Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005229.1 Kokia drynarioides strain JFW-HI SEQ_119114, 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: 22361
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:546 original size:29 final size:28
Alignment explanation
Indices: 514--603 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
504 AAAAATTATA
514 TTTTATCTCTAAACTTTCCAAAATTCCAT
1 TTTTA-CTCTAAACTTTCCAAAATTCCAT
* ** *
543 TTTTGAC-CTCGATTTTTCCAAAATTACAT
1 TTTT-ACTCT-AAACTTTCCAAAATTCCAT
572 TTTTAC-CTAGAACTTTCCAAAATTCCAT
1 TTTTACTCTA-AACTTTCCAAAATTCCAT
600 TTTT
1 TTTT
604 TACCCCAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 25 0.50
29 24 0.48
30 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTTACTCTAAACTTTCCAAAATTCCAT
Found at i:603 original size:28 final size:29
Alignment explanation
Indices: 525--603 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 29
515 TTTATCTCTA
*
525 AACTTTCCAAAATTCCATTTTTGACCTCG
1 AACTTTCCAAAATTCCATTTTTGACCTAG
** *
554 ATTTTTCCAAAATTACATTTTT-ACCTAG
1 AACTTTCCAAAATTCCATTTTTGACCTAG
582 AACTTTCCAAAATTCCATTTTT
1 AACTTTCCAAAATTCCATTTTT
604 TACCCCAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 24 0.56
29 19 0.44
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (29 bp):
AACTTTCCAAAATTCCATTTTTGACCTAG
Found at i:617 original size:58 final size:57
Alignment explanation
Indices: 529--814 Score: 258
Period size: 59 Copynumber: 4.9 Consensus size: 57
519 TCTCTAAACT
*
529 TTCCAAAATTCCATTTTTGACCTCGATTTTTCCAAAATTA-CATTTTTA-CCTAGAAC
1 TTCCAAAATTCCATTTTTGACCCCGATTTTTCCAAAATTACCA-TTTTACCCTAGAAC
* * ** * *
585 TTTCCAAAATTCCATTTTTTACCCCAATTTTTTTGAAAATTATCATTTTACTCCCA-AAC
1 -TTCCAAAATTCCATTTTTGACCCCGA-TTTTTCCAAAATTACCATTTTAC-CCTAGAAC
*
644 TTCCAAAAATTCCA-TTTTGACCCCGATTTTTCCAAAAATGACCATTTTACCCCT-GAAC
1 TTCC-AAAATTCCATTTTTGACCCCGATTTTTCC-AAAATTACCATTTTA-CCCTAGAAC
* * * **
702 TTCCAAAACTCCTATTTTTGACCCCGATTCTTCCAAAAGGTACCATTTTACCCCCGAAC
1 TTCCAAAATTCC-ATTTTTGACCCCGATTTTTCCAAAA-TTACCATTTTACCCTAGAAC
* * * * * * *
761 ATCTAAAAATTCCATTTTTGACCCCTAACTTTCCCAAAATTTCAATTTTACCCT
1 TTC-CAAAATTCCATTTTTGACCCC-GATTTTTCCAAAATTACCATTTTACCCT
815 CGAGTGACCA
Statistics
Matches: 186, Mismatches: 29, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
57 35 0.19
58 61 0.33
59 71 0.38
60 19 0.10
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (57 bp):
TTCCAAAATTCCATTTTTGACCCCGATTTTTCCAAAATTACCATTTTACCCTAGAAC
Found at i:676 original size:29 final size:28
Alignment explanation
Indices: 528--739 Score: 117
Period size: 29 Copynumber: 7.3 Consensus size: 28
518 ATCTCTAAAC
*
528 TTTCCAAAATTCCATTTTTGACCTCGATT
1 TTTCCAAAATTCCA-TTTTGACCCCGATT
* * ** **
557 TTTCCAAAATTACATTTTTACCTAGAAC
1 TTTCCAAAATTCCATTTTGACCCCGATT
* *
585 TTTCCAAAATTCCATTTTTTACCCCAATTT
1 TTTCCAAAATTCCA-TTTTGACCCCGA-TT
** * **
615 TTTTGAAAATTATCATTTT-ACTCCC-AAA
1 TTTCCAAAATT-CCATTTTGAC-CCCGATT
*
643 CTTCCAAAAATTCCATTTTGACCCCGATT
1 TTTCC-AAAATTCCATTTTGACCCCGATT
* *
672 TTTCCAAAAATGACCATTTT-ACCCCTGA-A
1 TTTCC-AAAAT-TCCATTTTGACCCC-GATT
* *
701 CTTCCAAAACTCCTATTTTTGACCCCGATT
1 TTTCCAAAATTCC-A-TTTTGACCCCGATT
*
731 CTTCCAAAA
1 TTTCCAAAA
740 GGTACCATTT
Statistics
Matches: 141, Mismatches: 29, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
27 2 0.01
28 39 0.28
29 59 0.42
30 39 0.28
31 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (28 bp):
TTTCCAAAATTCCATTTTGACCCCGATT
Found at i:758 original size:30 final size:29
Alignment explanation
Indices: 643--755 Score: 108
Period size: 29 Copynumber: 3.9 Consensus size: 29
633 TACTCCCAAA
*
643 CTTCCAAAAATTCCATTTTGACCCCGATT
1 CTTCCAAAAATACCATTTTGACCCCGATT
* *
672 TTTCCAAAAATGACCATTTT-ACCCCTGA-A
1 CTTCCAAAAAT-ACCATTTTGACCCC-GATT
*
701 CTTCCAAAACT-CCTATTTTTGACCCCGATT
1 CTTCCAAAAATACC-A-TTTTGACCCCGATT
*
731 CTTCCAAAAGGTACCATTTT-ACCCC
1 CTTCCAAAA-ATACCATTTTGACCCC
756 CGAACATCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.03
28 1 0.01
29 35 0.51
30 27 0.39
31 2 0.03
32 2 0.03
ACGTcount: A:0.28, C:0.32, G:0.07, T:0.33
Consensus pattern (29 bp):
CTTCCAAAAATACCATTTTGACCCCGATT
Found at i:6887 original size:6 final size:7
Alignment explanation
Indices: 6859--6885 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
6849 CGTAAAATAA
6859 AATTTTT
1 AATTTTT
6866 AATTTTT
1 AATTTTT
6873 AATTTTT
1 AATTTTT
6880 AATTTT
1 AATTTT
6886 AAGAATCGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
AATTTTT
Found at i:8311 original size:22 final size:22
Alignment explanation
Indices: 8286--8383 Score: 63
Period size: 22 Copynumber: 4.5 Consensus size: 22
8276 GTTTATACGA
*
8286 GTTTAGCACTTTTGTGCTCTTT
1 GTTTAGCACTTTGGTGCTCTTT
* ** *
8308 GTTTAGTACTACGGTACTCTTT
1 GTTTAGCACTTTGGTGCTCTTT
*** * *
8330 GACCAACACTTTGGTGCTCTCTC
1 GTTTAGCACTTTGGTGCTCT-TT
** *
8353 G-TTAGCACTTTTTTGCTCTAT
1 GTTTAGCACTTTGGTGCTCTTT
8374 GTTTAGCACT
1 GTTTAGCACT
8384 ACAGTGCTTT
Statistics
Matches: 53, Mismatches: 21, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
21 1 0.02
22 50 0.94
23 2 0.04
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.45
Consensus pattern (22 bp):
GTTTAGCACTTTGGTGCTCTTT
