Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3530
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: 47865
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Found at i:1729 original size:40 final size:40
Alignment explanation
Indices: 1674--1888 Score: 305
Period size: 40 Copynumber: 5.4 Consensus size: 40
1664 GATGATAACG
* *
1674 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
1714 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
1754 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
**
1794 GGGCTAAGT-CCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
1833 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
* *
1873 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
1889 TACTTGGTTT
Statistics
Matches: 164, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
39 53 0.32
40 110 0.67
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:1846 original size:79 final size:80
Alignment explanation
Indices: 1674--1888 Score: 305
Period size: 79 Copynumber: 2.7 Consensus size: 80
1664 GATGATAACG
* *
1674 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTTGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGT
**
1738 GCGAGTTACTAATTCC
65 GCGAACTACTAATTCC
1754 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTG
1818 CGAACTACT-ATATCC
66 CGAACTACTAAT-TCC
* * *
1833 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
1889 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
78 10 0.08
79 68 0.55
80 45 0.36
81 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTG
CGAACTACTAATTCC
Found at i:9635 original size:40 final size:40
Alignment explanation
Indices: 9580--9769 Score: 258
Period size: 40 Copynumber: 4.8 Consensus size: 40
9570 GATGATAACG
* **
9580 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGGCTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* * *
9620 GGGCTAAGTCTCGAAGTCATTCGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
9660 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATT-C
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCC
**
9700 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
* *
9740 GGACTAAGTCCCGAAGGCATTTGAGCGAGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT
9770 AGCTATATCC
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 126 0.95
41 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:9776 original size:40 final size:39
Alignment explanation
Indices: 9580--9795 Score: 249
Period size: 40 Copynumber: 5.4 Consensus size: 39
9570 GATGATAACG
* *
9580 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGGCTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATA-TCC
* * *
9620 GGGCTAAGTCTCGAAGTCATTCGTGCGAGTTACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATA-TCC
*
9660 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCC
*
9700 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATATCC
* *
9740 GGACTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATATCC
* *
9780 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
9796 TACTTGGTTT
Statistics
Matches: 155, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
39 16 0.10
40 136 0.88
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCC
Found at i:23106 original size:27 final size:26
Alignment explanation
Indices: 23076--23225 Score: 149
Period size: 27 Copynumber: 5.5 Consensus size: 26
23066 AAATTGTACA
*
23076 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTG
* *
23103 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCG-ATTGACTATG-TG
* *
23130 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTG
* *
23157 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTG
* *
23185 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTG
23212 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
23226 TGTTGATTGT
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.01
27 77 0.75
28 25 0.24
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTG
Found at i:23192 original size:82 final size:81
Alignment explanation
Indices: 23076--23225 Score: 212
Period size: 82 Copynumber: 1.8 Consensus size: 81
23066 AAATTGTACA
* * * *
23076 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
23140 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
23157 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
23222 TGCG
65 TGCG
23226 TGTTGATTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 18 0.30
82 42 0.70
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:23231 original size:27 final size:27
Alignment explanation
Indices: 23156--23233 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
23146 TTGACCATGC
* * * *
23156 GGCACTAAGTGTGCGAGTCTAACTATGT
1 GGCACTAAGTGTGCGTGT-TGATTACGT
*
23184 AGCACTAAGTGTGCGAT-TTGATTACGT
1 GGCACTAAGTGTGCG-TGTTGATTACGT
23211 GGCACTAAGTGTGCGTGTTGATT
1 GGCACTAAGTGTGCGTGTTGATT
23234 GTATAGCACT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
26 1 0.02
27 26 0.62
28 15 0.36
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32
Consensus pattern (27 bp):
GGCACTAAGTGTGCGTGTTGATTACGT
Found at i:23242 original size:27 final size:27
Alignment explanation
Indices: 23075--23252 Score: 85
Period size: 27 Copynumber: 6.6 Consensus size: 27
23065 TAAATTGTAC
* * **
23075 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATTTGATTACAT
* ** * *
23102 TGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGATTA-CAT
* *
23130 -GCACTAAGTGTGCGAATTGA--CCAT
1 AGCACTAAGTGTGCGATTTGATTACAT
* * * * **
23154 GCGGCACTAAGTGTGCGAGTCTAACTATGT
1 --AGCACTAAGTGTGCGA-TTTGATTACAT
*
23184 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTACAT
* **
23211 GGCACTAAGTGTGCG-TGTTGATTGTAT
1 AGCACTAAGTGTGCGAT-TTGATTACAT
*
23238 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
23253 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
24 2 0.02
26 1 0.01
27 94 0.81
28 18 0.16
30 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTACAT
Found at i:23243 original size:82 final size:81
Alignment explanation
Indices: 23068--23252 Score: 201
Period size: 82 Copynumber: 2.3 Consensus size: 81
23058 GCGGGATTAA
* * * *
23068 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
23133 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
23149 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
**
23213 CACTAAGTGTGCGTGTTG
64 CACTAAGTGTGCGAATTG
* *
23231 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
23253 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
81 21 0.26
82 60 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:32139 original size:29 final size:27
Alignment explanation
Indices: 32064--32145 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
32054 GCGAGACTGC
* *
32064 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGGCGAAGCCACCAGATA
* *
32091 CAGATATTGTGGCTAGGCCACCAGA-A
1 CAGATATTGTGGCGAAGCCACCAGATA
32117 CAGATATATATGTGGCGAAGCCACCAGAT
1 CAG--ATAT-TGTGGCGAAGCCACCAGAT
32146 TGCAGCGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.09
27 21 0.47
28 4 0.09
29 16 0.36
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGGCGAAGCCACCAGATA
Found at i:40257 original size:26 final size:27
Alignment explanation
Indices: 40227--40294 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 27
40217 TTATCCTCCG
*
40227 GGGTATATCAGTAGTCCTA-CCCTACA
1 GGGTATATCAGTAATCCTATCCCTACA
* * * *
40253 GGGTATTTCGGTAATTCTATCCTTACA
1 GGGTATATCAGTAATCCTATCCCTACA
* *
40280 GGGTATTTCAATAAT
1 GGGTATATCAGTAAT
40295 TCTACAACTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 15 0.44
27 19 0.56
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (27 bp):
GGGTATATCAGTAATCCTATCCCTACA
Found at i:42219 original size:47 final size:45
Alignment explanation
Indices: 42150--42270 Score: 131
Period size: 47 Copynumber: 2.7 Consensus size: 45
42140 CTCGTAGCCG
*
42150 ATGCATGTCCTAGACATGTCTTACACTAGCTCTACATCATCGAGGCCA
1 ATGCATGTCCTAAACATGTCTTACACTAGCT-TACATC--CGAGGCCA
* *
42198 ATGCATGTCC-AAACATGTCTTACACTGGCTTACATCCGAGGCCG
1 ATGCATGTCCTAAACATGTCTTACACTAGCTTACATCCGAGGCCA
* * * *
42242 ATGTATGTGCTAGATATG--TTACACTAGCT
1 ATGCATGTCCTAAACATGTCTTACACTAGCT
42271 CTCGGTCTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
43 10 0.16
44 15 0.23
45 5 0.08
46 6 0.09
47 18 0.28
48 10 0.16
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (45 bp):
ATGCATGTCCTAAACATGTCTTACACTAGCTTACATCCGAGGCCA
Done.