Origin IGS: tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacctcaatataacgtatagaactcttgttatgaaagtaaaactgttctgttgcatctttcaatgagcagaacaaagaaagcaaaaaataaaaacaatgtaaggctgatataaagagaggaaaataaaaaatattataaatatttttcacagacgcagatatcacataacta Mask Tandem Repeat Region ================================================ tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta Find is-nt database================================================ Query_seq: PI0902:PI0903|PI0902:PI0903:hypothetical protein:conserved hypothetical protein:->->:832641..832813 173 tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0902:PI0903|PI0902:PI0903:hypothetical protein:conserved hypothetical protein:->->:832641..832813 173 tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0902:PI0903|PI0902:PI0903:hypothetical protein:conserved hypothetical protein:->->:832641..832813 173 tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 8 End: 172 ....... M I S A S V K N I Y N I F Y F P L F I S A L H C F Y F L L S L F C S L K D A T E Q F Y F H N K S S I R Y I E V . tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta 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: 82 Start: 137 End: 166 ........................................................................................................................................TTTCATAACAAGAGTTCTATACGTTATATT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0902:PI0903|PI0902:PI0903:hypothetical protein:conserved hypothetical protein:->->:832641..832813 173 tagttatgtgatatctgcgtctgtgaaaaatatttataatattttttattttcctctctttatatcagccttacattgtttttattttttgctttctttgttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: pint_PI0902_PI0903|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[832641,832813]|173 HSP 1 e-value: 1.0E-34 bit: 147.0 Len: 74 Query Start:100 Query End:173 Subject Strand: POSITIVE Subject Start: 100 Subject End: 173 ...................................................................................................gttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta ...................................................................................................gttctgctcattgaaagatgcaacagaacagttttactttcataacaagagttctatacgttatattgaggtta HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 29 Query Start:1 Query End:29 Subject Strand: POSITIVE Subject Start: 1 Subject End: 29 tagttatgtgatatctgcgtctgtgaaaa................................................................................................................................................ tagttatgtgatatctgcgtctgtgaaaa................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAUGUGAUAUCUGCGUCUGUGAAAAAUAUUUAUAAUAUUUUUUAUUUUCCUCUCUUUAUAUCAGCCUUACAUUGUUUUUAUUUUUUGCUUUCUUUGUUCUGCUCAUUGAAAGAUGCAACAGAACAGUUUUACUUUCAUAACAAGAGUUCUAUACGUUAUAUUGAGGUUA .....((((((.....(.(...(((((((((((.....)))))))))))...)).....)))))).(((((((........................((((((((..((((....))))...))))))))..........(((((.............)))))..))))))). (-27.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCUCAAUAUAACGUAUAGAACUCUUGUUAUGAAAGUAAAACUGUUCUGUUGCAUCUUUCAAUGAGCAGAACAAAGAAAGCAAAAAAUAAAAACAAUGUAAGGCUGAUAUAAAGAGAGGAAAAUAAAAAAUAUUAUAAAUAUUUUUCACAGACGCAGAUAUCACAUAACUA ........((((..(((......(((((.(((((..(((.....(((((((((.(((......))))))))))))......(((..............)))...)))..))))).))))).......((((((((.....)))))))).....)))...)))).......... (-25.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 38 1 129 92 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 320 132 91 162 109 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 304 155 112 93 49 pint:PI0124|5end_outer_membrane_protein/protective_antigen_OMA87_114487..114717_POSITIVE 292 38 1 129 92 pint:PI0182|5end_hypothetical_protein_174093..174323_POSITIVE 287 128 88 216 171 pint:PI0562|5end_conserved_hypothetical_protein_509096..509326_POSITIVE 287 128 88 72 27 pint:PI0561|5end_hypothetical_protein_508952..509182_POSITIVE 282 38 1 129 92 pint:PI1733|5end_hypothetical_protein_1652160..1652390_POSITIVE 264 38 1 88 51 pint:PI1922|5end_hypothetical_protein_1865219..1865449_POSITIVE 262 126 87 81 39 pint:PI0584|5end_hypothetical_protein_527352..527582_POSITIVE 256 106 68 161 120 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 255 127 90 169 135 pint:PI1619|5end_two-component_system_response_regulator_1543210..1543440_POSITIVE 250 120 74 103 58 pint:PI0038|5end_transcriptional_regulator,_LysR_family_39578..39808_POSITIVE 242 38 1 129 92 pint:PI0061|5end_hypothetical_protein_60500..60730_POSITIVE 241 90 42 229 184 pint:PI2178|5end_1-hydroxy-2-methyl-2-(E)-butenyl_4-diphosphate_synthase,_GcpE_2117677..2117907_POSITIVE 239 120 74 144 89 pint:PI2091|5end_DNA_processing_protein_2048019..2048249_POSITIVE 239 104 63 62 16 pint:PI0071|5end_hypothetical_protein_69958..70188_POSITIVE 236 131 94 60 22 pint:PI0227|5end_ABC_transporter,_ATP-binding/permease_protein_223810..224040_POSITIVE 235 120 76 220 178 pint:PI1573|5end_transcription-repair_coupling_factor_1496429..1496659_POSITIVE 232 127 89 230 186 pint:PI1722|5end_possible_peptidyl-prolyl_cis-trans_isomerase_1639536..1639766_POSITIVE 231 97 54 231 194 pint:PI0327|5end_hypothetical_protein_308791..309021_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 38 1 82 45 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 321 38 1 42 5 pint:PI1424|3end_probable_peptidase_family_M48_1344044..1344194_POSITIVE 282 50 3 62 16 pint:PI1485|3end_hypothetical_protein_1405339..1405489_POSITIVE 274 125 83 151 101 pint:PI1156|3end_possible_glycerate_kinase_family_protein_1081781..1081931_POSITIVE 271 106 62 120 66 pint:PI0818|3end_alpha-amylase_759659..759809_POSITIVE 271 107 64 137 98 pint:PI0503|3end_mobilizable_transposon,_excision_protein_464198..464348_POSITIVE 264 110 68 128 93 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 255 127 90 43 9 pint:PI1617|3end_hypothetical_protein_1543164..1543314_POSITIVE 250 120 74 61 16 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE 244 128 99 151 126 pint:PI2061|3end_type_I_restriction_enzyme_restriction_subunit_2021647..2021797_POSITIVE 239 120 74 111 56 pint:PI2090|3end_thioesterase_family_protein_2048066..2048216_POSITIVE 239 104 63 132 86 pint:PI0070|3end_conserved_hypothetical_protein_70108..70258_POSITIVE 238 127 89 137 91 pint:PI2014|3end_conserved_hypothetical_protein_1972603..1972753_POSITIVE 236 131 94 54 16 pint:PI0226|3end_ABC_transporter,_ATP-binding_/_permease_protein_223884..224034_POSITIVE 232 135 91 63 15 pint:PI0399|3end_conserved_hypothetical_protein_364090..364240_POSITIVE 230 130 89 42 4 pint:PI1720|3end_conserved_hypothetical_protein_1637992..1638142_POSITIVE 224 38 2 70 34 pint:PI1600|3end_conserved_hypothetical_protein_1530275..1530425_POSITIVE 221 49 2 122 76 pint:PI0688|3end_hypothetical_protein_625750..625900_POSITIVE 219 137 91 79 29 pint:PI0959|3end_uridine_kinase_891204..891354_POSITIVE 216 103 61 151 109 pint:PI0621|3end_conserved_hypothetical_protein_571227..571377_POSITIVE