Origin IGS: taaatccctatcttcagatgttttaaatggaactgttcttctgcttgccgtcctttcctacaatgtcgggacaggcaggttgctcggatacggcaagcatcccaagagccgactgttgcggaagatagagtcgggcgacaggaatttctatcgtgaatttgtctctttctgccgatacaagggcaaagtcctcagaggtctcgtcaaacgacgaaaggtggagtttgccctgttttatgtaccctgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactttacgaactaaaatacgccttttgcatagaagatatttactgaacgtgaagagaaatagaaatagttggagaaaatcatat .........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 atatgattttctccaactatttctatttctcttcacgttcagtaaatatcttctatgcaaaaggcgtattttagttcgtaaagttactcatttataataagaaaggcaaagaaaacggcaagaaaacgcctcttgcgagcataaaaatgtcgcaagaggtgtatgtggtaatcagggtacataaaacagggcaaactccacctttcgtcgtttgacgagacctctgaggactttgcccttgtatcggcagaaagagacaaattcacgatagaaattcctgtcgcccgactctatcttccgcaacagtcggctcttgggatgcttgccgtatccgagcaacctgcctgtcccgacattgtaggaaaggacggcaagcagaagaacagttccatttaaaacatctgaagatagggattta Mask Tandem Repeat Region ================================================ taaatccctatcttcagatgttttaaatggaactgttcttctgcttgccgtcctttcctacaatgtcgggacaggcaggttgctcggatacggcaagcatcccaagagccgactgttgcggaagatagagtcgggcgacaggaatttctatcgtgaatttgtctctttctgccgatacaagggcaaagtcctcagaggtctcgtcaaacgacgaaaggtggagtttgccctgttttatgtaccctgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactttacgaactaaaatacgccttttgcatagaagatatttactgaacgtgaagagaaatagaaatagttggagaaaatcatat Find is-nt database================================================ Query_seq: PI0399:PI0400|PI0399:PI0400:conserved hypothetical protein:conserved hypothetical protein:->->:364151..364568 418 taaatccctatcttcagatgttttaaatggaactgttcttctgcttgccgtcctttcctacaatgtcgggacaggcaggttgctcggatacggcaagcatcccaagagccgactgttgcggaagatagagtcgggcgacaggaatttctatcgtgaatttgtctctttctgccgatacaagggcaaagtcctcagaggtctcgtcaaacgacgaaaggtggagtttgccctgttttatgtaccctgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactttacgaactaaaatacgccttttgcatagaagatatttactgaacgtgaagagaaatagaaatagttggagaaaatcatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0399:PI0400|PI0399:PI0400:conserved hypothetical protein:conserved hypothetical protein:->->:364151..364568 418 taaatccctatcttcagatgttttaaatggaactgttcttctgcttgccgtcctttcctacaatgtcgggacaggcaggttgctcggatacggcaagcatcccaagagccgactgttgcggaagatagagtcgggcgacaggaatttctatcgtgaatttgtctctttctgccgatacaagggcaaagtcctcagaggtctcgtcaaacgacgaaaggtggagtttgccctgttttatgtaccctgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactttacgaactaaaatacgccttttgcatagaagatatttactgaacgtgaagagaaatagaaatagttggagaaaatcatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0399:PI0400|PI0399:PI0400:conserved hypothetical protein:conserved hypothetical protein:->->:364151..364568 418 taaatccctatcttcagatgttttaaatggaactgttcttctgcttgccgtcctttcctacaatgtcgggacaggcaggttgctcggatacggcaagcatcccaagagccgactgttgcggaagatagagtcgggcgacaggaatttctatcgtgaatttgtctctttctgccgatacaagggcaaagtcctcagaggtctcgtcaaacgacgaaaggtggagtttgccctgttttatgtaccctgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactttacgaactaaaatacgccttttgcatagaagatatttactgaacgtgaagagaaatagaaatagttggagaaaatcatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 38 Max: 244 Len: 207 Subject: UniRef90_Q7MUQ4 Cluster: Lysozyme-related protein; n=1; Porphyromonas gingivalis|Rep: Lysozyme-related protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 6.0E-25 bit: 115.0 Len: 165 Query Start:80 Query End:244 Subject Strand: null Subject Start: 1 Subject End: 55 ............................................................................... L L G Y G K H P K S R L L R K I E S G D R N F Y R E F V S F C R Y K G K V L R G L V K R R K V E F A L F Y V P .............................................................................................................................................................................. ............................................................................... M L G Y G K H P K S R L L R K I E S G D R N F Y R E F V S F C R Y K G K V L R G L V K R R K V E F A L F Y V P .............................................................................................................................................................................. Subject: UniRef90_Q56VH1 Cluster: Lys; n=1; Bacteroides fragilis|Rep: Lys - Bacteroides fragilis HSP 1 e-value: 1.0E-18 bit: 94.0 Len: 207 Query Start:38 Query End:244 Subject Strand: null Subject Start: 107 Subject End: 175 ..................................... L L L A V L S Y N V G T G R L L G Y G K H P K S R L L R K I E S G D R N F Y R E F V S F C R Y K G K V L R G L V K R R K V E F A L F Y V P .............................................................................................................................................................................. ..................................... L L L A T L A N N V G P Y R L L G S G K I P K S T L I R K L E A G D R N I Y R E Y I A F C N Y K G K R H A M L L K R R K A E F A L L Y V P .............................................................................................................................................................................. Subject: UniRef90_Q650G3 Cluster: Probable lysozyme; n=1; Bacteroides fragilis|Rep: Probable lysozyme - Bacteroides fragilis HSP 1 e-value: 8.0E-17 bit: 88.2 Len: 207 Query Start:38 Query End:244 Subject Strand: null Subject Start: 106 Subject End: 174 ..................................... L L L A V L S Y N V G T G R L L G Y G K H P K S R L L R K I E S G D R N F Y R E F V S F C R Y K G K V L R G L V K R R K V E F A L F Y V P .............................................................................................................................................................................. ..................................... I L L G T L A Y N V G P A K L L G S K T I P K S T L I K K L E A G D R N I Y R E Y I A F C N Y K G K R H A M L L K R R K A E F A L L Y I P .............................................................................................................................................................................. taaatccctatcttcagatgttttaaatggaactgttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 27 End: 125 .......................... M E L F F C L P S F P T M S G Q A G C S D T A S I P R A D C C G R ..................................................................................................................................................................................................................................................................................................... Protein_Len: 50 Strand: + Start: 4 End: 153 ... M P I F R C F K W N C S S A C R P F L Q C R D R Q V A R I R Q A S Q E P T V A E D R V G R Q E F L S ......................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 41 End: 244 ........................................ M L A V L S Y N V G T G R L L G Y G K H P K S R L L R K I E S G D R N F Y R E F V S F C R Y K G K V L R G L V K R R K V .............................................................................................................................................................................. Protein_Len: 56 Strand: + Start: 157 End: 324 ............................................................................................................................................................ M C L F L P I Q G Q S P Q R S R Q T T K G G V C P V L C T L I T T Y T S C D I F M L A R G V F L P F S L P F L L .............................................................................................. Protein_Len: 60 Strand: + Start: 144 End: 332 ............................................................................................................................................... M S I V N L S L S A D T R A K S S E V S S N D E R W S L P C F M Y P D Y H I H L L R H F Y A R K R R F L A V F F A F L I ...................................................................................... Protein_Len: 41 Strand: - Start: 207 End: 329 .............................................................................................................................................................................................................. V V F P P T Q G T K H V R I V V Y V E Q S M K I S A L P T K K G N E K G K K N Y M ......................................................................................... Protein_Len: 60 Strand: - Start: 26 End: 238 ......................... V I D P C A P Q E S V A L M G L A S Q Q P L Y L R A V P I E I T F K D R E A S V L A F D E S T E D F S S L H L K G Q K M .................................................................................................................................................................................... Protein_Len: 58 Strand: - Start: 3 End: 176 .. I G I K L H K L H F Q E E A Q R G K R C H R S L C T A R I R C A D W S G V T A S S L T P R C S N R D H I Q R K R G M .................................................................................................................................................................................................................................................. taaatccctatcttcagatgttttaaatggaactgttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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================================================ taaatccctatcttcagatgttttaaatggaactgttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.3 Tail_Score: -4.70613 Start: 258 End: 292 Full_Region: CCTGATTACCACATA CACCTCTTGCGACAT TTTT ATGCTCGCAAGAGGCG TTTTCTTGCCGTTTT .................................................................................................................................................................................................................................................................CACCTCTTGCGACATTTTTATGCTCGCAAGAGGCG.............................................................................................................................. TransTerm Strand: - Conf: 89 HP_score: -14.5 Tail_Score: -2.96216 Start: 258 End: 292 Full_Region: aaaacggcaagaaaa cgcctcttgcgagcat aaaa atgtcgcaagaggtg tatgtggtaatcagg .................................................................................................................................................................................................................................................................cgcctcttgcgagcataaaaatgtcgcaagaggtg.............................................................................................................................. TransTerm Strand: + Conf: 86 HP_score: -13.5 Tail_Score: -2.6336 Start: 260 End: 290 Full_Region: TGATTACCACATACA CCTCTTGCGACAT TTTT ATGCTCGCAAGAGG CGTTTTCTTGCCGTT ...................................................................................................................................................................................................................................................................CCTCTTGCGACATTTTTATGCTCGCAAGAGG................................................................................................................................ TransTerm Strand: - Conf: 87 HP_score: -13.5 Tail_Score: -3.03443 Start: 260 End: 290 Full_Region: aacggcaagaaaacg cctcttgcgagcat aaaa atgtcgcaagagg tgtatgtggtaatca ...................................................................................................................................................................................................................................................................cctcttgcgagcataaaaatgtcgcaagagg................................................................................................................................ Find igs database================================================ Query_seq: PI0399:PI0400|PI0399:PI0400:conserved hypothetical protein:conserved hypothetical protein:->->:364151..364568 418 taaatccctatcttcagatgttttaaatggaactgttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 337 Len: 337 Subject: pint_PI0399_PI0400|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[364151,364568]|418 HSP 1 e-value: 2.0E-45 bit: 184.0 Len: 93 Query Start:245 Query End:337 Subject Strand: POSITIVE Subject Start: 245 Subject End: 337 ....................................................................................................................................................................................................................................................tgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaact................................................................................. ....................................................................................................................................................................................................................................................tgattaccacatacacctcttgcgacatttttatgctcgcaagaggcgttttcttgccgttttctttgcctttcttattataaatgagtaact................................................................................. HSP 2 e-value: 4.0E-12 bit: 73.8 Len: 37 Query Start:1 Query End:37 Subject Strand: POSITIVE Subject Start: 1 Subject End: 37 taaatccctatcttcagatgttttaaatggaactgtt............................................................................................................................................................................................................................................................................................................................................................................................. taaatccctatcttcagatgttttaaatggaactgtt............................................................................................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: tfor_TF0926_TF0927|conserved hypothetical protein; possible TraB protein:conserved hypothetical protein; possible ATPase of the AAA superfamily|POSITIVE:POSITIVE|[962998,963595]|598 HSP 1 e-value: 4.0E-12 bit: 73.8 Len: 37 Query Start:1 Query End:37 Subject Strand: POSITIVE Subject Start: 1 Subject End: 37 taaatccctatcttcagatgttttaaatggaactgtt............................................................................................................................................................................................................................................................................................................................................................................................. taaatccctatcttcagatgttttaaatggaactgtt............................................................................................................................................................................................................................................................................................................................................................................................. HSP 2 e-value: 3.0E-7 bit: 58.0 Len: 48 Query Start:255 Query End:302 Subject Strand: POSITIVE Subject Start: 228 Subject End: 276 ..............................................................................................................................................................................................................................................................atacacctcttgcgacatttttatgct-cgcaagaggcgttttcttgcc.................................................................................................................... ..............................................................................................................................................................................................................................................................atacacctcttgcgacatttttatgctccgcaaggggcatgttcttgcc.................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCCCUAUCUUCAGAUGUUUUAAAUGGAACUGUUCUUCUGCUUGCCGUCCUUUCCUACAAUGUCGGGACAGGCAGGUUGCUCGGAUACGGCAAGCAUCCCAAGAGCCGACUGUUGCGGAAGAUAGAGUCGGGCGACAGGAAUUUCUAUCGUGAAUUUGUCUCUUUCUGCCGAUACAAGGGCAAAGUCCUCAGAGGUCUCGUCAAACGACGAAAGGUGGAGUUUGCCCUGUUUUAUGUACCCUGAUUACCACAUACACCUCUUGCGACAUUUUUAUGCUCGCAAGAGGCGUUUUCUUGCC .......((((((((....(((((....))))).((((((.((((((((((....(((..(((((((......))))..)))...))).))))))))))....))))))...........)))))))).....(((((((((......(((((.(((.........)))...)))))..((((((((.(((.(.......(((((....)))))...).))).))))))))...........))))..........((.(((((((((((((....))).)))))))))).))....))))) (-97.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAAGAAAACGCCUCUUGCGAGCAUAAAAAUGUCGCAAGAGGUGUAUGUGGUAAUCAGGGUACAUAAAACAGGGCAAACUCCACCUUUCGUCGUUUGACGAGACCUCUGAGGACUUUGCCCUUGUAUCGGCAGAAAGAGACAAAUUCACGAUAGAAAUUCCUGUCGCCCGACUCUAUCUUCCGCAACAGUCGGCUCUUGGGAUGCUUGCCGUAUCCGAGCAACCUGCCUGUCCCGACAUUGUAGGAAAGGACGGCAAGCAGAAGAACAGUUCCAUUUAAAACAUCUGAAGAUAGGGAUUUA (((......(((((((((((((.(((....))))))))))))))))..........(((((..........((((((((.(((.(.(((((((....))))))).....).))).))))))))(.(((((...(((.........))).))))).)...)))))..)))...((((((((((.((........))...((((((((((((((..(((......(((((.(((....)))..)))))...)))))))))))).........)))))............))))))))))..... (-101.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 86 41 91 47 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 400 293 257 203 166 pint:PI0269|5end_conserved_hypothetical_protein_259835..260065_POSITIVE 382 119 73 210 152 pint:PI1437|5end_hypothetical_protein_1356088..1356318_POSITIVE 382 119 73 83 25 pint:PI1436|5end_hypothetical_protein_1355961..1356191_POSITIVE 378 137 91 202 143 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 374 119 71 122 82 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 371 138 91 220 164 pint:PI0857|5end_hypothetical_protein_790697..790927_POSITIVE 368 139 92 194 140 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 366 88 41 74 18 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 366 88 41 230 174 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 362 123 81 86 43 pint:PI1271|5end_transcriptional_regulator,__AraC/XylS_family_1190755..1190985_POSITIVE 357 140 92 90 54 pint:PI0536|5end_hypothetical_protein_492163..492393_POSITIVE 354 135 91 86 34 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 354 86 42 198 149 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 352 90 41 177 131 pint:PI0428|5end_hypothetical_protein_393080..393310_POSITIVE 352 119 73 83 25 pint:PI0037|5end_hypothetical_protein_39354..39584_POSITIVE 351 88 42 120 61 pint:PI0945|5end_sodium:solute_symporter_family_protein_876249..876479_POSITIVE 350 110 63 52 1 pint:PI1933|5end_hypothetical_protein_1879925..1880155_POSITIVE 346 110 67 191 137 pint:PI1644|5end_hypothetical_protein_1560372..1560602_POSITIVE 346 99 52 63 6 pint:PI0877|5end_hypothetical_protein_811378..811608_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 99 57 81 33 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 400 293 257 78 41 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 382 86 45 103 60 pint:PI0262|3end_conserved_hypothetical_protein_255094..255244_POSITIVE 372 144 102 104 54 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 366 99 52 102 67 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 366 86 41 145 99 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE 364 119 74 142 100 pint:PI0258|3end_conjugative_transposon_protein,_TraG_252285..252435_POSITIVE 362 123 81 80 37 pint:PI1270|3end_probable_dipeptidyl_peptidase_1190829..1190979_POSITIVE 354 138 91 60 14 pint:PI2079|3end_conserved_hypothetical_protein;_possible_ATPase_2037961..2038111_POSITIVE 352 90 41 105 59 pint:PI0427|3end_conserved_hypothetical_protein_393088..393238_POSITIVE 346 90 41 61 3 pint:PI1069|3end_hypothetical_protein_988458..988608_POSITIVE 346 110 67 78 31 pint:PI0130|3end_hypothetical_protein_122267..122417_POSITIVE 344 136 91 77 42 pint:PI0157|3end_hypothetical_protein_151387..151537_POSITIVE 341 120 73 151 105 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 340 88 42 56 2 pint:PI1766|3end_sugar_transporter,_possible_glucose/galactose_transporter_1694350..1694500_POSITIVE 339 120 73 62 11 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 338 141 101 58 9 pint:PI0274|3end_conserved_hypothetical_protein_263187..263337_POSITIVE 332 88 41 98 51 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 332 234 191 53 3 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 330 110 66 50 14 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE