Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1228
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: 29088
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Found at i:1114 original size:27 final size:27
Alignment explanation
Indices: 1084--1203 Score: 144
Period size: 27 Copynumber: 4.6 Consensus size: 27
1074 ATATTAAGTC
*
1084 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
1111 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
*
1139 CGCACACTTAGTGCT-GATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAA-CT
*
1166 CGCACACTTA-----ACATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
1189 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1204 GTACAATTTA
Statistics
Matches: 81, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
23 18 0.22
24 2 0.02
26 2 0.02
27 40 0.49
28 19 0.23
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:1201 original size:50 final size:50
Alignment explanation
Indices: 1084--1204 Score: 154
Period size: 50 Copynumber: 2.3 Consensus size: 50
1074 ATATTAAGTC
* * *
1084 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCT-GATAATCAACTCGCACACTTA--G--ACATAATCAAACT
1139 CGCACACTTAGTGCTGATAATCAAGCTCGCACACTTA-ACATAATCAAACT
1 CGCACACTTAGTGCTGATAATCAA-CTCGCACACTTAGACATAATCAAACT
1189 CGCACACTTAGTGCTG
1 CGCACACTTAGTGCTG
1205 TACAATTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
50 28 0.45
54 8 0.13
55 26 0.42
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (50 bp):
CGCACACTTAGTGCTGATAATCAACTCGCACACTTAGACATAATCAAACT
Found at i:9474 original size:28 final size:28
Alignment explanation
Indices: 9411--9561 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
9401 ATATTAAGTC
*
9411 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
9438 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
9466 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
*
9494 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * * *
9522 CGCACAGTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
9551 CGCACACTTAG
1 CGCACACTTAG
9562 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
27 22 0.20
28 74 0.67
29 15 0.14
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:14175 original size:40 final size:40
Alignment explanation
Indices: 13963--14168 Score: 344
Period size: 40 Copynumber: 5.2 Consensus size: 40
13953 AACCCAAGTA
* *
13963 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
14002 CCTTTGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
14042 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
14082 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
14122 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
14162 CCTTCGG
1 CCTTCGG
14169 ATCTTAGTCC
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 12 0.08
40 144 0.92
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:15599 original size:13 final size:13
Alignment explanation
Indices: 15583--15610 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15573 TTTATTATTT
15583 TTAACACAAAATA
1 TTAACACAAAATA
15596 TTAACACAAAATA
1 TTAACACAAAATA
15609 TT
1 TT
15611 TATAATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAACACAAAATA
Found at i:22260 original size:78 final size:79
Alignment explanation
Indices: 22121--22324 Score: 340
Period size: 78 Copynumber: 2.6 Consensus size: 79
22111 AACCCAAGTA
* *
22121 CCTTCGGGATTTAGCCGGATATAG-CAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
1 CCTTCGGGACTTAGCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAA
*
22185 TCACTAGCACAAATG
65 TAACTAGCACAAATG
*
22200 CCTTC-GGACTTAGCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAAT
22264 AACTAGCACAAATG
66 AACTAGCACAAATG
22278 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGG
1 CCTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAATGCCTTCGG
22325 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
78 72 0.61
79 14 0.12
80 32 0.27
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAAT
AACTAGCACAAATG
Found at i:22331 original size:40 final size:40
Alignment explanation
Indices: 22121--22324 Score: 335
Period size: 40 Copynumber: 5.2 Consensus size: 40
22111 AACCCAAGTA
* *
22121 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
22160 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
22200 CCTTC-GGACTTAG-CCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
22238 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
22278 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
22318 CCTTCGG
1 CCTTCGG
22325 ATCTTAGTCC
Statistics
Matches: 155, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
38 29 0.19
39 29 0.19
40 96 0.62
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:23752 original size:13 final size:13
Alignment explanation
Indices: 23736--23762 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23726 TTTATTATTT
23736 TTAACACAAAATA
1 TTAACACAAAATA
23749 TTAACACAAAATA
1 TTAACACAAAATA
23762 T
1 T
23763 AATATGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (13 bp):
TTAACACAAAATA
Done.