Multiple sequence alignment - TraesCS2B01G573700

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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 TraesCS2B01G573700 chr2B 100.000 3399 0 0 1 3399 763472911 763476309 0.000000e+00 6277.0
1 TraesCS2B01G573700 chr2B 86.687 969 90 17 1871 2829 763331158 763332097 0.000000e+00 1038.0
2 TraesCS2B01G573700 chr2B 89.029 556 36 14 2838 3388 763524621 763525156 0.000000e+00 665.0
3 TraesCS2B01G573700 chr2B 91.545 343 20 5 1 341 792126227 792126562 6.640000e-127 464.0
4 TraesCS2B01G573700 chr2B 86.809 235 28 3 1070 1302 39092875 39093108 3.360000e-65 259.0
5 TraesCS2B01G573700 chr2B 83.682 239 32 6 2838 3072 763444741 763444976 5.710000e-53 219.0
6 TraesCS2B01G573700 chr2B 76.527 311 48 16 2895 3204 763389965 763390251 2.730000e-31 147.0
7 TraesCS2B01G573700 chr2B 89.623 106 8 3 3099 3204 762834789 762834891 7.650000e-27 132.0
8 TraesCS2B01G573700 chr2B 89.524 105 9 2 3282 3384 763445151 763445255 7.650000e-27 132.0
9 TraesCS2B01G573700 chr2B 80.916 131 3 4 3156 3284 763444976 763445086 2.170000e-12 84.2
10 TraesCS2B01G573700 chr2A 90.579 2866 172 49 519 3320 753418717 753421548 0.000000e+00 3707.0
11 TraesCS2B01G573700 chr2A 89.254 335 30 4 2889 3218 753412474 753412807 6.790000e-112 414.0
12 TraesCS2B01G573700 chr2A 91.509 106 8 1 339 443 566861345 566861240 9.830000e-31 145.0
13 TraesCS2B01G573700 chr2A 95.122 82 4 0 3318 3399 753421867 753421948 2.750000e-26 130.0
14 TraesCS2B01G573700 chr2A 87.736 106 10 2 3099 3204 753409403 753409505 1.660000e-23 121.0
15 TraesCS2B01G573700 chr2D 92.105 1254 81 10 1578 2825 621634830 621636071 0.000000e+00 1751.0
16 TraesCS2B01G573700 chr2D 90.207 1256 81 24 339 1573 621615207 621616441 0.000000e+00 1600.0
17 TraesCS2B01G573700 chr2D 95.374 562 23 1 2838 3399 621667285 621667843 0.000000e+00 891.0
18 TraesCS2B01G573700 chr2D 81.013 158 5 5 3132 3284 621599953 621600090 6.000000e-18 102.0
19 TraesCS2B01G573700 chr2D 82.692 104 16 2 3283 3384 621600127 621600230 1.300000e-14 91.6
20 TraesCS2B01G573700 chr4B 91.520 342 22 6 1 342 117475368 117475702 6.640000e-127 464.0
21 TraesCS2B01G573700 chr4B 91.509 106 9 0 339 444 232098687 232098792 2.730000e-31 147.0
22 TraesCS2B01G573700 chr5B 91.471 340 23 4 1 340 694674751 694675084 2.390000e-126 462.0
23 TraesCS2B01G573700 chr5B 92.453 106 8 0 339 444 609842567 609842462 5.870000e-33 152.0
24 TraesCS2B01G573700 chr5B 78.182 110 24 0 1822 1931 573408257 573408148 1.690000e-08 71.3
25 TraesCS2B01G573700 chr3D 91.471 340 23 4 1 340 481074621 481074954 2.390000e-126 462.0
26 TraesCS2B01G573700 chr3D 100.000 28 0 0 1905 1932 22303816 22303789 6.000000e-03 52.8
27 TraesCS2B01G573700 chr1A 91.496 341 21 5 1 340 101280057 101280390 2.390000e-126 462.0
28 TraesCS2B01G573700 chr1A 82.707 399 58 8 1100 1491 553958031 553957637 9.030000e-91 344.0
29 TraesCS2B01G573700 chr1A 93.519 108 7 0 339 446 480593849 480593956 9.760000e-36 161.0
30 TraesCS2B01G573700 chr1A 80.645 124 21 3 1518 1639 248436155 248436033 3.610000e-15 93.5
31 TraesCS2B01G573700 chr6B 91.202 341 23 4 1 341 573274807 573274474 1.110000e-124 457.0
32 TraesCS2B01G573700 chr3A 91.014 345 21 6 1 345 201997958 201997624 1.110000e-124 457.0
33 TraesCS2B01G573700 chr3B 91.176 340 22 6 1 340 89378571 89378240 4.000000e-124 455.0
34 TraesCS2B01G573700 chr3B 90.936 342 25 6 1 342 434637129 434636794 4.000000e-124 455.0
35 TraesCS2B01G573700 chr1B 79.268 574 97 16 1822 2378 636738580 636738012 6.880000e-102 381.0
36 TraesCS2B01G573700 chr1B 80.603 464 64 14 1038 1491 636739118 636738671 5.430000e-88 335.0
37 TraesCS2B01G573700 chr1B 79.869 457 77 10 1038 1491 636727006 636726562 1.520000e-83 320.0
38 TraesCS2B01G573700 chr1D 82.524 412 56 9 1088 1491 462093071 462092668 6.980000e-92 348.0
39 TraesCS2B01G573700 chr1D 81.995 411 63 6 1088 1491 462107848 462107442 4.200000e-89 339.0
40 TraesCS2B01G573700 chr1D 78.671 572 76 23 942 1491 462115566 462115019 4.200000e-89 339.0
41 TraesCS2B01G573700 chr1D 91.509 106 9 0 339 444 199421410 199421305 2.730000e-31 147.0
42 TraesCS2B01G573700 chr7D 92.523 107 6 2 339 444 628667802 628667697 5.870000e-33 152.0
43 TraesCS2B01G573700 chr7D 80.247 162 25 5 1528 1686 58907445 58907602 7.710000e-22 115.0
44 TraesCS2B01G573700 chr4D 92.453 106 8 0 339 444 233079337 233079442 5.870000e-33 152.0
45 TraesCS2B01G573700 chr4D 81.356 177 27 5 1518 1689 70326445 70326270 4.570000e-29 139.0
46 TraesCS2B01G573700 chr5D 90.566 106 10 0 339 444 220730038 220729933 1.270000e-29 141.0
47 TraesCS2B01G573700 chr5D 81.884 138 20 5 1525 1658 454313174 454313310 9.970000e-21 111.0
48 TraesCS2B01G573700 chr5D 78.182 110 24 0 1822 1931 466569808 466569699 1.690000e-08 71.3


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 TraesCS2B01G573700 chr2B 763472911 763476309 3398 False 6277.0 6277 100.0000 1 3399 1 chr2B.!!$F5 3398
1 TraesCS2B01G573700 chr2B 763331158 763332097 939 False 1038.0 1038 86.6870 1871 2829 1 chr2B.!!$F3 958
2 TraesCS2B01G573700 chr2B 763524621 763525156 535 False 665.0 665 89.0290 2838 3388 1 chr2B.!!$F6 550
3 TraesCS2B01G573700 chr2A 753418717 753421948 3231 False 1918.5 3707 92.8505 519 3399 2 chr2A.!!$F2 2880
4 TraesCS2B01G573700 chr2A 753409403 753412807 3404 False 267.5 414 88.4950 2889 3218 2 chr2A.!!$F1 329
5 TraesCS2B01G573700 chr2D 621634830 621636071 1241 False 1751.0 1751 92.1050 1578 2825 1 chr2D.!!$F2 1247
6 TraesCS2B01G573700 chr2D 621615207 621616441 1234 False 1600.0 1600 90.2070 339 1573 1 chr2D.!!$F1 1234
7 TraesCS2B01G573700 chr2D 621667285 621667843 558 False 891.0 891 95.3740 2838 3399 1 chr2D.!!$F3 561
8 TraesCS2B01G573700 chr1B 636738012 636739118 1106 True 358.0 381 79.9355 1038 2378 2 chr1B.!!$R2 1340
9 TraesCS2B01G573700 chr1D 462115019 462115566 547 True 339.0 339 78.6710 942 1491 1 chr1D.!!$R4 549

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
255 256 0.037160 ATAAAACAGGACCGCGGGTT 59.963 50.0 31.76 20.53 35.25 4.11 F
256 257 0.885596 TAAAACAGGACCGCGGGTTG 60.886 55.0 31.76 24.78 35.25 3.77 F
266 267 0.953471 CCGCGGGTTGAATTCACTGA 60.953 55.0 20.10 0.00 0.00 3.41 F
1538 1598 0.391597 CCCTGGTTAGTGTCACACGT 59.608 55.0 1.22 0.00 39.64 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1140 1185 0.032403 TCAGGTACGAACGGTTGTGG 59.968 55.000 2.75 0.0 0.0 4.17 R
1257 1302 0.391263 GGTCGGCGAATTGGTTCTCT 60.391 55.000 12.92 0.0 32.0 3.10 R
1793 1884 2.046314 CGGTCCGGGCACAGAAAT 60.046 61.111 9.07 0.0 0.0 2.17 R
3084 3268 0.668535 ACTGAAGGAAAAACTGCCGC 59.331 50.000 0.00 0.0 0.0 6.53 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
26 27 8.141835 TCACATATAACATGTTCAAATCGGAG 57.858 34.615 15.85 0.00 0.00 4.63
27 28 7.768582 TCACATATAACATGTTCAAATCGGAGT 59.231 33.333 15.85 0.39 0.00 3.85
30 31 9.864034 CATATAACATGTTCAAATCGGAGTTAC 57.136 33.333 15.85 0.00 0.00 2.50
31 32 4.921470 ACATGTTCAAATCGGAGTTACG 57.079 40.909 0.00 0.00 0.00 3.18
33 34 3.389925 TGTTCAAATCGGAGTTACGGT 57.610 42.857 0.00 0.00 0.00 4.83
34 35 3.731089 TGTTCAAATCGGAGTTACGGTT 58.269 40.909 0.00 0.00 39.15 4.44
37 38 5.757320 TGTTCAAATCGGAGTTACGGTTTAA 59.243 36.000 0.00 0.00 44.52 1.52
39 40 6.857777 TCAAATCGGAGTTACGGTTTAAAA 57.142 33.333 0.00 0.00 44.52 1.52
41 42 6.705381 TCAAATCGGAGTTACGGTTTAAAAGA 59.295 34.615 0.00 0.00 44.52 2.52
42 43 7.388500 TCAAATCGGAGTTACGGTTTAAAAGAT 59.612 33.333 0.00 0.00 44.52 2.40
43 44 8.658609 CAAATCGGAGTTACGGTTTAAAAGATA 58.341 33.333 0.00 0.00 44.52 1.98
44 45 8.953368 AATCGGAGTTACGGTTTAAAAGATAT 57.047 30.769 0.00 0.00 32.43 1.63
45 46 7.760131 TCGGAGTTACGGTTTAAAAGATATG 57.240 36.000 0.00 0.00 0.00 1.78
46 47 6.757947 TCGGAGTTACGGTTTAAAAGATATGG 59.242 38.462 0.00 0.00 0.00 2.74
47 48 6.510638 CGGAGTTACGGTTTAAAAGATATGGC 60.511 42.308 0.00 0.00 0.00 4.40
49 50 7.316544 AGTTACGGTTTAAAAGATATGGCTG 57.683 36.000 0.00 0.00 0.00 4.85
50 51 7.107542 AGTTACGGTTTAAAAGATATGGCTGA 58.892 34.615 0.00 0.00 0.00 4.26
52 53 8.403236 GTTACGGTTTAAAAGATATGGCTGATT 58.597 33.333 0.00 0.00 0.00 2.57
53 54 7.404671 ACGGTTTAAAAGATATGGCTGATTT 57.595 32.000 0.00 0.00 0.00 2.17
56 57 9.796120 CGGTTTAAAAGATATGGCTGATTTAAA 57.204 29.630 0.00 0.00 32.75 1.52
88 89 8.950961 CATTGTTTGACTTAAATATGATCAGCG 58.049 33.333 0.09 0.00 30.74 5.18
89 90 7.015226 TGTTTGACTTAAATATGATCAGCGG 57.985 36.000 0.09 0.00 0.00 5.52
90 91 6.821160 TGTTTGACTTAAATATGATCAGCGGA 59.179 34.615 0.09 0.00 0.00 5.54
92 93 7.425577 TTGACTTAAATATGATCAGCGGATG 57.574 36.000 3.36 0.00 32.67 3.51
93 94 6.758254 TGACTTAAATATGATCAGCGGATGA 58.242 36.000 3.36 0.00 43.70 2.92
94 95 7.216494 TGACTTAAATATGATCAGCGGATGAA 58.784 34.615 3.36 0.00 42.53 2.57
95 96 7.879677 TGACTTAAATATGATCAGCGGATGAAT 59.120 33.333 3.36 0.57 42.53 2.57
96 97 8.627208 ACTTAAATATGATCAGCGGATGAATT 57.373 30.769 3.36 0.00 42.53 2.17
105 106 8.087982 TGATCAGCGGATGAATTATCTAAAAC 57.912 34.615 3.36 0.00 42.53 2.43
106 107 7.714813 TGATCAGCGGATGAATTATCTAAAACA 59.285 33.333 3.36 0.00 42.53 2.83
108 109 8.087982 TCAGCGGATGAATTATCTAAAACATC 57.912 34.615 0.00 0.00 34.02 3.06
109 110 7.714813 TCAGCGGATGAATTATCTAAAACATCA 59.285 33.333 0.00 0.00 35.54 3.07
110 111 8.013947 CAGCGGATGAATTATCTAAAACATCAG 58.986 37.037 0.00 0.00 35.54 2.90
112 113 7.573843 GCGGATGAATTATCTAAAACATCAGGG 60.574 40.741 0.00 0.00 35.54 4.45
113 114 7.094634 CGGATGAATTATCTAAAACATCAGGGG 60.095 40.741 0.00 0.00 35.54 4.79
114 115 7.177392 GGATGAATTATCTAAAACATCAGGGGG 59.823 40.741 0.00 0.00 35.54 5.40
133 134 4.587584 GGGGGTTTTCGACAAATGTAAA 57.412 40.909 0.00 0.00 0.00 2.01
