Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010693.1 Kokia drynarioides strain JFW-HI SEQ_125640, 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: 70081
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8935 original size:10 final size:10
Alignment explanation
Indices: 8920--8970 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
8910 GTCACTTAAA
8920 AAGAAAAAAT
1 AAGAAAAAAT
8930 AAGAAAAAGA-
1 AAGAAAAA-AT
*
8940 AAGAAAAAGAA
1 AAGAAAAA-AT
*
8951 AAGAAAAAAG
1 AAGAAAAAAT
8961 AA-AAAAAAT
1 AAGAAAAAAT
8970 A
1 A
8971 TGTTTGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
9 7 0.19
10 21 0.57
11 9 0.24
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (10 bp):
AAGAAAAAAT
Found at i:8938 original size:16 final size:15
Alignment explanation
Indices: 8917--8959 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
8907 TTAGTCACTT
8917 AAAAAGAAAAAATAAG
1 AAAAAGAAAAAA-AAG
8933 AAAAAGAAAGAAAAAG
1 AAAAAGAAA-AAAAAG
8949 -AAAAGAAAAAA
1 AAAAAGAAAAAA
8960 GAAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.12
15 8 0.31
16 12 0.46
17 3 0.12
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:8968 original size:16 final size:15
Alignment explanation
Indices: 8917--8968 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
8907 TTAGTCACTT
*
8917 AAAAAGAAAAAATAAG
1 AAAAAGAAAAAA-AAA
*
8933 AAAAAGAAAGAAAAA
1 AAAAAGAAAAAAAAA
*
8948 GAAAAGAAAAAAGAAA
1 AAAAAGAAAAAA-AAA
8964 AAAAA
1 AAAAA
8969 TATGTTTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:13062 original size:17 final size:17
Alignment explanation
Indices: 13036--13072 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13026 CCACCTTGAC
* *
13036 AAGAATTCTCTACGAAT
1 AAGAACTCTCAACGAAT
13053 AAGAACTCTCAACGAAT
1 AAGAACTCTCAACGAAT
13070 AAG
1 AAG
13073 TTCTCCACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (17 bp):
AAGAACTCTCAACGAAT
Found at i:15924 original size:19 final size:19
Alignment explanation
Indices: 15883--15924 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
15873 GGCAAAGGAG
*
15883 AAAAAAATTCACTAATATC
1 AAAAAAATTCAATAATATC
*
15902 AAAAAAATTGAATGAATAT-
1 AAAAAAATTCAAT-AATATC
15921 AAAA
1 AAAA
15925 GGATATGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAAAATTCAATAATATC
Found at i:21760 original size:22 final size:22
Alignment explanation
Indices: 21732--21779 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
21722 GTTTGGTTCG
*
21732 TTTATGTTCACGAACAAGCTTA
1 TTTATGTTCACGAACAAACTTA
*
21754 TTTATGTTCACGAACAAACTTG
1 TTTATGTTCACGAACAAACTTA
21776 TTTA
1 TTTA
21780 AAAGTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (22 bp):
TTTATGTTCACGAACAAACTTA
Found at i:21803 original size:12 final size:12
Alignment explanation
Indices: 21787--21840 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
21777 TTAAAAGTTT
21787 GTTTATTGGCTC
1 GTTTATTGGCTC
* **
21799 ATTTATAAGCTC
1 GTTTATTGGCTC
*
21811 GTTTATTGACTC
1 GTTTATTGGCTC
*
21823 GTTTA-TGACTC
1 GTTTATTGGCTC
21834 GTTTATT
1 GTTTATT
21841 TATTAATGAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 11 0.32
12 23 0.68
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.50
Consensus pattern (12 bp):
GTTTATTGGCTC
Found at i:21814 original size:24 final size:23
Alignment explanation
Indices: 21787--21840 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
