Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001176.1 Kokia drynarioides strain JFW-HI SEQ_112506, 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: 7201
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.33
Found at i:216 original size:21 final size:21
Alignment explanation
Indices: 192--243 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
182 TGTGGGTGAT
192 GGTGGTGAGTGCACT-AGTGGC
1 GGTGGTGAGTGCA-TGAGTGGC
* *
213 GGTGAG-GAGTGGATGAGTGGT
1 GGTG-GTGAGTGCATGAGTGGC
234 GGTGGTGAGT
1 GGTGGTGAGT
244 CCATAGGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.15, C:0.06, G:0.54, T:0.25
Consensus pattern (21 bp):
GGTGGTGAGTGCATGAGTGGC
Found at i:294 original size:42 final size:43
Alignment explanation
Indices: 188--295 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 43
178 AGTGTGTGGG
* * *
188 TGATGGTGGTGAGTGCACTA-GT-GGCGGTGAGGAGTGGATGAG
1 TGATGGTGGTGAGTGCAC-AGGTAGGCGGTGAAGAGTGGATAAC
* * *
230 TGGTGGTGGTGAGTCCATAGGTAGG-GGTGAAGAGTGGATAAC
1 TGATGGTGGTGAGTGCACAGGTAGGCGGTGAAGAGTGGATAAC
*
272 TGATGGTGGTGAGTGAACAGGTAG
1 TGATGGTGGTGAGTGCACAGGTAG
296 TGGTTGGGAG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.02
42 51 0.94
43 2 0.04
ACGTcount: A:0.22, C:0.06, G:0.47, T:0.24
Consensus pattern (43 bp):
TGATGGTGGTGAGTGCACAGGTAGGCGGTGAAGAGTGGATAAC
Found at i:1989 original size:77 final size:77
Alignment explanation
Indices: 1899--2128 Score: 343
Period size: 77 Copynumber: 3.0 Consensus size: 77
1889 TTTACCAAGT
* * * *
1899 ATAACTTGTATTTTCGATCTTTAGTTTACAATAGGTCAAATTATATTTTGGTCCTTATACCATTT
1 ATAACTTGTATTTTCTATCTTTAGTTTACAATAGGTTAAATTATATTTTGGTCCTTATACTATAT
1964 CTAAAATTCATG
66 CTAAAATTCATG
* *
1976 ATAACTTGTATTTTCTATCTTTAGTTTACAATAGATTATATTATATTTTGGTCCTTATACTATAT
1 ATAACTTGTATTTTCTATCTTTAGTTTACAATAGGTTAAATTATATTTTGGTCCTTATACTATAT
2041 CTAAAATTCATG
66 CTAAAATTCATG
* * * * * * *
2053 ATGACTTGTTTTTTCTATATTTAGTTGACAATAGGTTAAATTATATTATGGTCTTTATAATATAT
1 ATAACTTGTATTTTCTATCTTTAGTTTACAATAGGTTAAATTATATTTTGGTCCTTATACTATAT
2118 CTAAAATTCAT
66 CTAAAATTCAT
2129 TATTAAATTT
Statistics
Matches: 138, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 138 1.00
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (77 bp):
ATAACTTGTATTTTCTATCTTTAGTTTACAATAGGTTAAATTATATTTTGGTCCTTATACTATAT
CTAAAATTCATG
Found at i:3601 original size:16 final size:16
Alignment explanation
Indices: 3580--3617 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
3570 AAAAACATCA
*
3580 TTATAATAATATAGCT
1 TTATAAGAATATAGCT
3596 TTATAAGAATATAGCT
1 TTATAAGAATATAGCT
3612 TTATAA
1 TTATAA
3618 AATTATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (16 bp):
TTATAAGAATATAGCT
Found at i:5744 original size:42 final size:42
Alignment explanation
Indices: 5685--5925 Score: 313
Period size: 42 Copynumber: 5.7 Consensus size: 42
5675 TGATAGAGTT
* *
5685 GGTGGAGGTCGAGATTGTACTGGTGGTTG-TAGAGACCTAACG
1 GGTGGAGGTCGAGATTGTACTGGTGG-TGATAAAGACCTGACG
* * * *
5727 GGTGGAGGTCGAAATTGTATTGGTGGTGATAAAGAACTGACA
1 GGTGGAGGTCGAGATTGTACTGGTGGTGATAAAGACCTGACG
* * *
5769 GGTAGAGGGCGAGATTGTACTGGTGGTGATAGAGACCTGACG
1 GGTGGAGGTCGAGATTGTACTGGTGGTGATAAAGACCTGACG
* * * *
5811 GGTAGAGGGCGAGATTGTACTGGTGGTGATATAGACCTAACG
1 GGTGGAGGTCGAGATTGTACTGGTGGTGATAAAGACCTGACG
* * *
5853 GGTGGAGGTCGGGATTGTATTGGTGGTGATAAAGACTTGACG
1 GGTGGAGGTCGAGATTGTACTGGTGGTGATAAAGACCTGACG
*
5895 GGTGGAGGTCGAGATTGTAATGGTGGTGATA
1 GGTGGAGGTCGAGATTGTACTGGTGGTGATA
5926 GAAACTTGAC
Statistics
Matches: 174, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 2 0.01
42 172 0.99
ACGTcount: A:0.24, C:0.09, G:0.41, T:0.26
Consensus pattern (42 bp):
GGTGGAGGTCGAGATTGTACTGGTGGTGATAAAGACCTGACG
Found at i:5849 original size:126 final size:126
Alignment explanation
Indices: 5689--5927 Score: 374
Period size: 126 Copynumber: 1.9 Consensus size: 126
5679 AGAGTTGGTG
*
5689 GAGGTCGAGATTGTACTGGTGGTTGTAGAGACCTAACGGGTGGAGGTCGAAATTGTATTGGTGGT
1 GAGGGCGAGATTGTACTGGTGGTTGTAGAGACCTAACGGGTGGAGGTCGAAATTGTATTGGTGGT
*
5754 GATAAAGAAC-TGACAGGTAGAGGGCGAGATTGTACTGGTGGTGATAGAGACCTGACGGGTA
66 GATAAAG-ACTTGACAGGTAGAGGGCGAGATTGTAATGGTGGTGATAGAGACCTGACGGGTA
* **
5815 GAGGGCGAGATTGTACTGGTGG-TGATATAGACCTAACGGGTGGAGGTCGGGATTGTATTGGTGG
1 GAGGGCGAGATTGTACTGGTGGTTG-TAGAGACCTAACGGGTGGAGGTCGAAATTGTATTGGTGG
* * *
5879 TGATAAAGACTTGACGGGTGGAGGTCGAGATTGTAATGGTGGTGATAGA
65 TGATAAAGACTTGACAGGTAGAGGGCGAGATTGTAATGGTGGTGATAGA
5928 AACTTGACCG
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
125 4 0.04
126 99 0.96
ACGTcount: A:0.25, C:0.09, G:0.40, T:0.26
Consensus pattern (126 bp):
GAGGGCGAGATTGTACTGGTGGTTGTAGAGACCTAACGGGTGGAGGTCGAAATTGTATTGGTGGT
GATAAAGACTTGACAGGTAGAGGGCGAGATTGTAATGGTGGTGATAGAGACCTGACGGGTA
Found at i:5970 original size:60 final size:60
Alignment explanation
Indices: 5902--6017 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
5892 ACGGGTGGAG
* * * *
5902 GTCGAGATTGTAATGGTGG-TGATAGAAACTTGACCGATGGAGGTGATAGAGTTGGTGGCA
1 GTCGAGATTGTAATGGTGGTTG-TAGAAACCTAACCGATGAAGGTGATAAAGTTGGTGGCA
* * *
5962 GTCGAGATTGTACTGGTGGTTGTAGAGACCTAACCGGTGAAGGTGATAAAGTTGGT
1 GTCGAGATTGTAATGGTGGTTGTAGAAACCTAACCGATGAAGGTGATAAAGTTGGT
6018 AGTTTGAGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.37, T:0.28
Consensus pattern (60 bp):
GTCGAGATTGTAATGGTGGTTGTAGAAACCTAACCGATGAAGGTGATAAAGTTGGTGGCA
Found at i:6191 original size:102 final size:101
Alignment explanation
Indices: 5853--6182 Score: 336
Period size: 102 Copynumber: 3.3 Consensus size: 101
5843 AGACCTAACG
* * * * * *
5853 GGTGGAGGTCGGGATTGTATTGGTGGTGATAAAGACTTGACGGGTGGAGGTCGAGATTGT-AATG
1 GGTGGAGGTCGAGATTGTACTGGTGGTGATAGAGACCTAACGGGTGAAGGTCGAGATT-TAAATG
* *
5917 GTGGTGATAGAAACTTGACCGATGGAGGTGATAGAGTT
65 GTGGTGATAGAGACTTGA-AGATGGAGGTGATAGAGTT
*
5955 GGTGGCA-GTCGAGATTGTACTGGTGGTTG-TAGAGACCTAACCGGTGAAGGT---GA--TAAA-
1 GGTGG-AGGTCGAGATTGTACTGGTGG-TGATAGAGACCTAACGGGTGAAGGTCGAGATTTAAAT
* * * *
6012 GTTGGTAGTTTGAGAGACCTGAAGGGTGGAGGTGATAGAGTT
64 GGTGGT-G-AT-AGAGACTTGAA-GATGGAGGTGATAGAGTT
* *
6054 GGTAGATGTCGAGATTGTACTGGTGGTGATAGAGACCTAACGGGTGAAGGTCGAGATTTAAATGG
1 GGTGGAGGTCGAGATTGTACTGGTGGTGATAGAGACCTAACGGGTGAAGGTCGAGATTTAAATGG
* * * *
6119 TGGTGGTATAGATTTGAAAACTGGAGGTGATAGAGTT
66 TGGTGATAGAGACTTGAAGA-TGGAGGTGATAGAGTT
*
6156 GGTGGAGGTCGGGATTGTACTGGTGGT
1 GGTGGAGGTCGAGATTGTACTGGTGGT
6183 AGGAGAGACT
Statistics
Matches: 187, Mismatches: 25, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
96 6 0.03
97 3 0.02
98 4 0.02
99 71 0.38
102 89 0.48
103 4 0.02
104 5 0.03
105 5 0.03
ACGTcount: A:0.25, C:0.08, G:0.40, T:0.28
Consensus pattern (101 bp):
GGTGGAGGTCGAGATTGTACTGGTGGTGATAGAGACCTAACGGGTGAAGGTCGAGATTTAAATGG
TGGTGATAGAGACTTGAAGATGGAGGTGATAGAGTT
Found at i:6204 original size:60 final size:60
Alignment explanation
Indices: 6140--6375 Score: 350
Period size: 60 Copynumber: 3.9 Consensus size: 60
6130 ATTTGAAAAC
6140 TGGAGGTGATAGAGTTGGTGGAGGTCGGGATTGTACTGGTGGTAGG-AGAGACTTGACGTG
1 TGGAGGTGATAGAGTTGGTGGAGGTCGGGATTGTACTGGTGGT-GGTAGAGACTTGACGTG
* * *
6200 TGGAGGTGATAGAGTTGGTGGAGTTCGAGATTGTACTGGTGGTGGTAGAGACTTGA-TTG
1 TGGAGGTGATAGAGTTGGTGGAGGTCGGGATTGTACTGGTGGTGGTAGAGACTTGACGTG
* *
6259 ATGGAGGTGATAGAGTTAGTGGAGGTCGGGATTGTACTGGTGGTGGTAGAGACTTGACGGG
1 -TGGAGGTGATAGAGTTGGTGGAGGTCGGGATTGTACTGGTGGTGGTAGAGACTTGACGTG
* * * * *
6320 TGGAGGTAATAGAGTTGATGGAGGTTGGGATTGTATTTGTGGTGGTAGAGACTTGA
1 TGGAGGTGATAGAGTTGGTGGAGGTCGGGATTGTACTGGTGGTGGTAGAGACTTGA
6376 TTGATGGAGG
Statistics
Matches: 159, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.03
60 154 0.97
61 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.44, T:0.30
Consensus pattern (60 bp):
TGGAGGTGATAGAGTTGGTGGAGGTCGGGATTGTACTGGTGGTGGTAGAGACTTGACGTG
Found at i:6264 original size:120 final size:120
Alignment explanation
Indices: 6140--6387 Score: 401
Period size: 120 Copynumber: 2.1 Consensus size: 120
6130 ATTTGAAAAC
* *
6140 TGGAGGTGATAGAGTTGGTGGAGGTCGGGATTGTACTGGTGGTAGG-AGAGACTTGACGTGTGGA
1 TGGAGGTGATAGAGTTAGTGGAGGTCGGGATTGTACTGGTGGT-GGTAGAGACTTGACGGGTGGA
* *
6204 GGTGATAGAGTTGGTGGA-GTTCGAGATTGTACTGGTGGTGGTAGAGACTTGATTGA
65 GGTAATAGAGTTGATGGAGGTT-GAGATTGTACTGGTGGTGGTAGAGACTTGATTGA
6260 TGGAGGTGATAGAGTTAGTGGAGGTCGGGATTGTACTGGTGGTGGTAGAGACTTGACGGGTGGAG
1 TGGAGGTGATAGAGTTAGTGGAGGTCGGGATTGTACTGGTGGTGGTAGAGACTTGACGGGTGGAG
* * *
6325 GTAATAGAGTTGATGGAGGTTGGGATTGTATTTGTGGTGGTAGAGACTTGATTGA
66 GTAATAGAGTTGATGGAGGTTGAGATTGTACTGGTGGTGGTAGAGACTTGATTGA
6380 TGGAGGTG
1 TGGAGGTG
6388 GTGAATGGAG
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
119 2 0.02
120 114 0.96
121 3 0.03
ACGTcount: A:0.21, C:0.05, G:0.44, T:0.30
Consensus pattern (120 bp):
TGGAGGTGATAGAGTTAGTGGAGGTCGGGATTGTACTGGTGGTGGTAGAGACTTGACGGGTGGAG
GTAATAGAGTTGATGGAGGTTGAGATTGTACTGGTGGTGGTAGAGACTTGATTGA
Found at i:6571 original size:42 final size:42
Alignment explanation
Indices: 6520--7129 Score: 476
Period size: 42 Copynumber: 14.5 Consensus size: 42
6510 GTTGGTGACA
* *
6520 AGTGGACGGGTGGTGTTGGTAAGTCCACTAGTGAGGGTGAGG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
* * * * * *
6562 AGTGAACGGGTGGTGTTAGTGACTCCATTGGTGAGGGTGAGG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
* * * *
6604 AGTGGACGGATGGTGCTGGTGAATCCACTAGTGAGGGTGAGA
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
* * * *
6646 AGTGGACGGGTGGTAGAGGTGAGTCCATTGGTGAGGGTGATGG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGA-GG
* * * * *
6689 -GTGGAAGGGTGATGGTGGTGAGTCCACTGGTGAGGTTGAAG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
* * * * * * * *
6730 AGTAGACGGATGATGGTGGTAAGTCTATTGGTGAGGTTGAGG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
** * * * * *
6772 AGTGGATAGATGATGGTGATGAGTCCACTTGTGAGGGAGAGG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
** * * * *
6814 AGTGGATAGGTGATGGTGATGAGTCCACTAGTGAGGCTGAAG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
* * * * * *
6856 AGTGGACGAGTGATGGTGGTGAGTCTAATTGTGAGGTTGAGG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
* *
6898 AGTGGACGGGTGGTGGTGGTGAGTCCATTTGTG-GTGGTG-GAG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAG-GGTGAG-G
* * * * *
6940 AGTGTACGGG-GGATGGTTGTGAGTCCGCTAGTAAGGGTGAAG
1 AGTGGACGGGTGG-TGGTGGTGAGTCCACTAGTGAGGGTGAGG
* * * * * *
6982 AATGGACGGATGATGGTGGTGAGTCCACTAATGAGGGCGAGA
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
* * *
7024 AGTGGACGGGAAGG-GGTGGTGAGTCCATTGGTGAGGGTGAGG
1 AGTGGACGGG-TGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
* * * * * *
7066 AGTGGACGAGAGGTAGTGGTGTGTCCACT-GTTGAAGGTGATG
1 AGTGGACGGGTGGTGGTGGTGAGTCCACTAG-TGAGGGTGAGG
* *
7108 AGTGGATGGGTGGTGATGGTGA
1 AGTGGACGGGTGGTGGTGGTGA
7130 ATGTATTGAT
Statistics
Matches: 453, Mismatches: 104, Indels: 22
0.78 0.18 0.04
Matches are distributed among these distances:
41 9 0.02
42 440 0.97
43 4 0.01
ACGTcount: A:0.21, C:0.08, G:0.46, T:0.24
Consensus pattern (42 bp):
AGTGGACGGGTGGTGGTGGTGAGTCCACTAGTGAGGGTGAGG
Found at i:6837 original size:21 final size:21
Alignment explanation
Indices: 6771--6837 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
6761 TGAGGTTGAG
*
6771 GAGTGGATAGATGATGGTGAT
1 GAGTGGATAGGTGATGGTGAT
** * * * *
6792 GAGTCCACT-TGTGAGGGAGAG
1 GAGTGGA-TAGGTGATGGTGAT
6813 GAGTGGATAGGTGATGGTGAT
1 GAGTGGATAGGTGATGGTGAT
6834 GAGT
1 GAGT
6838 CCACTAGTGA
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.45, T:0.25
Consensus pattern (21 bp):
GAGTGGATAGGTGATGGTGAT
Found at i:6847 original size:21 final size:21
Alignment explanation
Indices: 6782--6880 Score: 67
Period size: 21 Copynumber: 4.7 Consensus size: 21
6772 AGTGGATAGA
*
6782 TGATGGTGATGAGTCCACTTG
1 TGATGGTGATGAGTCCACTAG
* * * **
6803 TGAGGGAGAGGAGTGGA-TAGG
1 TGATGGTGATGAGTCCACTA-G
6824 TGATGGTGATGAGTCCACTAG
1 TGATGGTGATGAGTCCACTAG
* ** *
6845 TGA-GGCTGAAGAGTGGACGAG
1 TGATGG-TGATGAGTCCACTAG
*
6866 TGATGGTGGTGAGTC
1 TGATGGTGATGAGTC
6881 TAATTGTGAG
Statistics
Matches: 56, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
20 3 0.05
21 49 0.88
22 4 0.07
ACGTcount: A:0.23, C:0.09, G:0.43, T:0.24
Consensus pattern (21 bp):
TGATGGTGATGAGTCCACTAG
Done.