Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012122.1 Kokia drynarioides strain JFW-HI SEQ_127121, 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: 16660
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:581 original size:30 final size:30
Alignment explanation
Indices: 547--617 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
537 GAAACCCGAG
547 CGGCGACGCGCAATGGCCACGCGCCGAGTT
1 CGGCGACGCGCAATGGCCACGCGCCGAGTT
*
577 CGGCGACGCGCAATTGCCACGCGCCGAGTT
1 CGGCGACGCGCAATGGCCACGCGCCGAGTT
*
607 CGCCGACGCGC
1 CGGCGACGCGC
618 GTGAGNNNNN
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.15, C:0.39, G:0.35, T:0.10
Consensus pattern (30 bp):
CGGCGACGCGCAATGGCCACGCGCCGAGTT
Found at i:587 original size:17 final size:17
Alignment explanation
Indices: 565--617 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
555 CGCAATGGCC
565 ACGCGCCGAGTTCGGCG
1 ACGCGCCGAGTTCGGCG
* *
582 ACGCG-C-AATT--GCC
1 ACGCGCCGAGTTCGGCG
*
595 ACGCGCCGAGTTCGCCG
1 ACGCGCCGAGTTCGGCG
612 ACGCGC
1 ACGCGC
618 GTGAGNNNNN
Statistics
Matches: 27, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
13 7 0.26
14 1 0.04
15 6 0.22
16 1 0.04
17 12 0.44
ACGTcount: A:0.15, C:0.40, G:0.34, T:0.11
Consensus pattern (17 bp):
ACGCGCCGAGTTCGGCG
Found at i:1315 original size:59 final size:59
Alignment explanation
Indices: 1229--1877 Score: 785
Period size: 59 Copynumber: 11.0 Consensus size: 59
1219 TCCCAGAGGT
* * * *
1229 CCCCGAACCTTCTAAAAATTA-TCATTTTACCCCCGAATTTCTAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACT-ATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* *
1288 CCCCGAACATTCCAAAAGTTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * * *
1347 CCTCAAACCTTCCAAAAATTAGTATTTTACCCTCGAACTTCCAAAAATCTCATTTTTAA
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1406 CCCCGAACCTTCCAAAAATTACTATTTTACCAC-CGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACTATTTTACC-CTCGAACTTCCAAAAATCCCATTTTTGA
* * *
1465 CCTCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGA
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * * *
1524 CCCCAAACCTTCCAAAATTTACTATTTTACCCCCGAACTCCCAAAATTCCCATTTTT-A
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * *
1582 GCCCCGAACCTTTCAAAAATTACCATTTTACTCTCGAAC-TCTCAAAAATCTCATTTTT-A
1 -CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTC-CAAAAATCCCATTTTTGA
* * *
1641 GCCTCGAACCTTCCAAAAATTATTGTTTTACCCTCGAAC-TCTCAAAAATCCCATTTTT-A
1 -CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTC-CAAAAATCCCATTTTTGA
* * *
1700 GCCCCGAACCTTCCAAAAATTATTGTTTTACCCTCGAACTCCCAAAAATCCCATTTTT-A
1 -CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * *
1759 GCCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAAC-TCTCAAAAATCCCATTTTTGA
1 -CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTC-CAAAAATCCCATTTTTGA
* * ** * * * * *
1819 CCTCGAATCTTTTAAAAATTACCATTTTACCCTCGAATTTCCCAAGATCCTATTTTTGA
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1878 TTCCGGACAT
Statistics
Matches: 523, Mismatches: 58, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
58 4 0.01
59 513 0.98
60 6 0.01
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (59 bp):
CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:1894 original size:177 final size:177
Alignment explanation
Indices: 1229--1877 Score: 896
Period size: 177 Copynumber: 3.7 Consensus size: 177
1219 TCCCAGAGGT
* * *
1229 CCCCGAACC-TTCTAAAAATTATCATTTTACCCCCGAA-TTTCTAAAAATCCCATTTTTGACCCC
1 CCCCGAACCTTTC-AAAAATTACCATTTTACCCCCGAACTCTC-AAAAATCCCATTTTTGACCTC
* * *
1292 GAACATTCCAAAAGTTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAAACCT
64 GAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
* * * *
1357 TCCAAAAATTAGTATTTTACCCTCGAACTTCCAAAAATCTCATTTTTAA
129 TCCAAAAATTACTATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAG
* * *
1406 CCCCGAACCTTCCAAAAATTACTATTTTACCACCGAACT-TCCAAAAATCCCATTTTTGACCTCG
1 CCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAACTCT-CAAAAATCCCATTTTTGACCTCG
* *
1470 AACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCCAAACCTT
65 AACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTT
* * *
1535 CCAAAATTTACTATTTTACCCCCGAACTCCCAAAATTCCCATTTTTAG
130 CCAAAAATTACTATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAG
* * *
1583 CCCCGAACCTTTCAAAAATTACCATTTTACTCTCGAACTCTCAAAAATCTCATTTTT-AGCCTCG
1 CCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAACTCTCAAAAATCCCATTTTTGA-CCTCG
* * *
1647 AACCTTCCAAAAATTATTGTTTTACCCTCGAAC-TCTCAAAAATCCCATTTTT-AGCCCCGAACC
65 AACCTTCCAAAAATTACTATTTTACCCTCGAACTTC-CAAAAATCCCATTTTTGA-CCCCAAACC
* *
1710 TTCCAAAAATTATTGTTTTACCCTCGAACTCCCAAAAATCCCATTTTTAG
128 TTCCAAAAATTACTATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAG
1760 CCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAACTCTCAAAAATCCCATTTTTGACCTCGA
1 CCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAACTCTCAAAAATCCCATTTTTGACCTCGA
* ** * * * * *
1825 ATCTTTTAAAAATTACCATTTTACCCTCGAATTTCCCAAGATCCTATTTTTGA
66 ACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1878 TTCCGGACAT
Statistics
Matches: 416, Mismatches: 46, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
176 4 0.01
177 403 0.97
178 9 0.02
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (177 bp):
CCCCGAACCTTTCAAAAATTACCATTTTACCCCCGAACTCTCAAAAATCCCATTTTTGACCTCGA
ACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTC
CAAAAATTACTATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAG
Found at i:3862 original size:31 final size:31
Alignment explanation
Indices: 3824--3885 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3814 TTTGGTAATG
3824 GAACTATTCAAAAGTTTTCT-TTTAAATCACT
1 GAACTATTCAAAAGTTTT-TATTTAAATCACT
* *
3855 GAACTATTCAATAGTTTTTATTTAAGTCACT
1 GAACTATTCAAAAGTTTTTATTTAAATCACT
3886 AGGTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.44
Consensus pattern (31 bp):
GAACTATTCAAAAGTTTTTATTTAAATCACT
Found at i:7588 original size:108 final size:108
Alignment explanation
Indices: 7399--7604 Score: 387
Period size: 108 Copynumber: 1.9 Consensus size: 108
7389 GTCTATTCAG
*
7399 TTACCAAGTGAGGCATTTTGAGTGAATGGTGGTCGTCCTCCATTCTAGCTAACAATCTCCATTAC
1 TTACCAAGTGAGGCATTTTGAGTGAATGGTGGTCGCCCTCCATTCTAGCTAACAATCTCCATTAC
7464 CACTGCTTGGAGAATTCAGTTCAGCTTCATCTTTAGGCCTCAA
66 CACTGCTTGGAGAATTCAGTTCAGCTTCATCTTTAGGCCTCAA
7507 TTACCAAGTGAGGCATTTTG-GTCGAATGGTGGTCGCCCTCCATTCTAGCTAACAATCTCCATTA
1 TTACCAAGTGAGGCATTTTGAGT-GAATGGTGGTCGCCCTCCATTCTAGCTAACAATCTCCATTA
7571 CCACTGCTTGGAGAATTCAGTTCAGCTTCATCTT
65 CCACTGCTTGGAGAATTCAGTTCAGCTTCATCTT
7605 CATCTTCATC
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
107 2 0.02
108 94 0.98
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (108 bp):
TTACCAAGTGAGGCATTTTGAGTGAATGGTGGTCGCCCTCCATTCTAGCTAACAATCTCCATTAC
CACTGCTTGGAGAATTCAGTTCAGCTTCATCTTTAGGCCTCAA
Found at i:7995 original size:14 final size:14
Alignment explanation
Indices: 7976--8005 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7966 CAATTATTTT
7976 AATTAAAATAATTA
1 AATTAAAATAATTA
*
7990 AATTAAATTAATTA
1 AATTAAAATAATTA
8004 AA
1 AA
8006 ATAAGACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAAAATAATTA
Found at i:9307 original size:19 final size:20
Alignment explanation
Indices: 9270--9307 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
9260 ATAAGATTAA
**
9270 TAAAAAAATATAATTATATT
1 TAAAAAAATATAAACATATT
9290 TAAAAAAA-ATAAACATAT
1 TAAAAAAATATAAACATAT
9308 GTTTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAAAATATAAACATATT
Found at i:16537 original size:14 final size:15
Alignment explanation
Indices: 16513--16545 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16503 CAAATTTGAG
16513 AATACATCATTTTTC
1 AATACATCATTTTTC
*
16528 AATA-ATCATTTTTT
1 AATACATCATTTTTC
16542 AATA
1 AATA
16546 GAGCGATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (15 bp):
AATACATCATTTTTC
Done.