Origin IGS: aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt .........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 aatttctatatttttgtccgtgacagtgcggaaagcataccggccgacagcgtctcggccggccttccgcctctattaacgacataaaagtaacgaatcgtatgggtctgaaaatccttttcccactgcaaaatctttccgttgatacaactaaagtcaataaaatagcagaagtcgtttcgcccgaagcactcaagcaaatcaaagacatcaagccttcgcaatggaccgagctgctcggccagtggggcggcaaggcgttgagcttcggtatcaaggtgctcatcgccctt Mask Tandem Repeat Region ================================================ aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt Find is-nt database================================================ Query_seq: PG1966:PG1967|PG1966:PG1967:hypothetical protein:TPR domain protein:<-->:2057015..2057307 293 aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1966:PG1967|PG1966:PG1967:hypothetical protein:TPR domain protein:<-->:2057015..2057307 293 aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1966:PG1967|PG1966:PG1967:hypothetical protein:TPR domain protein:<-->:2057015..2057307 293 aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 49 End: 285 ................................................ M A E Q L G P L R R L D V F D L L E C F G R N D F C Y F I D F S C I N G K I L Q W E K D F Q T H T I R Y F Y V V N R G G ........ Protein_Len: 60 Strand: + Start: 8 End: 292 ....... M S T L I P K L N A L P P H W P S S S V H C E G L M S L I C L S A S G E T T S A I L L T L V V S T E R F C S G K R I F R . Protein_Len: 60 Strand: - Start: 1 End: 219 G G W Q G L L E T W Q S P K I D K I Q K L A E P S V V E A I K N V K T T D V S L N Q L P F L I K L G M R N T V K I D N M .......................................................................... aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt 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================================================ aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -3.1 Tail_Score: -2.95919 Start: 73 End: 91 Full_Region: CAGCTCGGTCCATTG CGAAGGC TTGAT GTCTTTG ATTTGCTTGAGTGCT ........................................................................CGAAGGCTTGATGTCTTTG.......................................................................................................................................................................................................... TransTerm Strand: + Conf: 80 HP_score: -13.4 Tail_Score: -3.00704 Start: 232 End: 254 Full_Region: AATAGAGGCGGAAGG CCGGCCGAGA CGC TGTCGGCCGG TATGCTTTCCGCACT .......................................................................................................................................................................................................................................CCGGCCGAGACGCTGTCGGCCGG....................................... Find igs database================================================ Query_seq: PG1966:PG1967|PG1966:PG1967:hypothetical protein:TPR domain protein:<-->:2057015..2057307 293 aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 293 Len: 293 Subject: NC_002950_PG1966_PG1967|hypothetical protein:TPR domain protein|NEGATIVE:POSITIVE|[2057015,2057307]|293 HSP 1 e-value: 1.0E-165 bit: 581.0 Len: 293 Query Start:1 Query End:293 Subject Strand: POSITIVE Subject Start: 1 Subject End: 293 aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt aagggcgatgagcaccttgataccgaagctcaacgccttgccgccccactggccgagcagctcggtccattgcgaaggcttgatgtctttgatttgcttgagtgcttcgggcgaaacgacttctgctattttattgactttagttgtatcaacggaaagattttgcagtgggaaaaggattttcagacccatacgattcgttacttttatgtcgttaatagaggcggaaggccggccgagacgctgtcggccggtatgctttccgcactgtcacggacaaaaatatagaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGGCGAUGAGCACCUUGAUACCGAAGCUCAACGCCUUGCCGCCCCACUGGCCGAGCAGCUCGGUCCAUUGCGAAGGCUUGAUGUCUUUGAUUUGCUUGAGUGCUUCGGGCGAAACGACUUCUGCUAUUUUAUUGACUUUAGUUGUAUCAACGGAAAGAUUUUGCAGUGGGAAAAGGAUUUUCAGACCCAUACGAUUCGUUACUUUUAUGUCGUUAAUAGAGGCGGAAGGCCGGCCGAGACGCUGUCGGCCGGUAUGCUUUCCGCACUGUCACGGACAAAAAUAUAGAAAUU .((((((.(((((...(((....))).))))).)))))).((..(((((((....(((((...((((.....(((((((.....))))))).((((((((((...))))))))))..)))).)))))..........((((.((((...))))..))))......)))))))....))..................(((......(((.((((....((((..((((((((((((((((.......)))))))....))))))))).))))....)))).)))....)))... (-95.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCUAUAUUUUUGUCCGUGACAGUGCGGAAAGCAUACCGGCCGACAGCGUCUCGGCCGGCCUUCCGCCUCUAUUAACGACAUAAAAGUAACGAAUCGUAUGGGUCUGAAAAUCCUUUUCCCACUGCAAAAUCUUUCCGUUGAUACAACUAAAGUCAAUAAAAUAGCAGAAGUCGUUUCGCCCGAAGCACUCAAGCAAAUCAAAGACAUCAAGCCUUCGCAAUGGACCGAGCUGCUCGGCCAGUGGGGCGGCAAGGCGUUGAGCUUCGGUAUCAAGGUGCUCAUCGCCCUU ........(((((((((.(((...((.((((((.((....(((((((.......))))))))).))))))..))....)))..)))))))))..((...(((((((...(((.....))).)))).)))....(((((..((((((.........))))))......((...(((.(((((....))))))))...)).....)))))..))..(((.((.((.(((.(((((...)))))))).)).)).)))..((((.(((((.((........)).))))).))))... (-87.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1203 80 31 171 122 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 597 279 231 74 21 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 538 270 222 50 7 NC_002950:PG0736|5end_ribonuclease_HII_785608..785838_POSITIVE 499 270 221 193 140 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 496 270 221 205 140 NC_002950:PG1588|5end_hypothetical_protein_1666532..1666762_NEGATIVE 486 270 221 205 146 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 479 58 11 66 23 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 456 265 223 189 135 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 449 255 220 52 4 NC_002950:PG2000|5end_signal_peptidase-related_protein_2089468..2089698_NEGATIVE 449 270 223 107 57 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 448 265 223 161 118 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 441 277 232 183 135 NC_002950:PG1248|5end_hypothetical_protein_1326532..1326762_NEGATIVE 437 258 212 213 167 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 435 257 213 170 127 NC_002950:PG1977|5end_hypothetical_protein_2066693..2066923_NEGATIVE 434 260 219 221 157 NC_002950:PG1840|5end_hypothetical_protein_1937102..1937332_POSITIVE 427 278 231 199 147 NC_002950:PG1972|5end_hemagglutinin_protein_HagB_2060002..2060232_POSITIVE 424 276 231 55 6 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 423 270 224 174 131 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 423 56 11 73 14 NC_002950:PG0674|5end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724802..725032_NEGATIVE 422 278 234 180 137 NC_002950:PG1592|5end_HDIG_domain_protein_1669383..1669613_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 496 270 221 144 79 NC_002950:PG1589|3end_dihydropteroate_synthase_1666593..1666743_NEGATIVE 489 280 231 50 2 NC_002950:PG0735|3end_aminotransferase,_class_V_785677..785827_POSITIVE 460 273 231 93 47 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 460 265 223 146 96 NC_002950:PG0381|3end_cell_volume_regulation_protein_CvrA_411185..411335_NEGATIVE 455 260 218 113 58 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 452 54 12 72 21 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 449 255 220 62 14 NC_002950:PG2001|3end_signal_peptidase_I_2089458..2089608_NEGATIVE 449 270 223 127 61 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 447 275 233 127 76 NC_002950:PG2206|3end_ABC_transporter,_ATP-binding_protein_2317250..2317400_NEGATIVE 441 266 223 144 98 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 439 265 225 67 17 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 438 59 12 118 58 NC_002950:PG1175|3end_ABC_transporter,_ATP-binding_protein,_putative_1254170..1254320_NEGATIVE 437 258 212 151 105 NC_002950:PG0227|3end_DNA_repair_protein_RadA_262593..262743_NEGATIVE 435 257 213 140 97 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 434 259 211 143 96 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 433 270 223 127 71 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 422 270 225 72 19 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE 419 67 24 54 1 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 416 270 222 61 3 NC_002950:PG0125|3end_hypothetical_protein_146238..146388_NEGATIVE 415 273 231 93 43 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE