Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011774.1 Kokia drynarioides strain JFW-HI SEQ_126769, 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: 4863
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Found at i:3656 original size:30 final size:30
Alignment explanation
Indices: 3612--3937 Score: 198
Period size: 30 Copynumber: 10.9 Consensus size: 30
3602 AAGGTCGCTA
3612 AACTGTCCAAAAATTACATTTTTTACCCTCG
1 AACT-TCCAAAAATTACATTTTTTACCCTCG
* * * **
3643 AACTTCCCAAAATTCCATTTTTGA-CCTTA
1 AACTTCCAAAAATTACATTTTTTACCCTCG
* *
3672 AACTTTCCAAAAATTACA-ATTTTACCC-CTA
1 AAC-TTCCAAAAATTACATTTTTTACCCTC-G
* * * *
3702 AACTTTCC-AAAATTCCATTTTTAACTC-CA
1 AAC-TTCCAAAAATTACATTTTTTACCCTCG
*
3731 AACTTCCCAAAAATTACATTTTTGA-CCTCG
1 AACTT-CCAAAAATTACATTTTTTACCCTCG
* *
3761 AACTTTCCAAAAAAATACCA--TTTTACCCTTG
1 AAC-TTCC-AAAAATTA-CATTTTTTACCCTCG
* *
3792 AA-TTCCCAAAAATTCCATTTTTGACCC-CG
1 AACTT-CCAAAAATTACATTTTTTACCCTCG
*
3821 AACTTTTCAAAAATTACCA--TTTTACCCTCG
1 AAC-TTCCAAAAATTA-CATTTTTTACCCTCG
* *
3851 AACTTCCAAAAATT-CCTTTTTTAACCAT-G
1 AACTTCCAAAAATTACATTTTTT-ACCCTCG
* * *
3880 ATCTTTTCGAAAATTACCA--TTTTACCCTCG
1 AAC-TTCCAAAAATTA-CATTTTTTACCCTCG
* *
3910 AACTTCCAAAAATTCCATTTTTAACCCT
1 AACTTCCAAAAATTACATTTTTTACCCT
3938 AATTTTTTTA
Statistics
Matches: 227, Mismatches: 41, Indels: 55
0.70 0.13 0.17
Matches are distributed among these distances:
27 1 0.00
28 6 0.03
29 73 0.32
30 121 0.53
31 23 0.10
32 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (30 bp):
AACTTCCAAAAATTACATTTTTTACCCTCG
Found at i:3862 original size:59 final size:59
Alignment explanation
Indices: 3612--4082 Score: 365
Period size: 59 Copynumber: 7.9 Consensus size: 59
3602 AAGGTCGCTA
* * * * **
3612 AACTGTCCAAAAATTACATTTTTTACCCTCGAAC-TTCCCAAAATT-CCATTTTTGA-CCTTA
1 AACT-TCCAAAAATTCCATTTTTGACCC-CGAACTTTTCAAAAATTACCA-TTTT-ACCCTCG
* * * * * *
3672 AACTTTCCAAAAATTACAATTTT-ACCCCTAAAC-TTTCCAAAATT-CCATTTTTA-ACTCCA
1 AAC-TTCCAAAAATTCCATTTTTGACCCC-GAACTTTTCAAAAATTACCA-TTTTACCCT-CG
* * * * *
3731 AACTTCCCAAAAATTACATTTTTGACCTCGAACTTTCCAAAAAAATACCATTTTACCCTTG
1 AACTT-CCAAAAATTCCATTTTTGACCCCGAACTTTTC-AAAAATTACCATTTTACCCTCG
3792 AA-TTCCCAAAAATTCCATTTTTGACCCCGAACTTTTCAAAAATTACCATTTTACCCTCG
1 AACTT-CCAAAAATTCCATTTTTGACCCCGAACTTTTCAAAAATTACCATTTTACCCTCG
* * ** * *
3851 AACTTCCAAAAATTCCTTTTTTAACCATGATCTTTTCGAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCCGAACTTTTCAAAAATTACCATTTTACCCTCG
* * * * * *
3910 AACTTCCAAAAATTCCATTTTT-AACCCTAATTTTTTTAGAAAATTACCATTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTGACCCCGAA-CTTTTCA-AAAATTACCATTTTACCCTCG
* * * * * *
3970 AACTTCTACAAATTCCATTTTTGACCTCG-ATTTTTCCAAAATTA-CATTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTGACCCCGAACTTTTCAAAAATTACCATTTTACCCTCG
* * * *
4027 GACTTTCAAAAATTCCATTTTCGACCCCG-A-TTCTTCCAAAAAGTACCATTTTACCC
1 AACTTCCAAAAATTCCATTTTTGACCCCGAACTT-TT-CAAAAATTACCATTTTACCC
4083 CCAAGTAACC
Statistics
Matches: 343, Mismatches: 52, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
56 2 0.01
57 38 0.11
58 23 0.07
59 158 0.46
60 101 0.29
61 16 0.05
62 5 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTGACCCCGAACTTTTCAAAAATTACCATTTTACCCTCG
Found at i:3893 original size:149 final size:147
Alignment explanation
Indices: 3632--3921 Score: 349
Period size: 149 Copynumber: 2.0 Consensus size: 147
3622 AAATTACATT
**
3632 TTTTACCCTCGAACTTCCCAAAATTCCATTTTTGACCTTAAACTTTCCAAAAATTACAATTTTAC
1 TTTTACCCTCGAACTTCCCAAAATTCCATTTTTGACCCCAAACTTTCCAAAAATTACAATTTTAC
3697 CCCTAAACTTTCCAAAATTCCATTTTTAACTCCAAACTTCCCAAAAATTA-CATTTTTGA-CCTC
66 CCCTAAACTTTCCAAAATTCCATTTTTAAC-CCAAACTTCCCAAAAATTACCA-TTTT-ACCCTC
3760 GAACTTTCCAAAAAAATACCA
128 GAAC-TTCCAAAAAAATACCA
* * * *
3781 TTTTACCCTTGAA-TTCCCAAAAATTCCATTTTTGACCCCGAACTTTTCAAAAATTACCATTTTA
1 TTTTACCCTCGAACTTCCC-AAAATTCCATTTTTGACCCCAAACTTTCCAAAAATTACAATTTTA
* * * ** *
3845 -CCCTCGAAC-TTCCAAAAATTCCTTTTTTAA-CCATGATCTTTTCGAAAATTACCATTTTACCC
65 CCCCT-AAACTTTCC-AAAATTCCATTTTTAACCCA--AACTTCCCAAAAATTACCATTTTACCC
3907 TCGAACTTCCAAAAA
126 TCGAACTTCCAAAAA
3922 TTCCATTTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
147 3 0.02
148 23 0.19
149 94 0.77
150 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (147 bp):
TTTTACCCTCGAACTTCCCAAAATTCCATTTTTGACCCCAAACTTTCCAAAAATTACAATTTTAC
CCCTAAACTTTCCAAAATTCCATTTTTAACCCAAACTTCCCAAAAATTACCATTTTACCCTCGAA
CTTCCAAAAAAATACCA
Found at i:4067 original size:29 final size:27
Alignment explanation
Indices: 3979--4067 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 27
3969 AAACTTCTAC
*
3979 AAATTCCATTTTTGACCTCGATTTTTCCA
1 AAATTCCA-TTTTGACCCCGA-TTTTCCA
* * *
4008 AAATTACATTTT-ACCCCCGGACTTTCAA
1 AAATTCCATTTTGA-CCCC-GATTTTCCA
4036 AAATTCCATTTTCGACCCCGATTCTTCCA
1 AAATTCCATTTT-GACCCCGATT-TTCCA
4065 AAA
1 AAA
4068 AGTACCATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.02
28 26 0.54
29 20 0.42
30 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (27 bp):
AAATTCCATTTTGACCCCGATTTTCCA
Found at i:4067 original size:30 final size:27
Alignment explanation
Indices: 3617--4083 Score: 132
Period size: 30 Copynumber: 15.8 Consensus size: 27
3607 CGCTAAACTG
* *
3617 TCCAAAAATTACATTTTTTACCCTCGAACT
1 TCCAAAAATTCCA--TTTTACCC-CGATCT
* *** *
3647 TCCCAAAATTCCATTTTTGACCTTAAACTT
1 TCCAAAAATTCCA-TTTT-ACCCCGATC-T
* * *
3677 TCCAAAAATTACAATTTTACCCCTAAACTT
1 TCCAAAAATT-CCATTTTACCCC-GATC-T
* * *
3707 TCC-AAAATTCCATTTTTAACTCCAAACT
1 TCCAAAAATTCCA-TTTT-ACCCCGATCT
* * *
3735 TCCCAAAAATTACATTTTTGACCTCGAACTT
1 T-CCAAAAATTCCA-TTTT-ACCCCGATC-T
* *
3766 TCCAAAAAAATACCATTTTACCCTTGAAT-T
1 TCC--AAAAATTCCATTTTACCC-CG-ATCT
* *
3796 CCCAAAAATTCCATTTTTGACCCCGAACTT
1 TCCAAAAATTCCA-TTTT-ACCCCGATC-T
* *
3826 TTCAAAAATTACCATTTTACCCTCGAACT
1 TCCAAAAATT-CCATTTTACCC-CGATCT
* **
3855 TCCAAAAATTCCTTTTTTAACCATGATCTT
1 TCCAAAAATTCC-ATTTT-ACCCCGATC-T
* * *
3885 TTCGAAAATTACCATTTTACCCTCGAACT
1 TCCAAAAATT-CCATTTTACCC-CGATCT
** *
3914 TCCAAAAATTCCATTTTTAACCCTAATTTT
1 TCCAAAAATTCCA-TTTT-ACCCCGA-TCT
** * *
3944 TTTAGAAAATTACCATTTTACCCCCAAACT
1 TCCA-AAAATT-CCATTTTA-CCCCGATCT
* * * *
3974 TCTACAAATTCCATTTTTGACCTCGATTTT
1 TCCAAAAATTCCA-TTTT-ACCCCGA-TCT
*
4004 TCC-AAAATTACATTTTACCCCCGGA-CT
1 TCCAAAAATTCCATTTTA-CCCC-GATCT
*
4031 TTCAAAAATTCCATTTTCGACCCCGATTCT
1 TCCAAAAATTCCATTTT--ACCCCGA-TCT
*
4061 TCCAAAAAGTACCATTTTACCCC
1 TCCAAAAA-TTCCATTTTACCCC
4084 CAAGTAACCA
Statistics
Matches: 332, Mismatches: 64, Indels: 83
0.69 0.13 0.17
Matches are distributed among these distances:
27 4 0.01
28 43 0.13
29 101 0.30
30 135 0.41
31 37 0.11
32 12 0.04
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (27 bp):
TCCAAAAATTCCATTTTACCCCGATCT
Done.