Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002091.1 Kokia drynarioides strain JFW-HI SEQ_114006, 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: 44585
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:2015 original size:22 final size:22
Alignment explanation
Indices: 1987--2031 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1977 GTTGCTATCT
1987 TCACAAAGGAATGAAACTTTTG
1 TCACAAAGGAATGAAACTTTTG
2009 TCACAAAGGAATGAAACTTTTG
1 TCACAAAGGAATGAAACTTTTG
2031 T
1 T
2032 ACTAATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (22 bp):
TCACAAAGGAATGAAACTTTTG
Found at i:7429 original size:130 final size:131
Alignment explanation
Indices: 7151--7470 Score: 417
Period size: 131 Copynumber: 2.4 Consensus size: 131
7141 ATATTTAACG
* * * * ** *
7151 AATTTTCAATCCTTTTTCATTTTTCATGTTTTTTCTTAAAATTTCATTTAATTTCCCTTTGTTGA
1 AATTTTCAATTCTTTTTCATTTTCCATATTTTTTCTTAAAATTTCATTTTATTTTACTCTGTTGA
* * * * * **
7216 CTGATTTATTTTTTACTGCCTCCACCCGAAGAACTTTGTTACTATAAAAAACAACAAAATCAAAC
66 CTGAATTATTCTTCACTACCTCCACCCGAAAAACCCTGTTACTATAAAAAACAACAAAATCAAAC
7281 C
131 C
* *
7282 AATTTTCAATTCTTTTTCATTTTCCATATTTTTTCTTAAATTTTCATTTTCTTTTACTCTGTTGA
1 AATTTTCAATTCTTTTTCATTTTCCATATTTTTTCTTAAAATTTCATTTTATTTTACTCTGTTGA
* * *
7347 CTGAATTATTCTTCACTACCTCCACCTGAAAAACCCTGTTTCTGT-AAAAACAACAAAATCAAAC
66 CTGAATTATTCTTCACTACCTCCACCCGAAAAACCCTGTTACTATAAAAAACAACAAAATCAAAC
7411 C
131 C
*
7412 AATTTTCAATTCTTTTTCATTTTTCACATTTTTTTTTTCTTAAAATTTCATTTTATTTT
1 AATTTTCAATTCTTTTTCA-TTTTC-CA--TATTTTTTCTTAAAATTTCATTTTATTTT
7471 CCAGTTGATT
Statistics
Matches: 163, Mismatches: 22, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
130 39 0.24
131 96 0.59
132 2 0.01
134 26 0.16
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.48
Consensus pattern (131 bp):
AATTTTCAATTCTTTTTCATTTTCCATATTTTTTCTTAAAATTTCATTTTATTTTACTCTGTTGA
CTGAATTATTCTTCACTACCTCCACCCGAAAAACCCTGTTACTATAAAAAACAACAAAATCAAAC
C
Found at i:17326 original size:80 final size:80
Alignment explanation
Indices: 17193--17354 Score: 279
Period size: 80 Copynumber: 2.0 Consensus size: 80
17183 AATCTTGACT
* * *
17193 TATGAATCCTTCTCACAAGCCCTTAATATATCAATCTTATAGGACCCAAACTTGAATCGCTGATC
1 TATGAATCCTCCTCACAAGCCCTTAATATATCAACCTTATAGGACCCAAACTTGAATCGCAGATC
17258 AATAATTTGAGATTA
66 AATAATTTGAGATTA
* *
17273 TATGAATCCTCCTCACAAGCCCTTAATATATCTACCTTATAGGACCCAGACTTGAATCGCAGATC
1 TATGAATCCTCCTCACAAGCCCTTAATATATCAACCTTATAGGACCCAAACTTGAATCGCAGATC
17338 AATAATTTGAGATTA
66 AATAATTTGAGATTA
17353 TA
1 TA
17355 GCCAAATTTC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (80 bp):
TATGAATCCTCCTCACAAGCCCTTAATATATCAACCTTATAGGACCCAAACTTGAATCGCAGATC
AATAATTTGAGATTA
Found at i:21650 original size:21 final size:22
Alignment explanation
Indices: 21614--21661 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
21604 TTAAAGTAAT
21614 TTTATATTAAATAATAATT-AAA
1 TTTATATTAAATAAT-ATTAAAA
*
21636 TTTATATT-TATAATATTAAAA
1 TTTATATTAAATAATATTAAAA
21657 TTTAT
1 TTTAT
21662 GTATTTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 13 0.54
22 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATATTAAATAATATTAAAA
Found at i:21676 original size:23 final size:20
Alignment explanation
Indices: 21629--21676 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 20
21619 ATTAAATAAT
21629 AATT-AAATTTATATTTATA
1 AATTAAAATTTATATTTATA
21648 ATATTAAAATTTATGTATTTATCA
1 A-ATTAAAATTTA--TATTTAT-A
21672 AATTA
1 AATTA
21677 CTATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 7 0.29
23 11 0.46
24 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
AATTAAAATTTATATTTATA
Found at i:35358 original size:30 final size:31
Alignment explanation
Indices: 35323--35385 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
35313 GATTTCTCCC
* *
35323 TTAAAAGTTTTAATTAGACCTTTCAA-ATTT
1 TTAAAAATTCTAATTAGACCTTTCAATATTT
* * *
35353 TTAAAAATTCTCATTATACCTTTTAATATTT
1 TTAAAAATTCTAATTAGACCTTTCAATATTT
35384 TT
1 TT
35386 TTGGAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (31 bp):
TTAAAAATTCTAATTAGACCTTTCAATATTT
Found at i:44388 original size:2 final size:2
Alignment explanation
Indices: 44381--44408 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44371 GTGAACTTAC
44381 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
44409 ATACACCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:44509 original size:2 final size:2
Alignment explanation
Indices: 44502--44527 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44492 GTGAACTTAC
44502 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
44528 ATACACCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:44541 original size:119 final size:120
Alignment explanation
Indices: 44367--44585 Score: 422
Period size: 119 Copynumber: 1.8 Consensus size: 120
44357 TTGTTGGATT
44367 CCTTGTGAACTTACGTGTGTGTGTGTGTGTGTGTGTGTGTGTATACACCACCTTTTCTTTAATTA
1 CCTTGTGAACTTACG-GTGTGTGTGTGTGTGTGTGTGTGTGTATACACCACCTTTTCTTTAATTA
44432 AATTGTGCTCTTCACTGCTATTTTCAGATATAGTTTATACATATATATATATATAA
65 AATTGTGCTCTTCACTGCTATTTTCAGATATAGTTTATACATATATATATATATAA
44488 CCTTGTGAACTTAC-GTGTGTGTGTGTGTGTGTGTGTGTGTATACACCACCTTTTCTTTAATTAA
1 CCTTGTGAACTTACGGTGTGTGTGTGTGTGTGTGTGTGTGTATACACCACCTTTTCTTTAATTAA
44552 ATTGTGCTCTTCACTGCTATTTTCAGATATAGTT
66 ATTGTGCTCTTCACTGCTATTTTCAGATATAGTT
Statistics
Matches: 98, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
119 84 0.86
121 14 0.14
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (120 bp):
CCTTGTGAACTTACGGTGTGTGTGTGTGTGTGTGTGTGTGTATACACCACCTTTTCTTTAATTAA
ATTGTGCTCTTCACTGCTATTTTCAGATATAGTTTATACATATATATATATATAA
Done.