Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold719
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: 22031
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:2401 original size:1 final size:1
Alignment explanation
Indices: 2395--2453 Score: 118
Period size: 1 Copynumber: 59.0 Consensus size: 1
2385 GTTAAATCCG
2395 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2454 TTTTTCTGGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:10900 original size:2 final size:2
Alignment explanation
Indices: 10895--10921 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10885 TATATATATA
10895 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
10922 ATTTAAGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11244 original size:9 final size:9
Alignment explanation
Indices: 11230--11261 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
11220 TCCCAAGAAT
11230 TTTTTATTA
1 TTTTTATTA
11239 TTTTTATTA
1 TTTTTATTA
*
11248 TTATTATTA
1 TTTTTATTA
11257 TTTTT
1 TTTTT
11262 TATAACTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTATTA
Found at i:11861 original size:2 final size:2
Alignment explanation
Indices: 11856--11880 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11846 TTATATAAAA
11856 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11881 ATTAATAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12500 original size:4 final size:4
Alignment explanation
Indices: 12491--12525 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
12481 AGATTTCTTT
12491 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
12526 TATATATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:13141 original size:16 final size:17
Alignment explanation
Indices: 13116--13151 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
13106 ATAAATATGT
13116 TTTTTATTAATTGTTTA
1 TTTTTATTAATTGTTTA
*
13133 TTTTT-TTAATTTTTTA
1 TTTTTATTAATTGTTTA
13149 TTT
1 TTT
13152 AAAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTATTAATTGTTTA
Found at i:18780 original size:22 final size:22
Alignment explanation
Indices: 18755--18798 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18745 TTAAAAATAA
*
18755 ATTAAATTTAATTAATTTAAAT
1 ATTAAATTAAATTAATTTAAAT
*
18777 ATTAAATTAAATTGATTTAAAT
1 ATTAAATTAAATTAATTTAAAT
18799 TTATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTAAATTAAATTAATTTAAAT
Found at i:18863 original size:9 final size:9
Alignment explanation
Indices: 18849--18892 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
18839 TTAAAATAAT
18849 TTAATCTAA
1 TTAATCTAA
18858 TTAATCTAA
1 TTAATCTAA
* *
18867 TTCATTTAA
1 TTAATCTAA
18876 TTAAT-TAA
1 TTAATCTAA
*
18884 TTGATCTAA
1 TTAATCTAA
18893 AAATTTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (9 bp):
TTAATCTAA
Found at i:20221 original size:11 final size:11
Alignment explanation
Indices: 20205--20229 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20195 AAAGATTTTG
20205 TTAAATACCTT
1 TTAAATACCTT
20216 TTAAATACCTT
1 TTAAATACCTT
20227 TTA
1 TTA
20230 CTTTCTCCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATACCTT
Found at i:20477 original size:3 final size:3
Alignment explanation
Indices: 20471--20495 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20461 TTTTATTTTC
20471 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
20496 AAAGGAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:20701 original size:2 final size:2
Alignment explanation
Indices: 20689--20762 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
20679 CAACATCCTC
* *
20689 CT CT AT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20731 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20763 ATATATATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.01, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:20767 original size:2 final size:2
Alignment explanation
Indices: 20762--20788 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20752 TCTCTCTCTC
20762 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20789 TTCAGTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21449 original size:3 final size:3
Alignment explanation
Indices: 21441--21466 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21431 GGTTAGACTT
21441 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
21467 TGTTATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.