Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012428.1 Kokia drynarioides strain JFW-HI SEQ_127432, 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: 38684
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Found at i:299 original size:13 final size:13
Alignment explanation
Indices: 281--305 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
271 TTTTTGATAT
281 AAAAAATATTTTG
1 AAAAAATATTTTG
294 AAAAAATATTTT
1 AAAAAATATTTT
306 TTTATTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AAAAAATATTTTG
Found at i:11904 original size:30 final size:30
Alignment explanation
Indices: 11848--11999 Score: 123
Period size: 30 Copynumber: 5.1 Consensus size: 30
11838 TAAGGAAAAT
* * *
11848 GGGGTCAAA-ATGAAATTTTAGAAAGTTT-
1 GGGGTCAAATTTGAATTTTTGGAAAGTTTA
* * *
11876 GGGGGCTATATTTGAATTTTTGGAAAGTTCA
1 GGGGTC-AAATTTGAATTTTTGGAAAGTTTA
* * * * *
11907 AGGGTCAAATCTAAATTTTTGGGAAGTTTG
1 GGGGTCAAATTTGAATTTTTGGAAAGTTTA
11937 GGGGTCAAATCTT-AATTTTTGGAAAGTTTA
1 GGGGTCAAAT-TTGAATTTTTGGAAAGTTTA
* * *
11967 GGGGTCAAAATAT-AATTTCTAGAAAGTTTA
1 GGGGTC-AAATTTGAATTTTTGGAAAGTTTA
11997 GGG
1 GGG
12000 ACCTCTTGGG
Statistics
Matches: 98, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
28 5 0.05
29 2 0.02
30 82 0.84
31 9 0.09
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (30 bp):
GGGGTCAAATTTGAATTTTTGGAAAGTTTA
Found at i:11984 original size:60 final size:60
Alignment explanation
Indices: 11848--11995 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 60
11838 TAAGGAAAAT
*
11848 GGGGTCAAAATGA-AA-TTTTAGAAAGTTTGGGGGCTATATTTGAATTTTTGGAAAGTTCA
1 GGGGTCAAAAT-ATAATTTTTAGAAAGTTTGGGGGCTAAATTTGAATTTTTGGAAAGTTCA
* * * * *
11907 AGGGTC-AAATCTAAATTTTTGGGAAGTTTGGGGG-TCAAATCTT-AATTTTTGGAAAGTTTA
1 GGGGTCAAAATAT-AATTTTTAGAAAGTTTGGGGGCT-AAAT-TTGAATTTTTGGAAAGTTCA
*
11967 GGGGTCAAAATATAATTTCTAGAAAGTTT
1 GGGGTCAAAATATAATTTTTAGAAAGTTT
11996 AGGGACCTCT
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
58 4 0.06
59 8 0.11
60 53 0.74
61 7 0.10
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (60 bp):
GGGGTCAAAATATAATTTTTAGAAAGTTTGGGGGCTAAATTTGAATTTTTGGAAAGTTCA
Found at i:12753 original size:15 final size:16
Alignment explanation
Indices: 12735--12765 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12725 TATCGAAAAT
12735 ATAAAAA-ATAAATAG
1 ATAAAAATATAAATAG
12750 ATAAAAATATAAATAG
1 ATAAAAATATAAATAG
12766 GCATTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
ATAAAAATATAAATAG
Found at i:13352 original size:24 final size:24
Alignment explanation
Indices: 13325--13476 Score: 178
Period size: 24 Copynumber: 6.3 Consensus size: 24
13315 CATGTAGATA
*
13325 AGCGTAAATGTATTCATGCTAACG
1 AGCGTAAATGTATTCATGCTGACG
*
13349 AGCGTAAACGTATTCATGCTGACG
1 AGCGTAAATGTATTCATGCTGACG
* ** * *
13373 AGCATAAACATTTTCATGCTGACA
1 AGCGTAAATGTATTCATGCTGACG
* *
13397 AGCGTAAATCTATTCATGTTGACG
1 AGCGTAAATGTATTCATGCTGACG
* *
13421 AGCGTAAATGTATTAATGCTGATG
1 AGCGTAAATGTATTCATGCTGACG
