Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2067
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: 29616
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:605 original size:1 final size:1
Alignment explanation
Indices: 599--666 Score: 109
Period size: 1 Copynumber: 68.0 Consensus size: 1
589 TCCTTTGTTG
* * *
599 TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTGTTTTTTTTCTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
664 TTT
1 TTT
667 GGTGTGTGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.03, G:0.01, T:0.96
Consensus pattern (1 bp):
T
Found at i:629 original size:27 final size:27
Alignment explanation
Indices: 599--666 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
589 TCCTTTGTTG
599 TTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTCTTTTTTT
*
626 TTTTTTTTTTGTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTCTTTTTTT
653 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
667 GGTGTGTGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.00, C:0.03, G:0.01, T:0.96
Consensus pattern (27 bp):
TTTTTTTTTTTTTTTTTTTCTTTTTTT
Found at i:4735 original size:14 final size:14
Alignment explanation
Indices: 4716--4746 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4706 TACAATATAT
4716 ATAAGAATTATACG
1 ATAAGAATTATACG
4730 ATAAGAATTATACG
1 ATAAGAATTATACG
4744 ATA
1 ATA
4747 TATATCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:5376 original size:14 final size:14
Alignment explanation
Indices: 5359--5411 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
5349 ATATTTATAT
5359 TAAATATTATTAAA
1 TAAATATTATTAAA
5373 TAAATATTATTAAA
1 TAAATATTATTAAA
* *
5387 TTATTATTATTAAAA
1 TAAATATTATT-AAA
5402 TGAAATATTA
1 T-AAATATTA
5412 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 23 0.70
15 4 0.12
16 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATATTATTAAA
Found at i:10387 original size:3 final size:3
Alignment explanation
Indices: 10375--10484 Score: 61
Period size: 3 Copynumber: 37.7 Consensus size: 3
10365 AATTTTTTTT
* * *
10375 TTA TTAA TTA TTA TT- TTC TT- TTT TTT TTA TTA TT- TT- TTA TTAA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * * *
10418 TTA TTA TTA ATA TT- TTA TTAA TTA TTA TTA ATA TT- TTT TTA ATA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * *
10462 TTA ATA TTT TTA TTA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
10485 TCCTATTTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
2 12 0.14
3 64 0.75
4 9 0.11
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10390 original size:21 final size:21
Alignment explanation
Indices: 10366--10481 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 21
10356 AATTTAGTCA
10366 ATTTTTTTTTTATTAATTATT
1 ATTTTTTTTTTATTAATTATT
10387 ATTTTCTTTTTT-TT--TTATT
1 ATTTT-TTTTTTATTAATTATT
10406 A----TTTTTTATTAATTATT
1 ATTTTTTTTTTATTAATTATT
** *
10423 ATTAATATTTTATTAATTATT
1 ATTTTTTTTTTATTAATTATT
* *
10444 ATTAATATTTTT-TTAA-TATT
1 ATT-TTTTTTTTATTAATTATT
* *
10464 AATATTTTTATTATTAAT
1 -ATTTTTTTTTTATTAAT
10482 ATTTCCTATT
Statistics
Matches: 75, Mismatches: 8, Indels: 23
0.71 0.08 0.22
Matches are distributed among these distances:
14 6 0.08
15 2 0.03
17 6 0.08
19 6 0.08
20 9 0.12
21 35 0.47
22 11 0.15
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTTTTTTTATTAATTATT
Found at i:10410 original size:10 final size:10
Alignment explanation
Indices: 10368--10447 Score: 56
Period size: 10 Copynumber: 8.0 Consensus size: 10
10358 TTTAGTCAAT
*
10368 TTTTTTTTTA
1 TTTTTTATTA
**
10378 TTAATTATTA
1 TTTTTTATTA
10388 TTTTCTT-TT-
1 TTTT-TTATTA
10397 TTTTTTATTA
1 TTTTTTATTA
10407 TTTTTTATTA
1 TTTTTTATTA
* *
10417 ATTATTATTAA
1 TTTTTTATT-A
*
10428 TATTTTATTA
1 TTTTTTATTA
* *
10438 ATTATTATTA
1 TTTTTTATTA
10448 ATATTTTTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
8 2 0.04
9 6 0.11
10 36 0.68
11 9 0.17
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:10448 original size:10 final size:10
Alignment explanation
Indices: 10401--10449 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
10391 TCTTTTTTTT
* *
10401 TTATTATTTT
1 TTATTAATTA
10411 TTATTAATTA
1 TTATTAATTA
*
10421 TTATTAATATT
1 TTATTAAT-TA
10432 TTATTAATTA
1 TTATTAATTA
10442 TTATTAAT
1 TTATTAAT
10450 ATTTTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATTAATTA
Found at i:10482 original size:21 final size:21
Alignment explanation
Indices: 10409--10484 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
10399 TTTTATTATT
*
10409 TTTTATTAATTATTATTAATA
1 TTTTATTAATTAATATTAATA
*
10430 TTTTATTAATTATTATTAATA
1 TTTTATTAATTAATATTAATA
10451 -TTT-TT--TTAATATTAATA
1 TTTTATTAATTAATATTAATA
10468 TTTTTATT-ATTAATATT
1 -TTTTATTAATTAATATT
10485 TCCTATTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
17 11 0.22
19 5 0.10
20 5 0.10
21 29 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATTAATTAATATTAATA
Found at i:11140 original size:15 final size:15
Alignment explanation
Indices: 11120--11149 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11110 ATGTCTATGC
*
11120 ATGGAATTATAATGT
1 ATGGAATTAGAATGT
11135 ATGGAATTAGAATGT
1 ATGGAATTAGAATGT
11150 CAAAAAGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (15 bp):
ATGGAATTAGAATGT
Found at i:12183 original size:19 final size:19
Alignment explanation
Indices: 12167--12221 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
12157 TTTTATTATC
12167 CTTTTCTATTCTAATTAGA
1 CTTTTCTATTCTAATTAGA
12186 CTTTTCTATTCTAATTAGA
1 CTTTTCTATTCTAATTAGA
12205 CTTTTCTATTCTAATTA
1 CTTTTCTATTCTAATTA
12222 ATAAGAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (19 bp):
CTTTTCTATTCTAATTAGA
Found at i:12333 original size:17 final size:17
Alignment explanation
Indices: 12311--12344 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12301 CCTTGCATCT
12311 TCAAATAACCCGATAGA
1 TCAAATAACCCGATAGA
*
12328 TCAAATAACTCGATAGA
1 TCAAATAACCCGATAGA
12345 ATAGATCCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (17 bp):
TCAAATAACCCGATAGA
Found at i:13406 original size:13 final size:13
Alignment explanation
Indices: 13388--13414 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13378 TCAACTCTTA
13388 TTACAAGTTAATT
1 TTACAAGTTAATT
13401 TTACAAGTTAATT
1 TTACAAGTTAATT
13414 T
1 T
13415 CTGAAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTACAAGTTAATT
Found at i:13944 original size:13 final size:13
Alignment explanation
Indices: 13926--13951 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13916 GATTCTTAAT
13926 TTTATTATATAGA
1 TTTATTATATAGA
13939 TTTATTATATAGA
1 TTTATTATATAGA
13952 AGATAGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTATTATATAGA
Found at i:13980 original size:21 final size:21
Alignment explanation
Indices: 13954--13993 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13944 TATATAGAAG
13954 ATAGATATATACAACTTTTCT
1 ATAGATATATACAACTTTTCT
*
13975 ATAGATATATAGAACTTTT
1 ATAGATATATACAACTTTT
13994 ATCAGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (21 bp):
ATAGATATATACAACTTTTCT
Found at i:14025 original size:21 final size:21
Alignment explanation
Indices: 14001--14040 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13991 TTTATCAGTA
*
14001 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATTTATATTAT
* *
14022 ATTCTATATCATTTCTATT
1 ATTCCATATCATTTATATT
14041 CTATAGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTCCATATCATTTATATTAT
Found at i:15314 original size:24 final size:22
Alignment explanation
Indices: 15270--15314 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
15260 CTTATTTATA
*
15270 TTTTTTATATTTTCGATTTCCT
1 TTTTTTATATTTTCCATTTCCT
*
15292 TTTTTTTTATTTATCCATCTTCC
1 TTTTTTATATTT-TCCAT-TTCC
15315 ATTGAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.13, C:0.18, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTATATTTTCCATTTCCT
Found at i:15828 original size:20 final size:20
Alignment explanation
Indices: 15782--15821 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
15772 TCTATATAGA
*
15782 ATAATATTCTAAATTCTAAT
1 ATAATATTCTAAATTCGAAT
15802 ATAATATTCTAAATTCGAAT
1 ATAATATTCTAAATTCGAAT
15822 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (20 bp):
ATAATATTCTAAATTCGAAT
Found at i:15857 original size:12 final size:12
Alignment explanation
Indices: 15842--15866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15832 TATCTATATA
15842 TAATTAGATAAT
1 TAATTAGATAAT
15854 TAATTAGATAAT
1 TAATTAGATAAT
15866 T
1 T
15867 TTTCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TAATTAGATAAT
Found at i:15913 original size:19 final size:19
Alignment explanation
Indices: 15863--15913 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
15853 TTAATTAGAT
15863 AATTTTTCTATTTTTATTA
1 AATTTTTCTATTTTTATTA
* *
15882 AA-ATTTCTAATTTTATTTA
1 AATTTTTCTATTTTTA-TTA
15901 AATTTTTCTATTT
1 AATTTTTCTATTT
15914 AAATTTAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 11 0.42
19 7 0.27
20 8 0.31
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTTCTATTTTTATTA
Found at i:15914 original size:18 final size:19
Alignment explanation
Indices: 15863--15914 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
15853 TTAATTAGAT
*
15863 AATTTTTCTATTTTTATTA
1 AATTTTTCTATTTATATTA
*
15882 AA-ATTTCTAATTT-TATTTA
1 AATTTTTCT-ATTTATA-TTA
15901 AATTTTTCTATTTA
1 AATTTTTCTATTTA
15915 AATTTAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 7 0.26
19 15 0.56
20 5 0.19
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTCTATTTATATTA
Found at i:19020 original size:19 final size:18
Alignment explanation
Indices: 18996--19032 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
18986 TTTTTTTTAA
18996 TAAATTATTAATTTATTAT
1 TAAATTATTAA-TTATTAT
*
19015 TAAATTATTCATTATTAT
1 TAAATTATTAATTATTAT
19033 GAATTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAATTATTAATTATTAT
Found at i:22739 original size:8 final size:8
Alignment explanation
Indices: 22726--22751 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
22716 CTTTATTACT
22726 ATTAACAA
1 ATTAACAA
22734 ATTAACAA
1 ATTAACAA
22742 ATTAACAA
1 ATTAACAA
22750 AT
1 AT
22752 CAAATGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (8 bp):
ATTAACAA
Done.