Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2937
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: 31734
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Found at i:2053 original size:25 final size:23
Alignment explanation
Indices: 2025--2070 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2015 CAGGAAGGTT
2025 AGAGTTGATAAAGGGATAGGATTTA
1 AGAGTTGAT-AAGGGAT-GGATTTA
*
2050 AGAGTTGATGAGGGATGGATT
1 AGAGTTGATAAGGGATGGATT
2071 AGCAGCAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 6 0.30
25 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (23 bp):
AGAGTTGATAAGGGATGGATTTA
Found at i:2239 original size:30 final size:30
Alignment explanation
Indices: 2203--2259 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2193 CCACCATTAT
*
2203 CTTTTCTTTTCTT-TTCTTTCTCTCCATCCA
1 CTTTTCTGTTCTTCTTCTTTCTC-CCATCCA
2233 CTTTTCTGTTCTTCTTCTTTCTCCCAT
1 CTTTTCTGTTCTTCTTCTTTCTCCCAT
2260 AGTCGAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.05, C:0.33, G:0.02, T:0.60
Consensus pattern (30 bp):
CTTTTCTGTTCTTCTTCTTTCTCCCATCCA
Found at i:6193 original size:19 final size:20
Alignment explanation
Indices: 6164--6201 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6154 AAGGTGAGAA
6164 AAAAGAAAAAAAAAAGACAC
1 AAAAGAAAAAAAAAAGACAC
*
6184 AAAA-AAAAAAAAAGGACA
1 AAAAGAAAAAAAAAAGACA
6202 ACCACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAAAGACAC
Found at i:21512 original size:24 final size:24
Alignment explanation
Indices: 21480--21550 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
21470 CTGTCAGGAG
21480 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
21504 AGGATTTAGGAGTTGATGAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
21528 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
21551 GGAAATCTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.34, C:0.01, G:0.39, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:23047 original size:28 final size:27
Alignment explanation
Indices: 22954--23065 Score: 140
Period size: 27 Copynumber: 4.1 Consensus size: 27
22944 AGGAAGCGTC
*
22954 CTGGTGGCTATGCCACAATTATCTGATT
1 CTGGTGGCTCTGCCACAATTATCTG-TT
22982 -TGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGTT
*
23008 CTGGTGGTTCTGCCACAATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTGT-T
* *
23036 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGTT
23062 CTGG
1 CTGG
23066 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.13
27 48 0.64
28 17 0.23
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGTT
Found at i:26801 original size:30 final size:30
Alignment explanation
Indices: 26767--26824 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
26757 TGGATCCTAG
*
26767 AAAATTGAAGTAGTTTTGGAGTGGAAGCGA
1 AAAATTGAAGCAGTTTTGGAGTGGAAGCGA
26797 AAAATTGAAGCAGTTTTGGAGTGGAAGC
1 AAAATTGAAGCAGTTTTGGAGTGGAAGC
26825 CGCCTAGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (30 bp):
AAAATTGAAGCAGTTTTGGAGTGGAAGCGA
Found at i:29345 original size:24 final size:24
Alignment explanation
Indices: 29313--29382 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
29303 CTGTCAGGAG
29313 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
29337 AGGATTTAGGAGTTGATAA-GGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
29360 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
29383 GGAAATCTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 21 0.49
24 22 0.51
ACGTcount: A:0.36, C:0.01, G:0.37, T:0.26
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:29363 original size:23 final size:23
Alignment explanation
Indices: 29308--29380 Score: 110
Period size: 23 Copynumber: 3.1 Consensus size: 23
29298 AAAGTCTGTC
*
29308 AGGAGAGGATTTAGGAGTTGATA
1 AGGATAGGATTTAGGAGTTGATA
29331 AGGGATAGGATTTAGGAGTTGATA
1 A-GGATAGGATTTAGGAGTTGATA
**
29355 AGGATAGGATTTAGGAGCAGATA
1 AGGATAGGATTTAGGAGTTGATA
29378 AGG
1 AGG
29381 GAGGAAATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 24 0.52
24 22 0.48
ACGTcount: A:0.36, C:0.01, G:0.38, T:0.25
Consensus pattern (23 bp):
AGGATAGGATTTAGGAGTTGATA
Found at i:29394 original size:47 final size:47
Alignment explanation
Indices: 29308--29406 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 47
29298 AAAGTCTGTC
** * *
29308 AGGAGAGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-A
1 AGGAGAGGATTTAGGAGCAGATAAGGGA-AGGATCTAGGAGCTGATCA
*
29355 AGGATAGGATTTAGGAGCAGATAAGGG-AGGAAATCTAGGAGCTGATCA
1 AGGAGAGGATTTAGGAGCAGATAAGGGAAGG--ATCTAGGAGCTGATCA
29403 AGGA
1 AGGA
29407 ACAAGAGGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
45 3 0.07
47 36 0.82
48 5 0.11
ACGTcount: A:0.36, C:0.04, G:0.37, T:0.22
Consensus pattern (47 bp):
AGGAGAGGATTTAGGAGCAGATAAGGGAAGGATCTAGGAGCTGATCA
Found at i:30834 original size:27 final size:27
Alignment explanation
Indices: 30794--30903 Score: 120
Period size: 27 Copynumber: 4.1 Consensus size: 27
30784 AGGAAGCGTC
*
30794 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
30821 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
30848 CTGGTGG--CTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
30874 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
30900 CTGG
1 CTGG
30904 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
24 3 0.04
25 11 0.15
26 12 0.17
27 36 0.51
28 9 0.13
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:30898 original size:52 final size:53
Alignment explanation
Indices: 30794--30903 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 53
30784 AGGAAGCGTC
* *
30794 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGC-ATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* *
30848 CTGGTGGC-TGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
30900 CTGG
1 CTGG
30904 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
52 25 0.49
53 18 0.35
54 8 0.16
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (53 bp):
CTGGTGGCATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Done.