Multiple sequence alignment - TraesCS2B01G289000

Loading Multiple Alignment...

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 TraesCS2B01G289000 chr2B 100.000 3252 0 0 1 3252 399706198 399709449 0.000000e+00 6006.0
1 TraesCS2B01G289000 chr2B 84.762 105 11 4 2923 3023 736103153 736103256 2.060000e-17 100.0
2 TraesCS2B01G289000 chr2A 94.689 2617 91 20 173 2763 438298689 438301283 0.000000e+00 4019.0
3 TraesCS2B01G289000 chr2A 93.534 232 13 2 3022 3251 438301995 438302226 8.640000e-91 344.0
4 TraesCS2B01G289000 chr2A 85.345 116 15 2 1997 2111 686214510 686214396 5.700000e-23 119.0
5 TraesCS2B01G289000 chr2D 93.921 2418 89 20 197 2590 331177651 331180034 0.000000e+00 3598.0
6 TraesCS2B01G289000 chr2D 92.829 251 13 2 3004 3251 331181041 331181289 3.080000e-95 359.0
7 TraesCS2B01G289000 chr2D 87.119 295 26 8 2586 2868 331180550 331180844 1.130000e-84 324.0
8 TraesCS2B01G289000 chr2D 86.207 116 14 2 1997 2111 543429272 543429158 1.230000e-24 124.0
9 TraesCS2B01G289000 chr2D 86.735 98 8 5 2915 3010 524577111 524577017 1.600000e-18 104.0
10 TraesCS2B01G289000 chr4A 95.968 372 14 1 1498 1869 68460695 68460325 1.290000e-168 603.0
11 TraesCS2B01G289000 chr4A 89.655 87 7 1 2926 3010 507914725 507914811 3.430000e-20 110.0
12 TraesCS2B01G289000 chr1B 95.957 371 15 0 1498 1868 94164390 94164760 1.290000e-168 603.0
13 TraesCS2B01G289000 chr1B 95.161 372 16 2 1498 1868 450455772 450456142 1.300000e-163 586.0
14 TraesCS2B01G289000 chr1B 84.946 93 11 3 2942 3032 32394232 32394141 1.240000e-14 91.6
15 TraesCS2B01G289000 chr5B 94.892 372 19 0 1498 1869 56554029 56554400 1.680000e-162 582.0
16 TraesCS2B01G289000 chr5B 89.109 101 8 2 2926 3023 477498514 477498414 4.410000e-24 122.0
17 TraesCS2B01G289000 chr3B 92.183 371 18 3 1498 1868 321756844 321757203 6.220000e-142 514.0
18 TraesCS2B01G289000 chr7B 89.773 88 6 3 2925 3009 745107314 745107401 3.430000e-20 110.0
19 TraesCS2B01G289000 chr4B 89.655 87 7 1 2926 3010 531091954 531092040 3.430000e-20 110.0
20 TraesCS2B01G289000 chr6D 88.043 92 8 3 2922 3012 342467205 342467294 4.440000e-19 106.0
21 TraesCS2B01G289000 chr5D 88.636 88 8 2 2924 3010 192552320 192552234 4.440000e-19 106.0
22 TraesCS2B01G289000 chr5D 83.486 109 16 2 2004 2111 70520859 70520752 2.060000e-17 100.0
23 TraesCS2B01G289000 chr5A 83.486 109 16 2 2004 2111 60413598 60413491 2.060000e-17 100.0
24 TraesCS2B01G289000 chr5A 88.889 45 3 2 2889 2931 694880914 694880870 2.000000e-03 54.7
25 TraesCS2B01G289000 chr7D 100.000 28 0 0 2889 2916 510397778 510397751 6.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G289000 chr2B 399706198 399709449 3251 False 6006.0 6006 100.000000 1 3252 1 chr2B.!!$F1 3251
1 TraesCS2B01G289000 chr2A 438298689 438302226 3537 False 2181.5 4019 94.111500 173 3251 2 chr2A.!!$F1 3078
2 TraesCS2B01G289000 chr2D 331177651 331181289 3638 False 1427.0 3598 91.289667 197 3251 3 chr2D.!!$F1 3054

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
136 137 0.027716 TGCTCTCGTCGTAATCGCTC 59.972 55.0 0.0 0.0 36.96 5.03 F
144 145 0.317854 TCGTAATCGCTCGCTGGATG 60.318 55.0 0.0 0.0 36.96 3.51 F
145 146 0.317854 CGTAATCGCTCGCTGGATGA 60.318 55.0 0.0 0.0 0.00 2.92 F
420 424 0.677731 ACCTCACATCATTGGCACCG 60.678 55.0 0.0 0.0 0.00 4.94 F
1371 1392 0.759346 ACTTCACCAAGGCGTCTTCT 59.241 50.0 0.0 0.0 33.37 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 1935 0.253160 TACATGGTGGAGGGAAGCCT 60.253 55.000 0.00 0.0 0.00 4.58 R
1914 1936 0.623723 TTACATGGTGGAGGGAAGCC 59.376 55.000 0.00 0.0 0.00 4.35 R
1918 1940 1.203376 TGGTCTTACATGGTGGAGGGA 60.203 52.381 0.00 0.0 0.00 4.20 R
2205 2236 0.953960 AACGAAGGGAACATGGCGAC 60.954 55.000 0.00 0.0 0.00 5.19 R
2680 3245 0.311165 CAAGACGCTATCGACCGGAT 59.689 55.000 9.46 0.0 39.41 4.18 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 4.764143 GAATGGTGGTGGAAGGGG 57.236 61.111 0.00 0.00 0.00 4.79
18 19 1.774300 GAATGGTGGTGGAAGGGGT 59.226 57.895 0.00 0.00 0.00 4.95
19 20 0.996583 GAATGGTGGTGGAAGGGGTA 59.003 55.000 0.00 0.00 0.00 3.69
20 21 0.702316 AATGGTGGTGGAAGGGGTAC 59.298 55.000 0.00 0.00 0.00 3.34
21 22 1.559065 ATGGTGGTGGAAGGGGTACG 61.559 60.000 0.00 0.00 0.00 3.67
22 23 1.914764 GGTGGTGGAAGGGGTACGA 60.915 63.158 0.00 0.00 0.00 3.43
23 24 1.482748 GGTGGTGGAAGGGGTACGAA 61.483 60.000 0.00 0.00 0.00 3.85
24 25 0.397564 GTGGTGGAAGGGGTACGAAA 59.602 55.000 0.00 0.00 0.00 3.46
