Origin IGS: ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt .........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 aattttatattgttattgtttgttgtttcaaatctttccagtttccatcggcaaagataatggcgtgcgtacacctctcaaagccatggggaacagtagggaagtatcgggaacaatcgggaaaagagcaatccgtttcatcagttcacatttgcattttcctgtcccgtcttttttctttcattgcaaaattaatatcgggcatttcttattccatcacttttcattcaagtggcagcttgtggcgtcatagtggaataggttggcacagtaatccgatataaaatatgctccaatcaatagtttgtagatagttggagcaaaagactgcatctgaaagcaaacaacgacaatccgtatttctgttaacctttctttcctgtcatccgttttttgcttaatgagacgataa Mask Tandem Repeat Region ================================================ ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt Find is-nt database================================================ Query_seq: PI0378:PI0379|PI0378:PI0379:conserved hypothetical protein; possible helicase:conserved hypothetical protein:->->:349600..350011 412 ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0378:PI0379|PI0378:PI0379:conserved hypothetical protein; possible helicase:conserved hypothetical protein:->->:349600..350011 412 ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0378:PI0379|PI0378:PI0379:conserved hypothetical protein; possible helicase:conserved hypothetical protein:->->:349600..350011 412 ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 70 End: 162 ..................................................................... M L S D A V F C S N Y L Q T I D W S I F Y I G L L C Q P I P L .......................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 11 End: 193 .......... M K Q K T D D R K E R L T E I R I V V V C F Q M Q S F A P T I Y K L L I G A Y F I S D Y C A N L F H Y D A T S C H L N E ........................................................................................................................................................................................................................... Protein_Len: 38 Strand: + Start: 269 End: 382 ............................................................................................................................................................................................................................................................................ M M K R I A L F P I V P D T S L L F P M A L R G V R T P L S L P M E T G K I .............................. Protein_Len: 60 Strand: - Start: 163 End: 411 .................................................................................................................................................................. F F F S P V P F H L H S S I F R I A R K G I T G S V E R S N G M A K L P T R V G N D K G I S V P F I Q F L L C Y C Y L M . Protein_Len: 60 Strand: - Start: 132 End: 404 ................................................................................................................................... A I F S F L R S L F I C I H V S S V S Q E K G S Q E R Y K G V T G W P K S L H V C A M I K A S P F Q F S K F C C V I V M ........ ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt 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================================================ ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0378:PI0379|PI0378:PI0379:conserved hypothetical protein; possible helicase:conserved hypothetical protein:->->:349600..350011 412 ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 412 Len: 412 Subject: pint_PI0378_PI0379|conserved hypothetical protein; possible helicase:conserved hypothetical protein|POSITIVE:POSITIVE|[349600,350011]|412 HSP 1 e-value: 0.0 bit: 817.0 Len: 412 Query Start:1 Query End:412 Subject Strand: POSITIVE Subject Start: 1 Subject End: 412 ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt ttatcgtctcattaagcaaaaaacggatgacaggaaagaaaggttaacagaaatacggattgtcgttgtttgctttcagatgcagtcttttgctccaactatctacaaactattgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatattaattttgcaatgaaagaaaaaagacgggacaggaaaatgcaaatgtgaactgatgaaacggattgctcttttcccgattgttcccgatacttccctactgttccccatggctttgagaggtgtacgcacgccattatctttgccgatggaaactggaaagatttgaaacaacaaacaataacaatataaaatt Inter-species Hit: Count: 1 Min: 114 Max: 220 Len: 107 Subject: tfor_TF1634_TF1637|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1747139,1747245]|107 HSP 1 e-value: 1.0E-46 bit: 188.0 Len: 107 Query Start:114 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 .................................................................................................................tgattggagcatattttatatcggattactgtgccaacctattccactatgacgccacaagctgccacttgaatgaaaagtgatggaataagaaatgcccgatatta................................................................................................................................................................................................ .................................................................................................................tgattggagcatattttatctcggattactgtgccaacctattccactacgacgccacaagctgccacttgaatggaaagtgatggaataagaaatgcccgatatta................................................................................................................................................................................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUGGAGCAUAUUUUAUAUCGGAUUACUGUGCCAACCUAUUCCACUAUGACGCCACAAGCUGCCACUUGAAUGAAAAGUGAUGGAAUAAGAAAUGCCCGAUAUUA ..(((((.((((..........((((....)).))..(.(((((((.......((.....))...(((((.......))))).))))))).)..))))))))).... (-21.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUCGGGCAUUUCUUAUUCCAUCACUUUUCAUUCAAGUGGCAGCUUGUGGCGUCAUAGUGGAAUAGGUUGGCACAGUAAUCCGAUAUAAAAUAUGCUCCAAUCA ..(((((((((....(((((((((((((((.......)))))...((.....))......))))))))))...))........)))))))................. (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 792 97 53 202 158 pint:PI0742|5end_hypothetical_protein_672394..672624_POSITIVE 462 69 21 135 84 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 355 100 53 221 156 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 355 100 53 118 53 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 326 66 23 123 78 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 323 70 34 174 129 pint:PI1008|5end_cytochrome_c_nitrite_reductase,_small_subunit_928784..929014_POSITIVE 318 67 23 63 11 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 315 75 31 160 100 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 309 98 56 171 133 pint:PI1442|5end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1363949..1364179_POSITIVE 306 69 21 159 107 pint:PI0528|5end_hypothetical_protein_482791..483021_POSITIVE 301 68 21 57 10 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 276 71 45 36 9 pint:PI1551|5end_HesA/MoeB/ThiF_family_protein_1467787..1468017_POSITIVE 275 68 22 61 4 pint:PI0906|5end_hypothetical_protein_835653..835883_POSITIVE 266 99 54 110 69 pint:PI1283|5end_ATP_synthase,_alpha_subunit_1198204..1198434_POSITIVE 266 65 21 121 61 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 266 68 22 204 151 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 263 67 21 79 32 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 260 82 44 70 34 pint:PI1741|5end_lipid-A-disaccharide_synthase_1662754..1662984_POSITIVE 260 67 21 105 57 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 259 39 1 85 50 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 792 97 53 93 49 pint:PI0740|3end_hypothetical_protein_672365..672515_POSITIVE 462 69 21 125 74 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 355 100 53 96 31 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE 347 75 31 97 38 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 326 66 23 126 81 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 323 90 44 68 19 pint:PI1943|3end_hypothetical_protein_1902206..1902356_POSITIVE 316 67 28 51 3 pint:PI1067|3end_thymidylate_synthase_984811..984961_POSITIVE 278 68 39 33 7 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 266 99 54 95 54 pint:PI1282|3end_ATP_synthase,_gamma_subunit_(F0F1-ATPase,_gamma_subunit)_1198269..1198419_POSITIVE 266 68 22 147 94 pint:PI0535|3end_hypothetical_protein_489779..489929_POSITIVE 263 67 21 70 23 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 260 45 4 148 107 pint:PI1874|3end_hypothetical_protein_1818924..1819074_POSITIVE 260 70 22 129 91 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 257 98 52 88 51 pint:PI0783|3end_hypothetical_protein_723397..723547_POSITIVE 249 70 23 76 23 pint:PI2066|3end_hypothetical_protein_2027726..2027876_POSITIVE 244 70 23 120 84 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE 242 66 23 62 25 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 238 75 31 142 78 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 237 65 22 100 53 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 237 63 21 133 98 pint:PI0492|3end_hypothetical_protein_452458..452608_POSITIVE