Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3543
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: 42107
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:6303 original size:13 final size:12
Alignment explanation
Indices: 6273--6306 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6263 AATGTGAAAC
*
6273 AAAAAGAAATTG
1 AAAAAGAAGTTG
6285 AAAAAGAAGTTG
1 AAAAAGAAGTTG
6297 AAGAAAGAAG
1 AA-AAAGAAG
6307 AGAAATGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:7686 original size:6 final size:6
Alignment explanation
Indices: 7675--7707 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
7665 AGTTGTAAAG
7675 TTTTAT TTTTAT TTTTAT TATTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT TT
7708 ACTTAGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:7700 original size:13 final size:12
Alignment explanation
Indices: 7675--7707 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
7665 AGTTGTAAAG
7675 TTTTATTTTTAT
1 TTTTATTTTTAT
7687 TTTTATTATTTAT
1 TTTTATT-TTTAT
7700 TTTTATTT
1 TTTTATTT
7708 ACTTAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:16122 original size:20 final size:20
Alignment explanation
Indices: 16097--16151 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
16087 ACGAGTTAAA
* *
16097 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
16117 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
16137 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
16152 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:22641 original size:17 final size:17
Alignment explanation
Indices: 22621--22656 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
22611 ACCTATAAGC
22621 ATAATTAAACAAGTTAA
1 ATAATTAAACAAGTTAA
22638 ATAATTAAACAAGTTAA
1 ATAATTAAACAAGTTAA
22655 AT
1 AT
22657 GGCTGTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
ATAATTAAACAAGTTAA
Found at i:23565 original size:18 final size:17
Alignment explanation
Indices: 23544--23600 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
23534 TTTTTCAAAC
23544 TCATTTTCTTTTCTTTCT
1 TCATTTTCTTTTCTTT-T
* * *
23562 TCATTCTCACTCTCTTTT
1 TCATTTTC-TTTTCTTTT
*
23580 TCAATTTTCTTTTCTTGT
1 TC-ATTTTCTTTTCTTTT
23598 TCA
1 TCA
23601 CATTCTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
17 1 0.03
18 18 0.60
19 11 0.37
ACGTcount: A:0.11, C:0.25, G:0.02, T:0.63
Consensus pattern (17 bp):
TCATTTTCTTTTCTTTT
Found at i:25443 original size:20 final size:20
Alignment explanation
Indices: 25418--25472 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
25408 TGTGGTTCAA
*
25418 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
* *
25438 CTCATTCGTGCTCGAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
25458 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
25473 TTTAACTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:25564 original size:13 final size:13
Alignment explanation
Indices: 25543--25577 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
25533 ATAAGTTGCT
* *
25543 GTTAGTTAAATTA
1 GTTAATTAAATAA
25556 GTTAATTAAATAA
1 GTTAATTAAATAA
25569 GTTAATTAA
1 GTTAATTAA
25578 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:25835 original size:23 final size:23
Alignment explanation
Indices: 25801--25862 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
25791 TTTCTAGACA
*
25801 AATTTAATGTATGTCTT-TGGCCG
1 AATTTAAAGTATGT-TTCTGGCCG
25824 AATTTAAAGTATGTTTCTGGCCG
1 AATTTAAAGTATGTTTCTGGCCG
* *
25847 AATTTAATGCATGTTT
1 AATTTAAAGTATGTTT
25863 TAAATGGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (23 bp):
AATTTAAAGTATGTTTCTGGCCG
Found at i:28238 original size:23 final size:22
Alignment explanation
Indices: 28187--28238 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
28177 CCTCGTCTTT
*
28187 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
28209 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
28232 TTCTTTT
1 TTCTTTT
28239 TTAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33695 original size:16 final size:16
Alignment explanation
Indices: 33674--33718 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
33664 CTATATATTG
**
33674 AAAAAATAAAGAATTC
1 AAAAAATAAAGAATAA
*
33690 AAAAAATAAAAAATAA
1 AAAAAATAAAGAATAA
*
33706 AAAAAAGAAAGAA
1 AAAAAATAAAGAA
33719 AGAGTGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (16 bp):
AAAAAATAAAGAATAA
Found at i:34116 original size:10 final size:10
Alignment explanation
Indices: 34103--34148 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
34093 AGCTCACTTG
34103 AGCTCGTTTT
1 AGCTCGTTTT
* *
34113 AGCTTGTTTG
1 AGCTCGTTTT
*
34123 AGCTCGAATTT
1 AGCTCG-TTTT
34134 AGCTCGTTTT
1 AGCTCGTTTT
34144 AGCTC
1 AGCTC
34149 ATTCCTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:34136 original size:21 final size:20
Alignment explanation
Indices: 34100--34148 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
34090 ATCAGCTCAC
* *
34100 TTGAGCTCGTTTTAGCTTGT
1 TTGAGCTCGATTTAGCTCGT
34120 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
34141 TTTAGCTC
1 TTGAGCTC
34149 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Done.