Multiple sequence alignment - TraesCS3A01G509600

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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 TraesCS3A01G509600 chr3A 100.000 2625 0 0 453 3077 730117589 730114965 0.000000e+00 4848.0
1 TraesCS3A01G509600 chr3A 86.830 1511 124 50 707 2180 730657118 730655646 0.000000e+00 1618.0
2 TraesCS3A01G509600 chr3A 95.108 695 30 4 2384 3076 72894945 72894253 0.000000e+00 1092.0
3 TraesCS3A01G509600 chr3A 100.000 232 0 0 1 232 730118041 730117810 2.190000e-116 429.0
4 TraesCS3A01G509600 chr3A 88.028 142 15 2 2377 2516 598331646 598331505 1.900000e-37 167.0
5 TraesCS3A01G509600 chr3B 91.646 1975 85 27 453 2382 807975356 807977295 0.000000e+00 2660.0
6 TraesCS3A01G509600 chr3B 90.851 1093 88 10 1090 2180 808043606 808042524 0.000000e+00 1454.0
7 TraesCS3A01G509600 chr3B 89.412 85 7 1 521 605 808069187 808069105 4.200000e-19 106.0
8 TraesCS3A01G509600 chr3B 95.238 63 2 1 84 145 807975563 807975625 7.020000e-17 99.0
9 TraesCS3A01G509600 chr3D 89.704 1690 100 39 557 2213 600631841 600633489 0.000000e+00 2089.0
10 TraesCS3A01G509600 chr3D 90.778 1182 82 17 1008 2180 600820826 600819663 0.000000e+00 1554.0
11 TraesCS3A01G509600 chr2A 96.835 695 18 4 2384 3076 534620103 534620795 0.000000e+00 1158.0
12 TraesCS3A01G509600 chr2B 87.760 433 32 13 2400 2827 231020483 231020899 1.280000e-133 486.0
13 TraesCS3A01G509600 chr2B 93.782 193 11 1 2852 3044 231021113 231021304 3.880000e-74 289.0
14 TraesCS3A01G509600 chr2B 77.108 249 47 9 1762 2005 793141261 793141018 5.350000e-28 135.0
15 TraesCS3A01G509600 chr2B 93.478 46 2 1 2806 2850 231021046 231021091 1.980000e-07 67.6
16 TraesCS3A01G509600 chr2B 84.483 58 9 0 1600 1657 793129230 793129173 1.190000e-04 58.4
17 TraesCS3A01G509600 chr6A 92.720 261 16 3 2376 2634 157969932 157970191 1.040000e-99 374.0
18 TraesCS3A01G509600 chr6A 90.909 44 4 0 1605 1648 545883955 545883912 3.310000e-05 60.2
19 TraesCS3A01G509600 chrUn 72.057 977 216 44 1096 2044 90726853 90725906 3.970000e-59 239.0
20 TraesCS3A01G509600 chrUn 72.057 977 216 44 1096 2044 90939398 90938451 3.970000e-59 239.0
21 TraesCS3A01G509600 chrUn 78.187 353 67 8 1096 1443 401026723 401026376 1.860000e-52 217.0
22 TraesCS3A01G509600 chrUn 82.843 204 30 4 2369 2569 26237947 26238148 8.770000e-41 178.0
23 TraesCS3A01G509600 chr7D 79.525 337 59 7 1112 1443 37234993 37234662 6.640000e-57 231.0
24 TraesCS3A01G509600 chr6B 84.239 184 26 3 2386 2567 591186776 591186594 3.150000e-40 176.0
25 TraesCS3A01G509600 chr2D 77.642 246 51 4 1762 2005 644017110 644017353 2.470000e-31 147.0
26 TraesCS3A01G509600 chr2D 84.211 57 9 0 1601 1657 643924339 643924395 4.290000e-04 56.5
27 TraesCS3A01G509600 chr5D 80.729 192 32 5 2376 2564 228486285 228486474 8.890000e-31 145.0
28 TraesCS3A01G509600 chr5A 81.319 182 31 3 2385 2564 690639736 690639916 8.890000e-31 145.0
29 TraesCS3A01G509600 chr5A 84.354 147 21 2 2386 2530 643863922 643863776 3.200000e-30 143.0
30 TraesCS3A01G509600 chr5A 100.000 29 0 0 473 501 570251595 570251567 2.000000e-03 54.7
31 TraesCS3A01G509600 chr6D 93.182 44 3 0 1605 1648 400089324 400089281 7.120000e-07 65.8


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 TraesCS3A01G509600 chr3A 730114965 730118041 3076 True 2638.500000 4848 100.000000 1 3077 2 chr3A.!!$R4 3076
1 TraesCS3A01G509600 chr3A 730655646 730657118 1472 True 1618.000000 1618 86.830000 707 2180 1 chr3A.!!$R3 1473
2 TraesCS3A01G509600 chr3A 72894253 72894945 692 True 1092.000000 1092 95.108000 2384 3076 1 chr3A.!!$R1 692
3 TraesCS3A01G509600 chr3B 808042524 808043606 1082 True 1454.000000 1454 90.851000 1090 2180 1 chr3B.!!$R1 1090
4 TraesCS3A01G509600 chr3B 807975356 807977295 1939 False 1379.500000 2660 93.442000 84 2382 2 chr3B.!!$F1 2298
5 TraesCS3A01G509600 chr3D 600631841 600633489 1648 False 2089.000000 2089 89.704000 557 2213 1 chr3D.!!$F1 1656
6 TraesCS3A01G509600 chr3D 600819663 600820826 1163 True 1554.000000 1554 90.778000 1008 2180 1 chr3D.!!$R1 1172
7 TraesCS3A01G509600 chr2A 534620103 534620795 692 False 1158.000000 1158 96.835000 2384 3076 1 chr2A.!!$F1 692
8 TraesCS3A01G509600 chr2B 231020483 231021304 821 False 280.866667 486 91.673333 2400 3044 3 chr2B.!!$F1 644
9 TraesCS3A01G509600 chrUn 90725906 90726853 947 True 239.000000 239 72.057000 1096 2044 1 chrUn.!!$R1 948
10 TraesCS3A01G509600 chrUn 90938451 90939398 947 True 239.000000 239 72.057000 1096 2044 1 chrUn.!!$R2 948

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
106 107 0.031178 GCCACAGTGTTTCCTGCTTG 59.969 55.0 0.00 0.00 35.83 4.01 F
158 159 0.175760 TCCGGAGAGCAATGCTACAC 59.824 55.0 8.12 2.37 39.88 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 1963 3.302347 CTGGTCGAAGAAGGCGGCT 62.302 63.158 5.25 5.25 39.69 5.52 R
2103 2173 5.752955 GCCAAAACATAAAACAAGCTTGAGA 59.247 36.000 32.50 14.11 0.00 3.27 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.315246 TTGGTTTTTGCGCATTGGC 58.685 47.368 12.75 2.07 0.00 4.52
19 20 0.179062 TTGGTTTTTGCGCATTGGCT 60.179 45.000 12.75 0.00 38.10 4.75
20 21 0.179062 TGGTTTTTGCGCATTGGCTT 60.179 45.000 12.75 0.00 38.10 4.35
21 22 1.069204 TGGTTTTTGCGCATTGGCTTA 59.931 42.857 12.75 0.00 38.10 3.09
22 23 1.459209 GGTTTTTGCGCATTGGCTTAC 59.541 47.619 12.75 2.84 38.10 2.34
23 24 2.131183 GTTTTTGCGCATTGGCTTACA 58.869 42.857 12.75 0.00 38.10 2.41
24 25 2.736192 GTTTTTGCGCATTGGCTTACAT 59.264 40.909 12.75 0.00 38.10 2.29
25 26 1.993542 TTTGCGCATTGGCTTACATG 58.006 45.000 12.75 0.00 38.10 3.21
26 27 0.458197 TTGCGCATTGGCTTACATGC 60.458 50.000 12.75 0.00 38.10 4.06
27 28 1.139308 GCGCATTGGCTTACATGCA 59.861 52.632 0.30 0.00 39.80 3.96
28 29 0.458197 GCGCATTGGCTTACATGCAA 60.458 50.000 0.30 0.00 39.80 4.08
29 30 1.993542 CGCATTGGCTTACATGCAAA 58.006 45.000 0.00 0.00 39.80 3.68
30 31 2.335752 CGCATTGGCTTACATGCAAAA 58.664 42.857 0.00 0.00 39.80 2.44
31 32 2.931325 CGCATTGGCTTACATGCAAAAT 59.069 40.909 0.00 0.00 39.80 1.82
32 33 4.111198 CGCATTGGCTTACATGCAAAATA 58.889 39.130 0.00 0.00 39.80 1.40
33 34 4.565962 CGCATTGGCTTACATGCAAAATAA 59.434 37.500 0.00 0.00 39.80 1.40
34 35 5.500610 CGCATTGGCTTACATGCAAAATAAC 60.501 40.000 0.00 0.00 39.80 1.89
35 36 5.220643 GCATTGGCTTACATGCAAAATAACC 60.221 40.000 0.00 0.00 39.61 2.85
36 37 5.736951 TTGGCTTACATGCAAAATAACCT 57.263 34.783 0.00 0.00 34.04 3.50
37 38 5.323371 TGGCTTACATGCAAAATAACCTC 57.677 39.130 0.00 0.00 34.04 3.85
38 39 5.016173 TGGCTTACATGCAAAATAACCTCT 58.984 37.500 0.00 0.00 34.04 3.69
39 40 6.184068 TGGCTTACATGCAAAATAACCTCTA 58.816 36.000 0.00 0.00 34.04 2.43
40 41 6.833416 TGGCTTACATGCAAAATAACCTCTAT 59.167 34.615 0.00 0.00 34.04 1.98
41 42 7.341769 TGGCTTACATGCAAAATAACCTCTATT 59.658 33.333 0.00 0.00 34.04 1.73
42 43 8.197439 GGCTTACATGCAAAATAACCTCTATTT 58.803 33.333 0.00 0.00 34.04 1.40
50 51 9.905713 TGCAAAATAACCTCTATTTATGAGTCT 57.094 29.630 0.00 0.00 0.00 3.24
55 56 9.853177 AATAACCTCTATTTATGAGTCTTTGGG 57.147 33.333 0.00 0.00 0.00 4.12
56 57 6.893020 ACCTCTATTTATGAGTCTTTGGGT 57.107 37.500 0.00 0.00 0.00 4.51
57 58 7.272144 ACCTCTATTTATGAGTCTTTGGGTT 57.728 36.000 0.00 0.00 0.00 4.11
58 59 8.388656 ACCTCTATTTATGAGTCTTTGGGTTA 57.611 34.615 0.00 0.00 0.00 2.85
59 60 9.004231 ACCTCTATTTATGAGTCTTTGGGTTAT 57.996 33.333 0.00 0.00 0.00 1.89
60 61 9.853177 CCTCTATTTATGAGTCTTTGGGTTATT 57.147 33.333 0.00 0.00 0.00 1.40
69 70 8.934023 TGAGTCTTTGGGTTATTACTGAATTT 57.066 30.769 0.00 0.00 0.00 1.82
98 99 2.758736 TTTTTGCTGCCACAGTGTTT 57.241 40.000 0.00 0.00 33.43 2.83
99 100 2.292103 TTTTGCTGCCACAGTGTTTC 57.708 45.000 0.00 0.00 33.43 2.78
100 101 0.459489 TTTGCTGCCACAGTGTTTCC 59.541 50.000 0.00 0.00 33.43 3.13
101 102 0.395586 TTGCTGCCACAGTGTTTCCT 60.396 50.000 0.00 0.00 33.43 3.36
102 103 1.102809 TGCTGCCACAGTGTTTCCTG 61.103 55.000 0.00 0.00 38.45 3.86
103 104 1.656441 CTGCCACAGTGTTTCCTGC 59.344 57.895 0.00 0.00 35.83 4.85
104 105 0.820891 CTGCCACAGTGTTTCCTGCT 60.821 55.000 0.00 0.00 35.83 4.24
105 106 0.395586 TGCCACAGTGTTTCCTGCTT 60.396 50.000 0.00 0.00 35.83 3.91
106 107 0.031178 GCCACAGTGTTTCCTGCTTG 59.969 55.000 0.00 0.00 35.83 4.01
107 108 0.670162 CCACAGTGTTTCCTGCTTGG 59.330 55.000 0.00 0.00 35.83 3.61
108 109 1.392589 CACAGTGTTTCCTGCTTGGT 58.607 50.000 0.00 0.00 35.83 3.67
109 110 1.750778 CACAGTGTTTCCTGCTTGGTT 59.249 47.619 0.00 0.00 35.83 3.67
110 111 2.024414 ACAGTGTTTCCTGCTTGGTTC 58.976 47.619 0.00 0.00 35.83 3.62
111 112 2.023673 CAGTGTTTCCTGCTTGGTTCA 58.976 47.619 0.00 0.00 37.07 3.18
112 113 2.624838 CAGTGTTTCCTGCTTGGTTCAT 59.375 45.455 0.00 0.00 37.07 2.57
113 114 2.887152 AGTGTTTCCTGCTTGGTTCATC 59.113 45.455 0.00 0.00 37.07 2.92
114 115 2.029918 GTGTTTCCTGCTTGGTTCATCC 60.030 50.000 0.00 0.00 37.07 3.51
115 116 1.200020 GTTTCCTGCTTGGTTCATCCG 59.800 52.381 0.00 0.00 39.52 4.18
116 117 0.322456 TTCCTGCTTGGTTCATCCGG 60.322 55.000 0.00 0.00 39.52 5.14
117 118 2.409870 CCTGCTTGGTTCATCCGGC 61.410 63.158 0.00 0.00 39.52 6.13
118 119 2.361104 TGCTTGGTTCATCCGGCC 60.361 61.111 0.00 0.00 39.52 6.13
119 120 2.044946 GCTTGGTTCATCCGGCCT 60.045 61.111 0.00 0.00 39.52 5.19
120 121 1.678970 GCTTGGTTCATCCGGCCTT 60.679 57.895 0.00 0.00 39.52 4.35
121 122 0.393808 GCTTGGTTCATCCGGCCTTA 60.394 55.000 0.00 0.00 39.52 2.69
122 123 1.668419 CTTGGTTCATCCGGCCTTAG 58.332 55.000 0.00 0.00 39.52 2.18
123 124 1.209504 CTTGGTTCATCCGGCCTTAGA 59.790 52.381 0.00 0.00 39.52 2.10
124 125 1.507140 TGGTTCATCCGGCCTTAGAT 58.493 50.000 0.00 0.00 39.52 1.98
125 126 2.684943 TGGTTCATCCGGCCTTAGATA 58.315 47.619 0.00 0.00 39.52 1.98
126 127 2.367567 TGGTTCATCCGGCCTTAGATAC 59.632 50.000 0.00 0.00 39.52 2.24
127 128 2.609737 GGTTCATCCGGCCTTAGATACG 60.610 54.545 0.00 0.00 0.00 3.06
128 129 0.601558 TCATCCGGCCTTAGATACGC 59.398 55.000 0.00 0.00 0.00 4.42
129 130 0.603569 CATCCGGCCTTAGATACGCT 59.396 55.000 0.00 0.00 0.00 5.07
130 131 1.000955 CATCCGGCCTTAGATACGCTT 59.999 52.381 0.00 0.00 0.00 4.68
131 132 1.117150 TCCGGCCTTAGATACGCTTT 58.883 50.000 0.00 0.00 0.00 3.51
132 133 1.202486 TCCGGCCTTAGATACGCTTTG 60.202 52.381 0.00 0.00 0.00 2.77
133 134 1.217882 CGGCCTTAGATACGCTTTGG 58.782 55.000 0.00 0.00 0.00 3.28
134 135 1.202486 CGGCCTTAGATACGCTTTGGA 60.202 52.381 0.00 0.00 0.00 3.53
135 136 2.548067 CGGCCTTAGATACGCTTTGGAT 60.548 50.000 0.00 0.00 0.00 3.41
136 137 3.477530 GGCCTTAGATACGCTTTGGATT 58.522 45.455 0.00 0.00 0.00 3.01
137 138 3.883489 GGCCTTAGATACGCTTTGGATTT 59.117 43.478 0.00 0.00 0.00 2.17
138 139 4.023963 GGCCTTAGATACGCTTTGGATTTC 60.024 45.833 0.00 0.00 0.00 2.17
139 140 4.816925 GCCTTAGATACGCTTTGGATTTCT 59.183 41.667 0.00 0.00 0.00 2.52
140 141 5.050023 GCCTTAGATACGCTTTGGATTTCTC 60.050 44.000 0.00 0.00 0.00 2.87
141 142 5.467063 CCTTAGATACGCTTTGGATTTCTCC 59.533 44.000 0.00 0.00 42.45 3.71
142 143 3.458189 AGATACGCTTTGGATTTCTCCG 58.542 45.455 0.00 0.00 45.37 4.63
143 144 2.018542 TACGCTTTGGATTTCTCCGG 57.981 50.000 0.00 0.00 45.37 5.14
144 145 0.323629 ACGCTTTGGATTTCTCCGGA 59.676 50.000 2.93 2.93 45.37 5.14
145 146 1.009829 CGCTTTGGATTTCTCCGGAG 58.990 55.000 26.32 26.32 45.37 4.63
146 147 1.405526 CGCTTTGGATTTCTCCGGAGA 60.406 52.381 30.49 30.49 45.37 3.71
147 148 2.284190 GCTTTGGATTTCTCCGGAGAG 58.716 52.381 31.81 19.49 45.37 3.20
148 149 2.284190 CTTTGGATTTCTCCGGAGAGC 58.716 52.381 31.81 23.90 45.37 4.09
149 150 1.275666 TTGGATTTCTCCGGAGAGCA 58.724 50.000 31.81 23.33 45.37 4.26
150 151 1.275666 TGGATTTCTCCGGAGAGCAA 58.724 50.000 31.81 24.86 45.37 3.91
151 152 1.839994 TGGATTTCTCCGGAGAGCAAT 59.160 47.619 31.81 28.03 45.37 3.56
152 153 2.216898 GGATTTCTCCGGAGAGCAATG 58.783 52.381 31.81 6.25 36.30 2.82
153 154 1.601430 GATTTCTCCGGAGAGCAATGC 59.399 52.381 31.81 18.70 36.30 3.56
154 155 0.615331 TTTCTCCGGAGAGCAATGCT 59.385 50.000 31.81 7.79 43.88 3.79
155 156 1.485124 TTCTCCGGAGAGCAATGCTA 58.515 50.000 31.81 13.92 39.88 3.49
156 157 0.747255 TCTCCGGAGAGCAATGCTAC 59.253 55.000 30.49 5.50 39.88 3.58
157 158 0.461548 CTCCGGAGAGCAATGCTACA 59.538 55.000 28.21 0.00 39.88 2.74
158 159 0.175760 TCCGGAGAGCAATGCTACAC 59.824 55.000 8.12 2.37 39.88 2.90
159 160 0.176680 CCGGAGAGCAATGCTACACT 59.823 55.000 8.12 0.12 39.88 3.55
160 161 1.406069 CCGGAGAGCAATGCTACACTT 60.406 52.381 8.12 0.00 39.88 3.16
161 162 2.159099 CCGGAGAGCAATGCTACACTTA 60.159 50.000 8.12 0.00 39.88 2.24
162 163 2.860735 CGGAGAGCAATGCTACACTTAC 59.139 50.000 8.12 0.00 39.88 2.34
163 164 3.676049 CGGAGAGCAATGCTACACTTACA 60.676 47.826 8.12 0.00 39.88 2.41
164 165 3.619038 GGAGAGCAATGCTACACTTACAC 59.381 47.826 8.12 0.00 39.88 2.90
165 166 4.245660 GAGAGCAATGCTACACTTACACA 58.754 43.478 8.12 0.00 39.88 3.72
166 167 3.997021 AGAGCAATGCTACACTTACACAC 59.003 43.478 8.12 0.00 39.88 3.82
167 168 3.738982 AGCAATGCTACACTTACACACA 58.261 40.909 5.69 0.00 36.99 3.72
168 169 3.748048 AGCAATGCTACACTTACACACAG 59.252 43.478 5.69 0.00 36.99 3.66
169 170 3.745975 GCAATGCTACACTTACACACAGA 59.254 43.478 0.00 0.00 0.00 3.41
170 171 4.393062 GCAATGCTACACTTACACACAGAT 59.607 41.667 0.00 0.00 0.00 2.90
171 172 5.106555 GCAATGCTACACTTACACACAGATT 60.107 40.000 0.00 0.00 0.00 2.40
172 173 6.568462 GCAATGCTACACTTACACACAGATTT 60.568 38.462 0.00 0.00 0.00 2.17
173 174 7.362662 CAATGCTACACTTACACACAGATTTT 58.637 34.615 0.00 0.00 0.00 1.82
174 175 6.539649 TGCTACACTTACACACAGATTTTC 57.460 37.500 0.00 0.00 0.00 2.29
175 176 6.052360 TGCTACACTTACACACAGATTTTCA 58.948 36.000 0.00 0.00 0.00 2.69
176 177 6.018262 TGCTACACTTACACACAGATTTTCAC 60.018 38.462 0.00 0.00 0.00 3.18
177 178 5.403897 ACACTTACACACAGATTTTCACG 57.596 39.130 0.00 0.00 0.00 4.35
178 179 4.272504 ACACTTACACACAGATTTTCACGG 59.727 41.667 0.00 0.00 0.00 4.94
179 180 4.509970 CACTTACACACAGATTTTCACGGA 59.490 41.667 0.00 0.00 0.00 4.69
180 181 5.007234 CACTTACACACAGATTTTCACGGAA 59.993 40.000 0.00 0.00 0.00 4.30
181 182 5.763204 ACTTACACACAGATTTTCACGGAAT 59.237 36.000 0.00 0.00 0.00 3.01
182 183 6.932400 ACTTACACACAGATTTTCACGGAATA 59.068 34.615 0.00 0.00 0.00 1.75
183 184 7.442969 ACTTACACACAGATTTTCACGGAATAA 59.557 33.333 0.00 0.00 0.00 1.40
184 185 6.817765 ACACACAGATTTTCACGGAATAAT 57.182 33.333 0.00 0.00 0.00 1.28
185 186 6.611381 ACACACAGATTTTCACGGAATAATG 58.389 36.000 0.00 0.00 0.00 1.90
186 187 6.029607 CACACAGATTTTCACGGAATAATGG 58.970 40.000 0.00 0.00 0.00 3.16
187 188 5.710099 ACACAGATTTTCACGGAATAATGGT 59.290 36.000 0.00 0.00 0.00 3.55
188 189 6.208599 ACACAGATTTTCACGGAATAATGGTT 59.791 34.615 0.00 0.00 0.00 3.67
189 190 7.392113 ACACAGATTTTCACGGAATAATGGTTA 59.608 33.333 0.00 0.00 0.00 2.85
190 191 7.696453 CACAGATTTTCACGGAATAATGGTTAC 59.304 37.037 0.00 0.00 0.00 2.50
191 192 7.392113 ACAGATTTTCACGGAATAATGGTTACA 59.608 33.333 0.00 0.00 0.00 2.41
192 193 7.910162 CAGATTTTCACGGAATAATGGTTACAG 59.090 37.037 0.00 0.00 0.00 2.74
193 194 7.827236 AGATTTTCACGGAATAATGGTTACAGA 59.173 33.333 0.00 0.00 0.00 3.41
194 195 6.730960 TTTCACGGAATAATGGTTACAGAC 57.269 37.500 0.00 0.00 0.00 3.51
195 196 5.408880 TCACGGAATAATGGTTACAGACA 57.591 39.130 0.00 0.00 0.00 3.41
196 197 5.984725 TCACGGAATAATGGTTACAGACAT 58.015 37.500 0.00 0.00 0.00 3.06
197 198 5.815222 TCACGGAATAATGGTTACAGACATG 59.185 40.000 0.00 0.00 0.00 3.21
198 199 4.574828 ACGGAATAATGGTTACAGACATGC 59.425 41.667 0.00 0.00 0.00 4.06
199 200 4.574421 CGGAATAATGGTTACAGACATGCA 59.426 41.667 0.00 0.00 0.00 3.96
200 201 5.239306 CGGAATAATGGTTACAGACATGCAT 59.761 40.000 0.00 0.00 0.00 3.96
201 202 6.441274 GGAATAATGGTTACAGACATGCATG 58.559 40.000 25.09 25.09 0.00 4.06
202 203 6.395426 AATAATGGTTACAGACATGCATGG 57.605 37.500 29.41 14.96 0.00 3.66
203 204 1.462616 TGGTTACAGACATGCATGGC 58.537 50.000 29.41 27.74 35.53 4.40
204 205 1.271817 TGGTTACAGACATGCATGGCA 60.272 47.619 33.44 11.40 44.86 4.92
215 216 1.596603 TGCATGGCATCATTAGGTCG 58.403 50.000 0.00 0.00 31.71 4.79
216 217 0.877071 GCATGGCATCATTAGGTCGG 59.123 55.000 0.00 0.00 0.00 4.79
217 218 1.527034 CATGGCATCATTAGGTCGGG 58.473 55.000 0.00 0.00 0.00 5.14
218 219 0.401738 ATGGCATCATTAGGTCGGGG 59.598 55.000 0.00 0.00 0.00 5.73
219 220 1.073199 GGCATCATTAGGTCGGGGG 59.927 63.158 0.00 0.00 0.00 5.40
508 509 8.531622 TGTGGTAAGCAATTCAAAACATAATG 57.468 30.769 0.00 0.00 0.00 1.90
515 516 6.365789 AGCAATTCAAAACATAATGAACACCG 59.634 34.615 0.00 0.00 38.29 4.94
601 602 4.502016 GTTAGTTAACCACTCCCACTAGC 58.498 47.826 0.88 0.00 36.88 3.42
672 678 2.488937 TGAATATGCTGCCACAGTGTTG 59.511 45.455 0.00 0.00 33.43 3.33
717 728 3.871594 AGATACGCTTTGAATTTCTCCGG 59.128 43.478 0.00 0.00 0.00 5.14
795 813 7.629027 TTCAAATATTCGAGTCGATCAGATG 57.371 36.000 17.34 12.94 35.23 2.90
930 976 1.821759 CCACACGCACACCTCCAAA 60.822 57.895 0.00 0.00 0.00 3.28
942 988 0.250640 CCTCCAAAGCTCAGCACACT 60.251 55.000 0.00 0.00 0.00 3.55
948 994 0.755079 AAGCTCAGCACACTCACAGA 59.245 50.000 0.00 0.00 0.00 3.41
963 1009 3.352648 TCACAGACACATCGATCCTACA 58.647 45.455 0.00 0.00 0.00 2.74
965 1011 3.859961 CACAGACACATCGATCCTACAAC 59.140 47.826 0.00 0.00 0.00 3.32
966 1012 3.764434 ACAGACACATCGATCCTACAACT 59.236 43.478 0.00 0.00 0.00 3.16
968 1014 4.017126 AGACACATCGATCCTACAACTCA 58.983 43.478 0.00 0.00 0.00 3.41
969 1015 4.106197 GACACATCGATCCTACAACTCAC 58.894 47.826 0.00 0.00 0.00 3.51
970 1016 3.509967 ACACATCGATCCTACAACTCACA 59.490 43.478 0.00 0.00 0.00 3.58
971 1017 4.108336 CACATCGATCCTACAACTCACAG 58.892 47.826 0.00 0.00 0.00 3.66
972 1018 4.017126 ACATCGATCCTACAACTCACAGA 58.983 43.478 0.00 0.00 0.00 3.41
973 1019 4.097135 ACATCGATCCTACAACTCACAGAG 59.903 45.833 0.00 0.00 35.52 3.35
974 1020 3.951663 TCGATCCTACAACTCACAGAGA 58.048 45.455 0.31 0.00 33.32 3.10
983 1029 4.952482 TCACAGAGAGACCTGGCA 57.048 55.556 0.00 0.00 38.44 4.92
984 1030 3.147826 TCACAGAGAGACCTGGCAA 57.852 52.632 0.00 0.00 38.44 4.52
985 1031 0.972134 TCACAGAGAGACCTGGCAAG 59.028 55.000 0.00 0.00 38.44 4.01
986 1032 0.673022 CACAGAGAGACCTGGCAAGC 60.673 60.000 0.00 0.00 38.44 4.01
987 1033 0.835543 ACAGAGAGACCTGGCAAGCT 60.836 55.000 0.00 0.00 38.44 3.74
999 1045 1.067669 TGGCAAGCTAGCTAGATCACG 59.932 52.381 25.15 11.32 34.17 4.35
1010 1062 2.224161 GCTAGATCACGATGGCTTCCTT 60.224 50.000 0.00 0.00 0.00 3.36
1275 1339 2.586792 GATGGCTCCGTGCTCCTT 59.413 61.111 0.00 0.00 42.39 3.36
1323 1387 2.739132 GTGTCTCCCCCGAACGTT 59.261 61.111 0.00 0.00 0.00 3.99
1452 1516 2.115911 CGACTCCGTCCAGCTAGCT 61.116 63.158 12.68 12.68 0.00 3.32
1479 1543 4.802051 AGGTACGCCGTCCCGCTA 62.802 66.667 0.00 0.00 40.50 4.26
1584 1648 0.615331 TCAGCTTCCTCGCCAAGATT 59.385 50.000 0.00 0.00 0.00 2.40
1725 1789 2.753029 GGCCACCTCAAGCTCACT 59.247 61.111 0.00 0.00 0.00 3.41
1899 1963 3.608662 AGGTTCGCCGTCGACCAA 61.609 61.111 10.58 0.00 45.43 3.67
2058 2125 4.395583 GTCGTCGAGACCGCCGTT 62.396 66.667 0.00 0.00 43.95 4.44
2063 2130 2.504244 CGAGACCGCCGTTGAGAC 60.504 66.667 0.00 0.00 0.00 3.36
2064 2131 2.963371 GAGACCGCCGTTGAGACT 59.037 61.111 0.00 0.00 0.00 3.24
2067 2134 0.963962 AGACCGCCGTTGAGACTTTA 59.036 50.000 0.00 0.00 0.00 1.85
2100 2170 5.221661 GGTAGTAGGGTTTAGTCCATGGATG 60.222 48.000 19.62 0.00 0.00 3.51
2195 2267 0.868406 GCAAGACCGAACCAGTTGAG 59.132 55.000 0.00 0.00 0.00 3.02
2205 2277 4.868734 CCGAACCAGTTGAGTAATAAGGAC 59.131 45.833 0.00 0.00 0.00 3.85
2214 2286 8.621286 CAGTTGAGTAATAAGGACTTGTTTTGT 58.379 33.333 0.00 0.00 0.00 2.83
2222 2294 8.803397 AATAAGGACTTGTTTTGTATCTACCC 57.197 34.615 0.00 0.00 0.00 3.69
2223 2295 5.836024 AGGACTTGTTTTGTATCTACCCA 57.164 39.130 0.00 0.00 0.00 4.51
2224 2296 6.388619 AGGACTTGTTTTGTATCTACCCAT 57.611 37.500 0.00 0.00 0.00 4.00
2225 2297 6.180472 AGGACTTGTTTTGTATCTACCCATG 58.820 40.000 0.00 0.00 0.00 3.66
2226 2298 5.944007 GGACTTGTTTTGTATCTACCCATGT 59.056 40.000 0.00 0.00 0.00 3.21
2227 2299 7.037873 AGGACTTGTTTTGTATCTACCCATGTA 60.038 37.037 0.00 0.00 0.00 2.29
2228 2300 7.608761 GGACTTGTTTTGTATCTACCCATGTAA 59.391 37.037 0.00 0.00 0.00 2.41
2238 2310 9.006839 TGTATCTACCCATGTAATAACTAGACG 57.993 37.037 0.00 0.00 0.00 4.18
2239 2311 9.224267 GTATCTACCCATGTAATAACTAGACGA 57.776 37.037 0.00 0.00 0.00 4.20
2240 2312 8.701908 ATCTACCCATGTAATAACTAGACGAA 57.298 34.615 0.00 0.00 0.00 3.85
2242 2314 5.585390 ACCCATGTAATAACTAGACGAACG 58.415 41.667 0.00 0.00 0.00 3.95
2244 2316 5.279384 CCATGTAATAACTAGACGAACGCT 58.721 41.667 0.00 0.00 0.00 5.07
2246 2318 5.550232 TGTAATAACTAGACGAACGCTCA 57.450 39.130 0.00 0.00 0.00 4.26
2247 2319 6.127810 TGTAATAACTAGACGAACGCTCAT 57.872 37.500 0.00 0.00 0.00 2.90
2257 2329 2.548057 ACGAACGCTCATGTGAACATTT 59.452 40.909 0.00 0.00 33.61 2.32
2311 2383 2.358615 GCTCACCGTGTGCATGGA 60.359 61.111 18.37 0.00 39.90 3.41
2315 2387 2.138320 CTCACCGTGTGCATGGATATC 58.862 52.381 16.53 0.00 39.90 1.63
2330 2402 8.729756 TGCATGGATATCTTAAAAATACCGATG 58.270 33.333 2.05 0.00 0.00 3.84
2371 2444 6.523676 TCATTTTGAGGAAAATTTCGTTGC 57.476 33.333 2.32 0.00 39.34 4.17
2378 2451 5.691305 TGAGGAAAATTTCGTTGCTGATTTG 59.309 36.000 2.32 0.00 0.00 2.32
2382 2455 6.587608 GGAAAATTTCGTTGCTGATTTGATCT 59.412 34.615 0.00 0.00 0.00 2.75
2456 2530 3.000727 GCTAGAACTTGTGGCGTACATT 58.999 45.455 0.00 0.00 39.48 2.71
2483 2558 0.383949 GCAAAAACTTGACTCGGGCA 59.616 50.000 0.00 0.00 0.00 5.36
2503 2578 4.320421 GGCATGCAAATACGATGCTAATCA 60.320 41.667 21.36 0.00 44.14 2.57
2686 2764 6.643770 AGCAGAACACATTTTAATTGAGCAAG 59.356 34.615 0.00 0.00 0.00 4.01
2748 2826 0.914644 ATGAGTGTGCAGGTAGCCAT 59.085 50.000 0.00 0.00 44.83 4.40
2872 3141 4.465886 TGAGGTAAACAAGCAGGCTAAAA 58.534 39.130 0.00 0.00 0.00 1.52
2955 3224 0.171007 TACTCGTCGGCTAAAACGGG 59.829 55.000 0.00 0.00 44.80 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179062 AGCCAATGCGCAAAAACCAA 60.179 45.000 17.11 0.00 44.33 3.67
2 3 1.459209 GTAAGCCAATGCGCAAAAACC 59.541 47.619 17.11 1.81 44.33 3.27
3 4 2.131183 TGTAAGCCAATGCGCAAAAAC 58.869 42.857 17.11 4.75 44.33 2.43
4 5 2.515926 TGTAAGCCAATGCGCAAAAA 57.484 40.000 17.11 0.00 44.33 1.94
5 6 2.335752 CATGTAAGCCAATGCGCAAAA 58.664 42.857 17.11 0.00 44.33 2.44
6 7 1.993542 CATGTAAGCCAATGCGCAAA 58.006 45.000 17.11 0.00 44.33 3.68
7 8 0.458197 GCATGTAAGCCAATGCGCAA 60.458 50.000 17.11 0.00 44.33 4.85
8 9 1.139308 GCATGTAAGCCAATGCGCA 59.861 52.632 14.96 14.96 44.33 6.09
9 10 0.458197 TTGCATGTAAGCCAATGCGC 60.458 50.000 0.00 0.00 44.33 6.09
10 11 1.993542 TTTGCATGTAAGCCAATGCG 58.006 45.000 0.00 0.00 44.33 4.73
11 12 5.220643 GGTTATTTTGCATGTAAGCCAATGC 60.221 40.000 0.00 0.75 40.20 3.56
12 13 6.108015 AGGTTATTTTGCATGTAAGCCAATG 58.892 36.000 0.00 0.00 0.00 2.82
13 14 6.155049 AGAGGTTATTTTGCATGTAAGCCAAT 59.845 34.615 0.00 0.00 0.00 3.16
14 15 5.480073 AGAGGTTATTTTGCATGTAAGCCAA 59.520 36.000 0.00 0.00 0.00 4.52
15 16 5.016173 AGAGGTTATTTTGCATGTAAGCCA 58.984 37.500 0.00 0.00 0.00 4.75
16 17 5.582689 AGAGGTTATTTTGCATGTAAGCC 57.417 39.130 0.00 0.00 0.00 4.35
24 25 9.905713 AGACTCATAAATAGAGGTTATTTTGCA 57.094 29.630 0.00 0.00 37.43 4.08
29 30 9.853177 CCCAAAGACTCATAAATAGAGGTTATT 57.147 33.333 0.00 0.00 37.43 1.40
30 31 9.004231 ACCCAAAGACTCATAAATAGAGGTTAT 57.996 33.333 0.00 0.00 37.43 1.89
31 32 8.388656 ACCCAAAGACTCATAAATAGAGGTTA 57.611 34.615 0.00 0.00 37.43 2.85
32 33 7.272144 ACCCAAAGACTCATAAATAGAGGTT 57.728 36.000 0.00 0.00 37.43 3.50
33 34 6.893020 ACCCAAAGACTCATAAATAGAGGT 57.107 37.500 0.00 0.00 37.43 3.85
34 35 9.853177 AATAACCCAAAGACTCATAAATAGAGG 57.147 33.333 0.00 0.00 37.43 3.69
43 44 9.533831 AAATTCAGTAATAACCCAAAGACTCAT 57.466 29.630 0.00 0.00 0.00 2.90
44 45 8.934023 AAATTCAGTAATAACCCAAAGACTCA 57.066 30.769 0.00 0.00 0.00 3.41
79 80 2.615869 GAAACACTGTGGCAGCAAAAA 58.384 42.857 13.09 0.00 34.37 1.94
80 81 1.134848 GGAAACACTGTGGCAGCAAAA 60.135 47.619 13.09 0.00 34.37 2.44
81 82 0.459489 GGAAACACTGTGGCAGCAAA 59.541 50.000 13.09 0.00 34.37 3.68
82 83 0.395586 AGGAAACACTGTGGCAGCAA 60.396 50.000 13.09 0.00 34.37 3.91
83 84 1.102809 CAGGAAACACTGTGGCAGCA 61.103 55.000 13.09 0.00 34.37 4.41
84 85 1.656441 CAGGAAACACTGTGGCAGC 59.344 57.895 13.09 0.00 34.37 5.25
85 86 0.820891 AGCAGGAAACACTGTGGCAG 60.821 55.000 13.09 0.00 40.59 4.85
86 87 0.395586 AAGCAGGAAACACTGTGGCA 60.396 50.000 13.09 0.00 40.59 4.92
87 88 0.031178 CAAGCAGGAAACACTGTGGC 59.969 55.000 13.09 4.60 40.59 5.01
88 89 0.670162 CCAAGCAGGAAACACTGTGG 59.330 55.000 13.09 0.00 41.22 4.17
89 90 1.392589 ACCAAGCAGGAAACACTGTG 58.607 50.000 6.19 6.19 41.22 3.66
90 91 2.024414 GAACCAAGCAGGAAACACTGT 58.976 47.619 1.83 0.00 41.22 3.55
91 92 2.023673 TGAACCAAGCAGGAAACACTG 58.976 47.619 1.83 0.00 41.22 3.66
92 93 2.435372 TGAACCAAGCAGGAAACACT 57.565 45.000 1.83 0.00 41.22 3.55
93 94 2.029918 GGATGAACCAAGCAGGAAACAC 60.030 50.000 1.83 0.00 41.22 3.32
94 95 2.238521 GGATGAACCAAGCAGGAAACA 58.761 47.619 1.83 0.36 41.22 2.83
95 96 1.200020 CGGATGAACCAAGCAGGAAAC 59.800 52.381 1.83 0.00 41.22 2.78
96 97 1.533625 CGGATGAACCAAGCAGGAAA 58.466 50.000 1.83 0.00 41.22 3.13
97 98 0.322456 CCGGATGAACCAAGCAGGAA 60.322 55.000 0.00 0.00 41.22 3.36
98 99 1.299648 CCGGATGAACCAAGCAGGA 59.700 57.895 0.00 0.00 41.22 3.86
99 100 2.409870 GCCGGATGAACCAAGCAGG 61.410 63.158 5.05 0.00 45.67 4.85
100 101 2.409870 GGCCGGATGAACCAAGCAG 61.410 63.158 5.05 0.00 38.75 4.24
101 102 2.361104 GGCCGGATGAACCAAGCA 60.361 61.111 5.05 0.00 38.75 3.91
102 103 0.393808 TAAGGCCGGATGAACCAAGC 60.394 55.000 5.05 0.00 38.90 4.01
103 104 1.209504 TCTAAGGCCGGATGAACCAAG 59.790 52.381 5.05 0.00 38.90 3.61
104 105 1.281419 TCTAAGGCCGGATGAACCAA 58.719 50.000 5.05 0.00 38.90 3.67
105 106 1.507140 ATCTAAGGCCGGATGAACCA 58.493 50.000 5.05 0.00 38.90 3.67
106 107 2.609737 CGTATCTAAGGCCGGATGAACC 60.610 54.545 5.05 0.00 0.00 3.62
107 108 2.673833 CGTATCTAAGGCCGGATGAAC 58.326 52.381 5.05 8.41 0.00 3.18
108 109 1.000506 GCGTATCTAAGGCCGGATGAA 59.999 52.381 5.05 0.00 32.71 2.57
109 110 0.601558 GCGTATCTAAGGCCGGATGA 59.398 55.000 5.05 6.28 32.71 2.92
110 111 0.603569 AGCGTATCTAAGGCCGGATG 59.396 55.000 5.05 4.92 39.90 3.51
111 112 1.339097 AAGCGTATCTAAGGCCGGAT 58.661 50.000 5.05 12.19 39.90 4.18
112 113 1.117150 AAAGCGTATCTAAGGCCGGA 58.883 50.000 5.05 0.00 39.90 5.14
113 114 1.217882 CAAAGCGTATCTAAGGCCGG 58.782 55.000 0.00 0.00 39.90 6.13
114 115 1.202486 TCCAAAGCGTATCTAAGGCCG 60.202 52.381 0.00 0.00 39.90 6.13
115 116 2.614829 TCCAAAGCGTATCTAAGGCC 57.385 50.000 0.00 0.00 39.90 5.19
116 117 4.816925 AGAAATCCAAAGCGTATCTAAGGC 59.183 41.667 0.00 0.00 39.33 4.35
117 118 5.467063 GGAGAAATCCAAAGCGTATCTAAGG 59.533 44.000 0.00 0.00 0.00 2.69
118 119 5.175856 CGGAGAAATCCAAAGCGTATCTAAG 59.824 44.000 0.00 0.00 0.00 2.18
119 120 5.047847 CGGAGAAATCCAAAGCGTATCTAA 58.952 41.667 0.00 0.00 0.00 2.10
120 121 4.500887 CCGGAGAAATCCAAAGCGTATCTA 60.501 45.833 0.00 0.00 0.00 1.98
121 122 3.458189 CGGAGAAATCCAAAGCGTATCT 58.542 45.455 0.00 0.00 0.00 1.98
122 123 2.544267 CCGGAGAAATCCAAAGCGTATC 59.456 50.000 0.00 0.00 0.00 2.24
123 124 2.169769 TCCGGAGAAATCCAAAGCGTAT 59.830 45.455 0.00 0.00 0.00 3.06
124 125 1.551430 TCCGGAGAAATCCAAAGCGTA 59.449 47.619 0.00 0.00 0.00 4.42
125 126 0.323629 TCCGGAGAAATCCAAAGCGT 59.676 50.000 0.00 0.00 0.00 5.07
126 127 1.009829 CTCCGGAGAAATCCAAAGCG 58.990 55.000 28.21 0.00 0.00 4.68
127 128 2.284190 CTCTCCGGAGAAATCCAAAGC 58.716 52.381 32.94 0.00 41.86 3.51
128 129 2.284190 GCTCTCCGGAGAAATCCAAAG 58.716 52.381 32.94 20.05 41.86 2.77
129 130 1.628340 TGCTCTCCGGAGAAATCCAAA 59.372 47.619 32.94 10.24 41.86 3.28
130 131 1.275666 TGCTCTCCGGAGAAATCCAA 58.724 50.000 32.94 11.00 41.86 3.53
131 132 1.275666 TTGCTCTCCGGAGAAATCCA 58.724 50.000 32.94 23.15 41.86 3.41
132 133 2.216898 CATTGCTCTCCGGAGAAATCC 58.783 52.381 32.94 21.10 41.86 3.01
133 134 1.601430 GCATTGCTCTCCGGAGAAATC 59.399 52.381 32.94 23.81 41.86 2.17
134 135 1.211457 AGCATTGCTCTCCGGAGAAAT 59.789 47.619 32.94 26.40 41.86 2.17
135 136 0.615331 AGCATTGCTCTCCGGAGAAA 59.385 50.000 32.94 25.42 41.86 2.52
136 137 1.137086 GTAGCATTGCTCTCCGGAGAA 59.863 52.381 32.94 20.37 41.86 2.87
137 138 0.747255 GTAGCATTGCTCTCCGGAGA 59.253 55.000 31.67 31.67 41.86 3.71
138 139 0.461548 TGTAGCATTGCTCTCCGGAG 59.538 55.000 26.32 26.32 40.44 4.63
139 140 0.175760 GTGTAGCATTGCTCTCCGGA 59.824 55.000 15.81 2.93 40.44 5.14
140 141 0.176680 AGTGTAGCATTGCTCTCCGG 59.823 55.000 15.81 0.00 40.44 5.14
141 142 2.015736 AAGTGTAGCATTGCTCTCCG 57.984 50.000 15.81 0.00 40.44 4.63
142 143 3.619038 GTGTAAGTGTAGCATTGCTCTCC 59.381 47.826 15.81 5.24 40.44 3.71
143 144 4.092091 GTGTGTAAGTGTAGCATTGCTCTC 59.908 45.833 15.81 10.31 40.44 3.20
144 145 3.997021 GTGTGTAAGTGTAGCATTGCTCT 59.003 43.478 15.81 3.27 40.44 4.09
145 146 3.745975 TGTGTGTAAGTGTAGCATTGCTC 59.254 43.478 15.81 7.72 40.44 4.26
146 147 3.738982 TGTGTGTAAGTGTAGCATTGCT 58.261 40.909 16.63 16.63 43.41 3.91
147 148 3.745975 TCTGTGTGTAAGTGTAGCATTGC 59.254 43.478 0.00 0.00 0.00 3.56
148 149 6.486253 AATCTGTGTGTAAGTGTAGCATTG 57.514 37.500 0.00 0.00 0.00 2.82
149 150 7.228507 TGAAAATCTGTGTGTAAGTGTAGCATT 59.771 33.333 0.00 0.00 0.00 3.56
150 151 6.710295 TGAAAATCTGTGTGTAAGTGTAGCAT 59.290 34.615 0.00 0.00 0.00 3.79
151 152 6.018262 GTGAAAATCTGTGTGTAAGTGTAGCA 60.018 38.462 0.00 0.00 0.00 3.49
152 153 6.363473 GTGAAAATCTGTGTGTAAGTGTAGC 58.637 40.000 0.00 0.00 0.00 3.58
153 154 6.346598 CCGTGAAAATCTGTGTGTAAGTGTAG 60.347 42.308 0.00 0.00 0.00 2.74
154 155 5.464057 CCGTGAAAATCTGTGTGTAAGTGTA 59.536 40.000 0.00 0.00 0.00 2.90
155 156 4.272504 CCGTGAAAATCTGTGTGTAAGTGT 59.727 41.667 0.00 0.00 0.00 3.55
156 157 4.509970 TCCGTGAAAATCTGTGTGTAAGTG 59.490 41.667 0.00 0.00 0.00 3.16
157 158 4.699637 TCCGTGAAAATCTGTGTGTAAGT 58.300 39.130 0.00 0.00 0.00 2.24
158 159 5.666969 TTCCGTGAAAATCTGTGTGTAAG 57.333 39.130 0.00 0.00 0.00 2.34
159 160 7.731882 TTATTCCGTGAAAATCTGTGTGTAA 57.268 32.000 0.00 0.00 0.00 2.41
160 161 7.148323 CCATTATTCCGTGAAAATCTGTGTGTA 60.148 37.037 0.00 0.00 0.00 2.90
161 162 6.349280 CCATTATTCCGTGAAAATCTGTGTGT 60.349 38.462 0.00 0.00 0.00 3.72
162 163 6.029607 CCATTATTCCGTGAAAATCTGTGTG 58.970 40.000 0.00 0.00 0.00 3.82
163 164 5.710099 ACCATTATTCCGTGAAAATCTGTGT 59.290 36.000 0.00 0.00 0.00 3.72
164 165 6.194796 ACCATTATTCCGTGAAAATCTGTG 57.805 37.500 0.00 0.00 0.00 3.66
165 166 6.834168 AACCATTATTCCGTGAAAATCTGT 57.166 33.333 0.00 0.00 0.00 3.41
166 167 7.757526 TGTAACCATTATTCCGTGAAAATCTG 58.242 34.615 0.00 0.00 0.00 2.90
167 168 7.827236 TCTGTAACCATTATTCCGTGAAAATCT 59.173 33.333 0.00 0.00 0.00 2.40
168 169 7.908601 GTCTGTAACCATTATTCCGTGAAAATC 59.091 37.037 0.00 0.00 0.00 2.17
169 170 7.392113 TGTCTGTAACCATTATTCCGTGAAAAT 59.608 33.333 0.00 0.00 0.00 1.82
170 171 6.711194 TGTCTGTAACCATTATTCCGTGAAAA 59.289 34.615 0.00 0.00 0.00 2.29
171 172 6.231951 TGTCTGTAACCATTATTCCGTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
172 173 5.795972 TGTCTGTAACCATTATTCCGTGAA 58.204 37.500 0.00 0.00 0.00 3.18
173 174 5.408880 TGTCTGTAACCATTATTCCGTGA 57.591 39.130 0.00 0.00 0.00 4.35
174 175 5.504010 GCATGTCTGTAACCATTATTCCGTG 60.504 44.000 0.00 0.00 0.00 4.94
175 176 4.574828 GCATGTCTGTAACCATTATTCCGT 59.425 41.667 0.00 0.00 0.00 4.69
176 177 4.574421 TGCATGTCTGTAACCATTATTCCG 59.426 41.667 0.00 0.00 0.00 4.30
177 178 6.441274 CATGCATGTCTGTAACCATTATTCC 58.559 40.000 18.91 0.00 0.00 3.01
178 179 6.441274 CCATGCATGTCTGTAACCATTATTC 58.559 40.000 24.58 0.00 0.00 1.75
179 180 5.221303 GCCATGCATGTCTGTAACCATTATT 60.221 40.000 24.58 0.00 0.00 1.40
180 181 4.279169 GCCATGCATGTCTGTAACCATTAT 59.721 41.667 24.58 0.00 0.00 1.28
181 182 3.631686 GCCATGCATGTCTGTAACCATTA 59.368 43.478 24.58 0.00 0.00 1.90
182 183 2.428171 GCCATGCATGTCTGTAACCATT 59.572 45.455 24.58 0.00 0.00 3.16
183 184 2.026641 GCCATGCATGTCTGTAACCAT 58.973 47.619 24.58 0.00 0.00 3.55
184 185 1.271817 TGCCATGCATGTCTGTAACCA 60.272 47.619 24.58 6.26 31.71 3.67
185 186 1.462616 TGCCATGCATGTCTGTAACC 58.537 50.000 24.58 3.95 31.71 2.85
196 197 1.596603 CGACCTAATGATGCCATGCA 58.403 50.000 0.00 0.00 44.86 3.96
197 198 0.877071 CCGACCTAATGATGCCATGC 59.123 55.000 0.00 0.00 32.36 4.06
198 199 1.527034 CCCGACCTAATGATGCCATG 58.473 55.000 0.00 0.00 32.36 3.66
199 200 0.401738 CCCCGACCTAATGATGCCAT 59.598 55.000 0.00 0.00 33.66 4.40
200 201 1.705002 CCCCCGACCTAATGATGCCA 61.705 60.000 0.00 0.00 0.00 4.92
201 202 1.073199 CCCCCGACCTAATGATGCC 59.927 63.158 0.00 0.00 0.00 4.40
202 203 4.800554 CCCCCGACCTAATGATGC 57.199 61.111 0.00 0.00 0.00 3.91
452 453 7.445096 TCACTTGTGATGTTGTTGATTACTGAT 59.555 33.333 0.00 0.00 0.00 2.90
453 454 6.765512 TCACTTGTGATGTTGTTGATTACTGA 59.234 34.615 0.00 0.00 0.00 3.41
454 455 6.852853 GTCACTTGTGATGTTGTTGATTACTG 59.147 38.462 6.74 0.00 0.00 2.74
455 456 6.542005 TGTCACTTGTGATGTTGTTGATTACT 59.458 34.615 6.74 0.00 0.00 2.24
456 457 6.632834 GTGTCACTTGTGATGTTGTTGATTAC 59.367 38.462 6.74 0.00 0.00 1.89
515 516 1.239347 GCTTTGACAAGTCAGGGGAC 58.761 55.000 2.87 0.00 44.66 4.46
601 602 2.286559 CGTAACGATCGAGCGCCTG 61.287 63.158 24.71 6.90 33.86 4.85
672 678 1.941999 GCCAGATGAACCAAGCAGGC 61.942 60.000 0.00 0.00 43.14 4.85
717 728 2.874701 GAGTCATGGGTACACATGCATC 59.125 50.000 29.70 24.18 46.02 3.91
899 945 0.375803 CGTGTGGTTTTATAGGCGCC 59.624 55.000 21.89 21.89 0.00 6.53
930 976 0.033228 GTCTGTGAGTGTGCTGAGCT 59.967 55.000 5.83 0.00 0.00 4.09
942 988 3.352648 TGTAGGATCGATGTGTCTGTGA 58.647 45.455 0.54 0.00 0.00 3.58
948 994 3.509967 TGTGAGTTGTAGGATCGATGTGT 59.490 43.478 0.54 0.00 0.00 3.72
963 1009 0.972883 GCCAGGTCTCTCTGTGAGTT 59.027 55.000 6.63 0.00 43.13 3.01
965 1011 0.972134 TTGCCAGGTCTCTCTGTGAG 59.028 55.000 0.37 0.37 43.96 3.51
966 1012 0.972134 CTTGCCAGGTCTCTCTGTGA 59.028 55.000 0.00 0.00 33.14 3.58
968 1014 0.835543 AGCTTGCCAGGTCTCTCTGT 60.836 55.000 0.00 0.00 33.14 3.41
969 1015 1.136695 CTAGCTTGCCAGGTCTCTCTG 59.863 57.143 0.00 0.00 34.70 3.35
970 1016 1.484038 CTAGCTTGCCAGGTCTCTCT 58.516 55.000 0.00 0.00 31.45 3.10
971 1017 0.179086 GCTAGCTTGCCAGGTCTCTC 60.179 60.000 9.15 0.00 31.45 3.20
972 1018 0.617249 AGCTAGCTTGCCAGGTCTCT 60.617 55.000 12.68 0.00 31.45 3.10
973 1019 1.068434 CTAGCTAGCTTGCCAGGTCTC 59.932 57.143 24.88 0.00 31.45 3.36
974 1020 1.118838 CTAGCTAGCTTGCCAGGTCT 58.881 55.000 24.88 0.00 31.45 3.85
