Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009053.1 Kokia drynarioides strain JFW-HI SEQ_123752, 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: 6469
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Found at i:3807 original size:85 final size:85
Alignment explanation
Indices: 3664--3830 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 85
3654 CAAATCTCAT
* * * *
3664 CTTCCTAATAAGATACAAAGAAGTGGGTAAAAGCAACAAAGCGGCCATCTTCTTGATGAGATAGA
1 CTTCCTAATAAGATACAAAAAAGTGGATAAAAGCAACAAAGCGGCCATCTTCCTGATGAGATACA
*
3729 GAGAAGTGGAACAAATCCGC
66 GAGAAGTAGAACAAATCCGC
* * * * ** * *
3749 CTTCCTGATGAGATACAAAAAAGTGGATTAAATCAATGAAGTGGTCATCTTCCTGATGAGATACA
1 CTTCCTAATAAGATACAAAAAAGTGGATAAAAGCAACAAAGCGGCCATCTTCCTGATGAGATACA
*
3814 GAGAAGTAGACCAAATC
66 GAGAAGTAGAACAAATC
3831 AATAAAGCGA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (85 bp):
CTTCCTAATAAGATACAAAAAAGTGGATAAAAGCAACAAAGCGGCCATCTTCCTGATGAGATACA
GAGAAGTAGAACAAATCCGC
Found at i:3934 original size:208 final size:208
Alignment explanation
Indices: 3577--4237 Score: 901
Period size: 208 Copynumber: 3.2 Consensus size: 208
3567 AGTAAAAATG
* * *
3577 ATGAAGTGGTCATCTTCCTGATTAGATACAGAGAAGT-GACCAAATCAATGAAGCAAAGCTCAAT
1 ATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAAT
* * * * *
3641 ACGAATAAGACTTCAAATCTCATCTTCCTAATAAGATACAAAGAAGTGGGTAAAAGCAACAAAGC
66 ACGAATGAGACTTCAAACCTCATCTTCCTAATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGC
** * * * *
3706 GGCCATCTTCTTGATGAGATAGAGAGAAGTGGAACAAATCCGCCTTCCTGATGAGATACAAAAAA
131 TACCATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAA
3771 GTGGATTAAATCA
196 GTGGATTAAATCA
* *
3784 ATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATAAAGCGAAGCTCAAT
1 ATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAAT
* *
3849 ATGAATGAGACTTCAAACCTCATCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGC
66 ACGAATGAGACTTCAAACCTCATCTTCCTAATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGC
* * * *
3914 TATCATCTTCCTGATGAGATACAAAGAAGTGGACCAAATCCGCCTTCCTGATGAGATATAGAGAA
131 TACCATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAA
3979 GTGGATTAAATCA
196 GTGGATTAAATCA
* * * *
3992 ATGAAGCGATCATCTTCC---T--GATA-AGATAAGTAGACCAAATCAATGAAGTGAAGCTTAAT
1 ATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAAT
* *
4051 ACGAATGAGACTTGAAACCCCATCTTCCTAATGAGATACAAAGAAGTGGGTCAAAGCAATAAAG-
66 ACGAATGAGACTTCAAACCTCATCTTCCTAATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGC
* **
4115 TAGCCATCTTCTTGATGAGATATAGAGAAGTGGACCAAATTTGCCTTCCTGATGAGATACAGAGA
131 TA-CCATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGA
* **
4180 AGTGG-GTAGAAGAA
195 AGTGGATTA-AATCA
* *
4194 ATAAAGCGGTCATCTT-CTAGATGAGATACAGAGAAATAGACCAA
1 ATGAAGCGGTCATCTTCCT-GATGAGATACAGAGAAGTAGACCAA
4238 GAGATGAAGC
Statistics
Matches: 400, Mismatches: 44, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
201 5 0.01
202 169 0.42
203 4 0.01
205 2 0.00
207 40 0.10
208 180 0.45
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (208 bp):
ATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAAT
ACGAATGAGACTTCAAACCTCATCTTCCTAATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGC
TACCATCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAA
GTGGATTAAATCA
Found at i:4217 original size:85 final size:85
Alignment explanation
Indices: 4074--4237 Score: 222
Period size: 85 Copynumber: 1.9 Consensus size: 85
4064 GAAACCCCAT
* * * *
4074 CTTCCTAATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGTAGCCATCTTCTTGATGAGATATA
1 CTTCCTAATGAGATACAAAGAAGTGGGTCAAAGAAATAAAGCAGCCATCTTCTAGATGAGATACA
* *
4139 GAGAAGTGGACCAAATTTGC
66 GAGAAATAGACCAAATTTGC
* * * *
4159 CTTCCTGATGAGATACAGAGAAGTGGGT-AGAAGAAATAAAGCGGTCATCTTCTAGATGAGATAC
1 CTTCCTAATGAGATACAAAGAAGTGGGTCA-AAGAAATAAAGCAGCCATCTTCTAGATGAGATAC
4223 AGAGAAATAGACCAA
65 AGAGAAATAGACCAA
4238 GAGATGAAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 1 0.01
85 67 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (85 bp):
CTTCCTAATGAGATACAAAGAAGTGGGTCAAAGAAATAAAGCAGCCATCTTCTAGATGAGATACA
GAGAAATAGACCAAATTTGC
Found at i:4674 original size:42 final size:40
Alignment explanation
Indices: 4628--4706 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 40
4618 AATAAAACAA
* *
4628 ATTTTAAATTTTAATTTACTTTAAATTTTAAATGTCCAATAC
1 ATTTTAAATTTAAATTT-CTTTAAA-TTTAAAAGTCCAATAC
*
4670 ATTTTAAATTTAAATTTGTTTAAATTTAAAAGTCCAA
1 ATTTTAAATTTAAATTTCTTTAAATTTAAAAGTCCAA
4707 ATTACAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 12 0.35
41 6 0.18
42 16 0.47
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.48
Consensus pattern (40 bp):
ATTTTAAATTTAAATTTCTTTAAATTTAAAAGTCCAATAC
Found at i:4749 original size:13 final size:13
Alignment explanation
Indices: 4724--4772 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
4714 AATCCAATAC
4724 CACTAAA-CCAAA
1 CACTAAACCCAAA
4736 CACTAAACCCAAA
1 CACTAAACCCAAA
4749 CCCAC-AAACCCTAAA
1 --CACTAAACCC-AAA
4764 -ACTAAACCC
1 CACTAAACCC
4773 TAATTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 9 0.28
13 11 0.34
14 6 0.19
15 6 0.19
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.08
Consensus pattern (13 bp):
CACTAAACCCAAA
Found at i:4757 original size:21 final size:21
Alignment explanation
Indices: 4732--4772 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4722 ACCACTAAAC
*
4732 CAAACACTAAACCCAAACCCA
1 CAAACACTAAAACCAAACCCA
* *
4753 CAAACCCTAAAACTAAACCC
1 CAAACACTAAAACCAAACCC
4773 TAATTTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.07
Consensus pattern (21 bp):
CAAACACTAAAACCAAACCCA
Found at i:6323 original size:30 final size:30
Alignment explanation
Indices: 6266--6356 Score: 107
Period size: 29 Copynumber: 3.1 Consensus size: 30
6256 CTTAAGAGGA
*
6266 CCCTAAACTTTCCAAAAA-T-CTATTTTGAC
1 CCCTAAACTTTTCAAAAATTAC-ATTTTGAC
6295 CCCTAAACTTTTCAAAAATTACATTTTGA-
1 CCCTAAACTTTTCAAAAATTACATTTTGAC
* * * *
6324 CCCAAAATTTTTCTAAGATTACATTTTGAC
1 CCCTAAACTTTTCAAAAATTACATTTTGAC
6354 CCC
1 CCC
6357 AAATTCTTCG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 42 0.78
30 11 0.20
31 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
CCCTAAACTTTTCAAAAATTACATTTTGAC
Done.