Multiple sequence alignment - TraesCS2B01G415900

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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 TraesCS2B01G415900 chr2B 100.000 2633 0 0 1 2633 594685031 594682399 0.000000e+00 4863.0
1 TraesCS2B01G415900 chr2B 84.775 1110 100 34 768 1835 594261859 594260777 0.000000e+00 1050.0
2 TraesCS2B01G415900 chr2B 83.670 1041 99 39 793 1780 594205822 594204800 0.000000e+00 915.0
3 TraesCS2B01G415900 chr2A 87.588 1982 121 46 103 1990 651511468 651509518 0.000000e+00 2182.0
4 TraesCS2B01G415900 chr2A 82.971 1104 106 33 769 1835 651505822 651504764 0.000000e+00 922.0
5 TraesCS2B01G415900 chr2A 82.726 1071 113 43 769 1784 651396669 651395616 0.000000e+00 887.0
6 TraesCS2B01G415900 chr2A 82.633 1071 114 44 769 1784 651445339 651444286 0.000000e+00 881.0
7 TraesCS2B01G415900 chr2D 88.649 1850 100 48 122 1898 506759885 506758073 0.000000e+00 2152.0
8 TraesCS2B01G415900 chr2D 89.061 905 71 18 869 1765 506652218 506651334 0.000000e+00 1098.0
9 TraesCS2B01G415900 chr2D 84.327 1040 92 35 793 1784 506525008 506523992 0.000000e+00 952.0
10 TraesCS2B01G415900 chr2D 93.380 287 13 5 2255 2538 645036330 645036047 1.130000e-113 420.0
11 TraesCS2B01G415900 chr2D 93.182 220 15 0 1988 2207 506757925 506757706 9.090000e-85 324.0
12 TraesCS2B01G415900 chr2D 93.548 62 3 1 1930 1990 506758017 506757956 1.000000e-14 91.6
13 TraesCS2B01G415900 chr2D 87.671 73 7 2 21 93 201958174 201958104 1.680000e-12 84.2
14 TraesCS2B01G415900 chr2D 90.164 61 3 3 34 93 360766118 360766060 2.810000e-10 76.8
15 TraesCS2B01G415900 chrUn 82.633 1071 114 43 769 1784 323408374 323409427 0.000000e+00 881.0
16 TraesCS2B01G415900 chr1D 94.925 335 11 5 2259 2590 460411303 460411634 1.080000e-143 520.0
17 TraesCS2B01G415900 chr1D 94.681 282 9 5 2260 2538 181273226 181272948 1.450000e-117 433.0
18 TraesCS2B01G415900 chr1D 93.640 283 11 6 2259 2538 395812197 395812475 1.460000e-112 416.0
19 TraesCS2B01G415900 chr1D 96.078 51 1 1 34 83 434342492 434342442 6.040000e-12 82.4
20 TraesCS2B01G415900 chr1D 80.412 97 7 5 4 88 177084556 177084460 2.190000e-06 63.9
21 TraesCS2B01G415900 chr3D 90.050 402 9 8 2262 2633 603306449 603306049 2.350000e-135 492.0
22 TraesCS2B01G415900 chr3B 94.425 287 11 4 2254 2538 734161777 734162060 1.120000e-118 436.0
23 TraesCS2B01G415900 chr3B 96.753 154 5 0 2480 2633 734162038 734162191 9.350000e-65 257.0
24 TraesCS2B01G415900 chr5B 94.662 281 10 4 2260 2538 17675733 17675456 5.210000e-117 431.0
25 TraesCS2B01G415900 chr5B 97.403 154 4 0 2480 2633 17675478 17675325 2.010000e-66 263.0
26 TraesCS2B01G415900 chr6D 94.286 280 10 5 2262 2538 159022481 159022757 8.710000e-115 424.0
27 TraesCS2B01G415900 chr6D 93.993 283 11 5 2259 2538 262761129 262760850 8.710000e-115 424.0
28 TraesCS2B01G415900 chr4D 93.640 283 12 5 2259 2538 67329380 67329659 4.050000e-113 418.0
29 TraesCS2B01G415900 chr4D 96.753 154 5 0 2480 2633 67329637 67329790 9.350000e-65 257.0
30 TraesCS2B01G415900 chr4D 90.164 61 3 3 34 93 108608223 108608281 2.810000e-10 76.8
31 TraesCS2B01G415900 chr6B 97.403 154 4 0 2480 2633 704147023 704146870 2.010000e-66 263.0
32 TraesCS2B01G415900 chr6A 97.403 154 4 0 2480 2633 560204665 560204512 2.010000e-66 263.0
33 TraesCS2B01G415900 chr6A 96.753 154 5 0 2480 2633 480306438 480306591 9.350000e-65 257.0
34 TraesCS2B01G415900 chr5A 97.403 154 4 0 2480 2633 640623975 640623822 2.010000e-66 263.0
35 TraesCS2B01G415900 chr5A 84.615 91 11 3 4 93 392740668 392740756 1.300000e-13 87.9
36 TraesCS2B01G415900 chr7D 86.667 90 10 2 4 93 419908376 419908463 6.000000e-17 99.0
37 TraesCS2B01G415900 chr7D 90.164 61 3 3 34 93 578327430 578327488 2.810000e-10 76.8
38 TraesCS2B01G415900 chr5D 90.164 61 3 3 34 93 317158514 317158572 2.810000e-10 76.8
39 TraesCS2B01G415900 chr3A 90.164 61 3 3 34 93 530205795 530205853 2.810000e-10 76.8
40 TraesCS2B01G415900 chr3A 89.130 46 5 0 4 49 559552401 559552446 1.020000e-04 58.4


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 TraesCS2B01G415900 chr2B 594682399 594685031 2632 True 4863.000000 4863 100.0000 1 2633 1 chr2B.!!$R3 2632
1 TraesCS2B01G415900 chr2B 594260777 594261859 1082 True 1050.000000 1050 84.7750 768 1835 1 chr2B.!!$R2 1067
2 TraesCS2B01G415900 chr2B 594204800 594205822 1022 True 915.000000 915 83.6700 793 1780 1 chr2B.!!$R1 987
3 TraesCS2B01G415900 chr2A 651504764 651511468 6704 True 1552.000000 2182 85.2795 103 1990 2 chr2A.!!$R3 1887
4 TraesCS2B01G415900 chr2A 651395616 651396669 1053 True 887.000000 887 82.7260 769 1784 1 chr2A.!!$R1 1015
5 TraesCS2B01G415900 chr2A 651444286 651445339 1053 True 881.000000 881 82.6330 769 1784 1 chr2A.!!$R2 1015
6 TraesCS2B01G415900 chr2D 506651334 506652218 884 True 1098.000000 1098 89.0610 869 1765 1 chr2D.!!$R4 896
7 TraesCS2B01G415900 chr2D 506523992 506525008 1016 True 952.000000 952 84.3270 793 1784 1 chr2D.!!$R3 991
8 TraesCS2B01G415900 chr2D 506757706 506759885 2179 True 855.866667 2152 91.7930 122 2207 3 chr2D.!!$R6 2085
9 TraesCS2B01G415900 chrUn 323408374 323409427 1053 False 881.000000 881 82.6330 769 1784 1 chrUn.!!$F1 1015

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
32 33 0.606401 AACTCAATGCCCGGTGTCAG 60.606 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2122 0.179089 ACAGGCAGCGCTATTCTCAG 60.179 55.0 10.99 0.0 0.0 3.35 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
23 24 5.246307 AGTCTAACCTGTTAACTCAATGCC 58.754 41.667 7.22 0.00 0.00 4.40
24 25 4.395231 GTCTAACCTGTTAACTCAATGCCC 59.605 45.833 7.22 0.00 0.00 5.36
25 26 1.821216 ACCTGTTAACTCAATGCCCG 58.179 50.000 7.22 0.00 0.00 6.13
26 27 1.094785 CCTGTTAACTCAATGCCCGG 58.905 55.000 7.22 0.00 0.00 5.73
27 28 1.613255 CCTGTTAACTCAATGCCCGGT 60.613 52.381 7.22 0.00 0.00 5.28
28 29 1.468520 CTGTTAACTCAATGCCCGGTG 59.531 52.381 7.22 0.00 0.00 4.94
29 30 1.202830 TGTTAACTCAATGCCCGGTGT 60.203 47.619 7.22 0.00 0.00 4.16
30 31 1.467342 GTTAACTCAATGCCCGGTGTC 59.533 52.381 0.00 0.00 0.00 3.67
31 32 0.687920 TAACTCAATGCCCGGTGTCA 59.312 50.000 0.00 0.00 0.00 3.58
32 33 0.606401 AACTCAATGCCCGGTGTCAG 60.606 55.000 0.00 0.00 0.00 3.51
33 34 1.003355 CTCAATGCCCGGTGTCAGT 60.003 57.895 0.00 0.00 0.00 3.41
34 35 0.606401 CTCAATGCCCGGTGTCAGTT 60.606 55.000 0.00 0.00 0.00 3.16
35 36 0.888736 TCAATGCCCGGTGTCAGTTG 60.889 55.000 0.00 3.28 0.00 3.16
36 37 2.268076 AATGCCCGGTGTCAGTTGC 61.268 57.895 0.00 0.00 0.00 4.17
37 38 2.697147 AATGCCCGGTGTCAGTTGCT 62.697 55.000 0.00 0.00 0.00 3.91
38 39 3.357079 GCCCGGTGTCAGTTGCTG 61.357 66.667 0.00 0.00 0.00 4.41
39 40 2.111043 CCCGGTGTCAGTTGCTGT 59.889 61.111 0.00 0.00 32.61 4.40
40 41 1.525995 CCCGGTGTCAGTTGCTGTT 60.526 57.895 0.00 0.00 32.61 3.16
41 42 1.101049 CCCGGTGTCAGTTGCTGTTT 61.101 55.000 0.00 0.00 32.61 2.83
42 43 0.738389 CCGGTGTCAGTTGCTGTTTT 59.262 50.000 0.00 0.00 32.61 2.43
43 44 1.134175 CCGGTGTCAGTTGCTGTTTTT 59.866 47.619 0.00 0.00 32.61 1.94
65 66 7.414814 TTTTGCTTTTCGGAAAATCAATACC 57.585 32.000 24.59 7.76 37.91 2.73
66 67 5.713792 TGCTTTTCGGAAAATCAATACCA 57.286 34.783 15.64 3.59 0.00 3.25
67 68 6.090483 TGCTTTTCGGAAAATCAATACCAA 57.910 33.333 15.64 0.00 0.00 3.67
68 69 6.516718 TGCTTTTCGGAAAATCAATACCAAA 58.483 32.000 15.64 0.00 0.00 3.28
69 70 6.422400 TGCTTTTCGGAAAATCAATACCAAAC 59.578 34.615 15.64 0.00 0.00 2.93
70 71 6.399564 GCTTTTCGGAAAATCAATACCAAACG 60.400 38.462 15.64 1.95 0.00 3.60
71 72 5.943706 TTCGGAAAATCAATACCAAACGA 57.056 34.783 0.00 0.00 0.00 3.85
72 73 5.943706 TCGGAAAATCAATACCAAACGAA 57.056 34.783 0.00 0.00 0.00 3.85
73 74 5.933790 TCGGAAAATCAATACCAAACGAAG 58.066 37.500 0.00 0.00 0.00 3.79
75 76 5.793457 CGGAAAATCAATACCAAACGAAGTC 59.207 40.000 0.00 0.00 45.00 3.01
76 77 6.090783 GGAAAATCAATACCAAACGAAGTCC 58.909 40.000 0.00 0.00 45.00 3.85
77 78 6.294286 GGAAAATCAATACCAAACGAAGTCCA 60.294 38.462 0.00 0.00 45.00 4.02
78 79 6.642707 AAATCAATACCAAACGAAGTCCAA 57.357 33.333 0.00 0.00 45.00 3.53
79 80 6.642707 AATCAATACCAAACGAAGTCCAAA 57.357 33.333 0.00 0.00 45.00 3.28
80 81 5.427036 TCAATACCAAACGAAGTCCAAAC 57.573 39.130 0.00 0.00 45.00 2.93
81 82 4.882427 TCAATACCAAACGAAGTCCAAACA 59.118 37.500 0.00 0.00 45.00 2.83
82 83 5.357314 TCAATACCAAACGAAGTCCAAACAA 59.643 36.000 0.00 0.00 45.00 2.83
83 84 3.497297 ACCAAACGAAGTCCAAACAAC 57.503 42.857 0.00 0.00 45.00 3.32
84 85 2.164827 ACCAAACGAAGTCCAAACAACC 59.835 45.455 0.00 0.00 45.00 3.77
85 86 2.446282 CAAACGAAGTCCAAACAACCG 58.554 47.619 0.00 0.00 45.00 4.44
86 87 2.027003 AACGAAGTCCAAACAACCGA 57.973 45.000 0.00 0.00 45.00 4.69
87 88 2.027003 ACGAAGTCCAAACAACCGAA 57.973 45.000 0.00 0.00 29.74 4.30
88 89 1.937899 ACGAAGTCCAAACAACCGAAG 59.062 47.619 0.00 0.00 29.74 3.79
89 90 2.206750 CGAAGTCCAAACAACCGAAGA 58.793 47.619 0.00 0.00 0.00 2.87
90 91 2.610374 CGAAGTCCAAACAACCGAAGAA 59.390 45.455 0.00 0.00 0.00 2.52
91 92 3.064271 CGAAGTCCAAACAACCGAAGAAA 59.936 43.478 0.00 0.00 0.00 2.52
92 93 4.348656 GAAGTCCAAACAACCGAAGAAAC 58.651 43.478 0.00 0.00 0.00 2.78
93 94 2.353579 AGTCCAAACAACCGAAGAAACG 59.646 45.455 0.00 0.00 0.00 3.60
94 95 2.096335 GTCCAAACAACCGAAGAAACGT 59.904 45.455 0.00 0.00 0.00 3.99
95 96 2.096174 TCCAAACAACCGAAGAAACGTG 59.904 45.455 0.00 0.00 0.00 4.49
96 97 2.159490 CCAAACAACCGAAGAAACGTGT 60.159 45.455 0.00 0.00 0.00 4.49
97 98 3.494232 CAAACAACCGAAGAAACGTGTT 58.506 40.909 0.00 0.00 35.27 3.32
98 99 2.817538 ACAACCGAAGAAACGTGTTG 57.182 45.000 10.16 10.16 43.11 3.33
99 100 2.078392 ACAACCGAAGAAACGTGTTGT 58.922 42.857 11.27 11.27 44.19 3.32
100 101 2.094734 ACAACCGAAGAAACGTGTTGTC 59.905 45.455 11.27 0.00 44.89 3.18
101 102 1.292992 ACCGAAGAAACGTGTTGTCC 58.707 50.000 0.00 0.00 0.00 4.02
102 103 1.134610 ACCGAAGAAACGTGTTGTCCT 60.135 47.619 0.00 0.00 0.00 3.85
103 104 1.937899 CCGAAGAAACGTGTTGTCCTT 59.062 47.619 0.00 0.00 0.00 3.36
104 105 2.353579 CCGAAGAAACGTGTTGTCCTTT 59.646 45.455 0.00 0.00 0.00 3.11
105 106 3.556775 CCGAAGAAACGTGTTGTCCTTTA 59.443 43.478 0.00 0.00 0.00 1.85
106 107 4.034279 CCGAAGAAACGTGTTGTCCTTTAA 59.966 41.667 0.00 0.00 0.00 1.52
107 108 5.277634 CCGAAGAAACGTGTTGTCCTTTAAT 60.278 40.000 0.00 0.00 0.00 1.40
108 109 6.073657 CCGAAGAAACGTGTTGTCCTTTAATA 60.074 38.462 0.00 0.00 0.00 0.98
109 110 7.360607 CCGAAGAAACGTGTTGTCCTTTAATAT 60.361 37.037 0.00 0.00 0.00 1.28
110 111 8.649841 CGAAGAAACGTGTTGTCCTTTAATATA 58.350 33.333 0.00 0.00 0.00 0.86
157 162 8.703604 AACATATCATGACGCAATATACTACC 57.296 34.615 0.00 0.00 0.00 3.18
198 203 6.333416 GCCCTCATAAGAAAGTTCCAAAATC 58.667 40.000 0.00 0.00 0.00 2.17
247 268 9.933723 AATTTGAGTTATTTTTGAATCAGGAGG 57.066 29.630 0.00 0.00 0.00 4.30
303 324 1.322538 ATCAAATTGGAGCCGGGCAC 61.323 55.000 23.09 15.59 0.00 5.01
318 339 2.477845 GGCACCAATTTGCTCCAATT 57.522 45.000 2.32 0.00 42.56 2.32
319 340 2.781923 GGCACCAATTTGCTCCAATTT 58.218 42.857 2.32 0.00 42.56 1.82
320 341 2.485038 GGCACCAATTTGCTCCAATTTG 59.515 45.455 2.32 5.89 42.56 2.32
352 379 9.702494 GTATGAGATCATCACTATCAAACATGA 57.298 33.333 0.00 0.00 41.91 3.07
397 424 4.415881 ACATTCCGCCATACATCTTGTA 57.584 40.909 0.00 0.00 37.24 2.41
455 489 5.230306 CAGTTCGAAAGCTATCCGTAAAGAG 59.770 44.000 0.00 0.00 0.00 2.85
523 557 1.308998 CGTATCCAGATTGGCAACCC 58.691 55.000 0.00 0.00 37.47 4.11
580 618 2.263540 CCCTACACCCGTTCCACG 59.736 66.667 0.00 0.00 42.11 4.94
597 635 2.926242 GGAACACCGGGGAGTGGA 60.926 66.667 12.96 0.00 42.28 4.02
599 637 0.979187 GGAACACCGGGGAGTGGATA 60.979 60.000 12.96 0.00 42.28 2.59
618 669 4.285790 AGCCCCCAACCCAGAGGA 62.286 66.667 0.00 0.00 36.73 3.71
668 719 1.321074 GGAGTTCACCGACCCTCGAT 61.321 60.000 0.00 0.00 43.74 3.59
694 745 6.299604 CAGCGTTTTTGTTGACAGATAGTAG 58.700 40.000 0.00 0.00 0.00 2.57
696 747 7.115805 CAGCGTTTTTGTTGACAGATAGTAGTA 59.884 37.037 0.00 0.00 0.00 1.82
697 748 7.654520 AGCGTTTTTGTTGACAGATAGTAGTAA 59.345 33.333 0.00 0.00 0.00 2.24
698 749 8.440833 GCGTTTTTGTTGACAGATAGTAGTAAT 58.559 33.333 0.00 0.00 0.00 1.89
756 809 3.637544 ACCCCCTCCCCACCATCT 61.638 66.667 0.00 0.00 0.00 2.90
760 813 1.616327 CCCTCCCCACCATCTGACA 60.616 63.158 0.00 0.00 0.00 3.58
764 817 2.124983 CCCACCATCTGACAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
910 968 2.177016 TCCTCTCGAATCCATCCACCTA 59.823 50.000 0.00 0.00 0.00 3.08
935 999 4.499183 GAGCTCCTTCTCGAAATCTCAAA 58.501 43.478 0.87 0.00 0.00 2.69
940 1009 3.061429 CCTTCTCGAAATCTCAAAGCGAC 59.939 47.826 0.00 0.00 0.00 5.19
955 1024 3.712881 GACCACACCGCGCAAGTC 61.713 66.667 8.75 0.19 41.68 3.01
1162 1270 6.183360 CGATTGAATGGTTTTGATTGCGATTT 60.183 34.615 0.00 0.00 0.00 2.17
1326 1437 0.106469 AGATGCTCTCCGTCCAGCTA 60.106 55.000 0.00 0.00 36.53 3.32
1645 1790 1.067000 CCGCCTGATCTGATCTGATCC 60.067 57.143 29.27 18.11 41.42 3.36
1647 1792 1.067000 GCCTGATCTGATCTGATCCGG 60.067 57.143 31.53 31.53 45.01 5.14
1675 1820 1.276421 GCTGGTCTTAGGAGTGCTTGA 59.724 52.381 0.00 0.00 0.00 3.02
1737 1882 3.547746 TGTTTAGGTTTCGGTTCTGCTT 58.452 40.909 0.00 0.00 0.00 3.91
1843 1988 2.507484 TCTGCAGTTTCCTTCACCATG 58.493 47.619 14.67 0.00 0.00 3.66
1851 1996 1.702182 TCCTTCACCATGCAAGCAAA 58.298 45.000 0.00 0.00 0.00 3.68
1864 2009 2.026915 GCAAGCAAATTCCCAATCCCTT 60.027 45.455 0.00 0.00 0.00 3.95
1865 2010 3.197549 GCAAGCAAATTCCCAATCCCTTA 59.802 43.478 0.00 0.00 0.00 2.69
1866 2011 4.758688 CAAGCAAATTCCCAATCCCTTAC 58.241 43.478 0.00 0.00 0.00 2.34
1868 2013 4.687976 AGCAAATTCCCAATCCCTTACTT 58.312 39.130 0.00 0.00 0.00 2.24
1870 2015 4.141937 GCAAATTCCCAATCCCTTACTTCC 60.142 45.833 0.00 0.00 0.00 3.46
1871 2016 3.577805 ATTCCCAATCCCTTACTTCCG 57.422 47.619 0.00 0.00 0.00 4.30
1872 2017 1.961133 TCCCAATCCCTTACTTCCGT 58.039 50.000 0.00 0.00 0.00 4.69
1873 2018 2.271777 TCCCAATCCCTTACTTCCGTT 58.728 47.619 0.00 0.00 0.00 4.44
1874 2019 2.645797 TCCCAATCCCTTACTTCCGTTT 59.354 45.455 0.00 0.00 0.00 3.60
1875 2020 3.845398 TCCCAATCCCTTACTTCCGTTTA 59.155 43.478 0.00 0.00 0.00 2.01
1876 2021 4.289148 TCCCAATCCCTTACTTCCGTTTAA 59.711 41.667 0.00 0.00 0.00 1.52
1882 2032 8.395633 CAATCCCTTACTTCCGTTTAATTACTG 58.604 37.037 0.00 0.00 0.00 2.74
1884 2034 7.099120 TCCCTTACTTCCGTTTAATTACTGTC 58.901 38.462 0.00 0.00 0.00 3.51
1887 2037 7.064253 CCTTACTTCCGTTTAATTACTGTCTGG 59.936 40.741 0.00 0.00 0.00 3.86
1904 2054 4.341806 TGTCTGGCTTGTGATCATTTGTTT 59.658 37.500 0.00 0.00 0.00 2.83
1906 2056 4.583907 TCTGGCTTGTGATCATTTGTTTCA 59.416 37.500 0.00 0.00 0.00 2.69
1907 2057 5.068855 TCTGGCTTGTGATCATTTGTTTCAA 59.931 36.000 0.00 0.00 0.00 2.69
1908 2058 5.856156 TGGCTTGTGATCATTTGTTTCAAT 58.144 33.333 0.00 0.00 0.00 2.57
1909 2059 5.927689 TGGCTTGTGATCATTTGTTTCAATC 59.072 36.000 0.00 0.00 0.00 2.67
1924 2092 7.303634 TGTTTCAATCTTATTAAGGTCGCTC 57.696 36.000 3.66 0.00 0.00 5.03
1936 2110 3.884350 TCGCTCGGGGATTCGTCG 61.884 66.667 0.00 0.00 0.00 5.12
1948 2122 3.002348 GGGATTCGTCGTCAATTTGATCC 59.998 47.826 1.78 3.66 0.00 3.36
2053 2262 7.637511 AGTTCTGTTCTTATCCCAATTCATCT 58.362 34.615 0.00 0.00 0.00 2.90
2072 2281 4.895668 TCTGGTAGGGTATCGTTGTTTT 57.104 40.909 0.00 0.00 0.00 2.43
2105 2314 4.210537 GCTTAGAAACTGAGCACACGTAAA 59.789 41.667 9.94 0.00 41.75 2.01
2232 2443 4.899239 CGAGTGCGCCCCTCCATC 62.899 72.222 15.95 0.00 0.00 3.51
2235 2446 4.554036 GTGCGCCCCTCCATCCTC 62.554 72.222 4.18 0.00 0.00 3.71
2237 2448 3.797353 GCGCCCCTCCATCCTCAA 61.797 66.667 0.00 0.00 0.00 3.02
2238 2449 2.998097 CGCCCCTCCATCCTCAAA 59.002 61.111 0.00 0.00 0.00 2.69
2240 2451 1.626356 CGCCCCTCCATCCTCAAAGA 61.626 60.000 0.00 0.00 0.00 2.52
2241 2452 0.182299 GCCCCTCCATCCTCAAAGAG 59.818 60.000 0.00 0.00 0.00 2.85
2255 4398 4.398319 CTCAAAGAGGAAGCCTTTTACCA 58.602 43.478 0.00 0.00 31.76 3.25
2256 4399 4.998051 TCAAAGAGGAAGCCTTTTACCAT 58.002 39.130 0.00 0.00 31.76 3.55
2257 4400 4.766891 TCAAAGAGGAAGCCTTTTACCATG 59.233 41.667 0.00 0.00 31.76 3.66
2258 4401 2.728007 AGAGGAAGCCTTTTACCATGC 58.272 47.619 0.00 0.00 31.76 4.06
2259 4402 2.310052 AGAGGAAGCCTTTTACCATGCT 59.690 45.455 0.00 0.00 31.76 3.79
2260 4403 3.092301 GAGGAAGCCTTTTACCATGCTT 58.908 45.455 0.00 0.00 46.07 3.91
2261 4404 4.018415 AGAGGAAGCCTTTTACCATGCTTA 60.018 41.667 0.00 0.00 43.63 3.09
2262 4405 4.273318 AGGAAGCCTTTTACCATGCTTAG 58.727 43.478 0.00 0.00 43.63 2.18
2264 4407 4.705023 GGAAGCCTTTTACCATGCTTAGAA 59.295 41.667 0.00 0.00 43.63 2.10
2265 4408 5.393135 GGAAGCCTTTTACCATGCTTAGAAC 60.393 44.000 0.00 0.00 43.63 3.01
