Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011807.1 Kokia drynarioides strain JFW-HI SEQ_126802, 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: 282844
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 242 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:258222 original size:52 final size:52
Alignment explanation
Indices: 258166--258277 Score: 163
Period size: 52 Copynumber: 2.2 Consensus size: 52
258156 ATAAGAGCAT
258166 AACTCTGTACAG-GCTCGAATGAACTAAACTCTGTCTGGGCTTGAACAAGCTA
1 AACTCTGT-CAGAGCTCGAATGAACTAAACTCTGTCTGGGCTTGAACAAGCTA
* * * *
258218 AACTCTGTCTGAGCTCGAATGAGCTAAACTCTGTTTGGGCTTGAACGAGCTA
1 AACTCTGTCAGAGCTCGAATGAACTAAACTCTGTCTGGGCTTGAACAAGCTA
*
258270 AAGTCTGT
1 AACTCTGT
258278 TATGGGTTCG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 2 0.04
52 52 0.96
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (52 bp):
AACTCTGTCAGAGCTCGAATGAACTAAACTCTGTCTGGGCTTGAACAAGCTA
Found at i:258278 original size:26 final size:26
Alignment explanation
Indices: 258189--258277 Score: 124
Period size: 26 Copynumber: 3.4 Consensus size: 26
258179 CTCGAATGAA
*
258189 CTAAACTCTGTCTGGGCTTGAACAAG
1 CTAAACTCTGTCTGGGCTTGAACGAG
* * *
258215 CTAAACTCTGTCTGAGCTCGAATGAG
1 CTAAACTCTGTCTGGGCTTGAACGAG
*
258241 CTAAACTCTGTTTGGGCTTGAACGAG
1 CTAAACTCTGTCTGGGCTTGAACGAG
*
258267 CTAAAGTCTGT
1 CTAAACTCTGT
258278 TATGGGTTCG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (26 bp):
CTAAACTCTGTCTGGGCTTGAACGAG
Found at i:260011 original size:167 final size:168
Alignment explanation
Indices: 259715--260045 Score: 495
Period size: 167 Copynumber: 2.0 Consensus size: 168
259705 ATCAATCATG
259715 GTTAAGTCAGTTTAACAACTTAGATGAAGATTTATGAAAACCTAACAATCGACATTTACTTATTC
1 GTTAAGTCAGTTTAACAACTTAGATGAAGATTTATGAAAACCTAACAATCGACATTTACTTATTC
*
259780 AAAACCCAACATTCAACATAATATATTCAAAAAGTCTTAATCAATTTCTTTGCAGTGAAAATTAT
66 AAAACCCAACATTCAACATAATATATTCAAAAAGTCTTAATCAATTTCTTTGCAATGAAAATTAT
* * * *
259845 CAGTATCAATCAATATCTTATACTTAGCCATTTACATA
131 CAATATCAATCAATATCTCATAATTACCCATTTACATA
* *
259883 GTTAAGTCAG-TTAACAACTTAGCTGAAGATTTATGAAAACCTGACAATC-AGCATTTACTTATT
1 GTTAAGTCAGTTTAACAACTTAGATGAAGATTTATGAAAACCTAACAATCGA-CATTTACTTATT
* * * ** *** *
259946 CAAAACCCAACATTCAATATAATCTATTTAAAGTGTCTTAATTGGTTTCTTTGCAATGGAAATTA
65 CAAAACCCAACATTCAACATAATATATTCAAAAAGTCTTAATCAATTTCTTTGCAATGAAAATTA
260011 TCAATATCAATCAATATCTCATAATTACCCATTTA
130 TCAATATCAATCAATATCTCATAATTACCCATTTA
260046 GCATGCATAG
Statistics
Matches: 146, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
166 1 0.01
167 135 0.92
168 10 0.07
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (168 bp):
GTTAAGTCAGTTTAACAACTTAGATGAAGATTTATGAAAACCTAACAATCGACATTTACTTATTC
AAAACCCAACATTCAACATAATATATTCAAAAAGTCTTAATCAATTTCTTTGCAATGAAAATTAT
CAATATCAATCAATATCTCATAATTACCCATTTACATA
Found at i:269640 original size:15 final size:15
Alignment explanation
Indices: 269620--269649 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
269610 CACTTCGAAA
269620 TAATCTAAGTTTGGC
1 TAATCTAAGTTTGGC
269635 TAATCTAAGTTTGGC
1 TAATCTAAGTTTGGC
269650 ATCAGACCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
TAATCTAAGTTTGGC
Found at i:270279 original size:63 final size:63
Alignment explanation
Indices: 270180--270305 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
270170 TTTTTTATTG
270180 AATACAAACTTCACATTTATCCACAAACTCATCATTACTTAGACTAATATAACTATTCTTTTT
1 AATACAAACTTCACATTTATCCACAAACTCATCATTACTTAGACTAATATAACTATTCTTTTT
270243 AATACAAACTTCACATTTATCCACAAACTCATCATTACTTAGACTAATATAACTATTCTTTTT
1 AATACAAACTTCACATTTATCCACAAACTCATCATTACTTAGACTAATATAACTATTCTTTTT
270306 CATATATTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (63 bp):
AATACAAACTTCACATTTATCCACAAACTCATCATTACTTAGACTAATATAACTATTCTTTTT
Found at i:275329 original size:21 final size:21
Alignment explanation
Indices: 275305--275350 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
275295 ACAAAAGATA
275305 CAAAAAAATCAAAATAATTTT
1 CAAAAAAATCAAAATAATTTT
**
275326 C-AAAAGTTCAAAATAATTTT
1 CAAAAAAATCAAAATAATTTT
*
275346 TAAAA
1 CAAAA
275351 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (21 bp):
CAAAAAAATCAAAATAATTTT
Found at i:275336 original size:20 final size:20
Alignment explanation
Indices: 275313--275350 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
275303 TACAAAAAAA
275313 TCAAAATAATTTTCAAAAGT
1 TCAAAATAATTTTCAAAAGT
*
275333 TCAAAATAATTTTTAAAA
1 TCAAAATAATTTTCAAAA
275351 TAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (20 bp):
TCAAAATAATTTTCAAAAGT
Found at i:275359 original size:19 final size:20
Alignment explanation
Indices: 275315--275368 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
275305 CAAAAAAATC
* **
275315 AAAATAATTTTCAAAAGTTC
1 AAAATAATTTTTAAAAGTAA
275335 AAAATAATTTTTAAAA-TAA
1 AAAATAATTTTTAAAAGTAA
*
275354 AAAAT-ATTTATAAAA
1 AAAATAATTTTTAAAA
275369 ATTTCAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 9 0.30
19 6 0.20
20 15 0.50
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATAATTTTTAAAAGTAA
Found at i:275424 original size:18 final size:18
Alignment explanation
Indices: 275403--275452 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
275393 AAATTTCAAT
275403 ATTTATATTTTTAAAAAA
1 ATTTATATTTTTAAAAAA
**
275421 ATTTA-AAATTTAAAAAA
1 ATTTATATTTTTAAAAAA
*
275438 ATATT-TTTTTTTAAA
1 AT-TTATATTTTTAAA
275453 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATATTTTTAAAAAA
Found at i:275431 original size:25 final size:26
Alignment explanation
Indices: 275360--275432 Score: 121
Period size: 26 Copynumber: 2.8 Consensus size: 26
275350 ATAAAAAATA
*
275360 TTTATAAAAATTTCAATATTTATATT
1 TTTAAAAAAATTTCAATATTTATATT
275386 TTTAAAAAAATTTCAATATTTATATT
1 TTTAAAAAAATTTCAATATTTATATT
*
275412 TTTAAAAAAATTT-AAAATTTA
1 TTTAAAAAAATTTCAATATTTA
275433 AAAAAATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 7 0.16
26 38 0.84
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTAAAAAAATTTCAATATTTATATT
Done.