Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4608
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: 14228
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:132 original size:27 final size:27
Alignment explanation
Indices: 92--160 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
82 TTCACTTTTG
*
92 TTTTTTC-TTCTTTTTTTTAACTCGTTT
1 TTTTTTCATT-TTTTTTTTAACTCGATT
***
119 TTTTTTCATTTTTTTTTTTTTTCGATT
1 TTTTTTCATTTTTTTTTTAACTCGATT
146 TTTTTT-ATTTTTTTT
1 TTTTTTCATTTTTTTT
161 GAATTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 9 0.24
27 26 0.70
28 2 0.05
ACGTcount: A:0.07, C:0.09, G:0.03, T:0.81
Consensus pattern (27 bp):
TTTTTTCATTTTTTTTTTAACTCGATT
Found at i:135 original size:16 final size:17
Alignment explanation
Indices: 116--175 Score: 77
Period size: 19 Copynumber: 3.4 Consensus size: 17
106 TTTTAACTCG
116 TTTTTTTTTC-ATTTTT
1 TTTTTTTTTCGATTTTT
132 TTTTTTTTTCGATTTTTT
1 TTTTTTTTTCGA-TTTTT
*
150 TTATTTTTTTTGAATTTTT
1 TT-TTTTTTTCG-ATTTTT
169 TTTTTTT
1 TTTTTTT
176 CGTTGAACCT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
16 10 0.26
17 1 0.03
18 12 0.31
19 15 0.38
20 1 0.03
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTCGATTTTT
Found at i:147 original size:11 final size:10
Alignment explanation
Indices: 117--171 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 10
107 TTTAACTCGT
*
117 TTTTTTTTCA
1 TTTTTTTTGA
127 -TTTTTTT--
1 TTTTTTTTGA
*
134 TTTTTTTCGA
1 TTTTTTTTGA
144 TTTTTTTT-A
1 TTTTTTTTGA
153 TTTTTTTTGAA
1 TTTTTTTTG-A
164 TTTTTTTT
1 TTTTTTTT
172 TTTTCGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 6 0.16
9 16 0.42
10 7 0.18
11 9 0.24
ACGTcount: A:0.09, C:0.04, G:0.04, T:0.84
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:182 original size:19 final size:17
Alignment explanation
Indices: 116--175 Score: 68
Period size: 16 Copynumber: 3.4 Consensus size: 17
106 TTTTAACTCG
*
116 TTTTTTTTT-CATTTTT
1 TTTTTTTTTGAATTTTT
*
132 TTTTTTTTTCGATTTTTTT
1 TTTTTTTTT-GA-ATTTTT
151 TATTTTTTTTGAATTTTT
1 T-TTTTTTTTGAATTTTT
169 TTTTTTT
1 TTTTTTT
176 CGTTGAACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.24
17 6 0.16
18 6 0.16
19 8 0.22
20 8 0.22
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTGAATTTTT
Found at i:3268 original size:15 final size:15
Alignment explanation
Indices: 3248--3300 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
3238 CTTGCCTCTC
*
3248 TTTCTTTTTATTTTT
1 TTTCTTTTTCTTTTT
*
3263 TTTCTTTTTCTTCTT
1 TTTCTTTTTCTTTTT
3278 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTT-T
3294 TTTCTTT
1 TTTCTTT
3301 GTTTTCTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 26 0.76
16 8 0.24
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTTCTTTTT
Found at i:3270 original size:6 final size:6
Alignment explanation
Indices: 3248--3300 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
3238 CTTGCCTCTC
*
3248 TTTCTT TTTATT TTT-TT TCTT-TT TCTTCTT TTTCTT TTTC-T TTTC-T
1 TTTCTT TTTCTT TTTCTT T-TTCTT T-TTCTT TTTCTT TTTCTT TTTCTT
3294 TTTCTT T
1 TTTCTT T
3301 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
5 13 0.30
6 27 0.63
7 3 0.07
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:3310 original size:21 final size:20
Alignment explanation
Indices: 3243--3311 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
3233 TGCCTCTTGC
3243 CTCTCTTTCTTTTTATT-TTTT
1 CTCT-TTTCTTTTT-TTCTTTT
*
3264 TTCTTTTTCTTCTTTTTCTTTT
1 CTC-TTTTCTT-TTTTTCTTTT
*
3286 -TCTTTTCTTTTCTTTGTTTT
1 CTCTTTTCTTTT-TTTCTTTT
3306 CTCTTT
1 CTCTTT
3312 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 2 0.05
20 14 0.34
21 17 0.41
22 8 0.20
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (20 bp):
CTCTTTTCTTTTTTTCTTTT
Found at i:9098 original size:12 final size:12
Alignment explanation
Indices: 9081--9111 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
9071 AGGAAATTTG
9081 AAAAAAAAATTCA
1 AAAAAAAAATT-A
9094 AAAAAAAAATTA
1 AAAAAAAAATTA
9106 AAAAAA
1 AAAAAA
9112 TGAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:10058 original size:37 final size:37
Alignment explanation
Indices: 10007--10077 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
9997 CATTCTTGTA
10007 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
10044 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
10078 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:10077 original size:6 final size:6
Alignment explanation
Indices: 10017--10066 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
10007 AAGAGAAAAC
*
10017 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
10066 A
1 A
10067 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:10159 original size:11 final size:12
Alignment explanation
Indices: 10127--10157 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
10117 TTGAGAGAAC
10127 TTGAAAAAGCCT
1 TTGAAAAAGCCT
10139 TTGAAAAAGCCT
1 TTGAAAAAGCCT
10151 TTGAAAA
1 TTGAAAA
10158 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:13951 original size:20 final size:20
Alignment explanation
Indices: 13905--13951 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
13895 AGCTTGTTTC
*
13905 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
13925 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13945 CAGCTCA
1 CAGCTCA
13952 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Done.