Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014280.1 Kokia drynarioides strain JFW-HI SEQ_129313, 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: 37022
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 260 characters in sequence are not A, C, G, or T
Found at i:661 original size:66 final size:66
Alignment explanation
Indices: 527--662 Score: 164
Period size: 66 Copynumber: 2.1 Consensus size: 66
517 ATCGCGGCTG
* * * * *
527 AAATTATTCGGGTTCGCTAACATAAGATCATGACCTATGTAGCTCGCCGACCTAAAATCATAATC
1 AAATTATTCGGGTTCACTAACATAAGATCACGACCTATGTAGCTCGCCGAACTAAAATCACAACC
592 A
66 A
** * * * * *
593 AAATTATTCGGGTTCACTTGCATAAGATCGCGACCTATGTGGCTCGCCGAACTAAGATCGCAGCC
1 AAATTATTCGGGTTCACTAACATAAGATCACGACCTATGTAGCTCGCCGAACTAAAATCACAACC
658 A
66 A
659 AAAT
1 AAAT
663 CTCGTTGCTA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (66 bp):
AAATTATTCGGGTTCACTAACATAAGATCACGACCTATGTAGCTCGCCGAACTAAAATCACAACC
A
Found at i:3600 original size:16 final size:16
Alignment explanation
Indices: 3558--3622 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
3548 TTAGGGGTCG
*
3558 AAATTAAATTTTTA-T
1 AAATTAAAATTTTATT
* *
3573 ATATTTATAATTTTATT
1 A-AATTAAAATTTTATT
3590 AAATTAAAATTTTAATT
1 AAATTAAAATTTT-ATT
* *
3607 AAAATATAATTTTATT
1 AAATTAAAATTTTATT
3623 TTTATTAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.03
16 23 0.57
17 16 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTAAAATTTTATT
Found at i:3605 original size:22 final size:22
Alignment explanation
Indices: 3575--3641 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 22
3565 ATTTTTATAT
3575 ATTTATAATTTTATTAAATTAAA
1 ATTT-TAATTTTATTAAATTAAA
*
3598 ATTTTAA--TTA--AAA-TATA
1 ATTTTAATTTTATTAAATTAAA
*
3615 ATTTTATTTTTATT-AATTAAA
1 ATTTTAATTTTATTAAATTAAA
3636 ACTTTT
1 A-TTTT
3642 TAAAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
17 9 0.26
18 3 0.09
19 3 0.09
20 5 0.14
21 4 0.11
22 7 0.20
23 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTAATTTTATTAAATTAAA
Found at i:4762 original size:38 final size:38
Alignment explanation
Indices: 4716--4792 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
4706 CACAAAGCAA
4716 GAGATTTTTTAATTTTATTTTTGATATGTTATGAGTTT
1 GAGATTTTTTAATTTTATTTTTGATATGTTATGAGTTT
4754 GAGATTTTTTAATTTTATTTTTGATATGTTATGAGTTT
1 GAGATTTTTTAATTTTATTTTTGATATGTTATGAGTTT
4792 G
1 G
4793 GGTGAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (38 bp):
GAGATTTTTTAATTTTATTTTTGATATGTTATGAGTTT
Found at i:10695 original size:30 final size:27
Alignment explanation
Indices: 10624--10699 Score: 73
Period size: 30 Copynumber: 2.7 Consensus size: 27
10614 ACAAAAAGGT
*
10624 TTTATTT-TATTTTATTTTAAAATATA
1 TTTATTTATATTTAATTTTAAAATATA
* *
10650 TTTTTATTAGGATTTAATATTTAAAGATATTA
1 TTTAT-TTA-TATTTAAT-TTTAAA-ATA-TA
10682 TTTATTTATATTTAATTT
1 TTTATTTATATTTAATTT
10700 ATGTTTATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
26 4 0.10
27 2 0.05
29 8 0.21
30 13 0.33
31 6 0.15
32 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTATTTATATTTAATTTTAAAATATA
Found at i:12882 original size:3 final size:3
Alignment explanation
Indices: 12869--12901 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12859 TACAGGAAAA
*
12869 ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
12902 CAATTTGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:15550 original size:13 final size:13
Alignment explanation
Indices: 15532--15557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15522 TGCTACTCTC
15532 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
15545 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
15558 AGAACCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTCTTTTTCTTT
Found at i:18880 original size:23 final size:24
Alignment explanation
Indices: 18853--18897 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
18843 ATATTGCTAA
18853 TAAATTTTA-AAATAAAATCAAAT
1 TAAATTTTATAAATAAAATCAAAT
*
18876 TAAATTTTATATATAAAATCAA
1 TAAATTTTATAAATAAAATCAA
18898 GCCTCAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAATTTTATAAATAAAATCAAAT
Found at i:18951 original size:22 final size:22
Alignment explanation
Indices: 18920--18966 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 22
18910 ATATTTCATA
18920 TTAAATTAAAAT-TTATTTATTTT
1 TTAAATTAAAATATTA--TATTTT
18943 TTAAA-TAAAATATTATATTTT
1 TTAAATTAAAATATTATATTTT
18964 TTA
1 TTA
18967 TGAAGTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.39
22 6 0.26
23 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAATTAAAATATTATATTTT
Found at i:29246 original size:21 final size:22
Alignment explanation
Indices: 29209--29256 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
29199 AGATTTATCT
* *
29209 ATTTTTATTATATTC-AAATA-
1 ATTTTTATTAAAATCAAAATAG
29229 ATTTTTATTTAAAATCAAAATAG
1 ATTTTTA-TTAAAATCAAAATAG
29252 ATTTT
1 ATTTT
29257 GAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 5 0.22
23 5 0.22
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTTTATTAAAATCAAAATAG
Found at i:32859 original size:20 final size:19
Alignment explanation
Indices: 32836--32888 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
32826 AAAAAAGTGC
32836 AAAAATACAAAAAAATATGA
1 AAAAATACAAAAAAATAT-A
* *
32856 AAAATTACAAGAAAATATA
1 AAAAATACAAAAAAATATA
*
32875 ATAAAATATAAAAA
1 A-AAAATACAAAAA
32889 TATACGTACA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (19 bp):
AAAAATACAAAAAAATATA
Found at i:33372 original size:10 final size:10
Alignment explanation
Indices: 33310--33381 Score: 67
Period size: 10 Copynumber: 7.2 Consensus size: 10
33300 CACTTTCAAA
33310 TTTTTATAA-
1 TTTTTATAAT
33319 TTTTTATATAT
1 TTTTTATA-AT
* *
33330 TGTTTATGAT
1 TTTTTATAAT
33340 TTTCTT-TAAT
1 TTT-TTATAAT
**
33350 TTTTTATGCT
1 TTTTTATAAT
33360 TTTTTATAAT
1 TTTTTATAAT
*
33370 TTTTAATAAT
1 TTTTTATAAT
33380 TT
1 TT
33382 AAAATATAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
9 10 0.20
10 32 0.64
11 8 0.16
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:33380 original size:30 final size:29
Alignment explanation
Indices: 33308--33381 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
33298 TGCACTTTCA
33308 AATTTTTATAATTTTTATATATTGTTTAT
1 AATTTTTATAATTTTTATATATTGTTTAT
* * * *
33337 GATTTTCTTTAATTTTT-TATGCTTTTTTAT
1 AATTTT-TATAATTTTTATAT-ATTGTTTAT
33367 AATTTTTAATAATTT
1 AATTTTT-ATAATTT
33382 AAAATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 9 0.25
30 27 0.75
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (29 bp):
AATTTTTATAATTTTTATATATTGTTTAT
Found at i:36171 original size:25 final size:24
Alignment explanation
Indices: 36095--36163 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 24
36085 AACAAAAACG
*
36095 CATAAGTGCTGGAGAAACAGAAGCA
1 CATAAGTGCTGG-GAAACATAAGCA
36120 CATAAGTGCTGGGGAAACATAAGCA
1 CATAAGTGCT-GGGAAACATAAGCA
36145 CATAAGTGCTGGGAAACAT
1 CATAAGTGCTGGGAAACAT
36164 TAGGCACAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 9 0.21
25 31 0.74
26 2 0.05
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.16
Consensus pattern (24 bp):
CATAAGTGCTGGGAAACATAAGCA
Found at i:36205 original size:22 final size:22
Alignment explanation
Indices: 36178--36301 Score: 178
Period size: 22 Copynumber: 5.7 Consensus size: 22
36168 CACAGACAGT
36178 GTGCTGAACAGAAGCACACACA
1 GTGCTGAACAGAAGCACACACA
* * * *
36200 ATGCTGAACAAAATCGCACACA
1 GTGCTGAACAGAAGCACACACA
*
36222 GTGCTAAACAGAAGCACACACA
1 GTGCTGAACAGAAGCACACACA
*
36244 GTGCTGAATAGAAG-ACACACA
1 GTGCTGAACAGAAGCACACACA
*
36265 GTGCTGAACAGAAGCACACAAA
1 GTGCTGAACAGAAGCACACACA
36287 GTGCTGAACAGAAGC
1 GTGCTGAACAGAAGC
36302 GCGCTAGCGT
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
21 20 0.23
22 68 0.77
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (22 bp):
GTGCTGAACAGAAGCACACACA
Found at i:36271 original size:65 final size:66
Alignment explanation
Indices: 36178--36301 Score: 178
Period size: 65 Copynumber: 1.9 Consensus size: 66
36168 CACAGACAGT
* * *
36178 GTGCTGAACAGAAGCACACACAATGCTGAACAAAATCGCACACAGTGCTAAACAGAAGCACACAC
1 GTGCTGAACAGAAGCACACACAATGCTGAACAAAAGCACACAAAGTGCTAAACAGAAGCACACAC
36243 A
66 A
* * * *
36244 GTGCTGAATAGAAG-ACACACAGTGCTGAACAGAAGCACACAAAGTGCTGAACAGAAGC
1 GTGCTGAACAGAAGCACACACAATGCTGAACAAAAGCACACAAAGTGCTAAACAGAAGC
36302 GCGCTAGCGT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
65 38 0.75
66 13 0.25
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (66 bp):
GTGCTGAACAGAAGCACACACAATGCTGAACAAAAGCACACAAAGTGCTAAACAGAAGCACACAC
A
Found at i:36277 original size:43 final size:42
Alignment explanation
Indices: 36178--36301 Score: 176
Period size: 43 Copynumber: 2.9 Consensus size: 42
36168 CACAGACAGT
* *
36178 GTGCTGAACAGAAGCACACACAATGCTGAACAAAATCGCACACA
1 GTGCTGAACAGAAGCACACACAGTGCTGAACAGAA--GCACACA
* *
36222 GTGCTAAACAGAAGCACACACAGTGCTGAATAGAAGACACACA
1 GTGCTGAACAGAAGCACACACAGTGCTGAACAGAAG-CACACA
*
36265 GTGCTGAACAGAAGCACACAAAGTGCTGAACAGAAGC
1 GTGCTGAACAGAAGCACACACAGTGCTGAACAGAAGC
36302 GCGCTAGCGT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 2 0.03
43 39 0.54
44 31 0.43
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (42 bp):
GTGCTGAACAGAAGCACACACAGTGCTGAACAGAAGCACACA
Found at i:36509 original size:21 final size:21
Alignment explanation
Indices: 36485--36525 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36475 TGTCACCAAT
*
36485 TAATTACACA-ATCAATATTTA
1 TAATTAAACACAT-AATATTTA
36506 TAATTAAACACATAATATTT
1 TAATTAAACACATAATATTT
36526 CACATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAACACATAATATTTA
Done.