Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold981
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: 25196
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Found at i:12105 original size:25 final size:23
Alignment explanation
Indices: 12048--12105 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
12038 TCCATGTAAG
*
12048 AATTTA-ATTTATTTAATTGGGT
1 AATTTATATTTATTTAATTGGAT
*
12070 AATTTTTTATTTGATTTAATTGGAT
1 AA-TTTATATTT-ATTTAATTGGAT
12095 CAATTTATATT
1 -AATTTATATT
12106 AAAATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.07
23 3 0.10
24 4 0.14
25 18 0.62
26 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (23 bp):
AATTTATATTTATTTAATTGGAT
Found at i:12810 original size:29 final size:28
Alignment explanation
Indices: 12777--12842 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
12767 TATTATTAAA
12777 AAATTATTTCATTTATGA-T-TAATGATAGT
1 AAATTATTT-ATTTA-GATTGTAATGAT-GT
12806 AAATTTATTTATTTAGATTGTAATGATGT
1 AAA-TTATTTATTTAGATTGTAATGATGT
12835 -AATTATTT
1 AAATTATTT
12843 TAAAATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 6 0.18
28 4 0.12
29 11 0.32
30 13 0.38
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.52
Consensus pattern (28 bp):
AAATTATTTATTTAGATTGTAATGATGT
Found at i:12844 original size:28 final size:29
Alignment explanation
Indices: 12777--12844 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
12767 TATTATTAAA
*
12777 AAATTATTTCATTTATGATTAATGATAGT
1 AAATTATTTTATTTATGATTAATGATAGT
12806 AAATT-TATTTATTTA-GATTGTAATGAT-GT
1 AAATTAT-TTTATTTATGA-T-TAATGATAGT
12835 -AATTATTTTA
1 AAATTATTTTA
12845 AAATATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
28 11 0.32
29 16 0.47
30 7 0.21
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.51
Consensus pattern (29 bp):
AAATTATTTTATTTATGATTAATGATAGT
Found at i:12879 original size:13 final size:13
Alignment explanation
Indices: 12845--12887 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
12835 AATTATTTTA
12845 AAATATTTAATTT
1 AAATATTTAATTT
*
12858 AATTATTTAATTT
1 AAATATTTAATTT
*
12871 GAAAT-TTTATTTT
1 -AAATATTTAATTT
12884 AAAT
1 AAAT
12888 TGTACTCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 4 0.15
13 19 0.73
14 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
AAATATTTAATTT
Found at i:12933 original size:64 final size:64
Alignment explanation
Indices: 12813--12938 Score: 150
Period size: 64 Copynumber: 2.0 Consensus size: 64
12803 AGTAAATTTA
* * * *
12813 TTTATTTAGATTGTAATGATGTAATTATTTTAAAATATTTAATTTAATTATTTAATT-TGAAAT
1 TTTATTTAAATTGTAATCATGTAATTATTTTAAAATATTTAATTTAATCATCTAATTATGAAAT
* *
12876 TTTATTTTAAATTGTACTCATGTAATTATTTT-AAA-ATTTAGATTGTAATCGTCTAATTATGAA
1 TTTA-TTTAAATTGTAATCATGTAATTATTTTAAAATATTTA-ATT-TAATCATCTAATTATGAA
12939 GGGATATCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
62 5 0.09
63 10 0.19
64 34 0.64
65 4 0.08
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.52
Consensus pattern (64 bp):
TTTATTTAAATTGTAATCATGTAATTATTTTAAAATATTTAATTTAATCATCTAATTATGAAAT
Found at i:13052 original size:37 final size:38
Alignment explanation
Indices: 12985--13057 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
12975 AATTTAAAAT
* *
12985 AATTATAATTTTAAAAATAATTAAAAGATTATAACTTA
1 AATTAAAATTTTAAAAATAATTAAAAGATTACAACTTA
*
13023 AATTAAAATTTT-AAAATAATTAAATGATTACAACT
1 AATTAAAATTTTAAAAATAATTAAAAGATTACAACT
13058 CTTAATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 21 0.66
38 11 0.34
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (38 bp):
AATTAAAATTTTAAAAATAATTAAAAGATTACAACTTA
Found at i:13129 original size:13 final size:14
Alignment explanation
Indices: 13107--13148 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
13097 TTAGATGATT
13107 ACAACTTAAATTAA
1 ACAACTTAAATTAA
*
13121 A-ATCTTAAATTAA
1 ACAACTTAAATTAA
*
13134 ACAAATTAAATTAA
1 ACAACTTAAATTAA
13148 A
1 A
13149 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAACTTAAATTAA
Found at i:13546 original size:14 final size:13
Alignment explanation
Indices: 13523--13565 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
13513 AAAATAATAA
*
13523 TATTTCAATAATT
1 TATTTTAATAATT
13536 TATTTTAAATAATAT
1 TATTTT-AATAAT-T
*
13551 TATTTTGATAATT
1 TATTTTAATAATT
13564 TA
1 TA
13566 CTTAAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 8 0.31
14 11 0.42
15 7 0.27
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (13 bp):
TATTTTAATAATT
Found at i:13554 original size:28 final size:27
Alignment explanation
Indices: 13514--13573 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
13504 TTAAATATCA
*
13514 AAATAATAATATTTCAATAATTTATTTT
1 AAATAATAATATTTCAATAATTTA-CTT
* **
13542 AAATAATATTATTTTGATAATTTACTT
1 AAATAATAATATTTCAATAATTTACTT
13569 AAATA
1 AAATA
13574 TCATGAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (27 bp):
AAATAATAATATTTCAATAATTTACTT
Found at i:16745 original size:16 final size:17
Alignment explanation
Indices: 16715--16747 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16705 AACTGCTCCT
*
16715 TTTTCTCTCTTTCTTTC
1 TTTTCTCTCTCTCTTTC
16732 TTTTC-CTCTCTCTTTC
1 TTTTCTCTCTCTCTTTC
16748 ACACTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTCTCTCTCTCTTTC
Found at i:18501 original size:15 final size:15
Alignment explanation
Indices: 18481--18510 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18471 AACGACAGGC
18481 CAGGGAAAAGAGAAA
1 CAGGGAAAAGAGAAA
18496 CAGGGAAAAGAGAAA
1 CAGGGAAAAGAGAAA
18511 AAAAAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.33, T:0.00
Consensus pattern (15 bp):
CAGGGAAAAGAGAAA
Found at i:20633 original size:2 final size:2
Alignment explanation
Indices: 20626--20663 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20616 CAATACATAC
20626 AT AT AT 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 AT AT AT
20664 GTAAAAACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21450 original size:20 final size:19
Alignment explanation
Indices: 21425--21488 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 19
21415 TTTGGTTATT
21425 AAAAATTACATTTTTCATCC
1 AAAAA-TACATTTTTCATCC
*
21445 AAAAATGCATTCTTTCATCC
1 AAAAATACATT-TTTCATCC
* *
21465 AACCAATACATCATTTCATCC
1 AA-AAATACAT-TTTTCATCC
21486 AAA
1 AAA
21489 TATATCTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 5 0.14
20 15 0.42
21 16 0.44
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATACATTTTTCATCC
Done.