Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold531
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: 54309
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Found at i:3657 original size:41 final size:41
Alignment explanation
Indices: 3605--3767 Score: 209
Period size: 41 Copynumber: 4.0 Consensus size: 41
3595 GAGTGTAAAT
* * *
3605 AGAGGCACATATGTGCTATTTAGGGGCACCGAAGTACAAAC
1 AGAGGCACATATGTGCAATTTAGGGGTACCAAAGTACAAAC
* * **
3646 AGGGGCTCATATGTGCAATTTAGGGGTACCAAAGTGTAAAC
1 AGAGGCACATATGTGCAATTTAGGGGTACCAAAGTACAAAC
* * *
3687 AGAGGCACGTATGCGCAATTTAAGGGTACCAAAGTACAAAC
1 AGAGGCACATATGTGCAATTTAGGGGTACCAAAGTACAAAC
* * *
3728 AGAGGCACGTATGTGCAATTCAGGGGTACCGAAGTACAAA
1 AGAGGCACATATGTGCAATTTAGGGGTACCAAAGTACAAA
3768 AGGGGATAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 104 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20
Consensus pattern (41 bp):
AGAGGCACATATGTGCAATTTAGGGGTACCAAAGTACAAAC
Found at i:13875 original size:40 final size:40
Alignment explanation
Indices: 13801--13985 Score: 223
Period size: 40 Copynumber: 4.6 Consensus size: 40
13791 AACACAAGTA
* *
13801 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
* *
13840 CCTTCGGGTCTTATCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATG
*
13880 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATG
* * * *
13923 CCTTCGGAACTTCGCCCGGACATAGTC-ACTAGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATG
13963 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
13986 CATCTGAATA
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
39 12 0.10
40 76 0.61
41 1 0.01
43 34 0.27
44 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
Found at i:13924 original size:83 final size:80
Alignment explanation
Indices: 13793--13985 Score: 271
Period size: 83 Copynumber: 2.4 Consensus size: 80
13783 CACTTCCAAA
* * ** *
13793 CACAAGTACCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTATCCC
1 CACAAATACCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGAACTTAGCCC
*
13857 GGATATAGTCACTAG
66 GGACATAGTCACTAG
* * *
13872 CACAAATGCCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGAACTTCG
1 CACAAATACCTTCGGGACTTAGCCCGGATATAGC-A--ACTCGCACAAATGCCTTCGGAACTTAG
13937 CCCGGACATAGTCACTAG
63 CCCGGACATAGTCACTAG
13955 CACAAATACCTTCGGGACTTAGCCCGGATAT
1 CACAAATACCTTCGGGACTTAGCCCGGATAT
13986 CATCTGAATA
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
79 19 0.19
80 10 0.10
81 1 0.01
83 69 0.70
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (80 bp):
CACAAATACCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGAACTTAGCCC
GGACATAGTCACTAG
Found at i:21997 original size:40 final size:39
Alignment explanation
Indices: 21923--22147 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 39
21913 AACCCAAGTA
* *
21923 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTAGCACAAATG
* * *
21962 CCTTCGGGTCTTAGACCAGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
*
22002 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTA---GCACAAATG
* *
22045 CCTTCGGGACTTCGCCCGGACATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
* * *
22085 CCTTCAGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATA-GCACTAGCACAAATG
22125 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
22148 CATCCGAATA
Statistics
Matches: 161, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
39 13 0.08
40 110 0.68
41 2 0.01
43 35 0.22
44 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGCACTAGCACAAATG
Found at i:22043 original size:83 final size:80
Alignment explanation
Indices: 21923--22147 Score: 335
Period size: 83 Copynumber: 2.8 Consensus size: 80
21913 AACCCAAGTA
* * * *
21923 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGACCAGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
21987 TCACTAGCACAAATG
66 TCACTAGCACAAATG
* * *
22002 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGACA
1 CCTTCGGGACTTAGCCCGGATATAGC-A--ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
22067 TAGTCACTAGCACAAATG
63 TAGTCACTAGCACAAATG
* *
22085 CCTTCAGGACTTAGCCCGGATATAGGAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
22148 CATCCGAATA
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
79 13 0.10
80 44 0.34
81 1 0.01
82 1 0.01
83 71 0.55
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCACTAGCACAAATG
Found at i:24907 original size:41 final size:41
Alignment explanation
Indices: 24827--25121 Score: 172
Period size: 41 Copynumber: 7.2 Consensus size: 41
24817 ACCAGAGTGT
* * * *
24827 AAACAGGGGCACTTATATGCTATT-TAGGCGTACCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAAGG-GTACCGAAGTAC
*
24868 AAACAGGGGGCACGTATGTGCAATTCAAGGGTA-CAAAGTA-
1 AAACA-GGGGCACGTATGTGCAATTCAAGGGTACCGAAGTAC
* ** * * * * * *
24908 TAACTAGCAGAACATATGTACAATTCAAGGCTATCGAAGTAA
1 AAAC-AGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTAC
* * * *
24950 AAAAAGGTGCACGTATGTGCATTTCGA-GGTACCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTAC
* * **
24990 AAACAAGGGCACATATGTATAATTCAGAGGTGT--CGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCA-AGG-GTACCGAAGTAC
* * * * * *
25031 AAAGAGAGGCACGTATGTGCAATT-TAGAGTTATCGAAGTAT
1 AAACAGGGGCACGTATGTGCAATTCAAG-GGTACCGAAGTAC
** * * * * *
25072 AAACAAAGGCACGCATATGCAATTCAGGGGTACTGAAGTAA
1 AAACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTAC
25113 AAACAGGGG
1 AAACAGGGG
25122 ATAATTCAGT
Statistics
Matches: 188, Mismatches: 54, Indels: 24
0.71 0.20 0.09
Matches are distributed among these distances:
39 3 0.02
40 53 0.28
41 104 0.55
42 23 0.12
43 5 0.03
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (41 bp):
AAACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTAC
Found at i:24969 original size:81 final size:81
Alignment explanation
Indices: 24876--25054 Score: 195
Period size: 81 Copynumber: 2.2 Consensus size: 81
24866 ACAAACAGGG
* *
24876 GGCACGTATGTGCAATTCAAGGGTA-CAAAGTA-TAACTAGCAGAACATATGTACAATTCA-AGG
1 GGCACGTATGTGCAATTCAA-GGTACCAAAGTACAAACAAG-AGAACATATGTACAATTCAGAGG
24938 CTATCGAAGTAAAAAAAG-
64 -TATCGAAGTAAAAAAAGA
* * * * * *
24956 GTGCACGTATGTGCATTTCGAGGTACCGAAGTACAAACAAGGGCACATATGTATAATTCAGAGGT
1 G-GCACGTATGTGCAATTCAAGGTACCAAAGTACAAACAAGAGAACATATGTACAATTCAGAGGT
* * *
25021 GTCGAAGTACAAAGAGA
65 ATCGAAGTAAAAAAAGA
25038 GGCACGTATGTGCAATT
1 GGCACGTATGTGCAATT
25055 TAGAGTTATC
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
80 5 0.06
81 68 0.83
82 9 0.11
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (81 bp):
GGCACGTATGTGCAATTCAAGGTACCAAAGTACAAACAAGAGAACATATGTACAATTCAGAGGTA
TCGAAGTAAAAAAAGA
Found at i:25096 original size:82 final size:81
Alignment explanation
Indices: 24919--25115 Score: 199
Period size: 82 Copynumber: 2.4 Consensus size: 81
24909 AACTAGCAGA
*
24919 ACATATGTACAATTCA-AGGCTATCGAAGTAAAAAAAGGTGCACGTATGTGCATTTCGAGGTACC
1 ACATATG-ACAATTCAGAGGCTATCGAAGTAAAAAAAGGTGCACGTATGTGCATTTAGAGGTACC
*
24983 GAAGTACAAACAAGGGC
65 GAAGTACAAACAAAGGC
* * * * *
25000 ACATATGTATAATTCAGAGG-TGTCGAAGTACAAAGAGAG-GCACGTATGTGCAATTTAGAGTTA
1 ACATATG-ACAATTCAGAGGCTATCGAAGTAAAAAAAG-GTGCACGTATGTGC-ATTTAGAGGTA
* *
25063 TCGAAGTATAAACAAAGGC
63 CCGAAGTACAAACAAAGGC
*
25082 ACGCATATG-CAATTCAG-GGGTA-CTGAAGTAAAAA
1 A--CATATGACAATTCAGAGGCTATC-GAAGTAAAAA
25116 CAGGGGATAA
Statistics
Matches: 97, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
81 44 0.45
82 47 0.48
84 6 0.06
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (81 bp):
ACATATGACAATTCAGAGGCTATCGAAGTAAAAAAAGGTGCACGTATGTGCATTTAGAGGTACCG
AAGTACAAACAAAGGC
Found at i:27754 original size:40 final size:40
Alignment explanation
Indices: 27732--27913 Score: 294
Period size: 40 Copynumber: 4.5 Consensus size: 40
27722 ATGGTCGCTA
27732 GCACAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTC
*
27772 GCACAAATGCCTTCGAGACTTAGCCCGGAATTAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
27812 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
* * *
27852 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
* *
27892 GCACAAATGTCTTCGAGACTTA
1 GCACAAATGCCTTCGGGACTTA
