Multiple sequence alignment - TraesCS2B01G530400

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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 TraesCS2B01G530400 chr2B 100.000 3362 0 0 1 3362 725581285 725577924 0.000000e+00 6209.0
1 TraesCS2B01G530400 chr2B 100.000 2434 0 0 3728 6161 725577558 725575125 0.000000e+00 4495.0
2 TraesCS2B01G530400 chr2B 91.667 192 15 1 4234 4424 795598485 795598294 1.320000e-66 265.0
3 TraesCS2B01G530400 chr2B 91.429 70 4 1 5578 5645 71396490 71396559 1.830000e-15 95.3
4 TraesCS2B01G530400 chr2B 93.182 44 3 0 5575 5618 177083656 177083699 1.430000e-06 65.8
5 TraesCS2B01G530400 chr2D 95.788 2825 101 9 1 2824 596555115 596552308 0.000000e+00 4542.0
6 TraesCS2B01G530400 chr2D 97.260 1241 30 3 4414 5652 596550910 596549672 0.000000e+00 2100.0
7 TraesCS2B01G530400 chr2D 96.614 502 4 4 3736 4233 596551403 596550911 0.000000e+00 821.0
8 TraesCS2B01G530400 chr2D 93.983 482 22 4 2882 3362 596552303 596551828 0.000000e+00 723.0
9 TraesCS2B01G530400 chr2D 91.684 493 20 12 5670 6161 596549266 596548794 0.000000e+00 664.0
10 TraesCS2B01G530400 chr2D 91.525 59 3 2 5580 5637 326216609 326216552 5.120000e-11 80.5
11 TraesCS2B01G530400 chr2D 87.692 65 2 4 5578 5637 428662624 428662687 3.080000e-08 71.3
12 TraesCS2B01G530400 chr2D 94.444 36 2 0 2828 2863 577544724 577544689 8.630000e-04 56.5
13 TraesCS2B01G530400 chr2D 100.000 28 0 0 2848 2875 99197493 99197466 1.100000e-02 52.8
14 TraesCS2B01G530400 chr2A 93.133 2825 104 28 7 2779 730618412 730615626 0.000000e+00 4060.0
15 TraesCS2B01G530400 chr2A 90.941 850 42 14 4725 5556 730614200 730613368 0.000000e+00 1110.0
16 TraesCS2B01G530400 chr2A 95.870 460 15 2 3774 4233 730615084 730614629 0.000000e+00 741.0
17 TraesCS2B01G530400 chr2A 86.860 449 25 18 2915 3362 730615575 730615160 7.230000e-129 472.0
18 TraesCS2B01G530400 chr2A 90.734 259 18 4 4416 4669 730614624 730614367 2.130000e-89 340.0
19 TraesCS2B01G530400 chr2A 82.367 414 28 20 5753 6161 730612826 730612453 9.970000e-83 318.0
20 TraesCS2B01G530400 chr5D 94.536 183 10 0 4233 4415 401323327 401323145 3.640000e-72 283.0
21 TraesCS2B01G530400 chr5D 100.000 29 0 0 2829 2857 223960568 223960596 3.000000e-03 54.7
22 TraesCS2B01G530400 chr7D 94.972 179 9 0 4234 4412 17234601 17234423 1.310000e-71 281.0
23 TraesCS2B01G530400 chr7D 94.413 179 10 0 4234 4412 499739589 499739411 6.080000e-70 276.0
24 TraesCS2B01G530400 chr7B 93.194 191 12 1 4222 4412 12181404 12181593 4.700000e-71 279.0
25 TraesCS2B01G530400 chr7B 91.667 60 5 0 5578 5637 53250579 53250638 3.960000e-12 84.2
26 TraesCS2B01G530400 chr7B 96.970 33 0 1 2829 2861 443651147 443651116 3.000000e-03 54.7
27 TraesCS2B01G530400 chr6D 94.857 175 9 0 4238 4412 7488539 7488365 2.190000e-69 274.0
28 TraesCS2B01G530400 chr6D 87.850 107 9 4 1529 1631 111569452 111569346 8.390000e-24 122.0
29 TraesCS2B01G530400 chr3B 93.407 182 12 0 4234 4415 226083172 226082991 2.830000e-68 270.0
30 TraesCS2B01G530400 chr4A 93.855 179 10 1 4234 4412 735616180 735616357 1.020000e-67 268.0
31 TraesCS2B01G530400 chrUn 94.220 173 10 0 4240 4412 262705403 262705575 1.320000e-66 265.0
32 TraesCS2B01G530400 chrUn 78.862 123 25 1 2460 2581 293363190 293363312 1.420000e-11 82.4
33 TraesCS2B01G530400 chrUn 78.862 123 25 1 2460 2581 303118505 303118383 1.420000e-11 82.4
34 TraesCS2B01G530400 chrUn 78.862 123 25 1 2460 2581 322941820 322941698 1.420000e-11 82.4
35 TraesCS2B01G530400 chrUn 78.862 123 25 1 2460 2581 341924122 341924000 1.420000e-11 82.4
36 TraesCS2B01G530400 chrUn 94.444 36 2 0 2829 2864 41687640 41687675 8.630000e-04 56.5
37 TraesCS2B01G530400 chr6B 87.395 119 9 5 1519 1631 200511462 200511344 1.390000e-26 132.0
38 TraesCS2B01G530400 chr6A 89.524 105 8 2 1519 1620 136542093 136542197 5.010000e-26 130.0
39 TraesCS2B01G530400 chr1D 82.143 112 18 2 2471 2581 246042255 246042145 1.830000e-15 95.3
40 TraesCS2B01G530400 chr3A 92.857 56 4 0 5582 5637 210325924 210325869 1.420000e-11 82.4
41 TraesCS2B01G530400 chr3A 95.455 44 2 0 5578 5621 32446145 32446188 3.080000e-08 71.3
42 TraesCS2B01G530400 chr5B 93.478 46 2 1 2829 2873 537532960 537532915 3.990000e-07 67.6
43 TraesCS2B01G530400 chr5B 85.714 56 4 3 2780 2835 273140188 273140239 8.630000e-04 56.5
44 TraesCS2B01G530400 chr1B 93.333 45 3 0 2829 2873 24501985 24501941 3.990000e-07 67.6
45 TraesCS2B01G530400 chr1B 97.297 37 1 0 2781 2817 24501946 24501982 5.160000e-06 63.9
46 TraesCS2B01G530400 chr1B 94.737 38 2 0 2829 2866 94558748 94558785 6.670000e-05 60.2
47 TraesCS2B01G530400 chr4B 93.182 44 3 0 5578 5621 577918578 577918535 1.430000e-06 65.8
48 TraesCS2B01G530400 chr4B 97.297 37 1 0 2781 2817 646978758 646978794 5.160000e-06 63.9
49 TraesCS2B01G530400 chr4B 90.698 43 4 0 2775 2817 659335742 659335784 2.400000e-04 58.4
50 TraesCS2B01G530400 chr5A 100.000 30 0 0 2828 2857 257315276 257315247 8.630000e-04 56.5
51 TraesCS2B01G530400 chr5A 92.308 39 3 0 2829 2867 298808133 298808171 8.630000e-04 56.5
52 TraesCS2B01G530400 chr7A 100.000 28 0 0 1656 1683 170630644 170630671 1.100000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G530400 chr2B 725575125 725581285 6160 True 5352.0 6209 100.000000 1 6161 2 chr2B.!!$R2 6160
1 TraesCS2B01G530400 chr2D 596548794 596555115 6321 True 1770.0 4542 95.065800 1 6161 5 chr2D.!!$R4 6160
2 TraesCS2B01G530400 chr2A 730612453 730618412 5959 True 1173.5 4060 89.984167 7 6161 6 chr2A.!!$R1 6154

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
891 913 0.032678 CAGTGAGTGAGCGACCAAGT 59.967 55.0 0.00 0.00 0.00 3.16 F
1494 1519 1.732417 GCTACCGGACCTACTTCCCG 61.732 65.0 9.46 0.00 42.64 5.14 F
1762 1787 1.909376 CGTGTCTGATCGACCGATTT 58.091 50.0 6.36 0.00 42.13 2.17 F
2586 2641 0.814457 ACACCAACACACACGCAAAT 59.186 45.0 0.00 0.00 0.00 2.32 F
3154 3228 0.036952 TCTCTCCTCCTTTGCTTGCG 60.037 55.0 0.00 0.00 0.00 4.85 F
4339 4469 0.039437 GCCTCGCTAATAGCACGCTA 60.039 55.0 13.15 0.39 42.58 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2553 2608 0.179006 TGGTGTTGGCTGTGTGCATA 60.179 50.0 0.00 0.00 45.15 3.14 R
2586 2641 0.881118 GCTTTTTGCCGGTCTGATCA 59.119 50.0 1.90 0.00 35.15 2.92 R
2856 2915 2.040012 ACAAGTACTCTCTCCGTCCTGA 59.960 50.0 0.00 0.00 0.00 3.86 R
4320 4450 0.039437 TAGCGTGCTATTAGCGAGGC 60.039 55.0 17.41 17.41 46.26 4.70 R
5073 5340 0.825010 CCAAGCCTGGCTGTTCTTGT 60.825 55.0 24.16 0.52 39.62 3.16 R
5576 5851 0.105039 CATTACTGGACGGAGGGAGC 59.895 60.0 0.00 0.00 0.00 4.70 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
34 35 1.571919 CTGTAGATGGGTAGCAACGC 58.428 55.000 0.00 0.00 38.96 4.84
89 94 1.474498 CGTACTTCCCTGGCCATTACC 60.474 57.143 5.51 0.00 0.00 2.85
230 242 4.677832 CACATTATACATGCGTGCTACGTA 59.322 41.667 5.64 0.00 44.73 3.57
231 243 4.678287 ACATTATACATGCGTGCTACGTAC 59.322 41.667 5.64 0.00 44.73 3.67
232 244 1.750351 ATACATGCGTGCTACGTACG 58.250 50.000 15.01 15.01 44.73 3.67
233 245 0.447406 TACATGCGTGCTACGTACGT 59.553 50.000 25.98 25.98 44.73 3.57
344 359 0.963962 AAAGCTCGAAGACGGTGGTA 59.036 50.000 0.00 0.00 40.21 3.25
349 364 0.538057 TCGAAGACGGTGGTAGTGGT 60.538 55.000 0.00 0.00 40.21 4.16
484 506 4.156477 CCCCTCACCAAACTCCAATTAAA 58.844 43.478 0.00 0.00 0.00 1.52
485 507 4.220602 CCCCTCACCAAACTCCAATTAAAG 59.779 45.833 0.00 0.00 0.00 1.85
585 607 1.771255 ACAGATACAGCTTGATCCCCC 59.229 52.381 1.68 0.00 0.00 5.40
586 608 2.053244 CAGATACAGCTTGATCCCCCT 58.947 52.381 1.68 0.00 0.00 4.79
771 793 2.031333 CAGAAACAAGCTGCTTGGAGAC 60.031 50.000 36.97 25.95 44.81 3.36
778 800 1.900351 CTGCTTGGAGACCCATCGA 59.100 57.895 0.00 0.00 43.12 3.59
886 908 1.005630 AAGCCAGTGAGTGAGCGAC 60.006 57.895 0.00 0.00 0.00 5.19
891 913 0.032678 CAGTGAGTGAGCGACCAAGT 59.967 55.000 0.00 0.00 0.00 3.16
928 950 2.048597 TACTTGCACCGCGTCCTG 60.049 61.111 4.92 0.00 0.00 3.86
1141 1166 4.699522 GGGAGCACGACCACCACC 62.700 72.222 0.00 0.00 0.00 4.61
1142 1167 3.936203 GGAGCACGACCACCACCA 61.936 66.667 0.00 0.00 0.00 4.17
1143 1168 2.665185 GAGCACGACCACCACCAC 60.665 66.667 0.00 0.00 0.00 4.16
1278 1303 2.367202 CCCCACCTCGCACCACTAT 61.367 63.158 0.00 0.00 0.00 2.12
1494 1519 1.732417 GCTACCGGACCTACTTCCCG 61.732 65.000 9.46 0.00 42.64 5.14
1620 1645 2.743928 GAGCACCACTCCAAGGCG 60.744 66.667 0.00 0.00 39.75 5.52
1762 1787 1.909376 CGTGTCTGATCGACCGATTT 58.091 50.000 6.36 0.00 42.13 2.17
1787 1815 8.359875 TGCTATTCTAAAGAGAGATGGATAGG 57.640 38.462 0.00 0.00 31.77 2.57
1920 1948 4.494091 ACAATCCACCTCATCCTGTTAG 57.506 45.455 0.00 0.00 0.00 2.34
1967 1995 7.416326 GCCTTCAAATTACCCATTTAGTTCGAT 60.416 37.037 0.00 0.00 32.90 3.59
2092 2120 3.694566 ACAAAGACGAAATTATGGCCTCC 59.305 43.478 3.32 0.00 0.00 4.30
2095 2123 3.963129 AGACGAAATTATGGCCTCCAAA 58.037 40.909 3.32 0.00 36.95 3.28
2198 2227 3.442076 AGTTAGATTCCTCTTCCACGGT 58.558 45.455 0.00 0.00 32.66 4.83
2279 2308 3.851403 CGAAAATTTCGCATACCCTGTTG 59.149 43.478 15.33 0.00 46.97 3.33
2538 2569 6.071616 ACAAAACACAATGAGTAACACTTGGT 60.072 34.615 0.00 0.00 0.00 3.67
2553 2608 6.054860 ACACTTGGTCTCTGCATAGTTAAT 57.945 37.500 0.00 0.00 0.00 1.40
2586 2641 0.814457 ACACCAACACACACGCAAAT 59.186 45.000 0.00 0.00 0.00 2.32
2618 2673 2.119457 CAAAAAGCAAAGCCAGACGTC 58.881 47.619 7.70 7.70 0.00 4.34
2699 2758 3.997021 CGTAAGACTTGGCTTGACAATCT 59.003 43.478 0.00 0.00 43.02 2.40
2783 2842 8.107095 TCAGGCTCTACAATTTTGTATTACCTT 58.893 33.333 12.18 1.86 42.26 3.50
2787 2846 8.448615 GCTCTACAATTTTGTATTACCTTCGTT 58.551 33.333 3.76 0.00 42.26 3.85
2790 2849 6.604930 ACAATTTTGTATTACCTTCGTTCCG 58.395 36.000 0.00 0.00 40.16 4.30
2864 2923 7.611213 ATTTAAGACAAGTAATTCAGGACGG 57.389 36.000 0.00 0.00 0.00 4.79
2865 2924 4.884668 AAGACAAGTAATTCAGGACGGA 57.115 40.909 0.00 0.00 0.00 4.69
2866 2925 4.457834 AGACAAGTAATTCAGGACGGAG 57.542 45.455 0.00 0.00 0.00 4.63
2867 2926 4.087182 AGACAAGTAATTCAGGACGGAGA 58.913 43.478 0.00 0.00 0.00 3.71
2868 2927 4.158764 AGACAAGTAATTCAGGACGGAGAG 59.841 45.833 0.00 0.00 0.00 3.20
2869 2928 4.087182 ACAAGTAATTCAGGACGGAGAGA 58.913 43.478 0.00 0.00 0.00 3.10
2870 2929 4.158764 ACAAGTAATTCAGGACGGAGAGAG 59.841 45.833 0.00 0.00 0.00 3.20
2871 2930 3.970842 AGTAATTCAGGACGGAGAGAGT 58.029 45.455 0.00 0.00 0.00 3.24
2872 2931 5.113446 AGTAATTCAGGACGGAGAGAGTA 57.887 43.478 0.00 0.00 0.00 2.59
2873 2932 4.883006 AGTAATTCAGGACGGAGAGAGTAC 59.117 45.833 0.00 0.00 0.00 2.73
2874 2933 3.655615 ATTCAGGACGGAGAGAGTACT 57.344 47.619 0.00 0.00 31.85 2.73
2875 2934 3.436577 TTCAGGACGGAGAGAGTACTT 57.563 47.619 0.00 0.00 28.49 2.24
2876 2935 2.712709 TCAGGACGGAGAGAGTACTTG 58.287 52.381 0.00 0.00 28.49 3.16
2877 2936 2.040012 TCAGGACGGAGAGAGTACTTGT 59.960 50.000 0.00 0.00 28.49 3.16
2878 2937 2.820787 CAGGACGGAGAGAGTACTTGTT 59.179 50.000 0.00 0.00 28.49 2.83
2879 2938 4.008330 CAGGACGGAGAGAGTACTTGTTA 58.992 47.826 0.00 0.00 28.49 2.41
2880 2939 4.095185 CAGGACGGAGAGAGTACTTGTTAG 59.905 50.000 0.00 0.00 28.49 2.34
2886 2945 5.447548 CGGAGAGAGTACTTGTTAGTAGTGC 60.448 48.000 0.00 0.00 39.96 4.40
2903 2962 7.365840 AGTAGTGCACAATTTTAAGTAGCTC 57.634 36.000 21.04 0.00 0.00 4.09
3008 3081 7.428020 CGTGATTCAACCATCCAAATATGATT 58.572 34.615 0.00 0.00 0.00 2.57
3054 3128 4.672587 TCTACATATTTCGCTCTGCCTT 57.327 40.909 0.00 0.00 0.00 4.35
3066 3140 3.142174 GCTCTGCCTTTACTTGACAAGT 58.858 45.455 23.61 23.61 45.40 3.16
3068 3142 4.130118 CTCTGCCTTTACTTGACAAGTGT 58.870 43.478 27.44 8.08 42.84 3.55
3069 3143 4.127171 TCTGCCTTTACTTGACAAGTGTC 58.873 43.478 27.44 13.33 42.84 3.67
3154 3228 0.036952 TCTCTCCTCCTTTGCTTGCG 60.037 55.000 0.00 0.00 0.00 4.85
3155 3229 1.642952 CTCTCCTCCTTTGCTTGCGC 61.643 60.000 0.00 0.00 0.00 6.09
3238 3313 3.735237 AACAGTGTGACCTGTCTGTAG 57.265 47.619 0.00 0.00 44.74 2.74
3253 3328 1.142465 CTGTAGATGCATTGGCCTCCT 59.858 52.381 3.32 0.00 40.13 3.69
3295 3370 6.113411 GCTACTTTCTCCCTAAGTATTGCAA 58.887 40.000 0.00 0.00 37.44 4.08
3296 3371 6.598064 GCTACTTTCTCCCTAAGTATTGCAAA 59.402 38.462 1.71 0.00 37.44 3.68
3760 3886 1.133792 GGGCTGTGGCTGTGGTAATAT 60.134 52.381 0.00 0.00 38.73 1.28
3761 3887 2.105821 GGGCTGTGGCTGTGGTAATATA 59.894 50.000 0.00 0.00 38.73 0.86
3762 3888 3.244911 GGGCTGTGGCTGTGGTAATATAT 60.245 47.826 0.00 0.00 38.73 0.86
3764 3890 5.514136 GGGCTGTGGCTGTGGTAATATATAA 60.514 44.000 0.00 0.00 38.73 0.98
3765 3891 6.180472 GGCTGTGGCTGTGGTAATATATAAT 58.820 40.000 0.00 0.00 38.73 1.28
3766 3892 7.335627 GGCTGTGGCTGTGGTAATATATAATA 58.664 38.462 0.00 0.00 38.73 0.98
3767 3893 7.827236 GGCTGTGGCTGTGGTAATATATAATAA 59.173 37.037 0.00 0.00 38.73 1.40
3768 3894 9.396022 GCTGTGGCTGTGGTAATATATAATAAT 57.604 33.333 0.00 0.00 35.22 1.28
4036 4162 1.797046 CATCATTGCCTAGCTACTGCG 59.203 52.381 6.13 0.00 45.42 5.18
4096 4226 7.725818 TTGATCTCTGATCATGCACTAATTC 57.274 36.000 10.52 0.00 0.00 2.17
4169 4299 4.692625 GCCAGCGATAAACTGATGATACAT 59.307 41.667 0.00 0.00 37.32 2.29
4235 4365 8.772306 CACATTAGTATTTCATGTGTATGCAC 57.228 34.615 7.03 7.03 41.90 4.57
4236 4366 7.857389 CACATTAGTATTTCATGTGTATGCACC 59.143 37.037 11.66 0.00 44.65 5.01
4237 4367 6.597262 TTAGTATTTCATGTGTATGCACCG 57.403 37.500 11.66 2.91 44.65 4.94
4238 4368 4.765273 AGTATTTCATGTGTATGCACCGA 58.235 39.130 11.66 5.33 44.65 4.69
4239 4369 5.182487 AGTATTTCATGTGTATGCACCGAA 58.818 37.500 11.66 10.99 44.65 4.30
4240 4370 5.645929 AGTATTTCATGTGTATGCACCGAAA 59.354 36.000 22.00 22.00 43.57 3.46
4241 4371 4.837896 TTTCATGTGTATGCACCGAAAA 57.162 36.364 19.34 11.28 44.65 2.29
4242 4372 4.837896 TTCATGTGTATGCACCGAAAAA 57.162 36.364 11.66 0.00 44.65 1.94
4270 4400 1.582502 CGCTATAACGCCGCTAATAGC 59.417 52.381 13.04 13.04 42.10 2.97
4271 4401 2.602878 GCTATAACGCCGCTAATAGCA 58.397 47.619 13.15 0.00 43.98 3.49
4272 4402 2.344741 GCTATAACGCCGCTAATAGCAC 59.655 50.000 13.15 2.74 43.98 4.40
4273 4403 1.415374 ATAACGCCGCTAATAGCACG 58.585 50.000 18.94 18.94 42.58 5.34
4274 4404 1.210545 TAACGCCGCTAATAGCACGC 61.211 55.000 20.02 15.33 42.58 5.34
4275 4405 2.658593 CGCCGCTAATAGCACGCT 60.659 61.111 13.15 0.00 42.58 5.07
4276 4406 1.371267 CGCCGCTAATAGCACGCTA 60.371 57.895 13.15 0.39 42.58 4.26
4277 4407 0.732880 CGCCGCTAATAGCACGCTAT 60.733 55.000 13.15 5.72 42.58 2.97
4278 4408 1.466866 CGCCGCTAATAGCACGCTATA 60.467 52.381 13.15 1.16 42.58 1.31
4279 4409 2.186076 GCCGCTAATAGCACGCTATAG 58.814 52.381 13.15 10.32 42.58 1.31
4280 4410 2.186076 CCGCTAATAGCACGCTATAGC 58.814 52.381 15.09 15.09 42.58 2.97
4281 4411 2.415491 CCGCTAATAGCACGCTATAGCA 60.415 50.000 23.99 4.83 42.58 3.49
4282 4412 3.439293 CGCTAATAGCACGCTATAGCAT 58.561 45.455 23.99 6.50 42.58 3.79
4283 4413 4.497507 CCGCTAATAGCACGCTATAGCATA 60.498 45.833 23.99 11.14 42.58 3.14
4284 4414 5.215903 CGCTAATAGCACGCTATAGCATAT 58.784 41.667 23.99 12.75 42.58 1.78
4285 4415 6.371389 CGCTAATAGCACGCTATAGCATATA 58.629 40.000 23.99 11.13 42.58 0.86
4286 4416 6.521477 CGCTAATAGCACGCTATAGCATATAG 59.479 42.308 23.99 14.95 42.58 1.31
4287 4417 7.571428 CGCTAATAGCACGCTATAGCATATAGA 60.571 40.741 23.99 5.24 42.58 1.98
4288 4418 8.076781 GCTAATAGCACGCTATAGCATATAGAA 58.923 37.037 23.99 3.88 41.89 2.10
4289 4419 9.952188 CTAATAGCACGCTATAGCATATAGAAA 57.048 33.333 23.99 3.44 42.21 2.52
4291 4421 9.823647 AATAGCACGCTATAGCATATAGAAAAT 57.176 29.630 23.99 3.35 42.21 1.82
4292 4422 7.763172 AGCACGCTATAGCATATAGAAAATC 57.237 36.000 23.99 0.50 42.21 2.17
