Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1547
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: 10376
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Found at i:3131 original size:55 final size:55
Alignment explanation
Indices: 3038--3426 Score: 484
Period size: 55 Copynumber: 6.9 Consensus size: 55
3028 GACGCCTTTT
*
3038 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
3093 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
3148 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
3203 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTCCAGTCCTTAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
*
3257 CTTTTTCTTTTCAAAG-CC-CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACG
1 C-----C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
** * *
3316 CCTTTTCTTTTCAAAGCCCACATGAGTTGGTGACACCTTT-CAGTCCTCAAAGAGCAGGACG
1 -C----C-TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
* *
3377 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCA
3427 AGATGCACTA
Statistics
Matches: 303, Mismatches: 19, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
54 27 0.09
55 174 0.57
56 1 0.00
58 15 0.05
59 39 0.13
60 12 0.04
61 32 0.11
62 3 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
Found at i:3180 original size:27 final size:27
Alignment explanation
Indices: 3099--3234 Score: 76
Period size: 27 Copynumber: 5.0 Consensus size: 27
3089 GACGCCTTTC
3099 AAAGCCCACACAAGTTGGTGGCATTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT
** * * * ** ** *
3126 CCAGTCCTCAAAGAGCAGGACGCCTTTT
1 AAAGCCCACACA-AGTTGGTGGCATTTT
3154 AAAGCCCACACAAGTTGGTGGCATTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT
** * * * * * *
3181 CCAGTCCTCAAAGAGTAGGAT-GCCTTTC
1 AAAGCCCACACA-AGTTGG-TGGCATTTT
3209 AAAGCCCACACAAGTTGGTGGCATTT
1 AAAGCCCACACAAGTTGGTGGCATTT
3235 CCAGTCCTTA
Statistics
Matches: 70, Mismatches: 35, Indels: 8
0.62 0.31 0.07
Matches are distributed among these distances:
26 1 0.01
27 34 0.49
28 34 0.49
29 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (27 bp):
AAAGCCCACACAAGTTGGTGGCATTTT
Found at i:3366 original size:229 final size:225
Alignment explanation
Indices: 3012--3424 Score: 584
Period size: 229 Copynumber: 1.8 Consensus size: 225
3002 TTCACTTTTT
*
3012 AGTCCTCAAAGAGCATGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* *
3077 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
66 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGACACTTTCCAGTCCTCAAAGAGC
*
3142 AGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGTAGGATGCCT
131 AGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGTAGGATGCCT
3206 TTCAAAGCCCACACAAGTTGGTGGCATTTCC
195 TTCAAAGCCCACACAAGTTGGTGGCATTTCC
* * * * *
3237 AGTCCTTAAAGAGCAGGATGCTTTTTCTTTTCAAAG-CC-CACAAGTTGGTGGCA-TTTTCCAGT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGT
* **
3299 CCTCAAAGAGTAGGACGCCTTTTCTTTTCAAAGCCCACATGAGTTGGTGACACCTTT-CAGTCCT
65 CCTCAAAGAGCAGGACG-C----C-TTTCAAAGCCCACACAAGTTGGTGACA-CTTTCCAGTCCT
* *
3363 CAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAG
123 CAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAG
3425 CAAGATGCAC
Statistics
Matches: 165, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
222 3 0.02
223 35 0.21
224 3 0.02
225 31 0.19
228 1 0.01
229 85 0.52
230 7 0.04
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (225 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGACACTTTCCAGTCCTCAAAGAGC
AGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGTAGGATGCCTT
TCAAAGCCCACACAAGTTGGTGGCATTTCC
Found at i:9001 original size:19 final size:19
Alignment explanation
Indices: 8977--9016 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8967 ACAGTAAATG
8977 TACATAAGTGTTGTATCGA
1 TACATAAGTGTTGTATCGA
8996 TACATAAGTGTTGTATCGA
1 TACATAAGTGTTGTATCGA
9015 TA
1 TA
9017 TAGTGTATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (19 bp):
TACATAAGTGTTGTATCGA
Found at i:9039 original size:16 final size:16
Alignment explanation
Indices: 8987--9041 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 16
8977 TACATAAGTG
8987 TTGTATCGATACATAAGT
1 TTGTATCGATAC-TAA-T
9005 GTTGTATCGATA-T-A-
1 -TTGTATCGATACTAAT
*
9019 GTGTATCGATACTAAT
1 TTGTATCGATACTAAT
9035 TTGTATC
1 TTGTATC
9042 TACAATGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 10 0.32
14 1 0.03
15 1 0.03
16 7 0.23
17 1 0.03
19 11 0.35
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (16 bp):
TTGTATCGATACTAAT
Found at i:9097 original size:21 final size:21
Alignment explanation
Indices: 9071--9112 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9061 GCTACTACCA
9071 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
9092 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
9113 GATTTGTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:9172 original size:20 final size:21
Alignment explanation
Indices: 9139--9181 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
9129 TCCGAAAATT
9139 TTACCCAGATGTATCGATACA
1 TTACCCAGATGTATCGATACA
9160 TTACCCA-ATGTATCGATACA
1 TTACCCAGATGTATCGATACA
9180 TT
1 TT
9182 CAGGCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (21 bp):
TTACCCAGATGTATCGATACA
Done.