Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2543
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: 18823
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Found at i:15418 original size:44 final size:42
Alignment explanation
Indices: 15348--15776 Score: 200
Period size: 44 Copynumber: 10.1 Consensus size: 42
15338 GTGTTCGACT
* * * * *
15348 TGCTCCGCTGTAATCTTAGGGAGATAAGACCTCTGGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGA-CTCT-TCTTCGATC
* *
15392 TGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGA-CT-C--TTCTTCGATC
* * ** *
15438 TGTTCCACTGTAATCTCAGGGAGATAAGAC-CTGATGCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACTCTTCTTCGATC
* * * * * **
15479 TACTCTACTGTAACTTCAGAGAGATAAGA-TCCTTTATTTTAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACT-C-TT-CTTCGATC
* * * * *
15523 CGCTCCACTGTAACTTCAGGGAGATAGGATTATATCTTCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACTCT-TCTTCGATC
* * *
15566 TGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGA-CT--CTTCTTCGATC
* * **
15611 TGTTCCACTGTAATCTCAGGGAGATAAGAC-CTGATGT-GATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACTCTTCT-TCGATC
* * * **
15652 T--TCTACTGTAACTTCAGAGAGATAAGA-TC--CTTTAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACTCTTCTTCGATC
* * * * *
15689 CGCTCCA-T-TAATCTCA-GG-GATAGGATTACTATCTTTGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGACT-CT-TCTTCGATC
* * * *
15729 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGA-CTCT-TCTTCGATC
15773 TGCT
1 TGCT
15777 TCAATGCAAC
Statistics
Matches: 289, Mismatches: 69, Indels: 54
0.70 0.17 0.13
Matches are distributed among these distances:
35 6 0.02
36 3 0.01
37 11 0.04
38 1 0.00
39 26 0.09
40 12 0.04
41 36 0.12
42 10 0.03
43 35 0.12
44 76 0.26
45 38 0.13
46 34 0.12
47 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (42 bp):
TGCTCCACTGTAACCTCAGGGAGATAAGACTCTTCTTCGATC
Found at i:15585 original size:43 final size:45
Alignment explanation
Indices: 15384--15644 Score: 234
Period size: 45 Copynumber: 5.9 Consensus size: 45
15374 AGACCTCTGG
* *
15384 CTTCAATCTGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATT
1 CTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG-AATT
* * * *
15430 CTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG-A--
1 CTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAATT
* * * * * **
15472 -TGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATT
1 CTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGAATT
* * * *
15517 -TT-AATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-T--ATAT
1 CTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-T
*
15558 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAATT
1 CTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAATT
* * * *
15603 CTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGA
1 CTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA
15645 TGTGATCTTC
Statistics
Matches: 172, Mismatches: 33, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
40 2 0.01
41 29 0.17
42 5 0.03
43 30 0.17
44 30 0.17
45 39 0.23
46 37 0.22
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (45 bp):
CTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAATT
Found at i:15994 original size:42 final size:42
Alignment explanation
Indices: 15946--16082 Score: 130
Period size: 44 Copynumber: 3.2 Consensus size: 42
15936 CAAGATCTTT
15946 TGTCTTCAACCAGCTCTATCACAACGAAAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCTATCACAACGAAAGAGGCAAGGTTTG
* * * ** ** * * * * *
15988 TGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTT
1 TGTCTTCAACCAGC-TCTATCACAACGAAAG-AGGCAAGGT-TTG
16033 TGTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCTATCACAA-CGAAAGAGGCAAGGTTTG
16076 TGTCTTC
1 TGTCTTC
16083 GATCTGCTTC
Statistics
Matches: 67, Mismatches: 24, Indels: 7
0.68 0.24 0.07
Matches are distributed among these distances:
42 11 0.16
43 18 0.27
44 22 0.33
45 16 0.24
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (42 bp):
TGTCTTCAACCAGCTCTATCACAACGAAAGAGGCAAGGTTTG
Found at i:16006 original size:87 final size:88
Alignment explanation
Indices: 15892--16127 Score: 408
Period size: 87 Copynumber: 2.7 Consensus size: 88
15882 AACGATGGAT
*
15892 GCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
1 GCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
15955 CCAGCTCTATCACAA-CGAAAGAG
65 CCAGCTCTATCACAACCGAAAGAG
15978 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
16043 CAGCTCTATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
* *
16066 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATC-TTTGTCTTCA
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCA
16128 TTGTCTGTCC
Statistics
Matches: 144, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
85 5 0.03
86 7 0.05
87 74 0.51
88 58 0.40
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (88 bp):
GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
CAGCTCTATCACAACCGAAAGAG
Found at i:16122 original size:46 final size:46
Alignment explanation
Indices: 15984--16122 Score: 121
Period size: 44 Copynumber: 3.1 Consensus size: 46
15974 AGAGGCAAGG
* *
15984 TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATC
1 TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATC
* * * * * * *
16030 TTT-TGTCTTCAACCAGC-T--CTATCACA-ACCGAAAGAGGCAAG--G
1 TTTGTGTCTTCGATCTGCTTCGCTGTCA-ATGCAG-AA-AGGCAAGATC
16072 TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATC
1 TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATC
16118 TTTGT
1 TTTGT
16123 CTTCATTGTC
Statistics
Matches: 67, Mismatches: 16, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
42 9 0.13
43 13 0.19
44 16 0.24
45 14 0.21
46 15 0.22
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (46 bp):
TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATC
Done.