Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3621
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: 35853
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:12923 original size:68 final size:66
Alignment explanation
Indices: 12846--12992 Score: 172
Period size: 67 Copynumber: 2.2 Consensus size: 66
12836 CATCATGCGT
* * * *
12846 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC-AG-CA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
12909 TGTAG
62 TGTAG
* * *
12914 ACAAGAGAGCTACAGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
12979 AG
65 AG
12981 ACAAGAGAGCTA
1 ACAAGAGAGCTA
12993 TGAGATAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
64 24 0.35
65 3 0.04
66 3 0.04
67 26 0.38
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:15638 original size:80 final size:80
Alignment explanation
Indices: 15411--15639 Score: 259
Period size: 80 Copynumber: 2.8 Consensus size: 80
15401 TATTTAGGCA
* * * *
15411 TTGAGCCTAGCAAGCCTTGTGCTGGTGAATTTGATT-AGGCTTTATGCCTAGCAGACTTGTTACT
1 TTGAGTCTAGCAGGCCTTGTGCTGGTG--TGTGATTCAGGC-TTATGCCTAGCAG-GTT-TTACT
*
15475 --GGTGAATAAAATTAGACG
61 GCGGTGAATAAAATCAGACG
** ** *
15493 TTGAGTCTAGCAGGTTTTGTGCCAGTGTGTGATTCAGGCTTATGCCTAGCAGG-CTTACTGTCGG
1 TTGAGTCTAGCAGGCCTTGTGCTGGTGTGTGATTCAGGCTTATGCCTAGCAGGTTTTACTG-CGG
*
15557 TGAATAAAATCAGACT
65 TGAATAAAATCAGACG
* *
15573 TTGAGTCTAGCAGGCCTTGTGTTGGTGTGTGATTCAGGCTTATGCCTAGCAGGTTTTATTGCGGT
1 TTGAGTCTAGCAGGCCTTGTGCTGGTGTGTGATTCAGGCTTATGCCTAGCAGGTTTTACTGCGGT
15638 GA
66 GA
15640 TTTATTTTAA
Statistics
Matches: 124, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
77 5 0.04
80 89 0.72
81 9 0.07
82 21 0.17
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.34
Consensus pattern (80 bp):
TTGAGTCTAGCAGGCCTTGTGCTGGTGTGTGATTCAGGCTTATGCCTAGCAGGTTTTACTGCGGT
GAATAAAATCAGACG
Found at i:15773 original size:50 final size:50
Alignment explanation
Indices: 15714--15925 Score: 361
Period size: 50 Copynumber: 4.2 Consensus size: 50
15704 TAAATGATGA
* *
15714 TGTATATTCGGCCACATAGGTGTGTACATACGTGATGTTATATTTGATCT
1 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
*
15764 TGTATATTCGGCCACATAGGTATGTACATATGTGATATTATATTTGATCT
1 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
*
15814 TGTATATGCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
1 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
* *
15864 TGTATATTCGGCCATATAGGTATGTACATAGGTGATGTTATATTTGATCT
1 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
*
15914 TGTGTATTCGGC
1 TGTATATTCGGC
15926 TAAATGAGTG
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 153 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (50 bp):
TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
Found at i:20963 original size:47 final size:47
Alignment explanation
Indices: 20900--21119 Score: 341
Period size: 47 Copynumber: 4.7 Consensus size: 47
20890 CCCTTCGGGA
* *
20900 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
20947 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
20994 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
21041 CTTATCACATATATACACTTTCATATTCATCACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
21088 CCTATCACATATATACACTTTCACATTCATCA
1 CTTATCACATATATACACTTTCACATTCATCA
21120 TGTGACAGCC
Statistics
Matches: 158, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 158 1.00
ACGTcount: A:0.28, C:0.29, G:0.07, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:28842 original size:39 final size:40
Alignment explanation
Indices: 28757--29015 Score: 445
Period size: 39 Copynumber: 6.6 Consensus size: 40
28747 ATTTGAATAC
28757 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
28797 ATCCGGGCTAAGACCCGAAGGCATTTGTGC-AGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
28836 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
28876 ATCC-GGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
28915 ATCCGGGCTAAGACCCGAAGGCA-TTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
28954 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
28994 A-CCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
29016 ATTGAGCTTG
Statistics
Matches: 211, Mismatches: 5, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
39 136 0.64
40 75 0.36
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:28910 original size:79 final size:79
Alignment explanation
Indices: 28757--29015 Score: 443
Period size: 79 Copynumber: 3.3 Consensus size: 79
28747 ATTTGAATAC
28757 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
28822 TGTGCAGTTGATAT
66 TGTGCAGTTGATAT
*
28836 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCC-GGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
28900 TGTGCAAGTTGATAT
66 TGTGC-AGTTGATAT
28915 ATCCGGGCTAAGACCCGAAGGCA-TTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* *
28979 CGTGCGAGTTGCTAT
66 TGTGC-AGTTGATAT
*
28994 A-CCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
29016 ATTGAGCTTG
Statistics
Matches: 172, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
78 64 0.37
79 108 0.63
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (79 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAGTTGATAT
Found at i:29038 original size:118 final size:119
Alignment explanation
Indices: 28757--29015 Score: 461
Period size: 118 Copynumber: 2.2 Consensus size: 119
28747 ATTTGAATAC
28757 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
*
28822 TGTGCAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
66 TGTGCAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATAT
28876 ATCC-GGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCA-T
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
*
28939 TGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
66 TGTGC-AGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATAT
*
28994 A-CCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
29016 ATTGAGCTTG
Statistics
Matches: 135, Mismatches: 3, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
117 8 0.06
118 123 0.91
119 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (119 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATAT
Done.