Multiple sequence alignment - TraesCS4B01G171000

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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 TraesCS4B01G171000 chr4B 100.000 4882 0 0 1 4882 374217233 374212352 0.000000e+00 9016.0
1 TraesCS4B01G171000 chr4D 93.859 2459 116 23 2449 4882 300855346 300852898 0.000000e+00 3672.0
2 TraesCS4B01G171000 chr4D 96.394 1248 28 7 718 1965 300858934 300857704 0.000000e+00 2039.0
3 TraesCS4B01G171000 chr4D 93.228 694 42 4 1 690 300861198 300860506 0.000000e+00 1016.0
4 TraesCS4B01G171000 chr4D 83.575 207 20 6 3055 3247 300854651 300854445 1.080000e-41 182.0
5 TraesCS4B01G171000 chr4D 96.610 59 2 0 2399 2457 300857714 300857656 1.120000e-16 99.0
6 TraesCS4B01G171000 chr4A 90.916 2488 166 26 2399 4856 182058399 182060856 0.000000e+00 3288.0
7 TraesCS4B01G171000 chr4A 91.721 1679 65 27 299 1965 182056793 182058409 0.000000e+00 2263.0
8 TraesCS4B01G171000 chr4A 91.228 342 30 0 1 342 182056325 182056666 2.660000e-127 466.0
9 TraesCS4B01G171000 chr4A 89.000 100 11 0 3054 3153 182059212 182059311 1.850000e-24 124.0
10 TraesCS4B01G171000 chr5D 85.323 402 39 10 1966 2349 541959710 541960109 9.850000e-107 398.0
11 TraesCS4B01G171000 chr5D 86.420 324 38 6 1965 2283 433506382 433506704 2.800000e-92 350.0
12 TraesCS4B01G171000 chr2D 84.962 399 39 8 1969 2349 637586706 637586311 7.670000e-103 385.0
13 TraesCS4B01G171000 chr2D 87.195 328 37 5 1962 2286 344347839 344348164 7.720000e-98 368.0
14 TraesCS4B01G171000 chr2D 81.897 116 16 4 2486 2596 532496827 532496942 5.200000e-15 93.5
15 TraesCS4B01G171000 chr2D 87.302 63 6 2 1433 1494 35315542 35315603 2.440000e-08 71.3
16 TraesCS4B01G171000 chr2D 91.667 48 2 2 1448 1494 35241716 35241670 1.130000e-06 65.8
17 TraesCS4B01G171000 chr1A 84.131 397 50 10 1965 2349 31842489 31842094 5.970000e-99 372.0
18 TraesCS4B01G171000 chr3D 86.503 326 36 8 1965 2284 25967602 25967279 7.770000e-93 351.0
19 TraesCS4B01G171000 chr7D 86.751 317 37 5 1968 2281 16321361 16321047 1.010000e-91 348.0
20 TraesCS4B01G171000 chr7A 83.202 381 54 9 1978 2351 62841526 62841149 1.680000e-89 340.0
21 TraesCS4B01G171000 chr5A 82.821 390 50 12 1969 2349 62975775 62975394 2.820000e-87 333.0
22 TraesCS4B01G171000 chr2B 87.302 63 6 2 1433 1494 58091462 58091401 2.440000e-08 71.3
23 TraesCS4B01G171000 chr2B 87.302 63 6 2 1433 1494 58237001 58236940 2.440000e-08 71.3
24 TraesCS4B01G171000 chr2B 87.302 63 6 2 1433 1494 58311310 58311249 2.440000e-08 71.3
25 TraesCS4B01G171000 chr2B 91.489 47 4 0 1448 1494 58345078 58345124 1.130000e-06 65.8
26 TraesCS4B01G171000 chr2B 91.667 48 2 2 1448 1494 58537069 58537115 1.130000e-06 65.8


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 TraesCS4B01G171000 chr4B 374212352 374217233 4881 True 9016.00 9016 100.00000 1 4882 1 chr4B.!!$R1 4881
1 TraesCS4B01G171000 chr4D 300852898 300861198 8300 True 1401.60 3672 92.73320 1 4882 5 chr4D.!!$R1 4881
2 TraesCS4B01G171000 chr4A 182056325 182060856 4531 False 1535.25 3288 90.71625 1 4856 4 chr4A.!!$F1 4855

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
138 139 0.035881 AGTGTGTGCCATCTCCTGTG 59.964 55.000 0.00 0.0 0.00 3.66 F
768 2490 1.407851 GGTAAGATCCCGGAAACCCAC 60.408 57.143 0.73 0.0 0.00 4.61 F
1999 3729 0.179051 CTGCCCAAGCTCATCTCCTC 60.179 60.000 0.00 0.0 40.80 3.71 F
3623 7704 0.038526 GTCCCGATGACAACGTGACT 60.039 55.000 12.25 0.0 43.85 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 3423 0.108756 GGTCTCCACCTCGTACAAGC 60.109 60.000 0.0 0.0 40.00 4.01 R
2366 4096 0.106335 TACGGTCCGTGCCTCAAAAA 59.894 50.000 27.2 0.0 41.39 1.94 R
3668 7749 1.741706 TCTTTGACGAGGCGGTAGTAG 59.258 52.381 0.0 0.0 0.00 2.57 R
4764 8852 0.183492 GGCCCTATTCCTGACATGCA 59.817 55.000 0.0 0.0 0.00 3.96 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
42 43 6.557568 TGAGGGGTATTGATAACAAGGTTTT 58.442 36.000 0.00 0.00 39.46 2.43
64 65 2.837498 TCACATATTCTCATGGTGGCG 58.163 47.619 0.00 0.00 0.00 5.69
126 127 5.107453 TGCGGTTTTAAACAAAAAGTGTGTG 60.107 36.000 10.14 0.00 40.60 3.82
127 128 5.309707 CGGTTTTAAACAAAAAGTGTGTGC 58.690 37.500 10.14 0.00 40.60 4.57
138 139 0.035881 AGTGTGTGCCATCTCCTGTG 59.964 55.000 0.00 0.00 0.00 3.66
192 193 5.768164 TCGTACTTGGTATATCATGCAGAGA 59.232 40.000 0.00 0.00 0.00 3.10
221 222 4.287067 GGATAGGACCTCATTAAGATGGCA 59.713 45.833 0.00 0.00 33.93 4.92
251 254 4.038763 TGACGGTAGCATACAATTAGGAGG 59.961 45.833 0.00 0.00 45.43 4.30
362 535 6.917217 TTGACGTATTGATTATGTGCATCA 57.083 33.333 0.00 0.00 29.93 3.07
368 541 8.282592 ACGTATTGATTATGTGCATCATGTTAC 58.717 33.333 10.77 3.57 37.91 2.50
376 549 4.758688 TGTGCATCATGTTACGAAGAGAT 58.241 39.130 0.00 0.00 0.00 2.75
380 553 3.179443 TCATGTTACGAAGAGATGGGC 57.821 47.619 0.00 0.00 0.00 5.36
411 584 3.874543 GCACAATACGGTTGTATCATCCA 59.125 43.478 7.93 0.00 40.42 3.41
443 616 7.252708 TCGATTGAATTGAATGGAAATGTCAG 58.747 34.615 0.05 0.00 0.00 3.51
543 721 9.424319 ACGTAAACAAAGCAGGATATATATCAG 57.576 33.333 21.50 14.91 34.40 2.90
702 880 2.427453 CCGAAGTAGCAGTGGAGTACAT 59.573 50.000 0.00 0.00 0.00 2.29
704 882 4.278669 CCGAAGTAGCAGTGGAGTACATAT 59.721 45.833 0.00 0.00 0.00 1.78
706 884 6.348622 CCGAAGTAGCAGTGGAGTACATATAG 60.349 46.154 0.00 0.00 0.00 1.31
707 885 6.348622 CGAAGTAGCAGTGGAGTACATATAGG 60.349 46.154 0.00 0.00 0.00 2.57
709 887 6.242396 AGTAGCAGTGGAGTACATATAGGAG 58.758 44.000 0.00 0.00 0.00 3.69
