Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005363.1 Kokia drynarioides strain JFW-HI SEQ_119345, 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: 98599
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 169 characters in sequence are not A, C, G, or T
Found at i:8245 original size:7 final size:7
Alignment explanation
Indices: 8233--8257 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8223 TAACAAATGA
8233 GCCTAAT
1 GCCTAAT
8240 GCCTAAT
1 GCCTAAT
8247 GCCTAAT
1 GCCTAAT
8254 GCCT
1 GCCT
8258 CGAAGATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (7 bp):
GCCTAAT
Found at i:12014 original size:22 final size:23
Alignment explanation
Indices: 11989--12032 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11979 TAATAGGGAA
*
11989 TTATAAGTAATG-AATATTATGT
1 TTATAAGGAATGAAATATTATGT
*
12011 TTATATGGAATGAAATATTATG
1 TTATAAGGAATGAAATATTATG
12033 GATATTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (23 bp):
TTATAAGGAATGAAATATTATGT
Found at i:13769 original size:79 final size:79
Alignment explanation
Indices: 13564--13906 Score: 417
Period size: 79 Copynumber: 4.4 Consensus size: 79
13554 TTGACTAGTA
* * * *
13564 CTAGGCACACATTTGCGGTTTATCCGCTAGGCAGTGGGTGCCAAGATTTGACAGATATTGTTGGT
1 CTAGGCTCACATTTGCAGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATATTGTTGGT
13629 TAATCCAACTAGAG
66 TAATCCAACTAGAG
* * * * * *
13643 CT-GGACT--CATTTACAGTTTATCCGTTAGGCATTGGATGCCAGGATTTGACGGATATTGTTAG
1 CTAGG-CTCACATTTGCAGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATATTGTTGG
*
13705 TTAATCCAATTAGAG
65 TTAATCCAACTAGAG
* * *
13720 TTAGGCTCACATTTGC-GATTTATCCGCTAGGCACTGGGTGCAAAGATTTGATGGATATTGTTGG
1 CTAGGCTCACATTTGCAG-TTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATATTGTTGG
* *
13784 TTAATCCAACCAAAG
65 TTAATCCAACTAGAG
* * *
13799 CTGGGCTCACTTTTGCAGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACGGATATTGTTGGT
1 CTAGGCTCACATTTGCAGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATATTGTTGGT
13864 TAATCCAACTAGAG
66 TAATCCAACTAGAG
* * * *
13878 CT-GAACTCACAATTACAATTTATCCGCTA
1 CTAG-GCTCACATTTGCAGTTTATCCGCTA
13907 AGCATCGAGT
Statistics
Matches: 222, Mismatches: 35, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
77 64 0.29
78 6 0.03
79 151 0.68
80 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (79 bp):
CTAGGCTCACATTTGCAGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATATTGTTGGT
TAATCCAACTAGAG
Found at i:18831 original size:12 final size:12
Alignment explanation
Indices: 18811--18840 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18801 CTGACCCCAA
*
18811 TTTTCTTTCTTT
1 TTTTTTTTCTTT
18823 TTTTTTTTCTTT
1 TTTTTTTTCTTT
18835 TTTTTT
1 TTTTTT
18841 AGAAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:18832 original size:16 final size:15
Alignment explanation
Indices: 18811--18840 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18801 CTGACCCCAA
18811 TTTTCTTTCTTTTTTT
1 TTTTCTTT-TTTTTTT
18827 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
18841 AGAAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:20982 original size:3 final size:3
Alignment explanation
Indices: 20974--20999 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20964 ACAATTAGCC
20974 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
21000 ACCTACTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:38571 original size:19 final size:19
Alignment explanation
Indices: 38547--38606 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
38537 TGTTATATTC
*
38547 ATATTATTATTTATGTGTT
1 ATATTAATATTTATGTGTT
38566 ATATTAATATTTCAAT-T-TT
1 ATATTAATATTT--ATGTGTT
*
38585 AT-TTAAAATTTATGTGTT
1 ATATTAATATTTATGTGTT
38603 ATAT
1 ATAT
38607 ATAGTTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 12 0.35
19 16 0.47
20 1 0.03
21 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (19 bp):
ATATTAATATTTATGTGTT
Found at i:38604 original size:18 final size:19
Alignment explanation
Indices: 38555--38606 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
38545 TCATATTATT
*
38555 ATTTATGTGTTATATTAAT
1 ATTTATGTGTTATATTAAA
38574 ATTTCAAT-T-TTAT-TTAAA
1 ATTT--ATGTGTTATATTAAA
38592 ATTTATGTGTTATAT
1 ATTTATGTGTTATAT
38607 ATAGTTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
16 2 0.07
17 1 0.04
18 12 0.44
19 9 0.33
20 1 0.04
21 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTTATGTGTTATATTAAA
Found at i:39459 original size:18 final size:18
Alignment explanation
Indices: 39424--39459 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39414 ACACGCTTTC
*
39424 CTTCTGCCTTGTGACACG
1 CTTCTGCCTTATGACACG
*
39442 CTTCTGCCTTATGGCACG
1 CTTCTGCCTTATGACACG
39460 TTTTCATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.33, G:0.22, T:0.33
Consensus pattern (18 bp):
CTTCTGCCTTATGACACG
Found at i:57334 original size:14 final size:14
Alignment explanation
Indices: 57315--57350 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
57305 TTGTTTCATT
* *
57315 GAAAATGATTTTTG
1 GAAAATGATTTCTA
57329 GAAAATGATTTCTA
1 GAAAATGATTTCTA
57343 GAAAATGA
1 GAAAATGA
57351 CTTATTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCTA
Found at i:68610 original size:21 final size:21
Alignment explanation
Indices: 68581--68629 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
68571 TTTTAAAATT
*
68581 TAAAAATTATTAACAAAATCA
1 TAAAAATTATAAACAAAATCA
* *
68602 TAAATATTATAAACAAAATTTA
1 TAAAAATTATAAACAAAA-TCA
68624 TAAAAA
1 TAAAAA
68630 ATAAAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAAATTATAAACAAAATCA
Found at i:68641 original size:15 final size:16
Alignment explanation
Indices: 68616--68646 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
68606 TATTATAAAC
68616 AAAATTTATAAAAAAT
1 AAAATTTATAAAAAAT
68632 AAAA-TTATAAAAAAT
1 AAAATTTATAAAAAAT
68647 TTATTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTTATAAAAAAT
Found at i:68751 original size:19 final size:19
Alignment explanation
Indices: 68727--68763 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
68717 ATCTTTTAGT
68727 AAAAGAGTAGAG-GTTAAAC
1 AAAAGAGTA-AGTGTTAAAC
68746 AAAAGAGTAAGTGTTAAA
1 AAAAGAGTAAGTGTTAAA
68764 TTGAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (19 bp):
AAAAGAGTAAGTGTTAAAC
Found at i:69769 original size:27 final size:28
Alignment explanation
Indices: 69716--69771 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
69706 GTTTTACGAA
* *
69716 TTGTTTTAATATCGTTTTTAGTTTATTTG
1 TTGTTTTAATATC-TTTTAAGTGTATTTG
69745 TTGTTTTAATAT-TTTTAAGTGTATTTG
1 TTGTTTTAATATCTTTTAAGTGTATTTG
69772 ATATATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 13 0.52
29 12 0.48
ACGTcount: A:0.20, C:0.02, G:0.14, T:0.64
Consensus pattern (28 bp):
TTGTTTTAATATCTTTTAAGTGTATTTG
Found at i:80881 original size:4 final size:4
Alignment explanation
Indices: 80872--80896 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
80862 CCTTTGCAGC
80872 TGGG TGGG TGGG TGGG TGGG TGGG T
1 TGGG TGGG TGGG TGGG TGGG TGGG T
80897 TTGATTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.72, T:0.28
Consensus pattern (4 bp):
TGGG
Found at i:87641 original size:21 final size:21
Alignment explanation
Indices: 87610--87665 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
87600 ACGTTTCTTT
87610 ATTTTTT-TTTTATAA-AATTA
1 ATTTTTTATTTT-TAAGAATTA
*
87630 ATTTTTTATTTTTAAGAATTT
1 ATTTTTTATTTTTAAGAATTA
87651 ATTTGATTTATTTTT
1 ATTT--TTTATTTTT
87666 CAGACTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 10 0.32
21 12 0.39
23 9 0.29
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
ATTTTTTATTTTTAAGAATTA
Found at i:94645 original size:8 final size:8
Alignment explanation
Indices: 94632--94686 Score: 65
Period size: 8 Copynumber: 6.6 Consensus size: 8
94622 AGATAGAAAC
94632 AAATATAT
1 AAATATAT
94640 AAATATAT
1 AAATATAT
94648 ATATATATAT
1 A-A-ATATAT
*
94658 ATATATAT
1 AAATATAT
*
94666 ATATATAT
1 AAATATAT
*
94674 ATATATAT
1 AAATATAT
94682 AAATA
1 AAATA
94687 AATAGAGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 35 0.81
9 1 0.02
10 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATATAT
Found at i:94647 original size:2 final size:2
Alignment explanation
Indices: 94634--94682 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
94624 ATAGAAACAA
*
94634 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94676 AT AT AT A
1 AT AT AT A
94683 AATAAATAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:96466 original size:17 final size:19
Alignment explanation
Indices: 96446--96487 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
96436 ATTAATATAA
*
96446 TTAATATATT-TAT-TATT
1 TTAATAAATTATATATATT
96463 TTAATAAATTATATAATATT
1 TTAATAAATTATAT-ATATT
96483 TTAAT
1 TTAAT
96488 TTTATTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
20 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATAAATTATATATATT
Found at i:96466 original size:26 final size:26
Alignment explanation
Indices: 96432--96491 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
96422 TCATATAACA
96432 AATTATTAATATAATTA-AT-ATATTTAT
1 AATT-TTAATA-AATTATATAATATTT-T
*
96459 TATTTTAATAAATTATATAATATTTT
1 AATTTTAATAAATTATATAATATTTT
96485 AATTTTA
1 AATTTTA
96492 TTTTAGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 5 0.17
26 15 0.52
27 9 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATTTTAATAAATTATATAATATTTT
Found at i:96484 original size:20 final size:20
Alignment explanation
Indices: 96431--96487 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
96421 GTCATATAAC
*
96431 AAATTAT-TAATATAATTAAT
1 AAATTATATAATAT-TTTAAT
*
96451 ATATT-TAT--TATTTTAAT
1 AAATTATATAATATTTTAAT
96468 AAATTATATAATATTTTAAT
1 AAATTATATAATATTTTAAT
96488 TTTATTTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
17 9 0.30
18 6 0.20
19 1 0.03
20 14 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTATATAATATTTTAAT
Done.