Origin IGS: tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg .........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 cgctactgtagcgaggaagggtaaaaacgtttgtttcttcatgatttttttgtttttaatgattggtgatttaggataaaatagttttaattgattccgcccattttagtataagggcgaaccagttgcaaatataaatcttttttccaagaatagcaaggtattgcaagaatgattttgttagttcgtatattttctgtatttttgcattgtaaataagaaatccactatgtcagaacagataaaaaagaccgaacaggagtttaaggaaattctaaacgaatgccagtcgctcttctcaaagaaa Mask Tandem Repeat Region ================================================ tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Find is-nt database================================================ Query_seq: PI1493:PI1494|PI1493:PI1494:conserved hypothetical protein:conserved hypothetical protein:->->:1412879..1413185 307 tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1493:PI1494|PI1493:PI1494:conserved hypothetical protein:conserved hypothetical protein:->->:1412879..1413185 307 tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1493:PI1494|PI1493:PI1494:conserved hypothetical protein:conserved hypothetical protein:->->:1412879..1413185 307 tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 35 End: 124 .................................. M S L N S C S V F F I C S D I V D F L F T M Q K Y R K Y T N ....................................................................................................................................................................................... Protein_Len: 45 Strand: + Start: 84 End: 218 ................................................................................... M S Y L Q C K N T E N I R T N K I I L A I P C Y S W K K D L Y L Q L V R P Y T K M G G I N ......................................................................................... Protein_Len: 48 Strand: + Start: 91 End: 234 .......................................................................................... M Y N A K I Q K I Y E L T K S F L Q Y L A I L G K K I Y I C N W F A L I L K W A E S I K T I L S ......................................................................... Protein_Len: 37 Strand: - Start: 1 End: 111 K K S F L S Q C E N L I E K F E Q E T K K I Q E S M T S K K N V I C F Y M .................................................................................................................................................................................................... tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 176 End: 205 ...............................................................................................................................................................................TTTGCAACTGGTTCGCCCTTATACTAAAAT...................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 148 End: 177 ...................................................................................................................................................CTTGCTATTCTTGGAAAAAAGATTTATATT.................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1493:PI1494|PI1493:PI1494:conserved hypothetical protein:conserved hypothetical protein:->->:1412879..1413185 307 tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcattaaaaacaaaaaaatcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Intra-Species Hit: Count: 1 Min: 1 Max: 307 Len: 307 Subject: pint_PI1493_PI1494|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1412879,1413185]|307 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 250 Query Start:1 Query End:250 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcatt......................................................... tttctttgagaagagcgactggcattcgtttagaatttccttaaactcctgttcggtcttttttatctgttctgacatagtggatttcttatttacaatgcaaaaatacagaaaatatacgaactaacaaaatcattcttgcaataccttgctattcttggaaaaaagatttatatttgcaactggttcgcccttatactaaaatgggcggaatcaattaaaactattttatcctaaatcaccaatcatt......................................................... HSP 2 e-value: 2.0E-16 bit: 87.7 Len: 44 Query Start:264 Query End:307 Subject Strand: POSITIVE Subject Start: 264 Subject End: 307 .......................................................................................................................................................................................................................................................................tcatgaagaaacaaacgtttttacccttcctcgctacagtagcg .......................................................................................................................................................................................................................................................................tcatgaagaaacaaacgtttttacccttcctcgctacagtagcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUUGAGAAGAGCGACUGGCAUUCGUUUAGAAUUUCCUUAAACUCCUGUUCGGUCUUUUUUAUCUGUUCUGACAUAGUGGAUUUCUUAUUUACAAUGCAAAAAUACAGAAAAUAUACGAACUAACAAAAUCAUUCUUGCAAUACCUUGCUAUUCUUGGAAAAAAGAUUUAUAUUUGCAACUGGUUCGCCCUUAUACUAAAAUGGGCGGAAUCAAUUAAAACUAUUUUAUCCUAAAUCACCAAUCAUUAAAAACAAAAAAAUCAUGAAGAAACAAACGUUUUUACCCUUCCUCGCUACAGUAGCG ....((..((((.(((((...(((...((((((.......))))))....(((((......(((.(((((..((.(((.((((((.....)))))).))))).....))))))))....)))))...............)))......))))).))))..))................((.((((.(((((((............))))))).........................................................((((((....))))))..............)))).)). (-52.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUACUGUAGCGAGGAAGGGUAAAAACGUUUGUUUCUUCAUGAUUUUUUUGUUUUUAAUGAUUGGUGAUUUAGGAUAAAAUAGUUUUAAUUGAUUCCGCCCAUUUUAGUAUAAGGGCGAACCAGUUGCAAAUAUAAAUCUUUUUUCCAAGAAUAGCAAGGUAUUGCAAGAAUGAUUUUGUUAGUUCGUAUAUUUUCUGUAUUUUUGCAUUGUAAAUAAGAAAUCCACUAUGUCAGAACAGAUAAAAAAGACCGAACAGGAGUUUAAGGAAAUUCUAAACGAAUGCCAGUCGCUCUUCUCAAAGAAA (((((...))))).(((((((((((((((...(..((.....))..)...))))))))..((((((((.((((((((......((((((((((.(((.((((............))))))).)))))).)))).....(((((.((((.....((((((((((((.....))).)))))))))(((((.......(((((...(((((((.((..((.....))..)).))).)))))))))..........))))).))))...))))).))))))))....)))))))).)))))))........ (-64.53) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 213 173 170 128 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 315 185 141 168 122 pint:PI1247|5end_conserved_hypothetical_protein_1171630..1171860_POSITIVE 305 36 1 79 33 pint:PI1785|5end_conserved_hypothetical_protein_1717122..1717352_POSITIVE 295 216 175 68 24 pint:PI1084|5end_threonyl-tRNA_synthetase_1002664..1002894_POSITIVE 281 71 31 184 138 pint:PI1787|5end_conserved_hypothetical_protein_1718414..1718644_POSITIVE 277 57 12 121 63 pint:PI1279|5end_RNA_polymerase_sigma_factor/ECF_subfamily_(sigma-70)_1195215..1195445_POSITIVE 263 209 179 223 198 pint:PI0447|5end_DNA-directed_RNA_polymerase,_beta'_subunit_417314..417544_POSITIVE 262 67 21 142 83 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 258 77 31 212 155 pint:PI0659|5end_hypothetical_protein_603203..603433_POSITIVE 255 60 18 195 158 pint:PI0729|5end_integrase_661428..661658_POSITIVE 250 74 32 137 99 pint:PI1654|5end_hypothetical_protein_1567669..1567899_POSITIVE 248 60 11 73 35 pint:PI0772|5end_conserved_hypothetical_protein_707157..707387_POSITIVE 244 60 12 149 110 pint:PI0833|5end_conserved_hypothetical_protein_770059..770289_POSITIVE 243 83 47 52 12 pint:PI1312|5end_conserved_hypothetical_protein_1228851..1229081_POSITIVE 242 40 7 97 64 pint:PI0432|5end_hypothetical_protein_404781..405011_POSITIVE 242 40 7 40 7 pint:PI0433|5end_hypothetical_protein_404724..404954_POSITIVE 242 211 175 150 106 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 240 64 21 58 16 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 236 60 11 116 74 pint:PI1185|5end_hypothetical_protein_1106076..1106306_POSITIVE 235 208 170 109 59 pint:PI2120|5end_hypothetical_protein_2068839..2069069_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 213 173 57 15 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 305 36 1 72 26 pint:PI1784|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1717195..1717345_POSITIVE 281 71 31 70 24 pint:PI1786|3end_hypothetical_protein_1718380..1718530_POSITIVE 277 57 12 126 68 pint:PI1278|3end_ribulose-phosphate_3-epimerase_(pentose-5-phosphate-3-epimerase)_1195300..1195450_POSITIVE 256 69 24 71 22 pint:PI0187|3end_hypothetical_protein_178211..178361_POSITIVE 237 60 12 111 77 pint:PI1712|3end_hypothetical_protein_1627774..1627924_POSITIVE 237 210 178 58 27 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 236 60 11 123 81 pint:PI1184|3end_conserved_hypothetical_protein_1106163..1106313_POSITIVE 234 89 46 66 28 pint:PI1549|3end_conserved_hypothetical_protein_1467382..1467532_POSITIVE 233 194 155 131 87 pint:PI1073|3end_hemogluttinin_A-related_protein_(HagA)_993693..993843_POSITIVE 227 68 35 146 101 pint:PI0958|3end_G:T/U_mismatch-specific_DNA_glycosylase_890569..890719_POSITIVE 224 59 19 63 22 pint:PI2072|3end_possible_ISmav2-related_transposase_2031470..2031620_POSITIVE 224 199 153 93 39 pint:PI0051|3end_hypothetical_protein_53388..53538_POSITIVE 223 58 20 151 97 pint:PI1656|3end_hypothetical_protein_1570783..1570933_POSITIVE 223 59 19 148 116 pint:PI1492|3end_triosephosphate_isomerase_1412310..1412460_POSITIVE 222 298 255 59 13 pint:PI1153|3end_histidine_kinase_sensor_protein_1078638..1078788_POSITIVE 222 28 5 55 22 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE 221 214 183 101 74 pint:PI1916|3end_conserved_hypothetical_protein_1860740..1860890_POSITIVE 221 230 181 51 2 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 220 210 186 145 126 pint:PI0185|3end_conserved_hypothetical_protein_177821..177971_POSITIVE