Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1259
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: 11006
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Found at i:2914 original size:2 final size:2
Alignment explanation
Indices: 2907--2938 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2897 TATTTTAGAA
2907 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2939 ATTTCGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2928 original size:17 final size:17
Alignment explanation
Indices: 2906--2938 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2896 GTATTTTAGA
2906 AATATATATATATATAT
1 AATATATATATATATAT
2923 AATATATATATATATA
1 AATATATATATATATA
2939 ATTTCGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:2929 original size:15 final size:15
Alignment explanation
Indices: 2909--2940 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2899 TTTTAGAAAT
2909 ATATATATATATATA
1 ATATATATATATATA
2924 ATATATATATATATA
1 ATATATATATATATA
2939 AT
1 AT
2941 TTCGTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:5098 original size:2 final size:2
Alignment explanation
Indices: 5091--5116 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5081 ATGTCAAGGA
5091 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5117 GATTCTACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7138 original size:20 final size:18
Alignment explanation
Indices: 7092--7143 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
7082 TTTATAATTA
7092 AATTTAAA-TAAAAATAT
1 AATTTAAATTAAAAATAT
* *
7109 TATTTTAATTAATAAATAAT
1 AATTTAAATTAA-AAAT-AT
7129 AATTTAAATTAAAAA
1 AATTTAAATTAAAAA
7144 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 6 0.21
18 3 0.11
19 7 0.25
20 12 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTAAATTAAAAATAT
Found at i:8098 original size:2 final size:2
Alignment explanation
Indices: 8093--8124 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8083 TTTTCCCAGA
8093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8125 TATGGAAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9316 original size:21 final size:19
Alignment explanation
Indices: 9274--9311 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9264 ATTTCTTCAA
9274 AAATAAGTTAATTCTTTTT
1 AAATAAGTTAATTCTTTTT
9293 AAATAAGTTAATTCTTTTT
1 AAATAAGTTAATTCTTTTT
9312 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
AAATAAGTTAATTCTTTTT
Found at i:9704 original size:13 final size:13
Alignment explanation
Indices: 9686--9710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9676 TTGTTAAATA
9686 AATATTAAATATC
1 AATATTAAATATC
9699 AATATTAAATAT
1 AATATTAAATAT
9711 AAATCTTTTT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATTAAATATC
Found at i:10288 original size:2 final size:2
Alignment explanation
Indices: 10281--10379 Score: 130
Period size: 2 Copynumber: 50.5 Consensus size: 2
10271 TAATTTAGAT
*
10281 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
10322 CA AA TA TA TA TA TA TA TA TA AA TA TA TA -A AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
10363 TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA T
10380 GCAAACACAC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
1 2 0.02
2 83 0.98
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Done.