Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006713.1 Kokia drynarioides strain JFW-HI SEQ_121309, 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: 6392
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:3008 original size:16 final size:15
Alignment explanation
Indices: 2987--3018 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2977 TACTAAAACT
2987 ATTTTTTTAAAATATA
1 ATTTTTTT-AAATATA
3003 ATTTTTTTAAATATA
1 ATTTTTTTAAATATA
3018 A
1 A
3019 AATTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTTTTAAATATA
Found at i:3022 original size:17 final size:16
Alignment explanation
Indices: 2987--3022 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2977 TACTAAAACT
*
2987 ATTTTTTTAAAATATA
1 ATTTTTTTAAAATAAA
3003 ATTTTTTTAAATATAAA
1 ATTTTTTTAAA-ATAAA
3020 ATT
1 ATT
3023 ATTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTTTTAAAATAAA
Found at i:3125 original size:31 final size:33
Alignment explanation
Indices: 3090--3162 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
3080 CCCAATTTCA
3090 TCTTCTTCCT-CATTTTT-CATCTAACACCACT
1 TCTTCTTCCTACATTTTTCCATCTAACACCACT
* * *
3121 TCTTCTGCTTACCATTTTTCCATCTAACATCACT
1 TCTTCTTCCTA-CATTTTTCCATCTAACACCACT
3155 TCTTCTTC
1 TCTTCTTC
3163 TCACATTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.23
33 7 0.20
34 20 0.57
ACGTcount: A:0.18, C:0.34, G:0.01, T:0.47
Consensus pattern (33 bp):
TCTTCTTCCTACATTTTTCCATCTAACACCACT
Found at i:3840 original size:16 final size:14
Alignment explanation
Indices: 3813--3886 Score: 62
Period size: 16 Copynumber: 5.1 Consensus size: 14
3803 GATGATGATG
3813 ATTATAATTTTAAAA
1 ATTAT-ATTTTAAAA
3828 ATTTTATATTTTAAAA
1 A--TTATATTTTAAAA
3844 ATTA-ATTTT-AAA
1 ATTATATTTTAAAA
* *
3856 ATAATTTTTTAATAA
1 ATTATATTTTAA-AA
*
3871 TTCTATATTTTAAAA
1 AT-TATATTTTAAAA
3886 A
1 A
3887 AATAATTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
12 6 0.13
13 9 0.19
14 4 0.09
15 6 0.13
16 18 0.38
17 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATATTTTAAAA
Found at i:3878 original size:42 final size:41
Alignment explanation
Indices: 3820--3904 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 41
3810 ATGATTATAA
* *
3820 TTTTAAAAATTTTATATTTT-AAAAATTAATTTTAAAATAATT
1 TTTTAAAAATTCTATATTTTAAAAAAATAATTTT--AATAATT
*
3862 TTTTAATAATTCTATATTTTAAAAAAATAATTTTAATAATT
1 TTTTAAAAATTCTATATTTTAAAAAAATAATTTTAATAATT
3903 TT
1 TT
3905 AAAATGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 9 0.23
42 18 0.46
43 12 0.31
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (41 bp):
TTTTAAAAATTCTATATTTTAAAAAAATAATTTTAATAATT
Found at i:3891 original size:21 final size:23
Alignment explanation
Indices: 3866--3908 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3856 ATAATTTTTT
3866 AATAATTCT-AT-ATTTTAAAAA
1 AATAATTCTAATAATTTTAAAAA
*
3887 AATAATTTTAATAATTTTAAAA
1 AATAATTCTAATAATTTTAAAA
