Origin IGS: cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta .........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 taacaaaaaacgaaactcggtgtggctccaacagccattccccacaatcctaagggcgggtgtctttcccccgttagcatttcccaacgctgctaaagcgaacggaaagagtaagaccaccgcaagaacaaacttgttgcggtggtcttttttcatttatcctaataaggattaaaactgatatattatg Mask Tandem Repeat Region ================================================ cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta Find is-nt database================================================ Query_seq: PI0121:PI0122|PI0121:PI0122:outer membrane protein, ompH family:outer membrane protein, ompH family:->->:113269..113458 190 cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0121:PI0122|PI0121:PI0122:outer membrane protein, ompH family:outer membrane protein, ompH family:->->:113269..113458 190 cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0121:PI0122|PI0121:PI0122:outer membrane protein, ompH family:outer membrane protein, ompH family:->->:113269..113458 190 cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 7 End: 114 ...... M S V L I L I R I N E K R P P Q Q V C S C G G L T L S V R F S S V G K C ............................................................................ Protein_Len: 52 Strand: + Start: 35 End: 190 .................................. M K K D H R N K F V L A V V L L F P F A L A A L G N A N G G K T P A L R I V G N G C W S H T E F R F L L Protein_Len: 51 Strand: - Start: 19 End: 171 .................. D K N P Y I F F S W R L L N T R A T T K S K G N A K A A N P F A L P P F V G A R L I T P F P Q Q L W M ................... Protein_Len: 33 Strand: - Start: 3 End: 101 .. L I D T K I R I L I F S F L G G C C T Q E Q P P R V R E T R K L M ......................................................................................... cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta 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================================================ cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -7.2 Tail_Score: -3.79481 Start: 38 End: 82 Full_Region: TTATTAGGATAAATG AAAAAAGACCACCGCAACAA GTTTG TTCTTGCGGTGGTCTTACTC TTTCCGTTCGCTTTA .....................................AAAAAAGACCACCGCAACAAGTTTGTTCTTGCGGTGGTCTTACTC............................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -15.0 Tail_Score: -5.42514 Start: 44 End: 76 Full_Region: gaacggaaagagtaa gaccaccgcaagaa caaac ttgttgcggtggtc ttttttcatttatcc ...........................................gaccaccgcaagaacaaacttgttgcggtggtc.................................................................................................................. Find igs database================================================ Query_seq: PI0121:PI0122|PI0121:PI0122:outer membrane protein, ompH family:outer membrane protein, ompH family:->->:113269..113458 190 cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: pint_PI0121_PI0122|outer membrane protein, ompH family:outer membrane protein, ompH family|POSITIVE:POSITIVE|[113269,113458]|190 HSP 1 e-value: 1.0E-104 bit: 377.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta cataatatatcagttttaatccttattaggataaatgaaaaaagaccaccgcaacaagtttgttcttgcggtggtcttactctttccgttcgctttagcagcgttgggaaatgctaacgggggaaagacacccgcccttaggattgtggggaatggctgttggagccacaccgagtttcgttttttgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAAUAUAUCAGUUUUAAUCCUUAUUAGGAUAAAUGAAAAAAGACCACCGCAACAAGUUUGUUCUUGCGGUGGUCUUACUCUUUCCGUUCGCUUUAGCAGCGUUGGGAAAUGCUAACGGGGGAAAGACACCCGCCCUUAGGAUUGUGGGGAAUGGCUGUUGGAGCCACACCGAGUUUCGUUUUUUGUUA ..(((((...........(((((....)))))((((((((.(((((((((((((((....)))...))))))))))))..(((((((....((....))..((((((......))))))..)))))))..(((((((...))...)))))...(((((.....))))).......))))))))..))))) (-58.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAAAAACGAAACUCGGUGUGGCUCCAACAGCCAUUCCCCACAAUCCUAAGGGCGGGUGUCUUUCCCCCGUUAGCAUUUCCCAACGCUGCUAAAGCGAACGGAAAGAGUAAGACCACCGCAAGAACAAACUUGUUGCGGUGGUCUUUUUUCAUUUAUCCUAAUAAGGAUUAAAACUGAUAUAUUAUG ..................((.((((((.....)))))).))....((((((..(((.(((......)))))).((((..(((((...((((.....))))...)))))(((.(((((((((((((.((.....)).)))))))))))))..))).......))))..))))))................. (-59.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 135 92 84 26 pint:PI1799|5end_30S_ribosomal_protein_S2_1732900..1733130_POSITIVE 373 139 91 203 166 pint:PI2134|5end_hypothetical_protein_2082269..2082499_POSITIVE 364 159 113 211 165 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 357 167 121 62 15 pint:PI2086|5end_signal_peptidase_I_2041835..2042065_POSITIVE 357 85 41 169 130 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 351 175 133 178 124 pint:PI0132|5end_hypothetical_protein_123783..124013_POSITIVE 344 189 141 214 168 pint:PI0051|5end_hypothetical_protein_52607..52837_POSITIVE 340 150 101 198 149 pint:PI0222|5end_conserved_hypothetical_protein_217808..218038_POSITIVE 336 160 112 227 177 pint:PI0655|5end_Na+/H+_anitporter_597290..597520_POSITIVE 336 164 127 73 41 pint:PI0247|5end_conjugative_transposon_protein,_TraA_245373..245603_POSITIVE 334 127 81 175 127 pint:PI1343|5end_conserved_hypothetical_protein_1257782..1258012_POSITIVE 333 150 102 95 52 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 331 130 87 190 130 pint:PI0941|5end_hypothetical_protein_874443..874673_POSITIVE 330 175 133 76 29 pint:PI1916|5end_conserved_hypothetical_protein_1860211..1860441_POSITIVE 329 180 132 110 39 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 328 180 132 165 125 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 328 160 111 64 14 pint:PI1446|5end_conserved_hypothetical_protein_1369027..1369257_POSITIVE 326 180 134 216 169 pint:PI1528|5end_hypothetical_protein_1449685..1449915_POSITIVE 325 88 46 198 149 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 324 167 121 201 149 pint:PI0281|5end_conserved_hypothetical_protein_266309..266539_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 505 78 42 49 13 pint:PI0121|3end_outer_membrane_protein,_ompH_family_113208..113358_POSITIVE 382 188 145 146 83 pint:PI1686|3end_hypothetical_protein_1601898..1602048_POSITIVE 373 137 92 98 45 pint:PI2129|3end_octaprenyl-diphosphate_synthase_2077721..2077871_POSITIVE 351 179 131 109 41 pint:PI1503|3end_30S_ribosomal_protein_S15_1423780..1423930_POSITIVE 341 105 61 150 92 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 340 180 132 148 103 pint:PI1128|3end_probable_yrdC_domain_protein,_translation_factor_(SUA5)_1055055..1055205_POSITIVE 340 150 101 106 57 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 339 160 112 150 107 pint:PI0865|3end_possible_phosphoglycerol_transferase_803684..803834_POSITIVE 336 160 112 80 30 pint:PI0654|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_597223..597373_POSITIVE 334 127 81 112 64 pint:PI1342|3end_conserved_hypothetical_protein_1257799..1257949_POSITIVE 331 130 87 96 36 pint:PI0940|3end_ribonuclease_G_874429..874579_POSITIVE 324 176 140 69 31 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 323 109 62 64 9 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 319 109 61 124 81 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 318 99 51 76 27 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 316 109 67 43 1 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 313 157 115 95 65 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 312 174 131 46 1 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 311 138 92 111 67 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 307 187 156 53 22 pint:PI0337|3end_hypothetical_protein_315402..315552_POSITIVE