Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012249.1 Kokia drynarioides strain JFW-HI SEQ_127250, 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: 58208
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:10969 original size:16 final size:17
Alignment explanation
Indices: 10950--10984 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
10940 TTGTGTCTTT
*
10950 TTTTTTTTAAT-ATTTA
1 TTTTTTTAAATAATTTA
10966 TTTTTTTAAATAATTTA
1 TTTTTTTAAATAATTTA
10983 TT
1 TT
10985 ATAGCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTTAAATAATTTA
Found at i:14973 original size:23 final size:23
Alignment explanation
Indices: 14945--14992 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
14935 GAAATATATA
*
14945 TATTATTGTTATTTTAACAAAAT
1 TATTATTATTATTTTAACAAAAT
14968 TATTATTATTATTTTAACAAAAT
1 TATTATTATTATTTTAACAAAAT
14991 TA
1 TA
14993 CTAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTATTATTATTTTAACAAAAT
Found at i:19702 original size:23 final size:22
Alignment explanation
Indices: 19672--19750 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
19662 ACGCTAGCGC
19672 GCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTGTTT-GCACTAT-GTGT
*
19695 GCTTACTGATTTGCACTATGTGC
1 GCTTACTG-TTTGCACTATGTGT
* * *
19718 GCCTACTGATTGCACTGTGTGT
1 GCTTACTGTTTGCACTATGTGT
*
19740 GCTTATTGTTT
1 GCTTACTGTTT
19751 CCCTAGCACT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
22 19 0.41
23 23 0.50
24 4 0.09
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.43
Consensus pattern (22 bp):
GCTTACTGTTTGCACTATGTGT
Found at i:24069 original size:18 final size:18
Alignment explanation
Indices: 24048--24083 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24038 AGTTGATAGC
24048 GATGAGGAAGAGGAAGAG
1 GATGAGGAAGAGGAAGAG
* *
24066 GATGAGGATGAGGGAGAG
1 GATGAGGAAGAGGAAGAG
24084 AACGATTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.53, T:0.08
Consensus pattern (18 bp):
GATGAGGAAGAGGAAGAG
Found at i:26290 original size:28 final size:29
Alignment explanation
Indices: 26244--26301 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
26234 TATTTGGGAT
26244 TAAAAATAAATTGTATATT-TTTATAATAG
1 TAAAAATAAATTGTATATTATTT-TAATAG
26273 TAAAAATATAATT-T-TATTATTTTAATAG
1 TAAAAATA-AATTGTATATTATTTTAATAG
26301 T
1 T
26302 TCATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 11 0.41
29 12 0.44
30 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (29 bp):
TAAAAATAAATTGTATATTATTTTAATAG
Found at i:29125 original size:19 final size:19
Alignment explanation
Indices: 29083--29125 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
29073 AAAAAAACCC
* *
29083 AAAAATGTTGATTGAATTT
1 AAAAATGTTGAATGAATTA
*
29102 GAAAATGTTGAATGAATTA
1 AAAAATGTTGAATGAATTA
29121 AAAAA
1 AAAAA
29126 AGAAGAAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (19 bp):
AAAAATGTTGAATGAATTA
Found at i:32957 original size:72 final size:72
Alignment explanation
Indices: 32840--32983 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
32830 GGCCCTGGAA
32840 CCGATAACCTTGTGCGTGGCATATGAAACCTAACTATAATGACAAACTTCCAGGCTCAACAGTCA
1 CCGATAACCTTGTGCGTGGCATATGAAACCTAACTATAATGACAAACTTCCAGGCTCAACAGTCA
32905 ATGTAAT
66 ATGTAAT
32912 CCGATAACCTTGTGCGTGGCATATGAAACCTAACTATAATGACAAACTTCCAGGCTCAACAGTCA
1 CCGATAACCTTGTGCGTGGCATATGAAACCTAACTATAATGACAAACTTCCAGGCTCAACAGTCA
32977 ATGTAAT
66 ATGTAAT
32984 GCCCGGTTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (72 bp):
CCGATAACCTTGTGCGTGGCATATGAAACCTAACTATAATGACAAACTTCCAGGCTCAACAGTCA
ATGTAAT
Found at i:47077 original size:17 final size:18
Alignment explanation
Indices: 47055--47092 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
47045 GCGTTTTCTC
47055 ATTTTAGTCC-TAATATT
1 ATTTTAGTCCTTAATATT
*
47072 ATTTTAGTCCTTAATGTT
1 ATTTTAGTCCTTAATATT
47090 ATT
1 ATT
47093 AAAAGTTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (18 bp):
ATTTTAGTCCTTAATATT
Found at i:56483 original size:55 final size:55
Alignment explanation
Indices: 56380--56483 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
56370 TATGTATCAT
* * * **
56380 TCGATTTAAATATATAAACAATCGATTTAAAAGAAATAATATTTCAACATGACAA
1 TCGATTTAAACATATAAACAATCGAATTAAAAAAAATAATATCCCAACATGACAA
56435 TCGATTTAAACATATAATA-AATC-AATTAAAAAAAAGTAATATCCCAACA
1 TCGATTTAAACATATAA-ACAATCGAATTAAAAAAAA-TAATATCCCAACA
56484 ATTAAGACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
54 10 0.24
55 31 0.74
56 1 0.02
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (55 bp):
TCGATTTAAACATATAAACAATCGAATTAAAAAAAATAATATCCCAACATGACAA
Found at i:57745 original size:29 final size:29
Alignment explanation
Indices: 57670--57924 Score: 83
Period size: 30 Copynumber: 8.7 Consensus size: 29
57660 AATAAATTTG
* * *
57670 GAAAGTTTGGGGTTAAAATGTAATTTTCA
1 GAAAGTTTGAGGTCAAAATGTAATTTTTA
* * *
57699 AAAAG-TTCAGGGAT-AAAATGTGATTTTTA
1 GAAAGTTTGA-GG-TCAAAATGTAATTTTTA
** * *
57728 GAAAGTTTGAGGTCAAAATCAAAGTTATA
1 GAAAGTTTGAGGTCAAAATGTAATTTTTA
* * * * *
57757 GAAAATTTTGGGGTCAAAATATGATTTTCA
1 G-AAAGTTTGAGGTCAAAATGTAATTTTTA
* * * * *
57787 AAAAGTTT-AGGAGTTAAAATATAAATTTTG
1 GAAAGTTTGA-G-GTCAAAATGTAATTTTTA
* * * *
57817 GAAAATTTAGGGGTCAAAATGCAATTTTCA
1 GAAAGTTT-GAGGTCAAAATGTAATTTTTA
* *
57847 -AAGAGTTT-AGGGTCAAAAAGT-ATTTTAA
1 GAA-AGTTTGA-GGTCAAAATGTAATTTTTA
* * * *
57875 AAAAGTTCGGAGGTCAAAAT-TGATGTTTTG
1 GAAAGTT-TGAGGTCAAAATGTAAT-TTTTA
*
57905 GAAAGTTTGGGGGTCAAAAT
1 GAAAGTTT-GAGGTCAAAAT
57925 CGAAGTTTTA
Statistics
Matches: 160, Mismatches: 49, Indels: 33
0.66 0.20 0.14
Matches are distributed among these distances:
28 14 0.09
29 66 0.41
30 79 0.49
31 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (29 bp):
GAAAGTTTGAGGTCAAAATGTAATTTTTA
Found at i:57806 original size:30 final size:29
Alignment explanation
Indices: 57671--57881 Score: 121
Period size: 29 Copynumber: 7.2 Consensus size: 29
57661 ATAAATTTGG
* * *
57671 AAAGTTTGGGGTTAAAATGTAATTTTCAA
1 AAAGTTTAGGGTCAAAATATAATTTTCAA
* * * * *
57700 AAAGTTCAGGGAT-AAAATGTGATTTTTAG
1 AAAGTTTAGGG-TCAAAATATAATTTTCAA
*
57729 AAAGTTT-GAGGTCAAAATCA-AAGTTAT-AGA
1 AAAGTTTAG-GGTCAAAAT-ATAA-TTTTCA-A
* * *
57759 AAATTTTGGGGTCAAAATATGATTTTCAA
1 AAAGTTTAGGGTCAAAATATAATTTTCAA
* **
57788 AAAGTTTAGGAGTTAAAATATAAATTTTGGA
1 AAAGTTTAGG-GTCAAAATAT-AATTTTCAA
**
57819 AAA-TTTAGGGGTCAAAATGCAATTTTCAA
1 AAAGTTTA-GGGTCAAAATATAATTTTCAA
* *
57848 AGAGTTTAGGGTCAAAA-AGT-ATTTTAAA
1 AAAGTTTAGGGTCAAAATA-TAATTTTCAA
57876 AAAGTT
1 AAAGTT
57882 CGGAGGTCAA
Statistics
Matches: 139, Mismatches: 29, Indels: 29
0.71 0.15 0.15
Matches are distributed among these distances:
28 14 0.10
29 68 0.49
30 45 0.32
31 12 0.09
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
AAAGTTTAGGGTCAAAATATAATTTTCAA
Found at i:57910 original size:30 final size:30
Alignment explanation
Indices: 57876--57933 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
57866 GTATTTTAAA
* *
57876 AAAGTTCGGAGGTCAAAATTGATGTTTTGG
1 AAAGTTCGGAGGTCAAAATCGAAGTTTTGG
* *
57906 AAAGTTTGGGGGTCAAAATCGAAGTTTT
1 AAAGTTCGGAGGTCAAAATCGAAGTTTT
57934 AAATAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (30 bp):
AAAGTTCGGAGGTCAAAATCGAAGTTTTGG
Done.