Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012308.1 Kokia drynarioides strain JFW-HI SEQ_127309, 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: 19846
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:55 original size:3 final size:3
Alignment explanation
Indices: 1--44 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
45 TTGGATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3412 original size:18 final size:19
Alignment explanation
Indices: 3369--3416 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
3359 AGTCATTTTA
3369 AAAAAAAGAAAGAAAGAAG
1 AAAAAAAGAAAGAAAGAAG
** *
3388 AGGAAAAGAGA-AAAGAAG
1 AAAAAAAGAAAGAAAGAAG
3406 AAAAAAAGAAA
1 AAAAAAAGAAA
3417 TATATGCTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAGAAAGAAG
Found at i:11960 original size:20 final size:20
Alignment explanation
Indices: 11938--11976 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
11928 ATTTAATTTT
*
11938 TTTTATTTTT-TTTCTTCTC
1 TTTTATTTTTCTCTCTTCTC
11957 TTTTATTTTTCTCTCTTCTC
1 TTTTATTTTTCTCTCTTCTC
11977 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTTTCTCTCTTCTC
Found at i:14718 original size:22 final size:22
Alignment explanation
Indices: 14693--14750 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
14683 TGTTTAATCA
14693 TGTTTAATCGATGTTGA-TATTT
1 TGTTTAATCGATGTT-ACTATTT
* *
14715 TGTTTAATCGATATTACTGTTT
1 TGTTTAATCGATGTTACTATTT
14737 TGTTTAATCG-TGTT
1 TGTTTAATCGATGTT
14751 TAATCGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (22 bp):
TGTTTAATCGATGTTACTATTT
Found at i:14773 original size:31 final size:32
Alignment explanation
Indices: 14715--14777 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
14705 GTTGATATTT
14715 TGTTTAATCGATATTACTGTTTTGTTTAATCG
1 TGTTTAATCGATATTACTGTTTTGTTTAATCG
*
14747 TGTTTAATCGATATTGCTG-TTTGTTTAATCG
1 TGTTTAATCGATATTACTGTTTTGTTTAATCG
14778 ATGAGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (32 bp):
TGTTTAATCGATATTACTGTTTTGTTTAATCG
Found at i:18798 original size:45 final size:47
Alignment explanation
Indices: 18729--18862 Score: 119
Period size: 48 Copynumber: 2.9 Consensus size: 47
18719 CTGCCAGTAG
* * * ** * *
18729 CCTCACCACCTTTACTATCGGCTTCCTCACCATCATCTCC-C-TCAC
1 CCTCACCACCCTTACTACCAGCTTCCAAACCATCACCACCTCATCAC
*
18774 CCTCACCACCCTTACTACCAGCTTCCAAACCCTCACCACCTTCATCAC
1 CCTCACCACCCTTACTACCAGCTTCCAAACCATCACCACC-TCATCAC
* * * * * *
18822 CCTCACCACCCTTATTGCTAGCATCTAAACCCTCACCACCT
1 CCTCACCACCCTTACTACCAGCTTCCAAACCATCACCACCT
18863 TTACTGCCAA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
45 32 0.44
47 2 0.03
48 39 0.53
ACGTcount: A:0.22, C:0.49, G:0.04, T:0.25
Consensus pattern (47 bp):
CCTCACCACCCTTACTACCAGCTTCCAAACCATCACCACCTCATCAC
Found at i:18829 original size:48 final size:48
Alignment explanation
Indices: 18770--18863 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
18760 ATCATCTCCC
*
18770 TCACCCTCACCACCCTTACTACCAGCTTCCAAACCCTCACCACCTTCA
1 TCACCCTCACCACCCTTACTACCAGCATCCAAACCCTCACCACCTTCA
* * * *
18818 TCACCCTCACCACCCTTATTGCTAGCATCTAAACCCTCACCACCTT
1 TCACCCTCACCACCCTTACTACCAGCATCCAAACCCTCACCACCTT
18864 TACTGCCAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.24, C:0.49, G:0.03, T:0.23
Consensus pattern (48 bp):
TCACCCTCACCACCCTTACTACCAGCATCCAAACCCTCACCACCTTCA
Found at i:19636 original size:12 final size:12
Alignment explanation
Indices: 19619--19684 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
19609 TGATTATGAA
19619 ACATACATTTAC
1 ACATACATTTAC
*
19631 ACATACAGTT--
1 ACATACATTTAC
*
19641 GC-TACATTTAC
1 ACATACATTTAC
*
19652 ACATTA-ATTATGAA
1 ACA-TACATT-T-AC
19666 ACATACATTTAC
1 ACATACATTTAC
19678 ACATACA
1 ACATACA
19685 ATTGCTACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
9 6 0.15
10 1 0.02
11 1 0.02
12 20 0.49
13 6 0.15
14 7 0.17
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (12 bp):
ACATACATTTAC
Found at i:19648 original size:21 final size:21
Alignment explanation
Indices: 19622--19697 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 21
19612 TTATGAAACA
*
19622 TACATTTACACATACAGTTGC
1 TACATTTACACATACAATTGC
*
19643 TACATTTACACATTA-ATTATGAAAC
1 TACATTTACACA-TACAAT-TG---C
19668 ATACATTTACACATACAATTGC
1 -TACATTTACACATACAATTGC
19690 TACATTTA
1 TACATTTA
19698 ATGTACTGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
21 22 0.48
22 5 0.11
25 5 0.11
26 14 0.30
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (21 bp):
TACATTTACACATACAATTGC
Found at i:19673 original size:26 final size:27
Alignment explanation
Indices: 19611--19681 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 27
19601 AATCATATTG
19611 ATTATGAAACATACATTTACACA-TAC
1 ATTATGAAACATACATTTACACATTAC
*
19637 AGT-TG---C-TACATTTACACATTA-
1 ATTATGAAACATACATTTACACATTAC
19658 ATTATGAAACATACATTTACACAT
1 ATTATGAAACATACATTTACACAT
19682 ACAATTGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
21 14 0.38
22 5 0.14
25 3 0.08
26 15 0.41
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (27 bp):
ATTATGAAACATACATTTACACATTAC
Done.