Multiple sequence alignment - TraesCS2B01G238600

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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 TraesCS2B01G238600 chr2B 100.000 5005 0 0 1 5005 239931058 239926054 0.000000e+00 9243.0
1 TraesCS2B01G238600 chr2D 93.069 4617 145 59 326 4819 186777178 186772614 0.000000e+00 6591.0
2 TraesCS2B01G238600 chr2D 91.085 258 16 4 1 257 186778776 186778525 4.800000e-90 342.0
3 TraesCS2B01G238600 chr2A 92.115 4540 153 75 399 4819 199276390 199271937 0.000000e+00 6211.0
4 TraesCS2B01G238600 chr2A 91.667 72 6 0 246 317 199276594 199276523 3.190000e-17 100.0
5 TraesCS2B01G238600 chr4A 86.331 278 32 6 1 275 718425560 718425286 1.050000e-76 298.0
6 TraesCS2B01G238600 chr5D 91.228 57 4 1 2416 2471 476461292 476461348 5.370000e-10 76.8
7 TraesCS2B01G238600 chr3B 73.462 260 42 22 1 249 39794563 39794320 6.950000e-09 73.1
8 TraesCS2B01G238600 chr7D 100.000 29 0 0 4897 4925 25903216 25903188 3.000000e-03 54.7
9 TraesCS2B01G238600 chr7B 100.000 29 0 0 4897 4925 468211099 468211071 3.000000e-03 54.7
10 TraesCS2B01G238600 chr6B 100.000 28 0 0 4899 4926 70726704 70726677 9.000000e-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 TraesCS2B01G238600 chr2B 239926054 239931058 5004 True 9243.0 9243 100.000 1 5005 1 chr2B.!!$R1 5004
1 TraesCS2B01G238600 chr2D 186772614 186778776 6162 True 3466.5 6591 92.077 1 4819 2 chr2D.!!$R1 4818
2 TraesCS2B01G238600 chr2A 199271937 199276594 4657 True 3155.5 6211 91.891 246 4819 2 chr2A.!!$R1 4573

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
557 1899 0.036294 CCCCTCTTCGTCTTCAACCC 60.036 60.0 0.00 0.0 0.00 4.11 F
1249 2667 0.031111 CCTCTAGGGGGTGATGACCA 60.031 60.0 0.00 0.0 45.25 4.02 F
1251 2669 0.031111 TCTAGGGGGTGATGACCAGG 60.031 60.0 3.00 0.0 45.25 4.45 F
1634 3059 0.036765 TAAAATCACCCGCGCTGTCT 60.037 50.0 5.56 0.0 0.00 3.41 F
2324 3764 0.327924 TTGGATGATTGGCAGGACGT 59.672 50.0 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 3643 0.319900 CAAGGACAGCGTGCTACACT 60.320 55.000 0.00 0.00 31.83 3.55 R
2279 3719 0.459899 ATGAGAACGAGCACGCCATA 59.540 50.000 2.62 0.00 43.96 2.74 R
2717 4169 1.228228 GCAGGGATGGCCATCTGAA 59.772 57.895 37.94 2.69 37.92 3.02 R
3039 4491 1.286880 CAGGCCCTTGCAAGAAACG 59.713 57.895 28.05 10.63 40.13 3.60 R
4149 5610 1.021390 AACAGATTCGCCAAGCTCCG 61.021 55.000 0.00 0.00 0.00 4.63 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
29 30 5.278512 GGACATTTTTCTTCAGTTCAGGTCC 60.279 44.000 0.00 0.00 33.92 4.46
41 42 0.468226 TCAGGTCCAGTCTTTGCGTT 59.532 50.000 0.00 0.00 0.00 4.84
46 47 0.884704 TCCAGTCTTTGCGTTGCCTC 60.885 55.000 0.00 0.00 0.00 4.70
63 64 1.712018 CTCGGCCGACGTCATGACTA 61.712 60.000 27.28 0.00 44.69 2.59
70 71 1.304713 ACGTCATGACTACGGGGGT 60.305 57.895 22.95 9.15 44.48 4.95
71 72 1.141019 CGTCATGACTACGGGGGTG 59.859 63.158 22.95 0.89 36.71 4.61
72 73 1.601419 CGTCATGACTACGGGGGTGT 61.601 60.000 22.95 0.00 36.71 4.16
74 75 1.826720 GTCATGACTACGGGGGTGTTA 59.173 52.381 18.83 0.00 0.00 2.41
75 76 2.234414 GTCATGACTACGGGGGTGTTAA 59.766 50.000 18.83 0.00 0.00 2.01
76 77 2.905085 TCATGACTACGGGGGTGTTAAA 59.095 45.455 0.00 0.00 0.00 1.52
77 78 3.055675 TCATGACTACGGGGGTGTTAAAG 60.056 47.826 0.00 0.00 0.00 1.85
82 83 3.645687 ACTACGGGGGTGTTAAAGTACAA 59.354 43.478 0.00 0.00 0.00 2.41
118 119 9.309516 ACCGTACAATGTATGTATTTAGTCAAG 57.690 33.333 11.23 0.00 45.87 3.02
120 121 7.996551 CGTACAATGTATGTATTTAGTCAAGCG 59.003 37.037 4.52 0.00 45.87 4.68
126 127 8.176814 TGTATGTATTTAGTCAAGCGTTGTAC 57.823 34.615 0.00 0.00 0.00 2.90
215 216 5.566230 GCCTCCTGTAACCTGTATATTACCG 60.566 48.000 0.00 0.00 31.48 4.02
221 222 1.346722 ACCTGTATATTACCGCCAGCC 59.653 52.381 0.00 0.00 0.00 4.85
228 229 2.996168 ATTACCGCCAGCCGATGAGC 62.996 60.000 0.00 0.00 40.02 4.26
261 1534 4.019950 TGCATTGAGTCTCATTCCTTCTCA 60.020 41.667 2.68 0.00 34.08 3.27
294 1567 6.790319 ACACTAAACTTCCCACCATCTAATT 58.210 36.000 0.00 0.00 0.00 1.40
296 1569 7.827729 ACACTAAACTTCCCACCATCTAATTAC 59.172 37.037 0.00 0.00 0.00 1.89
299 1572 9.408648 CTAAACTTCCCACCATCTAATTACAAT 57.591 33.333 0.00 0.00 0.00 2.71
301 1574 8.747538 AACTTCCCACCATCTAATTACAATAC 57.252 34.615 0.00 0.00 0.00 1.89
317 1590 2.947652 CAATACCCACATGAGCCTTCAG 59.052 50.000 0.00 0.00 36.61 3.02
319 1592 1.067295 ACCCACATGAGCCTTCAGAA 58.933 50.000 0.00 0.00 36.61 3.02
320 1593 1.425066 ACCCACATGAGCCTTCAGAAA 59.575 47.619 0.00 0.00 36.61 2.52
321 1594 1.815003 CCCACATGAGCCTTCAGAAAC 59.185 52.381 0.00 0.00 36.61 2.78
322 1595 1.466167 CCACATGAGCCTTCAGAAACG 59.534 52.381 0.00 0.00 36.61 3.60
385 1687 1.665679 CAGCGATGGCAAAGATAACGT 59.334 47.619 1.50 0.00 43.41 3.99
396 1698 4.437390 GCAAAGATAACGTTCACATCAGGG 60.437 45.833 2.82 0.00 0.00 4.45
412 1736 4.119556 TCAGGGTATCAGGGTATCAGAG 57.880 50.000 0.00 0.00 0.00 3.35
457 1783 3.961480 TGACCCAACTCAGATACACTG 57.039 47.619 0.00 0.00 46.97 3.66
458 1784 2.028112 TGACCCAACTCAGATACACTGC 60.028 50.000 0.00 0.00 45.38 4.40
468 1794 6.578023 ACTCAGATACACTGCCTTCTTAATC 58.422 40.000 0.00 0.00 45.38 1.75
471 1802 6.100279 TCAGATACACTGCCTTCTTAATCCAT 59.900 38.462 0.00 0.00 45.38 3.41
524 1859 1.303643 CTTCACCAGCCCACTTCCC 60.304 63.158 0.00 0.00 0.00 3.97
526 1861 2.034687 CACCAGCCCACTTCCCAG 59.965 66.667 0.00 0.00 0.00 4.45
557 1899 0.036294 CCCCTCTTCGTCTTCAACCC 60.036 60.000 0.00 0.00 0.00 4.11
591 1947 3.508845 ACCACCCAAGGATACATATGC 57.491 47.619 1.58 0.00 41.41 3.14
661 2017 0.393402 TCCACTTGCATGCTAGCAGG 60.393 55.000 25.99 24.52 46.54 4.85
715 2071 2.125066 TTTGGCCCCTCTCCTCTCCT 62.125 60.000 0.00 0.00 0.00 3.69
808 2174 2.024846 TCAGTAAGGACTCTCCCAGAGG 60.025 54.545 5.54 0.00 46.45 3.69
809 2175 2.024846 CAGTAAGGACTCTCCCAGAGGA 60.025 54.545 5.54 0.00 46.45 3.71
817 2183 2.366167 TCCCAGAGGAGAGGCCAG 59.634 66.667 5.01 0.00 37.19 4.85
818 2184 3.478274 CCCAGAGGAGAGGCCAGC 61.478 72.222 5.01 0.00 40.02 4.85
819 2185 3.478274 CCAGAGGAGAGGCCAGCC 61.478 72.222 5.01 0.00 40.02 4.85
820 2186 2.686470 CAGAGGAGAGGCCAGCCA 60.686 66.667 12.03 0.00 40.02 4.75
821 2187 2.365370 AGAGGAGAGGCCAGCCAG 60.365 66.667 12.03 0.00 40.02 4.85
822 2188 2.364842 GAGGAGAGGCCAGCCAGA 60.365 66.667 12.03 0.00 40.02 3.86
823 2189 2.365370 AGGAGAGGCCAGCCAGAG 60.365 66.667 12.03 0.00 40.02 3.35
880 2246 2.563798 CGGCTTGGGCTTTTCTGCA 61.564 57.895 0.00 0.00 38.73 4.41
993 2386 1.354031 TGTTGGGGAATAGCAGCAGAA 59.646 47.619 0.00 0.00 0.00 3.02
994 2387 2.224992 TGTTGGGGAATAGCAGCAGAAA 60.225 45.455 0.00 0.00 0.00 2.52
995 2388 2.424956 GTTGGGGAATAGCAGCAGAAAG 59.575 50.000 0.00 0.00 0.00 2.62
1020 2413 1.194781 TGGGCTCTGTCCTTGAGGTC 61.195 60.000 0.00 0.00 36.34 3.85
1096 2510 1.609783 CTCCTCCCCCAATTTCGCT 59.390 57.895 0.00 0.00 0.00 4.93
1099 2513 1.078426 CTCCCCCAATTTCGCTCGT 60.078 57.895 0.00 0.00 0.00 4.18
1171 2588 6.503589 TTTCGTTTCTGTTTCTTCCTTTCA 57.496 33.333 0.00 0.00 0.00 2.69
1189 2606 5.522460 CCTTTCATATAGGTACCGTTGTGTG 59.478 44.000 6.18 2.70 0.00 3.82
1241 2659 0.631085 AGGTCTAGCCTCTAGGGGGT 60.631 60.000 19.29 19.29 46.96 4.95
1249 2667 0.031111 CCTCTAGGGGGTGATGACCA 60.031 60.000 0.00 0.00 45.25 4.02
1250 2668 1.418334 CTCTAGGGGGTGATGACCAG 58.582 60.000 3.00 0.00 45.25 4.00
1251 2669 0.031111 TCTAGGGGGTGATGACCAGG 60.031 60.000 3.00 0.00 45.25 4.45
1259 2677 0.107459 GTGATGACCAGGGAGGCTTC 60.107 60.000 0.00 0.00 43.14 3.86
1276 2694 2.546795 GCTTCGACATATCCTGGTGGAG 60.547 54.545 0.00 0.00 46.91 3.86
1278 2696 2.747177 TCGACATATCCTGGTGGAGTT 58.253 47.619 0.00 0.00 46.91 3.01
1290 2712 1.480545 GGTGGAGTTTGTGCCTGTTTT 59.519 47.619 0.00 0.00 0.00 2.43
1447 2871 2.076863 CATCGCTTCCTTTTCGACCTT 58.923 47.619 0.00 0.00 34.92 3.50
1625 3050 3.947834 CACTCCATGGACTAAAATCACCC 59.052 47.826 11.44 0.00 0.00 4.61
1626 3051 3.206150 CTCCATGGACTAAAATCACCCG 58.794 50.000 11.44 0.00 0.00 5.28
1628 3053 1.330521 CATGGACTAAAATCACCCGCG 59.669 52.381 0.00 0.00 0.00 6.46
1629 3054 1.022451 TGGACTAAAATCACCCGCGC 61.022 55.000 0.00 0.00 0.00 6.86
1630 3055 0.743345 GGACTAAAATCACCCGCGCT 60.743 55.000 5.56 0.00 0.00 5.92
1631 3056 0.373716 GACTAAAATCACCCGCGCTG 59.626 55.000 5.56 0.00 0.00 5.18
1632 3057 0.321298 ACTAAAATCACCCGCGCTGT 60.321 50.000 5.56 0.00 0.00 4.40
1633 3058 0.373716 CTAAAATCACCCGCGCTGTC 59.626 55.000 5.56 0.00 0.00 3.51
1634 3059 0.036765 TAAAATCACCCGCGCTGTCT 60.037 50.000 5.56 0.00 0.00 3.41
1635 3060 1.577328 AAAATCACCCGCGCTGTCTG 61.577 55.000 5.56 0.00 0.00 3.51
1636 3061 2.731691 AAATCACCCGCGCTGTCTGT 62.732 55.000 5.56 0.00 0.00 3.41
1637 3062 1.884075 AATCACCCGCGCTGTCTGTA 61.884 55.000 5.56 0.00 0.00 2.74
1638 3063 1.884075 ATCACCCGCGCTGTCTGTAA 61.884 55.000 5.56 0.00 0.00 2.41
1639 3064 1.447838 CACCCGCGCTGTCTGTAAT 60.448 57.895 5.56 0.00 0.00 1.89
1640 3065 1.447838 ACCCGCGCTGTCTGTAATG 60.448 57.895 5.56 0.00 0.00 1.90
1641 3066 1.447838 CCCGCGCTGTCTGTAATGT 60.448 57.895 5.56 0.00 0.00 2.71
1642 3067 1.421410 CCCGCGCTGTCTGTAATGTC 61.421 60.000 5.56 0.00 0.00 3.06
1643 3068 0.735978 CCGCGCTGTCTGTAATGTCA 60.736 55.000 5.56 0.00 0.00 3.58
1690 3117 3.745975 TGTAAATTTGCCTGACACTCTCG 59.254 43.478 0.00 0.00 0.00 4.04
1712 3139 9.715121 TCTCGTGTAACTGTAAATTTTAATCCT 57.285 29.630 0.00 0.00 31.75 3.24
1746 3177 3.861341 CTTCCGGAAAGGCATCTCA 57.139 52.632 19.39 0.00 40.77 3.27
1756 3187 2.803030 AGGCATCTCAATCTTGTGCT 57.197 45.000 0.00 0.00 36.15 4.40
2150 3590 2.103373 TCTCTGGAAAGGACCTGATCG 58.897 52.381 0.00 0.00 37.29 3.69
2152 3592 0.539051 CTGGAAAGGACCTGATCGCT 59.461 55.000 0.00 0.00 0.00 4.93
2279 3719 2.095853 CGTGGCGTGCTTCATTAATTCT 59.904 45.455 0.00 0.00 0.00 2.40
2324 3764 0.327924 TTGGATGATTGGCAGGACGT 59.672 50.000 0.00 0.00 0.00 4.34
2341 3781 1.771073 CGTTCTTGCACCGTTCAGCA 61.771 55.000 0.00 0.00 39.32 4.41
2360 3800 3.015327 GCAGCAGGATCAAGAATCTGTT 58.985 45.455 0.00 0.00 34.56 3.16
2367 3807 4.116238 GGATCAAGAATCTGTTCGAGGAC 58.884 47.826 0.00 0.00 39.38 3.85
2670 4122 2.664081 CCAGAGCCTCTTCCCGCTT 61.664 63.158 0.00 0.00 34.84 4.68
3039 4491 2.883621 GACCTCGACCGGAGTTCC 59.116 66.667 9.46 0.00 41.46 3.62
3168 4620 2.356313 ACGCTCGACAACCTGCTG 60.356 61.111 0.00 0.00 0.00 4.41
3435 4890 4.031611 ACTTCCAGGTACTACATTCTCCC 58.968 47.826 0.00 0.00 36.02 4.30
3440 4895 4.030913 CAGGTACTACATTCTCCCCAGAA 58.969 47.826 0.00 0.00 39.34 3.02
3479 4934 1.610522 AGAATTGAGTTGCACAGTGCC 59.389 47.619 23.06 8.39 44.23 5.01
3725 5184 4.697756 CACTCCGGCCCGCTGAAA 62.698 66.667 0.00 0.00 0.00 2.69
3781 5240 4.883300 GAGCTACGACGACGCCGG 62.883 72.222 8.74 0.00 43.96 6.13
4008 5467 1.667724 CCAGGATGTGTTCTTGATCGC 59.332 52.381 0.00 0.00 33.37 4.58
4027 5486 1.171308 CCCCATTTCACTCTGCACAG 58.829 55.000 0.00 0.00 0.00 3.66
4126 5587 6.724893 TTTATCTGTGTATCGATTCCTGGA 57.275 37.500 1.71 0.00 0.00 3.86
4149 5610 5.876612 GATTGATCTAATCTGATGTGGGC 57.123 43.478 9.36 0.00 41.61 5.36
4197 5658 5.672421 ACATCTCAGTGAACAGATGATCA 57.328 39.130 21.44 0.00 46.23 2.92
4204 5665 8.316946 TCTCAGTGAACAGATGATCAAATAACT 58.683 33.333 0.00 0.00 0.00 2.24
4325 5786 3.941483 ACAATTCAATCCATGACCTCGAC 59.059 43.478 0.00 0.00 37.92 4.20
4328 5789 2.179427 TCAATCCATGACCTCGACAGT 58.821 47.619 0.00 0.00 31.50 3.55
4332 5793 1.546029 TCCATGACCTCGACAGTTCAG 59.454 52.381 0.00 0.00 0.00 3.02
4335 5796 0.750249 TGACCTCGACAGTTCAGCAA 59.250 50.000 0.00 0.00 0.00 3.91
4477 5946 4.924305 ACAGTTGACTTGTAGACCGTAA 57.076 40.909 0.00 0.00 0.00 3.18
4486 5955 6.869913 TGACTTGTAGACCGTAAATTAACAGG 59.130 38.462 0.00 0.00 0.00 4.00
4623 6092 0.114954 AATTGGCAGGGGCTTTCTCA 59.885 50.000 0.00 0.00 40.87 3.27
4692 6164 2.075566 TGCAGTGTCCAACCTCCCA 61.076 57.895 0.00 0.00 0.00 4.37
4720 6204 9.890629 ATGTGCTCATCTAGTTACTTTTCATTA 57.109 29.630 0.00 0.00 0.00 1.90
4723 6207 9.719355 TGCTCATCTAGTTACTTTTCATTACAA 57.281 29.630 0.00 0.00 0.00 2.41
4794 6278 5.904362 ATTCTAACTCACCATTTGCTTCC 57.096 39.130 0.00 0.00 0.00 3.46
4819 6303 6.307800 CGTGCCTTGATATAAACTTTTTGTGG 59.692 38.462 0.00 0.00 0.00 4.17
4820 6304 6.090763 GTGCCTTGATATAAACTTTTTGTGGC 59.909 38.462 0.00 0.00 35.22 5.01
4821 6305 5.580691 GCCTTGATATAAACTTTTTGTGGCC 59.419 40.000 0.00 0.00 0.00 5.36
4822 6306 6.574269 GCCTTGATATAAACTTTTTGTGGCCT 60.574 38.462 3.32 0.00 0.00 5.19
4823 6307 7.386059 CCTTGATATAAACTTTTTGTGGCCTT 58.614 34.615 3.32 0.00 0.00 4.35
4824 6308 7.877612 CCTTGATATAAACTTTTTGTGGCCTTT 59.122 33.333 3.32 0.00 0.00 3.11
4825 6309 9.271828 CTTGATATAAACTTTTTGTGGCCTTTT 57.728 29.630 3.32 0.00 0.00 2.27
4826 6310 9.620259 TTGATATAAACTTTTTGTGGCCTTTTT 57.380 25.926 3.32 0.00 0.00 1.94
4847 6331 6.500684 TTTTTGGCTGCATTTGTTTGTAAA 57.499 29.167 0.50 0.00 0.00 2.01
4848 6332 6.690194 TTTTGGCTGCATTTGTTTGTAAAT 57.310 29.167 0.50 0.00 0.00 1.40
4849 6333 7.792374 TTTTGGCTGCATTTGTTTGTAAATA 57.208 28.000 0.50 0.00 0.00 1.40
4850 6334 7.418840 TTTGGCTGCATTTGTTTGTAAATAG 57.581 32.000 0.50 0.00 0.00 1.73
4851 6335 6.338214 TGGCTGCATTTGTTTGTAAATAGA 57.662 33.333 0.50 0.00 0.00 1.98
4852 6336 6.753180 TGGCTGCATTTGTTTGTAAATAGAA 58.247 32.000 0.50 0.00 0.00 2.10
4853 6337 6.867816 TGGCTGCATTTGTTTGTAAATAGAAG 59.132 34.615 0.50 0.00 0.00 2.85
4854 6338 7.090173 GGCTGCATTTGTTTGTAAATAGAAGA 58.910 34.615 0.50 0.00 0.00 2.87
4855 6339 7.761249 GGCTGCATTTGTTTGTAAATAGAAGAT 59.239 33.333 0.50 0.00 0.00 2.40
4856 6340 9.143631 GCTGCATTTGTTTGTAAATAGAAGATT 57.856 29.630 0.00 0.00 0.00 2.40
4902 6386 8.139350 TGCTTTACTTCTTTAAAACTTTAGGGC 58.861 33.333 0.00 0.00 0.00 5.19
4903 6387 8.139350 GCTTTACTTCTTTAAAACTTTAGGGCA 58.861 33.333 0.00 0.00 0.00 5.36
4906 6390 9.582648 TTACTTCTTTAAAACTTTAGGGCATCT 57.417 29.630 0.00 0.00 0.00 2.90
4907 6391 8.112016 ACTTCTTTAAAACTTTAGGGCATCTC 57.888 34.615 0.00 0.00 0.00 2.75
4908 6392 7.176865 ACTTCTTTAAAACTTTAGGGCATCTCC 59.823 37.037 0.00 0.00 0.00 3.71
4909 6393 6.548321 TCTTTAAAACTTTAGGGCATCTCCA 58.452 36.000 0.00 0.00 36.21 3.86
4910 6394 7.007723 TCTTTAAAACTTTAGGGCATCTCCAA 58.992 34.615 0.00 0.00 36.21 3.53
4911 6395 6.584185 TTAAAACTTTAGGGCATCTCCAAC 57.416 37.500 0.00 0.00 36.21 3.77
4912 6396 2.403252 ACTTTAGGGCATCTCCAACG 57.597 50.000 0.00 0.00 36.21 4.10
4913 6397 1.017387 CTTTAGGGCATCTCCAACGC 58.983 55.000 0.00 0.00 36.21 4.84
4914 6398 0.618458 TTTAGGGCATCTCCAACGCT 59.382 50.000 0.00 0.00 36.21 5.07
4915 6399 1.491668 TTAGGGCATCTCCAACGCTA 58.508 50.000 0.00 0.00 36.21 4.26
4916 6400 1.491668 TAGGGCATCTCCAACGCTAA 58.508 50.000 0.00 0.00 36.21 3.09
4917 6401 0.107654 AGGGCATCTCCAACGCTAAC 60.108 55.000 0.00 0.00 36.21 2.34
4918 6402 1.095807 GGGCATCTCCAACGCTAACC 61.096 60.000 0.00 0.00 36.21 2.85
4919 6403 1.095807 GGCATCTCCAACGCTAACCC 61.096 60.000 0.00 0.00 34.01 4.11
4920 6404 1.429148 GCATCTCCAACGCTAACCCG 61.429 60.000 0.00 0.00 0.00 5.28
4921 6405 1.153429 ATCTCCAACGCTAACCCGC 60.153 57.895 0.00 0.00 0.00 6.13
4922 6406 1.895020 ATCTCCAACGCTAACCCGCA 61.895 55.000 0.00 0.00 0.00 5.69
4923 6407 1.669760 CTCCAACGCTAACCCGCAA 60.670 57.895 0.00 0.00 0.00 4.85
4924 6408 1.227883 TCCAACGCTAACCCGCAAA 60.228 52.632 0.00 0.00 0.00 3.68
4925 6409 1.081708 CCAACGCTAACCCGCAAAC 60.082 57.895 0.00 0.00 0.00 2.93
4926 6410 1.081708 CAACGCTAACCCGCAAACC 60.082 57.895 0.00 0.00 0.00 3.27
4927 6411 1.526455 AACGCTAACCCGCAAACCA 60.526 52.632 0.00 0.00 0.00 3.67
4928 6412 1.512156 AACGCTAACCCGCAAACCAG 61.512 55.000 0.00 0.00 0.00 4.00
4929 6413 1.669760 CGCTAACCCGCAAACCAGA 60.670 57.895 0.00 0.00 0.00 3.86
4930 6414 1.873863 GCTAACCCGCAAACCAGAC 59.126 57.895 0.00 0.00 0.00 3.51
4931 6415 0.887387 GCTAACCCGCAAACCAGACA 60.887 55.000 0.00 0.00 0.00 3.41
4932 6416 0.872388 CTAACCCGCAAACCAGACAC 59.128 55.000 0.00 0.00 0.00 3.67
4933 6417 0.535553 TAACCCGCAAACCAGACACC 60.536 55.000 0.00 0.00 0.00 4.16
4934 6418 3.353836 CCCGCAAACCAGACACCG 61.354 66.667 0.00 0.00 0.00 4.94
4935 6419 4.025401 CCGCAAACCAGACACCGC 62.025 66.667 0.00 0.00 0.00 5.68
4936 6420 3.276091 CGCAAACCAGACACCGCA 61.276 61.111 0.00 0.00 0.00 5.69
4937 6421 2.331451 GCAAACCAGACACCGCAC 59.669 61.111 0.00 0.00 0.00 5.34
4938 6422 2.631428 CAAACCAGACACCGCACG 59.369 61.111 0.00 0.00 0.00 5.34
4939 6423 3.276846 AAACCAGACACCGCACGC 61.277 61.111 0.00 0.00 0.00 5.34
4940 6424 3.750373 AAACCAGACACCGCACGCT 62.750 57.895 0.00 0.00 0.00 5.07
4941 6425 4.664677 ACCAGACACCGCACGCTC 62.665 66.667 0.00 0.00 0.00 5.03
4943 6427 4.363990 CAGACACCGCACGCTCCT 62.364 66.667 0.00 0.00 0.00 3.69
4944 6428 4.057428 AGACACCGCACGCTCCTC 62.057 66.667 0.00 0.00 0.00 3.71
4947 6431 4.379243 CACCGCACGCTCCTCCTT 62.379 66.667 0.00 0.00 0.00 3.36
4948 6432 4.379243 ACCGCACGCTCCTCCTTG 62.379 66.667 0.00 0.00 0.00 3.61
4950 6434 4.069232 CGCACGCTCCTCCTTGGA 62.069 66.667 0.00 0.00 43.86 3.53
4951 6435 2.435059 GCACGCTCCTCCTTGGAC 60.435 66.667 0.00 0.00 40.56 4.02
4952 6436 3.059982 CACGCTCCTCCTTGGACA 58.940 61.111 0.00 0.00 40.56 4.02
4953 6437 1.374758 CACGCTCCTCCTTGGACAC 60.375 63.158 0.00 0.00 40.56 3.67
4954 6438 2.125912 CGCTCCTCCTTGGACACG 60.126 66.667 0.00 0.00 40.56 4.49
4955 6439 2.266055 GCTCCTCCTTGGACACGG 59.734 66.667 0.00 0.00 40.56 4.94
4956 6440 2.982130 CTCCTCCTTGGACACGGG 59.018 66.667 0.00 0.00 40.56 5.28
4957 6441 3.316573 CTCCTCCTTGGACACGGGC 62.317 68.421 0.00 0.00 40.56 6.13
4958 6442 4.410400 CCTCCTTGGACACGGGCC 62.410 72.222 0.00 0.00 38.35 5.80
4959 6443 4.410400 CTCCTTGGACACGGGCCC 62.410 72.222 13.57 13.57 0.00 5.80
4960 6444 4.974438 TCCTTGGACACGGGCCCT 62.974 66.667 22.43 0.00 0.00 5.19
4961 6445 4.410400 CCTTGGACACGGGCCCTC 62.410 72.222 22.43 11.01 0.00 4.30
4962 6446 4.760047 CTTGGACACGGGCCCTCG 62.760 72.222 22.43 13.39 0.00 4.63
4992 6476 4.072088 CGTCGCCAACGCCACTTC 62.072 66.667 0.00 0.00 45.76 3.01
4993 6477 3.723348 GTCGCCAACGCCACTTCC 61.723 66.667 0.00 0.00 39.84 3.46
4996 6480 2.975799 GCCAACGCCACTTCCGAA 60.976 61.111 0.00 0.00 0.00 4.30
4997 6481 2.966309 GCCAACGCCACTTCCGAAG 61.966 63.158 6.59 6.59 0.00 3.79
4998 6482 1.597027 CCAACGCCACTTCCGAAGT 60.597 57.895 8.03 8.03 44.06 3.01
4999 6483 0.320073 CCAACGCCACTTCCGAAGTA 60.320 55.000 13.47 0.00 40.46 2.24
5000 6484 0.788391 CAACGCCACTTCCGAAGTAC 59.212 55.000 13.47 8.18 40.46 2.73
5001 6485 0.677842 AACGCCACTTCCGAAGTACT 59.322 50.000 13.47 0.00 40.46 2.73
5002 6486 0.038526 ACGCCACTTCCGAAGTACTG 60.039 55.000 13.47 8.49 40.46 2.74
5003 6487 0.736325 CGCCACTTCCGAAGTACTGG 60.736 60.000 13.47 11.81 40.46 4.00
5004 6488 0.606604 GCCACTTCCGAAGTACTGGA 59.393 55.000 13.47 0.00 40.46 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.300286 ACTGGACCTGAACTGAAGAAAAATG 59.700 40.000 5.22 0.00 0.00 2.32
29 30 1.205064 CGAGGCAACGCAAAGACTG 59.795 57.895 0.00 0.00 46.39 3.51
46 47 1.585521 GTAGTCATGACGTCGGCCG 60.586 63.158 22.12 22.12 44.03 6.13
58 59 2.328319 ACTTTAACACCCCCGTAGTCA 58.672 47.619 0.00 0.00 0.00 3.41
63 64 3.181441 ACATTGTACTTTAACACCCCCGT 60.181 43.478 0.00 0.00 0.00 5.28
76 77 9.687210 CATTGTACGGTATATACACATTGTACT 57.313 33.333 14.70 2.81 35.42 2.73
77 78 9.467258 ACATTGTACGGTATATACACATTGTAC 57.533 33.333 20.03 18.19 35.42 2.90
120 121 4.464043 CGCGCTCGCACGTACAAC 62.464 66.667 14.80 0.00 42.06 3.32
157 158 0.179148 TCGTGCGCCACTACATACAG 60.179 55.000 4.18 0.00 31.34 2.74
215 216 0.590195 CAATTAGCTCATCGGCTGGC 59.410 55.000 0.00 0.00 43.01 4.85
221 222 4.744136 ATGCACATCAATTAGCTCATCG 57.256 40.909 0.00 0.00 0.00 3.84
228 229 6.673154 TGAGACTCAATGCACATCAATTAG 57.327 37.500 1.64 0.00 0.00 1.73
261 1534 4.165372 TGGGAAGTTTAGTGTTTGAGGAGT 59.835 41.667 0.00 0.00 0.00 3.85
294 1567 3.521531 TGAAGGCTCATGTGGGTATTGTA 59.478 43.478 0.00 0.00 0.00 2.41
296 1569 2.947652 CTGAAGGCTCATGTGGGTATTG 59.052 50.000 0.00 0.00 0.00 1.90
299 1572 1.951209 TCTGAAGGCTCATGTGGGTA 58.049 50.000 0.00 0.00 0.00 3.69
301 1574 1.815003 GTTTCTGAAGGCTCATGTGGG 59.185 52.381 0.00 0.00 0.00 4.61
317 1590 7.766723 CTGTTGAAATACAGATGAACGTTTC 57.233 36.000 0.46 0.00 46.72 2.78
385 1687 2.845659 ACCCTGATACCCTGATGTGAA 58.154 47.619 0.00 0.00 0.00 3.18
396 1698 6.150976 CACTGAGATCTCTGATACCCTGATAC 59.849 46.154 29.89 0.00 33.48 2.24
412 1736 3.446873 AGTCTCCATGTGACACTGAGATC 59.553 47.826 15.98 11.08 36.94 2.75
457 1783 3.065925 GTGCTGTCATGGATTAAGAAGGC 59.934 47.826 0.00 0.00 0.00 4.35
458 1784 4.264253 TGTGCTGTCATGGATTAAGAAGG 58.736 43.478 0.00 0.00 0.00 3.46
468 1794 1.162698 CAGTCCTTGTGCTGTCATGG 58.837 55.000 0.00 0.00 35.02 3.66
471 1802 0.109153 ATGCAGTCCTTGTGCTGTCA 59.891 50.000 0.00 0.00 41.78 3.58
524 1859 3.229697 AGAGGGGTGGTTTTCTTTCTG 57.770 47.619 0.00 0.00 0.00 3.02
526 1861 2.552743 CGAAGAGGGGTGGTTTTCTTTC 59.447 50.000 0.00 0.00 30.49 2.62
557 1899 4.924305 TGGGTGGTACTTTATACTAGCG 57.076 45.455 0.00 0.00 0.00 4.26
591 1947 2.158755 AGGCCGGGTCTTGATTTATCTG 60.159 50.000 2.18 0.00 0.00 2.90
661 2017 1.336632 ATCTGAGCTCCTGACAGCCC 61.337 60.000 12.15 0.00 40.65 5.19
715 2071 3.818210 GTGTGTGTGAGAGAGAGAGAGAA 59.182 47.826 0.00 0.00 0.00 2.87
808 2174 2.663423 GATGCTCTGGCTGGCCTCTC 62.663 65.000 13.05 0.00 39.59 3.20
809 2175 2.691623 ATGCTCTGGCTGGCCTCT 60.692 61.111 13.05 0.00 39.59 3.69
810 2176 2.203181 GATGCTCTGGCTGGCCTC 60.203 66.667 13.05 0.00 39.59 4.70
811 2177 2.691623 AGATGCTCTGGCTGGCCT 60.692 61.111 13.05 0.00 39.59 5.19
812 2178 2.516460 CAGATGCTCTGGCTGGCC 60.516 66.667 4.43 4.43 40.71 5.36
813 2179 3.210528 GCAGATGCTCTGGCTGGC 61.211 66.667 12.98 0.00 44.43 4.85
821 2187 1.153005 CAAGGGAGGGCAGATGCTC 60.153 63.158 4.59 0.00 43.28 4.26
822 2188 2.687610 CCAAGGGAGGGCAGATGCT 61.688 63.158 4.59 0.00 41.70 3.79
823 2189 2.123982 CCAAGGGAGGGCAGATGC 60.124 66.667 0.00 0.00 41.14 3.91
880 2246 3.168528 ACCACCCACACCTCGCTT 61.169 61.111 0.00 0.00 0.00 4.68
993 2386 0.915364 GGACAGAGCCCATCCTTCTT 59.085 55.000 0.00 0.00 0.00 2.52
994 2387 0.043940 AGGACAGAGCCCATCCTTCT 59.956 55.000 0.00 0.00 40.03 2.85
995 2388 2.614001 AGGACAGAGCCCATCCTTC 58.386 57.895 0.00 0.00 40.03 3.46
1020 2413 1.431488 CGGCTTCACCATCCACATCG 61.431 60.000 0.00 0.00 39.03 3.84
1060 2453 2.187163 GAAGTAGAGGCGGCCACC 59.813 66.667 23.09 12.52 0.00 4.61
1061 2454 2.187163 GGAAGTAGAGGCGGCCAC 59.813 66.667 23.09 15.87 0.00 5.01
1062 2455 2.038975 AGGAAGTAGAGGCGGCCA 59.961 61.111 23.09 0.00 0.00 5.36
1064 2457 1.740332 GAGGAGGAAGTAGAGGCGGC 61.740 65.000 0.00 0.00 0.00 6.53
1073 2466 1.641192 GAAATTGGGGGAGGAGGAAGT 59.359 52.381 0.00 0.00 0.00 3.01
1096 2510 3.893200 TGGAGGAAGAACAAGTAAGACGA 59.107 43.478 0.00 0.00 0.00 4.20
1099 2513 4.658901 ACCTTGGAGGAAGAACAAGTAAGA 59.341 41.667 0.07 0.00 39.85 2.10
1168 2585 4.681244 GCCACACAACGGTACCTATATGAA 60.681 45.833 10.90 0.00 0.00 2.57
1171 2588 3.036091 AGCCACACAACGGTACCTATAT 58.964 45.455 10.90 0.00 0.00 0.86
1189 2606 1.376037 ACGCTAGAAACCAGCAGCC 60.376 57.895 0.00 0.00 39.04 4.85
1241 2659 1.617018 CGAAGCCTCCCTGGTCATCA 61.617 60.000 0.00 0.00 38.35 3.07
1249 2667 1.133009 AGGATATGTCGAAGCCTCCCT 60.133 52.381 0.00 0.00 0.00 4.20
1250 2668 1.001406 CAGGATATGTCGAAGCCTCCC 59.999 57.143 0.00 0.00 0.00 4.30
1251 2669 1.001406 CCAGGATATGTCGAAGCCTCC 59.999 57.143 0.00 0.00 0.00 4.30
1259 2677 3.198068 CAAACTCCACCAGGATATGTCG 58.802 50.000 0.00 0.00 44.70 4.35
1276 2694 5.633601 GGCTAGAATTAAAACAGGCACAAAC 59.366 40.000 0.00 0.00 0.00 2.93
1278 2696 4.219725 GGGCTAGAATTAAAACAGGCACAA 59.780 41.667 0.00 0.00 33.74 3.33
1290 2712 4.018415 AGGAAGCAACAAGGGCTAGAATTA 60.018 41.667 0.00 0.00 41.66 1.40
1447 2871 1.667830 CGAAACCAAGCAGCTCGGA 60.668 57.895 6.33 0.00 0.00 4.55
1625 3050 1.005662 CATGACATTACAGACAGCGCG 60.006 52.381 0.00 0.00 0.00 6.86
1626 3051 2.002586 ACATGACATTACAGACAGCGC 58.997 47.619 0.00 0.00 0.00 5.92
1628 3053 2.939103 GGGACATGACATTACAGACAGC 59.061 50.000 0.00 0.00 0.00 4.40
1629 3054 3.198635 AGGGGACATGACATTACAGACAG 59.801 47.826 0.00 0.00 0.00 3.51
1630 3055 3.181329 AGGGGACATGACATTACAGACA 58.819 45.455 0.00 0.00 0.00 3.41
1631 3056 3.914426 AGGGGACATGACATTACAGAC 57.086 47.619 0.00 0.00 0.00 3.51
1632 3057 4.163458 GGTTAGGGGACATGACATTACAGA 59.837 45.833 0.00 0.00 0.00 3.41
1633 3058 4.080582 TGGTTAGGGGACATGACATTACAG 60.081 45.833 0.00 0.00 0.00 2.74
1634 3059 3.847184 TGGTTAGGGGACATGACATTACA 59.153 43.478 0.00 0.00 0.00 2.41
1635 3060 4.196971 GTGGTTAGGGGACATGACATTAC 58.803 47.826 0.00 0.00 0.00 1.89
1636 3061 3.847184 TGTGGTTAGGGGACATGACATTA 59.153 43.478 0.00 0.00 0.00 1.90
1637 3062 2.647299 TGTGGTTAGGGGACATGACATT 59.353 45.455 0.00 0.00 0.00 2.71
1638 3063 2.274542 TGTGGTTAGGGGACATGACAT 58.725 47.619 0.00 0.00 0.00 3.06
1639 3064 1.735926 TGTGGTTAGGGGACATGACA 58.264 50.000 0.00 0.00 0.00 3.58
1640 3065 2.026262 ACATGTGGTTAGGGGACATGAC 60.026 50.000 16.15 0.00 46.60 3.06
1641 3066 2.274542 ACATGTGGTTAGGGGACATGA 58.725 47.619 16.15 0.00 46.60 3.07
1643 3068 2.919602 AGAACATGTGGTTAGGGGACAT 59.080 45.455 0.00 0.00 40.63 3.06
1709 3136 4.887655 GGAAGGAAAAAGAAACAGACAGGA 59.112 41.667 0.00 0.00 0.00 3.86
1712 3139 4.893424 CGGAAGGAAAAAGAAACAGACA 57.107 40.909 0.00 0.00 0.00 3.41
1737 3165 2.803030 AGCACAAGATTGAGATGCCT 57.197 45.000 0.00 0.00 36.96 4.75
1739 3167 5.746307 TGAATAGCACAAGATTGAGATGC 57.254 39.130 0.00 0.00 36.52 3.91
2203 3643 0.319900 CAAGGACAGCGTGCTACACT 60.320 55.000 0.00 0.00 31.83 3.55
2279 3719 0.459899 ATGAGAACGAGCACGCCATA 59.540 50.000 2.62 0.00 43.96 2.74
2324 3764 1.785041 GCTGCTGAACGGTGCAAGAA 61.785 55.000 0.00 0.00 38.81 2.52
2341 3781 3.196469 TCGAACAGATTCTTGATCCTGCT 59.804 43.478 0.00 0.00 35.21 4.24
2360 3800 3.125573 CGACCAGCTCGTCCTCGA 61.126 66.667 5.85 0.00 44.12 4.04
2400 3840 1.254026 AGCCGTGCAACACTAGTCTA 58.746 50.000 0.00 0.00 35.74 2.59
2577 4029 2.180204 CGCCTTATCCGCCACCTTG 61.180 63.158 0.00 0.00 0.00 3.61
2717 4169 1.228228 GCAGGGATGGCCATCTGAA 59.772 57.895 37.94 2.69 37.92 3.02
2972 4424 2.657237 CCTTCTTGTCCTCGGCGT 59.343 61.111 6.85 0.00 0.00 5.68
3003 4455 1.815421 GGCAATGACGGTGATCGCT 60.815 57.895 6.18 0.00 43.89 4.93
3039 4491 1.286880 CAGGCCCTTGCAAGAAACG 59.713 57.895 28.05 10.63 40.13 3.60
3186 4638 2.048597 TCGTACAAGCTGCCCGTG 60.049 61.111 0.00 0.00 0.00 4.94
3435 4890 2.182827 TCTGACATCCCTGAGTTCTGG 58.817 52.381 0.00 0.00 35.06 3.86
3440 4895 1.554160 CTGCTTCTGACATCCCTGAGT 59.446 52.381 0.00 0.00 0.00 3.41
3545 5004 2.356194 TCGTCGTCCGTCAGTCGA 60.356 61.111 0.00 0.00 42.86 4.20
3629 5088 2.434774 GGGAAGCCGGAGTTGGTT 59.565 61.111 5.05 0.00 0.00 3.67
4008 5467 1.171308 CTGTGCAGAGTGAAATGGGG 58.829 55.000 1.91 0.00 0.00 4.96
4027 5486 7.273320 TCCTAGCAGTATGTACATTCACTAC 57.727 40.000 14.77 7.25 39.31 2.73
4101 5562 7.210174 TCCAGGAATCGATACACAGATAAAAG 58.790 38.462 0.00 0.00 0.00 2.27
4149 5610 1.021390 AACAGATTCGCCAAGCTCCG 61.021 55.000 0.00 0.00 0.00 4.63
4156 5617 3.734463 TGTAACAAGAACAGATTCGCCA 58.266 40.909 0.00 0.00 40.04 5.69
4159 5620 6.587990 ACTGAGATGTAACAAGAACAGATTCG 59.412 38.462 0.00 0.00 40.04 3.34
4229 5690 6.296026 TGTAGCAGTTGTACTTGGAATCTTT 58.704 36.000 0.00 0.00 0.00 2.52
4325 5786 6.095377 GGATTTGTTTATCCTTGCTGAACTG 58.905 40.000 0.00 0.00 40.81 3.16
4422 5889 1.671979 CCGCCATGATGTCATCTTGT 58.328 50.000 21.15 4.62 33.61 3.16
4423 5890 0.309922 GCCGCCATGATGTCATCTTG 59.690 55.000 17.75 17.75 33.61 3.02
4477 5946 2.903375 TTAACCCCGGCCTGTTAATT 57.097 45.000 14.50 0.12 33.31 1.40
4486 5955 2.375146 ACATCAATCTTTAACCCCGGC 58.625 47.619 0.00 0.00 0.00 6.13
4615 6084 3.993920 TCCAAAAAGCCAATGAGAAAGC 58.006 40.909 0.00 0.00 0.00 3.51
4623 6092 4.040706 TCAAAGAGCATCCAAAAAGCCAAT 59.959 37.500 0.00 0.00 33.66 3.16
4692 6164 7.161404 TGAAAAGTAACTAGATGAGCACATGT 58.839 34.615 0.00 0.00 36.82 3.21
4720 6204 1.547372 GCATGAGGAAGGCACAATTGT 59.453 47.619 4.92 4.92 0.00 2.71
4723 6207 2.097825 GAAGCATGAGGAAGGCACAAT 58.902 47.619 0.00 0.00 0.00 2.71
4778 6262 1.238439 CACGGAAGCAAATGGTGAGT 58.762 50.000 0.00 0.00 0.00 3.41
4785 6269 1.549203 ATCAAGGCACGGAAGCAAAT 58.451 45.000 0.00 0.00 35.83 2.32
4794 6278 6.307800 CCACAAAAAGTTTATATCAAGGCACG 59.692 38.462 0.00 0.00 0.00 5.34
4824 6308 6.500684 TTTACAAACAAATGCAGCCAAAAA 57.499 29.167 0.00 0.00 0.00 1.94
4825 6309 6.690194 ATTTACAAACAAATGCAGCCAAAA 57.310 29.167 0.00 0.00 0.00 2.44
4826 6310 7.212976 TCTATTTACAAACAAATGCAGCCAAA 58.787 30.769 0.00 0.00 30.84 3.28
4827 6311 6.753180 TCTATTTACAAACAAATGCAGCCAA 58.247 32.000 0.00 0.00 30.84 4.52
4828 6312 6.338214 TCTATTTACAAACAAATGCAGCCA 57.662 33.333 0.00 0.00 30.84 4.75
4829 6313 7.090173 TCTTCTATTTACAAACAAATGCAGCC 58.910 34.615 0.00 0.00 30.84 4.85
4830 6314 8.693542 ATCTTCTATTTACAAACAAATGCAGC 57.306 30.769 0.00 0.00 30.84 5.25
4876 6360 8.139350 GCCCTAAAGTTTTAAAGAAGTAAAGCA 58.861 33.333 0.00 0.00 29.39 3.91
4877 6361 8.139350 TGCCCTAAAGTTTTAAAGAAGTAAAGC 58.861 33.333 0.00 0.00 0.00 3.51
4880 6364 9.582648 AGATGCCCTAAAGTTTTAAAGAAGTAA 57.417 29.630 0.00 0.00 0.00 2.24
4881 6365 9.227777 GAGATGCCCTAAAGTTTTAAAGAAGTA 57.772 33.333 0.00 0.00 0.00 2.24
4882 6366 7.176865 GGAGATGCCCTAAAGTTTTAAAGAAGT 59.823 37.037 0.00 0.00 0.00 3.01
4883 6367 7.176690 TGGAGATGCCCTAAAGTTTTAAAGAAG 59.823 37.037 0.00 0.00 34.97 2.85
4884 6368 7.007723 TGGAGATGCCCTAAAGTTTTAAAGAA 58.992 34.615 0.00 0.00 34.97 2.52
4885 6369 6.548321 TGGAGATGCCCTAAAGTTTTAAAGA 58.452 36.000 0.00 0.00 34.97 2.52
4886 6370 6.834168 TGGAGATGCCCTAAAGTTTTAAAG 57.166 37.500 0.00 0.00 34.97 1.85
4887 6371 6.294286 CGTTGGAGATGCCCTAAAGTTTTAAA 60.294 38.462 0.00 0.00 34.97 1.52
4888 6372 5.182380 CGTTGGAGATGCCCTAAAGTTTTAA 59.818 40.000 0.00 0.00 34.97 1.52
4889 6373 4.698304 CGTTGGAGATGCCCTAAAGTTTTA 59.302 41.667 0.00 0.00 34.97 1.52
4890 6374 3.506067 CGTTGGAGATGCCCTAAAGTTTT 59.494 43.478 0.00 0.00 34.97 2.43
4891 6375 3.081804 CGTTGGAGATGCCCTAAAGTTT 58.918 45.455 0.00 0.00 34.97 2.66
4892 6376 2.711542 CGTTGGAGATGCCCTAAAGTT 58.288 47.619 0.00 0.00 34.97 2.66
4893 6377 1.679032 GCGTTGGAGATGCCCTAAAGT 60.679 52.381 0.00 0.00 34.03 2.66
4894 6378 1.017387 GCGTTGGAGATGCCCTAAAG 58.983 55.000 0.00 0.00 34.03 1.85
4895 6379 0.618458 AGCGTTGGAGATGCCCTAAA 59.382 50.000 0.00 0.00 41.38 1.85
4896 6380 1.491668 TAGCGTTGGAGATGCCCTAA 58.508 50.000 0.00 0.00 41.38 2.69
4897 6381 1.138266 GTTAGCGTTGGAGATGCCCTA 59.862 52.381 0.00 0.00 41.38 3.53
4898 6382 0.107654 GTTAGCGTTGGAGATGCCCT 60.108 55.000 0.00 0.00 41.38 5.19
4899 6383 1.095807 GGTTAGCGTTGGAGATGCCC 61.096 60.000 0.00 0.00 41.38 5.36
4900 6384 1.095807 GGGTTAGCGTTGGAGATGCC 61.096 60.000 0.00 0.00 41.38 4.40
4901 6385 1.429148 CGGGTTAGCGTTGGAGATGC 61.429 60.000 0.00 0.00 40.73 3.91
4902 6386 1.429148 GCGGGTTAGCGTTGGAGATG 61.429 60.000 0.00 0.00 0.00 2.90
4903 6387 1.153429 GCGGGTTAGCGTTGGAGAT 60.153 57.895 0.00 0.00 0.00 2.75
4904 6388 2.102109 TTGCGGGTTAGCGTTGGAGA 62.102 55.000 0.00 0.00 40.67 3.71
4905 6389 1.231958 TTTGCGGGTTAGCGTTGGAG 61.232 55.000 0.00 0.00 40.67 3.86
4906 6390 1.227883 TTTGCGGGTTAGCGTTGGA 60.228 52.632 0.00 0.00 40.67 3.53
4907 6391 1.081708 GTTTGCGGGTTAGCGTTGG 60.082 57.895 0.00 0.00 40.67 3.77
4908 6392 1.081708 GGTTTGCGGGTTAGCGTTG 60.082 57.895 0.00 0.00 40.67 4.10
4909 6393 1.512156 CTGGTTTGCGGGTTAGCGTT 61.512 55.000 0.00 0.00 40.67 4.84
4910 6394 1.964373 CTGGTTTGCGGGTTAGCGT 60.964 57.895 0.00 0.00 40.67 5.07
4911 6395 1.669760 TCTGGTTTGCGGGTTAGCG 60.670 57.895 0.00 0.00 40.67 4.26
4912 6396 0.887387 TGTCTGGTTTGCGGGTTAGC 60.887 55.000 0.00 0.00 37.71 3.09
4913 6397 0.872388 GTGTCTGGTTTGCGGGTTAG 59.128 55.000 0.00 0.00 0.00 2.34
4914 6398 0.535553 GGTGTCTGGTTTGCGGGTTA 60.536 55.000 0.00 0.00 0.00 2.85
4915 6399 1.826487 GGTGTCTGGTTTGCGGGTT 60.826 57.895 0.00 0.00 0.00 4.11
4916 6400 2.203294 GGTGTCTGGTTTGCGGGT 60.203 61.111 0.00 0.00 0.00 5.28
4917 6401 3.353836 CGGTGTCTGGTTTGCGGG 61.354 66.667 0.00 0.00 0.00 6.13
4918 6402 4.025401 GCGGTGTCTGGTTTGCGG 62.025 66.667 0.00 0.00 0.00 5.69
4919 6403 3.276091 TGCGGTGTCTGGTTTGCG 61.276 61.111 0.00 0.00 0.00 4.85
4920 6404 2.331451 GTGCGGTGTCTGGTTTGC 59.669 61.111 0.00 0.00 0.00 3.68
4921 6405 2.631428 CGTGCGGTGTCTGGTTTG 59.369 61.111 0.00 0.00 0.00 2.93
4922 6406 3.276846 GCGTGCGGTGTCTGGTTT 61.277 61.111 0.00 0.00 0.00 3.27
4923 6407 4.235762 AGCGTGCGGTGTCTGGTT 62.236 61.111 0.00 0.00 0.00 3.67
4924 6408 4.664677 GAGCGTGCGGTGTCTGGT 62.665 66.667 0.00 0.00 0.00 4.00
4926 6410 4.363990 AGGAGCGTGCGGTGTCTG 62.364 66.667 0.00 0.00 0.00 3.51
4927 6411 4.057428 GAGGAGCGTGCGGTGTCT 62.057 66.667 0.00 0.00 0.00 3.41
4930 6414 4.379243 AAGGAGGAGCGTGCGGTG 62.379 66.667 0.00 0.00 0.00 4.94
4931 6415 4.379243 CAAGGAGGAGCGTGCGGT 62.379 66.667 0.00 0.00 0.00 5.68
4933 6417 4.069232 TCCAAGGAGGAGCGTGCG 62.069 66.667 0.00 0.00 43.07 5.34
4940 6424 3.319198 GCCCGTGTCCAAGGAGGA 61.319 66.667 0.49 0.00 46.75 3.71
4941 6425 4.410400 GGCCCGTGTCCAAGGAGG 62.410 72.222 0.00 0.00 39.47 4.30
4942 6426 4.410400 GGGCCCGTGTCCAAGGAG 62.410 72.222 5.69 0.00 35.79 3.69
4943 6427 4.974438 AGGGCCCGTGTCCAAGGA 62.974 66.667 18.44 0.00 39.40 3.36
4944 6428 4.410400 GAGGGCCCGTGTCCAAGG 62.410 72.222 18.44 0.00 39.40 3.61
4945 6429 4.760047 CGAGGGCCCGTGTCCAAG 62.760 72.222 18.44 0.00 39.40 3.61
4979 6463 2.966309 CTTCGGAAGTGGCGTTGGC 61.966 63.158 9.61 0.00 38.90 4.52
4980 6464 0.320073 TACTTCGGAAGTGGCGTTGG 60.320 55.000 28.81 0.34 42.84 3.77
4981 6465 0.788391 GTACTTCGGAAGTGGCGTTG 59.212 55.000 28.81 1.05 42.84 4.10
4982 6466 0.677842 AGTACTTCGGAAGTGGCGTT 59.322 50.000 28.81 7.48 42.84 4.84
4983 6467 0.038526 CAGTACTTCGGAAGTGGCGT 60.039 55.000 28.81 10.92 42.84 5.68
4984 6468 0.736325 CCAGTACTTCGGAAGTGGCG 60.736 60.000 28.81 17.38 42.84 5.69
4985 6469 0.606604 TCCAGTACTTCGGAAGTGGC 59.393 55.000 28.81 21.25 42.84 5.01


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

AutoCloner maintained by Alex Coulton.