Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002365.1 Kokia drynarioides strain JFW-HI SEQ_114441, 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: 31220
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1872 original size:21 final size:20
Alignment explanation
Indices: 1827--1869 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1817 TTTTTTAAAA
*
1827 TTTAAAATCATTAAAATTAT
1 TTTAAAATCATTAAAAATAT
1847 TTTAAAA-CATATAAAAATAT
1 TTTAAAATCAT-TAAAAATAT
1867 TTT
1 TTT
1870 TAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAAATCATTAAAAATAT
Found at i:2012 original size:27 final size:26
Alignment explanation
Indices: 1967--2018 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1957 GTGATTTAAT
* **
1967 ATAAAATATAAATTTAAGAATTAAAAA
1 ATAAAAAATAAATGAAAG-ATTAAAAA
1994 ATAAAAAATAAATGAAAGATTAAAA
1 ATAAAAAATAAATGAAAGATTAAAA
2019 TAATTTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (26 bp):
ATAAAAAATAAATGAAAGATTAAAAA
Found at i:8358 original size:44 final size:45
Alignment explanation
Indices: 8309--8403 Score: 165
Period size: 44 Copynumber: 2.1 Consensus size: 45
8299 CTTGTATAGT
*
8309 TTCATTTGTAGCAACTATTTGCTTATTTCAATAATTAAAGAAACA
1 TTCATTTGTAGCAACTATTTCCTTATTTCAATAATTAAAGAAACA
*
8354 -TCATTTGTAGCAACTATTTCCTTATTTCAATAATTAAAGAAGCA
1 TTCATTTGTAGCAACTATTTCCTTATTTCAATAATTAAAGAAACA
8398 TTCATT
1 TTCATT
8404 ATAAAATATC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 42 0.89
45 5 0.11
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (45 bp):
TTCATTTGTAGCAACTATTTCCTTATTTCAATAATTAAAGAAACA
Found at i:8780 original size:18 final size:18
Alignment explanation
Indices: 8757--8808 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
8747 TTTTCAGTTG
* *
8757 TAATTAATTTAAATTTTT
1 TAATTAATTAAAATTATT
8775 TAATTAATTAAAATTATT
1 TAATTAATTAAAATTATT
8793 TAATTAA--AAAATTATT
1 TAATTAATTAAAATTATT
8809 CTCACTCGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.28
18 23 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:10533 original size:252 final size:252
Alignment explanation
Indices: 10088--10574 Score: 974
Period size: 252 Copynumber: 1.9 Consensus size: 252
10078 TAGTTCAATC
10088 GAATTATTTGAATTAGATTATAATCGTGTTCTCCATGAAAAATAGTAAGGGTCTAAGGGATCAGA
1 GAATTATTTGAATTAGATTATAATCGTGTTCTCCATGAAAAATAGTAAGGGTCTAAGGGATCAGA
10153 TAGCTTGGGATGTTTTGAGTAAATGTCAATAATTTTTGGTTAAGCGTTCCTTCAAAATGTTGCTA
66 TAGCTTGGGATGTTTTGAGTAAATGTCAATAATTTTTGGTTAAGCGTTCCTTCAAAATGTTGCTA
10218 ATGACTGAGTTTGCTATCAAAAATTGACAAAAGGAGACAATTTCGCATTTGTACAAAATTTTTAA
131 ATGACTGAGTTTGCTATCAAAAATTGACAAAAGGAGACAATTTCGCATTTGTACAAAATTTTTAA
10283 TTAGTAGGTATGCATCATGCTTGGGACATTTGTGTACAGGGTCTAAGGGAATTATTT
196 TTAGTAGGTATGCATCATGCTTGGGACATTTGTGTACAGGGTCTAAGGGAATTATTT
10340 GAATTATTTGAATTAGATTATAATCGTGTTCTCCATGAAAAATAGTAAGGGTCTAAGGGATCAGA
1 GAATTATTTGAATTAGATTATAATCGTGTTCTCCATGAAAAATAGTAAGGGTCTAAGGGATCAGA
10405 TAGCTTGGGATGTTTTGAGTAAATGTCAATAATTTTTGGTTAAGCGTTCCTTCAAAATGTTGCTA
66 TAGCTTGGGATGTTTTGAGTAAATGTCAATAATTTTTGGTTAAGCGTTCCTTCAAAATGTTGCTA
10470 ATGACTGAGTTTGCTATCAAAAATTGACAAAAGGAGACAATTTCGCATTTGTACAAAATTTTTAA
131 ATGACTGAGTTTGCTATCAAAAATTGACAAAAGGAGACAATTTCGCATTTGTACAAAATTTTTAA
10535 TTAGTAGGTATGCATCATGCTTGGGACATTTGTGTACAGG
196 TTAGTAGGTATGCATCATGCTTGGGACATTTGTGTACAGG
10575 CGCAAACATC
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
252 235 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (252 bp):
GAATTATTTGAATTAGATTATAATCGTGTTCTCCATGAAAAATAGTAAGGGTCTAAGGGATCAGA
TAGCTTGGGATGTTTTGAGTAAATGTCAATAATTTTTGGTTAAGCGTTCCTTCAAAATGTTGCTA
ATGACTGAGTTTGCTATCAAAAATTGACAAAAGGAGACAATTTCGCATTTGTACAAAATTTTTAA
TTAGTAGGTATGCATCATGCTTGGGACATTTGTGTACAGGGTCTAAGGGAATTATTT
Found at i:15220 original size:15 final size:16
Alignment explanation
Indices: 15195--15229 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
15185 AATCTAATTC
*
15195 ATTTGATATATTTAAT
1 ATTTGATATATTAAAT
15211 ATTT-ATATATTAAAT
1 ATTTGATATATTAAAT
15226 ATTT
1 ATTT
15230 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTGATATATTAAAT
Done.