Origin IGS: atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggttggagtgtgaattatcgcattcctaacatcaaagcgaactgttttacctaggatttctagtcttcctagaatccctataaacgttgaaccaatacataaaaacagcttcggttttgtaaagataattccaccgaaaaatgataatttcgat Mask Tandem Repeat Region ================================================ atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta Find is-nt database================================================ Query_seq: PI2011:PI2012|PI2011:PI2012:hypothetical protein:hypothetical protein:->->:1970791..1970946 156 atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2011:PI2012|PI2011:PI2012:hypothetical protein:hypothetical protein:->->:1970791..1970946 156 atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2011:PI2012|PI2011:PI2012:hypothetical protein:hypothetical protein:->->:1970791..1970946 156 atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 1 End: 105 M E I I I F R W N Y L Y K T E A V F M Y W F N V Y R D S R K T R N P R ................................................... Protein_Len: 43 Strand: + Start: 26 End: 154 ......................... M I F T K P K L F L C I G S T F I G I L G R L E I L G K T V R F D V R N A I I H T P T .. Protein_Len: 47 Strand: - Start: 1 End: 141 D F N D N K P P I I K V F G F S N K H I P E V N I P I R P L S S I R P L V T R K S T L F A I M ............... atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta 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================================================ atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2011:PI2012|PI2011:PI2012:hypothetical protein:hypothetical protein:->->:1970791..1970946 156 atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: pint_PI2011_PI2012|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1970791,1970946]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta atcgaaattatcatttttcggtggaattatctttacaaaaccgaagctgtttttatgtattggttcaacgtttatagggattctaggaagactagaaatcctaggtaaaacagttcgctttgatgttaggaatgcgataattcacactccaaccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAAAUUAUCAUUUUUCGGUGGAAUUAUCUUUACAAAACCGAAGCUGUUUUUAUGUAUUGGUUCAACGUUUAUAGGGAUUCUAGGAAGACUAGAAAUCCUAGGUAAAACAGUUCGCUUUGAUGUUAGGAAUGCGAUAAUUCACACUCCAACCUA ..(((((........)))))(((((((((((.((((..((((((.((.........)).)))))).........(((((.((((((.....)))))).))))).))))....((((.((........))))))..)))))))).)))......... (-36.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUUGGAGUGUGAAUUAUCGCAUUCCUAACAUCAAAGCGAACUGUUUUACCUAGGAUUUCUAGUCUUCCUAGAAUCCCUAUAAACGUUGAACCAAUACAUAAAAACAGCUUCGGUUUUGUAAAGAUAAUUCCACCGAAAAAUGAUAAUUUCGAU ...((((((((((((....))))))))).)))..((((((((((((((((...((((..((((((.....))))))..)))).....((((...)))).....))))))).))).))))))...............(((((........))))).. (-39.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 478 58 16 43 1 pint:PI0069|5end_hypothetical_protein_67072..67302_POSITIVE 446 47 3 178 134 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 435 47 1 78 32 pint:PI1182|5end_hypothetical_protein_1104025..1104255_POSITIVE 401 46 3 64 21 pint:PI0970|5end_hypothetical_protein_897254..897484_POSITIVE 392 48 1 231 184 pint:PI1804|5end_hypothetical_protein_1738109..1738339_POSITIVE 357 49 1 104 52 pint:PI0815|5end_hypothetical_protein_754475..754705_POSITIVE 356 50 1 141 92 pint:PI0037|5end_hypothetical_protein_39354..39584_POSITIVE 339 60 11 131 83 pint:PI0089|5end_hypothetical_protein_88162..88392_POSITIVE 338 50 8 45 3 pint:PI1072|5end_hypothetical_protein_990220..990450_POSITIVE 330 53 16 38 1 pint:PI1521|5end_hypothetical_protein_1441220..1441450_POSITIVE 326 50 1 141 92 pint:PI0926|5end_hypothetical_protein_856824..857054_POSITIVE 324 50 1 119 71 pint:PI1786|5end_hypothetical_protein_1718124..1718354_POSITIVE 324 50 3 88 36 pint:PI1041|5end_hypothetical_protein_960443..960673_POSITIVE 308 50 1 141 92 pint:PI0322|5end_hypothetical_protein_303508..303738_POSITIVE 305 49 3 121 75 pint:PI0568|5end_hypothetical_protein_512950..513180_POSITIVE 295 55 16 40 1 pint:PI0826|5end_hypothetical_protein_763738..763968_POSITIVE 287 46 3 63 21 pint:PI1540|5end_hypothetical_protein_1461362..1461592_POSITIVE 274 48 1 133 92 pint:PI1436|5end_hypothetical_protein_1355961..1356191_POSITIVE 271 150 111 166 128 pint:PI0902|5end_hypothetical_protein_832291..832521_POSITIVE 270 136 104 202 163 pint:PI1295|5end_hypothetical_protein_1208636..1208866_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 461 50 1 93 42 pint:PI0574|3end_hypothetical_protein_519444..519594_POSITIVE 421 50 1 105 56 pint:PI1520|3end_hypothetical_protein_1441370..1441520_POSITIVE 305 49 3 146 100 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 285 41 3 42 4 pint:PI0010|3end_conserved_hypothetical_protein_11679..11829_POSITIVE 281 66 24 50 6 pint:PI1577|3end_conserved_hypothetical_protein_1503879..1504029_POSITIVE 277 146 101 81 41 pint:PI0594|3end_possible_rare_lipoprotein_A_545157..545307_POSITIVE 267 79 36 145 97 pint:PI0135|3end_internalin-related_protein_127257..127407_POSITIVE 250 80 35 71 8 pint:PI1958|3end_hypothetical_protein_1917369..1917519_POSITIVE 249 72 40 74 30 pint:PI0109|3end_hypothetical_protein_107183..107333_POSITIVE 248 139 95 41 1 pint:PI1871|3end_glycosyl_transferase,_group_1_family_protein_1817133..1817283_POSITIVE 247 83 41 68 22 pint:PI1674|3end_hypothetical_protein_1588154..1588304_POSITIVE 243 150 107 48 5 pint:PI2088|3end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_2045815..2045965_POSITIVE 243 47 11 38 3 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 242 137 91 151 97 pint:PI0978|3end_hypothetical_protein_905114..905264_POSITIVE 240 68 29 32 1 pint:PI0945|3end_sodium:solute_symporter_family_protein_877624..877774_POSITIVE 237 150 101 141 93 pint:PI1661|3end_hypothetical_protein_1576817..1576967_POSITIVE 237 59 13 74 29 pint:PI1203|3end_conserved_hypothetical_protein_1124439..1124589_POSITIVE 235 150 102 145 105 pint:PI0379|3end_conserved_hypothetical_protein_350239..350389_POSITIVE 234 136 98 115 74 pint:PI1666|3end_conserved_hypothetical_protein_1579418..1579568_POSITIVE 233 90 42 63 11 pint:PI1758|3end_hypothetical_protein_1684057..1684207_POSITIVE