Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004008.1 Kokia drynarioides strain JFW-HI SEQ_117122, 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: 24092
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:5465 original size:138 final size:139
Alignment explanation
Indices: 5297--5578 Score: 419
Period size: 138 Copynumber: 2.0 Consensus size: 139
5287 ACATGGAGAA
* *
5297 AATTAATATATGAATTTGACTCATACAAAATATT-ATTCGTATGTATTTTATCGAAA-TTATTAA
1 AATTAATATATGAATTTGACTCATACAAAATATTAATT-GTATATATTTTA-CCAAATTTATTAA
* * *
5360 TATAAATAGTTATAATAATTAATTTCAG-TCCATATATAAAAGACATGGAAAATAATATTCTTTT
64 TATAAACAGTTATAATAATTAATTTC-GTTCAAAATATAAAAGACATGGAAAATAATATTCTTTT
*
5424 -GAAAAGAATAT
128 GGAAAAAAATAT
*
5435 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTGACTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* * *
5500 TAAACAGTTATATTAATTAATTTCGTTCAAAATATAAAAGACATGGAAATTAATATTTTTTTGGA
66 TAAACAGTTATAATAATTAATTTCGTTCAAAATATAAAAGACATGGAAAATAATATTCTTTTGGA
5565 AAAAAATAT
131 AAAAAATAT
5574 AATTA
1 AATTA
5579 TTTCTTCTAA
Statistics
Matches: 130, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
137 5 0.04
138 107 0.82
139 18 0.14
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (139 bp):
AATTAATATATGAATTTGACTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
TAAACAGTTATAATAATTAATTTCGTTCAAAATATAAAAGACATGGAAAATAATATTCTTTTGGA
AAAAAATAT
Found at i:6539 original size:14 final size:14
Alignment explanation
Indices: 6492--6540 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
6482 CATTTCATAA
*
6492 TCATTCTTCATTTC
1 TCATTCTTCATTTT
6506 TCATTCTCTCA--TT
1 TCATTCT-TCATTTT
6519 TCATTCTTCATTTT
1 TCATTCTTCATTTT
*
6533 TCTTTCTT
1 TCATTCTT
6541 TCTTTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 3 0.10
13 8 0.27
14 16 0.53
15 3 0.10
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (14 bp):
TCATTCTTCATTTT
Found at i:13835 original size:13 final size:13
Alignment explanation
Indices: 13817--13856 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
13807 ACAAACAACC
13817 ATTAAAATTTTATA
1 ATTAAAA-TTTATA
*
13831 A-TAAAATTTAAA
1 ATTAAAATTTATA
13843 ATTAAAATTTATA
1 ATTAAAATTTATA
13856 A
1 A
13857 GGTTGAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 16 0.70
14 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTAAAATTTATA
Found at i:18608 original size:29 final size:29
Alignment explanation
Indices: 18566--18621 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
18556 TTCACTTCTG
* *
18566 CCAGATTGGTACCTATAGTTTTTTTTGTC
1 CCAGATTGGTACCTAAACTTTTTTTTGTC
18595 CCAGATTGGTACCTAAACTTTTTTTTG
1 CCAGATTGGTACCTAAACTTTTTTTTG
18622 GTTTGGTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (29 bp):
CCAGATTGGTACCTAAACTTTTTTTTGTC
Found at i:21628 original size:14 final size:14
Alignment explanation
Indices: 21611--21662 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
21601 AAGTCAATGA
*
21611 TCAACGATCAACTG
1 TCAACGATCAACAG
* * *
21625 TCAATGGTCAACGG
1 TCAACGATCAACAG
*
21639 TCAACGGTCAACAG
1 TCAACGATCAACAG
*
21653 TCAATGATCA
1 TCAACGATCA
21663 GGTTCGATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (14 bp):
TCAACGATCAACAG
Found at i:21628 original size:21 final size:21
Alignment explanation
Indices: 21603--21649 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
21593 AACCTAAAAA
*
21603 GTCAATGATCAACGATCAACT
1 GTCAATGATCAACGATCAACG
* *
21624 GTCAATGGTCAACGGTCAACG
1 GTCAATGATCAACGATCAACG
21645 GTCAA
1 GTCAA
21650 CAGTCAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
GTCAATGATCAACGATCAACG
Found at i:21640 original size:7 final size:7
Alignment explanation
Indices: 21611--21656 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
21601 AAGTCAATGA
*
21611 TCAACGA
1 TCAACGG
*
21618 TCAACTG
1 TCAACGG
*
21625 TCAATGG
1 TCAACGG
21632 TCAACGG
1 TCAACGG
21639 TCAACGG
1 TCAACGG
*
21646 TCAACAG
1 TCAACGG
21653 TCAA
1 TCAA
21657 TGATCAGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (7 bp):
TCAACGG
Found at i:21655 original size:21 final size:21
Alignment explanation
Indices: 21611--21662 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
21601 AAGTCAATGA
* **
21611 TCAACGATCAACTGTCAATGG
1 TCAACGATCAACGGTCAACAG
*
21632 TCAACGGTCAACGGTCAACAG
1 TCAACGATCAACGGTCAACAG
*
21653 TCAATGATCA
1 TCAACGATCA
21663 GGTTCGATCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
TCAACGATCAACGGTCAACAG
Found at i:21749 original size:29 final size:29
Alignment explanation
Indices: 21716--21782 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
21706 TTGGGGGATT
* *
21716 TGGTTTTAGGGTTTTGGTATTTGTTTTTA
1 TGGTTTTAGGGTTTGGGTATTTATTTTTA
21745 TGGTTTTAGGGTTTGGGTATTTATTTTTA
1 TGGTTTTAGGGTTTGGGTATTTATTTTTA
21774 TGGTTTTAG
1 TGGTTTTAG
21783 CTTTACACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (29 bp):
TGGTTTTAGGGTTTGGGTATTTATTTTTA
Done.