Locus 107

Sequence ID	3L_DroMel_CAF1
Location	367,446 – 367,590
Length	144
Max. P	0.998084

overview

Window 1

Location	367,446 – 367,553
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.23
Mean single sequence MFE	-23.83
Consensus MFE	-7.51
Energy contribution	-9.07
Covariance contribution	1.56
Combinations/Pair	1.17
Mean z-score	-2.18
Structure conservation index	0.32
SVM decision value	1.07
SVM RNA-class probability	0.909958
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 367446 107 + 23771897
---AUAUUAUUUACCCUG------AACUACCUUCAAUGGCUA---GUUUUAUUGGGUCUGCCAGAUUGUUUU-UAAGGAUUGUUAAAUACAAACAUCCUAAUACUAGCAAUCCCAAUGAA
---...............------(((((((......)).))---)))((((((((..(((.((..((((..-..(((((.(((.......)))))))))))))).)))..)))))))). ( -24.10)
>DroSec_CAF1 21558 105 + 1
---AUAAUAUUUACCCUG------AACUACCAUCAAUGGCUG---AU-UAAUUG-GUCUGCCAGAUUGAUUU-UAGGGAUUGUUAAAUACAGAGAUCCUAAUACUAGCAAUCACAUUGAA
---...........((((------((.....(((((((((.(---((-(....)-))).))))..)))))))-))))((((((((.....((.....)).....))))))))........ ( -22.20)
>DroSim_CAF1 22373 106 + 1
---AUAAUAUUUACCCUG------AACUACCUUCAAUGGCUG---GU-CAAUUGGGUCUGCCAGAUUGAUUU-UAGGGAUUGUUAAACACAGACAUCCUAAUACUAGCAAUCACAUUGAA
---...............------........((((((((((---((-(((((.((....)).))))))...-..(((((.(((.......))))))))....))))).....)))))). ( -22.90)
>DroEre_CAF1 23029 104 + 1
GGUGUAUUA-UUAGCCUG------AAAUACCUUCAAACCCAG---GC-UUAUUGAGCCUGGUAGAUUGUUUC-UAGGGAUUGUUAAAUAC----AUUUUAAUACUAGCAAUCACAUCGAA
(((((....-....((((------(((((...((....((((---((-((...))))))))..)).))))))-.)))((((((((.....----..........)))))))))))))... ( -30.16)
>DroYak_CAF1 23213 114 + 1
UGUUUAUUA-UUACCCUUAUUAUUAACUGCCUUCAAACGCAGAUUGU-UUAUUUGGUCUGCCAGAUUGUUUUUUCGGUAUUGUUAAAUAC----ACUUUAAUACUAGCAAUCACAUUGAG
.........-......................((((..((((((((.-.....))))))))..(((((((.....(((((((........----....))))))))))))))...)))). ( -19.80)
>consensus
___AUAUUAUUUACCCUG______AACUACCUUCAAUGGCUG___GU_UUAUUGGGUCUGCCAGAUUGUUUU_UAGGGAUUGUUAAAUACA_A_AUCCUAAUACUAGCAAUCACAUUGAA
................................((((((((...................))))(((((((.....((((((((.....)))...)))))......)))))))...)))). ( -7.51 =  -9.07 +   1.56)

