Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009795.1 Kokia drynarioides strain JFW-HI SEQ_124516, 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: 45060
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:2902 original size:18 final size:18
Alignment explanation
Indices: 2879--2915 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2869 GGTTTTTTAT
2879 TGGGCTTTTCTACTTGGG
1 TGGGCTTTTCTACTTGGG
2897 TGGGCTTTTCTACTTGGG
1 TGGGCTTTTCTACTTGGG
2915 T
1 T
2916 TTTGGATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.16, G:0.32, T:0.46
Consensus pattern (18 bp):
TGGGCTTTTCTACTTGGG
Found at i:2936 original size:3 final size:3
Alignment explanation
Indices: 2928--2954 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2918 TGGATCCAAT
2928 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2955 GAATATACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12676 original size:44 final size:44
Alignment explanation
Indices: 12613--12699 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
12603 TGCTTAGTAG
12613 CTTACTTTTGAGATGGACAGATATTTTTAGAGGTATCAATTTAA
1 CTTACTTTTGAGATGGACAGATATTTTTAGAGGTATCAATTTAA
12657 CTTACTTTTGAGATGGACAGATATTTTTAGAGGTATCAATTTA
1 CTTACTTTTGAGATGGACAGATATTTTTAGAGGTATCAATTTA
12700 CTCAATATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.41
Consensus pattern (44 bp):
CTTACTTTTGAGATGGACAGATATTTTTAGAGGTATCAATTTAA
Found at i:27186 original size:31 final size:31
Alignment explanation
Indices: 27129--27187 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
27119 TCGTCCATAT
*
27129 TATTTTTTAATTTTTTAAAATATTTATATTA
1 TATTTTTTAATTATTTAAAATATTTATATTA
27160 TATTATTTTAA-TATTTAATAAT-TTTATA
1 TATT-TTTTAATTATTTAA-AATATTTATA
27188 CTTTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
TATTTTTTAATTATTTAAAATATTTATATTA
Found at i:34846 original size:10 final size:10
Alignment explanation
Indices: 34831--34857 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34821 TAATTAAGTT
34831 CAGGGGCTGG
1 CAGGGGCTGG
34841 CAGGGGCTGG
1 CAGGGGCTGG
34851 CAGGGGC
1 CAGGGGC
34858 CCTAGCCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.22, G:0.59, T:0.07
Consensus pattern (10 bp):
CAGGGGCTGG
Found at i:44542 original size:4 final size:4
Alignment explanation
Indices: 44526--44575 Score: 73
Period size: 4 Copynumber: 12.2 Consensus size: 4
44516 ACGAAAAATG
* *
44526 AAGA AAAA AAGA AAGA AAAA AGAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA AAGA AAGA AAGA
44575 A
1 A
44576 GGAAGAAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 38 0.93
5 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:44544 original size:21 final size:21
Alignment explanation
Indices: 44518--44575 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
44508 GGGGACCAAC
* *
44518 GAAAAATGAAGAAAAAAAGAAA
1 GAAAAAAG-AGAAAGAAAGAAA
44540 GAAAAAAGAGAAAGAAAGAAA
1 GAAAAAAGAGAAAGAAAGAAA
*
44561 GAAAGAA-AGAAAGAA
1 GAAAAAAGAGAAAGAA
44576 GGAAGAAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 8 0.24
21 18 0.55
22 7 0.21
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (21 bp):
GAAAAAAGAGAAAGAAAGAAA
Found at i:45005 original size:20 final size:21
Alignment explanation
Indices: 44964--45006 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
44954 TAATTTACTT
44964 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
44985 TAATTTAATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
45005 TA
1 TA
45007 GTAGTAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Done.