Multiple sequence alignment - TraesCS5A01G313300

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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 TraesCS5A01G313300 chr5A 100.000 2648 0 0 1 2648 524308394 524311041 0.000000e+00 4891.0
1 TraesCS5A01G313300 chr5A 88.340 1012 81 17 670 1656 524388941 524389940 0.000000e+00 1181.0
2 TraesCS5A01G313300 chr5A 94.118 51 1 2 299 347 48352806 48352856 2.830000e-10 76.8
3 TraesCS5A01G313300 chr5D 92.920 1356 51 13 342 1656 412448134 412449485 0.000000e+00 1930.0
4 TraesCS5A01G313300 chr5B 91.120 1036 55 7 654 1656 496549375 496550406 0.000000e+00 1369.0
5 TraesCS5A01G313300 chr5B 86.696 1120 93 23 670 1737 496805686 496806801 0.000000e+00 1192.0
6 TraesCS5A01G313300 chr5B 87.953 1021 78 22 670 1656 496569085 496570094 0.000000e+00 1162.0
7 TraesCS5A01G313300 chr5B 94.737 323 11 2 339 656 496549006 496549327 5.090000e-137 497.0
8 TraesCS5A01G313300 chr5B 99.203 251 0 2 1 250 694276646 694276397 4.020000e-123 451.0
9 TraesCS5A01G313300 chr5B 97.500 40 0 1 1769 1808 496806915 496806953 1.700000e-07 67.6
10 TraesCS5A01G313300 chr2A 98.945 758 8 0 1891 2648 447298102 447297345 0.000000e+00 1356.0
11 TraesCS5A01G313300 chr2B 98.811 757 9 0 1892 2648 53050500 53051256 0.000000e+00 1349.0
12 TraesCS5A01G313300 chr2B 98.810 252 0 2 1 250 444820004 444820254 1.870000e-121 446.0
13 TraesCS5A01G313300 chr7B 98.674 754 10 0 1895 2648 749839968 749840721 0.000000e+00 1338.0
14 TraesCS5A01G313300 chr7B 99.420 690 4 0 1959 2648 525623426 525624115 0.000000e+00 1253.0
15 TraesCS5A01G313300 chr7B 99.203 251 2 0 1 251 693350826 693350576 1.120000e-123 453.0
16 TraesCS5A01G313300 chr6B 98.287 759 11 2 1890 2648 158094994 158095750 0.000000e+00 1328.0
17 TraesCS5A01G313300 chr6B 97.632 760 14 1 1893 2648 486115574 486116333 0.000000e+00 1301.0
18 TraesCS5A01G313300 chr6B 96.306 758 26 2 1892 2648 37964563 37963807 0.000000e+00 1243.0
19 TraesCS5A01G313300 chr6B 99.203 251 0 2 1 250 152611647 152611896 4.020000e-123 451.0
20 TraesCS5A01G313300 chr6B 98.425 254 3 1 1 253 684030116 684030369 1.870000e-121 446.0
21 TraesCS5A01G313300 chrUn 98.146 755 13 1 1894 2648 150913429 150912676 0.000000e+00 1315.0
22 TraesCS5A01G313300 chrUn 94.517 766 29 7 1884 2648 208769007 208769760 0.000000e+00 1170.0
23 TraesCS5A01G313300 chrUn 78.844 1073 151 46 677 1701 60943030 60944074 0.000000e+00 654.0
24 TraesCS5A01G313300 chrUn 82.481 645 101 7 1000 1644 60947713 60947081 2.980000e-154 555.0
25 TraesCS5A01G313300 chrUn 79.676 679 119 14 995 1663 60935687 60936356 3.090000e-129 472.0
26 TraesCS5A01G313300 chrUn 89.286 84 7 2 723 804 60939704 60939787 1.300000e-18 104.0
27 TraesCS5A01G313300 chr4A 79.014 1034 135 42 677 1651 601177878 601178888 1.340000e-177 632.0
28 TraesCS5A01G313300 chr4A 98.425 254 2 2 1 253 646614231 646614483 1.870000e-121 446.0
29 TraesCS5A01G313300 chr4B 82.243 749 108 13 970 1701 5531978 5532718 8.050000e-175 623.0
30 TraesCS5A01G313300 chr4B 76.577 222 32 9 677 893 5531654 5531860 1.300000e-18 104.0
31 TraesCS5A01G313300 chr3B 99.200 250 2 0 1 250 15977413 15977164 4.020000e-123 451.0
32 TraesCS5A01G313300 chr3B 97.692 260 4 1 1 258 615465604 615465863 1.870000e-121 446.0
33 TraesCS5A01G313300 chr7A 98.810 252 1 2 1 251 653373534 653373284 5.200000e-122 448.0


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 TraesCS5A01G313300 chr5A 524308394 524311041 2647 False 4891.0 4891 100.0000 1 2648 1 chr5A.!!$F2 2647
1 TraesCS5A01G313300 chr5A 524388941 524389940 999 False 1181.0 1181 88.3400 670 1656 1 chr5A.!!$F3 986
2 TraesCS5A01G313300 chr5D 412448134 412449485 1351 False 1930.0 1930 92.9200 342 1656 1 chr5D.!!$F1 1314
3 TraesCS5A01G313300 chr5B 496569085 496570094 1009 False 1162.0 1162 87.9530 670 1656 1 chr5B.!!$F1 986
4 TraesCS5A01G313300 chr5B 496549006 496550406 1400 False 933.0 1369 92.9285 339 1656 2 chr5B.!!$F2 1317
5 TraesCS5A01G313300 chr5B 496805686 496806953 1267 False 629.8 1192 92.0980 670 1808 2 chr5B.!!$F3 1138
6 TraesCS5A01G313300 chr2A 447297345 447298102 757 True 1356.0 1356 98.9450 1891 2648 1 chr2A.!!$R1 757
7 TraesCS5A01G313300 chr2B 53050500 53051256 756 False 1349.0 1349 98.8110 1892 2648 1 chr2B.!!$F1 756
8 TraesCS5A01G313300 chr7B 749839968 749840721 753 False 1338.0 1338 98.6740 1895 2648 1 chr7B.!!$F2 753
9 TraesCS5A01G313300 chr7B 525623426 525624115 689 False 1253.0 1253 99.4200 1959 2648 1 chr7B.!!$F1 689
10 TraesCS5A01G313300 chr6B 158094994 158095750 756 False 1328.0 1328 98.2870 1890 2648 1 chr6B.!!$F2 758
11 TraesCS5A01G313300 chr6B 486115574 486116333 759 False 1301.0 1301 97.6320 1893 2648 1 chr6B.!!$F3 755
12 TraesCS5A01G313300 chr6B 37963807 37964563 756 True 1243.0 1243 96.3060 1892 2648 1 chr6B.!!$R1 756
13 TraesCS5A01G313300 chrUn 150912676 150913429 753 True 1315.0 1315 98.1460 1894 2648 1 chrUn.!!$R2 754
14 TraesCS5A01G313300 chrUn 208769007 208769760 753 False 1170.0 1170 94.5170 1884 2648 1 chrUn.!!$F1 764
15 TraesCS5A01G313300 chrUn 60947081 60947713 632 True 555.0 555 82.4810 1000 1644 1 chrUn.!!$R1 644
16 TraesCS5A01G313300 chrUn 60935687 60944074 8387 False 410.0 654 82.6020 677 1701 3 chrUn.!!$F2 1024
17 TraesCS5A01G313300 chr4A 601177878 601178888 1010 False 632.0 632 79.0140 677 1651 1 chr4A.!!$F1 974
18 TraesCS5A01G313300 chr4B 5531654 5532718 1064 False 363.5 623 79.4100 677 1701 2 chr4B.!!$F1 1024

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
222 223 0.096976 CTAATGGCAGTTGCGAACCG 59.903 55.0 0.0 0.0 43.26 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 8723 0.03779 TGACAATCGACCGCACATCA 60.038 50.0 0.0 0.0 0.0 3.07 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.096357 CAGGTTTAGGGGGTGGGG 58.904 66.667 0.00 0.00 0.00 4.96
18 19 2.204401 AGGTTTAGGGGGTGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
19 20 4.070265 GGTTTAGGGGGTGGGGGC 62.070 72.222 0.00 0.00 0.00 5.80
22 23 1.166281 TTTAGGGGGTGGGGGCTAA 59.834 57.895 0.00 0.00 0.00 3.09
23 24 0.479990 TTTAGGGGGTGGGGGCTAAA 60.480 55.000 0.00 0.00 0.00 1.85
25 26 1.216368 TAGGGGGTGGGGGCTAAAAC 61.216 60.000 0.00 0.00 0.00 2.43
26 27 2.038329 GGGGTGGGGGCTAAAACC 59.962 66.667 0.00 0.00 0.00 3.27
39 40 1.471287 CTAAAACCCTAAACCTGCGGC 59.529 52.381 0.00 0.00 0.00 6.53
41 42 3.912745 AACCCTAAACCTGCGGCGG 62.913 63.158 9.78 0.65 0.00 6.13
44 45 4.778143 CTAAACCTGCGGCGGCCT 62.778 66.667 18.34 0.00 38.85 5.19
47 48 2.466523 TAAACCTGCGGCGGCCTTTA 62.467 55.000 18.34 11.46 38.85 1.85
48 49 4.778143 ACCTGCGGCGGCCTTTAG 62.778 66.667 18.34 11.71 38.85 1.85
49 50 4.778143 CCTGCGGCGGCCTTTAGT 62.778 66.667 18.34 0.00 38.85 2.24
57 58 2.736682 CGGCCTTTAGTCGCGGTTG 61.737 63.158 6.13 0.00 0.00 3.77
58 59 2.396157 GGCCTTTAGTCGCGGTTGG 61.396 63.158 6.13 1.60 0.00 3.77
59 60 3.035576 GCCTTTAGTCGCGGTTGGC 62.036 63.158 6.13 8.44 38.69 4.52
61 62 1.669760 CTTTAGTCGCGGTTGGCCA 60.670 57.895 0.00 0.00 38.94 5.36
62 63 1.635663 CTTTAGTCGCGGTTGGCCAG 61.636 60.000 5.11 0.00 38.94 4.85
63 64 2.102109 TTTAGTCGCGGTTGGCCAGA 62.102 55.000 5.11 0.00 38.94 3.86
64 65 2.102109 TTAGTCGCGGTTGGCCAGAA 62.102 55.000 5.11 0.00 38.94 3.02
65 66 2.501223 TAGTCGCGGTTGGCCAGAAG 62.501 60.000 5.11 1.86 38.94 2.85
66 67 3.621805 TCGCGGTTGGCCAGAAGA 61.622 61.111 5.11 0.00 38.94 2.87
67 68 2.668212 CGCGGTTGGCCAGAAGAA 60.668 61.111 5.11 0.00 38.94 2.52
68 69 2.954611 GCGGTTGGCCAGAAGAAC 59.045 61.111 5.11 0.00 34.80 3.01
70 71 3.668386 GGTTGGCCAGAAGAACCG 58.332 61.111 5.11 0.00 30.33 4.44
71 72 2.626780 GGTTGGCCAGAAGAACCGC 61.627 63.158 5.11 0.00 30.33 5.68
72 73 2.668212 TTGGCCAGAAGAACCGCG 60.668 61.111 5.11 0.00 0.00 6.46
73 74 3.171828 TTGGCCAGAAGAACCGCGA 62.172 57.895 8.23 0.00 0.00 5.87
74 75 3.119096 GGCCAGAAGAACCGCGAC 61.119 66.667 8.23 0.00 0.00 5.19
76 77 1.214589 GCCAGAAGAACCGCGACTA 59.785 57.895 8.23 0.00 0.00 2.59
77 78 0.389426 GCCAGAAGAACCGCGACTAA 60.389 55.000 8.23 0.00 0.00 2.24
78 79 1.938016 GCCAGAAGAACCGCGACTAAA 60.938 52.381 8.23 0.00 0.00 1.85
81 82 1.617357 AGAAGAACCGCGACTAAAGGT 59.383 47.619 8.23 0.00 40.50 3.50
83 84 0.245813 AGAACCGCGACTAAAGGTCC 59.754 55.000 8.23 0.00 41.64 4.46
84 85 0.245813 GAACCGCGACTAAAGGTCCT 59.754 55.000 8.23 0.00 41.64 3.85
87 88 1.226603 CGCGACTAAAGGTCCTCCG 60.227 63.158 0.00 0.00 41.64 4.63
88 89 1.518792 GCGACTAAAGGTCCTCCGC 60.519 63.158 0.00 0.00 41.64 5.54
89 90 1.141234 CGACTAAAGGTCCTCCGCC 59.859 63.158 0.00 0.00 41.64 6.13
90 91 1.521141 GACTAAAGGTCCTCCGCCC 59.479 63.158 0.00 0.00 38.93 6.13
92 93 3.078836 TAAAGGTCCTCCGCCCCG 61.079 66.667 0.00 0.00 39.05 5.73
93 94 3.605412 TAAAGGTCCTCCGCCCCGA 62.605 63.158 0.00 0.00 39.05 5.14
125 126 4.636435 CCACGTGGACGGGCCTTT 62.636 66.667 31.31 0.00 42.34 3.11
126 127 2.344500 CACGTGGACGGGCCTTTA 59.656 61.111 7.95 0.00 44.95 1.85
128 129 2.212110 ACGTGGACGGGCCTTTAGT 61.212 57.895 0.84 0.00 44.95 2.24
129 130 1.447314 CGTGGACGGGCCTTTAGTC 60.447 63.158 0.84 7.66 37.63 2.59
130 131 1.447314 GTGGACGGGCCTTTAGTCG 60.447 63.158 0.84 0.00 37.63 4.18
131 132 2.510918 GGACGGGCCTTTAGTCGC 60.511 66.667 0.84 0.00 35.87 5.19
132 133 2.884207 GACGGGCCTTTAGTCGCG 60.884 66.667 0.84 0.00 43.02 5.87
134 135 4.446413 CGGGCCTTTAGTCGCGGT 62.446 66.667 6.13 0.00 35.43 5.68
135 136 2.046604 GGGCCTTTAGTCGCGGTT 60.047 61.111 6.13 0.00 0.00 4.44
136 137 2.104859 GGGCCTTTAGTCGCGGTTC 61.105 63.158 6.13 0.00 0.00 3.62
137 138 1.079336 GGCCTTTAGTCGCGGTTCT 60.079 57.895 6.13 5.42 0.00 3.01
139 140 1.404583 GGCCTTTAGTCGCGGTTCTTA 60.405 52.381 6.13 0.00 0.00 2.10
141 142 2.347755 GCCTTTAGTCGCGGTTCTTAAG 59.652 50.000 6.13 11.57 0.00 1.85
144 145 2.728690 TAGTCGCGGTTCTTAAGCAA 57.271 45.000 6.13 0.00 0.00 3.91
146 147 0.165295 GTCGCGGTTCTTAAGCAACC 59.835 55.000 19.09 19.09 40.12 3.77
150 151 2.535588 GGTTCTTAAGCAACCGCGA 58.464 52.632 8.23 0.00 45.49 5.87
152 153 1.145803 GTTCTTAAGCAACCGCGACT 58.854 50.000 8.23 0.00 45.49 4.18
154 155 2.728690 TCTTAAGCAACCGCGACTAA 57.271 45.000 8.23 0.00 45.49 2.24
155 156 3.029320 TCTTAAGCAACCGCGACTAAA 57.971 42.857 8.23 0.00 45.49 1.85
156 157 2.991190 TCTTAAGCAACCGCGACTAAAG 59.009 45.455 8.23 1.88 45.49 1.85
157 158 1.717194 TAAGCAACCGCGACTAAAGG 58.283 50.000 8.23 0.00 45.49 3.11
158 159 0.953960 AAGCAACCGCGACTAAAGGG 60.954 55.000 8.23 0.00 45.49 3.95
