Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006463.1 Kokia drynarioides strain JFW-HI SEQ_121046, 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: 43036
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1288 original size:6 final size:5
Alignment explanation
Indices: 1255--1281 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1245 TTTTAAAAAT
1255 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
1282 ATCAAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:2315 original size:31 final size:30
Alignment explanation
Indices: 2256--2449 Score: 205
Period size: 30 Copynumber: 6.4 Consensus size: 30
2246 AAAATTTTAG
2256 AAATTACCATTTTAACCACC-AAACTTTTCCA
1 AAATTA-CATTTTAACC-CCTAAACTTTTCCA
* *
2287 AAATTACATTTTGACCCCTAAACTTTTTCA
1 AAATTACATTTTAACCCCTAAACTTTTCCA
2317 AAATTACATTTTAACCCCCTAAACTTTTCCA
1 AAATTACATTTTAA-CCCCTAAACTTTTCCA
* * * **
2348 AAATCACATTTTTTATCTTTAAACTTTTCCA
1 AAATTACA-TTTTAACCCCTAAACTTTTCCA
* *
2379 AAATCACATTTTGACCCCTAAACTTTTCCA
1 AAATTACATTTTAACCCCTAAACTTTTCCA
* * *
2409 AAATCACA-TTTAACCCTTAAA-TTTCTCTA
1 AAATTACATTTTAACCCCTAAACTTT-TCCA
*
2438 AAATTTCATTTT
1 AAATTACATTTT
2450 CATCCCGAGT
Statistics
Matches: 140, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
28 3 0.02
29 22 0.16
30 61 0.44
31 49 0.35
32 5 0.04
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATTACATTTTAACCCCTAAACTTTTCCA
Found at i:2344 original size:61 final size:61
Alignment explanation
Indices: 2256--2449 Score: 225
Period size: 61 Copynumber: 3.2 Consensus size: 61
2246 AAAATTTTAG
* * * *
2256 AAATTACCATTTTAACCACC-AAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTTCA
1 AAATTA-CATTTTAACCCCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTTCA
* * * *
2317 AAATTACATTTTAACCCCCTAAACTTTTCCAAAATCACATTTTTTATCTTTAAACTTTTCCA
1 AAATTACATTTTAACCCCCTAAACTTTTCCAAAATCACA-TTTTAACCCTTAAACTTTTTCA
* * *
2379 AAATCACATTTTGA-CCCCTAAACTTTTCCAAAATCACA-TTTAACCCTTAAA-TTTCTCTA
1 AAATTACATTTTAACCCCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTTC-A
*
2438 AAATTTCATTTT
1 AAATTACATTTT
2450 CATCCCGAGT
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
58 4 0.04
59 21 0.18
60 12 0.11
61 48 0.42
62 29 0.25
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (61 bp):
AAATTACATTTTAACCCCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTTCA
Found at i:12370 original size:35 final size:35
Alignment explanation
Indices: 12306--12376 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
12296 ATAACTTATA
* *
12306 TAAATGAATTTTTATTATAGCAACGTATAAATGAAT
1 TAAATGAATTTTTATTATAACAACATAT-AATGAAT
12342 TAAATGAA-TTTTATTATAACAACATATAATGAAT
1 TAAATGAATTTTTATTATAACAACATATAATGAAT
12376 T
1 T
12377 TTCATTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 8 0.24
35 17 0.52
36 8 0.24
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.39
Consensus pattern (35 bp):
TAAATGAATTTTTATTATAACAACATATAATGAAT
Found at i:16835 original size:6 final size:6
Alignment explanation
Indices: 16824--16848 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16814 TCTGTGTGTT
16824 GAAAGA GAAAGA GAAAGA GAAAGA G
1 GAAAGA GAAAGA GAAAGA GAAAGA G
16849 GTGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:23842 original size:19 final size:20
Alignment explanation
Indices: 23802--23848 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
23792 TTGAAAAAAA
23802 AAGTATAATTAATCAAGATT
1 AAGTATAATTAATCAAGATT
* *
23822 AAGT-TAATTAATTAAGTTT
1 AAGTATAATTAATCAAGATT
*
23841 AATTATAA
1 AAGTATAA
23849 ACTAAACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (20 bp):
AAGTATAATTAATCAAGATT
Found at i:32967 original size:173 final size:173
Alignment explanation
Indices: 32676--33198 Score: 626
Period size: 173 Copynumber: 2.9 Consensus size: 173
32666 GTAAAGAAGT
* * * *
32676 TAACCACTGAGCCCCACTACCATAGGTGCATACATTAGCTTGTGCAGGTAGCCTGTAGAG-AGCA
1 TAACCACTGAGCCCCACT-GCATAGGTGCACACATTAGCTTGTGTAGGTGGCCTGTAG-GTAGCA
* *
32740 CTTTTGTAACCAGCATCAAACCGATAATAACACCTATCAACGAGGTGTCCCATCTTCCCATACAA
64 CTCTTGTAACCAGCATCAAACCGATAATAACACCTATCAACGAGGTGCCCCATCTTCCCATACAA
* * *
32805 CTGATATTAAACACTAGAGTTAGAGGTAAGCCCACT-G-CC-ATA
129 CTGACATTGAACACTAGAGATAGAGGTAAGCCCACTCGACCTATA
32847 GGTAACCACTGAGCCCCACTGCTATAGGTGCACACATTAGCTTGTGTAGGTGGCCTGTAGGTAGC
1 --TAACCACTGAGCCCCACTGC-ATAGGTGCACACATTAGCTTGTGTAGGTGGCCTGTAGGTAGC
*
32912 ACTCTTGTAACCAGCATCAAACCGATAATAACACCTATCAACAAGGTGCCCCATCTTCCCATACA
63 ACTCTTGTAACCAGCATCAAACCGATAATAACACCTATCAACGAGGTGCCCCATCTTCCCATACA
* *
32977 ACTGACATTGAACACTAGAGATAGAGGTATGCCCATGACCTCGACCTCTA
128 ACTGACATTGAACACTAGAGATAGAGGTAAGCCC---A-CTCGACCTATA
* *** * * *
33027 AAACCAAAC-GATGGCTTGTAAGCTGGCATA-GTCGGAGACGACTCAGCTTGTGTAGGTGGCCTG
1 TAACC--ACTGA--GC--CCCA-CT-GCATAGGT-GCACAC-A-TTAGCTTGTGTAGGTGGCCTG
**
33090 TAGGTAGCACTCTTGTAACCAGCATCAAATTGATAATAACACCTATCAACGAGGTGCCCCATCTT
55 TAGGTAGCACTCTTGTAACCAGCATCAAACCGATAATAACACCTATCAACGAGGTGCCCCATCTT
*
33155 CCCATACAACTGACATTGAACACTAGAGATAGAGGTACGCCCAC
120 CCCATACAACTGACATTGAACACTAGAGATAGAGGTAAGCCCAC
33199 GACCTCGACC
Statistics
Matches: 307, Mismatches: 23, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
172 2 0.01
173 147 0.48
176 1 0.00
177 2 0.01
178 5 0.02
179 4 0.01
180 4 0.01
181 2 0.01
182 1 0.00
183 4 0.01
184 9 0.03
185 3 0.01
186 123 0.40
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (173 bp):
TAACCACTGAGCCCCACTGCATAGGTGCACACATTAGCTTGTGTAGGTGGCCTGTAGGTAGCACT
CTTGTAACCAGCATCAAACCGATAATAACACCTATCAACGAGGTGCCCCATCTTCCCATACAACT
GACATTGAACACTAGAGATAGAGGTAAGCCCACTCGACCTATA
Found at i:33205 original size:186 final size:186
Alignment explanation
Indices: 32885--33258 Score: 703
Period size: 186 Copynumber: 2.0 Consensus size: 186
32875 TGCACACATT
32885 AGCTTGTGTAGGTGGCCTGTAGGTAGCACTCTTGTAACCAGCATCAAACCGATAATAACACCTAT
1 AGCTTGTGTAGGTGGCCTGTAGGTAGCACTCTTGTAACCAGCATCAAACCGATAATAACACCTAT
* *
32950 CAACAAGGTGCCCCATCTTCCCATACAACTGACATTGAACACTAGAGATAGAGGTATGCCCATGA
66 CAACAAGGTGCCCCATCTTCCCATACAACTGACATTGAACACTAGAGATAGAGGTACGCCCACGA
33015 CCTCGACCTCTAAAACCAAACGATGGCTTGTAAGCTGGCATAGTCGGAGACGACTC
131 CCTCGACCTCTAAAACCAAACGATGGCTTGTAAGCTGGCATAGTCGGAGACGACTC
**
33071 AGCTTGTGTAGGTGGCCTGTAGGTAGCACTCTTGTAACCAGCATCAAATTGATAATAACACCTAT
1 AGCTTGTGTAGGTGGCCTGTAGGTAGCACTCTTGTAACCAGCATCAAACCGATAATAACACCTAT
*
33136 CAACGAGGTGCCCCATCTTCCCATACAACTGACATTGAACACTAGAGATAGAGGTACGCCCACGA
66 CAACAAGGTGCCCCATCTTCCCATACAACTGACATTGAACACTAGAGATAGAGGTACGCCCACGA
33201 CCTCGACCTCTAAAACCAAACGATGGCTTGTAAGCTGGCATAGTCGGAGACGACTC
131 CCTCGACCTCTAAAACCAAACGATGGCTTGTAAGCTGGCATAGTCGGAGACGACTC
33257 AG
1 AG
33259 GCTGTTGATG
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
186 183 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (186 bp):
AGCTTGTGTAGGTGGCCTGTAGGTAGCACTCTTGTAACCAGCATCAAACCGATAATAACACCTAT
CAACAAGGTGCCCCATCTTCCCATACAACTGACATTGAACACTAGAGATAGAGGTACGCCCACGA
CCTCGACCTCTAAAACCAAACGATGGCTTGTAAGCTGGCATAGTCGGAGACGACTC
Found at i:39777 original size:19 final size:19
Alignment explanation
Indices: 39753--39795 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39743 AAACATAAAT
39753 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
39772 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
39791 TAAAT
1 TAAAT
39796 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:39825 original size:5 final size:5
Alignment explanation
Indices: 39815--39839 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39805 AATAATATTT
39815 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
39840 CCAAGTCTTT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:39831 original size:29 final size:31
Alignment explanation
Indices: 39766--39834 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
39756 ATACAAATTT
* *
39766 AAATAATAAATAATATCTTAAATATTAAATCC
1 AAATAA-AAATAATATCTTAAATATAAAATCA
* *
39798 TAATAAAAATAATATTTTAAA-ATAAAAT-A
1 AAATAAAAATAATATCTTAAATATAAAATCA
39827 AAATAAAA
1 AAATAAAA
39835 TAAAACCAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.22
30 6 0.19
31 14 0.44
32 5 0.16
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (31 bp):
AAATAAAAATAATATCTTAAATATAAAATCA
Found at i:41302 original size:5 final size:6
Alignment explanation
Indices: 41295--41339 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
41285 CACATATAAT
*
41295 AAAATA AATAAATG AAAATA AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AA--AATA AAAATA AAAATA AAAATA AAAATA AAAATA A
41340 TTGGGTTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 30 0.86
8 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAATA
Done.