27914 ACCCCATTAG
Statistics
Matches: 134, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 132 0.99
41 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
Found at i:30439 original size:40 final size:40
Alignment explanation
Indices: 30393--30577 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 40
30383 CTTGCGCAAG
* * * *
30393 GCCTTCGGGTCTTAGCCCGTATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
30433 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
30473 GCCTTCGGGTTTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * * *
30513 GCCTTCGGATCTTAGTCCGGTTGTAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
30554 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
30578 CATTCGAATA
Statistics
Matches: 118, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 89 0.75
41 28 0.24
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:30568 original size:121 final size:118
Alignment explanation
Indices: 30357--30577 Score: 300
Period size: 121 Copynumber: 1.8 Consensus size: 118
30347 CTCAAGTAAT
* * * * *
30357 CTTCGGGATTTAGCCGGATATAACTACTTGCGCAAGGCCTTCGGGTCTTAGCCCGTATGTGGTCA
1 CTTCGGGATTTAGCCGGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGTATGTAGTCA
* *
30422 CTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
66 CTAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
* * * *
30475 CTTCGGGTTTTAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCGGT-TGTAG
1 CTTCGGGATTTAG-CCGGATATAACAACTCGCAC-AAGGCCTTCGGATCTTAG-CCCGTATGTAG
30539 TCACCTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
63 TCA-CTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
30578 CATTCGAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
118 12 0.14
119 16 0.18
120 23 0.26
121 37 0.42
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (118 bp):
CTTCGGGATTTAGCCGGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGTATGTAGTCA
CTAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
Found at i:35347 original size:11 final size:11
Alignment explanation
Indices: 35331--35355 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35321 CATATCTATA
35331 TTGTAGAATTT
1 TTGTAGAATTT
35342 TTGTAGAATTT
1 TTGTAGAATTT
35353 TTG
1 TTG
35356 GCCTGGCCAA
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:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (11 bp):
TTGTAGAATTT
Found at i:36629 original size:28 final size:28
Alignment explanation
Indices: 36597--36694 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
36587 ATAATAAGCC
*
36597 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
36625 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
36653 CGCACACTTAGTGCTATAA-ATTTGAACC
1 CGCACACTTAGTGCT-TAATAATCGAACT
36681 CGCACACTTAGTGC
1 CGCACACTTAGTGC
36695 CAATCTCATG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.03
28 56 0.92
29 1 0.02
30 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:44617 original size:28 final size:29
Alignment explanation
Indices: 44585--44683 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
44575 ATAATAAGCC
*
44585 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
44613 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
44641 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
44670 CGCACACTTAGTGC
1 CGCACACTTAGTGC
44684 CAATCTCATG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:52507 original size:27 final size:27
Alignment explanation
Indices: 52412--52508 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 27
52402 TGTTAAGCCC
52412 CGCACACTTAGTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTATAA-A-TCGAACT
*
52440 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATA-AATCGAACT
*
52468 CGCACACTTAGTGCTATAAATTGAAC-
1 CGCACACTTAGTGCTATAAATCGAACT
52494 CAGCACACTTAGTGC
1 C-GCACACTTAGTGC
52509 CAATCTCATG
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
26 1 0.02
27 19 0.30
28 39 0.62
29 3 0.05
30 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATAAATCGAACT
Done.