Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1417
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: 13851
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:2659 original size:19 final size:18
Alignment explanation
Indices: 2635--2702 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2625 CAGTAGCTGA
2635 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2654 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2669 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
2686 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2703 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2675 original size:13 final size:13
Alignment explanation
Indices: 2657--2681 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2647 ACAATACTTA
2657 TGTATCGATACAT
1 TGTATCGATACAT
2670 TGTATCGATACA
1 TGTATCGATACA
2682 ACACTTATGT
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:2679 original size:32 final size:32
Alignment explanation
Indices: 2638--2700 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2628 TAGCTGATTA
*
2638 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
2670 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
2701 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:5508 original size:27 final size:28
Alignment explanation
Indices: 5477--5547 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
5467 TAATATGGAA
*
5477 ATAATTATATAATAAATTTTA-TTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
5504 ATAATAATAT-ATAAATTTTATTTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
*
5531 ATAATAATTTAATAAAT
1 ATAATAATATAATAAAT
5548 ATATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.25
27 24 0.60
28 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATAATATAATAAATTTTATTTTTAT
Found at i:5613 original size:10 final size:11
Alignment explanation
Indices: 5585--5618 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
5575 TAATATGAAT
5585 TAATAAATAATA
1 TAATAAA-AATA
5597 TAATAAAAATA
1 TAATAAAAATA
5608 -AATAAAAATA
1 TAATAAAAATA
5618 T
1 T
5619 CATTTGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 4 0.19
12 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAATAAAAATA
Found at i:7103 original size:21 final size:20
Alignment explanation
Indices: 7072--7110 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
7062 ATTTTTATTT
7072 TTTAAATTTTTAAGTTTTAC
1 TTTAAATTTTTAAGTTTTAC
*
7092 TTTAAGATTTTTATGTTTT
1 TTTAA-ATTTTTAAGTTTT
7111 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTAAATTTTTAAGTTTTAC
Found at i:7236 original size:21 final size:22
Alignment explanation
Indices: 7193--7242 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
7183 TGTGAATAAA
*
7193 TTTATTATTAAATTTATAAATT
1 TTTATTATAAAATTTATAAATT
*
7215 TTTATTATAAAATTT-TACATT
1 TTTATTATAAAATTTATAAATT
*
7236 TTCATTA
1 TTTATTA
7243 ACTTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATAAAATTTATAAATT
Found at i:7702 original size:9 final size:9
Alignment explanation
Indices: 7688--7728 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
7678 ACTCCAAAAT
*
7688 TTCCTCCTC
1 TTCCTCTTC
7697 TTCCTCTTC
1 TTCCTCTTC
7706 TTCCTCTTC
1 TTCCTCTTC
7715 TTCTCGTCTTC
1 TTC-C-TCTTC
7726 TTC
1 TTC
7729 AACTCCACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 20 0.69
10 1 0.03
11 8 0.28
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.54
Consensus pattern (9 bp):
TTCCTCTTC
Found at i:8286 original size:2 final size:2
Alignment explanation
Indices: 8281--8309 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8271 TCTCTCTCTC
8281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8310 GCACGCACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11004 original size:3 final size:3
Alignment explanation
Indices: 10996--11028 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
10986 GTGTTACCTT
10996 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
11029 TGTTAATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:13194 original size:20 final size:20
Alignment explanation
Indices: 13169--13210 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13159 TAAATCTCTT
** *
13169 TTTTTATTTGAATTCAAATA
1 TTTTTATTCCAATTAAAATA
13189 TTTTTATTCCAATTAAAATA
1 TTTTTATTCCAATTAAAATA
13209 TT
1 TT
13211 AACAATGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTATTCCAATTAAAATA
Done.