Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004281.1 Kokia drynarioides strain JFW-HI SEQ_117575, 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: 11005
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:3951 original size:30 final size:30
Alignment explanation
Indices: 3917--4069 Score: 136
Period size: 31 Copynumber: 5.1 Consensus size: 30
3907 ATTTAAAACC
*
3917 GGGTCAAATTTAAATTTTT-GAAAATTTTAG
1 GGGTCAAATTGAAATTTTTGGAAAA-TTTAG
* * *
3947 GGGTCAAA--GAAA-TTCTAGAAAGTTTAG
1 GGGTCAAATTGAAATTTTTGGAAAATTTAG
* *
3974 AGGTCAAATTGGAATTTTTTGGAAAATTTAG
1 GGGTCAAATT-GAAATTTTTGGAAAATTTAG
* *
4005 GGGTTAAATTCAAATTTTTTGGAAAATTTAG
1 GGGTCAAATTGAAA-TTTTTGGAAAATTTAG
* * *
4036 GGGTCGAATT-AGAATTTTTAGAAAATTTAA
1 GGGTCAAATTGA-AATTTTTGGAAAATTTAG
4066 GGGT
1 GGGT
4070 TAAAAAATTT
Statistics
Matches: 100, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
27 15 0.15
28 7 0.07
30 32 0.32
31 46 0.46
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (30 bp):
GGGTCAAATTGAAATTTTTGGAAAATTTAG
Found at i:5134 original size:12 final size:11
Alignment explanation
Indices: 5123--5152 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5113 TTATTTAATA
5123 AATAAAAAAAT
1 AATAAAAAAAT
5134 AATAAATAAAAT
1 AATAAA-AAAAT
5146 AATAAAA
1 AATAAAA
5153 TTTGGATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:5138 original size:15 final size:15
Alignment explanation
Indices: 5118--5150 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5108 TTTATTTATT
5118 TAATAAATAAAAAAA
1 TAATAAATAAAAAAA
*
5133 TAATAAATAAAATAA
1 TAATAAATAAAAAAA
5148 TAA
1 TAA
5151 AATTTGGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAATAAATAAAAAAA
Found at i:5647 original size:50 final size:50
Alignment explanation
Indices: 5589--5694 Score: 149
Period size: 50 Copynumber: 2.1 Consensus size: 50
5579 TGTGAGTTTT
*
5589 AATCTGCCCCTCTATTACTTTAGGGGTATAAGATTCGCTTTTGTAGCTTC
1 AATCTGCCCCTCTATAACTTTAGGGGTATAAGATTCGCTTTTGTAGCTTC
* * * * * *
5639 AATCTGCCCTTTTGTAATTTTAGGGGTATAAGATTTGCTTTTGTAGCTTT
1 AATCTGCCCCTCTATAACTTTAGGGGTATAAGATTCGCTTTTGTAGCTTC
5689 AATCTG
1 AATCTG
5695 TAGCTTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (50 bp):
AATCTGCCCCTCTATAACTTTAGGGGTATAAGATTCGCTTTTGTAGCTTC
Found at i:5698 original size:13 final size:13
Alignment explanation
Indices: 5680--5707 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5670 GATTTGCTTT
5680 TGTAGCTTTAATC
1 TGTAGCTTTAATC
5693 TGTAGCTTTAATC
1 TGTAGCTTTAATC
5706 TG
1 TG
5708 CCATTCTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (13 bp):
TGTAGCTTTAATC
Found at i:5729 original size:63 final size:63
Alignment explanation
Indices: 5630--5754 Score: 223
Period size: 63 Copynumber: 2.0 Consensus size: 63
5620 GATTCGCTTT
* *
5630 TGTAGCTTCAATCTGCCCTTTTGTAATTTTAGGGGTATAAGATTTGCTTTTGTAGCTTTAATC
1 TGTAGCTTCAATCTGCCATTCTGTAATTTTAGGGGTATAAGATTTGCTTTTGTAGCTTTAATC
*
5693 TGTAGCTTTAATCTGCCATTCTGTAATTTTAGGGGTATAAGATTTGCTTTTGTAGCTTTAAT
1 TGTAGCTTCAATCTGCCATTCTGTAATTTTAGGGGTATAAGATTTGCTTTTGTAGCTTTAAT
5755 TTATGTCTCT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (63 bp):
TGTAGCTTCAATCTGCCATTCTGTAATTTTAGGGGTATAAGATTTGCTTTTGTAGCTTTAATC
Found at i:5850 original size:40 final size:40
Alignment explanation
Indices: 5774--5948 Score: 167
Period size: 40 Copynumber: 4.4 Consensus size: 40
5764 TGTAACTTTA
* * * *
5774 GGGGTAAAAGATTGGATTGT-TTCAACCTGTCTCATGGTC
1 GGGGTAAAAGATTGGATTGTCTTCAATCTGCCCCATGGTT
* *
5813 GGGGTAAGAGATTGAATTGTCTTCAATCTGCCCCATGGTT
1 GGGGTAAAAGATTGGATTGTCTTCAATCTGCCCCATGGTT
* * * **
5853 GGAGTAAGAGATTGGATTGTCTTCAATTTGCCCTC-TAATT
1 GGGGTAAAAGATTGGATTGTCTTCAATCTGCCC-CATGGTT
* * *
5893 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAGTT
1 GGGGTAAAAGATTGGATTGTCTTCAATCTGCCC-CATGGTT
* *
5933 AGGGTAAGAGATTGGA
1 GGGGTAAAAGATTGGA
5949 GGTTGTAACT
Statistics
Matches: 116, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
39 18 0.16
40 97 0.84
41 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (40 bp):
GGGGTAAAAGATTGGATTGTCTTCAATCTGCCCCATGGTT
Found at i:6056 original size:50 final size:49
Alignment explanation
Indices: 6002--6129 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 49
5992 ATCCTTGTGA
6002 CTTCAATTTGCCCTTCTACAGCTTTAGGTGAATGAGATATGCCATTGCGG
1 CTTCAATTTGCCC-TCTACAGCTTTAGGTGAATGAGATATGCCATTGCGG
* * *
6052 CTTC-ATTCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCTTTGCGG
1 CTTCAATT-TG-CCCTCTACAGCTTTAGGTGAATGAGATATGCCATTGCGG
* * *
6102 TTTCAATCTGCACCTCTATAGCTTTAGG
1 CTTCAATTTGC-CCTCTACAGCTTTAGG
6130 GGTAAAAGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
49 4 0.06
50 59 0.87
51 5 0.07
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (49 bp):
CTTCAATTTGCCCTCTACAGCTTTAGGTGAATGAGATATGCCATTGCGG
Found at i:6140 original size:50 final size:50
Alignment explanation
Indices: 6002--6147 Score: 143
Period size: 50 Copynumber: 2.9 Consensus size: 50
5992 ATCCTTGTGA
* * * *
6002 CTTCAATTTGC-CCTTCTACAGCTTTAGGTG-AATGAGATATGCCATTGCGG
1 CTTCAATCTGCACC-TCTACAGCTTTAGGGGTAA-AAGATTTGCCATTGCGG
* * * ** *
6052 CTTCATTCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCTTTGCGG
1 CTTCAATCTGCACCTCTACAGCTTTAGGGGTAAAAGATTTGCCATTGCGG
* * *
6102 TTTCAATCTGCACCTCTATAGCTTTAGGGGTAAAAGATTTGTCATT
1 CTTCAATCTGCACCTCTACAGCTTTAGGGGTAAAAGATTTGCCATT
6148 CTATCGCCAT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
50 77 0.96
51 3 0.04
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (50 bp):
CTTCAATCTGCACCTCTACAGCTTTAGGGGTAAAAGATTTGCCATTGCGG
Done.