Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012243.1 Kokia drynarioides strain JFW-HI SEQ_127244, 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: 36775
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:5122 original size:205 final size:205
Alignment explanation
Indices: 4767--5411 Score: 835
Period size: 205 Copynumber: 3.1 Consensus size: 205
4757 CAATAATGCT
* *
4767 GTCATCTTCCTGATTAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTAAGCAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATC
* * * *
4832 TTCGAATCTCAGCTTCCTGATGAGACATTGAGAAGCAAGTCGAAGCAATAAACGATTAGCTTCTT
66 TTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAACGATTAGCTTCCT
* * *
4897 GATAAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACGGAGAAAAAGATTAAAAC
131 GATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAAGATTAAAAC
4962 AAATGACACG
196 AAATGACACG
*
4972 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCTATGTGAGCAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATC
* * *
5037 TTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGTAAGTCGAAGCAATAAACGGTTAGCTTCCT
66 TTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAACGATTAGCTTCCT
* * * *
5102 GATGAGATACTGATAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCAGATTGAAAC
131 GATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAAGATTAAAAC
*
5167 AAATGACGCG
196 AAATGACACG
* ** *
5177 GTCATCTTCATGATGAGATACTGAGAAGAAGACCAAATCAAATTCACGCTCGA--TGAACAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATC
* * * ** **
5240 TTCAAACCCCAGCTTCCTGTTGAGATACTGAGAAGCGGGTCGAAATAATAAAACGATTAGCTTCC
66 TTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAAT-AAACGATTAGCTTCC
* * * * * * * * * ** *
5305 TGAAGAAAATACGGGGAAGTAAACCAAAATCATCTTCCTGATGAAACACAGAGAAGTGGATCAAA
130 TGATG-AGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAAGATTAAA
* * *
5370 ACAAGTGATATG
194 ACAAATGACACG
** *
5382 GTCATCTTCCAAATGAGATACCGAGAAGAA
1 GTCATCTTCCTGATGAGATACTGAGAAGAA
5412 AGCCAAGTCA
Statistics
Matches: 382, Mismatches: 56, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
203 49 0.13
204 18 0.05
205 315 0.82
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (205 bp):
GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATC
TTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAACGATTAGCTTCCT
GATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAAGATTAAAAC
AAATGACACG
Found at i:5755 original size:17 final size:17
Alignment explanation
Indices: 5730--5811 Score: 101
Period size: 17 Copynumber: 4.8 Consensus size: 17
5720 CTGGGCCCAA
5730 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
5747 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
*
5764 TAAATTTAAAATTATTT
1 TAAATTTAAATTTATTT
* * *
5781 AAAATTTAAAATTATTA
1 TAAATTTAAATTTATTT
5798 TAAATTTAAATTTA
1 TAAATTTAAATTTA
5812 AAATCTATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:5773 original size:34 final size:34
Alignment explanation
Indices: 5729--5811 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
5719 TCTGGGCCCA
**
5729 ATAAATTTAAATTTATTTTAAAA-TTAAGTTTATT
1 ATAAATTTAAATTTA-TTTAAAATTTAAAATTATT
* *
5763 CTAAATTTAAAATTATTTAAAATTTAAAATTATT
1 ATAAATTTAAATTTATTTAAAATTTAAAATTATT
5797 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
5812 AAATCTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 7 0.17
34 35 0.83
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
ATAAATTTAAATTTATTTAAAATTTAAAATTATT
Found at i:5824 original size:23 final size:24
Alignment explanation
Indices: 5777--5825 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
5767 ATTTAAAATT
5777 ATTTAAAATTTAAAATTATTATAA
1 ATTTAAAATTTAAAATTATTATAA
5801 ATTT-AAATTTAAAATCTATT-TAA
1 ATTTAAAATTTAAAAT-TATTATAA
5824 AT
1 AT
5826 AATGTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTAAAATTTAAAATTATTATAA
Found at i:6517 original size:3 final size:3
Alignment explanation
Indices: 6509--6573 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
6499 AATAAGGTTT