25 26 1.138568 TGGTGGAAGGGGTACGAAAA 58.861 50.000 0.00 0.00 0.00 2.29
26 27 1.493871 TGGTGGAAGGGGTACGAAAAA 59.506 47.619 0.00 0.00 0.00 1.94
57 58 8.173321 GTCAAAAAGACCGGATAAAAATGATG 57.827 34.615 9.46 0.00 41.56 3.07
58 59 7.275560 GTCAAAAAGACCGGATAAAAATGATGG 59.724 37.037 9.46 0.00 41.56 3.51
59 60 7.177568 TCAAAAAGACCGGATAAAAATGATGGA 59.822 33.333 9.46 0.00 0.00 3.41
60 61 7.475137 AAAAGACCGGATAAAAATGATGGAA 57.525 32.000 9.46 0.00 0.00 3.53
61 62 7.660030 AAAGACCGGATAAAAATGATGGAAT 57.340 32.000 9.46 0.00 0.00 3.01
62 63 6.884280 AGACCGGATAAAAATGATGGAATC 57.116 37.500 9.46 0.00 45.83 2.52
78 79 7.684062 GATGGAATCAAAAATACCATGAACG 57.316 36.000 0.00 0.00 44.70 3.95
79 80 5.406649 TGGAATCAAAAATACCATGAACGC 58.593 37.500 0.00 0.00 0.00 4.84
80 81 5.047731 TGGAATCAAAAATACCATGAACGCA 60.048 36.000 0.00 0.00 0.00 5.24
81 82 5.866633 GGAATCAAAAATACCATGAACGCAA 59.133 36.000 0.00 0.00 0.00 4.85
82 83 6.534793 GGAATCAAAAATACCATGAACGCAAT 59.465 34.615 0.00 0.00 0.00 3.56
83 84 7.254084 GGAATCAAAAATACCATGAACGCAATC 60.254 37.037 0.00 0.00 0.00 2.67
84 85 5.406649 TCAAAAATACCATGAACGCAATCC 58.593 37.500 0.00 0.00 0.00 3.01
85 86 5.184864 TCAAAAATACCATGAACGCAATCCT 59.815 36.000 0.00 0.00 0.00 3.24
86 87 6.375736 TCAAAAATACCATGAACGCAATCCTA 59.624 34.615 0.00 0.00 0.00 2.94
87 88 5.751243 AAATACCATGAACGCAATCCTAC 57.249 39.130 0.00 0.00 0.00 3.18
88 89 4.689612 ATACCATGAACGCAATCCTACT 57.310 40.909 0.00 0.00 0.00 2.57
89 90 5.801531 ATACCATGAACGCAATCCTACTA 57.198 39.130 0.00 0.00 0.00 1.82
90 91 4.481368 ACCATGAACGCAATCCTACTAA 57.519 40.909 0.00 0.00 0.00 2.24
91 92 4.189231 ACCATGAACGCAATCCTACTAAC 58.811 43.478 0.00 0.00 0.00 2.34
92 93 4.081087 ACCATGAACGCAATCCTACTAACT 60.081 41.667 0.00 0.00 0.00 2.24
93 94 4.271049 CCATGAACGCAATCCTACTAACTG 59.729 45.833 0.00 0.00 0.00 3.16
94 95 3.259064 TGAACGCAATCCTACTAACTGC 58.741 45.455 0.00 0.00 0.00 4.40
95 96 3.056107 TGAACGCAATCCTACTAACTGCT 60.056 43.478 0.00 0.00 0.00 4.24
96 97 3.611766 ACGCAATCCTACTAACTGCTT 57.388 42.857 0.00 0.00 0.00 3.91
97 98 3.939066 ACGCAATCCTACTAACTGCTTT 58.061 40.909 0.00 0.00 0.00 3.51
98 99 5.080969 ACGCAATCCTACTAACTGCTTTA 57.919 39.130 0.00 0.00 0.00 1.85
99 100 5.671493 ACGCAATCCTACTAACTGCTTTAT 58.329 37.500 0.00 0.00 0.00 1.40
100 101 6.113411 ACGCAATCCTACTAACTGCTTTATT 58.887 36.000 0.00 0.00 0.00 1.40
101 102 7.270047 ACGCAATCCTACTAACTGCTTTATTA 58.730 34.615 0.00 0.00 0.00 0.98
102 103 7.767198 ACGCAATCCTACTAACTGCTTTATTAA 59.233 33.333 0.00 0.00 0.00 1.40
103 104 8.276325 CGCAATCCTACTAACTGCTTTATTAAG 58.724 37.037 0.00 0.00 34.36 1.85
104 105 9.326413 GCAATCCTACTAACTGCTTTATTAAGA 57.674 33.333 0.00 0.00 32.92 2.10
124 125 8.912787 TTAAGAGTAGAAATTAGTTGCTCTCG 57.087 34.615 0.00 0.00 32.22 4.04
125 126 6.518208 AGAGTAGAAATTAGTTGCTCTCGT 57.482 37.500 0.00 0.00 0.00 4.18
126 127 6.557110 AGAGTAGAAATTAGTTGCTCTCGTC 58.443 40.000 0.00 0.00 0.00 4.20
127 128 5.333513 AGTAGAAATTAGTTGCTCTCGTCG 58.666 41.667 0.00 0.00 0.00 5.12
128 129 4.175787 AGAAATTAGTTGCTCTCGTCGT 57.824 40.909 0.00 0.00 0.00 4.34
129 130 5.306532 AGAAATTAGTTGCTCTCGTCGTA 57.693 39.130 0.00 0.00 0.00 3.43
130 131 5.706916 AGAAATTAGTTGCTCTCGTCGTAA 58.293 37.500 0.00 0.00 0.00 3.18
131 132 6.331061 AGAAATTAGTTGCTCTCGTCGTAAT 58.669 36.000 0.00 0.00 0.00 1.89
132 133 6.472808 AGAAATTAGTTGCTCTCGTCGTAATC 59.527 38.462 0.00 0.00 0.00 1.75
133 134 2.175530 AGTTGCTCTCGTCGTAATCG 57.824 50.000 0.00 0.00 38.55 3.34
134 135 0.566593 GTTGCTCTCGTCGTAATCGC 59.433 55.000 0.00 0.00 36.96 4.58
135 136 0.450583 TTGCTCTCGTCGTAATCGCT 59.549 50.000 0.00 0.00 36.96 4.93
136 137 0.027716 TGCTCTCGTCGTAATCGCTC 59.972 55.000 0.00 0.00 36.96 5.03
137 138 0.987848 GCTCTCGTCGTAATCGCTCG 60.988 60.000 0.00 0.00 36.96 5.03
138 139 0.987848 CTCTCGTCGTAATCGCTCGC 60.988 60.000 0.00 0.00 35.57 5.03
139 140 1.011019 CTCGTCGTAATCGCTCGCT 60.011 57.895 0.00 0.00 35.57 4.93
140 141 1.256284 CTCGTCGTAATCGCTCGCTG 61.256 60.000 0.00 0.00 35.57 5.18
141 142 2.286559 CGTCGTAATCGCTCGCTGG 61.287 63.158 0.00 0.00 36.96 4.85
142 143 1.063649 GTCGTAATCGCTCGCTGGA 59.936 57.895 0.00 0.00 36.96 3.86
143 144 0.317938 GTCGTAATCGCTCGCTGGAT 60.318 55.000 0.00 0.00 36.96 3.41
144 145 0.317854 TCGTAATCGCTCGCTGGATG 60.318 55.000 0.00 0.00 36.96 3.51
145 146 0.317854 CGTAATCGCTCGCTGGATGA 60.318 55.000 0.00 0.00 0.00 2.92
146 147 1.852942 GTAATCGCTCGCTGGATGAA 58.147 50.000 0.00 0.00 0.00 2.57
147 148 2.201732 GTAATCGCTCGCTGGATGAAA 58.798 47.619 0.00 0.00 0.00 2.69
148 149 1.959042 AATCGCTCGCTGGATGAAAT 58.041 45.000 0.00 0.00 0.00 2.17
149 150 1.959042 ATCGCTCGCTGGATGAAATT 58.041 45.000 0.00 0.00 0.00 1.82
150 151 1.737838 TCGCTCGCTGGATGAAATTT 58.262 45.000 0.00 0.00 0.00 1.82
151 152 1.665679 TCGCTCGCTGGATGAAATTTC 59.334 47.619 11.41 11.41 0.00 2.17
152 153 1.398041 CGCTCGCTGGATGAAATTTCA 59.602 47.619 22.52 22.52 42.14 2.69
153 154 2.159531 CGCTCGCTGGATGAAATTTCAA 60.160 45.455 23.91 7.84 41.13 2.69
154 155 3.432782 GCTCGCTGGATGAAATTTCAAG 58.567 45.455 23.91 17.42 41.13 3.02
155 156 3.127548 GCTCGCTGGATGAAATTTCAAGA 59.872 43.478 23.91 14.48 41.13 3.02
156 157 4.656041 CTCGCTGGATGAAATTTCAAGAC 58.344 43.478 23.91 16.54 41.13 3.01
157 158 4.071423 TCGCTGGATGAAATTTCAAGACA 58.929 39.130 23.91 19.63 41.13 3.41
158 159 4.701651 TCGCTGGATGAAATTTCAAGACAT 59.298 37.500 23.91 7.93 41.13 3.06
159 160 5.032863 CGCTGGATGAAATTTCAAGACATC 58.967 41.667 23.91 15.86 41.13 3.06
160 161 5.392272 CGCTGGATGAAATTTCAAGACATCA 60.392 40.000 23.91 13.96 41.13 3.07
161 162 6.570692 GCTGGATGAAATTTCAAGACATCAT 58.429 36.000 23.91 5.69 41.13 2.45
162 163 7.039882 GCTGGATGAAATTTCAAGACATCATT 58.960 34.615 23.91 4.96 41.13 2.57
163 164 7.548075 GCTGGATGAAATTTCAAGACATCATTT 59.452 33.333 23.91 4.22 41.13 2.32
164 165 8.766000 TGGATGAAATTTCAAGACATCATTTG 57.234 30.769 23.91 0.00 41.13 2.32
165 166 7.820386 TGGATGAAATTTCAAGACATCATTTGG 59.180 33.333 23.91 0.00 41.13 3.28
166 167 7.279313 GGATGAAATTTCAAGACATCATTTGGG 59.721 37.037 23.91 0.00 41.13 4.12
167 168 7.065120 TGAAATTTCAAGACATCATTTGGGT 57.935 32.000 18.45 0.00 33.55 4.51
168 169 7.507829 TGAAATTTCAAGACATCATTTGGGTT 58.492 30.769 18.45 0.00 33.55 4.11
169 170 7.441760 TGAAATTTCAAGACATCATTTGGGTTG 59.558 33.333 18.45 0.00 33.55 3.77
170 171 4.870123 TTCAAGACATCATTTGGGTTGG 57.130 40.909 0.00 0.00 0.00 3.77
171 172 3.843422 TCAAGACATCATTTGGGTTGGT 58.157 40.909 0.00 0.00 0.00 3.67
175 176 4.589908 AGACATCATTTGGGTTGGTCTAC 58.410 43.478 0.00 0.00 32.80 2.59
188 189 3.134574 TGGTCTACGCATTTCCTTTGT 57.865 42.857 0.00 0.00 0.00 2.83
357 359 6.091437 GCCAAATCAGACTGAATGAAGAAAG 58.909 40.000 18.37 6.23 0.00 2.62
358 360 6.618811 CCAAATCAGACTGAATGAAGAAAGG 58.381 40.000 18.37 5.22 0.00 3.11
359 361 6.349944 CCAAATCAGACTGAATGAAGAAAGGG 60.350 42.308 18.37 3.78 0.00 3.95
360 362 5.768980 ATCAGACTGAATGAAGAAAGGGA 57.231 39.130 9.70 0.00 0.00 4.20
362 364 5.555017 TCAGACTGAATGAAGAAAGGGAAG 58.445 41.667 1.64 0.00 0.00 3.46
363 365 4.699257 CAGACTGAATGAAGAAAGGGAAGG 59.301 45.833 0.00 0.00 0.00 3.46
377 381 2.192263 GGGAAGGGAAGTCTCTGACAT 58.808 52.381 0.46 0.00 34.60 3.06
384 388 2.039084 GGAAGTCTCTGACATGTGGGTT 59.961 50.000 1.15 0.00 34.60 4.11
420 424 0.677731 ACCTCACATCATTGGCACCG 60.678 55.000 0.00 0.00 0.00 4.94
439 443 3.246699 ACCGTTCACATAACTGTTTCACG 59.753 43.478 0.00 0.00 31.62 4.35
440 444 3.246699 CCGTTCACATAACTGTTTCACGT 59.753 43.478 0.00 0.00 31.62 4.49
441 445 4.445052 CCGTTCACATAACTGTTTCACGTA 59.555 41.667 0.00 0.00 31.62 3.57
453 457 8.876275 AACTGTTTCACGTAGTAGTATTTCAA 57.124 30.769 0.00 0.00 41.61 2.69
761 777 2.063979 ATCCAACGGCGGGAGATGA 61.064 57.895 13.24 0.00 37.96 2.92
795 811 4.913126 GGTAAGCCCGTGTCTCTG 57.087 61.111 0.00 0.00 0.00 3.35
909 925 2.287103 CCGCCTCGCCTTCTTTTATAAC 59.713 50.000 0.00 0.00 0.00 1.89
944 960 2.823154 CGTCTCCCTCACTTCTTCTTCT 59.177 50.000 0.00 0.00 0.00 2.85
984 1000 2.414824 CGGCGAGCACCTATCTTATCTC 60.415 54.545 0.00 0.00 0.00 2.75
986 1002 2.226912 GCGAGCACCTATCTTATCTCGT 59.773 50.000 10.46 0.00 43.49 4.18
1200 1221 2.893489 CCGGGAGATCACTGATATGACA 59.107 50.000 0.00 0.00 0.00 3.58
1342 1363 2.097918 CGTCTTCGTCGAGGTCCG 59.902 66.667 4.85 4.78 40.25 4.79
1371 1392 0.759346 ACTTCACCAAGGCGTCTTCT 59.241 50.000 0.00 0.00 33.37 2.85
1496 1517 4.479993 GCTGATGCTCCCGCCACT 62.480 66.667 0.00 0.00 36.03 4.00
1690 1711 1.556911 AGCAGATTCGATTCACCCAGT 59.443 47.619 9.78 0.00 0.00 4.00
1716 1737 3.249080 GGATTTCGTTGTTCCGTTCTTCA 59.751 43.478 0.00 0.00 0.00 3.02
1722 1743 2.808543 GTTGTTCCGTTCTTCATCTGCT 59.191 45.455 0.00 0.00 0.00 4.24
1753 1774 7.649533 ATCCATGTTGCTAAAGAATGAATGA 57.350 32.000 0.00 0.00 0.00 2.57
1758 1780 6.632909 TGTTGCTAAAGAATGAATGAATGGG 58.367 36.000 0.00 0.00 0.00 4.00
1913 1935 2.614969 AGGCAGCATCCCTTCCCA 60.615 61.111 0.00 0.00 0.00 4.37
1914 1936 2.123982 GGCAGCATCCCTTCCCAG 60.124 66.667 0.00 0.00 0.00 4.45
1915 1937 2.123982 GCAGCATCCCTTCCCAGG 60.124 66.667 0.00 0.00 40.45 4.45
1916 1938 2.123982 CAGCATCCCTTCCCAGGC 60.124 66.667 0.00 0.00 39.20 4.85
1917 1939 2.286732 AGCATCCCTTCCCAGGCT 60.287 61.111 0.00 0.00 39.20 4.58
1918 1940 1.932757 AGCATCCCTTCCCAGGCTT 60.933 57.895 0.00 0.00 39.20 4.35
1919 1941 1.454663 GCATCCCTTCCCAGGCTTC 60.455 63.158 0.00 0.00 39.20 3.86
1920 1942 1.228510 CATCCCTTCCCAGGCTTCC 59.771 63.158 0.00 0.00 39.20 3.46
1921 1943 2.009302 ATCCCTTCCCAGGCTTCCC 61.009 63.158 0.00 0.00 39.20 3.97
1983 2013 1.266989 GAACTAACCACCAGTTGCTGC 59.733 52.381 0.00 0.00 39.67 5.25
2205 2236 7.752239 CCTCACATGTTAATTCAACTTAGCTTG 59.248 37.037 0.00 0.00 38.05 4.01
2208 2239 7.269084 CACATGTTAATTCAACTTAGCTTGTCG 59.731 37.037 0.00 0.00 38.05 4.35
2377 2411 1.045407 AGGTGCGTGGTAGACAAGAA 58.955 50.000 0.00 0.00 0.00 2.52
2378 2412 1.000955 AGGTGCGTGGTAGACAAGAAG 59.999 52.381 0.00 0.00 0.00 2.85
2379 2413 1.429463 GTGCGTGGTAGACAAGAAGG 58.571 55.000 0.00 0.00 0.00 3.46
2380 2414 1.000506 GTGCGTGGTAGACAAGAAGGA 59.999 52.381 0.00 0.00 0.00 3.36
2387 2421 5.509163 CGTGGTAGACAAGAAGGAGAAAGAA 60.509 44.000 0.00 0.00 0.00 2.52
2391 2425 7.998964 TGGTAGACAAGAAGGAGAAAGAAAAAT 59.001 33.333 0.00 0.00 0.00 1.82
2433 2470 1.903877 ATCCTGTGGCTCGGGTTCTG 61.904 60.000 13.78 0.00 42.90 3.02
2434 2471 2.046892 CTGTGGCTCGGGTTCTGG 60.047 66.667 0.00 0.00 0.00 3.86
2470 2507 2.482333 CGGTGGTTGAACGGGCAAA 61.482 57.895 0.00 0.00 0.00 3.68
2585 2622 0.597637 CGTTGACTCGTGTTGCTCCT 60.598 55.000 0.00 0.00 0.00 3.69
2620 3177 6.754209 TGCTCGATTATTGTTTGTTTGTTTGT 59.246 30.769 0.00 0.00 0.00 2.83
2680 3245 4.248842 CACCCGCCAGTGTGGACA 62.249 66.667 0.00 0.00 45.51 4.02
2720 3285 2.280592 GGTTCGCCAACGGTGTCT 60.281 61.111 0.00 0.00 40.63 3.41
2774 3375 1.657594 CGCAGTGCTGATAGTGTTGAG 59.342 52.381 14.33 0.00 0.00 3.02
2775 3376 1.396301 GCAGTGCTGATAGTGTTGAGC 59.604 52.381 8.18 0.00 0.00 4.26
2779 3380 4.931601 CAGTGCTGATAGTGTTGAGCTTTA 59.068 41.667 0.00 0.00 32.41 1.85
2780 3381 5.409520 CAGTGCTGATAGTGTTGAGCTTTAA 59.590 40.000 0.00 0.00 32.41 1.52
2781 3382 6.093219 CAGTGCTGATAGTGTTGAGCTTTAAT 59.907 38.462 0.00 0.00 32.41 1.40
2782 3383 6.093219 AGTGCTGATAGTGTTGAGCTTTAATG 59.907 38.462 0.00 0.00 32.41 1.90
2783 3384 5.163723 TGCTGATAGTGTTGAGCTTTAATGC 60.164 40.000 5.22 5.22 32.41 3.56
2793 3774 8.616076 GTGTTGAGCTTTAATGCTATATTGTCT 58.384 33.333 15.21 0.00 44.17 3.41
2846 3827 1.394618 ACTCCTGCGACCTCATCTAC 58.605 55.000 0.00 0.00 0.00 2.59
2868 3849 4.399934 ACAAACGCCGGGAATTTTACATAT 59.600 37.500 2.18 0.00 0.00 1.78
2869 3850 5.589452 ACAAACGCCGGGAATTTTACATATA 59.411 36.000 2.18 0.00 0.00 0.86
2870 3851 6.263617 ACAAACGCCGGGAATTTTACATATAT 59.736 34.615 2.18 0.00 0.00 0.86
2874 3855 6.935771 ACGCCGGGAATTTTACATATATACAA 59.064 34.615 2.18 0.00 0.00 2.41
2875 3856 7.095102 ACGCCGGGAATTTTACATATATACAAC 60.095 37.037 2.18 0.00 0.00 3.32
2876 3857 7.095144 CGCCGGGAATTTTACATATATACAACA 60.095 37.037 2.18 0.00 0.00 3.33
2877 3858 8.019094 GCCGGGAATTTTACATATATACAACAC 58.981 37.037 2.18 0.00 0.00 3.32
2896 3901 8.746922 ACAACACAAAATGCTGTTATTATGAG 57.253 30.769 0.00 0.00 33.72 2.90
2902 3907 6.851222 AAATGCTGTTATTATGAGACGGAG 57.149 37.500 0.00 0.00 0.00 4.63
2921 3926 5.954150 ACGGAGGGAGTAGTTCATAACTAAA 59.046 40.000 1.26 0.00 44.95 1.85
2922 3927 6.610425 ACGGAGGGAGTAGTTCATAACTAAAT 59.390 38.462 1.26 0.00 44.95 1.40
2923 3928 7.781693 ACGGAGGGAGTAGTTCATAACTAAATA 59.218 37.037 1.26 0.00 44.95 1.40
2924 3929 8.298140 CGGAGGGAGTAGTTCATAACTAAATAG 58.702 40.741 1.26 0.00 44.95 1.73
2925 3930 9.145442 GGAGGGAGTAGTTCATAACTAAATAGT 57.855 37.037 1.26 0.00 44.95 2.12
2938 3943 9.930693 CATAACTAAATAGTACTTCCTCCATCC 57.069 37.037 0.00 0.00 34.99 3.51
2939 3944 6.651975 ACTAAATAGTACTTCCTCCATCCG 57.348 41.667 0.00 0.00 34.13 4.18
2940 3945 4.338379 AAATAGTACTTCCTCCATCCGC 57.662 45.455 0.00 0.00 0.00 5.54
2941 3946 2.750141 TAGTACTTCCTCCATCCGCT 57.250 50.000 0.00 0.00 0.00 5.52
2942 3947 2.750141 AGTACTTCCTCCATCCGCTA 57.250 50.000 0.00 0.00 0.00 4.26
2945 3950 2.918712 ACTTCCTCCATCCGCTAATG 57.081 50.000 0.00 0.00 0.00 1.90
2949 3954 4.202264 ACTTCCTCCATCCGCTAATGTAAG 60.202 45.833 0.00 0.00 0.00 2.34
2950 3955 3.572642 TCCTCCATCCGCTAATGTAAGA 58.427 45.455 0.00 0.00 0.00 2.10
2951 3956 3.321111 TCCTCCATCCGCTAATGTAAGAC 59.679 47.826 0.00 0.00 0.00 3.01
2953 3958 2.691526 TCCATCCGCTAATGTAAGACGT 59.308 45.455 0.00 0.00 0.00 4.34
2954 3959 3.131577 TCCATCCGCTAATGTAAGACGTT 59.868 43.478 0.00 0.00 0.00 3.99
3077 4155 3.874543 TGCTAATTGTTTGTCTGTGACGT 59.125 39.130 0.00 0.00 34.95 4.34
3098 4176 2.124122 TGTCGACTGTCGTTTCACATG 58.876 47.619 27.16 0.00 41.35 3.21
3226 4304 6.566197 AAACAAGAAATAGGTGCTCTCTTG 57.434 37.500 11.14 11.14 45.46 3.02
3251 4329 3.891977 CTCACTCGATCCCATCTTTCCTA 59.108 47.826 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.996583 TACCCCTTCCACCACCATTC 59.003 55.000 0.00 0.00 0.00 2.67
1 2 0.702316 GTACCCCTTCCACCACCATT 59.298 55.000 0.00 0.00 0.00 3.16
2 3 1.559065 CGTACCCCTTCCACCACCAT 61.559 60.000 0.00 0.00 0.00 3.55
3 4 2.218454 CGTACCCCTTCCACCACCA 61.218 63.158 0.00 0.00 0.00 4.17
4 5 1.482748 TTCGTACCCCTTCCACCACC 61.483 60.000 0.00 0.00 0.00 4.61
5 6 0.397564 TTTCGTACCCCTTCCACCAC 59.602 55.000 0.00 0.00 0.00 4.16
6 7 1.138568 TTTTCGTACCCCTTCCACCA 58.861 50.000 0.00 0.00 0.00 4.17
7 8 2.275134 TTTTTCGTACCCCTTCCACC 57.725 50.000 0.00 0.00 0.00 4.61
31 32 7.519032 TCATTTTTATCCGGTCTTTTTGACT 57.481 32.000 0.00 0.00 44.74 3.41
32 33 7.275560 CCATCATTTTTATCCGGTCTTTTTGAC 59.724 37.037 0.00 0.00 44.63 3.18
33 34 7.177568 TCCATCATTTTTATCCGGTCTTTTTGA 59.822 33.333 0.00 0.00 0.00 2.69
34 35 7.319646 TCCATCATTTTTATCCGGTCTTTTTG 58.680 34.615 0.00 0.00 0.00 2.44
35 36 7.475137 TCCATCATTTTTATCCGGTCTTTTT 57.525 32.000 0.00 0.00 0.00 1.94
36 37 7.475137 TTCCATCATTTTTATCCGGTCTTTT 57.525 32.000 0.00 0.00 0.00 2.27
37 38 7.341769 TGATTCCATCATTTTTATCCGGTCTTT 59.658 33.333 0.00 0.00 33.59 2.52
38 39 6.833416 TGATTCCATCATTTTTATCCGGTCTT 59.167 34.615 0.00 0.00 33.59 3.01
39 40 6.364701 TGATTCCATCATTTTTATCCGGTCT 58.635 36.000 0.00 0.00 33.59 3.85
40 41 6.633500 TGATTCCATCATTTTTATCCGGTC 57.367 37.500 0.00 0.00 33.59 4.79
41 42 7.416964 TTTGATTCCATCATTTTTATCCGGT 57.583 32.000 0.00 0.00 39.39 5.28
42 43 8.715191 TTTTTGATTCCATCATTTTTATCCGG 57.285 30.769 0.00 0.00 39.39 5.14
51 52 9.603921 GTTCATGGTATTTTTGATTCCATCATT 57.396 29.630 0.00 0.00 39.39 2.57
52 53 7.922278 CGTTCATGGTATTTTTGATTCCATCAT 59.078 33.333 0.00 0.00 39.39 2.45
53 54 7.257003 CGTTCATGGTATTTTTGATTCCATCA 58.743 34.615 0.00 0.00 36.86 3.07
54 55 6.198966 GCGTTCATGGTATTTTTGATTCCATC 59.801 38.462 0.00 0.00 36.86 3.51
55 56 6.042143 GCGTTCATGGTATTTTTGATTCCAT 58.958 36.000 0.00 0.00 39.14 3.41
56 57 5.047731 TGCGTTCATGGTATTTTTGATTCCA 60.048 36.000 0.00 0.00 0.00 3.53
57 58 5.406649 TGCGTTCATGGTATTTTTGATTCC 58.593 37.500 0.00 0.00 0.00 3.01
58 59 6.942886 TTGCGTTCATGGTATTTTTGATTC 57.057 33.333 0.00 0.00 0.00 2.52
59 60 6.534793 GGATTGCGTTCATGGTATTTTTGATT 59.465 34.615 0.00 0.00 0.00 2.57
60 61 6.042143 GGATTGCGTTCATGGTATTTTTGAT 58.958 36.000 0.00 0.00 0.00 2.57
61 62 5.184864 AGGATTGCGTTCATGGTATTTTTGA 59.815 36.000 0.00 0.00 0.00 2.69
62 63 5.410067 AGGATTGCGTTCATGGTATTTTTG 58.590 37.500 0.00 0.00 0.00 2.44
63 64 5.659440 AGGATTGCGTTCATGGTATTTTT 57.341 34.783 0.00 0.00 0.00 1.94
64 65 5.885912 AGTAGGATTGCGTTCATGGTATTTT 59.114 36.000 0.00 0.00 0.00 1.82
65 66 5.437060 AGTAGGATTGCGTTCATGGTATTT 58.563 37.500 0.00 0.00 0.00 1.40
66 67 5.036117 AGTAGGATTGCGTTCATGGTATT 57.964 39.130 0.00 0.00 0.00 1.89
67 68 4.689612 AGTAGGATTGCGTTCATGGTAT 57.310 40.909 0.00 0.00 0.00 2.73
68 69 5.128171 AGTTAGTAGGATTGCGTTCATGGTA 59.872 40.000 0.00 0.00 0.00 3.25
69 70 4.081087 AGTTAGTAGGATTGCGTTCATGGT 60.081 41.667 0.00 0.00 0.00 3.55
70 71 4.271049 CAGTTAGTAGGATTGCGTTCATGG 59.729 45.833 0.00 0.00 0.00 3.66
71 72 4.260375 GCAGTTAGTAGGATTGCGTTCATG 60.260 45.833 0.00 0.00 0.00 3.07
72 73 3.871594 GCAGTTAGTAGGATTGCGTTCAT 59.128 43.478 0.00 0.00 0.00 2.57
73 74 3.056107 AGCAGTTAGTAGGATTGCGTTCA 60.056 43.478 0.00 0.00 39.63 3.18
74 75 3.522553 AGCAGTTAGTAGGATTGCGTTC 58.477 45.455 0.00 0.00 39.63 3.95
75 76 3.611766 AGCAGTTAGTAGGATTGCGTT 57.388 42.857 0.00 0.00 39.63 4.84
76 77 3.611766 AAGCAGTTAGTAGGATTGCGT 57.388 42.857 0.00 0.00 39.63 5.24
77 78 6.604735 AATAAAGCAGTTAGTAGGATTGCG 57.395 37.500 0.00 0.00 39.63 4.85
78 79 9.326413 TCTTAATAAAGCAGTTAGTAGGATTGC 57.674 33.333 0.00 0.00 27.30 3.56
98 99 9.522804 CGAGAGCAACTAATTTCTACTCTTAAT 57.477 33.333 0.00 0.00 33.37 1.40
99 100 8.521176 ACGAGAGCAACTAATTTCTACTCTTAA 58.479 33.333 0.00 0.00 33.37 1.85
100 101 8.053026 ACGAGAGCAACTAATTTCTACTCTTA 57.947 34.615 0.00 0.00 33.37 2.10
101 102 6.926313 ACGAGAGCAACTAATTTCTACTCTT 58.074 36.000 0.00 0.00 33.37 2.85
102 103 6.518208 ACGAGAGCAACTAATTTCTACTCT 57.482 37.500 0.00 0.00 35.80 3.24
103 104 5.452944 CGACGAGAGCAACTAATTTCTACTC 59.547 44.000 0.00 0.00 0.00 2.59
104 105 5.106237 ACGACGAGAGCAACTAATTTCTACT 60.106 40.000 0.00 0.00 0.00 2.57
105 106 5.094134 ACGACGAGAGCAACTAATTTCTAC 58.906 41.667 0.00 0.00 0.00 2.59
106 107 5.306532 ACGACGAGAGCAACTAATTTCTA 57.693 39.130 0.00 0.00 0.00 2.10
107 108 4.175787 ACGACGAGAGCAACTAATTTCT 57.824 40.909 0.00 0.00 0.00 2.52
108 109 6.558071 CGATTACGACGAGAGCAACTAATTTC 60.558 42.308 0.00 0.00 42.66 2.17
109 110 5.229469 CGATTACGACGAGAGCAACTAATTT 59.771 40.000 0.00 0.00 42.66 1.82
110 111 4.733887 CGATTACGACGAGAGCAACTAATT 59.266 41.667 0.00 0.00 42.66 1.40
111 112 4.280461 CGATTACGACGAGAGCAACTAAT 58.720 43.478 0.00 0.00 42.66 1.73
112 113 3.677601 CGATTACGACGAGAGCAACTAA 58.322 45.455 0.00 0.00 42.66 2.24
113 114 2.538333 GCGATTACGACGAGAGCAACTA 60.538 50.000 0.00 0.00 42.66 2.24
114 115 1.794437 GCGATTACGACGAGAGCAACT 60.794 52.381 0.00 0.00 42.66 3.16
115 116 0.566593 GCGATTACGACGAGAGCAAC 59.433 55.000 0.00 0.00 42.66 4.17
116 117 0.450583 AGCGATTACGACGAGAGCAA 59.549 50.000 0.00 0.00 42.66 3.91
117 118 0.027716 GAGCGATTACGACGAGAGCA 59.972 55.000 0.00 0.00 42.66 4.26
118 119 0.987848 CGAGCGATTACGACGAGAGC 60.988 60.000 0.00 0.00 42.66 4.09
119 120 0.987848 GCGAGCGATTACGACGAGAG 60.988 60.000 0.00 0.00 42.66 3.20
120 121 1.011463 GCGAGCGATTACGACGAGA 60.011 57.895 0.00 0.00 42.66 4.04
121 122 1.011019 AGCGAGCGATTACGACGAG 60.011 57.895 0.00 0.00 42.66 4.18
122 123 1.297378 CAGCGAGCGATTACGACGA 60.297 57.895 0.00 0.00 42.66 4.20
123 124 2.286559 CCAGCGAGCGATTACGACG 61.287 63.158 0.00 0.00 42.66 5.12
124 125 0.317938 ATCCAGCGAGCGATTACGAC 60.318 55.000 0.00 0.00 42.66 4.34
125 126 0.317854 CATCCAGCGAGCGATTACGA 60.318 55.000 0.00 0.00 42.66 3.43
126 127 0.317854 TCATCCAGCGAGCGATTACG 60.318 55.000 0.00 0.00 42.93 3.18
127 128 1.852942 TTCATCCAGCGAGCGATTAC 58.147 50.000 0.00 0.00 0.00 1.89
128 129 2.595124 TTTCATCCAGCGAGCGATTA 57.405 45.000 0.00 0.00 0.00 1.75
129 130 1.959042 ATTTCATCCAGCGAGCGATT 58.041 45.000 0.00 0.00 0.00 3.34
130 131 1.959042 AATTTCATCCAGCGAGCGAT 58.041 45.000 0.00 0.00 0.00 4.58
131 132 1.665679 GAAATTTCATCCAGCGAGCGA 59.334 47.619 13.40 0.00 0.00 4.93
132 133 1.398041 TGAAATTTCATCCAGCGAGCG 59.602 47.619 16.91 0.00 31.01 5.03
133 134 3.127548 TCTTGAAATTTCATCCAGCGAGC 59.872 43.478 21.10 0.00 37.00 5.03
134 135 4.154737 TGTCTTGAAATTTCATCCAGCGAG 59.845 41.667 21.10 13.38 37.00 5.03
135 136 4.071423 TGTCTTGAAATTTCATCCAGCGA 58.929 39.130 21.10 4.17 37.00 4.93
136 137 4.424061 TGTCTTGAAATTTCATCCAGCG 57.576 40.909 21.10 6.71 37.00 5.18
137 138 5.957798 TGATGTCTTGAAATTTCATCCAGC 58.042 37.500 21.10 18.56 37.00 4.85
138 139 8.869897 CAAATGATGTCTTGAAATTTCATCCAG 58.130 33.333 21.10 15.39 37.00 3.86
139 140 7.820386 CCAAATGATGTCTTGAAATTTCATCCA 59.180 33.333 21.10 16.82 37.00 3.41
140 141 7.279313 CCCAAATGATGTCTTGAAATTTCATCC 59.721 37.037 21.10 12.24 37.00 3.51
141 142 7.820872 ACCCAAATGATGTCTTGAAATTTCATC 59.179 33.333 21.10 15.14 37.00 2.92
142 143 7.682628 ACCCAAATGATGTCTTGAAATTTCAT 58.317 30.769 21.10 6.33 37.00 2.57
143 144 7.065120 ACCCAAATGATGTCTTGAAATTTCA 57.935 32.000 16.91 16.91 34.92 2.69
144 145 7.095102 CCAACCCAAATGATGTCTTGAAATTTC 60.095 37.037 11.41 11.41 0.00 2.17
145 146 6.711645 CCAACCCAAATGATGTCTTGAAATTT 59.288 34.615 0.00 0.00 0.00 1.82
146 147 6.183361 ACCAACCCAAATGATGTCTTGAAATT 60.183 34.615 0.00 0.00 0.00 1.82
147 148 5.307716 ACCAACCCAAATGATGTCTTGAAAT 59.692 36.000 0.00 0.00 0.00 2.17
148 149 4.653341 ACCAACCCAAATGATGTCTTGAAA 59.347 37.500 0.00 0.00 0.00 2.69
149 150 4.222336 ACCAACCCAAATGATGTCTTGAA 58.778 39.130 0.00 0.00 0.00 2.69
150 151 3.826157 GACCAACCCAAATGATGTCTTGA 59.174 43.478 0.00 0.00 0.00 3.02
151 152 3.828451 AGACCAACCCAAATGATGTCTTG 59.172 43.478 0.00 0.00 0.00 3.02
152 153 4.118168 AGACCAACCCAAATGATGTCTT 57.882 40.909 0.00 0.00 0.00 3.01
153 154 3.814504 AGACCAACCCAAATGATGTCT 57.185 42.857 0.00 0.00 0.00 3.41
154 155 3.374058 CGTAGACCAACCCAAATGATGTC 59.626 47.826 0.00 0.00 0.00 3.06
155 156 3.343617 CGTAGACCAACCCAAATGATGT 58.656 45.455 0.00 0.00 0.00 3.06
156 157 2.097466 GCGTAGACCAACCCAAATGATG 59.903 50.000 0.00 0.00 0.00 3.07
157 158 2.290641 TGCGTAGACCAACCCAAATGAT 60.291 45.455 0.00 0.00 0.00 2.45
158 159 1.072489 TGCGTAGACCAACCCAAATGA 59.928 47.619 0.00 0.00 0.00 2.57
159 160 1.529226 TGCGTAGACCAACCCAAATG 58.471 50.000 0.00 0.00 0.00 2.32
160 161 2.507407 ATGCGTAGACCAACCCAAAT 57.493 45.000 0.00 0.00 0.00 2.32
161 162 2.279935 AATGCGTAGACCAACCCAAA 57.720 45.000 0.00 0.00 0.00 3.28
162 163 2.156098 GAAATGCGTAGACCAACCCAA 58.844 47.619 0.00 0.00 0.00 4.12
163 164 1.612199 GGAAATGCGTAGACCAACCCA 60.612 52.381 0.00 0.00 0.00 4.51
164 165 1.092348 GGAAATGCGTAGACCAACCC 58.908 55.000 0.00 0.00 0.00 4.11
165 166 2.109425 AGGAAATGCGTAGACCAACC 57.891 50.000 0.00 0.00 0.00 3.77
166 167 3.252458 ACAAAGGAAATGCGTAGACCAAC 59.748 43.478 0.00 0.00 0.00 3.77
167 168 3.482436 ACAAAGGAAATGCGTAGACCAA 58.518 40.909 0.00 0.00 0.00 3.67
168 169 3.134574 ACAAAGGAAATGCGTAGACCA 57.865 42.857 0.00 0.00 0.00 4.02
169 170 4.329256 GTCTACAAAGGAAATGCGTAGACC 59.671 45.833 14.24 1.07 46.92 3.85
170 171 5.451828 GTCTACAAAGGAAATGCGTAGAC 57.548 43.478 11.07 11.07 46.78 2.59
171 172 4.020928 TGGTCTACAAAGGAAATGCGTAGA 60.021 41.667 0.00 0.00 36.97 2.59
175 176 3.334691 TCTGGTCTACAAAGGAAATGCG 58.665 45.455 0.00 0.00 0.00 4.73
188 189 1.134367 CGTCCTCGCATTTCTGGTCTA 59.866 52.381 0.00 0.00 0.00 2.59
235 236 7.229707 TCGTGGATTCAATTCAAGGACTAAAAA 59.770 33.333 0.00 0.00 0.00 1.94
236 237 6.712998 TCGTGGATTCAATTCAAGGACTAAAA 59.287 34.615 0.00 0.00 0.00 1.52
240 241 4.286297 TCGTGGATTCAATTCAAGGACT 57.714 40.909 0.00 0.00 0.00 3.85
246 247 3.058570 CGTTGGTTCGTGGATTCAATTCA 60.059 43.478 0.00 0.00 0.00 2.57
357 359 1.645710 TGTCAGAGACTTCCCTTCCC 58.354 55.000 0.00 0.00 33.15 3.97
358 360 2.569404 ACATGTCAGAGACTTCCCTTCC 59.431 50.000 0.00 0.00 33.15 3.46
359 361 3.594134 CACATGTCAGAGACTTCCCTTC 58.406 50.000 0.00 0.00 33.15 3.46
360 362 2.304180 CCACATGTCAGAGACTTCCCTT 59.696 50.000 0.00 0.00 33.15 3.95
362 364 1.065854 CCCACATGTCAGAGACTTCCC 60.066 57.143 0.00 0.00 33.15 3.97
363 365 1.625818 ACCCACATGTCAGAGACTTCC 59.374 52.381 0.00 0.00 33.15 3.46
377 381 1.116536 TGCTGGTCTCGTAACCCACA 61.117 55.000 6.53 2.80 38.65 4.17
384 388 1.289066 GTGCTGTGCTGGTCTCGTA 59.711 57.895 0.00 0.00 0.00 3.43
420 424 6.520792 ACTACGTGAAACAGTTATGTGAAC 57.479 37.500 0.00 0.00 40.39 3.18
439 443 6.970613 CGCCCCAAAAATTGAAATACTACTAC 59.029 38.462 0.00 0.00 0.00 2.73
440 444 6.885376 TCGCCCCAAAAATTGAAATACTACTA 59.115 34.615 0.00 0.00 0.00 1.82
441 445 5.712917 TCGCCCCAAAAATTGAAATACTACT 59.287 36.000 0.00 0.00 0.00 2.57
453 457 0.038618 GACGCTTTCGCCCCAAAAAT 60.039 50.000 0.00 0.00 39.84 1.82
565 570 4.156739 CCCAGGCTAGAAAACAACTGAATC 59.843 45.833 0.00 0.00 0.00 2.52
569 574 1.541588 GCCCAGGCTAGAAAACAACTG 59.458 52.381 0.08 0.00 38.26 3.16
703 719 6.126911 GGATGGAGAGAGGAAGTTGACTATTT 60.127 42.308 0.00 0.00 0.00 1.40
704 720 5.365314 GGATGGAGAGAGGAAGTTGACTATT 59.635 44.000 0.00 0.00 0.00 1.73
944 960 0.251430 GGACAACGGAAATGGGGGAA 60.251 55.000 0.00 0.00 0.00 3.97
1173 1194 2.060980 AGTGATCTCCCGGCAGTCC 61.061 63.158 0.00 0.00 0.00 3.85
1200 1221 3.199946 TCACCTTCTTGAACTTGGACACT 59.800 43.478 0.00 0.00 0.00 3.55
1342 1363 2.341846 TTGGTGAAGTCCAAGGTCAC 57.658 50.000 0.00 0.00 41.79 3.67
1371 1392 2.049248 GCGTCGTTTCCGTACCCA 60.049 61.111 0.00 0.00 35.01 4.51
1389 1410 4.742201 GCCGAGACGCTGAAGCCA 62.742 66.667 0.00 0.00 37.91 4.75
1569 1590 4.539083 TGGTCGTGGCACTTGCGT 62.539 61.111 16.72 0.00 43.26 5.24
1690 1711 2.773487 ACGGAACAACGAAATCCATCA 58.227 42.857 0.00 0.00 37.61 3.07
1716 1737 3.939740 ACATGGATAACACCAGCAGAT 57.060 42.857 0.00 0.00 43.49 2.90
1722 1743 5.565509 TCTTTAGCAACATGGATAACACCA 58.434 37.500 0.00 0.00 44.41 4.17
1753 1774 2.198304 GACTTCCTGCCGGTCCCATT 62.198 60.000 1.90 0.00 0.00 3.16
1913 1935 0.253160 TACATGGTGGAGGGAAGCCT 60.253 55.000 0.00 0.00 0.00 4.58
1914 1936 0.623723 TTACATGGTGGAGGGAAGCC 59.376 55.000 0.00 0.00 0.00 4.35
1915 1937 1.559682 TCTTACATGGTGGAGGGAAGC 59.440 52.381 0.00 0.00 0.00 3.86
1916 1938 2.092914 GGTCTTACATGGTGGAGGGAAG 60.093 54.545 0.00 0.00 0.00 3.46
1917 1939 1.913419 GGTCTTACATGGTGGAGGGAA 59.087 52.381 0.00 0.00 0.00 3.97
1918 1940 1.203376 TGGTCTTACATGGTGGAGGGA 60.203 52.381 0.00 0.00 0.00 4.20
1919 1941 1.210478 CTGGTCTTACATGGTGGAGGG 59.790 57.143 0.00 0.00 0.00 4.30
1920 1942 2.169352 CTCTGGTCTTACATGGTGGAGG 59.831 54.545 0.00 0.00 0.00 4.30
1921 1943 2.834549 ACTCTGGTCTTACATGGTGGAG 59.165 50.000 0.00 0.00 0.00 3.86
1983 2013 1.875009 ACCTCTGCATGCATATCACG 58.125 50.000 22.97 8.55 0.00 4.35
2205 2236 0.953960 AACGAAGGGAACATGGCGAC 60.954 55.000 0.00 0.00 0.00 5.19
2208 2239 1.737793 CAGTAACGAAGGGAACATGGC 59.262 52.381 0.00 0.00 0.00 4.40
2377 2411 9.354673 TCTGAAACACATATTTTTCTTTCTCCT 57.645 29.630 0.00 0.00 33.61 3.69
2378 2412 9.617975 CTCTGAAACACATATTTTTCTTTCTCC 57.382 33.333 0.00 0.00 33.61 3.71
2387 2421 5.313712 ACCCGACTCTGAAACACATATTTT 58.686 37.500 0.00 0.00 0.00 1.82
2391 2425 4.062293 CAAACCCGACTCTGAAACACATA 58.938 43.478 0.00 0.00 0.00 2.29
2406 2440 1.002134 AGCCACAGGATCAAACCCG 60.002 57.895 0.00 0.00 0.00 5.28
2470 2507 1.606313 CACCCGGGACCAAAAGCAT 60.606 57.895 32.02 0.00 0.00 3.79
2516 2553 3.011760 GCGTTCCTTGACCGCTTCG 62.012 63.158 0.00 0.00 43.81 3.79
2561 2598 1.226745 AACACGAGTCAACGACGCA 60.227 52.632 0.00 0.00 37.67 5.24
2585 2622 1.944234 TAATCGAGCAGAGCACCGCA 61.944 55.000 0.00 0.00 0.00 5.69
2620 3177 1.145819 GCCAAACCAGCCAAGCAAA 59.854 52.632 0.00 0.00 0.00 3.68
2657 3218 4.248842 CACTGGCGGGTGTGGACA 62.249 66.667 0.00 0.00 33.04 4.02
2680 3245 0.311165 CAAGACGCTATCGACCGGAT 59.689 55.000 9.46 0.00 39.41 4.18
2720 3285 1.335506 GCTCAACGCCCGATTTTCAAA 60.336 47.619 0.00 0.00 0.00 2.69
2757 3358 3.692257 AAGCTCAACACTATCAGCACT 57.308 42.857 0.00 0.00 34.08 4.40
2774 3375 6.347725 CCGGACAGACAATATAGCATTAAAGC 60.348 42.308 0.00 0.00 0.00 3.51
2775 3376 6.706270 ACCGGACAGACAATATAGCATTAAAG 59.294 38.462 9.46 0.00 0.00 1.85
2779 3380 4.100963 TGACCGGACAGACAATATAGCATT 59.899 41.667 9.46 0.00 0.00 3.56
2780 3381 3.641436 TGACCGGACAGACAATATAGCAT 59.359 43.478 9.46 0.00 0.00 3.79
2781 3382 3.028130 TGACCGGACAGACAATATAGCA 58.972 45.455 9.46 0.00 0.00 3.49
2782 3383 3.728076 TGACCGGACAGACAATATAGC 57.272 47.619 9.46 0.00 0.00 2.97
2783 3384 3.990469 GCATGACCGGACAGACAATATAG 59.010 47.826 9.46 0.00 0.00 1.31
2788 3769 0.320683 CTGCATGACCGGACAGACAA 60.321 55.000 9.46 0.00 31.67 3.18
2793 3774 2.358615 GTGCTGCATGACCGGACA 60.359 61.111 9.46 9.50 0.00 4.02
2814 3795 0.461961 CAGGAGTAGTGGTAGCAGCC 59.538 60.000 0.00 0.00 0.00 4.85
2846 3827 2.708386 TGTAAAATTCCCGGCGTTTG 57.292 45.000 6.01 0.00 0.00 2.93
2874 3855 7.243487 CGTCTCATAATAACAGCATTTTGTGT 58.757 34.615 0.00 0.00 0.00 3.72
2875 3856 6.688385 CCGTCTCATAATAACAGCATTTTGTG 59.312 38.462 0.00 0.00 0.00 3.33
2876 3857 6.597672 TCCGTCTCATAATAACAGCATTTTGT 59.402 34.615 0.00 0.00 0.00 2.83
2877 3858 7.015226 TCCGTCTCATAATAACAGCATTTTG 57.985 36.000 0.00 0.00 0.00 2.44
2879 3860 5.760253 CCTCCGTCTCATAATAACAGCATTT 59.240 40.000 0.00 0.00 0.00 2.32
2882 3863 3.069586 CCCTCCGTCTCATAATAACAGCA 59.930 47.826 0.00 0.00 0.00 4.41
2884 3865 4.585162 ACTCCCTCCGTCTCATAATAACAG 59.415 45.833 0.00 0.00 0.00 3.16
2886 3867 5.769162 ACTACTCCCTCCGTCTCATAATAAC 59.231 44.000 0.00 0.00 0.00 1.89
2896 3901 3.952967 AGTTATGAACTACTCCCTCCGTC 59.047 47.826 0.00 0.00 40.69 4.79
2921 3926 3.246416 AGCGGATGGAGGAAGTACTAT 57.754 47.619 0.00 0.00 0.00 2.12
2922 3927 2.750141 AGCGGATGGAGGAAGTACTA 57.250 50.000 0.00 0.00 0.00 1.82
2923 3928 2.750141 TAGCGGATGGAGGAAGTACT 57.250 50.000 0.00 0.00 0.00 2.73
2924 3929 3.069729 ACATTAGCGGATGGAGGAAGTAC 59.930 47.826 7.18 0.00 0.00 2.73
2925 3930 3.305720 ACATTAGCGGATGGAGGAAGTA 58.694 45.455 7.18 0.00 0.00 2.24
2927 3932 2.918712 ACATTAGCGGATGGAGGAAG 57.081 50.000 7.18 0.00 0.00 3.46
2929 3934 3.321111 GTCTTACATTAGCGGATGGAGGA 59.679 47.826 7.18 2.13 0.00 3.71
2930 3935 3.654414 GTCTTACATTAGCGGATGGAGG 58.346 50.000 7.18 0.00 0.00 4.30
2932 3937 2.691526 ACGTCTTACATTAGCGGATGGA 59.308 45.455 7.18 0.00 0.00 3.41
2933 3938 3.093717 ACGTCTTACATTAGCGGATGG 57.906 47.619 7.18 0.00 0.00 3.51
2934 3939 5.464965 AAAACGTCTTACATTAGCGGATG 57.535 39.130 0.00 1.44 0.00 3.51
2980 4036 8.012957 ACTCTCCGTCTCATAATGTAAGAATT 57.987 34.615 0.00 0.00 0.00 2.17
2982 4038 7.774157 ACTACTCTCCGTCTCATAATGTAAGAA 59.226 37.037 0.00 0.00 0.00 2.52
2988 4044 6.706716 TGAGTACTACTCTCCGTCTCATAATG 59.293 42.308 15.76 0.00 45.27 1.90
3044 4119 6.775708 ACAAACAATTAGCAGGAACCTAGTA 58.224 36.000 0.00 0.00 0.00 1.82
3077 4155 2.281140 TGTGAAACGACAGTCGACAA 57.719 45.000 29.53 8.92 43.74 3.18
3098 4176 0.583917 GAAGAATTCGATGCCGGCTC 59.416 55.000 29.70 20.55 34.17 4.70
3212 4290 2.763448 GTGAGTCCAAGAGAGCACCTAT 59.237 50.000 0.00 0.00 0.00 2.57
3220 4298 2.370349 GGATCGAGTGAGTCCAAGAGA 58.630 52.381 0.00 0.00 32.23 3.10
3226 4304 1.698506 AGATGGGATCGAGTGAGTCC 58.301 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.