Locus 3037

Sequence ID	3R_DroMel_CAF1
Location	8,085,049 – 8,085,431
Length	382
Max. P	0.989125

overview

Window 9

Location	8,085,049 – 8,085,155
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.27
Mean single sequence MFE	-26.20
Consensus MFE	-18.94
Energy contribution	-19.54
Covariance contribution	0.60
Combinations/Pair	1.10
Mean z-score	-1.60
Structure conservation index	0.72
SVM decision value	-0.00
SVM RNA-class probability	0.533140
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085049 106 + 27905053
AAAUACAUAAAUA------UAUACUCUACAGAUGUCGCAUCUUAUCA--------GUCCGCUGAGGACCCAAAGUGAUGUCCACAUCAGGCGAGAGCUGUGAGAUUAAUUCUACACAUAG
.............------....(((.((((.(.((((.........--------((((.....))))......(((((....))))).)))).).)))))))................. ( -25.40)
>DroSec_CAF1 9976 106 + 1
AAAUACACAAAUA------UAUACUCUACAGAUUUCGCAUCUUAUCA--------GUCCGCUGAGGACCCAAAGUGAUGUCCACAUCAGGCGAGAGUUGUGAGAUUAAUUCUGCACAUAG
.............------....(((.((((.((((((.........--------((((.....))))......(((((....))))).)))))).)))))))................. ( -24.80)
>DroSim_CAF1 8811 106 + 1
AAAUACAUAAAUA------UAUACUCUACAGAUGUCGCAUCUUAUCA--------GUCCGCUGAGGACCCAAAGUGAUGUCCACAUCAGGCGAGAGUUGUGAGAUUAAUUCUGCACAUAG
.............------...(((((.(.(((((.(((((......--------((((.....)))).......)))).).))))).)...)))))(((((((.....))).))))... ( -25.42)
>DroEre_CAF1 11732 115 + 1
AAAUACAUAAAUAUACGAGUAUACUAUACAAAUGUCGCAUCUUAUCAG-UCGUCAGUCCGCUGAGGACCCAAUGAGAUGUCCACAUCAGGCGAGAGUUGGGAGAUUAAUUCUACAC----
...............((.((((...))))..((((.(((((((((..(-((.((((....)))).)))...)))))))).).))))....))((((((((....))))))))....---- ( -26.50)
>DroYak_CAF1 5085 116 + 1
AAAUACAUAAAUACUCGCAUAUACUGUACAAAUGUCGCAUCUUAUCAGCUCGUCGGUCCGCUGAGGACCCAAAGUGAUGUCCACAUCAGGCGAGAGUUUUGAGAUUAAUUCUACAC----
................((((((.........)))).))((((((....(((((((((((.....))))).....(((((....))))))))))).....))))))...........---- ( -28.90)
>consensus
AAAUACAUAAAUA______UAUACUCUACAGAUGUCGCAUCUUAUCA________GUCCGCUGAGGACCCAAAGUGAUGUCCACAUCAGGCGAGAGUUGUGAGAUUAAUUCUACACAUAG
.......................(((.((((.(.((((.................((((.....))))......(((((....))))).)))).).)))))))................. (-18.94 = -19.54 +   0.60)

