Locus 1660

Sequence ID	2L_DroMel_CAF1
Location	4,485,362 – 4,485,507
Length	145
Max. P	0.999915

overview

Window 6

Location	4,485,362 – 4,485,473
Length	111
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	73.16
Mean single sequence MFE	-23.00
Consensus MFE	-13.44
Energy contribution	-15.30
Covariance contribution	1.86
Combinations/Pair	1.28
Mean z-score	-2.61
Structure conservation index	0.58
SVM decision value	3.11
SVM RNA-class probability	0.998470
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4485362 111 + 22407834
AAAAGCAAACUCAAAAGUAAAGCGUAUUUAAAUAAGUUGGAAUAAGGAGUACCA--AAAGCUGGGGUGGGUUGAGCUAUUGGACAGCUGUCUAACAAAUCAACCCACUCUAAG
........((((........(((.(((....))).)))........))))....--.....(((((((((((((....((((((....))))))....))))))))))))).. ( -32.59)
>DroSec_CAF1 670 89 + 1
AAAAGCAAACUCAAAAAUAAAGCGUAUUUAAUUAAU---UAAUGAGGAGUCCCA--AAAGAUAGGGUGGGUUGAUCU-------------------AAUCGACUCACUCUAGG
.........((((..(((.((..........)).))---)..))))........--.....((((((((((((((..-------------------.)))))))))))))).. ( -19.10)
>DroSim_CAF1 675 87 + 1
AAAAGCAAACUCAAAAAUAAAGCGUAUUUAAAUAAGCUGAAAUGACGAGUUCCA--AAAGCUAG-----GUUGAGCU-------------------AAUCAACCCACUCUAGG
...(((.(((((........(((.(((....))).)))........)))))...--...))).(-----(((((...-------------------..))))))......... ( -14.49)
>DroEre_CAF1 676 107 + 1
AAAAGCAAACUCAAAAGUAAAGGGUAU---AAUAAGCUGGAAUGA---AAUCCACCAAAGCUAUGGUGGAUUGAGUUAAUAGACAGCUGUCUAACAAAUCAACCCACUUUAAG
.............(((((...((((..---..........(((..---(((((((((......)))))))))..)))..(((((....)))))........)))))))))... ( -26.90)
>DroYak_CAF1 659 111 + 1
AAAAGCAAACUCAAAAGUAAAGCGUAUUUAAAUAAGCUGGAAUGAGGAGAUCCA--AAAGCUAUGUUGGGUUGAGUUAAUAGACAUCUGUCCAACAAAUCAACCCACUCUGGA
...(((....(((....(..(((.(((....))).)))..).)))((....)).--...)))....((((((((.......(((....))).......))))))))....... ( -21.94)
>consensus
AAAAGCAAACUCAAAAGUAAAGCGUAUUUAAAUAAGCUGGAAUGAGGAGUUCCA__AAAGCUAGGGUGGGUUGAGCUA_U_GACA_CUGUC_AACAAAUCAACCCACUCUAGG
.............................................................(((((((((((((.....(((((....))))).....))))))))))))).. (-13.44 = -15.30 +   1.86)

alignment

secondary structure

dotplot

Window 7

Location	4,485,362 – 4,485,473
Length	111
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	73.16
Mean single sequence MFE	-23.55
Consensus MFE	-9.84
Energy contribution	-11.76
Covariance contribution	1.92
Combinations/Pair	1.21
Mean z-score	-2.59
Structure conservation index	0.42
SVM decision value	2.87
SVM RNA-class probability	0.997473
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4485362 111 - 22407834
CUUAGAGUGGGUUGAUUUGUUAGACAGCUGUCCAAUAGCUCAACCCACCCCAGCUUU--UGGUACUCCUUAUUCCAACUUAUUUAAAUACGCUUUACUUUUGAGUUUGCUUUU
.((((((((((((((.(((((.(((....))).))))).)))))))))........(--(((...........))))....)))))....((...(((....)))..)).... ( -25.80)
>DroSec_CAF1 670 89 - 1
CCUAGAGUGAGUCGAUU-------------------AGAUCAACCCACCCUAUCUUU--UGGGACUCCUCAUUA---AUUAAUUAAAUACGCUUUAUUUUUGAGUUUGCUUUU
....(((.((((((((.-------------------..))).......((.......--.))))))))))....---.............((((.......))))........ ( -13.40)
>DroSim_CAF1 675 87 - 1
CCUAGAGUGGGUUGAUU-------------------AGCUCAAC-----CUAGCUUU--UGGAACUCGUCAUUUCAGCUUAUUUAAAUACGCUUUAUUUUUGAGUUUGCUUUU
((.((((((((((((..-------------------...)))))-----))).))))--.))((((((.......(((.(((....))).))).......))))))....... ( -21.34)
>DroEre_CAF1 676 107 - 1
CUUAAAGUGGGUUGAUUUGUUAGACAGCUGUCUAUUAACUCAAUCCACCAUAGCUUUGGUGGAUU---UCAUUCCAGCUUAUU---AUACCCUUUACUUUUGAGUUUGCUUUU
(((((((((((((((.(((.(((((....))))).))).))))))))).........(.((((..---....)))).).....---............))))))......... ( -28.00)
>DroYak_CAF1 659 111 - 1
UCCAGAGUGGGUUGAUUUGUUGGACAGAUGUCUAUUAACUCAACCCAACAUAGCUUU--UGGAUCUCCUCAUUCCAGCUUAUUUAAAUACGCUUUACUUUUGAGUUUGCUUUU
(((((((((((((((.(((.(((((....))))).))).)))))))).......)))--))))............(((..(((((((...........)))))))..)))... ( -29.21)
>consensus
CCUAGAGUGGGUUGAUUUGUU_GACAG_UGUC_A_UAGCUCAACCCACCCUAGCUUU__UGGAACUCCUCAUUCCAGCUUAUUUAAAUACGCUUUACUUUUGAGUUUGCUUUU
..(((((((((((((.(((.(((((....))))).))).))))))).....((((....(((......)))....))))...........))))))................. ( -9.84 = -11.76 +   1.92)

alignment

secondary structure

dotplot

Window 8

Location	4,485,395 – 4,485,507
Length	112
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	72.86
Mean single sequence MFE	-31.68
Consensus MFE	-17.16
Energy contribution	-22.34
Covariance contribution	5.18
Combinations/Pair	1.33
Mean z-score	-3.48
Structure conservation index	0.54
SVM decision value	4.53
SVM RNA-class probability	0.999915
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4485395 112 + 22407834
AAGUUGGAAUAAGGAGUACCA--AAAGCUGGGGUGGGUUGAGCUAUUGGACAGCUGUCUAACAAAUCAACCCACUCUAAGGCUUCUUUUGGUCUUUCCACCAGCCAUAUCUUAC
..(((((.....((((.((((--((((((((((((((((((....((((((....))))))....))))))))))))..))))...))))))..)))).))))).......... ( -44.40)
>DroSec_CAF1 703 90 + 1
AAU---UAAUGAGGAGUCCCA--AAAGAUAGGGUGGGUUGAUCU-------------------AAUCGACUCACUCUAGGGCUCCAUGUGAUCUUACUACCAGCCAUAUCUUAC
...---......(((((((..--.....((((((((((((((..-------------------.)))))))))))))))))))))(((((..............)))))..... ( -29.15)
>DroSim_CAF1 708 88 + 1
AAGCUGAAAUGACGAGUUCCA--AAAGCUAG-----GUUGAGCU-------------------AAUCAACCCACUCUAGGGCUCCAUGUGAUCUUUCCACCAGCCAUAUCUUAC
..((((.......((((((..--..((...(-----(((((...-------------------..))))))..))...))))))...(((.......))))))).......... ( -19.00)
>DroEre_CAF1 706 111 + 1
AAGCUGGAAUGA---AAUCCACCAAAGCUAUGGUGGAUUGAGUUAAUAGACAGCUGUCUAACAAAUCAACCCACUUUAAGGCUCCUUGUGAUCUUUCCACCAGUCAUAUCUUAC
..(((((...((---((..(((...((((..(((((.((((.....(((((....))))).....)))).)))))....))))....)))...))))..))))).......... ( -29.00)
>DroYak_CAF1 692 112 + 1
AAGCUGGAAUGAGGAGAUCCA--AAAGCUAUGUUGGGUUGAGUUAAUAGACAUCUGUCCAACAAAUCAACCCACUCUGGAGCUCCUUUUGAUCUUUCCACCAGCCAUAUCUUAC
..(((((..((..((((((.(--((((((..(.((((((((.......(((....))).......))))))))..)...))))..))).))))))..))))))).......... ( -36.84)
>consensus
AAGCUGGAAUGAGGAGUUCCA__AAAGCUAGGGUGGGUUGAGCUA_U_GACA_CUGUC_AACAAAUCAACCCACUCUAGGGCUCCUUGUGAUCUUUCCACCAGCCAUAUCUUAC
..(((((.(((((((((((.........(((((((((((((.....(((((....))))).....))))))))))))))))))))))))((....))..))))).......... (-17.16 = -22.34 +   5.18)

