Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005152.1 Kokia drynarioides strain JFW-HI SEQ_118997, 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: 57891
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:69 original size:14 final size:14
Alignment explanation
Indices: 33--75 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
23 TTAATTTTAA
33 TTTTTGTATTATATT
1 TTTTTGTATTAT-TT
** *
48 TTGGTGTATAATTT
1 TTTTTGTATTATTT
62 TTTTTGTATTATTT
1 TTTTTGTATTATTT
76 ATGTAAAAAC
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.70
Consensus pattern (14 bp):
TTTTTGTATTATTT
Found at i:179 original size:27 final size:27
Alignment explanation
Indices: 127--194 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
117 GGTTGATGCA
* *
127 GCCTGTCAGGTAGGCACCTCTAGTGCT
1 GCCTGTCAGGTAGGCACATCTAGTGCC
* * *
154 GCCTATCAGGTAGGCACATTTGGTGCC
1 GCCTGTCAGGTAGGCACATCTAGTGCC
*
181 GCCTGTCAGATAGG
1 GCCTGTCAGGTAGG
195 TACCACCCCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (27 bp):
GCCTGTCAGGTAGGCACATCTAGTGCC
Found at i:4104 original size:13 final size:13
Alignment explanation
Indices: 4086--4112 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4076 AATCCAATTT
4086 TTTATTATTTTTA
1 TTTATTATTTTTA
4099 TTTATTATTTTTA
1 TTTATTATTTTTA
4112 T
1 T
4113 GAATATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTATTTTTA
Found at i:4157 original size:63 final size:63
Alignment explanation
Indices: 4081--4270 Score: 242
Period size: 67 Copynumber: 2.9 Consensus size: 63
4071 ACTTAAATCC
4081 AATTTTTTATTATT-TTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATAGT
1 AATTTTTT-TTATTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATAGT
* *
4144 AATTTTATTTTATTATTT-TATTATTTATTACTGTATGAATATAAATAAATAAATGTAAAATAAT
1 AATTTT-TTTTATTATTTAT-TTA-TTATT--TTTATGAATATAAATAAATAAATATAAAATAAT
*
4208 ATT
61 AGT
* *
4211 AATTTTGTTTTATTATTTATTTATTA-TTTTATGAATATAGATAAATAAATAAATAAATAA
1 AATTTT-TTTTATTATTTATTTATTATTTTTATGAATATAAATAAATAAATATA-AAATAA
4271 CAAACCCAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
63 34 0.31
64 14 0.13
65 6 0.05
66 3 0.03
67 53 0.48
68 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (63 bp):
AATTTTTTTTATTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATAGT
Found at i:18914 original size:20 final size:21
Alignment explanation
Indices: 18874--18919 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
18864 ATCCGCATGA
* *
18874 ACTCATATTTCCTAGATTTTG
1 ACTCACATTTCCTAAATTTTG
18895 ACTCACATTTCC-AAATTTTG
1 ACTCACATTTCCTAAATTTTG
18915 ACTCA
1 ACTCA
18920 GTAAAACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (21 bp):
ACTCACATTTCCTAAATTTTG
Found at i:19956 original size:2 final size:2
Alignment explanation
Indices: 19949--19983 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19939 AATTGACATG
19949 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 T
19984 TCCCATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21298 original size:21 final size:20
Alignment explanation
Indices: 21273--21318 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
21263 AAAAATAATC
21273 ATAAA-CTATTTTTTGAAAATT
1 ATAAAGCTA-TTTTT-AAAATT
21294 ATAAAAGCTATTTTTAAAATT
1 AT-AAAGCTATTTTTAAAATT
21315 ATAA
1 ATAA
21319 GCATGCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.09
21 10 0.43
22 8 0.35
23 3 0.13
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
ATAAAGCTATTTTTAAAATT
Found at i:21567 original size:18 final size:19
Alignment explanation
Indices: 21544--21596 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
21534 AAAGTTTGGC
*
21544 ATATTTGTAATTTT-AAAA
1 ATATTTATAATTTTCAAAA
21562 ATATTTTATAATTTTCAAAA
1 ATA-TTTATAATTTTCAAAA
*
21582 ATATATTATGATTTT
1 ATAT-TTATAATTTT
21597 TAATTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 11 0.37
20 16 0.53
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
ATATTTATAATTTTCAAAA
Found at i:21575 original size:19 final size:20
Alignment explanation
Indices: 21551--21596 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21541 GGCATATTTG
*
21551 TAATTTT-AAAAATATTTTA
1 TAATTTTCAAAAATATATTA
21570 TAATTTTCAAAAATATATTA
1 TAATTTTCAAAAATATATTA
*
21590 TGATTTT
1 TAATTTT
21597 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTTTCAAAAATATATTA
Found at i:27312 original size:26 final size:26
Alignment explanation
Indices: 27282--27333 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
27272 AATGCAAATG
27282 AAGAGAACAAAAAAGGTTATTTCTTT
1 AAGAGAACAAAAAAGGTTATTTCTTT
27308 AAGAGAACAAAAAAGGTTATTTCTTT
1 AAGAGAACAAAAAAGGTTATTTCTTT
27334 GAATTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (26 bp):
AAGAGAACAAAAAAGGTTATTTCTTT
Found at i:34071 original size:22 final size:20
Alignment explanation
Indices: 34041--34109 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 20
34031 CAGTAAGAGG
34041 GAAACACTTGAGATTTTACAA
1 GAAA-ACTTGAGATTTTACAA
* * *
34062 GAAATTACTTGAGTTTTTATAG
1 GAAA--ACTTGAGATTTTACAA
34084 GAAAACTTG-GATTATTACAA
1 GAAAACTTGAGATT-TTACAA
34104 GGAAAA
1 -GAAAA
34110 ACCATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 3 0.08
20 9 0.24
21 9 0.24
22 17 0.45
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (20 bp):
GAAAACTTGAGATTTTACAA
Found at i:36041 original size:69 final size:69
Alignment explanation
Indices: 35968--36190 Score: 164
Period size: 69 Copynumber: 3.1 Consensus size: 69
35958 AAAAAATAAT
35968 ATTGAGATAATTTTGCCTCCACATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAA
1 ATTGAGATAATTTTGCCTCCACATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAA
36033 TCGG
66 TCGG
** * * * * ** *
36037 ATTGAGTTATTTGAATTATTCGAGCCAACTCGAATT-AGTAAGATCTCGAGTTCGAATT--ATGT
1 ATTGAG--A--T-AATT-TT---GCCTCCAC-ATTTAAGTAGGA-GT-GAG-TAAAATTCGATTT
* * ** ***
36099 AAATGGAAAAAAATAAT
53 GATTCAAAAAAAATCGG
36116 ATTGAGATAATTTTGCCTCCACATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAA
1 ATTGAGATAATTTTGCCTCCACATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAA
36181 TCGG
66 TCGG
36185 ATTGAG
1 ATTGAG
36191 TTATTTGAAT
Statistics
Matches: 106, Mismatches: 32, Indels: 32
0.62 0.19 0.19
Matches are distributed among these distances:
67 5 0.05
68 3 0.03
69 29 0.27
70 11 0.10
71 1 0.01
73 3 0.03
74 8 0.08
75 3 0.03
77 1 0.01
78 11 0.10
79 23 0.22
80 3 0.03
81 5 0.05
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (69 bp):
ATTGAGATAATTTTGCCTCCACATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAA
TCGG
Found at i:36101 original size:148 final size:148
Alignment explanation
Indices: 35924--36225 Score: 586
Period size: 148 Copynumber: 2.0 Consensus size: 148
35914 GATATCACTA
*
35924 AAGTAAGATTTCGAGTTCGAATTATGTAAATGGAAAAAAATAATATTGAGATAATTTTGCCTCCA
1 AAGTAAGATCTCGAGTTCGAATTATGTAAATGGAAAAAAATAATATTGAGATAATTTTGCCTCCA
35989 CATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAATCGGATTGAGTTATTTGAATT
66 CATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAATCGGATTGAGTTATTTGAATT
36054 ATTCGAGCCAACTCGAAT
131 ATTCGAGCCAACTCGAAT
*
36072 TAGTAAGATCTCGAGTTCGAATTATGTAAATGGAAAAAAATAATATTGAGATAATTTTGCCTCCA
1 AAGTAAGATCTCGAGTTCGAATTATGTAAATGGAAAAAAATAATATTGAGATAATTTTGCCTCCA
36137 CATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAATCGGATTGAGTTATTTGAATT
66 CATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAATCGGATTGAGTTATTTGAATT
36202 ATTCGAGCCAACTCGAAT
131 ATTCGAGCCAACTCGAAT
36220 AAGTAA
1 AAGTAA
36226 TTCGAGTCAA
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
148 151 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (148 bp):
AAGTAAGATCTCGAGTTCGAATTATGTAAATGGAAAAAAATAATATTGAGATAATTTTGCCTCCA
CATTTAAGTAGGAGTGAGTAAAATTCGATTTGATTCAAAAAAAATCGGATTGAGTTATTTGAATT
ATTCGAGCCAACTCGAAT
Found at i:36255 original size:23 final size:23
Alignment explanation
Indices: 36202--36255 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
36192 TATTTGAATT
*
36202 ATTCGAGCCAACTCGAATAAGTA
1 ATTCGAGTCAACTCGAATAAGTA
36225 ATTCGAGTCAACTCGAATAAGTA
1 ATTCGAGTCAACTCGAATAAGTA
36248 ATTCGAGT
1 ATTCGAGT
36256 TTCGAGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (23 bp):
ATTCGAGTCAACTCGAATAAGTA
Found at i:36395 original size:18 final size:19
Alignment explanation
Indices: 36346--36394 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
36336 TCTCTCAATA
*
36346 AAAATTACAAAATAATTTTT
1 AAAATT-CAAAATAATTTAT
36366 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
36384 AAAATTTCAAA
1 AAAA-TTCAAA
36395 TTTATATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:36584 original size:14 final size:15
Alignment explanation
Indices: 36565--36593 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
36555 GTTCTCAAAT
36565 ATATATG-GTTTTAA
1 ATATATGTGTTTTAA
36579 ATATATGTGTTTTAA
1 ATATATGTGTTTTAA
36594 TATGAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
ATATATGTGTTTTAA
Found at i:36682 original size:16 final size:15
Alignment explanation
Indices: 36646--36684 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
36636 TTTAAATTTT
*
36646 TTAATTTAACTCGAA
1 TTAATTTCACTCGAA
36661 -TAATTTCACTCGATA
1 TTAATTTCACTCGA-A
36676 TTAATTTCA
1 TTAATTTCA
36685 TTTCACTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (15 bp):
TTAATTTCACTCGAA
Found at i:43085 original size:20 final size:20
Alignment explanation
Indices: 43030--43085 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
43020 TATTTTCGGA
* *
43030 TTTTTTAAAATTTTTAGAAT
1 TTTTTTATAATATTTAGAAT
* * *
43050 TTTTATATATTCTTTAGAAT
1 TTTTTTATAATATTTAGAAT
43070 TTTTTTATAATATTTA
1 TTTTTTATAATATTTA
43086 TATTTGGTGG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTTATAATATTTAGAAT
Found at i:48758 original size:4 final size:4
Alignment explanation
Indices: 48749--48776 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
48739 ACAGTGCCGT
48749 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
48777 ACCAGAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Done.