Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009164.1 Kokia drynarioides strain JFW-HI SEQ_123869, 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: 11188
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4712 original size:28 final size:25
Alignment explanation
Indices: 4681--4744 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 25
4671 TGTTAAAAAC
4681 TTCATCCATTTTACTATCTATTAAAATT
1 TTCAT-CATTTT--TATCTATTAAAATT
* *
4709 TTCATC-TTTTTTTCTGTTAAAATT
1 TTCATCATTTTTATCTATTAAAATT
4733 TTCATTCATTTT
1 TTCA-TCATTTT
4745 GCTTGAGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 16 0.50
25 2 0.06
26 8 0.25
27 1 0.03
28 5 0.16
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.58
Consensus pattern (25 bp):
TTCATCATTTTTATCTATTAAAATT
Found at i:5501 original size:30 final size:28
Alignment explanation
Indices: 5466--5636 Score: 103
Period size: 30 Copynumber: 5.8 Consensus size: 28
5456 TTTGATCCAT
*
5466 AAACTTTCAAAAAATTCATATTTGACCCCC
1 AAACTTTC-AAAAATTCA-ATTTGACCCTC
* * * *
5496 GAACTTCCCAAAAATTTAGATTTGACCCTT
1 AAACTT-TCAAAAATTCA-ATTTGACCCTC
**
5526 AAACTTTTCAAAAATTTGGATTTGACCC-C
1 AAAC-TTTCAAAAA-TTCAATTTGACCCTC
* * *
5555 TAAATTTTCCAAAAAATAATATTTGA-CCTC
1 -AAACTTT-CAAAAATTCA-ATTTGACCCTC
** *
5585 GTACTTCCCAAAAATTCGAATTTGACCCTC
1 AAACTT-TCAAAAATTC-AATTTGACCCTC
5615 AAACTTTTCAAAAATTCAATTT
1 AAAC-TTTCAAAAATTCAATTT
5637 TCGACCTCAT
Statistics
Matches: 106, Mismatches: 24, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
29 27 0.25
30 72 0.68
31 7 0.07
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (28 bp):
AAACTTTCAAAAATTCAATTTGACCCTC
Found at i:5563 original size:29 final size:31
Alignment explanation
Indices: 5456--5569 Score: 110
Period size: 30 Copynumber: 3.8 Consensus size: 31
5446 AAAACTATGT
* * * * *
5456 TTTGATCCATAAAC-TTTCAAAAAATTCATA
1 TTTGACCCCTAAACTTTTCCAAAAATTTAGA
** *
5486 TTTGACCCCCGAAC-TTCCCAAAAATTTAGA
1 TTTGACCCCTAAACTTTTCCAAAAATTTAGA
* *
5516 TTTGACCCTTAAACTTTT-CAAAAATTTGGA
1 TTTGACCCCTAAACTTTTCCAAAAATTTAGA
5546 TTTGACCCCTAAA-TTTTCCAAAAA
1 TTTGACCCCTAAACTTTTCCAAAAA
5570 ATAATATTTG
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
29 4 0.06
30 62 0.91
31 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (31 bp):
TTTGACCCCTAAACTTTTCCAAAAATTTAGA
Found at i:5620 original size:89 final size:90
Alignment explanation
Indices: 5456--5630 Score: 239
Period size: 89 Copynumber: 2.0 Consensus size: 90
5446 AAAACTATGT
* * *
5456 TTTGATCCATAAACTTTCAAAAAATTCATATTTGACCCCCGAACTTCCCAAAAATTTAGATTTGA
1 TTTGACCCATAAACTTTCAAAAAATTAATATTTGACCCCCGAACTTCCCAAAAATTGAGATTTGA
*
5521 CCCTTAAACTTTTCAAAAATTTGGA
66 CCCTCAAACTTTTCAAAAATTTGGA
* * * *
5546 TTTGACCCCTAAATTTTCCAAAAAA-TAATATTTGA-CCTCGTACTTCCCAAAAATTCGA-ATTT
1 TTTGACCCATAAACTTT-CAAAAAATTAATATTTGACCCCCGAACTTCCCAAAAATT-GAGATTT
5608 GACCCTCAAACTTTTCAAAAATT
