Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012522.1 Kokia drynarioides strain JFW-HI SEQ_127529, 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: 32192
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:3443 original size:3 final size:3
Alignment explanation
Indices: 3437--3488 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
3427 GTGGTGGTAG
3437 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA ATGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA
3486 AGA
1 AGA
3489 TGAATGAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:9935 original size:17 final size:17
Alignment explanation
Indices: 9915--9957 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
9905 AAATGAACTA
*
9915 ACAAGTAAAATGCAACG
1 ACAACTAAAATGCAACG
*
9932 ACAACTAAAATGCAATG
1 ACAACTAAAATGCAACG
*
9949 ACAATTAAA
1 ACAACTAAA
9958 TGAGATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (17 bp):
ACAACTAAAATGCAACG
Found at i:21934 original size:40 final size:40
Alignment explanation
Indices: 21890--22111 Score: 255
Period size: 40 Copynumber: 5.5 Consensus size: 40
21880 GTAATATCAC
* *
21890 AGTGTTTACAGTGTCACTGCCAGTTTAGTGGTAGTATCGT
1 AGTGTTTACAATGTCACTGCCAATTTAGTGGTAGTATCGT
* * * *
21930 AGTGTTTACAGTGTCACTACCAATTTAGTTGTAATATCGT
1 AGTGTTTACAATGTCACTGCCAATTTAGTGGTAGTATCGT
* * *
21970 AGTATTTACAATGTCACTGCCAGTTTAGTGGTAGTACCGT
1 AGTGTTTACAATGTCACTGCCAATTTAGTGGTAGTATCGT
* * * * * *
22010 AGTGTTTATAGTGCCACTGCAAATTTAGTGATAGTATCGC
1 AGTGTTTACAATGTCACTGCCAATTTAGTGGTAGTATCGT
* * * * **
22050 AGTGTTTATAATGTCACAGCCAATTTAGTGATAATATCAC
1 AGTGTTTACAATGTCACTGCCAATTTAGTGGTAGTATCGT
22090 AGTGTTTACAATGTCACTGCCA
1 AGTGTTTACAATGTCACTGCCA
22112 GTTCGGTTGT
Statistics
Matches: 154, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 154 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (40 bp):
AGTGTTTACAATGTCACTGCCAATTTAGTGGTAGTATCGT
Found at i:21985 original size:80 final size:80
Alignment explanation
Indices: 21876--22127 Score: 299
Period size: 80 Copynumber: 3.1 Consensus size: 80
21866 GTGTCACTTC
* *
21876 AGTTGTAATATCACAGTGTTTACAGTGTCACTGCCAGTTTAGTGGTAGTATCGTAGTGTTTACAG
1 AGTTGTAATATCGCAGTGTTTACAATGTCACTGCCAGTTTAGTGGTAGTATCGTAGTGTTTACAG
*
21941 TGTCACTACCAATTT
66 TGTCACTGCCAATTT
* * * *
21956 AGTTGTAATATCGTAGTATTTACAATGTCACTGCCAGTTTAGTGGTAGTACCGTAGTGTTTATAG
1 AGTTGTAATATCGCAGTGTTTACAATGTCACTGCCAGTTTAGTGGTAGTATCGTAGTGTTTACAG
* *
22021 TGCCACTGCAAATTT
66 TGTCACTGCCAATTT
* * * * * * **
22036 AG-TGATAGTATCGCAGTGTTTATAATGTCACAGCCAATTTAGTGATAATATCACAGTGTTTACA
1 AGTTG-TAATATCGCAGTGTTTACAATGTCACTGCCAGTTTAGTGGTAGTATCGTAGTGTTTACA
* * *
22100 ATGTCACTGCCAGTTC
65 GTGTCACTGCCAATTT
*
22116 GGTTGTAATATC
1 AGTTGTAATATC
22128 AATTATTAAC
Statistics
Matches: 142, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
79 2 0.01
80 138 0.97
81 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (80 bp):
AGTTGTAATATCGCAGTGTTTACAATGTCACTGCCAGTTTAGTGGTAGTATCGTAGTGTTTACAG
TGTCACTGCCAATTT
Found at i:22065 original size:120 final size:120
Alignment explanation
Indices: 21890--22114 Score: 319
Period size: 120 Copynumber: 1.9 Consensus size: 120
21880 GTAATATCAC
* * * * * *
21890 AGTGTTTACAGTGTCACTGCCAGTTTAGTGGTAGTATCGTAGTGTTTACAGTGTCACTA-CCAAT
1 AGTGTTTACAGTGCCACTGCAAATTTAGTGATAGTATCGCAGTGTTTACAATGTCAC-AGCCAAT
**
21954 TTAGTTG-TAATATCGTAGTATTTACAATGTCACTGCCAGTTTAGTGGTAGTACCGT
65 TTAG-TGATAATATCACAGTATTTACAATGTCACTGCCAGTTTAGTGGTAGTACCGT
* *
22010 AGTGTTTATAGTGCCACTGCAAATTTAGTGATAGTATCGCAGTGTTTATAATGTCACAGCCAATT
1 AGTGTTTACAGTGCCACTGCAAATTTAGTGATAGTATCGCAGTGTTTACAATGTCACAGCCAATT
*
22075 TAGTGATAATATCACAGTGTTTACAATGTCACTGCCAGTT
66 TAGTGATAATATCACAGTATTTACAATGTCACTGCCAGTT
22115 CGGTTGTAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
119 3 0.03
120 89 0.97
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (120 bp):
AGTGTTTACAGTGCCACTGCAAATTTAGTGATAGTATCGCAGTGTTTACAATGTCACAGCCAATT
TAGTGATAATATCACAGTATTTACAATGTCACTGCCAGTTTAGTGGTAGTACCGT
Found at i:22128 original size:40 final size:40
Alignment explanation
Indices: 21876--22127 Score: 238
Period size: 40 Copynumber: 6.3 Consensus size: 40
21866 GTGTCACTTC
* * *
21876 AGTTGTAATATCACAGTGTTTACAGTGTCACTGCCAGTTT
1 AGTTGTAATATCGCAGTGTTTACAATGTCACTGCCAATTT
* * * * *
21916 AGTGGTAGTATCGTAGTGTTTACAGTGTCACTACCAATTT
1 AGTTGTAATATCGCAGTGTTTACAATGTCACTGCCAATTT
* * *
21956 AGTTGTAATATCGTAGTATTTACAATGTCACTGCCAGTTT
1 AGTTGTAATATCGCAGTGTTTACAATGTCACTGCCAATTT
* * * * * * * *
21996 AGTGGTAGTACCGTAGTGTTTATAGTGCCACTGCAAATTT
1 AGTTGTAATATCGCAGTGTTTACAATGTCACTGCCAATTT
* * *
22036 AG-TGATAGTATCGCAGTGTTTATAATGTCACAGCCAATTT
1 AGTTG-TAATATCGCAGTGTTTACAATGTCACTGCCAATTT
* * *
22076 AG-TGATAATATCACAGTGTTTACAATGTCACTGCCAGTTC
1 AGTTG-TAATATCGCAGTGTTTACAATGTCACTGCCAATTT
*
22116 GGTTGTAATATC
1 AGTTGTAATATC
22128 AATTATTAAC
Statistics
Matches: 175, Mismatches: 35, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 172 0.98
41 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (40 bp):
AGTTGTAATATCGCAGTGTTTACAATGTCACTGCCAATTT
Found at i:25100 original size:21 final size:21
Alignment explanation
Indices: 25074--25118 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
25064 ACGAAATGAG
25074 AAAAATGAAATCCTGAGATAT
1 AAAAATGAAATCCTGAGATAT
25095 AAAAATGAAATCCTGAGATAT
1 AAAAATGAAATCCTGAGATAT
25116 AAA
1 AAA
25119 GGACGACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (21 bp):
AAAAATGAAATCCTGAGATAT
Done.