Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015113.1 Kokia drynarioides strain JFW-HI SEQ_130157, whole genome shotgun sequence
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: 106898
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 231 characters in sequence are not A, C, G, or T
Found at i:6927 original size:38 final size:38
Alignment explanation
Indices: 6883--6961 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
6873 AGGAAGTATG
6883 AATTATTTCCTTTTGTCTTTATGTAGAAGAGAGTATCT
1 AATTATTTCCTTTTGTCTTTATGTAGAAGAGAGTATCT
6921 AATTATTTCCTTTTGTCTTTATGTAGAAGAGAGTATCT
1 AATTATTTCCTTTTGTCTTTATGTAGAAGAGAGTATCT
6959 AAT
1 AAT
6962 AGAATCAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (38 bp):
AATTATTTCCTTTTGTCTTTATGTAGAAGAGAGTATCT
Found at i:22981 original size:64 final size:65
Alignment explanation
Indices: 22880--23008 Score: 224
Period size: 64 Copynumber: 2.0 Consensus size: 65
22870 ACTGCACTCA
22880 ATCTAAAAGAAAAGAGTTATATTTCTGTAAATTCAAAATACAATTCAC-ATTTTTCTTAGAAAAT
1 ATCTAAAAGAAAAGAGTTATATTTCTGTAAATTCAAAATACAATTCACAATTTTTCTTAGAAAAT
* * *
22944 ATCTAAAAGAAAAGCGTTATGTTTCTTTAAATTCAAAATACAATTCACAATTTTTCTTAGAAAAT
1 ATCTAAAAGAAAAGAGTTATATTTCTGTAAATTCAAAATACAATTCACAATTTTTCTTAGAAAAT
23009 CGCAAACCTG
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 45 0.74
65 16 0.26
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (65 bp):
ATCTAAAAGAAAAGAGTTATATTTCTGTAAATTCAAAATACAATTCACAATTTTTCTTAGAAAAT
Found at i:28690 original size:18 final size:19
Alignment explanation
Indices: 28653--28692 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28643 GCACGAAGCA
*
28653 CATCTTAGCGCATAAAGTG
1 CATCCTAGCGCATAAAGTG
28672 CATCCTAGCGCAT-AAGTG
1 CATCCTAGCGCATAAAGTG
28690 CAT
1 CAT
28693 AAACCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (19 bp):
CATCCTAGCGCATAAAGTG
Found at i:30274 original size:6 final size:6
Alignment explanation
Indices: 30263--30291 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30253 CAAAGAAGAA
30263 TAATAG TAATAG TAATAG TAATAG TAATA
1 TAATAG TAATAG TAATAG TAATAG TAATA
30292 AAATCGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
TAATAG
Found at i:44638 original size:21 final size:20
Alignment explanation
Indices: 44596--44640 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44586 GGAAAAACTT
*
44596 AAATTAATTCTTAAAAATTA
1 AAATTAATTCTTAAAAAGTA
*
44616 AAATTAATTTTTAAAAAGGTA
1 AAATTAATTCTTAAAAA-GTA
44637 AAAT
1 AAAT
44641 GAGTGATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AAATTAATTCTTAAAAAGTA
Found at i:50363 original size:16 final size:16
Alignment explanation
Indices: 50342--50372 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50332 TCAACCACTT
50342 TTTTTATTTAATATTA
1 TTTTTATTTAATATTA
*
50358 TTTTTATTTTATATT
1 TTTTTATTTAATATT
50373 TAATTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATTTAATATTA
Found at i:50755 original size:27 final size:28
Alignment explanation
Indices: 50713--50778 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
50703 TAAAATCCCC
*
50713 AACCCTAAACCCAAAATATAAAACAC-TA
1 AACCC-AAACCCAAAACATAAAACACTTA
* * *
50741 AATCCAAACCCAAAACCTTAAACACTTA
1 AACCCAAACCCAAAACATAAAACACTTA
50769 AACCCAAACC
1 AACCCAAACC
50779 TTAAATCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (28 bp):
AACCCAAACCCAAAACATAAAACACTTA
Found at i:52704 original size:13 final size:11
Alignment explanation
Indices: 52676--52718 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
52666 AGTTAAATAT
52676 TATTTTATTAA
1 TATTTTATTAA
