Origin IGS: ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 nnnnngtaaaaagagtaggagtaataagtgtcttaatcaaagttaaaggtttaaaactacgtgtagcttataaaaatttccaaccaggaaagaaagaagaagtagatattgctgctaactattggaatgtaaataatcctgaagtgcaa Mask Tandem Repeat Region ================================================ ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn Find is-nt database================================================ Query_seq: SMT_2102:SMT_2103|SMT_2102:SMT_2103:hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor:<-<-:1994624..1994772 149 ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2102:SMT_2103|SMT_2102:SMT_2103:hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor:<-<-:1994624..1994772 149 ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2102:SMT_2103|SMT_2102:SMT_2103:hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor:<-<-:1994624..1994772 149 ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 1 End: 90 M H F R I I Y I P I V S S N I Y F F F L S W L E I F I S Y T ........................................................... Protein_Len: 42 Strand: - Start: 1 End: 126 Q V E P N N V N W Y N A A I D V E E K K G P Q F N K Y A V R L K L G K V K I L V S M ....................... ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn 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================================================ ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -4.3 Tail_Score: -4.85599 Start: 59 End: 73 Full_Region: TCTACTTCTTCTTTC TTTCC TGGTT GGAAA TTTTTATAAGCTACA ..........................................................TTTCCTGGTTGGAAA............................................................................ Find igs database================================================ Query_seq: SMT_2102:SMT_2103|SMT_2102:SMT_2103:hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor:<-<-:1994624..1994772 149 ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttacnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: smit_SMT_2102_SMT_2103|hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor|NEGATIVE:NEGATIVE|[1994624,1994772]|149 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttac..... ttgcacttcaggattatttacattccaatagttagcagcaatatctacttcttctttctttcctggttggaaatttttataagctacacgtagttttaaacctttaactttgattaagacacttattactcctactctttttac..... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCACUUCAGGAUUAUUUACAUUCCAAUAGUUAGCAGCAAUAUCUACUUCUUCUUUCUUUCCUGGUUGGAAAUUUUUAUAAGCUACACGUAGUUUUAAACCUUUAACUUUGAUUAAGACACUUAUUACUCCUACUCUUUUUAC (((((((...(((..........)))...)))..))))..............((((....((..(((((((..(((....((((((....)))))).)))..)))))))..))..))))......................... (-16.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAAAAGAGUAGGAGUAAUAAGUGUCUUAAUCAAAGUUAAAGGUUUAAAACUACGUGUAGCUUAUAAAAAUUUCCAACCAGGAAAGAAAGAAGAAGUAGAUAUUGCUGCUAACUAUUGGAAUGUAAAUAAUCCUGAAGUGCAA (((.....(((((.(((((((..((.(((..((.((((((.(.((........)).).)))))).......(((((.....)))))....))..)))))..))))))).)).)))...(((.((....)).))).....))).. (-23.