Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004835.1 Kokia drynarioides strain JFW-HI SEQ_118479, 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: 14437
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:183 original size:3 final size:3
Alignment explanation
Indices: 177--213 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
167 TATTATTAAA
177 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
214 GTGTTGCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3318 original size:29 final size:29
Alignment explanation
Indices: 3286--3349 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
3276 ATGGTTTAGT
*
3286 GTTTTGAATTTTAGGG-TTTAAATTTTAAG
1 GTTTTGAA-TTAAGGGTTTTAAATTTTAAG
*
3315 GTTTTGAATTAAGGGTTTTGAATTTTAAG
1 GTTTTGAATTAAGGGTTTTAAATTTTAAG
3344 GTTTTG
1 GTTTTG
3350 GGTTTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (29 bp):
GTTTTGAATTAAGGGTTTTAAATTTTAAG
Found at i:3355 original size:15 final size:16
Alignment explanation
Indices: 3286--3380 Score: 78
Period size: 15 Copynumber: 6.2 Consensus size: 16
3276 ATGGTTTAGT
3286 GTTTTGAATTTT-AGG
1 GTTTTGAATTTTAAGG
*
3301 G-TTTAAATTTTAA-G
1 GTTTTGAATTTTAAGG
3315 GTTTTGAA--TTAAGG
1 GTTTTGAATTTTAAGG
3329 GTTTTGAATTTTAA-G
1 GTTTTGAATTTTAAGG
**
3344 GTTTTGGGTTTTGAAAGG
1 GTTTTGAATTTT--AAGG
* *
3362 G-TTTCAAATTTAAGG
1 GTTTTGAATTTTAAGG
3377 GTTT
1 GTTT
3381 AAGGTTTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
13 4 0.06
14 20 0.32
15 23 0.37
16 6 0.10
17 8 0.13
18 2 0.03
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.48
Consensus pattern (16 bp):
GTTTTGAATTTTAAGG
Found at i:3387 original size:33 final size:35
Alignment explanation
Indices: 3309--3423 Score: 87
Period size: 36 Copynumber: 3.3 Consensus size: 35
3299 GGGTTTAAAT
* *
3309 TTTAAGGTTTTGAATTAAGGGTTTTGAATTTTAAGG
1 TTTAAGGTTTTGAA-TAAGGGTTTTCAAATTTAAGG
**
3345 TTTTGGGTTTTG-A-AAGGG-TTTCAAATTTAAGGG
1 TTTAAGGTTTTGAATAAGGGTTTTCAAATTTAA-GG
** *
3378 TTTAAGGTTTAAAATTTAA-GGTTTT-GAATTTAAGG
1 TTTAAGGTTTTGAA--TAAGGGTTTTCAAATTTAAGG
3413 TTTTAAGGTTT
1 -TTTAAGGTTT
3424 AGGGTTAAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
32 10 0.16
33 15 0.24
34 1 0.02
35 3 0.05
36 29 0.46
37 5 0.08
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.47
Consensus pattern (35 bp):
TTTAAGGTTTTGAATAAGGGTTTTCAAATTTAAGG
Found at i:3416 original size:14 final size:14
Alignment explanation
Indices: 3286--3416 Score: 69
Period size: 14 Copynumber: 9.4 Consensus size: 14
3276 ATGGTTTAGT
*
3286 GTTTTGAATTTTAG
1 GTTTTGAATTTAAG
* *
3300 GGTTTAAATTTTAAG
1 GTTTTGAA-TTTAAG
3315 GTTTTGAA-TTAAGG
1 GTTTTGAATTTAA-G
3329 GTTTTGAATTTTAAG
1 GTTTTGAA-TTTAAG
**
3344 GTTTTGGGTTTTGAAAGG
1 GTTTT-GAATTT--AA-G
**
3362 GTTTCAAATTTAAG
1 GTTTTGAATTTAAG
3376 G----G--TTTAAG
1 GTTTTGAATTTAAG
**
3384 GTTTAAAATTTAAG
1 GTTTTGAATTTAAG
3398 GTTTTGAATTTAAG
1 GTTTTGAATTTAAG
3412 GTTTT
1 GTTTT
3417 AAGGTTTAGG
Statistics
Matches: 88, Mismatches: 15, Indels: 28
0.67 0.11 0.21
Matches are distributed among these distances:
8 7 0.08
13 4 0.05
14 40 0.45
15 22 0.25
16 5 0.06
17 5 0.06
18 5 0.06
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.48
Consensus pattern (14 bp):
GTTTTGAATTTAAG
Found at i:6457 original size:4 final size:4
Alignment explanation
Indices: 6448--6500 Score: 56
Period size: 4 Copynumber: 13.5 Consensus size: 4
6438 TTTCTCATTC
* * *
6448 TTCT TTCT TTCCT CTCT TTC- TTCC TTCT TTC- TTCT TTCT TTCT TCCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
6495 TTCT TT
1 TTCT TT
6501 TTGGTGCCCG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
3 6 0.15
4 32 0.78
5 3 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTCT
Found at i:6478 original size:11 final size:11
Alignment explanation
Indices: 6447--6500 Score: 72
Period size: 11 Copynumber: 4.6 Consensus size: 11
6437 TTTTCTCATT
6447 CTTCTTTCTTTC
1 CTTCTTTC-TTC
6459 CTCTCTTTCTTC
1 CT-TCTTTCTTC
6471 CTTCTTTCTTC
1 CTTCTTTCTTC
*
6482 TTTCTTTCTTC
1 CTTCTTTCTTC
6493 CTTTCTTT
1 C-TTCTTT
6501 TTGGTGCCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 19 0.50
12 13 0.34
13 6 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
CTTCTTTCTTC
Found at i:9313 original size:13 final size:12
Alignment explanation
Indices: 9288--9339 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
9278 TTTTATAGAC
*
9288 AAATAAGAAAAT
1 AAATAATAAAAT
9300 AAATATATAAAAT
1 AAATA-ATAAAAT
*
9313 ATATAAATAAAAAT
1 AAAT-AAT-AAAAT
9327 AAA-AATAAAAT
1 AAATAATAAAAT
9338 AA
1 AA
9340 TTAGGTTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 7 0.21
12 8 0.24
13 11 0.32
14 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:9339 original size:21 final size:22
Alignment explanation
Indices: 9288--9339 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
9278 TTTTATAGAC
* *
9288 AAATAAGA-AAATAAATATATA
1 AAATAAAATAAATAAAAATATA
*
9309 AAAT-ATATAAATAAAAATA-A
1 AAATAAAATAAATAAAAATATA
9329 AAATAAAATAA
1 AAATAAAATAA
9340 TTAGGTTGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATAAAATAAATAAAAATATA
Done.