Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006235.1 Kokia drynarioides strain JFW-HI SEQ_120806, 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: 7497
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:974 original size:27 final size:27
Alignment explanation
Indices: 937--990 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
927 AAATTATGTA
* *
937 ATTAATTAAAAGGTATATCCTTTGATT
1 ATTAATCAAAAGGTATATCATTTGATT
*
964 ATTAATCAAAAGTTATATCATTTGATT
1 ATTAATCAAAAGGTATATCATTTGATT
991 TTTTACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (27 bp):
ATTAATCAAAAGGTATATCATTTGATT
Found at i:1006 original size:27 final size:27
Alignment explanation
Indices: 950--1007 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
940 AATTAAAAGG
* *
950 TATATCCTTTGATTATTAATCAAAAGT
1 TATATCATTTGATTATTAATCAAAAAT
* *
977 TATATCATTTGATTTTTTA-CAAAATAT
1 TATATCATTTGATTATTAATCAAAA-AT
1004 TATA
1 TATA
1008 ACTATTCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (27 bp):
TATATCATTTGATTATTAATCAAAAAT
Found at i:4253 original size:17 final size:18
Alignment explanation
Indices: 4231--4271 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
4221 TTTAATTTAT
*
4231 TTTAAATTTGATTT-AAA
1 TTTAAATTTAATTTCAAA
4248 TTTAAATTTAATTTCAAA
1 TTTAAATTTAATTTCAAA
*
4266 ATTAAA
1 TTTAAA
4272 AAGTCCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTAAATTTAATTTCAAA
Found at i:5111 original size:19 final size:19
Alignment explanation
Indices: 5072--5112 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5062 GTTTGTTAAG
*
5072 TAATTAATAATATAATTAA
1 TAATTAATAATATAATAAA
5091 TAATTAATAA-ATAAATAAA
1 TAATTAATAATAT-AATAAA
5110 TAA
1 TAA
5113 AACGAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATTAATAATATAATAAA
Found at i:6196 original size:59 final size:58
Alignment explanation
Indices: 6104--6899 Score: 588
Period size: 59 Copynumber: 13.6 Consensus size: 58
6094 TTACCCCAGA
* * *
6104 GACCCCGAAACTTTCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTTACCC-CAAACTTCCAAAAATCCCATTTTT
6163 GACCCCAAAACTTCCTAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTTACCCC-AAACTTCCAAAAATCCCA-TTTTT
* * *
6223 TACCCCAAAACTTCCTAAAATTACCATTTTACCCCCAAACTCCCAAAAATCTCATTTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCCCATTTTT
* * *
6282 AACCCCCAAAACTT-CTAAAAATACCATTTTACCCTCAAACTCCCAAAAATCCCATTTTT
1 GA-CCCCAAAACTTCCTAAAATTACCATTTTACCC-CAAACTTCCAAAAATCCCATTTTT
*
6341 GACCCCAAAACTT-CTAAAATTACCATTTTACCCACGAACTTCCAAAAATCCCATTTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTTACCC-CAAACTTCCAAAAATCCCATTTTT
* * * * * * * *
6399 GACCCCGAAACATCCAAAAATTACTATTTTACTCCCGAA-TGTCCGAAGA-CTCCGTTTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTTAC-CCCAAACT-TCCAAAAATC-CCATTTTT
* * * * ** * **** * ** *
6458 GACCTCGAAAC-T-CTCAAAATGGT-CC-TCTGACTTCAAGA-TGCCTTAGGGGCTGCCACGTGT
1 GACCCCAAAACTTCCT-AAAAT--TACCATTTTACCCCAA-ACTTCC--A-AAAATCCCATTTTT
* ****** ** *** *** * *
6518 CA-CCTGTTTTTTGGTTTTATTACC-TCGGAGGTCCCTAAACTATCCAAAAATTACCA-TTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTTA---CCCCAAACT-TCCAAAAA-TCCCATTTTT
** * *
6578 -ACCCCCTGAACTT-CTAAAAATCCCATTTTAACCCCAAACTTCCAAAAATCCCA-TTTT
1 GA-CCCCAAAACTTCCTAAAATTACCATTTT-ACCCCAAACTTCCAAAAATCCCATTTTT
*
6635 GACCCC-AAACTTCC-AAGAATTACCATTTTACCCCTAAACTTCCAAGAATCCCATTTTT
1 GACCCCAAAACTTCCTAA-AATTACCATTTTACCCC-AAACTTCCAAAAATCCCATTTTT
* *
6693 GACCACGAAACTTCC-AAAATTACCATTTTAACCCCAAACTTCCAAAAATCCCATTTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTT-ACCCCAAACTTCCAAAAATCCCATTTTT
* * * *
6751 AACCCCAAAACTTCCAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCA-TTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCCCATTTTT
* *
6809 GACCCCAAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
1 GACCCCAAAACTTCCTAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCCCATTTTT
* * *
6868 GATCCCGAAACTT-TTAAAAATTACCATTTTAC
1 GACCCCAAAACTTCCT-AAAATTACCATTTTAC
6900 TCCCGGATGT
Statistics
Matches: 599, Mismatches: 97, Indels: 83
0.77 0.12 0.11
Matches are distributed among these distances:
56 12 0.02
57 45 0.08
58 203 0.34
59 235 0.39
60 81 0.14
61 16 0.03
62 5 0.01
63 2 0.00
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.30
Consensus pattern (58 bp):
GACCCCAAAACTTCCTAAAATTACCATTTTACCCCAAACTTCCAAAAATCCCATTTTT
Found at i:6436 original size:30 final size:29
Alignment explanation
Indices: 6105--6437 Score: 179
Period size: 29 Copynumber: 11.3 Consensus size: 29
6095 TACCCCAGAG
* * *
6105 ACCCCGAAACTTTCTAAAATTACCATTTT
1 ACCCCGAAACATCCAAAAATTACCATTTT
* *
6134 ACCCTCG-AACTTCCAAAAA-TCCCATTTTT
1 ACCC-CGAAACATCCAAAAATTACCA-TTTT
* * *
6163 GACCCCAAAACTTCCTAAAATTACCATTTT
1 -ACCCCGAAACATCCAAAAATTACCATTTT
* * *
6193 ACCCCTAAACTTCCAAAAA-TCCCATTTTTTT
1 ACCCCGAAACATCCAAAAATTACCA---TTTT
* * *
6224 ACCCCAAAACTTCCTAAAATTACCATTTT
1 ACCCCGAAACATCCAAAAATTACCATTTT
*
6253 ACCCCCAAAC-TCCCAAAAA-T-CTCATTTTT
1 ACCCCGAAACAT-CCAAAAATTAC-CA-TTTT
* * *
6282 AACCCCCAAAACTTCTAAAAA-TACCATTTT
1 -A-CCCCGAAACATCCAAAAATTACCATTTT
*
6312 ACCCTC-AAAC-TCCCAAAAA-TCCCATTTTT
1 ACCC-CGAAACAT-CCAAAAATTACCA-TTTT
* * *
6341 GACCCCAAAAC-TTCTAAAATTACCATTTT
1 -ACCCCGAAACATCCAAAAATTACCATTTT
* *
6370 ACCCACG-AACTTCCAAAAA-TCCCATTTTT
1 ACCC-CGAAACATCCAAAAATTACCA-TTTT
*
6399 GACCCCGAAACATCCAAAAATTACTATTTT
1 -ACCCCGAAACATCCAAAAATTACCATTTT
6429 ACTCCCGAA
1 AC-CCCGAA
6438 TGTCCGAAGA
Statistics
Matches: 247, Mismatches: 28, Indels: 57
0.74 0.08 0.17
Matches are distributed among these distances:
27 2 0.01
28 40 0.16
29 90 0.36
30 64 0.26
31 45 0.18
32 6 0.02
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.29
Consensus pattern (29 bp):
ACCCCGAAACATCCAAAAATTACCATTTT
Found at i:6867 original size:29 final size:28
Alignment explanation
Indices: 6554--6866 Score: 322
Period size: 29 Copynumber: 10.8 Consensus size: 28
6544 GGAGGTCCCT
*
6554 AAACTATCCAAAAATTACCATTTTACCCCC
1 AAACT-TCCAAAAA-TCCCATTTTACCCCC
* * *
6584 TGAACTTCTAAAAATCCCATTTTAACCCC
1 -AAACTTCCAAAAATCCCATTTTACCCCC
6613 AAACTTCCAAAAATCCCATTTTGA-CCCC
1 AAACTTCCAAAAATCCCATTTT-ACCCCC
* * *
6641 AAACTTCCAAGAATTACCATTTTACCCCT
1 AAACTTCCAA-AAATCCCATTTTACCCCC
* * *
6670 AAACTTCCAAGAATCCCATTTTTGACCACG
1 AAACTTCCAAAAATCCCA-TTTT-ACCCCC
* * *
6700 AAACTTCCAAAATTACCATTTTAACCCC
1 AAACTTCCAAAAATCCCATTTTACCCCC
*
6728 AAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATCCCA-TTTT-ACCCCC
* * *
6758 AAACTTCCAAAAATTACCATTTTATCCTC
1 AAACTTCCAAAAA-TCCCATTTTACCCCC
* *
6787 GAACTTCCAAAAATCCCATTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTT-ACCCCC
*
6816 AAACTTCCAAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAA-TCCCATTTTACCCCC
*
6845 GAACTTCCAAAAATCCCATTTT
1 AAACTTCCAAAAATCCCATTTT
6867 TGATCCCGAA
Statistics
Matches: 234, Mismatches: 38, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
28 75 0.32
29 96 0.41
30 55 0.24
31 8 0.03
ACGTcount: A:0.37, C:0.32, G:0.03, T:0.28
Consensus pattern (28 bp):
AAACTTCCAAAAATCCCATTTTACCCCC
Found at i:6960 original size:117 final size:115
Alignment explanation
Indices: 6104--6904 Score: 484
Period size: 117 Copynumber: 6.8 Consensus size: 115
6094 TTACCCCAGA
* * *
6104 GACCCCGAAACTTTCTAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
1 GACCACGAAAC-TTCCAAAATTACCATTTTAACCC-CAAACTTCCAAAAATCCCATTTTTGA-CC
* * *
6168 CAAAACTTCCTAAAATTACCATTTTAC-CCCTAAACTTCCAAAAATCCCATTTTTT
63 CAAAACTTCCAAAAATTACCATTTTACTCCC-GAACTTCCAAGAATCCCA--TTTT
* * * * * * *
6223 TACCCCAAAACTTCCTAAAATTACCATTTTACCCCCAAACTCCCAAAAATCTCATTTTTAACCCC
1 GACCACGAAACTTCC-AAAATTACCATTTTAACCCCAAACTTCCAAAAATCCCATTTTTGA--CC
* * * *
6288 CAAAACTTCTAAAAA-TACCATTTTAC-CCTCAAACTCCCAAAAATCCCATTTTT
63 CAAAACTTCCAAAAATTACCATTTTACTCC-CGAACTTCCAAGAATCCCA-TTTT
* * * *
6341 GACCCCAAAACTTCTAAAATTACCATTTT-ACCCACGAACTTCCAAAAATCCCATTTTTGACCCC
1 GACCACGAAACTTCCAAAATTACCATTTTAACCC-CAAACTTCCAAAAATCCCATTTTTGA-CCC
* * * * **
6405 GAAACATCCAAAAATTACTATTTTACTCCCGAA-TGTCCGAAGACTCCGTTTTT
64 AAAACTTCCAAAAATTACCATTTTACTCCCGAACT-TCC-AAGAATCCCATTTT
* * * ** * **** * ** *
6458 GACCTCGAAAC-TCTCAAAATGGT-CC--TCTGACTTCAAGA-TGCCTTAGGGGCTGCCACGTGT
1 GACCACGAAACTTC-CAAAAT--TACCATTTTAACCCCAA-ACTTCC--A-AAAATCCCATTTTT
* ****** ****** *** * * * *
6518 CACCTGTTTTTTGGTTTTATTACC-TCGGAGGTCCCTAAACTATCCAAAAATTACCATTTT
59 GACCCAAAACTTCCAAAAATTACCATTTTA-CTCCC-GAACT-TCCAAGAA-TCCCATTTT
* * * *
6578 -ACCCCCTG-AACTTCTAAAAATCCCATTTTAACCCCAAACTTCCAAAAATCCCA-TTTTGACCC
1 GA-CCAC-GAAACTTCCAAAATTACCATTTTAACCCCAAACTTCCAAAAATCCCATTTTTGACCC
* * *
6640 CAAACTTCCAAGAATTACCATTTTAC-CCCTAAACTTCCAAGAATCCCATTTTT
64 AAAACTTCCAAAAATTACCATTTTACTCCC-GAACTTCCAAGAATCCCA-TTTT
*
6693 GACCACGAAACTTCCAAAATTACCATTTTAACCCCAAACTTCCAAAAATCCCATTTTTAACCCCA
1 GACCACGAAACTTCCAAAATTACCATTTTAACCCCAAACTTCCAAAAATCCCATTTTTGA-CCCA
*
6758 AAACTTCCAAAAATTACCATTTTA-TCCTCGAACTTCCAAAAATCCCATTTT
65 AAACTTCCAAAAATTACCATTTTACTCC-CGAACTTCCAAGAATCCCATTTT
* * * *
6809 GACCCCAAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCCC
1 GACCACGAAACTTCC-AAAATTACCATTTTAACCCCAAACTTCCAAAAATCCCATTTTTGA-CCC
* **
6874 GAAACTTTTAAAAATTACCATTTTACTCCCG
64 AAAACTTCCAAAAATTACCATTTTACTCCCG
6905 GATGTCCGAA
Statistics
Matches: 523, Mismatches: 121, Indels: 78
0.72 0.17 0.11
Matches are distributed among these distances:
114 5 0.01
115 56 0.11
116 60 0.11
117 200 0.38
118 56 0.11
119 92 0.18
120 41 0.08
121 13 0.02
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.30
Consensus pattern (115 bp):
GACCACGAAACTTCCAAAATTACCATTTTAACCCCAAACTTCCAAAAATCCCATTTTTGACCCAA
AACTTCCAAAAATTACCATTTTACTCCCGAACTTCCAAGAATCCCATTTT
Found at i:7359 original size:96 final size:96
Alignment explanation
Indices: 7221--7408 Score: 231
Period size: 96 Copynumber: 2.0 Consensus size: 96
7211 ATTAAAAATC
* **
7221 GAGGCAATGTTCTTTTATTTCGAGTTTTGAAATTTCGTGCCTTAACTCACTAGGCACAATTTTTC
1 GAGGCAATGTTCTTTTATTTCGAGTTTTGAAATTTCGCGCCTTAACTCACTAGGCACAACCTTTC
7286 TTCAAATCGAAATAATCGAATACCCTTAATT
66 TTCAAATCGAAATAATCGAATACCCTTAATT
* **
7317 GAGGCAATGTT-TTCTTATCTTCGA-TTCTT-AAATATT-GCGCCTTAACTTACTAGGTGCAACC
1 GAGGCAATGTTCTT-TTAT-TTCGAGTT-TTGAAAT-TTCGCGCCTTAACTCACTAGGCACAACC
* * *
7378 TTTCTTTAAATCGAGATAATCGAATATCCTT
62 TTTCTTCAAATCGAAATAATCGAATACCCTT
7409 TTGCAAAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
95 2 0.03
96 68 0.86
97 9 0.11
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (96 bp):
GAGGCAATGTTCTTTTATTTCGAGTTTTGAAATTTCGCGCCTTAACTCACTAGGCACAACCTTTC
TTCAAATCGAAATAATCGAATACCCTTAATT
Done.