Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009557.1 Kokia drynarioides strain JFW-HI SEQ_124269, 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: 11295
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:7295 original size:7 final size:8
Alignment explanation
Indices: 7280--7322 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
7270 ACCCACAAGA
7280 TATTTTTT
1 TATTTTTT
7288 TATTTTTT
1 TATTTTTT
7296 TATTTTTCT
1 TATTTTT-T
*
7305 CATATTTTT
1 TAT-TTTTT
*
7314 TCTTTTTT
1 TATTTTTT
7322 T
1 T
7323 CTCAACTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 21 0.70
9 5 0.17
10 4 0.13
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (8 bp):
TATTTTTT
Found at i:7312 original size:19 final size:20
Alignment explanation
Indices: 7288--7326 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7278 GATATTTTTT
7288 TATTTTTT-TATTTTTCTCA
1 TATTTTTTCTATTTTTCTCA
*
7307 TATTTTTTCTTTTTTTCTCA
1 TATTTTTTCTATTTTTCTCA
7327 ACTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTTTTTCTATTTTTCTCA
Found at i:8157 original size:25 final size:25
Alignment explanation
Indices: 8120--8171 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
8110 TTAAAACAAC
8120 TTCTAAAAAAAAAACTC-AAGAGCAA
1 TTCTAAAAAAAAAACTCAAAGAG-AA
* * *
8145 TTCTTAAAGAAAAATTCAAAGAGAA
1 TTCTAAAAAAAAAACTCAAAGAGAA
8170 TT
1 TT
8172 ATTATTAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.23
Consensus pattern (25 bp):
TTCTAAAAAAAAAACTCAAAGAGAA
Found at i:10934 original size:216 final size:214
Alignment explanation
Indices: 10368--11145 Score: 974
Period size: 216 Copynumber: 3.6 Consensus size: 214
10358 TCGTATCATA
* * * ** *
10368 TCCCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCATCACGAATAC-TCAGAGGAA
1 TCCCGAGCATGGAATGTTAGGAAAATTGC-TGAAGGAATGGATCGTCTTGAATACTTTA-AGGAA
* * *
10432 CTAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTC-AGAAGTTCGTCCAAAAACCAAGAGA
64 CCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTCGA-AAGTTTGTCCAAGAACCAAGAGA
* * *
10496 GAAACAATTATCACGTACATAAGTTTTTAATTCAAAGAACAAAACTTGTTTAGAAAATGACAAAA
128 GAAACAATTCTCACGTAAATAAG-TTTTAATTCAAAGAACAAAACTTGTTTACAAAATG------
10561 ACAAACTATTTAGACCAAAAGATGCGATT
186 ACAAACTATTTAGACCAAAAGATGCGATT
* * *
10590 TCCCGAGCATGGAATGTTTGGAAAATTGCTAGAAGGAATGGATTGTCTTGAAT-GTTTAAGGAAC
1 TCCCGAGCATGGAATGTTAGGAAAATTGCT-GAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
*
10654 CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTCGAAAGTTTGTCCAAGAACCAAGAGAGA
65 CAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTCGAAAGTTTGTCCAAGAACCAAGAGAGA
* * *
10719 CACAATTCTCACATATATAAGTTCTTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTA
130 AACAATTCTCACGTAAATAAGTT-TTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTA
10784 TTTAGACCAAAAGATGCGATT
194 TTTAGACCAAAAGATGCGATT
* *
10805 TCTCGAGCATGAAATGTTAGGAAAATTGCTGAAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
1 TCCCGAGCATGGAATGTTAGGAAAATTGCTG-AAGGAATGGATCGTCTTGAATACTTTAAGGAAC
* * * * *
10870 CGAAGCTATAAAAGAACTCGTAAAAGTTTGACTAGTTCGAAAGTTTGTCCTAGAACCAAGAGAGA
65 CAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTCGAAAGTTTGTCCAAGAACCAAGAGAGA
* * * * *
10935 AATAATTCTCACGTAAATAGGATTTTAATTTAAAG-ACTAAAACTTGTTTACATAATAACAAACT
130 AACAATTCTCACGTAAATAAG-TTTTAATTCAAAGAAC-AAAACTTGTTTACAAAATGACAAACT
10999 ATTTAGACCAAAAGATGCGATT
193 ATTTAGACCAAAAGATGCGATT
* * * * * * *
11021 TCGCGAGCGTTGAATGTTCA-GAATATTGCTCGAAGGAATGGATTGTCTTTAATACTTTAAGGAG
1 TCCCGAGCATGGAATGTT-AGGAAAATTGCT-GAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* * * * *
11085 CCAAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTGCAAG-ACCAAGA
64 CCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTCGAAAGTTTGTCCAAGAACCAAGA
11146 TGTCAAACTA
Statistics
Matches: 496, Mismatches: 50, Indels: 27
0.87 0.09 0.05
Matches are distributed among these distances:
214 1 0.00
215 85 0.17
216 241 0.49
217 4 0.01
220 2 0.00
221 115 0.23
222 48 0.10
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (214 bp):
TCCCGAGCATGGAATGTTAGGAAAATTGCTGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
AAAGTTATAAAAGAACTCGTAAAAGTTTGACAAATTCGAAAGTTTGTCCAAGAACCAAGAGAGAA
ACAATTCTCACGTAAATAAGTTTTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTATT
TAGACCAAAAGATGCGATT
Found at i:11277 original size:156 final size:156
Alignment explanation
Indices: 10993--11295 Score: 417
Period size: 156 Copynumber: 1.9 Consensus size: 156
10983 TACATAATAA
* * ** ** * * *
10993 CAAACTATTTAGACCAAAAGATGCGATTTCGCGAGCGTTGAATGTTCAGAATATTGCTCGAAGGA
1 CAAACTATTTAAACCAAAAGATACGATTTAACGAGAATGGAATGTTCAAAAAATTGCTCGAAGGA
** * * *
11058 ATGGATTGTCTTTAATACTTTAAGGAGCCAAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTT
66 ATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
*
11123 CGGAAGTTCGTGCAAGACCAAGATGT
131 CGGAAGTTCGTCCAAGACCAAGATGT
* * *
11149 CAAACTATTTAAACCAAATGATACGATTTAACGAGAATGGAATGTTCAAAAAATTGTTGGAAGGA
1 CAAACTATTTAAACCAAAAGATACGATTTAACGAGAATGGAATGTTCAAAAAATTGCTCGAAGGA
***
11214 ATGGATCATCTTGAATACTTTAAGGAATTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
66 ATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
11279 CGGAAGTTCGTCCAAGA
131 CGGAAGTTCGTCCAAGA
Statistics
Matches: 126, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
156 126 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (156 bp):
CAAACTATTTAAACCAAAAGATACGATTTAACGAGAATGGAATGTTCAAAAAATTGCTCGAAGGA
ATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
CGGAAGTTCGTCCAAGACCAAGATGT
Done.