Origin IGS: ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt .........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 acatacctccaaccgctcaatagaactattatactataaatgcagaagcatagcaaaagctattacatgatttcttatgcagaaaaaggactaagttttgcactcagtcccttttttccttgccttaaaattcttctctggcagatagtggttatagctgcatctcacgtgactggccag Mask Tandem Repeat Region ================================================ ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt Find is-nt database================================================ Query_seq: SSA_0022:SSA_0023|SSA_0022:SSA_0023:Surface protein cell wall anchor, sortase_B family, putative:Aspartate aminotransferase, putative:->->:28489..28668 180 ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0022:SSA_0023|SSA_0022:SSA_0023:Surface protein cell wall anchor, sortase_B family, putative:Aspartate aminotransferase, putative:->->:28489..28668 180 ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0022:SSA_0023|SSA_0022:SSA_0023:Surface protein cell wall anchor, sortase_B family, putative:Aspartate aminotransferase, putative:->->:28489..28668 180 ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 1 End: 141 Q G T V H S A A I V V I Q W L L I K L C P F F P S L A F S L G K E A Y S I M Y Y S K S H K Q M ....................................... ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt 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: 87 Start: 124 End: 153 ...........................................................................................................................TTTGCTATGCTTCTGCATTTATAGTATAAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -2.8 Tail_Score: -5.29385 Start: 70 End: 94 Full_Region: ttcttatgcagaaaa aggactaagt tttgc actcagtccc ttttttccttgcctt .....................................................................aggactaagttttgcactcagtccc...................................................................................... TransTerm Strand: + Conf: 90 HP_score: -8.5 Tail_Score: -4.87665 Start: 71 End: 93 Full_Region: AGGCAAGGAAAAAAG GGACTGAGT GCAAA ACTTAGTCC TTTTTCTGCATAAGA ......................................................................GGACTGAGTGCAAAACTTAGTCC....................................................................................... TransTerm Strand: - Conf: 64 HP_score: -6.3 Tail_Score: -3.76004 Start: 71 End: 93 Full_Region: tcttatgcagaaaaa ggactaagt tttgc actcagtcc cttttttccttgcct ......................................................................ggactaagttttgcactcagtcc....................................................................................... Find igs database================================================ Query_seq: SSA_0022:SSA_0023|SSA_0022:SSA_0023:Surface protein cell wall anchor, sortase_B family, putative:Aspartate aminotransferase, putative:->->:28489..28668 180 ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_009009_SSA_0022_SSA_0023|Surface protein cell wall anchor, sortase_B family, putative:Aspartate aminotransferase, putative|POSITIVE:POSITIVE|[28489,28668]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt ctggccagtcacgtgagatgcagctataaccactatctgccagagaagaattttaaggcaaggaaaaaagggactgagtgcaaaacttagtcctttttctgcataagaaatcatgtaatagcttttgctatgcttctgcatttatagtataatagttctattgagcggttggaggtatgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGGCCAGUCACGUGAGAUGCAGCUAUAACCACUAUCUGCCAGAGAAGAAUUUUAAGGCAAGGAAAAAAGGGACUGAGUGCAAAACUUAGUCCUUUUUCUGCAUAAGAAAUCAUGUAAUAGCUUUUGCUAUGCUUCUGCAUUUAUAGUAUAAUAGUUCUAUUGAGCGGUUGGAGGUAUGU ((..((((.(.(((..((((.((((((....(((((.(((.((((..((.((((...(((.(((((...((((((((((.....))))))))))))))))))...)))).)).....(((((....)))))..)))))))...)))))...)))))).))))..)))))))).))..... (-49.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUACCUCCAACCGCUCAAUAGAACUAUUAUACUAUAAAUGCAGAAGCAUAGCAAAAGCUAUUACAUGAUUUCUUAUGCAGAAAAAGGACUAAGUUUUGCACUCAGUCCCUUUUUUCCUUGCCUUAAAAUUCUUCUCUGGCAGAUAGUGGUUAUAGCUGCAUCUCACGUGACUGGCCAG ........(((..(((...((((..........))))..((((((....(((((....((((((.(((((....)))))..(((((((((((.(((.....))).)))))..))))))..((((...............)))))))))).)))))..)))))).....)))..))).... (-34.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 59 14 73 20 NC_009009:SSA_0918|5end_Conserved_uncharacterized_protein_930398..930628_POSITIVE 335 45 1 146 94 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 311 48 1 166 119 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 306 49 1 69 28 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 305 41 3 231 186 NC_009009:SSA_2072|5end_Phosphatidate_cytidylyltransferase,_putative_2075603..2075833_NEGATIVE 304 45 3 141 97 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 297 40 2 89 37 NC_009009:SSA_0270|5end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_262873..263103_POSITIVE 294 44 1 56 5 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 292 59 11 70 14 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 287 46 1 194 140 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 285 45 1 56 7 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 281 42 1 90 39 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 281 49 4 48 2 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 277 49 1 204 150 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 276 100 57 179 123 NC_009009:SSA_1166|5end_hypothetical_protein_1191929..1192159_POSITIVE 276 127 86 146 95 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 276 139 91 135 98 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 274 49 1 86 31 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 273 43 1 55 3 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 273 45 3 72 22 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 45 1 134 82 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 315 140 91 127 77 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 309 46 7 101 56 NC_009009:SSA_2166|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2163873..2164023_NEGATIVE 304 45 3 59 15 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 297 40 2 83 31 NC_009009:SSA_0269|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262947..263097_POSITIVE 296 139 91 69 13 NC_009009:SSA_0419|3end_Alpha-galactosidase,_putative_418530..418680_POSITIVE 292 99 67 89 55 NC_009009:SSA_0998|3end_hypothetical_protein_998758..998908_POSITIVE 285 45 1 54 5 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 281 42 1 81 30 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 278 47 1 139 83 NC_009009:SSA_0022|3end_Surface_protein_cell_wall_anchor,_sortase_B_family,_putative_28428..28578_POSITIVE 277 93 56 74 40 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 273 43 1 58 6 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 273 45 3 79 29 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 270 46 2 50 11 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 269 44 2 65 16 NC_009009:SSA_2393|3end_Transcriptional_regulator,_XRE_family,_putative_204339..204489_POSITIVE 266 143 120 143 117 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 263 100 56 103 60 NC_009009:SSA_1862|3end_hypothetical_protein_1857981..1858131_NEGATIVE 262 46 5 50 3 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 259 40 5 51 19 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 258 47 7 51 3 NC_009009:SSA_0422|3end_Phosphoglycerate_mutase_family_protein,_putative_420839..420989_POSITIVE