Origin IGS: acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt .........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 aaataactccttataaaaactttttgcaagtgtttatacaaccatactatactacactatacgtactgtcaagagcccgcatattctctatatctttttgaaatatatatcccttaaatatagacaaataataaaaaacaattaaaatataggttagataaaattcatttaggagaagatgt Mask Tandem Repeat Region ================================================ acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt Find is-nt database================================================ Query_seq: TDE0107:TDE0108|TDE0107:TDE0108:alpha-amylase family protein:hypothetical protein:<-->:128357..128538 182 acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0107:TDE0108|TDE0107:TDE0108:alpha-amylase family protein:hypothetical protein:<-->:128357..128538 182 acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0107:TDE0108|TDE0107:TDE0108:alpha-amylase family protein:hypothetical protein:<-->:128357..128538 182 acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 35 End: 133 .................................. M L I V F Y Y L S I F K G Y I F Q K D I E N M R A L D S T Y S V V ................................................. Protein_Len: 32 Strand: - Start: 85 End: 180 .................................................................................... F S I S F I R A R S L V Y L T T Y Y P Q I F V Q L F N K Y P T M .. Protein_Len: 34 Strand: - Start: 69 End: 170 .................................................................... P I Y I E F L Y L S Y A P E Q C Y T Y H L I T H N Y L C K C F T K M ............ Protein_Len: 33 Strand: - Start: 41 End: 139 ........................................ N N K I I Q R Y K L S I Y K L F I Y L I H P S K V T R I T Y Y L M ........................................... acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt 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: 86 Start: 110 End: 139 .............................................................................................................CTTGACAGTACGTATAGTGTAGTATAGTAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0107:TDE0108|TDE0107:TDE0108:alpha-amylase family protein:hypothetical protein:<-->:128357..128538 182 acatcttctcctaaatgaattttatctaacctatattttaattgttttttattatttgtctatatttaagggatatatatttcaaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt Intra-Species Hit: Count: 1 Min: 83 Max: 182 Len: 100 Subject: NC_002967_TDE0107_TDE0108|alpha-amylase family protein:hypothetical protein|NEGATIVE:POSITIVE|[128357,128538]|182 HSP 1 e-value: 5.0E-50 bit: 198.0 Len: 100 Query Start:83 Query End:182 Subject Strand: POSITIVE Subject Start: 83 Subject End: 182 ..................................................................................caaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt ..................................................................................caaaaagatatagagaatatgcgggctcttgacagtacgtatagtgtagtatagtatggttgtataaacacttgcaaaaagtttttataaggagttattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAAGAUAUAGAGAAUAUGCGGGCUCUUGACAGUACGUAUAGUGUAGUAUAGUAUGGUUGUAUAAACACUUGCAAAAAGUUUUUAUAAGGAGUUAUUU ........((((((((.((((((..((......))..))))))((((.((((((.....))))))..))))..........))))))))........... (-14.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAACUCCUUAUAAAAACUUUUUGCAAGUGUUUAUACAACCAUACUAUACUACACUAUACGUACUGUCAAGAGCCCGCAUAUUCUCUAUAUCUUUUUG ........................(((.(((((.((((.........))))..)))))....((.((....)).))..)))................... ( -7.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 865 50 1 223 174 NC_002967:TDE0107|5end_alpha-amylase_family_protein_128266..128496_NEGATIVE 285 87 45 47 6 NC_002967:TDE2557|5end_hypothetical_protein_2583383..2583613_NEGATIVE 282 60 13 94 34 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 256 97 53 47 5 NC_002967:TDE0995|5end_hypothetical_protein_1022576..1022806_NEGATIVE 251 58 14 115 74 NC_002967:TDE2122|5end_DHH_superfamily_protein_2155910..2156140_NEGATIVE 249 70 21 207 152 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 244 67 21 109 63 NC_002967:TDE1622|5end_hypothetical_protein_1670981..1671211_NEGATIVE 242 64 21 56 9 NC_002967:TDE2507|5end_hypothetical_protein_2531735..2531965_NEGATIVE 238 94 71 185 163 NC_002967:TDE1326|5end_hypothetical_protein_1361661..1361891_POSITIVE 233 53 19 131 97 NC_002967:TDE2229|5end_hypothetical_protein_2269077..2269307_NEGATIVE 233 34 1 224 187 NC_002967:TDE0969|5end_hypothetical_protein_993260..993490_POSITIVE 232 51 19 146 106 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 232 56 16 54 9 NC_002967:TDE1463|5end_hypothetical_protein_1513072..1513302_NEGATIVE 225 100 54 126 78 NC_002967:TDE1617|5end_hypothetical_protein_1664859..1665089_NEGATIVE 223 70 21 82 29 NC_002967:TDE2280|5end_transglycosylase,_SLT_family_2317358..2317588_NEGATIVE 223 64 21 191 140 NC_002967:TDE0678|5end_hypothetical_protein_716014..716244_POSITIVE 221 35 13 180 158 NC_002967:TDE2324|5end_DNA-binding_response_regulator_2359188..2359418_POSITIVE 218 68 24 194 144 NC_002967:TDE1911|5end_hypothetical_protein_1929098..1929328_NEGATIVE 217 60 11 217 166 NC_002967:TDE1859|5end_hypothetical_protein_1884957..1885187_POSITIVE 216 51 11 50 7 NC_002967:TDE2409|5end_hypothetical_protein_2436006..2436236_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 67 23 48 6 NC_002967:TDE1620|3end_hypothetical_protein_1666959..1667109_NEGATIVE 251 39 20 103 83 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 247 50 5 64 18 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 245 66 23 140 84 NC_002967:TDE0269|3end_hypothetical_protein_300196..300346_NEGATIVE 244 67 21 72 26 NC_002967:TDE1623|3end_hypothetical_protein_1671018..1671168_NEGATIVE 242 64 21 148 101 NC_002967:TDE2507|3end_hypothetical_protein_2531643..2531793_NEGATIVE 232 56 16 50 5 NC_002967:TDE1464|3end_SsrA-binding_protein_1513076..1513226_NEGATIVE 227 59 12 141 95 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE 227 52 22 149 111 NC_002967:TDE1071|3end_peptide_ABC_transporter,_peptide-binding_protein_OppA_1098813..1098963_NEGATIVE 223 64 21 148 97 NC_002967:TDE0677|3end_hypothetical_protein_716051..716201_POSITIVE 219 59 12 70 21 NC_002967:TDE2340|3end_FMN-binding_domain_protein_2377493..2377643_NEGATIVE 214 68 22 52 7 NC_002967:TDE2600|3end_hypothetical_protein_2638555..2638705_POSITIVE 211 50 10 144 102 NC_002967:TDE0031|3end_hypothetical_protein_38835..38985_NEGATIVE 208 41 4 64 31 NC_002967:TDE1134|3end_hypothetical_protein_1165062..1165212_NEGATIVE 207 62 21 101 57 NC_002967:TDE0496|3end_DNA-binding_protein,_putative_550971..551121_NEGATIVE 206 60 19 68 28 NC_002967:TDE2583|3end_hypothetical_protein_2616500..2616650_POSITIVE 204 68 21 87 42 NC_002967:TDE2723|3end_phosphoribosylpyrophosphate_synthetase_2780871..2781021_NEGATIVE 204 60 13 62 10 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 204 49 1 50 6 NC_002967:TDE2038|3end_UVR_domain_protein_2067704..2067854_NEGATIVE 202 60 12 82 34 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE