Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010370.1 Kokia drynarioides strain JFW-HI SEQ_125243, 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: 22470
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4557 original size:18 final size:18
Alignment explanation
Indices: 4534--4592 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
4524 ATGGTAAAAT
4534 AAATAAAATACATGAATA
1 AAATAAAATACATGAATA
* *
4552 AAATAAATTAAATGAATA
1 AAATAAAATACATGAATA
* *
4570 CAAT-TAATAACAT-AATA
1 AAATAAAAT-ACATGAATA
4587 AAATAA
1 AAATAA
4593 TAAATAGAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 9 0.29
18 22 0.71
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.25
Consensus pattern (18 bp):
AAATAAAATACATGAATA
Found at i:4826 original size:50 final size:48
Alignment explanation
Indices: 4762--4860 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 48
4752 AAAAAAAAAG
* **
4762 ACATATAAATAAATAAAAATATCAAACATAATGAAATTAAGGATAAATAA
1 ACATATAAATAAATAAAAAGAAAAAACATAA--AAATTAAGGATAAATAA
* * * *
4812 ACATGTAATTAAATAAAAAGAAAAAACATAAAATTTAATGATAAATAA
1 ACATATAAATAAATAAAAAGAAAAAACATAAAAATTAAGGATAAATAA
4860 A
1 A
4861 TAATTAAACA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 16 0.38
50 26 0.62
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.24
Consensus pattern (48 bp):
ACATATAAATAAATAAAAAGAAAAAACATAAAAATTAAGGATAAATAA
Found at i:5069 original size:15 final size:16
Alignment explanation
Indices: 5048--5083 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5038 ATTAGACATG
5048 AAAATAAAT-AACAAA
1 AAAATAAATAAACAAA
*
5063 TAAATAAATAAACAAA
1 AAAATAAATAAACAAA
5079 AAAAT
1 AAAAT
5084 TTAAATGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:6232 original size:46 final size:44
Alignment explanation
Indices: 5923--6502 Score: 396
Period size: 46 Copynumber: 12.6 Consensus size: 44
5913 TTCAATTTAC
* *
5923 CCCTCTGGATTTAAGGGGTATAAGATTGGATGCGGTAGCTTCAATCTG
1 CCCTCTGGATTT-A-GGGTAAAAGATTGGAT--GGTGGCTTCAATCTG
* * * *
5971 TCCCTCTAGATTTTGGGGTATAAGATTGGATGTGGTAGCTTCAATCTG
1 -CCCTCTGGA-TTTAGGGTAAAAGATTGGA--TGGTGGCTTCAATCTG
* * ** ** * *
6019 CCTTTATGGATTTAGGGGTAAAAGATTAAATTATGGCTTTAATCTAC
1 CC-CTCTGGATTTA-GGGTAAAAGATTGGATGGTGGCTTCAATCT-G
* * *
6066 CCCTCTAGATTAAGGGCAAAAGATTGGATGGTGGCTTCAATCTG
1 CCCTCTGGATTTAGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* * *
6110 TCCCTCTGGATTAAGGGTAAAAGGTTGGATGGTGGCTTTAATCTG
1 -CCCTCTGGATTTAGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* * *
6155 CCCCTCTAGA-TTAGAGGTAAAAGATTGGATGGTAGCTGCAATCTG
1 -CCCTCTGGATTTAG-GGTAAAAGATTGGATGGTGGCTTCAATCTG
* * ** *
6200 CCCTTTTGGATTTAGGGATAAAAGGTTGGATGGTGGCTTTGATCTA
1 CCC-TCTGGATTTAGGG-TAAAAGATTGGATGGTGGCTTCAATCTG
* * * *
6246 CCTCTTTAGATTTAGGGGTAAAAGATTGAATGGTGTCTTCAAAT-TG
1 CC-CTCTGGATTTA-GGGTAAAAGATTGGATGGTGGCTTC-AATCTG
* * * *
6292 CCCCTCTAGA-TTAGGGGTAAAAGATTGAATAGTGGCTTCAATCTAT
1 -CCCTCTGGATTTA-GGGTAAAAGATTGGATGGTGGCTTCAATCT-G
