Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006865.1 Kokia drynarioides strain JFW-HI SEQ_121464, 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: 18195
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:357 original size:130 final size:130
Alignment explanation
Indices: 124--367 Score: 425
Period size: 130 Copynumber: 1.9 Consensus size: 130
114 GATTTGCGAA
124 AGAGTCCAAGTTGCAAAACAAAATGAATAAATCCGATGATGTTTGGTAAATGGTTGAGGTGGTCT
1 AGAGTCCAAGTTGCAAAACAAAATGAATAAATCCGATGATGTTTGGTAAATGGTTGAGGTGGTCT
* * *
189 TGCATGTAATGTTCTGCCATGTAAACTGACATCGCCGTTAATCTAAACACGGATTTGTGAAATAG
66 TCCATGTAACGTTCTGCCATGTAAACTGACATCACCGTTAATCTAAACACGGATTTGTGAAATAG
* *
254 AGAGTCCTAGTTGCAAAACAAAATGAATAAATCCGATGATGTTTGGTAAATGGTTGAGGTGTTCT
1 AGAGTCCAAGTTGCAAAACAAAATGAATAAATCCGATGATGTTTGGTAAATGGTTGAGGTGGTCT
* *
319 TCCATGTTACGTTCTGCCATGTAAACTGACATCACCGTTATTCTAAACA
66 TCCATGTAACGTTCTGCCATGTAAACTGACATCACCGTTAATCTAAACA
368 TGTTAAGATA
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (130 bp):
AGAGTCCAAGTTGCAAAACAAAATGAATAAATCCGATGATGTTTGGTAAATGGTTGAGGTGGTCT
TCCATGTAACGTTCTGCCATGTAAACTGACATCACCGTTAATCTAAACACGGATTTGTGAAATAG
Found at i:1237 original size:17 final size:16
Alignment explanation
Indices: 1211--1242 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1201 GTAAAAATTA
1211 AGAAAAAATTTAATGC
1 AGAAAAAATTTAATGC
1227 AGAAGAAAATTTAATG
1 AGAA-AAAATTTAATG
1243 GACTTCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.16, T:0.25
Consensus pattern (16 bp):
AGAAAAAATTTAATGC
Found at i:12519 original size:24 final size:24
Alignment explanation
Indices: 12492--12553 Score: 61
Period size: 27 Copynumber: 2.5 Consensus size: 24
12482 TGTAATGACC
* *
12492 TCAGGTTCTTCTTCTACTTCCTCT
1 TCAGGTTCTTCTTCTACCTCCACT
*
12516 TCAGACCGTTCTTCTTCTTCCTCCACT
1 TCAG---GTTCTTCTTCTACCTCCACT
*
12543 TCAGCTTCTTC
1 TCAGGTTCTTC
12554 CTAGAATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 10 0.32
27 21 0.68
ACGTcount: A:0.10, C:0.37, G:0.08, T:0.45
Consensus pattern (24 bp):
TCAGGTTCTTCTTCTACCTCCACT
Found at i:14157 original size:85 final size:85
Alignment explanation
Indices: 14063--14331 Score: 226
Period size: 85 Copynumber: 3.1 Consensus size: 85
14053 ATATTAATCC
14063 TTTAATTATGTTGGTAAAATTTTAAAAAAGAAATTATTTTTCTTTTTTTTAAATGAAATTTTTTT
1 TTTAATTATGTTGGTAAAATTTTAAAAAAGAAATTATTTTTCTTTTTTTTAAATGAAATTTTTTT
14128 GAAGATTTATTTTGAAAAAT
66 GAAGATTTATTTTGAAAAAT
* * * * * * * * *
14148 TTTATTTATG-T--TAACATTTTATTTCAATACAAATTATAATTT-TTTGTTTAAATTATGTAAT
1 TTTAATTATGTTGGTAAAATTTTA---AAAAAGAAATTAT-TTTTCTTTTTTTTAA--ATGAAAT
**** * * * **
14209 CAAGTT-AAAATTTAATAT-ATTAAT
60 TTTTTTGAAGATTTATTTTGAAAAAT
*
14233 CCTTTAATTATGTTGGTAAAATTTTAAAAAAGAAATTATTTTTCTGTTTTTTAAATGAAATTTTT
1 --TTTAATTATGTTGGTAAAATTTTAAAAAAGAAATTATTTTTCTTTTTTTTAAATGAAATTTTT
* *
14298 ATGAAGATTTATTTTGAAAAAA
64 TTGAAGATTTATTTTGAAAAAT
*
14320 TTTATTTATGTT
1 TTTAATTATGTT
14332 AACATTTTAT
Statistics
Matches: 130, Mismatches: 40, Indels: 28
0.66 0.20 0.14
Matches are distributed among these distances:
82 9 0.07
84 1 0.01
85 49 0.38
86 24 0.18
87 37 0.28
88 1 0.01
90 9 0.07
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (85 bp):
TTTAATTATGTTGGTAAAATTTTAAAAAAGAAATTATTTTTCTTTTTTTTAAATGAAATTTTTTT
GAAGATTTATTTTGAAAAAT
Found at i:14314 original size:172 final size:172
Alignment explanation
Indices: 14028--14372 Score: 663
Period size: 172 Copynumber: 2.0 Consensus size: 172
14018 ATTTTTTTTT
14028 TTATGTAATCAAGTTAAAATTTAATATATTAATCCTTTAATTATGTTGGTAAAATTTTAAAAAAG
1 TTATGTAATCAAGTTAAAATTTAATATATTAATCCTTTAATTATGTTGGTAAAATTTTAAAAAAG
* * *
14093 AAATTATTTTTCTTTTTTTTAAATGAAATTTTTTTGAAGATTTATTTTGAAAAATTTTATTTATG
66 AAATTATTTTTCTGTTTTTTAAATGAAATTTTTATGAAGATTTATTTTGAAAAAATTTATTTATG
14158 TTAACATTTTATTTCAATACAAATTATAATTTTTTGTTTAAA
131 TTAACATTTTATTTCAATACAAATTATAATTTTTTGTTTAAA
14200 TTATGTAATCAAGTTAAAATTTAATATATTAATCCTTTAATTATGTTGGTAAAATTTTAAAAAAG
1 TTATGTAATCAAGTTAAAATTTAATATATTAATCCTTTAATTATGTTGGTAAAATTTTAAAAAAG
14265 AAATTATTTTTCTGTTTTTTAAATGAAATTTTTATGAAGATTTATTTTGAAAAAATTTATTTATG
66 AAATTATTTTTCTGTTTTTTAAATGAAATTTTTATGAAGATTTATTTTGAAAAAATTTATTTATG
14330 TTAACATTTTATTTCAATACAAATTATAATTTTTTGTTTAAA
131 TTAACATTTTATTTCAATACAAATTATAATTTTTTGTTTAAA
14372 T
1 T
14373 GAGAGATTAT
Statistics
Matches: 170, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
172 170 1.00
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.50
Consensus pattern (172 bp):
TTATGTAATCAAGTTAAAATTTAATATATTAATCCTTTAATTATGTTGGTAAAATTTTAAAAAAG
AAATTATTTTTCTGTTTTTTAAATGAAATTTTTATGAAGATTTATTTTGAAAAAATTTATTTATG
TTAACATTTTATTTCAATACAAATTATAATTTTTTGTTTAAA
Found at i:14354 original size:85 final size:84
Alignment explanation
Indices: 14093--14374 Score: 209
Period size: 85 Copynumber: 3.3 Consensus size: 84
14083 TTTAAAAAAG
* *
14093 AAATTATTTTTCTTTTTTTTAAATGAAATTTTTTTGAAGATTTATTTTGAAAAATTTTATTTATG
1 AAATTATTTTTC-TTTTTTTAAATGAAATTTTTATGAAGATTTATTTTGAAAAAATTTATTTATG
14158 TTAACATTTTATTTCAATAC
65 TTAACATTTTATTTCAATAC
* * * ** * ** * * *** *
14178 AAATTATAATTT-TTTGTTTAAATTATGTAATCAAGTTAAAATTTAATATATT--AATCCTTTAA
1 AAATTAT-TTTTCTTTTTTTAAATGAAAT-TTTTA-TGAAGATTT-AT-T-TTGAAAAAATTTAT
* * * *
14240 TTATGTTGGTAAAATTTTA---AAAAAG
60 TTATG-T--TAACATTTTATTTCAATAC
14265 AAATTATTTTTCTGTTTTTTAAATGAAATTTTTATGAAGATTTATTTTGAAAAAATTTATTTATG
1 AAATTATTTTTCT-TTTTTTAAATGAAATTTTTATGAAGATTTATTTTGAAAAAATTTATTTATG
14330 TTAACATTTTATTTCAATAC
65 TTAACATTTTATTTCAATAC
* *
14350 AAATTATAATTT-TTTGTTTAAATGA
1 AAATTAT-TTTTCTTTTTTTAAATGA
14375 GAGATTATTA
Statistics
Matches: 141, Mismatches: 39, Indels: 35
0.66 0.18 0.16
Matches are distributed among these distances:
82 9 0.06
83 2 0.01
84 25 0.18
85 32 0.23
86 23 0.16
87 26 0.18
88 13 0.09
89 2 0.01
90 9 0.06
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (84 bp):
AAATTATTTTTCTTTTTTTAAATGAAATTTTTATGAAGATTTATTTTGAAAAAATTTATTTATGT
TAACATTTTATTTCAATAC
Found at i:15713 original size:20 final size:20
Alignment explanation
Indices: 15684--15730 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
15674 TACTTTTTCT
*
15684 AAATTTTTAAAAAATA-ATTA
1 AAATTATTAAAAAATATA-TA
*
15704 AAATTATTAAGAAATATATA
1 AAATTATTAAAAAATATATA
15724 AAATTAT
1 AAATTAT
15731 AATAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATTATTAAAAAATATATA
Found at i:15969 original size:19 final size:19
Alignment explanation
Indices: 15945--16010 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
15935 CCAATTAAAT
15945 TTAAATTAACATTTAATAC
1 TTAAATTAACATTTAATAC
* *
15964 TTAAATT-CCACTTGAAT--
1 TTAAATTAACA-TTTAATAC
*
15981 TTGAATTAACATTTAATAC
1 TTAAATTAACATTTAATAC
16000 TTAAATTAACA
1 TTAAATTAACA
16011 ATTAGACTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
17 11 0.30
18 4 0.11
19 22 0.59
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (19 bp):
TTAAATTAACATTTAATAC
Found at i:15969 original size:36 final size:36
Alignment explanation
Indices: 15929--16006 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
15919 AAATTTTAAA
15929 TAAATTCCAATTAAATTTAAATTAACATTTAATACT
1 TAAATTCCAATTAAATTTAAATTAACATTTAATACT
* * *
15965 TAAATTCCACTTGAATTTGAATTAACATTTAATACT
1 TAAATTCCAATTAAATTTAAATTAACATTTAATACT
16001 TAAATT
1 TAAATT
16007 AACAATTAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.42
Consensus pattern (36 bp):
TAAATTCCAATTAAATTTAAATTAACATTTAATACT
Done.