Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008303.1 Kokia drynarioides strain JFW-HI SEQ_122968, 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: 6431
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Found at i:4762 original size:15 final size:14
Alignment explanation
Indices: 4729--4787 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
4719 TGTTTAAATC
* *
4729 AAGAAAAAAATACA
1 AAGAAAAAAAAAAA
* *
4743 AA-AAAAAAAGAAG
1 AAGAAAAAAAAAAA
4756 AAGAAAAAAGAAAAA
1 AAGAAAAAA-AAAAA
4771 AAGAAAAAAAGAAAA
1 AAGAAAAAAA-AAAA
4786 AA
1 AA
4788 AATAGAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
13 10 0.27
14 9 0.24
15 18 0.49
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAAAAA
Found at i:4772 original size:8 final size:8
Alignment explanation
Indices: 4729--4788 Score: 68
Period size: 8 Copynumber: 7.2 Consensus size: 8
4719 TGTTTAAATC
4729 AAGAAAAA
1 AAGAAAAA
*
4737 AATACAAAA
1 AAGA-AAAA
*
4746 AA-AAAAG
1 AAGAAAAA
4753 AAGAAGAAAA
1 AAG-A-AAAA
4763 AAGAAAAA
1 AAGAAAAA
4771 AAGAAAAA
1 AAGAAAAA
4779 AAGAAAAA
1 AAGAAAAA
4787 AA
1 AA
4789 ATAGAAAGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
7 5 0.11
8 26 0.58
9 8 0.18
10 6 0.13
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:4787 original size:18 final size:19
Alignment explanation
Indices: 4742--4795 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
4732 AAAAAAATAC
4742 AAAAAAAAAAGAAGAAGAAA
1 AAAAAAAAAAGAA-AAGAAA
4762 AAAGAAAAAAAGAAAA-AAA
1 AAA-AAAAAAAGAAAAGAAA
*
4781 GAAAAAAAATAGAAA
1 -AAAAAAAAAAGAAA
4796 GAGAGAGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 13 0.42
20 8 0.26
21 10 0.32
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAGAAA
Found at i:4796 original size:15 final size:14
Alignment explanation
Indices: 4743--4797 Score: 62
Period size: 13 Copynumber: 4.1 Consensus size: 14
4733 AAAAAATACA
4743 AAAAAAAAAG-AAG
1 AAAAAAAAAGAAAG
*
4756 AAGAAAAAAGAAA-
1 AAAAAAAAAGAAAG
*
4769 AAAAGAAAA-AAAG
1 AAAAAAAAAGAAAG
4782 AAAAAAAATAGAAAG
1 AAAAAAAA-AGAAAG
4797 A
1 A
4798 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:5282 original size:42 final size:42
Alignment explanation
Indices: 5242--5659 Score: 586
Period size: 42 Copynumber: 10.0 Consensus size: 42
5232 TGCGCCCACT
* * * * *
5242 TGTGGAGGTCCATTTACTTTTTACTGCATTTTGAGGCCCACG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
*
5284 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * * * **
5326 TGTGGAGGTCTATTTACTTTTCATTACATTTAAAGGCTTAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
5368 TGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCCTAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
*
5410 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* *
5452 TGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCGAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
5494 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCGAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
5536 TGTGGAGGCCCATTTACTATTCATTACATTTAGAGGCCTAGG
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
5578 TGTAGG-GGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TGT-GGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* *
5620 TGTGGAGGCCCATTTATTTTTCATTGCATTTAGAGACCCA
1 TGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCA
5660 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:5417 original size:126 final size:125
Alignment explanation
Indices: 5242--5855 Score: 653
Period size: 126 Copynumber: 5.1 Consensus size: 125
5232 TGCGCCCACT
* * * *
5242 TGTGGAGGTCCATTTACTTTTTACTGCATTTTGAGGCCCACGTGTGGAGGCCCATTTACTTTTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGG-CCAGGTGTGGAGGCCCATTTACTTTTCA
* * * * **
5307 TTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTTTTCATTACATTTAAAGGCTTAGG
65 TTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
*
5368 TGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCCTAGGTGTGGAGGCCCATTTACTTTTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCC-AGGTGTGGAGGCCCATTTACTTTTCA
* *
5433 TTGCATTTAGAGGCCCAAGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCGAGG
65 TTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
* *
5494 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCGAGGTGTGGAGGCCCATTTACTATTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGG-CCAGGTGTGGAGGCCCATTTACTTTTCA
* * *
5559 TTACATTTAGAGGCCTAGGTGTAGG-GGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
65 TTGCATTTAGAGGCCCAGGTGT-GGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
* *
5620 TGTGGAGGCCCATTTATTTTTCATTGCATTT--A-G--A------GA--CCCATTTACTTTTCAT
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCAGGTGTGGAGGCCCATTTACTTTTCAT
*
5672 TGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT--A-G---A--
66 TGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
* * * * *
5724 ----GA--CCCATTTACTTTTTATTGCATTTGGAGGCTCAGGTGTGAAGGCCTATTTACTTTTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGC-CAGGTGTGGAGGCCCATTTACTTTTCA
* * * * * *
5783 TTGCATTTAGAGACCCAAGTGTGGAGACCC----ACTTTTTATTGCATTTAGAGGCCTAGG
65 TTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTACATTTAGAGGCCCAGG
* *
5840 TGTAGAGGCCCATTTA
1 TGTGGAGGTCCATTTA
5856 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:5660 original size:70 final size:70
Alignment explanation
Indices: 5586--5799 Score: 374
Period size: 70 Copynumber: 3.1 Consensus size: 70
5576 GGTGTAGGGG
*
5586 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTATTTTTCATTGCATTT
1 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
5651 AGAGA
66 AGAGA
5656 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
1 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
5721 AGAGA
66 AGAGA
* * * * *
5726 CCCATTTACTTTTTATTGCATTTGGAGGCTCAGGTGTGAAGGCCTATTTACTTTTCATTGCATTT
1 CCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTT
5791 AGAGA
66 AGAGA
5796 CCCA
1 CCCA
5800 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:5668 original size:28 final size:28
Alignment explanation
Indices: 5628--5687 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
5618 GGTGTGGAGG
*
5628 CCCATTTATTTTTCATTGCATTTAGAGA
1 CCCATTTACTTTTCATTGCATTTAGAGA
*
5656 CCCATTTACTTTTCATTGCATTTAGAGG
1 CCCATTTACTTTTCATTGCATTTAGAGA
5684 CCCA
1 CCCA
5688 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.