Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007206.1 Kokia drynarioides strain JFW-HI SEQ_121820, 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: 19943
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:5358 original size:24 final size:22
Alignment explanation
Indices: 5306--5360 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
5296 TGCTGCTGAA
*
5306 GCTGTTGTTGCTGTGAGTTACT
1 GCTGCTGTTGCTGTGAGTTACT
* *
5328 G-TTCTGTTGCTGTTGCAGTTGCT
1 GCTGCTGTTGCTG-TG-AGTTACT
5351 GCTGCTGTTG
1 GCTGCTGTTG
5361 TTGCTGCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 3 0.12
23 7 0.27
24 7 0.27
ACGTcount: A:0.05, C:0.16, G:0.33, T:0.45
Consensus pattern (22 bp):
GCTGCTGTTGCTGTGAGTTACT
Found at i:5360 original size:12 final size:12
Alignment explanation
Indices: 5331--5369 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5321 AGTTACTGTT
*
5331 CTGTTGCTGTTG
1 CTGTTGCTGCTG
*
5343 CAGTTGCTGCTG
1 CTGTTGCTGCTG
*
5355 CTGTTGTTGCTG
1 CTGTTGCTGCTG
5367 CTG
1 CTG
5370 ATGCAACTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.21, G:0.33, T:0.44
Consensus pattern (12 bp):
CTGTTGCTGCTG
Found at i:7245 original size:6 final size:6
Alignment explanation
Indices: 7059--7242 Score: 194
Period size: 6 Copynumber: 31.2 Consensus size: 6
7049 TGCTGTGGTG
7059 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
* * * * * *
7107 GTTGCT GCTGCT GCTGCT GCTGTT GTTGTT GCTG-T --TGTT GTTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
* * * * * * * *
7152 GTTGTT GTTGTT GCTGCT GCTGCT GCTGCT GCTGCT GCTGCT GCTGCT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
* * *
7200 GCTGTT GCTGTT GCTGTT GCTGTT GTTGCT GCTGTT GTTGTT G
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT G
7243 TTGGGCATGC
Statistics
Matches: 161, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
3 2 0.01
4 1 0.01
5 1 0.01
6 157 0.98
ACGTcount: A:0.00, C:0.18, G:0.34, T:0.48
Consensus pattern (6 bp):
GCTGTT
Found at i:7286 original size:15 final size:15
Alignment explanation
Indices: 7268--7315 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
7258 CAATAAAAGC
7268 TGTTGCATCTGCAGT
1 TGTTGCATCTGCAGT
7283 TGTTGC-TGCTGC---
1 TGTTGCAT-CTGCAGT
7295 TGTTGCATCTGCAGT
1 TGTTGCATCTGCAGT
7310 TGTTGC
1 TGTTGC
7316 TGCTGCTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.08, C:0.21, G:0.29, T:0.42
Consensus pattern (15 bp):
TGTTGCATCTGCAGT
Found at i:7296 original size:27 final size:27
Alignment explanation
Indices: 7266--7327 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
7256 TGCAATAAAA
7266 GCTGTTGCATCTGCAGTTGTTGCTGCT
1 GCTGTTGCATCTGCAGTTGTTGCTGCT
7293 GCTGTTGCATCTGCAGTTGTTGCTGCT
1 GCTGTTGCATCTGCAGTTGTTGCTGCT
7320 GCTGTTGC
1 GCTGTTGC
7328 TGTTGCTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.06, C:0.23, G:0.31, T:0.40
Consensus pattern (27 bp):
GCTGTTGCATCTGCAGTTGTTGCTGCT
Found at i:7321 original size:15 final size:15
Alignment explanation
Indices: 7276--7336 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
7266 GCTGTTGCAT
7276 CTGCAGTTGTTGCTG
1 CTGCAGTTGTTGCTG
7291 CTGC---TGTTGCAT-
1 CTGCAGTTGTTGC-TG
7303 CTGCAGTTGTTGCTG
1 CTGCAGTTGTTGCTG
* * *
7318 CTGCTGTTGCTGTTG
1 CTGCAGTTGTTGCTG
7333 CTGC
1 CTGC
7337 TGCTGTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
12 10 0.26
13 1 0.03
14 1 0.03
15 26 0.68
ACGTcount: A:0.05, C:0.23, G:0.31, T:0.41
Consensus pattern (15 bp):
CTGCAGTTGTTGCTG
Found at i:7333 original size:18 final size:18
Alignment explanation
Indices: 7310--7391 Score: 98
Period size: 18 Copynumber: 4.7 Consensus size: 18
7300 CATCTGCAGT
*
7310 TGTTGCTGCTGCTGTTGC
1 TGTTGCTGCTGCTGTTGA
7328 TGTTGCTGCTGCTGTTGA
1 TGTTGCTGCTGCTGTTGA
*
7346 TGTTG-AG--GCTGTTGA
1 TGTTGCTGCTGCTGTTGA
* *
7361 GGTTGCTGCTGCTGTTGC
1 TGTTGCTGCTGCTGTTGA
*
7379 TGTTGTTGCTGCT
1 TGTTGCTGCTGCT
7392 CCCGTGCTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
15 12 0.22
16 1 0.02
17 1 0.02
18 40 0.74
ACGTcount: A:0.04, C:0.17, G:0.35, T:0.44
Consensus pattern (18 bp):
TGTTGCTGCTGCTGTTGA
Found at i:7334 original size:12 final size:12
Alignment explanation
Indices: 7310--7383 Score: 67
Period size: 12 Copynumber: 5.9 Consensus size: 12
7300 CATCTGCAGT
*
7310 TGTTGCTGCTGC
1 TGTTGCTGTTGC
7322 TGTTGCTGTTGC
1 TGTTGCTGTTGC
* *
7334 TGCTGCTGTTGA
1 TGTTGCTGTTGC
*
7346 TGTTGAGGCTGTTGA
1 TGTT---GCTGTTGC
* *
7361 GGTTGCTGCTGC
1 TGTTGCTGTTGC
7373 TGTTGCTGTTG
1 TGTTGCTGTTG
7384 TTGCTGCTCC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
12 39 0.78
15 11 0.22
ACGTcount: A:0.04, C:0.16, G:0.36, T:0.43
Consensus pattern (12 bp):
TGTTGCTGTTGC
Found at i:7391 original size:12 final size:12
Alignment explanation
Indices: 7283--7391 Score: 64
Period size: 12 Copynumber: 8.8 Consensus size: 12
7273 CATCTGCAGT
7283 TGTTGCTGCTGC
1 TGTTGCTGCTGC
7295 TGTTGCAT-CTGC
1 TGTTGC-TGCTGC
7307 AGTTGTTGCTGCTGC
1 ---TGTTGCTGCTGC
*
7322 TGTTGCTGTTGC
1 TGTTGCTGCTGC
* * *
7334 TGCTGCTGTTGA
1 TGTTGCTGCTGC
* *
7346 TGTTGAGGCTGTTGA
1 TGTT---GCTGCTGC
*
7361 GGTTGCTGCTGC
1 TGTTGCTGCTGC
7373 TGTTGCTG-T--
1 TGTTGCTGCTGC
7382 TGTTGCTGCT
1 TGTTGCTGCT
7392 CCCGTGCTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
9 8 0.10
10 1 0.01
11 1 0.01
12 47 0.59
13 1 0.01
14 1 0.01
15 21 0.26
ACGTcount: A:0.05, C:0.18, G:0.34, T:0.43
Consensus pattern (12 bp):
TGTTGCTGCTGC
Found at i:12738 original size:31 final size:30
Alignment explanation
Indices: 12698--12789 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 30
12688 TTTAAATGGG
* *
12698 TATAATTGAATCAATATTAAAGTTTCATGTA
1 TATAATTGAACCAA-ATAAAAGTTTCATGTA
* *
12729 TATATTTGAACCAAAATAAAAGTTTCATGTG
1 TATAATTGAACC-AAATAAAAGTTTCATGTA
* *
12760 TATAATTGCACCAAATCAAAG-TTCATGTA
1 TATAATTGAACCAAATAAAAGTTTCATGTA
12789 T
1 T
12790 CAAATTGCAC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
29 8 0.15
30 8 0.15
31 34 0.65
32 2 0.04
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (30 bp):
TATAATTGAACCAAATAAAAGTTTCATGTA
Found at i:12795 original size:29 final size:31
Alignment explanation
Indices: 12763--12820 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12753 TCATGTGTAT
*
12763 AATTGCAC-C-AAATCAAAGTTCATGTATCA
1 AATTGCACACTAAATCAAAATTCATGTATCA
*
12792 AATTGCACACTCAATCAAAATTCATGTAT
1 AATTGCACACTAAATCAAAATTCATGTAT
12821 AATTTTGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 1 0.04
31 16 0.64
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (31 bp):
AATTGCACACTAAATCAAAATTCATGTATCA
Found at i:12824 original size:29 final size:27
Alignment explanation
Indices: 12758--12824 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
12748 AAGTTTCATG
*
12758 TGTATAATTGCACCAAATCAAAGTTCA
1 TGTATAATTGCACCAAATCAAAATTCA
*
12785 TGTATCAAATTGCACACTCAATCAAAATTCA
1 TGTAT--AATTGCAC-C-AAATCAAAATTCA
12816 TGTATAATT
1 TGTATAATT
12825 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.35
30 1 0.03
31 16 0.47
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAATTCA
Done.