159 160 2.396157 GCAACCGCGACTAAAGGGG 61.396 63.158 8.23 0.00 45.85 4.79
160 161 1.743995 CAACCGCGACTAAAGGGGG 60.744 63.158 8.23 0.00 44.84 5.40
176 177 4.468689 GGGCCTTTAGTCGCGCCT 62.469 66.667 0.84 0.00 41.35 5.52
177 178 2.497770 GGCCTTTAGTCGCGCCTA 59.502 61.111 0.00 0.00 38.41 3.93
179 180 0.532196 GGCCTTTAGTCGCGCCTATT 60.532 55.000 0.00 0.00 38.41 1.73
181 182 1.003866 GCCTTTAGTCGCGCCTATTTG 60.004 52.381 0.00 0.00 0.00 2.32
182 183 1.597663 CCTTTAGTCGCGCCTATTTGG 59.402 52.381 0.00 0.00 39.35 3.28
183 184 2.277084 CTTTAGTCGCGCCTATTTGGT 58.723 47.619 0.00 0.00 38.35 3.67
185 186 0.248743 TAGTCGCGCCTATTTGGTCG 60.249 55.000 0.00 0.00 38.35 4.79
189 190 2.510691 CGCCTATTTGGTCGCGGT 60.511 61.111 6.13 0.00 40.91 5.68
190 191 2.104253 CGCCTATTTGGTCGCGGTT 61.104 57.895 6.13 0.00 40.91 4.44
191 192 1.427819 GCCTATTTGGTCGCGGTTG 59.572 57.895 6.13 0.00 38.35 3.77
210 211 2.403586 GCAACCGCGACTAATGGC 59.596 61.111 8.23 0.00 0.00 4.40
211 212 2.395360 GCAACCGCGACTAATGGCA 61.395 57.895 8.23 0.00 0.00 4.92
212 213 1.715585 CAACCGCGACTAATGGCAG 59.284 57.895 8.23 0.00 0.00 4.85
213 214 1.019278 CAACCGCGACTAATGGCAGT 61.019 55.000 8.23 0.00 0.00 4.40
214 215 0.321298 AACCGCGACTAATGGCAGTT 60.321 50.000 8.23 0.00 0.00 3.16
215 216 1.019278 ACCGCGACTAATGGCAGTTG 61.019 55.000 8.23 0.00 33.66 3.16
217 218 1.060937 GCGACTAATGGCAGTTGCG 59.939 57.895 0.00 0.70 44.02 4.85
219 220 1.075542 CGACTAATGGCAGTTGCGAA 58.924 50.000 0.00 0.00 43.26 4.70
220 221 1.201921 CGACTAATGGCAGTTGCGAAC 60.202 52.381 0.00 0.00 43.26 3.95
221 222 1.130561 GACTAATGGCAGTTGCGAACC 59.869 52.381 0.00 0.00 43.26 3.62
222 223 0.096976 CTAATGGCAGTTGCGAACCG 59.903 55.000 0.00 0.00 43.26 4.44
232 233 4.084888 GCGAACCGCGACCAAAGG 62.085 66.667 8.23 0.00 44.55 3.11
233 234 4.084888 CGAACCGCGACCAAAGGC 62.085 66.667 8.23 0.00 44.57 4.35
234 235 3.733960 GAACCGCGACCAAAGGCC 61.734 66.667 8.23 0.00 0.00 5.19
238 239 2.983592 CGCGACCAAAGGCCCTTT 60.984 61.111 1.93 1.93 33.58 3.11
239 240 2.561037 CGCGACCAAAGGCCCTTTT 61.561 57.895 5.84 0.00 30.60 2.27
240 241 1.745890 GCGACCAAAGGCCCTTTTT 59.254 52.632 5.84 0.00 30.60 1.94
241 242 0.319555 GCGACCAAAGGCCCTTTTTC 60.320 55.000 5.84 5.31 30.60 2.29
242 243 0.317160 CGACCAAAGGCCCTTTTTCC 59.683 55.000 5.84 0.00 30.60 3.13
243 244 1.419381 GACCAAAGGCCCTTTTTCCA 58.581 50.000 5.84 0.00 30.60 3.53
244 245 1.070134 GACCAAAGGCCCTTTTTCCAC 59.930 52.381 5.84 0.00 30.60 4.02
245 246 0.396435 CCAAAGGCCCTTTTTCCACC 59.604 55.000 5.84 0.00 30.60 4.61
246 247 1.127343 CAAAGGCCCTTTTTCCACCA 58.873 50.000 5.84 0.00 30.60 4.17
247 248 1.070601 CAAAGGCCCTTTTTCCACCAG 59.929 52.381 5.84 0.00 30.60 4.00
248 249 0.264657 AAGGCCCTTTTTCCACCAGT 59.735 50.000 0.00 0.00 0.00 4.00
249 250 0.469892 AGGCCCTTTTTCCACCAGTG 60.470 55.000 0.00 0.00 0.00 3.66
250 251 0.759060 GGCCCTTTTTCCACCAGTGT 60.759 55.000 0.00 0.00 0.00 3.55
251 252 0.673985 GCCCTTTTTCCACCAGTGTC 59.326 55.000 0.00 0.00 0.00 3.67
252 253 2.026905 GCCCTTTTTCCACCAGTGTCA 61.027 52.381 0.00 0.00 0.00 3.58
253 254 1.681264 CCCTTTTTCCACCAGTGTCAC 59.319 52.381 0.00 0.00 0.00 3.67
254 255 2.654863 CCTTTTTCCACCAGTGTCACT 58.345 47.619 0.00 0.00 0.00 3.41
255 256 3.434453 CCCTTTTTCCACCAGTGTCACTA 60.434 47.826 4.85 0.00 0.00 2.74
256 257 4.398319 CCTTTTTCCACCAGTGTCACTAT 58.602 43.478 4.85 0.00 0.00 2.12
257 258 4.455877 CCTTTTTCCACCAGTGTCACTATC 59.544 45.833 4.85 0.00 0.00 2.08
258 259 4.974645 TTTTCCACCAGTGTCACTATCT 57.025 40.909 4.85 0.00 0.00 1.98
259 260 4.974645 TTTCCACCAGTGTCACTATCTT 57.025 40.909 4.85 0.00 0.00 2.40
260 261 4.537135 TTCCACCAGTGTCACTATCTTC 57.463 45.455 4.85 0.00 0.00 2.87
261 262 2.832129 TCCACCAGTGTCACTATCTTCC 59.168 50.000 4.85 0.00 0.00 3.46
262 263 2.093447 CCACCAGTGTCACTATCTTCCC 60.093 54.545 4.85 0.00 0.00 3.97
265 266 2.774234 CCAGTGTCACTATCTTCCCCAT 59.226 50.000 4.85 0.00 0.00 4.00
266 267 3.432749 CCAGTGTCACTATCTTCCCCATG 60.433 52.174 4.85 0.00 0.00 3.66
267 268 3.198635 CAGTGTCACTATCTTCCCCATGT 59.801 47.826 4.85 0.00 0.00 3.21
268 269 3.198635 AGTGTCACTATCTTCCCCATGTG 59.801 47.826 2.87 0.00 0.00 3.21
269 270 3.055094 GTGTCACTATCTTCCCCATGTGT 60.055 47.826 0.00 0.00 0.00 3.72
270 271 3.197766 TGTCACTATCTTCCCCATGTGTC 59.802 47.826 0.00 0.00 0.00 3.67
271 272 3.197766 GTCACTATCTTCCCCATGTGTCA 59.802 47.826 0.00 0.00 0.00 3.58
272 273 3.843619 TCACTATCTTCCCCATGTGTCAA 59.156 43.478 0.00 0.00 0.00 3.18
273 274 4.474651 TCACTATCTTCCCCATGTGTCAAT 59.525 41.667 0.00 0.00 0.00 2.57
275 276 2.806945 TCTTCCCCATGTGTCAATCC 57.193 50.000 0.00 0.00 0.00 3.01
277 278 2.378208 TCTTCCCCATGTGTCAATCCAA 59.622 45.455 0.00 0.00 0.00 3.53
278 279 3.011595 TCTTCCCCATGTGTCAATCCAAT 59.988 43.478 0.00 0.00 0.00 3.16
279 280 3.471430 TCCCCATGTGTCAATCCAATT 57.529 42.857 0.00 0.00 0.00 2.32
280 281 3.788933 TCCCCATGTGTCAATCCAATTT 58.211 40.909 0.00 0.00 0.00 1.82
281 282 4.166539 TCCCCATGTGTCAATCCAATTTT 58.833 39.130 0.00 0.00 0.00 1.82
282 283 4.020396 TCCCCATGTGTCAATCCAATTTTG 60.020 41.667 0.00 0.00 0.00 2.44
283 284 4.020396 CCCCATGTGTCAATCCAATTTTGA 60.020 41.667 0.00 0.00 0.00 2.69
284 285 5.338544 CCCCATGTGTCAATCCAATTTTGAT 60.339 40.000 0.00 0.00 35.68 2.57
285 286 5.813672 CCCATGTGTCAATCCAATTTTGATC 59.186 40.000 0.00 0.00 35.68 2.92
286 287 6.399743 CCATGTGTCAATCCAATTTTGATCA 58.600 36.000 0.00 0.00 35.68 2.92
287 288 6.311935 CCATGTGTCAATCCAATTTTGATCAC 59.688 38.462 0.00 12.34 35.68 3.06
289 290 7.757941 TGTGTCAATCCAATTTTGATCACTA 57.242 32.000 16.31 0.00 36.79 2.74
291 292 8.245491 TGTGTCAATCCAATTTTGATCACTATG 58.755 33.333 16.31 0.00 36.79 2.23
292 293 8.461222 GTGTCAATCCAATTTTGATCACTATGA 58.539 33.333 0.00 0.00 35.68 2.15
293 294 9.022884 TGTCAATCCAATTTTGATCACTATGAA 57.977 29.630 0.00 0.00 35.68 2.57
294 295 9.859427 GTCAATCCAATTTTGATCACTATGAAA 57.141 29.630 0.00 0.00 35.68 2.69
299 300 9.022884 TCCAATTTTGATCACTATGAAATCACA 57.977 29.630 0.00 0.00 0.00 3.58
305 306 7.742556 TGATCACTATGAAATCACAACAACA 57.257 32.000 0.00 0.00 0.00 3.33
307 308 9.447157 TGATCACTATGAAATCACAACAACATA 57.553 29.630 0.00 0.00 0.00 2.29
311 312 8.839914 CACTATGAAATCACAACAACATAAACG 58.160 33.333 0.00 0.00 0.00 3.60
312 313 8.020819 ACTATGAAATCACAACAACATAAACGG 58.979 33.333 0.00 0.00 0.00 4.44
313 314 4.979197 TGAAATCACAACAACATAAACGGC 59.021 37.500 0.00 0.00 0.00 5.68
314 315 2.672188 TCACAACAACATAAACGGCG 57.328 45.000 4.80 4.80 0.00 6.46
316 317 0.663688 ACAACAACATAAACGGCGCA 59.336 45.000 10.83 0.00 0.00 6.09
317 318 1.326576 CAACAACATAAACGGCGCAG 58.673 50.000 10.83 8.25 0.00 5.18
446 447 3.119173 TGATTCGGATTGGTTCAATTGGC 60.119 43.478 5.42 0.00 33.90 4.52
563 569 5.245075 AGACTTTTGTGTTTGGACTTTGGAA 59.755 36.000 0.00 0.00 0.00 3.53
623 629 7.651027 ATTTCTCAGATTAATGAAGTTGGGG 57.349 36.000 0.00 0.00 0.00 4.96
649 655 1.299541 CACACTCACACACCCAAGTC 58.700 55.000 0.00 0.00 0.00 3.01
698 3998 9.927668 ACACCAAAGTTTTCATTATAATGGAAG 57.072 29.630 22.31 11.27 35.43 3.46
812 7499 7.281999 TCAGATGTGTGTCAAACTGTCAATTAA 59.718 33.333 0.00 0.00 36.60 1.40
896 7596 2.171237 CTCCATCACATCACTAGCCCAA 59.829 50.000 0.00 0.00 0.00 4.12
903 7603 2.237392 ACATCACTAGCCCAACTCTTCC 59.763 50.000 0.00 0.00 0.00 3.46
950 7683 3.689161 TCAACCACAGCCTTAATCAATCG 59.311 43.478 0.00 0.00 0.00 3.34
1055 7793 2.521708 GGTGGTTGCACTGGCCTT 60.522 61.111 3.32 0.00 40.13 4.35
1058 7796 2.521708 GGTTGCACTGGCCTTGGT 60.522 61.111 3.32 0.00 40.13 3.67
1107 7845 2.223735 GGACATCCTCAGCGATTTCGTA 60.224 50.000 1.55 0.00 42.22 3.43
1266 8025 1.070105 ACTCAACGGGCAAAGCGTA 59.930 52.632 0.00 0.00 0.00 4.42
1656 8415 2.821969 GCCCAAGAAGTGATTCATGTGT 59.178 45.455 0.00 0.00 0.00 3.72
1666 8425 6.551385 AGTGATTCATGTGTTCTTCTTCAC 57.449 37.500 0.00 0.00 35.43 3.18
1677 8448 1.075425 CTTCTTCACGCCGCTCTGAG 61.075 60.000 0.00 0.00 0.00 3.35
1737 8510 1.302192 GGTGCCGCCAAGTAGACAA 60.302 57.895 0.00 0.00 37.17 3.18
1739 8512 1.406341 GGTGCCGCCAAGTAGACAATA 60.406 52.381 0.00 0.00 37.17 1.90
1741 8514 2.943033 GTGCCGCCAAGTAGACAATAAT 59.057 45.455 0.00 0.00 0.00 1.28
1742 8515 4.124238 GTGCCGCCAAGTAGACAATAATA 58.876 43.478 0.00 0.00 0.00 0.98
1743 8516 4.755123 GTGCCGCCAAGTAGACAATAATAT 59.245 41.667 0.00 0.00 0.00 1.28
1744 8517 4.754618 TGCCGCCAAGTAGACAATAATATG 59.245 41.667 0.00 0.00 0.00 1.78
1746 8519 5.334105 GCCGCCAAGTAGACAATAATATGTG 60.334 44.000 0.00 0.00 32.57 3.21
1747 8520 5.989168 CCGCCAAGTAGACAATAATATGTGA 59.011 40.000 0.00 0.00 32.57 3.58
1748 8521 6.481976 CCGCCAAGTAGACAATAATATGTGAA 59.518 38.462 0.00 0.00 32.57 3.18
1749 8522 7.011950 CCGCCAAGTAGACAATAATATGTGAAA 59.988 37.037 0.00 0.00 32.57 2.69
1750 8523 8.559536 CGCCAAGTAGACAATAATATGTGAAAT 58.440 33.333 0.00 0.00 32.57 2.17
1800 8655 6.762187 TGTGATTGTGCTGATGTGAAATTTTT 59.238 30.769 0.00 0.00 0.00 1.94
1801 8656 7.924947 TGTGATTGTGCTGATGTGAAATTTTTA 59.075 29.630 0.00 0.00 0.00 1.52
1802 8657 8.928733 GTGATTGTGCTGATGTGAAATTTTTAT 58.071 29.630 0.00 0.00 0.00 1.40
1803 8658 9.142515 TGATTGTGCTGATGTGAAATTTTTATC 57.857 29.630 0.00 0.00 0.00 1.75
1804 8659 9.362539 GATTGTGCTGATGTGAAATTTTTATCT 57.637 29.630 0.00 0.00 0.00 1.98
1805 8660 8.523523 TTGTGCTGATGTGAAATTTTTATCTG 57.476 30.769 0.00 3.14 0.00 2.90
1806 8661 7.884257 TGTGCTGATGTGAAATTTTTATCTGA 58.116 30.769 15.04 0.00 0.00 3.27
1807 8662 8.525316 TGTGCTGATGTGAAATTTTTATCTGAT 58.475 29.630 15.04 0.00 0.00 2.90
1808 8663 9.362539 GTGCTGATGTGAAATTTTTATCTGATT 57.637 29.630 15.04 0.00 0.00 2.57
1809 8664 9.361315 TGCTGATGTGAAATTTTTATCTGATTG 57.639 29.630 15.04 0.00 0.00 2.67
1810 8665 9.577110 GCTGATGTGAAATTTTTATCTGATTGA 57.423 29.630 15.04 0.00 0.00 2.57
1822 8677 9.695526 TTTTTATCTGATTGAGATGTTGGTTTG 57.304 29.630 0.00 0.00 41.86 2.93
1823 8678 8.408043 TTTATCTGATTGAGATGTTGGTTTGT 57.592 30.769 0.00 0.00 41.86 2.83
1824 8679 5.947228 TCTGATTGAGATGTTGGTTTGTC 57.053 39.130 0.00 0.00 0.00 3.18
1825 8680 5.375773 TCTGATTGAGATGTTGGTTTGTCA 58.624 37.500 0.00 0.00 0.00 3.58
1826 8681 5.239306 TCTGATTGAGATGTTGGTTTGTCAC 59.761 40.000 0.00 0.00 0.00 3.67
1827 8682 8.920108 ATCTGATTGAGATGTTGGTTTGTCACC 61.920 40.741 0.00 0.00 42.22 4.02
1838 8693 4.663636 GGTTTGTCACCAATTCTACTCG 57.336 45.455 0.00 0.00 46.42 4.18
1839 8694 3.120304 GGTTTGTCACCAATTCTACTCGC 60.120 47.826 0.00 0.00 46.42 5.03
1840 8695 1.990799 TGTCACCAATTCTACTCGCG 58.009 50.000 0.00 0.00 0.00 5.87
1841 8696 0.645868 GTCACCAATTCTACTCGCGC 59.354 55.000 0.00 0.00 0.00 6.86
1842 8697 0.459585 TCACCAATTCTACTCGCGCC 60.460 55.000 0.00 0.00 0.00 6.53
1843 8698 0.460284 CACCAATTCTACTCGCGCCT 60.460 55.000 0.00 0.00 0.00 5.52
1844 8699 0.460284 ACCAATTCTACTCGCGCCTG 60.460 55.000 0.00 0.00 0.00 4.85
1845 8700 0.460284 CCAATTCTACTCGCGCCTGT 60.460 55.000 0.00 3.10 0.00 4.00
1846 8701 1.359848 CAATTCTACTCGCGCCTGTT 58.640 50.000 0.00 0.00 0.00 3.16
1847 8702 2.536365 CAATTCTACTCGCGCCTGTTA 58.464 47.619 0.00 0.00 0.00 2.41
1848 8703 3.123804 CAATTCTACTCGCGCCTGTTAT 58.876 45.455 0.00 0.00 0.00 1.89
1849 8704 2.203800 TTCTACTCGCGCCTGTTATG 57.796 50.000 0.00 0.00 0.00 1.90
1850 8705 0.248907 TCTACTCGCGCCTGTTATGC 60.249 55.000 0.00 0.00 0.00 3.14
1851 8706 0.527600 CTACTCGCGCCTGTTATGCA 60.528 55.000 0.00 0.00 0.00 3.96
1852 8707 0.804544 TACTCGCGCCTGTTATGCAC 60.805 55.000 0.00 0.00 0.00 4.57
1853 8708 2.047750 TCGCGCCTGTTATGCACA 60.048 55.556 0.00 0.00 0.00 4.57
1854 8709 1.431488 CTCGCGCCTGTTATGCACAT 61.431 55.000 0.00 0.00 33.76 3.21
1855 8710 1.010797 CGCGCCTGTTATGCACATC 60.011 57.895 0.00 0.00 33.76 3.06
1856 8711 1.431488 CGCGCCTGTTATGCACATCT 61.431 55.000 0.00 0.00 33.76 2.90
1857 8712 0.305922 GCGCCTGTTATGCACATCTC 59.694 55.000 0.00 0.00 33.76 2.75
1858 8713 1.945387 CGCCTGTTATGCACATCTCT 58.055 50.000 0.00 0.00 33.76 3.10
1859 8714 1.596260 CGCCTGTTATGCACATCTCTG 59.404 52.381 0.00 0.00 33.76 3.35
1860 8715 2.636830 GCCTGTTATGCACATCTCTGT 58.363 47.619 0.00 0.00 33.76 3.41
1875 8730 6.525628 CACATCTCTGTGTTTATTTGATGTGC 59.474 38.462 16.54 0.00 46.76 4.57
1876 8731 5.281693 TCTCTGTGTTTATTTGATGTGCG 57.718 39.130 0.00 0.00 0.00 5.34
1877 8732 4.154015 TCTCTGTGTTTATTTGATGTGCGG 59.846 41.667 0.00 0.00 0.00 5.69
1878 8733 3.818210 TCTGTGTTTATTTGATGTGCGGT 59.182 39.130 0.00 0.00 0.00 5.68
1879 8734 4.083537 TCTGTGTTTATTTGATGTGCGGTC 60.084 41.667 0.00 0.00 0.00 4.79
1880 8735 3.160545 GTGTTTATTTGATGTGCGGTCG 58.839 45.455 0.00 0.00 0.00 4.79
1881 8736 3.067833 TGTTTATTTGATGTGCGGTCGA 58.932 40.909 0.00 0.00 0.00 4.20
1882 8737 3.687212 TGTTTATTTGATGTGCGGTCGAT 59.313 39.130 0.00 0.00 0.00 3.59
1883 8738 4.155099 TGTTTATTTGATGTGCGGTCGATT 59.845 37.500 0.00 0.00 0.00 3.34
1884 8739 2.830772 ATTTGATGTGCGGTCGATTG 57.169 45.000 0.00 0.00 0.00 2.67
1885 8740 1.518325 TTTGATGTGCGGTCGATTGT 58.482 45.000 0.00 0.00 0.00 2.71
1886 8741 1.075542 TTGATGTGCGGTCGATTGTC 58.924 50.000 0.00 0.00 0.00 3.18
1887 8742 0.037790 TGATGTGCGGTCGATTGTCA 60.038 50.000 0.00 0.00 0.00 3.58
1888 8743 0.370273 GATGTGCGGTCGATTGTCAC 59.630 55.000 0.00 0.00 0.00 3.67
1889 8744 1.351430 ATGTGCGGTCGATTGTCACG 61.351 55.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.622447 CCCCCACCCCCTAAACCTG 61.622 68.421 0.00 0.00 0.00 4.00
1 2 2.204401 CCCCCACCCCCTAAACCT 60.204 66.667 0.00 0.00 0.00 3.50
2 3 4.070265 GCCCCCACCCCCTAAACC 62.070 72.222 0.00 0.00 0.00 3.27
3 4 1.216368 TTAGCCCCCACCCCCTAAAC 61.216 60.000 0.00 0.00 0.00 2.01
5 6 0.479990 TTTTAGCCCCCACCCCCTAA 60.480 55.000 0.00 0.00 0.00 2.69
7 8 2.120760 TTTTAGCCCCCACCCCCT 60.121 61.111 0.00 0.00 0.00 4.79
9 10 2.038329 GGTTTTAGCCCCCACCCC 59.962 66.667 0.00 0.00 0.00 4.95
10 11 2.038329 GGGTTTTAGCCCCCACCC 59.962 66.667 0.00 0.00 42.89 4.61
17 18 1.471287 CGCAGGTTTAGGGTTTTAGCC 59.529 52.381 0.00 0.00 35.59 3.93
18 19 2.913777 CGCAGGTTTAGGGTTTTAGC 57.086 50.000 0.00 0.00 0.00 3.09
33 34 3.195698 GACTAAAGGCCGCCGCAG 61.196 66.667 3.05 5.13 36.38 5.18
39 40 2.433664 AACCGCGACTAAAGGCCG 60.434 61.111 8.23 0.00 0.00 6.13
41 42 3.035576 GCCAACCGCGACTAAAGGC 62.036 63.158 8.23 8.51 0.00 4.35
42 43 2.396157 GGCCAACCGCGACTAAAGG 61.396 63.158 8.23 1.23 38.94 3.11
43 44 1.635663 CTGGCCAACCGCGACTAAAG 61.636 60.000 8.23 0.00 39.70 1.85
44 45 1.669760 CTGGCCAACCGCGACTAAA 60.670 57.895 8.23 0.00 39.70 1.85
47 48 3.883744 CTTCTGGCCAACCGCGACT 62.884 63.158 8.23 0.00 39.70 4.18
48 49 3.423154 CTTCTGGCCAACCGCGAC 61.423 66.667 8.23 0.00 39.70 5.19
49 50 3.171828 TTCTTCTGGCCAACCGCGA 62.172 57.895 8.23 0.00 39.70 5.87
51 52 2.626780 GGTTCTTCTGGCCAACCGC 61.627 63.158 7.01 0.00 39.70 5.68
52 53 3.668386 GGTTCTTCTGGCCAACCG 58.332 61.111 7.01 0.00 39.70 4.44
54 55 2.954611 GCGGTTCTTCTGGCCAAC 59.045 61.111 7.01 0.29 0.00 3.77
55 56 2.668212 CGCGGTTCTTCTGGCCAA 60.668 61.111 7.01 0.00 0.00 4.52
57 58 2.221906 TAGTCGCGGTTCTTCTGGCC 62.222 60.000 6.13 0.00 0.00 5.36
58 59 0.389426 TTAGTCGCGGTTCTTCTGGC 60.389 55.000 6.13 0.00 0.00 4.85
59 60 1.993370 CTTTAGTCGCGGTTCTTCTGG 59.007 52.381 6.13 0.00 0.00 3.86
61 62 1.617357 ACCTTTAGTCGCGGTTCTTCT 59.383 47.619 6.13 0.00 0.00 2.85
62 63 1.991264 GACCTTTAGTCGCGGTTCTTC 59.009 52.381 6.13 0.00 35.30 2.87
63 64 2.075979 GACCTTTAGTCGCGGTTCTT 57.924 50.000 6.13 0.00 35.30 2.52
64 65 3.808583 GACCTTTAGTCGCGGTTCT 57.191 52.632 6.13 5.42 35.30 3.01
72 73 1.521141 GGGCGGAGGACCTTTAGTC 59.479 63.158 0.00 0.00 45.51 2.59
73 74 1.993948 GGGGCGGAGGACCTTTAGT 60.994 63.158 0.00 0.00 43.03 2.24
74 75 2.908796 GGGGCGGAGGACCTTTAG 59.091 66.667 0.00 0.00 43.03 1.85
108 109 3.242897 TAAAGGCCCGTCCACGTGG 62.243 63.158 29.26 29.26 37.29 4.94
