Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1687
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: 15607
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Found at i:3246 original size:19 final size:18
Alignment explanation
Indices: 3224--3301 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 18
3214 ATTTTAATAC
3224 ATTTTTATATTT-T-TAT
1 ATTTTTATATTTATATAT
*
3240 CATATTTATATTATATATAT
1 -ATTTTTATATT-TATATAT
3260 ATTTTTATA-TTATATTAT
1 ATTTTTATATTTATA-TAT
3278 ATTTTTATA--TATATAT
1 ATTTTTATATTTATATAT
3294 ATTTTTAT
1 ATTTTTAT
3302 GAATACGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.20
17 18 0.33
18 14 0.25
19 9 0.16
20 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTATATTTATATAT
Found at i:3249 original size:17 final size:16
Alignment explanation
Indices: 3227--3301 Score: 79
Period size: 18 Copynumber: 4.8 Consensus size: 16
3217 TTAATACATT
3227 TTTATATTTTTATCATA
1 TTTATATTTTTAT-ATA
3244 TTTATA---TTATATA
1 TTTATATTTTTATATA
3257 --TATATTTTTATATTA
1 TTTATATTTTTATA-TA
3272 TATTATATTTTTATATA
1 T-TTATATTTTTATATA
*
3289 TATATATTTTTAT
1 TTTATATTTTTAT
3302 GAATACGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
11 4 0.08
13 3 0.06
14 9 0.18
15 2 0.04
16 11 0.22
17 9 0.18
18 12 0.24
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATATTTTTATATA
Found at i:3294 original size:34 final size:36
Alignment explanation
Indices: 3224--3301 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 36
3214 ATTTTAATAC
*
3224 ATTTTTATATTTTTATCATATTTATATTATATATAT
1 ATTTTTATATTTATATCATATTTATATTATATATAT
* *
3260 ATTTTTATA-TTATATTATATTTTTA-TATATATAT
1 ATTTTTATATTTATATCATATTTATATTATATATAT
3294 ATTTTTAT
1 ATTTTTAT
3302 GAATACGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
34 17 0.44
35 13 0.33
36 9 0.23
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (36 bp):
ATTTTTATATTTATATCATATTTATATTATATATAT
Found at i:3551 original size:11 final size:11
Alignment explanation
Indices: 3535--3560 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3525 TGCCGAAGGT
3535 TTTTTTTTTTA
1 TTTTTTTTTTA
3546 TTTTTTTTTTA
1 TTTTTTTTTTA
3557 TTTT
1 TTTT
3561 GGTTAGCATG
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:3743 original size:18 final size:19
Alignment explanation
Indices: 3712--3766 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 19
3702 TTAAAATATT
3712 ATATATTTATATAAATTTTA
1 ATATA-TTATATAAATTTTA
3732 ATATATTA-AT-AA--TT-
1 ATATATTATATAAATTTTA
3746 -TATATTATATAAATTTTA
1 ATATATTATATAAATTTTA
3764 ATA
1 ATA
3767 AATATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 13
0.69 0.00 0.31
Matches are distributed among these distances:
13 7 0.24
14 2 0.07
15 4 0.14
17 4 0.14
18 2 0.07
19 5 0.17
20 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATTATATAAATTTTA
Found at i:3771 original size:16 final size:16
Alignment explanation
Indices: 3719--3772 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
3709 ATTATATATT
3719 TATATAAATTTTAATA
1 TATATAAATTTTAATA
*
3735 TAT-TAATAATTT-ATA
1 TATATAA-ATTTTAATA
3750 TTATATAAATTTTAATA
1 -TATATAAATTTTAATA
*
3767 AATATA
1 TATATA
3773 TTCATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 6 0.19
16 19 0.61
17 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATAAATTTTAATA
Found at i:3783 original size:23 final size:24
Alignment explanation
Indices: 3737--3786 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
3727 TTTTAATATA
*
3737 TTAATAATTTATATTATATAAATT
1 TTAATAATATATATTATATAAATT
3761 TTAATAA-ATATATTCATAT-AATT
1 TTAATAATATATATT-ATATAAATT
3784 TTA
1 TTA
3787 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAATAATATATATTATATAAATT
Found at i:5332 original size:21 final size:19
Alignment explanation
