Origin IGS: caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta .........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 taaagcggtcggcaaatctgccgaccgctactttctttcgtgagcttcgagcggacaaagaaagtagcaaagaaacccgaagaaaagtacctcgttacttttgacagtgagttgggacggctcaaaagtaacaaaaagccaataagatataatatcattctctcaaatacaggtagatatgtttgttttagagggaacgttaagtcattgtttgtatttatctaaaaacacatgtggaatacagtatatatccctttttgctcttgtgtaagcaacgtaaagtttattccgggttgacggatttaattg Mask Tandem Repeat Region ================================================ caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta Find is-nt database================================================ Query_seq: PI0271:PI0272|PI0271:PI0272:hypothetical protein:conserved hypothetical protein:->->:262452..262760 309 caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0271:PI0272|PI0271:PI0272:hypothetical protein:conserved hypothetical protein:->->:262452..262760 309 caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0271:PI0272|PI0271:PI0272:hypothetical protein:conserved hypothetical protein:->->:262452..262760 309 caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 157 End: 279 ............................................................................................................................................................ M I S Y W L F V T F E P S Q L T V K S N E V L F F G F L C Y F L C P L E A H E R K .............................. Protein_Len: 60 Strand: + Start: 89 End: 307 ........................................................................................ M N T N N D L T F P L K Q T Y L P V F E R M I L Y L I G F L L L L S R P N S L S K V T R Y F S S G F F A T F F V R S K L .. Protein_Len: 60 Strand: - Start: 88 End: 294 ....................................................................................... G R F C V Y R G T N S L I I N Y R I P K K N S K L R G L E S D F T V L Y K E E P K K A V K K T R E F S V F S L L P R C M ............... Protein_Len: 40 Strand: - Start: 42 End: 161 ......................................... V L A F L S I Y Q I G C T N K S L Y L C H S L T G E L V F M D V Q I Q S F S I M .................................................................................................................................................... Protein_Len: 34 Strand: - Start: 2 End: 103 . I L D T L G S Y V K R Q K C L L L F P Y I S Y E V H T K L Y I C V M .............................................................................................................................................................................................................. caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta 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================================================ caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.4 Tail_Score: -2.54841 Start: 175 End: 219 Full_Region: ATATCTTATTGGCTT TTTGTTACTTTTGAGCCGT CCCAACTC ACTGTCAAAAGTAACGAG GTACTTTTCTTCGGG ..............................................................................................................................................................................TTTGTTACTTTTGAGCCGTCCCAACTCACTGTCAAAAGTAACGAG.......................................................................................... Find igs database================================================ Query_seq: PI0271:PI0272|PI0271:PI0272:hypothetical protein:conserved hypothetical protein:->->:262452..262760 309 caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta Intra-Species Hit: Count: 2 Min: 1 Max: 309 Len: 309 Subject: pint_PI0271_PI0272|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[262452,262760]|309 HSP 1 e-value: 1.0E-174 bit: 613.0 Len: 309 Query Start:1 Query End:309 Subject Strand: POSITIVE Subject Start: 1 Subject End: 309 caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta caattaaatccgtcaacccggaataaactttacgttgcttacacaagagcaaaaagggatatatactgtattccacatgtgtttttagataaatacaaacaatgacttaacgttccctctaaaacaaacatatctacctgtatttgagagaatgatattatatcttattggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttcttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta Subject: pint_PI0401_PI0402|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[367168,368031]|864 HSP 1 e-value: 3.0E-37 bit: 157.0 Len: 142 Query Start:168 Query End:309 Subject Strand: POSITIVE Subject Start: 20 Subject End: 162 .......................................................................................................................................................................ttggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttc-ttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta .......................................................................................................................................................................ttggctttttgttacttttgagctgtctcaactcactgtcaaaagtaacgaagtgtttttcattggggtttctttgctcctttctttgtccgcccgatgctcacgaaagagaggagcggtcggcaaatccgccgaccgcttta Inter-species Hit: Count: 1 Min: 168 Max: 309 Len: 142 Subject: NC_002950_PG1436_PG1439|ATPase, putative:hypothetical protein|POSITIVE:NEGATIVE|[1523815,1524674]|860 HSP 1 e-value: 3.0E-37 bit: 157.0 Len: 142 Query Start:168 Query End:309 Subject Strand: NEGATIVE Subject Start: 702 Subject End: 844 .......................................................................................................................................................................ttggctttttgttacttttgagccgtcccaactcactgtcaaaagtaacgaggtacttttc-ttcgggtttctttgctactttctttgtccgctcgaagctcacgaaagaaagtagcggtcggcagatttgccgaccgcttta .......................................................................................................................................................................ttggctttttgttacttttgagctgtctcaactcactgtcaaaagtaacgaagtgtttttcattggggtttctttgctcctttctttgtccgcccgatgctcacgaaagagaggagcggtcggcaaatccgccgaccgcttta Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGGCUUUUUGUUACUUUUGAGCCGUCCCAACUCACUGUCAAAAGUAACGAGGUACUUUUCUUCGGGUUUCUUUGCUACUUUCUUUGUCCGCUCGAAGCUCACGAAAGAAAGUAGCGGUCGGCAGAUUUGCCGACCGCUUUA .......((((((((((((((.(.((........)).))))))))))))))).((((((..((((((((((...((.((.......))..))..))))).).))))..))))))(((((((((......))))))))).... (-50.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGCGGUCGGCAAAUCUGCCGACCGCUACUUUCUUUCGUGAGCUUCGAGCGGACAAAGAAAGUAGCAAAGAAACCCGAAGAAAAGUACCUCGUUACUUUUGACAGUGAGUUGGGACGGCUCAAAAGUAACAAAAAGCCAA ......((((((((....))))))))((((((((((((.((..((.....))..)))))))))))))).........................(((((((((((..((........))...))))))))))).......... (-48.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 120 71 168 123 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 350 140 91 203 157 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 344 119 72 185 146 pint:PI0226|5end_ABC_transporter,_ATP-binding_/_permease_protein_222110..222340_POSITIVE 344 119 72 113 74 pint:PI0225|5end_conserved_hypothetical_protein_222038..222268_POSITIVE 343 130 82 62 6 pint:PI0041|5end_hypothetical_protein_41785..42015_POSITIVE 324 140 94 226 179 pint:PI1231|5end_hypothetical_protein_1153175..1153405_POSITIVE 323 134 94 48 1 pint:PI0817|5end_glycosyl_transferase,_group_1_family_protein_756861..757091_POSITIVE 321 137 94 205 157 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 317 69 21 180 137 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 316 99 56 186 130 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 314 119 71 61 6 pint:PI0485|5end_30S_ribosomal_protein_S4_444450..444680_POSITIVE 314 90 43 60 2 pint:PI0095|5end_hypothetical_protein_91444..91674_POSITIVE 313 124 85 219 165 pint:PI0937|5end_hypothetical_protein_869235..869465_POSITIVE 311 137 91 174 122 pint:PI0732|5end_conserved_hypothetical_protein_663598..663828_POSITIVE 308 140 93 66 15 pint:PI1501|5end_GTP-binding_elongation_factor_family_protein_TypA/BipA_1421424..1421654_POSITIVE 307 139 91 77 8 pint:PI1879|5end_uracil_phosphoribosyltransferase_1820671..1820901_POSITIVE 307 137 91 64 12 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 303 130 83 231 190 pint:PI1644|5end_hypothetical_protein_1560372..1560602_POSITIVE 301 137 94 157 101 pint:PI2032|5end_RNA_polymerase_sigma_factor,_ECF_subfamily_1986544..1986774_POSITIVE 300 138 91 229 171 pint:PI0320|5end_probable_cobalamin_adenosyltransferase_302027..302257_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 440 130 81 93 43 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 343 130 82 69 13 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 330 128 89 147 107 pint:PI0075|3end_uridine_kinase_75390..75540_POSITIVE 314 90 43 73 15 pint:PI0093|3end_riboflavin_biosynthesis_protein_91537..91687_POSITIVE 305 120 71 117 44 pint:PI1713|3end_ABC_transporter,_ATP-binding_protein_1630192..1630342_POSITIVE 295 104 61 145 102 pint:PI0700|3end_UDP-glucose_4-epimerase_638413..638563_POSITIVE 292 68 21 135 91 pint:PI1596|3end_conserved_hypothetical_protein_1525791..1525941_POSITIVE 286 138 91 123 76 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 286 137 94 145 98 pint:PI2031|3end_hypothetical_protein_1986621..1986771_POSITIVE 285 105 61 145 96 pint:PI0470|3end_50S_ribosomal_protein_L14_437813..437963_POSITIVE 284 137 91 115 53 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 284 93 56 145 107 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 282 138 91 134 61 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 282 134 95 147 97 pint:PI0590|3end_ribosomal_large_subunit_pseudouridine_synthase_B_538545..538695_POSITIVE 282 99 68 44 20 pint:PI0579|3end_hypothetical_protein_524209..524359_POSITIVE 276 67 27 131 74 pint:PI1918|3end_uracil-DNA_glycosylase_1862224..1862374_POSITIVE 276 130 85 74 12 pint:PI1608|3end_possible_Na+/H+_anti-porter_1536300..1536450_POSITIVE 276 122 81 134 102 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 275 117 71 142 94 pint:PI1705|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1622706..1622856_POSITIVE 274 39 1 127 75 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE