Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014687.1 Kokia drynarioides strain JFW-HI SEQ_129726, 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: 36531
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:2646 original size:39 final size:40
Alignment explanation
Indices: 2593--2672 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
2583 AAGAAGTATG
*
2593 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* * *
2633 TCCAATTTG-AAAGGGTTGTGACTCTTTAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
2672 T
1 T
2673 TAAGTGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Found at i:10456 original size:20 final size:19
Alignment explanation
Indices: 10424--10480 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
10414 ATATATGATG
10424 ATTTGATTT-TAATTTTTGTT
1 ATTT-ATTTATAATTTTT-TT
10444 ATTTATTTATAATTATTTTT
1 ATTTATTTATAATT-TTTTT
* * *
10464 ATCTACTAATAATTTTT
1 ATTTATTTATAATTTTT
10481 ATAGTAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.22
20 22 0.69
21 3 0.09
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
ATTTATTTATAATTTTTTT
Found at i:14875 original size:16 final size:17
Alignment explanation
Indices: 14854--14886 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
14844 ATGACTAGAG
14854 CATATAAATTT-AAATT
1 CATATAAATTTGAAATT
*
14870 CATATATATTTGAAATT
1 CATATAAATTTGAAATT
14887 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
CATATAAATTTGAAATT
Found at i:15998 original size:11 final size:12
Alignment explanation
Indices: 15974--16003 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
15964 TTTATTGGCC
15974 CGTTTATAAGCT
1 CGTTTATAAGCT
15986 CGTTTAT-AGCT
1 CGTTTATAAGCT
15997 CGTTTAT
1 CGTTTAT
16004 TTATTAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.47
Consensus pattern (12 bp):
CGTTTATAAGCT
Found at i:16121 original size:24 final size:23
Alignment explanation
Indices: 16094--16156 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
16084 TCATTAACAT
*
16094 TGTTCGTGAACGTGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* *
16118 TGTTCATGGACATGTTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
* *
16141 TGTTAGTGATCATGTT
1 TGTTCGTGAACATGTT
16157 TGATTAAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:30107 original size:43 final size:43
Alignment explanation
Indices: 30046--30131 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
30036 AAGGTGGTAG
30046 TTACCTTAATACTTGTTTCTCCATCTGCTGCTGCTACAAACTT
1 TTACCTTAATACTTGTTTCTCCATCTGCTGCTGCTACAAACTT
30089 TTACCTTAATACTTGTTTCTCCATCTGCTGCTGCTACAAACTT
1 TTACCTTAATACTTGTTTCTCCATCTGCTGCTGCTACAAACTT
30132 AGTCTCGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (43 bp):
TTACCTTAATACTTGTTTCTCCATCTGCTGCTGCTACAAACTT
Found at i:35542 original size:28 final size:30
Alignment explanation
Indices: 35507--35567 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
35497 TATGGCAATT
*
35507 AAAATAAAAACATTA-AATT-TAAAT-TTAA
1 AAAATAAAAA-ACTATAATTCTAAATATTAA
35535 AAAATAAAAAACTATAATTCTAAATATTAA
1 AAAATAAAAAACTATAATTCTAAATATTAA
35565 AAA
1 AAA
35568 TACCTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 14 0.48
29 5 0.17
30 7 0.24
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (30 bp):
AAAATAAAAAACTATAATTCTAAATATTAA
Found at i:36511 original size:16 final size:16
Alignment explanation
Indices: 36456--36529 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
36446 TTGTAAAATA
* *
36456 AATATTA-ATTTACTT
1 AATATTATAATTAATT
* *
36471 AATATT-TAAGTAAATA
1 AATATTATAA-TTAATT
*
36487 AATATTTATAATTTATT
1 AATA-TTATAATTAATT
*
36504 AATATTATTATTAATT
1 AATATTATAATTAATT
36520 AATATATATA
1 AATAT-TATA
36530 TA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
15 7 0.16
16 22 0.50
17 12 0.27
18 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (16 bp):
AATATTATAATTAATT
Done.