Locus 8426

Sequence ID	3L_DroMel_CAF1
Location	22,133,670 – 22,133,808
Length	138
Max. P	0.929580

overview

Window 0

Location	22,133,670 – 22,133,770
Length	100
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	77.63
Mean single sequence MFE	-17.93
Consensus MFE	-11.47
Energy contribution	-12.05
Covariance contribution	0.58
Combinations/Pair	1.14
Mean z-score	-1.90
Structure conservation index	0.64
SVM decision value	1.11
SVM RNA-class probability	0.917008
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22133670 100 + 23771897
AAUUUUUCGUCUU--UAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUUGUAUAAUGCGUUGGGCUAUCUCUGACGUCCCCGCCC--CCUUACCUACAUCAAAUG
.......((((.(--((.....)))....(((.....((((((((((...)))))))))).))).......)))).........--.................. ( -15.00)
>DroGri_CAF1 136987 81 + 1
AAUUUUUCGUCUUUUUAUAAUUUCAUUUUACUAUGAAAACGCAUUAUUAUGUAAUGCGCUGGGCUG-CGCU--CCGCGACGCUC--------------------
.......((((.........((((((......))))))..(((((((...)))))))((.((((..-.)))--).))))))...-------------------- ( -19.70)
>DroSec_CAF1 119492 100 + 1
AAUUUUUCGUCUU--UAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUUGUAUAAUGCGUUGGGCUAUCUCUGACUGCCCCGCCC--CCUUACCAACAUCAAACG
.............--..............((......((((((((((...))))))))))((((..((...))..)))).))..--.................. ( -17.40)
>DroSim_CAF1 127568 100 + 1
AAUUUUUCGUCUU--UAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUGGUAUAAUGCGUUGGGCUAUGUCUGACUGCCCCGCCC--CCUUACCUACAUCAAACG
.............--..............((......((((((((((...))))))))))((((...........)))).))..--.................. ( -17.00)
>DroEre_CAF1 119367 88 + 1
AAUUUUUCGUCUU--UAUAAUUUCAUUUUGCUAUAACAACGCAUUAUUGUAUAAUGCGUUGGGCU-AUUCUCACAGCCCC-------------ACCCCCCAGCG
.............--..............(((....(((((((((((...)))))))))))((((-........))))..-------------.......))). ( -20.50)
>DroYak_CAF1 166958 101 + 1
AAUUUUUCGUCUU--UAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUUGUAUAAUGCGUUGGGCUUGCUCUCUCAGCUACGCCAAACGCUA-CUCCCCCAAACG
.............--..............((......((((((((((...)))))))))).(((..(((.....)))...)))....))..-............ ( -18.00)
>consensus
AAUUUUUCGUCUU__UAUAAUUUAAUUUUGCUAUAAAAACGCAUUAUUGUAUAAUGCGUUGGGCUAUCUCUGACAGCCCCGCCC__CCUUA_CUACAUCAAACG
.....................................((((((((((...))))))))))((((...........))))......................... (-11.47 = -12.05 +   0.58)

alignment

secondary structure

dotplot

Window 1

Location	22,133,670 – 22,133,770
Length	100
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	77.63
Mean single sequence MFE	-23.53
Consensus MFE	-11.80
Energy contribution	-12.72
Covariance contribution	0.92
Combinations/Pair	1.13
Mean z-score	-2.43
Structure conservation index	0.50
SVM decision value	1.20
SVM RNA-class probability	0.929580
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22133670 100 - 23771897
CAUUUGAUGUAGGUAAGG--GGGCGGGGACGUCAGAGAUAGCCCAACGCAUUAUACAAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUA--AAGACGAAAAAUU
..((((.((((((...((--(((((....))))........)))((((((((((...)))))))))))))))).))))...........--............. ( -23.00)
>DroGri_CAF1 136987 81 - 1
--------------------GAGCGUCGCGG--AGCG-CAGCCCAGCGCAUUACAUAAUAAUGCGUUUUCAUAGUAAAAUGAAAUUAUAAAAAGACGAAAAAUU
--------------------...((((..((--.((.-..)))).((((((((.....))))))))((((((......)))))).........))))....... ( -18.60)
>DroSec_CAF1 119492 100 - 1
CGUUUGAUGUUGGUAAGG--GGGCGGGGCAGUCAGAGAUAGCCCAACGCAUUAUACAAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUA--AAGACGAAAAAUU
(((((........(((..--..((.((((.(((...))).))))((((((((((...))))))))))......))....))).......--.)))))....... ( -25.29)
>DroSim_CAF1 127568 100 - 1
CGUUUGAUGUAGGUAAGG--GGGCGGGGCAGUCAGACAUAGCCCAACGCAUUAUACCAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUA--AAGACGAAAAAUU
(((((..(((((.(((..--..((.((((...........))))((((((((((...))))))))))......))....)))..)))))--.)))))....... ( -24.00)
>DroEre_CAF1 119367 88 - 1
CGCUGGGGGGU-------------GGGGCUGUGAGAAU-AGCCCAACGCAUUAUACAAUAAUGCGUUGUUAUAGCAAAAUGAAAUUAUA--AAGACGAAAAAUU
.((((......-------------.(((((((....))-)))))((((((((((...))))))))))....))))..............--............. ( -26.20)
>DroYak_CAF1 166958 101 - 1
CGUUUGGGGGAG-UAGCGUUUGGCGUAGCUGAGAGAGCAAGCCCAACGCAUUAUACAAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUA--AAGACGAAAAAUU
((((..(...((-(.(((((.(((...(((.....)))..))).))))))))...)...))))(((((((((((..........)))))--))))))....... ( -24.10)
>consensus
CGUUUGAUGUAG_UAAGG__GGGCGGGGCAGUCAGAGAUAGCCCAACGCAUUAUACAAUAAUGCGUUUUUAUAGCAAAAUUAAAUUAUA__AAGACGAAAAAUU
......................((.((((...........))))(((((((((.....)))))))))......))............................. (-11.80 = -12.72 +   0.92)

alignment

secondary structure

dotplot

Window 2

Location	22,133,708 – 22,133,808
Length	100
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	78.66
Mean single sequence MFE	-24.74
Consensus MFE	-17.44
Energy contribution	-18.12
Covariance contribution	0.68
Combinations/Pair	1.09
Mean z-score	-1.63
Structure conservation index	0.71
SVM decision value	0.46
SVM RNA-class probability	0.746690
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22133708 100 + 23771897
GCAUUAUUGUAUAAUGCGUUGGGCUAUCUCUGACGUCCCCGCCC--CCUUACCUACAUCAAAUGCAGAGUACCAUCAUCAGCGUCAGCAUUCGCAUC-AGCAU-
(((((((...)))))))(((((((.....(((((((........--...(((((.(((...))).)).))).........))))))).....)).))-)))..- ( -22.35)
>DroSec_CAF1 119530 101 + 1
GCAUUAUUGUAUAAUGCGUUGGGCUAUCUCUGACUGCCCCGCCC--CCUUACCAACAUCAAACGCAGAGUGCUAUCAUCAGCGUCAGCAUUCGCAUCCAGCAU-
(((((((...)))))))((.((((..((...))..)))).))..--.................((.(((((((..(......)..))))))))).........- ( -24.70)
>DroSim_CAF1 127606 102 + 1
GCAUUAUGGUAUAAUGCGUUGGGCUAUGUCUGACUGCCCCGCCC--CCUUACCUACAUCAAACGCAGAGUGCCAUCAUCAGCGUCAGCAUUCGCAUCCAGCAUC
((...(((((((..((((((((((...((......))...))))--..............))))))..))))))).....(((........))).....))... ( -26.03)
>DroEre_CAF1 119405 82 + 1
GCAUUAUUGUAUAAUGCGUUGGGCU-AUUCUCACAGCCCC-------------ACCCCCCAGCGCAGAGUGCCAUCAUCAGCGACAGCACUCGCAU--------
(((((((...)))))))((.(((((-........))))).-------------))........((.((((((..((......))..))))))))..-------- ( -27.40)
>DroYak_CAF1 166996 95 + 1
GCAUUAUUGUAUAAUGCGUUGGGCUUGCUCUCUCAGCUACGCCAAACGCUA-CUCCCCCAAACGCAGAGUGCCAUCAUCAGCGUCAGCAUUCGCAU--------
(((((((...)))))))(((.(((..(((.....)))...))).)))....-...........((.((((((...(......)...))))))))..-------- ( -23.20)
>consensus
GCAUUAUUGUAUAAUGCGUUGGGCUAUCUCUGACAGCCCCGCCC__CCUUACCUACAUCAAACGCAGAGUGCCAUCAUCAGCGUCAGCAUUCGCAUC_AGCAU_
(((((((...)))))))((.((((...........)))).)).....................((.((((((...(......)...)))))))).......... (-17.44 = -18.12 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:05 2006