Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011039.1 Kokia drynarioides strain JFW-HI SEQ_126010, 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: 119344
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:14680 original size:7 final size:7
Alignment explanation
Indices: 14668--14693 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
14658 AAAGCAGTAC
14668 TGCACTG
1 TGCACTG
14675 TGCACTG
1 TGCACTG
14682 TGCACTG
1 TGCACTG
14689 TGCAC
1 TGCAC
14694 GAGACATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.31, G:0.27, T:0.27
Consensus pattern (7 bp):
TGCACTG
Found at i:17997 original size:21 final size:20
Alignment explanation
Indices: 17956--17996 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17946 ATTGTAACAA
17956 TAAAATTGTATTTTCACTTT
1 TAAAATTGTATTTTCACTTT
*
17976 TAAAATTTTATTATTCA-TTT
1 TAAAATTGTATT-TTCACTTT
17996 T
1 T
17997 TTACTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (20 bp):
TAAAATTGTATTTTCACTTT
Found at i:27333 original size:2 final size:2
Alignment explanation
Indices: 27326--27351 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27316 GTGGGAGAAA
27326 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27352 TCAATATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36876 original size:24 final size:24
Alignment explanation
Indices: 36843--36923 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 24
36833 TCCTTTTCCA
* *
36843 GCACCCGAGCCTTCCAGTCCCTTT
1 GCACCTGAGCCTTCTAGTCCCTTT
36867 GCACCTGAGCCTGATTCTAG-CCCTTTT
1 GCACCTGAGCC---TTCTAGTCCC-TTT
* * *
36894 GCACCAGAGCCTTCTAGTCCATGT
1 GCACCTGAGCCTTCTAGTCCCTTT
36918 GCACCT
1 GCACCT
36924 CCCCCCGCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
24 23 0.50
25 2 0.04
26 3 0.07
27 18 0.39
ACGTcount: A:0.16, C:0.38, G:0.19, T:0.27
Consensus pattern (24 bp):
GCACCTGAGCCTTCTAGTCCCTTT
Found at i:61190 original size:24 final size:24
Alignment explanation
Indices: 61163--61208 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
61153 TGATTTAATT
61163 CTATAAAAAAT-TTAAAAATATAGA
1 CTAT-AAAAATGTTAAAAATATAGA
* *
61187 CTATTAAAATGTTAAAATTATA
1 CTATAAAAATGTTAAAAATATA
61209 TTTTTACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
CTATAAAAATGTTAAAAATATAGA
Found at i:62205 original size:96 final size:97
Alignment explanation
Indices: 62028--62213 Score: 254
Period size: 96 Copynumber: 1.9 Consensus size: 97
62018 GGAAAGGATG
* * * *
62028 TTCGATTATCTCGATTTGAGGAAAAGGTTGCACCTAGTAAATTAAGGCGCAAATTTTCAGAATCG
1 TTCGATTATCTCAATTTGAAGAAAAGATTGCACATAGTAAATTAAGGCGCAAATTTTCAGAATCG
*
62093 AATATAAGGAAGCATTGCCTCGATTAGGGGTA
66 AATATAAAGAAGCATTGCCTCGATTAGGGGTA
* *
62125 TTCGATTATTTCAATTTGAAGAAAA-ATTGCACATAGTAAGTTAAGGCGCAAATTTTC-GAAACT
1 TTCGATTATCTCAATTTGAAGAAAAGATTGCACATAGTAAATTAAGGCGCAAATTTTCAG-AA-T
62188 CGAA-ATAATAGAA-CATTGCCTCGATT
64 CGAATATAA-AGAAGCATTGCCTCGATT
62214 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
95 1 0.01
96 48 0.61
97 30 0.38
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (97 bp):
TTCGATTATCTCAATTTGAAGAAAAGATTGCACATAGTAAATTAAGGCGCAAATTTTCAGAATCG
AATATAAAGAAGCATTGCCTCGATTAGGGGTA
Found at i:62467 original size:29 final size:27
Alignment explanation
Indices: 62433--62495 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
62423 AAATGAGACT
*
62433 TTTTGGATACCCGGGGGGCAAAATGGTAA
1 TTTTGGATACCC--GGGGAAAAATGGTAA
* *
62462 TTTTGGATTCTCGGGGAAAAATGGTAA
1 TTTTGGATACCCGGGGAAAAATGGTAA
62489 TTTTGGA
1 TTTTGGA
62496 AATTTTGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 21 0.68
29 10 0.32
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.32
Consensus pattern (27 bp):
TTTTGGATACCCGGGGAAAAATGGTAA
Found at i:62521 original size:29 final size:30
Alignment explanation
Indices: 62478--62702 Score: 217
Period size: 30 Copynumber: 7.6 Consensus size: 30
62468 ATTCTCGGGG
62478 AAAAATGGTAA-TTTTGGAAATTTTGGGGTC
1 AAAAATGG-AATTTTTGGAAATTTTGGGGTC
* * * *
62508 AAAAATGGTATTTTTGGAAGTTTTGGTGTT
1 AAAAATGGAATTTTTGGAAATTTTGGGGTC
* * *
62538 AAAAATGGAACTTTTGGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGAAATTTTGGGGTC
** **
62568 AAAAATGGAATTTTTGGAAGCTCGGGGGT-
1 AAAAATGGAATTTTTGGAAATTTTGGGGTC
**
62597 AAAAATGGAATTTTTGGAAATTTTAAGGTC
1 AAAAATGGAATTTTTGGAAATTTTGGGGTC
* * *
62627 AAAAATGAAATTTTTGG-AAGTTCGTGGGT-
1 AAAAATGGAATTTTTGGAAATTTTG-GGGTC
***
62656 AAAAATGGAATTTTTGGAAATTAAAGGGT-
1 AAAAATGGAATTTTTGGAAATTTTGGGGTC
*
62685 AAAAATAGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
62703 CAGTTTAGGG
Statistics
Matches: 160, Mismatches: 31, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
29 65 0.41
30 95 0.59
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAATTTTGGGGTC
Found at i:62626 original size:59 final size:59
Alignment explanation
Indices: 62452--62702 Score: 271
Period size: 59 Copynumber: 4.3 Consensus size: 59
62442 CCCGGGGGGC
** **
62452 AAAATGGTAA-TTTTGGATTCTC-GGGG-AAAAATGGTAA-TTTTGGAAATTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAGCTCGGGGGTAAAAATGG-AATTTTTGGAAATTTTAAGGTCA
* * * * * * * *
62509 AAAATGGTATTTTTGGAAGTTTTGGTGTTAAAAATGGAACTTTTGGAAGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAG-CTCGGGGGTAAAAATGGAATTTTTGGAAATTTTAAGGTCA
62569 AAAATGGAATTTTTGGAAGCTCGGGGGTAAAAATGGAATTTTTGGAAATTTTAAGGTCA
1 AAAATGGAATTTTTGGAAGCTCGGGGGTAAAAATGGAATTTTTGGAAATTTTAAGGTCA
* * * *
62628 AAAATGAAATTTTTGGAAGTTCGTGGGTAAAAATGGAATTTTTGGAAA-TTAAAGGGT-A
1 AAAATGGAATTTTTGGAAGCTCGGGGGTAAAAATGGAATTTTTGGAAATTTTAA-GGTCA
*
62686 AAAATAGAATTTTTGGA
1 AAAATGGAATTTTTGGA
62703 CAGTTTAGGG
Statistics
Matches: 165, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
56 1 0.01
57 14 0.08
58 21 0.13
59 85 0.52
60 44 0.27
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGCTCGGGGGTAAAAATGGAATTTTTGGAAATTTTAAGGTCA
Found at i:64556 original size:11 final size:11
Alignment explanation
Indices: 64534--64611 Score: 63
Period size: 11 Copynumber: 6.8 Consensus size: 11
64524 TAAATTTTGG
64534 AATTAAATTTA
1 AATTAAATTTA
64545 AATTTAAA-TTA
1 AA-TTAAATTTA
64556 AACTTAAATTTTA
1 AA-TTAAA-TTTA
64569 AGATT-AATTTA
1 A-ATTAAATTTA
*
64580 AATTTAAA-ATA
1 AA-TTAAATTTA
64591 AATCTAAATTTA
1 AAT-TAAATTTA
*
64603 AAATAAATT
1 AATTAAATT
64612 AAAAAGGGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
10 2 0.04
11 33 0.60
12 13 0.24
13 6 0.11
14 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:64556 original size:17 final size:17
Alignment explanation
Indices: 64534--64611 Score: 95
Period size: 17 Copynumber: 4.5 Consensus size: 17
64524 TAAATTTTGG
64534 AATTAAATTTAAATTTA
1 AATTAAATTTAAATTTA
*
64551 AATTAAACTTAAATTTTA
1 AATTAAATTTAAA-TTTA
64569 AGATT-AATTTAAATTTA
1 A-ATTAAATTTAAATTTA
* *
64586 AAATAAATCTAAATTTA
1 AATTAAATTTAAATTTA
*
64603 AAATAAATT
1 AATTAAATT
64612 AAAAAGGGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
16 2 0.04
17 36 0.68
18 12 0.23
19 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
AATTAAATTTAAATTTA
Found at i:64580 original size:18 final size:18
Alignment explanation
Indices: 64523--64611 Score: 87
Period size: 17 Copynumber: 5.1 Consensus size: 18
64513 TTTTGGACTC
*
64523 TTAAATTTTGGAATTAAAT
1 TTAAATTTT-AAATTAAAT
*
64542 TTAAA-TTTAAATTAAAC
1 TTAAATTTTAAATTAAAT
64559 TTAAATTTTAAGATT-AAT
1 TTAAATTTTAA-ATTAAAT
*
64577 TTAAA-TTTAAAATAAAT
1 TTAAATTTTAAATTAAAT
* *
64594 CTAAA-TTTAAAATAAAT
1 TTAAATTTTAAATTAAAT
64611 T
1 T
64612 AAAAAGGGGG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
16 2 0.03
17 36 0.59
18 15 0.25
19 8 0.13
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (18 bp):
TTAAATTTTAAATTAAAT
Found at i:64585 original size:35 final size:36
Alignment explanation
Indices: 64522--64601 Score: 103
Period size: 35 Copynumber: 2.2 Consensus size: 36
64512 CTTTTGGACT
* *
64522 CTTAAATTTTGGAATTAAATTTAAATTTAAATTAAA
1 CTTAAATTTTAGAATTAAATTTAAATTTAAAATAAA
64558 CTTAAATTTTA-AGATT-AATTTAAATTTAAAATAAA
1 CTTAAATTTTAGA-ATTAAATTTAAATTTAAAATAAA
64593 -TCTAAATTT
1 CT-TAAATTT
64602 AAAATAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 1 0.03
35 26 0.65
36 13 0.32
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (36 bp):
CTTAAATTTTAGAATTAAATTTAAATTTAAAATAAA
Found at i:64606 original size:7 final size:6
Alignment explanation
Indices: 64536--64604 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
64526 AATTTTGGAA
*
64536 TTAAAT TTAAAT TTAAA- TTAAAC TTAAATT TTAAGA- TT-AAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAA-AT TTAAAT TTAAAT
* *
64583 TTAAA- ATAAAT CTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA
64605 ATAAATTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
4 1 0.02
5 12 0.23
6 35 0.66
7 4 0.08
8 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:75130 original size:34 final size:34
Alignment explanation
Indices: 75086--75160 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
75076 GGATGTTCAA
** *
75086 CCTTACATCTCCCTTGACTTTTAACCTTCCATCTT
1 CCTTA-ATCTCCCTAAACCTTTAACCTTCCATCTT
*
75121 CCTTAATCTCCCTAAACCTTTAACCTTTCATCTT
1 CCTTAATCTCCCTAAACCTTTAACCTTCCATCTT
75155 CCTTAA
1 CCTTAA
75161 CTTTTCATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 31 0.86
35 5 0.14
ACGTcount: A:0.21, C:0.36, G:0.01, T:0.41
Consensus pattern (34 bp):
CCTTAATCTCCCTAAACCTTTAACCTTCCATCTT
Found at i:75662 original size:30 final size:30
Alignment explanation
Indices: 75626--75692 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 30
75616 TTCTATTATA
*
75626 TTATGTTTGC-AAGTTTTGTTAAGGGATTAC
1 TTATGTTTGCTAAG-TTTGTTAAGGGACTAC
75656 TTATGTTTGCTTGAAAGTTTGTTAAGGGACTAC
1 TTATGTTTGC-T--AAGTTTGTTAAGGGACTAC
75689 TTAT
1 TTAT
75693 ATTTATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.31
33 19 0.59
34 3 0.09
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (30 bp):
TTATGTTTGCTAAGTTTGTTAAGGGACTAC
Found at i:80615 original size:34 final size:34
Alignment explanation
Indices: 80572--80639 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
80562 AACCTTTCAT
*
80572 CTCCCTTGACTTTTAACCTTCCATCTTCCTTAAC
1 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
* *
80606 CTCCCTTGACCTTTAACCTTCTATTTTCCTTAAC
1 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
80640 TTTTCATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.18, C:0.37, G:0.03, T:0.43
Consensus pattern (34 bp):
CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
Found at i:86708 original size:17 final size:18
Alignment explanation
Indices: 86686--86719 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
86676 TAACTTTTCA
86686 ATTAT-AATAATTGAAAC
1 ATTATAAATAATTGAAAC
86703 ATTATAAATAATTGAAA
1 ATTATAAATAATTGAAA
86720 ATGTTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (18 bp):
ATTATAAATAATTGAAAC
Found at i:116264 original size:15 final size:15
Alignment explanation
Indices: 116233--116274 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
116223 AAATAACTCT
116233 AAAAAATC-AAAAAA
1 AAAAAATCTAAAAAA
* *
116247 AAAAAATCTAATATA
1 AAAAAATCTAAAAAA
116262 AAAAAATCTAAAA
1 AAAAAATCTAAAA
116275 CTAAATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAATCTAAAAAA
Done.