Multiple sequence alignment - TraesCS6A01G235200

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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 TraesCS6A01G235200 chr6A 100.000 6294 0 0 998 7291 445044647 445050940 0.000000e+00 11623.0
1 TraesCS6A01G235200 chr6A 100.000 748 0 0 1 748 445043650 445044397 0.000000e+00 1382.0
2 TraesCS6A01G235200 chr6A 100.000 142 0 0 7653 7794 445051302 445051443 6.000000e-66 263.0
3 TraesCS6A01G235200 chr6D 96.188 4119 122 13 2893 6992 307879463 307883565 0.000000e+00 6704.0
4 TraesCS6A01G235200 chr6D 97.158 1900 40 2 998 2897 307877539 307879424 0.000000e+00 3197.0
5 TraesCS6A01G235200 chr6D 89.791 764 35 18 1 748 307876753 307877489 0.000000e+00 939.0
6 TraesCS6A01G235200 chr6B 95.710 2634 73 13 4380 6992 475271186 475273800 0.000000e+00 4202.0
7 TraesCS6A01G235200 chr6B 96.737 1900 52 3 998 2897 475267927 475269816 0.000000e+00 3157.0
8 TraesCS6A01G235200 chr6B 92.184 806 38 5 2893 3682 475269855 475270651 0.000000e+00 1116.0
9 TraesCS6A01G235200 chr6B 91.576 641 23 9 101 720 475267222 475267852 0.000000e+00 856.0
10 TraesCS6A01G235200 chr6B 90.784 510 23 5 3684 4189 475270702 475271191 0.000000e+00 660.0
11 TraesCS6A01G235200 chr6B 100.000 29 0 0 2539 2567 32833412 32833384 4.000000e-03 54.7
12 TraesCS6A01G235200 chr2B 78.533 368 64 14 4570 4931 554455935 554455577 2.190000e-55 228.0
13 TraesCS6A01G235200 chr2A 78.474 367 66 12 4570 4931 615740272 615739914 2.190000e-55 228.0
14 TraesCS6A01G235200 chr2D 78.261 368 65 14 4570 4931 473716827 473716469 1.020000e-53 222.0
15 TraesCS6A01G235200 chr7D 92.958 142 8 1 7653 7794 565431719 565431580 1.030000e-48 206.0
16 TraesCS6A01G235200 chr7D 92.683 82 6 0 7008 7089 565434112 565434031 1.370000e-22 119.0
17 TraesCS6A01G235200 chr1A 93.478 138 6 3 7659 7793 30124102 30123965 1.330000e-47 202.0
18 TraesCS6A01G235200 chr1A 86.207 58 7 1 2515 2571 373311931 373311988 2.350000e-05 62.1
19 TraesCS6A01G235200 chr4A 90.667 150 14 0 7015 7164 583199661 583199810 4.770000e-47 200.0
20 TraesCS6A01G235200 chr5A 83.099 142 5 12 7656 7794 664975522 664975397 2.300000e-20 111.0
21 TraesCS6A01G235200 chr1D 82.443 131 5 9 7664 7794 375211510 375211622 1.790000e-16 99.0
22 TraesCS6A01G235200 chr7B 85.556 90 10 2 2322 2408 468947278 468947367 2.990000e-14 91.6
23 TraesCS6A01G235200 chr3B 85.714 91 8 4 2322 2408 198130752 198130663 2.990000e-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 TraesCS6A01G235200 chr6A 445043650 445051443 7793 False 4422.666667 11623 100.0000 1 7794 3 chr6A.!!$F1 7793
1 TraesCS6A01G235200 chr6D 307876753 307883565 6812 False 3613.333333 6704 94.3790 1 6992 3 chr6D.!!$F1 6991
2 TraesCS6A01G235200 chr6B 475267222 475273800 6578 False 1998.200000 4202 93.3982 101 6992 5 chr6B.!!$F1 6891

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
261 263 0.165079 AGCGGCGTCATAAAAACACG 59.835 50.0 9.37 0.00 36.60 4.49 F
1504 1540 0.694771 ACCCAAGCTGCTTGATCAGA 59.305 50.0 36.69 0.00 43.42 3.27 F
2660 2696 0.106708 GGCATCCTGATCTGGCGTAA 59.893 55.0 13.60 0.00 0.00 3.18 F
3936 4084 0.399833 TGCCAACTCAGCATGGTGTA 59.600 50.0 23.35 10.24 39.00 2.90 F
4095 4243 0.036388 TTCAGTTCGCTAGCCCAAGG 60.036 55.0 9.66 0.00 0.00 3.61 F
4096 4244 0.902984 TCAGTTCGCTAGCCCAAGGA 60.903 55.0 9.66 0.00 0.00 3.36 F
5636 5797 0.326264 ATGAGCCTGACTTCCACACC 59.674 55.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1966 1.518325 TGTATGACTTGCCGTTGTGG 58.482 50.000 0.00 0.0 42.50 4.17 R
2816 2852 1.073444 TGGACTCTCGTACACCTCTGT 59.927 52.381 0.00 0.0 0.00 3.41 R
4096 4244 0.249398 GTTCTGTACCATGGACGGCT 59.751 55.000 21.47 0.0 0.00 5.52 R
5604 5765 1.134075 GCTCATCAACAGCACGCAG 59.866 57.895 0.00 0.0 36.82 5.18 R
5610 5771 1.736681 GAAGTCAGGCTCATCAACAGC 59.263 52.381 0.00 0.0 36.02 4.40 R
5959 6120 2.639839 TCTTGCTTCCTGGAGTTAGCTT 59.360 45.455 17.27 0.0 34.77 3.74 R
7038 7214 0.038166 TTCTGTCCTCATTGCCACCC 59.962 55.000 0.00 0.0 0.00 4.61 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
38 39 4.918129 GCGCTGGCGGCATGATTG 62.918 66.667 19.92 0.50 41.91 2.67
56 57 3.666883 TTGCTACAAGTGTTGTGTTCG 57.333 42.857 2.50 0.00 45.03 3.95
61 62 2.912771 ACAAGTGTTGTGTTCGGATCA 58.087 42.857 0.00 0.00 43.48 2.92
67 68 3.311322 GTGTTGTGTTCGGATCAAAGACA 59.689 43.478 6.10 6.10 0.00 3.41
69 70 4.035091 TGTTGTGTTCGGATCAAAGACAAG 59.965 41.667 17.57 0.00 39.60 3.16
70 71 4.066646 TGTGTTCGGATCAAAGACAAGA 57.933 40.909 7.36 0.00 28.17 3.02
74 75 5.236478 GTGTTCGGATCAAAGACAAGAAGAA 59.764 40.000 0.00 0.00 0.00 2.52
77 78 7.659799 TGTTCGGATCAAAGACAAGAAGAAATA 59.340 33.333 0.00 0.00 0.00 1.40
86 87 9.748708 CAAAGACAAGAAGAAATAATCCAACAA 57.251 29.630 0.00 0.00 0.00 2.83
96 97 9.965824 AAGAAATAATCCAACAATATAAAGGCG 57.034 29.630 0.00 0.00 0.00 5.52
97 98 9.131791 AGAAATAATCCAACAATATAAAGGCGT 57.868 29.630 0.00 0.00 0.00 5.68
98 99 9.744468 GAAATAATCCAACAATATAAAGGCGTT 57.256 29.630 0.00 0.00 0.00 4.84
104 105 9.744468 ATCCAACAATATAAAGGCGTTTTAATC 57.256 29.630 10.01 0.00 35.03 1.75
105 106 8.192110 TCCAACAATATAAAGGCGTTTTAATCC 58.808 33.333 10.01 0.00 35.03 3.01
106 107 7.976734 CCAACAATATAAAGGCGTTTTAATCCA 59.023 33.333 10.01 0.00 35.03 3.41
107 108 9.360093 CAACAATATAAAGGCGTTTTAATCCAA 57.640 29.630 10.01 0.00 35.03 3.53
108 109 8.920509 ACAATATAAAGGCGTTTTAATCCAAC 57.079 30.769 10.01 0.00 35.03 3.77
109 110 8.524487 ACAATATAAAGGCGTTTTAATCCAACA 58.476 29.630 10.01 0.00 35.03 3.33
110 111 9.528018 CAATATAAAGGCGTTTTAATCCAACAT 57.472 29.630 10.01 0.00 35.03 2.71
161 162 2.196925 CGACCGGCTCCTAGCATCT 61.197 63.158 0.00 0.00 44.75 2.90
166 167 1.524002 GGCTCCTAGCATCTGCACA 59.476 57.895 4.79 0.00 44.75 4.57
195 196 5.128663 AGAAAGGGCAAAACAATTGTACTGT 59.871 36.000 12.39 0.00 0.00 3.55
196 197 6.322712 AGAAAGGGCAAAACAATTGTACTGTA 59.677 34.615 12.39 0.00 0.00 2.74
261 263 0.165079 AGCGGCGTCATAAAAACACG 59.835 50.000 9.37 0.00 36.60 4.49
305 307 2.735478 CGCGAGCGGTTGTTACCA 60.735 61.111 9.90 0.00 45.31 3.25
336 338 3.749609 CCGGACGGAACAAAATTTACTCT 59.250 43.478 4.40 0.00 37.50 3.24
479 507 3.475774 GGCAGTAACGACACCGCG 61.476 66.667 0.00 0.00 39.95 6.46
520 548 3.535962 GCAGGCGAGGGAGAGGAG 61.536 72.222 0.00 0.00 0.00 3.69
521 549 2.043450 CAGGCGAGGGAGAGGAGT 60.043 66.667 0.00 0.00 0.00 3.85
522 550 2.043450 AGGCGAGGGAGAGGAGTG 60.043 66.667 0.00 0.00 0.00 3.51
523 551 3.151022 GGCGAGGGAGAGGAGTGG 61.151 72.222 0.00 0.00 0.00 4.00
524 552 2.043852 GCGAGGGAGAGGAGTGGA 60.044 66.667 0.00 0.00 0.00 4.02
543 571 1.925185 GAGAGGACATTTTACCGCGAC 59.075 52.381 8.23 0.00 0.00 5.19
608 636 2.362503 GCGGGGGAAAGGAAAGGG 60.363 66.667 0.00 0.00 0.00 3.95
609 637 2.914310 GCGGGGGAAAGGAAAGGGA 61.914 63.158 0.00 0.00 0.00 4.20
610 638 1.303282 CGGGGGAAAGGAAAGGGAG 59.697 63.158 0.00 0.00 0.00 4.30
612 640 0.849540 GGGGGAAAGGAAAGGGAGGA 60.850 60.000 0.00 0.00 0.00 3.71
613 641 1.309876 GGGGAAAGGAAAGGGAGGAT 58.690 55.000 0.00 0.00 0.00 3.24
614 642 1.215673 GGGGAAAGGAAAGGGAGGATC 59.784 57.143 0.00 0.00 0.00 3.36
719 755 3.878667 CTTCGCCATCCCTCCCCC 61.879 72.222 0.00 0.00 0.00 5.40
720 756 4.431524 TTCGCCATCCCTCCCCCT 62.432 66.667 0.00 0.00 0.00 4.79
721 757 4.880426 TCGCCATCCCTCCCCCTC 62.880 72.222 0.00 0.00 0.00 4.30
725 761 3.795924 CATCCCTCCCCCTCCCCT 61.796 72.222 0.00 0.00 0.00 4.79
1504 1540 0.694771 ACCCAAGCTGCTTGATCAGA 59.305 50.000 36.69 0.00 43.42 3.27
1693 1729 2.424842 ATTCCCAAAGTGGCGCCTCA 62.425 55.000 29.70 4.80 35.79 3.86
1930 1966 3.712881 GACCGTGTCAAGGTGCGC 61.713 66.667 15.71 0.00 43.01 6.09
2072 2108 2.300152 GGAGAGGATTGCGTGATCCATA 59.700 50.000 17.66 0.00 46.61 2.74
2194 2230 1.331756 GAGCCAATGTTAGCATCGGTG 59.668 52.381 0.00 0.00 31.86 4.94
2223 2259 0.750911 GGCAGCCATTGGGAGAAGAG 60.751 60.000 6.55 0.00 35.59 2.85
2415 2451 5.382618 AGTCTTGCTTCAATTCCAATGTC 57.617 39.130 0.00 0.00 0.00 3.06
2575 2611 5.452255 ACGGAGGGAGTACATTTCTGTATA 58.548 41.667 0.00 0.00 39.93 1.47
2656 2692 0.106819 AGTTGGCATCCTGATCTGGC 60.107 55.000 13.60 6.53 38.35 4.85
2660 2696 0.106708 GGCATCCTGATCTGGCGTAA 59.893 55.000 13.60 0.00 0.00 3.18
2662 2698 2.498167 GCATCCTGATCTGGCGTAAAT 58.502 47.619 13.60 0.00 0.00 1.40
2715 2751 3.748083 TCAGGATTAGGCAATCTGATGC 58.252 45.455 8.75 0.00 45.67 3.91
2816 2852 9.449719 AACTGTTCTTCTACTTTCTTTCTTGAA 57.550 29.630 0.00 0.00 0.00 2.69
3047 3126 8.299570 AGGTTTGATGAAAAGTATAAGCAGTTG 58.700 33.333 0.00 0.00 0.00 3.16
3082 3161 3.443976 GTCAGTTTTGCAATGTCGGTTT 58.556 40.909 0.00 0.00 0.00 3.27
3089 3168 2.697431 GCAATGTCGGTTTGCTGTTA 57.303 45.000 9.61 0.00 44.71 2.41
3128 3207 9.617975 GCTCATTTATCACATTAAGGCTTAATC 57.382 33.333 25.67 9.40 33.73 1.75
3346 3435 2.498167 ACCTTCATCAGTGACACAAGC 58.502 47.619 8.59 0.00 33.11 4.01
3462 3551 3.426695 GCCATTCTGAATTTCTGACCACG 60.427 47.826 0.00 0.00 0.00 4.94
3565 3660 3.074412 CTGGTTAATATCATCCGCCACC 58.926 50.000 0.00 0.00 0.00 4.61
3736 3880 2.396590 AAATATTCGCGACCACACCT 57.603 45.000 9.15 0.00 0.00 4.00
3833 3977 2.030823 GCAATACCGTTAAAGTACCGCC 59.969 50.000 0.00 0.00 0.00 6.13
3936 4084 0.399833 TGCCAACTCAGCATGGTGTA 59.600 50.000 23.35 10.24 39.00 2.90
4080 4228 7.933396 TGCTGTCCATATCATTGTAAATTCAG 58.067 34.615 0.00 0.00 0.00 3.02
4095 4243 0.036388 TTCAGTTCGCTAGCCCAAGG 60.036 55.000 9.66 0.00 0.00 3.61
4096 4244 0.902984 TCAGTTCGCTAGCCCAAGGA 60.903 55.000 9.66 0.00 0.00 3.36
4249 4397 7.550597 TCATAGAGATCCTTCAATATGCACT 57.449 36.000 0.00 0.00 0.00 4.40
4253 4401 4.467769 AGATCCTTCAATATGCACTTGGG 58.532 43.478 10.13 5.70 0.00 4.12
4348 4496 7.611079 CACATTCAACAATTTATTGGGGGAATT 59.389 33.333 7.33 0.00 41.96 2.17
4349 4497 8.830741 ACATTCAACAATTTATTGGGGGAATTA 58.169 29.630 7.33 0.00 41.96 1.40
4370 4518 2.939103 AGCTGCATGAAAGACGAATACC 59.061 45.455 1.02 0.00 0.00 2.73
4507 4655 2.972625 TGTAGGAATGTAGCAGCACAC 58.027 47.619 0.00 0.00 0.00 3.82
4704 4852 7.846644 ACTATGCTTTCAGAAGATTTCTCTG 57.153 36.000 0.00 0.00 38.11 3.35
4709 4857 5.676584 GCTTTCAGAAGATTTCTCTGCATGG 60.677 44.000 0.00 0.00 38.11 3.66
4746 4894 6.006449 ACTGATAGCACTGTCCTGAAATTTT 58.994 36.000 0.00 0.00 0.00 1.82
4988 5136 7.042523 GGTTTATTGGCTTATTGCATGTTCATC 60.043 37.037 0.00 0.00 45.15 2.92
5077 5225 9.159364 GTGTATGACACGTCTGGTATATATCTA 57.841 37.037 0.00 0.00 39.53 1.98
5101 5259 6.121776 TCCCTCTCTAGTTGCATTGTTTTA 57.878 37.500 0.00 0.00 0.00 1.52
5161 5319 8.059798 AGTGCTGTTATCTAAAGATTGCATTT 57.940 30.769 0.00 0.00 36.05 2.32
5397 5557 5.719085 ACTGACACTGAATGATAGTTCCTCT 59.281 40.000 0.00 0.00 0.00 3.69
5419 5579 7.286215 TCTATAGTTTATCCCAGGAAGTTCG 57.714 40.000 0.00 0.00 0.00 3.95
5594 5754 1.152963 AATAGCACCGCATCCACCC 60.153 57.895 0.00 0.00 0.00 4.61
5636 5797 0.326264 ATGAGCCTGACTTCCACACC 59.674 55.000 0.00 0.00 0.00 4.16
5656 5817 4.022329 CACCATCTTTCCCTTTACAACACC 60.022 45.833 0.00 0.00 0.00 4.16
5657 5818 4.141018 ACCATCTTTCCCTTTACAACACCT 60.141 41.667 0.00 0.00 0.00 4.00
5710 5871 5.385198 ACCTTTTTCTATTCTGCCAGTTGA 58.615 37.500 0.00 0.00 0.00 3.18
5863 6024 3.885297 TCCAAACCAAGCAGAAAGAAGAG 59.115 43.478 0.00 0.00 0.00 2.85
5959 6120 3.466836 CCAGCGCCAGAATGACTAATAA 58.533 45.455 2.29 0.00 39.69 1.40
5965 6126 5.236478 GCGCCAGAATGACTAATAAAGCTAA 59.764 40.000 0.00 0.00 39.69 3.09
6023 6184 5.063880 GGTAATGGTCATGTACTTGGATCC 58.936 45.833 4.20 4.20 0.00 3.36
6266 6427 5.851047 ACTTCGGTTTTCCAAGTATAACG 57.149 39.130 0.00 0.00 38.52 3.18
6529 6691 3.106827 TCAGCTGGTTGGAGTGATATCA 58.893 45.455 15.13 0.00 0.00 2.15
6541 6703 4.467082 GGAGTGATATCATGCTCCTCTCAT 59.533 45.833 25.06 0.00 42.99 2.90
6656 6818 7.663081 TCTCAGTGCTACAGAAATGAGAAAATT 59.337 33.333 13.65 0.00 39.98 1.82
6733 6896 7.386851 TCTGAATGTAGGTAGAAGTGGAAAAG 58.613 38.462 0.00 0.00 0.00 2.27
6997 7173 5.643379 CTACAGAGCAAATTTTAGGCCAA 57.357 39.130 5.01 0.00 0.00 4.52
6998 7174 6.212888 CTACAGAGCAAATTTTAGGCCAAT 57.787 37.500 5.01 0.00 0.00 3.16
6999 7175 5.488262 ACAGAGCAAATTTTAGGCCAATT 57.512 34.783 5.01 0.00 0.00 2.32
7000 7176 5.482006 ACAGAGCAAATTTTAGGCCAATTC 58.518 37.500 5.01 0.00 0.00 2.17
7001 7177 4.872124 CAGAGCAAATTTTAGGCCAATTCC 59.128 41.667 5.01 0.00 0.00 3.01
7002 7178 4.531732 AGAGCAAATTTTAGGCCAATTCCA 59.468 37.500 5.01 0.00 0.00 3.53
7003 7179 4.578871 AGCAAATTTTAGGCCAATTCCAC 58.421 39.130 5.01 0.00 0.00 4.02
7004 7180 3.689161 GCAAATTTTAGGCCAATTCCACC 59.311 43.478 5.01 0.00 0.00 4.61
7005 7181 3.885724 AATTTTAGGCCAATTCCACCG 57.114 42.857 5.01 0.00 0.00 4.94
7006 7182 0.892063 TTTTAGGCCAATTCCACCGC 59.108 50.000 5.01 0.00 0.00 5.68
7007 7183 0.251386 TTTAGGCCAATTCCACCGCA 60.251 50.000 5.01 0.00 0.00 5.69
7008 7184 0.963355 TTAGGCCAATTCCACCGCAC 60.963 55.000 5.01 0.00 0.00 5.34
7009 7185 4.114997 GGCCAATTCCACCGCACG 62.115 66.667 0.00 0.00 0.00 5.34
7010 7186 3.361977 GCCAATTCCACCGCACGT 61.362 61.111 0.00 0.00 0.00 4.49
7011 7187 2.867472 CCAATTCCACCGCACGTC 59.133 61.111 0.00 0.00 0.00 4.34
7012 7188 2.686816 CCAATTCCACCGCACGTCC 61.687 63.158 0.00 0.00 0.00 4.79
7013 7189 2.740826 AATTCCACCGCACGTCCG 60.741 61.111 0.00 0.00 0.00 4.79
7014 7190 3.524648 AATTCCACCGCACGTCCGT 62.525 57.895 0.00 0.00 0.00 4.69
7015 7191 2.999739 AATTCCACCGCACGTCCGTT 63.000 55.000 0.00 0.00 0.00 4.44
7016 7192 2.999739 ATTCCACCGCACGTCCGTTT 63.000 55.000 0.00 0.00 0.00 3.60
7017 7193 3.273834 CCACCGCACGTCCGTTTT 61.274 61.111 0.00 0.00 0.00 2.43
7018 7194 2.052590 CACCGCACGTCCGTTTTG 60.053 61.111 0.00 0.00 0.00 2.44
7019 7195 2.512057 ACCGCACGTCCGTTTTGT 60.512 55.556 0.00 0.00 0.00 2.83
7020 7196 2.247267 CCGCACGTCCGTTTTGTC 59.753 61.111 0.00 0.00 0.00 3.18
7021 7197 2.247267 CGCACGTCCGTTTTGTCC 59.753 61.111 0.00 0.00 0.00 4.02
7022 7198 2.247267 GCACGTCCGTTTTGTCCG 59.753 61.111 0.00 0.00 0.00 4.79
7023 7199 2.932905 CACGTCCGTTTTGTCCGG 59.067 61.111 0.00 0.00 46.83 5.14
7032 7208 2.657184 CGTTTTGTCCGGAATTTGTCC 58.343 47.619 5.23 0.00 43.90 4.02
7042 7218 3.842732 GGAATTTGTCCGTTTAGGGTG 57.157 47.619 0.00 0.00 41.52 4.61
7043 7219 2.490509 GGAATTTGTCCGTTTAGGGTGG 59.509 50.000 0.00 0.00 41.52 4.61
7044 7220 1.541379 ATTTGTCCGTTTAGGGTGGC 58.459 50.000 0.00 0.00 41.52 5.01
7045 7221 0.183014 TTTGTCCGTTTAGGGTGGCA 59.817 50.000 0.00 0.00 41.52 4.92
7046 7222 0.183014 TTGTCCGTTTAGGGTGGCAA 59.817 50.000 0.00 0.00 41.52 4.52
7047 7223 0.402504 TGTCCGTTTAGGGTGGCAAT 59.597 50.000 0.00 0.00 41.52 3.56
7048 7224 0.808755 GTCCGTTTAGGGTGGCAATG 59.191 55.000 0.00 0.00 41.52 2.82
7049 7225 0.693622 TCCGTTTAGGGTGGCAATGA 59.306 50.000 0.00 0.00 41.52 2.57
7050 7226 1.094785 CCGTTTAGGGTGGCAATGAG 58.905 55.000 0.00 0.00 35.97 2.90
7051 7227 1.094785 CGTTTAGGGTGGCAATGAGG 58.905 55.000 0.00 0.00 0.00 3.86
7052 7228 1.339631 CGTTTAGGGTGGCAATGAGGA 60.340 52.381 0.00 0.00 0.00 3.71
7053 7229 2.092323 GTTTAGGGTGGCAATGAGGAC 58.908 52.381 0.00 0.00 0.00 3.85
7054 7230 1.367346 TTAGGGTGGCAATGAGGACA 58.633 50.000 0.00 0.00 0.00 4.02
7055 7231 0.911769 TAGGGTGGCAATGAGGACAG 59.088 55.000 0.00 0.00 0.00 3.51
7056 7232 0.842030 AGGGTGGCAATGAGGACAGA 60.842 55.000 0.00 0.00 0.00 3.41
7057 7233 0.038166 GGGTGGCAATGAGGACAGAA 59.962 55.000 0.00 0.00 0.00 3.02
7058 7234 1.547675 GGGTGGCAATGAGGACAGAAA 60.548 52.381 0.00 0.00 0.00 2.52
7059 7235 1.541588 GGTGGCAATGAGGACAGAAAC 59.458 52.381 0.00 0.00 0.00 2.78
7060 7236 1.197721 GTGGCAATGAGGACAGAAACG 59.802 52.381 0.00 0.00 0.00 3.60
7061 7237 0.804989 GGCAATGAGGACAGAAACGG 59.195 55.000 0.00 0.00 0.00 4.44
7062 7238 1.610624 GGCAATGAGGACAGAAACGGA 60.611 52.381 0.00 0.00 0.00 4.69
7063 7239 1.464997 GCAATGAGGACAGAAACGGAC 59.535 52.381 0.00 0.00 0.00 4.79
7064 7240 2.766313 CAATGAGGACAGAAACGGACA 58.234 47.619 0.00 0.00 0.00 4.02
7065 7241 3.338249 CAATGAGGACAGAAACGGACAT 58.662 45.455 0.00 0.00 0.00 3.06
7066 7242 2.455674 TGAGGACAGAAACGGACATG 57.544 50.000 0.00 0.00 0.00 3.21
7067 7243 1.079503 GAGGACAGAAACGGACATGC 58.920 55.000 0.00 0.00 0.00 4.06
7068 7244 0.670546 AGGACAGAAACGGACATGCG 60.671 55.000 0.00 0.00 0.00 4.73
7069 7245 0.949105 GGACAGAAACGGACATGCGT 60.949 55.000 0.00 0.00 0.00 5.24
7070 7246 0.163788 GACAGAAACGGACATGCGTG 59.836 55.000 3.82 3.82 0.00 5.34
7071 7247 0.531974 ACAGAAACGGACATGCGTGT 60.532 50.000 12.38 12.38 42.49 4.49
7079 7255 3.049674 ACATGCGTGTCCGGCTTG 61.050 61.111 5.51 0.00 40.30 4.01
7080 7256 4.465512 CATGCGTGTCCGGCTTGC 62.466 66.667 0.00 0.00 33.68 4.01
7084 7260 4.072088 CGTGTCCGGCTTGCGTTC 62.072 66.667 0.00 0.00 0.00 3.95
7085 7261 4.072088 GTGTCCGGCTTGCGTTCG 62.072 66.667 0.00 0.00 0.00 3.95
7086 7262 4.287781 TGTCCGGCTTGCGTTCGA 62.288 61.111 0.00 0.00 0.00 3.71
7087 7263 3.479269 GTCCGGCTTGCGTTCGAG 61.479 66.667 0.00 0.00 0.00 4.04
7088 7264 4.735132 TCCGGCTTGCGTTCGAGG 62.735 66.667 0.00 0.00 0.00 4.63
7097 7273 4.812476 CGTTCGAGGCGCCCATCA 62.812 66.667 26.15 1.45 0.00 3.07
7098 7274 3.195698 GTTCGAGGCGCCCATCAC 61.196 66.667 26.15 12.00 0.00 3.06
7099 7275 4.812476 TTCGAGGCGCCCATCACG 62.812 66.667 26.15 20.38 0.00 4.35
7102 7278 4.451150 GAGGCGCCCATCACGACA 62.451 66.667 26.15 0.00 42.43 4.35
7103 7279 4.457496 AGGCGCCCATCACGACAG 62.457 66.667 26.15 0.00 42.43 3.51
7104 7280 4.451150 GGCGCCCATCACGACAGA 62.451 66.667 18.11 0.00 38.80 3.41
7105 7281 2.434185 GCGCCCATCACGACAGAA 60.434 61.111 0.00 0.00 0.00 3.02
7106 7282 2.740714 GCGCCCATCACGACAGAAC 61.741 63.158 0.00 0.00 0.00 3.01
7107 7283 2.444624 CGCCCATCACGACAGAACG 61.445 63.158 0.00 0.00 39.31 3.95
7108 7284 1.080093 GCCCATCACGACAGAACGA 60.080 57.895 0.00 0.00 37.03 3.85
7109 7285 1.352156 GCCCATCACGACAGAACGAC 61.352 60.000 0.00 0.00 37.03 4.34
7110 7286 0.736325 CCCATCACGACAGAACGACC 60.736 60.000 0.00 0.00 37.03 4.79
7111 7287 0.736325 CCATCACGACAGAACGACCC 60.736 60.000 0.00 0.00 37.03 4.46
7112 7288 0.038618 CATCACGACAGAACGACCCA 60.039 55.000 0.00 0.00 37.03 4.51
7113 7289 0.677288 ATCACGACAGAACGACCCAA 59.323 50.000 0.00 0.00 37.03 4.12
7114 7290 0.460722 TCACGACAGAACGACCCAAA 59.539 50.000 0.00 0.00 37.03 3.28
7115 7291 1.134759 TCACGACAGAACGACCCAAAA 60.135 47.619 0.00 0.00 37.03 2.44
7116 7292 1.004292 CACGACAGAACGACCCAAAAC 60.004 52.381 0.00 0.00 37.03 2.43
7117 7293 0.231279 CGACAGAACGACCCAAAACG 59.769 55.000 0.00 0.00 35.09 3.60
7118 7294 1.292992 GACAGAACGACCCAAAACGT 58.707 50.000 0.00 0.00 44.57 3.99
7119 7295 1.259770 GACAGAACGACCCAAAACGTC 59.740 52.381 0.00 0.00 41.87 4.34
7120 7296 0.584876 CAGAACGACCCAAAACGTCC 59.415 55.000 0.00 0.00 41.87 4.79
7121 7297 0.877213 AGAACGACCCAAAACGTCCG 60.877 55.000 0.00 0.00 41.87 4.79
7122 7298 2.434225 GAACGACCCAAAACGTCCGC 62.434 60.000 0.00 0.00 41.87 5.54
7123 7299 3.719144 CGACCCAAAACGTCCGCC 61.719 66.667 0.00 0.00 0.00 6.13
7124 7300 3.719144 GACCCAAAACGTCCGCCG 61.719 66.667 0.00 0.00 44.03 6.46
7128 7304 4.084888 CAAAACGTCCGCCGCCTC 62.085 66.667 0.00 0.00 41.42 4.70
7152 7328 4.849329 CCACCCGCTCGTCGCTAC 62.849 72.222 0.00 0.00 36.73 3.58
7153 7329 4.111016 CACCCGCTCGTCGCTACA 62.111 66.667 0.00 0.00 36.73 2.74
7154 7330 4.112341 ACCCGCTCGTCGCTACAC 62.112 66.667 0.00 0.00 36.73 2.90
7155 7331 4.849329 CCCGCTCGTCGCTACACC 62.849 72.222 0.00 0.00 36.73 4.16
7156 7332 3.812019 CCGCTCGTCGCTACACCT 61.812 66.667 0.00 0.00 36.73 4.00
7157 7333 2.277373 CGCTCGTCGCTACACCTC 60.277 66.667 0.00 0.00 36.13 3.85
7158 7334 2.277373 GCTCGTCGCTACACCTCG 60.277 66.667 0.00 0.00 35.14 4.63
7159 7335 2.277373 CTCGTCGCTACACCTCGC 60.277 66.667 0.00 0.00 0.00 5.03
7160 7336 3.736482 CTCGTCGCTACACCTCGCC 62.736 68.421 0.00 0.00 0.00 5.54
7246 7422 4.487412 GCAGCAGCATTGGTCGCC 62.487 66.667 0.00 0.00 41.58 5.54
7247 7423 4.170062 CAGCAGCATTGGTCGCCG 62.170 66.667 0.00 0.00 31.36 6.46
7698 7874 4.864334 CCGCTGCCTCCACCCATC 62.864 72.222 0.00 0.00 0.00 3.51
7701 7877 4.864334 CTGCCTCCACCCATCGCC 62.864 72.222 0.00 0.00 0.00 5.54
7722 7898 4.454319 CTCGCTCCTGCTGCTGCT 62.454 66.667 17.00 0.00 40.48 4.24
7723 7899 3.070576 TCGCTCCTGCTGCTGCTA 61.071 61.111 17.00 2.62 40.48 3.49
7724 7900 2.889503 CGCTCCTGCTGCTGCTAC 60.890 66.667 17.00 1.14 40.48 3.58
7725 7901 2.889503 GCTCCTGCTGCTGCTACG 60.890 66.667 17.00 5.29 40.48 3.51
7726 7902 2.889503 CTCCTGCTGCTGCTACGC 60.890 66.667 17.00 1.65 40.48 4.42
7727 7903 4.457496 TCCTGCTGCTGCTACGCC 62.457 66.667 17.00 0.00 40.48 5.68
7728 7904 4.765449 CCTGCTGCTGCTACGCCA 62.765 66.667 17.00 0.00 40.48 5.69
7729 7905 2.513204 CTGCTGCTGCTACGCCAT 60.513 61.111 17.00 0.00 40.48 4.40
7730 7906 2.820619 CTGCTGCTGCTACGCCATG 61.821 63.158 17.00 0.00 40.48 3.66
7731 7907 4.247612 GCTGCTGCTACGCCATGC 62.248 66.667 8.53 0.00 36.03 4.06
7732 7908 2.513204 CTGCTGCTACGCCATGCT 60.513 61.111 0.00 0.00 0.00 3.79
7733 7909 2.820619 CTGCTGCTACGCCATGCTG 61.821 63.158 0.00 0.00 0.00 4.41
7734 7910 4.247612 GCTGCTACGCCATGCTGC 62.248 66.667 0.00 0.00 44.21 5.25
7735 7911 2.513204 CTGCTACGCCATGCTGCT 60.513 61.111 0.00 0.00 0.00 4.24
7736 7912 2.820619 CTGCTACGCCATGCTGCTG 61.821 63.158 0.00 0.00 0.00 4.41
7737 7913 4.247612 GCTACGCCATGCTGCTGC 62.248 66.667 8.89 8.89 40.20 5.25
7761 7937 3.219928 GCCGGGATGCGAGAGAGA 61.220 66.667 2.18 0.00 0.00 3.10
7762 7938 3.038280 CCGGGATGCGAGAGAGAG 58.962 66.667 0.00 0.00 0.00 3.20
7763 7939 1.527148 CCGGGATGCGAGAGAGAGA 60.527 63.158 0.00 0.00 0.00 3.10
7764 7940 1.514678 CCGGGATGCGAGAGAGAGAG 61.515 65.000 0.00 0.00 0.00 3.20
7765 7941 1.514678 CGGGATGCGAGAGAGAGAGG 61.515 65.000 0.00 0.00 0.00 3.69
7766 7942 0.179004 GGGATGCGAGAGAGAGAGGA 60.179 60.000 0.00 0.00 0.00 3.71
7767 7943 1.238439 GGATGCGAGAGAGAGAGGAG 58.762 60.000 0.00 0.00 0.00 3.69
7768 7944 1.202758 GGATGCGAGAGAGAGAGGAGA 60.203 57.143 0.00 0.00 0.00 3.71
7769 7945 2.146342 GATGCGAGAGAGAGAGGAGAG 58.854 57.143 0.00 0.00 0.00 3.20
7770 7946 1.199615 TGCGAGAGAGAGAGGAGAGA 58.800 55.000 0.00 0.00 0.00 3.10
7771 7947 1.138859 TGCGAGAGAGAGAGGAGAGAG 59.861 57.143 0.00 0.00 0.00 3.20
7772 7948 1.412710 GCGAGAGAGAGAGGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
7773 7949 2.546795 GCGAGAGAGAGAGGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
7774 7950 2.959030 CGAGAGAGAGAGGAGAGAGAGA 59.041 54.545 0.00 0.00 0.00 3.10
7775 7951 3.005261 CGAGAGAGAGAGGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
7776 7952 4.219115 GAGAGAGAGAGGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
7777 7953 4.624913 AGAGAGAGAGGAGAGAGAGAGAA 58.375 47.826 0.00 0.00 0.00 2.87
7778 7954 5.032846 AGAGAGAGAGGAGAGAGAGAGAAA 58.967 45.833 0.00 0.00 0.00 2.52
7779 7955 5.488919 AGAGAGAGAGGAGAGAGAGAGAAAA 59.511 44.000 0.00 0.00 0.00 2.29
7780 7956 5.749462 AGAGAGAGGAGAGAGAGAGAAAAG 58.251 45.833 0.00 0.00 0.00 2.27
7781 7957 5.251700 AGAGAGAGGAGAGAGAGAGAAAAGT 59.748 44.000 0.00 0.00 0.00 2.66
7782 7958 5.256474 AGAGAGGAGAGAGAGAGAAAAGTG 58.744 45.833 0.00 0.00 0.00 3.16
7783 7959 4.344104 AGAGGAGAGAGAGAGAAAAGTGG 58.656 47.826 0.00 0.00 0.00 4.00
7784 7960 3.440127 AGGAGAGAGAGAGAAAAGTGGG 58.560 50.000 0.00 0.00 0.00 4.61
7785 7961 2.499693 GGAGAGAGAGAGAAAAGTGGGG 59.500 54.545 0.00 0.00 0.00 4.96
7786 7962 3.169908 GAGAGAGAGAGAAAAGTGGGGT 58.830 50.000 0.00 0.00 0.00 4.95
7787 7963 4.345854 GAGAGAGAGAGAAAAGTGGGGTA 58.654 47.826 0.00 0.00 0.00 3.69
7788 7964 4.349365 AGAGAGAGAGAAAAGTGGGGTAG 58.651 47.826 0.00 0.00 0.00 3.18
7789 7965 3.445987 AGAGAGAGAAAAGTGGGGTAGG 58.554 50.000 0.00 0.00 0.00 3.18
7790 7966 3.174779 GAGAGAGAAAAGTGGGGTAGGT 58.825 50.000 0.00 0.00 0.00 3.08
7791 7967 2.907042 AGAGAGAAAAGTGGGGTAGGTG 59.093 50.000 0.00 0.00 0.00 4.00
7792 7968 1.985895 AGAGAAAAGTGGGGTAGGTGG 59.014 52.381 0.00 0.00 0.00 4.61
7793 7969 1.004394 GAGAAAAGTGGGGTAGGTGGG 59.996 57.143 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.385630 ACAACACTTGTAGCAATCATGCCG 62.386 45.833 0.00 0.00 44.59 5.69
32 33 5.560760 CGAACACAACACTTGTAGCAATCAT 60.561 40.000 0.00 0.00 43.23 2.45
38 39 2.206750 TCCGAACACAACACTTGTAGC 58.793 47.619 0.00 0.00 43.23 3.58
43 44 4.035208 GTCTTTGATCCGAACACAACACTT 59.965 41.667 0.00 0.00 0.00 3.16
56 57 8.960591 TGGATTATTTCTTCTTGTCTTTGATCC 58.039 33.333 0.00 0.00 0.00 3.36
70 71 9.965824 CGCCTTTATATTGTTGGATTATTTCTT 57.034 29.630 0.00 0.00 0.00 2.52
87 88 8.336806 CGTATGTTGGATTAAAACGCCTTTATA 58.663 33.333 0.00 0.00 29.52 0.98
88 89 7.190871 CGTATGTTGGATTAAAACGCCTTTAT 58.809 34.615 0.00 0.00 29.52 1.40
89 90 6.544622 CGTATGTTGGATTAAAACGCCTTTA 58.455 36.000 0.00 0.00 0.00 1.85
91 92 4.673320 GCGTATGTTGGATTAAAACGCCTT 60.673 41.667 5.70 0.00 46.07 4.35
93 94 3.103007 GCGTATGTTGGATTAAAACGCC 58.897 45.455 5.70 0.00 46.07 5.68
95 96 5.619607 GCTATGCGTATGTTGGATTAAAACG 59.380 40.000 0.00 0.00 0.00 3.60
96 97 6.969669 GCTATGCGTATGTTGGATTAAAAC 57.030 37.500 0.00 0.00 0.00 2.43
116 117 3.454587 AAATGCCGGCCGATCGCTA 62.455 57.895 30.73 12.66 37.74 4.26
117 118 4.856801 AAATGCCGGCCGATCGCT 62.857 61.111 30.73 8.79 37.74 4.93
129 130 3.810896 GTCGACCGGCCCAAATGC 61.811 66.667 3.51 0.00 0.00 3.56
130 131 3.131478 GGTCGACCGGCCCAAATG 61.131 66.667 20.85 0.00 32.85 2.32
305 307 4.648626 TCCGTCCGGTCCGACAGT 62.649 66.667 14.39 0.00 36.47 3.55
479 507 1.001020 TCATGGTGGTGATGGTGGC 60.001 57.895 0.00 0.00 0.00 5.01
520 548 2.007608 GCGGTAAAATGTCCTCTCCAC 58.992 52.381 0.00 0.00 0.00 4.02
521 549 1.404986 CGCGGTAAAATGTCCTCTCCA 60.405 52.381 0.00 0.00 0.00 3.86
522 550 1.134907 TCGCGGTAAAATGTCCTCTCC 60.135 52.381 6.13 0.00 0.00 3.71
523 551 1.925185 GTCGCGGTAAAATGTCCTCTC 59.075 52.381 6.13 0.00 0.00 3.20
524 552 1.734707 CGTCGCGGTAAAATGTCCTCT 60.735 52.381 6.13 0.00 0.00 3.69
608 636 0.179936 CTGTTGCCTCCCTGATCCTC 59.820 60.000 0.00 0.00 0.00 3.71
609 637 1.919600 GCTGTTGCCTCCCTGATCCT 61.920 60.000 0.00 0.00 0.00 3.24
610 638 1.452833 GCTGTTGCCTCCCTGATCC 60.453 63.158 0.00 0.00 0.00 3.36
612 640 2.270205 CGCTGTTGCCTCCCTGAT 59.730 61.111 0.00 0.00 35.36 2.90
613 641 4.020617 CCGCTGTTGCCTCCCTGA 62.021 66.667 0.00 0.00 35.36 3.86
1504 1540 2.049433 CTGCCGTCGTCGAGGTTT 60.049 61.111 13.41 0.00 39.71 3.27
1582 1618 2.145397 ATAGCTCGAACTCCTCCACA 57.855 50.000 0.00 0.00 0.00 4.17
1693 1729 1.619669 GGACCTCTCCATGGGGGTT 60.620 63.158 12.98 0.00 36.42 4.11
1930 1966 1.518325 TGTATGACTTGCCGTTGTGG 58.482 50.000 0.00 0.00 42.50 4.17
2072 2108 1.620822 GAGTGCAACACCTCCCAAAT 58.379 50.000 0.00 0.00 41.43 2.32
2223 2259 3.521796 GATCCTTTGCCGGCAGCC 61.522 66.667 30.75 12.15 42.71 4.85
2415 2451 8.928270 AGATTACACTCAAAACTAGTATTCGG 57.072 34.615 0.00 0.00 0.00 4.30
2442 2478 7.164122 TCTACTCAAAGAACATTCTGCATCTT 58.836 34.615 0.00 0.00 37.65 2.40
2715 2751 7.604164 TCCTAGTTCATAAGTCTTTTGCTTCAG 59.396 37.037 0.00 0.00 0.00 3.02
2810 2846 3.483421 TCTCGTACACCTCTGTTCAAGA 58.517 45.455 0.00 0.00 0.00 3.02
2816 2852 1.073444 TGGACTCTCGTACACCTCTGT 59.927 52.381 0.00 0.00 0.00 3.41
3026 3105 6.816134 TGCAACTGCTTATACTTTTCATCA 57.184 33.333 2.95 0.00 42.66 3.07
3033 3112 5.301805 ACAAGGTTTGCAACTGCTTATACTT 59.698 36.000 0.00 0.00 42.66 2.24
3047 3126 1.583054 ACTGACGAGACAAGGTTTGC 58.417 50.000 0.00 0.00 0.00 3.68
3089 3168 8.689061 TGTGATAAATGAGCAAGAAATAATGCT 58.311 29.630 0.00 0.00 40.68 3.79
3121 3200 5.450550 GCTCAAGGGTTTACATGGATTAAGC 60.451 44.000 0.00 0.00 0.00 3.09
3128 3207 3.356529 AGAGCTCAAGGGTTTACATGG 57.643 47.619 17.77 0.00 0.00 3.66
3184 3273 8.133024 AGTGCTTCAATAAATGGAACCAATTA 57.867 30.769 4.20 4.20 0.00 1.40
3346 3435 8.279103 GCTCATAATAGTTTTTCGGAATCTGAG 58.721 37.037 0.00 0.00 0.00 3.35
3462 3551 2.505337 TGCGCGTATCCGTGTGTC 60.505 61.111 8.43 0.00 46.08 3.67
3659 3754 5.689383 AACTATAACACACTGCAAACTGG 57.311 39.130 0.00 0.00 0.00 4.00
3833 3977 6.106673 AGACAAGTGATGGAGTAATTAACCG 58.893 40.000 5.77 0.00 0.00 4.44
3917 4065 0.399833 TACACCATGCTGAGTTGGCA 59.600 50.000 3.88 0.00 44.05 4.92
3936 4084 7.874016 TGCAAGCTGAAGTTCAATTGAAATTAT 59.126 29.630 28.14 12.39 41.62 1.28
4048 4196 5.532406 ACAATGATATGGACAGCATGGTAAC 59.468 40.000 0.00 0.00 43.62 2.50
4080 4228 1.815840 GCTCCTTGGGCTAGCGAAC 60.816 63.158 9.00 2.03 0.00 3.95
4095 4243 0.535335 TTCTGTACCATGGACGGCTC 59.465 55.000 21.47 2.43 0.00 4.70
4096 4244 0.249398 GTTCTGTACCATGGACGGCT 59.751 55.000 21.47 0.00 0.00 5.52
4118 4266 7.388224 TGCGTAGAAACCTGAAAATACATGTTA 59.612 33.333 2.30 0.00 30.87 2.41
4141 4289 5.004922 AGAGATTCCTAGAGTTTCTTGCG 57.995 43.478 0.00 0.00 0.00 4.85
4205 4353 9.379791 TCTATGATGCAATATATTCAGAAGCAG 57.620 33.333 11.61 1.20 33.69 4.24
4253 4401 5.968254 TGAACTTTTGGGACCAAAGTAAAC 58.032 37.500 15.37 8.99 45.15 2.01
4348 4496 4.119862 GGTATTCGTCTTTCATGCAGCTA 58.880 43.478 0.00 0.00 0.00 3.32
4349 4497 2.939103 GGTATTCGTCTTTCATGCAGCT 59.061 45.455 0.00 0.00 0.00 4.24
4370 4518 5.574830 TGGAATCGGTTAATTTGCAAATTCG 59.425 36.000 34.40 29.81 39.24 3.34
4431 4579 7.673926 AGGTCCCTGATTTTAAAATTAGCTTGA 59.326 33.333 21.46 15.61 32.44 3.02
4488 4636 3.252974 AGTGTGCTGCTACATTCCTAC 57.747 47.619 0.00 0.00 32.43 3.18
5077 5225 4.851639 AACAATGCAACTAGAGAGGGAT 57.148 40.909 0.00 0.00 0.00 3.85
5101 5259 3.924576 AAAAAGGGGTCACAGCAGT 57.075 47.368 0.00 0.00 0.00 4.40
5161 5319 2.293122 GCACAACTGGATAACAACAGCA 59.707 45.455 0.00 0.00 38.25 4.41
5248 5406 6.272318 TGCAGGTCAATTTGTTTCTTGTAAG 58.728 36.000 0.00 0.00 0.00 2.34
5397 5557 6.608405 TGACGAACTTCCTGGGATAAACTATA 59.392 38.462 0.00 0.00 0.00 1.31
5419 5579 4.614535 GCAGATGTGACAATGACCTTTGAC 60.615 45.833 5.47 0.00 0.00 3.18
5604 5765 1.134075 GCTCATCAACAGCACGCAG 59.866 57.895 0.00 0.00 36.82 5.18
5610 5771 1.736681 GAAGTCAGGCTCATCAACAGC 59.263 52.381 0.00 0.00 36.02 4.40
5636 5797 4.321230 GCAGGTGTTGTAAAGGGAAAGATG 60.321 45.833 0.00 0.00 0.00 2.90
5656 5817 7.194607 TCTTGAAAGTTGAAACAGATAGCAG 57.805 36.000 0.00 0.00 0.00 4.24
5657 5818 7.566760 TTCTTGAAAGTTGAAACAGATAGCA 57.433 32.000 0.00 0.00 0.00 3.49
5863 6024 4.485163 GGTATTTGTGACAGGAACAATGC 58.515 43.478 0.00 0.00 37.38 3.56
5940 6101 3.561725 GCTTTATTAGTCATTCTGGCGCT 59.438 43.478 7.64 0.00 0.00 5.92
5959 6120 2.639839 TCTTGCTTCCTGGAGTTAGCTT 59.360 45.455 17.27 0.00 34.77 3.74
5965 6126 3.054802 CAGGTTATCTTGCTTCCTGGAGT 60.055 47.826 0.00 0.00 41.10 3.85
6023 6184 3.131223 TCTCATCCTCTTTAGCAGGTTCG 59.869 47.826 0.00 0.00 32.20 3.95
6164 6325 2.010582 GCGGACTCGGAGCTTGATCT 62.011 60.000 4.58 0.00 36.79 2.75
6266 6427 2.157279 CGATACGGGTACTCAGATCGAC 59.843 54.545 17.35 0.00 38.71 4.20
6529 6691 0.759959 CTGCTGGATGAGAGGAGCAT 59.240 55.000 0.00 0.00 40.55 3.79
6541 6703 1.004560 CAAGGTCGAAGCTGCTGGA 60.005 57.895 1.35 0.58 0.00 3.86
6656 6818 7.233962 TCTGTCACCCTATGTGTAACTCTTTTA 59.766 37.037 0.00 0.00 45.61 1.52
6684 6847 0.321122 AGGAAAGCCAGCAGAACGAG 60.321 55.000 0.00 0.00 36.29 4.18
6733 6896 9.819267 AATGGTCTAAAAGCTACAGTAAGATAC 57.181 33.333 0.00 0.00 0.00 2.24
6765 6928 6.870439 AGATAAAGCAACAAAAGAATGCCTTC 59.130 34.615 0.00 0.00 40.93 3.46
6820 6985 9.220767 GAACTCAAGACATGGTAGAAATTAACT 57.779 33.333 0.00 0.00 0.00 2.24
6824 6989 5.122396 GCGAACTCAAGACATGGTAGAAATT 59.878 40.000 0.00 0.00 0.00 1.82
6887 7063 3.322369 TGATGCGTCGTTGACAAGTAAT 58.678 40.909 0.58 0.00 32.09 1.89
6888 7064 2.745102 TGATGCGTCGTTGACAAGTAA 58.255 42.857 0.58 0.00 32.09 2.24
6992 7168 4.114997 CGTGCGGTGGAATTGGCC 62.115 66.667 0.00 0.00 0.00 5.36
6993 7169 3.322706 GACGTGCGGTGGAATTGGC 62.323 63.158 0.00 0.00 0.00 4.52
6994 7170 2.686816 GGACGTGCGGTGGAATTGG 61.687 63.158 0.00 0.00 0.00 3.16
6995 7171 2.867472 GGACGTGCGGTGGAATTG 59.133 61.111 0.00 0.00 0.00 2.32
6996 7172 2.740826 CGGACGTGCGGTGGAATT 60.741 61.111 22.68 0.00 0.00 2.17
6997 7173 2.999739 AAACGGACGTGCGGTGGAAT 63.000 55.000 32.46 9.23 0.00 3.01
6998 7174 3.736732 AAACGGACGTGCGGTGGAA 62.737 57.895 32.46 0.00 0.00 3.53
6999 7175 3.736732 AAAACGGACGTGCGGTGGA 62.737 57.895 32.46 0.00 0.00 4.02
7000 7176 3.273834 AAAACGGACGTGCGGTGG 61.274 61.111 32.46 6.26 0.00 4.61
7001 7177 2.052590 CAAAACGGACGTGCGGTG 60.053 61.111 32.46 22.20 0.00 4.94
7002 7178 2.512057 ACAAAACGGACGTGCGGT 60.512 55.556 32.46 25.72 0.00 5.68
7003 7179 2.247267 GACAAAACGGACGTGCGG 59.753 61.111 32.46 17.35 0.00 5.69
7004 7180 2.247267 GGACAAAACGGACGTGCG 59.753 61.111 28.33 28.33 0.00 5.34
7005 7181 2.247267 CGGACAAAACGGACGTGC 59.753 61.111 0.00 0.00 0.00 5.34
7012 7188 2.657184 GGACAAATTCCGGACAAAACG 58.343 47.619 1.83 0.00 33.46 3.60
7022 7198 2.490509 CCACCCTAAACGGACAAATTCC 59.509 50.000 0.00 0.00 41.75 3.01
7023 7199 2.094906 GCCACCCTAAACGGACAAATTC 60.095 50.000 0.00 0.00 33.16 2.17
7024 7200 1.890489 GCCACCCTAAACGGACAAATT 59.110 47.619 0.00 0.00 33.16 1.82
7025 7201 1.202952 TGCCACCCTAAACGGACAAAT 60.203 47.619 0.00 0.00 33.16 2.32
7026 7202 0.183014 TGCCACCCTAAACGGACAAA 59.817 50.000 0.00 0.00 33.16 2.83
7027 7203 0.183014 TTGCCACCCTAAACGGACAA 59.817 50.000 0.00 0.00 33.16 3.18
7028 7204 0.402504 ATTGCCACCCTAAACGGACA 59.597 50.000 0.00 0.00 33.16 4.02
7029 7205 0.808755 CATTGCCACCCTAAACGGAC 59.191 55.000 0.00 0.00 33.16 4.79
7030 7206 0.693622 TCATTGCCACCCTAAACGGA 59.306 50.000 0.00 0.00 33.16 4.69
7031 7207 1.094785 CTCATTGCCACCCTAAACGG 58.905 55.000 0.00 0.00 0.00 4.44
7032 7208 1.094785 CCTCATTGCCACCCTAAACG 58.905 55.000 0.00 0.00 0.00 3.60
7033 7209 2.092323 GTCCTCATTGCCACCCTAAAC 58.908 52.381 0.00 0.00 0.00 2.01
7034 7210 1.707989 TGTCCTCATTGCCACCCTAAA 59.292 47.619 0.00 0.00 0.00 1.85
7035 7211 1.281867 CTGTCCTCATTGCCACCCTAA 59.718 52.381 0.00 0.00 0.00 2.69
7036 7212 0.911769 CTGTCCTCATTGCCACCCTA 59.088 55.000 0.00 0.00 0.00 3.53
7037 7213 0.842030 TCTGTCCTCATTGCCACCCT 60.842 55.000 0.00 0.00 0.00 4.34
7038 7214 0.038166 TTCTGTCCTCATTGCCACCC 59.962 55.000 0.00 0.00 0.00 4.61
7039 7215 1.541588 GTTTCTGTCCTCATTGCCACC 59.458 52.381 0.00 0.00 0.00 4.61
7040 7216 1.197721 CGTTTCTGTCCTCATTGCCAC 59.802 52.381 0.00 0.00 0.00 5.01
7041 7217 1.522668 CGTTTCTGTCCTCATTGCCA 58.477 50.000 0.00 0.00 0.00 4.92
7042 7218 0.804989 CCGTTTCTGTCCTCATTGCC 59.195 55.000 0.00 0.00 0.00 4.52
7043 7219 1.464997 GTCCGTTTCTGTCCTCATTGC 59.535 52.381 0.00 0.00 0.00 3.56
7044 7220 2.766313 TGTCCGTTTCTGTCCTCATTG 58.234 47.619 0.00 0.00 0.00 2.82
7045 7221 3.338249 CATGTCCGTTTCTGTCCTCATT 58.662 45.455 0.00 0.00 0.00 2.57
7046 7222 2.936993 GCATGTCCGTTTCTGTCCTCAT 60.937 50.000 0.00 0.00 0.00 2.90
7047 7223 1.608025 GCATGTCCGTTTCTGTCCTCA 60.608 52.381 0.00 0.00 0.00 3.86
7048 7224 1.079503 GCATGTCCGTTTCTGTCCTC 58.920 55.000 0.00 0.00 0.00 3.71
7049 7225 0.670546 CGCATGTCCGTTTCTGTCCT 60.671 55.000 0.00 0.00 0.00 3.85
7050 7226 0.949105 ACGCATGTCCGTTTCTGTCC 60.949 55.000 0.00 0.00 38.47 4.02
7051 7227 0.163788 CACGCATGTCCGTTTCTGTC 59.836 55.000 0.00 0.00 39.83 3.51
7052 7228 0.531974 ACACGCATGTCCGTTTCTGT 60.532 50.000 0.00 0.00 39.83 3.41
7053 7229 2.234613 ACACGCATGTCCGTTTCTG 58.765 52.632 0.00 0.00 39.83 3.02
7054 7230 4.771127 ACACGCATGTCCGTTTCT 57.229 50.000 0.00 0.00 39.83 2.52
7062 7238 3.049674 CAAGCCGGACACGCATGT 61.050 61.111 5.05 0.00 43.71 3.21
7063 7239 4.465512 GCAAGCCGGACACGCATG 62.466 66.667 5.05 0.00 39.22 4.06
7067 7243 4.072088 GAACGCAAGCCGGACACG 62.072 66.667 5.05 5.18 42.52 4.49
7068 7244 4.072088 CGAACGCAAGCCGGACAC 62.072 66.667 5.05 0.00 42.52 3.67
7069 7245 4.287781 TCGAACGCAAGCCGGACA 62.288 61.111 5.05 0.00 42.52 4.02
7070 7246 3.479269 CTCGAACGCAAGCCGGAC 61.479 66.667 5.05 0.00 42.52 4.79
7071 7247 4.735132 CCTCGAACGCAAGCCGGA 62.735 66.667 5.05 0.00 42.52 5.14
7080 7256 4.812476 TGATGGGCGCCTCGAACG 62.812 66.667 28.56 3.27 0.00 3.95
7081 7257 3.195698 GTGATGGGCGCCTCGAAC 61.196 66.667 28.56 16.17 0.00 3.95
7082 7258 4.812476 CGTGATGGGCGCCTCGAA 62.812 66.667 28.56 10.38 0.00 3.71
7085 7261 4.451150 TGTCGTGATGGGCGCCTC 62.451 66.667 28.56 18.02 0.00 4.70
7086 7262 4.457496 CTGTCGTGATGGGCGCCT 62.457 66.667 28.56 7.30 0.00 5.52
7087 7263 3.950794 TTCTGTCGTGATGGGCGCC 62.951 63.158 21.18 21.18 0.00 6.53
7088 7264 2.434185 TTCTGTCGTGATGGGCGC 60.434 61.111 0.00 0.00 0.00 6.53
7089 7265 2.444624 CGTTCTGTCGTGATGGGCG 61.445 63.158 0.00 0.00 0.00 6.13
7090 7266 1.080093 TCGTTCTGTCGTGATGGGC 60.080 57.895 0.00 0.00 0.00 5.36
7091 7267 0.736325 GGTCGTTCTGTCGTGATGGG 60.736 60.000 0.00 0.00 0.00 4.00
7092 7268 0.736325 GGGTCGTTCTGTCGTGATGG 60.736 60.000 0.00 0.00 0.00 3.51
7093 7269 0.038618 TGGGTCGTTCTGTCGTGATG 60.039 55.000 0.00 0.00 0.00 3.07
7094 7270 0.677288 TTGGGTCGTTCTGTCGTGAT 59.323 50.000 0.00 0.00 0.00 3.06
7095 7271 0.460722 TTTGGGTCGTTCTGTCGTGA 59.539 50.000 0.00 0.00 0.00 4.35
7096 7272 1.004292 GTTTTGGGTCGTTCTGTCGTG 60.004 52.381 0.00 0.00 0.00 4.35
7097 7273 1.292992 GTTTTGGGTCGTTCTGTCGT 58.707 50.000 0.00 0.00 0.00 4.34
7098 7274 0.231279 CGTTTTGGGTCGTTCTGTCG 59.769 55.000 0.00 0.00 0.00 4.35
7099 7275 1.259770 GACGTTTTGGGTCGTTCTGTC 59.740 52.381 0.00 0.00 40.39 3.51
7100 7276 1.292992 GACGTTTTGGGTCGTTCTGT 58.707 50.000 0.00 0.00 40.39 3.41
7101 7277 0.584876 GGACGTTTTGGGTCGTTCTG 59.415 55.000 0.00 0.00 40.39 3.02
7102 7278 0.877213 CGGACGTTTTGGGTCGTTCT 60.877 55.000 0.00 0.00 40.39 3.01
7103 7279 1.566077 CGGACGTTTTGGGTCGTTC 59.434 57.895 0.00 0.00 40.39 3.95
7104 7280 2.536673 GCGGACGTTTTGGGTCGTT 61.537 57.895 0.00 0.00 40.39 3.85
7105 7281 2.968697 GCGGACGTTTTGGGTCGT 60.969 61.111 0.00 0.00 43.00 4.34
7106 7282 3.719144 GGCGGACGTTTTGGGTCG 61.719 66.667 0.00 0.00 35.24 4.79
7107 7283 3.719144 CGGCGGACGTTTTGGGTC 61.719 66.667 0.00 0.00 37.93 4.46
7111 7287 4.084888 GAGGCGGCGGACGTTTTG 62.085 66.667 9.78 0.00 46.52 2.44
7142 7318 2.277373 GCGAGGTGTAGCGACGAG 60.277 66.667 0.00 0.00 0.00 4.18
7143 7319 3.807538 GGCGAGGTGTAGCGACGA 61.808 66.667 0.00 0.00 0.00 4.20
7229 7405 4.487412 GGCGACCAATGCTGCTGC 62.487 66.667 8.89 8.89 40.20 5.25
7230 7406 4.170062 CGGCGACCAATGCTGCTG 62.170 66.667 0.00 0.00 30.94 4.41
7681 7857 4.864334 GATGGGTGGAGGCAGCGG 62.864 72.222 0.00 0.00 0.00 5.52
7684 7860 4.864334 GGCGATGGGTGGAGGCAG 62.864 72.222 0.00 0.00 0.00 4.85
7708 7884 2.889503 CGTAGCAGCAGCAGGAGC 60.890 66.667 3.17 0.00 45.49 4.70
7744 7920 3.206211 CTCTCTCTCGCATCCCGGC 62.206 68.421 0.00 0.00 37.59 6.13
7745 7921 1.514678 CTCTCTCTCTCGCATCCCGG 61.515 65.000 0.00 0.00 37.59 5.73
7746 7922 1.514678 CCTCTCTCTCTCGCATCCCG 61.515 65.000 0.00 0.00 38.61 5.14
7747 7923 0.179004 TCCTCTCTCTCTCGCATCCC 60.179 60.000 0.00 0.00 0.00 3.85
7748 7924 1.202758 TCTCCTCTCTCTCTCGCATCC 60.203 57.143 0.00 0.00 0.00 3.51
7749 7925 2.146342 CTCTCCTCTCTCTCTCGCATC 58.854 57.143 0.00 0.00 0.00 3.91
7750 7926 1.768275 TCTCTCCTCTCTCTCTCGCAT 59.232 52.381 0.00 0.00 0.00 4.73
7751 7927 1.138859 CTCTCTCCTCTCTCTCTCGCA 59.861 57.143 0.00 0.00 0.00 5.10
7752 7928 1.412710 TCTCTCTCCTCTCTCTCTCGC 59.587 57.143 0.00 0.00 0.00 5.03
7753 7929 2.959030 TCTCTCTCTCCTCTCTCTCTCG 59.041 54.545 0.00 0.00 0.00 4.04
7754 7930 4.219115 TCTCTCTCTCTCCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
7755 7931 4.271807 TCTCTCTCTCTCCTCTCTCTCT 57.728 50.000 0.00 0.00 0.00 3.10
7756 7932 5.359194 TTTCTCTCTCTCTCCTCTCTCTC 57.641 47.826 0.00 0.00 0.00 3.20
7757 7933 5.251700 ACTTTTCTCTCTCTCTCCTCTCTCT 59.748 44.000 0.00 0.00 0.00 3.10
7758 7934 5.355350 CACTTTTCTCTCTCTCTCCTCTCTC 59.645 48.000 0.00 0.00 0.00 3.20
7759 7935 5.256474 CACTTTTCTCTCTCTCTCCTCTCT 58.744 45.833 0.00 0.00 0.00 3.10
7760 7936 4.399303 CCACTTTTCTCTCTCTCTCCTCTC 59.601 50.000 0.00 0.00 0.00 3.20
7761 7937 4.344104 CCACTTTTCTCTCTCTCTCCTCT 58.656 47.826 0.00 0.00 0.00 3.69
7762 7938 3.447229 CCCACTTTTCTCTCTCTCTCCTC 59.553 52.174 0.00 0.00 0.00 3.71
7763 7939 3.440127 CCCACTTTTCTCTCTCTCTCCT 58.560 50.000 0.00 0.00 0.00 3.69
7764 7940 2.499693 CCCCACTTTTCTCTCTCTCTCC 59.500 54.545 0.00 0.00 0.00 3.71
7765 7941 3.169908 ACCCCACTTTTCTCTCTCTCTC 58.830 50.000 0.00 0.00 0.00 3.20
7766 7942 3.268034 ACCCCACTTTTCTCTCTCTCT 57.732 47.619 0.00 0.00 0.00 3.10
7767 7943 3.449377 CCTACCCCACTTTTCTCTCTCTC 59.551 52.174 0.00 0.00 0.00 3.20
7768 7944 3.181405 ACCTACCCCACTTTTCTCTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
7769 7945 3.055747 CACCTACCCCACTTTTCTCTCTC 60.056 52.174 0.00 0.00 0.00 3.20
7770 7946 2.907042 CACCTACCCCACTTTTCTCTCT 59.093 50.000 0.00 0.00 0.00 3.10
7771 7947 2.027100 CCACCTACCCCACTTTTCTCTC 60.027 54.545 0.00 0.00 0.00 3.20
7772 7948 1.985895 CCACCTACCCCACTTTTCTCT 59.014 52.381 0.00 0.00 0.00 3.10
7773 7949 1.004394 CCCACCTACCCCACTTTTCTC 59.996 57.143 0.00 0.00 0.00 2.87
7774 7950 1.073098 CCCACCTACCCCACTTTTCT 58.927 55.000 0.00 0.00 0.00 2.52
7775 7951 3.664240 CCCACCTACCCCACTTTTC 57.336 57.895 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.