Origin IGS: aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggctctttcctttccagaatttcattttatttcaataaaatttactagcacagccagtgctaataaattctattgacacaaaggcgtctcaatttcaaaaagaagcgaccctacacggtcggatcgctcttaaattgtt Mask Tandem Repeat Region ================================================ aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc Find is-nt database================================================ Query_seq: SSA_1038:SSA_1039|SSA_1038:SSA_1039:Lipoprotein, putative:Sugar ABC transporter, ATP-binding protein, putative:->->:1053775..1053913 139 aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1038:SSA_1039|SSA_1038:SSA_1039:Lipoprotein, putative:Sugar ABC transporter, ATP-binding protein, putative:->->:1053775..1053913 139 aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1038:SSA_1039|SSA_1038:SSA_1039:Lipoprotein, putative:Sugar ABC transporter, ATP-binding protein, putative:->->:1053775..1053913 139 aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc Predict ORF larger than 30AA ================================================ aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc 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================================================ aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -8.9 Tail_Score: -4.65916 Start: 73 End: 99 Full_Region: TTTGTGTCAATAGAA TTTATTAGCAC TGGCT GTGCTAGTAAA TTTTATTGAAATAAA ........................................................................TTTATTAGCACTGGCTGTGCTAGTAAA........................................ TransTerm Strand: - Conf: 66 HP_score: -6.7 Tail_Score: -3.65812 Start: 73 End: 99 Full_Region: tttatttcaataaaa tttactagcac agcca gtgctaataaa ttctattgacacaaa ........................................................................tttactagcacagccagtgctaataaa........................................ Find igs database================================================ Query_seq: SSA_1038:SSA_1039|SSA_1038:SSA_1039:Lipoprotein, putative:Sugar ABC transporter, ATP-binding protein, putative:->->:1053775..1053913 139 aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: NC_009009_SSA_1038_SSA_1039|Lipoprotein, putative:Sugar ABC transporter, ATP-binding protein, putative|POSITIVE:POSITIVE|[1053775,1053913]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc aacaatttaagagcgatccgaccgtgtagggtcgcttctttttgaaattgagacgcctttgtgtcaatagaatttattagcactggctgtgctagtaaattttattgaaataaaatgaaattctggaaaggaaagagcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAUUUAAGAGCGAUCCGACCGUGUAGGGUCGCUUCUUUUUGAAAUUGAGACGCCUUUGUGUCAAUAGAAUUUAUUAGCACUGGCUGUGCUAGUAAAUUUUAUUGAAAUAAAAUGAAAUUCUGGAAAGGAAAGAGCC ..(((((((((((((((((.........))))))).))))....))))))....((.(((((.((((((((((((((((((((.....)))))))))))))))))))).)))))......((((....))))....)). (-47.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUCUUUCCUUUCCAGAAUUUCAUUUUAUUUCAAUAAAAUUUACUAGCACAGCCAGUGCUAAUAAAUUCUAUUGACACAAAGGCGUCUCAAUUUCAAAAAGAAGCGACCCUACACGGUCGGAUCGCUCUUAAAUUGUU ((((((((........(.....)........((((((.((((((.((((((.....)))))).)))))).))))))...))))).))).((((((....((((.((((.((.((...)).)).)))))))))))))).. (-30.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 70 21 225 161 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 330 56 13 89 36 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 319 95 54 46 3 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 301 52 11 67 27 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 298 64 22 110 55 NC_009009:SSA_2020|5end_hypothetical_protein_2019284..2019514_POSITIVE 296 60 13 54 9 NC_009009:SSA_2316|5end_General_secretory_pathway_protein_F,_putative_2318342..2318572_NEGATIVE 296 58 11 208 160 NC_009009:SSA_1479|5end_Transposase,_putative_1483180..1483410_POSITIVE 282 54 14 64 25 NC_009009:SSA_0592|5end_hypothetical_protein_583626..583856_POSITIVE 279 66 23 168 123 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 274 59 11 207 167 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 272 56 13 207 161 NC_009009:SSA_0106|5end_30S_ribosomal_protein_S10,_putative_107772..108002_POSITIVE 270 66 23 190 155 NC_009009:SSA_0694|5end_Mutator_protein,_putative_677730..677960_POSITIVE 269 40 5 42 7 NC_009009:SSA_1377|5end_Asparaginyl-tRNA_synthetase,_putative_1397614..1397844_NEGATIVE 266 58 12 51 5 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 266 42 4 158 126 NC_009009:SSA_0259|5end_Thiol_peroxidase,_putative_253543..253773_NEGATIVE 262 96 54 230 177 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 259 46 11 183 139 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 259 46 11 49 5 NC_009009:SSA_1552|5end_hypothetical_protein_1554913..1555143_POSITIVE 259 50 5 136 82 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 256 59 11 173 125 NC_009009:SSA_2269|5end_hypothetical_protein_2270327..2270557_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 50 3 88 41 NC_009009:SSA_1038|3end_Lipoprotein,_putative_1053714..1053864_POSITIVE 319 95 54 49 6 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 296 60 13 50 5 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 296 58 11 72 24 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 296 65 22 85 18 NC_009009:SSA_0100|3end_DNA_polymerase_I_-_3'-5'_exonuclease_and_polymerase_domains,_putative_103402..103552_POSITIVE 288 56 17 53 10 NC_009009:SSA_1224|3end_hypothetical_protein_1247251..1247401_NEGATIVE 282 54 14 52 13 NC_009009:SSA_0591|3end_Conserved_uncharacterized_protein_583694..583844_POSITIVE 266 42 4 45 13 NC_009009:SSA_0260|3end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_253656..253806_NEGATIVE 264 56 11 58 12 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 259 50 5 143 89 NC_009009:SSA_0023|3end_Aspartate_aminotransferase,_putative_29781..29931_POSITIVE 249 66 23 65 23 NC_009009:SSA_1057|3end_Aminotransferase,_class-V,_putative_1074993..1075143_POSITIVE 246 58 11 54 11 NC_009009:SSA_0585|3end_hypothetical_protein_577286..577436_POSITIVE 244 57 13 50 5 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 244 100 51 81 18 NC_009009:SSA_1722|3end_Thymidylate_kinase,_putative_1708025..1708175_NEGATIVE 244 57 11 54 5 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 243 57 19 144 98 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 240 96 53 146 113 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 239 44 6 80 23 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 235 67 21 61 9 NC_009009:SSA_0866|3end_Cation-transporting_ATPase,_E1-E_2_family,_putative_859831..859981_POSITIVE 233 40 4 89 50 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE