Locus 5781

Sequence ID	3R_DroMel_CAF1
Location	15,071,243 – 15,071,404
Length	161
Max. P	0.956566

overview

Window 8

Location	15,071,243 – 15,071,333
Length	90
Sequences	6
Columns	92
Reading direction	forward
Mean pairwise identity	78.87
Mean single sequence MFE	-19.62
Consensus MFE	-17.01
Energy contribution	-16.65
Covariance contribution	-0.36
Combinations/Pair	1.11
Mean z-score	-1.87
Structure conservation index	0.87
SVM decision value	1.26
SVM RNA-class probability	0.937666
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15071243 90 + 27905053
UAGGUUACUCUAACCUCUAUAGAU--ACUUACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAG
.((((((...))))))....((((--((((.(((((......)))))..))))))))(((((((....)))))))(.((((....))))).. ( -24.50)
>DroVir_CAF1 8995 69 + 1
-------------G--------GA--ACUUACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAG
-------------.--------((--((((........))))))...........(((((((((....)))))))))((((....))))... ( -17.50)
>DroGri_CAF1 10067 77 + 1
-------------GCUAAGCUAAC--ACUUACUUAAUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAG
-------------.....((....--((((.(((((......)))))..))))..(((((((((....))))))))).(((....))))).. ( -18.20)
>DroEre_CAF1 7869 84 + 1
------CCUAUUUCCUAUAAAAGC--ACUUACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAG
------................((--((((.(((((......)))))..))))..(((((((((....))))))))).(((....))))).. ( -18.40)
>DroWil_CAF1 8402 86 + 1
----AUACAAUUUCAAUCAGUUUC--ACUUACUUAAUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCAACGCCAGAGGGCGCGG
----................((((--.(..((((....))))..).)))).....(((((((((....)))))))))((((....))))... ( -19.00)
>DroAna_CAF1 8143 79 + 1
-------------AUUUUAAACCUAAACUCACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAG
-------------........(.(((((((........))))))).)........(((((((((....)))))))))((((....))))... ( -20.10)
>consensus
_____________CCUAUAAAAAC__ACUUACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAG
...............................(((((......)))))........(((((((((....)))))))))((((....))))... (-17.01 = -16.65 +  -0.36)

alignment

secondary structure

dotplot

Window 9

Location	15,071,243 – 15,071,333
Length	90
Sequences	6
Columns	92
Reading direction	reverse
Mean pairwise identity	78.87
Mean single sequence MFE	-16.93
Consensus MFE	-14.02
Energy contribution	-13.88
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-2.17
Structure conservation index	0.83
SVM decision value	1.47
SVM RNA-class probability	0.956566
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15071243 90 - 27905053
CUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUAAGU--AUCUAUAGAGGUUAGAGUAACCUA
..(((((....))))).(((((((....)))))))...((((((((((......((((.....)))--)......))))..))))))..... ( -20.40)
>DroVir_CAF1 8995 69 - 1
CUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUAAGU--UC--------C-------------
..(((((....))))).(((((((....)))))))...(((((...............)))))...--..--------.------------- ( -13.96)
>DroGri_CAF1 10067 77 - 1
CUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUAUUAAGUAAGU--GUUAGCUUAGC-------------
..(((((....))))).(((((((....))))))).(((((((..((.((......)).)).))))--)))........------------- ( -16.20)
>DroEre_CAF1 7869 84 - 1
CUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUAAGU--GCUUUUAUAGGAAAUAGG------
..(((((....))))).(((((((....)))))))......((((((.......((((.....)))--).......))))))....------ ( -15.84)
>DroWil_CAF1 8402 86 - 1
CCGCGCCCUCUGGCGUUGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUAUUAAGUAAGU--GAAACUGAUUGAAAUUGUAU----
..(((((....)))))((((((((....)))))))).((((..((.(((((((......))).((.--....))..))))))..))))---- ( -15.90)
>DroAna_CAF1 8143 79 - 1
CUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUGAGUUUAGGUUUAAAAU-------------
..(((((....))))).(((((((....)))))))..........(..((((((........))))))..)........------------- ( -19.30)
>consensus
CUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUAAGU__GCUUUUAAAGG_____________
..(((((....))))).(((((((....)))))))...(((((...............)))))............................. (-14.02 = -13.88 +  -0.14)

