Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015148.1 Kokia drynarioides strain JFW-HI SEQ_130192, 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: 29756
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:2729 original size:27 final size:27
Alignment explanation
Indices: 2699--2760 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
2689 TCAACATCTC
* *
2699 TGTTTTTGTTTCTATGAATGATTTTCA
1 TGTTTTTGTTTCAATGAATGATTTGCA
* *
2726 TGTTTTCGTTTGAATGAATGATTTGCA
1 TGTTTTTGTTTCAATGAATGATTTGCA
2753 TGTTTTTG
1 TGTTTTTG
2761 CGCACCCTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.06, G:0.19, T:0.56
Consensus pattern (27 bp):
TGTTTTTGTTTCAATGAATGATTTGCA
Found at i:6730 original size:27 final size:27
Alignment explanation
Indices: 6692--6768 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
6682 GACACTGGTA
6692 GAGGGATATCAAGTGGCGGCACCCTTG
1 GAGGGATATCAAGTGGCGGCACCCTTG
* *
6719 GAGGGATATCAAGTGACGACACCCTTG
1 GAGGGATATCAAGTGGCGGCACCCTTG
*
6746 GAGGGATATCAAGTGGGGGCACC
1 GAGGGATATCAAGTGGCGGCACC
6769 AATGTGTGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.26, C:0.21, G:0.36, T:0.17
Consensus pattern (27 bp):
GAGGGATATCAAGTGGCGGCACCCTTG
Found at i:6820 original size:3 final size:3
Alignment explanation
Indices: 6812--6841 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6802 TCATTTAAAT
6812 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6842 GTGGTGCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7506 original size:24 final size:24
Alignment explanation
Indices: 7474--7545 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
7464 TGTGGAACCA
7474 GTAGAAAATGAAGATCTAACTCCG
1 GTAGAAAATGAAGATCTAACTCCG
7498 GTAGAAAATGAAGATCTAACTCCG
1 GTAGAAAATGAAGATCTAACTCCG
*
7522 GTAGAAAATGAAGATCCAACTCCG
1 GTAGAAAATGAAGATCTAACTCCG
7546 TGTATACTGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (24 bp):
GTAGAAAATGAAGATCTAACTCCG
Found at i:8987 original size:29 final size:29
Alignment explanation
Indices: 8938--8994 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
8928 AGGTTTCAAA
*
8938 TTTAAGGTTTTGAATTAAAGGTTTTGAAT
1 TTTAAGGTTTAGAATTAAAGGTTTTGAAT
* *
8967 TTTAAGGTTTAGAGTTTAAGGTTTTGAA
1 TTTAAGGTTTAGAATTAAAGGTTTTGAA
8995 CTTAATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (29 bp):
TTTAAGGTTTAGAATTAAAGGTTTTGAAT
Found at i:8999 original size:14 final size:14
Alignment explanation
Indices: 8926--9012 Score: 102
Period size: 14 Copynumber: 6.1 Consensus size: 14
8916 CTATAACTTA
**
8926 TAAGGTTTCAAATT
1 TAAGGTTTTGAATT
8940 TAAGGTTTTGAATT
1 TAAGGTTTTGAATT
*
8954 AAAGGTTTTGAATTT
1 TAAGGTTTTGAA-TT
* *
8969 TAAGGTTTAGAGTT
1 TAAGGTTTTGAATT
*
8983 TAAGGTTTTGAACT
1 TAAGGTTTTGAATT
*
8997 TAATGTTTTGAATT
1 TAAGGTTTTGAATT
9011 TA
1 TA
9013 GGGTCTAAGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 50 0.82
15 11 0.18
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (14 bp):
TAAGGTTTTGAATT
Found at i:9095 original size:21 final size:20
Alignment explanation
Indices: 9021--9096 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
9011 TAGGGTCTAA
* *
9021 GGTTTAGATTTTAGAATTTAA
1 GGTTTAGGTTTTA-AATTTAG
* **
9042 GGTTCATGGTTTTTTATTTAG
1 GGTTTA-GGTTTTAAATTTAG
*
9063 GGTTTAATGTTTTAAATTTAG
1 GGTTT-AGGTTTTAAATTTAG
*
9084 GGTTTAGGGTTTA
1 GGTTTAGGTTTTA
9097 TACGTATGAA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
20 6 0.14
21 30 0.71
22 6 0.14
ACGTcount: A:0.24, C:0.01, G:0.24, T:0.51
Consensus pattern (20 bp):
GGTTTAGGTTTTAAATTTAG
Found at i:9348 original size:21 final size:22
Alignment explanation
Indices: 9324--9369 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
9314 TAGGGTTTAT
9324 TTGCCCCA-GAGGAGTAGAGTA
1 TTGCCCCAGGAGGAGTAGAGTA
*
9345 TTG-CCTAGGAGGAGTAGAGTA
1 TTGCCCCAGGAGGAGTAGAGTA
9366 TTGC
1 TTGC
9370 GGTGACTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (22 bp):
TTGCCCCAGGAGGAGTAGAGTA
Found at i:11845 original size:16 final size:16
Alignment explanation
Indices: 11815--11886 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
11805 TTTATACAAC
11815 TAAATAA-AAA-C-AT
1 TAAATAATAAATCAAT
11828 TAAATAATAAATCAAT
1 TAAATAATAAATCAAT
* *
11844 TAAA-AATTAAATTAAA
1 TAAATAA-TAAATCAAT
11860 T-AA-AATAAAT-AATT
1 TAAATAATAAATCAA-T
11874 TAAAATAATAAAT
1 T-AAATAATAAAT
11887 ACTAAACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
13 9 0.19
14 9 0.19
15 7 0.15
16 16 0.33
17 7 0.15
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATAATAAATCAAT
Found at i:11854 original size:23 final size:23
Alignment explanation
Indices: 11816--11887 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 23
11806 TTATACAACT
*
11816 AAATAAAAACATTAAATAATAAATC
1 AAAT-AAAA-ATTAAATAATAAATA
*
11841 AATTAAAAATTAAAT--TAAATA
1 AAATAAAAATTAAATAATAAATA
11862 AAATAAATAATTTAAAATAATAAATA
1 AAATAAA-AA-TT-AAATAATAAATA
11888 CTAAACAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 11 0.28
22 2 0.05
23 9 0.23
24 8 0.21
25 3 0.08
26 6 0.15
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATAAAAATTAAATAATAAATA
Found at i:13026 original size:29 final size:34
Alignment explanation
Indices: 12965--13041 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 34
12955 AAATAAAGAA
12965 AAAAGAGAAAGAAAGAAAGAAAGAAGGAAGAAGG
1 AAAAGAGAAAGAAAGAAAGAAAGAAGGAAGAAGG
12999 AAAA-AGAAAG-AAG-AAG-AAGAAGGGGAAGAAGG
1 AAAAGAGAAAGAAAGAAAGAAAGAA--GGAAGAAGG
*
13031 AGAATGAGAAA
1 A-AAAGAGAAA
13042 AAGGTAATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
30 5 0.13
31 3 0.08
32 13 0.34
33 8 0.21
34 9 0.24
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (34 bp):
AAAAGAGAAAGAAAGAAAGAAAGAAGGAAGAAGG
Found at i:13208 original size:18 final size:18
Alignment explanation
Indices: 13185--13219 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13175 GAAACAAATG
13185 TAAGTTT-GATTAATTTTT
1 TAAGTTTAG-TTAATTTTT
13203 TAAGTTTAGTTAATTTT
1 TAAGTTTAGTTAATTTT
13220 AAATTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (18 bp):
TAAGTTTAGTTAATTTTT
Found at i:14187 original size:16 final size:16
Alignment explanation
Indices: 14142--14191 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
14132 TAAACCTAGC
14142 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
14158 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
14172 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
14188 TAAT
1 TAAT
14192 ATCCCCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:16191 original size:45 final size:44
Alignment explanation
Indices: 16122--16254 Score: 167
Period size: 45 Copynumber: 3.0 Consensus size: 44
16112 CCATAGCTCA
* *
16122 TCAAGCCAAGGATATCAGCTTCAGTTTGACGAGCCACGATAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACG-CAATAC
*
16167 TCAAGCCAATGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCA-CGCAATAC
* ** * *
16212 TTAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCGCAAT
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCA-CGCAAT
16255 TCTCTACTCC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 76 0.97
46 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (44 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACGCAATAC
Found at i:16531 original size:7 final size:7
Alignment explanation
Indices: 16515--16548 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
16505 TTTCATAACA
16515 TTAAACC
1 TTAAACC
*
16522 TTAAAAC
1 TTAAACC
16529 TTAAACC
1 TTAAACC
16536 TTAAACC
1 TTAAACC
*
16543 CTAAAC
1 TTAAAC
16549 TTAGAACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (7 bp):
TTAAACC
Found at i:23728 original size:23 final size:23
Alignment explanation
Indices: 23678--23826 Score: 115
Period size: 23 Copynumber: 6.5 Consensus size: 23
23668 TATATGGAAC
* * *
23678 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
23700 -AACAGAGATCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* * *
23722 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* * * * *
23745 AATCAGAGAGCATATAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* *
23768 AATCAGAGAGCACACACGGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
23791 AATAACAGAGAGCACGAGACA-TGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
23816 AAACAGAGAGC
1 AAACAGAGAGC
23827 GCGCTAGTGT
Statistics
Matches: 102, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
21 10 0.10
22 7 0.07
23 65 0.64
24 2 0.02
25 15 0.15
26 3 0.03
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:23777 original size:46 final size:45
Alignment explanation
Indices: 23678--23783 Score: 133
Period size: 46 Copynumber: 2.4 Consensus size: 45
23668 TATATGGAAC
* * *
23678 AAACAGAGAGTAC-CAAAGTACTAACAGAGATCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAACAGAGAGCACACAAAGTACT
* *
23722 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCATATAAAGTACT
1 AAACAGAGAGTACACAAAGTACTAA-CAGAGAGCACACAAAGTACT
* *
23768 AATCAGAGAGCACACA
1 AAACAGAGAGTACACA
23784 CGGTGCTAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
44 13 0.25
45 11 0.21
46 29 0.55
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (45 bp):
AAACAGAGAGTACACAAAGTACTAACAGAGAGCACACAAAGTACT
Done.