Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005206.1 Kokia drynarioides strain JFW-HI SEQ_119074, 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: 20542
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3802 original size:24 final size:24
Alignment explanation
Indices: 3773--3819 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3763 TGGTTAACCT
3773 CTATCTGGGCTCGTAAGAGCTAAC
1 CTATCTGGGCTCGTAAGAGCTAAC
*
3797 CTATCTGGGCTCGTATGAGCTAA
1 CTATCTGGGCTCGTAAGAGCTAA
3820 TTTTGTCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (24 bp):
CTATCTGGGCTCGTAAGAGCTAAC
Found at i:3837 original size:25 final size:26
Alignment explanation
Indices: 3800--3849 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
3790 AGCTAACCTA
*
3800 TCTGGGCTCGTATGAGCT-AATTTTG
1 TCTGGGCTAGTATGAGCTAAATTTTG
3825 TCTGGGCTAGTATGAGCTAAATTTT
1 TCTGGGCTAGTATGAGCTAAATTTT
3850 TGGAAAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (26 bp):
TCTGGGCTAGTATGAGCTAAATTTTG
Found at i:4794 original size:30 final size:30
Alignment explanation
Indices: 4746--4852 Score: 94
Period size: 30 Copynumber: 3.5 Consensus size: 30
4736 AAAAAGAACG
4746 AAAAAAATCTAGATTAGTTGGGTGACCAAATTA
1 AAAAAAAT-T-GA-TAGTTGGGTGACCAAATTA
**
4779 AAAAAAATTGATAGTTGAATGACCAAA--A
1 AAAAAAATTGATAGTTGGGTGACCAAATTA
* ** *
4807 AAGAAAAGGGCAATAGTTAGGTGACCAAATT-
1 AAAAAAATTG--ATAGTTGGGTGACCAAATTA
4838 AAAAAAATTGATAGT
1 AAAAAAATTGATAGT
4853 CAAGTGGCCA
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 8 0.14
29 5 0.08
30 28 0.47
31 9 0.15
32 1 0.02
33 8 0.14
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.23
Consensus pattern (30 bp):
AAAAAAATTGATAGTTGGGTGACCAAATTA
Found at i:4871 original size:59 final size:60
Alignment explanation
Indices: 4760--4892 Score: 191
Period size: 60 Copynumber: 2.2 Consensus size: 60
4750 AAATCTAGAT
*
4760 TAGTTGGGTGACCAAATTAAAAAAAATTGATAGTTGAATGACCAAAAAAG-AAAAGGGCAA
1 TAGTT-GGTGACCAAATTAAAAAAAATTGATAGTTCAATGACCAAAAAAGAAAAAGGGCAA
*
4820 TAGTTAGGTGACCAAATT-AAAAAAATTGATAG-TCAAGTGGCCAAAAAAGAAAAAGGGCAA
1 TAGTT-GGTGACCAAATTAAAAAAAATTGATAGTTCAA-TGACCAAAAAAGAAAAAGGGCAA
4880 TAGTTGAGTGACC
1 TAGTTG-GTGACC
4893 TTTAATGCAG
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
58 3 0.04
59 26 0.39
60 38 0.57
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (60 bp):
TAGTTGGTGACCAAATTAAAAAAAATTGATAGTTCAATGACCAAAAAAGAAAAAGGGCAA
Found at i:11680 original size:14 final size:15
Alignment explanation
Indices: 11656--11701 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
11646 TAATAAATAA
11656 AAAACTATTAAATATT
1 AAAA-TATTAAATATT
11672 -AAATATTAAAT-TT
1 AAAATATTAAATATT
11685 AAAATAATTTAAATATT
1 AAAAT-A-TTAAATATT
11702 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.08
14 12 0.46
15 4 0.15
16 6 0.23
17 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATATTAAATATT
Found at i:11698 original size:23 final size:23
Alignment explanation
Indices: 11670--11715 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11660 CTATTAAATA
11670 TTAAATATTAAATTTAAAATAAT
1 TTAAATATTAAATTTAAAATAAT
***
11693 TTAAATATTTTTTTTAAAATAAT
1 TTAAATATTAAATTTAAAATAAT
11716 ATGAGCATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAATATTAAATTTAAAATAAT
Found at i:14229 original size:184 final size:184
Alignment explanation
Indices: 13920--14288 Score: 693
Period size: 184 Copynumber: 2.0 Consensus size: 184
13910 AACAACCCAT
13920 ACCCGGCCTAGACGTTAAGACCAAGTCCGAAGAGATACATTAAAACATTTCTAGAAAATCCAACC
1 ACCCGGCCTAGACGTTAAGACCAAGTCCGAAGAGATACATTAAAACATTTCTAGAAAATCCAACC
* *
13985 TTTATAAATGCAATTCAAACATATCTAAACCATATAAAAGATCTTAAACAATCACAAAATTATCC
66 TTTATAAATGCAATTCAAACAGATCTAAACCATATAAAAGATATTAAACAATCACAAAATTATCC
*
14050 AGTCAATAAAACAACAATCTTAGAAAGACATAGTACGATGGAATTACTGAAAAC
131 AGTCAATAAAACAACAATCTTAGAAAGACATAGTACGATGGAAATACTGAAAAC
* *
14104 ACCCGGCCTAGACTTTAAGACCAAGTCCGAAGAGCTACATTAAAACATTTCTAGAAAATCCAACC
1 ACCCGGCCTAGACGTTAAGACCAAGTCCGAAGAGATACATTAAAACATTTCTAGAAAATCCAACC
14169 TTTATAAATGCAATTCAAACAGATCTAAACCATATAAAAGATATTAAACAATCACAAAATTATCC
66 TTTATAAATGCAATTCAAACAGATCTAAACCATATAAAAGATATTAAACAATCACAAAATTATCC
14234 AGTCAATAAAACAACAATCTTAGAAAGACATAGTACGATGGAAATACTGAAAAC
131 AGTCAATAAAACAACAATCTTAGAAAGACATAGTACGATGGAAATACTGAAAAC
14288 A
1 A
14289 TAATAAGATG
Statistics
Matches: 180, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 180 1.00
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (184 bp):
ACCCGGCCTAGACGTTAAGACCAAGTCCGAAGAGATACATTAAAACATTTCTAGAAAATCCAACC
TTTATAAATGCAATTCAAACAGATCTAAACCATATAAAAGATATTAAACAATCACAAAATTATCC
AGTCAATAAAACAACAATCTTAGAAAGACATAGTACGATGGAAATACTGAAAAC
Done.