Origin IGS: tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaaagttaatactccgttttttttaattaaaagttcgacaatctatttattactcactaaaaataatccgaaaaagtgggacaaagataatgctttttttcgaagaggaagccgttctcggaagaaaatctttgaatttcaatttttttca Mask Tandem Repeat Region ================================================ tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa Find is-nt database================================================ Query_seq: TF2786:TF2787|TF2786:TF2787:hypothetical protein:30S ribosomal protein S1:->->:2970363..2970515 153 tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2786:TF2787|TF2786:TF2787:hypothetical protein:30S ribosomal protein S1:->->:2970363..2970515 153 tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2786:TF2787|TF2786:TF2787:hypothetical protein:30S ribosomal protein S1:->->:2970363..2970515 153 tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 10 End: 99 ......... M K F K D F L P R T A S S S K K S I I F V P L F R I I F S E ...................................................... Protein_Len: 35 Strand: - Start: 3 End: 107 .. F F N F N L S K R G L V A E E E F F L M I K T G S K R I I K L S Y Y M .............................................. Protein_Len: 42 Strand: - Start: 1 End: 126 S F F Q F E F I K K R S R S G R R F F A N D K D W K K P N N K T L L L Y I T S S K M ........................... tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa 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================================================ tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2786:TF2787|TF2786:TF2787:hypothetical protein:30S ribosomal protein S1:->->:2970363..2970515 153 tgaaaaaaattgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa Intra-Species Hit: Count: 1 Min: 10 Max: 153 Len: 144 Subject: tfor_TF2786_TF2787|hypothetical protein:30S ribosomal protein S1|POSITIVE:POSITIVE|[2970363,2970515]|153 HSP 1 e-value: 1.0E-49 bit: 196.0 Len: 144 Query Start:10 Query End:153 Subject Strand: POSITIVE Subject Start: 10 Subject End: 153 .........ttgaaattcaaagattttcttccgagaacggcttcctcttcgnnnnnnngcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattnnnnnnnncggagtattaactttaaa .........ttgaaattcaaagattttcttccgagaacggcttcctcttcgaaaaaaagcattatctttgtcccactttttcggattatttttagtgagtaataaatagattgtcgaacttttaattaaaaaaaacggagtattaactttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAAAUUCAAAGAUUUUCUUCCGAGAACGGCUUCCUCUUCGAAAAAAAGCAUUAUCUUUGUCCCACUUUUUCGGAUUAUUUUUAGUGAGUAAUAAAUAGAUUGUCGAACUUUUAAUUAAAAAAAACGGAGUAUUAACUUUAAA .........((((......(((((....((((.((.....(((((((..(((.......))).....))))))).(((((((.....))))))).....))..))))...((((......))))..)))))......))))... (-16.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAAGUUAAUACUCCGUUUUUUUUAAUUAAAAGUUCGACAAUCUAUUUAUUACUCACUAAAAAUAAUCCGAAAAAGUGGGACAAAGAUAAUGCUUUUUUUCGAAGAGGAAGCCGUUCUCGGAAGAAAAUCUUUGAAUUUCAA ................((..(((((.....)))))..))...............((((((................)))))).(((((((.....((((((((((..(.(....).)..)))))))))))))))))........ (-22.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 45 18 219 187 tfor:TF2683|5end_translation_initiation_factor_IF-2_2857722..2857952_POSITIVE 334 64 21 84 37 tfor:TF3120|5end_HD_superfamily_hydrolase_3353169..3353399_POSITIVE 301 68 22 189 135 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 301 53 22 68 32 tfor:TF0409|5end_conserved_hypothetical_protein_426240..426470_POSITIVE 289 42 6 199 160 tfor:TF0779|5end_possible_outer_membrane_protein_830346..830576_POSITIVE 283 65 23 87 43 tfor:TF3070|5end_conserved_hypothetical_protein_3294380..3294610_POSITIVE 283 42 1 224 177 tfor:TF2684|5end_conserved_hypothetical_protein;_possible_CvpA_family_protein_2860692..2860922_POSITIVE 283 60 15 173 129 tfor:TF1286|5end_hypothetical_protein_1369199..1369429_POSITIVE 279 52 17 186 146 tfor:TF1740|5end_hypothetical_protein_1868645..1868875_POSITIVE 273 42 1 164 119 tfor:TF3121|5end_nicotinate_phosphoribosyltransferase_3354815..3355045_POSITIVE 272 76 31 72 24 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 270 42 1 231 183 tfor:TF2387|5end_transposase_2554464..2554694_POSITIVE 266 43 1 160 113 tfor:TF2950|5end_chloromuconate_cycloisomerase_3157399..3157629_POSITIVE 266 70 22 159 102 tfor:TF1636|5end_hypothetical_protein_1747143..1747373_POSITIVE 266 70 22 122 65 tfor:TF1637|5end_hypothetical_protein_1747106..1747336_POSITIVE 265 75 31 57 7 tfor:TF2622|5end_methyltransferase_2797567..2797797_POSITIVE 258 52 15 48 15 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 257 77 36 76 26 tfor:TF0831|5end_conserved_hypothetical_protein_888183..888413_POSITIVE 257 38 18 151 131 tfor:TF0448|5end_hypothetical_protein_467664..467894_POSITIVE 256 64 22 76 30 tfor:TF2853|5end_2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_3040172..3040402_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 53 22 72 36 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 283 60 15 139 95 tfor:TF1285|3end_hypothetical_protein_1369245..1369395_POSITIVE 279 52 17 65 25 tfor:TF1739|3end_possible_sulfatase_1868604..1868754_POSITIVE 270 42 1 136 88 tfor:TF2386|3end_beta-galactosidase_2554449..2554599_POSITIVE 267 89 41 84 41 tfor:TF0219|3end_threonyl-tRNA_synthetase_245878..246028_POSITIVE 262 65 29 40 1 tfor:TF3069|3end_hypothetical_protein_3294413..3294563_POSITIVE 259 42 5 44 2 tfor:TF3120|3end_HD_superfamily_hydrolase_3354775..3354925_POSITIVE 258 52 15 48 15 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 257 77 36 63 13 tfor:TF0829|3end_conserved_hypothetical_protein_888250..888400_POSITIVE 256 41 16 148 114 tfor:TF2247|3end_transfer_region-related_protein,_TraA_2422625..2422775_POSITIVE 254 75 35 107 74 tfor:TF2891|3end_lipoprotein_3079381..3079531_POSITIVE 250 75 31 120 73 tfor:TF2189|3end_conserved_hypothetical_protein_2364884..2365034_POSITIVE 250 75 32 82 46 tfor:TF1876|3end_hypothetical_protein_2030054..2030204_POSITIVE 248 44 18 65 44 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 248 64 23 68 26 tfor:TF1554|3end_UDP-glucose_dehydrogenase_1661013..1661163_POSITIVE 247 65 26 62 25 tfor:TF2655|3end_DNA_topoisomerase_I_2826962..2827112_POSITIVE 242 76 34 97 44 tfor:TF2907|3end_CDP-diacylglycerol-serine-O-phosphatidyltransfera_se_3103681..3103831_POSITIVE 242 70 22 110 43 tfor:TF1185|3end_hypothetical_protein_1269563..1269713_POSITIVE 241 45 21 26 1 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 240 75 37 38 1 tfor:TF2621|3end_conserved_hypothetical_protein;_possible_SAM-dependent_methyltransferase_2797628..2797778_POSITIVE