Origin IGS: ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcctaggttcccattctaatataaggtttaaacgaggttgattttacctgttgttgcaataatttctagctttttcagacaaaaagtatcccaaaaacttacttaa Mask Tandem Repeat Region ================================================ ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag Find is-nt database================================================ Query_seq: SSA_0694:SSA_0695|SSA_0694:SSA_0695:Mutator protein, putative:hypothetical protein:->->:678482..678588 107 ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0694:SSA_0695|SSA_0694:SSA_0695:Mutator protein, putative:hypothetical protein:->->:678482..678588 107 ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0694:SSA_0695|SSA_0694:SSA_0695:Mutator protein, putative:hypothetical protein:->->:678482..678588 107 ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag Predict ORF larger than 30AA ================================================ ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag 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================================================ ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0694:SSA_0695|SSA_0694:SSA_0695:Mutator protein, putative:hypothetical protein:->->:678482..678588 107 ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_009009_SSA_0694_SSA_0695|Mutator protein, putative:hypothetical protein|POSITIVE:POSITIVE|[678482,678588]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag ttaagtaagtttttgggatactttttgtctgaaaaagctagaaattattgcaacaacaggtaaaatcaacctcgtttaaaccttatattagaatgggaacctaggag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAGUAAGUUUUUGGGAUACUUUUUGUCUGAAAAAGCUAGAAAUUAUUGCAACAACAGGUAAAAUCAACCUCGUUUAAACCUUAUAUUAGAAUGGGAACCUAGGAG ..........(((((((.....((((..(((.....((...........)).....)))..)))).....(((((((.............)))))))..))))))). (-15.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUAGGUUCCCAUUCUAAUAUAAGGUUUAAACGAGGUUGAUUUUACCUGUUGUUGCAAUAAUUUCUAGCUUUUUCAGACAAAAAGUAUCCCAAAAACUUACUUAA ....((((((................((...(((.((((.......)))))))...))...........(((((((.....)))))))........))))))..... (-12.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 56 13 231 190 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 265 60 13 157 112 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 250 42 5 170 125 NC_009009:SSA_0123|5end_50S_ribosomal_protein_L18P,_putative_116048..116278_POSITIVE 243 44 19 144 116 NC_009009:SSA_0145|5end_Transcriptional_regulator,_TetR_family,_putative_139380..139610_NEGATIVE 242 50 5 222 178 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 225 72 34 184 146 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 215 46 9 51 16 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 210 70 27 80 34 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 206 67 21 71 27 NC_009009:SSA_0969|5end_hypothetical_protein_977212..977442_POSITIVE 202 39 3 77 35 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 199 41 3 197 163 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 195 76 35 185 136 NC_009009:SSA_2098|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103617..2103847_NEGATIVE 195 51 11 149 111 NC_009009:SSA_0109|5end_50S_ribosomal_protein_L23,_putative_109439..109669_POSITIVE 194 51 15 88 46 NC_009009:SSA_1802|5end_Snf2_family_protein,_putative_1786470..1786700_NEGATIVE 193 70 31 44 11 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 193 60 14 187 137 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 193 48 4 154 120 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 192 99 70 166 133 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 189 90 46 229 186 NC_009009:SSA_2283|5end_Conserved_uncharacterized_protein_2285824..2286054_NEGATIVE 186 57 15 221 177 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 58 13 82 39 NC_009009:SSA_0746|3end_Glucosamine-6-phosphate_deaminase,_putative_727865..728015_POSITIVE 250 42 5 85 40 NC_009009:SSA_0122|3end_50S_ribosomal_protein_L6,_putative_116043..116193_POSITIVE 239 52 13 145 110 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 226 73 36 66 32 NC_009009:SSA_0177|3end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_182132..182282_POSITIVE 215 46 9 54 19 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 210 70 27 90 44 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 209 98 67 101 74 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 202 39 3 68 26 NC_009009:SSA_1420|3end_Homoserine_O-succinyltransferase,_putative_1429684..1429834_NEGATIVE 201 58 14 151 116 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 201 76 36 120 75 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 198 95 52 66 14 NC_009009:SSA_2284|3end_Histidyl-tRNA_synthetase,_putative_2285992..2286142_NEGATIVE 197 84 50 146 116 NC_009009:SSA_1939|3end_Acyl_carrier_protein,_putative_1925875..1926025_NEGATIVE 195 51 11 149 111 NC_009009:SSA_0108|3end_50S_ribosomal_protein_L4,_putative_109519..109669_POSITIVE 193 70 31 51 18 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE 193 48 4 135 101 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 187 42 11 33 1 NC_009009:SSA_1136|3end_ATPases_with_chaperone_activity,_ATP-binding_subunit,_putative_1164247..1164397_POSITIVE 184 50 3 71 13 NC_009009:SSA_0299|3end_hypothetical_protein_293342..293492_POSITIVE 181 86 49 66 30 NC_009009:SSA_1724|3end_CBS_domain_protein,_putative_1709897..1710047_NEGATIVE 181 42 7 77 46 NC_009009:SSA_0461|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_464905..465055_POSITIVE 172 61 26 42 5 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE