Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001314.1 Kokia drynarioides strain JFW-HI SEQ_112733, 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: 29505
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:103 original size:6 final size:6
Alignment explanation
Indices: 92--125 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
82 AGTCGAGCTG
92 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGG
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGG
126 GGGAGACCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:435 original size:3 final size:3
Alignment explanation
Indices: 427--457 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
417 CAAATATTAA
*
427 GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
458 GTGCAGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1548 original size:27 final size:27
Alignment explanation
Indices: 1514--1578 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
1504 CAAAAAATAA
*
1514 AAAAAAAAATTAAAATGTATTAAATTTT
1 AAAAAAAAA-TAAAATGTATTAAAATTT
* * *
1542 AATAAAAAATAACATTTATTAAAATTT
1 AAAAAAAAATAAAATGTATTAAAATTT
1569 AAAAAAAAAT
1 AAAAAAAAAT
1579 TATAAAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 24 0.75
28 8 0.25
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAAAAAATAAAATGTATTAAAATTT
Found at i:7798 original size:19 final size:19
Alignment explanation
Indices: 7776--7836 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
7766 TATTATTACG
7776 ATATAATTATATTAAAAAT
1 ATATAATTATATTAAAAAT
* *
7795 ATATAAATTGCA-ATTCAATAT
1 ATAT-AATT--ATATTAAAAAT
* *
7816 TTATTATTATATTAAAAAT
1 ATATAATTATATTAAAAAT
7835 AT
1 AT
7837 TAAAAAATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
18 1 0.03
19 12 0.39
20 7 0.23
21 10 0.32
22 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (19 bp):
ATATAATTATATTAAAAAT
Found at i:10589 original size:30 final size:31
Alignment explanation
Indices: 10553--10621 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
10543 ATATTTAACG
*
10553 AAACAGTCACTCAACTT-T-GAAAATGTGACA
1 AAACAGTCACTAAACTTATCGAAAA-GTGACA
*
10583 AAACAGTCACTAAAGTTATCGAAAAGTGACA
1 AAACAGTCACTAAACTTATCGAAAAGTGACA
10614 AAACAGTC
1 AAACAGTC
10622 CTCTTAGCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 15 0.43
31 15 0.43
32 5 0.14
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.20
Consensus pattern (31 bp):
AAACAGTCACTAAACTTATCGAAAAGTGACA
Found at i:13024 original size:147 final size:147
Alignment explanation
Indices: 12609--13027 Score: 513
Period size: 147 Copynumber: 2.9 Consensus size: 147
12599 TAGTTCAATC
* * * *
12609 TGGCATTTCATCGAACAATT-TAGATGCAGAAAA-CCTAATTAAGGAAGATAACCTGACATCTCA
1 TGGCATTTCATCGAAC-ATTGGAGATGCTGAAAATGC-AATTAAGGAAGATAACCTGACATCTGA
* * * *
12672 ACTTGAGGAGGAGGTTACTGAAATTGATGATTCTGGGGTTGTGGAAGTTAAAGTTAATGTAGCGA
64 ACTTAAGGAGGAGGTTACTGAAATGGATGATTCTGGGGTTGTGGAAGATAAAGTTAATGTAGCCA
*
12737 ACTCTACAATGGTTCAGTG
129 ACTCGACAATGGTTCAGTG
* ** *
12756 TGGCATTTCATCGAACATTGGAGATGCTGGAGGTGCAATTAAGGAAGATAACCTAACATCTGAAC
1 TGGCATTTCATCGAACATTGGAGATGCTGAAAATGCAATTAAGGAAGATAACCTGACATCTGAAC
** * * * * *
12821 TTAAGGAGGAGGTTA-TCGAAATGGATGATTCTGGGGTCATAGCAGATGAGGCTAATGTAGCCAA
66 TTAAGGAGGAGGTTACT-GAAATGGATGATTCTGGGGTTGTGGAAGATAAAGTTAATGTAGCCAA
* *
12885 GTGGACAATGGTTCAGTG
130 CTCGACAATGGTTCAGTG
* * *
12903 TGGCATTTCATCGAACATTGGAGATGCTGAAAATGCAATCAAGGAAGATAATCTGACGTCTGAAC
1 TGGCATTTCATCGAACATTGGAGATGCTGAAAATGCAATTAAGGAAGATAACCTGACATCTGAAC
* * * *
12968 TTAAGGAGGAGGTCACTGAAAGGGTTGATTCCT-TGGTTGTGGAAGATAAAGTTAATGTAG
66 TTAAGGAGGAGGTTACTGAAATGGATGATT-CTGGGGTTGTGGAAGATAAAGTTAATGTAG
13028 AAAAGAAAGA
Statistics
Matches: 227, Mismatches: 40, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
146 4 0.02
147 219 0.96
148 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.27
Consensus pattern (147 bp):
TGGCATTTCATCGAACATTGGAGATGCTGAAAATGCAATTAAGGAAGATAACCTGACATCTGAAC
TTAAGGAGGAGGTTACTGAAATGGATGATTCTGGGGTTGTGGAAGATAAAGTTAATGTAGCCAAC
TCGACAATGGTTCAGTG
Found at i:25981 original size:21 final size:22
Alignment explanation
Indices: 25939--25982 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
25929 ATGTAGAAGT
* *
25939 ACCATATTGAAAATTTTATTAA
1 ACCACATTGAAAAATTTATTAA
*
25961 ACCACATT-AAAAATTTGTTAA
1 ACCACATTGAAAAATTTATTAA
25982 A
1 A
25983 GTAGACAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (22 bp):
ACCACATTGAAAAATTTATTAA
Found at i:28012 original size:5 final size:5
Alignment explanation
Indices: 28002--28026 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27992 AAGTAAAATT
28002 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
28027 GAGAGTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:28260 original size:29 final size:30
Alignment explanation
Indices: 28206--28263 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
28196 ATCGATATAA
*
28206 TTTTAATACTTTAGAAATATAATTAAAATG
1 TTTTAAAACTTTAGAAATATAATTAAAATG
*
28236 TTTTAAAATTTTA-AAAT-TAATTTAAAAT
1 TTTTAAAACTTTAGAAATATAA-TTAAAAT
28264 AAAAATCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 11 0.44
30 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTTAAAACTTTAGAAATATAATTAAAATG
Found at i:28817 original size:2 final size:2
Alignment explanation
Indices: 28810--28837 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28800 CTAAAAATTA
28810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28838 GATCCATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.