Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3333
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: 17878
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Found at i:1024 original size:26 final size:26
Alignment explanation
Indices: 985--1092 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
975 TGGTACAAAT
985 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1011 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1037 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1063 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1089 TGAT
1 TGAT
1093 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2771 original size:21 final size:22
Alignment explanation
Indices: 2699--2798 Score: 101
Period size: 22 Copynumber: 4.1 Consensus size: 22
2689 AGGAAGCATC
2699 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCAC-A-TA--T-AT
*
2726 CTGGTGGCTCTGCCACATATAT
1 CTGGTGGCTATGCCACATATAT
2748 CTGGTGGCTATGCCACATTATCTGAT
1 CTGGTGGCTATGCCACA-TA--T-AT
*
2774 CTGGTGGCTCTGCCACATATAT
1 CTGGTGGCTATGCCACATATAT
2796 CTG
1 CTG
2799 TTTGGTGGCT
Statistics
Matches: 66, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
22 23 0.35
23 4 0.06
25 5 0.08
26 19 0.29
27 15 0.23
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (22 bp):
CTGGTGGCTATGCCACATATAT
Found at i:2780 original size:48 final size:48
Alignment explanation
Indices: 2699--2832 Score: 196
Period size: 48 Copynumber: 2.7 Consensus size: 48
2689 AGGAAGCATC
2699 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATAT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATAT
2748 CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATAT
1 CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATAT
* *
2796 CTGTTTGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 C----TGGTGGCTATGCCACATTATCTG-ATCTGGTG
2833 ACTTCGTCAC
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
48 33 0.42
49 16 0.21
52 21 0.27
53 8 0.10
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (48 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATAT
Found at i:2782 original size:26 final size:26
Alignment explanation
Indices: 2699--2832 Score: 170
Period size: 26 Copynumber: 5.2 Consensus size: 26
2689 AGGAAGCATC
*
2699 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
2726 CTGGTGGCTCTGCCACA-TA--T-AT
1 CTGGTGGCTCTGCCACATTATCTGAT
*
2748 CTGGTGGCTATGCCACATTATCTGAT
1 CTGGTGGCTCTGCCACATTATCTGAT
2774 CTGGTGGCTCTGCCACATATATCTG-T
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
2800 TTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
2827 CTGGTG
1 CTGGTG
2833 ACTTCGTCAC
Statistics
Matches: 94, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
22 18 0.19
23 3 0.03
25 9 0.10
26 37 0.39
27 27 0.29
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:8088 original size:26 final size:26
Alignment explanation
Indices: 8059--8166 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
8049 TGGTACAAAT
8059 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
8085 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
8111 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
8137 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
8163 TGAT
1 TGAT
8167 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:9795 original size:27 final size:26
Alignment explanation
Indices: 9746--9903 Score: 158
Period size: 27 Copynumber: 5.9 Consensus size: 26
9736 AGGAAGCGTC
*
9746 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAA-TATCTGAT
*
9773 CTGGTGGCTCTGTCC-CACATATCTGTT
1 CTGGTGGCTCTG-CCACA-ATATCTGAT
* * *
9800 CTGGAGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-AATATCTGAT
*
9827 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACA-ATATCTGAT
*
9854 CTGGAGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTG-AT
* *
9881 CTGGTGACT-TCGTCACAATATCT
1 CTGGTGGCTCT-GCCACAATATCT
9904 AGCAGCCTCG
Statistics
Matches: 109, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
26 11 0.10
27 94 0.86
28 4 0.04
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACAATATCTGAT
Found at i:9833 original size:54 final size:53
Alignment explanation
Indices: 9746--9886 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 53
9736 AGGAAGCGTC
*
9746 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCC-CACATATCTGTT
1 CTGGAGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTG-CCACACATATCTGTT
*
9800 CTGGAGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGAGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACACATATCTGTT
* *
9854 CTGGAGGCTCTGCCACAATATCTGTATCTGGTG
1 CTGGAGGCTATGCCACATTATCTG-ATCTGGTG
9887 ACTTCGTCAC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
53 9 0.11
54 71 0.89
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (53 bp):
CTGGAGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACACATATCTGTT
Found at i:15151 original size:26 final size:26
Alignment explanation
Indices: 15122--15228 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
15112 TGGTACAAAT
15122 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
15148 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
15174 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
15200 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
15225 TGAT
1 TGAT
15229 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 22 0.29
26 55 0.71
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:16906 original size:33 final size:29
Alignment explanation
Indices: 16841--16960 Score: 137
Period size: 27 Copynumber: 4.2 Consensus size: 29
16831 AGGAAGCGTC
*
16841 CTGGTGGCTATGCCACA-ATTATC--TGAT
1 CTGGTGGCTCTGCCACATA-TATCTGTGAT
16868 CTGGTGGCTCTGCCACATATATGGCTATGTGAT
1 CTGGTGGCTCTGCCACATATAT--C--TGTGAT
16901 CTGGTGGCTCTGCCACATATATCTGT--T
1 CTGGTGGCTCTGCCACATATATCTGTGAT
16928 CTGGTGGCTCTGCCACA-ATATCTGT-AT
1 CTGGTGGCTCTGCCACATATATCTGTGAT
16955 CTGGTG
1 CTGGTG
16961 ACTTCGTCAC
Statistics
Matches: 84, Mismatches: 1, Indels: 16
0.83 0.01 0.16
Matches are distributed among these distances:
26 8 0.10
27 44 0.52
28 1 0.01
29 4 0.05
31 1 0.01
33 26 0.31
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.34
Consensus pattern (29 bp):
CTGGTGGCTCTGCCACATATATCTGTGAT
Found at i:16971 original size:27 final size:26
Alignment explanation
Indices: 16922--16978 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
16912 GCCACATATA
*
16922 TCTGTTCTGGTGGCTCTGCCACAATA
1 TCTGTTCTGGTGACTCTGCCACAATA
*
16948 TCTGTATCTGGTGACT-TCGTCACAATA
1 TCTGT-TCTGGTGACTCT-GCCACAATA
16975 TCTG
1 TCTG
16979 GCAGCCTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TCTGTTCTGGTGACTCTGCCACAATA
Done.