Origin IGS: aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt .........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 actttcttatcggtatttttagaataaacctttaggaacacttttttacaaaaaaaatgctctttttacataaaaatttaaaaatttaagaaaaatttttaaatttttatgtaaccaaaagcccctaaatagttttgtttagtgtatgttgaacgacaacaaacaattcaatatacctcctttgcagtttcccgacaggtttttctcctccttttgcctgtcgggttttttattttcttgataacttatttcaaaaattactatattttatatataattattgacattatatataattatatataaaatataggtataaattaggaggtttt Mask Tandem Repeat Region ================================================ aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt Find is-nt database================================================ Query_seq: TDE0663:TDE0664|TDE0663:TDE0664:hypothetical protein:OmpA family protein:<-->:698188..698519 332 aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0663:TDE0664|TDE0663:TDE0664:hypothetical protein:OmpA family protein:<-->:698188..698519 332 aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0663:TDE0664|TDE0663:TDE0664:hypothetical protein:OmpA family protein:<-->:698188..698519 332 aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 69 End: 191 .................................................................... M V I F E I S Y Q E N K K P D R Q K E E K N L S G N C K G G I L N C L L S F N I H ............................................................................................................................................. Protein_Len: 31 Strand: - Start: 95 End: 187 .............................................................................................. S F L F G S L C F S S F F R D P F Q L P P I N F Q K N D N L M ................................................................................................................................................. Protein_Len: 37 Strand: - Start: 52 End: 162 ................................................... Y N Y I F Y L L K Q F L N D L F Y F V R C A F P P S F G T P F S C L L Y M .......................................................................................................................................................................... Protein_Len: 54 Strand: - Start: 30 End: 191 ............................. I Y N Y I I D I I I Y L I Y Y N K F Y T I L F I F F G V P L L L L F V Q R S V A F S T Y Q I T Q Q R E V Y M ............................................................................................................................................. aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt 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: 90 Start: 24 End: 53 .......................ATTGACATTATATATAATTATATATAAAAT....................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 55 End: 84 ......................................................TTTCAAAAATTACTATATTTTATATATAAT........................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -7.7 Tail_Score: -3.37188 Start: 17 End: 74 Full_Region: AAACCTCCTAATTTA TACCTATATTTTATATATAATTATATAT AAT GTCAATAATTATATATAAAATATAGTA ATTTTTGAAATAAGT ................TACCTATATTTTATATATAATTATATATAATGTCAATAATTATATATAAAATATAGTA.................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 71 HP_score: -5.8 Tail_Score: -4.63184 Start: 17 End: 75 Full_Region: AAACCTCCTAATTTA TACCTATATTTTATATATAATTATATAT AAT GTCAATAATTATATATAAAATATAGTAA TTTTTGAAATAAGTT ................TACCTATATTTTATATATAATTATATATAATGTCAATAATTATATATAAAATATAGTAA................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 62 HP_score: -7.1 Tail_Score: -2.53392 Start: 17 End: 74 Full_Region: acttatttcaaaaat tactatattttatatataattat tgacattatat ataattatatataaaatataggta taaattaggaggttt ................tactatattttatatataattattgacattatatataattatatataaaatataggta.................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 93 HP_score: -11.9 Tail_Score: -3.25166 Start: 20 End: 72 Full_Region: CCTCCTAATTTATAC CTATATTTTATATATAATTATATAT AAT GTCAATAATTATATATAAAATATAG TAATTTTTGAAATAA ...................CTATATTTTATATATAATTATATATAATGTCAATAATTATATATAAAATATAG.................