Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001951.1 Kokia drynarioides strain JFW-HI SEQ_113774, 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: 16829
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Found at i:8632 original size:124 final size:124
Alignment explanation
Indices: 8491--8793 Score: 453
Period size: 124 Copynumber: 2.4 Consensus size: 124
8481 GAGTGAAACA
* * * * *
8491 TCAAAACAATAAAGCGGTGATCTTCATGATGAGATATAGAGAAGTAGACCAAATCGATGAAATGA
1 TCAAATCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAACGA
* * **
8556 ATCTCAATGGGAGCGAAACTTCGAATCCCCATCTTTCTGATGAGATACTGAGAAGTGGG
66 AGCTCAATGGGAGCGAAACTCCGAATCCCCATCTTTCTGATGAGATACTGAGAAGTAAG
* *
8615 TCAAATCAATAAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCGATGAAGCGA
1 TCAAATCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAACGA
* *
8680 AGCTCAATGGGAGTGAAACTCCGAATCCCCATCTTTCTGATGAGATGCTGAGAAGTAAG
66 AGCTCAATGGGAGCGAAACTCCGAATCCCCATCTTTCTGATGAGATACTGAGAAGTAAG
* * * *
8739 TCAAATCAATAAAGCAGTCATCTTCCTAATGGGATACAGAGAAGTGGACCAAATC
1 TCAAATCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATC
8794 CATCTTGCTG
Statistics
Matches: 161, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
124 161 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (124 bp):
TCAAATCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAACGA
AGCTCAATGGGAGCGAAACTCCGAATCCCCATCTTTCTGATGAGATACTGAGAAGTAAG
Found at i:8668 original size:48 final size:48
Alignment explanation
Indices: 8585--8678 Score: 116
Period size: 48 Copynumber: 2.0 Consensus size: 48
8575 TTCGAATCCC
* ** * **
8585 CATCTTTCTGATGAGATACTGAGAAGTGGGTCAAATCAATAAAGCGGT
1 CATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAATAAAGCGGT
* *
8633 CATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCGATGAAGCG
1 CATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAATAAAGCG
8679 AAGCTCAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAATAAAGCGGT
Found at i:8851 original size:209 final size:210
Alignment explanation
Indices: 8605--9211 Score: 882
Period size: 209 Copynumber: 2.9 Consensus size: 210
8595 ATGAGATACT
* * *
8605 GAGAAGTGGGTCA-AATCAATAAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAT
1 GAGAAGTGGATCACAAT-AATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAAACCAAAT
* * * *
8669 CGATGAAGCGAAGCTCAATGGGAGTGAAACTCCGAATCCCCATCTTTCTGATGAGATGCTGAGAA
65 CGATGAAGCGAAGCTCAATAGGAGTGAAACTTCGAATCCCCATCTTCCTGATGAGATACTGAGAA
** * *
8734 GTAAGTCAAATCAATAAAGCAGTCATCTTCCTAATGGGATACAGAGAAGTGGACCAAATCCATCT
130 GTGGGTCAAATCAATAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCATCT
8799 TGC-TGATAAAATA-AA
195 T-CTTGATAAAATACAA
*
8814 GAGAAGTGGATCACAATAATGAAGCAGTCATCTTCCTGATGAGATACATAA-AAGTAAACCAAAT
1 GAGAAGTGGATCACAATAATGAAGCGGTCATCTTCCTGATGAGATACA-AAGAAGTAAACCAAAT
* * * *
8878 CGATGAAGTGAAGCTCAATAGGAGTGAAACTTTGAATCCCCATCTTCCTGATAAGATATTGAGAA
65 CGATGAAGCGAAGCTCAATAGGAGTGAAACTTCGAATCCCCATCTTCCTGATGAGATACTGAGAA
* *
8943 GTGGGTCAAATCAATAAAGCGGTCATCTCCCTAATGAGATACAGAGAAGTGGATCAAATCCATCT
130 GTGGGTCAAATCAATAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCATCT
* *
9008 TCTTGATGAGATACAA
195 TCTTGATAAAATACAA
* * * *
9024 -AGAAGTGGATCACAACAATGAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAAACCAAATC
1 GAGAAGTGGATCACAATAATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAAACCAAATC
* * * *
9088 AATGAAGCGAAGCTCAATTGGAGTGAAACTTCGAATCTCGATCTTCCTGATGAGATACTGAGAAG
66 GATGAAGCGAAGCTCAATAGGAGTGAAACTTCGAATCCCCATCTTCCTGATGAGATACTGAGAAG
* *
9153 TGGGTCAAATTAATAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATC
131 TGGGTCAAATCAATAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATC
9212 GATGAAGCAA
Statistics
Matches: 356, Mismatches: 37, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
208 2 0.01
209 347 0.97
210 7 0.02
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (210 bp):
GAGAAGTGGATCACAATAATGAAGCGGTCATCTTCCTGATGAGATACAAAGAAGTAAACCAAATC
GATGAAGCGAAGCTCAATAGGAGTGAAACTTCGAATCCCCATCTTCCTGATGAGATACTGAGAAG
TGGGTCAAATCAATAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCATCTT
CTTGATAAAATACAA
Found at i:9091 original size:48 final size:48
Alignment explanation
Indices: 9003--9094 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
8993 GGATCAAATC
** *
9003 CATCTTCTTGATGAGATACAAAGAAGTGGATCACAACAATGAAGTGGT
1 CATCTTCTTGATGAGATACAAAGAAGTAAACCACAACAATGAAGTGGT
*
9051 CATCTTCTTGATGAGATACAGAGAAGTAAACCA-AATCAATGAAG
1 CATCTTCTTGATGAGATACAAAGAAGTAAACCACAA-CAATGAAG
9095 CGAAGCTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 2 0.05
48 37 0.95
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (48 bp):
CATCTTCTTGATGAGATACAAAGAAGTAAACCACAACAATGAAGTGGT
Found at i:9153 original size:333 final size:332
Alignment explanation
Indices: 8813--9543 Score: 991
Period size: 333 Copynumber: 2.2 Consensus size: 332
8803 GATAAAATAA
* * * *
8813 AGAGAAGTGGATCACAATAATGAAGCAGTCATCTTCCTGATGAGATACATAAAAGTAAACCAAAT
1 AGAGAAGTGG-TCA-AATAATAAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAAT
** * * * ***
8878 CGATGAAGTGAAGCTCAATAGGAGTGAAACTTTGAATCCCCATCTTCCTGATAAGATATTGAGAA
64 CGATGAAGCAAAACTCAATAGGAGTGAAACTTCGAACCCCCATCTTCCTGATAAGATACAAAGAA
** * *
8943 GTGGGTCAAATCAATAAAGCGGTCATCTCCCTAATGAGATACAGAGAAGTGGATCAAATCCATCT
129 GTGGGTCAAAAAAATAAAGCGATCATCTCCCTAATGAGATACAGAGAAGTGGACCAAATCCATCT
* ** *
9008 TCTTGATGAGATACAAAGAAGTGGATCACAACAA-TGAAGTGGTCATCTTCTTGATGAGATACAG
194 TCTTGATGAGATACAAAGAAGTGGATCAAAACAAGTGAAGCAGTCATCTTCCTGATGAGATACAG
* *
9072 AGAAGTAAACCAAATCAATGAAGCGAAGCTCAATTG-GAGTGAAACTTCGAATCTCG-ATCTTCC
259 AGAAGTAAACCAAATCAATGAAGCGAAGCTCAA-TGAGAGTGAAACTTCGAAAC-CGCATATTCC
9135 TGATGAGATAC
322 TGATGAGATAC
* * *
9146 TGAGAAGTGGGTCAAATTAATAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAAT
1 AGAGAAGT-GGTCAAA-TAATAAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAAT
* * *
9211 CGATGAAGCAAAACTCAATATGAGTGAAACTTCGAACCCCCATCTTCTTGATGAGATACAAAGAA
64 CGATGAAGCAAAACTCAATAGGAGTGAAACTTCGAACCCCCATCTTCCTGATAAGATACAAAGAA
* * * * *
9276 GTGGGTCAAAAAAATAAAGCGATCGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCT
129 GTGGGTCAAAAAAATAAAGCGATCATCTCCCTAATGAGATACAGAGAAGTGGACCAAATCCATCT
* * * *
9341 TCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGCAGTCATCTTCCTGATGAGATATAG
194 TCTTGATGAGATACAAAGAAGTGGATCAAAACAAGTGAAGCAGTCATCTTCCTGATGAGATACAG
* *
9406 AGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGAGAGTGAAACTTCGAAACCGCTATATTCCT
259 AGAAGTAAACCAAATCAATGAAGCGAAGCTCAATGAGAGTGAAACTTCGAAACCGC-ATATTCCT
9471 GATGAGATAC
323 GATGAGATAC
* *
9481 AGAGAAGTAGGTCAAAACAATAAAGCGGTCATCTTCCTGATGAGATACAGATAAGTAGACCAA
1 AGAGAAGT-GGTC-AAATAATAAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGACCAA
9544 GAGATGAAGC
Statistics
Matches: 347, Mismatches: 44, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
332 2 0.01
333 197 0.57
334 74 0.21
335 71 0.20
336 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (332 bp):
AGAGAAGTGGTCAAATAATAAAGCGGTCATCTTCCTGATGAGATACAGAAAAGTAGACCAAATCG
ATGAAGCAAAACTCAATAGGAGTGAAACTTCGAACCCCCATCTTCCTGATAAGATACAAAGAAGT
GGGTCAAAAAAATAAAGCGATCATCTCCCTAATGAGATACAGAGAAGTGGACCAAATCCATCTTC
TTGATGAGATACAAAGAAGTGGATCAAAACAAGTGAAGCAGTCATCTTCCTGATGAGATACAGAG
AAGTAAACCAAATCAATGAAGCGAAGCTCAATGAGAGTGAAACTTCGAAACCGCATATTCCTGAT
GAGATAC
Found at i:9228 original size:124 final size:123
Alignment explanation
Indices: 9002--9334 Score: 443
Period size: 124 Copynumber: 2.7 Consensus size: 123
8992 TGGATCAAAT
* * * * *
9002 CCATCTTCTTGATGAGATACAAAGAAGTGGATCACAACAATGAAGTGGTCATCTTCTTGATGAGA
1 CCATCTTCTTGATGAGATACAAAGAAGTGGGTCA-AAAAATAAAGCGGTCATCTTCCTGATGAGA
* * * * *
9067 TACAGAGAAGTAAACCAAATCAATGAAGCGAAGCTCAAT-TGGAGTGAAACTTCGAATCT
65 TACAGAGAAGTAGACCAAATCAATGAAGCAAAACTCAATAT-GAGTGAAACTTCGAACCC
* * ** * *
9126 CGATCTTCCTGATGAGATACTGAGAAGTGGGTCAAATTAATAAAGCGGTCATCTTCCTAATGAGA
1 CCATCTTCTTGATGAGATACAAAGAAGTGGGTCAAA-AAATAAAGCGGTCATCTTCCTGATGAGA
*
9191 TACAGAGAAGTAGACCAAATCGATGAAGCAAAACTCAATATGAGTGAAACTTCGAACCC
65 TACAGAGAAGTAGACCAAATCAATGAAGCAAAACTCAATATGAGTGAAACTTCGAACCC
* *
9250 CCATCTTCTTGATGAGATACAAAGAAGTGGGTCAAAAAAATAAAGCGATCGTCTTCCTGATGAGA
1 CCATCTTCTTGATGAGATACAAAGAAGTGGGTC-AAAAAATAAAGCGGTCATCTTCCTGATGAGA
*
9315 TACAGAGAAGTGGACCAAAT
65 TACAGAGAAGTAGACCAAAT
9335 TCGTCTTCTT
Statistics
Matches: 181, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
123 2 0.01
124 175 0.97
125 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (123 bp):
CCATCTTCTTGATGAGATACAAAGAAGTGGGTCAAAAAATAAAGCGGTCATCTTCCTGATGAGAT
ACAGAGAAGTAGACCAAATCAATGAAGCAAAACTCAATATGAGTGAAACTTCGAACCC
Found at i:9417 original size:86 final size:85
Alignment explanation
Indices: 9253--9420 Score: 230
Period size: 86 Copynumber: 2.0 Consensus size: 85
9243 CGAACCCCCA
* *
9253 TCTTCTTGATGAGATACAAAGAAGTGGGTCAAAAAAATAAAGCGATCGTCTTCCTGATGAGATAC
1 TCTTCTTGATGAGATACAAAGAAGTGGATCAAAAAAATAAAGCGATCATCTTCCTGATGAGATAC
*
9318 AGAGAAGTGGACCAAATTCG
66 AGAGAAGTAGACCAAATTCG
* * * * *
9338 TCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGATGC-AGTCATCTTCCTGATGAGAT
1 TCTTCTTGATGAGATACAAAGAAGTGGATCAAAA-AAATAAAGCGA-TCATCTTCCTGATGAGAT
*
9402 ATAGAGAAGTAGACCAAAT
64 ACAGAGAAGTAGACCAAAT
9421 CGATGAAGCG
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
85 32 0.44
86 40 0.56
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (85 bp):
TCTTCTTGATGAGATACAAAGAAGTGGATCAAAAAAATAAAGCGATCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATTCG
Found at i:9977 original size:17 final size:18
Alignment explanation
Indices: 9946--9983 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
9936 AATAATAATA
9946 ATTTTAAATTTTAAATTT
1 ATTTTAAATTTTAAATTT
9964 ATTTTAAA-TTTAAATTT
1 ATTTTAAATTTTAAATTT
9981 ATT
1 ATT
9984 AATGTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAAATTTTAAATTT
Found at i:12156 original size:33 final size:33
Alignment explanation
Indices: 12119--12181 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
12109 TTGTCATCAA
* * *
12119 AAGATCTTCTTCATTTTCTTCATGATCTTCCTC
1 AAGATCCTCTTCATCTTCTTCAGGATCTTCCTC
*
12152 AAGATCCTCTTCGTCTTCTTCAGGATCTTC
1 AAGATCCTCTTCATCTTCTTCAGGATCTTC
12182 TTCTTCTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.17, C:0.29, G:0.10, T:0.44
Consensus pattern (33 bp):
AAGATCCTCTTCATCTTCTTCAGGATCTTCCTC
Found at i:12191 original size:21 final size:21
Alignment explanation
Indices: 12144--12195 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
12134 TTCTTCATGA
* *
12144 TCTTCCTCAAGATCCTCTTCG
1 TCTTCTTCAGGATCCTCTTCG
* *
12165 TCTTCTTCAGGATCTTCTTCT
1 TCTTCTTCAGGATCCTCTTCG
12186 TCTTCTTCAG
1 TCTTCTTCAG
12196 CTTGCTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.33, G:0.10, T:0.46
Consensus pattern (21 bp):
TCTTCTTCAGGATCCTCTTCG
Found at i:14473 original size:67 final size:67
Alignment explanation
Indices: 14402--14533 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 67
14392 TGACATCTCA
* *
14402 ATAATCAATTCAAATCTAACTAAATGATCCTATTCAATCGTATCAATATGCCTTCAATGGCACCT
1 ATAATAAATTCAAATCTAACTAAATGATCCTACTCAATCGTATCAATATGCCTTCAATGGCACCT
14467 CG
66 CG
* * *
14469 ATAATAAATTCAACTCTAACTAAGTGATTCTACTCAATCGTATCAATATGCCTTCAATGGCACCT
1 ATAATAAATTCAAATCTAACTAAATGATCCTACTCAATCGTATCAATATGCCTTCAATGGCACCT
14534 TAAATAAATC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (67 bp):
ATAATAAATTCAAATCTAACTAAATGATCCTACTCAATCGTATCAATATGCCTTCAATGGCACCT
CG
Done.