Locus 68

Sequence ID	2L_DroMel_CAF1
Location	243,026 – 243,154
Length	128
Max. P	0.966382

overview

Window 3

Location	243,026 – 243,133
Length	107
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	76.93
Mean single sequence MFE	-26.29
Consensus MFE	-19.03
Energy contribution	-18.79
Covariance contribution	-0.25
Combinations/Pair	1.11
Mean z-score	-1.66
Structure conservation index	0.72
SVM decision value	1.25
SVM RNA-class probability	0.935617
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 243026 107 + 22407834
ACUU----------UUCGUUGCAAUAGCUCUAACUUUUAAGGGGAAAAGCUAUACGCUUAUGAAUAUCA-CAGAAGGGCACAUAUAACGUACAGUUUUACCCCCCAAAAU-GUUGAGCA
....----------............((((.(((((((..((((.((((((.((((..((((....((.-.....))...))))...)))).)))))).))))..)))).-))))))). ( -27.80)
>DroPse_CAF1 43144 116 + 1
AAUUGUUGUUGCGA-UUGUUGCUGUUGCAUCAAGUUUUAAGGGGAAAAGCUAUACGCUUAUGAAUUUCG-AAUAUUGUCACAUAGAACGUACAGUUUGACCCCUCAAAUU-UUUGAGCA
((((((....))))-))........(((.(((((.(((.(((((..(((((.((((.(((((.......-..........)))))..)))).)))))..))))).)))..-)))))))) ( -26.73)
>DroGri_CAF1 42835 109 + 1
-----GACUU-UU-UAGGUUGCUAUCACUUCAACUUUUAAGGGGAAAAGCUAUACGCUUAUGAAUUUCU-U-CAUUUACACAUAUAACGUACAGUUUGACCCCCUAAACA-UUUGAGUG
-----((((.-..-..)))).....(((((.((..((((.((((..(((((.((((..((((.......-.-........))))...)))).)))))..)))).))))..-)).))))) ( -22.99)
>DroWil_CAF1 44371 112 + 1
A----UUGUUUACA-UUGUUGAUUUAACAUCAACUUUUAAGGGGAAAAGCUAUACGCUUAUGGAUUUCUUAAGAUUUGCACAUACAACGUACAGUUUAACCCCAUAA-AU-GUUGUGUA
.----.........-...........(((.((((.((((.((((..(((((.((((..(((((...((....))....).))))...)))).)))))..)))).)))-).-))))))). ( -25.30)
>DroAna_CAF1 41181 117 + 1
ACUU-UAGUUGAGAUUUGUUGACUUUGCUUCAACUUUUAAGGGGAAAAGCUAUACGCUUAUGAAUUUCU-AAGAUUGCCACAUAGAACGUACAGUUUGACCCCCCAAAAGGGUUGAGCU
....-.(((..(......)..)))..(((.((((((((..((((..(((((.((((.(((((((((...-..))))....)))))..)))).)))))....))))..))))))))))). ( -28.20)
>DroPer_CAF1 43601 116 + 1
AAUUGUUGUUGCGA-UUGUUGCUGUUGCAUCAAGUUUUAAGGGGAAAAGCUAUACGCUUAUGAAUUUCG-AAUAUUGUCACAUAGAACGUACAGUUUGACCCCUCAAAUU-UUUGAGCA
((((((....))))-))........(((.(((((.(((.(((((..(((((.((((.(((((.......-..........)))))..)))).)))))..))))).)))..-)))))))) ( -26.73)
>consensus
A_UU_UUGUUGAGA_UUGUUGCUAUUGCAUCAACUUUUAAGGGGAAAAGCUAUACGCUUAUGAAUUUCU_AAGAUUGGCACAUAGAACGUACAGUUUGACCCCCCAAAAU_GUUGAGCA
..........................((.(((((.(((..((((..(((((.((((..((((..................))))...)))).)))))..))))..)))...))))))). (-19.03 = -18.79 +  -0.25)

alignment

secondary structure

dotplot

Window 4

Location	243,026 – 243,133
Length	107
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	76.93
Mean single sequence MFE	-31.92
Consensus MFE	-25.90
Energy contribution	-25.62
Covariance contribution	-0.28
Combinations/Pair	1.13
Mean z-score	-4.02
Structure conservation index	0.81
SVM decision value	1.59
SVM RNA-class probability	0.966382
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 243026 107 - 22407834
UGCUCAAC-AUUUUGGGGGGUAAAACUGUACGUUAUAUGUGCCCUUCUG-UGAUAUUCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUAGAGCUAUUGCAACGAA----------AAGU
.(((((((-.((((((((((.(((((((((((((.((((..........-.......))))))))))))).))))))))))))))))).))))............----------.... ( -34.23)
>DroPse_CAF1 43144 116 - 1
UGCUCAAA-AAUUUGAGGGGUCAAACUGUACGUUCUAUGUGACAAUAUU-CGAAAUUCAUAAGCGUAUAGCUUUUCCCCUUAAAACUUGAUGCAACAGCAACAA-UCGCAACAACAAUU
(((.....-..(((((((((..((.(((((((((...(((((.......-......)))))))))))))).))..)))))))))..(((.(((....))).)))-..)))......... ( -31.22)
>DroGri_CAF1 42835 109 - 1
CACUCAAA-UGUUUAGGGGGUCAAACUGUACGUUAUAUGUGUAAAUG-A-AGAAAUUCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUGAAGUGAUAGCAACCUA-AA-AAGUC-----
(((((((.-..(((((((((..((.(((((((((.((....)).(((-(-(....))))).))))))))).))..)))))))))..))).))))...........-..-.....----- ( -32.80)
>DroWil_CAF1 44371 112 - 1
UACACAAC-AU-UUAUGGGGUUAAACUGUACGUUGUAUGUGCAAAUCUUAAGAAAUCCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUGAUGUUAAAUCAACAA-UGUAAACAA----U
((((....-.(-(((.((((..((.(((((((((.((((.(....((....))...)))))))))))))).))..)))).)))).((((((.....))))))..-)))).....----. ( -29.70)
>DroAna_CAF1 41181 117 - 1
AGCUCAACCCUUUUGGGGGGUCAAACUGUACGUUCUAUGUGGCAAUCUU-AGAAAUUCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUGAAGCAAAGUCAACAAAUCUCAACUA-AAGU
.(((((((..((((((((((..((.(((((((((.((((..........-.......))))))))))))).))..)))))))))))))).))).....................-.... ( -32.33)
>DroPer_CAF1 43601 116 - 1
UGCUCAAA-AAUUUGAGGGGUCAAACUGUACGUUCUAUGUGACAAUAUU-CGAAAUUCAUAAGCGUAUAGCUUUUCCCCUUAAAACUUGAUGCAACAGCAACAA-UCGCAACAACAAUU
(((.....-..(((((((((..((.(((((((((...(((((.......-......)))))))))))))).))..)))))))))..(((.(((....))).)))-..)))......... ( -31.22)
>consensus
UGCUCAAA_AUUUUGGGGGGUCAAACUGUACGUUCUAUGUGACAAUCUU_AGAAAUUCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUGAAGCAAAAGCAACAA_UCGCAACAA_AA_U
.((((((....(((((((((..((.(((((((((.((((..................))))))))))))).))..)))))))))..)))).)).......................... (-25.90 = -25.62 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	243,056 – 243,154
Length	98
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	75.12
Mean single sequence MFE	-20.60
Consensus MFE	-15.79
Energy contribution	-15.79
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.16
Structure conservation index	0.77
SVM decision value	0.94
SVM RNA-class probability	0.885809
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 243056 98 + 22407834
GGGGAAAAGCUAUACGCUUAUGAAUAUCA-CAGAAGGGCACAUAUAACGUACAGUUUUACCCCCCAAAAU-GUUGAGCAAUAUUGUCCAGAUU-GUACAAU---
((((.((((((.((((..((((....((.-.....))...))))...)))).)))))).)))).......-((((.(((((.........)))-)).))))--- ( -22.10)
>DroSim_CAF1 36420 98 + 1
GGGGAAAAGCUAUACGCUUAUGAAUUUCA-CAGAAGGGCACAUAUAACGUACAGUUUCACCCCCCAAAAU-GUUGAGCAAUUUUGUCCAGAUU-GUACAAG---
((((..(((((.((((..((((..((((.-..))))....))))...)))).)))))..)))).......-.(((.(((((((.....)))))-)).))).--- ( -22.50)
