Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold370
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: 21712
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:9530 original size:12 final size:12
Alignment explanation
Indices: 9513--9548 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
9503 TACTGACTTG
*
9513 AGTCACACGGCC
1 AGTCACACGCCC
9525 AGTCACACGCCC
1 AGTCACACGCCC
*
9537 AGTCAAACGCCC
1 AGTCACACGCCC
9549 GTGTGTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.44, G:0.19, T:0.08
Consensus pattern (12 bp):
AGTCACACGCCC
Found at i:10136 original size:25 final size:25
Alignment explanation
Indices: 10108--10182 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 25
10098 ACATTACTAA
10108 ACATATTCACACACTTCTAGCCTAT
1 ACATATTCACACACTTCTAGCCTAT
* * * *
10133 ACAT-TCCATACACAT-TA--CTAA
1 ACATATTCACACACTTCTAGCCTAT
10154 ACATATTCACACACTTCTAGCCTAT
1 ACATATTCACACACTTCTAGCCTAT
10179 ACAT
1 ACAT
10183 GCCATAGTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
21 7 0.18
22 8 0.21
23 4 0.11
24 8 0.21
25 11 0.29
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (25 bp):
ACATATTCACACACTTCTAGCCTAT
Found at i:10147 original size:46 final size:46
Alignment explanation
Indices: 10094--10188 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
10084 ATGGCTAAAT
*
10094 ATACACATTACTAAACATATTCACACACTTCTAGCCTATACATTCC
1 ATACACATTACTAAACATATTCACACACTTCTAGCCTATACATGCC
10140 ATACACATTACTAAACATATTCACACACTTCTAGCCTATACATGCC
1 ATACACATTACTAAACATATTCACACACTTCTAGCCTATACATGCC
10186 ATA
1 ATA
10189 GTTTAATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.29
Consensus pattern (46 bp):
ATACACATTACTAAACATATTCACACACTTCTAGCCTATACATGCC
Found at i:10724 original size:43 final size:42
Alignment explanation
Indices: 10661--10741 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
10651 ACAACACCAA
* *
10661 TGTCCTAGATGTGGTCTTACATGTAACCAAATATCGATGTTGC
1 TGTCCTAGATGTGGTCTTACACGAAACCAAATA-CGATGTTGC
* *
10704 TGTCCTAGATAG-GGTTTTACACGAAATCAAATACGATG
1 TGTCCTAGAT-GTGGTCTTACACGAAACCAAATACGATG
10742 CCAACATCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 5 0.15
43 27 0.82
44 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (42 bp):
TGTCCTAGATGTGGTCTTACACGAAACCAAATACGATGTTGC
Found at i:10783 original size:42 final size:44
Alignment explanation
Indices: 10737--10862 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 44
10727 AAATCAAATA
* *
10737 CGATGCCAACAT-CC-TACATGGTCTTACACGTGAAACATAAGT
1 CGATGCCAACATCCCAGACATGGTCTTACACGTAAAACATAAGT
** *
10779 CGATGCCAATGTCCCAGACGTGGTCTTACACGTAAAACATAAGT
1 CGATGCCAACATCCCAGACATGGTCTTACACGTAAAACATAAGT
** *
10823 CGATGCCAATGTCCCAGACGTGGTCTTACACG-AAAACATA
1 CGATGCCAACATCCCAGACATGGTCTTACACGTAAAACATA
10863 TATCGGATCC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
42 10 0.13
43 10 0.13
44 57 0.74
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (44 bp):
CGATGCCAACATCCCAGACATGGTCTTACACGTAAAACATAAGT
Found at i:10878 original size:43 final size:44
Alignment explanation
Indices: 10755--10862 Score: 200
Period size: 44 Copynumber: 2.5 Consensus size: 44
10745 ACATCCTACA
*
10755 TGGTCTTACACGTGAAACATAAGTCGATGCCAATGTCCCAGACG
1 TGGTCTTACACGTAAAACATAAGTCGATGCCAATGTCCCAGACG
10799 TGGTCTTACACGTAAAACATAAGTCGATGCCAATGTCCCAGACG
1 TGGTCTTACACGTAAAACATAAGTCGATGCCAATGTCCCAGACG
10843 TGGTCTTACACG-AAAACATA
1 TGGTCTTACACGTAAAACATA
10863 TATCGGATCC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
43 8 0.13
44 55 0.87
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (44 bp):
TGGTCTTACACGTAAAACATAAGTCGATGCCAATGTCCCAGACG
Found at i:13992 original size:29 final size:29
Alignment explanation
Indices: 13959--14017 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
13949 TCCTTAACTC
13959 AAAC-TTTGCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTT-CCCCT
* * *
13988 AAACTTTTGCATATTTACACTTTTCCCCT
1 AAACTTTTGCAAAATTACAATTTTCCCCT
14017 A
1 A
14018 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (29 bp):
AAACTTTTGCAAAATTACAATTTTCCCCT
Found at i:21300 original size:26 final size:25
Alignment explanation
Indices: 21271--21319 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
21261 TCCTATGATA
*
21271 AATTC-ATTTATGCTTGATTATGTTTG
1 AATTCAATTT-TGCTT-ATCATGTTTG
21297 AATTCAATTTTGCTTATCATGTT
1 AATTCAATTTTGCTTATCATGTT
21320 AAGTGCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 10 0.48
27 4 0.19
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.53
Consensus pattern (25 bp):
AATTCAATTTTGCTTATCATGTTTG
Done.