Locus 744

Sequence ID	3L_DroMel_CAF1
Location	2,232,251 – 2,232,438
Length	187
Max. P	0.967534

overview

Window 9

Location	2,232,251 – 2,232,358
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.73
Mean single sequence MFE	-32.82
Consensus MFE	-21.50
Energy contribution	-22.22
Covariance contribution	0.72
Combinations/Pair	1.14
Mean z-score	-2.11
Structure conservation index	0.66
SVM decision value	1.61
SVM RNA-class probability	0.967534
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2232251 107 + 23771897
UGAAGGUAGGCCAGGUAGACCAUCUUGUGUGGCUUAACCACUAAGAU-------------UGUUACCAAUUUCAGAACAAGUGUCAGAAUCUACGCCUGGAAUUGGCCUGCUCUCGCCUU
.((..(((((((.(((.(((.((((((.((((.....))))))))))-------------.))))))((((((((.....((((........)))))))))))))))))))..))..... ( -40.40)
>DroSec_CAF1 13187 106 + 1
UGAAGGUAGACCAGG-AUUCCGUCUUGUGUGGCUAACCCACUUAGAU-------------UGUUACCAAUUUCAGAACAAGUGCCAGAAGCUACGCCUGGAAUUGGCCUGCUCUCGCCUU
..((((((((.((((-.....((((...((((.....))))..))))-------------.....((((((((((.....((((.....)).))..)))))))))))))).))).))))) ( -33.30)
>DroSim_CAF1 13263 106 + 1
UGAAGGUAGACCAGG-AUUCUGUCUUGUGUGGCUUACCCACAUAGAU-------------UGUUACCAAUUUCAGAACAAGUGUCAGAAUCUUCGCCUGGAAUUGGCCUGCUCUCGCCUU
..((((((((.((((-.....((((.((((((.....))))))))))-------------.....((((((((((...(((.........)))...)))))))))))))).))).))))) ( -34.20)
>DroEre_CAF1 26240 117 + 1
UGAAGGUAGACCGGG-AUUCCAUCUG--AUGGCCCACCCACUUCAGUCUCCACCACGCUCUAAUUCCAAUUCCAGAGCAAGUGUCAGAGUCUACGCCUGGAAAUGGCCUGCUCCCACCUC
((..(((((.(((((-...((((...--)))))))..(((....((.(((...((((((((............)))))..)))...))).)).....)))....)).)))))..)).... ( -27.00)
>DroYak_CAF1 13714 109 + 1
UGAAGGUAGACCAGG-ACUCCAUCUCGUAUGGCCUACC-ACU--------CACCACU-UCCUAUUCCAAUUACAGGAUAAGUGCCAGAGUCUACGCCUGGAAAUGGCCUGCUCUCACCUC
...(((((((.((((-...((((.((....(((.....-(((--------(..((((-((((...........))))..))))...))))....)))..)).)))))))).))).)))). ( -29.20)
>consensus
UGAAGGUAGACCAGG_AUUCCAUCUUGUGUGGCUUACCCACUUAGAU_____________UGUUACCAAUUUCAGAACAAGUGUCAGAAUCUACGCCUGGAAUUGGCCUGCUCUCGCCUU
...(((((((.((((.............((((.....))))........................((((((((((.....(((..........))))))))))))))))).))).)))). (-21.50 = -22.22 +   0.72)

