Multiple sequence alignment - TraesCS6A01G385600

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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 TraesCS6A01G385600 chr6A 100.000 6962 0 0 1 6962 603192582 603185621 0.000000e+00 12857
1 TraesCS6A01G385600 chr6B 93.336 2476 116 28 3121 5562 694122961 694120501 0.000000e+00 3613
2 TraesCS6A01G385600 chr6B 90.596 1276 99 15 5567 6829 694120138 694118871 0.000000e+00 1672
3 TraesCS6A01G385600 chr6B 84.921 1638 161 49 205 1796 694125944 694124347 0.000000e+00 1578
4 TraesCS6A01G385600 chr6B 85.049 1331 113 35 1833 3117 694124346 694123056 0.000000e+00 1277
5 TraesCS6A01G385600 chr6B 94.444 90 3 2 6873 6962 694118775 694118688 3.390000e-28 137
6 TraesCS6A01G385600 chr6D 89.723 2744 173 46 426 3115 456463915 456461227 0.000000e+00 3404
7 TraesCS6A01G385600 chr6D 88.538 2783 210 56 4115 6829 456460133 456457392 0.000000e+00 3271
8 TraesCS6A01G385600 chr6D 86.337 1010 109 8 3121 4129 456461130 456460149 0.000000e+00 1074
9 TraesCS6A01G385600 chr6D 92.222 90 5 2 6873 6962 456457292 456457205 7.330000e-25 126
10 TraesCS6A01G385600 chr1B 86.549 736 75 15 1 729 232962293 232963011 0.000000e+00 789
11 TraesCS6A01G385600 chr4B 91.807 476 35 3 5 478 592539534 592539061 0.000000e+00 660
12 TraesCS6A01G385600 chr4B 89.979 479 44 3 1 478 473670339 473670814 3.570000e-172 616
13 TraesCS6A01G385600 chr4B 81.818 330 41 13 404 729 208020310 208020624 6.930000e-65 259
14 TraesCS6A01G385600 chr4B 81.818 330 40 14 404 729 363880120 363880433 6.930000e-65 259
15 TraesCS6A01G385600 chr4B 81.818 330 41 12 407 732 367070333 367070019 6.930000e-65 259
16 TraesCS6A01G385600 chr7B 91.476 481 36 4 1 480 483312143 483311667 0.000000e+00 656
17 TraesCS6A01G385600 chr7B 89.662 474 45 3 5 477 736345819 736346289 9.990000e-168 601
18 TraesCS6A01G385600 chr2B 91.042 480 41 2 1 478 16822094 16821615 0.000000e+00 647
19 TraesCS6A01G385600 chr2B 90.397 479 42 3 1 477 374399005 374398529 1.650000e-175 627
20 TraesCS6A01G385600 chr2B 89.792 480 43 5 1 478 322309864 322310339 1.660000e-170 610
21 TraesCS6A01G385600 chr2B 89.770 479 44 4 1 478 407861842 407862316 5.970000e-170 608
22 TraesCS6A01G385600 chr7A 84.286 280 35 5 387 666 598322087 598322357 1.490000e-66 265
23 TraesCS6A01G385600 chr3B 81.212 330 39 15 404 729 351867402 351867712 1.940000e-60 244
24 TraesCS6A01G385600 chr3B 80.896 335 40 16 404 732 705239681 705239997 6.980000e-60 243
25 TraesCS6A01G385600 chr3B 80.243 329 48 11 404 731 72567728 72568040 1.510000e-56 231
26 TraesCS6A01G385600 chr3B 96.721 61 1 1 3928 3988 1451465 1451524 4.440000e-17 100
27 TraesCS6A01G385600 chr2D 80.675 326 46 10 407 732 103678549 103678241 3.250000e-58 237
28 TraesCS6A01G385600 chr1D 92.920 113 2 6 624 732 473888592 473888482 7.230000e-35 159
29 TraesCS6A01G385600 chr1D 87.970 133 12 3 604 732 487325623 487325491 3.360000e-33 154
30 TraesCS6A01G385600 chr5B 93.396 106 5 2 624 729 435850041 435850144 9.350000e-34 156


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 TraesCS6A01G385600 chr6A 603185621 603192582 6961 True 12857.00 12857 100.0000 1 6962 1 chr6A.!!$R1 6961
1 TraesCS6A01G385600 chr6B 694118688 694125944 7256 True 1655.40 3613 89.6692 205 6962 5 chr6B.!!$R1 6757
2 TraesCS6A01G385600 chr6D 456457205 456463915 6710 True 1968.75 3404 89.2050 426 6962 4 chr6D.!!$R1 6536
3 TraesCS6A01G385600 chr1B 232962293 232963011 718 False 789.00 789 86.5490 1 729 1 chr1B.!!$F1 728

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
198 200 0.037590 ACCCCATGCGAGCTAACAAA 59.962 50.000 0.00 0.00 0.00 2.83 F
1303 1364 0.030504 CGCAGGATTTGTGTGTTGCA 59.969 50.000 0.00 0.00 32.55 4.08 F
1407 1469 0.248949 GACAGTACGAGGATTCCGCC 60.249 60.000 0.42 0.00 0.00 6.13 F
1410 1472 0.395311 AGTACGAGGATTCCGCCAGA 60.395 55.000 0.42 0.00 0.00 3.86 F
1843 1905 0.466372 TTGGTTGTGGGTCATTCGCA 60.466 50.000 0.00 0.00 36.65 5.10 F
2843 2951 1.601412 GCTTTGGCAGCTGACAAGAAC 60.601 52.381 32.49 22.18 44.95 3.01 F
3080 3188 2.031120 CCCTTTTGCACTGAAACCTCA 58.969 47.619 0.00 0.00 0.00 3.86 F
3732 3930 0.822164 AGTAGCGGCGGTAGTTCAAT 59.178 50.000 20.20 0.00 0.00 2.57 F
4737 4985 0.166814 GACGTTGTCATGCCAGCTTC 59.833 55.000 0.00 0.00 32.09 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 1572 0.111061 AAGCAGAACATCAGCACCCA 59.889 50.000 0.0 0.0 30.69 4.51 R
2578 2659 0.037975 AGAAATGCTGGGCAAAAGCG 60.038 50.000 0.0 0.0 43.62 4.68 R
2645 2730 0.111639 GCCCACTTGGTTTACAGGGA 59.888 55.000 0.0 0.0 34.73 4.20 R
3276 3474 0.322975 ACAGATCAGCAGGGACACAC 59.677 55.000 0.0 0.0 0.00 3.82 R
3593 3791 0.030638 CAGCACTGGGTGGTTTTTCG 59.969 55.000 0.0 0.0 41.72 3.46 R
3644 3842 0.323629 CCTTTCGGCAACCTCACCTA 59.676 55.000 0.0 0.0 0.00 3.08 R
3952 4152 1.131303 TGGAAGGCGGAAAAGGAGGA 61.131 55.000 0.0 0.0 0.00 3.71 R
4872 5120 1.228094 GCTATCTTGCCCAGGCCTC 60.228 63.158 0.0 0.0 41.09 4.70 R
6614 7303 0.746063 TGTCTTGGCTTTGTTGGCTG 59.254 50.000 0.0 0.0 0.00 4.85 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
46 47 0.801251 GCAGAGACATGCAACTGTCC 59.199 55.000 15.24 8.32 45.41 4.02
61 63 0.038166 TGTCCAAGGGTTCATCCAGC 59.962 55.000 0.00 0.00 38.11 4.85
85 87 5.562298 TCTAATACAATAACTCCCCAGCC 57.438 43.478 0.00 0.00 0.00 4.85
116 118 2.580322 TGGGAGGAAATCACCTTGCATA 59.420 45.455 0.00 0.00 40.73 3.14
120 122 4.096984 GGAGGAAATCACCTTGCATAACAG 59.903 45.833 0.00 0.00 40.73 3.16
132 134 5.453903 CCTTGCATAACAGCTCCTATACACT 60.454 44.000 0.00 0.00 34.99 3.55
136 138 6.183361 TGCATAACAGCTCCTATACACTGAAT 60.183 38.462 0.00 0.00 34.25 2.57
139 141 8.797438 CATAACAGCTCCTATACACTGAATAGA 58.203 37.037 0.00 0.00 34.25 1.98
154 156 9.209175 ACACTGAATAGAACATTTAACAGACTC 57.791 33.333 0.00 0.00 0.00 3.36
155 157 9.208022 CACTGAATAGAACATTTAACAGACTCA 57.792 33.333 0.00 0.00 0.00 3.41
184 186 7.899648 TCAAACAAAGAACTAATTTACCCCA 57.100 32.000 0.00 0.00 0.00 4.96
186 188 8.364142 TCAAACAAAGAACTAATTTACCCCATG 58.636 33.333 0.00 0.00 0.00 3.66
193 195 3.389983 ACTAATTTACCCCATGCGAGCTA 59.610 43.478 0.00 0.00 0.00 3.32
195 197 2.032680 TTTACCCCATGCGAGCTAAC 57.967 50.000 0.00 0.00 0.00 2.34
198 200 0.037590 ACCCCATGCGAGCTAACAAA 59.962 50.000 0.00 0.00 0.00 2.83
277 279 3.309954 GGCAACTTACAAGGATTAGAGCG 59.690 47.826 0.00 0.00 0.00 5.03
280 282 4.030134 ACTTACAAGGATTAGAGCGTCG 57.970 45.455 0.00 0.00 0.00 5.12
300 303 3.932710 TCGCAGATATGTTCACTTCCAAC 59.067 43.478 0.00 0.00 0.00 3.77
327 330 4.855340 TCTAAGGCCCTAAAGTGGATTTG 58.145 43.478 0.00 0.00 32.01 2.32
332 335 3.576550 GGCCCTAAAGTGGATTTGAACAA 59.423 43.478 0.00 0.00 32.01 2.83
374 378 2.095567 CCACATCAGTACAGCAAGCAAC 60.096 50.000 0.00 0.00 0.00 4.17
379 383 3.390135 TCAGTACAGCAAGCAACTACAC 58.610 45.455 0.00 0.00 0.00 2.90
385 389 2.033602 AAGCAACTACACGGGCCC 59.966 61.111 13.57 13.57 0.00 5.80
441 445 7.067496 TGAGTAGATCCATTCCTAAACATCC 57.933 40.000 0.00 0.00 0.00 3.51
448 452 6.485830 TCCATTCCTAAACATCCTCTACAG 57.514 41.667 0.00 0.00 0.00 2.74
454 458 8.721133 TTCCTAAACATCCTCTACAGCATATA 57.279 34.615 0.00 0.00 0.00 0.86
455 459 8.123639 TCCTAAACATCCTCTACAGCATATAC 57.876 38.462 0.00 0.00 0.00 1.47
533 538 3.686241 TCGCGACTACTAGTAGCAAGAAA 59.314 43.478 26.54 8.28 45.37 2.52
534 539 4.154737 TCGCGACTACTAGTAGCAAGAAAA 59.845 41.667 26.54 6.82 45.37 2.29
535 540 4.262510 CGCGACTACTAGTAGCAAGAAAAC 59.737 45.833 26.54 9.23 45.37 2.43
589 596 4.284860 CCGCGCGATCCATCCAGA 62.285 66.667 34.63 0.00 0.00 3.86
606 613 2.223066 CCAGAACTACGCTACGAGACTG 60.223 54.545 0.00 0.00 0.00 3.51
859 875 2.247311 CTTTGTAAGCCATGACACGC 57.753 50.000 0.00 0.00 0.00 5.34
873 889 4.729227 TGACACGCAAATGTAGGATAGA 57.271 40.909 0.00 0.00 31.24 1.98
885 902 1.665137 AGGATAGAACGGGGTGGTTT 58.335 50.000 0.00 0.00 0.00 3.27
887 904 2.502947 AGGATAGAACGGGGTGGTTTAC 59.497 50.000 0.00 0.00 0.00 2.01
893 910 1.596603 ACGGGGTGGTTTACGAAAAG 58.403 50.000 0.00 0.00 0.00 2.27
932 949 2.526624 GCTTTGGGTTTGGGGGCT 60.527 61.111 0.00 0.00 0.00 5.19
933 950 2.882677 GCTTTGGGTTTGGGGGCTG 61.883 63.158 0.00 0.00 0.00 4.85
934 951 2.122636 TTTGGGTTTGGGGGCTGG 60.123 61.111 0.00 0.00 0.00 4.85
976 994 1.449601 GAAGCCGGAATTGCGAGGA 60.450 57.895 21.76 0.00 0.00 3.71
990 1008 0.323908 CGAGGAAGGGGTCTGAGACT 60.324 60.000 12.92 0.00 32.47 3.24
1014 1038 2.785425 GGAAATGGCGGCCATGGAC 61.785 63.158 33.56 24.68 44.40 4.02
1153 1177 1.201647 CGCACTTCTTCGAGGAGGTAA 59.798 52.381 11.98 0.00 0.00 2.85
1210 1250 0.537653 GCTAGGTTTCGCCTCTTCCT 59.462 55.000 0.00 0.00 46.96 3.36
1217 1257 4.168291 CGCCTCTTCCTGCCCCTC 62.168 72.222 0.00 0.00 0.00 4.30
1222 1262 4.785453 CTTCCTGCCCCTCCACGC 62.785 72.222 0.00 0.00 0.00 5.34
1256 1317 2.778679 GTCTTCGATGTGCCGCAC 59.221 61.111 16.93 16.93 34.56 5.34
1277 1338 2.955881 GCAGTCCCAGCCCGTACTT 61.956 63.158 0.00 0.00 0.00 2.24
1303 1364 0.030504 CGCAGGATTTGTGTGTTGCA 59.969 50.000 0.00 0.00 32.55 4.08
1383 1445 0.318441 TCTTCAGGAACCTGCGTGAG 59.682 55.000 15.20 10.26 43.31 3.51
1389 1451 2.915659 AACCTGCGTGAGTCCGGA 60.916 61.111 0.00 0.00 0.00 5.14
1401 1463 0.255318 AGTCCGGACAGTACGAGGAT 59.745 55.000 35.00 8.65 33.15 3.24
1407 1469 0.248949 GACAGTACGAGGATTCCGCC 60.249 60.000 0.42 0.00 0.00 6.13
1410 1472 0.395311 AGTACGAGGATTCCGCCAGA 60.395 55.000 0.42 0.00 0.00 3.86
1483 1545 0.608035 GCTTCCCATGGACCGTTTCA 60.608 55.000 15.22 0.00 0.00 2.69
1537 1599 1.291877 GATGTTCTGCTTCGTGCCGT 61.292 55.000 1.30 0.00 42.00 5.68
1619 1681 3.068024 AGCATTTTCTGAAAGCCGAAACA 59.932 39.130 9.84 0.00 0.00 2.83
1652 1714 0.888619 ACATCCGTGCTCTTCTCGAA 59.111 50.000 0.00 0.00 33.89 3.71
1670 1732 3.861797 GCGGTCGTGGGGATGGAT 61.862 66.667 0.00 0.00 0.00 3.41
1676 1738 1.825474 GTCGTGGGGATGGATATCGAT 59.175 52.381 2.16 2.16 33.98 3.59
1678 1740 1.550524 CGTGGGGATGGATATCGATGT 59.449 52.381 8.54 0.00 33.98 3.06
1740 1802 5.598416 TGTGAAGTCGATCCTGAATATGT 57.402 39.130 0.00 0.00 0.00 2.29
1843 1905 0.466372 TTGGTTGTGGGTCATTCGCA 60.466 50.000 0.00 0.00 36.65 5.10
2009 2071 2.480419 CCCTTAAACACACTCAGCTTCG 59.520 50.000 0.00 0.00 0.00 3.79
2015 2077 2.688507 ACACACTCAGCTTCGGTATTG 58.311 47.619 0.00 0.00 0.00 1.90
2068 2131 5.022021 CAGTTTGAACTCACACGAAACTTC 58.978 41.667 0.00 0.00 37.08 3.01
2245 2308 6.019881 GTGTTTGAACCATTAACAGTTTCTGC 60.020 38.462 0.00 0.00 34.37 4.26
2428 2508 4.225942 TGGGACACATTGATAGAGAGCTTT 59.774 41.667 0.00 0.00 0.00 3.51
2439 2519 3.533606 AGAGAGCTTTGTGTCGCATAT 57.466 42.857 0.00 0.00 0.00 1.78
2529 2609 2.096496 GTGAATGCCCAGACAAGATTCG 59.904 50.000 0.00 0.00 0.00 3.34
