Multiple sequence alignment - TraesCS7A01G546300

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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 TraesCS7A01G546300 chr7A 100.000 2922 0 0 394 3315 721893016 721895937 0.000000e+00 5397.0
1 TraesCS7A01G546300 chr7A 86.194 1637 152 31 896 2501 721818118 721819711 0.000000e+00 1703.0
2 TraesCS7A01G546300 chr7A 82.388 829 120 17 1197 2012 721779777 721780592 0.000000e+00 699.0
3 TraesCS7A01G546300 chr7A 80.359 835 131 25 1196 2018 721719182 721719995 1.320000e-168 603.0
4 TraesCS7A01G546300 chr7A 79.037 353 19 18 567 893 721817733 721818056 1.210000e-44 191.0
5 TraesCS7A01G546300 chr7A 80.128 156 29 2 400 554 24770927 24770773 7.520000e-22 115.0
6 TraesCS7A01G546300 chr7A 86.667 105 13 1 464 567 61779349 61779245 7.520000e-22 115.0
7 TraesCS7A01G546300 chr7A 100.000 58 0 0 1 58 721892623 721892680 1.260000e-19 108.0
8 TraesCS7A01G546300 chr7D 92.898 2267 130 12 1064 3313 626298945 626301197 0.000000e+00 3265.0
9 TraesCS7A01G546300 chr7D 80.849 872 132 28 1196 2042 626233021 626233882 0.000000e+00 652.0
10 TraesCS7A01G546300 chr7D 80.072 838 131 24 1171 1987 626260098 626260920 1.020000e-164 590.0
11 TraesCS7A01G546300 chr7D 81.046 459 67 14 2873 3315 263658128 263657674 6.810000e-92 348.0
12 TraesCS7A01G546300 chr7D 81.140 456 61 15 2873 3315 143948076 143948519 3.170000e-90 342.0
13 TraesCS7A01G546300 chr7D 84.507 355 27 9 567 893 626298398 626298752 3.190000e-85 326.0
14 TraesCS7A01G546300 chr7D 79.565 460 66 17 2873 3315 231181023 231180575 1.490000e-78 303.0
15 TraesCS7A01G546300 chr7D 86.179 123 3 5 892 1002 626298813 626298933 1.620000e-23 121.0
16 TraesCS7A01G546300 chr7B 86.988 1514 120 30 985 2487 725813378 725811931 0.000000e+00 1633.0
17 TraesCS7A01G546300 chr7B 88.823 1342 116 10 1033 2358 726016591 726017914 0.000000e+00 1616.0
18 TraesCS7A01G546300 chr7B 80.238 840 140 19 1198 2021 726004603 726005432 2.830000e-170 608.0
19 TraesCS7A01G546300 chr7B 78.360 878 149 31 1189 2045 726009871 726010728 6.300000e-147 531.0
20 TraesCS7A01G546300 chr7B 83.420 386 62 1 2873 3258 323726091 323726474 1.130000e-94 357.0
21 TraesCS7A01G546300 chr7B 89.420 293 18 7 2437 2724 726017913 726018197 1.130000e-94 357.0
22 TraesCS7A01G546300 chr7B 81.093 439 66 15 2873 3305 494754897 494754470 5.300000e-88 335.0
23 TraesCS7A01G546300 chr7B 81.435 237 23 11 567 793 725813852 725813627 1.220000e-39 174.0
24 TraesCS7A01G546300 chr7B 84.076 157 5 5 757 893 726016259 726016415 2.070000e-27 134.0
25 TraesCS7A01G546300 chr7B 98.039 51 1 0 2728 2778 726018513 726018563 4.560000e-14 89.8
26 TraesCS7A01G546300 chr7B 98.000 50 1 0 2729 2778 726018476 726018525 1.640000e-13 87.9
27 TraesCS7A01G546300 chr7B 95.556 45 1 1 891 935 725813491 725813448 1.650000e-08 71.3
28 TraesCS7A01G546300 chrUn 89.109 1212 106 9 1186 2381 87863290 87864491 0.000000e+00 1483.0
29 TraesCS7A01G546300 chrUn 79.804 817 131 27 1198 1994 87838277 87839079 6.210000e-157 564.0
30 TraesCS7A01G546300 chrUn 94.737 57 3 0 837 893 87862965 87863021 4.560000e-14 89.8
31 TraesCS7A01G546300 chr1D 83.212 411 59 9 2873 3277 138311165 138310759 5.220000e-98 368.0
32 TraesCS7A01G546300 chr1D 81.713 432 67 10 2873 3299 384464648 384465072 1.890000e-92 350.0
33 TraesCS7A01G546300 chr2D 84.699 366 47 6 2873 3236 500642625 500642983 1.130000e-94 357.0
34 TraesCS7A01G546300 chr1B 83.516 364 54 5 2873 3234 193835312 193835671 5.300000e-88 335.0
35 TraesCS7A01G546300 chr3D 79.869 457 73 16 2873 3315 20109971 20110422 1.920000e-82 316.0
36 TraesCS7A01G546300 chr3D 78.993 457 76 12 2873 3315 171268386 171268836 8.990000e-76 294.0
37 TraesCS7A01G546300 chr3D 91.716 169 13 1 394 561 17695101 17695269 1.990000e-57 233.0
38 TraesCS7A01G546300 chr3A 79.295 454 71 17 2876 3315 525668711 525668267 2.500000e-76 296.0
39 TraesCS7A01G546300 chr6D 82.320 362 31 19 2963 3309 462837089 462837432 1.950000e-72 283.0
40 TraesCS7A01G546300 chr6D 95.402 174 7 1 394 566 124164603 124164776 3.260000e-70 276.0
41 TraesCS7A01G546300 chr6D 98.276 58 1 0 1 58 124164492 124164549 5.850000e-18 102.0
42 TraesCS7A01G546300 chr4D 87.500 232 25 4 2648 2877 461459047 461458818 7.050000e-67 265.0
43 TraesCS7A01G546300 chr3B 82.464 211 20 5 2574 2769 10099943 10100151 5.690000e-38 169.0
44 TraesCS7A01G546300 chr3B 76.301 173 35 4 397 567 633387951 633387783 1.640000e-13 87.9
45 TraesCS7A01G546300 chr6A 78.035 173 36 2 395 565 557925556 557925384 1.260000e-19 108.0
46 TraesCS7A01G546300 chr5A 86.869 99 10 2 472 567 47582631 47582729 1.260000e-19 108.0
47 TraesCS7A01G546300 chr5A 85.577 104 12 3 464 565 129983510 129983408 4.520000e-19 106.0
48 TraesCS7A01G546300 chr6B 85.047 107 13 2 472 575 460917473 460917367 4.520000e-19 106.0


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 TraesCS7A01G546300 chr7A 721892623 721895937 3314 False 2752.500000 5397 100.000000 1 3315 2 chr7A.!!$F4 3314
1 TraesCS7A01G546300 chr7A 721817733 721819711 1978 False 947.000000 1703 82.615500 567 2501 2 chr7A.!!$F3 1934
2 TraesCS7A01G546300 chr7A 721779777 721780592 815 False 699.000000 699 82.388000 1197 2012 1 chr7A.!!$F2 815
3 TraesCS7A01G546300 chr7A 721719182 721719995 813 False 603.000000 603 80.359000 1196 2018 1 chr7A.!!$F1 822
4 TraesCS7A01G546300 chr7D 626298398 626301197 2799 False 1237.333333 3265 87.861333 567 3313 3 chr7D.!!$F4 2746
5 TraesCS7A01G546300 chr7D 626233021 626233882 861 False 652.000000 652 80.849000 1196 2042 1 chr7D.!!$F2 846
6 TraesCS7A01G546300 chr7D 626260098 626260920 822 False 590.000000 590 80.072000 1171 1987 1 chr7D.!!$F3 816
7 TraesCS7A01G546300 chr7B 725811931 725813852 1921 True 626.100000 1633 87.993000 567 2487 3 chr7B.!!$R2 1920
8 TraesCS7A01G546300 chr7B 726004603 726005432 829 False 608.000000 608 80.238000 1198 2021 1 chr7B.!!$F2 823
9 TraesCS7A01G546300 chr7B 726009871 726010728 857 False 531.000000 531 78.360000 1189 2045 1 chr7B.!!$F3 856
10 TraesCS7A01G546300 chr7B 726016259 726018563 2304 False 456.940000 1616 91.671600 757 2778 5 chr7B.!!$F4 2021
11 TraesCS7A01G546300 chrUn 87862965 87864491 1526 False 786.400000 1483 91.923000 837 2381 2 chrUn.!!$F2 1544
12 TraesCS7A01G546300 chrUn 87838277 87839079 802 False 564.000000 564 79.804000 1198 1994 1 chrUn.!!$F1 796

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
451 452 0.098728 CGCCCGAATGATGTCCAAAC 59.901 55.0 0.00 0.0 0.00 2.93 F
562 563 0.244450 CAACGCACGGGGTTCTACTA 59.756 55.0 3.88 0.0 36.59 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1878 0.766131 TCCTCCACTTTAACCGCCAA 59.234 50.000 0.0 0.0 0.0 4.52 R
2381 2708 1.195448 CGAGCAGCCAAAACAGTAGTG 59.805 52.381 0.0 0.0 0.0 2.74 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
18 19 2.506065 TTTTTGTTGGGACCGTGGG 58.494 52.632 0.00 0.00 0.00 4.61
19 20 0.324460 TTTTTGTTGGGACCGTGGGT 60.324 50.000 0.00 0.00 39.44 4.51
20 21 0.324460 TTTTGTTGGGACCGTGGGTT 60.324 50.000 0.00 0.00 35.25 4.11
21 22 1.038130 TTTGTTGGGACCGTGGGTTG 61.038 55.000 0.00 0.00 35.25 3.77
22 23 1.923006 TTGTTGGGACCGTGGGTTGA 61.923 55.000 0.00 0.00 35.25 3.18
23 24 1.152922 GTTGGGACCGTGGGTTGAA 60.153 57.895 0.00 0.00 35.25 2.69
24 25 1.149627 TTGGGACCGTGGGTTGAAG 59.850 57.895 0.00 0.00 35.25 3.02
25 26 1.346479 TTGGGACCGTGGGTTGAAGA 61.346 55.000 0.00 0.00 35.25 2.87
26 27 1.131303 TGGGACCGTGGGTTGAAGAT 61.131 55.000 0.00 0.00 35.25 2.40
27 28 0.906775 GGGACCGTGGGTTGAAGATA 59.093 55.000 0.00 0.00 35.25 1.98
28 29 1.279846 GGGACCGTGGGTTGAAGATAA 59.720 52.381 0.00 0.00 35.25 1.75
29 30 2.353323 GGACCGTGGGTTGAAGATAAC 58.647 52.381 0.00 0.00 35.25 1.89
30 31 2.289819 GGACCGTGGGTTGAAGATAACA 60.290 50.000 0.00 0.00 35.25 2.41
31 32 2.740447 GACCGTGGGTTGAAGATAACAC 59.260 50.000 0.00 0.00 35.25 3.32
33 34 1.730064 CGTGGGTTGAAGATAACACGG 59.270 52.381 7.08 0.00 45.39 4.94
34 35 2.774687 GTGGGTTGAAGATAACACGGT 58.225 47.619 0.00 0.00 36.76 4.83
35 36 2.482721 GTGGGTTGAAGATAACACGGTG 59.517 50.000 6.58 6.58 36.76 4.94
36 37 2.081462 GGGTTGAAGATAACACGGTGG 58.919 52.381 13.48 0.00 32.22 4.61
37 38 2.289819 GGGTTGAAGATAACACGGTGGA 60.290 50.000 13.48 0.00 32.22 4.02
38 39 3.606687 GGTTGAAGATAACACGGTGGAT 58.393 45.455 13.48 5.31 32.22 3.41
39 40 4.383335 GGGTTGAAGATAACACGGTGGATA 60.383 45.833 13.48 5.77 32.22 2.59
40 41 4.809426 GGTTGAAGATAACACGGTGGATAG 59.191 45.833 13.48 0.00 32.22 2.08
41 42 5.416947 GTTGAAGATAACACGGTGGATAGT 58.583 41.667 13.48 0.00 0.00 2.12
42 43 6.406177 GGTTGAAGATAACACGGTGGATAGTA 60.406 42.308 13.48 0.00 32.22 1.82
43 44 6.140303 TGAAGATAACACGGTGGATAGTAC 57.860 41.667 13.48 0.24 0.00 2.73
44 45 5.653330 TGAAGATAACACGGTGGATAGTACA 59.347 40.000 13.48 2.80 0.00 2.90
45 46 6.153170 TGAAGATAACACGGTGGATAGTACAA 59.847 38.462 13.48 0.00 0.00 2.41
46 47 6.534475 AGATAACACGGTGGATAGTACAAA 57.466 37.500 13.48 0.00 0.00 2.83
47 48 6.335777 AGATAACACGGTGGATAGTACAAAC 58.664 40.000 13.48 0.00 0.00 2.93
48 49 4.339872 AACACGGTGGATAGTACAAACA 57.660 40.909 13.48 0.00 0.00 2.83
49 50 4.339872 ACACGGTGGATAGTACAAACAA 57.660 40.909 13.48 0.00 0.00 2.83
50 51 4.060205 ACACGGTGGATAGTACAAACAAC 58.940 43.478 13.48 0.00 0.00 3.32
51 52 3.434299 CACGGTGGATAGTACAAACAACC 59.566 47.826 0.00 0.00 0.00 3.77
52 53 3.071312 ACGGTGGATAGTACAAACAACCA 59.929 43.478 0.00 0.00 0.00 3.67
53 54 3.434299 CGGTGGATAGTACAAACAACCAC 59.566 47.826 0.00 0.00 40.86 4.16
54 55 4.391155 GGTGGATAGTACAAACAACCACA 58.609 43.478 18.53 0.00 42.07 4.17
55 56 5.007682 GGTGGATAGTACAAACAACCACAT 58.992 41.667 18.53 0.00 42.07 3.21
56 57 5.123344 GGTGGATAGTACAAACAACCACATC 59.877 44.000 18.53 6.29 42.07 3.06
57 58 5.703592 GTGGATAGTACAAACAACCACATCA 59.296 40.000 0.00 0.00 41.05 3.07
411 412 2.452116 TGGACTGTCCAGAGGGTTG 58.548 57.895 25.12 0.00 42.67 3.77
412 413 1.127567 TGGACTGTCCAGAGGGTTGG 61.128 60.000 25.12 0.00 42.67 3.77
413 414 0.836400 GGACTGTCCAGAGGGTTGGA 60.836 60.000 21.70 0.00 44.84 3.53
421 422 3.537337 TCCAGAGGGTTGGATTTTAGGA 58.463 45.455 0.00 0.00 42.24 2.94
422 423 3.523564 TCCAGAGGGTTGGATTTTAGGAG 59.476 47.826 0.00 0.00 42.24 3.69
423 424 3.282885 CAGAGGGTTGGATTTTAGGAGC 58.717 50.000 0.00 0.00 0.00 4.70
424 425 2.242452 AGAGGGTTGGATTTTAGGAGCC 59.758 50.000 0.00 0.00 0.00 4.70
425 426 1.288037 AGGGTTGGATTTTAGGAGCCC 59.712 52.381 0.00 0.00 35.26 5.19
426 427 1.389555 GGTTGGATTTTAGGAGCCCG 58.610 55.000 0.00 0.00 0.00 6.13
427 428 0.738975 GTTGGATTTTAGGAGCCCGC 59.261 55.000 0.00 0.00 0.00 6.13
428 429 0.746563 TTGGATTTTAGGAGCCCGCG 60.747 55.000 0.00 0.00 0.00 6.46
429 430 1.892391 GGATTTTAGGAGCCCGCGG 60.892 63.158 21.04 21.04 0.00 6.46
430 431 1.892391 GATTTTAGGAGCCCGCGGG 60.892 63.158 40.26 40.26 38.57 6.13
445 446 4.875713 GGGCCGCCCGAATGATGT 62.876 66.667 14.19 0.00 32.13 3.06
446 447 3.279875 GGCCGCCCGAATGATGTC 61.280 66.667 0.00 0.00 0.00 3.06
447 448 3.279875 GCCGCCCGAATGATGTCC 61.280 66.667 0.00 0.00 0.00 4.02
448 449 2.189257 CCGCCCGAATGATGTCCA 59.811 61.111 0.00 0.00 0.00 4.02
449 450 1.451207 CCGCCCGAATGATGTCCAA 60.451 57.895 0.00 0.00 0.00 3.53
450 451 1.029408 CCGCCCGAATGATGTCCAAA 61.029 55.000 0.00 0.00 0.00 3.28
451 452 0.098728 CGCCCGAATGATGTCCAAAC 59.901 55.000 0.00 0.00 0.00 2.93
452 453 1.173043 GCCCGAATGATGTCCAAACA 58.827 50.000 0.00 0.00 40.38 2.83
454 455 2.480073 GCCCGAATGATGTCCAAACATG 60.480 50.000 0.00 0.00 46.20 3.21
455 456 3.016031 CCCGAATGATGTCCAAACATGA 58.984 45.455 0.00 0.00 46.20 3.07
456 457 3.181497 CCCGAATGATGTCCAAACATGAC 60.181 47.826 0.00 0.00 46.20 3.06
457 458 3.181497 CCGAATGATGTCCAAACATGACC 60.181 47.826 0.00 0.00 46.20 4.02
458 459 3.485711 CGAATGATGTCCAAACATGACCG 60.486 47.826 0.00 0.00 46.20 4.79
459 460 1.164411 TGATGTCCAAACATGACCGC 58.836 50.000 0.00 0.00 46.20 5.68
460 461 1.164411 GATGTCCAAACATGACCGCA 58.836 50.000 0.00 0.00 46.20 5.69
461 462 0.881118 ATGTCCAAACATGACCGCAC 59.119 50.000 0.00 0.00 44.51 5.34
462 463 0.464554 TGTCCAAACATGACCGCACA 60.465 50.000 0.00 0.00 31.60 4.57
463 464 0.881118 GTCCAAACATGACCGCACAT 59.119 50.000 0.00 0.00 0.00 3.21
464 465 2.080693 GTCCAAACATGACCGCACATA 58.919 47.619 0.00 0.00 0.00 2.29
465 466 2.682856 GTCCAAACATGACCGCACATAT 59.317 45.455 0.00 0.00 0.00 1.78
466 467 3.874543 GTCCAAACATGACCGCACATATA 59.125 43.478 0.00 0.00 0.00 0.86
467 468 4.334203 GTCCAAACATGACCGCACATATAA 59.666 41.667 0.00 0.00 0.00 0.98
468 469 5.008613 GTCCAAACATGACCGCACATATAAT 59.991 40.000 0.00 0.00 0.00 1.28
469 470 6.203915 GTCCAAACATGACCGCACATATAATA 59.796 38.462 0.00 0.00 0.00 0.98
470 471 6.768381 TCCAAACATGACCGCACATATAATAA 59.232 34.615 0.00 0.00 0.00 1.40
471 472 7.283354 TCCAAACATGACCGCACATATAATAAA 59.717 33.333 0.00 0.00 0.00 1.40
472 473 7.591057 CCAAACATGACCGCACATATAATAAAG 59.409 37.037 0.00 0.00 0.00 1.85
473 474 8.341903 CAAACATGACCGCACATATAATAAAGA 58.658 33.333 0.00 0.00 0.00 2.52
474 475 8.445275 AACATGACCGCACATATAATAAAGAA 57.555 30.769 0.00 0.00 0.00 2.52
475 476 8.445275 ACATGACCGCACATATAATAAAGAAA 57.555 30.769 0.00 0.00 0.00 2.52
476 477 9.066892 ACATGACCGCACATATAATAAAGAAAT 57.933 29.630 0.00 0.00 0.00 2.17
477 478 9.333497 CATGACCGCACATATAATAAAGAAATG 57.667 33.333 0.00 0.00 0.00 2.32
478 479 8.669946 TGACCGCACATATAATAAAGAAATGA 57.330 30.769 0.00 0.00 0.00 2.57
479 480 9.114952 TGACCGCACATATAATAAAGAAATGAA 57.885 29.630 0.00 0.00 0.00 2.57
500 501 8.970859 ATGAATTTCGATCTTAAAGATGACCT 57.029 30.769 0.00 0.00 34.53 3.85
501 502 8.792830 TGAATTTCGATCTTAAAGATGACCTT 57.207 30.769 0.00 0.00 34.53 3.50
502 503 9.884636 TGAATTTCGATCTTAAAGATGACCTTA 57.115 29.630 0.00 0.00 34.53 2.69
506 507 9.884636 TTTCGATCTTAAAGATGACCTTAATCA 57.115 29.630 0.00 0.00 34.53 2.57
540 541 7.753309 TTTATTTACATGCATTATAGCCCGT 57.247 32.000 0.00 0.00 0.00 5.28
541 542 8.850007 TTTATTTACATGCATTATAGCCCGTA 57.150 30.769 0.00 0.00 0.00 4.02
542 543 6.985188 ATTTACATGCATTATAGCCCGTAG 57.015 37.500 0.00 0.00 0.00 3.51
543 544 2.699954 ACATGCATTATAGCCCGTAGC 58.300 47.619 0.00 0.00 44.25 3.58
556 557 2.667199 GTAGCAACGCACGGGGTT 60.667 61.111 0.00 0.00 39.22 4.11
557 558 2.357760 TAGCAACGCACGGGGTTC 60.358 61.111 3.88 1.39 36.59 3.62
558 559 2.874664 TAGCAACGCACGGGGTTCT 61.875 57.895 3.88 7.00 36.59 3.01
559 560 1.534336 TAGCAACGCACGGGGTTCTA 61.534 55.000 3.88 6.30 36.59 2.10
560 561 2.674084 GCAACGCACGGGGTTCTAC 61.674 63.158 3.88 0.00 36.59 2.59
561 562 1.005394 CAACGCACGGGGTTCTACT 60.005 57.895 3.88 0.00 36.59 2.57
562 563 0.244450 CAACGCACGGGGTTCTACTA 59.756 55.000 3.88 0.00 36.59 1.82
563 564 0.529378 AACGCACGGGGTTCTACTAG 59.471 55.000 0.00 0.00 33.50 2.57
564 565 0.610232 ACGCACGGGGTTCTACTAGT 60.610 55.000 0.00 0.00 0.00 2.57
565 566 1.340017 ACGCACGGGGTTCTACTAGTA 60.340 52.381 1.89 1.89 0.00 1.82
593 594 2.437343 GCACGAGTAGCTGTCGCAC 61.437 63.158 17.49 8.32 41.26 5.34
614 615 2.536130 CGGAAATTATTGTCGTCACGGC 60.536 50.000 0.00 0.00 0.00 5.68
640 641 1.441515 GCAATGCACGCAGTCACTG 60.442 57.895 0.00 0.00 41.61 3.66
748 750 3.179925 ATGCATGCATGGAGTTCGT 57.820 47.368 31.74 5.52 35.03 3.85
749 751 1.019673 ATGCATGCATGGAGTTCGTC 58.980 50.000 31.74 9.08 35.03 4.20
893 937 1.093159 AGCGATCGAGTTTACGACCT 58.907 50.000 21.57 0.00 44.84 3.85
894 938 1.063764 AGCGATCGAGTTTACGACCTC 59.936 52.381 21.57 0.00 44.84 3.85
992 1128 2.297597 CCTCTCCAACGAGTCTCAACTT 59.702 50.000 0.00 0.00 35.28 2.66
1002 1197 4.527038 ACGAGTCTCAACTTCCTTATCCAA 59.473 41.667 0.00 0.00 35.28 3.53
1006 1201 5.187967 AGTCTCAACTTCCTTATCCAACGAT 59.812 40.000 0.00 0.00 28.74 3.73
1008 1203 4.766375 TCAACTTCCTTATCCAACGATCC 58.234 43.478 0.00 0.00 0.00 3.36
1009 1204 3.454371 ACTTCCTTATCCAACGATCCG 57.546 47.619 0.00 0.00 0.00 4.18
1010 1205 2.135933 CTTCCTTATCCAACGATCCGC 58.864 52.381 0.00 0.00 0.00 5.54
1011 1206 1.410004 TCCTTATCCAACGATCCGCT 58.590 50.000 0.00 0.00 0.00 5.52
1012 1207 1.068588 TCCTTATCCAACGATCCGCTG 59.931 52.381 0.00 0.00 0.00 5.18
1013 1208 1.502231 CTTATCCAACGATCCGCTGG 58.498 55.000 2.68 2.68 43.45 4.85
1015 1210 2.577059 TCCAACGATCCGCTGGAC 59.423 61.111 7.32 0.00 45.33 4.02
1016 1211 2.885644 CCAACGATCCGCTGGACG 60.886 66.667 2.94 13.40 44.67 4.79
1025 1220 3.285371 CGCTGGACGGGACTAACT 58.715 61.111 0.00 0.00 38.44 2.24
1026 1221 2.485677 CGCTGGACGGGACTAACTA 58.514 57.895 0.00 0.00 38.44 2.24
1030 1225 0.333993 TGGACGGGACTAACTAGGCT 59.666 55.000 0.00 0.00 0.00 4.58
1031 1226 0.745468 GGACGGGACTAACTAGGCTG 59.255 60.000 0.00 0.00 0.00 4.85
1051 1246 2.771943 TGTCACATCCCTTCCATCTACC 59.228 50.000 0.00 0.00 0.00 3.18
1062 1257 1.002659 TCCATCTACCACAACCAACGG 59.997 52.381 0.00 0.00 0.00 4.44
1063 1258 0.802494 CATCTACCACAACCAACGGC 59.198 55.000 0.00 0.00 0.00 5.68
1064 1259 0.672401 ATCTACCACAACCAACGGCG 60.672 55.000 4.80 4.80 0.00 6.46
1065 1260 1.595929 CTACCACAACCAACGGCGT 60.596 57.895 6.77 6.77 0.00 5.68
1117 1312 2.838225 GATCCTCTTCCCCGCGGA 60.838 66.667 30.73 3.89 35.88 5.54
1358 1583 2.668550 GCCAGTTTCTTCCGCGGT 60.669 61.111 27.15 0.00 0.00 5.68
1390 1615 2.503061 CGCCTGCTACCAGCTGAT 59.497 61.111 17.39 0.00 41.94 2.90
1400 1625 2.672908 CAGCTGATGTGCAGGGGA 59.327 61.111 8.42 0.00 45.03 4.81
1481 1739 4.344865 ATGACCGGTGGTGGTGCC 62.345 66.667 14.63 0.00 44.01 5.01
1611 1878 2.135933 GCGTGTACAAGAGCAAGAACT 58.864 47.619 13.30 0.00 0.00 3.01
2046 2330 1.446792 CAGCTCCGATGACACGCTT 60.447 57.895 0.00 0.00 0.00 4.68
2050 2334 2.885644 CCGATGACACGCTTCCCG 60.886 66.667 0.00 0.00 44.21 5.14
2051 2335 2.885644 CGATGACACGCTTCCCGG 60.886 66.667 0.00 0.00 42.52 5.73
2052 2336 3.195698 GATGACACGCTTCCCGGC 61.196 66.667 0.00 0.00 42.52 6.13
2053 2337 3.950794 GATGACACGCTTCCCGGCA 62.951 63.158 0.00 0.00 42.52 5.69
2060 2344 2.829914 GCTTCCCGGCATGCATGA 60.830 61.111 30.64 9.49 0.00 3.07
2061 2345 2.198287 GCTTCCCGGCATGCATGAT 61.198 57.895 30.64 0.00 0.00 2.45
2073 2366 1.357690 GCATGATGCATCCACCACG 59.642 57.895 23.67 6.94 44.26 4.94
2289 2616 1.757699 GTCCCGCTCTAAACAGAGGAT 59.242 52.381 3.98 0.00 35.41 3.24
2359 2686 4.223700 AGAACATGTAGATGGCTCTGTTCA 59.776 41.667 13.70 5.77 35.05 3.18
2381 2708 2.421424 GGTCTTGGAATCACATGACAGC 59.579 50.000 0.00 0.00 43.44 4.40
2382 2709 3.076621 GTCTTGGAATCACATGACAGCA 58.923 45.455 0.00 0.00 42.10 4.41
2532 2867 9.619316 TTATGTTGTGCTGTGTTTATTTCATAC 57.381 29.630 0.00 0.00 0.00 2.39
2603 2941 2.416431 GCATGTTGCTGAGGGATGTTTC 60.416 50.000 0.00 0.00 40.96 2.78
2644 2982 0.107263 TTGTGGCACAGTTGAGCAGA 60.107 50.000 20.97 0.00 41.80 4.26
2694 3032 3.854286 CGATATGCTCGGTTGTTTACC 57.146 47.619 0.00 0.00 43.82 2.85
2771 3384 7.040132 TGTTGTGCAAATCCATACATCAAACTA 60.040 33.333 0.00 0.00 0.00 2.24
2813 3430 2.020720 ACACATCAAAACACTTGCCGA 58.979 42.857 0.00 0.00 0.00 5.54
2843 3460 2.516225 GCCTATCCGGTTGTGGGC 60.516 66.667 13.61 13.61 34.25 5.36
2856 3473 3.442625 GGTTGTGGGCCAATAGTAAACTC 59.557 47.826 8.40 0.00 35.02 3.01
2865 3482 7.348801 TGGGCCAATAGTAAACTCTCCTAATAA 59.651 37.037 2.13 0.00 0.00 1.40
2902 3519 4.274950 CGCCGGACAAAGGAAATTGTATAT 59.725 41.667 5.05 0.00 43.31 0.86
