Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002031.1 Kokia drynarioides strain JFW-HI SEQ_113912, 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: 63441
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:21047 original size:24 final size:24
Alignment explanation
Indices: 21001--21046 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
20991 TAACCAAACT
21001 TTTAATATGTAAATATAATTTTTA
1 TTTAATATGTAAATATAATTTTTA
21025 TTTAAT-TGTAAATATAATTTTT
1 TTTAATATGTAAATATAATTTTT
21047 TCTACATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTAATATGTAAATATAATTTTTA
Found at i:22335 original size:28 final size:32
Alignment explanation
Indices: 22278--22339 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 32
22268 ATTATTTTTT
*
22278 AAAACTTTAACTTTATTTATATATTCTTTAAA
1 AAAACTTTAAATTTATTTATATATTCTTTAAA
22310 AAAAC-TTAAATTT-TTTATA-ATT-TTTAAA
1 AAAACTTTAAATTTATTTATATATTCTTTAAA
22338 AA
1 AA
22340 TATATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 8 0.28
29 3 0.10
30 6 0.21
31 7 0.24
32 5 0.17
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (32 bp):
AAAACTTTAAATTTATTTATATATTCTTTAAA
Found at i:22370 original size:19 final size:19
Alignment explanation
Indices: 22342--22399 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
22332 TTTAAAAATA
*
22342 TATAAA-ATTTAGAATTTT
1 TATAAATATTTTGAATTTT
22360 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
* *
22379 AAAAAATATTTTGAAATTTT
1 TATAAATATTTTG-AATTTT
22399 T
1 T
22400 TGTAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.18
19 22 0.65
20 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:23247 original size:11 final size:11
Alignment explanation
Indices: 23221--23270 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
23211 TTTTGTTGTC
*
23221 ATTTTGTTATT
1 ATTTTGCTATT
* *
23232 GTTTTGCTATC
1 ATTTTGCTATT
*
23243 ATTTTTCTATT
1 ATTTTGCTATT
*
23254 ATATTGCTATT
1 ATTTTGCTATT
23265 ATTTTG
1 ATTTTG
23271 TTGTTATTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.64
Consensus pattern (11 bp):
ATTTTGCTATT
Found at i:23253 original size:22 final size:22
Alignment explanation
Indices: 23199--23272 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
23189 GTCGGACCTT
* *
23199 TTTTAGTTATTGTTTTGTTGTCA
1 TTTT-GTTATTGTTTTGCTATCA
23222 TTTTGTTATTGTTTTGCTATCA
1 TTTTGTTATTGTTTTGCTATCA
* * *
23244 TTTT-TCTATTATATTGCTATTA
1 TTTTGT-TATTGTTTTGCTATCA
23266 TTTTGTT
1 TTTTGTT
23273 GTTATTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.02
22 38 0.86
23 5 0.11
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.66
Consensus pattern (22 bp):
TTTTGTTATTGTTTTGCTATCA
Found at i:24035 original size:23 final size:20
Alignment explanation
Indices: 23996--24049 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
23986 ATTTTAGTGC
*
23996 TTTT-TTGTTGTTTTTACTGT
1 TTTTGTTGTT-TTTTTACTAT
24016 TTTGGTGTTGTTTTTGTTACTAT
1 TTT--TGTTGTTTTT-TTACTAT
24039 TTTTGTTGTTT
1 TTTTGTTGTTT
24050 GGATGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 3 0.10
21 8 0.28
22 4 0.14
23 14 0.48
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.72
Consensus pattern (20 bp):
TTTTGTTGTTTTTTTACTAT
Found at i:24263 original size:29 final size:27
Alignment explanation
Indices: 24188--24264 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 27
24178 TTTTAATGTA
* * *
24188 TTTTAAATTTGTTTATTTTTTAATGTT
1 TTTTAAATTTGTTTATATATTAATATT
* *
24215 TGTTTAAGTTTATTTGATATATTATATATT
1 T-TTTAAATTTGTTT-ATATATTA-ATATT
24245 TTTTAAATTTGTTGTATATA
1 TTTTAAATTTGTT-TATATA
24265 ATAAAATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.03
28 11 0.28
29 21 0.54
30 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (27 bp):
TTTTAAATTTGTTTATATATTAATATT
Found at i:26437 original size:81 final size:81
Alignment explanation
Indices: 26338--26498 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 81
26328 TATGTGGGCC
*
26338 TTTCAACTTAATTACAAAGTAATCTAATTATCATACCAGATTAGACTTCCACATCTATGAAATAA
1 TTTCAACTTAATTACAAAGTAATCTAATTATCATACAAGATTAGACTTCCACATCTATGAAATAA
*
26403 TATTCCATTGATTTTA
66 TATTCCATGGATTTTA
26419 TTTCAACTTAATTACAAAGTAATCTAATTATCATACAAGATTAGACTTCCACATCTATGAAATAA
1 TTTCAACTTAATTACAAAGTAATCTAATTATCATACAAGATTAGACTTCCACATCTATGAAATAA
26484 TATTCCATGGATTTT
66 TATTCCATGGATTTT
26499 GTTTTCCCTC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.38
Consensus pattern (81 bp):
TTTCAACTTAATTACAAAGTAATCTAATTATCATACAAGATTAGACTTCCACATCTATGAAATAA
TATTCCATGGATTTTA
Found at i:30804 original size:11 final size:12
Alignment explanation
Indices: 30790--30823 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
30780 CTCTAATGTA
30790 AATATTAAAAT-
1 AATATTAAAATG
30801 AATATTAAAATG
1 AATATTAAAATG
30813 AATATATAAAA
1 AATAT-TAAAA
30824 AATTTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 5 0.24
13 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AATATTAAAATG
Found at i:31774 original size:24 final size:24
Alignment explanation
Indices: 31742--31789 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
31732 CAAGGGCTGA
31742 ATTGAACAAATAAAAAACATGTTG
1 ATTGAACAAATAAAAAACATGTTG
31766 ATTGAACAAATAAAAAACATGTTG
1 ATTGAACAAATAAAAAACATGTTG
31790 TAAGACTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.25
Consensus pattern (24 bp):
ATTGAACAAATAAAAAACATGTTG
Found at i:32959 original size:5 final size:5
Alignment explanation
Indices: 32949--32993 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
32939 TTGTCACTCA
32949 CCAAC CCAAC CCAAC CCAAC CCAAC CCAAC CCAAC CCAAC CCAAC
1 CCAAC CCAAC CCAAC CCAAC CCAAC CCAAC CCAAC CCAAC CCAAC
32994 TAGTGATGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAC
Found at i:39431 original size:2 final size:2
Alignment explanation
Indices: 39424--39448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39414 TTAACTCAAG
39424 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
39449 GGAGGGATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:45884 original size:17 final size:17
Alignment explanation
Indices: 45862--45900 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
45852 AAGTGGAGAA
* *
45862 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
45879 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
45896 CTTGT
1 CTTGT
45901 CAGGGTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:59638 original size:20 final size:22
Alignment explanation
Indices: 59593--59639 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
59583 TTGAACTTTT
*
59593 CAAAAATGCTTTTGTGACAAAA
1 CAAAAATGCTTTTGTCACAAAA
59615 -AAAAATGC-TTTGTCA-AAAA
1 CAAAAATGCTTTTGTCACAAAA
59634 CAAAAA
1 CAAAAA
59640 CATAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 11 0.48
21 8 0.35
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (22 bp):
CAAAAATGCTTTTGTCACAAAA
Found at i:61852 original size:31 final size:31
Alignment explanation
Indices: 61816--61879 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
61806 AAAGGGCCAT
* * * *
61816 TAAACTATTCGAAAGTTTTTATTTAAGTTAC
1 TAAACTATTAGAAAATGTTTATTTAAGTCAC
61847 TAAACTATTAGAAAATGTTTATTTAAGTCAC
1 TAAACTATTAGAAAATGTTTATTTAAGTCAC
61878 TA
1 TA
61880 GTTTATTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (31 bp):
TAAACTATTAGAAAATGTTTATTTAAGTCAC
Done.