Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003873.1 Kokia drynarioides strain JFW-HI SEQ_116907, 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: 5219
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Found at i:1508 original size:45 final size:45
Alignment explanation
Indices: 1436--1659 Score: 213
Period size: 45 Copynumber: 5.0 Consensus size: 45
1426 GAATCTAAGT
* * * *
1436 CACCAGTGTATGAACCACCGAAA-AAAGA-AAAGCCTGAACCTAAGC
1 CACCAGTTTATGAACCTCC-AAAGAAAGAGAAA-CCTGAACCCAAAC
* *
1481 CACCTGTTTAT-ACACCTCCAAAGAAAGAGAAACTTGAACCCAAAC
1 CACCAGTTTATGA-ACCTCCAAAGAAAGAGAAACCTGAACCCAAAC
* * * ** * * *
1526 CACCAGTGTATGAACCTCCGAAGAAGGAGAAGTCTGAGCCTAAGC
1 CACCAGTTTATGAACCTCCAAAGAAAGAGAAACCTGAACCCAAAC
* * *
1571 CGCCAATTTAT-ACACCTCCAAAGAAAGAGAAACTTGAACCCAAAC
1 CACCAGTTTATGA-ACCTCCAAAGAAAGAGAAACCTGAACCCAAAC
* *
1616 CACCAGTATATGAACCACCAAAGAAAGAGAAACCTGAACCCAAA
1 CACCAGTTTATGAACCTCCAAAGAAAGAGAAACCTGAACCCAAA
1660 GAAAGAGAAA
Statistics
Matches: 141, Mismatches: 32, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
44 5 0.04
45 131 0.93
46 5 0.04
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (45 bp):
CACCAGTTTATGAACCTCCAAAGAAAGAGAAACCTGAACCCAAAC
Found at i:1568 original size:90 final size:90
Alignment explanation
Indices: 1436--1655 Score: 332
Period size: 90 Copynumber: 2.4 Consensus size: 90
1426 GAATCTAAGT
* * **
1436 CACCAGTGTATGAACCACCGAAAAAAGAAAAGCCTGAACCTAAGCCACCTGTTTATACACCTCCA
1 CACCAGTGTATGAACCACCGAAGAAAGAGAAGCCTGAACCTAAGCCACCAATTTATACACCTCCA
1501 AAGAAAGAGAAACTTGAACCCAAAC
66 AAGAAAGAGAAACTTGAACCCAAAC
* * * * *
1526 CACCAGTGTATGAACCTCCGAAGAAGGAGAAGTCTGAGCCTAAGCCGCCAATTTATACACCTCCA
1 CACCAGTGTATGAACCACCGAAGAAAGAGAAGCCTGAACCTAAGCCACCAATTTATACACCTCCA
1591 AAGAAAGAGAAACTTGAACCCAAAC
66 AAGAAAGAGAAACTTGAACCCAAAC
* * *
1616 CACCAGTATATGAACCACCAAAGAAAGAGAAACCTGAACC
1 CACCAGTGTATGAACCACCGAAGAAAGAGAAGCCTGAACC
1656 CAAAGAAAGA
Statistics
Matches: 114, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 114 1.00
ACGTcount: A:0.42, C:0.27, G:0.16, T:0.14
Consensus pattern (90 bp):
CACCAGTGTATGAACCACCGAAGAAAGAGAAGCCTGAACCTAAGCCACCAATTTATACACCTCCA
AAGAAAGAGAAACTTGAACCCAAAC
Found at i:1660 original size:22 final size:22
Alignment explanation
Indices: 1633--1681 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1623 ATATGAACCA
1633 CCAAAGAAAGAGAAACCTGAAC
1 CCAAAGAAAGAGAAACCTGAAC
1655 CCAAAGAAAGAGAAACCTGAAC
1 CCAAAGAAAGAGAAACCTGAAC
1677 CCAAA
1 CCAAA
1682 CCACCAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.55, C:0.24, G:0.16, T:0.04
Consensus pattern (22 bp):
CCAAAGAAAGAGAAACCTGAAC
Found at i:1666 original size:67 final size:67
Alignment explanation
Indices: 1588--1722 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
1578 TTATACACCT
* *
1588 CCAAAGAAAGAGAAACTTGAACCCAAACCACCAGTATATGAACCACCAAAGAAAGAGAAACCTGA
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCACCAAAAAAAGAGAAACCTGA
1653 AC
66 AC
*
1655 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCACCAAAAAAAGAGAAACCTGA
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCACCAAAAAAAGAGAAACCTGA
1720 AC
66 AC
1722 C
1 C
1723 TAAGCCATTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.50, C:0.27, G:0.15, T:0.08
Consensus pattern (67 bp):
CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGAACCACCAAAAAAAGAGAAACCTGA
AC
Found at i:1710 original size:45 final size:45
Alignment explanation
Indices: 1655--1932 Score: 263
Period size: 45 Copynumber: 6.2 Consensus size: 45
1645 AAACCTGAAC
*
1655 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCA
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCT
* * * *** *
1700 CCAAAAAAAGAGAAACCTGAACCTAAGCCATTGGTTTAT-ACACCT
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGA-ACCT
* * *
1745 CCAAAGAAAGAGAAACCTGAACCTAGATCACCAGTGTATGAACCT
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCT
* * * * ** * * *
1790 CCAAAGAAGGAGAAACTTGAGCCTAAGTCACCAATTTATGCACCT
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCT
* * *
1835 TCAAAGAAAGAGAAGCCTGAATCCAAACCACCAGTGTATGAACCGT
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACC-T
* * * * * *
1881 -CAAAGAAAGAAAAACCAGAGCCCAAATCACCAGTTTATGAGCCT
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCT
1925 CCAAAGAA
1 CCAAAGAA
1933 GCCACCGATG
Statistics
Matches: 185, Mismatches: 44, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
44 2 0.01
45 181 0.98
46 2 0.01
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.15
Consensus pattern (45 bp):
CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCT
Found at i:1785 original size:157 final size:157
Alignment explanation
Indices: 1498--1805 Score: 436
Period size: 157 Copynumber: 2.0 Consensus size: 157
1488 TTATACACCT
* * * * * **
1498 CCAAAGAAAGAGAAACTTGAACCCAAACCACCAGTGTATGAACCTCCGAAGAAGGAGAAGTCTGA
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCACCAAAAAAAGAGAAACCTGA
* * *
1563 GCCTAAGCCGCCAATTTATACACCTCCAAAGAAAGAGAAACTTGAACCCAAACCACCAGTATATG
66 ACCTAAGCCACCAATTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATG
1628 AACCACCAAAGAAAGAGAAACCTGAAC
131 AACCACCAAAGAAAGAGAAACCTGAAC
1655 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCACCAAAAAAAGAGAAACCTGA
1 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCACCAAAAAAAGAGAAACCTGA
**** * * * *
1720 ACCTAAGCCATTGGTTTATACACCTCCAAAGAAAGAGAAACCTGAACCTAGATCACCAGTGTATG
66 ACCTAAGCCACCAATTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATG
* *
1785 AACCTCCAAAGAAGGAGAAAC
131 AACCACCAAAGAAAGAGAAAC
1806 TTGAGCCTAA
Statistics
Matches: 131, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
157 131 1.00
ACGTcount: A:0.44, C:0.26, G:0.17, T:0.13
Consensus pattern (157 bp):
CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCACCAAAAAAAGAGAAACCTGA
ACCTAAGCCACCAATTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATG
AACCACCAAAGAAAGAGAAACCTGAAC
Found at i:1877 original size:247 final size:247
Alignment explanation
Indices: 1436--1906 Score: 705
Period size: 247 Copynumber: 1.9 Consensus size: 247
1426 GAATCTAAGT
*
1436 CACCAGTGTATGAACCACCGAAAAAAGAAAAGCCTGAACCTAAGCCACCTGTTTATACACCTCCA
1 CACCAGTGTATGAACCACCAAAAAAAGAAAAGCCTGAACCTAAGCCACCTGTTTATACACCTCCA
* * *
1501 AAGAAAGAGAAACTTGAACCCAAACCACCAGTGTATGAACCTCCGAAGAAGGAGAAGTCTGAGCC
66 AAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAACTCTGAGCC
* *
1566 TAAGCCGCCAATTTATACACCTCCAAAGAAAGAGAAACTTGAACCCAAACCACCAGTATATGAAC
131 TAAGCCACCAATTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGAAC
* *
1631 CACCAAAGAAAGAGAAACCTGAACCCAAAGAAAGAGAAACCTGAACCCAAAC
196 CACCAAAGAAAGAAAAACCAGAACCCAAAGAAAGAGAAACCTGAACCCAAAC
*
1683 CACCAGTGTATGAACCACCAAAAAAAGAGAAA-CCTGAACCTAAGCCA-TTGGTTTATACACCTC
1 CACCAGTGTATGAACCACCAAAAAAAGA-AAAGCCTGAACCTAAGCCACCT-GTTTATACACCTC
* * *
1746 CAAAGAAAGAGAAACCTGAACCTAGATCACCAGTGTATGAACCTCCAAAGAAGGAGAAACT-TGA
64 CAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAG-AACTCTGA
* * * * * *
1810 GCCTAAGTCACCAATTTATGCACCTTCAAAGAAAGAGAAGCCTGAATCCAAACCACCAGTGTATG
128 GCCTAAGCCACCAATTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATG
** *
1875 AACCGTCAAAGAAAGAAAAACCAGAGCCCAAA
193 AACCACCAAAGAAAGAAAAACCAGAACCCAAA
1907 TCACCAGTTT
Statistics
Matches: 200, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
246 1 0.00
247 193 0.96
248 6 0.03
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (247 bp):
CACCAGTGTATGAACCACCAAAAAAAGAAAAGCCTGAACCTAAGCCACCTGTTTATACACCTCCA
AAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAACTCTGAGCC
TAAGCCACCAATTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTATATGAAC
CACCAAAGAAAGAAAAACCAGAACCCAAAGAAAGAGAAACCTGAACCCAAAC
Found at i:1902 original size:90 final size:88
Alignment explanation
Indices: 1655--1932 Score: 315
Period size: 90 Copynumber: 3.1 Consensus size: 88
1645 AAACCTGAAC
* *
1655 CCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGAACCACCAAAAAAAGAGAAACCTGA
1 CCAAAGAAAGAGAAACCTGAA-CCAAACCACCAGTGTATGAACC-TCAAAGAAAGAGAAACCTGA
* * *** *
1720 ACCTAAGCCATTGGTTTATACACCT
64 GCCTAAGTCACCAGTTTATGCACCT
* * * *
1745 CCAAAGAAAGAGAAACCTGAACCTAGATCACCAGTGTATGAACCTCCAAAGAAGGAGAAACTTGA
1 CCAAAGAAAGAGAAACCTGAACC-AAACCACCAGTGTATGAACCT-CAAAGAAAGAGAAACCTGA
*
1810 GCCTAAGTCACCAATTTATGCACCT
64 GCCTAAGTCACCAGTTTATGCACCT
* * * *
1835 TCAAAGAAAGAGAAGCCTGAATCCAAACCACCAGTGTATGAACCGTCAAAGAAAGAAAAACCAGA
1 CCAAAGAAAGAGAAACCTGAA-CCAAACCACCAGTGTATGAACC-TCAAAGAAAGAGAAACCTGA
* *
1900 GCCCAAATCACCAGTTTATG-AGCCT
64 GCCTAAGTCACCAGTTTATGCA-CCT
1925 CCAAAGAA
1 CCAAAGAA
1933 GCCACCGATG
Statistics
Matches: 158, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
89 3 0.02
90 152 0.96
91 3 0.02
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.15
Consensus pattern (88 bp):
CCAAAGAAAGAGAAACCTGAACCAAACCACCAGTGTATGAACCTCAAAGAAAGAGAAACCTGAGC
CTAAGTCACCAGTTTATGCACCT
Done.