Multiple sequence alignment - TraesCS6A01G128200

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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 TraesCS6A01G128200 chr6A 100.000 2936 0 0 1 2936 100742178 100745113 0.000000e+00 5422.0
1 TraesCS6A01G128200 chr6A 88.368 1857 193 17 700 2537 100357576 100355724 0.000000e+00 2211.0
2 TraesCS6A01G128200 chr6A 84.519 1828 248 26 729 2537 100363718 100361907 0.000000e+00 1775.0
3 TraesCS6A01G128200 chr6A 80.159 1507 279 17 1039 2535 98813557 98812061 0.000000e+00 1109.0
4 TraesCS6A01G128200 chr6A 80.040 1503 291 9 1039 2535 98256385 98254886 0.000000e+00 1105.0
5 TraesCS6A01G128200 chr6A 79.761 1507 288 16 1039 2535 98249947 98248448 0.000000e+00 1077.0
6 TraesCS6A01G128200 chr6A 76.079 1668 360 33 889 2536 100229021 100227373 0.000000e+00 833.0
7 TraesCS6A01G128200 chr6A 81.081 111 15 5 383 490 100796407 100796514 1.880000e-12 84.2
8 TraesCS6A01G128200 chr6A 82.796 93 12 4 383 473 100754302 100754392 2.430000e-11 80.5
9 TraesCS6A01G128200 chr6B 92.538 2439 92 20 95 2532 159389589 159391938 0.000000e+00 3413.0
10 TraesCS6A01G128200 chr6B 87.211 1814 196 23 744 2537 158190176 158188379 0.000000e+00 2032.0
11 TraesCS6A01G128200 chr6B 80.465 1505 279 11 1039 2537 157027356 157025861 0.000000e+00 1136.0
12 TraesCS6A01G128200 chr6D 87.047 1822 196 27 739 2537 83205514 83203710 0.000000e+00 2021.0
13 TraesCS6A01G128200 chr6D 80.305 1508 279 16 1039 2537 82139084 82137586 0.000000e+00 1123.0
14 TraesCS6A01G128200 chr6D 76.531 1666 356 29 889 2536 83160551 83158903 0.000000e+00 878.0
15 TraesCS6A01G128200 chr6D 86.761 355 17 7 2546 2880 29207013 29207357 4.620000e-98 368.0
16 TraesCS6A01G128200 chr6D 85.675 363 28 12 2539 2877 111601122 111601484 7.740000e-96 361.0
17 TraesCS6A01G128200 chr6D 82.796 93 12 4 383 473 83524140 83524230 2.430000e-11 80.5
18 TraesCS6A01G128200 chr4A 87.679 349 34 6 2540 2880 248810683 248811030 5.900000e-107 398.0
19 TraesCS6A01G128200 chr4D 86.631 374 26 8 2531 2880 16932874 16933247 2.740000e-105 392.0
20 TraesCS6A01G128200 chr7A 85.714 392 28 11 2541 2907 336386556 336386168 3.550000e-104 388.0
21 TraesCS6A01G128200 chrUn 85.316 395 32 10 2539 2907 26517083 26516689 4.590000e-103 385.0
22 TraesCS6A01G128200 chr3D 86.486 370 26 9 2535 2880 24290561 24290930 4.590000e-103 385.0
23 TraesCS6A01G128200 chr3D 90.980 255 22 1 2626 2880 24336950 24337203 2.800000e-90 342.0
24 TraesCS6A01G128200 chr3D 83.686 331 39 13 2583 2907 587278079 587277758 6.150000e-77 298.0


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 TraesCS6A01G128200 chr6A 100742178 100745113 2935 False 5422 5422 100.000 1 2936 1 chr6A.!!$F1 2935
1 TraesCS6A01G128200 chr6A 100355724 100357576 1852 True 2211 2211 88.368 700 2537 1 chr6A.!!$R5 1837
2 TraesCS6A01G128200 chr6A 100361907 100363718 1811 True 1775 1775 84.519 729 2537 1 chr6A.!!$R6 1808
3 TraesCS6A01G128200 chr6A 98812061 98813557 1496 True 1109 1109 80.159 1039 2535 1 chr6A.!!$R3 1496
4 TraesCS6A01G128200 chr6A 98254886 98256385 1499 True 1105 1105 80.040 1039 2535 1 chr6A.!!$R2 1496
5 TraesCS6A01G128200 chr6A 98248448 98249947 1499 True 1077 1077 79.761 1039 2535 1 chr6A.!!$R1 1496
6 TraesCS6A01G128200 chr6A 100227373 100229021 1648 True 833 833 76.079 889 2536 1 chr6A.!!$R4 1647
7 TraesCS6A01G128200 chr6B 159389589 159391938 2349 False 3413 3413 92.538 95 2532 1 chr6B.!!$F1 2437
8 TraesCS6A01G128200 chr6B 158188379 158190176 1797 True 2032 2032 87.211 744 2537 1 chr6B.!!$R2 1793
9 TraesCS6A01G128200 chr6B 157025861 157027356 1495 True 1136 1136 80.465 1039 2537 1 chr6B.!!$R1 1498
10 TraesCS6A01G128200 chr6D 83203710 83205514 1804 True 2021 2021 87.047 739 2537 1 chr6D.!!$R3 1798
11 TraesCS6A01G128200 chr6D 82137586 82139084 1498 True 1123 1123 80.305 1039 2537 1 chr6D.!!$R1 1498
12 TraesCS6A01G128200 chr6D 83158903 83160551 1648 True 878 878 76.531 889 2536 1 chr6D.!!$R2 1647

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
80 81 0.185175 ATAAAGGGCGTGAATCCCCC 59.815 55.0 0.00 0.00 45.03 5.40 F
85 86 0.250770 GGGCGTGAATCCCCCTAATC 60.251 60.0 0.00 0.00 37.81 1.75 F
719 721 0.253044 ACCCTGACATCAATGACGGG 59.747 55.0 11.83 11.83 44.87 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1518 1.001503 GGTGGATGGAAATGGCCCA 59.998 57.895 0.00 0.00 38.19 5.36 R
1933 1960 1.227943 GTGTTGGTGGCAGCTCTCA 60.228 57.895 18.53 10.95 0.00 3.27 R
2714 2741 0.031314 CATCATCCGACTCCACCGAG 59.969 60.000 0.00 0.00 42.32 4.63 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 2.462301 TGCCTTGTGATGACTGGGA 58.538 52.632 0.00 0.00 0.00 4.37
19 20 0.770499 TGCCTTGTGATGACTGGGAA 59.230 50.000 0.00 0.00 0.00 3.97
20 21 1.271543 TGCCTTGTGATGACTGGGAAG 60.272 52.381 0.00 0.00 0.00 3.46
21 22 1.952367 GCCTTGTGATGACTGGGAAGG 60.952 57.143 0.00 0.00 34.30 3.46
22 23 1.457346 CTTGTGATGACTGGGAAGGC 58.543 55.000 0.00 0.00 0.00 4.35
23 24 1.004044 CTTGTGATGACTGGGAAGGCT 59.996 52.381 0.00 0.00 0.00 4.58
24 25 1.067295 TGTGATGACTGGGAAGGCTT 58.933 50.000 0.00 0.00 0.00 4.35
