Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2794
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: 38447
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:459 original size:41 final size:42
Alignment explanation
Indices: 402--483 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
392 AATGGCCCTG
* * *
402 CTCACACGAGCTGTGGGTCGGCATGT-AGCTACACGATGCTA
1 CTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATGCTA
443 CTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATGCT
1 CTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATGCT
484 GCTTACACGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 23 0.62
42 14 0.38
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (42 bp):
CTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATGCTA
Found at i:500 original size:42 final size:41
Alignment explanation
Indices: 399--500 Score: 141
Period size: 42 Copynumber: 2.5 Consensus size: 41
389 TGAAATGGCC
* *
399 CTGCTCACACGAGCTGTGGGTCGGCATGTAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
* *
440 CTACTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGT-AGCTACACGATG
* *
482 CTGCTTACACGAGTTGTGG
1 CTGCTCACACGAGCTGTGG
501 AGAATTCACA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 25 0.48
42 27 0.52
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (41 bp):
CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
Found at i:4351 original size:26 final size:27
Alignment explanation
Indices: 4322--4372 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
4312 GACCGTAATG
4322 CCCCTAGAGGGTAAATGACT-ATTTTT
1 CCCCTAGAGGGTAAATGACTGATTTTT
*
4348 CCCCTCGAGGGTAAATGACTGATTT
1 CCCCTAGAGGGTAAATGACTGATTT
4373 GTGCTATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (27 bp):
CCCCTAGAGGGTAAATGACTGATTTTT
Found at i:10110 original size:17 final size:17
Alignment explanation
Indices: 10088--10122 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10078 CATAGATATT
10088 AACTAACACAAAAATAA
1 AACTAACACAAAAATAA
**
10105 AACTAATGCAAAAATAA
1 AACTAACACAAAAATAA
10122 A
1 A
10123 TACATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.14, G:0.03, T:0.14
Consensus pattern (17 bp):
AACTAACACAAAAATAA
Found at i:17409 original size:11 final size:13
Alignment explanation
Indices: 17382--17424 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
17372 TATGGTCTAC
17382 AATTTCATTGAAA
1 AATTTCATTGAAA
17395 AATTTCA-TG-AA
1 AATTTCATTGAAA
* *
17406 AATTTCGTTCAAA
1 AATTTCATTGAAA
17419 AATTTC
1 AATTTC
17425 GACGTTTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 8 0.31
12 3 0.12
13 15 0.58
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (13 bp):
AATTTCATTGAAA
Found at i:18618 original size:102 final size:104
Alignment explanation
Indices: 18490--18719 Score: 374
Period size: 102 Copynumber: 2.2 Consensus size: 104
18480 GAATATAAAG
* * * *
18490 GGGGTTGCTAAGTGCTGAGTCCCCCAAGGGGTTGCTAAGTGTTGTTTCCCCGATTCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
*
18555 TGCTAAGTGCTGATTCCACCGTA-TTTTAAATGTG-AAA
66 TGCTAAGTGCTGATTCCACCATATTTTTAAATGTGAAAA
*
18592 GGGGTTACTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
*
18657 TGCTAAGTGCTGATTCCACCATATTTTTGAATGTGAAAA
66 TGCTAAGTGCTGATTCCACCATATTTTTAAATGTGAAAA
*
18696 GGGGTTGCTAAGTGCTAATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
18720 GAATCATTGG
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 82 0.70
103 10 0.09
104 25 0.21
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (104 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
TGCTAAGTGCTGATTCCACCATATTTTTAAATGTGAAAA
Found at i:18629 original size:27 final size:27
Alignment explanation
Indices: 18590--18642 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
18580 TTAAATGTGA
18590 AAGGGGTTACTAAGTGCTGATTCCCCC
1 AAGGGGTTACTAAGTGCTGATTCCCCC
*
18617 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTACTAAGTGCTGATTCCCC
18643 GAATCATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (27 bp):
AAGGGGTTACTAAGTGCTGATTCCCCC
Found at i:18663 original size:33 final size:33
Alignment explanation
Indices: 18621--18746 Score: 110
Period size: 33 Copynumber: 3.5 Consensus size: 33
18611 TCCCCCAAGG
18621 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
18654 GGTTGCTAAGTGCTGATTCCACC-ATATTTTTGAATGTGAAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-A----T-CAT-TG----GT
*
18698 GGTTGCTAAGTGCTAATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
18731 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
18747 ATCCACTGAT
Statistics
Matches: 74, Mismatches: 6, Indels: 26
0.70 0.06 0.25
Matches are distributed among these distances:
33 37 0.50
34 3 0.04
37 2 0.03
38 3 0.04
39 3 0.04
40 2 0.03
43 3 0.04
44 21 0.28
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:34503 original size:69 final size:68
Alignment explanation
Indices: 34423--34565 Score: 243
Period size: 70 Copynumber: 2.1 Consensus size: 68
34413 TATTATCTTC
34423 AAGTAAG-TTTTTTTATTTAAAAAACTTTATGAGCCAGATAATCAAAATAGAGACCCCAAATACG
1 AAGTAAGTTTTTTTTATTTAAAAAACTTTATGAGCCAGATAATCAAAATAGAGACCCCAAATA--
34487 GAAGA
64 GAAGA
* *
34492 AAGTAAGTTTTTTTTATTTAAAAAACTTTGTGAGCCAGATAATCAAAATAGAGACCCTAAATAGA
1 AAGTAAGTTTTTTTTATTTAAAAAACTTTATGAGCCAGATAATCAAAATAGAGACCCCAAATAGA
34557 AGA
66 AGA
34560 AAGTAA
1 AAGTAA
34566 ATCAACACAC
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
68 11 0.15
69 7 0.10
70 53 0.75
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (68 bp):
AAGTAAGTTTTTTTTATTTAAAAAACTTTATGAGCCAGATAATCAAAATAGAGACCCCAAATAGA
AGA
Found at i:38401 original size:20 final size:20
Alignment explanation
Indices: 38359--38401 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
38349 CTAACCAAAG
* *
38359 ATATACTATAAATATTAATA
1 ATATACTATAAATATAAAAA
38379 ATATACTATAAATATAAAAA
1 ATATACTATAAATATAAAAA
38399 ATA
1 ATA
38402 AATGCAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATACTATAAATATAAAAA
Done.