Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012864.1 Kokia drynarioides strain JFW-HI SEQ_127878, 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: 275618
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 12 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:247868 original size:31 final size:31
Alignment explanation
Indices: 247833--247911 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 31
247823 TTTTTTTAAT
247833 TTTTAAAGAATCTAAAAAATTTTTT-ACCAAC
1 TTTTAAAGAA-CTAAAAAATTTTTTCACCAAC
* * *
247864 TTTT-AAGAGACTTAAAATTTTTTTCTCCAAC
1 TTTTAAAGA-ACTAAAAAATTTTTTCACCAAC
*
247895 TTTTAAATAAACTAAAA
1 TTTTAAA-GAACTAAAA
247912 CCCCATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 16 0.41
31 14 0.36
32 8 0.21
33 1 0.03
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.41
Consensus pattern (31 bp):
TTTTAAAGAACTAAAAAATTTTTTCACCAAC
Found at i:258543 original size:18 final size:18
Alignment explanation
Indices: 258508--258546 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
258498 ATTAAGAATT
**
258508 TTAATAAATTGTTAAAAA
1 TTAATAAAAAGTTAAAAA
*
258526 TTAATAAAAAGTTTAAAA
1 TTAATAAAAAGTTAAAAA
258544 TTA
1 TTA
258547 CAATAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
TTAATAAAAAGTTAAAAA
Found at i:261680 original size:14 final size:14
Alignment explanation
Indices: 261661--261689 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
261651 ACGTTTGTCC
261661 AGTAAAATAGAATT
1 AGTAAAATAGAATT
261675 AGTAAAATAGAATT
1 AGTAAAATAGAATT
261689 A
1 A
261690 TAATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (14 bp):
AGTAAAATAGAATT
Found at i:261704 original size:16 final size:16
Alignment explanation
Indices: 261677--261720 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
261667 ATAGAATTAG
*
261677 TAAAATAGAATTATAA
1 TAAAATAAAATTATAA
*
261693 TGAAATAAAATTATAA
1 TAAAATAAAATTATAA
261709 TAAAATAAAATT
1 TAAAATAAAATT
261721 GATATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAAAATAAAATTATAA
Found at i:273172 original size:26 final size:25
Alignment explanation
Indices: 273129--273186 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
273119 AATAAAAAAA
273129 TAATATTA-AATTTATACATGAATTT
1 TAAT-TTATAATTTATACATGAATTT
*
273154 TAGTTTATAATTTGATACATGAATTT
1 TAATTTATAATTT-ATACATGAATTT
273180 TAATTTA
1 TAATTTA
273187 GTGTAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 3 0.10
25 8 0.28
26 18 0.62
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (25 bp):
TAATTTATAATTTATACATGAATTT
Found at i:274295 original size:2 final size:2
Alignment explanation
Indices: 274233--274280 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
274223 AGTAATCATA
274233 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
274275 AT AT AT
1 AT AT AT
274281 TCTAAGTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:274749 original size:27 final size:27
Alignment explanation
Indices: 274719--274796 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
274709 GGAATGAACT
274719 AATCATGAAATGGAAGTCTTTGTGACA
1 AATCATGAAATGGAAGTCTTTGTGACA
* * * *
274746 AATCATGAAATGAAAGCCCTTGTGACG
1 AATCATGAAATGGAAGTCTTTGTGACA
274773 AATCATGAAATGGAAGTCTTTGTG
1 AATCATGAAATGGAAGTCTTTGTG
274797 GTGCACTCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCATGAAATGGAAGTCTTTGTGACA
Found at i:275339 original size:82 final size:82
Alignment explanation
Indices: 275241--275395 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 82
275231 CTCTGACTTA
* * * **
275241 AGCGGCATTTATGAGAAAGCGCCGCAAAAGGTCAGAGCATTAGTGGTGTTTATGA-AAAAGTGCC
1 AGCGGCATTTATGAGAAAGCGCCGCAAAAGGTCAGAACA-TAGCGGTGCTTATGAGAAAAACGCC
275305 GCTAAAGGTCAGAGCATT
65 GCTAAAGGTCAGAGCATT
* ** *
275323 AGCGGCGTTTATGAGAAAGCGTTGCTAAAGGTCAGAACATAGCGGTGCTTATGAGAAAAACGCCG
1 AGCGGCATTTATGAGAAAGCGCCGCAAAAGGTCAGAACATAGCGGTGCTTATGAGAAAAACGCCG
275388 CTAAAGGT
66 CTAAAGGT
275396 TAAGAAATAG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
81 13 0.21
82 50 0.79
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (82 bp):
AGCGGCATTTATGAGAAAGCGCCGCAAAAGGTCAGAACATAGCGGTGCTTATGAGAAAAACGCCG
CTAAAGGTCAGAGCATT
Found at i:275377 original size:40 final size:41
Alignment explanation
Indices: 275248--275395 Score: 190
Period size: 41 Copynumber: 3.6 Consensus size: 41
275238 TTAAGCGGCA
* *
275248 TTTATGAGAAAGCGCCGCAAAAGGTCAGAGCATTAGTGGTG
1 TTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGGTG
* * *
275289 TTTATGAAAAAGTGCCGCTAAAGGTCAGAGCATTAGCGGCG
1 TTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGGTG
** *
275330 TTTATGAGAAAGCGTTGCTAAAGGTCAGAACA-TAGCGGTG
1 TTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGGTG
* *
275370 CTTATGAGAAAAACGCCGCTAAAGGT
1 TTTATGAG-AAAGCGCCGCTAAAGGT
275396 TAAGAAATAG
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 14 0.15
41 77 0.85
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (41 bp):
TTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGGTG
Done.