Multiple sequence alignment - TraesCS4A01G032700

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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 TraesCS4A01G032700 chr4A 100.000 2883 0 0 1 2883 24934572 24937454 0.000000e+00 5325.0
1 TraesCS4A01G032700 chr4A 88.851 1471 117 26 585 2020 24919886 24918428 0.000000e+00 1764.0
2 TraesCS4A01G032700 chr4A 81.470 1333 177 40 598 1883 26324660 26323351 0.000000e+00 1029.0
3 TraesCS4A01G032700 chr4D 88.674 2322 196 31 610 2883 442215768 442213466 0.000000e+00 2769.0
4 TraesCS4A01G032700 chr4D 91.770 1847 114 20 208 2027 442223828 442221993 0.000000e+00 2534.0
5 TraesCS4A01G032700 chr4D 90.269 1860 125 20 205 2027 442249631 442247791 0.000000e+00 2381.0
6 TraesCS4A01G032700 chr4D 90.473 1459 104 22 584 2020 442395655 442397100 0.000000e+00 1892.0
7 TraesCS4A01G032700 chr4B 87.640 2314 201 36 611 2883 550433469 550431200 0.000000e+00 2610.0
8 TraesCS4A01G032700 chr4B 90.041 1466 109 18 584 2020 550502382 550503839 0.000000e+00 1864.0
9 TraesCS4A01G032700 chr4B 90.550 836 75 4 1187 2019 550487561 550486727 0.000000e+00 1103.0
10 TraesCS4A01G032700 chr4B 91.901 568 35 7 621 1181 550488324 550487761 0.000000e+00 784.0
11 TraesCS4A01G032700 chr4B 88.971 408 23 5 205 595 550489304 550488902 4.320000e-133 484.0
12 TraesCS4A01G032700 chr4B 82.320 181 29 3 1 179 395999819 395999998 1.380000e-33 154.0
13 TraesCS4A01G032700 chr1A 81.868 364 34 18 834 1181 569356152 569355805 7.870000e-71 278.0
14 TraesCS4A01G032700 chr6D 87.755 196 24 0 10 205 290243951 290244146 2.230000e-56 230.0
15 TraesCS4A01G032700 chr6D 79.885 174 30 4 1 171 174381460 174381289 3.900000e-24 122.0
16 TraesCS4A01G032700 chr6D 77.679 112 21 4 2214 2323 368767264 368767373 6.670000e-07 65.8
17 TraesCS4A01G032700 chr3A 83.415 205 33 1 1 205 21173362 21173159 3.790000e-44 189.0
18 TraesCS4A01G032700 chr6B 81.643 207 34 4 1 204 394652635 394652430 4.940000e-38 169.0
19 TraesCS4A01G032700 chr6B 94.737 38 2 0 2287 2324 554808739 554808776 3.100000e-05 60.2
20 TraesCS4A01G032700 chr6A 81.643 207 34 4 1 204 228534385 228534590 4.940000e-38 169.0
21 TraesCS4A01G032700 chr5B 85.065 154 16 5 1 150 31137979 31138129 1.790000e-32 150.0
22 TraesCS4A01G032700 chr1B 79.327 208 38 4 1 205 325272599 325272394 1.080000e-29 141.0
23 TraesCS4A01G032700 chr3B 77.451 204 32 11 10 205 539096366 539096563 3.040000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G032700 chr4A 24934572 24937454 2882 False 5325.000000 5325 100.000 1 2883 1 chr4A.!!$F1 2882
1 TraesCS4A01G032700 chr4A 24918428 24919886 1458 True 1764.000000 1764 88.851 585 2020 1 chr4A.!!$R1 1435
2 TraesCS4A01G032700 chr4A 26323351 26324660 1309 True 1029.000000 1029 81.470 598 1883 1 chr4A.!!$R2 1285
3 TraesCS4A01G032700 chr4D 442213466 442215768 2302 True 2769.000000 2769 88.674 610 2883 1 chr4D.!!$R1 2273
4 TraesCS4A01G032700 chr4D 442221993 442223828 1835 True 2534.000000 2534 91.770 208 2027 1 chr4D.!!$R2 1819
5 TraesCS4A01G032700 chr4D 442247791 442249631 1840 True 2381.000000 2381 90.269 205 2027 1 chr4D.!!$R3 1822
6 TraesCS4A01G032700 chr4D 442395655 442397100 1445 False 1892.000000 1892 90.473 584 2020 1 chr4D.!!$F1 1436
7 TraesCS4A01G032700 chr4B 550431200 550433469 2269 True 2610.000000 2610 87.640 611 2883 1 chr4B.!!$R1 2272
8 TraesCS4A01G032700 chr4B 550502382 550503839 1457 False 1864.000000 1864 90.041 584 2020 1 chr4B.!!$F2 1436
9 TraesCS4A01G032700 chr4B 550486727 550489304 2577 True 790.333333 1103 90.474 205 2019 3 chr4B.!!$R2 1814

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
190 191 0.034089 CAAAGGCCCGGAGAAATCCT 60.034 55.0 0.73 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2991 0.251165 CCATCGGTGGTTTGAGGGTT 60.251 55.0 6.53 0.0 40.83 4.11 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
25 26 7.903145 TGGCGGTCTAATAATAGAATATGTGT 58.097 34.615 0.00 0.00 39.81 3.72
26 27 8.372459 TGGCGGTCTAATAATAGAATATGTGTT 58.628 33.333 0.00 0.00 39.81 3.32
27 28 9.216117 GGCGGTCTAATAATAGAATATGTGTTT 57.784 33.333 0.00 0.00 39.81 2.83
39 40 7.559590 AGAATATGTGTTTAGTCATCTTGGC 57.440 36.000 0.00 0.00 0.00 4.52
40 41 6.543831 AGAATATGTGTTTAGTCATCTTGGCC 59.456 38.462 0.00 0.00 0.00 5.36
41 42 3.788227 TGTGTTTAGTCATCTTGGCCT 57.212 42.857 3.32 0.00 0.00 5.19
42 43 4.901197 TGTGTTTAGTCATCTTGGCCTA 57.099 40.909 3.32 0.00 0.00 3.93
43 44 5.435686 TGTGTTTAGTCATCTTGGCCTAT 57.564 39.130 3.32 0.00 0.00 2.57
44 45 5.815581 TGTGTTTAGTCATCTTGGCCTATT 58.184 37.500 3.32 0.00 0.00 1.73
45 46 6.245408 TGTGTTTAGTCATCTTGGCCTATTT 58.755 36.000 3.32 0.00 0.00 1.40
46 47 6.719370 TGTGTTTAGTCATCTTGGCCTATTTT 59.281 34.615 3.32 0.00 0.00 1.82
47 48 7.232534 TGTGTTTAGTCATCTTGGCCTATTTTT 59.767 33.333 3.32 0.00 0.00 1.94
48 49 7.755373 GTGTTTAGTCATCTTGGCCTATTTTTC 59.245 37.037 3.32 0.00 0.00 2.29
49 50 6.677781 TTAGTCATCTTGGCCTATTTTTCG 57.322 37.500 3.32 0.00 0.00 3.46
50 51 3.378427 AGTCATCTTGGCCTATTTTTCGC 59.622 43.478 3.32 0.00 0.00 4.70
51 52 2.687935 TCATCTTGGCCTATTTTTCGCC 59.312 45.455 3.32 0.00 43.32 5.54
52 53 1.091537 TCTTGGCCTATTTTTCGCCG 58.908 50.000 3.32 0.00 46.12 6.46
53 54 0.100503 CTTGGCCTATTTTTCGCCGG 59.899 55.000 3.32 0.00 46.12 6.13
54 55 0.609681 TTGGCCTATTTTTCGCCGGT 60.610 50.000 3.32 0.00 46.12 5.28
55 56 0.609681 TGGCCTATTTTTCGCCGGTT 60.610 50.000 3.32 0.00 46.12 4.44
56 57 0.179148 GGCCTATTTTTCGCCGGTTG 60.179 55.000 1.90 0.00 31.92 3.77
57 58 0.524414 GCCTATTTTTCGCCGGTTGT 59.476 50.000 1.90 0.00 0.00 3.32
58 59 1.731098 GCCTATTTTTCGCCGGTTGTG 60.731 52.381 1.90 0.00 0.00 3.33
59 60 1.135517 CCTATTTTTCGCCGGTTGTGG 60.136 52.381 1.90 0.00 0.00 4.17
68 69 2.414750 CCGGTTGTGGCAGTTTTCT 58.585 52.632 0.00 0.00 0.00 2.52
69 70 0.744281 CCGGTTGTGGCAGTTTTCTT 59.256 50.000 0.00 0.00 0.00 2.52
70 71 1.136110 CCGGTTGTGGCAGTTTTCTTT 59.864 47.619 0.00 0.00 0.00 2.52
71 72 2.418060 CCGGTTGTGGCAGTTTTCTTTT 60.418 45.455 0.00 0.00 0.00 2.27
72 73 3.258228 CGGTTGTGGCAGTTTTCTTTTT 58.742 40.909 0.00 0.00 0.00 1.94
73 74 4.425520 CGGTTGTGGCAGTTTTCTTTTTA 58.574 39.130 0.00 0.00 0.00 1.52
74 75 4.266739 CGGTTGTGGCAGTTTTCTTTTTAC 59.733 41.667 0.00 0.00 0.00 2.01
75 76 5.416083 GGTTGTGGCAGTTTTCTTTTTACT 58.584 37.500 0.00 0.00 0.00 2.24
76 77 5.290885 GGTTGTGGCAGTTTTCTTTTTACTG 59.709 40.000 0.00 0.00 41.64 2.74
77 78 5.906113 TGTGGCAGTTTTCTTTTTACTGA 57.094 34.783 0.00 0.00 41.33 3.41
78 79 6.463995 TGTGGCAGTTTTCTTTTTACTGAT 57.536 33.333 0.00 0.00 41.33 2.90
79 80 6.872920 TGTGGCAGTTTTCTTTTTACTGATT 58.127 32.000 0.00 0.00 41.33 2.57
80 81 7.327214 TGTGGCAGTTTTCTTTTTACTGATTT 58.673 30.769 0.00 0.00 41.33 2.17
81 82 7.277539 TGTGGCAGTTTTCTTTTTACTGATTTG 59.722 33.333 0.00 0.00 41.33 2.32
82 83 7.277760 GTGGCAGTTTTCTTTTTACTGATTTGT 59.722 33.333 0.00 0.00 41.33 2.83
83 84 7.821846 TGGCAGTTTTCTTTTTACTGATTTGTT 59.178 29.630 0.00 0.00 41.33 2.83
84 85 8.664798 GGCAGTTTTCTTTTTACTGATTTGTTT 58.335 29.630 0.00 0.00 41.33 2.83
85 86 9.689075 GCAGTTTTCTTTTTACTGATTTGTTTC 57.311 29.630 0.00 0.00 41.33 2.78
90 91 9.598517 TTTCTTTTTACTGATTTGTTTCATGCT 57.401 25.926 0.00 0.00 0.00 3.79
91 92 8.801715 TCTTTTTACTGATTTGTTTCATGCTC 57.198 30.769 0.00 0.00 0.00 4.26
92 93 7.867403 TCTTTTTACTGATTTGTTTCATGCTCC 59.133 33.333 0.00 0.00 0.00 4.70
93 94 6.899393 TTTACTGATTTGTTTCATGCTCCT 57.101 33.333 0.00 0.00 0.00 3.69
94 95 6.899393 TTACTGATTTGTTTCATGCTCCTT 57.101 33.333 0.00 0.00 0.00 3.36
95 96 5.382618 ACTGATTTGTTTCATGCTCCTTC 57.617 39.130 0.00 0.00 0.00 3.46
96 97 4.219288 ACTGATTTGTTTCATGCTCCTTCC 59.781 41.667 0.00 0.00 0.00 3.46
97 98 3.191162 TGATTTGTTTCATGCTCCTTCCG 59.809 43.478 0.00 0.00 0.00 4.30
98 99 2.270352 TTGTTTCATGCTCCTTCCGT 57.730 45.000 0.00 0.00 0.00 4.69
99 100 1.522668 TGTTTCATGCTCCTTCCGTG 58.477 50.000 0.00 0.00 0.00 4.94
100 101 1.071542 TGTTTCATGCTCCTTCCGTGA 59.928 47.619 0.00 0.00 0.00 4.35
101 102 1.734465 GTTTCATGCTCCTTCCGTGAG 59.266 52.381 0.00 0.00 30.61 3.51
108 109 2.977405 CTCCTTCCGTGAGCTTTTTG 57.023 50.000 0.00 0.00 0.00 2.44
109 110 1.537202 CTCCTTCCGTGAGCTTTTTGG 59.463 52.381 0.00 0.00 0.00 3.28
110 111 1.142060 TCCTTCCGTGAGCTTTTTGGA 59.858 47.619 0.00 0.00 0.00 3.53
111 112 1.953686 CCTTCCGTGAGCTTTTTGGAA 59.046 47.619 9.42 9.42 37.20 3.53
112 113 2.287608 CCTTCCGTGAGCTTTTTGGAAC 60.288 50.000 6.58 0.00 35.06 3.62
113 114 2.341846 TCCGTGAGCTTTTTGGAACT 57.658 45.000 0.00 0.00 0.00 3.01
114 115 2.650322 TCCGTGAGCTTTTTGGAACTT 58.350 42.857 0.00 0.00 0.00 2.66
115 116 2.357637 TCCGTGAGCTTTTTGGAACTTG 59.642 45.455 0.00 0.00 0.00 3.16
116 117 2.543653 CCGTGAGCTTTTTGGAACTTGG 60.544 50.000 0.00 0.00 0.00 3.61
117 118 2.543653 CGTGAGCTTTTTGGAACTTGGG 60.544 50.000 0.00 0.00 0.00 4.12
118 119 2.693074 GTGAGCTTTTTGGAACTTGGGA 59.307 45.455 0.00 0.00 0.00 4.37
119 120 2.693074 TGAGCTTTTTGGAACTTGGGAC 59.307 45.455 0.00 0.00 0.00 4.46
120 121 2.959030 GAGCTTTTTGGAACTTGGGACT 59.041 45.455 0.00 0.00 0.00 3.85
121 122 3.374764 AGCTTTTTGGAACTTGGGACTT 58.625 40.909 0.00 0.00 0.00 3.01
122 123 3.774766 AGCTTTTTGGAACTTGGGACTTT 59.225 39.130 0.00 0.00 0.00 2.66
123 124 3.871006 GCTTTTTGGAACTTGGGACTTTG 59.129 43.478 0.00 0.00 0.00 2.77