alignment

secondary structure

dotplot

Window 0

Location	8,085,155 – 8,085,271
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.88
Mean single sequence MFE	-34.30
Consensus MFE	-32.56
Energy contribution	-31.68
Covariance contribution	-0.88
Combinations/Pair	1.16
Mean z-score	-1.31
Structure conservation index	0.95
SVM decision value	1.03
SVM RNA-class probability	0.903599
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085155 116 - 27905053
CGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAAAAAUUGAUGUCGCCAAAGAUCAGGGAAUGCGGCUGUUCGUCGCAGGACAAAAGUUCAGUGG----GCAGCCAUGUAUGUA
.(((((((.....)))))..((((((.((((((.((((.....(((.......))).....))))..((((((.....))))))))))))...))))))..----))............. ( -32.50)
>DroSec_CAF1 10082 116 - 1
CGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAAAAAUUGAUGUCGCCAAAGAUCAGGGAACGCGGCUGUUCGUCGCAGGACAAAAGUUCAGUGG----GUAGCCAUGUAUGUA
((((......)))).(((((.(((((.((((((.((((.....(((.......))).....))))...(((((.....))))).))))))...))))))))----))............. ( -32.00)
>DroSim_CAF1 8917 120 - 1
CGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAAAAAUUGAUGUCGCCAAAGAUCAGGGAACGCGGCUGUUCGUCGCAGGACAAAAGUUCAGUGGGCGGGCAGCCAUGUAUGUA
.(((((((.....)))))...........((((.((........((((.(......).))))))))))))(((((((((((((.((((....)))).)).)))))))))))......... ( -38.60)
>DroEre_CAF1 11847 113 - 1
CGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAAAAAUUGAUGUCGCCAAAGAUCAGGGAACGCGGCUGUUCGUCGCAGGACAAGAGUUCAGUGG----ACAGCCAUGUAU---
.(((((((.....)))))..((((((.((((((.((((.....(((.......))).....))))...(((((.....))))).))))))...))))))..----...)).......--- ( -32.20)
>DroYak_CAF1 5201 113 - 1
CGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAAAAAUUGAUGUCGCCAAAGAUCAGGGAACGCGGCUGUUCGCCGCAGGACAAAAGUUCAGCGG----ACAGCCAUGUAU---
.(((((((.....)))))...........((((.((........((((.(......).))))))))))))((((((((((....((((....)))).))))----))))))......--- ( -36.20)
>consensus
CGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAAAAAUUGAUGUCGCCAAAGAUCAGGGAACGCGGCUGUUCGUCGCAGGACAAAAGUUCAGUGG____GCAGCCAUGUAUGUA
.(((((((.....)))))...........((((.((........((((.(......).))))))))))))((((((...((((.((((....)))).))))....))))))......... (-32.56 = -31.68 +  -0.88)

alignment

secondary structure

dotplot

Window 1

Location	8,085,191 – 8,085,311
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.00
Mean single sequence MFE	-34.24
Consensus MFE	-33.48
Energy contribution	-33.68
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.85
Structure conservation index	0.98
SVM decision value	2.15
SVM RNA-class probability	0.989125
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085191 120 + 27905053
ACGAACAGCCGCAUUCCCUGAUCUUUGGCGACAUCAAUUUUUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAU
..........((...((((((...((((.....))))...)))))).....((((((((((.(((((.....)))))..))))))))))...)).((((............))))..... ( -31.30)
>DroSec_CAF1 10118 120 + 1
ACGAACAGCCGCGUUCCCUGAUCUUUGGCGACAUCAAUUUUUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAU
..........(((((((((((...((((.....))))...)))))).....((((((((((.(((((.....)))))..))))))))))))))).((((............))))..... ( -34.60)
>DroSim_CAF1 8957 120 + 1
ACGAACAGCCGCGUUCCCUGAUCUUUGGCGACAUCAAUUUUUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAU
..........(((((((((((...((((.....))))...)))))).....((((((((((.(((((.....)))))..))))))))))))))).((((............))))..... ( -34.60)
>DroEre_CAF1 11880 119 + 1
ACGAACAGCCGCGUUCCCUGAUCUUUGGCGACAUCAAUUUUUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCA-GUAGUUUCCCGCAGAUAAU
..........(((((((((((...((((.....))))...)))))).....((((((((((.(((((.....)))))..))))))))))))))).((((.-..........))))..... ( -34.70)
>DroYak_CAF1 5234 120 + 1
GCGAACAGCCGCGUUCCCUGAUCUUUGGCGACAUCAAUUUUUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAU
(((.......(((((((((((...((((.....))))...)))))).....((((((((((.(((((.....)))))..)))))))))))))))((((....))))....)))....... ( -36.00)
>consensus
ACGAACAGCCGCGUUCCCUGAUCUUUGGCGACAUCAAUUUUUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAU
..........(((((((((((...((((.....))))...)))))).....((((((((((.(((((.....)))))..))))))))))))))).((((............))))..... (-33.48 = -33.68 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	8,085,231 – 8,085,351
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.33
Mean single sequence MFE	-36.08
Consensus MFE	-34.62
Energy contribution	-34.82
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.96
SVM decision value	1.34
SVM RNA-class probability	0.944037
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085231 120 + 27905053
UUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAUGCAAUUGUUGUGUGUAUUUGCGUAUUCCGCACCGCCGGCU
....((((...((((((((((.(((((.....)))))..)))))))))).((((((.(((((((...((.....))...)))..)))).))))))...((((.....)))).)))).... ( -36.30)
>DroSec_CAF1 10158 120 + 1
UUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAUGCAAUUGUUGUGUGUAUUUGCGUAUUCCGCACCGCCGGCU
....((((...((((((((((.(((((.....)))))..)))))))))).((((((.(((((((...((.....))...)))..)))).))))))...((((.....)))).)))).... ( -36.30)
>DroSim_CAF1 8997 120 + 1
UUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAUGCAAUUGUUGUGUGUAUUUGCGUAUUCCGCACCGCCGGCU
....((((...((((((((((.(((((.....)))))..)))))))))).((((((.(((((((...((.....))...)))..)))).))))))...((((.....)))).)))).... ( -36.30)
>DroEre_CAF1 11920 119 + 1
UUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCA-GUAGUUUCCCGCAGAUAAUGCAAUUGUUGUGUGUAUUUGCGUAUUCCGCACCGCCGGCU
....((((...((((((((((.(((((.....)))))..)))))))))).((((((.(((-((.(.....)(((.....))).))))).))))))...((((.....)))).)))).... ( -37.20)
>DroYak_CAF1 5274 120 + 1
UUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAUGCAAUUGUUGUGUGUAUUUGCGUAUUCCACACCGCCGGCU
....((((...((((((((((.(((((.....)))))..)))))))))).((((((((....)))).....(((.(((((......))))).)))....))))......))))....... ( -34.30)
>consensus
UUAGGGUGAACAAUUUCAAUUAGGUUCACGUUGAACCGCGAUUGAGAUUAACGCACUGCAAGUAGUUUCCCGCAGAUAAUGCAAUUGUUGUGUGUAUUUGCGUAUUCCGCACCGCCGGCU
....((((...((((((((((.(((((.....)))))..))))))))))...((((((....))))....(((((((((((((.....))))).))))))))......))..)))).... (-34.62 = -34.82 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	8,085,231 – 8,085,351
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.33
Mean single sequence MFE	-31.00
Consensus MFE	-30.06
Energy contribution	-30.10
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.36
