Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3435
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: 39006
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1789 original size:13 final size:13
Alignment explanation
Indices: 1771--1798 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1761 TTTAATTAAA
1771 TTATGTGTATTTT
1 TTATGTGTATTTT
1784 TTATGTGTATTTT
1 TTATGTGTATTTT
1797 TT
1 TT
1799 GTTGGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (13 bp):
TTATGTGTATTTT
Found at i:2260 original size:43 final size:44
Alignment explanation
Indices: 2207--2289 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 44
2197 TCCGAGGTAT
*
2207 GATTTAGTGTAAGACCATGTCTGGGACATTGGCAT-TGATAAGA
1 GATTTAGTGTAAGACCATGCCTGGGACATTGGCATATGATAAGA
* * *
2250 GATTTTGTGTAAGATCATGCCTGGGATATTGGCATATGAT
1 GATTTAGTGTAAGACCATGCCTGGGACATTGGCATATGAT
2290 TATAACATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 31 0.89
44 4 0.11
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.34
Consensus pattern (44 bp):
GATTTAGTGTAAGACCATGCCTGGGACATTGGCATATGATAAGA
Found at i:18316 original size:49 final size:49
Alignment explanation
Indices: 18199--18322 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 49
18189 TATCCCAGAT
** * * * *
18199 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCACGT-CAAAAC
* *
18249 ATGGTCTTACGA-GAGACCTCTCATCTCGGTGCCAACGCCACGT-AAAGAC
1 ATGGTCTTAC-ATGGGACCTCTCATATCGGTGCCAACGCCACGTCAAA-AC
18298 ATGGTCTTACATGGGACCTCTCATA
1 ATGGTCTTACATGGGACCTCTCATA
18323 ACCTCAATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
48 3 0.05
49 23 0.38
50 34 0.56
51 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (49 bp):
ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCACGTCAAAAC
Found at i:26604 original size:26 final size:26
Alignment explanation
Indices: 26575--26635 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
26565 TCTCATTCCT
26575 ATTTTACTCCC-AATAAAATTTTGA-A
1 ATTTTAC-CCCTAATAAAATTTTGACA
*
26600 GATTTTACCCCTATTAAAATTTTGACA
1 -ATTTTACCCCTAATAAAATTTTGACA
26627 ATTTTACCC
1 ATTTTACCC
26636 ATGGTATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 3 0.09
26 28 0.88
27 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (26 bp):
ATTTTACCCCTAATAAAATTTTGACA
Found at i:35534 original size:99 final size:97
Alignment explanation
Indices: 35353--35659 Score: 324
Period size: 99 Copynumber: 3.1 Consensus size: 97
35343 AACCGTATGT
* * **
35353 GGTGGATCTCGCACTTAGCAACCACCGCTGAATCGGGGAA-CAGCACTTAGC-ACGCCTCGGGGG
1 GGTGGATCACACAC-TAGC-ACCACCAATGAATC-GGGAATCAGCACTTAGCAAC-CCTCGGGGG
*
35416 AATCAGCAC-CAGCAACCCTTTACATTTTCAAAGATA
62 AATCAGCACATAGCAACCCTTTACA-TTTCAAAGATA
* *
35452 GGTGGAT-ATCGCACTTAGCCCCGACCAATGAA-C-GG-ATCAGCACTTAGCAACCCTTCGGGGG
1 GGTGGATCA-CACAC-TAGCACC-ACCAATGAATCGGGAATCAGCACTTAGCAACCC-TCGGGGG
*
35513 AATCAGCACATAGCAACCCCTTTCACATTTCAACGATA
62 AATCAGCACATAGCAA-CCCTTT-ACATTTCAAAGATA
35551 TGGTGGATCACACACTAGCACCACCAATGAATCGGGGGAATCAGCACTTAGCAACCCTC-GGGGA
1 -GGTGGATCACACACTAGCACCACCAATGAATC--GGGAATCAGCACTTAGCAACCCTCGGGGGA
* * *
35615 ATCAGCCACATAGCAACCTTTTTCATTTCAAAGATT
63 ATCAG-CACATAGCAACCCTTTACATTTCAAAGATA
35651 GGTGGATCA
1 GGTGGATCA
35660 ACGAACATAG
Statistics
Matches: 180, Mismatches: 12, Indels: 32
0.80 0.05 0.14
Matches are distributed among these distances:
95 1 0.01
96 15 0.08
97 18 0.10
98 17 0.09
99 56 0.31
100 25 0.14
101 16 0.09
102 14 0.08
103 18 0.10
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (97 bp):
GGTGGATCACACACTAGCACCACCAATGAATCGGGAATCAGCACTTAGCAACCCTCGGGGGAATC
AGCACATAGCAACCCTTTACATTTCAAAGATA
Found at i:35682 original size:100 final size:99
Alignment explanation
Indices: 35381--35691 Score: 322
Period size: 100 Copynumber: 3.1 Consensus size: 99
35371 CAACCACCGC
* *
35381 TGAATCGGGGAA-CAGCACTTAGC-ACGCCTCGGGGGAATCAGCAC-CAGCAACCCTTTACATTT
1 TGAATCGGGGAATCAGCACTTAGCAAC-CCTCGGGGGAATCAGCACATAGCAACCTTTTACA-TT
* * * *
35443 TCAAAGATAGGTGGAT-ATCGCACTTAGCCCCGACCAA
64 TCAAAGATTGGTGGATCAACG-ACATAGCACC-ACCAA
*
35480 TGAA-C--GG-ATCAGCACTTAGCAACCCTTCGGGGGAATCAGCACATAGCAACCCCTTTCACAT
1 TGAATCGGGGAATCAGCACTTAGCAACCC-TCGGGGGAATCAGCACATAGCAA--CCTTTTACAT
*
35541 TTCAACGATATGGTGGATC-AC-ACACTAGCACCACCAA
63 TTCAAAGAT-TGGTGGATCAACGACA-TAGCACCACCAA
*
35578 TGAATCGGGGGAATCAGCACTTAGCAACCCTC-GGGGAATCAGCCACATAGCAACCTTTTTCATT
1 TGAATC-GGGGAATCAGCACTTAGCAACCCTCGGGGGAATCAG-CACATAGCAACCTTTTACATT
**
35642 TCAAAGATTGGTGGATCAACGAACATAG-AATACCAA
64 TCAAAGATTGGTGGATCAACG-ACATAGCACCACCAA
35678 TGAATCGGGAGAAT
1 TGAATCGGG-GAAT
35692 AACACACGCA
Statistics
Matches: 180, Mismatches: 13, Indels: 37
0.78 0.06 0.16
Matches are distributed among these distances:
95 1 0.01
96 15 0.08
97 18 0.10
98 17 0.09
99 32 0.18
100 49 0.27
101 13 0.07
102 17 0.09
103 18 0.10
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (99 bp):
TGAATCGGGGAATCAGCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCTTTTACATTTC
AAAGATTGGTGGATCAACGACATAGCACCACCAA
Found at i:36856 original size:28 final size:27
Alignment explanation
Indices: 36824--36899 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
36814 TTGTTCTTCT
*
36824 TTTATGTTTTTTAATTTTATTTAATAGA
1 TTTATGTTTTTTAATTTTATTTAA-AAA
* *
36852 TTTATGTTTATATTTATTTT-TATAAAAA
1 TTTATGTTT-T-TTAATTTTATTTAAAAA
36880 TTTATG--TTTTAATTTTATTT
1 TTTATGTTTTTTAATTTTATTT
36900 GTAAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
24 7 0.17
25 3 0.08
26 1 0.03
28 17 0.43
29 5 0.12
30 7 0.17
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (27 bp):
TTTATGTTTTTTAATTTTATTTAAAAA
Done.