Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002695.1 Kokia drynarioides strain JFW-HI SEQ_114971, 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: 8731
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:261 original size:15 final size:15
Alignment explanation
Indices: 241--272 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
231 TCTTACTTTC
241 TTCATTTTTCCACTT
1 TTCATTTTTCCACTT
256 TTCATTTTTCCACTT
1 TTCATTTTTCCACTT
271 TT
1 TT
273 GGTGGTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCATTTTTCCACTT
Found at i:1531 original size:100 final size:100
Alignment explanation
Indices: 1355--1553 Score: 344
Period size: 100 Copynumber: 2.0 Consensus size: 100
1345 TCATGATTAG
* **
1355 TCCCAAATTATAATAAACATGATATAATAAATAAATCATAGTGAAATATATCTGGTGATCTTTAA
1 TCCCAAATTATAATAAACATGATATAATAAATAAATCATAGTGAAATATACCTGAAGATCTTTAA
*
1420 CATCATTGTTATCACCTTAGCTATTATCATGAGCT
66 CATCATCGTTATCACCTTAGCTATTATCATGAGCT
*
1455 TCCCAAATTATAATAAACATTATATAATAAATAAATCATAGTGAAATATACCTGAAGATCTTTAA
1 TCCCAAATTATAATAAACATGATATAATAAATAAATCATAGTGAAATATACCTGAAGATCTTTAA
*
1520 TATCATCGTTATCACCTTAGCTATTATCATGAGC
66 CATCATCGTTATCACCTTAGCTATTATCATGAGC
1554 ACTGAGTAGT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (100 bp):
TCCCAAATTATAATAAACATGATATAATAAATAAATCATAGTGAAATATACCTGAAGATCTTTAA
CATCATCGTTATCACCTTAGCTATTATCATGAGCT
Found at i:1847 original size:6 final size:6
Alignment explanation
Indices: 1836--1867 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1826 ACCAAACCTT
*
1836 ATCTTG ATCTTG ATCTTT ATCTTG ATCTTG AT
1 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG AT
1868 GGACATCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (6 bp):
ATCTTG
Found at i:1918 original size:33 final size:33
Alignment explanation
Indices: 1876--1942 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1866 ATGGACATCC
1876 ATTTAATAAGATATTCATAACAGATCTAATATT
1 ATTTAATAAGATATTCATAACAGATCTAATATT
1909 ATTTAATAAGATATTCATAACAGATCTAATATT
1 ATTTAATAAGATATTCATAACAGATCTAATATT
1942 A
1 A
1943 ATATATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (33 bp):
ATTTAATAAGATATTCATAACAGATCTAATATT
Found at i:5450 original size:30 final size:29
Alignment explanation
Indices: 5409--5485 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
5399 TAAAAGTTTG
* * *
5409 TAAAGTATAATGATTAAAAATTAT-AAATT
1 TAAAATATAATGACTAAAAATGATCAAA-T
5438 ATAAAATATAATGACTAAAAATGATCAAAT
1 -TAAAATATAATGACTAAAAATGATCAAAT
*
5468 TAAAATAGAATGACTAAA
1 TAAAATATAATGACTAAA
5486 TCACAACTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.40
30 22 0.52
31 3 0.07
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (29 bp):
TAAAATATAATGACTAAAAATGATCAAAT
Found at i:7215 original size:3 final size:3
Alignment explanation
Indices: 7209--7233 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7199 CTCATCATCA
7209 TGT TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT T
7234 TTTTCTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:8539 original size:21 final size:21
Alignment explanation
Indices: 8515--8569 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 21
8505 GGACCAACGA
8515 AAAATGAAGGAAA-AAAGAAAG
1 AAAA-GAAGGAAAGAAAGAAAG
*
8536 AAAA-AAGAGAAAGAAAGAAATA
1 AAAAGAAG-GAAAGAAAGAAA-G
8558 AAGAAGAAGGAA
1 AA-AAGAAGGAA
8570 GAAGGAGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 3 0.11
20 4 0.14
21 11 0.39
22 2 0.07
23 5 0.18
24 3 0.11
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.04
Consensus pattern (21 bp):
AAAAGAAGGAAAGAAAGAAAG
Found at i:8550 original size:17 final size:18
Alignment explanation
Indices: 8528--8561 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
8518 ATGAAGGAAA
8528 AAAGAAAGAAA-AAAGAG
1 AAAGAAAGAAATAAAGAG
8545 AAAGAAAGAAATAAAGA
1 AAAGAAAGAAATAAAGA
8562 AGAAGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (18 bp):
AAAGAAAGAAATAAAGAG
Done.