Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006008.1 Kokia drynarioides strain JFW-HI SEQ_120443, 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: 51659
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7729 original size:81 final size:80
Alignment explanation
Indices: 7589--7753 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 80
7579 GAGAGAAAAA
7589 AAAGGAATGGAAAGGGTTTTTTTTTTAAAACAAATGAAATAAATGATTTTTTTGAAAAAAATTCA
1 AAAGGAATGGAAAGGGTTTTTTTTTTAAAACAAATGAAATAAATGATTTTTTTGAAAAAAATTCA
7654 CTTATATAGGCTTTC
66 CTTATATAGGCTTTC
7669 AANAGGAATGGAAAGGGTTTTTTTTTTTAAAACAAATGAAATAAATGATTTTTTTGAAAAAAATT
1 AA-AGGAATGGAAAGGG-TTTTTTTTTTAAAACAAATGAAATAAATGATTTTTTTGAAAAAAATT
7734 CACTTATATAGGCTTTC
64 CACTTATATAGGCTTTC
7751 AAA
1 AAA
7754 ACTACGTCGT
Statistics
Matches: 83, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
80 2 0.02
81 15 0.18
82 66 0.80
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (80 bp):
AAAGGAATGGAAAGGGTTTTTTTTTTAAAACAAATGAAATAAATGATTTTTTTGAAAAAAATTCA
CTTATATAGGCTTTC
Found at i:8178 original size:60 final size:60
Alignment explanation
Indices: 8107--8280 Score: 212
Period size: 60 Copynumber: 2.9 Consensus size: 60
8097 ACTTCCAAAT
8107 TTTCTAAAAATTTGAATTTGACCCCT-AAATTTTCTAAAAATTCAAATTTGACCCCTAAAC
1 TTTCTAAAAATTT-AATTTGACCCCTAAAATTTTCTAAAAATTCAAATTTGACCCCTAAAC
* * *
8167 TTTCTAAAAATTCAAATTTGACCTCTAAAATTTT-TCAAAAATTCTAATTTGA-CCCTAAAC
1 TTTCTAAAAATT-TAATTTGACCCCTAAAATTTTCT-AAAAATTCAAATTTGACCCCTAAAC
* * * *
8227 TTTTTGAACATTCTAATTTGACCCCCTAAAATTTTC-AAAAATTCAAAATTGACC
1 TTTCTAAAAATT-TAATTTGA-CCCCTAAAATTTTCTAAAAATTCAAATTTGACC
8281 AGGTTTTAAT
Statistics
Matches: 98, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
60 63 0.64
61 35 0.36
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (60 bp):
TTTCTAAAAATTTAATTTGACCCCTAAAATTTTCTAAAAATTCAAATTTGACCCCTAAAC
Found at i:8210 original size:31 final size:31
Alignment explanation
Indices: 8106--8280 Score: 182
Period size: 30 Copynumber: 5.7 Consensus size: 31
8096 AACTTCCAAA
**
8106 TTTTCTAAAAATTTGAATTTGACCCCT-AAA-
1 TTTTC-AAAAATTCAAATTTGACCCCTAAAAT
*
8136 TTTTCTAAAAATTCAAATTTGACCCCTAAACT
1 TTTTC-AAAAATTCAAATTTGACCCCTAAAAT
* *
8168 TTCT-AAAAATTCAAATTTGACCTCTAAAAT
1 TTTTCAAAAATTCAAATTTGACCCCTAAAAT
* *
8198 TTTTCAAAAATTCTAATTTGA-CCCTAAACT
1 TTTTCAAAAATTCAAATTTGACCCCTAAAAT
* * *
8228 TTTT-GAACATTCTAATTTGACCCCCTAAAA-
1 TTTTCAAAAATTCAAATTTGA-CCCCTAAAAT
*
8258 TTTTCAAAAATTCAAAATTGACC
1 TTTTCAAAAATTCAAATTTGACC
8281 AGGTTTTAAT
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
29 14 0.11
30 69 0.57
31 36 0.30
32 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (31 bp):
TTTTCAAAAATTCAAATTTGACCCCTAAAAT
Found at i:20617 original size:22 final size:20
Alignment explanation
Indices: 20590--20641 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
20580 TTAATTTCTA
*
20590 TTAATTTAACT-ATTTTTTATT
1 TTAATTTAA-TAATTTTGT-TT
20611 TTAAATTTAATAATTTTGTTT
1 TT-AATTTAATAATTTTGTTT
20632 TTAATTTAAT
1 TTAATTTAAT
20642 TTTTACATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 8 0.29
21 7 0.25
22 13 0.46
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTAATTTAATAATTTTGTTT
Found at i:20632 original size:20 final size:20
Alignment explanation
Indices: 20604--20641 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20594 TTTAACTATT
20604 TTTTATTTTAAATTTAATAA
1 TTTTATTTTAAATTTAATAA
* *
20624 TTTTGTTTTTAATTTAAT
1 TTTTATTTTAAATTTAAT
20642 TTTTACATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTATTTTAAATTTAATAA
Found at i:24279 original size:7 final size:8
Alignment explanation
Indices: 24266--24305 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 8
24256 TATATACATA
24266 TTTTTTTC
1 TTTTTTTC
24274 TTTTTTTCC
1 TTTTTTT-C
24283 TTTTTTTC
1 TTTTTTTC
*
24291 TATTTTTTA
1 T-TTTTTTC
24300 TTTTTT
1 TTTTTT
24306 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTC
Found at i:24303 original size:17 final size:16
Alignment explanation
Indices: 24264--24305 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
24254 AATATATACA
24264 TATTTTTTTCTTTTTT
1 TATTTTTTTCTTTTTT
*
24280 TCCTTTTTTTCTATTTTT
1 T-ATTTTTTTCT-TTTTT
24298 TATTTTTT
1 TATTTTTT
24306 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 15 0.68
18 6 0.27
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (16 bp):
TATTTTTTTCTTTTTT
Found at i:24306 original size:7 final size:7
Alignment explanation
Indices: 24285--24317 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
24275 TTTTTTCCTT
24285 TTTTTCTA
1 TTTTT-TA
24293 TTTTTTA
1 TTTTTTA
24300 TTTTTTA
1 TTTTTTA
24307 -TTTTTA
1 TTTTTTA
24313 TTTTT
1 TTTTT
24318 ATGTAACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 13 0.54
8 5 0.21
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:24892 original size:17 final size:17
Alignment explanation
Indices: 24862--24919 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
24852 TAATTTACAT
*
24862 TGACAAATGAAAATGCAA
1 TGAC-AATGTAAATGCAA
* *
24880 TGATAATGTAAATGCAG
1 TGACAATGTAAATGCAA
24897 TGACAAT-TAAAATGCAA
1 TGACAATGT-AAATGCAA
24914 TGACAA
1 TGACAA
24920 AGGGAATGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 1 0.03
17 30 0.88
18 3 0.09
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.22
Consensus pattern (17 bp):
TGACAATGTAAATGCAA
Found at i:35633 original size:25 final size:25
Alignment explanation
Indices: 35599--35649 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
35589 TCCGTGTCAC
35599 GACATAGCAAGCAGTATACTCCTTT
1 GACATAGCAAGCAGTATACTCCTTT
35624 GACATAGCAAGCAGTATACTCCTTT
1 GACATAGCAAGCAGTATACTCCTTT
35649 G
1 G
35650 GTGTGATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (25 bp):
GACATAGCAAGCAGTATACTCCTTT
Found at i:37376 original size:35 final size:35
Alignment explanation
Indices: 37336--37406 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
37326 TATACTGAAA
37336 CTACGACATGTGAATATGAATGTATTGATAAGATG
1 CTACGACATGTGAATATGAATGTATTGATAAGATG
37371 CTACGACATGTGAATATGAATGTATTGATAAGATG
1 CTACGACATGTGAATATGAATGTATTGATAAGATG
37406 C
1 C
37407 AAAATGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (35 bp):
CTACGACATGTGAATATGAATGTATTGATAAGATG
Found at i:48690 original size:15 final size:15
Alignment explanation
Indices: 48667--48696 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48657 TTCAAAAAAA
48667 AAAACAATAATAATT
1 AAAACAATAATAATT
*
48682 AAAATAATAATAATT
1 AAAACAATAATAATT
48697 TACAGACAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAACAATAATAATT
Found at i:49164 original size:17 final size:17
Alignment explanation
Indices: 49142--49178 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
49132 TCAATACAAT
49142 TTACAAACTGCAGCCGC
1 TTACAAACTGCAGCCGC
49159 TTACAAACTGCAGCCGC
1 TTACAAACTGCAGCCGC
49176 TTA
1 TTA
49179 GTATATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (17 bp):
TTACAAACTGCAGCCGC
Done.