Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007043.1 Kokia drynarioides strain JFW-HI SEQ_121651, 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: 4608
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Found at i:1019 original size:14 final size:13
Alignment explanation
Indices: 1000--1048 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
990 GTCGATTACA
1000 TTTGTCTTCTTGCT
1 TTTGTCTT-TTGCT
*
1014 TTTGTCTTGTTACT
1 TTTGTCTT-TTGCT
*
1028 CTTTATCTTTTGCT
1 -TTTGTCTTTTGCT
1042 TTTGTCT
1 TTTGTCT
1049 CTGTGTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 6 0.21
14 16 0.55
15 7 0.24
ACGTcount: A:0.04, C:0.18, G:0.12, T:0.65
Consensus pattern (13 bp):
TTTGTCTTTTGCT
Found at i:2012 original size:39 final size:39
Alignment explanation
Indices: 1837--2185 Score: 286
Period size: 38 Copynumber: 9.0 Consensus size: 39
1827 AAGATTGGAT
* * * **
1837 GATGTCTTCAATCTTCCCTATAATTGGGGTAAGAGATTG
1 GATGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTG
* *
1876 ATTGATGTCTTTAATCTACCCCATGATC-GAGGTAAGAGATTG
1 ---GATGTCTTCAATCTGCCCCATGATCAG-GGTAAGAGATTG
* * * *
1918 GTGTGTCTTCAATTTG-CCCACTAATTAGGGTATA-AGATTG
1 G-ATGTCTTCAATCTGCCCCA-TGATCAGGGTA-AGAGATTG
*
1958 GATG-CTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
1 GATGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTG
* * * *
1996 CATGTCTTCAATCTGCCTTC-TGATTAAGGTAAGAGATTG
1 GATGTCTTCAATCTGCC-CCATGATCAGGGTAAGAGATTG
* *
2035 GATG-CTTCAATCTGCCCCATGATCAAGGTAAGAGATTA
1 GATGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTG
* * * * * * *
2073 CATGTCTTCAATCTACCTTC-TGATTAAGTTAAAAGATTG
1 GATGTCTTCAATCTGCC-CCATGATCAGGGTAAGAGATTG
* *
2112 GATG-CTTCAATCTGTCCCATGATC-GGGTAAAAGATT-
1 GATGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTG
* *
2148 GATGTCTTCAATCTGCTCCATGATCGGGGTAAGAGATT
1 GATGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATT
2186 AAATGGTGTC
Statistics
Matches: 250, Mismatches: 42, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
36 4 0.02
37 31 0.12
38 83 0.33
39 71 0.28
40 26 0.10
41 3 0.01
42 32 0.13
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (39 bp):
GATGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTG
Found at i:2046 original size:77 final size:77
Alignment explanation
Indices: 1864--2163 Score: 372
Period size: 77 Copynumber: 3.9 Consensus size: 77
1854 CTATAATTGG
* * **
1864 GGTAAGAGATTGATTGATGTCTTTAATCTACCCCATGATCGAGGTAAGAGATTGGTGTGTCTTCA
1 GGTAAGAGATTG---GATG-CTTCAATCTGCCCCATGATCGAGGTAAGAGATT-GCATGTCTTCA
* ** * *
1929 ATTTGCCCACTAATTAG
61 ATCTGCCTTCTGATTAA
*
1946 GGTATA-AGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGCATGTCTTCAATCT
1 GGTA-AGAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGCATGTCTTCAATCT
2010 GCCTTCTGATTAA
65 GCCTTCTGATTAA
* * *
2023 GGTAAGAGATTGGATGCTTCAATCTGCCCCATGATCAAGGTAAGAGATTACATGTCTTCAATCTA
1 GGTAAGAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGCATGTCTTCAATCTG
2088 CCTTCTGATTAA
66 CCTTCTGATTAA
* * * *
2100 GTTAAAAGATTGGATGCTTCAATCTGTCCCATGATCG-GGTAAAAGATTG-ATGTCTTCAATCTG
1 GGTAAGAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGCATGTCTTCAATCTG
2163 C
66 C
2164 TCCATGATCG
Statistics
Matches: 195, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
75 14 0.07
76 11 0.06
77 125 0.64
78 30 0.15
79 4 0.02
82 10 0.05
83 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (77 bp):
GGTAAGAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGCATGTCTTCAATCTG
CCTTCTGATTAA
Found at i:2604 original size:50 final size:49
Alignment explanation
Indices: 2386--2958 Score: 426
Period size: 50 Copynumber: 11.7 Consensus size: 49
2376 ACAAGGTTCT
* * * * * **
2386 CGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCTT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCGGGTTCGC
* * * *
2435 CGTTGTGGCCTCAATCC-TTCCCATTACATCTTCTAAGGTACCGGGTTCAC
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTACCGGGTTCGC
* * * * * * *
2485 CATTGC-GACTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTTGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCGGGTTCGC
** * * * * *
2533 TATTGTGGCTTCAATCC-TTCCCATCGCATCTTCTAAGGTACCGAGTTCGC
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTACCGGGTTCGC
* * ** * *
2583 CATTGCGGCCTCAACCTTTCCCTTCATGTCTTCATGGTACAGGGTTCAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCGGGTTCGC
* * * ** *
2632 CGTTACGGCCTCAACCTTTCCCATCACGTCTTCCAAGGTATTGGGTTCAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTT-CATGGTACCGGGTTCGC
* * * * * * *
2682 CGTTACGGCCTTAACCTTTCTC-T-TCATCTTCATGGTATCGAGTTCGA
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCGGGTTCGC
* * * * * * *
2729 CATTACGACCTCAACCTTTCCTATCACATCTTCCAAGGTATCGGGTTCAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTT-CATGGTACCGGGTTCGC
* ** * * *
2779 CGTTACGATCTCAACCTTTTCC-T-TCATCTTCATGGTACCGAGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCGGGTTCGC
* * *
2826 CGTTGCGACCTCAACCTTTCCCATCACATCTTTCAAGGTATCGGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATC-TTCATGGTACCGGGTTCGC
* * * * *
2876 CATTACGGCTTCAACCTTTCCCTTCAC--CTTCATGGTACCGGGTTCGT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCGGGTTCGC
*
2923 CGTTGCGGCCTCAACCTTTCCCATTACATCTTCATG
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATG
2959 TTTCCTTGGT
Statistics
Matches: 411, Mismatches: 97, Indels: 32
0.76 0.18 0.06
Matches are distributed among these distances:
47 99 0.24
48 31 0.08
49 125 0.30
50 156 0.38
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (49 bp):
CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCGGGTTCGC
Found at i:2755 original size:97 final size:97
Alignment explanation
Indices: 2392--2955 Score: 530
Period size: 97 Copynumber: 5.8 Consensus size: 97
2382 TTCTCGTTGT
** ** *
2392 GGCCTCAACCTTTCCCTTCATATCTTCATGGTACC-AGATTCTTCGTTGTGGCCTCAATCC-TTC
1 GGCCTCAACCTTTCCCTTC--ATCTTCATGGTACCGAG-TTCGACGTTACGACCTCAA-CCTTTC
* * * * *
2455 CCATTACATCTTCTAAGGTACCGGGTTCACCATTGC
62 CCATCACATCTTCCAAGGTATCGGGTTCACCGTTAC
* * * ** * *
2491 -GACTCAACCTTTCCCTTCATATCTTCATGGTACC-AGATTTG-CTATTGTGGCTTCAATCC-TT
1 GGCCTCAACCTTTCCCTTC--ATCTTCATGGTACCGAG-TTCGAC-GTTACGACCTCAA-CCTTT
* * * * * * *
2552 CCCATCGCATCTTCTAAGGTACCGAGTTCGCCATTGC
61 CCCATCACATCTTCCAAGGTATCGGGTTCACCGTTAC
* * *
2589 GGCCTCAACCTTTCCCTTCATGTCTTCATGGTACAGGGTTC-ACCGTTACGGCCTCAACCTTTCC
1 GGCCTCAACCTTTCCCTTCA--TCTTCATGGTACCGAGTTCGA-CGTTACGACCTCAACCTTTCC
* *
2653 CATCACGTCTTCCAAGGTATTGGGTTCACCGTTAC
63 CATCACATCTTCCAAGGTATCGGGTTCACCGTTAC
* * * * *
2688 GGCCTTAACCTTTCTCTTCATCTTCATGGTATCGAGTTCGACATTACGACCTCAACCTTTCCTAT
1 GGCCTCAACCTTTCCCTTCATCTTCATGGTACCGAGTTCGACGTTACGACCTCAACCTTTCCCAT
2753 CACATCTTCCAAGGTATCGGGTTCACCGTTAC
66 CACATCTTCCAAGGTATCGGGTTCACCGTTAC
** * * *
2785 GATCTCAACCTTTTCCTTCATCTTCATGGTACCGAGTTCGCCGTTGCGACCTCAACCTTTCCCAT
1 GGCCTCAACCTTTCCCTTCATCTTCATGGTACCGAGTTCGACGTTACGACCTCAACCTTTCCCAT
* * *
2850 CACATCTTTCAAGGTATCGGGTTCGCCATTAC
66 CACATCTTCCAAGGTATCGGGTTCACCGTTAC
* * * * * *
2882 GGCTTCAACCTTTCCCTTCACCTTCATGGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCAT
1 GGCCTCAACCTTTCCCTTCATCTTCATGGTACCGAGTTCGACGTTACGACCTCAACCTTTCCCAT