710 888 5.068215 AGCAGTGGAGTACATATAGGAGT 57.932 43.478 0.00 0.00 0.00 3.85
713 891 5.106634 GCAGTGGAGTACATATAGGAGTACG 60.107 48.000 0.00 0.00 43.98 3.67
715 893 7.157347 CAGTGGAGTACATATAGGAGTACGTA 58.843 42.308 0.00 0.00 43.98 3.57
716 894 7.117523 CAGTGGAGTACATATAGGAGTACGTAC 59.882 44.444 18.10 18.10 43.98 3.67
768 2490 1.407851 GGTAAGATCCCGGAAACCCAC 60.408 57.143 0.73 0.00 0.00 4.61
809 2531 3.508840 GCCCATGACGGCCGAAAG 61.509 66.667 35.90 17.88 43.66 2.62
1035 2763 1.551452 CTCCTCTCGGTCTCAGGTTT 58.449 55.000 0.00 0.00 0.00 3.27
1045 2773 3.744530 CGGTCTCAGGTTTTCACTTCCTT 60.745 47.826 0.00 0.00 0.00 3.36
1046 2774 4.207955 GGTCTCAGGTTTTCACTTCCTTT 58.792 43.478 0.00 0.00 0.00 3.11
1047 2775 4.036852 GGTCTCAGGTTTTCACTTCCTTTG 59.963 45.833 0.00 0.00 0.00 2.77
1048 2776 3.632145 TCTCAGGTTTTCACTTCCTTTGC 59.368 43.478 0.00 0.00 0.00 3.68
1049 2777 3.631250 TCAGGTTTTCACTTCCTTTGCT 58.369 40.909 0.00 0.00 0.00 3.91
1050 2778 3.381272 TCAGGTTTTCACTTCCTTTGCTG 59.619 43.478 0.00 0.00 0.00 4.41
1051 2779 2.101415 AGGTTTTCACTTCCTTTGCTGC 59.899 45.455 0.00 0.00 0.00 5.25
1052 2780 2.101415 GGTTTTCACTTCCTTTGCTGCT 59.899 45.455 0.00 0.00 0.00 4.24
1053 2781 3.118542 GTTTTCACTTCCTTTGCTGCTG 58.881 45.455 0.00 0.00 0.00 4.41
1244 2972 3.627395 TGATTGCTTCGTCAGGGTAAT 57.373 42.857 0.00 0.00 0.00 1.89
1246 2974 5.092554 TGATTGCTTCGTCAGGGTAATAA 57.907 39.130 0.00 0.00 0.00 1.40
1247 2975 5.492895 TGATTGCTTCGTCAGGGTAATAAA 58.507 37.500 0.00 0.00 0.00 1.40
1248 2976 5.941058 TGATTGCTTCGTCAGGGTAATAAAA 59.059 36.000 0.00 0.00 0.00 1.52
1542 3271 5.619981 GCTGGTACACATTTAAGCCTCTTTG 60.620 44.000 0.00 0.00 0.00 2.77
1555 3284 2.641305 CCTCTTTGCCTCCATTCAGAG 58.359 52.381 0.00 0.00 0.00 3.35
1965 3695 1.470051 ACGGTTGCCCCAATTGTATC 58.530 50.000 4.43 0.00 0.00 2.24
1966 3696 0.380378 CGGTTGCCCCAATTGTATCG 59.620 55.000 4.43 0.00 0.00 2.92
1967 3697 0.744281 GGTTGCCCCAATTGTATCGG 59.256 55.000 4.43 0.00 0.00 4.18
1968 3698 1.683629 GGTTGCCCCAATTGTATCGGA 60.684 52.381 4.43 0.00 0.00 4.55
1969 3699 2.096248 GTTGCCCCAATTGTATCGGAA 58.904 47.619 4.43 0.00 0.00 4.30
1970 3700 2.494073 GTTGCCCCAATTGTATCGGAAA 59.506 45.455 4.43 0.00 0.00 3.13
1971 3701 3.025322 TGCCCCAATTGTATCGGAAAT 57.975 42.857 4.43 0.00 0.00 2.17
1972 3702 2.955660 TGCCCCAATTGTATCGGAAATC 59.044 45.455 4.43 0.00 0.00 2.17
1973 3703 2.296190 GCCCCAATTGTATCGGAAATCC 59.704 50.000 4.43 0.00 0.00 3.01
1974 3704 3.561143 CCCCAATTGTATCGGAAATCCA 58.439 45.455 4.43 0.00 35.14 3.41
1975 3705 3.957497 CCCCAATTGTATCGGAAATCCAA 59.043 43.478 4.43 0.00 35.14 3.53
1976 3706 4.202111 CCCCAATTGTATCGGAAATCCAAC 60.202 45.833 4.43 0.00 35.14 3.77
1977 3707 4.644685 CCCAATTGTATCGGAAATCCAACT 59.355 41.667 4.43 0.00 35.14 3.16
1978 3708 5.221048 CCCAATTGTATCGGAAATCCAACTC 60.221 44.000 4.43 0.00 35.14 3.01
1979 3709 5.501715 CAATTGTATCGGAAATCCAACTCG 58.498 41.667 0.00 0.00 35.14 4.18
1980 3710 2.546778 TGTATCGGAAATCCAACTCGC 58.453 47.619 0.00 0.00 35.14 5.03
1981 3711 2.167693 TGTATCGGAAATCCAACTCGCT 59.832 45.455 0.00 0.00 35.14 4.93
1982 3712 1.656652 ATCGGAAATCCAACTCGCTG 58.343 50.000 0.00 0.00 35.14 5.18
1983 3713 1.019278 TCGGAAATCCAACTCGCTGC 61.019 55.000 0.00 0.00 35.14 5.25
1984 3714 1.803289 GGAAATCCAACTCGCTGCC 59.197 57.895 0.00 0.00 35.64 4.85
1985 3715 1.657751 GGAAATCCAACTCGCTGCCC 61.658 60.000 0.00 0.00 35.64 5.36
1986 3716 0.960364 GAAATCCAACTCGCTGCCCA 60.960 55.000 0.00 0.00 0.00 5.36
1987 3717 0.539438 AAATCCAACTCGCTGCCCAA 60.539 50.000 0.00 0.00 0.00 4.12
1988 3718 0.962356 AATCCAACTCGCTGCCCAAG 60.962 55.000 0.00 0.00 0.00 3.61
1997 3727 4.555610 CTGCCCAAGCTCATCTCC 57.444 61.111 0.00 0.00 40.80 3.71
1998 3728 1.913722 CTGCCCAAGCTCATCTCCT 59.086 57.895 0.00 0.00 40.80 3.69
1999 3729 0.179051 CTGCCCAAGCTCATCTCCTC 60.179 60.000 0.00 0.00 40.80 3.71
2000 3730 1.148048 GCCCAAGCTCATCTCCTCC 59.852 63.158 0.00 0.00 35.50 4.30
2001 3731 1.835693 CCCAAGCTCATCTCCTCCC 59.164 63.158 0.00 0.00 0.00 4.30
2002 3732 1.445095 CCAAGCTCATCTCCTCCCG 59.555 63.158 0.00 0.00 0.00 5.14
2003 3733 1.445095 CAAGCTCATCTCCTCCCGG 59.555 63.158 0.00 0.00 0.00 5.73
2004 3734 1.002274 AAGCTCATCTCCTCCCGGT 59.998 57.895 0.00 0.00 0.00 5.28
2005 3735 1.045911 AAGCTCATCTCCTCCCGGTC 61.046 60.000 0.00 0.00 0.00 4.79
2006 3736 2.503382 GCTCATCTCCTCCCGGTCC 61.503 68.421 0.00 0.00 0.00 4.46
2007 3737 2.123854 TCATCTCCTCCCGGTCCG 60.124 66.667 3.60 3.60 0.00 4.79
2008 3738 2.123854 CATCTCCTCCCGGTCCGA 60.124 66.667 14.39 0.00 0.00 4.55
2009 3739 1.756950 CATCTCCTCCCGGTCCGAA 60.757 63.158 14.39 0.00 0.00 4.30
2010 3740 1.001248 ATCTCCTCCCGGTCCGAAA 59.999 57.895 14.39 0.00 0.00 3.46
2011 3741 0.616679 ATCTCCTCCCGGTCCGAAAA 60.617 55.000 14.39 0.00 0.00 2.29
2012 3742 0.832983 TCTCCTCCCGGTCCGAAAAA 60.833 55.000 14.39 0.00 0.00 1.94
2079 3809 6.449635 TTGGTGTGGTAGATAATTTGATGC 57.550 37.500 0.00 0.00 0.00 3.91
2080 3810 4.574421 TGGTGTGGTAGATAATTTGATGCG 59.426 41.667 0.00 0.00 0.00 4.73
2081 3811 4.574828 GGTGTGGTAGATAATTTGATGCGT 59.425 41.667 0.00 0.00 0.00 5.24
2082 3812 5.501715 GTGTGGTAGATAATTTGATGCGTG 58.498 41.667 0.00 0.00 0.00 5.34
2083 3813 5.293324 GTGTGGTAGATAATTTGATGCGTGA 59.707 40.000 0.00 0.00 0.00 4.35
2084 3814 5.523552 TGTGGTAGATAATTTGATGCGTGAG 59.476 40.000 0.00 0.00 0.00 3.51
2085 3815 5.050091 GTGGTAGATAATTTGATGCGTGAGG 60.050 44.000 0.00 0.00 0.00 3.86
2086 3816 5.057149 GGTAGATAATTTGATGCGTGAGGT 58.943 41.667 0.00 0.00 0.00 3.85
2087 3817 5.177696 GGTAGATAATTTGATGCGTGAGGTC 59.822 44.000 0.00 0.00 0.00 3.85
2088 3818 4.130118 AGATAATTTGATGCGTGAGGTCC 58.870 43.478 0.00 0.00 0.00 4.46
2089 3819 1.086696 AATTTGATGCGTGAGGTCCG 58.913 50.000 0.00 0.00 0.00 4.79
2096 3826 4.354155 CGTGAGGTCCGCTTCAAA 57.646 55.556 0.00 0.00 32.39 2.69
2097 3827 2.840974 CGTGAGGTCCGCTTCAAAT 58.159 52.632 0.00 0.00 32.39 2.32
2098 3828 1.156736 CGTGAGGTCCGCTTCAAATT 58.843 50.000 0.00 0.00 32.39 1.82
2099 3829 1.535462 CGTGAGGTCCGCTTCAAATTT 59.465 47.619 0.00 0.00 32.39 1.82
2100 3830 2.412847 CGTGAGGTCCGCTTCAAATTTC 60.413 50.000 0.00 0.00 32.39 2.17
2101 3831 2.552315 GTGAGGTCCGCTTCAAATTTCA 59.448 45.455 0.00 0.00 32.39 2.69
2102 3832 3.004315 GTGAGGTCCGCTTCAAATTTCAA 59.996 43.478 0.00 0.00 32.39 2.69
2103 3833 3.004315 TGAGGTCCGCTTCAAATTTCAAC 59.996 43.478 0.00 0.00 0.00 3.18
2104 3834 3.222603 AGGTCCGCTTCAAATTTCAACT 58.777 40.909 0.00 0.00 0.00 3.16
2105 3835 3.636764 AGGTCCGCTTCAAATTTCAACTT 59.363 39.130 0.00 0.00 0.00 2.66
2106 3836 4.825085 AGGTCCGCTTCAAATTTCAACTTA 59.175 37.500 0.00 0.00 0.00 2.24
2107 3837 5.476945 AGGTCCGCTTCAAATTTCAACTTAT 59.523 36.000 0.00 0.00 0.00 1.73
2108 3838 6.015434 AGGTCCGCTTCAAATTTCAACTTATT 60.015 34.615 0.00 0.00 0.00 1.40
2109 3839 6.645003 GGTCCGCTTCAAATTTCAACTTATTT 59.355 34.615 0.00 0.00 0.00 1.40
2110 3840 7.359181 GGTCCGCTTCAAATTTCAACTTATTTG 60.359 37.037 0.00 0.00 41.08 2.32
2111 3841 6.644592 TCCGCTTCAAATTTCAACTTATTTGG 59.355 34.615 0.00 0.00 40.46 3.28
2112 3842 6.644592 CCGCTTCAAATTTCAACTTATTTGGA 59.355 34.615 0.00 0.00 40.46 3.53
2113 3843 7.331687 CCGCTTCAAATTTCAACTTATTTGGAT 59.668 33.333 0.00 0.00 40.46 3.41
2114 3844 9.352784 CGCTTCAAATTTCAACTTATTTGGATA 57.647 29.630 0.00 0.00 40.46 2.59
2124 3854 9.851686 TTCAACTTATTTGGATATATGAGCAGT 57.148 29.630 0.00 0.00 35.69 4.40
2125 3855 9.851686 TCAACTTATTTGGATATATGAGCAGTT 57.148 29.630 0.00 0.00 35.69 3.16
2128 3858 9.717942 ACTTATTTGGATATATGAGCAGTTCTC 57.282 33.333 0.00 0.00 42.23 2.87
2153 3883 3.553828 AAAAAGACAAGTCGGGTCAGA 57.446 42.857 0.00 0.00 37.74 3.27
2154 3884 3.553828 AAAAGACAAGTCGGGTCAGAA 57.446 42.857 0.00 0.00 37.74 3.02
2155 3885 2.528041 AAGACAAGTCGGGTCAGAAC 57.472 50.000 0.00 0.00 37.74 3.01
2156 3886 0.680061 AGACAAGTCGGGTCAGAACC 59.320 55.000 0.00 0.00 45.65 3.62
2157 3887 0.680061 GACAAGTCGGGTCAGAACCT 59.320 55.000 2.07 0.00 45.66 3.50
2158 3888 1.070289 GACAAGTCGGGTCAGAACCTT 59.930 52.381 2.07 0.00 45.66 3.50
2159 3889 1.202651 ACAAGTCGGGTCAGAACCTTG 60.203 52.381 2.07 3.10 45.66 3.61
2160 3890 0.250338 AAGTCGGGTCAGAACCTTGC 60.250 55.000 2.07 0.00 45.66 4.01
2161 3891 2.027625 GTCGGGTCAGAACCTTGCG 61.028 63.158 2.07 0.00 45.66 4.85
2162 3892 2.030562 CGGGTCAGAACCTTGCGT 59.969 61.111 2.07 0.00 45.66 5.24
2163 3893 2.317609 CGGGTCAGAACCTTGCGTG 61.318 63.158 2.07 0.00 45.66 5.34
2164 3894 1.070786 GGGTCAGAACCTTGCGTGA 59.929 57.895 0.00 0.00 45.66 4.35
2165 3895 0.534203 GGGTCAGAACCTTGCGTGAA 60.534 55.000 0.00 0.00 45.66 3.18
2166 3896 0.586802 GGTCAGAACCTTGCGTGAAC 59.413 55.000 0.00 0.00 42.80 3.18
2167 3897 1.295792 GTCAGAACCTTGCGTGAACA 58.704 50.000 0.00 0.00 0.00 3.18
2168 3898 1.261619 GTCAGAACCTTGCGTGAACAG 59.738 52.381 0.00 0.00 0.00 3.16
2169 3899 1.134521 TCAGAACCTTGCGTGAACAGT 60.135 47.619 0.00 0.00 0.00 3.55
2170 3900 2.101750 TCAGAACCTTGCGTGAACAGTA 59.898 45.455 0.00 0.00 0.00 2.74
2171 3901 2.869801 CAGAACCTTGCGTGAACAGTAA 59.130 45.455 0.00 0.00 0.00 2.24
2172 3902 3.311322 CAGAACCTTGCGTGAACAGTAAA 59.689 43.478 0.00 0.00 0.00 2.01
2173 3903 3.311596 AGAACCTTGCGTGAACAGTAAAC 59.688 43.478 0.00 0.00 0.00 2.01
2174 3904 2.914059 ACCTTGCGTGAACAGTAAACT 58.086 42.857 0.00 0.00 0.00 2.66
2175 3905 3.275999 ACCTTGCGTGAACAGTAAACTT 58.724 40.909 0.00 0.00 0.00 2.66
2176 3906 3.692593 ACCTTGCGTGAACAGTAAACTTT 59.307 39.130 0.00 0.00 0.00 2.66
2177 3907 4.157105 ACCTTGCGTGAACAGTAAACTTTT 59.843 37.500 0.00 0.00 0.00 2.27
2178 3908 5.099575 CCTTGCGTGAACAGTAAACTTTTT 58.900 37.500 0.00 0.00 0.00 1.94
2222 3952 5.356882 TTTTACTGAGAGCGGTTCAAATG 57.643 39.130 0.00 0.00 34.79 2.32
2223 3953 2.550830 ACTGAGAGCGGTTCAAATGT 57.449 45.000 0.00 0.00 0.00 2.71
2224 3954 2.417719 ACTGAGAGCGGTTCAAATGTC 58.582 47.619 0.00 0.00 0.00 3.06
2225 3955 1.734465 CTGAGAGCGGTTCAAATGTCC 59.266 52.381 0.00 0.00 0.00 4.02
2226 3956 1.071542 TGAGAGCGGTTCAAATGTCCA 59.928 47.619 0.00 0.00 0.00 4.02
2227 3957 2.151202 GAGAGCGGTTCAAATGTCCAA 58.849 47.619 0.00 0.00 0.00 3.53
2228 3958 2.552315 GAGAGCGGTTCAAATGTCCAAA 59.448 45.455 0.00 0.00 0.00 3.28
2229 3959 3.157087 AGAGCGGTTCAAATGTCCAAAT 58.843 40.909 0.00 0.00 0.00 2.32
2230 3960 4.331968 AGAGCGGTTCAAATGTCCAAATA 58.668 39.130 0.00 0.00 0.00 1.40
2231 3961 4.764823 AGAGCGGTTCAAATGTCCAAATAA 59.235 37.500 0.00 0.00 0.00 1.40
2232 3962 5.059404 AGCGGTTCAAATGTCCAAATAAG 57.941 39.130 0.00 0.00 0.00 1.73
2233 3963 4.522789 AGCGGTTCAAATGTCCAAATAAGT 59.477 37.500 0.00 0.00 0.00 2.24
2234 3964 5.010617 AGCGGTTCAAATGTCCAAATAAGTT 59.989 36.000 0.00 0.00 0.00 2.66
2235 3965 5.118510 GCGGTTCAAATGTCCAAATAAGTTG 59.881 40.000 0.00 0.00 36.94 3.16
2236 3966 6.442952 CGGTTCAAATGTCCAAATAAGTTGA 58.557 36.000 0.00 0.00 39.87 3.18
2237 3967 6.920758 CGGTTCAAATGTCCAAATAAGTTGAA 59.079 34.615 0.00 0.00 39.87 2.69
2238 3968 7.436673 CGGTTCAAATGTCCAAATAAGTTGAAA 59.563 33.333 0.00 0.00 39.87 2.69
2239 3969 9.271828 GGTTCAAATGTCCAAATAAGTTGAAAT 57.728 29.630 0.00 0.00 39.87 2.17
2246 3976 8.364129 TGTCCAAATAAGTTGAAATTTGAAGC 57.636 30.769 10.02 0.00 42.90 3.86
2247 3977 7.168972 TGTCCAAATAAGTTGAAATTTGAAGCG 59.831 33.333 10.02 0.00 42.90 4.68
2248 3978 6.644592 TCCAAATAAGTTGAAATTTGAAGCGG 59.355 34.615 10.02 0.00 42.90 5.52
2249 3979 6.644592 CCAAATAAGTTGAAATTTGAAGCGGA 59.355 34.615 10.02 0.00 42.90 5.54
2250 3980 7.359181 CCAAATAAGTTGAAATTTGAAGCGGAC 60.359 37.037 10.02 0.00 42.90 4.79
2251 3981 3.643159 AGTTGAAATTTGAAGCGGACC 57.357 42.857 0.00 0.00 0.00 4.46
2252 3982 3.222603 AGTTGAAATTTGAAGCGGACCT 58.777 40.909 0.00 0.00 0.00 3.85
2253 3983 3.253432 AGTTGAAATTTGAAGCGGACCTC 59.747 43.478 0.00 0.00 0.00 3.85
2254 3984 2.857483 TGAAATTTGAAGCGGACCTCA 58.143 42.857 0.00 0.00 0.00 3.86
2255 3985 2.552315 TGAAATTTGAAGCGGACCTCAC 59.448 45.455 0.00 0.00 0.00 3.51
2256 3986 1.156736 AATTTGAAGCGGACCTCACG 58.843 50.000 0.00 0.00 0.00 4.35
2268 3998 5.018695 CGGACCTCACGCATTAAATTATC 57.981 43.478 0.00 0.00 0.00 1.75
2269 3999 4.750098 CGGACCTCACGCATTAAATTATCT 59.250 41.667 0.00 0.00 0.00 1.98
2270 4000 5.924254 CGGACCTCACGCATTAAATTATCTA 59.076 40.000 0.00 0.00 0.00 1.98
2271 4001 6.128902 CGGACCTCACGCATTAAATTATCTAC 60.129 42.308 0.00 0.00 0.00 2.59
2272 4002 6.147328 GGACCTCACGCATTAAATTATCTACC 59.853 42.308 0.00 0.00 0.00 3.18
2273 4003 6.588204 ACCTCACGCATTAAATTATCTACCA 58.412 36.000 0.00 0.00 0.00 3.25
2274 4004 6.482308 ACCTCACGCATTAAATTATCTACCAC 59.518 38.462 0.00 0.00 0.00 4.16
2275 4005 6.481976 CCTCACGCATTAAATTATCTACCACA 59.518 38.462 0.00 0.00 0.00 4.17
2276 4006 7.241663 TCACGCATTAAATTATCTACCACAC 57.758 36.000 0.00 0.00 0.00 3.82
2277 4007 6.819146 TCACGCATTAAATTATCTACCACACA 59.181 34.615 0.00 0.00 0.00 3.72
2278 4008 7.334671 TCACGCATTAAATTATCTACCACACAA 59.665 33.333 0.00 0.00 0.00 3.33
2279 4009 7.965655 CACGCATTAAATTATCTACCACACAAA 59.034 33.333 0.00 0.00 0.00 2.83
2280 4010 8.516234 ACGCATTAAATTATCTACCACACAAAA 58.484 29.630 0.00 0.00 0.00 2.44
2281 4011 9.347934 CGCATTAAATTATCTACCACACAAAAA 57.652 29.630 0.00 0.00 0.00 1.94
2339 4069 4.864334 GGGTGCAGCTGATCCCGG 62.864 72.222 24.06 0.00 0.00 5.73
2340 4070 4.864334 GGTGCAGCTGATCCCGGG 62.864 72.222 20.43 16.85 0.00 5.73
2341 4071 3.785859 GTGCAGCTGATCCCGGGA 61.786 66.667 29.18 29.18 0.00 5.14
2342 4072 3.473647 TGCAGCTGATCCCGGGAG 61.474 66.667 30.42 16.89 0.00 4.30
2343 4073 4.925861 GCAGCTGATCCCGGGAGC 62.926 72.222 32.10 32.10 0.00 4.70
2344 4074 3.473647 CAGCTGATCCCGGGAGCA 61.474 66.667 37.53 37.53 38.28 4.26
2348 4078 4.145436 TGATCCCGGGAGCAGAAA 57.855 55.556 37.01 15.50 35.47 2.52
2349 4079 2.620234 TGATCCCGGGAGCAGAAAT 58.380 52.632 37.01 14.60 35.47 2.17
2350 4080 0.181114 TGATCCCGGGAGCAGAAATG 59.819 55.000 37.01 0.00 35.47 2.32
2351 4081 0.181350 GATCCCGGGAGCAGAAATGT 59.819 55.000 33.57 10.94 0.00 2.71
2352 4082 0.625849 ATCCCGGGAGCAGAAATGTT 59.374 50.000 30.42 4.43 0.00 2.71
2353 4083 0.322456 TCCCGGGAGCAGAAATGTTG 60.322 55.000 22.63 0.00 0.00 3.33
2354 4084 1.508088 CCGGGAGCAGAAATGTTGC 59.492 57.895 0.00 0.00 41.83 4.17
2355 4085 1.243342 CCGGGAGCAGAAATGTTGCA 61.243 55.000 0.00 0.00 43.92 4.08
2356 4086 0.813184 CGGGAGCAGAAATGTTGCAT 59.187 50.000 0.00 0.00 43.92 3.96
2357 4087 1.202222 CGGGAGCAGAAATGTTGCATC 60.202 52.381 0.00 0.00 43.92 3.91
2358 4088 1.135721 GGGAGCAGAAATGTTGCATCC 59.864 52.381 0.00 4.14 43.92 3.51
2359 4089 1.135721 GGAGCAGAAATGTTGCATCCC 59.864 52.381 0.00 0.00 43.92 3.85
2360 4090 1.820519 GAGCAGAAATGTTGCATCCCA 59.179 47.619 0.00 0.00 43.92 4.37
2361 4091 2.231964 GAGCAGAAATGTTGCATCCCAA 59.768 45.455 0.00 0.00 43.92 4.12
2362 4092 2.835764 AGCAGAAATGTTGCATCCCAAT 59.164 40.909 0.00 0.00 43.92 3.16
2363 4093 3.262405 AGCAGAAATGTTGCATCCCAATT 59.738 39.130 0.00 0.00 43.92 2.32
2364 4094 4.004982 GCAGAAATGTTGCATCCCAATTT 58.995 39.130 0.00 0.00 41.17 1.82
2365 4095 4.456566 GCAGAAATGTTGCATCCCAATTTT 59.543 37.500 0.00 0.00 41.17 1.82
2366 4096 5.048573 GCAGAAATGTTGCATCCCAATTTTT 60.049 36.000 0.00 0.00 41.17 1.94
2383 4113 3.739167 TTTTTGAGGCACGGACCG 58.261 55.556 13.61 13.61 33.69 4.79
2384 4114 1.153127 TTTTTGAGGCACGGACCGT 60.153 52.632 15.37 15.37 42.36 4.83
2385 4115 0.106335 TTTTTGAGGCACGGACCGTA 59.894 50.000 21.25 0.00 38.32 4.02
2386 4116 0.320073 TTTTGAGGCACGGACCGTAG 60.320 55.000 21.25 15.00 38.32 3.51
2387 4117 1.180456 TTTGAGGCACGGACCGTAGA 61.180 55.000 21.25 0.00 38.32 2.59
2388 4118 1.180456 TTGAGGCACGGACCGTAGAA 61.180 55.000 21.25 5.30 38.32 2.10
2389 4119 1.180456 TGAGGCACGGACCGTAGAAA 61.180 55.000 21.25 1.65 38.32 2.52
2390 4120 0.175073 GAGGCACGGACCGTAGAAAT 59.825 55.000 21.25 4.08 38.32 2.17
2391 4121 0.108329 AGGCACGGACCGTAGAAATG 60.108 55.000 21.25 7.43 38.32 2.32
2392 4122 1.702491 GGCACGGACCGTAGAAATGC 61.702 60.000 21.25 17.36 38.32 3.56
2393 4123 0.739813 GCACGGACCGTAGAAATGCT 60.740 55.000 21.25 0.00 38.32 3.79
2394 4124 0.999406 CACGGACCGTAGAAATGCTG 59.001 55.000 21.25 0.00 38.32 4.41
2395 4125 0.739813 ACGGACCGTAGAAATGCTGC 60.740 55.000 20.23 0.00 38.73 5.25
2396 4126 0.739462 CGGACCGTAGAAATGCTGCA 60.739 55.000 4.13 4.13 0.00 4.41
2397 4127 1.668419 GGACCGTAGAAATGCTGCAT 58.332 50.000 9.81 9.81 0.00 3.96
2398 4128 1.599542 GGACCGTAGAAATGCTGCATC 59.400 52.381 16.55 5.28 0.00 3.91
2399 4129 1.599542 GACCGTAGAAATGCTGCATCC 59.400 52.381 16.55 10.87 0.00 3.51
2400 4130 0.947244 CCGTAGAAATGCTGCATCCC 59.053 55.000 16.55 10.52 0.00 3.85
2401 4131 0.583438 CGTAGAAATGCTGCATCCCG 59.417 55.000 16.55 9.77 0.00 5.14
2464 6512 3.088532 AGTGAATTAGAAAATGCCCGCA 58.911 40.909 0.00 0.00 0.00 5.69
2467 6515 5.359576 AGTGAATTAGAAAATGCCCGCATTA 59.640 36.000 14.92 0.10 44.86 1.90
2669 6721 8.413229 GCCCATACTTGTAACAATTGTATGAAT 58.587 33.333 12.39 0.00 41.46 2.57
2676 6728 9.438291 CTTGTAACAATTGTATGAATCGATTCC 57.562 33.333 30.16 17.98 35.97 3.01
2710 6762 0.593128 AAGACACGCAAACCTCATGC 59.407 50.000 0.00 0.00 40.41 4.06
2798 6855 3.101437 TGAGCCTTTTCCATGCATGATT 58.899 40.909 28.31 3.85 0.00 2.57
2835 6892 0.671251 TTTCCCGTGCATGGTTTGAC 59.329 50.000 23.39 0.00 0.00 3.18
2843 6900 3.190327 CGTGCATGGTTTGACCTTTGATA 59.810 43.478 0.00 0.00 39.58 2.15
2857 6922 4.147321 CCTTTGATATTGAGGGGACATGG 58.853 47.826 0.00 0.00 0.00 3.66
2882 6947 5.423015 AGATGATATCTCGTGTTTTGCTGT 58.577 37.500 3.98 0.00 33.42 4.40
2888 6953 1.403679 CTCGTGTTTTGCTGTGGGAAA 59.596 47.619 0.00 0.00 0.00 3.13
3012 7078 9.934190 AAAAATATGATGTTTTTGCAGTTCAAC 57.066 25.926 11.09 0.00 37.37 3.18
3015 7081 9.979578 AATATGATGTTTTTGCAGTTCAACTTA 57.020 25.926 0.00 0.00 33.73 2.24
3027 7093 9.646427 TTGCAGTTCAACTTAAACTACAAAAAT 57.354 25.926 0.00 0.00 37.17 1.82
3570 7651 1.272554 GGACCCTACCCTGGACAAGG 61.273 65.000 0.00 0.00 46.94 3.61
3623 7704 0.038526 GTCCCGATGACAACGTGACT 60.039 55.000 12.25 0.00 43.85 3.41
3668 7749 0.788645 CGACGACTTTCGACTCGACC 60.789 60.000 12.05 4.30 43.74 4.79
4094 8175 7.095144 ACGGATCTATCTATCGTGAGTAAACAG 60.095 40.741 0.00 0.00 0.00 3.16
4166 8249 6.841601 ACATATAACCATCCTTAGTGCATGT 58.158 36.000 0.00 0.00 0.00 3.21
4217 8301 8.990163 AAGAAGTATCAAGGAACTAAAAACCA 57.010 30.769 0.00 0.00 38.49 3.67
4219 8303 6.796705 AGTATCAAGGAACTAAAAACCACG 57.203 37.500 0.00 0.00 38.49 4.94
4318 8402 4.466015 TCACATGTACCATCTCTAAGTGCA 59.534 41.667 0.00 0.00 0.00 4.57
4349 8433 6.678568 AGACACCAGAATATCCCTTATCTG 57.321 41.667 0.00 0.00 0.00 2.90
4577 8664 0.738412 ATACCGAGCAAAACCCGTCG 60.738 55.000 0.00 0.00 0.00 5.12
4590 8677 1.672854 CCCGTCGCAACCCTCTGATA 61.673 60.000 0.00 0.00 0.00 2.15
4626 8714 6.999950 AGTATAAATCACACACACCACTACA 58.000 36.000 0.00 0.00 0.00 2.74
4673 8761 3.966215 CGTCATCGCCACCACTTT 58.034 55.556 0.00 0.00 0.00 2.66
4700 8788 0.880278 GCAAGTGACTCCGCTTCACA 60.880 55.000 10.69 0.00 45.00 3.58
4727 8815 1.141019 GCCGACATAGCTCGAACCA 59.859 57.895 0.00 0.00 35.58 3.67
4763 8851 4.482952 AGTCACATGCAGATCAATCAGA 57.517 40.909 0.00 0.00 0.00 3.27
4764 8852 5.037383 AGTCACATGCAGATCAATCAGAT 57.963 39.130 0.00 0.00 40.48 2.90
4765 8853 4.816925 AGTCACATGCAGATCAATCAGATG 59.183 41.667 0.00 0.00 37.00 2.90
4777 8865 4.788679 TCAATCAGATGCATGTCAGGAAT 58.211 39.130 2.46 0.00 0.00 3.01
4787 8875 2.270434 TGTCAGGAATAGGGCCTCTT 57.730 50.000 10.74 6.59 32.12 2.85
4810 8898 2.094649 GGATCCGGGATTGATCTACGAC 60.095 54.545 11.57 0.00 38.89 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.833346 TGTTATCAATACCCCTCAACCATA 57.167 37.500 0.00 0.00 0.00 2.74
42 43 3.627123 CGCCACCATGAGAATATGTGAAA 59.373 43.478 0.00 0.00 0.00 2.69
56 57 1.004277 ACATAAGGTTGTCGCCACCAT 59.996 47.619 3.62 0.00 0.00 3.55
64 65 3.795101 CACGTATCCGACATAAGGTTGTC 59.205 47.826 0.00 0.00 42.10 3.18
100 101 6.147985 ACACACTTTTTGTTTAAAACCGCATT 59.852 30.769 0.00 0.00 35.67 3.56
104 105 5.309707 GCACACACTTTTTGTTTAAAACCG 58.690 37.500 0.00 0.00 35.67 4.44
126 127 2.113860 TAAACTGCACAGGAGATGGC 57.886 50.000 2.21 0.00 0.00 4.40
127 128 4.264253 TGAATAAACTGCACAGGAGATGG 58.736 43.478 2.21 0.00 0.00 3.51
158 159 1.666553 CAAGTACGAAGCCGGTGCA 60.667 57.895 1.90 0.00 41.13 4.57
162 163 3.005050 TGATATACCAAGTACGAAGCCGG 59.995 47.826 0.00 0.00 40.78 6.13
192 193 2.777459 ATGAGGTCCTATCCTTCGGT 57.223 50.000 0.00 0.00 38.02 4.69
277 280 1.825474 TGAAGGAGGTCTCATCCGAAC 59.175 52.381 0.14 0.00 42.02 3.95
342 515 6.866010 ACATGATGCACATAATCAATACGT 57.134 33.333 0.00 0.00 37.58 3.57
353 526 4.758688 TCTCTTCGTAACATGATGCACAT 58.241 39.130 0.00 0.00 40.17 3.21
362 535 1.806623 GCGCCCATCTCTTCGTAACAT 60.807 52.381 0.00 0.00 0.00 2.71
368 541 1.741401 TTGTGCGCCCATCTCTTCG 60.741 57.895 4.18 0.00 0.00 3.79
419 592 7.031372 ACTGACATTTCCATTCAATTCAATCG 58.969 34.615 0.00 0.00 0.00 3.34
543 721 2.123428 GGATGCATGCAGACCCCAC 61.123 63.158 26.69 10.27 0.00 4.61
702 880 8.048514 TGGTGCATATATGTACGTACTCCTATA 58.951 37.037 25.12 20.50 43.16 1.31
704 882 6.149973 GTGGTGCATATATGTACGTACTCCTA 59.850 42.308 25.12 14.51 43.16 2.94
706 884 5.159209 GTGGTGCATATATGTACGTACTCC 58.841 45.833 25.12 11.80 43.16 3.85
707 885 5.765176 TGTGGTGCATATATGTACGTACTC 58.235 41.667 25.12 15.46 43.16 2.59
709 887 6.422701 ACATTGTGGTGCATATATGTACGTAC 59.577 38.462 22.59 22.18 43.16 3.67
710 888 6.422400 CACATTGTGGTGCATATATGTACGTA 59.578 38.462 22.59 14.07 43.16 3.57
768 2490 1.596603 TGATGCCATGTGATTAGCCG 58.403 50.000 0.00 0.00 0.00 5.52
793 2515 0.958382 TTTCTTTCGGCCGTCATGGG 60.958 55.000 27.15 10.63 38.63 4.00
806 2528 3.450578 TGACTAAGTGCGTCGTTTCTTT 58.549 40.909 0.00 0.00 34.17 2.52
809 2531 3.722123 CATTGACTAAGTGCGTCGTTTC 58.278 45.455 0.00 0.00 34.17 2.78
949 2677 2.378547 AGTCTGCCCTCTAGCTAGCTAT 59.621 50.000 24.36 3.01 0.00 2.97
1007 2735 3.775654 CGAGAGGAGGCACCCACC 61.776 72.222 0.00 0.00 40.05 4.61
1035 2763 0.670162 GCAGCAGCAAAGGAAGTGAA 59.330 50.000 0.00 0.00 41.58 3.18
