Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006656.1 Kokia drynarioides strain JFW-HI SEQ_121247, 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: 26865
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:2041 original size:10 final size:10
Alignment explanation
Indices: 2026--2052 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2016 CTCACAAAAA
2026 ATATATAAAT
1 ATATATAAAT
2036 ATATATAAAT
1 ATATATAAAT
2046 ATATATA
1 ATATATA
2053 TTTAAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATAAAT
Found at i:4159 original size:24 final size:23
Alignment explanation
Indices: 4127--4172 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
4117 ACCGGCCCGA
4127 ATTTATAATAATAATTTTATTTTT
1 ATTTATAATAATAATTTT-TTTTT
* *
4151 ATTTTTAATACTAATTTTTTTT
1 ATTTATAATAATAATTTTTTTT
4173 GCTTGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTATAATAATAATTTTTTTTT
Found at i:15677 original size:28 final size:27
Alignment explanation
Indices: 15638--15690 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
15628 ACTTTTATCA
* *
15638 AATATAAGTATCACATTGGACAAAAAAT
1 AATATAAATATCACATTAGA-AAAAAAT
*
15666 AATATAAATATCGCATTAGAAAAAA
1 AATATAAATATCACATTAGAAAAAA
15691 GTATCAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (27 bp):
AATATAAATATCACATTAGAAAAAAAT
Found at i:16874 original size:24 final size:23
Alignment explanation
Indices: 16842--16907 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 23
16832 AGTTTGGAGG
*
16842 TGAGGTTAAAAATCACGATGGCGA
1 TGAGATTAAAAAT-ACGATGGCGA
* * *
16866 TGAGATT--AACTACGATAGCGG
1 TGAGATTAAAAATACGATGGCGA
16887 TGAGATTAAAAATAACGATGG
1 TGAGATTAAAAAT-ACGATGG
16908 GTTGTGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 15 0.45
22 3 0.09
23 3 0.09
24 12 0.36
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (23 bp):
TGAGATTAAAAATACGATGGCGA
Found at i:18624 original size:12 final size:12
Alignment explanation
Indices: 18596--18642 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
18586 TCATTCATAA
*
18596 ATAAACGAG-TC
1 ATAAACGAGCTT
18607 ATAAACGAGCTT
1 ATAAACGAGCTT
**
18619 ATAAACGAGCCA
1 ATAAACGAGCTT
18631 ATAAACGAGCTT
1 ATAAACGAGCTT
18643 GTTCGTGAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:18626 original size:23 final size:24
Alignment explanation
Indices: 18596--18642 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
18586 TCATTCATAA
*
18596 ATAAACGAGTC-ATAAACGAGCTT
1 ATAAACGAGCCAATAAACGAGCTT
18619 ATAAACGAGCCAATAAACGAGCTT
1 ATAAACGAGCCAATAAACGAGCTT
18643 GTTCGTGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (24 bp):
ATAAACGAGCCAATAAACGAGCTT
Found at i:20353 original size:19 final size:18
Alignment explanation
Indices: 20301--20354 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
20291 AATCATTCCG
*
20301 TTTTCTAAATGAAT-TTTT
1 TTTTCT-AATTAATATTTT
20319 TTTT-TAATTCAA-ATTTAT
1 TTTTCTAATT-AATATTT-T
20337 TTTTCTAATTAATATTTT
1 TTTTCTAATTAATATTTT
20355 AAAATCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
16 3 0.10
17 6 0.20
18 12 0.40
19 9 0.30
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTCTAATTAATATTTT
Found at i:21949 original size:59 final size:59
Alignment explanation
Indices: 21857--21975 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 59
21847 GCGTTCGAGA
* *
21857 AAAAGAAATCTATTGATTTTCTCTCAATTGATTGGATCGTAGGTACGATGATTTACTTC
1 AAAAGAAATCTATTGATTCTCTCTCAATTGATTGGACCGTAGGTACGATGATTTACTTC
* *
21916 AAAAGAAATCTATTGATTCTCTCTCAATTGATTGGCCCGTAGGTGCGATGATTTACTTC
1 AAAAGAAATCTATTGATTCTCTCTCAATTGATTGGACCGTAGGTACGATGATTTACTTC
21975 A
1 A
21976 CGGGTGAAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (59 bp):
AAAAGAAATCTATTGATTCTCTCTCAATTGATTGGACCGTAGGTACGATGATTTACTTC
Done.