* ** * * * *
6338 CCTTCTATATTTAGAGCTAAAAAATTGGATGGTGACTTCAATCTAT
1 CCCTCTGGATTTAG-GGTAAAAGATTGGATGGTGGCTTCAATCT-G
* ** * *
6384 CCTTCTATATTTAGGGGTAAAAGATTGAATGGTGGCTTCAATCTTC
1 CCCTCTGGATTTA-GGGTAAAAGATTGGATGGTGGCTTCAATC-TG
* *
6430 CCCTCTGGATTTAGGGAGTAAAAG-TTAGATGGTGGTTTCAATCTG
1 CCCTCTGGATTTA-GG-GTAAAAGATTGGATGGTGGCTTCAATCTG
*
6475 CCTCTCTAGA-TTAGGGGTAAAAGATTGG
1 CC-CTCTGGATTTA-GGGTAAAAGATTGG
6503 GTGTTGTAGC
Statistics
Matches: 431, Mismatches: 76, Indels: 52
0.77 0.14 0.09
Matches are distributed among these distances:
44 16 0.04
45 152 0.35
46 181 0.42
47 24 0.06
48 46 0.11
49 8 0.02
50 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (44 bp):
CCCTCTGGATTTAGGGTAAAAGATTGGATGGTGGCTTCAATCTG
Found at i:6496 original size:137 final size:137
Alignment explanation
Indices: 5911--6502 Score: 527
Period size: 137 Copynumber: 4.3 Consensus size: 137
5901 GCTTTCTGTA
* * * * * * *
5911 GCTTCAATTTACCCCTCTGGATTTAAGGGGTATAAGATTGGATGCGGTAGCTTCAATCTGTCCCT
1 GCTTCAATCTGCCTCTCTAGATTT-AGGGGTAAAAGATTGGAT--GGTGGCTTCAATCTATCCCT
* * * * ** * *
5976 CTAGATTTTGGGGTATAAGATTGGATGTGGTAGCTTCAATCTGCCTTTATGGATTTAGGGGTAAA
63 CTAGATTTAGGGGTAAAAGATT-GA-ATGGTGGCTTCAATCTGCCCCTCTAGA-TTAGGGGTAAA
* **
6041 AGATTAAATTATG
125 AGATTAGATGGTG
* * * * * * *
6054 GCTTTAATCTACCCCTCTAGA-TTAAGGGCAAAAGATTGGATGGTGGCTTCAATCTGTCCCTCTG
1 GCTTCAATCTGCCTCTCTAGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTATCCCTCTA
* * * * * *
6118 GA-TTAAGGGTAAAAGGTTGGATGGTGGCTTTAATCTGCCCCTCTAGATTAGAGGTAAAAGATTG
66 GATTTAGGGGTAAAAGATTGAATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTA
*
6182 GATGGTA
131 GATGGTG
* * * * * ** *
6189 GCTGCAATCTGCC-CTTTTGGATTTAGGGATAAAAGGTTGGATGGTGGCTTTGATCTA-CCTCTT
1 GCTTCAATCTGCCTC-TCTAGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTATCC-CTC
*
6252 TAGATTTAGGGGTAAAAGATTGAATGGTGTCTTCAAAT-TGCCCCTCTAGATTAGGGGTAAAAGA
64 TAGATTTAGGGGTAAAAGATTGAATGGTGGCTTC-AATCTGCCCCTCTAGATTAGGGGTAAAAGA
*
6316 TT-GAATAGTG
128 TTAG-ATGGTG
* * * * * * *
6326 GCTTCAATCTATCCT-TCTATATTTAGAGCTAAAAAATTGGATGGTGACTTCAATCTATCCTTCT
1 GCTTCAATCT-GCCTCTCTAGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTATCCCTCT
* * *
6390 ATATTTAGGGGTAAAAGATTGAATGGTGGCTTCAATCTTCCCCTCTGGATTTAGGGAGTAAAAG-
65 AGATTTAGGGGTAAAAGATTGAATGGTGGCTTCAATCTGCCCCTCTAGA-TTAGGG-GTAAAAGA
6454 TTAGATGGTG
128 TTAGATGGTG
*
6464 GTTTCAATCTGCCTCTCTAGA-TTAGGGGTAAAAGATTGG
1 GCTTCAATCTGCCTCTCTAGATTTAGGGGTAAAAGATTGG
6503 GTGTTGTAGC
Statistics
Matches: 362, Mismatches: 73, Indels: 34
0.77 0.16 0.07
Matches are distributed among these distances:
134 1 0.00
135 34 0.09
136 57 0.16
137 158 0.44
138 46 0.13
139 31 0.09
141 15 0.04
142 2 0.01
143 18 0.05
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (137 bp):
GCTTCAATCTGCCTCTCTAGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTATCCCTCTA
GATTTAGGGGTAAAAGATTGAATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTA
GATGGTG
Done.