Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008415.1 Kokia drynarioides strain JFW-HI SEQ_123086, 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: 10416
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Found at i:139 original size:22 final size:20
Alignment explanation
Indices: 114--196 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 20
104 AAAAAACACC
*
114 AAAACAAAAACCAAAACAGTT
1 AAAAAAAAAACCAAAACAG-T
*
135 AAAAAAACAACACCAAAACAGC
1 AAAAAAA-AA-ACCAAAACAGT
*
157 AAAAAACACCAACCAAAACAGT
1 AAAAAA-A-AAACCAAAACAGT
**
179 AAAAAAAGCACCAAAACA
1 AAAAAAAAAACCAAAACA
197 ACAATATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.17
21 7 0.13
22 24 0.45
23 13 0.25
ACGTcount: A:0.67, C:0.24, G:0.05, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAACCAAAACAGT
Found at i:140 original size:23 final size:23
Alignment explanation
Indices: 114--185 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
104 AAAAAACACC
114 AAAACAAAAACCAAAACAGTTAAA
1 AAAACAAAAACCAAAACAG-TAAA
* *
138 AAAAC-AACACCAAAACAG-CAA
1 AAAACAAAAACCAAAACAGTAAA
**
159 AAAACACCAACCAAAACAGTAAA
1 AAAACAAAAACCAAAACAGTAAA
182 AAAA
1 AAAA
186 GCACCAAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 7 0.17
22 10 0.25
23 18 0.45
24 5 0.12
ACGTcount: A:0.69, C:0.22, G:0.04, T:0.04
Consensus pattern (23 bp):
AAAACAAAAACCAAAACAGTAAA
Found at i:883 original size:15 final size:15
Alignment explanation
Indices: 865--908 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
855 AAATTAATTT
865 AATAAAAATTATAAA
1 AATAAAAATTATAAA
* **
880 AATATAAATTATTCA
1 AATAAAAATTATAAA
895 AATATAAAATTATA
1 AATA-AAAATTATA
909 TTTTTAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAAAATTATAAA
Found at i:3511 original size:21 final size:21
Alignment explanation
Indices: 3484--3537 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
3474 CTAGGGATGG
*
3484 TTCTACCGATACAAGTGATAC
1 TTCTACCGATACAAGTCATAC
* * * *
3505 TTTTACCAAAACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
3526 TTCTACCGATAC
1 TTCTACCGATAC
3538 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:4282 original size:38 final size:37
Alignment explanation
Indices: 4180--4309 Score: 154
Period size: 37 Copynumber: 3.5 Consensus size: 37
4170 TTAATCCAGA
* * *
4180 ATTGCGCCCAAACATGTCGCTGCATAAGCACTTCTAG
1 ATTGCGCCCAAAAATGTCGCCGCATGAGCACTTCTAG
* *
4217 ATTGCGCCCAAACATGTCGCCGCATGAGCACCTCTAG
1 ATTGCGCCCAAAAATGTCGCCGCATGAGCACTTCTAG
* * *
4254 ATTGCGCCCAAAAATTGTCGCCACATGAGCAATTCCAG
1 ATTGCGCCCAAAAA-TGTCGCCGCATGAGCACTTCTAG
* *
4292 ATTGC-ACCAAAATTGTCG
1 ATTGCGCCCAAAAATGTCG
4310 ATGCACAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
36 5 0.06
37 53 0.65
38 24 0.29
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.22
Consensus pattern (37 bp):
ATTGCGCCCAAAAATGTCGCCGCATGAGCACTTCTAG
Found at i:7424 original size:25 final size:25
Alignment explanation
Indices: 7356--7505 Score: 124
Period size: 25 Copynumber: 5.9 Consensus size: 25
7346 TCATGCGAGC
**
7356 CCAGACAGAATCTA-GCTCTTACCAG
1 CCAGACAGAAT-TACGCTCTTATAAG
*
7381 CCCAGACAGAA-TATTGCTCTTATAAG
1 -CCAGACAGAATTA-CGCTCTTATAAG
* **
7407 CTAGACAGAATTACGCTCTTACGAG
1 CCAGACAGAATTACGCTCTTATAAG
* * *
7432 CCAGACAGAATTATGTTCTTACAAG
1 CCAGACAGAATTACGCTCTTATAAG
* *
7457 CCAGATAGAATTACGCTCTTATGAG
1 CCAGACAGAATTACGCTCTTATAAG
* *
7482 CCAAAATCAGAATTATGCTCTTAT
1 CC-AGA-CAGAATTACGCTCTTAT
7506 GTGCCAAAAT
Statistics
Matches: 101, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
24 2 0.02
25 61 0.60
26 23 0.23
27 15 0.15
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (25 bp):
CCAGACAGAATTACGCTCTTATAAG
Found at i:7467 original size:50 final size:50
Alignment explanation
Indices: 7356--7504 Score: 176
Period size: 50 Copynumber: 2.9 Consensus size: 50
7346 TCATGCGAGC
* *
7356 CCAGACAGAATCTA-GCTCTTACCAGCCCAGACAGAA-TATTGCTCTTATAAG
1 CCAGACAGAAT-TACGCTCTTACGAG-CCAGACAGAATTA-TGCTCTTACAAG
* *
7407 CTAGACAGAATTACGCTCTTACGAGCCAGACAGAATTATGTTCTTACAAG
1 CCAGACAGAATTACGCTCTTACGAGCCAGACAGAATTATGCTCTTACAAG
* * *
7457 CCAGATAGAATTACGCTCTTATGAGCCAAAATCAGAATTATGCTCTTA
1 CCAGACAGAATTACGCTCTTACGAGCC-AGA-CAGAATTATGCTCTTA
7505 TGTGCCAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
50 46 0.54
51 24 0.28
52 15 0.18
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (50 bp):
CCAGACAGAATTACGCTCTTACGAGCCAGACAGAATTATGCTCTTACAAG
Found at i:7501 original size:27 final size:26
Alignment explanation
Indices: 7412--7522 Score: 100
Period size: 25 Copynumber: 4.3 Consensus size: 26
7402 ATAAGCTAGA
*
7412 CAGAATTACGCTCTTACGAGCCAGA-
1 CAGAATTACGCTCTTACGAGCCAAAT
* * * *
7437 CAGAATTATGTTCTTACAAGCCAGAT
1 CAGAATTACGCTCTTACGAGCCAAAT
*
7463 -AGAATTACGCTCTTATGAGCCAAAAT
1 CAGAATTACGCTCTTACGAGCC-AAAT
* * *
7489 CAGAATTATGCTCTTATGTGCCAAAAT
1 CAGAATTACGCTCTTACGAGCC-AAAT
*
7516 CAAAATT
1 CAGAATT
7523 TCCTCGTCGT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
25 39 0.54
26 3 0.04
27 30 0.42
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (26 bp):
CAGAATTACGCTCTTACGAGCCAAAT
Found at i:9926 original size:33 final size:33
Alignment explanation
Indices: 9889--9951 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
9879 TGAATAGATT
*
9889 GCTCCCCCT-TAATAAAAGTCATTTTCAATTCAA
1 GCTCCCCCTAT-ATAAAAATCATTTTCAATTCAA
* *
9922 GCTCCTCCTATATAAAAATTATTTTCAATT
1 GCTCCCCCTATATAAAAATCATTTTCAATT
9952 TAAGGCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (33 bp):
GCTCCCCCTATATAAAAATCATTTTCAATTCAA
Done.