Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold51
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: 3712191
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.32
Warning! 131352 characters in sequence are not A, C, G, or T
File 23 of 23
Found at i:3697568 original size:52 final size:52
Alignment explanation
Indices: 3697507--3697657 Score: 149
Period size: 61 Copynumber: 2.7 Consensus size: 52
3697497 CCGATATCGG
* *
3697507 TGGCCTTGAATCAGCATATTGGCACATTTACCATTTTTAAGCCCAATGTCGC
1 TGGCCTTGAATCAGCATATTGGCACATTTACCATTTTTAAGCCCAATATCAC
* **
3697559 TGGCCTTGAATCAGCACATTGGCATCATTCTCATCCTTATTATCTTTAAGTTCAATATCAC
1 TGGCCTTGAATCAGCATATTGGCA-CATT-T-A-CC--A-T-T-TTTAAGCCCAATATCAC
* * *
3697620 TGGCCTTGAATCAGCATATTGGTACCTTTATCATTTTT
1 TGGCCTTGAATCAGCATATTGGCACATTTACCATTTTT
3697658 CTCATCTTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
52 26 0.32
53 5 0.06
54 2 0.02
55 2 0.02
56 2 0.02
57 1 0.01
58 2 0.02
59 2 0.02
60 4 0.05
61 35 0.43
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (52 bp):
TGGCCTTGAATCAGCATATTGGCACATTTACCATTTTTAAGCCCAATATCAC
Found at i:3697703 original size:122 final size:119
Alignment explanation
Indices: 3697545--3697777 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 119
3697535 TACCATTTTT
* * * *
3697545 AAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCATTCTC-ATCCTTATTATCTTTAAG
1 AAGCCCAATGTCGCTAGCCCTGAATCAACACATTGGCA-C-TTCTCAAT-CTTATT-TCTTTAAA
* * * *
3697609 TTCAATATCACTGGCCTTGAATCAGCATATTGGTACCTTTATCATTTTTCTCATCTTC
62 TCCAATATCACTAGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTCTCATCTTC
* * *
3697667 AAGCCCAATGTCGTTAGCCCTGAATCAACACATTGGCACTTGTCAAATCTTGTTTCTTTAAATCC
1 AAGCCCAATGTCGCTAGCCCTGAATCAACACATTGGCACTTCTC-AATCTTATTTCTTTAAATCC
* **
3697732 GATATTGCTAGCCTTGAATCAGCATATTGGCACCTTTACCATTTTT
65 AATATCACTAGCCTTGAATCAGCATATTGGCACCTTTACCATTTTT
3697778 AAACCCTATG
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
120 53 0.56
121 6 0.06
122 36 0.38
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (119 bp):
AAGCCCAATGTCGCTAGCCCTGAATCAACACATTGGCACTTCTCAATCTTATTTCTTTAAATCCA
ATATCACTAGCCTTGAATCAGCATATTGGCACCTTTACCATTTTTCTCATCTTC
Found at i:3697976 original size:52 final size:52
Alignment explanation
Indices: 3697891--3698316 Score: 283
Period size: 52 Copynumber: 7.9 Consensus size: 52
3697881 TCATTCTTCG
* *
3697891 TATCTTTAAGTCCAATGTCGTTTGCCTTAAATCAGCACATTGGCACTCTTTT
1 TATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTCTTTT
* * *
3697943 TATTTTTAAGTCCAATGTCGATGGCCTTGAATCAACACATTGGCACT-TTTT
1 TATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTCTTTT
* * * ** ** * * **
3697994 TCTTTCTTAAGTCCAATATCACTACCCTTAAATCAACGTATTGGCA-TCTTTGT
1 TATCT-TTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTCTTT-T
* *
3698047 CATCTTTAAGTCCAATGTCGTTGGCCTTGAATTAGCACATTGGCA-TCTTTGT
1 TATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTCTTT-T
* * * * *
3698099 CATCATTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCAC-CTTTAT
1 TATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTCTTT-T
* * * * * *
3698151 TATTCTTCTCATCTTCAAG-CCAGATATCGCTAGCCATGAATCAGCATATTGACACCTTTATCAT
1 TA------TC-T-TT-AAGTCCA-ATGTCGTTGGCCTTGAATCAGCACATTGGCA-C----TC-T
3698215 TCTT
50 T-TT
* *
3698219 CGCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTCTTTT
1 --TATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTCTTTT
*
3698273 TATCTTTAAGT-CAAGTGT-GTAGGCCTTGAATCTA-CACATTGGCA
1 TATCTTTAAGTCCAA-TGTCGTTGGCCTTGAATC-AGCACATTGGCA
3698317 TATCACAGAC
Statistics
Matches: 299, Mismatches: 48, Indels: 55
0.74 0.12 0.14
Matches are distributed among these distances:
51 34 0.11
52 174 0.58
53 3 0.01
54 2 0.01
55 2 0.01
56 2 0.01
58 2 0.01
60 6 0.02
61 59 0.20
62 6 0.02
63 1 0.00
64 2 0.01
67 1 0.00
68 3 0.01
69 1 0.00
70 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (52 bp):
TATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACTCTTTT
Found at i:3698193 original size:61 final size:61
Alignment explanation
Indices: 3698110--3698275 Score: 201
Period size: 61 Copynumber: 2.7 Consensus size: 61
3698100 ATCATTAAGC
* * * *
3698110 CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATTATTCTTCTCATCTTCAAG-
1 CCAATATCGCTAGCCATGAATCAGCATATTGGCACCTTTATTATTCTTCGCATCTTCAAGT
* * *
3698170 CCAGATATCGCTAGCCATGAATCAGCATATTGACACCTTTATCATTCTTCGCATCTTTAAGT
1 CCA-ATATCGCTAGCCATGAATCAGCATATTGGCACCTTTATTATTCTTCGCATCTTCAAGT
* * * *
3698232 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTCTTT-TTAT
1 CCAATATCGCTAGCCATGAATCAGCATATTGGCAC-CTTTATTAT
3698276 CTTTAAGTCA
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
60 3 0.03
61 80 0.89
62 7 0.08
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (61 bp):
CCAATATCGCTAGCCATGAATCAGCATATTGGCACCTTTATTATTCTTCGCATCTTCAAGT
Found at i:3698958 original size:20 final size:20
Alignment explanation
Indices: 3698912--3698965 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3698902 TTTTATGATT
* * *
3698912 TGTATCGATACAATTAGTGAC
1 TGTATCGATAC-ATAAATGAA
3698933 TGTATCGATACATAAATGAA
1 TGTATCGATACATAAATGAA
*
3698953 TGTATCGACACAT
1 TGTATCGATACAT
3698966 GCCTAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAATGAA
Found at i:3708307 original size:2 final size:2
Alignment explanation
Indices: 3708300--3708343 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3708290 CCAATTGTTA
3708300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3708342 AT
1 AT
3708344 CTTTATGGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3710944 original size:17 final size:17
Alignment explanation
Indices: 3710918--3710952 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3710908 ATGGATAGTT
*
3710918 ATTATCTTTTTTGTATA
1 ATTATATTTTTTGTATA
3710935 ATTATATTTTTTGTATA
1 ATTATATTTTTTGTATA
3710952 A
1 A
3710953 AAATCGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (17 bp):
ATTATATTTTTTGTATA
Done.