Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014557.1 Kokia drynarioides strain JFW-HI SEQ_129596, 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: 32003
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Warning! 94 characters in sequence are not A, C, G, or T
Found at i:5651 original size:30 final size:33
Alignment explanation
Indices: 5588--5653 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 33
5578 TAGTAATAGT
* *
5588 AAAATTACACTTTGACCCTTTCAAAAATGATAA
1 AAAATTACACTTTAACCCTTTCAAAAATAATAA
*
5621 AAAATTA-A-TTTAACCCTTT-TAAAATAATAA
1 AAAATTACACTTTAACCCTTTCAAAAATAATAA
5651 AAA
1 AAA
5654 TATAAGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 12 0.40
31 10 0.33
32 1 0.03
33 7 0.23
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.32
Consensus pattern (33 bp):
AAAATTACACTTTAACCCTTTCAAAAATAATAA
Found at i:14605 original size:68 final size:67
Alignment explanation
Indices: 14479--14623 Score: 200
Period size: 68 Copynumber: 2.1 Consensus size: 67
14469 AAGCTATATA
* * * ** *
14479 TATACATATAACTTAAGGAAACGGTGGGTATACGGCAATATATACATACTATATATAAAGAATAA
1 TATATATATAACTTAAAGAAACAGAAGGTATACGACAATATATACATACTATATATAAAGAATAA
14544 AC
66 AC
* *
14546 TATATATATAACTTAAAGAAACAGAAGGTATATGACAAATATATACATACTGTATATAAAGAATA
1 TATATATATAACTTAAAGAAACAGAAGGTATACGAC-AATATATACATACTATATATAAAGAATA
14611 AAC
65 AAC
*
14614 AATATATATA
1 TATATATATA
14624 TTATATATAA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 29 0.43
68 39 0.57
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (67 bp):
TATATATATAACTTAAAGAAACAGAAGGTATACGACAATATATACATACTATATATAAAGAATAA
AC
Found at i:16421 original size:39 final size:39
Alignment explanation
Indices: 16356--16649 Score: 270
Period size: 39 Copynumber: 7.5 Consensus size: 39
16346 TTCTATAACT
* * *
16356 TTAGGCGTAAAAG-TTTGATTGTTTCAATCTGCCCTCTGG
1 TTAGG-GTAAAAGATTGGATGGCTTCAATCTGCCCTCTGG
* *
16395 TTAGGGTAAAAGATTGGATGGCTTCAATCTACCC-CATAG
1 TTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTC-TGG
* * * * *
16434 -TCGGGATAAGAGATCGGATGATCTTCAATCTGCCCTCTGA
1 TTAGGG-TAAAAGATTGGATG-GCTTCAATCTGCCCTCTGG
* *
16474 TTAGGGTAAAAGATTGGATTGCTTCAATCTGTCCTCTGG
1 TTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTCTGG
* * * *
16513 TTAGGGTAAAAAATTGGATTGTTTCAATCTGCCCTATGG
1 TTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTCTGG
* * * * * *
16552 TTGGGGTAAGAGATTGGATTGTCTTCAATTTGCCCTTTGA
1 TTAGGGTAAAAGATTGGA-TGGCTTCAATCTGCCCTCTGG
* * * *
16592 TTAGGGTAAAAGTTTTGATGGTCTTCAATTTGCCTTCTGG
1 TTAGGGTAAAAGATTGGATGG-CTTCAATCTGCCCTCTGG
*
16632 TTAGGGTAAGAGATTGGA
1 TTAGGGTAAAAGATTGGA
16650 GGTTGTAACT
Statistics
Matches: 204, Mismatches: 43, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
38 12 0.06
39 104 0.51
40 83 0.41
41 5 0.02
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (39 bp):
TTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTCTGG
Found at i:16564 original size:118 final size:116
Alignment explanation
Indices: 16356--16649 Score: 365
Period size: 118 Copynumber: 2.5 Consensus size: 116
16346 TTCTATAACT
*
16356 TTAGGCGTAAAAGTTTGATTGTTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
1 TTAGG-GTAAAAGTTTGATTGCTTCAATCTG-CCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
16421 ATCTACCCCATAGTCGGGATAAGAGATCGGA-TGATCTTCAATCTGCCCTCTGA
64 ATCTACCCCATAGTCGGGATAAGAGATCGGATTG-TCTTCAATCTGCCCTCTGA
* * * *
16474 TTAGGGTAAAAGATTGGATTGCTTCAATCTGTCCTCTGGTTAGGGTAAAAAATTGGATTGTTTCA
1 TTAGGGTAAAAG-TTTGATTGCTTCAATCTG-CCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
* * * * * * * *
16539 ATCTGCCCTATGGTTGGGGTAAGAGATTGGATTGTCTTCAATTTGCCCTTTGA
64 ATCTACCCCATAGTCGGGATAAGAGATCGGATTGTCTTCAATCTGCCCTCTGA
* * *
16592 TTAGGGTAAAAGTTTTGATGGTCTTCAATTTGCCTTCTGGTTAGGGTAAGAGATTGGA
1 TTAGGGTAAAAG-TTTGATTG-CTTCAATCTGCC-TCTGGTTAGGGTAAAAGATTGGA
16650 GGTTGTAACT
Statistics
Matches: 152, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
117 7 0.05
118 113 0.74
119 32 0.21
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (116 bp):
TTAGGGTAAAAGTTTGATTGCTTCAATCTGCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAAT
CTACCCCATAGTCGGGATAAGAGATCGGATTGTCTTCAATCTGCCCTCTGA
Found at i:16826 original size:50 final size:50
Alignment explanation
Indices: 16703--16818 Score: 178
Period size: 50 Copynumber: 2.3 Consensus size: 50
16693 ATCCTTGTGA
*
16703 CTTCAATCTACCCCTCTACAGCTTTAGGTGAATGAGATTTGCCATTGCGG
1 CTTCAATCTACCCCTCTACAGCTTTAGGTAAATGAGATTTGCCATTGCGG
* * *
16753 CTTCATTCTGCCCCTCTACAGCTTTAGGTAAATGAGATTTGCCATTGTGG
1 CTTCAATCTACCCCTCTACAGCTTTAGGTAAATGAGATTTGCCATTGCGG
* *
16803 TTTCAATCTACACCTC
1 CTTCAATCTACCCCTC
16819 CATAGCTTCC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (50 bp):
CTTCAATCTACCCCTCTACAGCTTTAGGTAAATGAGATTTGCCATTGCGG
Found at i:26631 original size:23 final size:22
Alignment explanation
Indices: 26601--26650 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
26591 GCTGGGGAAA
*
26601 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACACTGCAAT
26623 CCAGTAAGCACACACACTGCAAT
1 -CAGTAAGCACACACACTGCAAT
26646 CAGTA
1 CAGTA
26651 GGCGCACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.40, C:0.30, G:0.16, T:0.14
Consensus pattern (22 bp):
CAGTAAGCACACACACTGCAAT
Found at i:30793 original size:17 final size:19
Alignment explanation
Indices: 30756--30800 Score: 67
Period size: 17 Copynumber: 2.4 Consensus size: 19
30746 AAGTTTATTC
30756 TAAATTTATTAGCTGAAATT
1 TAAATTTATTA-CTGAAATT
30776 TAAATTTATTA-T-AAATT
1 TAAATTTATTACTGAAATT
30793 TAAATTTA
1 TAAATTTA
30801 AAATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.52
18 1 0.04
20 11 0.44
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TAAATTTATTACTGAAATT
Done.