Origin IGS: taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgttcttatattcttgttattaattaatttgacaacaaaggtatgaataattgcttataaaacaaagagattatactgtttttacacaacaagggcaacgaagcgttagtttcgttgcccttgattcttttttatatgtttctatattctataccttta Mask Tandem Repeat Region ================================================ taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Find is-nt database================================================ Query_seq: PI0622:PI0623|PI0622:PI0623:hypothetical protein:hypothetical protein:->->:572148..572306 159 taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0622:PI0623|PI0622:PI0623:hypothetical protein:hypothetical protein:->->:572148..572306 159 taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0622:PI0623|PI0622:PI0623:hypothetical protein:hypothetical protein:->->:572148..572306 159 taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 35 End: 133 .................................. M K G N E T N A S L P L L C K N S I I S L F Y K Q L F I P L L S N .......................... Protein_Len: 36 Strand: - Start: 2 End: 109 . F T Y F I S V Y L F S D L A V F S V S R Q G Q Q T F V T Y D R Q K I L M .................................................. Protein_Len: 30 Strand: - Start: 1 End: 90 L P I S Y L F M Y F L I L P L S V L A E N G K N H L F L I M ..................................................................... taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 61 End: 90 ............................................................GTTGCCCTTGTTGTGTAAAAACAGTATAAT..................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.8 Tail_Score: -5.51046 Start: 33 End: 73 Full_Region: tatactgtttttaca caacaagggcaacgaagc gtta gtttcgttgcccttgattc ttttttatatgtttc ................................caacaagggcaacgaagcgttagtttcgttgcccttgattc...................................................................................... TransTerm Strand: - Conf: 100 HP_score: -17.0 Tail_Score: -4.78477 Start: 36 End: 71 Full_Region: tactgtttttacaca acaagggcaacgaagc gtta gtttcgttgcccttga ttcttttttatatgt ...................................acaagggcaacgaagcgttagtttcgttgcccttga........................................................................................ TransTerm Strand: + Conf: 100 HP_score: -18.3 Tail_Score: -3.48395 Start: 37 End: 70 Full_Region: CATATAAAAAAGAAT CAAGGGCAACGAAAC TAAC GCTTCGTTGCCCTTG TTGTGTAAAAACAGT ....................................CAAGGGCAACGAAACTAACGCTTCGTTGCCCTTG......................................................................................... TransTerm Strand: - Conf: 100 HP_score: -20.5 Tail_Score: -3.44646 Start: 37 End: 70 Full_Region: actgtttttacacaa caagggcaacgaagc gtta gtttcgttgcccttg attcttttttatatg ....................................caagggcaacgaagcgttagtttcgttgcccttg......................................................................................... TransTerm Strand: + Conf: 100 HP_score: -14.2 Tail_Score: -3.88232 Start: 40 End: 67 Full_Region: ATAAAAAAGAATCAA GGGCAACGAAAC TAAC GCTTCGTTGCCC TTGTTGTGTAAAAAC .......................................GGGCAACGAAACTAACGCTTCGTTGCCC............................................................................................ Find igs database================================================ Query_seq: PI0622:PI0623|PI0622:PI0623:hypothetical protein:hypothetical protein:->->:572148..572306 159 taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Intra-Species Hit: Count: 1 Min: 1 Max: 159 Len: 159 Subject: pint_PI0622_PI0623|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[572148,572306]|159 HSP 1 e-value: 2.0E-85 bit: 315.0 Len: 159 Query Start:1 Query End:159 Subject Strand: POSITIVE Subject Start: 1 Subject End: 159 taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca taaaggtatagaatatagaaacatataaaaaagaatcaagggcaacgaaactaacgcttcgttgcccttgttgtgtaaaaacagtataatctctttgttttataagcaattattcatacctttgttgtcaaattaattaataacaagaatataagaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGGUAUAGAAUAUAGAAACAUAUAAAAAAGAAUCAAGGGCAACGAAACUAACGCUUCGUUGCCCUUGUUGUGUAAAAACAGUAUAAUCUCUUUGUUUUAUAAGCAAUUAUUCAUACCUUUGUUGUCAAAUUAAUUAAUAACAAGAAUAUAAGAACA (((((((((.