Locus 3978

Sequence ID	3R_DroMel_CAF1
Location	10,775,534 – 10,775,641
Length	107
Max. P	0.933773

overview

Window 6

Location	10,775,534 – 10,775,627
Length	93
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.60
Mean single sequence MFE	-23.87
Consensus MFE	-16.69
Energy contribution	-17.00
Covariance contribution	0.31
Combinations/Pair	1.18
Mean z-score	-1.43
Structure conservation index	0.70
SVM decision value	0.72
SVM RNA-class probability	0.832830
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10775534 93 + 27905053
------------GG---UCGUG--------UG---AUGUGAGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUUGCCAAAAGCAUUCUGG-
------------..---.....--------..---.......(((((((..(((...((((........)))).))).....((((((((.......)))))))).....)).))))).- ( -24.20)
>DroVir_CAF1 66581 96 + 1
------------GG---GUGUG--------UGUCUGUGUAAGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCGAAUGUGCCAAAUGCGUUUGCCAAAAGCAUUGUGG-
------------..---...((--------(.(((((....))))).))).....((((((((((((..(((..........))).....((.....)))))))))....)))))....- ( -25.00)
>DroGri_CAF1 59699 80 + 1
----------------------------------UGUGUGAGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGUUCCAAAUGCGUUUGCCAAAAGC-----GG-
----------------------------------.......((....(((.......)))((((...((((((.....((.(((....))).))..))))))))))....))-----..- ( -18.70)
>DroWil_CAF1 53858 90 + 1
------------AUGCGAUGUU--------U----GUGUGAGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUGGCCAAACACAU------
------------..........--------(----((((..(((.((....))....)))(((...(((((((.....((.(((....))).))..))))))))))..))))).------ ( -24.60)
>DroMoj_CAF1 67222 116 + 1
GUGUAAGUGUCAGG---GUAUGCGUGCGAUUGUAUGUGCGAGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGUUCCAAAUGCGUUUGCCAAAAGCAUUGUGG-
((((..(((((...---...(((((..((((((.(.((....)).).))))))...)))))......)))))..........((((((((.......)))))))).....)))).....- ( -28.60)
>DroPer_CAF1 61604 96 + 1
------------AG-AGCUGUG--------UG---AUGUGAGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUGCCCAAAAGCAUCCUGUG
------------..-.(((..(--------..---(((((((((...((........((((........)))).........))...))))).....))))..).....)))........ ( -22.13)
>consensus
____________GG___GUGUG________UG___GUGUGAGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUUGCCAAAAGCAUU_UGG_
...................................((((........(((.......)))((((...((((((.....((.(((....))).))..))))))))))....))))...... (-16.69 = -17.00 +   0.31)

alignment

secondary structure

dotplot

Window 7

Location	10,775,534 – 10,775,627
Length	93
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.60
Mean single sequence MFE	-21.73
Consensus MFE	-13.77
Energy contribution	-14.30
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-1.91
Structure conservation index	0.63
SVM decision value	1.10
SVM RNA-class probability	0.914630
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10775534 93 - 27905053
-CCAGAAUGCUUUUGGCAAACGCAUUUGGAGCAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCUCACAU---CA--------CACGA---CC------------
-.(((((.......((((((((((..((((((....)))))).....)))))...)))))(((.......)))))))).......---..--------.....---..------------ ( -25.50)
>DroVir_CAF1 66581 96 - 1
-CCACAAUGCUUUUGGCAAACGCAUUUGGCACAUUCGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCUUACACAGACA--------CACAC---CC------------
-....(((((....(((((((((.....)).....(((..........)))..)))))))))))).....((..((((......))))..--------))...---..------------ ( -20.20)
>DroGri_CAF1 59699 80 - 1
-CC-----GCUUUUGGCAAACGCAUUUGGAACAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCUCACACA----------------------------------
-..-----((....((((((((((..((((.(....).)))).....)))))...)))))(((.......)))....)).......---------------------------------- ( -16.60)
>DroWil_CAF1 53858 90 - 1
------AUGUGUUUGGCCAACGCAUUUGGAGCAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCUCACAC----A--------AACAUCGCAU------------
------.(((((..((((.(((((..((((((....)))))).....))))).)...)))(((.......)))........))))----)--------..........------------ ( -23.10)
>DroMoj_CAF1 67222 116 - 1
-CCACAAUGCUUUUGGCAAACGCAUUUGGAACAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCUCGCACAUACAAUCGCACGCAUAC---CCUGACACUUACAC
-.....((((....((((((((((..((((.(....).)))).....)))))...)))))(((((.((..(((........)))..)).))).))..))))..---.............. ( -20.40)
>DroPer_CAF1 61604 96 - 1
CACAGGAUGCUUUUGGGCAACGCAUUUGGAGCAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCUCACAU---CA--------CACAGCU-CU------------
.....((((....(((((((((((..((((((....)))))).....)))))........(((.......)))...)))))))))---).--------.......-..------------ ( -24.60)
>consensus
_CCA_AAUGCUUUUGGCAAACGCAUUUGGAACAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCUCACAC___CA________CACAC___CC____________
........((....((((((((((..((((........)))).....)))))...)))))(((.......)))....))......................................... (-13.77 = -14.30 +   0.53)

alignment

secondary structure

dotplot

Window 8

Location	10,775,548 – 10,775,641
Length	93
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.19
Mean single sequence MFE	-25.01
Consensus MFE	-17.76
Energy contribution	-18.07
Covariance contribution	0.31
Combinations/Pair	1.10
Mean z-score	-1.60
Structure conservation index	0.71
SVM decision value	1.23
SVM RNA-class probability	0.933773
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10775548 93 + 27905053
AGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUUGCCAAAAGCAUUCUGG-----CCG---UGCGC-----AAGU------AU--------
..(((((((..(((...((((........)))).))).....((((((((.......)))))))).....)).))))).-----..(---(((..-----..))------))-------- ( -28.50)
>DroPse_CAF1 62001 101 + 1
AGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUGCCCAAAAGCAUCCUGUGGCCCCCU---UGCAC-----AUGUCCAUG-----------
.((((..(((.......)))(((...(((((((.....((.(((....))).))..))))))).......((.....)).)))...)---)))..-----.........----------- ( -22.10)
>DroGri_CAF1 59705 91 + 1
AGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGUUCCAAAUGCGUUUGCCAAAAGC-----GG-----GUAAGCUGUGAUGCAUG-------------------
.(((...(((.(((...(((((((...((((((.....((.(((....))).))..))))))))))....))-----).-----.)))..)))..)))...------------------- ( -22.60)
>DroMoj_CAF1 67259 102 + 1
AGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGUUCCAAAUGCGUUUGCCAAAAGCAUUGUGG-----GUUAACUGCAA-------------GGUUGUGCGGGC
.((....((((((....(((((..(((..((((((.......((((((((.......)))))))).......)))))).-----)))..))))).-------------))))))....)) ( -26.84)
>DroAna_CAF1 48954 93 + 1
AGCAGAAGCAAUUAAAAUGCGGCAAACGGCGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUUGCCAAAGGCAUUCUGU-----CCC---GGCAC-----UUGU------AU--------
.((((((((..(((...((((.(....).)))).))).....((((((((.......)))))))).....)).))))))-----...---.....-----....------..-------- ( -26.10)
>DroPer_CAF1 61620 107 + 1
AGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUGCCCAAAAGCAUCCUGUGGCCCCCU---UGCAC-----AUGUCCAUGUAUCUG-----
..((((.(((......(((..((((..((((((.....((.(((....))).))..))))))(((((.........)).)))....)---))).)-----)).....))).))))----- ( -23.90)
>consensus
AGCAGAAGCAAUUAAAAUGCGGCAAACGACGCAGUAAAUGAAGCAAAUGCUCCAAAUGCGUUUGCCAAAAGCAUUCUGG_____CCU___UGCAC_____AUGU______AU________
.((....(((.......)))((((...((((((.....((.(((....))).))..))))))))))....))................................................ (-17.76 = -18.07 +   0.31)

alignment

secondary structure

dotplot

Window 9

Location	10,775,548 – 10,775,641
Length	93
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.19
Mean single sequence MFE	-26.42
Consensus MFE	-17.37
Energy contribution	-18.37
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.66
SVM decision value	0.91
SVM RNA-class probability	0.879028
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10775548 93 - 27905053
--------AU------ACUU-----GCGCA---CGG-----CCAGAAUGCUUUUGGCAAACGCAUUUGGAGCAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCU
--------..------....-----..(((---.((-----(.(((((((....((((((((((..((((((....)))))).....)))))...))))))))))))....)))..))). ( -28.70)
>DroPse_CAF1 62001 101 - 1
-----------CAUGGACAU-----GUGCA---AGGGGGCCACAGGAUGCUUUUGGGCAACGCAUUUGGAGCAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCU
-----------.........-----..(((---..(((((...(((((((.....(((((((((..((((((....)))))).....)))))....)))))))))))....)))))))). ( -29.00)
>DroGri_CAF1 59705 91 - 1
-------------------CAUGCAUCACAGCUUAC-----CC-----GCUUUUGGCAAACGCAUUUGGAACAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCU
-------------------.((((.....(((....-----..-----)))...((((((((((..((((.(....).)))).....)))))...))))))))).......((....)). ( -19.20)
>DroMoj_CAF1 67259 102 - 1
GCCCGCACAACC-------------UUGCAGUUAAC-----CCACAAUGCUUUUGGCAAACGCAUUUGGAACAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCU
....(((.....-------------..((((((((.-----....(((((....((((((((((..((((.(....).)))).....)))))...))))))))))))))))))...))). ( -23.20)
>DroAna_CAF1 48954 93 - 1
--------AU------ACAA-----GUGCC---GGG-----ACAGAAUGCCUUUGGCAAACGCAUUUGGAGCAUUUGCUUCAUUUACUGCGCCGUUUGCCGCAUUUUAAUUGCUUCUGCU
--------..------..((-----((((.---(((-----.(.....))))..((((((((((..((((((....)))))).....)))...))))))))))))).....((....)). ( -25.90)
>DroPer_CAF1 61620 107 - 1
-----CAGAUACAUGGACAU-----GUGCA---AGGGGGCCACAGGAUGCUUUUGGGCAACGCAUUUGGAGCAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCU
-----((((..((..((.((-----(((((---((.(.(((.(((((...)))))))).(((((..((((((....)))))).....)))))).)))).))))).))...))..)))).. ( -32.50)
>consensus
________AU______ACAU_____GUGCA___AGG_____ACAGAAUGCUUUUGGCAAACGCAUUUGGAGCAUUUGCUUCAUUUACUGCGUCGUUUGCCGCAUUUUAAUUGCUUCUGCU
................................................((....((((((((((..((((((....)))))).....)))...)))))))(((.......)))....)). (-17.37 = -18.37 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:02 2006