Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004162.1 Kokia drynarioides strain JFW-HI SEQ_117388, 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: 80804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:32866 original size:38 final size:38
Alignment explanation
Indices: 32815--32891 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
32805 CATAGTTTCT
32815 TCATCTTACACACCATTAATTTGCTCAAAATACAGCTC
1 TCATCTTACACACCATTAATTTGCTCAAAATACAGCTC
32853 TCATCTTACACACCATTAATTTGCTCAAAATACAGCTC
1 TCATCTTACACACCATTAATTTGCTCAAAATACAGCTC
32891 T
1 T
32892 AGACCCATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (38 bp):
TCATCTTACACACCATTAATTTGCTCAAAATACAGCTC
Found at i:34993 original size:2 final size:2
Alignment explanation
Indices: 34986--35010 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34976 AAATAACATT
34986 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
35011 TTAAACCGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:45513 original size:25 final size:26
Alignment explanation
Indices: 45485--45539 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
45475 ATTATCGTGA
*
45485 TTTTAATT-TATCTATAATTTTGT-GG
1 TTTT-ATTCTATCTACAATTTTGTAGG
*
45510 TTTTATTCTCTCTACAATTTTGTAGG
1 TTTTATTCTATCTACAATTTTGTAGG
45536 TTTT
1 TTTT
45540 GTTTTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 3 0.12
25 17 0.65
26 6 0.23
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.60
Consensus pattern (26 bp):
TTTTATTCTATCTACAATTTTGTAGG
Found at i:45883 original size:3 final size:3
Alignment explanation
Indices: 45875--45934 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
45865 TGGATTAATC
45875 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45923 TAT TAT TAT TAT
1 TAT TAT TAT TAT
45935 AAACAACAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:48802 original size:17 final size:18
Alignment explanation
Indices: 48776--48839 Score: 75
Period size: 17 Copynumber: 3.7 Consensus size: 18
48766 AACTCAACCT
48776 TTAAATATTTTCAATATA
1 TTAAATATTTTCAATATA
48794 TTAAA-ATTTTC-AT-T-
1 TTAAATATTTTCAATATA
48808 TTGAAAATATTTTCAATATA
1 TT--AAATATTTTCAATATA
48828 TTAAA-ATTTTCA
1 TTAAATATTTTCA
48840 TTTTGAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.05
15 1 0.03
16 5 0.12
17 19 0.47
18 10 0.25
19 1 0.03
20 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAAATATTTTCAATATA
Found at i:48821 original size:34 final size:34
Alignment explanation
Indices: 48778--48847 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
48768 CTCAACCTTT
48778 AAATATTTTCAATATATTAAAATTTTCATTTTGA
1 AAATATTTTCAATATATTAAAATTTTCATTTTGA
48812 AAATATTTTCAATATATTAAAATTTTCATTTTGA
1 AAATATTTTCAATATATTAAAATTTTCATTTTGA
48846 AA
1 AA
48848 TTAAAAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (34 bp):
AAATATTTTCAATATATTAAAATTTTCATTTTGA
Found at i:49633 original size:28 final size:27
Alignment explanation
Indices: 49601--49664 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
49591 TATTTTTTAA
49601 TATTTTAATATTT-AATATT-ATAGTTTT
1 TATTTTAATATTTAAAT-TTAAT-GTTTT
49628 CTATTTTTAA-ATTTAAATTTAATGTTTT
1 -TA-TTTTAATATTTAAATTTAATGTTTT
49656 TATTTTAAT
1 TATTTTAAT
49665 TGTCACGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
26 6 0.19
27 2 0.06
28 13 0.41
29 11 0.34
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (27 bp):
TATTTTAATATTTAAATTTAATGTTTT
Found at i:50255 original size:6 final size:6
Alignment explanation
Indices: 50244--50276 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
50234 TATTAACATC
50244 GATGTT GATGTT GATGTT GATGTT GATGTT GAT
1 GATGTT GATGTT GATGTT GATGTT GATGTT GAT
50277 AAGTAAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (6 bp):
GATGTT
Found at i:59241 original size:10 final size:10
Alignment explanation
Indices: 59226--59250 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59216 TATTATTTAG
59226 ATTTTTTAAA
1 ATTTTTTAAA
59236 ATTTTTTAAA
1 ATTTTTTAAA
59246 ATTTT
1 ATTTT
59251 AAATTAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:59338 original size:15 final size:15
Alignment explanation
Indices: 59318--59356 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
59308 AATTTTTTAA
59318 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
59333 AAATTATTAAAAATT
1 AAATTATTAAAAATT
59348 AAATT-TTAA
1 AAATTATTAA
59357 TTTTGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.17
15 12 0.52
16 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:63225 original size:22 final size:22
Alignment explanation
Indices: 63193--63240 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
63183 CTTATTTAAG
*
63193 GGTTCAAGGTTCAAGTGTTTGA
1 GGTTCAAGGTTCAAGGGTTTGA
*
63215 GGTTCACGGTTCAAGGGTTTGA
1 GGTTCAAGGTTCAAGGGTTTGA
63237 GGTT
1 GGTT
63241 ATAAGCTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.10, G:0.35, T:0.35
Consensus pattern (22 bp):
GGTTCAAGGTTCAAGGGTTTGA
Found at i:67536 original size:30 final size:30
Alignment explanation
Indices: 67500--67564 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
67490 ACTTATTTTA
*
67500 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAGAGACAT
67530 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAGAGACAT
67560 TTGTT
1 TTGTT
67565 TGTTAAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGACAT
Found at i:70812 original size:16 final size:16
Alignment explanation
Indices: 70785--70817 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
70775 TTCACTTTTT
70785 TATTTTTAATTAATAAA
1 TATTTTTAATTAA-AAA
70802 TATTTTT-ATTAAAAA
1 TATTTTTAATTAAAAA
70817 T
1 T
70818 TAGAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTTAATTAAAAA
Found at i:71318 original size:16 final size:17
Alignment explanation
Indices: 71286--71318 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
71276 TCCGTTCAAT
*
71286 AATTTTATAATTTATAA
1 AATTTTATAATTAATAA
71303 AATTTTA-AATTAATAA
1 AATTTTATAATTAATAA
71319 CAATAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTTATAATTAATAA
Done.