Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3448
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: 18583
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Found at i:800 original size:18 final size:18
Alignment explanation
Indices: 769--842 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
759 GCGCATTTTG
769 TTAGCCTTT-T-GCATTT
1 TTAGCCTTTGTGGCATTT
*
785 TTAGTCTTTGTGGCATTT
1 TTAGCCTTTGTGGCATTT
*
803 TGATATGGCTTTGTGGCATTT
1 T--TA-GCCTTTGTGGCATTT
* *
824 TTAACCTTTGTGACATTT
1 TTAGCCTTTGTGGCATTT
842 T
1 T
843 ATATGGCATT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
16 8 0.17
17 1 0.02
18 20 0.42
19 2 0.04
20 2 0.04
21 15 0.31
ACGTcount: A:0.15, C:0.14, G:0.19, T:0.53
Consensus pattern (18 bp):
TTAGCCTTTGTGGCATTT
Found at i:816 original size:21 final size:20
Alignment explanation
Indices: 790--860 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 20
780 CATTTTTAGT
790 CTTTGTGGCATTTTGATATGG
1 CTTTGTGGCATTTT-ATATGG
**
811 CTTTGTGGCATTTT-TA-AC
1 CTTTGTGGCATTTTATATGG
*
829 CTTTGTGACATTTTATATGG
1 CTTTGTGGCATTTTATATGG
849 CATTT-TGGCATT
1 C-TTTGTGGCATT
861 CTGTTAACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 13 0.32
19 4 0.10
20 7 0.17
21 17 0.41
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (20 bp):
CTTTGTGGCATTTTATATGG
Found at i:858 original size:38 final size:38
Alignment explanation
Indices: 774--860 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 38
764 TTTTGTTAGC
** *
774 CTTTT-GCATTTTTAGTCTTTGTGGCATTTTGATATGG
1 CTTTTGGCATTTTTAACCTTTGTGACATTTTGATATGG
811 CTTTGTGGCATTTTTAACCTTTGTGACATTTT-ATATGG
1 CTTT-TGGCATTTTTAACCTTTGTGACATTTTGATATGG
849 CATTTTGGCATT
1 C-TTTTGGCATT
861 CTGTTAACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
37 4 0.09
38 15 0.34
39 25 0.57
ACGTcount: A:0.16, C:0.13, G:0.20, T:0.52
Consensus pattern (38 bp):
CTTTTGGCATTTTTAACCTTTGTGACATTTTGATATGG
Found at i:2822 original size:28 final size:28
Alignment explanation
Indices: 2791--2846 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2781 ATTCCAAAAG
2791 AACACTATTAGGATAACATTAGATTTAT
1 AACACTATTAGGATAACATTAGATTTAT
2819 AACACTATTAGGATAACATTAGATTTAT
1 AACACTATTAGGATAACATTAGATTTAT
2847 GTAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (28 bp):
AACACTATTAGGATAACATTAGATTTAT
Found at i:3390 original size:14 final size:14
Alignment explanation
Indices: 3371--3418 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
3361 TAAGTTAAAA
3371 ATAATATAAAATTT
1 ATAATATAAAATTT
*
3385 ATAATATATAACCTTT
1 ATAATATA-AA-ATTT
* *
3401 ATAAAAAAAAATTT
1 ATAATATAAAATTT
3415 ATAA
1 ATAA
3419 AGTGTCCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 15 0.54
15 4 0.14
16 9 0.32
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAAAATTT
Found at i:3395 original size:16 final size:15
Alignment explanation
Indices: 3373--3419 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
3363 AGTTAAAAAT
3373 AATATAAAATTTATA
1 AATATAAAATTTATA
**
3388 ATATATAACCTTTATA
1 A-ATATAAAATTTATA
*
3404 AA-AAAAAATTTATA
1 AATATAAAATTTATA
3418 AA
1 AA
3420 GTGTCCAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.42
15 2 0.08
16 13 0.50
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAAAATTTATA
Found at i:4046 original size:4 final size:4
Alignment explanation
Indices: 4032--4061 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
4022 ATTTTAAAAT
4032 ATTA TATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA -ATTA ATTA ATTA ATTA ATTA ATTA A
4062 CGAGAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:14914 original size:6 final size:6
Alignment explanation
Indices: 14900--14977 Score: 147
Period size: 6 Copynumber: 13.0 Consensus size: 6
14890 GCAAATGGAT
*
14900 CATTTC CATTCC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
14948 CATTTC CATTTC CATTTC CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC
14978 AAAATGATTC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.17, C:0.35, G:0.00, T:0.49
Consensus pattern (6 bp):
CATTTC
Found at i:15389 original size:12 final size:12
Alignment explanation
Indices: 15369--15399 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
15359 CAAATGAATA
15369 ATTTCCATTTTC
1 ATTTCCATTTTC
*
15381 ATTTTCATTTTC
1 ATTTCCATTTTC
15393 ATTTCCA
1 ATTTCCA
15400 AATGATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTCCATTTTC
Done.