Origin IGS: taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttaattgtcaatggttaattgtcattcagcagtcagcggtcagcattcagccatcggatacgtgtaggggcgaacatctcaacaatcaaacaactcaacaaatgattta Mask Tandem Repeat Region ================================================ taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta Find is-nt database================================================ Query_seq: TF2832:TF2833|TF2832:TF2833:possible proton/sodium:glutamate symporter protein:lipid A disaccharide synthase:->->:3024000..3024112 113 taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2832:TF2833|TF2832:TF2833:possible proton/sodium:glutamate symporter protein:lipid A disaccharide synthase:->->:3024000..3024112 113 taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2832:TF2833|TF2832:TF2833:possible proton/sodium:glutamate symporter protein:lipid A disaccharide synthase:->->:3024000..3024112 113 taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. I M Q Q T T Q N N L H E G R C T D S P Q I S V A S Q Q I V M ..................... taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta 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================================================ taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2832:TF2833|TF2832:TF2833:possible proton/sodium:glutamate symporter protein:lipid A disaccharide synthase:->->:3024000..3024112 113 taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: tfor_TF2832_TF2833|possible proton/sodium:glutamate symporter protein:lipid A disaccharide synthase|POSITIVE:POSITIVE|[3024000,3024112]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta taaatcatttgttgagttgtttgattgttgagatgttcgcccctacacgtatccgatggctgaatgctgaccgctgactgctgaatgacaattaaccattgacaattaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCAUUUGUUGAGUUGUUUGAUUGUUGAGAUGUUCGCCCCUACACGUAUCCGAUGGCUGAAUGCUGACCGCUGACUGCUGAAUGACAAUUAACCAUUGACAAUUAAAUUA ........((((..(..((.(((((((((.((.((((((((................))).)))))))....((.....)).....))))))))).)))..))))........ (-17.99) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAAUUGUCAAUGGUUAAUUGUCAUUCAGCAGUCAGCGGUCAGCAUUCAGCCAUCGGAUACGUGUAGGGGCGAACAUCUCAACAAUCAAACAACUCAACAAAUGAUUUA .........((((.((((((.(((((......)))))..((.....))....))))))..))))..(((.((((......)))).)))......................... (-14.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 109 64 188 133 tfor:TF2202|5end_hypothetical_protein_2378682..2378912_POSITIVE 407 69 21 209 156 tfor:TF2611|5end_conserved_hypothetical_protein_2787204..2787434_POSITIVE 401 85 42 142 88 tfor:TF0142|5end_subtilisin-like_serine_proteinase_149740..149970_POSITIVE 398 77 31 90 30 tfor:TF2438|5end_hypothetical_protein_2615781..2616011_POSITIVE 391 82 45 196 152 tfor:TF1577|5end_hypothetical_protein_1685960..1686190_POSITIVE 391 82 45 88 44 tfor:TF1576|5end_hypothetical_protein_1685852..1686082_POSITIVE 388 90 41 165 112 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 388 90 41 165 112 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 384 80 34 51 4 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 380 78 38 49 5 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 373 87 49 125 87 tfor:TF0598|5end_hypothetical_protein_629190..629420_POSITIVE 369 77 32 106 55 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 369 78 33 230 188 tfor:TF0433|5end_60_kDa_inner_membrane_protein_453357..453587_POSITIVE 366 109 61 175 122 tfor:TF0018|5end_hypothetical_protein_11250..11480_POSITIVE 366 109 61 87 34 tfor:TF0017|5end_hypothetical_protein_10504..10734_POSITIVE 364 77 51 101 75 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 362 83 41 166 118 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 362 83 41 160 112 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 362 83 41 160 112 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 362 83 41 160 112 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 431 77 31 69 2 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 401 85 55 79 49 tfor:TF1172|3end_ABC_transporter,_permease_component_1255213..1255363_POSITIVE 392 84 42 151 98 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 391 82 45 51 7 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE 384 80 34 51 4 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 373 87 49 85 47 tfor:TF0597|3end_hypothetical_protein_629230..629380_POSITIVE 372 110 72 52 17 tfor:TF2161|3end_conserved_hypothetical_protein_2338362..2338512_POSITIVE 366 109 61 76 23 tfor:TF0017|3end_hypothetical_protein_11231..11381_POSITIVE 366 109 61 84 31 tfor:TF0016|3end_hypothetical_protein_10581..10731_POSITIVE 362 83 41 56 8 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 357 68 23 77 24 tfor:TF0323|3end_NAD-dependent_epimerase/dehydratase_family_protein_351053..351203_POSITIVE 355 75 31 75 19 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 352 72 31 71 39 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 350 109 70 44 6 tfor:TF2817|3end_hypothetical_protein_3007626..3007776_POSITIVE 347 69 24 65 11 tfor:TF0490|3end_conserved_hypothetical_protein_513904..514054_POSITIVE 341 87 49 48 3 tfor:TF1587|3end_conserved_hypothetical_protein_1702022..1702172_POSITIVE 341 90 41 74 13 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 340 90 50 74 22 tfor:TF1166|3end_ABC_transporter,_permease_component_1248603..1248753_POSITIVE 336 70 26 151 101 tfor:TF1824|3end_ABC_transporter,_ATP-binding_protein_1973510..1973660_POSITIVE 335 80 31 64 3 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE