Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008302.1 Kokia drynarioides strain JFW-HI SEQ_122967, 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: 6430
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Found at i:4761 original size:15 final size:14
Alignment explanation
Indices: 4732--4786 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
4722 TTAAATCAAG
* *
4732 AAAAAAATACAAAA
1 AAAAAAAAAGAAAA
4746 AAAAAGAAGAAGAAAA
1 AAAAA-AA-AAGAAAA
4762 AAGAAAAAAAGAAAA
1 AA-AAAAAAAGAAAA
4777 AAAGAAAAAA
1 AAA-AAAAAA
4787 AATAGAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 6 0.17
15 17 0.49
16 9 0.26
17 3 0.09
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAGAAAA
Found at i:4763 original size:26 final size:26
Alignment explanation
Indices: 4729--4794 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
4719 TGTTTAAATC
*
4729 AAGAAAAAA-ATACAAAAA-AAAAGAAG
1 AAGAAAAAAGA-A-AAAAAGAAAAAAAG
4755 AAGAAAAAAGAAAAAAAGAAAAAAAG
1 AAGAAAAAAGAAAAAAAGAAAAAAAG
*
4781 AAAAAAAATAGAAA
1 AAGAAAAA-AGAAA
4795 GAGAGAGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 5 0.14
26 24 0.69
27 6 0.17
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (26 bp):
AAGAAAAAAGAAAAAAAGAAAAAAAG
Found at i:4771 original size:8 final size:8
Alignment explanation
Indices: 4729--4787 Score: 68
Period size: 8 Copynumber: 7.2 Consensus size: 8
4719 TGTTTAAATC
4729 AAGAAAAA
1 AAGAAAAA
*
4737 AATACAAAA
1 AAGA-AAAA
4746 AA-AAAGAA
1 AAGAAA-AA
4754 GAAG-AAAA
1 -AAGAAAAA
4762 AAGAAAAA
1 AAGAAAAA
4770 AAGAAAAA
1 AAGAAAAA
4778 AAGAAAAA
1 AAGAAAAA
4786 AA
1 AA
4788 ATAGAAAGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
7 5 0.11
8 30 0.67
9 10 0.22
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:4786 original size:18 final size:19
Alignment explanation
Indices: 4729--4794 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
4719 TGTTTAAATC
4729 AAGAAAA-AAATACAAAAAAA
1 AAGAAAAGAAA-A-AAAAAAA
4749 AAGAAGAAGAAAAAAGAAAAA
1 AAGAA-AAGAAAAAA-AAAAA
4770 AAGAAAA-AAAGAAAAAAAA
1 AAGAAAAGAAA-AAAAAAAA
*
4789 TAGAAA
1 AAGAAA
4795 GAGAGAGCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 13 0.32
20 12 0.29
21 13 0.32
22 3 0.07
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (19 bp):
AAGAAAAGAAAAAAAAAAA
Found at i:4795 original size:15 final size:14
Alignment explanation
Indices: 4742--4796 Score: 62
Period size: 13 Copynumber: 4.1 Consensus size: 14
4732 AAAAAAATAC
4742 AAAAAAAAAG-AAG
1 AAAAAAAAAGAAAG
*
4755 AAGAAAAAAGAAA-
1 AAAAAAAAAGAAAG
*
4768 AAAAGAAAA-AAAG
1 AAAAAAAAAGAAAG
4781 AAAAAAAATAGAAAG
1 AAAAAAAA-AGAAAG
4796 A
1 A
4797 GAGAGCAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 3 0.09
13 23 0.68
14 3 0.09
15 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:5281 original size:42 final size:42
Alignment explanation
Indices: 5241--5658 Score: 586
Period size: 42 Copynumber: 10.0 Consensus size: 42
5231 TGCGCCCACT
* * * * *
5241 TGTGGAGGTCCATTTACTTTTTACTGCATTTTGAGGCCCACG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
*
5283 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * * * **
5325 TGTGGAGGTCTATTTACTTTTCATTACATTTAAAGGCTTAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
5367 TGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCCTAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
*
5409 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* *
5451 TGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCGAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
5493 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCGAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
5535 TGTGGAGGCCCATTTACTATTCATTACATTTAGAGGCCTAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
5577 TGTAGG-GGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TGT-GGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* *
5619 TGTGGAGGCCCATTTATTTTTCATTGCATTTAGAGACCCA
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCA
5659 TTTACTTTTC
Statistics
Matches: 340, Mismatches: 34, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
41 2 0.01
42 336 0.99
43 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
Found at i:5416 original size:126 final size:125
Alignment explanation
Indices: 5241--5854 Score: 653
Period size: 126 Copynumber: 5.1 Consensus size: 125
5231 TGCGCCCACT
* * * *
5241 TGTGGAGGTCCATTTACTTTTTACTGCATTTTGAGGCCCACGTGTGGAGGCCCATTTACTTTTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGG-CCAGGTGTGGAGGCCCATTTACTTTTCA
* * * * **
5306 TTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTTTTCATTACATTTAAAGGCTTAGG
65 TTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
*
5367 TGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCCTAGGTGTGGAGGCCCATTTACTTTTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCC-AGGTGTGGAGGCCCATTTACTTTTCA
* *
5432 TTGCATTTAGAGGCCCAAGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCGAGG
65 TTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
* *
5493 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCGAGGTGTGGAGGCCCATTTACTATTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGG-CCAGGTGTGGAGGCCCATTTACTTTTCA
* * *
5558 TTACATTTAGAGGCCTAGGTGTAGG-GGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
65 TTGCATTTAGAGGCCCAGGTGT-GGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
* *
5619 TGTGGAGGCCCATTTATTTTTCATTGCATTT--A-G--A------GA--CCCATTTACTTTTCAT
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCAGGTGTGGAGGCCCATTTACTTTTCAT
*
5671 TGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT--A-G---A--
66 TGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
* * * * *
5723 ----GA--CCCATTTACTTTTTATTGCATTTGGAGGCTCAGGTGTGAAGGCCTATTTACTTTTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGC-CAGGTGTGGAGGCCCATTTACTTTTCA
* * * * * *
5782 TTGCATTTAGAGACCCAAGTGTGGAGACCC----ACTTTTTATTGCATTTAGAGGCCTAGG
65 TTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
* *
5839 TGTAGAGGCCCATTTA
1 TGTGGAGGTCCATTTA
5855 TTTATTTTTT
Statistics
Matches: 423, Mismatches: 33, Indels: 68
0.81 0.06 0.13
Matches are distributed among these distances:
98 21 0.05
100 3 0.01
101 1 0.00
104 1 0.00
106 1 0.00
108 15 0.04
109 1 0.00
110 3 0.01
111 3 0.01
112 100 0.24
114 3 0.01
120 3 0.01
122 8 0.02
123 1 0.00
124 1 0.00
125 2 0.00
126 253 0.60
127 3 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (125 bp):
TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCAGGTGTGGAGGCCCATTTACTTTTCAT
TGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
Found at i:5659 original size:70 final size:70
Alignment explanation
Indices: 5585--5798 Score: 374
Period size: 70 Copynumber: 3.1 Consensus size: 70
5575 GGTGTAGGGG
*
5585 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTATTTTTCATTGCATTT
1 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
5650 AGAGA
66 AGAGA
5655 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
1 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
5720 AGAGA
66 AGAGA
* * * * *
5725 CCCATTTACTTTTTATTGCATTTGGAGGCTCAGGTGTGAAGGCCTATTTACTTTTCATTGCATTT
1 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
5790 AGAGA
66 AGAGA
5795 CCCA
1 CCCA
5799 AGTGTGGAGA
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 138 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (70 bp):
CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
AGAGA
Found at i:5667 original size:28 final size:28
Alignment explanation
Indices: 5627--5686 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
5617 GGTGTGGAGG
*
5627 CCCATTTATTTTTCATTGCATTTAGAGA
1 CCCATTTACTTTTCATTGCATTTAGAGA
*
5655 CCCATTTACTTTTCATTGCATTTAGAGG
1 CCCATTTACTTTTCATTGCATTTAGAGA
5683 CCCA
1 CCCA
5687 GGTGTGGAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (28 bp):
CCCATTTACTTTTCATTGCATTTAGAGA
Done.