alignment

secondary structure

dotplot

Window 0

Location	15,071,255 – 15,071,373
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.07
Mean single sequence MFE	-29.48
Consensus MFE	-26.07
Energy contribution	-25.60
Covariance contribution	-0.47
Combinations/Pair	1.14
Mean z-score	-1.62
Structure conservation index	0.88
SVM decision value	0.45
SVM RNA-class probability	0.742084
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15071255 118 + 27905053
ACCUCUAUAGAU--ACUUACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGCAAGACGUUGUGCAGUAGACGAACGUGGUAUUCAUGAAG
.(((((..((((--((((.(((((......)))))..))))))))(((((((....)))))))......)))))((((((........))))))..........((((.....))))... ( -30.70)
>DroVir_CAF1 8995 109 + 1
-G--------GA--ACUUACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGUAAGACGUUGUGCAAGAGGCGUACAUGGUAUUCAUGAAG
-.--------((--((((........))))))............((((((((....))))))))(((((.....((((((........))))))....))))).((((.....))))... ( -28.00)
>DroGri_CAF1 10067 117 + 1
-GCUAAGCUAAC--ACUUACUUAAUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGUAAGACGUUGUGCAAUAGGCGUACAUGGUAUUCAUGAAG
-(((..((((((--.(((((((.....................(((((((((....)))))))))((((....)))).)))))))..)))).))....)))...((((.....))))... ( -28.90)
>DroWil_CAF1 8410 118 + 1
UCAAUCAGUUUC--ACUUACUUAAUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCAACGCCAGAGGGCGCGGGCAAGACAUUGUGCAAUAGGCGUACAUGGUAUUCAUGAAG
........((((--.(..((((....))))..).))))......((((((((....))))))))(((((.....((((((........))))))....))))).((((.....))))... ( -29.60)
>DroMoj_CAF1 8745 109 + 1
-G--------GA--GAUUACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGUAAGACAUUGUGCAAGAGGCGUACAUGAUAUUCAUGGAG
-.--------..--.....(((((......))))).........((((((((....))))))))(((((.....((((((........))))))....))))).((((.....))))... ( -28.70)
>DroAna_CAF1 8143 119 + 1
-AUUUUAAACCUAAACUCACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGUAAGACGUUGUGCAAAAGGCGUACAUGGUAUUCAUGAAG
-.......((((((((((........)))))))......(((.(((((((((....)))))))))((((.....((((((........))))))....)))))))..))).......... ( -31.00)
>consensus
_G_U__A___AA__ACUUACUUAGUAGAGUUUGAGAAAAGUAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGUAAGACGUUGUGCAAUAGGCGUACAUGGUAUUCAUGAAG
...................(((((......)))))........(((((((((....)))))))))((((.....((((((........))))))....))))..((((.....))))... (-26.07 = -25.60 +  -0.47)

alignment

secondary structure

dotplot

Window 1

Location	15,071,255 – 15,071,373
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.07
Mean single sequence MFE	-21.35
Consensus MFE	-18.01
Energy contribution	-17.85
Covariance contribution	-0.16
Combinations/Pair	1.13
Mean z-score	-1.62
Structure conservation index	0.84
SVM decision value	0.13
SVM RNA-class probability	0.599154
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15071255 118 - 27905053
CUUCAUGAAUACCACGUUCGUCUACUGCACAACGUCUUGCCUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUAAGU--AUCUAUAGAGGU
(((((((.((((.(((((.(((....).))))))).((((..(((((....))))).(((((((....))))))).........................))))))--)).))).)))). ( -22.70)
>DroVir_CAF1 8995 109 - 1
CUUCAUGAAUACCAUGUACGCCUCUUGCACAACGUCUUACCUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUAAGU--UC--------C-
...((((.....)))).......(((((..............(((((....))))).(((((((....))))))).........................))))).--..--------.- ( -19.40)
>DroGri_CAF1 10067 117 - 1
CUUCAUGAAUACCAUGUACGCCUAUUGCACAACGUCUUACCUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUAUUAAGUAAGU--GUUAGCUUAGC-
...((((.....)))).....(((..((..((((.(((((..(((((....))))).(((((((....))))))).........................))))))--))).)).))).- ( -23.50)
>DroWil_CAF1 8410 118 - 1
CUUCAUGAAUACCAUGUACGCCUAUUGCACAAUGUCUUGCCCGCGCCCUCUGGCGUUGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUAUUAAGUAAGU--GAAACUGAUUGA
...((((.....))))...((.....)).((((((.(..(..(((((....)))))((((((((....))))))))..(((((...............))))).).--.).))..)))). ( -19.96)
>DroMoj_CAF1 8745 109 - 1
CUCCAUGAAUAUCAUGUACGCCUCUUGCACAAUGUCUUACCUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUAAUC--UC--------C-
...((((.....)))).(((((....((.((..........)).)).....))))).(((((((....)))))))...(((((...............)))))...--..--------.- ( -18.86)
>DroAna_CAF1 8143 119 - 1
CUUCAUGAAUACCAUGUACGCCUUUUGCACAACGUCUUACCUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUGAGUUUAGGUUUAAAAU-
...((((.....))))...((.....))..........(((((((((....))))).(((((((....))))))).............((((((........)))))))))).......- ( -23.70)
>consensus
CUUCAUGAAUACCAUGUACGCCUAUUGCACAACGUCUUACCUGCGCCCUCUGGCGUCGAUAUUGCUAACAAUAUCAAAUACUUUUCUCAAACUCUACUAAGUAAGU__AC___U__A_C_
...((((.....))))...((.....)).......(((((..(((((....))))).(((((((....))))))).........................)))))............... (-18.01 = -17.85 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	15,071,293 – 15,071,404
Length	111
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	88.52
Mean single sequence MFE	-33.93
Consensus MFE	-27.16
Energy contribution	-26.43
Covariance contribution	-0.72
Combinations/Pair	1.15
Mean z-score	-2.07
Structure conservation index	0.80
SVM decision value	0.06
SVM RNA-class probability	0.564031
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15071293 111 + 27905053
UAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGCAAGACGUUGUGCAGUAGACGAACGUGGUAUUCAUGAAGGGCUCUCAGUUUUGCCUGAACUGAAA---GCAG--A
...(((((((((....)))))))))((((....))))((((((((((...(.((.(....)...((((.....))))....)).)...))))))))))..(((...---.)))--. ( -35.90)
>DroVir_CAF1 9024 116 + 1
UAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGUAAGACGUUGUGCAAGAGGCGUACAUGGUAUUCAUGAAGGGCUCUCAGUUUUGCCUGAACUGUAAUAAAUAAACA
...(((((((((....)))))))))((((....))))(((((((((((.....).((((.(.(.((((.....)))).).).))))..)))))))))).................. ( -36.80)
>DroPse_CAF1 7930 111 + 1
UAUUUGAUAUUGUUGGCAAUAUCAACGCCAGAGGGGGCGGGUAAGACAUUGUGCAAUAGACGUACGUGGUAGUCAUGAAGGGCUCUCAAUUUUGCCUGAACUGUAA---UAGG--A
...(((((((((....)))))))))..((..(.((..(((((((((....((((.......)))).((..((((......))))..)).)))))))))..)).)..---..))--. ( -31.50)
>DroWil_CAF1 8448 111 + 1
UAUUUGAUAUUGUUAGCAAUAUCAACGCCAGAGGGCGCGGGCAAGACAUUGUGCAAUAGGCGUACAUGGUAUUCAUGAAGGGCUCUCAAUUUUGCCUGAACUAUAA---AGAG--A
...(((((((((....)))))))))((((....))))(((((((((..(((.(....((.(.(.((((.....)))).).).))).))))))))))))........---....--. ( -31.30)
>DroMoj_CAF1 8774 111 + 1
UAUUUGAUAUUGUUAGCAAUAUCGACGCCAGAGGGCGCAGGUAAGACAUUGUGCAAGAGGCGUACAUGAUAUUCAUGGAGGGCUCUCAGUUUUGCCUGAACUGCGA---AUAG--A
...(((((((((....)))))))))((((....))))((((((((((..((....((((.(.(.((((.....)))).).).))))))))))))))))........---....--. ( -36.60)
>DroPer_CAF1 7942 111 + 1
UAUUUGAUAUUGUUGGCAAUAUCAACGCCAGAGGGGGCGGGUAAGACAUUGUGCAAUAGACGUACGUGGUAGUCAUGAAGGGCUCUCAAUUUUGCCUGAACUGUAA---UAGG--A
...(((((((((....)))))))))..((..(.((..(((((((((....((((.......)))).((..((((......))))..)).)))))))))..)).)..---..))--. ( -31.50)
>consensus
UAUUUGAUAUUGUUAGCAAUAUCAACGCCAGAGGGCGCAGGUAAGACAUUGUGCAAUAGACGUACAUGGUAUUCAUGAAGGGCUCUCAAUUUUGCCUGAACUGUAA___AAAG__A
...(((((((((....)))))))))((((....))))(((((((((..(((.(....((.(.(.((((.....)))).).).))).)))))))))))).................. (-27.16 = -26.43 +  -0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:36 2006