124 125 4.622933 GCTTTTTGGAACTTGGGACTTTGT 60.623 41.667 0.00 0.00 0.00 2.83
125 126 5.487433 CTTTTTGGAACTTGGGACTTTGTT 58.513 37.500 0.00 0.00 0.00 2.83
126 127 5.491323 TTTTGGAACTTGGGACTTTGTTT 57.509 34.783 0.00 0.00 0.00 2.83
127 128 5.491323 TTTGGAACTTGGGACTTTGTTTT 57.509 34.783 0.00 0.00 0.00 2.43
128 129 4.464069 TGGAACTTGGGACTTTGTTTTG 57.536 40.909 0.00 0.00 0.00 2.44
129 130 4.090090 TGGAACTTGGGACTTTGTTTTGA 58.910 39.130 0.00 0.00 0.00 2.69
130 131 4.528596 TGGAACTTGGGACTTTGTTTTGAA 59.471 37.500 0.00 0.00 0.00 2.69
131 132 5.012148 TGGAACTTGGGACTTTGTTTTGAAA 59.988 36.000 0.00 0.00 0.00 2.69
132 133 5.350365 GGAACTTGGGACTTTGTTTTGAAAC 59.650 40.000 0.00 0.00 39.33 2.78
133 134 5.738619 ACTTGGGACTTTGTTTTGAAACT 57.261 34.783 7.97 0.00 39.59 2.66
134 135 6.109156 ACTTGGGACTTTGTTTTGAAACTT 57.891 33.333 7.97 0.00 39.59 2.66
135 136 6.163476 ACTTGGGACTTTGTTTTGAAACTTC 58.837 36.000 7.97 0.69 39.59 3.01
136 137 5.730296 TGGGACTTTGTTTTGAAACTTCA 57.270 34.783 7.97 0.00 39.59 3.02
137 138 5.719173 TGGGACTTTGTTTTGAAACTTCAG 58.281 37.500 7.97 4.21 38.61 3.02
138 139 5.478679 TGGGACTTTGTTTTGAAACTTCAGA 59.521 36.000 7.97 0.00 38.61 3.27
139 140 6.154363 TGGGACTTTGTTTTGAAACTTCAGAT 59.846 34.615 7.97 0.00 38.61 2.90
140 141 6.697455 GGGACTTTGTTTTGAAACTTCAGATC 59.303 38.462 7.97 0.00 38.61 2.75
141 142 7.257722 GGACTTTGTTTTGAAACTTCAGATCA 58.742 34.615 7.97 0.00 38.61 2.92
142 143 7.759433 GGACTTTGTTTTGAAACTTCAGATCAA 59.241 33.333 7.97 3.57 38.61 2.57
143 144 9.305925 GACTTTGTTTTGAAACTTCAGATCAAT 57.694 29.630 7.97 0.00 38.61 2.57
157 158 9.850628 ACTTCAGATCAATAAAATGTTCACATG 57.149 29.630 0.00 0.00 36.56 3.21
158 159 9.850628 CTTCAGATCAATAAAATGTTCACATGT 57.149 29.630 0.00 0.00 36.56 3.21
172 173 9.872721 AATGTTCACATGTATTATTTTGATGCA 57.127 25.926 0.00 0.00 36.56 3.96
173 174 9.872721 ATGTTCACATGTATTATTTTGATGCAA 57.127 25.926 0.00 0.00 34.83 4.08
174 175 9.702494 TGTTCACATGTATTATTTTGATGCAAA 57.298 25.926 0.00 0.00 0.00 3.68
176 177 8.929827 TCACATGTATTATTTTGATGCAAAGG 57.070 30.769 0.00 0.00 34.72 3.11
177 178 7.492020 TCACATGTATTATTTTGATGCAAAGGC 59.508 33.333 0.00 0.00 34.72 4.35
178 179 6.762661 ACATGTATTATTTTGATGCAAAGGCC 59.237 34.615 0.00 0.00 40.13 5.19
179 180 5.669477 TGTATTATTTTGATGCAAAGGCCC 58.331 37.500 0.00 0.00 40.13 5.80
180 181 2.957491 TATTTTGATGCAAAGGCCCG 57.043 45.000 0.00 0.00 40.13 6.13
181 182 0.249955 ATTTTGATGCAAAGGCCCGG 59.750 50.000 0.00 0.00 40.13 5.73
182 183 0.829602 TTTTGATGCAAAGGCCCGGA 60.830 50.000 0.73 0.00 40.13 5.14
183 184 1.250154 TTTGATGCAAAGGCCCGGAG 61.250 55.000 0.73 0.00 40.13 4.63
184 185 2.135903 TTGATGCAAAGGCCCGGAGA 62.136 55.000 0.73 0.00 40.13 3.71
185 186 1.378514 GATGCAAAGGCCCGGAGAA 60.379 57.895 0.73 0.00 40.13 2.87
186 187 0.965363 GATGCAAAGGCCCGGAGAAA 60.965 55.000 0.73 0.00 40.13 2.52
187 188 0.324645 ATGCAAAGGCCCGGAGAAAT 60.325 50.000 0.73 0.00 40.13 2.17
188 189 0.965363 TGCAAAGGCCCGGAGAAATC 60.965 55.000 0.73 0.00 40.13 2.17
189 190 1.667154 GCAAAGGCCCGGAGAAATCC 61.667 60.000 0.73 0.00 0.00 3.01
190 191 0.034089 CAAAGGCCCGGAGAAATCCT 60.034 55.000 0.73 0.00 0.00 3.24
191 192 0.256177 AAAGGCCCGGAGAAATCCTC 59.744 55.000 0.73 0.00 41.22 3.71
226 227 8.871686 AAAATGTTGACTACTTCAATGGTTTC 57.128 30.769 0.00 0.00 46.14 2.78
259 273 4.096382 CGGTAGTTAGTTTAGAAGGCCGTA 59.904 45.833 0.00 0.00 0.00 4.02
273 287 2.304761 AGGCCGTACTTCAAGGATTTGA 59.695 45.455 0.00 0.00 41.44 2.69
293 307 1.973812 GGGAGTTGGGCTTGCAGTC 60.974 63.158 0.00 0.00 0.00 3.51
297 311 0.403271 AGTTGGGCTTGCAGTCAGAT 59.597 50.000 0.00 0.00 0.00 2.90
350 364 2.069273 CCAGCACTACCGAAAGAACAG 58.931 52.381 0.00 0.00 0.00 3.16
416 431 5.123186 TGCCTATCCAGTTGAAAATTGTACG 59.877 40.000 0.00 0.00 30.71 3.67
417 432 5.123344 GCCTATCCAGTTGAAAATTGTACGT 59.877 40.000 0.00 0.00 30.71 3.57
421 436 4.882427 TCCAGTTGAAAATTGTACGTTCCA 59.118 37.500 0.00 0.00 30.71 3.53
463 480 6.515272 AATTGAACGGTTGCATATTCTCTT 57.485 33.333 0.00 0.00 0.00 2.85
464 481 5.545658 TTGAACGGTTGCATATTCTCTTC 57.454 39.130 0.00 0.00 0.00 2.87
465 482 4.832248 TGAACGGTTGCATATTCTCTTCT 58.168 39.130 0.00 0.00 0.00 2.85
466 483 4.870426 TGAACGGTTGCATATTCTCTTCTC 59.130 41.667 0.00 0.00 0.00 2.87
467 484 4.744795 ACGGTTGCATATTCTCTTCTCT 57.255 40.909 0.00 0.00 0.00 3.10
519 537 3.005554 ACGGTTGCATCTTCTCTCAATG 58.994 45.455 0.00 0.00 0.00 2.82
582 603 7.283127 ACGGTTGCTGATCATTTCTAATTGTAT 59.717 33.333 0.00 0.00 0.00 2.29
717 1318 2.358267 GGAACGACATACCGATCAGACT 59.642 50.000 0.00 0.00 33.78 3.24
739 1340 2.652662 CGTTCAATGATTAGAGCGCC 57.347 50.000 2.29 0.00 32.14 6.53
