Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004392.1 Kokia drynarioides strain JFW-HI SEQ_117768, 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: 60205
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:147 original size:78 final size:77
Alignment explanation
Indices: 1--336 Score: 350
Period size: 78 Copynumber: 4.3 Consensus size: 77
* * * * * * * * * * *
1 TGCCTCAAGCTCGGGGTAAAAGATCGGATGGTTGTAATTTGCCCTAGGCTC-AGGGTAAGAGATT
1 TGCC-CAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGA-GGTAAAAGATC
*
65 GGATGACTGCAATC
64 GGATGACTGTAATC
* * *
79 TGTCTCGAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGAGCTAAAAGATCG
1 TG-CCCAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
*
144 GATGGCTGTAATC
65 GATGACTGTAATC
* * * *
157 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTACCCCAGGCTCGTGGTAAAAGATCG
1 TG-CCCAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
*
222 GATGGCTGTAATC
65 GATGACTGTAATC
* *
235 TGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCG
1 TG-CCCAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
* * *
300 GATGATTGTGATA
65 GATGACTGTAATC
* * *
313 TGCCCCATGATTGGGGTAAGAGAT
1 TG-CCCAAGCTCGGGGTAAGAGAT
337 CGGAATCTTC
Statistics
Matches: 220, Mismatches: 36, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
78 218 0.99
79 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (77 bp):
TGCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGG
ATGACTGTAATC
Found at i:337 original size:39 final size:39
Alignment explanation
Indices: 1--340 Score: 281
Period size: 39 Copynumber: 8.7 Consensus size: 39
* * * * * *
1 TGCCTCAAGCTCGGGGTAAAAGATCGGATGGTTGTAATT
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGATGGTGATC
* * * * **
40 TGCCCTAGGCTCAGGGTAAGAGATTGGATGACT-GCAATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGA-TGGTGATC
* * * * *
79 TGTCTCGAGCTCGGGGTAAGAGATTGGTTGATGGTGATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGATGGTGATC
* * * * *
118 TGCCCCAAGCTCGAGCTAAAAGATCGGATGGCT-GTAATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGAT-GATGGTGATC
* * *
157 TGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGATGGTGATC
* * * * * *
196 TACCCCAGGCTCGTGGTAAAAGATCGGATGGCT-GTAATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGAT-GATGGTGATC
* *
235 TGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGATGGTGATC
* * *
274 TGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTGATA
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGATGGTGATC
* * *
313 TGCCCCATGATTGGGGTAAGAGATCGGA
1 TGCCCCAAGCTCGGGGTAAGAGATCGGA
341 ATCTTCAATC
Statistics
Matches: 235, Mismatches: 60, Indels: 12
0.77 0.20 0.04
Matches are distributed among these distances:
38 5 0.02
39 225 0.96
40 5 0.02
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (39 bp):
TGCCCCAAGCTCGGGGTAAGAGATCGGATGATGGTGATC
Found at i:12080 original size:18 final size:19
Alignment explanation
Indices: 12052--12094 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
12042 AGAATCCGAA
12052 TAAAAAAAAA-GAT-TAAT
1 TAAAAAAAAAGGATATAAT
12069 TAAAAAACAAAGGATAATAAT
1 TAAAAAA-AAAGGAT-ATAAT
12090 TAAAA
1 TAAAA
12095 TTTATATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
18 3 0.14
19 3 0.14
21 9 0.41
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (19 bp):
TAAAAAAAAAGGATATAAT
Found at i:12203 original size:29 final size:29
Alignment explanation
Indices: 12163--12472 Score: 194
Period size: 30 Copynumber: 10.4 Consensus size: 29
12153 ATTCGAGGTT
*
12163 AAAATGTAATTTTATAAAAG-TTAGGGGTA
1 AAAATGTAATTTTAGAAAAGTTTA-GGGTA
* *
12192 AAAATGTAATTTTAGAGAAGTTTAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGGTA
* * * * *
12221 AAAATGTAATTTTGGAAAATTTTTGAGATC
1 AAAATGTAATTTTAGAAAAGTTTAG-GGTA
* * *
12251 AAAATGCT-ATTTTGGAAAAGTTCAAGGGTT
1 AAAATG-TAATTTTAGAAAAGTT-TAGGGTA
* *
12281 AAAATGTAATTTTAGAAATGTTTGGGTGTAA
1 AAAATGTAATTTTAGAAAAGTTTAGG-GT-A
* * * * *
12312 AAAATGTGATTTTGGGAAAGTTAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGTA
** * * *
12341 AAAATGTGGTTTTAGGAAAGTTTAAGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGTA
* *
12370 AAAATGTAATTTTGGATAAGTTTGAGGGT-
1 AAAATGTAATTTTAGAAAAGTTT-AGGGTA
* * * * *
12399 TAGATCGTAATGTTAGAAAAATTTAGGGGTT
1 AAAAT-GTAATTTTAGAAAAGTTTA-GGGTA
* * * * *
12430 AAAATGTATTTTTTGTAGAGTTTAGGGGTT
1 AAAATGTAATTTTAGAAAAGTTTA-GGGTA
12460 AAAATGTAATTTT
1 AAAATGTAATTTT
12473 TACAAAGTTC
Statistics
Matches: 220, Mismatches: 50, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
29 93 0.42
30 102 0.46
31 25 0.11
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGTA
Found at i:12255 original size:30 final size:29
Alignment explanation
Indices: 12163--12392 Score: 126
Period size: 29 Copynumber: 7.8 Consensus size: 29
12153 ATTCGAGGTT
** * *
12163 AAAATGTAATTTTATAAAAG-TTAGGGGTA
1 AAAATGTAATTTTGGAAAAGTTTA-GGATC
* * *
12192 AAAATGTAATTTTAGAGAAGTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGATC
* *
12221 AAAATGTAATTTTGGAAAATTTTTGAGATC
1 AAAATGTAATTTTGGAAAAGTTTAG-GATC
* * *
12251 AAAATGCT-ATTTTGGAAAAGTTCAAGGGTT
1 AAAATG-TAATTTTGGAAAAGTT-TAGGATC
* * * * *
12281 AAAATGTAATTTTAGAAATGTTTGGGTGTAA
1 AAAATGTAATTTTGGAAAAGTTTAGG-AT-C
* * * * *
12312 AAAATGTGATTTTGGGAAAGTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGATC
** *
12341 AAAATGTGGTTTTAGG-AAAGTTTAAGG-TT
1 AAAATGTAATTTT-GGAAAAGTTT-AGGATC
*
12370 AAAATGTAATTTTGGATAAGTTT
1 AAAATGTAATTTTGGAAAAGTTT
12393 GAGGGTTAGA
Statistics
Matches: 161, Mismatches: 30, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 83 0.52
30 54 0.34
31 22 0.14
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGATC
Found at i:12820 original size:162 final size:164
Alignment explanation
Indices: 12534--12834 Score: 378
Period size: 162 Copynumber: 1.8 Consensus size: 164
12524 AAGCAGTAAA
* * *
12534 CCCAAAAAAGAGTGACACGTGGTAGCTTCTCAGGCTTTCAAAAGTGAGTGGACCAAATTGAAAAA
1 CCCAAAAAAGAGTGACACGTGGTAGCTTCTCAAGCTTTCAAAAGTCAGGGGACCAAATTGAAAAA
* ** * **
12599 TAATTAAAATTACCAAACAAATTTGGAATAAAATAAAAGGTGATTTAAGGATGAAATTGAAACAA
66 TAATTAAAATTACCAAACAAAATTAAAATAAAATAAAAGATGATTTAAGGACCAAATTGAAACAA
12664 ATGAAAAATGGAAAGGATTAATCACAGAAATAAC
131 ATGAAAAATGGAAAGGATTAATCACAGAAATAAC
*
12698 CCCAAAAAAG-G-GACACGTGGTAGCTTCTCAAGCTTTCAGAAAGTCAGGGGACTAAATTGAAAA
1 CCCAAAAAAGAGTGACACGTGGTAGCTTCTCAAGCTTTCA-AAAGTCAGGGGACCAAATTGAAAA
****** * *
12761 GA-AATTAAAATTGTTGGGCAAAATTAAAATTAATTAAAA-AT-ATGTTAAGGACCAAATTGAAA
65 -ATAATTAAAATTACCAAACAAAATTAAAATAAAATAAAAGATGAT-TTAAGGACCAAATTGAAA
12823 CAAATGAAAAAT
128 CAAATGAAAAAT
12835 ACGGAAGGAC
Statistics
Matches: 116, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
161 2 0.02
162 55 0.47
163 48 0.41
164 11 0.09
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.23
Consensus pattern (164 bp):
CCCAAAAAAGAGTGACACGTGGTAGCTTCTCAAGCTTTCAAAAGTCAGGGGACCAAATTGAAAAA
TAATTAAAATTACCAAACAAAATTAAAATAAAATAAAAGATGATTTAAGGACCAAATTGAAACAA
ATGAAAAATGGAAAGGATTAATCACAGAAATAAC
Found at i:13975 original size:6 final size:6
Alignment explanation
Indices: 13942--13989 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
13932 GGGACATTAA
* *
13942 TAAATT TAAACT TAAATTT TAAA-- AAAATT TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT
13989 T
1 T
13990 TGTTTGGGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 3 0.09
6 27 0.77
7 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:16199 original size:51 final size:51
Alignment explanation
Indices: 16089--16375 Score: 360
Period size: 51 Copynumber: 5.6 Consensus size: 51
16079 TCATTTAATG
* * ** * *
16089 CTCACAATGACA-TATAGTCATCGGATCTCTTGTTCCATATAGGAATTCATATA
1 CTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATTTA
** * * * *
16142 CTCACGATGACACAAAGTCATCGAACCCTTAATCCATCATGGATTCATTTA
1 CTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTA
16193 CTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTA
1 CTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTA
16244 CTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTA
1 CTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTA
* * *** * *
16295 CTGATGATGACACTTAGTCATCGGACCTTTAATTTGTAAATGATTCATTTC
1 CTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTA
*
16346 CTCACGATGACACTTAGTCATCGGGCCTTT
1 CTCACGATGACACTTAGTCATCGGACCTTT
16376 TCGTTTATAG
Statistics
Matches: 205, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
51 175 0.85
52 9 0.04
53 21 0.10
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
CTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTA
Found at i:19618 original size:20 final size:18
Alignment explanation
Indices: 19571--19677 Score: 69
Period size: 19 Copynumber: 5.8 Consensus size: 18
19561 CAAGATAAAC
19571 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
19588 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
* *
19608 ATTAAATTAATAAATTACT
1 ATTAAATTAAT-ATTTAAT
*
19627 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
19644 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
* *
19664 ACTAAAATAATATT
1 ATTAAATTAATATT
19678 ATTTTTGGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
17 16 0.23
18 10 0.14
19 23 0.32
20 22 0.31
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:19789 original size:19 final size:20
Alignment explanation
Indices: 19765--19803 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19755 TATCATATTA
*
19765 ATTTGATT-AATTTAAATTT
1 ATTTGATTAAAATTAAATTT
19784 ATTTGATTAAAATTAAATTT
1 ATTTGATTAAAATTAAATTT
19804 CCAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTGATTAAAATTAAATTT
Found at i:26427 original size:21 final size:22
Alignment explanation
Indices: 26402--26474 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 22
26392 TGTGATAGTT
*
26402 CTACTGATACAAGT-ATGACTA
1 CTACTGATACAAGTCATCACTA
* *
26423 CTACTGAAACAA-TCATCACTT
1 CTACTGATACAAGTCATCACTA
* ** *
26444 CTACCGATACAAGTGTTCA-GA
1 CTACTGATACAAGTCATCACTA
26465 CTACTGATAC
1 CTACTGATAC
26475 TACTATGCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 35 0.88
22 4 0.10
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
CTACTGATACAAGTCATCACTA
Found at i:34907 original size:15 final size:16
Alignment explanation
Indices: 34889--34918 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34879 CTAGACCAAC
34889 CCCT-TTTGTTTTATA
1 CCCTATTTGTTTTATA
34904 CCCTATTTGTTTTAT
1 CCCTATTTGTTTTAT
34919 TTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.60
Consensus pattern (16 bp):
CCCTATTTGTTTTATA
Found at i:37350 original size:40 final size:39
Alignment explanation
Indices: 37295--37404 Score: 166
Period size: 40 Copynumber: 2.8 Consensus size: 39
37285 TTACAATATA
*
37295 ATTCAAGTTACGGCTTAGCAGGCTATGAGTTGGTGTTAAG
1 ATTCAAG-TACGGCTTAGCAGGCTATGAGTCGGTGTTAAG
* *
37335 ATTCAAGCTACGGCTTAGTAGGCTATGAGCCGGTGTTAAG
1 ATTCAAG-TACGGCTTAGCAGGCTATGAGTCGGTGTTAAG
*
37375 ATTCAAGTACGACTTAGCAGGCTATGAGTC
1 ATTCAAGTACGGCTTAGCAGGCTATGAGTC
37405 TGTAAATTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 20 0.32
40 43 0.68
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (39 bp):
ATTCAAGTACGGCTTAGCAGGCTATGAGTCGGTGTTAAG
Found at i:46080 original size:39 final size:39
Alignment explanation
Indices: 46037--46114 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
46027 TGTTCACTCA
46037 ATACAATCTTATTTTATCTTATTGTCACCATTGTGTCTT
1 ATACAATCTTATTTTATCTTATTGTCACCATTGTGTCTT
46076 ATACAATCTTATTTTATCTTATTGTCACCATTGTGTCTT
1 ATACAATCTTATTTTATCTTATTGTCACCATTGTGTCTT
46115 CTTAATGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (39 bp):
ATACAATCTTATTTTATCTTATTGTCACCATTGTGTCTT
Found at i:50300 original size:23 final size:24
Alignment explanation
Indices: 50274--50329 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
50264 AAGCAAAATC
*
50274 CTTAATGTATG-ATTTAACCATGA
1 CTTAATGTATGAATTTAACCATAA
50297 CTTAATG-A-GAAATTTAACCATAA
1 CTTAATGTATG-AATTTAACCATAA
50320 CTTAAT-TATG
1 CTTAATGTATG
50330 TTGGTGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 1 0.04
23 25 0.89
24 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (24 bp):
CTTAATGTATGAATTTAACCATAA
Found at i:55724 original size:8 final size:8
Alignment explanation
Indices: 55711--55742 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
55701 AGCTTTATTT
55711 ATTAGTTA
1 ATTAGTTA
55719 ATTAGTTA
1 ATTAGTTA
55727 ATTAGTTA
1 ATTAGTTA
55735 ATTAGTTA
1 ATTAGTTA
55743 TTTGATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
ATTAGTTA
Found at i:59604 original size:16 final size:15
Alignment explanation
Indices: 59583--59629 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
59573 TACATTTATG
59583 TTTATTTCTTTTTTA
1 TTTATTTCTTTTTTA
59598 CTTTATTTCTTCTTTTA
1 -TTTATTTCTT-TTTTA
* *
59615 TCTATTTTTTTTTTA
1 TTTATTTCTTTTTTA
59630 GATTCTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTCTTTTTTA
Done.