111 112 1.447314 GACTAAAGGCCCGTCCACG 60.447 63.158 0.00 0.00 37.29 4.94
112 113 1.447314 CGACTAAAGGCCCGTCCAC 60.447 63.158 0.00 0.00 37.29 4.02
113 114 2.975536 CGACTAAAGGCCCGTCCA 59.024 61.111 0.00 0.00 37.29 4.02
114 115 2.510918 GCGACTAAAGGCCCGTCC 60.511 66.667 0.00 0.00 0.00 4.79
115 116 2.884207 CGCGACTAAAGGCCCGTC 60.884 66.667 0.00 0.02 0.00 4.79
117 118 3.945304 AACCGCGACTAAAGGCCCG 62.945 63.158 8.23 0.00 0.00 6.13
118 119 2.046604 AACCGCGACTAAAGGCCC 60.047 61.111 8.23 0.00 0.00 5.80
119 120 0.672711 AAGAACCGCGACTAAAGGCC 60.673 55.000 8.23 0.00 0.00 5.19
120 121 2.000429 TAAGAACCGCGACTAAAGGC 58.000 50.000 8.23 0.00 0.00 4.35
121 122 2.347755 GCTTAAGAACCGCGACTAAAGG 59.652 50.000 8.23 0.00 0.00 3.11
122 123 2.991190 TGCTTAAGAACCGCGACTAAAG 59.009 45.455 8.23 4.60 0.00 1.85
123 124 3.029320 TGCTTAAGAACCGCGACTAAA 57.971 42.857 8.23 0.00 0.00 1.85
125 126 2.331194 GTTGCTTAAGAACCGCGACTA 58.669 47.619 8.23 0.00 35.64 2.59
126 127 1.145803 GTTGCTTAAGAACCGCGACT 58.854 50.000 8.23 0.30 35.64 4.18
128 129 2.535588 GGTTGCTTAAGAACCGCGA 58.464 52.632 8.23 0.00 33.85 5.87
132 133 0.165295 GTCGCGGTTGCTTAAGAACC 59.835 55.000 19.09 19.09 39.71 3.62
134 135 2.728690 TAGTCGCGGTTGCTTAAGAA 57.271 45.000 6.13 0.00 39.65 2.52
135 136 2.728690 TTAGTCGCGGTTGCTTAAGA 57.271 45.000 6.13 0.00 39.65 2.10
136 137 2.093783 CCTTTAGTCGCGGTTGCTTAAG 59.906 50.000 6.13 9.06 39.65 1.85
137 138 2.070783 CCTTTAGTCGCGGTTGCTTAA 58.929 47.619 6.13 0.00 39.65 1.85
139 140 0.953960 CCCTTTAGTCGCGGTTGCTT 60.954 55.000 6.13 0.00 39.65 3.91
141 142 2.396157 CCCCTTTAGTCGCGGTTGC 61.396 63.158 6.13 0.00 37.91 4.17
159 160 2.379030 ATAGGCGCGACTAAAGGCCC 62.379 60.000 28.10 5.53 46.75 5.80
160 161 0.532196 AATAGGCGCGACTAAAGGCC 60.532 55.000 28.10 6.29 45.91 5.19
161 162 1.003866 CAAATAGGCGCGACTAAAGGC 60.004 52.381 28.10 0.00 0.00 4.35
165 166 1.799917 CGACCAAATAGGCGCGACTAA 60.800 52.381 28.10 9.87 43.14 2.24
166 167 0.248743 CGACCAAATAGGCGCGACTA 60.249 55.000 26.49 26.49 43.14 2.59
168 169 3.003478 CGACCAAATAGGCGCGAC 58.997 61.111 12.10 7.34 43.14 5.19
169 170 2.888534 GCGACCAAATAGGCGCGA 60.889 61.111 12.10 0.00 46.90 5.87
173 174 1.427819 CAACCGCGACCAAATAGGC 59.572 57.895 8.23 0.00 43.14 3.93
174 175 1.427819 GCAACCGCGACCAAATAGG 59.572 57.895 8.23 0.00 45.67 2.57
193 194 2.309764 CTGCCATTAGTCGCGGTTGC 62.310 60.000 6.13 0.28 37.91 4.17
194 195 1.019278 ACTGCCATTAGTCGCGGTTG 61.019 55.000 6.13 0.00 41.86 3.77
195 196 1.295423 ACTGCCATTAGTCGCGGTT 59.705 52.632 6.13 0.00 41.86 4.44
196 197 1.019278 CAACTGCCATTAGTCGCGGT 61.019 55.000 6.13 0.00 46.47 5.68
199 200 1.060937 CGCAACTGCCATTAGTCGC 59.939 57.895 0.00 0.00 37.91 5.19
200 201 1.075542 TTCGCAACTGCCATTAGTCG 58.924 50.000 0.00 0.00 37.91 4.18
202 203 1.165270 GGTTCGCAACTGCCATTAGT 58.835 50.000 0.00 0.00 37.91 2.24
204 205 2.167161 CGGTTCGCAACTGCCATTA 58.833 52.632 0.00 0.00 37.91 1.90
205 206 2.953821 CGGTTCGCAACTGCCATT 59.046 55.556 0.00 0.00 37.91 3.16
216 217 4.084888 GCCTTTGGTCGCGGTTCG 62.085 66.667 6.13 0.00 40.15 3.95
217 218 3.733960 GGCCTTTGGTCGCGGTTC 61.734 66.667 6.13 0.00 0.00 3.62
221 222 2.082629 AAAAAGGGCCTTTGGTCGCG 62.083 55.000 31.06 0.00 33.64 5.87
222 223 0.319555 GAAAAAGGGCCTTTGGTCGC 60.320 55.000 31.06 14.98 33.64 5.19
223 224 0.317160 GGAAAAAGGGCCTTTGGTCG 59.683 55.000 31.06 0.00 33.64 4.79
224 225 1.070134 GTGGAAAAAGGGCCTTTGGTC 59.930 52.381 31.06 27.31 33.64 4.02
225 226 1.128200 GTGGAAAAAGGGCCTTTGGT 58.872 50.000 31.06 21.81 33.64 3.67
226 227 0.396435 GGTGGAAAAAGGGCCTTTGG 59.604 55.000 31.06 0.00 33.64 3.28
227 228 1.070601 CTGGTGGAAAAAGGGCCTTTG 59.929 52.381 31.06 12.80 33.64 2.77
229 230 0.264657 ACTGGTGGAAAAAGGGCCTT 59.735 50.000 14.48 14.48 0.00 4.35
230 231 0.469892 CACTGGTGGAAAAAGGGCCT 60.470 55.000 0.00 0.00 0.00 5.19
231 232 0.759060 ACACTGGTGGAAAAAGGGCC 60.759 55.000 0.00 0.00 34.19 5.80
232 233 0.673985 GACACTGGTGGAAAAAGGGC 59.326 55.000 5.70 0.00 34.19 5.19
233 234 1.681264 GTGACACTGGTGGAAAAAGGG 59.319 52.381 5.70 0.00 34.19 3.95
234 235 2.654863 AGTGACACTGGTGGAAAAAGG 58.345 47.619 7.47 0.00 34.19 3.11
236 237 5.304686 AGATAGTGACACTGGTGGAAAAA 57.695 39.130 18.58 0.00 34.19 1.94
238 239 4.262894 GGAAGATAGTGACACTGGTGGAAA 60.263 45.833 18.58 0.00 34.19 3.13
239 240 3.260884 GGAAGATAGTGACACTGGTGGAA 59.739 47.826 18.58 0.00 34.19 3.53
240 241 2.832129 GGAAGATAGTGACACTGGTGGA 59.168 50.000 18.58 0.00 34.19 4.02
241 242 2.093447 GGGAAGATAGTGACACTGGTGG 60.093 54.545 18.58 0.00 34.19 4.61
242 243 2.093447 GGGGAAGATAGTGACACTGGTG 60.093 54.545 18.58 0.00 0.00 4.17
243 244 2.188817 GGGGAAGATAGTGACACTGGT 58.811 52.381 18.58 6.69 0.00 4.00
244 245 2.187958 TGGGGAAGATAGTGACACTGG 58.812 52.381 18.58 0.00 0.00 4.00
245 246 3.198635 ACATGGGGAAGATAGTGACACTG 59.801 47.826 18.58 0.10 0.00 3.66
246 247 3.198635 CACATGGGGAAGATAGTGACACT 59.801 47.826 13.68 13.68 0.00 3.55
247 248 3.055094 ACACATGGGGAAGATAGTGACAC 60.055 47.826 0.00 0.00 0.00 3.67
248 249 3.181329 ACACATGGGGAAGATAGTGACA 58.819 45.455 0.00 0.00 0.00 3.58
249 250 3.197766 TGACACATGGGGAAGATAGTGAC 59.802 47.826 0.00 0.00 0.00 3.67
250 251 3.449918 TGACACATGGGGAAGATAGTGA 58.550 45.455 0.00 0.00 0.00 3.41
251 252 3.912496 TGACACATGGGGAAGATAGTG 57.088 47.619 0.00 0.00 0.00 2.74
252 253 4.141390 GGATTGACACATGGGGAAGATAGT 60.141 45.833 0.00 0.00 0.00 2.12
253 254 4.141413 TGGATTGACACATGGGGAAGATAG 60.141 45.833 0.00 0.00 0.00 2.08
254 255 3.785325 TGGATTGACACATGGGGAAGATA 59.215 43.478 0.00 0.00 0.00 1.98
255 256 2.582172 TGGATTGACACATGGGGAAGAT 59.418 45.455 0.00 0.00 0.00 2.40
256 257 1.991813 TGGATTGACACATGGGGAAGA 59.008 47.619 0.00 0.00 0.00 2.87
257 258 2.512692 TGGATTGACACATGGGGAAG 57.487 50.000 0.00 0.00 0.00 3.46
258 259 2.988636 TTGGATTGACACATGGGGAA 57.011 45.000 0.00 0.00 0.00 3.97
259 260 3.471430 AATTGGATTGACACATGGGGA 57.529 42.857 0.00 0.00 0.00 4.81
260 261 4.020396 TCAAAATTGGATTGACACATGGGG 60.020 41.667 0.00 0.00 32.10 4.96
261 262 5.149973 TCAAAATTGGATTGACACATGGG 57.850 39.130 0.00 0.00 32.10 4.00
262 263 6.311935 GTGATCAAAATTGGATTGACACATGG 59.688 38.462 0.00 0.00 39.43 3.66
265 266 6.653526 AGTGATCAAAATTGGATTGACACA 57.346 33.333 17.03 9.41 39.43 3.72
266 267 8.461222 TCATAGTGATCAAAATTGGATTGACAC 58.539 33.333 0.00 11.80 39.43 3.67
267 268 8.578448 TCATAGTGATCAAAATTGGATTGACA 57.422 30.769 0.00 0.00 39.43 3.58
268 269 9.859427 TTTCATAGTGATCAAAATTGGATTGAC 57.141 29.630 0.00 0.00 39.43 3.18
273 274 9.022884 TGTGATTTCATAGTGATCAAAATTGGA 57.977 29.630 0.00 0.00 32.14 3.53
278 279 9.462174 GTTGTTGTGATTTCATAGTGATCAAAA 57.538 29.630 0.00 0.00 32.14 2.44
279 280 8.628280 TGTTGTTGTGATTTCATAGTGATCAAA 58.372 29.630 0.00 0.00 32.14 2.69
280 281 8.164058 TGTTGTTGTGATTTCATAGTGATCAA 57.836 30.769 0.00 0.00 32.14 2.57
281 282 7.742556 TGTTGTTGTGATTTCATAGTGATCA 57.257 32.000 0.00 0.00 0.00 2.92
284 285 9.891828 GTTTATGTTGTTGTGATTTCATAGTGA 57.108 29.630 0.00 0.00 0.00 3.41
285 286 8.839914 CGTTTATGTTGTTGTGATTTCATAGTG 58.160 33.333 0.00 0.00 0.00 2.74
286 287 8.020819 CCGTTTATGTTGTTGTGATTTCATAGT 58.979 33.333 0.00 0.00 0.00 2.12
287 288 7.008266 GCCGTTTATGTTGTTGTGATTTCATAG 59.992 37.037 0.00 0.00 0.00 2.23
289 290 5.633182 GCCGTTTATGTTGTTGTGATTTCAT 59.367 36.000 0.00 0.00 0.00 2.57
291 292 4.087930 CGCCGTTTATGTTGTTGTGATTTC 59.912 41.667 0.00 0.00 0.00 2.17
292 293 3.978217 CGCCGTTTATGTTGTTGTGATTT 59.022 39.130 0.00 0.00 0.00 2.17
293 294 3.560503 CGCCGTTTATGTTGTTGTGATT 58.439 40.909 0.00 0.00 0.00 2.57
294 295 2.667171 GCGCCGTTTATGTTGTTGTGAT 60.667 45.455 0.00 0.00 0.00 3.06
295 296 1.334239 GCGCCGTTTATGTTGTTGTGA 60.334 47.619 0.00 0.00 0.00 3.58
296 297 1.049251 GCGCCGTTTATGTTGTTGTG 58.951 50.000 0.00 0.00 0.00 3.33
297 298 0.663688 TGCGCCGTTTATGTTGTTGT 59.336 45.000 4.18 0.00 0.00 3.32
299 300 0.386731 GCTGCGCCGTTTATGTTGTT 60.387 50.000 4.18 0.00 0.00 2.83
301 302 0.386605 TTGCTGCGCCGTTTATGTTG 60.387 50.000 4.18 0.00 0.00 3.33
302 303 0.312416 TTTGCTGCGCCGTTTATGTT 59.688 45.000 4.18 0.00 0.00 2.71
303 304 0.109781 CTTTGCTGCGCCGTTTATGT 60.110 50.000 4.18 0.00 0.00 2.29
305 306 1.154035 GCTTTGCTGCGCCGTTTAT 60.154 52.632 4.18 0.00 0.00 1.40
318 319 2.359900 AGAAGGATTAGGCACGCTTTG 58.640 47.619 0.00 0.00 0.00 2.77
319 320 2.789409 AGAAGGATTAGGCACGCTTT 57.211 45.000 0.00 0.00 0.00 3.51
321 322 2.389715 ACTAGAAGGATTAGGCACGCT 58.610 47.619 0.00 0.00 0.00 5.07
322 323 2.892784 ACTAGAAGGATTAGGCACGC 57.107 50.000 0.00 0.00 0.00 5.34
324 325 8.179509 TCATACTAACTAGAAGGATTAGGCAC 57.820 38.462 0.00 0.00 31.43 5.01
411 412 1.667236 CGAATCAGGCCATACAGCAA 58.333 50.000 5.01 0.00 0.00 3.91
446 447 0.388649 ACCAAACTAGCAGCGAGTCG 60.389 55.000 8.81 8.54 0.00 4.18
656 662 2.222027 GGTGTGTGTCCCTCAAGAAAG 58.778 52.381 0.00 0.00 0.00 2.62
657 663 1.562008 TGGTGTGTGTCCCTCAAGAAA 59.438 47.619 0.00 0.00 0.00 2.52
658 664 1.208706 TGGTGTGTGTCCCTCAAGAA 58.791 50.000 0.00 0.00 0.00 2.52
698 3998 2.534742 GCAGCGCGGAATTTATTTTTGC 60.535 45.455 13.03 2.23 0.00 3.68
896 7596 7.101054 TGCTGTGTTAATTTATACGGAAGAGT 58.899 34.615 4.56 0.00 0.00 3.24
903 7603 6.758149 ACGACTTGCTGTGTTAATTTATACG 58.242 36.000 0.00 0.00 0.00 3.06
983 7721 2.694628 GCCATTGGAAATGGATGTAGCA 59.305 45.455 20.60 0.00 41.64 3.49
1107 7845 0.179100 CGATCATGGAAGTCGGCACT 60.179 55.000 0.00 0.00 0.00 4.40
1656 8415 0.667487 CAGAGCGGCGTGAAGAAGAA 60.667 55.000 9.37 0.00 0.00 2.52
1666 8425 2.128035 CCTTATTAACTCAGAGCGGCG 58.872 52.381 0.51 0.51 0.00 6.46
1677 8448 4.101119 TCACTAGCTCAGGGCCTTATTAAC 59.899 45.833 1.32 0.00 43.05 2.01
1708 8481 3.131478 CGGCACCGGGATTGTTCC 61.131 66.667 6.32 0.00 41.77 3.62
1721 8494 2.772077 TTATTGTCTACTTGGCGGCA 57.228 45.000 7.97 7.97 0.00 5.69
1743 8516 9.409312 CAACAAGCACAGATTATTAATTTCACA 57.591 29.630 0.00 0.00 0.00 3.58
1744 8517 9.410556 ACAACAAGCACAGATTATTAATTTCAC 57.589 29.630 0.00 0.00 0.00 3.18
1746 8519 9.624697 TCACAACAAGCACAGATTATTAATTTC 57.375 29.630 0.00 0.00 0.00 2.17
1747 8520 9.630098 CTCACAACAAGCACAGATTATTAATTT 57.370 29.630 0.00 0.00 0.00 1.82
1748 8521 8.796475 ACTCACAACAAGCACAGATTATTAATT 58.204 29.630 0.00 0.00 0.00 1.40
1749 8522 8.340618 ACTCACAACAAGCACAGATTATTAAT 57.659 30.769 0.00 0.00 0.00 1.40
1750 8523 7.744087 ACTCACAACAAGCACAGATTATTAA 57.256 32.000 0.00 0.00 0.00 1.40
1756 8600 3.065786 CACAACTCACAACAAGCACAGAT 59.934 43.478 0.00 0.00 0.00 2.90
1758 8602 2.419673 TCACAACTCACAACAAGCACAG 59.580 45.455 0.00 0.00 0.00 3.66
1760 8604 3.698029 ATCACAACTCACAACAAGCAC 57.302 42.857 0.00 0.00 0.00 4.40
1800 8655 7.119699 GTGACAAACCAACATCTCAATCAGATA 59.880 37.037 0.00 0.00 40.20 1.98
1801 8656 6.005823 TGACAAACCAACATCTCAATCAGAT 58.994 36.000 0.00 0.00 43.33 2.90
1802 8657 5.239306 GTGACAAACCAACATCTCAATCAGA 59.761 40.000 0.00 0.00 34.78 3.27
1803 8658 5.455392 GTGACAAACCAACATCTCAATCAG 58.545 41.667 0.00 0.00 0.00 2.90
1804 8659 5.437289 GTGACAAACCAACATCTCAATCA 57.563 39.130 0.00 0.00 0.00 2.57
1821 8676 1.990799 CGCGAGTAGAATTGGTGACA 58.009 50.000 0.00 0.00 39.83 3.58
1822 8677 0.645868 GCGCGAGTAGAATTGGTGAC 59.354 55.000 12.10 0.00 0.00 3.67
1823 8678 0.459585 GGCGCGAGTAGAATTGGTGA 60.460 55.000 12.10 0.00 0.00 4.02
1824 8679 0.460284 AGGCGCGAGTAGAATTGGTG 60.460 55.000 12.10 0.00 0.00 4.17
1825 8680 0.460284 CAGGCGCGAGTAGAATTGGT 60.460 55.000 12.10 0.00 0.00 3.67
1826 8681 0.460284 ACAGGCGCGAGTAGAATTGG 60.460 55.000 12.10 0.00 0.00 3.16
1827 8682 1.359848 AACAGGCGCGAGTAGAATTG 58.640 50.000 12.10 0.00 0.00 2.32
1828 8683 2.953466 TAACAGGCGCGAGTAGAATT 57.047 45.000 12.10 0.00 0.00 2.17
1829 8684 2.743938 CATAACAGGCGCGAGTAGAAT 58.256 47.619 12.10 0.00 0.00 2.40
1830 8685 1.801395 GCATAACAGGCGCGAGTAGAA 60.801 52.381 12.10 0.00 0.00 2.10
1831 8686 0.248907 GCATAACAGGCGCGAGTAGA 60.249 55.000 12.10 0.00 0.00 2.59
1832 8687 0.527600 TGCATAACAGGCGCGAGTAG 60.528 55.000 12.10 0.00 0.00 2.57
1833 8688 0.804544 GTGCATAACAGGCGCGAGTA 60.805 55.000 12.10 0.00 31.50 2.59
1834 8689 2.100631 GTGCATAACAGGCGCGAGT 61.101 57.895 12.10 0.82 31.50 4.18
1835 8690 1.431488 ATGTGCATAACAGGCGCGAG 61.431 55.000 12.10 0.01 43.64 5.03
1836 8691 1.428370 GATGTGCATAACAGGCGCGA 61.428 55.000 12.10 0.00 43.64 5.87
1837 8692 1.010797 GATGTGCATAACAGGCGCG 60.011 57.895 0.00 0.00 43.64 6.86
1838 8693 0.305922 GAGATGTGCATAACAGGCGC 59.694 55.000 0.00 0.00 43.64 6.53
1839 8694 1.596260 CAGAGATGTGCATAACAGGCG 59.404 52.381 0.00 0.00 43.64 5.52
1840 8695 2.353889 CACAGAGATGTGCATAACAGGC 59.646 50.000 0.00 0.00 43.64 4.85
1841 8696 3.603532 ACACAGAGATGTGCATAACAGG 58.396 45.455 8.24 0.00 43.64 4.00
1842 8697 5.618056 AAACACAGAGATGTGCATAACAG 57.382 39.130 8.24 0.00 43.64 3.16
1843 8698 7.686438 AATAAACACAGAGATGTGCATAACA 57.314 32.000 8.24 0.00 43.13 2.41
1844 8699 8.236586 TCAAATAAACACAGAGATGTGCATAAC 58.763 33.333 8.24 0.00 43.13 1.89
1845 8700 8.334263 TCAAATAAACACAGAGATGTGCATAA 57.666 30.769 8.24 0.00 43.13 1.90
1846 8701 7.920160 TCAAATAAACACAGAGATGTGCATA 57.080 32.000 8.24 0.00 43.13 3.14
1847 8702 6.822667 TCAAATAAACACAGAGATGTGCAT 57.177 33.333 8.24 0.78 43.13 3.96
1848 8703 6.207221 ACATCAAATAAACACAGAGATGTGCA 59.793 34.615 8.24 0.00 41.91 4.57
1849 8704 6.615088 ACATCAAATAAACACAGAGATGTGC 58.385 36.000 8.24 0.00 41.91 4.57
1851 8706 6.615088 GCACATCAAATAAACACAGAGATGT 58.385 36.000 0.00 0.00 43.63 3.06
1852 8707 5.735892 CGCACATCAAATAAACACAGAGATG 59.264 40.000 0.00 0.00 37.85 2.90
1853 8708 5.163723 CCGCACATCAAATAAACACAGAGAT 60.164 40.000 0.00 0.00 0.00 2.75
1854 8709 4.154015 CCGCACATCAAATAAACACAGAGA 59.846 41.667 0.00 0.00 0.00 3.10
1855 8710 4.083324 ACCGCACATCAAATAAACACAGAG 60.083 41.667 0.00 0.00 0.00 3.35
1856 8711 3.818210 ACCGCACATCAAATAAACACAGA 59.182 39.130 0.00 0.00 0.00 3.41
1857 8712 4.158384 GACCGCACATCAAATAAACACAG 58.842 43.478 0.00 0.00 0.00 3.66
1858 8713 3.364465 CGACCGCACATCAAATAAACACA 60.364 43.478 0.00 0.00 0.00 3.72
1859 8714 3.120477 TCGACCGCACATCAAATAAACAC 60.120 43.478 0.00 0.00 0.00 3.32
1860 8715 3.067833 TCGACCGCACATCAAATAAACA 58.932 40.909 0.00 0.00 0.00 2.83
1861 8716 3.733024 TCGACCGCACATCAAATAAAC 57.267 42.857 0.00 0.00 0.00 2.01
1862 8717 4.155099 ACAATCGACCGCACATCAAATAAA 59.845 37.500 0.00 0.00 0.00 1.40
1863 8718 3.687212 ACAATCGACCGCACATCAAATAA 59.313 39.130 0.00 0.00 0.00 1.40
1864 8719 3.266636 ACAATCGACCGCACATCAAATA 58.733 40.909 0.00 0.00 0.00 1.40
1865 8720 2.083774 ACAATCGACCGCACATCAAAT 58.916 42.857 0.00 0.00 0.00 2.32
1866 8721 1.463056 GACAATCGACCGCACATCAAA 59.537 47.619 0.00 0.00 0.00 2.69
1867 8722 1.075542 GACAATCGACCGCACATCAA 58.924 50.000 0.00 0.00 0.00 2.57
1868 8723 0.037790 TGACAATCGACCGCACATCA 60.038 50.000 0.00 0.00 0.00 3.07
1869 8724 0.370273 GTGACAATCGACCGCACATC 59.630 55.000 0.00 0.00 0.00 3.06
1870 8725 1.351430 CGTGACAATCGACCGCACAT 61.351 55.000 9.30 0.00 0.00 3.21
1871 8726 2.019408 CGTGACAATCGACCGCACA 61.019 57.895 9.30 0.00 0.00 4.57
1872 8727 2.726691 CCGTGACAATCGACCGCAC 61.727 63.158 0.00 0.00 0.00 5.34
1873 8728 2.220615 ATCCGTGACAATCGACCGCA 62.221 55.000 0.00 0.00 0.00 5.69
1874 8729 1.082117 AATCCGTGACAATCGACCGC 61.082 55.000 0.00 0.00 0.00 5.68
1875 8730 1.355971 AAATCCGTGACAATCGACCG 58.644 50.000 0.00 0.00 0.00 4.79
1876 8731 3.824414 AAAAATCCGTGACAATCGACC 57.176 42.857 0.00 0.00 0.00 4.79
2138 8998 1.628340 TCATTGTCGGAGGTGGAACAT 59.372 47.619 0.00 0.00 44.52 2.71
2201 9062 4.276678 CAGTGATGTTCCATTGTGAGTTGT 59.723 41.667 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.