25 26 1.425066 TGTGATGACTGGGAAGGCTTT 59.575 47.619 0.00 0.00 0.00 3.51
26 27 1.815003 GTGATGACTGGGAAGGCTTTG 59.185 52.381 0.00 0.00 0.00 2.77
27 28 0.813821 GATGACTGGGAAGGCTTTGC 59.186 55.000 0.00 0.00 0.00 3.68
38 39 3.596362 GGCTTTGCCTTACCCAGAT 57.404 52.632 0.73 0.00 46.69 2.90
39 40 1.852633 GGCTTTGCCTTACCCAGATT 58.147 50.000 0.73 0.00 46.69 2.40
40 41 2.179427 GGCTTTGCCTTACCCAGATTT 58.821 47.619 0.73 0.00 46.69 2.17
41 42 2.094026 GGCTTTGCCTTACCCAGATTTG 60.094 50.000 0.73 0.00 46.69 2.32
42 43 2.094026 GCTTTGCCTTACCCAGATTTGG 60.094 50.000 0.00 0.00 44.60 3.28
52 53 2.816746 CAGATTTGGATGCCCCCAG 58.183 57.895 0.00 0.00 37.53 4.45
53 54 1.075748 AGATTTGGATGCCCCCAGC 60.076 57.895 0.00 0.00 44.14 4.85
54 55 1.075748 GATTTGGATGCCCCCAGCT 60.076 57.895 0.00 0.00 44.23 4.24
55 56 1.382146 ATTTGGATGCCCCCAGCTG 60.382 57.895 6.78 6.78 44.23 4.24
56 57 1.877672 ATTTGGATGCCCCCAGCTGA 61.878 55.000 17.39 0.00 44.23 4.26
57 58 2.091640 TTTGGATGCCCCCAGCTGAA 62.092 55.000 17.39 0.00 44.23 3.02
58 59 2.091640 TTGGATGCCCCCAGCTGAAA 62.092 55.000 17.39 0.00 44.23 2.69
59 60 1.755783 GGATGCCCCCAGCTGAAAG 60.756 63.158 17.39 3.71 44.23 2.62
72 73 2.549633 CTGAAAGCATAAAGGGCGTG 57.450 50.000 0.00 0.00 36.08 5.34
73 74 2.083774 CTGAAAGCATAAAGGGCGTGA 58.916 47.619 0.00 0.00 36.08 4.35
74 75 2.487762 CTGAAAGCATAAAGGGCGTGAA 59.512 45.455 0.00 0.00 36.08 3.18
75 76 3.088532 TGAAAGCATAAAGGGCGTGAAT 58.911 40.909 0.00 0.00 36.08 2.57
76 77 3.128589 TGAAAGCATAAAGGGCGTGAATC 59.871 43.478 0.00 0.00 36.08 2.52
77 78 1.680338 AGCATAAAGGGCGTGAATCC 58.320 50.000 0.00 0.00 36.08 3.01
78 79 0.668535 GCATAAAGGGCGTGAATCCC 59.331 55.000 0.00 0.00 44.25 3.85
79 80 1.318576 CATAAAGGGCGTGAATCCCC 58.681 55.000 0.00 0.00 45.03 4.81
80 81 0.185175 ATAAAGGGCGTGAATCCCCC 59.815 55.000 0.00 0.00 45.03 5.40
83 84 3.326900 GGGCGTGAATCCCCCTAA 58.673 61.111 0.00 0.00 37.81 2.69
84 85 1.844130 GGGCGTGAATCCCCCTAAT 59.156 57.895 0.00 0.00 37.81 1.73
85 86 0.250770 GGGCGTGAATCCCCCTAATC 60.251 60.000 0.00 0.00 37.81 1.75
86 87 0.472471 GGCGTGAATCCCCCTAATCA 59.528 55.000 0.00 0.00 0.00 2.57
87 88 1.133915 GGCGTGAATCCCCCTAATCAA 60.134 52.381 0.00 0.00 0.00 2.57
88 89 1.947456 GCGTGAATCCCCCTAATCAAC 59.053 52.381 0.00 0.00 0.00 3.18
89 90 2.421529 GCGTGAATCCCCCTAATCAACT 60.422 50.000 0.00 0.00 0.00 3.16
90 91 3.181458 GCGTGAATCCCCCTAATCAACTA 60.181 47.826 0.00 0.00 0.00 2.24
91 92 4.632153 CGTGAATCCCCCTAATCAACTAG 58.368 47.826 0.00 0.00 0.00 2.57
92 93 4.503296 CGTGAATCCCCCTAATCAACTAGG 60.503 50.000 0.00 0.00 38.61 3.02
137 138 1.541310 TTCCTCCATCGCGTCTTGGT 61.541 55.000 19.56 0.00 34.48 3.67
158 159 0.606401 CAGCTCACCAAACCCATCGT 60.606 55.000 0.00 0.00 0.00 3.73
162 163 1.953686 CTCACCAAACCCATCGTGTTT 59.046 47.619 0.00 0.00 36.40 2.83
192 193 7.378461 GCGAAGTGAAAACATTTGAAAGATACA 59.622 33.333 0.00 0.00 0.00 2.29
211 212 3.551846 ACACCTACAACAACTGGAAAGG 58.448 45.455 0.00 0.00 32.52 3.11
227 228 5.463154 TGGAAAGGAATTGAAGAGGGAAAA 58.537 37.500 0.00 0.00 0.00 2.29
245 246 9.143631 GAGGGAAAACATCAAAACAATATCAAG 57.856 33.333 0.00 0.00 0.00 3.02
334 335 6.870971 TGTAATAACAAAGATATTCCCCGC 57.129 37.500 0.00 0.00 30.91 6.13
335 336 6.358178 TGTAATAACAAAGATATTCCCCGCA 58.642 36.000 0.00 0.00 30.91 5.69
336 337 6.829298 TGTAATAACAAAGATATTCCCCGCAA 59.171 34.615 0.00 0.00 30.91 4.85
337 338 6.783708 AATAACAAAGATATTCCCCGCAAA 57.216 33.333 0.00 0.00 0.00 3.68
338 339 6.783708 ATAACAAAGATATTCCCCGCAAAA 57.216 33.333 0.00 0.00 0.00 2.44
339 340 5.476091 AACAAAGATATTCCCCGCAAAAA 57.524 34.783 0.00 0.00 0.00 1.94
466 467 4.398319 ACCAACTCTAGTCAAACCCAATG 58.602 43.478 0.00 0.00 0.00 2.82
477 479 4.828387 GTCAAACCCAATGTAACCCAACTA 59.172 41.667 0.00 0.00 0.00 2.24
482 484 9.362151 CAAACCCAATGTAACCCAACTATATAT 57.638 33.333 0.00 0.00 0.00 0.86
508 510 2.037641 TGTGTGATAGCTTCAGCACTGT 59.962 45.455 6.45 0.00 45.16 3.55
525 527 4.921515 GCACTGTCTTTTCTGTATACACGA 59.078 41.667 0.08 1.36 0.00 4.35
565 567 3.012518 GCAATGACCACTTACAGCTGAT 58.987 45.455 23.35 7.41 0.00 2.90
600 602 7.716799 AACTTAAATTGCACCTATTCCATCA 57.283 32.000 0.00 0.00 0.00 3.07
643 645 5.228635 GCGAGAAAATGCATACAATGTTCAG 59.771 40.000 0.00 0.00 0.00 3.02
644 646 6.317088 CGAGAAAATGCATACAATGTTCAGT 58.683 36.000 0.00 0.00 0.00 3.41
652 654 4.727734 GCATACAATGTTCAGTAAGCACCG 60.728 45.833 0.00 0.00 35.63 4.94
656 658 1.508632 TGTTCAGTAAGCACCGCTTC 58.491 50.000 4.16 0.00 46.77 3.86
719 721 0.253044 ACCCTGACATCAATGACGGG 59.747 55.000 11.83 11.83 44.87 5.28
817 825 8.268850 ACTCATGAACAAATTATAGTGGACAC 57.731 34.615 0.00 0.00 0.00 3.67
827 838 8.822855 CAAATTATAGTGGACACGCAATAGTAA 58.177 33.333 0.00 0.00 36.20 2.24
841 852 6.127140 ACGCAATAGTAACTAATCCTTCACCT 60.127 38.462 0.00 0.00 0.00 4.00
872 886 2.333688 TCACCACGATGACCAAAACA 57.666 45.000 0.00 0.00 0.00 2.83
874 888 1.946768 CACCACGATGACCAAAACAGT 59.053 47.619 0.00 0.00 0.00 3.55
878 892 3.303990 CCACGATGACCAAAACAGTTCAG 60.304 47.826 0.00 0.00 0.00 3.02
