Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000322.1 Kokia drynarioides strain JFW-HI SEQ_111086, 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: 23191
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Found at i:912 original size:58 final size:60
Alignment explanation
Indices: 797--923 Score: 177
Period size: 59 Copynumber: 2.1 Consensus size: 60
787 ATAAATTTAG
797 ATACCAAATTGAATCTAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGCTAAGTTCAA
1 ATACCAAATTGAATCTAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGCTAAGTTCAA
* * * * * *
857 GTACCAAATTGAGTC-CAAAAATGTTTAGGTACCAAATTAGGAAAAATTG-TAAGTTCAA
1 ATACCAAATTGAATCTAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGCTAAGTTCAA
*
915 ATATCAAAT
1 ATACCAAAT
924 ATTATATTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
58 16 0.27
59 30 0.51
60 13 0.22
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (60 bp):
ATACCAAATTGAATCTAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGCTAAGTTCAA
Found at i:4000 original size:94 final size:92
Alignment explanation
Indices: 3901--4103 Score: 250
Period size: 94 Copynumber: 2.2 Consensus size: 92
3891 AATCATATTT
* * * *
3901 AATAAATAATAACTTAATTTAGACGA-TATTATTAAATATAATTGATTGGATTTAGTATTTTTAT
1 AATAAATAATAACTTAATTTAGACAACT-TTATTAAATATAATTGATTGAATTTAATATTTCTA-
3965 TG-TAAATATTTTTTATTAAATGA-TTGATTG
64 TGAT-AA-ATTTTTTATTAAAT-ATTTGATTG
* *
3995 AATAAATAATAAATTAATTTAGACAACTTTATTAAATATGATTGATTGAATTTAATATTTCTATG
1 AATAAATAATAACTTAATTTAGACAACTTTATTAAATATAATTGATTGAATTTAATATTTCTATG
* *
4060 ATAAGTTTTTTCTTAAATATTTGATTG
66 ATAAATTTTTTATTAAATATTTGATTG
* *
4087 AATAAAAAAAAACTTAA
1 AATAAATAATAACTTAA
4104 AACAACATTA
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
91 1 0.01
92 33 0.35
93 4 0.04
94 56 0.59
95 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (92 bp):
AATAAATAATAACTTAATTTAGACAACTTTATTAAATATAATTGATTGAATTTAATATTTCTATG
ATAAATTTTTTATTAAATATTTGATTG
Found at i:10632 original size:123 final size:122
Alignment explanation
Indices: 10396--10801 Score: 530
Period size: 123 Copynumber: 3.3 Consensus size: 122
10386 AATGAAGTGA
* * ** * *
10396 TCATCTTTTTGATGAGATACAGAGAAGTATATCAAAGCAATGAAGCAAAGCTCAATGTGAGTGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTAGATCAAAAAAATGAAGAAAAGCTCAATGTCAGTGAA
* *
10461 ACTTCAAACCCCTATCTTCCTGATGAGATACAGAAAAGTGGATCAAACAATCAAGCAG
66 ACTTCAAACCCCT-TCTTCTTGATGAGATACAGAGAAGTGGATCAAACAATCAAGCAG
* * *
10519 TCATCTTCCTGATGAGATACAGAGAAGTAGA-CAAAAATAATGAAGAAAAGGTCAATTTCAGTGA
1 TCATCTTCTTGATGAGATACAGAGAAGTAGATCAAAAA-AATGAAGAAAAGCTCAATGTCAGTGA
* * *
10583 AACTTCAAACCGCTTCTTCTTGATGAGATGCAGAGAAGTGGATCAAAACAATGAA--ATG
65 AACTTCAAACCCCTTCTTCTTGATGAGATACAGAGAAGTGGATC-AAACAATCAAGCA-G
* * * *
10641 ATCATCATCTTGATGAGATACAGAGAAGTAGACCAAAAAAATGAAGTAAAGCTCAATGTCAGCGA
1 -TCATCTTCTTGATGAGATACAGAGAAGTAGATCAAAAAAATGAAGAAAAGCTCAATGTCAGTGA
* * *
10706 AACTTCAAACCCCCATCTTCTTGATGAGATATAGAGAAGTGGATCAAACAATCAAGCGG
65 AACTTCAAA-CCCCTTCTTCTTGATGAGATACAGAGAAGTGGATCAAACAATCAAGCAG
* *
10765 TCGTCTTCTTGATGAGATACAGAGAAGTGGATCAAAA
1 TCATCTTCTTGATGAGATACAGAGAAGTAGATCAAAA
10802 CAATTAAGTG
Statistics
Matches: 245, Mismatches: 30, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
121 1 0.00
122 32 0.13
123 174 0.71
124 38 0.16
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (122 bp):
TCATCTTCTTGATGAGATACAGAGAAGTAGATCAAAAAAATGAAGAAAAGCTCAATGTCAGTGAA
ACTTCAAACCCCTTCTTCTTGATGAGATACAGAGAAGTGGATCAAACAATCAAGCAG
Found at i:10801 original size:171 final size:170
Alignment explanation
Indices: 10597--10979 Score: 534
Period size: 171 Copynumber: 2.2 Consensus size: 170
10587 TCAAACCGCT
*
10597 TCTTCTTGATGAGATGCAGAGAAGTGGATCAAAACAATGAAATGATCATCATCTTGATGAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATGAAATGATCATCATCTTGATGAGATAC
* * *
10662 AGAGAAGTAGACCAAAAAAATGAAGTAAAGCTCAATGTCAGCGAAACTTCAAACCCCCATCTTCT
66 AGAGAAGTAGACCAAAAAAATGAAGCAAAGCTCAATATCAACG-AACTTCAAA-CCCCATCTTCT
* * *
10727 TGATGAGATATAGAGAAGTGGATC-AAACAATCAAGCGGTCG
129 TGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCGATCA
* * * *
10768 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATTAAGTGGTCATCTTCTTGATGAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATGAAATGATCATCATCTTGATGAGATAC
* * *
10833 ATAGAAGTAGACCAAAATAATGAAGCGAAGCTCAATATCAACGAACTTCAAACCCCATCTTCTTG
66 AGAGAAGTAGACCAAAAAAATGAAGCAAAGCTCAATATCAACGAACTTCAAACCCCATCTTCTTG
* * *
10898 ATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGATCA
131 ATGAGATACAGAGAAGTGGATCAAAACAATCAAGCGATCA
* * * * * *
10938 TCTTCCTGATGAGATACAAATAAGTAGACCAAAATAATGAAA
1 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATGAAA
10980 CAAAGCTCAA
Statistics
Matches: 186, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
169 34 0.18
170 55 0.30
171 97 0.52
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (170 bp):
TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATGAAATGATCATCATCTTGATGAGATAC
AGAGAAGTAGACCAAAAAAATGAAGCAAAGCTCAATATCAACGAACTTCAAACCCCATCTTCTTG
ATGAGATACAGAGAAGTGGATCAAAACAATCAAGCGATCA
Found at i:10822 original size:48 final size:48
Alignment explanation
Indices: 10719--10859 Score: 194
Period size: 48 Copynumber: 3.0 Consensus size: 48
10709 TTCAAACCCC
*
10719 CATCTTCTTGATGAGATATAGAGAAGTGGATC-AAACAATCAAGCGGT
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCGGT
* * *
10766 CGTCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATTAAGTGGT
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCGGT
* * * * *
10814 CATCTTCTTGATGAGATACATAGAAGTAGACCAAAATAATGAAGCG
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCG
10860 AAGCTCAATA
Statistics
Matches: 82, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 30 0.37
48 52 0.63
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (48 bp):
CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCGGT
Found at i:10914 original size:293 final size:294
Alignment explanation
Indices: 10474--11104 Score: 897
Period size: 293 Copynumber: 2.2 Consensus size: 294
10464 TCAAACCCCT
*
10474 ATCTTCCTGATGAGATACAGAAAAGTGGATC-AAACAATCAAGCAGTCATCTTCCTGATGAGATA
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCAGTCATCTTCCTGATGAGATA
* * ** * *
10538 CAGAGAAGTAGACAAAAATAATGAAGAAAAGGTCAATTTCAGTGAAACTTCAAACCGCTTCTTCT
66 CAGAGAAGTAGACAAAAATAATGAAGAAAAGCTCAATATCAACGAAACTTCAAACCCCATCTTCT
* * *
10603 TGATGAGATGCAGAGAAGTGGATCAAAACAATGAAATGATCATCATCTTGATGAGATACAGAGAA
131 TGATGAGATACAGAGAAGTGGATCAAAACAATGAAATGATCATCATCCTGATGAGATACAAAGAA
**
10668 GTAGACCAAAAAAATGAAGTAAAGCTCAATGTCAGCGAAACTTCAAACCCCCATCTTCTTGATGA
196 GTAGACCAAAAAAATGAAACAAAGCTCAATGTCAGCGAAACTTCAAACCCCCATCTTCTTGATGA
* *
10733 GATATAGAGAAGTGGATCAAACAATCAAGCGGTC
261 GATACAGAGAAGTGGATCAAACAATCAAACGGTC
* * * ** *
10767 GTCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATTAAGTGGTCATCTTCTTGATGAGATA
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCAGTCATCTTCCTGATGAGATA
* * **
