piRNA cluster 150

Predicted piRNA cluster no. 150 previous next

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================================= proTRAC ====================================
VERSION: .......... 2.4.4
LAST MODIFIED: .... 10. August 2019

Please cite:
Rosenkranz D, Zischler H. proTRAC - a software for probabilistic piRNA cluster
detection, visualization and analysis. 2012. BMC Bioinformatics 13:5.


Contact:
David Rosenkranz
Institute of Organismic and Molecular Evolutionary Biology
Dept. Anthropology, small RNA group
Johannes Gutenberg University Mainz
email: rosenkranz@uni-mainz.de

You can find the latest proTRAC version at:
http://sourceforge.net/projects/protrac/files
http://www.smallRNAgroup.uni-mainz.de
==============================================================================

PARAMETERS:
Map file: ...............PiRNAClusterAlignFemales/Curicó_X_Con.map.weighted-10000-1000-b-0
Genome file: ............ReferenceGenome//DsubobscuraReferenceGenome_1.fasta
RepeatMasker annotation: ReferenceGenome//DsubobscuraReferenceGenome.fasta.out
GeneSet:.................ReferenceGenome//Transcripts_ParentGene_HSP_NoTEs_Ensemble.gtf

Significant (p<=0.05) hit density will be calculated based
on observed hit distribution.

Sliding window size: ........................................ 5000 bp
Sliding window increament: .................................. 1000 bp
Normalize each hit by number of genomic hits: ............... yes
Normalize each hit by number of sequence reads: ............. yes
Normalize values (-> per million mapped reads): ............. yes
Min. fraction of hits with 1T(U) or 10A: .................... 0.3
Alternatively: Min. fraction of hits with 1T(U) and 10A: .... 0.5
Min. fraction of hits with typical piRNA length: ............ 0.75
Typical piRNA length: ....................................... 23-32 nt
Min. size of a piRNA cluster: ............................... 5000 bp.
Min. number of hits (absolute): ............................. 0
Min. number of hits (normalized): ........................... 0
Min. fraction of hits on the mainstrand: .................... 0.5
Top fraction of mapped sequences (in terms of read counts): . 5%
Top fraction accounts for max. n% of sequence reads: ........ 90%
Max. percentage of reads within any x bp sliding window: .... 50%
Size of sliding window with max x % of reads (see above): ... 1000 bp
Min. fraction of hits on each arm of a bidirectional cluster: 0.05
Output html file for each cluster: .......................... yes
Output a summary table: ..................................... yes
Output a FASTA file for each cluster (piRNA sequences): ..... yes
Output a FASTA file comprising cluster sequences: ........... yes
Output a GTF file for predicted piRNA clusters: ..............yes
Search DNA motifs in clusters: .............................. yes
Output flanking sequences: +/- .............................. 0 bp
Output ~.pTi file: .......................................... no
==============================================================================


Genome size (without gaps): ............ 126436220 bp
Gaps (N/X/-): .......................... 152 bp
Mapped reads: .......................... 24908081
Non-identical sequences: ............... 1270140
Genomic hits: .......................... 8891180
Significant densitiy of mapped reads: .. 284.883293433879 reads/kb

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1 hit

2-5 hits

6-10 hits

11-20 hits

21-50 hits

51-100 hits

> 100 hits

ChrU_v4

3044051

3053975

Gene Set

RepeatMasker

Mapped
Reads

13.73

plus strand

minus strand

13.73

RepeatMasker Color Code

100-98% Identity

<98-95% Identity

<95-90% Identity

<90-85% Identity

<85-80% Identity

<80-75% Identity

<75-70% Identity

<70% Identity

Gene Set Color Code

Gene

Pseudogene

Other

Topology/Coverage Color Code

Coverage Plus Strand

Coverage Minus Strand

Mainstrand: Plus

Mainstrand: Minus

Complementary Strand

Flanking Region
(if option -flank >0)

Gene Set Annotation

RepeatMasker Annotation

1. GYPSY-20_Dsub: 3044040-3044340 (-), Divergence to consensus: 0.3%
2. TE-576_Dsub: 3044337-3045964 (-), Divergence to consensus: 0%
3. GYPSY-20_Dsub: 3045965-3046103 (-), Divergence to consensus: 0.7%
4. TE-621_Dsub: 3046104-3052840 (-), Divergence to consensus: 0.4%
5. TE-576_Dsub: 3052804-3052840 (-), Divergence to consensus: 0%
6. GYPSY-20_Dsub: 3052841-3053276 (-), Divergence to consensus: 0.2%
7. TE-626_Dsub: 3053277-3054253 (-), Divergence to consensus: 19%

Transcription Factor Binding Sites

FOXP1 (Sequence: TGTTTAC (-): 3047810)
FOXP1 (Sequence: TGTTTAC (-): 3049723)
FIGLA (Sequence: TACAGGTGTA (-): 3047194)
Lhx8 (Sequence: TTAATTAA (-): 3046216)
Lhx8 (Sequence: TTAATTAA (-): 3049380)
Rhox11 (Sequence: TGCTGTTAT (+): 3050205)
Rhox11 (Sequence: CGCTGTTAT (+): 3050755)
FOXP1 (Sequence: GTAAACA (+): 3047384)
POU5F1 (Sequence: ATGCAAA (+): 3053361)
POU5F1 (Sequence: ATGCAAA (+): 3053840)
FOXO3_mmu (Sequence: TGTTTTCC (-): 3048047)
FOXO3_mmu (Sequence: TGTTTTCC (-): 3049920)
FOXO3_mmu (Sequence: TGTTTTCA (-): 3053542)
Nobox (Sequence: TAATTGCC (+): 3048078)
Nobox (Sequence: TAATTGGT (+): 3049385)
Nobox (Sequence: TAATTACC (+): 3050138)
RHOXF1 (Sequence: GGATCA (-): 3044271)
RHOXF1 (Sequence: AGCTTA (-): 3044637)
RHOXF1 (Sequence: AGATTA (-): 3047109)
RHOXF1 (Sequence: AGATCA (-): 3049650)
RHOXF1 (Sequence: AGCTTA (-): 3051730)
RHOXF1 (Sequence: GGCTTA (-): 3051931)
RHOXF1 (Sequence: GGCTCA (-): 3052547)
RHOXF1 (Sequence: GGATTA (-): 3052732)
RHOXF1 (Sequence: GGATCA (-): 3053072)
FOXO3_mmu (Sequence: TGTAAACA (+): 3047383)
FOXO3_mmu (Sequence: GGAAAACA (+): 3053744)
Sox5 (Sequence: ATTGTT (+): 3045048)
Sox5 (Sequence: ATTGTT (+): 3046430)
Sox5 (Sequence: ATTGTT (+): 3047210)
Sox5 (Sequence: ATTGTT (+): 3047843)
Sox5 (Sequence: ATTGTT (+): 3049562)
Sox5 (Sequence: ATTGTT (+): 3049610)
Sox5 (Sequence: ATTGTT (+): 3049937)
Sox5 (Sequence: ATTGTT (+): 3050059)
Sox5 (Sequence: ATTGTT (+): 3050173)
Sox5 (Sequence: ATTGTT (+): 3050645)
Sox5 (Sequence: ATTGTT (+): 3053879)
FOXO1 (Sequence: GAAAACAAC (-): 3053745)
POU2F1 (Sequence: ATTTACATA (-): 3046941)
POU2F1 (Sequence: ATTTGCATA (-): 3053588)
SOX9 (Sequence: TTATTGTT (+): 3047208)
SOX9 (Sequence: TTATTGTT (+): 3050057)
SOX9 (Sequence: TTATTGTT (+): 3050643)
POU5F1 (Sequence: TTTGCAT (-): 3052170)
POU5F1 (Sequence: TTTGCAT (-): 3053589)
RFX4_1 (Sequence: CTTGGCAAC (+): 3053791)
RHOXF1 (Sequence: TGATCT (+): 3044112)
RHOXF1 (Sequence: TGATCT (+): 3045159)
RHOXF1 (Sequence: TAAGCT (+): 3045665)
RHOXF1 (Sequence: TAAGCT (+): 3046622)
RHOXF1 (Sequence: TAATCT (+): 3046658)
RHOXF1 (Sequence: TGATCT (+): 3047143)
RHOXF1 (Sequence: TGAGCT (+): 3047983)
RHOXF1 (Sequence: TGATCT (+): 3048145)
RHOXF1 (Sequence: TAATCT (+): 3048358)
RHOXF1 (Sequence: TGAGCC (+): 3048781)
RHOXF1 (Sequence: TGATCC (+): 3048893)
RHOXF1 (Sequence: TGAGCT (+): 3049288)
RHOXF1 (Sequence: TGAGCT (+): 3049293)
RHOXF1 (Sequence: TGATCT (+): 3049538)
RHOXF1 (Sequence: TAAGCT (+): 3050273)
RHOXF1 (Sequence: TGATCC (+): 3050677)
RHOXF1 (Sequence: TAATCT (+): 3050685)
RHOXF1 (Sequence: TGATCT (+): 3050915)
RHOXF1 (Sequence: TGATCT (+): 3052913)
RHOXF1 (Sequence: TAAGCC (+): 3053464)
RHOXF1 (Sequence: TAATCT (+): 3053867)
RHOXF1 (Sequence: TAAGCT (+): 3053909)
RFX4_2 (Sequence: GTAACCACG (-): 3050218)
Gata4 (Sequence: AGATAAC (-): 3053855)
FOXO3_hsa (Sequence: TTGTTTAC (-): 3049722)
Gata4 (Sequence: CTTATCT (+): 3046525)
Sox5 (Sequence: AACAAT (-): 3051771)

Location	ChrU_v4
Coordinates	3044051-3053975
Size [bp]	9925
Sequence hit loci	16041
Mapped reads (normalized)	3467.4
Mapped reads (normalized) per kb	349.4
Normalized reads with 1T (1U)	89.6%
Normalized reads with 10A	29.3%
Normalized reads with length 23-32 nt	100%
Normalized reads on the main strand(s)	99.7%
Predicted directionality	mono:plus