Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011441.1 Kokia drynarioides strain JFW-HI SEQ_126425, 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: 80128
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:1380 original size:18 final size:19
Alignment explanation
Indices: 1357--1393 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
1347 TTAAAAAGCT
1357 TACATACAT-ATATATACA
1 TACATACATCATATATACA
1375 TACATACATGCATATATAC
1 TACATACAT-CATATATAC
1394 CTGCATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (19 bp):
TACATACATCATATATACA
Found at i:1400 original size:24 final size:24
Alignment explanation
Indices: 1357--1424 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1347 TTAAAAAGCT
* *
1357 TACATACATATATA--TACATACA
1 TACATGCATATATACCTGCATACA
*
1379 TACATGCATATATACCTGCATATA
1 TACATGCATATATACCTGCATACA
* *
1403 TTCCTGCATATATACCTGCATA
1 TACATGCATATATACCTGCATA
1425 TATATAATCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.33
24 26 0.67
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (24 bp):
TACATGCATATATACCTGCATACA
Found at i:1413 original size:10 final size:12
Alignment explanation
Indices: 1373--1428 Score: 85
Period size: 12 Copynumber: 4.7 Consensus size: 12
1363 CATATATATA
* *
1373 CATACATACATG
1 CATATATACCTG
1385 CATATATACCTG
1 CATATATACCTG
*
1397 CATATATTCCTG
1 CATATATACCTG
1409 CATATATACCTG
1 CATATATACCTG
1421 CATATATA
1 CATATATA
1429 TAATCCAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (12 bp):
CATATATACCTG
Found at i:6378 original size:18 final size:18
Alignment explanation
Indices: 6355--6395 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6345 TATTATACTT
*
6355 TAAAAAAAATTAAATCTA
1 TAAAAAAAATTAAATATA
* *
6373 TAAAAATATTTAAATATA
1 TAAAAAAAATTAAATATA
6391 TAAAA
1 TAAAA
6396 TATCGAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAAAATTAAATATA
Found at i:7791 original size:30 final size:32
Alignment explanation
Indices: 7742--7839 Score: 85
Period size: 33 Copynumber: 3.1 Consensus size: 32
7732 AGTCTAGATA
7742 TTTATAATTTTTAAAGGATT-AAAT-CAAATT
1 TTTATAATTTTTAAAGGATTGAAATACAAATT
* ** *
7772 TTTATCATTTTTATGGGATTGAAATATAAATT
1 TTTATAATTTTTAAAGGATTGAAATACAAATT
* * * *
7804 TTTTTAAAATTTTAAAGGGTTTAAATGA-AAATT
1 TTTAT-AATTTTTAAAGGATTGAAAT-ACAAATT
7837 TTT
1 TTT
7840 TTATTTTAGG
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
30 17 0.32
31 4 0.08
32 9 0.17
33 22 0.42
34 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (32 bp):
TTTATAATTTTTAAAGGATTGAAATACAAATT
Found at i:9079 original size:24 final size:23
Alignment explanation
Indices: 9039--9096 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
9029 TATACATTTT
*
9039 AATTAGAT-TTTATAAATAATTAA
1 AATTA-ATATTTAAAAATAATTAA
* *
9062 TATTAATTATTTAAAAATATTTAA
1 AATTAA-TATTTAAAAATAATTAA
9086 AATTAATATTT
1 AATTAATATTT
9097 CATATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 10 0.34
24 18 0.62
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAAAAATAATTAA
Found at i:15240 original size:27 final size:27
Alignment explanation
Indices: 15210--15266 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
15200 AGATTCTTCC
*
15210 GAAGAGGTTAAATGGTTTTATGAAGTA
1 GAAGAGGTTAAACGGTTTTATGAAGTA
15237 GAAGAGGTTAAACGGTTTTATGAAGTA
1 GAAGAGGTTAAACGGTTTTATGAAGTA
15264 GAA
1 GAA
15267 CTTGGGTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.02, G:0.30, T:0.30
Consensus pattern (27 bp):
GAAGAGGTTAAACGGTTTTATGAAGTA
Found at i:23342 original size:29 final size:30
Alignment explanation
Indices: 23308--23378 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
23298 ATGTGCGATA
*
23308 TCATATATAAATTTTGATTTGGTATAATTT
1 TCATATATAAATTTTGATTTGATATAATTT
* *
23338 T-ATATATGAAATTTTTATTTGATTTAATTT
1 TCATATAT-AAATTTTGATTTGATATAATTT
*
23368 TCATAAATAAA
1 TCATATATAAA
23379 CAACAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 6 0.17
30 24 0.69
31 5 0.14
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (30 bp):
TCATATATAAATTTTGATTTGATATAATTT
Found at i:23590 original size:25 final size:24
Alignment explanation
Indices: 23562--23609 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
23552 AATTGTATCA
23562 AATTAAAATTCATATATCAAATTAC
1 AATTAAAATTCATATAT-AAATTAC
23587 AATTAAAATTCATATATAAATTA
1 AATTAAAATTCATATATAAATTA
23610 GATATTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (24 bp):
AATTAAAATTCATATATAAATTAC
Found at i:23608 original size:12 final size:13
Alignment explanation
Indices: 23565--23606 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
23555 TGTATCAAAT
23565 TAAAATTCATATA
1 TAAAATTCATATA
*
23578 TCAAATTACA-AT-
1 TAAAATT-CATATA
23590 TAAAATTCATATA
1 TAAAATTCATATA
23603 TAAA
1 TAAA
23607 TTAGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 12 0.50
14 2 0.08
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAATTCATATA
Found at i:34391 original size:16 final size:16
Alignment explanation
Indices: 34351--34393 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
34341 AGGAAAAAAT
*
34351 AGTTACAAGAATATGAA
1 AGTTA-AAGAAGATGAA
*
34368 AGGTTAAAGAAGATGGA
1 A-GTTAAAGAAGATGAA
34385 AGTTAAAGA
1 AGTTAAAGA
34394 TCAAGGGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 11 0.48
18 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.26, T:0.21
Consensus pattern (16 bp):
AGTTAAAGAAGATGAA
Found at i:37319 original size:156 final size:156
Alignment explanation
Indices: 37035--37353 Score: 566
Period size: 156 Copynumber: 2.0 Consensus size: 156
37025 TAAATATAAC
*
37035 TTCTAATTCTTCAATAAAATTATATAAAATTACATCAGATTATTTTGCATCAACATTGACTCGGG
1 TTCTAATTCTTCAATAAAATCATATAAAATTACATCAGATTATTTTGCATCAACATTGACTCGGG
*
37100 ATAGTCTAACTGGTCATACCAACACTATGAACTTCTTTTCACTATCTCATATGTTATTCATATAA
66 ATAGTCTAACCGGTCATACCAACACTATGAACTTCTTTTCACTATCTCATATGTTATTCATATAA
*
37165 ATGTAATGTATCCCTTTTGGGAATAT
131 ATGTAATGTATCCCTTCTGGGAATAT
*
37191 TTCTAATTCTTCAATAAAATCATATAAAATTGCATCAGATTATTTTGCATCAACATTGACTCGGG
1 TTCTAATTCTTCAATAAAATCATATAAAATTACATCAGATTATTTTGCATCAACATTGACTCGGG
37256 ATAGTCTAACCGGTCATACCAACACTATGAACTTCTTTTCACTATCTCATATGTTATTCATATAA
66 ATAGTCTAACCGGTCATACCAACACTATGAACTTCTTTTCACTATCTCATATGTTATTCATATAA
* * *
37321 GTGTAATGTATTCCTTCTGTGAATAT
131 ATGTAATGTATCCCTTCTGGGAATAT
*
37347 TTATAAT
1 TTCTAAT
37354 ACAAAAACAT
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (156 bp):
TTCTAATTCTTCAATAAAATCATATAAAATTACATCAGATTATTTTGCATCAACATTGACTCGGG
ATAGTCTAACCGGTCATACCAACACTATGAACTTCTTTTCACTATCTCATATGTTATTCATATAA
ATGTAATGTATCCCTTCTGGGAATAT
Found at i:54170 original size:29 final size:30
Alignment explanation
Indices: 54137--54199 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
54127 TTTAAGACTA
*
54137 AAAATTATTAA-AGTATTATAAAAAATTAT-
1 AAAATTATTAATA-TATTATAAAAAAATATG
*
54166 AAAATTGTTAATATATTATAAAAAAATATG
1 AAAATTATTAATATATTATAAAAAAATATG
54196 AAAA
1 AAAA
54200 CAATAGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAATTATTAATATATTATAAAAAAATATG
Found at i:54308 original size:21 final size:19
Alignment explanation
Indices: 54264--54337 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
54254 GAAATTATAA
54264 ATTATAAAATTTATTAAAT
1 ATTATAAAATTTATTAAAT
* *
54283 ATTATAAAATATTGTTAATTT
1 ATTATAAAAT-TTATTAA-AT
* *
54304 ATTATGAAAA-TTATGAAAGA
1 ATTAT-AAAATTTATTAAA-T
*
54324 ATTATAAAAATTAT
1 ATTATAAAATTTAT
54338 GGAAAGTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 14 0.32
20 20 0.45
21 6 0.14
22 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATTATAAAATTTATTAAAT
Found at i:54333 original size:20 final size:21
Alignment explanation
Indices: 54304--54343 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
54294 TTGTTAATTT
*
54304 ATTATGAAAATTAT-GAAAGA
1 ATTATAAAAATTATGGAAAGA
54324 ATTATAAAAATTATGGAAAG
1 ATTATAAAAATTATGGAAAG
54344 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (21 bp):
ATTATAAAAATTATGGAAAGA
Found at i:54386 original size:11 final size:11
Alignment explanation
Indices: 54372--54408 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
54362 AATGATTAAA
54372 AAAAACTTATT
1 AAAAACTTATT
54383 AAAAA-TT-TT
1 AAAAACTTATT
54392 ATAAAACTTATT
1 A-AAAACTTATT
54404 AAAAA
1 AAAAA
54409 TTTGCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.13
10 6 0.26
11 11 0.48
12 3 0.13
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAAACTTATT
Found at i:56046 original size:34 final size:34
Alignment explanation
Indices: 56003--56081 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
55993 TTTCCCACCG
* *
56003 CATTATTCATGGTTCATTCT-CAACTGTTTAACAA
1 CATTATTCATGG-TCACTCTCCAACTATTTAACAA
*
56037 CATTATTCATGGTCCCTCTCCAACTATTTAACAA
1 CATTATTCATGGTCACTCTCCAACTATTTAACAA
* *
56071 CTTTTTTCATG
1 CATTATTCATG
56082 TCCTTCACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 5 0.13
34 34 0.87
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.42
Consensus pattern (34 bp):
CATTATTCATGGTCACTCTCCAACTATTTAACAA
Found at i:56345 original size:7 final size:7
Alignment explanation
Indices: 56304--56355 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
56294 TCGAGGCTCG
56304 AGGTTCA
1 AGGTTCA
* *
56311 CGGTTTA
1 AGGTTCA
*
56318 AGGTACA
1 AGGTTCA
* *
56325 ATGTTCG
1 AGGTTCA
56332 A-GTTCA
1 AGGTTCA
56338 AGGTTCA
1 AGGTTCA
56345 AGGTTCA
1 AGGTTCA
56352 AGGT
1 AGGT
56356 AAAATAATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (7 bp):
AGGTTCA
Found at i:61711 original size:19 final size:20
Alignment explanation
Indices: 61673--61711 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61663 AAAAAAATTA
**
61673 TTTTTTAAATTCTCATTTTT
1 TTTTTTAAATTAACATTTTT
61693 TTTTTTAAATTAACATTTT
1 TTTTTTAAATTAACATTTT
61712 GATATTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTTAAATTAACATTTTT
Found at i:65170 original size:21 final size:21
Alignment explanation
Indices: 65121--65170 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
65111 AAAAAATTAT
*
65121 TTAATT-AAAATAGTTAGATA
1 TTAATTAAAAATAATTAGATA
* *
65141 TAAAATAAAGAATAATTA-ATA
1 TTAATTAAA-AATAATTAGATA
65162 TTAATTAAA
1 TTAATTAAA
65171 CTTGAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (21 bp):
TTAATTAAAAATAATTAGATA
Found at i:67148 original size:47 final size:46
Alignment explanation
Indices: 67066--67164 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 46
67056 GATATCCATG
*
67066 TAACAAAAAATGACACTGTAATGAACTTAAATTTAATAAAAAAAAT
1 TAACAAAAAATGACACTGTAATGAACCTAAATTTAATAAAAAAAAT
* * * * * **
67112 TAACAAAAATATGGCATTGTATTGGACCTAAATTTAATAGAAAATTT
1 TAACAAAAA-ATGACACTGTAATGAACCTAAATTTAATAAAAAAAAT
67159 TAACAA
1 TAACAA
67165 TGTTAACAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 9 0.20
47 35 0.80
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (46 bp):
TAACAAAAAATGACACTGTAATGAACCTAAATTTAATAAAAAAAAT
Found at i:67519 original size:26 final size:24
Alignment explanation
Indices: 67490--67546 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
67480 TTTTTACAAA
67490 TTAAAAAAATATATATTTTTATAATT
1 TTAAAAAAATATATATTTTT-T-ATT
* * * *
67516 TTAATAAATTTTTTATTTTTTATT
1 TTAAAAAAATATATATTTTTTATT
67540 TTAAAAA
1 TTAAAAA
67547 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 9 0.35
25 1 0.04
26 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAAAAAATATATATTTTTTATT
Found at i:77156 original size:2 final size:2
Alignment explanation
Indices: 77151--77179 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
77141 GATAGTGTTG
77151 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
77180 AAGTAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Done.