Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012858.1 Kokia drynarioides strain JFW-HI SEQ_127872, 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: 12079
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Found at i:2225 original size:15 final size:16
Alignment explanation
Indices: 2199--2273 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 16
2189 AAATAAAATT
*
2199 TAATTAAAAGAAGAAA
1 TAATTTAAAGAAGAAA
*
2215 T-ATTTAAAGAATAAA
1 TAATTTAAAGAAGAAA
*
2230 TCAATTTAAAGTAATAAA
1 T-AATTTAAAG-AAGAAA
2248 TTAAATTTAAA-AA-AATA
1 -T-AATTTAAAGAAGAA-A
2265 TAATTTAAA
1 TAATTTAAA
2274 TTAACTAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
15 21 0.41
16 4 0.08
17 11 0.22
18 6 0.12
19 9 0.18
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATTTAAAGAAGAAA
Found at i:2238 original size:70 final size:71
Alignment explanation
Indices: 2159--2334 Score: 189
Period size: 74 Copynumber: 2.5 Consensus size: 71
2149 ATATTAAAAT
*
2159 ATCAATTTAAAGGAATAAAATTAAA-TT-ACAAAATAAAATTT-AATTAAAAGAAGAAATATTTA
1 ATCAATTTAAAGGAAT-AAATTAAATTTAAAAAAATAAAATTTAAATT-AAAGAAGAAATATTTA
2221 AAGAATAA
64 AAGAATAA
* * ** *
2229 ATCAATTTAAAGTAATAAATTAAATTTAAAAAAATATAATTTAAATTAACTAAGACATATTTAAA
1 ATCAATTTAAAGGAATAAATTAAATTTAAAAAAATAAAATTTAAATTAAAGAAGAAATATTTAAA
2294 GAATAATAA
66 G---AATAA
* * *
2303 ATTATTTTAAAGCAATAAACTT-AATTTAAAAA
1 ATCAATTTAAAGGAATAAA-TTAAATTTAAAAA
2335 TAGATATTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
69 8 0.09
70 17 0.19
71 28 0.31
72 4 0.04
74 31 0.34
75 2 0.02
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (71 bp):
ATCAATTTAAAGGAATAAATTAAATTTAAAAAAATAAAATTTAAATTAAAGAAGAAATATTTAAA
GAATAA
Found at i:3508 original size:16 final size:16
Alignment explanation
Indices: 3471--3513 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3461 AAATGGTCTG
3471 AAAATAAAT-AACAAC
1 AAAATAAATAAACAAC
*
3486 AAGATAAATAAACAA-
1 AAAATAAATAAACAAC
3501 ATAAATAAATAAA
1 A-AAATAAATAAA
3514 AATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAATAAATAAACAAC
Found at i:3522 original size:16 final size:15
Alignment explanation
Indices: 3471--3527 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
3461 AAATGGTCTG
* *
3471 AAAATAAATAACAAC
1 AAAATAAATAAAAAA
*
3486 AAGATAAATAAACAAA
1 AAAATAAATAAA-AAA
*
3502 TAAATAAATAAAAATA
1 AAAATAAATAAAAA-A
3518 AAAATTAAAT
1 AAAA-TAAAT
3528 GCTACAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 12 0.36
16 16 0.48
17 5 0.15
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAAAAA
Found at i:5348 original size:13 final size:13
Alignment explanation
Indices: 5289--5357 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
5279 TATATATATA
5289 TTCATATAACCAT
1 TTCATATAACCAT
*
5302 TTCATGA-AATCA-
1 TTCAT-ATAACCAT
5314 TTCATTATAACCAT
1 TTCA-TATAACCAT
* *
5328 ATT-TTATAATCAT
1 -TTCATATAACCAT
5341 TTCATAT-ACCAT
1 TTCATATAACCAT
5353 TTCAT
1 TTCAT
5358 TTATCCATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
12 16 0.36
13 25 0.57
14 1 0.02
15 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.01, T:0.43
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:5863 original size:158 final size:158
Alignment explanation
Indices: 5616--5944 Score: 419
Period size: 158 Copynumber: 2.1 Consensus size: 158
5606 GTAACCATAT
* *
5616 ATGCTCACACGAGCTGTGAAATGGGTCTGCTCACACAAGCTGTGGGTCGAGATGTAAGGCTACAC
1 ATGCTCACACGAGCTGTGAAATGGGTCTACTCACACAAGCTATGGGTCGAGATGTAAGGCTACAC
* *
5681 GATGCTGCTAACACAAGCTATGGAGAA-TCAGCAAT-AAATGCCGAAACTCAGCCATTGATAAGA
66 GATGCTGCTAACACAAGCTATGGAGAATTCA-C-ATCAAATGCAGAAACTCAGCCATCGATAAGA
* *
5744 CATCTAAGACTAGCACTCATATAACCTGTA
129 CATCTAAGACCAGCACCCATATAACCTGTA
* * * **
5774 ATGCTCACACGAGCTGTGGAATGGGTCTACTCACACGAGCTATGGGTCGAGATGTTAGGCTATGC
1 ATGCTCACACGAGCTGTGAAATGGGTCTACTCACACAAGCTATGGGTCGAGATGTAAGGCTACAC
* * * * * * **
5839 GATGCTGCTCACACGAGCTGTGGAGAATTCACATCAAATGCAGGACCTCAGCCATCGGTTGGACA
66 GATGCTGCTAACACAAGCTATGGAGAATTCACATCAAATGCAGAAACTCAGCCATCGATAAGACA
* *
5904 TTTAAGACCAGCACCCATATAACTTGTA
131 TCTAAGACCAGCACCCATATAACCTGTA
* *
5932 ATGGTCATACGAG
1 ATGCTCACACGAG
5945 TTGTAATTGT
Statistics
Matches: 146, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
157 2 0.01
158 141 0.97
159 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.22
Consensus pattern (158 bp):
ATGCTCACACGAGCTGTGAAATGGGTCTACTCACACAAGCTATGGGTCGAGATGTAAGGCTACAC
GATGCTGCTAACACAAGCTATGGAGAATTCACATCAAATGCAGAAACTCAGCCATCGATAAGACA
TCTAAGACCAGCACCCATATAACCTGTA
Found at i:10316 original size:24 final size:24
Alignment explanation
Indices: 10281--10326 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
10271 GATAAATAAA
*
10281 TAAATAAGATAATAACAATAAATG
1 TAAATAAGATAAAAACAATAAATG
*
10305 TAAATTAA-ATAAAAATAATAAA
1 TAAA-TAAGATAAAAACAATAAA
10327 AGAGATAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (24 bp):
TAAATAAGATAAAAACAATAAATG
Found at i:10367 original size:13 final size:13
Alignment explanation
Indices: 10349--10391 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
10339 AAAATGATCT
10349 AAAAATAAATAAC
1 AAAAATAAATAAC
10362 AAAAAT--A-AAC
1 AAAAATAAATAAC
10372 -AAAATAAATAA-
1 AAAAATAAATAAC
10383 AAAAATAAA
1 AAAAATAAA
10392 AATTAAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 2 0.08
12 10 0.38
13 6 0.23
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAATAAC
Found at i:10375 original size:22 final size:21
Alignment explanation
Indices: 10350--10391 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
10340 AAATGATCTA
10350 AAAATAAATAACAAAAATAAAC
1 AAAATAAATAA-AAAAATAAAC
10372 AAAATAAATAAAAAAATAAA
1 AAAATAAATAAAAAAATAAA
10392 AATTAAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAATAAATAAAAAAATAAAC
Found at i:10392 original size:40 final size:39
Alignment explanation
Indices: 10348--10436 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 39
10338 TAAAATGATC
10348 TAAAAATAAATAACAAAAATAAACAAAATAAATA-AAAAAA
1 TAAAAATAAAT-ACAAAAATAAA-AAAATAAATATAAAAAA
* * ** *
10388 TAAAAATTAAATGCTAAAATAAATTAATAAATATAAACAA
1 TAAAAA-TAAATACAAAAATAAAAAAATAAATATAAAAAA
10428 TAAAAATAA
1 TAAAAATAA
10437 TTGAGATTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
39 11 0.26
40 26 0.62
41 5 0.12
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.21
Consensus pattern (39 bp):
TAAAAATAAATACAAAAATAAAAAAATAAATATAAAAAA
Found at i:10435 original size:19 final size:18
Alignment explanation
Indices: 10348--10436 Score: 63
Period size: 19 Copynumber: 4.5 Consensus size: 18
10338 TAAAATGATC
*
10348 TAAAAATAAATAACAAAAA
1 TAAAAATAAAT-ATAAAAA
*
10367 TAAACAAAATAAATAAAAAAA
1 T--A-AAAATAAATATAAAAA
*
10388 TAAAAATTAAATGCT-AAAA
1 TAAAAA-TAAAT-ATAAAAA
10407 TAAATTAATAAATATAAACAA
1 TAAA--AATAAATATAAA-AA
10428 TAAAAATAA
1 TAAAAATAA
10437 TTGAGATTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
18 4 0.07
19 21 0.37
20 7 0.12
21 16 0.28
22 9 0.16
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.21
Consensus pattern (18 bp):
TAAAAATAAATATAAAAA
Found at i:11129 original size:7 final size:6
Alignment explanation
Indices: 11099--11138 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
11089 AAAAGGAAAA
11099 GGTGAT GGTGAT GGTGAT GGTGAT GGGTGAT GGATGAT GG
1 GGTGAT GGTGAT GGTGAT GGTGAT -GGTGAT GG-TGAT GG
11139 CTGAAAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 20 0.62
7 12 0.38
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTGAT
Done.