Origin IGS: tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaatctttagaaaataactgatgaaatatcaaaaaaaagaggttgggaacctcttttttatagctaaaattttattttcaaagttagttgtttgaagcca Mask Tandem Repeat Region ================================================ tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca Find is-nt database================================================ Query_seq: SSA_2169:SSA_2170|SSA_2169:SSA_2170:Glucose-1-phosphate uridylyltransferase, putative:hypothetical protein:-><-:2169546..2169646 101 tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2169:SSA_2170|SSA_2169:SSA_2170:Glucose-1-phosphate uridylyltransferase, putative:hypothetical protein:-><-:2169546..2169646 101 tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2169:SSA_2170|SSA_2169:SSA_2170:Glucose-1-phosphate uridylyltransferase, putative:hypothetical protein:-><-:2169546..2169646 101 tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca Predict ORF larger than 30AA ================================================ tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca 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================================================ tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -10.1 Tail_Score: -2.68381 Start: 39 End: 71 Full_Region: AAATAAAATTTTAGC TATAAAAAAGAGGTT CCC AACCTCTTTTTTTTG ATATTTCATCAGTTA ......................................TATAAAAAAGAGGTTCCCAACCTCTTTTTTTTG.............................. TransTerm Strand: + Conf: 100 HP_score: -8.6 Tail_Score: -5.9663 Start: 48 End: 62 Full_Region: TTTAGCTATAAAAAA GAGGTT CCC AACCTC TTTTTTTTGATATTT ...............................................GAGGTTCCCAACCTC....................................... Find igs database================================================ Query_seq: SSA_2169:SSA_2170|SSA_2169:SSA_2170:Glucose-1-phosphate uridylyltransferase, putative:hypothetical protein:-><-:2169546..2169646 101 tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_009009_SSA_2169_SSA_2170|Glucose-1-phosphate uridylyltransferase, putative:hypothetical protein|POSITIVE:NEGATIVE|[2169546,2169646]|101 HSP 1 e-value: 1.0E-36 bit: 153.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcnnnnnnnngatatttcatcagttattttctaaagattca tggcttcaaacaactaactttgaaaataaaattttagctataaaaaagaggttcccaacctcttttttttgatatttcatcagttattttctaaagattca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGCUUCAAACAACUAACUUUGAAAAUAAAAUUUUAGCUAUAAAAAAGAGGUUCCCAACCUCUUUUUUUUGAUAUUUCAUCAGUUAUUUUCUAAAGAUUCA .................((((((((((((............(((((((((((.....))))))))))).((((.....)))).)))))))).))))..... (-19.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUCUUUAGAAAAUAACUGAUGAAAUAUCAAAAAAAAGAGGUUGGGAACCUCUUUUUUAUAGCUAAAAUUUUAUUUUCAAAGUUAGUUGUUUGAAGCCA .....(((((((...(((((..(((((......(((((((((((.....))))))))))).....(((....))).))))).)))))....)))))))... (-20.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 208 99 51 131 95 NC_009009:SSA_0052|5end_Transcriptional_regulator,_GntR_family,_putative_56658..56888_NEGATIVE 206 64 35 206 167 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 200 99 58 152 101 NC_009009:SSA_1888|5end_hypothetical_protein_1886025..1886255_NEGATIVE 199 70 26 111 72 NC_009009:SSA_1724|5end_CBS_domain_protein,_putative_1710553..1710783_NEGATIVE 199 98 54 110 57 NC_009009:SSA_0935|5end_tRNA_pseudouridine_synthase_B,_putative_944015..944245_POSITIVE 199 78 34 64 9 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 197 66 37 104 71 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 195 85 46 161 125 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 193 82 47 186 159 NC_009009:SSA_1511|5end_Glycosyltransferase,_putative_1516697..1516927_NEGATIVE 192 82 43 169 134 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 192 61 38 143 116 NC_009009:SSA_1477|5end_Truncated_transposase,_putative_1482496..1482726_POSITIVE 192 84 50 132 96 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 192 100 54 82 22 NC_009009:SSA_0527|5end_Propanediol_utilization_protein_PduL_524625..524855_POSITIVE 191 49 2 169 124 NC_009009:SSA_1735|5end_UreX,_putative_1721072..1721302_NEGATIVE 191 70 30 216 164 NC_009009:SSA_1464|5end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1471516..1471746_NEGATIVE 190 88 47 77 26 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 188 97 59 133 97 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 188 80 31 180 119 NC_009009:SSA_1168|5end_hypothetical_protein_1194151..1194381_POSITIVE 188 85 47 79 40 NC_009009:SSA_0654|5end_Cell_division_protein_DivIB,_putative_637457..637687_POSITIVE 188 93 52 110 68 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 77 43 89 48 NC_009009:SSA_1533|3end_Glutathione_reductase,_putative_1542212..1542362_POSITIVE 235 76 36 92 50 NC_009009:SSA_0446|3end_hypothetical_protein_444764..444914_NEGATIVE 223 68 42 49 23 NC_009009:SSA_2169|3end_Glucose-1-phosphate_uridylyltransferase,_putative_2169485..2169635_POSITIVE 209 70 43 92 65 NC_009009:SSA_1707|3end_Conserved_uncharacterized_protein_1698248..1698398_POSITIVE 206 64 35 84 45 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 199 90 43 81 47 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 199 98 54 106 53 NC_009009:SSA_0934|3end_HydD,_putative_944091..944241_POSITIVE 199 78 34 71 16 NC_009009:SSA_0637|3end_Tryptophan_synthase_beta_chain,_putative_627022..627172_POSITIVE 198 84 43 131 82 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE 195 86 42 104 62 NC_009009:SSA_0680|3end_Serine/threonine_protein_phosphatase,_putative_663233..663383_POSITIVE 195 85 46 151 115 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 192 82 43 98 63 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 192 84 50 151 115 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 191 79 47 137 102 NC_009009:SSA_1479|3end_Transposase,_putative_1483889..1484039_POSITIVE 191 70 30 84 32 NC_009009:SSA_1465|3end_Conserved_uncharacterized_protein_1471648..1471798_NEGATIVE 190 88 47 99 48 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 189 100 58 58 7 NC_009009:SSA_0526|3end_hypothetical_protein_524681..524831_POSITIVE 188 70 37 81 45 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE 188 97 59 38 2 NC_009009:SSA_2063|3end_Aminopeptidase_PepS,_putative_2063616..2063766_NEGATIVE 188 80 31 120 59 NC_009009:SSA_1167|3end_SRP54,_signal_recognition_particle_GTPase_protein,_putative_1194171..1194321_POSITIVE