Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold540
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: 15200
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Found at i:198 original size:2 final size:2
Alignment explanation
Indices: 191--215 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
181 TAAAGAATTT
191 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
216 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:301 original size:18 final size:19
Alignment explanation
Indices: 273--317 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
263 TTTTCTTAAT
273 TTATATATTTTTT-ATAAAA
1 TTATAT-TTTTTTAATAAAA
292 TTA-ATTTTTTTAATAAAA
1 TTATATTTTTTTAATAAAA
310 TTATATTT
1 TTATATTT
318 ACATCCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 11 0.46
19 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTTTTTTAATAAAA
Found at i:348 original size:21 final size:21
Alignment explanation
Indices: 300--364 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
290 AATTAATTTT
*
300 TTTAATAAAATTATATTTACA
1 TTTAATAAAATAATATTTACA
** *
321 TCCAATAAAATAATATTTATA
1 TTTAATAAAATAATATTTACA
*
342 TTTAATAAAAATAATATATACA
1 TTTAAT-AAAATAATATTTACA
364 T
1 T
365 ATAACATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAATAAAATAATATTTACA
Found at i:10765 original size:22 final size:21
Alignment explanation
Indices: 10721--10765 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
10711 TTTGATTTTT
***
10721 TTCAATAAAATAATATGTTCA
1 TTCAATAAAATAATATACACA
10742 TTCAATAAAAATAATATACACA
1 TTCAAT-AAAATAATATACACA
10764 TT
1 TT
10766 TAGTAGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (21 bp):
TTCAATAAAATAATATACACA
Found at i:11341 original size:53 final size:53
Alignment explanation
Indices: 11268--11410 Score: 154
Period size: 50 Copynumber: 2.7 Consensus size: 53
11258 AGAATTTAAT
11268 TTTTTATAATTTTTTTATTATTATTTTAAATAGTAATTCAG-GA-TTAATATAAAA
1 TTTTTATAA--TTTTTATTATTATTTTAAATAGTAATT-AGAGATTTAATATAAAA
* * *
11322 TATTTT-TCAA--TTT-TTATTATTTTAAATTGTAATTTGAGATTTAATATACAA
1 T-TTTTAT-AATTTTTATTATTATTTTAAATAGTAATTAGAGATTTAATATAAAA
* *
11373 TTTTTATAATTTTTATAATTTTTTTAAATAGTAATTAG
1 TTTTTATAATTTTTATTATTATTTTAAATAGTAATTAG
11411 TAAAGATATG
Statistics
Matches: 74, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
49 1 0.01
50 28 0.38
51 15 0.20
52 3 0.04
53 19 0.26
54 2 0.03
55 6 0.08
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (53 bp):
TTTTTATAATTTTTATTATTATTTTAAATAGTAATTAGAGATTTAATATAAAA
Found at i:11398 original size:11 final size:9
Alignment explanation
Indices: 11371--11395 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11361 TTTAATATAC
11371 AATTTTTAT
1 AATTTTTAT
11380 AATTTTTAT
1 AATTTTTAT
11389 AATTTTT
1 AATTTTT
11396 TTAAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
AATTTTTAT
Found at i:12175 original size:2 final size:2
Alignment explanation
Indices: 12168--12209 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
12158 AATTCGGGGC
*
12168 AT AT AT AT AT AT AT AT AT AT AG AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12209 A
1 A
12210 GGGATAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:14585 original size:6 final size:6
Alignment explanation
Indices: 14570--14608 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
14560 AAAAAAATAC
*
14570 AAAAATG AAAAAG AAAAAG AAAAAG AAAGA- AAAAAG AAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
14609 GTGGAAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 4 0.14
6 20 0.69
7 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Done.