Origin IGS: aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggggaatttgttttggattgaattgtcccaatccataagaacattccgattattcctttgcaaagttgagcgaagctcaaggcttggcaggcgttgcggttttttatgtgagtaaatttgtttgtgtttgattgtaaacttatttaggcatgggaaggcc .........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 ggccttcccatgcctaaataagtttacaatcaaacacaaacaaatttactcacataaaaaaccgcaacgcctgccaagccttgagcttcgctcaactttgcaaaggaataatcggaatgttcttatggattgggacaattcaatccaaaacaaattcccccgaaaccttaaacccgcggggtttccaaaggggtgtcccctttggcagacggaaaaggaaggaggggtttggggaggaaggaaaacctgttctgtcggggtgtccttcctcccctaaacatggaggatttt Mask Tandem Repeat Region ================================================ aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggggaatttgttttggattgaattgtcccaatccataagaacattccgattattcctttgcaaagttgagcgaagctcaaggcttggcaggcgttgcggttttttatgtgagtaaatttgtttgtgtttgattgtaaacttatttaggcatgggaaggcc Find is-nt database================================================ Query_seq: TDE0741:TDE0742|TDE0741:TDE0742:hypothetical protein:hypothetical protein:<-<-:778249..778539 291 aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggggaatttgttttggattgaattgtcccaatccataagaacattccgattattcctttgcaaagttgagcgaagctcaaggcttggcaggcgttgcggttttttatgtgagtaaatttgtttgtgtttgattgtaaacttatttaggcatgggaaggcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0741:TDE0742|TDE0741:TDE0742:hypothetical protein:hypothetical protein:<-<-:778249..778539 291 aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggggaatttgttttggattgaattgtcccaatccataagaacattccgattattcctttgcaaagttgagcgaagctcaaggcttggcaggcgttgcggttttttatgtgagtaaatttgtttgtgtttgattgtaaacttatttaggcatgggaaggcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0741:TDE0742|TDE0741:TDE0742:hypothetical protein:hypothetical protein:<-<-:778249..778539 291 aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggggaatttgttttggattgaattgtcccaatccataagaacattccgattattcctttgcaaagttgagcgaagctcaaggcttggcaggcgttgcggttttttatgtgagtaaatttgtttgtgtttgattgtaaacttatttaggcatgggaaggcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 2 Min: 134 Max: 290 Len: 157 Subject: UniRef90_Q73P23 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 1.0E-11 bit: 71.2 Len: 105 Query Start:186 Query End:290 Subject Strand: null Subject Start: 63 Subject End: 97 ......................................................................................................................................................................................... A F P C L N K F T I K H K Q I Y S H K K P Q R L P S L E L R S T L Q R . ......................................................................................................................................................................................... A F P C L N K F T I K H K Q I Y S H K K P Q R S P S L E L R S T S Q R . Subject: UniRef90_Q73KF8 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 6.0E-7 bit: 55.5 Len: 126 Query Start:134 Query End:259 Subject Strand: null Subject Start: 10 Subject End: 51 ..................................................................................................................................... G I C F G L N C P N P * E H S D Y S F A K L S E A Q G L A G V A V F Y V S K F V C V ................................ ..................................................................................................................................... G L V F L I E L S Q S V G H A D Y C F A K L S E A Q C L A G V A V F Y V S K F V C V ................................ aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 11 End: 121 .......... M F R G G R T P R Q N R F S F L P K P L L P F P S A K G D T P L E T P R V .......................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 139 End: 243 .......................................................................................................................................... M F W I E L S Q S I R T F R L F L C K V E R S S R L G R R C G F L C E ................................................ Protein_Len: 60 Strand: - Start: 18 End: 263 ................. Q W L P C G K P F G A P K L N R P F K N Q I S N D W D M L V N R N N R Q L T S R L E L S P L R Q P K K H S Y I Q K H K M ............................ Protein_Len: 60 Strand: - Start: 2 End: 274 . V G R Q F G R P N L T E P S N T K S Q I T G I W L F M G I I G K C L Q A F S L A Q C A N R N K I H T F K N T N S Q L S M ................. Protein_Len: 33 Strand: - Start: 1 End: 99 F D E M N L P P L V G R C F L N E K R G L G R R G K G D A L P S M ................................................................................................................................................................................................ aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnc 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================================================ aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0741:TDE0742|TDE0741:TDE0742:hypothetical protein:hypothetical protein:<-<-:778249..778539 291 aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttcgggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnc Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002967_TDE0741_TDE0742|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[778249,778539]|291 HSP 1 e-value: 9.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttc................................................................................................................................................................. aaaatcctccatgtttaggggaggaaggacaccccgacagaacaggttttccttcctccccaaacccctccttccttttccgtctgccaaaggggacacccctttggaaaccccgcgggtttaaggtttc................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCCUCCAUGUUUAGGGGAGGAAGGACACCCCGACAGAACAGGUUUUCCUUCCUCCCCAAACCCCUCCUUCCUUUUCCGUCUGCCAAAGGGGACACCCCUUUGGAAACCCCGCGGGUUUAAGGUUUC ............((((.((((((((((((.(((...........)))..))))))))))))))))........((((.(((((...(((((((((...))))))))).......)))))...)))).... (-51.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAACCUUAAACCCGCGGGGUUUCCAAAGGGGUGUCCCCUUUGGCAGACGGAAAAGGAAGGAGGGGUUUGGGGAGGAAGGAAAACCUGUUCUGUCGGGGUGUCCUUCCUCCCCUAAACAUGGAGGAUUUU ....((((...((......(((((((((((((...))))))))).))))......))...)))).((((((((((((((((...((((......))))...)))))))))))).))))............ (-58.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1086 120 71 211 162 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 735 120 72 147 91 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 731 120 71 230 171 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 728 116 71 123 73 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 680 115 72 118 70 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 548 106 65 231 178 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 449 70 21 194 142 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 444 58 12 192 140 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 436 58 16 73 29 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 416 125 87 208 173 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 406 109 66 220 166 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 405 59 18 155 111 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 400 120 87 118 88 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 397 50 1 177 128 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 393 100 52 206 148 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 382 94 52 200 157 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 381 126 90 156 122 NC_002967:TDE2737|5end_hypothetical_protein_2791870..2792100_POSITIVE 365 104 65 199 167 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 364 119 72 147 86 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 363 100 52 155 102 NC_002967:TDE2205|5end_enoate_reductase,_putative_2244755..2244985_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 731 120 71 98 39 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 481 60 14 81 35 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 454 116 89 28 1 NC_002967:TDE1891|3end_hypothetical_protein_1912050..1912200_POSITIVE 444 58 12 138 86 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 436 58 16 86 42 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 420 54 12 132 89 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 413 129 81 76 29 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 397 50 1 90 41 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 394 59 14 84 37 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 392 59 17 83 37 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 371 60 13 116 67 NC_002967:TDE1008|3end_flagellar_protein,_putative_1032806..1032956_POSITIVE 366 114 71 148 98 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 365 104 65 122 90 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 348 95 56 66 23 NC_002967:TDE1534|3end_hypothetical_protein_1578667..1578817_NEGATIVE 346 118 73 80 26 NC_002967:TDE0437|3end_PBS_lyase_HEAT-like_repeat_domain_protein_492136..492286_NEGATIVE 339 54 23 54 23 NC_002967:TDE0862|3end_hypothetical_protein_884126..884276_POSITIVE 333 57 34 28 3 NC_002967:TDE1206|3end_TPR_domain_protein_1239312..1239462_POSITIVE 329 60 18 49 8 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 325 58 17 47 5 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 325 47 17 147 116 NC_002967:TDE0402|3end_hypothetical_protein_454248..454398_NEGATIVE