Origin IGS: caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt .........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 aaactcgtaaaagttatgtagcgagcaaaaaggagtatacagtattttctcactttttgtcaagagctttttaaaagttttttttattttttttaaccttttttgcagcttttaaactgccaaacttaagaagtcttaccttcattgaaaatgcaagacttgcaaaacttttctagtgttttctttgcttttctaggcacaccgtcttaacagacggtgtgagcgaatatacccctttctcaaacttttg Mask Tandem Repeat Region ================================================ caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt Find is-nt database================================================ Query_seq: TDE0578:TDE0579|TDE0578:TDE0579:hypothetical protein:hypothetical protein:-><-:609738..609987 250 caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0578:TDE0579|TDE0578:TDE0579:hypothetical protein:hypothetical protein:-><-:609738..609987 250 caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0578:TDE0579|TDE0578:TDE0579:hypothetical protein:hypothetical protein:-><-:609738..609987 250 caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 143 End: 250 .............................................................................................................................................. M Q K R L K K I K K T F K K L L T K S E K I L Y T P F C S L H N F Y E F caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt 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================================================ caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -6.3 Tail_Score: -4.18494 Start: 87 End: 99 Full_Region: ACACTAGAAAAGTTT TGCAA GTC TTGCA TTTTCAATGAAGGTA ......................................................................................TGCAAGTCTTGCA....................................................................................................................................................... TransTerm Strand: + Conf: 44 HP_score: -2.4 Tail_Score: -3.28269 Start: 108 End: 121 Full_Region: TCTTGCATTTTCAAT GAAG GTAAGA CTTC TTAAGTTTGGCAGTT ...........................................................................................................GAAGGTAAGACTTC................................................................................................................................. TransTerm Strand: - Conf: 78 HP_score: -2.2 Tail_Score: -5.82388 Start: 165 End: 179 Full_Region: ttgtcaagagctttt taaaag ttt ttttta ttttttttaaccttt ....................................................................................................................................................................taaaagtttttttta....................................................................... TransTerm Strand: - Conf: 95 HP_score: -4.0 Tail_Score: -6.47325 Start: 174 End: 184 Full_Region: actttttgtcaagag cttt tta aaag ttttttttatttttt .............................................................................................................................................................................ctttttaaaag.................................................................. Find igs database================================================ Query_seq: TDE0578:TDE0579|TDE0578:TDE0579:hypothetical protein:hypothetical protein:-><-:609738..609987 250 caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgcaaaaaaggttaaaaaaaataaaaaaaacttttaaaaagctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt Intra-Species Hit: Count: 2 Min: 1 Max: 250 Len: 250 Subject: NC_002967_TDE0578_TDE0579|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[609738,609987]|250 HSP 1 e-value: 2.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgc........................................................................................................ caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttcaatgaaggtaagacttcttaagtttggcagtttaaaagctgc........................................................................................................ HSP 2 e-value: 3.0E-30 bit: 133.0 Len: 67 Query Start:184 Query End:250 Subject Strand: POSITIVE Subject Start: 184 Subject End: 250 .......................................................................................................................................................................................gctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt .......................................................................................................................................................................................gctcttgacaaaaagtgagaaaatactgtatactcctttttgctcgctacataacttttacgagttt Subject: NC_002967_TDE1191_TDE1192|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1219279,1219471]|193 HSP 1 e-value: 4.0E-48 bit: 192.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 89 Subject End: 193 caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca................................................................................................................................................. caaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAGUUUGAGAAAGGGGUAUAUUCGCUCACACCGUCUGUUAAGACGGUGUGCCUAGAAAAGCAAAGAAAACACUAGAAAAGUUUUGCAAGUCUUGCAUUUUCAAUGAAGGUAAGACUUCUUAAGUUUGGCAGUUUAAAAGCUGCAAAAAAGGUUAAAAAAAAUAAAAAAAACUUUUAAAAAGCUCUUGACAAAAAGUGAGAAAAUACUGUAUACUCCUUUUUGCUCGCUACAUAACUUUUACGAGUUU .((((((((((((((((((((((((((((((((((((((....)))))))))).........(..((((.........(((((((((..(((((((((.(((.....))).))))))))).((((.(((.((((((....))))))....))).))))...........))))))))).......))))..)....))))).........))))))))))))...))))......)))))))........ (-65.29) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUCGUAAAAGUUAUGUAGCGAGCAAAAAGGAGUAUACAGUAUUUUCUCACUUUUUGUCAAGAGCUUUUUAAAAGUUUUUUUUAUUUUUUUUAACCUUUUUUGCAGCUUUUAAACUGCCAAACUUAAGAAGUCUUACCUUCAUUGAAAAUGCAAGACUUGCAAAACUUUUCUAGUGUUUUCUUUGCUUUUCUAGGCACACCGUCUUAACAGACGGUGUGAGCGAAUAUACCCCUUUCUCAAACUUUUG ...(((((............)))))...(((((.(((((..((((((((..............(.((..((((((((((...........................))))))))))..)))........((((......))))...)))))))).....((((.........((((.((.......))....)))).((((((((((....)))))))))).)))).))))).)))))............ (-53.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 53 30 167 144 NC_002967:TDE1192|5end_hypothetical_protein_1219332..1219562_POSITIVE 300 67 25 92 51 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 293 53 17 109 75 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 285 69 25 139 84 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 276 59 15 124 74 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 269 55 18 104 62 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 268 247 210 56 14 NC_002967:TDE1556|5end_hypothetical_protein_1598787..1599017_POSITIVE 266 65 33 157 127 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 262 56 16 56 26 NC_002967:TDE0793|5end_hypothetical_protein_818910..819140_POSITIVE 259 60 11 224 159 NC_002967:TDE2482|5end_hypothetical_protein_2505536..2505766_POSITIVE 259 49 4 67 24 NC_002967:TDE1029|5end_Hsp20/alpha_crystallin_family_protein_1058574..1058804_POSITIVE 258 47 16 226 192 NC_002967:TDE1398|5end_hypothetical_protein_1437192..1437422_POSITIVE 253 64 22 174 138 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 249 66 27 91 61 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 249 249 214 191 155 NC_002967:TDE1455|5end_prevent-host-death_family_protein_1502865..1503095_POSITIVE 246 239 196 120 74 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 246 56 23 51 12 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 245 49 9 69 27 NC_002967:TDE2045|5end_hypothetical_protein_2074933..2075163_NEGATIVE 243 145 104 42 1 NC_002967:TDE0009|5end_hypothetical_protein_14545..14775_NEGATIVE 242 100 52 194 145 NC_002967:TDE2608|5end_hypothetical_protein_2649275..2649505_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 824 230 181 70 21 NC_002967:TDE1193|3end_hypothetical_protein_1219526..1219676_NEGATIVE 330 56 15 108 63 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 312 53 30 61 38 NC_002967:TDE0578|3end_hypothetical_protein_609677..609827_POSITIVE 300 67 25 85 44 NC_002967:TDE0847|3end_hypothetical_protein_871342..871492_POSITIVE 285 75 33 69 26 NC_002967:TDE2141|3end_hypothetical_protein_2175583..2175733_NEGATIVE 285 69 25 58 3 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 284 70 26 81 36 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 278 148 104 147 96 NC_002967:TDE0937|3end_RNA_polymerase_sigma-70_factor_family_protein_960891..961041_POSITIVE 268 247 210 45 3 NC_002967:TDE1555|3end_hypothetical_protein_1598856..1599006_POSITIVE 262 56 16 72 42 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 259 55 17 117 70 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 259 54 11 108 56 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 259 49 4 74 31 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 249 66 27 78 48 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 249 249 214 128 92 NC_002967:TDE1454|3end_sugar_transporter_1502882..1503032_POSITIVE 247 55 12 146 96 NC_002967:TDE0009|3end_hypothetical_protein_13724..13874_NEGATIVE 246 239 196 98 52 NC_002967:TDE2767|3end_flagellar_protein-related_protein_2820896..2821046_NEGATIVE 243 60 14 71 15 NC_002967:TDE1022|3end_ISTde2,_transposase_1053912..1054062_NEGATIVE 242 64 24 49 8 NC_002967:TDE2483|3end_hypothetical_protein_2505880..2506030_NEGATIVE 242 55 11 116 69 NC_002967:TDE0735|3end_hypothetical_protein_774746..774896_NEGATIVE