Origin IGS: tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaatgtaccacgatgattgtgggacaggaaatgacaagcgacggttctatgatggtggcacgttccgaagactgggacgccatggaagcaaagaactacgaaatttacgaagataccacagaaggcgcaaccgaatatgttgcgaaagacagtcctttccgctgcgaactccccaaggaggct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcctccttggggagttcgcagcggaaaggactgtctttcgcaacatattcggttgcgccttctgtggtatcttcgtaaatttcgtagttctttgcttccatggcgtcccagtcttcggaacgtgccaccatcatagaaccgtcgcttgtcatttcctgtcccacaatcatcgtggtacattctgatggtaaattgcttaccaaaactttattttctttcataaatatatttgttttaagatataacttgtaagggcaaatgtaggcaaaataattggattgaagaaaggcttttgctgatttattgttattttacctaattgtaggtaatcgaaattatatcggaagtctttactaaacaaacttaaaaataggagctaaattcaataatttacataattaactaagaaaatcgggcagtatctaaagaattctaattaaatttgcagacaaa Mask Tandem Repeat Region ================================================ tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaatgtaccacgatgattgtgggacaggaaatgacaagcgacggttctatgatggtggcacgttccgaagactgggacgccatggaagcaaagaactacgaaatttacgaagataccacagaaggcgcaaccgaatatgttgcgaaagacagtcctttccgctgcgaactccccaaggaggct Find is-nt database================================================ Query_seq: PI0127:PI0128|PI0127:PI0128:conserved hypothetical protein:dipeptidase, pathogenicity island-encoded protein D:->->:120218..120671 454 tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaatgtaccacgatgattgtgggacaggaaatgacaagcgacggttctatgatggtggcacgttccgaagactgggacgccatggaagcaaagaactacgaaatttacgaagataccacagaaggcgcaaccgaatatgttgcgaaagacagtcctttccgctgcgaactccccaaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0127:PI0128|PI0127:PI0128:conserved hypothetical protein:dipeptidase, pathogenicity island-encoded protein D:->->:120218..120671 454 tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaatgtaccacgatgattgtgggacaggaaatgacaagcgacggttctatgatggtggcacgttccgaagactgggacgccatggaagcaaagaactacgaaatttacgaagataccacagaaggcgcaaccgaatatgttgcgaaagacagtcctttccgctgcgaactccccaaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0127:PI0128|PI0127:PI0128:conserved hypothetical protein:dipeptidase, pathogenicity island-encoded protein D:->->:120218..120671 454 tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaatgtaccacgatgattgtgggacaggaaatgacaagcgacggttctatgatggtggcacgttccgaagactgggacgccatggaagcaaagaactacgaaatttacgaagataccacagaaggcgcaaccgaatatgttgcgaaagacagtcctttccgctgcgaactccccaaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 275 Max: 454 Len: 180 Subject: UniRef90_A2F3K0 Cluster: Clan PB, family C69, PipD-like cysteine peptidase; n=1; Trichomonas vaginalis G3|Rep: Clan PB, family C69, PipD-like cysteine peptidase - Trichomonas vaginalis G3 HSP 1 e-value: 4.0E-10 bit: 65.9 Len: 171 Query Start:275 Query End:445 Subject Strand: null Subject Start: 6 Subject End: 62 .................................................................................................................................................................................................................................................................................. C T T M I V G Q E M T S D G S M M V A R S E D W D A M E A K N Y E I Y E D T T E G A T E Y V A K D S P F R C E L P ......... .................................................................................................................................................................................................................................................................................. C T T I I V G S K M S A D G S M M Y T R S D D S S S Y K A T K L M Y Y P E T D H G P E E F V A I D S P F R C K L P ......... Subject: UniRef90_Q047P9 Cluster: Dipeptidase; n=1; Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365|Rep: Dipeptidase - Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC BAA-365) HSP 1 e-value: 3.0E-7 bit: 56.6 Len: 180 Query Start:275 Query End:454 Subject Strand: null Subject Start: 25 Subject End: 83 .................................................................................................................................................................................................................................................................................. C T T M I V G Q E M T S D G S M M V A R S E D W D A M E A K N Y E I Y E D T T E G A T E Y V A K D S P F R C E L P K E A .................................................................................................................................................................................................................................................................................. C T T V V V G K K A T T D G S T L V A R N E D V G A W - S K H F Y V H Q A T S N G P T T Y V S E D N G L K T S L P K T A Subject: UniRef90_Q71J38 Cluster: Cytosol non-specific dipeptidase , truncation; n=1; Lactobacillus delbrueckii subsp. lactis|Rep: Cytosol non-specific dipeptidase , truncation - Lactobacillus delbrueckii subsp. lactis HSP 1 e-value: 4.0E-6 bit: 52.8 Len: 180 Query Start:275 Query End:454 Subject Strand: null Subject Start: 25 Subject End: 83 .................................................................................................................................................................................................................................................................................. C T T M I V G Q E M T S D G S M M V A R S E D W D A M E A K N Y E I Y E D T T E G A T E Y V A K D S P F R C E L P K E A .................................................................................................................................................................................................................................................................................. C T T V V D G K K A T T D G S T L V A R N E X V G A W X - K H F Y V H Q A T S N G P T T Y V S E D N V F K T S L P K T A tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 93 End: 233 ............................................................................................ M F S K D F R Y N F D Y L Q L G K I T I N Q Q K P F F N P I I L P T F A L T S Y I L K Q I Y L ............................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 268 End: 453 ........................................................................................................................................................................................................................................................................... M R M Y H D D C G T G N D K R R F Y D G G T F R R L G R H G S K E L R N L R R Y H R R R N R I C C E R Q S F P L R T P Q . Protein_Len: 60 Strand: + Start: 194 End: 454 ................................................................................................................................................................................................. M C P Y K L Y L K T N I F M K E N K V L V S N L P S E C T T M I V G Q E M T S D G S M M V A R S E D W D A M E A K N Y E Protein_Len: 46 Strand: - Start: 272 End: 409 ............................................................................................................................................................................................................................................................................... F T G R H N H S L F H C A V T R H H H C T G F V P V G H F C L V V F N V F I G C F A C G F M ............................................. Protein_Len: 50 Strand: - Start: 205 End: 354 ............................................................................................................................................................................................................ L N Y R L V F I N I F S F L T K T L L K G D S H V V I I T P C S I V L S P E I I T A R E S S Q S A M .................................................................................................... tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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================================================ tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0127:PI0128|PI0127:PI0128:conserved hypothetical protein:dipeptidase, pathogenicity island-encoded protein D:->->:120218..120671 454 tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 274 Len: 274 Subject: pint_PI0127_PI0128|conserved hypothetical protein:dipeptidase, pathogenicity island-encoded protein D|POSITIVE:POSITIVE|[120218,120671]|454 HSP 1 e-value: 1.0E-153 bit: 543.0 Len: 274 Query Start:1 Query End:274 Subject Strand: POSITIVE Subject Start: 1 Subject End: 274 tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaa.................................................................................................................................................................................... tttgtctgcaaatttaattagaattctttagatactgcccgattttcttagttaattatgtaaattattgaatttagctcctatttttaagtttgtttagtaaagacttccgatataatttcgattacctacaattaggtaaaataacaataaatcagcaaaagcctttcttcaatccaattattttgcctacatttgcccttacaagttatatcttaaaacaaatatatttatgaaagaaaataaagttttggtaagcaatttaccatcagaa.................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUCUGCAAAUUUAAUUAGAAUUCUUUAGAUACUGCCCGAUUUUCUUAGUUAAUUAUGUAAAUUAUUGAAUUUAGCUCCUAUUUUUAAGUUUGUUUAGUAAAGACUUCCGAUAUAAUUUCGAUUACCUACAAUUAGGUAAAAUAACAAUAAAUCAGCAAAAGCCUUUCUUCAAUCCAAUUAUUUUGCCUACAUUUGCCCUUACAAGUUAUAUCUUAAAACAAAUAUAUUUAUGAAAGAAAAUAAAGUUUUGGUAAGCAAUUUACCAUCAGAA ..((((((..(((((.....)))))...))))))(((....((((((((...(((.(((((...(((((((((..((((..........)))).)))))))))........((((((((((...(((((((....)))))))...............((((((....................))))))................)))))))))).........))))).)))...)))))))).......(((((((...))))))).))).. (-40.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGAUGGUAAAUUGCUUACCAAAACUUUAUUUUCUUUCAUAAAUAUAUUUGUUUUAAGAUAUAACUUGUAAGGGCAAAUGUAGGCAAAAUAAUUGGAUUGAAGAAAGGCUUUUGCUGAUUUAUUGUUAUUUUACCUAAUUGUAGGUAAUCGAAAUUAUAUCGGAAGUCUUUACUAAACAAACUUAAAAAUAGGAGCUAAAUUCAAUAAUUUACAUAAUUAACUAAGAAAAUCGGGCAGUAUCUAAAGAAUUCUAAUUAAAUUUGCAGACAAA .((((.((((((.....))))))...((..((((((((...(((.((((((((((((...(((.....))).))))))))))))....((((.((((((((..((((((((((...(((((.((...((...(((((((....)))))))...))..)).))))))))))))).)).......((((....)))).....)))))))).))))......)))...))))))))..)).............................)))).... (-48.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 199 161 208 175 pint:PI0833|5end_conserved_hypothetical_protein_770059..770289_POSITIVE 248 204 163 65 26 pint:PI0804|5end_conserved_hypothetical_protein;_possible_membrane_protein_741934..742164_POSITIVE 246 200 155 197 143 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 241 125 102 163 136 pint:PI0146|5end_transcription_elongation_factor_140338..140568_POSITIVE 237 208 164 212 161 pint:PI2026|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1979497..1979727_POSITIVE 234 200 152 163 108 pint:PI1002|5end_metal_dependent_hydrolase_923842..924072_POSITIVE 232 190 152 68 33 pint:PI0403|5end_probable_integrase_370089..370319_POSITIVE 228 200 156 99 57 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 227 199 155 67 24 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 225 42 7 46 5 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 224 200 158 46 4 pint:PI0817|5end_glycosyl_transferase,_group_1_family_protein_756861..757091_POSITIVE 222 195 163 179 146 pint:PI1620|5end__two-component_system_sensor_protein_1543956..1544186_POSITIVE 221 43 1 190 145 pint:PI0399|5end_conserved_hypothetical_protein_363585..363815_POSITIVE 219 215 176 214 165 pint:PI1615|5end_hypothetical_protein_1541462..1541692_POSITIVE 217 208 166 32 1 pint:PI0380|5end_conserved_hypothetical_protein_350162..350392_POSITIVE 216 240 192 218 173 pint:PI1350|5end_conserved_hypothetical_protein_1265817..1266047_POSITIVE 216 209 162 190 128 pint:PI1211|5end_ubiquinone/menaquinone_biosynthesis_methyltransferase_1129926..1130156_POSITIVE 214 209 184 148 112 pint:PI0726|5end_hypothetical_protein_659042..659272_POSITIVE 213 209 163 199 147 pint:PI0809|5end_hypothetical_protein_746630..746860_POSITIVE 212 206 163 208 149 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 208 164 87 36 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 221 200 157 146 110 pint:PI1548|3end_conserved_hypothetical_protein_1466886..1467036_POSITIVE 221 43 1 66 21 pint:PI0398|3end_hypothetical_protein_363541..363691_POSITIVE 219 215 176 80 31 pint:PI1614|3end_hypothetical_protein_1541408..1541558_POSITIVE 216 209 162 143 81 pint:PI1210|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_(SAICAR_synthetase)_1129959..1130109_POSITIVE 212 206 163 73 14 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 212 206 163 103 44 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 212 206 163 73 14 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 212 180 157 47 25 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE 210 168 121 55 1 pint:PI0772|3end_conserved_hypothetical_protein_708481..708631_POSITIVE 210 190 148 80 39 pint:PI0536|3end_hypothetical_protein_492623..492773_POSITIVE 210 202 162 130 90 pint:PI0284|3end_flavoprotein_A_270157..270307_POSITIVE 209 114 72 63 22 pint:PI1451|3end_outer_membrane_receptor_proteins,_tonB_dependent_(possibly_iron_transport_related)_1375365..1375515_POSITIVE 207 137 91 74 30 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 207 200 155 96 36 pint:PI0139|3end_pyridoxine_biosynthesis_protein_132724..132874_POSITIVE 205 200 157 151 104 pint:PI1060|3end_conserved_hypothetical_protein_979729..979879_POSITIVE 204 201 164 42 6 pint:PI1944|3end_hypothetical_protein_1901990..1902140_POSITIVE 201 191 156 44 7 pint:PI0024|3end_hypothetical_protein_28559..28709_POSITIVE 196 216 175 121 73 pint:PI0559|3end_conserved_hypothetical_protein_508740..508890_POSITIVE 195 112 75 109 65 pint:PI1481|3end_hypothetical_protein_1404232..1404382_POSITIVE