Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002055.1 Kokia drynarioides strain JFW-HI SEQ_113952, 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: 89302
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 79 characters in sequence are not A, C, G, or T
Found at i:443 original size:13 final size:13
Alignment explanation
Indices: 425--454 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
415 TCTTATTCTT
425 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
438 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
451 AAAA
1 AAAA
455 TCAATTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:1619 original size:26 final size:26
Alignment explanation
Indices: 1590--1642 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1580 TAACAGCTAA
1590 GAACGTCCTAGCCACCATATCTTCCT
1 GAACGTCCTAGCCACCATATCTTCCT
1616 GAACGTCCTAGCCACCATATCTTCCT
1 GAACGTCCTAGCCACCATATCTTCCT
1642 G
1 G
1643 TCGTAGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (26 bp):
GAACGTCCTAGCCACCATATCTTCCT
Found at i:11222 original size:9 final size:9
Alignment explanation
Indices: 11208--11233 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
11198 GGACAAATCT
11208 TCAAATCAC
1 TCAAATCAC
11217 TCAAATCAC
1 TCAAATCAC
11226 TCAAATCA
1 TCAAATCA
11234 TTTTTAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (9 bp):
TCAAATCAC
Found at i:12073 original size:6 final size:6
Alignment explanation
Indices: 12062--12087 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12052 CTCCTTTCCT
12062 TCCTCA TCCTCA TCCTCA TCCTCA TC
1 TCCTCA TCCTCA TCCTCA TCCTCA TC
12088 TTCTACCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCTCA
Found at i:27873 original size:30 final size:26
Alignment explanation
Indices: 27799--27873 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 26
27789 AAAAGTTGGT
* *
27799 AAAAAAATTTAACCTATAAAAATTAA
1 AAAAAAATTTAACTTTTAAAAATTAA
27825 AAAAAAATTTAGACCTTTTAAAAATTTTAAA
1 AAAAAAATTTA-A-CTTTTAAAAA--TT-AA
27856 AAAAAAATTTAAGCTTTT
1 AAAAAAATTTAA-CTTTT
27874 TTAATCTTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.27
27 1 0.02
28 8 0.20
30 8 0.20
31 13 0.32
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (26 bp):
AAAAAAATTTAACTTTTAAAAATTAA
Found at i:29362 original size:30 final size:29
Alignment explanation
Indices: 29326--29383 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
29316 ATAACGAGAG
29326 ATAATTT-TGGTATCAATTTGAAAAAAATAA
1 ATAATTTAT-GTATCAATTT-AAAAAAATAA
* *
29356 ATAATTTATGTATTAATTTATAAAAATA
1 ATAATTTATGTATCAATTTAAAAAAATA
29384 TATATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 16 0.64
31 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (29 bp):
ATAATTTATGTATCAATTTAAAAAAATAA
Found at i:29392 original size:22 final size:23
Alignment explanation
Indices: 29352--29394 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
29342 TTTGAAAAAA
* *
29352 ATAAATAATTTATGTATTAATTT
1 ATAAATAATATATATATTAATTT
29375 ATAAA-AATATATATATTAAT
1 ATAAATAATATATATATTAAT
29395 ATGAAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAAATAATATATATATTAATTT
Found at i:62262 original size:22 final size:20
Alignment explanation
Indices: 62228--62267 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
62218 ATGTTTTTAG
62228 AAAATTTTAGAATTTTATTC
1 AAAATTTTAGAATTTTATTC
62248 AAAACTTTTAAGAATTTTAT
1 AAAA-TTTT-AGAATTTTAT
62268 GGTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAATTTTAGAATTTTATTC
Found at i:64796 original size:18 final size:18
Alignment explanation
Indices: 64769--64811 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
64759 TAATATTATT
* *
64769 ATTATTACATTTTTTAAA
1 ATTATGACATCTTTTAAA
64787 ATTATGACATCTTTTAAA
1 ATTATGACATCTTTTAAA
*
64805 ATAATGA
1 ATTATGA
64812 ATAAAATGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (18 bp):
ATTATGACATCTTTTAAA
Found at i:67164 original size:20 final size:18
Alignment explanation
Indices: 67114--67186 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 18
67104 ATACCATCAG
67114 GGGCATCGAAGTGCATACA
1 GGGCATCGAAGTGCA-ACA
67133 GGGCCA-CAGAAGTGCAAGCAA
1 GGG-CATC-GAAGTGCAA-C-A
67154 GGGCATCGAAGTGCAAACA
1 GGGCATCGAAGTGC-AACA
*
67173 GGAGCACCGAAGTG
1 GG-GCATCGAAGTG
67187 AAAATATGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
19 8 0.17
20 31 0.67
21 7 0.15
ACGTcount: A:0.34, C:0.22, G:0.34, T:0.10
Consensus pattern (18 bp):
GGGCATCGAAGTGCAACA
Found at i:67198 original size:40 final size:40
Alignment explanation
Indices: 67114--67190 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
67104 ATACCATCAG
* * *
67114 GGGCATCGAAGTGCATACAGGGCCACAGAAGTGCAAGCAA
1 GGGCATCGAAGTGCAAACAGGGCCACAGAAGTGAAAACAA
*
67154 GGGCATCGAAGTGCAAACAGGAG-CACCGAAGTGAAAA
1 GGGCATCGAAGTGCAAACAGG-GCCACAGAAGTGAAAA
67191 TATGGGCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.32, T:0.09
Consensus pattern (40 bp):
GGGCATCGAAGTGCAAACAGGGCCACAGAAGTGAAAACAA
Found at i:68906 original size:19 final size:19
Alignment explanation
Indices: 68891--68927 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
68881 TATGTGCTAC
*
68891 GATGCATCTCATGTGCCAA
1 GATGCACCTCATGTGCCAA
*
68910 GATGCACCTCGTGTGCCA
1 GATGCACCTCATGTGCCA
68928 GTAATGTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.24
Consensus pattern (19 bp):
GATGCACCTCATGTGCCAA
Found at i:77074 original size:25 final size:25
Alignment explanation
Indices: 77043--77097 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
77033 TTGAATTGTC
*
77043 AAAATATTAATTATTTACATTTAAA
1 AAAATATTAATCATTTACATTTAAA
*
77068 AAAATATTAATCATTTACATTTTAA
1 AAAATATTAATCATTTACATTTAAA
77093 AAAAT
1 AAAAT
77098 CATATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAATATTAATCATTTACATTTAAA
Found at i:77524 original size:7 final size:7
Alignment explanation
Indices: 77512--77540 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
77502 TAAGTCAAAT
77512 ATATTTA
1 ATATTTA
77519 ATATTTA
1 ATATTTA
77526 ATATTTA
1 ATATTTA
77533 AT-TTTA
1 ATATTTA
77539 AT
1 AT
77541 TTAAATTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:84246 original size:16 final size:16
Alignment explanation
Indices: 84225--84262 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
84215 CCCACAGATT
84225 TTATTTTTAAATTAAA
1 TTATTTTTAAATTAAA
84241 TTATTTTTAAATTAAA
1 TTATTTTTAAATTAAA
84257 TTATTT
1 TTATTT
84263 GAACTCGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTTTTAAATTAAA
Found at i:85567 original size:16 final size:16
Alignment explanation
Indices: 85546--85577 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
85536 TGACAACTTT
85546 GGGTTAGGCTCTTGAA
1 GGGTTAGGCTCTTGAA
85562 GGGTTAGGCTCTTGAA
1 GGGTTAGGCTCTTGAA
85578 AGTATAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.38, T:0.31
Consensus pattern (16 bp):
GGGTTAGGCTCTTGAA
Done.