Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001421.1 Kokia drynarioides strain JFW-HI SEQ_112920, 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: 25094
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:5098 original size:59 final size:59
Alignment explanation
Indices: 4984--5100 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 59
4974 CATTGTTGTT
*
4984 TCTCTCTTTCATATAATATACATATCATATTACATATAAATAACTTTAAATTATAAGTAG
1 TCTCTCTTTCATATAATATACATA-CATATTACATATAAATAACTTTAAACTATAAGTAG
* *
5044 TCTCTCTTTCATATAATATAACATA-ATATTATATATAAAT-AGTTCTAAACTATAAGT
1 TCTCTCTTTCATATAATAT-ACATACATATTACATATAAATAACTT-TAAACTATAAGT
5101 CCTCGTGAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
58 3 0.06
59 25 0.48
60 19 0.37
61 5 0.10
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (59 bp):
TCTCTCTTTCATATAATATACATACATATTACATATAAATAACTTTAAACTATAAGTAG
Found at i:5114 original size:60 final size:59
Alignment explanation
Indices: 4990--5115 Score: 130
Period size: 59 Copynumber: 2.1 Consensus size: 59
4980 TGTTTCTCTC
* * **
4990 TTTCATATAATATACATATCATATTACATATAAATAACTTTAAATTATAAGTAGTCTCTC
1 TTTCATATAATATACATA-CATATTACATATAAATAACTTTAAACTATAAGTACTCTCAA
* * * *
5050 TTTCATATAATATAACATA-ATATTATATATAAAT-AGTTCTAAACTATAAGTCCTCGTGAA
1 TTTCATATAATAT-ACATACATATTACATATAAATAACTT-TAAACTATAAGTACTC-TCAA
5110 TTTCAT
1 TTTCAT
5116 TTCAATTGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
58 3 0.05
59 27 0.49
60 20 0.36
61 5 0.09
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTCATATAATATACATACATATTACATATAAATAACTTTAAACTATAAGTACTCTCAA
Found at i:5158 original size:9 final size:10
Alignment explanation
Indices: 5135--5159 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5125 AGAAACTCTA
5135 AAAAACTTAT
1 AAAAACTTAT
5145 AAAAACTTAT
1 AAAAACTTAT
5155 AAAAA
1 AAAAA
5160 GAATAAGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAACTTAT
Found at i:5240 original size:13 final size:14
Alignment explanation
Indices: 5222--5250 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5212 TCTTCAAATG
5222 AAAAAACTC-TAAA
1 AAAAAACTCATAAA
5235 AAAAAACTCATAAA
1 AAAAAACTCATAAA
5249 AA
1 AA
5251 TAATGAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAACTCATAAA
Found at i:7837 original size:19 final size:20
Alignment explanation
Indices: 7799--7838 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7789 ATAATCGTCT
*
7799 TTTTTAATTTAAATTTAATA
1 TTTTTAATTTAAATTAAATA
*
7819 TTTTTATTTTAAA-TAAATA
1 TTTTTAATTTAAATTAAATA
7838 T
1 T
7839 AATTTCCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTAATTTAAATTAAATA
Found at i:8960 original size:26 final size:26
Alignment explanation
Indices: 8922--8973 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
8912 TGACCGGACC
** *
8922 CCTTTAATTAATTTTCCTTAAAAAAT
1 CCTTTAAAAAATTTTCATTAAAAAAT
*
8948 CCTTTAAAAAATTTTCATTTAAAAAT
1 CCTTTAAAAAATTTTCATTAAAAAAT
8974 TTTCCTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (26 bp):
CCTTTAAAAAATTTTCATTAAAAAAT
Found at i:12152 original size:31 final size:32
Alignment explanation
Indices: 12114--12188 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
12104 ATATTTATCT
* *
12114 CATACATACATA-AAATACTAATATATCATAA
1 CATACATACATATAAACACTAAAATATCATAA
*
12145 CATACATA-ATATACACACTAAAATATCATAA
1 CATACATACATATAAACACTAAAATATCATAA
*
12176 CATAGATAACATA
1 CATACAT-ACATA