746 1347 1.195115 TGATTAGAGCGCCCAAGTCT 58.805 50.000 2.29 1.82 0.00 3.24
762 1373 0.527817 GTCTATCGGTGGAGGTTGCG 60.528 60.000 0.00 0.00 0.00 4.85
805 1416 7.152645 ACCGCGATCTCATATGTTAGTTAATT 58.847 34.615 8.23 0.00 0.00 1.40
806 1417 8.301720 ACCGCGATCTCATATGTTAGTTAATTA 58.698 33.333 8.23 0.00 0.00 1.40
900 1537 0.991920 TCCTCACCTCCAAATCCACC 59.008 55.000 0.00 0.00 0.00 4.61
921 1558 4.281182 ACCCTCGATCACCACAATATCTAC 59.719 45.833 0.00 0.00 0.00 2.59
1011 1660 2.066393 AGCTGGGATGCGCTTCCTA 61.066 57.895 33.51 28.87 35.97 2.94
1279 2159 3.567164 CGTGTGGGTACGAGAACCTATAT 59.433 47.826 0.00 0.00 46.46 0.86
1382 2262 0.671472 CATCTGCGACACCAGCAAGA 60.671 55.000 0.00 0.00 44.67 3.02
1507 2387 1.410882 TGACACCACTTCGACATGTCA 59.589 47.619 24.93 9.94 45.51 3.58
1639 2519 4.523083 TCAACTACTTTGAACTGGTGCTT 58.477 39.130 0.00 0.00 41.51 3.91
2026 2910 6.894339 ATTTTCATTAACTGTTCGGTTCCT 57.106 33.333 0.00 0.00 0.00 3.36
2028 2912 4.610605 TCATTAACTGTTCGGTTCCTCA 57.389 40.909 0.00 0.00 0.00 3.86
2032 2916 3.771577 AACTGTTCGGTTCCTCAATCT 57.228 42.857 0.00 0.00 0.00 2.40
2055 2939 6.893554 TCTACTGTAAATTGTAGCCTCACCTA 59.106 38.462 0.00 0.00 36.88 3.08
2062 2946 7.396540 AAATTGTAGCCTCACCTATTCAAAG 57.603 36.000 0.00 0.00 0.00 2.77
2072 2956 7.068716 GCCTCACCTATTCAAAGATTATTTGGT 59.931 37.037 4.08 0.00 0.00 3.67
2075 2959 8.956426 TCACCTATTCAAAGATTATTTGGTGTC 58.044 33.333 0.00 0.00 41.15 3.67
2088 2972 9.099454 GATTATTTGGTGTCAAACTACTAGAGG 57.901 37.037 0.00 0.00 44.53 3.69
2097 2981 6.071334 TGTCAAACTACTAGAGGAGACCAATG 60.071 42.308 0.00 0.00 0.00 2.82
2107 2991 9.213777 ACTAGAGGAGACCAATGTTTAATATGA 57.786 33.333 0.00 0.00 0.00 2.15
2109 2993 8.738645 AGAGGAGACCAATGTTTAATATGAAC 57.261 34.615 0.00 0.00 0.00 3.18
2117 3001 8.311109 ACCAATGTTTAATATGAACCCTCAAAC 58.689 33.333 0.00 0.00 34.49 2.93
2121 3005 6.209788 TGTTTAATATGAACCCTCAAACCACC 59.790 38.462 0.00 0.00 34.49 4.61
2138 3022 2.621055 CCACCGATGGTTTGTCTTGAAA 59.379 45.455 0.00 0.00 41.64 2.69
2167 3051 7.739498 TCATCAGACCTTTACAAACTTTACC 57.261 36.000 0.00 0.00 0.00 2.85
2170 3054 4.214758 CAGACCTTTACAAACTTTACCGGG 59.785 45.833 6.32 0.00 0.00 5.73
2171 3055 4.102996 AGACCTTTACAAACTTTACCGGGA 59.897 41.667 6.32 0.00 0.00 5.14
2172 3056 4.790937 ACCTTTACAAACTTTACCGGGAA 58.209 39.130 6.32 0.00 0.00 3.97
2176 3060 5.754543 TTACAAACTTTACCGGGAAACAG 57.245 39.130 8.09 1.38 0.00 3.16
2181 3065 1.265905 CTTTACCGGGAAACAGCACAC 59.734 52.381 8.09 0.00 0.00 3.82
2232 3124 4.017126 CCACCTAAGATTCCCAAAACTCC 58.983 47.826 0.00 0.00 0.00 3.85
2257 3149 6.074698 AGGGTAACAAGTTTGGTATAGCAT 57.925 37.500 5.28 0.00 32.20 3.79
2265 3157 7.280356 ACAAGTTTGGTATAGCATAAGTAGGG 58.720 38.462 5.28 3.61 0.00 3.53
2326 3218 4.218635 GGGTTCCTCTTTGAATCCTCAAAC 59.781 45.833 0.00 0.00 44.76 2.93
2331 3223 8.630037 GTTCCTCTTTGAATCCTCAAACTTTTA 58.370 33.333 0.00 0.00 44.76 1.52
2333 3225 9.367160 TCCTCTTTGAATCCTCAAACTTTTATT 57.633 29.630 0.00 0.00 44.76 1.40
2354 3246 2.091166 TGGAGGAATCAATGGGGAATGG 60.091 50.000 0.00 0.00 0.00 3.16
2407 3299 2.677836 CGGCTCAAATTTCGAGGATTGA 59.322 45.455 15.09 8.09 0.00 2.57
2439 3331 5.965091 GGTAGAGGAAGGGTGGCTTATATAT 59.035 44.000 0.00 0.00 0.00 0.86
2440 3332 7.035320 AGGTAGAGGAAGGGTGGCTTATATATA 60.035 40.741 0.00 0.00 0.00 0.86
2441 3333 7.622479 GGTAGAGGAAGGGTGGCTTATATATAA 59.378 40.741 5.10 5.10 0.00 0.98
2455 3347 9.417561 GGCTTATATATAACCCCCTTTAAATCC 57.582 37.037 0.81 0.00 0.00 3.01
2481 3373 2.969821 TTGTTATCCCCACTTGCAGT 57.030 45.000 0.00 0.00 0.00 4.40
2488 3380 1.228063 CCCACTTGCAGTGCACTCT 60.228 57.895 19.58 0.00 44.63 3.24
2489 3381 1.512996 CCCACTTGCAGTGCACTCTG 61.513 60.000 19.58 12.67 44.63 3.35
2520 3412 1.153989 CCGGAGCCCTAGAGATCCA 59.846 63.158 9.39 0.00 0.00 3.41
2521 3413 0.252012 CCGGAGCCCTAGAGATCCAT 60.252 60.000 9.39 0.00 0.00 3.41
2530 3422 4.635908 GCCCTAGAGATCCATCCTATCCAT 60.636 50.000 0.00 0.00 0.00 3.41
2556 3448 0.338814 AACCTGAGGGTCGGTATCCT 59.661 55.000 2.38 0.00 46.67 3.24
2580 3472 0.769776 ATCCTGGGTATGGAGCCCTG 60.770 60.000 1.85 1.37 46.22 4.45
2588 3480 0.542938 TATGGAGCCCTGGAGATCCG 60.543 60.000 12.68 0.00 39.43 4.18
2589 3481 2.444895 GGAGCCCTGGAGATCCGT 60.445 66.667 0.00 0.00 39.43 4.69
2595 3487 2.016905 CCCTGGAGATCCGTCCTATT 57.983 55.000 0.00 0.00 39.43 1.73
2596 3488 2.330216 CCCTGGAGATCCGTCCTATTT 58.670 52.381 0.00 0.00 39.43 1.40
2607 3499 4.607239 TCCGTCCTATTTAGAGAAGGTGT 58.393 43.478 0.00 0.00 31.89 4.16
2640 3533 1.768077 GAGATCCAGGGGTCAGGGG 60.768 68.421 0.72 0.00 0.00 4.79
2647 3540 2.181773 AGGGGTCAGGGGTGGAGTA 61.182 63.158 0.00 0.00 0.00 2.59
2649 3542 2.356780 GGGTCAGGGGTGGAGTACG 61.357 68.421 0.00 0.00 0.00 3.67
2671 3564 0.798776 GTGTCCAAAGGCGATGTCAG 59.201 55.000 0.00 0.00 0.00 3.51
2677 3570 0.036732 AAAGGCGATGTCAGCTGGAA 59.963 50.000 15.13 2.40 34.52 3.53
2679 3572 1.078848 GGCGATGTCAGCTGGAACT 60.079 57.895 15.13 0.00 34.52 3.01
2680 3573 0.175760 GGCGATGTCAGCTGGAACTA 59.824 55.000 15.13 0.00 34.52 2.24
2687 3581 3.974719 TGTCAGCTGGAACTAGAGATCT 58.025 45.455 15.13 0.00 0.00 2.75
2754 3648 0.603065 GTGTTGGGTTTGAGATGGGC 59.397 55.000 0.00 0.00 0.00 5.36
2846 3753 4.520179 ACCTAAACCCCGCTTAATAGTTG 58.480 43.478 0.00 0.00 0.00 3.16
2847 3754 3.881089 CCTAAACCCCGCTTAATAGTTGG 59.119 47.826 0.00 0.00 0.00 3.77
2857 3764 4.135306 GCTTAATAGTTGGGCCTTCCTAC 58.865 47.826 4.53 0.00 40.79 3.18
2860 3767 2.170012 TAGTTGGGCCTTCCTACGAT 57.830 50.000 4.53 0.00 44.30 3.73
2863 3770 0.544697 TTGGGCCTTCCTACGATTCC 59.455 55.000 4.53 0.00 36.20 3.01
2865 3772 0.106894 GGGCCTTCCTACGATTCCAG 59.893 60.000 0.84 0.00 0.00 3.86
2869 3777 2.742204 GCCTTCCTACGATTCCAGAACC 60.742 54.545 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.903145 ACACATATTCTATTATTAGACCGCCA 58.097 34.615 0.00 0.00 34.15 5.69
1 2 8.773404 AACACATATTCTATTATTAGACCGCC 57.227 34.615 0.00 0.00 34.15 6.13
13 14 9.277783 GCCAAGATGACTAAACACATATTCTAT 57.722 33.333 0.00 0.00 0.00 1.98
14 15 7.715249 GGCCAAGATGACTAAACACATATTCTA 59.285 37.037 0.00 0.00 0.00 2.10
15 16 6.543831 GGCCAAGATGACTAAACACATATTCT 59.456 38.462 0.00 0.00 0.00 2.40
16 17 6.543831 AGGCCAAGATGACTAAACACATATTC 59.456 38.462 5.01 0.00 0.00 1.75
17 18 6.426587 AGGCCAAGATGACTAAACACATATT 58.573 36.000 5.01 0.00 0.00 1.28
18 19 6.006275 AGGCCAAGATGACTAAACACATAT 57.994 37.500 5.01 0.00 0.00 1.78
19 20 5.435686 AGGCCAAGATGACTAAACACATA 57.564 39.130 5.01 0.00 0.00 2.29
20 21 4.307032 AGGCCAAGATGACTAAACACAT 57.693 40.909 5.01 0.00 0.00 3.21
21 22 3.788227 AGGCCAAGATGACTAAACACA 57.212 42.857 5.01 0.00 0.00 3.72
22 23 6.759497 AAATAGGCCAAGATGACTAAACAC 57.241 37.500 5.01 0.00 0.00 3.32
23 24 7.361713 CGAAAAATAGGCCAAGATGACTAAACA 60.362 37.037 5.01 0.00 0.00 2.83
24 25 6.967199 CGAAAAATAGGCCAAGATGACTAAAC 59.033 38.462 5.01 0.00 0.00 2.01
25 26 6.404293 GCGAAAAATAGGCCAAGATGACTAAA 60.404 38.462 5.01 0.00 0.00 1.85
26 27 5.065988 GCGAAAAATAGGCCAAGATGACTAA 59.934 40.000 5.01 0.00 0.00 2.24
27 28 4.574828 GCGAAAAATAGGCCAAGATGACTA 59.425 41.667 5.01 0.00 0.00 2.59
28 29 3.378427 GCGAAAAATAGGCCAAGATGACT 59.622 43.478 5.01 0.00 0.00 3.41
29 30 3.489229 GGCGAAAAATAGGCCAAGATGAC 60.489 47.826 5.01 0.00 46.13 3.06
30 31 2.687935 GGCGAAAAATAGGCCAAGATGA 59.312 45.455 5.01 0.00 46.13 2.92
31 32 3.084070 GGCGAAAAATAGGCCAAGATG 57.916 47.619 5.01 0.00 46.13 2.90
37 38 0.179148 CAACCGGCGAAAAATAGGCC 60.179 55.000 9.30 0.00 43.42 5.19
38 39 0.524414 ACAACCGGCGAAAAATAGGC 59.476 50.000 9.30 0.00 0.00 3.93
39 40 1.135517 CCACAACCGGCGAAAAATAGG 60.136 52.381 9.30 0.00 0.00 2.57
40 41 1.731098 GCCACAACCGGCGAAAAATAG 60.731 52.381 9.30 0.00 43.52 1.73
41 42 0.241481 GCCACAACCGGCGAAAAATA 59.759 50.000 9.30 0.00 43.52 1.40
42 43 1.006688 GCCACAACCGGCGAAAAAT 60.007 52.632 9.30 0.00 43.52 1.82
43 44 2.413765 GCCACAACCGGCGAAAAA 59.586 55.556 9.30 0.00 43.52 1.94
50 51 0.744281 AAGAAAACTGCCACAACCGG 59.256 50.000 0.00 0.00 0.00 5.28
51 52 2.577449 AAAGAAAACTGCCACAACCG 57.423 45.000 0.00 0.00 0.00 4.44
52 53 5.290885 CAGTAAAAAGAAAACTGCCACAACC 59.709 40.000 0.00 0.00 34.73 3.77
53 54 6.096695 TCAGTAAAAAGAAAACTGCCACAAC 58.903 36.000 0.00 0.00 40.34 3.32
54 55 6.274157 TCAGTAAAAAGAAAACTGCCACAA 57.726 33.333 0.00 0.00 40.34 3.33
55 56 5.906113 TCAGTAAAAAGAAAACTGCCACA 57.094 34.783 0.00 0.00 40.34 4.17
56 57 7.277760 ACAAATCAGTAAAAAGAAAACTGCCAC 59.722 33.333 0.00 0.00 40.34 5.01
57 58 7.327214 ACAAATCAGTAAAAAGAAAACTGCCA 58.673 30.769 0.00 0.00 40.34 4.92
58 59 7.770801 ACAAATCAGTAAAAAGAAAACTGCC 57.229 32.000 0.00 0.00 40.34 4.85
59 60 9.689075 GAAACAAATCAGTAAAAAGAAAACTGC 57.311 29.630 0.00 0.00 40.34 4.40
64 65 9.598517 AGCATGAAACAAATCAGTAAAAAGAAA 57.401 25.926 0.00 0.00 31.76 2.52
65 66 9.248291 GAGCATGAAACAAATCAGTAAAAAGAA 57.752 29.630 0.00 0.00 31.76 2.52
66 67 7.867403 GGAGCATGAAACAAATCAGTAAAAAGA 59.133 33.333 0.00 0.00 31.76 2.52
67 68 7.869429 AGGAGCATGAAACAAATCAGTAAAAAG 59.131 33.333 0.00 0.00 31.76 2.27
68 69 7.725251 AGGAGCATGAAACAAATCAGTAAAAA 58.275 30.769 0.00 0.00 31.76 1.94
69 70 7.288810 AGGAGCATGAAACAAATCAGTAAAA 57.711 32.000 0.00 0.00 31.76 1.52
70 71 6.899393 AGGAGCATGAAACAAATCAGTAAA 57.101 33.333 0.00 0.00 31.76 2.01
71 72 6.071952 GGAAGGAGCATGAAACAAATCAGTAA 60.072 38.462 0.00 0.00 31.76 2.24
72 73 5.415701 GGAAGGAGCATGAAACAAATCAGTA 59.584 40.000 0.00 0.00 31.76 2.74
73 74 4.219288 GGAAGGAGCATGAAACAAATCAGT 59.781 41.667 0.00 0.00 31.76 3.41
74 75 4.673580 CGGAAGGAGCATGAAACAAATCAG 60.674 45.833 0.00 0.00 31.76 2.90
75 76 3.191162 CGGAAGGAGCATGAAACAAATCA 59.809 43.478 0.00 0.00 0.00 2.57
76 77 3.191371 ACGGAAGGAGCATGAAACAAATC 59.809 43.478 0.00 0.00 0.00 2.17
77 78 3.057315 CACGGAAGGAGCATGAAACAAAT 60.057 43.478 0.00 0.00 0.00 2.32
78 79 2.293122 CACGGAAGGAGCATGAAACAAA 59.707 45.455 0.00 0.00 0.00 2.83
79 80 1.879380 CACGGAAGGAGCATGAAACAA 59.121 47.619 0.00 0.00 0.00 2.83
80 81 1.071542 TCACGGAAGGAGCATGAAACA 59.928 47.619 0.00 0.00 0.00 2.83
81 82 1.734465 CTCACGGAAGGAGCATGAAAC 59.266 52.381 0.00 0.00 0.00 2.78
82 83 2.099141 CTCACGGAAGGAGCATGAAA 57.901 50.000 0.00 0.00 0.00 2.69
83 84 3.840831 CTCACGGAAGGAGCATGAA 57.159 52.632 0.00 0.00 0.00 2.57
89 90 1.537202 CCAAAAAGCTCACGGAAGGAG 59.463 52.381 0.00 0.00 35.47 3.69
90 91 1.142060 TCCAAAAAGCTCACGGAAGGA 59.858 47.619 0.00 0.00 0.00 3.36
91 92 1.604604 TCCAAAAAGCTCACGGAAGG 58.395 50.000 0.00 0.00 0.00 3.46
92 93 2.618709 AGTTCCAAAAAGCTCACGGAAG 59.381 45.455 7.01 0.00 36.45 3.46
93 94 2.650322 AGTTCCAAAAAGCTCACGGAA 58.350 42.857 3.45 3.45 33.40 4.30
94 95 2.341846 AGTTCCAAAAAGCTCACGGA 57.658 45.000 0.00 0.00 0.00 4.69
95 96 2.543653 CCAAGTTCCAAAAAGCTCACGG 60.544 50.000 0.00 0.00 0.00 4.94
96 97 2.543653 CCCAAGTTCCAAAAAGCTCACG 60.544 50.000 0.00 0.00 0.00 4.35
97 98 2.693074 TCCCAAGTTCCAAAAAGCTCAC 59.307 45.455 0.00 0.00 0.00 3.51
98 99 2.693074 GTCCCAAGTTCCAAAAAGCTCA 59.307 45.455 0.00 0.00 0.00 4.26
99 100 2.959030 AGTCCCAAGTTCCAAAAAGCTC 59.041 45.455 0.00 0.00 0.00 4.09
100 101 3.032265 AGTCCCAAGTTCCAAAAAGCT 57.968 42.857 0.00 0.00 0.00 3.74
101 102 3.819564 AAGTCCCAAGTTCCAAAAAGC 57.180 42.857 0.00 0.00 0.00 3.51
102 103 5.084818 ACAAAGTCCCAAGTTCCAAAAAG 57.915 39.130 0.00 0.00 0.00 2.27
103 104 5.491323 AACAAAGTCCCAAGTTCCAAAAA 57.509 34.783 0.00 0.00 0.00 1.94
104 105 5.491323 AAACAAAGTCCCAAGTTCCAAAA 57.509 34.783 0.00 0.00 0.00 2.44
105 106 5.012148 TCAAAACAAAGTCCCAAGTTCCAAA 59.988 36.000 0.00 0.00 0.00 3.28
106 107 4.528596 TCAAAACAAAGTCCCAAGTTCCAA 59.471 37.500 0.00 0.00 0.00 3.53
107 108 4.090090 TCAAAACAAAGTCCCAAGTTCCA 58.910 39.130 0.00 0.00 0.00 3.53
108 109 4.729227 TCAAAACAAAGTCCCAAGTTCC 57.271 40.909 0.00 0.00 0.00 3.62
109 110 6.163476 AGTTTCAAAACAAAGTCCCAAGTTC 58.837 36.000 8.23 0.00 41.30 3.01
110 111 6.109156 AGTTTCAAAACAAAGTCCCAAGTT 57.891 33.333 8.23 0.00 41.30 2.66
111 112 5.738619 AGTTTCAAAACAAAGTCCCAAGT 57.261 34.783 8.23 0.00 41.30 3.16
112 113 6.162777 TGAAGTTTCAAAACAAAGTCCCAAG 58.837 36.000 8.23 0.00 41.30 3.61
113 114 6.015010 TCTGAAGTTTCAAAACAAAGTCCCAA 60.015 34.615 8.23 0.00 41.30 4.12
114 115 5.478679 TCTGAAGTTTCAAAACAAAGTCCCA 59.521 36.000 8.23 0.00 41.30 4.37
115 116 5.961272 TCTGAAGTTTCAAAACAAAGTCCC 58.039 37.500 8.23 0.00 41.30 4.46
116 117 7.257722 TGATCTGAAGTTTCAAAACAAAGTCC 58.742 34.615 8.23 1.44 41.30 3.85
117 118 8.687824 TTGATCTGAAGTTTCAAAACAAAGTC 57.312 30.769 8.23 1.44 41.30 3.01
131 132 9.850628 CATGTGAACATTTTATTGATCTGAAGT 57.149 29.630 0.00 0.00 33.61 3.01
132 133 9.850628 ACATGTGAACATTTTATTGATCTGAAG 57.149 29.630 0.00 0.00 33.61 3.02
146 147 9.872721 TGCATCAAAATAATACATGTGAACATT 57.127 25.926 9.11 2.55 33.61 2.71
147 148 9.872721 TTGCATCAAAATAATACATGTGAACAT 57.127 25.926 9.11 0.00 36.96 2.71
148 149 9.702494 TTTGCATCAAAATAATACATGTGAACA 57.298 25.926 9.11 0.00 29.89 3.18
150 151 9.368674 CCTTTGCATCAAAATAATACATGTGAA 57.631 29.630 9.11 0.00 32.75 3.18
151 152 7.492020 GCCTTTGCATCAAAATAATACATGTGA 59.508 33.333 9.11 0.00 37.47 3.58
152 153 7.254522 GGCCTTTGCATCAAAATAATACATGTG 60.255 37.037 9.11 0.00 40.13 3.21
153 154 6.762661 GGCCTTTGCATCAAAATAATACATGT 59.237 34.615 2.69 2.69 40.13 3.21
154 155 6.203338 GGGCCTTTGCATCAAAATAATACATG 59.797 38.462 0.84 0.00 40.13 3.21
155 156 6.290605 GGGCCTTTGCATCAAAATAATACAT 58.709 36.000 0.84 0.00 40.13 2.29
156 157 5.669477 GGGCCTTTGCATCAAAATAATACA 58.331 37.500 0.84 0.00 40.13 2.29
157 158 4.744631 CGGGCCTTTGCATCAAAATAATAC 59.255 41.667 0.84 0.00 40.13 1.89
158 159 4.202202 CCGGGCCTTTGCATCAAAATAATA 60.202 41.667 0.84 0.00 40.13 0.98
159 160 3.432046 CCGGGCCTTTGCATCAAAATAAT 60.432 43.478 0.84 0.00 40.13 1.28
160 161 2.093764 CCGGGCCTTTGCATCAAAATAA 60.094 45.455 0.84 0.00 40.13 1.40
161 162 1.480137 CCGGGCCTTTGCATCAAAATA 59.520 47.619 0.84 0.00 40.13 1.40
162 163 0.249955 CCGGGCCTTTGCATCAAAAT 59.750 50.000 0.84 0.00 40.13 1.82
