Origin IGS: tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca .........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 tgcatgaaagcatcggtccgcggagaaaagcagtgcgcccactgtcataccaattcggtattcatagcaacaaagttagcaaaaagcctttcgctcttatcaatcgcactcgtggggcagctcacccgtaagcgaccgaaccgagtgtgctacgccctccatttgtcataactatatttgtacgcaagcaagtgaaattcagata Mask Tandem Repeat Region ================================================ tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca Find is-nt database================================================ Query_seq: PG1943:PG1944|PG1943:PG1944:hypothetical protein:3-phosphoshikimate 1-carboxyvinyltransferase:<-->:2030351..2030555 205 tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1943:PG1944|PG1943:PG1944:hypothetical protein:3-phosphoshikimate 1-carboxyvinyltransferase:<-->:2030351..2030555 205 tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1943:PG1944|PG1943:PG1944:hypothetical protein:3-phosphoshikimate 1-carboxyvinyltransferase:<-->:2030351..2030555 205 tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 78 End: 194 ............................................................................. P H A A G R T R N I L A F P K K S V K N S H I G F Q Y S L P R V A K R R P G M ........... Protein_Len: 55 Strand: - Start: 38 End: 202 ..................................... S L H L A Y C V R N P R K R T L Q G V L A I S L L S L S K A L K T A I F V S N T H C H A C Q K E G R V S A K M ... tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca 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================================================ tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1943:PG1944|PG1943:PG1944:hypothetical protein:3-phosphoshikimate 1-carboxyvinyltransferase:<-->:2030351..2030555 205 tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_002950_PG1943_PG1944|hypothetical protein:3-phosphoshikimate 1-carboxyvinyltransferase|NEGATIVE:POSITIVE|[2030351, 2030555]|205 HSP 1 e-value: 1.0E-112 bit: 406.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca tatctgaatttcacttgcttgcgtacaaatatagttatgacaaatggagggcgtagcacactcggttcggtcgcttacgggtgagctgccccacgagtgcgattgataagagcgaaaggctttttgctaactttgttgctatgaataccgaattggtatgacagtgggcgcactgcttttctccgcggaccgatgctttcatgca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUGAAUUUCACUUGCUUGCGUACAAAUAUAGUUAUGACAAAUGGAGGGCGUAGCACACUCGGUUCGGUCGCUUACGGGUGAGCUGCCCCACGAGUGCGAUUGAUAAGAGCGAAAGGCUUUUUGCUAACUUUGUUGCUAUGAAUACCGAAUUGGUAUGACAGUGGGCGCACUGCUUUUCUCCGCGGACCGAUGCUUUCAUGCA ........(((((.((((..((...........))...).))).))))).((((((((...((((((((........((((.((((((((((((....(((((.......(((((((....)))))))......))))).....(((((.....)))))....))))).)))..))))...))))))))))))))))...)))). (-55.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAUGAAAGCAUCGGUCCGCGGAGAAAAGCAGUGCGCCCACUGUCAUACCAAUUCGGUAUUCAUAGCAACAAAGUUAGCAAAAAGCCUUUCGCUCUUAUCAAUCGCACUCGUGGGGCAGCUCACCCGUAAGCGACCGAACCGAGUGUGCUACGCCCUCCAUUUGUCAUAACUAUAUUUGUACGCAAGCAAGUGAAAUUCAGAUA ...((((.....(((((((((((.(...(((..(((.(((((....(((((.....))))).....((.........(((.(((....))).)))..........))....)))))))))))..)))))..).))))))...(((.(((...))).)))......)))).....(((((((......)))))))........... (-44.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1167 100 51 191 142 NC_002950:PG1943|5end_hypothetical_protein_2030260..2030490_NEGATIVE 515 100 51 46 1 NC_002950:PG1103|5end_ATPase,_AAA_family_1173605..1173835_POSITIVE 488 90 41 89 31 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 425 89 44 125 80 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 423 200 155 66 10 NC_002950:PG1942|5end_30S_ribosomal_protein_S12_2028350..2028580_NEGATIVE 420 120 73 169 118 NC_002950:PG1024|5end_hypothetical_protein_1086698..1086928_POSITIVE 418 107 63 67 21 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 405 89 44 166 125 NC_002950:PG0201|5end_ribonuclease_P_238770..239000_NEGATIVE 399 120 72 228 170 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 398 186 148 71 17 NC_002950:PG1738|5end_hypothetical_protein_1825131..1825361_NEGATIVE 398 85 48 182 154 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 397 100 51 218 149 NC_002950:PG2100|5end_immunoreactive_63_kDa_antigen_PG102_2210191..2210421_NEGATIVE 397 89 43 130 69 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 397 108 63 218 177 NC_002950:PG0305|5end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_340906..341136_POSITIVE 395 100 51 223 168 NC_002950:PG0854|5end_hypothetical_protein_914870..915100_POSITIVE 395 98 53 73 21 NC_002950:PG0714|5end_copper_homeostasis_protein_CutC_768671..768901_NEGATIVE 395 99 52 207 163 NC_002950:PG0430|5end_ferrodoxin_oxidoreductase_beta_subunit_467986..468216_POSITIVE 393 99 53 67 15 NC_002950:PG1910|5end_ribosomal_protein_L17_2010764..2010994_NEGATIVE 393 89 44 199 140 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 390 90 51 202 160 NC_002950:PG1072|5end_MutS_family_protein_1138976..1139206_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 488 90 41 82 24 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 427 200 155 147 100 NC_002950:PG0259|3end_hypothetical_protein_293701..293851_POSITIVE 425 89 44 80 35 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 399 120 72 69 11 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 398 186 148 74 20 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 397 100 51 131 62 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 397 89 43 116 55 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 395 98 53 68 16 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 393 99 53 61 9 NC_002950:PG1911|3end_DNA-directed_RNA_polymerase_alpha_subunit_2010770..2010920_NEGATIVE 392 89 48 97 47 NC_002950:PG1218|3end_hypothetical_protein_1296475..1296625_POSITIVE 383 100 51 60 4 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 377 197 163 44 3 NC_002950:PG2164|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2269568..2269718_NEGATIVE 374 101 62 79 42 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 371 87 46 62 10 NC_002950:PG0261|3end_ISPg3,_transposase_293862..294012_NEGATIVE 367 86 44 71 16 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 367 198 153 138 84 NC_002950:PG0099|3end_phenylalanyl-tRNA_synthetase_beta_subunit_115827..115977_NEGATIVE 366 83 44 72 35 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 365 97 56 144 85 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 362 88 45 81 32 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE 361 90 46 91 38 NC_002950:PG2224|3end_hypothetical_protein_2339500..2339650_POSITIVE