Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003196.1 Kokia drynarioides strain JFW-HI SEQ_115810, 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: 60184
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 224 characters in sequence are not A, C, G, or T
Found at i:3885 original size:18 final size:18
Alignment explanation
Indices: 3862--3899 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3852 TAGAGACACG
3862 ATTAAAGCCTACGGGAAT
1 ATTAAAGCCTACGGGAAT
3880 ATTAAAGCCTACGGGAAT
1 ATTAAAGCCTACGGGAAT
3898 AT
1 AT
3900 GTTGGGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTAAAGCCTACGGGAAT
Found at i:18509 original size:24 final size:24
Alignment explanation
Indices: 18446--18500 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
18436 ACTCTATCTG
*
18446 GGCTCGTAAAAGCTAACCATTCTA
1 GGCTCGTAAGAGCTAACCATTCTA
18470 GGCTCGTAAGAGCTAACCATTCT-
1 GGCTCGTAAGAGCTAACCATTCTA
18493 GGTCTCGT
1 GG-CTCGT
18501 GTGGGCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCATTCTA
Found at i:31986 original size:17 final size:17
Alignment explanation
Indices: 31973--32013 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
31963 CTTATTGTGC
31973 CTACATTTTAATTGTCT
1 CTACATTTTAATTGTCT
*
31990 CTGCATTTTAATTGTCT
1 CTACATTTTAATTGTCT
*
32007 CTGCATT
1 CTACATT
32014 CCTTTTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (17 bp):
CTACATTTTAATTGTCT
Found at i:33760 original size:10 final size:10
Alignment explanation
Indices: 33745--33773 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
33735 GTATTTTAAC
33745 ATAAAAATAT
1 ATAAAAATAT
33755 ATAAAAATAT
1 ATAAAAATAT
33765 -TAAAAATAT
1 ATAAAAATAT
33774 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:36603 original size:24 final size:24
Alignment explanation
Indices: 36575--36657 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
36565 TATACTAATA
36575 AGAGTTTAACTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
** *
36599 AGAGTTTATTTGAAGCAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* *
36623 AGAGTCTAA-TAGAAACAAATAAAC
1 AGAGTTTAACT-GAAACAAATAAAT
36647 AGAGTTTAACT
1 AGAGTTTAACT
36658 CGAAGATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
23 1 0.02
24 47 0.96
25 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:39899 original size:15 final size:15
Alignment explanation
Indices: 39881--39928 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
39871 ATGTTATAAA
39881 AATTATAATATAATT
1 AATTATAATATAATT
* *
39896 AATTATAAAATAA-A
1 AATTATAATATAATT
39910 ACACTTATAATATAATT
1 A-A-TTATAATATAATT
39927 AA
1 AA
39929 GCTTGTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 1 0.04
15 13 0.50
16 11 0.42
17 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATAATATAATT
Found at i:49661 original size:19 final size:19
Alignment explanation
Indices: 49637--49673 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
49627 TTAGAAATTT
*
49637 TTTTATAAAAATTGTAAAC
1 TTTTATAAAAATTATAAAC
49656 TTTTATAAAAATTATAAA
1 TTTTATAAAAATTATAAA
49674 AAATTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTTATAAAAATTATAAAC
Found at i:49680 original size:19 final size:19
Alignment explanation
Indices: 49639--49684 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
49629 AGAAATTTTT
* ***
49639 TTATAAAAATTGTAAACTT
1 TTATAAAAATTATAAAAAA
49658 TTATAAAAATTATAAAAAA
1 TTATAAAAATTATAAAAAA
49677 TTATAAAA
1 TTATAAAA
49685 TACATCGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
TTATAAAAATTATAAAAAA
Found at i:49900 original size:19 final size:19
Alignment explanation
Indices: 49876--49931 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
49866 AATTTTTAAA
49876 ATTTTTTTACGAATTTTAT
1 ATTTTTTTACGAATTTTAT
* *
49895 A-TTTTTTA-TATTTTTAT
1 ATTTTTTTACGAATTTTAT
*
49912 AATTTTCTTACG-ATTTTAT
1 -ATTTTTTTACGAATTTTAT
49931 A
1 A
49932 AAATTTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
17 7 0.24
18 9 0.31
19 13 0.45
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTTTTTTACGAATTTTAT
Found at i:49927 original size:29 final size:28
Alignment explanation
Indices: 49895--49966 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
49885 CGAATTTTAT
49895 ATTTTTTATATTTTTATAATTTTCTTACG
1 ATTTTTTATATTTTTATAATTTT-TTACG
* * * * *
49924 ATTTTATAAAATTTTATAATTTTTTTCT
1 ATTTTTTATATTTTTATAATTTTTTACG
*
49952 ATATTTTATATTTTT
1 ATTTTTTATATTTTT
49967 TTACGATTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
28 14 0.41
29 20 0.59
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (28 bp):
ATTTTTTATATTTTTATAATTTTTTACG
Found at i:49932 original size:19 final size:18
Alignment explanation
Indices: 49878--49932 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
49868 TTTTTAAAAT
49878 TTTTTTACGAATTTTAT-A
1 TTTTTTACG-ATTTTATAA
*
49896 TTTTTTA-TATTTTTATAA
1 TTTTTTACGA-TTTTATAA
49914 TTTTCTTACGATTTTATAA
1 TTTT-TTACGATTTTATAA
49933 AATTTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 1 0.03
17 6 0.19
18 12 0.39
19 11 0.35
20 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTTTTACGATTTTATAA
Found at i:49939 original size:37 final size:38
Alignment explanation
Indices: 49866--49947 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
49856 TTAGTACAAA
* **
49866 AATTTTTAAAATTTTTTTACGAATTTTATATTTTTTAT
1 AATTTTTAAAATTTTCTTACGAATTTTATAAATTTTAT
*
49904 -ATTTTTATAATTTTCTTACG-ATTTTATAAAATTTTAT
1 AATTTTTAAAATTTTCTTACGAATTTTAT-AAATTTTAT
49941 AATTTTT
1 AATTTTT
49948 TTCTATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 7 0.18
37 25 0.66
38 6 0.16
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (38 bp):
AATTTTTAAAATTTTCTTACGAATTTTATAAATTTTAT
Found at i:49957 original size:20 final size:21
Alignment explanation
Indices: 49934--49981 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
49924 ATTTTATAAA
*
49934 ATTTTATAATTTTTTT-CTAT
1 ATTTTATAATTTTTTTACGAT
49954 ATTTTAT-ATTTTTTTACGAT
1 ATTTTATAATTTTTTTACGAT
49974 -TTTTATAA
1 ATTTTATAA
49982 AACTTTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTATAATTTTTTTACGAT
Found at i:49996 original size:49 final size:48
Alignment explanation
Indices: 49896--50013 Score: 143
Period size: 48 Copynumber: 2.5 Consensus size: 48
49886 GAATTTTATA
*
49896 TTTTTTATATTTTTATAATTTTCTTACGATTTTATAAAATTTTATAAT
1 TTTTTTATATTTTTATAATTTTCTTACGATTTTATAAAACTTTATAAT
* * *
49944 TTTTTTCTATATTTTAT-ATTTTTTTACGATTTTTATAAAACTTTAT--G
1 TTTTTTATAT-TTTTATAATTTTCTTACGA-TTTTATAAAACTTTATAAT
*
49991 TTTTTTATAATTTTTCTAATTTT
1 TTTTTTAT-ATTTTTATAATTTT
50014 TAATAAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
47 12 0.20
48 27 0.45
49 21 0.35
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (48 bp):
TTTTTTATATTTTTATAATTTTCTTACGATTTTATAAAACTTTATAAT
Found at i:50057 original size:20 final size:21
Alignment explanation
Indices: 50007--50057 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
49997 ATAATTTTTC
*
50007 TAATTTTTAATAAAATTTAAA
1 TAATTTTTATTAAAATTTAAA
*
50028 TATTTTTTATTAAAATTT-AA
1 TAATTTTTATTAAAATTTAAA
50048 TAATTTTTAT
1 TAATTTTTAT
50058 AACTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTTTTATTAAAATTTAAA
Found at i:55491 original size:51 final size:51
Alignment explanation
Indices: 55375--55561 Score: 225
Period size: 51 Copynumber: 3.6 Consensus size: 51
55365 TTTCATTTAC
* * ** * *
55375 TACTCATGATGACA-TATAATCATCAGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCAGACCT-TTAATCCATAAAGG-ATTCATT
* * * *
55428 TACTCACTATGACA-TTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTT-AGTCATCAGACCTTTAATCCATAAAGGATTCATT
*
55479 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCATAAAGGATTCATT
55530 TACTCACGATGACACTTAGTCATCAGACCTTT
1 TACTCACGATGACACTTAGTCATCAGACCTTT
55562 TCGTTTATAG
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
51 81 0.69
52 12 0.10
53 24 0.21
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCAGACCTTTAATCCATAAAGGATTCATT
Found at i:59882 original size:16 final size:16
Alignment explanation
Indices: 59861--59914 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
59851 ATTTGTTCGC
*
59861 TGTAATGGAATAGAGT
1 TGTAATAGAATAGAGT
* *
59877 TGTAATTGAATAGAAT
1 TGTAATAGAATAGAGT
59893 TGTAATAGAATAG-GAT
1 TGTAATAGAATAGAG-T
59909 TGTAAT
1 TGTAAT
59915 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (16 bp):
TGTAATAGAATAGAGT
Done.