Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002908.1 Kokia drynarioides strain JFW-HI SEQ_115334, 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, 870
Length: 1450
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Found at i:642 original size:29 final size:29
Alignment explanation
Indices: 607--832 Score: 149
Period size: 29 Copynumber: 7.8 Consensus size: 29
597 CTGAACTGTT
*
607 CAAAAATTACATTTTTGCCCCCGAACTTC
1 CAAAAATTACATTTTTGACCCCGAACTTC
** * **
636 CAAAAATCCCATTTATGACTTCGAAACTTC
1 CAAAAATTACATTTTTGACCCCG-AACTTC
* * *
666 AAAAAATTATATTTTT-ACACTCGAACTTC
1 CAAAAATTACATTTTTGAC-CCCGAACTTC
** **
695 C-AAAATT-CTATTTTCAACCTTGAAACTTC
1 CAAAAATTAC-ATTTTTGACCCCG-AACTTC
* *
724 AAAAAATTACATTTTT--CCACTGAACTTC
1 CAAAAATTACATTTTTGACC-CCGAACTTC
* *
752 CAAAAATTTCATTTTTGACCCCGAAACTTT
1 CAAAAATTACATTTTTGACCCCG-AACTTC
** *
782 TGAAAATTACATTTTT-ACCCCTAAACTTC
1 CAAAAATTACATTTTTGACCCC-GAACTTC
* *
811 CAAAAATTCCGTTTTTGACCCC
1 CAAAAATTACATTTTTGACCCC
833 TAAACTCTCA
Statistics
Matches: 152, Mismatches: 32, Indels: 25
0.73 0.15 0.12
Matches are distributed among these distances:
28 36 0.24
29 59 0.39
30 56 0.37
31 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTTGACCCCGAACTTC
Found at i:690 original size:30 final size:30
Alignment explanation
Indices: 656--818 Score: 108
Period size: 28 Copynumber: 5.6 Consensus size: 30
646 ATTTATGACT
656 TCGAAACTTCAAAAAATTATATTTTTACAC
1 TCGAAACTTCAAAAAATTATATTTTTACAC
* * *
686 TCG-AACTTC-CAAAATTCTATTTTCA-ACC
1 TCGAAACTTCAAAAAATTATATTTTTACA-C
* * *
714 TTGAAACTTCAAAAAATTACATTTTTCCAC
1 TCGAAACTTCAAAAAATTATATTTTTACAC
*
744 T-G-AACTTCCAAAAATT-TCATTTTTGAC-C
1 TCGAAACTTCAAAAAATTAT-ATTTTT-ACAC
* *** *
772 CCGAAACTTTTGAAAATTACATTTTTAC-C
1 TCGAAACTTCAAAAAATTATATTTTTACAC
* * *
801 CCTAAACTTCCAAAAATT
1 TCGAAACTTCAAAAAATT
819 CCGTTTTTGA
Statistics
Matches: 103, Mismatches: 21, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
27 1 0.01
28 36 0.35
29 32 0.31
30 33 0.32
31 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.36
Consensus pattern (30 bp):
TCGAAACTTCAAAAAATTATATTTTTACAC
Found at i:828 original size:59 final size:59
Alignment explanation
Indices: 608--845 Score: 248
Period size: 58 Copynumber: 4.1 Consensus size: 59
598 TGAACTGTTC
* * * * **
608 AAAAATTACATTTTTGCCCCCGAACTTCCAAAAATCCCATTTATGACTTCGAAACTTCA
1 AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCA
* * * ** **
667 AAAAATTATATTTTTA-CACTCGAACTTCC-AAAATTCTATTTTCAACCTTGAAACTTCA
1 AAAAATTACATTTTTACCCCT-GAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCA
* * **
725 AAAAATTACATTTTT-CCACTGAACTTCCAAAAATTTCATTTTTGACCCCGAAACTTTT
1 AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCA
* * * *
783 GAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCGTTTTTGACCCCTAAACTCTCA
1 AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACT-TCA
843 AAA
1 AAA
846 TTACCCTTTT
Statistics
Matches: 145, Mismatches: 29, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
57 8 0.06
58 77 0.53
59 57 0.39
60 3 0.02
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCA
Found at i:834 original size:30 final size:30
Alignment explanation
Indices: 607--838 Score: 149
Period size: 30 Copynumber: 7.9 Consensus size: 30
597 CTGAACTGTT
**
607 CAAAAATTACATTTTTG-CCCCCGAACTTC
1 CAAAAATTACATTTTTGACCCCTAAACTTC
** * ** *
636 CAAAAATCCCATTTATGACTTCGAAACTTC
1 CAAAAATTACATTTTTGACCCCTAAACTTC
* * * *
666 AAAAAATTATATTTTT-A-CACTCGAACTTC
1 CAAAAATTACATTTTTGACCCCT-AAACTTC
* * *
695 C-AAAATT-C-TATTTTCAACCTTGAAACTTC
1 CAAAAATTACAT-TTTTGACCCCT-AAACTTC
* * *
724 AAAAAATTACATTTTT--CCACTGAACTTC
1 CAAAAATTACATTTTTGACCCCTAAACTTC
* * *
752 CAAAAATTTCATTTTTGACCCCGAAACTTT
1 CAAAAATTACATTTTTGACCCCTAAACTTC
**
782 TGAAAATTACATTTTT-ACCCCTAAACTTC
1 CAAAAATTACATTTTTGACCCCTAAACTTC
* *
811 CAAAAATTCCGTTTTTGACCCCTAAACT
1 CAAAAATTACATTTTTGACCCCTAAACT
839 CTCAAAATTA
Statistics
Matches: 150, Mismatches: 42, Indels: 21
0.70 0.20 0.10
Matches are distributed among these distances:
26 1 0.01
27 4 0.03
28 28 0.19
29 54 0.36
30 57 0.38
31 5 0.03
32 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (30 bp):
CAAAAATTACATTTTTGACCCCTAAACTTC
Found at i:855 original size:29 final size:28
Alignment explanation
Indices: 764--860 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 28
754 AAAATTTCAT
* *
764 TTTTGACCCCGAAACTTTTGAAAATTA-CA
1 TTTTGACCCCTAAAC--TTCAAAATTACCA
* *
793 TTTTTACCCCTAAACTTCCAAAAATT-CCGT
1 TTTTGACCCCTAAACTT-C-AAAATTACC-A
*
823 TTTTGACCCCTAAACTCTCAAAATTACCC
1 TTTTGACCCCTAAACT-TCAAAATTACCA
852 TTTT-ACCCC
1 TTTTGACCCC
861 CGGATGTCTA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.04
28 5 0.09
29 30 0.54
30 18 0.32
31 1 0.02
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (28 bp):
TTTTGACCCCTAAACTTCAAAATTACCA
Done.