Origin IGS: gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagtggcggcggacaaagccgccctactttctttcggtgagcatgacggcggacaaagaaagtagcaaagaaaccgctgtcccaatctacgatagtattcacaaaaacaagtttcaatc Mask Tandem Repeat Region ================================================ gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca Find is-nt database================================================ Query_seq: TF2270:TF2271|TF2270:TF2271:conserved hypothetical protein:conserved hypothetical protein:->->:2435822..2435941 120 gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2270:TF2271|TF2270:TF2271:conserved hypothetical protein:conserved hypothetical protein:->->:2435822..2435941 120 gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2270:TF2271|TF2270:TF2271:conserved hypothetical protein:conserved hypothetical protein:->->:2435822..2435941 120 gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 2 End: 118 . M E T C F C E Y Y R R L G Q R F L C Y F L C P P S C S P K E S R A A L S A A T .. Protein_Len: 39 Strand: + Start: 3 End: 119 .. M K L V F V N T I V D W D S G F F A T F F V R R H A H R K K V G R L C P P P L . gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca 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: 83 Start: 2 End: 31 .ATTGAAACTTGTTTTTGTGAATACTATCGT......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2270:TF2271|TF2270:TF2271:conserved hypothetical protein:conserved hypothetical protein:->->:2435822..2435941 120 gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: tfor_TF2270_TF2271|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2435822,2435941]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca gattgaaacttgtttttgtgaatactatcgtagattgggacagcggtttctttgctactttctttgtccgccgtcatgctcaccgaaagaaagtagggcggctttgtccgccgccactca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUGAAACUUGUUUUUGUGAAUACUAUCGUAGAUUGGGACAGCGGUUUCUUUGCUACUUUCUUUGUCCGCCGUCAUGCUCACCGAAAGAAAGUAGGGCGGCUUUGUCCGCCGCCACUCA ....(((((((((((..((...(((....))).))..)))))..))))))....(((((((((((((..((......))..))..)))))))))))((((((.......))))))..... (-33.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUGGCGGCGGACAAAGCCGCCCUACUUUCUUUCGGUGAGCAUGACGGCGGACAAAGAAAGUAGCAAAGAAACCGCUGUCCCAAUCUACGAUAGUAUUCACAAAAACAAGUUUCAAUC .((((((.(((((......))))))))))).((.(((..((....((((((((.....................))))))))....))..))).))........................ (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 525 119 71 59 3 tfor:TF3055|5end_hypothetical_protein_3278775..3279005_POSITIVE 437 110 63 69 7 tfor:TF3154|5end_conserved_hypothetical_protein_3389219..3389449_POSITIVE 415 120 72 115 60 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 394 110 70 212 164 tfor:TF1418|5end_cell_division_protein_1500027..1500257_POSITIVE 386 119 72 70 13 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 386 119 72 58 1 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 386 109 62 213 154 tfor:TF0333|5end_hypothetical_protein_359020..359250_POSITIVE 384 99 54 52 1 tfor:TF0287|5end_peptidase,_M23_family_315810..316040_POSITIVE 374 110 64 45 3 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 374 119 71 200 159 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 369 108 61 213 161 tfor:TF0996|5end_ribonuclease_D_1050882..1051112_POSITIVE 368 116 72 120 59 tfor:TF2272|5end_conserved_hypothetical_protein_2436156..2436386_POSITIVE 367 114 71 176 136 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 364 118 72 91 40 tfor:TF2499|5end_possible_thioesterase_family_protein_2673903..2674133_POSITIVE 364 110 64 225 158 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 364 118 71 224 181 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 359 119 71 167 131 tfor:TF2455|5end_conserved_hypothetical_protein;_possible_membrane_protein_2631959..2632189_POSITIVE 359 79 34 227 185 tfor:TF2448|5end_conserved_hypothetical_protein_2624962..2625192_POSITIVE 354 116 71 50 10 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 352 110 61 210 161 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 585 99 51 71 20 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 437 110 63 94 32 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 367 117 71 140 98 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 350 110 68 38 5 tfor:TF1471|3end_conserved_hypothetical_protein_1565521..1565671_POSITIVE 348 86 41 129 68 tfor:TF2889|3end_50S_ribosomal_protein_L27_3078688..3078838_POSITIVE 346 102 63 64 25 tfor:TF0855|3end_membrane_protein,_possible_exporter_908199..908349_POSITIVE 344 115 78 68 20 tfor:TF0537|3end_conserved_hypothetical_protein_566836..566986_POSITIVE 342 115 71 147 103 tfor:TF2253|3end_conjugative_transposon_protein,_TraG_2427531..2427681_POSITIVE 341 119 72 117 61 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 340 110 68 111 76 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 338 110 61 134 86 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 333 110 64 128 64 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 332 75 35 58 7 tfor:TF2322|3end_conserved_hypothetical_protein;_possible_lipoprotein_2483785..2483935_POSITIVE 332 113 74 135 99 tfor:TF1684|3end_zinc_protease_1800331..1800481_POSITIVE 331 116 74 78 9 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 330 79 35 86 32 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 326 120 72 90 47 tfor:TF1796|3end_ABC_transporter,_ATP-binding_protein_1937216..1937366_POSITIVE 326 108 65 68 17 tfor:TF0326|3end_hypothetical_protein_354317..354467_POSITIVE 324 79 32 122 59 tfor:TF2225|3end_CTn_excision_protein_2395602..2395752_POSITIVE 324 110 63 51 5 tfor:TF0111|3end_outer_membrane_protein_121309..121459_POSITIVE