Indices: 5281--5326 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
5271 TATGAATTTT
5281 AATTAAATTAAAAATTATATA
1 AATTAAATT--AAATTATATA
*
5302 ATTTAAATTAAATTATATTA
1 AATTAAATTAAATTATA-TA
5322 AATTA
1 AATTA
5327 TTATTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 8 0.36
20 6 0.27
21 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTAAATTAAATTATATA
Found at i:5793 original size:15 final size:15
Alignment explanation
Indices: 5773--5802 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5763 ACTCGATTCG
5773 AATATAATAAAAATA
1 AATATAATAAAAATA
5788 AATATAATAAAAATA
1 AATATAATAAAAATA
5803 TAGAAATATA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATAATAAAAATA
Found at i:5811 original size:19 final size:18
Alignment explanation
Indices: 5787--5822 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5777 TAATAAAAAT
5787 AAATATAATAAAAATATAG
1 AAATAT-ATAAAAATATAG
*
5806 AAATATATTAAAATATA
1 AAATATATAAAAATATA
5823 TGTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATATATAAAAATATAG
Found at i:6408 original size:52 final size:51
Alignment explanation
Indices: 6341--6453 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 51
6331 TTGATAAATT
* ** *
6341 TAATTTTTATTAATTAAATTTTAAATT-AATTTATATAAGTTATT-ATTTAATAA
1 TAATATTT-TTAATTAAATTTT-AATTAAAAATATATAA-TTATTAATATAA-AA
*
6394 TAATATTTTTAATTAAATTTTATTTAAAAATATATAATTATTAATATAAAA
1 TAATATTTTTAATTAAATTTTAATTAAAAATATATAATTATTAATATAAAA
6445 TAATATTTT
1 TAATATTTT
6454 AATAATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
51 19 0.36
52 27 0.51
53 7 0.13
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (51 bp):
TAATATTTTTAATTAAATTTTAATTAAAAATATATAATTATTAATATAAAA
Found at i:6418 original size:30 final size:33
Alignment explanation
Indices: 6364--6484 Score: 86
Period size: 35 Copynumber: 3.6 Consensus size: 33
6354 TTAAATTTTA
* * *
6364 AATTAATTTATATAAGTTATTATTTAATAATA-AT
1 AATT-ATTAATATAAATT-TTATTTAAAAATATAT
*
6398 -ATTTTTAAT-TAAATTTTATTTAAAAATATAT
1 AATTATTAATATAAATTTTATTTAAAAATATAT
** *
6429 AATTATTAATATAAAATAATATTTTAATAATATTAT
1 AATTATTAATAT-AAATTTTA-TTTAAAAATA-TAT
* * *
6465 AAATATTAAAATAAAATTTA
1 AATTATTAATATAAATTTTA
6485 AAATTAATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
30 12 0.18
31 7 0.10
32 12 0.18
33 4 0.06
34 6 0.09
35 14 0.21
36 13 0.19
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (33 bp):
AATTATTAATATAAATTTTATTTAAAAATATAT
Found at i:6477 original size:20 final size:18
Alignment explanation
Indices: 6454--6517 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 18
6444 ATAATATTTT
*
6454 AATAATATTATAAATATTAA
1 AATAAAATT-TAAA-ATTAA
6474 AATAAAATTTAAAATT-A
1 AATAAAATTTAAAATTAA
* *
6491 ATTTAAATTT-AAATTAA
1 AATAAAATTTAAAATTAA
**
6508 TTTAAAATTT
1 AATAAAATTT
6518 TTAAATCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.13
17 18 0.47
18 3 0.08
19 4 0.11
20 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAAAATTTAAAATTAA
Found at i:6506 original size:16 final size:17
Alignment explanation
Indices: 6478--6513 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
6468 TATTAAAATA
6478 AAATTTAAAATTAATTT
1 AAATTTAAAATTAATTT
6495 AAATTT-AAATTAATTT
1 AAATTTAAAATTAATTT
6511 AAA
1 AAA
6514 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTAAAATTAATTT
Found at i:6515 original size:17 final size:18
Alignment explanation
Indices: 6476--6517 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
6466 AATATTAAAA
6476 TAAAATTTAAAATTAATT
1 TAAAATTTAAAATTAATT
6494 T-AAATTT-AAATTAATT
1 TAAAATTTAAAATTAATT
6510 TAAAATTT
1 TAAAATTT
6518 TTAAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.43
17 12 0.52
18 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAAATTTAAAATTAATT
Done.