Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold191
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 315193
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:840 original size:16 final size:16
Alignment explanation
Indices: 819--859 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
809 ACAAAAAATC
819 AAAAAAATTGATTGAA
1 AAAAAAATTGATTGAA
835 AAAAAAATTGATTGAA
1 AAAAAAATTGATTGAA
851 AAAAAAATT
1 AAAAAAATT
860 CAAAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (16 bp):
AAAAAAATTGATTGAA
Found at i:927 original size:16 final size:17
Alignment explanation
Indices: 908--942 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
898 AAAAGAAAAA
908 AAGTGAAAAAAAAA-TG
1 AAGTGAAAAAAAAAGTG
*
924 AAGTTAAAAAAAAAGTG
1 AAGTGAAAAAAAAAGTG
941 AA
1 AA
943 AAGTCTTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (17 bp):
AAGTGAAAAAAAAAGTG
Found at i:944 original size:11 final size:11
Alignment explanation
Indices: 847--925 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
837 AAAAATTGAT
847 TGAAAAAAAAA
1 TGAAAAAAAAA
* *
858 TTCAAAAAAAAG
1 -TGAAAAAAAAA
870 TGAAAAAAAAA
1 TGAAAAAAAAA
**
881 TCGAGCAAAAAA
1 T-GAAAAAAAAA
*
893 --AAAGAAAAA
1 TGAAAAAAAAA
*
902 -G-AAAAAAAG
1 TGAAAAAAAAA
911 TGAAAAAAAAA
1 TGAAAAAAAAA
922 TGAA
1 TGAA
926 GTTAAAAAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
9 12 0.24
10 1 0.02
11 21 0.41
12 17 0.33
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.09
Consensus pattern (11 bp):
TGAAAAAAAAA
Found at i:3720 original size:17 final size:18
Alignment explanation
Indices: 3698--3734 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3688 TGGAATAAAC
3698 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
3715 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
3733 TT
1 TT
3735 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:11297 original size:13 final size:13
Alignment explanation
Indices: 11279--11324 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
11269 ACGAGATTGT
11279 AAAAAAAATTTCG
1 AAAAAAAATTTCG
11292 AAAAAAAAATTT-G
1 -AAAAAAAATTTCG
11305 AAAAATAAA-TTC-
1 AAAAA-AAATTTCG
11317 AAAAAAAA
1 AAAAAAAA
11325 ACAAAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.10
12 12 0.40
13 4 0.13
14 11 0.37
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAAAAAATTTCG
Found at i:11298 original size:14 final size:14
Alignment explanation
Indices: 11279--11325 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
11269 ACGAGATTGT
11279 AAAAAAAATTTCGA
1 AAAAAAAATTTCGA
11293 AAAAAAAATTT-GA
1 AAAAAAAATTTCGA
*
11306 AAAATAAA-TTC-A
1 AAAAAAAATTTCGA
11318 AAAAAAAA
1 AAAAAAAA
11326 CAAAAAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 10 0.33
13 9 0.30
14 11 0.37
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTTCGA
Found at i:12946 original size:19 final size:21
Alignment explanation
Indices: 12890--12949 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
12880 TTTGAACCAT
*
12890 TACCA-TTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
12911 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
12932 TA-CATTTCG-ACCAATTCC
1 TACCATTTCGTACCAATTCC
12950 CAAATACCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 9 0.24
20 7 0.19
21 13 0.35
22 8 0.22
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:13288 original size:12 final size:12
Alignment explanation
Indices: 13252--13288 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
13242 GTACGTAAAA
*
13252 AAAAAAAAAGTTC
1 AAAAAAAAA-TTG
13265 AAAAAAAAATTG
1 AAAAAAAAATTG
13277 AAAAAAAAATTG
1 AAAAAAAAATTG
13289 CATACGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:15534 original size:17 final size:17
Alignment explanation
Indices: 15489--15542 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
15479 AGAAAAGAGC
* *
15489 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
15506 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
15523 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
15540 GAA
1 GAA
15543 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:19777 original size:21 final size:21
Alignment explanation
Indices: 19732--19794 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
19722 TTTGAACCAT
* *
19732 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
19754 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
19775 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
19795 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:20748 original size:59 final size:63
Alignment explanation
Indices: 20685--20824 Score: 162
Period size: 70 Copynumber: 2.2 Consensus size: 63
20675 ATTTAAAGGG
* *
20685 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTA
*
20744 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTA
20809 ATGTA
59 ATGTA
20814 AAGCATAGACA
1 AAGCATAGACA
20825 ATATATTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 11
0.83 0.04 0.14
Matches are distributed among these distances:
59 12 0.18
60 5 0.07
64 1 0.01
67 1 0.01
70 48 0.72
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.23
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGAAGGTGTTGGCCGAATTTAATGTA
Found at i:23916 original size:20 final size:20
Alignment explanation
Indices: 23869--23916 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
23859 AGTAAGCTCG
23869 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
23889 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
23909 GTTGAGCT
1 GTTGAGCT
23917 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:25704 original size:15 final size:14
Alignment explanation
Indices: 25668--25722 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
25658 TCTATTGAGC
25668 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
25682 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
25696 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
25711 GAAAGAAAAGAA
1 GAGA-AAAAGAA
25723 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:25764 original size:23 final size:23
Alignment explanation
Indices: 25738--25787 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
25728 AGAGTGAGAT
25738 AAAAACAAGAGTGACAAAAGAAA
1 AAAAACAAGAGTGACAAAAGAAA
* ** *
25761 AAAAGCAAGAGTGTGAAAATAAA
1 AAAAACAAGAGTGACAAAAGAAA
25784 AAAA
1 AAAA
25788 TAAGTGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.68, C:0.06, G:0.18, T:0.08
Consensus pattern (23 bp):
AAAAACAAGAGTGACAAAAGAAA
Found at i:41016 original size:22 final size:22
Alignment explanation
Indices: 40988--41031 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40978 TTTTGAACCA
40988 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41010 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41032 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41420 original size:12 final size:12
Alignment explanation
Indices: 41403--41432 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
41393 CGAATGGCTG
41403 AAAACAGCCTTC
1 AAAACAGCCTTC
41415 AAAACAGCCTTC
1 AAAACAGCCTTC
41427 AAAACA
1 AAAACA
41433 AAATTTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.30, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAACAGCCTTC
Found at i:49704 original size:20 final size:19
Alignment explanation
Indices: 49681--49745 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
49671 AAGCTCAAAC
49681 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
49701 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
49721 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
49741 GAGCT
1 GAGCT
49746 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:54731 original size:21 final size:23
Alignment explanation
Indices: 54686--54732 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
54676 TCACCTGCAA
* *
54686 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
54709 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
54730 TAA
1 TAA
54733 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:57027 original size:27 final size:29
Alignment explanation
Indices: 56996--57052 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
56986 TTAGGACTTA
56996 TCTTTT-AATT-T-CTTGCTGTCAATTTTT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTT
57023 TCTTTTAAATTCTGCTTGTGTCAATTTTT
1 TCTTTTAAATTCTGCTTGTGTCAATTTTT
57052 T
1 T
57053 TAATCACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 6 0.22
28 4 0.15
29 13 0.48
30 4 0.15
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (29 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTT
Found at i:57878 original size:43 final size:45
Alignment explanation
Indices: 57793--57918 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 45
57783 ACCTCTTTGA
*
57793 ACCATTACCAATTCGTACCAAATACCATACCATTTCGTACCAAAT
1 ACCATTACCAATTCGTACCAAATACCATACCATTTCGAACCAAAT
* * *
57838 ACCA-TACCATTTCGTACC-AATTCCATACCATTTCGAACCAATT
1 ACCATTACCAATTCGTACCAAATACCATACCATTTCGAACCAAAT
* * **
57881 CCCAAATACCAAAACGTACCAAA-ACCAAATACCATTTC
1 ACC-ATTACCAATTCGTACCAAATACC--ATACCATTTC
57919 TTAATTATCC
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
43 24 0.36
44 14 0.21
45 17 0.25
46 2 0.03
47 10 0.15
ACGTcount: A:0.39, C:0.33, G:0.04, T:0.25
Consensus pattern (45 bp):
ACCATTACCAATTCGTACCAAATACCATACCATTTCGAACCAAAT
Found at i:57882 original size:21 final size:22
Alignment explanation
Indices: 57793--57878 Score: 129
Period size: 22 Copynumber: 3.9 Consensus size: 22
57783 ACCTCTTTGA
*
57793 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
57816 ACCATACCATTTCGTACCAAAT
1 ACCATACCATTTCGTACCAAAT
57838 ACCATACCATTTCGTACC-AAT
1 ACCATACCATTTCGTACCAAAT
* *
57859 TCCATACCATTTCGAACCAA
1 ACCATACCATTTCGTACCAA
57879 TTCCCAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
21 19 0.32
22 36 0.61
23 4 0.07
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.27
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:58714 original size:20 final size:20
Alignment explanation
Indices: 58668--58714 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
58658 AGCTTGTTTC
*
58668 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
58688 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
58708 CAGCTCA
1 CAGCTCA
58715 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:61135 original size:13 final size:15
Alignment explanation
Indices: 61119--61155 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
61109 AAAGGAGTTC
61119 GAAAAAAAAAAT-T-
1 GAAAAAAAAAATCTG
*
61132 GAAAAAAAAATTCTG
1 GAAAAAAAAAATCTG
61147 GAAAAAAAA
1 GAAAAAAAA
61156 TTGCATACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.52
14 1 0.05
15 9 0.43
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.14
Consensus pattern (15 bp):
GAAAAAAAAAATCTG
Found at i:61151 original size:14 final size:13
Alignment explanation
Indices: 61119--61157 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
61109 AAAGGAGTTC
*
61119 GAAAAAAAAAATT
1 GAAAAAAAAATTT
61132 GAAAAAAAAATTCT
1 GAAAAAAAAATT-T
*
61146 GGAAAAAAAATT
1 GAAAAAAAAATT
61158 GCATACGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (13 bp):
GAAAAAAAAATTT
Found at i:62396 original size:20 final size:20
Alignment explanation
Indices: 62350--62396 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
62340 AGCTCGTTTC
*
62350 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
62370 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
62390 CAGCTCA
1 CAGCTCA
62397 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:65072 original size:48 final size:47
Alignment explanation
Indices: 64993--65098 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
64983 GAGTGTCATG
*
64993 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
65041 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
65089 GAAAAAGAAA
1 GAAAAAGAAA
65099 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:66814 original size:20 final size:20
Alignment explanation
Indices: 66768--66814 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
66758 AGCTCGTTTC
*
66768 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
66788 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
66808 CAGCTCA
1 CAGCTCA
66815 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:69342 original size:17 final size:17
Alignment explanation
Indices: 69297--69342 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
69287 GCGAAAATAC
69297 AAAAGAAAAGA-AAAATT
1 AAAA-AAAAGAGAAAATT
69314 AAAAAAAA-AGAAAATT
1 AAAAAAAAGAGAAAATT
69330 AAAAAAAAGAGAA
1 AAAAAAAAGAGAA
69343 TGAAAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.04
16 18 0.67
17 8 0.30
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (17 bp):
AAAAAAAAGAGAAAATT
Found at i:69348 original size:15 final size:15
Alignment explanation
Indices: 69315--69348 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
69305 AGAAAAATTA
*
69315 AAAAAAAAGAAAATT
1 AAAAAAAAGAAAATG
*
69330 AAAAAAAAGAGAATG
1 AAAAAAAAGAAAATG
69345 AAAA
1 AAAA
69349 GAGAGCGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (15 bp):
AAAAAAAAGAAAATG
Found at i:73556 original size:22 final size:22
Alignment explanation
Indices: 73528--73571 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
73518 TTTTGAACCA
73528 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
73550 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
73572 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:78510 original size:15 final size:15
Alignment explanation
Indices: 78490--78544 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
78480 ACTCTCCTCA
*
78490 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
78505 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
78520 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
78534 TTCTTTT-TCTC
1 TTCTTTTCTCTC
78545 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:80602 original size:18 final size:18
Alignment explanation
Indices: 80581--80617 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
80571 TTCTTTTTCT
*
80581 TTTTTTTTTAATTCTGAA
1 TTTTTTTTTAATACTGAA
80599 TTTTTTTTTAATACTGAA
1 TTTTTTTTTAATACTGAA
80617 T
1 T
80618 ACACAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTTTTTTAATACTGAA
Found at i:82759 original size:11 final size:10
Alignment explanation
Indices: 82743--82772 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
82733 TTCGTAACGT
82743 AAAAAAAAGTC
1 AAAAAAAA-TC
82754 AAAAAAAATC
1 AAAAAAAATC
82764 AAAAAAAAT
1 AAAAAAAAT
82773 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:82890 original size:11 final size:11
Alignment explanation
Indices: 82860--82901 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
82850 ATAAATTTAG
82860 AAAAAAAAATTC
1 AAAAAAAAA-TC
82872 -AAAAAAAATC
1 AAAAAAAAATC
**
82882 AAAAAAAAAAG
1 AAAAAAAAATC
82893 AAAAAAAAA
1 AAAAAAAAA
82902 AGGTGAGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 2 0.07
11 25 0.93
ACGTcount: A:0.86, C:0.05, G:0.02, T:0.07
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:94847 original size:20 final size:20
Alignment explanation
Indices: 94824--94870 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
94814 GGGTTAAGAT
*
94824 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
94844 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
94864 TGAGCTG
1 TGAGCTG
94871 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:96590 original size:48 final size:47
Alignment explanation
Indices: 96537--96643 Score: 139
Period size: 48 Copynumber: 2.2 Consensus size: 47
96527 ATTGTCTTTT
*
96537 ATTTCTTTTTCAA-T-TTTCTCTTTTTCCTCACA-CTTTTGTTCAATCTCA
1 ATTTCTTTTTCAATTCTTTCTCTTTTT--T-ACATCCTTT-TTCAATCTCA
96585 ATTTCTTTTTCAATTTCTTTCTCTTTTTTACATCCTTTTTCAATCTCA
1 ATTTCTTTTTCAA-TTCTTTCTCTTTTTTACATCCTTTTTCAATCTCA
96633 ATTTCTTTTTC
1 ATTTCTTTTTC
96644 CATGACACTC
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
48 37 0.69
49 5 0.09
50 1 0.02
51 11 0.20
ACGTcount: A:0.16, C:0.23, G:0.01, T:0.60
Consensus pattern (47 bp):
ATTTCTTTTTCAATTCTTTCTCTTTTTTACATCCTTTTTCAATCTCA
Found at i:98212 original size:20 final size:20
Alignment explanation
Indices: 98189--98235 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
98179 GGGTTAAGAT
*
98189 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
98209 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
98229 TGAGCTG
1 TGAGCTG
98236 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:103397 original size:10 final size:10
Alignment explanation
Indices: 103381--103438 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
103371 CAACTCCGAC
103381 CAGCTCAATT
1 CAGCTCAATT
* *
103391 GAGCTCATTT
1 CAGCTCAATT
103401 CAGCTCAA-T
1 CAGCTCAATT
103410 CGAGCTCAATT
1 C-AGCTCAATT
*
103421 TAGCTACAATT
1 CAGCT-CAATT
103432 CAGCTCA
1 CAGCTCA
103439 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:103404 original size:20 final size:20
Alignment explanation
Indices: 103381--103441 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
103371 CAACTCCGAC
103381 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
103401 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
103422 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
103442 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:108326 original size:50 final size:54
Alignment explanation
Indices: 108201--108331 Score: 125
Period size: 50 Copynumber: 2.6 Consensus size: 54
108191 TGAACAAAAG
* * * *
108201 AGTTACTTAATGCAAG--ACTTAATTTAATGATGCAGACCTAAACTAACATGGG
1 AGTTACATAATGCATGTAACTTTATTTAATGATGCAGACCTAAACTAACATGGA
* * * *
108253 AGTTACATAATGCATGTTA--TTATTT-ATGATGCATA-CTTAACTAGCATGGA
1 AGTTACATAATGCATGTAACTTTATTTAATGATGCAGACCTAAACTAACATGGA
*
108303 AGTTACATAATGC-T-TAACTTTATTAAATG
1 AGTTACATAATGCATGTAACTTTATTTAATG
108332 CAAAACACAC
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
48 2 0.03
49 1 0.02
50 30 0.46
51 12 0.18
52 19 0.29
54 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (54 bp):
AGTTACATAATGCATGTAACTTTATTTAATGATGCAGACCTAAACTAACATGGA
Found at i:116686 original size:20 final size:20
Alignment explanation
Indices: 116650--116704 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
116640 AACTCAATCC
*
116650 AGCTCAATT-TTACCTCAATG
1 AGCTC-ATTCTTAGCTCAATG
*
116670 AGCTCGTTCTTAGCTCAATG
1 AGCTCATTCTTAGCTCAATG
*
116690 AGCTCATTTTTAGCT
1 AGCTCATTCTTAGCT
116705 TACTTTAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (20 bp):
AGCTCATTCTTAGCTCAATG
Found at i:119026 original size:15 final size:14
Alignment explanation
Indices: 118995--119024 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
118985 TTTAAAAAAT
118995 AATTTAAAAAAAGA
1 AATTTAAAAAAAGA
*
119009 AATTTGAAAAAAGA
1 AATTTAAAAAAAGA
119023 AA
1 AA
119025 ATCTAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (14 bp):
AATTTAAAAAAAGA
Found at i:122836 original size:23 final size:22
Alignment explanation
Indices: 122784--122836 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
122774 TCCACGTCTT
*
122784 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
122806 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
122829 TTTCTTTT
1 TTTCTTTT
122837 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:124143 original size:18 final size:19
Alignment explanation
Indices: 124112--124153 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
124102 TTTTTTTAAA
*
124112 TTTTTATTGAATTTCGTCTT
1 TTTTTATT-AATTTCGACTT
*
124132 TTTTTATT-ATTTTGACTT
1 TTTTTATTAATTTCGACTT
124150 TTTT
1 TTTT
124154 GACTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (19 bp):
TTTTTATTAATTTCGACTT
Found at i:125659 original size:21 final size:23
Alignment explanation
Indices: 125614--125660 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
125604 TCACCTGCAA
* *
125614 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
125637 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
125658 TAA
1 TAA
125661 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:130678 original size:19 final size:18
Alignment explanation
Indices: 130642--130681 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
130632 TTTCCACTCG
*
130642 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
130660 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
130679 TTT
1 TTT
130682 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:130796 original size:18 final size:18
Alignment explanation
Indices: 130754--130813 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
130744 GCACTCTTTC
* *
130754 TTTCTTTCTCCAATCTTTT
1 TTTCTTTTTCGAAT-TTTT
*
130773 TCTCTTTTTC-AATTTTT
1 TTTCTTTTTCGAATTTTT
*
130790 GTTTCTTTTTCGAGTTTTT
1 -TTTCTTTTTCGAATTTTT
130809 TTTCT
1 TTTCT
130814 CTCGTCACTC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 17 0.49
19 14 0.40
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTCTTTTTCGAATTTTT
Found at i:136617 original size:15 final size:16
Alignment explanation
Indices: 136597--136638 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
136587 TAGCTTCTTC
136597 TTTTTTTTTCACG-AA
1 TTTTTTTTTCACGAAA
136612 TTTTTTTTTCACGAAA
1 TTTTTTTTTCACGAAA
136628 TTTTTTTTTCA
1 TTTTTTTTTCA
136639 ACTTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTTTTTCACGAAA
Found at i:136695 original size:13 final size:12
Alignment explanation
Indices: 136675--136724 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
136665 AAAGGAAACC
136675 AATTTTTTTTTG
1 AATTTTTTTTTG
136687 AATTTTTTTTTG
1 AATTTTTTTTTG
*
136699 AATTTTTTTTTC
1 AATTTTTTTTTG
**
136711 AAAATTTTTTTG
1 AATTTTTTTTTG
136723 AA
1 AA
136725 GAAACTACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:137752 original size:21 final size:23
Alignment explanation
Indices: 137707--137753 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
137697 TCACCTGCAA
* *
137707 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
137730 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
137751 TAA
1 TAA
137754 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:138488 original size:18 final size:18
Alignment explanation
Indices: 138467--138558 Score: 53
Period size: 18 Copynumber: 5.0 Consensus size: 18
138457 AGAACAAGAA
138467 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGAGAGTGAG
*
138485 ATTGAAGAAAGA-AATGAG
1 ATTGAA-AAAGAGAGTGAG
* * **
138503 AGTGTAAAAGAAACGAGTGTC
1 ATTG-AAAA-AGA-GAGTGAG
* * *
138524 ATGGAAAAAGAGAGAGGG
1 ATTGAAAAAGAGAGTGAG
*
138542 TTTGAAAAAGAGA-TGAG
1 ATTGAAAAAGAGAGTGAG
138559 TAAAAAAGGA
Statistics
Matches: 53, Mismatches: 16, Indels: 11
0.66 0.20 0.14
Matches are distributed among these distances:
17 2 0.04
18 31 0.58
19 11 0.21
20 4 0.08
21 5 0.09
ACGTcount: A:0.49, C:0.02, G:0.33, T:0.16
Consensus pattern (18 bp):
ATTGAAAAAGAGAGTGAG
Found at i:147147 original size:25 final size:25
Alignment explanation
Indices: 147121--147190 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
147111 ACTTCTAAAG
147121 AAAACTCAAGAGAGAATTCTTGGAGA
1 AAAACTCAA-AGAGAATTCTTGGAGA
147147 AAAACTCAAAGAGAATTCTTGGAGA
1 AAAACTCAAAGAGAATTCTTGGAGA
147172 AAAACTCAAAGAGAATTCT
1 AAAACTCAAAGAGAATTCT
147191 ACACTTAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 35 0.80
26 9 0.20
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.20
Consensus pattern (25 bp):
AAAACTCAAAGAGAATTCTTGGAGA
Found at i:153908 original size:15 final size:14
Alignment explanation
Indices: 153872--153926 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
153862 TCTATTGATC
153872 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
153886 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
153900 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
153915 GAAAGAAAAGAA
1 GAGA-AAAAGAA
153927 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:165668 original size:18 final size:18
Alignment explanation
Indices: 165647--165689 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
165637 TCTCACTCTT
165647 TTTTTCTTTTTCAATGTC
1 TTTTTCTTTTTCAATGTC
* *
165665 TTTTTCTTTTTCGATTTC
1 TTTTTCTTTTTCAATGTC
165683 TTTTTCT
1 TTTTTCT
165690 CTCATCTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTTTCTTTTTCAATGTC
Found at i:168206 original size:20 final size:20
Alignment explanation
Indices: 168183--168229 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
168173 GGGTTAAGAT
*
168183 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
168203 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
168223 TGAGCTG
1 TGAGCTG
168230 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:170940 original size:14 final size:13
Alignment explanation
Indices: 170922--170968 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
170912 TTTTAACTTG
170922 ATTTTTTTTGCTC
1 ATTTTTTTTGCTC
170935 ACTTTTTTTT-CT-
1 A-TTTTTTTTGCTC
*
170947 TTTTTTTTTGCTC
1 ATTTTTTTTGCTC
170960 GATTTTTTT
1 -ATTTTTTT
170969 AACCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
11 8 0.29
12 2 0.07
13 3 0.11
14 15 0.54
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.74
Consensus pattern (13 bp):
ATTTTTTTTGCTC
Found at i:170951 original size:25 final size:27
Alignment explanation
Indices: 170904--170968 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
170894 GCAAGACTTT
170904 TCACTTTTTTTTAACTTGATTTTTTTTGC
1 TCACTTTTTTTT-ACTT-ATTTTTTTTGC
170933 TCACTTTTTTTT-CTT-TTTTTTTTGC
1 TCACTTTTTTTTACTTATTTTTTTTGC
170958 TCGA-TTTTTTT
1 TC-ACTTTTTTT
170969 AACCTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 19 0.54
26 1 0.03
27 3 0.09
29 12 0.34
ACGTcount: A:0.09, C:0.14, G:0.06, T:0.71
Consensus pattern (27 bp):
TCACTTTTTTTTACTTATTTTTTTTGC
Found at i:170976 original size:25 final size:25
Alignment explanation
Indices: 170923--170981 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
170913 TTTAACTTGA
* *
170923 TTTTTTTTGCTCACTTTTTTTTCTT
1 TTTTTTTTGCTCACTTTTTTTACTC
170948 TTTTTTTTGCTCGA-TTTTTTTAAC-C
1 TTTTTTTTGCTC-ACTTTTTTT-ACTC
170973 TTTTTTTTG
1 TTTTTTTTG
170982 AATTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 28 0.93
26 2 0.07
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.73
Consensus pattern (25 bp):
TTTTTTTTGCTCACTTTTTTTACTC
Found at i:170987 original size:11 final size:11
Alignment explanation
Indices: 170973--170997 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
170963 TTTTTTAACC
170973 TTTTTTTTGAA
1 TTTTTTTTGAA
170984 TTTTTTTTGAA
1 TTTTTTTTGAA
170995 TTT
1 TTT
170998 CGATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:172473 original size:20 final size:20
Alignment explanation
Indices: 172450--172496 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
172440 GGGTTAAGAT
*
172450 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
172470 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
172490 TGAGCTG
1 TGAGCTG
172497 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:174244 original size:20 final size:19
Alignment explanation
Indices: 174221--174285 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
174211 AAGCTCAAAC
174221 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
174241 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
174261 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
174281 GAGCT
1 GAGCT
174286 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:176099 original size:33 final size:33
Alignment explanation
Indices: 176061--176123 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
176051 GATTACTCAC
176061 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
176094 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
176124 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:176150 original size:21 final size:21
Alignment explanation
Indices: 176121--176176 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
176111 CAAGCTCTCT
*
176121 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
176142 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
176163 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
176177 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:176169 original size:14 final size:14
Alignment explanation
Indices: 176120--176176 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
176110 TCAAGCTCTC
176120 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
176133 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
176147 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
176161 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
176175 TT
1 TT
176177 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:176256 original size:6 final size:6
Alignment explanation
Indices: 176138--176243 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
176128 TCTTTTTTCG
* * * **
176138 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA C-TTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * **
176188 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT C-TTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
176235 -GTTTT CTTT
1 CTTTTT CTTT
176244 CAATTTCTTT
Statistics
Matches: 73, Mismatches: 22, Indels: 10
0.70 0.21 0.10
Matches are distributed among these distances:
5 11 0.15
6 50 0.68
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:176256 original size:16 final size:15
Alignment explanation
Indices: 176191--176254 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
176181 CACTTTTCGA
176191 TTTCTTTTTCTTTTGC
1 TTTCTTTTTCTTTT-C
176207 AATTTCTTTTTCTTTTTC
1 --TTTCTTTTTC-TTTTC
*
176225 TTTTCTTTTTGTTTTC
1 -TTTCTTTTTCTTTTC
**
176241 TTTCAATTTCTTTT
1 TTTCTTTTTCTTTT
176255 TCAATCTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 11 0.28
16 5 0.12
17 9 0.22
18 11 0.28
19 4 0.10
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:177332 original size:11 final size:11
Alignment explanation
Indices: 177317--177385 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 11
177307 TTTTTGCTCG
177317 ATTTTTTTTCA
1 ATTTTTTTTCA
* *
177328 CTTTTTTTTGA
1 ATTTTTTTTCA
177339 ATTTTTTTCAATCAA
1 ATTTTTTT---TC-A
177354 ATTTTTTTTTCGA
1 A-TTTTTTTTC-A
*
177367 ATTTTTTTT-G
1 ATTTTTTTTCA
177377 ATTTTTTTT
1 ATTTTTTTT
177386 GATACTCCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
10 9 0.19
11 16 0.34
12 8 0.17
13 4 0.09
14 1 0.02
15 2 0.04
16 7 0.15
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:177345 original size:13 final size:13
Alignment explanation
Indices: 177329--177375 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
177319 TTTTTTTCAC
177329 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
* *
177341 TTTTTTCAATCAAAT
1 TTTTTT--TTCGAAT
177356 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
177369 TTTTTTT
1 TTTTTTT
177376 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 6 0.21
13 12 0.43
14 1 0.04
15 9 0.32
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.70
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:179729 original size:30 final size:30
Alignment explanation
Indices: 179695--179791 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
179685 AGCTCACTCC
179695 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
179725 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
179755 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
179785 TAGCTCA
1 TAGCTCA
179792 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:182657 original size:18 final size:18
Alignment explanation
Indices: 182636--182670 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
182626 AGAAAAGAAA
182636 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
182654 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
182671 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:187855 original size:82 final size:81
Alignment explanation
Indices: 187739--187894 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
187729 AAATTGTACA
* * * *
187739 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
187803 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
187820 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
187885 TGCGAGTTGA
65 TGCGAATTGA
187895 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:187862 original size:55 final size:52
Alignment explanation
Indices: 187738--187891 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
187728 TAAATTGTAC
* *
187738 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
187791 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
187846 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
187892 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:187896 original size:27 final size:27
Alignment explanation
Indices: 187739--187894 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
187729 AAATTGTACA
*
187739 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
187766 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
187793 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
187820 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
187848 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
187875 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
187895 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:187905 original size:27 final size:27
Alignment explanation
Indices: 187731--187915 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
187721 GCGGGATTAA
*
187731 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
187758 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
187785 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
187812 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
187840 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
187867 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
187894 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
187916 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:187906 original size:82 final size:81
Alignment explanation
Indices: 187731--187915 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
187721 GCGGGATTAA
* * * *
187731 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
187796 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
187812 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
187876 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
187894 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
187916 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:204843 original size:27 final size:26
Alignment explanation
Indices: 204788--204844 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
204778 AATCACTCTC
* *
204788 TCTTTTTTTCATCATCTTTTTGTTTT
1 TCTTCTTTTCATCATCTTTTTGTTAT
*
204814 TCTTCTTTTCTTCACTCTTTTCT-TTAT
1 TCTTCTTTTCATCA-TCTTTT-TGTTAT
204841 TCTT
1 TCTT
204845 TTCTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 12 0.46
27 13 0.50
28 1 0.04
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.70
Consensus pattern (26 bp):
TCTTCTTTTCATCATCTTTTTGTTAT
Found at i:204850 original size:12 final size:12
Alignment explanation
Indices: 204816--204850 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
204806 TTTGTTTTTC
*
204816 TTCTTTTCTTCA
1 TTCTTTTCTTTA
*
204828 CTCTTTTCTTTA
1 TTCTTTTCTTTA
204840 TTCTTTTCTTT
1 TTCTTTTCTTT
204851 TTTGCTCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (12 bp):
TTCTTTTCTTTA
Found at i:207054 original size:11 final size:11
Alignment explanation
Indices: 207038--207090 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
207028 AGACCGTATG
207038 CAATTTTTTTT
1 CAATTTTTTTT
207049 CAA-TTTTTTT
1 CAATTTTTTTT
207059 CAATTTTTTTTT
1 CAA-TTTTTTTT
*
207071 CGATTTTTTTT
1 CAATTTTTTTT
207082 --ATTTTTTTT
1 CAATTTTTTTT
207091 GAATCTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
9 9 0.23
10 10 0.26
11 11 0.28
12 9 0.23
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:207058 original size:12 final size:12
Alignment explanation
Indices: 207041--207081 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
207031 CCGTATGCAA
207041 TTTTTTTTCAA-
1 TTTTTTTTCAAT
207052 -TTTTTTTCAAT
1 TTTTTTTTCAAT
*
207063 TTTTTTTTCGAT
1 TTTTTTTTCAAT
207075 TTTTTTT
1 TTTTTTT
207082 ATTTTTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.37
12 17 0.63
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:207080 original size:10 final size:10
Alignment explanation
Indices: 207042--207068 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
207032 CGTATGCAAT
207042 TTTTTTTCAA
1 TTTTTTTCAA
207052 TTTTTTTCAA
1 TTTTTTTCAA
207062 TTTTTTT
1 TTTTTTT
207069 TTCGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:208382 original size:12 final size:12
Alignment explanation
Indices: 208365--208389 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
208355 GTAATGAAAC
208365 TTATTTAAATGT
1 TTATTTAAATGT
208377 TTATTTAAATGT
1 TTATTTAAATGT
208389 T
1 T
208390 CTAAATTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TTATTTAAATGT
Found at i:213314 original size:46 final size:46
Alignment explanation
Indices: 213261--213372 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
213251 ATTAATAAGT
213261 TAAGTCATTTAATTTGTCTAAATTATTACAACAATTTAAGTTGTCC
1 TAAGTCATTTAATTTGTCTAAATTATTACAACAATTTAAGTTGTCC
* *
213307 TAAGTCATTTAATTTGTCTAAATTATTACAGCAATTTAAGTTGTCT
1 TAAGTCATTTAATTTGTCTAAATTATTACAACAATTTAAGTTGTCC
* *
213353 TAAACTAATTTAATTTGTCT
1 T-AAGTCATTTAATTTGTCT
213373 TGTTTACAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 45 0.74
47 16 0.26
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.46
Consensus pattern (46 bp):
TAAGTCATTTAATTTGTCTAAATTATTACAACAATTTAAGTTGTCC
Found at i:221810 original size:17 final size:17
Alignment explanation
Indices: 221788--221825 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
221778 AAAAAAATTC
221788 AAAAAAAAATTCGTGAA
1 AAAAAAAAATTCGTGAA
221805 AAAAAAAAATTCGTGAA
1 AAAAAAAAATTCGTGAA
221822 AAAA
1 AAAA
221826 GAAGAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (17 bp):
AAAAAAAAATTCGTGAA
Found at i:228408 original size:20 final size:20
Alignment explanation
Indices: 228385--228431 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
228375 GGGTTAAGAT
*
228385 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
228405 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
228425 TGAGCTG
1 TGAGCTG
228432 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:234513 original size:20 final size:20
Alignment explanation
Indices: 234467--234513 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
234457 AGCTTGTTTC
*
234467 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
234487 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
234507 CAGCTCA
1 CAGCTCA
234514 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:237088 original size:12 final size:13
Alignment explanation
Indices: 237063--237096 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
237053 TAGTTTCTTC
*
237063 AAAAAATTTCGAA
1 AAAAAAATTCGAA
237076 AAAAAAATT-GAA
1 AAAAAAATTCGAA
237088 AAAAAAATT
1 AAAAAAATT
237097 TGGTTTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:237154 original size:15 final size:15
Alignment explanation
Indices: 237134--237189 Score: 94
Period size: 15 Copynumber: 3.6 Consensus size: 15
237124 GATATCAAGT
237134 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
237149 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
237164 TGAAAAAAAAAATTTCG
1 TG-AAAAAAAAA-TTCG
237181 TGAAAAAAA
1 TGAAAAAAA
237190 GAAGAAGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 17 0.44
16 16 0.41
17 6 0.15
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:237158 original size:17 final size:17
Alignment explanation
Indices: 237136--237189 Score: 85
Period size: 17 Copynumber: 3.3 Consensus size: 17
237126 TATCAAGTTG
237136 AAAAAAAAATTCGTG--
1 AAAAAAAAATTCGTGAA
237151 AAAAAAAAATTCGTGAA
1 AAAAAAAAATTCGTGAA
*
237168 AAAAAAAATTTCGTGAA
1 AAAAAAAAATTCGTGAA
237185 AAAAA
1 AAAAA
237190 GAAGAAGAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
15 15 0.42
17 21 0.58
ACGTcount: A:0.65, C:0.06, G:0.11, T:0.19
Consensus pattern (17 bp):
AAAAAAAAATTCGTGAA
Found at i:243903 original size:13 final size:13
Alignment explanation
Indices: 243887--243921 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
243877 TTTAAACAAA
*
243887 TTAATTAACTTAT
1 TTAATTAACTAAT
243900 TTAATTAACTAAT
1 TTAATTAACTAAT
*
243913 TTAACTAAC
1 TTAATTAAC
243922 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:245573 original size:10 final size:10
Alignment explanation
Indices: 245558--245619 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
245548 TTTGAACCAT
245558 TACCAATTCG
1 TACCAATTCG
*
245568 TACCAAATACCG
1 TACC-AAT-TCG
* *
245580 TACCATTTCA
1 TACCAATTCG
*
245590 TACCAATTCCA
1 TACCAATT-CG
*
245601 TACCATTTCG
1 TACCAATTCG
245611 TACCAATTC
1 TACCAATTC
245620 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 21 0.51
11 14 0.34
12 6 0.15
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (10 bp):
TACCAATTCG
Found at i:245606 original size:21 final size:21
Alignment explanation
Indices: 245580--245620 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
245570 CCAAATACCG
245580 TACCATTTCATACCAATTCCA
1 TACCATTTCATACCAATTCCA
*
245601 TACCATTTCGTACCAATTCC
1 TACCATTTCATACCAATTCC
245621 CAAATACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.02, T:0.34
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:253021 original size:10 final size:10
Alignment explanation
Indices: 253006--253067 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
252996 TTTGAACCAT
*
253006 TACCAATTCG
1 TACCAATTCA
*
253016 TACCAAATACCA
1 TACC-AAT-TCA
*
253028 TACCATTTCA
1 TACCAATTCA
253038 TACCAATTCCA
1 TACCAATT-CA
* *
253049 TACCATTTCG
1 TACCAATTCA
253059 TACCAATTC
1 TACCAATTC
253068 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:253051 original size:21 final size:21
Alignment explanation
Indices: 253006--253068 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
252996 TTTGAACCAT
* *
253006 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
253028 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
253049 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
253069 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:258872 original size:21 final size:22
Alignment explanation
Indices: 258839--258881 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
258829 ACTCATTAAT
258839 AGCTGGATCACTTAGT-CATTA
1 AGCTGGATCACTTAGTCCATTA
* * *
258860 AGCTGGTTTACTTTGTCCATTA
1 AGCTGGATCACTTAGTCCATTA
258882 GGCTATCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (22 bp):
AGCTGGATCACTTAGTCCATTA
Found at i:260537 original size:18 final size:18
Alignment explanation
Indices: 260514--260553 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
260504 AAATCAAAAG
* *
260514 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCGA
260532 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
260550 AAAA
1 AAAA
260554 AGAGAGTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:262383 original size:21 final size:21
Alignment explanation
Indices: 262357--262419 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
262347 TTGGTATTTG
*
262357 GGAATTGGTACAAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
262378 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
262399 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
262420 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:264078 original size:13 final size:13
Alignment explanation
Indices: 264057--264091 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
264047 ATAAGTTGCT
* *
264057 GTTAGTTAAATTA
1 GTTAATTAAATAA
264070 GTTAATTAAATAA
1 GTTAATTAAATAA
264083 GTTAATTAA
1 GTTAATTAA
264092 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:265685 original size:157 final size:157
Alignment explanation
Indices: 265399--265712 Score: 601
Period size: 157 Copynumber: 2.0 Consensus size: 157
265389 AAGCTATGTG
265399 GAACGAGCTTGGGAAGAGGGAGTGGCCGAATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
1 GAACGAGCTTGGGAAGAGGGAGTGGCCGAATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
265464 TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
66 TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
265529 GTTACTGATCAATTAATTTAACTTATC
131 GTTACTGATCAATTAATTTAACTTATC
* *
265556 GAACGAGCTTGGGAAGAGGGAGTGGCTGGATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
1 GAACGAGCTTGGGAAGAGGGAGTGGCCGAATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
265621 TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
66 TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
*
265686 GTTGCTGATCAATTAATTTAACTTATC
131 GTTACTGATCAATTAATTTAACTTATC
265713 TTAAAGTTTT
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (157 bp):
GAACGAGCTTGGGAAGAGGGAGTGGCCGAATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
GTTACTGATCAATTAATTTAACTTATC
Found at i:266973 original size:9 final size:10
Alignment explanation
Indices: 266945--266996 Score: 77
Period size: 10 Copynumber: 5.0 Consensus size: 10
266935 TAGTAGTTTC
266945 TTCAAAAAAA
1 TTCAAAAAAA
266955 TTTCAAAAAAAA
1 -TTC-AAAAAAA
*
266967 ATCAAAAAAA
1 TTCAAAAAAA
266977 TTCAAAAAAA
1 TTCAAAAAAA
266987 TTCAAAAAAA
1 TTCAAAAAAA
266997 AAATTGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
10 26 0.68
11 5 0.13
12 7 0.18
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:267059 original size:15 final size:15
Alignment explanation
Indices: 267039--267089 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
267029 TATCAAGTTG
267039 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
267054 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
*
267069 AAAAAAATTTCGTGA
1 AAAAAAAATTCGTGA
267084 AAAAAA
1 AAAAAA
267090 GAAGAAGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.63, C:0.06, G:0.12, T:0.20
Consensus pattern (15 bp):
AAAAAAAATTCGTGA
Found at i:272353 original size:157 final size:157
Alignment explanation
Indices: 272067--272380 Score: 601
Period size: 157 Copynumber: 2.0 Consensus size: 157
272057 AAGCTATGTG
272067 GAACGAGCTTGGGAAGAGGGAGTGGCCAGATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
1 GAACGAGCTTGGGAAGAGGGAGTGGCCAGATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
272132 TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
66 TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
272197 GTTGCTGATCAATTAATTTAACTTATC
131 GTTGCTGATCAATTAATTTAACTTATC
* * *
272224 GAACGAGCTTGGGAAGAGGGAGTGGCCGGATTTGATAGTCGTGCTTCGAACTGTTCAAAAGGCGT
1 GAACGAGCTTGGGAAGAGGGAGTGGCCAGATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
272289 TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
66 TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
272354 GTTGCTGATCAATTAATTTAACTTATC
131 GTTGCTGATCAATTAATTTAACTTATC
272381 TTAAAGTTTT
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (157 bp):
GAACGAGCTTGGGAAGAGGGAGTGGCCAGATTTGATAGTCGTGCTTCAAACCGTTCAAAAGGCGT
TACTTGCAATTTATTGCAAGCTGAATTAGTTTCTTTTAATTAACTTGTTTTAGTTTAATAAATAA
GTTGCTGATCAATTAATTTAACTTATC
Found at i:273656 original size:18 final size:17
Alignment explanation
Indices: 273633--273678 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
273623 GACTTTTCAC
273633 TTTTTTTTT-TAACTTT
1 TTTTTTTTTCTAACTTT
*
273649 ATTTTTTTTTCTCACTTT
1 -TTTTTTTTTCTAACTTT
273667 TTTTTTCTTTCT
1 TTTTTT-TTTCT
273679 TTTTTTTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTTTCTAACTTT
Found at i:273667 original size:14 final size:14
Alignment explanation
Indices: 273650--273699 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
273640 TTTAACTTTA
273650 TTTTTTTTTCTCAC
1 TTTTTTTTTCTCAC
**
273664 TTTTTTTTTCTTTC
1 TTTTTTTTTCTCAC
273678 TTTTTTTTTGCTCGA-
1 TTTTTTTTT-CTC-AC
273693 TTTTTTT
1 TTTTTTT
273700 CACTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 21 0.70
15 9 0.30
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (14 bp):
TTTTTTTTTCTCAC
Found at i:273668 original size:15 final size:15
Alignment explanation
Indices: 273650--273699 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
273640 TTTAACTTTA
273650 TTTTTTTTTCTCAC-
1 TTTTTTTTTCTCACT
**
273664 TTTTTTTTTCTTTCT
1 TTTTTTTTTCTCACT
*
273679 TTTTTTTTGCTCGA-T
1 TTTTTTTTTCTC-ACT
273694 TTTTTT
1 TTTTTT
273700 CACTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (15 bp):
TTTTTTTTTCTCACT
Found at i:273705 original size:29 final size:27
Alignment explanation
Indices: 273636--273711 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
273626 TTTTCACTTT
273636 TTTTTTTAACTTTATTTTTTTTTCTCAC
1 TTTTTTTAACTTT-TTTTTTTTTCTCAC
**
273664 TTTTTTTTTCTTTCTTTTTTTTTGCTCGA-
1 TTTTTTTAACTTT-TTTTTTTTT-CTC-AC
*
273693 TTTTTTTCACTTTTTTTTT
1 TTTTTTTAACTTTTTTTTT
273712 GAATTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 26 0.63
29 14 0.34
30 1 0.02
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76
Consensus pattern (27 bp):
TTTTTTTAACTTTTTTTTTTTTCTCAC
Found at i:275250 original size:20 final size:20
Alignment explanation
Indices: 275227--275273 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
275217 GGGTTAAGAT
*
275227 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
275247 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
275267 TGAGCTG
1 TGAGCTG
275274 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:282882 original size:20 final size:20
Alignment explanation
Indices: 282836--282882 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
282826 AGCTTGTTTC
*
282836 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
282856 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
282876 CAGCTCA
1 CAGCTCA
282883 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:283702 original size:21 final size:23
Alignment explanation
Indices: 283657--283703 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
283647 TCACCTGCAA
* *
283657 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
283680 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
283701 TAA
1 TAA
283704 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:289049 original size:14 final size:15
Alignment explanation
Indices: 289017--289055 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
289007 AACTAGCTTC
289017 TTTTTTTCACGAAAAT
1 TTTTTTTCACG-AAAT
*
289033 TTTTTTTCACG-ATT
1 TTTTTTTCACGAAAT
289047 TTTTTTTCA
1 TTTTTTTCA
289056 ACTTGATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
16 11 0.50
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:289112 original size:10 final size:10
Alignment explanation
Indices: 289097--289133 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
289087 AAACCAAATT
289097 TTTTTTTGAA
1 TTTTTTTGAA
*
289107 TTTTTTTGAT
1 TTTTTTTGAA
289117 TTTTTTTGAA
1 TTTTTTTGAA
289127 TTTTTTT
1 TTTTTTT
289134 TCGAGAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:289121 original size:20 final size:20
Alignment explanation
Indices: 289096--289133 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
289086 GAAACCAAAT
289096 TTTTTTTTGAATTTTTTTGA
1 TTTTTTTTGAATTTTTTTGA
289116 TTTTTTTTGAATTTTTTT
1 TTTTTTTTGAATTTTTTT
289134 TCGAGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTTTTTGAATTTTTTTGA
Found at i:290171 original size:21 final size:23
Alignment explanation
Indices: 290126--290172 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
290116 TCACCTGCAA
* *
290126 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
290149 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
290170 TAA
1 TAA
290173 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:290566 original size:157 final size:157
Alignment explanation
Indices: 290371--290684 Score: 556
Period size: 157 Copynumber: 2.0 Consensus size: 157
290361 AAAACTTTAA
* *
290371 GATAAGTTAAATTAATTGATCAGTAACTTATTTATTAAATTAAAACAAGTTAACTAAAAGAAACA
1 GATAAGTTAAATTAATTGATCAGCAACTTATTTATTAAACTAAAACAAGTTAACTAAAAGAAACA
*
290436 AATTCAGCTTGCAATAAATTGCAAGTAATGCCTTTTGAACGGTTTGAAGCACGACTATCAAATCC
66 AATTCAGCTTGCAATAAATTGCAAGTAACGCCTTTTGAACGGTTTGAAGCACGACTATCAAATCC
* *
290501 GGCCATTCCCTCTTCCCAAGCTCGTTC
131 GGCCACTCCCTCTTCCCAAGATCGTTC
* * *
290528 GATAAGTTAAATTAATTGATCAGCAACTTATTTATTAAACTAAAACAATTTAATTAAAAGAAACT
1 GATAAGTTAAATTAATTGATCAGCAACTTATTTATTAAACTAAAACAAGTTAACTAAAAGAAACA
290593 AATTCAGCTTGCAATAAATTGCAAGTAACGCCTTTTGAACGGTTTGAAGCACGACTATCAAATCC
66 AATTCAGCTTGCAATAAATTGCAAGTAACGCCTTTTGAACGGTTTGAAGCACGACTATCAAATCC
290658 GGCCACTCCCTCTTCCCAAGATCGTTC
131 GGCCACTCCCTCTTCCCAAGATCGTTC
290685 CACATAGCTT
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 149 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (157 bp):
GATAAGTTAAATTAATTGATCAGCAACTTATTTATTAAACTAAAACAAGTTAACTAAAAGAAACA
AATTCAGCTTGCAATAAATTGCAAGTAACGCCTTTTGAACGGTTTGAAGCACGACTATCAAATCC
GGCCACTCCCTCTTCCCAAGATCGTTC
Found at i:298881 original size:48 final size:48
Alignment explanation
Indices: 298780--298885 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
298770 GAGTGTCATG
* *
298780 GAAAAAGAAATTGAGATTGGAAAAGGATGTGAAAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAAAAAGAGAAAGAAATC
* * *
298828 AAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAA-AGAGA-AAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA--AAAAGAGAAAGAAATC
298876 GAAAAAGAAA
1 GAAAAAGAAA
298886 GAAAAGACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 37 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (48 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAAAAAGAGAAAGAAATC
Found at i:300113 original size:20 final size:20
Alignment explanation
Indices: 300067--300113 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
300057 AGCTTGTTTC
*
300067 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
300087 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
300107 CAGCTCA
1 CAGCTCA
300114 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:304223 original size:16 final size:16
Alignment explanation
Indices: 304191--304224 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
304181 AAACACTCAA
**
304191 CACTCAAAAAGTTAAT
1 CACTCAAAAAGAAAAT
304207 CACTCAAAAAGAAAAT
1 CACTCAAAAAGAAAAT
304223 CA
1 CA
304225 AATTCTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.21, G:0.06, T:0.18
Consensus pattern (16 bp):
CACTCAAAAAGAAAAT
Found at i:310201 original size:45 final size:46
Alignment explanation
Indices: 310123--310234 Score: 163
Period size: 46 Copynumber: 2.4 Consensus size: 46
310113 GCTGTAAACA
* *
310123 AGACAAATTAAATTAGTTTAAGACAACTTAAATT-CTGTAATAATTT
1 AGACAAATTAAATGA-CTTAAGACAACTTAAATTGCTGTAATAATTT
* * *
310169 AGACAAATTAAATGACTTAGGACAACTTAAATTGTTGTAGTAATTT
1 AGACAAATTAAATGACTTAAGACAACTTAAATTGCTGTAATAATTT
310215 AGACAAATTAAATGACTTAA
1 AGACAAATTAAATGACTTAA
310235 CTTATTAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 16 0.27
46 43 0.73
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.34
Consensus pattern (46 bp):
AGACAAATTAAATGACTTAAGACAACTTAAATTGCTGTAATAATTT
Found at i:315040 original size:1 final size:1
Alignment explanation
Indices: 315036--315083 Score: 96
Period size: 1 Copynumber: 48.0 Consensus size: 1
315026 AAATAAAATT
315036 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
315084 CGGGGTATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.