Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold752
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: 19056
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3813 original size:22 final size:22
Alignment explanation
Indices: 3779--3836 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
3769 TTTTTATTTT
*
3779 ATGTAATATTTTATTAATTAAAA
1 ATGTAA-ATTTTATAAATTAAAA
*
3802 ATGTAAATTTTAATAAATTTAAA
1 ATGTAAATTTT-ATAAATTAAAA
3825 A--TAAATTTTATA
1 ATGTAAATTTTATA
3837 TTTTGATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.09
21 8 0.25
22 5 0.16
23 16 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
ATGTAAATTTTATAAATTAAAA
Found at i:3893 original size:57 final size:56
Alignment explanation
Indices: 3821--3936 Score: 214
Period size: 57 Copynumber: 2.1 Consensus size: 56
3811 TTAATAAATT
*
3821 TAAAATAAATTTTATATTTTGATAATTTAAAATTTTTGTATACGAAGTGTCAACTA
1 TAAAATAAATTTTATATTTTGATAATTTAAAATTTTTGTATACAAAGTGTCAACTA
3877 TAAAAGTAAATTTTATATTTTGATAATTTAAAATTTTTGTATACAAAGTGTCAACTA
1 TAAAA-TAAATTTTATATTTTGATAATTTAAAATTTTTGTATACAAAGTGTCAACTA
3934 TAA
1 TAA
3937 GTAAATATAT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 5 0.09
57 53 0.91
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (56 bp):
TAAAATAAATTTTATATTTTGATAATTTAAAATTTTTGTATACAAAGTGTCAACTA
Found at i:7486 original size:2 final size:2
Alignment explanation
Indices: 7479--7534 Score: 60
Period size: 2 Copynumber: 27.5 Consensus size: 2
7469 TAAAACTGCT
*
7479 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TGA CTA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA
* *
7522 TA TG TA TG TA TA T
1 TA TA TA TA TA TA T
7535 CATCACACGC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 1 0.02
2 41 0.91
3 2 0.04
4 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8886 original size:17 final size:18
Alignment explanation
Indices: 8849--8886 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
8839 TGCTTCTTAC
8849 TTTCATAATCTTTAGATT
1 TTTCATAATCTTTAGATT
* *
8867 TTTCTTAATTTTTA-ATT
1 TTTCATAATCTTTAGATT
8884 TTT
1 TTT
8887 ATATAATAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTCATAATCTTTAGATT
Found at i:8893 original size:18 final size:19
Alignment explanation
Indices: 8853--8893 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
8843 TCTTACTTTC
*
8853 ATAATCTTTAGATTTTTCT
1 ATAATCTTTAGATTTTTAT
*
8872 -TAATTTTTA-ATTTTTAT
1 ATAATCTTTAGATTTTTAT
8889 ATAAT
1 ATAAT
8894 AGCATTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
ATAATCTTTAGATTTTTAT
Found at i:13564 original size:32 final size:33
Alignment explanation
Indices: 13528--13611 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
13518 TTAATGACCG
*
13528 TTAAATTTATAAATAATTATATCT-AATATTTA
1 TTAAATTTATAAATAATTATATCTAAATACTTA
* * *
13560 TTAAATTTATGAATAATTTTATTTAAATACTTA
1 TTAAATTTATAAATAATTATATCTAAATACTTA
13593 TTAAATTTATAAATAATTA
1 TTAAATTTATAAATAATTA
13612 CATATAATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
32 21 0.47
33 24 0.53
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (33 bp):
TTAAATTTATAAATAATTATATCTAAATACTTA
Found at i:13650 original size:30 final size:30
Alignment explanation
Indices: 13607--13681 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
13597 ATTTATAAAT
13607 AATTACATATAATTCATCAAATGTACAATCA
1 AATTA-ATATAATTCATCAAATGTACAATCA
* * *
13638 AATTAATCTAATTCATCAAATTTATAATCA
1 AATTAATATAATTCATCAAATGTACAATCA
*
13668 ATATTAATTTAATT
1 A-ATTAATATAATT
13682 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 23 0.59
31 16 0.41
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (30 bp):
AATTAATATAATTCATCAAATGTACAATCA
Found at i:13964 original size:2 final size:2
Alignment explanation
Indices: 13957--13992 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13947 TACTTTCAAG
13957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13993 GGGTAGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.