Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1610
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: 53972
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:15830 original size:43 final size:43
Alignment explanation
Indices: 15740--15851 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 43
15730 TGATTACAAG
* * * *
15740 TAAGACCGTGTTTGGGACATTCGCATTGTATTGAGATTACGTG
1 TAAGACCATGTTTGGGAAATTCGCATTGTAATGAGATTACGTA
* * *
15783 TAAGACCATGTTTGGGAAATTGGCATTGTTAAT-CGATTTCGTA
1 TAAGACCATGTTTGGGAAATTCGCATTG-TAATGAGATTACGTA
* * * *
15826 TAAGACCCTGTCTGGGACAGTCGCAT
1 TAAGACCATGTTTGGGAAATTCGCAT
15852 CGATATGTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 53 0.95
44 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
TAAGACCATGTTTGGGAAATTCGCATTGTAATGAGATTACGTA
Found at i:15885 original size:86 final size:85
Alignment explanation
Indices: 15740--15896 Score: 199
Period size: 86 Copynumber: 1.8 Consensus size: 85
15730 TGATTACAAG
* * * * * * * *
15740 TAAGACCGTGTTTGGGACATTCGCATTGTATTGAGATTACGTGTAAGACCATGTTTGGGAAATTG
1 TAAGACCCTGTCTGGGACAGTCGCATCGTATTGAGATAACATGTAAGACCATATCTGGGAAA-TG
15805 GCATTGTTAATCGATTTCGTA
65 GCATTGTTAATCGATTTCGTA
* *
15826 TAAGACCCTGTCTGGGACAGTCGCATCG-ATATGTGATAACATGTAAGACCATATCTGGGATATG
1 TAAGACCCTGTCTGGGACAGTCGCATCGTAT-TGAGATAACATGTAAGACCATATCTGGGAAATG
15890 GCATTGT
65 GCATTGT
15897 ATTATCTTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
85 11 0.18
86 49 0.82
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (85 bp):
TAAGACCCTGTCTGGGACAGTCGCATCGTATTGAGATAACATGTAAGACCATATCTGGGAAATGG
CATTGTTAATCGATTTCGTA
Found at i:17008 original size:29 final size:29
Alignment explanation
Indices: 16962--17025 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
16952 GTCTATTGGC
*
16962 CGTGTATGGCACAAGGGCTAGCACATGGG
1 CGTGTGTGGCACAAGGGCTAGCACATGGG
* *
16991 CGTGTGTGGCACACGGGCTGGCACATGGG
1 CGTGTGTGGCACAAGGGCTAGCACATGGG
17020 CGTGTG
1 CGTGTG
17026 GTCGGCAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.17, C:0.22, G:0.42, T:0.19
Consensus pattern (29 bp):
CGTGTGTGGCACAAGGGCTAGCACATGGG
Found at i:19069 original size:16 final size:15
Alignment explanation
Indices: 19044--19073 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19034 GTACGTAAAA
19044 CTCATATGTGATGAG
1 CTCATATGTGATGAG
19059 CTCATTATGTGATGA
1 CTCA-TATGTGATGA
19074 ACCCTCAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (15 bp):
CTCATATGTGATGAG
Found at i:19106 original size:15 final size:16
Alignment explanation
Indices: 19080--19109 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19070 ATGAACCCTC
19080 AGTAAGGTTATGATTG
1 AGTAAGGTTATGATTG
19096 AGTAA-GTTATGATT
1 AGTAAGGTTATGATT
19110 ATAAGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (16 bp):
AGTAAGGTTATGATTG
Found at i:28446 original size:38 final size:38
Alignment explanation
Indices: 28368--28535 Score: 230
Period size: 38 Copynumber: 4.4 Consensus size: 38
28358 AAACCAAAAC
* ** *
28368 ATAACACCAGCATGAAGCCTACGGGACTTTAACCCGGAT
1 ATAATACCAGCACAAAGCCTGCGGGA-TTTAACCCGGAT
*
28407 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
*
28445 ATATTACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
* *
28483 ATATTACCAGCACAAAGCCTGCGGGATTTAACCCGGGT
1 ATAATACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
*
28521 ACAAT-CTCAGCACAA
1 ATAATAC-CAGCACAA
28536 TTTATTTTAT
Statistics
Matches: 120, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
37 1 0.01
38 96 0.80
39 23 0.19
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (38 bp):
ATAATACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
Found at i:32551 original size:31 final size:31
Alignment explanation
Indices: 32511--32572 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
32501 GTTCATATAA
32511 CATAGTACTTAACTTACCATTCATTCTAATT
1 CATAGTACTTAACTTACCATTCATTCTAATT
*
32542 CATATTACTTAACTTACCATTCATTCTAATT
1 CATAGTACTTAACTTACCATTCATTCTAATT
32573 TGAGGTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.44
Consensus pattern (31 bp):
CATAGTACTTAACTTACCATTCATTCTAATT
Found at i:33492 original size:51 final size:51
Alignment explanation
Indices: 33430--33534 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
33420 CGATTCCTCC
33430 TTTATTCAAATGAGATTTAACATTTCTCAAGCATTAACAAGGATGTGATTA
1 TTTATTCAAATGAGATTTAACATTTCTCAAGCATTAACAAGGATGTGATTA
*
33481 TTTATTTAAATGAGATTTAACATTTCTCAAGCATTAACAAGGATGTGATTA
1 TTTATTCAAATGAGATTTAACATTTCTCAAGCATTAACAAGGATGTGATTA
33532 TTT
1 TTT
33535 CTTACATCTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (51 bp):
TTTATTCAAATGAGATTTAACATTTCTCAAGCATTAACAAGGATGTGATTA
Found at i:43410 original size:27 final size:27
Alignment explanation
Indices: 43370--43488 Score: 139
Period size: 27 Copynumber: 4.4 Consensus size: 27
43360 TGGATAAGTT
*
43370 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
43397 ATAGAATTATCGAAATAGCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
43424 GTAGAAATACCAAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
43451 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
43478 GTAAAATTACC
1 GTAGAATTACC
43489 ATTTTGCCCC
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:44164 original size:26 final size:27
Alignment explanation
Indices: 44135--44194 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
44125 CCACATATAT
*
44135 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
44161 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
44188 ATATCTG
1 ATATCTG
44195 GCAGCTTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:47690 original size:28 final size:28
Alignment explanation
Indices: 47625--47723 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
47615 CATGAGATTG
* * *
47625 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
47654 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
47682 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
47710 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
47724 GGCGTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Done.