Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009222.1 Kokia drynarioides strain JFW-HI SEQ_123927, 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: 96281
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:543 original size:45 final size:45
Alignment explanation
Indices: 494--586 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
484 TGTTATTCCC
*
494 AAGAAATATAAAAAAGGTTGGGCAGCATAGTAAATTAAAAAGAGG
1 AAGAAATATAAAAAAGGTAGGGCAGCATAGTAAATTAAAAAGAGG
* *
539 AAGAAATATAAAAAAGGTAGGGCAGCATATTCAATTAAAAAGAGG
1 AAGAAATATAAAAAAGGTAGGGCAGCATAGTAAATTAAAAAGAGG
584 AAG
1 AAG
587 TCAAATGGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.54, C:0.05, G:0.24, T:0.17
Consensus pattern (45 bp):
AAGAAATATAAAAAAGGTAGGGCAGCATAGTAAATTAAAAAGAGG
Found at i:6124 original size:29 final size:30
Alignment explanation
Indices: 6090--6151 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
6080 GTTTCACGTG
* *
6090 TATAATT-GCATCAAATTAAAATTTATGTA
1 TATAATTAACATCAAATCAAAATTTATGTA
*
6119 TATAATTACACATTAAATCAAAATTTATGTA
1 TATAATTA-ACATCAAATCAAAATTTATGTA
6150 TA
1 TA
6152 ATTTTAGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.25
31 21 0.75
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (30 bp):
TATAATTAACATCAAATCAAAATTTATGTA
Found at i:6790 original size:15 final size:14
Alignment explanation
Indices: 6762--6796 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
6752 TCGTGCACAG
6762 AATTTAAATTTTAA
1 AATTTAAATTTTAA
6776 AATTTAAAGTTTTAA
1 AATTTAAA-TTTTAA
*
6791 TATTTA
1 AATTTA
6797 TTTATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
AATTTAAATTTTAA
Found at i:6825 original size:10 final size:10
Alignment explanation
Indices: 6790--6828 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
6780 TAAAGTTTTA
*
6790 ATATTTATTT
1 ATATTTAATT
*
6800 ATAATTAATT
1 ATATTTAATT
6810 ATTATTTAATT
1 A-TATTTAATT
6821 ATATTTAA
1 ATATTTAA
6829 ATAAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTAATT
Found at i:19875 original size:11 final size:11
Alignment explanation
Indices: 19859--19884 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19849 GCGGCTGGTT
19859 GAGGCTTTGAA
1 GAGGCTTTGAA
19870 GAGGCTTTGAA
1 GAGGCTTTGAA
19881 GAGG
1 GAGG
19885 AAAATATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.42, T:0.23
Consensus pattern (11 bp):
GAGGCTTTGAA
Found at i:23266 original size:28 final size:28
Alignment explanation
Indices: 23234--23290 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
23224 CTTTTTAATT
* * *
23234 TTTTAAAAATTAAAGTAAAATTTTATCA
1 TTTTAAAAATCAAAATAAAAATTTATCA
*
23262 TTTTAAAGATCAAAATAAAAATTTATCA
1 TTTTAAAAATCAAAATAAAAATTTATCA
23290 T
1 T
23291 ATACTAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (28 bp):
TTTTAAAAATCAAAATAAAAATTTATCA
Found at i:25290 original size:15 final size:15
Alignment explanation
Indices: 25249--25291 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
25239 AAAAATTTAG
25249 TTTAAGAATTTAATAT
1 TTTAA-AATTTAATAT
* **
25265 TTTTACTTTTAATAT
1 TTTAAAATTTAATAT
25280 TTTAAAATTTAA
1 TTTAAAATTTAA
25292 GTCTAATTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTAAAATTTAATAT
Found at i:25418 original size:30 final size:31
Alignment explanation
Indices: 25377--25436 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
25367 TTAAAAAGCT
25377 AAACATAAG-AAAAATATGTTGACCATGGCC
1 AAACATAAGAAAAAATATGTTGACCATGGCC
*
25407 AAACATGAGAAAAAATATGTTGACCATGGC
1 AAACATAAGAAAAAATATGTTGACCATGGC
25437 TTATCTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (31 bp):
AAACATAAGAAAAAATATGTTGACCATGGCC
Found at i:39717 original size:5 final size:5
Alignment explanation
Indices: 39709--39733 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39699 TTTTGTTCGA
39709 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
39734 TCTCTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:49444 original size:19 final size:20
Alignment explanation
Indices: 49410--49447 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
49400 AATTCTTAAC
49410 AATAATTCTCAAAAATAAAA
1 AATAATTCTCAAAAATAAAA
*
49430 AATAA-TCTTAAAAATAAA
1 AATAATTCTCAAAAATAAA
49448 TATAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAATTCTCAAAAATAAAA
Found at i:50752 original size:20 final size:19
Alignment explanation
Indices: 50724--50763 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
50714 AAAAAAATTC
*
50724 TTAACAATAATTCTAAAAAA
1 TTAAAAATAA-TCTAAAAAA
*
50744 TTAAAAATAATCTTAAAAA
1 TTAAAAATAATCTAAAAAA
50763 T
1 T
50764 AAATATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAATAATCTAAAAAA
Found at i:50773 original size:32 final size:32
Alignment explanation
Indices: 50712--50773 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
50702 TTTTTATTTT
* * *
50712 TTAAAAAAATTCTTAACAATAATTCTAAAAAA
1 TTAAAAAAATTCTTAAAAATAAATATAAAAAA
50744 TTAAAAATAA-TCTTAAAAATAAATATAAAA
1 TTAAAAA-AATTCTTAAAAATAAATATAAAA
50774 TTATGTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (32 bp):
TTAAAAAAATTCTTAAAAATAAATATAAAAAA
Found at i:67982 original size:20 final size:21
Alignment explanation
Indices: 67957--67996 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
67947 AATCGATTTA
* *
67957 ATTTAACATA-ATTTTTAATC
1 ATTTAAAATATATTTATAATC
67977 ATTTAAAATATATTTATAAT
1 ATTTAAAATATATTTATAAT
67997 TTATAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAAAATATATTTATAATC
Found at i:68004 original size:18 final size:18
Alignment explanation
Indices: 67977--68012 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
67967 ATTTTTAATC
*
67977 ATTTAAAATATATTTATA
1 ATTTAAAATATATATATA
*
67995 ATTTATAATATATATATA
1 ATTTAAAATATATATATA
68013 TTATTCAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAAAATATATATATA
Found at i:68671 original size:5 final size:5
Alignment explanation
Indices: 68661--68688 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
68651 ATGAAACAAT
68661 GGTGA GGTGA GGTGA GGTGA GGTGA GGT
1 GGTGA GGTGA GGTGA GGTGA GGTGA GGT
68689 CTGTTACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (5 bp):
GGTGA
Found at i:69364 original size:25 final size:22
Alignment explanation
Indices: 69336--69390 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 22
69326 ATCAAAAAAA
69336 AATTTTAGAGATAA-AAATTAATTAT
1 AATTTTA-AGATAATAAA--AATT-T
69361 AATTTTTAAGATAATAAAAATTT
1 AA-TTTTAAGATAATAAAAATTT
69384 AATTTTA
1 AATTTTA
69391 TTATTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 5 0.18
23 3 0.11
24 4 0.14
25 8 0.29
26 8 0.29
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
AATTTTAAGATAATAAAAATTT
Found at i:72632 original size:32 final size:33
Alignment explanation
Indices: 72569--72638 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
72559 AATATCAAGG
*
72569 CAAATATTTCTAAAGCTACTAATGAATCATTTA
1 CAAATATTTCTAAAGCTACTAATGAAACATTTA
72602 CAAATATTTCTAAAGCTACT-ATGAAACATTTA
1 CAAATATTTCTAAAGCTACTAATGAAACATTTA
72634 CAAAT
1 CAAAT
72639 TTGTTCTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (33 bp):
CAAATATTTCTAAAGCTACTAATGAAACATTTA
Found at i:77196 original size:20 final size:20
Alignment explanation
Indices: 77151--77208 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
77141 AATGATAACG
*
77151 TGAAATATTAATTTAAATGAT
1 TGAATTATTAATTTAAAT-AT
77172 T-AATTATTAATTT-AATATT
1 TGAATTATTAATTTAAATA-T
*
77191 TGAATTA-TAATTAAAATA
1 TGAATTATTAATTTAAATA
77209 ATATTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 10 0.31
20 20 0.62
21 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TGAATTATTAATTTAAATAT
Found at i:82856 original size:29 final size:29
Alignment explanation
Indices: 82814--82871 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
82804 TAATGTAAGA
*
82814 TTATTTAAAAATAATTTTTACACAATTAT
1 TTATTTAAAAATAAATTTTACACAATTAT
**
82843 TTATTTAAAAATAAATTTTATTCAATTAT
1 TTATTTAAAAATAAATTTTACACAATTAT
82872 CTTTATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (29 bp):
TTATTTAAAAATAAATTTTACACAATTAT
Found at i:87436 original size:18 final size:18
Alignment explanation
Indices: 87409--87447 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
87399 AATGTTTATA
87409 TATTTAAAATTA-TTTTTT
1 TATTTAAAA-TAGTTTTTT
*
87427 TATTTTAAATAGTTTTTT
1 TATTTAAAATAGTTTTTT
87445 TAT
1 TAT
87448 AATTTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TATTTAAAATAGTTTTTT
Found at i:87534 original size:15 final size:17
Alignment explanation
Indices: 87514--87551 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
87504 GGAAAATTAA
87514 TTTTAACTTTTT-TTT-
1 TTTTAACTTTTTATTTC
*
87529 TTTTAATTTTTTATTTC
1 TTTTAACTTTTTATTTC
87546 TTTTAA
1 TTTTAA
87552 AGAGAAAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 3 0.15
17 6 0.30
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTAACTTTTTATTTC
Done.