Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013046.1 Kokia drynarioides strain JFW-HI SEQ_128064, 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: 72435
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 75 characters in sequence are not A, C, G, or T
Found at i:3752 original size:17 final size:17
Alignment explanation
Indices: 3732--3787 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
3722 ATAAAACTAT
3732 AAAATATTAAAAATCCA
1 AAAATATTAAAAATCCA
3749 AAAATATTATAAAA-CCA
1 AAAATATTA-AAAATCCA
***
3766 ATAAAGCGTAAAAATCCA
1 A-AAATATTAAAAATCCA
3784 AAAA
1 AAAA
3788 ATAATTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.64, C:0.12, G:0.04, T:0.20
Consensus pattern (17 bp):
AAAATATTAAAAATCCA
Found at i:12044 original size:13 final size:13
Alignment explanation
Indices: 12026--12050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12016 TGATCAATAG
12026 AAAAAATAAAAAT
1 AAAAAATAAAAAT
12039 AAAAAATAAAAA
1 AAAAAATAAAAA
12051 CTTCGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:12742 original size:18 final size:20
Alignment explanation
Indices: 12706--12752 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
12696 ATAAAAATGG
*
12706 AAAAAGAAAACAAATGAAGCC
1 AAAAA-AAAACAAATGAAGAC
12727 AAAAAAAAA-AAA-GAAGAC
1 AAAAAAAAACAAATGAAGAC
12745 AAAAAAAA
1 AAAAAAAA
12753 CTCCCATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 13 0.52
19 3 0.12
20 4 0.16
21 5 0.20
ACGTcount: A:0.79, C:0.09, G:0.11, T:0.02
Consensus pattern (20 bp):
AAAAAAAAACAAATGAAGAC
Found at i:21761 original size:21 final size:21
Alignment explanation
Indices: 21736--21776 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21726 TGTCCTTCAA
* *
21736 TATCAGCTCCCTTTTTTTTCT
1 TATCAGCACCCTTTTATTTCT
21757 TATCAGCACCCTTTTATTTC
1 TATCAGCACCCTTTTATTTC
21777 CCCTATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.29, G:0.05, T:0.51
Consensus pattern (21 bp):
TATCAGCACCCTTTTATTTCT
Found at i:29930 original size:30 final size:30
Alignment explanation
Indices: 29894--29993 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 30
29884 AATTCATGTT
29894 TAAAATTTTGTATCTAAGGCTATGATCAAG
1 TAAAATTTTGTATCTAAGGCTATGATCAAG
* *
29924 TAAAATTGTT-TGATTCAAATGG-TA--ATTCATG
1 TAAAATT-TTGT-A-TCTAA-GGCTATGA-TCAAG
29955 TTTAAAATTTTGTATCTAAGGCTATGATCAAG
1 --TAAAATTTTGTATCTAAGGCTATGATCAAG
29987 TAAAATT
1 TAAAATT
29994 GGTTGATTCG
Statistics
Matches: 55, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
30 18 0.33
31 13 0.24
32 13 0.24
33 11 0.20
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (30 bp):
TAAAATTTTGTATCTAAGGCTATGATCAAG
Found at i:29975 original size:63 final size:63
Alignment explanation
Indices: 29876--30007 Score: 246
Period size: 63 Copynumber: 2.1 Consensus size: 63
29866 GCCGGTTTCA
*
29876 CAAATGGTAATTCATGTTTAAAATTTTGTATCTAAGGCTATGATCAAGTAAAATTGTTTGATT
1 CAAATGGTAATTCATGTTTAAAATTTTGTATCTAAGGCTATGATCAAGTAAAATTGGTTGATT
29939 CAAATGGTAATTCATGTTTAAAATTTTGTATCTAAGGCTATGATCAAGTAAAATTGGTTGATT
1 CAAATGGTAATTCATGTTTAAAATTTTGTATCTAAGGCTATGATCAAGTAAAATTGGTTGATT
*
30002 CGAATG
1 CAAATG
30008 CGTACCTGAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.39
Consensus pattern (63 bp):
CAAATGGTAATTCATGTTTAAAATTTTGTATCTAAGGCTATGATCAAGTAAAATTGGTTGATT
Found at i:32024 original size:29 final size:28
Alignment explanation
Indices: 31981--32052 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 28
31971 AAATAAATAC
* *
31981 TAATAATT-TTATTTAAACATAATTAGA
1 TAATAATTAATATTTAAACATAATTAAA
** *
32008 TAATAACTTAATATTTAATTATATTTAAA
1 TAATAA-TTAATATTTAAACATAATTAAA
*
32037 TAATTATTAATATTTA
1 TAATAATTAATATTTA
32053 TTTATAAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 6 0.16
28 12 0.32
29 19 0.51
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (28 bp):
TAATAATTAATATTTAAACATAATTAAA
Found at i:36197 original size:6 final size:6
Alignment explanation
Indices: 36186--36218 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
36176 TCATTAATTA
36186 AATTCT AATTCT AATTCT AATTCT AATTCT AAT
1 AATTCT AATTCT AATTCT AATTCT AATTCT AAT
36219 ATTTATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTCT
Found at i:39169 original size:103 final size:103
Alignment explanation
Indices: 38986--39230 Score: 438
Period size: 103 Copynumber: 2.4 Consensus size: 103
38976 GGTAGTTTTT
* * *
38986 AATTAAAAGTTCAAAATTTCAAATT-TCATGTATTGACTTGATGGTTAGGGTGTTCATCACTCCA
1 AATTAAAAGGTCAAAATTTCAAATTCT-ATGTATTGACCTGATGGTTAGGGTATTCATCACTCCA
*
39050 GATATGATTTGGATTCAAGTTACGTTAATCTAGATTCAA
65 GATATGATTTGAATTCAAGTTACGTTAATCTAGATTCAA
39089 AATTAAAAGGTCAAAATTTCAAATTCTATGTATTGACCTGATGGTTAGGGTATTCATCACTCCAG
1 AATTAAAAGGTCAAAATTTCAAATTCTATGTATTGACCTGATGGTTAGGGTATTCATCACTCCAG
39154 ATATGATTTGAATTCAAGTTACGTTAATCTAGATTCAA
66 ATATGATTTGAATTCAAGTTACGTTAATCTAGATTCAA
39192 AATTAAAAGGTCAAAATTTCAAATTCTATGTATTGACCT
1 AATTAAAAGGTCAAAATTTCAAATTCTATGTATTGACCT
39231 CCTCTAATAA
Statistics
Matches: 137, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 136 0.99
104 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (103 bp):
AATTAAAAGGTCAAAATTTCAAATTCTATGTATTGACCTGATGGTTAGGGTATTCATCACTCCAG
ATATGATTTGAATTCAAGTTACGTTAATCTAGATTCAA
Found at i:51112 original size:29 final size:30
Alignment explanation
Indices: 51070--51128 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
51060 GTTTGTTTAC
**
51070 AATTACGTTTTAGTTATCTAAT-TT-TCAAA
1 AATTACGTAATAGTTA-CTAATGTTATCAAA
51099 AATTACGTAATAGTTACTAATGTTATCAAA
1 AATTACGTAATAGTTACTAATGTTATCAAA
51129 TTATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 16 0.62
30 5 0.19
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (30 bp):
AATTACGTAATAGTTACTAATGTTATCAAA
Found at i:51316 original size:19 final size:21
Alignment explanation
Indices: 51294--51332 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
51284 AAAAATCTTA
51294 TAAAA-TATAAA-ATATTATT
1 TAAAATTATAAATATATTATT
*
51313 TAAAATTCTAAATATATTAT
1 TAAAATTATAAATATATTAT
51333 AAAAGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATTATAAATATATTATT
Found at i:55475 original size:18 final size:19
Alignment explanation
Indices: 55448--55493 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
55438 TGATTTTTTG
*
55448 TTTGAATTAATTCGAATAA
1 TTTGAATTAACTCGAATAA
55467 TTT-AATTAACTCGAATAA
1 TTTGAATTAACTCGAATAA
55485 TTTGAATTA
1 TTTGAATTA
55494 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (19 bp):
TTTGAATTAACTCGAATAA
Found at i:56487 original size:32 final size:32
Alignment explanation
Indices: 56442--56504 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
56432 AAAAAAAAAT
*
56442 CATAAGTATCAACTTGGGA-GAAAGTGACAAAC
1 CATAAGTACCAACTT-GGATGAAAGTGACAAAC
56474 CATAAGTACCAACTTGGATGAAAGTGACAAA
1 CATAAGTACCAACTTGGATGAAAGTGACAAA
56505 TTCAGGGGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (32 bp):
CATAAGTACCAACTTGGATGAAAGTGACAAAC
Found at i:60552 original size:15 final size:15
Alignment explanation
Indices: 60534--60567 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
60524 TTATTTTTAT
60534 TTCAATTTGTATTGA
1 TTCAATTTGTATTGA
60549 TTCAATTTGTATTGA
1 TTCAATTTGTATTGA
60564 TTCA
1 TTCA
60568 TAGGTCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (15 bp):
TTCAATTTGTATTGA
Found at i:65830 original size:19 final size:22
Alignment explanation
Indices: 65808--65853 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
65798 GTCTTATGAT
65808 TTTTAT-A-CTTTTT-ATAATA
1 TTTTATAAGCTTTTTAATAATA
* *
65827 TTTTGTAAGCTTTTTAATAATT
1 TTTTATAAGCTTTTTAATAATA
65849 TTTTA
1 TTTTA
65854 CATCTTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.24
20 1 0.05
21 6 0.29
22 9 0.43
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTTATAAGCTTTTTAATAATA
Done.