Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1107
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: 32868
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1849 original size:18 final size:17
Alignment explanation
Indices: 1771--1866 Score: 77
Period size: 18 Copynumber: 5.4 Consensus size: 17
1761 TATCATATCA
*
1771 CTCATTTCTTTTGCACT
1 CTCATTTCTTTTTCACT
*
1788 CTCATTTCTTTCTTCATT
1 CTCATTTCTTT-TTCACT
* *
1806 CTCAATCTCTTTTTCAGTT
1 CTC-ATTTCTTTTTCA-CT
* *
1825 CTCTTTTCTTTTTCACA
1 CTCATTTCTTTTTCACT
*
1842 CTCATTT-TTATTCTCAAT
1 CTCATTTCTT-TT-TCACT
1860 CTCATTT
1 CTCATTT
1867 TCAATTTTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
16 2 0.03
17 19 0.30
18 31 0.48
19 12 0.19
ACGTcount: A:0.15, C:0.27, G:0.02, T:0.56
Consensus pattern (17 bp):
CTCATTTCTTTTTCACT
Found at i:1858 original size:48 final size:48
Alignment explanation
Indices: 1803--1894 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
1793 TTCTTTCTTC
* * * *
1803 ATTCTCAATCTCTTTTTCAGTTCTCTTTTCTTTTTCACACTCATTTTT
1 ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCATTTTT
*
1851 ATTCTCAATCTCATTTTCAATTTTCTTTTCTATCTCACACTCAT
1 ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCAT
1895 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.01, T:0.54
Consensus pattern (48 bp):
ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCATTTTT
Found at i:1916 original size:15 final size:16
Alignment explanation
Indices: 1891--1922 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1881 TATCTCACAC
1891 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
1907 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
1922 T
1 T
1923 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:15679 original size:11 final size:10
Alignment explanation
Indices: 15654--15714 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
15644 ACCAATAAAA
15654 TAAA-TGAGC
1 TAAATTGAGC
*
15663 TGAATTGTAGC
1 TAAATTG-AGC
15674 TAAATTGAGC
1 TAAATTGAGC
**
15684 TCGATTGAGC
1 TAAATTGAGC
15694 TGAAA-TGAGC
1 T-AAATTGAGC
*
15704 TCAATTGAGC
1 TAAATTGAGC
15714 T
1 T
15715 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:15715 original size:20 final size:20
Alignment explanation
Indices: 15655--15715 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
15645 CCAATAAAAT
*
15655 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
15675 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
15696 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
15716 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:19758 original size:23 final size:22
Alignment explanation
Indices: 19706--19758 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
19696 TCCACGTCTT
*
19706 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
19728 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
19751 TTTCTTTT
1 TTTCTTTT
19759 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:23518 original size:12 final size:11
Alignment explanation
Indices: 23503--23570 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 11
23493 TTGCTCACCT
23503 TTTTTTTCTCGA
1 TTTTTTT-TCGA
23515 TTTTTTTTTC-A
1 -TTTTTTTTCGA
*
23526 TTTTTTTTCAATCAA
1 -TTTTTTT---TCGA
23541 TTTTTTTTCGAA
1 TTTTTTTTCG-A
23553 TTTTTTTT-GA
1 TTTTTTTTCGA
23563 TTTTTTTT
1 TTTTTTTT
23571 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
10 9 0.18
11 12 0.24
12 11 0.22
13 7 0.14
14 9 0.18
15 1 0.02
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:23565 original size:10 final size:11
Alignment explanation
Indices: 23539--23571 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
23529 TTTTTCAATC
23539 AATTTTTTTTCG
1 AATTTTTTTT-G
23551 AATTTTTTTTG
1 AATTTTTTTTG
23562 -ATTTTTTTTG
1 AATTTTTTTTG
23572 TTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 1 0.05
12 10 0.48
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:25932 original size:11 final size:10
Alignment explanation
Indices: 25907--25967 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
25897 ACCAATAAAA
25907 TAAA-TGAGC
1 TAAATTGAGC
*
25916 TGAATTGTAGC
1 TAAATTG-AGC
25927 TAAATTGAGC
1 TAAATTGAGC
**
25937 TCGATTGAGC
1 TAAATTGAGC
25947 TGAAA-TGAGC
1 T-AAATTGAGC
*
25957 TCAATTGAGC
1 TAAATTGAGC
25967 T
1 T
25968 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:25968 original size:20 final size:20
Alignment explanation
Indices: 25908--25968 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25898 CCAATAAAAT
*
25908 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
25928 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
25949 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
25969 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:29593 original size:46 final size:46
Alignment explanation
Indices: 29540--29633 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
29530 CAAAGAAAAG
* *
29540 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-AGGATAAGAACCTTGGTATATGATGA
29586 ACCTCGACCCACTATCAATGAGGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGAGGATAAGAACCTTGGTATATGATGA
29632 AC
1 AC
29634 GCCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGAGGATAAGAACCTTGGTATATGATGA
Done.