Multiple sequence alignment - TraesCS1D01G374600

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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 TraesCS1D01G374600 chr1D 100.000 4481 0 0 1 4481 451958789 451954309 0.000000e+00 8275.0
1 TraesCS1D01G374600 chr1D 100.000 28 0 0 2316 2343 223162011 223162038 8.000000e-03 52.8
2 TraesCS1D01G374600 chr1D 100.000 28 0 0 2316 2343 254483922 254483895 8.000000e-03 52.8
3 TraesCS1D01G374600 chr1B 92.201 2449 135 28 2 2437 621957975 621955570 0.000000e+00 3413.0
4 TraesCS1D01G374600 chr1B 92.744 1640 82 15 2468 4087 621955575 621953953 0.000000e+00 2335.0
5 TraesCS1D01G374600 chr1B 87.768 327 31 5 4160 4481 621953965 621953643 1.520000e-99 374.0
6 TraesCS1D01G374600 chr1B 87.805 82 6 4 4079 4157 523134842 523134762 4.770000e-15 93.5
7 TraesCS1D01G374600 chr1B 88.571 70 7 1 4086 4155 32128894 32128826 2.870000e-12 84.2
8 TraesCS1D01G374600 chr1A 93.820 1602 68 20 765 2356 546516917 546515337 0.000000e+00 2381.0
9 TraesCS1D01G374600 chr1A 89.759 1201 61 14 3311 4481 546514647 546513479 0.000000e+00 1480.0
10 TraesCS1D01G374600 chr1A 90.440 659 48 5 2468 3118 546515297 546514646 0.000000e+00 854.0
11 TraesCS1D01G374600 chr1A 91.111 45 4 0 2391 2435 546515338 546515294 1.350000e-05 62.1
12 TraesCS1D01G374600 chr7B 94.203 69 4 0 4090 4158 704799025 704799093 6.130000e-19 106.0
13 TraesCS1D01G374600 chr7B 89.706 68 7 0 4091 4158 641527026 641527093 2.220000e-13 87.9
14 TraesCS1D01G374600 chr6A 82.203 118 18 2 3826 3943 556975385 556975499 1.030000e-16 99.0
15 TraesCS1D01G374600 chr5A 91.667 72 4 2 4088 4158 14492639 14492569 1.030000e-16 99.0
16 TraesCS1D01G374600 chr6B 81.356 118 19 2 3826 3943 620180644 620180758 4.770000e-15 93.5
17 TraesCS1D01G374600 chr2A 95.000 60 2 1 4100 4159 30196695 30196753 4.770000e-15 93.5
18 TraesCS1D01G374600 chr2B 91.803 61 5 0 4099 4159 793314670 793314610 7.990000e-13 86.1
19 TraesCS1D01G374600 chrUn 100.000 28 0 0 2316 2343 443804163 443804190 8.000000e-03 52.8
20 TraesCS1D01G374600 chrUn 100.000 28 0 0 2316 2343 445362361 445362334 8.000000e-03 52.8
21 TraesCS1D01G374600 chr6D 100.000 28 0 0 2316 2343 336543396 336543369 8.000000e-03 52.8
22 TraesCS1D01G374600 chr6D 100.000 28 0 0 2316 2343 427829903 427829876 8.000000e-03 52.8
23 TraesCS1D01G374600 chr6D 100.000 28 0 0 2316 2343 431396953 431396980 8.000000e-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 TraesCS1D01G374600 chr1D 451954309 451958789 4480 True 8275.000000 8275 100.000000 1 4481 1 chr1D.!!$R2 4480
1 TraesCS1D01G374600 chr1B 621953643 621957975 4332 True 2040.666667 3413 90.904333 2 4481 3 chr1B.!!$R3 4479
2 TraesCS1D01G374600 chr1A 546513479 546516917 3438 True 1194.275000 2381 91.282500 765 4481 4 chr1A.!!$R1 3716

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
85 86 0.025770 CACAACTTTTCGTGCGTCGT 59.974 50.0 0.00 0.0 40.80 4.34 F
373 375 0.040067 GCTCCAAACCGAAGCTGTTG 60.040 55.0 0.00 0.0 33.23 3.33 F
458 460 0.322277 CAGTGATGGTTGAGGCTGCT 60.322 55.0 0.00 0.0 0.00 4.24 F
2034 2050 0.106419 TTGACCCAACCAGGTTCCAC 60.106 55.0 0.12 0.0 41.42 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1751 0.961019 TGCGCTTTTCCTTTGAGCAT 59.039 45.000 9.73 0.0 36.22 3.79 R
1922 1938 1.067916 CACAGCCAAACTTGCCACC 59.932 57.895 0.00 0.0 0.00 4.61 R
2104 2121 3.668447 ACAGGAATGCAACTAGTCACAG 58.332 45.455 0.00 0.0 0.00 3.66 R
3735 3782 0.843309 TGAAGACAAGGACAAGGCCA 59.157 50.000 5.01 0.0 0.00 5.36 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
31 32 3.242936 TGAGCCGAAAAAGAAAGGAAACG 60.243 43.478 0.00 0.00 0.00 3.60
41 42 6.648879 AAAGAAAGGAAACGATTGGAATCA 57.351 33.333 0.00 0.00 35.11 2.57
42 43 6.648879 AAGAAAGGAAACGATTGGAATCAA 57.351 33.333 0.00 0.00 35.11 2.57
59 60 5.337009 GGAATCAACAAGCCAATCTCACAAT 60.337 40.000 0.00 0.00 0.00 2.71
66 67 1.202268 GCCAATCTCACAATGAGCTGC 60.202 52.381 0.00 0.00 43.95 5.25
75 76 3.130869 TCACAATGAGCTGCACAACTTTT 59.869 39.130 3.43 0.00 0.00 2.27
76 77 3.488310 CACAATGAGCTGCACAACTTTTC 59.512 43.478 3.43 0.00 0.00 2.29
77 78 2.693797 ATGAGCTGCACAACTTTTCG 57.306 45.000 3.43 0.00 0.00 3.46
78 79 1.378531 TGAGCTGCACAACTTTTCGT 58.621 45.000 1.02 0.00 0.00 3.85
79 80 1.063912 TGAGCTGCACAACTTTTCGTG 59.936 47.619 1.02 0.00 36.18 4.35
84 85 2.753416 CACAACTTTTCGTGCGTCG 58.247 52.632 0.00 0.00 41.41 5.12
85 86 0.025770 CACAACTTTTCGTGCGTCGT 59.974 50.000 0.00 0.00 40.80 4.34
86 87 1.255859 CACAACTTTTCGTGCGTCGTA 59.744 47.619 0.00 0.00 40.80 3.43
87 88 2.097104 CACAACTTTTCGTGCGTCGTAT 60.097 45.455 0.00 0.00 40.80 3.06
88 89 2.540931 ACAACTTTTCGTGCGTCGTATT 59.459 40.909 0.00 0.00 40.80 1.89
89 90 3.001533 ACAACTTTTCGTGCGTCGTATTT 59.998 39.130 0.00 0.00 40.80 1.40
90 91 3.429061 ACTTTTCGTGCGTCGTATTTC 57.571 42.857 0.00 0.00 40.80 2.17
91 92 3.054878 ACTTTTCGTGCGTCGTATTTCT 58.945 40.909 0.00 0.00 40.80 2.52
92 93 4.229096 ACTTTTCGTGCGTCGTATTTCTA 58.771 39.130 0.00 0.00 40.80 2.10
103 104 4.261363 CGTCGTATTTCTACCCCTTCCTAC 60.261 50.000 0.00 0.00 0.00 3.18
120 121 3.805497 CCCTTACCCCTTCCCCGC 61.805 72.222 0.00 0.00 0.00 6.13
134 135 3.479203 CCGCCAGCCCTGTCCATA 61.479 66.667 0.00 0.00 0.00 2.74
137 138 1.533711 GCCAGCCCTGTCCATACAT 59.466 57.895 0.00 0.00 34.37 2.29
178 179 2.177669 CCCATCTCTCTCCCTCTCTTCT 59.822 54.545 0.00 0.00 0.00 2.85
187 188 5.015817 TCTCTCCCTCTCTTCTTCTACCTTT 59.984 44.000 0.00 0.00 0.00 3.11
189 190 4.017808 TCCCTCTCTTCTTCTACCTTTCG 58.982 47.826 0.00 0.00 0.00 3.46
192 193 2.496470 TCTCTTCTTCTACCTTTCGCCC 59.504 50.000 0.00 0.00 0.00 6.13
207 208 4.578898 CCCGCGCGCATGTACCTA 62.579 66.667 32.61 0.00 0.00 3.08
214 215 0.464452 GCGCATGTACCTACCTCCTT 59.536 55.000 0.30 0.00 0.00 3.36
237 238 1.911471 GCTCCTTCTCCCTCCCTTG 59.089 63.158 0.00 0.00 0.00 3.61
250 251 2.192861 CCCTTGTCGCAGCAACCAA 61.193 57.895 0.00 0.00 0.00 3.67
252 253 1.008538 CTTGTCGCAGCAACCAACC 60.009 57.895 0.00 0.00 0.00 3.77
253 254 1.723608 CTTGTCGCAGCAACCAACCA 61.724 55.000 0.00 0.00 0.00 3.67
254 255 1.723608 TTGTCGCAGCAACCAACCAG 61.724 55.000 0.00 0.00 0.00 4.00
255 256 3.286751 TCGCAGCAACCAACCAGC 61.287 61.111 0.00 0.00 0.00 4.85
277 279 0.625849 GGATGCTCCCCTTTTCCTCA 59.374 55.000 0.00 0.00 0.00 3.86
289 291 1.523154 TTTCCTCATGCGCAACCACC 61.523 55.000 17.11 0.00 0.00 4.61
343 345 4.960938 TGTTGTCAATCTACTGAAGCTGT 58.039 39.130 0.00 0.00 0.00 4.40
353 355 4.043200 GAAGCTGTTGCACGGGGC 62.043 66.667 0.00 0.00 42.74 5.80
367 369 3.431725 GGGCGCTCCAAACCGAAG 61.432 66.667 7.64 0.00 35.00 3.79
368 370 4.103103 GGCGCTCCAAACCGAAGC 62.103 66.667 7.64 0.00 0.00 3.86
373 375 0.040067 GCTCCAAACCGAAGCTGTTG 60.040 55.000 0.00 0.00 33.23 3.33
375 377 1.007387 CCAAACCGAAGCTGTTGCC 60.007 57.895 0.00 0.00 40.80 4.52
383 385 1.238439 GAAGCTGTTGCCAGTTAGCA 58.762 50.000 0.00 0.00 41.02 3.49
384 386 1.815003 GAAGCTGTTGCCAGTTAGCAT 59.185 47.619 0.00 0.00 43.64 3.79
386 388 0.883833 GCTGTTGCCAGTTAGCATGT 59.116 50.000 0.00 0.00 43.64 3.21
410 412 3.272847 GGGACCCCCAACCACCAT 61.273 66.667 0.00 0.00 44.65 3.55
413 415 1.155155 GACCCCCAACCACCATTGT 59.845 57.895 0.00 0.00 0.00 2.71
421 423 2.428902 CCACCATTGTTGCGTGCG 60.429 61.111 0.00 0.00 0.00 5.34
458 460 0.322277 CAGTGATGGTTGAGGCTGCT 60.322 55.000 0.00 0.00 0.00 4.24
574 576 7.653783 CAACCGACAATGATAAATTTTTCGAC 58.346 34.615 0.00 0.00 0.00 4.20
583 585 6.548171 TGATAAATTTTTCGACCGATGAACC 58.452 36.000 0.00 0.00 0.00 3.62
594 596 2.726691 GATGAACCGACGGTGTGCG 61.727 63.158 22.53 0.00 35.34 5.34
630 632 2.858974 CACCCCTCCACCCAACCT 60.859 66.667 0.00 0.00 0.00 3.50
671 673 2.095853 CGGTTCACATTCCCATTTCTCG 59.904 50.000 0.00 0.00 0.00 4.04
691 693 8.804688 TTCTCGTGTTATGTTTTAATTTTGGG 57.195 30.769 0.00 0.00 0.00 4.12
692 694 7.942990 TCTCGTGTTATGTTTTAATTTTGGGT 58.057 30.769 0.00 0.00 0.00 4.51