10832 CATAGAAGTAGACCAAAATAATGAAGCGAAGCTCAATATCAACG-AACTTCAAACCCCATCTTCT
66 CAGAGAAGTAGACAAAAATAATGAAGAAAAGCTCAATATCAACGAAACTTCAAACCCCATCTTCT
* * * *
10896 TGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGATCATCTTCCTGATGAGATACAAATAA
131 TGATGAGATACAGAGAAGTGGATCAAAACAATGAAATGATCATCATCCTGATGAGATACAAAGAA
* * * *
10961 GTAGACCAAAATAATGAAACAAAGCTCAATGTGAGTGAAACTTCAAACCTCCATCTTCTTGATGA
196 GTAGACCAAAAAAATGAAACAAAGCTCAATGTCAGCGAAACTTCAAACCCCCATCTTCTTGATGA
11026 GATACAGAGAAGTGGATCAAACAATCAAACGGTC
261 GATACAGAGAAGTGGATCAAACAATCAAACGGTC
* * * * * * *
11060 ACCTTCCTAATGAGATACAAAGAAGTAGACCAAAATAATGAAGCA
1 ATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCA
11105 AAGTTCAATG
Statistics
Matches: 294, Mismatches: 43, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
293 229 0.78
294 65 0.22
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (294 bp):
ATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGCAGTCATCTTCCTGATGAGATA
CAGAGAAGTAGACAAAAATAATGAAGAAAAGCTCAATATCAACGAAACTTCAAACCCCATCTTCT
TGATGAGATACAGAGAAGTGGATCAAAACAATGAAATGATCATCATCCTGATGAGATACAAAGAA
GTAGACCAAAAAAATGAAACAAAGCTCAATGTCAGCGAAACTTCAAACCCCCATCTTCTTGATGA
GATACAGAGAAGTGGATCAAACAATCAAACGGTC
Found at i:10986 original size:122 final size:123
Alignment explanation
Indices: 10768--11225 Score: 568
Period size: 123 Copynumber: 3.7 Consensus size: 123
10758 CAAGCGGTCG
* *
10768 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATTAAGTGGTCATCTTCTTGATGAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGTGGTCATCTTCCTGATGAGATAC
* * * * **
10833 ATAGAAGTAGACCAAAATAATGAAGCGAAGCTCAATATCAACG-AACTTCAAACCCCA
66 AAAGAAGTAGACCAAAATAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCA
* * *
10890 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGATCATCTTCCTGATGAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGTGGTCATCTTCCTGATGAGATAC
* *
10955 AAATAAGTAGACCAAAATAATGAAACAAAGCTCAATGTGAGTGAAACTTCAAACCTCCA
66 AAAGAAGTAGACCAAAATAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACC-CCA
** * *
11014 TCTTCTTGATGAGATACAGAGAAGTGGATC-AAACAATCAAACGGTCACCTTCCTAATGAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGTGGTCATCTTCCTGATGAGATAC
* *
11078 AAAGAAGTAGACCAAAATAATGAAGCAAAGTTCAATGTGAGTGAAACTTCAAAACCTCA
66 AAAGAAGTAGACCAAAATAATGAAGCAAAGCTCAATGTGAGTGAAACTTC-AAACCCCA
* * * * * * * *
11137 TCTTCCTAATGAGATACAGAGAAATTGG-TC-AAACAA-CAAAGTAGTCAACTTTCAGAGGAGAT
1 TCTTCTTGATGAGATACAGAG-AAGTGGATCAAAACAATC-AAGTGGTCATCTTCCTGATGAGAT
* * *
11199 ACAGAGAAGTAAATCAAAAT-ATGAAGC
64 ACAAAGAAGTAGACCAAAATAATGAAGC
11226 TACGACATCA
Statistics
Matches: 294, Mismatches: 37, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
122 104 0.35
123 147 0.50
124 43 0.15
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (123 bp):
TCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATCAAGTGGTCATCTTCCTGATGAGATAC
AAAGAAGTAGACCAAAATAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCCCA
Found at i:13049 original size:31 final size:30
Alignment explanation
Indices: 12810--13074 Score: 257
Period size: 30 Copynumber: 8.8 Consensus size: 30
12800 GTTTTGTCTA
* * * *
12810 AAAATCACATTTTGACCCCTTAACTTTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* **
12840 AAAATTACATTTTGACCCCTAAACTTCACC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * * *
12870 AAAAATTAAAATTTAACACCTAAACTTCTT-G
1 -AAAATTACATTTTAACCCCTAAACTT-TTCC
* * *
12901 AAAATTACATTTTGACCCTTAAACTTTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
