Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001940.1 Kokia drynarioides strain JFW-HI SEQ_113759, 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: 60372
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:963 original size:34 final size:34
Alignment explanation
Indices: 925--1014 Score: 137
Period size: 34 Copynumber: 2.7 Consensus size: 34
915 ACAACTCATT
*
925 TTGTAAGTTTTCAAGCTCAAGAAATCAATATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATCAATATGTA
* *
959 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATCAATATGTA
*
993 TTTTAAGTTTTCAAACT-AAGAA
1 TTGTAAGTTTTCAAACTCAAGAA
1015 TTAGTATGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 5 0.10
34 47 0.90
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (34 bp):
TTGTAAGTTTTCAAACTCAAGAAATCAATATGTA
Found at i:4048 original size:30 final size:30
Alignment explanation
Indices: 3984--4080 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
3974 AATTAATGCT
** * * * *
3984 CAATTTAGTCCTCGAATGTCATTAAAATTC
1 CAATTTAGTCCTAAAATTTCACTAAACTTA
4014 CAATTTA-TACCCTAAAATTT-ACTAAACTTA
1 CAATTTAGT--CCTAAAATTTCACTAAACTTA
* * *
4044 CAATTTAGTCCTTAAATTTCACTAAATTTC
1 CAATTTAGTCCTAAAATTTCACTAAACTTA
4074 CAATTTA
1 CAATTTA
4081 ATCTTTAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 10 0.19
30 36 0.67
31 8 0.15
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (30 bp):
CAATTTAGTCCTAAAATTTCACTAAACTTA
Found at i:4981 original size:20 final size:20
Alignment explanation
Indices: 4958--4997 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4948 TATATTAATT
* *
4958 ATAAATAGGTTTAATTAAAG
1 ATAAAAAGGGTTAATTAAAG
4978 ATAAAAAGGGTTAATTAAAG
1 ATAAAAAGGGTTAATTAAAG
4998 CTTAATGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (20 bp):
ATAAAAAGGGTTAATTAAAG
Found at i:8334 original size:21 final size:21
Alignment explanation
Indices: 8307--8381 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
8297 AGAGTTTTTA
8307 GTATCGGTAGAAGTATCACTT
1 GTATCGGTAGAAGTATCACTT
*
8328 GTTTCGGTAGAAGTGA-CACTT
1 GTATCGGTAGAAGT-ATCACTT
* * **
8349 GTATGGGTAGAACTATCACAA
1 GTATCGGTAGAAGTATCACTT
*
8370 GTATCGTTAGAA
1 GTATCGGTAGAA
8382 ATTTGCACTA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTATCACTT
Found at i:9785 original size:2 final size:2
Alignment explanation
Indices: 9778--9807 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9768 CCCAATTTTC
9778 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
9808 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12860 original size:60 final size:60
Alignment explanation
Indices: 12743--12860 Score: 141
Period size: 61 Copynumber: 1.9 Consensus size: 60
12733 TCCAATTGGA
* * *
12743 ATTTGATACTCACGATGACACTCAAGTCATTGGACCTTTAATCCATAATGGGATTCATTTC
1 ATTTGATACTCACGATGACACT-AAGTCATGGGACCTATAATCCATAATAGGATTCATTTC
* **
12804 ATTTGATACTTACGATGACAC-ATAGTCATGGGACCTCATAATCTGTAA-AGGATTCAT
1 ATTTGATACTCACGATGACACTA-AGTCATGGGACCT-ATAATCCATAATAGGATTCAT
12861 ATACTCACGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 1 0.02
60 20 0.41
61 28 0.57
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (60 bp):
ATTTGATACTCACGATGACACTAAGTCATGGGACCTATAATCCATAATAGGATTCATTTC
Found at i:26989 original size:219 final size:219
Alignment explanation
Indices: 26603--27044 Score: 674
Period size: 219 Copynumber: 2.0 Consensus size: 219
26593 ACTGCAATAC
* *
26603 TTCACTCCTTGGTTTCTTTTCCTTCTCCTACACCTTCTACTCACAACACAAGCAACTCCTTCCCA
1 TTCACTCCTTGGTTTCTTTTCCTTCTCCTACACCTGCGACTCACAACACAAGCAACTCCTTCCCA
*
26668 CCAACAAGTAAAAATTACATAAAAATCCTTTAAGAACATATTAAGCTCCAAAATGCAATGTTAAA
66 CCAACAAGTAAAAATAACATAAAAATCCTTTAAGAACATATTAAGCTCCAAAATGCAATGTTAAA
*
26733 GAAAATACAAATGAAATTTCCTAAAATGCAACTAAATTTACTTAAGTATAAACAAATAACCCAAT
131 GAAAATACAAATGAAATTTCCTAAAATGCAACTAAATTTACTTAAGTACAAACAAATAACCCAAT
*
26798 TTAAAGGCTTA-AAATACAACTCTT
196 TTAAAGGC-AAGAAATACAACTCTT
* * * * *
26822 TTCACTCCTTGGTTTCTTTTCCTTCTCTTGCACCTGCGACTCACGACACAAGCAACTCCTTTCTA
1 TTCACTCCTTGGTTTCTTTTCCTTCTCCTACACCTGCGACTCACAACACAAGCAACTCCTTCCCA
* *
26887 CCAACAAGT-AAAATAACATAAAATATCTTTTAAGCACATATTAAGCTCCAAAATGCAATGTTAA
66 CCAACAAGTAAAAATAACATAAAA-ATCCTTTAAGAACATATTAAGCTCCAAAATGCAATGTTAA
* * * * *
26951 AGAAAATGCAAAT-AAATTTTCCTAAAATGCAGCTAAATTTACTTAAGTACAAACAATTGACTCA
130 AGAAAATACAAATGAAA-TTTCCTAAAATGCAACTAAATTTACTTAAGTACAAACAAATAACCCA
*
27015 ATTTAAAGGCAAGAAATATAACTCTT
194 ATTTAAAGGCAAGAAATACAACTCTT
27041 TTCA
1 TTCA
27045 AGAGTTATCA
Statistics
Matches: 202, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
218 17 0.08
219 185 0.92
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (219 bp):
TTCACTCCTTGGTTTCTTTTCCTTCTCCTACACCTGCGACTCACAACACAAGCAACTCCTTCCCA
CCAACAAGTAAAAATAACATAAAAATCCTTTAAGAACATATTAAGCTCCAAAATGCAATGTTAAA
GAAAATACAAATGAAATTTCCTAAAATGCAACTAAATTTACTTAAGTACAAACAAATAACCCAAT
TTAAAGGCAAGAAATACAACTCTT
Found at i:30763 original size:9 final size:9
Alignment explanation
Indices: 30749--30773 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30739 CCCTTTCTTT
30749 TTTTTTTTC
1 TTTTTTTTC
30758 TTTTTTTTC
1 TTTTTTTTC
30767 TTTTTTT
1 TTTTTTT
30774 GTGTTGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:44423 original size:14 final size:14
Alignment explanation
Indices: 44404--44456 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
44394 GCTCAAATCG
*
44404 AAAACCATAACCTT
1 AAAACCATAAACTT
44418 AAAACCATAAACTT
1 AAAACCATAAACTT
* *
44432 TAAACCCTAATA-TT
1 AAAACCATAA-ACTT
*
44446 AAAACCCTAAA
1 AAAACCATAAA
44457 ACCTAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 1 0.03
14 32 0.94
15 1 0.03
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAACCATAAACTT
Found at i:51744 original size:17 final size:18
Alignment explanation
Indices: 51704--51745 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
51694 TAACAAATAT
51704 AAATAATATATTAACCAA
1 AAATAATATATTAACCAA
* * *
51722 ATATAA-ATATTATCTAA
1 AAATAATATATTAACCAA
51739 AAATAAT
1 AAATAAT
51746 CTTAATAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATATATTAACCAA
Found at i:56369 original size:18 final size:18
Alignment explanation
Indices: 56343--56392 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
56333 AATTTCCATA
*
56343 AAATTATAATAAATTTAT
1 AAATCATAATAAATTTAT
56361 AAATCATAATTATAA-TTAT
1 AAATCATAA-TA-AATTTAT
*
56380 -AACCATAATAAAT
1 AAATCATAATAAAT
56393 AATATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 15 0.56
19 6 0.22
20 2 0.07
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATCATAATAAATTTAT
Found at i:56782 original size:47 final size:46
Alignment explanation
Indices: 56714--56810 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 46
56704 ATGTAACATT
* ** *
56714 ACTGGCCGTAATGTCATATTTGGTGAACCAAACGCC-CGTAAATGTA
1 ACTGGCCGTAATGTCACATTTGGCAAACCAAACACCTC-TAAATGTA
*
56760 ACTGGACCGTAATGTTACATTTGGCAAACCAAACACCTCTAAATGTA
1 ACTGG-CCGTAATGTCACATTTGGCAAACCAAACACCTCTAAATGTA
56807 ACTG
1 ACTG
56811 TCATGATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
46 5 0.11
47 38 0.86
48 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (46 bp):
ACTGGCCGTAATGTCACATTTGGCAAACCAAACACCTCTAAATGTA
Done.