Origin IGS: gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca .........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 tgccccctgaaacagcttttatataagcattgtcaggcgacgaaaggtcaaaacagccgtgcgcgaaacgattgtcggctgacaatcgtttcctgcatcgtgcaggacgtgattgtcacgtgacgacggcttcctgcatcgtgcacggagtgattgtcacgtgacaacggcttcctgcatcatgcacggagtgattgtcacgtgacaacggcttccagcatcgtgcagggagcaagaaacagcctacaatcgtttcttaattcgctgc Mask Tandem Repeat Region ================================================ gcagcgaattaagaaacgattgtaggctgtttcttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca Find is-nt database================================================ Query_seq: PG1970:PG1972|PG1970:PG1972:hypothetical protein:hemagglutinin protein HagB:<-->:2059874..2060141 268 gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1970:PG1972|PG1970:PG1972:hypothetical protein:hemagglutinin protein HagB:<-->:2059874..2060141 268 gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1970:PG1972|PG1970:PG1972:hypothetical protein:hemagglutinin protein HagB:<-->:2059874..2060141 268 gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 19 End: 150 .................. M V G C F L L P A R C W K P L S R D N H S V H D A G S R C H V T I T P C T M Q E A V V T ...................................................................................................................... Protein_Len: 39 Strand: + Start: 102 End: 218 ..................................................................................................... M S R D N H S V H D A G S R R H V T I T S C T M Q E T I V S R Q S F R A R L F .................................................. Protein_Len: 38 Strand: - Start: 149 End: 262 .................................................................................................................................................... T V I V D Q V I C S V I T L R C D N R A R S N Q G K T A Q C H K Y L L Q K M ...... Protein_Len: 44 Strand: - Start: 108 End: 239 ........................................................................................................... T V I V G H V I C S A T T V H C D R G A R H L F R N D A S L R K A C P Q K S R E D G S M ............................. Protein_Len: 30 Strand: - Start: 67 End: 156 .................................................................. T V I V G H M I C S A T T V H C D S R A R H L F G D D R S M ................................................................................................................ Protein_Len: 38 Strand: - Start: 2 End: 115 . L S N L F S Q L S N R A G Q V I S S A T T V H C D S R A H H L F G N D R S M ......................................................................................................................................................... gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca 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================================================ gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -10.3 Tail_Score: -4.25074 Start: 164 End: 215 Full_Region: CGTGACAATCACGTC CTGCACGATGCAGGAAACGATTGTC AGCC GACAATCGTTTCGCGCACGGCTG TTTTGACCTTTCGTC ...................................................................................................................................................................CTGCACGATGCAGGAAACGATTGTCAGCCGACAATCGTTTCGCGCACGGCTG..................................................... TransTerm Strand: + Conf: 79 HP_score: -11.5 Tail_Score: -3.71804 Start: 166 End: 213 Full_Region: TGACAATCACGTCCT GCACGATGCAGGAAACGATTGTC AGCC GACAATCGTTTCGCGCACGGC TGTTTTGACCTTTCG .....................................................................................................................................................................GCACGATGCAGGAAACGATTGTCAGCCGACAATCGTTTCGCGCACGGC....................................................... TransTerm Strand: - Conf: 80 HP_score: -10.8 Tail_Score: -3.77196 Start: 181 End: 200 Full_Region: cagccgtgcgcgaaa cgattgtc ggct gacaatcg tttcctgcatcgtgc ....................................................................................................................................................................................cgattgtcggctgacaatcg.................................................................... Find igs database================================================ Query_seq: PG1970:PG1972|PG1970:PG1972:hypothetical protein:hemagglutinin protein HagB:<-->:2059874..2060141 268 gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca Intra-Species Hit: Count: 1 Min: 1 Max: 268 Len: 268 Subject: NC_002950_PG1970_PG1972|hypothetical protein:hemagglutinin protein HagB|NEGATIVE:POSITIVE|[2059874,2060141]|268 HSP 1 e-value: 1.0E-150 bit: 531.0 Len: 268 Query Start:1 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 268 gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca gcagcgaattaagaaacgattgtaggctgtttcttgctccctgcacgatgctggaagccgttgtcacgtgacaatcactccgtgcatgatgcaggaagccgttgtcacgtgacaatcactccgtgcacgatgcaggaagccgtcgtcacgtgacaatcacgtcctgcacgatgcaggaaacgattgtcagccgacaatcgtttcgcgcacggctgttttgacctttcgtcgcctgacaatgcttatataaaagctgtttcagggggca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGCGAAUUAAGAAACGAUUGUAGGCUGUUUCUUGCUCCCUGCACGAUGCUGGAAGCCGUUGUCACGUGACAAUCACUCCGUGCAUGAUGCAGGAAGCCGUUGUCACGUGACAAUCACUCCGUGCACGAUGCAGGAAGCCGUCGUCACGUGACAAUCACGUCCUGCACGAUGCAGGAAACGAUUGUCAGCCGACAAUCGUUUCGCGCACGGCUGUUUUGACCUUUCGUCGCCUGACAAUGCUUAUAUAAAAGCUGUUUCAGGGGGCA (((((.......