Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008471.1 Kokia drynarioides strain JFW-HI SEQ_123146, 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: 6841
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Found at i:1826 original size:16 final size:17
Alignment explanation
Indices: 1805--1842 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1795 TGGAATTCAA
*
1805 TTTTTTATGAT-TTAAT
1 TTTTTTATAATATTAAT
1821 TTTTTTATAATATTAAT
1 TTTTTTATAATATTAAT
1838 TTTTT
1 TTTTT
1843 ATTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTTATAATATTAAT
Found at i:1843 original size:16 final size:15
Alignment explanation
Indices: 1798--1844 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
1788 ATGACACTGG
*
1798 AATTCAATTTTTTAT
1 AATTTAATTTTTTAT
*
1813 GATTTAATTTTTTTAT
1 AATTTAA-TTTTTTAT
1829 AATATTAATTTTTTAT
1 AAT-TTAATTTTTTAT
1845 TTTTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 5 0.19
16 18 0.67
17 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (15 bp):
AATTTAATTTTTTAT
Found at i:2844 original size:142 final size:140
Alignment explanation
Indices: 2650--2973 Score: 343
Period size: 142 Copynumber: 2.3 Consensus size: 140
2640 AGTTTTTTTG
** * * * * **
2650 TTAGATGGTTAGATAGCTGCAATTACATCCTTGGGTCTTAGGTTCAATTCATCTCCTACTCATGT
1 TTAGATGGTTAGATAATTGCAATTACATCCTTGAGTCTAAGGTTCAATTCATCTACTAATCACAT
* * * * *
2715 TTGTATTTTTTATTTCATATTGTTTTAAGCTTTTAAAATTATATATTTAA-TATTCTTTTTTAAA
66 TTGTATTTTTTATTTCACATTGCTTCAAGCTTTT----TT-TATATTTAATTAATATTTTTTAAA
2779 T-TTA-ATTCTTTCA
126 TATTACATTCTTTCA
* * * *
2792 TTAGATGGTTAGATAATTGTAATTACATCCTTGAGTCTCAAGTTTGAA-TCATCTACTAATCGCA
1 TTAGATGGTTAGATAATTGCAATTACATCCTTGAGTCT-AAGGTTCAATTCATCTACTAATCACA
* * *
2856 TTTGTATTTTTTATTTCACGTTGCTTCAAGCTTTTTTTATTTTTAATTAATATTTTTTACATATT
65 TTTGTATTTTTTATTTCACATTGCTTCAAGCTTTTTTTATATTTAATTAATATTTTTTAAATATT
*
2921 ACCTTCTTTCA
130 ACATTCTTTCA
* * *
2932 TTAGATGATTAGATAATTGCAATTATAT-CTTGAGTCTGAGGT
1 TTAGATGGTTAGATAATTGCAATTACATCCTTGAGTCTAAGGT
2974 AGCATTATTT
Statistics
Matches: 152, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
137 8 0.05
138 17 0.11
139 12 0.08
140 33 0.22
142 76 0.50
143 6 0.04
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.49
Consensus pattern (140 bp):
TTAGATGGTTAGATAATTGCAATTACATCCTTGAGTCTAAGGTTCAATTCATCTACTAATCACAT
TTGTATTTTTTATTTCACATTGCTTCAAGCTTTTTTTATATTTAATTAATATTTTTTAAATATTA
CATTCTTTCA
Found at i:3083 original size:40 final size:37
Alignment explanation
Indices: 3024--3108 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 37
3014 TATTATTTCA
*
3024 AATT-TTTTTATTTTCAATTAATGTTTTGATGATATTTTT
1 AATTATTTTCATTTTCAATTAATGTTTT--T-ATATTTTT
* *
3063 AATTATTTTCATTTTTAATTAATGTTTTTTTATTTTT
1 AATTATTTTCATTTTCAATTAATGTTTTTATATTTTT
3100 AATTATTTT
1 AATTATTTT
3109 ATAAGCATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 16 0.38
38 1 0.02
39 4 0.10
40 21 0.50
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (37 bp):
AATTATTTTCATTTTCAATTAATGTTTTTATATTTTT
Found at i:3097 original size:21 final size:21
Alignment explanation
Indices: 3026--3104 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
3016 TTATTTCAAA
*
3026 TTTTTTTATTTTCAATTAATG
1 TTTTTTTATTTTTAATTAATG
* * *
3047 TTTTGATGATATTT--TTAAT-
1 TTTT-TTTATTTTTAATTAATG
* *
3066 TATTTTCATTTTTAATTAATG
1 TTTTTTTATTTTTAATTAATG
3087 TTTTTTTATTTTTAATTA
1 TTTTTTTATTTTTAATTA
3105 TTTTATAAGC
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
18 6 0.14
19 3 0.07
20 10 0.23
21 20 0.45
22 5 0.11
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTTTTATTTTTAATTAATG
Found at i:3108 original size:16 final size:16
Alignment explanation
Indices: 3056--3108 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
3046 GTTTTGATGA
3056 TATTTTTAATTATTTT
1 TATTTTTAATTATTTT
*
3072 CATTTTTAATTAATGTTTTTT
1 TATTTTTAATT-A----TTTT
3093 TATTTTTAATTATTTT
1 TATTTTTAATTATTTT
3109 ATAAGCATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
16 14 0.47
17 1 0.03
20 1 0.03
21 14 0.47
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (16 bp):
TATTTTTAATTATTTT
Done.