alignment

secondary structure

dotplot

Window 2

Location	367,477 – 367,590
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.66
Mean single sequence MFE	-25.65
Consensus MFE	-16.64
Energy contribution	-16.60
Covariance contribution	-0.04
Combinations/Pair	1.31
Mean z-score	-1.58
Structure conservation index	0.65
SVM decision value	0.06
SVM RNA-class probability	0.561636
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 367477 113 + 23771897
UA---GUUUUAUUGGGUCUGCCAGAUUGUUUU-UAAGGAUUGUUAAAUACAAACAUCCUAAUACUAGCAAUCCCAAUGAAU---CUCUAGCAUUAGCGAGUAUCUAUCAAAAGGCAGAAA
..---...........((((((.(((((((..-(((((((.(((.......))))))))..))..))))))).....((..---(((..((....)))))..))........)))))).. ( -25.00)
>DroSec_CAF1 21589 114 + 1
UG---AU-UAAUUG-GUCUGCCAGAUUGAUUU-UAGGGAUUGUUAAAUACAGAGAUCCUAAUACUAGCAAUCACAUUGAAUCAUCUCUAGCAUUAGCGAGUAUCUAACAAAAGGCAGAAC
..---..-......-.(((((((((.((((((-...(((((((((.....((.....)).....)))))))).)...))))))..))).((....))...............)))))).. ( -25.50)
>DroSim_CAF1 22404 112 + 1
UG---GU-CAAUUGGGUCUGCCAGAUUGAUUU-UAGGGAUUGUUAAACACAGACAUCCUAAUACUAGCAAUCACAUUGAAU---CUCUAGCAUUAGCGAGUAUCUAACAAAAGGCAGAAC
..---..-........((((((.(((((...(-(((((..((((.......))))))))))......))))).....((..---(((..((....)))))..))........)))))).. ( -24.70)
>DroEre_CAF1 23062 108 + 1
AG---GC-UUAUUGAGCCUGGUAGAUUGUUUC-UAGGGAUUGUUAAAUAC----AUUUUAAUACUAGCAAUCACAUCGAAG---CCUUGGCAUUAGCGGGGAUCUAACCAGAAACAGAAA
((---((-((...))))))......(((((((-(.((((((((((.....----..........)))))))).........---.(((.((....)).)))......))))))))))... ( -27.26)
>DroYak_CAF1 23252 111 + 1
AGAUUGU-UUAUUUGGUCUGCCAGAUUGUUUUUUCGGUAUUGUUAAAUAC----ACUUUAAUACUAGCAAUCACAUUGAGA---CUUUAGCAUUAGUGGGUUUCUA-UCAGAGGCAGAAA
.......-........((((((.(((((((.....(((((((........----....)))))))))))))).....((((---((...((....)).))))))..-.....)))))).. ( -25.80)
>consensus
UG___GU_UUAUUGGGUCUGCCAGAUUGUUUU_UAGGGAUUGUUAAAUACA_A_AUCCUAAUACUAGCAAUCACAUUGAAU___CUCUAGCAUUAGCGAGUAUCUAACAAAAGGCAGAAA
................((((((.(((((((.....((((((((.....)))...)))))......)))))))............(((..((....)))))............)))))).. (-16.64 = -16.60 +  -0.04)

alignment

secondary structure

dotplot

Window 3

Location	367,477 – 367,590
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.66
Mean single sequence MFE	-28.51
Consensus MFE	-15.99
Energy contribution	-17.99
Covariance contribution	2.00
Combinations/Pair	1.10
Mean z-score	-3.11
Structure conservation index	0.56
SVM decision value	3.00
SVM RNA-class probability	0.998084
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 367477 113 - 23771897
UUUCUGCCUUUUGAUAGAUACUCGCUAAUGCUAGAG---AUUCAUUGGGAUUGCUAGUAUUAGGAUGUUUGUAUUUAACAAUCCUUA-AAAACAAUCUGGCAGACCCAAUAAAAC---UA
..((((((..((((((((((.((.((((((((((..---((((....))))..))))))))))))))))))).(((((......)))-))..)))...))))))...........---.. ( -32.20)
>DroSec_CAF1 21589 114 - 1
GUUCUGCCUUUUGUUAGAUACUCGCUAAUGCUAGAGAUGAUUCAAUGUGAUUGCUAGUAUUAGGAUCUCUGUAUUUAACAAUCCCUA-AAAUCAAUCUGGCAGAC-CAAUUA-AU---CA
(.((((((..(((((((((((((.((((((((((..((.((.....)).))..)))))))))))).....)))))))))))......-..........)))))).-).....-..---.. ( -32.57)
>DroSim_CAF1 22404 112 - 1
GUUCUGCCUUUUGUUAGAUACUCGCUAAUGCUAGAG---AUUCAAUGUGAUUGCUAGUAUUAGGAUGUCUGUGUUUAACAAUCCCUA-AAAUCAAUCUGGCAGACCCAAUUG-AC---CA
..((((((..(((((((((((((.((((((((((..---(((......)))..)))))))))))).....)))))))))))......-..........))))))........-..---.. ( -31.07)
>DroEre_CAF1 23062 108 - 1
UUUCUGUUUCUGGUUAGAUCCCCGCUAAUGCCAAGG---CUUCGAUGUGAUUGCUAGUAUUAAAAU----GUAUUUAACAAUCCCUA-GAAACAAUCUACCAGGCUCAAUAA-GC---CU
....(((((((((...((..((.((....))...))---..)).....(((((..(((((......----)))))...))))).)))-)))))).......(((((.....)-))---)) ( -24.70)
>DroYak_CAF1 23252 111 - 1
UUUCUGCCUCUGA-UAGAAACCCACUAAUGCUAAAG---UCUCAAUGUGAUUGCUAGUAUUAAAGU----GUAUUUAACAAUACCGAAAAAACAAUCUGGCAGACCAAAUAA-ACAAUCU
..((((((...((-(.(........((((((((.((---((.......))))..))))))))..(.----(((((....)))))).......).))).))))))........-....... ( -22.00)
>consensus
UUUCUGCCUUUUGUUAGAUACUCGCUAAUGCUAGAG___AUUCAAUGUGAUUGCUAGUAUUAGGAU_U_UGUAUUUAACAAUCCCUA_AAAACAAUCUGGCAGACCCAAUAA_AC___CA
..((((((..(((((((((((...((((((((((.......((.....))...)))))))))).......))))))))))).................))))))................ (-15.99 = -17.99 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:38 2006