4293 4423 6.473778 AGCACGCTATAGCATATAGAAAATCG 59.526 38.462 23.99 5.79 42.21 3.34
4294 4424 6.253727 GCACGCTATAGCATATAGAAAATCGT 59.746 38.462 23.99 6.41 42.21 3.73
4295 4425 7.513814 GCACGCTATAGCATATAGAAAATCGTC 60.514 40.741 23.99 1.37 42.21 4.20
4296 4426 7.698550 CACGCTATAGCATATAGAAAATCGTCT 59.301 37.037 23.99 0.00 42.21 4.18
4297 4427 7.911205 ACGCTATAGCATATAGAAAATCGTCTC 59.089 37.037 23.99 0.00 42.21 3.36
4298 4428 7.110903 CGCTATAGCATATAGAAAATCGTCTCG 59.889 40.741 23.99 0.00 42.21 4.04
4299 4429 7.096803 GCTATAGCATATAGAAAATCGTCTCGC 60.097 40.741 20.01 0.00 41.59 5.03
4300 4430 5.127693 AGCATATAGAAAATCGTCTCGCT 57.872 39.130 0.00 0.00 0.00 4.93
4301 4431 6.255596 AGCATATAGAAAATCGTCTCGCTA 57.744 37.500 0.00 0.00 0.00 4.26
4302 4432 6.678878 AGCATATAGAAAATCGTCTCGCTAA 58.321 36.000 0.00 0.00 0.00 3.09
4303 4433 7.145985 AGCATATAGAAAATCGTCTCGCTAAA 58.854 34.615 0.00 0.00 0.00 1.85
4304 4434 7.815068 AGCATATAGAAAATCGTCTCGCTAAAT 59.185 33.333 0.00 0.00 0.00 1.40
4305 4435 9.073368 GCATATAGAAAATCGTCTCGCTAAATA 57.927 33.333 0.00 0.00 0.00 1.40
4310 4440 8.420374 AGAAAATCGTCTCGCTAAATAAATCA 57.580 30.769 0.00 0.00 0.00 2.57
4311 4441 8.879759 AGAAAATCGTCTCGCTAAATAAATCAA 58.120 29.630 0.00 0.00 0.00 2.57
4312 4442 9.651718 GAAAATCGTCTCGCTAAATAAATCAAT 57.348 29.630 0.00 0.00 0.00 2.57
4313 4443 8.993852 AAATCGTCTCGCTAAATAAATCAATG 57.006 30.769 0.00 0.00 0.00 2.82
4314 4444 7.715265 ATCGTCTCGCTAAATAAATCAATGT 57.285 32.000 0.00 0.00 0.00 2.71
4315 4445 8.812147 ATCGTCTCGCTAAATAAATCAATGTA 57.188 30.769 0.00 0.00 0.00 2.29
4316 4446 8.057812 TCGTCTCGCTAAATAAATCAATGTAC 57.942 34.615 0.00 0.00 0.00 2.90
4317 4447 7.703197 TCGTCTCGCTAAATAAATCAATGTACA 59.297 33.333 0.00 0.00 0.00 2.90
4318 4448 8.325282 CGTCTCGCTAAATAAATCAATGTACAA 58.675 33.333 0.00 0.00 0.00 2.41
4321 4451 8.781067 TCGCTAAATAAATCAATGTACAATGC 57.219 30.769 6.02 0.00 0.00 3.56
4322 4452 7.860373 TCGCTAAATAAATCAATGTACAATGCC 59.140 33.333 6.02 0.00 0.00 4.40
4323 4453 7.862372 CGCTAAATAAATCAATGTACAATGCCT 59.138 33.333 6.02 0.00 0.00 4.75
4324 4454 9.185192 GCTAAATAAATCAATGTACAATGCCTC 57.815 33.333 6.02 0.00 0.00 4.70
4325 4455 9.385902 CTAAATAAATCAATGTACAATGCCTCG 57.614 33.333 6.02 0.00 0.00 4.63
4326 4456 3.698029 AATCAATGTACAATGCCTCGC 57.302 42.857 6.02 0.00 0.00 5.03
4327 4457 2.401583 TCAATGTACAATGCCTCGCT 57.598 45.000 6.02 0.00 0.00 4.93
4328 4458 3.535280 TCAATGTACAATGCCTCGCTA 57.465 42.857 6.02 0.00 0.00 4.26
4329 4459 3.867857 TCAATGTACAATGCCTCGCTAA 58.132 40.909 6.02 0.00 0.00 3.09
4330 4460 4.450976 TCAATGTACAATGCCTCGCTAAT 58.549 39.130 6.02 0.00 0.00 1.73
4331 4461 5.606505 TCAATGTACAATGCCTCGCTAATA 58.393 37.500 6.02 0.00 0.00 0.98
4332 4462 5.696270 TCAATGTACAATGCCTCGCTAATAG 59.304 40.000 6.02 0.00 0.00 1.73
4333 4463 3.390135 TGTACAATGCCTCGCTAATAGC 58.610 45.455 1.41 1.41 38.02 2.97
4334 4464 2.620251 ACAATGCCTCGCTAATAGCA 57.380 45.000 13.15 0.00 42.58 3.49
4335 4465 2.213499 ACAATGCCTCGCTAATAGCAC 58.787 47.619 13.15 0.00 42.58 4.40
4336 4466 1.193203 CAATGCCTCGCTAATAGCACG 59.807 52.381 13.15 2.14 42.58 5.34
4337 4467 0.946221 ATGCCTCGCTAATAGCACGC 60.946 55.000 13.15 10.17 42.58 5.34
4338 4468 1.300233 GCCTCGCTAATAGCACGCT 60.300 57.895 13.15 0.00 42.58 5.07
4339 4469 0.039437 GCCTCGCTAATAGCACGCTA 60.039 55.000 13.15 0.39 42.58 4.26
4340 4470 1.402984 GCCTCGCTAATAGCACGCTAT 60.403 52.381 13.15 5.72 42.58 2.97
4341 4471 2.159421 GCCTCGCTAATAGCACGCTATA 60.159 50.000 13.15 1.16 42.58 1.31
4342 4472 3.686128 CCTCGCTAATAGCACGCTATAG 58.314 50.000 13.15 10.32 42.58 1.31
4343 4473 3.102276 CTCGCTAATAGCACGCTATAGC 58.898 50.000 15.09 15.09 42.58 2.97
4369 4499 7.451281 CGTTATAGCACGCTAATAGCATATT 57.549 36.000 13.15 0.00 42.58 1.28
4370 4500 7.895870 CGTTATAGCACGCTAATAGCATATTT 58.104 34.615 13.15 0.00 42.58 1.40
4371 4501 8.380644 CGTTATAGCACGCTAATAGCATATTTT 58.619 33.333 13.15 0.00 42.58 1.82
4375 4505 7.133891 AGCACGCTAATAGCATATTTTTAGG 57.866 36.000 13.15 0.00 42.58 2.69
4376 4506 6.149474 AGCACGCTAATAGCATATTTTTAGGG 59.851 38.462 13.15 1.60 42.58 3.53
4377 4507 6.072673 GCACGCTAATAGCATATTTTTAGGGT 60.073 38.462 13.15 2.21 44.01 4.34
4378 4508 7.519002 CACGCTAATAGCATATTTTTAGGGTC 58.481 38.462 13.15 0.00 42.42 4.46
4379 4509 6.653740 ACGCTAATAGCATATTTTTAGGGTCC 59.346 38.462 13.15 0.00 41.27 4.46
4380 4510 6.653320 CGCTAATAGCATATTTTTAGGGTCCA 59.347 38.462 13.15 0.00 42.58 4.02
4381 4511 7.360946 CGCTAATAGCATATTTTTAGGGTCCAC 60.361 40.741 13.15 0.00 42.58 4.02
4382 4512 6.877611 AATAGCATATTTTTAGGGTCCACG 57.122 37.500 0.00 0.00 0.00 4.94
4383 4513 2.949644 AGCATATTTTTAGGGTCCACGC 59.050 45.455 0.00 0.00 0.00 5.34
4384 4514 2.949644 GCATATTTTTAGGGTCCACGCT 59.050 45.455 1.52 1.52 42.15 5.07
4385 4515 4.131596 GCATATTTTTAGGGTCCACGCTA 58.868 43.478 0.00 0.00 39.91 4.26
4386 4516 4.760204 GCATATTTTTAGGGTCCACGCTAT 59.240 41.667 4.48 0.00 40.40 2.97
4387 4517 5.240844 GCATATTTTTAGGGTCCACGCTATT 59.759 40.000 4.48 0.00 40.40 1.73
4388 4518 6.238925 GCATATTTTTAGGGTCCACGCTATTT 60.239 38.462 4.48 0.00 40.40 1.40
4389 4519 7.683463 GCATATTTTTAGGGTCCACGCTATTTT 60.683 37.037 4.48 0.00 40.40 1.82
4390 4520 5.632244 TTTTTAGGGTCCACGCTATTTTC 57.368 39.130 4.48 0.00 40.40 2.29
4391 4521 4.563140 TTTAGGGTCCACGCTATTTTCT 57.437 40.909 4.48 0.00 40.40 2.52
4392 4522 2.403252 AGGGTCCACGCTATTTTCTG 57.597 50.000 0.00 0.00 37.38 3.02
4393 4523 1.628846 AGGGTCCACGCTATTTTCTGT 59.371 47.619 0.00 0.00 37.38 3.41
4394 4524 2.835764 AGGGTCCACGCTATTTTCTGTA 59.164 45.455 0.00 0.00 37.38 2.74
4395 4525 3.118738 AGGGTCCACGCTATTTTCTGTAG 60.119 47.826 0.00 0.00 37.38 2.74
4396 4526 2.608090 GGTCCACGCTATTTTCTGTAGC 59.392 50.000 0.00 0.00 40.83 3.58
4404 4534 5.659048 GCTATTTTCTGTAGCGTGCTATT 57.341 39.130 4.68 0.00 35.68 1.73
4405 4535 6.049263 GCTATTTTCTGTAGCGTGCTATTT 57.951 37.500 4.68 0.00 35.68 1.40
4406 4536 6.487103 GCTATTTTCTGTAGCGTGCTATTTT 58.513 36.000 4.68 0.00 35.68 1.82
4407 4537 6.967199 GCTATTTTCTGTAGCGTGCTATTTTT 59.033 34.615 4.68 0.00 35.68 1.94
4561 4693 1.394917 CGAAGGAAGTCAAAGCCATCG 59.605 52.381 0.00 0.00 36.72 3.84
4585 4717 2.169789 CGATGCCGCTGACAAGAGG 61.170 63.158 0.00 0.00 45.67 3.69
4612 4744 2.737376 GCCAGCAAAGCAGCAAGC 60.737 61.111 0.00 0.00 46.19 4.01
4971 5238 1.002888 CATGGTCTTCACCTGCAGAGT 59.997 52.381 17.39 8.77 44.17 3.24
5073 5340 2.441410 TCAAATATCGGCCAAGTGCAA 58.559 42.857 2.24 0.00 43.89 4.08
5255 5524 6.309251 GTCGATCGGATCATTTCTTTCTATCC 59.691 42.308 16.41 0.00 34.08 2.59
5374 5647 6.737254 CCAAAAGGTGGTACTAGTACAATG 57.263 41.667 29.38 15.72 43.20 2.82
5426 5699 6.294361 TCATGTACTTGGCAGTAGTTATGT 57.706 37.500 8.74 0.00 36.09 2.29
5546 5821 6.070881 TGCTTTTTATGGACCATATTGCACTT 60.071 34.615 15.05 0.00 0.00 3.16
5556 5831 6.756542 GGACCATATTGCACTTTAATCCAAAC 59.243 38.462 0.00 0.00 0.00 2.93
5559 5834 7.602265 ACCATATTGCACTTTAATCCAAACAAC 59.398 33.333 0.00 0.00 0.00 3.32
5652 5927 8.679725 TGGAGGGAGTAGATATTAACATAGTCT 58.320 37.037 0.00 0.00 0.00 3.24
5653 5928 9.536510 GGAGGGAGTAGATATTAACATAGTCTT 57.463 37.037 0.00 0.00 0.00 3.01
5826 6534 6.084326 ACAAAATTCATTGCCGACTTAACT 57.916 33.333 0.00 0.00 33.52 2.24
5867 6575 2.002586 CACGGCTGATCACGATTTCTT 58.997 47.619 12.18 0.00 0.00 2.52
6007 6715 4.206477 TCTTGCAAGCACATCTTAGCTA 57.794 40.909 21.99 0.00 40.90 3.32
6008 6716 4.186926 TCTTGCAAGCACATCTTAGCTAG 58.813 43.478 21.99 0.00 40.90 3.42
6009 6717 2.283298 TGCAAGCACATCTTAGCTAGC 58.717 47.619 6.62 6.62 40.90 3.42
6010 6718 2.093288 TGCAAGCACATCTTAGCTAGCT 60.093 45.455 23.12 23.12 40.90 3.32
6051 6759 8.504005 AGATCCTTGTAAACTAACAATTTGTCG 58.496 33.333 1.83 0.24 38.61 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 94 7.491696 ACGCATATATTCATGAGATGTGATCTG 59.508 37.037 20.30 10.41 40.38 2.90
233 245 2.891941 ATCGAGGGGGTACGCACGTA 62.892 60.000 12.45 0.00 45.96 3.57
337 352 2.047274 CCAGCACCACTACCACCG 60.047 66.667 0.00 0.00 0.00 4.94
387 402 2.808206 CCTCCGTATCCACTGGCCC 61.808 68.421 0.00 0.00 0.00 5.80
393 415 2.027751 GCTCGCCTCCGTATCCAC 59.972 66.667 0.00 0.00 35.54 4.02
484 506 2.143419 GGGATGGGAGCGATGGACT 61.143 63.158 0.00 0.00 0.00 3.85
485 507 2.427753 GGGATGGGAGCGATGGAC 59.572 66.667 0.00 0.00 0.00 4.02
585 607 1.528309 GAGAGGGCGAGGGAGAGAG 60.528 68.421 0.00 0.00 0.00 3.20
586 608 2.598467 GAGAGGGCGAGGGAGAGA 59.402 66.667 0.00 0.00 0.00 3.10
778 800 2.362503 TGGTGGAGCTCGACGGAT 60.363 61.111 20.78 0.00 0.00 4.18
928 950 0.927029 AGGGGTTAGGAATGGAAGCC 59.073 55.000 0.00 0.00 0.00 4.35
1720 1745 0.724549 TTCATCAACGAATTCCGGCG 59.275 50.000 0.00 0.00 43.93 6.46
1762 1787 7.952930 ACCTATCCATCTCTCTTTAGAATAGCA 59.047 37.037 0.00 0.00 0.00 3.49
1787 1815 2.288273 ACTCAACACGGCTCTACAAGAC 60.288 50.000 0.00 0.00 0.00 3.01
1920 1948 2.159467 ATTTTTGCGATCGAACGAGC 57.841 45.000 21.57 8.45 35.09 5.03
1967 1995 8.924511 ATCTCAAAACTTTCCTACTCATTCAA 57.075 30.769 0.00 0.00 0.00 2.69
2009 2037 3.490933 CGATGTTGGTATCACGATCCAGT 60.491 47.826 0.00 0.00 32.63 4.00
2279 2308 6.877611 TTTATTGAGGGAGAACAGTGAAAC 57.122 37.500 0.00 0.00 0.00 2.78
2333 2362 6.613755 ATTGTACAGTACACCAGTTGTTTC 57.386 37.500 13.26 0.00 39.91 2.78
2495 2526 9.167311 GTGTTTTGTATTCTCCTGATACTTCAT 57.833 33.333 0.00 0.00 0.00 2.57
2501 2532 9.166173 CTCATTGTGTTTTGTATTCTCCTGATA 57.834 33.333 0.00 0.00 0.00 2.15
2509 2540 9.730420 AAGTGTTACTCATTGTGTTTTGTATTC 57.270 29.630 0.00 0.00 0.00 1.75
2553 2608 0.179006 TGGTGTTGGCTGTGTGCATA 60.179 50.000 0.00 0.00 45.15 3.14
2586 2641 0.881118 GCTTTTTGCCGGTCTGATCA 59.119 50.000 1.90 0.00 35.15 2.92
2618 2673 3.752412 CATGAGTGCACAACCAGTATG 57.248 47.619 21.04 8.34 0.00 2.39
2699 2758 2.512692 ATCTTGCTTGCCCACATGTA 57.487 45.000 0.00 0.00 0.00 2.29
2760 2819 7.065443 ACGAAGGTAATACAAAATTGTAGAGCC 59.935 37.037 11.28 11.44 45.80 4.70
2814 2873 9.601810 TTTATCTAGATACACCCATATGTGTCT 57.398 33.333 12.12 9.63 46.15 3.41
2838 2897 8.512138 CCGTCCTGAATTACTTGTCTTAAATTT 58.488 33.333 0.00 0.00 0.00 1.82
2839 2898 7.881232 TCCGTCCTGAATTACTTGTCTTAAATT 59.119 33.333 0.00 0.00 0.00 1.82
2840 2899 7.391620 TCCGTCCTGAATTACTTGTCTTAAAT 58.608 34.615 0.00 0.00 0.00 1.40
2841 2900 6.761312 TCCGTCCTGAATTACTTGTCTTAAA 58.239 36.000 0.00 0.00 0.00 1.52
2842 2901 6.209986 TCTCCGTCCTGAATTACTTGTCTTAA 59.790 38.462 0.00 0.00 0.00 1.85
2843 2902 5.713389 TCTCCGTCCTGAATTACTTGTCTTA 59.287 40.000 0.00 0.00 0.00 2.10
2844 2903 4.527038 TCTCCGTCCTGAATTACTTGTCTT 59.473 41.667 0.00 0.00 0.00 3.01
2845 2904 4.087182 TCTCCGTCCTGAATTACTTGTCT 58.913 43.478 0.00 0.00 0.00 3.41
2846 2905 4.158025 TCTCTCCGTCCTGAATTACTTGTC 59.842 45.833 0.00 0.00 0.00 3.18
2847 2906 4.087182 TCTCTCCGTCCTGAATTACTTGT 58.913 43.478 0.00 0.00 0.00 3.16
2848 2907 4.158764 ACTCTCTCCGTCCTGAATTACTTG 59.841 45.833 0.00 0.00 0.00 3.16
2849 2908 4.345854 ACTCTCTCCGTCCTGAATTACTT 58.654 43.478 0.00 0.00 0.00 2.24
2850 2909 3.970842 ACTCTCTCCGTCCTGAATTACT 58.029 45.455 0.00 0.00 0.00 2.24
2851 2910 4.883006 AGTACTCTCTCCGTCCTGAATTAC 59.117 45.833 0.00 0.00 0.00 1.89
2852 2911 5.113446 AGTACTCTCTCCGTCCTGAATTA 57.887 43.478 0.00 0.00 0.00 1.40
2853 2912 3.970842 AGTACTCTCTCCGTCCTGAATT 58.029 45.455 0.00 0.00 0.00 2.17
2854 2913 3.655615 AGTACTCTCTCCGTCCTGAAT 57.344 47.619 0.00 0.00 0.00 2.57
2855 2914 3.082548 CAAGTACTCTCTCCGTCCTGAA 58.917 50.000 0.00 0.00 0.00 3.02
2856 2915 2.040012 ACAAGTACTCTCTCCGTCCTGA 59.960 50.000 0.00 0.00 0.00 3.86
2857 2916 2.438411 ACAAGTACTCTCTCCGTCCTG 58.562 52.381 0.00 0.00 0.00 3.86
2858 2917 2.883122 ACAAGTACTCTCTCCGTCCT 57.117 50.000 0.00 0.00 0.00 3.85
2859 2918 4.009002 ACTAACAAGTACTCTCTCCGTCC 58.991 47.826 0.00 0.00 0.00 4.79
2860 2919 5.874261 ACTACTAACAAGTACTCTCTCCGTC 59.126 44.000 0.00 0.00 0.00 4.79
2861 2920 5.642919 CACTACTAACAAGTACTCTCTCCGT 59.357 44.000 0.00 0.00 0.00 4.69
2862 2921 5.447548 GCACTACTAACAAGTACTCTCTCCG 60.448 48.000 0.00 0.00 0.00 4.63
2863 2922 5.415077 TGCACTACTAACAAGTACTCTCTCC 59.585 44.000 0.00 0.00 0.00 3.71
2864 2923 6.072618 TGTGCACTACTAACAAGTACTCTCTC 60.073 42.308 19.41 0.00 0.00 3.20
2865 2924 5.768662 TGTGCACTACTAACAAGTACTCTCT 59.231 40.000 19.41 0.00 0.00 3.10
2866 2925 6.010294 TGTGCACTACTAACAAGTACTCTC 57.990 41.667 19.41 0.00 0.00 3.20
2867 2926 6.401047 TTGTGCACTACTAACAAGTACTCT 57.599 37.500 19.41 0.00 30.62 3.24
2868 2927 7.653767 AATTGTGCACTACTAACAAGTACTC 57.346 36.000 19.41 0.00 37.24 2.59
2869 2928 8.446599 AAAATTGTGCACTACTAACAAGTACT 57.553 30.769 19.41 0.00 37.24 2.73
2872 2931 8.899771 ACTTAAAATTGTGCACTACTAACAAGT 58.100 29.630 19.41 14.95 37.24 3.16
2875 2934 8.500773 GCTACTTAAAATTGTGCACTACTAACA 58.499 33.333 19.41 0.00 0.00 2.41
2876 2935 8.718734 AGCTACTTAAAATTGTGCACTACTAAC 58.281 33.333 19.41 0.00 0.00 2.34
2877 2936 8.842358 AGCTACTTAAAATTGTGCACTACTAA 57.158 30.769 19.41 3.87 0.00 2.24
2878 2937 8.092068 TGAGCTACTTAAAATTGTGCACTACTA 58.908 33.333 19.41 1.09 0.00 1.82
2879 2938 6.934645 TGAGCTACTTAAAATTGTGCACTACT 59.065 34.615 19.41 0.00 0.00 2.57
2880 2939 7.129109 TGAGCTACTTAAAATTGTGCACTAC 57.871 36.000 19.41 0.00 0.00 2.73
2977 3050 2.292267 GATGGTTGAATCACGGAGCAT 58.708 47.619 0.00 0.00 33.38 3.79
3008 3081 7.443302 AAGGAGGAGATCACATGAATCTTTA 57.557 36.000 13.92 0.00 0.00 1.85
3078 3152 5.747197 CGTATAAGTGTTCCCTACATGTGAC 59.253 44.000 9.11 0.23 39.39 3.67
3111 3185 2.557920 AGGAGCAACTCAAAGGACAG 57.442 50.000 0.00 0.00 31.08 3.51
3154 3228 3.912496 AAAATAAATGGCAAGGAGGGC 57.088 42.857 0.00 0.00 0.00 5.19
3155 3229 3.940852 GCAAAAATAAATGGCAAGGAGGG 59.059 43.478 0.00 0.00 0.00 4.30
3253 3328 3.988976 AGCCATGCTTCTCTGACTTTA 57.011 42.857 0.00 0.00 33.89 1.85
3295 3370 3.242712 CGTTCGTACGTGGTACAAACTTT 59.757 43.478 16.05 0.00 44.16 2.66
3296 3371 2.788786 CGTTCGTACGTGGTACAAACTT 59.211 45.455 16.05 0.00 44.16 2.66
3760 3886 8.941977 GTCTGTCCAACACAACACATTATTATA 58.058 33.333 0.00 0.00 33.31 0.98
3761 3887 7.446931 TGTCTGTCCAACACAACACATTATTAT 59.553 33.333 0.00 0.00 33.31 1.28
3762 3888 6.768381 TGTCTGTCCAACACAACACATTATTA 59.232 34.615 0.00 0.00 33.31 0.98
3764 3890 5.129634 TGTCTGTCCAACACAACACATTAT 58.870 37.500 0.00 0.00 33.31 1.28
3765 3891 4.518249 TGTCTGTCCAACACAACACATTA 58.482 39.130 0.00 0.00 33.31 1.90
3766 3892 3.351740 TGTCTGTCCAACACAACACATT 58.648 40.909 0.00 0.00 33.31 2.71
3767 3893 2.945008 CTGTCTGTCCAACACAACACAT 59.055 45.455 0.00 0.00 33.31 3.21
3768 3894 2.355197 CTGTCTGTCCAACACAACACA 58.645 47.619 0.00 0.00 33.31 3.72
3769 3895 1.064060 GCTGTCTGTCCAACACAACAC 59.936 52.381 0.00 0.00 33.31 3.32
3770 3896 1.378531 GCTGTCTGTCCAACACAACA 58.621 50.000 0.00 0.00 33.31 3.33
3771 3897 0.304705 CGCTGTCTGTCCAACACAAC 59.695 55.000 0.00 0.00 33.31 3.32
3772 3898 0.107897 ACGCTGTCTGTCCAACACAA 60.108 50.000 0.00 0.00 33.31 3.33
4096 4226 6.651975 AATCCTAATCCTAGGTAAGACACG 57.348 41.667 9.08 0.00 44.70 4.49
4169 4299 1.908619 AGTAGGGACACATGTGCATGA 59.091 47.619 25.68 4.90 41.20 3.07
4250 4380 1.582502 GCTATTAGCGGCGTTATAGCG 59.417 52.381 23.43 4.42 37.00 4.26
4251 4381 2.344741 GTGCTATTAGCGGCGTTATAGC 59.655 50.000 27.31 27.31 46.26 2.97
4252 4382 2.592897 CGTGCTATTAGCGGCGTTATAG 59.407 50.000 18.29 13.57 46.26 1.31
4253 4383 2.587956 CGTGCTATTAGCGGCGTTATA 58.412 47.619 18.29 3.30 46.26 0.98
4254 4384 1.415374 CGTGCTATTAGCGGCGTTAT 58.585 50.000 18.29 2.16 46.26 1.89
4255 4385 1.210545 GCGTGCTATTAGCGGCGTTA 61.211 55.000 23.58 3.34 46.26 3.18
4256 4386 2.522638 GCGTGCTATTAGCGGCGTT 61.523 57.895 23.58 4.68 46.26 4.84
4257 4387 2.067091 TAGCGTGCTATTAGCGGCGT 62.067 55.000 23.58 16.42 46.26 5.68
4258 4388 0.732880 ATAGCGTGCTATTAGCGGCG 60.733 55.000 20.72 20.72 46.26 6.46
4259 4389 2.186076 CTATAGCGTGCTATTAGCGGC 58.814 52.381 18.62 18.55 46.26 6.53
4260 4390 2.186076 GCTATAGCGTGCTATTAGCGG 58.814 52.381 18.62 6.68 46.26 5.52
4261 4391 2.863739 TGCTATAGCGTGCTATTAGCG 58.136 47.619 18.62 7.48 44.30 4.26
4262 4392 7.585867 TCTATATGCTATAGCGTGCTATTAGC 58.414 38.462 26.43 21.07 45.83 3.09
4263 4393 9.952188 TTTCTATATGCTATAGCGTGCTATTAG 57.048 33.333 26.43 17.73 45.83 1.73
4265 4395 9.823647 ATTTTCTATATGCTATAGCGTGCTATT 57.176 29.630 26.43 10.41 45.83 1.73
4266 4396 9.469807 GATTTTCTATATGCTATAGCGTGCTAT 57.530 33.333 26.43 17.65 45.83 2.97
4267 4397 7.644157 CGATTTTCTATATGCTATAGCGTGCTA 59.356 37.037 26.43 16.86 45.83 3.49
4268 4398 6.473778 CGATTTTCTATATGCTATAGCGTGCT 59.526 38.462 26.43 16.66 45.83 4.40
4269 4399 6.253727 ACGATTTTCTATATGCTATAGCGTGC 59.746 38.462 26.43 2.18 45.83 5.34
4270 4400 7.698550 AGACGATTTTCTATATGCTATAGCGTG 59.301 37.037 26.43 12.19 45.83 5.34
4271 4401 7.763356 AGACGATTTTCTATATGCTATAGCGT 58.237 34.615 22.53 22.53 45.83 5.07
4272 4402 7.110903 CGAGACGATTTTCTATATGCTATAGCG 59.889 40.741 19.55 5.29 45.83 4.26
4273 4403 7.096803 GCGAGACGATTTTCTATATGCTATAGC 60.097 40.741 18.18 18.18 42.50 2.97
4274 4404 8.126074 AGCGAGACGATTTTCTATATGCTATAG 58.874 37.037 0.00 0.00 0.00 1.31
4275 4405 7.986562 AGCGAGACGATTTTCTATATGCTATA 58.013 34.615 0.00 0.00 0.00 1.31
4276 4406 6.857956 AGCGAGACGATTTTCTATATGCTAT 58.142 36.000 0.00 0.00 0.00 2.97
4277 4407 6.255596 AGCGAGACGATTTTCTATATGCTA 57.744 37.500 0.00 0.00 0.00 3.49
4278 4408 5.127693 AGCGAGACGATTTTCTATATGCT 57.872 39.130 0.00 0.00 0.00 3.79
4279 4409 6.929587 TTAGCGAGACGATTTTCTATATGC 57.070 37.500 0.00 0.00 0.00 3.14
4284 4414 9.524106 TGATTTATTTAGCGAGACGATTTTCTA 57.476 29.630 0.00 0.00 0.00 2.10
4285 4415 8.420374 TGATTTATTTAGCGAGACGATTTTCT 57.580 30.769 0.00 0.00 0.00 2.52
4286 4416 9.651718 ATTGATTTATTTAGCGAGACGATTTTC 57.348 29.630 0.00 0.00 0.00 2.29
4287 4417 9.438291 CATTGATTTATTTAGCGAGACGATTTT 57.562 29.630 0.00 0.00 0.00 1.82
4288 4418 8.612619 ACATTGATTTATTTAGCGAGACGATTT 58.387 29.630 0.00 0.00 0.00 2.17
4289 4419 8.142994 ACATTGATTTATTTAGCGAGACGATT 57.857 30.769 0.00 0.00 0.00 3.34
4290 4420 7.715265 ACATTGATTTATTTAGCGAGACGAT 57.285 32.000 0.00 0.00 0.00 3.73
4291 4421 7.703197 TGTACATTGATTTATTTAGCGAGACGA 59.297 33.333 0.00 0.00 0.00 4.20
4292 4422 7.837505 TGTACATTGATTTATTTAGCGAGACG 58.162 34.615 0.00 0.00 0.00 4.18
4295 4425 8.895845 GCATTGTACATTGATTTATTTAGCGAG 58.104 33.333 19.36 0.00 0.00 5.03
4296 4426 7.860373 GGCATTGTACATTGATTTATTTAGCGA 59.140 33.333 19.36 0.00 0.00 4.93
4297 4427 7.862372 AGGCATTGTACATTGATTTATTTAGCG 59.138 33.333 19.36 0.00 0.00 4.26
4298 4428 9.185192 GAGGCATTGTACATTGATTTATTTAGC 57.815 33.333 19.36 2.30 0.00 3.09
4299 4429 9.385902 CGAGGCATTGTACATTGATTTATTTAG 57.614 33.333 19.36 0.09 0.00 1.85
4300 4430 7.860373 GCGAGGCATTGTACATTGATTTATTTA 59.140 33.333 19.36 0.00 0.00 1.40
4301 4431 6.697019 GCGAGGCATTGTACATTGATTTATTT 59.303 34.615 19.36 0.00 0.00 1.40
4302 4432 6.039717 AGCGAGGCATTGTACATTGATTTATT 59.960 34.615 19.36 0.67 0.00 1.40
4303 4433 5.532406 AGCGAGGCATTGTACATTGATTTAT 59.468 36.000 19.36 0.00 0.00 1.40
4304 4434 4.881273 AGCGAGGCATTGTACATTGATTTA 59.119 37.500 19.36 0.00 0.00 1.40
4305 4435 3.696051 AGCGAGGCATTGTACATTGATTT 59.304 39.130 19.36 5.61 0.00 2.17
4306 4436 3.282021 AGCGAGGCATTGTACATTGATT 58.718 40.909 19.36 7.76 0.00 2.57
4307 4437 2.923121 AGCGAGGCATTGTACATTGAT 58.077 42.857 19.36 8.37 0.00 2.57
4308 4438 2.401583 AGCGAGGCATTGTACATTGA 57.598 45.000 19.36 0.00 0.00 2.57
4309 4439 4.818534 ATTAGCGAGGCATTGTACATTG 57.181 40.909 12.41 12.41 0.00 2.82
4310 4440 4.452455 GCTATTAGCGAGGCATTGTACATT 59.548 41.667 0.00 0.00 0.00 2.71
4311 4441 3.997021 GCTATTAGCGAGGCATTGTACAT 59.003 43.478 0.00 0.00 0.00 2.29
4312 4442 3.181470 TGCTATTAGCGAGGCATTGTACA 60.181 43.478 10.94 0.00 46.26 2.90
4313 4443 3.184581 GTGCTATTAGCGAGGCATTGTAC 59.815 47.826 10.94 0.00 46.26 2.90
4314 4444 3.390135 GTGCTATTAGCGAGGCATTGTA 58.610 45.455 10.94 0.00 46.26 2.41
4315 4445 2.213499 GTGCTATTAGCGAGGCATTGT 58.787 47.619 10.94 0.00 46.26 2.71
4316 4446 1.193203 CGTGCTATTAGCGAGGCATTG 59.807 52.381 10.94 0.00 46.26 2.82
4317 4447 1.502231 CGTGCTATTAGCGAGGCATT 58.498 50.000 10.94 0.00 46.26 3.56
4318 4448 0.946221 GCGTGCTATTAGCGAGGCAT 60.946 55.000 18.94 0.00 46.26 4.40
4319 4449 1.591594 GCGTGCTATTAGCGAGGCA 60.592 57.895 18.94 0.00 46.26 4.75
4320 4450 0.039437 TAGCGTGCTATTAGCGAGGC 60.039 55.000 17.41 17.41 46.26 4.70
4321 4451 2.638556 ATAGCGTGCTATTAGCGAGG 57.361 50.000 8.54 7.17 46.26 4.63
4322 4452 3.102276 GCTATAGCGTGCTATTAGCGAG 58.898 50.000 18.62 11.00 46.26 5.03
4323 4453 3.132629 GCTATAGCGTGCTATTAGCGA 57.867 47.619 18.62 0.92 46.26 4.93
