Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003034.1 Kokia drynarioides strain JFW-HI SEQ_115556, 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: 32026
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:1052 original size:31 final size:32
Alignment explanation
Indices: 1008--1147 Score: 98
Period size: 33 Copynumber: 4.5 Consensus size: 32
998 GGATCCCAAA
* * *
1008 AAGTTCAAGTACCAACTTA-AAAAAAATTGTC
1 AAGTTCAAATACCAAATTAGAAAAAAAATGTC
*
1039 AAGTTTAAATACCAAATTAGGAAAAAAAATGTC
1 AAGTTCAAATACCAAATTA-GAAAAAAAATGTC
* * * *
1072 AAGTTCGAGTGCTAAATT-GAACCAAAAAA----
1 AAGTTCAAATACCAAATTAGAA--AAAAAATGTC
* **
1101 AAATT-AAATATTAAATTAG-AAAAAAATGTC
1 AAGTTCAAATACCAAATTAGAAAAAAAATGTC
1131 AAGTTCAAATACCAAAT
1 AAGTTCAAATACCAAAT
1148 ATTATATTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
26 6 0.07
28 9 0.11
29 5 0.06
30 4 0.05
31 28 0.34
33 30 0.37
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (32 bp):
AAGTTCAAATACCAAATTAGAAAAAAAATGTC
Found at i:5072 original size:14 final size:13
Alignment explanation
Indices: 5049--5097 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
5039 TTTCTCGAAA
*
5049 AAAGTTAATGGGTC
1 AAAGTCAAT-GGTC
5063 AAAGTCAATGGTC
1 AAAGTCAATGGTC
*
5076 AACGATCAATGGTC
1 AAAG-TCAATGGTC
5090 AAAGTCAA
1 AAAGTCAA
5098 CGATCAATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGTCAATGGTC
Found at i:5094 original size:27 final size:26
Alignment explanation
Indices: 5059--5126 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 26
5049 AAAGTTAATG
5059 GGTCAAAGTCAATGGTCAACGATCAAT
1 GGTCAAAGTCAA-GGTCAACGATCAAT
5086 GGTC--A---AA-GTCAACGATCAAT
1 GGTCAAAGTCAAGGTCAACGATCAAT
5106 GGTCAAAGTCAACGGTCAACG
1 GGTCAAAGTCAA-GGTCAACG
5127 GATCGGGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
20 17 0.50
22 3 0.09
25 3 0.09
27 11 0.32
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
GGTCAAAGTCAAGGTCAACGATCAAT
Found at i:5096 original size:20 final size:20
Alignment explanation
Indices: 5073--5124 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5063 AAAGTCAATG
5073 GTCAACGATCAATGGTCAAA
1 GTCAACGATCAATGGTCAAA
5093 GTCAACGATCAATGGTCAAA
1 GTCAACGATCAATGGTCAAA
*
5113 GTCAACGGTCAA
1 GTCAACGATCAA
5125 CGGATCGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
GTCAACGATCAATGGTCAAA
Found at i:9769 original size:13 final size:12
Alignment explanation
Indices: 9751--9821 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 12
9741 AAGTCAATGG
*
9751 GTCAAAGTCTACA
1 GTCAAAGTC-AAA
9764 GTCAAAGTCAAA
1 GTCAAAGTCAAA
*
9776 GATCAAAGTCAAC
1 G-TCAAAGTCAAA
*
9789 GATCAACCGTCAAA
1 G-TCAA-AGTCAAA
9803 GTCAATAGTCAACA
1 GTCAA-AGTCAA-A
9817 GTCAA
1 GTCAA
9822 CGATTAACAG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
12 3 0.06
13 34 0.69
14 12 0.24
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (12 bp):
GTCAAAGTCAAA
Found at i:9814 original size:20 final size:20
Alignment explanation
Indices: 9763--9821 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
9753 CAAAGTCTAC
9763 AGTCAAAG-TCAA-AGATCAA
1 AGTCAAAGATCAACAG-TCAA
* *
9782 AGTCAACGATCAACCGTCAA
1 AGTCAAAGATCAACAGTCAA
9802 AGTCAATAG-TCAACAGTCAA
1 AGTCAA-AGATCAACAGTCAA
9822 CGATTAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 7 0.21
20 24 0.73
21 2 0.06
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17
Consensus pattern (20 bp):
AGTCAAAGATCAACAGTCAA
Found at i:9822 original size:7 final size:6
Alignment explanation
Indices: 9751--9821 Score: 61
Period size: 7 Copynumber: 10.8 Consensus size: 6
9741 AAGTCAATGG
* * *
9751 GTCAAA GTCTACA GTCAAA GTCAAA GATCAAA GTCAAC GATCAACC GTCAAA
1 GTCAAA GTC-AAA GTCAAA GTCAAA G-TCAAA GTCAAA G-TCAA-A GTCAAA
9803 GTCAATA GTCAACA GTCAA
1 GTCAA-A GTCAA-A GTCAA
9822 CGATTAACAG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
6 22 0.40
7 31 0.56
8 2 0.04
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (6 bp):
GTCAAA
Found at i:10901 original size:5 final size:5
Alignment explanation
Indices: 10888--10936 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
10878 TGCAATAAGA
* * *
10888 TTTAT TTTAC TTTA- TTTAT TTTAT TTTAT TTTCGT TTTAT TTTAG TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT TTTAT TTTA
10937 ACGTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 4 0.11
5 30 0.79
6 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:10906 original size:14 final size:14
Alignment explanation
Indices: 10887--10918 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
10877 TTGCAATAAG
10887 ATTTATTTTACTTT
1 ATTTATTTTACTTT
*
10901 ATTTATTTTATTTT
1 ATTTATTTTACTTT
10915 ATTT
1 ATTT
10919 TCGTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTATTTTACTTT
Found at i:17931 original size:17 final size:17
Alignment explanation
Indices: 17909--17947 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
17899 GGTGTTGCCA
17909 AAATACTCAAAATAACC
1 AAATACTCAAAATAACC
17926 AAATACTCAAAATAACC
1 AAATACTCAAAATAACC
17943 AAATA
1 AAATA
17948 TCCATTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATACTCAAAATAACC
Found at i:18267 original size:10 final size:10
Alignment explanation
Indices: 18252--18294 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
18242 CATGATGACC
18252 AAAAGAGAAA
1 AAAAGAGAAA
*
18262 AAAAGAAAAA
1 AAAAGAGAAA
*
18272 AAAAGTGAAA
1 AAAAGAGAAA
18282 AAAAG-GAAA
1 AAAAGAGAAA
18291 AAAA
1 AAAA
18295 TTAAGGAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAGAGAAA
Found at i:18281 original size:20 final size:21
Alignment explanation
Indices: 18252--18294 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
18242 CATGATGACC
18252 AAAAGAGAAAAAAA-GAAAAA
1 AAAAGAGAAAAAAAGGAAAAA
*
18272 AAAAGTGAAAAAAAGGAAAAA
1 AAAAGAGAAAAAAAGGAAAAA
18293 AA
1 AA
18295 TTAAGGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAAGAGAAAAAAAGGAAAAA
Found at i:22695 original size:5 final size:5
Alignment explanation
Indices: 22687--22736 Score: 73
Period size: 5 Copynumber: 9.8 Consensus size: 5
22677 TACAACAAGA
* *
22687 TTTAT TTTAC TTTAT TTTAT TTTAT TTTAT TTTCAT TTTAT TTTAG TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT TTTAT TTTA
22737 ATGTTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 36 0.88
6 5 0.12
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:23621 original size:22 final size:22
Alignment explanation
Indices: 23593--23638 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
23583 TAATGTCGCA
23593 ACTTCAACTGAGGTGAGTCACG
1 ACTTCAACTGAGGTGAGTCACG
23615 ACTTCAACTGAGGTGAGTCACG
1 ACTTCAACTGAGGTGAGTCACG
23637 AC
1 AC
23639 CTTAAAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (22 bp):
ACTTCAACTGAGGTGAGTCACG
Found at i:25795 original size:13 final size:13
Alignment explanation
Indices: 25777--25802 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25767 GAATCATATC
25777 AACTTAGTGAAAG
1 AACTTAGTGAAAG
25790 AACTTAGTGAAAG
1 AACTTAGTGAAAG
25803 CTCTAACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
AACTTAGTGAAAG
Found at i:27649 original size:20 final size:19
Alignment explanation
Indices: 27614--27675 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
27604 CTAGAACTCT
**
27614 AGTATCGATACCTTTTTAA
1 AGTATCGATATTTTTTTAA
27633 AGGTATCGATATTTTTTCTAA
1 A-GTATCGATATTTTTT-TAA
*
27654 AATATCGATACTTTTCTTTAA
1 AGTATCGATA-TTTT-TTTAA
27675 A
1 A
27676 ATCGAGACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.03
20 21 0.58
21 12 0.33
22 2 0.06
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (19 bp):
AGTATCGATATTTTTTTAA
Found at i:27668 original size:21 final size:20
Alignment explanation
Indices: 27636--27677 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
27626 TTTTTAAAGG
27636 TATCGATATTTT-TTCTAAAA
1 TATCGATATTTTCTT-TAAAA
27656 TATCGATACTTTTCTTTAAAA
1 TATCGATA-TTTTCTTTAAAA
27677 T
1 T
27678 CGAGACCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 10 0.50
22 2 0.10
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (20 bp):
TATCGATATTTTCTTTAAAA
Found at i:28322 original size:22 final size:22
Alignment explanation
Indices: 28292--28348 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
28282 TGCACAAATG
* *
28292 AACAAAGAGCACTGAGGTGCTA
1 AACAGAGAGCACTAAGGTGCTA
* * *
28314 AACAGAGAGCACAAATGTGTTA
1 AACAGAGAGCACTAAGGTGCTA
*
28336 AACGGAGAGCACT
1 AACAGAGAGCACT
28349 TTACGTGCTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACTAAGGTGCTA
Found at i:28367 original size:26 final size:27
Alignment explanation
Indices: 28336--28398 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
28326 AAATGTGTTA
*
28336 AACGGAGAGCACTTTACGTGCT-AA-T
1 AACGGAGAGCACTATACGTGCTAAATT
28361 AATCGGAGAGCACTATACGTGCTAAATT
1 AA-CGGAGAGCACTATACGTGCTAAATT
28389 AACGGAGAGC
1 AACGGAGAGC
28399 TTGCTAGCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 2 0.06
26 19 0.56
27 10 0.29
28 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (27 bp):
AACGGAGAGCACTATACGTGCTAAATT
Done.