alignment

secondary structure

dotplot

Window 0

Location	2,232,251 – 2,232,358
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.73
Mean single sequence MFE	-35.38
Consensus MFE	-20.54
Energy contribution	-20.74
Covariance contribution	0.20
Combinations/Pair	1.15
Mean z-score	-1.74
Structure conservation index	0.58
SVM decision value	0.26
SVM RNA-class probability	0.658660
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2232251 107 - 23771897
AAGGCGAGAGCAGGCCAAUUCCAGGCGUAGAUUCUGACACUUGUUCUGAAAUUGGUAACA-------------AUCUUAGUGGUUAAGCCACACAAGAUGGUCUACCUGGCCUACCUUCA
.((((.((.(.((((((....((((.......))))...(((((..(((.((((....))-------------)).)))((((.....))))))))).)))))).))).))))....... ( -31.90)
>DroSec_CAF1 13187 106 - 1
AAGGCGAGAGCAGGCCAAUUCCAGGCGUAGCUUCUGGCACUUGUUCUGAAAUUGGUAACA-------------AUCUAAGUGGGUUAGCCACACAAGACGGAAU-CCUGGUCUACCUUCA
((((..(((.((((...(((((.......((.....)).(((((......((((....))-------------))....((((.....)))))))))..)))))-)))).))).)))).. ( -29.70)
>DroSim_CAF1 13263 106 - 1
AAGGCGAGAGCAGGCCAAUUCCAGGCGAAGAUUCUGACACUUGUUCUGAAAUUGGUAACA-------------AUCUAUGUGGGUAAGCCACACAAGACAGAAU-CCUGGUCUACCUUCA
((((..(((.((((((.......)))...(((((((....(((((((......)).))))-------------)(((.((((((....)).)))))))))))))-)))).))).)))).. ( -33.20)
>DroEre_CAF1 26240 117 - 1
GAGGUGGGAGCAGGCCAUUUCCAGGCGUAGACUCUGACACUUGCUCUGGAAUUGGAAUUAGAGCGUGGUGGAGACUGAAGUGGGUGGGCCAU--CAGAUGGAAU-CCCGGUCUACCUUCA
((((((((....((((...((((....(((.((((..(((..(((((((........))))))))))..)))).)))...))))..))))..--....(((...-.))).)))))))).. ( -40.50)
>DroYak_CAF1 13714 109 - 1
GAGGUGAGAGCAGGCCAUUUCCAGGCGUAGACUCUGGCACUUAUCCUGUAAUUGGAAUAGGA-AGUGGUG--------AGU-GGUAGGCCAUACGAGAUGGAGU-CCUGGUCUACCUUCA
(((((.(((.(((((((((((..(((.((.((((.(.((((..((((((.......))))))-)))).))--------)))-..)).)))....)))))))...-)))).)))))))).. ( -41.60)
>consensus
AAGGCGAGAGCAGGCCAAUUCCAGGCGUAGAUUCUGACACUUGUUCUGAAAUUGGUAACA_____________AUCUAAGUGGGUAAGCCACACAAGAUGGAAU_CCUGGUCUACCUUCA
((((..(((.((((((((((.((((...((.........))...)))).))))))........................((((.....)))).............)))).))).)))).. (-20.54 = -20.74 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	2,232,291 – 2,232,398
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.03
Mean single sequence MFE	-33.68
Consensus MFE	-22.68
Energy contribution	-23.00
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-1.58
Structure conservation index	0.67
SVM decision value	0.01
SVM RNA-class probability	0.537164
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2232291 107 + 23771897
CUAAGAU-------------UGUUACCAAUUUCAGAACAAGUGUCAGAAUCUACGCCUGGAAUUGGCCUGCUCUCGCCUUCGUGAGCUGGCCCUGAUGUCGAAUGUGGUUCAAAUUAUUU
....(((-------------(...((((..(((.((......(((((..((((....))))...((((.((((.((....)).)))).))))))))).)))))..))))...)))).... ( -28.30)
>DroSec_CAF1 13226 107 + 1
CUUAGAU-------------UGUUACCAAUUUCAGAACAAGUGCCAGAAGCUACGCCUGGAAUUGGCCUGCUCUCGCCUUCGGGAGCUGGCCCUGAUGUCGAAUGUGGUUCAAAUUAUUU
....(((-------------(...((((..(((.((.(((((.((((.........)))).)))((((.(((((((....))))))).))))....)))))))..))))...)))).... ( -31.60)
>DroSim_CAF1 13302 107 + 1
CAUAGAU-------------UGUUACCAAUUUCAGAACAAGUGUCAGAAUCUUCGCCUGGAAUUGGCCUGCUCUCGCCUUCGGGAGCUGGCCCUGAUGUCGAAUGUGGUUCAAAUUAUUU
....(((-------------(...((((..(((.((......(((((..(((......)))...((((.(((((((....))))))).))))))))).)))))..))))...)))).... ( -31.40)
>DroEre_CAF1 26277 120 + 1
CUUCAGUCUCCACCACGCUCUAAUUCCAAUUCCAGAGCAAGUGUCAGAGUCUACGCCUGGAAAUGGCCUGCUCCCACCUCCGGGAGCUGGCGCUGAUGUCGAAUGUGGUCCAGAUCAUUU
.....((((..((((((.((......((.((((((.((..(((........))))))))))).))(((.((((((......)))))).))).........)).))))))..))))..... ( -41.20)
>DroYak_CAF1 13752 111 + 1
CU--------CACCACU-UCCUAUUCCAAUUACAGGAUAAGUGCCAGAGUCUACGCCUGGAAAUGGCCUGCUCUCACCUCCGGGAGCUGGCGCUGAUGUCGAAUGUGGUGCAAAUCAUUU
..--------(((((((-((....(((.......)))..(((((((........(((.......)))..((((((......)))))))))))))......))).)))))).......... ( -35.90)
>consensus
CUUAGAU_____________UGUUACCAAUUUCAGAACAAGUGUCAGAAUCUACGCCUGGAAUUGGCCUGCUCUCGCCUUCGGGAGCUGGCCCUGAUGUCGAAUGUGGUUCAAAUUAUUU
..........................(((((((((.....(((..........))))))))))))(((.((((((......)))))).))).............(((((....))))).. (-22.68 = -23.00 +   0.32)

