Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010531.1 Kokia drynarioides strain JFW-HI SEQ_125448, 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: 58730
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:2457 original size:44 final size:44
Alignment explanation
Indices: 2407--2499 Score: 186
Period size: 44 Copynumber: 2.1 Consensus size: 44
2397 ATAAAATAAT
2407 CTAGACTAATCAAAGTTTGATTAAAACAAATAAACAGAATTTAA
1 CTAGACTAATCAAAGTTTGATTAAAACAAATAAACAGAATTTAA
2451 CTAGACTAATCAAAGTTTGATTAAAACAAATAAACAGAATTTAA
1 CTAGACTAATCAAAGTTTGATTAAAACAAATAAACAGAATTTAA
2495 CTAGA
1 CTAGA
2500 AGATTATTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.27
Consensus pattern (44 bp):
CTAGACTAATCAAAGTTTGATTAAAACAAATAAACAGAATTTAA
Found at i:4175 original size:17 final size:19
Alignment explanation
Indices: 4131--4185 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
4121 ATTGAGAAAT
4131 TGAACACACAAATTTAACG
1 TGAACACACAAATTTAACG
4150 TGAACACACAAATTTAACG
1 TGAACACACAAATTTAACG
4169 TGAACACACAAATTTAA
1 TGAACACACAAATTTAA
4186 TAAAAACCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (19 bp):
TGAACACACAAATTTAACG
Found at i:5251 original size:39 final size:41
Alignment explanation
Indices: 5172--5261 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
5162 TAAAAAGTAT
* *
5172 TTATATTAAAAAACACTATCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
5213 TTATATTAAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
**
5252 TCGTATTAAA
1 TTATATTAAA
5262 TATAATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 28 0.62
40 1 0.02
41 16 0.36
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (41 bp):
TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
Found at i:29370 original size:2 final size:2
Alignment explanation
Indices: 29365--29389 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29355 TTTATAAACA
29365 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29390 ATTGAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42528 original size:22 final size:21
Alignment explanation
Indices: 42499--42540 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
42489 ATCAATTGTT
42499 ATTATTTATTTGA-AATTTTAA
1 ATTATTTATTT-ATAATTTTAA
42520 ATTAGTTTATTTATAATTTTA
1 ATTA-TTTATTTATAATTTTA
42541 TTTTGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTATTTATTTATAATTTTAA
Found at i:44173 original size:20 final size:20
Alignment explanation
Indices: 44133--44174 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44123 AGAAGCATAC
* * *
44133 TTGTATTGGTAGAATTGAAG
1 TTGTATTAGTAGAAGTAAAG
44153 TTGTATTAGTAGAAGTAAAG
1 TTGTATTAGTAGAAGTAAAG
44173 TT
1 TT
44175 CTACTGATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (20 bp):
TTGTATTAGTAGAAGTAAAG
Found at i:48411 original size:14 final size:14
Alignment explanation
Indices: 48394--48432 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
48384 TATTTCATTA
48394 TGTATATAAAGATT-
1 TGTATA-AAAGATTG
*
48408 TGTATAAAAAATTG
1 TGTATAAAAGATTG
48422 TGTATAAAAGA
1 TGTATAAAAGA
48433 ATGTTGAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (14 bp):
TGTATAAAAGATTG
Found at i:50924 original size:196 final size:196
Alignment explanation
Indices: 50480--50927 Score: 540
Period size: 196 Copynumber: 2.3 Consensus size: 196
50470 GAAATCGACG
* * * * * *
50480 CGATGGGTGAGGTACCGCATATGTTGCGAGTCCTT-GACAGCTCGTGTGAACAACATCATGAGTT
1 CGATGGCTGGGGTACCGCATATGTTGCGAGT-CTTCGACAGCTCATGTGAGCAGCATCATGAGTC
* * *
50544 GGGAAAATGAGAAATGAATCCAAGAATAGATTATAGGCCATACAATAGCTAAGATTTATGCATAA
65 GAGAAAATGAGAAATGAACCCAAGAATAGATTATAGGCCATACAATAGCTAAGATTCATGCATAA
* * * * * **
50609 ATGCATATTCTTAACAGCTTGTGTCAGCAGCATCGTTAGGGAACAGTTATATGCACAGAAACCGT
130 ATGCATATTCTCAACAACTCGTGTCAGCAGCATCGTCAGGGAACAATTATATGCACAGAAACCAA
50674 AT
195 AT
* * * * * *
50676 CGATGGC-GGAGGTAACGCATATGTTGCGAGTCCTCAACAACTCATGTGAGCAGTATCGTGAGTC
1 CGATGGCTGG-GGTACCGCATATGTTGCGAGTCTTCGACAGCTCATGTGAGCAGCATCATGAGTC
* * * * *
50740 GAGAAAATGAGAAATGAACCCAAGAATGGATTATAGGCCCTACGATGGCTGAGATTCATGCATAA
65 GAGAAAATGAGAAATGAACCCAAGAATAGATTATAGGCCATACAATAGCTAAGATTCATGCATAA
* * * * * *
50805 GTGCATATTCTCGACAACTCGTGTGAGCAGCATTGTCAGGGAACAATTATATGCATAGATACCAA
130 ATGCATATTCTCAACAACTCGTGTCAGCAGCATCGTCAGGGAACAATTATATGCACAGAAACCAA
50870 AT
195 AT
* * *
50872 CGATGGCTGGGGTACCGCATATGTTGCTAGTATTCGACAGCTCATATGAGCAGCAT
1 CGATGGCTGGGGTACCGCATATGTTGCGAGTCTTCGACAGCTCATGTGAGCAGCAT
50928 AAGTTGAAAT
Statistics
Matches: 208, Mismatches: 41, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
195 3 0.01
196 203 0.98
197 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (196 bp):
CGATGGCTGGGGTACCGCATATGTTGCGAGTCTTCGACAGCTCATGTGAGCAGCATCATGAGTCG
AGAAAATGAGAAATGAACCCAAGAATAGATTATAGGCCATACAATAGCTAAGATTCATGCATAAA
TGCATATTCTCAACAACTCGTGTCAGCAGCATCGTCAGGGAACAATTATATGCACAGAAACCAAA
T
Found at i:52929 original size:46 final size:46
Alignment explanation
Indices: 52877--52978 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 46
52867 TTGTTATTAA
*
52877 ATTTTAATAAGATTATTATTAAATATAATTTAATAAAAAAATAAAT
1 ATTTTAATAAGATTATTATTAAATACAATTTAATAAAAAAATAAAT
* * * * * *
52923 ATTTTAACATGATTGTTATTAAATACAATTTAATAAAATAGTATAT
1 ATTTTAATAAGATTATTATTAAATACAATTTAATAAAAAAATAAAT
*
52969 AATTTAATAA
1 ATTTTAATAA
52979 CATTTTAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (46 bp):
ATTTTAATAAGATTATTATTAAATACAATTTAATAAAAAAATAAAT
Found at i:53215 original size:14 final size:14
Alignment explanation
Indices: 53196--53223 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53186 TACATTCAAA
53196 CATAATCTATATGT
1 CATAATCTATATGT
53210 CATAATCTATATGT
1 CATAATCTATATGT
53224 TAAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
CATAATCTATATGT
Done.