Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1900
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: 21987
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:1626 original size:20 final size:21
Alignment explanation
Indices: 1600--1655 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1590 TATAAACAGT
*
1600 AAATGTATCGATACATAAGTG
1 AAATGTATCGATACATAACTG
* **
1621 -AATGTATAGATACATTTCTG
1 AAATGTATCGATACATAACTG
1641 AAATGTATCGATACA
1 AAATGTATCGATACA
1656 AGACCATGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (21 bp):
AAATGTATCGATACATAACTG
Found at i:1725 original size:20 final size:20
Alignment explanation
Indices: 1697--1744 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1687 AAAGAAAATG
*
1697 TATCAATATATTTTTCATTA
1 TATCGATATATTTTTCATTA
* *
1717 TATCGATATATTTTTTATTG
1 TATCGATATATTTTTCATTA
1737 TATCGATA
1 TATCGATA
1745 CATTCTGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.54
Consensus pattern (20 bp):
TATCGATATATTTTTCATTA
Found at i:8447 original size:20 final size:19
Alignment explanation
Indices: 8377--8454 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 19
8367 TTAAAAACAC
* *
8377 AGAATGTATCGATACAGTG
1 AGAATGTATCGATACATTT
8396 AGAAATGTATCGATACAATTGT
1 AG-AATGTATCGATAC-ATT-T
*
8418 AAGCATGTATCGATACATTT
1 -AGAATGTATCGATACATTT
*
8438 AGTAATGTATCCATACA
1 AG-AATGTATCGATACA
8455 ATTTCTTGGC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 4 0.08
20 26 0.53
21 5 0.10
22 12 0.24
23 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (19 bp):
AGAATGTATCGATACATTT
Found at i:9663 original size:26 final size:26
Alignment explanation
Indices: 9611--9663 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
9601 AAACTGTTTT
**
9611 TAAAAATCACAAAATGATATTTTGTG
1 TAAAAATCACAAAATGATATTCCGTG
9637 TAAAAATCACAAAATGATATTCCGTG
1 TAAAAATCACAAAATGATATTCCGTG
9663 T
1 T
9664 CATTATCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (26 bp):
TAAAAATCACAAAATGATATTCCGTG
Found at i:17540 original size:55 final size:54
Alignment explanation
Indices: 17417--17540 Score: 119
Period size: 55 Copynumber: 2.2 Consensus size: 54
17407 TAAATTATTA
* * * *
17417 AAATATAAAAATTTATATAAATTTATAATACTTTTAACATATCAAAATTAAAAATT
1 AAATATAAACATGTA-A-AAATTTATAATACTTTTAAAACATCAAAATTAAAAATT
*
17473 AAATTATTAACATGTAAAAATTTATAATA-TTTTAAAACA-CAAAAATAATAAAAATCT
1 AAA-TATAAACATGTAAAAATTTATAATACTTTTAAAACATC-AAAAT--TAAAAAT-T
17530 AAA-ATAAACAT
1 AAATATAAACAT
17541 ACAAAATTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
53 1 0.02
54 13 0.23
55 19 0.33
56 11 0.19
57 13 0.23
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (54 bp):
AAATATAAACATGTAAAAATTTATAATACTTTTAAAACATCAAAATTAAAAATT
Found at i:18381 original size:43 final size:43
Alignment explanation
Indices: 18318--18400 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
18308 ACAAGATTAA
*
18318 TAAAATGTGTGGTGTGGAATACTGGGATAGTACTTGTTTTTTC
1 TAAAATGTGTGGTGTGGAATACTGAGATAGTACTTGTTTTTTC
*
18361 TAAAATGTGTGGTGTTGAATACTGAGATAGTACTTGTTTT
1 TAAAATGTGTGGTGTGGAATACTGAGATAGTACTTGTTTT
18401 AGCCGACAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (43 bp):
TAAAATGTGTGGTGTGGAATACTGAGATAGTACTTGTTTTTTC
Found at i:19692 original size:17 final size:17
Alignment explanation
Indices: 19653--19694 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
19643 TAAATTACTT
*
19653 ATAAACTAACAAAAAAA
1 ATAAATTAACAAAAAAA
*
19670 AT-AATTAACAGAAAAA
1 ATAAATTAACAAAAAAA
19686 ATAAATTAA
1 ATAAATTAA
19695 GACATATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.19
Consensus pattern (17 bp):
ATAAATTAACAAAAAAA
Found at i:20727 original size:27 final size:27
Alignment explanation
Indices: 20681--20741 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
20671 ATAAATATTT
* *
20681 AATAATTTTAAATTTTAAA-TATTAAATA
1 AATAA-TTTAAATATAAAATTATTAAA-A
20709 AATAATTTAAATATAAAATTATTAAAA
1 AATAATTTAAATATAAAATTATTAAAA
20736 AATAAT
1 AATAAT
20742 AAATTAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 18 0.60
28 12 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATAATTTAAATATAAAATTATTAAAA
Done.