Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002293.1 Kokia drynarioides strain JFW-HI SEQ_114325, 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: 19082
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:52 original size:28 final size:31
Alignment explanation
Indices: 5--75 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 31
1 TTAA
* * *
5 TTAATAATAATAATTATT-A-AAACATTTA-
1 TTAATATTAATGATTATTAAGAAAAATTTAT
* *
33 TTACTATTAATGATTTTTAAGAAAAATTTAT
1 TTAATATTAATGATTATTAAGAAAAATTTAT
64 TTAATATTAATG
1 TTAATATTAATG
76 GGGTCATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 14 0.41
29 1 0.03
30 8 0.24
31 11 0.32
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (31 bp):
TTAATATTAATGATTATTAAGAAAAATTTAT
Found at i:754 original size:17 final size:17
Alignment explanation
Indices: 694--756 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
684 CGGACTTTTC
* *
694 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
*
711 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
728 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
745 TAAACTTAAATT
1 TAAATTTAAATT
757 CAATTTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:828 original size:10 final size:10
Alignment explanation
Indices: 801--849 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
791 AACATAATTT
801 TTTTAAAAAA
1 TTTTAAAAAA
* *
811 ATTCAAAAAA
1 TTTTAAAAAA
821 TTTTAAAAATTA
1 TTTTAAAAA--A
833 TTTTAAAAAA
1 TTTTAAAAAA
843 TTTTAAA
1 TTTTAAA
850 TTATTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 23 0.70
12 10 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:850 original size:20 final size:20
Alignment explanation
Indices: 801--860 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 20
791 AACATAATTT
** *
801 TTTTAAAAAAATTCAAAAAA
1 TTTTAAAATTATTTAAAAAA
821 TTTTAAAAATTATTTTAAAAAA
1 TTTT-AAAATTA-TTTAAAAAA
843 TTTT-AAATTATTTAAAAA
1 TTTTAAAATTATTTAAAAA
861 TATAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.23
20 10 0.29
21 5 0.14
22 12 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTTAAAATTATTTAAAAAA
Found at i:870 original size:20 final size:19
Alignment explanation
Indices: 825--876 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
815 AAAAAATTTT
*
825 AAAAATTATTTTAAAAAATT
1 AAAAATTA-TTTAAAAAATA
**
845 TTAAATTATTTAAAAATATA
1 AAAAATTATTTAAAAA-ATA
865 AAAAATATATTT
1 AAAAAT-TATTT
877 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 8 0.32
20 12 0.48
21 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTATTTAAAAAATA
Found at i:1339 original size:18 final size:18
Alignment explanation
Indices: 1316--1351 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1306 TTTATTTCTT
*
1316 TGTTTCTTTAATTTTTTA
1 TGTTTCTATAATTTTTTA
*
1334 TGTTTCTATAGTTTTTTA
1 TGTTTCTATAATTTTTTA
1352 ATATTTAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (18 bp):
TGTTTCTATAATTTTTTA
Found at i:1415 original size:22 final size:22
Alignment explanation
Indices: 1389--1434 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1379 TAGGATTTTA
1389 AAATTTTATAAAATAT-TTAATT
1 AAATTTTA-AAAATATATTAATT
*
1411 AAATTTTAAAATTATATTAATT
1 AAATTTTAAAAATATATTAATT
1433 AA
1 AA
1435 GTACAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATTTTAAAAATATATTAATT
Found at i:6297 original size:24 final size:23
Alignment explanation
Indices: 6243--6297 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
6233 AATTCTAGAT
6243 ATTTT-ATAAAAAAATGATAAAA
1 ATTTTAATAAAAAAATGATAAAA
* * *
6265 ACTTATAATAAAATTAATGTTAAAA
1 A-TTTTAATAAAA-AAATGATAAAA
6290 ATTTTAAT
1 ATTTTAAT
6298 TGAATAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 3 0.12
24 12 0.46
25 10 0.38
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
ATTTTAATAAAAAAATGATAAAA
Found at i:7647 original size:16 final size:15
Alignment explanation
Indices: 7622--7652 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
7612 TTTTATTTTA
7622 TTAAAAATATAAAAT
1 TTAAAAATATAAAAT
7637 TTAACAAATATAAAAT
1 TTAA-AAATATAAAAT
7653 GATTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAAATATAAAAT
Found at i:8195 original size:16 final size:16
Alignment explanation
Indices: 8156--8197 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
8146 AATCTATACA
8156 AATAAATAAAT--TTT
1 AATAAATAAATAATTT
*
8170 AATATA-AAATAATTT
1 AATAAATAAATAATTT
8185 AATAAATAAATAA
1 AATAAATAAATAA
8198 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 5 0.22
15 8 0.35
16 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAAATAAATAATTT
Found at i:9870 original size:16 final size:18
Alignment explanation
Indices: 9831--9864 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9821 TAAGTTTATA
9831 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
9848 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
9865 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:9991 original size:24 final size:22
Alignment explanation
Indices: 9964--10014 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
9954 AAAAAATTTC
9964 AATA-AAAAATATATATAATTATTA
1 AATATAAAAATA-ATATAA-TA-TA
*
9988 AATATTAAAATAATATAATATA
1 AATATAAAAATAATATAATATA
10010 AATAT
1 AATAT
10015 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 7 0.28
23 2 0.08
24 10 0.40
25 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAAAAATAATATAATATA
Found at i:9997 original size:26 final size:22
Alignment explanation
Indices: 9969--10015 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
9959 ATTTCAATAA
9969 AAAATATATATAATTATTAAATATT
1 AAAATA-ATATAA-TA-TAAATATT
9994 AAAATAATATAATATAAATATT
1 AAAATAATATAATATAAATATT
10016 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 6 0.27
25 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATAATATAATATAAATATT
Found at i:10251 original size:5 final size:5
Alignment explanation
Indices: 10241--10275 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
10231 TACTCTCTCC
10241 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT
10276 TCAACCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTCT
Found at i:15786 original size:20 final size:19
Alignment explanation
Indices: 15763--15807 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
15753 AAAAATATAT
15763 TTTTTAT-ATTTTCTTAATAA
1 TTTTTATAATTTT-TTAA-AA
15783 TTTTTATAATTTTTTAAAA
1 TTTTTATAATTTTTTAAAA
15802 TTTTTA
1 TTTTTA
15808 AAAATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.33
20 11 0.46
21 5 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTATAATTTTTTAAAA
Found at i:15798 original size:10 final size:10
Alignment explanation
Indices: 15761--15806 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
15751 TAAAAAATAT
15761 ATTTTTTAT-
1 ATTTTTTATA
15770 ATTTTCTTAATA
1 ATTTT-TT-ATA
15782 A-TTTTTATA
1 ATTTTTTATA
*
15791 ATTTTTTAAA
1 ATTTTTTATA
15801 ATTTTT
1 ATTTTT
15807 AAAAATTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 9 0.28
10 17 0.53
11 5 0.16
12 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:16359 original size:16 final size:16
Alignment explanation
Indices: 16338--16370 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16328 ATCTATTTTT
16338 TAAAAAATATAAAATC
1 TAAAAAATATAAAATC
*
16354 TAAAAAATATACAATC
1 TAAAAAATATAAAATC
16370 T
1 T
16371 CGAAGTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAATATAAAATC
Found at i:18677 original size:17 final size:17
Alignment explanation
Indices: 18655--18741 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
18645 CATACTCCCT
18655 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
18672 TTAAATTT-GTTTAAAA
1 TTAAATTTATTTTAAAA
*
18688 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
* **
18706 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
* *
18723 TTAAAGTTATTTTCAAA
1 TTAAATTTATTTTAAAA
18740 TT
1 TT
18742 TAAAATTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
16 7 0.12
17 45 0.78
18 6 0.10
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:18692 original size:34 final size:34
Alignment explanation
Indices: 18654--18751 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
18644 TCATACTCCC
*
18654 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAAATTAAATTTAATTT-AAA
* *
18688 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAAATTAAATTTAATTTAAA
* *
18722 TTTAAAGTTATTTTCAAATTTAAAATTTAA
1 TTTAAATTTATTTT-AAAATT-AAATTTAA
18752 AATAAAAACC
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 40 0.70
35 9 0.16
36 8 0.14
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAATTAAATTTAATTTAAA
Found at i:18702 original size:11 final size:11
Alignment explanation
Indices: 18688--18743 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
18678 TTGTTTAAAA
18688 TTTAAATTTAT
1 TTTAAATTTAT
*
18699 TTTAAATTTAAA
1 TTTAAATTT-AT
*
18711 TTT-AATTTAAG
1 TTTAAATTT-AT
*
18722 TTTAAAGTTAT
1 TTTAAATTTAT
18733 TTTCAAATTTA
1 TTT-AAATTTA
18744 AAATTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:18707 original size:7 final size:6
Alignment explanation
Indices: 18654--18752 Score: 66
Period size: 6 Copynumber: 17.0 Consensus size: 6
18644 TCATACTCCC
* * * *
18654 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
18699 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA GTT-AT TTTCAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTT-AAA
18747 TTTAAA
1 TTTAAA
18753 ATAAAAACCT
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
4 3 0.04
5 16 0.23
6 38 0.54
7 13 0.19
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Done.