Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010439.1 Kokia drynarioides strain JFW-HI SEQ_125330, 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: 4104
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.24
Warning! 87 characters in sequence are not A, C, G, or T
Found at i:1698 original size:139 final size:139
Alignment explanation
Indices: 1448--1811 Score: 665
Period size: 139 Copynumber: 2.6 Consensus size: 139
1438 ATCATAGGGT
1448 AAATCTTCCTGATGAGATACGGAGAAGTGAGCCAGATTCGTATTCCTGATGAGATACAGAGAAAC
1 AAATCTTCCTGATGAGATACGGAGAAGTGAGCCAGATTCGTATTCCTGATGAGATACAGAGAAAC
*
1513 GGATCGAAACAATGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTC
66 GGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTC
1578 GAAACGAGC
131 GAAACGAGC
1587 AAATCTTCCTGATGAGATACGGAGAAGTGAGCCAGATTCGTATTCCTGATGAGATACAGAGAAAC
1 AAATCTTCCTGATGAGATACGGAGAAGTGAGCCAGATTCGTATTCCTGATGAGATACAGAGAAAC
* *
1652 GGATCGAAATAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAATAAGGCTC
66 GGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTC
1717 GAAACGAGC
131 GAAACGAGC
* * * *
1726 AAATCTTCTTGATGAGATACGAAAAAGTGAGCCAGATTTGTATTCCTGATGAGATACAGAGAAAC
1 AAATCTTCCTGATGAGATACGGAGAAGTGAGCCAGATTCGTATTCCTGATGAGATACAGAGAAAC
1791 GGATCGAAACAATGATGGGAT
66 GGATCGAAACAATGATGGGAT
1812 NNNNNNNNNN
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 217 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (139 bp):
AAATCTTCCTGATGAGATACGGAGAAGTGAGCCAGATTCGTATTCCTGATGAGATACAGAGAAAC
GGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTC
GAAACGAGC
Found at i:2094 original size:54 final size:53
Alignment explanation
Indices: 2035--2215 Score: 176
Period size: 54 Copynumber: 3.5 Consensus size: 53
2025 CGATGGGATC
2035 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAA
1 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAAC-AGGCTCGAAACGAGCAA
* * ** * * * *** *
2089 ATCTTCCTGATGAGATACAGAGAA-ACGGATCGAAACA--AT-GATGGGATC--
1 ATCTTCCTGATGAGACACTGAGAAGA-AAACCCAAACAGGCTCGAAACGAGCAA
2137 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAA
1 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAAC-AGGCTCGAAACGAGCAA
* *
2191 ATCTTCCTGATGAGATACGGAGAAG
1 ATCTTCCTGATGAGACACTGAGAAG
2216 TGAACTAGAT
Statistics
Matches: 95, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
48 28 0.29
49 2 0.02
50 5 0.05
51 2 0.02
52 5 0.05
53 2 0.02
54 51 0.54
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (53 bp):
ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAGGCTCGAAACGAGCAA
Found at i:2166 original size:102 final size:102
Alignment explanation
Indices: 1990--2214 Score: 396
Period size: 102 Copynumber: 2.2 Consensus size: 102
1980 CAGATTCGTA
* * *
1990 TTCCTGATGAGATACAAAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
*
2055 AGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATC
*
2092 TTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
2157 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATC
*
2194 TTCCTGATGAGATACGGAGAA
1 TTCCTGATGAGATACAGAGAA
2215 GTGAACTAGA
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 117 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (102 bp):
TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATC
Found at i:2173 original size:48 final size:49
Alignment explanation
Indices: 2025--2174 Score: 133
Period size: 48 Copynumber: 3.0 Consensus size: 49
2015 GTCGAAACAG
*
2025 CGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCT
1 CGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAAC-A--AT
*** * * * ** * *
2077 CGAAACGAGCAAATCTTCCTGATGAGATACAGAGAA-ACGGATCGAAACAAT
1 CGATGGGATC--ATCTTCCTGATGAGACACTGAGAAGA-AAACCCAAACAAT
2128 -GATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAA
1 CGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAA
2175 GGCTCGAAAC
Statistics
Matches: 73, Mismatches: 21, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
48 30 0.41
49 1 0.01
50 5 0.07
51 1 0.01
52 6 0.08
53 2 0.03
54 28 0.38
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (49 bp):
CGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAT
Found at i:2285 original size:241 final size:241
Alignment explanation
Indices: 1862--2367 Score: 931
Period size: 241 Copynumber: 2.1 Consensus size: 241
1852 NNNNNNNNNN
*
1862 ATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTTCTGATGAGACACTGAGAAGAAAACC
1 ATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACC
1927 CAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAAAAGTGAACCAGATTCGTATT
66 CAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAAAAGTGAACCAGATTCGTATT
1992 CCTGATGAGATACAAAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAG
131 CCTGATGAGATACAAAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAG
* * *
2057 AAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAG
196 AAGAAAACCCAAACAACGCTCGAAACGAGCAAATCTTCCTAATGAG
2103 ATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACC
1 ATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACC
* *
2168 CAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACTAGATTCGTATT
66 CAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAAAAGTGAACCAGATTCGTATT
*
2233 CCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAG
131 CCTGATGAGATACAAAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAG
* *
2298 AAGAAAACCCAAACAACGCTGGAAACGAGTAAATCTTCCTAATGAG
196 AAGAAAACCCAAACAACGCTCGAAACGAGCAAATCTTCCTAATGAG
2344 ATACAGAGAAACGGATCGAAACAA
1 ATACAGAGAAACGGATCGAAACAA
2368 GGCTCGAAAC
Statistics
Matches: 256, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
241 256 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.18
Consensus pattern (241 bp):
ATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACC
CAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAAAAGTGAACCAGATTCGTATT
CCTGATGAGATACAAAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAG
AAGAAAACCCAAACAACGCTCGAAACGAGCAAATCTTCCTAATGAG
Found at i:2335 original size:54 final size:54
Alignment explanation
Indices: 2276--2398 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 54
2266 CGATGGGATC
* * *
2276 ATCTTCCTGATGAGACACTGAGAAGA-AAACCCAAACAACGCTGGAAACGAGTAA
1 ATCTTCCTGATGAGACACAGAGAA-ACAAACCCAAACAACGCTCGAAACGAGCAA
* * ** * * *
2330 ATCTTCCTAATGAGATACAGAGAAACGGATCGAAACAAGGCTCGAAACGAGCAA
1 ATCTTCCTGATGAGACACAGAGAAACAAACCCAAACAACGCTCGAAACGAGCAA
2384 ATCTTCCTGATGAGA
1 ATCTTCCTGATGAGA
2399 TATGGAGAAG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 1 0.02
54 56 0.98
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (54 bp):
ATCTTCCTGATGAGACACAGAGAAACAAACCCAAACAACGCTCGAAACGAGCAA
Found at i:2343 original size:139 final size:139
Alignment explanation
Indices: 2092--2353 Score: 452
Period size: 139 Copynumber: 1.9 Consensus size: 139
2082 CGAGCAAATC
*
2092 TTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
* * *
2157 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACT
66 AGAAGAAAACCCAAACAACGCTCGAAACGAGCAAATCTTCCTAATGAGATACAGAGAAGTGAACT
2222 AGATTCGTA
131 AGATTCGTA
* *
2231 TTCCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
* *
2296 AGAAGAAAACCCAAACAACGCTGGAAACGAGTAAATCTTCCTAATGAGATACAGAGAA
66 AGAAGAAAACCCAAACAACGCTCGAAACGAGCAAATCTTCCTAATGAGATACAGAGAA
2354 ACGGATCGAA
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
139 115 1.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (139 bp):
TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
AGAAGAAAACCCAAACAACGCTCGAAACGAGCAAATCTTCCTAATGAGATACAGAGAAGTGAACT
AGATTCGTA
Found at i:2381 original size:193 final size:193
Alignment explanation
Indices: 2169--2546 Score: 648
Period size: 193 Copynumber: 2.0 Consensus size: 193
2159 AAGAAAACCC
*
2169 AAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACTAGATTCGTATTC
1 AAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACTAGATTCATATTC
2234 CTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAGA
66 CTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAGA
* * *
2299 AGAAAACCCAAACAACGCTGGAAACGAGTAAATCTTCCTAATGAGATACAGAGAAACGGATCG
131 AGAAAACCCAAACAACGCTCGAAACAAGCAAATCTTCCTAATGAGATACAGAGAAACGGATCG
*
2362 AAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATATGGAGAAGTGAACTAGATTCATATTC
1 AAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACTAGATTCATATTC
*
2427 CTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGATACTGAGA
66 CTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAGA
** * * * *
2492 AGAAAACCCAAATGAGGCTCGAAGCAAGCAAATCTTCCTGATGAGATACTGAGAA
131 AGAAAACCCAAACAACGCTCGAAACAAGCAAATCTTCCTAATGAGATACAGAGAA
2547 GTGAACCAAA
Statistics
Matches: 173, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
193 173 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (193 bp):
AAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACTAGATTCATATTC
CTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTGAGA
AGAAAACCCAAACAACGCTCGAAACAAGCAAATCTTCCTAATGAGATACAGAGAAACGGATCG
Found at i:3078 original size:17 final size:17
Alignment explanation
Indices: 3056--3118 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
3046 TTGGAAATTG
*
3056 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
3073 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
3090 AATTTAAATTTATTGTA
1 AATTTAAATTTATTTTA
*
3107 AAATTAAATTTA
1 AATTTAAATTTA
3119 GAAAAGTCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:3180 original size:15 final size:15
Alignment explanation
Indices: 3162--3220 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
3152 AGTCCAAATT
3162 ACAAATGGCCCAATA
1 ACAAATGGCCCAATA
* * *
3177 ACAAATGACCCAGTT
1 ACAAATGGCCCAATA
*
3192 ACAGATGGCCCAA-A
1 ACAAATGGCCCAATA
*
3206 TACAAATGGTCCAAT
1 -ACAAATGGCCCAAT
3221 TATAAAGTGC
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (15 bp):
ACAAATGGCCCAATA
Found at i:3180 original size:30 final size:29
Alignment explanation
Indices: 3142--3211 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
3132 ACAAAAAAAT
*
3142 CCAAAACAAAAGTCCAAATTACAAATGGC
1 CCAAAACAAAAGACCAAATTACAAATGGC
* * * *
3171 CCAATAACAAATGACCCAGTTACAGATGGC
1 CCAA-AACAAAAGACCAAATTACAAATGGC
3201 CCAAATACAAA
1 CCAAA-ACAAA
3212 TGGTCCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.14
Consensus pattern (29 bp):
CCAAAACAAAAGACCAAATTACAAATGGC
Done.