Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013123.1 Kokia drynarioides strain JFW-HI SEQ_128142, 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: 2674
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Found at i:907 original size:6 final size:6
Alignment explanation
Indices: 892--983 Score: 68
Period size: 6 Copynumber: 15.7 Consensus size: 6
882 TGTAATTGAT
* * *
892 TTTAAA TTTAAG TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* * *
938 TTTAAAAA ATT-AA TTTAAA TTTAAA TTTAAA -GTAAA TTTAAT TTTA
1 TTT--AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
984 GAAATAAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
4 3 0.04
5 12 0.18
6 43 0.64
7 4 0.06
8 5 0.07
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:909 original size:12 final size:11
Alignment explanation
Indices: 892--983 Score: 60
Period size: 11 Copynumber: 7.9 Consensus size: 11
882 TGTAATTGAT
892 TTTAAATTTAA
1 TTTAAATTTAA
*
903 GTTTAAAATT-A
1 -TTTAAATTTAA
914 TTTCAAATTTAA
1 TTT-AAATTTAA
**
926 ACTAAATTTAAA
1 TTTAAATTT-AA
*
938 TTTAAAAAATTAA
1 TTT--AAATTTAA
951 TTTAAATTTAAA
1 TTTAAATTT-AA
* *
963 TTTAAAGTAAA
1 TTTAAATTTAA
*
974 TTTAATTTTA
1 TTTAAATTTA
984 GAAATAAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
10 3 0.05
11 26 0.43
12 22 0.36
13 5 0.08
14 5 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:958 original size:36 final size:34
Alignment explanation
Indices: 894--962 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 34
884 TAATTGATTT
*
894 TAAATTTAAGTTTAAAATTATTTCAAATTTAAAC
1 TAAATTTAAATTTAAAATTATTTCAAATTTAAAC
928 TAAATTTAAATTTAAAAAATTAATTT-AAATTTAAA
1 TAAATTTAAATTT--AAAATT-ATTTCAAATTTAAA
963 TTTAAAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 12 0.39
36 15 0.48
37 4 0.13
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (34 bp):
TAAATTTAAATTTAAAATTATTTCAAATTTAAAC
Found at i:998 original size:42 final size:43
Alignment explanation
Indices: 913--998 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 43
903 GTTTAAAATT
*
913 ATTTCAAATTTAAACTAAATTTAAATTTAAAAAATTAATTTAA
1 ATTTCAAATTTAAACTAAATTTAAATTTAAAAAATAAATTTAA
* * *
956 ATTT-AAATTTAAAGTAAATTT-AATTTTAGAAATAAATCTTAA
1 ATTTCAAATTTAAACTAAATTTAAATTTAAAAAATAAAT-TTAA
998 A
1 A
999 CCTATCTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 13 0.34
42 21 0.55
43 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (43 bp):
ATTTCAAATTTAAACTAAATTTAAATTTAAAAAATAAATTTAA
Found at i:1726 original size:206 final size:206
Alignment explanation
Indices: 1354--1960 Score: 815
Period size: 206 Copynumber: 3.0 Consensus size: 206
1344 TCTGGTTTCA
* * **
1354 TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATTACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTCAATCCACTT
* * * * * * * *
1419 CTCTATGTTTCATCAAGAAGATGGATTTGGTTCACTTTTCCGTATCTCATCAGGAAGCTAACCAC
66 CTCTATATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
1484 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCAT
1549 CGAGCATGGGT
196 CGAGCATGGGT
* * * * * * *
1560 TTGATTTGGTTTTCTTCTTAGTATTTCTTCAGGAAGATGATCACATCACTTGTTTCAATTCATTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTCAATCCACTT
* *
1625 CCCTGTATCTCATCAGGAAGACGAATTTGG-TCTACTTCTCAGTATCTCATCAGGAAGCTAACCA
66 CTCTATATCTCATCAGGAAGACGAATTTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTAACCA
** * * *
1689 TTTTATTACTTCGACCCACTTCTCAGTATCACATCAGGAAGTTGGGGTTCGATGATTTGCTCGCA
130 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCA
*
1754 TTGAGCATGGGT
195 TCGAGCATGGGT
* * * * * *
1766 TTGATTTGGTCTTCTTCTCAGTATCTCATAAAGAAGATGACCGCGTC-CTTTATTTCAATCCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCAC-TTGTTTCAATCCACT
* * *
1830 TCTCTATATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGATAACCG
65 TCTCTATATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* *
1895 TTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCT-TGGTTCGAAGATTTGCTCGCA
130 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCA
1959 TC
195 TC
1961 AAGTCCTGAG
Statistics
Matches: 343, Mismatches: 55, Indels: 7
0.85 0.14 0.02
Matches are distributed among these distances:
205 23 0.07
206 318 0.93
207 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTCAATCCACTT
CTCTATATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCAT
CGAGCATGGGT
Done.