Multiple sequence alignment - TraesCS2D01G564200

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 TraesCS2D01G564200 chr2D 100.000 3396 0 0 966 4361 634873651 634877046 0.000000e+00 6272.0
1 TraesCS2D01G564200 chr2D 100.000 534 0 0 1 534 634872686 634873219 0.000000e+00 987.0
2 TraesCS2D01G564200 chr2A 91.864 2704 165 28 966 3647 778428054 778425384 0.000000e+00 3723.0
3 TraesCS2D01G564200 chr2A 89.698 563 32 11 3700 4259 778425368 778424829 0.000000e+00 695.0
4 TraesCS2D01G564200 chr2A 94.355 124 3 4 408 528 778428207 778428085 2.070000e-43 187.0
5 TraesCS2D01G564200 chr2A 91.765 85 5 1 4264 4346 778424786 778424702 2.760000e-22 117.0
6 TraesCS2D01G564200 chr2A 84.615 91 14 0 3107 3197 24313701 24313791 1.670000e-14 91.6
7 TraesCS2D01G564200 chr2B 91.923 1981 106 21 1691 3647 778850650 778848700 0.000000e+00 2723.0
8 TraesCS2D01G564200 chr2B 88.275 742 41 10 966 1683 778851344 778850625 0.000000e+00 846.0
9 TraesCS2D01G564200 chr2B 92.986 442 21 7 3830 4262 778848575 778848135 1.710000e-178 636.0
10 TraesCS2D01G564200 chr2B 78.044 542 66 34 3 528 778851874 778851370 4.270000e-75 292.0
11 TraesCS2D01G564200 chr2B 88.235 85 8 1 4264 4346 778848096 778848012 2.780000e-17 100.0
12 TraesCS2D01G564200 chr2B 81.443 97 8 9 3700 3788 778848684 778848590 2.180000e-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 TraesCS2D01G564200 chr2D 634872686 634877046 4360 False 3629.50 6272 100.000000 1 4361 2 chr2D.!!$F1 4360
1 TraesCS2D01G564200 chr2A 778424702 778428207 3505 True 1180.50 3723 91.920500 408 4346 4 chr2A.!!$R1 3938
2 TraesCS2D01G564200 chr2B 778848012 778851874 3862 True 778.05 2723 86.817667 3 4346 6 chr2B.!!$R1 4343

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
158 167 0.037303 ATGGAGCTGTGAGGTGTTGG 59.963 55.0 0.0 0.0 0.00 3.77 F
514 533 0.179045 AAGTCACAGCACCAGTCCAC 60.179 55.0 0.0 0.0 0.00 4.02 F
1648 1703 0.608130 TCTCCCAAGTGTCATCGTGG 59.392 55.0 0.0 0.0 36.87 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1684 1.548719 TCTACCACGATGACACTTGGG 59.451 52.381 0.0 0.0 34.19 4.12 R
1810 1884 2.795231 ATGACAGCCATGTAAGCACT 57.205 45.000 0.0 0.0 40.68 4.40 R
3434 3535 0.251209 TACAGGACAGGCGACACTCT 60.251 55.000 0.0 0.0 0.00 3.24 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
28 30 9.154847 CGATTTGTAATCTCATGGATAAGCATA 57.845 33.333 0.00 0.00 33.71 3.14
30 32 7.889589 TTGTAATCTCATGGATAAGCATACG 57.110 36.000 0.00 0.00 33.71 3.06
34 36 7.468141 AATCTCATGGATAAGCATACGACTA 57.532 36.000 0.00 0.00 33.71 2.59
57 59 3.005684 GGCAACACTTGAATCATGTGGAA 59.994 43.478 26.03 0.00 41.69 3.53
61 63 4.978099 ACACTTGAATCATGTGGAAGACT 58.022 39.130 26.03 7.77 41.69 3.24
62 64 6.114187 ACACTTGAATCATGTGGAAGACTA 57.886 37.500 26.03 0.00 41.69 2.59
63 65 5.934625 ACACTTGAATCATGTGGAAGACTAC 59.065 40.000 26.03 0.00 41.69 2.73
64 66 6.169094 CACTTGAATCATGTGGAAGACTACT 58.831 40.000 18.17 0.00 36.36 2.57
67 69 6.850752 TGAATCATGTGGAAGACTACTACA 57.149 37.500 0.00 0.00 33.73 2.74
69 71 7.323420 TGAATCATGTGGAAGACTACTACAAG 58.677 38.462 0.00 0.00 33.03 3.16
85 87 1.226746 CAAGAAGGAGAAAACGCGGT 58.773 50.000 12.47 0.00 0.00 5.68
89 91 4.043037 AGAAGGAGAAAACGCGGTATAG 57.957 45.455 12.47 0.00 0.00 1.31
94 96 1.745087 AGAAAACGCGGTATAGGACGA 59.255 47.619 12.47 0.00 0.00 4.20
111 120 3.491104 GGACGAAGGCAAATACGAGAGAT 60.491 47.826 0.00 0.00 0.00 2.75
112 121 4.261489 GGACGAAGGCAAATACGAGAGATA 60.261 45.833 0.00 0.00 0.00 1.98
113 122 5.258456 ACGAAGGCAAATACGAGAGATAA 57.742 39.130 0.00 0.00 0.00 1.75
114 123 5.282510 ACGAAGGCAAATACGAGAGATAAG 58.717 41.667 0.00 0.00 0.00 1.73
115 124 4.149046 CGAAGGCAAATACGAGAGATAAGC 59.851 45.833 0.00 0.00 0.00 3.09
116 125 4.672587 AGGCAAATACGAGAGATAAGCA 57.327 40.909 0.00 0.00 0.00 3.91
117 126 5.023533 AGGCAAATACGAGAGATAAGCAA 57.976 39.130 0.00 0.00 0.00 3.91
118 127 5.053145 AGGCAAATACGAGAGATAAGCAAG 58.947 41.667 0.00 0.00 0.00 4.01
119 128 4.212214 GGCAAATACGAGAGATAAGCAAGG 59.788 45.833 0.00 0.00 0.00 3.61
120 129 5.050490 GCAAATACGAGAGATAAGCAAGGA 58.950 41.667 0.00 0.00 0.00 3.36
121 130 5.176590 GCAAATACGAGAGATAAGCAAGGAG 59.823 44.000 0.00 0.00 0.00 3.69
123 132 3.019799 ACGAGAGATAAGCAAGGAGGA 57.980 47.619 0.00 0.00 0.00 3.71
124 133 3.571590 ACGAGAGATAAGCAAGGAGGAT 58.428 45.455 0.00 0.00 0.00 3.24
126 135 3.663025 GAGAGATAAGCAAGGAGGATGC 58.337 50.000 0.00 0.00 44.15 3.91
131 140 3.512516 GCAAGGAGGATGCGCCAC 61.513 66.667 10.12 0.00 40.02 5.01
133 142 3.390521 AAGGAGGATGCGCCACGA 61.391 61.111 10.12 0.00 40.02 4.35
135 144 3.838271 GGAGGATGCGCCACGAGA 61.838 66.667 4.18 0.00 40.02 4.04
136 145 2.419198 GAGGATGCGCCACGAGAT 59.581 61.111 4.18 0.00 40.02 2.75
137 146 1.663074 GAGGATGCGCCACGAGATC 60.663 63.158 4.18 0.00 40.02 2.75
139 148 0.823769 AGGATGCGCCACGAGATCTA 60.824 55.000 4.18 0.00 40.02 1.98
140 149 0.244994 GGATGCGCCACGAGATCTAT 59.755 55.000 4.18 0.00 36.34 1.98
142 151 0.037882 ATGCGCCACGAGATCTATGG 60.038 55.000 17.71 17.71 36.51 2.74
