Origin IGS: tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg .........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 cccgcagagcgttcacggattatcccttttatcctctctcgaattgtgcttgagggaggagctggcccattgagagctaaaaactagatcccttggaaaaatttacagagccaagccaaaacctcagcccataaaaggagcatgggttctgaggtatcccgatctgctggaagatgcctaccggattactgtatatgaggaaaacggcatcgtgactgctcttacagggattgttctcccgtaacattgattttcgtatggaagcaaggggctgtgccaaaaatgaatttggtcacagcccctttgtcttttatactcggttgcctgtgctgctgcggccggcaggccggcatgggggagtgcgga Mask Tandem Repeat Region ================================================ tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg Find is-nt database================================================ Query_seq: PG1975:PG1977|PG1975:PG1977:hemagglutinin protein HagC:hypothetical protein:-><-:2064411..2064776 366 tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1975:PG1977|PG1975:PG1977:hemagglutinin protein HagC:hypothetical protein:-><-:2064411..2064776 366 tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1975:PG1977|PG1975:PG1977:hemagglutinin protein HagC:hypothetical protein:-><-:2064411..2064776 366 tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 14 End: 142 ............. M P A C R P Q Q H R Q P S I K D K G A V T K F I F G T A P C F H T K I N V T G E Q S L ................................................................................................................................................................................................................................ Protein_Len: 55 Strand: + Start: 22 End: 186 ..................... M P A A A A Q A T E Y K R Q R G C D Q I H F W H S P L L P Y E N Q C Y G R T I P V R A V T M P F S S Y T V I R .................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 87 End: 287 ...................................................................................... M A Q P L A S I R K S M L R E N N P C K S S H D A V F L I Y S N P V G I F Q Q I G I P Q N P C S F Y G L R F W L G S V N ............................................................................... Protein_Len: 36 Strand: - Start: 172 End: 279 ........................................................................................................................................................................... I C Y D P L C R G A S R S V E S G M S R K H A S T K A Q S Q L N K W P M ....................................................................................... Protein_Len: 47 Strand: - Start: 126 End: 266 ............................................................................................................................. P L V I G T L A T V I G N E E Y V T I R Y A D E L L D P Y R L V W A G K I P Q P K P K A R Y M .................................................................................................... Protein_Len: 50 Strand: - Start: 2 End: 151 . R V G G H R G A P R L L V P L R T Y F V F P S H G F E N K A C G R A E M R F D I N R S F L G Q L L M ....................................................................................................................................................................................................................... Protein_Len: 40 Strand: - Start: 1 End: 120 G C E G M G A Q R G C C C L C G L I F S L P A T V L N M K P V A G Q K W V F I M ...................................................................................................................................................................................................................................................... tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg 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================================================ tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -15.2 Tail_Score: -3.37344 Start: 65 End: 99 Full_Region: AGTATAAAAGACAAA GGGGCTGTGACCAAA TTCATT TTTGGCACAGCCCC TTGCTTCCATACGAA ................................................................GGGGCTGTGACCAAATTCATTTTTGGCACAGCCCC........................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -15.2 Tail_Score: -4.52142 Start: 65 End: 99 Full_Region: ttcgtatggaagcaa ggggctgtgccaaa aatgaa tttggtcacagcccc tttgtcttttatact ................................................................ggggctgtgccaaaaatgaatttggtcacagcccc........................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG1975:PG1977|PG1975:PG1977:hemagglutinin protein HagC:hypothetical protein:-><-:2064411..2064776 366 tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg Intra-Species Hit: Count: 1 Min: 1 Max: 366 Len: 366 Subject: NC_002950_PG1975_PG1977|hemagglutinin protein HagC:hypothetical protein|POSITIVE:NEGATIVE|[2064411,2064776]|366 HSP 1 e-value: 0.0 bit: 726.0 Len: 366 Query Start:1 Query End:366 Subject Strand: POSITIVE Subject Start: 1 Subject End: 366 tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg tccgcactcccccatgccggcctgccggccgcagcagcacaggcaaccgagtataaaagacaaaggggctgtgaccaaattcatttttggcacagccccttgcttccatacgaaaatcaatgttacgggagaacaatccctgtaagagcagtcacgatgccgttttcctcatatacagtaatccggtaggcatcttccagcagatcgggatacctcagaacccatgctccttttatgggctgaggttttggcttggctctgtaaatttttccaagggatctagtttttagctctcaatgggccagctcctccctcaagcacaattcgagagaggataaaagggataatccgtgaacgctctgcggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGCACUCCCCCAUGCCGGCCUGCCGGCCGCAGCAGCACAGGCAACCGAGUAUAAAAGACAAAGGGGCUGUGACCAAAUUCAUUUUUGGCACAGCCCCUUGCUUCCAUACGAAAAUCAAUGUUACGGGAGAACAAUCCCUGUAAGAGCAGUCACGAUGCCGUUUUCCUCAUAUACAGUAAUCCGGUAGGCAUCUUCCAGCAGAUCGGGAUACCUCAGAACCCAUGCUCCUUUUAUGGGCUGAGGUUUUGGCUUGGCUCUGUAAAUUUUUCCAAGGGAUCUAGUUUUUAGCUCUCAAUGGGCCAGCUCCUCCCUCAAGCACAAUUCGAGAGAGGAUAAAAGGGAUAAUCCGUGAACGCUCUGCGGG .((((.(((((...((((.((((((.....))))..))...)))).....((((..(((...(((((((((((.(((((......)))))))))))))))).)))..))))...............))))).............(((((..(((((((.((.((((((((...........((((((..((........))..))))))..(((((((..((((((.......))))))))))))).((((((((..................(((((...((((....((((.....)))).))))..)))))))))).))).......)))))..))).))...)).)))))..))))))))). (-131.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGCAGAGCGUUCACGGAUUAUCCCUUUUAUCCUCUCUCGAAUUGUGCUUGAGGGAGGAGCUGGCCCAUUGAGAGCUAAAAACUAGAUCCCUUGGAAAAAUUUACAGAGCCAAGCCAAAACCUCAGCCCAUAAAAGGAGCAUGGGUUCUGAGGUAUCCCGAUCUGCUGGAAGAUGCCUACCGGAUUACUGUAUAUGAGGAAAACGGCAUCGUGACUGCUCUUACAGGGAUUGUUCUCCCGUAACAUUGAUUUUCGUAUGGAAGCAAGGGGCUGUGCCAAAAAUGAAUUUGGUCACAGCCCCUUUGUCUUUUAUACUCGGUUGCCUGUGCUGCUGCGGCCGGCAGGCCGGCAUGGGGGAGUGCGGA .(((((...((....)).....((((((...(((((((((((.......)))))))))))(((((((...(((((((.......((((((.(((((..............))))).....((((((((((((.........)))))..))))))).....))))))......((((((..((..((........))..)).....))))))......)))))))..((((......))))...............((((((((((((((((((((((((((......))))).))))))))).))).))))))))).(((((((..(.....).)))))))...)))))))..)))))).))))). (-140.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 557 101 65 193 157 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 498 105 65 61 21 NC_002950:PG1234|5end_hypothetical_protein_1310112..1310342_POSITIVE 497 47 1 121 58 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 495 50 7 71 25 NC_002950:PG0714|5end_copper_homeostasis_protein_CutC_768671..768901_NEGATIVE 477 50 2 60 6 NC_002950:PG1787|5end_hypothetical_protein_1875908..1876138_NEGATIVE 449 49 1 220 151 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 446 50 1 127 68 NC_002950:PG1605|5end_aminopeptidase_C_1685179..1685409_POSITIVE 445 48 2 55 5 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 441 50 6 59 3 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 440 50 1 179 119 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 436 50 3 211 144 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 434 45 1 179 128 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 433 46 1 61 18 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 432 49 2 227 168 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 429 227 183 80 39 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 418 208 166 183 144 NC_002950:PG2062|5end_histidyl-tRNA_synthetase_2158971..2159201_POSITIVE 411 98 51 225 177 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 411 49 1 192 142 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 406 53 15 176 132 NC_002950:PG1979|5end_hypothetical_protein_2067272..2067502_POSITIVE 405 50 2 166 114 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 497 47 1 81 18 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 495 50 7 66 20 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 474 105 61 67 18 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 469 99 62 41 4 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 433 46 1 74 31 NC_002950:PG1622|3end_DNA_topoisomerase_IV_subunit_A_1701418..1701568_NEGATIVE 431 98 62 67 31 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 429 227 183 83 42 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 418 208 166 122 83 NC_002950:PG2061|3end_dihydrofolate_reductase_2158990..2159140_POSITIVE 408 49 2 145 101 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 406 37 2 143 101 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 403 100 64 50 13 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 400 50 3 72 6 NC_002950:PG1334|3end_band_7/Mec-2_family_protein_1415422..1415572_NEGATIVE 399 105 64 43 6 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 399 98 55 68 22 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 397 49 3 84 24 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 397 44 2 102 50 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 395 99 51 62 16 NC_002950:PG0186|3end_lipoprotein_RagB_222997..223147_POSITIVE 392 101 62 46 11 NC_002950:PG1809|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_1905491..1905641_NEGATIVE 389 99 51 68 10 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 387 104 62 62 16 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE