Origin IGS: tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgtttttttactatttatattatttgcaaagttactcattcataacaagaaaggcgaataaaacagcaagaaaacgcctcttgcggagcataaaaatgtcgcaagaggcgtgtttgaaaatca Mask Tandem Repeat Region ================================================ tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa Find is-nt database================================================ Query_seq: PI0268:PI0269|PI0268:PI0269:lysozyme-related protein:conserved hypothetical protein:->->:259851..259974 124 tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0268:PI0269|PI0268:PI0269:lysozyme-related protein:conserved hypothetical protein:->->:259851..259974 124 tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0268:PI0269|PI0268:PI0269:lysozyme-related protein:conserved hypothetical protein:->->:259851..259974 124 tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 2 End: 124 . I K L C A E Q S M K I S R L L R K R A T K N A K R T I F S Y S Q L Y Y L Y Y F F M tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -4.8 Tail_Score: -4.6971 Start: 38 End: 60 Full_Region: CGACATTTTTATGCT CCGCAAGAGG CGT TTTCTTGCTG TTTTATTCGCCTTTC .....................................CCGCAAGAGGCGTTTTCTTGCTG................................................................ Find igs database================================================ Query_seq: PI0268:PI0269|PI0268:PI0269:lysozyme-related protein:conserved hypothetical protein:->->:259851..259974 124 tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagtaaaaaaacaa Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: pint_PI0268_PI0269|lysozyme-related protein:conserved hypothetical protein|POSITIVE:POSITIVE|[259851,259974]|124 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagt.......... tgattttcaaacacgcctcttgcgacatttttatgctccgcaagaggcgttttcttgctgttttattcgcctttcttgttatgaatgagtaactttgcaaataatataaatagt.......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUCAAACACGCCUCUUGCGACAUUUUUAUGCUCCGCAAGAGGCGUUUUCUUGCUGUUUUAUUCGCCUUUCUUGUUAUGAAUGAGUAACUUUGCAAAUAAUAUAAAUAGU ............((((((((((((.(((....)))...))))))))))))....((((....(((((((...(((.......))))))))))....)))).............. (-30.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUUUAUAUUAUUUGCAAAGUUACUCAUUCAUAACAAGAAAGGCGAAUAAAACAGCAAGAAAACGCCUCUUGCGGAGCAUAAAAAUGUCGCAAGAGGCGUGUUUGAAAAUCA ..........((((((((...((((........)))).......)))))))).....((((...((((((((((((..((((....)))))))))))))))).))))....... (-33.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 60 11 103 42 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 349 60 13 152 106 pint:PI0213|5end_conserved_hypothetical_protein_207065..207295_POSITIVE 343 78 34 176 131 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 339 60 15 96 50 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 338 60 14 73 12 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 336 80 34 105 36 pint:PI2137|5end_RNA_methylase_SpoU_family_2083173..2083403_POSITIVE 334 58 14 199 141 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 317 59 12 176 118 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 315 78 33 61 18 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 309 58 15 74 30 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 302 70 33 222 181 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 296 79 34 206 150 pint:PI1488|5end_hypothetical_protein_1406994..1407224_POSITIVE 296 48 1 157 94 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 296 50 19 206 173 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 295 60 14 188 140 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 294 60 15 197 156 pint:PI2104|5end_carboxyl-terminal_protease_2057910..2058140_POSITIVE 291 58 11 200 140 pint:PI1630|5end_hypothetical_protein_1552127..1552357_POSITIVE 291 74 31 171 127 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 290 60 15 166 126 pint:PI1223|5end_conserved_hypothetical_protein_1143537..1143767_POSITIVE 290 58 12 89 29 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 448 50 13 78 41 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 369 60 11 119 58 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 336 80 34 105 36 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 323 57 13 60 18 pint:PI0927|3end_transglutaminase-related_protein_859696..859846_POSITIVE 317 59 12 74 16 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 315 78 33 61 18 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 308 60 17 53 1 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 307 60 11 131 78 pint:PI0962|3end_phosphoglycerate_mutase_892702..892852_POSITIVE 299 59 11 87 40 pint:PI1424|3end_probable_peptidase_family_M48_1344044..1344194_POSITIVE 298 58 14 109 61 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 294 60 15 141 100 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 293 71 34 97 57 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE 291 48 13 46 1 pint:PI0529|3end_hypothetical_protein_483741..483891_POSITIVE 290 58 12 98 38 pint:PI0300|3end_transposase_285761..285911_POSITIVE 289 79 36 66 15 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 287 80 33 62 2 pint:PI0501|3end_excisionase_461863..462013_POSITIVE 287 60 13 66 17 pint:PI0363|3end_hypothetical_protein_333760..333910_POSITIVE 285 50 10 55 22 pint:PI1338|3end_phosphoserine_phosphatase_1256594..1256744_POSITIVE 280 77 35 149 108 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 279 70 22 132 81 pint:PI0700|3end_UDP-glucose_4-epimerase_638413..638563_POSITIVE