4345 4475 7.451281 AATATGCTATTAGCGTGCTATAACG 57.549 36.000 18.61 0.00 46.26 3.18
4349 4479 8.883731 CCTAAAAATATGCTATTAGCGTGCTAT 58.116 33.333 18.61 5.81 46.26 2.97
4350 4480 7.333423 CCCTAAAAATATGCTATTAGCGTGCTA 59.667 37.037 18.61 0.00 46.26 3.49
4351 4481 6.149474 CCCTAAAAATATGCTATTAGCGTGCT 59.851 38.462 18.61 0.00 46.26 4.40
4352 4482 6.072673 ACCCTAAAAATATGCTATTAGCGTGC 60.073 38.462 18.61 0.00 46.26 5.34
4353 4483 7.360946 GGACCCTAAAAATATGCTATTAGCGTG 60.361 40.741 18.61 3.27 46.26 5.34
4354 4484 6.653740 GGACCCTAAAAATATGCTATTAGCGT 59.346 38.462 14.53 14.53 46.26 5.07
4355 4485 6.653320 TGGACCCTAAAAATATGCTATTAGCG 59.347 38.462 10.94 0.00 46.26 4.26
4356 4486 7.360946 CGTGGACCCTAAAAATATGCTATTAGC 60.361 40.741 8.80 8.80 42.82 3.09
4357 4487 7.360946 GCGTGGACCCTAAAAATATGCTATTAG 60.361 40.741 0.00 0.00 0.00 1.73
4358 4488 6.428771 GCGTGGACCCTAAAAATATGCTATTA 59.571 38.462 0.00 0.00 0.00 0.98
4359 4489 5.240844 GCGTGGACCCTAAAAATATGCTATT 59.759 40.000 0.00 0.00 0.00 1.73
4360 4490 4.760204 GCGTGGACCCTAAAAATATGCTAT 59.240 41.667 0.00 0.00 0.00 2.97
4361 4491 4.131596 GCGTGGACCCTAAAAATATGCTA 58.868 43.478 0.00 0.00 0.00 3.49
4362 4492 2.949644 GCGTGGACCCTAAAAATATGCT 59.050 45.455 0.00 0.00 0.00 3.79
4363 4493 2.949644 AGCGTGGACCCTAAAAATATGC 59.050 45.455 0.00 0.00 0.00 3.14
4364 4494 6.877611 AATAGCGTGGACCCTAAAAATATG 57.122 37.500 0.00 0.00 0.00 1.78
4365 4495 7.778382 AGAAAATAGCGTGGACCCTAAAAATAT 59.222 33.333 0.00 0.00 0.00 1.28
4366 4496 7.066525 CAGAAAATAGCGTGGACCCTAAAAATA 59.933 37.037 0.00 0.00 0.00 1.40
4367 4497 5.949952 AGAAAATAGCGTGGACCCTAAAAAT 59.050 36.000 0.00 0.00 0.00 1.82
4368 4498 5.182380 CAGAAAATAGCGTGGACCCTAAAAA 59.818 40.000 0.00 0.00 0.00 1.94
4369 4499 4.698304 CAGAAAATAGCGTGGACCCTAAAA 59.302 41.667 0.00 0.00 0.00 1.52
4370 4500 4.258543 CAGAAAATAGCGTGGACCCTAAA 58.741 43.478 0.00 0.00 0.00 1.85
4371 4501 3.262405 ACAGAAAATAGCGTGGACCCTAA 59.738 43.478 0.00 0.00 0.00 2.69
4372 4502 2.835764 ACAGAAAATAGCGTGGACCCTA 59.164 45.455 0.00 0.00 0.00 3.53
4373 4503 1.628846 ACAGAAAATAGCGTGGACCCT 59.371 47.619 0.00 0.00 0.00 4.34
4374 4504 2.109425 ACAGAAAATAGCGTGGACCC 57.891 50.000 0.00 0.00 0.00 4.46
4375 4505 2.608090 GCTACAGAAAATAGCGTGGACC 59.392 50.000 0.00 0.00 36.02 4.46
4376 4506 3.927552 GCTACAGAAAATAGCGTGGAC 57.072 47.619 0.00 0.00 36.02 4.02
4382 4512 5.659048 AATAGCACGCTACAGAAAATAGC 57.341 39.130 0.00 0.00 41.43 2.97
4445 4577 6.681777 ACCTGAACAAGAAAAGATAACATGC 58.318 36.000 0.00 0.00 0.00 4.06
4452 4584 7.655490 CAGATGAAACCTGAACAAGAAAAGAT 58.345 34.615 0.00 0.00 33.65 2.40
4461 4593 3.819368 TCAAGCAGATGAAACCTGAACA 58.181 40.909 0.00 0.00 33.65 3.18
4585 4717 1.228245 TTTGCTGGCCTGTGTCCTC 60.228 57.895 11.69 0.00 0.00 3.71
4612 4744 1.588674 TTCACGTACTGCCTTTGGTG 58.411 50.000 0.00 0.00 0.00 4.17
4971 5238 1.549950 GGGAAAGGGAAGCCATGTTGA 60.550 52.381 0.00 0.00 0.00 3.18
5073 5340 0.825010 CCAAGCCTGGCTGTTCTTGT 60.825 55.000 24.16 0.52 39.62 3.16
5426 5699 3.446310 TCAGCTGTGACGTACAAAGAA 57.554 42.857 14.67 0.00 39.20 2.52
5559 5834 4.038402 AGGGAGCACTCAACATTTTTCTTG 59.962 41.667 0.00 0.00 0.00 3.02
5576 5851 0.105039 CATTACTGGACGGAGGGAGC 59.895 60.000 0.00 0.00 0.00 4.70
5623 5898 9.707957 CTATGTTAATATCTACTCCCTCCATCT 57.292 37.037 0.00 0.00 0.00 2.90
5626 5901 8.679725 AGACTATGTTAATATCTACTCCCTCCA 58.320 37.037 0.00 0.00 0.00 3.86
5715 6383 7.273320 CAATGATGCTATGTTTCATTCCTCT 57.727 36.000 0.00 0.00 37.86 3.69
5794 6502 5.289193 CGGCAATGAATTTTGTATCAACTGG 59.711 40.000 0.00 0.00 0.00 4.00
5797 6505 6.092748 AGTCGGCAATGAATTTTGTATCAAC 58.907 36.000 0.00 0.00 0.00 3.18
5799 6507 5.895636 AGTCGGCAATGAATTTTGTATCA 57.104 34.783 0.00 0.00 0.00 2.15
5800 6508 7.968405 AGTTAAGTCGGCAATGAATTTTGTATC 59.032 33.333 0.00 0.00 0.00 2.24
5802 6510 7.209471 AGTTAAGTCGGCAATGAATTTTGTA 57.791 32.000 0.00 0.00 0.00 2.41
5803 6511 6.084326 AGTTAAGTCGGCAATGAATTTTGT 57.916 33.333 0.00 0.00 0.00 2.83
5804 6512 6.640499 TGAAGTTAAGTCGGCAATGAATTTTG 59.360 34.615 0.00 0.00 0.00 2.44
5805 6513 6.744112 TGAAGTTAAGTCGGCAATGAATTTT 58.256 32.000 0.00 0.00 0.00 1.82
5806 6514 6.325919 TGAAGTTAAGTCGGCAATGAATTT 57.674 33.333 0.00 0.00 0.00 1.82
5807 6515 5.957842 TGAAGTTAAGTCGGCAATGAATT 57.042 34.783 0.00 0.00 0.00 2.17
5808 6516 5.957842 TTGAAGTTAAGTCGGCAATGAAT 57.042 34.783 0.00 0.00 0.00 2.57
5809 6517 5.240623 ACATTGAAGTTAAGTCGGCAATGAA 59.759 36.000 24.92 0.00 42.99 2.57
5810 6518 4.759693 ACATTGAAGTTAAGTCGGCAATGA 59.240 37.500 24.92 0.00 42.99 2.57
5811 6519 5.046910 ACATTGAAGTTAAGTCGGCAATG 57.953 39.130 20.55 20.55 44.75 2.82
5812 6520 5.240623 TCAACATTGAAGTTAAGTCGGCAAT 59.759 36.000 0.00 0.00 33.55 3.56
5813 6521 4.576873 TCAACATTGAAGTTAAGTCGGCAA 59.423 37.500 0.00 0.00 33.55 4.52
5826 6534 6.865726 CCGTGGAATTTTGTATCAACATTGAA 59.134 34.615 0.00 0.00 41.13 2.69
6007 6715 9.118300 CAAGGATCTTTCATCATAAAAGTAGCT 57.882 33.333 0.00 0.00 35.64 3.32
6008 6716 8.897752 ACAAGGATCTTTCATCATAAAAGTAGC 58.102 33.333 0.00 0.00 35.64 3.58
6085 6794 4.790937 TGCCATAGGTCAAGAATGCAATA 58.209 39.130 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.