Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2013
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: 14813
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:10455 original size:60 final size:59
Alignment explanation
Indices: 10058--10568 Score: 274
Period size: 64 Copynumber: 8.4 Consensus size: 59
10048 AACCTTTTAT
* * * * *
10058 CCTTTCAGTCCTTGAAGAGCAAGATGACTTTTCCTTTT-AAAGCCTAC-C-AGTTGGTAGCA
1 CCTTTCAGTCCTTAAAGAGCAGGACG-C-TTT-CTTTTAAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
10117 GCTTTTAGTCTTTAAAGAGTAGGACGCTTTTTCCTTTCAAAGCCCACACAAGTTGG-GG-G
1 CCTTTCAGTCCTTAAAGAGCAGGACGC--TTTCTTTTAAAAGCCCACACAAGTTGGTGGCA
* * * * *
10176 CCTCTTCTAGTCCTCAAAGAGTAGGACTCTCTTTTTCTTTTTAAAAGCCCATACAAATTGGTGGC
1 CCT-TTC-AGTCCTTAAAGAGCAGGA--CGC--TTTC-TTTTAAAAGCCCACACAAGTTGGTGGC
10241 A
59 A
* * * * *
10242 CCTTCCAATCCTTAAAGAGCATGACGCTTTCTTTTCAAAGCCCACATAAG-TGGTGGCA
1 CCTTTCAGTCCTTAAAGAGCAGGACGCTTTCTTTTAAAAGCCCACACAAGTTGGTGGCA
** * * ** *
10300 CGATT-AGTCC-TCAAGAGCAAGAACTTTTTTCCCTTTT-AAAGCTCACACAA-TTGG-GGCA
1 CCTTTCAGTCCTTAAAGAGC-AGGAC-GCTTT--CTTTTAAAAGCCCACACAAGTTGGTGGCA
* * *
10358 CCTTTCAGTCCTCAAAAAAAGTAGGACGCCTTATCTTTT-AAAGCCCACCACAAGTTGGTGGCA
1 CCTTTCAGTCCT--TAAAGAGCAGGACG-CTT-TCTTTTAAAAGCCCA-CACAAGTTGGTGGCA
* ** * *
10421 CCTTTCAATCCTTAAAGAGCAGGACGCATTTCTTTTTAAAAGCCTCACTGAACTGGTGGCGGCA
1 CCTTTCAGTCCTTAAAGAGCAGGACGC-TTTC-TTTTAAAAGCC-CACACAA--GTTGGTGGCA
* * * * * *
10485 CCTTTTAGTCCTCAAAGAGCATGACGCTTTCTTCTTGCAAAGCTCACACAAGTTGATGGCA
1 CCTTTCAGTCCTTAAAGAGCAGGACGCTTTCTT-TT-AAAAGCCCACACAAGTTGGTGGCA
* *
10546 TCTTTC-GTCCCTAAAGAGCAGGA
1 CCTTTCAGTCCTTAAAGAGCAGGA
10569 AACGCTCCTT
Statistics
Matches: 343, Mismatches: 76, Indels: 65
0.71 0.16 0.13
Matches are distributed among these distances:
56 7 0.02
57 7 0.02
58 25 0.07
59 67 0.20
60 42 0.12
61 61 0.18
62 22 0.06
63 36 0.10
64 69 0.20
65 4 0.01
66 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (59 bp):
CCTTTCAGTCCTTAAAGAGCAGGACGCTTTCTTTTAAAAGCCCACACAAGTTGGTGGCA
Found at i:11190 original size:18 final size:18
Alignment explanation
Indices: 11167--11235 Score: 113
Period size: 18 Copynumber: 3.8 Consensus size: 18
11157 TAAAGTATGA
11167 AAAAAATCACATTTTGTG
1 AAAAAATCACATTTTGTG
11185 AAAAAATCACATTTTGTG
1 AAAAAATCACATTTTGTG
11203 -AAAAATCACATTTTTGTG
1 AAAAAATCACA-TTTTGTG
*
11221 AATAAATCACATTTT
1 AAAAAATCACATTTT
11236 TGCCAAAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
17 10 0.21
18 29 0.60
19 9 0.19
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (18 bp):
AAAAAATCACATTTTGTG
Found at i:13768 original size:78 final size:74
Alignment explanation
Indices: 13677--13863 Score: 191
Period size: 78 Copynumber: 2.5 Consensus size: 74
13667 ATTCATGTTT
* *
13677 TTATTTCCGAGGGGATACTCCAACCCTTAGTTATTTCCAAAACA-CTAATTTTTCACAATCGGGG
1 TTATTTTCGAGGGGATACTCCAACCC-TAGTTATTTCCAAAACATC-AA-TTTTCACAAT-GAGG
13741 ATACTCTAACCTCG
62 ATACTC-AACCTCG
* * * * * *
13755 TTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCACAATTAGGCT
1 TTATTTTCGAGGGGATACTCCAA-CCCTA-GTTATTTCCAAAACATCAATTTTCACAATGAGGAT
*
13820 ACTCCACCTCG
64 ACTCAACCTCG
* *
13831 TTA-TTTCGAGGGAATACTCTAACCCT-GTTATTT
1 TTATTTTCGAGGGGATACTCCAACCCTAGTTATTT
13864 TCGAGGGTCA
Statistics
Matches: 92, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
72 6 0.07
74 3 0.03
75 16 0.17
76 9 0.10
77 7 0.08
78 32 0.35
79 18 0.20
80 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.35
Consensus pattern (74 bp):
TTATTTTCGAGGGGATACTCCAACCCTAGTTATTTCCAAAACATCAATTTTCACAATGAGGATAC
TCAACCTCG
Found at i:14147 original size:73 final size:76
Alignment explanation
Indices: 13923--14147 Score: 172
Period size: 73 Copynumber: 2.9 Consensus size: 76
13913 TTTTTGGACA
* * * * * *
13923 ATTGGGGATACTCC-AACCCCGTTATTTTTGAGGAGATTCCTCCCAACCTCGGTTTTATTTCAAA
1 ATTGGGGATACTCCGAA-CCCGTTA-TTTCGAGGGGA-TACT-CCAACC-CGATTTTATCTCCAA
** * *
13987 ACACCAATTTTCCACAA
61 ACATAAATTTTACAC-C
* * * * * *
14004 ATCGGGGATACTCCGATCCCGTTATTTCGCGGGGATACTTCAACCCGATTTTATTTCCAAACATC
1 ATTGGGGATACTCCGAACCCGTTATTTCGAGGGGATACTCCAACCCGATTTTATCTCCAAACATA
*
14069 GATTTTACACC
66 AATTTTACACC
* * *
14080 ATTGGGGATACT-C-AACCCGTTATTTTGAGGGG-TACTCCGACTCC-ATTTTATCTCCAAATAT
1 ATTGGGGATACTCCGAACCCGTTATTTCGAGGGGATACTCCAAC-CCGATTTTATCTCCAAACAT
14141 AAATTTT
65 AAATTTT
14148 TCATCGGGAG
Statistics
Matches: 119, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
73 27 0.23
74 18 0.15
75 1 0.01
76 11 0.09
77 25 0.21
78 5 0.04
79 3 0.03
80 8 0.07
81 20 0.17
82 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (76 bp):
ATTGGGGATACTCCGAACCCGTTATTTCGAGGGGATACTCCAACCCGATTTTATCTCCAAACATA
AATTTTACACC
Done.