Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015078.1 Kokia drynarioides strain JFW-HI SEQ_130122, 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: 43575
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1685 original size:18 final size:17
Alignment explanation
Indices: 1662--1698 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1652 TTATATGAAA
1662 ATAAAAATTATAAAAATC
1 ATAAAAATTA-AAAAATC
*
1680 ATAAAAATTACAAAATC
1 ATAAAAATTAAAAAATC
1697 AT
1 AT
1699 TTTTTGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAATTAAAAAATC
Found at i:1750 original size:21 final size:21
Alignment explanation
Indices: 1708--1751 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1698 TTTTTTGGCA
* *
1708 TTATAATTTTTACATTTATTT
1 TTATAATTTTTAAATATATTT
1729 TTATAATTTTTAAATA-ATTT
1 TTATAATTTTTAAATATATTT
1749 TTA
1 TTA
1752 CAAAGTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATAATTTTTAAATATATTT
Found at i:1946 original size:84 final size:84
Alignment explanation
Indices: 1794--1947 Score: 211
Period size: 84 Copynumber: 1.8 Consensus size: 84
1784 AAAGAATTTT
* * *
1794 AGTATTTGGTTCCAAAGTTGAGTTTCCAATAAGAATTTTAGTATTTGATTACAGAGTTAAGTATA
1 AGTATTTGGTTCCAAAGTTGAGTTTCCAATAAGAATTATAGTATTTGATTACAAAGTTAAGTACA
1859 TGCACACACACAATTACAA
66 TGCACACACACAATTACAA
* * * * * *
1878 AGTATTTGGTTGCAAA-TTTAGGTTTGCAATAAGAATTATAGTATTTGGTTACAAATTTGAGTAC
1 AGTATTTGGTTCCAAAGTTGA-GTTTCCAATAAGAATTATAGTATTTGATTACAAAGTTAAGTAC
1942 ATGCAC
65 ATGCAC
1948 GATTACAAAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
83 3 0.05
84 57 0.95
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (84 bp):
AGTATTTGGTTCCAAAGTTGAGTTTCCAATAAGAATTATAGTATTTGATTACAAAGTTAAGTACA
TGCACACACACAATTACAA
Found at i:5798 original size:59 final size:59
Alignment explanation
Indices: 5698--5894 Score: 297
Period size: 59 Copynumber: 3.3 Consensus size: 59
5688 TATGCATTGA
* **
5698 TGAATATTTTTGTACACATTCTTTTTATATTGTATTTTTTAATAAAATAAATGTTCTTT
1 TGAATATTTTTGTACACATTCTTTTTATATTCTATCATTTAATAAAATAAATGTTCTTT
*
5757 TAAATATTTTTGTACACATTCTTTTTATATTCTATCATTTAATAAAATAGAA-GTTCTTT
1 TGAATATTTTTGTACACATTCTTTTTATATTCTATCATTTAATAAAATA-AATGTTCTTT
* *
5816 TGAATCTTTTAGTACACATTCTTTTTATATTCTATCATTTAATAAAATAAATGTTCTTT
1 TGAATATTTTTGTACACATTCTTTTTATATTCTATCATTTAATAAAATAAATGTTCTTT
* * *
5875 TGGATCTTTTTATACACATT
1 TGAATATTTTTGTACACATT
5895 GTGATTTTTG
Statistics
Matches: 126, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
58 2 0.02
59 122 0.97
60 2 0.02
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (59 bp):
TGAATATTTTTGTACACATTCTTTTTATATTCTATCATTTAATAAAATAAATGTTCTTT
Found at i:8410 original size:43 final size:43
Alignment explanation
Indices: 8334--8556 Score: 252
Period size: 43 Copynumber: 5.2 Consensus size: 43
8324 GAATCACTTA
* * * * * *
8334 ATGTATAAATGGAAGGCTCATGCCTCAAGATGAGCATGATGTT
1 ATGTTTAAAAGGAAGACTCATGTCTCGAGATGAGCATGAGGTT
* *
8377 ATGTTTAAAAGGAAGACTTATGTCTC-AGGATGAGCACGAGGTT
1 ATGTTTAAAAGGAAGACTCATGTCTCGA-GATGAGCATGAGGTT
8420 ATGTTTAAAAGGAAGACTCATGTCTCGAGATGAGCATGAGGTT
1 ATGTTTAAAAGGAAGACTCATGTCTCGAGATGAGCATGAGGTT
* * * * *
8463 ATGTTTAAAAGGAAGACTCGTGACTCGAAAAGAGCATGAGATT
1 ATGTTTAAAAGGAAGACTCATGTCTCGAGATGAGCATGAGGTT
* * * * * *
8506 ATGTTT-AAAGGAAGACTCGTGACTCGGGATAAGCACGAGATT
1 ATGTTTAAAAGGAAGACTCATGTCTCGAGATGAGCATGAGGTT
8548 ATGTTTAAA
1 ATGTTTAAA
8557 GAAAGATTTA
Statistics
Matches: 158, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
42 38 0.24
43 119 0.75
44 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (43 bp):
ATGTTTAAAAGGAAGACTCATGTCTCGAGATGAGCATGAGGTT
Found at i:10480 original size:120 final size:120
Alignment explanation
Indices: 10275--10500 Score: 326
Period size: 120 Copynumber: 1.9 Consensus size: 120
10265 TAATCCAAAT
* * *
10275 TTTCATCCTCATGTCTGTATCAACTTTGTTACCAATATACGATGCTACTCACATGAGCTGTCGAG
1 TTTCATCCTCATGTCTGTATCAACTCTGTTACCAATATACAATGCTACTCACACGAGCTGTCGAG
*
10340 GACTCGCAACATATGCGGTACCCCAGCCATCGATACGGTATGTTATAATCTAGAA
66 GACTCGCAACATATGCGGTACCCCAACCATCGATACGGTATGTTATAATCTAGAA
* * * * * *
10395 TTTCATTCTTATGTCTGTATCAACTCTGTTTCCAGTATGCAATGCTGCTCACACGAGCTGTCGAG
1 TTTCATCCTCATGTCTGTATCAACTCTGTTACCAATATACAATGCTACTCACACGAGCTGTCGAG
* * * *
10460 GTCTCGTAACATATGTGGTACCCCAACCATCGATATGGTAT
66 GACTCGCAACATATGCGGTACCCCAACCATCGATACGGTAT
10501 CTGTGCTTAT
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
120 92 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (120 bp):
TTTCATCCTCATGTCTGTATCAACTCTGTTACCAATATACAATGCTACTCACACGAGCTGTCGAG
GACTCGCAACATATGCGGTACCCCAACCATCGATACGGTATGTTATAATCTAGAA
Found at i:16491 original size:31 final size:31
Alignment explanation
Indices: 16450--16563 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 31
16440 AAATTAATCT
16450 AATGAATTAAATAAAAAGTTTTGAATAGTTC
1 AATGAATTAAATAAAAAGTTTTGAATAGTTC
* * *** *
16481 AATGACTTAAATGAATTTTTTTGAATAAAAAAATTAATC
1 AATGAATTAAATAAAAAGTTTTGAAT------AGT--TC
16520 TAATGAATTAAATAAAAAGTTTTGAATAGTTC
1 -AATGAATTAAATAAAAAGTTTTGAATAGTTC
*
16552 AATGACTTAAAT
1 AATGAATTAAAT
16564 GAATTTTTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
31 32 0.52
32 2 0.03
34 2 0.03
37 2 0.03
39 2 0.03
40 21 0.34
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (31 bp):
AATGAATTAAATAAAAAGTTTTGAATAGTTC
Found at i:16551 original size:71 final size:71
Alignment explanation
Indices: 16436--16580 Score: 290
Period size: 71 Copynumber: 2.0 Consensus size: 71
16426 TGGCAAATTA
16436 AAAAAAATTAATCTAATGAATTAAATAAAAAGTTTTGAATAGTTCAATGACTTAAATGAATTTTT
1 AAAAAAATTAATCTAATGAATTAAATAAAAAGTTTTGAATAGTTCAATGACTTAAATGAATTTTT
16501 TTGAAT
66 TTGAAT
16507 AAAAAAATTAATCTAATGAATTAAATAAAAAGTTTTGAATAGTTCAATGACTTAAATGAATTTTT
1 AAAAAAATTAATCTAATGAATTAAATAAAAAGTTTTGAATAGTTCAATGACTTAAATGAATTTTT
16572 TTGAAT
66 TTGAAT
16578 AAA
1 AAA
16581 TCAATGAATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (71 bp):
AAAAAAATTAATCTAATGAATTAAATAAAAAGTTTTGAATAGTTCAATGACTTAAATGAATTTTT
TTGAAT
Found at i:24457 original size:29 final size:30
Alignment explanation
Indices: 24425--24483 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
24415 TCACGTGTAT
*
24425 AATTGCACCA-AATTAAAA-TTCATGTATAC
1 AATTGCA-CATAAATAAAAGTTCATGTATAC
24454 AATTGCACATTAAATAAAAGTTCATGTATA
1 AATTGCACA-TAAATAAAAGTTCATGTATA
24484 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 7 0.27
30 7 0.27
31 10 0.38
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (30 bp):
AATTGCACATAAATAAAAGTTCATGTATAC
Found at i:24486 original size:29 final size:27
Alignment explanation
Indices: 24420--24486 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 27
24410 GAGTTTCACG
*
24420 TGTATAATTGCACCAAATTAAAATTCA
1 TGTATAATTGCACCAAAATAAAATTCA
24447 TGTATACAATTGCA-CATTAAATAAAAGTTCA
1 TGTAT--AATTGCACCA--AAATAAAA-TTCA
24478 TGTATAATT
1 TGTATAATT
24487 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 5 0.15
28 2 0.06
29 11 0.32
30 7 0.21
31 9 0.26
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (27 bp):
TGTATAATTGCACCAAAATAAAATTCA
Found at i:33241 original size:73 final size:73
Alignment explanation
Indices: 33122--33267 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
33112 GGTTAAGAAA
*
33122 GTATGAACATATATTATCATGTAATCATACCAGTATATTAAAAGAAAAAACAAGTTGGGACAGGT
1 GTATGAACATATATTATCATGTAATCATACCAATATATTAAAAGAAAAAACAAGTTGGGACAGGT
33187 TAGATATT
66 TAGATATT
*
33195 GTATGAACATATATTATCATGTAATCATATCAATATATTAAAAGAAAAAACAAGTTGGGACAGGT
1 GTATGAACATATATTATCATGTAATCATACCAATATATTAAAAGAAAAAACAAGTTGGGACAGGT
33260 TAGATATT
66 TAGATATT
33268 AAAGCTCAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.31
Consensus pattern (73 bp):
GTATGAACATATATTATCATGTAATCATACCAATATATTAAAAGAAAAAACAAGTTGGGACAGGT
TAGATATT
Found at i:36873 original size:42 final size:42
Alignment explanation
Indices: 36825--36927 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 42
36815 CTTCATTTAG
*
36825 CTGATGATGCACTTACGTGCCAGTATAATTGCTTCAGTATAT
1 CTGATGATGCACTTACGTGCCAGTATAATTGCTTCAGTACAT
* ** * *
36867 CTGATGATGAACTTACGTGTTAGTATATTTGTTTCAGTACAT
1 CTGATGATGCACTTACGTGCCAGTATAATTGCTTCAGTACAT
**
36909 CCAATGATGCACTTACGTG
1 CTGATGATGCACTTACGTG
36928 TCGACATGAT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.37
Consensus pattern (42 bp):
CTGATGATGCACTTACGTGCCAGTATAATTGCTTCAGTACAT
Found at i:40824 original size:25 final size:23
Alignment explanation
Indices: 40796--40841 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
40786 GCTGGATCCA
*
40796 AATTAAATTCTAAACAGATAATTTG
1 AATTAAA-TATAAACA-ATAATTTG
40821 AATTAAATATAAACAATAATT
1 AATTAAATATAAACAATAATT
40842 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATATAAACAATAATTTG
Found at i:40928 original size:13 final size:13
Alignment explanation
Indices: 40907--40940 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40897 ACAATATAAT
40907 AATAATAATCCTA
1 AATAATAATCCTA
*
40920 AATACTAATCCTA
1 AATAATAATCCTA
*
40933 AAAAATAA
1 AATAATAA
40941 AATTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:42869 original size:14 final size:14
Alignment explanation
Indices: 42850--42892 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
42840 TTGCATAATT
**
42850 AAAATAAAATTTAA
1 AAAATAAAATAAAA
42864 AAAATAAAATAAAA
1 AAAATAAAATAAAA
42878 ATAAATAAAAATAAA
1 A-AAAT-AAAATAAA
42893 TATGAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 4 0.16
16 8 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAAAATAAAA
Found at i:42883 original size:10 final size:10
Alignment explanation
Indices: 42863--42906 Score: 61
Period size: 10 Copynumber: 4.1 Consensus size: 10
42853 ATAAAATTTA
42863 AAAAATAAAAT
1 AAAAAT-AAAT
42874 AAAAATAAAT
1 AAAAATAAAT
42884 AAAAATAAAT
1 AAAAATAAAT
42894 ATGAAAATAAAT
1 A--AAAATAAAT
42906 A
1 A
42907 TACTAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 15 0.48
11 6 0.19
12 10 0.32
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:42900 original size:22 final size:21
Alignment explanation
Indices: 42863--42906 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
42853 ATAAAATTTA
42863 AAAAATAAAATAAAAATAAAT
1 AAAAATAAAATAAAAATAAAT
*
42884 AAAAATAAATATGAAAATAAAT
1 AAAAATAAA-ATAAAAATAAAT
42906 A
1 A
42907 TACTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAATAAAATAAAAATAAAT
Done.