Multiple sequence alignment - TraesCS3B01G231300

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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 TraesCS3B01G231300 chr3B 100.000 2147 0 0 1 2147 349745653 349747799 0.000000e+00 3965
1 TraesCS3B01G231300 chr3B 95.526 1453 60 3 700 2147 201534419 201532967 0.000000e+00 2318
2 TraesCS3B01G231300 chr3B 92.784 194 14 0 1 194 349655986 349656179 4.510000e-72 281
3 TraesCS3B01G231300 chr5D 93.781 1994 82 18 195 2147 503226148 503224156 0.000000e+00 2957
4 TraesCS3B01G231300 chr5D 95.530 1454 58 5 700 2147 503270937 503272389 0.000000e+00 2318
5 TraesCS3B01G231300 chr5D 95.320 1453 62 4 700 2147 503235924 503234473 0.000000e+00 2302
6 TraesCS3B01G231300 chr5D 92.603 1460 67 17 195 1614 503240714 503239256 0.000000e+00 2060
7 TraesCS3B01G231300 chr5D 92.192 1460 72 18 195 1614 503230932 503229475 0.000000e+00 2026
8 TraesCS3B01G231300 chr5D 94.971 517 20 4 195 706 503236465 503235950 0.000000e+00 806
9 TraesCS3B01G231300 chr5D 94.971 517 20 4 195 706 503270396 503270911 0.000000e+00 806
10 TraesCS3B01G231300 chr5B 92.420 1992 104 20 195 2147 432717685 432715702 0.000000e+00 2798
11 TraesCS3B01G231300 chr3D 93.307 1778 79 18 195 1934 589267989 589269764 0.000000e+00 2588
12 TraesCS3B01G231300 chr3A 95.458 1453 60 4 700 2147 66010233 66011684 0.000000e+00 2313
13 TraesCS3B01G231300 chrUn 95.110 1452 67 3 700 2147 216511218 216512669 0.000000e+00 2285
14 TraesCS3B01G231300 chrUn 95.110 1452 67 3 700 2147 286272165 286270714 0.000000e+00 2285
15 TraesCS3B01G231300 chr6D 95.045 1453 67 3 700 2147 458922704 458921252 0.000000e+00 2279
16 TraesCS3B01G231300 chr6D 92.671 1460 66 17 195 1614 389252607 389251149 0.000000e+00 2065
17 TraesCS3B01G231300 chr6D 85.128 195 26 3 1 193 69554169 69554362 1.680000e-46 196
18 TraesCS3B01G231300 chr6D 85.128 195 26 3 1 193 422465683 422465876 1.680000e-46 196
19 TraesCS3B01G231300 chr1A 94.976 1453 68 3 700 2147 278526850 278528302 0.000000e+00 2274
20 TraesCS3B01G231300 chr2A 91.548 1266 65 18 195 1421 335842752 335841490 0.000000e+00 1707
21 TraesCS3B01G231300 chr2D 88.889 189 20 1 7 194 344624557 344624369 4.610000e-57 231
22 TraesCS3B01G231300 chr2B 87.179 195 24 1 1 194 370844563 370844757 9.970000e-54 220
23 TraesCS3B01G231300 chr7B 86.224 196 26 1 1 195 391854729 391854924 6.000000e-51 211
24 TraesCS3B01G231300 chr7A 86.224 196 26 1 1 195 412003106 412003301 6.000000e-51 211
25 TraesCS3B01G231300 chr4D 86.294 197 21 5 1 195 243491654 243491846 2.160000e-50 209
26 TraesCS3B01G231300 chr4D 85.641 195 25 3 1 193 387903361 387903168 3.610000e-48 202


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 TraesCS3B01G231300 chr3B 349745653 349747799 2146 False 3965.0 3965 100.0000 1 2147 1 chr3B.!!$F2 2146
1 TraesCS3B01G231300 chr3B 201532967 201534419 1452 True 2318.0 2318 95.5260 700 2147 1 chr3B.!!$R1 1447
2 TraesCS3B01G231300 chr5D 503224156 503240714 16558 True 2030.2 2957 93.7734 195 2147 5 chr5D.!!$R1 1952
3 TraesCS3B01G231300 chr5D 503270396 503272389 1993 False 1562.0 2318 95.2505 195 2147 2 chr5D.!!$F1 1952
4 TraesCS3B01G231300 chr5B 432715702 432717685 1983 True 2798.0 2798 92.4200 195 2147 1 chr5B.!!$R1 1952
5 TraesCS3B01G231300 chr3D 589267989 589269764 1775 False 2588.0 2588 93.3070 195 1934 1 chr3D.!!$F1 1739
6 TraesCS3B01G231300 chr3A 66010233 66011684 1451 False 2313.0 2313 95.4580 700 2147 1 chr3A.!!$F1 1447
7 TraesCS3B01G231300 chrUn 216511218 216512669 1451 False 2285.0 2285 95.1100 700 2147 1 chrUn.!!$F1 1447
8 TraesCS3B01G231300 chrUn 286270714 286272165 1451 True 2285.0 2285 95.1100 700 2147 1 chrUn.!!$R1 1447
9 TraesCS3B01G231300 chr6D 458921252 458922704 1452 True 2279.0 2279 95.0450 700 2147 1 chr6D.!!$R2 1447
10 TraesCS3B01G231300 chr6D 389251149 389252607 1458 True 2065.0 2065 92.6710 195 1614 1 chr6D.!!$R1 1419
11 TraesCS3B01G231300 chr1A 278526850 278528302 1452 False 2274.0 2274 94.9760 700 2147 1 chr1A.!!$F1 1447
12 TraesCS3B01G231300 chr2A 335841490 335842752 1262 True 1707.0 1707 91.5480 195 1421 1 chr2A.!!$R1 1226

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
34 35 0.027194 CCATCAAGTCGAAGCATGCG 59.973 55.0 13.01 0.0 39.81 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 16081 0.461961 CCTCGAGAGGGCTTAGTTGG 59.538 60.0 15.71 0.0 44.87 3.77 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
17 18 2.930019 CCTGACAGCTGGGACCCA 60.930 66.667 19.93 14.08 0.00 4.51
18 19 2.304056 CCTGACAGCTGGGACCCAT 61.304 63.158 19.93 0.00 30.82 4.00
19 20 1.222936 CTGACAGCTGGGACCCATC 59.777 63.158 19.93 10.53 30.82 3.51
20 21 1.538629 TGACAGCTGGGACCCATCA 60.539 57.895 19.93 12.28 30.82 3.07
21 22 1.133181 TGACAGCTGGGACCCATCAA 61.133 55.000 19.93 0.00 30.82 2.57
22 23 0.393537 GACAGCTGGGACCCATCAAG 60.394 60.000 19.93 9.41 30.82 3.02
23 24 1.136329 ACAGCTGGGACCCATCAAGT 61.136 55.000 19.93 10.08 30.82 3.16
24 25 0.393537 CAGCTGGGACCCATCAAGTC 60.394 60.000 15.39 0.00 30.82 3.01
25 26 1.450312 GCTGGGACCCATCAAGTCG 60.450 63.158 15.39 0.87 34.97 4.18
26 27 1.899437 GCTGGGACCCATCAAGTCGA 61.899 60.000 15.39 0.00 34.97 4.20
27 28 0.613260 CTGGGACCCATCAAGTCGAA 59.387 55.000 15.39 0.00 34.97 3.71
28 29 0.613260 TGGGACCCATCAAGTCGAAG 59.387 55.000 9.95 0.00 34.97 3.79
29 30 0.744771 GGGACCCATCAAGTCGAAGC 60.745 60.000 5.33 0.00 34.97 3.86
30 31 0.036388 GGACCCATCAAGTCGAAGCA 60.036 55.000 0.00 0.00 34.97 3.91
31 32 1.407437 GGACCCATCAAGTCGAAGCAT 60.407 52.381 0.00 0.00 34.97 3.79
32 33 1.667724 GACCCATCAAGTCGAAGCATG 59.332 52.381 0.00 0.00 0.00 4.06
33 34 0.379669 CCCATCAAGTCGAAGCATGC 59.620 55.000 10.51 10.51 0.00 4.06
34 35 0.027194 CCATCAAGTCGAAGCATGCG 59.973 55.000 13.01 0.00 39.81 4.73
35 36 0.723414 CATCAAGTCGAAGCATGCGT 59.277 50.000 13.01 9.49 39.14 5.24
36 37 1.926510 CATCAAGTCGAAGCATGCGTA 59.073 47.619 13.01 0.00 39.14 4.42
37 38 1.629013 TCAAGTCGAAGCATGCGTAG 58.371 50.000 13.01 9.94 39.14 3.51
54 55 3.785599 CGTAGCGTTATCTGTCTAGTCG 58.214 50.000 0.00 0.00 0.00 4.18
55 56 2.759538 AGCGTTATCTGTCTAGTCGC 57.240 50.000 0.00 0.00 41.96 5.19
56 57 1.003759 AGCGTTATCTGTCTAGTCGCG 60.004 52.381 0.00 0.00 45.32 5.87
57 58 1.004185 GCGTTATCTGTCTAGTCGCGA 60.004 52.381 3.71 3.71 33.59 5.87
58 59 2.538333 GCGTTATCTGTCTAGTCGCGAA 60.538 50.000 12.06 0.00 33.59 4.70
59 60 3.027710 CGTTATCTGTCTAGTCGCGAAC 58.972 50.000 12.06 5.95 0.00 3.95
60 61 3.484721 CGTTATCTGTCTAGTCGCGAACA 60.485 47.826 12.06 11.18 0.00 3.18
61 62 4.599047 GTTATCTGTCTAGTCGCGAACAT 58.401 43.478 12.06 2.05 0.00 2.71
62 63 2.544480 TCTGTCTAGTCGCGAACATG 57.456 50.000 12.06 6.12 0.00 3.21
63 64 1.810755 TCTGTCTAGTCGCGAACATGT 59.189 47.619 12.06 0.00 0.00 3.21
64 65 3.004862 TCTGTCTAGTCGCGAACATGTA 58.995 45.455 12.06 0.00 0.00 2.29
65 66 3.099362 CTGTCTAGTCGCGAACATGTAC 58.901 50.000 12.06 5.48 0.00 2.90
66 67 2.099621 GTCTAGTCGCGAACATGTACG 58.900 52.381 12.06 3.98 0.00 3.67
67 68 1.733912 TCTAGTCGCGAACATGTACGT 59.266 47.619 12.06 0.00 0.00 3.57
68 69 2.929398 TCTAGTCGCGAACATGTACGTA 59.071 45.455 12.06 0.00 0.00 3.57
69 70 1.887320 AGTCGCGAACATGTACGTAC 58.113 50.000 18.90 18.90 0.00 3.67
70 71 1.197492 AGTCGCGAACATGTACGTACA 59.803 47.619 29.15 29.15 40.98 2.90
72 73 3.063861 AGTCGCGAACATGTACGTACATA 59.936 43.478 34.24 18.45 44.57 2.29
73 74 3.416674 GTCGCGAACATGTACGTACATAG 59.583 47.826 34.24 28.46 44.57 2.23
74 75 2.150611 CGCGAACATGTACGTACATAGC 59.849 50.000 34.24 30.70 44.57 2.97
75 76 2.150611 GCGAACATGTACGTACATAGCG 59.849 50.000 34.24 32.43 44.57 4.26
76 77 3.610495 CGAACATGTACGTACATAGCGA 58.390 45.455 34.24 11.84 44.57 4.93
77 78 4.216731 CGAACATGTACGTACATAGCGAT 58.783 43.478 34.24 20.20 44.57 4.58
78 79 4.673761 CGAACATGTACGTACATAGCGATT 59.326 41.667 34.24 23.53 44.57 3.34
79 80 5.386019 CGAACATGTACGTACATAGCGATTG 60.386 44.000 34.24 25.28 44.57 2.67
80 81 5.177725 ACATGTACGTACATAGCGATTGA 57.822 39.130 34.24 8.98 44.57 2.57
81 82 5.769367 ACATGTACGTACATAGCGATTGAT 58.231 37.500 34.24 12.36 44.57 2.57
82 83 6.213677 ACATGTACGTACATAGCGATTGATT 58.786 36.000 34.24 11.86 44.57 2.57
83 84 6.143919 ACATGTACGTACATAGCGATTGATTG 59.856 38.462 34.24 23.00 44.57 2.67
84 85 4.979815 TGTACGTACATAGCGATTGATTGG 59.020 41.667 24.10 0.00 0.00 3.16
85 86 4.054780 ACGTACATAGCGATTGATTGGT 57.945 40.909 0.00 0.00 0.00 3.67
86 87 4.049186 ACGTACATAGCGATTGATTGGTC 58.951 43.478 0.00 0.00 0.00 4.02
87 88 4.202121 ACGTACATAGCGATTGATTGGTCT 60.202 41.667 0.00 0.00 0.00 3.85
88 89 4.383052 CGTACATAGCGATTGATTGGTCTC 59.617 45.833 0.00 0.00 0.00 3.36
89 90 4.679373 ACATAGCGATTGATTGGTCTCT 57.321 40.909 0.00 0.00 0.00 3.10
90 91 4.626042 ACATAGCGATTGATTGGTCTCTC 58.374 43.478 0.00 0.00 0.00 3.20
91 92 4.343526 ACATAGCGATTGATTGGTCTCTCT 59.656 41.667 0.00 0.00 0.00 3.10
92 93 3.176552 AGCGATTGATTGGTCTCTCTG 57.823 47.619 0.00 0.00 0.00 3.35
93 94 1.596727 GCGATTGATTGGTCTCTCTGC 59.403 52.381 0.00 0.00 0.00 4.26
94 95 1.857217 CGATTGATTGGTCTCTCTGCG 59.143 52.381 0.00 0.00 0.00 5.18
95 96 2.208431 GATTGATTGGTCTCTCTGCGG 58.792 52.381 0.00 0.00 0.00 5.69
96 97 0.391661 TTGATTGGTCTCTCTGCGGC 60.392 55.000 0.00 0.00 0.00 6.53
97 98 1.880340 GATTGGTCTCTCTGCGGCG 60.880 63.158 0.51 0.51 0.00 6.46
98 99 2.284798 GATTGGTCTCTCTGCGGCGA 62.285 60.000 12.98 0.00 0.00 5.54
99 100 1.680522 ATTGGTCTCTCTGCGGCGAT 61.681 55.000 12.98 0.00 0.00 4.58
100 101 2.279120 GGTCTCTCTGCGGCGATG 60.279 66.667 12.98 1.33 0.00 3.84
101 102 2.775856 GGTCTCTCTGCGGCGATGA 61.776 63.158 12.98 6.59 0.00 2.92
102 103 1.139734 GTCTCTCTGCGGCGATGAA 59.860 57.895 12.98 0.00 0.00 2.57
103 104 1.139734 TCTCTCTGCGGCGATGAAC 59.860 57.895 12.98 0.00 0.00 3.18
104 105 1.880340 CTCTCTGCGGCGATGAACC 60.880 63.158 12.98 0.00 0.00 3.62
105 106 2.125552 CTCTGCGGCGATGAACCA 60.126 61.111 12.98 0.00 0.00 3.67
106 107 1.522355 CTCTGCGGCGATGAACCAT 60.522 57.895 12.98 0.00 0.00 3.55
107 108 1.769098 CTCTGCGGCGATGAACCATG 61.769 60.000 12.98 0.00 0.00 3.66
108 109 2.823593 TGCGGCGATGAACCATGG 60.824 61.111 12.98 11.19 0.00 3.66
109 110 4.256090 GCGGCGATGAACCATGGC 62.256 66.667 12.98 5.54 43.17 4.40
112 113 2.513666 GCGATGAACCATGGCCGA 60.514 61.111 13.04 0.00 39.16 5.54
113 114 2.537560 GCGATGAACCATGGCCGAG 61.538 63.158 13.04 0.00 39.16 4.63
114 115 1.153369 CGATGAACCATGGCCGAGT 60.153 57.895 13.04 0.00 0.00 4.18
115 116 0.104120 CGATGAACCATGGCCGAGTA 59.896 55.000 13.04 0.00 0.00 2.59
116 117 1.472552 CGATGAACCATGGCCGAGTAA 60.473 52.381 13.04 0.00 0.00 2.24
117 118 2.213499 GATGAACCATGGCCGAGTAAG 58.787 52.381 13.04 0.00 0.00 2.34
118 119 0.251916 TGAACCATGGCCGAGTAAGG 59.748 55.000 13.04 0.00 0.00 2.69
119 120 0.539986 GAACCATGGCCGAGTAAGGA 59.460 55.000 13.04 0.00 0.00 3.36
120 121 0.541863 AACCATGGCCGAGTAAGGAG 59.458 55.000 13.04 0.00 0.00 3.69
121 122 0.617820 ACCATGGCCGAGTAAGGAGT 60.618 55.000 13.04 0.00 0.00 3.85
122 123 0.179073 CCATGGCCGAGTAAGGAGTG 60.179 60.000 0.00 0.00 0.00 3.51
123 124 0.824109 CATGGCCGAGTAAGGAGTGA 59.176 55.000 0.00 0.00 0.00 3.41
124 125 0.824759 ATGGCCGAGTAAGGAGTGAC 59.175 55.000 0.00 0.00 0.00 3.67
125 126 0.541063 TGGCCGAGTAAGGAGTGACA 60.541 55.000 0.00 0.00 0.00 3.58
126 127 0.108756 GGCCGAGTAAGGAGTGACAC 60.109 60.000 0.00 0.00 0.00 3.67
127 128 0.601558 GCCGAGTAAGGAGTGACACA 59.398 55.000 8.59 0.00 0.00 3.72
128 129 1.204941 GCCGAGTAAGGAGTGACACAT 59.795 52.381 8.59 0.00 0.00 3.21
129 130 2.881074 CCGAGTAAGGAGTGACACATG 58.119 52.381 8.59 0.00 0.00 3.21
130 131 2.231478 CCGAGTAAGGAGTGACACATGT 59.769 50.000 8.59 0.00 0.00 3.21
131 132 3.502920 CGAGTAAGGAGTGACACATGTC 58.497 50.000 8.59 5.02 44.97 3.06
142 143 3.067721 GACACATGTCGTAGTAGAGCC 57.932 52.381 0.00 0.00 35.12 4.70
143 144 1.400846 ACACATGTCGTAGTAGAGCCG 59.599 52.381 0.00 0.00 0.00 5.52
144 145 0.381089 ACATGTCGTAGTAGAGCCGC 59.619 55.000 0.00 0.00 0.00 6.53
145 146 0.317938 CATGTCGTAGTAGAGCCGCC 60.318 60.000 0.00 0.00 0.00 6.13
146 147 0.750546 ATGTCGTAGTAGAGCCGCCA 60.751 55.000 0.00 0.00 0.00 5.69
147 148 0.750546 TGTCGTAGTAGAGCCGCCAT 60.751 55.000 0.00 0.00 0.00 4.40
148 149 0.317938 GTCGTAGTAGAGCCGCCATG 60.318 60.000 0.00 0.00 0.00 3.66
149 150 0.750546 TCGTAGTAGAGCCGCCATGT 60.751 55.000 0.00 0.00 0.00 3.21
150 151 0.949397 CGTAGTAGAGCCGCCATGTA 59.051 55.000 0.00 0.00 0.00 2.29
151 152 1.069159 CGTAGTAGAGCCGCCATGTAG 60.069 57.143 0.00 0.00 0.00 2.74
152 153 0.959553 TAGTAGAGCCGCCATGTAGC 59.040 55.000 0.00 0.00 0.00 3.58
153 154 1.043116 AGTAGAGCCGCCATGTAGCA 61.043 55.000 0.00 0.00 0.00 3.49
154 155 0.034059 GTAGAGCCGCCATGTAGCAT 59.966 55.000 0.00 0.00 0.00 3.79
155 156 0.033920 TAGAGCCGCCATGTAGCATG 59.966 55.000 2.38 2.38 0.00 4.06
156 157 1.524621 GAGCCGCCATGTAGCATGT 60.525 57.895 8.11 0.00 0.00 3.21
157 158 1.502163 GAGCCGCCATGTAGCATGTC 61.502 60.000 8.11 0.00 0.00 3.06
158 159 1.819208 GCCGCCATGTAGCATGTCA 60.819 57.895 8.11 0.00 0.00 3.58
159 160 2.016961 CCGCCATGTAGCATGTCAC 58.983 57.895 8.11 0.00 0.00 3.67
160 161 0.462581 CCGCCATGTAGCATGTCACT 60.463 55.000 8.11 0.00 0.00 3.41
161 162 0.933097 CGCCATGTAGCATGTCACTC 59.067 55.000 8.11 0.00 0.00 3.51
