Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003930.1 Kokia drynarioides strain JFW-HI SEQ_117011, 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: 2050
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Found at i:904 original size:205 final size:205
Alignment explanation
Indices: 643--1661 Score: 1592
Period size: 205 Copynumber: 5.0 Consensus size: 205
633 CCAACTCAAG
* * * * * * ***
643 GCTCGATGTGAGAAAATCTTCGAATCCCAACTTCCTGATGAGATACTGACAAGCAGGGCAAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTTGAAGCA
*
708 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * *
773 AGAGAAGC-AGATTGAAACAAACGACGCGGTCATCTTCCTGGTGAGATACTAAGAAGAAGACCAA
131 AGAGAAGCGA-ACTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
*
837 ATCAAATCCAC
195 ATCAAACCCAC
*
848 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACCGAGAAGCAGGTTGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTTGAAGCA
* * *
913 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGGTAT
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * *
978 AGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGGTGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGAACTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
*
1043 TCAAATCCAC
196 TCAAACCCAC
* ** *
1053 GCTCGATGTGAGTAAATCTTTTAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTTGAAGTA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTTGAAGCA
* *
1118 ATAAAAGGTTAGCTTCCTGTTAAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * *
1183 AGAGAAGCGAACTGAAACAAACGACGCGGCCATATTCCTGATGAGATATTGAGAAGAAGACCAAA
131 AGAGAAGCGAACTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
1248 TCAAACCCAC
196 TCAAACCCAC
*
1258 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTTGAAGTA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTTGAAGCA
1323 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
*
1388 AGAGAAGCGAACTGAAACAAACGACGC-GTCCATCTTCCTGATGAGATATTGAGAAGAAGACCAA
131 AGAGAAGCGAACTGAAACAAACGACGCGGT-CATCTTCCTGATGAGATACTGAGAAGAAGACCAA
1452 ATCAAACCCAC
195 ATCAAACCCAC
* *
1463 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAACAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTTGAAGCA
* * * * *
1528 ATAAAAAGTTAACTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATAT
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * * * * *
1593 AGAGAAGTGAACTAAAACATATGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAG
131 AGAGAAGCGAACTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
1658 TCAA
196 TCAA
1662 TGAAACCAGA
Statistics
Matches: 760, Mismatches: 51, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
204 1 0.00
205 757 1.00
206 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (205 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTTGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
AGAGAAGCGAACTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:2000 original size:6 final size:6
Alignment explanation
Indices: 1986--2049 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
1976 TTTAATTTAT
* *
1986 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
2032 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
2050 A
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
4 2 0.04
5 10 0.21
6 28 0.60
7 7 0.15
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:2002 original size:17 final size:17
Alignment explanation
Indices: 1979--2049 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
1969 CCCTTTTTTT
1979 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
1996 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
2013 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
* *
2030 AATTTAATTTCAAAATTA
1 AATTT-ATTTTAAATTTA
2048 AA
1 AA
2050 A
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 34 0.76
18 11 0.24
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:2018 original size:11 final size:12
Alignment explanation
Indices: 1986--2049 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 12
1976 TTTAATTTAT
*
1986 TTTAAATTTAGA
1 TTTAAATTTAAA
*
1998 TTT-ATTTTAAA
1 TTTAAATTTAAA
2009 TTTAAA-TT-AA
1 TTTAAATTTAAA
2019 TCTTAAATTTAAA
1 T-TTAAATTTAAA
2032 TTT-AATTTCAAA
1 TTTAAATTT-AAA
*
2044 ATTAAA
1 TTTAAA
2050 A
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 21 0.50
12 13 0.31
13 5 0.12
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTAAATTTAAA
Done.