Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004651.1 Kokia drynarioides strain JFW-HI SEQ_118182, 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: 71935
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:9825 original size:2 final size:2
Alignment explanation
Indices: 9818--9845 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9808 TTTAATTGTA
9818 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
9846 GGGATTTAAT
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:10097 original size:23 final size:23
Alignment explanation
Indices: 10071--10120 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
10061 ATGATATTTG
10071 AAATTATAATTTCATTTCATTAA
1 AAATTATAATTTCATTTCATTAA
* **
10094 AAA-TATAATTTTATTTTGTTAA
1 AAATTATAATTTCATTTCATTAA
10116 AAATT
1 AAATT
10121 TATGAAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATTATAATTTCATTTCATTAA
Found at i:10543 original size:22 final size:22
Alignment explanation
Indices: 10509--10553 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
10499 TTAGTGTTTA
10509 AAATATTAATATC-ATTTTAATT
1 AAATATTAATATCTA-TTTAATT
**
10531 AAATATTTTTATCTATTTAATT
1 AAATATTAATATCTATTTAATT
10553 A
1 A
10554 TATAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATATTAATATCTATTTAATT
Found at i:18116 original size:15 final size:15
Alignment explanation
Indices: 18096--18128 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18086 TTGCTTCGTC
*
18096 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTATT
18111 TTTTTCTTTTTTATT
1 TTTTTCTTTTTTATT
18126 TTT
1 TTT
18129 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTCTTTTTTATT
Found at i:18120 original size:21 final size:21
Alignment explanation
Indices: 18094--18134 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18084 CATTGCTTCG
*
18094 TCTTTTTCT-TTTTTCTTTTTT
1 TCTTTTT-TATTTTTATTTTTT
18115 TCTTTTTTATTTTTATTTTT
1 TCTTTTTTATTTTTATTTTT
18135 ATTTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (21 bp):
TCTTTTTTATTTTTATTTTTT
Found at i:24971 original size:22 final size:19
Alignment explanation
Indices: 24934--24977 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
24924 GGATCTCTCC
24934 TTATATTTTTATATTAATAT
1 TTATATTTTTATATTAA-AT
24954 TTATATGTTTTATAATTAAAT
1 TTATAT-TTTTAT-ATTAAAT
24975 TTA
1 TTA
24978 AATAAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATATTTTTATATTAAAT
Found at i:29978 original size:24 final size:26
Alignment explanation
Indices: 29931--29978 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
29921 CATGGAAAAT
29931 GACTTAATGGTTTTGTTTTGGTAGAA
1 GACTTAATGGTTTTGTTTTGGTAGAA
*
29957 GACTTGATGG-TTT-TTTTGGTAG
1 GACTTAATGGTTTTGTTTTGGTAG
29979 GTCAGGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 3 0.14
26 9 0.43
ACGTcount: A:0.19, C:0.04, G:0.29, T:0.48
Consensus pattern (26 bp):
GACTTAATGGTTTTGTTTTGGTAGAA
Found at i:35632 original size:25 final size:23
Alignment explanation
Indices: 35586--35636 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
35576 CTATTTCTAA
*
35586 TTTTTTAATGACATTTCAATAAT
1 TTTTTTAATGACATTACAATAAT
*
35609 TTTTTTAATGTCATTGACACATAAT
1 TTTTTTAATGACATT-ACA-ATAAT
35634 TTT
1 TTT
35637 GGTATTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 14 0.58
24 2 0.08
25 8 0.33
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (23 bp):
TTTTTTAATGACATTACAATAAT
Found at i:35927 original size:28 final size:27
Alignment explanation
Indices: 35868--35927 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
35858 CTAGATTCGA
* *
35868 GTTTAAATTTAGGGTTTAGAATTTGAG
1 GTTTAAATTTAGGGTTGAGAATTTAAG
*
35895 ATTTAAAGTTTAGGGTTCGA-AATTTAAG
1 GTTTAAA-TTTAGGGTT-GAGAATTTAAG
35923 GTTTA
1 GTTTA
35928 GGGTAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 6 0.22
28 20 0.74
29 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (27 bp):
GTTTAAATTTAGGGTTGAGAATTTAAG
Found at i:40294 original size:54 final size:53
Alignment explanation
Indices: 40189--40298 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
40179 TAATTACTCT
40189 AAGCTTTGTCCTTGTTTTTTTTTTTTCAGTGCTATTATTCCCCCTGGTTTTAA
1 AAGCTTTGTCCTTGTTTTTTTTTTTTCAGTGCTATTATTCCCCCTGGTTTTAA
*
40242 AAGCTTTGTCCTTGTTTTTTTTTTTTCAGTGCTATTATTCCCCCTGGTTTTTA
1 AAGCTTTGTCCTTGTTTTTTTTTTTTCAGTGCTATTATTCCCCCTGGTTTTAA
40295 AAGC
1 AAGC
40299 ATGCTTTATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.54
Consensus pattern (53 bp):
AAGCTTTGTCCTTGTTTTTTTTTTTTCAGTGCTATTATTCCCCCTGGTTTTAA
Found at i:43864 original size:22 final size:23
Alignment explanation
Indices: 43829--43891 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
43819 CTTGCAATAA
* *
43829 TAAAAATTT-GTTTTAATTCTT-
1 TAAAAATTTCATTTTAATTATTG
* *
43850 TAAAAATTTCATTTTTACTATTG
1 TAAAAATTTCATTTTAATTATTG
*
43873 TAAAAATTACATTTTAATT
1 TAAAAATTTCATTTTAATT
43892 TAGCCCTCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 9 0.27
22 8 0.24
23 16 0.48
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.52
Consensus pattern (23 bp):
TAAAAATTTCATTTTAATTATTG
Found at i:50484 original size:2 final size:2
Alignment explanation
Indices: 50477--50505 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
50467 GTTGCAGAGC
50477 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50506 TGTAGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56527 original size:4 final size:4
Alignment explanation
Indices: 56518--56542 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56508 TTTCAATTAT
56518 AACC AACC AACC AACC AACC AACC A
1 AACC AACC AACC AACC AACC AACC A
56543 TAGTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (4 bp):
AACC
Found at i:61659 original size:6 final size:7
Alignment explanation
Indices: 61642--61668 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
61632 ACCAAATAGT
61642 AAAAAAG
1 AAAAAAG
61649 AAAAAAG
1 AAAAAAG
61656 AAAAAAG
1 AAAAAAG
61663 AAAAAA
1 AAAAAA
61669 CGAACACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Done.