>DroEre_CAF1 36397 97 + 1
GGGGAAAAGCUAUACGCUUAUGAAUUUUA-CAGAAGGACACAUAUAACGUACAGUUUCACCCCCUAAAAU-GUUGAGCAAUUUUGUC-AGGUU-CUACAAG---
((((..(((((.((((..((((..((((.-....))))..))))...)))).)))))..))))......(-((.((((.........-..)))-).)))..--- ( -21.00)
>DroWil_CAF1 44406 96 + 1
GGGGAAAAGCUAUACGCUUAUGGAUUUCUUAAGAUUUGCACAUACAACGUACAGUUUAACCCCAUAA-AU-GUUGUGUAGAAUUG-----AUU-CUUUAAUUUA
((((..(((((.((((..(((((...((....))....).))))...)))).)))))..))))....-..-........((((((-----(..-..))))))). ( -20.20)
>DroMoj_CAF1 40173 91 + 1
GGGGAAAAGCUAUACGCUUAUGGAUUUCA-U-UGUUUACACAUACAACGUACAGUUUGACCCCCUAAACA-UUUGAGUGUUUUGUU-CACAUUUG---------
((((..(((((.((((..((((.......-.-........))))...)))).)))))..))))..(((((-(....))))))....-........--------- ( -19.09)
>DroAna_CAF1 41220 88 + 1
GGGGAAAAGCUAUACGCUUAUGAAUUUCU-AAGAUUGCCACAUAGAACGUACAGUUUGACCCCCCAAAAGGGUUGAGCU------UCCAGAA------AAC---
..((((((((.....))))......((((-(.(.......).)))))......(((..((((.......))))..))))------)))....------...--- ( -18.70)
>consensus
GGGGAAAAGCUAUACGCUUAUGAAUUUCA_CAGAAGGGCACAUAUAACGUACAGUUUCACCCCCCAAAAU_GUUGAGCAAUUUUGUCCAGAUU_GUACAAG___
((((..(((((.((((..((((..................))))...)))).)))))..))))......................................... (-15.79 = -15.79 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	243,056 – 243,154
Length	98
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	75.12
Mean single sequence MFE	-20.77
Consensus MFE	-18.22
Energy contribution	-18.22
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.17
Structure conservation index	0.88
SVM decision value	1.15
SVM RNA-class probability	0.922607
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 243056 98 - 22407834
---AUUGUAC-AAUCUGGACAAUAUUGCUCAAC-AUUUUGGGGGGUAAAACUGUACGUUAUAUGUGCCCUUCUG-UGAUAUUCAUAAGCGUAUAGCUUUUCCCC
---(((((.(-.....).)))))....(((((.-...)))))(((.(((((((((((((.((((..........-.......))))))))))))).))))))). ( -20.93)
>DroSim_CAF1 36420 98 - 1
---CUUGUAC-AAUCUGGACAAAAUUGCUCAAC-AUUUUGGGGGGUGAAACUGUACGUUAUAUGUGCCCUUCUG-UGAAAUUCAUAAGCGUAUAGCUUUUCCCC
---.......-........((((((........-)))))).((((.(((.(((((((((.((((..........-.......))))))))))))).))).)))) ( -21.63)
>DroEre_CAF1 36397 97 - 1
---CUUGUAG-AACCU-GACAAAAUUGCUCAAC-AUUUUAGGGGGUGAAACUGUACGUUAUAUGUGUCCUUCUG-UAAAAUUCAUAAGCGUAUAGCUUUUCCCC
---.((((..-.....-.))))...........-.......((((.(((.(((((((((.((((..........-.......))))))))))))).))).)))) ( -20.03)
>DroWil_CAF1 44406 96 - 1
UAAAUUAAAG-AAU-----CAAUUCUACACAAC-AU-UUAUGGGGUUAAACUGUACGUUGUAUGUGCAAAUCUUAAGAAAUCCAUAAGCGUAUAGCUUUUCCCC
........((-((.-----...)))).......-..-....((((..((.(((((((((.((((.(....((....))...)))))))))))))).))..)))) ( -19.70)
>DroMoj_CAF1 40173 91 - 1
---------CAAAUGUG-AACAAAACACUCAAA-UGUUUAGGGGGUCAAACUGUACGUUGUAUGUGUAAACA-A-UGAAAUCCAUAAGCGUAUAGCUUUUCCCC
---------....((..-..))(((((......-))))).(((((.....(((((((((...(((....)))-(-((.....))).)))))))))....))))) ( -20.20)
>DroAna_CAF1 41220 88 - 1
---GUU------UUCUGGA------AGCUCAACCCUUUUGGGGGGUCAAACUGUACGUUCUAUGUGGCAAUCUU-AGAAAUUCAUAAGCGUAUAGCUUUUCCCC
---...------..(..((------((.......))))..)((((..((.(((((((((.((((..........-.......))))))))))))).))..)))) ( -22.13)
>consensus
___AUUGUAC_AAUCUGGACAAAAUUGCUCAAC_AUUUUAGGGGGUCAAACUGUACGUUAUAUGUGCCAAUCUG_UGAAAUUCAUAAGCGUAUAGCUUUUCCCC
.........................................((((..((.(((((((((.((((..................))))))))))))).))..)))) (-18.22 = -18.22 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:57 2006