* *
13445 AGCGTAAAAGTATTCATGTTGACG
1 AGCGTAAATGTATTCATGCTGACG
*
13469 AGCATAAA
1 AGCGTAAA
13477 CGTAATGAAC
Statistics
Matches: 107, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 107 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (24 bp):
AGCGTAAATGTATTCATGCTGACG
Found at i:15164 original size:15 final size:16
Alignment explanation
Indices: 15138--15237 Score: 62
Period size: 17 Copynumber: 5.9 Consensus size: 16
15128 AAATAAAATT
* *
15138 TAATTAAAAGAATACA
1 TAATTTAAAGAATAAA
15154 T-ATTTAAAGAATAAA
1 TAATTTAAAGAATAAA
15169 TCAATTTAAAGAAATAAA
1 T-AATTTAAAG-AATAAA
*
15187 TTAAATTTTAAA-AA-ATA
1 -T-AA-TTTAAAGAATAAA
*
15204 TAATTTAAATTAAATAAA
1 TAATTTAAA--GAATAAA
*
15222 CATATTTAAAGAATAA
1 TA-ATTTAAAGAATAA
15238 TAAATTATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
14 6 0.09
15 15 0.22
16 2 0.03
17 17 0.25
18 11 0.16
19 10 0.15
20 6 0.09
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (16 bp):
TAATTTAAAGAATAAA
Found at i:15221 original size:53 final size:53
Alignment explanation
Indices: 15163--15270 Score: 134
Period size: 53 Copynumber: 2.0 Consensus size: 53
15153 ATATTTAAAG
15163 AATAAATCA-ATTTAAAG-A-AATAAATTAAATTTTAAA-AAATATAATTTAAATTA
1 AATAAA-CATATTTAAAGAATAATAAATT--ATTTTAAAGAAATA-AATTTAAATTA
* *
15216 AATAAACATATTTAAAGAATAATAAATTATTTTAAAGCAATAAATTTAATTTA
1 AATAAACATATTTAAAGAATAATAAATTATTTTAAAGAAATAAATTTAAATTA
15269 AA
1 AA
15271 AATAAAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
52 2 0.04
53 34 0.69
54 5 0.10
55 8 0.16
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (53 bp):
AATAAACATATTTAAAGAATAATAAATTATTTTAAAGAAATAAATTTAAATTA
Found at i:15267 original size:73 final size:70
Alignment explanation
Indices: 15100--15284 Score: 207
Period size: 71 Copynumber: 2.6 Consensus size: 70
15090 TATTAAAATC
* * *
15100 TCAATTAAAAGGAATAAATTTAAATT-AAAAATAAAATTTAATTAAAAGAATACATATTTAAAGA
1 TCAATTTAAAGAAATAAATTTAATTTAAAAAATAAAATTTAATTAAAAGAATACATATTTAAAGA
15164 ATAAA
66 ATAAA
* * *
15169 TCAATTTAAAGAAATAAATTAAATTTTAAAAAATATAATTTAAATT-AAATAA-ACATATTTAAA
1 TCAATTTAAAGAAATAAATTTAA-TTTAAAAAATAAAATTT-AATTAAAAGAATACATATTTAAA
15232 GAATAATAAA
64 G---AATAAA
* * * *
15242 TTATTTTAAAGCAATAAATTTAATTT-AAAAATAAAAATTAATT
1 TCAATTTAAAGAAATAAATTTAATTTAAAAAATAAAATTTAATT
15285 GAATTATGAA
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
69 20 0.20
70 18 0.18
71 28 0.29
72 7 0.07
73 25 0.26
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.35
Consensus pattern (70 bp):
TCAATTTAAAGAAATAAATTTAATTTAAAAAATAAAATTTAATTAAAAGAATACATATTTAAAGA
ATAAA
Found at i:15270 original size:19 final size:18
Alignment explanation
Indices: 15111--15276 Score: 100
Period size: 19 Copynumber: 9.4 Consensus size: 18
15101 CAATTAAAAG
*
15111 GAATAAATTTAAATTAAA
1 GAATAAATTTAATTTAAA
*
15129 -AATAAAATTTAATTAAAA
1 GAAT-AAATTTAATTTAAA
*
15147 GAATACA--T-ATTTAAA
1 GAATAAATTTAATTTAAA
*
15162 GAATAAA-TCAATTTAAA
1 GAATAAATTTAATTTAAA
*
15179 GAAATAAATTAAATTTTAAA
1 G-AATAAATTTAA-TTTAAA
* *
15199 AAATATAATTTAAATT--A
1 GAATA-AATTTAATTTAAA
**
15216 -AATAAACAT-ATTTAAA
1 GAATAAATTTAATTTAAA
* *
15232 GAATAATAAATTATTTTAAA
1 GAAT-A-AATTTAATTTAAA
15252 GCAATAAATTTAATTTAAA
1 G-AATAAATTTAATTTAAA
15271 -AATAAA
1 GAATAAA
15277 AATTAATTGA
Statistics
Matches: 115, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
14 3 0.03
15 15 0.13
16 6 0.05
17 21 0.18
18 21 0.18
19 26 0.23
20 20 0.17
21 3 0.03
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (18 bp):
GAATAAATTTAATTTAAA
Found at i:15284 original size:18 final size:19
Alignment explanation
Indices: 15119--15284 Score: 74
Period size: 18 Copynumber: 9.3 Consensus size: 19
15109 AGGAATAAAT
* *
15119 TTAAATTAAA-AATAAAAT
1 TTAATTTAAAGAATAAAAA
* *
15137 TTAATTAAAAGAAT--ACA
1 TTAATTTAAAGAATAAAAA
15154 -T-ATTTAAAGAAT--AAA
1 TTAATTTAAAGAATAAAAA
* *
15169 TCAATTTAAAGAA-ATAAA
1 TTAATTTAAAGAATAAAAA
* * *
15187 TTAAATTTTAAAAAATATAAT
1 TT-AA-TTTAAAGAATAAAAA
* *
15208 TTAAATT--A-AATAAACA
1 TTAATTTAAAGAATAAAAA
15224 -T-ATTTAAAGAATAATAAA
1 TTAATTTAAAGAATAA-AAA
* *
15242 TTATTTTAAAGCAAT-AAAT
1 TTAATTTAAAG-AATAAAAA
15261 TTAATTTAAA-AATAAAAA
1 TTAATTTAAAGAATAAAAA
15279 TTAATT
1 TTAATT
15285 GAATTATGAA
Statistics
Matches: 112, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
14 3 0.03
15 13 0.12
16 7 0.06
17 20 0.18
18 23 0.21
19 19 0.17
20 18 0.16
21 9 0.08
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (19 bp):
TTAATTTAAAGAATAAAAA
Found at i:15373 original size:12 final size:12
Alignment explanation
Indices: 15356--15408 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
15346 GAAAAAAAAT
15356 GTGATGATGATG
1 GTGATGATGATG
* *
15368 GTGATGGTGATA
1 GTGATGATGATG
*
15380 GTGATGGGTGATG
1 GTGAT-GATGATG
15393 GCTGATGATTGATG
1 G-TGATGA-TGATG
15407 GT
1 GT
15409 TGAAAAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
12 15 0.44
13 9 0.26
14 10 0.29
ACGTcount: A:0.21, C:0.02, G:0.43, T:0.34
Consensus pattern (12 bp):
GTGATGATGATG
Found at i:15392 original size:7 final size:6
Alignment explanation
Indices: 15356--15399 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
15346 GAAAAAAAAT
* *
15356 GTGATG ATGATG GTGATG GTGATA GTGATGG GTGATG GCTGATG
1 GTGATG GTGATG GTGATG GTGATG GTGAT-G GTGATG G-TGATG
15400 ATTGATGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
6 22 0.69
7 10 0.31
ACGTcount: A:0.20, C:0.02, G:0.45, T:0.32
Consensus pattern (6 bp):
GTGATG
Found at i:16046 original size:24 final size:22
Alignment explanation
Indices: 16006--16051 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
15996 AATACGATAA
16006 TTTATTTATATAGTTTATAATTG
1 TTTATTTATATAGTTTA-AATTG
16029 TTTATTT-TATAGAATTTAAATTG
1 TTTATTTATATAG--TTTAAATTG
16052 AATTTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (22 bp):
TTTATTTATATAGTTTAAATTG
Found at i:20311 original size:35 final size:33
Alignment explanation
Indices: 20202--20318 Score: 96
Period size: 35 Copynumber: 3.4 Consensus size: 33
20192 ACAATCGAAT
20202 TTTATAAAAATATCAATTTAAAGGAATAAATTTAAA
1 TTTA-AAAAATATCAATTTAAA-GAATAAA-TTAAA
* * * *
20238 -TTAAAAAATA-AAATTTAATTAGAAGGAAA-CATA
1 TTTAAAAAATATCAATTTAA--AGAA-TAAATTAAA
20271 TTTAAAAATATATCAATTTAAAGTAATAAATTAAA
1 TTTAAAAA-ATATCAATTTAAAG-AATAAATTAAA
20306 TTTAAAAATATAT
1 TTTAAAAA-ATAT
20319 TTTAAATTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
33 9 0.14
34 22 0.34
35 27 0.42
36 7 0.11
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (33 bp):
TTTAAAAAATATCAATTTAAAGAATAAATTAAA
Found at i:20342 original size:33 final size:32
Alignment explanation
Indices: 20264--20349 Score: 84
Period size: 35 Copynumber: 2.5 Consensus size: 32
20254 AATTAGAAGG
20264 AAACATATTTAAAAATATATCAATTTAAAGTAAT
1 AAACATATTTAAAAATATAT--ATTTAAAGTAAT
* * *
20298 AAATTAAATTTAAAAATATAT-TTTAAATTAAAT
1 AAA-CATATTTAAAAATATATATTTAAAGT-AAT
20331 AAGACATATTTAAAGAATA
1 AA-ACATATTTAAA-AATA
20350 ATAAATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
32 7 0.16
33 13 0.30
34 8 0.19
35 15 0.35
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (32 bp):
AAACATATTTAAAAATATATATTTAAAGTAAT
Found at i:20342 original size:68 final size:69
Alignment explanation
Indices: 20202--20400 Score: 192
Period size: 68 Copynumber: 2.8 Consensus size: 69
20192 ACAATCGAAT
20202 TTTATAAAA-ATATCAATTTAAAGGAATAAATTTAAATTAAAAAATAAAATTTAATTAGAAGGAA
1 TTTA-AAAATATATCAATTTAAAGGAATAAATTTAAATTAAAAAATAAAATTTAATTAGAAGGAA
20266 ACATA
65 ACATA
* * * * *
20271 TTTAAAAATATATCAATTTAAAGTAATAAA-TTAAATTTAAAAATATATTTTAAATTA-AA-TAA
1 TTTAAAAATATATCAATTTAAAGGAATAAATTTAAATTAAAAAATAAAATTT-AATTAGAAGGAA
20333 GACATA
65 -ACATA
* * * *
20339 TTTAAAGAATAATAAATTATTTTAAAGCAATAAATTTAATTTTTAAAAAATAGAAA-TTAATT
1 TTTAAA-AAT-AT--ATCAATTTAAAGGAATAAATTTAA--ATTAAAAAATA-AAATTTAATT
20401 TAATGAAGAA
Statistics
Matches: 107, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
67 2 0.02
68 35 0.33
69 32 0.30
70 2 0.02
72 16 0.15
73 4 0.04
74 4 0.04
75 11 0.10
76 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (69 bp):
TTTAAAAATATATCAATTTAAAGGAATAAATTTAAATTAAAAAATAAAATTTAATTAGAAGGAAA
CATA
Found at i:22019 original size:25 final size:25
Alignment explanation
Indices: 21969--22019 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
21959 GATAGTGAAG
*
21969 TAAGCATATGATAGCAGTCTAATGA
1 TAAGCATATGATAGCAGTCCAATGA
* *
21994 TAAGCATTTGATAGCAGTCCATTGA
1 TAAGCATATGATAGCAGTCCAATGA
22019 T
1 T
22020 CTGTTGTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (25 bp):
TAAGCATATGATAGCAGTCCAATGA
Found at i:29040 original size:13 final size:13
Alignment explanation
Indices: 29022--29057 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
29012 TAATTAAGAC
29022 TAATAAAATAATT
1 TAATAAAATAATT
* *
29035 TCATAAAAAAATT
1 TAATAAAATAATT
29048 TAATAAAATA
1 TAATAAAATA
29058 TATTCAAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
TAATAAAATAATT
Done.