Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010675.1 Kokia drynarioides strain JFW-HI SEQ_125621, 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: 35215
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:31 original size:23 final size:23
Alignment explanation
Indices: 1--46 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1 GATTGCACTGTGTGTGCCTACTG
1 GATTGCACTGTGTGTGCCTACTG
*
24 GATTGCACTGTGTGTGCTTACTG
1 GATTGCACTGTGTGTGCCTACTG
47 TTTCCCCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.20, G:0.30, T:0.37
Consensus pattern (23 bp):
GATTGCACTGTGTGTGCCTACTG
Found at i:1467 original size:22 final size:21
Alignment explanation
Indices: 1428--1498 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 21
1418 AAACGGAACA
* *
1428 AACAGAGAGTACCGAAGTACTG
1 AACAGAGAGCA-CAAAGTACTG
*
1450 AACAGAGAGCACATAAGTGCTGGG
1 AACAGAGAGCACA-AAGTACT--G
1474 CAACAGAGAGTACACAAAGTACTG
1 -AACAGAGAG--CACAAAGTACTG
1498 A
1 A
1499 GCACACAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
21 1 0.03
22 16 0.41
23 1 0.03
24 2 0.05
25 9 0.23
26 6 0.15
27 4 0.10
ACGTcount: A:0.42, C:0.18, G:0.27, T:0.13
Consensus pattern (21 bp):
AACAGAGAGCACAAAGTACTG
Found at i:1518 original size:39 final size:39
Alignment explanation
Indices: 1475--1567 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
1465 AGTGCTGGGC
*
1475 AACAGAGAGTACACAAAGTACTGAGCACACAAAGTGCTA
1 AACAGAGAGTACACAAAGTACTGAGCACACAAAGTGCAA
1514 AACAGAGAGTACACAAAGTACTGAGCACACAAAGTGCAA
1 AACAGAGAGTACACAAAGTACTGAGCACACAAAGTGCAA
*
1553 AACAGAGAGCACACA
1 AACAGAGAGTACACA
1568 CAGTGCTAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (39 bp):
AACAGAGAGTACACAAAGTACTGAGCACACAAAGTGCAA
Found at i:1531 original size:23 final size:23
Alignment explanation
Indices: 1497--1605 Score: 97
Period size: 23 Copynumber: 5.0 Consensus size: 23
1487 ACAAAGTACT
1497 GAGCACACAAAGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAACAGA
* *
1520 GAGTACACAAA--G-T--AC--T
1 GAGCACACAAAGTGCTAAACAGA
*
1536 GAGCACACAAAGTGCAAAACAGA
1 GAGCACACAAAGTGCTAAACAGA
* *
1559 GAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAAACAGA
* * *
1582 TAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAAACAGA
1605 G
1 G
1606 CGCGCGCTAG
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
16 10 0.14
18 3 0.04
20 1 0.01
21 3 0.04
23 52 0.75
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAAACAGA
Found at i:11982 original size:15 final size:15
Alignment explanation
Indices: 11936--11982 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
11926 GTAAAAAGTC
11936 TTATTATGGTAACTT
1 TTATTATGGTAACTT
* *
11951 TTATTTTTGGTGA-TT
1 TTA-TTATGGTAACTT
11966 TTATTATGGTAACTT
1 TTATTATGGTAACTT
11981 TT
1 TT
11983 CTCATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 7 0.27
15 12 0.46
16 7 0.27
ACGTcount: A:0.21, C:0.04, G:0.15, T:0.60
Consensus pattern (15 bp):
TTATTATGGTAACTT
Found at i:20642 original size:22 final size:23
Alignment explanation
Indices: 20616--20666 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
20606 AACAATAATA
20616 ATAATAATAATAA-TATAATTTT
1 ATAATAATAATAATTATAATTTT
** *
20638 ATAATTTTAATAATTTATATTTTT
1 ATAATAATAATAA-TTATAATTTT
20662 ATAAT
1 ATAAT
20667 TTTTAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
24 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAATAATAATAATTATAATTTT
Found at i:20652 original size:9 final size:8
Alignment explanation
Indices: 20629--20669 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
20619 ATAATAATAA
20629 TATAATTT
1 TATAATTT
20637 TATAATTT
1 TATAATTT
20645 TAATAA-TT
1 T-ATAATTT
*
20653 TATATTTT
1 TATAATTT
20661 TATAATTT
1 TATAATTT
20669 T
1 T
20670 TAAAAGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 3 0.10
8 22 0.76
9 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATAATTT
Found at i:20718 original size:80 final size:82
Alignment explanation
Indices: 20629--20778 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 82
20619 ATAATAATAA
* * * * * *
20629 TATAATTTTATAATT-TTAATAATTTATATTTTTATAATTTTTAAAAGA-TTAAAT-TAAA-TTT
1 TATAATTTTATAATTATT-A-AATTTAAAATTTTATAAATTATAAAAAACTTAAATAAAAATTTT
20690 TTATTTTTTTGAATTAAAG
64 TTATTTTTTTGAATTAAAG
20709 TATAATTTTATAATTATTAAATTTAAAATTTTATAAATTATAAAAAACTTAAATAAAAATTTTTT
1 TATAATTTTATAATTATTAAATTTAAAATTTTATAAATTATAAAAAACTTAAATAAAAATTTTTT
20774 ATTTT
66 ATTTT
20779 AAGGGTGGCG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
79 23 0.38
80 22 0.37
81 5 0.08
82 10 0.17
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (82 bp):
TATAATTTTATAATTATTAAATTTAAAATTTTATAAATTATAAAAAACTTAAATAAAAATTTTTT
ATTTTTTTGAATTAAAG
Found at i:26316 original size:24 final size:24
Alignment explanation
Indices: 26271--26315 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
26261 CATACATATA
*
26271 AATACATTTTAATACATATTTTAC
1 AATACATTCTAATACATATTTTAC
*
26295 AATACA-TCTAATATATATTTT
1 AATACATTCTAATACATATTTT
26316 TGGTTCAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (24 bp):
AATACATTCTAATACATATTTTAC
Found at i:28587 original size:28 final size:29
Alignment explanation
Indices: 28539--28596 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
28529 ACTTTTGGAT
*
28539 CCCTTAAAAGTTAGAGAAATTTTTTAGGC
1 CCCTTAAAAGTTAGAGAAATTATTTAGGC
* *
28568 CCCTTAAAAGTT-GATAAATTATTTGGGC
1 CCCTTAAAAGTTAGAGAAATTATTTAGGC
28596 C
1 C
28597 TCTTTCAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (29 bp):
CCCTTAAAAGTTAGAGAAATTATTTAGGC
Found at i:30661 original size:26 final size:26
Alignment explanation
Indices: 30632--30693 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
30622 AAAACTAGAC
30632 GTATTGCTTCAAAATTTCTATTCTAA
1 GTATTGCTTCAAAATTTCTATTCTAA
30658 GTATTGCTTCAAAATTTCTATTCTAA
1 GTATTGCTTCAAAATTTCTATTCTAA
30684 GTATTGCTTC
1 GTATTGCTTC
30694 TTCAGCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (26 bp):
GTATTGCTTCAAAATTTCTATTCTAA
Found at i:32001 original size:18 final size:18
Alignment explanation
Indices: 31975--32018 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
31965 TAAACGGACC
31975 TATATTTTTTTGACTCAAA
1 TATA-TTTTTTGACTCAAA
* *
31994 TATATTTTTTGAGTCTAA
1 TATATTTTTTGACTCAAA
32012 TAT-TTTT
1 TATATTTT
32019 CTAATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (18 bp):
TATATTTTTTGACTCAAA
Found at i:35070 original size:11 final size:11
Alignment explanation
Indices: 35054--35104 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
35044 GGGGACCAAC
* *
35054 GAAAAATGAAG
1 GAAAAAAGAAA
35065 GAAAAAAGAAA
1 GAAAAAAGAAA
35076 GAAAAAAGAGAAA
1 G-AAAAA-AGAAA
35089 GAAAGAAAGAAA
1 GAAA-AAAGAAA
35101 GAAA
1 GAAA
35105 GAGAAAGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 10 0.29
12 17 0.49
13 8 0.23
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:35078 original size:4 final size:4
Alignment explanation
Indices: 35065--35106 Score: 59
Period size: 4 Copynumber: 10.5 Consensus size: 4
35055 AAAAATGAAG
*
35065 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GA
35107 GAAAGGAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.82
5 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:35108 original size:22 final size:22
Alignment explanation
Indices: 35065--35126 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
35055 AAAAATGAAG
35065 GAAA-AAAGAAAGAAA-AAAGA
1 GAAAGAAAGAAAGAAAGAAAGA
35085 GAAAGAAAGAAAGAAAGAAAGA
1 GAAAGAAAGAAAGAAAGAAAGA
* *
35107 GAAAGGAAGAAGGAGAAGAA
1 GAAAGAAAGAAAGA-AAGAA
35127 GGGGCAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 4 0.11
21 11 0.30
22 17 0.46
23 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGAAAGAAAGAAAGA
Done.