Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002037.1 Kokia drynarioides strain JFW-HI SEQ_113922, 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: 9146
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4663 original size:50 final size:49
Alignment explanation
Indices: 4540--4668 Score: 109
Period size: 50 Copynumber: 2.6 Consensus size: 49
4530 TAGAGGAATG
* * *
4540 GATTGAAGCCGTAATGACAAATCTCATACTCCTAAAGTTATAAGGGGTCA
1 GATTGAAGTCGTAAGGAC-AATCTCATACACCTAAAGTTATAAGGGGTCA
* * * * * *
4590 GATTGAAATTGCAATGGTA-AATCTCATTCACCTAAAGTTGTCTAGGGG-CA
1 GATTGAAGTCGTAA-GG-ACAATCTCATACACCTAAAGTTAT-AAGGGGTCA
*
4640 GATTGAAGTCGTAAGGACGAATCTTATAC
1 GATTGAAGTCGTAAGGAC-AATCTCATAC
4669 TCTTGAAGCT
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
48 1 0.02
49 2 0.03
50 50 0.83
51 6 0.10
52 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (49 bp):
GATTGAAGTCGTAAGGACAATCTCATACACCTAAAGTTATAAGGGGTCA
Found at i:4775 original size:40 final size:40
Alignment explanation
Indices: 4708--5073 Score: 366
Period size: 40 Copynumber: 9.2 Consensus size: 40
4698 ACCCTAAATT
* ** * *
4708 TTTTATCCTAATCAAAGGGAAGGTTGAAGACCATCCAATC
1 TTTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATC
* ** * *
4748 TTCTACCCCGATCATGGGACAGATTGAAGACCATCCAATT
1 TTTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATC
* * *
4788 TTTTACCTTGACCATGGGGCAGATTGAAGACCATCCAATC
1 TTTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATC
* *
4828 TTTTACCCTAATTA-GAGGGTAGATTGAAGACCATCCAATC
1 TTTTACCCTAATCATG-GGGCAGATTGAAGACCATCCAATC
** * * *
4868 TTTTACCCTAATCAAAGGGCAAATTGAAGATCATTCAATC
1 TTTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATC
** * * *
4908 TTTTACCCCGACCATGGGGCAAATTGAAG-CAATCCAATC
1 TTTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATC
* *
4947 TTTTACCCTAATCA-GAGGGCAAATTAAAGACCATCCAATC
1 TTTTACCCTAATCATG-GGGCAGATTGAAGACCATCCAATC
* * * *
4987 TTTTATCCC-GACCATGGAGCAGATTGAAG-CAATCCAATC
1 TTTTA-CCCTAATCATGGGGCAGATTGAAGACCATCCAATC
*
5026 TTTTACCCTAATCA-GAGGGCAGATTGAAGACTATCCAATC
1 TTTTACCCTAATCATG-GGGCAGATTGAAGACCATCCAATC
5066 TTTTACCC
1 TTTTACCC
5074 CTAAAGCTAT
Statistics
Matches: 267, Mismatches: 50, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
38 5 0.02
39 60 0.22
40 198 0.74
41 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (40 bp):
TTTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATC
Found at i:4968 original size:79 final size:80
Alignment explanation
Indices: 4708--5074 Score: 429
Period size: 79 Copynumber: 4.6 Consensus size: 80
4698 ACCCTAAATT
* * * * * *
4708 TTTTATCCTAATCAAAGGG-AAGGTTGAAGACCATCCAATCTTCTACCCCGATCATGGGACAGAT
1 TTTTACCCTAATCAGAGGGCAA-ATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGCAGAT
* *
4772 TGAAGACCATCCAATT
65 TGAAGACAATCCAATC
* * * * ** ** *
4788 TTTTACCTTGACCATG-GGGCAGATTGAAGACCATCCAATCTTTTACCCTAATTA-GAGGGTAGA
1 TTTTACCCTAATCA-GAGGGCAAATTGAAGACCATCCAATCTTTTACCCCGACCATG-GGGCAGA
*
4851 TTGAAGACCATCCAATC
64 TTGAAGACAATCCAATC
* * * *
4868 TTTTACCCTAATCAAAGGGCAAATTGAAGATCATTCAATCTTTTACCCCGACCATGGGGCAAATT
1 TTTTACCCTAATCAGAGGGCAAATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGCAGATT
4933 GAAG-CAATCCAATC
66 GAAGACAATCCAATC
* * *
4947 TTTTACCCTAATCAGAGGGCAAATTAAAGACCATCCAATCTTTTATCCCGACCATGGAGCAGATT
1 TTTTACCCTAATCAGAGGGCAAATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGCAGATT
5012 GAAG-CAATCCAATC
66 GAAGACAATCCAATC
* *
5026 TTTTACCCTAATCAGAGGGCAGATTGAAGACTATCCAATCTTTTACCCC
1 TTTTACCCTAATCAGAGGGCAAATTGAAGACCATCCAATCTTTTACCCC
5075 TAAAGCTATA
Statistics
Matches: 243, Mismatches: 39, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
79 127 0.52
80 114 0.47
81 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (80 bp):
TTTTACCCTAATCAGAGGGCAAATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGCAGATT
GAAGACAATCCAATC
Found at i:6002 original size:16 final size:16
Alignment explanation
Indices: 5981--6011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5971 AACCCAATAC
5981 TACCTAAAAAACCCAA
1 TACCTAAAAAACCCAA
*
5997 TACCTAAACAACCCA
1 TACCTAAAAAACCCA
6012 TTTAATAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (16 bp):
TACCTAAAAAACCCAA
Found at i:7012 original size:30 final size:30
Alignment explanation
Indices: 6977--7193 Score: 235
Period size: 30 Copynumber: 7.3 Consensus size: 30
6967 AAAATTACAT
6977 TTTGACCCTCAAACTTTCCAAAAATTCAAA
1 TTTGACCCTCAAACTTTCCAAAAATTCAAA
*
7007 ATTGACCC-CTAAACTTTCCAAAAATTCAAA
1 TTTGACCCTC-AAACTTTCCAAAAATTCAAA
* *
7037 ATTGACCC-CTAAACTTTCCAAAAATTTAAA
1 TTTGACCCTC-AAACTTTCCAAAAATTCAAA
* * **
7067 TTTGACCCTCGAACTTTCTAAAAATTTGAA
1 TTTGACCCTCAAACTTTCCAAAAATTCAAA
* * * *
7097 TTTGAACTTCGAACTTTCCAAAAATTCCAA
1 TTTGACCCTCAAACTTTCCAAAAATTCAAA
* * *
7127 TTTCA-CCTCTAACTTTCCAAAAATTCCAA
1 TTTGACCCTCAAACTTTCCAAAAATTCAAA
* *
7156 TTTTACCC-CTAAACTTCCCAAAAATTCAAA
1 TTTGACCCTC-AAACTTTCCAAAAATTCAAA
7186 TTTGACCC
1 TTTGACCC
7194 GATTTTAATT
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
29 28 0.17
30 135 0.82
31 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (30 bp):
TTTGACCCTCAAACTTTCCAAAAATTCAAA
Found at i:7274 original size:3 final size:3
Alignment explanation
Indices: 7266--7306 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
7256 TTTATCTTGT
7266 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
7307 GATTCAATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.