Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001589.1 Kokia drynarioides strain JFW-HI SEQ_113202, 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: 7450
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:284 original size:22 final size:22
Alignment explanation
Indices: 241--300 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
231 ATTAGACCAC
**
241 CCAAT-TTCCAGCTCACTTAAA
1 CCAATATTCCAGCTCACGAAAA
*
262 CCAATATTCCAGCTCAGGAAAA
1 CCAATATTCCAGCTCACGAAAA
*
284 CCGAA-ATTCAAGCTCAC
1 CC-AATATTCCAGCTCAC
301 CAACACCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 5 0.16
22 25 0.78
23 2 0.06
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (22 bp):
CCAATATTCCAGCTCACGAAAA
Found at i:1708 original size:62 final size:60
Alignment explanation
Indices: 1632--2108 Score: 509
Period size: 62 Copynumber: 7.8 Consensus size: 60
1622 TTTCATTCCA
*
1632 CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTAATCTGATAATAGCGGGTGTCGG
1 CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTT-ATCTGATAAAAG-GGGTGTCGG
* * *
1694 CCATTGCATGGCCAACACGAAAAAAATTTAAAATTTTTTAT-TCGAAAAAAGGAGGTGTCGG
1 CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTATCT-GATAAAAGG-GGTGTCGG
* * * * *
1755 CCATTGCATGGCTAACATCC--AAAATTTTGAATTTTTTTTATCTGAAAAAAAGGAGTGTCGG
1 CCATTGCATGGCCAACA-CCAAAAAAATTTGAA-ATTTTTTATCTG-ATAAAAGGGGTGTCGG
** * *
1816 CCATTGCATGATCAACACCAAAAAAATTTGAAAATTTTTTATCTAATAATAGGGGATGTCGG
1 CCATTGCATGGCCAACACCAAAAAAATTTG-AAATTTTTTATCTGATAAAAGGGG-TGTCGG
* * *
1878 CCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCTGAAAAAAAGGGTGTCGA
1 CCATTGCATGGCCAACACCAAAAAAATTTG-AAATTTTTTATCTGATAAAAGGGGTGTCGG
* * * * * *
1939 CCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGA
1 CCATTGCATGGCCAACACCAAAAAAATTTGAAA-TTTTTTATCTGATAA-AAGGGGTGTCGG
* * * * *
2001 CCATTGCGTGGCCAACACAAAAAAAATTTGAAATTTTTTTATCAGATTAATAGGGATGTCGG
1 CCATTGCATGGCCAACACCAAAAAAATTTGAAA-TTTTTTATCTGA-TAAAAGGGGTGTCGG
* * *
2063 CCATTGTATGGCCAA-A-CAAAAAAA-TTG-TATTTTTTATCTGACAAAA
1 CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTATCTGATAAAA
2109 TGGCCAACAC
Statistics
Matches: 353, Mismatches: 49, Indels: 32
0.81 0.11 0.07
Matches are distributed among these distances:
56 3 0.01
57 11 0.03
58 1 0.00
59 3 0.01
60 23 0.07
61 116 0.33
62 192 0.54
63 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (60 bp):
CCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTATCTGATAAAAGGGGTGTCGG
Found at i:1792 original size:123 final size:121
Alignment explanation
Indices: 1632--2088 Score: 503
Period size: 123 Copynumber: 3.7 Consensus size: 121
1622 TTTCATTCCA
*
1632 CCATTGCATGGCCAACACCAAAAAAATTTG-AAATTTTTTAATCTGATAATAGCGGGTGTCGGCC
1 CCATTGCATGGCCAACACC-AAAAAATTTGAAAATTTTTT-ATCTGATAAAAG-GGGTGTCGGCC
* *
1696 ATTGCATGGCCAACACGAAAAAAATTT-AAAATTTTTTATTCGAAAAAAGGAGGTGTCGG
63 ATTGCATGACCAACACCAAAAAAATTTGAAAATTTTTTATTCGAAAAAAGG-GGTGTCGG
* * ** * *
1755 CCATTGCATGGCTAACATCC-AAAATTTTGAATTTTTTTTATCTGAAAAAAAGGAGTGTCGGCCA
1 CCATTGCATGGCCAACA-CCAAAAAATTTGAAAATTTTTTATCTG-ATAAAAGGGGTGTCGGCCA
* * *
1819 TTGCATGATCAACACCAAAAAAATTTGAAAATTTTTTA-TCTAATAATAGGGGATGTCGG
64 TTGCATGACCAACACCAAAAAAATTTGAAAATTTTTTATTCGAA-AAAAGGGG-TGTCGG
* * *
1878 CCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCTGAAAAAAAGGGTGTCGACCAT
1 CCATTGCATGGCCAACACC-AAAAAATTTGAAAATTTTTTATCTGATAAAAGGGGTGTCGGCCAT
* * * * * *
1943 TGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGA
65 TGCATGACCAACACCAAAAAAATTTGAAAATTTTTTATTCGA-AAAAAGGGGTGTCGG
* * * * * *
2001 CCATTGCGTGGCCAACACAAAAAAAATTTGAAATTTTTTTATCAGATTAATAGGGATGTCGGCCA
1 CCATTGCATGGCCAACAC-CAAAAAATTTGAAAATTTTTTATCTGA-TAAAAGGGGTGTCGGCCA
* *
2066 TTGTATGGCCAA-A-CAAAAAAATT
64 TTGCATGACCAACACCAAAAAAATT
2089 GTATTTTTTA
Statistics
Matches: 282, Mismatches: 40, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
122 64 0.23
123 164 0.58
124 53 0.19
125 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (121 bp):
CCATTGCATGGCCAACACCAAAAAATTTGAAAATTTTTTATCTGATAAAAGGGGTGTCGGCCATT
GCATGACCAACACCAAAAAAATTTGAAAATTTTTTATTCGAAAAAAGGGGTGTCGG
Found at i:3232 original size:24 final size:22
Alignment explanation
Indices: 3174--3233 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 22
3164 GTAATTATTA
3174 TAAATTATTTGTTTAGTTTAATG
1 TAAATTATTT-TTTAGTTTAATG
**
3197 TTTATGTGATTTTTTAGTTATAAATG
1 TAAAT-T-ATTTTTTAGTT-T-AATG
3223 TAAATTATTTT
1 TAAATTATTTT
3234 GTTATTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.10
24 13 0.45
25 6 0.21
26 7 0.24
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (22 bp):
TAAATTATTTTTTAGTTTAATG
Found at i:3276 original size:21 final size:21
Alignment explanation
Indices: 3252--3308 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3242 TTGTTAAAAT
3252 ATTTTATTTTAAAGTTATT-TA
1 ATTTTATTTTAAA-TTATTATA
* *
3273 ATTTTGTTTTTAATTATTATA
1 ATTTTATTTTAAATTATTATA
*
3294 A--TTATTATAAATTAT
1 ATTTTATTTTAAATTAT
3309 AAAGCATTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 11 0.37
20 5 0.17
21 14 0.47
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTTTATTTTAAATTATTATA
Done.