Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007275.1 Kokia drynarioides strain JFW-HI SEQ_121891, 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: 40185
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:6363 original size:31 final size:31
Alignment explanation
Indices: 6337--6416 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
6327 AAACTTAACG
6337 ATTGTTCTCATATTAGGGTTTGAACTTAGAA
1 ATTGTTCTCATATTAGGGTTTGAACTTAGAA
6368 ATTGTTCTCATATTAGGGTTTGAACTTAGAA
1 ATTGTTCTCATATTAGGGTTTGAACTTAGAA
*
6399 ATTGTTCTCACATTAGGG
1 ATTGTTCTCATATTAGGG
6417 CTTAAACTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (31 bp):
ATTGTTCTCATATTAGGGTTTGAACTTAGAA
Found at i:9190 original size:42 final size:43
Alignment explanation
Indices: 9121--9352 Score: 229
Period size: 42 Copynumber: 5.4 Consensus size: 43
9111 GAAACACTTA
*
9121 ATGTATAAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
1 ATGTTTAAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
* *
9164 AAGTTTAAAA-GAAGACTCATGACTCAGAATGAGCATGAG-AT
1 ATGTTTAAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
** * * *
9205 ATGTTTAAAAAATAAGACTCATGACTC-GAAATGTGCATGAAAAT
1 ATGTTT-AAAAGGAAGACTCATGTCTCAG-AATGAGCATGAGAAT
* * * * * * *
9249 ATGTTTAAAAATGAAGAATTATGTCTCCGGATGAGAATGAGATT
1 ATGTTT-AAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
* * * * *
9293 ATGTTT-AAAGGAAGATTCATGTCTCGGAATGAGCGTAAGATT
1 ATGTTTAAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
9335 ATGTTTAAAAGGAAGACT
1 ATGTTTAAAAGGAAGACT
9353 TATGCCTCGG
Statistics
Matches: 157, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
41 7 0.04
42 67 0.43
43 42 0.27
44 40 0.25
45 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (43 bp):
ATGTTTAAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
Found at i:9243 original size:43 final size:43
Alignment explanation
Indices: 9127--9391 Score: 186
Period size: 42 Copynumber: 6.2 Consensus size: 43
9117 CTTAATGTAT
* * *
9127 AAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAATAAGTTT-
1 AAAAAGAAGACTCATGACTCAGAATGAGCATGAG-ATATGTTTA
9170 -AAAAGAAGACTCATGACTCAGAATGAGCATGAGATATGTTTA
1 AAAAAGAAGACTCATGACTCAGAATGAGCATGAGATATGTTTA
* * *
9212 AAAAATAAGACTCATGACTC-GAAATGTGCATGAAAATATGTTTA
1 AAAAAGAAGACTCATGACTCAG-AATGAGCATG-AGATATGTTTA
* * * * * * *
9256 AAAATGAAGAATTATGTCTCCGGATGAGAATGAGATTATGTTT-
1 AAAAAGAAGACTCATGACTCAGAATGAGCATGAGA-TATGTTTA
* * * * * *
9299 -AAAGGAAGATTCATGTCTCGGAATGAGCGTAAGATTATGTTT-
1 AAAAAGAAGACTCATGACTCAGAATGAGCATGAGA-TATGTTTA
* * * * * * *
9341 AAAAGGAAGACTTATGCCTCGGTA-GAACATAAGAT-TGTTTA
1 AAAAAGAAGACTCATGACTCAGAATGAGCATGAGATATGTTTA
*
9382 AAAAGGAAGA
1 AAAAAGAAGA
9392 TTTATGAACC
Statistics
Matches: 185, Mismatches: 29, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
40 5 0.03
41 18 0.10
42 74 0.40
43 48 0.26
44 39 0.21
45 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.26
Consensus pattern (43 bp):
AAAAAGAAGACTCATGACTCAGAATGAGCATGAGATATGTTTA
Found at i:12065 original size:22 final size:22
Alignment explanation
Indices: 12005--12065 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
11995 TAGTGTCATT
* *
12005 AAAATCACATCAAACTATACCT
1 AAAATCACATCAAACTCTACCC
12027 AAAATCACATCAAACTCTACCC
1 AAAATCACATCAAACTCTACCC
12049 AAAATCACATCAAACTC
1 AAAATCACATCAAACTC
12066 GCAAAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAATCACATCAAACTCTACCC
Found at i:16421 original size:44 final size:43
Alignment explanation
Indices: 16293--16484 Score: 203
Period size: 44 Copynumber: 4.5 Consensus size: 43
16283 GGAACACTTG
* * *
16293 ATGTATAAAAGGAAGAATCATGTCTCGAAATGAGCATGAGAAT
1 ATGTTTAAAAGGAAGACTCATGACTCGAAATGAGCATGAGAAT
* * * * *
16336 AAGTTT--AAGGAAGACTCGTGACTCG-GATAAGCATAAGAAT
1 ATGTTTAAAAGGAAGACTCATGACTCGAAATGAGCATGAGAAT
* *
16376 ATGTTTAAAAAGGAATACTCATGACTCAAAATGAGCATGAGAAT
1 ATGTTT-AAAAGGAAGACTCATGACTCGAAATGAGCATGAGAAT
* * * *
16420 ATGTTTGAAAAGGAAGACTCATGTCTCGAGATGAGAATGAGATT
1 ATGTTT-AAAAGGAAGACTCATGACTCGAAATGAGCATGAGAAT
*
16464 ATATTT-AAAGGAAGACTCATG
1 ATGTTTAAAAGGAAGACTCATG
16485 TTTTTGAATG
Statistics
Matches: 122, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
40 17 0.14
41 16 0.13
42 15 0.12
43 20 0.16
44 54 0.44
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (43 bp):
ATGTTTAAAAGGAAGACTCATGACTCGAAATGAGCATGAGAAT
Found at i:16496 original size:42 final size:42
Alignment explanation
Indices: 16300--16523 Score: 193
Period size: 44 Copynumber: 5.3 Consensus size: 42
16290 TTGATGTATA
* * *
16300 AAAGGAAGAATCATGTCTCGAAATGAGCATGAGAATAAGTTT-
1 AAAGGAAGACTCATGTCTCG-AATGAGCATGAGATTATGTTTG
* * * * * * *
16342 -AAGGAAGACTCGTGACTCGGATAAGCATAAGAATATGTTTAA
1 AAAGGAAGACTCATGTCTCGAATGAGCATGAGATTATGTTT-G
* * * *
16384 AAAGGAATACTCATGACTCAAAATGAGCATGAGAATATGTTTG
1 AAAGGAAGACTCATGTCTC-GAATGAGCATGAGATTATGTTTG
* *
16427 AAAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATATTT-
1 -AAAGGAAGACTCATGTCTCGA-ATGAGCATGAGATTATGTTTG
* * * *
16470 AAAGGAAGACTCATGTTTTTGAATGAGCGTAAGATTATGTTTG
1 AAAGGAAGACTCATG-TCTCGAATGAGCATGAGATTATGTTTG
16513 AAAGGAAGACT
1 AAAGGAAGACT
16524 TATGCCTTAG
Statistics
Matches: 148, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
40 17 0.11
41 16 0.11
42 31 0.21
43 32 0.22
44 52 0.35
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAATGAGCATGAGATTATGTTTG
Found at i:16545 original size:42 final size:42
Alignment explanation
Indices: 16300--16564 Score: 162
Period size: 44 Copynumber: 6.3 Consensus size: 42
16290 TTGATGTATA
* * * * * *
16300 AAAGGAAGAATCATGTCTCGAAATGAGCATGAGAATAAGTTT-
1 AAAGGAAGACTCATGTCT-TAGATGAGCATAAGATTATGTTTG
* * ** * * *
16342 -AAGGAAGACTCGTGACTCGGATAAGCATAAGAATATGTTTAA
1 AAAGGAAGACTCATGTCTTAGATGAGCATAAGATTATGTTT-G
* * * * * *
16384 AAAGGAATACTCATGACTCAAAATGAGCATGAGAATATGTTTG
1 AAAGGAAGACTCATGTCT-TAGATGAGCATAAGATTATGTTTG
* * * *
16427 AAAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATATTT-
1 -AAAGGAAGACTCATGTCT-TAGATGAGCATAAGATTATGTTTG
* * *
16470 AAAGGAAGACTCATGTTTTTGAATGAGCGTAAGATTATGTTTG
1 AAAGGAAGACTCATGTCTTAG-ATGAGCATAAGATTATGTTTG
* * * *
16513 AAAGGAAGACTTATGCCTTAG-TAGAGCATAAGATTGT-TTTA
1 AAAGGAAGACTCATGTCTTAGAT-GAGCATAAGATTATGTTTG
16554 AAAGGAAGACT
1 AAAGGAAGACT
16565 TATGAACCTA
Statistics
Matches: 177, Mismatches: 38, Indels: 17
0.76 0.16 0.07
Matches are distributed among these distances:
40 17 0.10
41 30 0.17
42 45 0.25
43 32 0.18
44 53 0.30
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTTAGATGAGCATAAGATTATGTTTG
Found at i:18875 original size:54 final size:54
Alignment explanation
Indices: 18816--18923 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
18806 ACAACCCTAG
18816 AAAGTCTTCTAGGTGGGAATGAACCCAAAATTGGTATTGCCCATCCGTGAACCC
1 AAAGTCTTCTAGGTGGGAATGAACCCAAAATTGGTATTGCCCATCCGTGAACCC
18870 AAAGTCTTCTAGGTGGGAATGAACCCAAAATTGGTATTGCCCATCCGTGAACCC
1 AAAGTCTTCTAGGTGGGAATGAACCCAAAATTGGTATTGCCCATCCGTGAACCC
18924 TTATTCCCCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (54 bp):
AAAGTCTTCTAGGTGGGAATGAACCCAAAATTGGTATTGCCCATCCGTGAACCC
Found at i:19164 original size:17 final size:19
Alignment explanation
Indices: 19132--19170 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
19122 TCAATTTTTA
19132 CTTTATTTTATTTTAT-CT
1 CTTTATTTTATTTTATGCT
19150 CTTTATTTT-TTTTATGCT
1 CTTTATTTTATTTTATGCT
19168 CTT
1 CTT
19171 AAAAACACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.72
Consensus pattern (19 bp):
CTTTATTTTATTTTATGCT
Found at i:28022 original size:15 final size:14
Alignment explanation
Indices: 28002--28053 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
27992 ACAAACATAA
28002 TTTTTTTATTTTCAT
1 TTTTTTTATTTTC-T
28017 TTTTTTTATTTTCT
1 TTTTTTTATTTTCT
* * *
28031 TTTTCTCATTTTTT
1 TTTTTTTATTTTCT
28045 TTCTTTTTA
1 TT-TTTTTA
28054 AGTGACTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 14 0.45
15 17 0.55
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTATTTTCT
Found at i:35558 original size:42 final size:42
Alignment explanation
Indices: 35473--35563 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
35463 CTAGATTGCA
* **
35473 TGACTTTTTACCACCAACTTCATGCAATACTGACTTTTTGTG
1 TGACTTTTTACCACCAACTTCACGCAATACTGACTTTCAGTG
* * *
35515 TGACTTTTTACCGCCTACTTCGCGCAATACTGACTTTCAGTG
1 TGACTTTTTACCACCAACTTCACGCAATACTGACTTTCAGTG
35557 TGGACTT
1 T-GACTT
35564 AAATTGTCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 37 0.88
43 5 0.12
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (42 bp):
TGACTTTTTACCACCAACTTCACGCAATACTGACTTTCAGTG
Done.