Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004667.1 Kokia drynarioides strain JFW-HI SEQ_118215, 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: 124482
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:16165 original size:7 final size:7
Alignment explanation
Indices: 16153--16180 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
16143 TAAATCAAAT
16153 GTGTTGA
1 GTGTTGA
16160 GTGTTGA
1 GTGTTGA
16167 GTGTTGA
1 GTGTTGA
16174 GTGTTGA
1 GTGTTGA
16181 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTGTTGA
Found at i:22429 original size:20 final size:21
Alignment explanation
Indices: 22390--22429 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
22380 CTTCACAACG
22390 CTTTAGAACAACCTCTAAATT
1 CTTTAGAACAACCTCTAAATT
22411 CTTTA-AACAATCCTC-AAAT
1 CTTTAGAACAA-CCTCTAAAT
22430 GTATCTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (21 bp):
CTTTAGAACAACCTCTAAATT
Found at i:27835 original size:166 final size:166
Alignment explanation
Indices: 27556--27888 Score: 639
Period size: 166 Copynumber: 2.0 Consensus size: 166
27546 CTGAGATTTA
*
27556 GTCGGCATCTGGAAAGTCATCTTCTGGGGAAGAGTACCATCCAACTGAGGAAGAGGAAGAACAGA
1 GTCGACATCTGGAAAGTCATCTTCTGGGGAAGAGTACCATCCAACTGAGGAAGAGGAAGAACAGA
*
27621 CGAAGGACAATGAGATTGATGAATTGATGATAGTGCTATTGTGAAGGAGAAATCTCAACACCGCC
66 CGAAGGACAATGAGATTGATGAATTGATGATAGTCCTATTGTGAAGGAGAAATCTCAACACCGCC
*
27686 AGCAAAGAATGTGACACCCAAGAAACTTGTAACAGC
131 AGCAAAGAATGTGACACCCAAGAAACCTGTAACAGC
27722 GTCGACATCTGGAAAGTCATCTTCTGGGGAAGAGTACCATCCAACTGAGGAAGAGGAAGAACAGA
1 GTCGACATCTGGAAAGTCATCTTCTGGGGAAGAGTACCATCCAACTGAGGAAGAGGAAGAACAGA
27787 CGAAGGACAATGAGATTGATGAATTGATGATAGTCCTATTGTGAAGGAGAAATCTCAACACCGCC
66 CGAAGGACAATGAGATTGATGAATTGATGATAGTCCTATTGTGAAGGAGAAATCTCAACACCGCC
27852 AGCAAAGAATGTGACACCCAAGAAACCTGTAACAGC
131 AGCAAAGAATGTGACACCCAAGAAACCTGTAACAGC
27888 G
1 G
27889 AAAGTGTTTG
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 164 1.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (166 bp):
GTCGACATCTGGAAAGTCATCTTCTGGGGAAGAGTACCATCCAACTGAGGAAGAGGAAGAACAGA
CGAAGGACAATGAGATTGATGAATTGATGATAGTCCTATTGTGAAGGAGAAATCTCAACACCGCC
AGCAAAGAATGTGACACCCAAGAAACCTGTAACAGC
Found at i:31758 original size:18 final size:18
Alignment explanation
Indices: 31735--31780 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
31725 ATATTTTTTT
31735 TTCTTCTTTTCTC-ATTTC
1 TTCTTCTTTT-TCGATTTC
*
31753 TTCTTCTTTTTCGTTTTC
1 TTCTTCTTTTTCGATTTC
31771 TTC-TCTTTTT
1 TTCTTCTTTTT
31781 ATTTTACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.72
Consensus pattern (18 bp):
TTCTTCTTTTTCGATTTC
Found at i:32353 original size:17 final size:17
Alignment explanation
Indices: 32328--32389 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
32318 TACATATCAT
*
32328 AATGGAAATGCAACTAC
1 AATGAAAATGCAACTAC
32345 AATGAAAATGC-ACTA-
1 AATGAAAATGCAACTAC
32360 AAT-AAAATGCAA-TGAC
1 AATGAAAATGCAACT-AC
*
32376 AAATAAAAATGCAA
1 -AATGAAAATGCAA
32390 TGATAACTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
14 8 0.21
15 5 0.13
16 4 0.10
17 13 0.33
18 9 0.23
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (17 bp):
AATGAAAATGCAACTAC
Found at i:32382 original size:21 final size:21
Alignment explanation
Indices: 32358--32409 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 21
32348 GAAAATGCAC
32358 TAAATAAAATGCAATGACAAA
1 TAAATAAAATGCAATGACAAA
* *
32379 T--A-AAAATGCAATGATAAC
1 TAAATAAAATGCAATGACAAA
*
32397 TAAATAAGATGCA
1 TAAATAAAATGCA
32410 TGCAACTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
18 15 0.60
19 1 0.04
20 1 0.04
21 8 0.32
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.21
Consensus pattern (21 bp):
TAAATAAAATGCAATGACAAA
Found at i:32400 original size:18 final size:18
Alignment explanation
Indices: 32359--32392 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32349 AAAATGCACT
32359 AAAT-AAAATGCAATGAC
1 AAATAAAAATGCAATGAC
32376 AAATAAAAATGCAATGA
1 AAATAAAAATGCAATGA
32393 TAACTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.18
Consensus pattern (18 bp):
AAATAAAAATGCAATGAC
Found at i:32863 original size:18 final size:18
Alignment explanation
Indices: 32849--32886 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
32839 TTTCTTCTCT
*
32849 TCCTCAATTTCCTTCTTC
1 TCCTCAAGTTCCTTCTTC
*
32867 TCCTCAAGTTCCTCCTTC
1 TCCTCAAGTTCCTTCTTC
32885 TC
1 TC
32887 AACTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.42, G:0.03, T:0.45
Consensus pattern (18 bp):
TCCTCAAGTTCCTTCTTC
Found at i:48895 original size:21 final size:21
Alignment explanation
Indices: 48871--48929 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
48861 AGTGTTCTAC
48871 CGATAGAAGTCTTAGTTGTAT
1 CGATAGAAGTCTTAGTTGTAT
** **
48892 CGATAGAACCCAGAGTTGTAT
1 CGATAGAAGTCTTAGTTGTAT
* *
48913 CGGTAGATGTCTTAGTT
1 CGATAGAAGTCTTAGTT
48930 CTACTGGTAG
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (21 bp):
CGATAGAAGTCTTAGTTGTAT
Found at i:56245 original size:32 final size:31
Alignment explanation
Indices: 56184--56247 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 31
56174 AAATACTTCA
*
56184 TTTTTTAAATTATATTTAAAGTAAGTTTTTT
1 TTTTTTAAATTATATTTAAAGTAAATTTTTT
56215 TTTTTTAAATTA-AGTTTTAAA-TATAATTTTTT
1 TTTTTTAAATTATA--TTTAAAGTA-AATTTTTT
56247 T
1 T
56248 GTCATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 1 0.03
31 14 0.48
32 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (31 bp):
TTTTTTAAATTATATTTAAAGTAAATTTTTT
Found at i:56259 original size:3 final size:3
Alignment explanation
Indices: 56253--56286 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
56243 TTTTTGTCAT
56253 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56287 TAAAGTGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:68043 original size:12 final size:12
Alignment explanation
Indices: 68026--68051 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
68016 GGAAAATGAA
68026 GAAGAAGAGAAT
1 GAAGAAGAGAAT
68038 GAAGAAGAGAAT
1 GAAGAAGAGAAT
68050 GA
1 GA
68052 CCCTATTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08
Consensus pattern (12 bp):
GAAGAAGAGAAT
Found at i:68617 original size:26 final size:26
Alignment explanation
Indices: 68588--68638 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
68578 TTAAGTTTGA
68588 GGGGAGATAATGTGAAATGGACATGT
1 GGGGAGATAATGTGAAATGGACATGT
*
68614 GGGGAGATAATGTGACATGGACATG
1 GGGGAGATAATGTGAAATGGACATG
68639 CAATTACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.39, T:0.22
Consensus pattern (26 bp):
GGGGAGATAATGTGAAATGGACATGT
Found at i:73608 original size:37 final size:37
Alignment explanation
Indices: 73567--73644 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
73557 CATTGCTACT
*
73567 ACAACTCATCTTCTTTGTCGTTTTTACCCTTACTTTC
1 ACAACTCATCTTCTTTGTCGTTTTTACCCTTACTCTC
*
73604 ACAACTCATCTTCTTTGTTGTTTTTACCCTTACTCTC
1 ACAACTCATCTTCTTTGTCGTTTTTACCCTTACTCTC
73641 ACAA
1 ACAA
73645 GTTTATTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.19, C:0.29, G:0.05, T:0.46
Consensus pattern (37 bp):
ACAACTCATCTTCTTTGTCGTTTTTACCCTTACTCTC
Found at i:82796 original size:45 final size:44
Alignment explanation
Indices: 82737--82832 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 44
82727 TGTTGCACCC
* * *
82737 ACATCTTTGGTGCATTGAGAGTGTCTTCAGTTGTTTCTTTCTTA
1 ACATCTTAGGTGCATTGACAGTGTCTTCAGTTGTTTCTTTCTCA
*
82781 ACATCTTCAGGTGCATTGACAGTGTCTTCAGTTTTTTCTTTCTCA
1 ACATCTT-AGGTGCATTGACAGTGTCTTCAGTTGTTTCTTTCTCA
82826 ACATCTT
1 ACATCTT
82833 TTTCCTTCTC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 7 0.15
45 40 0.85
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.46
Consensus pattern (44 bp):
ACATCTTAGGTGCATTGACAGTGTCTTCAGTTGTTTCTTTCTCA
Found at i:116530 original size:374 final size:374
Alignment explanation
Indices: 116009--116762 Score: 1463
Period size: 374 Copynumber: 2.0 Consensus size: 374
115999 ATGTCACAAC
*
116009 AATTGTGTAAGCGAACACTTGTCGATGCAAGTATAGTTGATAGGTTTAAAACTATTAGATAACGA
1 AATTGTGTAAGCGAACACTTGTCGATGCAAGTATAGTTCATAGGTTTAAAACTATTAGATAACGA
*
116074 TCCCATAGAGATGGTTGTTTATGTCTATAATTATTGATTCAATTACAATTAAACTAAGAGAAATT
66 TCCCATAGAGATGGTTGTTTATGTCTATAATAATTGATTCAATTACAATTAAACTAAGAGAAATT
*
116139 ATATGAATAAGTCAGCATAATTAAAATAAAGAGTGTAGAAATGAGTGAACTAAACTGTCAATATT
131 ATATGAATAAGTCAGCATAATTAAAATAAAGAGTGTAGAAATGAATGAACTAAACTGTCAATATT
116204 GCCAAACTGTAATAAAATATGTCGAACCAAATTGATAAGAAATGAAAAGAAAGTTGAAAATAATT
196 GCCAAACTGTAATAAAATATGTCGAACCAAATTGATAAGAAATGAAAAGAAAGTTGAAAATAATT
116269 TGTCGATGCAATTTAAGCGAAATGAAGATGTAAGAACAATGAAAATATAATGGGGGATCCCTGAC
261 TGTCGATGCAATTTAAGCGAAATGAAGATGTAAGAACAATGAAAATATAATGGGGGATCCCTGAC
116334 TTCACAATTCGTCAACTTCTAAATGTGAACACAAGGTGAGTAAGAGATA
326 TTCACAATTCGTCAACTTCTAAATGTGAACACAAGGTGAGTAAGAGATA
116383 AATTGTGTAAGCGAACACTTGTCGATGCAAGTATAGTTCATAGGTTTAAAACTATTAGATAACGA
1 AATTGTGTAAGCGAACACTTGTCGATGCAAGTATAGTTCATAGGTTTAAAACTATTAGATAACGA
116448 TCCCATAGAGATGGTTGTTTATGTCTATAATAATTGATTCAATTACAATTAAACTAAGAGAAATT
66 TCCCATAGAGATGGTTGTTTATGTCTATAATAATTGATTCAATTACAATTAAACTAAGAGAAATT
*
116513 ATATGAATAAGTCAGCATAATTAAAATAAAGAGTGTAGAAATGAATGAACTAAACTGTCAGTATT
131 ATATGAATAAGTCAGCATAATTAAAATAAAGAGTGTAGAAATGAATGAACTAAACTGTCAATATT
116578 GCCAAACTGTAATAAAATATGTCGAACCAAATTGATAAGAAATGAAAAGAAAGTTGAAAATAATT
196 GCCAAACTGTAATAAAATATGTCGAACCAAATTGATAAGAAATGAAAAGAAAGTTGAAAATAATT
116643 TGTCGATGCAATTTAAGCGAAATGAAGATGTAAGAACAATGAAAATATAATGGGGGATCCCTGAC
261 TGTCGATGCAATTTAAGCGAAATGAAGATGTAAGAACAATGAAAATATAATGGGGGATCCCTGAC
*
116708 TTGACAATTCGTCAACTTCTAAATGTGAACACAAGGTGAGTAAGAGATA
326 TTCACAATTCGTCAACTTCTAAATGTGAACACAAGGTGAGTAAGAGATA
116757 AATTGT
1 AATTGT
116763 CGCCACAATT
Statistics
Matches: 375, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
374 375 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.28
Consensus pattern (374 bp):
AATTGTGTAAGCGAACACTTGTCGATGCAAGTATAGTTCATAGGTTTAAAACTATTAGATAACGA
TCCCATAGAGATGGTTGTTTATGTCTATAATAATTGATTCAATTACAATTAAACTAAGAGAAATT
ATATGAATAAGTCAGCATAATTAAAATAAAGAGTGTAGAAATGAATGAACTAAACTGTCAATATT
GCCAAACTGTAATAAAATATGTCGAACCAAATTGATAAGAAATGAAAAGAAAGTTGAAAATAATT
TGTCGATGCAATTTAAGCGAAATGAAGATGTAAGAACAATGAAAATATAATGGGGGATCCCTGAC
TTCACAATTCGTCAACTTCTAAATGTGAACACAAGGTGAGTAAGAGATA
Done.