Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold250
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: 185408
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:167674 original size:13 final size:13
Alignment explanation
Indices: 167656--167681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
167646 CAAGTTTTTG
167656 TGTATCGATACAT
1 TGTATCGATACAT
167669 TGTATCGATACAT
1 TGTATCGATACAT
167682 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:167746 original size:21 final size:21
Alignment explanation
Indices: 167720--167795 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
167710 CTGCCAAGAA
167720 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTT
*****
167741 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTT
167761 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTT
167782 ATGTATCGATACAT
1 ATGTATCGATACAT
167796 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTT
Found at i:167766 original size:20 final size:20
Alignment explanation
Indices: 167741--167813 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
167731 CATCTTTTTT
167741 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*****
167761 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TGCAAC
167782 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
167802 ATGTATCGATAC
1 ATGTATCGATAC
167814 TTTGAATTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:167777 original size:41 final size:41
Alignment explanation
Indices: 167720--167813 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
167710 CTGCCAAGAA
167720 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
167761 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
167802 ATGTATCGATAC
1 ATGTATCGATAC
167814 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
Found at i:168670 original size:12 final size:12
Alignment explanation
Indices: 168653--168684 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
168643 AACTTTTACA
168653 TCATATACTACT
1 TCATATACTACT
168665 TCATATACTACT
1 TCATATACTACT
168677 TCATATAC
1 TCATATAC
168685 ATTATTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.41
Consensus pattern (12 bp):
TCATATACTACT
Found at i:171030 original size:19 final size:19
Alignment explanation
Indices: 170973--171022 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
170963 TTTAAAATAA
* *
170973 AATAAAATGATTATTATTAT
1 AATAAAATAATTA-TATGAT
* *
170993 TATAATATAATTATATGAT
1 AATAAAATAATTATATGAT
171012 AATAAAATAAT
1 AATAAAATAAT
171023 ATCATGATTG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
AATAAAATAATTATATGAT
Found at i:171050 original size:29 final size:26
Alignment explanation
Indices: 171008--171066 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
170998 TATAATTATA
*
171008 TGATAATAAAATAATATCATGATTGGTCT
1 TGATAATAAAATAA-A--ATGATTGGCCT
171037 TGATAATAAAATAAAATGATTGGCCT
1 TGATAATAAAATAAAATGATTGGCCT
171063 TGAT
1 TGAT
171067 TATTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 14 0.48
28 1 0.03
29 14 0.48
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (26 bp):
TGATAATAAAATAAAATGATTGGCCT
Found at i:172146 original size:33 final size:33
Alignment explanation
Indices: 172104--172168 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
172094 GTTGAAGCAA
172104 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGT-ATCATGTATCGATACAT
*
172137 TGTATCGATATAATGTATCATGTATCGATACA
1 TGTATCGATACAATGTATCATGTATCGATACA
172169 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTATCATGTATCGATACAT
Found at i:172153 original size:13 final size:13
Alignment explanation
Indices: 172101--172155 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
172091 GCCGTTGAAG
172101 CAATGTATCGATA
1 CAATGTATCGATA
172114 CAA--T-TC-AT-
1 CAATGTATCGATA
172122 C-ATGTATCGATA
1 CAATGTATCGATA
*
172134 CATTGTATCGATA
1 CAATGTATCGATA
*
172147 TAATGTATC
1 CAATGTATC
172156 ATGTATCGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:172242 original size:19 final size:20
Alignment explanation
Indices: 172198--172270 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
172188 ATGCTAGTTT
* * *
172198 CATGTATTGATACAATTATC
1 CATGTATCGATACAATGATA
172218 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
*
172237 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-ATA
172258 -ATGTATCGATACA
1 CATGTATCGATACA
172271 TCTGGGTGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.34
20 30 0.64
21 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:178378 original size:13 final size:15
Alignment explanation
Indices: 178346--178377 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
178336 GTTTTTTTTC
*
178346 CTCTCTTTTTGTATT
1 CTCTTTTTTTGTATT
178361 CTCTTTTTTTGTATT
1 CTCTTTTTTTGTATT
178376 CT
1 CT
178378 TGAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.69
Consensus pattern (15 bp):
CTCTTTTTTTGTATT
Found at i:179514 original size:21 final size:20
Alignment explanation
Indices: 179479--179530 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
179469 TTTGTTGGTG
* *
179479 ATTTTGATGAAAAATGAAGT
1 ATTTTGAAGAAAAATGAAGA
179499 ATTTTGAAGTAAAAATGAAGA
1 ATTTTGAAG-AAAAATGAAGA
*
179520 AATTTGAAGAA
1 ATTTTGAAGAA
179531 GATTTGATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (20 bp):
ATTTTGAAGAAAAATGAAGA
Done.