Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010063.1 Kokia drynarioides strain JFW-HI SEQ_124837, 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: 10761
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1792 original size:49 final size:49
Alignment explanation
Indices: 1672--2107 Score: 278
Period size: 49 Copynumber: 8.9 Consensus size: 49
1662 CTACAGGTCT
* * * *
1672 CAGTACCACA-AAACATGAAA-GGAAAGATTTAAGCCGCAATGGCAAATC
1 CAGTACCACAGAGACAT-AAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* ** * * *
1720 CAGTACCA-AGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACTG
1 CAGTACCACAG-AGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAA-TC
* * *
1770 TA-TACCTCAGA-AGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
1 CAGTACCACAGAGA-CATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * *
1818 CAGTACCACAGAGACATAAAGGGAAAAATCTAAGTCGCAACGACGAATT
1 CAGTACCACAGAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * * *
1867 TAGTACTGTAAAGATACA-AAAGGGAGAGATTTAAG-CTGCAACAGCGAATC
1 CAGTAC--CACAGAGACATAAAGGGAAAGATTTAAGTC-GCAACGGCGAATC
* * * *
1917 CAGTACCA-AGAAGATATAAAGGGAAGGGTTTAAGTCGCAACGACGAA-C
1 CAGTACCACAG-AGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * ** * * *
1965 CTAGTACCTCAGAGACATGAAGGGAAGGATCTAAACCGTAACCGCGGATC
1 C-AGTACCACAGAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * * * * *
2015 TAATACCACAAAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATC
1 CAGTACCACAGAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * * *
2064 TAGTACCGCAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGC
1 CAGTACCACAGAGACATAAAGGGAAAGATTTAAGTCGCAACGGC
2108 AAACCTTGTA
Statistics
Matches: 297, Mismatches: 74, Indels: 33
0.74 0.18 0.08
Matches are distributed among these distances:
47 3 0.01
48 18 0.06
49 231 0.78
50 38 0.13
51 7 0.02
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (49 bp):
CAGTACCACAGAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
Found at i:1970 original size:99 final size:98
Alignment explanation
Indices: 1692--2107 Score: 333
Period size: 98 Copynumber: 4.2 Consensus size: 98
1682 AAACATGAAA
* * **
1692 GGAAAGATTTAAGCCGCAATGGCAAATCCAGTACCAAGAAGATATGGAGGGAAAGGTTTAAGTCG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAAGAAGATATAAAGGGAAAGGTTTAAGTCG
** * *
1757 CAACGGTGAACTGTA-TACCTCAGAAGCATAAAG
66 CAACGACGAAC-CTAGTACCTAAGAAGCATAAAG
* ** *
1790 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAG-AGACATAAAGGGAAAAATCTAAGTC
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA-AGAAGATATAAAGGGAAAGGTTTAAGTC
** *
1854 GCAACGACGAATTTAGTACTGTAAAGATA-CA-AAAG
65 GCAACGACGAACCTAGTAC-CT-AAGA-AGCATAAAG
* * * *
1889 GGAGAGATTTAAGCTGCAACAGCGAATCCAGTACCAAGAAGATATAAAGGGAAGGGTTTAAGTCG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAAGAAGATATAAAGGGAAAGGTTTAAGTCG
* *
1954 CAACGACGAACCTAGTACCTCAG-AGACATGAAG
66 CAACGACGAACCTAGTACCTAAGAAG-CATAAAG
* * * * * * * * * * * * *
1987 GGAAGGATCTAAACCGTAACCGCGGATCTAATACCACA-AAGACATGAAGGGAAAGATCTAAGCC
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA-AGAAGATATAAAGGGAAAGGTTTAAGTC
* * ** *
2051 GCAACGACGGATCTAGTACCGCA-AAGACACAAAG
65 GCAACGACGAACCTAGTACCTAAGAAG-CATAAAG
* * *
2085 GGAAGGGTTTAAGTCGCAACGGC
1 GGAAAGATTTAAGCCGCAACGGC
2108 AAACCTTGTA
Statistics
Matches: 253, Mismatches: 54, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
95 1 0.00
97 6 0.02
98 162 0.64
99 78 0.31
100 5 0.02
101 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (98 bp):
GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAAGAAGATATAAAGGGAAAGGTTTAAGTCG
CAACGACGAACCTAGTACCTAAGAAGCATAAAG
Found at i:2039 original size:197 final size:196
Alignment explanation
Indices: 1696--2110 Score: 494
Period size: 197 Copynumber: 2.1 Consensus size: 196
1686 ATGAAAGGAA
** **
1696 AGATTTAAGCCGCAATGGCAAATCCAGTACCAAGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
1 AGATTTAAGCCGCAACAGCAAATCCAGTACCAAGAAGATATAAAGGGAAAGGTTTAAGTCGCAAC
** * * * * *
1761 GGTGAACTGTATACCTCAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
66 GACGAACTCTATACCTCAGAAGCATAAAGGGAAAGATCTAAACCGCAACCGCGAATCCAATACCA
* * * * * *
1826 CAGAGACATAAAGGGAAAAATCTAAGTCGCAACGACGAATTTAGTACTGTAAAGATACAAAAGGG
131 CAAAGACATAAAGGGAAAAATCTAAGCCGCAACGACGAATCTAGTACCGCAAAGACAC-AAAGGG
1891 AG
195 AG
* * *
1893 AGATTTAAGCTGCAACAGCGAATCCAGTACCAAGAAGATATAAAGGGAAGGGTTTAAGTCGCAAC
1 AGATTTAAGCCGCAACAGCAAATCCAGTACCAAGAAGATATAAAGGGAAAGGTTTAAGTCGCAAC
* * * * *
1958 GACGAAC-CTAGTACCTCAG-AGACATGAAGGGAAGGATCTAAACCGTAACCGCGGATCTAATAC
66 GACGAACTCTA-TACCTCAGAAG-CATAAAGGGAAAGATCTAAACCGCAACCGCGAATCCAATAC
* * *
2021 CACAAAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCGCAAAGACACAAAGG
129 CACAAAGACATAAAGGGAAAAATCTAAGCCGCAACGACGAATCTAGTACCGCAAAGACACAAAGG
2086 GA-
194 GAG
* * *
2088 AGGGTTTAAGTCGCAACGGCAAA
1 A-GATTTAAGCCGCAACAGCAAA
2111 CCTTGTACCT
Statistics
Matches: 182, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
195 1 0.01
196 27 0.15
197 154 0.85
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (196 bp):
AGATTTAAGCCGCAACAGCAAATCCAGTACCAAGAAGATATAAAGGGAAAGGTTTAAGTCGCAAC
GACGAACTCTATACCTCAGAAGCATAAAGGGAAAGATCTAAACCGCAACCGCGAATCCAATACCA
CAAAGACATAAAGGGAAAAATCTAAGCCGCAACGACGAATCTAGTACCGCAAAGACACAAAGGGA
G
Found at i:2876 original size:17 final size:17
Alignment explanation
Indices: 2854--2904 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
2844 AACTTTTCTT
2854 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
* *
2871 TTAAGTTTAAATGTAAT
1 TTAAGTTTAAATTTAAA
2888 TTGAA-TTTAAATTTAAA
1 TT-AAGTTTAAATTTAAA
2905 AATCCAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:2894 original size:6 final size:6
Alignment explanation
Indices: 2853--2904 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
2843 AAACTTTTCT
* * * *
2853 TTTAAG TTTAAA TTTAAA -TTAAG TTTAAA TGT-AA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2899 TTTAAA
1 TTTAAA
2905 AATCCAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
5 8 0.21
6 30 0.79
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:3724 original size:23 final size:20
Alignment explanation
Indices: 3697--3747 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 20
3687 AAATGGTAGC
*
3697 AATAAATATCATTAATAAATATT
1 AATAAAAAT-ATTAAT-AATA-T
3720 AATAAAAATATTAATAATAT
1 AATAAAAATATTAATAATAT
3740 AATAAAAA
1 AATAAAAA
3748 AAGAAAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.33
21 4 0.15
22 6 0.22
23 8 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAAATATTAATAATAT
Found at i:3748 original size:22 final size:22
Alignment explanation
Indices: 3697--3749 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
3687 AAATGGTAGC
* *
3697 AATAAATATCATTAATAAATATT
1 AATAAAAAT-ATTAATAAATAAT
3720 AATAAAAATATTAATAATATAAT
1 AATAAAAATATTAATAA-ATAAT
3743 AA-AAAAA
1 AATAAAAA
3750 GAAAGTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAAAAATATTAATAAATAAT
Found at i:4891 original size:58 final size:58
Alignment explanation
Indices: 4829--5107 Score: 221
Period size: 59 Copynumber: 4.8 Consensus size: 58
4819 TAAACTTTCC
*
4829 AAAATTCCATTTTTGACCTTGATTTTTGT-AAAATTA-TATTTTTACCCTCGAACTTCTA
1 AAAATTCCATTTTTGACCTTGATTTTT-TCAAAATTACCA-TTTTACCCTCGAACTTCTA
* * * *
4887 AAAATTCCATTTTT-ACCTTGTTTTTTTCCAAAAATTACTATTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTGACCTTGATTTTTT-C-AAAATTACCATTTTACCCTCGAACTTCTA
* ** * * * *
4946 AAGATTCCATCATTGA--TTCCCATTTTTCCAAAAATTACCATTTTACCCACTAACTT-TCA
1 AAAATTCCATTTTTGACCTT--GATTTTTTC-AAAATTACCATTTTACCCTCGAACTTCT-A
** * *
5005 AAAATTCCATTTTTGACCCCGATTTTTTCAAAATTACCATTTTACCCTTGGA-TGTCTA
1 AAAATTCCATTTTTGACCTTGATTTTTTCAAAATTACCATTTTACCCTCGAACT-TCTA
** *** *
5063 AAAATTCCATTTTAAACCTTGAACCTTCCGAAAATTACCATTTTA
1 AAAATTCCATTTTTGACCTTGATTTTTTC-AAAATTACCATTTTA
5108 TTCCCGAAGC
Statistics
Matches: 176, Mismatches: 32, Indels: 25
0.76 0.14 0.11
Matches are distributed among these distances:
56 1 0.01
57 12 0.07
58 58 0.33
59 97 0.55
60 8 0.05
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTTGATTTTTTCAAAATTACCATTTTACCCTCGAACTTCTA
Found at i:5010 original size:29 final size:29
Alignment explanation
Indices: 4974--5051 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
4964 CCCATTTTTC
*
4974 CAAAAATTACCATTTTACCCACTA-ACTTT
1 CAAAAATTACCATTTTACCC-CGATACTTT
**
5003 CAAAAATT-CCATTTTTGACCCCGATTTTTT
1 CAAAAATTACCA-TTTT-ACCCCGATACTTT
5033 C-AAAATTACCATTTTACCC
1 CAAAAATTACCATTTTACCC
5052 TTGGATGTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
28 7 0.17
29 24 0.57
30 11 0.26
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCGATACTTT
Found at i:5129 original size:29 final size:28
Alignment explanation
Indices: 5093--5153 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
5083 GAACCTTCCG
*
5093 AAAATTACCATTTTATTCCCGAAGCATCC
1 AAAATTACCATTTTACTCCC-AAGCATCC
* * *
5122 AAAATTACCGTTTTACTCTCAAGCATCT
1 AAAATTACCATTTTACTCCCAAGCATCC
5150 AAAA
1 AAAA
5154 ATCATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.31
Consensus pattern (28 bp):
AAAATTACCATTTTACTCCCAAGCATCC
Found at i:6957 original size:21 final size:22
Alignment explanation
Indices: 6933--6974 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
6923 GTGTTATCTT
*
6933 TTGTATTGCTTGTTG-GAATTG
1 TTGTATTCCTTGTTGTGAATTG
*
6954 TTGTTTTCCTTGTTGTGAATT
1 TTGTATTCCTTGTTGTGAATT
6975 TTAGTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.12, C:0.07, G:0.24, T:0.57
Consensus pattern (22 bp):
TTGTATTCCTTGTTGTGAATTG
Found at i:10278 original size:17 final size:17
Alignment explanation
Indices: 10246--10279 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10236 GAAAAAATTC
*
10246 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
*
10263 ATTTAAATATTGTTTAA
1 ATTTAAATATTATTTAA
10280 TCATGTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Done.