Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010418.1 Kokia drynarioides strain JFW-HI SEQ_125304, 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: 50692
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:802 original size:18 final size:18
Alignment explanation
Indices: 779--815 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
769 TTTGTGATCA
779 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
797 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
815 A
1 A
816 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:965 original size:41 final size:40
Alignment explanation
Indices: 917--1018 Score: 102
Period size: 38 Copynumber: 2.6 Consensus size: 40
907 TCGACCTTGA
*
917 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCATTACTTTACTTCGGATAG
* ** ** *
957 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCATTACTTTACTTCGGATAG
*
995 GCCGATGAGACACTGGGTGTCATT
1 GTCGATGAGACACTGGGTGTCATT
1019 TTATTGCTTT
Statistics
Matches: 45, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.38
39 4 0.09
40 3 0.07
41 11 0.24
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCATTACTTTACTTCGGATAG
Found at i:4701 original size:4 final size:4
Alignment explanation
Indices: 4692--4717 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4682 AGCGCAATAT
4692 TGCA TGCA TGCA TGCA TGCA TGCA TG
1 TGCA TGCA TGCA TGCA TGCA TGCA TG
4718 ACGTGAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (4 bp):
TGCA
Found at i:7571 original size:6 final size:6
Alignment explanation
Indices: 7560--7585 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7550 TACTAGAGAA
7560 ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT AT
7586 GATATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:10945 original size:15 final size:15
Alignment explanation
Indices: 10909--10939 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10899 ATGAAGAACT
10909 AACTTACCAAATACA
1 AACTTACCAAATACA
10924 AACTTACCAAATACA
1 AACTTACCAAATACA
10939 A
1 A
10940 GTTTACACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
AACTTACCAAATACA
Found at i:24469 original size:14 final size:14
Alignment explanation
Indices: 24414--24472 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
24404 ATTTTTCGTA
24414 TTTTTATAAACTTTT
1 TTTTTATAAA-TTTT
*
24429 TTTTATATATATTTT
1 TTTT-TATAAATTTT
24444 TAGTTTT-T-AATTTT
1 T--TTTTATAAATTTT
24458 TTTTTATAAATTTT
1 TTTTTATAAATTTT
24472 T
1 T
24473 AATTATTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
12 4 0.11
13 1 0.03
14 13 0.35
15 10 0.27
16 6 0.16
17 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTATAAATTTT
Found at i:28539 original size:23 final size:23
Alignment explanation
Indices: 28513--28563 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
28503 AAATTATAAA
28513 TTAATATATCATAAAATCTAT-AT
1 TTAATATATCA-AAAATCTATGAT
* *
28536 TTAATATCTCAAAAATTTATGAT
1 TTAATATATCAAAAATCTATGAT
28559 TTAAT
1 TTAAT
28564 CTTGACTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAATATATCAAAAATCTATGAT
Found at i:31223 original size:12 final size:12
Alignment explanation
Indices: 31206--31232 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31196 TTAGAAATTA
31206 AAAGAGAGAGAG
1 AAAGAGAGAGAG
31218 AAAGAGAGAGAG
1 AAAGAGAGAGAG
31230 AAA
1 AAA
31233 TCGTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (12 bp):
AAAGAGAGAGAG
Found at i:34002 original size:31 final size:31
Alignment explanation
Indices: 33935--34002 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
33925 TTTTTTAGTT
* *
33935 AAATTTGATCCTTAAACTATTTAAAAGAATT
1 AAATTTGATCATTAAACTATTTAAAAGAATC
* * *
33966 GAATTTGATCATTAATCT-TTTAAATAGAGTC
1 AAATTTGATCATTAAACTATTTAAA-AGAATC
33997 AAATTT
1 AAATTT
34003 TTGTTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (31 bp):
AAATTTGATCATTAAACTATTTAAAAGAATC
Found at i:47717 original size:12 final size:12
Alignment explanation
Indices: 47701--47740 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
47691 AAGTGTCTAG
*
47701 GAGAGGGAGAGG
1 GAGAGGGAGAGA
*
47713 GAGAGGGGGAGA
1 GAGAGGGAGAGA
*
47725 GAGAGAGAGAGA
1 GAGAGGGAGAGA
47737 GAGA
1 GAGA
47741 CTGAGGGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (12 bp):
GAGAGGGAGAGA
Done.