Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012994.1 Kokia drynarioides strain JFW-HI SEQ_128012, 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: 77394
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:737 original size:30 final size:26
Alignment explanation
Indices: 701--767 Score: 71
Period size: 30 Copynumber: 2.4 Consensus size: 26
691 CATATTATTT
701 TTTTTTTATTTTTTAAAAATATTTATA
1 TTTTTTTATTTTTTAAAAAT-TTTATA
* * *
728 CTGTATTTTTAATATTTAATAATTTTATA
1 -T-T-TTTTTATTTTTTAAAAATTTTATA
757 TTTTTTTATTT
1 TTTTTTTATTT
768 ATTGAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
26 7 0.22
27 1 0.03
28 2 0.06
29 7 0.22
30 15 0.47
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (26 bp):
TTTTTTTATTTTTTAAAAATTTTATA
Found at i:10176 original size:23 final size:22
Alignment explanation
Indices: 10131--10176 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
10121 TAATGTGATG
* * *
10131 TTTAAAAATAAATTTATGTTTT
1 TTTAAAAATAAAATAATGATTT
10153 TTTAATAAATAAAATAATGATTT
1 TTTAA-AAATAAAATAATGATTT
10176 T
1 T
10177 AAATATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTAAAAATAAAATAATGATTT
Found at i:14353 original size:19 final size:20
Alignment explanation
Indices: 14326--14384 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
14316 AAATAATGTT
14326 TTAAA-TAAATTATAATA-A
1 TTAAATTAAATTATAATATA
* *
14344 TTAATTTAAA-TATAATATT
1 TTAAATTAAATTATAATATA
*
14363 TTAAATTAAATCATAATCATA
1 TTAAATTAAATTATAAT-ATA
14384 T
1 T
14385 ATTAAGTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 11 0.34
19 13 0.41
20 5 0.16
21 3 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAATTAAATTATAATATA
Found at i:18932 original size:60 final size:60
Alignment explanation
Indices: 18799--18938 Score: 149
Period size: 60 Copynumber: 2.3 Consensus size: 60
18789 TTTTTTTGTT
* * * **
18799 TCAATTTAGTACTTAAGTTTGATTTTAATATTTAGTTTAATACTTAAGTTTTTATTTACC
1 TCAATTAAGTACCTAAGTTTGATTTTAATATTCAAATTAATACTTAAGTTTTTATTTACC
* * * * *
18859 TCACA-TAACTACCTAAGTTTGATTTTAATATTCAAATTAGTACTTGAGTTTTTCTTTTATC
1 TCA-ATTAAGTACCTAAGTTTGATTTTAATATTCAAATTAATACTTAAGTTTTT-ATTTACC
*
18920 -CAATTAAGTACCTATGTTT
1 TCAATTAAGTACCTAAGTTT
18939 TTTTTATTAG
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
59 1 0.02
60 58 0.89
61 6 0.09
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (60 bp):
TCAATTAAGTACCTAAGTTTGATTTTAATATTCAAATTAATACTTAAGTTTTTATTTACC
Found at i:24315 original size:5 final size:5
Alignment explanation
Indices: 24305--24342 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
24295 CATATAAAAT
*
24305 TAATA TAATA TAATA TAATA TAATA TAATA TATTA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
24343 ATTTAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:30344 original size:58 final size:58
Alignment explanation
Indices: 30246--30365 Score: 204
Period size: 58 Copynumber: 2.1 Consensus size: 58
30236 GATTTGTCAA
* * *
30246 CTTAACCCTTAGGTCAAATCAGCGAGCTTGGTTTGAATCTGCAACCCTACCTTGTGAG
1 CTTAACCCTTAGATCAAATCAGCGAGCTTGGTCTGAATCTGCAACCCTACCCTGTGAG
*
30304 CTTAACCCTTAGATCAAATCAGCGAGCTTGGTCTGGATCTGCAACCCTACCCTGTGAG
1 CTTAACCCTTAGATCAAATCAGCGAGCTTGGTCTGAATCTGCAACCCTACCCTGTGAG
30362 CTTA
1 CTTA
30366 CTAGAATTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (58 bp):
CTTAACCCTTAGATCAAATCAGCGAGCTTGGTCTGAATCTGCAACCCTACCCTGTGAG
Found at i:34733 original size:17 final size:17
Alignment explanation
Indices: 34682--34773 Score: 75
Period size: 17 Copynumber: 5.4 Consensus size: 17
34672 TTCATTTTGG
*
34682 GTTTAAATTTAATTTAAA
1 GTTTAAATTTAAATT-AA
**
34700 GTTTAAACTTT-TCTTAA
1 GTTTAAA-TTTAAATTAA
34717 GTTTAAATTTAAATTAA
1 GTTTAAATTTAAATTAA
* *
34734 GTTTAAAATTAATTTGAA
1 GTTTAAATTTAAATT-AA
34752 -TTTAAAATTT-AATTAA
1 GTTT-AAATTTAAATTAA
34768 -TTTAAA
1 GTTTAAA
34774 AAAGTCCAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
15 3 0.05
16 8 0.13
17 32 0.52
18 16 0.26
19 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (17 bp):
GTTTAAATTTAAATTAA
Found at i:34756 original size:34 final size:34
Alignment explanation
Indices: 34682--34774 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 34
34672 TTCATTTTGG
* * *
34682 GTTTAAATTTAATTTAAAGTTTAAACTTTTCTTAA
1 GTTTAAATTTAAATT-AAGTTTAAAATTTTCTGAA
34717 GTTTAAATTTAAATTAAGTTTAAAATTAATT-TGAA
1 GTTTAAATTTAAATTAAGTTTAAAATT--TTCTGAA
34752 -TTTAAAATTT-AATTAA-TTTAAAA
1 GTTT-AAATTTAAATTAAGTTTAAAA
34775 AAGTCCAGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
33 7 0.13
34 20 0.38
35 23 0.44
36 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (34 bp):
GTTTAAATTTAAATTAAGTTTAAAATTTTCTGAA
Found at i:34854 original size:16 final size:16
Alignment explanation
Indices: 34833--34872 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
34823 GCTAACCTAA
34833 GCCCAAATTCTAAAAG
1 GCCCAAATTCTAAAAG
* *
34849 GCCCAAA-CCTAAATG
1 GCCCAAATTCTAAAAG
34864 GCCCAAATT
1 GCCCAAATT
34873 GGCCCAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.17
Consensus pattern (16 bp):
GCCCAAATTCTAAAAG
Found at i:36647 original size:29 final size:28
Alignment explanation
Indices: 36577--36736 Score: 146
Period size: 29 Copynumber: 5.5 Consensus size: 28
36567 GAGGTTCCTA
*
36577 AACTGTCCCAAAATTACCATTTTACCTCCG
1 AACT-TCCAAAAATTACCATTTTACC-CCG
*
36607 AACTTCCAAAAA-TCCCATTTTGACCCCG
1 AACTTCCAAAAATTACCATTTT-ACCCCG
* *
36635 AACCCTCCCAAAATTACCATTTTACCCTCG
1 AA-CTTCCAAAAATTACCATTTTACCC-CG
*
36665 AACTTCCAAAAA-T-CTCATTTTTGGCCCCG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCCG
* *
36694 AACCTTCTAAAAATTACCATATTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTA-CCCCG
36724 AACTTCCAAAAAT
1 AACTTCCAAAAAT
36737 CTCATTTTTG
Statistics
Matches: 107, Mismatches: 12, Indels: 23
0.75 0.08 0.16
Matches are distributed among these distances:
27 1 0.01
28 16 0.15
29 48 0.45
30 38 0.36
31 3 0.03
32 1 0.01
ACGTcount: A:0.33, C:0.34, G:0.06, T:0.28
Consensus pattern (28 bp):
AACTTCCAAAAATTACCATTTTACCCCG
Found at i:36655 original size:30 final size:28
Alignment explanation
Indices: 36582--36736 Score: 109
Period size: 30 Copynumber: 5.3 Consensus size: 28
36572 TCCTAAACTG
36582 TCCCAAAATTACCATTTTACCTCCGAA-C
1 TCCCAAAATTACCATTTTACC-CCGAACC
* * *
36610 TTCCAAAAATCCCATTTTGACCCCGAACCC
1 TCCCAAAATTACCATTTT-ACCCCGAA-CC
36640 TCCCAAAATTACCATTTTACCCTCGAA-C
1 TCCCAAAATTACCATTTTACCC-CGAACC
* * *
36668 TTCCAAAAAT-CTCATTTTTGGCCCCGAACC
1 TCCCAAAATTAC-CA-TTTT-ACCCCGAACC
** * *
36698 TTCTAAAAATTACCATATTACCCCCGAACT
1 -TCCCAAAATTACCATTTTA-CCCCGAACC
*
36728 TCCAAAAAT
1 TCCCAAAAT
36737 CTCATTTTTG
Statistics
Matches: 99, Mismatches: 17, Indels: 21
0.72 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 31 0.31
29 23 0.23
30 35 0.35
31 8 0.08
32 1 0.01
ACGTcount: A:0.33, C:0.34, G:0.05, T:0.28
Consensus pattern (28 bp):
TCCCAAAATTACCATTTTACCCCGAACC
Found at i:36672 original size:58 final size:59
Alignment explanation
Indices: 36582--36807 Score: 269
Period size: 58 Copynumber: 3.9 Consensus size: 59
36572 TCCTAAACTG
36582 TCCCAAAATTACCATTTTA-CCTCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACCC
1 TCCCAAAATTACCATTTTACCCT-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACCC
* * *
36640 TCCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGGCCCCGAACCT
1 TCCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCC
** * * * **
36699 TCTAAAAATTACCATATTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTTGAA-CC
1 TCCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCC
*** * * * *
36757 TTTTAAAAATACCATTTTACCCTCGGACCTCCTAAAATCCCATTTTTGACC
1 TCCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACC
36808 TCAAGATATC
Statistics
Matches: 146, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
58 80 0.55
59 66 0.45
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.31
Consensus pattern (59 bp):
TCCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCC
Found at i:36719 original size:59 final size:59
Alignment explanation
Indices: 36586--36807 Score: 288
Period size: 59 Copynumber: 3.8 Consensus size: 59
36576 AAACTGTCCC
* **
36586 AAAATTACCATTTTA-CCTCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACCCTCCC
1 AAAATTACCATTTTACCCT-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* *
36644 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGGCCCCGAACCTTCTA
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* * * ** *
36703 AAAATTACCATATTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTTGAACCTTTTA
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* * *
36762 AAAA-TACCATTTTACCCTCGGACCTCCTAAAATCCCATTTTTGACC
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACC
36808 TCAAGATATC
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
58 69 0.48
59 76 0.52
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.31
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
Found at i:36794 original size:117 final size:117
Alignment explanation
Indices: 36586--36804 Score: 305
Period size: 117 Copynumber: 1.9 Consensus size: 117
36576 AAACTGTCCC
* * *
36586 AAAATTACCATTTTACCTCCGAACTTCCAAAAATCCCATTTTGACCCCGAACCCTCCCAAAATTA
1 AAAATTACCATATTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCGAACCCTCCCAAAAATA
* *
36651 CCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGGCCCCGAACCTTCTA
66 CCATTTTACCCTCGAACCTCCAAAAATCCCATTTTTGGCCCCGAACCTTCTA
* ** ***
36703 AAAATTACCATATTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTTGAA-CCTTTTAAAAAT
1 AAAATTACCATATTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACCCTCCCAAAAAT
* *
36767 ACCATTTTACCCTCGGACCTCCTAAAATCCCATTTTTG
65 ACCATTTTACCCTCGAACCTCCAAAAATCCCATTTTTG
36805 ACCTCAAGAT
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
117 77 0.88
118 11 0.12
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.31
Consensus pattern (117 bp):
AAAATTACCATATTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCGAACCCTCCCAAAAATA
CCATTTTACCCTCGAACCTCCAAAAATCCCATTTTTGGCCCCGAACCTTCTA
Found at i:36809 original size:29 final size:30
Alignment explanation
Indices: 36596--36809 Score: 110
Period size: 29 Copynumber: 7.3 Consensus size: 30
36586 AAAATTACCA
*
36596 TTTT-ACCTCCGAACTTCC-AAAAATCCCA-
1 TTTTGACCT-CGAACCTCCTAAAAATCCCAT
* * * *
36624 TTTTGACCCCGAACCCTCCCAAAATTACCA-
1 TTTTGACCTCGAA-CCTCCTAAAAATCCCAT
* *
36654 TTTT-ACCCTCGAACTTCC-AAAAATCTCAT
1 TTTTGA-CCTCGAACCTCCTAAAAATCCCAT
* * * *
36683 TTTTGGCCCCGAACCTTCTAAAAATTACCA-
1 TTTTGACCTCGAACCTCCTAAAAA-TCCCAT
* * * *
36713 TATT-ACCCCCGAACTTCC-AAAAATCTCAT
1 TTTTGA-CCTCGAACCTCCTAAAAATCCCAT
* ** *
36742 TTTTGACCTTGAACCTTTTAAAAATACCA-
1 TTTTGACCTCGAACCTCCTAAAAATCCCAT
*
36771 TTTT-ACCCTCGGACCTCCT-AAAATCCCAT
1 TTTTGA-CCTCGAACCTCCTAAAAATCCCAT
36800 TTTTGACCTC
1 TTTTGACCTC
36810 AAGATATCCA
Statistics
Matches: 137, Mismatches: 34, Indels: 29
0.69 0.17 0.14
Matches are distributed among these distances:
28 27 0.20
29 61 0.45
30 46 0.34
31 3 0.02
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.31
Consensus pattern (30 bp):
TTTTGACCTCGAACCTCCTAAAAATCCCAT
Found at i:36923 original size:28 final size:28
Alignment explanation
Indices: 36881--36936 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
36871 AAAACTCTCA
*
36881 AAATTACCAT-TTTTACCCCTGAATGTTTC
1 AAATTACCATCTTTAACCCC-GAAT-TTTC
36910 AAATT-CCATCTTTAACCCCGAATTTTC
1 AAATTACCATCTTTAACCCCGAATTTTC
36937 TCGAAACTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.16
28 8 0.32
29 13 0.52
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (28 bp):
AAATTACCATCTTTAACCCCGAATTTTC
Found at i:46150 original size:34 final size:34
Alignment explanation
Indices: 46107--46172 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
46097 TTGATGGAGA
*
46107 AATGGTACTATTGTTTCCTTTATCGCCGCAATTT
1 AATGGTACTATTGTTTCCTTTATCGCCACAATTT
46141 AATGGTACTATTGTTTCCTTTATCGCCACAAT
1 AATGGTACTATTGTTTCCTTTATCGCCACAAT
46173 GTAGATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (34 bp):
AATGGTACTATTGTTTCCTTTATCGCCACAATTT
Found at i:58089 original size:41 final size:40
Alignment explanation
Indices: 57994--58091 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 40
57984 AATTTTTTAT
* * *
57994 TTTTTAAATTTAAAAAATTATAAGAATATTTTTTGAAAAA
1 TTTTAAAATTTTAAAAATTATAAAAATATTTTTTGAAAAA
* *
58034 -TTAAAAATCATTAAAAATATATAAAAATATTTTTT-AAAATA
1 TTTTAAAAT-TTTAAAAAT-TATAAAAATATTTTTTGAAAA-A
58075 TTTTAAAATTTTAAAAA
1 TTTTAAAATTTTAAAAA
58092 ATTAATTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
39 6 0.13
40 11 0.23
41 23 0.49
42 7 0.15
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (40 bp):
TTTTAAAATTTTAAAAATTATAAAAATATTTTTTGAAAAA
Found at i:58901 original size:20 final size:20
Alignment explanation
Indices: 58876--58927 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
58866 TAATTTATAA
**
58876 AATTTTTACTATGTAAAAAT
1 AATTTTTAAAATGTAAAAAT
* *
58896 AATTTTTAAAATTTGAAAAT
1 AATTTTTAAAATGTAAAAAT
58916 AATTTTTAAAAT
1 AATTTTTAAAAT
58928 TCATAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (20 bp):
AATTTTTAAAATGTAAAAAT
Found at i:58928 original size:20 final size:20
Alignment explanation
Indices: 58891--58928 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
58881 TTACTATGTA
58891 AAAATAATTTTTAAAATTTG
1 AAAATAATTTTTAAAATTTG
58911 AAAATAATTTTTAAAATT
1 AAAATAATTTTTAAAATT
58929 CATAATATTT
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:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAATAATTTTTAAAATTTG
Found at i:58935 original size:19 final size:19
Alignment explanation
Indices: 58893--58956 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
58883 ACTATGTAAA
* *
58893 AATAATTTTTAAAATTTGAA
1 AATAATTTTTAAAA-TTCAT
58913 AATAATTTTTAAAATTCAT
1 AATAATTTTTAAAATTCAT
*
58932 AAT-ATTTATAAAAATTC-T
1 AATAATTT-TTAAAATTCAT
58950 AA-AATTT
1 AATAATTT
58957 GTATTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 11 0.28
19 14 0.36
20 14 0.36
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (19 bp):
AATAATTTTTAAAATTCAT
Found at i:71264 original size:29 final size:29
Alignment explanation
Indices: 71231--71286 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
71221 ATTATTAAAA
**
71231 ATAAAATTATGTTTTAATTCTTTAAAATG
1 ATAAAATTATAATTTAATTCTTTAAAATG
*
71260 ATAAAATTTTAATTTAATTCTTTAAAA
1 ATAAAATTATAATTTAATTCTTTAAAA
71287 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (29 bp):
ATAAAATTATAATTTAATTCTTTAAAATG
Found at i:71290 original size:22 final size:23
Alignment explanation
Indices: 71262--71323 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
71252 TTAAAATGAT
*
71262 AAAATTTTAATTTAATTCTT-TA
1 AAAATTTTAATTTAATTATTGTA
* * *
71284 AAAATTTTATTTTTACTATTGTA
1 AAAATTTTAATTTAATTATTGTA
*
71307 AAAATTATAATTTAATT
1 AAAATTTTAATTTAATT
71324 TAGACCTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (23 bp):
AAAATTTTAATTTAATTATTGTA
Found at i:72208 original size:28 final size:26
Alignment explanation
Indices: 72176--72243 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
72166 ACTTTTAATA
* **
72176 ATTTTTAAAATTTGTTTTGATTTTTTAT
1 ATTTTTAAAATTTCTAAT-ATTTTTT-T
*
72204 ATTTTTTAAATTTCTAATATTTTTTT
1 ATTTTTAAAATTTCTAATATTTTTTT
72230 ATTTTTTAAAATTT
1 A-TTTTTAAAATTT
72244 TTTAGTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.06
27 18 0.53
28 14 0.41
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (26 bp):
ATTTTTAAAATTTCTAATATTTTTTT
Found at i:72216 original size:18 final size:17
Alignment explanation
Indices: 72178--72282 Score: 84
Period size: 17 Copynumber: 5.8 Consensus size: 17
72168 TTTTAATAAT
*
72178 TTTTAAAATTTGTTTTGAT
1 TTTTTAAATTT-TTTT-AT
* * *
72197 TTTTTATATTTTTTAAA
1 TTTTTAAATTTTTTTAT
*
72214 TTTCTAATATTTTTTTAT
1 TTTTTAA-ATTTTTTTAT
* *
72232 TTTTTAAAATTTTTTAG
1 TTTTTAAATTTTTTTAT
72249 TTTTTAAATGTTTTTTTTAT
1 TTTTTAAA---TTTTTTTAT
72269 TTTTTAATATTTTT
1 TTTTTAA-ATTTTT
72283 AATTCTTATT
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
17 22 0.32
18 22 0.32
19 9 0.13
20 14 0.21
21 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (17 bp):
TTTTTAAATTTTTTTAT
Found at i:72246 original size:37 final size:35
Alignment explanation
Indices: 72174--72286 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 35
72164 GAACTTTTAA
*
72174 TAATTTTTAAAATTTGTTTTGATTTTTT-ATATTTTT
1 TAATTTTTAATATTT-TTTT-ATTTTTTAATATTTTT
* *
72210 TAAATTTCTAATATTTTTTTATTTTTTAAAATTTTT
1 T-AATTTTTAATATTTTTTTATTTTTTAATATTTTT
* *
72246 TAGTTTTTAAATGTTTTTTTTATTTTTTAATA-TTTT
1 TAATTTTT-AAT-ATTTTTTTATTTTTTAATATTTTT
72282 TAATT
1 TAATT
72287 CTTATTCACT
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
35 12 0.18
36 24 0.37
37 29 0.45
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.69
Consensus pattern (35 bp):
TAATTTTTAATATTTTTTTATTTTTTAATATTTTT
Found at i:72310 original size:9 final size:9
Alignment explanation
Indices: 72158--72311 Score: 50
Period size: 9 Copynumber: 16.8 Consensus size: 9
72148 GTAAGTGTTT
*
72158 TTTTTAGAA
1 TTTTTATAA
*
72167 CTTTTAATAA
1 -TTTTTATAA
*
72177 TTTTTAAAA
1 TTTTTATAA
* *
72186 TTTGTTTTGAT
1 TTT-TTAT-AA
*
72197 TTTTTATAT
1 TTTTTATAA
72206 TTTTTA-AA
1 TTTTTATAA
*
72214 TTTCTA-ATA
1 TTTTTATA-A
* *
72223 TTTTTTTAT
1 TTTTTATAA
*
72232 TTTTTAAAA
1 TTTTTATAA
*
72241 TTTTT-TAG
1 TTTTTATAA
72249 TTTTTA-AA
1 TTTTTATAA
* *
72257 TGTTTTTTTTA
1 --TTTTTATAA
72268 TTTTT-TAA
1 TTTTTATAA
72276 TATTTT-TAA
1 T-TTTTATAA
* *
72285 TTCTTATTCAC
1 TTTTTA-T-AA
72296 TTTTTATAA
1 TTTTTATAA
72305 TTTTTAT
1 TTTTTAT
72312 CTTTTACTTT
Statistics
Matches: 106, Mismatches: 26, Indels: 25
0.68 0.17 0.16
Matches are distributed among these distances:
8 20 0.19
9 55 0.52
10 20 0.19
11 11 0.10
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:72347 original size:19 final size:18
Alignment explanation
Indices: 72319--72383 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 18
72309 TATCTTTTAC
72319 TTTAATTTTTTTCATAAT
1 TTTAATTTTTTTCATAAT
**
72337 TTTAATGTTTTTTTGTAAT
1 TTTAAT-TTTTTTCATAAT
*
72356 TTTAA-ATTTTT-ATAAT
1 TTTAATTTTTTTCATAAT
*
72372 TTTGATTTTTTT
1 TTTAATTTTTTT
72384 TTTTTTTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 8 0.21
17 10 0.26
18 6 0.15
19 15 0.38
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTAATTTTTTTCATAAT
Found at i:72381 original size:16 final size:16
Alignment explanation
Indices: 72319--72382 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 16
72309 TATCTTTTAC