* ** *
6509 TAA TAA TAA TAA TAA TAA TAAA TAA TAA CT-G TTT TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA TAA TAA TAA TAA
*
6555 TAT TAA TTAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA
6574 AAAGAAACGA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 1 0.02
3 44 0.85
4 7 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:6543 original size:34 final size:34
Alignment explanation
Indices: 6505--6570 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
6495 AATAAATAAG
6505 GTTTTAATAATAATAATAATAATAAATAATAACT
1 GTTTTAATAATAATAATAATAATAAATAATAACT
* * *
6539 GTTTTAATAATAATATTATTAATTAATAATAA
1 GTTTTAATAATAATAATAATAATAAATAATAA
6571 TAAAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (34 bp):
GTTTTAATAATAATAATAATAATAAATAATAACT
Found at i:7649 original size:58 final size:58
Alignment explanation
Indices: 7550--7885 Score: 207
Period size: 59 Copynumber: 5.9 Consensus size: 58
7540 GAGGTCCTTA
* *** *
7550 AACTATCCAAAAATTTTGTTTTTACCCTCAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTGTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATTCCATTTTTACCCTCG
* * *
7609 AACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCTAAAAAATCCATTTTTTACCC-CAA
1 AACTGTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATTCCA-TTTTTACCCTC-G
* ** *
7668 AACT-TTCAAAAACCCCATTTTTA---C---C--CCAAAACTTCCATTTTTACCCTCG
1 AACTGTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTACCCTCG
* * * * * *
7717 AACT-TCCAAAAATTCCATTTTCGACCCCGTAACTCCCAAAAATTCTAGTTTTGCCCCCG
1 AACTGTCCAAAAATTCCATTTT-TACCCCG-AACTTCCAAAAATTCCATTTTTACCCTCG
* * * * * **
7776 GA-TGTCTAAAAACTCTATTTTTGACCTCGAAAC-TCCAAAAATTTTATTTTTACCCTCG
1 AACTGTCCAAAAATTCCATTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
7834 AA-TGTCTAAAAATTTCATTTTTAACCCCGAATTTTCCCAAAATTACCATTTT
1 AACTGTCCAAAAATTCCATTTTT-ACCCCGAA-CTTCCAAAAATT-CCATTTT
7886 AGCCCCGAGT
Statistics
Matches: 214, Mismatches: 45, Indels: 35
0.73 0.15 0.12
Matches are distributed among these distances:
49 27 0.13
50 11 0.05
52 1 0.00
53 1 0.00
55 1 0.00
57 3 0.01
58 81 0.38
59 84 0.39
60 5 0.02
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (58 bp):
AACTGTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:7660 original size:30 final size:29
Alignment explanation
Indices: 7550--7885 Score: 209
Period size: 29 Copynumber: 11.7 Consensus size: 29
7540 GAGGTCCTTA
*** *
7550 AACTATCCAAAAATTTTGTTTTTACCCTCA
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
7580 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
7609 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
7638 AACTTCTAAAAAATCCATTTTTTACCC-CAA
1 AACTTCCAAAAATTCCA-TTTTTACCCTC-G
* **
7668 AACTTTCAAAAACCCCATTTTTA----C-
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
7692 --C--CCAAAACTTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
7717 AACTTCCAAAAATTCCATTTTCGACCC-CG
1 AACTTCCAAAAATTCCATTTT-TACCCTCG
* * * * *
7746 TAACTCCCAAAAATTCTAGTTTTGCCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
7776 GA-TGTCTAAAAACTCTATTTTTGA-CCTCG
1 AACT-TCCAAAAATTCCATTTTT-ACCCTCG
**
7805 AAAC-TCCAAAAATTTTATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* *
7834 AA-TGTCTAAAAATTTCATTTTTAACCC-CG
1 AACT-TCCAAAAATTCCATTTTT-ACCCTCG
* *
7863 AATTTTCCCAAAATTACCATTTT
1 AA-CTTCCAAAAATT-CCATTTT
7886 AGCCCCGAGT
Statistics
Matches: 243, Mismatches: 38, Indels: 49
0.74 0.12 0.15
Matches are distributed among these distances:
20 14 0.06
22 1 0.00
24 1 0.00
26 1 0.00
27 1 0.00
28 4 0.02
29 151 0.62
30 63 0.26
31 7 0.03
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:26532 original size:20 final size:20
Alignment explanation
Indices: 26504--26557 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
26494 CTGGTACATG
*
26504 CCAAAATTTTTAAAGATTTA
1 CCAATATTTTTAAAGATTTA
*
26524 CCAATATTTTTAAAGGTTTA
1 CCAATATTTTTAAAGATTTA
** *
26544 TTAGTATTTTTAAA
1 CCAATATTTTTAAA
26558 TGTTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (20 bp):
CCAATATTTTTAAAGATTTA
Done.