Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005772.1 Kokia drynarioides strain JFW-HI SEQ_120039, 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: 2009
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Found at i:416 original size:207 final size:205
Alignment explanation
Indices: 1--484 Score: 588
Period size: 207 Copynumber: 2.4 Consensus size: 205
* * ** * * * *
1 TGATGAGATACAGAGAAGC-GAGTTGAAATAAATAACGCGGTCATCTTCTTGATGAAACACTGAG
1 TGATGAGATACAGAGAAACAGA-TTGAAACAAACGACGTGGTCATCTCCCTGATGAGACACTGAG
* * *
65 AAGAAGACCCAAA-C--G---AGGCTCAAAACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAG
65 AAGAAGA-CCAAATCAAGCCCACGCTCAAAACGAGAAAATCTTCGAACCCCAGCTTCCTGATAAG
* * * *
124 ACACCGAGAAGCAGGTCGAAGCAGTAAACGGTTAGCTTCCAGATGAGATACTGAGGAGTGAACCA
129 ACACCGAGAAGCAGGTCGAAGCAATAAACGGATAGCTCCCAGATGAGATACTGAGGAGTAAACCA
189 AATTCGCCTTCC
194 AATTCGCCTTCC
* * * * *
201 TGATGAGATACAGAGAAGCAGATTGAAACAAGCGATGTGGTCATCTTTCC-GATGAGATACTGAG
1 TGATGAGATACAGAGAAACAGATTGAAACAAACGACGTGGTCATC-TCCCTGATGAGACACTGAG
* *
265 AAGAAGACCAAATCAAGCCCACGCTCAAAGCGAGTAAAATCTTCGAACCCCAGCTTCTTGATAAG
65 AAGAAGACCAAATCAAGCCCACGCTCAAAACGAG-AAAATCTTCGAACCCCAGCTTCCTGATAAG
* * * * *
330 ACACTGAGAAGTAGGTCGAAGTAATAAAATGGATAGCTCCCTGATGAGATACTGAGGAGTAAACC
129 ACACCGAGAAGCAGGTCGAAGCAAT-AAACGGATAGCTCCCAGATGAGATACTGAGGAGTAAACC
*
395 AAATTCGTCTTCC
193 AAATTCGCCTTCC
* *
408 TGATGAGATGCAGAGAAACAGATTGAAACAAACGACGTGGTCATCTCCCTGATGAGACATTGAGA
1 TGATGAGATACAGAGAAACAGATTGAAACAAACGACGTGGTCATCTCCCTGATGAGACACTGAGA
*
473 AGAAGTCCAAAT
66 AGAAGACCAAAT
485 TAAACCCATG
Statistics
Matches: 241, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
199 5 0.02
200 56 0.23
201 5 0.02
202 1 0.00
205 12 0.05
206 51 0.21
207 111 0.46
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (205 bp):
TGATGAGATACAGAGAAACAGATTGAAACAAACGACGTGGTCATCTCCCTGATGAGACACTGAGA
AGAAGACCAAATCAAGCCCACGCTCAAAACGAGAAAATCTTCGAACCCCAGCTTCCTGATAAGAC
ACCGAGAAGCAGGTCGAAGCAATAAACGGATAGCTCCCAGATGAGATACTGAGGAGTAAACCAAA
TTCGCCTTCC
Found at i:871 original size:6 final size:6
Alignment explanation
Indices: 850--896 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
840 TTTAATTTAT
* *
850 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA -TTGAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
895 TT
1 TT
897 AAAAAGTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
5 13 0.37
6 22 0.63
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:885 original size:17 final size:17
Alignment explanation
Indices: 850--899 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
840 TTTAATTTAT
* *
850 TTTAAATTTGATTTAAA
1 TTTAAATTTAAATTAAA
*
867 TTTAAATTTAAATTGAA
1 TTTAAATTTAAATTAAA
884 TTT-AATTTAAATTAAA
1 TTTAAATTTAAATTAAA
900 AAGTCCAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:896 original size:11 final size:11
Alignment explanation
Indices: 843--899 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
833 GGCCTTTTTT
*
843 AATTTATTTTA
1 AATTTAATTTA
*
854 AATTTGATTTA
1 AATTTAATTTA
865 AATTTAAATTTA
1 AATTT-AATTTA
*
877 AATTGAATTT-
1 AATTTAATTTA
*
887 AATTTAAATTA
1 AATTTAATTTA
898 AA
1 AA
900 AAGTCCAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
10 8 0.21
11 21 0.55
12 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (11 bp):
AATTTAATTTA
Done.