52687 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
52700 TA-TTTATTAT
1 TATTTTATTAA
52710 TATTTTATT
1 TATTTTATT
52719 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:52705 original size:23 final size:23
Alignment explanation
Indices: 52679--52722 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
52669 TAAATATTAT
52679 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
52702 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
52723 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:58243 original size:21 final size:21
Alignment explanation
Indices: 58218--58281 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
58208 AGTTATCTCA
58218 AATAATATAAAATATTATATT
1 AATAATATAAAATATTATATT
* * *
58239 AATAATATTAAAAGTAATAAATA
1 AATAATA-TAAAA-TATTATATT
58262 AATAAT-TAAAA-ATTAATATT
1 AATAATATAAAATATT-ATATT
58282 TATTTTCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 12 0.35
22 5 0.15
23 12 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AATAATATAAAATATTATATT
Found at i:64683 original size:17 final size:18
Alignment explanation
Indices: 64661--64697 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
64651 GAGTAGGACC
*
64661 AGTTGCC-TATTAGCTTG
1 AGTTGCCGTATGAGCTTG
64678 AGTTGCCGTATGAGCTTG
1 AGTTGCCGTATGAGCTTG
64696 AG
1 AG
64698 CGGATTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (18 bp):
AGTTGCCGTATGAGCTTG
Found at i:65934 original size:7 final size:7
Alignment explanation
Indices: 65918--66045 Score: 101
Period size: 7 Copynumber: 19.0 Consensus size: 7
65908 AACCGAACTC
65918 GTTGACT
1 GTTGACT
*
65925 GTTGATT
1 GTTGACT
65932 GTTGACT
1 GTTGACT
65939 -TTGA-T
1 GTTGACT
65944 CGTTGACT
1 -GTTGACT
* *
65952 GGTGACC
1 GTTGACT
65959 GTTGACT
1 GTTGACT
65966 -TTGACT
1 GTTGACT
65972 GTTGACT
1 GTTGACT
*
65979 ATTGACT
1 GTTGACT
*
65986 GTTAACT
1 GTTGACT
*
65993 -TTGACC
1 GTTGACT
65999 GTTGACT
1 GTTGACT
*
66006 -TTGATT
1 GTTGACT
66012 GTTGA-T
1 GTTGACT
66018 CGTTGACT
1 -GTTGACT
66026 -TTGACCT
1 GTTGA-CT
66033 -TTGACT
1 GTTGACT
*
66039 ATTGACT
1 GTTGACT
66046 TTTTTGAGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
5 1 0.01
6 26 0.27
7 69 0.70
8 2 0.02
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (7 bp):
GTTGACT
Found at i:65962 original size:27 final size:27
Alignment explanation
Indices: 65916--66047 Score: 119
Period size: 27 Copynumber: 4.9 Consensus size: 27
65906 CAAACCGAAC
*
65916 TCGTTGACTGTTGATTGTTGACTTTGA
1 TCGTTGACTGTTGACTGTTGACTTTGA
* *
65943 TCGTTGACTGGTGACCGTTGACTTTGA
1 TCGTTGACTGTTGACTGTTGACTTTGA
* *
65970 -CTGTTGACTATTGACTGTTAACTTTGA
1 TC-GTTGACTGTTGACTGTTGACTTTGA
* * *
65997 CCGTTGACT-TTGATTGTTGATCGTTGA
1 TCGTTGACTGTTGACTGTTGA-CTTTGA
* *
66024 -CTTTGACCT-TTGACTATTGACTTT
1 TCGTTGA-CTGTTGACTGTTGACTTT
66048 TTTGAGAAAC
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
26 18 0.21
27 68 0.78
28 1 0.01
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.45
Consensus pattern (27 bp):
TCGTTGACTGTTGACTGTTGACTTTGA
Found at i:65969 original size:20 final size:20
Alignment explanation
Indices: 65917--66030 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
65907 AAACCGAACT
*
65917 CGTTGACTGTTGATTGTTGA-
1 CGTTGACT-TTGACTGTTGAC
* * *
65937 CTTTGATCGTTGACTGGTGAC
1 CGTTGA-CTTTGACTGTTGAC
65958 CGTTGACTTTGACTGTTGAC
1 CGTTGACTTTGACTGTTGAC
** *
65978 TATTGACTGTTAACT-TTGAC
1 CGTTGACT-TTGACTGTTGAC
* *
65998 CGTTGACTTTGATTGTTGAT
1 CGTTGACTTTGACTGTTGAC
66018 CGTTGACTTTGAC
1 CGTTGACTTTGAC
66031 CTTTGACTAT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
19 4 0.05
20 59 0.80
21 11 0.15
ACGTcount: A:0.17, C:0.16, G:0.25, T:0.43
Consensus pattern (20 bp):
CGTTGACTTTGACTGTTGAC
Found at i:66036 original size:20 final size:19
Alignment explanation
Indices: 65954--66047 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 19
65944 CGTTGACTGG
65954 TGACCGTTGACTTTGACTGT
1 TGACCGTTGACTTTGACT-T
** *
65974 TGACTATTGACTGTTAACTT
1 TGACCGTTGACT-TTGACTT
*
65994 TGACCGTTGACTTTGATTGT
1 TGACCGTTGACTTTGACT-T
*
66014 TGATCGTTGACTTTGACCTT
1 TGACCGTTGACTTTGA-CTT
**
66034 TGACTATTGACTTT
1 TGACCGTTGACTTT
66048 TTTGAGAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
19 4 0.07
20 49 0.83
21 6 0.10
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (19 bp):
TGACCGTTGACTTTGACTT
Found at i:67211 original size:23 final size:22
Alignment explanation
Indices: 67158--67212 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
67148 TTGTAAATAC
* *
67158 ATTTTGTTTTGGGGATTTTGAT
1 ATTTTATTTTGGGGATTTAGAT
67180 ATTTTATTTTGGGAGATTTAG-T
1 ATTTTATTTTGGG-GATTTAGAT
67202 ATTTTAATTTT
1 ATTTT-ATTTT
67213 ATTAGAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (22 bp):
ATTTTATTTTGGGGATTTAGAT
Found at i:73077 original size:20 final size:20
Alignment explanation
Indices: 73052--73149 Score: 99
Period size: 20 Copynumber: 4.9 Consensus size: 20
73042 CTAATCGAAC
73052 CCGTTGATCGTTAACTTTGA
1 CCGTTGATCGTTAACTTTGA
*
73072 CCGTTGATCGTTGACTTTGA
1 CCGTTGATCGTTAACTTTGA
* * *
73092 CCATTGATCATTGACTTTGA
1 CCGTTGATCGTTAACTTTGA
* * * *
73112 CTGTTGATCATTGATCGTTGA
1 CCGTTGATCGTT-AACTTTGA
*
73133 -CTTTGATCGTTAACTTT
1 CCGTTGATCGTTAACTTT
73150 TCTGAGAAAC
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.06
20 55 0.86
21 5 0.08
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.43
Consensus pattern (20 bp):
CCGTTGATCGTTAACTTTGA
Found at i:73098 original size:27 final size:27
Alignment explanation
Indices: 73068--73138 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
73058 ATCGTTAACT
*
73068 TTGACCGTTGATCGTTGACT-TTGACCA
1 TTGATCGTTGA-CGTTGACTGTTGACCA
* * *
73095 TTGATCATTGACTTTGACTGTTGATCA
1 TTGATCGTTGACGTTGACTGTTGACCA
*
73122 TTGATCGTTGACTTTGA
1 TTGATCGTTGACGTTGA
73139 TCGTTAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 7 0.18
27 31 0.82
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (27 bp):
TTGATCGTTGACGTTGACTGTTGACCA
Found at i:73099 original size:40 final size:40
Alignment explanation
Indices: 73055--73149 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
73045 ATCGAACCCG
* *
73055 TTGATCGTTAACTTTGACCGTTGATCGTTGA-CTTTGACCA
1 TTGATCGTTAACTTTGACCGTTGATCATTGATCGTTGA-CA
* * * *
73095 TTGATCATTGACTTTGACTGTTGATCATTGATCGTTGACT
1 TTGATCGTTAACTTTGACCGTTGATCATTGATCGTTGACA
73135 TTGATCGTTAACTTT
1 TTGATCGTTAACTTT
73150 TCTGAGAAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 41 0.89
41 5 0.11
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (40 bp):
TTGATCGTTAACTTTGACCGTTGATCATTGATCGTTGACA
Found at i:73539 original size:7 final size:7
Alignment explanation
Indices: 73529--73615 Score: 59
Period size: 7 Copynumber: 12.3 Consensus size: 7
73519 CTAAACCCAT
73529 AACCTTA
1 AACCTTA
* *
73536 AACCCTC
1 AACCTTA
73543 AACC-TA
1 AACCTTA
*
73549 AAACTCTA
1 AACCT-TA
*
73557 TACCTTA
1 AACCTTA
* *
73564 AAGCATA
1 AACCTTA
*
73571 AACCATA
1 AACCTTA
*
73578 AACCATA
1 AACCTTA
*
73585 AACCATA
1 AACCTTA
*
73592 AACTTTA
1 AACCTTA
73599 AATCCTTA
1 AA-CCTTA
73607 AACCTTA
1 AACCTTA
73614 AA
1 AA
73616 ATTAAAGCCC
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
6 4 0.06
7 49 0.77
8 11 0.17
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (7 bp):
AACCTTA
Found at i:73678 original size:68 final size:68
Alignment explanation
Indices: 73596--73834 Score: 285
Period size: 68 Copynumber: 3.6 Consensus size: 68
73586 ACCATAAACT
* * * *
73596 TTAAATCCTT-AAACCTTAAAATTAAAGCCCTTAAAAATCATAAAACGCTAAACTCATTAATTTA
1 TTAAATCCTTAAAACCTTAAAATCAAAACCCTTAAAAATCATAAAAC-CTAAACTCATCACTTTA
*
73660 AACC
65 AATC
* *
73664 CTAAA-CCTTAAAACCTTAAAATCAAAACCCTTAAAAATC-TAAAACC--AACTCATCACTTTGA
1 TTAAATCCTTAAAACCTTAAAATCAAAACCCTTAAAAATCATAAAACCTAAACTCATCACTTTAA
73725 ATC
66 ATC
* * * *
73728 TTAAATCCTTAAAACCCTAAAATCAAAACCTTTAAAAAT-ATAATACCCTAAACTAATCACTTTA
1 TTAAATCCTTAAAACCTTAAAATCAAAACCCTTAAAAATCATAA-AACCTAAACTCATCACTTTA
73792 AATC
65 AATC
* *
73796 TTAAATCCATAAAA-CTCTAAACTCAAAACCCTTAAAAAT
1 TTAAATCCTTAAAACCT-TAAAATCAAAACCCTTAAAAAT
73835 ATGATATTAT
Statistics
Matches: 147, Mismatches: 17, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
64 18 0.12
65 34 0.23
66 4 0.03
67 11 0.07
68 80 0.54
ACGTcount: A:0.48, C:0.23, G:0.01, T:0.28
Consensus pattern (68 bp):
TTAAATCCTTAAAACCTTAAAATCAAAACCCTTAAAAATCATAAAACCTAAACTCATCACTTTAA
ATC
Found at i:73695 original size:15 final size:17
Alignment explanation
Indices: 73672--73709 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
73662 CCCTAAACCT
73672 TAAAA-CCTT-AAAATC
1 TAAAACCCTTAAAAATC
73687 -AAAACCCTTAAAAATC
1 TAAAACCCTTAAAAATC
73703 TAAAACC
1 TAAAACC
73710 AACTCATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 4 0.20
16 6 0.30
17 6 0.30
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAACCCTTAAAAATC
Found at i:73793 original size:132 final size:133
Alignment explanation
Indices: 73596--73834 Score: 322
Period size: 133 Copynumber: 1.8 Consensus size: 133
73586 ACCATAAACT
* * * * * *
73596 TTAAATCCTTAAACCTTAAAATTAAAGCCCTTAAAAATCATAAAACGCTAAACTCATTAATTTAA
1 TTAAATCCTTAAACCCTAAAATCAAAACCCTTAAAAATCATAAAACCCTAAACTAATCAATTTAA
*
73661 ACCCTAAA-CCTTAAAAC-CTTAAAATCAAAACCCTTAAAAATCTAAAACCAACTCATCACTTTG
66 ACCCTAAATCCATAAAACTC-TAAAATCAAAACCCTTAAAAATCTAAAACCAACTCATCACTTTG
73724 AATC
130 AATC
* * *
73728 TTAAATCCTTAAAACCCTAAAATCAAAACCTTTAAAAAT-ATAATACCCTAAACTAATCACTTTA
1 TTAAATCCTT-AAACCCTAAAATCAAAACCCTTAAAAATCATAAAACCCTAAACTAATCAATTTA
* * *
73792 AATCTTAAATCCATAAAACTCTAAACTCAAAACCCTTAAAAAT
65 AACCCTAAATCCATAAAACTCTAAAATCAAAACCCTTAAAAAT
73835 ATGATATTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
132 37 0.41
133 53 0.58
134 1 0.01
ACGTcount: A:0.48, C:0.23, G:0.01, T:0.28
Consensus pattern (133 bp):
TTAAATCCTTAAACCCTAAAATCAAAACCCTTAAAAATCATAAAACCCTAAACTAATCAATTTAA
ACCCTAAATCCATAAAACTCTAAAATCAAAACCCTTAAAAATCTAAAACCAACTCATCACTTTGA
ATC
Found at i:78296 original size:18 final size:18
Alignment explanation
Indices: 78273--78309 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
78263 TTTGTGATCA
78273 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
78291 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
78309 A
1 A
78310 TATGAATTGT
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:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:78298 original size:12 final size:12
Alignment explanation
Indices: 78273--78309 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
78263 TTTGTGATCA
78273 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
78285 AAAGTGAAATTG
1 AAATTGAAAGTG
78297 AAATTGAAAGTG
1 AAATTGAAAGTG
78309 A
1 A
78310 TATGAATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:80383 original size:52 final size:52
Alignment explanation
Indices: 80274--80551 Score: 319
Period size: 52 Copynumber: 5.4 Consensus size: 52
80264 TTCATTTAAA
* * ** * * *
80274 ACTCACGATGACA--TAGTTATCGGACCTCTTGTTTCGTAAAGAAATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCATAAAG-GATTCATAT
* * * *
80325 ACTCACGATGACACTTAATCATCAGACCTCACAATCCATATAGGATTCAGT-T
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCATAAAGGATTCA-TAT
* * *
80377 ACTCACGCTAACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
* * ***
80429 ACTCAAGAAGACACTTAGTCATCGGACCTCATAATCTGCAAAGGATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
* * *
80481 ACTCACGATGACACTTAGTCATCGGACCTAATAATCCGTAAAAGATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
80533 ACTCACGATGACACTTAGT
1 ACTCACGATGACACTTAGT
80552 TTCATTTACG
Statistics
Matches: 193, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
51 14 0.07
52 160 0.83
53 19 0.10
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
ACTCACGATGACACTTAGTCATCGGACCTCATAATCCATAAAGGATTCATAT
Found at i:83018 original size:56 final size:58
Alignment explanation
Indices: 82943--83129 Score: 154
Period size: 57 Copynumber: 3.2 Consensus size: 58
82933 AGTTTGGGGT
* *
82943 TAAAACGTAATTTTAGAAAGATTTAATGGT-AAAATGT-AATTTTGGGAAAGTTC-AGGG
1 TAAAACGTAATTTTAGAAAGATTTAAGGGTAAAAATGTCAA-TTTGAGAAAGTTCGA-GG
* * *
83000 TAAAA-GTAATTTTGGAAAGTTTTAGGGGTAAAAATGTCAATTTGAGAAAGTTCGAGG
1 TAAAACGTAATTTTAGAAAGATTTAAGGGTAAAAATGTCAATTTGAGAAAGTTCGAGG
* * * * ***
83057 TAAAAATGTGATTTTTAG-AAG-TTTGAGGGTAAAAATGT-GATTTTTTAAAGTTCGAGGG
1 T-AAAACGT-AATTTTAGAAAGATTTAAGGGTAAAAATGTCAATTTGAGAAAGTTCGA-GG
*
83115 TAAAAATGTAATTTT
1 T-AAAACGTAATTTT
83130 TAAGAAGTTC
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
56 20 0.18
57 45 0.41
58 33 0.30
59 5 0.05
60 6 0.06
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
TAAAACGTAATTTTAGAAAGATTTAAGGGTAAAAATGTCAATTTGAGAAAGTTCGAGG
Found at i:83059 original size:29 final size:29
Alignment explanation
Indices: 82916--83249 Score: 226
Period size: 29 Copynumber: 11.6 Consensus size: 29
82906 AAAAGGGTCG
* * *
82916 AAAATG-AAGTTTTAGAGAGTTTG-GGGTT
1 AAAATGTAA-TTTTAGAAAGTTCGAGGGTA
* ** *
82944 AAAACGTAATTTTAGAAAGATTTAATGGT-
1 AAAATGTAATTTTAGAAAG-TTCGAGGGTA
*
82973 AAAATGTAATTTTGGGAAAGTTC-AGGGT-
1 AAAATGTAATTTT-AGAAAGTTCGAGGGTA
* **
83001 AAAA-GTAATTTTGGAAAGTTTTAGGGGTA
1 AAAATGTAATTTTAGAAAGTTCGA-GGGTA
*
83030 AAAATGTCAATTTGAGAAAGTTCGA-GGTA
1 AAAATGT-AATTTTAGAAAGTTCGAGGGTA
* *
83059 AAAATGTGATTTTTAG-AAGTTTGAGGGTA
1 AAAATGT-AATTTTAGAAAGTTCGAGGGTA
* **
83088 AAAATGTGATTTTTTAAAGTTCGAGGGTA
1 AAAATGTAATTTTAGAAAGTTCGAGGGTA
*
83117 AAAATGTAATTTTTA-AGAAGTTCGGGGGTA
1 AAAATGTAA-TTTTAGA-AAGTTCGAGGGTA
* * *
83147 AAAATATGATTTTTAG-AAGTTC-AGGGCA
1 AAAATGT-AATTTTAGAAAGTTCGAGGGTA
*
83175 AAAATGTAATTTTTAG-AAGTTCGGGGGT-
1 AAAATGTAA-TTTTAGAAAGTTCGAGGGTA
* * * * * *
83203 AAAATGTGATTTTTGGAAGTTTGAAGGTC
1 AAAATGTAATTTTAGAAAGTTCGAGGGTA
*
83232 AAAATGTGATTTTAGAAA
1 AAAATGTAATTTTAGAAA
83250 AGTTTAATGG
Statistics
Matches: 247, Mismatches: 40, Indels: 37
0.76 0.12 0.11
Matches are distributed among these distances:
26 8 0.03
27 15 0.06
28 76 0.31
29 97 0.39
30 37 0.15
31 14 0.06
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAGTTCGAGGGTA
Found at i:93870 original size:30 final size:30
Alignment explanation
Indices: 93834--94325 Score: 184
Period size: 30 Copynumber: 16.6 Consensus size: 30
93824 TACCCCCGAA
* *
93834 CTTCCAAAAATCTCATTTTTGACTTTAAAC
1 CTTCCAAAAATCCCATTTTTGACTCTAAAC
* **
93864 CTTCCAAAAATCCCATTTTTGACCCCGAAC
1 CTTCCAAAAATCCCATTTTTGACTCTAAAC
* *
93894 CTTCTAAAAATTACCATTTTT-ACTCCTAAA-
1 CTTCCAAAAA-TCCCATTTTTGACT-CTAAAC
*
93924 CTTCCAAAAATCCCATTTTTGAACTC-GAAC
1 CTTCCAAAAATCCCATTTTTG-ACTCTAAAC
* * * *
93954 CTTCTAAAAATTACCA-TTTT-ACCCCCAAA-
1 CTTCCAAAAA-TCCCATTTTTGA-CTCTAAAC
* **
93983 CTTCCAAAAATCCCATTTTTGACCCCGAAC
1 CTTCCAAAAATCCCATTTTTGACTCTAAAC
* * * **
94013 CTTCTAAAAATTACCA-TTTT-ACCCCCGAA-
1 CTTCCAAAAA-TCCCATTTTTGA-CTCTAAAC
**
94042 CTTCCAAAAATCCCATTTTTGACTCCGAAC
1 CTTCCAAAAATCCCATTTTTGACTCTAAAC
** * * * ***
94072 CTTTTAAAAATTACCA-TCTT-ACCCCCGGA-
1 CTTCCAAAAA-TCCCATTTTTGA-CTCTAAAC
**
94101 CTTCCAAAAATCCCATTTTTGAC-CCGAAC
1 CTTCCAAAAATCCCATTTTTGACTCTAAAC
* * * *
94130 CTTCTAAAAATTACCA-TTTT-ACCCTCGAA-
1 CTTCCAAAAA-TCCCATTTTTGACTCT-AAAC
*
94159 CTTCCAAAAATCCCATTTTTGAC-CTCGAAC
1 CTTCCAAAAATCCCATTTTTGACTCT-AAAC
* * * * *
94189 CTTTCTAAAATTACCA-TTTT-ACCCTCGAA-
1 C-TTCCAAAAATCCCATTTTTGACTCT-AAAC
* **
94218 CTTCCAAAAATCTCATTTTTGACTCCCAAC
1 CTTCCAAAAATCCCATTTTTGACTCTAAAC
* * * **
94248 CTTCTAAAAATTACCA-TTTT-ACCCCCGAA-
1 CTTCCAAAAA-TCCCATTTTTGA-CTCTAAAC
* **
94277 CTTCCAAAACTCCCATTTTTGACTCCGAAC
1 CTTCCAAAAATCCCATTTTTGACTCTAAAC
* *
94307 CTTCCAAAACTACCATTTT
1 CTTCCAAAAATCCCATTTT
94326 ACCCCCGTGC
Statistics
Matches: 364, Mismatches: 61, Indels: 74
0.73 0.12 0.15
Matches are distributed among these distances:
28 37 0.10
29 126 0.35
30 160 0.44
31 41 0.11
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.32
Consensus pattern (30 bp):
CTTCCAAAAATCCCATTTTTGACTCTAAAC
Found at i:94180 original size:176 final size:176
Alignment explanation
Indices: 93864--94331 Score: 733
Period size: 176 Copynumber: 2.6 Consensus size: 176
93854 GACTTTAAAC
* * **
93864 CTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTTACTCCTAAACTTCC
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCA-TTTTACCCCCGAACTTCC
*
93929 AAAAATCCCATTTTTGAACTCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAAT
65 AAAAATCCCATTTTTG-ACCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAAT
93994 CCCATTTTTGACCCCGAACC-TTCTAAAAATTACCATTTTACCCCCGAA
129 CCCATTTTTGACCCCGAACCTTTCT-AAAATTACCATTTTACCCCCGAA
* * *
94042 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTTTAAAAATTACCATCTTACCCCCGGACTTCCA
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCA
* *
94107 AAAATCCCATTTTTGACCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCC
66 AAAATCCCATTTTTGACCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCC
* *
94172 CATTTTTGACCTCGAACCTTTCTAAAATTACCATTTTACCCTCGAA
131 CATTTTTGACCCCGAACCTTTCTAAAATTACCATTTTACCCCCGAA
* *
94218 CTTCCAAAAATCTCATTTTTGACTCCCAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCA
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCA
* * *
94283 AAACTCCCATTTTTGACTCCGAACCTTC-CAAAACTACCATTTTACCCCC
66 AAAATCCCATTTTTGAC-CCGAACCTTCTAAAAATTACCATTTTACCCCC
94332 GTGCATCCGA
Statistics
Matches: 267, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
176 180 0.67
177 43 0.16
178 44 0.16
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.31
Consensus pattern (176 bp):
CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCA
AAAATCCCATTTTTGACCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCC
CATTTTTGACCCCGAACCTTTCTAAAATTACCATTTTACCCCCGAA
Found at i:94363 original size:59 final size:59
Alignment explanation
Indices: 93864--94332 Score: 723
Period size: 59 Copynumber: 8.0 Consensus size: 59
93854 GACTTTAAAC
* * **
93864 CTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTTACTCCTAAA
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCA-TTTTACCCCCGAA
*
93924 CTTCCAAAAATCCCATTTTTGAACT-CGAACCTTCTAAAAATTACCATTTTACCCCCAAA
1 CTTCCAAAAATCCCATTTTTG-ACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAA
*
93983 CTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAA
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAA
* * *
94042 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTTTAAAAATTACCATCTTACCCCCGGA
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAA
*
94101 CTTCCAAAAATCCCATTTTTGAC-CCGAACCTTCTAAAAATTACCATTTTACCCTCGAA
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAA
*
94159 CTTCCAAAAATCCCATTTTTGAC-CTCGAACCTTTCT-AAAATTACCATTTTACCCTCGAA
1 CTTCCAAAAATCCCATTTTTGACTC-CGAACC-TTCTAAAAATTACCATTTTACCCCCGAA
* *
94218 CTTCCAAAAATCTCATTTTTGACTCCCAACCTTCTAAAAATTACCATTTTACCCCCGAA
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAA
* * *
94277 CTTCCAAAACTCCCATTTTTGACTCCGAACCTTC-CAAAACTACCATTTTACCCCCG
1 CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCG
94333 TGCATCCGAA
Statistics
Matches: 382, Mismatches: 21, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
58 81 0.21
59 252 0.66
60 47 0.12
61 2 0.01
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (59 bp):
CTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAAAATTACCATTTTACCCCCGAA
Found at i:105435 original size:27 final size:26
Alignment explanation
Indices: 105404--105457 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
105394 TCAATTAAGG
*
105404 ATTGTTTCCTTTGATCCTCCTTTTAAT
1 ATTGTTTCCTTCGATCCT-CTTTTAAT
105431 ATTGTTTCCTTCGATCCTCTTTTAAT
1 ATTGTTTCCTTCGATCCTCTTTTAAT
105457 A
1 A
105458 GAATTCTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.17, C:0.22, G:0.07, T:0.54
Consensus pattern (26 bp):
ATTGTTTCCTTCGATCCTCTTTTAAT
Found at i:106303 original size:207 final size:205
Alignment explanation
Indices: 105939--106399 Score: 577
Period size: 207 Copynumber: 2.2 Consensus size: 205
105929 ATTATCCACA
* * * * * *
105939 AAACGGCGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAACCAAACCCATGCACGATG
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCACAAAG
** * * * *
106004 TGAGCAAGTCTTCGAATCCCAGCTTCCTGATGACACACCGAGAAGTAAATCGGAGCAATAAACGG
66 CAAACAAATCTTCGAACCCCAGCTTCCTGATGACACACCGAGAAGCAAATCGGAGCAATAAACGG
* * *
106069 TTAGCTTCCTGATGAGATACAGAGAAGT-AGACCAAATTCGTCTTCCTGATGAGATGCAGAGAAG
131 TCAGCTTCCTAATGAGATACAGAGAAGTGA-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
106133 CGGATTGAAAC
195 CGGATTGAAAC
* *
106144 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCGAACCCACGCTCAAAG
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCACAAAG
* * * **
106209 CAAACAAAATCTTCGAACCCTCAGCTTCCTGA-GAAGATACTGAGAAGCAGGT-GGAAGCAATAA
66 CAAAC-AAATCTTCGAACCC-CAGCTTCCTGATG-ACACACCGAGAAGCAAATCGG-AGCAATAA
* *
106272 ATGGTCAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
127 ACGGTCAGCTTCCTAATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
106337 AAGCGGATTGAAAC
192 AAGCGGATTGAAAC
* * * * * *
106351 AAGCGATGTGGTCATTTTCCTGATGAGACACTGAAAAGAAGACCCAAAT
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA-CCAAAT
106400 GAGACACTGA
Statistics
Matches: 220, Mismatches: 30, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
205 59 0.27
206 15 0.07
207 139 0.63
208 7 0.03
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (205 bp):
AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCACAAAG
CAAACAAATCTTCGAACCCCAGCTTCCTGATGACACACCGAGAAGCAAATCGGAGCAATAAACGG
TCAGCTTCCTAATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
GGATTGAAAC
Found at i:106548 original size:158 final size:157
Alignment explanation
Indices: 106247--106531 Score: 435
Period size: 158 Copynumber: 1.8 Consensus size: 157
106237 CTGAGAAGAT
106247 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTAATGAGATACTGAGAAGTGAACCAAA
1 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTAATGAGATACTGAGAAGTGAACCAAA
* * ** * *******
106312 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGA
66 TTCGTCTTCCCGATGAGATACAGAGAAGCGGATTGAAACAAGCGAAGACGTAAAGCAAAGGATGA
106377 GACACTGAAAAGAAGACCCAAATGAGAC
131 GACACTG-AAAGAAGACCCAAATGAGAC
*
106405 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGAACCAAA
1 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTAATGAGATACTGAGAAGTGAACCAAA
106470 TTCGTCTTCCCGATGAGATACAGAGAAGCGGATTGAAACAAGCGACAGACGTAAAGCAAAGG
66 TTCGTCTTCCCGATGAGATACAGAGAAGCGGATTGAAACAAGCGA-AGACGTAAAGCAAAGG
106532 GTGGACCAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
158 108 0.96
159 5 0.04
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (157 bp):
ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTAATGAGATACTGAGAAGTGAACCAAA
TTCGTCTTCCCGATGAGATACAGAGAAGCGGATTGAAACAAGCGAAGACGTAAAGCAAAGGATGA
GACACTGAAAGAAGACCCAAATGAGAC
Found at i:106701 original size:17 final size:17
Alignment explanation
Indices: 106679--106738 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
106669 CATACTCCCT
106679 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
106696 TTAAATTT-GTTTAAAA
1 TTAAATTTATTTTAAAA
* *
106712 TTTAAATTTATTTTCAAT
1 -TTAAATTTATTTTAAAA
106730 TTAAATTTA
1 TTAAATTTA
106739 AATTAAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 7 0.19
17 25 0.68
18 5 0.14
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:106710 original size:16 final size:18
Alignment explanation
Indices: 106678--106774 Score: 76
Period size: 17 Copynumber: 5.6 Consensus size: 18
106668 CCATACTCCC
*
106678 TTTAAATTTATTTTAAAA
1 TTTAAATTTAGTTTAAAA
106696 -TTAAATTT-GTTTAAAA
1 TTTAAATTTAGTTTAAAA
**
106712 TTTAAATTTA-TTTTCAA
1 TTTAAATTTAGTTTAAAA
** *
106729 TTTAAATTTAAATT-AAG
1 TTTAAATTTAGTTTAAAA
* * *
106746 TTTAAAATTATTTTCAAA
1 TTTAAATTTAGTTTAAAA
106764 TTTAAAATTTA
1 TTT-AAATTTA
106775 AAATAAATAA
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
16 7 0.11
17 43 0.68
18 7 0.11
19 6 0.10
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTAGTTTAAAA
Found at i:106718 original size:6 final size:6
Alignment explanation
Indices: 106678--106776 Score: 57
Period size: 6 Copynumber: 17.0 Consensus size: 6
106668 CCATACTCCC
* * * *
106678 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * * *
106723 TTTCAA TTTAAA TTTAAA -TTAAG TTTAAA ATT-AT TTTCAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTT-AAA
106771 TTTAAA
1 TTTAAA
106777 ATAAATAAAA
Statistics
Matches: 69, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
4 3 0.04
5 15 0.22
6 38 0.55
7 13 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:106750 original size:34 final size:35
Alignment explanation
Indices: 106678--106781 Score: 113
Period size: 34 Copynumber: 3.0 Consensus size: 35
106668 CCATACTCCC
* * **
106678 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTCAATTTAAATTTAAATTAAAA
*
106712 TTTAAATTTATTTTCAATTTAAATTTAAATT-AAG
1 TTTAAATTTATTTTCAATTTAAATTTAAATTAAAA
* *
106746 TTTAAAATTATTTTCAAATTTAAAATTTAAAATAAA
1 TTTAAATTTATTTTC-AATTT-AAATTTAAATTAAA
106782 TAAAACCCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
34 40 0.68
35 7 0.12
36 10 0.17
37 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (35 bp):
TTTAAATTTATTTTCAATTTAAATTTAAATTAAAA
Done.