Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014489.1 Kokia drynarioides strain JFW-HI SEQ_129528, 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: 76765
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:6291 original size:21 final size:20
Alignment explanation
Indices: 6250--6292 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6240 ATTTATATTC
* *
6250 ATTTTTCATTTGTATTTATT
1 ATTTTTCATTTGAATTAATT
6270 ATTTTTCATTTGAAATTAATT
1 ATTTTTCATTTG-AATTAATT
6291 AT
1 AT
6293 GTTTATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTTTTCATTTGAATTAATT
Found at i:6315 original size:34 final size:33
Alignment explanation
Indices: 6277--6371 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 33
6267 ATTATTTTTC
6277 ATTTGAAATTAATTATGTTTATGTTTATGAATGA
1 ATTTG-AATTAATTATGTTTATGTTTATGAATGA
** *
6311 ATTTGGAATTAATTATGTTTATGTTTATGTTTGT
1 ATTT-GAATTAATTATGTTTATGTTTATGAATGA
* *
6345 ATTT-AATTAATTATATTTATGCTTATG
1 ATTTGAATTAATTATGTTTATGTTTATG
6372 TTTATGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 21 0.38
34 33 0.60
35 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (33 bp):
ATTTGAATTAATTATGTTTATGTTTATGAATGA
Found at i:6781 original size:22 final size:23
Alignment explanation
Indices: 6756--6798 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
6746 ACAGAGATTA
*
6756 AGAATATCACATT-AAAAAGTAC
1 AGAATATCAAATTCAAAAAGTAC
6778 AGAATATCAAATTCAAAAAGT
1 AGAATATCAAATTCAAAAAGT
6799 CTTGATCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (23 bp):
AGAATATCAAATTCAAAAAGTAC
Found at i:6873 original size:26 final size:26
Alignment explanation
Indices: 6844--6895 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
6834 TCATAAACCA
*
6844 AAATACAAATATAAAAATTATTAATT
1 AAATACAAATATAAAAATAATTAATT
* *
6870 AAATACAAATTTAAACATAATTAATT
1 AAATACAAATATAAAAATAATTAATT
6896 TCAAATTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATACAAATATAAAAATAATTAATT
Found at i:10380 original size:12 final size:12
Alignment explanation
Indices: 10363--10388 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10353 AATTTGTTTG
10363 TTGTTTTAATAT
1 TTGTTTTAATAT
10375 TTGTTTTAATAT
1 TTGTTTTAATAT
10387 TT
1 TT
10389 TTAAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:10721 original size:29 final size:29
Alignment explanation
Indices: 10666--10720 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
10656 GGGAGAGTGC
* *
10666 ATTATTTTGATAAATAATTATTATTTTGT
1 ATTATTTGGATAAATAAATATTATTTTGT
*
10695 ATTATTTGGATAAA-AAATCTTATTTT
1 ATTATTTGGATAAATAAATATTATTTT
10721 TATCATCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (29 bp):
ATTATTTGGATAAATAAATATTATTTTGT
Found at i:16301 original size:36 final size:35
Alignment explanation
Indices: 16253--16323 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
16243 TCCCCCTGAG
*
16253 CAGTAGCTTCCCCTTGATCAATGGTGTTTTTTGGAA
1 CAGTAGCTTCCCCTTGAACAATGGTG-TTTTTGGAA
16289 CAGTAG-TCTCCCCTTGAACAATGGTGTTTTTGGAA
1 CAGTAGCT-TCCCCTTGAACAATGGTGTTTTTGGAA
16324 TAAGGTTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 10 0.30
36 23 0.70
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (35 bp):
CAGTAGCTTCCCCTTGAACAATGGTGTTTTTGGAA
Found at i:16359 original size:30 final size:30
Alignment explanation
Indices: 16323--16381 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
16313 TGTTTTTGGA
16323 ATAAGGTTTTCAATAGTTATTGAGTCAGGG
1 ATAAGGTTTTCAATAGTTATTGAGTCAGGG
16353 ATAAGGTTTTCAATAGTTATTGAGTCAGG
1 ATAAGGTTTTCAATAGTTATTGAGTCAGG
16382 TATCATTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.37
Consensus pattern (30 bp):
ATAAGGTTTTCAATAGTTATTGAGTCAGGG
Found at i:38936 original size:33 final size:33
Alignment explanation
Indices: 38894--38960 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
38884 GTGTGCGTTG
38894 TCAAAGGATTAAGAAAGTATGAACATATACTAC
1 TCAAAGGATTAAGAAAGTATGAACATATACTAC
38927 TCAAAGGATTAAGAAAGTATGAACATATACTAC
1 TCAAAGGATTAAGAAAGTATGAACATATACTAC
38960 T
1 T
38961 ATGTAATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (33 bp):
TCAAAGGATTAAGAAAGTATGAACATATACTAC
Found at i:49500 original size:30 final size:28
Alignment explanation
Indices: 49465--49715 Score: 154
Period size: 29 Copynumber: 8.5 Consensus size: 28
49455 AAATGGTAAT
*
49465 TTTTTGGAAGTATCGGGGTCAAAAATGAGA
1 TTTTTGGAAGTTTCGGGGT--AAAATGAGA
**
49495 TTTTTGGAAGTTTAAGGGTAAAATG-GTA
1 TTTTTGGAAGTTTCGGGGTAAAATGAG-A
* *
49523 TTTTTTAGAAGTTTTGGGGTCAAAAAAT-AGA
1 -TTTTTGGAAGTTTCGGGGT---AAAATGAGA
* *
49554 TTTTTTAGAAGTTTGGGGGTAAAATG-GTAA
1 -TTTTTGGAAGTTTCGGGGTAAAATGAG--A
*
49584 TTTTTGGAAGTTTCGAGGTCAAAAATGAGA
1 TTTTTGGAAGTTTCGGGGT--AAAATGAGA
* *
49614 TTTTTAGAAG-TTCATGGGTAAAATG-GTAA
1 TTTTTGGAAGTTTC-GGGGTAAAATGAG--A
* *
49643 TTTTTGGAAGTTTTGGGGTCAAAAATGGGA
1 TTTTTGGAAGTTTCGGGGT--AAAATGAGA
* *
49673 TTTTTAGAAG-TTCGAGGGTAAAATGATAA
1 TTTTTGGAAGTTTCG-GGGTAAAATGA-GA
49702 TTTTTGGACAGTTT
1 TTTTTGGA-AGTTT
49716 AGGGACCTTC
Statistics
Matches: 177, Mismatches: 21, Indels: 45
0.73 0.09 0.19
Matches are distributed among these distances:
27 2 0.01
28 25 0.14
29 60 0.34
30 48 0.27
31 34 0.19
32 8 0.05
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (28 bp):
TTTTTGGAAGTTTCGGGGTAAAATGAGA
Found at i:49549 original size:60 final size:59
Alignment explanation
Indices: 49452--49715 Score: 350
Period size: 59 Copynumber: 4.4 Consensus size: 59
49442 ACCTCCAGGA
* * *
49452 GTAAAATGGTAATTTTTTGGAAGTATCGGGGTCAAAAATGAGATTTTTGGAAGTTTAAGG
1 GTAAAATGGTAA-TTTTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTAGAAGTTCAAGG
* * * ***
49512 GTAAAATGGTATTTTTTAGAAGTTTTGGGGTCAAAAAAT-AGATTTTTTAGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTC-AAAAATGAGA-TTTTTAGAAGTTCAAGG
* *
49572 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAAGTTCATGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTAGAAGTTCAAGG
* * *
49631 GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTAGAAGTTCAAGG
*
49690 GTAAAATGATAATTTTTGGACAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
49716 AGGGACCTTC
Statistics
Matches: 180, Mismatches: 20, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
59 113 0.63
60 67 0.37
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTAGAAGTTCAAGG
Found at i:49605 original size:119 final size:118
Alignment explanation
Indices: 49452--49715 Score: 386
Period size: 119 Copynumber: 2.2 Consensus size: 118
49442 ACCTCCAGGA
* * * *
49452 GTAAAATGGTAATTTTTTGGAAGTATCGGGGTCAAAAATGAGATTTTTGGAAGTTTAAGGGTAAA
1 GTAAAATGGTAA-TTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAAGTTCAAGGGTAAA
* * *
49517 ATGGTATTTTTTAGAAGTTTTGGGGTCAAAAAAT-AGATTTTTTAGAAGTTTGGGG
65 ATGGTAATTTTTAGAAGTTTTGGGGTC-AAAAATGAGA-TTTTTAGAAGTTCGAGG
*
49572 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAAGTTCATGGGTAAAA
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAAGTTCAAGGGTAAAA
* *
49637 TGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTCGAGG
66 TGGTAATTTTTAGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTCGAGG
*
49690 GTAAAATGATAATTTTTGGACAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
49716 AGGGACCTTC
Statistics
Matches: 131, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
118 40 0.31
119 79 0.60
120 12 0.09
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (118 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAAGTTCAAGGGTAAAA
TGGTAATTTTTAGAAGTTTTGGGGTCAAAAATGAGATTTTTAGAAGTTCGAGG
Found at i:52933 original size:2 final size:2
Alignment explanation
Indices: 52921--52957 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
52911 GCCAGTACTT
*
52921 TA TA TA CA TA 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 TA TA T
52958 TACAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:60250 original size:5 final size:5
Alignment explanation
Indices: 60240--60264 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
60230 CAACAGCATG
60240 TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA
60265 GTCAAGTCAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:70726 original size:14 final size:14
Alignment explanation
Indices: 70689--70729 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
70679 TTTTACATAA
70689 ATAATA-AAAAAAT
1 ATAATACAAAAAAT
70702 -T-ATACATAAAAAT
1 ATAATACA-AAAAAT
70715 ATAATACAAAAAAT
1 ATAATACAAAAAAT
70729 A
1 A
70730 AAATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.12
12 2 0.08
13 6 0.25
14 8 0.33
15 5 0.21
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAATACAAAAAAT
Found at i:71108 original size:27 final size:27
Alignment explanation
Indices: 71048--71113 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
71038 AATTTGACAG
*
71048 GTGGTGCCTTTGGGATAGGTGGCACCA
1 GTGGTGCCTTTGGGATAGGCGGCACCA
* * *
71075 ATAGTGCCTATTGGG-TAGGCGGCACTA
1 GTGGTGCCT-TTGGGATAGGCGGCACCA
71102 GTGGTGCCTTTG
1 GTGGTGCCTTTG
71114 TCAAAACTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 3 0.09
27 24 0.75
28 5 0.16
ACGTcount: A:0.15, C:0.18, G:0.38, T:0.29
Consensus pattern (27 bp):
GTGGTGCCTTTGGGATAGGCGGCACCA
Found at i:74055 original size:28 final size:28
Alignment explanation
Indices: 74002--74059 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
73992 CATTTTTCAA
*
74002 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATAATTGAAT
**
74030 TTGGAATTAATTCTGTTTA-AATTTGAAT
1 TTGGAATTAATTAAGTTTATAA-TTGAAT
74058 TT
1 TT
74060 ATTTAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATAATTGAAT
Found at i:74192 original size:6 final size:6
Alignment explanation
Indices: 74168--74206 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
74158 ATTTGCATAT
*
74168 ATAAAC ATAAAT A-AGAAC ATAAAC ATAAAC ATAAAC ATA
1 ATAAAC ATAAAC ATA-AAC ATAAAC ATAAAC ATAAAC ATA
74207 TTTAATTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.03
6 27 0.93
7 1 0.03
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAC
Done.