Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007803.1 Kokia drynarioides strain JFW-HI SEQ_122438, 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: 8482
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:614 original size:17 final size:17
Alignment explanation
Indices: 589--677 Score: 81
Period size: 17 Copynumber: 5.1 Consensus size: 17
579 GTCTTTTTAA
* **
589 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
606 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
623 TTAAA-TTTAAAGGAAAT
1 TTAAATTTTAAA-TAAAT
*
640 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
*
659 TTAAATTTAAAATAAAT
1 TTAAATTTTAAATAAAT
676 TT
1 TT
678 GAATCAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.08
17 35 0.58
18 5 0.08
19 14 0.23
20 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:618 original size:6 final size:6
Alignment explanation
Indices: 604--669 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
594 TTTTAAATCC
* **
604 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GGAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
**
651 AGATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
670 ATAAATTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
5 7 0.15
6 36 0.77
7 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:660 original size:19 final size:18
Alignment explanation
Indices: 604--677 Score: 91
Period size: 17 Copynumber: 4.2 Consensus size: 18
594 TTTTAAATCC
* *
604 ATTTAAATTT-TAATTAA
1 ATTTAAATTTAAAAGTAA
*
621 ATTTAAATTT-AAAGGAA
1 ATTTAAATTTAAAAGTAA
638 ATTTAAATTTAAAAGATAA
1 ATTTAAATTTAAAAG-TAA
657 ATTTAAATTTAAAA-TAA
1 ATTTAAATTTAAAAGTAA
674 ATTT
1 ATTT
678 GAATCAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
17 31 0.61
18 4 0.08
19 16 0.31
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTTAAATTTAAAAGTAA
Found at i:1512 original size:3 final size:3
Alignment explanation
Indices: 1504--1544 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1494 GCATTAATAC
1504 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1545 ACTATTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2462 original size:17 final size:17
Alignment explanation
Indices: 2440--2499 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
2430 ATTAATTTTA
2440 ATTAAAAAAATTTAAAT
1 ATTAAAAAAATTTAAAT
*
2457 ATTAAAAAAGAGTATAAAAT
1 ATTAAAAAA-A-T-TTAAAT
*
2477 ATTAAAAATAATATAAA-
1 ATTAAAAA-AATTTAAAT
2494 ATTAAA
1 ATTAAA
2500 TGAATTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 15 0.42
18 4 0.11
19 2 0.06
20 14 0.39
21 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
ATTAAAAAAATTTAAAT
Found at i:2491 original size:19 final size:18
Alignment explanation
Indices: 2440--2495 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 18
2430 ATTAATTTTA
*
2440 ATTAAAAAAAT-TTAAAT
1 ATTAAAAAAATATAAAAT
2457 ATTAAAAAAGAGTATAAAAT
1 ATTAAAAAA-A-TATAAAAT
2477 ATTAAAAATAATATAAAAT
1 ATTAAAAA-AATATAAAAT
2496 TAAATGAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 9 0.26
18 1 0.03
19 9 0.26
20 14 0.41
21 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
ATTAAAAAAATATAAAAT
Found at i:2772 original size:14 final size:15
Alignment explanation
Indices: 2736--2777 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
2726 TTAGATTATT
2736 ATTTTTTATATGCCTCA
1 ATTTTTTATAT--CTCA
*
2753 AGTTTTTATAT-TCA
1 ATTTTTTATATCTCA
2767 ATTTTTTATAT
1 ATTTTTTATAT
2778 ACCTCTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 13 0.57
17 10 0.43
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.60
Consensus pattern (15 bp):
ATTTTTTATATCTCA
Found at i:3226 original size:23 final size:21
Alignment explanation
Indices: 3178--3218 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
3168 ATCATCTTTT
3178 AATTAATAAATAT-ATTTTATA
1 AATT-ATAAATATAATTTTATA
3199 AATTATAAATATAATATTTA
1 AATTATAAATATAAT-TTTA
3219 ATGAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTATAAATATAATTTTATA
Done.