12189 CATAATATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 30 0.81
32 1 0.03
33 3 0.08
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.27
Consensus pattern (32 bp):
CATACATACATATAAACACTAAAATATCATAA
Found at i:12159 original size:40 final size:40
Alignment explanation
Indices: 12115--12227 Score: 149
Period size: 40 Copynumber: 2.8 Consensus size: 40
12105 TATTTATCTC
*
12115 ATACATACATAAAATA-C-TAATATATCATAACATACATAAT
1 ATACATAC-TAAAATATCATAACATA-CATAACATACATAAT
* *
12155 ATACACACTAAAATATCATAACATAGATAACATACATAAT
1 ATACATACTAAAATATCATAACATACATAACATACATAAT
* *
12195 ATACATATTAATATATCATAACATACATAACAT
1 ATACATACTAAAATATCATAACATACATAACAT
12228 GTAACATCCC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
39 7 0.11
40 51 0.80
41 6 0.09
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.29
Consensus pattern (40 bp):
ATACATACTAAAATATCATAACATACATAACATACATAAT
Found at i:12190 original size:31 final size:31
Alignment explanation
Indices: 12130--12190 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
12120 TACATAAAAT
* *
12130 ACTAATATATCATAACATACATAATATACAC
1 ACTAAAATATCATAACATACATAACATACAC
*
12161 ACTAAAATATCATAACATAGATAACATACA
1 ACTAAAATATCATAACATACATAACATACA
12191 TAATATACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.26
Consensus pattern (31 bp):
ACTAAAATATCATAACATACATAACATACAC
Found at i:13311 original size:15 final size:15
Alignment explanation
Indices: 13291--13329 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
13281 AAGTCAAGGT
13291 ATGATGAGTTCATGA
1 ATGATGAGTTCATGA
*
13306 ATGATGGGTTCATGA
1 ATGATGAGTTCATGA
13321 ATGATGAGT
1 ATGATGAGT
13330 CTATGTATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (15 bp):
ATGATGAGTTCATGA
Found at i:13645 original size:28 final size:27
Alignment explanation
Indices: 13603--13700 Score: 101
Period size: 28 Copynumber: 3.6 Consensus size: 27
13593 AAACACTAGT
* *
13603 AAGGAAGCCTGTGTGGCTATCTCTGTTA
1 AAGGAAGCCTTTGTGGCAATCTCT-TTA
* *
13631 AAGGAAGCCTTTGTGACAATCTCTATA
1 AAGGAAGCCTTTGTGGCAATCTCTTTA
*
13658 AAGGACA-CCTTTGAGGCAAATCTC-TTA
1 AAGGA-AGCCTTTGTGGC-AATCTCTTTA
13685 AAGGAAAGCCTTTGTG
1 AAGG-AAGCCTTTGTG
13701 ATGAGTACTA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
27 22 0.38
28 36 0.62
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (27 bp):
AAGGAAGCCTTTGTGGCAATCTCTTTA
Found at i:13668 original size:27 final size:27
Alignment explanation
Indices: 13628--13701 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
13618 GCTATCTCTG
13628 TTAAAGGAAGCCTTTGTGAC-AATCTC
1 TTAAAGGAAGCCTTTGTGACAAATCTC
* *
13654 TATAAAGGACA-CCTTTGAGGCAAATCTC
1 T-TAAAGGA-AGCCTTTGTGACAAATCTC
13682 TTAAAGGAAAGCCTTTGTGA
1 TTAAAGG-AAGCCTTTGTGA
13702 TGAGTACTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.03
27 22 0.56
28 16 0.41
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (27 bp):
TTAAAGGAAGCCTTTGTGACAAATCTC
Found at i:22006 original size:16 final size:16
Alignment explanation
Indices: 21987--22039 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
21977 ATATGCTTAT
21987 AAAATAATTAAAAATAAAA
1 AAAATAATTAAAAAT---A
*
22006 AAACATTAATTAAAAATG
1 AAA-A-TAATTAAAAATA
22024 AAAATAATTAAAAATA
1 AAAATAATTAAAAATA
22040 TCATCAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 11 0.37
17 1 0.03
18 3 0.10
19 3 0.10
20 1 0.03
21 11 0.37
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAATAATTAAAAATA
Found at i:22033 original size:20 final size:21
Alignment explanation
Indices: 21991--22069 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
21981 GCTTATAAAA
21991 TAATTAAAAATAAAAAAACAT
1 TAATTAAAAATAAAAAAACAT
* *
22012 TAATTAAAAATGAAAATA-AT
1 TAATTAAAAATAAAAAAACAT
* **
22032 TAA--AAATATCATCAAAACAT
1 TAATTAAAAAT-AAAAAAACAT
*
22052 TAATTGAAAATAAAAAAA
1 TAATTAAAAATAAAAAAA
22070 TTTGAAATAA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
18 5 0.12
19 3 0.07
20 10 0.23
21 21 0.49
22 4 0.09
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (21 bp):
TAATTAAAAATAAAAAAACAT
Found at i:22062 original size:40 final size:36
Alignment explanation
Indices: 21985--22071 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 36
21975 TAATATGCTT
21985 ATAAAATAATTAAAAATAAAAAAACATTAATTAAAA
1 ATAAAATAATTAAAAATAAAAAAACATTAATTAAAA
* *
22021 ATGAAAATAATTAAAAATATCATCAAAACATTAATTGAAA
1 AT-AAAATAATTAAAAATA--A-AAAAACATTAATTAAAA
*
22061 ATAAAAAAATT
1 ATAAAATAATT
22072 TGAAATAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
36 2 0.05
37 16 0.36
39 9 0.20
40 17 0.39
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (36 bp):
ATAAAATAATTAAAAATAAAAAAACATTAATTAAAA
Found at i:22396 original size:142 final size:140
Alignment explanation
Indices: 22122--22445 Score: 343
Period size: 142 Copynumber: 2.3 Consensus size: 140
22112 AAATAATGCT
* * *
22122 ACCTCAGACTCAA-GATATAATTGCAATTATCTAATCATCTAATGAAAGAAGGTAATATGTAAAA
1 ACCTAAGACTCAAGGATGTAATTGCAATTATCTAACCATCTAATGAAAGAAGGTAATATGTAAAA
* * * * * ** * *
22186 AATATTAATTAAAAATAAAAAAAGCTTGAAGCAACGTGAAATAAAAAATACAAATGCGATTAGTA
66 AAGAATAATTAAAAATAAAAAAAGCTTAAAACAACATGAAATAAAAAATACAAACACGAGTAGGA
22251 GATG-ATTCAA
131 GATGAATT-AA
* * * * *
22261 ACTTGAGACTCAAGGATGTAATTACAATTATCTAACCATCTAATGAAAGAA-TTAA-ATTTAAAA
1 ACCTAAGACTCAAGGATGTAATTGCAATTATCTAACCATCTAATGAAAGAAGGTAATATGTAAAA
* * *
22324 AAGAAT-ATTAAATATATAATTTTAAAAGCTTAAAACAATATGAAATAAAAAATACAAACATGAG
66 AAGAATAATTAAA-A-ATAA---AAAAAGCTTAAAACAACATGAAATAAAAAATACAAACACGAG
*
22388 TAGGAGATGAATTGA
126 TAGGAGATGAATTAA
* **
22403 ACCTAAGACCCAAGGATGTAATTGCAGCTATCTAACCATCTAA
1 ACCTAAGACTCAAGGATGTAATTGCAATTATCTAACCATCTAA
22446 CAAAAAAACT
Statistics
Matches: 152, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
137 6 0.04
138 12 0.08
139 18 0.12
140 34 0.22
142 79 0.52
143 3 0.02
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.27
Consensus pattern (140 bp):
ACCTAAGACTCAAGGATGTAATTGCAATTATCTAACCATCTAATGAAAGAAGGTAATATGTAAAA
AAGAATAATTAAAAATAAAAAAAGCTTAAAACAACATGAAATAAAAAATACAAACACGAGTAGGA
GATGAATTAA
Found at i:23272 original size:16 final size:15
Alignment explanation
Indices: 23251--23292 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
23241 AAATATAAAA
*
23251 ATAAAAAATTAATATT
1 ATAAAAAATTAA-ATC
23267 ATAAAAAAATTAAATC
1 AT-AAAAAATTAAATC
23283 ATAAAAAATT
1 ATAAAAAATT
23293 GAATTCCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 10 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAAAATTAAATC
Found at i:23275 original size:17 final size:16
Alignment explanation
Indices: 23253--23290 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
23243 ATATAAAAAT
*
23253 AAAAAATTAATATTATA
1 AAAAAATTAA-ATCATA
23270 AAAAAATTAAATCATA
1 AAAAAATTAAATCATA
23286 AAAAA
1 AAAAA
23291 TTGAATTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAATTAAATCATA
Done.