134 135 4.946445 GGGGGTTTTCGACAAATGTAAAA 58.054 39.130 0.00 0.00 0.00 1.52
136 137 6.689554 GGGGGTTTTCGACAAATGTAAAATA 58.310 36.000 0.00 0.00 0.00 1.40
137 138 7.153315 GGGGGTTTTCGACAAATGTAAAATAA 58.847 34.615 0.00 0.00 0.00 1.40
138 139 7.116662 GGGGGTTTTCGACAAATGTAAAATAAC 59.883 37.037 0.00 0.00 0.00 1.89
139 140 7.148934 GGGGTTTTCGACAAATGTAAAATAACG 60.149 37.037 0.00 0.00 0.00 3.18
141 142 7.379262 GGTTTTCGACAAATGTAAAATAACGGT 59.621 33.333 0.00 0.00 0.00 4.83
142 143 8.744923 GTTTTCGACAAATGTAAAATAACGGTT 58.255 29.630 0.00 0.00 0.00 4.44
143 144 8.491605 TTTCGACAAATGTAAAATAACGGTTC 57.508 30.769 0.00 0.00 0.00 3.62
144 145 6.298103 TCGACAAATGTAAAATAACGGTTCG 58.702 36.000 0.00 0.00 0.00 3.95
146 147 6.557291 ACAAATGTAAAATAACGGTTCGGA 57.443 33.333 0.00 0.00 0.00 4.55
147 148 7.148355 ACAAATGTAAAATAACGGTTCGGAT 57.852 32.000 0.00 0.00 0.00 4.18
148 149 7.024768 ACAAATGTAAAATAACGGTTCGGATG 58.975 34.615 0.00 0.00 0.00 3.51
149 150 6.746745 AATGTAAAATAACGGTTCGGATGT 57.253 33.333 0.00 0.00 0.00 3.06
150 151 5.533533 TGTAAAATAACGGTTCGGATGTG 57.466 39.130 0.00 0.00 0.00 3.21
151 152 5.236282 TGTAAAATAACGGTTCGGATGTGA 58.764 37.500 0.00 0.00 0.00 3.58
155 156 4.724074 ATAACGGTTCGGATGTGACTTA 57.276 40.909 0.00 0.00 0.00 2.24
156 157 3.389925 AACGGTTCGGATGTGACTTAA 57.610 42.857 0.00 0.00 0.00 1.85
157 158 3.389925 ACGGTTCGGATGTGACTTAAA 57.610 42.857 0.00 0.00 0.00 1.52
158 159 3.934068 ACGGTTCGGATGTGACTTAAAT 58.066 40.909 0.00 0.00 0.00 1.40
159 160 3.930848 ACGGTTCGGATGTGACTTAAATC 59.069 43.478 0.00 0.00 0.00 2.17
160 161 3.308866 CGGTTCGGATGTGACTTAAATCC 59.691 47.826 0.00 0.00 37.17 3.01
165 166 4.138487 GGATGTGACTTAAATCCGGACT 57.862 45.455 6.12 0.00 31.11 3.85
166 167 5.272283 GGATGTGACTTAAATCCGGACTA 57.728 43.478 6.12 0.00 31.11 2.59
167 168 5.048507 GGATGTGACTTAAATCCGGACTAC 58.951 45.833 6.12 0.00 31.11 2.73
168 169 4.100707 TGTGACTTAAATCCGGACTACG 57.899 45.455 6.12 1.45 43.80 3.51
178 179 3.413522 CGGACTACGGGTTGACTTC 57.586 57.895 0.00 0.00 39.42 3.01
180 181 1.000060 CGGACTACGGGTTGACTTCAA 60.000 52.381 0.00 0.00 39.42 2.69
182 183 2.298163 GGACTACGGGTTGACTTCAAGA 59.702 50.000 0.00 0.00 36.39 3.02
183 184 3.243975 GGACTACGGGTTGACTTCAAGAA 60.244 47.826 0.00 0.00 36.39 2.52
185 186 4.773013 ACTACGGGTTGACTTCAAGAAAA 58.227 39.130 0.00 0.00 36.39 2.29
186 187 4.573607 ACTACGGGTTGACTTCAAGAAAAC 59.426 41.667 0.00 0.00 36.39 2.43
187 188 3.349022 ACGGGTTGACTTCAAGAAAACA 58.651 40.909 0.00 0.00 36.39 2.83
189 190 3.127895 CGGGTTGACTTCAAGAAAACACA 59.872 43.478 9.07 0.00 36.39 3.72
190 191 4.672409 GGGTTGACTTCAAGAAAACACAG 58.328 43.478 0.00 0.00 36.39 3.66
191 192 4.440112 GGGTTGACTTCAAGAAAACACAGG 60.440 45.833 0.00 0.00 36.39 4.00
192 193 4.440112 GGTTGACTTCAAGAAAACACAGGG 60.440 45.833 0.00 0.00 36.39 4.45
193 194 4.229304 TGACTTCAAGAAAACACAGGGA 57.771 40.909 0.00 0.00 0.00 4.20
194 195 3.945285 TGACTTCAAGAAAACACAGGGAC 59.055 43.478 0.00 0.00 0.00 4.46
195 196 4.200092 GACTTCAAGAAAACACAGGGACT 58.800 43.478 0.00 0.00 43.88 3.85
196 197 4.600062 ACTTCAAGAAAACACAGGGACTT 58.400 39.130 0.00 0.00 34.60 3.01
197 198 5.016831 ACTTCAAGAAAACACAGGGACTTT 58.983 37.500 0.00 0.00 34.60 2.66
199 200 5.323371 TCAAGAAAACACAGGGACTTTTG 57.677 39.130 0.00 0.00 34.60 2.44
200 201 4.770010 TCAAGAAAACACAGGGACTTTTGT 59.230 37.500 0.00 0.00 34.60 2.83
211 212 7.881142 CACAGGGACTTTTGTGTAAAATATGA 58.119 34.615 0.00 0.00 39.77 2.15
213 214 8.919145 ACAGGGACTTTTGTGTAAAATATGAAA 58.081 29.630 0.00 0.00 34.60 2.69
249 250 8.804688 TTTCATTTTAACATAAAACAGGACCG 57.195 30.769 0.00 0.00 0.00 4.79
250 251 6.383415 TCATTTTAACATAAAACAGGACCGC 58.617 36.000 0.00 0.00 0.00 5.68
251 252 4.407496 TTTAACATAAAACAGGACCGCG 57.593 40.909 0.00 0.00 0.00 6.46
252 253 1.161843 AACATAAAACAGGACCGCGG 58.838 50.000 26.86 26.86 0.00 6.46
253 254 0.675522 ACATAAAACAGGACCGCGGG 60.676 55.000 31.76 14.36 0.00 6.13
254 255 0.675522 CATAAAACAGGACCGCGGGT 60.676 55.000 31.76 15.13 39.44 5.28
255 256 0.037160 ATAAAACAGGACCGCGGGTT 59.963 50.000 31.76 20.53 35.25 4.11
256 257 0.885596 TAAAACAGGACCGCGGGTTG 60.886 55.000 31.76 24.78 35.25 3.77
257 258 2.612095 AAAACAGGACCGCGGGTTGA 62.612 55.000 31.76 0.00 35.25 3.18
258 259 2.612095 AAACAGGACCGCGGGTTGAA 62.612 55.000 31.76 0.00 35.25 2.69
259 260 2.046314 CAGGACCGCGGGTTGAAT 60.046 61.111 31.76 6.78 35.25 2.57
260 261 1.674322 CAGGACCGCGGGTTGAATT 60.674 57.895 31.76 5.85 35.25 2.17
261 262 1.376812 AGGACCGCGGGTTGAATTC 60.377 57.895 31.76 15.78 35.25 2.17
262 263 1.673009 GGACCGCGGGTTGAATTCA 60.673 57.895 31.76 3.38 35.25 2.57
265 266 1.234615 ACCGCGGGTTGAATTCACTG 61.235 55.000 31.76 4.05 27.29 3.66
266 267 0.953471 CCGCGGGTTGAATTCACTGA 60.953 55.000 20.10 0.00 0.00 3.41
268 269 1.265635 CGCGGGTTGAATTCACTGAAA 59.734 47.619 7.89 0.00 0.00 2.69
