Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014887.1 Kokia drynarioides strain JFW-HI SEQ_129930, 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: 6663
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:2407 original size:11 final size:10
Alignment explanation
Indices: 2341--2458 Score: 66
Period size: 10 Copynumber: 11.9 Consensus size: 10
2331 TTAAATTTTA
2341 ATAAAAAAAT
1 ATAAAAAAAT
*
2351 AT-AGAAAAT
1 ATAAAAAAAT
** *
2360 ATTTAAAATT
1 ATAAAAAAAT
*
2370 AGAAAAAAAT
1 ATAAAAAAAT
2380 ATAAAAAAAT
1 ATAAAAAAAT
*
2390 -TATAAAAAT
1 ATAAAAAAAT
2399 CATAAAAAAATT
1 -ATAAAAAAA-T
*
2411 ATTTAAAAAAT
1 A-TAAAAAAAT
* *
2422 GT-AATAAAT
1 ATAAAAAAAT
*
2431 -T-ATAAAAT
1 ATAAAAAAAT
*
2439 ATAGAAAAAT
1 ATAAAAAAAT
2449 ATAGAAAAAA
1 ATA-AAAAAA
2459 AAATTATAAA
Statistics
Matches: 81, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
8 6 0.07
9 23 0.28
10 30 0.37
11 14 0.17
12 8 0.10
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (10 bp):
ATAAAAAAAT
Found at i:2409 original size:41 final size:42
Alignment explanation
Indices: 2364--2519 Score: 117
Period size: 41 Copynumber: 3.8 Consensus size: 42
2354 GAAAATATTT
2364 AAAATTA-GAAAAAAATATAAAAAAATTATAAAAATCATAAA
1 AAAATTATGAAAAAAATATAAAAAAATTATAAAAATCATAAA
** * * *
2405 AAAATTATTTAAAAAATGT-AATAAATTAT-AAAAT-ATAGA
1 AAAATTATGAAAAAAATATAAAAAAATTATAAAAATCATAAA
* * * * ** *
2444 AAAA-TATAGAAAAAAAAATTATAAAATTTTATAAAGCCATAAG
1 AAAATTAT-GAAAAAAATATAAAAAAATTATA-AAAATCATAAA
* * *
2487 AAAATTATAAAAAAAATGTAAATAAA-TATAAAA
1 AAAATTATGAAAAAAATATAAAAAAATTATAAAA
2520 TTTTTAAAGA
Statistics
Matches: 85, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 3 0.04
39 15 0.18
40 12 0.14
41 19 0.22
42 14 0.16
43 19 0.22
44 3 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (42 bp):
AAAATTATGAAAAAAATATAAAAAAATTATAAAAATCATAAA
Found at i:2491 original size:82 final size:80
Alignment explanation
Indices: 2364--2520 Score: 199
Period size: 82 Copynumber: 1.9 Consensus size: 80
2354 GAAAATATTT
* * **
2364 AAAATTAGAAAAAAATATAAAAAAATTATAAAAATCATAAAAAAATTATTTAAAAAATGT-AATA
1 AAAATTAGAAAAAAAAATAAAAAAATTATAAAAACCATAAAAAAATTATAAAAAAAATGTAAATA
2428 AATTATAAAATATAGA
66 AA-TATAAAATATAGA
* * * * *
2444 AAAATATAGAAAAAAAAATTATAAAATTTTATAAAGCCATAAGAAAATTATAAAAAAAATGTAAA
1 AAAAT-TAGAAAAAAAAATAAAAAAATTATA-AAAACCATAAAAAAATTATAAAAAAAATGTAAA
2509 TAAATATAAAAT
64 TAAATATAAAAT
2521 TTTTAAAGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 5 0.08
81 21 0.32
82 33 0.51
83 6 0.09
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (80 bp):
AAAATTAGAAAAAAAAATAAAAAAATTATAAAAACCATAAAAAAATTATAAAAAAAATGTAAATA
AATATAAAATATAGA
Found at i:2613 original size:17 final size:16
Alignment explanation
Indices: 2559--2615 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
2549 CTAAAAAAAC
*
2559 ATTTTATATTTTTCTAT
1 ATTTTTTATTTTT-TAT
*
2576 AATTTTTATTGATTTT-T
1 ATTTTTTATT--TTTTAT
2593 ATTTTTTATTTTTTAT
1 ATTTTTTATTTTTTAT
2609 CATTTTT
1 -ATTTTT
2616 CGTTACATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 24 0.73
18 1 0.03
19 3 0.09
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (16 bp):
ATTTTTTATTTTTTAT
Found at i:2780 original size:27 final size:28
Alignment explanation
Indices: 2736--2802 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 28
2726 ATGCAGTTTA
*
2736 TAATTTTTTTCTAATTTTTAATAAAATT
1 TAATTTTTTTATAATTTTTAATAAAATT
* *
2764 T-ATTTTTTTATATTTTTTATTAAAATT
1 TAATTTTTTTATAATTTTTAATAAAATT
2791 TAATTTTTTTAT
1 TAATTTTTTTAT
2803 CACATACCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 24 0.69
28 11 0.31
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (28 bp):
TAATTTTTTTATAATTTTTAATAAAATT
Found at i:3141 original size:92 final size:90
Alignment explanation
Indices: 2968--3154 Score: 236
Period size: 92 Copynumber: 2.1 Consensus size: 90
2958 GCTTAATTAC
* * * * *
2968 TTTTTTTTAAGTTTGAGGCTTTTTTGATGTATTTTGAAAGTTTAAGTATCTAATTGAATGCAAAA
1 TTTTTTTTAAGTTTGAGGCTTTTTTGATGCATTTTAAAAGTTAAAGTATCAAAGTGAATGCAAAA
**
3033 TAAAAGCAGAGGCTTAATTGCTTCTTT
66 TAAAAGCAGAAACTTAATTG-TT-TTT
*
3060 TTTTTTTTAA-TTTGCGAGCATTTTTT-ATGCATTTTAAAAGTTAAAGTATCAAAGTGAATGCAA
1 TTTTTTTTAAGTTTGAG-GC-TTTTTTGATGCATTTTAAAAGTTAAAGTATCAAAGTGAATGCAA
3123 AATAAAAGCA-ATAACTTAATTGTTTTT
64 AATAAAAGCAGA-AACTTAATTGTTTTT
3150 TTTTT
1 TTTTT
3155 AAGTTTGATA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
90 8 0.10
91 8 0.10
92 62 0.74
93 6 0.07
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (90 bp):
TTTTTTTTAAGTTTGAGGCTTTTTTGATGCATTTTAAAAGTTAAAGTATCAAAGTGAATGCAAAA
TAAAAGCAGAAACTTAATTGTTTTT
Done.