Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009409.1 Kokia drynarioides strain JFW-HI SEQ_124116, 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: 13102
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1121 original size:14 final size:16
Alignment explanation
Indices: 1097--1128 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1087 ACAACCGAAT
1097 GATGCGAGTAC-CTCC
1 GATGCGAGTACACTCC
1112 GATG-GAGTACACTCC
1 GATGCGAGTACACTCC
1127 GA
1 GA
1129 ATTTACAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (16 bp):
GATGCGAGTACACTCC
Found at i:1438 original size:45 final size:45
Alignment explanation
Indices: 1373--1507 Score: 189
Period size: 45 Copynumber: 3.0 Consensus size: 45
1363 ATAGCTCATT
* * *
1373 AAGCCAAGGATATCAACCTCAGTTTGACGAGCCATCGTAATACTC
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTC
*
1418 AAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACTC
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTC
** * * *
1463 AAGGGAAGGATATCAGGCTTAGTTTGACGAGCCACCGCGATACTC
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTC
1508 TATTCCTCCC
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (45 bp):
AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTC
Found at i:1528 original size:21 final size:21
Alignment explanation
Indices: 1502--1544 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1492 AGCCACCGCG
*
1502 ATACTCTATTCCTCCCGGGCA
1 ATACTCTACTCCTCCCGGGCA
*
1523 ATACTCTACTCCTCCGGGGCA
1 ATACTCTACTCCTCCCGGGCA
1544 A
1 A
1545 ATGAACCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (21 bp):
ATACTCTACTCCTCCCGGGCA
Found at i:1818 original size:28 final size:28
Alignment explanation
Indices: 1787--1850 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
1777 CCTAAATTAC
1787 AAACACTAAACTTAAAA-TCTTAAACCGT
1 AAACACTAAACTTAAAACTC-TAAACCGT
* *
1815 AAACACTAAACTTGAAACTCTAAATCGT
1 AAACACTAAACTTAAAACTCTAAACCGT
*
1843 AGACACTA
1 AAACACTA
1851 GATTGATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.23
Consensus pattern (28 bp):
AAACACTAAACTTAAAACTCTAAACCGT
Found at i:4900 original size:9 final size:9
Alignment explanation
Indices: 4888--4943 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
4878 AAACACATTA
4888 CCTTTCTTT
1 CCTTTCTTT
4897 CC-TTC-TT
1 CCTTTCTTT
4904 -CTTTCTTT
1 CCTTTCTTT
* *
4912 CCTCTCATT
1 CCTTTCTTT
4921 CCTTTCTTT
1 CCTTTCTTT
4930 CCTTTCTTT
1 CCTTTCTTT
4939 -CTTTC
1 CCTTTC
4944 CCGTTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 1 0.03
7 5 0.12
8 10 0.25
9 24 0.60
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (9 bp):
CCTTTCTTT
Found at i:7807 original size:2 final size:2
Alignment explanation
Indices: 7800--7826 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7790 CTCAGACATC
7800 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
7827 CCTCCCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:12797 original size:20 final size:21
Alignment explanation
Indices: 12772--12814 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
12762 ATTCAAGGGA
* *
12772 TGAAATATATTT-TTTATAAT
1 TGAAATAAATTTCTGTATAAT
12792 TGAAATAAATTTCTGTATAAT
1 TGAAATAAATTTCTGTATAAT
12813 TG
1 TG
12815 TAAAACGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (21 bp):
TGAAATAAATTTCTGTATAAT
Done.