Locus 2629

Sequence ID	3R_DroMel_CAF1
Location	7,098,228 – 7,098,345
Length	117
Max. P	0.963648

overview

Window 8

Location	7,098,228 – 7,098,320
Length	92
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	76.85
Mean single sequence MFE	-32.80
Consensus MFE	-14.92
Energy contribution	-16.77
Covariance contribution	1.85
Combinations/Pair	1.23
Mean z-score	-2.66
Structure conservation index	0.45
SVM decision value	1.56
SVM RNA-class probability	0.963648
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7098228 92 + 27905053
UGGGGCACCCACUGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUCGGAUCUGGGUCCUUGGU-UUGGGUUCCCGGGUU-----
.((((.((((.(((((((((((.....)))))))).)))........(((((((((.((((....)))).)))))))-)))))))))).....----- ( -32.20)
>DroSec_CAF1 31264 92 + 1
UGGGGCACCCACUGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUCGGAUCUGGGGCUCUGUU-UUGGGUUCCCGGGUU-----
.((((.((((.(((((((((((.....)))))))).)))..((((((.((((((..(....)..))..)))).))))-)))))))))).....----- ( -32.90)
>DroSim_CAF1 35102 97 + 1
UGGGGCACCCACUGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUCGGAUCUGGGGCUCUGGU-UUGGGUUCCCGGGUUCUCCG
.((((.((((.(((((((((((.....)))))))).)))........((((((((((((((....))))))))))))-))((....)))))).)))). ( -41.00)
>DroEre_CAF1 32124 79 + 1
UGGGGCACCCACUGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUCAGGUUUGGGUGCCCGG-UU------UG------------
..((((((((.(((((((((((.....)))))))).)))...((((..(((....)))...))))))))))))..-..------..------------ ( -31.30)
>DroYak_CAF1 33373 93 + 1
UGGGGCACCCACUGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUGGGAUCUGGGGCCCAGGUUUUGGGUUGCCUAGUC-----
..(((((.((.(((((((((((.....)))))))).)))......(((((((.((((((.(....).)))))).))))))))).)))))....----- ( -37.10)
>DroMoj_CAF1 37677 70 + 1
UG-GGUAACCAGUGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCAGGCUGGCAG-GUUG---------C-CUGG----------------
.(-(((((((....((((((((.....))))))))..............(((.....))).)-))))---------)-))..---------------- ( -22.30)
>consensus
UGGGGCACCCACUGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUCGGAUCUGGGGCCCUGGU_UUGGGUUCCCGGGUU_____
..((((.((((((((((((..........((((((............)))))).))))))))...))))))))......................... (-14.92 = -16.77 +   1.85)