21777 TTAAAAGTTT
*
21787 GTTTATTGGCTCATTTATAAGCTC
1 GTTTATTGACTCATTTATAA-CTC
* *
21811 GTTTATTGACTCGTTTATGACTC
1 GTTTATTGACTCATTTATAACTC
21834 GTTTATT
1 GTTTATT
21841 TATTAATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.50
Consensus pattern (23 bp):
GTTTATTGACTCATTTATAACTC
Found at i:21833 original size:11 final size:11
Alignment explanation
Indices: 21808--21839 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
21798 CATTTATAAG
21808 CTCGTTTATTGA
1 CTCGTTTA-TGA
21820 CTCGTTTATGA
1 CTCGTTTATGA
21831 CTCGTTTAT
1 CTCGTTTAT
21840 TTATTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (11 bp):
CTCGTTTATGA
Found at i:21892 original size:4 final size:4
Alignment explanation
Indices: 21883--21911 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
21873 ATATTATCTT
21883 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
21912 TTGTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:22746 original size:22 final size:22
Alignment explanation
Indices: 22721--22765 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
22711 GTATTATCAC
22721 ATATTATTCACAAAAAACTTGT
1 ATATTATTCACAAAAAACTTGT
22743 ATATTATTCACAAAAAACTTGT
1 ATATTATTCACAAAAAACTTGT
22765 A
1 A
22766 AAGCCTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (22 bp):
ATATTATTCACAAAAAACTTGT
Found at i:24930 original size:20 final size:21
Alignment explanation
Indices: 24891--24932 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
24881 CAAACAATGA
*
24891 CAAAAAGTATCGATACCTTTT
1 CAAAAAATATCGATACCTTTT
*
24912 CAAAAAATATCGATACTTTTT
1 CAAAAAATATCGATACCTTTT
24933 ATTAGGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
CAAAAAATATCGATACCTTTT
Found at i:27140 original size:24 final size:24
Alignment explanation
Indices: 27106--27184 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
27096 GGCTCATAAC
27106 AGCTAATCTATCTAGGCCCGTAAG
1 AGCTAATCTATCTAGGCCCGTAAG
* * * **
27130 ATCTAACCTATCTGGGCTTGTAAG
1 AGCTAATCTATCTAGGCCCGTAAG
* * *
27154 AGCTAATTCTATCTAGACTCGTATG
1 AGCTAA-TCTATCTAGGCCCGTAAG
27179 AGCTAA
1 AGCTAA
27185 ATTTCTAGAA
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 24 0.56
25 19 0.44
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (24 bp):
AGCTAATCTATCTAGGCCCGTAAG
Found at i:31687 original size:21 final size:21
Alignment explanation
Indices: 31662--31702 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31652 TTCCTTTTTA
* * *
31662 TGCTTCTTCTTTTTGTCCTTG
1 TGCTTCCTCTTCTTATCCTTG
31683 TGCTTCCTCTTCTTATCCTT
1 TGCTTCCTCTTCTTATCCTT
31703 CGAACCAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.29, G:0.10, T:0.59
Consensus pattern (21 bp):
TGCTTCCTCTTCTTATCCTTG
Found at i:40823 original size:23 final size:20
Alignment explanation
Indices: 40775--40823 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 20
40765 GCTATACATA
*
40775 TAACCAATCATACATCAAAT
1 TAACCAATCATACAACAAAT
40795 TAACCAATCATTCACAACAATAT
1 TAACCAATCA-T-ACAACAA-AT
40818 TAACCA
1 TAACCA
40824 TACAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 1 0.04
22 6 0.24
23 8 0.32
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (20 bp):
TAACCAATCATACAACAAAT
Found at i:42800 original size:55 final size:55
Alignment explanation
Indices: 42703--42819 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 55
42693 ACATATGTTT
* *
42703 CTCAAAATAATATACACACACGGCTTGGAACACTCCCGTGTGTCTGCCAGTGAGC
1 CTCAAAATAATATACACACACGGCTTAGAACACGCCCGTGTGTCTGCCAGTGAGC
* * * * *
42758 CTCAAAATAATATACACACAC-GATCTAGCACACGCCTC-TGTGTTTGCCCGTGTGC
1 CTCAAAATAATATACACACACGGCT-TAGAACACGCC-CGTGTGTCTGCCAGTGAGC
42813 CTCAAAA
1 CTCAAAA
42820 CAGTATGCAG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 2 0.04
55 50 0.94
56 1 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (55 bp):
CTCAAAATAATATACACACACGGCTTAGAACACGCCCGTGTGTCTGCCAGTGAGC
Found at i:46346 original size:21 final size:21
Alignment explanation
Indices: 46320--46365 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
46310 AGACTAAGAC
46320 TAACATAAATCTTCCGAGAAA
1 TAACATAAATCTTCCGAGAAA
*
46341 TAACATAAATCTTCTGAGAAA
1 TAACATAAATCTTCCGAGAAA
46362 -AACA
1 TAACA
46366 CCCTAAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (21 bp):
TAACATAAATCTTCCGAGAAA
Found at i:46834 original size:18 final size:18
Alignment explanation
Indices: 46811--46879 Score: 95
Period size: 18 Copynumber: 3.8 Consensus size: 18
46801 AAATACAGAA
46811 ACAAATTCAGATGCAAGT
1 ACAAATTCAGATGCAAGT
*
46829 ACAAATTCAAATGCAAGT
1 ACAAATTCAGATGCAAGT
* *
46847 ACAGATTTAGATGCAAGT
1 ACAAATTCAGATGCAAGT
46865 A-AAGATTCAGATGCA
1 ACAA-ATTCAGATGCA
46880 GTTATTTTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
17 1 0.02
18 43 0.98
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.23
Consensus pattern (18 bp):
ACAAATTCAGATGCAAGT
Found at i:48061 original size:22 final size:22
Alignment explanation
Indices: 48036--48081 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
48026 TAATGCTTGG
48036 TTTAATTTTCTTTAATTTTATC
1 TTTAATTTTCTTTAATTTTATC
48058 TTTAATTTTCTTTAATTTTATC
1 TTTAATTTTCTTTAATTTTATC
48080 TT
1 TT
48082 GTTTTTGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTAATTTTCTTTAATTTTATC
Found at i:48081 original size:12 final size:10
Alignment explanation
Indices: 48036--48076 Score: 64
Period size: 10 Copynumber: 3.9 Consensus size: 10
48026 TAATGCTTGG
48036 TTTAATTTTC
1 TTTAATTTTC
48046 TTTAATTTTATC
1 TTTAA-TTT-TC
48058 TTTAATTTTC
1 TTTAATTTTC
48068 TTTAATTTT
1 TTTAATTTT
48077 ATCTTGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 16 0.55
11 6 0.21
12 7 0.24
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTAATTTTC
Found at i:50712 original size:16 final size:18
Alignment explanation
Indices: 50675--50712 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50665 ATTTAGATAT
*
50675 GGAAATTTTTCGAGCCAA
1 GGAAATTTTTCGAGCAAA
50693 GGAAATTTTT-GA-CAAA
1 GGAAATTTTTCGAGCAAA
50709 GGAA
1 GGAA
50713 TTATAATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 10 0.53
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (18 bp):
GGAAATTTTTCGAGCAAA
Found at i:65184 original size:44 final size:44
Alignment explanation
Indices: 65122--65206 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
65112 TGATTTCTAC
65122 TTTGTTTGGCTTCACTTGCTCCACTTCTTTGCTATCATCAAGAG
1 TTTGTTTGGCTTCACTTGCTCCACTTCTTTGCTATCATCAAGAG
65166 TTTGTTTGGCTTCACTTGCTCCACTTCTTTGCTATCATCAA
1 TTTGTTTGGCTTCACTTGCTCCACTTCTTTGCTATCATCAA
65207 CAGCAACCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.15, C:0.26, G:0.14, T:0.45
Consensus pattern (44 bp):
TTTGTTTGGCTTCACTTGCTCCACTTCTTTGCTATCATCAAGAG
Done.