Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010994.1 Kokia drynarioides strain JFW-HI SEQ_125964, 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: 33142
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:872 original size:14 final size:15
Alignment explanation
Indices: 839--878 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
829 TTTTTAATTT
839 GAAAAATTAAGTACCA
1 GAAAAATTAAGTA-CA
855 -AAAAATTAAGTA-A
1 GAAAAATTAAGTACA
868 GAAAAATTAAG
1 GAAAAATTAAG
879 GGTTGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 10 0.43
15 12 0.52
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (15 bp):
GAAAAATTAAGTACA
Found at i:6916 original size:27 final size:25
Alignment explanation
Indices: 6868--6920 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
6858 GAATTTCATT
6868 AAAAATAATGTGATTGAAAAAAATTG
1 AAAAATAATGTGATTG-AAAAAATTG
* *
6894 AAAAACTAATGTGATTTATAAAATTG
1 AAAAA-TAATGTGATTGAAAAAATTG
6920 A
1 A
6921 CTTTTAAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.30
Consensus pattern (25 bp):
AAAAATAATGTGATTGAAAAAATTG
Found at i:12147 original size:21 final size:21
Alignment explanation
Indices: 12121--12161 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12111 CGTTAAAAAC
* * *
12121 TGATATGGTTAACGAAATAAT
1 TGATATAGCTAACAAAATAAT
12142 TGATATAGCTAACAAAATAA
1 TGATATAGCTAACAAAATAA
12162 CTATACTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (21 bp):
TGATATAGCTAACAAAATAAT
Found at i:13899 original size:84 final size:84
Alignment explanation
Indices: 13754--13940 Score: 268
Period size: 84 Copynumber: 2.2 Consensus size: 84
13744 ATCGACCGAA
** * *
13754 AACAGCAGTCCGTTGGCGCCATCTTGTACTTGAGGTGTCGCCCTCCCAAGCTGTCGAAGGTTTCC
1 AACAGCAGTCCGTCCGCGCCATCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTCGAAGGTTTCC
*
13819 TGTAGATTCGAGGCTGGAC
66 TGTAGATTCCAGGCTGGAC
* * *
13838 AACGGCAGTCCGTCCGCGCCATAC-TGTACTTCAGGCGTCGCCCTCCCAGGCTGTCTAAGGTTTC
1 AACAGCAGTCCGTCCGCGCCAT-CTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTCGAAGGTTTC
*
13902 CTGTAGGTTCCAGGCTGGAC
65 CTGTAGATTCCAGGCTGGAC
*
13922 AACAGCGGTCCGTCCGCGC
1 AACAGCAGTCCGTCCGCGC
13941 TAGTTTCTAC
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
84 90 0.99
85 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.24
Consensus pattern (84 bp):
AACAGCAGTCCGTCCGCGCCATCTTGTACTTCAGGCGTCGCCCTCCCAAGCTGTCGAAGGTTTCC
TGTAGATTCCAGGCTGGAC
Found at i:16240 original size:93 final size:92
Alignment explanation
Indices: 16024--16261 Score: 271
Period size: 92 Copynumber: 2.6 Consensus size: 92
16014 GAACATGGTC
* * * *
16024 AATATTATTAAATGCAACATAGACTTGATTCAAGAAGAAGATGACTAACTGTGGACACTGATTAC
1 AATATTATTAAATGCAACATAGACCTGATTCAAGAAGAAGATGATTAACTTTGGACACAGATTAC
* **
16089 GATTTACACAAAAAGGCGGTTGAACCT
66 GATTGACACAAAAAGGCGGTCAAACCT
* * * * * * * *
16116 AATATTATTAAATGCAACGTAAACCTAATTCAAGCAGAAGATGATTGACTTTGGAGAGAGATTAT
1 AATATTATTAAATGCAACATAGACCTGATTCAAGAAGAAGATGATTAACTTTGGACACAGATTAC
* *
16181 GGTTGACAC-AAGAGAGCGGGTCAAACCT
66 GATTGACACAAAAAG-GC-GGTCAAACCT
* **
16209 AATATTACTAAATGCAACATAGACCTGATTCAATTAGAAGATGATTAACTTTG
1 AATATTATTAAATGCAACATAGACCTGATTCAAGAAGAAGATGATTAACTTTG
16262 AAAAAACTAC
Statistics
Matches: 120, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
91 4 0.03
92 62 0.52
93 54 0.45
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (92 bp):
AATATTATTAAATGCAACATAGACCTGATTCAAGAAGAAGATGATTAACTTTGGACACAGATTAC
GATTGACACAAAAAGGCGGTCAAACCT
Found at i:18592 original size:20 final size:21
Alignment explanation
Indices: 18552--18592 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18542 TGGTACTAAT
18552 ATTTTATATTAATAGTATATA
1 ATTTTATATTAATAGTATATA
* *
18573 ATTTTA-ATTGATATTATATA
1 ATTTTATATTAATAGTATATA
18593 TAACAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
ATTTTATATTAATAGTATATA
Found at i:19408 original size:39 final size:38
Alignment explanation
Indices: 19365--19500 Score: 143
Period size: 39 Copynumber: 3.5 Consensus size: 38
19355 ATATGAACTA
*
19365 ATAAATTTTGAAAAAAGATTAAAAATAAAACACGAATTG
1 ATAAATTTTGAAAAAATATTAAAAATAAAACA-GAATTG
* *
19404 ATAAATTTTGAAAGACATTTTAAAAA-AAATACA-AATTG
1 ATAAATTTTGAAA-AAATATTAAAAATAAA-ACAGAATTG
* *
19442 A-AAATTTTTGAAAAAATATTAAAAATAAAATATGAACTG
1 ATAAA-TTTTGAAAAAATATTAAAAATAAAACA-GAATTG
* *
19481 ATAAATTTTGGAACAATATT
1 ATAAATTTTGAAAAAATATT
19501 TTTTACTCAT
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
37 15 0.19
38 17 0.21
39 34 0.42
40 15 0.19
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (38 bp):
ATAAATTTTGAAAAAATATTAAAAATAAAACAGAATTG
Found at i:31739 original size:95 final size:92
Alignment explanation
Indices: 31524--31793 Score: 327
Period size: 95 Copynumber: 2.9 Consensus size: 92
31514 CTGTTGATCA
* * *
31524 TTGTACAGATCTGGGAAATTTAACTCAGATCAAATGATGAATCAAAAACAATCGAATCGAAAATA
1 TTGTACAGATCTGGGAAATTTAACTCAGATCAGATGATGAAT-AAAAATAATCGAATCAAAAATA
*
31589 T---AACAAGTAAATTAACGGCACCACATC
65 TAAGAACAAGTAAATCAAC-G-ACCACATC
* *
31616 TTGTACAGGTCTGGGAAATTTAACTCAGATCAGATGATAGAATAAAAAATAAGCGAATCAAAAAT
1 TTGTACAGATCTGGGAAATTTAACTCAGATCAGATGAT-GAAT-AAAAATAATCGAATCAAAAAT
*
31681 ATGAAGAACAAGTAAATCAACGACCGCATC
64 AT-AAGAACAAGTAAATCAACGACCACATC
* * * * *
31711 TTGTACAGATCTGGAAAATTTAACTCAGATCAGATGATG---AAAATTAATCAAATAAAAAACAT
1 TTGTACAGATCTGGGAAATTTAACTCAGATCAGATGATGAATAAAAATAATCGAATCAAAAATAT
31773 AAAGAACAAGTAAATCAACGA
66 -AAGAACAAGTAAATCAACGA
31794 TACCGAAACG
Statistics
Matches: 157, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
90 38 0.24
92 36 0.23
93 24 0.15
94 1 0.01
95 43 0.27
96 1 0.01
97 14 0.09
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (92 bp):
TTGTACAGATCTGGGAAATTTAACTCAGATCAGATGATGAATAAAAATAATCGAATCAAAAATAT
AAGAACAAGTAAATCAACGACCACATC
Done.