Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003491.1 Kokia drynarioides strain JFW-HI SEQ_116312, 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: 40907
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:5551 original size:115 final size:116
Alignment explanation
Indices: 5349--5587 Score: 381
Period size: 115 Copynumber: 2.1 Consensus size: 116
5339 CTTCTTTACC
* * * *
5349 GTGTAAAAGAGATCTGGAGCTGTAGGTGCATTTATATAACCTCTTTTAAGTTCTTGAGTAGATTC
1 GTGTAATAGAGATCTGGAGCTGTAGGTGCATTTACATAACCTCTTTTAAGTTCTTGAATAGATGC
5414 TAGGTTATGTTGTGTTTACAAAGAGTGG-CCCTTGCTAGGTCAGCATCTCT
66 TAGGTTATGTTGTGTTTACAAAGAGTGGCCCCTTGCTAGGTCAGCATCTCT
* * * * *
5464 GTGTAATAGAGGTCTGGAGCTGTAGGTGGATTTGCATAACCTCTTTTAGGTTCTTGAATAGCTGC
1 GTGTAATAGAGATCTGGAGCTGTAGGTGCATTTACATAACCTCTTTTAAGTTCTTGAATAGATGC
5529 TAGGTTATGTTGTGTTTACAAAGAGTGGCCCCTTGCTAGGTCAGCATCTCT
66 TAGGTTATGTTGTGTTTACAAAGAGTGGCCCCTTGCTAGGTCAGCATCTCT
5580 GTGGTAAT
1 GT-GTAAT
5588 CCCTAGGCAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
115 84 0.74
116 24 0.21
117 5 0.04
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (116 bp):
GTGTAATAGAGATCTGGAGCTGTAGGTGCATTTACATAACCTCTTTTAAGTTCTTGAATAGATGC
TAGGTTATGTTGTGTTTACAAAGAGTGGCCCCTTGCTAGGTCAGCATCTCT
Found at i:6825 original size:39 final size:39
Alignment explanation
Indices: 6771--6849 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
6761 CTGTCGGTGA
6771 AAGGATTATGTGGATGAGTATGGTCTTGTACACATGCAT
1 AAGGATTATGTGGATGAGTATGGTCTTGTACACATGCAT
6810 AAGGATTATGTGGATGAGTATGGTCTTGTACACATGCAT
1 AAGGATTATGTGGATGAGTATGGTCTTGTACACATGCAT
6849 A
1 A
6850 CTAATTTAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.33
Consensus pattern (39 bp):
AAGGATTATGTGGATGAGTATGGTCTTGTACACATGCAT
Found at i:8992 original size:30 final size:30
Alignment explanation
Indices: 8956--9017 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
8946 TGAAAGATAC
8956 GATAAATGACTCTTAATAAAATATTAAAAA
1 GATAAATGACTCTTAATAAAATATTAAAAA
* * * *
8986 GATAAATGATTTTTAGTAAAATATTAAGAA
1 GATAAATGACTCTTAATAAAATATTAAAAA
9016 GA
1 GA
9018 GAAGGAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.32
Consensus pattern (30 bp):
GATAAATGACTCTTAATAAAATATTAAAAA
Found at i:25172 original size:27 final size:27
Alignment explanation
Indices: 25122--25203 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 27
25112 TATTTAATTT
*
25122 TTTTTTTAATTTGGTATCTAAAATTGATA
1 TTTTTTTAATTTGATAT-T-AAATTGATA
* *
25151 TTTTTTTAATCTGATATTAAATT--TT
1 TTTTTTTAATTTGATATTAAATTGATA
25176 TTTTTTCTAATTTGATACTTAAAGTTGA
1 TTTTTT-TAATTTGATA-TTAAA-TTGA
25204 CACTTTTTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
25 7 0.16
26 9 0.20
27 10 0.23
28 3 0.07
29 15 0.34
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.57
Consensus pattern (27 bp):
TTTTTTTAATTTGATATTAAATTGATA
Found at i:26177 original size:17 final size:16
Alignment explanation
Indices: 26146--26185 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
26136 AGATAATAAC
*
26146 AAAAAATTATCAAATT
1 AAAAAATTATAAAATT
26162 AAAAAATATATAAAATT
1 AAAAAAT-TATAAAATT
26179 AATAAAA
1 AA-AAAA
26186 AAGTACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 10 0.48
18 4 0.19
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAATTATAAAATT
Found at i:29153 original size:18 final size:17
Alignment explanation
Indices: 29109--29155 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
29099 TACGAAATTT
*
29109 AAATTTTTTAGATTTTTA
1 AAATTTATTA-ATTTTTA
29127 AAA--TATTAATATTTTA
1 AAATTTATTAAT-TTTTA
29143 AAATTTATTAATT
1 AAATTTATTAATT
29156 CGAAAATGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.08
16 12 0.48
17 1 0.04
18 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AAATTTATTAATTTTTA
Found at i:29282 original size:30 final size:31
Alignment explanation
Indices: 29237--29295 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
29227 TTACAAAATA
* *
29237 AAAAATAATTATAAAAGAAAGATAATTATGAT
1 AAAAATAATTATAAAA-AAAAATAAATATGAT
29269 AAAAA-AA-TATAAAAAAAAATAAATATG
1 AAAAATAATTATAAAAAAAAATAAATATG
29296 GATATCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.44
30 7 0.28
31 2 0.08
32 5 0.20
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (31 bp):
AAAAATAATTATAAAAAAAAATAAATATGAT
Found at i:30002 original size:11 final size:11
Alignment explanation
Indices: 29986--30015 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
29976 TTATCTTGTC
29986 AAAATATTAAA
1 AAAATATTAAA
29997 AAAATA-TAAA
1 AAAATATTAAA
30007 AAAATATTA
1 AAAATATTA
30016 TCATATAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:33115 original size:21 final size:21
Alignment explanation
Indices: 33085--33138 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
33075 TCTCATCTAA
* * *
33085 AATAATAAATTTTTAATTATT
1 AATAAAAAATTTTAAATTAAT
* *
33106 TATAAAAAATATTAAATTAAT
1 AATAAAAAATTTTAAATTAAT
33127 AATAATAAAATT
1 AATAA-AAAATT
33139 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAAAAAATTTTAAATTAAT
Found at i:33165 original size:30 final size:30
Alignment explanation
Indices: 33122--33201 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
33112 AAATATTAAA
* * *
33122 TTAATAATAATAAAATTATATTTTAATCTT
1 TTAAAAATAATAAAATTATAATTTAATATT
*
33152 TTAAAAATGATAAAAATT-TAATTTAATATT
1 TTAAAAATAAT-AAAATTATAATTTAATATT
* *
33182 TT-AAAATTATAAAAATATAA
1 TTAAAAATAATAAAATTATAA
33202 ATTATTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 5 0.12
29 10 0.24
30 21 0.50
31 6 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATATT
Found at i:33194 original size:8 final size:8
Alignment explanation
Indices: 33183--33224 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
33173 TTTAATATTT
33183 TAAAATTA
1 TAAAATTA
*
33191 TAAAAATA
1 TAAAATTA
33199 T-AAATTA
1 TAAAATTA
*
33206 TTAAAATAA
1 -TAAAATTA
33215 TAAAATTA
1 TAAAATTA
33223 TA
1 TA
33225 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:33203 original size:15 final size:17
Alignment explanation
Indices: 33183--33224 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
33173 TTTAATATTT
33183 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATAA
*
33199 T-AAATTATTAAAATAA
1 TAAAATTATAAAAATAA
33215 TAAAATTATA
1 TAAAATTATA
33225 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 3 0.14
17 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:34303 original size:15 final size:15
Alignment explanation
Indices: 34283--34334 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
34273 ATGAAAAGTG
* *
34283 CTTCTTCCTCTTCCT
1 CTTCTTCCCCTTCCC
34298 CTTCTTCCCCTTCCC
1 CTTCTTCCCCTTCCC
34313 CTTCCCCTTCCCCTTCCC
1 CTT---CTTCCCCTTCCC
34331 CTTC
1 CTTC
34335 CCCTTTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 17 0.53
18 15 0.47
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (15 bp):
CTTCTTCCCCTTCCC
Found at i:34310 original size:6 final size:6
Alignment explanation
Indices: 34301--34339 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
34291 TCTTCCTCTT
34301 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTT
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTT
34340 TTTCTTATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CTTCCC
Found at i:38740 original size:5 final size:5
Alignment explanation
Indices: 38732--38776 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
38722 TAAACTAAAT
38732 ACACC ACACC ACACC ACACC ACACC ACACC ACACC ACACC ACACC
1 ACACC ACACC ACACC ACACC ACACC ACACC ACACC ACACC ACACC
38777 GTCCATCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (5 bp):
ACACC
Found at i:40428 original size:58 final size:58
Alignment explanation
Indices: 40366--40485 Score: 161
Period size: 58 Copynumber: 2.1 Consensus size: 58
40356 AATAAGATTT
* * *
40366 TTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATAATTA
1 TTATTAAATACAATTTAAT-AAAATAATAAATAATTTAATAACATTTTTAACATAATTA
* ** *
40424 TTATTAAATGCAATTTAATAAAATAATATGTAATTTAATAACATTTTTAATATAATTA
1 TTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATAATTA
40482 TTAT
1 TTAT
40486 CAAAATATGA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 20 0.37
58 34 0.63
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.46
Consensus pattern (58 bp):
TTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATAATTA
Done.