Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006529.1 Kokia drynarioides strain JFW-HI SEQ_121113, 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: 79470
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 188 characters in sequence are not A, C, G, or T
Found at i:3663 original size:6 final size:6
Alignment explanation
Indices: 3663--3697 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
3653 TAAAATTAAA
3663 AAATTC AAA-TC GAAATTC AAATTC AAATTC AAATT
1 AAATTC AAATTC -AAATTC AAATTC AAATTC AAATT
3698 AAAAACTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.07
6 23 0.85
7 2 0.07
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (6 bp):
AAATTC
Found at i:5238 original size:2 final size:2
Alignment explanation
Indices: 5231--5268 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5221 TTCTAATGAA
5231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5269 TGATTTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5481 original size:18 final size:17
Alignment explanation
Indices: 5458--5491 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5448 AATTAATATA
*
5458 AAATAAATAACTAAATTC
1 AAATAAA-AAATAAATTC
5476 AAATAAAAAATAAATT
1 AAATAAAAAATAAATT
5492 GAACACAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAAAATAAATTC
Found at i:7664 original size:26 final size:26
Alignment explanation
Indices: 7602--7686 Score: 65
Period size: 26 Copynumber: 3.4 Consensus size: 26
7592 GCCCACCCAT
*
7602 ATTTT-TATTTTTTTAAATATTT-AT-
1 ATTTTATATATTTTT-AATATTTAATA
*
7626 ATTATAT-TA-TTTTAATATTTAATA
1 ATTTTATATATTTTTAATATTTAATA
* *
7650 ATTTTATATATTTTTTATTTATTAA-A
1 ATTTTATATATTTTTAATAT-TTAATA
*
7676 ATTTTTTATAT
1 ATTTTATATAT
7687 AGTCATCTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
22 7 0.14
23 6 0.12
24 11 0.22
25 3 0.06
26 18 0.37
27 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
ATTTTATATATTTTTAATATTTAATA
Found at i:18870 original size:2 final size:2
Alignment explanation
Indices: 18863--18890 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18853 GTTAGTATTC
18863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18891 TCTTTAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18923 original size:13 final size:13
Alignment explanation
Indices: 18905--18929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18895 TAACCTATGG
18905 GATAAGTGTTTCA
1 GATAAGTGTTTCA
18918 GATAAGTGTTTC
1 GATAAGTGTTTC
18930 TCTTCAGTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (13 bp):
GATAAGTGTTTCA
Found at i:32897 original size:61 final size:54
Alignment explanation
Indices: 32828--32948 Score: 190
Period size: 54 Copynumber: 2.2 Consensus size: 54
32818 AACATCGAAT
* * * *
32828 CTCGAATCTCAAATATTAAACCCT-GACCCTAAATTAAAACCTTAGTCTTTAAAC
1 CTCGAATCCCAAATCTTAAACCCTAG-CCCTAAATTAAAACCATAATCTTTAAAC
32882 CTCGAATCCCAAATCTTAAACCCTAGCCCTAAATTAAAACCATAATCTTTAAAC
1 CTCGAATCCCAAATCTTAAACCCTAGCCCTAAATTAAAACCATAATCTTTAAAC
32936 CTCGAATCCCAAA
1 CTCGAATCCCAAA
32949 CTTGGGGTCT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
54 61 0.98
55 1 0.02
ACGTcount: A:0.40, C:0.29, G:0.05, T:0.26
Consensus pattern (54 bp):
CTCGAATCCCAAATCTTAAACCCTAGCCCTAAATTAAAACCATAATCTTTAAAC
Found at i:40181 original size:7 final size:7
Alignment explanation
Indices: 40169--40201 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
40159 TAAATCTTAT
40169 TTTTTTA
1 TTTTTTA
40176 TTTTTTA
1 TTTTTTA
40183 TTTTTTA
1 TTTTTTA
40190 TTTTTTA
1 TTTTTTA
40197 TTTTT
1 TTTTT
40202 GCAATGTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:41296 original size:29 final size:26
Alignment explanation
Indices: 41264--41329 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 26
41254 ATTGAACCCG
41264 AATTTTAAAATCTAAAAAATAGAAGATTA
1 AATTTTAAAA--TAAAAAATAGAA-ATTA
**
41293 AATTTCTTAAAATAAAGTATAGAAATTA
1 AA-TT-TTAAAATAAAAAATAGAAATTA
41321 AATTTTAAA
1 AATTTTAAA
41330 TTTATGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 5 0.15
27 2 0.06
28 6 0.18
29 12 0.36
30 2 0.06
31 6 0.18
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (26 bp):
AATTTTAAAATAAAAAATAGAAATTA
Found at i:42092 original size:21 final size:21
Alignment explanation
Indices: 42066--42109 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
42056 ATCTTAACCA
*
42066 ATGAAATTATATTTGTAAATT
1 ATGAAATTATATTTGAAAATT
42087 ATGAAATTATATTTGAAAATT
1 ATGAAATTATATTTGAAAATT
42108 AT
1 AT
42110 ATAAAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (21 bp):
ATGAAATTATATTTGAAAATT
Found at i:42562 original size:22 final size:23
Alignment explanation
Indices: 42537--42579 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
42527 TTAATTGTTA
42537 TAATTACAATCAAATT-TATTAG
1 TAATTACAATCAAATTATATTAG
* *
42559 TAATTATAATTAAATTATATT
1 TAATTACAATCAAATTATATT
42580 TTTTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATTACAATCAAATTATATTAG
Found at i:52838 original size:12 final size:13
Alignment explanation
Indices: 52821--52849 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52811 GGACGGATCC
52821 AAAAAAGTAC-GT
1 AAAAAAGTACTGT
52833 AAAAAAGTACTGT
1 AAAAAAGTACTGT
52846 AAAA
1 AAAA
52850 TCACCGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.17
Consensus pattern (13 bp):
AAAAAAGTACTGT
Found at i:63832 original size:69 final size:69
Alignment explanation
Indices: 63712--63847 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
63702 ATTTCAAAAT
* *
63712 TACTCGTCAAAGTTCGATGGACTTCTTTATGGGTTGGTATCAGCCCCTGTTAGAAACATGACGAG
1 TACTCGTCAAAGTTCGATAGACTTCTTTATGGGTTGGTATCAGCCCCTGTTAGAAACATGACAAG
63777 CCTA
66 CCTA
* *
63781 TACTCGTCAAAAG-TCGATAGACTTTTTTATGGGTTGGTATC-GTCCCTTGTTAGAAACATGACA
1 TACTCGTC-AAAGTTCGATAGACTTCTTTATGGGTTGGTATCAG-CCCCTGTTAGAAACATGACA
63844 AGCC
64 AGCC
63848 GAACACACCC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
68 1 0.02
69 56 0.92
70 4 0.07
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (69 bp):
TACTCGTCAAAGTTCGATAGACTTCTTTATGGGTTGGTATCAGCCCCTGTTAGAAACATGACAAG
CCTA
Found at i:64290 original size:72 final size:73
Alignment explanation
Indices: 64197--64337 Score: 230
Period size: 72 Copynumber: 1.9 Consensus size: 73
64187 TTAGTGGCCA
*
64197 TTGGATTGTTGATAAATGTCATCATCCTTGCCATTGATTTTACAAATATCTAATAGCTAGAATGT
1 TTGGATTGTTGATAAATGTCATCATCCTTACCATTGATTTTACAAATATCTAATAGCTAGAATGT
64262 TCATTCCC
66 TCATTCCC
* * * *
64270 TTGGATT-TTGATATATGTCATTATCCTTACCATTGATTTTACAAATATCTAATAGTTAGACTGT
1 TTGGATTGTTGATAAATGTCATCATCCTTACCATTGATTTTACAAATATCTAATAGCTAGAATGT
64334 TCAT
66 TCAT
64338 CTAGAAGTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 56 0.89
73 7 0.11
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (73 bp):
TTGGATTGTTGATAAATGTCATCATCCTTACCATTGATTTTACAAATATCTAATAGCTAGAATGT
TCATTCCC
Found at i:73511 original size:21 final size:21
Alignment explanation
Indices: 73487--73569 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
73477 AATAACAACC
*
73487 AAAACAGCAGCAAAACAACAA
1 AAAACAGCACCAAAACAACAA
* ** *
73508 AAAATAGCAATAAAAATAACAGCA
1 AAAACAGC-ACCAAAACAACA--A
* **
73532 AAAACAACACCAAAACAGTAA
1 AAAACAGCACCAAAACAACAA
73553 AAAACAGCACCAAAACA
1 AAAACAGCACCAAAACA
73570 TAAATCAAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
21 24 0.51
22 9 0.19
23 7 0.15
24 7 0.15
ACGTcount: A:0.66, C:0.22, G:0.07, T:0.05
Consensus pattern (21 bp):
AAAACAGCACCAAAACAACAA
Found at i:73513 original size:33 final size:34
Alignment explanation
Indices: 73475--73540 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 34
73465 CCAAACAATC
* *
73475 AAAATAACAACCAAAACAGCAGC-AAAACAACAA
1 AAAATAACAACAAAAACAACAGCAAAAACAACAA
* * *
73508 AAAATAGCAATAAAAATAACAGCAAAAACAACA
1 AAAATAACAACAAAAACAACAGCAAAAACAACA
73541 CCAAAACAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.68, C:0.20, G:0.06, T:0.06
Consensus pattern (34 bp):
AAAATAACAACAAAAACAACAGCAAAAACAACAA
Found at i:73555 original size:45 final size:45
Alignment explanation
Indices: 73470--73561 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
73460 AATATCCAAA
* * * * *
73470 CAATCAAAATAACAACCAAAACAGCAGCAAAACAACAAAAAATAG
1 CAATAAAAATAACAACAAAAACAACACCAAAACAACAAAAAACAG
* **
73515 CAATAAAAATAACAGCAAAAACAACACCAAAACAGTAAAAAACAG
1 CAATAAAAATAACAACAAAAACAACACCAAAACAACAAAAAACAG
73560 CA
1 CA
73562 CCAAAACATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.65, C:0.22, G:0.07, T:0.07
Consensus pattern (45 bp):
CAATAAAAATAACAACAAAAACAACACCAAAACAACAAAAAACAG
Found at i:73568 original size:32 final size:32
Alignment explanation
Indices: 73487--73609 Score: 112
Period size: 32 Copynumber: 3.8 Consensus size: 32
73477 AATAACAACC
* * *
73487 AAAACAGCAGCAAAACAACAAAAAATAGCAATAAA
1 AAAACAGCACCAAAACAACAACAAA-A-CAGT-AA
*
73522 AATAACAGCA--AAAACAACACCAAAACAGTAA
1 AA-AACAGCACCAAAACAACAACAAAACAGTAA
*
73553 AAAACAGCACCAAAACATA-AATCAAAATAGTAA
1 AAAACAGCACCAAAACA-ACAA-CAAAACAGTAA
73586 AAAA-AGCACCAAAACAACAA-AAAA
1 AAAACAGCACCAAAACAACAACAAAA
73610 TACCAAAATA
Statistics
Matches: 77, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
30 11 0.14
31 5 0.06
32 24 0.31
33 16 0.21
34 12 0.16
35 2 0.03
36 7 0.09
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (32 bp):
AAAACAGCACCAAAACAACAACAAAACAGTAA
Found at i:73614 original size:18 final size:18
Alignment explanation
Indices: 73593--73641 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
73583 TAAAAAAAGC
73593 ACCAAAACAACAAAAA-A
1 ACCAAAACAACAAAAACA
* *
73610 TACCAAAATAGCAAAAACA
1 -ACCAAAACAACAAAAACA
*
73629 GCCAAAACAACAA
1 ACCAAAACAACAA
73642 TCAAAACAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.24, G:0.04, T:0.04
Consensus pattern (18 bp):
ACCAAAACAACAAAAACA
Found at i:75679 original size:14 final size:14
Alignment explanation
Indices: 75660--75691 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
75650 GGTAGTATTA
75660 TATTATGTATATGT
1 TATTATGTATATGT
75674 TATTATGTATATGT
1 TATTATGTATATGT
75688 TATT
1 TATT
75692 TAATTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (14 bp):
TATTATGTATATGT
Done.