Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010911.1 Kokia drynarioides strain JFW-HI SEQ_125879, 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: 28092
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7605 original size:41 final size:43
Alignment explanation
Indices: 7549--7682 Score: 202
Period size: 43 Copynumber: 3.2 Consensus size: 43
7539 CACAAGGGCT
7549 GGCACACAGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTTGA
1 GGCACACAGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTTGA
* * *
7592 GGCACACGGGTGTGTGTCAA-G-GTGTGTGTATACTGTCTTGA
1 GGCACACAGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTTGA
*
7633 GGCACACAGGCGTGTGTCAGGGTGTGTGTGTATA-TGGTTTTGA
1 GGCACACAGGCGTGTGTCAAGGTGTGTGTGTATACT-GTTTTGA
7676 GGCACAC
1 GGCACAC
7683 GGGTTGGCAC
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
41 36 0.44
42 3 0.04
43 42 0.52
ACGTcount: A:0.18, C:0.15, G:0.37, T:0.31
Consensus pattern (43 bp):
GGCACACAGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTTGA
Found at i:9648 original size:19 final size:18
Alignment explanation
Indices: 9605--9648 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
9595 GGTTGAATCG
*
9605 ATTTTTTTTTATTTTTAA
1 ATTTTTTTTAATTTTTAA
*
9623 ATGTTTTTTTAATTTTATGA
1 AT-TTTTTTTAATTTT-TAA
9643 ATTTTT
1 ATTTTT
9649 AATAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 16 0.73
20 4 0.18
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
ATTTTTTTTAATTTTTAA
Found at i:14260 original size:3 final size:3
Alignment explanation
Indices: 14252--14282 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
14242 GTAAATATTA
*
14252 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
14283 TTTACTGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:14908 original size:2 final size:2
Alignment explanation
Indices: 14901--14928 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14891 GGACATTCAA
14901 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
14929 CTAATAAAAT
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:23427 original size:6 final size:6
Alignment explanation
Indices: 23418--23464 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
23408 CAAATTTATT
** *
23418 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
23464 T
1 T
23465 GGATTGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 26 0.79
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:23440 original size:17 final size:17
Alignment explanation
Indices: 23418--23464 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
23408 CAAATTTATT
**
23418 TTTAAATTTAAATTTGC
1 TTTAAATTTAAATTTAA
23435 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
*
23452 TTAAAATTTAAAT
1 TTTAAATTTAAAT
23465 GGATTGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:23804 original size:26 final size:26
Alignment explanation
Indices: 23774--23824 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
23764 GTAACATTAA
*
23774 TAGTAATA-ATGGTTAATAATAAGTAG
1 TAGTAATATATAG-TAATAATAAGTAG
*
23800 TAGTAATATATAGTATTAATAAGTA
1 TAGTAATATATAGTAATAATAAGTA
23825 TTAATACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (26 bp):
TAGTAATATATAGTAATAATAAGTAG
Found at i:25018 original size:30 final size:29
Alignment explanation
Indices: 24895--25114 Score: 205
Period size: 30 Copynumber: 7.5 Consensus size: 29
24885 GGAGGTCCAT
*
24895 AAACTATCCAAAATTTCCATTTTTACCCTC
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
* * * *
24925 GAACTTCTAAAAATCCCATTTTTGACCCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
** * *
24955 AAAACTTTTAAAAATTACA-TTTTACCCTT
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* *
24984 AAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
25014 AAACTTCCAAAAATTCCA-TTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
25042 GAACTTCCAAAAATGT-CATTTTTTA-TCTC
1 AAACTTCCAAAAAT-TCCA-TTTTTACCCTC
* *
25071 GAAACTTCCAAAAAATCCTTTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
*
25101 GAACTTCCAAAAAT
1 AAACTTCCAAAAAT
25115 GCCCTCGAAC
Statistics
Matches: 154, Mismatches: 26, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
28 34 0.22
29 50 0.32
30 56 0.36
31 14 0.09
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:25047 original size:58 final size:58
Alignment explanation
Indices: 24895--25114 Score: 244
Period size: 58 Copynumber: 3.7 Consensus size: 58
24885 GGAGGTCCAT
* * * *
24895 AAACTATCCAAAATTTCCATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCCA
1 AAACT-TCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTT-AACCCTA
** * **
24956 AAACTTTTAAAAATTACATTTTACCCTTAAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTA
** * * *
25014 AAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATGTCATTTTTTA-TCTCG
1 AAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCT-A
* *
25072 AAACTTCCAAAAAATCCTTTTTTACCCTCGAACTTCCAAAAAT
1 AAACTTCCAAAAATTCC-ATTTTACCCTCGAACTTCCAAAAAT
25115 GCCCTCGAAC
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
57 2 0.01
58 66 0.49
59 54 0.40
60 9 0.07
61 5 0.04
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTA
Found at i:25121 original size:20 final size:20
Alignment explanation
Indices: 25096--25137 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
25086 TCCTTTTTTA
25096 CCCTCGAACTTCCAAAAATG
1 CCCTCGAACTTCCAAAAATG
25116 CCCTCGAACTTCCAAAAATG
1 CCCTCGAACTTCCAAAAATG
25136 CC
1 CC
25138 ATTTTTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.38, G:0.10, T:0.19
Consensus pattern (20 bp):
CCCTCGAACTTCCAAAAATG
Found at i:25159 original size:79 final size:79
Alignment explanation
Indices: 25037--25183 Score: 233
Period size: 79 Copynumber: 1.9 Consensus size: 79
25027 TTCCATTTTA
* * *
25037 CCCTCGAACTTCCAAAAATGTCATTTTTTATCTCGAAACTTCCAAAAAATCCTTTTTTACCCTCG
1 CCCTCGAACTTCCAAAAATGCCATTTTTGATCTCGAAACTTCCAAAAAATCCGTTTTTACCCTCG
25102 AACTTCCAAAAATG
66 AACTTCCAAAAATG
* *
25116 CCCTCGAACTTCCAAAAATGCCATTTTTGA-CTCCGAAATTTCCAAAAATTCCGTTTTTACCCTC
1 CCCTCGAACTTCCAAAAATGCCATTTTTGATCT-CGAAACTTCCAAAAAATCCGTTTTTACCCTC
25180 GAAC
65 GAAC
25184 CTTTAAAACC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 2 0.03
79 60 0.97
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.32
Consensus pattern (79 bp):
CCCTCGAACTTCCAAAAATGCCATTTTTGATCTCGAAACTTCCAAAAAATCCGTTTTTACCCTCG
AACTTCCAAAAATG
Found at i:25231 original size:29 final size:29
Alignment explanation
Indices: 25199--25261 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
25189 AAACCTCTAT
*
25199 TTTTTAT-CTCGAA-ATCTTAAAAATTACCC
1 TTTTTATCCCCGAAGATC-TAAAAATT-CCC
*
25228 -TTTTATCCCCGAAGGTCTAAAAATTCCC
1 TTTTTATCCCCGAAGATCTAAAAATTCCC
25256 TTTTTA
1 TTTTTA
25262 AATCTCAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
28 9 0.31
29 18 0.62
30 2 0.07
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.41
Consensus pattern (29 bp):
TTTTTATCCCCGAAGATCTAAAAATTCCC
Done.