269 270 2.095263 CGCGGGTTGAATTCACTGAAAT 60.095 45.455 7.89 0.00 0.00 2.17
270 271 3.126171 CGCGGGTTGAATTCACTGAAATA 59.874 43.478 7.89 0.00 0.00 1.40
272 273 4.394920 GCGGGTTGAATTCACTGAAATAGA 59.605 41.667 7.89 0.00 0.00 1.98
273 274 5.447818 GCGGGTTGAATTCACTGAAATAGAG 60.448 44.000 7.89 0.00 0.00 2.43
274 275 5.065218 CGGGTTGAATTCACTGAAATAGAGG 59.935 44.000 7.89 0.00 0.00 3.69
276 277 6.180472 GGTTGAATTCACTGAAATAGAGGGA 58.820 40.000 7.89 0.00 0.00 4.20
277 278 6.094186 GGTTGAATTCACTGAAATAGAGGGAC 59.906 42.308 7.89 0.00 0.00 4.46
279 280 7.020827 TGAATTCACTGAAATAGAGGGACTT 57.979 36.000 3.38 0.00 41.55 3.01
282 283 7.929941 ATTCACTGAAATAGAGGGACTTTTC 57.070 36.000 0.00 0.00 41.55 2.29
283 284 6.688073 TCACTGAAATAGAGGGACTTTTCT 57.312 37.500 0.00 0.00 41.55 2.52
284 285 6.467677 TCACTGAAATAGAGGGACTTTTCTG 58.532 40.000 0.00 0.00 41.55 3.02
285 286 6.270000 TCACTGAAATAGAGGGACTTTTCTGA 59.730 38.462 0.00 0.00 41.55 3.27
286 287 6.936900 CACTGAAATAGAGGGACTTTTCTGAA 59.063 38.462 0.00 0.00 41.55 3.02
287 288 7.445402 CACTGAAATAGAGGGACTTTTCTGAAA 59.555 37.037 0.00 0.00 41.55 2.69
288 289 7.998964 ACTGAAATAGAGGGACTTTTCTGAAAA 59.001 33.333 14.31 14.31 41.55 2.29
290 291 9.367160 TGAAATAGAGGGACTTTTCTGAAAAAT 57.633 29.630 15.67 6.78 41.55 1.82
293 294 6.396829 AGAGGGACTTTTCTGAAAAATGTG 57.603 37.500 15.67 7.48 41.55 3.21
294 295 6.129179 AGAGGGACTTTTCTGAAAAATGTGA 58.871 36.000 15.67 0.00 41.55 3.58
296 297 6.752168 AGGGACTTTTCTGAAAAATGTGATG 58.248 36.000 15.67 5.91 34.00 3.07
297 298 6.550854 AGGGACTTTTCTGAAAAATGTGATGA 59.449 34.615 15.67 0.00 34.00 2.92
298 299 6.642540 GGGACTTTTCTGAAAAATGTGATGAC 59.357 38.462 15.67 4.16 34.00 3.06
299 300 6.360681 GGACTTTTCTGAAAAATGTGATGACG 59.639 38.462 15.67 4.03 34.00 4.35
301 302 6.039270 ACTTTTCTGAAAAATGTGATGACGGA 59.961 34.615 15.67 0.00 34.00 4.69
303 304 3.431912 TCTGAAAAATGTGATGACGGACG 59.568 43.478 0.00 0.00 0.00 4.79
304 305 3.394719 TGAAAAATGTGATGACGGACGA 58.605 40.909 0.00 0.00 0.00 4.20
306 307 4.273724 TGAAAAATGTGATGACGGACGAAA 59.726 37.500 0.00 0.00 0.00 3.46
307 308 4.404507 AAAATGTGATGACGGACGAAAG 57.595 40.909 0.00 0.00 0.00 2.62
308 309 3.313012 AATGTGATGACGGACGAAAGA 57.687 42.857 0.00 0.00 0.00 2.52
311 312 3.659786 TGTGATGACGGACGAAAGAAAT 58.340 40.909 0.00 0.00 0.00 2.17
312 313 3.678072 TGTGATGACGGACGAAAGAAATC 59.322 43.478 0.00 0.00 0.00 2.17
314 315 2.823924 TGACGGACGAAAGAAATCCA 57.176 45.000 0.00 0.00 32.35 3.41
315 316 3.114668 TGACGGACGAAAGAAATCCAA 57.885 42.857 0.00 0.00 32.35 3.53
316 317 3.670625 TGACGGACGAAAGAAATCCAAT 58.329 40.909 0.00 0.00 32.35 3.16
317 318 4.069304 TGACGGACGAAAGAAATCCAATT 58.931 39.130 0.00 0.00 32.35 2.32
318 319 4.517453 TGACGGACGAAAGAAATCCAATTT 59.483 37.500 0.00 0.00 34.64 1.82
319 320 4.794169 ACGGACGAAAGAAATCCAATTTG 58.206 39.130 0.00 0.00 31.47 2.32
321 322 4.615912 CGGACGAAAGAAATCCAATTTGCT 60.616 41.667 0.00 0.00 31.47 3.91
322 323 5.230182 GGACGAAAGAAATCCAATTTGCTT 58.770 37.500 0.00 0.00 31.47 3.91
323 324 5.696270 GGACGAAAGAAATCCAATTTGCTTT 59.304 36.000 0.00 0.00 34.94 3.51
324 325 6.866248 GGACGAAAGAAATCCAATTTGCTTTA 59.134 34.615 0.00 0.00 33.72 1.85
326 327 8.831715 ACGAAAGAAATCCAATTTGCTTTATT 57.168 26.923 0.00 0.00 33.72 1.40
327 328 9.921637 ACGAAAGAAATCCAATTTGCTTTATTA 57.078 25.926 0.00 0.00 33.72 0.98
413 414 8.463930 TGTAAAGTTTGACTTGATCCAAATCT 57.536 30.769 0.00 0.00 38.66 2.40
427 428 5.518848 TCCAAATCTAATACGCGGAGTAA 57.481 39.130 12.47 0.00 39.04 2.24
435 436 6.567050 TCTAATACGCGGAGTAAAAATGACT 58.433 36.000 12.47 0.00 39.04 3.41
478 479 5.558273 CGCTTGTAGTGTGTTTCTCGAAAAT 60.558 40.000 0.00 0.00 31.33 1.82
513 515 2.546195 AAGCGTACTCGAGCTGTAAG 57.454 50.000 13.61 2.06 43.78 2.34
538 540 4.517952 TTGTGTTGGTAAATCCTGCATG 57.482 40.909 0.00 0.00 37.07 4.06
542 544 3.253230 GTTGGTAAATCCTGCATGTTGC 58.747 45.455 0.00 0.00 45.29 4.17
613 615 5.147162 GCTAAGTTGATATTTGGTATGCGC 58.853 41.667 0.00 0.00 0.00 6.09
656 658 3.593442 TGTTGACAGAATTGGGAAGGT 57.407 42.857 0.00 0.00 0.00 3.50
702 704 3.151710 CGGTGTCCGGCCCTGATA 61.152 66.667 0.00 0.00 44.15 2.15
704 706 1.837090 GGTGTCCGGCCCTGATAAT 59.163 57.895 0.00 0.00 0.00 1.28
751 757 4.457834 ACCAACTCGATCTTCTTTCGAT 57.542 40.909 0.00 0.00 43.93 3.59
753 759 3.799420 CCAACTCGATCTTCTTTCGATCC 59.201 47.826 0.00 0.00 43.93 3.36
898 904 3.890674 GGCCGACACTGCCTAAAG 58.109 61.111 0.00 0.00 45.70 1.85
937 970 1.337821 GCGCGCTCTATATAAACGCT 58.662 50.000 26.67 0.00 46.91 5.07
938 971 1.317904 GCGCGCTCTATATAAACGCTC 59.682 52.381 26.67 9.02 46.91 5.03
939 972 1.573596 CGCGCTCTATATAAACGCTCG 59.426 52.381 5.56 8.17 46.91 5.03
1257 1302 1.451567 CCTCACCTACGAGCTCGGA 60.452 63.158 36.93 30.28 44.95 4.55
1308 1353 1.731969 GTTCGTCGCAAGGTACGCT 60.732 57.895 0.00 0.00 38.94 5.07
1495 1555 2.601314 TCGCAATGCTGTACGTATTCAC 59.399 45.455 2.94 0.00 0.00 3.18
1538 1598 0.391597 CCCTGGTTAGTGTCACACGT 59.608 55.000 1.22 0.00 39.64 4.49
1539 1599 1.202604 CCCTGGTTAGTGTCACACGTT 60.203 52.381 1.22 0.00 39.64 3.99
1546 1606 4.347813 GTTAGTGTCACACGTTTTTGCAT 58.652 39.130 1.22 0.00 39.64 3.96
1598 1660 6.100279 AGGCATGTTTAGTTATCTGAGGATGA 59.900 38.462 0.00 0.00 33.71 2.92
1641 1707 3.559655 GTCAACTTTTTGTTTGGATGGCC 59.440 43.478 0.00 0.00 36.63 5.36
1647 1713 3.922171 TTTGTTTGGATGGCCAGTTTT 57.078 38.095 13.05 0.00 46.91 2.43
1735 1812 5.907207 TGGTGACACTTATCATTAGAGCTC 58.093 41.667 5.27 5.27 33.40 4.09
1741 1819 7.282450 TGACACTTATCATTAGAGCTCGTTAGA 59.718 37.037 8.37 6.27 0.00 2.10
1752 1830 4.892934 AGAGCTCGTTAGAGGAATCTCATT 59.107 41.667 8.37 0.00 44.51 2.57
1828 1919 3.127533 GACCGGGTGCATGCAGTC 61.128 66.667 23.41 20.42 0.00 3.51
1966 2057 0.464452 GCAACCGAGGCTACTACCAT 59.536 55.000 0.00 0.00 0.00 3.55
2101 2204 4.796495 GCGGCGGTCCCCAAGAAT 62.796 66.667 9.78 0.00 0.00 2.40
2188 2291 0.037326 TGCAGTTCTACAAGAGCGGG 60.037 55.000 0.00 0.00 30.21 6.13
2403 2506 0.828022 TACCCGACCATGTGATGTCC 59.172 55.000 0.00 0.00 0.00 4.02
2455 2567 0.175760 TAAGTAAGCTCGCAGGCAGG 59.824 55.000 0.00 0.00 34.17 4.85
2456 2568 3.198489 GTAAGCTCGCAGGCAGGC 61.198 66.667 0.00 0.00 34.17 4.85
2501 2613 1.069296 CCATCGTGCATTTGTGACGTT 60.069 47.619 0.00 0.00 34.69 3.99
2635 2756 3.534554 CAAAAGGGCTGCAAAAAGTCTT 58.465 40.909 0.50 0.00 0.00 3.01
2637 2758 2.896745 AGGGCTGCAAAAAGTCTTTG 57.103 45.000 0.50 0.00 0.00 2.77
2639 2760 2.159057 AGGGCTGCAAAAAGTCTTTGTG 60.159 45.455 10.71 10.71 0.00 3.33
2643 2764 4.202010 GGCTGCAAAAAGTCTTTGTGTCTA 60.202 41.667 15.48 3.99 0.00 2.59
2644 2765 5.339990 GCTGCAAAAAGTCTTTGTGTCTAA 58.660 37.500 15.48 1.28 0.00 2.10
2645 2766 5.230097 GCTGCAAAAAGTCTTTGTGTCTAAC 59.770 40.000 15.48 1.31 0.00 2.34
2692 2816 6.803807 GCAAGGTAAAATATAGCATGCTAAGC 59.196 38.462 30.06 20.88 36.90 3.09
2704 2828 1.157870 TGCTAAGCGAAATAGCGGCC 61.158 55.000 0.00 0.00 46.93 6.13
2755 2883 4.651994 GCATGCCAATAACGTGCTATATC 58.348 43.478 6.36 0.00 44.79 1.63
2863 2991 2.806244 AGTTTTTCTTCGGGATGACACG 59.194 45.455 0.00 0.00 45.08 4.49
2907 3091 2.095768 CGCAACGATTGGAAAGTCACAT 60.096 45.455 0.00 0.00 0.00 3.21
3006 3190 2.704190 TCCCTCCAGTATCCCAGATC 57.296 55.000 0.00 0.00 0.00 2.75
3023 3207 6.070021 TCCCAGATCTGACAAATACATTGAGT 60.070 38.462 24.62 0.00 41.85 3.41
3084 3268 4.212847 CGCAAGGATTATCACTCCAATCTG 59.787 45.833 0.00 0.00 35.08 2.90
3216 3410 4.225042 TGCAAATCATGTACCAGTAGGAGT 59.775 41.667 0.00 0.00 38.69 3.85
3217 3411 5.186198 GCAAATCATGTACCAGTAGGAGTT 58.814 41.667 0.00 0.00 38.69 3.01
3218 3412 5.648092 GCAAATCATGTACCAGTAGGAGTTT 59.352 40.000 0.00 0.00 38.69 2.66
3247 3441 6.573664 TTTAGGAGTTCATGTGGAAACATG 57.426 37.500 11.70 11.70 46.14 3.21
3261 3459 5.640357 GTGGAAACATGTTGATTTCATGCAT 59.360 36.000 12.82 0.00 46.14 3.96
3262 3460 5.639931 TGGAAACATGTTGATTTCATGCATG 59.360 36.000 21.07 21.07 44.26 4.06
3263 3461 5.446741 GGAAACATGTTGATTTCATGCATGC 60.447 40.000 22.25 11.82 44.26 4.06
3264 3462 4.195225 ACATGTTGATTTCATGCATGCA 57.805 36.364 25.04 25.04 44.26 3.96
3391 3910 4.081087 TCAATCTCCACCTTTGGTACTAGC 60.081 45.833 0.00 0.00 44.35 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.864034 GTAACTCCGATTTGAACATGTTATATG 57.136 33.333 11.95 0.00 0.00 1.78
5 6 8.761497 CGTAACTCCGATTTGAACATGTTATAT 58.239 33.333 11.95 5.21 0.00 0.86
6 7 7.223193 CCGTAACTCCGATTTGAACATGTTATA 59.777 37.037 11.95 0.57 0.00 0.98
8 9 5.349270 CCGTAACTCCGATTTGAACATGTTA 59.651 40.000 11.95 0.00 0.00 2.41
9 10 4.153475 CCGTAACTCCGATTTGAACATGTT 59.847 41.667 11.78 11.78 0.00 2.71
10 11 3.682858 CCGTAACTCCGATTTGAACATGT 59.317 43.478 0.00 0.00 0.00 3.21
11 12 3.682858 ACCGTAACTCCGATTTGAACATG 59.317 43.478 0.00 0.00 0.00 3.21
12 13 3.934068 ACCGTAACTCCGATTTGAACAT 58.066 40.909 0.00 0.00 0.00 2.71
14 15 4.737353 AAACCGTAACTCCGATTTGAAC 57.263 40.909 0.00 0.00 0.00 3.18
15 16 6.857777 TTTAAACCGTAACTCCGATTTGAA 57.142 33.333 0.00 0.00 0.00 2.69
16 17 6.705381 TCTTTTAAACCGTAACTCCGATTTGA 59.295 34.615 0.00 0.00 0.00 2.69
17 18 6.890558 TCTTTTAAACCGTAACTCCGATTTG 58.109 36.000 0.00 0.00 0.00 2.32
19 20 8.823818 CATATCTTTTAAACCGTAACTCCGATT 58.176 33.333 0.00 0.00 0.00 3.34
20 21 7.440255 CCATATCTTTTAAACCGTAACTCCGAT 59.560 37.037 0.00 0.00 0.00 4.18
21 22 6.757947 CCATATCTTTTAAACCGTAACTCCGA 59.242 38.462 0.00 0.00 0.00 4.55
22 23 6.510638 GCCATATCTTTTAAACCGTAACTCCG 60.511 42.308 0.00 0.00 0.00 4.63
23 24 6.541278 AGCCATATCTTTTAAACCGTAACTCC 59.459 38.462 0.00 0.00 0.00 3.85
24 25 7.279313 TCAGCCATATCTTTTAAACCGTAACTC 59.721 37.037 0.00 0.00 0.00 3.01
26 27 7.311364 TCAGCCATATCTTTTAAACCGTAAC 57.689 36.000 0.00 0.00 0.00 2.50
