Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3047
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: 36139
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:8628 original size:14 final size:13
Alignment explanation
Indices: 8609--8655 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
8599 GCTTCTTCTT
8609 TTTTTTTCACGAAA
1 TTTTTTTCAC-AAA
8623 TTTTTTTTCAC-AA
1 -TTTTTTTCACAAA
**
8636 TTTTTTTTTCAAA
1 TTTTTTTCACAAA
8649 TTTTTTT
1 TTTTTTT
8656 TCAACTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 11 0.38
15 10 0.34
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.66
Consensus pattern (13 bp):
TTTTTTTCACAAA
Found at i:8637 original size:13 final size:13
Alignment explanation
Indices: 8608--8658 Score: 68
Period size: 15 Copynumber: 3.8 Consensus size: 13
8598 AGCTTCTTCT
8608 TTTTTTTTCACGAAA
1 TTTTTTTTCAC--AA
8623 TTTTTTTTCACAA
1 TTTTTTTTCACAA
8636 TTTTTTTTTCA-AA
1 -TTTTTTTTCACAA
8649 TTTTTTTTCA
1 TTTTTTTTCA
8659 ACTTGATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.29
13 4 0.11
14 10 0.29
15 11 0.31
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:8656 original size:12 final size:12
Alignment explanation
Indices: 8620--8659 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
8610 TTTTTTCACG
8620 AAATTTTTTTTC
1 AAATTTTTTTTC
8632 ACAATTTTTTTTTC
1 A-AA-TTTTTTTTC
8646 AAATTTTTTTTC
1 AAATTTTTTTTC
8658 AA
1 AA
8660 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.46
13 4 0.15
14 10 0.38
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (12 bp):
AAATTTTTTTTC
Found at i:8656 original size:14 final size:14
Alignment explanation
Indices: 8607--8656 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
8597 TAGCTTCTTC
8607 TTTTTTTTTCACGAA
1 TTTTTTTTTCAC-AA
*
8622 ATTTTTTTTCACAA
1 TTTTTTTTTCACAA
8636 TTTTTTTTTCA-AA
1 TTTTTTTTTCACAA
8649 TTTTTTTT
1 TTTTTTTT
8657 CAACTTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 10 0.30
14 12 0.36
15 11 0.33
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:8741 original size:10 final size:11
Alignment explanation
Indices: 8699--8738 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
8689 GAAACCAAAT
8699 TTTTTTTTGAA
1 TTTTTTTTGAA
8710 TTTTTTTTGAA
1 TTTTTTTTGAA
8721 TTTTTTTTGAA
1 TTTTTTTTGAA
8732 TTTTTTT
1 TTTTTTT
8739 GAAGAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:9776 original size:21 final size:23
Alignment explanation
Indices: 9731--9777 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
9721 TCACCTGCAA
* *
9731 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
9754 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
9775 TAA
1 TAA
9778 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:10694 original size:10 final size:10
Alignment explanation
Indices: 10679--10727 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
10669 TTGGGTTAAG
10679 ATTGAGCTGA
1 ATTGAGCTGA
10689 ATTGAGCTCGA
1 ATTGAGCT-GA
10700 A-TGAGCTGA
1 ATTGAGCTGA
* *
10709 CTTGAGCTCA
1 ATTGAGCTGA
*
10719 AGTGAGCTG
1 ATTGAGCTG
10728 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:10704 original size:20 final size:20
Alignment explanation
Indices: 10681--10727 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
10671 GGGTTAAGAT
10681 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
10701 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
10721 TGAGCTG
1 TGAGCTG
10728 GAAACGAGCT
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:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:11072 original size:18 final size:17
Alignment explanation
Indices: 11049--11087 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
11039 CTCTTTTTGC
11049 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
11067 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
11085 TCT
1 TCT
11088 GTCTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:16356 original size:22 final size:22
Alignment explanation
Indices: 16328--16371 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16318 TTTTGAACCA
16328 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
16350 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
16372 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:18956 original size:18 final size:18
Alignment explanation
Indices: 18910--18963 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
18900 AGAAAAGAGC
*
18910 GAAAATACAAAAGAAAAGA
1 GAAAATTCAAAA-AAAAGA
*
18929 -AAAA-TGAAAAAAAAGA
1 GAAAATTCAAAAAAAAGA
18945 GAAAATTC-AAAAAAAGA
1 GAAAATTCAAAAAAAAGA
18962 GA
1 GA
18964 GCGATAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 6 0.20
17 19 0.63
18 5 0.17
ACGTcount: A:0.74, C:0.04, G:0.15, T:0.07
Consensus pattern (18 bp):
GAAAATTCAAAAAAAAGA
Found at i:25590 original size:10 final size:10
Alignment explanation
Indices: 25575--25636 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
25565 TTTGAACCAT
*
25575 TACCAATTCG
1 TACCAATTCA
*
25585 TACCAAATACCA
1 TACC-AAT-TCA
*
25597 TACCATTTCA
1 TACCAATTCA
25607 TACCAATTCCA
1 TACCAATT-CA
* *
25618 TACCATTTCG
1 TACCAATTCA
25628 TACCAATTC
1 TACCAATTC
25637 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:25620 original size:21 final size:21
Alignment explanation
Indices: 25575--25637 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25565 TTTGAACCAT
* *
25575 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
25597 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
25618 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
25638 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:26709 original size:15 final size:15
Alignment explanation
Indices: 26677--26710 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
26667 GTTCAACGAA
*
26677 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
26692 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
26707 GAGG
1 GAGG
26711 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:30457 original size:10 final size:10
Alignment explanation
Indices: 30442--30503 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
30432 TTTGAACCAT
*
30442 TACCAATTCG
1 TACCAATTCA
*
30452 TACCAAATACCA
1 TACC-AAT-TCA
*
30464 TACCATTTCA
1 TACCAATTCA
30474 TACCAATTCCA
1 TACCAATT-CA
* *
30485 TACCATTTCG
1 TACCAATTCA
30495 TACCAATTC
1 TACCAATTC
30504 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:30487 original size:21 final size:21
Alignment explanation
Indices: 30442--30504 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
30432 TTTGAACCAT
* *
30442 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
30464 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
30485 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
30505 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
Done.