Origin IGS: cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaagtttattgtgcgtttttgcggttttggctaagtctttggcggcttttagtaggcttctatcgtttttgtgagtgcattttaatgcttgtagttcaaataaaaagcagtatctttgcagtatgaaaataggaacgatagattttggagaacgccctttgttcttggcaccg Mask Tandem Repeat Region ================================================ cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc Find is-nt database================================================ Query_seq: PI2037:PI2038|PI2037:PI2038:TIM-barrel protein, NifR3 family:conserved hypothetical protein; possible internalin-related protein:->->:1990430..1990602 173 cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2037:PI2038|PI2037:PI2038:TIM-barrel protein, NifR3 family:conserved hypothetical protein; possible internalin-related protein:->->:1990430..1990602 173 cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2037:PI2038|PI2037:PI2038:TIM-barrel protein, NifR3 family:conserved hypothetical protein; possible internalin-related protein:->->:1990430..1990602 173 cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 35 End: 172 .................................. M V P I F I L Q R Y C F L F E L Q A L K C T H K N D R S L L K A A K D L A K T A K T H N K L . Protein_Len: 35 Strand: - Start: 51 End: 155 .................................................. V A F I S S K I Q V V L M L I C E C F R Y F G V L L R W L S L W F R M .................. Protein_Len: 33 Strand: - Start: 1 End: 99 P A L F L P R E G F D I T G I K M S C L Y Q K K N S S C A N F H M .......................................................................... cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc 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================================================ cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2037:PI2038|PI2037:PI2038:TIM-barrel protein, NifR3 family:conserved hypothetical protein; possible internalin-related protein:->->:1990430..1990602 173 cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: pint_PI2037_PI2038|TIM-barrel protein, NifR3 family:conserved hypothetical protein; possible internalin-related protein|POSITIVE:POSITIVE|[1990430,1990602]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc cggtgccaagaacaaagggcgttctccaaaatctatcgttcctattttcatactgcaaagatactgctttttatttgaactacaagcattaaaatgcactcacaaaaacgatagaagcctactaaaagccgccaaagacttagccaaaaccgcaaaaacgcacaataaacttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUGCCAAGAACAAAGGGCGUUCUCCAAAAUCUAUCGUUCCUAUUUUCAUACUGCAAAGAUACUGCUUUUUAUUUGAACUACAAGCAUUAAAAUGCACUCACAAAAACGAUAGAAGCCUACUAAAAGCCGCCAAAGACUUAGCCAAAACCGCAAAAACGCACAAUAAACUUC ..((((...........((((..........(((((((((......((((...((.((((......)))).))..))))......((((....)))).........))))))))).((.........)))))).........((.......))......)))).......... (-26.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUUUAUUGUGCGUUUUUGCGGUUUUGGCUAAGUCUUUGGCGGCUUUUAGUAGGCUUCUAUCGUUUUUGUGAGUGCAUUUUAAUGCUUGUAGUUCAAAUAAAAAGCAGUAUCUUUGCAGUAUGAAAAUAGGAACGAUAGAUUUUGGAGAACGCCCUUUGUUCUUGGCACCG .....................((((....((((((.....((((..((((((......((((((((((((((.(.((((......(((((..............))))).......)))).)......))))))))))))))..))))))..)))).......)))))))))) (-43.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 60 19 175 124 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 302 89 47 126 87 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 295 60 16 118 78 pint:PI0868|5end_exodeoxyribonuclease_VII,_large_subunit_804201..804431_POSITIVE 288 36 2 153 118 pint:PI0278|5end_hypothetical_protein_265414..265644_POSITIVE 275 79 35 148 99 pint:PI1530|5end_conserved_hypothetical_protein_1450439..1450669_POSITIVE 274 50 1 113 64 pint:PI0943|5end_conserved_hypothetical_protein_875153..875383_POSITIVE 269 159 114 124 68 pint:PI0005|5end_hypothetical_protein_6984..7214_POSITIVE 266 139 99 98 54 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 265 146 101 229 175 pint:PI1925|5end_conserved_hypothetical_protein_1866387..1866617_POSITIVE 265 160 116 142 102 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 263 72 35 113 75 pint:PI1689|5end_conserved_hypothetical_protein_1604310..1604540_POSITIVE 262 153 118 154 117 pint:PI1834|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1774861..1775091_POSITIVE 260 149 107 87 32 pint:PI1898|5end_S-adenosyl-methyltransferase_1841288..1841518_POSITIVE 258 145 103 151 106 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 256 151 116 65 41 pint:PI1651|5end_hypothetical_protein_1563845..1564075_POSITIVE 256 27 3 228 204 pint:PI0167|5end_hypothetical_protein_163164..163394_POSITIVE 256 47 2 198 133 pint:PI0027|5end_aminopeptidase_C_30468..30698_POSITIVE 251 160 117 68 38 pint:PI1586|5end_possible_HesA/MoeB/ThiF_family_protein_1514372..1514602_POSITIVE 249 155 117 81 35 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 249 49 1 182 144 pint:PI1388|5end_transcriptional_regulator,_LuxR_family_1309354..1309584_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 89 47 113 74 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 288 36 2 132 97 pint:PI0277|3end_hypothetical_protein_265473..265623_POSITIVE 274 48 4 147 100 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 274 50 1 129 80 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 274 145 101 125 78 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 273 147 105 141 108 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 265 160 116 145 105 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 265 90 49 105 64 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 258 145 103 87 42 pint:PI0603|3end_3-dehydroquinate_synthase_550841..550991_POSITIVE 256 151 116 41 17 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE 253 160 112 139 82 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 252 41 1 133 108 pint:PI0113|3end_arginyl-tRNA_synthetase_110082..110232_POSITIVE 248 43 1 70 34 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 246 86 53 68 34 pint:PI0437|3end_conserved_hypothetical_protein;_possible_ribosomal_subunit_interface_protein_408543..408693_POSITIVE 246 154 113 129 78 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE 243 60 18 39 1 pint:PI0867|3end_hypothetical_protein_804202..804352_POSITIVE 238 156 113 124 76 pint:PI0191|3end_O-methyltransferase_181785..181935_POSITIVE 234 29 2 64 44 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 229 67 27 145 101 pint:PI1691|3end_hypothetical_protein_1605736..1605886_POSITIVE 225 124 86 150 104 pint:PI0136|3end_surface_antigen_BspA_128084..128234_POSITIVE