Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016451.1 Corchorus olitorius cultivar O-4 contig16484, 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: 2975
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Found at i:1869 original size:81 final size:79
Alignment explanation
Indices: 1727--2975 Score: 1208
Period size: 81 Copynumber: 15.3 Consensus size: 79
1717 GTAGGGCCTC
* * *
1727 TAGTTGCATATTTAGTAGGGCCATATAGTTACATATTCGGTAGGGTCATATAGTTGCATATTCAG
1 TAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGTCATATAGTTGCATATTCAG
1792 TAGGCTCATAATCATA
66 TAGG--CATAATCATA
* * * * *
1808 TAGTGGCATATTCGGTAGGGCCATGTAGTCGCATATTCAGTAGGGTCATATAGTTGTATATTCAG
1 TAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGTCATATAGTTGCATATTCAG
*
1873 TAGGGTCATAATCACA
66 TA-GG-CATAATCATA
*
1889 TAGTTAG-ATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGTCATATAGATGCA
1 TAGTT-GCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGGTCATATAGTTGCA
* *
1953 TATTCAGTAGG----GTCGTA
59 TATTCAGTAGGCATAATCATA
*
1970 TAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGAGCCATATAGTTGCA
1 TAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGG-GTCATATAGTTGCA
*
2035 TATTCAGTAGG----GTCATA
59 TATTCAGTAGGCATAATCATA
* * * *
2052 TAGTTGCATATTCAGTAGAGCCATATAGTTACATATTCAGTAGGGCCATATAGTTGCATATACAG
1 TAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGTCATATAGTTGCATATTCAG
2117 TAGGGCCATAATCATA
66 TA-GG-CATAATCATA
*
2133 TAGTTGCATATTCAGTAGGTTCATAATCATATAGTTGCATATTCAGTAGGGGATCATATAGTTGC
1 TAGTTGCATATTCAGTAGG-GC-----CATATAGTTGCATATTCAGTA-GGG-TCATATAGTTGC
**
2198 ATATTCAGTAGG--GGATCATA
58 ATATTCAGTAGGCATAATCATA
* * *
2218 TAGTTGCATATTCAGTAGGGGATCATATAGTTGCATATTCAGTAGGAAATCATGTAGTTGCATAT
1 TAGTTGCATATTCAGTA-GGG-CCATATAGTTGCATATTCAGTAGG--GTCATATAGTTGCATAT
***
2283 TCAGTAGG---GGGCATA
62 TCAGTAGGCATAATCATA
* * *
2298 TAGTTGCATATTCAGTAGGGCCATATATTTGCATATTTAGTAGGGGATCATATAGTTGCATATTT
1 TAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTA-GGG-TCATATAGTTGCATATTC
**
2363 AGTAGG--GGATCATA
64 AGTAGGCATAATCATA
* * * *
2377 TAGTTGCATATTCAGTAGGGGGCATATAGTTGCATATTCAGTAGGGCCATATATTTGCATATTTA
1 TAGTTGCATATTCAGTA-GGGCCATATAGTTGCATATTCAGTAGGGTCATATAGTTGCATATTCA
2442 GTAGGGC----T-ATA
65 GTA-GGCATAATCATA
*
2453 TAGTTGCATATTCAGTAGGGTCATATAGTTGCATATTCAGTAGGGAATCATATAGTTGCATATTC
1 TAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGG--TCATATAGTTGCATATTC
2518 AGTAGGGC-----CATA
64 AGTA-GGCATAATCATA
* *
2530 TGGTTGCATATTCAGTAGGGAATCATATAGTTGCATATTCAGTAGGGAATCATATAGTTGCATAT
1 TAGTTGCATATTCAGTAGGG--CCATATAGTTGCATATTCAGTAGGG--TCATATAGTTGCATAT
2595 TCAGTAGGGCCATAATCATA
62 TCAGTA-GG-CATAATCATA
*
2615 TAGTTGCATATTCAGTAGGGAATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGC
1 TAGTTGCATATTCAGTAGGG--CCATATAGTTGCATATTCAGTAGGG------TCATATAGTTGC
2680 ATATTCAGTAGGGTCATAATCATA
58 ATATTCAGTA-GG-CATAATCATA
* *
2704 TAGTTGCATATTCAGTAGGGCCATATAATTGCATATTCAGTAAGGCCATAATCATATAGTTGCAT
1 TAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGT-AGG-----GTCATATAGTTGCAT
2769 ATTCAGTAGGGTCATAATCATA
60 ATTCAGTA-GG-CATAATCATA
*
2791 TAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCAT
1 TAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGGTCATATAGTTGCAT
* *
2856 ATTCAGTAGGACCATTATTATA
60 ATTCAGTAGG--CATAATCATA
* *
2878 TAGTTGGATATTCAGTAGGGCCATATAGTTGCATATTCATTAGGGTCATATAGTTGCATATTCAG
1 TAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGTCATATAGTTGCATATTCAG
* *
2943 TAGG----GTCATG
66 TAGGCATAATCATA
2953 TAGTTGCATATTCAGTAGGGCCA
1 TAGTTGCATATTCAGTAGGGCCA
Statistics
Matches: 1032, Mismatches: 74, Indels: 130
0.83 0.06 0.11
Matches are distributed among these distances:
75 74 0.07
76 44 0.04
77 46 0.04
78 61 0.06
79 84 0.08
80 48 0.05
81 250 0.24
82 52 0.05
85 73 0.07
86 7 0.01
87 185 0.18
88 9 0.01
89 77 0.07
92 3 0.00
93 19 0.02
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (79 bp):
TAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGTCATATAGTTGCATATTCAG
TAGGCATAATCATA
Found at i:2972 original size:25 final size:25
Alignment explanation
Indices: 1685--2972 Score: 1196
Period size: 25 Copynumber: 47.5 Consensus size: 25
1675 CATATCGCTT
* *
1685 ATATTCAATAGGATCATATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
* * *
1710 ATATCCAGTAGGG-CCTCTAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
* * *
1734 ATATTTAGTAGGGCCATATAGTTAC
1 ATATTCAGTAGGGTCATATAGTTGC
*
1759 ATATTCGGTAGGGTCATATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
* *
1784 ATATTCAGTAGGCTCATAATCATATAGTGGC
1 ATATTCAGTAGG------GTCATATAGTTGC
* * * *
1815 ATATTCGGTAGGGCCATGTAGTCGC
1 ATATTCAGTAGGGTCATATAGTTGC
*
1840 ATATTCAGTAGGGTCATATAGTTGT
1 ATATTCAGTAGGGTCATATAGTTGC
1865 ATATTCAGTAGGGTCATAATCACATAGTTAG-
1 ATATTCAGTAGGGTC---AT---ATAGTT-GC
1896 ATATTCAGTAGGGCCATAATCATATAGTTGC
1 ATATTCAGTAGGG------TCATATAGTTGC
*
1927 ATATTCAGTAGGGTCATATAGATGC
1 ATATTCAGTAGGGTCATATAGTTGC
*
1952 ATATTCAGTAGGGTCGTATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
1977 ATATTCAGTAGGGCCATAATCATATAGTTGC
1 ATATTCAGTAGGG------TCATATAGTTGC
*
2008 ATATTCAGTAGGAGCCATATAGTTGC
1 ATATTCAGTAGG-GTCATATAGTTGC
2034 ATATTCAGTAGGGTCATATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
* * *
2059 ATATTCAGTAGAGCCATATAGTTAC
1 ATATTCAGTAGGGTCATATAGTTGC
*
2084 ATATTCAGTAGGGCCATATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
*
2109 ATATACAGTAGGGCCATAATCATATAGTTGC
1 ATATTCAGTAGGG------TCATATAGTTGC
*
2140 ATATTCAGTAGGTTCATAATCATATAGTTGC
1 ATATTCAGTAGG------GTCATATAGTTGC
2171 ATATTCAGTAGGGGATCATATAGTTGC
1 ATATTCAGTA-GGG-TCATATAGTTGC
2198 ATATTCAGTAGGGGATCATATAGTTGC
1 ATATTCAGTA-GGG-TCATATAGTTGC
2225 ATATTCAGTAGGGGATCATATAGTTGC
1 ATATTCAGTA-GGG-TCATATAGTTGC
* *
2252 ATATTCAGTAGGAAATCATGTAGTTGC
1 ATATTCAGTAGG--GTCATATAGTTGC
*
2279 ATATTCAGTAGGGGGCATATAGTTGC
1 ATATTCAGTA-GGGTCATATAGTTGC
* *
2305 ATATTCAGTAGGGCCATATATTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
*
2330 ATATTTAGTAGGGGATCATATAGTTGC
1 ATATTCAGTA-GGG-TCATATAGTTGC
*
2357 ATATTTAGTAGGGGATCATATAGTTGC
1 ATATTCAGTA-GGG-TCATATAGTTGC
*
2384 ATATTCAGTAGGGGGCATATAGTTGC
1 ATATTCAGTA-GGGTCATATAGTTGC
* *
2410 ATATTCAGTAGGGCCATATATTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
*
2435 ATATTTAGTAGGG-CTATATAGTTGC
1 ATATTCAGTAGGGTC-ATATAGTTGC
2460 ATATTCAGTAGGGTCATATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
2485 ATATTCAGTAGGGAATCATATAGTTGC
1 ATATTCAGTAGGG--TCATATAGTTGC
* *
2512 ATATTCAGTAGGGCCATATGGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
2537 ATATTCAGTAGGGAATCATATAGTTGC
1 ATATTCAGTAGGG--TCATATAGTTGC
2564 ATATTCAGTAGGGAATCATATAGTTGC
1 ATATTCAGTAGGG--TCATATAGTTGC
2591 ATATTCAGTAGGGCCATAATCATATAGTTGC
1 ATATTCAGTAGGG------TCATATAGTTGC
2622 ATATTCAGTAGGGAATCATATAGTTGC
1 ATATTCAGTAGGG--TCATATAGTTGC
2649 ATATTCAGTAGGGCCATAATCATATAGTTGC
1 ATATTCAGTAGGG------TCATATAGTTGC
2680 ATATTCAGTAGGGTCATAATCATATAGTTGC
1 ATATTCAGTAGGG------TCATATAGTTGC
* *
2711 ATATTCAGTAGGGCCATATAATTGC
1 ATATTCAGTAGGGTCATATAGTTGC
*
2736 ATATTCAGTAAGGCCATAATCATATAGTTGC
1 ATATTCAGT-AGG-----GTCATATAGTTGC
2767 ATATTCAGTAGGGTCATAATCATATAGTTGC
1 ATATTCAGTAGGG------TCATATAGTTGC
2798 ATATTCAGTAGGGTCATAATCATATAGTTGC
1 ATATTCAGTAGGG------TCATATAGTTGC
*
2829 ATATTCAGTAGGGCCATATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
* * *
2854 ATATTCAGTAGGACCATTATTATATAGTTGG
1 ATATTCAGTAGG------GTCATATAGTTGC
*
2885 ATATTCAGTAGGGCCATATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
*
2910 ATATTCATTAGGGTCATATAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
*
2935 ATATTCAGTAGGGTCATGTAGTTGC
1 ATATTCAGTAGGGTCATATAGTTGC
2960 ATATTCAGTAGGG
1 ATATTCAGTAGGG
2973 CCA
Statistics
Matches: 1100, Mismatches: 84, Indels: 158
0.82 0.06 0.12
Matches are distributed among these distances:
24 21 0.02
25 434 0.39
26 73 0.07
27 249 0.23
28 4 0.00
30 4 0.00
31 307 0.28
32 4 0.00
34 2 0.00
37 2 0.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (25 bp):
ATATTCAGTAGGGTCATATAGTTGC
Done.