Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002802.1 Kokia drynarioides strain JFW-HI SEQ_115146, 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: 49003
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:121 original size:4 final size:4
Alignment explanation
Indices: 65--141 Score: 68
Period size: 4 Copynumber: 19.2 Consensus size: 4
55 AACACATTAC
* * * * * *
65 CTTT CTTT CCTT C-TT CTTT CCTT C-TT CTTT ATTT CCTCT CCTT CTTC
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT
112 CTTT CTTT CTTT CTTT CCTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C
142 CTGTTTATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
3 6 0.10
4 47 0.80
5 6 0.10
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:141 original size:17 final size:16
Alignment explanation
Indices: 64--137 Score: 71
Period size: 17 Copynumber: 4.6 Consensus size: 16
54 AAACACATTA
64 CCTTTCTTTCCTTCTT
1 CCTTTCTTTCCTTCTT
*
80 -CTTTCCTT-CTTCTT
1 CCTTTCTTTCCTTCTT
** *
94 TATTTCCTCTCCTTCTT
1 CCTTT-CTTTCCTTCTT
*
111 CCTTTCTTTCTTTCTTT
1 CCTTTCTTTCCTTC-TT
128 CCTTTCTTTC
1 CCTTTCTTTC
138 TTTCCTGTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
14 6 0.13
15 10 0.22
16 9 0.20
17 21 0.46
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (16 bp):
CCTTTCTTTCCTTCTT
Found at i:5884 original size:119 final size:120
Alignment explanation
Indices: 5759--6003 Score: 438
Period size: 119 Copynumber: 2.0 Consensus size: 120
5749 AGTTAATATA
5759 TTATATACATAAATAATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACA
1 TTATATACATAAATAATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACA
*
5824 ATACAATAAGCATTATTATAATTTTTAAAATTCATATATAACTTTAATGTTTA-T
66 ATACAACAAGCATTATTATAATTTTTAAAATTCATATATAACTTTAATGTTTATT
* *
5878 TTATATACATAACTAATTATATCAATTCAATATAAAAATAAACGTGAGTATTCTTTTTTTACACA
1 TTATATACATAAATAATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACA
* *
5943 ATACAACAAGCATTATTATAATTTTTAAAGTTCATATATAATTTTAATGTTTATT
66 ATACAACAAGCATTATTATAATTTTTAAAATTCATATATAACTTTAATGTTTATT
5998 TTATAT
1 TTATAT
6004 TAAAAATACC
Statistics
Matches: 120, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
119 113 0.94
120 7 0.06
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (120 bp):
TTATATACATAAATAATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACA
ATACAACAAGCATTATTATAATTTTTAAAATTCATATATAACTTTAATGTTTATT
Found at i:5947 original size:61 final size:60
Alignment explanation
Indices: 5763--5947 Score: 143
Period size: 61 Copynumber: 3.1 Consensus size: 60
5753 AATATATTAT
*
5763 ATACATAAATAATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACA
1 ATACATAACTAATTATATCAATTCAATATAAAAATAAAC-TGAGTATTCTTTTTTTACACA
* * ** * * * * *
5824 ATACAATAAGC--ATTATTAT-AATTTTTAAAATTCATATATAACT--TTAATGTTTATTT--A-
1 ATAC-ATAA-CTAATTA-TATCAA--TTCAATATAAAAATA-AACTGAGTATTCTTTTTTTACAC
*
5881 T
60 A
5882 ATACATAACTAATTATATCAATTCAATATAAAAATAAACGTGAGTATTCTTTTTTTACACA
1 ATACATAACTAATTATATCAATTCAATATAAAAATAAAC-TGAGTATTCTTTTTTTACACA
5943 ATACA
1 ATACA
5948 ACAAGCATTA
Statistics
Matches: 88, Mismatches: 21, Indels: 30
0.63 0.15 0.22
Matches are distributed among these distances:
55 3 0.03
56 12 0.14
57 7 0.08
58 19 0.22
59 1 0.01
60 1 0.01
61 24 0.27
62 7 0.08
63 11 0.12
64 3 0.03
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (60 bp):
ATACATAACTAATTATATCAATTCAATATAAAAATAAACTGAGTATTCTTTTTTTACACA
Found at i:5958 original size:61 final size:61
Alignment explanation
Indices: 5774--5958 Score: 150
Period size: 56 Copynumber: 3.1 Consensus size: 61
5764 TACATAAATA
*
5774 ATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACAATACAATAAGC
1 ATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACAATACAACAAGC
* * ** * * * * * * * * *
5835 ATTATTAT-AATTTTTAAAATTCATATATAACTTTAATGTT-TATTTATATAC-AT--AACTA--
1 ATTA-TATCAA--TTCAATATAAAAATA-AACATGAGTATTCTTTTTTTACACAATACAACAAGC
*
5893 ATTATATCAATTCAATATAAAAATAAACGTGAGTATTCTTTTTTTACACAATACAACAAGC
1 ATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACAATACAACAAGC
5954 ATTAT
1 ATTAT
5959 TATAATTTTT
Statistics
Matches: 86, Mismatches: 27, Indels: 22
0.64 0.20 0.16
Matches are distributed among these distances:
55 8 0.09
56 18 0.21
57 5 0.06
58 6 0.07
59 4 0.05
60 3 0.03
61 11 0.13
62 5 0.06
63 18 0.21
64 8 0.09
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (61 bp):
ATTATATCAATTCAATATAAAAATAAACATGAGTATTCTTTTTTTACACAATACAACAAGC
Found at i:6424 original size:24 final size:26
Alignment explanation
Indices: 6366--6424 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
6356 TATTCTATTA
*
6366 TAAATATTAAAATAATCTTAAGATGAT
1 TAAATATTAAAAT-ATATTAAGATGAT
6393 T--ATA-TAAAAT-TATTAA-ATGAT
1 TAAATATTAAAATATATTAAGATGAT
6414 TAAATATTAAA
1 TAAATATTAAA
6425 TAATATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
21 6 0.21
22 5 0.18
23 3 0.11
24 10 0.36
25 3 0.11
27 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (26 bp):
TAAATATTAAAATATATTAAGATGAT
Found at i:7138 original size:17 final size:17
Alignment explanation
Indices: 7118--7176 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
7108 AAATAAACAC
7118 TTAAAATAATTTATTTT
1 TTAAAATAATTTATTTT
* *
7135 TTAAAATAA--AATTTGA
1 TTAAAATAATTTATTT-T
*
7151 TTAAAATAATTTTTTTT
1 TTAAAATAATTTATTTT
*
7168 TTTAAATAA
1 TTAAAATAA
7177 AATTCGATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 4 0.12
16 9 0.27
17 17 0.52
18 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAAATAATTTATTTT
Found at i:7160 original size:33 final size:33
Alignment explanation
Indices: 7118--7185 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
7108 AAATAAACAC
*
7118 TTAAAATAATTTATTTTTTAAAATAAAATTTGA
1 TTAAAATAATTTATTTTTTAAAATAAAATTCGA
* *
7151 TTAAAATAATTTTTTTTTTTAAATAAAATTCGA
1 TTAAAATAATTTATTTTTTAAAATAAAATTCGA
7184 TT
1 TT
7186 CAACTCAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (33 bp):
TTAAAATAATTTATTTTTTAAAATAAAATTCGA
Found at i:7236 original size:2 final size:2
Alignment explanation
Indices: 7229--7259 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
7219 TATCACAAAT
*
7229 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7260 TAACTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16549 original size:2 final size:2
Alignment explanation
Indices: 16542--16576 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16532 TACTTGATTC
16542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16577 TTTATTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20925 original size:21 final size:18
Alignment explanation
Indices: 20868--20917 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
20858 AGGATCATAC
*
20868 TTAAGAAAAATGAGTGCT
1 TTAAGAAAAATGAGTCCT
20886 TTAAGAAAAATGAGTCCT
1 TTAAGAAAAATGAGTCCT
20904 TTAAGAAAAATGAG
1 TTAAGAAAAATGAG
20918 AAGTCCTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (18 bp):
TTAAGAAAAATGAGTCCT
Found at i:27371 original size:6 final size:6
Alignment explanation
Indices: 27360--27399 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
27350 TAATCACTTA
27360 CACAGG CACAGG CACAGG CACAGG CACAGG CACAGG CACA
1 CACAGG CACAGG CACAGG CACAGG CACAGG CACAGG CACA
27400 ACCCAATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.35, C:0.35, G:0.30, T:0.00
Consensus pattern (6 bp):
CACAGG
Found at i:31550 original size:7 final size:7
Alignment explanation
Indices: 31539--31573 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
31529 AATTATTAAA
*
31539 TATTTAA
1 TATTTAT
31546 TATTTAT
1 TATTTAT
31553 TATTTAT
1 TATTTAT
31560 TATTTAT
1 TATTTAT
31567 TATTTAT
1 TATTTAT
31574 AAACAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATTTAT
Found at i:31556 original size:21 final size:21
Alignment explanation
Indices: 31530--31573 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
31520 TAAAAATTAA
31530 ATTATTAAATATTTAATATTT
1 ATTATTAAATATTTAATATTT
* * *
31551 ATTATTTATTATTTATTATTT
1 ATTATTAAATATTTAATATTT
31572 AT
1 AT
31574 AAACAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTAAATATTTAATATTT
Found at i:35516 original size:13 final size:13
Alignment explanation
Indices: 35498--35541 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
35488 TGGTTTGACC
35498 AATTGATTCTATT
1 AATTGATTCTATT
*
35511 AATTGATT-TGATC
1 AATTGATTCT-ATT
*
35524 AACTGATTCTATT
1 AATTGATTCTATT
35537 AATTG
1 AATTG
35542 TTTATTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (13 bp):
AATTGATTCTATT
Found at i:35530 original size:26 final size:26
Alignment explanation
Indices: 35491--35541 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
35481 TAGTGGTTGG
*
35491 TTTGACCAATTGATTCTATTAATTGA
1 TTTGACCAACTGATTCTATTAATTGA
*
35517 TTTGATCAACTGATTCTATTAATTG
1 TTTGACCAACTGATTCTATTAATTG
35542 TTTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (26 bp):
TTTGACCAACTGATTCTATTAATTGA
Found at i:46085 original size:26 final size:28
Alignment explanation
Indices: 46056--46119 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 28
46046 TTTATATATT
46056 TTTTAAAAATTTTAATAAA-A-TATAAA
1 TTTTAAAAATTTTAATAAATATTATAAA
* *
46082 TTTT-AAAATTTTTATAAATATTTTAAA
1 TTTTAAAAATTTTAATAAATATTATAAA
*
46109 ATTTAAAAATT
1 TTTTAAAAATT
46120 ATTTTGTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 13 0.41
26 5 0.16
27 8 0.25
28 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTTAAAAATTTTAATAAATATTATAAA
Found at i:46124 original size:19 final size:19
Alignment explanation
Indices: 46081--46124 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
46071 TAAAATATAA
*
46081 ATTTTAAAATTTTTATAAAT
1 ATTTTAAAA-TTTTAAAAAT
46101 ATTTTAAAA-TTTAAAAATT
1 ATTTTAAAATTTTAAAAA-T
46120 ATTTT
1 ATTTT
46125 GTATTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTAAAATTTTAAAAAT
Found at i:46630 original size:13 final size:13
Alignment explanation
Indices: 46591--46621 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
46581 ACTTTATTAA
46591 AGTTTGAAATTTG
1 AGTTTGAAATTTG
46604 AGTTTGAAATTTG
1 AGTTTGAAATTTG
46617 AGTTT
1 AGTTT
46622 TGACATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (13 bp):
AGTTTGAAATTTG
Found at i:47552 original size:10 final size:10
Alignment explanation
Indices: 47537--47565 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
47527 GCTTAGCCCT
47537 TGTGTGTATG
1 TGTGTGTATG
47547 TGTGTGTATG
1 TGTGTGTATG
47557 TGTGTGTAT
1 TGTGTGTAT
47566 AACACTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.38, T:0.52
Consensus pattern (10 bp):
TGTGTGTATG
Done.