72319 TTTAATTTTTTTCATAAT
1 TTTAA-TTTTTT-ATAAT
*
72337 TTTAATGTTTTTTTGTAAT
1 TTTAA---TTTTTTATAAT
*
72356 TTTAAATTTTTATAAT
1 TTTAATTTTTTATAAT
*
72372 TTTGATTTTTT
1 TTTAATTTTTT
72383 TTTTTTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 18 0.46
18 5 0.13
19 9 0.23
20 7 0.18
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTAATTTTTTATAAT
Found at i:74577 original size:57 final size:57
Alignment explanation
Indices: 74506--74622 Score: 189
Period size: 57 Copynumber: 2.1 Consensus size: 57
74496 TATCAAGTAA
* ** * *
74506 TTATTGTACAAATAAACTAAGAGTTAATACAATTCTTAACTAATTAGATTATTTGAT
1 TTATTGAACAAATAAACTAAGAGTTAATACAATTAATAACAAATTAGATTACTTGAT
74563 TTATTGAACAAATAAACTAAGAGTTAATACAATTAATAACAAATTAGATTACTTGAT
1 TTATTGAACAAATAAACTAAGAGTTAATACAATTAATAACAAATTAGATTACTTGAT
74620 TTA
1 TTA
74623 AAATTCGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (57 bp):
TTATTGAACAAATAAACTAAGAGTTAATACAATTAATAACAAATTAGATTACTTGAT
Found at i:75011 original size:27 final size:28
Alignment explanation
Indices: 74975--75027 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
74965 CTTTTTAATA
* *
74975 TAATATATAAAAAAT-ATTTTATTTATT
1 TAATAAATAAAAAATAATTTAATTTATT
*
75002 TAATAAATAAAATATAATTTAATTTA
1 TAATAAATAAAAAATAATTTAATTTA
75028 ACTATTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATAAATAAAAAATAATTTAATTTATT
Found at i:75158 original size:27 final size:29
Alignment explanation
Indices: 75119--75185 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
75109 AAATTTTAAA
* *
75119 TTAATAATGATAAAATTAT-ATTT-TATTT
1 TTAA-AATAATAAAATTATAATTTATATCT
*
75147 TTAAAATAATAAAATTTTAATTTAATATCT
1 TTAAAATAATAAAATTATAATTT-ATATCT
75177 TTAAAATAA
1 TTAAAATAA
75186 AAATAATCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 12 0.36
28 8 0.24
30 13 0.39
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TTAAAATAATAAAATTATAATTTATATCT
Found at i:76743 original size:77 final size:69
Alignment explanation
Indices: 76575--76713 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
76565 TTCTAAATAG
76575 AGATAATTAGAGTTAAAATCTTTGTATGCATTTATATATTTTATCATTATATAAATGAAATGATA
1 AGATAATTAGAGTTAAAATCTTTGTATGCATTTATATATTTTATCATTATATAAATGAAATGATA
76640 CGTT
66 CGTT
76644 AGATAATTAGAGTTAAAATCTTTGTATGCATTTATATATTTTATCATTATATAAATGAAATGATA
1 AGATAATTAGAGTTAAAATCTTTGTATGCATTTATATATTTTATCATTATATAAATGAAATGATA
76709 CGTT
66 CGTT
76713 A
1 A
76714 TAAGTCTAGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.43
Consensus pattern (69 bp):
AGATAATTAGAGTTAAAATCTTTGTATGCATTTATATATTTTATCATTATATAAATGAAATGATA
CGTT
Found at i:77367 original size:18 final size:16
Alignment explanation
Indices: 77333--77383 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 16
77323 ATGGTTTCGC
*
77333 ATAAAAAAGAAAAAAA
1 ATAAAAAAGAAAGAAA
77349 ATAAATAAACGAAAGAAA
1 ATAAA-AAA-GAAAGAAA
77367 ATAAACAAATGAAAGAA
1 ATAAA-AAA-GAAAGAA
77384 GGGGGAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 5 0.17
17 3 0.10
18 22 0.73
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (16 bp):
ATAAAAAAGAAAGAAA
Done.