Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2568
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: 27071
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:1611 original size:17 final size:16
Alignment explanation
Indices: 1570--1614 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1560 AGCTTTATTA
*
1570 TTTTA-TTACTAAAAT
1 TTTTATTTATTAAAAT
1585 TTTTATTTATTAAAAT
1 TTTTATTTATTAAAAT
*
1601 TTTTGTCTTATTAA
1 TTTTAT-TTATTAA
1615 GAATATTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 5 0.19
16 14 0.54
17 7 0.27
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTATTTATTAAAAT
Found at i:2510 original size:34 final size:35
Alignment explanation
Indices: 2446--2511 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
2436 AATCCAAAAA
* *
2446 TAAAATTAATAAATTATTATTGATTAAATTTTTTT
1 TAAAATTAATAAAATATTATTAATTAAATTTTTTT
*
2481 TAAAA-TAATAAAATA-TATTAAATTTAATTTT
1 TAAAATTAATAAAATATTATT-AATTAAATTTT
2512 ATCTATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.15
34 18 0.67
35 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (35 bp):
TAAAATTAATAAAATATTATTAATTAAATTTTTTT
Found at i:2848 original size:14 final size:16
Alignment explanation
Indices: 2817--2850 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
2807 TTTAGTATTA
2817 TTATGATTATTAAATT
1 TTATGATTATTAAATT
2833 TTATGA-TATT-AATT
1 TTATGATTATTAAATT
2847 TTAT
1 TTAT
2851 TAATAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 4 0.22
16 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TTATGATTATTAAATT
Found at i:2986 original size:19 final size:20
Alignment explanation
Indices: 2959--3011 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
2949 TATAATTATG
*
2959 TAATTTTTTAAAAT-AAAAT
1 TAATATTTTAAAATAAAAAT
**
2978 TAATATTTTTTAATAAAAAT
1 TAATATTTTAAAATAAAAAT
*
2998 AAATAATTTTAAAA
1 TAAT-ATTTTAAAA
3012 AAATTATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 11 0.42
20 8 0.31
21 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATTTTAAAATAAAAAT
Found at i:2996 original size:20 final size:19
Alignment explanation
Indices: 2961--3017 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2951 TAATTATGTA
2961 ATTTTTTAAAATAAAATTAAT
1 ATTTTTT-AAA-AAAATTAAT
*
2982 ATTTTTTAATAAAAATAAAT
1 ATTTTTTAA-AAAAATTAAT
*
3002 A-ATTTTAAAAAAATTA
1 ATTTTTTAAAAAAATTA
3018 TAAATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 7 0.22
19 6 0.19
20 11 0.34
21 8 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTTTAAAAAAATTAAT
Found at i:3014 original size:19 final size:19
Alignment explanation
Indices: 2964--3024 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 19
2954 TTATGTAATT
* *
2964 TTTTAAAATAAAATTAATATT
1 TTTTAAAA-AAAATAAATA-A
*
2985 TTTTAATAAAAATAAATAA
1 TTTTAAAAAAAATAAATAA
3004 TTTTAAAAAAATTATAAATAA
1 TTTTAAAAAAA--ATAAATAA
3025 AAAATTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 10 0.29
20 9 0.26
21 15 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTTAAAAAAAATAAATAA
Found at i:8975 original size:26 final size:26
Alignment explanation
Indices: 8946--8997 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
8936 AAACCTGCTT
8946 GACATGTCGCTGAAGATTTATTGTTG
1 GACATGTCGCTGAAGATTTATTGTTG
8972 GACATGTCGCTGAAGATTTATTGTTG
1 GACATGTCGCTGAAGATTTATTGTTG
8998 ATTGAACTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (26 bp):
GACATGTCGCTGAAGATTTATTGTTG
Found at i:18403 original size:24 final size:25
Alignment explanation
Indices: 18363--18409 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
18353 TAATTTCATT
* *
18363 ATTTATATAATATAAATTATATAAA
1 ATTTATATAATAAAAATAATATAAA
18388 ATTTATA-AATAAAAATAATATA
1 ATTTATATAATAAAAATAATATA
18410 TTATATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTTATATAATAAAAATAATATAAA
Found at i:18549 original size:10 final size:11
Alignment explanation
Indices: 18497--18549 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
18487 AATATTAATT
18497 TTTTATTTAAA
1 TTTTATTTAAA
*
18508 TTTATTTTTAAA
1 TTT-TATTTAAA
*
18520 -TTTA-AT-AA
1 TTTTATTTAAA
18528 TTTTATTTAAA
1 TTTTATTTAAA
18539 TTTTA-TTAAA
1 TTTTATTTAAA
18549 T
1 T
18550 ATCAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
8 2 0.06
9 5 0.15
10 8 0.24
11 12 0.35
12 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTATTTAAA
Found at i:18558 original size:31 final size:29
Alignment explanation
Indices: 18497--18571 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
18487 AATATTAATT
* *
18497 TTTTATTTAAATTTATTTTTAAATTTAATAA
1 TTTTATTTAAA-TT-TTATTAAATTAAATAA
18528 TTTTATTTAAATTTTATTAAATATCAAATAA
1 TTTTATTTAAATTTTATTAAAT-T-AAATAA
*
18559 TTTT-TTAAAATTT
1 TTTTATTTAAATTT
18572 AGATAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.21
30 11 0.28
31 20 0.51
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTATTTAAATTTTATTAAATTAAATAA
Found at i:18579 original size:30 final size:31
Alignment explanation
Indices: 18523--18580 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
18513 TTTTAAATTT
* *
18523 AATAATTTTATTTAAATTTTATTAAATATCA
1 AATAATTTTATTTAAAATTTAATAAATATCA
18554 AATAA-TTT-TTTAAAATTTAGATAAATA
1 AATAATTTTATTTAAAATTTA-ATAAATA
18581 ATTAGATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 9 0.38
31 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
AATAATTTTATTTAAAATTTAATAAATATCA
Found at i:18762 original size:2 final size:2
Alignment explanation
Indices: 18755--18820 Score: 77
Period size: 2 Copynumber: 35.0 Consensus size: 2
18745 TTGATAAAAT
*
18755 TA TA TA TA TA TA TA TA TA TA TA -A AA T- TA TA TA TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
18793 TA TA TA TA TA TA TA TA GA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18821 ATTTAAAGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:18777 original size:26 final size:28
Alignment explanation
Indices: 18748--18804 Score: 100
Period size: 26 Copynumber: 2.1 Consensus size: 28
18738 TGTTTTGTTG
18748 ATAAAATTATATATAT-A-TATATATAT
1 ATAAAATTATATATATAATTATATATAT
18774 ATAAAATTATATATATAATTATATATAT
1 ATAAAATTATATATATAATTATATATAT
18802 ATA
1 ATA
18805 TATAGATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 16 0.55
27 1 0.03
28 12 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAAAATTATATATATAATTATATATAT
Found at i:19581 original size:15 final size:16
Alignment explanation
Indices: 19550--19591 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
19540 CAATTATATG
19550 ATCAC-TATAAAAAAT
1 ATCACTTATAAAAAAT
19565 AT-A-TTATAAAAATAT
1 ATCACTTATAAAAA-AT
19580 ATCACTTATAAA
1 ATCACTTATAAA
19592 TATAAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 9 0.39
15 6 0.26
16 1 0.04
17 7 0.30
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
ATCACTTATAAAAAAT
Found at i:20490 original size:2 final size:2
Alignment explanation
Indices: 20483--20517 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
20473 CATTTTCCTT
*
20483 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20518 TAAAAGCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21325 original size:20 final size:19
Alignment explanation
Indices: 21273--21675 Score: 78
Period size: 19 Copynumber: 21.2 Consensus size: 19
21263 AATAAAAATA
21273 AAAATT-TAAAAAAATTATT
1 AAAATTATAAAAAAATTA-T
* **
21292 CAAATTATTTAAAAATTAT
1 AAAATTATAAAAAAATTAT
21311 AAAATTATAAAAAAATATAT
1 AAAATTATAAAAAAAT-TAT
*
21331 AAAA-TAAAAATAAAATT-T
1 AAAATTATAAA-AAAATTAT
*
21349 CAAAA--AT-ATAAAATCTAT
1 -AAAATTATAAAAAAAT-TAT
*
21367 AAAATT-CAAAAAAATTAT
1 AAAATTATAAAAAAATTAT
* *
21385 GAAAAACTAAAAAATAAAATT-T
1 --AAAA-TTATAAA-AAAATTAT
21407 CAAAAGATTATAAAAATATATT-T
1 --AAA-ATTATAAAAA-A-ATTAT
*
21430 AAAA-T-TCAAAAAA-TAT
1 AAAATTATAAAAAAATTAT
*
21446 AAAAATTTTAAAATAAA--AT
1 -AAAATTATAAAA-AAATTAT
* *
21465 AAAA-TACAAAAAAATGA-
1 AAAATTATAAAAAAATTAT
21482 AAAATCTAT---AAAATTA-
1 AAAAT-TATAAAAAAATTAT
21498 AAAACGCTTATAAAAATACAAATTAT
1 AAAA---TTAT--AAA-A-AAATTAT
*
21524 AAAAATTAT-AAAAATTCTAT
1 -AAAATTATAAAAAAAT-TAT
21544 AAAATTATAAAAAAATGT-T
1 AAAATTATAAAAAAAT-TAT
* *
21563 AAAATCA-AATTGAGAAAATTAC
1 AAAATTATAA---A-AAAATTAT
*
21585 AAAA-GATCAATAAAAATTA-
1 AAAATTAT-AA-AAAAATTAT
* *
21604 AAAATT-TTAAAAAGTTA-
1 AAAATTATAAAAAAATTAT
* *
21621 AAAA-TAT---AAATTTAG
1 AAAATTATAAAAAAATTAT
* *
21636 AAAATAATAAAAAAACTAT
1 AAAATTATAAAAAAATTAT
*
21655 AAAATTA-AAAAAAACTAT
1 AAAATTATAAAAAAATTAT
21673 AAA
1 AAA
21676 CGATAATAAA
Statistics
Matches: 292, Mismatches: 38, Indels: 109
0.67 0.09 0.25
Matches are distributed among these distances:
14 6 0.02
15 5 0.02
16 23 0.08
17 32 0.11
18 37 0.13
19 79 0.27
20 47 0.16
21 12 0.04
22 23 0.08
23 13 0.04
24 5 0.02
25 6 0.02
27 4 0.01
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATTATAAAAAAATTAT
Found at i:21495 original size:124 final size:122
Alignment explanation
Indices: 21242--21555 Score: 294
Period size: 127 Copynumber: 2.6 Consensus size: 122
21232 AAGAAAATAA
**
21242 AAAATTTATAAAAAATTTAAAAATAAAAATAAAAATTTAAAAAAATTATTCAAATTATTTAAAAA
1 AAAA-TTA-AAAAAATTTAAAAATAAAAATAAAAATTTAAAAAAATTATAAAAATTATTTAAAAA
* *
21307 TTATAAAATTATAAAAAAATATATAAAATAAAAATAAAATTTCAAAAATATAAAATCTAT
64 TTATAAAA-TATAAAAAAATATATAAAATAAAAATAAAATTACAAAAAAATAAAATCTAT
* *
21367 AAAATTCAAAAAAATTATGAAAAACTAAAAA-ATAAAATTTCAAAAGATTATAAAAATATATTT-
1 AAAATT-AAAAAAATT-T-AAAAA-TAAAAATA-AAAATTTAAAAAAATTATAAAAAT-TATTTA
* *
21430 AAAATTCA-AAAA-ATATAAAAAT-TTTAAAAT-AAAATAAAA-TACAAAAAAATGAAAAATCTA
60 AAAATT-ATAAAATATAAAAAAATATATAAAATAAAAATAAAATTACAAAAAAAT--AAAATCTA
21490 T
122 T
*** * * * *
21491 AAAATTAAAAACGCTT----ATAAAAATACAAA-TTATAAAAATTATAAAAATTCTAT-AAAATT
1 AAAATTAAAAAAATTTAAAAATAAAAATAAAAATTTAAAAAAATTATAAAAATTATTTAAAAATT
21550 ATAAAA
66 ATAAAA
21556 AAATGTTAAA
Statistics
Matches: 161, Mismatches: 17, Indels: 33
0.76 0.08 0.16
Matches are distributed among these distances:
113 1 0.01
114 13 0.08
115 16 0.10
116 9 0.06
117 2 0.01
122 10 0.06
123 15 0.09
124 32 0.20
125 15 0.09
126 6 0.04
127 36 0.22
128 6 0.04
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (122 bp):
AAAATTAAAAAAATTTAAAAATAAAAATAAAAATTTAAAAAAATTATAAAAATTATTTAAAAATT
ATAAAATATAAAAAAATATATAAAATAAAAATAAAATTACAAAAAAATAAAATCTAT
Found at i:21547 original size:10 final size:9
Alignment explanation
Indices: 21219--21556 Score: 79
Period size: 9 Copynumber: 38.2 Consensus size: 9
21209 TTATTTTATT
*
21219 AATTTTAAA
1 AATTATAAA
21228 AATTA-AGAA
1 AATTATA-AA
21237 AA-TA-AAA
1 AATTATAAA
21244 AATTTATAAAA
1 AA-TTAT-AAA
21255 AATT-T-AA
1 AATTATAAA
21262 AA--ATAAA
1 AATTATAAA
21269 AA-TA-AAA
1 AATTATAAA
* *
21276 ATTTAAAAA
1 AATTATAAA
**
21285 AATTATTCA
1 AATTATAAA
21294 AATTATTTAAA
1 AATTA--TAAA
21305 AATTAT-AA
1 AATTATAAA
21313 AATTATAAAA
1 AATTAT-AAA
*
21323 AAATATATAA
1 AATTATA-AA
* *
21333 AATAAAAATAA
1 AAT-TATA-AA
21344 AATT-TCAAA
1 AATTAT-AAA
21353 AA-TAT-AA
1 AATTATAAA
21360 AATCTAT-AA
1 AAT-TATAAA
*
21369 AATTCAAAAA
1 AATT-ATAAA
21379 AATTATGAAA
1 AATTAT-AAA
*
21389 AA--CTAAA
1 AATTATAAA
21396 AA--AT-AA
1 AATTATAAA
21402 AATT-TCAAA
1 AATTAT-AAA
21411 AGATTATAAA
1 A-ATTATAAA
*
21421 AATATATTTAA
1 AAT-TA-TAAA
21432 AATTCA-AAA
1 AATT-ATAAA
21441 AA-TATAAA
1 AATTATAAA
*
21449 AATT-TTAA
1 AATTATAAA
*
21457 AA-TAAAATA
1 AATTATAA-A
* *
21466 AAATACAAA
1 AATTATAAA
*
21475 AA-AATGAAA
1 AATTAT-AAA
21484 AATCTAT-AA
1 AAT-TATAAA
21493 AATTA-AAA
1 AATTATAAA
*
21501 ACGCTTAT-AA
1 A--ATTATAAA
*
21511 AA--ATACA
1 AATTATAAA
21518 AATTATAAA
1 AATTATAAA
21527 AATTATAAA
1 AATTATAAA
*
21536 AATTCTATAA
1 AATTATA-AA
21546 AATTATAAA
1 AATTATAAA
21555 AA
1 AA
21557 AATGTTAAAA
Statistics
Matches: 248, Mismatches: 33, Indels: 96
0.66 0.09 0.25
Matches are distributed among these distances:
6 7 0.03
7 32 0.13
8 36 0.15
9 90 0.36
10 53 0.21
11 30 0.12
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (9 bp):
AATTATAAA
Done.