Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014445.1 Kokia drynarioides strain JFW-HI SEQ_129484, 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: 47119
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8247 original size:11 final size:10
Alignment explanation
Indices: 8204--8251 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
8194 TAAGGGAGAG
8204 AAGAGAAGAA
1 AAGAGAAGAA
*
8214 ATG-GAAGAA
1 AAGAGAAGAA
8223 AAGAGAAGAA
1 AAGAGAAGAA
*
8233 AAGAGGAGAAA
1 AAGAGAAG-AA
8244 AAGAGAAG
1 AAGAGAAG
8252 GGAAGCCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 8 0.25
10 15 0.47
11 9 0.28
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (10 bp):
AAGAGAAGAA
Found at i:8247 original size:21 final size:19
Alignment explanation
Indices: 8204--8251 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
8194 TAAGGGAGAG
*
8204 AAGAGAAGAAATGGAAGAA
1 AAGAGAAGAAAAGGAAGAA
*
8223 AAGAGAAGAAAAGAGGAGAAA
1 AAGAGAAGAAAAG-GAAG-AA
8244 AAGAGAAG
1 AAGAGAAG
8252 GGAAGCCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.48
20 3 0.12
21 10 0.40
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (19 bp):
AAGAGAAGAAAAGGAAGAA
Found at i:13942 original size:286 final size:286
Alignment explanation
Indices: 13425--13991 Score: 1008
Period size: 286 Copynumber: 2.0 Consensus size: 286
13415 GAGCTTAAGT
*
13425 CCATGTGTTGTGCTTGTGCTATTGGTACCTAAGAAGGATGGCTCTTAGCACTTATGCATTGACTA
1 CCATGTGTTGTGCTTGTGCTATTGGTACCTAAGAAGGATGGCTCTTAGCACATATGCATTGACTA
* *
13490 TTGCGCGGTCAATAAGATTACCATCAAGTATCGACGCTCGATCCCACCTTTAGATGATATGCTGG
66 TCGCGCGGTCAATAAGATTACCATCAAGTATCGACGCCCGATCCCACCTTTAGATGATATGCTGG
13555 ACGAGCTAAGTGGAGCTCGCATTTTCTCCAAAGTTGATCTCAAGAGTGGTTATCATCAAATACGA
131 ACGAGCTAAGTGGAGCTCGCATTTTCTCCAAAGTTGATCTCAAGAGTGGTTATCATCAAATACGA
13620 ATGAGAGAAGGAGTCGAATGGAAGATTGCATCCAAAACCAAAAATGGTTTGTATGAGTGGTTGGT
196 ATGAGAGAAGGAGTCGAATGGAAGATTGCATCCAAAACCAAAAATGGTTTGTATGAGTGGTTGGT
13685 TATGCCCTTTGGCCTAACTAATGCAC
261 TATGCCCTTTGGCCTAACTAATGCAC
* * * *
13711 CCATGTGTTGTGCTTGTGCTATTGGTACCTAAGAAGGATGGCTCTTGGCGCATGTGCATTGACTG
1 CCATGTGTTGTGCTTGTGCTATTGGTACCTAAGAAGGATGGCTCTTAGCACATATGCATTGACTA
* * *
13776 TCGCGCTGTCAATAAGATTACCATCAAGTATCGATGCCCGATCCCACCTTTAGATGATATGTTGG
66 TCGCGCGGTCAATAAGATTACCATCAAGTATCGACGCCCGATCCCACCTTTAGATGATATGCTGG
* *
13841 ACGAGCTAAGTGGAGCTCGCATTTTCTCCAAAGTTGATCTCAATAGTGGTTATCATCAAATATGA
131 ACGAGCTAAGTGGAGCTCGCATTTTCTCCAAAGTTGATCTCAAGAGTGGTTATCATCAAATACGA
* *
13906 ATGAGAGAAGGAGTCGAATGGAAGATTGCTTCCAAAACCAAACATGGTTTGTATGAGTGGTTGGT
196 ATGAGAGAAGGAGTCGAATGGAAGATTGCATCCAAAACCAAAAATGGTTTGTATGAGTGGTTGGT
13971 TATGCCCTTTGGCCTAACTAA
261 TATGCCCTTTGGCCTAACTAA
13992 CGCATCCAGC
Statistics
Matches: 267, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
286 267 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (286 bp):
CCATGTGTTGTGCTTGTGCTATTGGTACCTAAGAAGGATGGCTCTTAGCACATATGCATTGACTA
TCGCGCGGTCAATAAGATTACCATCAAGTATCGACGCCCGATCCCACCTTTAGATGATATGCTGG
ACGAGCTAAGTGGAGCTCGCATTTTCTCCAAAGTTGATCTCAAGAGTGGTTATCATCAAATACGA
ATGAGAGAAGGAGTCGAATGGAAGATTGCATCCAAAACCAAAAATGGTTTGTATGAGTGGTTGGT
TATGCCCTTTGGCCTAACTAATGCAC
Found at i:15464 original size:26 final size:26
Alignment explanation
Indices: 15432--15483 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
15422 ACTAAGAACA
15432 ATTGTGTTAGATCGCGATGCAAAATT
1 ATTGTGTTAGATCGCGATGCAAAATT
15458 ATTGTGTTAGATCGCGATGCAAAATT
1 ATTGTGTTAGATCGCGATGCAAAATT
15484 TCTTAGCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (26 bp):
ATTGTGTTAGATCGCGATGCAAAATT
Found at i:15644 original size:18 final size:18
Alignment explanation
Indices: 15621--15663 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
15611 GCAATCATTT
15621 GGAAGAACTTGAAACATG
1 GGAAGAACTTGAAACATG
15639 GGAAGAACTTGAAACATG
1 GGAAGAACTTGAAACATG
15657 GGAAGAA
1 GGAAGAA
15664 TGCTTGCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.47, C:0.09, G:0.30, T:0.14
Consensus pattern (18 bp):
GGAAGAACTTGAAACATG
Found at i:22785 original size:31 final size:30
Alignment explanation
Indices: 22719--22803 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
22709 ATATAAAATA
**
22719 TTTTAAAAAATGCATATAATAATAATTAAG
1 TTTTAAAAAATTAATATAATAATAATTAAG
* * **
22749 ATTTAAAAAATTAATATAATGATAAATTATT
1 TTTTAAAAAATTAATATAATAAT-AATTAAG
* *
22780 TTTTAATAATTTAATATAATAATA
1 TTTTAAAAAATTAATATAATAATA
22804 TATAAATTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
30 20 0.45
31 24 0.55
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (30 bp):
TTTTAAAAAATTAATATAATAATAATTAAG
Found at i:23093 original size:16 final size:16
Alignment explanation
Indices: 23051--23093 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
23041 TTTTTCTTTA
* *
23051 TTTTCCAAAATCATTT
1 TTTTACAAAATAATTT
*
23067 TATTTATAAAATAATTT
1 T-TTTACAAAATAATTT
23084 TTTTACAAAA
1 TTTTACAAAA
23094 ATTTTAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTACAAAATAATTT
Found at i:26895 original size:60 final size:60
Alignment explanation
Indices: 26802--26924 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
26792 GTCTTTACTT
26802 TGGGTTGAACAATTATTTCATGGAAGTCTGCTAAACAGACGTGTATTGCTCGCTCCACGA
1 TGGGTTGAACAATTATTTCATGGAAGTCTGCTAAACAGACGTGTATTGCTCGCTCCACGA
26862 TGGGTTGAACAATTATTTCATGGAAGTCTGCTAAACAGACGTGTATTGCTCGCTCCACGA
1 TGGGTTGAACAATTATTTCATGGAAGTCTGCTAAACAGACGTGTATTGCTCGCTCCACGA
26922 TGG
1 TGG
26925 AATCAGAGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (60 bp):
TGGGTTGAACAATTATTTCATGGAAGTCTGCTAAACAGACGTGTATTGCTCGCTCCACGA
Found at i:27803 original size:28 final size:28
Alignment explanation
Indices: 27769--27831 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
27759 CTGATTGTTA
27769 CAATATGACCGTTGGAACTTGACCATTG
1 CAATATGACCGTTGGAACTTGACCATTG
* * * * *
27797 CACTATGATCTTTGGAATTTGCCCATTG
1 CAATATGACCGTTGGAACTTGACCATTG
27825 CAATATG
1 CAATATG
27832 GTCGTTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (28 bp):
CAATATGACCGTTGGAACTTGACCATTG
Found at i:29918 original size:67 final size:66
Alignment explanation
Indices: 29788--29919 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 66
29778 TTAATATTCT
* * *
29788 TTTGGAAAGAATATAATTCCTCTTTCAACTTTCCATTTGCCTTCTTTATTAATAAATGAATAATC
1 TTTGGAAAGAATATAATTCCTCTTTCAACTTTCCATTTGCCTTATCTATTAATAAAGGAATAATC
29853 A
66 A
* * * * *
29854 TTTGGAAAGAATATCATTCCAT-TTTCTATCTTTTCATTTGCCTTATCTATTAATAAGGGTATAA
1 TTTGGAAAGAATATAATTCC-TCTTTC-AACTTTCCATTTGCCTTATCTATTAATAAAGGAATAA
29918 TC
64 TC
29920 CTAGTTTTCC
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
66 23 0.41
67 33 0.59
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (66 bp):
TTTGGAAAGAATATAATTCCTCTTTCAACTTTCCATTTGCCTTATCTATTAATAAAGGAATAATC
A
Found at i:34816 original size:15 final size:16
Alignment explanation
Indices: 34787--34816 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34777 TACTTTCACA
34787 CTAAATCGTGTTCAAT
1 CTAAATCGTGTTCAAT
34803 CTAAATCG-GTTCAA
1 CTAAATCGTGTTCAA
34817 AAGACACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (16 bp):
CTAAATCGTGTTCAAT
Found at i:38086 original size:138 final size:137
Alignment explanation
Indices: 37916--38194 Score: 389
Period size: 138 Copynumber: 2.0 Consensus size: 137
37906 ACATATATAA
* * *
37916 AATTAATATATGAATTTGATTCATATAAAATATTAATTGTATATATTTGACCGAGTTTATTAATA
1 AATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTGACCAAATTTATTAATA
* *
37981 TAAACAACTATATTAATTAATTTTGGTCAAAATATAAAAGATAT-GAAAATTAATATTCTTTTGG
66 TAAACAACTATATTAAGTAATTTTGGTCAAAAT-TAAAAGACATGGAAAA-TAATATTCTTTTGG
*
38045 AAATAATAT
129 AAAGAATAT
* * * *
38054 AATTAATATATGAATTTTATTTATAAAAAATATTAATTGTATATATTTTATCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTGACCAAATTTATTAATA
* ** * * *
38119 TAAATAGTTATATTAAGTAATTTTGGTGAAAATTAAAATACATGGAACATAATATTCTTTTGGAA
66 TAAACAACTATATTAAGTAATTTTGGTCAAAATTAAAAGACATGGAAAATAATATTCTTTTGGAA
38184 AGAATAT
131 AGAATAT
38191 AATT
1 AATT
38195 CGTTTTTATA
Statistics
Matches: 124, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
137 34 0.27
138 90 0.73
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (137 bp):
AATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTGACCAAATTTATTAATA
TAAACAACTATATTAAGTAATTTTGGTCAAAATTAAAAGACATGGAAAATAATATTCTTTTGGAA
AGAATAT
Found at i:39928 original size:16 final size:17
Alignment explanation
Indices: 39904--39941 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
39894 ATCCTCAAGC
39904 AAAAAAAAGA-AAAAAG
1 AAAAAAAAGATAAAAAG
* *
39920 AAAACAAAGATCAAAAG
1 AAAAAAAAGATAAAAAG
39937 AAAAA
1 AAAAA
39942 CTAAGAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAAAAGATAAAAAG
Found at i:47091 original size:2 final size:2
Alignment explanation
Indices: 47084--47119 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47074 GAGTAATGGG
47084 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.