Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2511
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: 27824
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:2402 original size:49 final size:49
Alignment explanation
Indices: 2347--2541 Score: 302
Period size: 49 Copynumber: 4.0 Consensus size: 49
2337 TTCGTTTTCT
* ** *
2347 CGATGCCATAGTCCAATTATGGTCTTACACGTAATCACA-ATTCACATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATA-TCACATAC
* *
2396 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACATAC
*
2445 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACATAC
2494 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAT-ATCACAT
2542 GTTCACATGT
Statistics
Matches: 137, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
49 130 0.95
50 7 0.05
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (49 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACATAC
Found at i:3856 original size:37 final size:37
Alignment explanation
Indices: 3791--3936 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
3781 TACGTATGAT
* *
3791 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
3826 CACCTATCACTTTGTTTCTTGATCACATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
3863 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
3900 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
3937 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:3953 original size:46 final size:46
Alignment explanation
Indices: 3900--4115 Score: 263
Period size: 46 Copynumber: 4.6 Consensus size: 46
3890 TAAGTGTAGC
* * *
3900 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
*
3946 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
* *
3992 CACTTATCACTTTATCAC-TGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
* * * * *
4037 TACTTATCACTTTCCACTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
*
4089 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
4116 AGTACTCAAA
Statistics
Matches: 148, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
45 36 0.24
46 73 0.49
47 1 0.01
50 1 0.01
51 6 0.04
52 31 0.21
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
Found at i:4048 original size:52 final size:53
Alignment explanation
Indices: 3989--4113 Score: 139
Period size: 52 Copynumber: 2.4 Consensus size: 53
3979 TAGCCGAAGC
* * **
3989 TATCACTTATCACTTTATCAC-TGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTATCACTTTATCACTTGATCAAATAAGTATAGCCAAAGCTACCACT
* * *
4041 TATCACTT-TCCAC-TTGTCACTTGATCAAATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTAT-CACTTTATCACTTGATCAAATAAGTATAGCCAAAGCTACCACT
*
4093 TATCACTTTATCACTTGATCA
1 TATCAC-TTATCACTTTATCA
4114 GAAGTACTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
51 7 0.12
52 42 0.71
53 5 0.08
54 5 0.08
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.35
Consensus pattern (53 bp):
TATCACTTATCACTTTATCACTTGATCAAATAAGTATAGCCAAAGCTACCACT
Found at i:4094 original size:97 final size:92
Alignment explanation
Indices: 3899--4115 Score: 274
Period size: 97 Copynumber: 2.3 Consensus size: 92
3889 ATAAGTGTAG
* * * *
3899 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCAC
1 CCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTGTCAC
* *
3964 TTGATCAGATAAGTATAGCCGAAGCTA
66 TTGATCAAATAAGTATAGCCAAAGCTA
* * *
3991 TCACTTATCACTTTATCAC-TGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCAC--T----T
* *
4055 TGTCACTTGATCAAATAAGTGTAGCTAAAGCTA
60 TGTCACTTGATCAAATAAGTATAGCCAAAGCTA
4088 CCACTTATCACTTTATCACTTGATCAGA
1 CCACTTATCACTTTATCACTTGATCAGA
4116 AGTACTCAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
91 33 0.31
92 16 0.15
93 1 0.01
97 48 0.45
98 8 0.08
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (92 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTGTCAC
TTGATCAAATAAGTATAGCCAAAGCTA
Found at i:19444 original size:27 final size:28
Alignment explanation
Indices: 19360--19457 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
19350 CATGAGATTG
* * * *
19360 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
19389 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
19417 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
19444 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
19458 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:19468 original size:27 final size:27
Alignment explanation
Indices: 19388--19470 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
19378 TAAATTGTAC
* *
19388 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
19416 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
19443 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
19470 A
1 A
19471 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:19471 original size:29 final size:27
Alignment explanation
Indices: 19360--19471 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
19350 CATGAGATTG
** * *
19360 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
19389 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
19417 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
19444 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
19472 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:27561 original size:27 final size:28
Alignment explanation
Indices: 27506--27574 Score: 122
Period size: 27 Copynumber: 2.5 Consensus size: 28
27496 CATGAGATTG
27506 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
27534 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
27561 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
27575 GACTTAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:27588 original size:29 final size:27
Alignment explanation
Indices: 27506--27588 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
27496 CATGAGATTG
* *
27506 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
27534 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
27561 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
27589 TTTTGAATCA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.47
28 21 0.43
29 5 0.10
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Done.