alignment

secondary structure

dotplot

Window 2

Location	2,232,318 – 2,232,438
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.42
Mean single sequence MFE	-37.50
Consensus MFE	-28.80
Energy contribution	-30.28
Covariance contribution	1.48
Combinations/Pair	1.09
Mean z-score	-2.18
Structure conservation index	0.77
SVM decision value	1.07
SVM RNA-class probability	0.909669
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2232318 120 - 23771897
AGCAGAAUCACGUGAGCUACCAUCAAUAGUUCCACAUGCCAAAUAAUUUGAACCACAUUCGACAUCAGGGCCAGCUCACGAAGGCGAGAGCAGGCCAAUUCCAGGCGUAGAUUCUGACAC
.((((((((..((((((((.......))))).)))(((((.......(((((.....)))))......((((.((((.((....)).)))).)))).......))))).))))))).).. ( -39.60)
>DroSec_CAF1 13253 120 - 1
AGCAGAAUCACGUGAGCUACCAUCAAGAGUUCCACAUGCCAAAUAAUUUGAACCACAUUCGACAUCAGGGCCAGCUCCCGAAGGCGAGAGCAGGCCAAUUCCAGGCGUAGCUUCUGGCAC
..(((((.(..(((((((.........)))).)))(((((.......(((((.....)))))......((((.((((.((....)).)))).)))).......))))).).))))).... ( -33.80)
>DroSim_CAF1 13329 120 - 1
AGCAGAAUCACGUGAGCUACCAUCAAGAGUUCCACAUGCCAAAUAAUUUGAACCACAUUCGACAUCAGGGCCAGCUCCCGAAGGCGAGAGCAGGCCAAUUCCAGGCGAAGAUUCUGACAC
.((((((((..(((((((.........)))).))).((((.......(((((.....)))))......((((.((((.((....)).)))).)))).......))))..))))))).).. ( -37.10)
>DroEre_CAF1 26317 120 - 1
AACAGAAUCAUGUGAGCUACCAUCAGUAGUUCCACCUGCCAAAUGAUCUGGACCACAUUCGACAUCAGCGCCAGCUCCCGGAGGUGGGAGCAGGCCAUUUCCAGGCGUAGACUCUGACAC
..((((.((.((.(((((((.....)))))))))...(((...((((.(.((......)).).))))(.(((.(((((((....))))))).)))).......)))...)).)))).... ( -40.60)
>DroYak_CAF1 13783 120 - 1
AACAGAAUCACGUGGGAUACCAUCAACAGUUCCACAUGCCAAAUGAUUUGCACCACAUUCGACAUCAGCGCCAGCUCCCGGAGGUGAGAGCAGGCCAUUUCCAGGCGUAGACUCUGGCAC
..((((.((..(((((((..........)))))))((((((((((..((((.((((.((((.....(((....)))..)))).))).).))))..)))))...))))).)).)))).... ( -36.40)
>consensus
AGCAGAAUCACGUGAGCUACCAUCAAGAGUUCCACAUGCCAAAUAAUUUGAACCACAUUCGACAUCAGGGCCAGCUCCCGAAGGCGAGAGCAGGCCAAUUCCAGGCGUAGAUUCUGACAC
..(((((((..(((((((.........)))).)))(((((.......(((((.....)))))......((((.((((.((....)).)))).)))).......))))).))))))).... (-28.80 = -30.28 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:03 2006