Origin IGS: tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta .........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 taataggggctcatagatgtcagaaacgtgataaatgatgccccttataatgggtgtgcgttgctcgcaatgtagaacgaggagggcaaggggggcaattttgccataaaacatctgcgggactacctattgaaaggcagtcccgcagatgttttttgtggtatgagaagtttctcaaccaagcggaaatattcta Mask Tandem Repeat Region ================================================ tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta Find is-nt database================================================ Query_seq: PI1748:PI1749|PI1748:PI1749:guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase/possible (p)ppgpp synthetase II:conserved hypothetical protein:->->:1670983..1671178 196 tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1748:PI1749|PI1748:PI1749:guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase/possible (p)ppgpp synthetase II:conserved hypothetical protein:->->:1670983..1671178 196 tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1748:PI1749|PI1748:PI1749:guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase/possible (p)ppgpp synthetase II:conserved hypothetical protein:->->:1670983..1671178 196 tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 7 End: 174 ...... M S A W L R N F S Y H K K H L R D C L S I G S P A D V L W Q N C P P C P P R S T L R A T H T H Y K G H H L S R F ...................... Protein_Len: 38 Strand: + Start: 83 End: 196 .................................................................................. M F Y G K I A P L A L L V L H C E Q R T P I I R G I I Y H V S D I Y E P L L Protein_Len: 47 Strand: - Start: 3 End: 143 .. F I E A Q N L F K E Y W L F C R R S Q R E I P L G A S T K H C F Q G G Q G G R E V N R A V C M ..................................................... Protein_Len: 30 Strand: - Start: 2 End: 91 . S Y K R K T S F S R M G C F V D A P S G K L L Y D R L H K M ......................................................................................................... tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta 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================================================ tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -24.2 Tail_Score: -2.63112 Start: 39 End: 92 Full_Region: ggggggcaattttgc cataaaacatctgcgggactacct attgaa aggcagtcccgcagatgttttttg tggtatgagaagttt ......................................cataaaacatctgcgggactacctattgaaaggcagtcccgcagatgttttttg........................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -23.1 Tail_Score: -4.37658 Start: 46 End: 85 Full_Region: TCATACCACAAAAAA CATCTGCGGGACTGCCT TTCAAT AGGTAGTCCCGCAGATG TTTTATGGCAAAATT .............................................CATCTGCGGGACTGCCTTTCAATAGGTAGTCCCGCAGATG............................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -20.9 Tail_Score: -5.34555 Start: 46 End: 85 Full_Region: aattttgccataaaa catctgcgggactacct attgaa aggcagtcccgcagatg ttttttgtggtatga .............................................catctgcgggactacctattgaaaggcagtcccgcagatg............................................................................................................... Find igs database================================================ Query_seq: PI1748:PI1749|PI1748:PI1749:guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase/possible (p)ppgpp synthetase II:conserved hypothetical protein:->->:1670983..1671178 196 tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: pint_PI1748_PI1749|guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase/possible (p)ppgpp synthetase II:conserved hypothetical protein|POSITIVE:POSITIVE|[1670983,1671178]|196 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta tagaatatttccgcttggttgagaaacttctcataccacaaaaaacatctgcgggactgcctttcaataggtagtcccgcagatgttttatggcaaaattgccccccttgccctcctcgttctacattgcgagcaacgcacacccattataaggggcatcatttatcacgtttctgacatctatgagcccctatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAUAUUUCCGCUUGGUUGAGAAACUUCUCAUACCACAAAAAACAUCUGCGGGACUGCCUUUCAAUAGGUAGUCCCGCAGAUGUUUUAUGGCAAAAUUGCCCCCCUUGCCCUCCUCGUUCUACAUUGCGAGCAACGCACACCCAUUAUAAGGGGCAUCAUUUAUCACGUUUCUGACAUCUAUGAGCCCCUAUUA ...............(((((((((....))))).))))...(((((((((((((((((((((......)))))))))))))))))))))..((((....)))).....(((....(((((........)))))....)))...........((((((.((((...(((......))).....)))))))))).... (-74.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAGGGGCUCAUAGAUGUCAGAAACGUGAUAAAUGAUGCCCCUUAUAAUGGGUGUGCGUUGCUCGCAAUGUAGAACGAGGAGGGCAAGGGGGGCAAUUUUGCCAUAAAACAUCUGCGGGACUACCUAUUGAAAGGCAGUCCCGCAGAUGUUUUUUGUGGUAUGAGAAGUUUCUCAACCAAGCGGAAAUAUUCUA ....((((((((((...(((((......))))).)))).)))))).....(((...(((.((.((((..........)))).)).))).(((..((..((.(((((((((((((((((((((((.(((......))).))))))))))))))..))))))))).))...))..)))..)))............... (-78.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 508 88 41 156 110 pint:PI0820|5end_hypothetical_protein_759694..759924_POSITIVE 491 89 48 160 119 pint:PI2129|5end_octaprenyl-diphosphate_synthase_2076808..2077038_POSITIVE 438 84 47 230 193 pint:PI0294|5end_conserved_hypothetical_protein_276223..276453_POSITIVE 393 188 145 125 78 pint:PI0933|5end_hypothetical_protein_865700..865930_POSITIVE 336 120 78 99 64 pint:PI0834|5end_conserved_hypothetical_protein_770785..771015_POSITIVE 328 138 92 89 48 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 327 188 152 58 23 pint:PI0175|5end_succinyl-CoA_synthetase_beta_subunit_167023..167253_POSITIVE 326 147 101 202 132 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 322 97 51 136 72 pint:PI2136|5end_hypothetical_protein_2082605..2082835_POSITIVE 318 168 121 221 167 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 318 146 101 164 113 pint:PI0118|5end_hypothetical_protein_111321..111551_POSITIVE 311 136 98 227 190 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 311 136 98 60 23 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 308 120 71 150 103 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 308 138 98 49 8 pint:PI0314|5end_conserved_hypothetical_protein_295552..295782_POSITIVE 307 117 71 69 18 pint:PI0378|5end_conserved_hypothetical_protein;_possible_helicase_348026..348256_POSITIVE 306 92 51 119 74 pint:PI1005|5end_hypothetical_protein_926201..926431_POSITIVE 306 156 112 108 59 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 306 156 112 50 1 pint:PI0565|5end_hypothetical_protein_511479..511709_POSITIVE 304 85 46 185 135 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 724 89 42 49 2 pint:PI1748|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase/possible_(p)ppgpp_synthetase_II_1670922..1671072_POSITIVE 712 190 141 84 35 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 491 89 48 97 56 pint:PI2128|3end_hypothetical_protein_2076825..2076975_POSITIVE 468 88 50 41 3 pint:PI0818|3end_alpha-amylase_759659..759809_POSITIVE 336 119 77 136 94 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 320 144 101 144 96 pint:PI0019|3end_conserved_hypothetical_protein_24454..24604_POSITIVE 318 146 101 77 26 pint:PI0117|3end_ribonuclease_HI_111314..111464_POSITIVE 311 181 152 42 13 pint:PI1820|3end_hypothetical_protein_1760377..1760527_POSITIVE 306 92 51 55 10 pint:PI1004|3end_conserved_hypothetical_protein_926217..926367_POSITIVE 306 156 112 148 99 pint:PI0565|3end_hypothetical_protein_511657..511807_POSITIVE 305 158 115 73 36 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 300 148 101 79 13 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 298 126 92 151 112 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 298 139 91 143 86 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 295 138 91 136 92 pint:PI1184|3end_conserved_hypothetical_protein_1106163..1106313_POSITIVE 292 156 117 140 92 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 285 142 106 62 29 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 284 160 112 42 3 pint:PI1381|3end_conserved_hypothetical_protein_1303676..1303826_POSITIVE 284 168 123 54 7 pint:PI1003|3end_conserved_hypothetical_protein_925718..925868_POSITIVE 284 90 43 54 7 pint:PI0099|3end_hypothetical_protein_95777..95927_POSITIVE