.00 0.00 3.85
884 887 5.917541 TTTCTGGAAGCAACTAGTTAACG 57.082 39.130 8.04 0.00 0.00 3.18
885 888 8.451748 CCTAATTTCTGGAAGCAACTAGTTAAC 58.548 37.037 8.04 3.72 0.00 2.01
886 889 8.161425 ACCTAATTTCTGGAAGCAACTAGTTAA 58.839 33.333 8.04 0.00 0.00 2.01
887 890 7.686434 ACCTAATTTCTGGAAGCAACTAGTTA 58.314 34.615 8.04 0.00 0.00 2.24
888 891 6.543735 ACCTAATTTCTGGAAGCAACTAGTT 58.456 36.000 1.12 1.12 0.00 2.24
889 892 6.128138 ACCTAATTTCTGGAAGCAACTAGT 57.872 37.500 0.00 0.00 0.00 2.57
890 893 5.292101 CGACCTAATTTCTGGAAGCAACTAG 59.708 44.000 0.00 0.00 0.00 2.57
891 894 5.175859 CGACCTAATTTCTGGAAGCAACTA 58.824 41.667 0.00 0.00 0.00 2.24
892 895 4.003648 CGACCTAATTTCTGGAAGCAACT 58.996 43.478 0.00 0.00 0.00 3.16
893 896 3.426292 GCGACCTAATTTCTGGAAGCAAC 60.426 47.826 0.00 0.00 32.81 4.17
894 897 2.747446 GCGACCTAATTTCTGGAAGCAA 59.253 45.455 0.00 0.00 32.81 3.91
895 898 2.290008 TGCGACCTAATTTCTGGAAGCA 60.290 45.455 0.00 11.33 37.12 3.91
896 899 2.356135 TGCGACCTAATTTCTGGAAGC 58.644 47.619 0.00 0.00 0.00 3.86
897 900 4.191544 TGATGCGACCTAATTTCTGGAAG 58.808 43.478 0.00 0.00 0.00 3.46
898 901 4.214986 TGATGCGACCTAATTTCTGGAA 57.785 40.909 0.00 0.00 0.00 3.53
899 902 3.904800 TGATGCGACCTAATTTCTGGA 57.095 42.857 0.00 0.00 0.00 3.86
900 903 3.065371 GGTTGATGCGACCTAATTTCTGG 59.935 47.826 0.00 0.00 35.15 3.86
901 904 3.689161 TGGTTGATGCGACCTAATTTCTG 59.311 43.478 5.51 0.00 38.66 3.02
902 905 3.950397 TGGTTGATGCGACCTAATTTCT 58.050 40.909 5.51 0.00 38.66 2.52
903 906 4.498009 CCATGGTTGATGCGACCTAATTTC 60.498 45.833 2.57 0.00 38.66 2.17
904 907 3.381272 CCATGGTTGATGCGACCTAATTT 59.619 43.478 2.57 0.00 38.66 1.82
905 908 2.951642 CCATGGTTGATGCGACCTAATT 59.048 45.455 2.57 0.00 38.66 1.40
906 909 2.092429 ACCATGGTTGATGCGACCTAAT 60.092 45.455 13.00 0.00 38.66 1.73
907 910 1.280710 ACCATGGTTGATGCGACCTAA 59.719 47.619 13.00 0.00 38.66 2.69
908 911 0.908910 ACCATGGTTGATGCGACCTA 59.091 50.000 13.00 0.00 38.66 3.08
918 921 4.082245 GGAACTGGACATAAACCATGGTTG 60.082 45.833 30.44 20.98 39.13 3.77
1246 1252 0.836400 AGGGAGTTGGCGAGGAAAGA 60.836 55.000 0.00 0.00 0.00 2.52
1557 1563 3.723235 ATAGGTGGTGAGCAGCGCG 62.723 63.158 8.25 0.00 39.95 6.86
1757 1763 3.560251 AGTTCACGGCCAGCCTGT 61.560 61.111 2.24 3.79 0.00 4.00
1765 1771 1.857364 CCACGTAACAGTTCACGGC 59.143 57.895 15.29 0.00 42.35 5.68
1788 1794 2.159226 GGTGTACATCTCTACAAGCGCT 60.159 50.000 2.64 2.64 0.00 5.92
1869 1875 1.298863 CATGGCATTGTAGCAGCGC 60.299 57.895 0.00 0.00 35.83 5.92
1961 1967 0.248907 CGTGACGCTATCAATCGGGT 60.249 55.000 0.00 0.00 39.72 5.28
1966 1972 0.175760 AGCACCGTGACGCTATCAAT 59.824 50.000 1.65 0.00 39.72 2.57
2010 2016 0.251297 CTTCATCCACCAACCCAGCA 60.251 55.000 0.00 0.00 0.00 4.41
2046 2052 4.540099 ACCCCAAACTGAATCTCCATTCTA 59.460 41.667 0.00 0.00 39.49 2.10
2140 2146 2.370189 CCATCCCTCGGATAAGCTTCTT 59.630 50.000 0.00 0.00 40.98 2.52
2312 2318 4.219115 GTCCTCCCATAGTCTCATTCTCA 58.781 47.826 0.00 0.00 0.00 3.27
2385 2391 4.330056 TCAAGGAGGCTTGACCCA 57.670 55.556 0.00 0.00 40.58 4.51
2409 2415 2.738846 CAAGAACTCATGGAGAACACCG 59.261 50.000 0.00 0.00 33.32 4.94
2466 2472 2.380084 TCTCTTGAACCATGGCGTAC 57.620 50.000 13.04 1.21 0.00 3.67
2880 2886 0.876777 TTCGTGTTCATGACGCCGTT 60.877 50.000 0.00 0.00 36.75 4.44
2889 2895 2.034879 CCGGCTGCTTCGTGTTCAT 61.035 57.895 0.00 0.00 0.00 2.57
3001 3007 8.510243 TGACACTTGATATTGCAACATTATCT 57.490 30.769 15.90 0.00 31.77 1.98
3002 3008 9.229784 CTTGACACTTGATATTGCAACATTATC 57.770 33.333 0.00 6.44 31.39 1.75
3015 3021 5.545063 TCCTTGACACTTGACACTTGATA 57.455 39.130 0.00 0.00 0.00 2.15
3016 3022 4.422073 TCCTTGACACTTGACACTTGAT 57.578 40.909 0.00 0.00 0.00 2.57
3017 3023 3.904800 TCCTTGACACTTGACACTTGA 57.095 42.857 0.00 0.00 0.00 3.02
3018 3024 4.129380 TCATCCTTGACACTTGACACTTG 58.871 43.478 0.00 0.00 0.00 3.16
3019 3025 4.101585 TCTCATCCTTGACACTTGACACTT 59.898 41.667 0.00 0.00 0.00 3.16
3020 3026 3.643320 TCTCATCCTTGACACTTGACACT 59.357 43.478 0.00 0.00 0.00 3.55
3021 3027 3.995199 TCTCATCCTTGACACTTGACAC 58.005 45.455 0.00 0.00 0.00 3.67
3115 3122 9.865152 TCCCAATGAATCTATCAATAACATTCA 57.135 29.630 0.00 0.00 42.54 2.57
3195 3202 2.830923 CCCATACAGTTTGATTGGCCAA 59.169 45.455 23.00 23.00 0.00 4.52
3227 3234 1.153369 GCTCCGCCACTGAATGCTA 60.153 57.895 0.00 0.00 0.00 3.49
3240 3247 2.160417 CAGCTTTTCTTTGGTAGCTCCG 59.840 50.000 0.00 0.00 41.76 4.63
3262 3269 1.476845 TTTCTACTCTGTGGCCCGCA 61.477 55.000 0.00 0.00 0.00 5.69
3317 3333 9.188588 CTGAAGCAAAAATAATAATCGCATGAT 57.811 29.630 0.00 0.00 35.98 2.45
3322 3338 7.166473 CAGGACTGAAGCAAAAATAATAATCGC 59.834 37.037 0.00 0.00 0.00 4.58
3324 3340 7.922811 CCCAGGACTGAAGCAAAAATAATAATC 59.077 37.037 0.00 0.00 0.00 1.75
3383 3399 1.262417 TGTCATGCTAACACCGGAGA 58.738 50.000 9.46 0.00 0.00 3.71
3385 3401 1.070914 TGTTGTCATGCTAACACCGGA 59.929 47.619 9.46 0.00 32.30 5.14
3399 3415 2.494059 TGAGCTAAGCAGGTTGTTGTC 58.506 47.619 0.00 0.00 30.99 3.18
3408 3424 4.070009 TGGCATATTCATGAGCTAAGCAG 58.930 43.478 13.29 0.00 33.67 4.24
3413 3429 4.961438 TCTGTGGCATATTCATGAGCTA 57.039 40.909 4.84 0.00 33.67 3.32
3559 3576 3.976169 TGTCAACATGCTGGCTTTTAAC 58.024 40.909 1.92 0.00 0.00 2.01
3721 3742 0.319211 CAACCACACCTTCGCGTAGA 60.319 55.000 14.87 0.00 0.00 2.59
3736 3757 4.590850 AAAACTTGATCTTGCTCCAACC 57.409 40.909 0.00 0.00 0.00 3.77
3765 3786 4.442052 CGGAGCCATTCACTCTATTTCTCA 60.442 45.833 0.00 0.00 34.46 3.27


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

AutoCloner maintained by Alex Coulton.