2904 3521 5.298276 GCCGGACAAAGGAAATTGTATATGA 59.702 40.000 5.05 0.00 43.31 2.15
2935 3552 3.036026 CCTCGACATCGTGGTTCAG 57.964 57.895 13.02 0.00 45.02 3.02
2953 3570 6.038356 GGTTCAGACCGATAAAAATCTACGA 58.962 40.000 0.00 0.00 35.91 3.43
2969 3586 2.859165 ACGATGAATGTGTGGGAGTT 57.141 45.000 0.00 0.00 0.00 3.01
3007 3624 5.940470 AGGTTCCGCTATTGATTATTGATCC 59.060 40.000 0.00 0.00 33.60 3.36
3008 3625 5.163854 GGTTCCGCTATTGATTATTGATCCG 60.164 44.000 0.00 0.00 33.60 4.18
3028 3645 1.133407 GAGAGGTGTCTCGGTCATGTC 59.867 57.143 0.00 0.00 44.47 3.06
3029 3646 0.179161 GAGGTGTCTCGGTCATGTCG 60.179 60.000 0.00 0.00 0.00 4.35
3049 3666 1.278238 GCATGTTCTCGAACCCGTAG 58.722 55.000 7.28 0.00 40.46 3.51
3067 3684 4.817517 CGTAGGATCACACACTTAAGGTT 58.182 43.478 7.53 0.00 0.00 3.50
3069 3686 5.336531 CGTAGGATCACACACTTAAGGTTCT 60.337 44.000 7.53 0.00 0.00 3.01
3070 3687 5.153950 AGGATCACACACTTAAGGTTCTC 57.846 43.478 7.53 0.00 0.00 2.87
3071 3688 3.927142 GGATCACACACTTAAGGTTCTCG 59.073 47.826 7.53 0.00 0.00 4.04
3113 3730 5.386060 TGGGATATTCATACTGACGAGACT 58.614 41.667 0.00 0.00 0.00 3.24
3121 3738 8.809159 ATTCATACTGACGAGACTGAATATTG 57.191 34.615 0.00 0.00 34.74 1.90
3124 3741 8.251026 TCATACTGACGAGACTGAATATTGTTT 58.749 33.333 0.00 0.00 0.00 2.83
3133 3750 7.009179 AGACTGAATATTGTTTGGAGTCTCA 57.991 36.000 1.47 0.00 34.94 3.27
3141 3758 3.184628 TGTTTGGAGTCTCAGATGGGAT 58.815 45.455 1.47 0.00 0.00 3.85
3145 3762 1.479573 GGAGTCTCAGATGGGATCCGA 60.480 57.143 5.45 1.07 0.00 4.55
3153 3770 2.566279 CAGATGGGATCCGAGACATCAT 59.434 50.000 22.95 12.54 41.55 2.45
3154 3771 2.566279 AGATGGGATCCGAGACATCATG 59.434 50.000 22.95 0.00 41.55 3.07
3170 3787 0.250209 CATGAGGAGCTCCGGAATGG 60.250 60.000 26.95 11.89 42.08 3.16
3172 3789 0.909610 TGAGGAGCTCCGGAATGGTT 60.910 55.000 26.95 6.87 42.08 3.67
3174 3791 0.909610 AGGAGCTCCGGAATGGTTCA 60.910 55.000 26.95 0.00 42.08 3.18
3216 3833 4.109766 GGAAAGTGTTTTTCAGGGTTTCG 58.890 43.478 2.52 0.00 0.00 3.46
3225 3842 7.328982 GTGTTTTTCAGGGTTTCGAAAAAGTTA 59.671 33.333 13.10 0.00 46.29 2.24
3228 3845 4.139038 TCAGGGTTTCGAAAAAGTTAGGG 58.861 43.478 13.10 0.00 0.00 3.53
3235 3852 7.496591 GGGTTTCGAAAAAGTTAGGGAATTTTT 59.503 33.333 13.10 0.00 38.47 1.94
3269 3886 2.033602 GGTTCAGGGGTTCCACCG 59.966 66.667 0.00 0.00 39.83 4.94
3313 3930 1.219124 CCACATGGACCGAGGAGTG 59.781 63.158 0.00 0.00 37.39 3.51
3314 3931 1.219124 CACATGGACCGAGGAGTGG 59.781 63.158 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.324460 ACCCACGGTCCCAACAAAAA 60.324 50.000 0.00 0.00 0.00 1.94
1 2 0.324460 AACCCACGGTCCCAACAAAA 60.324 50.000 0.00 0.00 33.12 2.44
2 3 1.038130 CAACCCACGGTCCCAACAAA 61.038 55.000 0.00 0.00 33.12 2.83
3 4 1.454111 CAACCCACGGTCCCAACAA 60.454 57.895 0.00 0.00 33.12 2.83
4 5 1.923006 TTCAACCCACGGTCCCAACA 61.923 55.000 0.00 0.00 33.12 3.33
5 6 1.152922 TTCAACCCACGGTCCCAAC 60.153 57.895 0.00 0.00 33.12 3.77
6 7 1.149627 CTTCAACCCACGGTCCCAA 59.850 57.895 0.00 0.00 33.12 4.12
7 8 1.131303 ATCTTCAACCCACGGTCCCA 61.131 55.000 0.00 0.00 33.12 4.37
8 9 0.906775 TATCTTCAACCCACGGTCCC 59.093 55.000 0.00 0.00 33.12 4.46
9 10 2.289819 TGTTATCTTCAACCCACGGTCC 60.290 50.000 0.00 0.00 33.12 4.46
10 11 2.740447 GTGTTATCTTCAACCCACGGTC 59.260 50.000 0.00 0.00 33.12 4.79
11 12 2.774687 GTGTTATCTTCAACCCACGGT 58.225 47.619 0.00 0.00 37.65 4.83
12 13 1.730064 CGTGTTATCTTCAACCCACGG 59.270 52.381 0.00 0.00 29.23 4.94
13 14 1.730064 CCGTGTTATCTTCAACCCACG 59.270 52.381 0.00 0.00 31.36 4.94
14 15 2.482721 CACCGTGTTATCTTCAACCCAC 59.517 50.000 0.00 0.00 0.00 4.61
15 16 2.551287 CCACCGTGTTATCTTCAACCCA 60.551 50.000 0.00 0.00 0.00 4.51
16 17 2.081462 CCACCGTGTTATCTTCAACCC 58.919 52.381 0.00 0.00 0.00 4.11
17 18 3.048337 TCCACCGTGTTATCTTCAACC 57.952 47.619 0.00 0.00 0.00 3.77
18 19 5.416947 ACTATCCACCGTGTTATCTTCAAC 58.583 41.667 0.00 0.00 0.00 3.18
19 20 5.670792 ACTATCCACCGTGTTATCTTCAA 57.329 39.130 0.00 0.00 0.00 2.69
20 21 5.653330 TGTACTATCCACCGTGTTATCTTCA 59.347 40.000 0.00 0.00 0.00 3.02
21 22 6.140303 TGTACTATCCACCGTGTTATCTTC 57.860 41.667 0.00 0.00 0.00 2.87
22 23 6.534475 TTGTACTATCCACCGTGTTATCTT 57.466 37.500 0.00 0.00 0.00 2.40
23 24 6.071221 TGTTTGTACTATCCACCGTGTTATCT 60.071 38.462 0.00 0.00 0.00 1.98
24 25 6.101332 TGTTTGTACTATCCACCGTGTTATC 58.899 40.000 0.00 0.00 0.00 1.75
25 26 6.040209 TGTTTGTACTATCCACCGTGTTAT 57.960 37.500 0.00 0.00 0.00 1.89
26 27 5.465532 TGTTTGTACTATCCACCGTGTTA 57.534 39.130 0.00 0.00 0.00 2.41
27 28 4.339872 TGTTTGTACTATCCACCGTGTT 57.660 40.909 0.00 0.00 0.00 3.32
28 29 4.060205 GTTGTTTGTACTATCCACCGTGT 58.940 43.478 0.00 0.00 0.00 4.49
29 30 3.434299 GGTTGTTTGTACTATCCACCGTG 59.566 47.826 0.00 0.00 0.00 4.94
30 31 3.071312 TGGTTGTTTGTACTATCCACCGT 59.929 43.478 0.00 0.00 0.00 4.83
31 32 3.434299 GTGGTTGTTTGTACTATCCACCG 59.566 47.826 0.00 0.00 35.78 4.94
32 33 4.391155 TGTGGTTGTTTGTACTATCCACC 58.609 43.478 8.59 9.68 38.21 4.61
33 34 5.703592 TGATGTGGTTGTTTGTACTATCCAC 59.296 40.000 0.00 0.00 38.78 4.02
34 35 5.870706 TGATGTGGTTGTTTGTACTATCCA 58.129 37.500 0.00 0.00 0.00 3.41
393 394 1.127567 CCAACCCTCTGGACAGTCCA 61.128 60.000 21.68 21.68 45.98 4.02
394 395 0.836400 TCCAACCCTCTGGACAGTCC 60.836 60.000 13.35 13.35 40.71 3.85
395 396 2.759985 TCCAACCCTCTGGACAGTC 58.240 57.895 0.00 0.00 40.71 3.51
401 402 3.891049 CTCCTAAAATCCAACCCTCTGG 58.109 50.000 0.00 0.00 37.87 3.86
402 403 3.282885 GCTCCTAAAATCCAACCCTCTG 58.717 50.000 0.00 0.00 0.00 3.35
403 404 2.242452 GGCTCCTAAAATCCAACCCTCT 59.758 50.000 0.00 0.00 0.00 3.69
404 405 2.656002 GGCTCCTAAAATCCAACCCTC 58.344 52.381 0.00 0.00 0.00 4.30
405 406 1.288037 GGGCTCCTAAAATCCAACCCT 59.712 52.381 0.00 0.00 33.11 4.34
406 407 1.776662 GGGCTCCTAAAATCCAACCC 58.223 55.000 0.00 0.00 0.00 4.11
407 408 1.389555 CGGGCTCCTAAAATCCAACC 58.610 55.000 0.00 0.00 0.00 3.77
408 409 0.738975 GCGGGCTCCTAAAATCCAAC 59.261 55.000 0.00 0.00 0.00 3.77
409 410 0.746563 CGCGGGCTCCTAAAATCCAA 60.747 55.000 0.00 0.00 0.00 3.53
410 411 1.153249 CGCGGGCTCCTAAAATCCA 60.153 57.895 0.00 0.00 0.00 3.41
411 412 1.892391 CCGCGGGCTCCTAAAATCC 60.892 63.158 20.10 0.00 0.00 3.01
412 413 1.892391 CCCGCGGGCTCCTAAAATC 60.892 63.158 34.96 0.00 0.00 2.17
413 414 2.192175 CCCGCGGGCTCCTAAAAT 59.808 61.111 34.96 0.00 0.00 1.82
428 429 4.875713 ACATCATTCGGGCGGCCC 62.876 66.667 28.61 28.61 41.09 5.80
429 430 3.279875 GACATCATTCGGGCGGCC 61.280 66.667 20.04 20.04 0.00 6.13
430 431 3.279875 GGACATCATTCGGGCGGC 61.280 66.667 0.00 0.00 0.00 6.53
431 432 1.029408 TTTGGACATCATTCGGGCGG 61.029 55.000 0.00 0.00 0.00 6.13
432 433 0.098728 GTTTGGACATCATTCGGGCG 59.901 55.000 0.00 0.00 0.00 6.13
433 434 1.173043 TGTTTGGACATCATTCGGGC 58.827 50.000 0.00 0.00 0.00 6.13
434 435 3.016031 TCATGTTTGGACATCATTCGGG 58.984 45.455 0.00 0.00 44.55 5.14
435 436 3.181497 GGTCATGTTTGGACATCATTCGG 60.181 47.826 0.00 0.00 44.55 4.30
436 437 3.485711 CGGTCATGTTTGGACATCATTCG 60.486 47.826 0.00 0.00 44.55 3.34
437 438 3.731867 GCGGTCATGTTTGGACATCATTC 60.732 47.826 0.00 0.00 44.55 2.67
438 439 2.164219 GCGGTCATGTTTGGACATCATT 59.836 45.455 0.00 0.00 44.55 2.57
439 440 1.745087 GCGGTCATGTTTGGACATCAT 59.255 47.619 0.00 0.00 44.55 2.45
440 441 1.164411 GCGGTCATGTTTGGACATCA 58.836 50.000 0.00 0.00 44.55 3.07
441 442 1.135689 GTGCGGTCATGTTTGGACATC 60.136 52.381 0.00 0.00 44.55 3.06
443 444 0.464554 TGTGCGGTCATGTTTGGACA 60.465 50.000 0.00 0.00 40.71 4.02
444 445 0.881118 ATGTGCGGTCATGTTTGGAC 59.119 50.000 0.00 0.00 34.52 4.02
445 446 2.481289 TATGTGCGGTCATGTTTGGA 57.519 45.000 0.00 0.00 0.00 3.53
446 447 4.891627 TTATATGTGCGGTCATGTTTGG 57.108 40.909 0.00 0.00 0.00 3.28
447 448 8.341903 TCTTTATTATATGTGCGGTCATGTTTG 58.658 33.333 0.00 0.00 0.00 2.93
448 449 8.445275 TCTTTATTATATGTGCGGTCATGTTT 57.555 30.769 0.00 0.00 0.00 2.83
449 450 8.445275 TTCTTTATTATATGTGCGGTCATGTT 57.555 30.769 0.00 0.00 0.00 2.71
450 451 8.445275 TTTCTTTATTATATGTGCGGTCATGT 57.555 30.769 0.00 0.00 0.00 3.21
451 452 9.333497 CATTTCTTTATTATATGTGCGGTCATG 57.667 33.333 0.00 0.00 0.00 3.07
452 453 9.283768 TCATTTCTTTATTATATGTGCGGTCAT 57.716 29.630 0.00 0.00 0.00 3.06
453 454 8.669946 TCATTTCTTTATTATATGTGCGGTCA 57.330 30.769 0.00 0.00 0.00 4.02
474 475 9.401058 AGGTCATCTTTAAGATCGAAATTCATT 57.599 29.630 4.24 0.00 31.32 2.57
475 476 8.970859 AGGTCATCTTTAAGATCGAAATTCAT 57.029 30.769 4.24 0.00 31.32 2.57
476 477 8.792830 AAGGTCATCTTTAAGATCGAAATTCA 57.207 30.769 4.24 0.00 31.32 2.57
480 481 9.884636 TGATTAAGGTCATCTTTAAGATCGAAA 57.115 29.630 4.24 0.00 36.93 3.46
514 515 9.456147 ACGGGCTATAATGCATGTAAATAAATA 57.544 29.630 0.00 0.00 34.04 1.40
515 516 8.348285 ACGGGCTATAATGCATGTAAATAAAT 57.652 30.769 0.00 0.00 34.04 1.40
516 517 7.753309 ACGGGCTATAATGCATGTAAATAAA 57.247 32.000 0.00 0.00 34.04 1.40
517 518 7.065324 GCTACGGGCTATAATGCATGTAAATAA 59.935 37.037 0.00 0.00 38.06 1.40
518 519 6.537301 GCTACGGGCTATAATGCATGTAAATA 59.463 38.462 0.00 0.00 38.06 1.40
519 520 5.354234 GCTACGGGCTATAATGCATGTAAAT 59.646 40.000 0.00 0.00 38.06 1.40
520 521 4.693566 GCTACGGGCTATAATGCATGTAAA 59.306 41.667 0.00 0.00 38.06 2.01
521 522 4.250464 GCTACGGGCTATAATGCATGTAA 58.750 43.478 0.00 0.00 38.06 2.41
522 523 3.259625 TGCTACGGGCTATAATGCATGTA 59.740 43.478 0.00 0.00 42.39 2.29
523 524 2.038426 TGCTACGGGCTATAATGCATGT 59.962 45.455 0.00 0.00 42.39 3.21
524 525 2.698803 TGCTACGGGCTATAATGCATG 58.301 47.619 0.00 0.00 42.39 4.06
525 526 3.074412 GTTGCTACGGGCTATAATGCAT 58.926 45.455 0.00 0.00 42.39 3.96
526 527 2.489971 GTTGCTACGGGCTATAATGCA 58.510 47.619 0.00 0.00 42.39 3.96
527 528 1.459592 CGTTGCTACGGGCTATAATGC 59.540 52.381 13.04 0.00 43.94 3.56
539 540 2.667199 AACCCCGTGCGTTGCTAC 60.667 61.111 0.00 0.00 0.00 3.58
540 541 1.534336 TAGAACCCCGTGCGTTGCTA 61.534 55.000 0.00 0.00 0.00 3.49
541 542 2.874664 TAGAACCCCGTGCGTTGCT 61.875 57.895 0.00 0.00 0.00 3.91
542 543 2.357760 TAGAACCCCGTGCGTTGC 60.358 61.111 0.00 0.00 0.00 4.17
543 544 0.244450 TAGTAGAACCCCGTGCGTTG 59.756 55.000 0.00 0.00 0.00 4.10
544 545 0.529378 CTAGTAGAACCCCGTGCGTT 59.471 55.000 0.00 0.00 0.00 4.84
545 546 0.610232 ACTAGTAGAACCCCGTGCGT 60.610 55.000 3.59 0.00 0.00 5.24
546 547 1.382522 TACTAGTAGAACCCCGTGCG 58.617 55.000 3.59 0.00 0.00 5.34
547 548 3.874392 TTTACTAGTAGAACCCCGTGC 57.126 47.619 3.59 0.00 0.00 5.34
548 549 5.334724 ACATTTACTAGTAGAACCCCGTG 57.665 43.478 3.59 0.00 0.00 4.94
549 550 6.665248 ACTTACATTTACTAGTAGAACCCCGT 59.335 38.462 3.59 0.00 0.00 5.28
550 551 6.976925 CACTTACATTTACTAGTAGAACCCCG 59.023 42.308 3.59 0.00 0.00 5.73
551 552 6.760298 GCACTTACATTTACTAGTAGAACCCC 59.240 42.308 3.59 0.00 0.00 4.95
552 553 7.277319 GTGCACTTACATTTACTAGTAGAACCC 59.723 40.741 10.32 0.00 0.00 4.11
553 554 7.008992 CGTGCACTTACATTTACTAGTAGAACC 59.991 40.741 16.19 0.00 0.00 3.62
554 555 7.752239 TCGTGCACTTACATTTACTAGTAGAAC 59.248 37.037 16.19 0.00 0.00 3.01
555 556 7.819644 TCGTGCACTTACATTTACTAGTAGAA 58.180 34.615 16.19 1.88 0.00 2.10
556 557 7.120285 ACTCGTGCACTTACATTTACTAGTAGA 59.880 37.037 16.19 0.00 0.00 2.59
557 558 7.249147 ACTCGTGCACTTACATTTACTAGTAG 58.751 38.462 16.19 0.00 0.00 2.57
558 559 7.149569 ACTCGTGCACTTACATTTACTAGTA 57.850 36.000 16.19 0.00 0.00 1.82
559 560 6.022163 ACTCGTGCACTTACATTTACTAGT 57.978 37.500 16.19 0.00 0.00 2.57
560 561 6.196724 GCTACTCGTGCACTTACATTTACTAG 59.803 42.308 16.19 0.00 0.00 2.57
561 562 6.032094 GCTACTCGTGCACTTACATTTACTA 58.968 40.000 16.19 0.00 0.00 1.82
562 563 4.863131 GCTACTCGTGCACTTACATTTACT 59.137 41.667 16.19 0.00 0.00 2.24
563 564 4.863131 AGCTACTCGTGCACTTACATTTAC 59.137 41.667 16.19 0.00 0.00 2.01
564 565 4.862574 CAGCTACTCGTGCACTTACATTTA 59.137 41.667 16.19 0.00 0.00 1.40
565 566 3.679980 CAGCTACTCGTGCACTTACATTT 59.320 43.478 16.19 0.00 0.00 2.32
593 594 2.536130 GCCGTGACGACAATAATTTCCG 60.536 50.000 6.54 0.00 0.00 4.30
640 641 0.931005 GATTCCGTCCGTGATCTTGC 59.069 55.000 0.00 0.00 0.00 4.01
739 741 0.387929 GACACACAGGACGAACTCCA 59.612 55.000 0.00 0.00 42.46 3.86
740 742 0.663568 CGACACACAGGACGAACTCC 60.664 60.000 0.00 0.00 39.81 3.85
741 743 0.309922 TCGACACACAGGACGAACTC 59.690 55.000 0.00 0.00 0.00 3.01
742 744 0.030369 GTCGACACACAGGACGAACT 59.970 55.000 11.55 0.00 36.57 3.01
744 746 1.361271 GGTCGACACACAGGACGAA 59.639 57.895 18.91 0.00 36.57 3.85
746 748 2.049433 GGGTCGACACACAGGACG 60.049 66.667 18.91 0.00 0.00 4.79
747 749 2.049433 CGGGTCGACACACAGGAC 60.049 66.667 19.62 0.00 0.00 3.85
748 750 2.520020 ACGGGTCGACACACAGGA 60.520 61.111 19.62 0.00 0.00 3.86
749 751 2.355837 CACGGGTCGACACACAGG 60.356 66.667 19.62 3.51 0.00 4.00
750 752 1.949133 CACACGGGTCGACACACAG 60.949 63.158 19.62 9.09 0.00 3.66
751 753 2.105328 CACACGGGTCGACACACA 59.895 61.111 19.62 0.00 0.00 3.72
752 754 1.947642 GACACACGGGTCGACACAC 60.948 63.158 19.62 6.34 0.00 3.82
753 755 2.414179 GACACACGGGTCGACACA 59.586 61.111 19.62 0.00 0.00 3.72
893 937 1.456196 GGGAGCACGATCGATCCAGA 61.456 60.000 27.42 0.00 33.24 3.86
894 938 1.006805 GGGAGCACGATCGATCCAG 60.007 63.158 27.42 12.85 33.24 3.86
937 1069 0.601057 GCCTGCGTGGTGGTTTAAAT 59.399 50.000 0.00 0.00 38.35 1.40
992 1128 1.068588 CAGCGGATCGTTGGATAAGGA 59.931 52.381 0.00 0.00 34.62 3.36
1008 1203 0.381089 CTAGTTAGTCCCGTCCAGCG 59.619 60.000 0.00 0.00 40.95 5.18
1009 1204 0.745468 CCTAGTTAGTCCCGTCCAGC 59.255 60.000 0.00 0.00 0.00 4.85
1010 1205 0.745468 GCCTAGTTAGTCCCGTCCAG 59.255 60.000 0.00 0.00 0.00 3.86
1011 1206 0.333993 AGCCTAGTTAGTCCCGTCCA 59.666 55.000 0.00 0.00 0.00 4.02
1012 1207 0.745468 CAGCCTAGTTAGTCCCGTCC 59.255 60.000 0.00 0.00 0.00 4.79
1013 1208 1.404748 GACAGCCTAGTTAGTCCCGTC 59.595 57.143 0.00 0.00 0.00 4.79
1014 1209 1.272313 TGACAGCCTAGTTAGTCCCGT 60.272 52.381 0.00 0.00 0.00 5.28
1015 1210 1.134560 GTGACAGCCTAGTTAGTCCCG 59.865 57.143 0.00 0.00 0.00 5.14
1016 1211 2.176889 TGTGACAGCCTAGTTAGTCCC 58.823 52.381 0.00 0.00 0.00 4.46
1017 1212 3.181474 GGATGTGACAGCCTAGTTAGTCC 60.181 52.174 13.46 0.00 36.92 3.85
1018 1213 3.181474 GGGATGTGACAGCCTAGTTAGTC 60.181 52.174 20.23 0.00 40.16 2.59
1019 1214 2.766828 GGGATGTGACAGCCTAGTTAGT 59.233 50.000 20.23 0.00 40.16 2.24
1020 1215 3.034635 AGGGATGTGACAGCCTAGTTAG 58.965 50.000 20.23 0.00 40.16 2.34
1021 1216 3.116096 AGGGATGTGACAGCCTAGTTA 57.884 47.619 20.23 0.00 40.16 2.24
1022 1217 1.958288 AGGGATGTGACAGCCTAGTT 58.042 50.000 20.23 0.47 40.16 2.24
1023 1218 1.834263 GAAGGGATGTGACAGCCTAGT 59.166 52.381 20.23 5.01 40.16 2.57
1024 1219 1.139853 GGAAGGGATGTGACAGCCTAG 59.860 57.143 20.23 0.00 40.16 3.02
1025 1220 1.204146 GGAAGGGATGTGACAGCCTA 58.796 55.000 20.23 0.00 40.16 3.93
1026 1221 0.842030 TGGAAGGGATGTGACAGCCT 60.842 55.000 20.23 0.00 40.16 4.58
1030 1225 2.771943 GGTAGATGGAAGGGATGTGACA 59.228 50.000 0.00 0.00 0.00 3.58
1031 1226 2.771943 TGGTAGATGGAAGGGATGTGAC 59.228 50.000 0.00 0.00 0.00 3.67
1051 1246 4.007940 CCGACGCCGTTGGTTGTG 62.008 66.667 15.61 0.00 32.65 3.33
1062 1257 3.712881 GGCCATTATCGCCGACGC 61.713 66.667 0.00 0.00 39.84 5.19
1117 1312 3.637273 GGGTCAGGACGGCAACCT 61.637 66.667 6.66 0.00 38.40 3.50
1320 1545 3.499737 GACGGCCGCAATGTGGAG 61.500 66.667 28.58 11.80 34.74 3.86
1344 1569 2.668550 GCCACCGCGGAAGAAACT 60.669 61.111 35.90 3.57 36.56 2.66
1611 1878 0.766131 TCCTCCACTTTAACCGCCAA 59.234 50.000 0.00 0.00 0.00 4.52
1733 2000 3.276091 TCGTTGTTGGTGCCGCTG 61.276 61.111 0.00 0.00 0.00 5.18
2067 2351 1.588932 CATCGATCGGTCCGTGGTG 60.589 63.158 16.41 5.53 0.00 4.17
2233 2548 1.911293 TAACCGGAACTCGTCGTCGG 61.911 60.000 9.46 0.00 45.42 4.79
2289 2616 2.029815 TGAAGCTACGCGCCAACA 59.970 55.556 5.73 0.00 40.39 3.33
2359 2686 3.871463 GCTGTCATGTGATTCCAAGACCT 60.871 47.826 0.00 0.00 0.00 3.85
2381 2708 1.195448 CGAGCAGCCAAAACAGTAGTG 59.805 52.381 0.00 0.00 0.00 2.74
2382 2709 1.202651 ACGAGCAGCCAAAACAGTAGT 60.203 47.619 0.00 0.00 0.00 2.73
2562 2897 3.516300 TGCGGGGTATCTAGTTTTTCTCA 59.484 43.478 0.00 0.00 0.00 3.27
2603 2941 5.919272 ACATCTCATTCATACTTGATGCG 57.081 39.130 0.00 0.00 35.93 4.73
2644 2982 7.634671 TCATGAGTATTTGTCTGATTGCAAT 57.365 32.000 12.83 12.83 0.00 3.56
2771 3384 6.015434 GTGTGGATTTGGTTCATACCTCTTTT 60.015 38.462 0.00 0.00 45.27 2.27
2813 3430 4.956075 ACCGGATAGGCAAGAAATGATTTT 59.044 37.500 9.46 0.00 46.52 1.82
2856 3473 8.660373 GGCGATATGTTCATTCTTTATTAGGAG 58.340 37.037 0.00 0.00 0.00 3.69
2865 3482 3.131396 GTCCGGCGATATGTTCATTCTT 58.869 45.455 9.30 0.00 0.00 2.52
2879 3496 0.596082 ACAATTTCCTTTGTCCGGCG 59.404 50.000 0.00 0.00 34.83 6.46
2902 3519 5.914898 TGTCGAGGATTCAGTTAATCTCA 57.085 39.130 0.00 0.00 43.14 3.27
2904 3521 5.067936 ACGATGTCGAGGATTCAGTTAATCT 59.932 40.000 9.67 0.00 41.80 2.40
2935 3552 8.004344 CACATTCATCGTAGATTTTTATCGGTC 58.996 37.037 0.00 0.00 45.12 4.79
2950 3567 2.038426 TGAACTCCCACACATTCATCGT 59.962 45.455 0.00 0.00 0.00 3.73
2953 3570 5.135383 CCATATGAACTCCCACACATTCAT 58.865 41.667 3.65 3.99 42.79 2.57
2969 3586 1.425066 GGAACCTGGATGCCCATATGA 59.575 52.381 3.65 0.00 42.59 2.15
2987 3604 5.185056 TCTCGGATCAATAATCAATAGCGGA 59.815 40.000 0.00 0.00 35.96 5.54
3008 3625 1.133407 GACATGACCGAGACACCTCTC 59.867 57.143 0.00 0.00 39.86 3.20
3028 3645 2.452813 CGGGTTCGAGAACATGCCG 61.453 63.158 16.56 15.33 42.85 5.69
3029 3646 0.108520 TACGGGTTCGAGAACATGCC 60.109 55.000 16.56 8.53 42.85 4.40
3049 3666 3.927142 CGAGAACCTTAAGTGTGTGATCC 59.073 47.826 0.97 0.00 0.00 3.36
3057 3674 2.665052 GCGTTACCGAGAACCTTAAGTG 59.335 50.000 0.97 0.00 35.63 3.16
3064 3681 0.101939 CCCTAGCGTTACCGAGAACC 59.898 60.000 0.00 0.00 35.63 3.62
3067 3684 1.210478 ACTACCCTAGCGTTACCGAGA 59.790 52.381 0.00 0.00 35.63 4.04
3069 3686 3.492102 ATACTACCCTAGCGTTACCGA 57.508 47.619 0.00 0.00 35.63 4.69
3070 3687 3.304928 CCAATACTACCCTAGCGTTACCG 60.305 52.174 0.00 0.00 37.07 4.02
3071 3688 3.006217 CCCAATACTACCCTAGCGTTACC 59.994 52.174 0.00 0.00 0.00 2.85
3079 3696 9.488762 CAGTATGAATATCCCAATACTACCCTA 57.511 37.037 0.00 0.00 39.69 3.53
3113 3730 6.825213 CCATCTGAGACTCCAAACAATATTCA 59.175 38.462 0.00 0.00 0.00 2.57
3121 3738 3.432890 GGATCCCATCTGAGACTCCAAAC 60.433 52.174 0.00 0.00 0.00 2.93
3124 3741 1.755621 CGGATCCCATCTGAGACTCCA 60.756 57.143 6.06 0.00 37.90 3.86
3133 3750 2.388526 TGATGTCTCGGATCCCATCT 57.611 50.000 21.96 0.00 35.76 2.90
3141 3758 1.035923 GCTCCTCATGATGTCTCGGA 58.964 55.000 0.00 0.00 0.00 4.55
3145 3762 1.039068 CGGAGCTCCTCATGATGTCT 58.961 55.000 29.73 0.00 31.08 3.41
3153 3770 0.909610 AACCATTCCGGAGCTCCTCA 60.910 55.000 29.73 13.64 38.63 3.86
3154 3771 0.179070 GAACCATTCCGGAGCTCCTC 60.179 60.000 29.73 14.34 38.63 3.71
3193 3810 4.381079 CGAAACCCTGAAAAACACTTTCCA 60.381 41.667 0.00 0.00 0.00 3.53
3194 3811 4.109766 CGAAACCCTGAAAAACACTTTCC 58.890 43.478 0.00 0.00 0.00 3.13
3248 3865 0.771755 GTGGAACCCCTGAACCTTCT 59.228 55.000 0.00 0.00 0.00 2.85
3269 3886 2.362889 CAGGTCATTGGGCCCCAC 60.363 66.667 22.27 10.62 30.78 4.61


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

AutoCloner maintained by Alex Coulton.