Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010008.1 Kokia drynarioides strain JFW-HI SEQ_124769, 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: 41027
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:489 original size:4 final size:4
Alignment explanation
Indices: 470--549 Score: 65
Period size: 4 Copynumber: 19.8 Consensus size: 4
460 ACACATTACA
* * * *
470 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC -TTC TTTC TTTCC TCTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTT-C TTTC
* *
518 CTTC TTCC TTTC TTTC TTTC TTTCC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTT
550 TTTTGCCGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
3 6 0.10
4 45 0.74
5 10 0.16
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:537 original size:25 final size:20
Alignment explanation
Indices: 476--533 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
466 TACATTTCTT
476 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
496 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
516 TCCTTCTTCCTTTCTTTC
1 TCCTTCTT-CTTTCTTTC
534 TTTCTTTCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 28 0.76
21 9 0.24
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (20 bp):
TCCTTCTTCTTTCTTTCCTC
Found at i:542 original size:17 final size:17
Alignment explanation
Indices: 470--549 Score: 80
Period size: 17 Copynumber: 4.9 Consensus size: 17
460 ACACATTACA
470 TTTCTTTCC-TTC-TTC
1 TTTCTTTCCTTTCTTTC
* *
485 TTTCTTTCCTCTCCTTC
1 TTTCTTTCCTTTCTTTC
*
502 -TTCTTT-CTTTCCTCTC
1 TTTCTTTCCTTT-CTTTC
*
518 CTTC-TTCCTTTCTTTC
1 TTTCTTTCCTTTCTTTC
534 TTTCTTTCCTTTCTTT
1 TTTCTTTCCTTTCTTT
550 TTTTGCCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.23
16 20 0.38
17 21 0.40
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTTCCTTTCTTTC
Found at i:3257 original size:23 final size:23
Alignment explanation
Indices: 3230--3275 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3220 ATCAATGCTT
*
3230 ATTATGTTGCTTAGATCATAATC
1 ATTATGTTCCTTAGATCATAATC
*
3253 ATTATGTTCCTTGGATCATAATC
1 ATTATGTTCCTTAGATCATAATC
3276 CAAAGGTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (23 bp):
ATTATGTTCCTTAGATCATAATC
Found at i:11805 original size:23 final size:21
Alignment explanation
Indices: 11763--11805 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
11753 CTGAAATTGG
*
11763 AAAGTTCTAAATTCTAACTTA
1 AAAGTTCTAAATCCTAACTTA
*
11784 AAAGTGTCTCAAATCCTTACTT
1 AAAGT-TCT-AAATCCTAACTT
11806 TCTGGAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (21 bp):
AAAGTTCTAAATCCTAACTTA
Found at i:18413 original size:5 final size:5
Alignment explanation
Indices: 18403--18428 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
18393 CACCACCAAA
18403 GTTAG GTTAG GTTAG GTTAG GTTAG G
1 GTTAG GTTAG GTTAG GTTAG GTTAG G
18429 GGATCGCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTTAG
Found at i:18849 original size:21 final size:21
Alignment explanation
Indices: 18804--18849 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
18794 CTTATTTGGA
* *
18804 ATTATTATTGCATGATAAAGC
1 ATTATTATTGAATCATAAAGC
18825 ATTATTATTGTAATCATAAAG-
1 ATTATTATTG-AATCATAAAGC
18846 ATTA
1 ATTA
18850 GACTCCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (21 bp):
ATTATTATTGAATCATAAAGC
Found at i:19219 original size:2 final size:2
Alignment explanation
Indices: 19212--19240 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19202 AAGTTTTATT
19212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19241 TAAATATAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35276 original size:2 final size:2
Alignment explanation
Indices: 35269--35294 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35259 TTAAAAATTA
35269 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
35295 TTTACCAAGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36743 original size:6 final size:6
Alignment explanation
Indices: 36732--36773 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
36722 AGACAAGGAT
*
36732 AAAGAG AAAGAG AAAGAG AAAGAG -AAGA- AGAGAG AAA-AG AAA
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAA
36774 AATCAGAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 12 0.38
6 20 0.62
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:36753 original size:18 final size:17
Alignment explanation
Indices: 36732--36773 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
36722 AGACAAGGAT
36732 AAAGAGAAAGAGAAAGAG
1 AAAGAGAAAGA-AAAGAG
*
36750 AAAGAG-AAGAAGAGAG
1 AAAGAGAAAGAAAAGAG
36766 AAA-AGAAA
1 AAAGAGAAA
36774 AATCAGAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.09
16 10 0.45
17 4 0.18
18 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGAGAAAGAAAAGAG
Done.