Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3407
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: 31099
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2045 original size:17 final size:17
Alignment explanation
Indices: 2020--2072 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2010 GCTCTTTTCA
*
2020 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
2037 TTC-TTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
2053 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
2070 TTC
1 TTC
2073 GCTCTTTTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:2046 original size:16 final size:16
Alignment explanation
Indices: 2020--2072 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2010 GCTCTTTTCA
2020 TTCTCTTTTTTTGAATT
1 TTCT-TTTTTTTGAATT
* *
2037 TTCTTTTTTTTCATTT
1 TTCTTTTTTTTGAATT
*
2053 TTCTTTTCTTTTGTATT
1 TTCTTTT-TTTTGAATT
2070 TTC
1 TTC
2073 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (16 bp):
TTCTTTTTTTTGAATT
Found at i:2052 original size:15 final size:15
Alignment explanation
Indices: 1982--2064 Score: 58
Period size: 15 Copynumber: 5.3 Consensus size: 15
1972 TTTCACTCAC
* *
1982 TTTTTCTTTTTCTTC
1 TTTTTCATTTTCTTT
* **
1997 TTTTTCTTTTATCGCT
1 TTTTTCATTT-TCTTT
* *
2013 CTTTTCATTCTCTTT
1 TTTTTCATTTTCTTT
**
2028 TTTTGAATTTTCTTT
1 TTTTTCATTTTCTTT
2043 TTTTTCATTTTTCTTT
1 TTTTTCA-TTTTCTTT
2059 TCTTTT
1 T-TTTT
2065 GTATTTTCGC
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
15 29 0.57
16 18 0.35
17 4 0.08
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTTCATTTTCTTT
Found at i:3096 original size:4 final size:4
Alignment explanation
Indices: 3087--3114 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3077 TTAAACTAAG
3087 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
3115 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:4517 original size:23 final size:22
Alignment explanation
Indices: 4465--4517 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4455 TCCACGTCTT
*
4465 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
4487 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
4510 TTTCTTTT
1 TTTCTTTT
4518 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:6854 original size:12 final size:13
Alignment explanation
Indices: 6837--6865 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6827 TTAAACTAAG
6837 TAAATAAAT-AAA
1 TAAATAAATAAAA
6849 TAAATAAATAAAA
1 TAAATAAATAAAA
6862 TAAA
1 TAAA
6866 AAAAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:8982 original size:12 final size:12
Alignment explanation
Indices: 8965--9023 Score: 54
Period size: 11 Copynumber: 5.0 Consensus size: 12
8955 AAACCGTATG
8965 CAATTTTTTTTT
1 CAATTTTTTTTT
8977 CAA-TTTTTTTT
1 CAATTTTTTTTT
8988 -AA-TTTTTTTT
1 CAATTTTTTTTT
*
8998 C-TTTTTTTTTT
1 CAATTTTTTTTT
9009 CGAACTCTTTTTTTT
1 C-AA-T-TTTTTTTT
9024 TACGTATCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 10 0.26
11 17 0.44
12 3 0.08
14 1 0.03
15 8 0.21
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.75
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:8985 original size:11 final size:11
Alignment explanation
Indices: 8969--9009 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
8959 CGTATGCAAT
8969 TTTTTTTTCAA
1 TTTTTTTTCAA
8980 TTTTTTTT-AA
1 TTTTTTTTCAA
**
8990 TTTTTTTTCTT
1 TTTTTTTTCAA
9001 TTTTTTTTC
1 TTTTTTTTC
9010 GAACTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:8995 original size:21 final size:21
Alignment explanation
Indices: 8969--9008 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8959 CGTATGCAAT
8969 TTTTTTTTCAATTTTTTTTAA
1 TTTTTTTTCAATTTTTTTTAA
**
8990 TTTTTTTTCTTTTTTTTTT
1 TTTTTTTTCAATTTTTTTT
9009 CGAACTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTTTTTCAATTTTTTTTAA
Found at i:9007 original size:10 final size:10
Alignment explanation
Indices: 8969--9006 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
8959 CGTATGCAAT
8969 TTTTTTTTCAA
1 TTTTTTTTC-A
*
8980 TTTTTTTTAA
1 TTTTTTTTCA
8990 TTTTTTTTC-
1 TTTTTTTTCA
8999 TTTTTTTT
1 TTTTTTTT
9007 TTCGAACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 9 0.36
11 8 0.32
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:9349 original size:20 final size:20
Alignment explanation
Indices: 9324--9378 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
9314 TGGTATTTGG
*
9324 GAATTGGTTCGAAATAGTAT
1 GAATTGGTACGAAATAGTAT
*
9344 GAATTGGTACGAAATGGTAT
1 GAATTGGTACGAAATAGTAT
*
9364 GGTATTTGGTACGAA
1 -G-AATTGGTACGAA
9379 TTGGTAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 18 0.60
21 1 0.03
22 11 0.37
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (20 bp):
GAATTGGTACGAAATAGTAT
Found at i:9375 original size:22 final size:23
Alignment explanation
Indices: 9347--9389 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
9337 ATAGTATGAA
9347 TTGGTACGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
*
9369 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGTAATGGT
9390 TGAAAAGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.37
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:16068 original size:23 final size:22
Alignment explanation
Indices: 16016--16068 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
16006 TCCACGTCTT
*
16016 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
16038 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
16061 TTTCTTTT
1 TTTCTTTT
16069 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:26765 original size:18 final size:21
Alignment explanation
Indices: 26730--26770 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 21
26720 TTCTTGAAGG
*
26730 CAAGTCCCAATAAGAAGATTC
1 CAAGTCCCAATAAGAAGAATC
26751 CAAG-CCCAAT-A-AAGAATC
1 CAAGTCCCAATAAGAAGAATC
26769 CA
1 CA
26771 CACCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 6 0.32
21 4 0.21
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (21 bp):
CAAGTCCCAATAAGAAGAATC
Found at i:26847 original size:15 final size:15
Alignment explanation
Indices: 26827--26856 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26817 AGTTGTAAAG
*
26827 TTTATTTTTTATTTA
1 TTTATTTATTATTTA
26842 TTTATTTATTATTTA
1 TTTATTTATTATTTA
26857 CTTAGTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTATTATTTA
Done.