Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3768
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: 42114
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:10332 original size:27 final size:26
Alignment explanation
Indices: 10288--10338 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
10278 CTAGCTGCAA
*
10288 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
10315 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
10339 AGTAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:17897 original size:27 final size:26
Alignment explanation
Indices: 17845--17902 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
17835 CCACATATAT
*
17845 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
17871 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
17898 ATATC
1 ATATC
17903 CGGCAGCCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:19582 original size:40 final size:40
Alignment explanation
Indices: 19536--19612 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
19526 ATAGCTGAAT
19536 ATACTTTTAATTTAAACTTATAATACATGCAGATAAATAG
1 ATACTTTTAATTTAAACTTATAATACATGCAGATAAATAG
19576 ATACTTTTAATTTAAACTTATAATACATGCAGATAAA
1 ATACTTTTAATTTAAACTTATAATACATGCAGATAAA
19613 CAGACTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.38
Consensus pattern (40 bp):
ATACTTTTAATTTAAACTTATAATACATGCAGATAAATAG
Found at i:21237 original size:42 final size:41
Alignment explanation
Indices: 21127--21289 Score: 213
Period size: 42 Copynumber: 3.9 Consensus size: 41
21117 CTTGTATAAA
* *
21127 ACACCGGCA-AAGAGCCTGCTAGGTAATAAACCTGAT-TCAAT
1 ACACCGGCATAA-AGCCTGCTAGGCAATAAGCCTGATATC-AT
* * *
21168 ACACCGGCATAAAGCCTACTAGACAATAAGTCTGATATCAT
1 ACACCGGCATAAAGCCTGCTAGGCAATAAGCCTGATATCAT
*
21209 ACACCGGCATCAAAGCCTGCTAGGCAATAAGCCTGATATCTT
1 ACACCGGCAT-AAAGCCTGCTAGGCAATAAGCCTGATATCAT
*
21251 ACACCGGCATCAAAGCCTGCAAGGCAATAAGCCTGATAT
1 ACACCGGCAT-AAAGCCTGCTAGGCAATAAGCCTGATAT
21290 ATCACTGTTA
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
41 40 0.37
42 69 0.63
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (41 bp):
ACACCGGCATAAAGCCTGCTAGGCAATAAGCCTGATATCAT
Found at i:21238 original size:83 final size:83
Alignment explanation
Indices: 21127--21289 Score: 215
Period size: 83 Copynumber: 2.0 Consensus size: 83
21117 CTTGTATAAA
* *
21127 ACACCGGCAAAGAGCCTGCTAGGTAATAAACCTGAT-TCAATACACCGGCAT-AAAGCCTACTAG
1 ACACCGGCAAAGAGCCTGCTAGGCAATAAACCTGATATC-ATACACCGGCATCAAAGCCTACAAG
*
21190 ACAATAAGTCTGATATCAT
65 ACAATAAGCCTGATATCAT
* * *
21209 ACACCGGCATCAA-AGCCTGCTAGGCAATAAGCCTGATATCTTACACCGGCATCAAAGCCTGCAA
1 ACACCGGCA--AAGAGCCTGCTAGGCAATAAACCTGATATCATACACCGGCATCAAAGCCTACAA
*
21273 GGCAATAAGCCTGATAT
64 GACAATAAGCCTGATAT
21290 ATCACTGTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
82 9 0.13
83 33 0.47
84 28 0.40
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (83 bp):
ACACCGGCAAAGAGCCTGCTAGGCAATAAACCTGATATCATACACCGGCATCAAAGCCTACAAGA
CAATAAGCCTGATATCAT
Found at i:25198 original size:47 final size:47
Alignment explanation
Indices: 25126--25267 Score: 259
Period size: 47 Copynumber: 3.0 Consensus size: 47
25116 GTTGAATTTA
25126 AAGCTTGTTAAA-TTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
25172 AAGCTTGTTAAATTTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
* *
25219 AAGCTTGTTAAATTTGCCCTTATTATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
25266 AA
1 AA
25268 AGAAAATTTT
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
46 12 0.13
47 81 0.87
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
Found at i:26829 original size:13 final size:13
Alignment explanation
Indices: 26811--26836 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26801 TATTTTGAGA
26811 CGTCTTTGTATAT
1 CGTCTTTGTATAT
26824 CGTCTTTGTATAT
1 CGTCTTTGTATAT
26837 AAGCCATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
CGTCTTTGTATAT
Found at i:29066 original size:46 final size:48
Alignment explanation
Indices: 28959--29069 Score: 127
Period size: 48 Copynumber: 2.4 Consensus size: 48
28949 TGTCTTCGAC
** * * *
28959 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATACAAT
* * *
29007 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATA-A-CCGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATACAAT
*
29053 ATGGACTTGCATGGCTC
1 ATGGACTTACATGGCTC
29070 CTTTCTGTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 17 0.32
47 1 0.02
48 35 0.66
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATACAAT
Found at i:30673 original size:28 final size:28
Alignment explanation
Indices: 30608--30702 Score: 111
Period size: 27 Copynumber: 3.4 Consensus size: 28
30598 GAGATTGGCG
* * * *
30608 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
30637 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
30665 CTAAGTGTGAGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
**
30692 CGGAGTGTGCG
1 CTAAGTGTGCG
30703 GACTTAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 22 0.38
28 21 0.36
29 15 0.26
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:30689 original size:27 final size:28
Alignment explanation
Indices: 30633--30692 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
30623 TAAATTGTAC
*
30633 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGAGAGTTTGATTATAT
30661 AGCACTAAGTGTGAGAG-TTGATTATAT
1 AGCACTAAGTGTGAGAGTTTGATTATAT
30688 AGCAC
1 AGCAC
30693 GGAGTGTGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGAGAGTTTGATTATAT
Done.