Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011707.1 Kokia drynarioides strain JFW-HI SEQ_126701, 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: 74500
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:28837 original size:14 final size:14
Alignment explanation
Indices: 28818--28850 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
28808 ATGGAAGATC
28818 GAGTTTTCTTCTTT
1 GAGTTTTCTTCTTT
28832 GAGTTTTCTTCTTT
1 GAGTTTTCTTCTTT
28846 GAGTT
1 GAGTT
28851 AGTCATTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.12, G:0.18, T:0.61
Consensus pattern (14 bp):
GAGTTTTCTTCTTT
Found at i:39104 original size:134 final size:134
Alignment explanation
Indices: 38864--39131 Score: 520
Period size: 134 Copynumber: 2.0 Consensus size: 134
38854 CTTTCCAGTT
38864 TTTCACTTCTTTTTTTTTCTGTAGGTGCATGAAATTTCAAAGAGAAAAATGGGCACCTCCATTGC
1 TTTCACTTCTTTTTTTTTCTGTAGGTGCATGAAATTTCAAAGAGAAAAATGGGCACCTCCATTGC
38929 TACTCTAAATTCATCTTAAAATTGGGAAAAATTGAGCAAAGACACATAAAAATCAACTAAATCTA
66 TACTCTAAATTCATCTTAAAATTGGGAAAAATTGAGCAAAGACACATAAAAATCAACTAAATCTA
38994 TTTA
131 TTTA
38998 TTTCACTTC-TTTTTTTTCTGTAGGTGCATGAAATTTCAAAGAGAAAAATGGGGCACCTCCATTG
1 TTTCACTTCTTTTTTTTTCTGTAGGTGCATGAAATTTCAAAGAGAAAAAT-GGGCACCTCCATTG
39062 CTACTCTAAATTCATCTTAAAATTGGGAAAAATTGAGCAAAGACACATAAAAATCAACTAAATCT
65 CTACTCTAAATTCATCTTAAAATTGGGAAAAATTGAGCAAAGACACATAAAAATCAACTAAATCT
39127 ATTTA
130 ATTTA
39132 ATTAACTAAC
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
133 40 0.30
134 93 0.70
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (134 bp):
TTTCACTTCTTTTTTTTTCTGTAGGTGCATGAAATTTCAAAGAGAAAAATGGGCACCTCCATTGC
TACTCTAAATTCATCTTAAAATTGGGAAAAATTGAGCAAAGACACATAAAAATCAACTAAATCTA
TTTA
Found at i:45598 original size:29 final size:29
Alignment explanation
Indices: 45535--45599 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
45525 AATTAATAAC
* *
45535 ACAATAAAAATATAATTATAGTATTAAAT
1 ACAATAAAAATATAATCATAGTAATAAAT
* *
45564 AAAATAACAATATAATCATAGTAAT-AAT
1 ACAATAAAAATATAATCATAGTAATAAAT
45592 GACAATAA
1 -ACAATAA
45600 TATTAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (29 bp):
ACAATAAAAATATAATCATAGTAATAAAT
Found at i:45981 original size:13 final size:13
Alignment explanation
Indices: 45963--46018 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
45953 CAAGATAAAT
45963 TAAAAAATAAAAA
1 TAAAAAATAAAAA
*
45976 TAAAAAGCT-AAAA
1 TAAAAA-ATAAAAA
* *
45989 TAAACAAACAAATA
1 TAAA-AAATAAAAA
*
46003 TAAACAATAAAAA
1 TAAAAAATAAAAA
46016 TAA
1 TAA
46019 TTGGGATTAG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:45987 original size:26 final size:26
Alignment explanation
Indices: 45939--46014 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 26
45929 AAATGGCATG
* * *
45939 AAAATAAATAACAACAAGATAAATTAA
1 AAAATAAA-AATAAAAAGATAAAATAA
*
45966 AAAATAAAAATAAAAAGCTAAAATAA
1 AAAATAAAAATAAAAAGATAAAATAA
* * *
45992 ACAAACAAATATAAACA-ATAAAA
1 A-AAATAAAAATAAAAAGATAAAA
46015 ATAATTGGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 20 0.50
27 20 0.50
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.16
Consensus pattern (26 bp):
AAAATAAAAATAAAAAGATAAAATAA
Found at i:46089 original size:25 final size:26
Alignment explanation
Indices: 46061--46109 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
46051 AATAAATAAA
46061 CAAAAAAAATCAA-TAAAT-TAAATGT
1 CAAAAAAAA-CAACTAAATATAAATGT
*
46086 CAAAATAAACAACTAAATATAAAT
1 CAAAAAAAACAACTAAATATAAAT
46110 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.22
Consensus pattern (26 bp):
CAAAAAAAACAACTAAATATAAATGT
Found at i:51005 original size:21 final size:20
Alignment explanation
Indices: 50976--51018 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
50966 ATATATTAGT
*
50976 TAATGAATTAAAATATAAATA
1 TAATCAATTAAAA-ATAAATA
*
50997 TAATCAATTAAAAATCAATA
1 TAATCAATTAAAAATAAATA
51017 TA
1 TA
51019 GGAACATACG
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:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (20 bp):
TAATCAATTAAAAATAAATA
Found at i:51985 original size:20 final size:23
Alignment explanation
Indices: 51946--51986 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
51936 TTTACAAAAC
51946 ATTAGTAGATTAATTATCATTTA
1 ATTAGTAGATTAATTATCATTTA
51969 ATTAGT-GATT-A-TATCATT
1 ATTAGTAGATTAATTATCATT
51987 GTTAAATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 4 0.22
23 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (23 bp):
ATTAGTAGATTAATTATCATTTA
Found at i:52362 original size:17 final size:18
Alignment explanation
Indices: 52342--52382 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
52332 TTTTTTAACC
52342 TCTTTTTCTTTT-TATTT
1 TCTTTTTCTTTTCTATTT
*
52359 TC-TTTTCTTTTCTTTTT
1 TCTTTTTCTTTTCTATTT
52376 TCTTTTT
1 TCTTTTT
52383 TTCTACCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 8 0.38
18 4 0.19
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (18 bp):
TCTTTTTCTTTTCTATTT
Found at i:52364 original size:16 final size:17
Alignment explanation
Indices: 52345--52381 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
52335 TTTAACCTCT
52345 TTTTCTTTT-TATTTTC
1 TTTTCTTTTCTATTTTC
*
52361 TTTTCTTTTCTTTTTTC
1 TTTTCTTTTCTATTTTC
52378 TTTT
1 TTTT
52382 TTTCTACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTCTTTTCTATTTTC
Found at i:55420 original size:37 final size:37
Alignment explanation
Indices: 55368--55442 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
55358 GGCAGATCAA
*
55368 AACCTTCACAGCCAAATACCATAAAATCTAACTATCT
1 AACCTTCACAACCAAATACCATAAAATCTAACTATCT
*
55405 AACCTTTACAACCAAATACCATAAAATCTAACTATCT
1 AACCTTCACAACCAAATACCATAAAATCTAACTATCT
55442 A
1 A
55443 TACAGTCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.25
Consensus pattern (37 bp):
AACCTTCACAACCAAATACCATAAAATCTAACTATCT
Found at i:73844 original size:11 final size:11
Alignment explanation
Indices: 73816--73846 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
73806 GCAAAAAGAA
*
73816 CGAAAAACGAG
1 CGAAAATCGAG
73827 CGAAAATCGAG
1 CGAAAATCGAG
73838 CGAAAATCG
1 CGAAAATCG
73847 GAGCATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.48, C:0.19, G:0.26, T:0.06
Consensus pattern (11 bp):
CGAAAATCGAG
Done.