975 1021 1.115467 TCTAGCTAGCTTGCCAGGTC 58.885 55.000 24.88 0.00 31.45 3.85
976 1022 1.691434 GATCTAGCTAGCTTGCCAGGT 59.309 52.381 24.88 10.47 34.24 4.00
977 1023 1.690893 TGATCTAGCTAGCTTGCCAGG 59.309 52.381 24.88 7.32 0.00 4.45
978 1024 2.753296 GTGATCTAGCTAGCTTGCCAG 58.247 52.381 24.88 14.33 0.00 4.85
979 1025 1.067669 CGTGATCTAGCTAGCTTGCCA 59.932 52.381 24.88 17.83 0.00 4.92
980 1026 1.338337 TCGTGATCTAGCTAGCTTGCC 59.662 52.381 24.88 15.55 0.00 4.52
981 1027 2.783828 TCGTGATCTAGCTAGCTTGC 57.216 50.000 24.88 12.54 0.00 4.01
982 1028 3.573598 CCATCGTGATCTAGCTAGCTTG 58.426 50.000 24.88 21.44 0.00 4.01
983 1029 2.029470 GCCATCGTGATCTAGCTAGCTT 60.029 50.000 24.88 4.46 0.00 3.74
984 1030 1.543802 GCCATCGTGATCTAGCTAGCT 59.456 52.381 23.12 23.12 0.00 3.32
985 1031 1.543802 AGCCATCGTGATCTAGCTAGC 59.456 52.381 16.35 6.62 0.00 3.42
986 1032 3.366883 GGAAGCCATCGTGATCTAGCTAG 60.367 52.174 15.01 15.01 0.00 3.42
987 1033 2.558795 GGAAGCCATCGTGATCTAGCTA 59.441 50.000 0.00 0.00 0.00 3.32
999 1045 0.464554 CCGAGGGAAAGGAAGCCATC 60.465 60.000 0.00 0.00 0.00 3.51
1010 1062 3.760035 GACGAGCAGCCGAGGGAA 61.760 66.667 9.87 0.00 0.00 3.97
1057 1118 4.373116 GGCGGACACGGAGCTCAA 62.373 66.667 17.19 0.00 41.36 3.02
1275 1339 3.509137 GACGCCGTTGGTCCTGTCA 62.509 63.158 0.00 0.00 0.00 3.58
1899 1963 3.302347 CTGGTCGAAGAAGGCGGCT 62.302 63.158 5.25 5.25 39.69 5.52
2058 2125 7.392673 CCTACTACCTACAACACTAAAGTCTCA 59.607 40.741 0.00 0.00 0.00 3.27
2063 2130 6.847421 ACCCTACTACCTACAACACTAAAG 57.153 41.667 0.00 0.00 0.00 1.85
2064 2131 7.616528 AAACCCTACTACCTACAACACTAAA 57.383 36.000 0.00 0.00 0.00 1.85
2067 2134 6.318112 ACTAAACCCTACTACCTACAACACT 58.682 40.000 0.00 0.00 0.00 3.55
2100 2170 7.116805 CCAAAACATAAAACAAGCTTGAGATCC 59.883 37.037 32.50 0.00 0.00 3.36
2101 2171 7.359514 GCCAAAACATAAAACAAGCTTGAGATC 60.360 37.037 32.50 3.29 0.00 2.75
2102 2172 6.424812 GCCAAAACATAAAACAAGCTTGAGAT 59.575 34.615 32.50 18.37 0.00 2.75
2103 2173 5.752955 GCCAAAACATAAAACAAGCTTGAGA 59.247 36.000 32.50 14.11 0.00 3.27
2214 2286 9.797642 TTCGTCTAGTTATTACATGGGTAGATA 57.202 33.333 0.00 0.00 0.00 1.98
2216 2288 7.254898 CGTTCGTCTAGTTATTACATGGGTAGA 60.255 40.741 0.00 0.00 0.00 2.59
2217 2289 6.854892 CGTTCGTCTAGTTATTACATGGGTAG 59.145 42.308 0.00 0.00 0.00 3.18
2218 2290 6.728200 CGTTCGTCTAGTTATTACATGGGTA 58.272 40.000 0.00 0.00 0.00 3.69
2219 2291 5.585390 CGTTCGTCTAGTTATTACATGGGT 58.415 41.667 0.00 0.00 0.00 4.51
2221 2293 5.279384 AGCGTTCGTCTAGTTATTACATGG 58.721 41.667 0.00 0.00 0.00 3.66
2222 2294 5.969435 TGAGCGTTCGTCTAGTTATTACATG 59.031 40.000 0.00 0.00 0.00 3.21
2223 2295 6.127810 TGAGCGTTCGTCTAGTTATTACAT 57.872 37.500 0.00 0.00 0.00 2.29
2224 2296 5.550232 TGAGCGTTCGTCTAGTTATTACA 57.450 39.130 0.00 0.00 0.00 2.41
2225 2297 5.970023 ACATGAGCGTTCGTCTAGTTATTAC 59.030 40.000 0.00 0.00 0.00 1.89
2226 2298 5.969435 CACATGAGCGTTCGTCTAGTTATTA 59.031 40.000 0.00 0.00 0.00 0.98
2227 2299 4.798907 CACATGAGCGTTCGTCTAGTTATT 59.201 41.667 0.00 0.00 0.00 1.40
2228 2300 4.095932 TCACATGAGCGTTCGTCTAGTTAT 59.904 41.667 0.00 0.00 0.00 1.89
2230 2302 2.228103 TCACATGAGCGTTCGTCTAGTT 59.772 45.455 0.00 0.00 0.00 2.24
2232 2304 2.544480 TCACATGAGCGTTCGTCTAG 57.456 50.000 0.00 0.00 0.00 2.43
2233 2305 2.030628 TGTTCACATGAGCGTTCGTCTA 60.031 45.455 0.00 0.00 0.00 2.59
2235 2307 1.136690 TGTTCACATGAGCGTTCGTC 58.863 50.000 0.00 0.00 0.00 4.20
2237 2309 2.880822 AATGTTCACATGAGCGTTCG 57.119 45.000 0.00 0.00 36.56 3.95
2238 2310 3.236816 CCAAATGTTCACATGAGCGTTC 58.763 45.455 0.00 0.00 34.17 3.95
2239 2311 2.622942 ACCAAATGTTCACATGAGCGTT 59.377 40.909 0.00 0.00 36.30 4.84
2240 2312 2.229792 ACCAAATGTTCACATGAGCGT 58.770 42.857 0.00 0.00 36.56 5.07
2242 2314 4.241590 TCAACCAAATGTTCACATGAGC 57.758 40.909 0.00 0.00 36.56 4.26
2244 2316 6.593268 ATCATCAACCAAATGTTCACATGA 57.407 33.333 0.00 0.00 36.56 3.07
2246 2318 7.443477 TCAAATCATCAACCAAATGTTCACAT 58.557 30.769 0.00 0.00 38.41 3.21
2247 2319 6.814043 TCAAATCATCAACCAAATGTTCACA 58.186 32.000 0.00 0.00 34.00 3.58
2301 2373 7.803189 CGGTATTTTTAAGATATCCATGCACAC 59.197 37.037 0.00 0.00 0.00 3.82
2371 2444 9.552114 GTGTAATTGACTCAAAGATCAAATCAG 57.448 33.333 0.00 0.00 38.29 2.90
2378 2451 6.428159 ACCACAGTGTAATTGACTCAAAGATC 59.572 38.462 0.00 0.00 0.00 2.75
2382 2455 5.749596 CACCACAGTGTAATTGACTCAAA 57.250 39.130 0.00 0.00 39.30 2.69
2456 2530 4.681744 GAGTCAAGTTTTTGCACCATTCA 58.318 39.130 0.00 0.00 34.21 2.57
2483 2558 4.511454 ACGTGATTAGCATCGTATTTGCAT 59.489 37.500 0.00 0.00 42.62 3.96
2503 2578 2.346244 CGTTGCGGTCATATACAAACGT 59.654 45.455 0.00 0.00 36.75 3.99
2748 2826 4.730081 CGGCGAGATTCGGATCAA 57.270 55.556 6.44 0.00 40.84 2.57
2937 3206 1.080298 CCCGTTTTAGCCGACGAGT 60.080 57.895 0.00 0.00 41.53 4.18
2955 3224 2.399356 GGGCCGCACTAAGTTCTGC 61.399 63.158 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.