Origin IGS: tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa .........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 tttgaaatctctttctgtgtttagtattgcgaactcacaattacttctattttatcataattctagaggagtatcgcacaaaaagtcggaagcccgactttttgttatttcatagtatagatgcttattctagtttagcagggtgaatgaatcacttatctgagaaaaagtagttttctcaaggaaaga Mask Tandem Repeat Region ================================================ tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa Find is-nt database================================================ Query_seq: SMT_635:SMT_636|SMT_635:SMT_636:ribonucleoside-diphosphate reductase alpha chain:ribonucleoside-diphosphate reductase beta chain:->->:541104..541292 189 tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_635:SMT_636|SMT_635:SMT_636:ribonucleoside-diphosphate reductase alpha chain:ribonucleoside-diphosphate reductase beta chain:->->:541104..541292 189 tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_635:SMT_636|SMT_635:SMT_636:ribonucleoside-diphosphate reductase alpha chain:ribonucleoside-diphosphate reductase beta chain:->->:541104..541292 189 tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 78 End: 188 ............................................................................. S I V F L R A E S K K H S V G R S N H Y F L L L Q S N A I S F V S L S K M . Protein_Len: 43 Strand: - Start: 47 End: 175 .............................................. G A L S S Y A D I S H F L L F D P K R S K T R Y E E L I I I F Y F Y N H T R L V L C M .............. tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa 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================================================ tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.9 Tail_Score: -4.03811 Start: 86 End: 111 Full_Region: tagaggagtatcgca caaaaagtcgg aagc ccgactttttg ttatttcatagtata .....................................................................................caaaaagtcggaagcccgactttttg.............................................................................. TransTerm Strand: - Conf: 93 HP_score: -8.1 Tail_Score: -5.39905 Start: 92 End: 105 Full_Region: agtatcgcacaaaaa gtcgg aagc ccgac tttttgttatttcat ...........................................................................................gtcggaagcccgac.................................................................................... Find igs database================================================ Query_seq: SMT_635:SMT_636|SMT_635:SMT_636:ribonucleoside-diphosphate reductase alpha chain:ribonucleoside-diphosphate reductase beta chain:->->:541104..541292 189 tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: smit_SMT_635_SMT_636|ribonucleoside-diphosphate reductase alpha chain:ribonucleoside-diphosphate reductase beta chain|POSITIVE:POSITIVE|[541104,541292]|189 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 189 tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa tctttccttgagaaaactactttttctcagataagtgattcattcaccctgctaaactagaataagcatctatactatgaaataacaaaaagtcgggcttccgactttttgtgcgatactcctctagaattatgataaaatagaagtaattgtgagttcgcaatactaaacacagaaagagatttcaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCCUUGAGAAAACUACUUUUUCUCAGAUAAGUGAUUCAUUCACCCUGCUAAACUAGAAUAAGCAUCUAUACUAUGAAAUAACAAAAAGUCGGGCUUCCGACUUUUUGUGCGAUACUCCUCUAGAAUUAUGAUAAAAUAGAAGUAAUUGUGAGUUCGCAAUACUAAACACAGAAAGAGAUUUCAAA ((((((.(((((((((.....)))))))))....(((.(((((......((((...........))))........)))))...((((((((((((....))))))))))))((((.((((....(.((((((............)))))).))))))))).........))).))))))......... (-44.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAAAUCUCUUUCUGUGUUUAGUAUUGCGAACUCACAAUUACUUCUAUUUUAUCAUAAUUCUAGAGGAGUAUCGCACAAAAAGUCGGAAGCCCGACUUUUUGUUAUUUCAUAGUAUAGAUGCUUAUUCUAGUUUAGCAGGGUGAAUGAAUCACUUAUCUGAGAAAAAGUAGUUUUCUCAAGGAAAGA .........((((((((((...(((((((.(....).))).))))((...((((((.(((..(((((((((((((..((((((((((((....))))))))))))