Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015116.1 Kokia drynarioides strain JFW-HI SEQ_130160, 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: 89842
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:97 original size:19 final size:19
Alignment explanation
Indices: 73--111 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
63 AGGAGATTTT
73 TTATTTAATATTAATA-TAA
1 TTATTTAAT-TTAATAGTAA
*
92 TTATTTTATTTAATAGTAA
1 TTATTTAATTTAATAGTAA
111 T
1 T
112 GTAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTTAATTTAATAGTAA
Found at i:102 original size:24 final size:24
Alignment explanation
Indices: 71--120 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
61 GGAGGAGATT
* *
71 TTTTATTTAATATTAATATAATTA
1 TTTTATTTAATAGTAATATAAATA
*
95 TTTTATTTAATAGTAATGTAAATA
1 TTTTATTTAATAGTAATATAAATA
119 TT
1 TT
121 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTATTTAATAGTAATATAAATA
Found at i:126 original size:24 final size:24
Alignment explanation
Indices: 75--128 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
65 GAGATTTTTT
* * **
75 ATTTAATATTAATATAATTATTTT
1 ATTTAATAGTAATATAAATATTAA
*
99 ATTTAATAGTAATGTAAATATTAA
1 ATTTAATAGTAATATAAATATTAA
123 ATTTAA
1 ATTTAA
129 ATTTATTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTTAATAGTAATATAAATATTAA
Found at i:578 original size:21 final size:21
Alignment explanation
Indices: 554--593 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
544 TATTATAACA
554 ATTTAAACCCTATAAATTTTG
1 ATTTAAACCCTATAAATTTTG
* *
575 ATTTAATCCCTATCAATTT
1 ATTTAAACCCTATAAATTT
594 CGAAATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTTAAACCCTATAAATTTTG
Found at i:7239 original size:54 final size:54
Alignment explanation
Indices: 7175--7283 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
7165 ATCAACAAAT
* *
7175 TTAGCCCTTCTGTTTTTTCCTCCATTTTCCTTTGATACCTTCTTCAATCTAAGC
1 TTAGCCCTTCTGTTTTTTCCTCCATTTTCATTTGATACCTGCTTCAATCTAAGC
7229 TTAGCCCTTCTGTTTTTTCCTCCATTTTCATTTGATACCTGCTTCAATCTAAGC
1 TTAGCCCTTCTGTTTTTTCCTCCATTTTCATTTGATACCTGCTTCAATCTAAGC
7283 T
1 T
7284 CTCCCCTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (54 bp):
TTAGCCCTTCTGTTTTTTCCTCCATTTTCATTTGATACCTGCTTCAATCTAAGC
Found at i:38545 original size:18 final size:18
Alignment explanation
Indices: 38522--38556 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38512 CCTTCGATTG
38522 GAAGATAAAGAAGGAGAA
1 GAAGATAAAGAAGGAGAA
* *
38540 GAAGATGATGAAGGAGA
1 GAAGATAAAGAAGGAGA
38557 CCGCGAGGGG
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:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (18 bp):
GAAGATAAAGAAGGAGAA
Found at i:39055 original size:17 final size:17
Alignment explanation
Indices: 39033--39066 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39023 GTCGAAGTTT
39033 TAGGAGGTGAAAAACAG
1 TAGGAGGTGAAAAACAG
39050 TAGGAGGTGAAAAACAG
1 TAGGAGGTGAAAAACAG
39067 AAAACAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.35, T:0.12
Consensus pattern (17 bp):
TAGGAGGTGAAAAACAG
Found at i:42928 original size:18 final size:18
Alignment explanation
Indices: 42905--42939 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42895 TAGTTTATAA
42905 TTTAAAAAAATTAATTAT
1 TTTAAAAAAATTAATTAT
* *
42923 TTTAAATAATTTAATTA
1 TTTAAAAAAATTAATTA
42940 ATATTAAATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAAAATTAATTAT
Found at i:46788 original size:21 final size:21
Alignment explanation
Indices: 46762--46803 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
46752 TTAAATTGAG
46762 TAATGTATGGATGAGACCATT
1 TAATGTATGGATGAGACCATT
*
46783 TAATGTATGTATGAGACCATT
1 TAATGTATGGATGAGACCATT
46804 AAAAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (21 bp):
TAATGTATGGATGAGACCATT
Found at i:46867 original size:18 final size:19
Alignment explanation
Indices: 46844--46882 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
46834 TTTCAGTTAA
46844 AAATTAAAATAA-TTGATT
1 AAATTAAAATAATTTGATT
**
46862 AAATTAATCTAATTTGATT
1 AAATTAAAATAATTTGATT
46881 AA
1 AA
46883 TCGATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
AAATTAAAATAATTTGATT
Found at i:51047 original size:16 final size:15
Alignment explanation
Indices: 51013--51065 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
51003 TACGATGATT
*
51013 ATAAAAAATTTTAATAA
1 ATAAAAAATATT-A-AA
51030 ATAAAAAATATATAAA
1 ATAAAAAATAT-TAAA
*
51046 ATTAATAAATATTAAA
1 A-TAAAAAATATTAAA
51062 ATAA
1 ATAA
51066 TATAATACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 3 0.09
16 8 0.25
17 20 0.62
18 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAAAATATTAAA
Found at i:51055 original size:17 final size:15
Alignment explanation
Indices: 51028--51072 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
51018 AAATTTTAAT
*
51028 AAATAAAAAATATATA
1 AAATAATAAATAT-TA
51044 AAATTAATAAATATTA
1 AAA-TAATAAATATTA
51060 AAATAATATAATA
1 AAATAATA-AATA
51073 CAAATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 5 0.19
16 12 0.46
17 9 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATAAATATTA
Found at i:51055 original size:24 final size:26
Alignment explanation
Indices: 51023--51070 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
51013 ATAAAAAATT
51023 TTAATAAATA-AAAAAT-ATATAAAA
1 TTAATAAATATAAAAATAATATAAAA
*
51047 TTAATAAATATTAAAATAATATAA
1 TTAATAAATATAAAAATAATATAA
51071 TACAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 5 0.24
26 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
TTAATAAATATAAAAATAATATAAAA
Found at i:54813 original size:55 final size:55
Alignment explanation
Indices: 54659--54845 Score: 254
Period size: 55 Copynumber: 3.5 Consensus size: 55
54649 TTACCATAAT
* *
54659 AATCGATTCAAAAGAAACAATATTTCAACATAACAATTGATTTAAACATATAAAT
1 AATCGATTCAAAAGAAACAGTATTTCAACATAACAATTGATTTAAACATATAAAC
* * *
54714 AATCGATTCAAAAG--A-AGTATTCCAACACAACAATTGACTTAAACATATAAAC
1 AATCGATTCAAAAGAAACAGTATTTCAACATAACAATTGATTTAAACATATAAAC
* * * *
54766 AATCAATTCAAAAGAAACAGTATTTTAACATGACAATTGATTTAAACATAAAAAC
1 AATCGATTCAAAAGAAACAGTATTTCAACATAACAATTGATTTAAACATATAAAC
* *
54821 AATCTATCCAAAAGAAACAGTATTT
1 AATCGATTCAAAAGAAACAGTATTT
54846 TTGAGAAATT
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
52 45 0.39
53 1 0.01
54 1 0.01
55 68 0.59
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (55 bp):
AATCGATTCAAAAGAAACAGTATTTCAACATAACAATTGATTTAAACATATAAAC
Found at i:77124 original size:29 final size:29
Alignment explanation
Indices: 77065--77123 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
77055 TTTGTTCTAA
* *
77065 TGTATAATCTTATACATTAATTTTAATTT
1 TGTATAATCTTAAACATGAATTTTAATTT
* *
77094 TGTATAATTTTAAACATGAACTTTTGATTT
1 TGTATAATCTTAAACATGAA-TTTTAATTT
77124 GATTTAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.53
Consensus pattern (29 bp):
TGTATAATCTTAAACATGAATTTTAATTT
Found at i:88636 original size:18 final size:18
Alignment explanation
Indices: 88589--88670 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 18
88579 CGAGCTTAGT
*
88589 AAAAAGTGCGA-CTCTGC
1 AAAATGTGCGAGCTCTGC
*
88606 TCAAA-GTGCGAGCTCTGC
1 -AAAATGTGCGAGCTCTGC
* *
88624 AAAATGTGTGAGCTCAGC
1 AAAATGTGCGAGCTCTGC
* * *
88642 AAAAGGTGCGAGCTTTGG
1 AAAATGTGCGAGCTCTGC
88660 AAAATGTGCGA
1 AAAATGTGCGA
88671 TCAATCAAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
17 9 0.17
18 43 0.83
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (18 bp):
AAAATGTGCGAGCTCTGC
Found at i:88730 original size:33 final size:33
Alignment explanation
Indices: 88606--88733 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 33
88596 GCGACTCTGC
* * *
88606 TCAAAGTGCGAGCTCTGCAAAATGTGTGAGCTCA
1 TCAAAGTGCGAGCTCTGAAAAAGGTGCGAGCT-A
* * * * * *
88640 GCAAAAGGTGCGAGCTTTGGAAAATGTGCGATCAA
1 TC-AAA-GTGCGAGCTCTGAAAAAGGTGCGAGCTA
* * *
88675 TCAAAGTGCGGGCACAGAAAAAGGTGCGAGCTA
1 TCAAAGTGCGAGCTCTGAAAAAGGTGCGAGCTA
*
88708 TCAAAGTGCGAGCTCTGTAAAAGGTG
1 TCAAAGTGCGAGCTCTGAAAAAGGTG
88734 GGAACCTTGC
Statistics
Matches: 73, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
33 42 0.58
34 4 0.05
35 5 0.07
36 22 0.30
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (33 bp):
TCAAAGTGCGAGCTCTGAAAAAGGTGCGAGCTA
Found at i:88910 original size:44 final size:44
Alignment explanation
Indices: 88806--88910 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
88796 CCTGCCGAAA
** ** *
88806 TGCAAGCCAAAATGGAAAATGGTCTAAATACAAGCCTGAGTGGG
1 TGCAAGCCAAAATGGCGAACAGTCTAAATACAAGCCCGAGTGGG
* *
88850 TGCAAGCCAAAGTGGCGAACAGTCTAAATGCAAGCCCGAGTGGG
1 TGCAAGCCAAAATGGCGAACAGTCTAAATACAAGCCCGAGTGGG
*
88894 TGCAAGCTAAAATGGCG
1 TGCAAGCCAAAATGGCG
88911 GACTAAAGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.35, C:0.19, G:0.30, T:0.16
Consensus pattern (44 bp):
TGCAAGCCAAAATGGCGAACAGTCTAAATACAAGCCCGAGTGGG
Done.