Origin IGS: gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc .........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 ggttcttattcttatgaatctgtaaaaatgtagatgaaaagtctatctgtaattcgtttactttttctctcatcaacatctcctgaaaagggagatgttttgttttctttaagttttctttatctttcttttaagttttcatctttaaaattgcattacattcaagaaagatagagaggtgagaagccc Mask Tandem Repeat Region ================================================ gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc Find is-nt database================================================ Query_seq: SSA_2342:SSA_2343|SSA_2342:SSA_2343:SPX domain-like protein, putative:hypothetical protein:<-<-:2343604..2343792 189 gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2342:SSA_2343|SSA_2342:SSA_2343:SPX domain-like protein, putative:hypothetical protein:<-<-:2343604..2343792 189 gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2342:SSA_2343|SSA_2342:SSA_2343:SPX domain-like protein, putative:hypothetical protein:<-<-:2343604..2343792 189 gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: - Start: 19 End: 156 .................. R E Q I Y H L K L S S F K F S L Y L F S L S F L V D G K E P S T S S L F L L R I V S L S K M ................................. gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc 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================================================ gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -7.6 Tail_Score: -5.34857 Start: 93 End: 113 Full_Region: tttttctctcatcaa catctcct gaaaa gggagatg ttttgttttctttaa ............................................................................................catctcctgaaaagggagatg............................................................................ Find igs database================================================ Query_seq: SSA_2342:SSA_2343|SSA_2342:SSA_2343:SPX domain-like protein, putative:hypothetical protein:<-<-:2343604..2343792 189 gggcttctcacctctctatctttcttgaatgtaatgcaattttaaagatgaaaacttaaaagaaagataaagaaaacttaaagaaaacaaaacatctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: NC_009009_SSA_2342_SSA_2343|SPX domain-like protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2343604,2343792]|189 HSP 1 e-value: 1.0E-47 bit: 190.0 Len: 96 Query Start:94 Query End:189 Subject Strand: POSITIVE Subject Start: 94 Subject End: 189 .............................................................................................atctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc .............................................................................................atctcccttttcaggagatgttgatgagagaaaaagtaaacgaattacagatagacttttcatctacatttttacagattcataagaataagaacc HSP 2 e-value: 2.0E-15 bit: 83.8 Len: 42 Query Start:1 Query End:42 Subject Strand: POSITIVE Subject Start: 1 Subject End: 42 gggcttctcacctctctatctttcttgaatgtaatgcaattt................................................................................................................................................... gggcttctcacctctctatctttcttgaatgtaatgcaattt................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGCUUCUCACCUCUCUAUCUUUCUUGAAUGUAAUGCAAUUUUAAAGAUGAAAACUUAAAAGAAAGAUAAAGAAAACUUAAAGAAAACAAAACAUCUCCCUUUUCAGGAGAUGUUGAUGAGAGAAAAAGUAAACGAAUUACAGAUAGACUUUUCAUCUACAUUUUUACAGAUUCAUAAGAAUAAGAACC .((.((((....(((.((((((((((....((....((..........))...))....)))))))))).)))...((((..(((.....(((((((((.......)))))))))(((((((..((((((...(........)....))))))..))).))))........))).))))....)))))) (-35.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUCUUAUUCUUAUGAAUCUGUAAAAAUGUAGAUGAAAAGUCUAUCUGUAAUUCGUUUACUUUUUCUCUCAUCAACAUCUCCUGAAAAGGGAGAUGUUUUGUUUUCUUUAAGUUUUCUUUAUCUUUCUUUUAAGUUUUCAUCUUUAAAAUUGCAUUACAUUCAAGAAAGAUAGAGAGGUGAGAAGCCC (((((.((....)).)))))...(((((.(((((((((.((.....))....)))))))))))))).(((((((.(((((((((.....)))))))))..................((((((((((((((..(.((..(((..........)).)..)).)..)))))))))))))))))))))..... (-46.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 825 50 1 141 92 NC_009009:SSA_2342|5end_SPX_domain-like_protein,_putative_2343513..2343743_NEGATIVE 278 29 1 156 122 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 256 147 106 69 22 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 242 144 106 197 151 NC_009009:SSA_1503|5end_Ferredoxin,_putative_1506209..1506439_POSITIVE 234 150 106 185 138 NC_009009:SSA_1762|5end_Permease,_putative_1750052..1750282_NEGATIVE 232 120 87 66 25 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 231 123 95 231 193 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 229 137 92 134 96 NC_009009:SSA_0910|5end_ABC-type_multidrug_transporter,_ATPase_component,_putative_921356..921586_POSITIVE 227 130 94 188 148 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 223 129 96 187 151 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 222 38 1 56 26 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 220 123 95 45 9 NC_009009:SSA_1026|5end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1042794..1043024_POSITIVE 212 28 1 221 192 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 210 49 1 230 169 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 208 35 3 55 19 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 204 37 3 215 187 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 202 28 3 112 92 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 201 54 13 219 172 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 201 118 89 167 132 NC_009009:SSA_0975|5end_2-isopropylmalate_synthase,_putative_980971..981201_POSITIVE 201 48 3 129 93 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 29 1 77 43 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 258 115 84 81 44 NC_009009:SSA_1221|3end_L-lactate_dehydrogenase,_putative_1245022..1245172_POSITIVE 256 147 106 76 29 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 224 159 113 76 28 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 221 100 61 42 7 NC_009009:SSA_1387|3end_hypothetical_protein_1403497..1403647_NEGATIVE 217 119 96 133 108 NC_009009:SSA_2243|3end_Conserved_uncharacterized_protein_2238769..2238919_NEGATIVE 212 28 1 87 58 NC_009009:SSA_0085|3end_V-type_sodium_ATPase,_subunit_I,_putative_87785..87935_POSITIVE 208 35 3 45 9 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 206 31 3 147 107 NC_009009:SSA_1372|3end_hypothetical_protein_1388946..1389096_NEGATIVE 205 38 1 119 78 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 204 150 106 58 20 NC_009009:SSA_0167|3end_Hypothetical_protein_(Asparagine/proline-rich)_166335..166485_POSITIVE 203 106 61 93 40 NC_009009:SSA_0596|3end_hypothetical_protein_587352..587502_POSITIVE 202 28 3 125 105 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 201 48 3 117 81 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 198 48 3 134 84 NC_009009:SSA_0241|3end_Ribosomal_protein_L11_methyltransferase,_putative_235057..235207_POSITIVE 197 37 1 38 5 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 194 27 2 145 118 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 193 37 1 104 69 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 193 37 4 134 99 NC_009009:SSA_1490|3end_Ribonuclease_BN,_putative_1495821..1495971_NEGATIVE 193 34 5 100 76 NC_009009:SSA_0532|3end_Propanediol_utilization_protein_PduB,_putative_529028..529178_POSITIVE