Origin IGS: gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgtcatctattatttgaaaggctctataatttacgttatttaatttttccgttttttcgataatggaagggtaggggatttttaccgataaggtataggttttcgaaaagccattatcatctttttctgcttcaatgtttgtaataagtaagttattggtaccgtttattacctcatctccgatataaatttgagtgtatttatttttacagattttttttgtatcgattctttttccgtttaagtataagaaaaaattctttacattttcggtataaaaataaacatagccctgtcccgtataagccttaaaagggataaaaccgtttggtaaaattgaaggatcatatttttctttttccggaggaaagcttacatccgtctgaaagcctgaaaagccgccttcggtttcttccgatttataaatgtctgcgtctgccggatcggtctttatctttgatatttgagccgagcggc Mask Tandem Repeat Region ================================================ gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt Find is-nt database================================================ Query_seq: TDE2094:TDE2095|TDE2094:TDE2095:hypothetical protein:hypothetical protein:<-->:2121410..2121888 479 gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2094:TDE2095|TDE2094:TDE2095:hypothetical protein:hypothetical protein:<-->:2121410..2121888 479 gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2094:TDE2095|TDE2094:TDE2095:hypothetical protein:hypothetical protein:<-->:2121410..2121888 479 gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 15 End: 479 .............. M S K I K T D P A D A D I Y K S E E T E G G F S G F Q T D V S F P P E K E K Y D P S I L P N G F I P F K A Y T G Q G Y V Protein_Len: 37 Strand: - Start: 169 End: 279 ........................................................................................................................................................................ P K Y P V P S H K N K Y R F H L S N K R I S L R F F F R Y L F F R Y F Y M ........................................................................................................................................................................................................ Protein_Len: 50 Strand: - Start: 1 End: 150 G S P E F I L S L S R D P L R L C K Y I P L F R L R S K L S E S P H L S E E P F L F I H D K L K V M ......................................................................................................................................................................................................................................................................................................................................... gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt 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================================================ gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 50 HP_score: -2.1 Tail_Score: -3.72576 Start: 88 End: 107 Full_Region: AAGGCGGCTTTTCAG GCTTTCA GACGGA TGTAAGC TTTCCTCCGGAAAAA .......................................................................................GCTTTCAGACGGATGTAAGC.................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TDE2094:TDE2095|TDE2094:TDE2095:hypothetical protein:hypothetical protein:<-->:2121410..2121888 479 gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt Intra-Species Hit: Count: 1 Min: 1 Max: 479 Len: 479 Subject: NC_002967_TDE2094_TDE2095|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2121410,2121888]|479 HSP 1 e-value: 0.0 bit: 902.0 Len: 479 Query Start:1 Query End:479 Subject Strand: POSITIVE Subject Start: 1 Subject End: 479 gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacnnnnnnnntctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt gccgctcggctcaaatatcaaagataaagaccgatccggcagacgcagacatttataaatcggaagaaaccgaaggcggcttttcaggctttcagacggatgtaagctttcctccggaaaaagaaaaatatgatccttcaattttaccaaacggttttatcccttttaaggcttatacgggacagggctatgtttatttttataccgaaaatgtaaagaattttttcttatacttaaacggaaaaagaatcgatacaaaaaaaatctgtaaaaataaatacactcaaatttatatcggagatgaggtaataaacggtaccaataacttacttattacaaacattgaagcagaaaaagatgataatggcttttcgaaaacctataccttatcggtaaaaatcccctacccttccattatcgaaaaaacggaaaaattaaataacgtaaattatagagcctttcaaataatagatgacatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGCUCGGCUCAAAUAUCAAAGAUAAAGACCGAUCCGGCAGACGCAGACAUUUAUAAAUCGGAAGAAACCGAAGGCGGCUUUUCAGGCUUUCAGACGGAUGUAAGCUUUCCUCCGGAAAAAGAAAAAUAUGAUCCUUCAAUUUUACCAAACGGUUUUAUCCCUUUUAAGGCUUAUACGGGACAGGGCUAUGUUUAUUUUUAUACCGAAAAUGUAAAGAAUUUUUUCUUAUACUUAAACGGAAAAAGAAUCGAUACAAAAAAAAUCUGUAAAAAUAAAUACACUCAAAUUUAUAUCGGAGAUGAGGUAAUAAACGGUACCAAUAACUUACUUAUUACAAACAUUGAAGCAGAAAAAGAUGAUAAUGGCUUUUCGAAAACCUAUACCUUAUCGGUAAAAAUCCCCUACCCUUCCAUUAUCGAAAAAACGGAAAAAUUAAAUAACGUAAAUUAUAGAGCCUUUCAAAUAAUAGAUGACAUU (((....))).....((((...(((((.(((((.(((((..((.((..((((((.....((....))....((((((..........))))))....))))))..))..))..)))))......(((((.(((....))))))))......))))))))))......(((((((....((((.((((((((..((((((((...(((.....((((((((....))))).))).....))).......................(((((....((((((........))))))......((((..(((((((..(((.......)))...)))))))...))))...))))).))))))))..))))))))...........((((.....))))....))))......((((.((........)).))))......................)))))))..........))))..... (-93.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUCAUCUAUUAUUUGAAAGGCUCUAUAAUUUACGUUAUUUAAUUUUUCCGUUUUUUCGAUAAUGGAAGGGUAGGGGAUUUUUACCGAUAAGGUAUAGGUUUUCGAAAAGCCAUUAUCAUCUUUUUCUGCUUCAAUGUUUGUAAUAAGUAAGUUAUUGGUACCGUUUAUUACCUCAUCUCCGAUAUAAAUUUGAGUGUAUUUAUUUUUACAGAUUUUUUUUGUAUCGAUUCUUUUUCCGUUUAAGUAUAAGAAAAAAUUCUUUACAUUUUCGGUAUAAAAAUAAACAUAGCCCUGUCCCGUAUAAGCCUUAAAAGGGAUAAAACCGUUUGGUAAAAUUGAAGGAUCAUAUUUUUCUUUUUCCGGAGGAAAGCUUACAUCCGUCUGAAAGCCUGAAAAGCCGCCUUCGGUUUCUUCCGAUUUAUAAAUGUCUGCGUCUGCCGGAUCGGUCUUUAUCUUUGAUAUUUGAGCCGAGCGGC ((((((.............((((((.((((..................(((((((........)))))))((((((((......(((((((((((((..(((((.....)))))..)))).........(((((.............)))))..)))))))))..(((((((..........(((((((((...((.((((........))))..))...))))))))).........(((.....(((.(((((....)))))))).....)))......)))))))....))))).))).))))))))))...((((((((((((((((((((.....((((((........))))))...((((((((.((((.((......)).)))).......((((....))))))))))))...................))))))).)))).)))))))))))))))...(((....))) (-109.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1035 50 1 141 92 NC_002967:TDE2094|5end_hypothetical_protein_2121319..2121549_NEGATIVE 447 80 36 182 144 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 356 79 32 191 131 NC_002967:TDE1233|5end_hypothetical_protein_1267203..1267433_POSITIVE 355 117 73 69 27 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 346 117 71 172 128 NC_002967:TDE2407|5end_amidophosphoribosyltransferase_2435107..2435337_NEGATIVE 332 115 76 100 57 NC_002967:TDE2406|5end_TldD/PmbA_family_protein_2433513..2433743_NEGATIVE 327 110 61 192 139 NC_002967:TDE1336|5end_hypothetical_protein_1372303..1372533_POSITIVE 323 115 71 175 136 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 321 80 31 68 15 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 317 115 71 223 187 NC_002967:TDE0469|5end_hypothetical_protein_523987..524217_NEGATIVE 311 80 41 198 155 NC_002967:TDE2248|5end_HesA/MoeB/ThiF_family_protein_2287478..2287708_NEGATIVE 311 103 62 95 49 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 306 180 147 178 144 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 303 80 33 228 176 NC_002967:TDE2475|5end_MATE_efflux_family_protein_2498521..2498751_NEGATIVE 302 77 35 221 184 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 299 80 31 152 97 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 299 79 37 196 164 NC_002967:TDE0769|5end_ribosomal_protein_L23_807634..807864_POSITIVE 297 80 31 209 168 NC_002967:TDE2614|5end_ApbE_family_protein_2657133..2657363_NEGATIVE 295 117 72 52 13 NC_002967:TDE0872|5end_recA_protein_894841..895071_POSITIVE 294 191 152 61 20 NC_002967:TDE2551|5end_hypothetical_protein_2577282..2577512_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 100 54 79 26 NC_002967:TDE1844|3end_DNA_integrase_1873197..1873347_NEGATIVE 361 117 71 55 2 NC_002967:TDE1980|3end_hypothetical_protein_1991960..1992110_NEGATIVE 355 116 73 112 64 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 346 117 71 62 18 NC_002967:TDE2408|3end_hypothetical_protein_2435217..2435367_NEGATIVE 334 117 71 132 79 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 321 80 31 54 1 NC_002967:TDE0907|3end_hypothetical_protein_925320..925470_POSITIVE 318 98 55 103 54 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 317 79 35 47 1 NC_002967:TDE1856|3end_radical_SAM_domain_protein_1883956..1884106_POSITIVE 316 110 61 91 40 NC_002967:TDE2729|3end_hypothetical_protein_2785756..2785906_NEGATIVE 312 117 75 132 85 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 311 103 62 74 28 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 302 109 61 60 24 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 300 100 59 55 9 NC_002967:TDE1771|3end_hypothetical_protein_1814579..1814729_NEGATIVE 296 98 55 81 35 NC_002967:TDE0238|3end_thioredoxin,_selenocysteine-containing_271783..271933_POSITIVE 294 119 71 77 25 NC_002967:TDE1347|3end_hypothetical_protein_1388032..1388182_POSITIVE 290 49 3 119 76 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 289 119 74 79 30 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 288 116 71 108 51 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 286 99 61 48 15 NC_002967:TDE1051|3end_hypothetical_protein_1078212..1078362_NEGATIVE 285 118 75 42 4 NC_002967:TDE2144|3end_hypothetical_protein_2180451..2180601_NEGATIVE