Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012727.1 Kokia drynarioides strain JFW-HI SEQ_127738, 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: 65529
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:1474 original size:23 final size:25
Alignment explanation
Indices: 1448--1493 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1438 CCAATTAGGG
1448 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
1471 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
1494 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:9560 original size:4 final size:4
Alignment explanation
Indices: 9553--9585 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
9543 ACACACTTGA
9553 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
9586 CCACTAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:19640 original size:24 final size:24
Alignment explanation
Indices: 19595--19640 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19585 TTCAGGGCGT
* *
19595 AGTGAAGGAGGAGCCTCTTTTGAG
1 AGTGAAGGAAGAGCCTCATTTGAG
*
19619 AGTGAAGGAAGAGCCTGATTTG
1 AGTGAAGGAAGAGCCTCATTTG
19641 GGGTTTGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.37, T:0.24
Consensus pattern (24 bp):
AGTGAAGGAAGAGCCTCATTTGAG
Found at i:24820 original size:12 final size:13
Alignment explanation
Indices: 24786--24827 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
24776 AATACAAGAA
24786 AAAAAAAAGAGAG
1 AAAAAAAAGAGAG
24799 AAAAGAAAAGAG-G
1 AAAA-AAAAGAGAG
* *
24812 AAAATAAAGAAAG
1 AAAAAAAAGAGAG
24825 AAA
1 AAA
24828 GCTACAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 5 0.20
13 13 0.52
14 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGAGAG
Found at i:32317 original size:20 final size:21
Alignment explanation
Indices: 32292--32336 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
32282 AAATTTAAAA
32292 TTTTTATAAA-TATTTTGA-AT
1 TTTTTA-AAATTATTTTGATAT
32312 TTTTTAAAATTATTTTGATAT
1 TTTTTAAAATTATTTTGATAT
32333 TTTT
1 TTTT
32337 GTTTTGAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.13
20 14 0.61
21 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTAAAATTATTTTGATAT
Found at i:32488 original size:23 final size:23
Alignment explanation
Indices: 32462--32510 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
32452 CGAACTTAAG
*
32462 ACTCGAATTACTT-ATTCGAGTTA
1 ACTCGAATAACTTGATTCGA-TTA
*
32485 ACTCGAATAACTTGATTTGATTA
1 ACTCGAATAACTTGATTCGATTA
32508 ACT
1 ACT
32511 AGAAATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (23 bp):
ACTCGAATAACTTGATTCGATTA
Found at i:35024 original size:2 final size:2
Alignment explanation
Indices: 35017--35041 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35007 CAACCCATTA
35017 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35042 CACCTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51885 original size:12 final size:12
Alignment explanation
Indices: 51868--51900 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
51858 TCAATCCAAC
51868 AATAATTAAATA
1 AATAATTAAATA
51880 AATAATTAAA-A
1 AATAATTAAATA
51891 AA-AATTAAAT
1 AATAATTAAAT
51901 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 3 0.15
12 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATAATTAAATA
Found at i:62678 original size:17 final size:17
Alignment explanation
Indices: 62653--62700 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
62643 CTGAGCCCAA
*
62653 TAAACTTAAATTTATTT
1 TAAACTTAAATTTATTC
* *
62670 TAAAGTTAAGTTTATTC
1 TAAACTTAAATTTATTC
*
62687 TAAATTTAAATTTA
1 TAAACTTAAATTTA
62701 GCTGAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (17 bp):
TAAACTTAAATTTATTC
Found at i:64539 original size:29 final size:28
Alignment explanation
Indices: 64488--64720 Score: 261
Period size: 29 Copynumber: 8.0 Consensus size: 28
64478 GGAGACCTCG
* *
64488 AAACTTCCAAAAAATTCTATTTTTACCTCC
1 AAACTTCC-AAAAATCCCATTTTTACC-CC
*
64518 AAACTTCCAAAAATCTCATTTTTAACCCC
1 AAACTTCCAAAAATCCCATTTTT-ACCCC
*
64547 GAAACTTCCAAAAATTCCATTTTTACCCTC
1 -AAACTTCCAAAAATCCCATTTTTACCC-C
* *
64577 AAACTTCCAAAAATCCCATTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTTACC-CC
* *
64606 AAACTTCCAAAAATCCCATTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTTACC-CC
* *
64635 GAACTTCCAAAAATCCCGTTTTTACCCC
1 AAACTTCCAAAAATCCCATTTTTACCCC
64663 GAAACTTCCAAAAATCCCATTTTTGACCCC
1 -AAACTTCCAAAAATCCCATTTTT-ACCCC
* *
64693 GAAACTTCCAAAAATTCTA-TTTTACCCC
1 -AAACTTCCAAAAATCCCATTTTTACCCC
64721 TGGATATCCA
Statistics
Matches: 181, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
28 6 0.03
29 119 0.66
30 56 0.31
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.30
Consensus pattern (28 bp):
AAACTTCCAAAAATCCCATTTTTACCCC
Found at i:64731 original size:58 final size:58
Alignment explanation
Indices: 64487--64756 Score: 213
Period size: 58 Copynumber: 4.6 Consensus size: 58
64477 TGGAGACCTC
* *
64487 GAAACTTCCAAAAAATTCTATTTTT-ACCTCC-AAACTTCCAAAAAT-CTCATTTTTAACCCC-
1 GAAAC-TCC-AAAAATCCCATTTTTGACC-CCGAAACTTCCAAAAATCCT-A-TTTT-ACCCCT
* * *
64547 GAAACTTCCAAAAATTCCATTTTT-ACCCTC-AAACTTCCAAAAATCCCATTTTGACCTC-
1 GAAAC-TCCAAAAATCCCATTTTTGACCC-CGAAACTTCCAAAAATCCTATTTT-ACCCCT
* *
64605 GAAACTTCCAAAAATCCCA-TTTTGACCTCGGAACTTCCAAAAATCCCGT-TTTTACCCC-
1 GAAAC-TCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAAT-CC-TATTTTACCCCT
*
64663 GAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTACCCCT
1 GAAAC-TCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATCCTATTTTACCCCT
* * * *
64722 GGATA-TCCAAAAA-CTCCATCTTCGACCTCGAAACT
1 -GAAACTCCAAAAATC-CCATTTTTGACCCCGAAACT
64757 CTCAAAATTA
Statistics
Matches: 183, Mismatches: 16, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
57 7 0.04
58 101 0.55
59 62 0.34
60 13 0.07
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.30
Consensus pattern (58 bp):
GAAACTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATCCTATTTTACCCCT
Found at i:64774 original size:116 final size:114
Alignment explanation
Indices: 64481--64833 Score: 310
Period size: 116 Copynumber: 3.0 Consensus size: 114
64471 TTGCCTTGGA
* * ** * **
64481 GACCTCGAAACTTCCAAAAAATTCTATTTTTACCTCCAAACTTCCAAAAATCTCATTTTTAACCC
1 GACCTCGAAAC-TCC-AAAAATCCCATTTCGACCTCGAAACTTCCAAAAATC-CCGTTTT-ACCC
*
64546 CGAAACTTCCAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATCCCATTTT
62 CGAAACTTCCAAAAATTCCATTTTTACCC-CGAAACTTCCAAAAATTCCATTTT
* *
64599 GACCTCGAAACTTCCAAAAATCCCATTTTGACCTCGGAACTTCCAAAAATCCCGTTTTTACCCCG
1 GACCTCGAAAC-TCCAAAAATCCCATTTCGACCTCGAAACTTCCAAAAATCCCG-TTTTACCCCG
* *
64664 AAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTT
64 AAACTTCCAAAAATTCCATTTTT-ACCCCGAAACTTCCAAAAATTCCATTTT
* * *
64716 -ACCCCTGGATA-TCCAAAAA-CTCCATCTTCGACCTCGAAAC-TCTCAAAATTACCC-TTTTAC
1 GA--CCTCGAAACTCCAAAAATC-CCAT-TTCGACCTCGAAACTTC-CAAAAAT-CCCGTTTTAC
* * *
64776 CCTCG-AA-TGTCTAAAAATTCTATTTTTAACCCCG-AACTTTCCCAAAATTCCCATTTT
60 CC-CGAAACT-TCCAAAAATTCCATTTTT-ACCCCGAAAC-TTCCAAAAATT-CCATTTT
64833 G
1 G
64834 CCCCCATAAG
Statistics
Matches: 200, Mismatches: 21, Indels: 28
0.80 0.08 0.11
Matches are distributed among these distances:
115 5 0.03
116 86 0.43
117 85 0.43
118 24 0.12
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.31
Consensus pattern (114 bp):
GACCTCGAAACTCCAAAAATCCCATTTCGACCTCGAAACTTCCAAAAATCCCGTTTTACCCCGAA
ACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCCATTTT
Found at i:64780 original size:146 final size:145
Alignment explanation
Indices: 64481--64832 Score: 391
Period size: 146 Copynumber: 2.4 Consensus size: 145
64471 TTGCCTTGGA
* *
64481 GACCTCGAAACTTCCAAAAAATTCTATTTTTACCTCC-AAACTTCCAAAAATCTCATTTTTAACC
1 GACCTCGGAACTTCC-AAAAATTCTATTTTTACC-CCGAAACTTCCAAAAATCCCATTTTTAACC
*
64545 CCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTGACCTCGAAAC
64 CCGAAACTTCCAAAAATTCCATTTTTACCCTCAAAC-TCCAAAAATCCCATTTCGACCTCGAAAC
64610 TTCCAAAAATCCCATTTT
128 TTCCAAAAATCCCATTTT
* ** *
64628 GACCTCGGAACTTCCAAAAATCCCGTTTTTACCCCGAAACTTCCAAAAATCCCATTTTTGACCCC
1 GACCTCGGAACTTCCAAAAATTCTATTTTTACCCCGAAACTTCCAAAAATCCCATTTTTAACCCC
* * *
64693 GAAACTTCCAAAAATTCTA-TTTTACCCCTGGATA-TCCAAAAA-CTCCATCTTCGACCTCGAAA
66 GAAACTTCCAAAAATTCCATTTTTA-CCCT-CAAACTCCAAAAATC-CCAT-TTCGACCTCGAAA
*
64755 C-TCTCAAAATTACCC-TTTT
127 CTTC-CAAAAAT-CCCATTTT
* *
64774 -ACCCTC-GAA-TGTCTAAAAATTCTATTTTTAACCCCG-AACTTTCCCAAAATTCCCATTTT
1 GA-CCTCGGAACT-TCCAAAAATTCTATTTTT-ACCCCGAAAC-TT-CCAAAAATCCCATTTT
64833 GCCCCCATAA
Statistics
Matches: 177, Mismatches: 16, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
144 2 0.01
145 42 0.24
146 99 0.56
147 34 0.19
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (145 bp):
GACCTCGGAACTTCCAAAAATTCTATTTTTACCCCGAAACTTCCAAAAATCCCATTTTTAACCCC
GAAACTTCCAAAAATTCCATTTTTACCCTCAAACTCCAAAAATCCCATTTCGACCTCGAAACTTC
CAAAAATCCCATTTT
Done.