Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2780
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: 41227
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5083 original size:10 final size:10
Alignment explanation
Indices: 5068--5129 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
5058 TTTGAACCAT
*
5068 TACCAATTCG
1 TACCAATTCA
*
5078 TACCAAATACCA
1 TACC-AAT-TCA
*
5090 TACCATTTCA
1 TACCAATTCA
5100 TACCAATTCCA
1 TACCAATT-CA
* *
5111 TACCATTTCG
1 TACCAATTCA
5121 TACCAATTC
1 TACCAATTC
5130 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:5113 original size:21 final size:21
Alignment explanation
Indices: 5068--5130 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
5058 TTTGAACCAT
* *
5068 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
5090 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
5111 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
5131 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:6200 original size:15 final size:15
Alignment explanation
Indices: 6168--6201 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6158 GTTCAACGAA
*
6168 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
6183 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
6198 GAGG
1 GAGG
6202 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:9952 original size:10 final size:10
Alignment explanation
Indices: 9937--9998 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
9927 TTTGAACCAT
*
9937 TACCAATTCG
1 TACCAATTCA
*
9947 TACCAAATACCA
1 TACC-AAT-TCA
*
9959 TACCATTTCA
1 TACCAATTCA
9969 TACCAATTCCA
1 TACCAATT-CA
* *
9980 TACCATTTCG
1 TACCAATTCA
9990 TACCAATTC
1 TACCAATTC
9999 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:9982 original size:21 final size:21
Alignment explanation
Indices: 9937--9999 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
9927 TTTGAACCAT
* *
9937 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
9959 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
9980 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
10000 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:17495 original size:15 final size:15
Alignment explanation
Indices: 17470--17516 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
17460 AGAAAAGAAT
17470 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
17486 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
*
17501 AAA-AATGTGAAAATG
1 AAAGAA-ATGAAAATG
17516 A
1 A
17517 GATTTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.07
15 21 0.78
16 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:17505 original size:28 final size:29
Alignment explanation
Indices: 17460--17516 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
17450 ATTTTGAGCG
17460 AGAAAAGAATAAAGAAAA-TGAAAATGAA
1 AGAAAAGAATAAAGAAAAGTGAAAATGAA
*
17488 AGAAATGAA-AAAGAAAAATGTGAAAATGA
1 AGAAAAGAATAAAG-AAAA-GTGAAAATGA
17517 GATTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.16
28 12 0.48
30 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.12
Consensus pattern (29 bp):
AGAAAAGAATAAAGAAAAGTGAAAATGAA
Found at i:17563 original size:12 final size:12
Alignment explanation
Indices: 17546--17621 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
17536 AGTGAAAAGC
17546 AAAAAGAGATTG
1 AAAAAGAGATTG
*
17558 AAAAAGAAATT-
1 AAAAAGAGATTG
*
17569 -AAAAGAGA-AG
1 AAAAAGAGATTG
*
17579 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
17594 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
17606 AAAGAGAGCTTG
1 AAAAAGAGATTG
17618 AAAA
1 AAAA
17622 GAAATCGAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
10 7 0.15
11 5 0.10
12 24 0.50
13 5 0.10
15 7 0.15
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:17583 original size:21 final size:22
Alignment explanation
Indices: 17547--17587 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
17537 GTGAAAAGCA
*
17547 AAAAGAGATTGAAAAAGAAATT
1 AAAAGAGATAGAAAAAGAAATT
17569 AAAAGAGA-AGAAAAAGAAA
1 AAAAGAGATAGAAAAAGAAA
17588 GAGTGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.10
Consensus pattern (22 bp):
AAAAGAGATAGAAAAAGAAATT
Found at i:19522 original size:10 final size:10
Alignment explanation
Indices: 19498--19546 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
19488 AGCTCGTTTC
*
19498 CAGCTCACTT
1 CAGCTCAATT
* *
19508 GAGCTCAAGT
1 CAGCTCAATT
19518 CAGCTC-ATT
1 CAGCTCAATT
19527 CGAGCTCAATT
1 C-AGCTCAATT
19538 CAGCTCAAT
1 CAGCTCAAT
19547 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:19523 original size:20 final size:20
Alignment explanation
Indices: 19498--19544 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
19488 AGCTCGTTTC
19498 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
19518 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
19538 CAGCTCA
1 CAGCTCA
19545 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:25921 original size:21 final size:22
Alignment explanation
Indices: 25895--25958 Score: 85
Period size: 21 Copynumber: 2.9 Consensus size: 22
25885 GTATTTGGTT
25895 TTGGTACGAAATGGTATGG-AA
1 TTGGTACGAAATGGTATGGTAA
* *
25916 TTGGTATGAAATGGTATGGTAT
1 TTGGTACGAAATGGTATGGTAA
*
25938 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGT-ATGGT
25959 TCAAAGAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 18 0.49
22 14 0.38
23 5 0.14
ACGTcount: A:0.28, C:0.03, G:0.33, T:0.36
Consensus pattern (22 bp):
TTGGTACGAAATGGTATGGTAA
Found at i:37885 original size:13 final size:13
Alignment explanation
Indices: 37869--37904 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
37859 TTTATACTTC
37869 AATTTTTTTTTTG
1 AATTTTTTTTTTG
37882 AATTTTTTTTTTG
1 AATTTTTTTTTTG
37895 -ATTTTTTTTT
1 AATTTTTTTTT
37905 CAAATTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (13 bp):
AATTTTTTTTTTG
Done.