Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008645.1 Kokia drynarioides strain JFW-HI SEQ_123325, 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: 3945
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Found at i:858 original size:19 final size:19
Alignment explanation
Indices: 834--875 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
824 TTAAGCAGAC
834 ATAATTATGATTAATGAAG
1 ATAATTATGATTAATGAAG
853 ATAATTATGATTAATGAAG
1 ATAATTATGATTAATGAAG
872 ATAA
1 ATAA
876 CCCTATCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (19 bp):
ATAATTATGATTAATGAAG
Found at i:1394 original size:104 final size:106
Alignment explanation
Indices: 1201--1605 Score: 510
Period size: 110 Copynumber: 3.8 Consensus size: 106
1191 TATGGAAAAA
** *
1201 AATAAATTAAGAGTGTGTTGGGCAGAGTAACCGGGATGGGGTGCTTGGGTTGTCATTCCATTTCG
1 AATAAATT-AGAGTGTGTTGGGTTGAGTAACCGGGATGGAGTGCTTGGGTTGTCATTCCATTTCG
* *
1266 CGTCAAAATGACCAATACATTCTTAAGT-AAAAAATGATGAT
65 CGTCAAAAGGGCCAATACATTCTTAAGTAAAAAAATGATGAT
* * * *
1307 AATAAATT-GAGTGTGTTGGATTGAGTAATCGGGATGGAGTGCTTGGGTTGTCATTTCATTTTGC
1 AATAAATTAGAGTGTGTTGGGTTGAGTAACCGGGATGGAGTGCTTGGGTTGTCATTCCATTTCGC
* * * *
1371 GTCAAAAGGGTCAATACACTCTTAAGTAAAATAATAATAATAAT
66 GTCAAAAGGGCCAATACATTCTTAAGT-AAA-AA-AATGATGAT
* *
1415 AATAAATTGAGAGTGTGTTGGGTTGAGTAACCGGGATAGAGTGCTTGGGTTGTCATTCCATTTCT
1 AATAAATT-AGAGTGTGTTGGGTTGAGTAACCGGGATGGAGTGCTTGGGTTGTCATTCCATTTCG
*
1480 CATCAAAAGGGCCAATACATTCTTAAGTAAAAAAAAATGATGAT
65 CGTCAAAAGGGCCAATACATTCTTAAGT--AAAAAAATGATGAT
* * * * *
1524 AATAAATTTAGAATATGTTGGGTTGAGTAATCGAGAT-GAGGTGCTTGGATTGTCATTCCATTTC
1 AATAAA-TTAGAGTGTGTTGGGTTGAGTAACCGGGATGGA-GTGCTTGGGTTGTCATTCCATTTC
*
1588 GCGTCAAAAGGGTCAATA
64 GCGTCAAAAGGGCCAATA
1606 TACAAAAAAT
Statistics
Matches: 258, Mismatches: 32, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
104 72 0.28
106 10 0.04
107 2 0.01
108 17 0.07
109 75 0.29
110 78 0.30
111 4 0.02
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (106 bp):
AATAAATTAGAGTGTGTTGGGTTGAGTAACCGGGATGGAGTGCTTGGGTTGTCATTCCATTTCGC
GTCAAAAGGGCCAATACATTCTTAAGTAAAAAAATGATGAT
Found at i:1581 original size:109 final size:110
Alignment explanation
Indices: 1201--1605 Score: 522
Period size: 109 Copynumber: 3.8 Consensus size: 110
1191 TATGGAAAAA
* ** *
1201 AATAAATTAAGAGTGTGTTGGGCAGAGTAACCGGGATG-GGGTGCTTGGGTTGTCATTCCATTTC
1 AATAAATTTAGAGTGTGTTGGGTTGAGTAACCGGGATGAGAGTGCTTGGGTTGTCATTCCATTTC
* *
1265 GCGTCAAAATGACCAATACATTCTTAAGT---AAAAAATGATGAT
66 GCGTCAAAAGGGCCAATACATTCTTAAGTAAAAAAAAATGATGAT
* * * *
1307 AATAAA-TT-GAGTGTGTTGGATTGAGTAATCGGGATG-GAGTGCTTGGGTTGTCATTTCATTTT
1 AATAAATTTAGAGTGTGTTGGGTTGAGTAACCGGGATGAGAGTGCTTGGGTTGTCATTCCATTTC
* * * * *
1369 GCGTCAAAAGGGTCAATACACTCTTAAGTAAAATAATAATAATAAT
66 GCGTCAAAAGGGCCAATACATTCTTAAGTAAAA-AAAAATGATGAT
*
1415 AATAAATTGAGAGTGTGTTGGGTTGAGTAACCGGGAT-AGAGTGCTTGGGTTGTCATTCCATTTC
1 AATAAATTTAGAGTGTGTTGGGTTGAGTAACCGGGATGAGAGTGCTTGGGTTGTCATTCCATTTC
* *
1479 TCATCAAAAGGGCCAATACATTCTTAAGTAAAAAAAAATGATGAT
66 GCGTCAAAAGGGCCAATACATTCTTAAGTAAAAAAAAATGATGAT
* * * * *
1524 AATAAATTTAGAATATGTTGGGTTGAGTAATCGAGATGAG-GTGCTTGGATTGTCATTCCATTTC
1 AATAAATTTAGAGTGTGTTGGGTTGAGTAACCGGGATGAGAGTGCTTGGGTTGTCATTCCATTTC
*
1588 GCGTCAAAAGGGTCAATA
66 GCGTCAAAAGGGCCAATA
1606 TACAAAAAAT
Statistics
Matches: 255, Mismatches: 36, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
104 72 0.28
105 1 0.00
106 6 0.02
107 1 0.00
108 15 0.06
109 80 0.31
110 80 0.31
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (110 bp):
AATAAATTTAGAGTGTGTTGGGTTGAGTAACCGGGATGAGAGTGCTTGGGTTGTCATTCCATTTC
GCGTCAAAAGGGCCAATACATTCTTAAGTAAAAAAAAATGATGAT
Done.