163 164 0.829602 TCCGGGCCTTTGCATCAAAA 60.830 50.000 0.84 0.00 40.13 2.44
164 165 1.228706 TCCGGGCCTTTGCATCAAA 60.229 52.632 0.84 0.00 40.13 2.69
165 166 1.678635 CTCCGGGCCTTTGCATCAA 60.679 57.895 0.84 0.00 40.13 2.57
166 167 2.045045 CTCCGGGCCTTTGCATCA 60.045 61.111 0.84 0.00 40.13 3.07
167 168 0.965363 TTTCTCCGGGCCTTTGCATC 60.965 55.000 0.84 0.00 40.13 3.91
168 169 0.324645 ATTTCTCCGGGCCTTTGCAT 60.325 50.000 0.84 0.00 40.13 3.96
169 170 0.965363 GATTTCTCCGGGCCTTTGCA 60.965 55.000 0.84 0.00 40.13 4.08
170 171 1.667154 GGATTTCTCCGGGCCTTTGC 61.667 60.000 0.84 0.00 0.00 3.68
171 172 2.493547 GGATTTCTCCGGGCCTTTG 58.506 57.895 0.84 0.00 0.00 2.77
181 182 8.363390 ACATTTTTCTGAAAAGGAGGATTTCTC 58.637 33.333 14.52 0.00 38.46 2.87
182 183 8.255111 ACATTTTTCTGAAAAGGAGGATTTCT 57.745 30.769 14.52 0.00 38.46 2.52
183 184 8.768019 CAACATTTTTCTGAAAAGGAGGATTTC 58.232 33.333 14.52 0.00 38.46 2.17
184 185 8.485392 TCAACATTTTTCTGAAAAGGAGGATTT 58.515 29.630 14.52 0.00 38.46 2.17
185 186 7.928167 GTCAACATTTTTCTGAAAAGGAGGATT 59.072 33.333 14.52 4.15 38.46 3.01
186 187 7.288621 AGTCAACATTTTTCTGAAAAGGAGGAT 59.711 33.333 14.52 3.88 38.46 3.24
187 188 6.607198 AGTCAACATTTTTCTGAAAAGGAGGA 59.393 34.615 14.52 11.05 38.46 3.71
188 189 6.809869 AGTCAACATTTTTCTGAAAAGGAGG 58.190 36.000 14.52 6.66 38.46 4.30
189 190 8.624776 AGTAGTCAACATTTTTCTGAAAAGGAG 58.375 33.333 14.52 11.18 38.46 3.69
190 191 8.519799 AGTAGTCAACATTTTTCTGAAAAGGA 57.480 30.769 14.52 3.06 38.46 3.36
191 192 9.237846 GAAGTAGTCAACATTTTTCTGAAAAGG 57.762 33.333 14.52 13.26 41.10 3.11
192 193 9.787532 TGAAGTAGTCAACATTTTTCTGAAAAG 57.212 29.630 14.52 7.87 34.14 2.27
226 227 2.848691 ACTAACTACCGGAGATCGAGG 58.151 52.381 9.46 3.18 42.43 4.63
273 287 1.228675 CTGCAAGCCCAACTCCCTT 60.229 57.895 0.00 0.00 0.00 3.95
293 307 7.387948 AGCCAACACTAACTAAAACTGTATCTG 59.612 37.037 0.00 0.00 0.00 2.90
297 311 6.647895 GCTAGCCAACACTAACTAAAACTGTA 59.352 38.462 2.29 0.00 0.00 2.74
350 364 7.587629 AGCCGGAGTACTTTTACATTAAAAAC 58.412 34.615 5.05 0.00 37.22 2.43
416 431 6.569179 TTCTTTGCTACCTACATTTGGAAC 57.431 37.500 0.00 0.00 0.00 3.62
417 432 7.589958 TTTTCTTTGCTACCTACATTTGGAA 57.410 32.000 0.00 0.00 0.00 3.53
421 436 9.476202 GTTCAATTTTCTTTGCTACCTACATTT 57.524 29.630 0.00 0.00 0.00 2.32
463 480 5.970317 TCAGTCGTATTTTACACCAGAGA 57.030 39.130 0.00 0.00 0.00 3.10
464 481 5.005779 GCATCAGTCGTATTTTACACCAGAG 59.994 44.000 0.00 0.00 0.00 3.35
465 482 4.868171 GCATCAGTCGTATTTTACACCAGA 59.132 41.667 0.00 0.00 0.00 3.86
466 483 4.034048 GGCATCAGTCGTATTTTACACCAG 59.966 45.833 0.00 0.00 0.00 4.00
467 484 3.936453 GGCATCAGTCGTATTTTACACCA 59.064 43.478 0.00 0.00 0.00 4.17
519 537 5.794726 GGGAGAGAACTTCTTCCTATACC 57.205 47.826 14.56 0.00 46.84 2.73
687 1271 7.436080 TGATCGGTATGTCGTTCCTTAATTAAC 59.564 37.037 0.00 0.00 0.00 2.01
717 1318 2.223021 GCGCTCTAATCATTGAACGCAA 60.223 45.455 0.00 0.00 44.12 4.85
739 1340 1.486211 ACCTCCACCGATAGACTTGG 58.514 55.000 0.00 0.00 39.76 3.61
746 1347 1.514087 GACGCAACCTCCACCGATA 59.486 57.895 0.00 0.00 0.00 2.92
762 1373 2.199236 GGTTCCAACGATCGTATGGAC 58.801 52.381 32.85 27.76 42.71 4.02
805 1416 6.485648 TCGAGAGGAATGATTGTCGTCTTATA 59.514 38.462 0.00 0.00 39.64 0.98
806 1417 5.299531 TCGAGAGGAATGATTGTCGTCTTAT 59.700 40.000 0.00 0.00 39.64 1.73
900 1537 4.280929 TGGTAGATATTGTGGTGATCGAGG 59.719 45.833 0.00 0.00 0.00 4.63
1206 2069 2.510464 AGACACGCACACACGCAA 60.510 55.556 0.00 0.00 36.19 4.85
1279 2159 1.195442 TGATCCCGTACCCTGCAACA 61.195 55.000 0.00 0.00 0.00 3.33
1322 2202 2.225467 TGATGCACCGTCATTGAACAA 58.775 42.857 0.00 0.00 0.00 2.83
1359 2239 1.434622 GCTGGTGTCGCAGATGATGG 61.435 60.000 0.00 0.00 40.67 3.51
1382 2262 1.523711 CGGGCTTGCACATATCCGT 60.524 57.895 0.00 0.00 33.63 4.69
1487 2367 1.410882 TGACATGTCGAAGTGGTGTCA 59.589 47.619 20.54 12.58 44.74 3.58
1597 2477 1.669760 GCCGTTGATGGTGAACCGA 60.670 57.895 0.00 0.00 39.43 4.69
1630 2510 2.127232 GTTGGCCACAAGCACCAGT 61.127 57.895 3.88 0.00 46.50 4.00
1666 2546 4.396166 CCTTTCACCGACATGCTCTTAATT 59.604 41.667 0.00 0.00 0.00 1.40
1925 2806 7.118971 ACCTCGTCGATAATAATAGTGGTAGTC 59.881 40.741 0.00 0.00 0.00 2.59
2008 2892 5.643777 AGATTGAGGAACCGAACAGTTAATG 59.356 40.000 0.00 0.00 0.00 1.90
2026 2910 7.764443 GTGAGGCTACAATTTACAGTAGATTGA 59.236 37.037 24.06 11.15 40.02 2.57
2028 2912 7.048512 GGTGAGGCTACAATTTACAGTAGATT 58.951 38.462 0.00 0.00 40.02 2.40
2032 2916 7.670605 ATAGGTGAGGCTACAATTTACAGTA 57.329 36.000 0.00 0.00 0.00 2.74
2062 2946 9.099454 CCTCTAGTAGTTTGACACCAAATAATC 57.901 37.037 0.00 0.00 43.37 1.75
