Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003306.1 Kokia drynarioides strain JFW-HI SEQ_115990, 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: 2807
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Found at i:671 original size:18 final size:18
Alignment explanation
Indices: 625--675 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
615 AATTTTAAAC
*
625 TTAAATTAAATTTAAATTT
1 TTAAAATAAATTT-AATTT
**
644 TT-AAGCAAATTTAATTT
1 TTAAAATAAATTTAATTT
661 TTAAAATAAATTTAA
1 TTAAAATAAATTTAA
676 AGGGAGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.26
18 18 0.67
19 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAAAATAAATTTAATTT
Found at i:1384 original size:139 final size:139
Alignment explanation
Indices: 1145--2128 Score: 1551
Period size: 139 Copynumber: 7.1 Consensus size: 139
1135 TTCTTAGTGT
* ** *
1145 CTCATCTGGAAGATTTGCTAATTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCACCAGGAA
1 CTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
*
1210 GATGATCCCATCACTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
66 GATGATCCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
1275 TCTCAGTAC
131 TCTCAGTAC
* *
1284 CTCATCTGAAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTTAGTGTCTCATCAGGAA
1 CTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
* * *
1349 GATGATCCCATCATTGTTCCAATCCGCTTTTCTGTATCTCATCAGGAAGGCGTATTTGGTTCACT
66 GATGATCCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
1414 TCTCAGTAC
131 TCTCAGTAC
* * **
1423 CCCATCTGGAAGATTCACTCGTTTTAAGCCTCG-TTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
1 CTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
* * * *
1487 GATGATCCCATCATTATTCCAATCCGCTTTTCTGTATCTCATCAGGAAGGCGTATTTGGTTCACT
66 GATGATCCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
1552 TCTCAGTAC
131 TCTCAGTAC
* *
1561 C-CTATCTGGAAGATTCGCTCGTTTCGAGCCTTGTTTGGGTCTTCTTCTCAGTGTCTTATCAGGA
1 CTC-ATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGA
* * * *
1625 AGATGATCCCATCATTG-TTCGAATCTGCTTTTTTGTATCTCATCAGGAAGGCGTATTTGGTTCA
65 AGATGATCCCATCATTGTTTC-AATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCA
1689 CTTCTCAGTAC
129 CTTCTCAGTAC
* *
1700 CTCATCTGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATTAGGAA
1 CTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
*
1765 GATGATGCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
66 GATGATCCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
1830 TCTCAGTAC
131 TCTCAGTAC
1839 CTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
1 CTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
* *
1904 GATGATCCCATCATTATTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACT
66 GATGATCCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
*
1969 TCTTAGTAC
131 TCTCAGTAC
* * *
1978 CTCATCTAGAAGATTTGCTCGTTTCGAGCCTCGGTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
1 CTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
* * * ***
2043 GATGATCCAATCATTGTTTCAATCCGCTTCTCTATATCTCATCAAGAAGAAAAATTTGGTTCACT
66 GATGATCCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
* *
2108 TCTTAGTAT
131 TCTCAGTAC
*
2117 CTCATCAGGAAG
1 CTCATCTGGAAG
2129 CTAACCTTTT
Statistics
Matches: 787, Mismatches: 53, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
137 1 0.00
138 132 0.17
139 650 0.83
140 4 0.01
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.36
Consensus pattern (139 bp):
CTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAA
GATGATCCCATCATTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACT
TCTCAGTAC
Found at i:2371 original size:206 final size:205
Alignment explanation
Indices: 2010--2677 Score: 939
Period size: 205 Copynumber: 3.3 Consensus size: 205
2000 TTCGAGCCTC
* * *** * *
2010 GGTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCC-AATC-ATTGTTTCAATCCGCTTC
1 GGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA-CCGCGCCGTTTGTTTCAATTCGCTTC
* * * * *
2073 TCTATATCTCATCAAGAAGAA-AAATTTGGTTCACTTCTTAGTATCTCATCAGGAAGCTAACCTT
65 TCTGTATCTCATCAGGAA-AACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * * ** **
2137 TTATTGCTTCGATCTGCTTCTTGGTGTGTCATTAGGAAGCTGGGATTCGAAGATTTTGCTCATGT
129 TTATTGCTTCAATCTGCTTCTCGGTGTGTCATTCGGAAGCTGGGATCCGAAGA-CCTGCTCACAT
*
2202 CGAGCATGGGTTT
193 CGAGCGTGGGTTT
2215 GGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGCCGTTTGTTTCAATTCGCTTCT
1 GGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGCCGTTTGTTTCAATTCGCTTCT
* *
2280 CTGTATCTCATCAGGAAAACGAATTTGG-TCTACTTCTCCGTATCTCATCAGGAAGCTAACCGTT
66 CTGTATCTCATCAGGAAAACGAATTTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTAACCATT
* *
2344 TATTGCTTCAATCTGTTTCTCGGTGTGTCATCCGGAAGCTGGGATCCGAAGACCTGCTCACATCG
130 TATTGCTTCAATCTGCTTCTCGGTGTGTCATTCGGAAGCTGGGATCCGAAGACCTGCTCACATCG
2409 AGCGTGGGTTT
195 AGCGTGGGTTT
* * *
2420 GGTTTGGTCTTTTTGTCAGTATCTCATCAGGAAGATGACCGCGCCGTTTGTTTCAACTCGCTTCT
1 GGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGCCGTTTGTTTCAATTCGCTTCT
* **
2485 CTGCATCTCATCAGGAAGGCGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTT
66 CTGTATCTCATCAGGAAAACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTT
* * *
2550 ATTACTTCCACCTGCTTCTCGGTGTGTCATTCGGAAGCTGGGATCCGAAGACCTGCTCACATCGA
131 ATTGCTTCAATCTGCTTCTCGGTGTGTCATTCGGAAGCTGGGATCCGAAGACCTGCTCACATCGA
2615 GCGTGGGTTT
196 GCGTGGGTTT
* *
2625 GGTTTGGTCTTTTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTCTTGTT
1 GGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGCCGT-TTGTT
2678 GGATAATCGC
Statistics
Matches: 418, Mismatches: 39, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
204 2 0.00
205 294 0.70
206 122 0.29
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (205 bp):
GGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGCCGTTTGTTTCAATTCGCTTCT
CTGTATCTCATCAGGAAAACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTT
ATTGCTTCAATCTGCTTCTCGGTGTGTCATTCGGAAGCTGGGATCCGAAGACCTGCTCACATCGA
GCGTGGGTTT
Done.