Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1824
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: 8668
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:217 original size:14 final size:14
Alignment explanation
Indices: 195--250 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
185 TTTTGAATGC
*
195 CATACTTAATATAA
1 CATATTTAATATAA
209 CATATTTAATATAA
1 CATATTTAATATAA
*
223 TA-ATCTTAATATAA
1 CATAT-TTAATATAA
237 CATATTTAATATAA
1 CATATTTAATATAA
251 TAATGGTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 2 0.05
14 33 0.89
15 2 0.05
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
CATATTTAATATAA
Found at i:231 original size:28 final size:28
Alignment explanation
Indices: 199--254 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
189 GAATGCCATA
199 CTTAATATAACATATTTAATATAATAAT
1 CTTAATATAACATATTTAATATAATAAT
227 CTTAATATAACATATTTAATATAATAAT
1 CTTAATATAACATATTTAATATAATAAT
255 GGTAGATTCA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (28 bp):
CTTAATATAACATATTTAATATAATAAT
Found at i:277 original size:12 final size:12
Alignment explanation
Indices: 260--286 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
250 ATAATGGTAG
260 ATTCAATCTAAT
1 ATTCAATCTAAT
272 ATTCAATCTAAT
1 ATTCAATCTAAT
284 ATT
1 ATT
287 GATAGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTCAATCTAAT
Found at i:357 original size:9 final size:8
Alignment explanation
Indices: 345--383 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 8
335 AAATTTTAAA
345 AATTAGTTT
1 AATTA-TTT
354 AATTATTTT
1 AATTA-TTT
363 AATTATTT
1 AATTATTT
371 AAATTATTT
1 -AATTATTT
380 AATT
1 AATT
384 CTATTTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
AATTATTT
Found at i:394 original size:19 final size:18
Alignment explanation
Indices: 345--383 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
335 AAATTTTAAA
345 AATTAGTTT-AATTATTTT
1 AATTA-TTTAAATTATTTT
363 AATTATTTAAATTA-TTT
1 AATTATTTAAATTATTTT
380 AATT
1 AATT
384 CTATTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTATTTAAATTATTTT
Found at i:869 original size:18 final size:18
Alignment explanation
Indices: 846--888 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 18
836 CCATAAAAGA
846 AAAGAAAATAAATAAATG
1 AAAGAAAATAAATAAATG
864 AAAGAAAATAAATAAATG
1 AAAGAAAATAAATAAATG
882 ACAAGAA
1 A-AAGAA
889 GGGAAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (18 bp):
AAAGAAAATAAATAAATG
Found at i:5006 original size:13 final size:13
Alignment explanation
Indices: 4964--5032 Score: 61
Period size: 13 Copynumber: 5.2 Consensus size: 13
4954 AAATTTTATT
*
4964 TTATATCTATAT-
1 TTATTTCTATATA
*
4976 TTATAATCTATATA
1 TTAT-TTCTATATA
4990 -TATTTCTATATA
1 TTATTTCTATATA
*
5002 TTATTTAGACTCTATA
1 TTATTT---CTATATA
5018 TTATTTCTATATA
1 TTATTTCTATATA
5031 TT
1 TT
5033 TAATATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 12 0.25
13 24 0.50
16 12 0.25
ACGTcount: A:0.33, C:0.09, G:0.01, T:0.57
Consensus pattern (13 bp):
TTATTTCTATATA
Found at i:5031 original size:29 final size:29
Alignment explanation
Indices: 4959--5032 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
4949 GAATCAAATT
* *
4959 TTATTT-TATATCTATATTTATAATCTATA
1 TTATTTCTATATAT-TATTTAGAATCTATA
*
4988 TATATTTCTATATATTATTTAGACTCTATA
1 T-TATTTCTATATATTATTTAGAATCTATA
5018 TTATTTCTATATATT
1 TTATTTCTATATATT
5033 TAATATATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 15 0.38
30 19 0.47
31 6 0.15
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (29 bp):
TTATTTCTATATATTATTTAGAATCTATA
Found at i:5056 original size:11 final size:11
Alignment explanation
Indices: 5025--5056 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
5015 ATATTATTTC
5025 TATATATTTAA
1 TATATATTTAA
5036 TATATATTTAA
1 TATATATTTAA
5047 TATATATTTA
1 TATATATTTA
5057 TGAGATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATTTAA
Done.