Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009962.1 Kokia drynarioides strain JFW-HI SEQ_124710, 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: 2870
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.36
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:842 original size:52 final size:52
Alignment explanation
Indices: 781--890 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 52
771 CTTTATTTAT
** * *
781 TTTAAATTTATGAT-AATTTTAAATTTGAAA-ATAATGTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAAATTTGAAACA-AAT-TTAAACTTAAAATAAA
* **
833 TTTAAATTTAAAATAAATTTAAAATTTTAAACAAATTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAAATTTGAAACAAATTTAAACTTAAAATAAA
885 TTTAAA
1 TTTAAA
891 GGGAGTTTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
52 31 0.63
53 17 0.35
54 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAAATTTGAAACAAATTTAAACTTAAAATAAA
Found at i:843 original size:17 final size:17
Alignment explanation
Indices: 781--890 Score: 114
Period size: 17 Copynumber: 6.4 Consensus size: 17
771 CTTTATTTAT
** *
781 TTTAAATTTATGATAAT
1 TTTAAATTTAAAATAAA
798 TTTAAATTTGAAAAT-AA
1 TTTAAATTT-AAAATAAA
* *
815 TGTTAAACTTAAATTAAA
1 T-TTAAATTTAAAATAAA
833 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
850 TTTAAAATTTTAAACAAA
1 TTT-AAATTTAAAATAAA
*
868 TTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
885 TTTAAA
1 TTTAAA
891 GGGAGTTTGG
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
17 48 0.63
18 28 0.37
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1824 original size:201 final size:203
Alignment explanation
Indices: 1310--1825 Score: 691
Period size: 201 Copynumber: 2.5 Consensus size: 203
1300 TTTCATCAGG
* * * *
1310 ATTTGGTTCACTTCTCTGTATCTCATCA-GATAGCTAACCACTTTATGGCTTCAACCTGCTTCTC
1 ATTTGGTTCACTTCTCAGTATCTCATCAGGA-AGCTAACC-TTTTATTGCTTCGACCTGCTTCTC
* *
1374 AGCATCTCATCAGGAAGCTGGGGTTCAAAGA-TTTGCTCGTTTTGAGCCTCGTTTAGGTCTTCTT
64 AGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCGCTTTGAGCCTCGTTTAGGTCTTCTT
** *
1438 CTCAGTACCTCATCAGGAAGATGATTACATCACTGTTTGTTTCAATTCGCTCCTCCGTATCTCAT
129 CTCAGTACCTCATCAGGAAGATGACCACAT-ACTGTTTGTTTCAACTCGCTCCTCCGTATCTCAT
*
1503 CCGAAAGACGA
193 CAGAAAGACGA
* *
1514 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTATCAG
1 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
* * * *
1579 TGTCTCATCAAGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
66 TATCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCGCTTTGAGCCTCGTTTAGGTCTTCTTCT
** * * * * *
1644 CAGTGTCTCATCAGGAAGATGACCGCGT-C-GTTTGTTTCAACTCGCTTCTCTGTATCTCATTAG
131 CAGTACCTCATCAGGAAGATGACCACATACTGTTTGTTTCAACTCGCTCCTCCGTATCTCATCAG
* *
1707 GAAGGCGA
196 AAAGACGA
1715 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
* * * * *
1780 TATCTTC-TCAGGAAGCTGAGGTTCGAATATTTTGTTTGCTTTGAGC
66 TATC-TCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCGCTTTGAGC
1826 GTGGTGTTGA
Statistics
Matches: 274, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
201 133 0.49
202 3 0.01
203 48 0.18
204 88 0.32
205 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (203 bp):
ATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG
TATCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCGCTTTGAGCCTCGTTTAGGTCTTCTTCT
CAGTACCTCATCAGGAAGATGACCACATACTGTTTGTTTCAACTCGCTCCTCCGTATCTCATCAG
AAAGACGA
Done.