Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1489
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: 32931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1595 original size:10 final size:10
Alignment explanation
Indices: 1582--1642 Score: 61
Period size: 10 Copynumber: 5.8 Consensus size: 10
1572 ATTTTCCTTT
1582 TCTCTTCTTC
1 TCTCTTCTTC
*
1592 TCTCTTCTTT
1 TCTCTTCTTC
*
1602 TCTTTCTCTTC
1 TCTCT-TCTTC
1613 TCTCTATC-TC
1 TCTCT-TCTTC
1623 TCTCTTGCTCTC
1 TCTCTT-CT-TC
1635 TCTCTTCT
1 TCTCTTCT
1643 CCTTTGCTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 1 0.02
10 21 0.50
11 12 0.29
12 8 0.19
ACGTcount: A:0.02, C:0.38, G:0.02, T:0.59
Consensus pattern (10 bp):
TCTCTTCTTC
Found at i:1614 original size:29 final size:29
Alignment explanation
Indices: 1581--1643 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1571 CATTTTCCTT
* *
1581 TTCTCTTCT-TCTCTCTTCTT-TTCTTTCTC
1 TTCTC-TCTATCTCTC-TCTTGCTCTCTCTC
1610 TTCTCTCTATCTCTCTCTTGCTCTCTCTC
1 TTCTCTCTATCTCTCTCTTGCTCTCTCTC
1639 TTCTC
1 TTCTC
1644 CTTTGCTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.02, C:0.38, G:0.02, T:0.59
Consensus pattern (29 bp):
TTCTCTCTATCTCTCTCTTGCTCTCTCTC
Found at i:4990 original size:2 final size:2
Alignment explanation
Indices: 4973--5017 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4963 ATAAACTTAC
* *
4973 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5015 AT A
1 AT A
5018 GTGCTGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:8508 original size:22 final size:21
Alignment explanation
Indices: 8469--8510 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
8459 AGAAAATTAA
*
8469 AGTACTCCGAGAACGCACAAG
1 AGTACTCCAAGAACGCACAAG
*
8490 AGTACTCCAAAGAATGCACAA
1 AGTACTCC-AAGAACGCACAA
8511 TGTGCAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.12
Consensus pattern (21 bp):
AGTACTCCAAGAACGCACAAG
Found at i:9036 original size:1 final size:1
Alignment explanation
Indices: 9032--9062 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
9022 TTTTTTATTT
*
9032 GGGGGCGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
9063 CATATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:16933 original size:38 final size:38
Alignment explanation
Indices: 16876--17044 Score: 232
Period size: 38 Copynumber: 4.4 Consensus size: 38
16866 GTTCAATTTG
** * *
16876 GAATTCTCTAGCCACCAGCCACCGGCCAATTCCAAATT
1 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
* *
16914 GAATTCTCTAGTCGTCAGCCGCCGGCCAATTCCAAATT
1 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
*
16952 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTTCAAATT
1 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
* * *
16990 GAATTCTCTAGCCGTCAGCTGCCAGTCAATTTCAAATT
1 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
17028 GAATTCTCT-GACCGTCA
1 GAATTCTCTAG-CCGTCA
17045 ACTAATTCAA
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
37 1 0.01
38 120 0.99
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (38 bp):
GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
Found at i:22404 original size:2 final size:2
Alignment explanation
Indices: 22399--22435 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
22389 ACAAAGTGTG
22399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22436 AGTTTGAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23743 original size:1 final size:1
Alignment explanation
Indices: 23737--23767 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
23727 CTTGACCTCG
*
23737 TTTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23768 CCTTACCAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:29941 original size:37 final size:38
Alignment explanation
Indices: 29780--29952 Score: 215
Period size: 38 Copynumber: 4.6 Consensus size: 38
29770 TTGAATTAGT
* * * *
29780 TGACGG-TCAGAGAATTCAATTTGAAATTGACTGGCAGC
1 TGACGGCT-AGAGAATTCAATTTGGAATTGGCCGGCGGC
* *
29818 TGACGGCTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGGCCGGCGGC
*
29856 TGACGTCTAGAGAATTCAATTTGGAATTGGCCGGCGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGGCCGGCGGC
* *
29894 TGACGACTAGAG-ATTCAATTTGGAATTGGCCGGTGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGGCCGGCGGC
**
29931 TGGTGGCTAGAGAATTCCAATT
1 TGACGGCTAGAGAATT-CAATT
29953 GAACTCTCTT
Statistics
Matches: 122, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
37 33 0.27
38 83 0.68
39 6 0.05
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGGAATTGGCCGGCGGC
Done.