12931 AAAATTATATTTTAAACCCTAAACCTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
*
12961 AAAATTA-AGTTTTAACCCTTAAACTTTTCC
1 AAAATTACA-TTTTAACCCCTAAACTTTTCC
*
12991 AAAATTTCATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* *
13021 ATATTATTACATTTTGACCCC-AAACTTTTCC
1 A-A-AATTACATTTTAACCCCTAAACTTTTCC
**
13052 AAAATTATGTTTTAACCCCTAAA
1 AAAATTACATTTTAACCCCTAAA
13075 ATGCTCTAAA
Statistics
Matches: 191, Mismatches: 36, Indels: 16
0.79 0.15 0.07
Matches are distributed among these distances:
29 16 0.08
30 126 0.66
31 35 0.18
32 14 0.07
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTCC
Found at i:13091 original size:91 final size:88
Alignment explanation
Indices: 12817--13094 Score: 288
Period size: 91 Copynumber: 3.1 Consensus size: 88
12807 CTAAAAATCA
* ** **
12817 CATTTTGACCCCTTAACTTTTCTAAAATTACATTTTGACCCCTAAACTTCACCAAAAATTAAAAT
1 CATTTTGACCCCTAAACTTTTCTAAAATTACATTTTGACCCC-AAACTTTTCC-AAAATTAAGTT
*
12882 TTAACACCTAAACTTCT-TGAAAATT
64 TTAACCCCTAAACTTCTCT-AAAATT
* * * * *
12907 ACATTTTGACCCTTAAACTTTTCTAAAATTATATTTTAAACCCTAAACCTTTCCAAAATTAAGTT
1 -CATTTTGACCCCTAAACTTTTCTAAAATTACATTTT-GACCCCAAACTTTTCCAAAATTAAGTT
* * *
12972 TTAACCCTTAAACTTTTCCAAAATTT
64 TTAACCCCTAAACTTCTCTAAAA-TT
* ** *
12998 CATTTTAACCCCTAAACTTTTCCATATTATTACATTTTGACCCCAAACTTTTCCAAAATTATGTT
1 CATTTTGACCCCTAAACTTTT-C-TAAAATTACATTTTGACCCCAAACTTTTCCAAAATTAAGTT
* *
13063 TTAACCCCTAAAATGCTCTAAAACTT
64 TTAACCCCTAAACTTCTCTAAAA-TT
13089 CATTTT
1 CATTTT
13095 TTACTCTTTT
Statistics
Matches: 153, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
90 46 0.30
91 92 0.60
92 15 0.10
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (88 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTACATTTTGACCCCAAACTTTTCCAAAATTAAGTTTT
AACCCCTAAACTTCTCTAAAATT
Found at i:13322 original size:18 final size:19
Alignment explanation
Indices: 13287--13323 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
13277 ACATTAATTG
13287 CACAATCATATTTAATTTA
1 CACAATCATATTTAATTTA
*
13306 CACACTCAT-TTTAATTTA
1 CACAATCATATTTAATTTA
13324 ATTAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (19 bp):
CACAATCATATTTAATTTA
Found at i:15019 original size:31 final size:31
Alignment explanation
Indices: 14975--15049 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
14965 CATGTTCGAA
* *
14975 CTTGGTTCGTTTATTATTTGGTGTGTTCGGG
1 CTTGATTCGTTTATTATTTGGTGTCTTCGGG
* *
15006 CTTGATTCATTTATTATTTGGTGTCTTTGGG
1 CTTGATTCGTTTATTATTTGGTGTCTTCGGG
*
15037 CTCGATTCGTTTA
1 CTTGATTCGTTTA
15050 GTGTTCACGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.11, C:0.12, G:0.25, T:0.52
Consensus pattern (31 bp):
CTTGATTCGTTTATTATTTGGTGTCTTCGGG
Found at i:15068 original size:23 final size:23
Alignment explanation
Indices: 15059--15118 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
15049 AGTGTTCACG
15059 AACATGTTCGTTTAACGTTCGCA
1 AACATGTTCGTTTAACGTTCGCA
15082 AACATGTTCGTTTAACGTTCGCA
1 AACATGTTCGTTTAACGTTCGCA
15105 AACATGTTCGTTTA
1 AACATGTTCGTTTA
15119 TGTTTGCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (23 bp):
AACATGTTCGTTTAACGTTCGCA
Found at i:15912 original size:15 final size:15
Alignment explanation
Indices: 15892--15923 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15882 AACATTGCTG
15892 ACATCACTTTCTTGC
1 ACATCACTTTCTTGC
*
15907 ACATCATTTTCTTGC
1 ACATCACTTTCTTGC
15922 AC
1 AC
15924 CTCTCAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.41
Consensus pattern (15 bp):
ACATCACTTTCTTGC
Done.