Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006475.1 Kokia drynarioides strain JFW-HI SEQ_121058, 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: 39222
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1469 original size:2 final size:2
Alignment explanation
Indices: 1462--1502 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1452 GTTGTTATTT
1462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1503 TTTAATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5832 original size:21 final size:21
Alignment explanation
Indices: 5793--5833 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5783 TTTTTTTAAT
5793 TTTAAATTTCTTTATATATTC
1 TTTAAATTTCTTTATATATTC
*
5814 TTTAGAATTTTTTTA-ATATT
1 TTTA-AATTTCTTTATATATT
5834 TATAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTAAATTTCTTTATATATTC
Found at i:11057 original size:22 final size:22
Alignment explanation
Indices: 11032--11084 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
11022 TATAATAACC
**
11032 AAATAATAACAAAATGATAGCA
1 AAATAATAACAAAACAATAGCA
* * * *
11054 AAATGACATCAAAACAATAGTA
1 AAATAATAACAAAACAATAGCA
11076 AAATAATAA
1 AAATAATAA
11085 TAATAAAAAT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.08, T:0.19
Consensus pattern (22 bp):
AAATAATAACAAAACAATAGCA
Found at i:11505 original size:18 final size:18
Alignment explanation
Indices: 11471--11519 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
11461 TAATTTTAGG
* *
11471 TTATTTAATTAAATAAATT
1 TTATTTTATT-AATAAATA
11490 TTATTTTATTAATAAATA
1 TTATTTTATTAATAAATA
*
11508 TAATTTTATTAA
1 TTATTTTATTAA
11520 AGATTTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTTTATTAATAAATA
Found at i:11516 original size:23 final size:25
Alignment explanation
Indices: 11458--11517 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 25
11448 GATTATAAAT
**
11458 ATATAATTTTAGGTTATTTAATTAA
1 ATATAATTTTATTTTATTTAATTAA
11483 ATA-AATTTTATTTTA-TTAA-TAA
1 ATATAATTTTATTTTATTTAATTAA
11505 ATATAATTTTATT
1 ATATAATTTTATT
11518 AAAGATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 6 0.19
23 13 0.41
24 10 0.31
25 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
ATATAATTTTATTTTATTTAATTAA
Found at i:21196 original size:20 final size:19
Alignment explanation
Indices: 21136--21205 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 19
21126 TGAGCCAACT
* *
21136 GCATCAGCTAGCATTTAGCA
1 GCATCAGCAAGCA-TTGGCA
*
21156 GCATCAGGCAA-CATCGAGCA
1 GCATCA-GCAAGCATTG-GCA
21176 GCATCAGCAAGCAGTTGGCA
1 GCATCAGCAAGCA-TTGGCA
21196 G-AGTCAGCAA
1 GCA-TCAGCAA
21206 CTTTTTGGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 6 0.15
20 30 0.73
21 5 0.12
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (19 bp):
GCATCAGCAAGCATTGGCA
Found at i:33572 original size:43 final size:43
Alignment explanation
Indices: 33516--33761 Score: 296
Period size: 43 Copynumber: 5.6 Consensus size: 43
33506 GAAAAATACT
* * *
33516 GCTATAGAACATGGTCTTTAGCGGCGCTTCTCCCACAAATGCT
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATGCC
* *
33559 GCTAAAGATCATGGTCTTTAGCGGCGCTTTTTCCACAAACGCCGTTAGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAA------T-GCC
33609 GCTAAAGAACATGGTCTTTAGCGGCG-TTTTCCCCACAAATGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTT-CCCACAAATGCC
* * * *
33652 GTTAAAGAACATGATCTTTAGCGGCGCTTTTCCCCCAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATGCC
* * *
33695 GCTAAGGAACATGGTCTTTAGCGACGCTTTTCCCACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATGCC
*
33738 GCTAAAGAACACGGTCTTTAGCGG
1 GCTAAAGAACATGGTCTTTAGCGG
33762 TCTTTAGCGG
Statistics
Matches: 175, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
43 131 0.75
44 5 0.03
49 5 0.03
50 34 0.19
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (43 bp):
GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATGCC
Found at i:33627 original size:93 final size:86
Alignment explanation
Indices: 33516--33761 Score: 305
Period size: 93 Copynumber: 2.8 Consensus size: 86
33506 GAAAAATACT
* * * *
33516 GCTATAGAACATGGTCTTTAGCGGCGCTTCTCCCACAAATGCTGCTAAAGATCATGGTCTTTAGC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGAACATGGTCTTTAGC
*
33581 GGCGCTTTTTCCACAAACGCCGTTAGCC
66 GGCGCTTTTCCCACAAA---C----GCC
* *
33609 GCTAAAGAACATGGTCTTTAGCGGCG-TTTTCCCCACAAATGCCGTTAAAGAACATGATCTTTAG
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTT-CCCACAAATGCCGCTAAAGAACATGGTCTTTAG
*
33673 CGGCGCTTTTCCCCCAAACGCC
65 CGGCGCTTTTCCCACAAACGCC
* * * *
33695 GCTAAGGAACATGGTCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGAACACGGTCTTTAGC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGAACATGGTCTTTAGC
33760 GG
66 GG
33762 TCTTTAGCGG
Statistics
Matches: 137, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
86 59 0.43
87 4 0.03
90 1 0.01
92 3 0.02
93 70 0.51
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (86 bp):
GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGAACATGGTCTTTAGC
GGCGCTTTTCCCACAAACGCC
Found at i:34123 original size:21 final size:20
Alignment explanation
Indices: 34095--34139 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
34085 CCTCTGCTTC
*
34095 CCTCGCTTGCCTCGCTGCTG
1 CCTCGCTTCCCTCGCTGCTG
*
34115 CCTCTGCTTCCCTCGTTGCTG
1 CCTC-GCTTCCCTCGCTGCTG
34136 CCTC
1 CCTC
34140 CACTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.00, C:0.47, G:0.20, T:0.33
Consensus pattern (20 bp):
CCTCGCTTCCCTCGCTGCTG
Found at i:37620 original size:40 final size:40
Alignment explanation
Indices: 37574--37680 Score: 151
Period size: 40 Copynumber: 2.7 Consensus size: 40
37564 CTTTTTCTAT
* *
37574 AAACGCCGCTATTGCTTTACCTTTTGCAGTGTTTATATAA
1 AAACGCCGCTATTGCTTTACCTTTTGCAGCGTTTATAGAA
* *
37614 AAACGCCGCTATTGCTTTACCTTTTGCGGCGTTTATCGAA
1 AAACGCCGCTATTGCTTTACCTTTTGCAGCGTTTATAGAA
* * *
37654 AAACACCACTATTGATTTACCTTTTGC
1 AAACGCCGCTATTGCTTTACCTTTTGC
37681 CGCTAATAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (40 bp):
AAACGCCGCTATTGCTTTACCTTTTGCAGCGTTTATAGAA
Done.