Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003486.1 Kokia drynarioides strain JFW-HI SEQ_116298, 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: 60259
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:57 original size:20 final size:21
Alignment explanation
Indices: 16--58 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6 TAATTTACTT
16 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
37 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
57 TA
1 TA
59 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:17275 original size:64 final size:64
Alignment explanation
Indices: 17118--17264 Score: 181
Period size: 64 Copynumber: 2.3 Consensus size: 64
17108 CGTTGATGTC
* * * * *
17118 GAGATAATCGTAGTCCACTGCACAAGGGAGAACTAAAATGGTGAGCAGTTTCATTAATGGCGAG
1 GAGATAACCATAGTCCACTGCACAAGGGAGAACTAAAATGGCGAGCAGCTTCATTAATGGAGAG
** * *
17182 GAGATAACCATAGTCTGCTGCACAAGGGAGAACTAAAATGGCGAGTC-GCTTCATTGATAGTAG-
1 GAGATAACCATAGTCCACTGCACAAGGGAGAACTAAAATGGCGAG-CAGCTTCATTAAT-GGAGA
17245 G
64 G
17246 GAGATAACCATAGTCCACT
1 GAGATAACCATAGTCCACT
17265 ACATAGGGGA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 67 0.96
65 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (64 bp):
GAGATAACCATAGTCCACTGCACAAGGGAGAACTAAAATGGCGAGCAGCTTCATTAATGGAGAG
Found at i:22768 original size:22 final size:21
Alignment explanation
Indices: 22743--22797 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
22733 GTGAAATGAT
22743 AGCAAAACAATAAAAAA-ATAGC
1 AGCAAAACAATAAAAAACA-A-C
* *
22765 AGCAAAATAGTAAAAAACAAC
1 AGCAAAACAATAAAAAACAAC
*
22786 AACAAAACAATA
1 AGCAAAACAATA
22798 GAGTTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 10 0.37
22 16 0.59
23 1 0.04
ACGTcount: A:0.69, C:0.15, G:0.07, T:0.09
Consensus pattern (21 bp):
AGCAAAACAATAAAAAACAAC
Found at i:26611 original size:2 final size:2
Alignment explanation
Indices: 26604--26629 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26594 TGCCTAGCGC
26604 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
26630 GCATACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27126 original size:20 final size:20
Alignment explanation
Indices: 27103--27141 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27093 GTTTATATAA
27103 TTTTT-TAAAATATTTTTATG
1 TTTTTATAAAAT-TTTTTATG
*
27123 TTTTTATATAATTTTTTAT
1 TTTTTATAAAATTTTTTAT
27142 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTATAAAATTTTTTATG
Found at i:27377 original size:22 final size:23
Alignment explanation
Indices: 27352--27399 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
27342 AATCATCAAT
27352 ATTTATATATTTT-GTT-AATTTA
1 ATTTATAT-TTTTAGTTAAATTTA
*
27374 ATTTATATTTTTATTTAAATTTA
1 ATTTATATTTTTAGTTAAATTTA
27397 ATT
1 ATT
27400 ATTAACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 10 0.43
23 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTTATATTTTTAGTTAAATTTA
Found at i:49051 original size:29 final size:30
Alignment explanation
Indices: 49019--49081 Score: 119
Period size: 29 Copynumber: 2.1 Consensus size: 30
49009 TTAAAAACTC
49019 AAAATCATTGAAATTATTAAAAAATATA-T
1 AAAATCATTGAAATTATTAAAAAATATACT
49048 AAAATCATTGAAATTATTAAAAAATATACT
1 AAAATCATTGAAATTATTAAAAAATATACT
49078 AAAA
1 AAAA
49082 AATTAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAATCATTGAAATTATTAAAAAATATACT
Found at i:49089 original size:27 final size:28
Alignment explanation
Indices: 49019--49095 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
49009 TTAAAAACTC
*
49019 AAAATCATTGAAATTATTAAAAAATATAT
1 AAAATAATT-AAATTATTAAAAAATATAT
*
49048 AAAATCATTGAAATTATTAAAAAATATACT
1 AAAATAATT-AAATTATTAAAAAATATA-T
*
49078 AAAA-AATT-AATTTTTAAA
1 AAAATAATTAAATTATTAAA
49096 TATTTTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 9 0.20
29 31 0.69
30 5 0.11
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATAATTAAATTATTAAAAAATATAT
Done.