alignment

secondary structure

dotplot

Window 9

Location	4,485,395 – 4,485,507
Length	112
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	72.86
Mean single sequence MFE	-31.88
Consensus MFE	-16.06
Energy contribution	-20.22
Covariance contribution	4.16
Combinations/Pair	1.19
Mean z-score	-2.45
Structure conservation index	0.50
SVM decision value	2.60
SVM RNA-class probability	0.995653
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4485395 112 - 22407834
GUAAGAUAUGGCUGGUGGAAAGACCAAAAGAAGCCUUAGAGUGGGUUGAUUUGUUAGACAGCUGUCCAAUAGCUCAACCCACCCCAGCUUU--UGGUACUCCUUAUUCCAACUU
........(((.....(((...((((((((....((..(.(((((((((.(((((.(((....))).))))).))))))))))..))))))--))))..))).....))).... ( -36.20)
>DroSec_CAF1 703 90 - 1
GUAAGAUAUGGCUGGUAGUAAGAUCACAUGGAGCCCUAGAGUGAGUCGAUU-------------------AGAUCAACCCACCCUAUCUUU--UGGGACUCCUCAUUA---AUU
....(((...((.....))...)))....(((((((.((((((.((.(((.-------------------..))).)).)))....)))..--.))).))))......---... ( -18.80)
>DroSim_CAF1 708 88 - 1
GUAAGAUAUGGCUGGUGGAAAGAUCACAUGGAGCCCUAGAGUGGGUUGAUU-------------------AGCUCAAC-----CUAGCUUU--UGGAACUCGUCAUUUCAGCUU
....((.(((((..((((.....))))...(((.((.((((((((((((..-------------------...)))))-----))).))))--.))..)))))))).))..... ( -25.80)
>DroEre_CAF1 706 111 - 1
GUAAGAUAUGACUGGUGGAAAGAUCACAAGGAGCCUUAAAGUGGGUUGAUUUGUUAGACAGCUGUCUAUUAACUCAAUCCACCAUAGCUUUGGUGGAUU---UCAUUCCAGCUU
...........((((..((((..((((...((((......(((((((((.(((.(((((....))))).))).)))))))))....))))..)))).))---))...))))... ( -35.40)
>DroYak_CAF1 692 112 - 1
GUAAGAUAUGGCUGGUGGAAAGAUCAAAAGGAGCUCCAGAGUGGGUUGAUUUGUUGGACAGAUGUCUAUUAACUCAACCCAACAUAGCUUU--UGGAUCUCCUCAUUCCAGCUU
.........((((((..((.(((((...(((((((......((((((((.(((.(((((....))))).))).))))))))....))))))--).)))))..))...)))))). ( -43.20)
>consensus
GUAAGAUAUGGCUGGUGGAAAGAUCACAAGGAGCCCUAGAGUGGGUUGAUUUGUU_GACAG_UGUC_A_UAGCUCAACCCACCCUAGCUUU__UGGAACUCCUCAUUCCAGCUU
.........((((((..((....(((...(((((..(((.(((((((((.(((.(((((....))))).))).))))))))).))))))))..)))......))...)))))). (-16.06 = -20.22 +   4.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:49 2006