Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1993
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: 42655
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:7340 original size:40 final size:39
Alignment explanation
Indices: 7296--7400 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
7286 AGTGACCATA
*
7296 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
7336 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
7374 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
7401 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:7357 original size:39 final size:40
Alignment explanation
Indices: 7256--7419 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 40
7246 TTGAATGATG
* *
7256 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
7296 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA
*
7335 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* * **
7375 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATA-CTATA
7415 TCCGG
1 TCCGG
7420 TTAAATTCCG
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 36 0.34
40 59 0.56
41 10 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
Found at i:7419 original size:79 final size:80
Alignment explanation
Indices: 7256--7406 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
7246 TTGAATGATG
*
7256 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
7321 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
7336 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
7398 TTGAACGAG
64 TTGAACGAG
7407 TAGCTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.69
80 18 0.30
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:12611 original size:40 final size:40
Alignment explanation
Indices: 12556--12700 Score: 247
Period size: 40 Copynumber: 3.6 Consensus size: 40
12546 CGGATGATAA
* *
12556 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
12596 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
12636 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
12676 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
12701 AGCAAGTAGT
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 100 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:12715 original size:80 final size:80
Alignment explanation
Indices: 12556--12732 Score: 243
Period size: 80 Copynumber: 2.2 Consensus size: 80
12546 CGGATGATAA
* *
12556 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCATTTG
* *
12621 TGCGAGTTACTATAT
66 AGCAAGTTACTATAT
*
12636 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAGTCCCGAAGGCATTT
*
12700 GAGCAAG-TAGTTATAT
65 GAGCAAGTTA-CTATAT
* *
12716 TC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
12733 ATGCTTGGGT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
79 18 0.21
80 69 0.79
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCATTTG
AGCAAGTTACTATAT
Found at i:13000 original size:22 final size:21
Alignment explanation
Indices: 12959--13002 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
12949 GAATGTGCAT
12959 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
12981 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
13003 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:20912 original size:43 final size:44
Alignment explanation
Indices: 20858--20980 Score: 117
Period size: 43 Copynumber: 2.8 Consensus size: 44
20848 ACCGAGATGA
* * * *
20858 GATTACATGTAAGACTAAGTCTCAGACATTGGCATTG-TATTTT
1 GATTACGTGTAAGACCAAGTCTCAGACATTGGCATCGTTATATT
* * **
20901 GATTACGTGTAAAACCATGTCTGGGACATTGGCATCGTTATATT
1 GATTACGTGTAAGACCAAGTCTCAGACATTGGCATCGTTATATT
* * *
20945 -ATTTCGTGTAAGACCATGT-ACAGGACATTGGCATCG
1 GATTACGTGTAAGACCAAGTCTCA-GACATTGGCATCG
20981 ATATGTGATA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 60 0.92
44 5 0.08
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (44 bp):
GATTACGTGTAAGACCAAGTCTCAGACATTGGCATCGTTATATT
Found at i:28561 original size:27 final size:26
Alignment explanation
Indices: 28530--28707 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
28520 TAAATTGTAC
28530 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
28557 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
28583 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
28611 GGCACTAAGTGTGCGAGGTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
28639 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
28666 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
28693 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28708 GGCTCAATAT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 102 0.80
28 25 0.20
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:28591 original size:54 final size:54
Alignment explanation
Indices: 28530--28707 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 54
28520 TAAATTGTAC
* **
28530 AGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-GACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* ** *
28585 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGGTTGACTATG-T
1 AGCACTAAGTGTGCG-ATTGACTATGTAGCACTAAGTGTGCGA-GTTGAATATGAT
* * *
28639 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
28693 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28708 GGCTCAATAT
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
54 60 0.57
55 45 0.43
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:28646 original size:82 final size:81
Alignment explanation
Indices: 28531--28686 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 81
28521 AAATTGTACA
* *
28531 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28595 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28612 GCACTAAGTGTGCGAGGTT-GACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAGTGTGCGA--TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
28676 GTGCGAGTTGA
64 GTGCGAATTGA
28687 TTATATAGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 15 0.23
82 48 0.73
83 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28698 original size:82 final size:81
Alignment explanation
Indices: 28527--28707 Score: 213
Period size: 82 Copynumber: 2.2 Consensus size: 81
28517 GATTAAATTG
* *
28527 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28592 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28608 TGCGGCACTAAGTGTGCGAGGTT-GACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA--TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
28671 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
28690 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28708 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 18 0.22
82 63 0.76
83 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28718 original size:27 final size:27
Alignment explanation
Indices: 28612--28718 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
28602 TGACCATGCG
* * * *
28612 GCACTAAGTGTGCGAGGTTGACTATGTA
1 GCACTAAGTGTGCGA-GCTCAATATATA
** * * **
28640 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
28667 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
28694 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
28719 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:31507 original size:21 final size:20
Alignment explanation
Indices: 31483--31521 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31473 AAAATATGTG
31483 TTTG-TGGACTAAATTGAATGA
1 TTTGATGGA-TAAA-TGAATGA
31504 TTTGATGGATAAATGAAT
1 TTTGATGGATAAATGAAT
31522 AAATTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (20 bp):
TTTGATGGATAAATGAATGA
Found at i:31862 original size:43 final size:44
Alignment explanation
Indices: 31814--31956 Score: 202
Period size: 43 Copynumber: 3.3 Consensus size: 44
31804 ACCAAGATGA
*
31814 GATTACATGTAAGTCCATGTCTGGGACATTGGCATTGTAT-TGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATATGT
* *
31857 GATTACGTGTAAGACCATGTCTGGGACATTGGCATTGT-TATAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATATGT
* * *
31900 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCG-ATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATATGT
*
31943 GATAACATGTAAGA
1 GATTACATGTAAGA
31957 TCATATTTGG
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.01
43 88 0.99
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (44 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATATGT
Found at i:34747 original size:43 final size:42
Alignment explanation
Indices: 34637--34749 Score: 102
Period size: 43 Copynumber: 2.7 Consensus size: 42
34627 TGATTTATGC
* ** ** * *
34637 GTAAGACCATGTCTGGGACATTGATATTGTACTTGATTTCGT
1 GTAAGACCATGTCTGGGACGTTGGCATAATACTTGATTACAT
* * * *
34679 GTAAGACCCTGTCTAGGATAG-TGGCATCAATATTTGATTACAT
1 GTAAGACCATGTCTGGGA-CGTTGGCAT-AATACTTGATTACAT
34722 GTAAGACCATGTCTGGGACGTTGGCATA
1 GTAAGACCATGTCTGGGACGTTGGCATA
34750 GTACGAGCTT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
42 22 0.41
43 32 0.59
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (42 bp):
GTAAGACCATGTCTGGGACGTTGGCATAATACTTGATTACAT
Found at i:40971 original size:15 final size:15
Alignment explanation
Indices: 40947--40976 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40937 CTAATGTATT
40947 TTTTGAGGTTTCGGC
1 TTTTGAGGTTTCGGC
*
40962 TTTTGTGGTTTCGGC
1 TTTTGAGGTTTCGGC
40977 ACAAGTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.33, T:0.50
Consensus pattern (15 bp):
TTTTGAGGTTTCGGC
Done.