Locus 1115

Sequence ID	3R_DroMel_CAF1
Location	3,374,782 – 3,375,098
Length	316
Max. P	0.982950

overview

Window 3

Location	3,374,782 – 3,374,882
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.58
Mean single sequence MFE	-38.54
Consensus MFE	-26.04
Energy contribution	-27.36
Covariance contribution	1.32
Combinations/Pair	1.08
Mean z-score	-2.01
Structure conservation index	0.68
SVM decision value	0.63
SVM RNA-class probability	0.804015
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3374782 100 - 27905053
AGCCGCUACUGAAUCGAGGCUGCUGCGGG-CUU----A--C-----UGGCAGUCGAACUGAUGGAUCCGAUUGUUCGGUUCU--------CAUUGCGCGAUUCAGUUGUUCCUCGUCGAU
....((.(((((((((..((.(((((.((-...----.--)-----).)))))......((((((.((((....)))).)).--------)))))).))))))))).))........... ( -34.00)
>DroSec_CAF1 3173 102 - 1
AGCGGCAACUGAAUCGAGGCUGCUGCGGG-CUU----ACAC-----UGGCAGUCGAACUGAUGGAUCCGAUUGUUCGGUUCU--------CAUUGCGCGAUUCAGUUGUUCCUCGUCGAU
((..((((((((((((..((.(((((.((-...----...)-----).)))))......((((((.((((....)))).)).--------)))))).))))))))))))..))....... ( -40.00)
>DroAna_CAF1 7931 118 - 1
AACCGCAACUGAAUUGGGGCUGCUGUGGGGCUUGCUUGCACCGCUCCGCCACUCGAACUGAUAGAUCCGAUUCUACG-UUCUCGGUGUUCCAGUGCC-CAGUCAGUUGUUCCUCGUCGAU
....((((((((.(((((((((..(((((((.((....))..)))))))((((.((((.(.((((......))))))-)))..))))...)))).))-)))))))))))........... ( -41.10)
>DroSim_CAF1 4000 102 - 1
AGCGGCAACUGAAUCGAGGCUGCUGCGGG-CUU----ACAC-----UGGCAGUCGAACUGAUGGAUCCGAUUGUUCGGUUCU--------CAUUGCGCGAUUCAGUUGUUCCUCGUCGAU
((..((((((((((((..((.(((((.((-...----...)-----).)))))......((((((.((((....)))).)).--------)))))).))))))))))))..))....... ( -40.00)
>DroEre_CAF1 3448 99 - 1
AGCCACAACUGAAUUGAGGCUGCUGUGGG-CUC------AC-----UGGCAGUCGAACUGAUGGAUCGGAUUGUUCGGUUC---------CAUUGCACGAUUCAGUUGUUCCUCGUCAAU
....((((((((((((.((((((((((..-..)------))-----.))))))).....((((((.(.((....)).).))---------))))...))))))))))))........... ( -37.60)
>consensus
AGCCGCAACUGAAUCGAGGCUGCUGCGGG_CUU____ACAC_____UGGCAGUCGAACUGAUGGAUCCGAUUGUUCGGUUCU________CAUUGCGCGAUUCAGUUGUUCCUCGUCGAU
....((((((((((((.(((((((.......................)))))))(((((((.............)))))))................))))))))))))........... (-26.04 = -27.36 +   1.32)

alignment

secondary structure

dotplot

Window 4

Location	3,374,882 – 3,374,996
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.93
Mean single sequence MFE	-38.84
Consensus MFE	-23.28
Energy contribution	-25.12
Covariance contribution	1.84
Combinations/Pair	1.14
Mean z-score	-1.80
Structure conservation index	0.60
SVM decision value	0.09
SVM RNA-class probability	0.579412
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3374882 114 + 27905053
UUAAUCACGACCGCCGCUUAUCGCAAUGUGAGUUGCUGCUAUCGCU---GCAGCGAAACAUAUGGCGCAGAAUAUUGGAGUAGAAUAUCGCGACUGAUAAGCGGAGCGGACCGAAC---U
.......((.((((((((((((((.(((((..(((((((.......---)))))))..))))).))((.((.((((.......))))))))....))))))))..))))..))...---. ( -39.40)
>DroSec_CAF1 3275 114 + 1
UUAAUCACGACCGCCGCUUAUCGCAAUGUGAGUUGCUGC---CGCU---GCAGCGAAACAUAUGGCGCAGAAUAUUGGAGUAGAAUAUCGCGACUGAUAAGCGGAACGGGCCGAACCGCU
.......((.((((((((((((((.(((((..(((((((---....---)))))))..))))).))((.((.((((.......))))))))....)))))))))..)))..))....... ( -40.00)
>DroAna_CAF1 8049 109 + 1
UUAAUCACGCUCGCCGCUUAUCG-ACGCUGAGUUGAUGUUGUUGUUGGCGGUGCGAAACAUAUGGCCGGG------GAAGUAGAACAUCGGGACUGAUAAGCGGAGAGCUCUGAAC----
....(((.((((.((((((((((-((.....)))((((((.((.(((((.(((.......))).))))).------)).....))))))......))))))))).))))..)))..---- ( -39.00)
>DroSim_CAF1 4102 114 + 1
UUAAUCACGACCGCCGCUUAUCGCAAUGUGAGUUGCUGC---CGCU---GCAGCGAAACAUAUGGCGCAGAAUAUUGGAGUAGAAUAUCGCGACUGAUAAGCGGAGCGGGCCGAACUGCU
.............(((((((((((.(((((..(((((((---....---)))))))..))))).))((.((.((((.......))))))))....)))))))))(((((......))))) ( -40.90)
>DroEre_CAF1 3547 110 + 1
UUAAUCACGAUUGCCCCUUAUCGCAAUAUGGGUUGC-GC---CGCU---GCACCGAAACAUAUGGCGCAGAAUCUUGGAGCUGAAUAUCGCGACUGAUAAGCGGCGAGGGCAGAGC---U
..........((((((.((..(((..(((.((((((-(.---..((---((.(((.......))).))))..((........))....))))))).))).)))..))))))))...---. ( -34.90)
>consensus
UUAAUCACGACCGCCGCUUAUCGCAAUGUGAGUUGCUGC___CGCU___GCAGCGAAACAUAUGGCGCAGAAUAUUGGAGUAGAAUAUCGCGACUGAUAAGCGGAGCGGGCCGAAC___U
..........((.(((((((((((.(((((..(((((((..........)))))))..))))).))............(((.(.....)...))))))))))))...))........... (-23.28 = -25.12 +   1.84)

alignment

secondary structure

dotplot

Window 5

Location	3,374,996 – 3,375,098
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.49
Mean single sequence MFE	-31.80
Consensus MFE	-17.18
Energy contribution	-20.10
Covariance contribution	2.92
Combinations/Pair	1.07
Mean z-score	-1.88
Structure conservation index	0.54
SVM decision value	0.13
SVM RNA-class probability	0.598047
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3374996 102 + 27905053
GCUCACAGAAGACAGCUGUUUCGCGUCUUCUGGGUAAUU--GCUUUUUAAUGAUCACUCUGCGUGCUCUCGUAAGUGAU--AUAAAGUCGCAGGUC-------A----UGUGGACGG---
.....((((((((.((......)))))))))).....((--((.(((((...((((((.((((......))))))))))--.)))))..))))(((-------.----....)))..--- ( -30.00)
>DroSec_CAF1 3389 102 + 1
GCUCACAGAAGACAGCUGUUUGGCGUCUUCUGUGUAAUU--GCUUUUUAAUGAUCACUCUGCGUGCUCUCGUAAGUGAU--AUAAAGUCGCAGGUU-------A----UGUGGACGG---
((.((((((((((.(((....))))))))))))).....--)).........((((((.((((......))))))))))--.....((((((....-------.----))).)))..--- ( -33.50)
>DroAna_CAF1 8158 119 + 1
ACAGACCGAAGACAGCUGUUUCGCCGGUUGUGUGUAAUUACGCUUUUUAACGCUC-CACUCACUGCUCUCGCAUGUGGCUCAAAAAGUCAGAUUUUCAGACUUAUCUUUGAGAUCUGUCA
(((((.((...(((((((......)))))))((((....)))).......))..(-(((....(((....))).))))(((((((((((.(.....).)))))...)))))).))))).. ( -27.70)
>DroSim_CAF1 4216 102 + 1
GCUCACAGAAGACAGCUGUUUCGCGUCUUCUGUGUAAUU--GCUUUUUAAUGAUCACUCUGCGUGCUCUCGUAAGUGAU--AUUAAGUAGCAGGUC-------A----UGUGGACGG---
...((((((((((.((......))))))))))))...((--(((.(((((((.(((((.((((......))))))))))--)))))).)))))(((-------.----....)))..--- ( -37.70)
>DroEre_CAF1 3657 102 + 1
GCUCACAGAAGACAGCUGUUUCGCGUCUUCCGUGUAAUU--GCUUUUUAAUGAUCACUCUGCGAGCUCUCGAAAGUGAU--AUAAAGUCGCAGUUC-------A----UGUGCACUG---
((.....((((((.((......))))))))((((.((((--((.(((((...((((((...(((....)))..))))))--.)))))..)))))))-------)----)).))....--- ( -30.10)
>consensus
GCUCACAGAAGACAGCUGUUUCGCGUCUUCUGUGUAAUU__GCUUUUUAAUGAUCACUCUGCGUGCUCUCGUAAGUGAU__AUAAAGUCGCAGGUC_______A____UGUGGACGG___
((.((((((((((.((......)))))))))))).......(((((......((((((.((((......))))))))))....))))).))............................. (-17.18 = -20.10 +   2.92)

alignment

secondary structure

dotplot

Window 6

Location	3,374,996 – 3,375,098
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.49
Mean single sequence MFE	-30.80
Consensus MFE	-15.76
Energy contribution	-17.72
Covariance contribution	1.96
Combinations/Pair	1.09
Mean z-score	-2.73
Structure conservation index	0.51
SVM decision value	1.93
SVM RNA-class probability	0.982950
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3374996 102 - 27905053
---CCGUCCACA----U-------GACCUGCGACUUUAU--AUCACUUACGAGAGCACGCAGAGUGAUCAUUAAAAAGC--AAUUACCCAGAAGACGCGAAACAGCUGUCUUCUGUGAGC
---..(..(((.----.-------....(((...((((.--(((((((.((......))..)))))))...))))..))--).......(((((((((......)).))))))))))..) ( -25.20)
>DroSec_CAF1 3389 102 - 1
---CCGUCCACA----U-------AACCUGCGACUUUAU--AUCACUUACGAGAGCACGCAGAGUGAUCAUUAAAAAGC--AAUUACACAGAAGACGCCAAACAGCUGUCUUCUGUGAGC
---.........----.-------....(((...((((.--(((((((.((......))..)))))))...))))..))--)....((((((((((((......)).))))))))))... ( -27.80)
>DroAna_CAF1 8158 119 - 1
UGACAGAUCUCAAAGAUAAGUCUGAAAAUCUGACUUUUUGAGCCACAUGCGAGAGCAGUGAGUG-GAGCGUUAAAAAGCGUAAUUACACACAACCGGCGAAACAGCUGUCUUCGGUCUGU
..((((((((((((...(((((.(.....).))))))))))(((...(((....)))(((.(((-(.(((((....)))))..)))).)))....)))(((((....)).)))))))))) ( -34.30)
>DroSim_CAF1 4216 102 - 1
---CCGUCCACA----U-------GACCUGCUACUUAAU--AUCACUUACGAGAGCACGCAGAGUGAUCAUUAAAAAGC--AAUUACACAGAAGACGCGAAACAGCUGUCUUCUGUGAGC
---..(((....----.-------))).((((..(((((--(((((((.((......))..))))))).)))))..)))--)....((((((((((((......)).))))))))))... ( -33.30)
>DroEre_CAF1 3657 102 - 1
---CAGUGCACA----U-------GAACUGCGACUUUAU--AUCACUUUCGAGAGCUCGCAGAGUGAUCAUUAAAAAGC--AAUUACACGGAAGACGCGAAACAGCUGUCUUCUGUGAGC
---....((...----.-------....(((...((((.--(((((((((((....))).))))))))...))))..))--)....((((((((((((......)).)))))))))).)) ( -33.40)
>consensus
___CCGUCCACA____U_______GACCUGCGACUUUAU__AUCACUUACGAGAGCACGCAGAGUGAUCAUUAAAAAGC__AAUUACACAGAAGACGCGAAACAGCUGUCUUCUGUGAGC
..................................((((...(((((((.............)))))))...))))...........((((((((((((......)).))))))))))... (-15.76 = -17.72 +   1.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:18 2006