Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009816.1 Kokia drynarioides strain JFW-HI SEQ_124537, 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: 2883
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Found at i:1812 original size:45 final size:45
Alignment explanation
Indices: 1759--2123 Score: 355
Period size: 45 Copynumber: 8.1 Consensus size: 45
1749 CACCGGTGGC
* ** *
1759 TTCTTTGGAGGCT-TATAAACTGGTGGTTTGGGTTTTGGTTTTTCT
1 TTCTTTGGAGG-TGTATAAACTGGTGGTTTGGGCTCAGGCTTTTCT
* * * *
1804 TTCTTTGGAGGTGCATAAACTGGTGGTTTAGGTTCAGGCTTTTCC
1 TTCTTTGGAGGTGTATAAACTGGTGGTTTGGGCTCAGGCTTTTCT
* * * *
1849 TTCTTTGGCA-GT-TCATACACGGGTGGCTTGGGCTCAGGCTTCTCT
1 TTCTTTGG-AGGTGT-ATAAACTGGTGGTTTGGGCTCAGGCTTTTCT
* * * *
1894 TTCTTTGGTGGTGTATAAACTGGTGGCTTAGGCTCAGGCTTTTCC
1 TTCTTTGGAGGTGTATAAACTGGTGGTTTGGGCTCAGGCTTTTCT
* *
1939 TTCTTTGGAGGT-TCATATACTGGTGGTTTGGGCTCAGGCTTCTCT
1 TTCTTTGGAGGTGT-ATAAACTGGTGGTTTGGGCTCAGGCTTTTCT
* * *
1984 TTCTTTGGTGGTGTATAAACTGGTGGCTTAGGCTCAGGCTTTTCCT
1 TTCTTTGGAGGTGTATAAACTGGTGGTTTGGGCTCAGGCTTTT-CT
* * *
2030 TT-TTTGGGGGT-TCATATACTGGTGGTTTGGGCTCAGGCTTCTCT
1 TTCTTTGGAGGTGT-ATAAACTGGTGGTTTGGGCTCAGGCTTTTCT
* * * * * * *
2074 TTCTTTGGTGGTGTATAAACTGATGGCTTAGGTTCAGGCTTCTCC
1 TTCTTTGGAGGTGTATAAACTGGTGGTTTGGGCTCAGGCTTTTCT
2119 TTCTT
1 TTCTT
2124 CGGTGGTTCA
Statistics
Matches: 266, Mismatches: 43, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
44 7 0.03
45 251 0.94
46 8 0.03
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.42
Consensus pattern (45 bp):
TTCTTTGGAGGTGTATAAACTGGTGGTTTGGGCTCAGGCTTTTCT
Found at i:2132 original size:90 final size:90
Alignment explanation
Indices: 1758--2135 Score: 544
Period size: 90 Copynumber: 4.2 Consensus size: 90
1748 ACACCGGTGG
* * ** * * * *
1758 CTTCTTTGGAGGCTT-ATAAACTGGTGGTTTGGGTTTTGGTTTTTCTTTCTTTGGAGGTGCATAA
1 CTTCTTTGGAGG-TTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAA
* *
1822 ACTGGTGGTTTAGGTTCAGGCTTTTC
65 ACTGGTGGCTTAGGCTCAGGCTTTTC
* * *
1848 CTTCTTTGGCA-GTTCATACACGGGTGGCTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAA
1 CTTCTTTGG-AGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAA
1912 ACTGGTGGCTTAGGCTCAGGCTTTTC
65 ACTGGTGGCTTAGGCTCAGGCTTTTC
1938 CTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
2003 CTGGTGGCTTAGGCTCAGGCTTTTC
66 CTGGTGGCTTAGGCTCAGGCTTTTC
* *
2028 CTTTTTTGGGGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
* * *
2093 CTGATGGCTTAGGTTCAGGCTTCTC
66 CTGGTGGCTTAGGCTCAGGCTTTTC
* *
2118 CTTCTTCGGTGGTTCATA
1 CTTCTTTGGAGGTTCATA
2136 GACAGGAGGC
Statistics
Matches: 262, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
89 3 0.01
90 258 0.98
91 1 0.00
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.42
Consensus pattern (90 bp):
CTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
CTGGTGGCTTAGGCTCAGGCTTTTC
Found at i:2147 original size:135 final size:135
Alignment explanation
Indices: 1759--2148 Score: 430
Period size: 135 Copynumber: 2.9 Consensus size: 135
1749 CACCGGTGGC
* * ** * *
1759 TTCTTTGGAGGCT-TATAAACTGGTGGTTTGGGTTTTGGTTTTTCTTTCTTTGGAGGTGCATAAA
1 TTCTTTGG-GGGTGTATAAACTGGTGGTTTGGGCTCAGGCTTTTCTTTCTTTGGAGGTGTATAAA
* ** * * *
1823 CTGGTGGTTTAGGTTCAGGCTTTTCCTTCTTTGGCAGTTCATACACGGGTGGCTTGGGCTCAGGC
65 CTGGTGGTTTAGGTTCAGGCTTCTCCTTCTTTGGTGGTTCATAAACAGGTGGCTTAGGCTCAGGC
1888 TTCTCT
130 TTCTCT
* * * * *
1894 TTCTTTGGTGGTGTATAAACTGGTGGCTTAGGCTCAGGCTTTTCCTTCTTTGGAGGT-TCATATA
1 TTCTTTGGGGGTGTATAAACTGGTGGTTTGGGCTCAGGCTTTTCTTTCTTTGGAGGTGT-ATAAA
* * * *
1958 CTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGCTCAGG
65 CTGGTGGTTTAGGTTCAGGCTTCTCCTTCTTTGGTGGT-TCATAAACAGGTGGCTTAGGCTCAGG
*
2022 CTTTTCCT
129 CTTCT-CT
* * *
2030 TT-TTTGGGGGT-TCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
1 TTCTTTGGGGGTGT-ATAAACTGGTGGTTTGGGCTCAGGCTTTTCTTTCTTTGGAGGTGTATAAA
* * * * *
2093 CTGATGGCTTAGGTTCAGGCTTCTCCTTCTTCGGTGGTTCATAGACAGGAGGCTTA
65 CTGGTGGTTTAGGTTCAGGCTTCTCCTTCTTTGGTGGTTCATAAACAGGTGGCTTA
2149 TGTTCATAAG
Statistics
Matches: 210, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
134 4 0.02
135 200 0.95
136 6 0.03
ACGTcount: A:0.13, C:0.17, G:0.29, T:0.41
Consensus pattern (135 bp):
TTCTTTGGGGGTGTATAAACTGGTGGTTTGGGCTCAGGCTTTTCTTTCTTTGGAGGTGTATAAAC
TGGTGGTTTAGGTTCAGGCTTCTCCTTCTTTGGTGGTTCATAAACAGGTGGCTTAGGCTCAGGCT
TCTCT
Found at i:2154 original size:45 final size:45
Alignment explanation
Indices: 1804--2135 Score: 373
Period size: 45 Copynumber: 7.4 Consensus size: 45
1794 TGGTTTTTCT
* * * * *
1804 TTCTTTGGAGGTGCATAAACTGGTGGTTTAGGTTCAGGCTTTTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTCTCC
** * * * *
1849 TTCTTTGGCAGTTCATACACGGGTGGCTTGGGCTCAGGCTTCTCT
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTCTCC
*
1894 TTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGCTCAGGCTTTTCC
1 TTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCAGGCTTCTCC
* * * * *
1939 TTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCT
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTCTCC
*
1984 TTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGCTCAGGCTTTTCC
1 TTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCAGGCTTCTCC
* * * * * *
2029 TTTTTTGGGGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCT
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTCTCC
* *
2074 TTCTTTGGTGGTGT-ATAAACTGATGGCTTAGGTTCAGGCTTCTCC
1 TTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCAGGCTTCTCC
*
2119 TTCTTCGGTGGTTCATA
1 TTCTTTGGTGGTTCATA
2136 GACAGGAGGC
Statistics
Matches: 236, Mismatches: 45, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
44 3 0.01
45 230 0.97
46 3 0.01
ACGTcount: A:0.13, C:0.18, G:0.29, T:0.41
Consensus pattern (45 bp):
TTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTCTCC
Done.