Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014163.1 Kokia drynarioides strain JFW-HI SEQ_129196, 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: 46634
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:2180 original size:10 final size:10
Alignment explanation
Indices: 2167--2191 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2157 AATAAAATAG
2167 AATATATATA
1 AATATATATA
2177 AATATATATA
1 AATATATATA
2187 AATAT
1 AATAT
2192 CAAAATAAAC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATATATA
Found at i:4181 original size:10 final size:10
Alignment explanation
Indices: 4166--4195 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
4156 CAATACTTAA
4166 TTTTTTTATT
1 TTTTTTTATT
4176 TTTTTTTATT
1 TTTTTTTATT
4186 TTTTTATTAT
1 TTTTT-TTAT
4196 ACGACTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:12933 original size:17 final size:17
Alignment explanation
Indices: 12911--12955 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
12901 TATTATTTTT
12911 CAAAAATATTTTTGAGA
1 CAAAAATATTTTTGAGA
12928 CAAAAAATATTTTTGAGA
1 C-AAAAATATTTTTGAGA
* *
12946 TAAAAGTATT
1 CAAAAATATT
12956 ACTAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (17 bp):
CAAAAATATTTTTGAGA
Found at i:12935 original size:18 final size:18
Alignment explanation
Indices: 12912--12950 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12902 ATTATTTTTC
12912 AAAAATATTTTTGAGACA
1 AAAAATATTTTTGAGACA
*
12930 AAAAATATTTTTGAGATA
1 AAAAATATTTTTGAGACA
12948 AAA
1 AAA
12951 GTATTACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (18 bp):
AAAAATATTTTTGAGACA
Found at i:14884 original size:6 final size:6
Alignment explanation
Indices: 14875--14899 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14865 TGATTTTTTT
14875 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
14900 ATTGATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:21721 original size:13 final size:12
Alignment explanation
Indices: 21706--21754 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 12
21696 AATTAATTAT
21706 TTTTTAAATATA
1 TTTTTAAATATA
*
21718 TTTTTTTAAAAATA
1 --TTTTTAAATATA
*
21732 TTTTAAAAT-TA
1 TTTTTAAATATA
21743 TTTTTAAATATA
1 TTTTTAAATATA
21755 AAATTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.33
12 9 0.30
14 11 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTTAAATATA
Found at i:23930 original size:3 final size:3
Alignment explanation
Indices: 23922--23948 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
23912 ATGTGATTAC
23922 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
23949 TTTATTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28664 original size:10 final size:10
Alignment explanation
Indices: 28649--28678 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28639 AATAAATCTC
28649 TATTTTTTTA
1 TATTTTTTTA
28659 TA-TTTTTTA
1 TATTTTTTTA
28668 TATTTTTTTA
1 TATTTTTTTA
28678 T
1 T
28679 TGCGCGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:29307 original size:20 final size:20
Alignment explanation
Indices: 29284--29321 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29274 AAAATACAAT
*
29284 TTATATTATCCTTTTTAACG
1 TTATATTATCATTTTTAACG
29304 TTATATTATCATTTTTAA
1 TTATATTATCATTTTTAA
29322 TAAAAACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (20 bp):
TTATATTATCATTTTTAACG
Found at i:31713 original size:30 final size:30
Alignment explanation
Indices: 31659--31716 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
31649 ATTTTTACAA
*
31659 TTTTAAAAGGATTAAATCAAAATTTTATAT
1 TTTTAAAAGGATAAAATCAAAATTTTATAT
*
31689 TTTTAAAAGGATCAAAAT-ATAATTTTAT
1 TTTTAAAAGGAT-AAAATCAAAATTTTAT
31717 CTTTATGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTTAAAAGGATAAAATCAAAATTTTATAT
Found at i:32644 original size:16 final size:18
Alignment explanation
Indices: 32618--32654 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
32608 TAAATAAAAA
*
32618 TTTACTTTTAA-ATTATT
1 TTTACTTTTAAGATAATT
32635 TTTA-TTTTAAGATAATT
1 TTTACTTTTAAGATAATT
32652 TTT
1 TTT
32655 TTAACGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTACTTTTAAGATAATT
Found at i:39684 original size:37 final size:37
Alignment explanation
Indices: 39643--39714 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
39633 ATAAAAAAAT
39643 ATATTTTCACTATTTTAAATATAAAATATTGATTTAA
1 ATATTTTCACTATTTTAAATATAAAATATTGATTTAA
*
39680 ATATTTTCACTATTTTAAATATAAAATATTTATTT
1 ATATTTTCACTATTTTAAATATAAAATATTGATTT
39715 TTATATCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (37 bp):
ATATTTTCACTATTTTAAATATAAAATATTGATTTAA
Found at i:42331 original size:36 final size:35
Alignment explanation
Indices: 42268--42337 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 35
42258 ATGCTTTTGA
* *
42268 GCTTTTAAAAAGTGATTTTAAGACAAAAAAAAAAT
1 GCTTTCAAAAAGTAATTTTAAGACAAAAAAAAAAT
* * *
42303 GCTTTCAAAAAGTAAATTTTTAGCCAAAAATAAAA
1 GCTTTCAAAAAGT-AATTTTAAGACAAAAAAAAAA
42338 GTAAAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.29
Consensus pattern (35 bp):
GCTTTCAAAAAGTAATTTTAAGACAAAAAAAAAAT
Done.