Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014493.1 Kokia drynarioides strain JFW-HI SEQ_129532, 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: 13274
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Found at i:58 original size:21 final size:22
Alignment explanation
Indices: 4--58 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
1 TAC
*
4 TGTTATTTTTGCTGTTGTTTTGGT
1 TGTTATTTTT--TGTTGTTTTGGA
28 TGTTA-TTTTTGTTG-TTTGGA
1 TGTTATTTTTTGTTGTTTTGGA
48 TGTTATTTTTT
1 TGTTATTTTTT
59 ATGCGTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.34
21 10 0.34
23 4 0.14
24 5 0.17
ACGTcount: A:0.07, C:0.02, G:0.22, T:0.69
Consensus pattern (22 bp):
TGTTATTTTTTGTTGTTTTGGA
Found at i:231 original size:10 final size:9
Alignment explanation
Indices: 166--232 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 9
156 TATCTTAATA
166 TAAT-TTTT
1 TAATGTTTT
174 TAATGTATTT
1 TAATGT-TTT
184 TAAAT-TTTT
1 T-AATGTTTT
*
193 TTAT-TTTT
1 TAATGTTTT
201 TAATGTTTGTTT
1 TAATG--T-TTT
213 TAATGTTTT
1 TAATGTTTT
222 TAAGTGTTTT
1 TAA-TGTTTT
232 T
1 T
233 GATATATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
8 13 0.27
9 11 0.22
10 13 0.27
11 4 0.08
12 8 0.16
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (9 bp):
TAATGTTTT
Found at i:321 original size:17 final size:17
Alignment explanation
Indices: 291--338 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
281 TGGGCCCAAC
*
291 AAAATTTAAATTTATTTT
1 AAAA-TTAAATTTATTAT
*
309 AAAATTAAGTTTATTAT
1 AAAATTAAATTTATTAT
*
326 AAATTTAAATTTA
1 AAAATTAAATTTA
339 AATTTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AAAATTAAATTTATTAT
Found at i:332 original size:23 final size:22
Alignment explanation
Indices: 306--351 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
296 TTAAATTTAT
*
306 TTTAAAATTAAGTTTATTATAAA
1 TTTAAAATTAAATTTATT-TAAA
*
329 TTTAAATTTAAATTTATTTAAA
1 TTTAAAATTAAATTTATTTAAA
351 T
1 T
352 AATGTCCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTAAAATTAAATTTATTTAAA
Found at i:981 original size:22 final size:21
Alignment explanation
Indices: 940--982 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
930 CCTAGACAAA
*
940 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
961 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
983 GCAGGGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Found at i:8906 original size:206 final size:206
Alignment explanation
Indices: 8124--8890 Score: 1178
Period size: 206 Copynumber: 3.7 Consensus size: 206
8114 GACCATCCAC
* * * *
8124 AAAC-AGCGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACGAGG
1 AAACAAGCGATGCGATCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATC-A--AACCCACG
* * * * **
8188 CTCAAAGCGAGCAAATCTTCGAACCCCAGCTTCTTAACGAGATACTGAGAAGCAGGTCGAAGCAA
63 CTCGATGCGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAATAA
** * *
8253 TAAAACAGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTATTCCTGATGAGATAC
128 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAT
*
8318 AGAGAAACGGATTG
193 AGAGAAGCGGATTG
* *
8332 AAACAAGAGATGCGATCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCTACGCTC
1 AAACAAGCGATGCGATCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* *
8397 GATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAATAA
66 GATGCGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAATAATAA
* *
8462 AATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCCTCCTGATGAGATATAGA
131 AATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGA
8527 GAAGCGGATTG
196 GAAGCGGATTG
* * * *
8538 AAACAAGCAATGC-AGTCATCTTCCTGATAAGATACTGAAAAGAAGACCAAATCAAACCCACGCT
1 AAACAAGCGATGCGA-TCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCT
* *
8602 CGATGTGAGCAAATCTTCGAACCCCATCTTCCTAATGAGATACTGAGAAGCAGGTCGAAATAATA
65 CGATGCGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAATAATA
* *
8667 AAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAATCAAATTCGTCTTCTTGATGAGATATAG
130 AAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAG
*
8732 AGAAGCAGATTG
195 AGAAGCGGATTG
*
8744 AAACAAGCGATGCGATCACCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAGCGATGCGATCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * *
8809 GATGTGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAATAA
66 GATGCGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAATAATAA
8874 AATGGTTAGCTTCCTGA
131 AATGGTTAGCTTCCTGA
8891 CAAGATATAG
Statistics
Matches: 513, Mismatches: 43, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
205 1 0.00
206 460 0.90
207 1 0.00
208 5 0.01
209 46 0.09
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (206 bp):
AAACAAGCGATGCGATCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
GATGCGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAATAATAA
AATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGA
GAAGCGGATTG
Found at i:8995 original size:321 final size:320
Alignment explanation
Indices: 8599--9286 Score: 1110
Period size: 321 Copynumber: 2.1 Consensus size: 320
8589 TCAAACCCAC
* * *
8599 GCTCGATGTGAGCAAATCTTCGAACCCCATCTTCCTAATGAGATACTGAGAAGCAGGTCGAAATA
1 GCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAATA
*
8664 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAATCAAATTCGTCTTCTTGATGAGATA
65 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATA
* * * *
8729 TAGAGAAGCAGATTGAAACAAGCGATGCGATCACCTTCTTGATGAGATA-CTGAGAAGAAGACCA
130 CAGAGAAGCAGATTGAAACAAGCAATGCGATCACCTTCCTGATAAGATATC-GAGAAGAAGACCA
*
8793 AATCAAACCCACGCTCGATGTGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
194 AATCAAACCCACGCTCAATGTGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
8858 CAGGTCGAAATAATAAAATGGTTAGCTTCCTGACAAGATATAGAGAAGTATACCAACTC-AG
259 CAGGTCGAAATAATAAAATGGTTAGCTTCCTGACAAGATATAGAGAAGTATACCAACTCAAG
* * * *
8919 GACTCGATGCGAGCAAATCTTCGAACCCTAGCTTTCTGATGAGGTACTAAGAAGCAGGTCGAAGT
1 G-CTCGATGTGAGCAAATCTTCGAACCC-AGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAAT
*
8984 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCGAATTCGTCTTCTTGATGAGAT
64 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGAT
* * *
9049 ACAGAGAAGCGGATTGAAACAAGCAATGCGGTCATCTTCCTGATAAGATATCGAGAAGAAGACCA
129 ACAGAGAAGCAGATTGAAACAAGCAATGCGATCACCTTCCTGATAAGATATCGAGAAGAAGACCA
*
9114 AATCAAACCCACGCTCAATGTGAGCAAATCCTCGAACCCCAGCTTTCTGATGAGATACTGAGAAG
194 AATCAAACCCACGCTCAATGTGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
**
9179 CAGGTCGAAATAATAAAATGGTTAGCTTCCTGATGAGATATAGAGAAGTATACCAACTCAAG
259 CAGGTCGAAATAATAAAATGGTTAGCTTCCTGACAAGATATAGAGAAGTATACCAACTCAAG
* * *
9241 GCTCGATATGATCAAACCTTCGAATCCCAGCTTCCTGATGAGATAC
1 GCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATAC
9287 AGAGAAGTAG
Statistics
Matches: 337, Mismatches: 26, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
320 4 0.01
321 326 0.97
322 7 0.02
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (320 bp):
GCTCGATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAATAA
TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATAC
AGAGAAGCAGATTGAAACAAGCAATGCGATCACCTTCCTGATAAGATATCGAGAAGAAGACCAAA
TCAAACCCACGCTCAATGTGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
GGTCGAAATAATAAAATGGTTAGCTTCCTGACAAGATATAGAGAAGTATACCAACTCAAG
Found at i:9012 original size:115 final size:115
Alignment explanation
Indices: 8806--9021 Score: 335
Period size: 115 Copynumber: 1.9 Consensus size: 115
8796 CAAACCCACG
* *
8806 CTCGATGTGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAA
1 CTCGATGCGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAATAA
8871 TAAAATGGTTAGCTTCCTGACAAGATA-TAGAGAAGTATACCAACTCAGGA
66 TAAAATGGTTAGCTTCCTGACAAGATACT-GAGAAGTATACCAACTCAGGA
* * * * *
8921 CTCGATGCGAGCAAATCTTCGAACCCTAGCTTTCTGATGAGGTACTAAGAAGCAGGTCGAAGTAA
1 CTCGATGCGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAATAA
**
8986 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGT
66 TAAAATGGTTAGCTTCCTGACAAGATACTGAGAAGT
9022 GAACCGAATT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
115 90 0.99
116 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (115 bp):
CTCGATGCGAGCAAATCCTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAATAA
TAAAATGGTTAGCTTCCTGACAAGATACTGAGAAGTATACCAACTCAGGA
Found at i:9292 original size:115 final size:116
Alignment explanation
Indices: 9035--9383 Score: 303
Period size: 116 Copynumber: 3.0 Consensus size: 116
9025 CCGAATTCGT
* * * * * * *
