Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013516.1 Kokia drynarioides strain JFW-HI SEQ_128542, 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: 46133
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Warning! 91 characters in sequence are not A, C, G, or T
Found at i:2135 original size:28 final size:28
Alignment explanation
Indices: 2095--2152 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2085 CATCCTTTTC
2095 TAGAATGGTAAATAAACAACAATTAGAA
1 TAGAATGGTAAATAAACAACAATTAGAA
2123 TAGAATGGTAAATAAACAACAATTAGAA
1 TAGAATGGTAAATAAACAACAATTAGAA
2151 TA
1 TA
2153 AAATATTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.22
Consensus pattern (28 bp):
TAGAATGGTAAATAAACAACAATTAGAA
Found at i:7628 original size:7 final size:7
Alignment explanation
Indices: 7616--7642 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
7606 TTAAACCACA
7616 CATCTTT
1 CATCTTT
7623 CATCTTT
1 CATCTTT
7630 CATCTTT
1 CATCTTT
7637 CATCTT
1 CATCTT
7643 ATTTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.56
Consensus pattern (7 bp):
CATCTTT
Found at i:7954 original size:83 final size:85
Alignment explanation
Indices: 7828--7992 Score: 217
Period size: 83 Copynumber: 2.0 Consensus size: 85
7818 ATAATTAATA
* * **
7828 CTCCACATTCTGTAAGCTCATTAGAGAAGTAGATGCTGGTCACGAATTTTAAATTTACTCCATAC
1 CTCCACATTCTGTAAGCCCATTAGAGAAGTAGATACTGGTCACGAATTTTAAAACTACTCCATAC
*
7893 TCAAGGCGAGGATCGAAATC
66 TCAAGACGAGGATCGAAATC
* * * * *
7913 CTCCGCATTCTGTAGGCCCATTA-AG-GGTAGATATTGGTCACGAATTTTAAAACTGCTCCATAC
1 CTCCACATTCTGTAAGCCCATTAGAGAAGTAGATACTGGTCACGAATTTTAAAACTACTCCATAC
*
7976 TCAAGACGATGATCGAA
66 TCAAGACGAGGATCGAA
7993 CCCTCGACTA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
83 47 0.68
84 2 0.03
85 20 0.29
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (85 bp):
CTCCACATTCTGTAAGCCCATTAGAGAAGTAGATACTGGTCACGAATTTTAAAACTACTCCATAC
TCAAGACGAGGATCGAAATC
Found at i:8229 original size:15 final size:15
Alignment explanation
Indices: 8191--8234 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
8181 TATAAATTAA
*
8191 TTTAAATATAAAATT
1 TTTAAATTTAAAATT
8206 TTTACAATTTAAAATT
1 TTTA-AATTTAAAATT
*
8222 TTTAAATTCAAAA
1 TTTAAATTTAAAA
8235 ATATAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAAATTTAAAATT
Found at i:8251 original size:24 final size:23
Alignment explanation
Indices: 8224--8280 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
8214 TTAAAATTTT
8224 TAAATTCAAAAATATAAATAATTA
1 TAAATTCAAAAAT-TAAATAATTA
* *
8248 TAAATTTTAATAATTAAATAATTA
1 TAAA-TTCAAAAATTAAATAATTA
*
8272 -AATTTCAAA
1 TAAATTCAAA
8281 TATAAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 4 0.15
23 2 0.07
24 14 0.52
25 7 0.26
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATTCAAAAATTAAATAATTA
Found at i:8882 original size:18 final size:18
Alignment explanation
Indices: 8859--8900 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
8849 AAATAATTTT
8859 AAAAATATGAAAAATATA
1 AAAAATATGAAAAATATA
* * *
8877 AAAAATTTTAAAAATTTA
1 AAAAATATGAAAAATATA
8895 AAAAAT
1 AAAAAT
8901 GTGTTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAATATGAAAAATATA
Found at i:8883 original size:27 final size:27
Alignment explanation
Indices: 8848--8900 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
8838 AATTTTGTTT
* *
8848 TAAATAATTTTAAAAATATGAAAAATA
1 TAAAAAATTTTAAAAATATAAAAAATA
*
8875 TAAAAAATTTTAAAAATTTAAAAAAT
1 TAAAAAATTTTAAAAATATAAAAAAT
8901 GTGTTATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
TAAAAAATTTTAAAAATATAAAAAATA
Found at i:9553 original size:12 final size:12
Alignment explanation
Indices: 9536--9577 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
9526 AACCCAATTC
9536 TATTTTTATTAT
1 TATTTTTATTAT
9548 TATTTTTA-T-T
1 TATTTTTATTAT
*
9558 TATTTAT-TTAT
1 TATTTTTATTAT
9569 TATTTTTAT
1 TATTTTTAT
9578 GAATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 8 0.32
11 8 0.32
12 9 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:9731 original size:71 final size:72
Alignment explanation
Indices: 9592--9727 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 72
9582 ATAAATAAAT
9592 AAATAAATATTAATTTTGTTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAAT
1 AAATAAATATTAATTTTGTTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAAT
9657 AAATGTA
66 AAATGTA
** *
9664 AAAT-AATATTAATTTTGTTTTATTATTTATTTA-TTA-T-TT-TATGAATATGGATAAATAGAT
1 AAATAAATATTAATTTTGTTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAAT
9724 AAAT
66 AAAT
9728 AAATAACAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
67 22 0.36
68 2 0.03
69 1 0.02
70 3 0.05
71 29 0.48
72 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (72 bp):
AAATAAATATTAATTTTGTTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAAT
AAATGTA
Found at i:9942 original size:63 final size:63
Alignment explanation
Indices: 9865--9992 Score: 229
Period size: 63 Copynumber: 2.0 Consensus size: 63
9855 TAGTTTCAAG
* *
9865 CAAACTTTGAACTAGTCAAAGTGCTCAAAGGGTGGCTGGCCATGGAATTGAGTGGTTGAAATT
1 CAAACTTTGAACTAGTCAAAGTGCTCAAAGGGTGGCCGACCATGGAATTGAGTGGTTGAAATT
*
9928 CAAACTTTGAACTAGTCAAAGTGCTCAAAGGGTGGCCGATCATGGAATTGAGTGGTTGAAATT
1 CAAACTTTGAACTAGTCAAAGTGCTCAAAGGGTGGCCGACCATGGAATTGAGTGGTTGAAATT
9991 CA
1 CA
9993 TTTTCTAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (63 bp):
CAAACTTTGAACTAGTCAAAGTGCTCAAAGGGTGGCCGACCATGGAATTGAGTGGTTGAAATT
Found at i:11333 original size:15 final size:14
Alignment explanation
Indices: 11285--11336 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
11275 GTTGGAATTG
* *
11285 AATTTTTTATCAAG
1 AATTTTTTATAAAA
*
11299 AATTTTTTACAAAA
1 AATTTTTTATAAAA
*
11313 GTATTTTTTGATAAAA
1 -AATTTTTT-ATAAAA
11329 AATTTTTT
1 AATTTTTT
11337 TGGACTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 11 0.37
15 14 0.47
16 5 0.17
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (14 bp):
AATTTTTTATAAAA
Found at i:21869 original size:21 final size:22
Alignment explanation
Indices: 21823--21866 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21813 TGTTAAGTGG
*
21823 ATTTTTTAAAATATTTTATGAA
1 ATTTTTAAAAATATTTTATGAA
21845 ATTTTTAAATAATATTTT-TGAA
1 ATTTTTAAA-AATATTTTATGAA
21867 TTTCCATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTTAAAAATATTTTATGAA
Found at i:23928 original size:29 final size:29
Alignment explanation
Indices: 23896--23956 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
23886 AAAAATGTTG
*
23896 AATAAGATT-TTATTTTATTAAAAAATAA-A
1 AATAA-ATTATTATTTT-TGAAAAAATAAGA
23925 AATAAATTATTATTTTTGAAAAAATAAGA
1 AATAAATTATTATTTTTGAAAAAATAAGA
23954 AAT
1 AAT
23957 TCAAATTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (29 bp):
AATAAATTATTATTTTTGAAAAAATAAGA
Found at i:25624 original size:29 final size:28
Alignment explanation
Indices: 25578--25671 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 28
25568 TAAGATGATT
** *
25578 ATATAAAAAAATTTAATAAATAAAAAATA
1 ATATAAAATTATTAAATAAA-AAAAAATA
*
25607 ATATAAAATTATTAAATATTAAAATAATATA
1 ATATAAAATTATTAAATA--AAAA-AAAATA
* *
25638 ATATAAATATTTTTAAAAAAAATAAAAATA
1 ATATAAA-ATTATTAAATAAAA-AAAAATA
25668 ATAT
1 ATAT
25672 GGACGGATCT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
29 15 0.28
30 14 0.26
31 15 0.28
32 9 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
ATATAAAATTATTAAATAAAAAAAAATA
Found at i:31326 original size:6 final size:6
Alignment explanation
Indices: 31315--31339 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31305 TCTCTTTACC
31315 ATCATT ATCATT ATCATT ATCATT A
1 ATCATT ATCATT ATCATT ATCATT A
31340 ACTGACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATCATT
Found at i:32411 original size:25 final size:26
Alignment explanation
Indices: 32383--32431 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
32373 AATTGTAAAG
*
32383 ATTTTAATTTTAAATG-TAATAATTT
1 ATTTTAATTTTAAACGATAATAATTT
*
32408 ATTTTATTTTTAAACGATAATAAT
1 ATTTTAATTTTAAACGATAATAAT
32432 ACAATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTTAATTTTAAACGATAATAATTT
Found at i:33266 original size:24 final size:25
Alignment explanation
Indices: 33239--33301 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
33229 ATATTTTAAA
33239 ATTTTAAATACA-ATAA-AAAATTAT
1 ATTTTAAATA-ATATAATAAAATTAT
* *
33263 A-TTTAAATAATTTAATATAATTAT
1 ATTTTAAATAATATAATAAAATTAT
33287 ATTTATAAATAATAT
1 ATTT-TAAATAATAT
33302 TTAAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
24 9 0.28
25 2 0.06
26 9 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTTTAAATAATATAATAAAATTAT
Found at i:33310 original size:26 final size:22
Alignment explanation
Indices: 33254--33310 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 22
33244 AAATACAATA
33254 AAAAATTATATTTAAATAATTT
1 AAAAATTATATTTAAATAATTT
33276 AATATAATTATATTTATAAATAATATTT
1 AA-A-AATTATA-TT-TAAAT-A-ATTT
33304 AAAAATT
1 AAAAATT
33311 TAAATATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 2 0.07
23 1 0.03
24 7 0.24
25 2 0.07
26 9 0.31
27 2 0.07
28 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAAATTATATTTAAATAATTT
Found at i:34585 original size:28 final size:28
Alignment explanation
Indices: 34547--34650 Score: 95
Period size: 28 Copynumber: 3.8 Consensus size: 28
34537 CAATTAATTA
*
34547 ATTTTTTAAAATTTAAAAATTAAAAAAT
1 ATTTTTAAAAATTTAAAAATTAAAAAAT
* *** ***
34575 ATTTTTAAAAAATT-AAAAGCCATTCAT
1 ATTTTTAAAAATTTAAAAATTAAAAAAT
* *
34602 ATTATTAAAAATATAAAAATTAAAAAAT
1 ATTTTTAAAAATTTAAAAATTAAAAAAT
34630 ATTTTT-AAAATTATAAAAATT
1 ATTTTTAAAAATT-TAAAAATT
34651 TAATTGAATG
Statistics
Matches: 55, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
27 23 0.42
28 32 0.58
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (28 bp):
ATTTTTAAAAATTTAAAAATTAAAAAAT
Found at i:36015 original size:16 final size:16
Alignment explanation
Indices: 35994--36041 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
35984 TCAATTAATA
35994 TAATAATAATATATTT
1 TAATAATAATATATTT
*
36010 TAATAA-ATATATTTTT
1 TAATAATA-ATATATTT
*
36026 TAAT-ATAAAATATTT
1 TAATAATAATATATTT
36041 T
1 T
36042 CATCTATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATAATAATATATTT
Found at i:41892 original size:3 final size:3
Alignment explanation
Indices: 41884--41908 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41874 TATTAAGTGT
41884 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
41909 ACTCTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42546 original size:28 final size:27
Alignment explanation
Indices: 42489--42573 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 27
42479 TTAAGATGAC
*
42489 TATATAAAATTTTCAATAAATAAAAAA
1 TATATAAAATTTTAAATAAATAAAAAA
*
42516 TATATAAAATTATTAAAT-ATTAGAATAATA
1 TATATAAAATT-TTAAATAAATA-AA-AA-A
42546 TAATATAAATATTTTTAAA-AAATAAAAA
1 T-ATATAAA-A-TTTTAAATAAATAAAAA
42574 TAATATGGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
27 14 0.30
28 7 0.15
29 2 0.04
30 4 0.09
31 9 0.19
32 9 0.19
33 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (27 bp):
TATATAAAATTTTAAATAAATAAAAAA
Found at i:43018 original size:34 final size:34
Alignment explanation
Indices: 42978--43081 Score: 131
Period size: 34 Copynumber: 3.1 Consensus size: 34
42968 AATCTTTCAT
* *
42978 CTCCCTTGATTTTTAATCTTTC-ATCTTTCTTAAC
1 CTCCCTTGATCTTTAA-CTTTCTATCTTCCTTAAC
43012 CTCCCTT-AGTCTTTAACTTTCTATCTTCCTTAAC
1 CTCCCTTGA-TCTTTAACTTTCTATCTTCCTTAAC
* * *
43046 CTACCTTGACCTTTAACCTTCTATCTTCCTTAAC
1 CTCCCTTGATCTTTAACTTTCTATCTTCCTTAAC
43080 CT
1 CT
43082 TTCATATTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
33 6 0.10
34 55 0.89
35 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.03, T:0.47
Consensus pattern (34 bp):
CTCCCTTGATCTTTAACTTTCTATCTTCCTTAAC
Found at i:45291 original size:18 final size:18
Alignment explanation
Indices: 45268--45310 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
45258 ATAATTCATA
45268 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * *
45286 TCACTTTCAGTTTCAGTT
1 TCACTTTCAATTCCAATT
45304 TCACTTT
1 TCACTTT
45311 TACTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Done.