Origin IGS: atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcaaatacaaaaatttcggtgtgtaaactaaccggatcaagaaacgagcaagcttctcttcaaaaaggtccttattgttttgatgaaaagctcttaagcttttgatcgagaagtaaaaactactactgattattctccaatatagtatcctctttttattcgatgaagtcgatttttatcttggtatcttggtaaaggggaggaagcttttcgtatggtttcgatccaaacggagtcggtcgaatcggttttgagcttacttcagcggaagcacctgtgtctgtggttgtcggaaagggggggcagatgagtcggactaatgttgtatttttggcgcatggaaagccgtttttaatataatagtat Mask Tandem Repeat Region ================================================ atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca Find is-nt database================================================ Query_seq: PG0312:PG0313|PG0312:PG0313:hypothetical protein:hypothetical protein:<-->:347139..347505 367 atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0312:PG0313|PG0312:PG0313:hypothetical protein:hypothetical protein:<-->:347139..347505 367 atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0312:PG0313|PG0312:PG0313:hypothetical protein:hypothetical protein:<-->:347139..347505 367 atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 11 End: 208 .......... M K N G F P C A K N T T L V R L I C P P F P T T T D T G A S A E V S S K P I R P T P F G S K P Y E K L P P L Y Q D T K I ............................................................................................................................................................... Protein_Len: 31 Strand: + Start: 142 End: 234 ............................................................................................................................................. M E T I R K A S S P L P R Y Q D K N R L H R I K R G Y Y I G E ..................................................................................................................................... Protein_Len: 49 Strand: + Start: 219 End: 365 .......................................................................................................................................................................................................................... M L Y W R I I S S S F Y F S I K S L R A F H Q N N K D L F E E K L A R F L I R L V Y T P K F L Y L .. Protein_Len: 30 Strand: - Start: 265 End: 354 ........................................................................................................................................................................................................................................................................ F S L L K E D F C Y P G K Q L S A Q E N R S G T L K C V S M ............. Protein_Len: 42 Strand: - Start: 116 End: 241 ................................................................................................................... F R N S R S R K S R F W V F L K R G K V L I G L Y F D V E D F L F L I S Y Q L I I M .............................................................................................................................. Protein_Len: 31 Strand: - Start: 60 End: 152 ........................................................... R G G R E S L W L C L H K R Q L L S L V S E V S E T Q I S V M ....................................................................................................................................................................................................................... Protein_Len: 38 Strand: - Start: 10 End: 123 ......... I L F P K G H A L F V V N T R S M Q G G K G V V V S V P A E A S T L E F G M .................................................................................................................................................................................................................................................... atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca 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================================================ atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -4.1 Tail_Score: -5.13344 Start: 195 End: 207 Full_Region: gtatcctctttttat tcgat gaa gtcga tttttatcttggtat ..................................................................................................................................................................................................tcgatgaagtcga................................................................................................................................................................ Find igs database================================================ Query_seq: PG0312:PG0313|PG0312:PG0313:hypothetical protein:hypothetical protein:<-->:347139..347505 367 atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca Intra-Species Hit: Count: 1 Min: 1 Max: 367 Len: 367 Subject: NC_002950_PG0312_PG0313|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[347139,347505]|367 HSP 1 e-value: 0.0 bit: 686.0 Len: 367 Query Start:1 Query End:367 Subject Strand: POSITIVE Subject Start: 1 Subject End: 367 atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgnnnnnnntttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca atactattatattaaaaacggctttccatgcgccaaaaatacaacattagtccgactcatctgccccccctttccgacaaccacagacacaggtgcttccgctgaagtaagctcaaaaccgattcgaccgactccgtttggatcgaaaccatacgaaaagcttcctcccctttaccaagataccaagataaaaatcgacttcatcgaataaaaagaggatactatattggagaataatcagtagtagtttttacttctcgatcaaaagcttaagagcttttcatcaaaacaataaggacctttttgaagagaagcttgctcgtttcttgatccggttagtttacacaccgaaatttttgtatttgca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACUAUUAUAUUAAAAACGGCUUUCCAUGCGCCAAAAAUACAACAUUAGUCCGACUCAUCUGCCCCCCCUUUCCGACAACCACAGACACAGGUGCUUCCGCUGAAGUAAGCUCAAAACCGAUUCGACCGACUCCGUUUGGAUCGAAACCAUACGAAAAGCUUCCUCCCCUUUACCAAGAUACCAAGAUAAAAAUCGACUUCAUCGAAUAAAAAGAGGAUACUAUAUUGGAGAAUAAUCAGUAGUAGUUUUUACUUCUCGAUCAAAAGCUUAAGAGCUUUUCAUCAAAACAAUAAGGACCUUUUUGAAGAGAAGCUUGCUCGUUUCUUGAUCCGGUUAGUUUACACACCGAAAUUUUUGUAUUUGCA ...................(((.........)))..((((((((..(((((..((..((((((..........................))))))..)).))))).(((((((...(((((.(((((((((......)))).)))))..((.((((.(((((((.((...........................((((.....))))....(((((((...((.(((((..........(((((......)))))....(((.(((((((....))))))).)))....)))))))..)))))))...)))))))))..))))....))...))))))))))))............))))))))... (-74.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAAAUACAAAAAUUUCGGUGUGUAAACUAACCGGAUCAAGAAACGAGCAAGCUUCUCUUCAAAAAGGUCCUUAUUGUUUUGAUGAAAAGCUCUUAAGCUUUUGAUCGAGAAGUAAAAACUACUACUGAUUAUUCUCCAAUAUAGUAUCCUCUUUUUAUUCGAUGAAGUCGAUUUUUAUCUUGGUAUCUUGGUAAAGGGGAGGAAGCUUUUCGUAUGGUUUCGAUCCAAACGGAGUCGGUCGAAUCGGUUUUGAGCUUACUUCAGCGGAAGCACCUGUGUCUGUGGUUGUCGGAAAGGGGGGGCAGAUGAGUCGGACUAAUGUUGUAUUUUUGGCGCAUGGAAAGCCGUUUUUAAUAUAAUAGUAU .....((((......((((((..........))))))...(((((((.((..(((((((((......(((..(((((.(((((((.(((((((....))))))).))))))))))))..)))....(((((....(..((((((((..((((((((((..((((.((..((((........))))..))))))..)))))))))).(((((.(((.(((.......)))...(((((.(((((((.....))))).)).))))).))))))))..)))))).))..)..)))))..)))))))))..(((.((((((.............)))))).))).....))))))))).........)))) (-93.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1096 100 51 191 142 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 400 178 132 170 123 NC_002950:PG2222|5end_acyltransferase,_HtrB/MsbB_family_2336757..2336987_POSITIVE 372 138 91 74 22 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 352 104 65 210 164 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 351 99 53 216 159 NC_002950:PG1696|5end_type_II_DNA_modification_methyltransferase,_putative_1779973..1780203_POSITIVE 351 110 71 195 150 NC_002950:PG0009|5end_ISPg5_transposase_Orf1_8466..8696_NEGATIVE 345 140 91 222 167 NC_002950:PG1578|5end_quinolinate_synthetase_1655466..1655696_POSITIVE 338 206 162 93 43 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 337 96 55 198 154 NC_002950:PG2043|5end_conserved_hypothetical_protein_TIGR00486_2142218..2142448_POSITIVE 334 150 101 211 152 NC_002950:PG0285|5end_hypothetical_protein_318459..318689_POSITIVE 332 71 32 198 151 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 322 103 61 60 4 NC_002950:PG1846|5end_hypothetical_protein_1946037..1946267_POSITIVE 321 147 101 76 36 NC_002950:PG1753|5end_selenide,_water_dikinase_1838615..1838845_POSITIVE 317 136 91 109 57 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 317 138 92 54 9 NC_002950:PG0661|5end_hypothetical_protein_709853..710083_NEGATIVE 317 138 92 212 167 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 315 78 32 225 169 NC_002950:PG0090|5end_Dps_family_protein_105524..105754_POSITIVE 314 69 21 153 100 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 314 170 124 179 123 NC_002950:PG0293|5end_secretion_activator_protein,_putative_328671..328901_NEGATIVE 313 151 112 167 127 NC_002950:PG1687|5end_HIT_family_protein_1774201..1774431_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 104 65 109 63 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 352 130 85 145 88 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 338 206 162 80 30 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 334 130 84 145 95 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 328 127 84 47 1 NC_002950:PG0309|3end_thiamine_biosynthesis_lipoprotein_ApbE_344010..344160_NEGATIVE 324 103 62 56 3 NC_002950:PG2136|3end_hypothetical_protein_2245104..2245254_POSITIVE 321 147 101 79 39 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 313 103 70 69 19 NC_002950:PG2100|3end_immunoreactive_63_kDa_antigen_PG102_2208527..2208677_NEGATIVE 313 138 94 55 1 NC_002950:PG1541|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620855..1621005_POSITIVE 309 338 295 151 97 NC_002950:PG1179|3end_hypothetical_protein_1260341..1260491_NEGATIVE 309 105 62 140 84 NC_002950:PG0056|3end_hypothetical_protein_69782..69932_POSITIVE 305 336 297 107 61 NC_002950:PG0734|3end_nitroreductase_family_protein_784404..784554_POSITIVE 304 170 121 107 48 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 303 136 96 133 96 NC_002950:PG0711|3end_hypothetical_protein_766281..766431_POSITIVE 303 140 91 121 64 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 302 137 92 63 14 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 297 170 125 53 1 NC_002950:PG0397|3end_hypothetical_protein_434312..434462_NEGATIVE 296 150 112 151 112 NC_002950:PG1688|3end_transcription_elongation_factor_GreA_1774216..1774366_NEGATIVE 294 108 61 112 58 NC_002950:PG0063|3end_outer_membrane_efflux_protein_75878..76028_NEGATIVE 292 136 92 133 100 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE