Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1763
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: 27168
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9037 original size:21 final size:21
Alignment explanation
Indices: 9011--9053 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9001 AGCCAACACT
9011 TAGGCTATTTTCCAAGCCTTA
1 TAGGCTATTTTCCAAGCCTTA
9032 TAGGCTATTTTCCAAGCCTTA
1 TAGGCTATTTTCCAAGCCTTA
9053 T
1 T
9054 GTTGTCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (21 bp):
TAGGCTATTTTCCAAGCCTTA
Found at i:10539 original size:50 final size:50
Alignment explanation
Indices: 10471--10864 Score: 373
Period size: 50 Copynumber: 7.9 Consensus size: 50
10461 ACTAAAGCTC
* *
10471 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
** * * * *
10521 TCTGGTACATGTAATAGCCTGCACTTAGTACTACACATGTGACTTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
** * * *** *
10571 TCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATAGAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * * *
10623 -CGGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* ** * * *
10672 TCTAGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGA-CTAAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCT-ATCAA
* * * ** *
10722 TCTGATACACATAG-AGCTTACACTTAGTACTACACATGTGATCAAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * * *
10773 -CAGGTACGCATAGTAGCCTGCACTTAGTATTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* *
10822 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGAC
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGAC
10865 TCACAACGAA
Statistics
Matches: 268, Mismatches: 67, Indels: 18
0.76 0.19 0.05
Matches are distributed among these distances:
49 32 0.12
50 177 0.66
51 58 0.22
52 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
Found at i:10657 original size:101 final size:100
Alignment explanation
Indices: 10482--10864 Score: 302
Period size: 101 Copynumber: 3.8 Consensus size: 100
10472 CTGGTACGCA
* * * ** * *
10482 TAGTAGCCTGCACTTAGTACTACACATGCGACCT--ATCAATCTGG-TACATGTAATAGCCTGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CTAAACCAA-C-GGATACACATAGTAGCCTACA
* *
10544 CTTAGTACTACACATGTGACTTAACCATCTAATACACG
63 CTTAGTACTACACATGTGACCTAACAATCTAATACACG
** * *
10582 TAGTAGCCTGCACTTAGTACTACACACGTGA-TAGAAGTTAACGGGTACGCATAGTAGCCTACAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTA-AA-CCAACGGATACACATAGTAGCCTACAC
* * * *
10646 TTAGTACTACACATGCGACCTATCAATCTAGTACATG
64 TTAGTACTACACATGTGACCTAACAATCTAATACACG
* * *
10683 TAGTAGCCTGCACTTAGTACTACACACGTGACTAAACCATCTGATACACATAG-AGCTTACACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTAAACCAACGGATACACATAGTAGCCTACACTT
* * * *
10747 AGTACTACACATGTGATC-AA-AGT-TAACAGGTACGCA
66 AGTACTACACATGTGACCTAACAATCT-A-A--TACACG
* * * * * *
10783 TAGTAGCCTGCACTTAGTATTACACATGCGACCT--ATCAATCTGG-TACGCATAGTAGCCTGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CTAAACCAA-C-GGATACACATAGTAGCCTACA
*
10845 CTTAGTACTACACACGTGAC
63 CTTAGTACTACACATGTGAC
10865 TCACAACGAA
Statistics
Matches: 229, Mismatches: 40, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
96 1 0.00
97 3 0.01
98 2 0.01
99 29 0.13
100 82 0.36
101 107 0.47
102 5 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (100 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACTAAACCAACGGATACACATAGTAGCCTACACTT
AGTACTACACATGTGACCTAACAATCTAATACACG
Found at i:10837 original size:150 final size:151
Alignment explanation
Indices: 10474--10865 Score: 626
Period size: 150 Copynumber: 2.6 Consensus size: 151
10464 AAAGCTCTCT
*
10474 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAATAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
* * * *
10539 CTGCACTTAGTACTACACATGTGACTTAACCATCTAATACACGTAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTAAACCATCTAATACACATAGTAGCCTACACTTAGTACTA
*
10604 CACACGTGATAGAAGTTAACG
131 CACACGTGATAGAAGTTAACA
* *
10625 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTATCAATCTAGTACATGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
* *
10690 CTGCACTTAGTACTACACACGTGACTAAACCATCTGATACACATAG-AGCTTACACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTAAACCATCTAATACACATAGTAGCCTACACTTAGTACTA
*
10754 CACATGTGATCA-AAGTTAACA
131 CACACGTGAT-AGAAGTTAACA
* ***
10775 GGTACGCATAGTAGCCTGCACTTAGTATTACACATGCGACCTATCAATCTGGTACGCATAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
10840 CTGCACTTAGTACTACACACGTGACT
66 CTGCACTTAGTACTACACACGTGACT
10866 CACAACGAAT
Statistics
Matches: 223, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
150 118 0.53
151 105 0.47
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
CTGCACTTAGTACTACACACGTGACTAAACCATCTAATACACATAGTAGCCTACACTTAGTACTA
CACACGTGATAGAAGTTAACA
Found at i:11238 original size:19 final size:19
Alignment explanation
Indices: 11216--11252 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11206 ATGTTATATC
11216 ATCAAAATAATCACATAGT
1 ATCAAAATAATCACATAGT
* *
11235 ATCAAATTATTCACATAG
1 ATCAAAATAATCACATAG
11253 CATTCAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (19 bp):
ATCAAAATAATCACATAGT
Found at i:16835 original size:18 final size:18
Alignment explanation
Indices: 16808--16871 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
16798 TACTTAGTTA
*
16808 AAAATCTTTTTCTTCACC
1 AAAATATTTTTCTTCACC
** *
16826 AAAATA-TTTT-TAAATC
1 AAAATATTTTTCTTCACC
16842 AAAATATTTTTCTTCACC
1 AAAATATTTTTCTTCACC
*
16860 AAAGTATTTTTC
1 AAAATATTTTTC
16872 ATTACATTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 9 0.25
17 8 0.22
18 19 0.53
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (18 bp):
AAAATATTTTTCTTCACC
Found at i:18701 original size:19 final size:19
Alignment explanation
Indices: 18665--18704 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18655 TGAAAATGTG
**
18665 TAAGTTATGTCTACAAATT
1 TAAGTTATACCTACAAATT
*
18684 TAAGTTATACCTATAAATT
1 TAAGTTATACCTACAAATT
18703 TA
1 TA
18705 TGATGACACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (19 bp):
TAAGTTATACCTACAAATT
Done.