Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011270.1 Kokia drynarioides strain JFW-HI SEQ_126249, 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: 25538
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:9083 original size:14 final size:14
Alignment explanation
Indices: 9066--9095 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9056 TTGCTATTTG
*
9066 AATTTTTTAGAAAT
1 AATTTTTTAAAAAT
9080 AATTTTTTAAAAAT
1 AATTTTTTAAAAAT
9094 AA
1 AA
9096 AAAATTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AATTTTTTAAAAAT
Found at i:10298 original size:2 final size:2
Alignment explanation
Indices: 10291--10318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10281 CAAATCATTG
10291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10319 TGAAACAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11029 original size:8 final size:8
Alignment explanation
Indices: 11018--11047 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
11008 AAAAGTAAAA
11018 AAAAAATT
1 AAAAAATT
11026 AAAAAATT
1 AAAAAATT
*
11034 AAAAGATT
1 AAAAAATT
11042 AAAAAA
1 AAAAAA
11048 AAGAAGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (8 bp):
AAAAAATT
Found at i:12101 original size:14 final size:13
Alignment explanation
Indices: 12063--12101 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
12053 TATATTCTTA
*
12063 AATTTTTATTCAT
1 AATTTTTATTTAT
*
12076 AATTTTTTTTTAT
1 AATTTTTATTTAT
12089 AATTTTTACTTTA
1 AATTTTTA-TTTA
12102 GAACATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (13 bp):
AATTTTTATTTAT
Found at i:12291 original size:26 final size:26
Alignment explanation
Indices: 12262--12321 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
12252 CACATTGATA
12262 GAATTTATCAAATTCGAGTGCTAAAT
1 GAATTTATCAAATTCGAGTGCTAAAT
12288 GAATTTATCAAATTCGAGTGCTAAAT
1 GAATTTATCAAATTCGAGTGCTAAAT
12314 GAATTTAT
1 GAATTTAT
12322 TAACCGCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (26 bp):
GAATTTATCAAATTCGAGTGCTAAAT
Found at i:21686 original size:19 final size:19
Alignment explanation
Indices: 21664--21702 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21654 CAGATTTAGA
* *
21664 ATTTTGGCTTTGAATTTGG
1 ATTTTGACTTTGAAATTGG
*
21683 ATTTTGATTTTGAAATTGG
1 ATTTTGACTTTGAAATTGG
21702 A
1 A
21703 GATAACGAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (19 bp):
ATTTTGACTTTGAAATTGG
Found at i:22187 original size:16 final size:15
Alignment explanation
Indices: 22168--22209 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
22158 TAATATTAAA
22168 TAAATAAAAAATTATT
1 TAAATAAAAAATT-TT
22184 TAAATAATAAAA-TTT
1 TAAATAA-AAAATTTT
22199 TAAA-AAAAAAT
1 TAAATAAAAAAT
22210 ATTGATACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 2 0.08
15 6 0.25
16 8 0.33
17 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATAAAAAATTTT
Found at i:22304 original size:27 final size:27
Alignment explanation
Indices: 22266--22317 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
22256 TATTTTTGGT
* *
22266 TGGTGCTTACCTGATAAGCGGCACCAA
1 TGGTGCTTACCTAACAAGCGGCACCAA
22293 TGGTGCTTACCTAACAAGCGGCACC
1 TGGTGCTTACCTAACAAGCGGCACC
22318 TAGTCCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (27 bp):
TGGTGCTTACCTAACAAGCGGCACCAA
Found at i:22649 original size:17 final size:16
Alignment explanation
Indices: 22627--22661 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
22617 GAAAAAATTT
*
22627 ATTTAAATGTTATTTAA
1 ATTTAAATATTA-TTAA
22644 ATTTAAATATTATTAA
1 ATTTAAATATTATTAA
22660 AT
1 AT
22662 AATGTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTAAATATTATTAA
Found at i:25151 original size:6 final size:6
Alignment explanation
Indices: 25140--25167 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
25130 GCTTTCAGTC
25140 GCCTGA GCCTGA GCCTGA GCCTGA GCCT
1 GCCTGA GCCTGA GCCTGA GCCTGA GCCT
25168 TAGCTGCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.32, T:0.18
Consensus pattern (6 bp):
GCCTGA
Done.