Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011863.1 Kokia drynarioides strain JFW-HI SEQ_126860, 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: 2094
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.37
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:765 original size:59 final size:59
Alignment explanation
Indices: 692--824 Score: 230
Period size: 59 Copynumber: 2.3 Consensus size: 59
682 ATTTTGTACC
692 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAA
1 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAA
* * *
751 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAA
*
810 ATTTTGGTAATTAAT
1 ATTTTGGTAAATAAT
825 TAGCTAAGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.52
Consensus pattern (59 bp):
ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAA
Found at i:794 original size:29 final size:29
Alignment explanation
Indices: 692--794 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 29
682 ATTTTGTACC
* *
692 ATTTTGGTAAATAATATGATGGGGATATT
1 ATTTTGATAATTAATATGATGGGGATATT
* ****
721 ATTTTCATAATTAAT-T-ATTTTTTATATT
1 ATTTTGATAATTAATATGA-TGGGGATATT
*
749 AAATTTTGGTCAA-TAATATGATGGGGATATT
1 --ATTTTGAT-AATTAATATGATGGGGATATT
780 ATTTTGATAATTAAT
1 ATTTTGATAATTAAT
795 TATTTTTTAT
Statistics
Matches: 53, Mismatches: 14, Indels: 14
0.65 0.17 0.17
Matches are distributed among these distances:
27 1 0.02
28 9 0.17
29 23 0.43
30 10 0.19
31 9 0.17
32 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.49
Consensus pattern (29 bp):
ATTTTGATAATTAATATGATGGGGATATT
Found at i:798 original size:16 final size:16
Alignment explanation
Indices: 777--826 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
767 TGATGGGGAT
777 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
793 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
808 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
823 ATTA
1 ATTA
827 GCTAAGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:815 original size:30 final size:30
Alignment explanation
Indices: 720--826 Score: 87
Period size: 30 Copynumber: 3.6 Consensus size: 30
710 ATGGGGATAT
*
720 TATTTTCATAATTAATTATTTTTTATATTA
1 TATTTTGATAATTAATTATTTTTTATATTA
* * ****
750 AATTTTGGTCAA-TAA-TATGATGGGGATA-T-
1 TATTTTGAT-AATTAATTAT--TTTTTATATTA
779 TATTTTGATAATTAATTATTTTTTATATTA
1 TATTTTGATAATTAATTATTTTTTATATTA
*
809 TATTTTGGTAATTAATTA
1 TATTTTGATAATTAATTA
827 GCTAAGTTTA
Statistics
Matches: 56, Mismatches: 14, Indels: 14
0.67 0.17 0.17
Matches are distributed among these distances:
28 6 0.11
29 14 0.25
30 30 0.54
31 6 0.11
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (30 bp):
TATTTTGATAATTAATTATTTTTTATATTA
Found at i:1617 original size:21 final size:20
Alignment explanation
Indices: 1582--1639 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
1572 TACTTACTAC
1582 TACTAACAACAAAATAAAAT
1 TACTAACAACAAAATAAAAT
* *
1602 TACTAACTAGCAAAATTAAAT
1 TACTAAC-AACAAAATAAAAT
* * *
1623 TAATAATAACATAATAA
1 TACTAACAACAAAATAA
1640 CAAACTTACA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (20 bp):
TACTAACAACAAAATAAAAT
Found at i:1712 original size:11 final size:12
Alignment explanation
Indices: 1688--1721 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1678 CTATAACAAC
*
1688 ATTAAATAAAAA
1 ATTAAATTAAAA
1700 ATT-AATTAAAA
1 ATTAAATTAAAA
1711 ATTAAATTAAA
1 ATTAAATTAAA
1722 GAAAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATTAAAA
Found at i:2005 original size:18 final size:18
Alignment explanation
Indices: 1956--2023 Score: 52
Period size: 18 Copynumber: 3.7 Consensus size: 18
1946 ACCTTTTTTT
*
1956 TTCTTTCTCCTTCTTCC-CC
1 TTCTTTCT--TTCTTCCTTC
*
1975 TTCTTCTCCTTCTTCCTTC
1 TTCTT-TCTTTCTTCCTTC
*
1994 TTCTTTCTTTCTTTCTATC
1 TTCTTTCTTTCTTCCT-TC
2013 -TCTTT-TTTCTT
1 TTCTTTCTTTCTT
2024 TCTTTTTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 6 0.14
18 21 0.50
19 13 0.31
20 2 0.05
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.63
Consensus pattern (18 bp):
TTCTTTCTTTCTTCCTTC
Found at i:2029 original size:11 final size:11
Alignment explanation
Indices: 1994--2043 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
1984 TTCTTCCTTC
1994 TTCTTTCTTTCT
1 TTCTTTCTTT-T
2006 TTCTATCTCTTTT
1 TTCT-T-TCTTTT
2019 TTCTTTCTTTT
1 TTCTTTCTTTT
* *
2030 TTCCTTCATTT
1 TTCTTTCTTTT
2041 TTC
1 TTC
2044 GTTGGTCCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 18 0.53
12 5 0.15
13 6 0.18
14 5 0.15
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:2041 original size:21 final size:21
Alignment explanation
Indices: 1987--2041 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 21
1977 CTTCTCCTTC
1987 TTCCTTCTTCTTTCTTTCTTTCT
1 TTCCTTC-T-TTTCTTTCTTTCT
*
2010 ATCTCTT-TTTTCTTTCTTT-T
1 TTC-CTTCTTTTCTTTCTTTCT
2030 TTCCTTCATTTT
1 TTCCTTC-TTTT
2042 TCGTTGGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
19 3 0.11
20 3 0.11
21 15 0.56
22 1 0.04
23 2 0.07
24 3 0.11
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCCTTCTTTTCTTTCTTTCT
Done.