64 GACCCTCAAACTTTTCAAAAATT
5631 CAATTTTCGA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 44 0.59
90 24 0.32
91 7 0.09
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (90 bp):
TTTGACCCATAAACTTTCAAAAAATTAATATTTGACCCCCGAACTTCCCAAAAATTGAGATTTGA
CCCTCAAACTTTTCAAAAATTTGGA
Found at i:6735 original size:29 final size:28
Alignment explanation
Indices: 6671--6726 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
6661 AAGTCCGAGA
6671 AGTAAAATCGTGAAAAAATAAAAATTTT
1 AGTAAAATCGTGAAAAAATAAAAATTTT
6699 AGTAAAATCGTGAAAAAATAAAAATTTT
1 AGTAAAATCGTGAAAAAATAAAAATTTT
6727 CTTTCAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.29
Consensus pattern (28 bp):
AGTAAAATCGTGAAAAAATAAAAATTTT
Found at i:7857 original size:23 final size:23
Alignment explanation
Indices: 7755--7859 Score: 97
Period size: 23 Copynumber: 4.6 Consensus size: 23
7745 TACCGAGGTA
* *
7755 CTAAACAGCGAGCACACAAAGTG
1 CTAAATAGAGAGCACACAAAGTG
* *
7778 CTAAAT-GAAGAGTACACAAAGTA
1 CTAAATAG-AGAGCACACAAAGTG
* *
7801 CT-AATCGGAGAGCACACAAAATG
1 CTAAAT-AGAGAGCACACAAAGTG
* * *
7824 CTAATTGGAGAGCACACACAGTG
1 CTAAATAGAGAGCACACAAAGTG
7847 CTAAATAGAGAGC
1 CTAAATAGAGAGC
7860 GCGCAAAGGT
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.06
23 59 0.89
24 3 0.05
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (23 bp):
CTAAATAGAGAGCACACAAAGTG
Found at i:7858 original size:46 final size:46
Alignment explanation
Indices: 7752--7859 Score: 119
Period size: 46 Copynumber: 2.3 Consensus size: 46
7742 GAGTACCGAG
* * * *
7752 GTACTAAACAGCGAGCACACAAAGTGCTAAATGAAGAGTACACAAA
1 GTACTAAATAGAGAGCACACAAAATGCTAAATGAAGAGCACACAAA
* * * *
7798 GTACT-AATCGGAGAGCACACAAAATGCTAATTGGAGAGCACACACA
1 GTACTAAAT-AGAGAGCACACAAAATGCTAAATGAAGAGCACACAAA
*
7844 GTGCTAAATAGAGAGC
1 GTACTAAATAGAGAGC
7860 GCGCAAAGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
45 2 0.04
46 45 0.90
47 3 0.06
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (46 bp):
GTACTAAATAGAGAGCACACAAAATGCTAAATGAAGAGCACACAAA
Found at i:9239 original size:58 final size:58
Alignment explanation
Indices: 9149--9265 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
9139 TCACTAATCA
9149 CCACAATTACTATGGTGACTCATCTTTTGTTTTGGACTAATTATCCTTTTAGTCCCTT
1 CCACAATTACTATGGTGACTCATCTTTTGTTTTGGACTAATTATCCTTTTAGTCCCTT
9207 CCACAATTACTATGGTGACTCATCTTTTGTTTTGGACTAATTATCCTTTTAGTCCCTT
1 CCACAATTACTATGGTGACTCATCTTTTGTTTTGGACTAATTATCCTTTTAGTCCCTT
9265 C
1 C
9266 TTCTTTCTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (58 bp):
CCACAATTACTATGGTGACTCATCTTTTGTTTTGGACTAATTATCCTTTTAGTCCCTT
Found at i:10053 original size:2 final size:2
Alignment explanation
Indices: 10046--10073 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10036 AAGATGCGTG
10046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10074 GTGTTTTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.