3909 TGATTTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AATAATTCTAATAATTTTAAAAA
Found at i:4452 original size:46 final size:46
Alignment explanation
Indices: 4328--5097 Score: 545
Period size: 46 Copynumber: 16.9 Consensus size: 46
4318 AGATAATAGT
* * * * * *
4328 TTCAATTTCCCCCTCTCGA-TTAGGGGTAAAAGATTGGAAGATGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * * *
4373 TTCAATCT-ACCC-CATG-GTT-GGGGTAAGAGATTGGATGGTGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * *
4415 TTCAATCTACCCCCCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * * *
4461 TTCAATTTG--CCTCATGA--TCGGGGTAAGAA-ATTGGATAGTATGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAA-AAGATTGGAT-G-GTGTC
4505 TTCAATCTAG-CCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTC
1 TTCAATCT-GCCCCTCTTGACTTAGGGGTAAAAGATTGGAT-G-G-TGTC
* * * * * * *
4554 TTCAATTTGCCCCTCTTGAATTAAGGGTAAAAGATCGAATGATGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * * * * * *
4600 TTCAATTTG-CCC-CATG--GTCGGGGTAAGAGATTGGGTGGTGTT
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * *
4642 TTCAATCTGCCCTTCTTAACTTAGGGGTAAAAGATTGGATGGTGAC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* * * *
4688 TTTAATCTGCCCCTTTTGACTTAGGGGTAAAAGGTTGGGTGGTGATGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAT-G-G-TGTC
* * * * *
4737 TTCAATTTGTCCCTCTTGACTTAGGGGTAAAATATTAGATGAT-TGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGT-C
* * * * *
4783 TTCAATCTG--CTTCATG-GTTA-GGGTAAGAGATTGGATGGTATC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* *
4825 TTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
* *
4871 TTCAATCTG-CCC-CATGA--TAGGGGTAAGAA-ATTAGATAGTGTTGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAA-AAGATTGGAT-G-G-TGTC
* * * *
4916 TCCAATCTACCCTTCTTAACTTAGGGGTAAAAGATTGGATGGTGATGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAT-G-G-TGTC
* * *
4965 TTCAATCTACACCTCTTTACTTAGGGGTAAAAGATTAGGTGATGGT-T-
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATT--G-GATGGTGTC
* * * * *
5012 TT-AATCTGCCCCTTTTAACTTAAGGGTAAAACATTAGATGGTAG-C
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGT-GTC
* *
5057 TTCAATCTGCCCTTCTTGACTTAGGGGTAAAAGATTAGATG
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATG
5098 ATGATGTAAC
Statistics
Matches: 571, Mismatches: 110, Indels: 87
0.74 0.14 0.11
Matches are distributed among these distances:
42 106 0.19
43 25 0.04
44 42 0.07
45 32 0.06
46 201 0.35
47 8 0.01
48 24 0.04
49 127 0.22
50 1 0.00
51 2 0.00
52 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (46 bp):
TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGTC
Found at i:4541 original size:90 final size:88
Alignment explanation
Indices: 4328--4566 Score: 300
Period size: 88 Copynumber: 2.7 Consensus size: 88
4318 AGATAATAGT
* * * * * * * * *
4328 TTCAATTTCCCCCTCTCGA-TTAGGGGTAAAAGATTGGAAGATGGCTTCAATCTACCCCATGGTT
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCATGATC
* *
4392 GGGGTAAGAGATTGGATGGTGTC
66 GGGGTAAGAAATTGGATGATGTC
* *
4415 TTCAATCTACCCCCCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCTCATGATC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCATGATC
4480 GGGGTAAGAAATTGGATAGTATGTC
66 GGGGTAAGAAATTGGAT-G-ATGTC
*
4505 TTCAATCTAGCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTG--G-CTTCAATTTGCCCC
4567 TCTTGAATTA
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
87 15 0.12
88 54 0.42
89 1 0.01
90 46 0.35
92 1 0.01
93 13 0.10
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (88 bp):
TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGCCCCATGATC
GGGGTAAGAAATTGGATGATGTC
Found at i:4699 original size:88 final size:88
Alignment explanation
Indices: 4526--4960 Score: 385
Period size: 88 Copynumber: 4.8 Consensus size: 88
4516 CCTCTTGACT
* * * *
4526 TAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCTCTTGAA-TTAAGGGTAAAAGATC
1 TAGGGGTAAGAGATTGGATGGTG-T-TCTTCAATCTG-CCCTCTT-AACTTAGGGGTAAAAGATT
* * * *
4590 GAATGATGGCTTCAATTTGCCCCATGG
62 GGATGGTGACTTCAATCTGCCCCATGG
* *
4617 TCGGGGTAAGAGATTGGGTGGTGTT-TTCAATCTGCCCTTCTTAACTTAGGGGTAAAAGATTGGA
1 TAGGGGTAAGAGATTGGATGGTGTTCTTCAATCTGCCC-TCTTAACTTAGGGGTAAAAGATTGGA
* * *
4681 TGGTGACTTTAATCTGCCCCTTTTGACT
65 TGGTGACTTCAATCTGCCCC--ATG--G
* * * * * * *
4709 TAGGGGTAAAAGGTTGGGTGGTGATGTCTTCAATTTGTCCCTCTTGACTTAGGGGTAAAATATTA
1 TAGGGGTAAGAGATTGGATGGTG-T-TCTTCAATCTG-CCCTCTTAACTTAGGGGTAAAAGATTG
* **
4774 GATGATTG-CTTCAATCTGCTTCATGG
63 GATG-GTGACTTCAATCTGCCCCATGG
* *
4800 TTA-GGGTAAGAGATTGGATGGT-ATCTTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGG
1 -TAGGGGTAAGAGATTGGATGGTGTTCTTCAATCTG-CCCTCTTAACTTAGGGGTAAAAGATTGG
* *
4863 ATGGTGGCTTCAATCTGCCCCATGA
64 ATGGTGACTTCAATCTGCCCCATGG
* * * * *
4888 TAGGGGTAAGAAATTAGATAGTGTTGTCTCCAATCTACCCTTCTTAACTTAGGGGTAAAAGATTG
1 TAGGGGTAAGAGATTGGATGGTG-T-TCTTCAATCTGCCC-TCTTAACTTAGGGGTAAAAGATTG
4953 GATGGTGA
63 GATGGTGA
4961 TGTCTTCAAT
Statistics
Matches: 281, Mismatches: 45, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
87 9 0.03
88 115 0.41
89 1 0.00
90 6 0.02
91 75 0.27
92 22 0.08
93 3 0.01
94 1 0.00
95 44 0.16
96 5 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (88 bp):
TAGGGGTAAGAGATTGGATGGTGTTCTTCAATCTGCCCTCTTAACTTAGGGGTAAAAGATTGGAT
GGTGACTTCAATCTGCCCCATGG
Found at i:4733 original size:183 final size:183
Alignment explanation
Indices: 4504--5104 Score: 562
Period size: 183 Copynumber: 3.3 Consensus size: 183
4494 GATAGTATGT
4504 CTTCAATCTAG-CCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCT
1 CTTCAATCT-GCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCT
* *
4568 CTTGAATTAAGGGTAAAAGATCGA-ATGATGGCTTCAATTTGCCCCATGGTCGGGGTAAGAGATT
65 CTTGAATTAAGGGTAAAAGAT-GAGATGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATT
* * *
4632 GGGTGGTGTTTTCAATCTG-CCCTTCTTAACTTAGGGGTAAAAGATTGGATGGTGA
129 GGATGGTATCTTCAATCTGTCCC-TCTTAACTTAGGGGTAAAAGATTGGATGGTGA
* * * * *
4687 CTTTAATCTGCCCCTTTTGACTTAGGGGTAAAAGGTTGGGTGGTGATGTCTTCAATTTGTCCCTC
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCTC
* * * * * ** *
4752 TTGACTTAGGGGTAAAATATTAGATGATTGCTTCAATCTGCTTCATGGTTAGGGTAAGAGATTGG
66 TTGAATTAAGGGTAAAAGATGAGATGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGG
* *
4817 ATGGTATCTTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGG
131 ATGGTATCTTCAATCTGTCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGA
* * * * * * * *
4870 CTTCAATCTG-CCC-CATGA--TAGGGGTAAGAA-ATTAGATAGTGTTGTCTCCAATCTACCCTT
1 CTTCAATCTGCCCCTCTTGACTTAGGGGTAA-AAGATTGGATGGTGATGTCTTCAATTTGCCCCT
* * * * * ** *
4930 CTT-AACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATCTACACCTCTTTACTTAGGGGTA
65 CTTGAA-TTAAGGGTAAAAGA-T-GA-GATGATGGCTTCAATCTGC-CC-C-ATGGTCA-GGGTA
* * * * * *
4994 AAAGATTAGGTGATGGT-T-TT-AATCTGCCCCTTTTAACTTAAGGGTAAAACATTAGATGGT-A
122 AGAGATT--G-GATGGTATCTTCAATCTGTCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGA
* * *
5055 GCTTCAATCTGCCCTTCTTGACTTAGGGGTAAAAGATTAGATGATGATGT
1 -CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGT
5105 AACTTTACTC
Statistics
Matches: 339, Mismatches: 58, Indels: 35
0.78 0.13 0.08
Matches are distributed among these distances:
178 1 0.00
179 45 0.13
180 3 0.01
181 4 0.01
182 20 0.06
183 164 0.48
184 4 0.01
185 4 0.01
186 55 0.16
187 4 0.01
188 6 0.02
189 8 0.02
190 21 0.06
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (183 bp):
CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGATGTCTTCAATTTGCCCCTC
TTGAATTAAGGGTAAAAGATGAGATGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGG
ATGGTATCTTCAATCTGTCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGA
Found at i:5332 original size:95 final size:95
Alignment explanation
Indices: 5111--5395 Score: 344
Period size: 95 Copynumber: 3.0 Consensus size: 95
5101 ATGTAACTTT
* * * * * * * *
5111 ACTCCATTCCACAGTAGCCTCAAGGACGTTGAGATCT-ATTACCTT-TTTTGACCCACTTCTCTG
1 ACTCCACTCCACTGTAACCTCAAGGACATTGAGCTCTGCTT-CATTGTTTTGATCCACTTCTCTG
5174 TATCTCATCAGGAAGAT-GGTTTGAAGTTTC
65 TATCTCATCAGGAAGATGGGTTTGAAGTTTC
* * * *
5204 GCTCCACTTCACTGTAACCTCAGGGACATTGAGCTCTGCTTCATTGTTTTGATCCACTTCTTTGT
1 ACTCCACTCCACTGTAACCTCAAGGACATTGAGCTCTGCTTCATTGTTTTGATCCACTTCTCTGT
* *
5269 ATGTCATTAGGAAGATGGGTTTGAAGTTTC
66 ATCTCATCAGGAAGATGGGTTTGAAGTTTC
* ** *
5299 ACTCTACTCCACTGTAACC-CTAAGGATGTTGAGCTTTGCTTCATTGTTTTGATCCACTTCTCTG
1 ACTCCACTCCACTGTAACCTC-AAGGACATTGAGCTCTGCTTCATTGTTTTGATCCACTTCTCTG
*
5363 TATCTCATCAAGAAGATGGGGTTTGAAGTTTC
65 TATCTCATCAGGAAGAT-GGGTTTGAAGTTTC
5395 A
1 A
5396 TTGTTGTGAC
Statistics
Matches: 162, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
93 32 0.20
94 34 0.21
95 81 0.50
96 15 0.09
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (95 bp):
ACTCCACTCCACTGTAACCTCAAGGACATTGAGCTCTGCTTCATTGTTTTGATCCACTTCTCTGT
ATCTCATCAGGAAGATGGGTTTGAAGTTTC
Done.