Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013763.1 Kokia drynarioides strain JFW-HI SEQ_128791, 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: 53090
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:13753 original size:6 final size:6
Alignment explanation
Indices: 13742--13771 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
13732 ATTGTATCTC
*
13742 TAATTA TAATTA TAATTA TAATCA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA
13772 ATTTGCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATTA
Found at i:15029 original size:67 final size:66
Alignment explanation
Indices: 14953--15139 Score: 266
Period size: 71 Copynumber: 2.7 Consensus size: 66
14943 TTTGTTATTT
*
14953 ATTTATTTATTTATCTATATTCATAAGATAATAAATAAATAATAAAACAAAATTAATATTATTTT
1 ATTTATTTATTTATTTATATTCATAA-ATAATAAATAAATAATAAAACAAAATTAATATTATTTT
15018 AC
65 AC
*
15020 ATTTATTTATTTATTTATATTCATACAATAATAAATAAATAAGTAATAAAATAAAATTAATATTA
1 ATTTATTTATTTATTTATATTCATA-AATAATAAAT--A-AA-TAATAAAACAAAATTAATATTA
15085 TTTTAC
61 TTTTAC
*
15091 ATTTATTTATTTATTTATATTCATAAAAATAATGAATAAATGAATAAAA
1 ATTTATTTATTTATTTATATTCAT--AAATAATAAATAAAT-AATAAAA
15140 ATAATAAGAA
Statistics
Matches: 109, Mismatches: 3, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
67 33 0.30
68 2 0.02
69 10 0.09
70 3 0.03
71 51 0.47
72 9 0.08
73 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (66 bp):
ATTTATTTATTTATTTATATTCATAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTA
C
Found at i:18079 original size:14 final size:15
Alignment explanation
Indices: 18060--18088 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18050 GAAAATGAAG
18060 TTTAATT-TTTAAAT
1 TTTAATTATTTAAAT
18074 TTTAATTATTTAAAT
1 TTTAATTATTTAAAT
18089 GATTGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATTATTTAAAT
Found at i:28025 original size:19 final size:20
Alignment explanation
Indices: 28001--28039 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27991 TTAAAAATAA
28001 AAAAATATT-AAAATTATTT
1 AAAAATATTAAAAATTATTT
*
28020 AAAAATTTTAAAAATTATTT
1 AAAAATATTAAAAATTATTT
28040 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAATATTAAAAATTATTT
Found at i:28050 original size:9 final size:10
Alignment explanation
Indices: 27985--28063 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 10
27975 ATTAATTAAT
27985 AAAAT-TTTA
1 AAAATATTTA
*
27994 AAAATA--AA
1 AAAATATTTA
28002 AAAATA-TTA
1 AAAATATTTA
*
28011 AAATTATTTA
1 AAAATATTTA
28021 AAAAT-TTTA
1 AAAATATTTA
*
28030 AAAATTATTTTTT
1 AAAA-TA--TTTA
28043 AAAAT-TTTA
1 AAAATATTTA
*
28052 AAAATAATTA
1 AAAATATTTA
28062 AA
1 AA
28064 TGCTGACATG
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
8 7 0.13
9 27 0.49
10 13 0.24
12 1 0.02
13 7 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAAATATTTA
Found at i:32979 original size:20 final size:20
Alignment explanation
Indices: 32943--32982 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
32933 AATAAAATAT
*
32943 AATTTAAAAAATTAAATTAA
1 AATTTAAAAAATCAAATTAA
32963 AATTATAAAAAA-CAAATTAA
1 AATT-TAAAAAATCAAATTAA
32983 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AATTTAAAAAATCAAATTAA
Found at i:35875 original size:107 final size:107
Alignment explanation
Indices: 35684--35898 Score: 358
Period size: 107 Copynumber: 2.0 Consensus size: 107
35674 ATATTCAAGA
* * *
35684 TCGTTGTAATTATAGAGAGTGTTTTACACCTTTTTGTGAGTGCCCTATGAGATTTAGGGTTTTAT
1 TCGTCGTAATTACAGAGAGTATTTTACACCTTTTTGTGAGTGCCCTATGAGATTTAGGGTTTTAT
35749 TTACTGGTTTGCTCTTTGGGATTTTGAACTTTGTATTTAGAG
66 TTACTGGTTTGCTCTTTGGGATTTTGAACTTTGTATTTAGAG
* * * *
35791 TCGTCGTAATTACGGAGAGTATTTTACACCTTTTTGTGAGTGCCTTGTGAGATTTAGGGTTTTGT
1 TCGTCGTAATTACAGAGAGTATTTTACACCTTTTTGTGAGTGCCCTATGAGATTTAGGGTTTTAT
*
35856 TTATTGGTTTGCTCTTTGGGATTTTGAACTTTGTATTTAGAG
66 TTACTGGTTTGCTCTTTGGGATTTTGAACTTTGTATTTAGAG
35898 T
1 T
35899 TTTGGGTAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (107 bp):
TCGTCGTAATTACAGAGAGTATTTTACACCTTTTTGTGAGTGCCCTATGAGATTTAGGGTTTTAT
TTACTGGTTTGCTCTTTGGGATTTTGAACTTTGTATTTAGAG
Found at i:37859 original size:19 final size:20
Alignment explanation
Indices: 37837--37890 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 20
37827 ATATGCAATA
37837 TATAAATATAA-AATTGTGT
1 TATAAATATAAGAATTGTGT
*
37856 TAT--AT-TAATAATTGTGT
1 TATAAATATAAGAATTGTGT
*
37873 TAATAATTATAAGAATTG
1 T-ATAAATATAAGAATTG
37891 AATCAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 2 0.07
19 3 0.11
20 1 0.04
21 8 0.29
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (20 bp):
TATAAATATAAGAATTGTGT
Found at i:48417 original size:54 final size:54
Alignment explanation
Indices: 48335--48443 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
48325 AGAAACAAGA
* * *
48335 GTTAAGAAGCAGAAAAATACATTGAATATAAGCATAAGCAAGAAGGCACCAAAT
1 GTTAAGAAGCAGAAAAATACACTGAATATAAGCATAAGAAAAAAGGCACCAAAT
48389 GTTAAGAAGCAGAAAAATACACTGAATATAAGCATAAGAAAAAAGGCACCAAAT
1 GTTAAGAAGCAGAAAAATACACTGAATATAAGCATAAGAAAAAAGGCACCAAAT
48443 G
1 G
48444 ACCTTAGAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (54 bp):
GTTAAGAAGCAGAAAAATACACTGAATATAAGCATAAGAAAAAAGGCACCAAAT
Done.