Origin IGS: cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttactactatttaaacactattatatttgtttatacttttccaaattcgggtggcaaagatacggacttttttttatccgacaagcatttcttcaaaaaaaattggatttcaatgcttttcttcgcctcccataagacaaaggaagccctctacggatgccaatccacccgtcaaacaacttcttgcttaccccgatactcttccggcaggaaggataacgactcctcctctctctcatagcagcacatctttttttcttcatttatcccaaattacgcgatacaccgttcggcgtttatcatataataatagacgtacgaatatacgacaagggttacgtcagacttacaaccctccgccgagacgcg Mask Tandem Repeat Region ================================================ cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa Find is-nt database================================================ Query_seq: TF2547:TF2548|TF2547:TF2548:hypothetical protein:30S ribosomal protein S12:->->:2731008..2731377 370 cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2547:TF2548|TF2547:TF2548:hypothetical protein:30S ribosomal protein S12:->->:2731008..2731377 370 cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2547:TF2548|TF2547:TF2548:hypothetical protein:30S ribosomal protein S12:->->:2731008..2731377 370 cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 103 End: 195 ...................................................................................................... M N E E K K M C C Y E R E E E S L S F L P E E Y R G K Q E V V ............................................................................................................................................................................... Protein_Len: 56 Strand: + Start: 107 End: 274 .......................................................................................................... M K K K R C A A M R E R R S R Y P S C R K S I G V S K K L F D G W I G I R R G L P L S Y G R R R K A L K S N F F ................................................................................................ Protein_Len: 36 Strand: - Start: 238 End: 345 ............................................................................................................................................................................................................................................. P L R L F A N F D L K K Q L F A Q R I F F L G Y R Q W G F K S F Y L C M ......................... Protein_Len: 60 Strand: - Start: 132 End: 350 ................................................................................................................................... Y R P L C S T T Q R T S Q C G Y L A E K T K H S A F F L M S I W N K K F F H K D S L F F D T D K G G S N P F T Y V F I M .................... Protein_Len: 60 Strand: - Start: 2 End: 343 . P L T D P Y A L L Q K V P P N A D T S P K R Q R I P P S S F C Q F G I K K S S I S T P Y F F T R I K A V R I Q F L I F M ........................... Protein_Len: 44 Strand: - Start: 1 End: 132 A D R R L T T L R V Y G K D Y I R V D I I I H Y V G F P T D R L K P Y I F F F L H A A M .............................................................................................................................................................................................................................................. cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa 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: 84 Start: 37 End: 66 ....................................CTTGTCGTATATTCGTACGTCTATTATTAT................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2547:TF2548|TF2547:TF2548:hypothetical protein:30S ribosomal protein S12:->->:2731008..2731377 370 cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa Intra-Species Hit: Count: 6 Min: 1 Max: 370 Len: 370 Subject: tfor_TF2547_TF2548|hypothetical protein:30S ribosomal protein S12|POSITIVE:POSITIVE|[2731008,2731377]|370 HSP 1 e-value: 1.0E-169 bit: 597.0 Len: 370 Query Start:1 Query End:370 Subject Strand: POSITIVE Subject Start: 1 Subject End: 370 cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagnnnnnnngatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaannnnnnnngaagaaatgcttgtcggatnnnnnnnngtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaatgaagaaaaaaagatgtgctgctatgagagagaggaggagtcgttatccttcctgccggaagagtatcggggtaagcaagaagttgtttgacgggtggattggcatccgtagagggcttcctttgtcttatgggaggcgaagaaaagcattgaaatccaattttttttgaagaaatgcttgtcggataaaaaaaagtccgtatctttgccacccgaatttggaaaagtataaacaaatataatagtgtttaaatagtagtaaa Subject: tfor_TF0029_TF0030|hypothetical protein:N-acetylneuraminate lyase|POSITIVE:POSITIVE|[25123,25909]|787 HSP 1 e-value: 1.0E-24 bit: 115.0 Len: 102 Query Start:5 Query End:106 Subject Strand: POSITIVE Subject Start: 447 Subject End: 547 ....tctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataa........................................................................................................................................................................................................................................................................ ....tctcggcggagggctgtaagcttgacgtaaccattgtcgtacattcgtacgtccattatta-atggtaaacaccgaacagtgtatcgcgtaatttgggataa........................................................................................................................................................................................................................................................................ Subject: tfor_TF1273_TF1274|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1357523,1357760]|238 HSP 1 e-value: 2.0E-23 bit: 111.0 Len: 100 Query Start:8 Query End:107 Subject Strand: NEGATIVE Subject Start: 93 Subject End: 191 .......cggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaa....................................................................................................................................................................................................................................................................... .......cggcggagggctgtaagcctgacgtaaccattgtcgtgcattcgtacgtccatgatta-atggtaaacgccgaacagtgtatcgcgtaatttgggataaa....................................................................................................................................................................................................................................................................... Subject: tfor_TF0179_TF0180|pyrophosphate-energized proton pump:carboxynorspermidine decarboxylase|POSITIVE:POSITIVE|[190752,191406]|655 HSP 1 e-value: 7.0E-23 bit: 109.0 Len: 108 Query Start:1 Query End:108 Subject Strand: NEGATIVE Subject Start: 126 Subject End: 237 cgcgtctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattatta----tatgataaacgccgaacggtgtatcgcgtaatttgggataaat...................................................................................................................................................................................................................................................................... cgcgtctcggcggagggctgtaagcctgacgtaacccttgtcgtacattcgtacgtacattattaatgtaatggtaaacgcccaacagtgtatcgcgtaatttggggtaaat...................................................................................................................................................................................................................................................................... Subject: tfor_TF0467_TF0468|acetyltransferase-related protein:hypothetical protein|POSITIVE:POSITIVE|[486604,487068]|465 HSP 1 e-value: 1.0E-18 bit: 95.6 Len: 103 Query Start:5 Query End:107 Subject Strand: NEGATIVE Subject Start: 19 Subject End: 121 ....tctcggcggagggttgtaa-gtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaa....................................................................................................................................................................................................................................................................... ....tctcggcggagggctgaaaagcctgacgtaaccattgtcgtacattcgcacgtccattatta-atggtaaacgccgaacaatgtatcgcgtaatttgggataaa....................................................................................................................................................................................................................................................................... Subject: tfor_TF1473_TF1474|hypothetical protein:6- phosphogluconolactonase|POSITIVE:POSITIVE|[1567027, 1567481]|455 HSP 1 e-value: 1.0E-15 bit: 85.7 Len: 103 Query Start:5 Query End:107 Subject Strand: NEGATIVE Subject Start: 29 Subject End: 130 ....tctcggcggagggttgtaagtctgacgtaacccttgtcgtatattcgtacgtctattattatatgataaacgccgaacggtgtatcgcgtaatttgggataaa....................................................................................................................................................................................................................................................................... ....tctcggcggagggctgtaagcctgacgtaaccattgtcgtacattcatacgtccattatta-atggaaaacgcccaacagtatatcgcgtgatttgggttaaa....................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCGUCUCGGCGGAGGGUUGUAAGUCUGACGUAACCCUUGUCGUAUAUUCGUACGUCUAUUAUUAUAUGAUAAACGCCGAACGGUGUAUCGCGUAAUUUGGGAUAAAUGAAGAAAAAAAGAUGUGCUGCUAUGAGAGAGAGGAGGAGUCGUUAUCCUUCCUGCCGGAAGAGUAUCGGGGUAAGCAAGAAGUUGUUUGACGGGUGGAUUGGCAUCCGUAGAGGGCUUCCUUUGUCUUAUGGGAGGCGAAGAAAAGCAUUGAAAUCCAAUUUUUUUUGAAGAAAUGCUUGUCGGAUAAAAAAAAGUCCGUAUCUUUGCCACCCGAAUUUGGAAAAGUAUAAACAAAUAUAAUAGUGUUUAAAUAGUAGUAAA .(((((((((((.(((((((...(.....).))))))))))))....(((((..((((...((((..((((..(((((....)))))))))..))))...))))..))))).......))))))((((((((((((.((((((((..(((.((..(((((....)))))..)).)))..(((((((....)))))))(((((((......)))))))......)))))))).))))).(((.((((((((.(((((((......(((......)))....)))))))..(((((........)))))..)))))))).)))...............((((((..........))))))..)))))))... (-111.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUACUAUUUAAACACUAUUAUAUUUGUUUAUACUUUUCCAAAUUCGGGUGGCAAAGAUACGGACUUUUUUUUAUCCGACAAGCAUUUCUUCAAAAAAAAUUGGAUUUCAAUGCUUUUCUUCGCCUCCCAUAAGACAAAGGAAGCCCUCUACGGAUGCCAAUCCACCCGUCAAACAACUUCUUGCUUACCCCGAUACUCUUCCGGCAGGAAGGAUAACGACUCCUCCUCUCUCUCAUAGCAGCACAUCUUUUUUUCUUCAUUUAUCCCAAAUUACGCGAUACACCGUUCGGCGUUUAUCAUAUAAUAAUAGACGUACGAAUAUACGACAAGGGUUACGUCAGACUUACAACCCUCCGCCGAGACGCG ............((((((..........))))))...............(((.(((.((((..((((..........))))..(((((((..(((((......)))))....))))))).)))).))).)))..((((.((((((.(..(((((.((((....))))....(((......(((((((((.................)))))))))......)))...............))).))..).))))))..))))................((((.......(((((((((((((.........)))))))).)))))...((.(.((((((.............))))))..).))...)))) (-73.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 858 50 1 110 61 tfor:TF2640|5end_hypothetical_protein_2809106..2809336_POSITIVE 839 50 1 181 132 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 789 60 12 91 43 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 702 100 51 78 25 tfor:TF2639|5end_hypothetical_protein_2809020..2809250_POSITIVE 648 100 51 57 9 tfor:TF2025|5end_hypothetical_protein_2181933..2182163_POSITIVE 497 29 1 224 196 tfor:TF2641|5end_riboflavin_kinase/FAD_synthase_2809681..2809911_POSITIVE 430 29 1 187 159 tfor:TF0499|5end_hypothetical_protein_526257..526487_POSITIVE 419 322 281 208 168 tfor:TF1313|5end_conserved_hypothetical_protein_1388880..1389110_POSITIVE 414 204 163 74 23 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 405 170 122 167 101 tfor:TF0861|5end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_913377..913607_POSITIVE 398 180 132 74 21 tfor:TF3103|5end_outer_membrane_protein_3332982..3333212_POSITIVE 380 240 191 161 114 tfor:TF2754|5end_hypothetical_protein_2940446..2940676_POSITIVE 379 179 132 116 64 tfor:TF2348|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2511088..2511318_POSITIVE 378 46 1 80 35 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 377 185 144 159 122 tfor:TF2129|5end_possible_3-oxoacyl-(acyl-carrier-protein)_synthase_2305464..2305694_POSITIVE 374 190 141 215 153 tfor:TF1508|5end_anti-sigma_factor_1616345..1616575_POSITIVE 372 57 11 61 6 tfor:TF1888|5end_RNA_polymerase_ECF-type_sigma_factor_2040940..2041170_POSITIVE 370 226 182 178 119 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 370 29 6 192 168 tfor:TF0350|5end_hypothetical_protein_370794..371024_POSITIVE 362 58 11 180 127 tfor:TF3126|5end_glycosyltransferase,_group_2_family_3360439..3360669_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 835 56 11 50 5 tfor:TF0339|3end_hypothetical_protein_363747..363897_POSITIVE 778 60 11 54 5 tfor:TF2047|3end_hypothetical_protein_2210298..2210448_POSITIVE 683 100 51 65 17 tfor:TF0467|3end_acetyltransferase-related_protein_486543..486693_POSITIVE 599 120 71 53 2 tfor:TF1540|3end_possible_ATPase_1645987..1646137_POSITIVE 594 117 72 42 1 tfor:TF2638|3end_cation_transport_protein_2809051..2809201_POSITIVE 518 42 2 95 45 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 515 26 1 151 126 tfor:TF2025|3end_hypothetical_protein_2182180..2182330_POSITIVE 507 34 2 58 21 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE 477 90 45 45 1 tfor:TF1473|3end_hypothetical_protein_1566966..1567116_POSITIVE 472 111 76 36 1 tfor:TF1515|3end_hypothetical_protein_1626184..1626334_POSITIVE 443 29 2 71 40 tfor:TF2922|3end_surface_antigen_BspA_3121538..3121688_POSITIVE 421 248 205 150 111 tfor:TF2937|3end_translation_elongation_factor_Tu_3140502..3140652_POSITIVE 408 100 74 84 58 tfor:TF0724|3end_possible_transcriptional_regulator_776333..776483_POSITIVE 405 170 122 79 13 tfor:TF0860|3end_conserved_hypothetical_protein_913369..913519_POSITIVE 387 259 211 134 89 tfor:TF1296|3end_possible_DNA-binding_protein,_histone-like_family_1378982..1379132_POSITIVE 383 110 78 33 1 tfor:TF2024|3end_conserved_hypothetical_protein_2181979..2182129_POSITIVE 381 167 126 109 58 tfor:TF0779|3end_possible_outer_membrane_protein_831874..832024_POSITIVE 380 240 191 83 36 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 377 185 144 149 112 tfor:TF2128|3end_3-oxoacyl-(acyl-carrier_protein)_synthase_2305534..2305684_POSITIVE 377 29 2 81 51 tfor:TF0344|3end_hypothetical_protein_366963..367113_POSITIVE