Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012071.1 Kokia drynarioides strain JFW-HI SEQ_127069, 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: 32530
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:198 original size:17 final size:17
Alignment explanation
Indices: 138--200 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
128 CGGACTTCTC
* *
138 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
*
155 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
172 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
189 TAAACTTAAATT
1 TAAATTTAAATT
201 CAATTTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1290 original size:16 final size:16
Alignment explanation
Indices: 1266--1302 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1256 ATTTAGACTG
* *
1266 TGTGTCTAGTAGGCTT
1 TGTGCCTAGTAAGCTT
1282 TGTGCCTAGTAAGCTT
1 TGTGCCTAGTAAGCTT
1298 TGTGC
1 TGTGC
1303 TGGTGAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.41
Consensus pattern (16 bp):
TGTGCCTAGTAAGCTT
Found at i:5328 original size:113 final size:113
Alignment explanation
Indices: 5126--5368 Score: 387
Period size: 113 Copynumber: 2.2 Consensus size: 113
5116 CATGACCAAG
* *
5126 TAAGCAAATAACATAAGAAGGTTATGCACATTTTCTAAATGGCCTCACCTCCATCGGTTGCTTCC
1 TAAGCAAATAACATAAGAAGGCTATGCACATTTTCTAAATGGCCTCACCTCCATCGGTTACTTCC
* *
5191 TGCTCTATCCAAACAAATCTCTCACAACACATTTTCTAAGAATCTAAC
66 TACTCTATCCAAACAAATCACTCACAACACATTTTCTAAGAATCTAAC
* * * *
5239 TAAGCAAATAACATAAGAAGGCTATGCACATTTTCTAAATGGTCTCCCCTTCATCGGTTACTTCT
1 TAAGCAAATAACATAAGAAGGCTATGCACATTTTCTAAATGGCCTCACCTCCATCGGTTACTTCC
* * *
5304 TACTCTATCCAAACAAATCACTCACAACACATTTTTTAGGAATCTAGC
66 TACTCTATCCAAACAAATCACTCACAACACATTTTCTAAGAATCTAAC
5352 TAAGCAAATAACATAAG
1 TAAGCAAATAACATAAG
5369 GATATGCACA
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 119 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (113 bp):
TAAGCAAATAACATAAGAAGGCTATGCACATTTTCTAAATGGCCTCACCTCCATCGGTTACTTCC
TACTCTATCCAAACAAATCACTCACAACACATTTTCTAAGAATCTAAC
Found at i:10801 original size:51 final size:51
Alignment explanation
Indices: 10715--10856 Score: 185
Period size: 51 Copynumber: 2.8 Consensus size: 51
10705 GCTATAAACA
* * * * * *
10715 AAAGAGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGACGAATT
10767 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGACGAATT
* * * *
10818 TAAGGTCCGATGACTCAGTGTCATCATAAGTATATGAAT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAAT
10857 TCCTATACGG
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 76 0.95
52 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCATGACGAATT
Found at i:15163 original size:26 final size:29
Alignment explanation
Indices: 15133--15187 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 29
15123 CGATTGATTA
*
15133 AAAAATCAT-TAAAAA-ATATTT-TAAAT
1 AAAAATAATATAAAAAGATATTTATAAAT
15159 AAAAATAATAGTAAAAAGATATTTATAAA
1 AAAAATAATA-TAAAAAGATATTTATAAA
15188 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.33
28 6 0.25
29 6 0.25
30 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATAATATAAAAAGATATTTATAAAT
Found at i:16703 original size:20 final size:20
Alignment explanation
Indices: 16678--16723 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
16668 AATTTTTACC
* *
16678 AATTTTAATA-TCTTTAAAT
1 AATTTTAAAATTCTCTAAAT
16697 GAATTTTAAAATTCTCTAAAT
1 -AATTTTAAAATTCTCTAAAT
16718 AATTTT
1 AATTTT
16724 TTTATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (20 bp):
AATTTTAAAATTCTCTAAAT
Found at i:17802 original size:18 final size:16
Alignment explanation
Indices: 17778--17826 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 16
17768 AATATATAAT
17778 ATATAAATTAATAACAA
1 ATATAAATT-ATAACAA
17795 ATTATAAAATTATAACAA
1 A-TAT-AAATTATAACAA
17813 ATATAAATATATAA
1 ATATAAAT-TATAA
17827 AAGAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.14
17 9 0.31
18 11 0.38
19 5 0.17
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAATTATAACAA
Found at i:22716 original size:20 final size:19
Alignment explanation
Indices: 22678--22717 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
22668 ATAAAAACGC
*
22678 ATAAAAAAATAACATCCAA
1 ATAAAAAAATAACAACCAA
*
22697 ATAACAAAAATAATAACCAA
1 ATAA-AAAAATAACAACCAA
22717 A
1 A
22718 ACAGCAGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (19 bp):
ATAAAAAAATAACAACCAA
Found at i:22730 original size:12 final size:12
Alignment explanation
Indices: 22715--22799 Score: 65
Period size: 12 Copynumber: 7.6 Consensus size: 12
22705 AATAATAACC
*
22715 AAAACAGCAGCA
1 AAAACAACAGCA
*
22727 AAAATAACAGC-
1 AAAACAACAGCA
22738 AAAAC-A-A-CA
1 AAAACAACAGCA
*
22747 AAAACAACAACA
1 AAAACAACAGCA
* *
22759 ATAATAACAGCA
1 AAAACAACAGCA
*
22771 AAAACAACATC-
1 AAAACAACAGCA
*
22782 AAAACAACA-AA
1 AAAACAACAGCA
22793 AAAACAA
1 AAAACAA
22800 TCAGAAACAG
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
8 1 0.02
9 6 0.10
10 2 0.03
11 21 0.36
12 28 0.48
ACGTcount: A:0.69, C:0.21, G:0.05, T:0.05
Consensus pattern (12 bp):
AAAACAACAGCA
Found at i:22752 original size:9 final size:9
Alignment explanation
Indices: 22738--22799 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
22728 AAATAACAGC
22738 AAAACAACA
1 AAAACAACA
22747 AAAACAAC-
1 AAAACAACA
*
22755 --AACAATA
1 AAAACAACA
* *
22762 ATAACAGCA
1 AAAACAACA
22771 AAAACAACA
1 AAAACAACA
22780 TCAAAACAACA
1 --AAAACAACA
22791 AAAA-AACA
1 AAAACAACA
22799 A
1 A
22800 TCAGAAACAG
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
6 5 0.12
8 5 0.12
9 24 0.56
11 9 0.21
ACGTcount: A:0.73, C:0.21, G:0.02, T:0.05
Consensus pattern (9 bp):
AAAACAACA
Found at i:22765 original size:32 final size:34
Alignment explanation
Indices: 22714--22796 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 34
22704 AAATAATAAC
* *
22714 CAAAACAGCAGCAAAAATAACAGC-AAAACAACA
1 CAAAACAACAACAAAAATAACAGCAAAAACAACA
*
22747 -AAAACAACAACAATAATAACAGCAAAAACAACA
1 CAAAACAACAACAAAAATAACAGCAAAAACAACA
22780 TCAAAACAACAA-AAAAA
1 -CAAAACAACAACAAAAA
22797 CAATCAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
32 20 0.47
33 9 0.21
34 4 0.09
35 10 0.23
ACGTcount: A:0.69, C:0.22, G:0.05, T:0.05
Consensus pattern (34 bp):
CAAAACAACAACAAAAATAACAGCAAAAACAACA
Found at i:22770 original size:44 final size:43
Alignment explanation
Indices: 22682--22808 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 43
22672 AAACGCATAA
* * * *
22682 AAAAATAACATCCAAATAACAAAAATAATAACCAAAACAGCAGC
1 AAAAATAACATCAAAACAACAAAAA-AACAACCAAAACAACAGC
* *
22726 AAAAATAACAGCAAAACAACAAAAACAACAA-CAATAATAACAGC
1 AAAAATAACATCAAAACAACAAAAA-AACAACCAA-AACAACAGC
* *
22770 AAAAACAACATCAAAACAACAAAAAAACAATCAGAAACA
1 AAAAATAACATCAAAACAACAAAAAAACAACCA-AAACA
22809 GCAATATATT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 8 0.11
44 61 0.87
45 1 0.01
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.08
Consensus pattern (43 bp):
AAAAATAACATCAAAACAACAAAAAAACAACCAAAACAACAGC
Found at i:23460 original size:19 final size:19
Alignment explanation
Indices: 23425--23479 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
23415 TTTTAAAAAA
*
23425 TATAAATTTTAAAATTT-T
1 TATAAATTTTTAAATTTAT
23443 TATAAATATTTTAAATTTAT
1 TATAAAT-TTTTAAATTTAT
* *
23463 TTTGAATTTTTAAATTT
1 TATAAATTTTTAAATTT
23480 GTTGAAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.22
19 19 0.59
20 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATAAATTTTTAAATTTAT
Found at i:26899 original size:4 final size:4
Alignment explanation
Indices: 26890--26950 Score: 54
Period size: 4 Copynumber: 15.0 Consensus size: 4
26880 AAATAAACGG
* *
26890 GAAA GAAA GAAA GAAAA GAAA GAAA -AGAA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GA-AA GAAA GA-AA GAAA GAAA GAAA
*
26939 GAAT GAAA GAAA
1 GAAA GAAA GAAA
26951 AGTAATGTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
3 4 0.08
4 35 0.73
5 9 0.19
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:30501 original size:45 final size:45
Alignment explanation
Indices: 30450--30547 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
30440 AAACTCAGCT
* *
30450 TGATATCCATCCCTTGAGTATTGCGGTGGCTCGTCAAATTGAGGC
1 TGATATCCATCCCTTGAATATTGCGGTGGCTCGTCAAACTGAGGC
* ** *
30495 TGATATCCTTGGCTTTAATATTGCGGTGGCTCGTCAAACTGAGGC
1 TGATATCCATCCCTTGAATATTGCGGTGGCTCGTCAAACTGAGGC
30540 TGATATCC
1 TGATATCC
30548 TTGGCTTGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (45 bp):
TGATATCCATCCCTTGAATATTGCGGTGGCTCGTCAAACTGAGGC
Found at i:30548 original size:45 final size:45
Alignment explanation
Indices: 30468--30554 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
30458 ATCCCTTGAG
*
30468 TATTGCGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTTTAA
1 TATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTTAA
30513 TATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 TATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
30555 GATGAGCTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (45 bp):
TATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTTAA
Found at i:30878 original size:15 final size:15
Alignment explanation
Indices: 30858--30886 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30848 ATAAACATAT
30858 TGTCCATGCACACTA
1 TGTCCATGCACACTA
30873 TGTCCATGCACACT
1 TGTCCATGCACACT
30887 CCCCCAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (15 bp):
TGTCCATGCACACTA
Done.