Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2410
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: 22719
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:4576 original size:40 final size:40
Alignment explanation
Indices: 4515--4738 Score: 236
Period size: 40 Copynumber: 5.5 Consensus size: 40
4505 TATTTGGATG
** * *
4515 ATATCCGGGCTAAGTGTCGAAGGTATTTCTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
4555 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* *
4598 ATA-CTCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATC-CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * ** * *
4638 ATATCCGGGCTAAGTCTCGAAGGTATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
4678 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
4718 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
4739 ATACTTGGGT
Statistics
Matches: 155, Mismatches: 24, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
39 13 0.08
40 104 0.67
41 2 0.01
42 1 0.01
43 35 0.23
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:4659 original size:83 final size:80
Alignment explanation
Indices: 4515--4738 Score: 240
Period size: 83 Copynumber: 2.8 Consensus size: 80
4505 TATTTGGATG
** * * * *
4515 ATATCCGGGCTAAGTGTCGAAGGTATTTCTGCAAGTTACTATATCCGGGTTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
**
4580 TTTGTGCGAGTAGTTG-CT
66 TTCATGC---TAG-TGACT
* * *
4598 ATA-CTCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCTCGAAGGT
1 ATATC-CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGC
4662 ATTCATGCTAGTGACT
65 ATTCATGCTAGTGACT
* * *
4678 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
4739 ATACTTGGGT
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
79 15 0.12
80 44 0.36
81 3 0.02
82 1 0.01
83 59 0.48
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
TTCATGCTAGTGACT
Found at i:5520 original size:11 final size:12
Alignment explanation
Indices: 5495--5527 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5485 AAAATAGTAG
5495 TAATGTAATTAAA
1 TAATGTAA-TAAA
5508 TAAT-TAATAAA
1 TAATGTAATAAA
5519 TAATGTAAT
1 TAATGTAAT
5528 CGAACCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 7 0.37
13 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (12 bp):
TAATGTAATAAA
Found at i:11215 original size:29 final size:28
Alignment explanation
Indices: 11173--11231 Score: 109
Period size: 29 Copynumber: 2.1 Consensus size: 28
11163 ATTTTGTGTT
11173 AATGTTTTATGTTAGAAATAATAAAATAA
1 AATGTTTTATGTTAGAAATAAT-AAATAA
11202 AATGTTTTATGTTAGAAATAATAAATAA
1 AATGTTTTATGTTAGAAATAATAAATAA
11230 AA
1 AA
11232 GGTTAGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (28 bp):
AATGTTTTATGTTAGAAATAATAAATAA
Found at i:12667 original size:39 final size:40
Alignment explanation
Indices: 12557--12769 Score: 304
Period size: 40 Copynumber: 5.6 Consensus size: 40
12547 TATTCGAATG
12557 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
12597 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
12637 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
12676 -TATCCGGGCTAA-TCCCGAAGG-ATTTGTGCTAGTG---
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
12710 ATATCCGGGCTAAG-ACCGAAGGTATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
12749 ATATCC-GGCTAAAT-CCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
12770 TACTTGGGTT
Statistics
Matches: 162, Mismatches: 3, Indels: 18
0.89 0.02 0.10
Matches are distributed among these distances:
35 19 0.12
36 10 0.06
37 16 0.10
38 32 0.20
39 30 0.19
40 55 0.34
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:12737 original size:73 final size:75
Alignment explanation
Indices: 12555--12769 Score: 296
Period size: 73 Copynumber: 2.8 Consensus size: 75
12545 ATTATTCGAA
*
12555 TGATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 TGATATCCGGGCTAAG-ACCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAA-TCCCGAAGG
12620 CATTTGTGCTAG
64 CATTTGTGCTAG
*
12632 TGACTATATCCGGGCTAAGTCCGAAGGCATTTGTGCTAGTGACT-TATCCGGGCTAATCCCGAAG
1 TG---ATATCCGGGCTAAGACCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAATCCCGAAG
12696 G-ATTTGTGCTAG
63 GCATTTGTGCTAG
* *
12708 TGATATCCGGGCTAAGACCGAAGGTATTTGTGCGAGTTG-CTATATCC-GGCTAAAT-CCGAAGG
1 TGATATCCGGGCTAAGACCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCT-AATCCCGAAGG
12770 TACTTGGGTT
Statistics
Matches: 128, Mismatches: 4, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
73 44 0.34
74 10 0.08
76 13 0.10
77 11 0.09
78 12 0.09
79 24 0.19
80 14 0.11
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (75 bp):
TGATATCCGGGCTAAGACCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAATCCCGAAGGCA
TTTGTGCTAG
Found at i:20562 original size:40 final size:40
Alignment explanation
Indices: 20507--20727 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
20497 TATTCGAATG
20507 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
20547 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
20587 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
20627 ATATCCGGGCTAAAT-CCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
20666 ATATCCGGGCTAAGACCCGAAGGTATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
20706 ATATCC-GACTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
20728 TACTTGGGTT
Statistics
Matches: 171, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 50 0.29
40 119 0.70
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:20694 original size:79 final size:80
Alignment explanation
Indices: 20507--20727 Score: 367
Period size: 79 Copynumber: 2.8 Consensus size: 80
20497 TATTCGAATG
*
20507 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAATCCCGAAGGCA
20572 TTTGTGCTAGTGACT
66 TTTGTGCTAGTGACT
20587 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAT-CCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAATCCCGAAGGCA
20651 TTTGTGCTAGTGACT
66 TTTGTGCTAGTGACT
* * * *
20666 ATATCCGGGCTAAGACCCGAAGGTATTTGTGCGAGTTG-CTATATCC-GACTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAATCCCGAAGG
20728 TACTTGGGTT
Statistics
Matches: 134, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
78 7 0.05
79 71 0.53
80 56 0.42
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAATCCCGAAGGCA
TTTGTGCTAGTGACT
Done.