Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1918
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: 30290
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:2644 original size:2 final size:2
Alignment explanation
Indices: 2637--2678 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2627 TAATTTGTAT
2637 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2679 AAAGCAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3254 original size:4 final size:4
Alignment explanation
Indices: 3247--3276 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
3237 CATCCCTACT
3247 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
3277 GTTCAATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:10380 original size:13 final size:13
Alignment explanation
Indices: 10362--10389 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10352 ATACAAAGAT
10362 CAATGTATCGATA
1 CAATGTATCGATA
10375 CAATGTATCGATA
1 CAATGTATCGATA
10388 CA
1 CA
10390 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:10469 original size:33 final size:33
Alignment explanation
Indices: 10432--10496 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
10422 TAGCTTCAAA
10432 TGTATCGATACAAAAAAATATGTATCGATACAT
1 TGTATCGATACAAAAAAATATGTATCGATACAT
* ***
10465 TGTATCGATACAACATTTTATGTATCGATACA
1 TGTATCGATACAAAAAAATATGTATCGATACA
10497 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAAAAAATATGTATCGATACAT
Found at i:10470 original size:13 final size:13
Alignment explanation
Indices: 10452--10476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10442 CAAAAAAATA
10452 TGTATCGATACAT
1 TGTATCGATACAT
10465 TGTATCGATACA
1 TGTATCGATACA
10477 ACATTTTATG
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:12540 original size:17 final size:17
Alignment explanation
Indices: 12514--12554 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
12504 TGAAGGGTCC
*
12514 AAAATATTGTATTTT-T
1 AAAATTTTGTATTTTAT
12530 GAAAATTTTGTATTTTAT
1 -AAAATTTTGTATTTTAT
12548 AAAATTT
1 AAAATTT
12555 CATATGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (17 bp):
AAAATTTTGTATTTTAT
Found at i:13008 original size:32 final size:33
Alignment explanation
Indices: 12950--13012 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
12940 CACCAAGATG
*
12950 TATCGATACATGCTGCTTTGTATCGATACATTA
1 TATCGATACATGCTGCATTGTATCGATACATTA
*
12983 TATCGATACATG-TTCATTGTATCGATACAT
1 TATCGATACATGCTGCATTGTATCGATACAT
13013 GGCCAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (33 bp):
TATCGATACATGCTGCATTGTATCGATACATTA
Found at i:19268 original size:13 final size:13
Alignment explanation
Indices: 19250--19317 Score: 118
Period size: 13 Copynumber: 5.2 Consensus size: 13
19240 ACAATATTCC
*
19250 TTGTATCGATAAA
1 TTGTATCGATACA
19263 TTGTATCGATACA
1 TTGTATCGATACA
*
19276 TTGTATCGATAAA
1 TTGTATCGATACA
19289 TTGTATCGATACA
1 TTGTATCGATACA
19302 TTGTATCGATACA
1 TTGTATCGATACA
19315 TTG
1 TTG
19318 GGTACTATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:21807 original size:32 final size:33
Alignment explanation
Indices: 21749--21811 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
21739 CACCCAGATG
*
21749 TATCGATACATGCTGTTTTGTATCGATACATTA
1 TATCGATACATGCTGTATTGTATCGATACATTA
21782 TATCGATACATG-T-TCATTGTATCGATACAT
1 TATCGATACATGCTGT-ATTGTATCGATACAT
21812 GGCCAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.04
32 15 0.54
33 12 0.43
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (33 bp):
TATCGATACATGCTGTATTGTATCGATACATTA
Found at i:24120 original size:19 final size:20
Alignment explanation
Indices: 24098--24143 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
24088 ACATTGTATT
*
24098 GATACATGTTC-ATTATATC
1 GATACATGCTCAATTATATC
* *
24117 GATACATGCTCAATTGTATT
1 GATACATGCTCAATTATATC
24137 GATACAT
1 GATACAT
24144 AAAACTGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
GATACATGCTCAATTATATC
Found at i:24142 original size:20 final size:19
Alignment explanation
Indices: 24089--24143 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
24079 TGTATCGATA
*
24089 CATTGTATTGATACATGTT
1 CATTGTATTGATACATGCT
* *
24108 CATTATATCGATACATGCT
1 CATTGTATTGATACATGCT
24127 CAATTGTATTGATACAT
1 C-ATTGTATTGATACAT
24144 AAAACTGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (19 bp):
CATTGTATTGATACATGCT
Done.