Locus 3447

Sequence ID	2L_DroMel_CAF1
Location	10,038,553 – 10,038,657
Length	104
Max. P	0.917586

overview

Window 4

Location	10,038,553 – 10,038,657
Length	104
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	76.87
Mean single sequence MFE	-32.20
Consensus MFE	-22.53
Energy contribution	-23.03
Covariance contribution	0.50
Combinations/Pair	1.18
Mean z-score	-1.63
Structure conservation index	0.70
SVM decision value	1.12
SVM RNA-class probability	0.917586
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10038553 104 + 22407834
UGGGCCAGGUCUUCGACGAGGAGAAGGAGACCUGCGACUGGGCACGCAAGGUGCCAGAUUGGUAAGCUAUAGU----UAUCCCUAAUAUAAAGUACUAUUGG-GAAUUU
..((((((((((((..(.....)..)))))))))(((((((.(((.....))))))).)))....))).....----..((((.((((........))))))-)).... ( -32.90)
>DroVir_CAF1 37790 94 + 1
UCGGCCAGGUGUUCGAUGAGGAGAACAAAACCUGCGACUGGGCACGUAAGGUGCCAGAUUGGUAAGAUUUGCCGUGUCGAACAAAAUGU-----------GGCGA----
...((((.(((((((((..((..((....(((.....((((.(((.....)))))))...)))....))..))..))))))))...).)-----------)))..---- ( -30.30)
>DroSec_CAF1 34429 104 + 1
UGGGCCAGGUCUUCGACGAGGAGAAGGAGACCUGCGACUGGGCACGCAAGGUGCCAGAUUGGUAAGCUAUAGU----UACACCUAAUAUAAAGUACUAUUCCUGAAUU-
((((.(((((((((..(.....)..))))))))).((((((((((.....)))))....(((....)))))))----)...)))).......................- ( -29.30)
>DroSim_CAF1 36789 104 + 1
UGGGCCAGGUCUUCGACGAGGAGAAGGAGACCUGCGACUGGGCACGCAAGGUGCCAGAUUGGUAAGCUAUAGU----CACACCUAAUAUAAAGUAUUAUUGCUGAAUU-
((((.(((((((((..(.....)..))))))))).((((((((((.....)))))....(((....)))))))----)...))))......((((....)))).....- ( -33.50)
>DroEre_CAF1 34388 104 + 1
UGGGCCAGGUCUUCGACGAGGAGAAGGAGACCUGCGACUGGGCACGCAAGGUGCCCGAUUGGUAAGAUAUGGU----UAUCCCCAAUAUUUAGUACUACCAG-AAGUUC
(((((.((((((((..(.....)..)))))))))).(((((((((.....)))))).(((((...((((....----)))).)))))....)))....))).-...... ( -36.30)
>DroYak_CAF1 35087 87 + 1
UGGGCCAGGUCUUCGACGAGGAGAAGGAGACCUGCGACUGGGCACGCAAGGUGCCCGACUGGUAAUAUAUGGU----UAUCCUUCCUACUU------------------
((((((((((((((..(.....)..))))))))).)..(((((((.....)))))))...((((((.....))----))))...))))...------------------ ( -30.90)
>consensus
UGGGCCAGGUCUUCGACGAGGAGAAGGAGACCUGCGACUGGGCACGCAAGGUGCCAGAUUGGUAAGAUAUAGU____UAUACCUAAUAUAAAGUACUAUUGG_GAAUU_
((((.(((((((((..(.....)..)))))))))(((...(((((.....)))))...)))....................))))........................ (-22.53 = -23.03 +   0.50)

alignment

secondary structure

dotplot

Window 5

Location	10,038,553 – 10,038,657
Length	104
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	76.87
Mean single sequence MFE	-25.33
Consensus MFE	-16.47
Energy contribution	-16.13
Covariance contribution	-0.33
Combinations/Pair	1.12
Mean z-score	-1.14
Structure conservation index	0.65
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10038553 104 - 22407834
AAAUUC-CCAAUAGUACUUUAUAUUAGGGAUA----ACUAUAGCUUACCAAUCUGGCACCUUGCGUGCCCAGUCGCAGGUCUCCUUCUCCUCGUCGAAGACCUGGCCCA
....((-((((((........)))).))))..----......((........(((((((.....))).))))...(((((((.(..(.....)..).)))))))))... ( -24.80)
>DroVir_CAF1 37790 94 - 1
----UCGCC-----------ACAUUUUGUUCGACACGGCAAAUCUUACCAAUCUGGCACCUUACGUGCCCAGUCGCAGGUUUUGUUCUCCUCAUCGAACACCUGGCCGA
----..(((-----------(.....(((((((...((..(((...(((...(((((((.....))).)))).....)))...)))..))...)))))))..))))... ( -25.50)
>DroSec_CAF1 34429 104 - 1
-AAUUCAGGAAUAGUACUUUAUAUUAGGUGUA----ACUAUAGCUUACCAAUCUGGCACCUUGCGUGCCCAGUCGCAGGUCUCCUUCUCCUCGUCGAAGACCUGGCCCA
-......((.(((((((((......))))...----))))).((........(((((((.....))).))))...(((((((.(..(.....)..).))))))))))). ( -23.70)
>DroSim_CAF1 36789 104 - 1
-AAUUCAGCAAUAAUACUUUAUAUUAGGUGUG----ACUAUAGCUUACCAAUCUGGCACCUUGCGUGCCCAGUCGCAGGUCUCCUUCUCCUCGUCGAAGACCUGGCCCA
-......((....((((((......))))))(----(((...(.....).....(((((.....))))).)))).(((((((.(..(.....)..).)))))))))... ( -22.70)
>DroEre_CAF1 34388 104 - 1
GAACUU-CUGGUAGUACUAAAUAUUGGGGAUA----ACCAUAUCUUACCAAUCGGGCACCUUGCGUGCCCAGUCGCAGGUCUCCUUCUCCUCGUCGAAGACCUGGCCCA
......-..(((.(.(((....((((((((((----....)))))..))))).((((((.....)))))))))).(((((((.(..(.....)..).)))))))))).. ( -30.40)
>DroYak_CAF1 35087 87 - 1
------------------AAGUAGGAAGGAUA----ACCAUAUAUUACCAGUCGGGCACCUUGCGUGCCCAGUCGCAGGUCUCCUUCUCCUCGUCGAAGACCUGGCCCA
------------------.....((..((...----.))........((((((((((((.....)))))).(.((.(((.........))))).)...)).)))).)). ( -24.90)
>consensus
_AAUUC_CCAAUAGUACUUUAUAUUAGGGAUA____ACCAUAGCUUACCAAUCUGGCACCUUGCGUGCCCAGUCGCAGGUCUCCUUCUCCUCGUCGAAGACCUGGCCCA
..........................((..........................(((((.....)))))......(((((...((((........)))))))))..)). (-16.47 = -16.13 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:44 2006