Multiple sequence alignment - TraesCS1B01G263600

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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 TraesCS1B01G263600 chr1B 100.000 8572 0 0 440 9011 464128656 464137227 0.000000e+00 15830.0
1 TraesCS1B01G263600 chr1B 78.926 242 51 0 6401 6642 464149706 464149947 2.010000e-36 165.0
2 TraesCS1B01G263600 chr1B 78.099 242 53 0 6401 6642 464479706 464479947 4.360000e-33 154.0
3 TraesCS1B01G263600 chr1B 100.000 80 0 0 1 80 464128217 464128296 2.030000e-31 148.0
4 TraesCS1B01G263600 chr1B 76.882 186 41 2 1823 2007 464477687 464477871 4.450000e-18 104.0
5 TraesCS1B01G263600 chr1B 76.364 165 39 0 1843 2007 464147712 464147876 1.250000e-13 89.8
6 TraesCS1B01G263600 chr1A 92.982 4674 202 42 1266 5896 446130059 446125469 0.000000e+00 6698.0
7 TraesCS1B01G263600 chr1A 97.131 1429 35 5 5969 7397 446125469 446124047 0.000000e+00 2407.0
8 TraesCS1B01G263600 chr1A 91.207 1433 72 10 7544 8946 446124038 446122630 0.000000e+00 1899.0
9 TraesCS1B01G263600 chr1A 89.286 140 13 2 8868 9006 446122612 446122474 3.340000e-39 174.0
10 TraesCS1B01G263600 chr1A 79.339 242 50 0 6401 6642 445919190 445918949 4.330000e-38 171.0
11 TraesCS1B01G263600 chr1A 79.699 133 24 3 5285 5416 445919758 445919628 9.630000e-15 93.5
12 TraesCS1B01G263600 chr1A 75.556 180 42 2 1829 2007 445930760 445930582 4.480000e-13 87.9
13 TraesCS1B01G263600 chr1A 78.049 123 27 0 1888 2010 445938033 445937911 2.700000e-10 78.7
14 TraesCS1B01G263600 chr1D 94.541 2986 98 23 5975 8925 345812404 345809449 0.000000e+00 4551.0
15 TraesCS1B01G263600 chr1D 93.412 2201 89 23 3737 5927 345814568 345812414 0.000000e+00 3210.0
16 TraesCS1B01G263600 chr1D 95.562 1104 40 5 2649 3750 345815815 345814719 0.000000e+00 1759.0
17 TraesCS1B01G263600 chr1D 95.116 860 23 2 1490 2338 345816665 345815814 0.000000e+00 1338.0
18 TraesCS1B01G263600 chr1D 96.751 554 15 3 515 1066 345817661 345817109 0.000000e+00 920.0
19 TraesCS1B01G263600 chr1D 90.315 413 19 11 1067 1461 345817068 345816659 1.040000e-143 521.0
20 TraesCS1B01G263600 chr1D 79.339 242 50 0 6401 6642 345716800 345716559 4.330000e-38 171.0
21 TraesCS1B01G263600 chr1D 79.583 240 48 1 6404 6642 345722815 345722576 4.330000e-38 171.0
22 TraesCS1B01G263600 chr1D 75.556 180 42 2 1829 2007 345718886 345718708 4.480000e-13 87.9
23 TraesCS1B01G263600 chr1D 75.758 165 40 0 1843 2007 345724821 345724657 5.800000e-12 84.2
24 TraesCS1B01G263600 chr3B 85.642 592 68 14 6572 7158 101256194 101255615 2.780000e-169 606.0
25 TraesCS1B01G263600 chr5B 84.603 604 66 17 6572 7158 125268814 125268221 7.850000e-160 575.0
26 TraesCS1B01G263600 chr4D 84.864 588 68 12 6572 7158 180785380 180785947 2.820000e-159 573.0
27 TraesCS1B01G263600 chr5A 86.571 417 39 9 6742 7158 122409465 122409864 2.310000e-120 444.0
28 TraesCS1B01G263600 chr5A 88.701 177 19 1 6572 6747 122393372 122393548 1.970000e-51 215.0
29 TraesCS1B01G263600 chr3D 82.796 93 12 4 698 787 581358802 581358711 7.500000e-11 80.5
30 TraesCS1B01G263600 chr2A 82.759 87 8 3 5893 5972 608910806 608910720 4.510000e-08 71.3


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 TraesCS1B01G263600 chr1B 464128217 464137227 9010 False 7989.000000 15830 100.000000 1 9011 2 chr1B.!!$F1 9010
1 TraesCS1B01G263600 chr1A 446122474 446130059 7585 True 2794.500000 6698 92.651500 1266 9006 4 chr1A.!!$R4 7740
2 TraesCS1B01G263600 chr1D 345809449 345817661 8212 True 2049.833333 4551 94.282833 515 8925 6 chr1D.!!$R2 8410
3 TraesCS1B01G263600 chr3B 101255615 101256194 579 True 606.000000 606 85.642000 6572 7158 1 chr3B.!!$R1 586
4 TraesCS1B01G263600 chr5B 125268221 125268814 593 True 575.000000 575 84.603000 6572 7158 1 chr5B.!!$R1 586
5 TraesCS1B01G263600 chr4D 180785380 180785947 567 False 573.000000 573 84.864000 6572 7158 1 chr4D.!!$F1 586

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
59 60 1.003545 CTGTGCACTTCAGAAACCGTG 60.004 52.381 19.41 0.00 35.20 4.94 F
1166 1220 0.035820 TGTAGTGGATTTGGGCCGTC 60.036 55.000 0.00 0.00 0.00 4.79 F
1544 1620 0.111446 TTGAATCTTGCCCGTTCCCA 59.889 50.000 0.00 0.00 0.00 4.37 F
2508 2613 0.322648 GCTGCCCTTTTTGCTGGAAT 59.677 50.000 0.00 0.00 0.00 3.01 F
3093 3199 1.691976 ACAACCGTCATTCTCACAGGA 59.308 47.619 0.00 0.00 0.00 3.86 F
3554 3661 2.100749 TCCATGCTGACATACACGGTAG 59.899 50.000 0.00 0.00 33.67 3.18 F
5421 5703 0.714180 TCCTAGAGGTAAGCCCCACA 59.286 55.000 0.00 0.00 36.34 4.17 F
6319 6601 0.671163 GGTACCAATTGTCGGCGACA 60.671 55.000 36.29 36.29 41.09 4.35 F
6338 6620 2.093890 CAATGCAGTAATGTGCCTCCA 58.906 47.619 0.00 0.00 43.28 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1741 0.039256 CAAATGCACAACCACCTCCG 60.039 55.000 0.00 0.0 0.00 4.63 R
2833 2938 1.074775 GGCTGGTTCACCATGGACA 59.925 57.895 21.47 8.1 46.46 4.02 R
2961 3066 1.839424 ATTGGTAACTTGGAGCTGGC 58.161 50.000 0.00 0.0 37.61 4.85 R
3745 3852 2.160721 CTAGGAGGAACTAGGCACCA 57.839 55.000 0.00 0.0 41.55 4.17 R
4653 4930 0.825010 GGGCAATAGCAGGACATGGG 60.825 60.000 0.00 0.0 44.61 4.00 R
5483 5765 2.831685 AACTTGTGTCTCGGTGCATA 57.168 45.000 0.00 0.0 0.00 3.14 R
6538 6820 1.002888 AGCACTGACATACTTGCAGCT 59.997 47.619 0.00 0.0 37.44 4.24 R
7969 8283 0.394762 GGTTGCCTGCTCCATGATGA 60.395 55.000 0.00 0.0 0.00 2.92 R
8071 8385 2.300152 TCCGATAAGCTTGGGCATCTAG 59.700 50.000 9.86 0.0 41.70 2.43 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
21 22 4.882671 CGGAGGGAGTATGATTTTGTTG 57.117 45.455 0.00 0.00 0.00 3.33
22 23 3.627577 CGGAGGGAGTATGATTTTGTTGG 59.372 47.826 0.00 0.00 0.00 3.77
23 24 3.954258 GGAGGGAGTATGATTTTGTTGGG 59.046 47.826 0.00 0.00 0.00 4.12
24 25 4.569865 GGAGGGAGTATGATTTTGTTGGGT 60.570 45.833 0.00 0.00 0.00 4.51
25 26 5.339695 GGAGGGAGTATGATTTTGTTGGGTA 60.340 44.000 0.00 0.00 0.00 3.69
26 27 6.147437 AGGGAGTATGATTTTGTTGGGTAA 57.853 37.500 0.00 0.00 0.00 2.85
27 28 5.949952 AGGGAGTATGATTTTGTTGGGTAAC 59.050 40.000 0.00 0.00 37.32 2.50
28 29 5.949952 GGGAGTATGATTTTGTTGGGTAACT 59.050 40.000 0.00 0.00 37.68 2.24
29 30 6.127730 GGGAGTATGATTTTGTTGGGTAACTG 60.128 42.308 0.00 0.00 37.68 3.16
30 31 6.433093 GGAGTATGATTTTGTTGGGTAACTGT 59.567 38.462 0.00 0.00 37.68 3.55
31 32 7.039993 GGAGTATGATTTTGTTGGGTAACTGTT 60.040 37.037 0.00 0.00 37.68 3.16
32 33 7.657336 AGTATGATTTTGTTGGGTAACTGTTG 58.343 34.615 2.69 0.00 37.68 3.33
33 34 5.923733 TGATTTTGTTGGGTAACTGTTGT 57.076 34.783 2.69 0.00 37.68 3.32
34 35 5.897050 TGATTTTGTTGGGTAACTGTTGTC 58.103 37.500 2.69 0.00 37.68 3.18
35 36 5.419155 TGATTTTGTTGGGTAACTGTTGTCA 59.581 36.000 2.69 0.00 37.68 3.58
36 37 5.723672 TTTTGTTGGGTAACTGTTGTCAA 57.276 34.783 2.69 2.57 37.68 3.18
37 38 5.723672 TTTGTTGGGTAACTGTTGTCAAA 57.276 34.783 2.69 3.66 37.68 2.69
38 39 5.723672 TTGTTGGGTAACTGTTGTCAAAA 57.276 34.783 2.69 0.00 37.68 2.44
39 40 5.061920 TGTTGGGTAACTGTTGTCAAAAC 57.938 39.130 2.69 2.79 37.68 2.43
40 41 4.767928 TGTTGGGTAACTGTTGTCAAAACT 59.232 37.500 2.69 0.00 37.68 2.66
41 42 4.974368 TGGGTAACTGTTGTCAAAACTG 57.026 40.909 2.69 0.00 0.00 3.16
42 43 4.337145 TGGGTAACTGTTGTCAAAACTGT 58.663 39.130 2.69 0.00 34.47 3.55
43 44 4.156922 TGGGTAACTGTTGTCAAAACTGTG 59.843 41.667 2.69 0.00 33.55 3.66
44 45 4.102649 GGTAACTGTTGTCAAAACTGTGC 58.897 43.478 2.69 0.00 33.55 4.57
45 46 3.932545 AACTGTTGTCAAAACTGTGCA 57.067 38.095 0.00 0.00 33.55 4.57
46 47 3.216147 ACTGTTGTCAAAACTGTGCAC 57.784 42.857 10.75 10.75 32.32 4.57
47 48 2.819608 ACTGTTGTCAAAACTGTGCACT 59.180 40.909 19.41 0.00 32.32 4.40
48 49 3.255642 ACTGTTGTCAAAACTGTGCACTT 59.744 39.130 19.41 1.32 32.32 3.16
49 50 3.832276 TGTTGTCAAAACTGTGCACTTC 58.168 40.909 19.41 0.00 0.00 3.01
50 51 3.254411 TGTTGTCAAAACTGTGCACTTCA 59.746 39.130 19.41 0.00 0.00 3.02
51 52 3.763097 TGTCAAAACTGTGCACTTCAG 57.237 42.857 19.41 9.90 38.68 3.02
52 53 3.342719 TGTCAAAACTGTGCACTTCAGA 58.657 40.909 19.41 5.84 36.81 3.27
53 54 3.755905 TGTCAAAACTGTGCACTTCAGAA 59.244 39.130 19.41 0.00 36.81 3.02
54 55 4.217334 TGTCAAAACTGTGCACTTCAGAAA 59.783 37.500 19.41 1.12 36.81 2.52
55 56 4.558860 GTCAAAACTGTGCACTTCAGAAAC 59.441 41.667 19.41 5.60 36.81 2.78
56 57 3.782889 AAACTGTGCACTTCAGAAACC 57.217 42.857 19.41 0.00 36.81 3.27
57 58 1.299541 ACTGTGCACTTCAGAAACCG 58.700 50.000 19.41 0.00 36.81 4.44
58 59 1.299541 CTGTGCACTTCAGAAACCGT 58.700 50.000 19.41 0.00 35.20 4.83
59 60 1.003545 CTGTGCACTTCAGAAACCGTG 60.004 52.381 19.41 0.00 35.20 4.94
60 61 1.014352 GTGCACTTCAGAAACCGTGT 58.986 50.000 10.32 0.00 0.00 4.49
61 62 1.003866 GTGCACTTCAGAAACCGTGTC 60.004 52.381 10.32 0.00 0.00 3.67
62 63 1.295792 GCACTTCAGAAACCGTGTCA 58.704 50.000 3.65 0.00 0.00 3.58
63 64 1.668751 GCACTTCAGAAACCGTGTCAA 59.331 47.619 3.65 0.00 0.00 3.18
64 65 2.290641 GCACTTCAGAAACCGTGTCAAT 59.709 45.455 3.65 0.00 0.00 2.57
65 66 3.849645 GCACTTCAGAAACCGTGTCAATG 60.850 47.826 3.65 0.00 0.00 2.82
66 67 3.559655 CACTTCAGAAACCGTGTCAATGA 59.440 43.478 0.00 0.00 0.00 2.57
67 68 3.809832 ACTTCAGAAACCGTGTCAATGAG 59.190 43.478 0.00 0.00 0.00 2.90
68 69 3.469008 TCAGAAACCGTGTCAATGAGT 57.531 42.857 0.00 0.00 0.00 3.41
69 70 4.594123 TCAGAAACCGTGTCAATGAGTA 57.406 40.909 0.00 0.00 0.00 2.59
70 71 4.951254 TCAGAAACCGTGTCAATGAGTAA 58.049 39.130 0.00 0.00 0.00 2.24
71 72 5.361427 TCAGAAACCGTGTCAATGAGTAAA 58.639 37.500 0.00 0.00 0.00 2.01
72 73 5.995282 TCAGAAACCGTGTCAATGAGTAAAT 59.005 36.000 0.00 0.00 0.00 1.40
73 74 7.156000 TCAGAAACCGTGTCAATGAGTAAATA 58.844 34.615 0.00 0.00 0.00 1.40
74 75 7.117236 TCAGAAACCGTGTCAATGAGTAAATAC 59.883 37.037 0.00 0.00 0.00 1.89
75 76 6.370718 AGAAACCGTGTCAATGAGTAAATACC 59.629 38.462 0.00 0.00 0.00 2.73
76 77 5.155278 ACCGTGTCAATGAGTAAATACCA 57.845 39.130 0.00 0.00 0.00 3.25
77 78 5.741011 ACCGTGTCAATGAGTAAATACCAT 58.259 37.500 0.00 0.00 0.00 3.55
78 79 6.177610 ACCGTGTCAATGAGTAAATACCATT 58.822 36.000 0.00 0.00 31.69 3.16
79 80 6.657541 ACCGTGTCAATGAGTAAATACCATTT 59.342 34.615 0.00 0.00 30.23 2.32
755 757 7.918076 TCAACCCACTCTATTTCTCTTAACAT 58.082 34.615 0.00 0.00 0.00 2.71
923 926 4.082081 TCAAAATACCAATTCCTGCAGCAG 60.082 41.667 16.23 16.23 0.00 4.24
1021 1024 3.029320 TGTGCTGTGATTTGGAAATGC 57.971 42.857 0.00 0.00 0.00 3.56
1131 1174 2.929161 GCCGGCCCAAATACAGAAAAAC 60.929 50.000 18.11 0.00 0.00 2.43
1133 1176 3.574614 CGGCCCAAATACAGAAAAACAG 58.425 45.455 0.00 0.00 0.00 3.16
1136 1179 4.280929 GGCCCAAATACAGAAAAACAGAGT 59.719 41.667 0.00 0.00 0.00 3.24
1137 1180 5.221441 GGCCCAAATACAGAAAAACAGAGTT 60.221 40.000 0.00 0.00 0.00 3.01
1138 1181 6.015772 GGCCCAAATACAGAAAAACAGAGTTA 60.016 38.462 0.00 0.00 0.00 2.24
1150 1204 9.066892 AGAAAAACAGAGTTATTGCTGATTGTA 57.933 29.630 0.00 0.00 36.07 2.41
1166 1220 0.035820 TGTAGTGGATTTGGGCCGTC 60.036 55.000 0.00 0.00 0.00 4.79
1214 1273 4.223032 AGTTACCCACTTCTCGATTGATGT 59.777 41.667 0.00 0.00 27.32 3.06
1249 1309 4.367023 CCGCGTCGGTTCCCTCAA 62.367 66.667 4.92 0.00 42.73 3.02
1345 1413 1.135859 GTAGCGTACTAGCGTGTGTGT 60.136 52.381 0.00 0.00 43.00 3.72
1424 1498 1.648467 GGGTGCAGGCTCATCGAAAC 61.648 60.000 0.00 0.00 0.00 2.78
1454 1528 2.114411 TTGGTGCCCCCGTCTTTC 59.886 61.111 0.00 0.00 35.15 2.62
1536 1612 3.421844 AGTGGTTAGGTTGAATCTTGCC 58.578 45.455 0.00 0.00 0.00 4.52
1544 1620 0.111446 TTGAATCTTGCCCGTTCCCA 59.889 50.000 0.00 0.00 0.00 4.37
1651 1741 1.402259 TCGAATCGGAGAGCTGTCTTC 59.598 52.381 11.11 6.09 43.63 2.87
1665 1755 1.070786 TCTTCGGAGGTGGTTGTGC 59.929 57.895 0.00 0.00 0.00 4.57
1839 1930 2.357009 CTGCAGGCAGTTACCATCAATC 59.643 50.000 13.02 0.00 39.10 2.67
1880 1971 1.337071 GGGCATGCTGTGAATCATCTG 59.663 52.381 18.92 0.00 0.00 2.90
2147 2249 3.073274 ACTTTAGGGGATCACAACTGC 57.927 47.619 0.00 0.00 0.00 4.40
2226 2328 4.715534 TGACACAAACTGGGGAATTAGA 57.284 40.909 0.00 0.00 0.00 2.10
2374 2476 8.804912 ATCATTCTATGAAGCAGAAAGAAGTT 57.195 30.769 0.00 0.00 43.50 2.66
2376 2478 9.071276 TCATTCTATGAAGCAGAAAGAAGTTTT 57.929 29.630 0.00 0.00 35.73 2.43
2452 2554 7.984050 TCACACATAACATTTTCCAAACAACAT 59.016 29.630 0.00 0.00 0.00 2.71
2494 2599 1.033746 TTGCATCCTAAGCTGCTGCC 61.034 55.000 12.44 0.00 40.80 4.85
2496 2601 1.530771 CATCCTAAGCTGCTGCCCT 59.469 57.895 12.44 2.45 40.80 5.19
2508 2613 0.322648 GCTGCCCTTTTTGCTGGAAT 59.677 50.000 0.00 0.00 0.00 3.01
2540 2645 5.723672 TCAGACTTATCGACAGTTTTCCT 57.276 39.130 0.76 0.00 0.00 3.36
2549 2654 2.732597 CGACAGTTTTCCTAGAGCTCCG 60.733 54.545 10.93 1.40 0.00 4.63
2566 2671 4.033019 GCTCCGTTTGTGTTACTGTTTTC 58.967 43.478 0.00 0.00 0.00 2.29
2600 2705 8.246430 TCTATCGTTAGGACTTACATCCATTT 57.754 34.615 0.80 0.00 41.73 2.32
2601 2706 8.701895 TCTATCGTTAGGACTTACATCCATTTT 58.298 33.333 0.80 0.00 41.73 1.82
2682 2787 9.530129 GAAGTTGTTTATTTGTCTAATGTCTCG 57.470 33.333 0.00 0.00 0.00 4.04
2768 2873 6.119536 TCTGTGGTGATAAGTGAAAACACTT 58.880 36.000 17.41 17.41 46.05 3.16
2821 2926 4.081198 TGTTTTTGTTGCCCTCACAGAAAT 60.081 37.500 0.00 0.00 0.00 2.17
2876 2981 2.883386 GGGCCAAACAATGCAATTTGAA 59.117 40.909 18.12 0.00 37.91 2.69
2885 2990 9.801714 CAAACAATGCAATTTGAAGAATACTTC 57.198 29.630 13.43 0.00 43.01 3.01
2910 3015 7.227314 TCTGATATCAAACCATCACATTAGTGC 59.773 37.037 6.90 0.00 45.49 4.40
2932 3037 4.204012 CCCTTTCCGTAAGAAATATGCCA 58.796 43.478 0.00 0.00 43.50 4.92
2961 3066 7.783090 ACTCTGCTTATCTGTGTATTCATTG 57.217 36.000 0.00 0.00 0.00 2.82
3037 3142 2.552315 ACCATTTCAGCAACCTACAACG 59.448 45.455 0.00 0.00 0.00 4.10
3093 3199 1.691976 ACAACCGTCATTCTCACAGGA 59.308 47.619 0.00 0.00 0.00 3.86
3264 3370 4.967084 ATGCGGTGATATTGGTAACCTA 57.033 40.909 0.00 0.00 0.00 3.08
3414 3520 9.936759 AACTTTGAAAGTGGAATTTCTTGTTTA 57.063 25.926 11.83 0.00 41.91 2.01
3423 3529 8.194769 AGTGGAATTTCTTGTTTACGACAAATT 58.805 29.630 0.00 0.00 46.99 1.82
3553 3660 2.104170 TCCATGCTGACATACACGGTA 58.896 47.619 0.00 0.00 33.67 4.02
3554 3661 2.100749 TCCATGCTGACATACACGGTAG 59.899 50.000 0.00 0.00 33.67 3.18
3555 3662 2.100749 CCATGCTGACATACACGGTAGA 59.899 50.000 0.00 0.00 33.67 2.59
3556 3663 3.243873 CCATGCTGACATACACGGTAGAT 60.244 47.826 0.00 0.00 33.67 1.98
3557 3664 4.371786 CATGCTGACATACACGGTAGATT 58.628 43.478 0.00 0.00 33.67 2.40
3558 3665 4.465632 TGCTGACATACACGGTAGATTT 57.534 40.909 0.00 0.00 0.00 2.17
3559 3666 5.585820 TGCTGACATACACGGTAGATTTA 57.414 39.130 0.00 0.00 0.00 1.40
3594 3701 2.896685 CCCTTTTGTGATTAACTGCCCA 59.103 45.455 0.00 0.00 0.00 5.36
3944 4218 9.722056 GTGTCTCTTTAGTATGCCAATAAATTG 57.278 33.333 0.00 0.00 37.52 2.32
4179 4456 5.407995 TCTTCGCCCTTGCAAAATTTTAATG 59.592 36.000 2.44 0.00 37.32 1.90
4343 4620 5.680408 GCATGGAAATGATTTTGCTGAGCTA 60.680 40.000 5.83 0.00 34.54 3.32
4454 4731 4.377021 CCAAGTTTGGTCTTAAAAAGGGC 58.623 43.478 2.66 0.00 43.43 5.19
4637 4914 7.083875 TGAAGCTACATTAAATTTTCTCCGG 57.916 36.000 0.00 0.00 0.00 5.14
4651 4928 4.993705 TTCTCCGGCCCATATCTTTATT 57.006 40.909 0.00 0.00 0.00 1.40
4653 4930 4.906618 TCTCCGGCCCATATCTTTATTTC 58.093 43.478 0.00 0.00 0.00 2.17
4788 5066 6.863126 GGAAATTGGTGATGTTTTAGACACTG 59.137 38.462 0.00 0.00 42.04 3.66
4826 5108 4.663636 ATCTTTGACCGTCGCTTTTTAG 57.336 40.909 0.00 0.00 0.00 1.85
4827 5109 3.460103 TCTTTGACCGTCGCTTTTTAGT 58.540 40.909 0.00 0.00 0.00 2.24
4828 5110 3.872771 TCTTTGACCGTCGCTTTTTAGTT 59.127 39.130 0.00 0.00 0.00 2.24
4829 5111 4.333372 TCTTTGACCGTCGCTTTTTAGTTT 59.667 37.500 0.00 0.00 0.00 2.66
4830 5112 4.619437 TTGACCGTCGCTTTTTAGTTTT 57.381 36.364 0.00 0.00 0.00 2.43
4831 5113 4.619437 TGACCGTCGCTTTTTAGTTTTT 57.381 36.364 0.00 0.00 0.00 1.94
4832 5114 5.731599 TGACCGTCGCTTTTTAGTTTTTA 57.268 34.783 0.00 0.00 0.00 1.52
4870 5152 6.446909 AAAAGGGCTCAAATTTCCCAAATA 57.553 33.333 14.23 0.00 42.52 1.40
4976 5258 9.311676 TCCACCCTCACATTTTATACGTATATA 57.688 33.333 15.77 8.74 0.00 0.86
5070 5352 9.660180 TGCCTTACCAATCCAAATTTATTTTAC 57.340 29.630 0.00 0.00 0.00 2.01
5203 5485 3.120304 GCTGTTTAATGGTGGACGAAGAC 60.120 47.826 0.00 0.00 0.00 3.01
5204 5486 4.315803 CTGTTTAATGGTGGACGAAGACT 58.684 43.478 0.00 0.00 0.00 3.24
5205 5487 4.312443 TGTTTAATGGTGGACGAAGACTC 58.688 43.478 0.00 0.00 0.00 3.36
5232 5514 1.680735 TGTTCCCATGTTGCAAGTGAC 59.319 47.619 0.00 0.00 0.00 3.67
5273 5555 8.511321 TGTGTATGAAAAACTACTGGCTAATTG 58.489 33.333 0.00 0.00 0.00 2.32
5421 5703 0.714180 TCCTAGAGGTAAGCCCCACA 59.286 55.000 0.00 0.00 36.34 4.17
5483 5765 9.628500 ACAAGGTTAATAGTTCTCTTCTTTGTT 57.372 29.630 0.00 0.00 0.00 2.83
5514 5796 5.172053 CGAGACACAAGTTTTGCAATTTCTC 59.828 40.000 0.00 0.77 0.00 2.87
5648 5930 4.210331 AGTTGCATCCATATTCCTCCAAC 58.790 43.478 0.00 0.00 33.46 3.77
5700 5982 7.336931 TCTGATTTTGAGCTTGTTTATCCTACC 59.663 37.037 0.00 0.00 0.00 3.18
5734 6016 3.385193 CCAAAATGGAGTTGGGTTGAC 57.615 47.619 0.00 0.00 40.96 3.18
5907 6189 6.097915 CAGAGTTGTACTCCCTCTGTAAAA 57.902 41.667 19.94 0.00 46.18 1.52
5967 6249 9.906660 AGATCTTATATTTCTTTACAGAGCGAG 57.093 33.333 0.00 0.00 0.00 5.03
5982 6264 1.402259 AGCGAGTACATGGAAGAGTCG 59.598 52.381 0.00 4.98 0.00 4.18
6018 6300 7.793888 GCACTCACATACATGTAATATGAAACG 59.206 37.037 10.14 5.41 39.39 3.60
6028 6310 6.993786 TGTAATATGAAACGAAATCTGCCA 57.006 33.333 0.00 0.00 0.00 4.92
6047 6329 3.055591 CCACTAAGCATGTCAGCTATCG 58.944 50.000 0.00 0.00 45.89 2.92
6313 6595 5.880054 AGATTTGAAGGTACCAATTGTCG 57.120 39.130 15.94 0.00 0.00 4.35
6319 6601 0.671163 GGTACCAATTGTCGGCGACA 60.671 55.000 36.29 36.29 41.09 4.35
6338 6620 2.093890 CAATGCAGTAATGTGCCTCCA 58.906 47.619 0.00 0.00 43.28 3.86
6513 6795 2.594592 GTTGGCCGTGGCACTTCT 60.595 61.111 16.72 0.00 44.11 2.85
6538 6820 2.419574 GCGTTAGGCACTGGAATCCTTA 60.420 50.000 0.00 0.00 41.52 2.69
6818 7103 5.890334 TGAAGTTTGGCAGTCTGTTAAAAG 58.110 37.500 0.93 0.00 0.00 2.27
6886 7185 8.602472 ACCTCTTACAAATTTGGCCAATATTA 57.398 30.769 21.26 4.13 0.00 0.98
7354 7663 4.163458 TCATATGGTAAAGGTCTTCGGCTT 59.837 41.667 2.13 0.00 0.00 4.35
7427 7736 9.905713 AAAGTTCATAGTTTATATCAGCTTCCA 57.094 29.630 0.00 0.00 0.00 3.53
7456 7765 9.994432 CTGTCTGAACTGGTTATATTTCAAATC 57.006 33.333 0.00 0.00 0.00 2.17
7457 7766 9.513906 TGTCTGAACTGGTTATATTTCAAATCA 57.486 29.630 0.00 0.00 0.00 2.57
7496 7805 3.922850 GGCGTACTTACTTTCTGTGTACC 59.077 47.826 0.00 0.00 32.39 3.34
7500 7809 4.682778 ACTTACTTTCTGTGTACCTGCA 57.317 40.909 0.00 0.00 0.00 4.41
7518 7827 4.341235 CCTGCATCATGATTTCTGACCATT 59.659 41.667 5.16 0.00 0.00 3.16
7523 7832 6.641314 GCATCATGATTTCTGACCATTGAATC 59.359 38.462 5.16 0.00 0.00 2.52
7524 7833 7.683463 GCATCATGATTTCTGACCATTGAATCA 60.683 37.037 5.16 3.48 0.00 2.57
7594 7905 2.250921 TACCGAGGATACCAAACCCA 57.749 50.000 0.00 0.00 37.17 4.51
7631 7942 4.193826 TCCATCTCAAACTGCTGTAGTC 57.806 45.455 0.00 0.00 39.18 2.59
7634 7945 5.658634 TCCATCTCAAACTGCTGTAGTCTAT 59.341 40.000 0.00 0.00 39.18 1.98
7636 7947 6.478344 CCATCTCAAACTGCTGTAGTCTATTC 59.522 42.308 0.00 0.00 39.18 1.75
7705 8019 2.602217 GCCCGCGAATTGTCATAATCAC 60.602 50.000 8.23 0.00 0.00 3.06
7969 8283 3.118038 TGGTAGTTTTGCAGAACAGAGGT 60.118 43.478 20.91 3.75 31.94 3.85
8048 8362 7.272978 AGTATTAGCGGTACTGAAATGAACAT 58.727 34.615 5.68 0.00 31.47 2.71
8071 8385 9.614792 ACATATAGTTCATTTTCCTTACTGGAC 57.385 33.333 0.00 0.00 46.14 4.02
8081 8395 2.023404 TCCTTACTGGACTAGATGCCCA 60.023 50.000 0.00 0.00 40.56 5.36
8107 8421 1.183549 TCGGAAGAGTGTAAGCCCTC 58.816 55.000 0.00 0.00 34.84 4.30
8298 8617 4.351111 GGTATCATATCAAGTTCCCCTGGT 59.649 45.833 0.00 0.00 0.00 4.00
8335 8654 8.197592 TGTACTCTACAGTTTTCCCTGAATTA 57.802 34.615 0.00 0.00 36.30 1.40
8336 8655 8.311836 TGTACTCTACAGTTTTCCCTGAATTAG 58.688 37.037 0.00 0.00 36.30 1.73
8353 8672 7.335422 CCTGAATTAGTGCTATGTTTGACTCTT 59.665 37.037 0.00 0.00 0.00 2.85
8407 8726 5.409643 AGTATGATTCAGCGGAAAATTCG 57.590 39.130 2.68 0.00 36.43 3.34
8485 8805 0.394216 TCAATTGGCCACCCATCTCG 60.394 55.000 3.88 0.00 41.78 4.04
8612 8932 0.617820 CTCGGGGGAAAGAGGAGGAA 60.618 60.000 0.00 0.00 0.00 3.36
8613 8933 0.908180 TCGGGGGAAAGAGGAGGAAC 60.908 60.000 0.00 0.00 0.00 3.62
8614 8934 1.911702 CGGGGGAAAGAGGAGGAACC 61.912 65.000 0.00 0.00 39.35 3.62
8615 8935 1.572689 GGGGGAAAGAGGAGGAACCC 61.573 65.000 0.00 0.00 40.05 4.11
8616 8936 0.845102 GGGGAAAGAGGAGGAACCCA 60.845 60.000 0.00 0.00 39.10 4.51
8624 8944 0.496841 AGGAGGAACCCAAGTACCCT 59.503 55.000 0.00 0.00 40.05 4.34
8660 8980 1.076533 TCGCTTGTCGGAATTCTCGC 61.077 55.000 5.23 5.00 39.05 5.03
8683 9003 3.420893 GACTGGTGGATGATTTGGAACA 58.579 45.455 0.00 0.00 0.00 3.18
8684 9004 3.157087 ACTGGTGGATGATTTGGAACAC 58.843 45.455 0.00 0.00 39.29 3.32
8771 9113 1.079875 GTTGCAATGCTTCATGGGCG 61.080 55.000 6.82 0.00 30.81 6.13
8868 9214 8.752005 TTTTTAGCTATCCAATGCTAGTCATT 57.248 30.769 0.00 6.58 45.82 2.57
8885 9231 6.121776 AGTCATTAAATGTGTGGACTGGTA 57.878 37.500 0.00 0.00 34.57 3.25
8950 9392 0.524862 CGGGGAAGTCCGTATATCCG 59.475 60.000 0.00 0.00 44.60 4.18
8958 9400 3.379445 CGTATATCCGGCCGGCCT 61.379 66.667 41.01 29.21 34.68 5.19
8962 9404 0.625316 TATATCCGGCCGGCCTACTA 59.375 55.000 41.01 27.80 34.68 1.82
8969 9411 1.336609 CGGCCGGCCTACTATTAGTTC 60.337 57.143 41.01 12.17 0.00 3.01
9006 9448 1.556911 AGACCATGTGTCCCACTCATC 59.443 52.381 9.80 0.00 45.68 2.92
9007 9449 1.556911 GACCATGTGTCCCACTCATCT 59.443 52.381 3.65 0.00 38.09 2.90
9008 9450 1.556911 ACCATGTGTCCCACTCATCTC 59.443 52.381 0.00 0.00 35.11 2.75
9009 9451 1.836166 CCATGTGTCCCACTCATCTCT 59.164 52.381 0.00 0.00 35.11 3.10
9010 9452 2.238144 CCATGTGTCCCACTCATCTCTT 59.762 50.000 0.00 0.00 35.11 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.627577 CCAACAAAATCATACTCCCTCCG 59.372 47.826 0.00 0.00 0.00 4.63
1 2 3.954258 CCCAACAAAATCATACTCCCTCC 59.046 47.826 0.00 0.00 0.00 4.30
2 3 4.600062 ACCCAACAAAATCATACTCCCTC 58.400 43.478 0.00 0.00 0.00 4.30
3 4 4.675063 ACCCAACAAAATCATACTCCCT 57.325 40.909 0.00 0.00 0.00 4.20
4 5 5.949952 AGTTACCCAACAAAATCATACTCCC 59.050 40.000 0.00 0.00 37.10 4.30
5 6 6.433093 ACAGTTACCCAACAAAATCATACTCC 59.567 38.462 0.00 0.00 37.10 3.85
6 7 7.448748 ACAGTTACCCAACAAAATCATACTC 57.551 36.000 0.00 0.00 37.10 2.59
7 8 7.286775 ACAACAGTTACCCAACAAAATCATACT 59.713 33.333 0.00 0.00 37.10 2.12
8 9 7.430441 ACAACAGTTACCCAACAAAATCATAC 58.570 34.615 0.00 0.00 37.10 2.39
9 10 7.285629 TGACAACAGTTACCCAACAAAATCATA 59.714 33.333 0.00 0.00 37.10 2.15
10 11 6.097554 TGACAACAGTTACCCAACAAAATCAT 59.902 34.615 0.00 0.00 37.10 2.45
11 12 5.419155 TGACAACAGTTACCCAACAAAATCA 59.581 36.000 0.00 0.00 37.10 2.57
12 13 5.897050 TGACAACAGTTACCCAACAAAATC 58.103 37.500 0.00 0.00 37.10 2.17
13 14 5.923733 TGACAACAGTTACCCAACAAAAT 57.076 34.783 0.00 0.00 37.10 1.82
14 15 5.723672 TTGACAACAGTTACCCAACAAAA 57.276 34.783 0.00 0.00 37.10 2.44
15 16 5.723672 TTTGACAACAGTTACCCAACAAA 57.276 34.783 0.00 0.00 37.10 2.83
16 17 5.244178 AGTTTTGACAACAGTTACCCAACAA 59.756 36.000 0.00 0.00 37.10 2.83
17 18 4.767928 AGTTTTGACAACAGTTACCCAACA 59.232 37.500 0.00 0.00 37.10 3.33
18 19 5.099575 CAGTTTTGACAACAGTTACCCAAC 58.900 41.667 0.00 0.00 34.67 3.77
19 20 4.767928 ACAGTTTTGACAACAGTTACCCAA 59.232 37.500 0.00 0.00 0.00 4.12
20 21 4.156922 CACAGTTTTGACAACAGTTACCCA 59.843 41.667 0.00 0.00 0.00 4.51
21 22 4.668289 CACAGTTTTGACAACAGTTACCC 58.332 43.478 0.00 0.00 0.00 3.69
22 23 4.102649 GCACAGTTTTGACAACAGTTACC 58.897 43.478 0.00 0.00 0.00 2.85
23 24 4.557301 GTGCACAGTTTTGACAACAGTTAC 59.443 41.667 13.17 0.00 0.00 2.50
24 25 4.457603 AGTGCACAGTTTTGACAACAGTTA 59.542 37.500 21.04 0.00 0.00 2.24
25 26 3.255642 AGTGCACAGTTTTGACAACAGTT 59.744 39.130 21.04 0.00 0.00 3.16
26 27 2.819608 AGTGCACAGTTTTGACAACAGT 59.180 40.909 21.04 0.00 0.00 3.55
27 28 3.492421 AGTGCACAGTTTTGACAACAG 57.508 42.857 21.04 0.00 0.00 3.16
28 29 3.254411 TGAAGTGCACAGTTTTGACAACA 59.746 39.130 21.04 0.00 0.00 3.33
29 30 3.832276 TGAAGTGCACAGTTTTGACAAC 58.168 40.909 21.04 0.00 0.00 3.32
30 31 3.755905 TCTGAAGTGCACAGTTTTGACAA 59.244 39.130 21.04 0.00 36.81 3.18
31 32 3.342719 TCTGAAGTGCACAGTTTTGACA 58.657 40.909 21.04 5.96 36.81 3.58
32 33 4.355543 TTCTGAAGTGCACAGTTTTGAC 57.644 40.909 21.04 1.55 36.81 3.18
33 34 4.380444 GGTTTCTGAAGTGCACAGTTTTGA 60.380 41.667 21.04 6.41 36.81 2.69
34 35 3.859386 GGTTTCTGAAGTGCACAGTTTTG 59.141 43.478 21.04 4.01 36.81 2.44
35 36 3.427503 CGGTTTCTGAAGTGCACAGTTTT 60.428 43.478 21.04 3.86 36.81 2.43
36 37 2.097466 CGGTTTCTGAAGTGCACAGTTT 59.903 45.455 21.04 4.29 36.81 2.66
37 38 1.670811 CGGTTTCTGAAGTGCACAGTT 59.329 47.619 21.04 5.15 36.81 3.16
38 39 1.299541 CGGTTTCTGAAGTGCACAGT 58.700 50.000 21.04 6.13 36.81 3.55
39 40 1.003545 CACGGTTTCTGAAGTGCACAG 60.004 52.381 21.04 8.13 36.80 3.66
40 41 1.013596 CACGGTTTCTGAAGTGCACA 58.986 50.000 21.04 0.00 0.00 4.57
41 42 1.003866 GACACGGTTTCTGAAGTGCAC 60.004 52.381 9.40 9.40 38.08 4.57
42 43 1.295792 GACACGGTTTCTGAAGTGCA 58.704 50.000 7.84 0.00 38.08 4.57
43 44 1.295792 TGACACGGTTTCTGAAGTGC 58.704 50.000 7.84 3.33 38.08 4.40
44 45 3.559655 TCATTGACACGGTTTCTGAAGTG 59.440 43.478 6.70 6.70 40.17 3.16
45 46 3.804036 TCATTGACACGGTTTCTGAAGT 58.196 40.909 0.00 0.00 0.00 3.01
46 47 3.809832 ACTCATTGACACGGTTTCTGAAG 59.190 43.478 0.00 0.00 0.00 3.02
47 48 3.804036 ACTCATTGACACGGTTTCTGAA 58.196 40.909 0.00 0.00 0.00 3.02
48 49 3.469008 ACTCATTGACACGGTTTCTGA 57.531 42.857 0.00 0.00 0.00 3.27
49 50 5.666969 TTTACTCATTGACACGGTTTCTG 57.333 39.130 0.00 0.00 0.00 3.02
50 51 6.370718 GGTATTTACTCATTGACACGGTTTCT 59.629 38.462 0.00 0.00 0.00 2.52
51 52 6.148150 TGGTATTTACTCATTGACACGGTTTC 59.852 38.462 0.00 0.00 0.00 2.78
52 53 5.998981 TGGTATTTACTCATTGACACGGTTT 59.001 36.000 0.00 0.00 0.00 3.27
53 54 5.553123 TGGTATTTACTCATTGACACGGTT 58.447 37.500 0.00 0.00 0.00 4.44
54 55 5.155278 TGGTATTTACTCATTGACACGGT 57.845 39.130 0.00 0.00 0.00 4.83
55 56 6.677781 AATGGTATTTACTCATTGACACGG 57.322 37.500 0.00 0.00 30.96 4.94
696 698 5.221880 TGTGTGCATGTTGAAAGAAATAGC 58.778 37.500 0.00 0.00 0.00 2.97
705 707 4.019792 AGTAGGATGTGTGCATGTTGAA 57.980 40.909 0.00 0.00 35.07 2.69
845 848 9.770097 TGAGAATGAAGGCTAGAAATACATAAG 57.230 33.333 0.00 0.00 0.00 1.73
856 859 8.728833 GGATTTGAATATGAGAATGAAGGCTAG 58.271 37.037 0.00 0.00 0.00 3.42
923 926 2.960819 ACAAGAAGATACCTCACGTGC 58.039 47.619 11.67 0.00 0.00 5.34
977 980 0.908910 AGATGATGCCCCGTACACAA 59.091 50.000 0.00 0.00 0.00 3.33
989 992 7.307811 CCAAATCACAGCACATACTAGATGATG 60.308 40.741 0.00 0.82 35.87 3.07
1021 1024 6.039616 TCAAACAAACAAAAATCTTCCTCCG 58.960 36.000 0.00 0.00 0.00 4.63
1131 1174 6.108687 TCCACTACAATCAGCAATAACTCTG 58.891 40.000 0.00 0.00 0.00 3.35
1133 1176 7.559590 AATCCACTACAATCAGCAATAACTC 57.440 36.000 0.00 0.00 0.00 3.01
1136 1179 6.096705 CCCAAATCCACTACAATCAGCAATAA 59.903 38.462 0.00 0.00 0.00 1.40
1137 1180 5.593909 CCCAAATCCACTACAATCAGCAATA 59.406 40.000 0.00 0.00 0.00 1.90
1138 1181 4.403432 CCCAAATCCACTACAATCAGCAAT 59.597 41.667 0.00 0.00 0.00 3.56
1150 1204 2.046314 CGACGGCCCAAATCCACT 60.046 61.111 0.00 0.00 0.00 4.00
1166 1220 2.541588 CCAGTTCACAAGTTTTGAGCCG 60.542 50.000 2.62 0.00 0.00 5.52
1207 1261 1.066858 ACTTCGCCGTCAGACATCAAT 60.067 47.619 0.41 0.00 0.00 2.57
1208 1262 0.317160 ACTTCGCCGTCAGACATCAA 59.683 50.000 0.41 0.00 0.00 2.57
1214 1273 3.744719 CCCGACTTCGCCGTCAGA 61.745 66.667 0.00 0.00 38.18 3.27
1258 1318 2.257067 CGACGGCGGCCAAAATTT 59.743 55.556 20.71 0.00 0.00 1.82
1321 1389 1.541147 ACACGCTAGTACGCTACCAAA 59.459 47.619 0.00 0.00 36.19 3.28
1345 1413 2.580815 CTCAGCATCGCCCACTGA 59.419 61.111 0.00 0.00 38.09 3.41
1544 1620 4.760204 CACCGTTAATTCTCTTTGTTCCCT 59.240 41.667 0.00 0.00 0.00 4.20
1651 1741 0.039256 CAAATGCACAACCACCTCCG 60.039 55.000 0.00 0.00 0.00 4.63
1665 1755 7.905604 TCCTAGTGTAACAAGATCACAAATG 57.094 36.000 0.00 0.00 41.43 2.32
1757 1848 3.902881 ACTGCAAGAGAACCATCTAGG 57.097 47.619 0.00 0.00 40.11 3.02
1839 1930 1.959899 GCATCACTCCACGCGTTCAG 61.960 60.000 10.22 11.22 0.00 3.02
1880 1971 6.463614 GGCCCATCATGTAGAGGATATCATAC 60.464 46.154 4.83 5.23 0.00 2.39
2241 2343 1.594293 GCACGCGGCATATACCTGT 60.594 57.895 12.47 0.00 43.97 4.00
2374 2476 6.017523 TGCATCTCGATTGTTCAGTTGTTAAA 60.018 34.615 0.00 0.00 0.00 1.52
2376 2478 4.994217 TGCATCTCGATTGTTCAGTTGTTA 59.006 37.500 0.00 0.00 0.00 2.41
2390 2492 1.676006 TCAACGATAGCTGCATCTCGA 59.324 47.619 20.11 7.66 42.67 4.04
2452 2554 3.820557 AGAGGTAAAACAGAGCAAAGCA 58.179 40.909 0.00 0.00 0.00 3.91
2494 2599 6.101650 AGTTCCTTTATTCCAGCAAAAAGG 57.898 37.500 6.39 6.39 46.14 3.11
2496 2601 7.069331 TCTGAAGTTCCTTTATTCCAGCAAAAA 59.931 33.333 0.00 0.00 0.00 1.94
2508 2613 7.039923 ACTGTCGATAAGTCTGAAGTTCCTTTA 60.040 37.037 0.00 0.00 0.00 1.85
2518 2623 5.723672 AGGAAAACTGTCGATAAGTCTGA 57.276 39.130 4.41 0.00 0.00 3.27
2519 2624 6.853720 TCTAGGAAAACTGTCGATAAGTCTG 58.146 40.000 4.41 0.00 0.00 3.51
2523 2628 5.897050 AGCTCTAGGAAAACTGTCGATAAG 58.103 41.667 0.00 0.00 0.00 1.73
2540 2645 3.319972 ACAGTAACACAAACGGAGCTCTA 59.680 43.478 14.64 0.00 0.00 2.43
2580 2685 8.195436 TCTAGAAAATGGATGTAAGTCCTAACG 58.805 37.037 0.00 0.00 39.12 3.18
2656 2761 9.530129 CGAGACATTAGACAAATAAACAACTTC 57.470 33.333 0.00 0.00 0.00 3.01
2768 2873 9.679661 TGGCTATATTGTGTCTTTTTATCAGAA 57.320 29.630 0.00 0.00 0.00 3.02
2821 2926 9.733556 GGTTCACCATGGACAATATACATATTA 57.266 33.333 21.47 0.00 32.23 0.98
2833 2938 1.074775 GGCTGGTTCACCATGGACA 59.925 57.895 21.47 8.10 46.46 4.02
2838 2943 2.765969 CCAGGGCTGGTTCACCAT 59.234 61.111 0.00 0.00 46.46 3.55
2885 2990 7.358066 GCACTAATGTGATGGTTTGATATCAG 58.642 38.462 5.39 0.00 46.55 2.90
2910 3015 4.204012 TGGCATATTTCTTACGGAAAGGG 58.796 43.478 0.61 0.00 45.61 3.95
2932 3037 6.985653 ATACACAGATAAGCAGAGTACCAT 57.014 37.500 0.00 0.00 0.00 3.55
2961 3066 1.839424 ATTGGTAACTTGGAGCTGGC 58.161 50.000 0.00 0.00 37.61 4.85
3037 3142 4.340894 TTTGTCGATCATTACTTGCTGC 57.659 40.909 0.00 0.00 0.00 5.25
3093 3199 6.650390 GGAAAATGGCAAAGTTTGTATGTGAT 59.350 34.615 16.70 0.00 0.00 3.06
3180 3286 2.022195 CCTGTCGGGTTCTTCGATCTA 58.978 52.381 0.00 0.00 38.93 1.98
3264 3370 8.159229 AGGGATTGGTACTGTAACTAGAAAAT 57.841 34.615 4.27 0.00 0.00 1.82
3529 3635 3.002656 CCGTGTATGTCAGCATGGAATTC 59.997 47.826 11.15 0.00 42.72 2.17
3588 3695 5.125356 TCTACAATATGATTGTGTGGGCAG 58.875 41.667 13.75 3.83 34.11 4.85
3745 3852 2.160721 CTAGGAGGAACTAGGCACCA 57.839 55.000 0.00 0.00 41.55 4.17
3795 4068 3.044156 AGAAGAATCATAGCTCCTGGCA 58.956 45.455 0.00 0.00 44.79 4.92
3885 4158 8.888579 AATAAAGACAGGTTCCAGTATAATCG 57.111 34.615 0.00 0.00 0.00 3.34
4133 4407 6.058183 AGAATATGAACCTACTGCATGGAAC 58.942 40.000 7.42 2.61 0.00 3.62
4209 4486 9.733556 AAGAAAACAAAAAGGAAATGGTAAGTT 57.266 25.926 0.00 0.00 0.00 2.66
4210 4487 9.161629 CAAGAAAACAAAAAGGAAATGGTAAGT 57.838 29.630 0.00 0.00 0.00 2.24
4454 4731 3.526931 ACATGACCACTATGAACTCCG 57.473 47.619 0.00 0.00 0.00 4.63
4637 4914 5.185828 GGACATGGGAAATAAAGATATGGGC 59.814 44.000 0.00 0.00 0.00 5.36
4651 4928 1.410083 GGCAATAGCAGGACATGGGAA 60.410 52.381 0.00 0.00 44.61 3.97
4653 4930 0.825010 GGGCAATAGCAGGACATGGG 60.825 60.000 0.00 0.00 44.61 4.00
4743 5021 9.990868 AATTTCCCAACAGAGGTAGTAAATTAT 57.009 29.630 0.00 0.00 0.00 1.28
4744 5022 9.238368 CAATTTCCCAACAGAGGTAGTAAATTA 57.762 33.333 0.00 0.00 0.00 1.40
4788 5066 6.091441 GTCAAAGATACATGTTGGAGACTGTC 59.909 42.308 2.30 0.00 0.00 3.51
5070 5352 5.499139 TTTCCTAACTTTGACTTGCAGTG 57.501 39.130 0.00 0.00 0.00 3.66
5072 5354 7.706179 TCAAAATTTCCTAACTTTGACTTGCAG 59.294 33.333 0.00 0.00 33.90 4.41
5149 5431 6.489700 TGCACCATTCTTCTACTTCATTTCAA 59.510 34.615 0.00 0.00 0.00 2.69
5256 5538 9.908152 GAACAAATACAATTAGCCAGTAGTTTT 57.092 29.630 0.00 0.00 0.00 2.43
5483 5765 2.831685 AACTTGTGTCTCGGTGCATA 57.168 45.000 0.00 0.00 0.00 3.14
5514 5796 7.915508 TGTACAGGCTACATTGATATTTTTCG 58.084 34.615 0.00 0.00 0.00 3.46
5582 5864 7.094377 GGAATCAAATTAGTTGGAAGCTGTACA 60.094 37.037 0.00 0.00 37.85 2.90
5700 5982 3.259123 CCATTTTGGGGAGGTTTTCTGAG 59.741 47.826 0.00 0.00 32.67 3.35
5724 6006 2.203294 AGTGGCGGTCAACCCAAC 60.203 61.111 0.00 0.00 31.90 3.77
5730 6012 3.059982 CTCAGGAGTGGCGGTCAA 58.940 61.111 0.00 0.00 0.00 3.18
5734 6016 3.368190 CTGAGCTCAGGAGTGGCGG 62.368 68.421 32.30 7.60 40.20 6.13
5851 6133 8.591114 AGTACATAGTTTAGGTTGCTCTTAGA 57.409 34.615 0.00 0.00 0.00 2.10
5941 6223 9.906660 CTCGCTCTGTAAAGAAATATAAGATCT 57.093 33.333 0.00 0.00 0.00 2.75
5942 6224 9.685828 ACTCGCTCTGTAAAGAAATATAAGATC 57.314 33.333 0.00 0.00 0.00 2.75
5944 6226 9.947669 GTACTCGCTCTGTAAAGAAATATAAGA 57.052 33.333 0.00 0.00 0.00 2.10
5945 6227 9.731819 TGTACTCGCTCTGTAAAGAAATATAAG 57.268 33.333 0.00 0.00 0.00 1.73
5947 6229 9.678941 CATGTACTCGCTCTGTAAAGAAATATA 57.321 33.333 0.00 0.00 0.00 0.86
5948 6230 7.653713 CCATGTACTCGCTCTGTAAAGAAATAT 59.346 37.037 0.00 0.00 0.00 1.28
5949 6231 6.978659 CCATGTACTCGCTCTGTAAAGAAATA 59.021 38.462 0.00 0.00 0.00 1.40
5950 6232 5.812642 CCATGTACTCGCTCTGTAAAGAAAT 59.187 40.000 0.00 0.00 0.00 2.17
5951 6233 5.047590 TCCATGTACTCGCTCTGTAAAGAAA 60.048 40.000 0.00 0.00 0.00 2.52
5952 6234 4.461431 TCCATGTACTCGCTCTGTAAAGAA 59.539 41.667 0.00 0.00 0.00 2.52
5953 6235 4.014406 TCCATGTACTCGCTCTGTAAAGA 58.986 43.478 0.00 0.00 0.00 2.52
5954 6236 4.371855 TCCATGTACTCGCTCTGTAAAG 57.628 45.455 0.00 0.00 0.00 1.85
5955 6237 4.461431 TCTTCCATGTACTCGCTCTGTAAA 59.539 41.667 0.00 0.00 0.00 2.01
5956 6238 4.014406 TCTTCCATGTACTCGCTCTGTAA 58.986 43.478 0.00 0.00 0.00 2.41
