Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004171.1 Kokia drynarioides strain JFW-HI SEQ_117403, 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, 957
Length: 1596
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Found at i:636 original size:49 final size:49
Alignment explanation
Indices: 561--822 Score: 221
Period size: 49 Copynumber: 5.3 Consensus size: 49
551 TATGAAGATT
* * * * * *
561 TGAAGGGAAAGGTTTAAGTTGCAATGGCGAACCTAGTTCCTTAGAGATA
1 TGAAGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACA
* * * *
610 TGAAGGGAAAGATCTAAGTCGGAATGGCGGATCC-AATACCGC-GAAGACA
1 TGAAGGGAAAGATCTAAGTCGCAATGGC-GAACCTAGTACCTCAG-AGACA
* * *
659 T-AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGCACCTCAGAGACA
1 TGAAGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACA
* * * * * *
707 TGAAGGGAAAGATCTAAGCCGCAACGGAGGATCTAGTACCGC-GAAGACA
1 TGAAGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAG-AGACA
* * *
756 TGAAGGGAAA-AGTTTAAGTCGCAATGGTGAACCTAGTACCTCA-AAAGCA
1 TGAAGGGAAAGA-TCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGA-CA
*
805 TAAAAGGGAAAGATCTAA
1 T-GAAGGGAAAGATCTAA
823 ACCGTAACGG
Statistics
Matches: 166, Mismatches: 36, Indels: 21
0.74 0.16 0.09
Matches are distributed among these distances:
47 4 0.02
48 39 0.23
49 106 0.64
50 16 0.10
51 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (49 bp):
TGAAGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACA
Found at i:676 original size:48 final size:49
Alignment explanation
Indices: 609--971 Score: 204
Period size: 48 Copynumber: 7.4 Consensus size: 49
599 CCTTAGAGAT
* *
609 ATGAAGGGAAAGATCTAAGTCGGAATGGCGGATCCAATACCGCGAAGAC
1 ATGAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAGTACCGCGAAGAC
* * * * *
658 AT-AAGGGAAAGGTTTAAGTCGCAATGGC-GAACCTAGCACCTC-AGAGAC
1 ATGAAGGGAAAGATCTAAGTCGCAATGGCGGATCC-AGTACCGCGA-AGAC
* * * *
706 ATGAAGGGAAAGATCTAAGCCGCAACGGAGGATCTAGTACCGCGAAGAC
1 ATGAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAGTACCGCGAAGAC
* * * * *
755 ATGAAGGGAAA-AGTTTAAGTCGCAATGG-TGAACCTAGTACCTC-AAAAGC
1 ATGAAGGGAAAGA-TCTAAGTCGCAATGGCGGATCC-AGTACCGCGAAGA-C
* ** * * * *
804 ATAAAAGGGAAAGATCTAAACCGTAACGGCGGATCCAATACCACGAAGAC
1 AT-GAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAGTACCGCGAAGAC
* * * * * ** * * *
854 ACG-AGGGAAAGACCTAAGCCGCTACGATGGATCCAATACCACGAAGAT
1 ATGAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAGTACCGCGAAGAC
* * * * * **
902 A-CAATGGAAGGATCTAAGCCGCAATGGCAGATCC-GATACCATGAAGAC
1 ATGAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAG-TACCGCGAAGAC
** * *
950 ACAAAGGGAAAGGTTTAAGTCG
1 ATGAAGGGAAAGATCTAAGTCG
972 TAGACGAACC
Statistics
Matches: 237, Mismatches: 62, Indels: 30
0.72 0.19 0.09
Matches are distributed among these distances:
47 5 0.02
48 114 0.48
49 80 0.34
50 30 0.13
51 8 0.03
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (49 bp):
ATGAAGGGAAAGATCTAAGTCGCAATGGCGGATCCAGTACCGCGAAGAC
Found at i:739 original size:97 final size:97
Alignment explanation
Indices: 563--864 Score: 390
Period size: 97 Copynumber: 3.1 Consensus size: 97
553 TGAAGATTTG
* * * *
563 AAGGGAAAGGTTTAAGTTGCAATGGCGAACCTAGTTCCTTAGAGATATGAAGGGAAAGATCTAAG
1 AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAG
* * *
628 TCGGAATGGCGGATCCAATACCGCGAAGACAT
66 CCGCAACGGCGGATCCAATACCGCGAAGACAT
*
660 AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGCACCTCAGAGACATGAAGGGAAAGATCTAAG
1 AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAG
* * *
725 CCGCAACGGAGGATCTAGTACCGCGAAGACAT
66 CCGCAACGGCGGATCCAATACCGCGAAGACAT
* * * *
757 GAAGGGAAAAGTTTAAGTCGCAATGGTGAACCTAGTACCTCA-AAAGCATAAAAGGGAAAGATCT
1 -AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGA-CAT-GAAGGGAAAGATCT
* * * *
821 AAACCGTAACGGCGGATCCAATACCACGAAGACAC
63 AAGCCGCAACGGCGGATCCAATACCGCGAAGACAT
*
856 GAGGGAAAG
1 AAGGGAAAG
865 ACCTAAGCCG
Statistics
Matches: 177, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
97 88 0.50
98 48 0.27
99 41 0.23
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.16
Consensus pattern (97 bp):
AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAG
CCGCAACGGCGGATCCAATACCGCGAAGACAT
Found at i:1349 original size:39 final size:39
Alignment explanation
Indices: 1250--1519 Score: 139
Period size: 39 Copynumber: 6.9 Consensus size: 39
1240 AATGGAGTTA
* * *
1250 CATCGTCAACCAATTTTTTACCCCTAGCTTGGGGCAAAT
1 CATCGTCAACCAATCTCTTACCCCGAGCTTGGGGCAAAT
*
1289 --T-G-CAACCATTTGATCTTTTACCCCGAGCTTGGGGCAAAT
1 CATCGTCAACCA----ATCTCTTACCCCGAGCTTGGGGCAAAT
* * * ** *
1328 CATCGTCAACCAATCTCTTACCCCGAACCTAGTTCAGAT
1 CATCGTCAACCAATCTCTTACCCCGAGCTTGGGGCAAAT
* * * * *
1367 --T-G-CAGCCATTTGTTCTTTCACCCCGAGCTTGGGGTAGAT
1 CATCGTCAACCA-AT-CTC-TT-ACCCCGAGCTTGGGGCAAAT
* * *
1406 CATCGTCAACCAATCTCTTACCCCGAGCCTAGGGCAGATT
1 CATCGTCAACCAATCTCTTACCCCGAGCTTGGGGCA-AAT
* * * *
1446 GCAAC--CATCCGA-CTTTTTACCCCGAGCTTGGGGCAAAT
1 -CATCGTCAACCAATC-TCTTACCCCGAGCTTGGGGCAAAT
* * *
1484 CACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCA
1 CATCGTCAACCAATCTCTTACCCCGAGCTTGGGGCA
1520 GATTGTAGTT
Statistics
Matches: 172, Mismatches: 37, Indels: 44
0.68 0.15 0.17
Matches are distributed among these distances:
35 11 0.06
36 3 0.02
37 7 0.04
38 5 0.03
39 121 0.70
40 4 0.02
41 7 0.04
42 3 0.02
43 11 0.06
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (39 bp):
CATCGTCAACCAATCTCTTACCCCGAGCTTGGGGCAAAT
Found at i:1384 original size:78 final size:77
Alignment explanation
Indices: 1250--1524 Score: 316
Period size: 78 Copynumber: 3.5 Consensus size: 77
1240 AATGGAGTTA
* * * * * * *
1250 CATCGTCAACCAATTTTTTACCCCTAGCTTGGGGCAAATTGCAACCATTTGATCTTTTACCCCGA
1 CATCGTCAACCAATCTCTTACCCCGAACCTAGGGCAGATTGCAACCATTTG-TCTTTTACCCCGA
1315 GCTTGGGGCAAAT
65 GCTTGGGGCAAAT
** * *
1328 CATCGTCAACCAATCTCTTACCCCGAACCTAGTTCAGATTGCAGCCATTTGTTCTTTCACCCCGA
1 CATCGTCAACCAATCTCTTACCCCGAACCTAGGGCAGATTGCAACCATTTG-TCTTTTACCCCGA
* *
1393 GCTTGGGGTAGAT
65 GCTTGGGGCAAAT
* ** *
1406 CATCGTCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATCCGACTTTTTACCCCGA
1 CATCGTCAACCAATCTCTTACCCCGAACCTAGGGCAGATTGCAACCATTTGTC-TTTTACCCCGA
1471 GCTTGGGGCAAAT
65 GCTTGGGGCAAAT
* * * * * *
1484 CACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTG
1 CATCGTCAACCAATCTCTTACCCCGAACCTAGGGCAGATTG
1525 TAGTTATCCA
Statistics
Matches: 167, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
77 1 0.01
78 166 0.99
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (77 bp):
CATCGTCAACCAATCTCTTACCCCGAACCTAGGGCAGATTGCAACCATTTGTCTTTTACCCCGAG
CTTGGGGCAAAT
Done.