Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1665
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: 62063
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5874 original size:40 final size:39
Alignment explanation
Indices: 5830--6054 Score: 263
Period size: 40 Copynumber: 5.7 Consensus size: 39
5820 GCCACTAGCT
*
5830 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
5870 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
** * *
5909 CAAATGCCTTCGGGACTTAGCCCAGACATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGTATAGTAACTCGCA
* * *
5949 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
5989 CAAATGCCTTCGGGACTTAGCCCAGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
6029 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
6055 TATCATCCGA
Statistics
Matches: 161, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 39 0.24
40 122 0.76
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:10723 original size:38 final size:38
Alignment explanation
Indices: 10666--10773 Score: 153
Period size: 38 Copynumber: 2.8 Consensus size: 38
10656 AACGTAATGT
* *
10666 TATTCGGGCTCTGTCCCTAGCAGGCTTTGTGCTGGTGA
1 TATTCCGGCTCTGTGCCTAGCAGGCTTTGTGCTGGTGA
* *
10704 TATTCCTGCTTTGTGCCTAGCAGGCTTTGTGCTGGTGA
1 TATTCCGGCTCTGTGCCTAGCAGGCTTTGTGCTGGTGA
* * *
10742 TATTCGGGCTCTGTGCCTAGTAGGCTTCGTGC
1 TATTCCGGCTCTGTGCCTAGCAGGCTTTGTGC
10774 CAGTGTATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 61 1.00
ACGTcount: A:0.10, C:0.23, G:0.31, T:0.36
Consensus pattern (38 bp):
TATTCCGGCTCTGTGCCTAGCAGGCTTTGTGCTGGTGA
Found at i:11259 original size:21 final size:21
Alignment explanation
Indices: 11233--11273 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11223 ATATGTGAGA
11233 AATTTA-CTTAAGTTATGGATG
1 AATTTATC-TAAGTTATGGATG
*
11254 AATTTATCTAGGTTATGGAT
1 AATTTATCTAAGTTATGGAT
11274 AAATACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (21 bp):
AATTTATCTAAGTTATGGATG
Found at i:18326 original size:20 final size:20
Alignment explanation
Indices: 18303--18341 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18293 TTTTTTGTCC
*
18303 ATTTTTTATATTTATATTTA
1 ATTTTTAATATTTATATTTA
*
18323 ATTTTTAATTTTTATATTT
1 ATTTTTAATATTTATATTT
18342 TAGCTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTAATATTTATATTTA
Found at i:25884 original size:25 final size:25
Alignment explanation
Indices: 25856--25904 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
25846 CTAGAAGACC
*
25856 AATCACATAACTCATGATAATGATT
1 AATCACATAACTCATCATAATGATT
* * *
25881 AATCACGTAATTCTTCATAATGAT
1 AATCACATAACTCATCATAATGAT
25905 AATAATAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (25 bp):
AATCACATAACTCATCATAATGATT
Found at i:36688 original size:18 final size:17
Alignment explanation
Indices: 36661--36694 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
36651 TAAATTGGAA
36661 ATGAAAATAATTAAAAG
1 ATGAAAATAATTAAAAG
36678 ATGATAAATAATTAAAA
1 ATGA-AAATAATTAAAA
36695 AAATATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
ATGAAAATAATTAAAAG
Found at i:37040 original size:19 final size:19
Alignment explanation
Indices: 36996--37042 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
36986 AATTTTCATG
* *
36996 AAATTGTGATTTAAGGATT
1 AAATTGTAATTTAAGGACT
37015 AAATTGTAATTTAAGGACT
1 AAATTGTAATTTAAGGACT
*
37034 AATTTGTAA
1 AAATTGTAA
37043 ATATGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.40
Consensus pattern (19 bp):
AAATTGTAATTTAAGGACT
Found at i:38647 original size:23 final size:22
Alignment explanation
Indices: 38604--38647 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
38594 ATGTGTTTTG
* *
38604 ATATGATTAAGTAGTAGATGAT
1 ATATGATTAAATAGTAAATGAT
*
38626 ATATGTATTAAATGGTAAATGA
1 ATATG-ATTAAATAGTAAATGA
38648 ATTTGAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.36
Consensus pattern (22 bp):
ATATGATTAAATAGTAAATGAT
Found at i:50434 original size:40 final size:40
Alignment explanation
Indices: 50383--50468 Score: 172
Period size: 40 Copynumber: 2.1 Consensus size: 40
50373 TCATTCTTTT
50383 ATTCATAAACATATCACACAAAACAATAATTACCAAATTC
1 ATTCATAAACATATCACACAAAACAATAATTACCAAATTC
50423 ATTCATAAACATATCACACAAAACAATAATTACCAAATTC
