Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014496.1 Kokia drynarioides strain JFW-HI SEQ_129535, whole genome shotgun sequence
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: 55163
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7887 original size:22 final size:22
Alignment explanation
Indices: 7862--7908 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
7852 TTTAAAAACA
7862 TTTG-AGGAGATTAATGAGAATT
1 TTTGTAGG-GATTAATGAGAATT
* *
7884 TTTGTAGGGCTTAATTAGAATT
1 TTTGTAGGGATTAATGAGAATT
7906 TTT
1 TTT
7909 ATAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (22 bp):
TTTGTAGGGATTAATGAGAATT
Found at i:23036 original size:3 final size:3
Alignment explanation
Indices: 23023--23058 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
23013 AGTAGCTAAA
23023 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23059 AAGTAGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28492 original size:2 final size:2
Alignment explanation
Indices: 28487--28518 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28477 ATATCACAAC
28487 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28519 TATATACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:33539 original size:2 final size:2
Alignment explanation
Indices: 33532--33565 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33522 AGCATACTCC
33532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33566 GGGAGATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33647 original size:17 final size:17
Alignment explanation
Indices: 33617--33653 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
33607 AAGTAGTTAC
*
33617 AAGAATATGAAAGATTA
1 AAGAAGATGAAAGATTA
*
33634 AAGAAGATGGAAGATTA
1 AAGAAGATGAAAGATTA
33651 AAG
1 AAG
33654 GTTAAGGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAGATTA
Found at i:34163 original size:3 final size:3
Alignment explanation
Indices: 34155--34189 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
34145 ACTTGGATAT
34155 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
34190 TTCGTAGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:37629 original size:16 final size:18
Alignment explanation
Indices: 37599--37651 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
37589 AAAAAAATTT
* *
37599 AAATTTAATTTAATTATA
1 AAATATAATATAATTATA
37617 AAATAT-ATA-AATTATA
1 AAATATAATATAATTATA
*
37633 AATTATAATATAATTATA
1 AAATATAATATAATTATA
37651 A
1 A
37652 TATTTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 12 0.40
17 5 0.17
18 13 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATAATATAATTATA
Done.