143 152 1.106944 TGCGCCACGAGATCTATGGA 61.107 55.000 23.81 5.70 35.33 3.41
144 153 0.387878 GCGCCACGAGATCTATGGAG 60.388 60.000 23.81 21.50 35.33 3.86
145 154 0.387878 CGCCACGAGATCTATGGAGC 60.388 60.000 23.81 12.88 35.33 4.70
146 155 0.965439 GCCACGAGATCTATGGAGCT 59.035 55.000 23.81 0.00 41.28 4.09
147 156 1.336702 GCCACGAGATCTATGGAGCTG 60.337 57.143 23.81 0.00 38.42 4.24
148 157 1.959985 CCACGAGATCTATGGAGCTGT 59.040 52.381 17.28 0.00 38.42 4.40
149 158 2.288091 CCACGAGATCTATGGAGCTGTG 60.288 54.545 17.28 10.18 38.42 3.66
150 159 2.620585 CACGAGATCTATGGAGCTGTGA 59.379 50.000 16.26 0.00 38.42 3.58
152 161 2.228582 CGAGATCTATGGAGCTGTGAGG 59.771 54.545 0.00 0.00 38.42 3.86
153 162 3.230134 GAGATCTATGGAGCTGTGAGGT 58.770 50.000 0.00 0.00 38.42 3.85
156 165 2.540383 TCTATGGAGCTGTGAGGTGTT 58.460 47.619 0.00 0.00 0.00 3.32
157 166 2.234661 TCTATGGAGCTGTGAGGTGTTG 59.765 50.000 0.00 0.00 0.00 3.33
158 167 0.037303 ATGGAGCTGTGAGGTGTTGG 59.963 55.000 0.00 0.00 0.00 3.77
161 170 0.394565 GAGCTGTGAGGTGTTGGTCT 59.605 55.000 0.00 0.00 0.00 3.85
162 171 0.839946 AGCTGTGAGGTGTTGGTCTT 59.160 50.000 0.00 0.00 0.00 3.01
163 172 1.212935 AGCTGTGAGGTGTTGGTCTTT 59.787 47.619 0.00 0.00 0.00 2.52
164 173 2.024414 GCTGTGAGGTGTTGGTCTTTT 58.976 47.619 0.00 0.00 0.00 2.27
165 174 2.427095 GCTGTGAGGTGTTGGTCTTTTT 59.573 45.455 0.00 0.00 0.00 1.94
220 229 3.797256 ACTTGACGTCTTCTTTTCTCACG 59.203 43.478 17.92 0.00 36.54 4.35
226 235 4.166523 CGTCTTCTTTTCTCACGCTGATA 58.833 43.478 0.00 0.00 0.00 2.15
227 236 4.030753 CGTCTTCTTTTCTCACGCTGATAC 59.969 45.833 0.00 0.00 0.00 2.24
232 241 4.393990 TCTTTTCTCACGCTGATACGTAGA 59.606 41.667 0.08 0.00 46.34 2.59
233 242 3.946308 TTCTCACGCTGATACGTAGAG 57.054 47.619 0.08 0.57 46.34 2.43
234 243 2.210961 TCTCACGCTGATACGTAGAGG 58.789 52.381 0.08 0.00 46.34 3.69
235 244 2.159000 TCTCACGCTGATACGTAGAGGA 60.159 50.000 0.08 0.00 46.34 3.71
236 245 2.210961 TCACGCTGATACGTAGAGGAG 58.789 52.381 0.08 0.00 46.34 3.69
237 246 2.159000 TCACGCTGATACGTAGAGGAGA 60.159 50.000 0.08 0.00 46.34 3.71
238 247 2.809119 CACGCTGATACGTAGAGGAGAT 59.191 50.000 0.08 0.00 46.34 2.75
239 248 3.995048 CACGCTGATACGTAGAGGAGATA 59.005 47.826 0.08 0.00 46.34 1.98
240 249 4.451435 CACGCTGATACGTAGAGGAGATAA 59.549 45.833 0.08 0.00 46.34 1.75
241 250 4.691685 ACGCTGATACGTAGAGGAGATAAG 59.308 45.833 0.08 0.00 46.19 1.73
242 251 4.436317 CGCTGATACGTAGAGGAGATAAGC 60.436 50.000 0.08 0.00 0.00 3.09
246 255 1.957877 ACGTAGAGGAGATAAGCTGCC 59.042 52.381 0.00 0.00 35.18 4.85
249 258 0.397816 AGAGGAGATAAGCTGCCGGT 60.398 55.000 1.90 0.00 35.18 5.28
255 264 1.432270 GATAAGCTGCCGGTGTGAGC 61.432 60.000 1.90 6.04 0.00 4.26
268 277 4.927782 TGAGCGTGCCAGCGGTTT 62.928 61.111 0.00 0.00 42.89 3.27
272 281 2.613506 GCGTGCCAGCGGTTTAGTT 61.614 57.895 0.00 0.00 0.00 2.24
273 282 1.293267 GCGTGCCAGCGGTTTAGTTA 61.293 55.000 0.00 0.00 0.00 2.24
304 313 4.424711 GCCCATGGAAGCCACCGA 62.425 66.667 15.22 0.00 35.80 4.69
307 316 2.825836 CATGGAAGCCACCGAGCC 60.826 66.667 0.00 0.00 35.80 4.70
315 324 3.411351 CCACCGAGCCAACGTTCG 61.411 66.667 0.00 0.00 41.85 3.95
318 327 3.041940 CCGAGCCAACGTTCGCTT 61.042 61.111 21.37 5.75 40.96 4.68
320 329 1.286354 CCGAGCCAACGTTCGCTTTA 61.286 55.000 21.37 0.00 40.96 1.85
324 333 3.184541 GAGCCAACGTTCGCTTTATAGA 58.815 45.455 21.37 0.00 34.84 1.98
325 334 3.592059 AGCCAACGTTCGCTTTATAGAA 58.408 40.909 15.01 0.00 28.56 2.10
326 335 4.189231 AGCCAACGTTCGCTTTATAGAAT 58.811 39.130 15.01 0.00 28.56 2.40
327 336 4.634443 AGCCAACGTTCGCTTTATAGAATT 59.366 37.500 15.01 0.00 28.56 2.17
328 337 5.123344 AGCCAACGTTCGCTTTATAGAATTT 59.877 36.000 15.01 0.00 28.56 1.82
330 339 6.237201 GCCAACGTTCGCTTTATAGAATTTTG 60.237 38.462 10.84 0.00 0.00 2.44
333 342 9.320406 CAACGTTCGCTTTATAGAATTTTGTTA 57.680 29.630 0.00 0.00 0.00 2.41
469 487 1.428869 CAAATCCAAAACCACCCCCA 58.571 50.000 0.00 0.00 0.00 4.96
514 533 0.179045 AAGTCACAGCACCAGTCCAC 60.179 55.000 0.00 0.00 0.00 4.02
517 536 3.570212 ACAGCACCAGTCCACCCC 61.570 66.667 0.00 0.00 0.00 4.95
518 537 3.569210 CAGCACCAGTCCACCCCA 61.569 66.667 0.00 0.00 0.00 4.96
519 538 3.570212 AGCACCAGTCCACCCCAC 61.570 66.667 0.00 0.00 0.00 4.61
984 1014 4.024984 CTCCCTCCCTCCCCACCA 62.025 72.222 0.00 0.00 0.00 4.17
1098 1128 3.823330 GAGGACGACGCCACCGAT 61.823 66.667 10.28 0.00 38.29 4.18
1157 1190 4.849329 CGCGGACGCAGGGTACTC 62.849 72.222 17.35 0.00 42.06 2.59
1524 1576 4.846779 TGTTCAGTTAATTCAGCAACCC 57.153 40.909 0.00 0.00 0.00 4.11
1526 1578 1.810151 TCAGTTAATTCAGCAACCCGC 59.190 47.619 0.00 0.00 42.91 6.13
1597 1649 4.112634 TGTTTGCTCGATTCGATTAGGAG 58.887 43.478 9.54 0.00 34.61 3.69
1599 1651 2.583143 TGCTCGATTCGATTAGGAGGA 58.417 47.619 9.54 0.00 34.61 3.71
1639 1691 3.984508 GATGATTGCATCTCCCAAGTG 57.015 47.619 0.00 0.00 45.93 3.16
1648 1703 0.608130 TCTCCCAAGTGTCATCGTGG 59.392 55.000 0.00 0.00 36.87 4.94
1684 1758 7.877003 TCTGCTAATTACAGTCTATCTACAGC 58.123 38.462 12.04 0.00 36.50 4.40
1693 1767 9.967346 TTACAGTCTATCTACAGCATTACAATC 57.033 33.333 0.00 0.00 0.00 2.67
1694 1768 8.243961 ACAGTCTATCTACAGCATTACAATCT 57.756 34.615 0.00 0.00 0.00 2.40
1695 1769 8.140628 ACAGTCTATCTACAGCATTACAATCTG 58.859 37.037 0.00 0.00 0.00 2.90
1696 1770 7.116090 CAGTCTATCTACAGCATTACAATCTGC 59.884 40.741 0.00 0.00 38.69 4.26
1698 1772 8.300286 GTCTATCTACAGCATTACAATCTGCTA 58.700 37.037 0.00 0.00 46.62 3.49
1699 1773 8.860088 TCTATCTACAGCATTACAATCTGCTAA 58.140 33.333 0.00 0.00 46.62 3.09
1700 1774 9.650539 CTATCTACAGCATTACAATCTGCTAAT 57.349 33.333 0.00 0.00 46.62 1.73
1701 1775 8.915057 ATCTACAGCATTACAATCTGCTAATT 57.085 30.769 0.00 0.00 46.62 1.40
1703 1777 9.261180 TCTACAGCATTACAATCTGCTAATTAC 57.739 33.333 0.00 0.00 46.62 1.89
1704 1778 6.948353 ACAGCATTACAATCTGCTAATTACG 58.052 36.000 0.00 0.00 46.62 3.18
1705 1779 6.017934 ACAGCATTACAATCTGCTAATTACGG 60.018 38.462 0.00 0.00 46.62 4.02
1706 1780 6.017934 CAGCATTACAATCTGCTAATTACGGT 60.018 38.462 0.00 0.00 46.62 4.83
1707 1781 6.202954 AGCATTACAATCTGCTAATTACGGTC 59.797 38.462 0.00 0.00 46.49 4.79
1708 1782 6.202954 GCATTACAATCTGCTAATTACGGTCT 59.797 38.462 0.00 0.00 35.49 3.85
1709 1783 7.384115 GCATTACAATCTGCTAATTACGGTCTA 59.616 37.037 0.00 0.00 35.49 2.59
1710 1784 9.424319 CATTACAATCTGCTAATTACGGTCTAT 57.576 33.333 0.00 0.00 0.00 1.98
1711 1785 9.640963 ATTACAATCTGCTAATTACGGTCTATC 57.359 33.333 0.00 0.00 0.00 2.08
1712 1786 7.291411 ACAATCTGCTAATTACGGTCTATCT 57.709 36.000 0.00 0.00 0.00 1.98
1713 1787 8.405418 ACAATCTGCTAATTACGGTCTATCTA 57.595 34.615 0.00 0.00 0.00 1.98
1714 1788 8.298140 ACAATCTGCTAATTACGGTCTATCTAC 58.702 37.037 0.00 0.00 0.00 2.59
1715 1789 7.997773 ATCTGCTAATTACGGTCTATCTACA 57.002 36.000 0.00 0.00 0.00 2.74
1716 1790 7.436430 TCTGCTAATTACGGTCTATCTACAG 57.564 40.000 0.00 0.00 0.00 2.74
1717 1791 6.996879 TCTGCTAATTACGGTCTATCTACAGT 59.003 38.462 0.00 0.00 0.00 3.55
1718 1792 8.152898 TCTGCTAATTACGGTCTATCTACAGTA 58.847 37.037 0.00 0.00 0.00 2.74
1719 1793 8.859236 TGCTAATTACGGTCTATCTACAGTAT 57.141 34.615 0.00 0.00 31.55 2.12
1720 1794 9.293404 TGCTAATTACGGTCTATCTACAGTATT 57.707 33.333 0.00 0.00 31.55 1.89
1823 1897 6.927294 ATTTAGAGTAAGTGCTTACATGGC 57.073 37.500 20.14 9.32 45.79 4.40
1845 1919 4.034975 GCTGTCATAGAAAAGTGCTGGATC 59.965 45.833 0.00 0.00 0.00 3.36
1846 1920 5.164620 TGTCATAGAAAAGTGCTGGATCA 57.835 39.130 0.00 0.00 0.00 2.92
1902 1977 8.537858 AGTTCCTTAGAGTAAATCGTGGTTTAT 58.462 33.333 0.00 0.00 0.00 1.40
1903 1978 9.159364 GTTCCTTAGAGTAAATCGTGGTTTATT 57.841 33.333 0.00 0.00 0.00 1.40
1904 1979 9.729281 TTCCTTAGAGTAAATCGTGGTTTATTT 57.271 29.630 0.00 0.00 0.00 1.40
2008 2083 3.724374 TGTATGCTACCGATAGTTTGGC 58.276 45.455 0.00 0.00 0.00 4.52
2013 2088 3.376859 TGCTACCGATAGTTTGGCATTTG 59.623 43.478 0.00 0.00 0.00 2.32
2047 2126 3.234353 CTCAGTACCCCATGATGAGCTA 58.766 50.000 0.00 0.00 31.83 3.32
2104 2183 9.136952 CTGTAGCGTAACTGATACTTTACTTTT 57.863 33.333 0.00 0.00 32.13 2.27
2211 2293 4.683334 GAACACAACGCAGCCGCC 62.683 66.667 0.00 0.00 38.22 6.13
2287 2369 3.246226 GTGGCATATTCTTGTACTCTGCG 59.754 47.826 0.00 0.00 0.00 5.18
2312 2394 4.300803 TGCATTGCTTTTCTGAACATGTC 58.699 39.130 10.49 0.00 0.00 3.06
2314 2396 5.241285 TGCATTGCTTTTCTGAACATGTCTA 59.759 36.000 10.49 0.00 0.00 2.59
2364 2456 7.329717 CCTATCGGCAACTCTAATTCTGTATTC 59.670 40.741 0.00 0.00 0.00 1.75
2410 2502 7.416817 TGTAGACTTGATGAATTTGTGTTGTG 58.583 34.615 0.00 0.00 0.00 3.33
2455 2547 1.950828 CTCTGTGTGATCTGGGCATC 58.049 55.000 0.00 0.00 0.00 3.91
2463 2555 0.394192 GATCTGGGCATCGTGATGGA 59.606 55.000 11.54 1.18 39.16 3.41
2497 2589 6.129009 GCTTCATTTTTGCTGTGATAGTTGTG 60.129 38.462 0.00 0.00 0.00 3.33
2554 2646 4.476846 TCCTTGGATAATGGCCTTGAGTTA 59.523 41.667 3.32 0.00 0.00 2.24
2674 2766 4.533919 TTCCCTTGCATGGTGTAAATTG 57.466 40.909 16.81 0.04 0.00 2.32
2689 2781 6.371548 GGTGTAAATTGTGCTCTGTCTATGAA 59.628 38.462 0.00 0.00 0.00 2.57
2703 2797 9.227490 CTCTGTCTATGAACTATAGTTTGAACG 57.773 37.037 18.96 7.77 39.83 3.95
2899 2993 1.743394 CGTGAGGGGGCATTTCTTAAC 59.257 52.381 0.00 0.00 0.00 2.01
2906 3000 6.002653 AGGGGGCATTTCTTAACTAAGTAG 57.997 41.667 0.00 0.00 34.93 2.57
2967 3061 2.948979 TGGTGTTCTGCAGATTTTCGTT 59.051 40.909 19.04 0.00 0.00 3.85
3030 3124 3.706594 ACTGGAAATCAATCTCGGAGCTA 59.293 43.478 0.00 0.00 0.00 3.32
3111 3205 0.107508 CCATCGCAGTCATTCAGGGT 60.108 55.000 0.00 0.00 0.00 4.34
3150 3244 3.148279 GACCTCTCCCGGATGCGT 61.148 66.667 0.73 0.00 0.00 5.24
3418 3519 7.671302 TGACTATGCTTAGACTGAAACTTCTT 58.329 34.615 13.22 0.00 0.00 2.52
3434 3535 9.137459 TGAAACTTCTTATGTTTTCAATACCCA 57.863 29.630 0.00 0.00 37.70 4.51
3475 3577 5.344743 AGCGATCTTTTTGTAGAGATCCA 57.655 39.130 7.54 0.00 43.34 3.41
3478 3580 5.220491 GCGATCTTTTTGTAGAGATCCACAC 60.220 44.000 7.54 0.00 43.34 3.82
3480 3582 5.560722 TCTTTTTGTAGAGATCCACACCA 57.439 39.130 0.00 0.00 0.00 4.17
3630 3732 5.619625 AAGCTGAGAAGTTAACTGAATGC 57.380 39.130 9.34 10.25 0.00 3.56
3647 3749 1.018910 TGCGATGACATGCCTGATTG 58.981 50.000 0.00 0.00 0.00 2.67
3648 3750 1.302366 GCGATGACATGCCTGATTGA 58.698 50.000 0.00 0.00 0.00 2.57
3649 3751 1.878088 GCGATGACATGCCTGATTGAT 59.122 47.619 0.00 0.00 0.00 2.57
3650 3752 2.350484 GCGATGACATGCCTGATTGATG 60.350 50.000 0.00 0.00 0.00 3.07
3651 3753 3.135994 CGATGACATGCCTGATTGATGA 58.864 45.455 0.00 0.00 0.00 2.92
3652 3754 3.059120 CGATGACATGCCTGATTGATGAC 60.059 47.826 0.00 0.00 0.00 3.06
3655 3757 3.199289 TGACATGCCTGATTGATGACTCT 59.801 43.478 0.00 0.00 0.00 3.24
3656 3758 3.542648 ACATGCCTGATTGATGACTCTG 58.457 45.455 0.00 0.00 0.00 3.35
3657 3759 2.034104 TGCCTGATTGATGACTCTGC 57.966 50.000 0.00 0.00 0.00 4.26
3658 3760 1.279846 TGCCTGATTGATGACTCTGCA 59.720 47.619 0.00 0.00 0.00 4.41
3659 3761 2.290450 TGCCTGATTGATGACTCTGCAA 60.290 45.455 0.00 0.00 0.00 4.08
3660 3762 2.751259 GCCTGATTGATGACTCTGCAAA 59.249 45.455 0.00 0.00 0.00 3.68
3661 3763 3.380637 GCCTGATTGATGACTCTGCAAAT 59.619 43.478 0.00 0.00 0.00 2.32
3662 3764 4.733815 GCCTGATTGATGACTCTGCAAATG 60.734 45.833 0.00 0.00 0.00 2.32
3663 3765 4.352039 CTGATTGATGACTCTGCAAATGC 58.648 43.478 0.00 0.00 42.50 3.56
3664 3766 4.014406 TGATTGATGACTCTGCAAATGCT 58.986 39.130 6.97 0.00 42.66 3.79
3665 3767 5.187687 TGATTGATGACTCTGCAAATGCTA 58.812 37.500 6.97 0.00 42.66 3.49
3666 3768 5.826208 TGATTGATGACTCTGCAAATGCTAT 59.174 36.000 6.97 0.00 42.66 2.97
3667 3769 6.320418 TGATTGATGACTCTGCAAATGCTATT 59.680 34.615 6.97 0.00 42.66 1.73
3668 3770 5.746307 TGATGACTCTGCAAATGCTATTC 57.254 39.130 6.97 0.34 42.66 1.75
3669 3771 5.187687 TGATGACTCTGCAAATGCTATTCA 58.812 37.500 6.97 5.60 42.66 2.57
3670 3772 5.648960 TGATGACTCTGCAAATGCTATTCAA 59.351 36.000 6.97 0.00 42.66 2.69
3671 3773 5.300969 TGACTCTGCAAATGCTATTCAAC 57.699 39.130 6.97 0.00 42.66 3.18
3672 3774 5.005740 TGACTCTGCAAATGCTATTCAACT 58.994 37.500 6.97 0.00 42.66 3.16
3673 3775 6.172630 TGACTCTGCAAATGCTATTCAACTA 58.827 36.000 6.97 0.00 42.66 2.24
3674 3776 6.092670 TGACTCTGCAAATGCTATTCAACTAC 59.907 38.462 6.97 0.00 42.66 2.73
3675 3777 6.176183 ACTCTGCAAATGCTATTCAACTACT 58.824 36.000 6.97 0.00 42.66 2.57
3676 3778 6.314896 ACTCTGCAAATGCTATTCAACTACTC 59.685 38.462 6.97 0.00 42.66 2.59
3677 3779 5.586243 TCTGCAAATGCTATTCAACTACTCC 59.414 40.000 6.97 0.00 42.66 3.85
3678 3780 5.252547 TGCAAATGCTATTCAACTACTCCA 58.747 37.500 6.97 0.00 42.66 3.86
3679 3781 5.123820 TGCAAATGCTATTCAACTACTCCAC 59.876 40.000 6.97 0.00 42.66 4.02
3680 3782 5.355350 GCAAATGCTATTCAACTACTCCACT 59.645 40.000 0.00 0.00 38.21 4.00
3681 3783 6.127897 GCAAATGCTATTCAACTACTCCACTT 60.128 38.462 0.00 0.00 38.21 3.16
3682 3784 7.467623 CAAATGCTATTCAACTACTCCACTTC 58.532 38.462 0.00 0.00 0.00 3.01
3683 3785 5.738619 TGCTATTCAACTACTCCACTTCA 57.261 39.130 0.00 0.00 0.00 3.02
3684 3786 6.299805 TGCTATTCAACTACTCCACTTCAT 57.700 37.500 0.00 0.00 0.00 2.57
3685 3787 6.108687 TGCTATTCAACTACTCCACTTCATG 58.891 40.000 0.00 0.00 0.00 3.07
3686 3788 5.007136 GCTATTCAACTACTCCACTTCATGC 59.993 44.000 0.00 0.00 0.00 4.06
3687 3789 4.623932 TTCAACTACTCCACTTCATGCT 57.376 40.909 0.00 0.00 0.00 3.79
3688 3790 3.930336 TCAACTACTCCACTTCATGCTG 58.070 45.455 0.00 0.00 0.00 4.41
3689 3791 3.324846 TCAACTACTCCACTTCATGCTGT 59.675 43.478 0.00 0.00 0.00 4.40
3690 3792 3.601443 ACTACTCCACTTCATGCTGTC 57.399 47.619 0.00 0.00 0.00 3.51
3691 3793 2.234908 ACTACTCCACTTCATGCTGTCC 59.765 50.000 0.00 0.00 0.00 4.02
3692 3794 1.059098 ACTCCACTTCATGCTGTCCA 58.941 50.000 0.00 0.00 0.00 4.02
3693 3795 1.421268 ACTCCACTTCATGCTGTCCAA 59.579 47.619 0.00 0.00 0.00 3.53
3694 3796 2.158623 ACTCCACTTCATGCTGTCCAAA 60.159 45.455 0.00 0.00 0.00 3.28
3695 3797 2.227388 CTCCACTTCATGCTGTCCAAAC 59.773 50.000 0.00 0.00 0.00 2.93
3696 3798 1.955778 CCACTTCATGCTGTCCAAACA 59.044 47.619 0.00 0.00 0.00 2.83
3697 3799 2.361757 CCACTTCATGCTGTCCAAACAA 59.638 45.455 0.00 0.00 34.24 2.83
3698 3800 3.551454 CCACTTCATGCTGTCCAAACAAG 60.551 47.826 0.00 0.00 34.24 3.16
3733 3835 1.602311 GCCCTGGCATGAATCACTAG 58.398 55.000 2.58 0.00 41.49 2.57
3738 3840 4.285517 CCCTGGCATGAATCACTAGTCTAT 59.714 45.833 0.00 0.00 0.00 1.98
3760 3868 6.604735 ATTATTTACAGCTTCTACTTGCCG 57.395 37.500 0.00 0.00 0.00 5.69
3763 3871 0.036010 ACAGCTTCTACTTGCCGCAT 60.036 50.000 0.00 0.00 0.00 4.73
3765 3873 1.089920 AGCTTCTACTTGCCGCATTG 58.910 50.000 0.00 0.00 0.00 2.82
3767 3875 1.202076 GCTTCTACTTGCCGCATTGAC 60.202 52.381 0.00 0.00 0.00 3.18
3769 3877 1.438651 TCTACTTGCCGCATTGACAC 58.561 50.000 0.00 0.00 0.00 3.67
3770 3878 1.155889 CTACTTGCCGCATTGACACA 58.844 50.000 0.00 0.00 0.00 3.72
3772 3880 0.743688 ACTTGCCGCATTGACACAAA 59.256 45.000 0.00 0.00 0.00 2.83
3773 3881 1.130955 CTTGCCGCATTGACACAAAC 58.869 50.000 0.00 0.00 0.00 2.93
3775 3883 0.248825 TGCCGCATTGACACAAACAC 60.249 50.000 0.00 0.00 0.00 3.32
3781 3889 3.365832 GCATTGACACAAACACACTCAG 58.634 45.455 0.00 0.00 0.00 3.35
3788 3896 1.233019 CAAACACACTCAGGAGCAGG 58.767 55.000 0.00 0.00 0.00 4.85
3793 3901 1.375652 CACTCAGGAGCAGGCACAG 60.376 63.158 0.00 0.00 0.00 3.66
3796 3904 3.054503 CAGGAGCAGGCACAGTGC 61.055 66.667 17.97 17.97 44.08 4.40
3811 3919 6.220579 GCACAGTGCACATATCTAAGTATG 57.779 41.667 21.22 6.19 44.26 2.39
3812 3920 5.755375 GCACAGTGCACATATCTAAGTATGT 59.245 40.000 21.22 6.88 44.26 2.29
3833 3941 1.069358 GCTGCCCTCTATGGTACTGTC 59.931 57.143 0.00 0.00 0.00 3.51
3842 3950 4.275810 TCTATGGTACTGTCACCCTACAC 58.724 47.826 0.00 0.00 37.84 2.90
3846 3956 4.418359 TGGTACTGTCACCCTACACAATA 58.582 43.478 0.00 0.00 37.84 1.90
3847 3957 4.839550 TGGTACTGTCACCCTACACAATAA 59.160 41.667 0.00 0.00 37.84 1.40
3848 3958 5.486063 TGGTACTGTCACCCTACACAATAAT 59.514 40.000 0.00 0.00 37.84 1.28
3849 3959 5.815740 GGTACTGTCACCCTACACAATAATG 59.184 44.000 0.00 0.00 31.91 1.90
3850 3960 4.261801 ACTGTCACCCTACACAATAATGC 58.738 43.478 0.00 0.00 0.00 3.56
3851 3961 4.260985 CTGTCACCCTACACAATAATGCA 58.739 43.478 0.00 0.00 0.00 3.96
3853 3963 4.699735 TGTCACCCTACACAATAATGCAAG 59.300 41.667 0.00 0.00 0.00 4.01
3854 3964 4.700213 GTCACCCTACACAATAATGCAAGT 59.300 41.667 0.00 0.00 0.00 3.16
3857 3968 4.943705 ACCCTACACAATAATGCAAGTGAG 59.056 41.667 11.72 0.00 35.97 3.51
3903 4015 2.025887 CCTTGTTTCACCTAGGGCTGAT 60.026 50.000 14.81 0.00 0.00 2.90
4033 4145 5.069251 GCTATTGTACTCACTGATGTACCCT 59.931 44.000 12.47 6.19 38.48 4.34
4039 4151 2.586079 CTGATGTACCCTGGCGCG 60.586 66.667 0.00 0.00 0.00 6.86
4210 4322 2.087646 GGATCAACCAGTTCCTTGAGC 58.912 52.381 0.00 0.00 38.79 4.26
4262 4378 4.974645 TGTCAATGTTCAGGGTTAGACT 57.025 40.909 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.041848 TGCTTATCCATGAGATTACAAATCGTG 60.042 37.037 0.00 0.00 36.33 4.35
1 2 6.992123 TGCTTATCCATGAGATTACAAATCGT 59.008 34.615 0.00 0.00 36.33 3.73
7 8 7.039714 AGTCGTATGCTTATCCATGAGATTACA 60.040 37.037 0.00 0.00 36.33 2.41
10 11 6.352016 AGTCGTATGCTTATCCATGAGATT 57.648 37.500 0.00 0.00 36.33 2.40
11 12 5.991933 AGTCGTATGCTTATCCATGAGAT 57.008 39.130 0.00 0.00 39.15 2.75
20 21 4.099573 AGTGTTGCCTAGTCGTATGCTTAT 59.900 41.667 0.00 0.00 0.00 1.73
21 22 3.446161 AGTGTTGCCTAGTCGTATGCTTA 59.554 43.478 0.00 0.00 0.00 3.09
28 30 2.902705 TTCAAGTGTTGCCTAGTCGT 57.097 45.000 0.00 0.00 0.00 4.34
30 32 4.697352 ACATGATTCAAGTGTTGCCTAGTC 59.303 41.667 0.00 0.00 0.00 2.59
34 36 2.559668 CCACATGATTCAAGTGTTGCCT 59.440 45.455 17.88 0.00 32.14 4.75
57 59 6.679843 CGTTTTCTCCTTCTTGTAGTAGTCT 58.320 40.000 0.00 0.00 0.00 3.24
61 63 4.232221 CGCGTTTTCTCCTTCTTGTAGTA 58.768 43.478 0.00 0.00 0.00 1.82
62 64 3.057734 CGCGTTTTCTCCTTCTTGTAGT 58.942 45.455 0.00 0.00 0.00 2.73
63 65 2.412089 CCGCGTTTTCTCCTTCTTGTAG 59.588 50.000 4.92 0.00 0.00 2.74
64 66 2.224113 ACCGCGTTTTCTCCTTCTTGTA 60.224 45.455 4.92 0.00 0.00 2.41
67 69 2.825861 TACCGCGTTTTCTCCTTCTT 57.174 45.000 4.92 0.00 0.00 2.52
69 71 3.121544 CCTATACCGCGTTTTCTCCTTC 58.878 50.000 4.92 0.00 0.00 3.46
85 87 4.823442 TCTCGTATTTGCCTTCGTCCTATA 59.177 41.667 0.00 0.00 0.00 1.31
89 91 2.159282 TCTCTCGTATTTGCCTTCGTCC 60.159 50.000 0.00 0.00 0.00 4.79
94 96 5.023533 TGCTTATCTCTCGTATTTGCCTT 57.976 39.130 0.00 0.00 0.00 4.35
111 120 1.153168 GGCGCATCCTCCTTGCTTA 60.153 57.895 10.83 0.00 37.96 3.09
112 121 2.439156 GGCGCATCCTCCTTGCTT 60.439 61.111 10.83 0.00 37.96 3.91
113 122 3.720601 TGGCGCATCCTCCTTGCT 61.721 61.111 10.83 0.00 37.96 3.91
114 123 3.512516 GTGGCGCATCCTCCTTGC 61.513 66.667 10.83 0.00 36.74 4.01
115 124 3.197790 CGTGGCGCATCCTCCTTG 61.198 66.667 10.83 0.00 35.26 3.61
116 125 3.376935 CTCGTGGCGCATCCTCCTT 62.377 63.158 10.83 0.00 35.26 3.36
117 126 3.842923 CTCGTGGCGCATCCTCCT 61.843 66.667 10.83 0.00 35.26 3.69
118 127 3.157217 ATCTCGTGGCGCATCCTCC 62.157 63.158 10.83 0.00 35.26 4.30
119 128 1.663074 GATCTCGTGGCGCATCCTC 60.663 63.158 10.83 0.00 35.26 3.71
120 129 0.823769 TAGATCTCGTGGCGCATCCT 60.824 55.000 10.83 0.00 35.26 3.24
121 130 0.244994 ATAGATCTCGTGGCGCATCC 59.755 55.000 10.83 0.00 0.00 3.51
123 132 0.037882 CCATAGATCTCGTGGCGCAT 60.038 55.000 10.83 0.00 0.00 4.73
124 133 1.106944 TCCATAGATCTCGTGGCGCA 61.107 55.000 18.03 3.45 33.01 6.09
126 135 0.387878 GCTCCATAGATCTCGTGGCG 60.388 60.000 18.03 14.50 33.01 5.69
127 136 0.965439 AGCTCCATAGATCTCGTGGC 59.035 55.000 18.03 10.20 33.01 5.01
128 137 1.959985 ACAGCTCCATAGATCTCGTGG 59.040 52.381 17.13 17.13 0.00 4.94
129 138 2.620585 TCACAGCTCCATAGATCTCGTG 59.379 50.000 0.00 0.00 0.00 4.35
130 139 2.884012 CTCACAGCTCCATAGATCTCGT 59.116 50.000 0.00 0.00 0.00 4.18
131 140 2.228582 CCTCACAGCTCCATAGATCTCG 59.771 54.545 0.00 0.00 0.00 4.04
133 142 2.964464 CACCTCACAGCTCCATAGATCT 59.036 50.000 0.00 0.00 0.00 2.75
135 144 2.756907 ACACCTCACAGCTCCATAGAT 58.243 47.619 0.00 0.00 0.00 1.98
136 145 2.234661 CAACACCTCACAGCTCCATAGA 59.765 50.000 0.00 0.00 0.00 1.98
137 146 2.625737 CAACACCTCACAGCTCCATAG 58.374 52.381 0.00 0.00 0.00 2.23
139 148 0.037303 CCAACACCTCACAGCTCCAT 59.963 55.000 0.00 0.00 0.00 3.41
140 149 1.344953 ACCAACACCTCACAGCTCCA 61.345 55.000 0.00 0.00 0.00 3.86
142 151 0.394565 AGACCAACACCTCACAGCTC 59.605 55.000 0.00 0.00 0.00 4.09
143 152 0.839946 AAGACCAACACCTCACAGCT 59.160 50.000 0.00 0.00 0.00 4.24
144 153 1.680338 AAAGACCAACACCTCACAGC 58.320 50.000 0.00 0.00 0.00 4.40
162 171 5.928976 TCTCTCCATGAGTGTTGAGAAAAA 58.071 37.500 0.00 0.00 43.13 1.94
163 172 5.305386 TCTCTCTCCATGAGTGTTGAGAAAA 59.695 40.000 0.00 0.00 43.13 2.29
164 173 4.835056 TCTCTCTCCATGAGTGTTGAGAAA 59.165 41.667 0.00 0.00 43.13 2.52
165 174 4.411013 TCTCTCTCCATGAGTGTTGAGAA 58.589 43.478 0.00 0.00 43.13 2.87
166 175 4.039603 TCTCTCTCCATGAGTGTTGAGA 57.960 45.455 0.00 0.00 43.13 3.27
167 176 4.401837 TCATCTCTCTCCATGAGTGTTGAG 59.598 45.833 0.00 0.00 43.13 3.02
168 177 4.347607 TCATCTCTCTCCATGAGTGTTGA 58.652 43.478 0.00 0.00 43.13 3.18
169 178 4.441773 CCTCATCTCTCTCCATGAGTGTTG 60.442 50.000 0.00 0.00 43.14 3.33
170 179 3.705579 CCTCATCTCTCTCCATGAGTGTT 59.294 47.826 0.00 0.00 43.14 3.32
171 180 3.053019 TCCTCATCTCTCTCCATGAGTGT 60.053 47.826 0.00 0.00 43.14 3.55
172 181 3.564264 TCCTCATCTCTCTCCATGAGTG 58.436 50.000 0.00 1.31 43.14 3.51
173 182 3.969466 TCCTCATCTCTCTCCATGAGT 57.031 47.619 0.00 0.00 43.14 3.41
174 183 3.575256 CCTTCCTCATCTCTCTCCATGAG 59.425 52.174 0.00 2.48 43.94 2.90
175 184 3.574749 CCTTCCTCATCTCTCTCCATGA 58.425 50.000 0.00 0.00 0.00 3.07
176 185 2.633967 CCCTTCCTCATCTCTCTCCATG 59.366 54.545 0.00 0.00 0.00 3.66
177 186 2.521841 TCCCTTCCTCATCTCTCTCCAT 59.478 50.000 0.00 0.00 0.00 3.41
184 193 2.159170 CGTCAAGTCCCTTCCTCATCTC 60.159 54.545 0.00 0.00 0.00 2.75
201 210 2.124903 GCGTGAGAAAAGAAGACGTCA 58.875 47.619 19.50 0.00 32.66 4.35
209 218 3.570926 ACGTATCAGCGTGAGAAAAGA 57.429 42.857 0.00 0.00 43.99 2.52
220 229 4.698304 AGCTTATCTCCTCTACGTATCAGC 59.302 45.833 0.00 0.00 0.00 4.26
226 235 1.957877 GGCAGCTTATCTCCTCTACGT 59.042 52.381 0.00 0.00 0.00 3.57
227 236 1.068885 CGGCAGCTTATCTCCTCTACG 60.069 57.143 0.00 0.00 0.00 3.51
229 238 1.133450 ACCGGCAGCTTATCTCCTCTA 60.133 52.381 0.00 0.00 0.00 2.43
232 241 0.978146 ACACCGGCAGCTTATCTCCT 60.978 55.000 0.00 0.00 0.00 3.69
233 242 0.811616 CACACCGGCAGCTTATCTCC 60.812 60.000 0.00 0.00 0.00 3.71
234 243 0.175760 TCACACCGGCAGCTTATCTC 59.824 55.000 0.00 0.00 0.00 2.75
235 244 0.176680 CTCACACCGGCAGCTTATCT 59.823 55.000 0.00 0.00 0.00 1.98
236 245 1.432270 GCTCACACCGGCAGCTTATC 61.432 60.000 0.00 0.00 0.00 1.75
237 246 1.450312 GCTCACACCGGCAGCTTAT 60.450 57.895 0.00 0.00 0.00 1.73
238 247 2.047274 GCTCACACCGGCAGCTTA 60.047 61.111 0.00 0.00 0.00 3.09
255 264 0.441145 GTAACTAAACCGCTGGCACG 59.559 55.000 3.06 3.06 0.00 5.34
263 272 2.160065 CGCGTTCACTGTAACTAAACCG 60.160 50.000 0.00 0.00 0.00 4.44
268 277 1.954437 CGACGCGTTCACTGTAACTA 58.046 50.000 15.53 0.00 0.00 2.24
272 281 2.429571 GGCGACGCGTTCACTGTA 60.430 61.111 15.53 0.00 0.00 2.74
291 300 2.905996 TTGGCTCGGTGGCTTCCAT 61.906 57.895 5.23 0.00 42.34 3.41
304 313 3.241067 TCTATAAAGCGAACGTTGGCT 57.759 42.857 29.12 29.12 44.37 4.75
307 316 7.775729 ACAAAATTCTATAAAGCGAACGTTG 57.224 32.000 5.00 0.00 0.00 4.10
397 414 1.298339 ACGCGCTGCTTTTGTTCAC 60.298 52.632 5.73 0.00 0.00 3.18
401 418 4.629115 GCCACGCGCTGCTTTTGT 62.629 61.111 5.73 0.00 0.00 2.83
494 512 0.546122 TGGACTGGTGCTGTGACTTT 59.454 50.000 0.00 0.00 0.00 2.66
1368 1419 2.045926 GGTTCTCACCTGCGCCAT 60.046 61.111 4.18 0.00 40.44 4.40
1434 1486 2.584608 CCGGAACCCTAGCACTGG 59.415 66.667 0.00 0.00 0.00 4.00
1526 1578 1.845809 GCAACCGAGTTCAGCACCTG 61.846 60.000 0.00 0.00 0.00 4.00
1597 1649 5.313712 TCCACTACTCAATTTCCAGTTTCC 58.686 41.667 0.00 0.00 0.00 3.13
1599 1651 6.542821 TCATCCACTACTCAATTTCCAGTTT 58.457 36.000 0.00 0.00 0.00 2.66
1632 1684 1.548719 TCTACCACGATGACACTTGGG 59.451 52.381 0.00 0.00 34.19 4.12
1639 1691 4.800993 CAGATTCAGTTCTACCACGATGAC 59.199 45.833 0.00 0.00 0.00 3.06
1648 1703 8.934507 ACTGTAATTAGCAGATTCAGTTCTAC 57.065 34.615 16.84 0.00 37.40 2.59
1683 1757 6.202954 AGACCGTAATTAGCAGATTGTAATGC 59.797 38.462 0.00 0.00 42.87 3.56
1684 1758 7.715265 AGACCGTAATTAGCAGATTGTAATG 57.285 36.000 0.00 0.00 0.00 1.90
1688 1762 7.291411 AGATAGACCGTAATTAGCAGATTGT 57.709 36.000 0.00 0.00 0.00 2.71
1689 1763 8.297426 TGTAGATAGACCGTAATTAGCAGATTG 58.703 37.037 0.00 0.00 0.00 2.67
1690 1764 8.405418 TGTAGATAGACCGTAATTAGCAGATT 57.595 34.615 0.00 0.00 0.00 2.40
1691 1765 7.666388 ACTGTAGATAGACCGTAATTAGCAGAT 59.334 37.037 0.00 0.00 0.00 2.90
1692 1766 6.996879 ACTGTAGATAGACCGTAATTAGCAGA 59.003 38.462 0.00 0.00 0.00 4.26
1693 1767 7.204496 ACTGTAGATAGACCGTAATTAGCAG 57.796 40.000 0.00 0.00 0.00 4.24
1694 1768 8.859236 ATACTGTAGATAGACCGTAATTAGCA 57.141 34.615 0.00 0.00 0.00 3.49
1700 1774 9.618890 AGTTGTAATACTGTAGATAGACCGTAA 57.381 33.333 0.00 0.00 0.00 3.18
1701 1775 9.265901 GAGTTGTAATACTGTAGATAGACCGTA 57.734 37.037 0.00 0.00 0.00 4.02
1702 1776 7.992033 AGAGTTGTAATACTGTAGATAGACCGT 59.008 37.037 0.00 0.00 0.00 4.83
1703 1777 8.283992 CAGAGTTGTAATACTGTAGATAGACCG 58.716 40.741 0.00 0.00 0.00 4.79
1704 1778 8.077386 GCAGAGTTGTAATACTGTAGATAGACC 58.923 40.741 0.00 0.00 33.57 3.85
1705 1779 8.622157 TGCAGAGTTGTAATACTGTAGATAGAC 58.378 37.037 0.00 0.00 33.57 2.59
1706 1780 8.747538 TGCAGAGTTGTAATACTGTAGATAGA 57.252 34.615 0.00 0.00 33.57 1.98
1707 1781 9.239002 GTTGCAGAGTTGTAATACTGTAGATAG 57.761 37.037 0.00 0.00 31.49 2.08
1708 1782 8.967918 AGTTGCAGAGTTGTAATACTGTAGATA 58.032 33.333 0.00 0.00 31.49 1.98
1709 1783 7.841956 AGTTGCAGAGTTGTAATACTGTAGAT 58.158 34.615 0.00 0.00 31.49 1.98
1710 1784 7.176865 AGAGTTGCAGAGTTGTAATACTGTAGA 59.823 37.037 0.00 0.00 31.49 2.59
1711 1785 7.274468 CAGAGTTGCAGAGTTGTAATACTGTAG 59.726 40.741 0.00 0.00 34.21 2.74
1712 1786 7.090808 CAGAGTTGCAGAGTTGTAATACTGTA 58.909 38.462 0.00 0.00 34.21 2.74
1713 1787 5.928839 CAGAGTTGCAGAGTTGTAATACTGT 59.071 40.000 0.00 0.00 34.21 3.55
1714 1788 6.400579 CAGAGTTGCAGAGTTGTAATACTG 57.599 41.667 0.00 0.00 33.21 2.74
1801 1875 5.874810 CAGCCATGTAAGCACTTACTCTAAA 59.125 40.000 18.60 1.94 44.21 1.85
1810 1884 2.795231 ATGACAGCCATGTAAGCACT 57.205 45.000 0.00 0.00 40.68 4.40
1823 1897 5.064452 GTGATCCAGCACTTTTCTATGACAG 59.936 44.000 0.00 0.00 35.91 3.51
1867 1942 9.924650 GATTTACTCTAAGGAACTGAACAAGTA 57.075 33.333 0.00 0.00 40.86 2.24
2008 2083 4.825634 ACTGAGCATGATATCACCCAAATG 59.174 41.667 7.78 2.37 0.00 2.32
2013 2088 3.307059 GGGTACTGAGCATGATATCACCC 60.307 52.174 7.78 7.01 0.00 4.61
2047 2126 5.010516 AGCAGCTGAAAGAGACGATATGTAT 59.989 40.000 20.43 0.00 34.07 2.29
2226 2308 5.865013 CAGAAACACAAATAATGCATGCTCA 59.135 36.000 20.33 0.00 0.00 4.26
2287 2369 3.125316 TGTTCAGAAAAGCAATGCAAGC 58.875 40.909 8.35 6.40 0.00 4.01
2391 2483 7.703298 AATCACACAACACAAATTCATCAAG 57.297 32.000 0.00 0.00 0.00 3.02
2410 2502 2.813172 CCACAAATTTGGGCCAAATCAC 59.187 45.455 37.21 0.00 42.32 3.06
2455 2547 4.682787 TGAAGCATACTACTTCCATCACG 58.317 43.478 0.00 0.00 42.35 4.35
2463 2555 7.040478 TCACAGCAAAAATGAAGCATACTACTT 60.040 33.333 0.00 0.00 0.00 2.24
2497 2589 5.595133 ACTAGTTTACTGGGCTCTCTGTATC 59.405 44.000 0.00 0.00 0.00 2.24
2554 2646 2.774234 CAGGGTTCAGGTATCAGGACAT 59.226 50.000 0.00 0.00 0.00 3.06
2674 2766 8.191446 TCAAACTATAGTTCATAGACAGAGCAC 58.809 37.037 18.28 0.00 39.29 4.40
2689 2781 5.938125 ACAATGAAGCCGTTCAAACTATAGT 59.062 36.000 0.00 0.00 45.88 2.12
2703 2797 1.337167 GCCTGAAACCACAATGAAGCC 60.337 52.381 0.00 0.00 0.00 4.35
2967 3061 3.524095 TGGAATTTCTCCTGGCTTTCA 57.476 42.857 0.00 0.00 45.64 2.69
3030 3124 3.214328 GGTAGCGATTTCATGTGGGATT 58.786 45.455 0.00 0.00 0.00 3.01
3150 3244 2.604912 TGAGCTTCACTAGGACCTGA 57.395 50.000 3.53 0.00 0.00 3.86
3418 3519 5.872617 CGACACTCTGGGTATTGAAAACATA 59.127 40.000 0.00 0.00 0.00 2.29
3434 3535 0.251209 TACAGGACAGGCGACACTCT 60.251 55.000 0.00 0.00 0.00 3.24
3475 3577 3.244215 CGATACATAGCCATCCTTGGTGT 60.244 47.826 0.00 0.00 45.57 4.16
3478 3580 3.961480 TCGATACATAGCCATCCTTGG 57.039 47.619 0.00 0.00 46.66 3.61
3480 3582 4.382470 GCTGATCGATACATAGCCATCCTT 60.382 45.833 0.00 0.00 0.00 3.36
3630 3732 3.059120 GTCATCAATCAGGCATGTCATCG 60.059 47.826 0.00 0.00 0.00 3.84
3647 3749 5.746307 TGAATAGCATTTGCAGAGTCATC 57.254 39.130 5.20 0.00 45.16 2.92
3648 3750 5.651139 AGTTGAATAGCATTTGCAGAGTCAT 59.349 36.000 5.20 0.00 45.16 3.06
3649 3751 5.005740 AGTTGAATAGCATTTGCAGAGTCA 58.994 37.500 5.20 4.64 45.16 3.41
3650 3752 5.557891 AGTTGAATAGCATTTGCAGAGTC 57.442 39.130 5.20 2.10 45.16 3.36
3651 3753 6.176183 AGTAGTTGAATAGCATTTGCAGAGT 58.824 36.000 5.20 0.00 45.16 3.24
3652 3754 6.238320 GGAGTAGTTGAATAGCATTTGCAGAG 60.238 42.308 5.20 0.00 45.16 3.35
3655 3757 5.123820 GTGGAGTAGTTGAATAGCATTTGCA 59.876 40.000 5.20 0.00 45.16 4.08
3656 3758 5.355350 AGTGGAGTAGTTGAATAGCATTTGC 59.645 40.000 0.00 0.00 42.49 3.68
3657 3759 6.992063 AGTGGAGTAGTTGAATAGCATTTG 57.008 37.500 0.00 0.00 0.00 2.32
3658 3760 7.168219 TGAAGTGGAGTAGTTGAATAGCATTT 58.832 34.615 0.00 0.00 0.00 2.32
3659 3761 6.711277 TGAAGTGGAGTAGTTGAATAGCATT 58.289 36.000 0.00 0.00 0.00 3.56
3660 3762 6.299805 TGAAGTGGAGTAGTTGAATAGCAT 57.700 37.500 0.00 0.00 0.00 3.79
3661 3763 5.738619 TGAAGTGGAGTAGTTGAATAGCA 57.261 39.130 0.00 0.00 0.00 3.49
3662 3764 5.007136 GCATGAAGTGGAGTAGTTGAATAGC 59.993 44.000 0.00 0.00 0.00 2.97
3663 3765 6.257411 CAGCATGAAGTGGAGTAGTTGAATAG 59.743 42.308 0.00 0.00 39.69 1.73
3664 3766 6.108687 CAGCATGAAGTGGAGTAGTTGAATA 58.891 40.000 0.00 0.00 39.69 1.75
3665 3767 4.940046 CAGCATGAAGTGGAGTAGTTGAAT 59.060 41.667 0.00 0.00 39.69 2.57
3666 3768 4.202357 ACAGCATGAAGTGGAGTAGTTGAA 60.202 41.667 0.00 0.00 39.69 2.69
3667 3769 3.324846 ACAGCATGAAGTGGAGTAGTTGA 59.675 43.478 0.00 0.00 39.69 3.18
3668 3770 3.668447 ACAGCATGAAGTGGAGTAGTTG 58.332 45.455 0.00 0.00 39.69 3.16
3669 3771 3.307059 GGACAGCATGAAGTGGAGTAGTT 60.307 47.826 0.00 0.00 39.69 2.24
3670 3772 2.234908 GGACAGCATGAAGTGGAGTAGT 59.765 50.000 0.00 0.00 39.69 2.73
3671 3773 2.234661 TGGACAGCATGAAGTGGAGTAG 59.765 50.000 0.00 0.00 39.69 2.57
3672 3774 2.256306 TGGACAGCATGAAGTGGAGTA 58.744 47.619 0.00 0.00 39.69 2.59
3673 3775 1.059098 TGGACAGCATGAAGTGGAGT 58.941 50.000 0.00 0.00 39.69 3.85
3674 3776 2.189594 TTGGACAGCATGAAGTGGAG 57.810 50.000 0.00 0.00 39.69 3.86
3675 3777 2.229792 GTTTGGACAGCATGAAGTGGA 58.770 47.619 0.00 0.00 39.69 4.02
3676 3778 1.955778 TGTTTGGACAGCATGAAGTGG 59.044 47.619 0.00 0.00 39.69 4.00
3677 3779 3.635331 CTTGTTTGGACAGCATGAAGTG 58.365 45.455 0.00 0.00 39.69 3.16
3678 3780 2.035066 GCTTGTTTGGACAGCATGAAGT 59.965 45.455 0.00 0.00 39.69 3.01
3679 3781 2.034939 TGCTTGTTTGGACAGCATGAAG 59.965 45.455 0.00 0.00 39.69 3.02
3680 3782 2.030371 TGCTTGTTTGGACAGCATGAA 58.970 42.857 0.00 0.00 39.69 2.57
3681 3783 1.610038 CTGCTTGTTTGGACAGCATGA 59.390 47.619 0.00 0.00 39.69 3.07
3682 3784 2.060326 CTGCTTGTTTGGACAGCATG 57.940 50.000 0.00 0.00 46.00 4.06
3686 3788 2.806608 ATTGCTGCTTGTTTGGACAG 57.193 45.000 0.00 0.00 37.04 3.51
3687 3789 3.540314 AAATTGCTGCTTGTTTGGACA 57.460 38.095 0.00 0.00 0.00 4.02
3688 3790 4.808364 TGTAAAATTGCTGCTTGTTTGGAC 59.192 37.500 0.00 3.18 0.00 4.02
3689 3791 5.016051 TGTAAAATTGCTGCTTGTTTGGA 57.984 34.783 0.00 0.00 0.00 3.53
3690 3792 5.927954 ATGTAAAATTGCTGCTTGTTTGG 57.072 34.783 0.00 0.00 0.00 3.28
3733 3835 8.766151 GGCAAGTAGAAGCTGTAAATAATAGAC 58.234 37.037 0.00 0.00 0.00 2.59
3738 3840 4.331717 GCGGCAAGTAGAAGCTGTAAATAA 59.668 41.667 0.00 0.00 39.31 1.40
3747 3854 1.086696 TCAATGCGGCAAGTAGAAGC 58.913 50.000 6.82 0.00 0.00 3.86
3760 3868 3.365832 CTGAGTGTGTTTGTGTCAATGC 58.634 45.455 0.00 0.00 0.00 3.56
3763 3871 3.270027 CTCCTGAGTGTGTTTGTGTCAA 58.730 45.455 0.00 0.00 0.00 3.18
3765 3873 1.599542 GCTCCTGAGTGTGTTTGTGTC 59.400 52.381 0.00 0.00 0.00 3.67
3767 3875 1.600957 CTGCTCCTGAGTGTGTTTGTG 59.399 52.381 0.00 0.00 0.00 3.33
3769 3877 1.233019 CCTGCTCCTGAGTGTGTTTG 58.767 55.000 0.00 0.00 0.00 2.93
3770 3878 0.536006 GCCTGCTCCTGAGTGTGTTT 60.536 55.000 0.00 0.00 0.00 2.83
3772 3880 2.142761 TGCCTGCTCCTGAGTGTGT 61.143 57.895 0.00 0.00 0.00 3.72
3773 3881 1.670406 GTGCCTGCTCCTGAGTGTG 60.670 63.158 0.00 0.00 0.00 3.82
3775 3883 1.375652 CTGTGCCTGCTCCTGAGTG 60.376 63.158 0.00 0.00 0.00 3.51
3781 3889 3.360340 GTGCACTGTGCCTGCTCC 61.360 66.667 28.17 7.04 44.23 4.70
3788 3896 5.755375 ACATACTTAGATATGTGCACTGTGC 59.245 40.000 25.15 25.15 42.84 4.57
3797 3905 4.594920 AGGGCAGCACATACTTAGATATGT 59.405 41.667 0.00 0.00 44.84 2.29
3798 3906 5.046735 AGAGGGCAGCACATACTTAGATATG 60.047 44.000 0.00 0.00 38.34 1.78
3799 3907 5.090139 AGAGGGCAGCACATACTTAGATAT 58.910 41.667 0.00 0.00 0.00 1.63
3800 3908 4.483950 AGAGGGCAGCACATACTTAGATA 58.516 43.478 0.00 0.00 0.00 1.98
3801 3909 3.312890 AGAGGGCAGCACATACTTAGAT 58.687 45.455 0.00 0.00 0.00 1.98
3802 3910 2.752030 AGAGGGCAGCACATACTTAGA 58.248 47.619 0.00 0.00 0.00 2.10
3803 3911 4.562347 CCATAGAGGGCAGCACATACTTAG 60.562 50.000 0.00 0.00 0.00 2.18
3804 3912 3.324846 CCATAGAGGGCAGCACATACTTA 59.675 47.826 0.00 0.00 0.00 2.24
3805 3913 2.105477 CCATAGAGGGCAGCACATACTT 59.895 50.000 0.00 0.00 0.00 2.24
3806 3914 1.696336 CCATAGAGGGCAGCACATACT 59.304 52.381 0.00 0.00 0.00 2.12
3807 3915 1.417890 ACCATAGAGGGCAGCACATAC 59.582 52.381 0.00 0.00 43.89 2.39
3808 3916 1.806496 ACCATAGAGGGCAGCACATA 58.194 50.000 0.00 0.00 43.89 2.29
3809 3917 1.417890 GTACCATAGAGGGCAGCACAT 59.582 52.381 0.00 0.00 43.89 3.21
3810 3918 0.830648 GTACCATAGAGGGCAGCACA 59.169 55.000 0.00 0.00 43.89 4.57
3811 3919 1.123928 AGTACCATAGAGGGCAGCAC 58.876 55.000 0.00 0.00 43.89 4.40
3812 3920 1.123077 CAGTACCATAGAGGGCAGCA 58.877 55.000 0.00 0.00 43.89 4.41
3813 3921 1.069358 GACAGTACCATAGAGGGCAGC 59.931 57.143 0.00 0.00 43.89 5.25
3814 3922 2.101582 GTGACAGTACCATAGAGGGCAG 59.898 54.545 0.00 0.00 43.89 4.85
3833 3941 4.699735 TCACTTGCATTATTGTGTAGGGTG 59.300 41.667 0.00 0.00 0.00 4.61
3842 3950 4.239304 TGCTTTGCTCACTTGCATTATTG 58.761 39.130 0.00 0.00 42.96 1.90
3846 3956 1.958579 TCTGCTTTGCTCACTTGCATT 59.041 42.857 0.00 0.00 42.96 3.56
3847 3957 1.268899 GTCTGCTTTGCTCACTTGCAT 59.731 47.619 0.00 0.00 42.96 3.96
3848 3958 0.664761 GTCTGCTTTGCTCACTTGCA 59.335 50.000 0.00 0.00 41.65 4.08
3849 3959 0.039708 GGTCTGCTTTGCTCACTTGC 60.040 55.000 0.00 0.00 0.00 4.01
3850 3960 1.002033 GTGGTCTGCTTTGCTCACTTG 60.002 52.381 0.00 0.00 0.00 3.16
3851 3961 1.312815 GTGGTCTGCTTTGCTCACTT 58.687 50.000 0.00 0.00 0.00 3.16
3853 3963 1.518903 GGGTGGTCTGCTTTGCTCAC 61.519 60.000 0.00 0.00 0.00 3.51
3854 3964 1.228245 GGGTGGTCTGCTTTGCTCA 60.228 57.895 0.00 0.00 0.00 4.26
3857 3968 1.973812 GGAGGGTGGTCTGCTTTGC 60.974 63.158 0.00 0.00 0.00 3.68
4039 4151 1.169577 TCAACGAGAGAGAGCTGACC 58.830 55.000 0.00 0.00 0.00 4.02
4210 4322 2.559440 GAGCTGTATGAAGCAGGGAAG 58.441 52.381 0.00 0.00 46.08 3.46
4262 4378 8.956426 CCTGACTTTATGCCAGTAAAAAGATTA 58.044 33.333 0.00 0.00 33.98 1.75


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

AutoCloner maintained by Alex Coulton.