27 28 8.514330 AATCAGCCATATCTTTTAAACCGTAA 57.486 30.769 0.00 0.00 0.00 3.18
30 31 9.796120 TTTAAATCAGCCATATCTTTTAAACCG 57.204 29.630 0.00 0.00 0.00 4.44
61 62 8.749499 GCTGATCATATTTAAGTCAAACAATGC 58.251 33.333 0.00 0.00 0.00 3.56
62 63 8.950961 CGCTGATCATATTTAAGTCAAACAATG 58.049 33.333 0.00 0.00 0.00 2.82
63 64 8.131100 CCGCTGATCATATTTAAGTCAAACAAT 58.869 33.333 0.00 0.00 0.00 2.71
67 68 7.714813 TCATCCGCTGATCATATTTAAGTCAAA 59.285 33.333 0.00 0.00 0.00 2.69
68 69 7.216494 TCATCCGCTGATCATATTTAAGTCAA 58.784 34.615 0.00 0.00 0.00 3.18
71 72 8.627208 AATTCATCCGCTGATCATATTTAAGT 57.373 30.769 0.00 0.00 32.72 2.24
78 79 9.942850 TTTTAGATAATTCATCCGCTGATCATA 57.057 29.630 0.00 0.00 33.75 2.15
80 81 7.714813 TGTTTTAGATAATTCATCCGCTGATCA 59.285 33.333 0.00 0.00 33.75 2.92
81 82 8.087982 TGTTTTAGATAATTCATCCGCTGATC 57.912 34.615 0.00 0.00 33.75 2.92
82 83 8.627208 ATGTTTTAGATAATTCATCCGCTGAT 57.373 30.769 0.00 0.00 33.75 2.90
83 84 7.714813 TGATGTTTTAGATAATTCATCCGCTGA 59.285 33.333 0.00 0.00 33.75 4.26
84 85 7.864686 TGATGTTTTAGATAATTCATCCGCTG 58.135 34.615 0.00 0.00 33.75 5.18
85 86 7.173907 CCTGATGTTTTAGATAATTCATCCGCT 59.826 37.037 0.00 0.00 33.75 5.52
86 87 7.301054 CCTGATGTTTTAGATAATTCATCCGC 58.699 38.462 0.00 0.00 33.75 5.54
88 89 7.177392 CCCCCTGATGTTTTAGATAATTCATCC 59.823 40.741 0.00 0.00 33.75 3.51
89 90 8.115490 CCCCCTGATGTTTTAGATAATTCATC 57.885 38.462 0.00 0.00 34.28 2.92
112 113 4.587584 TTTACATTTGTCGAAAACCCCC 57.412 40.909 0.00 0.00 0.00 5.40
113 114 7.148934 CGTTATTTTACATTTGTCGAAAACCCC 60.149 37.037 0.00 0.00 0.00 4.95
114 115 7.148934 CCGTTATTTTACATTTGTCGAAAACCC 60.149 37.037 0.00 0.00 0.00 4.11
115 116 7.379262 ACCGTTATTTTACATTTGTCGAAAACC 59.621 33.333 0.00 0.00 0.00 3.27
117 118 8.853469 AACCGTTATTTTACATTTGTCGAAAA 57.147 26.923 0.00 0.00 0.00 2.29
118 119 7.320797 CGAACCGTTATTTTACATTTGTCGAAA 59.679 33.333 0.00 0.00 0.00 3.46
122 123 6.601264 TCCGAACCGTTATTTTACATTTGTC 58.399 36.000 0.00 0.00 0.00 3.18
123 124 6.557291 TCCGAACCGTTATTTTACATTTGT 57.443 33.333 0.00 0.00 0.00 2.83
124 125 7.007905 CACATCCGAACCGTTATTTTACATTTG 59.992 37.037 0.00 0.00 0.00 2.32
125 126 7.024768 CACATCCGAACCGTTATTTTACATTT 58.975 34.615 0.00 0.00 0.00 2.32
126 127 6.372103 TCACATCCGAACCGTTATTTTACATT 59.628 34.615 0.00 0.00 0.00 2.71
127 128 5.875910 TCACATCCGAACCGTTATTTTACAT 59.124 36.000 0.00 0.00 0.00 2.29
128 129 5.120519 GTCACATCCGAACCGTTATTTTACA 59.879 40.000 0.00 0.00 0.00 2.41
129 130 5.349543 AGTCACATCCGAACCGTTATTTTAC 59.650 40.000 0.00 0.00 0.00 2.01
130 131 5.481105 AGTCACATCCGAACCGTTATTTTA 58.519 37.500 0.00 0.00 0.00 1.52
131 132 4.320870 AGTCACATCCGAACCGTTATTTT 58.679 39.130 0.00 0.00 0.00 1.82
133 134 3.604875 AGTCACATCCGAACCGTTATT 57.395 42.857 0.00 0.00 0.00 1.40
134 135 3.604875 AAGTCACATCCGAACCGTTAT 57.395 42.857 0.00 0.00 0.00 1.89
136 137 3.389925 TTAAGTCACATCCGAACCGTT 57.610 42.857 0.00 0.00 0.00 4.44
137 138 3.389925 TTTAAGTCACATCCGAACCGT 57.610 42.857 0.00 0.00 0.00 4.83
138 139 3.308866 GGATTTAAGTCACATCCGAACCG 59.691 47.826 0.03 0.00 0.00 4.44
139 140 4.877323 GGATTTAAGTCACATCCGAACC 57.123 45.455 0.03 0.00 0.00 3.62
144 145 4.138487 AGTCCGGATTTAAGTCACATCC 57.862 45.455 7.81 0.00 34.18 3.51
146 147 4.679662 CGTAGTCCGGATTTAAGTCACAT 58.320 43.478 7.81 0.00 0.00 3.21
147 148 4.100707 CGTAGTCCGGATTTAAGTCACA 57.899 45.455 7.81 0.00 0.00 3.58
160 161 0.599558 TGAAGTCAACCCGTAGTCCG 59.400 55.000 0.00 0.00 0.00 4.79
163 164 4.411256 TTTCTTGAAGTCAACCCGTAGT 57.589 40.909 0.00 0.00 0.00 2.73
165 166 4.333372 GTGTTTTCTTGAAGTCAACCCGTA 59.667 41.667 0.00 0.00 0.00 4.02
166 167 3.128068 GTGTTTTCTTGAAGTCAACCCGT 59.872 43.478 0.00 0.00 0.00 5.28
167 168 3.127895 TGTGTTTTCTTGAAGTCAACCCG 59.872 43.478 0.00 0.00 0.00 5.28
168 169 4.440112 CCTGTGTTTTCTTGAAGTCAACCC 60.440 45.833 0.00 0.00 0.00 4.11
169 170 4.440112 CCCTGTGTTTTCTTGAAGTCAACC 60.440 45.833 0.00 0.00 0.00 3.77
170 171 4.398044 TCCCTGTGTTTTCTTGAAGTCAAC 59.602 41.667 0.00 0.00 0.00 3.18
171 172 4.398044 GTCCCTGTGTTTTCTTGAAGTCAA 59.602 41.667 0.00 0.00 0.00 3.18
172 173 3.945285 GTCCCTGTGTTTTCTTGAAGTCA 59.055 43.478 0.00 0.00 0.00 3.41
173 174 4.200092 AGTCCCTGTGTTTTCTTGAAGTC 58.800 43.478 0.00 0.00 0.00 3.01
174 175 4.236527 AGTCCCTGTGTTTTCTTGAAGT 57.763 40.909 0.00 0.00 0.00 3.01
175 176 5.582689 AAAGTCCCTGTGTTTTCTTGAAG 57.417 39.130 0.00 0.00 0.00 3.02
176 177 5.245075 ACAAAAGTCCCTGTGTTTTCTTGAA 59.755 36.000 0.00 0.00 0.00 2.69
178 179 4.864247 CACAAAAGTCCCTGTGTTTTCTTG 59.136 41.667 0.00 0.00 38.49 3.02
180 181 4.718940 CACAAAAGTCCCTGTGTTTTCT 57.281 40.909 0.00 0.00 38.49 2.52
186 187 7.881142 TCATATTTTACACAAAAGTCCCTGTG 58.119 34.615 0.81 0.81 46.76 3.66
187 188 8.472007 TTCATATTTTACACAAAAGTCCCTGT 57.528 30.769 0.00 0.00 37.08 4.00
224 225 7.382759 GCGGTCCTGTTTTATGTTAAAATGAAA 59.617 33.333 0.00 0.00 0.00 2.69
