Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009830.1 Kokia drynarioides strain JFW-HI SEQ_124551, 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: 2593
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Found at i:1680 original size:15 final size:17
Alignment explanation
Indices: 1662--1694 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1652 GCAATCCTAG
1662 CTCAAGC-TCTCC-TTT
1 CTCAAGCATCTCCGTTT
1677 CTCAAGCATCTCCGTTT
1 CTCAAGCATCTCCGTTT
1694 C
1 C
1695 AATAGCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.15, C:0.39, G:0.09, T:0.36
Consensus pattern (17 bp):
CTCAAGCATCTCCGTTT
Found at i:2051 original size:383 final size:383
Alignment explanation
Indices: 1332--2097 Score: 1275
Period size: 383 Copynumber: 2.0 Consensus size: 383
1322 CATATTGATT
1332 ACTAAAACTCTTTACAACCAGTCTTGCCTTCGGTCTGTTGAGTGAACCATCGAGATTGAGTTTGG
1 ACTAAAACTCTTTACAACCAGTCTTGCCTTCGGTCTGTTGAGTGAACCATCGAGATTGAGTTTGG
* * * *
1397 TTTTGAACACCCATTCGATGCTAATAACCTTTTTGTGTGATGGCCTATCAATAAGTTCCCATATC
66 TTCTGAACACCCATTCGATGCTAATAACCCTTTTGTGTGATGGCCTATCAACAAGTTCCCACATC
* *
1462 TGGTTCTTGTAAATCATATTTAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTTCAGC
131 TGGTTCTTGCAAATCATATTCAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTTCAGC
** * * *
1527 TTCTTCGGAGTTCACAGATTTAAGAGTTTCTACCTCTACTCTTTGGTAAATTTCAACAATTGGTC
196 TTCTTCAAAGTTCACAGATTTAAGAGTTGCTACCTCTAATCTTCGGTAAATTTCAACAATTGGTC
*
1592 GCGTACCCCTAAATGGTATATCATTGAAGTCTTCTTCTTCAACTTGATTATCCCCAAGTTGCAAT
261 GCGTACCCCTAAATGGCATATCATTGAAGTCTTCTTCTTCAACTTGATTATCCCCAAGTTGCAAT
* * *
1657 CCTAGCTCAAGCTCTCCTTTCTCAAGCATCTCCGTTTCAATAGCTTCCCATTTCCATG
326 CCTAGCTCAAGCTCTCCCTTCTCAAGCATCTCAGTTTCAATAGCATCCCATTTCCATG
* *
1715 ACTAAAACTCTTTACAACCAGTCTTGCCTTTGGTCTGTTGAGTGAACCATTGACG-TTGAGTTTG
1 ACTAAAACTCTTTACAACCAGTCTTGCCTTCGGTCTGTTGAGTGAACCATCGA-GATTGAGTTTG
*
1779 GTTCTGAACACCCATTTGATGCTAATAACCCTTTTGTGTGATGGCCTATCAACAAGTTCCCACAT
65 GTTCTGAACACCCATTCGATGCTAATAACCCTTTTGTGTGATGGCCTATCAACAAGTTCCCACAT
*
1844 CTGGTTCTTGCAAATCATATTCAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTTCAT
130 CTGGTTCTTGCAAATCATATTCAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTTCAG
* *
1909 CTTCTTCAAAGTTCACAGGTTTAAGAGTTGCTACCTCTAATCTTCGGTAAATTTTAACAATTGGT
195 CTTCTTCAAAGTTCACAGATTTAAGAGTTGCTACCTCTAATCTTCGGTAAATTTCAACAATTGGT
* * *
1974 CGCGTACCCCTAAATGGCATGTCATTGAAGTCTTTTTCTTCAACTTGATTATCCCTAAGTTGCAA
260 CGCGTACCCCTAAATGGCATATCATTGAAGTCTTCTTCTTCAACTTGATTATCCCCAAGTTGCAA
*
2039 -CCTTATCTCAAGCTCTCCCTTCTCAAGCATCTCAGTTTCAATAGCATCCCATTTCCATG
325 TCC-TAGCTCAAGCTCTCCCTTCTCAAGCATCTCAGTTTCAATAGCATCCCATTTCCATG
2098 TTTTTTCTTC
Statistics
Matches: 356, Mismatches: 25, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
382 2 0.01
383 353 0.99
384 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (383 bp):
ACTAAAACTCTTTACAACCAGTCTTGCCTTCGGTCTGTTGAGTGAACCATCGAGATTGAGTTTGG
TTCTGAACACCCATTCGATGCTAATAACCCTTTTGTGTGATGGCCTATCAACAAGTTCCCACATC
TGGTTCTTGCAAATCATATTCAACTCAGCTTGCATAGCTTCTTTCAAGCCTTTTGTTGCTTCAGC
TTCTTCAAAGTTCACAGATTTAAGAGTTGCTACCTCTAATCTTCGGTAAATTTCAACAATTGGTC
GCGTACCCCTAAATGGCATATCATTGAAGTCTTCTTCTTCAACTTGATTATCCCCAAGTTGCAAT
CCTAGCTCAAGCTCTCCCTTCTCAAGCATCTCAGTTTCAATAGCATCCCATTTCCATG
Done.