Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014395.1 Kokia drynarioides strain JFW-HI SEQ_129433, 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: 266598
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 106 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:233438 original size:26 final size:26
Alignment explanation
Indices: 233407--233464 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
233397 AATATTTAGC
233407 CAATTCAATCATCATATTTTATATTT
1 CAATTCAATCATCATATTTTATATTT
*
233433 CAATTCAATCATTATATTTTATATTT
1 CAATTCAATCATCATATTTTATATTT
233459 -AATTCA
1 CAATTCA
233465 TATAGATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 6 0.19
26 25 0.81
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (26 bp):
CAATTCAATCATCATATTTTATATTT
Found at i:235292 original size:2 final size:2
Alignment explanation
Indices: 235285--235324 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
235275 ACATACATAC
235285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
235325 CATGTTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244718 original size:13 final size:13
Alignment explanation
Indices: 244691--244728 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
244681 CATTTAAATT
244691 AAAAAAACA-AAA
1 AAAAAAACATAAA
* *
244703 AAACAAATATAAA
1 AAAAAAACATAAA
244716 AAAAAAACATAAA
1 AAAAAAACATAAA
244729 CATATCTATC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAAACATAAA
Found at i:245438 original size:10 final size:10
Alignment explanation
Indices: 245423--245447 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
245413 TTTTTGAGTG
245423 ATTTGTCGTA
1 ATTTGTCGTA
245433 ATTTGTCGTA
1 ATTTGTCGTA
245443 ATTTG
1 ATTTG
245448 ATACAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
ATTTGTCGTA
Found at i:247401 original size:40 final size:40
Alignment explanation
Indices: 247346--247426 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
247336 TCTAGGAGTC
247346 ATCCGCTTCGATACCCAAGACAGGGCATCTCCAGAATTGG
1 ATCCGCTTCGATACCCAAGACAGGGCATCTCCAGAATTGG
247386 ATCCGCTTCGATACCCAAGACAGGGCATCTCCAGAATTGG
1 ATCCGCTTCGATACCCAAGACAGGGCATCTCCAGAATTGG
247426 A
1 A
247427 CTTGATAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (40 bp):
ATCCGCTTCGATACCCAAGACAGGGCATCTCCAGAATTGG
Found at i:249388 original size:15 final size:16
Alignment explanation
Indices: 249370--249404 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
249360 GGGTTTGGAC
249370 TTGGTTCAATT-GGGT
1 TTGGTTCAATTCGGGT
*
249385 TTGGTTCACTTCGGGT
1 TTGGTTCAATTCGGGT
249401 TTGG
1 TTGG
249405 GTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.09, C:0.11, G:0.34, T:0.46
Consensus pattern (16 bp):
TTGGTTCAATTCGGGT
Found at i:256518 original size:14 final size:13
Alignment explanation
Indices: 256495--256554 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
256485 GAGGTCAAAG
*
256495 TCAAGGTCAACGA
1 TCAACGTCAACGA
256508 TCAACGATCAACTG-
1 TCAACG-TCAAC-GA
* *
256522 TCAACGTCTACGG
1 TCAACGTCAACGA
256535 TCAACTGTCAACGA
1 TCAAC-GTCAACGA
*
256549 CCAACG
1 TCAACG
256555 GTTGGTCAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 1 0.03
13 15 0.39
14 21 0.55
15 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (13 bp):
TCAACGTCAACGA
Found at i:256518 original size:20 final size:21
Alignment explanation
Indices: 256500--256554 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
256490 CAAAGTCAAG
256500 GTCAACGATCAACGATCAACT
1 GTCAACGATCAACGATCAACT
* *
256521 GTCAACG-TCTACGGTCAACT
1 GTCAACGATCAACGATCAACT
*
256541 GTCAACGACCAACG
1 GTCAACGATCAACG
256555 GTTGGTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (21 bp):
GTCAACGATCAACGATCAACT
Found at i:256620 original size:16 final size:15
Alignment explanation
Indices: 256590--256640 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
256580 GGGTTTGAAC
256590 TTGGTTCAATTGGGT
1 TTGGTTCAATTGGGT
*
256605 TTGGTTCACTTTGGGT
1 TTGGTTCA-ATTGGGT
256621 TTGGTTCTCAATT-GGT
1 TTGG-T-TCAATTGGGT
256637 TTGG
1 TTGG
256641 GCTTAATGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 3 0.10
18 3 0.10
ACGTcount: A:0.10, C:0.10, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAATTGGGT
Found at i:258090 original size:12 final size:12
Alignment explanation
Indices: 258075--258099 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
258065 ATGATGAGTG
258075 GATGGAAATGTT
1 GATGGAAATGTT
258087 GATGGAAATGTT
1 GATGGAAATGTT
258099 G
1 G
258100 CTTGGTTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (12 bp):
GATGGAAATGTT
Found at i:260982 original size:6 final size:6
Alignment explanation
Indices: 260939--260981 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
260929 CCTTGAAATT
* *
260939 TAAAAA TTAAAA -AAAAA TAAAAA TAAAAA TAAAAA TATAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
260982 TCATAATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
TAAAAA
Found at i:262538 original size:21 final size:21
Alignment explanation
Indices: 262513--262554 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
262503 TAAGTCAAAT
262513 ATTCTAGTTTATCTAATTAAC
1 ATTCTAGTTTATCTAATTAAC
262534 ATTCTAGTTTATCTAATTAAC
1 ATTCTAGTTTATCTAATTAAC
262555 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
ATTCTAGTTTATCTAATTAAC
Found at i:264856 original size:29 final size:30
Alignment explanation
Indices: 264783--265102 Score: 281
Period size: 29 Copynumber: 11.0 Consensus size: 30
264773 CATTCGGGAT
264783 TAAAAATGGTAATTTTTGGAAGTTTCG-GGG
1 TAAAAATGGTAATTTTTGGAAGTTT-GAGGG
*
264813 TCAAAAATGG-GATTTTTGGAAGTTTGAGGG
1 T-AAAAATGGTAATTTTTGGAAGTTTGAGGG
264843 T-AAAATGGTAA-TTTTGGAAGTTTTG-GGG
1 TAAAAATGGTAATTTTTGGAAG-TTTGAGGG
* *
264871 TCAAAAT-G-AGATTTTTGGAAGTTCGAGGG
1 TAAAAATGGTA-ATTTTTGGAAGTTTGAGGG
*
264900 T-AAAATGGTAATTTTTGAAAGTTTCG-GGG
1 TAAAAATGGTAATTTTTGGAAGTTT-GAGGG
* *
264929 TCAAAAATGAT-ATTTTTGGAAG-TTCAGGGG
1 T-AAAAATGGTAATTTTTGGAAGTTTGA-GGG
*
264959 T-AAAATGGTAATTTTTGGAAGTTT-CGGG
1 TAAAAATGGTAATTTTTGGAAGTTTGAGGG
*
264987 TCAAAAAT-G-AGATTTTTGGAAGTTCGAGGG
1 T-AAAAATGGTA-ATTTTTGGAAGTTTGAGGG
*
265017 T--AAATGATAATTTTTGGAAGGTTT-AGGG
1 TAAAAATGGTAATTTTTGGAA-GTTTGAGGG
265045 TTAAAAAT-G-AGATTTTTGGAAGTTT-AGGGG
1 -TAAAAATGGTA-ATTTTTGGAAGTTTGA-GGG
265075 T-AAAATGGTAATTTTTGGAAGTTT-AGGG
1 TAAAAATGGTAATTTTTGGAAGTTTGAGGG
265103 ACCTCCGGGG
Statistics
Matches: 244, Mismatches: 15, Indels: 64
0.76 0.05 0.20
Matches are distributed among these distances:
27 5 0.02
28 64 0.26
29 96 0.39
30 60 0.25
31 19 0.08
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (30 bp):
TAAAAATGGTAATTTTTGGAAGTTTGAGGG
Found at i:264876 original size:58 final size:59
Alignment explanation
Indices: 264785--265098 Score: 451
Period size: 58 Copynumber: 5.4 Consensus size: 59
264775 TTCGGGATTA
* *
264785 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTGAGGGT
*
264844 AAAATGGTAA-TTTTGGAAGTTTTGGGGTC-AAAATGAGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTGAGGGT
* * * *
264901 AAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGATATTTTTGGAAG-TTCAGGGGT
1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTGA-GGGT
* *
264960 AAAATGGTAATTTTTGGAAG-TTTCGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTGAGGGT
* * * *
265018 -AAATGATAATTTTTGGAAGGTTTAGGGTTAAAAATGAGATTTTTGGAAGTTT-AGGGGT
1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTGA-GGGT
265076 AAAATGGTAATTTTTGGAAGTTT
1 AAAATGGTAATTTTTGGAAGTTT
265099 AGGGACCTCC
Statistics
Matches: 228, Mismatches: 20, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
57 55 0.24
58 100 0.44
59 73 0.32
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.36
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTGAGGGT
Done.