225 226 6.864165 GCGGTCCTGTTTTATGTTAAAATGAA 59.136 34.615 0.00 0.00 0.00 2.57
226 227 6.383415 GCGGTCCTGTTTTATGTTAAAATGA 58.617 36.000 0.00 0.00 0.00 2.57
227 228 5.285134 CGCGGTCCTGTTTTATGTTAAAATG 59.715 40.000 0.00 0.00 0.00 2.32
228 229 5.395642 CGCGGTCCTGTTTTATGTTAAAAT 58.604 37.500 0.00 0.00 0.00 1.82
229 230 4.320348 CCGCGGTCCTGTTTTATGTTAAAA 60.320 41.667 19.50 0.00 0.00 1.52
230 231 3.188873 CCGCGGTCCTGTTTTATGTTAAA 59.811 43.478 19.50 0.00 0.00 1.52
231 232 2.743126 CCGCGGTCCTGTTTTATGTTAA 59.257 45.455 19.50 0.00 0.00 2.01
232 233 2.348660 CCGCGGTCCTGTTTTATGTTA 58.651 47.619 19.50 0.00 0.00 2.41
233 234 1.161843 CCGCGGTCCTGTTTTATGTT 58.838 50.000 19.50 0.00 0.00 2.71
234 235 0.675522 CCCGCGGTCCTGTTTTATGT 60.676 55.000 26.12 0.00 0.00 2.29
237 238 0.885596 CAACCCGCGGTCCTGTTTTA 60.886 55.000 26.12 0.00 33.12 1.52
239 240 2.593436 CAACCCGCGGTCCTGTTT 60.593 61.111 26.12 3.96 33.12 2.83
241 242 2.406002 AATTCAACCCGCGGTCCTGT 62.406 55.000 26.12 12.13 33.12 4.00
242 243 1.644786 GAATTCAACCCGCGGTCCTG 61.645 60.000 26.12 17.56 33.12 3.86
243 244 1.376812 GAATTCAACCCGCGGTCCT 60.377 57.895 26.12 4.48 33.12 3.85
244 245 1.673009 TGAATTCAACCCGCGGTCC 60.673 57.895 26.12 4.01 33.12 4.46
245 246 0.953960 AGTGAATTCAACCCGCGGTC 60.954 55.000 26.12 13.68 33.12 4.79
246 247 1.072505 AGTGAATTCAACCCGCGGT 59.927 52.632 26.12 9.63 37.65 5.68
247 248 0.953471 TCAGTGAATTCAACCCGCGG 60.953 55.000 21.04 21.04 0.00 6.46
248 249 0.871722 TTCAGTGAATTCAACCCGCG 59.128 50.000 10.35 0.00 0.00 6.46
249 250 3.575965 ATTTCAGTGAATTCAACCCGC 57.424 42.857 10.35 0.00 0.00 6.13
250 251 5.065218 CCTCTATTTCAGTGAATTCAACCCG 59.935 44.000 10.35 0.00 0.00 5.28
251 252 5.358160 CCCTCTATTTCAGTGAATTCAACCC 59.642 44.000 10.35 0.00 0.00 4.11
252 253 6.094186 GTCCCTCTATTTCAGTGAATTCAACC 59.906 42.308 10.35 0.00 0.00 3.77
253 254 6.881602 AGTCCCTCTATTTCAGTGAATTCAAC 59.118 38.462 10.35 4.88 0.00 3.18
254 255 7.020827 AGTCCCTCTATTTCAGTGAATTCAA 57.979 36.000 10.35 0.00 0.00 2.69
255 256 6.627087 AGTCCCTCTATTTCAGTGAATTCA 57.373 37.500 6.36 3.38 0.00 2.57
256 257 7.929941 AAAGTCCCTCTATTTCAGTGAATTC 57.070 36.000 6.36 0.00 0.00 2.17
257 258 8.166726 AGAAAAGTCCCTCTATTTCAGTGAATT 58.833 33.333 6.36 5.94 34.91 2.17
258 259 7.609532 CAGAAAAGTCCCTCTATTTCAGTGAAT 59.390 37.037 6.36 0.01 34.91 2.57
259 260 6.936900 CAGAAAAGTCCCTCTATTTCAGTGAA 59.063 38.462 0.08 0.08 34.91 3.18
260 261 6.270000 TCAGAAAAGTCCCTCTATTTCAGTGA 59.730 38.462 0.00 0.00 34.91 3.41
261 262 6.467677 TCAGAAAAGTCCCTCTATTTCAGTG 58.532 40.000 0.00 0.00 34.91 3.66
262 263 6.688073 TCAGAAAAGTCCCTCTATTTCAGT 57.312 37.500 0.00 0.00 34.91 3.41
265 266 9.631452 CATTTTTCAGAAAAGTCCCTCTATTTC 57.369 33.333 8.34 0.00 38.09 2.17
266 267 9.147732 ACATTTTTCAGAAAAGTCCCTCTATTT 57.852 29.630 8.34 0.00 38.09 1.40
268 269 7.944554 TCACATTTTTCAGAAAAGTCCCTCTAT 59.055 33.333 8.34 0.00 38.09 1.98
269 270 7.287061 TCACATTTTTCAGAAAAGTCCCTCTA 58.713 34.615 8.34 0.00 38.09 2.43
270 271 6.129179 TCACATTTTTCAGAAAAGTCCCTCT 58.871 36.000 8.34 0.00 38.09 3.69
272 273 6.550854 TCATCACATTTTTCAGAAAAGTCCCT 59.449 34.615 8.34 0.00 38.09 4.20
273 274 6.642540 GTCATCACATTTTTCAGAAAAGTCCC 59.357 38.462 8.34 0.00 38.09 4.46
274 275 6.360681 CGTCATCACATTTTTCAGAAAAGTCC 59.639 38.462 8.34 0.00 38.09 3.85
276 277 6.039270 TCCGTCATCACATTTTTCAGAAAAGT 59.961 34.615 8.34 3.20 38.09 2.66
277 278 6.360681 GTCCGTCATCACATTTTTCAGAAAAG 59.639 38.462 8.34 1.42 38.09 2.27
278 279 6.205784 GTCCGTCATCACATTTTTCAGAAAA 58.794 36.000 4.06 4.06 38.96 2.29
279 280 5.559991 CGTCCGTCATCACATTTTTCAGAAA 60.560 40.000 0.00 0.00 0.00 2.52
282 283 3.431912 TCGTCCGTCATCACATTTTTCAG 59.568 43.478 0.00 0.00 0.00 3.02
283 284 3.394719 TCGTCCGTCATCACATTTTTCA 58.605 40.909 0.00 0.00 0.00 2.69
284 285 4.398549 TTCGTCCGTCATCACATTTTTC 57.601 40.909 0.00 0.00 0.00 2.29
285 286 4.513692 TCTTTCGTCCGTCATCACATTTTT 59.486 37.500 0.00 0.00 0.00 1.94
286 287 4.062293 TCTTTCGTCCGTCATCACATTTT 58.938 39.130 0.00 0.00 0.00 1.82
287 288 3.659786 TCTTTCGTCCGTCATCACATTT 58.340 40.909 0.00 0.00 0.00 2.32
288 289 3.313012 TCTTTCGTCCGTCATCACATT 57.687 42.857 0.00 0.00 0.00 2.71
290 291 2.804697 TTCTTTCGTCCGTCATCACA 57.195 45.000 0.00 0.00 0.00 3.58
293 294 3.259064 TGGATTTCTTTCGTCCGTCATC 58.741 45.455 0.00 0.00 34.72 2.92
294 295 3.328382 TGGATTTCTTTCGTCCGTCAT 57.672 42.857 0.00 0.00 34.72 3.06
296 297 4.680171 AATTGGATTTCTTTCGTCCGTC 57.320 40.909 0.00 0.00 34.72 4.79
297 298 4.794169 CAAATTGGATTTCTTTCGTCCGT 58.206 39.130 0.00 0.00 34.72 4.69
298 299 3.608073 GCAAATTGGATTTCTTTCGTCCG 59.392 43.478 0.00 0.00 34.72 4.79
299 300 4.809673 AGCAAATTGGATTTCTTTCGTCC 58.190 39.130 0.00 0.00 0.00 4.79
301 302 8.831715 AATAAAGCAAATTGGATTTCTTTCGT 57.168 26.923 0.00 0.00 34.54 3.85
413 414 5.521010 CCAGTCATTTTTACTCCGCGTATTA 59.479 40.000 4.92 0.00 0.00 0.98
427 428 1.005215 CCTGCTCCCTCCAGTCATTTT 59.995 52.381 0.00 0.00 0.00 1.82
435 436 2.607750 GGACACCTGCTCCCTCCA 60.608 66.667 0.00 0.00 0.00 3.86
455 456 4.789095 TTTCGAGAAACACACTACAAGC 57.211 40.909 0.00 0.00 0.00 4.01
513 515 3.740832 GCAGGATTTACCAACACAAAAGC 59.259 43.478 0.00 0.00 42.04 3.51
538 540 6.012658 TGATAAGTTCAACTGATTGGCAAC 57.987 37.500 0.00 0.00 36.39 4.17
613 615 3.560902 TTCGTCTTCTAGCACAGTGAG 57.439 47.619 4.15 0.00 0.00 3.51
656 658 7.842982 TGTATACTAACTAATGCACCTTGTCA 58.157 34.615 4.17 0.00 0.00 3.58
702 704 1.895131 CCTTGCCCTGCACACTAAATT 59.105 47.619 0.00 0.00 38.71 1.82
704 706 1.178534 GCCTTGCCCTGCACACTAAA 61.179 55.000 0.00 0.00 38.71 1.85
751 757 2.677524 GCATGCCTTGGCACAGGA 60.678 61.111 17.22 0.15 42.39 3.86
753 759 1.153647 CATGCATGCCTTGGCACAG 60.154 57.895 17.22 13.25 43.75 3.66
790 796 5.499004 TTCTCTTGGTGCCTTAGTTGTAT 57.501 39.130 0.00 0.00 0.00 2.29
796 802 2.095718 GCGTTTTCTCTTGGTGCCTTAG 60.096 50.000 0.00 0.00 0.00 2.18
897 903 2.969628 CGGGAGCATGTCTTTAGACT 57.030 50.000 10.92 0.00 44.99 3.24
937 970 3.332493 GAAGGTGTAGACGCGCCGA 62.332 63.158 5.73 0.00 43.39 5.54
938 971 2.879462 GAAGGTGTAGACGCGCCG 60.879 66.667 5.73 0.00 43.39 6.46
939 972 1.153628 ATGAAGGTGTAGACGCGCC 60.154 57.895 5.73 0.00 39.22 6.53
1096 1141 1.596260 GTCCATCATCAGCATGTCACG 59.404 52.381 0.00 0.00 37.40 4.35
1140 1185 0.032403 TCAGGTACGAACGGTTGTGG 59.968 55.000 2.75 0.00 0.00 4.17
1257 1302 0.391263 GGTCGGCGAATTGGTTCTCT 60.391 55.000 12.92 0.00 32.00 3.10
1526 1586 3.623510 TCATGCAAAAACGTGTGACACTA 59.376 39.130 14.42 0.00 31.34 2.74
1531 1591 4.362932 TTCTTCATGCAAAAACGTGTGA 57.637 36.364 0.00 0.00 0.00 3.58
1538 1598 4.756135 GGGCAGAATTTCTTCATGCAAAAA 59.244 37.500 9.66 0.00 37.31 1.94
1539 1599 4.040706 AGGGCAGAATTTCTTCATGCAAAA 59.959 37.500 9.66 0.00 37.31 2.44
1546 1606 2.224523 ACGTCAGGGCAGAATTTCTTCA 60.225 45.455 0.00 0.00 33.56 3.02
1573 1633 5.957771 TCCTCAGATAACTAAACATGCCT 57.042 39.130 0.00 0.00 0.00 4.75
1598 1660 9.410556 GTTGACATGCTTCATAAATAAAGTTGT 57.589 29.630 0.00 0.00 0.00 3.32
1685 1762 2.820059 ACATCGCTCTGACTGAACAA 57.180 45.000 0.00 0.00 0.00 2.83
1686 1763 2.820059 AACATCGCTCTGACTGAACA 57.180 45.000 0.00 0.00 0.00 3.18
1687 1764 5.499334 CGAAATAACATCGCTCTGACTGAAC 60.499 44.000 0.00 0.00 33.07 3.18
1688 1765 4.562789 CGAAATAACATCGCTCTGACTGAA 59.437 41.667 0.00 0.00 33.07 3.02
1690 1767 3.859961 ACGAAATAACATCGCTCTGACTG 59.140 43.478 0.00 0.00 43.88 3.51
1691 1768 3.859961 CACGAAATAACATCGCTCTGACT 59.140 43.478 0.00 0.00 43.88 3.41
1735 1812 7.776933 TGAAATGAATGAGATTCCTCTAACG 57.223 36.000 0.00 0.00 40.10 3.18
1752 1830 6.821665 GGCCAGTACTTACATAGTTGAAATGA 59.178 38.462 0.00 0.00 38.33 2.57
1793 1884 2.046314 CGGTCCGGGCACAGAAAT 60.046 61.111 9.07 0.00 0.00 2.17
1828 1919 3.123620 GAGAACGCCCAGCAGCTG 61.124 66.667 16.23 16.23 0.00 4.24
1898 1989 3.699894 CTGCTGCTCCGACAGGGT 61.700 66.667 0.00 0.00 38.16 4.34
1966 2057 2.550277 TGATCCACTGGAAGGCTCTA 57.450 50.000 0.66 0.00 39.30 2.43
2101 2204 2.752358 CTCTGCAGGGCCAGTTCA 59.248 61.111 15.13 0.00 34.47 3.18
2188 2291 3.787001 CAGGGGGCCGAGAAGACC 61.787 72.222 0.00 0.00 0.00 3.85
2473 2585 3.378112 ACAAATGCACGATGGAATACTGG 59.622 43.478 0.00 0.00 0.00 4.00
2474 2586 4.094739 TCACAAATGCACGATGGAATACTG 59.905 41.667 0.00 0.00 0.00 2.74
2479 2591 1.196581 CGTCACAAATGCACGATGGAA 59.803 47.619 0.00 0.00 33.75 3.53
2501 2613 4.968812 TGTAATCGACGACATAGGTTGA 57.031 40.909 0.00 0.00 32.60 3.18
2608 2722 2.042404 TTGCAGCCCTTTTGCTTGGG 62.042 55.000 0.00 0.00 46.00 4.12
2692 2816 3.338676 GAGGCGGCCGCTATTTCG 61.339 66.667 45.23 10.47 41.60 3.46
2836 2964 6.148811 TGTCATCCCGAAGAAAAACTATTGTC 59.851 38.462 0.00 0.00 0.00 3.18
2863 2991 3.244976 CATTGCCGGTTGAGAAAATGAC 58.755 45.455 1.90 0.00 0.00 3.06
2887 3015 3.236816 CATGTGACTTTCCAATCGTTGC 58.763 45.455 0.00 0.00 0.00 4.17
2907 3091 7.488792 GCAAGATTATTCATGTGTTGTATTGCA 59.511 33.333 14.39 0.00 0.00 4.08
3006 3190 6.558771 TTCACCACTCAATGTATTTGTCAG 57.441 37.500 0.00 0.00 36.65 3.51
3023 3207 5.838521 AGCCTTAAATTTCTTCCTTTCACCA 59.161 36.000 0.00 0.00 0.00 4.17
3084 3268 0.668535 ACTGAAGGAAAAACTGCCGC 59.331 50.000 0.00 0.00 0.00 6.53
3261 3459 4.917385 ACCACTAAAGGAACATACATGCA 58.083 39.130 0.00 0.00 0.00 3.96
3262 3460 6.346096 TCTACCACTAAAGGAACATACATGC 58.654 40.000 0.00 0.00 0.00 4.06
3263 3461 8.786826 TTTCTACCACTAAAGGAACATACATG 57.213 34.615 0.00 0.00 0.00 3.21
3264 3462 9.396022 CATTTCTACCACTAAAGGAACATACAT 57.604 33.333 0.00 0.00 0.00 2.29
3274 3472 6.091713 CACGGGTAACATTTCTACCACTAAAG 59.908 42.308 1.73 0.00 40.64 1.85


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

AutoCloner maintained by Alex Coulton.