162 163 1.740043 CGCCATGTAGCATGTCACTCA 60.740 52.381 8.11 0.00 0.00 3.41
163 164 1.938577 GCCATGTAGCATGTCACTCAG 59.061 52.381 8.11 0.00 0.00 3.35
164 165 1.938577 CCATGTAGCATGTCACTCAGC 59.061 52.381 8.11 0.00 0.00 4.26
165 166 1.938577 CATGTAGCATGTCACTCAGCC 59.061 52.381 0.00 0.00 0.00 4.85
166 167 0.250234 TGTAGCATGTCACTCAGCCC 59.750 55.000 0.00 0.00 0.00 5.19
167 168 0.462759 GTAGCATGTCACTCAGCCCC 60.463 60.000 0.00 0.00 0.00 5.80
168 169 1.960040 TAGCATGTCACTCAGCCCCG 61.960 60.000 0.00 0.00 0.00 5.73
169 170 2.665000 CATGTCACTCAGCCCCGT 59.335 61.111 0.00 0.00 0.00 5.28
170 171 1.448540 CATGTCACTCAGCCCCGTC 60.449 63.158 0.00 0.00 0.00 4.79
171 172 1.610673 ATGTCACTCAGCCCCGTCT 60.611 57.895 0.00 0.00 0.00 4.18
172 173 0.324368 ATGTCACTCAGCCCCGTCTA 60.324 55.000 0.00 0.00 0.00 2.59
173 174 0.324368 TGTCACTCAGCCCCGTCTAT 60.324 55.000 0.00 0.00 0.00 1.98
174 175 1.064240 TGTCACTCAGCCCCGTCTATA 60.064 52.381 0.00 0.00 0.00 1.31
175 176 2.240279 GTCACTCAGCCCCGTCTATAT 58.760 52.381 0.00 0.00 0.00 0.86
176 177 2.229302 GTCACTCAGCCCCGTCTATATC 59.771 54.545 0.00 0.00 0.00 1.63
177 178 1.200252 CACTCAGCCCCGTCTATATCG 59.800 57.143 0.00 0.00 0.00 2.92
178 179 1.202903 ACTCAGCCCCGTCTATATCGT 60.203 52.381 0.00 0.00 0.00 3.73
179 180 1.200252 CTCAGCCCCGTCTATATCGTG 59.800 57.143 0.00 0.00 0.00 4.35
180 181 0.959553 CAGCCCCGTCTATATCGTGT 59.040 55.000 0.00 0.00 0.00 4.49
181 182 2.156917 CAGCCCCGTCTATATCGTGTA 58.843 52.381 0.00 0.00 0.00 2.90
182 183 2.095364 CAGCCCCGTCTATATCGTGTAC 60.095 54.545 0.00 0.00 0.00 2.90
183 184 1.881973 GCCCCGTCTATATCGTGTACA 59.118 52.381 0.00 0.00 0.00 2.90
184 185 2.351157 GCCCCGTCTATATCGTGTACAC 60.351 54.545 16.32 16.32 0.00 2.90
207 208 5.111293 CGTACGTACAAAGGATTTACCCAT 58.889 41.667 24.50 0.00 35.03 4.00
209 210 6.756074 CGTACGTACAAAGGATTTACCCATTA 59.244 38.462 24.50 0.00 35.03 1.90
294 295 3.546670 CGTTCTAGTGCGTTGTAGATTCC 59.453 47.826 0.00 0.00 0.00 3.01
334 335 5.361285 TCATTTGATGATGCCATGTGAATCA 59.639 36.000 7.16 7.16 33.59 2.57
358 359 6.873605 CACTAGAAACATGTGAAGTGTATGGA 59.126 38.462 16.25 0.00 33.95 3.41
407 411 1.055040 GGAGCAGGCTACCATGAGAT 58.945 55.000 0.00 0.00 0.00 2.75
457 461 6.208797 TCGATTCGGAACTCTTATATGTCCAT 59.791 38.462 6.18 0.00 0.00 3.41
483 487 7.890127 TGGTCAATATGGAAATTCTTTCAGAGT 59.110 33.333 2.39 0.00 41.43 3.24
500 505 9.110502 CTTTCAGAGTTTTACCTTACTTTGTCT 57.889 33.333 0.00 0.00 30.80 3.41
528 533 7.136119 GTCAACAAACAATTCGAAATACCTCA 58.864 34.615 0.00 0.00 0.00 3.86
582 588 5.403466 GCAATGATTCGAAGCACTTCTTTTT 59.597 36.000 19.71 4.21 37.44 1.94
619 625 6.785337 TTCATAAACCTAAGGACTCGATCA 57.215 37.500 0.00 0.00 0.00 2.92
673 679 0.538746 GCGGGAAAAGGAGGGAAACA 60.539 55.000 0.00 0.00 0.00 2.83
736 774 5.116882 AGCCCTATTCAATGAAAGTCGTAC 58.883 41.667 0.00 0.00 0.00 3.67
765 803 6.078664 GTCTTGGAGGGAGATCTTTCCTATA 58.921 44.000 15.78 7.67 37.40 1.31
770 808 7.749666 TGGAGGGAGATCTTTCCTATATTTTG 58.250 38.462 15.78 0.00 37.40 2.44
996 10822 9.440773 TCATTGGATTATCAAATTCTCTATCGG 57.559 33.333 0.00 0.00 0.00 4.18
1008 10834 4.437682 TCTCTATCGGGCCATGAAAAAT 57.562 40.909 4.39 0.00 0.00 1.82
1039 10865 8.062065 ACAAAAGACAGAAACAAATCCACTAA 57.938 30.769 0.00 0.00 0.00 2.24
1061 10887 5.950758 ATGGTTTTACGTCAAGCAATACA 57.049 34.783 14.23 0.00 35.38 2.29
1143 15753 4.674281 AGTTCCGACTGAAATAGGATCC 57.326 45.455 2.48 2.48 33.94 3.36
1144 15754 4.290942 AGTTCCGACTGAAATAGGATCCT 58.709 43.478 20.48 20.48 33.94 3.24
1190 15802 4.163458 TCGTTGGTTATTAGAAGCATCCCT 59.837 41.667 0.00 0.00 0.00 4.20
1198 15810 5.546621 ATTAGAAGCATCCCTAAAGCGTA 57.453 39.130 0.00 0.00 0.00 4.42
1199 15811 5.546621 TTAGAAGCATCCCTAAAGCGTAT 57.453 39.130 0.00 0.00 0.00 3.06
1204 15816 2.748465 GCATCCCTAAAGCGTATGGGTT 60.748 50.000 9.09 0.16 40.48 4.11
1218 15830 5.681179 GCGTATGGGTTGAAATATGGCTTTT 60.681 40.000 0.00 0.00 0.00 2.27
1222 15834 9.313118 GTATGGGTTGAAATATGGCTTTTAAAG 57.687 33.333 0.00 0.00 0.00 1.85
1318 15930 3.181461 GGCAGAGGCAAATAGAGCTCTTA 60.181 47.826 23.84 8.44 43.71 2.10
1371 15983 7.010160 TCTATGTATGTAGACACATGGATCCA 58.990 38.462 18.88 18.88 45.17 3.41
1383 15995 5.012458 ACACATGGATCCATACATCTCGATT 59.988 40.000 26.87 0.00 34.91 3.34
1421 16033 4.457603 AGAAGGAGAATCGGACGATATCTG 59.542 45.833 17.56 0.00 34.37 2.90
