Multiple sequence alignment - TraesCS5D01G151700

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 TraesCS5D01G151700 chr5D 100.000 5487 0 0 1 5487 240851485 240845999 0.000000e+00 10133.0
1 TraesCS5D01G151700 chr5D 98.113 53 1 0 4689 4741 240846742 240846690 5.850000e-15 93.5
2 TraesCS5D01G151700 chr5D 98.113 53 1 0 4744 4796 240846797 240846745 5.850000e-15 93.5
3 TraesCS5D01G151700 chr5A 95.275 4762 186 23 1 4741 312918320 312923063 0.000000e+00 7511.0
4 TraesCS5D01G151700 chr5A 86.446 332 22 12 4744 5069 312923012 312923326 5.260000e-90 342.0
5 TraesCS5D01G151700 chr5A 79.600 250 31 9 5133 5363 312923327 312923575 1.580000e-35 161.0
6 TraesCS5D01G151700 chr5B 93.962 1739 80 13 3 1736 262821260 262822978 0.000000e+00 2606.0
7 TraesCS5D01G151700 chr5B 94.977 1493 65 6 3255 4741 262824602 262826090 0.000000e+00 2333.0
8 TraesCS5D01G151700 chr5B 97.547 1060 22 2 2200 3259 262823349 262824404 0.000000e+00 1810.0
9 TraesCS5D01G151700 chr5B 94.580 369 19 1 1799 2167 262822984 262823351 2.220000e-158 569.0
10 TraesCS5D01G151700 chr5B 91.185 329 15 6 4744 5069 262826039 262826356 8.440000e-118 435.0
11 TraesCS5D01G151700 chr5B 80.749 374 44 12 5093 5439 262826344 262826716 3.260000e-67 267.0
12 TraesCS5D01G151700 chr5B 83.682 239 25 13 1810 2042 111200336 111200106 4.310000e-51 213.0
13 TraesCS5D01G151700 chr5B 83.404 235 33 5 1812 2042 355609947 355610179 4.310000e-51 213.0
14 TraesCS5D01G151700 chr4B 84.685 222 31 3 1811 2031 82417414 82417633 9.250000e-53 219.0
15 TraesCS5D01G151700 chr1B 84.279 229 26 9 1821 2042 383801419 383801194 1.200000e-51 215.0
16 TraesCS5D01G151700 chr1D 82.500 240 26 12 1811 2042 282290847 282290616 4.340000e-46 196.0
17 TraesCS5D01G151700 chr1D 91.045 67 5 1 4961 5027 180150047 180149982 7.570000e-14 89.8
18 TraesCS5D01G151700 chr4D 81.513 238 34 9 1810 2042 417623135 417622903 2.610000e-43 187.0
19 TraesCS5D01G151700 chr2B 80.913 241 39 6 1807 2042 750016756 750016994 3.380000e-42 183.0
20 TraesCS5D01G151700 chr7D 92.188 64 5 0 4961 5024 622166355 622166418 2.100000e-14 91.6


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 TraesCS5D01G151700 chr5D 240845999 240851485 5486 True 10133.000000 10133 100.000000 1 5487 1 chr5D.!!$R1 5486
1 TraesCS5D01G151700 chr5A 312918320 312923575 5255 False 2671.333333 7511 87.107000 1 5363 3 chr5A.!!$F1 5362
2 TraesCS5D01G151700 chr5B 262821260 262826716 5456 False 1336.666667 2606 92.166667 3 5439 6 chr5B.!!$F2 5436

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
833 835 0.391597 TTTCCTTCTCGCCTTCGTGT 59.608 50.000 0.00 0.00 36.96 4.49 F
1351 1355 0.798776 GTGTGGGTTCTGATGCTTCG 59.201 55.000 0.00 0.00 0.00 3.79 F
2884 2893 1.001974 TCCCTGACACTGTGTATGTGC 59.998 52.381 14.31 1.37 38.86 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1824 0.106167 GAGGAGGCCCAATAAACCCC 60.106 60.000 0.00 0.0 33.88 4.95 R
3161 3171 3.161067 TGCAAGGGCTACAAAATTAGCA 58.839 40.909 4.63 0.0 45.52 3.49 R
4740 4964 0.106708 AAGAAGCACCGTGAAGCTCA 59.893 50.000 1.65 0.0 40.90 4.26 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
96 97 1.065491 TCACACAAACCACTCACAGCT 60.065 47.619 0.00 0.00 0.00 4.24
134 135 7.416964 AAAAATGTGGGATATTTGGATCGAA 57.583 32.000 0.00 0.00 0.00 3.71
142 143 6.934645 TGGGATATTTGGATCGAACATAACTC 59.065 38.462 0.00 0.00 0.00 3.01
153 154 8.879759 GGATCGAACATAACTCAAACAAGATTA 58.120 33.333 0.00 0.00 0.00 1.75
177 178 7.581213 AGACAGATTTAACATTTTGGTGTGA 57.419 32.000 0.00 0.00 31.49 3.58
226 227 1.586042 CGTTTGCCACACAGTGCAC 60.586 57.895 9.40 9.40 31.34 4.57
292 293 4.900154 AGCACAGTTCGCTCTAGC 57.100 55.556 0.00 0.00 33.35 3.42
544 545 3.944015 GGTTGGATCTCTCATTTCCACAG 59.056 47.826 0.00 0.00 39.21 3.66
551 552 6.771749 GGATCTCTCATTTCCACAGAATTCAT 59.228 38.462 8.44 0.00 0.00 2.57
555 556 3.063861 TCATTTCCACAGAATTCATCGCG 59.936 43.478 8.44 0.00 0.00 5.87
620 621 0.958382 CGGAGCTAGGGATCGAGAGG 60.958 65.000 0.00 0.00 0.00 3.69
833 835 0.391597 TTTCCTTCTCGCCTTCGTGT 59.608 50.000 0.00 0.00 36.96 4.49
890 892 2.074547 GACGAATGGTCCGAACTTCA 57.925 50.000 0.00 0.00 39.90 3.02
891 893 2.618053 GACGAATGGTCCGAACTTCAT 58.382 47.619 0.00 0.00 39.90 2.57
899 901 1.011968 TCCGAACTTCATTCACGCGG 61.012 55.000 12.47 0.00 37.12 6.46
1058 1062 3.522731 CTCCCGCTCCTCCTCGTG 61.523 72.222 0.00 0.00 0.00 4.35
1082 1086 1.152943 CCCCATCGTCTCTCCGAGA 60.153 63.158 0.00 0.00 40.68 4.04
1298 1302 3.134127 GTGGCCTGGTGATTCCGC 61.134 66.667 3.32 0.00 39.52 5.54
1351 1355 0.798776 GTGTGGGTTCTGATGCTTCG 59.201 55.000 0.00 0.00 0.00 3.79
1355 1359 1.626321 TGGGTTCTGATGCTTCGGTAA 59.374 47.619 8.19 0.08 0.00 2.85
1372 1376 4.040706 TCGGTAAAATACTGACACTGGGTT 59.959 41.667 0.00 0.00 39.06 4.11
1500 1504 2.092291 TTCGTCGATGCCAACGCTC 61.092 57.895 0.00 0.00 38.72 5.03
1503 1507 1.421485 GTCGATGCCAACGCTCTTG 59.579 57.895 0.00 0.00 35.36 3.02
1504 1508 1.005037 TCGATGCCAACGCTCTTGT 60.005 52.632 0.00 0.00 35.36 3.16
1616 1620 3.378427 ACCTCTTGTTCAGTTCTGTTTGC 59.622 43.478 0.00 0.00 0.00 3.68
1624 1628 4.071961 TCAGTTCTGTTTGCAGCTTCTA 57.928 40.909 0.00 0.00 42.29 2.10
1626 1630 2.810852 AGTTCTGTTTGCAGCTTCTAGC 59.189 45.455 0.00 0.00 42.29 3.42
1682 1686 7.487822 TCTTCAGGAACTAGATCAGTCAATT 57.512 36.000 0.00 0.00 36.04 2.32
1726 1732 8.362639 AGAGTTTGAATGTTAAACATGCTGAAT 58.637 29.630 2.42 0.00 37.97 2.57
1805 1811 5.506317 GGTGGAAGAGTGTATTTATGCATGC 60.506 44.000 11.82 11.82 0.00 4.06
1871 1877 7.906327 AGCCAAACTTTGACCATATGTAAAAT 58.094 30.769 2.87 0.00 0.00 1.82
2068 2074 2.571653 TGTAGTCTGGTAATGGCAAGCT 59.428 45.455 0.00 0.00 0.00 3.74
2097 2103 8.383318 ACTATTATTCATTCAAGAATGGACCG 57.617 34.615 19.46 7.48 46.08 4.79
2104 2110 2.104967 TCAAGAATGGACCGGTATCGT 58.895 47.619 7.34 0.84 33.95 3.73
2161 2167 7.568349 TCTACATGCTTGTCTTCTATTCCATT 58.432 34.615 8.74 0.00 37.28 3.16
2275 2281 2.668001 GCGTGATGCATGCTTGTGTAAA 60.668 45.455 20.33 0.00 42.44 2.01
2335 2344 3.334691 TGTGAAATTTAGGACGAGCAGG 58.665 45.455 0.00 0.00 0.00 4.85
2336 2345 3.244422 TGTGAAATTTAGGACGAGCAGGT 60.244 43.478 0.00 0.00 0.00 4.00
2356 2365 6.151691 CAGGTGTGTAATTGACAATCCTTTG 58.848 40.000 0.05 0.00 39.76 2.77
2484 2493 4.853196 CGTTGCATTTCTGGTAATCTTGTG 59.147 41.667 0.00 0.00 0.00 3.33
2516 2525 4.577693 TCTGCAGAAATTATGGTGATCAGC 59.422 41.667 15.67 18.01 0.00 4.26
2699 2708 7.890515 TGAGTTGTTTTTATGTCCATTGCATA 58.109 30.769 0.00 0.00 0.00 3.14
2884 2893 1.001974 TCCCTGACACTGTGTATGTGC 59.998 52.381 14.31 1.37 38.86 4.57
3114 3123 7.665559 CCCTTTATATAGTTTTGGCATGCTCTA 59.334 37.037 18.92 12.33 0.00 2.43
3307 3519 3.672808 AGTTCTTCAGTCCTCTTGCATG 58.327 45.455 0.00 0.00 0.00 4.06
3308 3520 2.746362 GTTCTTCAGTCCTCTTGCATGG 59.254 50.000 0.00 0.00 0.00 3.66
3378 3591 6.164408 TCATCACATAGTAACAAAAGTGCG 57.836 37.500 0.00 0.00 0.00 5.34
3568 3782 3.162666 ACGGTGTCTTTCCTGATCACTA 58.837 45.455 0.00 0.00 0.00 2.74
3772 3986 1.811965 CTCATGCCGATGTGGTTGAAA 59.188 47.619 0.00 0.00 41.21 2.69
3884 4098 2.728007 AGACTTAATTTCTGCCAGCCC 58.272 47.619 0.00 0.00 0.00 5.19
4034 4248 3.118038 TCTTTTGTACCTTGTGGCTGAGT 60.118 43.478 0.00 0.00 36.63 3.41
4114 4328 6.048509 CCTTTTGACTTGTAAGTTTGGCATT 58.951 36.000 0.00 0.00 39.88 3.56
4127 4341 2.602257 TGGCATTGGAGTATGACTCG 57.398 50.000 0.73 0.00 45.96 4.18
4306 4523 1.075212 GTAGACTCTAGGGCGGGGTAT 59.925 57.143 0.00 0.00 0.00 2.73
4309 4526 1.353694 GACTCTAGGGCGGGGTATCTA 59.646 57.143 0.00 0.00 0.00 1.98
4342 4559 0.464373 ATGTGGCGATGTAAGGCTGG 60.464 55.000 0.00 0.00 35.01 4.85
4356 4573 7.208064 TGTAAGGCTGGAAGAATAAACCTAT 57.792 36.000 0.00 0.00 34.07 2.57
4388 4605 0.039798 TGGCGTCTCGTCTGTGTTAC 60.040 55.000 0.00 0.00 30.55 2.50
4391 4608 0.594602 CGTCTCGTCTGTGTTACCCA 59.405 55.000 0.00 0.00 0.00 4.51
4403 4620 2.096119 GTGTTACCCAACCGATGAAACG 60.096 50.000 0.00 0.00 33.41 3.60
4405 4622 0.674269 TACCCAACCGATGAAACGCC 60.674 55.000 0.00 0.00 0.00 5.68
4409 4626 2.332654 AACCGATGAAACGCCTGCC 61.333 57.895 0.00 0.00 0.00 4.85
4426 4649 6.259387 ACGCCTGCCTAGTATTGTAAATTAAC 59.741 38.462 0.00 0.00 0.00 2.01
4468 4691 2.186826 GCCCGCGATGCCAGTTAAT 61.187 57.895 8.23 0.00 0.00 1.40
4480 4703 3.126171 TGCCAGTTAATCATGCGTTGTAC 59.874 43.478 0.00 0.00 0.00 2.90
4487 4710 6.371548 AGTTAATCATGCGTTGTACAATCTGT 59.628 34.615 12.26 0.00 0.00 3.41
4525 4748 2.567985 GAGGTTGTTCTTGGTTTCCGA 58.432 47.619 0.00 0.00 0.00 4.55
4537 4760 8.508875 GTTCTTGGTTTCCGAAGAATTACATAA 58.491 33.333 0.00 0.00 39.69 1.90
4626 4850 1.091771 CAGTTGATGGCCGATTCGCT 61.092 55.000 0.00 0.00 0.00 4.93
4649 4873 1.141019 GCCGATGCCGTAGAGTTGA 59.859 57.895 0.00 0.00 0.00 3.18
4654 4878 3.181520 CCGATGCCGTAGAGTTGAAAAAG 60.182 47.826 0.00 0.00 0.00 2.27
4736 4960 4.105754 TCACTGATCCATCTATCCGTCT 57.894 45.455 0.00 0.00 0.00 4.18
4737 4961 3.823304 TCACTGATCCATCTATCCGTCTG 59.177 47.826 0.00 0.00 0.00 3.51
4738 4962 3.823304 CACTGATCCATCTATCCGTCTGA 59.177 47.826 0.00 0.00 0.00 3.27
4739 4963 3.823873 ACTGATCCATCTATCCGTCTGAC 59.176 47.826 0.00 0.00 0.00 3.51
4740 4964 4.078537 CTGATCCATCTATCCGTCTGACT 58.921 47.826 6.21 0.00 0.00 3.41
4741 4965 3.823304 TGATCCATCTATCCGTCTGACTG 59.177 47.826 6.21 0.00 0.00 3.51
4742 4966 3.577805 TCCATCTATCCGTCTGACTGA 57.422 47.619 6.21 5.26 0.00 3.41
4743 4967 3.481453 TCCATCTATCCGTCTGACTGAG 58.519 50.000 6.21 0.00 0.00 3.35
4744 4968 2.030363 CCATCTATCCGTCTGACTGAGC 60.030 54.545 6.21 0.00 0.00 4.26
4745 4969 2.719531 TCTATCCGTCTGACTGAGCT 57.280 50.000 6.21 0.00 0.00 4.09
4746 4970 3.006112 TCTATCCGTCTGACTGAGCTT 57.994 47.619 6.21 0.00 0.00 3.74
4747 4971 2.946329 TCTATCCGTCTGACTGAGCTTC 59.054 50.000 6.21 0.00 0.00 3.86
4748 4972 1.550327 ATCCGTCTGACTGAGCTTCA 58.450 50.000 6.21 0.00 0.00 3.02
4749 4973 0.598562 TCCGTCTGACTGAGCTTCAC 59.401 55.000 6.21 0.00 0.00 3.18
4750 4974 0.730834 CCGTCTGACTGAGCTTCACG 60.731 60.000 6.21 0.00 0.00 4.35
4751 4975 0.730834 CGTCTGACTGAGCTTCACGG 60.731 60.000 6.21 0.00 0.00 4.94
4752 4976 0.315568 GTCTGACTGAGCTTCACGGT 59.684 55.000 0.00 0.00 0.00 4.83
4753 4977 0.315251 TCTGACTGAGCTTCACGGTG 59.685 55.000 0.56 0.56 0.00 4.94
4754 4978 1.287730 CTGACTGAGCTTCACGGTGC 61.288 60.000 2.51 0.00 0.00 5.01
4755 4979 1.005630 GACTGAGCTTCACGGTGCT 60.006 57.895 2.51 0.00 42.82 4.40
4756 4980 0.601311 GACTGAGCTTCACGGTGCTT 60.601 55.000 2.51 0.00 39.91 3.91
4757 4981 0.601311 ACTGAGCTTCACGGTGCTTC 60.601 55.000 2.51 0.00 39.91 3.86
4758 4982 0.320247 CTGAGCTTCACGGTGCTTCT 60.320 55.000 2.51 0.00 39.91 2.85
4759 4983 0.106708 TGAGCTTCACGGTGCTTCTT 59.893 50.000 2.51 0.00 39.91 2.52
4760 4984 1.230324 GAGCTTCACGGTGCTTCTTT 58.770 50.000 2.51 0.00 39.91 2.52
4761 4985 0.947244 AGCTTCACGGTGCTTCTTTG 59.053 50.000 2.51 0.00 35.86 2.77
4762 4986 0.663153 GCTTCACGGTGCTTCTTTGT 59.337 50.000 2.51 0.00 0.00 2.83
4763 4987 1.334149 GCTTCACGGTGCTTCTTTGTC 60.334 52.381 2.51 0.00 0.00 3.18
4764 4988 2.213499 CTTCACGGTGCTTCTTTGTCT 58.787 47.619 2.51 0.00 0.00 3.41
4765 4989 1.865865 TCACGGTGCTTCTTTGTCTC 58.134 50.000 2.51 0.00 0.00 3.36
4766 4990 1.412710 TCACGGTGCTTCTTTGTCTCT 59.587 47.619 2.51 0.00 0.00 3.10
4767 4991 1.528586 CACGGTGCTTCTTTGTCTCTG 59.471 52.381 0.00 0.00 0.00 3.35
4768 4992 0.514691 CGGTGCTTCTTTGTCTCTGC 59.485 55.000 0.00 0.00 0.00 4.26
4769 4993 1.875576 CGGTGCTTCTTTGTCTCTGCT 60.876 52.381 0.00 0.00 0.00 4.24
4770 4994 2.225467 GGTGCTTCTTTGTCTCTGCTT 58.775 47.619 0.00 0.00 0.00 3.91
4771 4995 2.225255 GGTGCTTCTTTGTCTCTGCTTC 59.775 50.000 0.00 0.00 0.00 3.86
4772 4996 2.874701 GTGCTTCTTTGTCTCTGCTTCA 59.125 45.455 0.00 0.00 0.00 3.02
4773 4997 2.874701 TGCTTCTTTGTCTCTGCTTCAC 59.125 45.455 0.00 0.00 0.00 3.18
4774 4998 3.137533 GCTTCTTTGTCTCTGCTTCACT 58.862 45.455 0.00 0.00 0.00 3.41
4775 4999 3.059051 GCTTCTTTGTCTCTGCTTCACTG 60.059 47.826 0.00 0.00 0.00 3.66
4776 5000 4.375272 CTTCTTTGTCTCTGCTTCACTGA 58.625 43.478 0.00 0.00 0.00 3.41
4777 5001 3.722147 TCTTTGTCTCTGCTTCACTGAC 58.278 45.455 0.00 0.00 0.00 3.51
4778 5002 2.533266 TTGTCTCTGCTTCACTGACC 57.467 50.000 0.00 0.00 0.00 4.02
4779 5003 0.681733 TGTCTCTGCTTCACTGACCC 59.318 55.000 0.00 0.00 0.00 4.46
4780 5004 0.681733 GTCTCTGCTTCACTGACCCA 59.318 55.000 0.00 0.00 0.00 4.51
4781 5005 1.277557 GTCTCTGCTTCACTGACCCAT 59.722 52.381 0.00 0.00 0.00 4.00
4782 5006 1.552337 TCTCTGCTTCACTGACCCATC 59.448 52.381 0.00 0.00 0.00 3.51
4783 5007 1.554160 CTCTGCTTCACTGACCCATCT 59.446 52.381 0.00 0.00 0.00 2.90
4784 5008 2.762887 CTCTGCTTCACTGACCCATCTA 59.237 50.000 0.00 0.00 0.00 1.98
4785 5009 3.378512 TCTGCTTCACTGACCCATCTAT 58.621 45.455 0.00 0.00 0.00 1.98
4786 5010 3.386078 TCTGCTTCACTGACCCATCTATC 59.614 47.826 0.00 0.00 0.00 2.08
4787 5011 2.435805 TGCTTCACTGACCCATCTATCC 59.564 50.000 0.00 0.00 0.00 2.59
4788 5012 2.546795 GCTTCACTGACCCATCTATCCG 60.547 54.545 0.00 0.00 0.00 4.18
4789 5013 2.454336 TCACTGACCCATCTATCCGT 57.546 50.000 0.00 0.00 0.00 4.69
4790 5014 2.307768 TCACTGACCCATCTATCCGTC 58.692 52.381 0.00 0.00 0.00 4.79
4791 5015 2.091830 TCACTGACCCATCTATCCGTCT 60.092 50.000 0.00 0.00 0.00 4.18
4869 5094 1.094785 GTGGCTGTGAATAACCGCAT 58.905 50.000 0.00 0.00 40.53 4.73
4904 5132 5.005203 CGAGCAGCTAACTTTGACTGAATAG 59.995 44.000 0.00 0.00 31.67 1.73
4909 5137 7.545965 GCAGCTAACTTTGACTGAATAGTTCTA 59.454 37.037 0.00 0.00 37.25 2.10
4933 5161 2.307098 CCCCAGGTGAAGAAGAAGATGT 59.693 50.000 0.00 0.00 0.00 3.06
4949 5177 5.541484 AGAAGATGTTGAAAAGAAATGGCCT 59.459 36.000 3.32 0.00 0.00 5.19
4951 5179 4.590222 AGATGTTGAAAAGAAATGGCCTGT 59.410 37.500 3.32 0.00 0.00 4.00
4952 5180 4.751767 TGTTGAAAAGAAATGGCCTGTT 57.248 36.364 3.32 0.00 0.00 3.16
4953 5181 5.860941 TGTTGAAAAGAAATGGCCTGTTA 57.139 34.783 3.32 0.00 0.00 2.41
4954 5182 6.227298 TGTTGAAAAGAAATGGCCTGTTAA 57.773 33.333 3.32 0.00 0.00 2.01
4955 5183 6.825610 TGTTGAAAAGAAATGGCCTGTTAAT 58.174 32.000 3.32 0.00 0.00 1.40
4976 5204 9.626045 GTTAATGGAGTTTTGATTTAGTTGAGG 57.374 33.333 0.00 0.00 0.00 3.86
4996 5224 8.882736 GTTGAGGTTTTGACAAGATTTCATTTT 58.117 29.630 0.00 0.00 0.00 1.82
5030 5258 0.615331 ATGCAGGACGTGAGGAATGT 59.385 50.000 0.00 0.00 0.00 2.71
5046 5274 2.533266 ATGTGTGTGTGTGAGGAGAC 57.467 50.000 0.00 0.00 0.00 3.36
5048 5276 0.597637 GTGTGTGTGTGAGGAGACGG 60.598 60.000 0.00 0.00 0.00 4.79
5069 5299 2.277084 GGGCGAAGACGAATGTACAAT 58.723 47.619 0.00 0.00 42.66 2.71
5070 5300 2.030457 GGGCGAAGACGAATGTACAATG 59.970 50.000 0.00 0.00 42.66 2.82
5071 5301 2.927477 GGCGAAGACGAATGTACAATGA 59.073 45.455 0.00 0.00 42.66 2.57
5072 5302 3.555956 GGCGAAGACGAATGTACAATGAT 59.444 43.478 0.00 0.00 42.66 2.45
5073 5303 4.034048 GGCGAAGACGAATGTACAATGATT 59.966 41.667 0.00 0.00 42.66 2.57
5074 5304 5.447279 GGCGAAGACGAATGTACAATGATTT 60.447 40.000 0.00 0.00 42.66 2.17
5075 5305 6.021596 GCGAAGACGAATGTACAATGATTTT 58.978 36.000 0.00 0.00 42.66 1.82
5076 5306 6.523201 GCGAAGACGAATGTACAATGATTTTT 59.477 34.615 0.00 0.00 42.66 1.94
5175 5406 5.162000 GGAATCTTAGAGCAATTCCAACG 57.838 43.478 7.29 0.00 45.13 4.10
5227 5475 7.740805 ACTAAGAGAAACTTTTGTCAGATCCT 58.259 34.615 2.10 0.00 39.72 3.24
5232 5481 7.993183 AGAGAAACTTTTGTCAGATCCTGTAAA 59.007 33.333 2.10 0.00 33.31 2.01
5287 5537 8.990163 AACTTTTCCATTAAACAAGTCTAGGA 57.010 30.769 0.00 0.00 0.00 2.94
5306 5556 2.310233 CCCGCAAGTCAGTGACACG 61.310 63.158 24.73 22.08 34.60 4.49
5310 5560 1.227527 CAAGTCAGTGACACGGGCA 60.228 57.895 24.73 0.00 34.60 5.36
5319 5569 1.822186 GACACGGGCAAGTTGTGGT 60.822 57.895 4.48 0.00 37.92 4.16
5332 5582 3.376078 GTGGTACGACGGGGAGCA 61.376 66.667 0.00 0.00 0.00 4.26
5408 5665 2.126228 CGTATGACGGCGTGGTGT 60.126 61.111 21.19 2.43 38.08 4.16
5430 5687 2.330393 GCATACGACGGCGAGCTA 59.670 61.111 22.49 0.00 41.64 3.32
5449 5706 4.803426 GGCAGTCCGGCGAGTGAG 62.803 72.222 9.30 0.00 41.32 3.51
5450 5707 4.803426 GCAGTCCGGCGAGTGAGG 62.803 72.222 9.30 0.00 41.32 3.86
5451 5708 4.803426 CAGTCCGGCGAGTGAGGC 62.803 72.222 9.30 0.00 41.32 4.70
5453 5710 4.070552 GTCCGGCGAGTGAGGCTT 62.071 66.667 9.30 0.00 34.19 4.35
5454 5711 4.069232 TCCGGCGAGTGAGGCTTG 62.069 66.667 9.30 0.00 34.19 4.01
5455 5712 4.069232 CCGGCGAGTGAGGCTTGA 62.069 66.667 9.30 0.00 34.19 3.02
5456 5713 2.048222 CGGCGAGTGAGGCTTGAA 60.048 61.111 0.00 0.00 34.19 2.69
5457 5714 2.097038 CGGCGAGTGAGGCTTGAAG 61.097 63.158 0.00 0.00 34.19 3.02
5458 5715 1.004440 GGCGAGTGAGGCTTGAAGT 60.004 57.895 0.00 0.00 0.00 3.01
5459 5716 0.603975 GGCGAGTGAGGCTTGAAGTT 60.604 55.000 0.00 0.00 0.00 2.66
5460 5717 1.230324 GCGAGTGAGGCTTGAAGTTT 58.770 50.000 0.00 0.00 0.00 2.66
5461 5718 1.195674 GCGAGTGAGGCTTGAAGTTTC 59.804 52.381 0.00 0.00 0.00 2.78
5462 5719 2.483876 CGAGTGAGGCTTGAAGTTTCA 58.516 47.619 0.00 0.00 34.92 2.69
5463 5720 3.070018 CGAGTGAGGCTTGAAGTTTCAT 58.930 45.455 4.57 0.00 37.00 2.57
5464 5721 4.245660 CGAGTGAGGCTTGAAGTTTCATA 58.754 43.478 4.57 0.00 37.00 2.15
5465 5722 4.092091 CGAGTGAGGCTTGAAGTTTCATAC 59.908 45.833 4.57 2.63 37.00 2.39
5466 5723 3.997021 AGTGAGGCTTGAAGTTTCATACG 59.003 43.478 4.57 0.00 37.00 3.06
5467 5724 3.125316 GTGAGGCTTGAAGTTTCATACGG 59.875 47.826 4.57 0.00 37.00 4.02
5468 5725 2.084546 AGGCTTGAAGTTTCATACGGC 58.915 47.619 0.00 1.16 37.00 5.68
5469 5726 1.132453 GGCTTGAAGTTTCATACGGCC 59.868 52.381 0.00 0.00 37.00 6.13
5470 5727 1.202031 GCTTGAAGTTTCATACGGCCG 60.202 52.381 26.86 26.86 37.00 6.13
5471 5728 0.800012 TTGAAGTTTCATACGGCCGC 59.200 50.000 28.58 6.84 37.00 6.53
5472 5729 1.022451 TGAAGTTTCATACGGCCGCC 61.022 55.000 28.58 0.00 31.01 6.13
5473 5730 1.003112 AAGTTTCATACGGCCGCCA 60.003 52.632 28.58 14.80 0.00 5.69
5474 5731 0.606944 AAGTTTCATACGGCCGCCAA 60.607 50.000 28.58 12.10 0.00 4.52
5475 5732 0.606944 AGTTTCATACGGCCGCCAAA 60.607 50.000 28.58 15.83 0.00 3.28
5476 5733 0.241481 GTTTCATACGGCCGCCAAAA 59.759 50.000 28.58 17.60 0.00 2.44
5477 5734 0.523966 TTTCATACGGCCGCCAAAAG 59.476 50.000 28.58 9.76 0.00 2.27
5478 5735 0.606944 TTCATACGGCCGCCAAAAGT 60.607 50.000 28.58 6.16 0.00 2.66
5479 5736 0.606944 TCATACGGCCGCCAAAAGTT 60.607 50.000 28.58 5.26 0.00 2.66
5480 5737 1.088306 CATACGGCCGCCAAAAGTTA 58.912 50.000 28.58 7.81 0.00 2.24
5481 5738 1.469308 CATACGGCCGCCAAAAGTTAA 59.531 47.619 28.58 0.00 0.00 2.01
5482 5739 1.158434 TACGGCCGCCAAAAGTTAAG 58.842 50.000 28.58 0.00 0.00 1.85
5483 5740 1.211709 CGGCCGCCAAAAGTTAAGG 59.788 57.895 14.67 0.00 0.00 2.69
5484 5741 1.238625 CGGCCGCCAAAAGTTAAGGA 61.239 55.000 14.67 0.00 0.00 3.36
5485 5742 0.963225 GGCCGCCAAAAGTTAAGGAA 59.037 50.000 3.91 0.00 0.00 3.36
5486 5743 1.067846 GGCCGCCAAAAGTTAAGGAAG 60.068 52.381 3.91 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 9.950496 ATCTGTCTAATCTTGTTTGAGTTATGT 57.050 29.630 0.00 0.00 0.00 2.29
153 154 7.581213 TCACACCAAAATGTTAAATCTGTCT 57.419 32.000 0.00 0.00 0.00 3.41
177 178 3.508845 TCCTAGGCAAGCTTCAAACTT 57.491 42.857 2.96 0.00 0.00 2.66
473 474 5.047306 TCCTCCATATACGGTTGATGATCAC 60.047 44.000 0.00 0.00 0.00 3.06
478 479 4.600692 TGTCCTCCATATACGGTTGATG 57.399 45.455 0.00 0.00 0.00 3.07
544 545 1.063912 TGATGTTGGCGCGATGAATTC 59.936 47.619 12.10 0.00 0.00 2.17
551 552 2.553770 CGTTTGATGTTGGCGCGA 59.446 55.556 12.10 0.00 0.00 5.87
555 556 2.126502 CGGCCGTTTGATGTTGGC 60.127 61.111 19.50 0.00 46.82 4.52
620 621 0.462759 GCCATGGAGCAGTCAGTACC 60.463 60.000 18.40 0.00 0.00 3.34
877 879 1.790755 CGTGAATGAAGTTCGGACCA 58.209 50.000 0.00 0.00 39.80 4.02
884 886 1.798813 GTCTTCCGCGTGAATGAAGTT 59.201 47.619 17.65 0.00 37.39 2.66
885 887 1.429463 GTCTTCCGCGTGAATGAAGT 58.571 50.000 17.65 0.00 37.39 3.01
886 888 0.366871 CGTCTTCCGCGTGAATGAAG 59.633 55.000 13.73 13.73 37.44 3.02
887 889 0.038983 TCGTCTTCCGCGTGAATGAA 60.039 50.000 4.92 0.00 36.19 2.57
888 890 0.038983 TTCGTCTTCCGCGTGAATGA 60.039 50.000 4.92 5.56 36.19 2.57
889 891 0.999406 ATTCGTCTTCCGCGTGAATG 59.001 50.000 4.92 3.41 36.19 2.67
890 892 0.999406 CATTCGTCTTCCGCGTGAAT 59.001 50.000 4.92 1.92 36.19 2.57
891 893 1.011968 CCATTCGTCTTCCGCGTGAA 61.012 55.000 4.92 7.62 36.19 3.18
899 901 1.134946 CATTTGGGCCCATTCGTCTTC 59.865 52.381 29.23 0.00 0.00 2.87
1106 1110 3.684628 AGGGGAGCGGAGAGGGAA 61.685 66.667 0.00 0.00 0.00 3.97
1196 1200 3.385384 CAGGAGGCTGCGTGGAGA 61.385 66.667 0.00 0.00 0.00 3.71
1298 1302 4.260170 CAAGGAATGAAGAAGAGGTCCAG 58.740 47.826 0.00 0.00 0.00 3.86
1351 1355 5.533528 ACAAACCCAGTGTCAGTATTTTACC 59.466 40.000 0.00 0.00 0.00 2.85
1355 1359 5.197451 TCAACAAACCCAGTGTCAGTATTT 58.803 37.500 0.00 0.00 0.00 1.40
1372 1376 1.284408 GTCGCGGCCATTTCAACAA 59.716 52.632 6.13 0.00 0.00 2.83
1500 1504 2.880890 ACACTCTAAGGCAGCAAACAAG 59.119 45.455 0.00 0.00 0.00 3.16
1503 1507 1.537202 CCACACTCTAAGGCAGCAAAC 59.463 52.381 0.00 0.00 0.00 2.93
1504 1508 1.142870 ACCACACTCTAAGGCAGCAAA 59.857 47.619 0.00 0.00 0.00 3.68
1616 1620 7.493743 AATCATTCACTAATGCTAGAAGCTG 57.506 36.000 0.00 0.00 42.97 4.24
1624 1628 5.133221 GTGGGGTAATCATTCACTAATGCT 58.867 41.667 0.00 0.00 41.96 3.79
1626 1630 5.445069 TGGTGGGGTAATCATTCACTAATG 58.555 41.667 0.00 0.00 43.32 1.90
1705 1711 6.709145 GCATTCAGCATGTTTAACATTCAA 57.291 33.333 7.97 0.00 44.79 2.69
1769 1775 3.916989 ACTCTTCCACCCTGATTTTACCT 59.083 43.478 0.00 0.00 0.00 3.08
1818 1824 0.106167 GAGGAGGCCCAATAAACCCC 60.106 60.000 0.00 0.00 33.88 4.95
2068 2074 9.919416 TCCATTCTTGAATGAATAATAGTTCCA 57.081 29.630 20.95 0.00 35.18 3.53
2097 2103 5.470098 AGACATATGGCAAAATCACGATACC 59.530 40.000 12.11 0.00 0.00 2.73
2104 2110 8.065473 ACAATACAAGACATATGGCAAAATCA 57.935 30.769 12.11 0.00 0.00 2.57
2148 2154 8.928448 AGTAGCAGACATAAATGGAATAGAAGA 58.072 33.333 0.00 0.00 0.00 2.87
2356 2365 8.587111 CAAGCTTCAACAAAAGAAAAAGTAGAC 58.413 33.333 0.00 0.00 0.00 2.59
2484 2493 7.912250 CACCATAATTTCTGCAGAATAGACAAC 59.088 37.037 28.89 0.00 33.54 3.32
2516 2525 5.116180 TCAAACAAGACCAGACACTAACTG 58.884 41.667 0.00 0.00 35.43 3.16
2976 2985 7.669722 AGCTTCTGTGGGACAAAATAGAAATTA 59.330 33.333 0.00 0.00 44.16 1.40
3071 3080 4.592997 AAGGGGCAGAAAATAGCTAAGT 57.407 40.909 0.00 0.00 0.00 2.24
3114 3123 4.223923 AGCAGTTAGGTGAGAGCAATACTT 59.776 41.667 0.00 0.00 0.00 2.24
3149 3158 4.342092 ACAAAATTAGCAGCAAGAACCTGT 59.658 37.500 0.00 0.00 32.93 4.00
3161 3171 3.161067 TGCAAGGGCTACAAAATTAGCA 58.839 40.909 4.63 0.00 45.52 3.49
3354 3567 6.675486 GCGCACTTTTGTTACTATGTGATGAT 60.675 38.462 0.30 0.00 0.00 2.45
3378 3591 4.261801 TGGAAATAGTAGGCAGACAAAGC 58.738 43.478 0.00 0.00 0.00 3.51
3568 3782 4.334552 TGAATTGCAGTGTCACCACATAT 58.665 39.130 0.00 0.00 44.39 1.78
3772 3986 3.132925 GCAAGACCACAAATGCAATTGT 58.867 40.909 14.42 14.42 44.08 2.71
3884 4098 3.409026 AGTCCACAAGGTAGCTTTCAG 57.591 47.619 3.96 0.00 35.89 3.02
4034 4248 4.947388 ACTCACTTGTGTTTTGCCTCTAAA 59.053 37.500 0.46 0.00 0.00 1.85
4076 4290 5.169836 GTCAAAAGGACAGTGTTTCGAAT 57.830 39.130 0.00 0.00 46.19 3.34
4077 4291 4.609691 GTCAAAAGGACAGTGTTTCGAA 57.390 40.909 0.00 0.00 46.19 3.71
4114 4328 4.570772 GCTTAAAATGCGAGTCATACTCCA 59.429 41.667 1.63 1.98 42.12 3.86
4127 4341 4.329801 GCCAATGTTACCAGCTTAAAATGC 59.670 41.667 0.00 0.00 0.00 3.56
4306 4523 1.164411 CATGTTGCAACCGGCTTAGA 58.836 50.000 26.14 5.77 45.15 2.10
4309 4526 1.363443 CACATGTTGCAACCGGCTT 59.637 52.632 26.14 3.92 45.15 4.35
4368 4585 0.240145 TAACACAGACGAGACGCCAG 59.760 55.000 0.00 0.00 0.00 4.85
4388 4605 1.674322 AGGCGTTTCATCGGTTGGG 60.674 57.895 0.00 0.00 0.00 4.12
4391 4608 2.332654 GGCAGGCGTTTCATCGGTT 61.333 57.895 0.00 0.00 0.00 4.44
4403 4620 6.259387 ACGTTAATTTACAATACTAGGCAGGC 59.741 38.462 0.00 0.00 0.00 4.85
4405 4622 7.493320 TGGACGTTAATTTACAATACTAGGCAG 59.507 37.037 0.00 0.00 0.00 4.85
4426 4649 1.200252 ACTCGACAGACAAGATGGACG 59.800 52.381 0.00 0.00 0.00 4.79
4456 4679 3.181497 ACAACGCATGATTAACTGGCATC 60.181 43.478 0.00 0.00 0.00 3.91
4462 4685 6.371548 ACAGATTGTACAACGCATGATTAACT 59.628 34.615 11.22 0.00 0.00 2.24
4468 4691 6.256975 GGTTATACAGATTGTACAACGCATGA 59.743 38.462 11.22 0.00 40.19 3.07
4480 4703 6.458206 CCCATCACAAACGGTTATACAGATTG 60.458 42.308 0.00 0.00 33.69 2.67
4487 4710 3.520317 ACCTCCCATCACAAACGGTTATA 59.480 43.478 0.00 0.00 0.00 0.98
4537 4760 5.201243 GCTAGGAACCCCAGAATTTTACAT 58.799 41.667 0.00 0.00 33.88 2.29
4551 4774 5.335976 CCTGAGTTTTGATTTGCTAGGAACC 60.336 44.000 0.00 0.00 0.00 3.62
4636 4860 2.548057 CAGCTTTTTCAACTCTACGGCA 59.452 45.455 0.00 0.00 0.00 5.69
4639 4863 2.411547 CCGCAGCTTTTTCAACTCTACG 60.412 50.000 0.00 0.00 0.00 3.51
4641 4865 2.548057 CACCGCAGCTTTTTCAACTCTA 59.452 45.455 0.00 0.00 0.00 2.43
4649 4873 1.441311 CCAACCACCGCAGCTTTTT 59.559 52.632 0.00 0.00 0.00 1.94
4736 4960 1.300931 GCACCGTGAAGCTCAGTCA 60.301 57.895 1.65 0.00 0.00 3.41
4737 4961 0.601311 AAGCACCGTGAAGCTCAGTC 60.601 55.000 1.65 0.00 40.90 3.51
4738 4962 0.601311 GAAGCACCGTGAAGCTCAGT 60.601 55.000 1.65 0.00 40.90 3.41
4739 4963 0.320247 AGAAGCACCGTGAAGCTCAG 60.320 55.000 1.65 0.00 40.90 3.35
4740 4964 0.106708 AAGAAGCACCGTGAAGCTCA 59.893 50.000 1.65 0.00 40.90 4.26
4741 4965 1.069636 CAAAGAAGCACCGTGAAGCTC 60.070 52.381 1.65 0.00 40.90 4.09
4742 4966 0.947244 CAAAGAAGCACCGTGAAGCT 59.053 50.000 1.65 0.00 44.31 3.74
4743 4967 0.663153 ACAAAGAAGCACCGTGAAGC 59.337 50.000 1.65 0.00 0.00 3.86
4744 4968 2.213499 AGACAAAGAAGCACCGTGAAG 58.787 47.619 1.65 0.00 0.00 3.02
4745 4969 2.158957 AGAGACAAAGAAGCACCGTGAA 60.159 45.455 1.65 0.00 0.00 3.18
4746 4970 1.412710 AGAGACAAAGAAGCACCGTGA 59.587 47.619 1.65 0.00 0.00 4.35
4747 4971 1.528586 CAGAGACAAAGAAGCACCGTG 59.471 52.381 0.00 0.00 0.00 4.94
4748 4972 1.871080 CAGAGACAAAGAAGCACCGT 58.129 50.000 0.00 0.00 0.00 4.83
4749 4973 0.514691 GCAGAGACAAAGAAGCACCG 59.485 55.000 0.00 0.00 0.00 4.94
4750 4974 1.889545 AGCAGAGACAAAGAAGCACC 58.110 50.000 0.00 0.00 0.00 5.01
4751 4975 2.874701 TGAAGCAGAGACAAAGAAGCAC 59.125 45.455 0.00 0.00 0.00 4.40
4752 4976 2.874701 GTGAAGCAGAGACAAAGAAGCA 59.125 45.455 0.00 0.00 0.00 3.91
4753 4977 3.059051 CAGTGAAGCAGAGACAAAGAAGC 60.059 47.826 0.00 0.00 0.00 3.86
4754 4978 4.210955 GTCAGTGAAGCAGAGACAAAGAAG 59.789 45.833 0.00 0.00 0.00 2.85
4755 4979 4.122776 GTCAGTGAAGCAGAGACAAAGAA 58.877 43.478 0.00 0.00 0.00 2.52
4756 4980 3.493350 GGTCAGTGAAGCAGAGACAAAGA 60.493 47.826 0.00 0.00 0.00 2.52
4757 4981 2.805099 GGTCAGTGAAGCAGAGACAAAG 59.195 50.000 0.00 0.00 0.00 2.77
4758 4982 2.485479 GGGTCAGTGAAGCAGAGACAAA 60.485 50.000 0.00 0.00 0.00 2.83
4759 4983 1.070758 GGGTCAGTGAAGCAGAGACAA 59.929 52.381 0.00 0.00 0.00 3.18
4760 4984 0.681733 GGGTCAGTGAAGCAGAGACA 59.318 55.000 0.00 0.00 0.00 3.41
4761 4985 0.681733 TGGGTCAGTGAAGCAGAGAC 59.318 55.000 0.00 0.00 0.00 3.36
4762 4986 1.552337 GATGGGTCAGTGAAGCAGAGA 59.448 52.381 0.00 0.00 0.00 3.10
4763 4987 1.554160 AGATGGGTCAGTGAAGCAGAG 59.446 52.381 0.00 0.00 0.00 3.35
4764 4988 1.649321 AGATGGGTCAGTGAAGCAGA 58.351 50.000 0.00 0.00 0.00 4.26
4765 4989 3.494048 GGATAGATGGGTCAGTGAAGCAG 60.494 52.174 0.00 0.00 0.00 4.24
4766 4990 2.435805 GGATAGATGGGTCAGTGAAGCA 59.564 50.000 0.00 0.00 0.00 3.91
4767 4991 2.546795 CGGATAGATGGGTCAGTGAAGC 60.547 54.545 0.00 0.00 0.00 3.86
4768 4992 2.695666 ACGGATAGATGGGTCAGTGAAG 59.304 50.000 0.00 0.00 0.00 3.02
4769 4993 2.693591 GACGGATAGATGGGTCAGTGAA 59.306 50.000 0.00 0.00 0.00 3.18
4770 4994 2.091830 AGACGGATAGATGGGTCAGTGA 60.092 50.000 0.00 0.00 31.93 3.41
4771 4995 2.035193 CAGACGGATAGATGGGTCAGTG 59.965 54.545 0.00 0.00 31.93 3.66
4772 4996 2.091830 TCAGACGGATAGATGGGTCAGT 60.092 50.000 0.00 0.00 31.93 3.41
4773 4997 2.294791 GTCAGACGGATAGATGGGTCAG 59.705 54.545 0.00 0.00 31.93 3.51
4774 4998 2.091830 AGTCAGACGGATAGATGGGTCA 60.092 50.000 0.00 0.00 31.93 4.02
4775 4999 2.588620 AGTCAGACGGATAGATGGGTC 58.411 52.381 0.00 0.00 0.00 4.46
4776 5000 2.757894 AGTCAGACGGATAGATGGGT 57.242 50.000 0.00 0.00 0.00 4.51
4777 5001 3.754323 GTCTAGTCAGACGGATAGATGGG 59.246 52.174 0.00 0.00 41.79 4.00
4789 5013 3.010696 ACTCAGGACCATGTCTAGTCAGA 59.989 47.826 0.00 0.18 34.58 3.27
4790 5014 3.360867 ACTCAGGACCATGTCTAGTCAG 58.639 50.000 0.00 0.00 34.58 3.51
4791 5015 3.010696 AGACTCAGGACCATGTCTAGTCA 59.989 47.826 18.15 0.00 38.23 3.41
4869 5094 2.999485 GCTGCTCGAGAGGCTGTCA 61.999 63.158 18.75 1.15 0.00 3.58
4904 5132 3.782656 TCTTCACCTGGGGTTTAGAAC 57.217 47.619 0.00 0.00 31.02 3.01
4909 5137 2.783510 TCTTCTTCTTCACCTGGGGTTT 59.216 45.455 0.00 0.00 31.02 3.27
4933 5161 6.042552 TCCATTAACAGGCCATTTCTTTTCAA 59.957 34.615 5.01 0.00 0.00 2.69
4951 5179 9.362151 ACCTCAACTAAATCAAAACTCCATTAA 57.638 29.630 0.00 0.00 0.00 1.40
4952 5180 8.934023 ACCTCAACTAAATCAAAACTCCATTA 57.066 30.769 0.00 0.00 0.00 1.90
4953 5181 7.839680 ACCTCAACTAAATCAAAACTCCATT 57.160 32.000 0.00 0.00 0.00 3.16
4954 5182 7.839680 AACCTCAACTAAATCAAAACTCCAT 57.160 32.000 0.00 0.00 0.00 3.41
4955 5183 7.654022 AAACCTCAACTAAATCAAAACTCCA 57.346 32.000 0.00 0.00 0.00 3.86
4996 5224 6.597672 ACGTCCTGCATTAACTCAATCAAATA 59.402 34.615 0.00 0.00 0.00 1.40
5016 5244 1.148310 CACACACATTCCTCACGTCC 58.852 55.000 0.00 0.00 0.00 4.79
5030 5258 1.739667 CCGTCTCCTCACACACACA 59.260 57.895 0.00 0.00 0.00 3.72
5046 5274 2.287457 TACATTCGTCTTCGCCCCCG 62.287 60.000 0.00 0.00 36.96 5.73
5048 5276 0.108520 TGTACATTCGTCTTCGCCCC 60.109 55.000 0.00 0.00 36.96 5.80
5128 5358 5.933187 TTACAATACGAACAAGTGTGCAT 57.067 34.783 0.00 0.00 0.00 3.96
5129 5359 5.736486 TTTACAATACGAACAAGTGTGCA 57.264 34.783 0.00 0.00 0.00 4.57
5130 5360 5.623673 CCTTTTACAATACGAACAAGTGTGC 59.376 40.000 0.00 0.00 0.00 4.57
5131 5361 6.950545 TCCTTTTACAATACGAACAAGTGTG 58.049 36.000 0.00 0.00 0.00 3.82
5168 5399 6.378848 CCTAAAATTTAGGGGAATCGTTGGAA 59.621 38.462 21.11 0.00 0.00 3.53
5205 5453 6.360618 ACAGGATCTGACAAAAGTTTCTCTT 58.639 36.000 1.59 0.00 35.11 2.85
5287 5537 1.227556 GTGTCACTGACTTGCGGGT 60.228 57.895 10.54 0.00 33.15 5.28
5306 5556 1.562575 CGTCGTACCACAACTTGCCC 61.563 60.000 0.00 0.00 0.00 5.36
5310 5560 1.114722 TCCCCGTCGTACCACAACTT 61.115 55.000 0.00 0.00 0.00 2.66
5367 5617 3.083997 GCTCCACCCCGACTCCAT 61.084 66.667 0.00 0.00 0.00 3.41
5390 5640 3.550992 CACCACGCCGTCATACGC 61.551 66.667 0.00 0.00 40.91 4.42
5391 5641 2.126228 ACACCACGCCGTCATACG 60.126 61.111 0.00 0.00 42.11 3.06
5392 5642 2.098233 CCACACCACGCCGTCATAC 61.098 63.158 0.00 0.00 0.00 2.39
5393 5643 2.263227 CCACACCACGCCGTCATA 59.737 61.111 0.00 0.00 0.00 2.15
5401 5651 3.496131 GTATGCCGCCACACCACG 61.496 66.667 0.00 0.00 0.00 4.94
5415 5672 2.630317 CGTAGCTCGCCGTCGTAT 59.370 61.111 0.00 0.00 36.96 3.06
5416 5673 3.566853 CCGTAGCTCGCCGTCGTA 61.567 66.667 0.00 0.00 38.35 3.43
5439 5696 2.048222 TTCAAGCCTCACTCGCCG 60.048 61.111 0.00 0.00 0.00 6.46
5440 5697 0.603975 AACTTCAAGCCTCACTCGCC 60.604 55.000 0.00 0.00 0.00 5.54
5441 5698 1.195674 GAAACTTCAAGCCTCACTCGC 59.804 52.381 0.00 0.00 0.00 5.03
5442 5699 2.483876 TGAAACTTCAAGCCTCACTCG 58.516 47.619 0.00 0.00 33.55 4.18
5443 5700 4.092091 CGTATGAAACTTCAAGCCTCACTC 59.908 45.833 0.00 0.00 41.13 3.51
5444 5701 3.997021 CGTATGAAACTTCAAGCCTCACT 59.003 43.478 0.00 0.00 41.13 3.41
5445 5702 3.125316 CCGTATGAAACTTCAAGCCTCAC 59.875 47.826 0.00 0.00 41.13 3.51
5446 5703 3.334691 CCGTATGAAACTTCAAGCCTCA 58.665 45.455 0.00 0.00 41.13 3.86
5447 5704 2.096013 GCCGTATGAAACTTCAAGCCTC 59.904 50.000 0.00 0.00 41.13 4.70
5448 5705 2.084546 GCCGTATGAAACTTCAAGCCT 58.915 47.619 0.00 0.00 41.13 4.58
5449 5706 1.132453 GGCCGTATGAAACTTCAAGCC 59.868 52.381 9.16 9.16 41.13 4.35
5450 5707 1.202031 CGGCCGTATGAAACTTCAAGC 60.202 52.381 19.50 0.00 41.13 4.01
5451 5708 1.202031 GCGGCCGTATGAAACTTCAAG 60.202 52.381 28.70 0.00 41.13 3.02
5452 5709 0.800012 GCGGCCGTATGAAACTTCAA 59.200 50.000 28.70 0.00 41.13 2.69
5453 5710 1.022451 GGCGGCCGTATGAAACTTCA 61.022 55.000 28.70 0.00 42.14 3.02
5454 5711 1.022451 TGGCGGCCGTATGAAACTTC 61.022 55.000 28.70 5.15 0.00 3.01
5455 5712 0.606944 TTGGCGGCCGTATGAAACTT 60.607 50.000 28.70 0.00 0.00 2.66
5456 5713 0.606944 TTTGGCGGCCGTATGAAACT 60.607 50.000 28.70 0.00 0.00 2.66
5457 5714 0.241481 TTTTGGCGGCCGTATGAAAC 59.759 50.000 28.70 7.66 0.00 2.78
5458 5715 0.523966 CTTTTGGCGGCCGTATGAAA 59.476 50.000 28.70 19.75 0.00 2.69
5459 5716 0.606944 ACTTTTGGCGGCCGTATGAA 60.607 50.000 28.70 15.52 0.00 2.57
5460 5717 0.606944 AACTTTTGGCGGCCGTATGA 60.607 50.000 28.70 8.23 0.00 2.15
5461 5718 1.088306 TAACTTTTGGCGGCCGTATG 58.912 50.000 28.70 13.39 0.00 2.39
5462 5719 1.741145 CTTAACTTTTGGCGGCCGTAT 59.259 47.619 28.70 6.68 0.00 3.06
5463 5720 1.158434 CTTAACTTTTGGCGGCCGTA 58.842 50.000 28.70 14.00 0.00 4.02
5464 5721 1.520600 CCTTAACTTTTGGCGGCCGT 61.521 55.000 28.70 6.42 0.00 5.68
5465 5722 1.211709 CCTTAACTTTTGGCGGCCG 59.788 57.895 24.05 24.05 0.00 6.13
5466 5723 0.963225 TTCCTTAACTTTTGGCGGCC 59.037 50.000 13.32 13.32 0.00 6.13
5467 5724 2.347697 CTTCCTTAACTTTTGGCGGC 57.652 50.000 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.