1 ATTCATAAACATATCACACAAAACAATAATTACCAAATTC
50463 ATTCAT
1 ATTCAT
50469 TCTTTGTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (40 bp):
ATTCATAAACATATCACACAAAACAATAATTACCAAATTC
Found at i:52860 original size:56 final size:57
Alignment explanation
Indices: 52798--53003 Score: 262
Period size: 56 Copynumber: 3.7 Consensus size: 57
52788 GAGATTGGCG
* * *
52798 CTAAGTGTGCGGGTTTAAAT-TGTGCAGCACTAAGTGTGCGA-ATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATGTG-AGCACTAAGTGTGCGAGTTTGACTATGTAGCA
*
52854 CTAAGTGTGCGAGTTTGACTATGT-AGCACTAAGTGTGCGAGTTTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATGTGAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
* * * *
52910 CTAAGTGTGCGAGCTTGATTATGTG-GCACTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGAATATGTGAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
* * *
52966 CTAAGTGTGCGAG-TTGATTATAT-AGCACTGAGTGTGCG
1 CTAAGTGTGCGAGTTTGAATATGTGAGCACTAAGTGTGCG
53004 GACTTATTAT
Statistics
Matches: 136, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
55 38 0.28
56 95 0.70
57 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (57 bp):
CTAAGTGTGCGAGTTTGAATATGTGAGCACTAAGTGTGCGAGTTTGACTATGTAGCA
Found at i:52880 original size:28 final size:28
Alignment explanation
Indices: 52823--53003 Score: 267
Period size: 28 Copynumber: 6.5 Consensus size: 28
52813 TAAATTGTGC
*
52823 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
52850 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
52878 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
52906 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* * *
52934 GGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
52962 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
52989 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53004 GACTTATTAT
Statistics
Matches: 145, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
27 40 0.28
28 105 0.72
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:60003 original size:27 final size:27
Alignment explanation
Indices: 59966--60144 Score: 277
Period size: 27 Copynumber: 6.6 Consensus size: 27
59956 TAAATTGTGC
*
59966 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
59993 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
60021 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
60048 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
60076 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
60103 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
60130 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
60145 GACTTATTAT
Statistics
Matches: 146, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
27 93 0.64
28 53 0.36
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:60031 original size:55 final size:54
Alignment explanation
Indices: 59966--60144 Score: 286
Period size: 55 Copynumber: 3.3 Consensus size: 54
59956 TAAATTGTGC
* *
59966 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAG-TTGATTATGT
60021 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAG-TTGATTATGT
* * *
60076 AGCACTAAGTGTGCGAGTTGATTATATAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTGATTATGT
*
60130 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
60145 GACTTATTAT
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
54 23 0.20
55 94 0.80
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (54 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTGATTATGT
Found at i:60109 original size:82 final size:82
Alignment explanation
Indices: 59966--60144 Score: 279
Period size: 82 Copynumber: 2.2 Consensus size: 82
59956 TAAATTGTGC
*
59966 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATATAGCACTAAGT
*
60031 GTGCGAGTTGACTATGT
66 GTGCGAGTTGACTATAT
* * *
60048 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAG-TTGATTATATAGCACTAAG
1 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATATAGCACTAAG
*
60112 TGTGCGAGTTGATTATAT
65 TGTGCGAGTTGACTATAT
*
60130 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
60145 GACTTATTAT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 63 0.71
83 26 0.29
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATATAGCACTAAGT
GTGCGAGTTGACTATAT
Done.