693 695 8.077386 TCTCGTGTTATGTTTTAATTTTGGGTC 58.923 33.333 0.00 0.00 0.00 4.46
694 696 7.942990 TCGTGTTATGTTTTAATTTTGGGTCT 58.057 30.769 0.00 0.00 0.00 3.85
695 697 7.863375 TCGTGTTATGTTTTAATTTTGGGTCTG 59.137 33.333 0.00 0.00 0.00 3.51
696 698 7.863375 CGTGTTATGTTTTAATTTTGGGTCTGA 59.137 33.333 0.00 0.00 0.00 3.27
697 699 9.535878 GTGTTATGTTTTAATTTTGGGTCTGAA 57.464 29.630 0.00 0.00 0.00 3.02
780 782 9.770097 TTATGTCATGAAAGATTCAGACCTATC 57.230 33.333 0.00 0.00 43.98 2.08
788 795 7.550551 TGAAAGATTCAGACCTATCACACATTC 59.449 37.037 0.00 0.00 34.08 2.67
798 805 6.411376 ACCTATCACACATTCGTAAAATGGA 58.589 36.000 3.12 0.00 32.14 3.41
813 820 7.757624 TCGTAAAATGGATAAATCAAAACAGGC 59.242 33.333 0.00 0.00 0.00 4.85
907 914 2.024871 GCGACAGACGATCCCGAG 59.975 66.667 0.00 0.00 45.77 4.63
1294 1306 1.360551 CTCCTGCGATCCGGTAGTG 59.639 63.158 0.00 0.00 0.00 2.74
1347 1359 0.329596 AGGGTTCCCTCTTGTGATGC 59.670 55.000 4.31 0.00 0.00 3.91
1407 1419 2.049433 CGTTCACGGCGGAGACTT 60.049 61.111 13.24 0.00 35.37 3.01
1630 1642 4.994852 TGCACGAGATTAGTACTGCTTTTT 59.005 37.500 5.39 0.00 0.00 1.94
1645 1658 3.761218 TGCTTTTTCAAACCACTCAGTGA 59.239 39.130 6.30 0.00 35.23 3.41
1880 1896 4.419282 AGAAGAAATGGGATGCAAGGAAA 58.581 39.130 0.00 0.00 0.00 3.13
1922 1938 1.078709 TTTCATCTCTTTCTGCGGCG 58.921 50.000 0.51 0.51 0.00 6.46
2034 2050 0.106419 TTGACCCAACCAGGTTCCAC 60.106 55.000 0.12 0.00 41.42 4.02
2074 2090 4.400845 CAAGTGAATGTCGCAATCAAGAG 58.599 43.478 0.21 0.00 0.00 2.85
2094 2111 4.058817 GAGAGTGCTTTTTCTCTCGGAAA 58.941 43.478 6.46 0.00 44.28 3.13
2104 2121 8.070769 GCTTTTTCTCTCGGAAATTGATATACC 58.929 37.037 0.00 0.00 42.63 2.73
2105 2122 9.331282 CTTTTTCTCTCGGAAATTGATATACCT 57.669 33.333 0.00 0.00 42.63 3.08
2120 2137 7.124573 TGATATACCTGTGACTAGTTGCATT 57.875 36.000 0.00 0.00 0.00 3.56
2121 2138 7.210174 TGATATACCTGTGACTAGTTGCATTC 58.790 38.462 0.00 0.00 0.00 2.67
2123 2140 2.639839 ACCTGTGACTAGTTGCATTCCT 59.360 45.455 0.00 0.00 0.00 3.36
2129 2146 5.468746 TGTGACTAGTTGCATTCCTGTAAAC 59.531 40.000 0.00 0.00 0.00 2.01
2133 2150 7.880713 TGACTAGTTGCATTCCTGTAAACAATA 59.119 33.333 0.00 0.00 0.00 1.90
2134 2151 8.268850 ACTAGTTGCATTCCTGTAAACAATAG 57.731 34.615 0.00 0.00 0.00 1.73
2136 2153 9.378551 CTAGTTGCATTCCTGTAAACAATAGTA 57.621 33.333 0.00 0.00 0.00 1.82
2137 2154 8.268850 AGTTGCATTCCTGTAAACAATAGTAG 57.731 34.615 0.00 0.00 0.00 2.57
2138 2155 7.336931 AGTTGCATTCCTGTAAACAATAGTAGG 59.663 37.037 0.00 0.00 0.00 3.18
2139 2156 6.953101 TGCATTCCTGTAAACAATAGTAGGA 58.047 36.000 0.00 0.00 32.81 2.94
2140 2157 7.573710 TGCATTCCTGTAAACAATAGTAGGAT 58.426 34.615 0.00 0.00 34.57 3.24
2141 2158 8.052748 TGCATTCCTGTAAACAATAGTAGGATT 58.947 33.333 0.00 0.00 34.57 3.01
2142 2159 9.555727 GCATTCCTGTAAACAATAGTAGGATTA 57.444 33.333 0.00 0.00 34.57 1.75
2174 2191 4.815040 TTGGCATCATTTGTTGCTTTTG 57.185 36.364 12.04 0.00 39.85 2.44
2181 2201 6.358558 GCATCATTTGTTGCTTTTGAAATGTG 59.641 34.615 6.40 0.00 37.19 3.21
2188 2208 5.199726 GTTGCTTTTGAAATGTGCATGTTC 58.800 37.500 0.00 0.00 33.50 3.18
2216 2236 4.601406 ACCCCAATTCAGTAGGCATTTA 57.399 40.909 0.00 0.00 0.00 1.40
2238 2258 0.467844 TGCTTCTTGCTTTGCTGGGA 60.468 50.000 0.00 0.00 43.37 4.37
2243 2263 0.248289 CTTGCTTTGCTGGGAATGGG 59.752 55.000 0.00 0.00 0.00 4.00
2372 2392 9.864034 CCTTGTCATTAACGTTTGTCATATATC 57.136 33.333 5.91 0.00 0.00 1.63
2421 2441 5.124936 GGTGGTTAACTACTTTTATGGCCAG 59.875 44.000 19.90 0.00 0.00 4.85
2423 2443 4.097437 GGTTAACTACTTTTATGGCCAGCC 59.903 45.833 13.05 0.38 0.00 4.85
2431 2451 4.166144 ACTTTTATGGCCAGCCTGTATAGT 59.834 41.667 13.05 3.53 36.94 2.12
2432 2452 4.788925 TTTATGGCCAGCCTGTATAGTT 57.211 40.909 13.05 0.00 36.94 2.24
2433 2453 2.645838 ATGGCCAGCCTGTATAGTTG 57.354 50.000 13.05 0.00 36.94 3.16
2434 2454 1.285280 TGGCCAGCCTGTATAGTTGT 58.715 50.000 0.00 0.00 36.94 3.32
2435 2455 2.473070 TGGCCAGCCTGTATAGTTGTA 58.527 47.619 0.00 0.00 36.94 2.41
2436 2456 2.169769 TGGCCAGCCTGTATAGTTGTAC 59.830 50.000 0.00 0.00 36.94 2.90
2437 2457 2.434702 GGCCAGCCTGTATAGTTGTACT 59.565 50.000 0.00 0.00 0.00 2.73
2438 2458 3.118371 GGCCAGCCTGTATAGTTGTACTT 60.118 47.826 0.00 0.00 0.00 2.24
2439 2459 4.514401 GCCAGCCTGTATAGTTGTACTTT 58.486 43.478 0.00 0.00 0.00 2.66
2440 2460 4.941873 GCCAGCCTGTATAGTTGTACTTTT 59.058 41.667 0.00 0.00 0.00 2.27
2441 2461 5.064834 GCCAGCCTGTATAGTTGTACTTTTC 59.935 44.000 0.00 0.00 0.00 2.29
2442 2462 6.407202 CCAGCCTGTATAGTTGTACTTTTCT 58.593 40.000 0.00 0.00 0.00 2.52
2443 2463 6.879458 CCAGCCTGTATAGTTGTACTTTTCTT 59.121 38.462 0.00 0.00 0.00 2.52
2444 2464 7.390718 CCAGCCTGTATAGTTGTACTTTTCTTT 59.609 37.037 0.00 0.00 0.00 2.52
2445 2465 8.784043 CAGCCTGTATAGTTGTACTTTTCTTTT 58.216 33.333 0.00 0.00 0.00 2.27
2446 2466 9.350951 AGCCTGTATAGTTGTACTTTTCTTTTT 57.649 29.630 0.00 0.00 0.00 1.94
2508 2528 4.943705 TGTTCACATCTTCATCCTAAAGCC 59.056 41.667 0.00 0.00 0.00 4.35
2569 2589 9.884465 AAGAGCTAATTTCGAATAATAATGTGC 57.116 29.630 0.00 0.00 0.00 4.57
2585 2605 8.651589 AATAATGTGCTAGGAGCTACTGTATA 57.348 34.615 9.36 0.00 42.97 1.47
2592 2612 5.708230 GCTAGGAGCTACTGTATATGTGAGT 59.292 44.000 9.36 0.00 38.45 3.41
2593 2613 6.207810 GCTAGGAGCTACTGTATATGTGAGTT 59.792 42.308 9.36 0.00 38.45 3.01
2594 2614 6.642707 AGGAGCTACTGTATATGTGAGTTC 57.357 41.667 0.00 0.00 0.00 3.01
2595 2615 6.129874 AGGAGCTACTGTATATGTGAGTTCA 58.870 40.000 0.00 0.00 0.00 3.18
2596 2616 6.039941 AGGAGCTACTGTATATGTGAGTTCAC 59.960 42.308 0.00 5.33 46.59 3.18
2632 2652 6.646240 TGGTCCGTAACTTGTGTACTTTAATC 59.354 38.462 0.00 0.00 0.00 1.75
2780 2801 4.331108 AGCTCTTTTCTCAGAATGGGTTC 58.669 43.478 0.00 0.00 38.22 3.62
2787 2808 3.454858 TCTCAGAATGGGTTCCTAAGCT 58.545 45.455 0.00 0.00 38.22 3.74
2888 2909 2.284263 TTTGCACGCACATTGTTCAA 57.716 40.000 0.00 0.00 0.00 2.69
2900 2921 5.389098 GCACATTGTTCAAATCAGTGATTGC 60.389 40.000 18.94 10.70 32.14 3.56
2903 2924 5.518848 TTGTTCAAATCAGTGATTGCTGT 57.481 34.783 18.94 0.41 37.70 4.40
2970 3012 7.362834 CCATGTTGCTAATGGTCTATTGTTTCA 60.363 37.037 5.11 0.00 39.87 2.69
3119 3161 5.180868 CCATTTCAGGTAGCTCTATTCATGC 59.819 44.000 0.00 0.00 0.00 4.06
3120 3162 5.620738 TTTCAGGTAGCTCTATTCATGCT 57.379 39.130 0.00 0.00 40.43 3.79
3130 3172 6.882656 AGCTCTATTCATGCTTCTTCTGTAA 58.117 36.000 0.00 0.00 32.61 2.41
3191 3233 6.642950 CGAAAAGAATATCGGAGTAATCAGCT 59.357 38.462 0.00 0.00 35.49 4.24
3227 3269 9.374711 TGGAGGTTAGATTATTTTGTTTCCTTT 57.625 29.630 0.00 0.00 0.00 3.11
3228 3270 9.639601 GGAGGTTAGATTATTTTGTTTCCTTTG 57.360 33.333 0.00 0.00 0.00 2.77
3230 3272 9.374711 AGGTTAGATTATTTTGTTTCCTTTGGA 57.625 29.630 0.00 0.00 0.00 3.53
3260 3302 8.084073 CACATAATGAAATTGACTTCCACTTGT 58.916 33.333 0.00 0.00 36.99 3.16
3271 3313 5.473162 TGACTTCCACTTGTATCAAATGTGG 59.527 40.000 11.92 11.92 46.71 4.17
3273 3315 5.833131 ACTTCCACTTGTATCAAATGTGGTT 59.167 36.000 15.43 4.83 45.82 3.67
3299 3341 0.176449 GCCCCTTTGCATTCCATGAC 59.824 55.000 0.00 0.00 0.00 3.06
3369 3411 4.037089 TCAGACTTGTTACACTCGCAACTA 59.963 41.667 0.00 0.00 0.00 2.24
3370 3412 4.743151 CAGACTTGTTACACTCGCAACTAA 59.257 41.667 0.00 0.00 0.00 2.24
3375 3417 2.074547 TACACTCGCAACTAACAGCC 57.925 50.000 0.00 0.00 0.00 4.85
3394 3436 5.764192 ACAGCCATTTTTAGGTGTACGTTTA 59.236 36.000 0.00 0.00 42.55 2.01
3456 3500 3.058570 CGCTTGTTGGTTGTACAATAGCA 60.059 43.478 12.26 9.55 39.11 3.49
3470 3514 8.862325 TGTACAATAGCATATTTAATGGGGAG 57.138 34.615 0.00 0.00 0.00 4.30
3489 3536 6.495181 TGGGGAGATCTGTATGAGAAATACTC 59.505 42.308 0.00 0.00 45.11 2.59
3500 3547 5.344743 TGAGAAATACTCCTAGTTGGCAG 57.655 43.478 0.00 0.00 44.34 4.85
3581 3628 8.099537 AGTCTATTTTGTATCTCTGGCCATATG 58.900 37.037 5.51 0.00 0.00 1.78
3600 3647 3.228188 TGAAGTGCCCTTCTGTTGAAT 57.772 42.857 10.38 0.00 46.07 2.57
3615 3662 2.926838 GTTGAATTGGTTGCGTGTGTTT 59.073 40.909 0.00 0.00 0.00 2.83
3674 3721 5.043903 ACAGATGATGGTCGTCGAATTTAG 58.956 41.667 0.00 0.00 37.48 1.85
3795 3868 4.408921 TGAACTTCTCTGAGGTTTCTCCAA 59.591 41.667 4.59 0.00 39.23 3.53
3803 3876 3.674997 TGAGGTTTCTCCAAATTCTCCG 58.325 45.455 0.00 0.00 39.23 4.63
3891 3964 2.551270 TCTCTTTGGGCTATGACCACT 58.449 47.619 0.00 0.00 42.46 4.00
3917 3990 2.623418 TGGAGGTATGTCCACTCACT 57.377 50.000 0.00 0.00 41.99 3.41
3918 3991 2.179427 TGGAGGTATGTCCACTCACTG 58.821 52.381 0.00 0.00 41.99 3.66
3991 4064 3.760035 GCGACGCTTCTCCCTGGA 61.760 66.667 13.73 0.00 0.00 3.86
4032 4106 0.326595 TGCCCCTCGCATTGTTAAGA 59.673 50.000 0.00 0.00 44.64 2.10
4107 4181 8.446273 CGATTCAAAACAGACTGATGTATTTCT 58.554 33.333 10.08 0.00 31.70 2.52
4108 4182 9.552114 GATTCAAAACAGACTGATGTATTTCTG 57.448 33.333 10.08 0.00 41.14 3.02
4131 4205 9.334947 TCTGTTGATTGCAAAATTAATGGAAAA 57.665 25.926 1.71 0.00 35.42 2.29
4177 4251 5.898630 AAATTGGTTTTCGATTCGGTTTG 57.101 34.783 6.18 0.00 0.00 2.93
4231 4305 0.671796 TCGATATACACAGGTGGCGG 59.328 55.000 4.24 0.00 34.19 6.13
4238 4312 2.847234 ACAGGTGGCGGTTCCTCA 60.847 61.111 0.00 0.00 35.26 3.86
4254 4328 2.640826 TCCTCACCCGGTGACTATTTTT 59.359 45.455 16.73 0.00 37.67 1.94
4279 4358 2.550978 ACGACAGTTCTGAAAGTGGTG 58.449 47.619 6.83 3.51 39.69 4.17
4394 4473 6.754209 CAGTAAGACTCGCATCTTTTATCTGT 59.246 38.462 6.35 0.00 39.65 3.41
4397 4476 5.105752 AGACTCGCATCTTTTATCTGTCAC 58.894 41.667 0.00 0.00 0.00 3.67
4416 4495 6.319715 TGTCACTATACCCAGGAGCATTATA 58.680 40.000 0.00 0.00 0.00 0.98
4425 4504 4.539870 CCAGGAGCATTATACATTTTGCG 58.460 43.478 0.00 0.00 40.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.651704 TGATTCCAATCGTTTCCTTTCTTTTTC 59.348 33.333 0.00 0.00 38.26 2.29
24 25 4.321230 GCTTGTTGATTCCAATCGTTTCCT 60.321 41.667 0.00 0.00 38.26 3.36
59 60 1.063912 CACGAAAAGTTGTGCAGCTCA 59.936 47.619 0.00 0.00 0.00 4.26
66 67 0.025770 ACGACGCACGAAAAGTTGTG 59.974 50.000 9.43 0.00 45.77 3.33
75 76 1.202177 GGGTAGAAATACGACGCACGA 60.202 52.381 9.43 0.00 45.77 4.35
77 78 1.135721 AGGGGTAGAAATACGACGCAC 59.864 52.381 0.00 0.00 38.40 5.34
78 79 1.477553 AGGGGTAGAAATACGACGCA 58.522 50.000 0.00 0.00 38.40 5.24
79 80 2.467838 GAAGGGGTAGAAATACGACGC 58.532 52.381 0.00 0.00 36.62 5.19
80 81 2.692041 AGGAAGGGGTAGAAATACGACG 59.308 50.000 0.00 0.00 0.00 5.12
81 82 4.038522 GGTAGGAAGGGGTAGAAATACGAC 59.961 50.000 0.00 0.00 0.00 4.34
83 84 3.323115 GGGTAGGAAGGGGTAGAAATACG 59.677 52.174 0.00 0.00 0.00 3.06
84 85 4.564799 AGGGTAGGAAGGGGTAGAAATAC 58.435 47.826 0.00 0.00 0.00 1.89
85 86 4.932291 AGGGTAGGAAGGGGTAGAAATA 57.068 45.455 0.00 0.00 0.00 1.40
86 87 3.816967 AGGGTAGGAAGGGGTAGAAAT 57.183 47.619 0.00 0.00 0.00 2.17
87 88 3.590432 AAGGGTAGGAAGGGGTAGAAA 57.410 47.619 0.00 0.00 0.00 2.52
88 89 3.310879 GGTAAGGGTAGGAAGGGGTAGAA 60.311 52.174 0.00 0.00 0.00 2.10
89 90 2.248423 GGTAAGGGTAGGAAGGGGTAGA 59.752 54.545 0.00 0.00 0.00 2.59
90 91 2.687297 GGTAAGGGTAGGAAGGGGTAG 58.313 57.143 0.00 0.00 0.00 3.18
91 92 1.294986 GGGTAAGGGTAGGAAGGGGTA 59.705 57.143 0.00 0.00 0.00 3.69
92 93 0.045316 GGGTAAGGGTAGGAAGGGGT 59.955 60.000 0.00 0.00 0.00 4.95
103 104 3.805497 GCGGGGAAGGGGTAAGGG 61.805 72.222 0.00 0.00 0.00 3.95
120 121 2.442236 AAATGTATGGACAGGGCTGG 57.558 50.000 0.00 0.00 39.50 4.85
178 179 2.125832 CGCGGGCGAAAGGTAGAA 60.126 61.111 7.38 0.00 42.83 2.10
192 193 3.327754 GGTAGGTACATGCGCGCG 61.328 66.667 28.44 28.44 0.00 6.86
197 198 2.037381 GCCTAAGGAGGTAGGTACATGC 59.963 54.545 0.00 0.00 45.78 4.06
207 208 1.306226 AAGGAGCGCCTAAGGAGGT 60.306 57.895 10.31 0.00 46.28 3.85
214 215 1.455959 GAGGGAGAAGGAGCGCCTA 60.456 63.158 10.31 0.00 46.28 3.93
217 218 3.855853 GGGAGGGAGAAGGAGCGC 61.856 72.222 0.00 0.00 0.00 5.92
219 220 0.912006 ACAAGGGAGGGAGAAGGAGC 60.912 60.000 0.00 0.00 0.00 4.70
237 238 2.639286 CTGGTTGGTTGCTGCGAC 59.361 61.111 11.66 11.66 0.00 5.19
273 274 3.803082 CGGTGGTTGCGCATGAGG 61.803 66.667 12.75 0.00 0.00 3.86
289 291 3.217743 GTAGGACCCCTCCTCGCG 61.218 72.222 0.00 0.00 44.59 5.87
300 302 5.756734 ACATGTGTGTGCCTTTTGTAGGAC 61.757 45.833 0.00 0.00 46.59 3.85
302 304 3.068024 AACATGTGTGTGCCTTTTGTAGG 59.932 43.478 0.00 0.00 41.77 3.18
373 375 2.793946 CGGCACATGCTAACTGGC 59.206 61.111 3.48 0.00 41.70 4.85
375 377 2.793946 GGCGGCACATGCTAACTG 59.206 61.111 3.07 0.00 41.70 3.16
400 402 0.597118 CACGCAACAATGGTGGTTGG 60.597 55.000 0.00 1.14 44.41 3.77
409 411 3.430862 ATCGCCGCACGCAACAAT 61.431 55.556 0.00 0.00 43.23 2.71
410 412 4.382114 CATCGCCGCACGCAACAA 62.382 61.111 0.00 0.00 43.23 2.83
426 428 3.585020 CACTGCTTGTGGCGCACA 61.585 61.111 10.83 9.30 45.43 4.57
447 449 1.288127 CCTTGCAAGCAGCCTCAAC 59.712 57.895 21.43 0.00 44.83 3.18
458 460 1.275856 GTTGAATCATGGCCCTTGCAA 59.724 47.619 0.00 0.00 40.13 4.08
530 532 4.722700 AGCCATCGTGGTGCCACC 62.723 66.667 7.01 7.01 43.49 4.61
537 539 3.803082 CGGTTGCAGCCATCGTGG 61.803 66.667 20.42 0.00 41.55 4.94
620 622 0.039180 GGAGGGTTAAGGTTGGGTGG 59.961 60.000 0.00 0.00 0.00 4.61
630 632 0.337428 AGGGTAGCTCGGAGGGTTAA 59.663 55.000 7.20 0.00 0.00 2.01
671 673 9.535878 TTCAGACCCAAAATTAAAACATAACAC 57.464 29.630 0.00 0.00 0.00 3.32
724 726 7.411486 ACAAGAATATATCATACTCCCTCCG 57.589 40.000 0.00 0.00 0.00 4.63
755 757 8.927411 TGATAGGTCTGAATCTTTCATGACATA 58.073 33.333 0.00 13.74 39.30 2.29
757 759 7.044181 GTGATAGGTCTGAATCTTTCATGACA 58.956 38.462 0.00 0.00 39.30 3.58
779 781 8.951243 TGATTTATCCATTTTACGAATGTGTGA 58.049 29.630 0.00 0.00 0.00 3.58
780 782 9.566530 TTGATTTATCCATTTTACGAATGTGTG 57.433 29.630 0.00 0.00 0.00 3.82
788 795 7.253618 CGCCTGTTTTGATTTATCCATTTTACG 60.254 37.037 0.00 0.00 0.00 3.18
798 805 2.415357 CGGTGCGCCTGTTTTGATTTAT 60.415 45.455 15.69 0.00 0.00 1.40
1305 1317 1.722011 GCTACGCTTTCTACCAGCAA 58.278 50.000 0.00 0.00 37.07 3.91
1311 1323 1.925185 CCCTTTCGCTACGCTTTCTAC 59.075 52.381 0.00 0.00 0.00 2.59
1334 1346 1.372087 GCTTCCGCATCACAAGAGGG 61.372 60.000 0.00 0.00 35.78 4.30
1407 1419 1.348696 TGCAGCCAAGTTCATCTCTGA 59.651 47.619 0.00 0.00 0.00 3.27
1630 1642 3.054728 TCTGGTTTCACTGAGTGGTTTGA 60.055 43.478 13.33 1.80 33.87 2.69
1645 1658 2.488153 GCAGCGGAAATAGTTCTGGTTT 59.512 45.455 13.39 0.00 46.39 3.27
1731 1747 3.181497 GCGCTTTTCCTTTGAGCATGATA 60.181 43.478 0.00 0.00 36.22 2.15
1732 1748 2.416431 GCGCTTTTCCTTTGAGCATGAT 60.416 45.455 0.00 0.00 36.22 2.45
1733 1749 1.068333 GCGCTTTTCCTTTGAGCATGA 60.068 47.619 0.00 0.00 36.22 3.07
1734 1750 1.336148 TGCGCTTTTCCTTTGAGCATG 60.336 47.619 9.73 0.00 36.22 4.06
1735 1751 0.961019 TGCGCTTTTCCTTTGAGCAT 59.039 45.000 9.73 0.00 36.22 3.79
1922 1938 1.067916 CACAGCCAAACTTGCCACC 59.932 57.895 0.00 0.00 0.00 4.61
2034 2050 3.803778 ACTTGCTTGAAAAAGGAAATGCG 59.196 39.130 0.00 0.00 29.74 4.73
2090 2107 9.046296 CAACTAGTCACAGGTATATCAATTTCC 57.954 37.037 0.00 0.00 0.00 3.13
2094 2111 7.124573 TGCAACTAGTCACAGGTATATCAAT 57.875 36.000 0.00 0.00 0.00 2.57
2104 2121 3.668447 ACAGGAATGCAACTAGTCACAG 58.332 45.455 0.00 0.00 0.00 3.66
2105 2122 3.769739 ACAGGAATGCAACTAGTCACA 57.230 42.857 0.00 0.00 0.00 3.58
2137 2154 9.783081 AATGATGCCAAAATAGGAAAATAATCC 57.217 29.630 0.00 0.00 39.96 3.01
2140 2157 9.956640 ACAAATGATGCCAAAATAGGAAAATAA 57.043 25.926 0.00 0.00 0.00 1.40
2141 2158 9.956640 AACAAATGATGCCAAAATAGGAAAATA 57.043 25.926 0.00 0.00 0.00 1.40
2142 2159 8.732531 CAACAAATGATGCCAAAATAGGAAAAT 58.267 29.630 0.00 0.00 0.00 1.82
2143 2160 7.308469 GCAACAAATGATGCCAAAATAGGAAAA 60.308 33.333 4.48 0.00 37.80 2.29
2144 2161 6.149142 GCAACAAATGATGCCAAAATAGGAAA 59.851 34.615 4.48 0.00 37.80 3.13
2145 2162 5.642919 GCAACAAATGATGCCAAAATAGGAA 59.357 36.000 4.48 0.00 37.80 3.36
2146 2163 5.046448 AGCAACAAATGATGCCAAAATAGGA 60.046 36.000 11.43 0.00 43.71 2.94
2147 2164 5.180271 AGCAACAAATGATGCCAAAATAGG 58.820 37.500 11.43 0.00 43.71 2.57
2148 2165 6.730960 AAGCAACAAATGATGCCAAAATAG 57.269 33.333 11.43 0.00 43.71 1.73
2149 2166 7.228108 TCAAAAGCAACAAATGATGCCAAAATA 59.772 29.630 11.43 0.00 43.71 1.40
2150 2167 6.039493 TCAAAAGCAACAAATGATGCCAAAAT 59.961 30.769 11.43 0.00 43.71 1.82
2157 2174 6.358558 GCACATTTCAAAAGCAACAAATGATG 59.641 34.615 9.60 6.08 38.12 3.07
2160 2177 5.570344 TGCACATTTCAAAAGCAACAAATG 58.430 33.333 0.00 0.00 40.55 2.32
2174 2191 5.750067 GGGTATTGATGAACATGCACATTTC 59.250 40.000 6.66 0.00 0.00 2.17
2181 2201 4.942761 ATTGGGGTATTGATGAACATGC 57.057 40.909 0.00 0.00 0.00 4.06
2188 2208 4.520492 GCCTACTGAATTGGGGTATTGATG 59.480 45.833 0.00 0.00 0.00 3.07
2309 2329 9.237846 GGAATTTTCTTATTATCCTTTTGCTCG 57.762 33.333 0.00 0.00 0.00 5.03
2449 2469 9.991906 ACTGTACAAGTACAACTATACAACATT 57.008 29.630 13.45 0.00 44.47 2.71
2450 2470 9.419297 CACTGTACAAGTACAACTATACAACAT 57.581 33.333 13.45 0.00 44.47 2.71
2451 2471 8.631797 TCACTGTACAAGTACAACTATACAACA 58.368 33.333 13.45 0.00 44.47 3.33
2452 2472 9.635520 ATCACTGTACAAGTACAACTATACAAC 57.364 33.333 13.45 0.00 44.47 3.32
2453 2473 9.634163 CATCACTGTACAAGTACAACTATACAA 57.366 33.333 13.45 0.00 44.47 2.41
2454 2474 7.758076 GCATCACTGTACAAGTACAACTATACA 59.242 37.037 13.45 0.00 44.47 2.29
2455 2475 7.974501 AGCATCACTGTACAAGTACAACTATAC 59.025 37.037 13.45 3.99 44.47 1.47
2456 2476 7.973944 CAGCATCACTGTACAAGTACAACTATA 59.026 37.037 13.45 0.33 44.47 1.31
2457 2477 6.813649 CAGCATCACTGTACAAGTACAACTAT 59.186 38.462 13.45 5.24 44.47 2.12
2458 2478 6.156519 CAGCATCACTGTACAAGTACAACTA 58.843 40.000 13.45 3.35 44.47 2.24
2459 2479 4.991056 CAGCATCACTGTACAAGTACAACT 59.009 41.667 13.45 0.47 44.47 3.16
2460 2480 4.152402 CCAGCATCACTGTACAAGTACAAC 59.848 45.833 13.45 1.37 45.68 3.32
2461 2481 4.314961 CCAGCATCACTGTACAAGTACAA 58.685 43.478 13.45 0.78 45.68 2.41
2462 2482 3.306710 CCCAGCATCACTGTACAAGTACA 60.307 47.826 12.09 12.09 45.68 2.90
2463 2483 3.262420 CCCAGCATCACTGTACAAGTAC 58.738 50.000 0.00 3.47 45.68 2.73
2464 2484 2.903784 ACCCAGCATCACTGTACAAGTA 59.096 45.455 0.00 0.00 45.68 2.24
2465 2485 1.699634 ACCCAGCATCACTGTACAAGT 59.300 47.619 0.00 0.00 45.68 3.16
2466 2486 2.079158 CACCCAGCATCACTGTACAAG 58.921 52.381 0.00 0.00 45.68 3.16
2484 2504 5.163713 GGCTTTAGGATGAAGATGTGAACAC 60.164 44.000 0.00 0.00 0.00 3.32
2488 2508 4.842531 TGGCTTTAGGATGAAGATGTGA 57.157 40.909 0.00 0.00 0.00 3.58
2565 2585 5.241728 CACATATACAGTAGCTCCTAGCACA 59.758 44.000 0.00 0.00 45.56 4.57
2569 2589 7.445707 TGAACTCACATATACAGTAGCTCCTAG 59.554 40.741 0.00 0.00 0.00 3.02
2592 2612 2.229792 GGACCAGCTTGTGAATGTGAA 58.770 47.619 0.00 0.00 0.00 3.18
2593 2613 1.877680 CGGACCAGCTTGTGAATGTGA 60.878 52.381 0.00 0.00 0.00 3.58
2594 2614 0.518636 CGGACCAGCTTGTGAATGTG 59.481 55.000 0.00 0.00 0.00 3.21
2595 2615 0.108585 ACGGACCAGCTTGTGAATGT 59.891 50.000 0.00 0.00 0.00 2.71
2596 2616 2.093306 TACGGACCAGCTTGTGAATG 57.907 50.000 0.00 0.00 0.00 2.67
2597 2617 2.038557 AGTTACGGACCAGCTTGTGAAT 59.961 45.455 0.00 0.00 0.00 2.57
2632 2652 1.210931 CAGACTTGGCATGGCAACG 59.789 57.895 29.00 24.53 42.51 4.10
2780 2801 7.091443 CCTGTAACGAGGAATATAAGCTTAGG 58.909 42.308 12.54 0.00 34.69 2.69
2932 2974 7.276218 CCATTAGCAACATGGTAAGTGAAAATG 59.724 37.037 7.87 1.60 42.61 2.32
2987 3029 4.550076 ACTGCAGCAGAAAGTAGAAGAT 57.450 40.909 29.70 0.00 35.18 2.40
2991 3033 3.475566 ACAACTGCAGCAGAAAGTAGA 57.524 42.857 29.70 0.00 35.18 2.59
2992 3034 5.673337 TTAACAACTGCAGCAGAAAGTAG 57.327 39.130 29.70 12.94 35.18 2.57
2995 3037 5.522456 TGATTTAACAACTGCAGCAGAAAG 58.478 37.500 29.70 18.61 35.18 2.62
2996 3038 5.512753 TGATTTAACAACTGCAGCAGAAA 57.487 34.783 29.70 17.77 35.18 2.52
3130 3172 8.632679 CAACAACTTGAGGGCATGTAATATATT 58.367 33.333 2.97 2.97 32.68 1.28
3141 3183 3.568007 GTGATTACAACAACTTGAGGGCA 59.432 43.478 0.00 0.00 0.00 5.36
3153 3195 7.634817 CGATATTCTTTTCGTGGTGATTACAAC 59.365 37.037 0.00 0.00 0.00 3.32
3210 3252 6.878389 TGCCATCCAAAGGAAACAAAATAATC 59.122 34.615 0.00 0.00 34.34 1.75
3227 3269 5.657745 AGTCAATTTCATTATGTGCCATCCA 59.342 36.000 0.00 0.00 0.00 3.41
3228 3270 6.152932 AGTCAATTTCATTATGTGCCATCC 57.847 37.500 0.00 0.00 0.00 3.51
3230 3272 6.154877 TGGAAGTCAATTTCATTATGTGCCAT 59.845 34.615 0.00 0.00 0.00 4.40
3231 3273 5.479724 TGGAAGTCAATTTCATTATGTGCCA 59.520 36.000 0.00 0.00 0.00 4.92
3238 3280 9.513906 TGATACAAGTGGAAGTCAATTTCATTA 57.486 29.630 0.00 0.00 30.52 1.90
3260 3302 5.046950 GGGGCTGTTAAAACCACATTTGATA 60.047 40.000 0.00 0.00 0.00 2.15
3271 3313 2.900716 TGCAAAGGGGCTGTTAAAAC 57.099 45.000 0.00 0.00 34.04 2.43
3273 3315 2.301583 GGAATGCAAAGGGGCTGTTAAA 59.698 45.455 0.00 0.00 34.04 1.52
3299 3341 4.574421 TGGCGTGAAATATTCCACACTATG 59.426 41.667 5.62 0.00 33.13 2.23
3369 3411 4.139038 ACGTACACCTAAAAATGGCTGTT 58.861 39.130 0.00 0.00 0.00 3.16
3370 3412 3.746940 ACGTACACCTAAAAATGGCTGT 58.253 40.909 0.00 0.00 0.00 4.40
3375 3417 7.480542 GTCAGCATAAACGTACACCTAAAAATG 59.519 37.037 0.00 0.00 0.00 2.32
3428 3472 1.034838 ACAACCAACAAGCGCTCCAA 61.035 50.000 12.06 0.00 0.00 3.53
3456 3500 9.566331 TCTCATACAGATCTCCCCATTAAATAT 57.434 33.333 0.00 0.00 0.00 1.28
3470 3514 9.906660 CAACTAGGAGTATTTCTCATACAGATC 57.093 37.037 0.00 0.00 44.40 2.75
3500 3547 9.032420 GTAGTGTAATCTGAGTATAAGGCAAAC 57.968 37.037 0.00 0.00 0.00 2.93
3600 3647 3.305398 AAGAAAAACACACGCAACCAA 57.695 38.095 0.00 0.00 0.00 3.67
3674 3721 3.446570 GGCAGCTGCATGGTGTCC 61.447 66.667 37.63 15.84 45.23 4.02
3735 3782 0.843309 TGAAGACAAGGACAAGGCCA 59.157 50.000 5.01 0.00 0.00 5.36
3738 3785 2.619074 GGGGATGAAGACAAGGACAAGG 60.619 54.545 0.00 0.00 0.00 3.61
3739 3786 2.307098 AGGGGATGAAGACAAGGACAAG 59.693 50.000 0.00 0.00 0.00 3.16
3740 3787 2.305927 GAGGGGATGAAGACAAGGACAA 59.694 50.000 0.00 0.00 0.00 3.18
3741 3788 1.909302 GAGGGGATGAAGACAAGGACA 59.091 52.381 0.00 0.00 0.00 4.02
3743 3790 1.584724 GGAGGGGATGAAGACAAGGA 58.415 55.000 0.00 0.00 0.00 3.36
3795 3868 1.600023 TGGCGTTTTGACGGAGAATT 58.400 45.000 0.93 0.00 0.00 2.17
3803 3876 2.225491 TGCTACTGAATGGCGTTTTGAC 59.775 45.455 0.00 0.00 37.70 3.18
3891 3964 0.899720 GGACATACCTCCACCAACGA 59.100 55.000 0.00 0.00 35.41 3.85
3917 3990 6.581171 AGTGATATGATCGTAGAGAATGCA 57.419 37.500 0.41 0.00 43.63 3.96
3918 3991 7.087007 TGAAGTGATATGATCGTAGAGAATGC 58.913 38.462 0.41 0.00 43.63 3.56
4032 4106 7.044798 TGAGAAACCAAAACCGAATCAAAAAT 58.955 30.769 0.00 0.00 0.00 1.82
4048 4122 6.227522 TGATTCAGTTTACGATGAGAAACCA 58.772 36.000 0.00 0.00 36.41 3.67
4107 4181 8.566260 CCTTTTCCATTAATTTTGCAATCAACA 58.434 29.630 0.00 0.00 30.75 3.33
4108 4182 8.022550 CCCTTTTCCATTAATTTTGCAATCAAC 58.977 33.333 0.00 0.00 30.75 3.18
4124 4198 1.678970 GGCTCGCACCCTTTTCCAT 60.679 57.895 0.00 0.00 0.00 3.41
4158 4232 4.373348 AACAAACCGAATCGAAAACCAA 57.627 36.364 3.36 0.00 0.00 3.67
4159 4233 4.334759 TGTAACAAACCGAATCGAAAACCA 59.665 37.500 3.36 0.00 0.00 3.67
4177 4251 8.122952 CAGAAAGAATGATCCGGTTTATGTAAC 58.877 37.037 0.00 0.00 35.94 2.50
4220 4294 2.358737 GAGGAACCGCCACCTGTG 60.359 66.667 0.00 0.00 40.02 3.66
4221 4295 2.847234 TGAGGAACCGCCACCTGT 60.847 61.111 0.00 0.00 40.02 4.00
4231 4305 1.192428 ATAGTCACCGGGTGAGGAAC 58.808 55.000 29.42 18.09 43.57 3.62
4238 4312 5.530543 TCGTTTTTAAAAATAGTCACCGGGT 59.469 36.000 16.02 0.00 0.00 5.28
4254 4328 5.644636 ACCACTTTCAGAACTGTCGTTTTTA 59.355 36.000 1.73 0.00 32.39 1.52
4279 4358 5.858581 GTGTGCAGTTTATCAATCTTTCCAC 59.141 40.000 0.00 0.00 0.00 4.02
4394 4473 6.319715 TGTATAATGCTCCTGGGTATAGTGA 58.680 40.000 0.00 0.00 0.00 3.41
4397 4476 8.950210 CAAAATGTATAATGCTCCTGGGTATAG 58.050 37.037 0.00 0.00 0.00 1.31
4416 4495 2.292103 AGTTGTGCAACGCAAAATGT 57.708 40.000 9.10 0.00 45.50 2.71
4425 4504 3.983344 CCAGAAGCATTTAGTTGTGCAAC 59.017 43.478 6.94 6.94 43.63 4.17


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

AutoCloner maintained by Alex Coulton.