Origin IGS: ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca .........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 tgaaagagataaaagctatatatacgatatgttgacatattcaaatgagaaattgcttccaaatctataccggaactaattaatttgctaaattcaaaaaaatttatatgagtatcttaaaccttattgacaaaaaattagaatttatgtagactatctagctagataactcgttataccatttgcggttaaattaagtgagtgactatttaccgctccgaatatgacttttgtcactggtaaaacgggtaaaaaatatgtaaacttacagaaatgtaaggcggaaagttaaaatgtaagctatagtaa Mask Tandem Repeat Region ================================================ ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca Find is-nt database================================================ Query_seq: TDE1853:TDE1854|TDE1853:TDE1854:hypothetical protein:nucleotidyltransferase family protein:<-<-:1882173..1882481 309 ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1853:TDE1854|TDE1853:TDE1854:hypothetical protein:nucleotidyltransferase family protein:<-<-:1882173..1882481 309 ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1853:TDE1854|TDE1853:TDE1854:hypothetical protein:nucleotidyltransferase family protein:<-<-:1882173..1882481 309 ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 203 End: 307 .......................................................................................................................................................................................................... M N F F E F S K L I S S G I D L E A I S H L N M S T Y R I Y S F Y L F .. ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca 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: 85 Start: 155 End: 184 ..........................................................................................................................................................ATTGACAAAAAATTAGAATTTATGTAGACT............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1853:TDE1854|TDE1853:TDE1854:hypothetical protein:nucleotidyltransferase family protein:<-<-:1882173..1882481 309 ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca Intra-Species Hit: Count: 1 Min: 1 Max: 309 Len: 309 Subject: NC_002967_TDE1853_TDE1854|hypothetical protein:nucleotidyltransferase family protein|NEGATIVE:NEGATIVE|[1882173,1882481]|309 HSP 1 e-value: 1.0E-162 bit: 571.0 Len: 309 Query Start:1 Query End:309 Subject Strand: POSITIVE Subject Start: 1 Subject End: 309 ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaannnnnnngaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca ttactatagcttacattttaactttccgccttacatttctgtaagtttacatattttttacccgttttaccagtgacaaaagtcatattcggagcggtaaatagtcactcacttaatttaaccgcaaatggtataacgagttatctagctagatagtctacataaattctaattttttgtcaataaggtttaagatactcatataaatttttttgaatttagcaaattaattagttccggtatagatttggaagcaatttctcatttgaatatgtcaacatatcgtatatatagcttttatctctttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACUAUAGCUUACAUUUUAACUUUCCGCCUUACAUUUCUGUAAGUUUACAUAUUUUUUACCCGUUUUACCAGUGACAAAAGUCAUAUUCGGAGCGGUAAAUAGUCACUCACUUAAUUUAACCGCAAAUGGUAUAACGAGUUAUCUAGCUAGAUAGUCUACAUAAAUUCUAAUUUUUUGUCAAUAAGGUUUAAGAUACUCAUAUAAAUUUUUUUGAAUUUAGCAAAUUAAUUAGUUCCGGUAUAGAUUUGGAAGCAAUUUCUCAUUUGAAUAUGUCAACAUAUCGUAUAUAUAGCUUUUAUCUCUUUCA ...(((((...(((...............((((((....))))))...((((((((...((.((((.((((((((((....))))).......((((((((((((.....)))..)))).)))))...))))).)))).))......(((....((((((.((.....((((((.(((((.....((((((((((...............)))))))))).)))))..)))))).....)).))))))....)))............)))))))).........)))..)))))............... (-55.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAGAGAUAAAAGCUAUAUAUACGAUAUGUUGACAUAUUCAAAUGAGAAAUUGCUUCCAAAUCUAUACCGGAACUAAUUAAUUUGCUAAAUUCAAAAAAAUUUAUAUGAGUAUCUUAAACCUUAUUGACAAAAAAUUAGAAUUUAUGUAGACUAUCUAGCUAGAUAACUCGUUAUACCAUUUGCGGUUAAAUUAAGUGAGUGACUAUUUACCGCUCCGAAUAUGACUUUUGUCACUGGUAAAACGGGUAAAAAAUAUGUAAACUUACAGAAAUGUAAGGCGGAAAGUUAAAAUGUAAGCUAUAGUAA .............((((.(((((.(((((..((((.(((((((.(((((.(((((.((((...........)))).)))))..((((.......))))....))))).))))))).))))....)))))......................((((.(((.((......(((((((.(((((...(((((.((((..(((.....))))))))))))........((((....)))).))))).)))))))..............((((((....))))))))))).))))...)))))))))....... (-60.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 907 110 61 201 152 NC_002967:TDE1853|5end_hypothetical_protein_1882082..1882312_NEGATIVE 263 128 82 76 36 NC_002967:TDE2529|5end_hypothetical_protein_2557238..2557468_NEGATIVE 263 63 25 160 121 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 260 79 36 124 73 NC_002967:TDE0820|5end_transcriptional_regulator,_TetR_family_844373..844603_NEGATIVE 254 267 237 69 33 NC_002967:TDE1033|5end_polyA_polymerase_family_protein_1061069..1061299_POSITIVE 247 43 4 185 138 NC_002967:TDE0920|5end_transcriptional_regulator,_AraC_family_940041..940271_NEGATIVE 244 270 227 189 145 NC_002967:TDE0533|5end_hypothetical_protein_575910..576140_POSITIVE 242 110 62 157 102 NC_002967:TDE1217|5end_flagellar_assembly_protein_1249511..1249741_POSITIVE 238 129 86 106 62 NC_002967:TDE1238|5end_translocase_1270815..1271045_POSITIVE 238 106 61 165 120 NC_002967:TDE1100|5end_acetyltransferase,_GNAT_family_1134672..1134902_NEGATIVE 236 133 91 44 5 NC_002967:TDE1712|5end_flagellar_filament_outer_layer_protein_1767915..1768145_NEGATIVE 235 139 91 72 32 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 231 111 78 42 8 NC_002967:TDE0553|5end_hypothetical_protein_590307..590537_NEGATIVE 230 108 61 121 58 NC_002967:TDE1824|5end_hypothetical_protein_1857011..1857241_POSITIVE 229 68 21 206 170 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 229 147 103 192 157 NC_002967:TDE0194|5end_hypothetical_protein_231881..232111_NEGATIVE 227 69 22 108 63 NC_002967:TDE0685|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_722620..722850_NEGATIVE 226 130 90 122 89 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 226 130 90 198 165 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 226 95 53 123 82 NC_002967:TDE1449|5end_GTPase_YjeQ_1494352..1494582_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 262 221 137 98 NC_002967:TDE0359|3end_ABC_transporter,_ATP-binding/permease_protein_402193..402343_NEGATIVE 260 95 64 90 59 NC_002967:TDE2306|3end_hypothetical_protein_2344138..2344288_NEGATIVE 260 120 73 106 48 NC_002967:TDE1771|3end_hypothetical_protein_1814579..1814729_NEGATIVE 255 110 62 87 33 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 250 98 52 139 92 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 247 43 4 108 61 NC_002967:TDE0921|3end_ABC_transporter,_ATP-binding/permease_protein_940118..940268_NEGATIVE 244 270 227 151 107 NC_002967:TDE0532|3end_TPR_domain_protein_575952..576102_POSITIVE 242 110 62 136 81 NC_002967:TDE1216|3end_flagellar_motor_protein_1249570..1249720_POSITIVE 235 139 91 61 21 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 231 129 84 60 13 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE 229 68 21 129 93 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 229 98 53 38 1 NC_002967:TDE0812|3end_ABC_transporter,_ATP-binding/permease_protein_834137..834287_POSITIVE 229 147 103 131 96 NC_002967:TDE0195|3end_acetyltransferase,_GNAT_family_231942..232092_NEGATIVE 226 95 53 121 80 NC_002967:TDE1448|3end_glutamate_racemase,_putative_1494430..1494580_POSITIVE 224 64 21 121 76 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 223 270 227 139 87 NC_002967:TDE0994|3end_hypothetical_protein_1022447..1022597_POSITIVE 222 255 218 147 115 NC_002967:TDE1050|3end_hypothetical_protein_1078150..1078300_POSITIVE 221 295 252 143 93 NC_002967:TDE2626|3end_ABC_transporter,_ATP-binding/permease_protein_2666657..2666807_NEGATIVE 220 97 62 87 41 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 220 157 122 141 104 NC_002967:TDE0702|3end_ABC_transporter,_ATP-binding_protein_737244..737394_NEGATIVE