Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013968.1 Kokia drynarioides strain JFW-HI SEQ_128999, 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: 9675
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:707 original size:18 final size:17
Alignment explanation
Indices: 686--773 Score: 79
Period size: 17 Copynumber: 5.1 Consensus size: 17
676 TAATAAGTTT
686 TAAATTTAAATATAAATC
1 TAAATTTAAA-ATAAATC
* *
704 TAAATTTAAATTAAATT
1 TAAATTTAAAATAAATC
* *
721 TAAATTTTAAAAAAAATT
1 TAAA-TTTAAAATAAATC
* *
739 TAAATTCAAAATCAAT-
1 TAAATTTAAAATAAATC
*
755 TTAATCTTAAAATAAATC
1 TAAAT-TTAAAATAAATC
773 T
1 T
774 TAAAATGGGT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
16 4 0.07
17 27 0.47
18 26 0.46
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAAATAAATC
Found at i:723 original size:35 final size:34
Alignment explanation
Indices: 684--773 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 34
674 TATAATAAGT
* *
684 TTTAAATTTAAATATAAATCTAAATTTAAATTAAA
1 TTTAAATTTAAA-ATAAATCTAAATTCAAAATAAA
* * *
719 TTTAAATTTTAAAAAAAATTTAAATTCAAAATCAA
1 TTTAAA-TTTAAAATAAATCTAAATTCAAAATAAA
754 TTT-AATCTTAAAATAAATCT
1 TTTAAAT-TTAAAATAAATCT
774 TAAAATGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
33 1 0.02
34 13 0.28
35 26 0.57
36 6 0.13
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATCTAAATTCAAAATAAA
Found at i:744 original size:6 final size:6
Alignment explanation
Indices: 684--727 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
674 TATAATAAGT
* *
684 TTTAAA TTTAAA TATAAA TCTAAA TTTAAA -TTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
728 TAAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:1200 original size:37 final size:37
Alignment explanation
Indices: 1150--1220 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
1140 CATATCACTT
* * * *
1150 GTTTTGATCCACTTCTCTGTGTTTTATCAGGAAGACG
1 GTTTTGATCCACTTCCCCGTATTTCATCAGGAAGACG
* *
1187 GTTTTGGTTCACTTCCCCGTATTTCATCAGGAAG
1 GTTTTGATCCACTTCCCCGTATTTCATCAGGAAG
1221 CTAACCGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (37 bp):
GTTTTGATCCACTTCCCCGTATTTCATCAGGAAGACG
Found at i:1899 original size:115 final size:114
Alignment explanation
Indices: 1704--1918 Score: 349
Period size: 115 Copynumber: 1.9 Consensus size: 114
1694 AATTTGGTCC
* * *
1704 ACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATC
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
* *
1769 AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGTCTTAAGTTGGTAT
66 AGGAAGCTGGAGTTCGAAGATTTGCTCACATCGAGTCTTAAGTTGGTAT
* * *
1818 ACTTCTTTGTATCTCATCAGGAAGCTAACCATTTTATTTCTTTGACCTACTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTACTTCTCAGTATCTCAT
1883 CAGGAAGCTGGAGTTCGAAGATTTGCTCACATCGAG
65 CAGGAAGCTGGAGTTCGAAGATTTGCTCACATCGAG
1919 CGTGGGTTTG
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 29 0.32
115 63 0.68
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (114 bp):
ACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
AGGAAGCTGGAGTTCGAAGATTTGCTCACATCGAGTCTTAAGTTGGTAT
Found at i:2026 original size:320 final size:319
Alignment explanation
Indices: 1205--2123 Score: 1302
Period size: 320 Copynumber: 2.9 Consensus size: 319
1195 TCACTTCCCC
* * *
1205 GTATTTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTACTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTTCTTCGACCTACTTCTCAGTATCTCATCAGGAAGC
* * *
1270 TGGGGTTCGAAGATTTGCTCATATCAAGCGTGGGTTTGA--T--TCTTC-TCT-GTATC-CTATC
66 TGGAGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTAGTATCTC-ATC
