Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1667
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: 26177
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:6631 original size:24 final size:21
Alignment explanation
Indices: 6603--6691 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
6593 ACAAAAAAGA
*
6603 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCCAAGTCACTTC---TCTT
*
6627 TTTGTCCAAGTTACTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
**
6648 TTTGTCCAAGTTGCTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
* **
6669 TTTGTCTATCTCACTTC-CTT
1 TTTGTCCAAGTCACTTCTCTT
6689 TTT
1 TTT
6692 TCTTTGTGAG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
20 6 0.11
21 36 0.63
24 15 0.26
ACGTcount: A:0.11, C:0.24, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTGTCCAAGTCACTTCTCTT
Found at i:6649 original size:21 final size:21
Alignment explanation
Indices: 6623--6674 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
6613 TCACTTCGTT
6623 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
6644 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
6665 TCTTTTTGTC
1 TCTTTTTGTC
6675 TATCTCACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.10, C:0.23, G:0.12, T:0.56
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:10009 original size:93 final size:93
Alignment explanation
Indices: 9897--10068 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
9887 GCCCATAAGT
* *
9897 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
9962 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* *
9990 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATTCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
10055 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
10069 CAAATATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:10064 original size:46 final size:46
Alignment explanation
Indices: 9890--10064 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
9880 GTAACCCGCC
* * *
9890 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATC
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATT
* *
9936 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-C-TAGTT
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCA-TT
* * *
9981 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATT
1 -CA--TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATT
*
10029 CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
10065 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
44 1 0.01
45 4 0.04
46 67 0.61
47 32 0.29
48 5 0.05
49 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATT
Found at i:12015 original size:15 final size:16
Alignment explanation
Indices: 11989--12051 Score: 78
Period size: 15 Copynumber: 4.1 Consensus size: 16
11979 CAAGGAAACC
11989 GAATAAAGAAATCCAA
1 GAATAAAGAAATCCAA
*
12005 G-ATAGAGAAATCC-A
1 GAATAAAGAAATCCAA
*
12019 GAATAAAGAAAT-CTA
1 GAATAAAGAAATCCAA
*
12034 GAATAAAGAAACCCAA
1 GAATAAAGAAATCCAA
12050 GA
1 GA
12052 TACGATACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 3 0.08
15 32 0.80
16 5 0.12
ACGTcount: A:0.59, C:0.13, G:0.16, T:0.13
Consensus pattern (16 bp):
GAATAAAGAAATCCAA
Found at i:14905 original size:93 final size:93
Alignment explanation
Indices: 14776--14947 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
14766 GCCCATAAGT
* * * *
14776 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCAA
14841 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* *
14869 GAACTCAGACTGAACTCAACGAGTTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
14934 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
14948 CAAATATCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:14943 original size:46 final size:46
Alignment explanation
Indices: 14768--14943 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 46
14758 TGTAACCCGC
* * *
14768 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
* * * *
14814 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGACG-CTCGCAT
* ** * * * *
14860 ACATCTCACGAACTCAGACTGAACTCAACGAGTTCGGACGCTCGCAT
1 CCAT-AAATGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
*
14907 CCATAAATGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGA
14944 TGCCCAAATA
Statistics
Matches: 105, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
46 72 0.69
47 33 0.31
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
Found at i:16055 original size:18 final size:18
Alignment explanation
Indices: 16020--16110 Score: 107
Period size: 18 Copynumber: 5.2 Consensus size: 18
16010 AAGGTTTTCT
16020 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
*
16035 TATTGATGATAGTGACAA
1 TATTGATGATAGTGACGA
* *
16053 TATTGATGCTAGTGATGA
1 TATTGATGATAGTGACGA
* *
16071 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
*
16089 TATTGATGATAGTGACGC
1 TATTGATGATAGTGACGA
16107 TATT
1 TATT
16111 CATCGTGACC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.17
16 1 0.02
18 54 0.82
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:16077 original size:9 final size:9
Alignment explanation
Indices: 16033--16099 Score: 53
Period size: 9 Copynumber: 7.4 Consensus size: 9
16023 TGATGATATC
16033 GATATTGAT
1 GATATTGAT
* *
16042 GATAGTGAC
1 GATATTGAT
*
16051 AATATTGAT
1 GATATTGAT
* *
16060 GCTAGTGAT
1 GATATTGAT
16069 GATATTGAT
1 GATATTGAT
* * *
16078 GCTAGTGAC
1 GATATTGAT
*
16087 GCTATTGAT
1 GATATTGAT
16096 GATA
1 GATA
16100 GTGACGCTAT
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (9 bp):
GATATTGAT
Found at i:16108 original size:27 final size:27
Alignment explanation
Indices: 16035--16108 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
16025 ATGATATCGA
** * *
16035 TATTGATGATAGTGACAATATTGATGC
1 TATTGATGATAGTGACGCTAGTGACGC
* * *
16062 TAGTGATGATATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGCTAGTGACGC
16089 TATTGATGATAGTGACGCTA
1 TATTGATGATAGTGACGCTA
16109 TTCATCGTGA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (27 bp):
TATTGATGATAGTGACGCTAGTGACGC
Found at i:24424 original size:14 final size:14
Alignment explanation
Indices: 24405--24431 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24395 TTATTAAGTA
24405 TTTCTATTCTATTT
1 TTTCTATTCTATTT
24419 TTTCTATTCTATT
1 TTTCTATTCTATT
24432 AGTATTAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTCTATTCTATTT
Done.