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 850 70 21 161 112 smit:SMT_2102|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1994533..1994763_NEGATIVE 748 50 1 141 92 smit:SMT_2025|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1941765..1941995_NEGATIVE 297 68 23 112 74 smit:SMT_1795|5end_DNA_polymerase_III,_delta_subunit_1769847..1770077_NEGATIVE 283 97 51 80 22 smit:SMT_893|5end_leucine_rich_protein_841311..841541_NEGATIVE 249 74 32 57 9 smit:SMT_2011|5end_lysyl-tRNA_synthetase_1930409..1930639_NEGATIVE 249 46 1 153 110 smit:SMT_579|5end_ribosomal_large_subunit_pseudouridine_synthase_D_496512..496742_POSITIVE 248 103 63 209 168 smit:SMT_1653|5end_hydrolase_1641328..1641558_POSITIVE 243 68 21 170 132 smit:SMT_1861|5end_sucrose_operon_repressor_(SCR_operon_regulatory_protein)_1823713..1823943_POSITIVE 234 69 22 176 130 smit:SMT_278|5end_tyrosine-protein_kinase_220264..220494_POSITIVE 229 79 32 60 15 smit:SMT_1597|5end_K02032_peptide/nickel_transport_system_ATP-binding_protein_1586981..1587211_POSITIVE 228 73 32 69 27 smit:SMT_153|5end_sensor_histidine_kinase,_putative_101443..101673_POSITIVE 226 70 21 56 7 smit:SMT_1069|5end_acetyl_xylan_esterase,_putative_1009330..1009560_POSITIVE 225 76 38 169 123 smit:SMT_1205|5end_response_regulator_1165700..1165930_NEGATIVE 223 68 21 67 19 smit:SMT_1949|5end_IS1381_transposase_protein_B_1883518..1883748_POSITIVE 223 97 53 139 93 smit:SMT_843|5end_hypothetical_protein_789638..789868_NEGATIVE 221 67 26 103 56 smit:SMT_1105|5end_K03217_preprotein_translocase_YidC_subunit_1047632..1047862_NEGATIVE 221 68 32 216 180 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 220 70 29 210 170 smit:SMT_1784|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1760755..1760985_POSITIVE 219 76 55 208 184 smit:SMT_1383|5end_ribonucleoside-diphosphate_reductase_alpha_chain_1361928..1362158_NEGATIVE 218 45 3 202 154 smit:SMT_862|5end_hypothetical_protein_predicted_by_Glimmer/Critica_808587..808817_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 68 23 78 40 smit:SMT_1796|3end_dihydroorotate_dehydrogenase_A_1769881..1770031_NEGATIVE 283 97 51 76 18 smit:SMT_894|3end_hypothetical_protein_841315..841465_NEGATIVE 260 68 49 20 1 smit:SMT_2026|3end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1941905..1942055_NEGATIVE 229 79 32 49 4 smit:SMT_1596|3end_oligopeptide_transport_ATP-binding_protein_OppD_1587050..1587200_POSITIVE 223 68 21 50 2 smit:SMT_1948|3end_IS1381_transposase_protein_A_1883581..1883731_POSITIVE 223 49 1 95 48 smit:SMT_1230|3end_hypothetical_protein_1192342..1192492_POSITIVE 223 97 53 65 19 smit:SMT_844|3end_putative_phospho-sugar_mutase_789712..789862_NEGATIVE 221 67 26 134 87 smit:SMT_1106|3end_ribonuclease_P_protein_component_1047601..1047751_NEGATIVE 220 70 29 149 109 smit:SMT_1783|3end_peptide_methionine_sulfoxide_reductase_1760774..1760924_POSITIVE 219 76 55 127 103 smit:SMT_1384|3end_glutaredoxin_1362009..1362159_NEGATIVE 219 70 25 47 1 smit:SMT_987|3end_N-acetylmannosamine_kinase_/_transcriptional_regulator_931655..931805_NEGATIVE 216 61 21 92 45 smit:SMT_487|3end_transcriptional_regulator,_TetR_family_423017..423167_POSITIVE 210 36 6 35 10 smit:SMT_404|3end_hypothetical_protein_334029..334179_POSITIVE 209 68 24 149 105 smit:SMT_1544|3end_mevalonate_kinase_1528006..1528156_NEGATIVE 208 91 55 51 19 smit:SMT_1183|3end_K02795_PTS_system,_mannose-specific_IIC_component_1140629..1140779_NEGATIVE 207 68 46 92 70 smit:SMT_181|3end_50S_ribosomal_protein_L24_120510..120660_POSITIVE 205 68 29 104 66 smit:SMT_1525|3end_pneumococcal_histidine_triad_protein_A_precursor_1505873..1506023_NEGATIVE 204 110 63 148 114 smit:SMT_488|3end_dCMP_deaminase_423416..423566_POSITIVE 203 80 31 94 36 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 201 50 7 131 75 smit:SMT_2076|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1978482..1978632_NEGATIVE