2549 2629 8.076178 AGATTCGTAATTTGAAGGTTCTTTGTG 58.924 33.333 0.00 0.00 0.00 3.33
2552 2632 6.540914 TCGTAATTTGAAGGTTCTTTGTGTCT 59.459 34.615 0.00 0.00 0.00 3.41
2578 2659 5.557891 ATCTTATGTCTTGTTTGCAGCTC 57.442 39.130 0.00 0.00 0.00 4.09
2588 2669 2.697992 TTTGCAGCTCGCTTTTGCCC 62.698 55.000 9.12 0.00 43.93 5.36
2591 2672 3.368571 AGCTCGCTTTTGCCCAGC 61.369 61.111 0.00 0.00 44.11 4.85
2619 2704 3.779759 TGCAAACATCAGTTTTGGTGAC 58.220 40.909 0.00 0.00 45.32 3.67
2628 2713 5.843673 TCAGTTTTGGTGACAGCATTTTA 57.156 34.783 8.39 0.00 44.54 1.52
2688 2773 6.268566 CAGCTATGCAAATTTAGGAAGAACC 58.731 40.000 0.00 0.00 39.35 3.62
2712 2797 6.039270 CCTCAAAAACAGTTACACCTCAATGA 59.961 38.462 0.00 0.00 0.00 2.57
2714 2799 6.375736 TCAAAAACAGTTACACCTCAATGACA 59.624 34.615 0.00 0.00 0.00 3.58
2748 2833 5.423015 AGCACCATTGTGTCAACTATCTAG 58.577 41.667 0.00 0.00 44.65 2.43
2753 2838 6.211584 ACCATTGTGTCAACTATCTAGTGTCT 59.788 38.462 0.00 0.00 36.50 3.41
2756 2841 8.678199 CATTGTGTCAACTATCTAGTGTCTCTA 58.322 37.037 0.00 0.00 36.50 2.43
2757 2842 8.631480 TTGTGTCAACTATCTAGTGTCTCTAA 57.369 34.615 0.00 0.00 36.50 2.10
2758 2843 8.809468 TGTGTCAACTATCTAGTGTCTCTAAT 57.191 34.615 0.00 0.00 36.50 1.73
2759 2844 9.901172 TGTGTCAACTATCTAGTGTCTCTAATA 57.099 33.333 0.00 0.00 36.50 0.98
2763 2848 9.916360 TCAACTATCTAGTGTCTCTAATAACCA 57.084 33.333 0.00 0.00 36.50 3.67
2785 2893 6.884836 ACCAGATGAAAGGAACACTAATAACC 59.115 38.462 0.00 0.00 0.00 2.85
2843 2951 1.601412 GCTTTGGCAGCTGACAAGAAC 60.601 52.381 32.49 22.18 44.95 3.01
2865 2973 5.003160 ACTTGACATCGACCATTCATTGAA 58.997 37.500 0.75 0.75 0.00 2.69
2921 3029 6.542370 TCAAAATTGAGTAATAGGCTACTGGC 59.458 38.462 0.00 0.00 32.14 4.85
2922 3030 7.583416 TCAAAATTGAGTAATAGGCTACTGGCT 60.583 37.037 0.00 0.00 41.19 4.75
2945 3053 3.491447 GCCTGCTGCCTTTATTGGTTATG 60.491 47.826 0.00 0.00 0.00 1.90
2972 3080 4.923178 TAAGGAGCATGCCTTTCAGGGC 62.923 54.545 15.66 0.00 45.85 5.19
2997 3105 8.897752 GCTTTCTCAGGAAGTAAAATATGTGAT 58.102 33.333 0.00 0.00 32.61 3.06
3039 3147 8.940952 GTGAAATCTAGTATTTTTCTCTGCTGT 58.059 33.333 0.00 0.00 32.02 4.40
3041 3149 7.763172 AATCTAGTATTTTTCTCTGCTGTCG 57.237 36.000 0.00 0.00 0.00 4.35
3042 3150 6.510879 TCTAGTATTTTTCTCTGCTGTCGA 57.489 37.500 0.00 0.00 0.00 4.20
3053 3161 4.447724 TCTCTGCTGTCGATTTGTTGTTAC 59.552 41.667 0.00 0.00 0.00 2.50
3072 3180 2.242043 ACCATCTTCCCTTTTGCACTG 58.758 47.619 0.00 0.00 0.00 3.66
3080 3188 2.031120 CCCTTTTGCACTGAAACCTCA 58.969 47.619 0.00 0.00 0.00 3.86
3083 3191 3.489738 CCTTTTGCACTGAAACCTCACAG 60.490 47.826 0.00 0.00 39.65 3.66
3105 3213 8.988934 CACAGTTTCTTGAAGCTGTTAGTATAA 58.011 33.333 23.52 0.00 39.82 0.98
3107 3215 8.443937 CAGTTTCTTGAAGCTGTTAGTATAACC 58.556 37.037 15.79 0.00 0.00 2.85
3108 3216 8.154856 AGTTTCTTGAAGCTGTTAGTATAACCA 58.845 33.333 0.00 0.00 0.00 3.67
3109 3217 8.947115 GTTTCTTGAAGCTGTTAGTATAACCAT 58.053 33.333 0.00 0.00 0.00 3.55
3110 3218 8.718102 TTCTTGAAGCTGTTAGTATAACCATC 57.282 34.615 0.00 0.00 0.00 3.51
3112 3220 8.540388 TCTTGAAGCTGTTAGTATAACCATCTT 58.460 33.333 0.00 0.00 0.00 2.40
3113 3221 8.492673 TTGAAGCTGTTAGTATAACCATCTTG 57.507 34.615 0.00 0.00 0.00 3.02
3116 3224 9.162764 GAAGCTGTTAGTATAACCATCTTGAAA 57.837 33.333 0.00 0.00 0.00 2.69
3118 3226 8.322091 AGCTGTTAGTATAACCATCTTGAAAGT 58.678 33.333 0.00 0.00 0.00 2.66
3133 3331 8.817100 CATCTTGAAAGTTTCTTTAACCAAACC 58.183 33.333 16.33 0.00 37.46 3.27
3136 3334 8.766000 TTGAAAGTTTCTTTAACCAAACCTTC 57.234 30.769 16.33 10.38 37.46 3.46
3178 3376 4.081406 ACATTCTTGAGTATGCAAGGCAA 58.919 39.130 0.00 0.00 43.62 4.52
3184 3382 4.642445 TGAGTATGCAAGGCAATCATTG 57.358 40.909 0.00 0.00 43.62 2.82
3191 3389 2.997986 GCAAGGCAATCATTGGAAAGTG 59.002 45.455 0.00 0.00 0.00 3.16
3214 3412 3.141398 ACCGCACATATTATGGCTTCTG 58.859 45.455 8.48 0.00 33.60 3.02
3292 3490 2.191128 AAAGTGTGTCCCTGCTGATC 57.809 50.000 0.00 0.00 0.00 2.92
3343 3541 4.682787 TGCATTGTATCTTGTAGGTCGAG 58.317 43.478 0.00 0.00 0.00 4.04
3365 3563 6.403636 CGAGCTTGTTTGAAATATACCTTGCT 60.404 38.462 0.00 0.00 0.00 3.91
3397 3595 8.092687 AGATAAGCAATTTGATGAAGCTGTTTT 58.907 29.630 0.00 0.00 35.42 2.43
3476 3674 4.235360 AGTTTTCGTACCAGTTCTCATCG 58.765 43.478 0.00 0.00 0.00 3.84
3482 3680 3.608506 CGTACCAGTTCTCATCGTGAAAG 59.391 47.826 0.00 0.00 0.00 2.62
3487 3685 6.231211 ACCAGTTCTCATCGTGAAAGTTTAT 58.769 36.000 0.00 0.00 0.00 1.40
3498 3696 7.621832 TCGTGAAAGTTTATTGCTTCAATTG 57.378 32.000 0.00 0.00 35.54 2.32
3593 3791 8.290325 ACTACTCCGTTTCTCAAATTTCAAATC 58.710 33.333 0.00 0.00 0.00 2.17
3603 3801 8.125728 TCTCAAATTTCAAATCGAAAAACCAC 57.874 30.769 0.00 0.00 46.48 4.16
3693 3891 3.614616 GTCTCTACGCTTTCCATGTTCAG 59.385 47.826 0.00 0.00 0.00 3.02
3712 3910 2.564062 CAGCAACCTCATCCAATGGTTT 59.436 45.455 0.00 0.00 41.57 3.27
3718 3916 4.781934 ACCTCATCCAATGGTTTAGTAGC 58.218 43.478 0.00 0.00 0.00 3.58
3732 3930 0.822164 AGTAGCGGCGGTAGTTCAAT 59.178 50.000 20.20 0.00 0.00 2.57
3744 3942 5.813672 GCGGTAGTTCAATACAATACAGGAA 59.186 40.000 0.00 0.00 0.00 3.36
3768 3966 1.133253 CAATGTGCGCTTCCACTCG 59.867 57.895 9.73 0.00 36.68 4.18
3925 4124 5.683876 AGTCACTGCATATAAACTGGTCT 57.316 39.130 0.00 0.00 0.00 3.85
3994 4194 8.680001 TCCAAGTTGACAATCTATGATGAAATG 58.320 33.333 3.87 0.00 0.00 2.32
4036 4236 8.303156 CCAACACATGTTCAATTTAGGTGATTA 58.697 33.333 0.00 0.00 35.83 1.75
4124 4353 2.879646 GGGTGTTTGTTGGACAATCGTA 59.120 45.455 0.00 0.00 38.00 3.43
4147 4376 6.734104 AGTTTGACTGATGTCTGCTAAATC 57.266 37.500 0.00 0.00 43.29 2.17
4148 4377 6.233434 AGTTTGACTGATGTCTGCTAAATCA 58.767 36.000 0.00 0.00 43.29 2.57
4268 4503 3.421844 ACCAACCAAAGCACTCCTTATC 58.578 45.455 0.00 0.00 32.20 1.75
4291 4526 5.958380 TCTTGATCTACATAAGGTGTCCACT 59.042 40.000 0.00 0.00 42.29 4.00
4296 4531 7.618117 TGATCTACATAAGGTGTCCACTCTTTA 59.382 37.037 0.00 1.36 42.29 1.85
4300 4535 7.745620 ACATAAGGTGTCCACTCTTTAAAAG 57.254 36.000 6.51 0.00 35.77 2.27
4372 4607 9.834628 TTACAAATTCACAACGATAGGAAAATC 57.165 29.630 0.00 0.00 43.77 2.17
4396 4631 8.596271 TCTTTTAAAGTACGAATGACATGTCA 57.404 30.769 29.67 29.67 44.59 3.58
4459 4695 5.393027 GCGGTCAAAGTGTAAATCATGGAAT 60.393 40.000 0.00 0.00 0.00 3.01
4514 4762 9.007901 CCTCTGATGAAGTTACTGAAGAAAATT 57.992 33.333 0.00 0.00 0.00 1.82
4548 4796 3.181470 TGCATCTAACCAATACGCAGCTA 60.181 43.478 0.00 0.00 0.00 3.32
4737 4985 0.166814 GACGTTGTCATGCCAGCTTC 59.833 55.000 0.00 0.00 32.09 3.86
4863 5111 4.264253 TGCTTCATCCACATGGTTTAGAG 58.736 43.478 0.00 0.00 36.34 2.43
4903 5151 3.556004 GCAAGATAGCTCTACCATGTCCC 60.556 52.174 0.00 0.00 0.00 4.46
4933 5181 5.049954 TGCTTTTATGTAACCGTGTCAGTTC 60.050 40.000 0.00 0.00 0.00 3.01
5006 5255 4.062293 TGTATTTCGGTCAGACCAAACTG 58.938 43.478 20.13 2.72 38.47 3.16
5036 5291 2.736670 ATCTGTTGCCATAGTTCCCC 57.263 50.000 0.00 0.00 0.00 4.81
5118 5434 2.164219 CTGGGTGGTTGATGCATACAAC 59.836 50.000 22.96 22.96 44.40 3.32
5220 5536 9.927668 AAATGGAGTCAGTTTAAAATATTGGTG 57.072 29.630 0.00 0.00 0.00 4.17
5246 5562 7.600752 GGACTATCTGCTTGATGGTTATAGAAC 59.399 40.741 9.66 0.00 45.11 3.01
5319 5635 0.844661 ACCCTCCCCTATGCACACAA 60.845 55.000 0.00 0.00 0.00 3.33
5364 5680 2.781667 AGCCCCTGAATTGATCCTAGT 58.218 47.619 0.00 0.00 0.00 2.57
5406 5722 9.807921 AAAACTTTAATCCCTGTTCTTCTATGA 57.192 29.630 0.00 0.00 0.00 2.15
5450 5766 8.873830 ACAAGTAAGTATCAACATCGATTCAAG 58.126 33.333 0.00 0.00 0.00 3.02
5477 5793 2.738846 CTGTAACAGCAACGCAGAATCT 59.261 45.455 0.00 0.00 0.00 2.40
5478 5794 2.480037 TGTAACAGCAACGCAGAATCTG 59.520 45.455 5.78 5.78 34.12 2.90
5557 5875 8.544622 AGTTATTTGTTTCCCCTTCAAAGAAAA 58.455 29.630 0.00 0.00 35.26 2.29
5559 5877 7.864108 ATTTGTTTCCCCTTCAAAGAAAAAG 57.136 32.000 0.00 0.00 35.14 2.27
5560 5878 6.613153 TTGTTTCCCCTTCAAAGAAAAAGA 57.387 33.333 0.00 0.00 31.71 2.52
5561 5879 6.806668 TGTTTCCCCTTCAAAGAAAAAGAT 57.193 33.333 0.00 0.00 31.71 2.40
5562 5880 6.581712 TGTTTCCCCTTCAAAGAAAAAGATG 58.418 36.000 0.00 0.00 31.71 2.90
5563 5881 6.382570 TGTTTCCCCTTCAAAGAAAAAGATGA 59.617 34.615 0.00 0.00 31.71 2.92
5564 5882 7.071071 TGTTTCCCCTTCAAAGAAAAAGATGAT 59.929 33.333 0.00 0.00 31.71 2.45
5565 5883 7.616528 TTCCCCTTCAAAGAAAAAGATGATT 57.383 32.000 0.00 0.00 0.00 2.57
5566 5884 7.616528 TCCCCTTCAAAGAAAAAGATGATTT 57.383 32.000 0.00 0.00 0.00 2.17
5567 5885 8.719645 TCCCCTTCAAAGAAAAAGATGATTTA 57.280 30.769 0.00 0.00 0.00 1.40
5568 5886 8.806146 TCCCCTTCAAAGAAAAAGATGATTTAG 58.194 33.333 0.00 0.00 0.00 1.85
5649 6326 4.156739 GGGCTTGTTCTATTCAGTTCTTGG 59.843 45.833 0.00 0.00 0.00 3.61
5706 6385 7.064866 AGAAGGGATTGAATCTGCAAATCATA 58.935 34.615 5.03 0.00 0.00 2.15
5760 6439 7.724305 TGTTCCTGTTACTTCTTGATTACAC 57.276 36.000 0.00 0.00 0.00 2.90
5761 6440 7.276658 TGTTCCTGTTACTTCTTGATTACACA 58.723 34.615 0.00 0.00 0.00 3.72
5982 6670 4.792521 AGACAAATTCTCGCTAGTCAGT 57.207 40.909 0.00 0.00 0.00 3.41
5983 6671 4.489810 AGACAAATTCTCGCTAGTCAGTG 58.510 43.478 0.00 0.00 0.00 3.66
6029 6717 6.968904 CCAATTATCTCAACGATTGAACAAGG 59.031 38.462 0.00 0.00 39.58 3.61
6073 6762 7.862873 CACTGTTTTCCTTTCCAAGTTAGAATC 59.137 37.037 0.00 0.00 0.00 2.52
6074 6763 7.014326 ACTGTTTTCCTTTCCAAGTTAGAATCC 59.986 37.037 0.00 0.00 0.00 3.01
6078 6767 6.062258 TCCTTTCCAAGTTAGAATCCGATT 57.938 37.500 0.00 0.00 0.00 3.34
6093 6782 1.065418 CCGATTGGCCCTTACACTTCT 60.065 52.381 0.00 0.00 0.00 2.85
6106 6795 6.708054 CCCTTACACTTCTCCAATGATATGAC 59.292 42.308 0.00 0.00 0.00 3.06
6107 6796 7.275183 CCTTACACTTCTCCAATGATATGACA 58.725 38.462 0.00 0.00 0.00 3.58
6108 6797 7.440556 CCTTACACTTCTCCAATGATATGACAG 59.559 40.741 0.00 0.00 0.00 3.51
6115 6804 7.852550 TCTCCAATGATATGACAGAAGATCT 57.147 36.000 0.00 0.00 0.00 2.75
6159 6848 0.774276 TCCAAGGGGTAATGCACACA 59.226 50.000 0.00 0.00 34.93 3.72
6187 6876 9.112725 CCATACATCAATAATGAGTCAGTTTCA 57.887 33.333 0.00 0.00 39.39 2.69
6191 6880 9.017509 ACATCAATAATGAGTCAGTTTCACAAT 57.982 29.630 0.00 0.00 39.39 2.71
6257 6946 4.083003 CCAGTACTCTCTGAAGTCACAGTC 60.083 50.000 0.00 0.00 38.79 3.51
6267 6956 5.130477 TCTGAAGTCACAGTCCCTAGTTTTT 59.870 40.000 0.00 0.00 38.79 1.94
6303 6992 7.939039 GGACATCTTACATTGAAAGGGATATGA 59.061 37.037 0.00 0.00 0.00 2.15
6306 6995 7.141758 TCTTACATTGAAAGGGATATGAGCT 57.858 36.000 0.00 0.00 0.00 4.09
6333 7022 5.244178 AGTTCTATCACCTCATTCGATACCC 59.756 44.000 0.00 0.00 0.00 3.69
6338 7027 3.258372 TCACCTCATTCGATACCCTATGC 59.742 47.826 0.00 0.00 0.00 3.14
6393 7082 6.042777 TCAGATCTTCGTATCAACAATGGAC 58.957 40.000 0.00 0.00 0.00 4.02
6481 7170 4.217767 GCCATCAGCACATTCATCATACAT 59.782 41.667 0.00 0.00 42.97 2.29
6484 7173 3.566742 TCAGCACATTCATCATACATGGC 59.433 43.478 0.00 0.00 0.00 4.40
6527 7216 6.678568 ATGGTCTATCCCAAAGTATCTGAG 57.321 41.667 0.00 0.00 38.20 3.35
6529 7218 4.284746 GGTCTATCCCAAAGTATCTGAGGG 59.715 50.000 0.00 0.00 40.98 4.30
6538 7227 7.036863 TCCCAAAGTATCTGAGGGAATAAACTT 60.037 37.037 0.00 0.00 45.19 2.66
6588 7277 5.581350 TGGATATCCAGCAACCATTGATA 57.419 39.130 20.98 0.00 42.01 2.15
6605 7294 8.906867 ACCATTGATATTTCTGATCAACGAAAT 58.093 29.630 20.47 20.47 44.03 2.17
6614 7303 6.169419 TCTGATCAACGAAATGTGATTGTC 57.831 37.500 0.00 0.00 0.00 3.18
6704 7393 2.435069 CTCATCTGGGAGTTCAGAGCAT 59.565 50.000 0.00 0.00 45.60 3.79
6722 7411 2.893489 GCATTTTCTGGGAAGTTCAGGT 59.107 45.455 5.01 0.00 33.36 4.00
6763 7452 7.172361 GCTTAAGGTATCCATCTCATTTGACTC 59.828 40.741 4.29 0.00 0.00 3.36
6764 7453 6.821616 AAGGTATCCATCTCATTTGACTCT 57.178 37.500 0.00 0.00 0.00 3.24
6769 7458 8.401709 GGTATCCATCTCATTTGACTCTTTTTC 58.598 37.037 0.00 0.00 0.00 2.29
6770 7459 9.171877 GTATCCATCTCATTTGACTCTTTTTCT 57.828 33.333 0.00 0.00 0.00 2.52
6774 7463 6.551385 TCTCATTTGACTCTTTTTCTGCTC 57.449 37.500 0.00 0.00 0.00 4.26
6785 7474 3.542712 TTTTCTGCTCGTGATTTGCTC 57.457 42.857 0.00 0.00 0.00 4.26
6791 7480 5.660460 TCTGCTCGTGATTTGCTCTAATTA 58.340 37.500 0.00 0.00 0.00 1.40
6799 7488 8.638873 TCGTGATTTGCTCTAATTATTCTAGGA 58.361 33.333 0.00 0.00 0.00 2.94
6807 7496 9.823647 TGCTCTAATTATTCTAGGAGTTTTCAG 57.176 33.333 0.00 0.00 0.00 3.02
6822 7511 6.238511 GGAGTTTTCAGTGTCTTCTCTTTTCC 60.239 42.308 0.00 0.00 0.00 3.13
6823 7512 6.180472 AGTTTTCAGTGTCTTCTCTTTTCCA 58.820 36.000 0.00 0.00 0.00 3.53
6826 7515 7.645058 TTTCAGTGTCTTCTCTTTTCCATTT 57.355 32.000 0.00 0.00 0.00 2.32
6828 7517 5.532406 TCAGTGTCTTCTCTTTTCCATTTGG 59.468 40.000 0.00 0.00 0.00 3.28
6829 7518 4.829492 AGTGTCTTCTCTTTTCCATTTGGG 59.171 41.667 0.00 0.00 35.41 4.12
6830 7519 4.827284 GTGTCTTCTCTTTTCCATTTGGGA 59.173 41.667 0.00 0.00 46.61 4.37
6859 7617 0.990374 ACCTTCTTGCAGCTCCAGAT 59.010 50.000 0.00 0.00 0.00 2.90
6860 7618 1.339824 ACCTTCTTGCAGCTCCAGATG 60.340 52.381 0.00 0.00 34.00 2.90
6867 7625 3.261250 CAGCTCCAGATGCAACCTT 57.739 52.632 0.00 0.00 0.00 3.50
6868 7626 1.542492 CAGCTCCAGATGCAACCTTT 58.458 50.000 0.00 0.00 0.00 3.11
6869 7627 1.891150 CAGCTCCAGATGCAACCTTTT 59.109 47.619 0.00 0.00 0.00 2.27
6870 7628 2.298163 CAGCTCCAGATGCAACCTTTTT 59.702 45.455 0.00 0.00 0.00 1.94
6871 7629 2.560105 AGCTCCAGATGCAACCTTTTTC 59.440 45.455 0.00 0.00 0.00 2.29
6872 7630 2.297033 GCTCCAGATGCAACCTTTTTCA 59.703 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.679002 CTGCCCAAGTGGACAGATGG 60.679 60.000 7.85 0.00 39.32 3.51
16 17 1.053835 TGTCTCTGCCCAAGTGGACA 61.054 55.000 0.00 0.00 37.37 4.02
41 42 1.952367 GCTGGATGAACCCTTGGACAG 60.952 57.143 0.00 0.00 38.00 3.51
43 44 0.038166 TGCTGGATGAACCCTTGGAC 59.962 55.000 0.00 0.00 38.00 4.02
44 45 1.002069 ATGCTGGATGAACCCTTGGA 58.998 50.000 0.00 0.00 38.00 3.53
46 47 2.431954 AGATGCTGGATGAACCCTTG 57.568 50.000 0.00 0.00 38.00 3.61
61 63 5.940470 GGCTGGGGAGTTATTGTATTAGATG 59.060 44.000 0.00 0.00 0.00 2.90
85 87 4.016444 TGATTTCCTCCCATTTTTCCTCG 58.984 43.478 0.00 0.00 0.00 4.63
116 118 7.124298 TGTTCTATTCAGTGTATAGGAGCTGTT 59.876 37.037 14.65 0.00 0.00 3.16
120 122 8.894768 AAATGTTCTATTCAGTGTATAGGAGC 57.105 34.615 14.65 7.62 0.00 4.70
170 172 2.949644 GCTCGCATGGGGTAAATTAGTT 59.050 45.455 10.21 0.00 0.00 2.24
182 184 2.679837 AGATGTTTGTTAGCTCGCATGG 59.320 45.455 0.00 0.00 0.00 3.66
184 186 5.605534 AGATAGATGTTTGTTAGCTCGCAT 58.394 37.500 0.00 0.00 0.00 4.73
186 188 5.117897 GCTAGATAGATGTTTGTTAGCTCGC 59.882 44.000 0.00 0.00 31.73 5.03
193 195 6.402550 CGCTTGTTGCTAGATAGATGTTTGTT 60.403 38.462 0.00 0.00 40.11 2.83
195 197 5.063944 ACGCTTGTTGCTAGATAGATGTTTG 59.936 40.000 0.00 0.00 40.11 2.93
198 200 4.115516 CACGCTTGTTGCTAGATAGATGT 58.884 43.478 0.00 0.00 40.11 3.06
262 264 1.746787 TGCGACGCTCTAATCCTTGTA 59.253 47.619 22.08 0.00 0.00 2.41
265 267 1.103803 TCTGCGACGCTCTAATCCTT 58.896 50.000 22.08 0.00 0.00 3.36
271 273 2.616842 TGAACATATCTGCGACGCTCTA 59.383 45.455 22.08 9.92 0.00 2.43
277 279 3.521560 TGGAAGTGAACATATCTGCGAC 58.478 45.455 0.00 0.00 0.00 5.19
280 282 3.378427 GGGTTGGAAGTGAACATATCTGC 59.622 47.826 0.00 0.00 0.00 4.26
300 303 1.141185 CTTTAGGGCCTTAGAGGGGG 58.859 60.000 13.45 0.00 35.37 5.40
327 330 1.007387 CGTTGCCTTGCCCTTGTTC 60.007 57.895 0.00 0.00 0.00 3.18
332 335 2.044946 GGATCGTTGCCTTGCCCT 60.045 61.111 0.00 0.00 0.00 5.19
374 378 4.473520 CCTGCTGGGCCCGTGTAG 62.474 72.222 19.37 20.13 0.00 2.74
441 445 5.050490 GGTGGTTGTGTATATGCTGTAGAG 58.950 45.833 0.00 0.00 0.00 2.43
448 452 1.591158 CGTCGGTGGTTGTGTATATGC 59.409 52.381 0.00 0.00 0.00 3.14
454 458 1.005394 GATCCGTCGGTGGTTGTGT 60.005 57.895 11.88 0.00 0.00 3.72
455 459 0.528924 TAGATCCGTCGGTGGTTGTG 59.471 55.000 11.88 0.00 0.00 3.33
533 538 3.944233 GGCCGAACGCGTGTTGTT 61.944 61.111 20.80 0.00 38.78 2.83
534 539 4.903010 AGGCCGAACGCGTGTTGT 62.903 61.111 20.80 0.00 38.78 3.32
535 540 4.072088 GAGGCCGAACGCGTGTTG 62.072 66.667 20.80 11.26 38.78 3.33
584 591 2.005451 GTCTCGTAGCGTAGTTCTGGA 58.995 52.381 0.00 0.00 0.00 3.86
589 596 0.450983 GGCAGTCTCGTAGCGTAGTT 59.549 55.000 0.00 0.00 0.00 2.24
719 731 4.523282 GCCTCCCATCCTCCCCCT 62.523 72.222 0.00 0.00 0.00 4.79
850 866 5.049828 TCTATCCTACATTTGCGTGTCATG 58.950 41.667 0.00 0.00 33.62 3.07
859 875 4.127171 CACCCCGTTCTATCCTACATTTG 58.873 47.826 0.00 0.00 0.00 2.32
873 889 1.948834 CTTTTCGTAAACCACCCCGTT 59.051 47.619 0.00 0.00 0.00 4.44
885 902 2.125832 CGCGCCCTCCTTTTCGTA 60.126 61.111 0.00 0.00 0.00 3.43
887 904 4.752879 TCCGCGCCCTCCTTTTCG 62.753 66.667 0.00 0.00 0.00 3.46
893 910 0.463116 TAATTTCTTCCGCGCCCTCC 60.463 55.000 0.00 0.00 0.00 4.30
932 949 0.672401 GACGGATCGGCAAGAAACCA 60.672 55.000 0.00 0.00 33.63 3.67
933 950 1.366854 GGACGGATCGGCAAGAAACC 61.367 60.000 0.00 0.00 36.10 3.27
934 951 1.366854 GGGACGGATCGGCAAGAAAC 61.367 60.000 0.00 0.00 36.10 2.78
976 994 0.787084 TCCTCAGTCTCAGACCCCTT 59.213 55.000 0.00 0.00 32.18 3.95
990 1008 2.272146 GCCGCCATTTCCTCCTCA 59.728 61.111 0.00 0.00 0.00 3.86
1136 1160 4.401837 GTGGTATTACCTCCTCGAAGAAGT 59.598 45.833 13.90 0.00 39.58 3.01
1222 1262 3.202001 CGGTAACCAGCGCCATGG 61.202 66.667 13.77 13.77 46.47 3.66
1260 1321 1.079127 CAAGTACGGGCTGGGACTG 60.079 63.158 0.00 0.00 0.00 3.51
1264 1325 4.028490 TGGCAAGTACGGGCTGGG 62.028 66.667 13.61 0.00 0.00 4.45
1266 1327 2.746277 GGTGGCAAGTACGGGCTG 60.746 66.667 13.61 0.00 0.00 4.85
1301 1362 2.353889 CACCTCACATACAGCATTCTGC 59.646 50.000 0.00 0.00 44.10 4.26
1303 1364 2.636830 GCACCTCACATACAGCATTCT 58.363 47.619 0.00 0.00 0.00 2.40
1356 1418 1.344763 AGGTTCCTGAAGACCTGAACG 59.655 52.381 0.00 0.00 44.40 3.95
1383 1445 1.065251 GAATCCTCGTACTGTCCGGAC 59.935 57.143 28.17 28.17 0.00 4.79
1389 1451 0.968901 TGGCGGAATCCTCGTACTGT 60.969 55.000 0.00 0.00 0.00 3.55
1401 1463 1.585006 GTCGAACTCTCTGGCGGAA 59.415 57.895 0.00 0.00 0.00 4.30
1407 1469 2.876645 GCCGCGTCGAACTCTCTG 60.877 66.667 4.92 0.00 0.00 3.35
1510 1572 0.111061 AAGCAGAACATCAGCACCCA 59.889 50.000 0.00 0.00 30.69 4.51
1619 1681 0.389948 GGATGTTCTCCACGCTCGTT 60.390 55.000 0.00 0.00 44.26 3.85
1640 1702 1.213013 GACCGCTTCGAGAAGAGCA 59.787 57.895 16.23 0.00 40.79 4.26
1652 1714 2.939760 TATCCATCCCCACGACCGCT 62.940 60.000 0.00 0.00 0.00 5.52
1670 1732 2.170397 ACCAGCACCAATGACATCGATA 59.830 45.455 0.00 0.00 0.00 2.92
1676 1738 0.822944 CACCACCAGCACCAATGACA 60.823 55.000 0.00 0.00 0.00 3.58
1678 1740 1.228521 CCACCACCAGCACCAATGA 60.229 57.895 0.00 0.00 0.00 2.57
1700 1762 1.091197 CATACTGCTGGCACGCATCA 61.091 55.000 11.13 4.31 37.26 3.07
1712 1774 3.119291 CAGGATCGACTTCACATACTGC 58.881 50.000 0.00 0.00 0.00 4.40
1713 1775 4.639135 TCAGGATCGACTTCACATACTG 57.361 45.455 0.00 0.00 0.00 2.74
1740 1802 1.403647 CCGCGTCAAACCAGACAGATA 60.404 52.381 4.92 0.00 38.43 1.98
2009 2071 6.018343 CCATGGAAAACAAACAACACAATACC 60.018 38.462 5.56 0.00 0.00 2.73
2015 2077 4.506288 GCTACCATGGAAAACAAACAACAC 59.494 41.667 21.47 0.00 0.00 3.32
2068 2131 3.670055 GGTTTGTGATTTTCTGCATCGTG 59.330 43.478 0.00 0.00 0.00 4.35
2163 2226 6.380079 AAAACTAGATCCAGACACAATCCT 57.620 37.500 0.00 0.00 0.00 3.24
2245 2308 2.027377 AGGCCACTCTGACAAGAATCTG 60.027 50.000 5.01 0.00 30.03 2.90
2284 2347 9.301897 GGTGATTAAAGGATAAGCCAAGAATAT 57.698 33.333 0.00 0.00 40.02 1.28
2411 2491 4.867047 CGACACAAAGCTCTCTATCAATGT 59.133 41.667 0.00 0.00 0.00 2.71
2428 2508 5.250200 AGGGAACTAAAAATATGCGACACA 58.750 37.500 0.00 0.00 40.61 3.72
2439 2519 7.778382 GCTTGGATATAGGAAGGGAACTAAAAA 59.222 37.037 0.00 0.00 42.68 1.94
2529 2609 8.926715 AAAGACACAAAGAACCTTCAAATTAC 57.073 30.769 0.00 0.00 0.00 1.89
2549 2629 9.334693 CTGCAAACAAGACATAAGATAAAAGAC 57.665 33.333 0.00 0.00 0.00 3.01
2552 2632 7.885297 AGCTGCAAACAAGACATAAGATAAAA 58.115 30.769 1.02 0.00 0.00 1.52
2578 2659 0.037975 AGAAATGCTGGGCAAAAGCG 60.038 50.000 0.00 0.00 43.62 4.68
2588 2669 5.235616 AAACTGATGTTTGCAAGAAATGCTG 59.764 36.000 0.00 0.00 44.90 4.41
2591 2672 6.037391 ACCAAAACTGATGTTTGCAAGAAATG 59.963 34.615 0.00 0.00 44.70 2.32
2628 2713 6.347061 ACAGGGATAGGATTCCTTCATTTT 57.653 37.500 11.25 0.00 35.97 1.82
2645 2730 0.111639 GCCCACTTGGTTTACAGGGA 59.888 55.000 0.00 0.00 34.73 4.20
2688 2773 6.912591 GTCATTGAGGTGTAACTGTTTTTGAG 59.087 38.462 0.00 0.00 36.74 3.02
2696 2781 6.146184 CAGTACTTGTCATTGAGGTGTAACTG 59.854 42.308 0.00 0.00 36.74 3.16
2712 2797 5.008613 CACAATGGTGCTTAACAGTACTTGT 59.991 40.000 0.00 0.00 38.99 3.16
2714 2799 5.689383 CACAATGGTGCTTAACAGTACTT 57.311 39.130 0.00 0.00 38.37 2.24
2748 2833 7.556844 TCCTTTCATCTGGTTATTAGAGACAC 58.443 38.462 0.00 0.00 0.00 3.67
2753 2838 7.918076 AGTGTTCCTTTCATCTGGTTATTAGA 58.082 34.615 0.00 0.00 0.00 2.10
2758 2843 9.444600 GTTATTAGTGTTCCTTTCATCTGGTTA 57.555 33.333 0.00 0.00 0.00 2.85
2759 2844 7.393515 GGTTATTAGTGTTCCTTTCATCTGGTT 59.606 37.037 0.00 0.00 0.00 3.67
2760 2845 6.884836 GGTTATTAGTGTTCCTTTCATCTGGT 59.115 38.462 0.00 0.00 0.00 4.00
2761 2846 6.884295 TGGTTATTAGTGTTCCTTTCATCTGG 59.116 38.462 0.00 0.00 0.00 3.86
2763 2848 7.918076 TCTGGTTATTAGTGTTCCTTTCATCT 58.082 34.615 0.00 0.00 0.00 2.90
2764 2849 8.616076 CATCTGGTTATTAGTGTTCCTTTCATC 58.384 37.037 0.00 0.00 0.00 2.92
2765 2850 8.328758 TCATCTGGTTATTAGTGTTCCTTTCAT 58.671 33.333 0.00 0.00 0.00 2.57
2785 2893 6.497437 TGTATTGCGGATTTGATTTCATCTG 58.503 36.000 0.00 0.00 0.00 2.90
2843 2951 5.352293 TCTTCAATGAATGGTCGATGTCAAG 59.648 40.000 0.00 0.00 0.00 3.02
2865 2973 2.592102 TGGAAATTTGGCAGCTCTCT 57.408 45.000 0.00 0.00 0.00 3.10
2923 3031 0.897621 AACCAATAAAGGCAGCAGGC 59.102 50.000 0.00 0.00 43.74 4.85
2924 3032 3.953612 TCATAACCAATAAAGGCAGCAGG 59.046 43.478 0.00 0.00 0.00 4.85
2925 3033 5.779529 ATCATAACCAATAAAGGCAGCAG 57.220 39.130 0.00 0.00 0.00 4.24
2926 3034 6.543430 AAATCATAACCAATAAAGGCAGCA 57.457 33.333 0.00 0.00 0.00 4.41
2945 3053 6.639632 TGAAAGGCATGCTCCTTATAAATC 57.360 37.500 18.92 7.82 45.25 2.17
3011 3119 9.678260 AGCAGAGAAAAATACTAGATTTCACAT 57.322 29.630 0.00 0.00 35.91 3.21
3012 3120 8.939929 CAGCAGAGAAAAATACTAGATTTCACA 58.060 33.333 0.00 0.00 35.91 3.58
3013 3121 8.940952 ACAGCAGAGAAAAATACTAGATTTCAC 58.059 33.333 0.00 1.29 35.91 3.18
3014 3122 9.155975 GACAGCAGAGAAAAATACTAGATTTCA 57.844 33.333 0.00 0.00 35.91 2.69
3023 3131 6.603095 ACAAATCGACAGCAGAGAAAAATAC 58.397 36.000 0.00 0.00 0.00 1.89
3053 3161 2.517959 TCAGTGCAAAAGGGAAGATGG 58.482 47.619 0.00 0.00 0.00 3.51
3080 3188 8.989980 GTTATACTAACAGCTTCAAGAAACTGT 58.010 33.333 11.86 11.86 44.96 3.55
3083 3191 8.319143 TGGTTATACTAACAGCTTCAAGAAAC 57.681 34.615 0.00 0.00 0.00 2.78
3089 3197 7.847096 TCAAGATGGTTATACTAACAGCTTCA 58.153 34.615 0.00 0.00 37.46 3.02
3090 3198 8.718102 TTCAAGATGGTTATACTAACAGCTTC 57.282 34.615 0.00 0.00 37.46 3.86
3105 3213 7.654022 TGGTTAAAGAAACTTTCAAGATGGT 57.346 32.000 4.34 0.00 38.23 3.55
3107 3215 8.817100 GGTTTGGTTAAAGAAACTTTCAAGATG 58.183 33.333 4.34 0.00 38.23 2.90
3108 3216 8.758829 AGGTTTGGTTAAAGAAACTTTCAAGAT 58.241 29.630 4.34 0.00 38.23 2.40
3109 3217 8.129496 AGGTTTGGTTAAAGAAACTTTCAAGA 57.871 30.769 4.34 0.00 38.23 3.02
3110 3218 8.771920 AAGGTTTGGTTAAAGAAACTTTCAAG 57.228 30.769 4.34 0.00 38.23 3.02
3112 3220 7.038941 TGGAAGGTTTGGTTAAAGAAACTTTCA 60.039 33.333 23.04 14.53 44.12 2.69
3113 3221 7.324935 TGGAAGGTTTGGTTAAAGAAACTTTC 58.675 34.615 18.16 18.16 42.77 2.62
3116 3224 6.439375 AGTTGGAAGGTTTGGTTAAAGAAACT 59.561 34.615 9.36 0.00 38.23 2.66
3118 3226 6.127281 GGAGTTGGAAGGTTTGGTTAAAGAAA 60.127 38.462 0.00 0.00 0.00 2.52
3133 3331 4.584325 TCATTTTCCTGTTGGAGTTGGAAG 59.416 41.667 0.00 0.00 44.24 3.46
3136 3334 3.636300 TGTCATTTTCCTGTTGGAGTTGG 59.364 43.478 0.00 0.00 44.24 3.77
3178 3376 2.228822 GTGCGGTTCACTTTCCAATGAT 59.771 45.455 0.00 0.00 42.38 2.45
3184 3382 5.505654 CCATAATATGTGCGGTTCACTTTCC 60.506 44.000 0.00 0.00 45.81 3.13
3191 3389 3.815401 AGAAGCCATAATATGTGCGGTTC 59.185 43.478 10.06 10.06 33.53 3.62
3257 3455 5.889289 ACACACTTTAGGGTAAAGAGCAAAA 59.111 36.000 12.33 0.00 46.19 2.44
3276 3474 0.322975 ACAGATCAGCAGGGACACAC 59.677 55.000 0.00 0.00 0.00 3.82
3328 3526 5.047590 TCAAACAAGCTCGACCTACAAGATA 60.048 40.000 0.00 0.00 0.00 1.98
3332 3530 3.462483 TCAAACAAGCTCGACCTACAA 57.538 42.857 0.00 0.00 0.00 2.41
3343 3541 6.620678 TCAGCAAGGTATATTTCAAACAAGC 58.379 36.000 0.00 0.00 0.00 4.01
3365 3563 9.740239 GCTTCATCAAATTGCTTATCTATTTCA 57.260 29.630 0.00 0.00 29.78 2.69
3397 3595 5.353938 GCTATTGGTAATACCGTTCTGTGA 58.646 41.667 4.83 0.00 42.58 3.58
3476 3674 7.176285 TGCAATTGAAGCAATAAACTTTCAC 57.824 32.000 10.34 0.00 39.39 3.18
3482 3680 6.783892 TTTCCTGCAATTGAAGCAATAAAC 57.216 33.333 10.34 0.00 42.17 2.01
3487 3685 4.339872 ACATTTCCTGCAATTGAAGCAA 57.660 36.364 10.34 0.00 42.17 3.91
3498 3696 5.124457 TCTCTTCTGCAATTACATTTCCTGC 59.876 40.000 0.00 0.00 0.00 4.85
3593 3791 0.030638 CAGCACTGGGTGGTTTTTCG 59.969 55.000 0.00 0.00 41.72 3.46
3603 3801 1.739562 GAGAGTTCGCAGCACTGGG 60.740 63.158 8.32 8.32 43.85 4.45
3644 3842 0.323629 CCTTTCGGCAACCTCACCTA 59.676 55.000 0.00 0.00 0.00 3.08
3693 3891 3.763897 ACTAAACCATTGGATGAGGTTGC 59.236 43.478 10.37 0.00 44.44 4.17
3712 3910 1.462616 TTGAACTACCGCCGCTACTA 58.537 50.000 0.00 0.00 0.00 1.82
3718 3916 4.114073 TGTATTGTATTGAACTACCGCCG 58.886 43.478 0.00 0.00 0.00 6.46
3732 3930 6.589523 GCACATTGCAAATTTCCTGTATTGTA 59.410 34.615 1.71 0.00 44.26 2.41
3744 3942 1.270199 TGGAAGCGCACATTGCAAATT 60.270 42.857 11.47 0.00 45.36 1.82
3768 3966 6.042777 GCCAGCCTGGAAAATAAATTACTTC 58.957 40.000 16.85 0.00 40.96 3.01
3952 4152 1.131303 TGGAAGGCGGAAAAGGAGGA 61.131 55.000 0.00 0.00 0.00 3.71
3994 4194 4.515191 TGTGTTGGACAAGAAGATAGTTGC 59.485 41.667 0.00 0.00 0.00 4.17
4171 4406 6.013293 AGGCTAGATTAAAGAGACTGGTTTGT 60.013 38.462 0.00 0.00 0.00 2.83
4268 4503 6.097554 AGAGTGGACACCTTATGTAGATCAAG 59.902 42.308 0.00 0.00 43.56 3.02
4291 4526 7.469537 TGGTCAAAGTTCAACCTTTTAAAGA 57.530 32.000 6.24 0.00 32.42 2.52
4296 4531 7.847096 AGTTTATGGTCAAAGTTCAACCTTTT 58.153 30.769 7.83 0.00 32.42 2.27
4300 4535 6.569780 ACAAGTTTATGGTCAAAGTTCAACC 58.430 36.000 0.65 0.65 30.40 3.77
4372 4607 9.825972 ATTGACATGTCATTCGTACTTTAAAAG 57.174 29.630 28.32 0.00 39.64 2.27
4459 4695 1.810151 GCAGTCCCGCTGTTGATTTAA 59.190 47.619 0.00 0.00 46.64 1.52
4515 4763 9.382275 GTATTGGTTAGATGCAAATTGGAAAAT 57.618 29.630 0.00 0.00 0.00 1.82
4548 4796 8.825774 AGGCAAAATAATAGGGAAGAAAATGTT 58.174 29.630 0.00 0.00 0.00 2.71
4648 4896 5.692115 TGAATAGGAACAGCTGGAATACA 57.308 39.130 19.93 4.96 0.00 2.29
4737 4985 5.240623 TGGCATGTAACAGAAGGTTGTTTAG 59.759 40.000 0.00 0.00 41.31 1.85
4872 5120 1.228094 GCTATCTTGCCCAGGCCTC 60.228 63.158 0.00 0.00 41.09 4.70
4903 5151 4.843984 CACGGTTACATAAAAGCAGTTTCG 59.156 41.667 0.00 0.00 0.00 3.46
4944 5193 3.795623 TTACACCGATCAGTTAGGAGC 57.204 47.619 0.00 0.00 0.00 4.70
5006 5255 1.876156 GGCAACAGATATACAGCTGCC 59.124 52.381 15.27 0.80 42.09 4.85
5036 5291 7.114882 GCAGAACATAGATATACACTGCAAG 57.885 40.000 0.00 0.00 45.48 4.01
5118 5434 2.119801 ACCTGCCAGCTATTGACTTG 57.880 50.000 0.00 0.00 0.00 3.16
5220 5536 7.233389 TCTATAACCATCAAGCAGATAGTCC 57.767 40.000 0.00 0.00 34.43 3.85
5246 5562 8.997323 CCCTGAATCTGCTAAATGTATCTAAAG 58.003 37.037 0.00 0.00 0.00 1.85
5319 5635 5.629079 GAATGGAAAGGAGTTCAATTCGT 57.371 39.130 1.47 0.00 43.58 3.85
5406 5722 3.502123 TGTTTCTTTGGAGAACGGGAT 57.498 42.857 0.00 0.00 41.46 3.85
5450 5766 4.151689 TCTGCGTTGCTGTTACAGAATTAC 59.848 41.667 17.40 0.54 34.59 1.89
5567 5885 9.965902 ATTGATGTAATAGAAGAACCAAGAACT 57.034 29.630 0.00 0.00 0.00 3.01
5706 6385 3.693807 AGGATTGAGACACATGTGCAAT 58.306 40.909 25.68 23.73 34.44 3.56
5760 6439 6.809196 AGAGACTGCGAGTAAACTAAAGATTG 59.191 38.462 0.00 0.00 0.00 2.67
5761 6440 6.926313 AGAGACTGCGAGTAAACTAAAGATT 58.074 36.000 0.00 0.00 0.00 2.40
5767 6446 6.171921 ACTTCTAGAGACTGCGAGTAAACTA 58.828 40.000 0.00 0.00 0.00 2.24
5827 6506 6.834168 AAATCATAGTTGAACACCGGAATT 57.166 33.333 9.46 0.27 34.96 2.17
5954 6642 6.868622 ACTAGCGAGAATTTGTCTTCTACAT 58.131 36.000 0.00 0.00 38.10 2.29
5982 6670 2.304761 AGCGTCTTATTTTCCCAGGTCA 59.695 45.455 0.00 0.00 0.00 4.02
5983 6671 2.937149 GAGCGTCTTATTTTCCCAGGTC 59.063 50.000 0.00 0.00 0.00 3.85
6073 6762 1.065418 AGAAGTGTAAGGGCCAATCGG 60.065 52.381 6.18 0.00 0.00 4.18
6074 6763 2.280628 GAGAAGTGTAAGGGCCAATCG 58.719 52.381 6.18 0.00 0.00 3.34
6078 6767 1.440618 TTGGAGAAGTGTAAGGGCCA 58.559 50.000 6.18 0.00 0.00 5.36
6106 6795 7.174599 CCTCAGCCCATTAAAATAGATCTTCTG 59.825 40.741 0.00 0.00 0.00 3.02
6107 6796 7.147230 ACCTCAGCCCATTAAAATAGATCTTCT 60.147 37.037 0.00 0.00 0.00 2.85
6108 6797 7.001073 ACCTCAGCCCATTAAAATAGATCTTC 58.999 38.462 0.00 0.00 0.00 2.87
6115 6804 4.871871 TCCACCTCAGCCCATTAAAATA 57.128 40.909 0.00 0.00 0.00 1.40
6159 6848 6.835174 ACTGACTCATTATTGATGTATGGCT 58.165 36.000 0.00 0.00 37.06 4.75
6228 6917 6.314400 GTGACTTCAGAGAGTACTGGTACTAG 59.686 46.154 12.61 4.44 45.63 2.57
6257 6946 7.419711 TGTCCTATACTCTGAAAAACTAGGG 57.580 40.000 0.00 0.00 0.00 3.53
6267 6956 8.996651 TCAATGTAAGATGTCCTATACTCTGA 57.003 34.615 0.00 0.00 0.00 3.27
6303 6992 5.221145 CGAATGAGGTGATAGAACTACAGCT 60.221 44.000 0.00 0.00 43.42 4.24
6306 6995 6.961360 ATCGAATGAGGTGATAGAACTACA 57.039 37.500 0.00 0.00 0.00 2.74
6333 7022 3.875727 GCTGACATATATGGCTGGCATAG 59.124 47.826 25.12 15.96 36.54 2.23
6338 7027 3.244665 TGGAAGCTGACATATATGGCTGG 60.245 47.826 22.70 14.98 36.54 4.85
6393 7082 3.790089 AGACAGTTTCCCTTTAGGTGG 57.210 47.619 0.00 0.00 36.75 4.61
6527 7216 4.219944 GGTTCTTGACCCAAGTTTATTCCC 59.780 45.833 6.59 0.00 43.06 3.97
6568 7257 8.242053 CAGAAATATCAATGGTTGCTGGATATC 58.758 37.037 0.00 0.00 31.76 1.63
6588 7277 7.596494 ACAATCACATTTCGTTGATCAGAAAT 58.404 30.769 14.18 14.18 44.91 2.17
6605 7294 2.223782 GCTTTGTTGGCTGACAATCACA 60.224 45.455 0.00 0.00 41.95 3.58
6614 7303 0.746063 TGTCTTGGCTTTGTTGGCTG 59.254 50.000 0.00 0.00 0.00 4.85
6704 7393 4.207165 CAGAACCTGAACTTCCCAGAAAA 58.793 43.478 0.00 0.00 32.44 2.29
6722 7411 3.307691 CCTTAAGCACAGATCCACCAGAA 60.308 47.826 0.00 0.00 0.00 3.02
6763 7452 3.893720 AGCAAATCACGAGCAGAAAAAG 58.106 40.909 0.00 0.00 0.00 2.27
6764 7453 3.565482 AGAGCAAATCACGAGCAGAAAAA 59.435 39.130 0.00 0.00 0.00 1.94
6769 7458 4.871993 AATTAGAGCAAATCACGAGCAG 57.128 40.909 0.00 0.00 0.00 4.24
6770 7459 6.763135 AGAATAATTAGAGCAAATCACGAGCA 59.237 34.615 0.00 0.00 0.00 4.26
6774 7463 8.818141 TCCTAGAATAATTAGAGCAAATCACG 57.182 34.615 0.00 0.00 0.00 4.35
6791 7480 7.234577 AGAGAAGACACTGAAAACTCCTAGAAT 59.765 37.037 0.00 0.00 0.00 2.40
6799 7488 6.180472 TGGAAAAGAGAAGACACTGAAAACT 58.820 36.000 0.00 0.00 0.00 2.66
6803 7492 6.039717 CCAAATGGAAAAGAGAAGACACTGAA 59.960 38.462 0.00 0.00 37.39 3.02
6807 7496 4.827284 TCCCAAATGGAAAAGAGAAGACAC 59.173 41.667 0.00 0.00 41.40 3.67
6809 7498 5.316987 TCTCCCAAATGGAAAAGAGAAGAC 58.683 41.667 0.00 0.00 44.57 3.01
6829 7518 2.147150 GCAAGAAGGTGGAGTGTTCTC 58.853 52.381 0.00 0.00 39.76 2.87
6830 7519 1.490490 TGCAAGAAGGTGGAGTGTTCT 59.510 47.619 0.00 0.00 31.71 3.01
6831 7520 1.876156 CTGCAAGAAGGTGGAGTGTTC 59.124 52.381 0.00 0.00 34.07 3.18
6833 7522 0.536006 GCTGCAAGAAGGTGGAGTGT 60.536 55.000 0.00 0.00 39.05 3.55
6859 7617 9.421806 CAACAATATTATCTGAAAAAGGTTGCA 57.578 29.630 0.00 0.00 0.00 4.08
6860 7618 9.638239 TCAACAATATTATCTGAAAAAGGTTGC 57.362 29.630 0.00 0.00 32.93 4.17
6870 7628 8.956426 GGGACAAACTTCAACAATATTATCTGA 58.044 33.333 0.00 0.00 0.00 3.27
6871 7629 8.739039 TGGGACAAACTTCAACAATATTATCTG 58.261 33.333 0.00 0.00 31.92 2.90
6872 7630 8.739972 GTGGGACAAACTTCAACAATATTATCT 58.260 33.333 0.00 0.00 44.16 1.98
6888 7646 4.782019 TCATTAAGCATGTGGGACAAAC 57.218 40.909 0.00 0.00 44.16 2.93
6893 7651 4.947388 GGTAACTTCATTAAGCATGTGGGA 59.053 41.667 0.00 0.00 36.05 4.37
6894 7652 4.704540 TGGTAACTTCATTAAGCATGTGGG 59.295 41.667 0.00 0.00 36.05 4.61


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

AutoCloner maintained by Alex Coulton.