Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008564.1 Kokia drynarioides strain JFW-HI SEQ_123242, 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: 6266
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Found at i:4065 original size:19 final size:19
Alignment explanation
Indices: 4031--4069 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4021 TTCTAAATGG
4031 TTTATCGTAAAATTTTGATA
1 TTTATCGTAAAATTTT-ATA
*
4051 TTTAT-GTAAATTTTTATA
1 TTTATCGTAAAATTTTATA
4069 T
1 T
4070 GAATGGCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (19 bp):
TTTATCGTAAAATTTTATA
Found at i:4406 original size:22 final size:24
Alignment explanation
Indices: 4379--4429 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
4369 AAATGTTTCA
4379 AAAATA-TT-ATGTTAGTAATATC
1 AAAATATTTCATGTTAGTAATATC
*
4401 AAAATATTTTCATGTTAGTAATATT
1 AAAATA-TTTCATGTTAGTAATATC
4426 AAAA
1 AAAA
4430 CATTCTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
24 2 0.08
25 17 0.68
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (24 bp):
AAAATATTTCATGTTAGTAATATC
Found at i:5208 original size:12 final size:12
Alignment explanation
Indices: 5191--5216 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5181 TATTAGTGGT
5191 AAAAAGGAAAGA
1 AAAAAGGAAAGA
5203 AAAAAGGAAAGA
1 AAAAAGGAAAGA
5215 AA
1 AA
5217 CAAAAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAAGGAAAGA
Found at i:6001 original size:24 final size:24
Alignment explanation
Indices: 5974--6242 Score: 203
Period size: 24 Copynumber: 11.4 Consensus size: 24
5964 ATGTGGAAGT
5974 TGACAAGCGTAAATGTATATAAGC
1 TGACAAGCGTAAATGTATATAAGC
* *
5998 TGACGAGCGTAAACGTATATAAGC
1 TGACAAGCGTAAATGTATATAAGC
* * ** * **
6022 TGACGAGCATAAACATGTGCAAGC
1 TGACAAGCGTAAATGTATATAAGC
* * *
6046 TGACAAGCAT-AA---A-CTAAGT
1 TGACAAGCGTAAATGTATATAAGC
* * * **
6065 TGACGAGCGTAAATCTGTGCAAGC
1 TGACAAGCGTAAATGTATATAAGC
*
6089 TGACAAGCGTAAACGTATATAAGC
1 TGACAAGCGTAAATGTATATAAGC
* **
6113 TGACGAGCGTAAGCATG--TGCAAGC
1 TGACAAGCGTAA--ATGTATATAAGC
*
6137 TGACGAGCGTAAATGTATATAAGC
1 TGACAAGCGTAAATGTATATAAGC
* * * *
6161 TAACAAGCGTAAACGTGT-TCAATC
1 TGACAAGCGTAAATGTATAT-AAGC
*
6185 TAACAAGCGTAAATGTATATAAGC
1 TGACAAGCGTAAATGTATATAAGC
6209 TGACAAGCGTAAATGTATATAAGC
1 TGACAAGCGTAAATGTATATAAGC
*
6233 TGACGAGCGT
1 TGACAAGCGT
6243 GAACATGTGC
Statistics
Matches: 194, Mismatches: 40, Indels: 22
0.76 0.16 0.09
Matches are distributed among these distances:
19 11 0.06
20 2 0.01
22 3 0.02
23 3 0.02
24 172 0.89
25 1 0.01
26 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (24 bp):
TGACAAGCGTAAATGTATATAAGC
Found at i:6049 original size:48 final size:48
Alignment explanation
Indices: 5994--6221 Score: 270
Period size: 48 Copynumber: 4.9 Consensus size: 48
5984 AAATGTATAT
* *
5994 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCATAAACATGTGC
1 AAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAACATGTGC
* *
6042 AAGCTGACAAGCATAAAC-----TAAGTTGACGAGCGTAAATC-TGTGC
1 AAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAA-CATGTGC
*
6085 AAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAGCATGTGC
1 AAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAACATGTGC
* * * * * *
6133 AAGCTGACGAGCGTAAATGTATATAAGCTAACAAGCGTAAACGTGTTC
1 AAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAACATGTGC
* * * *
6181 AATCTAACAAGCGTAAATGTATATAAGCTGACAAGCGTAAA
1 AAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAA
6222 TGTATATAAG
Statistics
Matches: 155, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
43 38 0.25
44 1 0.01
47 1 0.01
48 115 0.74
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (48 bp):
AAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAACATGTGC
Found at i:6084 original size:43 final size:43
Alignment explanation
Indices: 6017--6149 Score: 142
Period size: 43 Copynumber: 3.0 Consensus size: 43
6007 TAAACGTATA
6017 TAAGCTGACGAGCATAAACATGTGCAAGCTGACAAGCATAAAC
1 TAAGCTGACGAGCATAAACATGTGCAAGCTGACAAGCATAAAC
* * *
6060 TAAGTTGACGAGCGTAAATC-TGTGCAAGCTGACAAGCGTAAAC
1 TAAGCTGACGAGCATAAA-CATGTGCAAGCTGACAAGCATAAAC
* * * *
6103 GTATATAAGCTGACGAGCGTAAGCATGTGCAAGCTGACGAGCGTAAA
1 -----TAAGCTGACGAGCATAAACATGTGCAAGCTGACAAGCATAAA
6150 TGTATATAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
43 38 0.49
44 1 0.01
47 1 0.01
48 37 0.48
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (43 bp):
TAAGCTGACGAGCATAAACATGTGCAAGCTGACAAGCATAAAC
Found at i:6130 original size:91 final size:94
Alignment explanation
Indices: 5970--6221 Score: 287
Period size: 91 Copynumber: 2.7 Consensus size: 94
5960 GTATATGTGG
* * * * *
5970 AAGTTGACAAGCGTAAATGTATATAAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCATAAA
1 AAGTTGACAAGCGTAAATCTGTACAAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAA
*
6035 CATGTGCAAGCTGACAAGCAT-AA-A-CT
66 CATGTGCAAGCTGACAAGCATAAATATAT
* * *
6061 AAGTTGACGAGCGTAAATCTGTGCAAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAG
1 AAGTTGACAAGCGTAAATCTGTACAAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAA
* *
6126 CATGTGCAAGCTGACGAGCGTAAATGTATAT
66 CATGTGCAAGCTGACAAGCATAAA--TATAT
* * * * * * *
6157 AAGCTAACAAGCGTAAA-CGTGTTCAATCTAACAAGCGTAAATGTATATAAGCTGACAAGCGTAA
1 AAGTTGACAAGCGTAAATC-TGTACAAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAA
6221 A
65 A
6222 TGTATATAAG
Statistics
Matches: 135, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
91 76 0.56
92 2 0.01
95 2 0.01
96 55 0.41
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (94 bp):
AAGTTGACAAGCGTAAATCTGTACAAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAA
CATGTGCAAGCTGACAAGCATAAATATAT
Found at i:6161 original size:72 final size:68
Alignment explanation
Indices: 5964--6266 Score: 257
Period size: 72 Copynumber: 4.3 Consensus size: 68
5954 TAATATGTAT
* * * *
5964 ATGTGGAAGTTGACAAGCGTAAATGTATATAAGCTGACGAGCGTAAACGTATATAAGCTGACGAG
1 ATGTGCAAGCTGACAAGCGTAAATG----TAAGCTGACGAGCGTAAATGTATATAAGCTGACAAG
*
6029 CATAAAC
62 CGTAAAC
* * * * * **
6036 ATGTGCAAGCTGACAAGCATAAA-CTAAGTTGACGAGCGTAAATCTGTGCAAGCTGACAAGCGTA
1 ATGTGCAAGCTGACAAGCGTAAATGTAAGCTGACGAGCGTAAATGTATATAAGCTGACAAGCGTA
6100 AAC
66 AAC
* * ** * *
6103 GTATATAAGCTGACGAGCGTAAGCATGTGCAAGCTGACGAGCGTAAATGTATATAAGCTAACAAG
1 ATGTGCAAGCTGACAAGCGTAA--ATGT--AAGCTGACGAGCGTAAATGTATATAAGCTGACAAG
6168 CGTAAAC
62 CGTAAAC
* * * * * *
6175 GTGTTCAATCTAACAAGCGTAAATGTATATAAGCTGACAAGCGTAAATGTATATAAGCTGACGAG
1 ATGTGCAAGCTGACAAGCGTAAATG----TAAGCTGACGAGCGTAAATGTATATAAGCTGACAAG
*
6240 CGTGAAC
62 CGTAAAC
*
6247 ATGTGCAAGCTGACGAGCGT
1 ATGTGCAAGCTGACAAGCGT
Statistics
Matches: 182, Mismatches: 40, Indels: 18
0.76 0.17 0.08
Matches are distributed among these distances:
67 51 0.28
69 1 0.01
70 4 0.02
72 125 0.69
74 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.22
Consensus pattern (68 bp):
ATGTGCAAGCTGACAAGCGTAAATGTAAGCTGACGAGCGTAAATGTATATAAGCTGACAAGCGTA
AAC
Found at i:6242 original size:48 final size:48
Alignment explanation
Indices: 5974--6242 Score: 251
Period size: 48 Copynumber: 5.7 Consensus size: 48
5964 ATGTGGAAGT
* ** *
5974 TGACAAGCGTAAATGTATATAAGCTGACGAGCGTAAACGTATATAAGC
1 TGACAAGCGTAAATGTGTGCAAGCTGACAAGCGTAAACGTATATAAGC
* * ** * *
6022 TGACGAGCATAAACATGTGCAAGCTGACAAGCATAAAC-----TAAGT
1 TGACAAGCGTAAATGTGTGCAAGCTGACAAGCGTAAACGTATATAAGC
* *
6065 TGACGAGCGTAAATCTGTGCAAGCTGACAAGCGTAAACGTATATAAGC
1 TGACAAGCGTAAATGTGTGCAAGCTGACAAGCGTAAACGTATATAAGC
* *** * *
6113 TGACGAGCGTAAGCATGTGCAAGCTGACGAGCGTAAATGTATATAAGC
1 TGACAAGCGTAAATGTGTGCAAGCTGACAAGCGTAAACGTATATAAGC
* * * * * *
6161 TAACAAGCGTAAACGTGTTCAATCTAACAAGCGTAAATGTATATAAGC
1 TGACAAGCGTAAATGTGTGCAAGCTGACAAGCGTAAACGTATATAAGC
* ** *
6209 TGACAAGCGTAAATGTATATAAGCTGACGAGCGT
1 TGACAAGCGTAAATGTGTGCAAGCTGACAAGCGT
6243 GAACATGTGC
Statistics
Matches: 180, Mismatches: 36, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
43 38 0.21
48 142 0.79
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (48 bp):
TGACAAGCGTAAATGTGTGCAAGCTGACAAGCGTAAACGTATATAAGC
Done.