885 899 5.465935 TGACCAAAACAGTTCAGACAAAAC 58.534 37.500 0.00 0.00 0.00 2.43
886 900 4.816392 ACCAAAACAGTTCAGACAAAACC 58.184 39.130 0.00 0.00 0.00 3.27
1010 1034 2.012673 CTCAAGAACCATGCAGCTACC 58.987 52.381 0.00 0.00 0.00 3.18
1035 1059 3.184581 GTCACTCACACAAGAACCGATTC 59.815 47.826 0.00 0.00 34.78 2.52
1037 1061 2.368875 ACTCACACAAGAACCGATTCCT 59.631 45.455 0.00 0.00 35.18 3.36
1084 1108 2.100087 GTGCTACTAGTCTCCTTGGCTC 59.900 54.545 0.00 0.00 0.00 4.70
1231 1258 3.827008 TTACCTGCAGCCTCAATAGAG 57.173 47.619 8.66 0.00 41.72 2.43
1560 1587 1.131126 CTCAACGCCAGCAATAACAGG 59.869 52.381 0.00 0.00 0.00 4.00
1804 1831 3.009473 ACAGGGTGTTCTTGATAGTGCAT 59.991 43.478 0.00 0.00 0.00 3.96
1834 1861 1.066143 GCCTCAGAAATCTCCGAACCA 60.066 52.381 0.00 0.00 0.00 3.67
1933 1960 0.827507 GGGCCACAACAACCTGTCAT 60.828 55.000 4.39 0.00 0.00 3.06
1935 1962 1.317613 GCCACAACAACCTGTCATGA 58.682 50.000 0.00 0.00 0.00 3.07
1962 1989 1.667236 CACCAACACTGAGCAACTGA 58.333 50.000 0.00 0.00 0.00 3.41
2192 2219 7.069986 AGAATAGGCAACCTGAAGTATCTCTA 58.930 38.462 0.00 0.00 34.61 2.43
2253 2280 8.529424 TCAGAAATGCATTTCAGATCCTTAAT 57.471 30.769 39.58 21.03 46.50 1.40
2412 2439 4.081972 CCTCTATGGATATCAAGGGTCACG 60.082 50.000 4.83 0.00 38.35 4.35
2456 2483 4.660168 AGAAGCAATCAACTCATTGGACT 58.340 39.130 0.00 0.00 36.39 3.85
2559 2586 4.058721 GAGATGGCTCCTTTCTCTTCTC 57.941 50.000 10.30 0.00 35.01 2.87
2560 2587 3.706086 GAGATGGCTCCTTTCTCTTCTCT 59.294 47.826 10.30 0.00 35.01 3.10
2561 2588 3.706086 AGATGGCTCCTTTCTCTTCTCTC 59.294 47.826 0.00 0.00 0.00 3.20
2562 2589 2.183679 TGGCTCCTTTCTCTTCTCTCC 58.816 52.381 0.00 0.00 0.00 3.71
2563 2590 1.484653 GGCTCCTTTCTCTTCTCTCCC 59.515 57.143 0.00 0.00 0.00 4.30
2564 2591 2.466846 GCTCCTTTCTCTTCTCTCCCT 58.533 52.381 0.00 0.00 0.00 4.20
2565 2592 2.837591 GCTCCTTTCTCTTCTCTCCCTT 59.162 50.000 0.00 0.00 0.00 3.95
2566 2593 3.118775 GCTCCTTTCTCTTCTCTCCCTTC 60.119 52.174 0.00 0.00 0.00 3.46
2567 2594 3.093057 TCCTTTCTCTTCTCTCCCTTCG 58.907 50.000 0.00 0.00 0.00 3.79
2568 2595 2.829120 CCTTTCTCTTCTCTCCCTTCGT 59.171 50.000 0.00 0.00 0.00 3.85
2569 2596 3.119280 CCTTTCTCTTCTCTCCCTTCGTC 60.119 52.174 0.00 0.00 0.00 4.20
2570 2597 2.131776 TCTCTTCTCTCCCTTCGTCC 57.868 55.000 0.00 0.00 0.00 4.79
2571 2598 1.107945 CTCTTCTCTCCCTTCGTCCC 58.892 60.000 0.00 0.00 0.00 4.46
2572 2599 0.324460 TCTTCTCTCCCTTCGTCCCC 60.324 60.000 0.00 0.00 0.00 4.81
2573 2600 1.305887 TTCTCTCCCTTCGTCCCCC 60.306 63.158 0.00 0.00 0.00 5.40
2599 2626 4.890306 GCTCCCCTCCTCCTCCCC 62.890 77.778 0.00 0.00 0.00 4.81
2600 2627 3.039526 CTCCCCTCCTCCTCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
2601 2628 3.368501 TCCCCTCCTCCTCCCCTG 61.369 72.222 0.00 0.00 0.00 4.45
2605 2632 4.101077 CTCCTCCTCCCCTGCCCT 62.101 72.222 0.00 0.00 0.00 5.19
2606 2633 3.626596 TCCTCCTCCCCTGCCCTT 61.627 66.667 0.00 0.00 0.00 3.95
2607 2634 3.415087 CCTCCTCCCCTGCCCTTG 61.415 72.222 0.00 0.00 0.00 3.61
2608 2635 4.120755 CTCCTCCCCTGCCCTTGC 62.121 72.222 0.00 0.00 38.26 4.01
2646 2673 4.452733 CCCGGTCTTCTGCGGGTC 62.453 72.222 0.00 0.00 35.05 4.46
2647 2674 4.796231 CCGGTCTTCTGCGGGTCG 62.796 72.222 0.00 0.00 0.00 4.79
2648 2675 4.796231 CGGTCTTCTGCGGGTCGG 62.796 72.222 0.00 0.00 0.00 4.79
2649 2676 4.452733 GGTCTTCTGCGGGTCGGG 62.453 72.222 0.00 0.00 0.00 5.14
2650 2677 3.692406 GTCTTCTGCGGGTCGGGT 61.692 66.667 0.00 0.00 0.00 5.28
2651 2678 2.920912 TCTTCTGCGGGTCGGGTT 60.921 61.111 0.00 0.00 0.00 4.11
2652 2679 2.742372 CTTCTGCGGGTCGGGTTG 60.742 66.667 0.00 0.00 0.00 3.77
2653 2680 4.323477 TTCTGCGGGTCGGGTTGG 62.323 66.667 0.00 0.00 0.00 3.77
2658 2685 4.452733 CGGGTCGGGTTGGCTCTC 62.453 72.222 0.00 0.00 0.00 3.20
2659 2686 4.097361 GGGTCGGGTTGGCTCTCC 62.097 72.222 0.00 0.00 0.00 3.71
2660 2687 3.003763 GGTCGGGTTGGCTCTCCT 61.004 66.667 0.00 0.00 0.00 3.69
2661 2688 2.593956 GGTCGGGTTGGCTCTCCTT 61.594 63.158 0.00 0.00 0.00 3.36
2662 2689 1.376037 GTCGGGTTGGCTCTCCTTG 60.376 63.158 0.00 0.00 0.00 3.61
2663 2690 2.747855 CGGGTTGGCTCTCCTTGC 60.748 66.667 0.00 0.00 0.00 4.01
2664 2691 2.759795 GGGTTGGCTCTCCTTGCT 59.240 61.111 0.00 0.00 0.00 3.91
2665 2692 1.377856 GGGTTGGCTCTCCTTGCTC 60.378 63.158 0.00 0.00 0.00 4.26
2666 2693 1.682257 GGTTGGCTCTCCTTGCTCT 59.318 57.895 0.00 0.00 0.00 4.09
2667 2694 0.037447 GGTTGGCTCTCCTTGCTCTT 59.963 55.000 0.00 0.00 0.00 2.85
2668 2695 1.447945 GTTGGCTCTCCTTGCTCTTC 58.552 55.000 0.00 0.00 0.00 2.87
2669 2696 1.003003 GTTGGCTCTCCTTGCTCTTCT 59.997 52.381 0.00 0.00 0.00 2.85
2670 2697 2.234908 GTTGGCTCTCCTTGCTCTTCTA 59.765 50.000 0.00 0.00 0.00 2.10
2671 2698 1.827969 TGGCTCTCCTTGCTCTTCTAC 59.172 52.381 0.00 0.00 0.00 2.59
2672 2699 1.202359 GGCTCTCCTTGCTCTTCTACG 60.202 57.143 0.00 0.00 0.00 3.51
2673 2700 1.801025 GCTCTCCTTGCTCTTCTACGC 60.801 57.143 0.00 0.00 0.00 4.42
2674 2701 0.818296 TCTCCTTGCTCTTCTACGCC 59.182 55.000 0.00 0.00 0.00 5.68
2675 2702 0.526524 CTCCTTGCTCTTCTACGCCG 60.527 60.000 0.00 0.00 0.00 6.46
2676 2703 1.519455 CCTTGCTCTTCTACGCCGG 60.519 63.158 0.00 0.00 0.00 6.13
2677 2704 2.125673 TTGCTCTTCTACGCCGGC 60.126 61.111 19.07 19.07 0.00 6.13
2678 2705 3.982372 TTGCTCTTCTACGCCGGCG 62.982 63.158 44.88 44.88 46.03 6.46
2696 2723 4.016706 CCCTTCCCTGGTTCGCGT 62.017 66.667 5.77 0.00 0.00 6.01
2697 2724 2.032071 CCTTCCCTGGTTCGCGTT 59.968 61.111 5.77 0.00 0.00 4.84
2698 2725 1.599797 CCTTCCCTGGTTCGCGTTT 60.600 57.895 5.77 0.00 0.00 3.60
2699 2726 1.170290 CCTTCCCTGGTTCGCGTTTT 61.170 55.000 5.77 0.00 0.00 2.43
2700 2727 0.666374 CTTCCCTGGTTCGCGTTTTT 59.334 50.000 5.77 0.00 0.00 1.94
2701 2728 0.382515 TTCCCTGGTTCGCGTTTTTG 59.617 50.000 5.77 0.00 0.00 2.44
2702 2729 1.007849 CCCTGGTTCGCGTTTTTGG 60.008 57.895 5.77 4.60 0.00 3.28
2703 2730 1.007849 CCTGGTTCGCGTTTTTGGG 60.008 57.895 5.77 0.00 0.00 4.12
2704 2731 1.660264 CTGGTTCGCGTTTTTGGGC 60.660 57.895 5.77 0.00 0.00 5.36
2723 2750 4.135153 CTGGGCGACTCGGTGGAG 62.135 72.222 0.00 0.00 46.13 3.86
2731 2758 3.920031 CTCGGTGGAGTCGGATGA 58.080 61.111 0.00 0.00 35.48 2.92
2732 2759 2.420138 CTCGGTGGAGTCGGATGAT 58.580 57.895 0.00 0.00 35.48 2.45
2733 2760 0.031314 CTCGGTGGAGTCGGATGATG 59.969 60.000 0.00 0.00 35.48 3.07
2734 2761 0.395173 TCGGTGGAGTCGGATGATGA 60.395 55.000 0.00 0.00 0.00 2.92
2735 2762 0.676184 CGGTGGAGTCGGATGATGAT 59.324 55.000 0.00 0.00 0.00 2.45
2736 2763 1.069204 CGGTGGAGTCGGATGATGATT 59.931 52.381 0.00 0.00 0.00 2.57
2737 2764 2.760374 GGTGGAGTCGGATGATGATTC 58.240 52.381 0.00 0.00 0.00 2.52
2738 2765 2.398498 GTGGAGTCGGATGATGATTCG 58.602 52.381 0.00 0.00 31.02 3.34
2739 2766 1.341209 TGGAGTCGGATGATGATTCGG 59.659 52.381 0.00 0.00 30.71 4.30
2740 2767 1.613925 GGAGTCGGATGATGATTCGGA 59.386 52.381 0.00 0.00 30.71 4.55
2741 2768 2.352225 GGAGTCGGATGATGATTCGGAG 60.352 54.545 0.00 0.00 30.71 4.63
2742 2769 1.615883 AGTCGGATGATGATTCGGAGG 59.384 52.381 0.00 0.00 30.71 4.30
2743 2770 1.341531 GTCGGATGATGATTCGGAGGT 59.658 52.381 0.00 0.00 30.71 3.85
2744 2771 1.341209 TCGGATGATGATTCGGAGGTG 59.659 52.381 0.00 0.00 30.71 4.00
2745 2772 1.069204 CGGATGATGATTCGGAGGTGT 59.931 52.381 0.00 0.00 0.00 4.16
2746 2773 2.487934 GGATGATGATTCGGAGGTGTG 58.512 52.381 0.00 0.00 0.00 3.82
2747 2774 1.869767 GATGATGATTCGGAGGTGTGC 59.130 52.381 0.00 0.00 0.00 4.57
2748 2775 0.460109 TGATGATTCGGAGGTGTGCG 60.460 55.000 0.00 0.00 39.23 5.34
2749 2776 1.766143 GATGATTCGGAGGTGTGCGC 61.766 60.000 0.00 0.00 37.45 6.09
2750 2777 2.125512 GATTCGGAGGTGTGCGCT 60.126 61.111 9.73 0.00 37.45 5.92
2751 2778 2.125512 ATTCGGAGGTGTGCGCTC 60.126 61.111 9.73 5.51 37.45 5.03
2752 2779 3.665675 ATTCGGAGGTGTGCGCTCC 62.666 63.158 9.73 10.40 37.45 4.70
2755 2782 4.459089 GGAGGTGTGCGCTCCCTC 62.459 72.222 25.95 25.95 43.35 4.30
2756 2783 4.803426 GAGGTGTGCGCTCCCTCG 62.803 72.222 22.46 0.00 35.79 4.63
2758 2785 4.148825 GGTGTGCGCTCCCTCGAT 62.149 66.667 9.73 0.00 0.00 3.59
2759 2786 2.887568 GTGTGCGCTCCCTCGATG 60.888 66.667 9.73 0.00 0.00 3.84
2760 2787 4.147449 TGTGCGCTCCCTCGATGG 62.147 66.667 9.73 0.00 0.00 3.51
2761 2788 4.148825 GTGCGCTCCCTCGATGGT 62.149 66.667 9.73 0.00 0.00 3.55
2762 2789 4.147449 TGCGCTCCCTCGATGGTG 62.147 66.667 9.73 5.56 0.00 4.17
2763 2790 4.899239 GCGCTCCCTCGATGGTGG 62.899 72.222 6.63 2.89 0.00 4.61
2764 2791 3.461773 CGCTCCCTCGATGGTGGT 61.462 66.667 6.63 0.00 0.00 4.16
2765 2792 2.187946 GCTCCCTCGATGGTGGTG 59.812 66.667 6.63 0.00 0.00 4.17
2766 2793 2.187946 CTCCCTCGATGGTGGTGC 59.812 66.667 6.63 0.00 0.00 5.01
2767 2794 3.391665 CTCCCTCGATGGTGGTGCC 62.392 68.421 6.63 0.00 37.90 5.01
2768 2795 4.838152 CCCTCGATGGTGGTGCCG 62.838 72.222 0.00 0.00 41.21 5.69
2769 2796 4.838152 CCTCGATGGTGGTGCCGG 62.838 72.222 0.00 0.00 41.21 6.13
2770 2797 4.082523 CTCGATGGTGGTGCCGGT 62.083 66.667 1.90 0.00 41.21 5.28
2771 2798 4.386951 TCGATGGTGGTGCCGGTG 62.387 66.667 1.90 0.00 41.21 4.94
2773 2800 4.344865 GATGGTGGTGCCGGTGGT 62.345 66.667 1.90 0.00 41.21 4.16
2774 2801 4.659172 ATGGTGGTGCCGGTGGTG 62.659 66.667 1.90 0.00 41.21 4.17
2813 2840 4.025401 CGCGCCCGAAAGTTTGCT 62.025 61.111 0.00 0.00 36.29 3.91
2814 2841 2.126850 GCGCCCGAAAGTTTGCTC 60.127 61.111 0.00 0.00 0.00 4.26
2815 2842 2.561373 CGCCCGAAAGTTTGCTCC 59.439 61.111 0.00 0.00 0.00 4.70
2816 2843 2.561373 GCCCGAAAGTTTGCTCCG 59.439 61.111 0.00 0.00 0.00 4.63
2817 2844 2.978018 GCCCGAAAGTTTGCTCCGG 61.978 63.158 0.00 0.00 39.85 5.14
2818 2845 3.263941 CCGAAAGTTTGCTCCGGG 58.736 61.111 0.00 0.00 36.81 5.73
2819 2846 1.599797 CCGAAAGTTTGCTCCGGGT 60.600 57.895 0.00 0.00 36.81 5.28
2820 2847 1.574428 CGAAAGTTTGCTCCGGGTG 59.426 57.895 0.00 0.00 0.00 4.61
2821 2848 1.852067 CGAAAGTTTGCTCCGGGTGG 61.852 60.000 0.00 0.00 0.00 4.61
2822 2849 2.142357 GAAAGTTTGCTCCGGGTGGC 62.142 60.000 0.00 4.70 34.14 5.01
2823 2850 4.660938 AGTTTGCTCCGGGTGGCC 62.661 66.667 0.00 0.00 34.14 5.36
2844 2871 3.723348 GCCAGCCGGTGTCGTTTC 61.723 66.667 1.90 0.00 33.95 2.78
2845 2872 3.047877 CCAGCCGGTGTCGTTTCC 61.048 66.667 1.90 0.00 33.95 3.13
2846 2873 3.047877 CAGCCGGTGTCGTTTCCC 61.048 66.667 1.90 0.00 33.95 3.97
2847 2874 3.239253 AGCCGGTGTCGTTTCCCT 61.239 61.111 1.90 0.00 33.95 4.20
2848 2875 2.741211 GCCGGTGTCGTTTCCCTC 60.741 66.667 1.90 0.00 33.95 4.30
2849 2876 3.057337 CCGGTGTCGTTTCCCTCT 58.943 61.111 0.00 0.00 33.95 3.69
2850 2877 1.374252 CCGGTGTCGTTTCCCTCTG 60.374 63.158 0.00 0.00 33.95 3.35
2851 2878 1.374252 CGGTGTCGTTTCCCTCTGG 60.374 63.158 0.00 0.00 0.00 3.86
2852 2879 1.003718 GGTGTCGTTTCCCTCTGGG 60.004 63.158 0.00 0.00 46.11 4.45
2853 2880 1.752833 GTGTCGTTTCCCTCTGGGT 59.247 57.895 2.25 0.00 44.74 4.51
2854 2881 0.320508 GTGTCGTTTCCCTCTGGGTC 60.321 60.000 2.25 0.00 44.74 4.46
2855 2882 1.080025 GTCGTTTCCCTCTGGGTCG 60.080 63.158 2.25 6.86 44.74 4.79
2856 2883 1.532316 TCGTTTCCCTCTGGGTCGT 60.532 57.895 2.25 0.00 44.74 4.34
2857 2884 1.080025 CGTTTCCCTCTGGGTCGTC 60.080 63.158 2.25 0.00 44.74 4.20
2858 2885 1.080025 GTTTCCCTCTGGGTCGTCG 60.080 63.158 2.25 0.00 44.74 5.12
2859 2886 2.280552 TTTCCCTCTGGGTCGTCGG 61.281 63.158 2.25 0.00 44.74 4.79
2860 2887 4.753662 TCCCTCTGGGTCGTCGGG 62.754 72.222 2.25 0.00 44.74 5.14
2863 2890 3.760035 CTCTGGGTCGTCGGGGTG 61.760 72.222 0.00 0.00 0.00 4.61
2869 2896 4.675029 GTCGTCGGGGTGGTGGTG 62.675 72.222 0.00 0.00 0.00 4.17
2876 2903 4.887190 GGGTGGTGGTGCGTTGGT 62.887 66.667 0.00 0.00 0.00 3.67
2877 2904 3.284449 GGTGGTGGTGCGTTGGTC 61.284 66.667 0.00 0.00 0.00 4.02
2878 2905 3.645975 GTGGTGGTGCGTTGGTCG 61.646 66.667 0.00 0.00 43.12 4.79
2879 2906 4.920112 TGGTGGTGCGTTGGTCGG 62.920 66.667 0.00 0.00 40.26 4.79
2888 2915 3.881104 GTTGGTCGGGGTGGTGGT 61.881 66.667 0.00 0.00 0.00 4.16
2889 2916 3.879885 TTGGTCGGGGTGGTGGTG 61.880 66.667 0.00 0.00 0.00 4.17
2896 2923 4.887190 GGGTGGTGGTGCGTTGGT 62.887 66.667 0.00 0.00 0.00 3.67
2897 2924 3.284449 GGTGGTGGTGCGTTGGTC 61.284 66.667 0.00 0.00 0.00 4.02
2898 2925 3.645975 GTGGTGGTGCGTTGGTCG 61.646 66.667 0.00 0.00 43.12 4.79
2899 2926 4.920112 TGGTGGTGCGTTGGTCGG 62.920 66.667 0.00 0.00 40.26 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.952367 GCCTTCCCAGTCATCACAAGG 60.952 57.143 0.00 0.00 34.62 3.61
3 4 1.004044 AGCCTTCCCAGTCATCACAAG 59.996 52.381 0.00 0.00 0.00 3.16
4 5 1.067295 AGCCTTCCCAGTCATCACAA 58.933 50.000 0.00 0.00 0.00 3.33
5 6 1.067295 AAGCCTTCCCAGTCATCACA 58.933 50.000 0.00 0.00 0.00 3.58
7 8 1.887956 GCAAAGCCTTCCCAGTCATCA 60.888 52.381 0.00 0.00 0.00 3.07
8 9 0.813821 GCAAAGCCTTCCCAGTCATC 59.186 55.000 0.00 0.00 0.00 2.92
9 10 0.613012 GGCAAAGCCTTCCCAGTCAT 60.613 55.000 0.00 0.00 46.69 3.06
10 11 1.228552 GGCAAAGCCTTCCCAGTCA 60.229 57.895 0.00 0.00 46.69 3.41
11 12 3.686760 GGCAAAGCCTTCCCAGTC 58.313 61.111 0.00 0.00 46.69 3.51
20 21 5.244862 CCAAATCTGGGTAAGGCAAAGCC 62.245 52.174 0.00 0.00 43.62 4.35
21 22 2.094026 CCAAATCTGGGTAAGGCAAAGC 60.094 50.000 0.00 0.00 39.30 3.51
22 23 3.430453 TCCAAATCTGGGTAAGGCAAAG 58.570 45.455 0.00 0.00 43.71 2.77
23 24 3.534357 TCCAAATCTGGGTAAGGCAAA 57.466 42.857 0.00 0.00 43.71 3.68
24 25 3.364549 CATCCAAATCTGGGTAAGGCAA 58.635 45.455 0.00 0.00 43.71 4.52
25 26 2.949963 GCATCCAAATCTGGGTAAGGCA 60.950 50.000 0.00 0.00 43.71 4.75
26 27 1.683385 GCATCCAAATCTGGGTAAGGC 59.317 52.381 0.00 0.00 43.71 4.35
27 28 2.310538 GGCATCCAAATCTGGGTAAGG 58.689 52.381 0.00 0.00 43.71 2.69
28 29 2.310538 GGGCATCCAAATCTGGGTAAG 58.689 52.381 0.00 0.00 43.71 2.34
29 30 1.063266 GGGGCATCCAAATCTGGGTAA 60.063 52.381 0.00 0.00 43.71 2.85
30 31 0.555769 GGGGCATCCAAATCTGGGTA 59.444 55.000 0.00 0.00 43.71 3.69
31 32 1.311059 GGGGCATCCAAATCTGGGT 59.689 57.895 0.00 0.00 43.71 4.51
32 33 1.458209 GGGGGCATCCAAATCTGGG 60.458 63.158 0.00 0.00 43.71 4.45
33 34 0.757935 CTGGGGGCATCCAAATCTGG 60.758 60.000 0.65 0.00 45.08 3.86
34 35 1.397390 GCTGGGGGCATCCAAATCTG 61.397 60.000 0.65 0.00 41.35 2.90
35 36 1.075748 GCTGGGGGCATCCAAATCT 60.076 57.895 0.65 0.00 41.35 2.40
36 37 1.075748 AGCTGGGGGCATCCAAATC 60.076 57.895 0.00 0.00 44.79 2.17
37 38 1.382146 CAGCTGGGGGCATCCAAAT 60.382 57.895 5.57 0.00 44.79 2.32
38 39 2.037687 CAGCTGGGGGCATCCAAA 59.962 61.111 5.57 0.00 44.79 3.28
39 40 2.091640 TTTCAGCTGGGGGCATCCAA 62.092 55.000 15.13 0.00 44.79 3.53
40 41 2.503846 CTTTCAGCTGGGGGCATCCA 62.504 60.000 15.13 0.00 44.79 3.41
41 42 1.755783 CTTTCAGCTGGGGGCATCC 60.756 63.158 15.13 0.00 44.79 3.51
42 43 2.421399 GCTTTCAGCTGGGGGCATC 61.421 63.158 15.13 0.00 44.79 3.91
43 44 2.363406 GCTTTCAGCTGGGGGCAT 60.363 61.111 15.13 0.00 44.79 4.40
44 45 1.862049 TATGCTTTCAGCTGGGGGCA 61.862 55.000 22.77 22.77 42.97 5.36
45 46 0.684153 TTATGCTTTCAGCTGGGGGC 60.684 55.000 15.13 15.18 42.97 5.80
46 47 1.753073 CTTTATGCTTTCAGCTGGGGG 59.247 52.381 15.13 5.16 42.97 5.40
47 48 1.753073 CCTTTATGCTTTCAGCTGGGG 59.247 52.381 15.13 5.53 42.97 4.96
48 49 1.753073 CCCTTTATGCTTTCAGCTGGG 59.247 52.381 15.13 5.90 42.97 4.45
49 50 1.135721 GCCCTTTATGCTTTCAGCTGG 59.864 52.381 15.13 0.00 42.97 4.85
50 51 1.202222 CGCCCTTTATGCTTTCAGCTG 60.202 52.381 7.63 7.63 42.97 4.24
51 52 1.098050 CGCCCTTTATGCTTTCAGCT 58.902 50.000 0.00 0.00 42.97 4.24
52 53 0.811281 ACGCCCTTTATGCTTTCAGC 59.189 50.000 0.00 0.00 42.82 4.26
53 54 2.083774 TCACGCCCTTTATGCTTTCAG 58.916 47.619 0.00 0.00 0.00 3.02
54 55 2.192664 TCACGCCCTTTATGCTTTCA 57.807 45.000 0.00 0.00 0.00 2.69
55 56 3.489229 GGATTCACGCCCTTTATGCTTTC 60.489 47.826 0.00 0.00 0.00 2.62
56 57 2.427095 GGATTCACGCCCTTTATGCTTT 59.573 45.455 0.00 0.00 0.00 3.51
57 58 2.024414 GGATTCACGCCCTTTATGCTT 58.976 47.619 0.00 0.00 0.00 3.91
58 59 1.680338 GGATTCACGCCCTTTATGCT 58.320 50.000 0.00 0.00 0.00 3.79
59 60 0.668535 GGGATTCACGCCCTTTATGC 59.331 55.000 0.00 0.00 42.56 3.14
60 61 1.318576 GGGGATTCACGCCCTTTATG 58.681 55.000 0.00 0.00 45.30 1.90
61 62 3.821306 GGGGATTCACGCCCTTTAT 57.179 52.632 0.00 0.00 45.30 1.40
68 69 1.947456 GTTGATTAGGGGGATTCACGC 59.053 52.381 0.00 0.00 0.00 5.34
69 70 3.560636 AGTTGATTAGGGGGATTCACG 57.439 47.619 0.00 0.00 0.00 4.35
70 71 4.974399 CCTAGTTGATTAGGGGGATTCAC 58.026 47.826 0.00 0.00 37.20 3.18
79 80 1.843851 TGGCCACCCTAGTTGATTAGG 59.156 52.381 0.00 0.00 39.99 2.69
80 81 3.480470 CATGGCCACCCTAGTTGATTAG 58.520 50.000 8.16 0.00 0.00 1.73
81 82 2.422803 GCATGGCCACCCTAGTTGATTA 60.423 50.000 8.16 0.00 0.00 1.75
82 83 1.686115 GCATGGCCACCCTAGTTGATT 60.686 52.381 8.16 0.00 0.00 2.57
83 84 0.106519 GCATGGCCACCCTAGTTGAT 60.107 55.000 8.16 0.00 0.00 2.57
84 85 1.302949 GCATGGCCACCCTAGTTGA 59.697 57.895 8.16 0.00 0.00 3.18
85 86 3.924507 GCATGGCCACCCTAGTTG 58.075 61.111 8.16 0.48 0.00 3.16
137 138 0.038166 GATGGGTTTGGTGAGCTGGA 59.962 55.000 0.00 0.00 0.00 3.86
158 159 1.135333 GTTTTCACTTCGCCCCAAACA 59.865 47.619 0.00 0.00 0.00 2.83
162 163 1.698506 AATGTTTTCACTTCGCCCCA 58.301 45.000 0.00 0.00 0.00 4.96
192 193 4.513406 TTCCTTTCCAGTTGTTGTAGGT 57.487 40.909 0.00 0.00 0.00 3.08
211 212 7.710475 TGTTTTGATGTTTTCCCTCTTCAATTC 59.290 33.333 0.00 0.00 31.38 2.17
227 228 7.208777 TGTGTTGCTTGATATTGTTTTGATGT 58.791 30.769 0.00 0.00 0.00 3.06
245 246 5.257864 GTTTGAATTGCTTTCTTGTGTTGC 58.742 37.500 0.00 0.00 35.23 4.17
282 283 5.172934 ACGAATCAAATAACCAGCGTAAGA 58.827 37.500 0.00 0.00 43.02 2.10
345 346 9.860898 GCACCAAGAATCTTTAATATCTTTGTT 57.139 29.630 0.00 0.00 28.64 2.83
346 347 9.023962 TGCACCAAGAATCTTTAATATCTTTGT 57.976 29.630 0.00 0.00 30.53 2.83
349 350 9.638176 AGATGCACCAAGAATCTTTAATATCTT 57.362 29.630 0.00 0.00 32.55 2.40
442 443 3.314693 TGGGTTTGACTAGAGTTGGTCT 58.685 45.455 0.00 0.00 35.94 3.85
466 467 9.424319 CACACATCAGATATATAGTTGGGTTAC 57.576 37.037 2.43 0.00 0.00 2.50
477 479 7.980662 GCTGAAGCTATCACACATCAGATATAT 59.019 37.037 11.11 0.00 37.14 0.86
482 484 3.196254 TGCTGAAGCTATCACACATCAGA 59.804 43.478 11.11 0.00 42.66 3.27
508 510 5.404366 GTGCAACTCGTGTATACAGAAAAGA 59.596 40.000 5.62 0.87 0.00 2.52
575 577 8.133024 TGATGGAATAGGTGCAATTTAAGTTT 57.867 30.769 0.00 0.00 0.00 2.66
583 585 4.508551 TGTCTGATGGAATAGGTGCAAT 57.491 40.909 0.00 0.00 0.00 3.56
584 586 3.998913 TGTCTGATGGAATAGGTGCAA 57.001 42.857 0.00 0.00 0.00 4.08
599 601 8.302965 TCTCGCAATTTAGATTATCATGTCTG 57.697 34.615 0.00 0.00 0.00 3.51
600 602 8.893219 TTCTCGCAATTTAGATTATCATGTCT 57.107 30.769 0.00 0.00 0.00 3.41
617 619 5.058149 ACATTGTATGCATTTTCTCGCAA 57.942 34.783 3.54 0.27 42.37 4.85
652 654 3.550656 CGTGGAGGAACGTGAAGC 58.449 61.111 0.00 0.00 38.74 3.86
719 721 8.948631 TCTTCTACCATTCTACAATTCACATC 57.051 34.615 0.00 0.00 0.00 3.06
817 825 6.201044 CAGGTGAAGGATTAGTTACTATTGCG 59.799 42.308 0.00 0.00 0.00 4.85
827 838 8.712228 AAAAAGAATTCAGGTGAAGGATTAGT 57.288 30.769 8.44 0.00 37.48 2.24
872 886 2.169769 TGGTCTCGGTTTTGTCTGAACT 59.830 45.455 0.00 0.00 0.00 3.01
874 888 2.432874 TCTGGTCTCGGTTTTGTCTGAA 59.567 45.455 0.00 0.00 0.00 3.02
878 892 1.149148 GCTCTGGTCTCGGTTTTGTC 58.851 55.000 0.00 0.00 0.00 3.18
885 899 1.115467 ATAACCTGCTCTGGTCTCGG 58.885 55.000 0.00 0.00 39.83 4.63
886 900 2.482142 GGAATAACCTGCTCTGGTCTCG 60.482 54.545 0.00 0.00 39.83 4.04
1010 1034 2.213499 GGTTCTTGTGTGAGTGACTGG 58.787 52.381 0.00 0.00 0.00 4.00
1231 1258 1.195448 CAGTGAAACATCAGTGACCGC 59.805 52.381 7.70 0.00 42.10 5.68
1491 1518 1.001503 GGTGGATGGAAATGGCCCA 59.998 57.895 0.00 0.00 38.19 5.36
1560 1587 2.011947 GTTGGTATCGCCCCAGTAAAC 58.988 52.381 0.00 0.00 36.04 2.01
1804 1831 5.045012 AGATTTCTGAGGCTGAATATGCA 57.955 39.130 0.00 0.00 0.00 3.96
1834 1861 6.394345 AAAGTAGTTCCCTCCAAGATCAAT 57.606 37.500 0.00 0.00 0.00 2.57
1933 1960 1.227943 GTGTTGGTGGCAGCTCTCA 60.228 57.895 18.53 10.95 0.00 3.27
1935 1962 1.228063 CAGTGTTGGTGGCAGCTCT 60.228 57.895 18.53 8.12 0.00 4.09
2192 2219 4.799564 TTTTTGCCAAGTGACAAGAAGT 57.200 36.364 0.00 0.00 0.00 3.01
2253 2280 3.074412 GGTGCTAAGTTTCTTGCTGCTA 58.926 45.455 0.00 0.00 0.00 3.49
2450 2477 2.840511 TCCAGCCTGGTATTAGTCCAA 58.159 47.619 11.27 0.00 39.03 3.53
2456 2483 4.689612 GAGTTGATCCAGCCTGGTATTA 57.310 45.455 11.27 0.00 39.03 0.98
2538 2565 3.706086 AGAGAAGAGAAAGGAGCCATCTC 59.294 47.826 12.02 12.02 39.88 2.75
2539 2566 3.706086 GAGAGAAGAGAAAGGAGCCATCT 59.294 47.826 0.00 0.00 0.00 2.90
2540 2567 3.181466 GGAGAGAAGAGAAAGGAGCCATC 60.181 52.174 0.00 0.00 0.00 3.51
2541 2568 2.771372 GGAGAGAAGAGAAAGGAGCCAT 59.229 50.000 0.00 0.00 0.00 4.40
