Origin IGS: aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatatcatatttgcgaacaagatagcattgtctgaaaggtctgatgggtcagacttgcccgacaatgctattttctttttatccatctcttcctttacaacaattcgatt Mask Tandem Repeat Region ================================================ aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta Find is-nt database================================================ Query_seq: PI2085:PI2086|PI2085:PI2086:conserved hypothetical protein:signal peptidase I:->->:2041864..2041974 111 aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2085:PI2086|PI2085:PI2086:conserved hypothetical protein:signal peptidase I:->->:2041864..2041974 111 aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2085:PI2086|PI2085:PI2086:conserved hypothetical protein:signal peptidase I:->->:2041864..2041974 111 aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 7 End: 111 ...... M V V K E E M D K K K I A L S G K S D P S D L S D N A I L F A N M I L Protein_Len: 35 Strand: - Start: 3 End: 107 .. R I T T F S S I S L F F I A N D P L D S G D S R E S L A I K N A F I M .... aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta 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================================================ aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.6 Tail_Score: -5.35224 Start: 41 End: 88 Full_Region: tatttgcgaacaaga tagcattgtctgaaaggtctga tggg tcagacttgcccgacaatgcta ttttctttttatcca ........................................tagcattgtctgaaaggtctgatgggtcagacttgcccgacaatgcta....................... Find igs database================================================ Query_seq: PI2085:PI2086|PI2085:PI2086:conserved hypothetical protein:signal peptidase I:->->:2041864..2041974 111 aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: pint_PI2085_PI2086|conserved hypothetical protein:signal peptidase I|POSITIVE:POSITIVE|[2041864,2041974]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta aatcgaattgttgtaaaggaagagatggataaaaagaaaatagcattgtcgggcaagtctgacccatcagacctttcagacaatgctatcttgttcgcaaatatgatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGAAUUGUUGUAAAGGAAGAGAUGGAUAAAAAGAAAAUAGCAUUGUCGGGCAAGUCUGACCCAUCAGACCUUUCAGACAAUGCUAUCUUGUUCGCAAAUAUGAUAUUA .((((.....((((...(((.((((...............((((((((((.((...((((((....))))))...)).)))))))))))))).)))))))...)))).... (-25.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUCAUAUUUGCGAACAAGAUAGCAUUGUCUGAAAGGUCUGAUGGGUCAGACUUGCCCGACAAUGCUAUUUUCUUUUUAUCCAUCUCUUCCUUUACAACAAUUCGAUU ...............(((.((((((((((((((.(..((((((((....))))))))..).)))))))))))))).)))................................ (-29.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 76 32 99 54 pint:PI1725|5end_hypothetical_protein_1643024..1643254_POSITIVE 290 97 52 188 128 pint:PI0433|5end_hypothetical_protein_404724..404954_POSITIVE 281 86 42 117 59 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 278 68 22 202 158 pint:PI1510|5end_cell_division_protein_1428412..1428642_POSITIVE 276 68 24 117 60 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 271 99 55 217 172 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 269 60 17 214 169 pint:PI1898|5end_S-adenosyl-methyltransferase_1841288..1841518_POSITIVE 267 84 41 198 164 pint:PI1670|5end_hypothetical_protein_1583725..1583955_POSITIVE 262 98 53 206 158 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 261 82 44 213 155 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 260 87 44 227 188 pint:PI0878|5end_hypothetical_protein_812762..812992_POSITIVE 259 69 23 208 166 pint:PI1200|5end_carbon-nitrogen_hydrolase/beta-alanine_synthase_1115662..1115892_POSITIVE 257 87 43 161 109 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 255 86 45 191 145 pint:PI1785|5end_conserved_hypothetical_protein_1717122..1717352_POSITIVE 255 77 47 132 99 pint:PI1332|5end_aminotransferase,_possible_pyridoxal-phosphate-dependent_aminotransferase_1249374..1249604_POSITIVE 255 99 51 132 72 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 254 98 51 213 156 pint:PI0275|5end_hypothetical_protein_263138..263368_POSITIVE 253 68 21 230 188 pint:PI0942|5end_DNA-binding_protein_HU_874624..874854_POSITIVE 253 68 21 49 7 pint:PI0941|5end_hypothetical_protein_874443..874673_POSITIVE 252 85 42 53 4 pint:PI1736|5end_topoisomerase_IV,_subunit_A_1654254..1654484_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 89 41 51 3 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 280 88 43 70 37 pint:PI0316|3end_conserved_hypothetical_protein_299082..299232_POSITIVE 278 68 22 132 88 pint:PI1509|3end_conserved_hypothetical_protein_1428422..1428572_POSITIVE 270 90 47 104 49 pint:PI1265|3end_hypothetical_protein_1185512..1185662_POSITIVE 269 60 17 81 36 pint:PI1897|3end_conserved_hypothetical_protein_1841235..1841385_POSITIVE 266 97 52 69 25 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 264 85 45 93 54 pint:PI0879|3end_hypothetical_protein_814051..814201_POSITIVE 259 60 17 143 90 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 255 77 47 141 108 pint:PI1331|3end_conserved_hypothetical_protein_1249463..1249613_POSITIVE 252 71 40 44 3 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 251 99 51 122 70 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE 251 80 40 91 40 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 250 98 51 103 54 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 246 73 39 121 92 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 246 76 43 36 3 pint:PI0096|3end_glycerol-3-phosphate_cytidylyltransferase_93305..93455_POSITIVE 245 87 43 95 53 pint:PI0225|3end_conserved_hypothetical_protein_222759..222909_POSITIVE 244 89 46 87 54 pint:PI2072|3end_possible_ISmav2-related_transposase_2031470..2031620_POSITIVE 244 67 21 125 78 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 242 86 42 145 100 pint:PI1568|3end_OmpA_family_protein_1491043..1491193_POSITIVE 238 54 13 148 110 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE