Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1645
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: 23406
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:12373 original size:22 final size:22
Alignment explanation
Indices: 12331--12373 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12321 ATACAAATAG
*
12331 ATAACAATTGGTATTTATTTTA
1 ATAACAATTGGTATGTATTTTA
* *
12353 ATAATAATTGGTATGTCTTTT
1 ATAACAATTGGTATGTATTTT
12374 CTGCTCATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (22 bp):
ATAACAATTGGTATGTATTTTA
Found at i:16377 original size:19 final size:18
Alignment explanation
Indices: 16353--16420 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
16343 CAGTAGCTGA
16353 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
16372 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
16387 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
16404 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
16421 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:16393 original size:13 final size:13
Alignment explanation
Indices: 16375--16399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16365 ACAATACTTA
16375 TGTATCGATACAT
1 TGTATCGATACAT
16388 TGTATCGATACA
1 TGTATCGATACA
16400 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16397 original size:32 final size:32
Alignment explanation
Indices: 16356--16418 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
16346 TAGCTGATTA
*
16356 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
16388 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
16419 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:19233 original size:25 final size:27
Alignment explanation
Indices: 19191--19257 Score: 93
Period size: 26 Copynumber: 2.5 Consensus size: 27
19181 TAATATGGAA
19191 ATAATTATATAATAAATTTTA-TTTTAT
1 ATAA-TATATAATAAATTTTATTTTTAT
19218 ATAATATAT-ATAAATTTTATTTTTAT
1 ATAATATATAATAAATTTTATTTTTAT
*
19244 ATAATTTAATAATA
1 ATAATAT-ATAATA
19258 TATAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 10 0.28
26 17 0.47
27 6 0.17
28 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATAATATATAATAAATTTTATTTTTAT
Found at i:19287 original size:34 final size:32
Alignment explanation
Indices: 19219--19288 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
19209 TTATTTTATA
* * *
19219 TAAT-ATATATAAATTTTATTTTTATATAATT
1 TAATAATATATAAAATTTATTATTATATAAAT
19250 TAATAATATATAAAATTTATTATTATTATGAAAT
1 TAATAATATATAAAATTTATTATTA-TAT-AAAT
19284 TAATA
1 TAATA
19289 TGAATTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 4 0.12
32 18 0.55
33 3 0.09
34 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
TAATAATATATAAAATTTATTATTATATAAAT
Found at i:20802 original size:21 final size:20
Alignment explanation
Indices: 20771--20809 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
20761 ATTTTTATTT
20771 TTTAAATTTTTAAGTTTTAC
1 TTTAAATTTTTAAGTTTTAC
*
20791 TTTAAGATTTTTATGTTTT
1 TTTAA-ATTTTTAAGTTTT
20810 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTAAATTTTTAAGTTTTAC
Found at i:20936 original size:21 final size:22
Alignment explanation
Indices: 20893--20942 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
20883 TGTGAATAAA
*
20893 TTTATTATTAAATTTATAAATT
1 TTTATTATAAAATTTATAAATT
*
20915 TTTATTATAAAATTT-TACATT
1 TTTATTATAAAATTTATAAATT
*
20936 TTCATTA
1 TTTATTA
20943 ACTTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATAAAATTTATAAATT
Found at i:21403 original size:9 final size:9
Alignment explanation
Indices: 21389--21418 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
21379 ACTCCCAAAT
*
21389 TTCCTCCTC
1 TTCCTCTTC
21398 TTCCTCTTC
1 TTCCTCTTC
21407 TTCCTCTTC
1 TTCCTCTTC
21416 TTC
1 TTC
21419 TTCGTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TTCCTCTTC
Done.