Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010469.1 Kokia drynarioides strain JFW-HI SEQ_125369, 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: 69112
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 312 characters in sequence are not A, C, G, or T
Found at i:152 original size:23 final size:23
Alignment explanation
Indices: 126--272 Score: 172
Period size: 23 Copynumber: 6.3 Consensus size: 23
116 ACACTAGCGC
126 GCTCTCTGATTAGCATTGTGTGT
1 GCTCTCTGATTAGCATTGTGTGT
* *
149 GCTCTCTGTTTAGCA-TGTCTCGT
1 GCTCTCTGATTAGCATTGTGT-GT
172 GCTCTCTGTTATTAGCATTGTGTGT
1 GCTCTCTG--ATTAGCATTGTGTGT
*
197 GCTCTCTGATTAGCATTTTGTGT
1 GCTCTCTGATTAGCATTGTGTGT
* *
220 GCTCTCTGACTAGTACTT-TGTGT
1 GCTCTCTGATTAGCA-TTGTGTGT
* * *
243 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCATTGTGTGT
266 GCTCTCT
1 GCTCTCT
273 ATTGCCCAGC
Statistics
Matches: 105, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
22 5 0.05
23 78 0.74
24 2 0.02
25 16 0.15
26 4 0.04
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (23 bp):
GCTCTCTGATTAGCATTGTGTGT
Found at i:248 original size:71 final size:69
Alignment explanation
Indices: 126--272 Score: 188
Period size: 71 Copynumber: 2.1 Consensus size: 69
116 ACACTAGCGC
** * *
126 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGTTTAGCATGTCTCGTGCTCTCTGTTATTAGCATT
1 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGACTAGCATGTCTCGTACTCTCTG-T-TTAGCACT
191 GTGTGT
64 GTGTGT
* * * *
197 GCTCTCTGATTAGCATTTTGTGTGCTCTCTGACTAGTACTTTGT-GTACTCTCTGTTTAGCACTG
1 GCTCTCTGATTAGCATTGTGTGTGCTCTCTGACTAGCA-TGTCTCGTACTCTCTGTTTAGCACTG
261 TGTGT
65 TGTGT
266 GCTCTCT
1 GCTCTCT
273 ATTGCCCAGC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
69 20 0.30
70 1 0.01
71 43 0.64
72 3 0.04
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (69 bp):
GCTCTCTGATTAGCATTGTGTGTGCTCTCTGACTAGCATGTCTCGTACTCTCTGTTTAGCACTGT
GTGT
Found at i:31106 original size:33 final size:32
Alignment explanation
Indices: 31042--31106 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
31032 ATATGTACTG
* *
31042 ATTAAATACAATCTGATTTTTTATTAGAAATA
1 ATTAAATACAATCTGATTTTTTATAAAAAATA
31074 ATTAAATACAATCTGATTTTTTAGTAAAAAATA
1 ATTAAATACAATCTGATTTTTTA-TAAAAAATA
31107 TAGATAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (32 bp):
ATTAAATACAATCTGATTTTTTATAAAAAATA
Found at i:39294 original size:31 final size:31
Alignment explanation
Indices: 39245--39305 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
39235 AGTCCCAATA
* *
39245 TGGGAAAAGTTGTTAAGTTTAAGTTTTAATG
1 TGGGAAAAGTTGTCAAGTTTAAGATTTAATG
39276 TGGGAATAA-TTGTCAAGTTTAAGATTTAAT
1 TGGGAA-AAGTTGTCAAGTTTAAGATTTAAT
39306 TTGAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (31 bp):
TGGGAAAAGTTGTCAAGTTTAAGATTTAATG
Found at i:41784 original size:7 final size:7
Alignment explanation
Indices: 41772--41797 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41762 TTCACTCAAC
41772 TTTTCTA
1 TTTTCTA
41779 TTTTCTA
1 TTTTCTA
41786 TTTTCTA
1 TTTTCTA
41793 TTTTC
1 TTTTC
41798 AAAAGAAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTCTA
Found at i:42768 original size:10 final size:10
Alignment explanation
Indices: 42753--42781 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
42743 NNNNNNNNNC
42753 TTTTCTTTTT
1 TTTTCTTTTT
42763 TTTTCTTTTT
1 TTTTCTTTTT
42773 TTTT-TTTTT
1 TTTTCTTTTT
42782 ATACATACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:42781 original size:15 final size:15
Alignment explanation
Indices: 42752--42780 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42742 NNNNNNNNNN
42752 CTTTTCTTTTTTTTT
1 CTTTTCTTTTTTTTT
42767 CTTTT-TTTTTTTTT
1 CTTTTCTTTTTTTTT
42781 TATACATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
CTTTTCTTTTTTTTT
Found at i:46665 original size:6 final size:6
Alignment explanation
Indices: 46654--46694 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
46644 AAATTATTGA
*
46654 TTTCTT TTTCTT TCTCTT TTT-TT TTT-TT TTT-TT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
46695 CAGTTTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 15 0.47
6 17 0.53
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTCTT
Found at i:49852 original size:8 final size:8
Alignment explanation
Indices: 49839--49865 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
49829 GTACAAATAT
49839 ATTGATAA
1 ATTGATAA
49847 ATTGATAA
1 ATTGATAA
49855 ATTGATAA
1 ATTGATAA
49863 ATT
1 ATT
49866 CAACGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (8 bp):
ATTGATAA
Found at i:66114 original size:18 final size:18
Alignment explanation
Indices: 66091--66144 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
66081 ATAAGTAAAT
66091 AATTTTAAAAAAAATTTA
1 AATTTTAAAAAAAATTTA
* * *
66109 AATTTTATAAAATATAATA
1 AATTTTAAAAAAAAT-TTA
*
66128 AATTCTTTAAAAAAATT
1 AATT-TTAAAAAAAATT
66145 AACTTCATGA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
18 13 0.48
19 6 0.22
20 8 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTTAAAAAAAATTTA
Found at i:66186 original size:22 final size:23
Alignment explanation
Indices: 66159--66202 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
66149 TCATGAATGA
*
66159 TAATAAAATTCCCTTA-ATTTTT
1 TAATAAAATCCCCTTATATTTTT
66181 TAATAAAATCCCCTTATATTTT
1 TAATAAAATCCCCTTATATTTT
66203 GAAATATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATAAAATCCCCTTATATTTTT
Found at i:66208 original size:23 final size:22
Alignment explanation
Indices: 66160--66208 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
66150 CATGAATGAT
* **
66160 AATAAAATTCCCTTAATTTTTT
1 AATAAAATCCCCTTAATTTTGA
66182 AATAAAATCCCCTTATATTTTGA
1 AATAAAATCCCCTTA-ATTTTGA
66205 AATA
1 AATA
66209 TTTGTTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (22 bp):
AATAAAATCCCCTTAATTTTGA
Found at i:67807 original size:41 final size:38
Alignment explanation
Indices: 67709--67807 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 38
67699 AACAATAAAG
* *
67709 TGACACCCAGTGTCTCATCG-ACCTAGCCAAAGCAAAG
1 TGACACCCAGTGTCTCATCGAACCTAGCCAAAGAAAAA
* ** * * *
67746 TGATACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAACCTAGCCAAAG--AAA-AA
67787 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
67808 CTCGAGGTCG
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 17 0.36
38 9 0.19
40 2 0.04
41 19 0.40
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.21
Consensus pattern (38 bp):
TGACACCCAGTGTCTCATCGAACCTAGCCAAAGAAAAA
Done.