(((((((((((.(((........(((.((((((((.(((((((.(..((((((((((((((((..((((.(((.....))))).))..))))))))))))))))..))))).))))).)))))).)))..........((((((((...((((((.....))))))...))))))))))).))))))))))).......)))))...........(((.(((((....((((......))))....))))).))). (-121.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCCCCCUGAAACAGCUUUUAUAUAAGCAUUGUCAGGCGACGAAAGGUCAAAACAGCCGUGCGCGAAACGAUUGUCGGCUGACAAUCGUUUCCUGCAUCGUGCAGGACGUGAUUGUCACGUGACGACGGCUUCCUGCAUCGUGCACGGAGUGAUUGUCACGUGACAACGGCUUCCUGCAUCAUGCACGGAGUGAUUGUCACGUGACAACGGCUUCCAGCAUCGUGCAGGGAGCAAGAAACAGCCUACAAUCGUUUCUUAAUUCGCUGC .....(((((....((((......))))....))))).(((.....)))....((((.......(((((((((((.(((((......(((((((((((.((((.(((.((..((((((((((((((..(((((.(((((.(((((.(((((..(((((....)))))..))))).))))).))))).)))))..))))))))))))))..)).))).)))).)))))))))))......))))).))))))))))).......)))). (-127.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1073 140 91 231 182 NC_002950:PG1970|5end_hypothetical_protein_2059783..2060013_NEGATIVE 700 55 11 228 183 NC_002950:PG1974|5end_hypothetical_protein_2063055..2063285_NEGATIVE 578 60 18 62 19 NC_002950:PG2114|5end_hypothetical_protein_2224158..2224388_NEGATIVE 467 204 162 210 167 NC_002950:PG1975|5end_hemagglutinin_protein_HagC_2063218..2063448_POSITIVE 423 62 21 225 184 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 417 147 103 186 136 NC_002950:PG1372|5end_hypothetical_protein_1454722..1454952_NEGATIVE 408 178 132 61 7 NC_002950:PG1104|5end_hypothetical_protein_1174935..1175165_POSITIVE 406 146 108 226 187 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 401 213 171 186 153 NC_002950:PG0497|5end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase_537257..537487_POSITIVE 401 213 171 97 64 NC_002950:PG0496|5end_hypothetical_protein_537168..537398_POSITIVE 388 229 181 83 29 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 386 145 101 172 120 NC_002950:PG1977|5end_hypothetical_protein_2066693..2066923_NEGATIVE 386 220 172 160 118 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 384 220 173 217 169 NC_002950:PG1815|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1911433..1911663_NEGATIVE 374 149 101 231 174 NC_002950:PG0310|5end_nitroreductase_family_protein_345559..345789_NEGATIVE 373 168 121 175 127 NC_002950:PG0999|5end_hypothetical_protein_1057026..1057256_POSITIVE 373 168 121 78 30 NC_002950:PG0998|5end_hypothetical_protein_1056929..1057159_POSITIVE 368 215 172 52 6 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 367 177 132 93 52 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 366 68 21 165 109 NC_002950:PG1132|5end_valyl-tRNA_synthetase_1210912..1211142_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 60 15 141 99 NC_002950:PG0363|3end_hypothetical_protein_398377..398527_POSITIVE 411 208 164 131 91 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 403 230 181 92 43 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 388 229 181 86 32 NC_002950:PG0214|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_251543..251693_POSITIVE 386 145 101 142 90 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 381 70 27 142 85 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 381 65 26 150 112 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 376 170 121 53 1 NC_002950:PG0599|3end_3,4-dihydroxy-2-butanone_4-phosphate_synthase/GTP_cyclohydrolase_II_657732..657882_POSITIVE 373 168 121 81 33 NC_002950:PG0997|3end_transcriptional_regulator,_putative_1057012..1057162_POSITIVE 363 168 121 125 74 NC_002950:PG1649|3end_hypothetical_protein_1730030..1730180_NEGATIVE 361 140 91 74 20 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 359 68 25 63 14 NC_002950:PG2164|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2269568..2269718_NEGATIVE 359 99 52 116 71 NC_002950:PG0263|3end_tyrosyl-tRNA_synthetase_297035..297185_POSITIVE 357 241 205 39 5 NC_002950:PG1256|3end_ribonuclease,_Rne/Rng_family_1332748..1332898_NEGATIVE 355 167 121 47 4 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 354 208 163 99 47 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 353 230 181 126 70 NC_002950:PG2121|3end_L-asparaginase_2228545..2228695_NEGATIVE 353 69 21 91 27 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 347 232 191 78 38 NC_002950:PG0243|3end_hypothetical_protein_278976..279126_NEGATIVE 344 210 161 147 87 NC_002950:PG1589|3end_dihydropteroate_synthase_1666593..1666743_NEGATIVE