Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001412.1 Kokia drynarioides strain JFW-HI SEQ_112905, 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: 50549
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 280 characters in sequence are not A, C, G, or T
Found at i:405 original size:16 final size:16
Alignment explanation
Indices: 384--428 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
374 TCCCTCTTCC
384 CCTTCTTCTCTTTCTT
1 CCTTCTTCTCTTTCTT
*
400 CCTTCTTCT-TTTTTT
1 CCTTCTTCTCTTTCTT
*
415 CTTTCTTTCTCTTT
1 CCTTC-TTCTCTTT
429 TTTCTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.36
16 13 0.52
17 3 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
CCTTCTTCTCTTTCTT
Found at i:415 original size:18 final size:18
Alignment explanation
Indices: 394--431 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
384 CCTTCTTCTC
394 TTTCTTCC-TTCTTCTTTT
1 TTTCTTCCTTTC-TCTTTT
*
412 TTTCTTTCTTTCTCTTTT
1 TTTCTTCCTTTCTCTTTT
430 TT
1 TT
432 CTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTTCCTTTCTCTTTT
Found at i:418 original size:8 final size:8
Alignment explanation
Indices: 405--439 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
395 TTCTTCCTTC
405 TTCTTTTT
1 TTCTTTTT
*
413 TTCTTTCT
1 TTCTTTTT
421 TTCTCTTTT
1 TTCT-TTTT
430 TTCTTTTT
1 TTCTTTTT
438 TT
1 TT
440 TTTCCTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTCTTTTT
Found at i:434 original size:13 final size:11
Alignment explanation
Indices: 405--443 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 11
395 TTCTTCCTTC
405 TTCTTTTTTTCT
1 TTCTTTTTTT-T
417 TTCTTTCTCTTTT
1 TTCTTT-T-TTTT
430 TTCTTTTTTTT
1 TTCTTTTTTTT
441 TTC
1 TTC
444 CTTCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.28
12 7 0.28
13 8 0.32
14 3 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:453 original size:24 final size:25
Alignment explanation
Indices: 405--453 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
395 TTCTTCCTTC
* **
405 TTCTTTTTTTCTTTCTTTCTCTTTT
1 TTCTTTTTTTCTTTCCTTCAATTTT
430 TTCTTTTTTT-TTTCCTTCAATTTT
1 TTCTTTTTTTCTTTCCTTCAATTTT
454 CGTTGGTCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (25 bp):
TTCTTTTTTTCTTTCCTTCAATTTT
Found at i:6602 original size:3 final size:3
Alignment explanation
Indices: 6594--6633 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6584 AACGAAACAC
6594 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
6634 AAACATAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:10873 original size:8 final size:8
Alignment explanation
Indices: 10860--10889 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
10850 TGCCGAAATG
10860 AAAAAAGA
1 AAAAAAGA
10868 AAAAAAGA
1 AAAAAAGA
10876 AAAAAAGA
1 AAAAAAGA
10884 AAAAAA
1 AAAAAA
10890 ACCAGCTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:11416 original size:1 final size:1
Alignment explanation
Indices: 11410--11439 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
11400 NNNNNNNNNN
11410 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11440 GAGAATATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14654 original size:29 final size:28
Alignment explanation
Indices: 14609--14684 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
14599 GTTATGTATT
14609 ATATTC-AAGTAAATTATGTTTTTCTTTA
1 ATATTCAAAGTAAATTATGTTTTT-TTTA
*
14637 ATATTCAAAATAAATTATG-TTTTTTTA
1 ATATTCAAAGTAAATTATGTTTTTTTTA
*
14664 ATATCCAAAGTAAATTATGTT
1 ATATTCAAAGTAAATTATGTT
14685 ACATTGGGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 21 0.49
28 11 0.26
29 11 0.26
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (28 bp):
ATATTCAAAGTAAATTATGTTTTTTTTA
Found at i:16329 original size:19 final size:19
Alignment explanation
Indices: 16284--16329 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
16274 ACATTCCCTT
16284 ATAATTTTAGTACTCCATC
1 ATAATTTTAGTACTCCATC
**
16303 ATGTTTTTAGTACTCTC-TC
1 ATAATTTTAGTACTC-CATC
16322 ATAATTTT
1 ATAATTTT
16330 GGTATTCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (19 bp):
ATAATTTTAGTACTCCATC
Found at i:37681 original size:105 final size:105
Alignment explanation
Indices: 37564--37778 Score: 385
Period size: 105 Copynumber: 2.0 Consensus size: 105
37554 AGATGTAAAG
* *
37564 GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAGGAGAGGTTTTTGATGA
1 GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAAGAGAAGTTTTTGATGA
37629 GATGGTAAGGGATATTGAGCAGCAGCGGCAGCAAACTGCT
66 GATGGTAAGGGATATTGAGCAGCAGCGGCAGCAAACTGCT
*
37669 GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAAGAGAAGTTTTTTATGA
1 GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAAGAGAAGTTTTTGATGA
* *
37734 GATGGTAAGGGATTTTGAGCAGCAGGGGCAGCAAACTGCT
66 GATGGTAAGGGATATTGAGCAGCAGCGGCAGCAAACTGCT
37774 GAAGA
1 GAAGA
37779 GGTTGAATTC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.34, C:0.09, G:0.33, T:0.23
Consensus pattern (105 bp):
GAAGATGGTGAAACACATGATGTTATTGAAGAGGAATTGGTGGAAACAAGAGAAGTTTTTGATGA
GATGGTAAGGGATATTGAGCAGCAGCGGCAGCAAACTGCT
Found at i:41336 original size:16 final size:15
Alignment explanation
Indices: 41317--41347 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41307 TTAGTTTTTT
*
41317 AAAATTTTAAATTAA
1 AAAAATTTAAATTAA
41332 AAAAATTTAAATTAA
1 AAAAATTTAAATTAA
41347 A
1 A
41348 TTTTGACTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATTTAAATTAA
Done.