Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002748.1 Kokia drynarioides strain JFW-HI SEQ_115062, 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: 100926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:1948 original size:28 final size:28
Alignment explanation
Indices: 1892--1948 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1882 TACTGGTAAC
*
1892 AAGCATGACCTTTGGGACAACAGGGAGT
1 AAGCATGACCTTTGGGACAACAGGAAGT
* *
1920 AAGCATGACCTTTGGGTCAATAGGAAGT
1 AAGCATGACCTTTGGGACAACAGGAAGT
1948 A
1 A
1949 GATCAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (28 bp):
AAGCATGACCTTTGGGACAACAGGAAGT
Found at i:6774 original size:37 final size:37
Alignment explanation
Indices: 6733--6808 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
6723 TATTTTGGTT
6733 AGTCTAAATTTTTTTGTCAATTTAGTCACTCTAATTA
1 AGTCTAAATTTTTTTGTCAATTTAGTCACTCTAATTA
6770 AGTCTAAATTTTTTTGTCAATTTAGTCACTCTAATTA
1 AGTCTAAATTTTTTTGTCAATTTAGTCACTCTAATTA
6807 AG
1 AG
6809 ATAATTGCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (37 bp):
AGTCTAAATTTTTTTGTCAATTTAGTCACTCTAATTA
Found at i:15513 original size:64 final size:65
Alignment explanation
Indices: 15401--15534 Score: 216
Period size: 64 Copynumber: 2.1 Consensus size: 65
15391 GAAATTTATG
* * *
15401 ATAACTTAAATATTCAATTTAAATTAAGATAAAAAATAATAAGTACTAATAAATTAAACCCTCCA
1 ATAACTTAAATATTCAATTAAAATTAAGACAAAAAATAATAAGAACTAATAAATTAAACCCTCCA
* *
15466 ATAACTTAAATATTC-ATTAAAATTAAGACCAAAAATTATAAGAACTAATAAATTAAACCCTCCA
1 ATAACTTAAATATTCAATTAAAATTAAGACAAAAAATAATAAGAACTAATAAATTAAACCCTCCA
15530 ATAAC
1 ATAAC
15535 ATTTCAATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
64 49 0.77
65 15 0.23
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (65 bp):
ATAACTTAAATATTCAATTAAAATTAAGACAAAAAATAATAAGAACTAATAAATTAAACCCTCCA
Found at i:18524 original size:12 final size:12
Alignment explanation
Indices: 18509--18538 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18499 CGTATATATG
18509 GTCTCAGTCTCC
1 GTCTCAGTCTCC
*
18521 GTCTCCGTCTCC
1 GTCTCAGTCTCC
18533 GTCTCA
1 GTCTCA
18539 AGCTGTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.43, G:0.17, T:0.33
Consensus pattern (12 bp):
GTCTCAGTCTCC
Found at i:23506 original size:27 final size:26
Alignment explanation
Indices: 23456--23507 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
23446 CTTAAACTAA
*
23456 ACTTTTCAAAATTACTTCTGAAAGTT
1 ACTTTTCAAAATTACTTCTAAAAGTT
* *
23482 ACTTTTCCAAATTACCTTTTAAAAGT
1 ACTTTTCAAAATTA-CTTCTAAAAGT
23508 ATTTCTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (26 bp):
ACTTTTCAAAATTACTTCTAAAAGTT
Found at i:23938 original size:22 final size:22
Alignment explanation
Indices: 23912--23968 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
23902 TCTAGGGCTA
23912 TTGTCTTGAGACAAAAGCCTAT
1 TTGTCTTGAGACAAAAGCCTAT
* *
23934 TTGTCTTGAAACAAAAGTCTAT
1 TTGTCTTGAGACAAAAGCCTAT
*
23956 ATGTCTTGAGACA
1 TTGTCTTGAGACA
23969 TGGCCTGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (22 bp):
TTGTCTTGAGACAAAAGCCTAT
Found at i:25601 original size:551 final size:546
