Origin IGS: gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc .........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 gcagcatctctcataccatttcttacccttcagtcgctcgcccattcctaagggatggtcgtagtgaaatgcctaaattgaattaaccgaagtatctgtccggcataagtgcattgtggagaaggggaagagattgccaaacaggcaaacatctcctccccccaatcgacaaaaaaccctctttagatactccggtacttttctcagaaactaccgctttgggtgtgctgaaaaataagtcttacccaaggaagc Mask Tandem Repeat Region ================================================ gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc Find is-nt database================================================ Query_seq: PG0411:PG0412|PG0411:PG0412:hemagglutinin, putative:DNA mismatch repair protein MutL:-><-:449419..449673 255 gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0411:PG0412|PG0411:PG0412:hemagglutinin, putative:DNA mismatch repair protein MutL:-><-:449419..449673 255 gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0411:PG0412|PG0411:PG0412:hemagglutinin, putative:DNA mismatch repair protein MutL:-><-:449419..449673 255 gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 49 End: 180 ................................................ M R K V P E Y L K R V F C R L G G G D V C L F G N L F P F S T M H L C R T D T S V N S I ........................................................................... Protein_Len: 34 Strand: + Start: 104 End: 205 ....................................................................................................... M F A C L A I S S P S P Q C T Y A G Q I L R L I Q F R H F T T T I P .................................................. Protein_Len: 53 Strand: - Start: 21 End: 179 .................... K E A C G F R Y N R L F T G S Y R F L T K Q R N P P P S T Q R N P L R K G K E V I C K H R V S V E T L E M ............................................................................ Protein_Len: 53 Strand: - Start: 2 End: 160 . K R P Y S K N K L V G L A T T E S F L V P T D L S P K K D I P P L L H K G T Q C D R G R R W L A S I G S M ............................................................................................... gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc 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================================================ gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -4.7 Tail_Score: -3.30124 Start: 97 End: 132 Full_Region: TTTTGTCGATTGGGG GGAGGAGATGTTTGCC TGTTT GGCAATCTCTTCCCC TTCTCCACAATGCAC ................................................................................................GGAGGAGATGTTTGCCTGTTTGGCAATCTCTTCCCC........................................................................................................................... Find igs database================================================ Query_seq: PG0411:PG0412|PG0411:PG0412:hemagglutinin, putative:DNA mismatch repair protein MutL:-><-:449419..449673 255 gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc Intra-Species Hit: Count: 1 Min: 1 Max: 255 Len: 255 Subject: NC_002950_PG0411_PG0412|hemagglutinin, putative:DNA mismatch repair protein MutL|POSITIVE:NEGATIVE|[449419,449673]|255 HSP 1 e-value: 1.0E-142 bit: 505.0 Len: 255 Query Start:1 Query End:255 Subject Strand: POSITIVE Subject Start: 1 Subject End: 255 gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc gcttccttgggtaagacttatttttcagcacacccaaagcggtagtttctgagaaaagtaccggagtatctaaagagggttttttgtcgattggggggaggagatgtttgcctgtttggcaatctcttccccttctccacaatgcacttatgccggacagatacttcggttaattcaatttaggcatttcactacgaccatcccttaggaatgggcgagcgactgaagggtaagaaatggtatgagagatgctgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUCCUUGGGUAAGACUUAUUUUUCAGCACACCCAAAGCGGUAGUUUCUGAGAAAAGUACCGGAGUAUCUAAAGAGGGUUUUUUGUCGAUUGGGGGGAGGAGAUGUUUGCCUGUUUGGCAAUCUCUUCCCCUUCUCCACAAUGCACUUAUGCCGGACAGAUACUUCGGUUAAUUCAAUUUAGGCAUUUCACUACGACCAUCCCUUAGGAAUGGGCGAGCGACUGAAGGGUAAGAAAUGGUAUGAGAGAUGCUGC ......((((((........((((((((.(((((......))).))..))))))))...((((((((((((............((((.((..(((((((((((((...((((.....))))))))))))))))).)).)))).(((....))).....))))))))))))..))))))....((((((((.(....((((((((((((..............))).))))......)))))..).)))))))).. (-79.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGCAUCUCUCAUACCAUUUCUUACCCUUCAGUCGCUCGCCCAUUCCUAAGGGAUGGUCGUAGUGAAAUGCCUAAAUUGAAUUAACCGAAGUAUCUGUCCGGCAUAAGUGCAUUGUGGAGAAGGGGAAGAGAUUGCCAAACAGGCAAACAUCUCCUCCCCCCAAUCGACAAAAAACCCUCUUUAGAUACUCCGGUACUUUUCUCAGAAACUACCGCUUUGGGUGUGCUGAAAAAUAAGUCUUACCCAAGGAAGC ...((.............(((((..........(((((((.(((((((...))))))).)).)))))............(((...((((.((((((((....(((....))).((((.((...(((((.(((((((((.....))))...))))).)))))....)).))))...........)))))))).))))....)))..)))))......(((((((((.(((........)))..)))))))))..)) (-77.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 138 95 224 168 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 392 120 74 203 159 NC_002950:PG2080|5end_adenosylmethionine--8-amino-7-oxononanoate_transaminase_2180679..2180909_NEGATIVE 370 128 87 220 176 NC_002950:PG1961|5end_hypothetical_protein_2051153..2051383_NEGATIVE 369 100 61 81 44 NC_002950:PG1774|5end_transcription-repair_coupling_factor_1864547..1864777_NEGATIVE 365 137 93 226 170 NC_002950:PG1088|5end_acetyltransferase,_GNAT_family_1155426..1155656_NEGATIVE 364 118 75 228 181 NC_002950:PG1603|5end_HAM1_protein_1682165..1682395_POSITIVE 357 120 77 224 173 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 356 229 183 224 168 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 350 228 185 71 32 NC_002950:PG1330|5end_large_conductance_mechanosensitive_channel_protein_1409666..1409896_POSITIVE 349 119 74 208 161 NC_002950:PG1741|5end_aspartate_ammonia-lyase_1827283..1827513_NEGATIVE 347 131 91 103 59 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 345 230 183 159 113 NC_002950:PG2149|5end_hypothetical_protein_2257658..2257888_NEGATIVE 344 140 92 91 34 NC_002950:PG0617|5end_hypothetical_protein_670059..670289_POSITIVE 342 43 2 228 190 NC_002950:PG0214|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_250963..251193_POSITIVE 340 249 201 61 17 NC_002950:PG1525|5end_isochorismate_synthase,_putative_1603865..1604095_NEGATIVE 336 160 115 219 167 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 336 129 87 55 3 NC_002950:PG1577|5end_nicotinate-nucleotide_pyrophosphorylase_1654619..1654849_POSITIVE 335 135 93 140 95 NC_002950:PG1672|5end_hypothetical_protein_1757637..1757867_POSITIVE 335 135 93 140 95 NC_002950:PG0100|5end_hypothetical_protein_119219..119449_NEGATIVE 335 137 94 150 112 NC_002950:PG0032|5end_beta-mannosidase,_putative_40212..40442_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 112 78 68 36 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 384 240 198 63 16 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 366 119 75 148 112 NC_002950:PG0867|3end_hypothetical_protein_930238..930388_NEGATIVE 365 137 93 129 73 NC_002950:PG1089|3end_DNA-binding_response_regulator_RprY_1155523..1155673_NEGATIVE 345 230 183 150 104 NC_002950:PG2150|3end_LysM_domain_protein_2257667..2257817_NEGATIVE 339 109 61 54 12 NC_002950:PG1117|3end_MATE_efflux_family_protein_1191541..1191691_POSITIVE 337 120 72 138 77 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 336 138 93 58 18 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 335 137 94 120 82 NC_002950:PG0033|3end_RmuC_domain_protein_40242..40392_NEGATIVE 332 110 61 113 58 NC_002950:PG0532|3end_hypothetical_protein_581249..581399_NEGATIVE 329 171 131 64 20 NC_002950:PG2224|3end_hypothetical_protein_2339500..2339650_POSITIVE 329 227 182 67 7 NC_002950:PG1657|3end_methylmalonyl-CoA_mutase_1741571..1741721_POSITIVE 329 240 191 72 27 NC_002950:PG0146|3end_hypothetical_protein_168408..168558_NEGATIVE 328 130 82 115 66 NC_002950:PG1189|3end_hypothetical_protein_1271952..1272102_POSITIVE 328 121 85 64 29 NC_002950:PG1103|3end_ATPase,_AAA_family_1174989..1175139_POSITIVE 327 114 78 148 98 NC_002950:PG1301|3end_hypothetical_protein_1379106..1379256_NEGATIVE 326 140 93 129 61 NC_002950:PG0309|3end_thiamine_biosynthesis_lipoprotein_ApbE_344010..344160_NEGATIVE 324 250 207 140 98 NC_002950:PG1769|3end_hypothetical_protein_1857010..1857160_POSITIVE 323 130 87 104 70 NC_002950:PG0272|3end_CBS_domain_protein_305738..305888_POSITIVE 320 120 76 72 34 NC_002950:PG2114|3end_hypothetical_protein_2223982..2224132_NEGATIVE