Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold324
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: 35433
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:1348 original size:21 final size:21
Alignment explanation
Indices: 1319--1361 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1309 ATATCTCTGT
*
1319 TGGTCTAATCTTACATTACGG
1 TGGTCTAATCTTACAATACGG
* *
1340 TGGTTTAATCTTATAATACGG
1 TGGTCTAATCTTACAATACGG
1361 T
1 T
1362 TTGTAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (21 bp):
TGGTCTAATCTTACAATACGG
Found at i:2842 original size:21 final size:21
Alignment explanation
Indices: 2816--2855 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2806 CTGATCTCGA
2816 CAGACAACACTTCAAAAACAT
1 CAGACAACACTTCAAAAACAT
2837 CAGACAACACTTCAAAAAC
1 CAGACAACACTTCAAAAAC
2856 TTTTCTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.30, G:0.05, T:0.12
Consensus pattern (21 bp):
CAGACAACACTTCAAAAACAT
Found at i:4744 original size:3 final size:3
Alignment explanation
Indices: 4730--4771 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
4720 TATTTTAATG
* *
4730 TTA TTG TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4772 GTTTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:11334 original size:10 final size:11
Alignment explanation
Indices: 11318--11343 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11308 TTTAAAATAC
11318 TTTTTTTTTAA
1 TTTTTTTTTAA
11329 TTTTTTTTTAA
1 TTTTTTTTTAA
11340 TTTT
1 TTTT
11344 AAAAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:11343 original size:86 final size:85
Alignment explanation
Indices: 11245--11408 Score: 260
Period size: 86 Copynumber: 1.9 Consensus size: 85
11235 AATATATTTA
* *
11245 TTTTTTTAATTTT-AAAATATTTTTTACATAC-TTTTTTAATTTTTTTTAAAATTTTAAAATATT
1 TTTTTTTAATTTTAAAAATATTTTTAAAATACTTTTTTTAA-TTTTTTT--AATTTTAAAATATT
11308 TTTAAAATACTTTTTTTTTAATT
63 TTTAAAATACTTTTTTTTTAATT
11331 TTTTTTTAATTTTAAAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTT
1 TTTTTTTAATTTT-AAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTT
11396 TAAAATACTTTTT
65 TAAAATACTTTTT
11409 AAAATTTAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
86 42 0.58
88 23 0.32
89 8 0.11
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (85 bp):
TTTTTTTAATTTTAAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTT
AAAATACTTTTTTTTTAATT
Found at i:11367 original size:12 final size:11
Alignment explanation
Indices: 11346--11413 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
11336 TTAATTTTAA
11346 AAAATATTTTT
1 AAAATATTTTT
11357 AAAATACTTTTT
1 AAAATA-TTTTT
**
11369 TTAAT-TTTTT
1 AAAATATTTTT
*
11379 ----TAATTTT
1 AAAATATTTTT
11386 AAAATATTTTT
1 AAAATATTTTT
11397 AAAATACTTTTT
1 AAAATA-TTTTT
11409 AAAAT
1 AAAAT
11414 TTAAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
10 5 0.11
11 18 0.39
12 18 0.39
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:11407 original size:29 final size:30
Alignment explanation
Indices: 11353--11421 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
11343 TAAAAAATAT
** *
11353 TTTTAAAATACTTTTTTTAAT-TTTTTTAA
1 TTTTAAAATACTTTTTAAAATCTTTTTAAA
11382 TTTTAAAATA-TTTTTAAAATACTTTTTAAA
1 TTTTAAAATACTTTTTAAAAT-CTTTTTAAA
*
11412 ATTTAAAATA
1 TTTTAAAATA
11422 AAAATGGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.24
29 10 0.29
30 16 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTAAAATACTTTTTAAAATCTTTTTAAA
Found at i:15367 original size:15 final size:14
Alignment explanation
Indices: 15342--15376 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
15332 ATTTCTTCTT
*
15342 ATATTTTACAGTAG
1 ATATTTCACAGTAG
15356 ATTATTTCACAGTAG
1 A-TATTTCACAGTAG
15371 ATATTT
1 ATATTT
15377 TTTGATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (14 bp):
ATATTTCACAGTAG
Found at i:19031 original size:29 final size:29
Alignment explanation
Indices: 18984--19040 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
18974 TGATTGATAG
* *
18984 TTCAGCTCATCAAAGGGAGACTGAAACCT
1 TTCAGCTCATCAAAAGGAGACTAAAACCT
*
19013 TTCAGCTCATTAAAAGGAGACTAAAACC
1 TTCAGCTCATCAAAAGGAGACTAAAACC
19041 ACAAGACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (29 bp):
TTCAGCTCATCAAAAGGAGACTAAAACCT
Found at i:21438 original size:15 final size:15
Alignment explanation
Indices: 21418--21447 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21408 CAAACATATT
21418 ACTGGATCATTGGTA
1 ACTGGATCATTGGTA
21433 ACTGGATCATTGGTA
1 ACTGGATCATTGGTA
21448 CTTTATTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
ACTGGATCATTGGTA
Found at i:21564 original size:16 final size:16
Alignment explanation
Indices: 21531--21564 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21521 ATTCATTGTT
* *
21531 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
21547 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
21563 AA
1 AA
21565 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:24388 original size:21 final size:21
Alignment explanation
Indices: 24362--24402 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24352 AGACGAGCAA
* *
24362 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
24383 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
24403 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:26340 original size:16 final size:16
Alignment explanation
Indices: 26307--26340 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26297 GGAGATTGTT
* *
26307 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
26323 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
26339 AA
1 AA
26341 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:30116 original size:16 final size:17
Alignment explanation
Indices: 30095--30129 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30085 GGAAATATTG
30095 ATCA-TTTCAATATTTT
1 ATCATTTTCAATATTTT
*
30111 ATCATTTTGAATATTTT
1 ATCATTTTCAATATTTT
30128 AT
1 AT
30130 GTTTTATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (17 bp):
ATCATTTTCAATATTTT
Found at i:31044 original size:19 final size:20
Alignment explanation
Indices: 31007--31045 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30997 AAGTTGTAAC
*
31007 AAAAATTTATATTATAAATA
1 AAAAAATTATATTATAAATA
31027 AAAAAATTATATTA-AAATA
1 AAAAAATTATATTATAAATA
31046 TTTAGATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATTATATTATAAATA
Found at i:31399 original size:18 final size:18
Alignment explanation
Indices: 31374--31443 Score: 70
Period size: 18 Copynumber: 3.6 Consensus size: 18
31364 ATTATATTGA
31374 TAAT-TTTTTATAGTAAT
1 TAATATTTTTATAGTAAT
31391 TAATATTTTTAAAATTATGTAAAT
1 TAATATTTTT---A-TA-GT-AAT
*
31415 TAATATTTTTATAATAAT
1 TAATATTTTTATAGTAAT
31433 TAATATTTTTA
1 TAATATTTTTA
31444 AATTATGTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
17 4 0.09
18 19 0.42
19 1 0.02
20 2 0.04
21 2 0.04
22 2 0.04
23 2 0.04
24 13 0.29
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TAATATTTTTATAGTAAT
Found at i:31415 original size:24 final size:23
Alignment explanation
Indices: 31388--31466 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 23
31378 TTTTTATAGT
31388 AATTAATATTTTTAAAATTATGTA
1 AATTAATATTTTT-AAATTATGTA
*
31412 AATTAATATTTTT--A-TA-AT-
1 AATTAATATTTTTAAATTATGTA
31430 AATTAATATTTTTAAATTATGTA
1 AATTAATATTTTTAAATTATGTA
* *
31453 AATAAACATTTTTA
1 AATTAATATTTTTA
31467 TAGCATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 13 0.28
19 1 0.02
20 3 0.07
21 3 0.07
22 1 0.02
23 12 0.26
24 13 0.28
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
AATTAATATTTTTAAATTATGTA
Found at i:31427 original size:42 final size:42
Alignment explanation
Indices: 31374--31485 Score: 156
Period size: 41 Copynumber: 2.7 Consensus size: 42
31364 ATTATATTGA
31374 TAAT-TTTTTATAGTAATTAATATTTTTAAAATTATGTAAAT
1 TAATATTTTTATAGTAATTAATATTTTTAAAATTATGTAAAT
*
31415 TAATATTTTTATAATAATTAATATTTTT-AAATTATGTAAAT
1 TAATATTTTTATAGTAATTAATATTTTTAAAATTATGTAAAT
* * * * *
31456 AAACATTTTTATAGCATTTAATTTTTTTAA
1 TAATATTTTTATAGTAATTAATATTTTTAA
31486 TTTAAATTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 39 0.63
42 23 0.37
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (42 bp):
TAATATTTTTATAGTAATTAATATTTTTAAAATTATGTAAAT
Done.