Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold536
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: 13440
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:5499 original size:37 final size:37
Alignment explanation
Indices: 5449--5527 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
5439 TTATTACGAA
* *
5449 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
5486 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
5523 GTCTT
1 GTCTT
5528 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:5763 original size:47 final size:47
Alignment explanation
Indices: 5646--6118 Score: 831
Period size: 47 Copynumber: 10.1 Consensus size: 47
5636 CCCTTCGGGA
* * * * * * *
5646 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
5693 C-CGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5739 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5786 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5833 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5880 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5927 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5974 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6021 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6068 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6115 CTTA
1 CTTA
6119 CTATCATTTC
Statistics
Matches: 410, Mismatches: 15, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
46 37 0.09
47 373 0.91
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:9915 original size:40 final size:40
Alignment explanation
Indices: 9791--9926 Score: 195
Period size: 40 Copynumber: 3.5 Consensus size: 40
9781 CGAATACACG
* * * * *
9791 TCACCAGCATGATTGCTCTTCGGGATTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
9831 TCACTAGCACGAATGCTCTTC-GAACTTAG-CCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
9869 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
9909 TCACTAGCATGAATGCTC
1 TCACTAGCATGAATGCTC
9927 GGACTAGCCC
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
38 27 0.32
39 13 0.15
40 45 0.53
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:10361 original size:29 final size:29
Alignment explanation
Indices: 10322--10400 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
10312 CTTAATAATC
*
10322 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
10352 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
10381 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
10401 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:10443 original size:43 final size:43
Alignment explanation
Indices: 10382--10483 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
10372 TGCATTTCAA
10382 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
10425 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
10468 G-CCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
10484 TGAAAACTCT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 15 0.25
43 44 0.75
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:12364 original size:37 final size:37
Alignment explanation
Indices: 12314--12392 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
12304 TTATTACGAA
* *
12314 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
12351 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
12388 GTCTT
1 GTCTT
12393 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:12628 original size:47 final size:47
Alignment explanation
Indices: 12511--12914 Score: 665
Period size: 47 Copynumber: 8.7 Consensus size: 47
12501 CCCTTCGGGA
* * * * * * *
12511 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
12558 C-CGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12604 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12651 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12696 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12743 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12790 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12837 CTTATCACACATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12884 CTTATCAC--ATATACACTTTCACATTCATCAC
1 CTTATCACATATATACACTTTCACATTCATCAC
12915 TTCACATTCA
Statistics
Matches: 338, Mismatches: 16, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
45 67 0.20
46 37 0.11
47 234 0.69
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12660 original size:22 final size:22
Alignment explanation
Indices: 12632--12705 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
12622 TTTCACATTC
12632 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
*** * *
12654 ATCACATATACACTTTCA--CATT
1 ATCACATCGGC-CATT-AGGCCTT
12676 CATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
12699 ATCACAT
1 ATCACAT
12706 ATATACACTT
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 1 0.03
22 21 0.57
23 14 0.38
24 1 0.03
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:12783 original size:94 final size:94
Alignment explanation
Indices: 12511--13038 Score: 805
Period size: 94 Copynumber: 5.5 Consensus size: 94
12501 CCCTTCGGGA
* * * * * * * **
12511 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCC-CGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
12575 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
12604 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
12667 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
12696 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
12761 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * *
12790 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
12855 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
12884 CTTATCACATATACACTTTCACATTCATCACTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 CTTATCACATAT--A---T-ACA--C-T---TTCACATTCATCACATCGGCCATTAGGCCTTATC
12949 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12990 CTTATCACATATATACACTTT--CATTCATCACATCGGCCATTAGGCCTTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
13039 CTATCATCAT
Statistics
Matches: 405, Mismatches: 15, Indels: 31
0.90 0.03 0.07
Matches are distributed among these distances:
92 120 0.30
93 41 0.10
94 146 0.36
96 1 0.00
97 1 0.00
98 1 0.00
99 1 0.00
100 6 0.01
101 1 0.00
102 1 0.00
103 1 0.00
104 1 0.00
106 84 0.21
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:12918 original size:14 final size:14
Alignment explanation
Indices: 12901--12928 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12891 CATATACACT
12901 TTCACATTCATCAC
1 TTCACATTCATCAC
12915 TTCACATTCATCAC
1 TTCACATTCATCAC
12929 ATCGGCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (14 bp):
TTCACATTCATCAC
Found at i:12919 original size:59 final size:60
Alignment explanation
Indices: 12856--12975 Score: 224
Period size: 59 Copynumber: 2.0 Consensus size: 60
12846 CATATATACT
12856 TTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATACACTTTCACATTCATCAC
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATACACTTTCACATTCATCAC
12915 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATACACTTTCACATTCATCAC
12976 ATCGGCCATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 36 0.61
61 23 0.39
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.33
Consensus pattern (60 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATACACTTTCACATTCATCAC
Found at i:12945 original size:153 final size:151
Alignment explanation
Indices: 12762--13038 Score: 509
Period size: 153 Copynumber: 1.8 Consensus size: 151
12752 TATATACACT
12762 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
* *
12827 GCTATTAGGCCTTATCACACATATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
66 GCCATTAGGCCTTATCACACATATACACTTT--CATTCATCACATCGGCCATTAGGCCTTATCAC
12892 ATATACACTTTCACATTCATCAC
129 ATATACACTTTCACATTCATCAC
12915 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
*
12980 GCCATTAGGCCTTATCACATATATACACTTTCATTCATCACATCGGCCATTAGGCCTTA
66 GCCATTAGGCCTTATCACACATATACACTTTCATTCATCACATCGGCCATTAGGCCTTA
13039 CTATCATCAT
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
151 28 0.23
153 93 0.77
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (151 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
GCCATTAGGCCTTATCACACATATACACTTTCATTCATCACATCGGCCATTAGGCCTTATCACAT
ATACACTTTCACATTCATCAC
Found at i:12967 original size:47 final size:47
Alignment explanation
Indices: 12915--13038 Score: 234
Period size: 47 Copynumber: 2.7 Consensus size: 47
12905 CATTCATCAC
12915 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
12962 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
13009 TT--CATTCATCACATCGGCCATTAGGCCTTA
1 TTCACATTCATCACATCGGCCATTAGGCCTTA
13039 CTATCATCAT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
45 28 0.36
47 49 0.64
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
Found at i:12994 original size:106 final size:105
Alignment explanation
Indices: 12809--13020 Score: 363
Period size: 106 Copynumber: 2.0 Consensus size: 105
12799 TATATACACT
* *
12809 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATATACTTTCACATTCATCACATCG
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG
12874 GCCATTAGGCCTTATCAC-ATATACACTTTCACATTCATCAC
66 GCCATTAGGCCTTATCACAATATACACTTT--CATTCATCAC
*
12915 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
1 TTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG
12980 GCCATTAGGCCTTATCACATATATACACTTTCATTCATCAC
66 GCCATTAGGCCTTATCACA-ATATACACTTTCATTCATCAC
13021 ATCGGCCATT
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
106 90 0.89
108 11 0.11
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (105 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG
GCCATTAGGCCTTATCACAATATACACTTTCATTCATCAC
Done.