Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003908.1 Kokia drynarioides strain JFW-HI SEQ_116971, 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: 4418
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Found at i:2962 original size:220 final size:220
Alignment explanation
Indices: 2581--3356 Score: 1277
Period size: 220 Copynumber: 3.5 Consensus size: 220
2571 AAGCGATGCG
* * *
2581 GTCATCTTCTCGATGAGATACTAAGAAGAAGACCAAACCAAACTCACGCTCGATGTAAGCAAAA-
1 GTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAAAG
* ** *
2645 CTTTGAATCCCAGCGCCCTGATGAGGTACTAAGAAGCAAGTCGAAGTAATAAAACGGTTGGCTTC
66 CTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAACGGTTGGCTTC
*
2710 CTGATCATCTTCATGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTTCCTGATGAGATACAGA
131 CTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTTCCTGATGAGATACAGA
*
2775 GAAACAAATTGAAACCAACGACACA
196 GAAACGAATTGAAACCAACGACACA
* *
2800 GTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAACCAAACTCACGCTTGATGTGAGCAAAAG
1 GTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAAAG
2865 CTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAACGGTTGGCTTC
66 CTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAACGGTTGGCTTC
* *
2930 CTGACCATTTTCATGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTTTCTGATGAGATACAGA
131 CTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTTCCTGATGAGATACAGA
2995 GAAACGAATTGAAACCAACGACACA
196 GAAACGAATTGAAACCAACGACACA
* * *
3020 GTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAACCAAACTTACGCTAGATGTGAGCAAAAG
1 GTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAAAG
3085 CTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAACGGTTGGCTTC
66 CTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAACGGTTGGCTTC
* *
3150 CTGACCATCTTCATGATGAGGTACAGAGAAGTGGACCAAATTCGTCTTTCCTGAGGAGATACAGA
131 CTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTTCCTGATGAGATACAGA
3215 GAAACGAATTGAAACCAACGACACA
196 GAAACGAATTGAAACCAACGACACA
* * * * * *
3240 GTCATCTTCCCGATGAGATACTGAGAAGAAGACTAAATCAAACTCACGCCCAATGTGAAC-AAAT
1 GTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAAAG
* ** * *
3304 CTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
66 CTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAA
3357 GTGGTTAGCT
Statistics
Matches: 523, Mismatches: 33, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
219 110 0.21
220 413 0.79
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (220 bp):
GTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAACCAAACTCACGCTCGATGTGAGCAAAAG
CTTCGAATCCCAGCTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGTAATAAAACGGTTGGCTTC
CTGACCATCTTCATGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTTCCTGATGAGATACAGA
GAAACGAATTGAAACCAACGACACA
Found at i:3836 original size:18 final size:17
Alignment explanation
Indices: 3807--3889 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
3797 TTAAGTTTAT
*
3807 TTTAAAAATTAAATTTG
1 TTTAAAATTTAAATTTG
*
3824 TTTAAAATTTTAAATTTA
1 TTTAAAA-TTTAAATTTG
**
3842 TTTTGAATTTAAATTTG
1 TTTAAAATTTAAATTTG
* *
3859 ATTT-AAGTTTAAATTTAT
1 -TTTAAAATTTAAATTT-G
*
3877 TTTCAAATTTAAA
1 TTTAAAATTTAAA
3890 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
17 29 0.55
18 24 0.45
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTAAAATTTAAATTTG
Found at i:3874 original size:12 final size:12
Alignment explanation
Indices: 3829--3888 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 12
3819 ATTTGTTTAA
3829 AATTTTAAATTT
1 AATTTTAAATTT
*
3841 -ATTTTGAATTT
1 AATTTTAAATTT
* *
3852 AAATTT-GATTT
1 AATTTTAAATTT
*
3863 AAGTTTAAATTT
1 AATTTTAAATTT
3875 -ATTTTCAAATTT
1 AATTTT-AAATTT
3887 AA
1 AA
3889 AATTATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
11 23 0.61
12 14 0.37
13 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (12 bp):
AATTTTAAATTT
Found at i:3886 original size:35 final size:34
Alignment explanation
Indices: 3796--3906 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 34
3786 CCAAACTCCC
* *
3796 TTTAAGTTTATTTTAAAAATTAAATTTG-TTTAAAA
1 TTTAAATTTATTTT-AAATTTAAATTTGATTT-AAA
* *
3831 TTTTAAATTTATTTTGAATTTAAATTTGATTTAAG
1 -TTTAAATTTATTTTAAATTTAAATTTGATTTAAA
*
3866 TTTAAATTTATTTTCAAATTTAAAATT-ATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTGATT-TAAA
3901 TTTAAA
1 TTTAAA
3907 ATAAGTAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
34 17 0.26
35 32 0.49
36 16 0.25
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTGATTTAAA
Found at i:3908 original size:17 final size:17
Alignment explanation
Indices: 3796--3906 Score: 107
Period size: 18 Copynumber: 6.4 Consensus size: 17
3786 CCAAACTCCC
*
3796 TTTAAGTTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
3814 ATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
*
3831 TTTTAAATTTATTTTGAA
1 -TTTAAATTTATTTTAAA
*
3849 TTTAAATTTGA-TTTAAG
1 TTTAAATTT-ATTTTAAA
3866 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
3884 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
3901 TTTAAA
1 TTTAAA
3907 ATAAGTAAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
16 1 0.01
17 37 0.49
18 38 0.50
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Done.