Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012102.1 Kokia drynarioides strain JFW-HI SEQ_127101, 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: 8143
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1031 original size:295 final size:292
Alignment explanation
Indices: 428--1013 Score: 649
Period size: 288 Copynumber: 2.0 Consensus size: 292
418 TCCAAAATGA
428 TGAAATGGAGGATAATTGTTTCAGAAAAAAATGAAAATTGTCAATATGATGCTAAAGTTGGCTAT
1 TGAAATGGAGGATAATTGTTTCAGAAAAAAATGAAAATTGTCAATATGATGCTAAAGTTGGCTAT
493 GCATACAAGGATGATTAATATGTATTTAGTTTGTGTTAAAATTTTGTTGATCCAAGCAGTGAAAT
66 GCATACAAGGATGATT-ATA--TATTTAGTTTGTGTTAAAATTTTGTTGATCCAAGCAGTGAAAT
558 TTAATTGTTTGATTTAAGAACCATTAAAATCAGTGTCTACTTGATATTTGCTTGGGGATGATATA
128 TTAATTGTTTGATTTAAGAACCATTAAAATCAGTGTCTACTTGATATTTGCTTGGGGATGATATA
***************
623 TTATCTAACCATAGTGATTTATTAGTAATATTAATTTATTATTTATTATGNNNNNNNNNNNNNNN
193 TTATCTAACCATAGTGATTTATTAGTAATATTAATTTATTATTTATTATGTAATATATGTTTTAT
***********************************
688 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
258 TTATACCTATTCATTTTATTTTTATATGAATACAT
723 TGAAATGGAGGATAATTGTTTCAGAAAAAAATGAAAATTGTCAATATGATGCTAAAGTTGGCTAT
1 TGAAATGGAGGATAATTGTTTCAGAAAAAAATGAAAATTGTCAATATGATGCTAAAGTTGGCTAT
788 GCATACAAGGATGA-T-TA-A-TTAGTTTGTGTTAAAATTTTGTTGATCCAAGCAGTGAAATTTA
66 GCATACAAGGATGATTATATATTTAGTTTGTGTTAAAATTTTGTTGATCCAAGCAGTGAAATTTA
849 ATTGTTTGATTTAAGAACCATTAAAATCAGTGTCTACTTGATATTTGCTTGGGGATGATATATTA
131 ATTGTTTGATTTAAGAACCATTAAAATCAGTGTCTACTTGATATTTGCTTGGGGATGATATATTA
914 TCTAACCATAGTGATTTATTAGTAATATTAATTTATTATTTATTATGTTTAATATATGTTTTATT
196 TCTAACCATAGTGATTTATTAGTAATATTAATTTATTATTTATTATG--TAATATATGTTTTATT
979 TATACCTATTCATTTTATTTTTATATGAATACAT
259 TATACCTATTCATTTTATTTTTATATGAATACAT
1013 T
1 T
1014 AAGTATTCAT
Statistics
Matches: 239, Mismatches: 50, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
288 155 0.65
289 1 0.00
290 1 0.00
292 2 0.01
294 1 0.00
295 79 0.33
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.38
Consensus pattern (292 bp):
TGAAATGGAGGATAATTGTTTCAGAAAAAAATGAAAATTGTCAATATGATGCTAAAGTTGGCTAT
GCATACAAGGATGATTATATATTTAGTTTGTGTTAAAATTTTGTTGATCCAAGCAGTGAAATTTA
ATTGTTTGATTTAAGAACCATTAAAATCAGTGTCTACTTGATATTTGCTTGGGGATGATATATTA
TCTAACCATAGTGATTTATTAGTAATATTAATTTATTATTTATTATGTAATATATGTTTTATTTA
TACCTATTCATTTTATTTTTATATGAATACAT
Found at i:4061 original size:17 final size:17
Alignment explanation
Indices: 4041--4100 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
4031 TCCTTGACTT
4041 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
*
4058 TTAACCTCTCC-T-TGACC
1 TTAACCT-TCCATCT-TCC
4075 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
*
4093 TCAACCTT
1 TTAACCTT
4101 TCATATTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 1 0.03
17 20 0.57
18 13 0.37
19 1 0.03
ACGTcount: A:0.18, C:0.40, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:4079 original size:35 final size:35
Alignment explanation
Indices: 4031--4099 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
4021 CCTTTCATCT
* *
4031 TCCTTGACTTTTAACCTTCCATCTTCCTTAACCTC
1 TCCTTGACCTTTAACCTTCCATCTTCCTCAACCTC
4066 TCCTTGACCTTTAACCTTCCATCTTCCTCAACCT
1 TCCTTGACCTTTAACCTTCCATCTTCCTCAACCT
4100 TTCATATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.17, C:0.39, G:0.03, T:0.41
Consensus pattern (35 bp):
TCCTTGACCTTTAACCTTCCATCTTCCTCAACCTC
Found at i:4718 original size:3 final size:3
Alignment explanation
Indices: 4710--4737 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4700 CCTTGGGCCC
4710 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4738 GATGATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4742 original size:3 final size:3
Alignment explanation
Indices: 4736--4779 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
4726 AATAATAATA
* *
4736 ATG ATG ATG ATG ATG ATA ATG ATG ATG ATG ATG ATG ATA ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
4780 AATAATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:4780 original size:6 final size:6
Alignment explanation
Indices: 4710--4782 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
4700 CCTTGGGCCC
* * * * * *
4710 TAATAA TAATAA TAATAA TAATAA TAATGA TGATGA TGATGA TAATGA
1 TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA
*
4758 TGATGATGA TGATGA TAATGA TAAT
1 T-A--ATGA TAATGA TAATGA TAAT
4783 AATTTAGGCC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
6 53 0.90
7 1 0.02
9 5 0.08
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
TAATGA
Found at i:4784 original size:9 final size:9
Alignment explanation
Indices: 4710--4785 Score: 62
Period size: 9 Copynumber: 8.4 Consensus size: 9
4700 CCTTGGGCCC
*
4710 TAATAATAA
1 TAATGATAA
*
4719 TAATAATAA
1 TAATGATAA
*
4728 TAATAATAA
1 TAATGATAA
* *
4737 TGATGATGA
1 TAATGATAA
*
4746 TGATGATAA
1 TAATGATAA
* *
4755 TGATGATGA
1 TAATGATAA
* *
4764 TGATGATGA
1 TAATGATAA
4773 TAATGATAA
1 TAATGATAA
4782 TAAT
1 TAAT
4786 TTAGGCCTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (9 bp):
TAATGATAA
Done.