Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014768.1 Kokia drynarioides strain JFW-HI SEQ_129808, 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: 51856
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7140 original size:47 final size:47
Alignment explanation
Indices: 7085--7180 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
7075 TTTTACCAAC
7085 AGGATCATTTTCAATATCAATGTATCATTTCACTTACTACATAACAG
1 AGGATCATTTTCAATATCAATGTATCATTTCACTTACTACATAACAG
7132 AGGATCATTTTCAATATCAATGTATCATTTCACTTACTACATAACAG
1 AGGATCATTTTCAATATCAATGTATCATTTCACTTACTACATAACAG
7179 AG
1 AG
7181 TATCGATGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (47 bp):
AGGATCATTTTCAATATCAATGTATCATTTCACTTACTACATAACAG
Found at i:20449 original size:29 final size:29
Alignment explanation
Indices: 20375--20483 Score: 73
Period size: 30 Copynumber: 3.7 Consensus size: 29
20365 AACTTGATAT
* *
20375 TTTTTTTTTAATTTGGTACTTAAATTT--
1 TTTTTTTTTAAGTTGGTACTCAAATTTAA
*
20402 TTTTTTTATCCAA-TGTGGTACTCAAATTTAAA
1 TTTTTTT-T-TAAGT-TGGTACTCAAATTT-AA
* * *
20434 TTTTTTTTTAA-TTGGTACCTGAACTTGATA
1 TTTTTTTTTAAGTTGGTA-CTCAAATTTA-A
*
20464 CTTTTTTTTAAGTTGGTACT
1 TTTTTTTTTAAGTTGGTACT
20484 TAAACTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.11
28 2 0.03
29 21 0.32
30 22 0.33
31 7 0.11
32 7 0.11
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (29 bp):
TTTTTTTTTAAGTTGGTACTCAAATTTAA
Found at i:22709 original size:13 final size:14
Alignment explanation
Indices: 22680--22713 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
22670 TAAGGCAAAT
22680 TTTTTTATTTGTAA
1 TTTTTTATTTGTAA
22694 TTTTTTATTTGT-A
1 TTTTTTATTTGTAA
22707 TTTTTTA
1 TTTTTTA
22714 CAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (14 bp):
TTTTTTATTTGTAA
Found at i:23762 original size:5 final size:5
Alignment explanation
Indices: 23752--23778 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
23742 AGCCATTATT
23752 TGCCA TGCCA TGCCA TGCCA TGCCA TG
1 TGCCA TGCCA TGCCA TGCCA TGCCA TG
23779 TAGGTTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.37, G:0.22, T:0.22
Consensus pattern (5 bp):
TGCCA
Found at i:25590 original size:3 final size:3
Alignment explanation
Indices: 25582--25609 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25572 GCTACAGCCT
25582 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
25610 TAATAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29391 original size:2 final size:2
Alignment explanation
Indices: 29384--29408 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29374 AGTTTTCAAG
29384 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 T
29409 CCTTTCCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32179 original size:21 final size:23
Alignment explanation
Indices: 32131--32179 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
32121 AACATCATTT
*
32131 TATATTTATATATTATATACATA
1 TATAATTATATATTATATACATA
* *
32154 AATAATTATAT-TTATCTA-ATA
1 TATAATTATATATTATATACATA
32175 TATAA
1 TATAA
32180 AATTGATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.32
22 6 0.27
23 9 0.41
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TATAATTATATATTATATACATA
Found at i:32488 original size:20 final size:22
Alignment explanation
Indices: 32454--32493 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
32444 TATCACTATA
32454 TTTTAACTTTATA-TTGATTTT
1 TTTTAACTTTATATTTGATTTT
*
32475 TTTTCACTTT-TATTTGATT
1 TTTTAACTTTATATTTGATT
32494 GCTTTTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTAACTTTATATTTGATTTT
Found at i:37629 original size:100 final size:100
Alignment explanation
Indices: 37454--37652 Score: 308
Period size: 100 Copynumber: 2.0 Consensus size: 100
37444 ATCACCCAGC
* *
37454 ACTTAATACATGCTCAACTGTAACAACTGAGCATCAATGACGAGCAGTATTAAACTTCCAAAATG
1 ACTTAATACATGCTCAACTGTAACAACTGAGCACCAATCACGAGCAGTATTAAACTTCCAAAATG
* *
37519 TATTGCTAAATCCCAGTAAGCAAGTTAGCCAAGCA
66 TATTGATAAATCCCAGTAAGCAACTTAGCCAAGCA
* * * *
37554 ACTTAATCCATGCTCAACTGTAATAACTGAGCACCAGTCAGGAGCAGTATTAAACTTCCAAAATG
1 ACTTAATACATGCTCAACTGTAACAACTGAGCACCAATCACGAGCAGTATTAAACTTCCAAAATG
* *
37619 TATTGATAAATTCTAGTAAGCAACTTAGCCAAGC
66 TATTGATAAATCCCAGTAAGCAACTTAGCCAAGC
37653 CAAAACTAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (100 bp):
ACTTAATACATGCTCAACTGTAACAACTGAGCACCAATCACGAGCAGTATTAAACTTCCAAAATG
TATTGATAAATCCCAGTAAGCAACTTAGCCAAGCA
Found at i:46490 original size:89 final size:91
Alignment explanation
Indices: 46337--46529 Score: 232
Period size: 89 Copynumber: 2.1 Consensus size: 91
46327 TTAATATAAC
* * * * *
46337 ATTTGGTACCTAAACTTGATACTTTTTTTCTAATTTGGTACCTAAACTCTTTTTGGTCCAATTTG
1 ATTTGGTACCTAAACATGATACATTTTTTATAAGTTGGTACCTAAACTCTTTTGGGTCCAATTTG
* * *
46402 GTACTCAAATTTGA-TACTTTTTCCTG
66 ATACTCAAACTTGACT-CTTTTTCCTA
*
46428 ATTTGGTACCTAAACAT-A-ACATTTTTTATAAGTTGGTACTTAAACT-TTTTGGGGTCCAATTT
1 ATTTGGTACCTAAACATGATACATTTTTTATAAGTTGGTACCTAAACTCTTTT-GGGTCCAATTT
**
46490 GATACTTGAACTTGACTCTTTTTCCTA
65 GATACTCAAACTTGACTCTTTTTCCTA
*
46517 ATTTGATACCTAA
1 ATTTGGTACCTAA
46530 TATTTTTTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
88 4 0.05
89 66 0.75
90 2 0.02
91 16 0.18
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (91 bp):
ATTTGGTACCTAAACATGATACATTTTTTATAAGTTGGTACCTAAACTCTTTTGGGTCCAATTTG
ATACTCAAACTTGACTCTTTTTCCTA
Found at i:46771 original size:57 final size:58
Alignment explanation
Indices: 46696--46832 Score: 188
Period size: 58 Copynumber: 2.4 Consensus size: 58
46686 AAATTGAATC
* * *
46696 TAAAAAAAGTTTAGGTACCAAAATAGG-AAAAATACCAAGTTCAGGTACCAATTTGGG
1 TAAAAAAAGTTTAGGTACCAAAATAGGAAAAAATACAAAGTTCAAGTACCAATTTAGG
* * ** *
46753 TAAAAAAAGTTTAGGTACCGAATTAGGAAAAAATGTAAAGTTCAAGTATCAATTTAGG
1 TAAAAAAAGTTTAGGTACCAAAATAGGAAAAAATACAAAGTTCAAGTACCAATTTAGG
46811 TAAAAAAAGTTTAGGTA-CAAAA
1 TAAAAAAAGTTTAGGTACCAAAA
46833 CTAATAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
57 28 0.41
58 41 0.59
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (58 bp):
TAAAAAAAGTTTAGGTACCAAAATAGGAAAAAATACAAAGTTCAAGTACCAATTTAGG
Found at i:46852 original size:58 final size:57
Alignment explanation
Indices: 46696--46852 Score: 181
Period size: 58 Copynumber: 2.7 Consensus size: 57
46686 AAATTGAATC
* * * *
46696 TAAAAAAAGTTTAGGTACCAAAAT-AGGAAAAATACCAAGTTCAGGTACCAATTTGGG
1 TAAAAAAAGTTTAGGTA-CAAAATAAGAAAAAATATCAAGTTCAAGTACCAATTTAGG
* * * * * *
46753 TAAAAAAAGTTTAGGTACCGAATTAGGAAAAAATGTAAAGTTCAAGTATCAATTTAGG
1 TAAAAAAAGTTTAGGTA-CAAAATAAGAAAAAATATCAAGTTCAAGTACCAATTTAGG
*
46811 TAAAAAAAGTTTAGGTACAAAACTAATAAAAAATATCAAGTT
1 TAAAAAAAGTTTAGGTACAAAA-TAAGAAAAAATATCAAGTT
46853 TAGATACCAA
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
57 25 0.30
58 57 0.70
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (57 bp):
TAAAAAAAGTTTAGGTACAAAATAAGAAAAAATATCAAGTTCAAGTACCAATTTAGG
Done.