2266 4409 4.662278 AGCCTTTTACCATGCTTAGAACA 58.338 39.130 0.00 0.00 0.00 3.18
2267 4410 5.264395 AGCCTTTTACCATGCTTAGAACAT 58.736 37.500 0.00 0.00 0.00 2.71
2268 4411 5.358160 AGCCTTTTACCATGCTTAGAACATC 59.642 40.000 0.00 0.00 0.00 3.06
2269 4412 5.358160 GCCTTTTACCATGCTTAGAACATCT 59.642 40.000 0.00 0.00 0.00 2.90
2272 4415 8.616076 CCTTTTACCATGCTTAGAACATCTTAG 58.384 37.037 0.00 0.00 0.00 2.18
2274 4417 8.492673 TTTACCATGCTTAGAACATCTTAGTG 57.507 34.615 0.00 0.00 0.00 2.74
2275 4418 5.431765 ACCATGCTTAGAACATCTTAGTGG 58.568 41.667 0.00 0.00 30.36 4.00
2276 4419 5.189736 ACCATGCTTAGAACATCTTAGTGGA 59.810 40.000 8.93 0.00 29.38 4.02
2277 4420 6.126652 ACCATGCTTAGAACATCTTAGTGGAT 60.127 38.462 8.93 0.00 29.38 3.41
2278 4421 6.204301 CCATGCTTAGAACATCTTAGTGGATG 59.796 42.308 0.00 0.00 45.96 3.51
2280 4423 5.189736 TGCTTAGAACATCTTAGTGGATGGT 59.810 40.000 8.91 2.39 45.13 3.55
2282 4425 6.620877 TTAGAACATCTTAGTGGATGGTGT 57.379 37.500 8.91 3.90 42.86 4.16
2283 4426 7.632898 GCTTAGAACATCTTAGTGGATGGTGTA 60.633 40.741 8.91 3.03 42.86 2.90
2284 4427 6.814954 AGAACATCTTAGTGGATGGTGTAT 57.185 37.500 8.91 0.00 42.86 2.29
2285 4428 7.914427 AGAACATCTTAGTGGATGGTGTATA 57.086 36.000 8.91 0.00 42.86 1.47
2286 4429 8.497910 AGAACATCTTAGTGGATGGTGTATAT 57.502 34.615 8.91 0.00 42.86 0.86
2287 4430 8.370940 AGAACATCTTAGTGGATGGTGTATATG 58.629 37.037 8.91 0.00 42.86 1.78
2288 4431 7.009179 ACATCTTAGTGGATGGTGTATATGG 57.991 40.000 8.91 0.00 45.11 2.74
2289 4432 6.787458 ACATCTTAGTGGATGGTGTATATGGA 59.213 38.462 8.91 0.00 45.11 3.41
2290 4433 6.918067 TCTTAGTGGATGGTGTATATGGAG 57.082 41.667 0.00 0.00 0.00 3.86
2292 4435 3.941629 AGTGGATGGTGTATATGGAGGT 58.058 45.455 0.00 0.00 0.00 3.85
2293 4436 3.648067 AGTGGATGGTGTATATGGAGGTG 59.352 47.826 0.00 0.00 0.00 4.00
2295 4438 3.248024 GGATGGTGTATATGGAGGTGGA 58.752 50.000 0.00 0.00 0.00 4.02
2296 4439 3.846588 GGATGGTGTATATGGAGGTGGAT 59.153 47.826 0.00 0.00 0.00 3.41
2297 4440 4.323792 GGATGGTGTATATGGAGGTGGATG 60.324 50.000 0.00 0.00 0.00 3.51
2298 4441 2.371841 TGGTGTATATGGAGGTGGATGC 59.628 50.000 0.00 0.00 0.00 3.91
2299 4442 2.639839 GGTGTATATGGAGGTGGATGCT 59.360 50.000 0.00 0.00 0.00 3.79
2300 4443 3.838317 GGTGTATATGGAGGTGGATGCTA 59.162 47.826 0.00 0.00 0.00 3.49
2301 4444 4.286032 GGTGTATATGGAGGTGGATGCTAA 59.714 45.833 0.00 0.00 0.00 3.09
2302 4445 5.221843 GGTGTATATGGAGGTGGATGCTAAA 60.222 44.000 0.00 0.00 0.00 1.85
2303 4446 6.476378 GTGTATATGGAGGTGGATGCTAAAT 58.524 40.000 0.00 0.00 0.00 1.40
2305 4448 8.267894 GTGTATATGGAGGTGGATGCTAAATAT 58.732 37.037 0.00 0.00 0.00 1.28
2307 4450 9.765795 GTATATGGAGGTGGATGCTAAATATAC 57.234 37.037 0.00 0.00 0.00 1.47
2308 4451 6.702449 ATGGAGGTGGATGCTAAATATACA 57.298 37.500 0.00 0.00 0.00 2.29
2310 4453 4.929808 GGAGGTGGATGCTAAATATACACG 59.070 45.833 0.00 0.00 39.73 4.49
2311 4454 5.279306 GGAGGTGGATGCTAAATATACACGA 60.279 44.000 0.00 0.00 39.73 4.35
2312 4455 6.360370 AGGTGGATGCTAAATATACACGAT 57.640 37.500 0.00 0.00 39.73 3.73
2313 4456 6.398918 AGGTGGATGCTAAATATACACGATC 58.601 40.000 0.00 0.00 39.73 3.69
2314 4457 6.014584 AGGTGGATGCTAAATATACACGATCA 60.015 38.462 0.00 0.00 39.73 2.92
2315 4458 6.649141 GGTGGATGCTAAATATACACGATCAA 59.351 38.462 0.00 0.00 39.73 2.57
2316 4459 7.172532 GGTGGATGCTAAATATACACGATCAAA 59.827 37.037 0.00 0.00 39.73 2.69
2318 4461 9.283768 TGGATGCTAAATATACACGATCAAAAT 57.716 29.630 0.00 0.00 0.00 1.82
2343 5194 5.529581 AAAAATGTTTTCCAGTGGATCGT 57.470 34.783 14.00 5.62 0.00 3.73
2345 5196 2.631160 TGTTTTCCAGTGGATCGTGT 57.369 45.000 14.00 0.00 0.00 4.49
2346 5197 3.755112 TGTTTTCCAGTGGATCGTGTA 57.245 42.857 14.00 0.00 0.00 2.90
2348 5199 4.250464 TGTTTTCCAGTGGATCGTGTATC 58.750 43.478 14.00 0.00 0.00 2.24
2350 5201 3.801114 TTCCAGTGGATCGTGTATCAG 57.199 47.619 14.00 0.00 36.20 2.90
2351 5202 2.031870 TCCAGTGGATCGTGTATCAGG 58.968 52.381 8.12 0.00 36.20 3.86
2353 5204 2.223829 CCAGTGGATCGTGTATCAGGTC 60.224 54.545 1.68 0.00 36.20 3.85
2358 5209 2.615447 GGATCGTGTATCAGGTCGTGTA 59.385 50.000 0.00 0.00 36.20 2.90
2375 5226 1.942657 TGTACCTATACACGTCGCTCC 59.057 52.381 0.00 0.00 36.34 4.70
2376 5227 1.265365 GTACCTATACACGTCGCTCCC 59.735 57.143 0.00 0.00 0.00 4.30
2377 5228 0.394762 ACCTATACACGTCGCTCCCA 60.395 55.000 0.00 0.00 0.00 4.37
2378 5229 0.030369 CCTATACACGTCGCTCCCAC 59.970 60.000 0.00 0.00 0.00 4.61
2379 5230 0.316772 CTATACACGTCGCTCCCACG 60.317 60.000 0.00 0.00 43.13 4.94
2381 5232 1.989966 ATACACGTCGCTCCCACGAG 61.990 60.000 0.23 0.00 43.89 4.18
2390 5241 3.064987 CTCCCACGAGCGTACCTGG 62.065 68.421 0.00 0.00 0.00 4.45
2394 5245 4.415332 ACGAGCGTACCTGGCGTG 62.415 66.667 0.00 0.00 33.52 5.34
2399 5250 3.379445 CGTACCTGGCGTGGGACT 61.379 66.667 9.54 0.00 38.78 3.85
2400 5251 2.048023 CGTACCTGGCGTGGGACTA 61.048 63.158 9.54 0.00 38.78 2.59
2401 5252 1.597797 CGTACCTGGCGTGGGACTAA 61.598 60.000 9.54 0.00 38.78 2.24
2402 5253 0.609662 GTACCTGGCGTGGGACTAAA 59.390 55.000 4.66 0.00 37.93 1.85
2403 5254 0.609662 TACCTGGCGTGGGACTAAAC 59.390 55.000 0.00 0.00 0.00 2.01
2404 5255 1.373435 CCTGGCGTGGGACTAAACA 59.627 57.895 0.00 0.00 0.00 2.83
2405 5256 0.953960 CCTGGCGTGGGACTAAACAC 60.954 60.000 0.00 0.00 0.00 3.32
2410 5261 2.818350 GTGGGACTAAACACGACCG 58.182 57.895 0.00 0.00 0.00 4.79
2411 5262 0.314935 GTGGGACTAAACACGACCGA 59.685 55.000 0.00 0.00 0.00 4.69
2412 5263 1.039068 TGGGACTAAACACGACCGAA 58.961 50.000 0.00 0.00 0.00 4.30
