Origin IGS: atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtacttgaaggagttcgacagttatgtcttaaccactcctaaacggcagtacaaagatactgcaaatacttttatttccattcttttttatgttataaaatatttttccttcgtttttcacttttaaaacagcgtaaacttaaaaacccctattggtttttcgctgtttattaacatgatttattattgcgctgaaattatttcgatgttttccaatggataatattttatttctttgtatatttgcatacataaaacaaactaatagttttaaaaaggaaaaaatcaagat Mask Tandem Repeat Region ================================================ atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca Find is-nt database================================================ Query_seq: PI0306:PI0307|PI0306:PI0307:conserved hypothetical protein:RNA polymerase sigma-70 factor, ECF subfamily:->->:289889..290181 293 atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0306:PI0307|PI0306:PI0307:conserved hypothetical protein:RNA polymerase sigma-70 factor, ECF subfamily:->->:289889..290181 293 atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0306:PI0307|PI0306:PI0307:conserved hypothetical protein:RNA polymerase sigma-70 factor, ECF subfamily:->->:289889..290181 293 atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 1 End: 150 M L I F S F L K L L V C F M Y A N I Q R N K I L S I G K H R N N F S A I I N H V N K Q R K T N R G F ............................................................................................................................................... Protein_Len: 30 Strand: + Start: 172 End: 261 ........................................................................................................................................................................... M K N E G K I F Y N I K K N G N K S I C S I F V L P F R S G ................................ Protein_Len: 40 Strand: - Start: 169 End: 288 ........................................................................................................................................................................ F H F V F S F Y K I V Y F L I S I F T N A T D K Y Q R K P T T L V Y S D F E K M ..... Protein_Len: 36 Strand: - Start: 3 End: 110 .. K I K E K K F S N T Q K I Y A F I C L F L I N D M P F C R F L K L A I M ....................................................................................................................................................................................... atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca 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================================================ atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0306:PI0307|PI0306:PI0307:conserved hypothetical protein:RNA polymerase sigma-70 factor, ECF subfamily:->->:289889..290181 293 atcttgattttttcctttttaaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaataggggtttttaagtttacgctgttttaaaagtgaaaaacgaaggaaaaatattttataacataaaaaagaatggaaataaaagtatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca Intra-Species Hit: Count: 1 Min: 21 Max: 293 Len: 273 Subject: pint_PI0306_PI0307|conserved hypothetical protein:RNA polymerase sigma-70 factor, ECF subfamily|POSITIVE:POSITIVE|[289889,290181]|293 HSP 1 e-value: 2.0E-65 bit: 250.0 Len: 126 Query Start:21 Query End:146 Subject Strand: POSITIVE Subject Start: 21 Subject End: 146 ....................aaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaatagggg................................................................................................................................................... ....................aaaactattagtttgttttatgtatgcaaatatacaaagaaataaaatattatccattggaaaacatcgaaataatttcagcgcaataataaatcatgttaataaacagcgaaaaaccaatagggg................................................................................................................................................... HSP 2 e-value: 2.0E-31 bit: 137.0 Len: 69 Query Start:225 Query End:293 Subject Strand: POSITIVE Subject Start: 225 Subject End: 293 ................................................................................................................................................................................................................................tatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca ................................................................................................................................................................................................................................tatttgcagtatctttgtactgccgtttaggagtggttaagacataactgtcgaactccttcaagtaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUAUUAGUUUGUUUUAUGUAUGCAAAUAUACAAAGAAAUAAAAUAUUAUCCAUUGGAAAACAUCGAAAUAAUUUCAGCGCAAUAAUAAAUCAUGUUAAUAAACAGCGAAAAACCAAUAGGGGUUUUUAAGUUUACGCUGUUUUAAAAGUGAAAAACGAAGGAAAAAUAUUUUAUAACAUAAAAAAGAAUGGAAAUAAAAGUAUUUGCAGUAUCUUUGUACUGCCGUUUAGGAGUGGUUAAGACAUAACUGUCGAACUCCUUCAAGUACA ....(((((..(((((....((((((....)))))).....((((((((((.(((.(((.........(((.....)))..............((((......(((((((((((((((......))))))).......)))))))).....))))....))).)))..))))))))))...)))))....)))))........(((((((((((((....))))))).....((((((......((((....))))..))))))..)))))). (-56.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUACUUGAAGGAGUUCGACAGUUAUGUCUUAACCACUCCUAAACGGCAGUACAAAGAUACUGCAAAUACUUUUAUUUCCAUUCUUUUUUAUGUUAUAAAAUAUUUUUCCUUCGUUUUUCACUUUUAAAACAGCGUAAACUUAAAAACCCCUAUUGGUUUUUCGCUGUUUAUUAACAUGAUUUAUUAUUGCGCUGAAAUUAUUUCGAUGUUUUCCAAUGGAUAAUAUUUUAUUUCUUUGUAUAUUUGCAUACAUAAAACAAACUAAUAGUUUU .(((.....((((((..((((....))))......)))))).....((((((......))))))...)))................((((((((.((((((((((..(((....................((((((((.....((((((......))))))(((.((((....))))))).......))))))))..........((.....))....))).)))))))))).....((((....)))).))))))))............... (-48.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 239 193 205 161 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 340 240 193 173 124 pint:PI1165|5end_hypothetical_protein_1089389..1089619_POSITIVE 340 240 193 89 40 pint:PI1166|5end_hypothetical_protein_1089305..1089535_POSITIVE 294 239 193 99 45 pint:PI0761|5end_hypothetical_protein_696173..696403_POSITIVE 277 248 210 223 177 pint:PI0018|5end_hypothetical_protein_23022..23252_POSITIVE 274 240 193 56 6 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 268 264 226 58 6 pint:PI1066|5end_dihydrofolate_reductase_983427..983657_POSITIVE 264 267 221 112 64 pint:PI0353|5end_hypothetical_protein_324610..324840_POSITIVE 263 269 226 47 7 pint:PI0224|5end_conserved_hypothetical_protein_220541..220771_POSITIVE 254 231 210 226 204 pint:PI1887|5end_cell_division_protein_1829115..1829345_POSITIVE 252 261 224 57 24 pint:PI0562|5end_conserved_hypothetical_protein_509096..509326_POSITIVE 250 242 204 137 88 pint:PI1213|5end_phosphoribosylformylglycinamidine_cyclo-ligase_(AIR_synthase)_1131597..1131827_POSITIVE 248 133 93 119 80 pint:PI1065|5end_hypothetical_protein_983382..983612_POSITIVE 245 257 214 115 68 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 239 230 186 187 140 pint:PI0404|5end_integrase_371295..371525_POSITIVE 238 87 51 186 145 pint:PI0518|5end_5'-nucleotidase_precursor_477076..477306_POSITIVE 237 269 227 216 162 pint:PI0373|5end_hypothetical_protein_344293..344523_POSITIVE 236 230 186 160 100 pint:PI1722|5end_possible_peptidyl-prolyl_cis-trans_isomerase_1639536..1639766_POSITIVE 236 257 212 52 11 pint:PI0221|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_212356..212586_POSITIVE 233 241 210 230 198 pint:PI2038|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1990463..1990693_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 239 203 123 87 pint:PI1995|3end_hypothetical_protein_1950212..1950362_POSITIVE 285 264 225 121 79 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 282 257 211 111 50 pint:PI1941|3end_outer_membrane_receptor;_ragA_protein_1900619..1900769_POSITIVE 274 240 193 53 3 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 271 242 209 138 104 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE 264 267 222 45 3 pint:PI0218|3end_conserved_hypothetical_protein_211149..211299_POSITIVE 263 238 206 81 49 pint:PI0149|3end_conserved_hypothetical_protein_143237..143387_POSITIVE 262 224 204 67 47 pint:PI1678|3end_conserved_hypothetical_protein_1594320..1594470_POSITIVE 256 142 115 71 44 pint:PI0754|3end_possible_outer_membrane_receptor_686424..686574_POSITIVE 254 259 222 133 89 pint:PI0240|3end_conserved_hypothetical_protein_239342..239492_POSITIVE 246 246 210 61 16 pint:PI1758|3end_hypothetical_protein_1684057..1684207_POSITIVE 245 257 214 131 84 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 244 246 210 59 24 pint:PI2037|3end_TIM-barrel_protein,_NifR3_family_1990369..1990519_POSITIVE 240 265 225 40 2 pint:PI1729|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1649935..1650085_POSITIVE 238 87 51 114 73 pint:PI0517|3end_apparent_PorT_homolog_477084..477234_POSITIVE 236 230 186 140 80 pint:PI1721|3end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_1639596..1639746_POSITIVE 235 242 207 108 61 pint:PI2072|3end_possible_ISmav2-related_transposase_2031470..2031620_POSITIVE 233 169 123 59 17 pint:PI2031|3end_hypothetical_protein_1986621..1986771_POSITIVE 231 238 192 126 72 pint:PI2077|3end_hypothetical_protein_2036070..2036220_POSITIVE 231 85 47 142 101 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE