Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001913.1 Kokia drynarioides strain JFW-HI SEQ_113706, 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: 29987
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:176 original size:30 final size:30
Alignment explanation
Indices: 142--236 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
132 AAATGGTACA
*
142 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
* * * * *
172 AAAT-AAT-TGTGTGTGGATACCATTTTGGT
1 AAATAAATATATATTTTG-TACCATTTTAGT
*
201 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
231 AAATAA
1 AAATAA
237 CCTATTTTGG
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
28 5 0.10
29 17 0.34
30 23 0.46
31 5 0.10
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACCATTTTAGT
Found at i:1464 original size:43 final size:43
Alignment explanation
Indices: 1382--1466 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
1372 ATTAACATGT
* *
1382 TAAATTATATTACTTGACTTGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
*
1425 TAAATTATATTACTTTACTCT-TATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACT-TGTATTAATATGCTTG-CATGTTA
1467 TTAATTGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.08
43 33 0.89
44 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
Found at i:2098 original size:45 final size:45
Alignment explanation
Indices: 2033--2168 Score: 209
Period size: 45 Copynumber: 3.0 Consensus size: 45
2023 CCCTTACTCA
2033 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* *
2078 TCAAGCCAAGGATATTAGCCTTAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * ** *
2123 TTAAGCCAAGGATGTCAGGTTGAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
2168 T
1 T
2169 TTACTCCTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:2460 original size:28 final size:28
Alignment explanation
Indices: 2424--2497 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
2414 CCTTAAACCC
*
2424 TAAAA-CCTAAACCTAAAACCTTAAACT
1 TAAAACCCTAAACCTAAAACCCTAAACT
**
2451 TGGAACCCTAAACCCT-AAACCCTAAACT
1 TAAAACCCTAAA-CCTAAAACCCTAAACT
*
2479 TAAAACCTTAAACCATAAA
1 TAAAACCCTAAACC-TAAA
2498 TCCTATACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.14
28 27 0.73
29 5 0.14
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.20
Consensus pattern (28 bp):
TAAAACCCTAAACCTAAAACCCTAAACT
Found at i:2491 original size:7 final size:7
Alignment explanation
Indices: 2412--2497 Score: 61
Period size: 7 Copynumber: 12.3 Consensus size: 7
2402 TAAATTTCAT
2412 AACCTTA
1 AACCTTA
*
2419 AACCCTAA
1 AA-CCTTA
2427 AACC-TA
1 AACCTTA
*
2433 AACCTAA
1 AACCTTA
2440 AACCTTA
1 AACCTTA
*
2447 AA-CTTGG
1 AACCTT-A
*
2454 AACCCTA
1 AACCTTA
*
2461 AACCCTA
1 AACCTTA
*
2468 AACCCTA
1 AACCTTA
2475 AA-CTTAA
1 AACCTT-A
2482 AACCTTA
1 AACCTTA
*
2489 AACCATA
1 AACCTTA
2496 AA
1 AA
2498 TCCTATACAT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
6 10 0.16
7 43 0.67
8 11 0.17
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (7 bp):
AACCTTA
Found at i:2512 original size:28 final size:28
Alignment explanation
Indices: 2424--2512 Score: 65
Period size: 28 Copynumber: 3.2 Consensus size: 28
2414 CCTTAAACCC
* *
2424 TAAAA-CCTAAACC-TAAAACCTTAAACT
1 TAAAACCCTAAACCAT-AAACCCTAAACA
** * *
2451 TGGAACCCTAAACCCTAAACCCTAAACT
1 TAAAACCCTAAACCATAAACCCTAAACA
* * *
2479 TAAAACCTTAAACCATAAATCCTATACA
1 TAAAACCCTAAACCATAAACCCTAAACA
*
2507 TGAAAC
1 TAAAAC
2513 ATTTTTAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
27 3 0.06
28 45 0.92
29 1 0.02
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.21
Consensus pattern (28 bp):
TAAAACCCTAAACCATAAACCCTAAACA
Found at i:5514 original size:4 final size:4
Alignment explanation
Indices: 5492--5556 Score: 64
Period size: 4 Copynumber: 16.5 Consensus size: 4
5482 AAACACATTA
* * *
5492 TCTT TCTCT TC-T T-TT TCTT TCTT TCTT TCTT TCTT ACCTT TCTC TCCT
1 TCTT TCT-T TCTT TCTT TCTT TCTT TCTT TCTT TCTT -TCTT TCTT TCTT
5540 TC-T TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TC
5557 CTATTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
3 7 0.14
4 38 0.75
5 6 0.12
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.68
Consensus pattern (4 bp):
TCTT
Found at i:5666 original size:17 final size:17
Alignment explanation
Indices: 5644--5678 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5634 TTTACAATAA
*
5644 AAATAAAATATACACAC
1 AAATAAAATAAACACAC
5661 AAATAAAATAAACACAC
1 AAATAAAATAAACACAC
5678 A
1 A
5679 CACTGCACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (17 bp):
AAATAAAATAAACACAC
Found at i:7444 original size:3 final size:3
Alignment explanation
Indices: 7436--7461 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7426 ATTAGTTATG
7436 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
7462 TTATATTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:19713 original size:24 final size:24
Alignment explanation
Indices: 19627--19701 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
19617 AGAAATAATC
* * *
19627 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTTTATTTATTTG
*
19651 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTTTATTTATTTG
19675 TTTCAATTAAACTTTATTTATTTG
1 TTTCAATTAAACTTTATTTATTTG
19699 TTT
1 TTT
19702 GAGTCAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTTTATTTATTTG
Found at i:21665 original size:24 final size:24
Alignment explanation
Indices: 21637--21699 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
21627 AGAAATAATC
21637 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
21661 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
21685 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
21700 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:23669 original size:22 final size:22
Alignment explanation
Indices: 23644--23715 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
23634 GCATATTTTG
23644 TCCATCACATGGTAAATTATCA
1 TCCATCACATGGTAAATTATCA
* * *
23666 TCCATGATTCCAT-GTATATT-TCG
1 TCCATCA---CATGGTAAATTATCA
*
23689 TCCATCACATGATAAATTATCA
1 TCCATCACATGGTAAATTATCA
23711 TCCAT
1 TCCAT
23716 TTAAATTTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
20 3 0.08
21 5 0.13
22 13 0.34
23 8 0.21
24 6 0.16
25 3 0.08
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (22 bp):
TCCATCACATGGTAAATTATCA
Found at i:23692 original size:45 final size:45
Alignment explanation
Indices: 23626--23715 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
23616 TTAAAAAATG
* *
23626 GATTCCATGCATATTTTGTCCATCACATGGTAAATTATCATCCAT
1 GATTCCATGCATATTTCGTCCATCACATGATAAATTATCATCCAT
*
23671 GATTCCATGTATATTTCGTCCATCACATGATAAATTATCATCCAT
1 GATTCCATGCATATTTCGTCCATCACATGATAAATTATCATCCAT
23716 TTAAATTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (45 bp):
GATTCCATGCATATTTCGTCCATCACATGATAAATTATCATCCAT
Found at i:23970 original size:40 final size:38
Alignment explanation
Indices: 23926--24031 Score: 110
Period size: 38 Copynumber: 2.7 Consensus size: 38
23916 AGCACCAAGC
*
23926 CTGCTAGGCAGTAAGCTCGATAAATACA-TCGACACTAAG
1 CTGCTAGGCACTAAGC-CGATAAATACATTCGA-ACTAAG
*
23965 TCTGCTAGGCACTAAGCCTGAT-AA-ACATTGGAACTAAG
1 -CTGCTAGGCACTAAGCC-GATAAATACATTCGAACTAAG
*
24003 CTTGCTAGGCATTAAGCCCGATAAATACA
1 C-TGCTAGGCACTAAG-CCGATAAATACA
24032 CTGGCAAGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
37 1 0.02
38 25 0.44
39 10 0.18
40 21 0.37
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (38 bp):
CTGCTAGGCACTAAGCCGATAAATACATTCGAACTAAG
Found at i:24010 original size:38 final size:37
Alignment explanation
Indices: 23969--24107 Score: 134
Period size: 38 Copynumber: 3.6 Consensus size: 37
23959 ACTAAGTCTG
* * *
23969 CTAGGCACTAAGCCTGATAAACATTGGAACTAAGCTTG
1 CTAGGCACTAAGCCCGATAAACATTGGAA-TAAGCCTA
* * *
24007 CTAGGCATTAAGCCCGATAAATACACTGGCAAGAAGCCTA
1 CTAGGCACTAAGCCCGAT-AA-ACATTGG-AATAAGCCTA
* * * *
24047 TTAGGCACTAAACCTGATAAACATTGGCATGAAGCCTA
1 CTAGGCACTAAGCCCGATAAACATTGGAAT-AAGCCTA
*
24085 CTAGGCACTACGCCCGATAAACA
1 CTAGGCACTAAGCCCGATAAACA
24108 CCGGGGAATT
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
37 1 0.01
38 48 0.60
39 4 0.05
40 25 0.31
41 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (37 bp):
CTAGGCACTAAGCCCGATAAACATTGGAATAAGCCTA
Found at i:24031 original size:78 final size:78
Alignment explanation
Indices: 23922--24105 Score: 210
Period size: 78 Copynumber: 2.4 Consensus size: 78
23912 CACCAGCACC
* * ** * * *
23922 AAGCCTGCTAGGCAGTAAGCTCGATAAATACA-TCGACACTAAGTCTGCTAGGCACTAAGCCTGA
1 AAGCCTGCTAGGCACTAAGCCCGATAAATACACT-GACAAGAAGCCTACTAGGCACTAAACCTGA
23986 TAAACATTGGAACT-
65 TAAACATTGGAA-TG
* * * *
24000 AAGCTTGCTAGGCATTAAGCCCGATAAATACACTGGCAAGAAGCCTATTAGGCACTAAACCTGAT
1 AAGCCTGCTAGGCACTAAGCCCGATAAATACACTGACAAGAAGCCTACTAGGCACTAAACCTGAT
*
24065 AAACATTGGCATG
66 AAACATTGGAATG
* *
24078 AAGCCTACTAGGCACTACGCCCGATAAA
1 AAGCCTGCTAGGCACTAAGCCCGATAAA
24106 CACCGGGGAA
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
77 1 0.01
78 87 0.98
79 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (78 bp):
AAGCCTGCTAGGCACTAAGCCCGATAAATACACTGACAAGAAGCCTACTAGGCACTAAACCTGAT
AAACATTGGAATG
Done.