Origin IGS: ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatacataaaataaattatgtaatatatggtttttaaaaaagaagctggtcctacaaccaacttctttttgatttatccaactaccgcttcagcgatttcttcacggctaataccagcgaaatagcgtgtgatatcaatggtttctaacgccttaaggacnnnnnttaattaa Mask Tandem Repeat Region ================================================ ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt Find is-nt database================================================ Query_seq: SMT_2106:SMT_2107|SMT_2106:SMT_2107:unknown, predicted membrane protein (TMS5):tyrosine recombinase:-><-:1997975..1998147 173 ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2106:SMT_2107|SMT_2106:SMT_2107:unknown, predicted membrane protein (TMS5):tyrosine recombinase:-><-:1997975..1998147 173 ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2106:SMT_2107|SMT_2106:SMT_2107:unknown, predicted membrane protein (TMS5):tyrosine recombinase:-><-:1997975..1998147 173 ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 52 End: 147 ................................................... K A P I L R S S I A S A T T P Y I L F F N T T P G A E K K F V M .......................... ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt 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================================================ ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -8.2 Tail_Score: -5.00884 Start: 109 End: 132 Full_Region: TGGATAAATCAAAAA GAAGTTGGTT GTAG GACCAGCTTC TTTTTTAAAAACCAT ............................................................................................................GAAGTTGGTTGTAGGACCAGCTTC......................................... TransTerm Strand: - Conf: 79 HP_score: -5.3 Tail_Score: -5.04601 Start: 109 End: 132 Full_Region: atggtttttaaaaaa gaagctggt cctaca accaacttc tttttgatttatcca ............................................................................................................gaagctggtcctacaaccaacttc......................................... Find igs database================================================ Query_seq: SMT_2106:SMT_2107|SMT_2106:SMT_2107:unknown, predicted membrane protein (TMS5):tyrosine recombinase:-><-:1997975..1998147 173 ttaattaannnnngtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt Intra-Species Hit: Count: 1 Min: 14 Max: 173 Len: 160 Subject: smit_SMT_2106_SMT_2107|unknown, predicted membrane protein (TMS5):tyrosine recombinase|POSITIVE:NEGATIVE|[1997975,1998147]|173 HSP 1 e-value: 7.0E-86 bit: 317.0 Len: 160 Query Start:14 Query End:173 Subject Strand: POSITIVE Subject Start: 14 Subject End: 173 .............gtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt .............gtccttaaggcgttagaaaccattgatatcacacgctatttcgctggtattagccgtgaagaaatcgctgaagcggtagttggataaatcaaaaagaagttggttgtaggaccagcttcttttttaaaaaccatatattacataatttattttatgtatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCCUUAAGGCGUUAGAAACCAUUGAUAUCACACGCUAUUUCGCUGGUAUUAGCCGUGAAGAAAUCGCUGAAGCGGUAGUUGGAUAAAUCAAAAAGAAGUUGGUUGUAGGACCAGCUUCUUUUUUAAAAACCAUAUAUUACAUAAUUUAUUUUAUGUAUU ((((....(((((..((...........))..))))).((((((.(((....)))))))))..(((((....)))))....)))).....(((((((((((((((....)))))))))))))))..............(((((((......))))))).. (-42.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACAUAAAAUAAAUUAUGUAAUAUAUGGUUUUUAAAAAAGAAGCUGGUCCUACAACCAACUUCUUUUUGAUUUAUCCAACUACCGCUUCAGCGAUUUCUUCACGGCUAAUACCAGCGAAAUAGCGUGUGAUAUCAAUGGUUUCUAACGCCUUAAGGAC ..(((((((......))))))).....(((......(((((((((.((((......)))).))))))))).......))).....(((....)))..(((((...(((....(((.((......))...((....))..))).......)))..))))). (-33.