Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002028.1 Kokia drynarioides strain JFW-HI SEQ_113909, 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: 47361
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 316 characters in sequence are not A, C, G, or T
Found at i:21039 original size:23 final size:23
Alignment explanation
Indices: 21013--21058 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
21003 GAACCAATCA
* *
21013 AAAATCTTATTTGGAGTAAATTT
1 AAAAGCTTATTTAGAGTAAATTT
21036 AAAAGCTTATTTAGAGTAAATTT
1 AAAAGCTTATTTAGAGTAAATTT
21059 GGATATTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (23 bp):
AAAAGCTTATTTAGAGTAAATTT
Found at i:29732 original size:18 final size:18
Alignment explanation
Indices: 29693--29742 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
29683 TGCTTGATAT
29693 TGAAATGGCAAA-G-GATG
1 TGAAATGG-AAATGAGATG
*
29710 AGAAATGGAAATGAGATG
1 TGAAATGGAAATGAGATG
29728 TGAAATGGAATATGA
1 TGAAATGGAA-ATGA
29743 AATGGTAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 8 0.29
18 13 0.46
19 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.32, T:0.20
Consensus pattern (18 bp):
TGAAATGGAAATGAGATG
Found at i:29941 original size:24 final size:23
Alignment explanation
Indices: 29914--29958 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29904 GAATGATGAA
* *
29914 ATTTATATAACATTACTTATTTGC
1 ATTTATACAAC-TTAATTATTTGC
*
29938 ATTTTTACAACTTAATTATTT
1 ATTTATACAACTTAATTATTT
29959 ATATCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTATACAACTTAATTATTTGC
Found at i:31278 original size:20 final size:22
Alignment explanation
Indices: 31250--31294 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
31240 TTAATCTATT
31250 AAAAAATTA-TATAA-AC-ATA
1 AAAAAATTATTATAACACAATA
31269 AAAAACATTATTATAACACAATA
1 AAAAA-ATTATTATAACACAATA
31292 AAA
1 AAA
31295 TGCTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
20 4 0.18
21 5 0.23
22 2 0.09
23 6 0.27
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAATTATTATAACACAATA
Found at i:36805 original size:18 final size:18
Alignment explanation
Indices: 36784--36818 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36774 AAATTATTAT
*
36784 AATTTTTAAAATTTTCAA
1 AATTCTTAAAATTTTCAA
*
36802 AATTCTTATAATTTTCA
1 AATTCTTAAAATTTTCA
36819 CAAAATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTCTTAAAATTTTCAA
Found at i:37656 original size:20 final size:20
Alignment explanation
Indices: 37607--37662 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
37597 AACCCATCAC
37607 AAGCCC-AATACCTAAA--A
1 AAGCCCAAATACCTAAACCA
* * *
37624 AAACCCAATTACCTAAACCT
1 AAGCCCAAATACCTAAACCA
*
37644 AAGCCCAAATACCAAAACC
1 AAGCCCAAATACCTAAACC
37663 CCATTACTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
20 16 0.53
ACGTcount: A:0.50, C:0.34, G:0.04, T:0.12
Consensus pattern (20 bp):
AAGCCCAAATACCTAAACCA
Found at i:40131 original size:219 final size:219
Alignment explanation
Indices: 39752--40173 Score: 763
Period size: 219 Copynumber: 1.9 Consensus size: 219
39742 AGGTTTAAAT
* *
39752 AATTTAATTTGTAATTCCCTATCCAGCCTAGAAGATATTACCGAATTTAAAATGTCACAATCGCA
1 AATTTAATTTGTAATCCCCTACCCAGCCTAGAAGATATTACCGAATTTAAAATGTCACAATCGCA
39817 ATTTCACCCTAAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATAAATTAAGACATA
66 ATTTCACCCTAAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATAAATTAAGACATA
*
39882 GTAAAAAAGTTAATTCCACACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
131 GGAAAAAAGTTAATTCCACACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
39947 TATACAAAAAAAGTTAATTTTTTA
196 TATACAAAAAAAGTTAATTTTTTA
* *
39971 AATTTAATTTGTAATCCCCTACCCAGCCTAGAAGATATTACCGAATTTAGAATGTCACTATCGCA
1 AATTTAATTTGTAATCCCCTACCCAGCCTAGAAGATATTACCGAATTTAAAATGTCACAATCGCA
* *
40036 ATTTCACCCTCAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATGAATTAAGACATA
66 ATTTCACCCTAAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATAAATTAAGACATA
*
40101 GGAAAAAAGTTAATTCCCCACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
131 GGAAAAAAGTTAATTCCACACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
*
40166 TATGCAAA
196 TATACAAA
40174 TATCCAAAAT
Statistics
Matches: 194, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
219 194 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (219 bp):
AATTTAATTTGTAATCCCCTACCCAGCCTAGAAGATATTACCGAATTTAAAATGTCACAATCGCA
ATTTCACCCTAAAAAACCATTTAAAACAGTTATATAATTTAATTTTGTAAATAAATTAAGACATA
GGAAAAAAGTTAATTCCACACATTTCTGAATAACTTCAAACTTACAAATTATCAATCAAATGCCT
TATACAAAAAAAGTTAATTTTTTA
Done.