alignment

secondary structure

dotplot

Window 9

Location	7,098,228 – 7,098,320
Length	92
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	76.85
Mean single sequence MFE	-22.93
Consensus MFE	-9.11
Energy contribution	-8.69
Covariance contribution	-0.42
Combinations/Pair	1.17
Mean z-score	-2.17
Structure conservation index	0.40
SVM decision value	0.03
SVM RNA-class probability	0.547980
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7098228 92 - 27905053
-----AACCCGGGAACCCAA-ACCAAGGACCCAGAUCCGAAGCCCCGGCUUUGUCUUUUCUAUAAACCAUUAUGCAAAUAGCCUCAGUGGGUGCCCCA
-----.....(((.(((((.-....(((....(((..((((((....)))))))))(((.(((((....))))).)))...)))...)))))..))). ( -23.50)
>DroSec_CAF1 31264 92 - 1
-----AACCCGGGAACCCAA-AACAGAGCCCCAGAUCCGAAGCCCCGGCUUUGUCUUUUCUAUAAACCAUUAUGCAAAUAGCCUCAGUGGGUGCCCCA
-----.....(((.(((((.-...((.((...(((..((((((....)))))))))(((.(((((....))))).)))..))))...)))))..))). ( -23.40)
>DroSim_CAF1 35102 97 - 1
CGGAGAACCCGGGAACCCAA-ACCAGAGCCCCAGAUCCGAAGCCCCGGCUUUGUCUUUUCUAUAAACCAUUAUGCAAAUAGCCUCAGUGGGUGCCCCA
.((.....))(((.(((((.-...((.((...(((..((((((....)))))))))(((.(((((....))))).)))..))))...)))))..))). ( -24.60)
>DroEre_CAF1 32124 79 - 1
------------CA------AA-CCGGGCACCCAAACCUGAGCCCCGGCUUUGUCUUUUCUAUAAACCAUUAUGCAAAUAGCCUCAGUGGGUGCCCCA
------------..------..-..(((((((((...(((((....((.(((((.......))))))).....((.....)))))))))))))))).. ( -27.30)
>DroYak_CAF1 33373 93 - 1
-----GACUAGGCAACCCAAAACCUGGGCCCCAGAUCCCAAGCCCCGGCUUUGUCUUUUCUAUAAACCAUUAUGCAAAUAGCCUCAGUGGGUGCCCCA
-----.....((((.((((....((((((...((((...((((....)))).))))(((.(((((....))))).)))..))).)))))))))))... ( -24.40)
>DroMoj_CAF1 37677 70 - 1
----------------CCAG-G---------CAAC-CUGCCAGCCUGGCUUUGUCUUUUCUAUAAACCAUUAUGCAAAUAGCCUCACUGGUUACC-CA
----------------((((-(---------(...-......))))))................(((((....((.....)).....)))))...-.. ( -14.40)
>consensus
_____AACCCGGGAACCCAA_ACCAGGGCCCCAGAUCCGAAGCCCCGGCUUUGUCUUUUCUAUAAACCAUUAUGCAAAUAGCCUCAGUGGGUGCCCCA
.........................................((((.((((((((...................))))..)))).....))))...... ( -9.11 =  -8.69 +  -0.42)

alignment

secondary structure

dotplot

Window 0

Location	7,098,248 – 7,098,345
Length	97
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	82.59
Mean single sequence MFE	-33.00
Consensus MFE	-23.38
Energy contribution	-24.75
Covariance contribution	1.38
Combinations/Pair	1.13
Mean z-score	-1.49
Structure conservation index	0.71
SVM decision value	-0.05
SVM RNA-class probability	0.509453
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7098248 97 + 27905053
UUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUCGGAUCUGGGUCCUUGGU-UUGGGUUCCCGGGUU--------CUCGGGUUCCUGGGUUCUCGGUUGC
...(((.....((((.......))))..((((.(((((..((((....))))..)))-)).)))).(((((..--------(((((....)))))..))))).))) ( -31.20)
>DroSec_CAF1 31284 97 + 1
UUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUCGGAUCUGGGGCUCUGUU-UUGGGUUCCCGGGUU--------CUCGGGUUCCUGGGUUCUCGGUUGC
...(((............(((....((((((.(((((((((....))))))))))))-)))..)))(((((..--------(((((....)))))..))))).))) ( -33.80)
>DroSim_CAF1 35122 105 + 1
UUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUCGGAUCUGGGGCUCUGGU-UUGGGUUCCCGGGUUCUCCGGUUCUCGGGUUCCUGGGUUCUCGGUUGC
...(((.....((((.......)))).((((((((((((((....))))))))))))-))(((..((((((..(.(((.....))))..))))))..)))...))) ( -41.00)
>DroYak_CAF1 33393 82 + 1
UUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUGGGAUCUGGGGCCCAGGUUUUGGGUUGCCUAGUC--------CUCGGGUU----------------C
.........((((((............))))))((((((((((.(((((((((((...))))))..)))))))--------).))))))----------------) ( -26.00)
>consensus
UUUGCAUAAUGGUUUAUAGAAAAGACAAAGCCGGGGCUUCGGAUCUGGGGCCCUGGU_UUGGGUUCCCGGGUU________CUCGGGUUCCUGGGUUCUCGGUUGC
.........................(((.((((((((((((....)))))))))))).)))((..((((((..........))))))..))............... (-23.38 = -24.75 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:57 2006