Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014890.1 Kokia drynarioides strain JFW-HI SEQ_129933, 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: 25351
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:2693 original size:18 final size:18
Alignment explanation
Indices: 2670--2704 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2660 GATACTACAT
2670 CAAAATTCAC-ATATTCTG
1 CAAAA-TCACAATATTCTG
2688 CAAAATCACAATATTCT
1 CAAAATCACAATATTCT
2705 CCATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.23, G:0.03, T:0.31
Consensus pattern (18 bp):
CAAAATCACAATATTCTG
Found at i:3095 original size:253 final size:254
Alignment explanation
Indices: 2643--3148 Score: 856
Period size: 253 Copynumber: 2.0 Consensus size: 254
2633 TAGTTGGTTG
*
2643 AGGGACCTTGCCCAATGGATACTACATCAAAATTCACATATTCTGCAAAATCACAATATTCTCCA
1 AGGGACCTTGCCCAATGGATACTACATCAAAATTCACATATTCTGCAAAACCACAATATTCTCCA
*
2708 TTCACTTCTTCACTGCTGTAACTCAGAAAAGCTCCCCATCACAACACTCTCAGTAGAAAACCCAC
66 TTCACTTCTTCACTGCTGTAACTCAGAAAAGCTCCCCATAACAACACTCTCAGTAGAAAACCCAC
** *
2773 CTTATTACCATCAATTGTTCGTGCTCTTTTTGTCATAGTCAATCCAAGATTGCTGCTCTACCAAC
131 CTTATTACCATCAATTGTTCACGCTCTTTTTGTCATAGTCAATCCAAGATTGCTACTCTACCAAC
*
2838 CATCAATCTTGCAGAGACATACTAAGGTAATCTTAGGAGTTTTTGTCATCATCAATCTT
196 CATCAATCTTGCAGAGACATAATAAGGTAATCTTAGGAGTTTTTGTCATCATCAATCTT
* * *
2897 AGGGACCTTGCCTAATGGATACTACATTACAATTCACATATTCTG-AAATACCACAATATTCTCC
1 AGGGACCTTGCCCAATGGATACTACATCAAAATTCACATATTCTGCAAA-ACCACAATATTCTCC
*
2961 ATTCACTTCTTCACTGCTGTAACTCAG-AAAGC-CCCTCATAACAACACTCTCAGTAGAAAATCC
65 ATTCACTTCTTCACTGCTGTAACTCAGAAAAGCTCCC-CATAACAACACTCTCAGTAGAAAACCC
*
3024 ACCTTATTACCATCAATTGTTCACGCTCTTTTTGTCATAGTCAATCCAAGATTGCTACTCTACCG
129 ACCTTATTACCATCAATTGTTCACGCTCTTTTTGTCATAGTCAATCCAAGATTGCTACTCTACCA
* *
3089 ACCATCAATCTTGCAGAGAGATAATAATGTAATCTTAGGAGTTTTTGTCATCATCAATCT
194 ACCATCAATCTTGCAGAGACATAATAAGGTAATCTTAGGAGTTTTTGTCATCATCAATCT
3149 AAGATTGCTT
Statistics
Matches: 237, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
252 3 0.01
253 151 0.64
254 83 0.35
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (254 bp):
AGGGACCTTGCCCAATGGATACTACATCAAAATTCACATATTCTGCAAAACCACAATATTCTCCA
TTCACTTCTTCACTGCTGTAACTCAGAAAAGCTCCCCATAACAACACTCTCAGTAGAAAACCCAC
CTTATTACCATCAATTGTTCACGCTCTTTTTGTCATAGTCAATCCAAGATTGCTACTCTACCAAC
CATCAATCTTGCAGAGACATAATAAGGTAATCTTAGGAGTTTTTGTCATCATCAATCTT
Found at i:3199 original size:78 final size:78
Alignment explanation
Indices: 3052--3203 Score: 202
Period size: 78 Copynumber: 1.9 Consensus size: 78
3042 GTTCACGCTC
* *
3052 TTTTTGTCATAGTCAATCCAAGATTGCTACTCTACCGACCATCAATCTTGCAGAGAGATAATAAT
1 TTTTTGTCATAGTCAATCCAAGATTGCTACTCTACCGACCATCAAGCTTGCAGAGAGATAATAAG
3117 GTAATCTTAGGAG
66 GTAATCTTAGGAG
* * * *
3130 TTTTTGTCATCA-TCAATCTAAGATTGCTTCTCTACCGGCCATCAAGCTTGTCAG-G-GCATACT
1 TTTTTGTCAT-AGTCAATCCAAGATTGCTACTCTACCGACCATCAAGCTTG-CAGAGAG-ATAAT
3192 AAGGTAATCTTA
63 AAGGTAATCTTA
3204 TGATTAACTG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
77 1 0.02
78 60 0.92
79 4 0.06
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (78 bp):
TTTTTGTCATAGTCAATCCAAGATTGCTACTCTACCGACCATCAAGCTTGCAGAGAGATAATAAG
GTAATCTTAGGAG
Found at i:3467 original size:167 final size:168
Alignment explanation
Indices: 3262--3596 Score: 546
Period size: 167 Copynumber: 2.0 Consensus size: 168
3252 CAGAATGGAT
*
3262 CATGAGAACTCAACCATATTAAAGAATCCCCAAGAGATCCTAAACTTAATCATTAAGATTCAATT
1 CATGAGAACTCAACCATATTAAAGAATCCCCAAGAGATCCCAAACTTAATCATTAAGATTCAATT
* * *
3327 CTTACCAATCTCATTCATATTAAAGAGCCCAAAAA-ATCCAAAATTTAATCATTATAAATTTGTG
66 CTTACCAATCTCATTCATATTAAAGAGCCCAAAAACATCCAAAACTTAATCATCATAAATTTGTA
**
3391 TTTAGCACCACCTTCATTTGCCTCAAATTTAGGAATGA
131 ACTAGCACCACCTTCATTTGCCTCAAATTTAGGAATGA
* *
3429 CATGAGAACTCAACCATATTAAAGAATCCCTAAGAGATCCCAAACTTAATCATTAAGATTCACTT
1 CATGAGAACTCAACCATATTAAAGAATCCCCAAGAGATCCCAAACTTAATCATTAAGATTCAATT
* ** *
3494 TTTACCAATCTCATTTGTATTAAAGATCCCAAAAACATCCAAAACTTAATCATCATAAATTTGTA
66 CTTACCAATCTCATTCATATTAAAGAGCCCAAAAACATCCAAAACTTAATCATCATAAATTTGTA
*
3559 ACTAGCACCGCCTTCATTTGCCTCAAATTTAGGAATGA
131 ACTAGCACCACCTTCATTTGCCTCAAATTTAGGAATGA
3597 TAGGCCTATC
Statistics
Matches: 154, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
167 93 0.60
168 61 0.40
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (168 bp):
CATGAGAACTCAACCATATTAAAGAATCCCCAAGAGATCCCAAACTTAATCATTAAGATTCAATT
CTTACCAATCTCATTCATATTAAAGAGCCCAAAAACATCCAAAACTTAATCATCATAAATTTGTA
ACTAGCACCACCTTCATTTGCCTCAAATTTAGGAATGA
Found at i:4972 original size:2 final size:2
Alignment explanation
Indices: 4967--4992 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4957 CAAATATATT
4967 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
4993 TCATAGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11735 original size:5 final size:5
Alignment explanation
Indices: 11725--11760 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
11715 AATCTGTGTT
11725 CACCC CACCC CACCC CACCC CACCC CACCC CACCC C
1 CACCC CACCC CACCC CACCC CACCC CACCC CACCC C
11761 TTGTATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.81, G:0.00, T:0.00
Consensus pattern (5 bp):
CACCC
Found at i:18732 original size:37 final size:37
Alignment explanation
Indices: 18666--18744 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
18656 TCTTATCATT
18666 ATGT-ATTTTTAAATTAAAAAATATATTAAATGAAAAA
1 ATGTGATTTTTAAATTAAAAAATATATTAAA-GAAAAA
* * * *
18703 ATGTGATTTTTTAA-TAAAAATTATTTTAAAGATAAA
1 ATGTGATTTTTAAATTAAAAAATATATTAAAGAAAAA
18739 ATGTGA
1 ATGTGA
18745 AATTGATACC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 11 0.30
37 18 0.49
38 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.41
Consensus pattern (37 bp):
ATGTGATTTTTAAATTAAAAAATATATTAAAGAAAAA
Found at i:19055 original size:14 final size:16
Alignment explanation
Indices: 19036--19071 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
19026 GAGAATTTTT
19036 GGGGGAAGT-AAA-TG
1 GGGGGAAGTAAAATTG
19050 GGGGG-AGTAAAATTG
1 GGGGGAAGTAAAATTG
19065 GGGGGAA
1 GGGGGAA
19072 ATGGGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.16
14 8 0.42
15 7 0.37
16 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.53, T:0.14
Consensus pattern (16 bp):
GGGGGAAGTAAAATTG
Found at i:19151 original size:31 final size:31
Alignment explanation
Indices: 19098--19159 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
19088 TGATGGTGAG
19098 ATGGGAGGGGAGAAAAAATTTTGGGGGAGAAA
1 ATGGGAGGGGAGAAAAAATTTTGGGGG-GAAA
* *
19130 ATGGGA-GGGAGTAAAAGTTTTGGGGGGAAA
1 ATGGGAGGGGAGAAAAAATTTTGGGGGGAAA
19160 GTAAAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 18 0.64
32 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.45, T:0.18
Consensus pattern (31 bp):
ATGGGAGGGGAGAAAAAATTTTGGGGGGAAA
Found at i:20971 original size:22 final size:22
Alignment explanation
Indices: 20937--20982 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
20927 TTGACTCTAA
* * *
20937 TGTCTCTAGTACTAACATTTTT
1 TGTCCCTAATACTAACATTCTT
*
20959 TGTCCCTAATACTGACATTCTT
1 TGTCCCTAATACTAACATTCTT
20981 TG
1 TG
20983 CGAACTCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (22 bp):
TGTCCCTAATACTAACATTCTT
Done.