Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014679.1 Kokia drynarioides strain JFW-HI SEQ_129718, 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: 331910
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 120 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:314536 original size:24 final size:24
Alignment explanation
Indices: 314495--314572 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
314485 CCCGCACGAA
* * *
314495 CCCAAATTGATTATCTCTTACAAG
1 CCCAAAATGGTTAGCTCTTACAAG
* *
314519 CCCAGAATGGTTAGCTCTTACGAG
1 CCCAAAATGGTTAGCTCTTACAAG
**
314543 CCCAAAATGGTTAGCTCTTATGAG
1 CCCAAAATGGTTAGCTCTTACAAG
314567 CCCAAA
1 CCCAAA
314573 CAGAGTTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (24 bp):
CCCAAAATGGTTAGCTCTTACAAG
Found at i:315805 original size:21 final size:21
Alignment explanation
Indices: 315779--315850 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
315769 ATGCCATAGG
315779 TTAATTTACCTATTTGATCCT
1 TTAATTTACCTATTTGATCCT
** ***
315800 TTAA-TTACACTAAAATGCCATAGG
1 TTAATTTAC-CT-ATTTG--ATCCT
315824 TTAATTTACCTATTTGATCCT
1 TTAATTTACCTATTTGATCCT
315845 TTAATT
1 TTAATT
315851 ATATTAAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 4 0.11
21 14 0.39
22 3 0.08
23 3 0.08
24 8 0.22
25 4 0.11
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.46
Consensus pattern (21 bp):
TTAATTTACCTATTTGATCCT
Found at i:315812 original size:45 final size:45
Alignment explanation
Indices: 315762--315851 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
315752 ATAATCCACC
315762 CACTAAAATGCCATAGGTTAATTTACCTATTTGATCCTTTAATTA
1 CACTAAAATGCCATAGGTTAATTTACCTATTTGATCCTTTAATTA
315807 CACTAAAATGCCATAGGTTAATTTACCTATTTGATCCTTTAATTA
1 CACTAAAATGCCATAGGTTAATTTACCTATTTGATCCTTTAATTA
315852 TATTAAATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (45 bp):
CACTAAAATGCCATAGGTTAATTTACCTATTTGATCCTTTAATTA
Found at i:316683 original size:19 final size:19
Alignment explanation
Indices: 316661--316705 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
316651 TTTTATTAGG
316661 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
316680 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
316699 ATTTAAT
1 ATTTAAT
316706 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:320129 original size:22 final size:22
Alignment explanation
Indices: 320101--320144 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
320091 TGACATGTCA
320101 GTAATAGATTATGAGTGGGAAT
1 GTAATAGATTATGAGTGGGAAT
320123 GTAATAGATTATGAGTGGGAAT
1 GTAATAGATTATGAGTGGGAAT
320145 TCTCAAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (22 bp):
GTAATAGATTATGAGTGGGAAT
Found at i:324753 original size:13 final size:12
Alignment explanation
Indices: 324744--324799 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
324734 TATATAATAT
324744 AAAAGAATAAAG
1 AAAAGAATAAAG
324756 AAAAGAA-AAAG
1 AAAAGAATAAAG
* * *
324767 AAACAAAAGAAGG
1 AAA-AGAATAAAG
*
324780 AATAGAATAACAG
1 AAAAGAATAA-AG
324793 AAAAGAA
1 AAAAGAA
324800 GCTCAAATGA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 7 0.21
12 15 0.44
13 12 0.35
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (12 bp):
AAAAGAATAAAG
Found at i:324767 original size:18 final size:18
Alignment explanation
Indices: 324744--324799 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
324734 TATATAATAT
324744 AAAAGAATAAAGAAAAGA
1 AAAAGAATAAAGAAAAGA
*
324762 AAAAGAA-ACAA-AAGAAGG
1 AAAAGAATA-AAGAA-AAGA
*
324780 AATAGAATAACAGAAAAGA
1 AAAAGAATAA-AGAAAAGA
324799 A
1 A
324800 GCTCAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
17 3 0.10
18 19 0.63
19 6 0.20
20 2 0.07
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (18 bp):
AAAAGAATAAAGAAAAGA
Found at i:325241 original size:17 final size:18
Alignment explanation
Indices: 325219--325252 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
325209 TAAATGAGTT
325219 AATTAGGAT-TAAATTGA
1 AATTAGGATATAAATTGA
*
325236 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
325253 GATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGA
Found at i:331818 original size:2 final size:2
Alignment explanation
Indices: 331813--331841 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
331803 GATTAATGAA
331813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
331842 AATTAAAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.