Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2831
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: 43193
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:14004 original size:16 final size:16
Alignment explanation
Indices: 13985--14015 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13975 TATGAAAAAC
13985 TTTGAGCTCGAGAAAG
1 TTTGAGCTCGAGAAAG
*
14001 TTTGGGCTCGAGAAA
1 TTTGAGCTCGAGAAA
14016 ATCCAAGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (16 bp):
TTTGAGCTCGAGAAAG
Found at i:15424 original size:15 final size:15
Alignment explanation
Indices: 15404--15434 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15394 AAATATGAAA
15404 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
15419 GATATGTTTTGTATT
1 GATATGTTTTGGATT
15434 G
1 G
15435 GAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:16073 original size:45 final size:45
Alignment explanation
Indices: 15983--16073 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
15973 GTAGGATTTT
* * * * *
15983 GATATATGTGTTTTCGAGTAAGACCACGTCTGGGATATTGGCATC
1 GATATATGTGGTTACGAGTAAGACCACGTCTGGGACATCGACATC
* *
16028 GATATATGTGGTTACGTGTAAGACCATGTCTGGGACATCGACATC
1 GATATATGTGGTTACGAGTAAGACCACGTCTGGGACATCGACATC
16073 G
1 G
16074 TATTTGATTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (45 bp):
GATATATGTGGTTACGAGTAAGACCACGTCTGGGACATCGACATC
Found at i:23236 original size:15 final size:15
Alignment explanation
Indices: 23216--23246 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23206 AAATATGAAA
23216 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
23231 GATATGTTTTGTATT
1 GATATGTTTTGGATT
23246 G
1 G
23247 GAATTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:23884 original size:45 final size:45
Alignment explanation
Indices: 23797--23885 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
23787 TAGGATTCTG
* * * *
23797 ATATATGTGTTTTCGAGGAAGACCACGTCTGGAACGTTGGCATCA
1 ATATATGTGATTACGAGGAAGACCACGTCTGGAACATCGGCATCA
* * * *
23842 ATATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 ATATATGTGATTACGAGGAAGACCACGTCTGGAACATCGGCATC
23886 GTATTTGCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (45 bp):
ATATATGTGATTACGAGGAAGACCACGTCTGGAACATCGGCATCA
Found at i:24353 original size:41 final size:41
Alignment explanation
Indices: 24251--24372 Score: 194
Period size: 40 Copynumber: 3.0 Consensus size: 41
24241 AAAATCGAAT
* * *
24251 AGAT-TGAGTATTAGCGGCGTTTTTAAGAAAGCACAGCTAA
1 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
24291 AGATC-GAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
1 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
*
24331 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGTGCCGCTAA
1 AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
24372 A
1 A
24373 AGATTAAGCA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
40 41 0.54
41 35 0.46
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (41 bp):
AGATCTGAGCATTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
Found at i:25232 original size:23 final size:23
Alignment explanation
Indices: 25179--25234 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
25169 TAATCCCAAC
*
25179 ACCT-TAAACCC-TAAATCTCAA
1 ACCTATAAACCCTTAAAACTCAA
* *
25200 ATC-ATAAACCCTTAAAACTCCA
1 ACCTATAAACCCTTAAAACTCAA
25222 ACCTATAAACCCT
1 ACCTATAAACCCT
25235 AACACACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 9 0.32
22 10 0.36
23 9 0.32
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (23 bp):
ACCTATAAACCCTTAAAACTCAA
Found at i:25546 original size:8 final size:8
Alignment explanation
Indices: 25522--25588 Score: 102
Period size: 8 Copynumber: 8.5 Consensus size: 8
25512 ATAAAAATCT
25522 TTAAAATAA
1 TTAAAA-AA
25531 TT-AAAAA
1 TTAAAAAA
25538 TTAAAAAA
1 TTAAAAAA
25546 TTAAAAAA
1 TTAAAAAA
25554 TTAAAAAA
1 TTAAAAAA
25562 TTAAAAAA
1 TTAAAAAA
25570 TT-AAAAA
1 TTAAAAAA
*
25577 TTAAAAAT
1 TTAAAAAA
25585 TTAA
1 TTAA
25589 TATTTTAGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
7 11 0.20
8 42 0.76
9 2 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
TTAAAAAA
Found at i:25718 original size:17 final size:17
Alignment explanation
Indices: 25683--25730 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
25673 TTTTGGAAGA
*
25683 AAAAATAAAAAAATGTT
1 AAAAATAAAAAAATATT
25700 AAAAATGAAAAAAA-ATT
1 AAAAAT-AAAAAAATATT
*
25717 AAAATTAAATAAAA
1 AAAAATAAA-AAAA
25731 AGTTTAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 17 0.63
18 7 0.26
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAAAATATT
Found at i:29704 original size:28 final size:28
Alignment explanation
Indices: 29641--29875 Score: 373
Period size: 28 Copynumber: 8.4 Consensus size: 28
29631 ATATTAAGTC
* *
29641 CGCACACTCAGTGTTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
29668 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
29696 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
29724 CGCACACTTAGTGCTATATAATTAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
29752 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
29780 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
29808 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
29836 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
29865 CGCACACTTAG
1 CGCACACTTAG
29876 CGCCAATCTC
Statistics
Matches: 194, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
27 21 0.11
28 157 0.81
29 16 0.08
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:37597 original size:28 final size:28
Alignment explanation
Indices: 37534--37681 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
37524 ATATTAAGTC
*
37534 CGCACACTCAGT--TATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
37559 CGCACA-TTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
37586 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
37614 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
37642 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
37671 CGCACACTTAG
1 CGCACACTTAG
37682 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
24 4 0.04
25 6 0.05
26 9 0.08
27 10 0.09
28 66 0.59
29 16 0.14
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.