Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010490.1 Kokia drynarioides strain JFW-HI SEQ_125398, 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: 6672
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1824 original size:58 final size:59
Alignment explanation
Indices: 1749--2240 Score: 521
Period size: 58 Copynumber: 8.4 Consensus size: 59
1739 GATCCCAAAA
*
1749 TTTTCCAAAAA-TACCATTTTGACCCTCGAAC-TTCCAAAATTCCATTTTTGACTCCGAT
1 TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGAC-CCGAT
* * *
1807 TTTTCCAAAAA-TACCATTTTGACCCTTGAAC-TTCAAAAATTCCATTTTTGACCCCGAT
1 TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGA-CCCGAT
* * *
1865 TTTTCCAAAAATTA-CATTTTTACTCTTGAACTTTCCAAAATTCCATTTTTAACCTCGAT
1 TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACC-CGAT
* * * *
1924 TTCTCTAAAAATTA--ATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAT
1 TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCCGAT
* *
1981 TTTTCAAAAAATTA-CATTTTTACCCTTGAACTTTCCAAAATTCCATTTTTGACCCCGAT
1 TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGA-CCCGAT
* *
2040 TTTTCCAAAAATTA-CATTTTTACCCTCGAACTTTCTAAAAATTCCA-TTTTGACCTCAAT
1 TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTC-CAAAATTCCATTTTTGACC-CGAT
* * * *
2099 TTTTCC-AAAATTACCA-TTTTACCCCCAAACTTTCAAAAATTCCATTTTTTACCCTGATT
1 TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCC-GA-T
** * * * * * * *
2158 TTTTTTAAAAATTA-CAATTTTACCCCCGAA-TGTCTAAAATTTCCATTTTTTACCCCAAA
1 TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAA-TTCCATTTTTGA-CCCGAT
*
2217 CTTTCC-AAAATTACCA-TTTTACCC
1 TTTTCCAAAAATTACCATTTTTACCC
2241 CCGGGTATCC
Statistics
Matches: 383, Mismatches: 34, Indels: 34
0.85 0.08 0.08
Matches are distributed among these distances:
57 26 0.07
58 202 0.53
59 111 0.29
60 41 0.11
61 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (59 bp):
TTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCCGAT
Found at i:1967 original size:117 final size:119
Alignment explanation
Indices: 1735--2240 Score: 567
Period size: 117 Copynumber: 4.3 Consensus size: 119
1725 AGAAGTCCTA
* * *
1735 TTTTGATCCCAAAATTTTCCAAAAA-TACCATTTTGACCCTCGAAC-TTCCAAAATTCCATTTTT
1 TTTTGA-CCCCAATTTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTT
* *
1798 GA-CTCCGATTTTTCCAAAAA-TACCATTTTGACCCTTGAAC-TTCAAAAATTCCAT
65 GACCT-CGATTTTTCCAAAAATTA-CATTTTTACCCTCGAACTTTCAAAAATTCCAT
* * * *
1852 TTTTGACCCCGATTTTTCCAAAAATTA-CATTTTTACTCTTGAACTTTCCAAAATTCCATTTTTA
1 TTTTGACCCCAATTTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTG
* * *
1916 ACCTCGATTTCTCTAAAAATTA-ATTTTTACCCTCGAACTTTCCAAAATTCCAT
66 ACCTCGATTTTTCCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATTCCAT
* * *
1969 TTTTAACCCC-ATTTTTCAAAAAATTA-CATTTTTACCCTTGAACTTTCCAAAATTCCATTTTTG
1 TTTTGACCCCAATTTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTG
*
2032 ACCCCGATTTTTCCAAAAATTACATTTTTACCCTCGAACTTTCTAAAAATTCCA-
66 ACCTCGATTTTTCCAAAAATTACATTTTTACCCTCGAACTTTC-AAAAATTCCAT
* * * * *
2086 TTTTGACCTCAATTTTTCC-AAAATTACCA-TTTTACCCCCAAACTTTCAAAAATTCCATTTTTT
1 TTTTGACCCCAATTTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTG
** * * * *
2149 ACC-CTGATTTTTTTTAAAAATTACAATTTTACCCCCGAA-TGTCTAAAATTTCCAT
66 ACCTC-GA-TTTTTCCAAAAATTACATTTTTACCCTCGAACTTTC-AAAAATTCCAT
* **
2204 TTTTTACCCCAAACTTTCC-AAAATTACCA-TTTTACCC
1 TTTTGACCCCAATTTTTCCAAAAATTACCATTTTTACCC
2241 CCGGGTATCC
Statistics
Matches: 339, Mismatches: 38, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
116 113 0.33
117 144 0.42
118 82 0.24
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (119 bp):
TTTTGACCCCAATTTTTCCAAAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTG
ACCTCGATTTTTCCAAAAATTACATTTTTACCCTCGAACTTTCAAAAATTCCAT
Found at i:2147 original size:29 final size:29
Alignment explanation
Indices: 1754--2240 Score: 313
Period size: 29 Copynumber: 16.7 Consensus size: 29
1744 CAAAATTTTC
* *
1754 CAAAAATACCATTTTGACCCTCGAAC-TT
1 CAAAAATTCCATTTTTACCCTCGAACTTT
* * **
1782 CCAAAATTCCATTTTTGACTC-CGATTTTT
1 CAAAAATTCCATTTTT-ACCCTCGAACTTT
* * *
1811 CCAAAAATACCATTTTGACCCTTGAAC-TT
1 -CAAAAATTCCATTTTTACCCTCGAACTTT
**
1840 CAAAAATTCCATTTTTGACCC-CGATTTTT
1 CAAAAATTCCATTTTT-ACCCTCGAACTTT
* * *
1869 CCAAAAATTACATTTTTACTCTTGAACTTT
1 -CAAAAATTCCATTTTTACCCTCGAACTTT
* * *
1899 CCAAAATTCCATTTTTAACCTCG-ATTTCT
1 CAAAAATTCCATTTTTACCCTCGAACTT-T
*
1928 CTAAAAATT-AATTTTTACCCTCGAACTTT
1 C-AAAAATTCCATTTTTACCCTCGAACTTT
* **
1957 CCAAAATTCCATTTTTAACCC-C-ATTTTT
1 CAAAAATTCCATTTTT-ACCCTCGAACTTT
* *
1985 CAAAAAATTACATTTTTACCCTTGAACTTT
1 C-AAAAATTCCATTTTTACCCTCGAACTTT
* **
2015 CCAAAATTCCATTTTTGACCC-CGATTTTT
1 CAAAAATTCCATTTTT-ACCCTCGAACTTT
*
2044 CCAAAAATTACATTTTTACCCTCGAACTTT
1 -CAAAAATTCCATTTTTACCCTCGAACTTT
* *
2074 CTAAAAATTCCATTTTGA-CCTC-AATTTTT
1 C-AAAAATTCCATTTTTACCCTCGAA-CTTT
* * *
2103 CCAAAATTACCA-TTTTACCCCCAAACTTT
1 CAAAAATT-CCATTTTTACCCTCGAACTTT
**
2132 CAAAAATTCCATTTTTTACCCT-GATTTTTTT
1 CAAAAATTCCA-TTTTTACCCTCGA--ACTTT
* * * * *
2163 TAAAAATTACAATTTTACCCCCGAA-TGT
1 CAAAAATTCCATTTTTACCCTCGAACTTT
* *
2191 CTAAAATTTCCATTTTTTACCC-CAAACTTT
1 C-AAAAATTCCA-TTTTTACCCTCGAACTTT
*
2221 CCAAAATTACCA-TTTTACCC
1 CAAAAATT-CCATTTTTACCC
2241 CCGGGTATCC
Statistics
Matches: 349, Mismatches: 77, Indels: 66
0.71 0.16 0.13
Matches are distributed among these distances:
28 75 0.21
29 137 0.39
30 123 0.35
31 14 0.04
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCGAACTTT
Found at i:2656 original size:30 final size:30
Alignment explanation
Indices: 2615--2818 Score: 122
Period size: 30 Copynumber: 6.9 Consensus size: 30
2605 NNNNNNNNNN
*
2615 TTTCCAAAAATTACATTTTTACCCTCGAAC
1 TTTCTAAAAATTACATTTTTACCCTCGAAC
* *
2645 TTTCTAAAAATTCCATTTTGA-CCTC-AA-
1 TTTCTAAAAATTACATTTTTACCCTCGAAC
* * *
2672 TTTTTCCAAAATTACCA-TTTTACCCCCGAAC
1 TTTCT-AAAAATTA-CATTTTTACCCTCGAAC
* **
2703 TTTC-AAAAATTCCATTTTTTACCCT-GATT
1 TTTCTAAAAATTACA-TTTTTACCCTCGAAC
* * *
2732 TTTTTAAAAAATTACAATTTTACCCCCGAA-
1 TTTCT-AAAAATTACATTTTTACCCTCGAAC
* * * *
2762 TGTCTAAAATTTCCATTTTTTACCC-CAAAC
1 TTTCTAAAAATTACA-TTTTTACCCTCGAAC
* *
2792 TTTC-CAAAATTACCA-TTTTGCCCTCGA
1 TTTCTAAAAATTA-CATTTTTACCCTCGA
2819 GTGTCCAAAA
Statistics
Matches: 129, Mismatches: 31, Indels: 29
0.68 0.16 0.15
Matches are distributed among these distances:
27 4 0.03
28 21 0.16
29 38 0.29
30 52 0.40
31 14 0.11
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTCTAAAAATTACATTTTTACCCTCGAAC
Found at i:2706 original size:58 final size:59
Alignment explanation
Indices: 2615--2810 Score: 220
Period size: 58 Copynumber: 3.3 Consensus size: 59
2605 NNNNNNNNNN
* *
2615 TTTCCAAAAATTA-CATTTTTACCCTCGAACTTTCTAAAAATTCCA-TTTTGACCTCAATT
1 TTTCC-AAAATTACCA-TTTTACCCCCGAACTTTCTAAAAATTCCATTTTTTACCTCAATT
* *
2674 TTTCCAAAATTACCATTTTACCCCCGAACTTTC-AAAAATTCCATTTTTTACCCTGATTTT
1 TTTCCAAAATTACCATTTTACCCCCGAACTTTCTAAAAATTCCATTTTTTA-CCTCA-ATT
** * * * * **
2734 TTTAAAAAATTACAATTTTACCCCCGAA-TGTCTAAAATTTCCATTTTTTACCCCAAAC
1 TTTCCAAAATTACCATTTTACCCCCGAACTTTCTAAAAATTCCATTTTTTACCTCAATT
2792 TTTCCAAAATTACCATTTT
1 TTTCCAAAATTACCATTTT
2811 GCCCTCGAGT
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
57 10 0.09
58 45 0.39
59 17 0.15
60 43 0.37
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.40
Consensus pattern (59 bp):
TTTCCAAAATTACCATTTTACCCCCGAACTTTCTAAAAATTCCATTTTTTACCTCAATT
Found at i:2709 original size:28 final size:28
Alignment explanation
Indices: 2621--2843 Score: 86
Period size: 28 Copynumber: 7.7 Consensus size: 28
2611 NNNNTTTCCA
*
2621 AAAATTA-CATTTTTACCCTCGAACTTTC
1 AAAATTACCA-TTTTACCCCCGAACTTTC
* *
2649 TAAAAATT-CCATTTTGA-CCTC-AATTTTTCC
1 --AAAATTACCATTTT-ACCCCCGAA-CTTT-C
2679 AAAATTACCATTTTACCCCCGAACTTTC
1 AAAATTACCATTTTACCCCCGAACTTTC
* ** *
2707 AAAAATT-CCATTTTTTA-CCCTGATTTTTTTAA
1 -AAAATTACCA--TTTTACCCCCGA--ACTTT-C
* *
2739 AAAATTACAATTTTACCCCCGAA-TGTC
1 AAAATTACCATTTTACCCCCGAACTTTC
* *
2766 TAAAATTTCCATTTTTTA-CCCCAAACTTTCC
1 -AAAATTACCA--TTTTACCCCCGAACTTT-C
* * * *
2797 AAAATTACCATTTTGCCCTCG-AGTGTCC
1 AAAATTACCATTTTACCCCCGAACT-TTC
*
2825 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
2844 TAGGTATCCA
Statistics
Matches: 148, Mismatches: 23, Indels: 46
0.68 0.11 0.21
Matches are distributed among these distances:
28 48 0.32
29 45 0.30
30 38 0.26
31 15 0.10
32 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAACTTTC
Found at i:2754 original size:60 final size:60
Alignment explanation
Indices: 2620--2786 Score: 207
Period size: 60 Copynumber: 2.8 Consensus size: 60
2610 NNNNNTTTCC
* * * *
2620 AAAAATTACATTTTTACCCTCGAACTTTCTAAAAATTCCA-TTTTGA-CCTCAATTTTTC
1 AAAAATTACAATTTTACCCCCGAACTTTCTAAAAATTCCATTTTTTACCCTCAATTTTTA
* * * *
2678 CAAAATTACCATTTTACCCCCGAACTTTC-AAAAATTCCATTTTTTACCCTGATTTTTTTA
1 AAAAATTACAATTTTACCCCCGAACTTTCTAAAAATTCCATTTTTTACCCTCA-ATTTTTA
* *
2738 AAAAATTACAATTTTACCCCCGAA-TGTCTAAAATTTCCATTTTTTACCC
1 AAAAATTACAATTTTACCCCCGAACTTTCTAAAAATTCCATTTTTTACCC
2787 CAAACTTTCC
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 10 0.11
58 30 0.32
59 7 0.08
60 46 0.49
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (60 bp):
AAAAATTACAATTTTACCCCCGAACTTTCTAAAAATTCCATTTTTTACCCTCAATTTTTA
Found at i:2828 original size:118 final size:118
Alignment explanation
Indices: 2620--2838 Score: 282
Period size: 118 Copynumber: 1.9 Consensus size: 118
2610 NNNNNTTTCC
* * * * **
2620 AAAAATTACATTTTTACCCTCGAACTTTCTAAAAATTCCATTTTGACCTCAATTTTTCCAAAATT
1 AAAAATTACAATTTTACCCCCGAACTGTCTAAAAATTCCATTTTGACCCCAAACTTTCCAAAATT
*
2685 ACCATTTTACCCCCGAACTTTCAAAAATT-CCATTTTTTACCCTGATTTTTTTA
66 ACCATTTTACCCCCGAAC-TTCCAAAATTACCATTTTTTACCCTGATTTTTTTA
* *
2738 AAAAATTACAATTTTACCCCCGAA-TGTCTAAAATTTCCATTTTTTACCCCAAACTTTCCAAAAT
1 AAAAATTACAATTTTACCCCCGAACTGTCTAAAAATTCCA-TTTTGACCCCAAACTTTCCAAAAT
* * *
2802 TACCATTTTGCCCTCG-AGTGTCCAAAATTACCATTTT
65 TACCATTTTACCCCCGAACT-TCCAAAATTACCATTTT
2839 GCCCCTAGGT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
116 1 0.01
117 22 0.26
118 63 0.73
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.39
Consensus pattern (118 bp):
AAAAATTACAATTTTACCCCCGAACTGTCTAAAAATTCCATTTTGACCCCAAACTTTCCAAAATT
ACCATTTTACCCCCGAACTTCCAAAATTACCATTTTTTACCCTGATTTTTTTA
Found at i:2858 original size:29 final size:28
Alignment explanation
Indices: 2794--2856 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
2784 CCCCAAACTT
* *
2794 TCCAAAATTACCATTTTGCCCTCGAGTG
1 TCCAAAATTACCATTTTGCCCTAGAGTA
2822 TCCAAAATTACCATTTTGCCCCTAG-GTA
1 TCCAAAATTACCATTTTG-CCCTAGAGTA
2850 TCCAAAA
1 TCCAAAA
2857 ATCTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCTAGAGTA
Done.