Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2247
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: 55108
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:448 original size:39 final size:38
Alignment explanation
Indices: 359--481 Score: 151
Period size: 39 Copynumber: 3.2 Consensus size: 38
349 GGGACTTTAG
* * * * *
359 CCGGACATATTTCCAGCACGTAGCC-G-AACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGACCCTAAGT
395 CCGGATATAATTCCAGCACATAGCCTGCGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGACCCTAAGT
*
433 CTCGGATATAATTCCAGGACATAGCCTGCGGACCCTAAGT
1 C-CGGATATAATTCCAGCACATAGCCTGC-GACCCTAAGT
*
473 CCAGATATA
1 CCGGATATA
482 CATCACTGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
36 22 0.29
37 1 0.01
38 9 0.12
39 33 0.43
40 11 0.14
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (38 bp):
CCGGATATAATTCCAGCACATAGCCTGCGACCCTAAGT
Found at i:8609 original size:39 final size:40
Alignment explanation
Indices: 8560--8708 Score: 107
Period size: 39 Copynumber: 3.8 Consensus size: 40
8550 TAAACCAGGT
* *
8560 ATAATACCAGCTCGAAGCCTGCGGGA-CTTTAGCCTGGAC
1 ATAATTCCAGCTCGAAGCCTGCGGGACCTTAAGCCTGGAC
* * * *
8599 ATATTTCCAGCAT-GTAGCCTGC-GGACCTTAAGTCTGGAT
1 ATAATTCCAGC-TCGAAGCCTGCGGGACCTTAAGCCTGGAC
* * *
8638 ATAATTCCAGCAC-ATAGCCTGC-GGACCCTAAGTCC-GGAT
1 ATAATTCCAGCTCGA-AGCCTGCGGGACCTTAAG-CCTGGAC
* *
8677 ATAATTCCAGCAC-ATAGCCTGC-GGACCCTAAG
1 ATAATTCCAGCTCGA-AGCCTGCGGGACCTTAAG
8709 TCCGGATATA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
38 3 0.03
39 89 0.95
40 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
ATAATTCCAGCTCGAAGCCTGCGGGACCTTAAGCCTGGAC
Found at i:8709 original size:39 final size:39
Alignment explanation
Indices: 8603--8718 Score: 196
Period size: 39 Copynumber: 3.0 Consensus size: 39
8593 CTGGACATAT
** * *
8603 TTCCAGCATGTAGCCTGCGGACCTTAAGTCTGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
8642 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
8681 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATA
8719 CATCACTGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:23644 original size:13 final size:13
Alignment explanation
Indices: 23628--23660 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
23618 TTCAATTAAA
*
23628 TTAGTTAATTAGT
1 TTAGATAATTAGT
23641 TTAGATAATTAGT
1 TTAGATAATTAGT
23654 TTA-ATAA
1 TTAGATAA
23661 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:25477 original size:46 final size:46
Alignment explanation
Indices: 25329--25484 Score: 133
Period size: 46 Copynumber: 3.3 Consensus size: 46
25319 TGTGTGAGCT
* * *
25329 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTA-TGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGAGT-A-AGCC
* * * **
25375 AGTGTAAGACCATGTCTGGGACATGGCATCAACATTTAGATGAGT-A-TT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGC--CTCGATGAGTAAGCC
*
25423 AATGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGA-GTAAGCC
25469 AGTGTAAGACATGTCT
1 AGTGTAAGACATGTCT
25485 AGACATAGAT
Statistics
Matches: 86, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
43 2 0.02
44 5 0.06
45 1 0.01
46 31 0.36
47 28 0.33
48 14 0.16
49 1 0.01
51 3 0.03
52 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGAGTAAGCC
Found at i:28167 original size:39 final size:39
Alignment explanation
Indices: 28124--28239 Score: 178
Period size: 39 Copynumber: 3.0 Consensus size: 39
28114 CGGGACATAT
* * *
28124 TTCCAGCACGTAGCCTACGAACCTTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGAACCCTAAGTCCGGATATAA
*
28163 TTCCAGCACATAGCCTGCGAACCCTAACTCCGGATATAA
1 TTCCAGCACATAGCCTGCGAACCCTAAGTCCGGATATAA
* *
28202 TTCCAGGACATAGCCTGCGGACCCTAAGTCCGGATATA
1 TTCCAGCACATAGCCTGCGAACCCTAAGTCCGGATATA
28240 CATCACTGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGAACCCTAAGTCCGGATATAA
Found at i:36294 original size:39 final size:39
Alignment explanation
Indices: 36198--36392 Score: 193
Period size: 39 Copynumber: 5.0 Consensus size: 39
36188 ACTTGAAACC
** *
36198 AATTACCAGCACA-AGCCTGCGGGAATTTAA-ACCGG-TAT
1 AATT-CCAGCACATAGCCTGC-GGACCTTAAGTCCGGATAT
* * * * *
36236 AATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCGGACAT
1 AATTCCAGCAC-ATAGCCTGC-GGACCTTAAGTCCGGATAT
* * * *
36275 ATTTCCAGCACGTAGCCTGCAGACCTTAAGTCTGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
*
36314 AATTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
*
36353 AATTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
36392 A
1 A
36393 CATCACTGAA
Statistics
Matches: 132, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
37 9 0.07
38 21 0.16
39 102 0.77
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (39 bp):
AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
Found at i:50672 original size:28 final size:27
Alignment explanation
Indices: 50616--50712 Score: 92
Period size: 28 Copynumber: 3.4 Consensus size: 27
50606 GTACAAGAAC
*
50616 CTAAG-GTGCGAGTTTGGTTAATAGCA
1 CTAAGTGTGCGAGTTTGATTAATAGCA
50642 CTAAGTGTGCGAG-TTGATTCATATAGCA
1 CTAAGTGTGCGAGTTTGATT-A-ATAGCA
50670 CTAAGTGTGC-AGTATTGATCTATTATAGCAA
1 CTAAGTGTGCGAGT-TTGAT-TA--ATAGC-A
*
50701 CTGAGTGTGCGA
1 CTAAGTGTGCGA
50713 CTTATATTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
26 10 0.17
27 10 0.17
28 16 0.27
29 6 0.10
30 7 0.12
31 10 0.17
32 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (27 bp):
CTAAGTGTGCGAGTTTGATTAATAGCA
Done.