Structure conservation index	0.97
SVM decision value	0.45
SVM RNA-class probability	0.740499
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085231 120 - 27905053
AGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGCAUUAUCUGCGGGAAACUACUUGCAGUGCGUUAAUCUCAAUCGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAA
....((.((((((.....)))..........((((((((((....(((((((......)))))))))).......(((((...(((((.....)))))..)))))))))))).))))).. ( -31.00)
>DroSec_CAF1 10158 120 - 1
AGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGCAUUAUCUGCGGGAAACUACUUGCAGUGCGUUAAUCUCAAUCGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAA
....((.((((((.....)))..........((((((((((....(((((((......)))))))))).......(((((...(((((.....)))))..)))))))))))).))))).. ( -31.00)
>DroSim_CAF1 8997 120 - 1
AGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGCAUUAUCUGCGGGAAACUACUUGCAGUGCGUUAAUCUCAAUCGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAA
....((.((((((.....)))..........((((((((((....(((((((......)))))))))).......(((((...(((((.....)))))..)))))))))))).))))).. ( -31.00)
>DroEre_CAF1 11920 119 - 1
AGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGCAUUAUCUGCGGGAAACUAC-UGCAGUGCGUUAAUCUCAAUCGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAA
....((.((((((.....)))..........((((((((((....((((((.......)-)))))))).......(((((...(((((.....)))))..)))))))))))).))))).. ( -31.30)
>DroYak_CAF1 5274 120 - 1
AGCCGGCGGUGUGGAAUACGCAAAUACACACAACAAUUGCAUUAUCUGCGGGAAACUACUUGCAGUGCGUUAAUCUCAAUCGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAA
....((.((((((.............)))))((((((((((....(((((((......)))))))))).......(((((...(((((.....)))))..))))))))))))).)).... ( -30.72)
>consensus
AGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGCAUUAUCUGCGGGAAACUACUUGCAGUGCGUUAAUCUCAAUCGCGGUUCAACGUGAACCUAAUUGAAAUUGUUCACCCUAA
....((.((((((.....)))..........((((((((((....(((((((......)))))))))).......(((((...(((((.....)))))..)))))))))))).))))).. (-30.06 = -30.10 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	8,085,311 – 8,085,431
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-38.80
Consensus MFE	-38.42
Energy contribution	-38.46
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.66
Structure conservation index	0.99
SVM decision value	2.09
SVM RNA-class probability	0.987790
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085311 120 - 27905053
CAUCUAUUGUCCCUCGCCAAUCGACGGCCAUUGUCUUUCGAUUCUAGGCGUGGGAUACUGCUAACCGUUUGGCGUUUUCCAGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGC
.......((((((.((((((((((.(((....)))..))))))...)))).))))))((((..((((((.(((........))))))))))))).....((((.............)))) ( -39.92)
>DroSec_CAF1 10238 120 - 1
CAUCUAUUGUCCCUCGCCAAUCGACGGCCUUUGUCUUUCGAUUCGAGGCGUGGGAUACUGCUAACCGUUUGGCGUUUUCCAGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGC
.......((((((.((((((((((.(((....)))..))))))...)))).))))))((((..((((((.(((........))))))))))))).....((((.............)))) ( -39.92)
>DroSim_CAF1 9077 120 - 1
CAUCUAUUGUCCCUCGCCAAUCGACGGCCUUUGUCUUUCGAUUCGAGGCGUGGGAUACUGCUAACCGUUUGGCGUUUUCCAGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGC
.......((((((.((((((((((.(((....)))..))))))...)))).))))))((((..((((((.(((........))))))))))))).....((((.............)))) ( -39.92)
>DroEre_CAF1 11999 119 - 1
CAUCUAUUGUCCCUCGCCAAUCGACGGCCUUUGUCUUUCGAUUCGAGGCGUGGGAUACUGCUAACCGUUUGGCGUUUU-CAGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGC
.......((((((.((((((((((.(((....)))..))))))...)))).))))))((((..((((((.(((.....-..))))))))))))).....((((.............)))) ( -39.62)
>DroYak_CAF1 5354 120 - 1
CAUCUAUUGUCCCUCGCCAAUCGACGCCCAUUGUCUUUCGAUUCGAGGCGUGGGAUACUGCUAACCGUUUGGCAUUUUCCAGCCGGCGGUGUGGAAUACGCAAAUACACACAACAAUUGC
..(((((((((((.((((((((((.((.....))...))))))...)))).))))))......((((((.(((........))))))))))))))....((((.............)))) ( -34.62)
>consensus
CAUCUAUUGUCCCUCGCCAAUCGACGGCCUUUGUCUUUCGAUUCGAGGCGUGGGAUACUGCUAACCGUUUGGCGUUUUCCAGCCGGCGGUGCGGAAUACGCAAAUACACACAACAAUUGC
.......((((((.((((((((((.(((....)))..))))))...)))).))))))((((..((((((.(((........))))))))))))).....((((.............)))) (-38.42 = -38.46 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:54 2006