Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3759
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: 20185
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:126 original size:36 final size:35
Alignment explanation
Indices: 76--147 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
66 TCTCTATGTC
*
76 GGTTGCATCAACATTAATGGAAGACAATTAATAAT
1 GGTTGCATCAACATTAATGGAAGACAATCAATAAT
* *
111 GGTTGCCATTAACATTAATGGGAGACAATCAATAAT
1 GGTTG-CATCAACATTAATGGAAGACAATCAATAAT
147 G
1 G
148 ACAACCACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 5 0.15
36 28 0.85
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (35 bp):
GGTTGCATCAACATTAATGGAAGACAATCAATAAT
Found at i:2948 original size:21 final size:21
Alignment explanation
Indices: 2922--2962 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2912 AGACGAGCAA
* *
2922 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2943 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2963 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6572 original size:31 final size:31
Alignment explanation
Indices: 6536--6598 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
6526 AGCATAATAC
6536 GGACAAAACGATGATTGAGAGATTTGAAGCT
1 GGACAAAACGATGATTGAGAGATTTGAAGCT
6567 GGACAAAACGATGATTGAGAGATTTGAAGCT
1 GGACAAAACGATGATTGAGAGATTTGAAGCT
6598 G
1 G
6599 CAATTGCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.30, T:0.22
Consensus pattern (31 bp):
GGACAAAACGATGATTGAGAGATTTGAAGCT
Found at i:10886 original size:17 final size:19
Alignment explanation
Indices: 10861--10897 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
10851 ATATACACTC
10861 TTTATATATAGTAT-TATT
1 TTTATATATAGTATATATT
*
10879 TTTA-ATATATTATATATT
1 TTTATATATAGTATATATT
10897 T
1 T
10898 ATTTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTATATATAGTATATATT
Found at i:10899 original size:22 final size:22
Alignment explanation
Indices: 10865--10939 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 22
10855 ACACTCTTTA
10865 TATATAGTATTATTTTTAATATAT
1 TATATA-T-TTATTTTTAATATAT
*
10889 TATATATTTATTTTTTAACATAT
1 TATATATTTA-TTTTTAATATAT
* *
10912 ATATGTATATATTTATGTAATATTAT
1 -TATATATTTATTT-T-TAATA-TAT
10938 TA
1 TA
10940 ACAATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
22 3 0.07
23 15 0.36
24 15 0.36
25 6 0.14
26 3 0.07
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (22 bp):
TATATATTTATTTTTAATATAT
Found at i:11098 original size:23 final size:22
Alignment explanation
Indices: 11066--11114 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
11056 TATCATATGT
11066 ATATTTTATGTACATACTTTTA
1 ATATTTTATGTACATACTTTTA
** *
11088 ATATTATTATGTATTTATTTTTA
1 ATATT-TTATGTACATACTTTTA
11111 ATAT
1 ATAT
11115 ATGTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (22 bp):
ATATTTTATGTACATACTTTTA
Found at i:11125 original size:23 final size:23
Alignment explanation
Indices: 11083--11128 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
11073 ATGTACATAC
*
11083 TTTTAATATTATTATGTATTTAT
1 TTTTAATATTATTATATATTTAT
11106 TTTTAATA-TATGTATATATTTAT
1 TTTTAATATTAT-TATATATTTAT
11129 GTAGTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTAATATTATTATATATTTAT
Found at i:11209 original size:13 final size:13
Alignment explanation
Indices: 11164--11233 Score: 60
Period size: 13 Copynumber: 5.6 Consensus size: 13
11154 TCTTCTAATA
11164 GTATATATATTAT
1 GTATATATATTAT
11177 GTA-A-ATATT-T
1 GTATATATATTAT
11187 -TAATACTATATTAT
1 GT-ATA-TATATTAT
11201 GTATATATA-TAT
1 GTATATATATTAT
* *
11213 TTATATATGTTAT
1 GTATATATATTAT
*
11226 GTACATAT
1 GTATATAT
11234 TTTTTAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
9 1 0.02
10 2 0.04
11 6 0.13
12 11 0.24
13 21 0.46
14 4 0.09
15 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (13 bp):
GTATATATATTAT
Found at i:11251 original size:16 final size:16
Alignment explanation
Indices: 11230--11263 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
11220 TGTTATGTAC
11230 ATATTTTTTAAATATT
1 ATATTTTTTAAATATT
*
11246 ATATTTTTTATATATT
1 ATATTTTTTAAATATT
11262 AT
1 AT
11264 GATGTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTTTTTAAATATT
Found at i:11271 original size:23 final size:22
Alignment explanation
Indices: 11245--11304 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
11235 TTTTAAATAT
*
11245 TATATTTTTTATATATTATGATG
1 TATATTTTTTATATATCATGA-G
*
11268 TATA--TTTTA-ATATCATTAG
1 TATATTTTTTATATATCATGAG
11287 TATATTTTTTATACTATC
1 TATATTTTTTATA-TATC
11305 TTATGTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 5 0.16
20 7 0.23
21 10 0.32
22 1 0.03
23 8 0.26
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (22 bp):
TATATTTTTTATATATCATGAG
Found at i:11496 original size:25 final size:25
Alignment explanation
Indices: 11433--11585 Score: 127
Period size: 25 Copynumber: 6.1 Consensus size: 25
11423 AATATATATA
* **
11433 TATATCATGTATATATGATTTTTTTA-
1 TATATTATGTATATAT--TTTTAATAC
*
11459 TATATTATGTATATATCTTTAATAC
1 TATATTATGTATATATTTTTAATAC
**
11484 TATATTAT-T-TATATTTTTCTTAC
1 TATATTATGTATATATTTTTAATAC
* * *
11507 -ATATTATCTTATGTATATTTAATAAC
1 TATATTAT-GTATATATTTTTAAT-AC
*
11533 TATATTATGTATGTATTTTTAACT-C
1 TATATTATGTATATATTTTTAA-TAC
*
11558 TATATTATGTACATATTTTTAATAC
1 TATATTATGTATATATTTTTAATAC
11583 TAT
1 TAT
11586 GTATATACTT
Statistics
Matches: 104, Mismatches: 15, Indels: 17
0.76 0.11 0.12
Matches are distributed among these distances:
22 7 0.07
23 11 0.11
24 8 0.08
25 41 0.39
26 29 0.28
27 8 0.08
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (25 bp):
TATATTATGTATATATTTTTAATAC
Found at i:11504 original size:27 final size:27
Alignment explanation
Indices: 11459--11526 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
11449 GATTTTTTTA
* *
11459 TATATTATGTATATATCT-TTA-ATAC
1 TATATTATGTATATTTTTCTTACATAC
* *
11484 TATATTATTTATATTTTTCTTACATAT
1 TATATTATGTATATTTTTCTTACATAC
*
11511 TATCTTATGTATATTT
1 TATATTATGTATATTT
11527 AATAACTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 15 0.43
26 3 0.09
27 17 0.49
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (27 bp):
TATATTATGTATATTTTTCTTACATAC
Found at i:11518 original size:23 final size:21
Alignment explanation
Indices: 11450--11518 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 21
11440 TGTATATATG
*
11450 ATTTTTTTATATATTATGTATAT
1 ATTTTTTTACATATTAT-T-TAT
**
11473 ATCTTTAATACTATATTATTTAT
1 AT-TTTTTTAC-ATATTATTTAT
11496 ATTTTTCTTACATATTATCTTAT
1 ATTTTT-TTACATATTAT-TTAT
11519 GTATATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
22 10 0.27
23 14 0.38
24 6 0.16
25 7 0.19
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.61
Consensus pattern (21 bp):
ATTTTTTTACATATTATTTAT
Found at i:12892 original size:20 final size:20
Alignment explanation
Indices: 12867--12904 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12857 TGGAAAAGTT
12867 ATATTATCAATTAGAACCAG
1 ATATTATCAATTAGAACCAG
12887 ATATTATCAATTAGAACC
1 ATATTATCAATTAGAACC
12905 GGATCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (20 bp):
ATATTATCAATTAGAACCAG
Found at i:16582 original size:17 final size:18
Alignment explanation
Indices: 16560--16595 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
16550 GAGACTTTAA
16560 TGAAAGAGGTGA-AATGT
1 TGAAAGAGGTGATAATGT
*
16577 TGAAAGTGGTGATAATGT
1 TGAAAGAGGTGATAATGT
16595 T
1 T
16596 TCCCTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (18 bp):
TGAAAGAGGTGATAATGT
Done.