* * *** * * *
1328 AGGAAGATGTCCGCCTTACTTGTTTCAATCCACTTCTCTGTACCTCATCAGGAAAACGAATTTGG
130 AGGAAGATGACCGCATCGTTTGTTTCAATTCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
* * * * * *
1393 TCCACTTCTCAATATCTCATTAGGAAGCTAACCTTTTATTACTTCGCCCTGCTTCTCAGTATCTC
195 TCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTC
* *
1458 ATCAGGAAGCTGGGATTCGAAGATTTGCTCACATC-ATGTCCTGAGTTGGTATACTTCTCT
260 ATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGA-GTCCTAAGTTGGTATACTTCTCT
* *
1518 GTATCTCATTAGGAAGCTAACCATTTTATTTCTTCGACCTGCTTCTCAG-------T-----AGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTTCTTCGACCTACTTCTCAGTATCTCATCAGGAAGC
** *
1571 TGGAGTTTTAAGATTTGCTCACATCGAGTGTGGGTTTGATTTGGTCTTCTTCTTAGTATCTCATC
66 TGGAGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTC-TAGTATCTCATC
** * *
1636 AGGAAGATGACCGTGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATTAGGAAGACGAATTTGG
130 AGGAAGATGACCGCATCGTTTGTTTCAATTCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
*
1701 TCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTC
195 TCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTC
* * *
1766 ATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGTCTTAAGTTGGTATACTTCTTT
260 ATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGTCCTAAGTTGGTATACTTCTCT
*
1826 GTATCTCATCAGGAAGCTAACCATTTTATTTCTTTGACCTACTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTTCTTCGACCTACTTCTCAGTATCTCATCAGGAAGC
1891 TGGAGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
66 TGGAGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCT-AGTATCTCATC
*
1956 AGGAAGATGACCGCATCGTTTGTTTCAATTCACTTCTCTGTATCTCATCAGGAAGATGAATTTGG
130 AGGAAGATGACCGCATCGTTTGTTTCAATTCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
*
2021 TCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTA
195 TCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTC
* *
2086 ATCAGGAAGCTAGGGTTCAAAGATTTGCTCACATCGAG
260 ATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAG
2124 CGTGGGTTTG
Statistics
Matches: 534, Mismatches: 50, Indels: 37
0.86 0.08 0.06
Matches are distributed among these distances:
301 36 0.07
303 1 0.00
305 5 0.01
306 3 0.01
307 1 0.00
308 219 0.41
309 2 0.00
313 44 0.08
315 1 0.00
319 1 0.00
320 221 0.41
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (319 bp):
GTATCTCATCAGGAAGCTAACCATTTTATTTCTTCGACCTACTTCTCAGTATCTCATCAGGAAGC
TGGAGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTAGTATCTCATCA
GGAAGATGACCGCATCGTTTGTTTCAATTCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGT
CCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCA
TCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGTCCTAAGTTGGTATACTTCTCT
Found at i:4789 original size:27 final size:27
Alignment explanation
Indices: 4755--4810 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
4745 GCCCCAACCC
4755 CATTACCTATGGCATTTGAAGCTCCAT
1 CATTACCTATGGCATTTGAAGCTCCAT
4782 CATTACCTATGGCATTTGAAGCTCCAT
1 CATTACCTATGGCATTTGAAGCTCCAT
4809 CA
1 CA
4811 AAGTTCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (27 bp):
CATTACCTATGGCATTTGAAGCTCCAT
Found at i:7868 original size:27 final size:27
Alignment explanation
Indices: 7834--7889 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
7824 GCCCCAACCC
7834 CATTACCTATGGCATTTGAAGCTCCAT
1 CATTACCTATGGCATTTGAAGCTCCAT
7861 CATTACCTATGGCATTTGAAGCTCCAT
1 CATTACCTATGGCATTTGAAGCTCCAT
7888 CA
1 CA
7890 AAGTTCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (27 bp):
CATTACCTATGGCATTTGAAGCTCCAT
Done.