Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014468.1 Kokia drynarioides strain JFW-HI SEQ_129507, 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: 16573
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.34
Warning! 212 characters in sequence are not A, C, G, or T
Found at i:1172 original size:43 final size:43
Alignment explanation
Indices: 1123--1205 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
1113 ATTAACATGT
*
1123 TAAATTATATTACTTGACTCGTGTTAATATGATTG-CATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATAT-ATTGACATGTTAC
* *
1166 TAAATTATATTACTTTACTCTTATTAATATATTGACATGT
1 TAAATTATATTACTTGACTCGTATTAATATATTGACATGT
1206 AATTAATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 4 0.11
43 32 0.89
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATATTGACATGTTAC
Found at i:1841 original size:45 final size:45
Alignment explanation
Indices: 1774--1909 Score: 186
Period size: 45 Copynumber: 3.0 Consensus size: 45
1764 GCATAGCTCA
*
1774 TCAAGCCAAGGATATCATCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
*
1819 TCAAGCCAAGGATATCAGCCTCAATTTGACGAG-CACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * *
1863 TCAAGGGAAGGATATCATG-CTGAGTTTGACGAGCCATCGCGATAC
1 TCAAGCCAAGGATATCA-GCCTCAGTTTGACGAGCCACCGCAATAC
1908 TC
1 TC
1910 TATTCCTCCC
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
44 38 0.47
45 43 0.53
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:1874 original size:44 final size:44
Alignment explanation
Indices: 1774--1896 Score: 176
Period size: 44 Copynumber: 2.8 Consensus size: 44
1764 GCATAGCTCA
*
1774 TCAAGCCAAGGATATCATCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAG-CACCGCAATAC
*
1819 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCACCGCAATAC
** *
1863 TCAAGGGAAGGATATCATG-CTGAGTTTGACGAGC
1 TCAAGCCAAGGATATCA-GCCTCAGTTTGACGAGC
1897 CATCGCGATA
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
44 39 0.55
45 32 0.45
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (44 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCACCGCAATAC
Found at i:1930 original size:21 final size:21
Alignment explanation
Indices: 1904--1946 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1894 AGCCATCGCG
*
1904 ATACTCTATTCCTCCCGGGCA
1 ATACTCTACTCCTCCCGGGCA
*
1925 ATACTCTACTCCTCCGGGGCA
1 ATACTCTACTCCTCCCGGGCA
1946 A
1 A
1947 ATGGACCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (21 bp):
ATACTCTACTCCTCCCGGGCA
Found at i:5403 original size:4 final size:4
Alignment explanation
Indices: 5394--5454 Score: 70
Period size: 4 Copynumber: 15.0 Consensus size: 4
5384 ACACATTACT
* * *
5394 TTTC TTTC TTTC -TTC TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC -TTTC
5443 TTTC TTTC TTTC
1 TTTC TTTC TTTC
5455 CCGTTTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
4 38 0.79
5 7 0.15
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:5443 original size:17 final size:16
Alignment explanation
Indices: 5394--5454 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 16
5384 ACACATTACT
5394 TTTCTTTC-TTTCTTC
1 TTTCTTTCTTTTCTTC
5409 TTTCTTTCCTCTCCTTCTTCC
1 TTTCTTT-CT-T--TTCTT-C
5430 TTTCTTTCTTTTCTTTC
1 TTTCTTTCTTTTC-TTC
5447 TTTCTTTC
1 TTTCTTTC
5455 CCGTTTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 7 0.18
16 1 0.03
17 12 0.31
18 3 0.08
19 1 0.03
20 7 0.18
21 8 0.21
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTCTTTCTTTTCTTC
Found at i:8629 original size:25 final size:27
Alignment explanation
Indices: 8582--8633 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
8572 CATACTATTT
8582 TTTTTAGTTTTTATGAACTTTTTATAA
1 TTTTTAGTTTTTATGAACTTTTTATAA
8609 TTTTTA-TTTTT-TGAA-TATTTTATAA
1 TTTTTAGTTTTTATGAACT-TTTTATAA
8634 ATGTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 1 0.04
25 12 0.50
26 5 0.21
27 6 0.25
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (27 bp):
TTTTTAGTTTTTATGAACTTTTTATAA
Found at i:9121 original size:4 final size:4
Alignment explanation
Indices: 9107--9146 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
9097 TGTTGCTAAT
*
9107 ATAA A-AA ATAA ATAA AAAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
9147 CGTGAGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:11002 original size:22 final size:22
Alignment explanation
Indices: 10968--11010 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10958 GAGATCTAGA
*
10968 TCTTATATACAAGACCCTAAAC
1 TCTTAAATACAAGACCCTAAAC
* *
10990 TCTTAAATTCAAGATCCTAAA
1 TCTTAAATACAAGACCCTAAA
11011 TCTGAGAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (22 bp):
TCTTAAATACAAGACCCTAAAC
Found at i:13352 original size:23 final size:22
Alignment explanation
Indices: 13243--13363 Score: 102
Period size: 23 Copynumber: 5.3 Consensus size: 22
13233 CTGGGAAAAT
* *
13243 AGTAAGCACACACAGTGCAATCC
1 AGTAAGCACACAAAGTGCAA-AC
* *
13266 AGTAGGCACACACAA-TGCAATC
1 AGTAAGCACACA-AAGTGCAAAC
* *
13288 AGTAGGCGCACATAA-TGCAAATC
1 AGTAAGCACACA-AAGTGCAAA-C
*
13311 AGTAAGCACACGAAGTGCGAAAC
1 AGTAAGCACACAAAGTGC-AAAC
13334 AGTAAGCACACAAAGTGCGAAAC
1 AGTAAGCACACAAAGTGC-AAAC
*
13357 AATAAGC
1 AGTAAGC
13364 TCGCTAGCGT
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
22 21 0.25
23 58 0.70
24 4 0.05
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.12
Consensus pattern (22 bp):
AGTAAGCACACAAAGTGCAAAC
Found at i:15178 original size:19 final size:19
Alignment explanation
Indices: 15154--15192 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15144 TTGATTTTTG
*
15154 TTAATTATTTATA-ATATTT
1 TTAATT-TTTAAACATATTT
15173 TTAATTTTTAAACATATTT
1 TTAATTTTTAAACATATTT
15192 T
1 T
15193 GTCAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATTTTTAAACATATTT
Found at i:16540 original size:2 final size:2
Alignment explanation
Indices: 16535--16573 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16525 TTTACATCTC
16535 AT AT AT AT AT AT AT 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 AT AT AT AT A
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.