Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000944.1 Kokia drynarioides strain JFW-HI SEQ_112109, 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: 30331
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:191 original size:3 final size:3
Alignment explanation
Indices: 183--231 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
173 TTTTCCTTTT
* * *
183 TTA TTA TTA TTA TTA ATG CTA TTA TTAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
229 TTA
1 TTA
232 ATGACTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:995 original size:6 final size:6
Alignment explanation
Indices: 967--1027 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
957 TTATAATAAT
* *
967 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1014 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
1028 TAAAACAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.26
6 31 0.67
7 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:1003 original size:17 final size:17
Alignment explanation
Indices: 950--1059 Score: 132
Period size: 17 Copynumber: 6.4 Consensus size: 17
940 CTTTATTTAT
* * *
950 TTTATATTTATAATAAT
1 TTTAAATTTAAAATAAA
967 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
985 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
1002 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
1019 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
1037 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
1054 TTTAAA
1 TTTAAA
1060 ATGAGTTTGG
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
16 1 0.01
17 50 0.62
18 29 0.36
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1006 original size:11 final size:11
Alignment explanation
Indices: 968--1026 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
958 TATAATAATT
968 TTAAATTTGAAA
1 TTAAATTT-AAA
*
980 ATAAATTTAAA
1 TTAAATTTAAA
991 CTTAAA-TTAAA
1 -TTAAATTTAAA
1002 TTTAAATTTAAA
1 -TTAAATTTAAA
*
1014 ATAAATTTAAA
1 TTAAATTTAAA
1025 TT
1 TT
1027 TTAAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:1009 original size:35 final size:35
Alignment explanation
Indices: 967--1059 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 35
957 TTATAATAAT
**
967 TTTAAATTTGAAAATAAATTTAAA-CTTAAATTAAA
1 TTTAAATTT-AAAATAAATTTAAATCTTAAAACAAA
*
1002 TTTAAATTTAAAATAAATTTAAATTTTAAAACAAA
1 TTTAAATTTAAAATAAATTTAAATCTTAAAACAAA
1037 TTT-AATCTTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
1060 ATGAGTTTGG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 17 0.32
35 36 0.68
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (35 bp):
TTTAAATTTAAAATAAATTTAAATCTTAAAACAAA
Found at i:1023 original size:52 final size:52
Alignment explanation
Indices: 950--1059 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
940 CTTTATTTAT
* * * * *
950 TTTATATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
* *
1002 TTTAAATTTAAAATAAATTTAAATTTTAAAACAAATTTAATCTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
1054 TTTAAA
1 TTTAAA
1060 ATGAGTTTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
Found at i:3007 original size:48 final size:48
Alignment explanation
Indices: 2952--3047 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2942 GGAATGGAAT
2952 CCAATCTTACATCATCCTAAATAGATACATGCACCTAAGCAATCTCTA
1 CCAATCTTACATCATCCTAAATAGATACATGCACCTAAGCAATCTCTA
3000 CCAATCTTACATCATCCTAAATAGATACATGCACCTAAGCAATCTCTA
1 CCAATCTTACATCATCCTAAATAGATACATGCACCTAAGCAATCTCTA
3048 GGTTTATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.27
Consensus pattern (48 bp):
CCAATCTTACATCATCCTAAATAGATACATGCACCTAAGCAATCTCTA
Found at i:4875 original size:28 final size:28
Alignment explanation
Indices: 4829--4908 Score: 142
Period size: 28 Copynumber: 2.8 Consensus size: 28
4819 AACAAAACGA
*
4829 AAACATAAATGACTAAAACGTAACATTTC
1 AAACATAAGT-ACTAAAACGTAACATTTC
4858 AAACATAAGTACTAAAACGTAACATTTC
1 AAACATAAGTACTAAAACGTAACATTTC
4886 AAACATAAGTACTAAAACGTAAC
1 AAACATAAGTACTAAAACGTAAC
4909 CCGAGACAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 41 0.82
29 9 0.18
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23
Consensus pattern (28 bp):
AAACATAAGTACTAAAACGTAACATTTC
Found at i:8326 original size:19 final size:19
Alignment explanation
Indices: 8291--8327 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8281 ATTAAATTCG
*
8291 AAATAAATTTAGGTAAAAA
1 AAATAAATTTAGATAAAAA
*
8310 AAATAAATTTATATAAAA
1 AAATAAATTTAGATAAAA
8328 TATGAATTAA
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:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATAAATTTAGATAAAAA
Found at i:12431 original size:28 final size:28
Alignment explanation
Indices: 12396--12459 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
12386 AAGTTCAGTC
12396 AAGCCCAAGTTATTTTAAAGTCATCTCG
1 AAGCCCAAGTTATTTTAAAGTCATCTCG
* *
12424 AGGCCCAAGTTATTTTAAAGTCATCTTG
1 AAGCCCAAGTTATTTTAAAGTCATCTCG
12452 AAGCCCAA
1 AAGCCCAA
12460 ATTGAACCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (28 bp):
AAGCCCAAGTTATTTTAAAGTCATCTCG
Found at i:13589 original size:33 final size:34
Alignment explanation
Indices: 13547--13622 Score: 100
Period size: 36 Copynumber: 2.2 Consensus size: 34
13537 CAAGTACAAT
* *
13547 TATATTGATA-AAAATAATATTCAAATAATTTAA
1 TATAATGATATAAAATAATATTAAAATAATTTAA
*
13580 TATAATGATATTTTAAATAATATTAAAATAATTTAA
1 TATAATGATA--TAAAATAATATTAAAATAATTTAA
13616 TATAATG
1 TATAATG
13623 TTACATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 9 0.24
36 28 0.76
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (34 bp):
TATAATGATATAAAATAATATTAAAATAATTTAA
Found at i:13634 original size:36 final size:36
Alignment explanation
Indices: 13557--13634 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
13547 TATATTGATA
* **
13557 AAAATAATATTCAAATAATTTAATATAATGATATTT
1 AAAATAATATTAAAATAATTTAATATAATGATACAT
* *
13593 TAAATAATATTAAAATAATTTAATATAATGTTACAT
1 AAAATAATATTAAAATAATTTAATATAATGATACAT
13629 AAAATA
1 AAAATA
13635 TAAATTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (36 bp):
AAAATAATATTAAAATAATTTAATATAATGATACAT
Found at i:21722 original size:29 final size:30
Alignment explanation
Indices: 21684--21741 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
21674 CACTTCTTTT
* *
21684 AAATTGATA-CCTAAATTTTTTTTTATCCC
1 AAATTAATACCCTAAATTTTTTTCTATCCC
*
21713 AAATTAATACCCTAAGTTTTTTTCTATCC
1 AAATTAATACCCTAAATTTTTTTCTATCC
21742 ATTAATTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (30 bp):
AAATTAATACCCTAAATTTTTTTCTATCCC
Found at i:21952 original size:16 final size:16
Alignment explanation
Indices: 21931--21962 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21921 TCTGTAGTGT
21931 CTTCTTTTTCTTCTTC
1 CTTCTTTTTCTTCTTC
21947 CTTCTTTTTCTTCTTC
1 CTTCTTTTTCTTCTTC
21963 TTAAATCCTC
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
CTTCTTTTTCTTCTTC
Found at i:22764 original size:3 final size:3
Alignment explanation
Indices: 22756--22786 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
22746 TTAGGGATTT
22756 AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG
22787 GACGATAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.