Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013788.1 Kokia drynarioides strain JFW-HI SEQ_128816, 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: 248684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 75 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:241362 original size:28 final size:29
Alignment explanation
Indices: 241224--241362 Score: 119
Period size: 28 Copynumber: 4.8 Consensus size: 29
241214 TTTTGGATAC
* *
241224 TCGGGGGTAAAATGGTAATTTTGGACA-C
1 TCGGGGGTAAAATGGTAATTTTGGAAAGT
*
241252 TCGAGGGTAAAATGGTAATTTTGGGAAAGT
1 TCGGGGGTAAAATGGTAATTTT-GGAAAGT
*
241282 TC-GGGGTAAAAAT-GTAATTTTTGGAAAAT
1 TCGGGGGT-AAAATGGTAA-TTTTGGAAAGT
* *
241311 ATC-AGGGTCAAAAAT-GAAATTTTTGG-AAGT
1 -TCGGGGGT--AAAATGGTAA-TTTTGGAAAGT
241341 TCGGGGGTAAAATGGTAATTTT
1 TCGGGGGTAAAATGGTAATTTT
241363 TAGAAAAATA
Statistics
Matches: 93, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
28 30 0.32
29 23 0.25
30 24 0.26
31 16 0.17
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.32
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTGGAAAGT
Found at i:241761 original size:13 final size:13
Alignment explanation
Indices: 241743--241768 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
241733 ACCCCGATCT
241743 TTTCTTTCTAAAA
1 TTTCTTTCTAAAA
241756 TTTCTTTCTAAAA
1 TTTCTTTCTAAAA
241769 GGTTTTTTAG
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:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTCTTTCTAAAA
Found at i:241879 original size:7 final size:7
Alignment explanation
Indices: 241867--241896 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
241857 AAGGTTTAAG
241867 TTTGATT
1 TTTGATT
241874 TTTGATT
1 TTTGATT
241881 TTTGATT
1 TTTGATT
*
241888 TTCGATT
1 TTTGATT
241895 TT
1 TT
241897 ATTTTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.03, G:0.13, T:0.70
Consensus pattern (7 bp):
TTTGATT
Found at i:242086 original size:3 final size:3
Alignment explanation
Indices: 242074--242149 Score: 59
Period size: 3 Copynumber: 25.7 Consensus size: 3
242064 ATTTATTAAA
* * *
242074 TAT T-T TAT TAT TAT TAT TAT TA- AAT TCAT TAT TAC TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* * *
242118 TAA TAT TAT TAT T-T TAGT TAA TAT CAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
242150 ATGATAGTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
2 5 0.09
3 45 0.80
4 6 0.11
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:242105 original size:24 final size:22
Alignment explanation
Indices: 242057--242133 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 22
242047 TGTTTTCTTT
*
242057 TTATTTTATTTATTAAATATTTTA
1 TTATTTTA-TTATTAAAT-TATTA
242081 TTATTATTATTATTAAATTCATTA
1 TTATT-TTATTATTAAATT-ATTA
*
242105 TTACTGTTATTATT-AA-TATTA
1 TTA-TTTTATTATTAAATTATTA
242126 TTATTTTA
1 TTATTTTA
242134 GTTAATATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.09
21 7 0.15
22 1 0.02
23 3 0.06
24 28 0.60
25 4 0.09
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (22 bp):
TTATTTTATTATTAAATTATTA
Found at i:242116 original size:12 final size:12
Alignment explanation
Indices: 242066--242130 Score: 71
Period size: 12 Copynumber: 5.4 Consensus size: 12
242056 TTTATTTTAT
242066 TTATTAAATATT-
1 TTATT-AATATTA
*
242078 TTATTATTATTA
1 TTATTAATATTA
242090 TTATTAA-ATTCA
1 TTATTAATATT-A
* *
242102 TTATTACTGTTA
1 TTATTAATATTA
242114 TTATTAATATTA
1 TTATTAATATTA
242126 TTATT
1 TTATT
242131 TTAGTTAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 8 0.18
12 34 0.77
13 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:242137 original size:24 final size:25
Alignment explanation
Indices: 242066--242137 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 25
242056 TTTATTTTAT
242066 TTATTAAATATT-TTATTATTA-TTA
1 TTATT-AATATTATTATTATTAGTTA
*
242090 TTATTAA-ATTCATTATTACT-GTTA
1 TTATTAATATT-ATTATTATTAGTTA
242114 TTATTAATATTATTATT-TTAGTTA
1 TTATTAATATTATTATTATTAGTTA
242138 ATATCATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 32 0.78
25 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (25 bp):
TTATTAATATTATTATTATTAGTTA
Found at i:242846 original size:6 final size:6
Alignment explanation
Indices: 242837--242901 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
242827 AAGTTTTAAA
* * **
242837 TAAATT TAAATT TAAA-G CAAATT TAAATT TAAGAAGA TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT T-A-AATT TAAATT TAAATT
**
242886 TAAAAA TAAATT TAAA
1 TAAATT TAAATT TAAA
242902 CCAATTTAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
5 3 0.07
6 36 0.82
7 2 0.05
8 3 0.07
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (6 bp):
TAAATT
Done.