Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007572.1 Kokia drynarioides strain JFW-HI SEQ_122200, 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: 2564
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Found at i:147 original size:84 final size:84
Alignment explanation
Indices: 4--536 Score: 739
Period size: 84 Copynumber: 6.3 Consensus size: 84
1 AAA
* * *
4 AAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTGTTGATTTGACAATATATTATTTA
1 AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATATATTATTTA
*
69 TTAAATTCGAATATTTAAAT
65 TTAAATTTGAATATTTAAAT
* * * *
89 TAAAAATTATTATTATATGACAATTTTTATTAAATAATATGTTGATTTGATAATATATTATTTAT
1 AAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATATATTATTTAT
*
154 TAAATTCGAATATTTAAAT
66 TAAATTTGAATATTTAAAT
* * **
173 TAAAAATTATTATTATATTACAATTTTTATCATATAATATGTTGATTTGACAATGCATTATTTAT
1 AAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATATATTATTTAT
* *
238 CAAATTTTAATATTTAAAT
66 TAAATTTGAATATTTAAAT
* **
257 AAAAAATTATTATTATATTACAGTTTTTATCAAATAATATGTTGATTTGACAATGCATTATTTAT
1 AAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATATATTATTTAT
* **
322 CAAATATT-AATATGAAAAT
66 TAAAT-TTGAATATTTAAAT
* * *
341 AAAAAATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTTGACAATGTATTATTTAT
1 AAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATATATTATTTAT
* *
406 TAAATTTTAATATGTAAAT
66 TAAATTTGAATATTTAAAT
* * *
425 AAAAAATTATTATTATATTATC-A-TTTTATCAAATAATGTGTTGATTTGATAATAAATTATTTA
1 AAAAAATTATTATTATATTA-CAATTTTTATCAAATAATATGTTGATTTGACAATATATTATTTA
*
488 CTAAATTTGAATATTTAAAT
65 TTAAATTTGAATATTTAAAT
*
508 AAAAAATTATTATTATATTATAATTTTTA
1 AAAAAATTATTATTATATTACAATTTTTA
537 CTAAATTTGA
Statistics
Matches: 408, Mismatches: 35, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
83 77 0.19
84 325 0.80
85 6 0.01
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (84 bp):
AAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATATATTATTTAT
TAAATTTGAATATTTAAAT
Found at i:537 original size:49 final size:49
Alignment explanation
Indices: 479--585 Score: 205
Period size: 49 Copynumber: 2.2 Consensus size: 49
469 TTTGATAATA
479 AATTATTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTAT
1 AATT-TTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTAT
529 AATTTTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTAT
1 AATTTTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTAT
578 AATTTTTA
1 AATTTTTA
586 TCAAATAATG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 53 0.93
50 4 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (49 bp):
AATTTTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTAT
Found at i:658 original size:71 final size:72
Alignment explanation
Indices: 541--909 Score: 335
Period size: 84 Copynumber: 4.7 Consensus size: 72
531 TTTTTACTAA
* *
541 ATTTGAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTG
1 ATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTG
606 ACAATAC
66 ACAATAC
613 ATTTGAATATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTG
1 ATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTG
677 ACAATACATTATTTAC
66 -----ACA--A--TAC
* *
693 TAAATTTGAATATTTAAATAAAAAATTATTATTATATTACAAATTTTATCAAATAATATGTTTAT
1 ---ATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGAT
758 TTGACAATACATTATTTAC
63 TTG-----ACA--A--TAC
** *
777 TAAATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAACGTGTTAAT
1 ---ATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGAT
*
842 TTGATAATAC
63 TTGACAATAC
* ** *
852 ATTATTTAATAAATTTAAATATTTAAATAAAAATTATTATTTTACAATTTTTATCAAA
1 A-T-TTGAAT--ATTTAAATA---AAA-AATTATTATTATATTACAATTTTTATCAAA
910 ATTTAAATTT
Statistics
Matches: 263, Mismatches: 13, Indels: 34
0.85 0.04 0.11
Matches are distributed among these distances:
71 46 0.17
72 17 0.06
73 1 0.00
74 5 0.02
75 3 0.01
76 12 0.05
77 1 0.00
78 1 0.00
79 5 0.02
80 30 0.11
83 16 0.06
84 126 0.48
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (72 bp):
ATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTG
ACAATAC
Found at i:713 original size:155 final size:160
Alignment explanation
Indices: 533--909 Score: 529
Period size: 168 Copynumber: 2.4 Consensus size: 160
523 TATTATAATT
* *
533 TTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAATGTG
1 TTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATG
598 TTGATTTG-ACA-A-TAC-ATTTGAATATTTAAAT-AAAAATTATTATTATATTACAATTTTTAT
66 TTGATTTGAACATATTACAATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTAT
* *
658 CAAATAATATGTTGATTTGACAATACATTA
131 CAAATAACATGTTAATTTGACAATACATTA
*
688 TTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTACAAATTTTATCAAATAATATG
1 TTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATG
*
753 TTTATTTGACAATACATTATTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTACA
66 TTGATTTG---A-ACA-TA-TTAC--AATTTGAATATTTAAATAAAAAATTATTATTATATTACA
* *
818 ATTTTTATCAAATAACGTGTTAATTTGATAATACATTA
123 ATTTTTATCAAATAACATGTTAATTTGACAATACATTA
* *
856 TTTAATAAATTTAAATATTTAAAT-AAAAATTATTA-T-T-TTACAATTTTTATCAAA
1 TTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAA
910 ATTTAAATTT
Statistics
Matches: 198, Mismatches: 11, Indels: 17
0.88 0.05 0.08
Matches are distributed among these distances:
155 69 0.35
160 3 0.02
162 1 0.01
164 19 0.10
165 1 0.01
166 1 0.01
167 27 0.14
168 77 0.39
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (160 bp):
TTTACTAAATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATG
TTGATTTGAACATATTACAATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTAT
CAAATAACATGTTAATTTGACAATACATTA
Found at i:740 original size:84 final size:83
Alignment explanation
Indices: 613--909 Score: 483
Period size: 84 Copynumber: 3.6 Consensus size: 83
603 TTGACAATAC
*
613 ATTTGAATATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGA
1 ATTTGAATATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTAATTTGA
678 CAATACATTATTTACTAA
66 CAATACATTATTTACTAA
* *
696 ATTTGAATATTTAAATAAAAAATTATTATTATATTACAAATTTTATCAAATAATATGTTTATTTG
1 ATTTGAATATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTAATTTG
761 ACAATACATTATTTACTAA
65 ACAATACATTATTTACTAA
**
780 ATTTGAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAACGTGTTAATTTG
1 ATTTGAATATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTAATTTG
* *
845 ATAATACATTATTTAATAA
65 ACAATACATTATTTACTAA
*
864 ATTTAAATATTTAAATAAAAATTATTA-T-T-TTACAATTTTTATCAAA
1 ATTTGAATATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAA
910 ATTTAAATTT
Statistics
Matches: 204, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
80 17 0.08
81 1 0.00
82 1 0.00
83 27 0.13
84 158 0.77
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (83 bp):
ATTTGAATATTTAAATAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTAATTTGA
CAATACATTATTTACTAA
Found at i:1035 original size:22 final size:22
Alignment explanation
Indices: 1003--1060 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
993 TGGACCACCT
* *
1003 AAATTCCAGCTCACCTAAACCG
1 AAATTCCAGCTCACCAAAACCA
* * *
1025 AAATTCTAGCTCATCAAAATCA
1 AAATTCCAGCTCACCAAAACCA
1047 AAATTCCAGCTCAC
1 AAATTCCAGCTCAC
1061 GAACACCTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (22 bp):
AAATTCCAGCTCACCAAAACCA
Found at i:2192 original size:15 final size:15
Alignment explanation
Indices: 2172--2227 Score: 69
Period size: 15 Copynumber: 3.6 Consensus size: 15
2162 ATATCTGATA
2172 TTTTTTACAAATATT
1 TTTTTTACAAATATT
*
2187 TTTTTTA-ATAACTGATA
1 TTTTTTACA-AA-T-ATT
2204 TTTTTTACAAATATT
1 TTTTTTACAAATATT
2219 TTTTTTACA
1 TTTTTTACA
2228 TTTTATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 1 0.03
15 20 0.57
16 2 0.06
17 11 0.31
18 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (15 bp):
TTTTTTACAAATATT
Found at i:2205 original size:32 final size:32
Alignment explanation
Indices: 2161--2225 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
2151 TTAAAAAATA
*
2161 AATATCTGATATTTTTTACAAATATTTTTTTT
1 AATAACTGATATTTTTTACAAATATTTTTTTT
2193 AATAACTGATATTTTTTACAAATATTTTTTTT
1 AATAACTGATATTTTTTACAAATATTTTTTTT
2225 A
1 A
2226 CATTTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (32 bp):
AATAACTGATATTTTTTACAAATATTTTTTTT
Done.