1244 2972 5.942826 CCCAAGGCCAAGCATTTTAATTTTA 59.057 36.000 5.01 0.00 27.16 1.52
1246 2974 4.202556 ACCCAAGGCCAAGCATTTTAATTT 60.203 37.500 5.01 0.00 27.16 1.82
1247 2975 3.330405 ACCCAAGGCCAAGCATTTTAATT 59.670 39.130 5.01 0.00 27.16 1.40
1248 2976 2.912295 ACCCAAGGCCAAGCATTTTAAT 59.088 40.909 5.01 0.00 27.16 1.40
1542 3271 1.307097 GATGCACTCTGAATGGAGGC 58.693 55.000 0.00 0.00 37.63 4.70
1583 3312 4.142315 ACGCTAGCTTTGATTGATGCATTT 60.142 37.500 13.93 0.00 0.00 2.32
1693 3423 0.108756 GGTCTCCACCTCGTACAAGC 60.109 60.000 0.00 0.00 40.00 4.01
1766 3496 6.682362 GCTTCTGGATTTCATCAAAGGAATCC 60.682 42.308 6.99 6.99 0.00 3.01
1965 3695 1.425428 GCAGCGAGTTGGATTTCCG 59.575 57.895 0.00 0.00 39.43 4.30
1966 3696 1.657751 GGGCAGCGAGTTGGATTTCC 61.658 60.000 0.00 0.00 0.00 3.13
1967 3697 0.960364 TGGGCAGCGAGTTGGATTTC 60.960 55.000 0.00 0.00 0.00 2.17
1968 3698 0.539438 TTGGGCAGCGAGTTGGATTT 60.539 50.000 0.00 0.00 0.00 2.17
1969 3699 0.962356 CTTGGGCAGCGAGTTGGATT 60.962 55.000 0.00 0.00 0.00 3.01
1970 3700 1.377725 CTTGGGCAGCGAGTTGGAT 60.378 57.895 0.00 0.00 0.00 3.41
1971 3701 2.032528 CTTGGGCAGCGAGTTGGA 59.967 61.111 0.00 0.00 0.00 3.53
1972 3702 3.741476 GCTTGGGCAGCGAGTTGG 61.741 66.667 0.00 0.00 39.29 3.77
1980 3710 0.179051 GAGGAGATGAGCTTGGGCAG 60.179 60.000 0.00 0.00 41.70 4.85
1981 3711 1.630126 GGAGGAGATGAGCTTGGGCA 61.630 60.000 0.00 0.00 41.70 5.36
1982 3712 1.148048 GGAGGAGATGAGCTTGGGC 59.852 63.158 0.00 0.00 39.06 5.36
1983 3713 1.835693 GGGAGGAGATGAGCTTGGG 59.164 63.158 0.00 0.00 0.00 4.12
1984 3714 1.445095 CGGGAGGAGATGAGCTTGG 59.555 63.158 0.00 0.00 0.00 3.61
2053 3783 7.816995 GCATCAAATTATCTACCACACCAAAAA 59.183 33.333 0.00 0.00 0.00 1.94
2054 3784 7.319646 GCATCAAATTATCTACCACACCAAAA 58.680 34.615 0.00 0.00 0.00 2.44
2055 3785 6.404184 CGCATCAAATTATCTACCACACCAAA 60.404 38.462 0.00 0.00 0.00 3.28
2056 3786 5.065859 CGCATCAAATTATCTACCACACCAA 59.934 40.000 0.00 0.00 0.00 3.67
2057 3787 4.574421 CGCATCAAATTATCTACCACACCA 59.426 41.667 0.00 0.00 0.00 4.17
2058 3788 4.574828 ACGCATCAAATTATCTACCACACC 59.425 41.667 0.00 0.00 0.00 4.16
2059 3789 5.293324 TCACGCATCAAATTATCTACCACAC 59.707 40.000 0.00 0.00 0.00 3.82
2060 3790 5.423886 TCACGCATCAAATTATCTACCACA 58.576 37.500 0.00 0.00 0.00 4.17
2061 3791 5.050091 CCTCACGCATCAAATTATCTACCAC 60.050 44.000 0.00 0.00 0.00 4.16
2062 3792 5.056480 CCTCACGCATCAAATTATCTACCA 58.944 41.667 0.00 0.00 0.00 3.25
2063 3793 5.057149 ACCTCACGCATCAAATTATCTACC 58.943 41.667 0.00 0.00 0.00 3.18
2064 3794 5.177696 GGACCTCACGCATCAAATTATCTAC 59.822 44.000 0.00 0.00 0.00 2.59
2065 3795 5.297547 GGACCTCACGCATCAAATTATCTA 58.702 41.667 0.00 0.00 0.00 1.98
2066 3796 4.130118 GGACCTCACGCATCAAATTATCT 58.870 43.478 0.00 0.00 0.00 1.98
2067 3797 3.059597 CGGACCTCACGCATCAAATTATC 60.060 47.826 0.00 0.00 0.00 1.75
2068 3798 2.872245 CGGACCTCACGCATCAAATTAT 59.128 45.455 0.00 0.00 0.00 1.28
2069 3799 2.276201 CGGACCTCACGCATCAAATTA 58.724 47.619 0.00 0.00 0.00 1.40
2070 3800 1.086696 CGGACCTCACGCATCAAATT 58.913 50.000 0.00 0.00 0.00 1.82
2071 3801 2.767536 CGGACCTCACGCATCAAAT 58.232 52.632 0.00 0.00 0.00 2.32
2072 3802 4.277239 CGGACCTCACGCATCAAA 57.723 55.556 0.00 0.00 0.00 2.69
2079 3809 1.156736 AATTTGAAGCGGACCTCACG 58.843 50.000 0.00 0.00 0.00 4.35
2080 3810 2.552315 TGAAATTTGAAGCGGACCTCAC 59.448 45.455 0.00 0.00 0.00 3.51
2081 3811 2.857483 TGAAATTTGAAGCGGACCTCA 58.143 42.857 0.00 0.00 0.00 3.86
2082 3812 3.253432 AGTTGAAATTTGAAGCGGACCTC 59.747 43.478 0.00 0.00 0.00 3.85
2083 3813 3.222603 AGTTGAAATTTGAAGCGGACCT 58.777 40.909 0.00 0.00 0.00 3.85
2084 3814 3.643159 AGTTGAAATTTGAAGCGGACC 57.357 42.857 0.00 0.00 0.00 4.46
2085 3815 7.359181 CCAAATAAGTTGAAATTTGAAGCGGAC 60.359 37.037 10.02 0.00 42.90 4.79
2086 3816 6.644592 CCAAATAAGTTGAAATTTGAAGCGGA 59.355 34.615 10.02 0.00 42.90 5.54
2087 3817 6.644592 TCCAAATAAGTTGAAATTTGAAGCGG 59.355 34.615 10.02 0.00 42.90 5.52
2088 3818 7.636259 TCCAAATAAGTTGAAATTTGAAGCG 57.364 32.000 10.02 0.00 42.90 4.68
2098 3828 9.851686 ACTGCTCATATATCCAAATAAGTTGAA 57.148 29.630 0.00 0.00 39.87 2.69
2099 3829 9.851686 AACTGCTCATATATCCAAATAAGTTGA 57.148 29.630 0.00 0.00 39.87 3.18
2102 3832 9.717942 GAGAACTGCTCATATATCCAAATAAGT 57.282 33.333 0.00 0.00 43.38 2.24
2133 3863 3.553828 TCTGACCCGACTTGTCTTTTT 57.446 42.857 0.00 0.00 33.83 1.94
2134 3864 3.203716 GTTCTGACCCGACTTGTCTTTT 58.796 45.455 0.00 0.00 33.83 2.27
2135 3865 2.484947 GGTTCTGACCCGACTTGTCTTT 60.485 50.000 0.00 0.00 40.25 2.52
2136 3866 1.070289 GGTTCTGACCCGACTTGTCTT 59.930 52.381 0.00 0.00 40.25 3.01
2137 3867 0.680061 GGTTCTGACCCGACTTGTCT 59.320 55.000 0.00 0.00 40.25 3.41
2138 3868 3.212450 GGTTCTGACCCGACTTGTC 57.788 57.895 0.00 0.00 40.25 3.18
2147 3877 0.586802 GTTCACGCAAGGTTCTGACC 59.413 55.000 0.00 0.00 46.92 4.02
2148 3878 1.261619 CTGTTCACGCAAGGTTCTGAC 59.738 52.381 0.00 0.00 46.39 3.51
2149 3879 1.134521 ACTGTTCACGCAAGGTTCTGA 60.135 47.619 0.00 0.00 46.39 3.27
2150 3880 1.299541 ACTGTTCACGCAAGGTTCTG 58.700 50.000 0.00 0.00 46.39 3.02
2151 3881 2.902705 TACTGTTCACGCAAGGTTCT 57.097 45.000 0.00 0.00 46.39 3.01
2152 3882 3.311596 AGTTTACTGTTCACGCAAGGTTC 59.688 43.478 0.00 0.00 46.39 3.62
2153 3883 3.275999 AGTTTACTGTTCACGCAAGGTT 58.724 40.909 0.00 0.00 46.39 3.50
2154 3884 2.914059 AGTTTACTGTTCACGCAAGGT 58.086 42.857 0.00 0.00 46.39 3.50
2155 3885 3.963383 AAGTTTACTGTTCACGCAAGG 57.037 42.857 0.00 0.00 46.39 3.61
2199 3929 5.298276 ACATTTGAACCGCTCTCAGTAAAAA 59.702 36.000 0.00 0.00 0.00 1.94
2200 3930 4.819630 ACATTTGAACCGCTCTCAGTAAAA 59.180 37.500 0.00 0.00 0.00 1.52
2201 3931 4.385825 ACATTTGAACCGCTCTCAGTAAA 58.614 39.130 0.00 0.00 0.00 2.01
2202 3932 3.994392 GACATTTGAACCGCTCTCAGTAA 59.006 43.478 0.00 0.00 0.00 2.24
2203 3933 3.585862 GACATTTGAACCGCTCTCAGTA 58.414 45.455 0.00 0.00 0.00 2.74
2204 3934 2.417719 GACATTTGAACCGCTCTCAGT 58.582 47.619 0.00 0.00 0.00 3.41
2205 3935 1.734465 GGACATTTGAACCGCTCTCAG 59.266 52.381 0.00 0.00 0.00 3.35
2206 3936 1.071542 TGGACATTTGAACCGCTCTCA 59.928 47.619 0.00 0.00 0.00 3.27
2207 3937 1.808411 TGGACATTTGAACCGCTCTC 58.192 50.000 0.00 0.00 0.00 3.20
2208 3938 2.270352 TTGGACATTTGAACCGCTCT 57.730 45.000 0.00 0.00 0.00 4.09
2209 3939 3.575965 ATTTGGACATTTGAACCGCTC 57.424 42.857 0.00 0.00 0.00 5.03
2210 3940 4.522789 ACTTATTTGGACATTTGAACCGCT 59.477 37.500 0.00 0.00 0.00 5.52
2211 3941 4.805219 ACTTATTTGGACATTTGAACCGC 58.195 39.130 0.00 0.00 0.00 5.68
2212 3942 6.442952 TCAACTTATTTGGACATTTGAACCG 58.557 36.000 0.00 0.00 35.69 4.44
2213 3943 8.655651 TTTCAACTTATTTGGACATTTGAACC 57.344 30.769 0.00 0.00 35.69 3.62
2220 3950 8.992073 GCTTCAAATTTCAACTTATTTGGACAT 58.008 29.630 0.00 0.00 40.46 3.06
2221 3951 7.168972 CGCTTCAAATTTCAACTTATTTGGACA 59.831 33.333 0.00 0.00 40.46 4.02
2222 3952 7.359181 CCGCTTCAAATTTCAACTTATTTGGAC 60.359 37.037 0.00 0.00 40.46 4.02
2223 3953 6.644592 CCGCTTCAAATTTCAACTTATTTGGA 59.355 34.615 0.00 0.00 40.46 3.53
2224 3954 6.644592 TCCGCTTCAAATTTCAACTTATTTGG 59.355 34.615 0.00 0.00 40.46 3.28
2225 3955 7.359181 GGTCCGCTTCAAATTTCAACTTATTTG 60.359 37.037 0.00 0.00 41.08 2.32
2226 3956 6.645003 GGTCCGCTTCAAATTTCAACTTATTT 59.355 34.615 0.00 0.00 0.00 1.40
2227 3957 6.015434 AGGTCCGCTTCAAATTTCAACTTATT 60.015 34.615 0.00 0.00 0.00 1.40
2228 3958 5.476945 AGGTCCGCTTCAAATTTCAACTTAT 59.523 36.000 0.00 0.00 0.00 1.73
2229 3959 4.825085 AGGTCCGCTTCAAATTTCAACTTA 59.175 37.500 0.00 0.00 0.00 2.24
2230 3960 3.636764 AGGTCCGCTTCAAATTTCAACTT 59.363 39.130 0.00 0.00 0.00 2.66
2231 3961 3.222603 AGGTCCGCTTCAAATTTCAACT 58.777 40.909 0.00 0.00 0.00 3.16
2232 3962 3.004315 TGAGGTCCGCTTCAAATTTCAAC 59.996 43.478 0.00 0.00 0.00 3.18
2233 3963 3.004315 GTGAGGTCCGCTTCAAATTTCAA 59.996 43.478 0.00 0.00 32.39 2.69
2234 3964 2.552315 GTGAGGTCCGCTTCAAATTTCA 59.448 45.455 0.00 0.00 32.39 2.69
2235 3965 2.412847 CGTGAGGTCCGCTTCAAATTTC 60.413 50.000 0.00 0.00 32.39 2.17
2236 3966 1.535462 CGTGAGGTCCGCTTCAAATTT 59.465 47.619 0.00 0.00 32.39 1.82
2237 3967 1.156736 CGTGAGGTCCGCTTCAAATT 58.843 50.000 0.00 0.00 32.39 1.82
2238 3968 2.840974 CGTGAGGTCCGCTTCAAAT 58.159 52.632 0.00 0.00 32.39 2.32
2239 3969 4.354155 CGTGAGGTCCGCTTCAAA 57.646 55.556 0.00 0.00 32.39 2.69
2246 3976 4.750098 AGATAATTTAATGCGTGAGGTCCG 59.250 41.667 0.00 0.00 0.00 4.79
2247 3977 6.147328 GGTAGATAATTTAATGCGTGAGGTCC 59.853 42.308 0.00 0.00 0.00 4.46
2248 3978 6.704493 TGGTAGATAATTTAATGCGTGAGGTC 59.296 38.462 0.00 0.00 0.00 3.85
2249 3979 6.482308 GTGGTAGATAATTTAATGCGTGAGGT 59.518 38.462 0.00 0.00 0.00 3.85
2250 3980 6.481976 TGTGGTAGATAATTTAATGCGTGAGG 59.518 38.462 0.00 0.00 0.00 3.86
2251 3981 7.011016 TGTGTGGTAGATAATTTAATGCGTGAG 59.989 37.037 0.00 0.00 0.00 3.51
2252 3982 6.819146 TGTGTGGTAGATAATTTAATGCGTGA 59.181 34.615 0.00 0.00 0.00 4.35
2253 3983 7.010697 TGTGTGGTAGATAATTTAATGCGTG 57.989 36.000 0.00 0.00 0.00 5.34
2254 3984 7.618502 TTGTGTGGTAGATAATTTAATGCGT 57.381 32.000 0.00 0.00 0.00 5.24
2255 3985 8.903570 TTTTGTGTGGTAGATAATTTAATGCG 57.096 30.769 0.00 0.00 0.00 4.73
2322 4052 4.864334 CCGGGATCAGCTGCACCC 62.864 72.222 27.20 27.20 39.02 4.61
2323 4053 4.864334 CCCGGGATCAGCTGCACC 62.864 72.222 18.48 14.20 0.00 5.01
2324 4054 3.746949 CTCCCGGGATCAGCTGCAC 62.747 68.421 27.07 5.09 0.00 4.57
2325 4055 3.473647 CTCCCGGGATCAGCTGCA 61.474 66.667 27.07 0.00 0.00 4.41
2326 4056 4.925861 GCTCCCGGGATCAGCTGC 62.926 72.222 27.07 19.50 0.00 5.25
2327 4057 3.457625 CTGCTCCCGGGATCAGCTG 62.458 68.421 34.84 27.43 32.72 4.24
2328 4058 3.160047 CTGCTCCCGGGATCAGCT 61.160 66.667 34.84 0.00 32.72 4.24
2329 4059 2.257409 TTTCTGCTCCCGGGATCAGC 62.257 60.000 38.45 31.17 38.02 4.26
2330 4060 0.471617 ATTTCTGCTCCCGGGATCAG 59.528 55.000 37.87 37.87 39.07 2.90
2331 4061 0.181114 CATTTCTGCTCCCGGGATCA 59.819 55.000 27.07 25.90 0.00 2.92
2332 4062 0.181350 ACATTTCTGCTCCCGGGATC 59.819 55.000 27.07 22.07 0.00 3.36
2333 4063 0.625849 AACATTTCTGCTCCCGGGAT 59.374 50.000 27.07 3.56 0.00 3.85
2334 4064 0.322456 CAACATTTCTGCTCCCGGGA 60.322 55.000 25.06 25.06 0.00 5.14
2335 4065 1.937546 GCAACATTTCTGCTCCCGGG 61.938 60.000 16.85 16.85 36.84 5.73
2336 4066 1.243342 TGCAACATTTCTGCTCCCGG 61.243 55.000 0.00 0.00 40.59 5.73
2337 4067 0.813184 ATGCAACATTTCTGCTCCCG 59.187 50.000 0.00 0.00 40.59 5.14
2338 4068 1.135721 GGATGCAACATTTCTGCTCCC 59.864 52.381 0.00 0.00 40.59 4.30
2339 4069 1.135721 GGGATGCAACATTTCTGCTCC 59.864 52.381 0.00 0.00 40.59 4.70
2340 4070 1.820519 TGGGATGCAACATTTCTGCTC 59.179 47.619 0.00 0.00 40.59 4.26
2341 4071 1.927487 TGGGATGCAACATTTCTGCT 58.073 45.000 0.00 0.00 40.59 4.24
2342 4072 2.747396 TTGGGATGCAACATTTCTGC 57.253 45.000 0.00 0.00 40.35 4.26
2343 4073 6.563222 AAAAATTGGGATGCAACATTTCTG 57.437 33.333 0.00 0.00 0.00 3.02
2366 4096 0.106335 TACGGTCCGTGCCTCAAAAA 59.894 50.000 27.20 0.00 41.39 1.94
2367 4097 0.320073 CTACGGTCCGTGCCTCAAAA 60.320 55.000 27.20 2.95 41.39 2.44
2368 4098 1.180456 TCTACGGTCCGTGCCTCAAA 61.180 55.000 27.20 3.75 41.39 2.69
2369 4099 1.180456 TTCTACGGTCCGTGCCTCAA 61.180 55.000 27.20 8.92 41.39 3.02
2370 4100 1.180456 TTTCTACGGTCCGTGCCTCA 61.180 55.000 27.20 5.34 41.39 3.86
2371 4101 0.175073 ATTTCTACGGTCCGTGCCTC 59.825 55.000 27.20 0.00 41.39 4.70
2372 4102 0.108329 CATTTCTACGGTCCGTGCCT 60.108 55.000 27.20 1.80 41.39 4.75
2373 4103 1.702491 GCATTTCTACGGTCCGTGCC 61.702 60.000 27.20 3.42 41.39 5.01
2374 4104 0.739813 AGCATTTCTACGGTCCGTGC 60.740 55.000 27.20 19.41 41.39 5.34
2375 4105 0.999406 CAGCATTTCTACGGTCCGTG 59.001 55.000 27.20 16.13 41.39 4.94
2376 4106 0.739813 GCAGCATTTCTACGGTCCGT 60.740 55.000 22.66 22.66 44.35 4.69
2377 4107 0.739462 TGCAGCATTTCTACGGTCCG 60.739 55.000 10.48 10.48 0.00 4.79
2378 4108 1.599542 GATGCAGCATTTCTACGGTCC 59.400 52.381 9.90 0.00 0.00 4.46
2379 4109 1.599542 GGATGCAGCATTTCTACGGTC 59.400 52.381 9.90 0.00 0.00 4.79
2380 4110 1.668419 GGATGCAGCATTTCTACGGT 58.332 50.000 9.90 0.00 0.00 4.83
2381 4111 0.947244 GGGATGCAGCATTTCTACGG 59.053 55.000 9.90 0.00 0.00 4.02
2382 4112 0.583438 CGGGATGCAGCATTTCTACG 59.417 55.000 9.90 6.54 0.00 3.51
2383 4113 1.953559 TCGGGATGCAGCATTTCTAC 58.046 50.000 9.90 0.00 0.00 2.59
2384 4114 2.880268 CAATCGGGATGCAGCATTTCTA 59.120 45.455 9.90 0.00 0.00 2.10
2385 4115 1.679680 CAATCGGGATGCAGCATTTCT 59.320 47.619 9.90 0.00 0.00 2.52
2386 4116 1.406539 ACAATCGGGATGCAGCATTTC 59.593 47.619 9.90 5.27 0.00 2.17
2387 4117 1.477553 ACAATCGGGATGCAGCATTT 58.522 45.000 9.90 0.00 0.00 2.32
2388 4118 2.346766 TACAATCGGGATGCAGCATT 57.653 45.000 9.90 0.00 0.00 3.56
2389 4119 2.156917 CATACAATCGGGATGCAGCAT 58.843 47.619 7.91 7.91 0.00 3.79
2390 4120 1.134128 ACATACAATCGGGATGCAGCA 60.134 47.619 3.51 0.00 0.00 4.41
2391 4121 1.597742 ACATACAATCGGGATGCAGC 58.402 50.000 0.00 0.00 0.00 5.25
2392 4122 3.995199 AGTACATACAATCGGGATGCAG 58.005 45.455 0.00 0.00 0.00 4.41
2393 4123 4.587262 AGTAGTACATACAATCGGGATGCA 59.413 41.667 2.52 0.00 36.79 3.96
2394 4124 5.135508 AGTAGTACATACAATCGGGATGC 57.864 43.478 2.52 0.00 36.79 3.91
2395 4125 6.150318 GTGAGTAGTACATACAATCGGGATG 58.850 44.000 2.52 0.00 36.79 3.51
2396 4126 5.048921 CGTGAGTAGTACATACAATCGGGAT 60.049 44.000 2.52 0.00 36.79 3.85
2397 4127 4.274214 CGTGAGTAGTACATACAATCGGGA 59.726 45.833 2.52 0.00 36.79 5.14
2398 4128 4.274214 TCGTGAGTAGTACATACAATCGGG 59.726 45.833 2.52 0.00 36.79 5.14
2399 4129 5.203370 GTCGTGAGTAGTACATACAATCGG 58.797 45.833 2.52 0.00 36.79 4.18
2400 4130 5.203370 GGTCGTGAGTAGTACATACAATCG 58.797 45.833 2.52 2.01 36.79 3.34
2401 4131 5.506982 GGGGTCGTGAGTAGTACATACAATC 60.507 48.000 2.52 0.00 36.79 2.67
2464 6512 4.522789 ACCAGGAAATGTTTTCGCAGTAAT 59.477 37.500 0.00 0.00 0.00 1.89
2467 6515 2.306847 ACCAGGAAATGTTTTCGCAGT 58.693 42.857 0.00 0.00 0.00 4.40
2482 6530 9.436957 AAGCTAATCGAAATATATTGTACCAGG 57.563 33.333 0.00 0.00 0.00 4.45
2669 6721 7.976734 GTCTTTTCATTAAGAGAGAGGAATCGA 59.023 37.037 0.00 0.00 34.95 3.59
2676 6728 5.635280 TGCGTGTCTTTTCATTAAGAGAGAG 59.365 40.000 0.00 0.00 34.95 3.20
2748 6805 7.459486 GTTGACATTCTGTTATGCTACTTCTG 58.541 38.462 0.00 0.00 0.00 3.02
2798 6855 4.401202 GGGAAAAGTTCACCTCAAAAGTCA 59.599 41.667 0.00 0.00 0.00 3.41
2835 6892 4.147321 CCATGTCCCCTCAATATCAAAGG 58.853 47.826 0.00 0.00 0.00 3.11
2843 6900 3.668821 TCATCTACCATGTCCCCTCAAT 58.331 45.455 0.00 0.00 0.00 2.57
2857 6922 6.477033 ACAGCAAAACACGAGATATCATCTAC 59.523 38.462 5.32 0.00 40.38 2.59
2989 7055 8.891671 AAGTTGAACTGCAAAAACATCATATT 57.108 26.923 0.00 0.00 38.44 1.28
3027 7093 8.772250 ACTCCCTCTGAATCAAAATATAAGTCA 58.228 33.333 0.00 0.00 0.00 3.41
3570 7651 1.888958 TTTAGTGTTGCCGCGTACGC 61.889 55.000 29.83 29.83 38.22 4.42
3668 7749 1.741706 TCTTTGACGAGGCGGTAGTAG 59.258 52.381 0.00 0.00 0.00 2.57
4115 8196 3.788227 TGATGCAAAGACTGGGTACTT 57.212 42.857 0.00 0.00 0.00 2.24
4159 8242 7.734924 TCTTATAAGGATTGATGACATGCAC 57.265 36.000 12.54 0.00 0.00 4.57
4259 8343 8.677300 CCAGTTTGTATTGTTGTCTAGCAATAT 58.323 33.333 4.49 4.40 40.52 1.28
4318 8402 4.040952 GGATATTCTGGTGTCTAGGTGCAT 59.959 45.833 0.00 0.00 0.00 3.96
4368 8455 8.942338 ATACTAATCACTTGATTTGTAAGCGA 57.058 30.769 21.86 8.52 46.95 4.93
4496 8583 6.033966 ACAAGTCTTTGCCTCGTTTAAAAAG 58.966 36.000 0.00 0.00 37.85 2.27
4577 8664 4.513442 TGTGTGTATTATCAGAGGGTTGC 58.487 43.478 0.00 0.00 0.00 4.17
4626 8714 4.214545 TGCAACCTCGACGATGTTTTTATT 59.785 37.500 14.72 0.00 0.00 1.40
4673 8761 1.810031 CGGAGTCACTTGCTTGTGGAA 60.810 52.381 9.17 0.00 38.40 3.53
4700 8788 0.810031 GCTATGTCGGCGGTCACAAT 60.810 55.000 7.21 0.00 0.00 2.71
4727 8815 1.940613 GTGACTTCTTGCGACCTTTGT 59.059 47.619 0.00 0.00 0.00 2.83
4734 8822 1.150827 CTGCATGTGACTTCTTGCGA 58.849 50.000 0.00 0.00 40.02 5.10
4763 8851 1.202976 GGCCCTATTCCTGACATGCAT 60.203 52.381 0.00 0.00 0.00 3.96
4764 8852 0.183492 GGCCCTATTCCTGACATGCA 59.817 55.000 0.00 0.00 0.00 3.96
4765 8853 0.475906 AGGCCCTATTCCTGACATGC 59.524 55.000 0.00 0.00 31.53 4.06
4777 8865 1.530891 CGGATCCGAAGAGGCCCTA 60.531 63.158 30.62 0.00 42.83 3.53
4787 8875 2.168496 GTAGATCAATCCCGGATCCGA 58.832 52.381 35.42 17.32 41.64 4.55
4810 8898 6.267070 GGTTCTAGTCTTTCATAGTTCTCCG 58.733 44.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.