2413 5264 1.269726 TGGGACTAAACACGACCGAAC 60.270 52.381 0.00 0.00 0.00 3.95
2415 5266 1.269726 GGACTAAACACGACCGAACCA 60.270 52.381 0.00 0.00 0.00 3.67
2416 5267 1.788886 GACTAAACACGACCGAACCAC 59.211 52.381 0.00 0.00 0.00 4.16
2417 5268 0.780002 CTAAACACGACCGAACCACG 59.220 55.000 0.00 0.00 42.18 4.94
2418 5269 1.214373 TAAACACGACCGAACCACGC 61.214 55.000 0.00 0.00 41.07 5.34
2420 5271 3.103911 CACGACCGAACCACGCTC 61.104 66.667 0.00 0.00 41.07 5.03
2422 5273 4.695231 CGACCGAACCACGCTCGT 62.695 66.667 0.00 0.00 42.63 4.18
2424 5275 2.654912 GACCGAACCACGCTCGTTG 61.655 63.158 0.00 0.00 41.07 4.10
2425 5276 4.072088 CCGAACCACGCTCGTTGC 62.072 66.667 0.00 0.00 41.07 4.17
2427 5278 2.853914 GAACCACGCTCGTTGCTC 59.146 61.111 0.00 0.00 40.11 4.26
2428 5279 3.000080 GAACCACGCTCGTTGCTCG 62.000 63.158 0.00 0.00 40.11 5.03
2434 5285 3.403057 GCTCGTTGCTCGCGAACA 61.403 61.111 11.33 9.78 37.93 3.18
2435 5286 2.765785 CTCGTTGCTCGCGAACAG 59.234 61.111 11.33 0.77 37.93 3.16
2436 5287 1.729484 CTCGTTGCTCGCGAACAGA 60.729 57.895 11.33 5.75 37.93 3.41
2437 5288 1.275471 CTCGTTGCTCGCGAACAGAA 61.275 55.000 11.33 0.00 37.93 3.02
2438 5289 1.128611 CGTTGCTCGCGAACAGAAG 59.871 57.895 11.33 3.43 0.00 2.85
2439 5290 1.493311 GTTGCTCGCGAACAGAAGG 59.507 57.895 11.33 0.00 0.00 3.46
2441 5292 2.094757 TTGCTCGCGAACAGAAGGGA 62.095 55.000 11.33 0.00 0.00 4.20
2444 5295 1.508632 CTCGCGAACAGAAGGGAAAA 58.491 50.000 11.33 0.00 0.00 2.29
2445 5296 1.461127 CTCGCGAACAGAAGGGAAAAG 59.539 52.381 11.33 0.00 0.00 2.27
2446 5297 1.069513 TCGCGAACAGAAGGGAAAAGA 59.930 47.619 6.20 0.00 0.00 2.52
2447 5298 1.871039 CGCGAACAGAAGGGAAAAGAA 59.129 47.619 0.00 0.00 0.00 2.52
2448 5299 2.096218 CGCGAACAGAAGGGAAAAGAAG 60.096 50.000 0.00 0.00 0.00 2.85
2449 5300 3.139077 GCGAACAGAAGGGAAAAGAAGA 58.861 45.455 0.00 0.00 0.00 2.87
2450 5301 3.187432 GCGAACAGAAGGGAAAAGAAGAG 59.813 47.826 0.00 0.00 0.00 2.85
2451 5302 4.632153 CGAACAGAAGGGAAAAGAAGAGA 58.368 43.478 0.00 0.00 0.00 3.10
2452 5303 5.057149 CGAACAGAAGGGAAAAGAAGAGAA 58.943 41.667 0.00 0.00 0.00 2.87
2453 5304 5.527582 CGAACAGAAGGGAAAAGAAGAGAAA 59.472 40.000 0.00 0.00 0.00 2.52
2454 5305 6.038271 CGAACAGAAGGGAAAAGAAGAGAAAA 59.962 38.462 0.00 0.00 0.00 2.29
2482 5333 3.391382 CTCCCGCTCCCGTTCCTT 61.391 66.667 0.00 0.00 0.00 3.36
2483 5334 2.926242 TCCCGCTCCCGTTCCTTT 60.926 61.111 0.00 0.00 0.00 3.11
2484 5335 2.436115 CCCGCTCCCGTTCCTTTC 60.436 66.667 0.00 0.00 0.00 2.62
2486 5337 2.813908 CGCTCCCGTTCCTTTCCG 60.814 66.667 0.00 0.00 0.00 4.30
2487 5338 2.436115 GCTCCCGTTCCTTTCCGG 60.436 66.667 0.00 0.00 43.82 5.14
2488 5339 2.436115 CTCCCGTTCCTTTCCGGC 60.436 66.667 0.00 0.00 42.87 6.13
2489 5340 3.971109 CTCCCGTTCCTTTCCGGCC 62.971 68.421 0.00 0.00 42.87 6.13
2540 6716 2.675075 GCCGCTGCCCAAGGTAAA 60.675 61.111 0.00 0.00 0.00 2.01
2541 6717 2.989881 GCCGCTGCCCAAGGTAAAC 61.990 63.158 0.00 0.00 0.00 2.01
2543 6719 0.965363 CCGCTGCCCAAGGTAAACAT 60.965 55.000 0.00 0.00 0.00 2.71
2544 6720 0.887933 CGCTGCCCAAGGTAAACATT 59.112 50.000 0.00 0.00 0.00 2.71
2546 6722 2.288763 CGCTGCCCAAGGTAAACATTTT 60.289 45.455 0.00 0.00 0.00 1.82
2547 6723 3.738982 GCTGCCCAAGGTAAACATTTTT 58.261 40.909 0.00 0.00 0.00 1.94
2563 6739 0.511221 TTTTTCCTTTCTCGCGAGCG 59.489 50.000 30.97 19.84 41.35 5.03
2564 6740 1.289109 TTTTCCTTTCTCGCGAGCGG 61.289 55.000 30.97 26.86 40.25 5.52
2565 6741 3.642778 TTCCTTTCTCGCGAGCGGG 62.643 63.158 30.97 27.43 42.03 6.13
2603 6779 3.537874 ACGCCCTACAGCCCGATC 61.538 66.667 0.00 0.00 0.00 3.69
2606 6782 3.142393 CCCTACAGCCCGATCTGG 58.858 66.667 0.00 0.00 38.36 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.246307 GGCATTGAGTTAACAGGTTAGACT 58.754 41.667 8.61 6.69 0.00 3.24
1 2 4.395231 GGGCATTGAGTTAACAGGTTAGAC 59.605 45.833 8.61 0.00 0.00 2.59
3 4 3.374058 CGGGCATTGAGTTAACAGGTTAG 59.626 47.826 8.61 0.00 0.00 2.34
4 5 3.340034 CGGGCATTGAGTTAACAGGTTA 58.660 45.455 8.61 0.00 0.00 2.85
5 6 2.159382 CGGGCATTGAGTTAACAGGTT 58.841 47.619 8.61 0.00 0.00 3.50
7 8 1.094785 CCGGGCATTGAGTTAACAGG 58.905 55.000 8.61 0.00 0.00 4.00
9 10 1.202830 ACACCGGGCATTGAGTTAACA 60.203 47.619 6.32 0.00 0.00 2.41
11 12 1.072489 TGACACCGGGCATTGAGTTAA 59.928 47.619 6.32 0.00 0.00 2.01
12 13 0.687920 TGACACCGGGCATTGAGTTA 59.312 50.000 6.32 0.00 0.00 2.24
13 14 0.606401 CTGACACCGGGCATTGAGTT 60.606 55.000 6.32 0.00 0.00 3.01
14 15 1.003355 CTGACACCGGGCATTGAGT 60.003 57.895 6.32 0.00 0.00 3.41
15 16 0.606401 AACTGACACCGGGCATTGAG 60.606 55.000 6.32 0.00 0.00 3.02
16 17 0.888736 CAACTGACACCGGGCATTGA 60.889 55.000 6.32 0.00 0.00 2.57
17 18 1.580942 CAACTGACACCGGGCATTG 59.419 57.895 6.32 0.00 0.00 2.82
18 19 2.268076 GCAACTGACACCGGGCATT 61.268 57.895 6.32 0.00 0.00 3.56
19 20 2.672996 GCAACTGACACCGGGCAT 60.673 61.111 6.32 0.00 0.00 4.40
20 21 3.872603 AGCAACTGACACCGGGCA 61.873 61.111 6.32 0.00 0.00 5.36
21 22 3.357079 CAGCAACTGACACCGGGC 61.357 66.667 6.32 0.00 32.44 6.13
22 23 1.101049 AAACAGCAACTGACACCGGG 61.101 55.000 6.32 0.00 35.18 5.73
23 24 0.738389 AAAACAGCAACTGACACCGG 59.262 50.000 0.00 0.00 35.18 5.28
24 25 2.559998 AAAAACAGCAACTGACACCG 57.440 45.000 0.78 0.00 35.18 4.94
44 45 5.713792 TGGTATTGATTTTCCGAAAAGCA 57.286 34.783 18.25 18.25 44.14 3.91
45 46 6.399564 CGTTTGGTATTGATTTTCCGAAAAGC 60.400 38.462 13.72 13.72 37.30 3.51
46 47 6.858993 TCGTTTGGTATTGATTTTCCGAAAAG 59.141 34.615 11.76 0.00 33.22 2.27
47 48 6.736123 TCGTTTGGTATTGATTTTCCGAAAA 58.264 32.000 8.71 8.71 34.41 2.29
48 49 6.315091 TCGTTTGGTATTGATTTTCCGAAA 57.685 33.333 0.00 0.00 0.00 3.46
49 50 5.943706 TCGTTTGGTATTGATTTTCCGAA 57.056 34.783 0.00 0.00 0.00 4.30
50 51 5.470777 ACTTCGTTTGGTATTGATTTTCCGA 59.529 36.000 0.00 0.00 0.00 4.55
51 52 5.695818 ACTTCGTTTGGTATTGATTTTCCG 58.304 37.500 0.00 0.00 0.00 4.30
52 53 6.090783 GGACTTCGTTTGGTATTGATTTTCC 58.909 40.000 0.00 0.00 0.00 3.13
53 54 6.674066 TGGACTTCGTTTGGTATTGATTTTC 58.326 36.000 0.00 0.00 0.00 2.29
54 55 6.642707 TGGACTTCGTTTGGTATTGATTTT 57.357 33.333 0.00 0.00 0.00 1.82
55 56 6.642707 TTGGACTTCGTTTGGTATTGATTT 57.357 33.333 0.00 0.00 0.00 2.17
56 57 6.039941 TGTTTGGACTTCGTTTGGTATTGATT 59.960 34.615 0.00 0.00 0.00 2.57
57 58 5.533154 TGTTTGGACTTCGTTTGGTATTGAT 59.467 36.000 0.00 0.00 0.00 2.57
58 59 4.882427 TGTTTGGACTTCGTTTGGTATTGA 59.118 37.500 0.00 0.00 0.00 2.57
59 60 5.176407 TGTTTGGACTTCGTTTGGTATTG 57.824 39.130 0.00 0.00 0.00 1.90
60 61 5.450826 GGTTGTTTGGACTTCGTTTGGTATT 60.451 40.000 0.00 0.00 0.00 1.89
61 62 4.037089 GGTTGTTTGGACTTCGTTTGGTAT 59.963 41.667 0.00 0.00 0.00 2.73
62 63 3.377798 GGTTGTTTGGACTTCGTTTGGTA 59.622 43.478 0.00 0.00 0.00 3.25
63 64 2.164827 GGTTGTTTGGACTTCGTTTGGT 59.835 45.455 0.00 0.00 0.00 3.67
64 65 2.793237 CGGTTGTTTGGACTTCGTTTGG 60.793 50.000 0.00 0.00 0.00 3.28
65 66 2.096174 TCGGTTGTTTGGACTTCGTTTG 59.904 45.455 0.00 0.00 0.00 2.93
66 67 2.358015 TCGGTTGTTTGGACTTCGTTT 58.642 42.857 0.00 0.00 0.00 3.60
67 68 2.027003 TCGGTTGTTTGGACTTCGTT 57.973 45.000 0.00 0.00 0.00 3.85
68 69 1.937899 CTTCGGTTGTTTGGACTTCGT 59.062 47.619 0.00 0.00 0.00 3.85
69 70 2.206750 TCTTCGGTTGTTTGGACTTCG 58.793 47.619 0.00 0.00 0.00 3.79
70 71 4.348656 GTTTCTTCGGTTGTTTGGACTTC 58.651 43.478 0.00 0.00 0.00 3.01
71 72 3.181504 CGTTTCTTCGGTTGTTTGGACTT 60.182 43.478 0.00 0.00 0.00 3.01
72 73 2.353579 CGTTTCTTCGGTTGTTTGGACT 59.646 45.455 0.00 0.00 0.00 3.85
73 74 2.096335 ACGTTTCTTCGGTTGTTTGGAC 59.904 45.455 0.00 0.00 34.94 4.02
74 75 2.096174 CACGTTTCTTCGGTTGTTTGGA 59.904 45.455 0.00 0.00 34.94 3.53
75 76 2.159490 ACACGTTTCTTCGGTTGTTTGG 60.159 45.455 0.00 0.00 34.94 3.28
76 77 3.125698 ACACGTTTCTTCGGTTGTTTG 57.874 42.857 0.00 0.00 34.94 2.93
77 78 3.058085 ACAACACGTTTCTTCGGTTGTTT 60.058 39.130 11.27 0.00 44.20 2.83
78 79 2.485038 ACAACACGTTTCTTCGGTTGTT 59.515 40.909 11.27 5.33 44.20 2.83
79 80 2.078392 ACAACACGTTTCTTCGGTTGT 58.922 42.857 11.27 11.27 43.15 3.32
80 81 2.538132 GGACAACACGTTTCTTCGGTTG 60.538 50.000 10.16 10.16 42.07 3.77
81 82 1.667212 GGACAACACGTTTCTTCGGTT 59.333 47.619 0.00 0.00 34.94 4.44
82 83 1.134610 AGGACAACACGTTTCTTCGGT 60.135 47.619 0.00 0.00 34.94 4.69
83 84 1.578583 AGGACAACACGTTTCTTCGG 58.421 50.000 0.00 0.00 34.94 4.30
84 85 3.668596 AAAGGACAACACGTTTCTTCG 57.331 42.857 0.00 0.00 0.00 3.79
87 88 9.444600 ACATATATTAAAGGACAACACGTTTCT 57.555 29.630 0.00 0.00 0.00 2.52
133 134 7.836842 TGGTAGTATATTGCGTCATGATATGT 58.163 34.615 0.00 0.00 0.00 2.29
157 162 4.161565 TGAGGGCCTTGTATTGTACTACTG 59.838 45.833 7.89 0.00 0.00 2.74
221 230 9.933723 CCTCCTGATTCAAAAATAACTCAAATT 57.066 29.630 0.00 0.00 0.00 1.82
222 231 8.037166 GCCTCCTGATTCAAAAATAACTCAAAT 58.963 33.333 0.00 0.00 0.00 2.32
223 232 7.378181 GCCTCCTGATTCAAAAATAACTCAAA 58.622 34.615 0.00 0.00 0.00 2.69
247 268 1.943340 GCACCAAGCTCATAGTTAGGC 59.057 52.381 0.00 0.00 41.15 3.93
303 324 4.327898 CGACATCAAATTGGAGCAAATTGG 59.672 41.667 0.00 0.00 35.64 3.16
311 332 6.703165 TGATCTCATACGACATCAAATTGGAG 59.297 38.462 0.00 0.00 0.00 3.86
312 333 6.581712 TGATCTCATACGACATCAAATTGGA 58.418 36.000 0.00 0.00 0.00 3.53
313 334 6.849588 TGATCTCATACGACATCAAATTGG 57.150 37.500 0.00 0.00 0.00 3.16
314 335 8.008279 GTGATGATCTCATACGACATCAAATTG 58.992 37.037 0.00 0.00 45.22 2.32
315 336 7.930325 AGTGATGATCTCATACGACATCAAATT 59.070 33.333 0.00 0.00 45.22 1.82
316 337 7.440198 AGTGATGATCTCATACGACATCAAAT 58.560 34.615 0.00 0.00 45.22 2.32
317 338 6.809869 AGTGATGATCTCATACGACATCAAA 58.190 36.000 0.00 0.00 45.22 2.69
318 339 6.396829 AGTGATGATCTCATACGACATCAA 57.603 37.500 0.00 0.00 45.22 2.57
319 340 7.391554 TGATAGTGATGATCTCATACGACATCA 59.608 37.037 0.00 0.00 42.85 3.07
320 341 7.756558 TGATAGTGATGATCTCATACGACATC 58.243 38.462 0.00 0.00 36.57 3.06
352 379 7.704472 TGTTGCAAGTTTTGATCGACTTTAAAT 59.296 29.630 0.00 0.00 34.04 1.40
365 392 1.526464 GGCGGAATGTTGCAAGTTTTG 59.474 47.619 0.00 0.00 0.00 2.44
404 431 1.299541 CTGTGCACAGTTCCGAGTTT 58.700 50.000 34.04 0.00 39.09 2.66
405 432 1.160329 GCTGTGCACAGTTCCGAGTT 61.160 55.000 39.30 0.00 45.45 3.01
406 433 1.595382 GCTGTGCACAGTTCCGAGT 60.595 57.895 39.30 0.00 45.45 4.18
407 434 1.159713 TTGCTGTGCACAGTTCCGAG 61.160 55.000 39.30 19.97 45.45 4.63
433 463 5.338365 TCTCTTTACGGATAGCTTTCGAAC 58.662 41.667 0.00 0.00 0.00 3.95
474 508 1.855360 GTGCTATTCGAGAGCTTTCGG 59.145 52.381 24.53 10.94 40.76 4.30
580 618 0.979187 TATCCACTCCCCGGTGTTCC 60.979 60.000 0.00 0.00 35.63 3.62
597 635 1.230149 TCTGGGTTGGGGGCTGTAT 60.230 57.895 0.00 0.00 0.00 2.29
599 637 3.260100 CTCTGGGTTGGGGGCTGT 61.260 66.667 0.00 0.00 0.00 4.40
604 642 2.276740 GCATCCTCTGGGTTGGGG 59.723 66.667 0.00 0.00 33.97 4.96
668 719 2.360844 TCTGTCAACAAAAACGCTGGA 58.639 42.857 0.00 0.00 0.00 3.86
865 920 4.322499 CCGGGTCGAGGCTTATTTATACAT 60.322 45.833 0.00 0.00 0.00 2.29
955 1024 2.032054 TGAAACTGAAACTGAAGCTGCG 59.968 45.455 0.00 0.00 0.00 5.18
1162 1270 4.531339 TCCAATTCAAAATCCAATCAGCCA 59.469 37.500 0.00 0.00 0.00 4.75
1432 1570 4.697756 CTTGGCGGCGTCCTTGGA 62.698 66.667 9.84 0.00 0.00 3.53
1645 1790 1.267261 CTAAGACCAGCTATCGGACCG 59.733 57.143 7.84 7.84 0.00 4.79
1647 1792 2.554893 CTCCTAAGACCAGCTATCGGAC 59.445 54.545 0.00 0.00 0.00 4.79
1675 1820 4.447138 TTTGTACAGACCCTTGGAACAT 57.553 40.909 0.00 0.00 39.30 2.71
1737 1882 3.275143 CCCACGATACATAAACTTGCCA 58.725 45.455 0.00 0.00 0.00 4.92
1800 1945 9.053840 CAGATTCATTTCACATAGTTAGAGCAT 57.946 33.333 0.00 0.00 0.00 3.79
1801 1946 7.011763 GCAGATTCATTTCACATAGTTAGAGCA 59.988 37.037 0.00 0.00 0.00 4.26
1811 1956 5.479375 AGGAAACTGCAGATTCATTTCACAT 59.521 36.000 30.48 13.08 41.13 3.21
1843 1988 1.556451 AGGGATTGGGAATTTGCTTGC 59.444 47.619 0.00 0.00 0.00 4.01
1851 1996 2.850568 ACGGAAGTAAGGGATTGGGAAT 59.149 45.455 0.00 0.00 46.88 3.01
1866 2011 4.935808 AGCCAGACAGTAATTAAACGGAAG 59.064 41.667 0.00 0.00 0.00 3.46
1868 2013 4.546829 AGCCAGACAGTAATTAAACGGA 57.453 40.909 0.00 0.00 0.00 4.69
1870 2015 5.178623 TCACAAGCCAGACAGTAATTAAACG 59.821 40.000 0.00 0.00 0.00 3.60
1871 2016 6.554334 TCACAAGCCAGACAGTAATTAAAC 57.446 37.500 0.00 0.00 0.00 2.01
1872 2017 6.939730 TGATCACAAGCCAGACAGTAATTAAA 59.060 34.615 0.00 0.00 0.00 1.52
1873 2018 6.472016 TGATCACAAGCCAGACAGTAATTAA 58.528 36.000 0.00 0.00 0.00 1.40
1874 2019 6.048732 TGATCACAAGCCAGACAGTAATTA 57.951 37.500 0.00 0.00 0.00 1.40
1875 2020 4.910195 TGATCACAAGCCAGACAGTAATT 58.090 39.130 0.00 0.00 0.00 1.40
1876 2021 4.558226 TGATCACAAGCCAGACAGTAAT 57.442 40.909 0.00 0.00 0.00 1.89
1882 2032 4.510038 AACAAATGATCACAAGCCAGAC 57.490 40.909 0.00 0.00 0.00 3.51
1884 2034 4.873817 TGAAACAAATGATCACAAGCCAG 58.126 39.130 0.00 0.00 0.00 4.85
1887 2037 7.647907 AAGATTGAAACAAATGATCACAAGC 57.352 32.000 0.00 0.00 0.00 4.01
1904 2054 4.500887 CCCGAGCGACCTTAATAAGATTGA 60.501 45.833 0.83 0.00 0.00 2.57
1906 2056 3.244112 CCCCGAGCGACCTTAATAAGATT 60.244 47.826 0.83 0.00 0.00 2.40
1907 2057 2.299297 CCCCGAGCGACCTTAATAAGAT 59.701 50.000 0.83 0.00 0.00 2.40
1908 2058 1.684983 CCCCGAGCGACCTTAATAAGA 59.315 52.381 0.83 0.00 0.00 2.10
1909 2059 1.684983 TCCCCGAGCGACCTTAATAAG 59.315 52.381 0.00 0.00 0.00 1.73
1924 2092 1.062002 CAAATTGACGACGAATCCCCG 59.938 52.381 0.00 0.00 0.00 5.73
1936 2110 5.559799 GCGCTATTCTCAGGATCAAATTGAC 60.560 44.000 0.00 0.00 0.00 3.18
1948 2122 0.179089 ACAGGCAGCGCTATTCTCAG 60.179 55.000 10.99 0.00 0.00 3.35
2003 2211 0.467384 AGGGATGGCGAACAGAGATG 59.533 55.000 0.00 0.00 0.00 2.90
2072 2281 5.221048 GCTCAGTTTCTAAGCCAAGTGAAAA 60.221 40.000 0.00 0.00 33.03 2.29
2082 2291 2.135933 ACGTGTGCTCAGTTTCTAAGC 58.864 47.619 0.00 0.00 36.56 3.09
2105 2314 4.142004 GGATAATAACAGTGTGTCTCCCGT 60.142 45.833 0.00 0.00 0.00 5.28
2113 2322 4.402056 ACCGAGGGATAATAACAGTGTG 57.598 45.455 0.00 0.00 0.00 3.82
2141 2350 4.018649 TCGATACGACGCACAGAAAATA 57.981 40.909 0.00 0.00 0.00 1.40
2142 2351 2.852413 CTCGATACGACGCACAGAAAAT 59.148 45.455 0.00 0.00 0.00 1.82
2148 2357 2.767445 CCCCTCGATACGACGCACA 61.767 63.158 0.00 0.00 0.00 4.57
2221 2432 1.153086 CTTTGAGGATGGAGGGGCG 60.153 63.158 0.00 0.00 0.00 6.13
2222 2433 0.182299 CTCTTTGAGGATGGAGGGGC 59.818 60.000 0.00 0.00 0.00 5.80
2234 2445 4.447138 TGGTAAAAGGCTTCCTCTTTGA 57.553 40.909 0.00 0.00 34.99 2.69
2235 2446 4.619160 GCATGGTAAAAGGCTTCCTCTTTG 60.619 45.833 0.00 0.00 34.99 2.77
2237 2448 3.092301 GCATGGTAAAAGGCTTCCTCTT 58.908 45.455 0.00 0.00 30.89 2.85
2238 2449 2.310052 AGCATGGTAAAAGGCTTCCTCT 59.690 45.455 0.00 0.00 31.34 3.69
2240 2451 2.907458 AGCATGGTAAAAGGCTTCCT 57.093 45.000 0.00 0.00 31.34 3.36
2241 2452 4.270008 TCTAAGCATGGTAAAAGGCTTCC 58.730 43.478 0.00 0.00 44.75 3.46
2246 4389 7.396540 AAGATGTTCTAAGCATGGTAAAAGG 57.603 36.000 0.00 0.00 0.00 3.11
2255 4398 6.126652 ACCATCCACTAAGATGTTCTAAGCAT 60.127 38.462 1.26 0.00 41.79 3.79
2256 4399 5.189736 ACCATCCACTAAGATGTTCTAAGCA 59.810 40.000 1.26 0.00 41.79 3.91
2257 4400 5.525378 CACCATCCACTAAGATGTTCTAAGC 59.475 44.000 1.26 0.00 41.79 3.09
2258 4401 6.644347 ACACCATCCACTAAGATGTTCTAAG 58.356 40.000 1.26 0.00 41.79 2.18
2259 4402 6.620877 ACACCATCCACTAAGATGTTCTAA 57.379 37.500 1.26 0.00 41.79 2.10
2260 4403 7.914427 ATACACCATCCACTAAGATGTTCTA 57.086 36.000 1.26 0.00 41.79 2.10
2261 4404 6.814954 ATACACCATCCACTAAGATGTTCT 57.185 37.500 1.26 0.00 41.79 3.01
2262 4405 7.604164 CCATATACACCATCCACTAAGATGTTC 59.396 40.741 1.26 0.00 41.79 3.18
2264 4407 6.787458 TCCATATACACCATCCACTAAGATGT 59.213 38.462 1.26 0.00 41.79 3.06
2265 4408 7.244886 TCCATATACACCATCCACTAAGATG 57.755 40.000 0.00 0.00 42.79 2.90
2266 4409 6.441924 CCTCCATATACACCATCCACTAAGAT 59.558 42.308 0.00 0.00 0.00 2.40
2267 4410 5.780282 CCTCCATATACACCATCCACTAAGA 59.220 44.000 0.00 0.00 0.00 2.10
2268 4411 5.544176 ACCTCCATATACACCATCCACTAAG 59.456 44.000 0.00 0.00 0.00 2.18
2269 4412 5.306937 CACCTCCATATACACCATCCACTAA 59.693 44.000 0.00 0.00 0.00 2.24
2272 4415 3.244561 CCACCTCCATATACACCATCCAC 60.245 52.174 0.00 0.00 0.00 4.02
2274 4417 3.248024 TCCACCTCCATATACACCATCC 58.752 50.000 0.00 0.00 0.00 3.51
2275 4418 4.836825 CATCCACCTCCATATACACCATC 58.163 47.826 0.00 0.00 0.00 3.51
2276 4419 3.009473 GCATCCACCTCCATATACACCAT 59.991 47.826 0.00 0.00 0.00 3.55
2277 4420 2.371841 GCATCCACCTCCATATACACCA 59.628 50.000 0.00 0.00 0.00 4.17
2278 4421 2.639839 AGCATCCACCTCCATATACACC 59.360 50.000 0.00 0.00 0.00 4.16
2280 4423 6.702449 ATTTAGCATCCACCTCCATATACA 57.298 37.500 0.00 0.00 0.00 2.29
2282 4425 9.500701 TGTATATTTAGCATCCACCTCCATATA 57.499 33.333 0.00 0.00 0.00 0.86
2283 4426 8.267894 GTGTATATTTAGCATCCACCTCCATAT 58.732 37.037 0.00 0.00 0.00 1.78
2284 4427 7.578763 CGTGTATATTTAGCATCCACCTCCATA 60.579 40.741 0.00 0.00 0.00 2.74
2285 4428 6.476378 GTGTATATTTAGCATCCACCTCCAT 58.524 40.000 0.00 0.00 0.00 3.41
2286 4429 5.510690 CGTGTATATTTAGCATCCACCTCCA 60.511 44.000 0.00 0.00 0.00 3.86
2287 4430 4.929808 CGTGTATATTTAGCATCCACCTCC 59.070 45.833 0.00 0.00 0.00 4.30
2288 4431 5.779922 TCGTGTATATTTAGCATCCACCTC 58.220 41.667 0.00 0.00 0.00 3.85
2289 4432 5.801531 TCGTGTATATTTAGCATCCACCT 57.198 39.130 0.00 0.00 0.00 4.00
2290 4433 6.163476 TGATCGTGTATATTTAGCATCCACC 58.837 40.000 0.00 0.00 0.00 4.61
2292 4435 8.669946 TTTTGATCGTGTATATTTAGCATCCA 57.330 30.769 0.00 0.00 0.00 3.41
2332 5183 1.757118 ACCTGATACACGATCCACTGG 59.243 52.381 0.00 0.00 33.07 4.00
2333 5184 2.541794 CGACCTGATACACGATCCACTG 60.542 54.545 0.00 0.00 33.07 3.66
2335 5186 1.404391 ACGACCTGATACACGATCCAC 59.596 52.381 0.00 0.00 33.07 4.02
2336 5187 1.404035 CACGACCTGATACACGATCCA 59.596 52.381 0.00 0.00 33.07 3.41
2337 5188 1.404391 ACACGACCTGATACACGATCC 59.596 52.381 0.00 0.00 33.07 3.36
2338 5189 2.846039 ACACGACCTGATACACGATC 57.154 50.000 0.00 0.00 34.84 3.69
2339 5190 2.357009 GGTACACGACCTGATACACGAT 59.643 50.000 0.00 0.00 45.89 3.73
2341 5192 2.184385 GGTACACGACCTGATACACG 57.816 55.000 0.00 0.00 45.89 4.49
2358 5209 0.394762 TGGGAGCGACGTGTATAGGT 60.395 55.000 0.00 0.00 0.00 3.08
2360 5211 0.316772 CGTGGGAGCGACGTGTATAG 60.317 60.000 0.00 0.00 31.38 1.31
2361 5212 0.744057 TCGTGGGAGCGACGTGTATA 60.744 55.000 0.00 0.00 36.95 1.47
2362 5213 1.989966 CTCGTGGGAGCGACGTGTAT 61.990 60.000 0.00 0.00 36.95 2.29
2364 5215 4.039357 CTCGTGGGAGCGACGTGT 62.039 66.667 0.00 0.00 36.95 4.49
2373 5224 3.066190 CCAGGTACGCTCGTGGGA 61.066 66.667 8.64 0.00 39.00 4.37
2374 5225 4.814294 GCCAGGTACGCTCGTGGG 62.814 72.222 16.80 0.00 41.78 4.61
2376 5227 4.415332 ACGCCAGGTACGCTCGTG 62.415 66.667 5.05 0.00 31.45 4.35
2377 5228 4.415332 CACGCCAGGTACGCTCGT 62.415 66.667 0.00 0.00 0.00 4.18
2379 5230 4.814294 CCCACGCCAGGTACGCTC 62.814 72.222 0.00 0.00 0.00 5.03
2383 5234 0.609662 TTTAGTCCCACGCCAGGTAC 59.390 55.000 0.00 0.00 0.00 3.34
2385 5236 1.373812 GTTTAGTCCCACGCCAGGT 59.626 57.895 0.00 0.00 0.00 4.00
2386 5237 0.953960 GTGTTTAGTCCCACGCCAGG 60.954 60.000 0.00 0.00 0.00 4.45
2388 5239 1.301087 CGTGTTTAGTCCCACGCCA 60.301 57.895 0.00 0.00 46.45 5.69
2392 5243 0.314935 TCGGTCGTGTTTAGTCCCAC 59.685 55.000 0.00 0.00 0.00 4.61
2394 5245 1.422388 GTTCGGTCGTGTTTAGTCCC 58.578 55.000 0.00 0.00 0.00 4.46
2395 5246 1.269726 TGGTTCGGTCGTGTTTAGTCC 60.270 52.381 0.00 0.00 0.00 3.85
2397 5248 1.856802 GTGGTTCGGTCGTGTTTAGT 58.143 50.000 0.00 0.00 0.00 2.24
2398 5249 0.780002 CGTGGTTCGGTCGTGTTTAG 59.220 55.000 0.00 0.00 35.71 1.85
2399 5250 1.214373 GCGTGGTTCGGTCGTGTTTA 61.214 55.000 0.00 0.00 40.26 2.01
2400 5251 2.527867 GCGTGGTTCGGTCGTGTTT 61.528 57.895 0.00 0.00 40.26 2.83
2401 5252 2.963320 GCGTGGTTCGGTCGTGTT 60.963 61.111 0.00 0.00 40.26 3.32
2408 5259 4.072088 GCAACGAGCGTGGTTCGG 62.072 66.667 6.80 0.00 40.38 4.30
2417 5268 3.340721 CTGTTCGCGAGCAACGAGC 62.341 63.158 25.68 5.38 45.77 5.03
2418 5269 1.275471 TTCTGTTCGCGAGCAACGAG 61.275 55.000 25.68 14.50 45.77 4.18
2420 5271 1.128611 CTTCTGTTCGCGAGCAACG 59.871 57.895 25.68 15.56 45.66 4.10
2422 5273 1.667830 CCCTTCTGTTCGCGAGCAA 60.668 57.895 25.68 11.85 0.00 3.91
2424 5275 0.949105 TTTCCCTTCTGTTCGCGAGC 60.949 55.000 16.69 16.69 0.00 5.03
2425 5276 1.461127 CTTTTCCCTTCTGTTCGCGAG 59.539 52.381 9.59 0.00 0.00 5.03
2427 5278 1.508632 TCTTTTCCCTTCTGTTCGCG 58.491 50.000 0.00 0.00 0.00 5.87
2428 5279 3.139077 TCTTCTTTTCCCTTCTGTTCGC 58.861 45.455 0.00 0.00 0.00 4.70
2430 5281 6.944234 TTTCTCTTCTTTTCCCTTCTGTTC 57.056 37.500 0.00 0.00 0.00 3.18
2431 5282 7.718334 TTTTTCTCTTCTTTTCCCTTCTGTT 57.282 32.000 0.00 0.00 0.00 3.16
2465 5316 2.854187 GAAAGGAACGGGAGCGGGAG 62.854 65.000 0.00 0.00 0.00 4.30
2467 5318 2.436115 GAAAGGAACGGGAGCGGG 60.436 66.667 0.00 0.00 0.00 6.13
2468 5319 2.436115 GGAAAGGAACGGGAGCGG 60.436 66.667 0.00 0.00 0.00 5.52
2469 5320 2.813908 CGGAAAGGAACGGGAGCG 60.814 66.667 0.00 0.00 0.00 5.03
2470 5321 2.436115 CCGGAAAGGAACGGGAGC 60.436 66.667 0.00 0.00 46.08 4.70
2504 5355 3.878519 GGAGAGGAGACGCGACGG 61.879 72.222 15.93 0.00 34.13 4.79
2505 5356 4.225340 CGGAGAGGAGACGCGACG 62.225 72.222 15.93 0.00 34.13 5.12
2506 5357 3.878519 CCGGAGAGGAGACGCGAC 61.879 72.222 15.93 6.86 45.00 5.19
2544 6720 0.511221 CGCTCGCGAGAAAGGAAAAA 59.489 50.000 38.74 0.00 42.83 1.94
2546 6722 1.736645 CCGCTCGCGAGAAAGGAAA 60.737 57.895 38.74 0.00 42.83 3.13
2547 6723 2.126071 CCGCTCGCGAGAAAGGAA 60.126 61.111 38.74 0.00 42.83 3.36
2548 6724 4.129737 CCCGCTCGCGAGAAAGGA 62.130 66.667 38.74 0.00 42.83 3.36
2550 6726 2.580867 CTCCCGCTCGCGAGAAAG 60.581 66.667 38.74 26.12 42.83 2.62
2551 6727 4.796231 GCTCCCGCTCGCGAGAAA 62.796 66.667 38.74 18.42 42.83 2.52
2585 6761 3.792053 GATCGGGCTGTAGGGCGTG 62.792 68.421 0.00 0.00 41.87 5.34
2586 6762 3.537874 GATCGGGCTGTAGGGCGT 61.538 66.667 0.00 0.00 41.87 5.68
2587 6763 3.227276 AGATCGGGCTGTAGGGCG 61.227 66.667 0.00 0.00 41.87 6.13
2588 6764 2.423446 CAGATCGGGCTGTAGGGC 59.577 66.667 0.00 0.00 40.05 5.19
2589 6765 3.142393 CCAGATCGGGCTGTAGGG 58.858 66.667 0.00 0.00 34.06 3.53


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

AutoCloner maintained by Alex Coulton.