Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2877
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: 41345
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3720 original size:11 final size:11
Alignment explanation
Indices: 3704--3760 Score: 96
Period size: 11 Copynumber: 5.0 Consensus size: 11
3694 TAGTAGTTTC
3704 TTCAAAAAAAA
1 TTCAAAAAAAA
3715 TTCAAAAAAAAA
1 TTC-AAAAAAAA
3727 TTCAAAAAAAA
1 TTCAAAAAAAA
3738 TTCAAAAAAAAA
1 TTC-AAAAAAAA
3750 TTCAAAAAAAA
1 TTCAAAAAAAA
3761 ATTTGGTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
11 22 0.50
12 22 0.50
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:3724 original size:12 final size:12
Alignment explanation
Indices: 3707--3763 Score: 107
Period size: 12 Copynumber: 4.8 Consensus size: 12
3697 TAGTTTCTTC
3707 AAAAAAAATTCA
1 AAAAAAAATTCA
3719 AAAAAAAATTC-
1 AAAAAAAATTCA
3730 AAAAAAAATTCA
1 AAAAAAAATTCA
3742 AAAAAAAATTCA
1 AAAAAAAATTCA
3754 AAAAAAAATT
1 AAAAAAAATT
3764 TGGTTTCCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.25
12 33 0.75
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:3734 original size:23 final size:23
Alignment explanation
Indices: 3704--3760 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
3694 TAGTAGTTTC
3704 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
3727 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
3750 TTCAAAAAAAA
1 TTCAAAAAAAA
3761 ATTTGGTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (23 bp):
TTCAAAAAAAATTCAAAAAAAAA
Found at i:3823 original size:14 final size:14
Alignment explanation
Indices: 3804--3852 Score: 98
Period size: 14 Copynumber: 3.5 Consensus size: 14
3794 ATCAAGTTGA
3804 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
3818 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
3832 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
3846 AAAAAAA
1 AAAAAAA
3853 GAAAAGCTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.63, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:4868 original size:22 final size:22
Alignment explanation
Indices: 4817--4882 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
4807 GGTATTTGGG
* *
4817 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
4838 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
4860 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
4883 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:5250 original size:21 final size:22
Alignment explanation
Indices: 5210--5250 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5200 TAGATTCGGC
*
5210 TGAACTTGGAGCTTGGGGGACT
1 TGAACTTGGAGCTTGAGGGACT
5232 TGAACTTGG-GCTTGAGGGA
1 TGAACTTGGAGCTTGAGGGA
5251 GTAAATGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.20, C:0.12, G:0.41, T:0.27
Consensus pattern (22 bp):
TGAACTTGGAGCTTGAGGGACT
Found at i:8998 original size:17 final size:17
Alignment explanation
Indices: 8976--9023 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
8966 TTTCATTCTC
8976 TTTTTTGAATTTTCTTT
1 TTTTTTGAATTTTCTTT
* *
8993 TTTTTTCATTTTTCTTT
1 TTTTTTGAATTTTCTTT
* *
9010 TCTTTTGTATTTTC
1 TTTTTTGAATTTTC
9024 GCTCTTTTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTTGAATTTTCTTT
Found at i:10775 original size:14 final size:14
Alignment explanation
Indices: 10756--10782 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10746 GACATGTAAA
10756 TAAAAACCTCACAG
1 TAAAAACCTCACAG
10770 TAAAAACCTCACA
1 TAAAAACCTCACA
10783 AAATCTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.30, G:0.04, T:0.15
Consensus pattern (14 bp):
TAAAAACCTCACAG
Found at i:11253 original size:12 final size:12
Alignment explanation
Indices: 11223--11247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11213 AAACCGTATG
11223 CAATTTTTTTTT
1 CAATTTTTTTTT
11235 CAATTTTTTTTT
1 CAATTTTTTTTT
11247 C
1 C
11248 TTTTTTCTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:11621 original size:22 final size:22
Alignment explanation
Indices: 11570--11635 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
11560 GGTATTTGGG
* *
11570 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
11591 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
11613 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
11636 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:18626 original size:12 final size:11
Alignment explanation
Indices: 18585--18625 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
18575 TAGTTTCTCG
*
18585 AAAAAAACTCA
1 AAAAAAATTCA
18596 AAAAAAATTCTA
1 AAAAAAATTC-A
18608 AAAAAAATTCA
1 AAAAAAATTCA
18619 AAAAAAA
1 AAAAAAA
18626 ACTAGTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:18687 original size:13 final size:13
Alignment explanation
Indices: 18669--18715 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
18659 TCAAGTTGTG
18669 AAAAAAAATTTGA
1 AAAAAAAATTTGA
18682 AAAAAAAATTCTGA
1 AAAAAAAATT-TGA
*
18696 AAAAAAAAATTGA
1 AAAAAAAATTTGA
18709 AAAAAAA
1 AAAAAAA
18716 GAGAGCTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 20 0.62
14 12 0.38
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:25861 original size:23 final size:22
Alignment explanation
Indices: 25810--25861 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
25800 CCTCGTCTTT
*
25810 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
25832 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
25855 TTCTTTT
1 TTCTTTT
25862 TCAATTTTGT
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:32463 original size:20 final size:19
Alignment explanation
Indices: 32440--32504 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
32430 AAGCTCAAAC
32440 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
32460 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * *
32480 AAGCTCATGTGAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
32500 GAGCT
1 GAGCT
32505 GGGAAAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 31 0.84
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:32464 original size:10 final size:10
Alignment explanation
Indices: 32440--32504 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
32430 AAGCTCAAAC
*
32440 GAGCTAAAGT
1 GAGCTAAATT
*
32450 AAGCTAAATT
1 GAGCTAAATT
*
32460 GAGCTCAAA-C
1 GAGCT-AAATT
32470 GAGCTAAATT
1 GAGCTAAATT
* *
32480 AAGCT-CATGT
1 GAGCTAAAT-T
32490 GAGCTAAATT
1 GAGCTAAATT
32500 GAGCT
1 GAGCT
32505 GGGAAAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 5 0.12
10 32 0.76
11 5 0.12
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (10 bp):
GAGCTAAATT
Done.