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -2.1 Tail_Score: -5.92399 Start: 108 End: 142 Full_Region: cctcctttgcagttt cccgacaggtt tttctcctccttt tgcctgtcggg ttttttattttcttg ...........................................................................................................cccgacaggtttttctcctccttttgcctgtcggg.............................................................................................................................................................................................. TransTerm Strand: + Conf: 80 HP_score: -6.9 Tail_Score: -4.96848 Start: 230 End: 256 Full_Region: TTGGTTACATAAAAA TTTAAAAATTT TTCTT AAATTTTTAAA TTTTTATGTAAAAAG .....................................................................................................................................................................................................................................TTTAAAAATTTTTCTTAAATTTTTAAA............................................................................ TransTerm Strand: - Conf: 80 HP_score: -6.9 Tail_Score: -4.96848 Start: 230 End: 256 Full_Region: ctttttacataaaaa tttaaaaattt aagaa aaatttttaaa tttttatgtaaccaa .....................................................................................................................................................................................................................................tttaaaaatttaagaaaaatttttaaa............................................................................ Find igs database================================================ Query_seq: TDE0663:TDE0664|TDE0663:TDE0664:hypothetical protein:OmpA family protein:<-->:698188..698519 332 aaaacctcctaatttatacctatattttatatataattatatataatgtcaataattatatataaaatatagtaatttttgaaataagttatcaagaaaataaaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacactaaacaaaactatttaggggcttttggttacataaaaatttaaaaatttttcttaaatttttaaatttttatgtaaaaagagcattttttttgtaaaaaagtgttcctaaaggtttattctaaaaataccgataagaaagt Intra-Species Hit: Count: 1 Min: 103 Max: 332 Len: 230 Subject: NC_002967_TDE0663_TDE0664|hypothetical protein:OmpA family protein|NEGATIVE:POSITIVE|[698188,698519]|332 HSP 1 e-value: 3.0E-43 bit: 176.0 Len: 89 Query Start:103 Query End:191 Subject Strand: POSITIVE Subject Start: 103 Subject End: 191 ......................................................................................................aaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacac............................................................................................................................................. ......................................................................................................aaaaacccgacaggcaaaaggaggagaaaaacctgtcgggaaactgcaaaggaggtatattgaattgtttgttgtcgttcaacatacac............................................................................................................................................. HSP 2 e-value: 1.0E-14 bit: 81.8 Len: 41 Query Start:292 Query End:332 Subject Strand: POSITIVE Subject Start: 292 Subject End: 332 ...................................................................................................................................................................................................................................................................................................gtgttcctaaaggtttattctaaaaataccgataagaaagt ...................................................................................................................................................................................................................................................................................................gtgttcctaaaggtttattctaaaaataccgataagaaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCCGACAGGCAAAAGGAGGAGAAAAACCUGUCGGGAAACUGCAAAGGAGGUAUAUUGAAUUGUUUGUUGUCGUUCAACAUACACUAAACAAAACUAUUUAGGGGCUUUUGGUUACAUAAAAAUUUAAAAAUUUUUCUUAAAUUUUUAAAUUUUUAUGUAAAAAGAGCAUUUUUUUUGUAAAAAAGUGUUCCUAAAGGUUUAUUCUAAAAAUACCGAUAAGAAAGU .....(((((((((.................)))))))))..(((........(((((.......(((.(((((.....))))).))).............(((((((((((((((((((((((((((((((((((((.....))))))))))))))))))))))...(((((((((((.....)))))))))))))))))))...))))))).)))))........))) (-64.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUCUUAUCGGUAUUUUUAGAAUAAACCUUUAGGAACACUUUUUUACAAAAAAAAUGCUCUUUUUACAUAAAAAUUUAAAAAUUUAAGAAAAAUUUUUAAAUUUUUAUGUAACCAAAAGCCCCUAAAUAGUUUUGUUUAGUGUAUGUUGAACGACAACAAACAAUUCAAUAUACCUCCUUUGCAGUUUCCCGACAGGUUUUUCUCCUCCUUUUGCCUGUCGGGUUUUU ...........(((((.....(((((((.(((((((.....((((((....)))))).(((....((((((((((((((((((((((.....)))))))))))))))))))))).....))).)))))..)).)))))))..(((.(((((.....))))).))).......))))).............((((((((((...............))))))))))..... (-56.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 687 38 1 231 194 NC_002967:TDE0663|5end_hypothetical_protein_698097..698327_NEGATIVE 323 49 4 159 106 NC_002967:TDE2426|5end_transcription_antitermination_protein_NusG_2455799..2456029_NEGATIVE 317 77 32 78 15 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 307 47 6 53 3 NC_002967:TDE2335|5end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_2369641..2369871_POSITIVE 301 55 11 184 145 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 298 60 11 80 26 NC_002967:TDE2630|5end_peptide_ABC_transporter,_permease_protein,_putative_2670879..2671109_POSITIVE 285 46 2 174 132 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 283 47 7 170 119 NC_002967:TDE2129|5end_hypothetical_protein_2161463..2161693_POSITIVE 267 59 12 164 120 NC_002967:TDE0214|5end_hypothetical_protein_250449..250679_NEGATIVE 266 41 8 36 4 NC_002967:TDE1585|5end_hypothetical_protein_1633399..1633629_NEGATIVE 262 42 6 66 27 NC_002967:TDE0899|5end_ABC_transporter,_permease_protein,_putative_916481..916711_POSITIVE 261 55 12 231 173 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 256 50 6 74 26 NC_002967:TDE1616|5end_glycerate_dehydrogenase_1664723..1664953_NEGATIVE 256 48 6 203 170 NC_002967:TDE1314|5end_penicillin-binding_protein_1351174..1351404_POSITIVE 255 50 6 193 133 NC_002967:TDE2262|5end_peptidase,_U32_family_2299277..2299507_NEGATIVE 254 46 2 134 92 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 253 47 9 165 112 NC_002967:TDE1714|5end_N-acetylmuramoyl-L-alanine_amidase,_family_3_1769496..1769726_NEGATIVE 253 46 7 172 127 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 251 47 7 64 28 NC_002967:TDE0156|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_183571..183801_NEGATIVE 250 79 37 198 156 NC_002967:TDE1175|5end_chaperonin_GroEL_1205151..1205381_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 77 32 88 25 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 298 60 11 83 29 NC_002967:TDE2629|3end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2670962..2671112_POSITIVE 297 60 12 60 23 NC_002967:TDE2082|3end_hypothetical_protein_2112489..2112639_NEGATIVE 295 53 12 64 34 NC_002967:TDE2075|3end_GGDEF_domain/EAL_domain_protein_2101504..2101654_NEGATIVE 285 47 4 150 102 NC_002967:TDE2427|3end_preprotein_translocase,_SecE_subunit_2455803..2455953_NEGATIVE 281 48 8 147 101 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 265 48 7 150 97 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 262 42 6 62 23 NC_002967:TDE0898|3end_hypothetical_protein_916557..916707_POSITIVE 262 50 10 70 34 NC_002967:TDE0474|3end_hypothetical_protein_531134..531284_POSITIVE 256 50 6 81 33 NC_002967:TDE1617|3end_hypothetical_protein_1664716..1664866_NEGATIVE 255 58 11 54 3 NC_002967:TDE1505|3end_hypothetical_protein_1554137..1554287_POSITIVE 254 46 2 66 24 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 253 46 7 145 100 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 251 43 11 42 3 NC_002967:TDE1230|3end_hypothetical_protein_1263505..1263655_POSITIVE 250 79 37 67 25 NC_002967:TDE1176|3end_oxygen-independent_coproporphyrinogen_III_oxidase,_putative_1205282..1205432_NEGATIVE 248 52 12 149 111 NC_002967:TDE2324|3end_DNA-binding_response_regulator_2359921..2360071_POSITIVE 247 53 13 69 36 NC_002967:TDE2069|3end_endoribonuclease_L-PSP,_putative_2097089..2097239_POSITIVE 245 52 12 149 108 NC_002967:TDE2529|3end_hypothetical_protein_2556978..2557128_NEGATIVE 244 78 33 89 27 NC_002967:TDE0962|3end_hypothetical_protein_985973..986123_POSITIVE 242 55 13 50 10 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE