Origin IGS: atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcgcccgctcttattttctttacattgtagttcatcaaatgccttcctaaatgtttgtaagcaaaggcttttattcctgacacttcctgatgatgatgtttcagcaattcatccggagaatcccatactccaaaatcctgagtaattccattttcatatgt .........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 acatatgaaaatggaattactcaggattttggagtatgggattctccggatgaattgctgaaacatcatcatcaggaagtgtcaggaataaaagcctttgcttacaaacatttaggaaggcatttgatgaactacaatgtaaagaaaataagagcgggcgctactctctgacgtttgatttgaattgataaatagaatggaatatgatataattttattcaaatcaatttgaataaaattaatttgaatcaaactattaatgaggatatacat Mask Tandem Repeat Region ================================================ atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcgcccgctcttattttctttacattgtagttcatcaaatgccttcctaaatgtttgtaagcaaaggcttttattcctgacacttcctgatgatgatgtttcagcaattcatccggagaatcccatactccaaaatcctgagtaattccattttcatatgt Find is-nt database================================================ Query_seq: TDE0498:TDE0499|TDE0498:TDE0499:hypothetical protein:hypothetical protein:<-<-:552334..552606 273 atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcgcccgctcttattttctttacattgtagttcatcaaatgccttcctaaatgtttgtaagcaaaggcttttattcctgacacttcctgatgatgatgtttcagcaattcatccggagaatcccatactccaaaatcctgagtaattccattttcatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0498:TDE0499|TDE0498:TDE0499:hypothetical protein:hypothetical protein:<-<-:552334..552606 273 atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcgcccgctcttattttctttacattgtagttcatcaaatgccttcctaaatgtttgtaagcaaaggcttttattcctgacacttcctgatgatgatgtttcagcaattcatccggagaatcccatactccaaaatcctgagtaattccattttcatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0498:TDE0499|TDE0498:TDE0499:hypothetical protein:hypothetical protein:<-<-:552334..552606 273 atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcgcccgctcttattttctttacattgtagttcatcaaatgccttcctaaatgtttgtaagcaaaggcttttattcctgacacttcctgatgatgatgtttcagcaattcatccggagaatcccatactccaaaatcctgagtaattccattttcatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 6 Min: 115 Max: 267 Len: 153 Subject: UniRef90_Q24Z43 Cluster: Hypothetical protein; n=2; Desulfitobacterium hafniense|Rep: Hypothetical protein - Desulfitobacterium hafniense (strain Y51) HSP 1 e-value: 3.0E-9 bit: 63.2 Len: 150 Query Start:118 Query End:267 Subject Strand: null Subject Start: 193 Subject End: 242 ..................................................................................................................... E N G I T Q D F G V W D S P D E L L K H H H Q E V S G I K A F A Y K H L G R H L M N Y N V K K I R A ...... ..................................................................................................................... K E G I N Q D F G V F D S P D E F L A V H Q Q Q L S P L R K W A Y Q N V G R K L M N R N V E K I R S ...... Subject: UniRef90_Q3CB60 Cluster: Hypothetical protein; n=1; Alkaliphilus metalliredigenes QYMF|Rep: Hypothetical protein - Alkaliphilus metalliredigenes QYMF HSP 1 e-value: 6.0E-7 bit: 55.5 Len: 147 Query Start:121 Query End:267 Subject Strand: null Subject Start: 182 Subject End: 230 ........................................................................................................................ E N G I T Q D F G V W D S P D E L L K H H H Q E V S G I K A F A Y K H L G R H L M N Y N V K K I R ...... ........................................................................................................................ K E G I N D D F G V F N S P D E F F E K Y Q Q Q L S P L K K W I Y R N I G R K L M N R N V E R I R ...... Subject: UniRef90_Q1FM42 Cluster: Transglutaminase-like; n=1; Clostridium phytofermentans ISDg|Rep: Transglutaminase-like - Clostridium phytofermentans ISDg HSP 1 e-value: 1.0E-6 bit: 54.3 Len: 147 Query Start:121 Query End:267 Subject Strand: null Subject Start: 182 Subject End: 230 ........................................................................................................................ E N G I T Q D F G V W D S P D E L L K H H H Q E V S G I K A F A Y K H L G R H L M N Y N V K K I R ...... ........................................................................................................................ K E S I N E D Y G T F D N P D A L F S N Y P Q K L S L L K R F L Y R H F G R H I M N R R V D K I R ...... Subject: UniRef90_A4ET33 Cluster: Hypothetical protein; n=1; Roseobacter sp. SK209-2-6|Rep: Hypothetical protein - Roseobacter sp. SK209-2-6 HSP 1 e-value: 2.0E-6 bit: 53.9 Len: 147 Query Start:115 Query End:261 Subject Strand: null Subject Start: 186 Subject End: 234 .................................................................................................................. G I T Q D F G V W D S P D E L L K H H H Q E V S G I K A F A Y K H L G R H L M N Y N V K K I R A G ............ .................................................................................................................. G I A E D L G L W D T P D D F Y A H H Q Q D F G P V K T L L Y R Y A L R H W M N G R V R N I R R G ............ Subject: UniRef90_A2SGC7 Cluster: Hypothetical protein; n=1; Methylibium petroleiphilum PM1|Rep: Hypothetical protein - Methylibium petroleiphilum (strain PM1) HSP 1 e-value: 3.0E-6 bit: 53.1 Len: 150 Query Start:118 Query End:267 Subject Strand: null Subject Start: 185 Subject End: 234 ..................................................................................................................... E N G I T Q D F G V W D S P D E L L K H H H Q E V S G I K A F A Y K H L G R H L M N Y N V K K I R A ...... ..................................................................................................................... K E G I A D D F G V F D S P D A F Y A R H G S N L S G V K R W L Y E R V I R H R M N R N V A R V R A ...... Subject: UniRef90_A1W5M8 Cluster: Hypothetical protein; n=1; Acidovorax sp. JS42|Rep: Hypothetical protein - Acidovorax sp. (strain JS42) HSP 1 e-value: 5.0E-6 bit: 52.4 Len: 150 Query Start:118 Query End:267 Subject Strand: null Subject Start: 184 Subject End: 233 ..................................................................................................................... E N G I T Q D F G V W D S P D E L L K H H H Q E V S G I K A F A Y K H L G R H L M N Y N V K K I R A ...... ..................................................................................................................... K D G I A D D F G V F D S P D E F Y A R H G S N L S G L K R W L F T Q V I R H R M N A Q V R R I R A ...... atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatatgt Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 1 End: 159 M Y I L I N S L I Q I N F I Q I D L N K I I S Y S I L F I N S N Q T S E S S A R S Y F L Y I V V H Q M P S .................................................................................................................. Protein_Len: 51 Strand: - Start: 106 End: 258 ......................................................................................................... L T A G A R I K K V N Y N M L H R G L H K Y A F A K I G S V E Q H H H K L L E D P S D W V G F D Q T M ............... Protein_Len: 44 Strand: - Start: 89 End: 220 ........................................................................................ N L D F T L S Y R G S K N E K C Q L E D F A K R F T Q L C L S K N R V S G S S S T E A M ..................................................... atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatatgt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 90 Start: 61 End: 90 ............................................................ATTGATAAATAGAATGGAATATGATATAAT....................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 66 End: 95 .................................................................TTTGAATTGATAAATAGAATGGAATATGAT.................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatatgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -8.5 Tail_Score: -3.65529 Start: 32 End: 65 Full_Region: agaatggaatatgat ataattttattcaaa tcaa tttgaataaaattaa tttgaatcaaactat ...............................ataattttattcaaatcaatttgaataaaattaa................................................................................................................................................................................................................ TransTerm Strand: + Conf: 90 HP_score: -12.0 Tail_Score: -2.93236 Start: 33 End: 64 Full_Region: TAGTTTGATTCAAAT TAATTTTATTCAAA TTGA TTTGAATAAAATTA TATCATATTCCATTC ................................TAATTTTATTCAAATTGATTTGAATAAAATTA................................................................................................................................................................................................................. TransTerm Strand: - Conf: 89 HP_score: -12.0 Tail_Score: -2.78996 Start: 33 End: 64 Full_Region: gaatggaatatgata taattttattcaaa tcaa tttgaataaaatta atttgaatcaaacta ................................taattttattcaaatcaatttgaataaaatta................................................................................................................................................................................................................. TransTerm Strand: + Conf: 81 HP_score: -9.3 Tail_Score: -3.60348 Start: 36 End: 61 Full_Region: TTTGATTCAAATTAA TTTTATTCAAA TTGA TTTGAATAAAA TTATATCATATTCCA ...................................TTTTATTCAAATTGATTTGAATAAAA.................................................................................................................................................................................................................... TransTerm Strand: - Conf: 81 HP_score: -9.3 Tail_Score: -3.54408 Start: 36 End: 61 Full_Region: tggaatatgatataa ttttattcaaa tcaa tttgaataaaa ttaatttgaatcaaa ...................................ttttattcaaatcaatttgaataaaa.................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TDE0498:TDE0499|TDE0498:TDE0499:hypothetical protein:hypothetical protein:<-<-:552334..552606 273 atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatatgt Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_002967_TDE0498_TDE0499|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[552334,552606]|273 HSP 1 e-value: 3.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagc............................................................................................................................................................... atgtatatcctcattaatagtttgattcaaattaattttattcaaattgatttgaataaaattatatcatattccattctatttatcaattcaaatcaaacgtcagagagtagc............................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUAUAUCCUCAUUAAUAGUUUGAUUCAAAUUAAUUUUAUUCAAAUUGAUUUGAAUAAAAUUAUAUCAUAUUCCAUUCUAUUUAUCAAUUCAAAUCAAACGUCAGAGAGUAGC .....((..(((.......((((((((..(((((((((((((((((....))))))))))))))........................)))..))))))))....)))..)).. (-18.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUACUCUCUGACGUUUGAUUUGAAUUGAUAAAUAGAAUGGAAUAUGAUAUAAUUUUAUUCAAAUCAAUUUGAAUAAAAUUAAUUUGAAUCAAACUAUUAAUGAGGAUAUACAU ....(((..(((.((((((((..(((((((.....(((((((((........)))))))))...((.....)).....)))))))..))))))))..)))..)))......... (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 723 110 61 201 152 NC_002967:TDE0498|5end_hypothetical_protein_552243..552473_NEGATIVE 199 90 48 135 80 NC_002967:TDE0290|5end_hypothetical_protein_320794..321024_NEGATIVE 198 49 1 171 125 NC_002967:TDE0583|5end_hypothetical_protein_622199..622429_NEGATIVE 183 44 4 90 40 NC_002967:TDE1302|5end_hemerythrin_family_protein_1339644..1339874_NEGATIVE 176 108 61 147 95 NC_002967:TDE1416|5end_ABC_transporter,_permease_protein_1459796..1460026_POSITIVE 173 110 61 152 97 NC_002967:TDE2545|5end_hypothetical_protein_2571814..2572044_NEGATIVE 168 89 46 117 74 NC_002967:TDE2013|5end_hypothetical_protein_2034706..2034936_NEGATIVE 167 107 72 101 58 NC_002967:TDE2047|5end_hypothetical_protein_2076351..2076581_NEGATIVE 160 87 42 108 66 NC_002967:TDE0077|5end_glycine_reductase_complex_proprotein_GrdE1_88732..88962_NEGATIVE 157 110 74 37 6 NC_002967:TDE2378|5end_ABC_transporter,_ATP-binding_protein,_putative_2407719..2407949_POSITIVE 154 110 79 224 187 NC_002967:TDE1033|5end_polyA_polymerase_family_protein_1061069..1061299_POSITIVE 151 93 67 217 184 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 150 110 64 57 13 NC_002967:TDE1876|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_1897679..1897909_NEGATIVE 149 90 45 153 113 NC_002967:TDE2459|5end_hypothetical_protein_2485934..2486164_NEGATIVE 147 110 69 49 9 NC_002967:TDE0158|5end_hypothetical_protein_185948..186178_NEGATIVE 146 106 67 94 60 NC_002967:TDE1228|5end_pentapeptide_repeat_family_protein_1261889..1262119_POSITIVE 144 110 63 129 74 NC_002967:TDE0769|5end_ribosomal_protein_L23_807634..807864_POSITIVE 142 104 61 187 140 NC_002967:TDE1306|5end_hypothetical_protein_1340874..1341104_NEGATIVE 141 108 62 134 84 NC_002967:TDE2336|5end_sodium/dicarboxylate_symporter_family_protein_2373196..2373426_NEGATIVE 141 86 51 189 150 NC_002967:TDE1571|5end_hypothetical_protein_1620668..1620898_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 199 90 48 135 80 NC_002967:TDE0291|3end_hypothetical_protein_320794..320944_NEGATIVE 183 44 4 85 35 NC_002967:TDE1303|3end_hypothetical_protein_1339649..1339799_NEGATIVE 176 108 61 142 90 NC_002967:TDE1415|3end_nucleotidyl_transferase/aminotransferase,_class_V_1459871..1460021_POSITIVE 173 110 61 89 34 NC_002967:TDE2546|3end_hypothetical_protein_2571877..2572027_NEGATIVE 171 36 4 50 17 NC_002967:TDE2750|3end_GTP-binding_protein_HflX,_truncation_2807288..2807438_POSITIVE 160 87 42 95 53 NC_002967:TDE0078|3end_glycine_reductase_complex_selenoprotein_GrdB1_88745..88895_NEGATIVE 155 45 8 72 31 NC_002967:TDE2588|3end_integrase_domain_protein_2624778..2624928_POSITIVE 151 104 76 120 83 NC_002967:TDE1306|3end_hypothetical_protein_1340452..1340602_NEGATIVE 150 110 64 76 32 NC_002967:TDE1877|3end_conserved_hypothetical_protein_TIGR00046_1897660..1897810_NEGATIVE 148 107 80 136 108 NC_002967:TDE2287|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2324309..2324459_NEGATIVE 146 105 61 121 78 NC_002967:TDE1722|3end_hypothetical_protein_1776518..1776668_POSITIVE 146 106 67 52 18 NC_002967:TDE1227|3end_hypothetical_protein_1261927..1262077_POSITIVE 144 110 63 126 71 NC_002967:TDE0768|3end_50S_ribosomal_protein_L4_807711..807861_POSITIVE 143 92 51 108 73 NC_002967:TDE0519|3end_hypothetical_protein_565438..565588_NEGATIVE 141 86 51 47 8 NC_002967:TDE1570|3end_hypothetical_protein_1620606..1620756_POSITIVE 137 29 2 75 50 NC_002967:TDE1697|3end_phosphoglycerate_mutase_1755516..1755666_NEGATIVE 137 80 39 41 4 NC_002967:TDE0507|3end_hypothetical_protein_558783..558933_NEGATIVE 136 109 64 52 9 NC_002967:TDE0567|3end_hypothetical_protein_598916..599066_POSITIVE 135 104 70 123 92 NC_002967:TDE2424|3end_50S_ribosomal_protein_L1_2454037..2454187_NEGATIVE 135 54 19 57 18 NC_002967:TDE0893|3end_ABC_transporter,_ATP-binding_protein_910451..910601_POSITIVE