*
2947 TACATCTTC
66 CACATCTTC
2956 ATGTTTCCTT
Statistics
Matches: 397, Mismatches: 59, Indels: 20
0.83 0.12 0.04
Matches are distributed among these distances:
97 217 0.55
98 90 0.23
99 88 0.22
100 2 0.01
ACGTcount: A:0.18, C:0.33, G:0.16, T:0.34
Consensus pattern (97 bp):
GGCCTCAACCTTTCCCTTCATCTTCATGGTACCGAGTTCGACGTTACGACCTCAACCTTTCCCAT
CACATCTTCCAAGGTATCGGGTTCACCGTTAC
Found at i:2868 original size:147 final size:144
Alignment explanation
Indices: 2386--2958 Score: 423
Period size: 147 Copynumber: 3.9 Consensus size: 144
2376 ACAAGGTTCT
* * * * * ** * **
2386 CGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTA-CCAGATTCTTCGTTGTGGCCTCAAT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCAAGGTATCGAG-TTCGCCATTACGGCCTCAA-
* * * * *
2450 CC-TTCCCATTACATCTTCTAAGGTACCGGGTTCACCATTGCGACTCAACCTTTCCCTTCATATC
64 CCTTTCCTATCACATCTTCCAAGGTA-CGGGTTCACCGTTACGACTCAACCTTTCCCTTC--ATC
*
2514 TTCATGGTACC-AGATTTGC
126 TTCATGGTACCGAG-TTCGC
** * * * * *
2533 TATTGTGGCTTCAATCC-TTCCCATCGCATCTTCTAAGGTACCGAGTTCGCCATTGCGGCCTCAA
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-AAGGTATCGAGTTCGCCATTACGGCCTCAA
** * * *
2597 CCTTTCCCT-TCATGTCTT-CATGGTACAGGGTTCACCGTTACGGCCTCAACCTTTCCCATCACG
64 CCTTT-CCTATCACATCTTCCAAGGTAC-GGGTTCACCGTTAC-GACTCAACCTTTCCCTTCA--
* ** * *
2660 TCTTCCAAGGTATTGGGTTCAC
124 TCTT-CATGGTACCGAGTTCGC
* * * * * * *
2682 CGTTACGGCCTTAACCTTTCTC-T-TCATCTTCATGGTATCGAGTTCGACATTACGACCTCAACC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCAAGGTATCGAGTTCGCCATTACGGCCTCAACC
*
2745 TTTCCTATCACATCTTCCAAGGTATCGGGTTCACCGTTACGATCTCAACCTTTTCCTTCATCTTC
66 TTTCCTATCACATCTTCCAAGGTA-CGGGTTCACCGTTACGA-CTCAACCTTTCCCTTCATCTTC
2810 ATGGTACCGAGTTCGC
129 ATGGTACCGAGTTCGC
* * *
2826 CGTTGCGACCTCAACCTTTCCCATCACATCTTTCAAGGTATCGGGTTCGCCATTACGGCTTCAAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATC-TTCAAGGTATCGAGTTCGCCATTACGGCCTCAAC
* ** * *
2891 CTTTCCCT-TCAC--CTT-CATGGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATTACAT
65 CTTT-CCTATCACATCTTCCAAGGTA-CGGGTTCACCGTTAC-GACTCAACCTTTCCC-TT-CAT
2952 CTTCATG
125 CTTCATG
2959 TTTCCTTGGT
Statistics
Matches: 334, Mismatches: 69, Indels: 47
0.74 0.15 0.10
Matches are distributed among these distances:
144 60 0.18
145 14 0.04
146 54 0.16
147 122 0.37
148 57 0.17
149 26 0.08
150 1 0.00
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (144 bp):
CGTTGCGGCCTCAACCTTTCCCATCACATCTTCAAGGTATCGAGTTCGCCATTACGGCCTCAACC
TTTCCTATCACATCTTCCAAGGTACGGGTTCACCGTTACGACTCAACCTTTCCCTTCATCTTCAT
GGTACCGAGTTCGC
Found at i:3912 original size:14 final size:13
Alignment explanation
Indices: 3893--3941 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
3883 GTTTATTACA
3893 TTTGTCTTCTTGCT
1 TTTGTCTT-TTGCT
3907 TTTGTCTTGTTGTTCT
1 TTTGTCTT-TTG--CT
3923 TTT-TCTTTTGCT
1 TTTGTCTTTTGCT
3935 TTTGTCT
1 TTTGTCT
3942 CTATGTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.16
13 3 0.10
14 14 0.45
15 4 0.13
16 5 0.16
ACGTcount: A:0.00, C:0.16, G:0.14, T:0.69
Consensus pattern (13 bp):
TTTGTCTTTTGCT
Found at i:3948 original size:28 final size:29
Alignment explanation
Indices: 3897--3961 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 29
3887 ATTACATTTG
*
3897 TCTTCTTGCTTTTGTCTTGTTGTTCTTT-T-
1 TCTT-TTGCTTTTGTCTTGATGTT-TTTCTC
3926 TCTTTTGCTTTTGTCTCT-ATGTTTTTCTC
1 TCTTTTGCTTTTGTCT-TGATGTTTTTCTC
3955 TCTTTTG
1 TCTTTTG
3962 AAGGCGTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 17 0.53
29 12 0.38
ACGTcount: A:0.02, C:0.18, G:0.12, T:0.68
Consensus pattern (29 bp):
TCTTTTGCTTTTGTCTTGATGTTTTTCTC
Done.