Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006116.1 Kokia drynarioides strain JFW-HI SEQ_120632, 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: 7036
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:628 original size:41 final size:41
Alignment explanation
Indices: 569--906 Score: 317
Period size: 41 Copynumber: 8.5 Consensus size: 41
559 GAAAGCTCCA
* **
569 CTATTGCTCTGACTTTTAGCGGCGCATT-TTCATAAGCGCCG
1 CTATTGCTCTGACCTTTAGCGGCGC-TTGCCCATAAGCGCCG
* *
610 CTATTGCTCTGACCTTTAGCGGCACTTGCCCTTAAGCGCCG
1 CTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
* * * *
651 CTATTGCTCTGATCTGTAGCGGCGCTTGCTCATAAGCGTC-
1 CTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
* *
691 CTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGCGCCG
1 CTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
732 CTATTGCAT-TGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
1 CTATTGC-TCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
* * * ** *
773 CTATTGCTCTAACATTTAGCGGCGC-TGCTC-T--G-ATCT
1 CTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
* * * * *
809 TTATTGCTCTAACCTTTAGCGGCGC-TGCTC-T--G-GTCT
1 CTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
* * * *
845 TTATTGCTCTGACCTTTAGCGGCGCTTCCCCATAAGCACTG
1 CTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
*
886 CTATTGCTCT-ACCTTTTGCGG
1 CTATTGCTCTGACCTTTAGCGG
907 TGTTTATGTA
Statistics
Matches: 251, Mismatches: 37, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
36 58 0.23
37 4 0.02
38 1 0.00
39 1 0.00
40 52 0.21
41 134 0.53
42 1 0.00
ACGTcount: A:0.15, C:0.30, G:0.22, T:0.33
Consensus pattern (41 bp):
CTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCG
Found at i:732 original size:81 final size:81
Alignment explanation
Indices: 569--895 Score: 311
Period size: 81 Copynumber: 4.1 Consensus size: 81
559 GAAAGCTCCA
*
569 CTATTGCTCTGACTTTTAGCGGCGCATT-TTCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGC
1 CTATTGCTCTGAC-TTTAGCGGCGC-TTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGC
* *
633 ACTTGCCCTTAAGCGCCG
64 GCTTGCCCATAAGCGCCG
* * *
651 CTATTGCTCTGATCTGTAGCGGCGCTTGCTCATAAGCGTC-CTATTGCTCTGACCTTTAGCAGCG
1 CTATTGCTCTGA-CTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
*
715 CTTTCCCATAAGCGCCG
65 CTTGCCCATAAGCGCCG
* * *
732 CTATTGCAT-TGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTAACATTTAGCGGC
1 CTATTGC-TCTGA-CTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGC
* ** *
796 GC-TGCTC-T--G-ATCT
64 GCTTGCCCATAAGCGCCG
* * * **
809 TTATTGCTCTAACCTTTAGCGGCGC-TGCTC-T--G-GTCTTTATTGCTCTGACCTTTAGCGGCG
1 CTATTGCTCTGA-CTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
* * *
869 CTTCCCCATAAGCACTG
65 CTTGCCCATAAGCGCCG
886 CTATTGCTCT
1 CTATTGCTCT
896 ACCTTTTGCG
Statistics
Matches: 202, Mismatches: 33, Indels: 25
0.78 0.13 0.10
Matches are distributed among these distances:
72 24 0.12
73 4 0.02
74 1 0.00
75 1 0.00
76 6 0.03
77 32 0.16
78 1 0.00
80 1 0.00
81 76 0.38
82 55 0.27
83 1 0.00
ACGTcount: A:0.16, C:0.30, G:0.21, T:0.33
Consensus pattern (81 bp):
CTATTGCTCTGACTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
TTGCCCATAAGCGCCG
Found at i:793 original size:122 final size:121
Alignment explanation
Indices: 569--802 Score: 348
Period size: 122 Copynumber: 1.9 Consensus size: 121
559 GAAAGCTCCA
* * *
569 CTATTGCTCTGACTTTTAGCGGCGCATTTTCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCA
1 CTATTGCTCTGACCTTTAGCAGCGCATTTCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCA
* *
634 CTTGCCCTTAAGCGCCGCTATTGCTCTGATCTGTAGCGGCGCTTGCTCATAAGCGTC
66 CTTGCCCATAAGCGCCGCTATTGCTCTGAACTGTAGCGGCGC-TGCTCATAAGCGTC
691 CTATTGCTCTGACCTTTAGCAGCGC-TTTCCCATAAGCGCCGCTATTGCAT-TGACCTTTAGCGG
1 CTATTGCTCTGACCTTTAGCAGCGCATTT-CCATAAGCGCCGCTATTGC-TCTGACCTTTAGCGG
* *
754 CGCTTGCCCATAAGCGCCGCTATTGCTCT-AACATTTAGCGGCGCTGCTC
64 CACTTGCCCATAAGCGCCGCTATTGCTCTGAAC-TGTAGCGGCGCTGCTC
803 TGATCTTTAT
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
121 10 0.10
122 91 0.89
123 1 0.01
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (121 bp):
CTATTGCTCTGACCTTTAGCAGCGCATTTCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCA
CTTGCCCATAAGCGCCGCTATTGCTCTGAACTGTAGCGGCGCTGCTCATAAGCGTC
Found at i:821 original size:36 final size:36
Alignment explanation
Indices: 774--870 Score: 167
Period size: 36 Copynumber: 2.7 Consensus size: 36
764 TAAGCGCCGC
*
774 TATTGCTCTAACATTTAGCGGCGCTGCTCTGATCTT
1 TATTGCTCTAACCTTTAGCGGCGCTGCTCTGATCTT
*
810 TATTGCTCTAACCTTTAGCGGCGCTGCTCTGGTCTT
1 TATTGCTCTAACCTTTAGCGGCGCTGCTCTGATCTT
*
846 TATTGCTCTGACCTTTAGCGGCGCT
1 TATTGCTCTAACCTTTAGCGGCGCT
871 TCCCCATAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (36 bp):
TATTGCTCTAACCTTTAGCGGCGCTGCTCTGATCTT
Found at i:1183 original size:49 final size:49
Alignment explanation
Indices: 1126--1219 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
1116 AGAATCCGTG
1126 CTTAACTCTTTTCAACCCGAGTATTCATCAATTCTCTGTAATACGGGAT
1 CTTAACTCTTTTCAACCCGAGTATTCATCAATTCTCTGTAATACGGGAT
1175 CTTAACTCTTTTCAACCCGAGTATTCATCAATTCTCTGTAATACG
1 CTTAACTCTTTTCAACCCGAGTATTCATCAATTCTCTGTAATACG
1220 TGATTGACGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.37
Consensus pattern (49 bp):
CTTAACTCTTTTCAACCCGAGTATTCATCAATTCTCTGTAATACGGGAT
Found at i:1689 original size:22 final size:22
Alignment explanation
Indices: 1649--1708 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
1639 TTCGACTTTC
*
1649 CTATTTTCTATT-TTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
1670 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
1692 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
1709 CCTCAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 25 0.69
22 11 0.31
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:6320 original size:6 final size:6
Alignment explanation
Indices: 6311--6387 Score: 65
Period size: 6 Copynumber: 13.7 Consensus size: 6
6301 TTGTTTTAGG
* * * * *
6311 TTTAAA TTT-AT TTTAAA GTTAAA -TTAAT TTTAAG TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
6356 TTTAAA TTTAAA ATT--A TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
6388 TTCAAATCTA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 41 0.73
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:6325 original size:11 final size:11
Alignment explanation
Indices: 6311--6365 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
6301 TTGTTTTAGG
6311 TTTAAATTTAT
1 TTTAAATTTAT
* *
6322 TTTAAAGTTAA
1 TTTAAATTTAT
* * *
6333 ATTAATTTTAAG
1 TTTAAATTT-AT
6345 TTTAAATTTAT
1 TTTAAATTTAT
6356 TTTAAATTTA
1 TTTAAATTTA
6366 AAATTATTTA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 26 0.76
12 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:6394 original size:16 final size:17
Alignment explanation
Indices: 6294--6389 Score: 122
Period size: 17 Copynumber: 5.7 Consensus size: 17
6284 TGAACTTATT
* **
6294 TTTAAATTTGTTTTAGG
1 TTTAAATTTATTTTAAA
6311 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
6328 GTTAAATTAATTTTAAG
1 TTTAAATTTATTTTAAA
6345 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
6362 TTTAAAATTA-TTTAAA
1 TTTAAATTTATTTTAAA
6378 TTTAAATTTATT
1 TTTAAATTTATT
6390 CAAATCTAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
16 15 0.22
17 52 0.78
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:6399 original size:16 final size:16
Alignment explanation
Indices: 6311--6399 Score: 97
Period size: 17 Copynumber: 5.4 Consensus size: 16
6301 TTGTTTTAGG
6311 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
* * *
6328 GTTAAATTAATTTTAAG
1 TTTAAATTTA-TTTAAA
6345 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
6362 TTTAAAATTATTTAAA
1 TTTAAATTTATTTAAA
*
6378 TTTAAATTTATTCAAA
1 TTTAAATTTATTTAAA
*
6394 TCTAAA
1 TTTAAA
6400 ATAAATAATG
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
16 25 0.40
17 37 0.60
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Done.