Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011823.1 Kokia drynarioides strain JFW-HI SEQ_126818, 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: 26505
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.33
Warning! 257 characters in sequence are not A, C, G, or T
Found at i:6153 original size:24 final size:24
Alignment explanation
Indices: 6106--6148 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
6096 AATTAATAAT
6106 ATTAACAACTTAATAATTATATTA
1 ATTAACAACTTAATAATTATATTA
6130 ATTAA-AA-TTAATAA-TATAT
1 ATTAACAACTTAATAATTATAT
6149 CATTACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 2 0.11
24 5 0.26
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTAACAACTTAATAATTATATTA
Found at i:8946 original size:24 final size:23
Alignment explanation
Indices: 8899--8947 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
8889 TAATATTAAT
8899 AATTAAATTTAACTAAAAAGAAAA
1 AATTAAATTT-ACTAAAAAGAAAA
*
8923 AATTAAATTT-CTAAAATAGTAAA
1 AATTAAATTTACTAAAA-AGAAAA
8946 AA
1 AA
8948 GAATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 7 0.30
24 10 0.43
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
AATTAAATTTACTAAAAAGAAAA
Found at i:19115 original size:16 final size:16
Alignment explanation
Indices: 19094--19129 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19084 AGTTTTGAAT
19094 TTTTTTTATATTTTAA
1 TTTTTTTATATTTTAA
* *
19110 TTTTTTTTTTTTTTAA
1 TTTTTTTATATTTTAA
19126 TTTT
1 TTTT
19130 AAGGAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTATATTTTAA
Found at i:21424 original size:167 final size:168
Alignment explanation
Indices: 21002--21531 Score: 1026
Period size: 168 Copynumber: 3.2 Consensus size: 168
20992 TAATAATTTC
21002 CATTGCAAGCAAAGCCTTGGAGGACTAGGTTTGGGTTTTGGTACCCACATACATAATTGGGTGTG
1 CATTGCAAGCAAAGCCTTGGAGGACTAGGTTTGGGTTTTGGTACCCACATACATAATTGGGTGTG
*
21067 CATAGAGTTAGGAACCATTCAACTTTCTAGTACAAAATCTAGGCATGAATAACATTAGAAATGTC
66 CATAGAGTTAGGAACCATTCAACTTTCTAGGACAAAATCTAGGCATGAATAACATTAGAAATGTC
21132 TACTTTCAAGAAAAGAAAAAAAAAACATTACAAAAAGT
131 TACTTTCAAGAAAAGAAAAAAAAAACATTACAAAAAGT
*
21170 CATTGCAAGCAAAGCCTTGGAGGACTAGGTTTGGCTTTTGGTACCCACATACATAATTGGGTGTG
1 CATTGCAAGCAAAGCCTTGGAGGACTAGGTTTGGGTTTTGGTACCCACATACATAATTGGGTGTG
21235 CATAGAGTTAGGAACCATTCAACTTTCTAGGACAAAATCTAGGCATGAATAACATTAGAAATGTC
66 CATAGAGTTAGGAACCATTCAACTTTCTAGGACAAAATCTAGGCATGAATAACATTAGAAATGTC
*
21300 TACTTTCAAGAAAAG-AAAAAAAACCATTACAAAAAGT
131 TACTTTCAAGAAAAGAAAAAAAAAACATTACAAAAAGT
21337 CATTGCAAGCAAAGCCTTGGAGGACTAGGTTTGGGTTTTGGTACCCACATACATAATTGGGTGTG
1 CATTGCAAGCAAAGCCTTGGAGGACTAGGTTTGGGTTTTGGTACCCACATACATAATTGGGTGTG
21402 CATAGAGTTAGGAACCATTCAACTTTCTAGGACAAAATCTAGGCATGAATAACATTAGAAATGTC
66 CATAGAGTTAGGAACCATTCAACTTTCTAGGACAAAATCTAGGCATGAATAACATTAGAAATGTC
21467 TACTTTCAAGAAAAGAAAAAAAAAACATTACAAAAAGT
131 TACTTTCAAGAAAAGAAAAAAAAAACATTACAAAAAGT
21505 CATTGCAAGCAAAGCCTTGGAGGACTA
1 CATTGCAAGCAAAGCCTTGGAGGACTA
21532 AGGCATGAAT
Statistics
Matches: 356, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
167 165 0.46
168 191 0.54
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (168 bp):
CATTGCAAGCAAAGCCTTGGAGGACTAGGTTTGGGTTTTGGTACCCACATACATAATTGGGTGTG
CATAGAGTTAGGAACCATTCAACTTTCTAGGACAAAATCTAGGCATGAATAACATTAGAAATGTC
TACTTTCAAGAAAAGAAAAAAAAAACATTACAAAAAGT
Found at i:21617 original size:89 final size:89
Alignment explanation
Indices: 21442--21663 Score: 392
Period size: 89 Copynumber: 2.5 Consensus size: 89
21432 GACAAAATCT
* *
21442 AGGCATGAATAACATTAGAAATGTCTACTTTCAAGAAAAGAAAAAAAAAACATTACAAAAAGTCA
1 AGGCATGAATAACATTAGAAAAGCCTACTTTCAAGAAAAG-AAAAAAAAACATTACAAAAAGTCA
21507 TTGCAAGCAAAGCCTTGGAGGACTA
65 TTGCAAGCAAAGCCTTGGAGGACTA
* *
21532 AGGCATGAATAATATTAGAAAAGCCTACTTTCAAGAAAAGAAAAAAAAACATTGCAAAAAGTCAT
1 AGGCATGAATAACATTAGAAAAGCCTACTTTCAAGAAAAGAAAAAAAAACATTACAAAAAGTCAT
21597 TGCAAGCAAAGCCTTGGAGGACTA
66 TGCAAGCAAAGCCTTGGAGGACTA
21621 AGGCATGAATAACATTAGAAAAGCCTACTTTCAAGAAAA-AAAA
1 AGGCATGAATAACATTAGAAAAGCCTACTTTCAAGAAAAGAAAA
21664 CATTACAAAA
Statistics
Matches: 127, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
88 4 0.03
89 86 0.68
90 37 0.29
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (89 bp):
AGGCATGAATAACATTAGAAAAGCCTACTTTCAAGAAAAGAAAAAAAAACATTACAAAAAGTCAT
TGCAAGCAAAGCCTTGGAGGACTA
Found at i:24160 original size:21 final size:21
Alignment explanation
Indices: 24126--24165 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
24116 TAATTTAAAT
24126 TTTTATTATGTAAAAATAAACA
1 TTTTATTATGT-AAAATAAACA
*
24148 TTTTA-TATTTAAAATAAA
1 TTTTATTATGTAAAATAAA
24166 GAGACAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTTATTATGTAAAATAAACA
Done.