Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015104.1 Kokia drynarioides strain JFW-HI SEQ_130148, 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: 58135
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:7379 original size:20 final size:20
Alignment explanation
Indices: 7338--7393 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
7328 GAGTTGTAGA
7338 AAATTATTAAA-AATATTAAG
1 AAATTA-TAAATAATATTAAG
* *
7358 AAATTATAAATAATTTTTAG
1 AAATTATAAATAATATTAAG
7378 -AATTATCAAATTAATA
1 AAATTAT-AAA-TAATA
7394 ATAAAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 10 0.33
20 16 0.53
21 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (20 bp):
AAATTATAAATAATATTAAG
Found at i:10873 original size:21 final size:21
Alignment explanation
Indices: 10844--10887 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10834 TATTTTATAA
*
10844 TATTAATTAATAA-ATTATTAT
1 TATTAATT-ATAAGACTATTAT
*
10865 TATTTATTATAAGACTATTAT
1 TATTAATTATAAGACTATTAT
10886 TA
1 TA
10888 ATGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTAATTATAAGACTATTAT
Found at i:15035 original size:30 final size:30
Alignment explanation
Indices: 14988--15140 Score: 125
Period size: 30 Copynumber: 5.1 Consensus size: 30
14978 TTTTATTTAG
* *
14988 AAATTTTATTTTAACCCTTAAACTTTCCAA
1 AAATTATATTTTGACCCTTAAACTTTCCAA
* * *
15018 AAATTATATGTTGACCCTCTGAACTTTTCAA
1 AAATTATATTTTGACCCT-TAAACTTTCCAA
* *
15049 AAATTAT-TTTTAAACCC-TAAATTTTCCAA
1 AAATTATATTTT-GACCCTTAAACTTTCCAA
* * *
15078 AAAATATATTTTGGCACCTT-AACTTTCTAA
1 AAATTATATTTTGAC-CCTTAAACTTTCCAA
* * *
15108 AAGTT-TGATTTTGACCCCTAAACTTTCTAA
1 AAATTAT-ATTTTGACCCTTAAACTTTCCAA
15138 AAA
1 AAA
15141 AGTCATTTTG
Statistics
Matches: 96, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
29 20 0.21
30 54 0.56
31 22 0.23
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (30 bp):
AAATTATATTTTGACCCTTAAACTTTCCAA
Found at i:15198 original size:29 final size:29
Alignment explanation
Indices: 15159--15214 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
15149 TGACCCCTTG
15159 AACTTTTTGAAAATTACATTTTAACCCCA
1 AACTTTTTGAAAATTACATTTTAACCCCA
*
15188 AACTTTTTGAAAGTTACATTTTAACCC
1 AACTTTTTGAAAATTACATTTTAACCC
15215 TCAAGCTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (29 bp):
AACTTTTTGAAAATTACATTTTAACCCCA
Found at i:15312 original size:1 final size:1
Alignment explanation
Indices: 15264--15295 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
15254 NNNNNNNNNN
15264 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15296 CTTATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25112 original size:68 final size:68
Alignment explanation
Indices: 25003--25139 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
24993 GAACTTGTTG
25003 AGATAAGGAAAGAATCCACTCAATAAAAATAAGAAAAGAATGTTGAGATATATCTTACTGCAGAT
1 AGATAAGGAAAGAATCCACTCAATAAAAATAAGAAAAGAATGTTGAGATATATCTTACTGCAGAT
25068 GTC
66 GTC
*
25071 AGATAAGGAAAGAATCCACTCAATAAAAATAAGGAAAGAATGTTGAGATATATCTTACTGCAGAT
1 AGATAAGGAAAGAATCCACTCAATAAAAATAAGAAAAGAATGTTGAGATATATCTTACTGCAGAT
25136 GTC
66 GTC
25139 A
1 A
25140 CCTCTGACAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (68 bp):
AGATAAGGAAAGAATCCACTCAATAAAAATAAGAAAAGAATGTTGAGATATATCTTACTGCAGAT
GTC
Found at i:25346 original size:33 final size:33
Alignment explanation
Indices: 25309--25423 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
25299 CAGCTGTTCG
25309 TTATTCATTGATTCATCTTCAATAACGGTAGGT
1 TTATTCATTGATTCATCTTCAATAACGGTAGGT
*
25342 TTATTCATTGATTCATCTTCAATAATGGTAGGT
1 TTATTCATTGATTCATCTTCAATAACGGTAGGT
*
25375 TTATTCATTGATTCATCTTCAATAACAGTAGGT
1 TTATTCATTGATTCATCTTCAATAACGGTAGGT
25408 TTATTCATTGATTCAT
1 TTATTCATTGATTCAT
25424 TGTCAACAAC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (33 bp):
TTATTCATTGATTCATCTTCAATAACGGTAGGT
Found at i:26203 original size:21 final size:21
Alignment explanation
Indices: 26170--26226 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
26160 ACTCTTTTGT
* * *
26170 TTCCTCAAGCTCAAGTTGCAT
1 TTCCTGAAACTCAAGTTGCAG
* *
26191 TTTCTGAAACTCAACTTGCAG
1 TTCCTGAAACTCAAGTTGCAG
26212 TTCCTGAAACTCAAG
1 TTCCTGAAACTCAAG
26227 ATCCTTCTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (21 bp):
TTCCTGAAACTCAAGTTGCAG
Found at i:26332 original size:66 final size:66
Alignment explanation
Indices: 26212--26356 Score: 202
Period size: 66 Copynumber: 2.2 Consensus size: 66
26202 CAACTTGCAG
26212 TTCCTGAAACTCAAGATCCTTCTTGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTT-TTCTG
1 TTCCTGAAACTCAAGATCCTTCTTGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTGTT-TG
26276 GA
65 GA
* * * * * * *
26278 TTCCTGAAATTCAAGTTCCTTCTTGTGCAAAGTAGATTCTAGTGTTTCTTTTTCCTGTTGTTTGG
1 TTCCTGAAACTCAAGATCCTTCTTGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTGTTTGG
26343 A
66 A
*
26344 TTCCTCAAACTCA
1 TTCCTGAAACTCA
26357 CGTTGCAGTG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 67 0.97
67 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.42
Consensus pattern (66 bp):
TTCCTGAAACTCAAGATCCTTCTTGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTGTTTGG
A
Found at i:26396 original size:21 final size:21
Alignment explanation
Indices: 26350--26396 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
26340 TGGATTCCTC
**
26350 AAACTCACGTTGCAGTGTCTG
1 AAACTCAAATTGCAGTGTCTG
*
26371 CAACTCAAATTGCAGT-TGCTG
1 AAACTCAAATTGCAGTGT-CTG
26392 AAACT
1 AAACT
26397 GAAGTTCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
AAACTCAAATTGCAGTGTCTG
Found at i:26468 original size:174 final size:174
Alignment explanation
Indices: 26170--26537 Score: 452
Period size: 174 Copynumber: 2.1 Consensus size: 174
26160 ACTCTTTTGT
* * * *
26170 TTCCTCAAGCTCAAGTTGCATTTTCTGAAACTCAACTTGCAGTTCCTGAAACTCAAGATCCTTCT
1 TTCCTCAAACTCAAGTTGCAGTGTCTGAAACTCAAATTGCAGTTCCTGAAACTCAAGATCCTTCT
* * *
26235 TGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTTTCTGGATTCCTGAAATTCAAGTTCCTTC
66 TGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTTTCTGGATTCCTCAAACTCAAGTTCCATC
* *** **
26300 TTGTGCAAAGTAGATTCTAGTGTTTCTTTTTCCTGTTGTTTGGA
131 TTGTGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTGTTTGGA
* * * * *
26344 TTCCTCAAACTCACGTTGCAGTGTCTGCAACTCAAATTGCAGTTGCTGAAACTGAAGTTCCTT-T
1 TTCCTCAAACTCAAGTTGCAGTGTCTGAAACTCAAATTGCAGTTCCTGAAACTCAAGATCCTTCT
* * * *
26408 CTGTGCAAAGTAGATTCAAACT-TTGCTCTTTCTTGTTTTTTGGATTCCTCAAACTCAAGTTGCA
66 -TGTACAAAGTAGATTCAAA-TGTTGCTCTTTCCTGTTTTCTGGATTCCTCAAACTCAAGTTCCA
* *** *
26472 TCTTTTGCGTGGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGA
129 TCTTGTGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTGTTTGGA
*
26518 TTCCTCACACTCAAGTTGCA
1 TTCCTCAAACTCAAGTTGCA
26538 TCTTGTGGAA
Statistics
Matches: 163, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
173 1 0.01
174 161 0.99
175 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (174 bp):
TTCCTCAAACTCAAGTTGCAGTGTCTGAAACTCAAATTGCAGTTCCTGAAACTCAAGATCCTTCT
TGTACAAAGTAGATTCAAATGTTGCTCTTTCCTGTTTTCTGGATTCCTCAAACTCAAGTTCCATC
TTGTGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTGTTTGGA
Found at i:26505 original size:66 final size:66
Alignment explanation
Indices: 26411--26789 Score: 530
Period size: 66 Copynumber: 5.7 Consensus size: 66
26401 TTCCTTTCTG
* *
26411 TGCAAAGTAGATTCAAA-CTTTGCTCTTTCTTGTTTTTTGGATTCCTCAAACTCAAGTTGCATCT
1 TGCAAAGTAGATTCAAACCTTT-CACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATCT
26475 TT
65 TT
*** *
26477 TGCGTGGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCCTCACACTCAAGTTGCATCTT
1 TGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATCTT
*
26542 G
66 T
* * *
26543 TGGAAAGTAGATTCAAACCTTTCACTTTCCTTTTTTTTCGATTCCTCAAACTCAAGTTGCATCTT
1 TGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATCTT
*
26608 G
66 T
* * *
26609 TGCAAAGTTGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTCCTTCTT
1 TGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATCTT
26674 T
66 T
* * *
26675 TGCAAAATAGATTCAAACCTTGCACTTTCCT-TTTTCTTCGATTCCTCAAACTCAAGTTGCATCT
1 TGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTT-TTGGATTCCTCAAACTCAAGTTGCATCT
26739 TT
65 TT
* * *
26741 TGTATAGTAGATTCAAACCTTGCACTTTCCTGCTTTTTT-GATTCCTCAA
1 TGCAAAGTAGATTCAAACCTTTCACTTTCCTG-TTTTTTGGATTCCTCAA
26790 GGTCAACCTG
Statistics
Matches: 279, Mismatches: 30, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
65 4 0.01
66 265 0.95
67 6 0.02
68 4 0.01
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.42
Consensus pattern (66 bp):
TGCAAAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTGGATTCCTCAAACTCAAGTTGCATCTT
T
Found at i:34012 original size:108 final size:105
Alignment explanation
Indices: 33822--34040 Score: 280
Period size: 108 Copynumber: 2.1 Consensus size: 105
33812 AAGGATTTAC
* **
33822 AGCAATCAATATATTTCCTGTGTAGGACTGGAATAAACATCAGCACATTTAGCTTCAAACAACAA
1 AGCAACCAATATATTTCCCATGTAGGACTGGAATAAACATCAGCACATTTAGCTTCAAACAACAA
*
33887 TACATATCCCAAAAAAAAAACAAACAGCCACACAACAAACTAA
66 TACATATCCC--AAAAAAAA-AAACAGCCACAAAACAAACTAA
* *
33930 AGCAACCAATATATTTCCCATGTAGGTCTGGAATAAACATCAGCACATTTAGCTTCAAACAA-TA
1 AGCAACCAATATATTTCCCATGTAGGACTGGAATAAACATCAGCACATTTAGCTTCAAACAACAA
* * * * *
33994 -ACATGTACCTCTAGAAAAAAAACAGGCACAAAACAAATTAA
66 TACATAT-CC-CAAAAAAAAAAACAGCCACAAAACAAACTAA
34035 AGCAAC
1 AGCAAC
34041 ATATTCACAC
Statistics
Matches: 98, Mismatches: 11, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
105 25 0.26
106 11 0.11
107 3 0.03
108 59 0.60
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (105 bp):
AGCAACCAATATATTTCCCATGTAGGACTGGAATAAACATCAGCACATTTAGCTTCAAACAACAA
TACATATCCCAAAAAAAAAAACAGCCACAAAACAAACTAA
Found at i:44051 original size:20 final size:22
Alignment explanation
Indices: 43997--44052 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 22
43987 ATCCCCAAAC
43997 ACTTAGAATTTGTTTAAAAATG
1 ACTTAGAATTTGTTTAAAAATG
* *
44019 ATTCTA-AA-GTGTTT-AAAATG
1 ACT-TAGAATTTGTTTAAAAATG
44039 ACTT-GAATTTGTTT
1 ACTTAGAATTTGTTT
44053 TTAATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
19 3 0.11
20 13 0.48
21 5 0.19
22 4 0.15
23 2 0.07
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (22 bp):
ACTTAGAATTTGTTTAAAAATG
Found at i:46676 original size:19 final size:19
Alignment explanation
Indices: 46649--46693 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
46639 ATATTTGAGG
*
46649 TTTAGTTTTTATTTAAATT
1 TTTAATTTTTATTTAAATT
*
46668 TTTAATTTTTTTTTAAATT
1 TTTAATTTTTATTTAAATT
*
46687 TTAAATT
1 TTTAATT
46694 AATAAAAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTAATTTTTATTTAAATT
Found at i:47197 original size:21 final size:21
Alignment explanation
Indices: 47166--47205 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
47156 GATATGCATG
47166 CAAAAACTATAAATTTAAAACA
1 CAAAAACTAT-AATTTAAAACA
*
47188 CAAAAA-TATATTTTAAAA
1 CAAAAACTATAATTTAAAA
47206 TAAACATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (21 bp):
CAAAAACTATAATTTAAAACA
Done.