Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013678.1 Kokia drynarioides strain JFW-HI SEQ_128706, 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: 13898
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:164 original size:23 final size:23
Alignment explanation
Indices: 28--164 Score: 113
Period size: 23 Copynumber: 5.9 Consensus size: 23
18 CGAAGTACTT
28 AACAGTAAGCACACA-AGTGCTAGGGA
1 AACAGTAAGCACACACAGTGC-A---A
54 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACACAGTGCAA
* * ** *
76 ATCAGTAGGTGCACATAGTGCAA
1 AACAGTAAGCACACACAGTGCAA
* *
99 ATCAGT-AG-ACACACGAGGTGCGA
1 AACAGTAAGCACACAC-A-GTGCAA
122 AACAGTAAGCACACGA-AGTGCAA
1 AACAGTAAGCACAC-ACAGTGCAA
145 AACAGTAAGCACACACAGTG
1 AACAGTAAGCACACACAGTG
165 TTGAACAGTA
Statistics
Matches: 92, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
21 4 0.04
22 20 0.22
23 40 0.43
24 3 0.03
25 4 0.04
26 16 0.17
27 5 0.05
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACACAGTGCAA
Found at i:172 original size:46 final size:44
Alignment explanation
Indices: 28--177 Score: 126
Period size: 46 Copynumber: 3.2 Consensus size: 44
18 CGAAGTACTT
*
28 AACAGTAAGCACACAAGTGCTAGGGAAACAGTAAGCACACACAGTG-C
1 AACAGTAAGCACACAAGTGC-A---AAACAGTAAGCACACACAGTGTG
* ** * *
75 AATCAGTAGGTGCACATAGTGCAAATCAGT-AG-ACACACGAGGTGCG
1 AA-CAGTAAGCACACA-AGTGCAAAACAGTAAGCACACAC-A-GTGTG
121 AAACAGTAAGCACACGAAGTGCAAAACAGTAAGCACACACAGTGTTG
1 -AACAGTAAGCACAC-AAGTGCAAAACAGTAAGCACACACAGTG-TG
168 AACAGTAAGC
1 AACAGTAAGC
178 GCGTTAGCGT
Statistics
Matches: 83, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
43 6 0.07
44 3 0.04
45 9 0.11
46 34 0.41
47 9 0.11
48 17 0.20
49 5 0.06
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.13
Consensus pattern (44 bp):
AACAGTAAGCACACAAGTGCAAAACAGTAAGCACACACAGTGTG
Found at i:278 original size:24 final size:26
Alignment explanation
Indices: 240--287 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
230 TCTACATGGG
240 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
266 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
288 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:4366 original size:340 final size:340
Alignment explanation
Indices: 3746--4422 Score: 1228
Period size: 340 Copynumber: 2.0 Consensus size: 340
3736 ATCCATCACG
*
3746 ATTTTCTACTTCAAATTTATTGTTTCTTTTGCTTAAATTTGTTTTCTTTGGATTGTGAAGAGGTT
1 ATTTTCTACGTCAAATTTATTGTTTCTTTTGCTTAAATTTGTTTTCTTTGGATTGTGAAGAGGTT
* * *
3811 GATGGAGTCAAATTCAAATGATTAGAGGAGTTTTCTTATTATTAGTACAAAGTACTCTTTAGATT
66 GATGGAGTCAAATTCAAATGATTAGAGGAGTCTTCTTACTATTAGTACAAAGTAATCTTTAGATT
* *
3876 TTTCCTTCCCAATTTGTGAAGAAATTGTTATTGTAAAGTATTCGAAGAAGGCATTTCAATTTAAA
131 TTTCCTCCCCAATTTGTGAAGAAATTGTTATTGTAAAGTATTCGAAGAAAGCATTTCAATTTAAA
*
3941 AACTTGCAATTTGATAGCTCATTTCCTCAAAAAATTTGAAATTTTGAATGAATGAAGAGATCGGT
196 AACTTACAATTTGATAGCTCATTTCCTCAAAAAATTTGAAATTTTGAATGAATGAAGAGATCGGT
4006 TAATACATTATTCGAGAGGAACGGAACTCTAAAATGTCAAGTTAATGAAAAACACTTTGTATATT
261 TAATACATTATTCGAGAGGAACGGAACTCTAAAATGTCAAGTTAATGAAAAACACTTTGTATATT
4071 TTTCAGTTCAAAACC
326 TTTCAGTTCAAAACC
4086 ATTTTCTACGTCAAATTTATTGTTTCTTTTGCTTAAATTTGTTTTCTTTGGATTGTGAAGAGGTT
1 ATTTTCTACGTCAAATTTATTGTTTCTTTTGCTTAAATTTGTTTTCTTTGGATTGTGAAGAGGTT
*
4151 GATGGAGTCAAATTCAAATGATTAGAGGAGTCTTCTTACTATTAGTACAAAGTAATCTTTGGATT
66 GATGGAGTCAAATTCAAATGATTAGAGGAGTCTTCTTACTATTAGTACAAAGTAATCTTTAGATT
* *
4216 TTTCCTCCCCAATTTGTGAAGAAATTGTTATTGTAAAGTATTCGAAGAAAGCATTTTAATTTAAC
131 TTTCCTCCCCAATTTGTGAAGAAATTGTTATTGTAAAGTATTCGAAGAAAGCATTTCAATTTAAA
* * *
4281 AACTTACAATTTGATAGTTCATTTCCTCAAAAATTTTGAAATTTTGAATGAATGAAGAGATTGGT
196 AACTTACAATTTGATAGCTCATTTCCTCAAAAAATTTGAAATTTTGAATGAATGAAGAGATCGGT
*
4346 TAATACATTATTCGAGAGGAACGGGACTCTAAAATGTCAAGTTAATGAAAAACACTTTGTATATT
261 TAATACATTATTCGAGAGGAACGGAACTCTAAAATGTCAAGTTAATGAAAAACACTTTGTATATT
4411 TTTCAGTTCAAA
326 TTTCAGTTCAAA
4423 GATTCGAAAG
Statistics
Matches: 323, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
340 323 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (340 bp):
ATTTTCTACGTCAAATTTATTGTTTCTTTTGCTTAAATTTGTTTTCTTTGGATTGTGAAGAGGTT
GATGGAGTCAAATTCAAATGATTAGAGGAGTCTTCTTACTATTAGTACAAAGTAATCTTTAGATT
TTTCCTCCCCAATTTGTGAAGAAATTGTTATTGTAAAGTATTCGAAGAAAGCATTTCAATTTAAA
AACTTACAATTTGATAGCTCATTTCCTCAAAAAATTTGAAATTTTGAATGAATGAAGAGATCGGT
TAATACATTATTCGAGAGGAACGGAACTCTAAAATGTCAAGTTAATGAAAAACACTTTGTATATT
TTTCAGTTCAAAACC
Found at i:6941 original size:164 final size:164
Alignment explanation
Indices: 6496--7205 Score: 693
Period size: 164 Copynumber: 4.3 Consensus size: 164
6486 GTTATTGGAC
* * * * * * * *
6496 AGTATATGCATTCATTGATTGTGTTGTCATGTATTGTTAGTGGCATATATGTCATG-CTCATATT
1 AGTATAGGCATTCTTTGATTTTATTGTTATGTATTGTTGGTGGCATATATGTCATGTC-CATGTC
* * *
6560 TCTCCAAAC-AGTCGGTGGTTGTCTCGGGTTTGTGTTCTATAGGACTTTAGTTTGACTGATTGAA
65 TCTCC-AACGAGTCGGCGGTTGTCTCGGGTTTGTGTTCCATAGTACTTTAGTTTGACTGATTGAA
* *
6624 AGTTGGTT-AGAT-AAGTGGAGATTTAGTCTTTA-TGTT
129 AGTTGGTTGA-ATGTA-TGAAGATTTAGTCTTTATTG-T
* * * * *
6660 A-CACAGGCATTCTTTGATTGTGTTGTTATATATTGTTAGTGGCATATATGGCATATATGTCATG
1 AGTATAGGCATTCTTTGATTTTATTGTTATGTATTG-T--TGG------TGGCATATATGTCATG
** * * * * *
6724 TCCATGT-TCCTCTGACAAGTTGGTGGTTGTCTTGGGTTTGTGTTCCGTAGTACTTTAGTTTGAC
57 TCCATGTCT-CTCCAACGAGTCGGCGGTTGTCTCGGGTTTGTGTTCCATAGTACTTTAGTTTGAC
*
6788 TGATTGGAAGTTGGTTGAATGTATGGAA-ATTTAGTCTTTATTGT
121 TGATTGAAAGTTGGTTGAATGTAT-GAAGATTTAGTCTTTATTGT
* * * *
6832 AGTATAGGCTTTCTTTGATTTTATTTTTGTGTATTGTTGGTGGCATATATGTCATGTCCGTGTCT
1 AGTATAGGCATTCTTTGATTTTATTGTTATGTATTGTTGGTGGCATATATGTCATGTCCATGTCT
* * *
6897 CTCCAACGTGTCTGCGGTTGTCTCGGGTTTGTGTTCCATAGTACTTTAGTTTGACCGATTGAAAG
66 CTCCAACGAGTCGGCGGTTGTCTCGGGTTTGTGTTCCATAGTACTTTAGTTTGACTGATTGAAAG
* *
6962 TTGGTTGGATGTGTGAAGATTTAGTCTTTATTGT
131 TTGGTTGAATGTATGAAGATTTAGTCTTTATTGT
* * ** *
6996 AGTATTGGCATTCTTTGATTTTATTGTTGTGTATTGTTGGTGGCATATATGTTGTGTTCATGT-T
1 AGTATAGGCATTCTTTGATTTTATTGTTATGTATTGTTGGTGGCATATATGTCATGTCCATGTCT
* * * **
7060 CCTCCGACAAGTC-GCTGGTTGTTTCGGGTTTGTGTTCTGTAGTACTTTAGTTTGACTGATTGAA
66 -CTCCAACGAGTCGGC-GGTTGTCTCGGGTTTGTGTTCCATAGTACTTTAGTTTGACTGATTGAA
*** * * * *
7124 AGCCAGATGGATGTGTGAAGATTTAGTCTTTATTGC
129 AGTTGGTTGAATGTATGAAGATTTAGTCTTTATTGT
* * *
7160 AGTATGGGCATTCTTTGATTTTATTATCATGTATTGTTGGTGGCAT
1 AGTATAGGCATTCTTTGATTTTATTGTTATGTATTGTTGGTGGCAT
7206 TGTTCATGTG
Statistics
Matches: 462, Mismatches: 63, Indels: 42
0.81 0.11 0.07
Matches are distributed among these distances:
163 34 0.07
164 288 0.62
165 1 0.00
166 2 0.00
170 3 0.01
171 3 0.01
172 98 0.21
173 33 0.07
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.44
Consensus pattern (164 bp):
AGTATAGGCATTCTTTGATTTTATTGTTATGTATTGTTGGTGGCATATATGTCATGTCCATGTCT
CTCCAACGAGTCGGCGGTTGTCTCGGGTTTGTGTTCCATAGTACTTTAGTTTGACTGATTGAAAG
TTGGTTGAATGTATGAAGATTTAGTCTTTATTGT
Found at i:7179 original size:328 final size:331
Alignment explanation
Indices: 6495--7205 Score: 855
Period size: 336 Copynumber: 2.1 Consensus size: 331
6485 GGTTATTGGA
* * * * * * *
6495 CAGTATATGCATTCATTGATTGTGTTGTCATGTATTGTTAGTGGCATATATGTCATGCTCATATT
1 CAGTATAGGCATTCTTTGATTTTATTATCATGTATTGTTGGTGGCATATATGTCATGCTCATATC
* * *
6560 TCTCCAAACAGTCGGTGGTTGTCTCGGGTTTGTGTTCTATAGGACTTTAGTTTGACTGATTGAAA
66 TCTCCAAACAGTCGGCGGTTGTCTCGGGTTTGTGTTCCATAGGACTTTAGTTTGACCGATTGAAA
* *
6625 GTTGGTTAGATAAGTGGAGATTTAGTCTTTATGTTACACAGGCATTCTTTGATTGTGTTGTTATA
131 GTTGGTTAGATAAGTGAAGATTTAGTCTTTATGTTACACAGGCATTCTTTGATTGTATTGTTATA
* * *
6690 TATTGTTAGTGGCATATATGGCATATATGTCATGTCCATGTTCCTCTGACAAGTTGGTGGTTGTC
196 TATTGTTAGTGGCATATATGG---ATATG--ATGTCCATGTTCCTCCGACAAGTCGCTGGTTGTC
* *** *
6755 TTGGGTTTGTGTTCCGTAGTACTTTAGTTTGACTGATTGGAAGTTGGTTGAATGTATGGAAATTT
256 TTGGGTTTGTGTTCCGTAGTACTTTAGTTTGACTGATTGAAAGCCAGATGAATGTATGGAAATTT
6820 AGTCTTTATTG
321 AGTCTTTATTG
* * * ** * *
6831 TAGTATAGGCTTTCTTTGATTTTATTTTTGTGTATTGTTGGTGGCATATATGTCATG-TCCGTGT
1 CAGTATAGGCATTCTTTGATTTTATTATCATGTATTGTTGGTGGCATATATGTCATGCT-CATAT
* * *
6895 CTCTCC-AACGTGTCTGCGGTTGTCTCGGGTTTGTGTTCCATAGTACTTTAGTTTGACCGATTGA
65 CTCTCCAAAC-AGTCGGCGGTTGTCTCGGGTTTGTGTTCCATAGGACTTTAGTTTGACCGATTGA
* ** * ** *
6959 AAGTTGGTTGGATGTGTGAAGATTTAGTCTTTAT-TGTAGTATTGGCATTCTTTGATTTTATTGT
129 AAGTTGGTTAGATAAGTGAAGATTTAGTCTTTATGT-TA-CACAGGCATTCTTTGATTGTATTGT
* * * *
7023 TGTGTATTGTTGGTGGCATATAT-G-T-TG-TGTTCATGTTCCTCCGACAAGTCGCTGGTTGT-T
192 TATATATTGTTAGTGGCATATATGGATATGATGTCCATGTTCCTCCGACAAGTCGCTGGTTGTCT
* * *
7083 TCGGGTTTGTGTTCTGTAGTACTTTAGTTTGACTGATTGAAAGCCAGATGGATGTGT-GAAGATT
257 T-GGGTTTGTGTTCCGTAGTACTTTAGTTTGACTGATTGAAAGCCAGATGAATGTATGGAA-ATT
7147 TAGTCTTTATTG
320 TAGTCTTTATTG
*
7159 CAGTATGGGCATTCTTTGATTTTATTATCATGTATTGTTGGTGGCAT
1 CAGTATAGGCATTCTTTGATTTTATTATCATGTATTGTTGGTGGCAT
7206 TGTTCATGTG
Statistics
Matches: 320, Mismatches: 49, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
327 5 0.02
328 131 0.41
331 2 0.01
332 1 0.00
335 5 0.02
336 136 0.43
337 40 0.12
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (331 bp):
CAGTATAGGCATTCTTTGATTTTATTATCATGTATTGTTGGTGGCATATATGTCATGCTCATATC
TCTCCAAACAGTCGGCGGTTGTCTCGGGTTTGTGTTCCATAGGACTTTAGTTTGACCGATTGAAA
GTTGGTTAGATAAGTGAAGATTTAGTCTTTATGTTACACAGGCATTCTTTGATTGTATTGTTATA
TATTGTTAGTGGCATATATGGATATGATGTCCATGTTCCTCCGACAAGTCGCTGGTTGTCTTGGG
TTTGTGTTCCGTAGTACTTTAGTTTGACTGATTGAAAGCCAGATGAATGTATGGAAATTTAGTCT
TTATTG
Found at i:7663 original size:147 final size:147
Alignment explanation
Indices: 7391--7678 Score: 434
Period size: 147 Copynumber: 2.0 Consensus size: 147
7381 ATGTCGTATT
**
7391 CGTGTTTCTATGACATGTCTGCAGTTATCCGGGCTTGACTCCCATATTTCTTTAGTTTCACTGAT
1 CGTGTTTCTATGACATGTCTGCAGTTATCCGGGCTTGACTCCCATATTTCTTTAGTTTCACAAAT
* * *
7456 TGGGATAACTGAAAGATGGTTGGTTATTTGAAGATACAGTCTTCATTTCAGTACAGACATTCTTT
66 TGGGATAACTGAAAGACGGTTGGTTATGTGAAGATACAGTCTTCATTTCAGTACAAACATTCTTT
*
7521 GATTGTGTTGTTGGTGG
131 GATTGTATTGTTGGTGG
* * * *
7538 CGTGTTTCTATGACATGTCTGCAGTTATCTGGGTTTGAGTTCCATATTTCTTTAGTTTCACAAAT
1 CGTGTTTCTATGACATGTCTGCAGTTATCCGGGCTTGACTCCCATATTTCTTTAGTTTCACAAAT
* ** *
7603 TGGGATAA-TAGAAAGACGGTTGGTTATGTGAAGGTTTAGTCTTTATTTCAGTACAAACATTCTT
66 TGGGATAACT-GAAAGACGGTTGGTTATGTGAAGATACAGTCTTCATTTCAGTACAAACATTCTT
7667 TGATTGTATTGT
130 TGATTGTATTGT
7679 CATGTATTGT
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
146 1 0.01
147 125 0.99
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (147 bp):
CGTGTTTCTATGACATGTCTGCAGTTATCCGGGCTTGACTCCCATATTTCTTTAGTTTCACAAAT
TGGGATAACTGAAAGACGGTTGGTTATGTGAAGATACAGTCTTCATTTCAGTACAAACATTCTTT
GATTGTATTGTTGGTGG
Found at i:7826 original size:172 final size:172
Alignment explanation
Indices: 7551--7860 Score: 455
Period size: 172 Copynumber: 1.8 Consensus size: 172
7541 GTTTCTATGA
* *
7551 CATGTCTGCAGTTATCTGGGTTTGAGTTCCATATTTCTTTAGTTTCACAAATTGGGATAATAGAA
1 CATGTCTGCAGTTATCTGGGTTTGAGTTCCATAGTTCTTTAGTTTCACAAATTAGGATAATAGAA
* * * *
7616 AGACGGTTGGTTATGTGAAGGTTTAGTCTTTATTTCAGTACAAACATTCTTTGATTG-TATTGTC
66 AGACAGTTGGTTATGTGAAGATTTAGTATTTATTTCAGTACAAACATTATTTGATTGTTA-TGTC
7680 ATGTATTGTTAGTGGCATAGATGTTGTGTTCATGTTTCTCCTC
130 ATGTATTGTTAGTGGCATAGATGTTGTGTTCATGTTTCTCCTC
* * *
7723 CATGTCTGCAGTTATCTTGGTTTTGAGTTCCATAGTTCTTTAGTTTCACAGATTAGGA-AATCGA
1 CATGTCTGCAGTTATC-TGGGTTTGAGTTCCATAGTTCTTTAGTTTCACAAATTAGGATAATAGA
* * * *
7787 AAGACAGTTGGATT-TTTTAAGATTTAGTATTTATTTCAGTACAAGCATTATTTGGTTGTTATGT
65 AAGACAGTTGG-TTATGTGAAGATTTAGTATTTATTTCAGTACAAACATTATTTGATTGTTATGT
7851 CATGTATTGT
129 CATGTATTGT
7861 CGGTGACATT
Statistics
Matches: 122, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
172 81 0.66
173 41 0.34
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.44
Consensus pattern (172 bp):
CATGTCTGCAGTTATCTGGGTTTGAGTTCCATAGTTCTTTAGTTTCACAAATTAGGATAATAGAA
AGACAGTTGGTTATGTGAAGATTTAGTATTTATTTCAGTACAAACATTATTTGATTGTTATGTCA
TGTATTGTTAGTGGCATAGATGTTGTGTTCATGTTTCTCCTC
Done.