Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3523
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: 46080
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:11522 original size:16 final size:15
Alignment explanation
Indices: 11503--11532 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11493 AGTATCAATT
11503 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
11519 TTTGATTGGGATGA
1 TTTGATTGGGATGA
11533 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:12442 original size:20 final size:20
Alignment explanation
Indices: 12417--12471 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
12407 TGTGGTTCAA
*
12417 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
12437 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
12457 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
12472 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:19230 original size:23 final size:24
Alignment explanation
Indices: 19184--19229 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
19174 AAAAGAGCGT
*
19184 GAAAAACATATTGAGAAGAAAAAA
1 GAAAAACATAATGAGAAGAAAAAA
19208 GAAAAACA-AATGAG-AGAAAAAA
1 GAAAAACATAATGAGAAGAAAAAA
19230 ATAAATTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 5 0.24
24 8 0.38
ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09
Consensus pattern (24 bp):
GAAAAACATAATGAGAAGAAAAAA
Found at i:26348 original size:70 final size:70
Alignment explanation
Indices: 26227--26363 Score: 238
Period size: 70 Copynumber: 2.0 Consensus size: 70
26217 TTGCATGCCC
* *
26227 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAGCACCTTCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
26292 TGTTG
66 TGTTG
* *
26297 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
26362 TG
66 TG
26364 ATTTAATTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:31202 original size:21 final size:21
Alignment explanation
Indices: 31178--31218 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31168 TTTCAACCAT
*
31178 TACCAATTCGTACCAATTCCA
1 TACCAATTCGAACCAATTCCA
*
31199 TACCATTTCGAACCAATTCC
1 TACCAATTCGAACCAATTCC
31219 CAAATACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCAATTCGAACCAATTCCA
Found at i:37720 original size:11 final size:10
Alignment explanation
Indices: 37695--37755 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
37685 ACCAATAAAA
37695 TAAA-TGAGC
1 TAAATTGAGC
*
37704 TGAATTGTAGC
1 TAAATTG-AGC
37715 TAAATTGAGC
1 TAAATTGAGC
**
37725 TCGATTGAGC
1 TAAATTGAGC
37735 TGAAA-TGAGC
1 T-AAATTGAGC
*
37745 TCAATTGAGC
1 TAAATTGAGC
37755 T
1 T
37756 GGTCGAAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:37756 original size:20 final size:20
Alignment explanation
Indices: 37696--37756 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
37686 CCAATAAAAT
*
37696 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
37716 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
37737 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
37757 GTCGAAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:38514 original size:37 final size:37
Alignment explanation
Indices: 38454--38535 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
38444 TTTTATTTTC
** *
38454 TTTTTTTTTGATCGATTTCTTTTTC-ACTTTTTTTGAA
1 TTTTTTTTCAATCAATTTCTTTTTCAACTTTTTTTG-A
* *
38491 TTTTTTTTCAATCAATTTTTTTTTCAAATTTTTTTTGA
1 TTTTTTTTCAATCAATTTCTTTTTC-AACTTTTTTTGA
38529 TTTTTTT
1 TTTTTTT
38536 GTTCCTCCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 21 0.55
38 8 0.21
39 9 0.24
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.71
Consensus pattern (37 bp):
TTTTTTTTCAATCAATTTCTTTTTCAACTTTTTTTGA
Found at i:44307 original size:14 final size:16
Alignment explanation
Indices: 44288--44319 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
44278 TGCTGTTTTT
44288 TTTTCTTT-CTT-TAC
1 TTTTCTTTGCTTATAC
44302 TTTTCTTTGCTTATAC
1 TTTTCTTTGCTTATAC
44318 TT
1 TT
44320 GTGCCGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTCTTTGCTTATAC
Done.