Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013232.1 Kokia drynarioides strain JFW-HI SEQ_128251, 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: 16333
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Found at i:546 original size:20 final size:19
Alignment explanation
Indices: 523--568 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
513 TTCAAAACAG
*
523 AAAACAATAAATAAAAATAT
1 AAAACAATAAAT-AAAATAC
* *
543 AAAACGATTAATAAAATAC
1 AAAACAATAAATAAAATAC
562 AAAACAA
1 AAAACAA
569 ATTAAAAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAACAATAAATAAAATAC
Found at i:572 original size:20 final size:20
Alignment explanation
Indices: 523--573 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
513 TTCAAAACAG
* *
523 AAAACAATAAATAAAAATAT
1 AAAACAATTAATAAAAATAC
*
543 AAAACGATTAAT-AAAATAC
1 AAAACAATTAATAAAAATAC
562 AAAACAAATTAA
1 AAAAC-AATTAA
574 AAGGAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAACAATTAATAAAAATAC
Found at i:7556 original size:23 final size:23
Alignment explanation
Indices: 7526--7579 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
7516 ACACTAGCGC
*
7526 GCTTACTGTTTCGTACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
7549 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
7572 GCCTACTG
1 GCTTACTG
7580 ATTTGTGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:7628 original size:21 final size:20
Alignment explanation
Indices: 7567--7636 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 20
7557 TTTCGCACTT
7567 TGTGTGCCTACTGATTTGTGCTA-
1 TGTGTGCCTACTGA--T-TGC-AC
*
7590 TGTGCGCCTACTGATTGCAC
1 TGTGTGCCTACTGATTGCAC
7610 TGTGTGCCTACTGGATTGCAC
1 TGTGTGCCTACT-GATTGCAC
7631 TGTGTG
1 TGTGTG
7637 TGCTTACTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.02
20 14 0.33
21 15 0.35
23 13 0.30
ACGTcount: A:0.13, C:0.21, G:0.29, T:0.37
Consensus pattern (20 bp):
TGTGTGCCTACTGATTGCAC
Found at i:7644 original size:23 final size:21
Alignment explanation
Indices: 7540--7645 Score: 88
Period size: 23 Copynumber: 4.8 Consensus size: 21
7530 ACTGTTTCGT
* *
7540 ACTTCGTGTGCTTACTGTTTCGC
1 ACTT-GTGTGCCTACTGATT-GC
*
7563 ACTTTGTGTGCCTACTGATTTGT
1 AC-TTGTGTGCCTACTGA-TTGC
* *
7586 GCTATGTGCGCCTACTGATTGC
1 ACT-TGTGTGCCTACTGATTGC
7608 AC-TGTGTGCCTACTGGATTGC
1 ACTTGTGTGCCTACT-GATTGC
*
7629 ACTGTGTGTGCTTACTG
1 ACT-TGTGTGCCTACTG
7646 TTTCCCCAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
20 11 0.16
21 8 0.12
22 6 0.09
23 39 0.57
24 4 0.06
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (21 bp):
ACTTGTGTGCCTACTGATTGC
Found at i:7645 original size:43 final size:45
Alignment explanation
Indices: 7545--7645 Score: 109
Period size: 43 Copynumber: 2.3 Consensus size: 45
7535 TTCGTACTTC
* **
7545 GTGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGATTTGTGCTAT
1 GTGTGCTTACTGATTCGCAC-TTGTGTGCCTACTGATTTGCACTAT
* * *
7591 GTGCGCCTACTGATT-GCAC-TGTGTGCCTACTGGA-TTGCACTGT
1 GTGTGCTTACTGATTCGCACTTGTGTGCCTACT-GATTTGCACTAT
7634 GTGTGCTTACTG
1 GTGTGCTTACTG
7646 TTTCCCCAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 28 0.61
44 2 0.04
45 4 0.09
46 12 0.26
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.40
Consensus pattern (45 bp):
GTGTGCTTACTGATTCGCACTTGTGTGCCTACTGATTTGCACTAT
Found at i:15441 original size:85 final size:85
Alignment explanation
Indices: 15228--15485 Score: 275
Period size: 87 Copynumber: 3.0 Consensus size: 85
15218 CTTCAAACCC
* * * *
15228 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAGTAAAGCAGTTACCTTCTTGATGAGA
1 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATGAAGCGGTCACCTTCTTGATGAGA
* * *
15293 TACAGAAAAGTGAACCAAACCT
66 TATAGAGAAGTAAACCAAA--T
* * *
15315 CCATATTCCTGATAAGATACAGAGAAGTGGGTCAATGCAATGAAGCGGTCACCTTCTTGATGAGA
1 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATGAAGCGGTCACCTTCTTGATGAGA
15380 TATAGAGAAGTAAACCAAAT
66 TATAGAGAAGTAAACCAAAT
** * *** * * * * * *
15400 CTGTCTTCCTGATGAGATACAAAGAAGTAAATTAAAACAATGAGGCGGTCATCTTCCTGATGTGA
1 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATGAAGCGGTCACCTTCTTGATGAGA
*
15465 TACT-GAGAAGTAGACCAAAT
66 TA-TAGAGAAGTAAACCAAAT
15485 C
1 C
15486 GATGAAGCAA
Statistics
Matches: 144, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
85 69 0.48
86 1 0.01
87 74 0.51
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (85 bp):
CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATGAAGCGGTCACCTTCTTGATGAGA
TATAGAGAAGTAAACCAAAT
Found at i:15588 original size:209 final size:209
Alignment explanation
Indices: 15320--15909 Score: 856
Period size: 209 Copynumber: 2.8 Consensus size: 209
15310 AACCTCCATA
* * * * * *
15320 TTCCTGATAAGATACAGAGAAGTGGGTCAATGCAATGAAGCGGTCACCTTCTTGATGAGATATAG
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCCTGATGAGATACAG
*
15385 AGAAGTAAACCAAATCTGTCTTCCTGATGAGATACAAAGAAGTAAATTAAAACAATGAGGCGGTC
66 AGAAGTGAACCAAATCTGTCTTCCTGATGAGATACAAAGAAGTAAATTAAAACAATGAGGCGGTC
* *
15450 ATCTTCCTGATGTGATACTGAGAAGTAGACCAAATCGATGAAGCAAAGCTCAATGTGAGTGAAAC
131 ATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCGATGAAGCAAAGCTCAATGTGAGTGAAAC
* *
15515 TTTAAACCCATATC
196 TTCAAACCCACATC
* *
15529 TTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCAGTCCCCTTCCTGATGAGATACAG
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCCTGATGAGATACAG
* *
15594 AGAAGTGAACCAAATCTGTCTTCCTGATGAGATACAAAGAAGTATATTAAAACAATGAGGCGATC
66 AGAAGTGAACCAAATCTGTCTTCCTGATGAGATACAAAGAAGTAAATTAAAACAATGAGGCGGTC
* *
15659 ATCTTCTTGATGAGATACTGAGAAATAAACCAAATCGATGAAGCAAAGCTCAATGTGAGTGAAAC
131 ATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCGATGAAGCAAAGCTCAATGTGAGTGAAAC
*
15724 TTCAAACCCCCATC
196 TTCAAACCCACATC
* * ** *
15738 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAGGAAGTCATATTCCTGATGAGATACAT
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCCTGATGAGATACAG
** * * ** * *
15803 AGAAGTGAGTCAAATCCGTCTTCCTGATGAGATACAAAAAAGTGGATCAAAACAATGAGGCAGTC
66 AGAAGTGAACCAAATCTGTCTTCCTGATGAGATACAAAGAAGTAAATTAAAACAATGAGGCGGTC
* ** * *
15868 ATCTTTTTGATGAGATACAAAGAAGTTGACCAAATCAATGAA
131 ATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCGATGAA
15910 ACAGAGATTG
Statistics
Matches: 340, Mismatches: 41, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
209 340 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (209 bp):
TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCCTGATGAGATACAG
AGAAGTGAACCAAATCTGTCTTCCTGATGAGATACAAAGAAGTAAATTAAAACAATGAGGCGGTC
ATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCGATGAAGCAAAGCTCAATGTGAGTGAAAC
TTCAAACCCACATC
Found at i:15836 original size:85 final size:85
Alignment explanation
Indices: 15736--15893 Score: 226
Period size: 85 Copynumber: 1.9 Consensus size: 85
15726 CAAACCCCCA
* * * *
15736 TCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAGGAAGTCATATTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAAAAAAGTGGATCAAAACAATAAGGAAGTCATATTCCTGATGAGATAC
*
15801 ATAGAAGTGAGTCAAATCCG
66 AAAGAAGTGAGTCAAATCCG
* * * **
15821 TCTTCCTGATGAGATACAAAAAAGTGGATCAAAACAATGAGGCAGTCATCTTTTTGATGAGATAC
1 TCTTCCTGATGAGATACAAAAAAGTGGATCAAAACAATAAGGAAGTCATATTCCTGATGAGATAC
15886 AAAGAAGT
66 AAAGAAGT
15894 TGACCAAATC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 63 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAAAAAAGTGGATCAAAACAATAAGGAAGTCATATTCCTGATGAGATAC
AAAGAAGTGAGTCAAATCCG
Found at i:16238 original size:13 final size:13
Alignment explanation
Indices: 16220--16245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16210 TTAACCCATT
16220 TACACCAACCCAA
1 TACACCAACCCAA
16233 TACACCAACCCAA
1 TACACCAACCCAA
16246 GTTTCAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (13 bp):
TACACCAACCCAA
Done.