Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014884.1 Kokia drynarioides strain JFW-HI SEQ_129927, 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: 80485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 123 characters in sequence are not A, C, G, or T
Found at i:2161 original size:6 final size:6
Alignment explanation
Indices: 2150--2175 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2140 TTTAGAGTTG
2150 GAAATT GAAATT GAAATT GAAATT GA
1 GAAATT GAAATT GAAATT GAAATT GA
2176 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (6 bp):
GAAATT
Found at i:3487 original size:25 final size:25
Alignment explanation
Indices: 3450--3500 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3440 TATTAGAGTA
* * *
3450 AAACCTATTATCCATGCTAAACAAT
1 AAACCCATGATCCATACTAAACAAT
3475 AAACCCATGATCCATACTAAACAAT
1 AAACCCATGATCCATACTAAACAAT
3500 A
1 A
3501 TAGAGAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (25 bp):
AAACCCATGATCCATACTAAACAAT
Found at i:5716 original size:111 final size:111
Alignment explanation
Indices: 5539--5760 Score: 354
Period size: 111 Copynumber: 2.0 Consensus size: 111
5529 TCTGCTATAA
* * * * * *
5539 AATTTAGACTCGATCATGAATCATTTGATATAAGTAGTATTGAATGAGGTTTTGTTAAAGAACTC
1 AATTTAGACTCGATCATGAACCATTTAATATAAGAAATATTAAATGAGGTTTTGTTAAAAAACTC
* * *
5604 ACAGTTCAAAACTTTTTTTTTCATCTAATAAAATATTTTTCAGCAT
66 ACAGTTCAAAACCTTTATTTTCATCTAATAAAATATTTTCCAGCAT
*
5650 AATTTAGACTCGATCATGAACCATTTAATATAAGAAATATTAAATGGGGTTTTGTTAAAAAACTC
1 AATTTAGACTCGATCATGAACCATTTAATATAAGAAATATTAAATGAGGTTTTGTTAAAAAACTC
5715 ACAGTTCAAAACCTTTATTTTCATCTAATAAAATATTTTCCAGCAT
66 ACAGTTCAAAACCTTTATTTTCATCTAATAAAATATTTTCCAGCAT
5761 TTGTTAAAAC
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (111 bp):
AATTTAGACTCGATCATGAACCATTTAATATAAGAAATATTAAATGAGGTTTTGTTAAAAAACTC
ACAGTTCAAAACCTTTATTTTCATCTAATAAAATATTTTCCAGCAT
Found at i:6739 original size:29 final size:31
Alignment explanation
Indices: 6647--6741 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 31
6637 AAATAATGAA
* *
6647 AATTTTGAATTCTTTTAATAAATATTTACTT
1 AATTTTGAAGTGTTTTAATAAATATTTACTT
* * *
6678 AA-TTTGAAGTGTTTTTATTAGTATTTA-TGT
1 AATTTTGAAGTGTTTTAATAAATATTTACT-T
* *
6708 AATTTTG-AGT-TTTTAATCAATATCTACTT
1 AATTTTGAAGTGTTTTAATAAATATTTACTT
6737 AATTT
1 AATTT
6742 AAAATTTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
29 19 0.37
30 27 0.52
31 6 0.12
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (31 bp):
AATTTTGAAGTGTTTTAATAAATATTTACTT
Found at i:14856 original size:26 final size:26
Alignment explanation
Indices: 14803--14872 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 26
14793 ACAAAGTACT
14803 AACAGAGA-ACACATAAGTGCTGGAC
1 AACAGAGAGACACATAAGTGCTGGAC
*
14828 AACAGAGAGCACACAT-AGTGCTGGGC
1 AACAGAGAG-ACACATAAGTGCTGGAC
14854 AACAGAGAGTACACA-AAGT
1 AACAGAGAG-ACACATAAGT
14873 ATTAATCAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.20
26 26 0.65
27 6 0.15
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (26 bp):
AACAGAGAGACACATAAGTGCTGGAC
Found at i:14901 original size:23 final size:23
Alignment explanation
Indices: 14784--14913 Score: 63
Period size: 26 Copynumber: 5.4 Consensus size: 23
14774 ATGGAACAAA
* *
14784 CAGAGAGTA-ACAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
*
14805 CAGAGA--ACACATAAGTGCTGGACAA
1 CAGAGAGCACACA-AAGTGCT--A-AT
*
14830 CAGAGAGCACACATAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTGCT----AAT
* **
14856 CAGAGAGTACACAAAGTATTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
14879 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
14902 AACAGAGAGCAC
1 --CAGAGAGCAC
14914 GCTAGTGTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 12 0.14
22 2 0.02
23 20 0.24
24 1 0.01
25 16 0.19
26 22 0.26
27 6 0.07
28 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:14907 original size:25 final size:25
Alignment explanation
Indices: 14802--14913 Score: 79
Period size: 26 Copynumber: 4.5 Consensus size: 25
14792 AACAAAGTAC
* * *
14802 TAACAGAGAACACATAAGTGCTGGA
1 TAACAGAGAGCACACAAGTGCTGAA
* **
14827 CAACAGAGAGCACACATAGTGCTGGG
1 TAACAGAGAGCACACA-AGTGCTGAA
* * * *
14853 CAACAGAGAGTACACAA-AG-T-AT
1 TAACAGAGAGCACACAAGTGCTGAA
14875 TAATCAGAGAGCACACACAGTGCT-AA
1 TAA-CAGAGAGCACACA-AGTGCTGAA
14901 TAACAGAGAGCAC
1 TAACAGAGAGCAC
14914 GCTAGTGTTC
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.03
23 13 0.19
24 2 0.03
25 25 0.36
26 28 0.40
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (25 bp):
TAACAGAGAGCACACAAGTGCTGAA
Found at i:15541 original size:42 final size:42
Alignment explanation
Indices: 15482--15564 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
15472 TTTTCTTTCA
15482 CTGTTATTTCCAAACTGTTTTACTAAATCACAAATTCATCCT
1 CTGTTATTTCCAAACTGTTTTACTAAATCACAAATTCATCCT
15524 CTGTTATTTCCAAACTGTTTTACTAAATCACAAATTCATCC
1 CTGTTATTTCCAAACTGTTTTACTAAATCACAAATTCATCC
15565 CTTCATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (42 bp):
CTGTTATTTCCAAACTGTTTTACTAAATCACAAATTCATCCT
Found at i:27802 original size:19 final size:19
Alignment explanation
Indices: 27777--27820 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
27767 TAAATTTTTT
* *
27777 TAAATAACAAATTATATATC
1 TAAATAA-AAAGTAAATATC
27797 -AAATAAAAAGTAAATATC
1 TAAATAAAAAGTAAATATC
27815 TAAATA
1 TAAATA
27821 GGAATATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAATAAAAAGTAAATATC
Found at i:56065 original size:21 final size:21
Alignment explanation
Indices: 56023--56090 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
56013 CGGAGACACC
* *
56023 GAGGATGATGAGGAT-GAGGAT
1 GAGGAAGATGAAGATGGA-GAT
56044 GAGGAAGATGAAGCA-GGAGAT
1 GAGGAAGATGAAG-ATGGAGAT
** *
56065 GATCAAGATGAAGATGTAGAT
1 GAGGAAGATGAAGATGGAGAT
56086 GAGGA
1 GAGGA
56091 GGAGGATGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.03
21 33 0.89
22 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.41, T:0.16
Consensus pattern (21 bp):
GAGGAAGATGAAGATGGAGAT
Found at i:56238 original size:9 final size:9
Alignment explanation
Indices: 56227--56274 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
56217 TGATGGTGAG
*
56227 GAAGAGGAG
1 GAAGAGGAA
*
56236 GAAGAAGAA
1 GAAGAGGAA
56245 GAAGAGGAA
1 GAAGAGGAA
* *
56254 GACGAGGAC
1 GAAGAGGAA
56263 GAAGAGGAA
1 GAAGAGGAA
56272 GAA
1 GAA
56275 CTTCAGCCAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.52, C:0.04, G:0.44, T:0.00
Consensus pattern (9 bp):
GAAGAGGAA
Found at i:60931 original size:28 final size:29
Alignment explanation
Indices: 60890--60945 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
60880 AATTGGTTAT
60890 CCTGAAAAACTAT-AGTTAAAACATCAAA
1 CCTGAAAAACTATAAGTTAAAACATCAAA
60918 CCTGAATAAA-TATAGAGTTAAAACATCA
1 CCTGAA-AAACTATA-AGTTAAAACATCA
60946 TTTGTAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 9 0.36
29 3 0.12
30 13 0.52
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.23
Consensus pattern (29 bp):
CCTGAAAAACTATAAGTTAAAACATCAAA
Done.