Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1478
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: 19442
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:7298 original size:27 final size:27
Alignment explanation
Indices: 7228--7324 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 27
7218 TTAGCTACCA
*
7228 ATTTTTGACAAACA-ACAA-G--CCACA
1 ATTTTTGACAAACACA-AAGGAACCACC
* * **
7252 ATTTTTGATAAACAAAAAAGGATTCACC
1 ATTTTTGACAAAC-ACAAAGGAACCACC
* *
7280 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAACACAAAGGAACCACC
7307 ATTTTTGACAAACACAAA
1 ATTTTTGACAAACACAAA
7325 AGGTGGTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
24 12 0.21
25 3 0.05
26 2 0.03
27 27 0.47
28 14 0.24
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.26
Consensus pattern (27 bp):
ATTTTTGACAAACACAAAGGAACCACC
Found at i:12311 original size:12 final size:12
Alignment explanation
Indices: 12279--12330 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
12269 TTAATGTATT
12279 TATATTT-AATA
1 TATATTTAAATA
*
12290 TTTATGTTAAATA
1 TATAT-TTAAATA
12303 TATATTTAAATA
1 TATATTTAAATA
* * *
12315 TAAATATAAAAA
1 TATATTTAAATA
12327 TATA
1 TATA
12331 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 4 0.12
12 21 0.64
13 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
TATATTTAAATA
Found at i:14831 original size:22 final size:23
Alignment explanation
Indices: 14806--14852 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
14796 TACTTTTTTT
*
14806 ATAAAAGAAATT-TCAA-ATTAAG
1 ATAAAA-AAATTATAAATATTAAG
14828 ATAAAAAAATTATAAATATTAAG
1 ATAAAAAAATTATAAATATTAAG
14851 AT
1 AT
14853 TTTAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 8 0.36
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAAAAAAATTATAAATATTAAG
Found at i:16080 original size:18 final size:17
Alignment explanation
Indices: 16031--16083 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
16021 ATTTTGTTAA
16031 GTATATAAA-TTAAATT
1 GTATATAAATTTAAATT
16047 -TATGATAATTATTTAAATT
1 GTAT-ATAA--ATTTAAATT
16066 CGTATATAAATTTAAATT
1 -GTATATAAATTTAAATT
16084 AACTTATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.10
16 4 0.13
18 10 0.32
19 7 0.23
20 4 0.13
21 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (17 bp):
GTATATAAATTTAAATT
Found at i:16561 original size:2 final size:2
Alignment explanation
Indices: 16554--16597 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
16544 TAAAAATTGA
16554 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
16596 AT
1 AT
16598 TCTTGACCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16580 original size:17 final size:17
Alignment explanation
Indices: 16554--16597 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
16544 TAAAAATTGA
16554 ATAT-ATATATATATAT
1 ATATAATATATATATAT
16570 ATATAATATATATATAT
1 ATATAATATATATATAT
*
16587 ATATACTATAT
1 ATATAATATAT
16598 TCTTGACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATAATATATATATAT
Done.