((((....))))..))))))).)))))).)))....)))))).))..))).....((((((((.....)))))))).))))))) (-48.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 105 69 114 72 smit:SMT_577|5end_transcriptional_regulator,_LysR_family_495324..495554_POSITIVE 262 117 90 168 139 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 255 136 91 113 68 smit:SMT_126|5end_hypothetical_membrane_associated_protein_78250..78480_NEGATIVE 252 132 91 75 28 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 250 127 95 77 38 smit:SMT_1961|5end_K07485_transposase_1894206..1894436_POSITIVE 247 126 92 217 182 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 246 135 92 141 93 smit:SMT_771|5end_spermidine/putrescine_transport_system_permease_protein_PotB_682183..682413_NEGATIVE 246 73 36 136 104 smit:SMT_136|5end_hypothetical_protein_predicted_by_Glimmer/Critica_87314..87544_POSITIVE 244 127 90 155 111 smit:SMT_206|5end_K07720_two-component_system,_response_regulator_YesN_138237..138467_NEGATIVE 241 50 1 231 181 smit:SMT_1016|5end_alcohol_dehydrogenase,_zinc-containing_954094..954324_NEGATIVE 235 49 5 75 18 smit:SMT_1461|5end_putative_phosphate_ABC_transporter_(ATP-binding_protein)_1442324..1442554_POSITIVE 232 52 25 47 19 smit:SMT_513|5end_16S_rRNA_processing_protein_RimM_440869..441099_POSITIVE 232 130 83 214 145 smit:SMT_160|5end_folylpolyglutamate_synthase_104741..104971_POSITIVE 231 124 92 102 60 smit:SMT_1890|5end_hypothetical_protein_1843407..1843637_POSITIVE 229 88 48 193 159 smit:SMT_1962|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1895639..1895869_NEGATIVE 229 88 48 193 159 smit:SMT_823|5end_putative_mucus_binding_protein_746790..747020_NEGATIVE 226 156 111 204 160 smit:SMT_1781|5end_transcriptional_regulator,_xre_family_1758365..1758595_POSITIVE 225 115 88 110 83 smit:SMT_1107|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1048081..1048311_NEGATIVE 225 115 88 219 192 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 224 132 91 84 46 smit:SMT_1979|5end_possible_cell_surface_protein_1911052..1911282_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 105 69 117 75 smit:SMT_576|3end_transcriptional_regulator,_LysR_family_495407..495557_POSITIVE 285 123 93 84 52 smit:SMT_2046|3end_choline_binding_protein_C_1957280..1957430_NEGATIVE 261 51 17 108 75 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 255 136 91 126 81 smit:SMT_127|3end_transcriptional_regulator,_PadR_family_78237..78387_NEGATIVE 252 132 91 63 16 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 236 70 29 60 13 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 235 49 5 64 7 smit:SMT_1460|3end_K02038_phosphate_transport_system_permease_protein_1442393..1442543_POSITIVE 234 134 92 126 73 smit:SMT_1517|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1498497..1498647_POSITIVE 231 124 92 82 40 smit:SMT_1889|3end_hypothetical_protein_1843467..1843617_POSITIVE 225 115 88 69 42 smit:SMT_1108|3end_acetate_kinase_1048122..1048272_NEGATIVE 224 48 9 108 63 smit:SMT_1253|3end_beta-galactosidase_1212912..1213062_NEGATIVE 223 110 65 67 12 smit:SMT_134|3end_LysM_domain_protein_86157..86307_POSITIVE 222 114 78 58 12 smit:SMT_1300|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1262614..1262764_NEGATIVE 221 118 91 44 6 smit:SMT_1484|3end_exonuclease_RexA_1464256..1464406_NEGATIVE 221 53 18 90 43 smit:SMT_1337|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1312054..1312204_NEGATIVE 214 49 9 105 65 smit:SMT_146|3end_sugar_transport_system_permease_protein_97382..97532_POSITIVE 214 49 9 105 65 smit:SMT_118|3end_K02026_multiple_sugar_transport_system_permease_protein_70433..70583_POSITIVE 211 126 91 65 23 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 209 123 95 84 51 smit:SMT_1391|3end_dihydroxyacetone_kinase_1368589..1368739_POSITIVE 209 115 78 144 109 smit:SMT_187|3end_30S_ribosomal_protein_S5_123571..123721_POSITIVE