Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014993.1 Kokia drynarioides strain JFW-HI SEQ_130037, 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: 99419
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 380 characters in sequence are not A, C, G, or T
Found at i:2904 original size:6 final size:6
Alignment explanation
Indices: 2888--2917 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2878 AAGTCACTAT
*
2888 CTCTAC ATCTAC CTCTAC CTCTAC CTCTAC
1 CTCTAC CTCTAC CTCTAC CTCTAC CTCTAC
2918 AAAGGCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.47, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTAC
Found at i:2947 original size:6 final size:6
Alignment explanation
Indices: 2936--2960 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2926 CAAACAGCTA
2936 GTTGCT GTTGCT GTTGCT GTTGCT G
1 GTTGCT GTTGCT GTTGCT GTTGCT G
2961 GTTTTGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.36, T:0.48
Consensus pattern (6 bp):
GTTGCT
Found at i:6422 original size:88 final size:88
Alignment explanation
Indices: 6273--6451 Score: 340
Period size: 88 Copynumber: 2.0 Consensus size: 88
6263 ATGTTTATTA
6273 TAATAAAAATAGAAAGAGGAAATAAGGTGAGGGCGCATGTTATGGTATCATCCTTAATGCATGGC
1 TAATAAAAATAGAAAGAGGAAATAAGGTGAGGGCGCATGTTATGGTATCATCCTTAATGCATGGC
*
6338 AGGACGATGGGTGCGGTGTAGCC
66 AGGACGATGGGTGCGGTGTAACC
*
6361 TAATAAAAATAGAAAGAGGAAATAAGGTGAGGGCGCATGTTATGGTATCTTCCTTAATGCATGGC
1 TAATAAAAATAGAAAGAGGAAATAAGGTGAGGGCGCATGTTATGGTATCATCCTTAATGCATGGC
6426 AGGACGATGGGTGCGGTGTAACC
66 AGGACGATGGGTGCGGTGTAACC
6449 TAA
1 TAA
6452 GAATGTGTGC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.23
Consensus pattern (88 bp):
TAATAAAAATAGAAAGAGGAAATAAGGTGAGGGCGCATGTTATGGTATCATCCTTAATGCATGGC
AGGACGATGGGTGCGGTGTAACC
Found at i:6981 original size:30 final size:30
Alignment explanation
Indices: 6941--7002 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
6931 ACTTATTTTA
* * *
6941 TTGTTAATTTTGTTATTATTTTATAGGCAT
1 TTGTGAATTTTGTTACTATTTTAGAGGCAT
*
6971 TTGTGAATTTTGTTACTATTTTAGAGGTAT
1 TTGTGAATTTTGTTACTATTTTAGAGGCAT
7001 TT
1 TT
7003 ATTTGTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.03, G:0.16, T:0.58
Consensus pattern (30 bp):
TTGTGAATTTTGTTACTATTTTAGAGGCAT
Found at i:8607 original size:62 final size:62
Alignment explanation
Indices: 8509--8632 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
8499 ACTACCAAGT
*
8509 GCATTATACCATATATATATATATATATATATACACACGTCAAGGAGAGATGTACTATAAAA
1 GCATTATACCATATATATATATATATATATACACACACGTCAAGGAGAGATGTACTATAAAA
*
8571 GCATTATACCATATATATATATATATGTATACACACACGTCAAGGAGAGATGTACTATAAAA
1 GCATTATACCATATATATATATATATATATACACACACGTCAAGGAGAGATGTACTATAAAA
8633 TATTATATAC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (62 bp):
GCATTATACCATATATATATATATATATATACACACACGTCAAGGAGAGATGTACTATAAAA
Found at i:12853 original size:30 final size:30
Alignment explanation
Indices: 12813--12994 Score: 197
Period size: 30 Copynumber: 6.1 Consensus size: 30
12803 AAGTCCACCT
*
12813 CCCTTGCCAATCCCACCACCAAGGCCTCCA
1 CCCTTTCCAATCCCACCACCAAGGCCTCCA
* *
12843 CCTTTTCCAATCCCACCGCCAAGGCCTCCA
1 CCCTTTCCAATCCCACCACCAAGGCCTCCA
* *
12873 CCCTTTCCAATCCCACCACCAAGACCGCCA
1 CCCTTTCCAATCCCACCACCAAGGCCTCCA
* * * * *
12903 CCATTGCCAATGCCACCACCAAGGCCCCCT
1 CCCTTTCCAATCCCACCACCAAGGCCTCCA
* *
12933 CCCTTTCCTATCCCACCACCAAGCCCTCCA
1 CCCTTTCCAATCCCACCACCAAGGCCTCCA
* * *
12963 -CCTGCTCC-ACCGCCACCACCAAGCCCTCCA
1 CCCT-TTCCAATC-CCACCACCAAGGCCTCCA
12993 CC
1 CC
12995 GGCTCCACCT
Statistics
Matches: 127, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
29 5 0.04
30 121 0.95
31 1 0.01
ACGTcount: A:0.22, C:0.54, G:0.09, T:0.15
Consensus pattern (30 bp):
CCCTTTCCAATCCCACCACCAAGGCCTCCA
Found at i:12979 original size:90 final size:90
Alignment explanation
Indices: 12816--12994 Score: 227
Period size: 90 Copynumber: 2.0 Consensus size: 90
12806 TCCACCTCCC
* * * * *
12816 TTGCCAATCCCACCACCAAGGCCTCCACCTTTTCCAATCCCACCGCCAAGGCCTCCACCCTTTCC
1 TTGCCAATCCCACCACCAAGGCCCCCACCCTTTCCAATCCCACCACCAAGCCCTCCACCCTCTCC
*
12881 AATCCCACCACCAAGACCGCCACCA
66 AACCCCACCACCAAGACCGCCACCA
* * *
12906 TTGCCAATGCCACCACCAAGGCCCCCTCCCTTTCCTATCCCACCACCAAGCCCTCCA-CCTGCTC
1 TTGCCAATCCCACCACCAAGGCCCCCACCCTTTCCAATCCCACCACCAAGCCCTCCACCCT-CTC
* *
12970 C-ACCGCCACCACCAAGCCCTCCACC
65 CAACC-CCACCACCAAGACCGCCACC
12995 GGCTCCACCT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 5 0.07
90 71 0.93
ACGTcount: A:0.22, C:0.54, G:0.09, T:0.15
Consensus pattern (90 bp):
TTGCCAATCCCACCACCAAGGCCCCCACCCTTTCCAATCCCACCACCAAGCCCTCCACCCTCTCC
AACCCCACCACCAAGACCGCCACCA
Found at i:13000 original size:30 final size:30
Alignment explanation
Indices: 12945--13024 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
12935 CTTTCCTATC
*
12945 CCACCACCAAGCCCTCCACCTGCTCCACCG
1 CCACCACCAAGCCCTCCACCGGCTCCACCG
*
12975 CCACCACCAAGCCCTCCACCGGCTCCACCT
1 CCACCACCAAGCCCTCCACCGGCTCCACCG
* * *
13005 CCACCTCCAAGTCCACCACC
1 CCACCACCAAGCCCTCCACC
13025 ACCAGCAGCT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.21, C:0.60, G:0.09, T:0.10
Consensus pattern (30 bp):
CCACCACCAAGCCCTCCACCGGCTCCACCG
Found at i:13067 original size:18 final size:18
Alignment explanation
Indices: 12990--13067 Score: 68
Period size: 18 Copynumber: 4.3 Consensus size: 18
12980 ACCAAGCCCT
* *
12990 CCACCGGCTCCACCTCCA
1 CCACCAGCTCCACCACCA
*
13008 CCTCCAAG-TCCACCACCA
1 CCACC-AGCTCCACCACCA
*
13026 CCAGCAGCTCCACCACCA
1 CCACCAGCTCCACCACCA
** *
13044 AAACCAGCTCCACCTCCA
1 CCACCAGCTCCACCACCA
*
13062 GCACCA
1 CCACCA
13068 CCGCCGAAAC
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
17 2 0.04
18 44 0.94
19 1 0.02
ACGTcount: A:0.27, C:0.55, G:0.09, T:0.09
Consensus pattern (18 bp):
CCACCAGCTCCACCACCA
Found at i:13190 original size:15 final size:15
Alignment explanation
Indices: 13170--13207 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
13160 ATCCGTATTT
13170 ACCACATTC-CTAGCA
1 ACCACATTCACTA-CA
13185 ACCACATTCACTACA
1 ACCACATTCACTACA
*
13200 AACACATT
1 ACCACATT
13208 AAAGCAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.39, C:0.37, G:0.03, T:0.21
Consensus pattern (15 bp):
ACCACATTCACTACA
Found at i:21839 original size:14 final size:14
Alignment explanation
Indices: 21820--21858 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
21810 AATAGAGAGC
21820 AAAAAAGAAAAAGA
1 AAAAAAGAAAAAGA
**
21834 AAAAAAGAAAATTA
1 AAAAAAGAAAAAGA
21848 AAAAAA-AAAAA
1 AAAAAAGAAAAA
21859 AAGTCAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:26616 original size:27 final size:27
Alignment explanation
Indices: 26586--26640 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
26576 AGTTAGGCAC
26586 ATTGGTGAATGATTACATCCAATTCAA
1 ATTGGTGAATGATTACATCCAATTCAA
26613 ATTGGTGAATGATTACATCCAATTCAA
1 ATTGGTGAATGATTACATCCAATTCAA
26640 A
1 A
26641 ACACTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
ATTGGTGAATGATTACATCCAATTCAA
Found at i:26968 original size:22 final size:23
Alignment explanation
Indices: 26917--26970 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
26907 ACTTAAATTT
* *
26917 TTAAAATCTAAAAAATAAAGATA
1 TTAAATTCTAAAAAATAAAGAAA
* *
26940 TTGAATTCTCAAAAATAAA-AAA
1 TTAAATTCTAAAAAATAAAGAAA
26962 TTAAATTCT
1 TTAAATTCT
26971 GAATTTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.31
Consensus pattern (23 bp):
TTAAATTCTAAAAAATAAAGAAA
Found at i:31859 original size:31 final size:31
Alignment explanation
Indices: 31824--31887 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
31814 CTTAACAATC
**
31824 CAGTGACTTAAATAAAAAATTTTTAATAGTT
1 CAGTGACTTAAATAAAAAATTTCGAATAGTT
* *
31855 CAGTGACTTAAATGAAAACTTTCGAATAGTT
1 CAGTGACTTAAATAAAAAATTTCGAATAGTT
31886 CA
1 CA
31888 ATGATCATTT
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:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAAATTTCGAATAGTT
Found at i:32343 original size:2 final size:2
Alignment explanation
Indices: 32330--32362 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
32320 ATAATTTCCT
*
32330 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32363 TTGTGGTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32787 original size:20 final size:20
Alignment explanation
Indices: 32745--32801 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
32735 ATTTTTTATA
*
32745 TTAATATTTTATAATTAAGT
1 TTAATATTTTAAAATTAAGT
* **
32765 TTAAAATTTTAAAATTATTT
1 TTAATATTTTAAAATTAAGT
*
32785 TTATTA-TTTAAAATTAA
1 TTAATATTTTAAAATTAA
32802 TATTAATAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAATATTTTAAAATTAAGT
Found at i:36854 original size:24 final size:24
Alignment explanation
Indices: 36809--36854 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
36799 TATTATGATA
* *
36809 AATTTAAAATTTAATCTATATTTT
1 AATTTAAAAGTTAATATATATTTT
36833 AATTTAAATAGTTAATAT-TATT
1 AATTTAAA-AGTTAATATATATT
36855 AACTATTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AATTTAAAAGTTAATATATATTTT
Found at i:55871 original size:16 final size:16
Alignment explanation
Indices: 55839--55882 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
55829 GATTTTGAAT
*
55839 TTCAAATTATTTCAAA
1 TTCAAATCATTTCAAA
55855 TTCAAATCATATT-AAA
1 TTCAAATCAT-TTCAAA
*
55871 TTCGAATCATTT
1 TTCAAATCATTT
55883 TAGTTTAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (16 bp):
TTCAAATCATTTCAAA
Found at i:57607 original size:28 final size:28
Alignment explanation
Indices: 57551--57626 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 28
57541 AAGACTTATA
*
57551 TAATTATGTTAATAATAAAAGATTAAA-T
1 TAATTAT-TTAATAATAAAAGAATAAATT
*
57579 TAATCTATTTAATAATAAATCGAAT-AATT
1 TAAT-TATTTAATAATAAA-AGAATAAATT
57608 TAATTTAATTTATATAATA
1 TAA-TT-ATTTA-ATAATA
57627 TATAAATCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 17 0.43
29 11 0.28
30 6 0.15
31 6 0.15
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (28 bp):
TAATTATTTAATAATAAAAGAATAAATT
Found at i:59854 original size:23 final size:22
Alignment explanation
Indices: 59814--59856 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
59804 TATATTTTAA
*
59814 GTTTAAATATAATAATTAAAAT
1 GTTTAAATAAAATAATTAAAAT
59836 GTTTAAGATAAAATAATTAAA
1 GTTTAA-ATAAAATAATTAAA
59857 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
GTTTAAATAAAATAATTAAAAT
Found at i:65368 original size:55 final size:55
Alignment explanation
Indices: 65283--65394 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
65273 AGATACCAGA
65283 AAAAAAAAAAAAAAAGACTGCCTAAAGATATTCTGGTTTTTATGGCACATATGAT
1 AAAAAAAAAAAAAAAGACTGCCTAAAGATATTCTGGTTTTTATGGCACATATGAT
* *
65338 AAAAATAAAAAAAAAGACTGCCTAAGGATATTCTGGTTTTTATGGCACATATGAT
1 AAAAAAAAAAAAAAAGACTGCCTAAAGATATTCTGGTTTTTATGGCACATATGAT
65393 AA
1 AA
65395 CTCCGTTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (55 bp):
AAAAAAAAAAAAAAAGACTGCCTAAAGATATTCTGGTTTTTATGGCACATATGAT
Found at i:66369 original size:19 final size:19
Alignment explanation
Indices: 66333--66371 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
66323 TAAATTTGGC
**
66333 ATTTAATTTTTATTATTTT
1 ATTTAATTTTTAAGATTTT
*
66352 ATTTTATTTTTAAGATTTT
1 ATTTAATTTTTAAGATTTT
66371 A
1 A
66372 ATCTTCATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
ATTTAATTTTTAAGATTTT
Found at i:81829 original size:16 final size:16
Alignment explanation
Indices: 81806--81846 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
81796 AAAATCAAAG
*
81806 TATAAATTTATCATTA
1 TATAAATTTATAATTA
* *
81822 TATTAATTTATAATTG
1 TATAAATTTATAATTA
81838 TATAAATTT
1 TATAAATTT
81847 TAACTGAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TATAAATTTATAATTA
Found at i:82387 original size:14 final size:15
Alignment explanation
Indices: 82358--82391 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
82348 CTTATGTTCT
82358 TTTTTCAATTTTTTAA
1 TTTTTCAA-TTTTTAA
82374 TTTTTCAA-TTTTAA
1 TTTTTCAATTTTTAA
82388 TTTT
1 TTTT
82392 AACTTGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTCAATTTTTAA
Found at i:98367 original size:22 final size:22
Alignment explanation
Indices: 98324--98367 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
98314 TCCACATTAG
*
98324 TTAAATCAAAATTAAATTAATT
1 TTAAATCAAAATTAAATGAATT
*
98346 TTAAAT-AAAATTCATATGAATT
1 TTAAATCAAAATT-AAATGAATT
98368 ATTCAACGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAAATCAAAATTAAATGAATT
Done.