Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002062.1 Kokia drynarioides strain JFW-HI SEQ_113966, 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: 32820
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:575 original size:8 final size:8
Alignment explanation
Indices: 562--622 Score: 72
Period size: 8 Copynumber: 7.6 Consensus size: 8
552 ACTTTTTTAA
562 ATATTGTT
1 ATATTGTT
570 ATATTGTT
1 ATATTGTT
*
578 ATATT-TAA
1 ATATTGT-T
586 ATATTGTT
1 ATATTGTT
594 ATATTGTT
1 ATATTGTT
*
602 ATATT-TAA
1 ATATTGT-T
610 ATATTGTT
1 ATATTGTT
618 ATATT
1 ATATT
623 TATAAGTGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 2 0.04
8 41 0.91
9 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (8 bp):
ATATTGTT
Found at i:589 original size:16 final size:16
Alignment explanation
Indices: 557--624 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
547 GCCAAACTTT
557 TTTAAATATTGTTATA
1 TTTAAATATTGTTATA
* *
573 TTGT-TATATT-TAAATA
1 TT-TAAATATTGT-TATA
*
589 TTGTTA-TATTGTTATA
1 TT-TAAATATTGTTATA
605 TTTAAATATTGTTATA
1 TTTAAATATTGTTATA
621 TTTA
1 TTTA
625 TAAGTGGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
15 3 0.07
16 37 0.88
17 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (16 bp):
TTTAAATATTGTTATA
Found at i:589 original size:24 final size:24
Alignment explanation
Indices: 557--622 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
547 GCCAAACTTT
557 TTTAAATATTGTTATATTGTTATA
1 TTTAAATATTGTTATATTGTTATA
581 TTTAAATATTGTTATATTGTTATA
1 TTTAAATATTGTTATATTGTTATA
605 TTTAAATATTGTTATATT
1 TTTAAATATTGTTATATT
623 TATAAGTGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (24 bp):
TTTAAATATTGTTATATTGTTATA
Found at i:738 original size:23 final size:23
Alignment explanation
Indices: 712--767 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
702 AAAATGATTA
** *
712 TTGAATTATTTTAAAGTTTTTCT
1 TTGAATTATTCAAAAGATTTTCT
735 TTGAATTATTCAAAAGATTTTCT
1 TTGAATTATTCAAAAGATTTTCT
758 TT-AAGTTATT
1 TTGAA-TTATT
768 GGATTGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55
Consensus pattern (23 bp):
TTGAATTATTCAAAAGATTTTCT
Found at i:846 original size:13 final size:13
Alignment explanation
Indices: 828--880 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 13
818 ATGATAATTT
828 TTTAAAAAAGTTA
1 TTTAAAAAAGTTA
*
841 TTT-AAATA-TATA
1 TTTAAAAAAGT-TA
853 TTTAAAAAAGTTA
1 TTTAAAAAAGTTA
*
866 TTCAAAAAAAGTTA
1 TT-TAAAAAAGTTA
880 T
1 T
881 ATTTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 1 0.03
12 9 0.27
13 11 0.33
14 12 0.36
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTAAAAAAGTTA
Found at i:985 original size:23 final size:23
Alignment explanation
Indices: 959--1014 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
949 AAAATGATTA
** *
959 TTGAATTATTTTAAAGTTTTTCT
1 TTGAATTATTCAAAAGATTTTCT
982 TTGAATTATTCAAAAGATTTTCT
1 TTGAATTATTCAAAAGATTTTCT
1005 TT-AAGTTATT
1 TTGAA-TTATT
1015 GGATTGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55
Consensus pattern (23 bp):
TTGAATTATTCAAAAGATTTTCT
Found at i:1105 original size:8 final size:8
Alignment explanation
Indices: 1092--1161 Score: 56
Period size: 8 Copynumber: 8.6 Consensus size: 8
1082 AAGTTATAAA
1092 ATATTGTT
1 ATATTGTT
1100 ATATTGTT
1 ATATTGTT
*
1108 ATATTTTT
1 ATATTGTT
* *
1116 TTA-AGTT
1 ATATTGTT
1123 ATTGGATTGTT
1 A-T--ATTGTT
1134 ATATT-TT
1 ATATTGTT
1141 -TGATTGTT
1 AT-ATTGTT
1149 ATATTGTT
1 ATATTGTT
1157 ATATT
1 ATATT
1162 TTTTTTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
6 1 0.02
7 7 0.14
8 34 0.69
9 1 0.02
10 2 0.04
11 4 0.08
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (8 bp):
ATATTGTT
Found at i:1167 original size:26 final size:25
Alignment explanation
Indices: 1094--1166 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 25
1084 GTTATAAAAT
1094 ATTGTTATATTGTTATATTTTTTTA
1 ATTGTTATATTGTTATATTTTTTTA
* ** *
1119 AGTTATTGGATTGTTATA--TTTTTG
1 A-TTGTTATATTGTTATATTTTTTTA
1143 ATTGTTATATTGTTATATTTTTTT
1 ATTGTTATATTGTTATATTTTTTT
1167 TTAAAGATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
23 13 0.34
24 6 0.16
25 6 0.16
26 13 0.34
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (25 bp):
ATTGTTATATTGTTATATTTTTTTA
Found at i:8394 original size:39 final size:39
Alignment explanation
Indices: 8340--8420 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
8330 GTAACTTAAC
8340 ATGGTATCAAGAGCTTAAAAAAATTGATCTTGAGGGACT
1 ATGGTATCAAGAGCTTAAAAAAATTGATCTTGAGGGACT
8379 ATGGTATCAAGAGCTTAAAAAAATTGATCTTGAGGGACT
1 ATGGTATCAAGAGCTTAAAAAAATTGATCTTGAGGGACT
8418 ATG
1 ATG
8421 TGAGCTGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (39 bp):
ATGGTATCAAGAGCTTAAAAAAATTGATCTTGAGGGACT
Found at i:17455 original size:15 final size:13
Alignment explanation
Indices: 17422--17465 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
17412 TAGTCATTAT
17422 TTTTTAATTTTTA
1 TTTTTAATTTTTA
17435 TATTTTAATTTAGTTA
1 T-TTTTAATTT--TTA
*
17451 TTTTTAATCTTTA
1 TTTTTAATTTTTA
17464 TT
1 TT
17466 AAAATGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 6 0.22
14 9 0.33
15 8 0.30
16 4 0.15
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTTAATTTTTA
Found at i:18269 original size:28 final size:25
Alignment explanation
Indices: 18229--18281 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
18219 TTTTTCTATT
18229 TCCCCCATTTACTATAACAAAATTAAAA
1 TCCCCCATTTAC--TAA-AAAATTAAAA
18257 TCCCCC-TTATACTAAAAAATTAAAA
1 TCCCCCATT-TACTAAAAAATTAAAA
18282 GATGTCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 2 0.08
28 9 0.38
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (25 bp):
TCCCCCATTTACTAAAAAATTAAAA
Found at i:18970 original size:3 final size:3
Alignment explanation
Indices: 18962--18986 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18952 GCGTTACTTG
18962 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
18987 ACAAGCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:25219 original size:29 final size:29
Alignment explanation
Indices: 25187--25248 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
25177 CGCAAGTAAC
*
25187 TAAAACGTAACATT-TCAAACATAAGTGAT
1 TAAAACGTAAC-TTGTCAAACAAAAGTGAT
25216 TAAAACGTAACTTGAGTCAAACAAAAGTGAT
1 TAAAACGTAACTT--GTCAAACAAAAGTGAT
25247 TA
1 TA
25249 TTTTAATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 11 0.38
31 16 0.55
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (29 bp):
TAAAACGTAACTTGTCAAACAAAAGTGAT
Found at i:28753 original size:3 final size:3
Alignment explanation
Indices: 28745--28778 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
28735 TGTGATAACA
* *
28745 ATG ATG ATG ATG ATG ATG ATG ATA ATG ATA ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
28779 CAAGTCACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (3 bp):
ATG
Done.