Alignment explanation
Indices: 24560--25654 Score: 1769
Period size: 551 Copynumber: 2.0 Consensus size: 546
24550 TAGAAAAGTC
* * *
24560 TGCAAAAAAAATTTAAAATACTAATTCACACCCTCTTGATATTTTCGGGCCTAGCAAAATAGTAT
1 TGCAAAAAAAATTGAAAACACTAATTCACACCCTCTTGATATTTTCGGGCCTAACAAAATAGTAT
* * *
24625 CTGTTCATACTTTCTTAACCCTTTAACAACACACACACCTTGTACACACAGATGCTCGAACTCGG
66 CTGTTCATACTTTCTTAACACTTTAACAACACACACACCTTGCACACACAGATGCTCGAACTCAG
* *
24690 GTCTAATAGGATGAACATCATCCTCTTTTCCACTGGAATTACTCGTTGAGTTTTACTTAGATGGT
131 GTCTAATAGGATGAACATCATCCTCTTTTCCACTGGAATCACTCGTTGAGTTTTACTTAGATGCT
* ** *
24755 AATTGATTGAATATATCCAACAATTGAATGTTATTTATAAAGCTAAATTTAACTTTAATTGATAT
196 AATTGACTGAATATATCCAACAATTGAATACTATTTATAAAGCTAAATTTAACTTCAATTGATAT
*
24820 ATGACTCTAACATTAATTAAGTGATAATCAATAGATAAATATTTTTTTTATACTTAAGAGTACTA
261 ATGACTCTAACATTAATTAAGTGATAATCAATAGATAAATACTTTTTTTATACTTAAGAGTACTA
*
24885 CTCAAATTAAAACTCTATTTAGATTAATAGATAAATCTCTTTTCTCATGCATAAAGTTTTATTTA
326 CTCAAATTAAAACTCTATTTAGATTAATAGATAAATCTCTTTTCTCATGCATAAAGTTTTATTAA
* * * * **
24950 AATTTAACTTCTTTTTAAAAAATTCAAGAGTGCTTTCTTTGTTTTCTCTAGAGAATCGGTGGCTG
391 AATTTAACTTCTCTTTAAAAAAGTCAAGAGTGCTTTCTTTATTTTCTCTAGAGAACCAATGGCTG
* **
25015 CTGCGACTATGGTTTGGGGTGAAGTGGTGACTTTTTGTTGTTGACAATGGAGGAAGATGAGGTTT
456 CTGCGACTAGGGTTTGGGGTGAAGCAGTGACTTTTTGTTGTTGACAATGGAGGAAGATGAGGTTT
*
25080 CTTTGTTAGAACGAGAACTTATTCTT
521 CTTAGTTAGAACGAGAACTTATTCTT
* *
25106 TGCAAAAAAAATTGAAAACACTAATTCACCCCCTCTTGGTATTTTCGGGCCTAACAAAATAGTAT
1 TGCAAAAAAAATTGAAAACACTAATTCACACCCTCTTGATATTTTCGGGCCTAACAAAATAGTAT
* * ** *
25171 CTGTTCATACTTTCTTAACACTTTGACAACACACACACTTTGCACATGCAGATGCTTGAACTCAG
66 CTGTTCATACTTTCTTAACACTTTAACAACACACACACCTTGCACACACAGATGCTCGAACTCAG
**
25236 GTCTTCTAGGATGAACATCATCCTCTTTTCCACTGGAATCACTCGTTGAGTTTAATTTTACTTAG
131 GTCTAATAGGATGAACATCATCCTCTTTTCCACTGGAATCACTCGTTGAG-----TTTTACTTAG
25301 ATGCTAATTGACTGAATATATCCAACAATTGAATACTATTTATAAAGCTAAATTTAACTTCAATT
191 ATGCTAATTGACTGAATATATCCAACAATTGAATACTATTTATAAAGCTAAATTTAACTTCAATT
*
25366 GATATATGACTCTAACATTAATTAAGTGATAATCAATAGATAAA-CCTTTTTTTATACTTAAAGA
256 GATATATGACTCTAACATTAATTAAGTGATAATCAATAGATAAATACTTTTTTTATACTT-AAGA
*
25430 GTACTACTCAAATTAAAACTCTATTTAGATTAATAGATAAATCTCTTTTTTCATGCATAAAGTTT
320 GTACTACTCAAATTAAAACTCTATTTAGATTAATAGATAAATCTCTTTTCTCATGCATAAAGTTT
25495 TATTAAAATTTAACTTCTCTTTAAAAAAGTCAAGAGTGCTTTCTTTATTTTCTCTAGAGAACCAA
385 TATTAAAATTTAACTTCTCTTTAAAAAAGTCAAGAGTGCTTTCTTTATTTTCTCTAGAGAACCAA
* * * * *
25560 TGGTTGCTGTGGCTAGGGTTTGGGGTGAAGCAGTTACTTTTTGTTGTTGACGATGGAGGAAGATG
450 TGGCTGCTGCGACTAGGGTTTGGGGTGAAGCAGTGACTTTTTGTTGTTGACAATGGAGGAAGATG
25625 AGGTTTCTTAGTTAGAACGAGAACTTATTC
515 AGGTTTCTTAGTTAGAACGAGAACTTATTC
25655 AGCTTTCTGT
Statistics
Matches: 503, Mismatches: 40, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
546 164 0.33
550 13 0.03
551 326 0.65
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (546 bp):
TGCAAAAAAAATTGAAAACACTAATTCACACCCTCTTGATATTTTCGGGCCTAACAAAATAGTAT
CTGTTCATACTTTCTTAACACTTTAACAACACACACACCTTGCACACACAGATGCTCGAACTCAG
GTCTAATAGGATGAACATCATCCTCTTTTCCACTGGAATCACTCGTTGAGTTTTACTTAGATGCT
AATTGACTGAATATATCCAACAATTGAATACTATTTATAAAGCTAAATTTAACTTCAATTGATAT
ATGACTCTAACATTAATTAAGTGATAATCAATAGATAAATACTTTTTTTATACTTAAGAGTACTA
CTCAAATTAAAACTCTATTTAGATTAATAGATAAATCTCTTTTCTCATGCATAAAGTTTTATTAA
AATTTAACTTCTCTTTAAAAAAGTCAAGAGTGCTTTCTTTATTTTCTCTAGAGAACCAATGGCTG
CTGCGACTAGGGTTTGGGGTGAAGCAGTGACTTTTTGTTGTTGACAATGGAGGAAGATGAGGTTT
CTTAGTTAGAACGAGAACTTATTCTT
Found at i:27123 original size:6 final size:6
Alignment explanation
Indices: 27112--27140 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
27102 ATATCACTTT
27112 CAATTC CAATTC CAATTC CAATTC CAATT
1 CAATTC CAATTC CAATTC CAATTC CAATT
27141 TCACTTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
CAATTC
Found at i:43212 original size:17 final size:17
Alignment explanation
Indices: 43177--43215 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
43167 AGATGAAGAA
** *
43177 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAAAGAATT
43194 CTTGTTCGTAAAGAATT
1 CTTGTTCGTAAAGAATT
43211 CTTGT
1 CTTGT
43216 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAAAGAATT
Found at i:45272 original size:44 final size:44
Alignment explanation
Indices: 45209--45301 Score: 186
Period size: 44 Copynumber: 2.1 Consensus size: 44
45199 AATATAATAC
45209 TTATCAATATTTTTGAAATTCTATTCATAGTTAAATTAATCAAG
1 TTATCAATATTTTTGAAATTCTATTCATAGTTAAATTAATCAAG
45253 TTATCAATATTTTTGAAATTCTATTCATAGTTAAATTAATCAAG
1 TTATCAATATTTTTGAAATTCTATTCATAGTTAAATTAATCAAG
45297 TTATC
1 TTATC
45302 GATCTTTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (44 bp):
TTATCAATATTTTTGAAATTCTATTCATAGTTAAATTAATCAAG
Found at i:45436 original size:5 final size:5
Alignment explanation
Indices: 45426--45450 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
45416 TCAATTAATT
45426 TTCAA TTCAA TTCAA TTCAA TTCAA
1 TTCAA TTCAA TTCAA TTCAA TTCAA
45451 ATAACACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TTCAA
Found at i:53664 original size:24 final size:24
Alignment explanation
Indices: 53632--53678 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
53622 AGTTTTAAAC
53632 TTAATTAATAGTATATATGAGTCT
1 TTAATTAATAGTATATATGAGTCT
*
53656 TTAATTAATATTATATATGAGTC
1 TTAATTAATAGTATATATGAGTC
53679 CAATATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
TTAATTAATAGTATATATGAGTCT
Found at i:53686 original size:24 final size:24
Alignment explanation
Indices: 53633--53690 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
53623 GTTTTAAACT
* **
53633 TAATTAATAGTATATATGAGTCTT
1 TAATTAATATTATATATGAGTCAA
53657 TAATTAATATTATATATGAGTCCAA
1 TAATTAATATTATATATGAGT-CAA
53682 T-ATT-ATATT
1 TAATTAATATT
53691 TATTAGCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.17
24 23 0.77
25 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (24 bp):
TAATTAATATTATATATGAGTCAA
Found at i:53969 original size:27 final size:27
Alignment explanation
Indices: 53918--53968 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
53908 TTTTGAGTTT
53918 ATAAATTCTCTTTGAGTTTTTTTTTCA
1 ATAAATTCTCTTTGAGTTTTTTTTTCA
*
53945 ATAATTTCTC-TTGAGTTTTTTTTT
1 ATAAATTCTCTTTGAGTTTTTTTTT
53969 TTAGAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.63
Consensus pattern (27 bp):
ATAAATTCTCTTTGAGTTTTTTTTTCA
Found at i:60551 original size:21 final size:21
Alignment explanation
Indices: 60512--60551 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
60502 TTTCAGCAAA
*
60512 TTATTCTTCTTTTTCTTTTCT
1 TTATTCTTCTTTCTCTTTTCT
60533 TTATTCTT-TTTCTCATTTT
1 TTATTCTTCTTTCTC-TTTT
60552 TGTTTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTCTTCTTTCTCTTTTCT
Found at i:61651 original size:30 final size:30
Alignment explanation
Indices: 61595--61651 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
61585 CCTCGGCAGG
** * *
61595 TTCTTTTTCTTCTTTCTTTTTTTCCTTTCC
1 TTCTTTTTCTTCTTGATCTTTCTCCTTTCC
61625 TTCTTTTTCTTCTTGATCTTTCTCCTT
1 TTCTTTTTCTTCTTGATCTTTCTCCTT
61652 CAACTAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (30 bp):
TTCTTTTTCTTCTTGATCTTTCTCCTTTCC
Found at i:76742 original size:29 final size:29
Alignment explanation
Indices: 76693--76751 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
76683 GATCCACACC
* *
76693 TTGTGTGATATTATTTTGTGTTATGTTAT
1 TTGTGTGATATTAATTGGTGTTATGTTAT
* *
76722 TTGTGTGATTTTAATTGGTGTTGTGTTAT
1 TTGTGTGATATTAATTGGTGTTATGTTAT
76751 T
1 T
76752 ACATGTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (29 bp):
TTGTGTGATATTAATTGGTGTTATGTTAT
Found at i:78311 original size:20 final size:21
Alignment explanation
Indices: 78286--78331 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
78276 AACTTAAACC
*
78286 GTTGATCGTTGACC-TTGACT
1 GTTGATCCTTGACCGTTGACT
*
78306 GTTGATCCTTGACCGTTGATT
1 GTTGATCCTTGACCGTTGACT
78327 GTTGA
1 GTTGA
78332 CATTTACGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.41
Consensus pattern (21 bp):
GTTGATCCTTGACCGTTGACT
Found at i:78332 original size:14 final size:14
Alignment explanation
Indices: 78287--78325 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
78277 ACTTAAACCG
*
78287 TTGATCGTTGA-CC
1 TTGACCGTTGATCC
*
78300 TTGACTGTTGATCC
1 TTGACCGTTGATCC
78314 TTGACCGTTGAT
1 TTGACCGTTGAT
78326 TGTTGACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (14 bp):
TTGACCGTTGATCC
Found at i:82385 original size:24 final size:25
Alignment explanation
Indices: 82332--82392 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
82322 AACTAATAAG
* *
82332 AGTTTAACTGAAACAAAAAAATAGA
1 AGTTTAATTGAAACAAAAAAACAGA
*
82357 A-TTTAATTGAAACAAATAAACA-A
1 AGTTTAATTGAAACAAAAAAACAGA
82380 AGTTTAATTGAAA
1 AGTTTAATTGAAA
82393 TATTATTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 29 0.91
25 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (25 bp):
AGTTTAATTGAAACAAAAAAACAGA
Found at i:99747 original size:40 final size:40
Alignment explanation
Indices: 99692--99771 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
99682 TGATCGGTGA
99692 AAGGATGAGTTCGACACCTTGTTAGGTGTGAACATCCTCT
1 AAGGATGAGTTCGACACCTTGTTAGGTGTGAACATCCTCT
99732 AAGGATGAGTTCGACACCTTGTTAGGTGTGAACATCCTCT
1 AAGGATGAGTTCGACACCTTGTTAGGTGTGAACATCCTCT
99772 GTCATATTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (40 bp):
AAGGATGAGTTCGACACCTTGTTAGGTGTGAACATCCTCT
Done.