Multiple sequence alignment - TraesCS5B01G248100

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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 TraesCS5B01G248100 chr5B 100.000 7861 0 0 1 7861 430472979 430465119 0.000000e+00 14517.0
1 TraesCS5B01G248100 chr5B 91.492 764 46 15 6365 7119 430376586 430375833 0.000000e+00 1033.0
2 TraesCS5B01G248100 chr5B 96.607 501 13 2 5863 6363 430378761 430378265 0.000000e+00 828.0
3 TraesCS5B01G248100 chr5B 86.168 441 47 8 5682 6122 430246444 430246018 1.550000e-126 464.0
4 TraesCS5B01G248100 chr5B 86.158 419 44 8 5704 6122 430141933 430141529 2.600000e-119 440.0
5 TraesCS5B01G248100 chr5B 96.552 203 7 0 7659 7861 430141910 430141708 3.510000e-88 337.0
6 TraesCS5B01G248100 chr5B 96.552 203 7 0 7659 7861 430246399 430246197 3.510000e-88 337.0
7 TraesCS5B01G248100 chr5B 95.745 47 2 0 3753 3799 430469146 430469100 8.460000e-10 76.8
8 TraesCS5B01G248100 chr5B 95.745 47 2 0 3834 3880 430469227 430469181 8.460000e-10 76.8
9 TraesCS5B01G248100 chr5B 100.000 34 0 0 3796 3829 430469133 430469100 6.590000e-06 63.9
10 TraesCS5B01G248100 chr5B 100.000 34 0 0 3847 3880 430469184 430469151 6.590000e-06 63.9
11 TraesCS5B01G248100 chr5A 94.830 3404 127 22 3834 7204 465542501 465539114 0.000000e+00 5265.0
12 TraesCS5B01G248100 chr5A 96.471 2550 65 9 1 2540 465548088 465545554 0.000000e+00 4187.0
13 TraesCS5B01G248100 chr5A 95.133 678 30 2 5866 6542 465313861 465313186 0.000000e+00 1066.0
14 TraesCS5B01G248100 chr5A 95.161 558 17 5 6186 6739 465278589 465278038 0.000000e+00 872.0
15 TraesCS5B01G248100 chr5A 88.252 698 51 18 6537 7213 465310916 465310229 0.000000e+00 806.0
16 TraesCS5B01G248100 chr5A 96.010 401 16 0 3400 3800 465542854 465542454 0.000000e+00 652.0
17 TraesCS5B01G248100 chr5A 94.299 421 17 5 2974 3394 465543410 465542997 8.600000e-179 638.0
18 TraesCS5B01G248100 chr5A 96.793 343 9 1 5863 6205 465279084 465278744 8.850000e-159 571.0
19 TraesCS5B01G248100 chr5A 84.800 500 37 18 6735 7204 465277809 465277319 4.300000e-127 466.0
20 TraesCS5B01G248100 chr5A 90.148 203 17 1 7662 7861 465540602 465540400 2.180000e-65 261.0
21 TraesCS5B01G248100 chr5A 96.129 155 5 1 2808 2962 465543893 465543740 1.310000e-62 252.0
22 TraesCS5B01G248100 chr5A 91.837 147 10 1 2528 2674 465544030 465543886 3.720000e-48 204.0
23 TraesCS5B01G248100 chr5A 84.375 128 9 9 7340 7467 465309155 465309039 1.790000e-21 115.0
24 TraesCS5B01G248100 chr5A 97.143 35 1 0 3796 3830 465542488 465542454 8.520000e-05 60.2
25 TraesCS5B01G248100 chr5D 96.405 2976 78 8 1 2965 364401485 364398528 0.000000e+00 4876.0
26 TraesCS5B01G248100 chr5D 96.695 2481 72 5 3834 6310 364397616 364395142 0.000000e+00 4119.0
27 TraesCS5B01G248100 chr5D 96.068 941 30 4 6350 7285 364395145 364394207 0.000000e+00 1526.0
28 TraesCS5B01G248100 chr5D 93.712 827 26 10 2974 3800 364398369 364397569 0.000000e+00 1216.0
29 TraesCS5B01G248100 chr5D 98.330 539 9 0 7323 7861 364394205 364393667 0.000000e+00 946.0
30 TraesCS5B01G248100 chr7D 88.471 798 90 2 3 799 318251751 318252547 0.000000e+00 963.0
31 TraesCS5B01G248100 chr7B 86.375 800 106 3 1 799 302546507 302545710 0.000000e+00 870.0
32 TraesCS5B01G248100 chr7B 87.126 769 96 3 1 768 302513292 302512526 0.000000e+00 869.0
33 TraesCS5B01G248100 chrUn 86.036 444 48 8 5679 6122 369774136 369774565 1.550000e-126 464.0
34 TraesCS5B01G248100 chrUn 86.168 441 47 8 5682 6122 400072315 400071889 1.550000e-126 464.0
35 TraesCS5B01G248100 chrUn 85.941 441 48 8 5682 6122 361244582 361244156 7.190000e-125 459.0
36 TraesCS5B01G248100 chrUn 85.941 441 48 8 5682 6122 399317465 399317039 7.190000e-125 459.0
37 TraesCS5B01G248100 chrUn 96.552 203 7 0 7659 7861 361244537 361244335 3.510000e-88 337.0
38 TraesCS5B01G248100 chrUn 96.552 203 7 0 7659 7861 369774184 369774386 3.510000e-88 337.0
39 TraesCS5B01G248100 chrUn 96.552 203 7 0 7659 7861 399317420 399317218 3.510000e-88 337.0
40 TraesCS5B01G248100 chrUn 96.552 203 7 0 7659 7861 400072270 400072068 3.510000e-88 337.0
41 TraesCS5B01G248100 chrUn 87.500 80 8 2 3521 3600 48471376 48471453 3.020000e-14 91.6
42 TraesCS5B01G248100 chrUn 87.500 80 8 2 3521 3600 48498154 48498231 3.020000e-14 91.6
43 TraesCS5B01G248100 chrUn 87.500 80 8 2 3521 3600 235113477 235113554 3.020000e-14 91.6
44 TraesCS5B01G248100 chrUn 89.041 73 8 0 3528 3600 237211180 237211108 3.020000e-14 91.6
45 TraesCS5B01G248100 chrUn 89.041 73 8 0 3528 3600 346824056 346823984 3.020000e-14 91.6
46 TraesCS5B01G248100 chr6B 94.366 71 2 1 3522 3590 195461855 195461925 3.000000e-19 108.0
47 TraesCS5B01G248100 chr6B 90.411 73 4 2 3524 3594 166127579 166127650 8.400000e-15 93.5


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 TraesCS5B01G248100 chr5B 430465119 430472979 7860 True 2959.680000 14517 98.298000 1 7861 5 chr5B.!!$R4 7860
1 TraesCS5B01G248100 chr5B 430375833 430378761 2928 True 930.500000 1033 94.049500 5863 7119 2 chr5B.!!$R3 1256
2 TraesCS5B01G248100 chr5A 465539114 465548088 8974 True 1439.900000 5265 94.608375 1 7861 8 chr5A.!!$R3 7860
3 TraesCS5B01G248100 chr5A 465309039 465313861 4822 True 662.333333 1066 89.253333 5866 7467 3 chr5A.!!$R2 1601
4 TraesCS5B01G248100 chr5A 465277319 465279084 1765 True 636.333333 872 92.251333 5863 7204 3 chr5A.!!$R1 1341
5 TraesCS5B01G248100 chr5D 364393667 364401485 7818 True 2536.600000 4876 96.242000 1 7861 5 chr5D.!!$R1 7860
6 TraesCS5B01G248100 chr7D 318251751 318252547 796 False 963.000000 963 88.471000 3 799 1 chr7D.!!$F1 796
7 TraesCS5B01G248100 chr7B 302545710 302546507 797 True 870.000000 870 86.375000 1 799 1 chr7B.!!$R2 798
8 TraesCS5B01G248100 chr7B 302512526 302513292 766 True 869.000000 869 87.126000 1 768 1 chr7B.!!$R1 767

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
885 891 2.231380 GGAGGAGTTGGGGGCTCAA 61.231 63.158 0.00 0.0 34.83 3.02 F
1644 1650 1.271762 CCGTATGGGGAGGAGATACGA 60.272 57.143 11.32 0.0 44.94 3.43 F
2970 4519 0.776080 AGAGTGTTTGGGTGGGGGAT 60.776 55.000 0.00 0.0 0.00 3.85 F
3591 5595 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.0 0.00 2.73 F
3794 5798 0.744281 TCGTGACTTGAGTGCTGTGA 59.256 50.000 0.00 0.0 0.00 3.58 F
3824 5828 0.744281 TCGTGACTTGAGTGCTGTGA 59.256 50.000 0.00 0.0 0.00 3.58 F
3832 5836 0.764271 TGAGTGCTGTGAATGTGGGA 59.236 50.000 0.00 0.0 0.00 4.37 F
3834 5838 0.767375 AGTGCTGTGAATGTGGGAGT 59.233 50.000 0.00 0.0 0.00 3.85 F
5829 7836 0.741326 TCGAGGCTCTGGAAAGATCG 59.259 55.000 13.50 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2685 4233 0.824759 AGTACGCATGAGGGGTCTTC 59.175 55.000 0.00 0.0 42.41 2.87 R
3063 4930 1.404583 GCCATGTTGCCATCAAGGTTC 60.405 52.381 0.00 0.0 40.61 3.62 R
3840 5844 0.391597 ACGAACTCCCACATCGTTGT 59.608 50.000 0.00 0.0 46.66 3.32 R
5090 7097 0.037326 GGCAGTCACTCCACGATCAA 60.037 55.000 0.00 0.0 0.00 2.57 R
5416 7423 5.130145 CCACACTAATTTGAGGAGGAGAGAT 59.870 44.000 0.00 0.0 29.11 2.75 R
5727 7734 6.934645 CACTTACAAAAGAACTCCTCATACCA 59.065 38.462 0.00 0.0 36.50 3.25 R
5829 7836 1.070786 TGTTTCCAGGTCGCTGTCC 59.929 57.895 0.00 0.0 0.00 4.02 R
5913 7920 5.163530 GGTGTGCATGGACATAAAATCATCA 60.164 40.000 23.52 0.0 0.00 3.07 R
7306 14091 0.315251 GCCTGTGCCAAACTTTCCTC 59.685 55.000 0.00 0.0 0.00 3.71 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
885 891 2.231380 GGAGGAGTTGGGGGCTCAA 61.231 63.158 0.00 0.00 34.83 3.02
1513 1519 3.776781 CCACGATACCGGTGCCCA 61.777 66.667 19.93 0.00 40.78 5.36
1578 1584 1.747745 CCGGGATTTGACGAACCCC 60.748 63.158 0.00 0.00 39.20 4.95
1602 1608 1.293179 GGTGGCTGTTGATTTGGCC 59.707 57.895 0.00 0.00 44.31 5.36
1617 1623 2.811317 GCCAGACTCGCGGAGTTG 60.811 66.667 6.13 9.37 43.53 3.16
1644 1650 1.271762 CCGTATGGGGAGGAGATACGA 60.272 57.143 11.32 0.00 44.94 3.43
1839 1845 1.819208 CTGGATCAATTGCCGCCGA 60.819 57.895 0.00 0.00 0.00 5.54
1888 1894 8.703604 TGTGTATAGTTTGTTCTGATTCTAGC 57.296 34.615 0.00 0.00 0.00 3.42
1898 1904 5.216648 GTTCTGATTCTAGCGATAGTGGAC 58.783 45.833 7.70 0.00 39.35 4.02
2153 2159 9.851686 ACATATTAGAAACATAAGCATCAGGAA 57.148 29.630 0.00 0.00 0.00 3.36
2229 2235 4.683781 GCATTTGCAAGGTGTTATTTCGAA 59.316 37.500 13.36 0.00 41.59 3.71
2231 2237 6.292596 GCATTTGCAAGGTGTTATTTCGAAAA 60.293 34.615 15.66 1.71 41.59 2.29
2297 2303 4.460263 ACATAGTGCTCCTGTTTGTTTCA 58.540 39.130 0.00 0.00 0.00 2.69
2338 2344 3.245284 GTGTTGCATGCATACCTAGTACG 59.755 47.826 23.37 0.00 0.00 3.67
2382 2394 4.839668 TTGTTGGTCCTATTTGGTTTCG 57.160 40.909 0.00 0.00 37.07 3.46
2521 2533 3.889815 CCTCTGCCAATTTCCATGTCTA 58.110 45.455 0.00 0.00 0.00 2.59
2522 2534 4.272489 CCTCTGCCAATTTCCATGTCTAA 58.728 43.478 0.00 0.00 0.00 2.10
2577 4125 8.225603 TGTGCTGATAAGGATTTTAGGATTTC 57.774 34.615 0.00 0.00 0.00 2.17
2594 4142 9.558396 TTAGGATTTCCGTTTTCTAAAGTAACA 57.442 29.630 0.00 0.00 42.08 2.41
2698 4246 2.200373 AAAACCGAAGACCCCTCATG 57.800 50.000 0.00 0.00 0.00 3.07
2700 4248 2.202932 CCGAAGACCCCTCATGCG 60.203 66.667 0.00 0.00 0.00 4.73
2712 4260 4.398044 ACCCCTCATGCGTACTTTATTTTG 59.602 41.667 0.00 0.00 0.00 2.44
2749 4297 5.249622 TGTGTTCTGGGTATATGAACCTTGA 59.750 40.000 0.00 0.00 39.24 3.02
2751 4299 6.316390 GTGTTCTGGGTATATGAACCTTGAAG 59.684 42.308 0.00 0.00 39.24 3.02
2867 4415 6.879400 AGTAGCTGAAAATAGAACCTCGAAT 58.121 36.000 0.00 0.00 0.00 3.34
2887 4435 8.130671 TCGAATAGTTAATTGTAGGGGGATAG 57.869 38.462 0.00 0.00 0.00 2.08
2906 4454 7.266400 GGGATAGTTTAGTCCTGTGTTAAGAG 58.734 42.308 0.00 0.00 34.84 2.85
2965 4514 2.292828 ATCCAAGAGTGTTTGGGTGG 57.707 50.000 5.06 0.00 46.16 4.61
2967 4516 0.827507 CCAAGAGTGTTTGGGTGGGG 60.828 60.000 0.00 0.00 43.16 4.96
2969 4518 0.996762 AAGAGTGTTTGGGTGGGGGA 60.997 55.000 0.00 0.00 0.00 4.81
2970 4519 0.776080 AGAGTGTTTGGGTGGGGGAT 60.776 55.000 0.00 0.00 0.00 3.85
2971 4520 0.996583 GAGTGTTTGGGTGGGGGATA 59.003 55.000 0.00 0.00 0.00 2.59
3054 4921 6.498538 TCTCTAATCCCTCTCTTCTTCAACT 58.501 40.000 0.00 0.00 0.00 3.16
3059 4926 3.103742 CCCTCTCTTCTTCAACTAGCCT 58.896 50.000 0.00 0.00 0.00 4.58
3063 4930 5.398603 TCTCTTCTTCAACTAGCCTTCAG 57.601 43.478 0.00 0.00 0.00 3.02
3072 4939 4.287067 TCAACTAGCCTTCAGAACCTTGAT 59.713 41.667 0.00 0.00 0.00 2.57
3131 4998 8.403236 CCATATTATGCACATACCATCTTGATG 58.597 37.037 3.77 3.77 0.00 3.07
3134 5001 2.946990 TGCACATACCATCTTGATGCTG 59.053 45.455 5.16 5.22 32.81 4.41
3191 5058 5.010012 AGCGATTCCACTTTTTCTTGAATGT 59.990 36.000 0.00 0.00 0.00 2.71
3317 5184 8.511604 AACTCAGTGATTTTTCTCTCTTTTCA 57.488 30.769 0.00 0.00 0.00 2.69
3359 5226 6.923012 TCATTGTGCTTTGCATAAGTTATGT 58.077 32.000 21.15 0.00 42.32 2.29
3381 5248 7.123355 TGTTTTTGGAGAAAAAGATCCATGT 57.877 32.000 0.00 0.00 44.87 3.21
3511 5515 5.528043 TGCTACATGGTTTGTGATGTTTT 57.472 34.783 0.00 0.00 39.48 2.43
3538 5542 4.246712 TCTAATCAAGTACTCCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
3591 5595 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
3604 5608 6.348213 CGGAGGGAGTAGTAAATTGTGTTTTG 60.348 42.308 0.00 0.00 0.00 2.44
3626 5630 6.734502 TGCATGTTGATTTCCCATTATCAT 57.265 33.333 0.00 0.00 31.34 2.45
3649 5653 3.848272 TTGCCTTAGCTAATTGTGCAC 57.152 42.857 10.75 10.75 40.80 4.57
3652 5656 2.749621 GCCTTAGCTAATTGTGCACACT 59.250 45.455 21.56 12.30 35.50 3.55
3691 5695 3.763897 GGGGACATCAATTTGCTACTTGT 59.236 43.478 0.00 0.00 0.00 3.16
3760 5764 1.680338 AGCCAACCACTGTTCAGAAC 58.320 50.000 6.32 6.32 30.42 3.01
3761 5765 1.064758 AGCCAACCACTGTTCAGAACA 60.065 47.619 15.39 15.39 39.52 3.18
3762 5766 1.748493 GCCAACCACTGTTCAGAACAA 59.252 47.619 16.85 1.86 41.61 2.83
3763 5767 2.362077 GCCAACCACTGTTCAGAACAAT 59.638 45.455 16.85 4.25 41.61 2.71
3764 5768 3.796504 GCCAACCACTGTTCAGAACAATG 60.797 47.826 16.36 16.36 41.61 2.82
3765 5769 3.631686 CCAACCACTGTTCAGAACAATGA 59.368 43.478 23.34 0.00 40.84 2.57
3766 5770 4.279169 CCAACCACTGTTCAGAACAATGAT 59.721 41.667 23.34 6.02 40.84 2.45
3767 5771 5.473162 CCAACCACTGTTCAGAACAATGATA 59.527 40.000 23.34 0.00 40.84 2.15
3768 5772 6.151648 CCAACCACTGTTCAGAACAATGATAT 59.848 38.462 23.34 8.01 40.84 1.63
3769 5773 6.748333 ACCACTGTTCAGAACAATGATATG 57.252 37.500 23.34 10.80 40.84 1.78
3770 5774 5.649395 ACCACTGTTCAGAACAATGATATGG 59.351 40.000 23.34 19.55 40.84 2.74
3771 5775 5.066893 CCACTGTTCAGAACAATGATATGGG 59.933 44.000 23.34 8.68 40.84 4.00
3772 5776 5.882000 CACTGTTCAGAACAATGATATGGGA 59.118 40.000 18.09 0.00 40.84 4.37
3773 5777 6.037940 CACTGTTCAGAACAATGATATGGGAG 59.962 42.308 18.09 4.37 40.84 4.30
3774 5778 6.065976 TGTTCAGAACAATGATATGGGAGT 57.934 37.500 13.90 0.00 38.72 3.85
3775 5779 6.484288 TGTTCAGAACAATGATATGGGAGTT 58.516 36.000 13.90 0.00 38.72 3.01
3776 5780 6.599244 TGTTCAGAACAATGATATGGGAGTTC 59.401 38.462 13.90 0.00 38.72 3.01
3777 5781 5.359756 TCAGAACAATGATATGGGAGTTCG 58.640 41.667 0.00 0.00 40.03 3.95
3778 5782 5.104941 TCAGAACAATGATATGGGAGTTCGT 60.105 40.000 0.00 0.00 40.03 3.85
3779 5783 5.007039 CAGAACAATGATATGGGAGTTCGTG 59.993 44.000 0.00 0.00 40.03 4.35
3780 5784 4.753516 ACAATGATATGGGAGTTCGTGA 57.246 40.909 0.00 0.00 0.00 4.35
3781 5785 4.442706 ACAATGATATGGGAGTTCGTGAC 58.557 43.478 0.00 0.00 0.00 3.67
3782 5786 4.162320 ACAATGATATGGGAGTTCGTGACT 59.838 41.667 0.00 0.00 42.70 3.41
3783 5787 5.118990 CAATGATATGGGAGTTCGTGACTT 58.881 41.667 0.00 0.00 39.19 3.01
3784 5788 4.123497 TGATATGGGAGTTCGTGACTTG 57.877 45.455 0.00 0.00 39.19 3.16
3785 5789 3.767131 TGATATGGGAGTTCGTGACTTGA 59.233 43.478 0.00 0.00 39.19 3.02
3786 5790 2.751166 ATGGGAGTTCGTGACTTGAG 57.249 50.000 0.00 0.00 39.19 3.02
3787 5791 1.410004 TGGGAGTTCGTGACTTGAGT 58.590 50.000 0.00 0.00 39.19 3.41
3788 5792 1.068588 TGGGAGTTCGTGACTTGAGTG 59.931 52.381 0.00 0.00 39.19 3.51
3789 5793 1.140816 GGAGTTCGTGACTTGAGTGC 58.859 55.000 0.00 0.00 39.19 4.40
3790 5794 1.269831 GGAGTTCGTGACTTGAGTGCT 60.270 52.381 0.00 0.00 39.19 4.40
3791 5795 1.789464 GAGTTCGTGACTTGAGTGCTG 59.211 52.381 0.00 0.00 39.19 4.41
3792 5796 1.137086 AGTTCGTGACTTGAGTGCTGT 59.863 47.619 0.00 0.00 33.92 4.40
3793 5797 1.258982 GTTCGTGACTTGAGTGCTGTG 59.741 52.381 0.00 0.00 0.00 3.66
3794 5798 0.744281 TCGTGACTTGAGTGCTGTGA 59.256 50.000 0.00 0.00 0.00 3.58
3795 5799 1.136110 TCGTGACTTGAGTGCTGTGAA 59.864 47.619 0.00 0.00 0.00 3.18
3796 5800 2.138320 CGTGACTTGAGTGCTGTGAAT 58.862 47.619 0.00 0.00 0.00 2.57
3797 5801 2.096565 CGTGACTTGAGTGCTGTGAATG 60.097 50.000 0.00 0.00 0.00 2.67
3798 5802 2.874701 GTGACTTGAGTGCTGTGAATGT 59.125 45.455 0.00 0.00 0.00 2.71
3799 5803 2.874086 TGACTTGAGTGCTGTGAATGTG 59.126 45.455 0.00 0.00 0.00 3.21
3800 5804 2.224606 ACTTGAGTGCTGTGAATGTGG 58.775 47.619 0.00 0.00 0.00 4.17
3801 5805 1.538512 CTTGAGTGCTGTGAATGTGGG 59.461 52.381 0.00 0.00 0.00 4.61
3802 5806 0.764271 TGAGTGCTGTGAATGTGGGA 59.236 50.000 0.00 0.00 0.00 4.37
3803 5807 1.271001 TGAGTGCTGTGAATGTGGGAG 60.271 52.381 0.00 0.00 0.00 4.30
3804 5808 0.767375 AGTGCTGTGAATGTGGGAGT 59.233 50.000 0.00 0.00 0.00 3.85
3805 5809 1.143684 AGTGCTGTGAATGTGGGAGTT 59.856 47.619 0.00 0.00 0.00 3.01
3806 5810 1.537202 GTGCTGTGAATGTGGGAGTTC 59.463 52.381 0.00 0.00 0.00 3.01
3807 5811 0.798776 GCTGTGAATGTGGGAGTTCG 59.201 55.000 0.00 0.00 0.00 3.95
3808 5812 1.878102 GCTGTGAATGTGGGAGTTCGT 60.878 52.381 0.00 0.00 0.00 3.85
3809 5813 1.800586 CTGTGAATGTGGGAGTTCGTG 59.199 52.381 0.00 0.00 0.00 4.35
3810 5814 1.414550 TGTGAATGTGGGAGTTCGTGA 59.585 47.619 0.00 0.00 0.00 4.35
3811 5815 1.798813 GTGAATGTGGGAGTTCGTGAC 59.201 52.381 0.00 0.00 0.00 3.67
3812 5816 1.691976 TGAATGTGGGAGTTCGTGACT 59.308 47.619 0.00 0.00 42.70 3.41
3813 5817 2.104111 TGAATGTGGGAGTTCGTGACTT 59.896 45.455 0.00 0.00 39.19 3.01
3814 5818 2.169832 ATGTGGGAGTTCGTGACTTG 57.830 50.000 0.00 0.00 39.19 3.16
3815 5819 1.116308 TGTGGGAGTTCGTGACTTGA 58.884 50.000 0.00 0.00 39.19 3.02
3816 5820 1.068588 TGTGGGAGTTCGTGACTTGAG 59.931 52.381 0.00 0.00 39.19 3.02
3817 5821 1.068741 GTGGGAGTTCGTGACTTGAGT 59.931 52.381 0.00 0.00 39.19 3.41
3818 5822 1.068588 TGGGAGTTCGTGACTTGAGTG 59.931 52.381 0.00 0.00 39.19 3.51
3819 5823 1.140816 GGAGTTCGTGACTTGAGTGC 58.859 55.000 0.00 0.00 39.19 4.40
3820 5824 1.269831 GGAGTTCGTGACTTGAGTGCT 60.270 52.381 0.00 0.00 39.19 4.40
3821 5825 1.789464 GAGTTCGTGACTTGAGTGCTG 59.211 52.381 0.00 0.00 39.19 4.41
3822 5826 1.137086 AGTTCGTGACTTGAGTGCTGT 59.863 47.619 0.00 0.00 33.92 4.40
3823 5827 1.258982 GTTCGTGACTTGAGTGCTGTG 59.741 52.381 0.00 0.00 0.00 3.66
3824 5828 0.744281 TCGTGACTTGAGTGCTGTGA 59.256 50.000 0.00 0.00 0.00 3.58
3825 5829 1.136110 TCGTGACTTGAGTGCTGTGAA 59.864 47.619 0.00 0.00 0.00 3.18
3826 5830 2.138320 CGTGACTTGAGTGCTGTGAAT 58.862 47.619 0.00 0.00 0.00 2.57
3827 5831 2.096565 CGTGACTTGAGTGCTGTGAATG 60.097 50.000 0.00 0.00 0.00 2.67
3828 5832 2.874701 GTGACTTGAGTGCTGTGAATGT 59.125 45.455 0.00 0.00 0.00 2.71
3829 5833 2.874086 TGACTTGAGTGCTGTGAATGTG 59.126 45.455 0.00 0.00 0.00 3.21
3830 5834 2.224606 ACTTGAGTGCTGTGAATGTGG 58.775 47.619 0.00 0.00 0.00 4.17
3831 5835 1.538512 CTTGAGTGCTGTGAATGTGGG 59.461 52.381 0.00 0.00 0.00 4.61
3832 5836 0.764271 TGAGTGCTGTGAATGTGGGA 59.236 50.000 0.00 0.00 0.00 4.37
3833 5837 1.271001 TGAGTGCTGTGAATGTGGGAG 60.271 52.381 0.00 0.00 0.00 4.30
3834 5838 0.767375 AGTGCTGTGAATGTGGGAGT 59.233 50.000 0.00 0.00 0.00 3.85
3835 5839 1.143684 AGTGCTGTGAATGTGGGAGTT 59.856 47.619 0.00 0.00 0.00 3.01
3836 5840 1.537202 GTGCTGTGAATGTGGGAGTTC 59.463 52.381 0.00 0.00 0.00 3.01
3837 5841 1.142667 TGCTGTGAATGTGGGAGTTCA 59.857 47.619 0.00 0.00 32.31 3.18
3838 5842 1.808945 GCTGTGAATGTGGGAGTTCAG 59.191 52.381 0.00 0.00 35.22 3.02
3839 5843 2.550855 GCTGTGAATGTGGGAGTTCAGA 60.551 50.000 0.00 0.00 35.22 3.27
3840 5844 3.743521 CTGTGAATGTGGGAGTTCAGAA 58.256 45.455 0.00 0.00 35.22 3.02
3852 5856 2.480419 GAGTTCAGAACAACGATGTGGG 59.520 50.000 15.85 0.00 40.46 4.61
3880 5884 4.058124 GTGACTTGAGTGCTGTGAATGTA 58.942 43.478 0.00 0.00 0.00 2.29
3909 5913 7.591006 TTTTCTTAGTACGCACCTTATCTTG 57.409 36.000 0.00 0.00 0.00 3.02
3935 5939 3.316308 GTCTGCACTTTCATTTCCACTGT 59.684 43.478 0.00 0.00 0.00 3.55
3994 5998 6.489700 TCTTCACCAGCAAAATGATTCAACTA 59.510 34.615 0.00 0.00 0.00 2.24
4035 6039 4.994852 GTGTCAGCCACTTCTGTTACATTA 59.005 41.667 0.00 0.00 41.11 1.90
4036 6040 5.643777 GTGTCAGCCACTTCTGTTACATTAT 59.356 40.000 0.00 0.00 41.11 1.28
4170 6174 1.097232 GTGCCTATGTGCAGCATCAA 58.903 50.000 0.00 0.00 43.02 2.57
4176 6180 3.630769 CCTATGTGCAGCATCAATTGTCT 59.369 43.478 5.13 0.00 38.94 3.41
4218 6222 1.670811 AGGCGCAAGGTTGATAAATCG 59.329 47.619 10.83 0.00 38.28 3.34
4219 6223 1.668751 GGCGCAAGGTTGATAAATCGA 59.331 47.619 10.83 0.00 38.28 3.59
4224 6228 4.201910 CGCAAGGTTGATAAATCGATTGGT 60.202 41.667 12.25 3.16 0.00 3.67
4234 6238 1.866015 ATCGATTGGTCTGGGAGTCA 58.134 50.000 0.00 0.00 0.00 3.41
4248 6252 5.309543 TCTGGGAGTCAGTAAAGATGGAAAA 59.690 40.000 0.00 0.00 43.76 2.29
4260 6264 7.993183 AGTAAAGATGGAAAACTTGAGACTCAA 59.007 33.333 16.86 16.86 34.79 3.02
4302 6306 6.252995 TGAAGATAAACCTGGCTATTTTGGT 58.747 36.000 0.00 0.00 0.00 3.67
4386 6390 2.382882 TCAGGAGATGTAGGTGCTCAG 58.617 52.381 0.00 0.00 0.00 3.35
4430 6434 2.162408 GTGGGTTGCAAGAGATAACTGC 59.838 50.000 0.00 0.00 0.00 4.40
4455 6459 1.902508 CCTGAACAGGTAGAAGAGCCA 59.097 52.381 12.21 0.00 43.61 4.75
4529 6536 5.511363 TGGTTTACCTCAACAGGAAAAAGA 58.489 37.500 0.00 0.00 43.65 2.52
4649 6656 1.067354 GCCTCTTGCCTTTGATGTTGG 60.067 52.381 0.00 0.00 0.00 3.77
4798 6805 3.198635 ACCTCAGGATGTTCCATGTACTG 59.801 47.826 0.00 0.00 39.61 2.74
4946 6953 2.883026 TGGTTTTAATGACCAGGTGGG 58.117 47.619 0.00 0.00 42.06 4.61
4950 6957 4.530553 GGTTTTAATGACCAGGTGGGAAAT 59.469 41.667 0.00 0.00 41.15 2.17
5041 7048 1.533625 AGCTTGCAAGTTTGGCGATA 58.466 45.000 26.55 0.00 0.00 2.92
5055 7062 3.664107 TGGCGATATGCTGAATTCTACC 58.336 45.455 7.05 0.00 45.43 3.18
5090 7097 7.722949 ATGATAAACCTGTTGTGGATCAAAT 57.277 32.000 0.00 0.00 37.81 2.32
5124 7131 2.919229 GACTGCCTTGAAAAATGATGCG 59.081 45.455 0.00 0.00 0.00 4.73
5172 7179 7.177878 ACATTGATGTCAGAATAAAGGAGGTT 58.822 34.615 0.00 0.00 35.87 3.50
5364 7371 8.962884 ACAATGTTTCTAAGGCTGAAATTTTT 57.037 26.923 3.66 0.00 36.10 1.94
5416 7423 8.592529 TCAATCCAATTTGAACATGAATCCTA 57.407 30.769 0.00 0.00 32.82 2.94
5705 7712 1.738099 CGCTGACTGGTGGTACTGC 60.738 63.158 0.00 0.00 0.00 4.40
5829 7836 0.741326 TCGAGGCTCTGGAAAGATCG 59.259 55.000 13.50 0.00 0.00 3.69
5913 7920 1.102978 GCACAAGTGGGACAAGTGTT 58.897 50.000 2.00 0.00 44.16 3.32
6050 8057 3.305964 CTCACATGCTGTTTTTGCTCAG 58.694 45.455 0.00 0.00 35.12 3.35
6276 8457 3.206150 GAGGTCACAGTGTCACACAATT 58.794 45.455 11.40 0.00 36.74 2.32
6286 8467 5.978919 CAGTGTCACACAATTTAGCATGTTT 59.021 36.000 11.40 0.00 36.74 2.83
6310 8492 6.364701 TGGGTAACTATTGCAATAGCTGAAT 58.635 36.000 35.65 22.57 41.62 2.57
6378 10237 7.387397 ACATTCTCTCTTAAATATAGCAGCAGC 59.613 37.037 0.00 0.00 42.56 5.25
6440 10300 2.412870 TGCGTGTTGACTCTGGTAATG 58.587 47.619 0.00 0.00 0.00 1.90
6455 10315 8.154856 ACTCTGGTAATGTATTTTGTACAGTGT 58.845 33.333 0.00 0.00 0.00 3.55
6548 12684 2.359230 GCTGGAGCTCCGCAGTTT 60.359 61.111 31.47 0.00 39.43 2.66
6803 13172 3.381136 GGCTTCATTTGCCCCGCA 61.381 61.111 0.00 0.00 44.32 5.69
6896 13265 6.114767 TGCTGCTGTTTTCATCATATGTAGA 58.885 36.000 1.90 0.00 0.00 2.59
6965 13343 6.775594 TCTGAGCTAGCAAATTCTAGTGTA 57.224 37.500 18.83 0.00 38.58 2.90
6982 13360 1.543358 TGTATGTGCGGTGGTTACGTA 59.457 47.619 0.00 0.00 0.00 3.57
6983 13361 2.166050 TGTATGTGCGGTGGTTACGTAT 59.834 45.455 0.00 0.00 0.00 3.06
6984 13362 1.647346 ATGTGCGGTGGTTACGTATG 58.353 50.000 0.00 0.00 0.00 2.39
6985 13363 0.317799 TGTGCGGTGGTTACGTATGT 59.682 50.000 0.00 0.00 0.00 2.29
7027 13418 4.025979 CGGTCGTTTACTGATTTGGCTATC 60.026 45.833 0.00 0.00 36.47 2.08
7076 13467 2.093075 AGTGCTGATGTCCAGATTGAGG 60.093 50.000 0.00 0.00 45.78 3.86
7200 13611 1.672881 GCATATGGAAGTGCTGGTCAC 59.327 52.381 4.56 0.00 45.98 3.67
7208 13619 3.826729 GGAAGTGCTGGTCACCTTTTAAT 59.173 43.478 0.00 0.00 46.81 1.40
7285 14070 5.106555 GGATTCGGTGCACCATATTCTTATG 60.107 44.000 34.16 14.59 35.87 1.90
7292 14077 5.834169 TGCACCATATTCTTATGCAATGTG 58.166 37.500 0.00 0.00 43.00 3.21
7302 14087 3.092841 GCAATGTGTGCGTGTGCG 61.093 61.111 0.00 0.00 45.10 5.34
7312 14097 3.334751 CGTGTGCGCGTGAGGAAA 61.335 61.111 8.43 0.00 0.00 3.13
7313 14098 2.551270 GTGTGCGCGTGAGGAAAG 59.449 61.111 8.43 0.00 0.00 2.62
7316 14101 1.092921 TGTGCGCGTGAGGAAAGTTT 61.093 50.000 8.43 0.00 0.00 2.66
7317 14102 0.657368 GTGCGCGTGAGGAAAGTTTG 60.657 55.000 8.43 0.00 0.00 2.93
7318 14103 1.082104 GCGCGTGAGGAAAGTTTGG 60.082 57.895 8.43 0.00 0.00 3.28
7319 14104 1.082104 CGCGTGAGGAAAGTTTGGC 60.082 57.895 0.00 0.00 0.00 4.52
7321 14106 0.317854 GCGTGAGGAAAGTTTGGCAC 60.318 55.000 0.00 0.00 0.00 5.01
7347 14706 2.608090 GCCTTTTCCGAGTTAAGGATCG 59.392 50.000 0.00 0.00 40.71 3.69
7353 14712 4.041740 TCCGAGTTAAGGATCGAATGTG 57.958 45.455 6.30 0.00 41.40 3.21
7525 14888 0.887933 TAGACTGCAGTGCACGATCA 59.112 50.000 27.27 9.65 33.79 2.92
7566 14929 1.187974 TTGCAGAATGGCAGGAATGG 58.812 50.000 0.00 0.00 45.88 3.16
7722 15085 7.041916 TGCAATGAACCAAATGAACTTGATTTC 60.042 33.333 0.00 0.00 0.00 2.17
7833 15196 3.677648 CCTGTGGCTGGCACAAGC 61.678 66.667 32.33 10.23 38.70 4.01
7849 15212 0.537188 AAGCGGGAGTGTCGATGATT 59.463 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
384 386 3.561213 CCGCTCATGTGCTCGCTG 61.561 66.667 16.99 1.89 0.00 5.18
867 869 1.575447 ATTGAGCCCCCAACTCCTCC 61.575 60.000 0.00 0.00 32.98 4.30
868 870 0.394899 CATTGAGCCCCCAACTCCTC 60.395 60.000 0.00 0.00 32.98 3.71
869 871 1.142688 ACATTGAGCCCCCAACTCCT 61.143 55.000 0.00 0.00 32.98 3.69
885 891 5.620654 CGCTCCACTGATCAAATTGAAACAT 60.621 40.000 0.00 0.00 0.00 2.71
1365 1371 0.753867 GGTTCTCGGAATCCTCCTCC 59.246 60.000 0.00 0.00 39.93 4.30
1578 1584 0.542702 AATCAACAGCCACCCCCTTG 60.543 55.000 0.00 0.00 0.00 3.61
1602 1608 1.734477 CACCAACTCCGCGAGTCTG 60.734 63.158 8.23 10.00 42.59 3.51
1617 1623 1.481056 CCTCCCCATACGGATCCACC 61.481 65.000 13.41 0.00 0.00 4.61
1644 1650 0.036010 CCAGTCCTGCAGTCCGATTT 60.036 55.000 13.81 0.00 0.00 2.17
1839 1845 5.730550 TCGAGCAGAACAAACCTAACATAT 58.269 37.500 0.00 0.00 0.00 1.78
1888 1894 2.159296 TGTCAACCATCGTCCACTATCG 60.159 50.000 0.00 0.00 0.00 2.92
1898 1904 3.618594 CACCTATCAAGTGTCAACCATCG 59.381 47.826 0.00 0.00 0.00 3.84
2153 2159 6.922540 ACTTATATAGCCAGAAACCCCATTT 58.077 36.000 0.00 0.00 0.00 2.32
2297 2303 4.655963 ACACAATCAGAGGTGCTTACAAT 58.344 39.130 5.18 0.00 38.57 2.71
2463 2475 3.761218 CCAAACATGTGGTTAGGCATACA 59.239 43.478 0.00 0.00 39.29 2.29
2555 4103 6.486993 ACGGAAATCCTAAAATCCTTATCAGC 59.513 38.462 0.00 0.00 0.00 4.26
2577 4125 8.126700 ACATTGTTCTGTTACTTTAGAAAACGG 58.873 33.333 0.00 0.00 34.95 4.44
2610 4158 6.688637 ACCCTAGAACTAAAACAAACACAC 57.311 37.500 0.00 0.00 0.00 3.82
2612 4160 7.324354 TGAACCCTAGAACTAAAACAAACAC 57.676 36.000 0.00 0.00 0.00 3.32
2613 4161 6.544564 CCTGAACCCTAGAACTAAAACAAACA 59.455 38.462 0.00 0.00 0.00 2.83
2614 4162 6.514541 GCCTGAACCCTAGAACTAAAACAAAC 60.515 42.308 0.00 0.00 0.00 2.93
2685 4233 0.824759 AGTACGCATGAGGGGTCTTC 59.175 55.000 0.00 0.00 42.41 2.87
2698 4246 7.631915 AATGTCAAACCAAAATAAAGTACGC 57.368 32.000 0.00 0.00 0.00 4.42
2712 4260 4.023193 CCCAGAACACAGTAATGTCAAACC 60.023 45.833 0.00 0.00 30.55 3.27
2749 4297 2.634453 CTGGAAAAGGATTTGTGGGCTT 59.366 45.455 0.00 0.00 39.02 4.35
2751 4299 1.970640 ACTGGAAAAGGATTTGTGGGC 59.029 47.619 0.00 0.00 39.02 5.36
2833 4381 6.899075 TCTATTTTCAGCTACTACCCCAGTTA 59.101 38.462 0.00 0.00 38.80 2.24
2841 4389 6.793349 TCGAGGTTCTATTTTCAGCTACTAC 58.207 40.000 0.00 0.00 0.00 2.73
2867 4415 9.733907 ACTAAACTATCCCCCTACAATTAACTA 57.266 33.333 0.00 0.00 0.00 2.24
2887 4435 5.298347 AGCACTCTTAACACAGGACTAAAC 58.702 41.667 0.00 0.00 0.00 2.01
2906 4454 3.055747 ACCTGGCTAGAGTCTTTTAGCAC 60.056 47.826 13.97 5.64 43.14 4.40
2965 4514 5.221661 CCTTATGTACAAGACACCTATCCCC 60.222 48.000 0.00 0.00 42.17 4.81
2967 4516 5.070580 AGCCTTATGTACAAGACACCTATCC 59.929 44.000 0.00 0.00 42.17 2.59
2969 4518 7.670605 TTAGCCTTATGTACAAGACACCTAT 57.329 36.000 0.00 0.00 42.17 2.57
2970 4519 7.343574 TGATTAGCCTTATGTACAAGACACCTA 59.656 37.037 0.00 0.00 42.17 3.08
2971 4520 6.156256 TGATTAGCCTTATGTACAAGACACCT 59.844 38.462 0.00 0.00 42.17 4.00
3054 4921 3.634397 CCATCAAGGTTCTGAAGGCTA 57.366 47.619 0.00 0.00 28.16 3.93
3059 4926 2.942804 TGTTGCCATCAAGGTTCTGAA 58.057 42.857 0.00 0.00 40.61 3.02
3063 4930 1.404583 GCCATGTTGCCATCAAGGTTC 60.405 52.381 0.00 0.00 40.61 3.62
3222 5089 5.221682 TGTCTAATAAAAACACCCACGGAGA 60.222 40.000 0.00 0.00 0.00 3.71
3291 5158 9.613428 TGAAAAGAGAGAAAAATCACTGAGTTA 57.387 29.630 0.00 0.00 0.00 2.24
3317 5184 8.462016 GCACAATGAGAGTGGTAATAAATCTTT 58.538 33.333 0.00 0.00 37.46 2.52
3511 5515 7.565680 GGAGGGAGTACTTGATTAGATGAAAA 58.434 38.462 0.00 0.00 0.00 2.29
3538 5542 6.361433 TGAAGTTGAGACACTTATTTTGGGA 58.639 36.000 0.00 0.00 37.11 4.37
3591 5595 8.341173 GGAAATCAACATGCAAAACACAATTTA 58.659 29.630 0.00 0.00 0.00 1.40
3604 5608 6.518493 ACATGATAATGGGAAATCAACATGC 58.482 36.000 0.00 0.00 35.82 4.06
3626 5630 3.571828 TGCACAATTAGCTAAGGCAAACA 59.428 39.130 12.54 3.39 41.70 2.83
3649 5653 2.158755 CCTGGGGCTGGAAAGTATAGTG 60.159 54.545 0.00 0.00 0.00 2.74
3652 5656 1.518367 CCCTGGGGCTGGAAAGTATA 58.482 55.000 4.27 0.00 0.00 1.47
3691 5695 9.877178 GACATGAAATAGGAAGAAACTTCTCTA 57.123 33.333 0.00 10.22 36.28 2.43
3760 5764 4.697514 AGTCACGAACTCCCATATCATTG 58.302 43.478 0.00 0.00 30.02 2.82
3761 5765 5.104941 TCAAGTCACGAACTCCCATATCATT 60.105 40.000 0.00 0.00 37.17 2.57
3762 5766 4.405680 TCAAGTCACGAACTCCCATATCAT 59.594 41.667 0.00 0.00 37.17 2.45
3763 5767 3.767131 TCAAGTCACGAACTCCCATATCA 59.233 43.478 0.00 0.00 37.17 2.15
3764 5768 4.142138 ACTCAAGTCACGAACTCCCATATC 60.142 45.833 0.00 0.00 37.17 1.63
3765 5769 3.769844 ACTCAAGTCACGAACTCCCATAT 59.230 43.478 0.00 0.00 37.17 1.78
3766 5770 3.056821 CACTCAAGTCACGAACTCCCATA 60.057 47.826 0.00 0.00 37.17 2.74
3767 5771 1.971357 ACTCAAGTCACGAACTCCCAT 59.029 47.619 0.00 0.00 37.17 4.00
3768 5772 1.068588 CACTCAAGTCACGAACTCCCA 59.931 52.381 0.00 0.00 37.17 4.37
3769 5773 1.784525 CACTCAAGTCACGAACTCCC 58.215 55.000 0.00 0.00 37.17 4.30
3770 5774 1.140816 GCACTCAAGTCACGAACTCC 58.859 55.000 0.00 0.00 37.17 3.85
3771 5775 1.789464 CAGCACTCAAGTCACGAACTC 59.211 52.381 0.00 0.00 37.17 3.01
3772 5776 1.137086 ACAGCACTCAAGTCACGAACT 59.863 47.619 0.00 0.00 41.10 3.01
3773 5777 1.258982 CACAGCACTCAAGTCACGAAC 59.741 52.381 0.00 0.00 0.00 3.95
3774 5778 1.136110 TCACAGCACTCAAGTCACGAA 59.864 47.619 0.00 0.00 0.00 3.85
3775 5779 0.744281 TCACAGCACTCAAGTCACGA 59.256 50.000 0.00 0.00 0.00 4.35
3776 5780 1.570813 TTCACAGCACTCAAGTCACG 58.429 50.000 0.00 0.00 0.00 4.35
3777 5781 2.874701 ACATTCACAGCACTCAAGTCAC 59.125 45.455 0.00 0.00 0.00 3.67
3778 5782 2.874086 CACATTCACAGCACTCAAGTCA 59.126 45.455 0.00 0.00 0.00 3.41
3779 5783 2.225019 CCACATTCACAGCACTCAAGTC 59.775 50.000 0.00 0.00 0.00 3.01
3780 5784 2.224606 CCACATTCACAGCACTCAAGT 58.775 47.619 0.00 0.00 0.00 3.16
3781 5785 1.538512 CCCACATTCACAGCACTCAAG 59.461 52.381 0.00 0.00 0.00 3.02
3782 5786 1.142667 TCCCACATTCACAGCACTCAA 59.857 47.619 0.00 0.00 0.00 3.02
3783 5787 0.764271 TCCCACATTCACAGCACTCA 59.236 50.000 0.00 0.00 0.00 3.41
3784 5788 1.271054 ACTCCCACATTCACAGCACTC 60.271 52.381 0.00 0.00 0.00 3.51
3785 5789 0.767375 ACTCCCACATTCACAGCACT 59.233 50.000 0.00 0.00 0.00 4.40
3786 5790 1.537202 GAACTCCCACATTCACAGCAC 59.463 52.381 0.00 0.00 0.00 4.40
3787 5791 1.877680 CGAACTCCCACATTCACAGCA 60.878 52.381 0.00 0.00 0.00 4.41
3788 5792 0.798776 CGAACTCCCACATTCACAGC 59.201 55.000 0.00 0.00 0.00 4.40
3789 5793 1.800586 CACGAACTCCCACATTCACAG 59.199 52.381 0.00 0.00 0.00 3.66
3790 5794 1.414550 TCACGAACTCCCACATTCACA 59.585 47.619 0.00 0.00 0.00 3.58
3791 5795 1.798813 GTCACGAACTCCCACATTCAC 59.201 52.381 0.00 0.00 0.00 3.18
3792 5796 1.691976 AGTCACGAACTCCCACATTCA 59.308 47.619 0.00 0.00 30.02 2.57
3793 5797 2.457366 AGTCACGAACTCCCACATTC 57.543 50.000 0.00 0.00 30.02 2.67
3794 5798 2.104111 TCAAGTCACGAACTCCCACATT 59.896 45.455 0.00 0.00 37.17 2.71
3795 5799 1.691976 TCAAGTCACGAACTCCCACAT 59.308 47.619 0.00 0.00 37.17 3.21
3796 5800 1.068588 CTCAAGTCACGAACTCCCACA 59.931 52.381 0.00 0.00 37.17 4.17
3797 5801 1.068741 ACTCAAGTCACGAACTCCCAC 59.931 52.381 0.00 0.00 37.17 4.61
3798 5802 1.068588 CACTCAAGTCACGAACTCCCA 59.931 52.381 0.00 0.00 37.17 4.37
3799 5803 1.784525 CACTCAAGTCACGAACTCCC 58.215 55.000 0.00 0.00 37.17 4.30
3800 5804 1.140816 GCACTCAAGTCACGAACTCC 58.859 55.000 0.00 0.00 37.17 3.85
3801 5805 1.789464 CAGCACTCAAGTCACGAACTC 59.211 52.381 0.00 0.00 37.17 3.01
3802 5806 1.137086 ACAGCACTCAAGTCACGAACT 59.863 47.619 0.00 0.00 41.10 3.01
3803 5807 1.258982 CACAGCACTCAAGTCACGAAC 59.741 52.381 0.00 0.00 0.00 3.95
3804 5808 1.136110 TCACAGCACTCAAGTCACGAA 59.864 47.619 0.00 0.00 0.00 3.85
3805 5809 0.744281 TCACAGCACTCAAGTCACGA 59.256 50.000 0.00 0.00 0.00 4.35
3806 5810 1.570813 TTCACAGCACTCAAGTCACG 58.429 50.000 0.00 0.00 0.00 4.35
3807 5811 2.874701 ACATTCACAGCACTCAAGTCAC 59.125 45.455 0.00 0.00 0.00 3.67
3808 5812 2.874086 CACATTCACAGCACTCAAGTCA 59.126 45.455 0.00 0.00 0.00 3.41
3809 5813 2.225019 CCACATTCACAGCACTCAAGTC 59.775 50.000 0.00 0.00 0.00 3.01
3810 5814 2.224606 CCACATTCACAGCACTCAAGT 58.775 47.619 0.00 0.00 0.00 3.16
3811 5815 1.538512 CCCACATTCACAGCACTCAAG 59.461 52.381 0.00 0.00 0.00 3.02
3812 5816 1.142667 TCCCACATTCACAGCACTCAA 59.857 47.619 0.00 0.00 0.00 3.02
3813 5817 0.764271 TCCCACATTCACAGCACTCA 59.236 50.000 0.00 0.00 0.00 3.41
3814 5818 1.271054 ACTCCCACATTCACAGCACTC 60.271 52.381 0.00 0.00 0.00 3.51
3815 5819 0.767375 ACTCCCACATTCACAGCACT 59.233 50.000 0.00 0.00 0.00 4.40
3816 5820 1.537202 GAACTCCCACATTCACAGCAC 59.463 52.381 0.00 0.00 0.00 4.40
3817 5821 1.142667 TGAACTCCCACATTCACAGCA 59.857 47.619 0.00 0.00 29.89 4.41
3818 5822 1.808945 CTGAACTCCCACATTCACAGC 59.191 52.381 0.00 0.00 31.62 4.40
3819 5823 3.407424 TCTGAACTCCCACATTCACAG 57.593 47.619 0.00 0.00 31.62 3.66
3820 5824 3.118075 TGTTCTGAACTCCCACATTCACA 60.118 43.478 20.18 0.00 31.62 3.58
3821 5825 3.476552 TGTTCTGAACTCCCACATTCAC 58.523 45.455 20.18 0.00 31.62 3.18
3822 5826 3.855255 TGTTCTGAACTCCCACATTCA 57.145 42.857 20.18 0.00 33.82 2.57
3823 5827 3.058914 CGTTGTTCTGAACTCCCACATTC 60.059 47.826 20.18 1.82 0.00 2.67
3824 5828 2.878406 CGTTGTTCTGAACTCCCACATT 59.122 45.455 20.18 0.00 0.00 2.71
3825 5829 2.104111 TCGTTGTTCTGAACTCCCACAT 59.896 45.455 20.18 0.00 0.00 3.21
3826 5830 1.483004 TCGTTGTTCTGAACTCCCACA 59.517 47.619 20.18 0.00 0.00 4.17
3827 5831 2.234300 TCGTTGTTCTGAACTCCCAC 57.766 50.000 20.18 11.00 0.00 4.61
3828 5832 2.104111 ACATCGTTGTTCTGAACTCCCA 59.896 45.455 20.18 4.11 29.55 4.37
3829 5833 2.480419 CACATCGTTGTTCTGAACTCCC 59.520 50.000 20.18 8.01 32.34 4.30
3830 5834 2.480419 CCACATCGTTGTTCTGAACTCC 59.520 50.000 20.18 10.21 32.34 3.85
3831 5835 2.480419 CCCACATCGTTGTTCTGAACTC 59.520 50.000 20.18 12.50 32.34 3.01
3832 5836 2.104111 TCCCACATCGTTGTTCTGAACT 59.896 45.455 20.18 0.00 32.34 3.01
3833 5837 2.480419 CTCCCACATCGTTGTTCTGAAC 59.520 50.000 13.49 13.49 32.34 3.18
3834 5838 2.104111 ACTCCCACATCGTTGTTCTGAA 59.896 45.455 0.00 0.00 32.34 3.02
3835 5839 1.691976 ACTCCCACATCGTTGTTCTGA 59.308 47.619 0.00 0.00 32.34 3.27
3836 5840 2.169832 ACTCCCACATCGTTGTTCTG 57.830 50.000 0.00 0.00 32.34 3.02
3837 5841 2.767505 GAACTCCCACATCGTTGTTCT 58.232 47.619 0.00 0.00 32.34 3.01
3838 5842 1.459592 CGAACTCCCACATCGTTGTTC 59.540 52.381 0.00 0.00 32.34 3.18
3839 5843 1.202604 ACGAACTCCCACATCGTTGTT 60.203 47.619 0.00 0.00 46.66 2.83
3840 5844 0.391597 ACGAACTCCCACATCGTTGT 59.608 50.000 0.00 0.00 46.66 3.32
3852 5856 1.789464 CAGCACTCAAGTCACGAACTC 59.211 52.381 0.00 0.00 37.17 3.01
3896 5900 1.009829 GACTGCCAAGATAAGGTGCG 58.990 55.000 0.00 0.00 0.00 5.34
3909 5913 2.352127 GGAAATGAAAGTGCAGACTGCC 60.352 50.000 24.33 15.26 44.23 4.85
3924 5928 8.870160 TTTCATGAAGTTAAACAGTGGAAATG 57.130 30.769 8.41 0.00 38.30 2.32
4176 6180 6.705825 GCCTTTTAGCTTTCCTTTGATGAAAA 59.294 34.615 0.00 0.00 31.77 2.29
4218 6222 4.223032 TCTTTACTGACTCCCAGACCAATC 59.777 45.833 0.00 0.00 45.78 2.67
4219 6223 4.168101 TCTTTACTGACTCCCAGACCAAT 58.832 43.478 0.00 0.00 45.78 3.16
4224 6228 4.061131 TCCATCTTTACTGACTCCCAGA 57.939 45.455 0.00 0.00 45.78 3.86
4234 6238 7.509546 TGAGTCTCAAGTTTTCCATCTTTACT 58.490 34.615 0.00 0.00 0.00 2.24
4248 6252 9.295308 GTCCTCTGACTTTCTTGAGTCTCAAGT 62.295 44.444 32.10 19.93 44.26 3.16
4302 6306 6.237901 ACTTTTAACATCAGCTACACCATGA 58.762 36.000 0.00 0.00 0.00 3.07
4386 6390 1.452651 TGCTGCAGCCAAGGATAGC 60.453 57.895 34.64 8.33 41.18 2.97
4430 6434 4.382147 GCTCTTCTACCTGTTCAGGTAAGG 60.382 50.000 25.48 17.71 43.14 2.69
4557 6564 8.483307 AATTATCAACATGTTCCTTTTGATGC 57.517 30.769 8.48 0.00 38.75 3.91
4649 6656 4.515567 ACTTGCAAGTACTAAGGTTGCTTC 59.484 41.667 30.25 0.00 45.56 3.86
4798 6805 1.538047 TTTTCACCTGGAGCATCTGC 58.462 50.000 0.00 0.00 42.49 4.26
4825 6832 3.683564 GCACAGTCCATTGGATCATCAGA 60.684 47.826 9.01 0.00 32.73 3.27
4827 6834 2.240414 AGCACAGTCCATTGGATCATCA 59.760 45.455 9.01 0.00 32.73 3.07
4946 6953 4.702131 AGTTGGCAGACAGTGGATTATTTC 59.298 41.667 0.00 0.00 0.00 2.17
4950 6957 3.411446 CAAGTTGGCAGACAGTGGATTA 58.589 45.455 0.00 0.00 0.00 1.75
5034 7041 3.070878 TGGTAGAATTCAGCATATCGCCA 59.929 43.478 8.44 0.00 44.04 5.69
5055 7062 7.281774 ACAACAGGTTTATCATATTCAGAGCTG 59.718 37.037 0.00 0.00 37.23 4.24
5090 7097 0.037326 GGCAGTCACTCCACGATCAA 60.037 55.000 0.00 0.00 0.00 2.57
5124 7131 6.040054 TGTTCATCCCATCATCAATGTTGATC 59.960 38.462 5.30 0.00 45.62 2.92
5172 7179 9.851686 ATTGTATCTAAGCATGAATTGAGGTTA 57.148 29.630 0.00 0.00 0.00 2.85
5288 7295 7.978982 ACAAACATTGTCATCATTAGAGCTAC 58.021 34.615 0.00 0.00 40.56 3.58
5416 7423 5.130145 CCACACTAATTTGAGGAGGAGAGAT 59.870 44.000 0.00 0.00 29.11 2.75
5454 7461 9.850628 TTCTTAATTTCAGAATTCATTGAGCAG 57.149 29.630 8.44 0.00 36.82 4.24
5727 7734 6.934645 CACTTACAAAAGAACTCCTCATACCA 59.065 38.462 0.00 0.00 36.50 3.25
5829 7836 1.070786 TGTTTCCAGGTCGCTGTCC 59.929 57.895 0.00 0.00 0.00 4.02
5913 7920 5.163530 GGTGTGCATGGACATAAAATCATCA 60.164 40.000 23.52 0.00 0.00 3.07
6019 8026 0.471617 AGCATGTGAGGATACCCAGC 59.528 55.000 0.00 0.00 33.88 4.85
6276 8457 5.712446 TGCAATAGTTACCCAAACATGCTAA 59.288 36.000 0.00 0.00 41.33 3.09
6286 8467 5.366482 TCAGCTATTGCAATAGTTACCCA 57.634 39.130 35.32 18.40 40.37 4.51
6310 8492 7.545615 CGATGGTTATAGCAGCAATTACATCTA 59.454 37.037 0.00 0.00 30.42 1.98
6378 10237 4.634004 ACACATAATGGATAACGGTGTGTG 59.366 41.667 7.36 0.00 44.70 3.82
6440 10300 7.647715 AGTTGCAAATCACACTGTACAAAATAC 59.352 33.333 0.00 0.00 0.00 1.89
6455 10315 4.378774 CACCAAATCCAAGTTGCAAATCA 58.621 39.130 0.00 0.00 0.00 2.57
6548 12684 1.074775 GTGTCTGCCCATGTTCCCA 59.925 57.895 0.00 0.00 0.00 4.37
6803 13172 2.040813 ACCAGATGTCTTGTCCTTGCAT 59.959 45.455 0.00 0.00 0.00 3.96
6913 13290 6.264067 CAGTCTACACTATGATCCACATGAGA 59.736 42.308 0.00 0.00 39.77 3.27
6914 13291 6.445475 CAGTCTACACTATGATCCACATGAG 58.555 44.000 0.00 0.00 39.77 2.90
6916 13293 5.302823 TCCAGTCTACACTATGATCCACATG 59.697 44.000 0.00 0.00 39.77 3.21
6917 13294 5.458595 TCCAGTCTACACTATGATCCACAT 58.541 41.667 0.00 0.00 42.39 3.21
6918 13295 4.867086 TCCAGTCTACACTATGATCCACA 58.133 43.478 0.00 0.00 0.00 4.17
6920 13297 6.266330 CAGATTCCAGTCTACACTATGATCCA 59.734 42.308 0.00 0.00 0.00 3.41
6921 13298 6.491745 TCAGATTCCAGTCTACACTATGATCC 59.508 42.308 0.00 0.00 0.00 3.36
6922 13299 7.517614 TCAGATTCCAGTCTACACTATGATC 57.482 40.000 0.00 0.00 0.00 2.92
6925 13302 5.301551 AGCTCAGATTCCAGTCTACACTATG 59.698 44.000 0.00 0.00 0.00 2.23
6926 13303 5.454062 AGCTCAGATTCCAGTCTACACTAT 58.546 41.667 0.00 0.00 0.00 2.12
6930 13307 3.634448 GCTAGCTCAGATTCCAGTCTACA 59.366 47.826 7.70 0.00 0.00 2.74
6965 13343 1.066716 ACATACGTAACCACCGCACAT 60.067 47.619 0.00 0.00 0.00 3.21
6982 13360 7.262048 ACCGAAAACAGTGTCATTTAAAACAT 58.738 30.769 0.00 0.00 0.00 2.71
6983 13361 6.622549 ACCGAAAACAGTGTCATTTAAAACA 58.377 32.000 0.00 0.00 0.00 2.83
6984 13362 6.075780 CGACCGAAAACAGTGTCATTTAAAAC 60.076 38.462 0.00 0.00 0.00 2.43
6985 13363 5.966503 CGACCGAAAACAGTGTCATTTAAAA 59.033 36.000 0.00 0.00 0.00 1.52
7054 13445 3.133542 CCTCAATCTGGACATCAGCACTA 59.866 47.826 0.00 0.00 43.06 2.74
7056 13447 2.286872 CCTCAATCTGGACATCAGCAC 58.713 52.381 0.00 0.00 43.06 4.40
7076 13467 2.158928 AGAGAATCATGCACCTCTCAGC 60.159 50.000 14.92 0.00 37.39 4.26
7200 13611 1.994916 CAGCCCGTGCAATTAAAAGG 58.005 50.000 0.00 0.00 41.13 3.11
7295 14080 3.281751 CTTTCCTCACGCGCACACG 62.282 63.158 5.73 0.00 44.07 4.49
7296 14081 1.772063 AACTTTCCTCACGCGCACAC 61.772 55.000 5.73 0.00 0.00 3.82
7297 14082 1.092921 AAACTTTCCTCACGCGCACA 61.093 50.000 5.73 0.00 0.00 4.57
7298 14083 0.657368 CAAACTTTCCTCACGCGCAC 60.657 55.000 5.73 0.00 0.00 5.34
7299 14084 1.646540 CAAACTTTCCTCACGCGCA 59.353 52.632 5.73 0.00 0.00 6.09
7300 14085 1.082104 CCAAACTTTCCTCACGCGC 60.082 57.895 5.73 0.00 0.00 6.86
7301 14086 1.082104 GCCAAACTTTCCTCACGCG 60.082 57.895 3.53 3.53 0.00 6.01
7302 14087 0.317854 GTGCCAAACTTTCCTCACGC 60.318 55.000 0.00 0.00 0.00 5.34
7303 14088 1.002468 CTGTGCCAAACTTTCCTCACG 60.002 52.381 0.00 0.00 0.00 4.35
7304 14089 1.338020 CCTGTGCCAAACTTTCCTCAC 59.662 52.381 0.00 0.00 0.00 3.51
7305 14090 1.691196 CCTGTGCCAAACTTTCCTCA 58.309 50.000 0.00 0.00 0.00 3.86
7306 14091 0.315251 GCCTGTGCCAAACTTTCCTC 59.685 55.000 0.00 0.00 0.00 3.71
7307 14092 1.455383 CGCCTGTGCCAAACTTTCCT 61.455 55.000 0.00 0.00 0.00 3.36
7308 14093 1.007387 CGCCTGTGCCAAACTTTCC 60.007 57.895 0.00 0.00 0.00 3.13
7310 14095 2.417097 GCGCCTGTGCCAAACTTT 59.583 55.556 0.00 0.00 0.00 2.66
7318 14103 4.404654 CGGAAAAGGCGCCTGTGC 62.405 66.667 33.60 25.45 0.00 4.57
7319 14104 2.668212 TCGGAAAAGGCGCCTGTG 60.668 61.111 33.60 17.97 0.00 3.66
7321 14106 0.672401 TAACTCGGAAAAGGCGCCTG 60.672 55.000 33.60 17.89 0.00 4.85
7334 14119 2.540101 GGCACATTCGATCCTTAACTCG 59.460 50.000 0.00 0.00 36.25 4.18
7347 14706 1.811860 GTCTGGGCATGGCACATTC 59.188 57.895 22.06 3.43 42.76 2.67
7353 14712 1.078426 AGTTACGTCTGGGCATGGC 60.078 57.895 11.56 11.56 0.00 4.40
7525 14888 8.644216 TGCAAATATCAATTCCAGCATTCTATT 58.356 29.630 0.00 0.00 0.00 1.73
7566 14929 2.684843 CGCCAGCTCCAGCAAGTTC 61.685 63.158 0.48 0.00 45.16 3.01
7722 15085 1.134098 AGCATGGAACCCTTGGTATCG 60.134 52.381 0.00 0.00 37.57 2.92
7833 15196 4.119862 ACATAAAATCATCGACACTCCCG 58.880 43.478 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.