Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012534.1 Kokia drynarioides strain JFW-HI SEQ_127542, 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: 47799
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:882 original size:34 final size:34
Alignment explanation
Indices: 844--909 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
834 GAAAAAAATT
* ***
844 TTAGGTCTCCTAAAAATTGGTAAAAAAAAATAAA
1 TTAGGACTCCTAAAAATTAAAAAAAAAAAATAAA
*
878 TTAGGACTCTTAAAAATTAAAAAAAAAAAATA
1 TTAGGACTCCTAAAAATTAAAAAAAAAAAATA
910 TTGGGGCCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.58, C:0.08, G:0.09, T:0.26
Consensus pattern (34 bp):
TTAGGACTCCTAAAAATTAAAAAAAAAAAATAAA
Found at i:901 original size:32 final size:32
Alignment explanation
Indices: 864--927 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
854 TAAAAATTGG
* *
864 TAAAAAAAAATAA-ATTAGGACTCTTAAAAAT
1 TAAAAAAAAAAAATATTAGGACCCTTAAAAAT
* *
895 TAAAAAAAAAAAATATTGGGGCCCTTAAAAAT
1 TAAAAAAAAAAAATATTAGGACCCTTAAAAAT
927 T
1 T
928 GATAAAAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.58, C:0.08, G:0.09, T:0.25
Consensus pattern (32 bp):
TAAAAAAAAAAAATATTAGGACCCTTAAAAAT
Found at i:1845 original size:12 final size:11
Alignment explanation
Indices: 1824--1866 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1814 TGGTTGAGTG
1824 AAAAAATAAAA
1 AAAAAATAAAA
*
1835 AAAAAATTAAA
1 AAAAAATAAAA
**
1846 AAAAGGTAAAA
1 AAAAAATAAAA
*
1857 ATAAAATAAA
1 AAAAAATAAA
1867 TTTTGAAGTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:9007 original size:3 final size:3
Alignment explanation
Indices: 8999--9028 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
8989 TTGAATCTTG
8999 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9029 ATTTTCTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9811 original size:31 final size:31
Alignment explanation
Indices: 9751--9811 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
9741 CAAGTAGCAA
* *
9751 AAAGATATTTATATTAATTTGATTGAATATG
1 AAAGATATTTATATTAATTAGATTCAATATG
9782 AAAGATATTTATATTAAATTAG-TTCAATAT
1 AAAGATATTTATATT-AATTAGATTCAATAT
9812 TTTAATTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (31 bp):
AAAGATATTTATATTAATTAGATTCAATATG
Found at i:13072 original size:6 final size:6
Alignment explanation
Indices: 13061--13096 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
13051 CAATGAAGTT
13061 TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC
1 TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC
13097 GTTTGAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.33, T:0.50
Consensus pattern (6 bp):
TGTTGC
Found at i:13202 original size:27 final size:27
Alignment explanation
Indices: 13166--13365 Score: 193
Period size: 27 Copynumber: 7.4 Consensus size: 27
13156 CGGTGTTGAT
* *
13166 GGAGTTCCAAAAGCCGGTGTCGAGGAC
1 GGAGTTCCAAACGCCGGTGTCGAAGAC
*
13193 GGAGTTCCAAACGCCGGCGTCGAAGAC
1 GGAGTTCCAAACGCCGGTGTCGAAGAC
* *** *
13220 TGAAACCCAAACGCAGGTGTCGAAGAC
1 GGAGTTCCAAACGCCGGTGTCGAAGAC
*
13247 GGAGTGCCAAACGCCGGTGTCGAAGAC
1 GGAGTTCCAAACGCCGGTGTCGAAGAC
* * *
13274 GGAGTGCCAAATGCCGGTGTCGAAGAA
1 GGAGTTCCAAACGCCGGTGTCGAAGAC
* * ** * *
13301 GGAGTCCCAAAAGCCGGACTGGAAGAA
1 GGAGTTCCAAACGCCGGTGTCGAAGAC
* * * *
13328 GGAGTTCCAAAGGCCGGGGTGGAAGAA
1 GGAGTTCCAAACGCCGGTGTCGAAGAC
*
13355 GGAGTGCCAAA
1 GGAGTTCCAAA
13366 GGCAGGGGTG
Statistics
Matches: 147, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 147 1.00
ACGTcount: A:0.30, C:0.23, G:0.35, T:0.12
Consensus pattern (27 bp):
GGAGTTCCAAACGCCGGTGTCGAAGAC
Found at i:13310 original size:81 final size:81
Alignment explanation
Indices: 13166--13386 Score: 226
Period size: 81 Copynumber: 2.7 Consensus size: 81
13156 CGGTGTTGAT
* * ** **
13166 GGAGTTCCAAAAGCCGGTGTCGAGGACGGAGTTCCAAACGCCGGCGTCGAAGACTGAAACCCAAA
1 GGAGTTCCAAAAGCCGGTGTCGAAGACGGAGTGCCAAACGCCGGCGTCGAAGAAGGAGTCCCAAA
* ** *
13231 CGCAGGTGTCGAAGAC
66 AGCAGGACTCGAAGAA
* * * *
13247 GGAGTGCCAAACGCCGGTGTCGAAGACGGAGTGCCAAATGCCGGTGTCGAAGAAGGAGTCCCAAA
1 GGAGTTCCAAAAGCCGGTGTCGAAGACGGAGTGCCAAACGCCGGCGTCGAAGAAGGAGTCCCAAA
* *
13312 AGCCGGACTGGAAGAA
66 AGCAGGACTCGAAGAA
* * * * * * * *
13328 GGAGTTCCAAAGGCCGGGGTGGAAGAAGGAGTGCCAAAGGCAGGGGTGGAAGAAGGAGT
1 GGAGTTCCAAAAGCCGGTGTCGAAGACGGAGTGCCAAACGCCGGCGTCGAAGAAGGAGT
13387 GCCGAAGGCA
Statistics
Matches: 115, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 115 1.00
ACGTcount: A:0.30, C:0.21, G:0.38, T:0.11
Consensus pattern (81 bp):
GGAGTTCCAAAAGCCGGTGTCGAAGACGGAGTGCCAAACGCCGGCGTCGAAGAAGGAGTCCCAAA
AGCAGGACTCGAAGAA
Found at i:13326 original size:54 final size:53
Alignment explanation
Indices: 13166--13389 Score: 178
Period size: 54 Copynumber: 4.2 Consensus size: 53
13156 CGGTGTTGAT
* * * * *
13166 GGAGTTCCAAAAGCCGGTGTCGAGGACGGAGTTCCAAACGCCGGCGTCGAAGAC
1 GGAGTGCCAAAAGCCGGTGTCGAAGAAGGAGTGCCAAACGCCGGC-TCGAAGAA
* *** * * * * *
13220 TGAAACCCAAACGCAGGTGTCGAAGACGGAGTGCCAAACGCCGGTGTCGAAGAC
1 GGAGTGCCAAAAGCCGGTGTCGAAGAAGGAGTGCCAAACGCCGG-CTCGAAGAA
* * * *
13274 GGAGTGCCAAATGCCGGTGTCGAAGAAGGAGTCCCAAAAGCCGGACTGGAAGAA
1 GGAGTGCCAAAAGCCGGTGTCGAAGAAGGAGTGCCAAACGCCGG-CTCGAAGAA
* * * * * * * *
13328 GGAGTTCCAAAGGCCGGGGTGGAAGAAGGAGTGCCAAAGGCAGGGGTGGAAGAA
1 GGAGTGCCAAAAGCCGGTGTCGAAGAAGGAGTGCCAAACGC-CGGCTCGAAGAA
13382 GGAGTGCC
1 GGAGTGCC
13390 GAAGGCAGAA
Statistics
Matches: 137, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
54 135 0.99
55 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.38, T:0.11
Consensus pattern (53 bp):
GGAGTGCCAAAAGCCGGTGTCGAAGAAGGAGTGCCAAACGCCGGCTCGAAGAA
Found at i:13366 original size:27 final size:27
Alignment explanation
Indices: 13241--13395 Score: 175
Period size: 27 Copynumber: 5.7 Consensus size: 27
13231 CGCAGGTGTC
* * * *
13241 GAAGACGGAGTGCCAAACGCCGGTGTC
1 GAAGAAGGAGTGCCAAAGGCCGGGGTG
* * * *
13268 GAAGACGGAGTGCCAAATGCCGGTGTC
1 GAAGAAGGAGTGCCAAAGGCCGGGGTG
* * **
13295 GAAGAAGGAGTCCCAAAAGCCGGACTG
1 GAAGAAGGAGTGCCAAAGGCCGGGGTG
*
13322 GAAGAAGGAGTTCCAAAGGCCGGGGTG
1 GAAGAAGGAGTGCCAAAGGCCGGGGTG
*
13349 GAAGAAGGAGTGCCAAAGGCAGGGGTG
1 GAAGAAGGAGTGCCAAAGGCCGGGGTG
*
13376 GAAGAAGGAGTGCCGAAGGC
1 GAAGAAGGAGTGCCAAAGGC
13396 AGAAGTGGAA
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 114 1.00
ACGTcount: A:0.31, C:0.19, G:0.41, T:0.10
Consensus pattern (27 bp):
GAAGAAGGAGTGCCAAAGGCCGGGGTG
Found at i:13396 original size:27 final size:27
Alignment explanation
Indices: 13226--13406 Score: 155
Period size: 27 Copynumber: 6.7 Consensus size: 27
13216 AGACTGAAAC
* * * *
13226 CCAAACGCAGGTGTCGAAGACGGAGTG
1 CCAAAGGCAGGGGTGGAAGAAGGAGTG
* * * * *
13253 CCAAACGCCGGTGTCGAAGACGGAGTG
1 CCAAAGGCAGGGGTGGAAGAAGGAGTG
* * * * *
13280 CCAAATGCCGGTGTCGAAGAAGGAGTC
1 CCAAAGGCAGGGGTGGAAGAAGGAGTG
* * ** *
13307 CCAAAAGCCGGACTGGAAGAAGGAGTT
1 CCAAAGGCAGGGGTGGAAGAAGGAGTG
*
13334 CCAAAGGCCGGGGTGGAAGAAGGAGTG
1 CCAAAGGCAGGGGTGGAAGAAGGAGTG
13361 CCAAAGGCAGGGGTGGAAGAAGGAGTG
1 CCAAAGGCAGGGGTGGAAGAAGGAGTG
* **
13388 CCGAAGGCAGAAGTGGAAG
1 CCAAAGGCAGGGGTGGAAG
13407 CTTGAGCTCC
Statistics
Matches: 137, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 137 1.00
ACGTcount: A:0.31, C:0.19, G:0.40, T:0.10
Consensus pattern (27 bp):
CCAAAGGCAGGGGTGGAAGAAGGAGTG
Found at i:14841 original size:287 final size:286
Alignment explanation
Indices: 14316--14883 Score: 820
Period size: 287 Copynumber: 2.0 Consensus size: 286
14306 ATTTTCGTCT
* * *
14316 TGATTTTCAACATTTTCATCTTGAAAAAAATCAAATAAAGATGAAAATCTTGAAATTCAAAATGA
1 TGATTTTCAACATTTTCATCTTAAAAAAAATCAAATAAAGATGAAAATCCTCAAATTCAAAATGA
* *
14381 AATTATTGATGTGACATATAACTATTAAAAAATATATCTCTATTTCATACAATTCTTTCTCAGAT
66 AATTATTGATGCGACATAAAACTATTAAAAAATATATCTCTATTTCATACAATTCTTTCTCAGAT
** *
14446 CATTTAATGTAAAAATAATAAATAATACCAAGTGAAAAAATAAAACTATATTTGTTTATCTATAT
131 CATACAATGTAAAAATAATAAATAATACCAAGCGAAAAAATAAAACTATATTTGTTTATCTATAT
* *
14511 GCTAAACAAAATTATAAAACAAAATACTTTTATAAATTGAAAATTTTTCCTTTTTAACAATTGTA
196 GCTAAACAAAATCATAAAACAAAATACTTTTATAAATTGAAAATTTTACCTTTTTAACAATTGTA
*
14576 TGAGATACAAAATCATAAAATCATCC
261 TGAGAAACAAAATCATAAAATCATCC
* * * *
14602 TGATTTTTAATATTTTCATCTTAAAAAAAATCAAATTCAA-ATGAAAATCCTCAAATTTAAAATG
1 TGATTTTCAACATTTTCATCTTAAAAAAAATCAAA-TAAAGATGAAAATCCTCAAATTCAAAATG
* * ** * * * * *
14666 AAATTATTGATGCGACATAAAATTATT-TAATTTTTTTTTTTATTTCATACAATT-TTTCTCATA
65 AAATTATTGATGCGACATAAAACTATTAAAAAATATATCTCTATTTCATACAATTCTTTCTCAGA
*
14729 TTATACAATGTAAAAATAATAAATAATACCAAGCG-AAAAATAAAACTATACGTATTTGTTTATC
130 TCATACAATGTAAAAATAATAAATAATACCAAGCGAAAAAATAAAAC--TA--TATTTGTTTATC
* *
14793 TATATGCTAAACAAAATCATAAAACAAACTACTTTTATGAATTGAAAATTTTACCTTTTTAACAA
191 TATATGCTAAACAAAATCATAAAACAAAATACTTTTATAAATTGAAAATTTTACCTTTTTAACAA
14858 TTGTATGAGAAACAAAATCATAAAAT
256 TTGTATGAGAAACAAAATCATAAAAT
14884 AATTTATTTT
Statistics
Matches: 250, Mismatches: 27, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
283 11 0.04
284 39 0.16
285 22 0.09
286 77 0.31
287 101 0.40
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (286 bp):
TGATTTTCAACATTTTCATCTTAAAAAAAATCAAATAAAGATGAAAATCCTCAAATTCAAAATGA
AATTATTGATGCGACATAAAACTATTAAAAAATATATCTCTATTTCATACAATTCTTTCTCAGAT
CATACAATGTAAAAATAATAAATAATACCAAGCGAAAAAATAAAACTATATTTGTTTATCTATAT
GCTAAACAAAATCATAAAACAAAATACTTTTATAAATTGAAAATTTTACCTTTTTAACAATTGTA
TGAGAAACAAAATCATAAAATCATCC
Found at i:16489 original size:23 final size:23
Alignment explanation
Indices: 16463--16587 Score: 139
Period size: 23 Copynumber: 5.3 Consensus size: 23
16453 AAGTACTTAA
16463 CAGAGGGCACACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
16486 CAGAGGGCACACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
***
16509 CAGAGGGCACGTGAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
16532 AACAGAGGGCACACACAGTGCTGAA-
1 --CAGAGGGCACACAAAGTGCT-AAT
*
16557 CAGAGGGCACGA-AACA-TGCTAAA
1 CAGAGGGCAC-ACAA-AGTGCTAAT
16580 CAGAGGGC
1 CAGAGGGC
16588 GCGCTAGTGT
Statistics
Matches: 88, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
22 2 0.02
23 66 0.75
24 2 0.02
25 16 0.18
26 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.30, T:0.11
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:16561 original size:48 final size:45
Alignment explanation
Indices: 16460--16587 Score: 150
Period size: 48 Copynumber: 2.8 Consensus size: 45
16450 CCGAAGTACT
*
16460 TAACAGAGGGCACACAAAGTGCTAATCAGAGGGCACACAAAGTGC
1 TAACAGAGGGCACGCAAAGTGCTAATCAGAGGGCACACAAAGTGC
** *
16505 TAATCAGAGGGCACGTGAAGTGCTAATAACAGAGGGCACACACAGTGC
1 TAA-CAGAGGGCACGCAAAGTGCTAAT--CAGAGGGCACACAAAGTGC
* *
16553 TGAACAGAGGGCACG-AAACATGCTAAACAGAGGGC
1 T-AACAGAGGGCACGCAAA-GTGCTAATCAGAGGGC
16588 GCGCTAGTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
45 3 0.04
46 28 0.39
47 2 0.03
48 36 0.51
49 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.29, T:0.12
Consensus pattern (45 bp):
TAACAGAGGGCACGCAAAGTGCTAATCAGAGGGCACACAAAGTGC
Found at i:28548 original size:6 final size:6
Alignment explanation
Indices: 28537--28565 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28527 ATCCTGAGGC
28537 CAACAG CAACAG CAACAG CAACAG CAACA
1 CAACAG CAACAG CAACAG CAACAG CAACA
28566 CCATTCTCTT
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:0.52, C:0.34, G:0.14, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:32234 original size:3 final size:3
Alignment explanation
Indices: 32220--32269 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
32210 TAACCTATTC
* *
32220 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
32268 TA
1 TA
32270 GTGACCGAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Done.