5957 6239 3.617284 TCTTCCATGTACTCGCTCTGTA 58.383 45.455 0.00 0.00 0.00 2.74
5958 6240 2.425312 CTCTTCCATGTACTCGCTCTGT 59.575 50.000 0.00 0.00 0.00 3.41
5959 6241 2.425312 ACTCTTCCATGTACTCGCTCTG 59.575 50.000 0.00 0.00 0.00 3.35
5960 6242 2.685897 GACTCTTCCATGTACTCGCTCT 59.314 50.000 0.00 0.00 0.00 4.09
5961 6243 2.539953 CGACTCTTCCATGTACTCGCTC 60.540 54.545 0.00 0.00 0.00 5.03
5962 6244 1.402259 CGACTCTTCCATGTACTCGCT 59.598 52.381 0.00 0.00 0.00 4.93
5963 6245 1.400846 TCGACTCTTCCATGTACTCGC 59.599 52.381 0.00 0.00 0.00 5.03
5964 6246 3.622828 CATCGACTCTTCCATGTACTCG 58.377 50.000 0.00 0.00 0.00 4.18
5965 6247 3.181486 TGCATCGACTCTTCCATGTACTC 60.181 47.826 0.00 0.00 0.00 2.59
5966 6248 2.760650 TGCATCGACTCTTCCATGTACT 59.239 45.455 0.00 0.00 0.00 2.73
5967 6249 2.860735 GTGCATCGACTCTTCCATGTAC 59.139 50.000 0.00 0.00 0.00 2.90
6018 6300 3.691118 TGACATGCTTAGTGGCAGATTTC 59.309 43.478 0.00 0.00 45.75 2.17
6028 6310 4.392921 AACGATAGCTGACATGCTTAGT 57.607 40.909 0.00 2.04 43.74 2.24
6043 6325 5.935206 ACCAATATGACACACACAAACGATA 59.065 36.000 0.00 0.00 0.00 2.92
6047 6329 6.072112 AGAACCAATATGACACACACAAAC 57.928 37.500 0.00 0.00 0.00 2.93
6313 6595 1.795162 GCACATTACTGCATTGTCGCC 60.795 52.381 0.00 0.00 37.11 5.54
6319 6601 2.512692 TGGAGGCACATTACTGCATT 57.487 45.000 0.00 0.00 39.08 3.56
6513 6795 1.534336 TTCCAGTGCCTAACGCGGTA 61.534 55.000 12.47 7.63 42.08 4.02
6538 6820 1.002888 AGCACTGACATACTTGCAGCT 59.997 47.619 0.00 0.00 37.44 4.24
6714 6999 5.039480 CTGAATTTTCAGCAGTGTACCTG 57.961 43.478 7.34 6.91 46.97 4.00
6886 7185 1.558294 TGCATTCCTGTCAGAGAGCAT 59.442 47.619 0.00 0.00 0.00 3.79
7354 7663 9.391006 AGTAAGTTGTAACAAATGAACAGAAGA 57.609 29.630 0.00 0.00 0.00 2.87
7427 7736 7.112122 TGAAATATAACCAGTTCAGACAGCAT 58.888 34.615 0.00 0.00 0.00 3.79
7456 7765 1.734477 CAGTTCGTCGGCAGGAGTG 60.734 63.158 0.00 0.00 0.00 3.51
7457 7766 2.651361 CAGTTCGTCGGCAGGAGT 59.349 61.111 0.00 0.00 0.00 3.85
7496 7805 5.067283 TCAATGGTCAGAAATCATGATGCAG 59.933 40.000 9.46 2.10 0.00 4.41
7500 7809 7.891498 TGATTCAATGGTCAGAAATCATGAT 57.109 32.000 1.18 1.18 0.00 2.45
7523 7832 5.307204 TGGGCTCCTCAAAAATCAAAATTG 58.693 37.500 0.00 0.00 0.00 2.32
7524 7833 5.565455 TGGGCTCCTCAAAAATCAAAATT 57.435 34.783 0.00 0.00 0.00 1.82
7594 7905 5.013079 TGAGATGGAATAGTTGTGGTCTTGT 59.987 40.000 0.00 0.00 0.00 3.16
7661 7974 9.059260 GGGCCGAAAAATATGATAAGTACTTAA 57.941 33.333 18.88 4.50 0.00 1.85
7662 7975 7.385752 CGGGCCGAAAAATATGATAAGTACTTA 59.614 37.037 24.41 17.41 0.00 2.24
7682 7996 1.433053 TTATGACAATTCGCGGGCCG 61.433 55.000 24.35 24.35 38.61 6.13
7705 8019 5.896073 AGTTCTCCCAGAAATATACCCTG 57.104 43.478 0.00 0.00 35.75 4.45
7969 8283 0.394762 GGTTGCCTGCTCCATGATGA 60.395 55.000 0.00 0.00 0.00 2.92
8071 8385 2.300152 TCCGATAAGCTTGGGCATCTAG 59.700 50.000 9.86 0.00 41.70 2.43
8081 8395 4.434520 GCTTACACTCTTCCGATAAGCTT 58.565 43.478 3.48 3.48 42.80 3.74
8113 8427 9.692325 AAGAACTTTCCTATCAATGCTAAGAAT 57.308 29.630 0.00 0.00 0.00 2.40
8298 8617 8.958119 AACTGTAGAGTACAATGTTTTCTTCA 57.042 30.769 0.00 0.00 38.38 3.02
8335 8654 4.238514 GTCGAAGAGTCAAACATAGCACT 58.761 43.478 0.00 0.00 36.95 4.40
8336 8655 3.987868 TGTCGAAGAGTCAAACATAGCAC 59.012 43.478 0.00 0.00 36.95 4.40
8353 8672 1.929230 TTGAAGCTTTGTCGTGTCGA 58.071 45.000 0.00 0.00 0.00 4.20
8428 8748 0.460109 TCCACGATCTTGACATGCCG 60.460 55.000 0.00 0.00 0.00 5.69
8485 8805 1.432514 TCAACGCATCTGTTCTGCTC 58.567 50.000 0.00 0.00 37.48 4.26
8548 8868 2.086251 ATTGTGGTTGCAAGGCACCG 62.086 55.000 0.00 0.00 38.71 4.94
8612 8932 1.652947 CCACTGTAGGGTACTTGGGT 58.347 55.000 0.00 0.00 32.29 4.51
8613 8933 0.909623 CCCACTGTAGGGTACTTGGG 59.090 60.000 8.92 8.92 44.24 4.12
8660 8980 1.065491 TCCAAATCATCCACCAGTCGG 60.065 52.381 0.00 0.00 38.77 4.79
8707 9027 1.267806 CCATCGTATTGCCTGCCATTC 59.732 52.381 0.00 0.00 0.00 2.67
8851 9197 8.839343 CACACATTTAATGACTAGCATTGGATA 58.161 33.333 12.28 1.31 46.38 2.59
8868 9214 2.898612 TCCGTACCAGTCCACACATTTA 59.101 45.455 0.00 0.00 0.00 1.40
8949 9391 0.677842 AACTAATAGTAGGCCGGCCG 59.322 55.000 38.88 24.25 41.95 6.13
8950 9392 1.336609 CGAACTAATAGTAGGCCGGCC 60.337 57.143 39.29 39.29 0.00 6.13
8951 9393 1.339291 ACGAACTAATAGTAGGCCGGC 59.661 52.381 21.18 21.18 33.37 6.13
8953 9395 4.040376 GTGAACGAACTAATAGTAGGCCG 58.960 47.826 0.00 7.00 34.48 6.13
8954 9396 5.002464 TGTGAACGAACTAATAGTAGGCC 57.998 43.478 0.00 0.00 0.00 5.19
8958 9400 9.346005 TGGAGATATGTGAACGAACTAATAGTA 57.654 33.333 0.00 0.00 0.00 1.82
8962 9404 6.873997 TGTGGAGATATGTGAACGAACTAAT 58.126 36.000 0.00 0.00 0.00 1.73
8969 9411 3.119137 TGGTCTGTGGAGATATGTGAACG 60.119 47.826 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.