Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005959.1 Kokia drynarioides strain JFW-HI SEQ_120355, 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: 46638
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1758 original size:62 final size:62
Alignment explanation
Indices: 1639--2080 Score: 570
Period size: 62 Copynumber: 7.4 Consensus size: 62
1629 GTGTTGGCTA
* * *
1639 TGAAATTTTTTTATCCAATAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
1 TGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
* * * *
1701 TGAAATTTTTTTATCTGA-AAAAAGAGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATT
1 TGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
* * * * *
1762 TGAAAATTTTTTATCCGAGAATAGGGGGTGTCGACCATTGCATGGCAAACACCAAAAAAATT
1 TGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
* * * **
1824 TGAAATTTTTTTATCTGA-AAAAGGAGGTATCGGCCATTGCATGACCAACATAAAAAAAATT
1 TGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
* *
1885 TGAAA-TTTTTTATCTGAGAATAGGGGGTGTCGGCCATTGCATGACCAACACC---------
1 TGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
* *
1937 --AAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAATACCAAAAAAATT
1 TGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
* *
1997 TGAAAATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
1 TGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
*
2059 TGAAATATTTTTATCCGAGAAA
1 TGAAATTTTTTTATCCGAGAAA
2081 TGGCCAACAC
Statistics
Matches: 327, Mismatches: 39, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
50 3 0.01
51 43 0.13
60 12 0.04
61 124 0.38
62 145 0.44
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (62 bp):
TGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATT
Found at i:1858 original size:123 final size:123
Alignment explanation
Indices: 1639--2073 Score: 615
Period size: 123 Copynumber: 3.6 Consensus size: 123
1629 GTGTTGGCTA
* * *
1639 TGAAATTTTTTTATCCAATAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGA
1 TGAAAATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGA
*
1704 AATTTTTTTATCTGAAAAAAGAGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATT
66 AATTTTTTTATCTGAAAAAGGAGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATT
* * * *
1762 TGAAAATTTTTTATCCGAGAATAGGGGGTGTCGACCATTGCATGGCAAACACCAAAAAAATTTGA
1 TGAAAATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGA
* * **
1827 AATTTTTTTATCTGAAAAAGGAGGTATCGGCCATTGCATGACCAACATAAAAAAAATT
66 AATTTTTTTATCTGAAAAAGGAGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATT
* *
1885 TG-AAATTTTTTATCTGAGAATAGGGGGTGTCGGCCATTGCATGACCAACACC-----------A
1 TGAAAATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGA
* * *
1938 AATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAATACCAAAAAAATT
66 AATTTTTTTATCTGA-AAAAGGAGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATT
1997 TGAAAATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGA
1 TGAAAATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGA
*
2062 AATATTTTTATC
66 AATTTTTTTATC
2074 CGAGAAATGG
Statistics
Matches: 273, Mismatches: 26, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
111 15 0.05
112 39 0.14
113 48 0.18
122 46 0.17
123 113 0.41
124 12 0.04
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (123 bp):
TGAAAATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGA
AATTTTTTTATCTGAAAAAGGAGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATT
Found at i:1962 original size:51 final size:53
Alignment explanation
Indices: 1645--2052 Score: 203
Period size: 61 Copynumber: 6.9 Consensus size: 53
1635 GCTATGAAAT
* * *
1645 TTTTTTATCCAATAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGAAA
1 TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC----AAA-TT---A
* * * *
1706 TTTTTTTATCTGA-AAAAAGAGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAA
1 -TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC----AAA-TT----A
* * * *
1768 TTTTTTATCCGAGAATAGGGGGTGTCGACCATTGCATGGCAAACACCAAAAAAATTTGAAA
1 TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC----AAA-TT---A
* * * **
1829 TTTTTTTATCTGA-AAAAGGAGGTATCGGCCATTGCATGACCAACATAAAAAAAATTTGAAA
1 -TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAAC----ACCAAA-TT---A
* *
1890 TTTTTTATCTGAGAATAGGGGGTGTCGGCCATTGCATGACCAACACCAAA-T-
1 TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAATTA
* *
1941 TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAATACCAAAAAAATTTGAAAA
1 TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC----AAA-TT----A
*
2003 TTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACCAAA
1 TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAA
2053 AAAATTTGAA
Statistics
Matches: 292, Mismatches: 35, Indels: 42
0.79 0.09 0.11
Matches are distributed among these distances:
51 43 0.15
55 4 0.01
57 5 0.02
58 3 0.01
60 12 0.04
61 117 0.40
62 107 0.37
65 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (53 bp):
TTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAAATTA
Found at i:2029 original size:113 final size:111
Alignment explanation
Indices: 1826--2052 Score: 355
Period size: 113 Copynumber: 2.0 Consensus size: 111
1816 AAAAAATTTG
* *
1826 AAATTTTTTTATCTGAAAAAGGAGGTATCGGCCATTGCATGACCAACATAAAAAAAATTTGAAAT
1 AAATTTTTTTATCCGAAAAAGGAGGTATCGGCCATTGCATGACCAACACAAAAAAAATTTGAAAT
* *
1891 TTTTTATCTGAGAATAGGGGGTGTCGGCCATTGCATGACCAACACC
66 TTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACC
* * * * *
1937 AAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAATACCAAAAAAATTTGAAA
1 AAATTTTTTTATCCGA-AAAAGGAGGTATCGGCCATTGCATGACCAACACAAAAAAAATTTG-AA
2002 ATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACC
64 ATTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACC
2050 AAA
1 AAA
2053 AAAATTTGAA
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
111 15 0.14
112 39 0.37
113 51 0.49
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (111 bp):
AAATTTTTTTATCCGAAAAAGGAGGTATCGGCCATTGCATGACCAACACAAAAAAAATTTGAAAT
TTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGACCAACACC
Found at i:2292 original size:61 final size:60
Alignment explanation
Indices: 2136--2338 Score: 277
Period size: 62 Copynumber: 3.4 Consensus size: 60
2126 GATGTCGACC
* *
2136 ATTTGAAATTTTTTTAT-TCGAGAACAGGGGGTGTCGGCCATTGCATGGCTAACACCAAAAAA
1 ATTTGAAATTTTTTTATCT-GA-AAAAGGGGGTGTCGGCCATTGCATGGCCAACACC-AAAAA
* *
2198 ATTTGAAATTTTTTTATCCGTAAAAAGGAGGTGTCGGCCATTGCATGGCCAACACCAAAAA
1 ATTTGAAATTTTTTTATCTG-AAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCAAAAA
* **
2259 ATTTTGAAATTTTTTTATCTGAAAAAGGGGGTGTCGGCCATTGCATGGGCAACACCCGAAA
1 A-TTTGAAATTTTTTTATCTGAAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCAAAAA
2320 ATTT--AATTTTTTTATCTGA
1 ATTTGAAATTTTTTTATCTGA
2339 TAAATAAGAG
Statistics
Matches: 129, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
58 15 0.12
60 3 0.02
61 43 0.33
62 67 0.52
63 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (60 bp):
ATTTGAAATTTTTTTATCTGAAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCAAAAA
Found at i:2298 original size:123 final size:121
Alignment explanation
Indices: 2137--2381 Score: 311
Period size: 120 Copynumber: 2.0 Consensus size: 121
2127 ATGTCGACCA
*
2137 TTTGAAATTTTTTTATTCGAGAACAGGGGGTGTCGGCCATTGCAT-GGCTAACACCAAAAAAATT
1 TTTGAAATTTTTTTATTCGAGAAAAGGGGGTGTCGGCCATTGCATGGGC-AACACC-AAAAAATT
* *
2201 TGAAATTTTTTTATCCG-TAAA-AAGGAGGTGTCGGCCATTGCATGGCCAACACCAAAAAAT
64 T--AATTTTTTTATCCGATAAATAA-GA-GTGTCGGCCATTGCATAGCCAACACAAAAAAAT
**
2261 TTTGAAATTTTTTTA-TCTGA-AAAAGGGGGTGTCGGCCATTGCATGGGCAACACCCGAAAATTT
1 TTTGAAATTTTTTTATTC-GAGAAAAGGGGGTGTCGGCCATTGCATGGGCAACACCAAAAAATTT
* ** *
2324 AATTTTTTTATCTGATAAATAAGAGTGTCGTTCATTGTATAGCCAACACAAAAAAAT
65 AATTTTTTTATCCGATAAATAAGAGTGTCGGCCATTGCATAGCCAACACAAAAAAAT
2381 T
1 T
2382 GTATTTTTTA
Statistics
Matches: 108, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
120 42 0.39
121 6 0.06
122 9 0.08
123 31 0.29
124 20 0.19
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (121 bp):
TTTGAAATTTTTTTATTCGAGAAAAGGGGGTGTCGGCCATTGCATGGGCAACACCAAAAAATTTA
ATTTTTTTATCCGATAAATAAGAGTGTCGGCCATTGCATAGCCAACACAAAAAAAT
Found at i:2371 original size:59 final size:59
Alignment explanation
Indices: 2166--2402 Score: 234
Period size: 62 Copynumber: 4.0 Consensus size: 59
2156 AGAACAGGGG
* *
2166 GTGTCGGCCATTGCATGGCTAACACCAAAAAAATTTGAAATTTTTTTATCCG-TAAAAAGGA
1 GTGTCGGCCATTGCATGGCCAACACC-AAAAAATTT-AAATTTTTTTATCTGATAAAAA-GA
* *
2227 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAGGGG
1 -GTGTCGGCCATTGCATGGCCAACACCAAAAAA-TTT-AAATTTTTTTATCTGATAAAA-AGA
* **
2289 GTGTCGGCCATTGCATGGGCAACACCCGAAAATTT-AATTTTTTTATCTGATAAATAAGA
1 GTGTCGGCCATTGCATGGCCAACACCAAAAAATTTAAATTTTTTTATCTGATAAA-AAGA
** * * * *
2348 GTGTCGTTCATTGTATAGCCAACACAAAAAAATTGT--A-TTTTTTATCTGACAAAAA
1 GTGTCGGCCATTGCATGGCCAACACCAAAAAATT-TAAATTTTTTTATCTGATAAAAA
2403 AGGGGTTTTT
Statistics
Matches: 151, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
57 2 0.01
58 30 0.20
59 31 0.21
60 5 0.03
61 35 0.23
62 48 0.32
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (59 bp):
GTGTCGGCCATTGCATGGCCAACACCAAAAAATTTAAATTTTTTTATCTGATAAAAAGA
Found at i:10450 original size:20 final size:20
Alignment explanation
Indices: 10425--10464 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
10415 TTACGTGTTT
*
10425 TTCTTTTTATTGCAATTTTA
1 TTCTTTTTATTACAATTTTA
10445 TTCTTTTTATTACAATTTTA
1 TTCTTTTTATTACAATTTTA
10465 AACATAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65
Consensus pattern (20 bp):
TTCTTTTTATTACAATTTTA
Found at i:24341 original size:30 final size:30
Alignment explanation
Indices: 24297--24355 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
24287 AATTTGGAGA
* *
24297 TTTTAGGTTGTTGAATTTGG-GAATTTTGGG
1 TTTTAGGTGGTTGAATGTGGAG-ATTTTGGG
*
24327 TTTTGGGTGGTTGAATGTGGAGATTTTGG
1 TTTTAGGTGGTTGAATGTGGAGATTTTGG
24356 ATAAGAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.47
Consensus pattern (30 bp):
TTTTAGGTGGTTGAATGTGGAGATTTTGGG
Found at i:34619 original size:31 final size:29
Alignment explanation
Indices: 34584--34643 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
34574 GTGATCACTT
34584 CGTAACAAAATACTAACATAAGTGACTAAAA
1 CGTAACAAAATA--AACATAAGTGACTAAAA
***
34615 CGTAACATTTTAAACATAAGTGACTAAAA
1 CGTAACAAAATAAACATAAGTGACTAAAA
34644 AATAATCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
31 9 0.35
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (29 bp):
CGTAACAAAATAAACATAAGTGACTAAAA
Found at i:35833 original size:23 final size:23
Alignment explanation
Indices: 35713--35839 Score: 139
Period size: 23 Copynumber: 5.4 Consensus size: 23
35703 TGTGCTGGGC
*
35713 AACAGAGAGCACACACAGTGCTC
1 AACAGAGAGCACACACAGTGCTA
* *
35736 AACAGAGAGTACACACAGTACTA
1 AACAGAGAGCACACACAGTGCTA
** *
35759 ATTAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
35782 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
35806 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
*
35830 AACAAAGAGC
1 AACAGAGAGC
35840 GCGCTAGTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 67 0.76
24 2 0.02
25 16 0.18
26 3 0.03
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:41661 original size:4 final size:4
Alignment explanation
Indices: 41641--41679 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
41631 TCTGGGAGGG
*
41641 TTCT TT-T TCTCT CTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT T-TCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
41680 AAGTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 28 0.90
5 1 0.03
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:45724 original size:77 final size:77
Alignment explanation
Indices: 45633--45786 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
45623 AATATGCTTG
*
45633 ATACAAATGTATATATGTTATGTTGAGATCTTATATCATGTTGAATTGTGTTATAATGGTGAGAA
1 ATACAAATGTATATATGTTATGTTGAGATCTTATATCATGTTGAATCGTGTTATAATGGTGAGAA
45698 TGATGATCATAC
66 TGATGATCATAC
*
45710 ATACAAATGTATATATGTTATGTTGAGATCTTATATCATGTTGAATCGTGTTGTAATGGTGAGAA
1 ATACAAATGTATATATGTTATGTTGAGATCTTATATCATGTTGAATCGTGTTATAATGGTGAGAA
45775 TGATGATCATAC
66 TGATGATCATAC
45787 CCTGGTAAAC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (77 bp):
ATACAAATGTATATATGTTATGTTGAGATCTTATATCATGTTGAATCGTGTTATAATGGTGAGAA
TGATGATCATAC
Found at i:45748 original size:41 final size:39
Alignment explanation
Indices: 45633--45748 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 39
45623 AATATGCTTG
45633 ATACAAATGTATATATGTTATGTTGAGATCTTATATCAT
1 ATACAAATGTATATATGTTATGTTGAGATCTTATATCAT
* ** * * * * * *
45672 GTTGAATTGTGT-TA--TAATGGTGAGA-ATGATGATCAT
1 ATACAAATGTATATATGTTATGTTGAGATCTTAT-ATCAT
45708 ACATACAAATGTATATATGTTATGTTGAGATCTTATATCAT
1 --ATACAAATGTATATATGTTATGTTGAGATCTTATATCAT
45749 GTTGAATCGT
Statistics
Matches: 52, Mismatches: 18, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
35 3 0.06
36 14 0.27
38 9 0.17
39 9 0.17
41 14 0.27
42 3 0.06
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (39 bp):
ATACAAATGTATATATGTTATGTTGAGATCTTATATCAT
Done.