Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011987.1 Kokia drynarioides strain JFW-HI SEQ_126985, 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: 6906
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:2727 original size:49 final size:49
Alignment explanation
Indices: 2553--3125 Score: 343
Period size: 49 Copynumber: 11.6 Consensus size: 49
2543 CTACAGGTTT
* * * * *
2553 CAGTACCACGAA-ACATGAAGGAAAAGATTTAAGTCGTAACGGCGAATC
1 CAGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
2601 CAGTACCA-AGAAGATATGGAA-GGAAAGGTTTAAGTCGCAACGGTGAA-C
1 CAGTACCACA-AAGACAT-AAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* ** * * *
2649 CGTGTACCTTAGAAGACACAAAGGGAAAGATTTAAGCCGCAATGGAGAATC
1 C-AGTACCACA-AAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *
2700 CAGTACCACAAAGACATAAAGGGAAAGATCTAAGCCGCAACGGCGGATC
1 CAGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * *
2749 CAGTACCACAAAGAAATAAAGGGAAGGGTTTAAGTCGCAATGGTGAA-C
1 CAGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
** ** * *
2797 CTAGTACCTTAGGGACATAAAGGGAAAGATCTAAGCCGCAACGGCGGATC
1 C-AGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
** * * * * * * **
2847 TTGTACCACGAAGACA-CAAGGGAAAGGTTTAAGTCGTAATGATGAA-C
1 CAGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * * *
2894 CTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGCCGCAACGGTGGATN
1 C-AGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* ** * * * * * *
2944 TAGTACCGGAAAGACACAAAGGGAAGGGTTTAAGTCGTAACGGTGAA-C
1 CAGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * **
2992 CTTGTACCTCAAAAACATGAAGGGAAAGATCTAAGCCAAAACGGCGAATC
1 C-AGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *
3042 CAGTACCGCAAAGAAACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
1 CAGTA-C-C------ACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
3099 CAGTACCACGAAGGCACAAAGGGAAAG
1 CAGTACCACAAAGACATAAAGGGAAAG
3126 GCACCTTAGA
Statistics
Matches: 393, Mismatches: 110, Indels: 43
0.72 0.20 0.08
Matches are distributed among these distances:
47 1 0.00
48 46 0.12
49 258 0.66
50 42 0.11
51 3 0.01
55 1 0.00
56 1 0.00
57 41 0.10
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.15
Consensus pattern (49 bp):
CAGTACCACAAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:2814 original size:98 final size:97
Alignment explanation
Indices: 2668--3057 Score: 449
Period size: 98 Copynumber: 4.0 Consensus size: 97
2658 TAGAAGACAC
* * * *
2668 AAAGGGAAAGATTTAAGCCGCAATGGAGAATCC-AGTACCACAAAGACATAAAGGGAAAGATCTA
1 AAAGGGAAAGGTTTAAGTCGCAATGGTGAA-CCTAGTACCTCAAAGACATAAAGGGAAAGATCTA
2732 AGCCGCAACGGCGGATCCAGTACCACAAAGAAA
65 AGCCGCAACGGCGGATCCAGTACCACAAAGAAA
* * **
2765 TAAAGGGAAGGGTTTAAGTCGCAATGGTGAACCTAGTACCTTAGGGACATAAAGGGAAAGATCTA
1 -AAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTAGTACCTCAAAGACATAAAGGGAAAGATCTA
** * *
2830 AGCCGCAACGGCGGATCTTGTACCACGAAGACA
65 AGCCGCAACGGCGGATCCAGTACCACAAAGAAA
* * * * *
2863 CAAGGGAAAGGTTTAAGTCGTAATGATGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAA
1 AAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTAGTACCTCAAAGACATAAAGGGAAAGATCTAA
* ** ** *
2928 GCCGCAACGGTGGATNTAGTACCGGAAAGACAC
66 GCCGCAACGGCGGATCCAGTACCACAAAGA-AA
* * * * * *
2961 AAAGGGAAGGGTTTAAGTCGTAACGGTGAACCTTGTACCTCAAAAACATGAAGGGAAAGATCTAA
1 AAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTAGTACCTCAAAGACATAAAGGGAAAGATCTAA
** * *
3026 GCCAAAACGGCGAATCCAGTACCGCAAAGAAA
66 GCCGCAACGGCGGATCCAGTACCACAAAGAAA
3058 CGAAGACATG
Statistics
Matches: 248, Mismatches: 42, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
97 85 0.34
98 163 0.66
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (97 bp):
AAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTAGTACCTCAAAGACATAAAGGGAAAGATCTAA
GCCGCAACGGCGGATCCAGTACCACAAAGAAA
Found at i:2923 original size:195 final size:196
Alignment explanation
Indices: 2660--3125 Score: 524
Period size: 195 Copynumber: 2.3 Consensus size: 196
2650 GTGTACCTTA
2660 GAAGACACAAAGGGAAAGATTTAAGCCGCAATGGAGAATCCAGTACCACAAAGACATAAAGGGAA
1 GAAGACACAAAGGGAAAGATTTAAGCCGCAATGGAGAATCCAGTACCACAAAGACATAAAGGGAA
* *
2725 AGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGAAATAAAGGGAAGGGTTTAAGTCGCAAT
66 AGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGAAACAAAGGGAAGGGTTTAAGTCGCAAC
* *** **
2790 GGTGAACCTAGTACCTTAGGGACATAAAGGGAAAGATCTAAGCCGCAACGGCGGATCTTGTACCA
131 GGTGAACCTAGTACCTCAAAAACATAAAGGGAAAGATCTAAGCCAAAACGGCGGATCTTGTACCA
2855 C
196 C
* * * * * *
2856 GAAGACAC-AAGGGAAAGGTTTAAGTCGTAAT-GATGAA-CCTAGTACCTCAGAGACATGAAGGG
1 GAAGACACAAAGGGAAAGATTTAAGCCGCAATGGA-GAATCC-AGTACCACAAAGACATAAAGGG
* ** ** * *
2918 AAAGATCTAAGCCGCAACGGTGGATNTAGTACCGGAAAGACACAAAGGGAAGGGTTTAAGTCGTA
64 AAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGAAACAAAGGGAAGGGTTTAAGTCGCA
* * * **
2983 ACGGTGAACCTTGTACCTCAAAAACATGAAGGGAAAGATCTAAGCCAAAACGGCGAATCCAGTAC
129 ACGGTGAACCTAGTACCTCAAAAACATAAAGGGAAAGATCTAAGCCAAAACGGCGGATCTTGTA-
3048 CGCAAAGAAAC
193 C-C------AC
** * * * * *
3059 GAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGGCACAAAGGGAA
1 GAAGACACAAAGGGAAAGATTTAAGCCGCAATGGAGAATCCAGTACCACAAAGACATAAAGGGAA
3124 AG
66 AG
3126 GCACCTTAGA
Statistics
Matches: 219, Mismatches: 38, Indels: 18
0.80 0.14 0.07
Matches are distributed among these distances:
194 4 0.02
195 151 0.69
196 9 0.04
197 1 0.00
203 9 0.04
204 42 0.19
205 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (196 bp):
GAAGACACAAAGGGAAAGATTTAAGCCGCAATGGAGAATCCAGTACCACAAAGACATAAAGGGAA
AGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGAAACAAAGGGAAGGGTTTAAGTCGCAAC
GGTGAACCTAGTACCTCAAAAACATAAAGGGAAAGATCTAAGCCAAAACGGCGGATCTTGTACCA
C
Found at i:3747 original size:53 final size:52
Alignment explanation
Indices: 3667--3773 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 52
3657 TGAAGAGATG
3667 AGACCCGACAAAATTGGGCATCCTTTTGGTCTTTGCTCCATTCCTGTTACAC
1 AGACCCGACAAAATTGGGCATCCTTTTGGTCTTTGCTCCATTCCTGTTACAC
*
3719 NAGACCCGACAAAATTTGGCATCCTTTTGGTCTTTGCTCCATTCCTGTTACAC
1 -AGACCCGACAAAATTGGGCATCCTTTTGGTCTTTGCTCCATTCCTGTTACAC
3772 AG
1 AG
3774 CAACGAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 2 0.04
53 51 0.96
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.33
Consensus pattern (52 bp):
AGACCCGACAAAATTGGGCATCCTTTTGGTCTTTGCTCCATTCCTGTTACAC
Found at i:3866 original size:17 final size:16
Alignment explanation
Indices: 3846--3900 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
3836 TTAAACCAAG
3846 TTTAGAATTATTTTAAA
1 TTTA-AATTATTTTAAA
* *
3863 TTTAAATT-TATTAAG
1 TTTAAATTATTTTAAA
3878 TTTAAATTTATTTTAAA
1 TTTAAA-TTATTTTAAA
3895 TTTAAA
1 TTTAAA
3901 ATTTGAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 11 0.34
16 6 0.19
17 15 0.47
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:3881 original size:15 final size:15
Alignment explanation
Indices: 3843--3889 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
3833 AAATTAAACC
*
3843 AAGTTTAGAATTATTTT
1 AAGTTTA-AATT-TATT
*
3860 AAATTTAAATTTATT
1 AAGTTTAAATTTATT
3875 AAGTTTAAATTTATT
1 AAGTTTAAATTTATT
3890 TTAAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 17 0.63
16 4 0.15
17 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
AAGTTTAAATTTATT
Found at i:6003 original size:29 final size:28
Alignment explanation
Indices: 5962--6298 Score: 141
Period size: 29 Copynumber: 11.5 Consensus size: 28
5952 AAATTGTACA
*
5962 AAAATTACATTTTTACCCTCAAACTTTCC
1 AAAATTCCATTTTTACCC-CAAACTTTCC
* ** **
5991 AAAATTCCATTTTCGACCTTAAACTTTTTG
1 AAAATTCCATTTT-TACCCCAAAC-TTTCC
** * *
6021 AAAATTATATTCTTACCCCTAAATTTTCC
1 AAAATTCCATTTTTACCCC-AAACTTTCC
* **
6050 AAAATTCCATTTTTGACCCCGATTTTTCC
1 AAAATTCCATTTTT-ACCCCAAACTTTCC
*
6079 AAAAATTACATTTTTA-CCCATAACTTTCC
1 -AAAATTCCATTTTTACCCCA-AACTTTCC
** * *
6108 AAAATTCCATTTTTGACCTTAATCTCTCC
1 AAAATTCCATTTTT-ACCCCAAACTTTCC
*
6137 AAAAATT--ATCGTTTTACCCCTGAAC-TTCC
1 -AAAATTCCAT--TTTTACCCC-AAACTTTCC
* **
6166 AAAAATTCCATTTTTGACCCCGATTTTTCC
1 -AAAATTCCATTTTT-ACCCCAAACTTTCC
* * *
6196 AAAATTTTCA-TTTTACTCTCGAAC-TTCC
1 AAAA-TTCCATTTTTAC-CCCAAACTTTCC
* * **
6224 ACAAATTCTATTTTTTACCCTAATTTTTCC
1 A-AAATTCCA-TTTTTACCCCAAACTTTCC
6254 AAAAATTACCA-TTTTACCCCCCAAAC-TTCC
1 -AAAATT-CCATTTTTA--CCCCAAACTTTCC
*
6284 AAAAAATCCATTTTT
1 -AAAATTCCATTTTT
6299 TAACCTCGAT
Statistics
Matches: 229, Mismatches: 52, Indels: 53
0.69 0.16 0.16
Matches are distributed among these distances:
28 28 0.12
29 98 0.43
30 93 0.41
31 10 0.04
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCAAACTTTCC
Found at i:6054 original size:59 final size:59
Alignment explanation
Indices: 5951--6298 Score: 238
Period size: 59 Copynumber: 5.9 Consensus size: 59
5941 GTTCTTGGTC
* * *
5951 TAAATTGTACAAAAATTACATTTTTA-CCCTCAAACTTTCCAAAATTCCATTTTCGACCT
1 TAAATTTTTCAAAAATTACATTTTTACCCCT-AAACTTTCCAAAATTCCATTTTTGACCT
* * * *
6010 TAAACTTTTT-GAAAATTATATTCTTACCCCTAAATTTTCCAAAATTCCATTTTTGACC-
1 TAAA-TTTTTCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCT
*** *
6068 CCGATTTTTCCAAAAATTACATTTTTACCCAT-AACTTTCCAAAATTCCATTTTTGACCT
1 TAAATTTTT-CAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCT
* * * *
6127 T-AATCTCTCCAAAAATTATC-GTTTTACCCCTGAAC-TTCCAAAAATTCCATTTTTGACC-
1 TAAAT-TTTTCAAAAATTA-CATTTTTACCCCTAAACTTTCC-AAAATTCCATTTTTGACCT
*** * * * * * * *
6185 CCGATTTTTCCAAAATTTTCA-TTTTA-CTCTCGAAC-TTCCACAAATTCTATTTTTTACCC
1 TAAATTTTT-CAAAAATTACATTTTTACCCCT-AAACTTTCCA-AAATTCCATTTTTGACCT
* *
6244 T-AATTTTTCCAAAAATTACCA-TTTTACCCCCCAAAC-TTCCAAAAAATCCATTTTT
1 TAAATTTTT-CAAAAATTA-CATTTTTA-CCCCTAAACTTTCC-AAAATTCCATTTTT
6299 TAACCTCGAT
Statistics
Matches: 231, Mismatches: 39, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
57 9 0.04
58 95 0.41
59 99 0.43
60 25 0.11
61 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (59 bp):
TAAATTTTTCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCT
Found at i:6171 original size:117 final size:116
Alignment explanation
Indices: 5960--6328 Score: 406
Period size: 117 Copynumber: 3.1 Consensus size: 116
5950 CTAAATTGTA
* * ***
5960 CAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTCGACCTTAAACTTTTTGAAAA
1 CAAAAATTACATTTTTACCCT--AACTTTCCAAAATTCCATTTTTGACCTTAATCTTTCCAAAAA
*
6025 TTAT-ATTCTTACCCCTAAATTTTCC-AAAATTCCATTTTTGACCCCGATTTTTC
64 TTATCATT-TTACCCCTAAA-CTTCCAAAAATTCCATTTTTGACCCCGATTTTTC
*
6078 CAAAAATTACATTTTTACCCATAACTTTCCAAAATTCCATTTTTGACCTTAATCTCTCCAAAAAT
1 CAAAAATTACATTTTTACCC-TAACTTTCCAAAATTCCATTTTTGACCTTAATCTTTCCAAAAAT
* *
6143 TATCGTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTC
65 TATCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTC
* * * * * * *
6195 CAAAATTTTCA-TTTTACTCTCGAAC-TTCCACAAATTCTATTTTTTACCCTAATTTTTCCAAAA
1 CAAAAATTACATTTTTAC-C-CTAACTTTCCA-AAATTCCATTTTTGACCTTAATCTTTCCAAAA
* * * * *
6258 ATTACCATTTTACCCCCCAAACTTCCAAAAAATCCATTTTTTAACCTCGA-TTTTC
63 ATTATCATTTTA-CCCCTAAACTTCCAAAAATTCCA-TTTTTGACCCCGATTTTTC
*
6313 CCAAAATTACCATTTT
1 CAAAAATTA-CATTTT
6329 ATTCGGATGT
Statistics
Matches: 214, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
116 15 0.07
117 128 0.60
118 54 0.25
119 14 0.07
120 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (116 bp):
CAAAAATTACATTTTTACCCTAACTTTCCAAAATTCCATTTTTGACCTTAATCTTTCCAAAAATT
ATCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTC
Done.