2072 2956 4.994282 TGGTCTCCTCTAGTAGTTTGACA 58.006 43.478 0.00 0.00 0.00 3.58
2075 2959 6.287589 ACATTGGTCTCCTCTAGTAGTTTG 57.712 41.667 0.00 0.00 0.00 2.93
2086 2970 6.833933 GGGTTCATATTAAACATTGGTCTCCT 59.166 38.462 1.34 0.00 0.00 3.69
2088 2972 7.556275 TGAGGGTTCATATTAAACATTGGTCTC 59.444 37.037 1.34 0.00 0.00 3.36
2097 2981 6.624204 CGGTGGTTTGAGGGTTCATATTAAAC 60.624 42.308 0.00 0.00 32.27 2.01
2106 2990 1.165270 CATCGGTGGTTTGAGGGTTC 58.835 55.000 0.00 0.00 0.00 3.62
2107 2991 0.251165 CCATCGGTGGTTTGAGGGTT 60.251 55.000 6.53 0.00 40.83 4.11
2109 2993 4.319133 CCATCGGTGGTTTGAGGG 57.681 61.111 6.53 0.00 40.83 4.30
2121 3005 3.624326 TGCTTTCAAGACAAACCATCG 57.376 42.857 0.00 0.00 0.00 3.84
2138 3022 6.006449 AGTTTGTAAAGGTCTGATGATTGCT 58.994 36.000 0.00 0.00 0.00 3.91
2167 3051 2.715864 CTTGCGTGTGCTGTTTCCCG 62.716 60.000 0.00 0.00 43.34 5.14
2170 3054 0.593128 ATCCTTGCGTGTGCTGTTTC 59.407 50.000 0.00 0.00 43.34 2.78
2171 3055 1.535462 GTATCCTTGCGTGTGCTGTTT 59.465 47.619 0.00 0.00 43.34 2.83
2172 3056 1.156736 GTATCCTTGCGTGTGCTGTT 58.843 50.000 0.00 0.00 43.34 3.16
2176 3060 0.727398 GGAAGTATCCTTGCGTGTGC 59.273 55.000 0.00 0.00 42.93 4.57
2181 3065 2.691409 TTCCTGGAAGTATCCTTGCG 57.309 50.000 4.68 0.00 46.70 4.85
2209 3093 3.431415 AGTTTTGGGAATCTTAGGTGGC 58.569 45.455 0.00 0.00 0.00 5.01
2232 3124 5.708230 TGCTATACCAAACTTGTTACCCTTG 59.292 40.000 0.00 0.00 0.00 3.61
2280 3172 6.472887 CCTAGATCTACAGTTCCACCAAAAA 58.527 40.000 0.00 0.00 0.00 1.94
2281 3173 5.045869 CCCTAGATCTACAGTTCCACCAAAA 60.046 44.000 0.00 0.00 0.00 2.44
2326 3218 5.898972 TCCCCATTGATTCCTCCAATAAAAG 59.101 40.000 0.00 0.00 33.35 2.27
2331 3223 4.228824 CATTCCCCATTGATTCCTCCAAT 58.771 43.478 0.00 0.00 34.83 3.16
2333 3225 2.091166 CCATTCCCCATTGATTCCTCCA 60.091 50.000 0.00 0.00 0.00 3.86
2382 3274 0.179189 CTCGAAATTTGAGCCGCACC 60.179 55.000 0.00 0.00 0.00 5.01
2384 3276 0.321210 TCCTCGAAATTTGAGCCGCA 60.321 50.000 4.71 0.00 31.98 5.69
2407 3299 3.203487 CACCCTTCCTCTACCTCTAGACT 59.797 52.174 0.00 0.00 0.00 3.24
2439 3331 9.395068 ACAATTAAAAGGATTTAAAGGGGGTTA 57.605 29.630 0.00 0.00 42.57 2.85
2440 3332 8.282801 ACAATTAAAAGGATTTAAAGGGGGTT 57.717 30.769 0.00 0.00 42.57 4.11
2441 3333 7.881912 ACAATTAAAAGGATTTAAAGGGGGT 57.118 32.000 0.00 0.00 42.57 4.95
2455 3347 6.696411 TGCAAGTGGGGATAACAATTAAAAG 58.304 36.000 0.00 0.00 0.00 2.27
2456 3348 6.672266 TGCAAGTGGGGATAACAATTAAAA 57.328 33.333 0.00 0.00 0.00 1.52
2457 3349 6.279513 CTGCAAGTGGGGATAACAATTAAA 57.720 37.500 0.00 0.00 0.00 1.52
2458 3350 5.913137 CTGCAAGTGGGGATAACAATTAA 57.087 39.130 0.00 0.00 0.00 1.40
2481 3373 1.915266 CCCTGACCTCCAGAGTGCA 60.915 63.158 0.00 0.00 45.78 4.57
2488 3380 4.715130 CCGGACCCCTGACCTCCA 62.715 72.222 0.00 0.00 0.00 3.86
2489 3381 4.393778 TCCGGACCCCTGACCTCC 62.394 72.222 0.00 0.00 0.00 4.30
2501 3393 1.361176 TGGATCTCTAGGGCTCCGGA 61.361 60.000 2.93 2.93 0.00 5.14
2512 3404 5.920347 TGGTTATGGATAGGATGGATCTCT 58.080 41.667 0.00 0.00 0.00 3.10
2520 3412 6.410853 CCTCAGGTTTTGGTTATGGATAGGAT 60.411 42.308 0.00 0.00 0.00 3.24
2521 3413 5.104109 CCTCAGGTTTTGGTTATGGATAGGA 60.104 44.000 0.00 0.00 0.00 2.94
2556 3448 1.762827 GCTCCATACCCAGGATCTCCA 60.763 57.143 0.00 0.00 38.89 3.86
2580 3472 5.184287 CCTTCTCTAAATAGGACGGATCTCC 59.816 48.000 0.00 0.00 0.00 3.71
2588 3480 6.763610 CCAATGACACCTTCTCTAAATAGGAC 59.236 42.308 0.00 0.00 33.21 3.85
2589 3481 6.126768 CCCAATGACACCTTCTCTAAATAGGA 60.127 42.308 0.00 0.00 33.21 2.94
2595 3487 4.224370 GGTACCCAATGACACCTTCTCTAA 59.776 45.833 0.00 0.00 0.00 2.10
2596 3488 3.773119 GGTACCCAATGACACCTTCTCTA 59.227 47.826 0.00 0.00 0.00 2.43
2621 3513 1.316266 CCCTGACCCCTGGATCTCT 59.684 63.158 0.00 0.00 33.65 3.10
2622 3514 1.768077 CCCCTGACCCCTGGATCTC 60.768 68.421 0.00 0.00 33.65 2.75
2640 3533 1.474332 TTGGACACCCCGTACTCCAC 61.474 60.000 0.00 0.00 37.93 4.02
2647 3540 4.636435 CGCCTTTGGACACCCCGT 62.636 66.667 0.00 0.00 37.93 5.28
2649 3542 2.046285 CATCGCCTTTGGACACCCC 61.046 63.158 0.00 0.00 0.00 4.95
2671 3564 1.691434 CCCCAGATCTCTAGTTCCAGC 59.309 57.143 0.00 0.00 0.00 4.85
2677 3570 0.644937 AAGGCCCCCAGATCTCTAGT 59.355 55.000 0.00 0.00 0.00 2.57
2679 3572 0.400525 CCAAGGCCCCCAGATCTCTA 60.401 60.000 0.00 0.00 0.00 2.43
2680 3573 1.695597 CCAAGGCCCCCAGATCTCT 60.696 63.158 0.00 0.00 0.00 3.10
2754 3648 6.808212 CCATACACAAAGCCATGTTAGAAAAG 59.192 38.462 0.00 0.00 0.00 2.27
2846 3753 0.106894 CTGGAATCGTAGGAAGGCCC 59.893 60.000 0.00 0.00 33.31 5.80
2847 3754 1.120530 TCTGGAATCGTAGGAAGGCC 58.879 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.