9035 CTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAGCAATGCGGTCATCTTCCTGATAAGATAT
1 CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAGTAATGCGATCAGCTTCCTGATGAGATA-
* * * * * **
9100 C-GAGAAGAAGACCAAATCAAACCCACGCTCAATGTGAGCAAATCC-TCGAACCCCAG
65 CAAAGAAGAATACCAACTC-AA--GA--CTCGATACGAGCAAA-CCTTCGAACCCCAG
* * * * *
9156 CTTTCTGATGAGATACTGAGAAGCAGGTCGAAATAA-TAAAATG-G-TTAGCTTCCTGATGAGAT
1 CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAGT--AATGCGATCAGCTTCCTGATGAGAT
* * * * * * *
9218 ATAGAGAAGTATACCAACTCAAGGCTCGATATGATCAAACCTTCGAATCCCAG
64 ACAAAGAAGAATACCAACTCAAGACTCGATACGAGCAAACCTTCGAACCCCAG
* * *
9271 CTTCCTGATGAGATACAGAGAAGTAGATTGAAACAAGTAATGCGATCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAGTAATGCGATCAGCTTCCTGATGAGATAC
* *
9336 AAAGAAGAATATCAACTCAAGACTCGATACGAGCAAATCTTCGAACCC
66 AAAGAAGAATACCAACTCAAGACTCGATACGAGCAAACCTTCGAACCC
9384 TAGCAAATTA
Statistics
Matches: 183, Mismatches: 38, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
114 6 0.03
115 53 0.29
116 58 0.32
119 2 0.01
120 30 0.16
121 30 0.16
122 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (116 bp):
CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAGTAATGCGATCAGCTTCCTGATGAGATAC
AAAGAAGAATACCAACTCAAGACTCGATACGAGCAAACCTTCGAACCCCAG
Found at i:9362 original size:116 final size:114
Alignment explanation
Indices: 9035--9383 Score: 335
Period size: 115 Copynumber: 3.0 Consensus size: 114
9025 CCGAATTCGT
* * * *
9035 CTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAGCAATGCGGTCATCTTCCTGATAAGATAT
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTAATGC-GTCATCTTCCTGATGAGATA-
* * * * *
9100 CGAGAAGAAGACCAAATCAAACCCACGCTCAATGTGAGCAAATCC-TCGAACCCCAG
64 C-A-AAGAAGA--ATATC-AACTCAAGCTCGATATGAGCAAA-CCTTCGAACCCCAG
* * * * * * *
9156 CTTTCTGATGAGATACTGAGAAGCAGGTCGAAATAA-TAAAATG-GTTAGCTTCCTGATGAGATA
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGT--AATGCGTCATCTTCCTGATGAGATA
* * * * * *
9219 TAGAGAAGTATACCAACTCAAGGCTCGATATGATCAAACCTTCGAATCCCAG
64 CAAAGAAGAATATCAACTCAA-GCTCGATATGAGCAAACCTTCGAACCCCAG
*
9271 CTTCCTGATGAGATACAGAGAAGTAGATTGAAACAAGTAATGCGATCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTAATGCG-TCATCTTCCTGATGAGATAC
* *
9336 AAAGAAGAATATCAACTCAAGACTCGATACGAGCAAATCTTCGAACCC
65 AAAGAAGAATATCAACTCAAG-CTCGATATGAGCAAACCTTCGAACCC
9384 TAGCAAATTA
Statistics
Matches: 182, Mismatches: 38, Indels: 21
0.76 0.16 0.09
Matches are distributed among these distances:
114 11 0.06
115 58 0.32
116 57 0.31
117 5 0.03
118 1 0.01
120 17 0.09
121 29 0.16
122 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (114 bp):
CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTAATGCGTCATCTTCCTGATGAGATACA
AAGAAGAATATCAACTCAAGCTCGATATGAGCAAACCTTCGAACCCCAG
Found at i:9670 original size:17 final size:17
Alignment explanation
Indices: 9640--9687 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
9630 TGGGCCCAAC
*
9640 AAAATTTAAATTTATTTT
1 AAAA-TTAAATTTATTTG
*
9658 AAAATTAAGTTTATTTG
1 AAAATTAAATTTATTTG
*
9675 AAATTTAAATTTA
1 AAAATTAAATTTA
9688 AATTTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
AAAATTAAATTTATTTG
Found at i:9681 original size:23 final size:22
Alignment explanation
Indices: 9655--9700 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
9645 TTAAATTTAT
*
9655 TTTAAAATTAAGTTTATTTGAAA
1 TTTAAAATTAAATTTATTT-AAA
*
9678 TTTAAATTTAAATTTATTTAAA
1 TTTAAAATTAAATTTATTTAAA
9700 T
1 T
9701 AATGTCCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTAAAATTAAATTTATTTAAA
Found at i:10980 original size:83 final size:83
Alignment explanation
Indices: 10841--11007 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
10831 GTTGAGAGGG
10841 TTTCCAGAGGTTGGCAACATGATTATGTAGAACTCCATACCCTATATTGAACCCCAATAACTTGA
1 TTTCCAGAGGTTGGCAACATGATTATGTAGAACTCCATACCCTATATTGAACCCCAATAACTTGA
10906 CAACAGCAATAGTCCCCA
66 CAACAGCAATAGTCCCCA
10924 TTTCCAGAGGTTGGCAACATGATTATGTAGAACTCCATACCCTATATTGAACCCCAATAACTTGA
1 TTTCCAGAGGTTGGCAACATGATTATGTAGAACTCCATACCCTATATTGAACCCCAATAACTTGA
*
10989 CAACAGCAATAGTTCCCA
66 CAACAGCAATAGTCCCCA
11007 T
1 T
11008 GTCCTTTACC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (83 bp):
TTTCCAGAGGTTGGCAACATGATTATGTAGAACTCCATACCCTATATTGAACCCCAATAACTTGA
CAACAGCAATAGTCCCCA
Done.