Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007487.1 Kokia drynarioides strain JFW-HI SEQ_122111, 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: 28642
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:13071 original size:16 final size:17
Alignment explanation
Indices: 13050--13083 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13040 TTTAAAACCC
*
13050 TAAATA-CTAATCATTA
1 TAAATATCTAAACATTA
13066 TAAATATCTAAACATTA
1 TAAATATCTAAACATTA
13083 T
1 T
13084 TGTAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATATCTAAACATTA
Found at i:21487 original size:16 final size:17
Alignment explanation
Indices: 21466--21499 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21456 TTGAAAACCC
*
21466 TAAATA-CTAACCATTA
1 TAAATATCTAAACATTA
21482 TAAATATCTAAACATTA
1 TAAATATCTAAACATTA
21499 T
1 T
21500 TCTAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATATCTAAACATTA
Found at i:24314 original size:141 final size:140
Alignment explanation
Indices: 24054--24316 Score: 373
Period size: 141 Copynumber: 1.9 Consensus size: 140
24044 ATTTTTGGAG
* * * *
24054 AGTGTCGGGATAGACTTGCTAACATATGCTTTGGCCAACTCTTTGTATATGAGTTGGGGTATGCA
1 AGTGTCGGCATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGAGTTGGGATATGCA
* * * * *
24119 TGCCTAAGATAACGCTTAAATAAGAGTCCGCTTTGTTCAACACTATGTCGACACTTTTGGGGCAA
66 TGCCTAAGACAACGCTTAAATAAGAGTCAGCTTTGTCCAACACTATGGCAACACTTTTGGGGCAA
24184 CACTTTCCTA
131 CACTTTCCTA
* * * *
24194 AGTGTTGGCATAGACTTGCCGACATATGCTTTTGCCAACTCTTTTGTATAAGGGTTGGGATATGC
1 AGTGTCGGCATAGACTTGCCAACATATGCTTTGGCCAACTC-TTTGTATAAGAGTTGGGATATGC
* * *
24259 ATGCTTAAGGCAACGCTTAAATAAGAGTTAGCTTTGTCCAACACTATGGCAACACTTT
65 ATGCCTAAGACAACGCTTAAATAAGAGTCAGCTTTGTCCAACACTATGGCAACACTTT
24317 CCTAAGTGTT
Statistics
Matches: 106, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
140 36 0.34
141 70 0.66
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (140 bp):
AGTGTCGGCATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGAGTTGGGATATGCA
TGCCTAAGACAACGCTTAAATAAGAGTCAGCTTTGTCCAACACTATGGCAACACTTTTGGGGCAA
CACTTTCCTA
Found at i:24412 original size:126 final size:127
Alignment explanation
Indices: 24179--24441 Score: 388
Period size: 126 Copynumber: 2.1 Consensus size: 127
24169 ACACTTTTGG
** * *
24179 GGCAACACTTTCCTAAGTGTTGGCATAGACTTGCCGACATATGCTTTTGCCAACTCTTTTGTATA
1 GGCAACACTTTCCTAAGTGTTGGCATAGACTTGCCGACATACACTTTGGCCAACTCTTATGTATA
* * *
24244 AGGGTTGGGATATGCATGCTTAAGGCAACGCTTAAATAAGAGTTAGCTTTGTCCAACACTAT
66 AGGGTTGGCATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTAGCTTTATCCAACACTAT
*
24306 GGCAACACTTTCCTAAGTGTTAGG-ATAGACTTGCCGGCATACACTTTGGCCAACTC-TATGTAT
1 GGCAACACTTTCCTAAGTGTT-GGCATAGACTTGCCGACATACACTTTGGCCAACTCTTATGTAT
* * *
24369 AAGGGTTGGCATATGCATGCCTAAGGCAATGCTTAAATGAGAGTTGGCTTTATCCAACACTAT
65 AAGGGTTGGCATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTAGCTTTATCCAACACTAT
*
24432 GCCAAC-CTTT
1 GGCAACACTTT
24442 TTAAGGTTGC
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
125 4 0.03
126 68 0.55
127 49 0.40
128 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (127 bp):
GGCAACACTTTCCTAAGTGTTGGCATAGACTTGCCGACATACACTTTGGCCAACTCTTATGTATA
AGGGTTGGCATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTAGCTTTATCCAACACTAT
Found at i:24512 original size:74 final size:74
Alignment explanation
Indices: 24428--24803 Score: 464
Period size: 74 Copynumber: 5.1 Consensus size: 74
24418 TTATCCAACA
* * *
24428 CTATGCCAACCTTTTT-AAGGTTGCCTTAAACAAGGTCTATCCTAACATTTTTAAATGGTTGCCT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAAACAAGGTCTATCCCAACCTTTTTAAA-GGTTGCCT
24492 TAGATAAGGT
65 TAGATAAGGT
** * *
24502 CTATATCAACCTTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTCCTTTAAAGGTTGCCT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAAACAAGGTCTATCCCAACCT-TTTTAAAGGTTGCCT
* *
24566 CAAATAAGGT
65 TAGATAAGGT
*
24576 CTATCCCAACCTTTTTTAAAGGTTGCCTCAAACAAGGTCTATCCCAACC-TTTT-AAGGTTGCCT
1 CTATCCCAACC-TTTTTAAAGGTTGCCTTAAACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCT
24639 TAGATAAGGT
65 TAGATAAGGT
* *
24649 CTATCCCAA-CTTTTTGAAGGTTGCCTTAAAC-AGGTCTATCCCAACTTTTTTAAAGGTTGCCTT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAAACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
*
24712 AGA-CAGGT
66 AGATAAGGT
* * * * *
24720 CTATCCCAACCTTTTTTAAAGCTTGCCTTAGAGAAGGCCTACCCCAACCTTTTTAAA-GTTGCCT
1 CTATCCCAACC-TTTTTAAAGGTTGCCTTAAACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCT
***
24784 TAGGCGA-GT
65 TAGATAAGGT
24793 CTATCCCAACC
1 CTATCCCAACC
24804 ATTCAGTAAA
Statistics
Matches: 265, Mismatches: 28, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
70 14 0.05
71 36 0.14
72 16 0.06
73 67 0.25
74 92 0.35
75 11 0.04
76 29 0.11
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (74 bp):
CTATCCCAACCTTTTTAAAGGTTGCCTTAAACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTT
AGATAAGGT
Found at i:24531 original size:36 final size:37
Alignment explanation
Indices: 24428--24803 Score: 446
Period size: 38 Copynumber: 10.3 Consensus size: 37
24418 TTATCCAACA
* *
24428 CTATGCCAACCTTTTT-AAGGTTGCCTTAAACAAGGT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
* * *
24464 CTATCCTAACATTTTTAAATGGTTGCCTTAGATAAGGT
1 CTATCCCAACCTTTTTAAA-GGTTGCCTTAGACAAGGT
**
24502 CTATATCAACCTTTTT-AAGGTTGCCTTAGACAAGGT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
* * * *
24538 CTATCCCAACCTCCTTTAAAGGTTGCCTCAAATAAGGT
1 CTATCCCAACCT-TTTTAAAGGTTGCCTTAGACAAGGT
* *
24576 CTATCCCAACCTTTTTTAAAGGTTGCCTCAAACAAGGT
1 CTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGGT
*
24614 CTATCCCAACC-TTTT-AAGGTTGCCTTAGATAAGGT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
* *
24649 CTATCCCAA-CTTTTTGAAGGTTGCCTTAAAC-AGGT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
*
24684 CTATCCCAACTTTTTTAAAGGTTGCCTTAGAC-AGGT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
* * *
24720 CTATCCCAACCTTTTTTAAAGCTTGCCTTAGAGAAGGC
1 CTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGGT
* * *
24758 CTACCCCAACCTTTTTAAA-GTTGCCTTAGGCGA-GT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
24793 CTATCCCAACC
1 CTATCCCAACC
24804 ATTCAGTAAA
Statistics
Matches: 293, Mismatches: 37, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.00
35 54 0.18
36 100 0.34
37 34 0.12
38 103 0.35
39 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (37 bp):
CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
Found at i:25233 original size:21 final size:21
Alignment explanation
Indices: 25192--25235 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25182 CTGAACACTA
*
25192 AACCCCAAACTCATAACCCAT
1 AACCCCAAACTCATAAACCAT
*
25213 AACCCCAAA-TCCTTAAACCAT
1 AACCCCAAACT-CATAAACCAT
25234 AA
1 AA
25236 ACATGAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (21 bp):
AACCCCAAACTCATAAACCAT
Found at i:26588 original size:2 final size:2
Alignment explanation
Indices: 26581--26608 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26571 GTTATCACTT
26581 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
26609 TATCACCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:26815 original size:21 final size:20
Alignment explanation
Indices: 26769--26821 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
26759 TTGTGATAGC
*
26769 TCTATCGATACAAGTATGAA
1 TCTACCGATACAAGTATGAA
26789 TTCTACCGATACAAGTTATGCAA
1 -TCTACCGATACAAG-TATG-AA
26812 -CTACCGATAC
1 TCTACCGATAC
26822 CAAAAACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 23 0.79
22 4 0.14
23 2 0.07
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (20 bp):
TCTACCGATACAAGTATGAA
Done.