Found at i:13465 original size:460 final size:460
Alignment explanation
Indices: 12453--13837 Score: 2360
Period size: 460 Copynumber: 3.0 Consensus size: 460
12443 TTTTAAATGA
12453 TGATGACAAAATTGATAAAAGATATTTCAGGGATCAACATTTAGCTTAAATTTAATTATTGATAA
1 TGATGACAAAATTGATAAAAGATATTTCAGGGATCAACATTTAGCTTAAATTTAATTATTGATAA
* *
12518 ACGTTTGGGCTCTTTATCAGGTTAAAATTGAATTAACCAACCGAAACGATCTAATTAGTTTAATC
66 ACGTTTGGGCTCTTTATCAGGCTAAAATCGAATTAACCAACCGAAACGATCTAATTAGTTTAATC
* *
12583 GGTCGGTTAATTGATCTAATTCGGTCGAAAGTCGATTAATGATTTTTTTAAAGTTTAATTATCGG
131 GGTCGGTTAACTGATCTAATTCGGTCGAAAGTCGATTAATGATTTTTTTAAAGTTTAATTATCGA
*
12648 TTAATTCGGTTCGAAATTGGGTAATTAATCGAATTAATCAATCTTAATAATTAATAATACAAATT
196 TTAATTCGGTTCGAAATTGGGTAATTAATCGAATTAATCAAACTTAATAATTAATAATACAAATT
* * * *
12713 ATATATACTTTTAATTCAGTTAATTCGGTCAAATAAACATTATTAAGTTATTTATTTTTTTTATG
261 ATATGTACTTTTAATTCAGTTAATTCGATCAAATAAACATTATCAAGTTATTTATTTTTTATATG
12778 TTTTATACTTGTTTTAATCAAAAGATAAAAACATAAAAATTTTGATTAATT-TGATTAATCAACT
326 TTTTATACTTGTTTTAATCAAAAGATAAAAACATAAAAATTTTGATTAATTCTG-TTAATCAACT
* *
12842 GCATTACCGAAATATTTCGATTCGATTAATTTGTTTTTGAAAAATTTCAGTTCAATTAACGATTA
390 GCATTACCGAAATATTTCGATTCGGTTAATTT-TTTTTGAAAAATTTCAGTTCGATTAACGATTA
12907 AAAAGTT
454 AAAAGTT
* * *
12914 TGATGACAAAATTGATAAAATATATTTGAGGGATCAACATTTAGCTCAAATTTAATTATTGATAA
1 TGATGACAAAATTGATAAAAGATATTTCAGGGATCAACATTTAGCTTAAATTTAATTATTGATAA
* * * * *
12979 ATGTTTGGGCTATTTATCAAGCTAAAATCGAATTAAACAATCGAAACGATCTAATTAGTTTAATC
66 ACGTTTGGGCTCTTTATCAGGCTAAAATCGAATTAACCAACCGAAACGATCTAATTAGTTTAATC
** * *
13044 AATCGGTTAACTAATCTAATTCAGTCGAAAGTCGATTAATGATTTTTTTAAAGTTTAATTATCGA
131 GGTCGGTTAACTGATCTAATTCGGTCGAAAGTCGATTAATGATTTTTTTAAAGTTTAATTATCGA
* *
13109 TTAATTCGGTTCAAAATTAGGTAATTAATCGAATTAATCAAACTTAATAATTAATAATACAAATT
196 TTAATTCGGTTCGAAATTGGGTAATTAATCGAATTAATCAAACTTAATAATTAATAATACAAATT
* *
13174 ATATGTACTTTTAATTCAATTAATTCGATCAAATAAACATTATCAAGTTATTTA-TTTTTATATA
261 ATATGTACTTTTAATTCAGTTAATTCGATCAAATAAACATTATCAAGTTATTTATTTTTTATATG
13238 TTTTATACTTGTTTTAATCAAAAGATAAAAACATAAAAATTTTGATTAATTCTGTTAATCAACTG
326 TTTTATACTTGTTTTAATCAAAAGATAAAAACATAAAAATTTTGATTAATTCTGTTAATCAACTG
*
13303 CATTACCGAAATATTTCGATCCGGTTAATTTATTTTTGAAAAATTTCAGTTCGATTAACGATTAA
391 CATTACCGAAATATTTCGATTCGGTTAATTT-TTTTTGAAAAATTTCAGTTCGATTAACGATTAA
13368 AAAGTT
455 AAAGTT
* *
13374 TGATGACAAAATTGATAAAAGATATTTTAGGGATCAATATTTAGCTTAAATTTAATTATTGATAA
1 TGATGACAAAATTGATAAAAGATATTTCAGGGATCAACATTTAGCTTAAATTTAATTATTGATAA
*
13439 ACGTTTGGGCTCTTTATCAGGCTAAAATCGAATTAACCGACCGAAACGATCTAATTAGTTTAATC
66 ACGTTTGGGCTCTTTATCAGGCTAAAATCGAATTAACCAACCGAAACGATCTAATTAGTTTAATC
*
13504 GGTCGGTTAACTGATCTAATTCGGTCGAAAGTCGATTAATGATTTTTTTAAAGTTTAATTATTGA
131 GGTCGGTTAACTGATCTAATTCGGTCGAAAGTCGATTAATGATTTTTTTAAAGTTTAATTATCGA
13569 TTAATTCGGTTCGAAATTGGGTAATTAATCGAATTAATCAAACTTAATAATTAATAATACAAATT
196 TTAATTCGGTTCGAAATTGGGTAATTAATCGAATTAATCAAACTTAATAATTAATAATACAAATT
* *
13634 ATATGTACTTTTAATTCAGTTAATTTGATCAAATAAACATTATCAAATTATTTATTTTTTATATG
261 ATATGTACTTTTAATTCAGTTAATTCGATCAAATAAACATTATCAAGTTATTTATTTTTTATATG
* * *
13699 TTTTATACTTGTTTTAATCAAAAGATAAAAACATAAAAATTTTTATTAATTCGGTTAATCAATTG
326 TTTTATACTTGTTTTAATCAAAAGATAAAAACATAAAAATTTTGATTAATTCTGTTAATCAACTG
* * * *
13764 CATTACCAAAATATTTCGATTCAGTTAATTTTTTTTGAAAATTTTCATTTCGATTAACGATTAAA
391 CATTACCGAAATATTTCGATTCGGTTAATTTTTTTTGAAAAATTTCAGTTCGATTAACGATTAAA
13829 AAGTT
456 AAGTT
13834 TGAT
1 TGAT
13838 TAATTCGATT
Statistics
Matches: 864, Mismatches: 58, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
460 472 0.55
461 392 0.45
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (460 bp):
TGATGACAAAATTGATAAAAGATATTTCAGGGATCAACATTTAGCTTAAATTTAATTATTGATAA
ACGTTTGGGCTCTTTATCAGGCTAAAATCGAATTAACCAACCGAAACGATCTAATTAGTTTAATC
GGTCGGTTAACTGATCTAATTCGGTCGAAAGTCGATTAATGATTTTTTTAAAGTTTAATTATCGA
TTAATTCGGTTCGAAATTGGGTAATTAATCGAATTAATCAAACTTAATAATTAATAATACAAATT
ATATGTACTTTTAATTCAGTTAATTCGATCAAATAAACATTATCAAGTTATTTATTTTTTATATG
TTTTATACTTGTTTTAATCAAAAGATAAAAACATAAAAATTTTGATTAATTCTGTTAATCAACTG
CATTACCGAAATATTTCGATTCGGTTAATTTTTTTTGAAAAATTTCAGTTCGATTAACGATTAAA
AAGTT
Found at i:14471 original size:20 final size:20
Alignment explanation
Indices: 14435--14472 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14425 AATATTTTTT
*
14435 AATTCGATTCAATTCGATTC
1 AATTCGATTCAACTCGATTC
*
14455 AATTCGATTCGACTCGAT
1 AATTCGATTCAACTCGAT
14473 CGAATACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (20 bp):
AATTCGATTCAACTCGATTC
Found at i:14472 original size:10 final size:10
Alignment explanation
Indices: 14435--14464 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
14425 AATATTTTTT
14435 AATTCGATTC
1 AATTCGATTC
14445 AATTCGATTC
1 AATTCGATTC
14455 AATTCGATTC
1 AATTCGATTC
14465 GACTCGATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (10 bp):
AATTCGATTC
Found at i:18968 original size:13 final size:13
Alignment explanation
Indices: 18950--18974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18940 TAAAATTAAT
18950 AATTCTTAAATTA
1 AATTCTTAAATTA
18963 AATTCTTAAATT
1 AATTCTTAAATT
18975 TTAAAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTCTTAAATTA
Done.