Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014484.1 Kokia drynarioides strain JFW-HI SEQ_129523, 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: 4836
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:51 original size:17 final size:18
Alignment explanation
Indices: 29--71 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
19 AACTTTATTT
29 ATTTTAAA-TTCATAATA
1 ATTTTAAATTTCATAATA
*
46 ATTTTAAATTTGATAATA
1 ATTTTAAATTTCATAATA
*
64 AATTTAAA
1 ATTTTAAA
72 CTTAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTTAAATTTCATAATA
Found at i:99 original size:17 final size:17
Alignment explanation
Indices: 74--152 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
64 AATTTAAACT
74 TAAATTTAAATCTAAAA
1 TAAATTTAAATCTAAAA
* *
91 TACATTTAAATTTAAAA
1 TAAATTTAAATCTAAAA
* *
108 TAAATTTAAATTTTTAAA
1 TAAATTTAAA-TCTAAAA
*
126 CAAATTT-AATCTTAAAA
1 TAAATTTAAATC-TAAAA
143 TAAATTTAAA
1 TAAATTTAAA
153 GGGGAGCTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 1 0.02
17 36 0.71
18 14 0.27
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATCTAAAA
Found at i:108 original size:7 final size:6
Alignment explanation
Indices: 62--120 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
52 AATTTGATAA
* * * * *
62 TAAATT TAAACT TAAATT TAAATC TAAA-A TACATT TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
108 TAAATT TAAATT T
1 TAAATT TAAATT T
121 TTAAACAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
5 7 0.17
6 35 0.83
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:133 original size:35 final size:34
Alignment explanation
Indices: 62--152 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 34
52 AATTTGATAA
* * *
62 TAAATTTAAACTTAAATTTAAATCTAAAATACATT
1 TAAATTTAAA-ATAAATTTAAATCTAAAACAAATT
* *
97 TAAATTTAAAATAAATTTAAATTTTTAAACAAATT
1 TAAATTTAAAATAAATTTAAA-TCTAAAACAAATT
132 T-AATCTTAAAATAAATTTAAA
1 TAAAT-TTAAAATAAATTTAAA
153 GGGGAGCTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 13 0.27
35 36 0.73
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (34 bp):
TAAATTTAAAATAAATTTAAATCTAAAACAAATT
Found at i:789 original size:37 final size:37
Alignment explanation
Indices: 748--834 Score: 174
Period size: 37 Copynumber: 2.4 Consensus size: 37
738 TTCTCTGTAT
748 CTCATCAGGAAGACGAATTTGGTCCACTTCTACGTAC
1 CTCATCAGGAAGACGAATTTGGTCCACTTCTACGTAC
785 CTCATCAGGAAGACGAATTTGGTCCACTTCTACGTAC
1 CTCATCAGGAAGACGAATTTGGTCCACTTCTACGTAC
822 CTCATCAGGAAGA
1 CTCATCAGGAAGA
835 TGGTCCGGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (37 bp):
CTCATCAGGAAGACGAATTTGGTCCACTTCTACGTAC
Found at i:1150 original size:218 final size:218
Alignment explanation
Indices: 772--1852 Score: 1880
Period size: 218 Copynumber: 5.0 Consensus size: 218
762 GAATTTGGTC
* *
772 CACTTCTAC-GTACCTCATCAGGAAGACGAATTTGGTCCACTTCTACGTACCTCATCAGGAAGAT
1 CACTTCT-CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGAT
836 GGTCCGGAAGCTAACCGTTTTATTACTTCGGCACGCTTCTCAGTATCTCATCAGGAAGCTATGGT
65 GGTCCGGAAGCTAACCGTTTTATTACTTCGGCACGCTTCTCAGTATCTCATCAGGAAGCTATGGT
* *
901 TCGAAGATTTCCTCACATCGAGCATGGGTTTGGTTCGATCTTCTTCTCAGTATCTCATCGGGAAG
130 TCGAAGATTTGCTCACATCGAGCATGGGTTTGGTTCGGTCTTCTTCTCAGTATCTCATCGGGAAG
*
966 ATGACTGCGTCATTTGTTTCAATT
195 ATGACTGCGTCGTTTGTTTCAATT
990 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
1 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
* * ** *
1055 GTCAGGAAGCCAACCGTTTTATTACTTCAACACGCTTCTCAGTATCTCATCAGGAAGCTGTGGTT
66 GTCCGGAAGCTAACCGTTTTATTACTTCGGCACGCTTCTCAGTATCTCATCAGGAAGCTATGGTT
*
1120 CGAAGATTTGCTCACATCGAGCATGGGTTTGGTTCGATCTTCTTCTCAGTATCTCATCGGGAAGA
131 CGAAGATTTGCTCACATCGAGCATGGGTTTGGTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGA
*
1185 TGA-TGGCGTTGTTTGTTTCAATT
196 TGACT-GCGTCGTTTGTTTCAATT
1208 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
1 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
* *
1273 GTCCGGAAGCTAACCGTTTTATTACTTTGGCACGTTTCTCAGTATCTCATCAGGAAGCTATGGTT
66 GTCCGGAAGCTAACCGTTTTATTACTTCGGCACGCTTCTCAGTATCTCATCAGGAAGCTATGGTT
*
1338 CGAAGATTTCCTCACATCGAGCATGGGTTTGGTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGA
131 CGAAGATTTGCTCACATCGAGCATGGGTTTGGTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGA
1403 TGACTGCGTCGTTTGTTTCAATT
196 TGACTGCGTCGTTTGTTTCAATT
1426 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
1 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
* * *
1491 GTCAGGAAG-TCAACCGTTTTATTACTTCGACACGCTTCTCAGTATCTCATCAGGAAGCTGTGGT
66 GTCCGGAAGCT-AACCGTTTTATTACTTCGGCACGCTTCTCAGTATCTCATCAGGAAGCTATGGT
*
1555 TCGAAGATTTGCTCACATCGAGCATGGCTTTGGTTCGGTCTTCTTCTCAGTATCTCATCGGGAAG
130 TCGAAGATTTGCTCACATCGAGCATGGGTTTGGTTCGGTCTTCTTCTCAGTATCTCATCGGGAAG
*
1620 ATGACTGCATCGTTTGTTTCAATT
195 ATGACTGCGTCGTTTGTTTCAATT
* *
1644 CACTTCTCTATATCTCATCAGGAAAACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
1 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
*
1709 GTCCGGAAGCTAACCGTTTTATTACTTCGGCACGTTTCTCAGTATCTCATCAGGAAGCTATGGTT
66 GTCCGGAAGCTAACCGTTTTATTACTTCGGCACGCTTCTCAGTATCTCATCAGGAAGCTATGGTT
* *
1774 TGAAGATTTGCTCACATCGAGCATGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCGGGAAGA
131 CGAAGATTTGCTCACATCGAGCATGGGTTTGGTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGA
*
1839 TGACTGCATCGTTT
196 TGACTGCGTCGTTT
1853 TGTGGATAAT
Statistics
Matches: 821, Mismatches: 37, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
217 3 0.00
218 816 0.99
219 2 0.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (218 bp):
CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATG
GTCCGGAAGCTAACCGTTTTATTACTTCGGCACGCTTCTCAGTATCTCATCAGGAAGCTATGGTT
CGAAGATTTGCTCACATCGAGCATGGGTTTGGTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGA
TGACTGCGTCGTTTGTTTCAATT
Done.