Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008518.1 Kokia drynarioides strain JFW-HI SEQ_123194, 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: 21751
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Found at i:2085 original size:135 final size:133
Alignment explanation
Indices: 1836--2334 Score: 549
Period size: 135 Copynumber: 3.8 Consensus size: 133
1826 ACTGTCCAAA
* * * * * *
1836 TTCGCTTTAATGTCCATAAAAAGATTGCAATTTTCCTTTTTAGTCTCCGGAGGGCTTCTTTC-GA
1 TTCGCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAG-
* * *
1900 TCATTGCCTCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACCGCACTGTCCAAATTTCTGAGT
65 TCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACTGAACTGTCCAAATTTCTGAG-
1965 TTTGT
129 TTTGT
* * * *
1970 TTCAGCTTTAACGTTCATAAAAAGATCACAGCTTTCCTTCTTAGTCTCTTGAGGGCTTCTTTCGG
1 TTC-GCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAG
* **
2035 TCATTGCATTCTTCTTAGTCTCCTGAGGGCTTCTTTTAGTCACTGAACTGTCCAAATTTCTGCA-
65 TCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACTGAACTGTCCAAATTTCTG-AG
2099 TTTGT
129 TTTGT
* * * * *
2104 TCCGTGCTCTATCGTTCAAAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCA
1 TTC--GCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCA
* * * * *
2169 GTCATTGCATTCTTCTCACTCTCCTGAGGGCTTCTTTCGGTCA-TCACACTGTCCAAGTTTCT--
64 GTCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACTGA-ACTGTCCAAATTTCTGA
*
2231 G-CT-T
128 GTTTGT
* *
2235 TT-G-----ACGTTCATGAAAAGACCGCAGTTTTCCTTCTTAGTCT-CTCGAGGGCTTCTTTCAG
1 TTCGCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCT-GAGGGCTTCTTTCAG
* *
2293 TCATTGCATCCTTCTTATTCTCCTGAGGGATTCTTTCGGTCA
65 TCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCA
2335 TCGCACCATC
Statistics
Matches: 316, Mismatches: 42, Indels: 25
0.83 0.11 0.07
Matches are distributed among these distances:
122 2 0.01
123 85 0.27
128 1 0.00
131 2 0.01
132 1 0.00
134 12 0.04
135 211 0.67
136 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.39
Consensus pattern (133 bp):
TTCGCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGT
CATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACTGAACTGTCCAAATTTCTGAGTT
TGT
Found at i:2347 original size:123 final size:123
Alignment explanation
Indices: 2124--2353 Score: 354
Period size: 123 Copynumber: 1.9 Consensus size: 123
2114 ATCGTTCAAA
* *
2124 AAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATTCTTCTCACT
1 AAAAGACCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATCCTTCTCACT
* ** *
2189 CTCCTGAGGGCTTCTTTCGGTCATCACACTGTCCAAGTTTCTGCTTTTGACGTTCATG
66 CTCCTGAGGGATTCTTTCGGTCATCACACCATCCAAATTTCTGCTTTTGACGTTCATG
* * *
2247 AAAAGACCGCAGTTTTCCTTCTTAGTCT-CTCGAGGGCTTCTTTCAGTCATTGCATCCTTCTTAT
1 AAAAGACCGCAGTTTTCCTTCTTAGTCTCCT-GAGGGCTACTTTCAGTCATTGCATCCTTCTCAC
*
2311 TCTCCTGAGGGATTCTTTCGGTCATCGCACCATCCAAATTTCT
65 TCTCCTGAGGGATTCTTTCGGTCATCACACCATCCAAATTTCT
2354 ACGTTTGCTC
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
122 2 0.02
123 94 0.98
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (123 bp):
AAAAGACCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATCCTTCTCACT
CTCCTGAGGGATTCTTTCGGTCATCACACCATCCAAATTTCTGCTTTTGACGTTCATG
Found at i:3585 original size:3 final size:3
Alignment explanation
Indices: 3565--3628 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
3555 TCAATAAATA
* *
3565 TAT TTT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3613 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
3629 CACTTAGGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3881 original size:53 final size:54
Alignment explanation
Indices: 3823--3938 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 54
3813 TAACAATCAT
* * * * *
3823 TCAATTATTAGTATTTTTTAT-T-ATTTAATTTTGAAAAGTTATAAAATATTCAC
1 TCAATTATTAGAATTTTTTATGTCATTTAATTAT-AAAAGTTACAAAATAATAAC
* *
3876 TCAATTATTAGAATTTTTTTTGTCATTTAATTATAAAAGTTACAAAATAATAAT
1 TCAATTATTAGAATTTTTTATGTCATTTAATTATAAAAGTTACAAAATAATAAC
3930 TCAATTATT
1 TCAATTATT
3939 CAATTTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 19 0.35
54 26 0.48
55 9 0.17
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (54 bp):
TCAATTATTAGAATTTTTTATGTCATTTAATTATAAAAGTTACAAAATAATAAC
Found at i:4226 original size:5 final size:5
Alignment explanation
Indices: 4216--4249 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4206 ACAGTTATTA
* *
4216 TTTGT TTTGT TTTGT TTTGT TCTGT TTTAT TTTG
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTG
4250 GGATAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.03, C:0.03, G:0.18, T:0.76
Consensus pattern (5 bp):
TTTGT
Found at i:4303 original size:2 final size:2
Alignment explanation
Indices: 4296--4334 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4286 TTTTGGTACT
4296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4335 TTGTTCACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7068 original size:22 final size:22
Alignment explanation
Indices: 7043--7090 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
7033 TTAATTTAGT
*
7043 ATTTATACATTTTTATAATTAA
1 ATTTAAACATTTTTATAATTAA
* * *
7065 ATTTAAATATTTTTATTATTTA
1 ATTTAAACATTTTTATAATTAA
7087 ATTT
1 ATTT
7091 GAATTCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTAAACATTTTTATAATTAA
Found at i:13865 original size:135 final size:133
Alignment explanation
Indices: 13616--14114 Score: 549
Period size: 135 Copynumber: 3.8 Consensus size: 133
13606 ACTGTCCAAA
* * * * * *
13616 TTCGCTTTAATGTCCATAAAAAGATTGCAATTTTCCTTTTTAGTCTCCGGAGGGCTTCTTTC-GA
1 TTCGCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAG-
* * *
13680 TCATTGCCTCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACCGCACTGTCCAAATTTCTGAGT
65 TCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACTGAACTGTCCAAATTTCTGAG-
13745 TTTGT
129 TTTGT
* * * *
13750 TTCAGCTTTAACGTTCATAAAAAGATCACAGCTTTCCTTCTTAGTCTCTTGAGGGCTTCTTTCGG
1 TTC-GCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAG
* **
13815 TCATTGCATTCTTCTTAGTCTCCTGAGGGCTTCTTTTAGTCACTGAACTGTCCAAATTTCTGCA-
65 TCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACTGAACTGTCCAAATTTCTG-AG
13879 TTTGT
129 TTTGT
* * * * *
13884 TCCGTGCTCTATCGTTCAAAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCA
1 TTC--GCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCA
* * * * *
13949 GTCATTGCATTCTTCTCACTCTCCTGAGGGCTTCTTTCGGTCA-TCACACTGTCCAAGTTTCT--
64 GTCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACTGA-ACTGTCCAAATTTCTGA
*
14011 G-CT-T
128 GTTTGT
* *
14015 TT-G-----ACGTTCATGAAAAGACCGCAGTTTTCCTTCTTAGTCT-CTCGAGGGCTTCTTTCAG
1 TTCGCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCT-GAGGGCTTCTTTCAG
* *
14073 TCATTGCATCCTTCTTATTCTCCTGAGGGATTCTTTCGGTCA
65 TCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCA
14115 TCGCACCATC
Statistics
Matches: 316, Mismatches: 42, Indels: 25
0.83 0.11 0.07
Matches are distributed among these distances:
122 2 0.01
123 85 0.27
128 1 0.00
131 2 0.01
132 1 0.00
134 12 0.04
135 211 0.67
136 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.39
Consensus pattern (133 bp):
TTCGCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGT
CATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCGGTCACTGAACTGTCCAAATTTCTGAGTT
TGT
Found at i:14127 original size:123 final size:123
Alignment explanation
Indices: 13904--14133 Score: 354
Period size: 123 Copynumber: 1.9 Consensus size: 123
13894 ATCGTTCAAA
* *
13904 AAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATTCTTCTCACT
1 AAAAGACCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATCCTTCTCACT
* ** *
13969 CTCCTGAGGGCTTCTTTCGGTCATCACACTGTCCAAGTTTCTGCTTTTGACGTTCATG
66 CTCCTGAGGGATTCTTTCGGTCATCACACCATCCAAATTTCTGCTTTTGACGTTCATG
* * *
14027 AAAAGACCGCAGTTTTCCTTCTTAGTCT-CTCGAGGGCTTCTTTCAGTCATTGCATCCTTCTTAT
1 AAAAGACCGCAGTTTTCCTTCTTAGTCTCCT-GAGGGCTACTTTCAGTCATTGCATCCTTCTCAC
*
14091 TCTCCTGAGGGATTCTTTCGGTCATCGCACCATCCAAATTTCT
65 TCTCCTGAGGGATTCTTTCGGTCATCACACCATCCAAATTTCT
14134 ACGTTTGCTC
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
122 2 0.02
123 94 0.98
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (123 bp):
AAAAGACCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATCCTTCTCACT
CTCCTGAGGGATTCTTTCGGTCATCACACCATCCAAATTTCTGCTTTTGACGTTCATG
Found at i:15365 original size:3 final size:3
Alignment explanation
Indices: 15345--15408 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
15335 TCAATAAATA
* *
15345 TAT TTT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15393 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
15409 CACTTAGGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:15661 original size:53 final size:54
Alignment explanation
Indices: 15603--15718 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 54
15593 TAACAATCAT
* * * * *
15603 TCAATTATTAGTATTTTTTAT-T-ATTTAATTTTGAAAAGTTATAAAATATTCAC
1 TCAATTATTAGAATTTTTTATGTCATTTAATTAT-AAAAGTTACAAAATAATAAC
* *
15656 TCAATTATTAGAATTTTTTTTGTCATTTAATTATAAAAGTTACAAAATAATAAT
1 TCAATTATTAGAATTTTTTATGTCATTTAATTATAAAAGTTACAAAATAATAAC
15710 TCAATTATT
1 TCAATTATT
15719 CAATTTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 19 0.35
54 26 0.48
55 9 0.17
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (54 bp):
TCAATTATTAGAATTTTTTATGTCATTTAATTATAAAAGTTACAAAATAATAAC
Found at i:16006 original size:5 final size:5
Alignment explanation
Indices: 15996--16029 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
15986 ACAGTTATTA
* *
15996 TTTGT TTTGT TTTGT TTTGT TCTGT TTTAT TTTG
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTG
16030 GGATAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.03, C:0.03, G:0.18, T:0.76
Consensus pattern (5 bp):
TTTGT
Found at i:16083 original size:2 final size:2
Alignment explanation
Indices: 16076--16114 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16066 TTTTGGTACT
16076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16115 TTGTTCACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18848 original size:22 final size:22
Alignment explanation
Indices: 18823--18870 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
18813 TTAATTTAGT
*
18823 ATTTATACATTTTTATAATTAA
1 ATTTAAACATTTTTATAATTAA
* * *
18845 ATTTAAATATTTTTATTATTTA
1 ATTTAAACATTTTTATAATTAA
18867 ATTT
1 ATTT
18871 GAATTCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTAAACATTTTTATAATTAA
Done.