1431 16043 3.002451 CGGACGATATCTGTCTCGAAACT 59.998 47.826 19.79 0.00 38.24 2.66
1451 16063 8.592155 CGAAACTAACAAAAAGGAAAAGAAAGG 58.408 33.333 0.00 0.00 0.00 3.11
1469 16081 6.986250 AGAAAGGGAAAACAGAAATCATGAC 58.014 36.000 0.00 0.00 0.00 3.06
1573 16185 3.550820 TCATGGGGATTCCGTAAATGTG 58.449 45.455 0.00 0.00 38.76 3.21
1607 16219 5.782893 ATCAAAACAATCGGGACTTTTCA 57.217 34.783 0.00 0.00 0.00 2.69
1800 16412 8.413309 TGATTCAACCTCTGATCAAAAAGATT 57.587 30.769 0.00 0.00 37.00 2.40
1859 16471 7.248743 AGTAATAAGCATAACGGCCCTATTA 57.751 36.000 0.00 0.00 0.00 0.98
1928 16540 7.194278 TCCAAACGAACAATTTCAACGAAATA 58.806 30.769 2.56 0.00 40.77 1.40
2020 16633 8.540388 ACAGAAATGGCTATAACAGAGTTTCTA 58.460 33.333 0.00 0.00 33.09 2.10
2059 16672 4.882427 GCTACTCTAGGGGGAATGTTTTTC 59.118 45.833 0.00 0.00 0.00 2.29
2130 16743 6.597562 TCAGTTTGTGTTCCTACCTATTGTT 58.402 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.262774 GATGGGTCCCAGCTGTCAGG 62.263 65.000 19.44 7.08 36.92 3.86
1 2 1.222936 GATGGGTCCCAGCTGTCAG 59.777 63.158 19.44 0.78 36.92 3.51
2 3 1.133181 TTGATGGGTCCCAGCTGTCA 61.133 55.000 26.24 16.84 41.01 3.58
3 4 0.393537 CTTGATGGGTCCCAGCTGTC 60.394 60.000 26.24 14.38 41.01 3.51
4 5 1.136329 ACTTGATGGGTCCCAGCTGT 61.136 55.000 26.24 20.62 41.01 4.40
5 6 0.393537 GACTTGATGGGTCCCAGCTG 60.394 60.000 26.24 20.01 41.01 4.24
6 7 1.903877 CGACTTGATGGGTCCCAGCT 61.904 60.000 26.24 6.93 41.01 4.24
7 8 1.450312 CGACTTGATGGGTCCCAGC 60.450 63.158 19.90 19.90 40.77 4.85
8 9 0.613260 TTCGACTTGATGGGTCCCAG 59.387 55.000 17.70 4.95 36.75 4.45
9 10 0.613260 CTTCGACTTGATGGGTCCCA 59.387 55.000 14.64 14.64 38.19 4.37
10 11 0.744771 GCTTCGACTTGATGGGTCCC 60.745 60.000 0.00 0.00 0.00 4.46
11 12 0.036388 TGCTTCGACTTGATGGGTCC 60.036 55.000 0.00 0.00 0.00 4.46
12 13 1.667724 CATGCTTCGACTTGATGGGTC 59.332 52.381 0.00 0.00 0.00 4.46
13 14 1.742761 CATGCTTCGACTTGATGGGT 58.257 50.000 0.00 0.00 0.00 4.51
14 15 0.379669 GCATGCTTCGACTTGATGGG 59.620 55.000 11.37 0.00 0.00 4.00
15 16 0.027194 CGCATGCTTCGACTTGATGG 59.973 55.000 17.13 0.00 0.00 3.51
16 17 0.723414 ACGCATGCTTCGACTTGATG 59.277 50.000 17.13 0.00 0.00 3.07
17 18 2.196749 CTACGCATGCTTCGACTTGAT 58.803 47.619 17.13 0.00 0.00 2.57
18 19 1.629013 CTACGCATGCTTCGACTTGA 58.371 50.000 17.13 0.00 0.00 3.02
19 20 0.025513 GCTACGCATGCTTCGACTTG 59.974 55.000 17.13 0.00 0.00 3.16
20 21 1.413767 CGCTACGCATGCTTCGACTT 61.414 55.000 17.13 0.00 0.00 3.01
21 22 1.874019 CGCTACGCATGCTTCGACT 60.874 57.895 17.13 0.00 0.00 4.18
22 23 1.683790 AACGCTACGCATGCTTCGAC 61.684 55.000 17.13 0.26 0.00 4.20
23 24 0.179158 TAACGCTACGCATGCTTCGA 60.179 50.000 17.13 0.00 0.00 3.71
24 25 0.852777 ATAACGCTACGCATGCTTCG 59.147 50.000 17.13 14.89 0.00 3.79
25 26 2.097202 CAGATAACGCTACGCATGCTTC 60.097 50.000 17.13 0.79 0.00 3.86
26 27 1.860950 CAGATAACGCTACGCATGCTT 59.139 47.619 17.13 9.37 0.00 3.91
27 28 1.202417 ACAGATAACGCTACGCATGCT 60.202 47.619 17.13 5.50 0.00 3.79
28 29 1.190323 GACAGATAACGCTACGCATGC 59.810 52.381 7.91 7.91 0.00 4.06
29 30 2.732366 AGACAGATAACGCTACGCATG 58.268 47.619 0.00 0.00 0.00 4.06
30 31 3.564644 ACTAGACAGATAACGCTACGCAT 59.435 43.478 0.00 0.00 0.00 4.73
31 32 2.941064 ACTAGACAGATAACGCTACGCA 59.059 45.455 0.00 0.00 0.00 5.24
32 33 3.543670 GACTAGACAGATAACGCTACGC 58.456 50.000 0.00 0.00 0.00 4.42
33 34 3.785599 CGACTAGACAGATAACGCTACG 58.214 50.000 0.00 0.00 0.00 3.51
34 35 3.543670 GCGACTAGACAGATAACGCTAC 58.456 50.000 0.00 0.00 41.07 3.58
35 36 2.220363 CGCGACTAGACAGATAACGCTA 59.780 50.000 0.00 0.00 41.88 4.26
36 37 1.003759 CGCGACTAGACAGATAACGCT 60.004 52.381 0.00 0.00 41.88 5.07
37 38 1.004185 TCGCGACTAGACAGATAACGC 60.004 52.381 3.71 0.00 40.91 4.84
38 39 3.027710 GTTCGCGACTAGACAGATAACG 58.972 50.000 9.15 0.00 0.00 3.18
39 40 4.012319 TGTTCGCGACTAGACAGATAAC 57.988 45.455 9.15 0.00 0.00 1.89
40 41 4.095932 ACATGTTCGCGACTAGACAGATAA 59.904 41.667 9.15 0.00 0.00 1.75
41 42 3.626217 ACATGTTCGCGACTAGACAGATA 59.374 43.478 9.15 0.00 0.00 1.98
42 43 2.423892 ACATGTTCGCGACTAGACAGAT 59.576 45.455 9.15 0.00 0.00 2.90
43 44 1.810755 ACATGTTCGCGACTAGACAGA 59.189 47.619 9.15 0.00 0.00 3.41
44 45 2.264109 ACATGTTCGCGACTAGACAG 57.736 50.000 9.15 7.37 0.00 3.51
45 46 2.475022 CGTACATGTTCGCGACTAGACA 60.475 50.000 9.15 11.67 0.00 3.41
46 47 2.099621 CGTACATGTTCGCGACTAGAC 58.900 52.381 9.15 4.70 0.00 2.59
47 48 1.733912 ACGTACATGTTCGCGACTAGA 59.266 47.619 22.67 0.00 0.00 2.43
48 49 2.169663 ACGTACATGTTCGCGACTAG 57.830 50.000 22.67 1.29 0.00 2.57
49 50 2.414825 TGTACGTACATGTTCGCGACTA 59.585 45.455 24.10 0.00 0.00 2.59
50 51 1.197492 TGTACGTACATGTTCGCGACT 59.803 47.619 24.10 7.72 0.00 4.18
51 52 1.605500 TGTACGTACATGTTCGCGAC 58.394 50.000 24.10 19.96 0.00 5.19
52 53 2.547913 ATGTACGTACATGTTCGCGA 57.452 45.000 34.29 3.71 44.66 5.87
53 54 2.150611 GCTATGTACGTACATGTTCGCG 59.849 50.000 38.87 23.92 45.77 5.87
54 55 2.150611 CGCTATGTACGTACATGTTCGC 59.849 50.000 38.87 31.77 45.77 4.70
55 56 3.610495 TCGCTATGTACGTACATGTTCG 58.390 45.455 38.87 34.23 45.77 3.95
56 57 5.684184 TCAATCGCTATGTACGTACATGTTC 59.316 40.000 38.87 27.76 45.77 3.18
57 58 5.584442 TCAATCGCTATGTACGTACATGTT 58.416 37.500 38.87 25.16 45.77 2.71
58 59 5.177725 TCAATCGCTATGTACGTACATGT 57.822 39.130 38.87 24.45 45.77 3.21
59 60 6.399986 CCAATCAATCGCTATGTACGTACATG 60.400 42.308 38.87 30.11 45.77 3.21
61 62 4.979815 CCAATCAATCGCTATGTACGTACA 59.020 41.667 29.15 29.15 40.98 2.90
62 63 4.980434 ACCAATCAATCGCTATGTACGTAC 59.020 41.667 18.90 18.90 0.00 3.67
63 64 5.009310 AGACCAATCAATCGCTATGTACGTA 59.991 40.000 0.00 0.00 0.00 3.57
64 65 4.049186 GACCAATCAATCGCTATGTACGT 58.951 43.478 0.00 0.00 0.00 3.57
65 66 4.299155 AGACCAATCAATCGCTATGTACG 58.701 43.478 0.00 0.00 0.00 3.67
66 67 5.533482 AGAGACCAATCAATCGCTATGTAC 58.467 41.667 0.00 0.00 0.00 2.90
67 68 5.536538 AGAGAGACCAATCAATCGCTATGTA 59.463 40.000 0.00 0.00 0.00 2.29
68 69 4.343526 AGAGAGACCAATCAATCGCTATGT 59.656 41.667 0.00 0.00 0.00 2.29
69 70 4.685165 CAGAGAGACCAATCAATCGCTATG 59.315 45.833 0.00 0.00 29.72 2.23
70 71 4.798924 GCAGAGAGACCAATCAATCGCTAT 60.799 45.833 0.00 0.00 0.00 2.97
71 72 3.491619 GCAGAGAGACCAATCAATCGCTA 60.492 47.826 0.00 0.00 0.00 4.26
72 73 2.741228 GCAGAGAGACCAATCAATCGCT 60.741 50.000 0.00 0.00 0.00 4.93
73 74 1.596727 GCAGAGAGACCAATCAATCGC 59.403 52.381 0.00 0.00 0.00 4.58
74 75 1.857217 CGCAGAGAGACCAATCAATCG 59.143 52.381 0.00 0.00 0.00 3.34
75 76 2.208431 CCGCAGAGAGACCAATCAATC 58.792 52.381 0.00 0.00 0.00 2.67
76 77 1.745141 GCCGCAGAGAGACCAATCAAT 60.745 52.381 0.00 0.00 0.00 2.57
77 78 0.391661 GCCGCAGAGAGACCAATCAA 60.392 55.000 0.00 0.00 0.00 2.57
78 79 1.219124 GCCGCAGAGAGACCAATCA 59.781 57.895 0.00 0.00 0.00 2.57
79 80 1.880340 CGCCGCAGAGAGACCAATC 60.880 63.158 0.00 0.00 0.00 2.67
80 81 1.680522 ATCGCCGCAGAGAGACCAAT 61.681 55.000 0.00 0.00 0.00 3.16
81 82 2.351244 ATCGCCGCAGAGAGACCAA 61.351 57.895 0.00 0.00 0.00 3.67
82 83 2.755876 ATCGCCGCAGAGAGACCA 60.756 61.111 0.00 0.00 0.00 4.02
83 84 2.279120 CATCGCCGCAGAGAGACC 60.279 66.667 0.00 0.00 0.00 3.85
84 85 1.139734 TTCATCGCCGCAGAGAGAC 59.860 57.895 0.00 0.00 0.00 3.36
85 86 1.139734 GTTCATCGCCGCAGAGAGA 59.860 57.895 0.00 0.00 0.00 3.10
86 87 1.880340 GGTTCATCGCCGCAGAGAG 60.880 63.158 0.00 0.00 0.00 3.20
87 88 1.960040 ATGGTTCATCGCCGCAGAGA 61.960 55.000 0.00 0.00 0.00 3.10
88 89 1.522355 ATGGTTCATCGCCGCAGAG 60.522 57.895 0.00 0.00 0.00 3.35
89 90 1.815003 CATGGTTCATCGCCGCAGA 60.815 57.895 0.00 0.00 0.00 4.26
90 91 2.711311 CATGGTTCATCGCCGCAG 59.289 61.111 0.00 0.00 0.00 5.18
91 92 2.823593 CCATGGTTCATCGCCGCA 60.824 61.111 2.57 0.00 0.00 5.69
92 93 4.256090 GCCATGGTTCATCGCCGC 62.256 66.667 14.67 0.00 0.00 6.53
93 94 3.585990 GGCCATGGTTCATCGCCG 61.586 66.667 14.67 0.00 38.24 6.46
94 95 3.585990 CGGCCATGGTTCATCGCC 61.586 66.667 14.67 5.16 43.07 5.54
95 96 2.513666 TCGGCCATGGTTCATCGC 60.514 61.111 14.67 0.00 0.00 4.58
96 97 0.104120 TACTCGGCCATGGTTCATCG 59.896 55.000 14.67 9.98 0.00 3.84
97 98 2.213499 CTTACTCGGCCATGGTTCATC 58.787 52.381 14.67 0.00 0.00 2.92
98 99 1.134098 CCTTACTCGGCCATGGTTCAT 60.134 52.381 14.67 0.00 0.00 2.57
99 100 0.251916 CCTTACTCGGCCATGGTTCA 59.748 55.000 14.67 0.00 0.00 3.18
100 101 0.539986 TCCTTACTCGGCCATGGTTC 59.460 55.000 14.67 5.37 0.00 3.62
101 102 0.541863 CTCCTTACTCGGCCATGGTT 59.458 55.000 14.67 0.00 0.00 3.67
102 103 0.617820 ACTCCTTACTCGGCCATGGT 60.618 55.000 14.67 0.00 0.00 3.55
103 104 0.179073 CACTCCTTACTCGGCCATGG 60.179 60.000 7.63 7.63 0.00 3.66
104 105 0.824109 TCACTCCTTACTCGGCCATG 59.176 55.000 2.24 0.00 0.00 3.66
105 106 0.824759 GTCACTCCTTACTCGGCCAT 59.175 55.000 2.24 0.00 0.00 4.40
106 107 0.541063 TGTCACTCCTTACTCGGCCA 60.541 55.000 2.24 0.00 0.00 5.36
107 108 0.108756 GTGTCACTCCTTACTCGGCC 60.109 60.000 0.00 0.00 0.00 6.13
108 109 0.601558 TGTGTCACTCCTTACTCGGC 59.398 55.000 4.27 0.00 0.00 5.54
109 110 2.231478 ACATGTGTCACTCCTTACTCGG 59.769 50.000 0.00 0.00 0.00 4.63
110 111 3.502920 GACATGTGTCACTCCTTACTCG 58.497 50.000 1.15 0.00 44.18 4.18
111 112 3.057456 ACGACATGTGTCACTCCTTACTC 60.057 47.826 1.15 0.00 44.99 2.59
112 113 2.891580 ACGACATGTGTCACTCCTTACT 59.108 45.455 1.15 0.00 44.99 2.24
113 114 3.299340 ACGACATGTGTCACTCCTTAC 57.701 47.619 1.15 0.00 44.99 2.34
114 115 4.077108 ACTACGACATGTGTCACTCCTTA 58.923 43.478 1.15 0.00 44.99 2.69
115 116 2.891580 ACTACGACATGTGTCACTCCTT 59.108 45.455 1.15 0.00 44.99 3.36
116 117 2.515854 ACTACGACATGTGTCACTCCT 58.484 47.619 1.15 0.00 44.99 3.69
117 118 3.688185 TCTACTACGACATGTGTCACTCC 59.312 47.826 1.15 0.00 44.99 3.85
118 119 4.728307 GCTCTACTACGACATGTGTCACTC 60.728 50.000 1.15 0.00 44.99 3.51
119 120 3.127203 GCTCTACTACGACATGTGTCACT 59.873 47.826 1.15 0.65 44.99 3.41
120 121 3.427243 GCTCTACTACGACATGTGTCAC 58.573 50.000 1.15 0.00 44.99 3.67
121 122 2.422479 GGCTCTACTACGACATGTGTCA 59.578 50.000 1.15 0.00 44.99 3.58
122 123 2.539142 CGGCTCTACTACGACATGTGTC 60.539 54.545 1.15 3.07 41.47 3.67
123 124 1.400846 CGGCTCTACTACGACATGTGT 59.599 52.381 1.15 4.54 0.00 3.72
124 125 1.860399 GCGGCTCTACTACGACATGTG 60.860 57.143 1.15 0.00 0.00 3.21
125 126 0.381089 GCGGCTCTACTACGACATGT 59.619 55.000 0.00 0.00 0.00 3.21
126 127 0.317938 GGCGGCTCTACTACGACATG 60.318 60.000 0.00 0.00 35.30 3.21
127 128 0.750546 TGGCGGCTCTACTACGACAT 60.751 55.000 11.43 0.00 41.27 3.06
128 129 1.377594 TGGCGGCTCTACTACGACA 60.378 57.895 11.43 0.00 44.35 4.35
129 130 0.317938 CATGGCGGCTCTACTACGAC 60.318 60.000 11.43 0.00 35.88 4.34
130 131 0.750546 ACATGGCGGCTCTACTACGA 60.751 55.000 11.43 0.00 0.00 3.43
131 132 0.949397 TACATGGCGGCTCTACTACG 59.051 55.000 11.43 0.00 0.00 3.51
132 133 1.336056 GCTACATGGCGGCTCTACTAC 60.336 57.143 11.43 0.00 0.00 2.73
133 134 0.959553 GCTACATGGCGGCTCTACTA 59.040 55.000 11.43 0.00 0.00 1.82
134 135 1.043116 TGCTACATGGCGGCTCTACT 61.043 55.000 11.43 0.00 34.52 2.57
135 136 0.034059 ATGCTACATGGCGGCTCTAC 59.966 55.000 11.43 0.00 34.52 2.59
136 137 0.033920 CATGCTACATGGCGGCTCTA 59.966 55.000 11.43 0.00 34.52 2.43
137 138 1.227764 CATGCTACATGGCGGCTCT 60.228 57.895 11.43 0.00 34.52 4.09
138 139 1.502163 GACATGCTACATGGCGGCTC 61.502 60.000 11.43 0.00 34.52 4.70
139 140 1.524621 GACATGCTACATGGCGGCT 60.525 57.895 11.43 0.00 34.52 5.52
140 141 1.819208 TGACATGCTACATGGCGGC 60.819 57.895 11.91 0.00 34.52 6.53
141 142 0.462581 AGTGACATGCTACATGGCGG 60.463 55.000 11.91 0.00 34.52 6.13
142 143 0.933097 GAGTGACATGCTACATGGCG 59.067 55.000 11.91 0.00 34.52 5.69
143 144 1.938577 CTGAGTGACATGCTACATGGC 59.061 52.381 11.91 9.36 0.00 4.40
144 145 1.938577 GCTGAGTGACATGCTACATGG 59.061 52.381 11.91 0.00 0.00 3.66
145 146 1.938577 GGCTGAGTGACATGCTACATG 59.061 52.381 6.03 6.03 0.00 3.21
146 147 1.134280 GGGCTGAGTGACATGCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
147 148 0.250234 GGGCTGAGTGACATGCTACA 59.750 55.000 0.00 0.00 0.00 2.74
148 149 0.462759 GGGGCTGAGTGACATGCTAC 60.463 60.000 0.00 0.00 0.00 3.58
149 150 1.907739 GGGGCTGAGTGACATGCTA 59.092 57.895 0.00 0.00 0.00 3.49
150 151 2.673523 GGGGCTGAGTGACATGCT 59.326 61.111 0.00 0.00 0.00 3.79
151 152 2.821366 CGGGGCTGAGTGACATGC 60.821 66.667 0.00 0.00 0.00 4.06
152 153 1.448540 GACGGGGCTGAGTGACATG 60.449 63.158 0.00 0.00 0.00 3.21
153 154 0.324368 TAGACGGGGCTGAGTGACAT 60.324 55.000 0.00 0.00 0.00 3.06
154 155 0.324368 ATAGACGGGGCTGAGTGACA 60.324 55.000 0.00 0.00 0.00 3.58
155 156 1.688772 TATAGACGGGGCTGAGTGAC 58.311 55.000 0.00 0.00 0.00 3.67
156 157 2.515854 GATATAGACGGGGCTGAGTGA 58.484 52.381 0.00 0.00 0.00 3.41
157 158 1.200252 CGATATAGACGGGGCTGAGTG 59.800 57.143 0.00 0.00 0.00 3.51
158 159 1.202903 ACGATATAGACGGGGCTGAGT 60.203 52.381 0.00 0.00 34.93 3.41
159 160 1.200252 CACGATATAGACGGGGCTGAG 59.800 57.143 0.00 0.00 34.93 3.35
160 161 1.244816 CACGATATAGACGGGGCTGA 58.755 55.000 0.00 0.00 34.93 4.26
161 162 0.959553 ACACGATATAGACGGGGCTG 59.040 55.000 8.74 1.00 38.55 4.85
162 163 2.157738 GTACACGATATAGACGGGGCT 58.842 52.381 8.74 0.00 38.55 5.19
163 164 1.881973 TGTACACGATATAGACGGGGC 59.118 52.381 8.74 3.09 38.55 5.80
164 165 3.549299 GTGTACACGATATAGACGGGG 57.451 52.381 10.84 3.15 38.55 5.73
179 180 6.033513 GGTAAATCCTTTGTACGTACGTGTAC 59.966 42.308 30.25 21.19 43.95 2.90
180 181 6.090129 GGTAAATCCTTTGTACGTACGTGTA 58.910 40.000 30.25 16.00 0.00 2.90
181 182 4.923281 GGTAAATCCTTTGTACGTACGTGT 59.077 41.667 30.25 7.45 0.00 4.49
182 183 4.327087 GGGTAAATCCTTTGTACGTACGTG 59.673 45.833 30.25 13.17 36.25 4.49
183 184 4.021544 TGGGTAAATCCTTTGTACGTACGT 60.022 41.667 25.98 25.98 36.25 3.57
184 185 4.493547 TGGGTAAATCCTTTGTACGTACG 58.506 43.478 20.18 15.01 36.25 3.67
185 186 6.990341 AATGGGTAAATCCTTTGTACGTAC 57.010 37.500 18.90 18.90 36.25 3.67
186 187 8.484575 TCATAATGGGTAAATCCTTTGTACGTA 58.515 33.333 0.00 0.00 36.25 3.57
187 188 7.340256 TCATAATGGGTAAATCCTTTGTACGT 58.660 34.615 0.00 0.00 36.25 3.57
188 189 7.713507 TCTCATAATGGGTAAATCCTTTGTACG 59.286 37.037 0.00 0.00 36.25 3.67
189 190 8.974060 TCTCATAATGGGTAAATCCTTTGTAC 57.026 34.615 0.00 0.00 36.25 2.90
193 194 9.672673 CGATATCTCATAATGGGTAAATCCTTT 57.327 33.333 0.34 0.00 36.25 3.11
207 208 7.996385 TCCTCGAATAATGCGATATCTCATAA 58.004 34.615 8.57 0.00 37.13 1.90
209 210 6.456795 TCCTCGAATAATGCGATATCTCAT 57.543 37.500 2.25 2.25 37.13 2.90
294 295 9.551734 TCATCAAATGATACAAGTCTTGGATAG 57.448 33.333 16.85 3.16 33.33 2.08
334 335 7.004555 TCCATACACTTCACATGTTTCTAGT 57.995 36.000 0.00 0.00 0.00 2.57
483 487 7.390996 TGTTGACACAGACAAAGTAAGGTAAAA 59.609 33.333 0.00 0.00 0.00 1.52
487 491 4.839121 TGTTGACACAGACAAAGTAAGGT 58.161 39.130 0.00 0.00 0.00 3.50
500 505 6.693545 GGTATTTCGAATTGTTTGTTGACACA 59.306 34.615 0.00 0.00 0.00 3.72
528 533 3.877508 CTCGGACCTGTTCTGAAAAAGTT 59.122 43.478 0.00 0.00 39.28 2.66
599 605 7.674348 TCCATATGATCGAGTCCTTAGGTTTAT 59.326 37.037 3.65 0.00 0.00 1.40
600 606 7.008332 TCCATATGATCGAGTCCTTAGGTTTA 58.992 38.462 3.65 0.00 0.00 2.01
736 774 1.334243 GATCTCCCTCCAAGACGTACG 59.666 57.143 15.01 15.01 0.00 3.67
742 780 3.498614 AGGAAAGATCTCCCTCCAAGA 57.501 47.619 16.69 0.00 35.95 3.02
832 875 7.436118 TGAAAGAGGTTCAAGAATCCATTTTG 58.564 34.615 0.00 0.00 43.43 2.44
996 10822 8.229811 GTCTTTTGTTGAATATTTTTCATGGCC 58.770 33.333 0.00 0.00 0.00 5.36
1008 10834 9.528018 GGATTTGTTTCTGTCTTTTGTTGAATA 57.472 29.630 0.00 0.00 0.00 1.75
1039 10865 5.950758 TGTATTGCTTGACGTAAAACCAT 57.049 34.783 0.00 0.00 0.00 3.55
1143 15753 2.485814 GGCAAGTGCTCTTCCTTGTTAG 59.514 50.000 2.85 0.00 40.13 2.34
1144 15754 2.158682 TGGCAAGTGCTCTTCCTTGTTA 60.159 45.455 2.85 0.00 40.13 2.41
1190 15802 5.009210 GCCATATTTCAACCCATACGCTTTA 59.991 40.000 0.00 0.00 0.00 1.85
1198 15810 7.917003 ACTTTAAAAGCCATATTTCAACCCAT 58.083 30.769 0.00 0.00 0.00 4.00
1199 15811 7.309770 ACTTTAAAAGCCATATTTCAACCCA 57.690 32.000 0.00 0.00 0.00 4.51
1218 15830 9.525409 GCATCTACTAATTCGGAACTTACTTTA 57.475 33.333 0.00 0.00 0.00 1.85
1222 15834 6.074249 GCAGCATCTACTAATTCGGAACTTAC 60.074 42.308 0.00 0.00 0.00 2.34
1318 15930 6.976088 TGTTCATGGATTAACGAAAATGTGT 58.024 32.000 0.00 0.00 0.00 3.72
1371 15983 8.737168 TTGATTCTTTTCCAATCGAGATGTAT 57.263 30.769 0.00 0.00 33.57 2.29
1383 15995 9.401058 GATTCTCCTTCTATTGATTCTTTTCCA 57.599 33.333 0.00 0.00 0.00 3.53
1421 16033 8.179615 TCTTTTCCTTTTTGTTAGTTTCGAGAC 58.820 33.333 0.00 0.00 0.00 3.36
1431 16043 9.221933 GTTTTCCCTTTCTTTTCCTTTTTGTTA 57.778 29.630 0.00 0.00 0.00 2.41
1451 16063 6.089249 AGTTGGTCATGATTTCTGTTTTCC 57.911 37.500 0.00 0.00 0.00 3.13
1469 16081 0.461961 CCTCGAGAGGGCTTAGTTGG 59.538 60.000 15.71 0.00 44.87 3.77
1517 16129 6.240894 ACGTCATTCCATGCTATTTCCATAT 58.759 36.000 0.00 0.00 0.00 1.78
1537 16149 3.815401 CCCCATGAATAGGATCAAACGTC 59.185 47.826 0.00 0.00 32.06 4.34
1539 16151 4.085357 TCCCCATGAATAGGATCAAACG 57.915 45.455 0.00 0.00 32.06 3.60
1573 16185 6.578172 CCGATTGTTTTGATTTTTGAAATGGC 59.422 34.615 0.00 0.00 0.00 4.40
1607 16219 7.568349 TGAATTAGTAACTGCATCCAATCTCT 58.432 34.615 0.00 0.00 0.00 3.10
1693 16305 6.040729 TCCATTGAAGAGAAGCAAATGAAACA 59.959 34.615 0.00 0.00 0.00 2.83
1743 16355 9.927668 CAGAAGAAGAATTAGGCCAAAAATTAA 57.072 29.630 5.01 0.00 0.00 1.40
1800 16412 6.627087 AGAGATGAAATAGAACCAAGGTCA 57.373 37.500 0.00 0.00 0.00 4.02
1859 16471 3.379452 AGGTTCTTCTCTCCATCGGAAT 58.621 45.455 0.00 0.00 0.00 3.01
2059 16672 7.303634 AGTTATTAAATCGTTAGCACCACAG 57.696 36.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.