2542 2569 2.183679 GGAGAGAAGAGAAAGGAGCCA 58.816 52.381 0.00 0.00 0.00 4.75
2543 2570 1.484653 GGGAGAGAAGAGAAAGGAGCC 59.515 57.143 0.00 0.00 0.00 4.70
2544 2571 2.466846 AGGGAGAGAAGAGAAAGGAGC 58.533 52.381 0.00 0.00 0.00 4.70
2545 2572 3.130340 CGAAGGGAGAGAAGAGAAAGGAG 59.870 52.174 0.00 0.00 0.00 3.69
2546 2573 3.093057 CGAAGGGAGAGAAGAGAAAGGA 58.907 50.000 0.00 0.00 0.00 3.36
2547 2574 2.829120 ACGAAGGGAGAGAAGAGAAAGG 59.171 50.000 0.00 0.00 0.00 3.11
2548 2575 3.119280 GGACGAAGGGAGAGAAGAGAAAG 60.119 52.174 0.00 0.00 0.00 2.62
2549 2576 2.826725 GGACGAAGGGAGAGAAGAGAAA 59.173 50.000 0.00 0.00 0.00 2.52
2550 2577 2.448453 GGACGAAGGGAGAGAAGAGAA 58.552 52.381 0.00 0.00 0.00 2.87
2551 2578 1.341187 GGGACGAAGGGAGAGAAGAGA 60.341 57.143 0.00 0.00 0.00 3.10
2552 2579 1.107945 GGGACGAAGGGAGAGAAGAG 58.892 60.000 0.00 0.00 0.00 2.85
2553 2580 0.324460 GGGGACGAAGGGAGAGAAGA 60.324 60.000 0.00 0.00 0.00 2.87
2554 2581 1.331399 GGGGGACGAAGGGAGAGAAG 61.331 65.000 0.00 0.00 0.00 2.85
2555 2582 1.305887 GGGGGACGAAGGGAGAGAA 60.306 63.158 0.00 0.00 0.00 2.87
2556 2583 2.363361 GGGGGACGAAGGGAGAGA 59.637 66.667 0.00 0.00 0.00 3.10
2582 2609 4.890306 GGGGAGGAGGAGGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
2583 2610 3.039526 AGGGGAGGAGGAGGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
2584 2611 3.368501 CAGGGGAGGAGGAGGGGA 61.369 72.222 0.00 0.00 0.00 4.81
2588 2615 3.649652 AAGGGCAGGGGAGGAGGAG 62.650 68.421 0.00 0.00 0.00 3.69
2589 2616 3.626596 AAGGGCAGGGGAGGAGGA 61.627 66.667 0.00 0.00 0.00 3.71
2590 2617 3.415087 CAAGGGCAGGGGAGGAGG 61.415 72.222 0.00 0.00 0.00 4.30
2591 2618 4.120755 GCAAGGGCAGGGGAGGAG 62.121 72.222 0.00 0.00 40.72 3.69
2630 2657 4.796231 CGACCCGCAGAAGACCGG 62.796 72.222 0.00 0.00 43.97 5.28
2631 2658 4.796231 CCGACCCGCAGAAGACCG 62.796 72.222 0.00 0.00 0.00 4.79
2632 2659 4.452733 CCCGACCCGCAGAAGACC 62.453 72.222 0.00 0.00 0.00 3.85
2633 2660 3.236003 AACCCGACCCGCAGAAGAC 62.236 63.158 0.00 0.00 0.00 3.01
2634 2661 2.920912 AACCCGACCCGCAGAAGA 60.921 61.111 0.00 0.00 0.00 2.87
2635 2662 2.742372 CAACCCGACCCGCAGAAG 60.742 66.667 0.00 0.00 0.00 2.85
2636 2663 4.323477 CCAACCCGACCCGCAGAA 62.323 66.667 0.00 0.00 0.00 3.02
2641 2668 4.452733 GAGAGCCAACCCGACCCG 62.453 72.222 0.00 0.00 0.00 5.28
2642 2669 4.097361 GGAGAGCCAACCCGACCC 62.097 72.222 0.00 0.00 0.00 4.46
2643 2670 2.593956 AAGGAGAGCCAACCCGACC 61.594 63.158 0.00 0.00 36.29 4.79
2644 2671 1.376037 CAAGGAGAGCCAACCCGAC 60.376 63.158 0.00 0.00 36.29 4.79
2645 2672 3.068881 CAAGGAGAGCCAACCCGA 58.931 61.111 0.00 0.00 36.29 5.14
2646 2673 2.747855 GCAAGGAGAGCCAACCCG 60.748 66.667 0.00 0.00 36.29 5.28
2647 2674 1.377856 GAGCAAGGAGAGCCAACCC 60.378 63.158 0.00 0.00 36.29 4.11
2648 2675 0.037447 AAGAGCAAGGAGAGCCAACC 59.963 55.000 0.00 0.00 36.29 3.77
2649 2676 1.003003 AGAAGAGCAAGGAGAGCCAAC 59.997 52.381 0.00 0.00 36.29 3.77
2650 2677 1.356124 AGAAGAGCAAGGAGAGCCAA 58.644 50.000 0.00 0.00 36.29 4.52
2651 2678 1.827969 GTAGAAGAGCAAGGAGAGCCA 59.172 52.381 0.00 0.00 36.29 4.75
2652 2679 1.202359 CGTAGAAGAGCAAGGAGAGCC 60.202 57.143 0.00 0.00 0.00 4.70
2653 2680 1.801025 GCGTAGAAGAGCAAGGAGAGC 60.801 57.143 0.00 0.00 0.00 4.09
2654 2681 1.202359 GGCGTAGAAGAGCAAGGAGAG 60.202 57.143 0.00 0.00 34.54 3.20
2655 2682 0.818296 GGCGTAGAAGAGCAAGGAGA 59.182 55.000 0.00 0.00 34.54 3.71
2656 2683 0.526524 CGGCGTAGAAGAGCAAGGAG 60.527 60.000 0.00 0.00 34.54 3.69
2657 2684 1.511305 CGGCGTAGAAGAGCAAGGA 59.489 57.895 0.00 0.00 34.54 3.36
2658 2685 1.519455 CCGGCGTAGAAGAGCAAGG 60.519 63.158 6.01 0.00 34.54 3.61
2659 2686 2.167861 GCCGGCGTAGAAGAGCAAG 61.168 63.158 12.58 0.00 34.54 4.01
2660 2687 2.125673 GCCGGCGTAGAAGAGCAA 60.126 61.111 12.58 0.00 34.54 3.91
2661 2688 4.492160 CGCCGGCGTAGAAGAGCA 62.492 66.667 39.71 0.00 34.54 4.26
2679 2706 3.546714 AACGCGAACCAGGGAAGGG 62.547 63.158 15.93 0.00 0.00 3.95
2680 2707 1.170290 AAAACGCGAACCAGGGAAGG 61.170 55.000 15.93 0.00 0.00 3.46
2681 2708 0.666374 AAAAACGCGAACCAGGGAAG 59.334 50.000 15.93 0.00 0.00 3.46
2682 2709 0.382515 CAAAAACGCGAACCAGGGAA 59.617 50.000 15.93 0.00 0.00 3.97
2683 2710 1.448922 CCAAAAACGCGAACCAGGGA 61.449 55.000 15.93 0.00 0.00 4.20
2684 2711 1.007849 CCAAAAACGCGAACCAGGG 60.008 57.895 15.93 2.74 0.00 4.45
2685 2712 1.007849 CCCAAAAACGCGAACCAGG 60.008 57.895 15.93 8.99 0.00 4.45
2686 2713 1.660264 GCCCAAAAACGCGAACCAG 60.660 57.895 15.93 0.00 0.00 4.00
2687 2714 2.413765 GCCCAAAAACGCGAACCA 59.586 55.556 15.93 0.00 0.00 3.67
2706 2733 4.135153 CTCCACCGAGTCGCCCAG 62.135 72.222 7.12 0.00 0.00 4.45
2707 2734 4.988716 ACTCCACCGAGTCGCCCA 62.989 66.667 7.12 0.00 46.90 5.36
2714 2741 0.031314 CATCATCCGACTCCACCGAG 59.969 60.000 0.00 0.00 42.32 4.63
2715 2742 0.395173 TCATCATCCGACTCCACCGA 60.395 55.000 0.00 0.00 0.00 4.69
2716 2743 0.676184 ATCATCATCCGACTCCACCG 59.324 55.000 0.00 0.00 0.00 4.94
2717 2744 2.760374 GAATCATCATCCGACTCCACC 58.240 52.381 0.00 0.00 0.00 4.61
2718 2745 2.398498 CGAATCATCATCCGACTCCAC 58.602 52.381 0.00 0.00 0.00 4.02