(((((........(((((((((((..(((((((((((((.(....).))))))))))))).(((......)))........))))..)))))))......))))))))))))))................................... (-40.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUUAUAUUCUUGUUAUUAAUUAAUUUGACAACAAAGGUAUGAAUAAUUGCUUAUAAAACAAAGAGAUUAUACUGUUUUUACACAACAAGGGCAACGAAGCGUUAGUUUCGUUGCCCUUGAUUCUUUUUUAUAUGUUUCUAUAUUCUAUACCUUUA .............((((((..........)))))).(((((((((((((...((.(((((((..(((((.......(((....)))...(((((((((((((((....))))))))))))))).)))))))))))).)).....))))).)))))))). (-46.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 453 69 37 156 124 pint:PI0625|5end_possible_membrane_transport_protein_573104..573334_POSITIVE 357 75 38 164 125 pint:PI0897|5end_ferredoxin,_4Fe-4S_828227..828457_POSITIVE 305 78 31 207 167 pint:PI0300|5end_transposase_285163..285393_POSITIVE 293 73 41 199 154 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 284 80 32 131 81 pint:PI0882|5end_conserved_hypothetical_protein;_possible_para-aminobenzoate_synthase_component_I_815545..815775_POSITIVE 281 75 41 125 79 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 278 72 36 107 60 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 275 89 50 72 32 pint:PI0291|5end_hypothetical_protein_274067..274297_POSITIVE 272 84 42 69 34 pint:PI2153|5end_hypothetical_protein_2099392..2099622_POSITIVE 272 84 42 69 34 pint:PI1567|5end_hypothetical_protein_1489229..1489459_POSITIVE 272 74 32 155 112 pint:PI1522|5end_thioredoxin_M_1441646..1441876_POSITIVE 272 84 42 195 160 pint:PI0788|5end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726152..726382_POSITIVE 272 84 42 200 165 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 270 76 36 158 112 pint:PI1134|5end_ABC_transporter,_ATP-binding_protein_1060374..1060604_POSITIVE 267 76 40 181 136 pint:PI0228|5end_outer_membrane_cobalamin_receptor_protein_225752..225982_POSITIVE 263 70 35 151 122 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 262 78 39 223 175 pint:PI1257|5end_dTDP-4-dehydrorhamnose_reductase_1177971..1178201_POSITIVE 261 78 42 55 14 pint:PI1530|5end_conserved_hypothetical_protein_1450439..1450669_POSITIVE 261 76 39 203 166 pint:PI1187|5end_conserved_hypothetical_protein_1106692..1106922_POSITIVE 259 94 55 213 179 pint:PI0147|5end_HIT_family_protein_140833..141063_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 402 70 37 54 21 pint:PI0622|3end_hypothetical_protein_572087..572237_POSITIVE 399 74 37 62 20 pint:PI0620|3end_hypothetical_protein_570630..570780_POSITIVE 357 75 38 133 94 pint:PI0896|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_828276..828426_POSITIVE 305 78 31 50 10 pint:PI0299|3end_hypothetical_protein_285086..285236_POSITIVE 297 89 41 151 103 pint:PI0981|3end_outer_membrane_protein,_TonB_dependent_receptor_909390..909540_POSITIVE 279 79 38 76 32 pint:PI0447|3end_DNA-directed_RNA_polymerase,_beta'_subunit_421755..421905_POSITIVE 278 92 54 105 57 pint:PI1620|3end__two-component_system_sensor_protein_1545160..1545310_POSITIVE 275 89 50 56 16 pint:PI0290|3end_conserved_hypothetical_protein_274131..274281_POSITIVE 272 84 42 151 116 pint:PI1814|3end_hypothetical_protein_1753233..1753383_POSITIVE 270 76 36 108 62 pint:PI1133|3end_GrpE_protein_1060404..1060554_POSITIVE 267 79 31 131 77 pint:PI2018|3end_50S_ribosomal_protein_L34_1975989..1976139_POSITIVE 263 70 35 145 116 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 261 73 32 115 74 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 255 75 39 106 68 pint:PI1726|3end_ATP-dependent_DNA_helicase_1645542..1645692_POSITIVE 255 69 21 61 9 pint:PI0596|3end_hypothetical_protein_546608..546758_POSITIVE 251 75 31 85 41 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 248 84 42 151 116 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE 247 78 38 56 17 pint:PI1700|3end_hypothetical_protein_1619243..1619393_POSITIVE 236 70 21 118 61 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 234 72 32 143 100 pint:PI0698|3end_conserved_hypothetical_protein_636711..636861_POSITIVE