Locus 8597

Sequence ID	3L_DroMel_CAF1
Location	22,386,136 – 22,386,315
Length	179
Max. P	0.987493

overview

Window 5

Location	22,386,136 – 22,386,239
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.23
Mean single sequence MFE	-34.18
Consensus MFE	-19.45
Energy contribution	-19.40
Covariance contribution	-0.05
Combinations/Pair	1.13
Mean z-score	-3.05
Structure conservation index	0.57
SVM decision value	2.08
SVM RNA-class probability	0.987493
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22386136 103 + 23771897
AAAUAAGUCAAC--------ACUGG------CGAGUGGAUGUAUAUAUAUGCGUCUG---CUGGAAAAGUUUCCCCGACGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCC
......(((...--------.(((.------((((..(((((((....)))))))..---))((((....)))).)).)))............(((.(((((....))))).))).))). ( -29.50)
>DroPse_CAF1 91503 118 + 1
AAAUAAGUCAGCCAGCACACACACACGUACACAGAAGAAUGUCGG--UGUAUGUCUGGCACUGGGAGACUCCUCCUAGUGGACCCCAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCC
......(((.(((((.(((.((((.((.(((........))))))--))).))))))))((((((((....)))))))).)))..........(((.(((((....))))).)))..... ( -43.50)
>DroSim_CAF1 52847 99 + 1
AAAUAAGUCAAC--------ACUGG------CGAGAGGAUGUA----UGUGCGUCUG---CUGGAAAAGUUUCCCCGGCGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCC
............--------...((------(...........----((((.(((((---((((..........)))))))))))))......(((.(((((....))))).)))..))) ( -33.00)
>DroEre_CAF1 53512 99 + 1
AAAUAAGUCAAC--------ACUGG------CGAGAGGAUGUG----UGUGCGUCUG---CUGGAAAAGUUUCCCCGACGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCC
............--------...((------(.......((((----.((.((((..---..((((....))))..)))).))))))......(((.(((((....))))).)))..))) ( -28.20)
>DroYak_CAF1 53802 99 + 1
AAAUAAGUCAAC--------ACUGG------CUACAGGAUGUA----UGUGCGUCUG---CUGGAAAAGUUUCCCCGACGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCC
......(((...--------.(((.------...)))......----((((.(((((---(.((((....))))..).)))))))))......(((.(((((....))))).))).))). ( -27.40)
>DroPer_CAF1 94104 118 + 1
AAAUAAGUCAGCCAGCACACACACACGUACACAGAAGAAUGUCGG--UGUAUGUCUGGCACUGGGAGACUCCUCCUAGUGGACCCCAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCC
......(((.(((((.(((.((((.((.(((........))))))--))).))))))))((((((((....)))))))).)))..........(((.(((((....))))).)))..... ( -43.50)
>consensus
AAAUAAGUCAAC________ACUGG______CGAGAGGAUGUA____UGUGCGUCUG___CUGGAAAAGUUUCCCCGACGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCC
......(((......................................((((.(((((.....(((......)))....)))))))))......(((.(((((....))))).))).))). (-19.45 = -19.40 +  -0.05)

alignment

secondary structure

dotplot

Window 6

Location	22,386,136 – 22,386,239
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.23
Mean single sequence MFE	-33.98
Consensus MFE	-16.55
Energy contribution	-15.75
Covariance contribution	-0.80
Combinations/Pair	1.26
Mean z-score	-2.57
Structure conservation index	0.49
SVM decision value	1.19
SVM RNA-class probability	0.928926
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22386136 103 - 23771897
GGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGUCGGGGAAACUUUUCCAG---CAGACGCAUAUAUAUACAUCCACUCG------CCAGU--------GUUGACUUAUUU
(((..(((.(((((....))))).)))......(((((((.((.((..(....)..)).)---).))).))))...............)------))...--------............ ( -25.70)
>DroPse_CAF1 91503 118 - 1
GGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGGGGUCCACUAGGAGGAGUCUCCCAGUGCCAGACAUACA--CCGACAUUCUUCUGUGUACGUGUGUGUGUGCUGGCUGACUUAUUU
((((((((.(((((....))))).)))........))))).(((.((((....)))).)))((((((((((((--(((((((......)))).)).)))))))).))))).......... ( -46.20)
>DroSim_CAF1 52847 99 - 1
GGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGCCGGGGAAACUUUUCCAG---CAGACGCACA----UACAUCCUCUCG------CCAGU--------GUUGACUUAUUU
(((..(((.(((((....))))).)))......(((((((.((.((..(....)..)).)---).))).))))----...........)------))...--------............ ( -29.20)
>DroEre_CAF1 53512 99 - 1
GGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGUCGGGGAAACUUUUCCAG---CAGACGCACA----CACAUCCUCUCG------CCAGU--------GUUGACUUAUUU
(((..(((.(((((....))))).)))......((((((.((((..((((....))))..---..)))).)).----)))).......)------))...--------............ ( -29.10)
>DroYak_CAF1 53802 99 - 1
GGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGUCGGGGAAACUUUUCCAG---CAGACGCACA----UACAUCCUGUAG------CCAGU--------GUUGACUUAUUU
(((..(((.(((((....))))).)))......(((((((.((.((..(....)..)).)---).))).))))----...........)------))...--------............ ( -27.50)
>DroPer_CAF1 94104 118 - 1
GGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGGGGUCCACUAGGAGGAGUCUCCCAGUGCCAGACAUACA--CCGACAUUCUUCUGUGUACGUGUGUGUGUGCUGGCUGACUUAUUU
((((((((.(((((....))))).)))........))))).(((.((((....)))).)))((((((((((((--(((((((......)))).)).)))))))).))))).......... ( -46.20)
>consensus
GGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGCCGGGGAAACUUUUCCAG___CAGACGCACA____UACAUCCUCUCG______CCAGU________GUUGACUUAUUU
(((..(((.(((((....))))).)))......(((((((....(((((....))))).......))).))))...................................)))......... (-16.55 = -15.75 +  -0.80)

alignment

secondary structure

dotplot

Window 7

Location	22,386,162 – 22,386,279
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.91
Mean single sequence MFE	-42.67
Consensus MFE	-27.56
Energy contribution	-26.62
Covariance contribution	-0.94
Combinations/Pair	1.15
Mean z-score	-3.27
Structure conservation index	0.65
SVM decision value	0.87
SVM RNA-class probability	0.870735
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22386162 117 + 23771897
GUAUAUAUAUGCGUCUG---CUGGAAAAGUUUCCCCGACGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCCUUUGUAAUGGGGCCUUUGGGUUCUUCUCCAGCC
((((....))))....(---(((((.(((....(((((...............(((.(((((....))))).)))((((((((.((....))..)))))))))))))..))).)))))). ( -40.10)
>DroPse_CAF1 91543 114 + 1
GUCGG--UGUAUGUCUGGCACUGGGAGACUCCUCCUAGUGGACCCCAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCUUUUGUAAUGGGCCCUUUGGGUCCAACUCC----
(((((--.......)))))((((((((....))))))))((((((........(((.(((((....))))).))).(((((...((....))...)))))....))))))......---- ( -46.80)
>DroSim_CAF1 52873 113 + 1
GUA----UGUGCGUCUG---CUGGAAAAGUUUCCCCGGCGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCCUUUGUAAUGGGCCCUUUGGGUCCUUCGCCAGCC
...----((((.(((((---((((..........)))))))))))))...((((((.(((((....))))).)))((((.....)))).......((((((...)))))))))....... ( -42.90)
>DroEre_CAF1 53538 113 + 1
GUG----UGUGCGUCUG---CUGGAAAAGUUUCCCCGACGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCCAUUGUAAUGGGGCCUUUGGGUCCUCCUCCAGCC
...----.........(---(((((...(((.....)))(((((.((((....(((.(((((....))))).))).(((((((.((....))..))))))))))))))))...)))))). ( -41.80)
>DroYak_CAF1 53828 104 + 1
GUA----UGUGCGUCUG---CUGGAAAAGUUUCCCCGACGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCCUAAGCCAUUGUAAUGGGGCCUUUGGGUCCU---------
...----.....(((..---..((((....))))..)))(((((.((((....(((.(((((....))))).))).(((((((.((....))..)))))))))))))))).--------- ( -37.60)
>DroPer_CAF1 94144 114 + 1
GUCGG--UGUAUGUCUGGCACUGGGAGACUCCUCCUAGUGGACCCCAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCUUUUGUAAUGGGCCCUUUGGGUCCAACUCC----
(((((--.......)))))((((((((....))))))))((((((........(((.(((((....))))).))).(((((...((....))...)))))....))))))......---- ( -46.80)
>consensus
GUA____UGUGCGUCUG___CUGGAAAAGUUUCCCCGACGGACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCCUUUGUAAUGGGCCCUUUGGGUCCUACUCC____
......................(((......))).....(((((.((((....(((.(((((....))))).))).(((((...((....))...))).))))))))))).......... (-27.56 = -26.62 +  -0.94)

alignment

secondary structure

dotplot

Window 8

Location	22,386,162 – 22,386,279
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.91
Mean single sequence MFE	-42.53
Consensus MFE	-27.07
Energy contribution	-26.85
Covariance contribution	-0.22
Combinations/Pair	1.11
Mean z-score	-3.34
Structure conservation index	0.64
SVM decision value	0.89
SVM RNA-class probability	0.874484
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22386162 117 - 23771897
GGCUGGAGAAGAACCCAAAGGCCCCAUUACAAAGGCUUGAGGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGUCGGGGAAACUUUUCCAG---CAGACGCAUAUAUAUAC
.((((((((((..(((...(((...(((((((((((.....))).(((.(((((....))))).)))....))))))))..))).)))...)))))))))---)................ ( -43.40)
>DroPse_CAF1 91543 114 - 1
----GGAGUUGGACCCAAAGGGCCCAUUACAAAAGCUUGAGGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGGGGUCCACUAGGAGGAGUCUCCCAGUGCCAGACAUACA--CCGAC
----...(((((.(((((((((((((...........)).)))))(((.(((((....))))).)))....))))))(((((((.((((....)))).))))...))).....--))))) ( -43.00)
>DroSim_CAF1 52873 113 - 1
GGCUGGCGAAGGACCCAAAGGGCCCAUUACAAAGGCUUGAGGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGCCGGGGAAACUUUUCCAG---CAGACGCACA----UAC
.(((((.((((..(((...(((((....((((((((.....))).(((.(((((....))))).)))....))))))))))....)))...)))).))))---).........----... ( -43.00)
>DroEre_CAF1 53538 113 - 1
GGCUGGAGGAGGACCCAAAGGCCCCAUUACAAUGGCUUGAGGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGUCGGGGAAACUUUUCCAG---CAGACGCACA----CAC
.(((((((..(((((((((((((((((....)))).....)))).(((.(((((....))))).)))....)))).)))))..)(((....))).)))))---).........----... ( -45.00)
>DroYak_CAF1 53828 104 - 1
---------AGGACCCAAAGGCCCCAUUACAAUGGCUUAGGGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGUCGGGGAAACUUUUCCAG---CAGACGCACA----UAC
---------.((((((((((((((...............))))).(((.(((((....))))).)))....)))).)))))(((..((((....))))..---..))).....----... ( -37.76)
>DroPer_CAF1 94144 114 - 1
----GGAGUUGGACCCAAAGGGCCCAUUACAAAAGCUUGAGGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGGGGUCCACUAGGAGGAGUCUCCCAGUGCCAGACAUACA--CCGAC
----...(((((.(((((((((((((...........)).)))))(((.(((((....))))).)))....))))))(((((((.((((....)))).))))...))).....--))))) ( -43.00)
>consensus
____GGAGAAGGACCCAAAGGCCCCAUUACAAAGGCUUGAGGCCUUCAAAUGCCUUUUGGCAUAUGAUUCAUUUGUGGUCCGCCGGGGAAACUUUUCCAG___CAGACGCACA____UAC
..........(((((((((((.((((...........)).)))).(((.(((((....))))).)))....)))).)))))...(((((....)))))...................... (-27.07 = -26.85 +  -0.22)

alignment

secondary structure

dotplot

Window 9

Location	22,386,199 – 22,386,315
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.69
Mean single sequence MFE	-29.30
Consensus MFE	-22.23
Energy contribution	-21.78
Covariance contribution	-0.44
Combinations/Pair	1.15
Mean z-score	-1.54
Structure conservation index	0.76
SVM decision value	0.34
SVM RNA-class probability	0.693940
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22386199 116 + 23771897
GACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCCUUUGUAAUGGGGCCUUUGGGUUCUUCUCCAGCCCACC-UCCAU---CCUCCUCGACAUGUCUGCGCCAACAUG
.............(((.(((((....))))).)))((((((((.((....))..)))))))).((((((.......))))))..-.....---.........(((((........))))) ( -29.70)
>DroPse_CAF1 91581 111 + 1
GACCCCAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCUUUUGUAAUGGGCCCUUUGGGUCCAACUCC---------UUCAUUUCACUCCUGGUUUUGUCUGCCUCAAAAUG
(((((........(((.(((((....))))).))).(((((...((....))...)))))....))))).......---------...............((((((.......)))))). ( -28.60)
>DroSim_CAF1 52906 116 + 1
GACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCCUUUGUAAUGGGCCCUUUGGGUCCUUCGCCAGCCCACC-UCCAU---CCUCCUCGCCAUGUCUGCGCCAACAUG
....(((((....(((.(((((....))))).))).(((.....))))))))..(((((....(((........))))))))..-.....---.........(((((........))))) ( -27.00)
>DroEre_CAF1 53571 117 + 1
GACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCCAUUGUAAUGGGGCCUUUGGGUCCUCCUCCAGCCCAUCAUCCGU---CCUCCUCGCCAUGUCAGCGCCAACAUG
(((.....((((.(((.(((((....))))).)))((((((((.((....))..)))))))).(((((.........)))))))))..))---)........(((((........))))) ( -30.80)
>DroYak_CAF1 53861 95 + 1
GACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCCUAAGCCAUUGUAAUGGGGCCUUUGGGUCCU-------------------------CCUCGCCAUGUCAGCCCCAACAUG
((((.((((....(((.(((((....))))).))).(((((((.((....))..)))))))))))))))..-------------------------......(((((........))))) ( -31.10)
>DroPer_CAF1 94182 111 + 1
GACCCCAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCUUUUGUAAUGGGCCCUUUGGGUCCAACUCC---------UUCAUUUCACUCCUGGUUUUGUCUGCCUCAAAAUG
(((((........(((.(((((....))))).))).(((((...((....))...)))))....))))).......---------...............((((((.......)))))). ( -28.60)
>consensus
GACCACAAAUGAAUCAUAUGCCAAAAGGCAUUUGAAGGCCUCAAGCCUUUGUAAUGGGCCCUUUGGGUCCUACUCC_________UCCAU___CCUCCUCGCCAUGUCUGCCCCAACAUG
((((.((((....(((.(((((....))))).))).(((((...((....))...))).))))))))))..............................(((.......)))........ (-22.23 = -21.78 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:59 2006