Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3392
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: 43163
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:2526 original size:21 final size:21
Alignment explanation
Indices: 2464--2532 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
2454 CAAATAATTT
2464 AAAAATTATAAAAAATGTT-AAA
1 AAAAATTAT-AAAAA-GTTCAAA
* *
2486 AATAAAATATTCAAAA-TTCAAA
1 AA-AAATTA-TAAAAAGTTCAAA
*
2508 AAAAATTATAAAAAGTTCATA
1 AAAAATTATAAAAAGTTCAAA
2529 AAAA
1 AAAA
2533 TTTCAAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
20 5 0.13
21 16 0.42
22 7 0.18
23 9 0.24
24 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAAATTATAAAAAGTTCAAA
Found at i:9998 original size:21 final size:21
Alignment explanation
Indices: 9957--10000 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9947 AAATATTAAA
*
9957 TATTTATTTTCTTAATATATT
1 TATTTATATTCTTAATATATT
*
9978 TATTTATATT-TTATATTTATT
1 TATTTATATTCTTA-ATATATT
9999 TA
1 TA
10001 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATATTCTTAATATATT
Found at i:13278 original size:15 final size:15
Alignment explanation
Indices: 13260--13297 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
13250 CAGATAAAAT
13260 TATTTTAAATAACAG
1 TATTTTAAATAACAG
*
13275 TATTTTAAATAATAG
1 TATTTTAAATAACAG
*
13290 TAGTTTAA
1 TATTTTAA
13298 TTTTTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (15 bp):
TATTTTAAATAACAG
Found at i:17206 original size:21 final size:20
Alignment explanation
Indices: 17182--17220 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17172 TTGGGTAAAA
17182 GTTTGGAAATAGAAAAAAATT
1 GTTT-GAAATAGAAAAAAATT
* *
17203 GTTTTAAATATAAAAAAA
1 GTTTGAAATAGAAAAAAA
17221 ATCAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (20 bp):
GTTTGAAATAGAAAAAAATT
Found at i:19980 original size:23 final size:21
Alignment explanation
Indices: 19953--20006 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
19943 ACTTGTATAT
19953 TTAATTTTTATACTTTAATTTAA
1 TTAATTTTTATAC-TTAATTT-A
* * *
19976 TTAATTTTTGTTCTTAATTTT
1 TTAATTTTTATACTTAATTTA
19997 TTAATTTTTA
1 TTAATTTTTA
20007 AAATTTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 9 0.33
22 7 0.26
23 11 0.41
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
TTAATTTTTATACTTAATTTA
Found at i:23703 original size:23 final size:22
Alignment explanation
Indices: 23677--23719 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
23667 TTAGATTTGA
23677 ATTAATTCACAAACGGATTCAGT
1 ATTAATTCA-AAACGGATTCAGT
*
23700 ATTAATTCAAATCGGATTCA
1 ATTAATTCAAAACGGATTCA
23720 ATTCAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
ATTAATTCAAAACGGATTCAGT
Found at i:25186 original size:50 final size:50
Alignment explanation
Indices: 25068--25304 Score: 348
Period size: 50 Copynumber: 4.7 Consensus size: 50
25058 ACATGCTAAA
** * * *
25068 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAAT
** * *
25119 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
*
25169 GTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
*
25219 GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* *
25269 GCTATGTCCCAGACATGGTCTTACATGGGGCCTCTC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
25305 TATCCAAATG
Statistics
Matches: 167, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 139 0.83
51 28 0.17
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
Found at i:25419 original size:13 final size:13
Alignment explanation
Indices: 25398--25427 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25388 GCTTGGATCA
25398 TCATCAAATAAAT
1 TCATCAAATAAAT
*
25411 TCATGAAATAAAT
1 TCATCAAATAAAT
25424 TCAT
1 TCAT
25428 AGTTGCTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:26983 original size:17 final size:17
Alignment explanation
Indices: 26961--26994 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
26951 TGGGAATGAA
26961 CCCAAGTTCTCGTGCTT
1 CCCAAGTTCTCGTGCTT
26978 CCCAAGTTCTCGTGCTT
1 CCCAAGTTCTCGTGCTT
26995 ACTAGCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.18, T:0.35
Consensus pattern (17 bp):
CCCAAGTTCTCGTGCTT
Found at i:27961 original size:44 final size:44
Alignment explanation
Indices: 27912--28025 Score: 176
Period size: 44 Copynumber: 2.6 Consensus size: 44
27902 TGGCTTTCTA
*
27912 ATTCTCGAATCTGTGTTTCTGATCATTTCCTTTTTTGCTTCCAT
1 ATTCTCGAATCTGTGTTTGTGATCATTTCCTTTTTTGCTTCCAT
* *
27956 ATTCTCAAATCTGTGTTTGTGGTCATTTCCTTTTTTGCTTCCAT
1 ATTCTCGAATCTGTGTTTGTGATCATTTCCTTTTTTGCTTCCAT
*
28000 ATTCT-GAAATCTGTGTCTGTGATCAT
1 ATTCTCG-AATCTGTGTTTGTGATCAT
28026 ACCTTAAAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.50
Consensus pattern (44 bp):
ATTCTCGAATCTGTGTTTGTGATCATTTCCTTTTTTGCTTCCAT
Found at i:31613 original size:28 final size:28
Alignment explanation
Indices: 31576--31632 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
31566 TAAGTGTTAT
*
31576 ATATATATATATATTAAAGTAAATATTAAA
1 ATATATATA-ATATTAAA-TAAAAATTAAA
*
31606 ATATATATAATATTCAATAAAAATTAA
1 ATATATATAATATTAAATAAAAATTAA
31633 TTAAGGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.36
29 7 0.28
30 9 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
ATATATATAATATTAAATAAAAATTAAA
Done.