2719 2746 1.341209 CCGAATCATCATCCGACTCCA 59.659 52.381 0.00 0.00 0.00 3.86
2720 2747 1.613925 TCCGAATCATCATCCGACTCC 59.386 52.381 0.00 0.00 0.00 3.85
2721 2748 2.352225 CCTCCGAATCATCATCCGACTC 60.352 54.545 0.00 0.00 0.00 3.36
2722 2749 1.615883 CCTCCGAATCATCATCCGACT 59.384 52.381 0.00 0.00 0.00 4.18
2723 2750 1.341531 ACCTCCGAATCATCATCCGAC 59.658 52.381 0.00 0.00 0.00 4.79
2724 2751 1.341209 CACCTCCGAATCATCATCCGA 59.659 52.381 0.00 0.00 0.00 4.55
2725 2752 1.069204 ACACCTCCGAATCATCATCCG 59.931 52.381 0.00 0.00 0.00 4.18
2726 2753 2.487934 CACACCTCCGAATCATCATCC 58.512 52.381 0.00 0.00 0.00 3.51
2727 2754 1.869767 GCACACCTCCGAATCATCATC 59.130 52.381 0.00 0.00 0.00 2.92
2728 2755 1.807755 CGCACACCTCCGAATCATCAT 60.808 52.381 0.00 0.00 0.00 2.45
2729 2756 0.460109 CGCACACCTCCGAATCATCA 60.460 55.000 0.00 0.00 0.00 3.07
2730 2757 1.766143 GCGCACACCTCCGAATCATC 61.766 60.000 0.30 0.00 0.00 2.92
2731 2758 1.815421 GCGCACACCTCCGAATCAT 60.815 57.895 0.30 0.00 0.00 2.45
2732 2759 2.434185 GCGCACACCTCCGAATCA 60.434 61.111 0.30 0.00 0.00 2.57
2733 2760 2.125512 AGCGCACACCTCCGAATC 60.126 61.111 11.47 0.00 0.00 2.52
2734 2761 2.125512 GAGCGCACACCTCCGAAT 60.126 61.111 11.47 0.00 0.00 3.34
2735 2762 4.373116 GGAGCGCACACCTCCGAA 62.373 66.667 11.47 0.00 39.50 4.30
2738 2765 4.459089 GAGGGAGCGCACACCTCC 62.459 72.222 25.58 16.72 46.54 4.30
2739 2766 4.803426 CGAGGGAGCGCACACCTC 62.803 72.222 25.90 25.90 45.73 3.85
2741 2768 4.148825 ATCGAGGGAGCGCACACC 62.149 66.667 11.47 8.75 0.00 4.16
2742 2769 2.887568 CATCGAGGGAGCGCACAC 60.888 66.667 11.47 3.80 0.00 3.82
2743 2770 4.147449 CCATCGAGGGAGCGCACA 62.147 66.667 11.55 0.00 0.00 4.57
2744 2771 4.148825 ACCATCGAGGGAGCGCAC 62.149 66.667 25.24 1.97 43.89 5.34
2745 2772 4.147449 CACCATCGAGGGAGCGCA 62.147 66.667 25.24 0.00 43.89 6.09
2746 2773 4.899239 CCACCATCGAGGGAGCGC 62.899 72.222 25.24 0.00 43.89 5.92
2747 2774 3.461773 ACCACCATCGAGGGAGCG 61.462 66.667 25.24 11.44 43.89 5.03
2748 2775 2.187946 CACCACCATCGAGGGAGC 59.812 66.667 25.24 0.00 43.89 4.70
2749 2776 2.187946 GCACCACCATCGAGGGAG 59.812 66.667 25.24 15.63 43.89 4.30
2750 2777 3.399181 GGCACCACCATCGAGGGA 61.399 66.667 25.24 0.00 43.89 4.20
2751 2778 4.838152 CGGCACCACCATCGAGGG 62.838 72.222 15.94 15.94 43.89 4.30
2752 2779 4.838152 CCGGCACCACCATCGAGG 62.838 72.222 0.00 0.00 45.67 4.63
2753 2780 4.082523 ACCGGCACCACCATCGAG 62.083 66.667 0.00 0.00 39.03 4.04
2754 2781 4.386951 CACCGGCACCACCATCGA 62.387 66.667 0.00 0.00 39.03 3.59
2756 2783 4.344865 ACCACCGGCACCACCATC 62.345 66.667 0.00 0.00 39.03 3.51
2757 2784 4.659172 CACCACCGGCACCACCAT 62.659 66.667 0.00 0.00 39.03 3.55
2796 2823 3.928618 GAGCAAACTTTCGGGCGCG 62.929 63.158 18.21 18.21 0.00 6.86
2797 2824 2.126850 GAGCAAACTTTCGGGCGC 60.127 61.111 0.00 0.00 0.00 6.53
2798 2825 2.561373 GGAGCAAACTTTCGGGCG 59.439 61.111 0.00 0.00 0.00 6.13
2799 2826 2.561373 CGGAGCAAACTTTCGGGC 59.439 61.111 0.00 0.00 0.00 6.13
2800 2827 3.263941 CCGGAGCAAACTTTCGGG 58.736 61.111 0.00 0.00 38.53 5.14
2801 2828 1.599797 ACCCGGAGCAAACTTTCGG 60.600 57.895 0.73 0.00 40.49 4.30
2802 2829 1.574428 CACCCGGAGCAAACTTTCG 59.426 57.895 0.73 0.00 0.00 3.46
2803 2830 1.956802 CCACCCGGAGCAAACTTTC 59.043 57.895 0.73 0.00 0.00 2.62
2804 2831 2.200337 GCCACCCGGAGCAAACTTT 61.200 57.895 0.73 0.00 0.00 2.66
2805 2832 2.597510 GCCACCCGGAGCAAACTT 60.598 61.111 0.73 0.00 0.00 2.66
2806 2833 4.660938 GGCCACCCGGAGCAAACT 62.661 66.667 0.73 0.00 0.00 2.66
2827 2854 3.723348 GAAACGACACCGGCTGGC 61.723 66.667 12.89 0.00 39.70 4.85
2828 2855 3.047877 GGAAACGACACCGGCTGG 61.048 66.667 11.02 11.02 40.78 4.85
2829 2856 3.047877 GGGAAACGACACCGGCTG 61.048 66.667 0.00 1.20 40.78 4.85
2830 2857 3.236003 GAGGGAAACGACACCGGCT 62.236 63.158 0.00 0.00 40.78 5.52
2831 2858 2.741211 GAGGGAAACGACACCGGC 60.741 66.667 0.00 0.00 40.78 6.13
2832 2859 1.374252 CAGAGGGAAACGACACCGG 60.374 63.158 0.00 0.00 40.78 5.28
2833 2860 1.374252 CCAGAGGGAAACGACACCG 60.374 63.158 0.00 0.00 37.97 4.94
2834 2861 4.695560 CCAGAGGGAAACGACACC 57.304 61.111 0.00 0.00 35.59 4.16
2846 2873 3.760035 CACCCCGACGACCCAGAG 61.760 72.222 0.00 0.00 0.00 3.35
2852 2879 4.675029 CACCACCACCCCGACGAC 62.675 72.222 0.00 0.00 0.00 4.34
2859 2886 4.887190 ACCAACGCACCACCACCC 62.887 66.667 0.00 0.00 0.00 4.61
2860 2887 3.284449 GACCAACGCACCACCACC 61.284 66.667 0.00 0.00 0.00 4.61
2861 2888 3.645975 CGACCAACGCACCACCAC 61.646 66.667 0.00 0.00 34.51 4.16
2862 2889 4.920112 CCGACCAACGCACCACCA 62.920 66.667 0.00 0.00 41.07 4.17
2871 2898 3.881104 ACCACCACCCCGACCAAC 61.881 66.667 0.00 0.00 0.00 3.77
2872 2899 3.879885 CACCACCACCCCGACCAA 61.880 66.667 0.00 0.00 0.00 3.67
2879 2906 4.887190 ACCAACGCACCACCACCC 62.887 66.667 0.00 0.00 0.00 4.61
2880 2907 3.284449 GACCAACGCACCACCACC 61.284 66.667 0.00 0.00 0.00 4.61
2881 2908 3.645975 CGACCAACGCACCACCAC 61.646 66.667 0.00 0.00 34.51 4.16
2882 2909 4.920112 CCGACCAACGCACCACCA 62.920 66.667 0.00 0.00 41.07 4.17


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

AutoCloner maintained by Alex Coulton.