Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1770
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: 5454
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Found at i:3165 original size:13 final size:12
Alignment explanation
Indices: 3142--3187 Score: 65
Period size: 13 Copynumber: 3.6 Consensus size: 12
3132 CCGTTACACC
3142 CAAAAAAAAAAA
1 CAAAAAAAAAAA
3154 CAAAACAAAAAAA
1 CAAAA-AAAAAAA
3167 CAAAAAAAAAATA
1 CAAAAAAAAAA-A
3180 GCAAAAAA
1 -CAAAAAA
3188 TAGAAGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.35
13 13 0.42
14 7 0.23
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:4810 original size:32 final size:32
Alignment explanation
Indices: 4408--5454 Score: 1196
Period size: 32 Copynumber: 34.6 Consensus size: 32
4398 TGTTCATCCC
*
4408 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * *
4437 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
4466 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
4494 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
4522 TTTCAAAGCCCACA-AAGT--G-GGC-ACTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
4548 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
4576 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
4604 -TTC-AAG-CC-CACAAG-C-ATGGC-A-TC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
4627 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
4655 -TTC-AAG-CC-CACAAGCCAGTGGC-ACCTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACC-CA
*
4683 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
4712 TTTC-AAG--C-CACAAGTC-GTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
4739 GTTC--AGCCCACAACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCAC-ACAAGTCGGTGGCAACCCA
4770 TTTC-AAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
4801 TTTCAAAGCCCACACAAGTCGGTGGCAAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGC-AACCCA
*
4834 TTCCAAAG-CCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
4865 TTCCAAAGCCCACACAAGGCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
4897 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
4929 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
4961 TTTCCAAAGCCCACACAAGTC-GTGGCAACCCA
1 TTT-CAAAGCCCACACAAGTCGGTGGCAACCCA
4993 -TTCAAAGCCCACAC-AG-CGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5022 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5054 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5086 TTTCAAAG-CC-CACAAGTCGGTGGGCAAACCCA
1 TTTCAAAGCCCACACAAGTCGGT-GGC-AACCCA
5118 TTTCAAAG-CCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5149 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5181 TTCCAAAGCCCACACAAGTC-GTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
5212 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5244 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
5276 TTCCAAAAACCCACAACAAGTCGGTGGCAACACCA
1 TTTC-AAAGCCCAC-ACAAGTCGGTGGCAAC-CCA
5311 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5342 TTTCAAAG-CCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5373 TTTCAAAGCCCA-ACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
5404 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
5435 TTCCAAAAG-CCAAACAAGTC
1 TTTC-AAAGCCCACACAAGTC
Statistics
Matches: 942, Mismatches: 26, Indels: 97
0.88 0.02 0.09
Matches are distributed among these distances:
23 1 0.00
24 10 0.01
25 18 0.02
26 55 0.06
27 30 0.03
28 82 0.09
29 64 0.07
30 81 0.09
31 180 0.19
32 339 0.36
33 61 0.06
34 18 0.02
35 3 0.00
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.16
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Done.