Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003311.1 Kokia drynarioides strain JFW-HI SEQ_115997, 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: 19492
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5012 original size:21 final size:21
Alignment explanation
Indices: 4988--5044 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
4978 CCAAATGCGG
4988 TACTACCTCTACTAGAAACAA
1 TACTACCTCTACTAGAAACAA
* *
5009 TACTACCTCTGCTAGAAACAG
1 TACTACCTCTACTAGAAACAA
5030 TACTACCTCTACTAG
1 TACTACCTCTACTAG
5045 TGTCTTGACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (21 bp):
TACTACCTCTACTAGAAACAA
Found at i:7728 original size:26 final size:26
Alignment explanation
Indices: 7699--7753 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
7689 AATCAGATAG
* * *
7699 CAGCTGATAGCAGTTCAGTCAGAGAT
1 CAGCAGATAACAGATCAGTCAGAGAT
* *
7725 CAGCAGGTAACAGATCAGTCATAGAT
1 CAGCAGATAACAGATCAGTCAGAGAT
7751 CAG
1 CAG
7754 TTAACACAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (26 bp):
CAGCAGATAACAGATCAGTCAGAGAT
Found at i:8500 original size:40 final size:39
Alignment explanation
Indices: 8416--8509 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 39
8406 TAATAGTACG
* * *
8416 GTGTTTATAGTGTCATTGCCAGTCAGTTGTCATACTGCA
1 GTGTTTATAGTGTCATTACCAGTAAGTTGTCATACTACA
* * * * *
8455 ATGTTTACAGTGTCATTACTAGTTAAGTTTTCATATTACA
1 GTGTTTATAGTGTCATTACCAG-TAAGTTGTCATACTACA
8495 GTGTTTATAGTGTCA
1 GTGTTTATAGTGTCA
8510 CTGCAAGTTC
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
39 18 0.41
40 26 0.59
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (39 bp):
GTGTTTATAGTGTCATTACCAGTAAGTTGTCATACTACA
Found at i:8538 original size:40 final size:40
Alignment explanation
Indices: 8487--8591 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
8477 TTAAGTTTTC
* *
8487 ATATTACAGTGTTTATAGTGTCACTGCAAGTTCAGTAATA
1 ATATCACAGTGTTTACAGTGTCACTGCAAGTTCAGTAATA
** * * *
8527 ATATCGTAGTGTTTACAGTGTCACTTCCAGTTGAGTAATA
1 ATATCACAGTGTTTACAGTGTCACTGCAAGTTCAGTAATA
*
8567 ATATCACAGTGTTTGCAGTGTCACT
1 ATATCACAGTGTTTACAGTGTCACT
8592 ACCAATAAGC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (40 bp):
ATATCACAGTGTTTACAGTGTCACTGCAAGTTCAGTAATA
Found at i:12104 original size:14 final size:15
Alignment explanation
Indices: 12085--12122 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
12075 CGAACTTTTG
12085 GAAAATTTGA-TGTC
1 GAAAATTTGACTGTC
* *
12099 GAAAATGTGACTTTC
1 GAAAATTTGACTGTC
12114 GAAAATTTG
1 GAAAATTTG
12123 GGTAAAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (15 bp):
GAAAATTTGACTGTC
Found at i:12186 original size:29 final size:29
Alignment explanation
Indices: 12030--12414 Score: 238
Period size: 29 Copynumber: 13.1 Consensus size: 29
12020 TTTCGAGGAA
*
12030 TTTGGGGATCAAAATTGAAATTTTTGGAAAA-
1 TTTGGGG-TCAAAA-TGTAA-TTTTGGAAAAG
* *
12061 TTTGGGATTAAAATCG-AACTTTTGGAAAA-
1 TTTGGGGTCAAAAT-GTAA-TTTTGGAAAAG
** * * *
12090 TTTGATGTCGAAAATGTGACTTTCGAAAA-
1 TTTGGGGTC-AAAATGTAATTTTGGAAAAG
* *
12119 TTT-GGGT-AAAATAGTGATTTTTGG-ATA-
1 TTTGGGGTCAAAAT-GT-AATTTTGGAAAAG
* **
12146 TTCAGGGG-CAAAATGGTAATTTTGG-TGAG
1 TT-TGGGGTCAAAAT-GTAATTTTGGAAAAG
*
12175 TTTGGGGTCAAAATATAATTTTAGG--AAG
1 TTTGGGGTCAAAATGTAATTTT-GGAAAAG
12203 TTTGGGAGTCAAAAATGTAATTTTGGAAAAG
1 TTTGGG-GTC-AAAATGTAATTTTGGAAAAG
*
12234 TTTGGGGTTAAAATGTAATTTTGGAAAAG
1 TTTGGGGTCAAAATGTAATTTTGGAAAAG
* * * * *
12263 TTTAGGGTCAAAATATGATTTTAGAGAAG
1 TTTGGGGTCAAAATGTAATTTTGGAAAAG
* * * * *
12292 TTTAAGGTGT-TAAATGTAAATTTGGCAATG
1 TTT--GGGGTCAAAATGTAATTTTGGAAAAG
* * *
12322 TTTAAGGGCCAAAATGTGATTTTGGAAAAG
1 TTT-GGGGTCAAAATGTAATTTTGGAAAAG
*
12352 TTTAGGCGGTTAAAATGTAATTTTGGAAAAG
1 TTT-GG-GGTCAAAATGTAATTTTGGAAAAG
*
12383 TTTGGGCGTCAAAATGTGATTTTGGAAAAG
1 TTTGGG-GTCAAAATGTAATTTTGGAAAAG
12413 TT
1 TT
12415 CAGGGGTTTT
Statistics
Matches: 277, Mismatches: 57, Indels: 41
0.74 0.15 0.11
Matches are distributed among these distances:
26 5 0.02
27 6 0.02
28 33 0.12
29 105 0.38
30 86 0.31
31 42 0.15
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTGGGGTCAAAATGTAATTTTGGAAAAG
Found at i:12216 original size:58 final size:57
Alignment explanation
Indices: 12051--12414 Score: 206
Period size: 59 Copynumber: 6.2 Consensus size: 57
12041 AAATTGAAAT
* * ** * * *
12051 TTTTGGAAAA-TTTGGGATTAAAATCGAACTTTTGGAAAATTT-GATGTCGAAAATGTGA
1 TTTTGGAAAAGTTTGGGGTCAAAATATAA-TTTTGGAAAGTTTAG-GGTC-AAAATGTAA
* * * * * *
12109 CTTTCGAAAA-TTT-GGGT-AAAATAGTGATTTTTGGATA-TTCAGGGGCAAAATGGTAA
1 TTTTGGAAAAGTTTGGGGTCAAAATA-T-AATTTTGGAAAGTTTAGGGTCAAAAT-GTAA
** *
12165 TTTTGG-TGAGTTTGGGGTCAAAATATAATTTTAGG-AAGTTTGGGAGTCAAAAATGTAA
1 TTTTGGAAAAGTTTGGGGTCAAAATATAATTTT-GGAAAGTTTAGG-GTC-AAAATGTAA
* * * *
12223 TTTTGGAAAAGTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTCAAAATATGA
1 TTTTGGAAAAGTTTGGGGTCAAAATATAATTTTGG-AAAGTTTAGGGTCAAAATGTAA
* * * * * * * * *
12281 TTTTAGAGAAGTTTAAGGTGT-TAAATGTAAATTTGGCAATGTTTAAGGGCCAAAATGTGA
1 TTTTGGAAAAGTTT--GGGGTCAAAATATAATTTTGG-AAAGTTT-AGGGTCAAAATGTAA
* * * *
12341 TTTTGGAAAAGTTTAGGCGGTTAAAATGTAATTTTGGAAAAGTTTGGGCGTCAAAATGTGA
1 TTTTGGAAAAGTTT-GG-GGTCAAAATATAATTTTGG-AAAGTTTAGG-GTCAAAATGTAA
12402 TTTTGGAAAAGTT
1 TTTTGGAAAAGTT
12415 CAGGGGTTTT
Statistics
Matches: 241, Mismatches: 45, Indels: 37
0.75 0.14 0.11
Matches are distributed among these distances:
55 6 0.02
56 25 0.10
57 23 0.10
58 51 0.21
59 52 0.22
60 41 0.17
61 43 0.18
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (57 bp):
TTTTGGAAAAGTTTGGGGTCAAAATATAATTTTGGAAAGTTTAGGGTCAAAATGTAA
Found at i:12314 original size:60 final size:60
Alignment explanation
Indices: 12184--12422 Score: 258
Period size: 60 Copynumber: 4.0 Consensus size: 60
12174 GTTTGGGGTC
* * *
12184 AAAATATAATTTTAGG--AAGTTTGGGAGTCAAAAATGTAATTTTGGAAAAGTTT-GG-GGTT
1 AAAATGTAATTTT-GGAAAAGTTTAGG-GTC-AAAATGTGATTTTGGAAAAGTTTAGGCGGTT
* * * *
12243 AAAATGTAATTTTGGAAAAGTTTAGGGTCAAAATATGATTTTAGAGAAGTTTAAGG-TGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTCAAAATGTGATTTTGGAAAAGTTT-AGGCGGTT
* * * *
12303 -AAATGTAAATTTGGCAATGTTTAAGGGCCAAAATGTGATTTTGGAAAAGTTTAGGCGGTT
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTCAAAATGTGATTTTGGAAAAGTTTAGGCGGTT
* *
12363 AAAATGTAATTTTGGAAAAGTTTGGGCGTCAAAATGTGATTTTGGAAAAGTTCAGG-GGTT
1 AAAATGTAATTTTGGAAAAGTTTAGG-GTCAAAATGTGATTTTGGAAAAGTTTAGGCGGTT
12423 TTTGTGTAAT
Statistics
Matches: 151, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
58 21 0.14
59 37 0.25
60 47 0.31
61 46 0.30
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (60 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTCAAAATGTGATTTTGGAAAAGTTTAGGCGGTT
Found at i:12346 original size:30 final size:30
Alignment explanation
Indices: 12214--12414 Score: 169
Period size: 30 Copynumber: 6.7 Consensus size: 30
12204 TTGGGAGTCA
* **
12214 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGCC
*
12243 AAAATGTAATTTTGGAAAAGTTT-AGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGCC
* * * * *
12272 AAAATATGATTTTAGAGAAGTTTAAGGTG-T
1 AAAATGTAATTTTGGAAAAGTTTAAGG-GCC
* * * *
12302 TAAATGTAAATTTGGCAATGTTTAAGGGCC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGCC
* * **
12332 AAAATGTGATTTTGGAAAAGTTTAGGCGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAG-GGCC
12363 AAAATGTAATTTTGGAAAAGTTT--GGGCGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGC--C
*
12393 AAAATGTGATTTTGGAAAAGTT
1 AAAATGTAATTTTGGAAAAGTT
12415 CAGGGGTTTT
Statistics
Matches: 138, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
28 2 0.01
29 48 0.35
30 63 0.46
31 25 0.18
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAAGGGCC
Found at i:14806 original size:52 final size:53
Alignment explanation
Indices: 14702--14815 Score: 133
Period size: 52 Copynumber: 2.2 Consensus size: 53
14692 TTTTCTTTTG
* *
14702 ATTAAAAAAAAATCACTACTTTACTTAAAAATTCAAACTTTTATTTCGAAATA
1 ATTAAAAAAAAATCACAACTTTACTTAAAAATTCAAACTTTTATTTCAAAATA
* ** * *
14755 ATTAAAAAAAAATTA-AACTTTTTTTAAAAATTTAAACTTTT-TCTTTAAAATA
1 ATTAAAAAAAAATCACAACTTTACTTAAAAATTCAAACTTTTAT-TTCAAAATA
*
14807 ACTAAAAAA
1 ATTAAAAAA
14816 CAGATTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
51 1 0.02
52 37 0.71
53 14 0.27
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.38
Consensus pattern (53 bp):
ATTAAAAAAAAATCACAACTTTACTTAAAAATTCAAACTTTTATTTCAAAATA
Found at i:14990 original size:141 final size:140
Alignment explanation
Indices: 14810--15066 Score: 383
Period size: 141 Copynumber: 1.8 Consensus size: 140
14800 TAAAATAACT
* *
14810 AAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTTAATAAAAATCGCTATTTT-
1 AAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAT-AAAATCACTATTTTA
*
14874 CTTAAAAATCTAAA-CTTTTATTTCGAAATAGTTAAAAAAAAAATCAAAACTTTGTTTAAAAATT
65 CTTAAAAAT-AAAAGCTTTTATTTCGAAATAGTTAAAAAAAAAAT-AAAACTTTGTTTAAAAATT
14938 TAAACTTTTCTAA
128 TAAACTTTTCTAA
*
14951 AAAAAACAGATTTTTATTTTTAAAAATCTAAACTTTCTCTTTTTTAAATAAAATCACTATTTTAC
1 AAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAATAAAATCACTATTTTAC
* * * * * *
15016 TTGAAAATAAAAGTTTTTATTTCGAAATTGTTTAAATAAAACTAAAACTTT
66 TTAAAAATAAAAGCTTTTATTTCGAAATAGTTAAAAAAAAAATAAAACTTT
15067 TCCCAAAATC
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
140 24 0.23
141 80 0.77
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (140 bp):
AAAAAACAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAATAAAATCACTATTTTAC
TTAAAAATAAAAGCTTTTATTTCGAAATAGTTAAAAAAAAAATAAAACTTTGTTTAAAAATTTAA
ACTTTTCTAA
Found at i:15501 original size:3 final size:3
Alignment explanation
Indices: 15493--15529 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
15483 CATGAAACCC
* *
15493 TAA TAA TAA TAA TAA TAA TAG TAA TGA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
15530 TTGAGTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17956 original size:12 final size:12
Alignment explanation
Indices: 17919--17960 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
17909 TGGAGTATTC
* *
17919 TTTTTCCTTCTG
1 TTTTTTCTTCTT
*
17931 TTTTCTCTTCTT
1 TTTTTTCTTCTT
17943 TTTTTTCTT-TT
1 TTTTTTCTTCTT
17954 TTTTTTC
1 TTTTTTC
17961 CAAATGAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTTTCTTCTT
Done.