Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003509.1 Kokia drynarioides strain JFW-HI SEQ_116345, 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: 25008
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:7884 original size:109 final size:109
Alignment explanation
Indices: 7751--7965 Score: 313
Period size: 109 Copynumber: 2.0 Consensus size: 109
7741 AACAAAAAAC
* * * * *
7751 ATTTATCGGTTTTAAATAGGATATTGAATTATTTAGGTTCAAGGAAAAATCATACCCAATACGTT
1 ATTTATCGATTTTAAATAGAATATTCAATTATTTAGGTTCAAAGAAAAACCATACCCAATACGTT
* * ** * *
7816 AGGGCACAATTTTTCGAGTTCCCTAAAATAACAGAATATTGAGT
66 AGGGCACAATTTCTCGAATTCCAAAAAATAAAAGAACATTGAGT
*
7860 ATTTATCGATTTTGAATAGAATATTCAATTATTTAGGTTCAAAGAAAAACCATACCCAATACGTT
1 ATTTATCGATTTTAAATAGAATATTCAATTATTTAGGTTCAAAGAAAAACCATACCCAATACGTT
*
7925 AGTGCACAATTTCTCGAATTCCAAAAAATAAAAGAACATTG
66 AGGGCACAATTTCTCGAATTCCAAAAAATAAAAGAACATTG
7966 CCTTGGTTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
109 93 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (109 bp):
ATTTATCGATTTTAAATAGAATATTCAATTATTTAGGTTCAAAGAAAAACCATACCCAATACGTT
AGGGCACAATTTCTCGAATTCCAAAAAATAAAAGAACATTGAGT
Found at i:12443 original size:2 final size:2
Alignment explanation
Indices: 12436--12463 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12426 ATCATCATAA
12436 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12464 TTATATATAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:14271 original size:21 final size:21
Alignment explanation
Indices: 14245--14294 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
14235 GATACTTGAA
*
14245 ATACTTCTACCGATACAAGT-
1 ATACTTCTACCGAAACAAGTC
14265 ATAACTTCTACCGAAACAAGTC
1 AT-ACTTCTACCGAAACAAGTC
14287 ATACTTCT
1 ATACTTCT
14295 TCAGATACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (21 bp):
ATACTTCTACCGAAACAAGTC
Found at i:15046 original size:25 final size:25
Alignment explanation
Indices: 15010--15102 Score: 132
Period size: 25 Copynumber: 3.7 Consensus size: 25
15000 ATATCGCTCA
* *
15010 TACGAGCTAGACAGAATTATGCTTT
1 TACGAGCCAGACAGAATTACGCTTT
* *
15035 TGCGAGCCAGACAGAATTACGCTCT
1 TACGAGCCAGACAGAATTACGCTTT
15060 TACGAGCCAGACAGAATTACGCTTT
1 TACGAGCCAGACAGAATTACGCTTT
* *
15085 TACGAGCCAAATAGAATT
1 TACGAGCCAGACAGAATT
15103 TCATTCTTAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (25 bp):
TACGAGCCAGACAGAATTACGCTTT
Found at i:15064 original size:50 final size:50
Alignment explanation
Indices: 15004--15127 Score: 149
Period size: 50 Copynumber: 2.5 Consensus size: 50
14994 GATAAAATAT
* * * * *
15004 CGCTCATACGAGCTAGACAGAATTATGCTTTTGCGAGCCAGACAGAATTA
1 CGCTCTTACGAGCCAGACAGAATTACGCTTTTACGAGCCAAACAGAATTA
* *
15054 CGCTCTTACGAGCCAGACAGAATTACGCTTTTACGAGCCAAATAGAATTT
1 CGCTCTTACGAGCCAGACAGAATTACGCTTTTACGAGCCAAACAGAATTA
** * *
15104 CATTCTTACGAGCCTGATAGAATT
1 CGCTCTTACGAGCCAGACAGAATT
15128 TTGTTCTTAC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (50 bp):
CGCTCTTACGAGCCAGACAGAATTACGCTTTTACGAGCCAAACAGAATTA
Found at i:15112 original size:25 final size:25
Alignment explanation
Indices: 15037--15140 Score: 93
Period size: 25 Copynumber: 4.2 Consensus size: 25
15027 TATGCTTTTG
* * **
15037 CGAGCCAGACAGAATTACGCTCTTA
1 CGAGCCAGATAGAATTTCATTCTTA
* * *
15062 CGAGCCAGACAGAATTACGCTT-TTA
1 CGAGCCAGATAGAATTTC-ATTCTTA
*
15087 CGAGCCAAATAGAATTTCATTCTTA
1 CGAGCCAGATAGAATTTCATTCTTA
* **
15112 CGAGCCTGATAGAATTTTGTTCTTA
1 CGAGCCAGATAGAATTTCATTCTTA
15137 CGAG
1 CGAG
15141 TCGTGCAGAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
24 2 0.03
25 64 0.96
26 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (25 bp):
CGAGCCAGATAGAATTTCATTCTTA
Found at i:15811 original size:54 final size:54
Alignment explanation
Indices: 15729--15838 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
15719 TGGCAAGTTT
15729 TATAACATTTTACATATTCACAAACTAGACCTTGAGTTAGCTAGATTAAGCTAA
1 TATAACATTTTACATATTCACAAACTAGACCTTGAGTTAGCTAGATTAAGCTAA
15783 TATAACATTTTACATATTCACAAACTAGACCTTGAGTTAGCTAGATTAAGCTAA
1 TATAACATTTTACATATTCACAAACTAGACCTTGAGTTAGCTAGATTAAGCTAA
15837 TA
1 TA
15839 CGGACTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (54 bp):
TATAACATTTTACATATTCACAAACTAGACCTTGAGTTAGCTAGATTAAGCTAA
Found at i:20836 original size:10 final size:10
Alignment explanation
Indices: 20818--20851 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20808 TCTTAATCAT
*
20818 CATAAACACA
1 CATACACACA
20828 CATACACACA
1 CATACACACA
*
20838 CACACACACA
1 CATACACACA
20848 CATA
1 CATA
20852 TATAAAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.53, C:0.38, G:0.00, T:0.09
Consensus pattern (10 bp):
CATACACACA
Done.