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 86 41 61 18 smit:SMT_2078|5end_acetyl_xylan_esterase,_putative_1979571..1979801_POSITIVE 330 83 41 230 186 smit:SMT_422|5end_K02004_363781..364011_POSITIVE 295 85 41 87 49 smit:SMT_2111|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999303..1999533_POSITIVE 292 55 15 219 171 smit:SMT_1353|5end_GTP-binding_protein_1331589..1331819_NEGATIVE 292 120 72 104 44 smit:SMT_1107|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1048081..1048311_NEGATIVE 292 120 72 213 153 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 288 48 2 104 51 smit:SMT_2017|5end_exonuclease_RexA_1936785..1937015_NEGATIVE 288 48 2 104 51 smit:SMT_1798|5end_exonuclease_RexA_1773441..1773671_NEGATIVE 288 78 42 41 7 smit:SMT_888|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_835459..835689_POSITIVE 283 56 20 181 136 smit:SMT_1202|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1164097..1164327_NEGATIVE 279 87 41 207 152 smit:SMT_1048|5end_K06518_holin-like_protein_988142..988372_POSITIVE 275 79 32 226 180 smit:SMT_1838|5end_response_regulator_1805400..1805630_NEGATIVE 273 116 71 67 31 smit:SMT_204|5end_K02012_iron(III)_transport_system_substrate-binding_protein_135971..136201_NEGATIVE 272 76 31 109 56 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 268 83 44 133 73 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 267 85 43 64 18 smit:SMT_1638|5end_UTP-glucose-1-phosphate_uridylyltransferase_1624781..1625011_NEGATIVE 266 44 3 123 76 smit:SMT_2079|5end_single_strand_binding_protein_1980144..1980374_POSITIVE 266 82 44 153 112 smit:SMT_1647|5end_3-isopropylmalate_dehydratase_small_subunit_1633403..1633633_POSITIVE 264 49 1 153 107 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 263 90 45 221 173 smit:SMT_1669|5end_potassium_uptake_protein_KtrB_1658577..1658807_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 875 120 71 50 1 smit:SMT_1405|3end_tyrosine_recombinase_1382080..1382230_NEGATIVE 401 79 31 146 93 smit:SMT_862|3end_hypothetical_protein_predicted_by_Glimmer/Critica_809191..809341_POSITIVE 299 124 91 87 54 smit:SMT_1404|3end_lipoate-protein_ligase_A_1382036..1382186_POSITIVE 295 85 41 48 10 smit:SMT_2110|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999344..1999494_POSITIVE 292 120 72 63 3 smit:SMT_1108|3end_acetate_kinase_1048122..1048272_NEGATIVE 283 79 33 55 4 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 283 56 20 57 12 smit:SMT_1203|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1164221..1164371_NEGATIVE 283 79 41 44 1 smit:SMT_822|3end_putative_mucus_binding_protein_734047..734197_NEGATIVE 272 86 45 145 105 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 268 83 44 140 80 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 266 82 44 143 102 smit:SMT_1646|3end_3-isopropylmalate_dehydratase_large_subunit_1633473..1633623_POSITIVE 264 49 1 141 95 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE 264 85 43 42 5 smit:SMT_1639|3end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1624803..1624953_NEGATIVE 262 59 19 58 25 smit:SMT_601|3end_hypothetical_protein_517255..517405_POSITIVE 257 79 35 72 24 smit:SMT_229|3end_mechanosensitive_ion_channel_165429..165579_NEGATIVE 252 57 22 56 14 smit:SMT_955|3end_acyltransferase_family_protein_904703..904853_POSITIVE 250 89 42 88 39 smit:SMT_735|3end_putative_transposase,_ISSmu1_641395..641545_POSITIVE 248 86 54 151 115 smit:SMT_306|3end_3-oxoacyl-_249117..249267_POSITIVE 247 86 50 136 104 smit:SMT_1346|3end_tellurite_resistance_protein_TehB_1323843..1323993_NEGATIVE 243 45 11 112 74 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE