Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007984.1 Kokia drynarioides strain JFW-HI SEQ_122635, 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: 98999
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:1356 original size:17 final size:18
Alignment explanation
Indices: 1326--1359 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1316 ATAGATACGA
*
1326 TTCTCTTTATTTTTTTTC
1 TTCTCTTTAATTTTTTTC
1344 TTCT-TTTAATTTTTTT
1 TTCTCTTTAATTTTTTT
1360 TCCTTTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (18 bp):
TTCTCTTTAATTTTTTTC
Found at i:10069 original size:23 final size:22
Alignment explanation
Indices: 10043--10086 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
10033 AAAATATTTT
*
10043 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
10066 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
10087 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:15680 original size:28 final size:28
Alignment explanation
Indices: 15648--15773 Score: 130
Period size: 28 Copynumber: 4.5 Consensus size: 28
15638 TTAAGAACGA
* * *
15648 TATTTTGTATTCTAGCTCAAAAGAGTGT
1 TATTCTGTATTCTAGCTCGAAAGAGCGT
* * ***
15676 TATTTTGTATAT-TGGCTCGAAAGATTAT
1 TATTCTGTAT-TCTAGCTCGAAAGAGCGT
15704 TATTCTGTATAT-TAGCTCGAAAGAGCGT
1 TATTCTGTAT-TCTAGCTCGAAAGAGCGT
*
15732 TATTCTATATTCTAGCTCGAAAGAGCGT
1 TATTCTGTATTCTAGCTCGAAAGAGCGT
*
15760 TATTCTGTGTTCTA
1 TATTCTGTATTCTA
15774 AACTGAAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.01
28 82 0.98
29 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (28 bp):
TATTCTGTATTCTAGCTCGAAAGAGCGT
Found at i:15781 original size:28 final size:28
Alignment explanation
Indices: 15719--15798 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
15709 TGTATATTAG
*
15719 CTCGAAAGAGCGTTATTCTATATTCTAG
1 CTCGAAAGAGCGTTATTCTATATTCTAA
* *
15747 CTCGAAAGAGCGTTATTCTGTGTTCTAAA
1 CTCGAAAGAGCGTTATTCTATATTCT-AA
* * *
15776 CT-GAAAAAGCATTATTCTTTATT
1 CTCGAAAGAGCGTTATTCTATATT
15799 TGGCTCGAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 41 0.93
29 3 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (28 bp):
CTCGAAAGAGCGTTATTCTATATTCTAA
Found at i:20664 original size:3 final size:3
Alignment explanation
Indices: 20656--20687 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
20646 AAATATCAAC
*
20656 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20688 CATATATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:20910 original size:23 final size:23
Alignment explanation
Indices: 20875--21156 Score: 402
Period size: 23 Copynumber: 12.3 Consensus size: 23
20865 ATCTTAATTC
20875 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
20898 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
20921 TTCAAACACAAATCAAATTAATA
1 TTTAAGCACAAATCACATTAATA
*
20944 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
20967 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
20990 TTTAAGCACATATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
21013 TTTAAGGACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21036 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21059 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21082 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
21105 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
21128 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
21151 TTTAAG
1 TTTAAG
21157 TACGGATATA
Statistics
Matches: 227, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 227 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:28154 original size:35 final size:35
Alignment explanation
Indices: 28108--28178 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
28098 CAACCGACCT
28108 ATTGGCTCAGTTGAAATTGGACGAGGAATCACCCG
1 ATTGGCTCAGTTGAAATTGGACGAGGAATCACCCG
28143 ATTGGCTCAGTTGAAATTGGACGAGGAATCACCCG
1 ATTGGCTCAGTTGAAATTGGACGAGGAATCACCCG
28178 A
1 A
28179 CTTCTGGGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (35 bp):
ATTGGCTCAGTTGAAATTGGACGAGGAATCACCCG
Found at i:37561 original size:12 final size:13
Alignment explanation
Indices: 37532--37574 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
37522 GAGCTTGTAT
37532 TTTTATTATAATA
1 TTTTATTATAATA
37545 TTTTATTATCAAT-
1 TTTTATTAT-AATA
*
37558 TTTATTTTATAATA
1 TTT-TATTATAATA
37572 TTT
1 TTT
37575 ATGTTAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTATTATAATA
Found at i:37575 original size:14 final size:14
Alignment explanation
Indices: 37529--37576 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
37519 GAAGAGCTTG
*
37529 TATTTTTATTATAA
1 TATTTATATTATAA
37543 TATTT-TATTATCAA
1 TATTTATATTAT-AA
*
37557 T-TTTATTTTATAA
1 TATTTATATTATAA
37570 TATTTAT
1 TATTTAT
37577 GTTAAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTATATTATAA
Found at i:40939 original size:21 final size:20
Alignment explanation
Indices: 40899--40936 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40889 TGGATGTTAC
40899 TTTTTCAAAAAACATTCCTT
1 TTTTTCAAAAAACATTCCTT
*
40919 TTTTTTAACAAAA-ATTCC
1 TTTTTCAA-AAAACATTCC
40937 CTTCAGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTTCAAAAAACATTCCTT
Found at i:74850 original size:16 final size:17
Alignment explanation
Indices: 74811--74851 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
74801 ATTTTAATAT
74811 AAAAT-ATATAAATTTA
1 AAAATAATATAAATTTA
*
74827 AATTATAATA-AAATTTA
1 AA-AATAATATAAATTTA
74844 AAAATAAT
1 AAAATAAT
74852 TTATTAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 7 0.33
17 11 0.52
18 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATAATATAAATTTA
Found at i:75008 original size:17 final size:18
Alignment explanation
Indices: 74988--75023 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
74978 TTAATATTAA
74988 AATATATTAAT-TTATTT
1 AATATATTAATATTATTT
*
75005 AATATTTTAATATTATTT
1 AATATATTAATATTATTT
75023 A
1 A
75024 TTAATAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATATATTAATATTATTT
Found at i:75139 original size:23 final size:23
Alignment explanation
Indices: 75113--75160 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
75103 ATATATATTG
75113 ATTTTAATTAT-AAATTTAAAAAT
1 ATTTTAA-TATGAAATTTAAAAAT
* *
75136 ATTTTAATATGCATTTTAAAAAT
1 ATTTTAATATGAAATTTAAAAAT
75159 AT
1 AT
75161 GTTGTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTTAATATGAAATTTAAAAAT
Found at i:76039 original size:24 final size:24
Alignment explanation
Indices: 76011--76072 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
76001 AGAAATAATT
* * *
76011 TTTCAGTTAAAGTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
76035 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
76059 TTTCAA-CAAACTCT
1 TTTCAATTAAACTCT
76073 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.21
24 27 0.79
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:81653 original size:19 final size:20
Alignment explanation
Indices: 81601--81653 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
81591 TAAAAGTCTG
* * *
81601 CAAGAAAATATTGATAAATA
1 CAAGAATATAGTGAAAAATA
*
81621 -AAGCATATAGTGAAAAATA
1 CAAGAATATAGTGAAAAATA
81640 CAAGAATATA-TGAA
1 CAAGAATATAGTGAA
81654 TTTTGAAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (20 bp):
CAAGAATATAGTGAAAAATA
Found at i:82129 original size:28 final size:28
Alignment explanation
Indices: 82083--82183 Score: 123
Period size: 28 Copynumber: 3.6 Consensus size: 28
82073 CTACGTGTAT
* *
82083 TTAGCACTTTGTGTACTCTCTGTTCTGA
1 TTAGCACTTCGTGTGCTCTCTGTTCTGA
* *
82111 TTAGCACTTCGCGTGCTCTTTGTTCTGA
1 TTAGCACTTCGTGTGCTCTCTGTTCTGA
* *
82139 TTAGCACTTTGTGTGCTCTCTATTCTGTA
1 TTAGCACTTCGTGTGCTCTCTGTTCTG-A
*
82168 ATAGCACTTCG-GTGCT
1 TTAGCACTTCGTGTGCT
82184 TCGTGATACG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
28 52 0.84
29 10 0.16
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (28 bp):
TTAGCACTTCGTGTGCTCTCTGTTCTGA
Found at i:82451 original size:2 final size:2
Alignment explanation
Indices: 82441--82471 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
82431 AAAAAAAAAA
*
82441 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
82472 CAAGATCGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:95924 original size:21 final size:21
Alignment explanation
Indices: 95871--95935 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
95861 ACCCAAAAAG
*
95871 TCAATGGTCAACAGTCAACTA
1 TCAATGGTCAATAGTCAACTA
95892 TCAATGGTCAATAGTCAACTA
1 TCAATGGTCAATAGTCAACTA
95913 TCAATGGTCAAT-GTTCAACTA
1 TCAATGGTCAATAG-TCAACTA
95934 TC
1 TC
95936 TACGATCAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (21 bp):
TCAATGGTCAATAGTCAACTA
Found at i:95993 original size:22 final size:21
Alignment explanation
Indices: 95963--96013 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
95953 TCAAATCAAA
* *
95963 TTGGGTTTAATGTTTGGGTGAT
1 TTGGTTTTAAGGTTTGGGT-AT
*
95985 TTGGTTTTAGGGTTTGGGTAT
1 TTGGTTTTAAGGTTTGGGTAT
*
96006 TGGGTTTT
1 TTGGTTTT
96014 CATGGTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.10, C:0.00, G:0.37, T:0.53
Consensus pattern (21 bp):
TTGGTTTTAAGGTTTGGGTAT
Found at i:96020 original size:22 final size:22
Alignment explanation
Indices: 95962--96026 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
95952 GTCAAATCAA
*
95962 ATTGGGTTTAAT-GTTTGGGTG
1 ATTGGGTTTTATGGTTTGGGTG
* *
95983 ATTTGGTTTTAGGGTTTGGGT-
1 ATTGGGTTTTATGGTTTGGGTG
96004 ATTGGGTTTTCATGGTTTTGGGT
1 ATTGGGTTTT-ATGG-TTTGGGT
96027 TTACACATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 18 0.50
22 11 0.31
23 7 0.19
ACGTcount: A:0.11, C:0.02, G:0.37, T:0.51
Consensus pattern (22 bp):
ATTGGGTTTTATGGTTTGGGTG
Done.