Locus 7132

Sequence ID	2L_DroMel_CAF1
Location	19,989,363 – 19,989,555
Length	192
Max. P	0.994264

overview

Window 3

Location	19,989,363 – 19,989,482
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.41
Mean single sequence MFE	-38.40
Consensus MFE	-36.70
Energy contribution	-36.22
Covariance contribution	-0.48
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.96
SVM decision value	2.27
SVM RNA-class probability	0.991423
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19989363 119 + 22407834
GAAGUGAGUACUAAAUGCACCCAGCUGGCGCUCAUAUU-UGUAUGUUCGCUAAUUUGCAGCUGAAUGGAGCUUAAACGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUU
..((((((((.....(((.(.(((((((((..((((..-..))))..))))..((((((((((..(.........)..))))))))))......))))).)))).......)))).)))) ( -35.90)
>DroSec_CAF1 172148 119 + 1
GAAGUGAGUACUAAAUGCACCCAGCUGGCGCUCAUAUU-UGUAUGUUCGCUAAUUUGCAGCUGAAUGUCGCUUAAAUGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUU
..((((((((.....(((.(.(((((((((..((((..-..))))..))))..((((((((((.((.........)).))))))))))......))))).)))).......)))).)))) ( -36.40)
>DroSim_CAF1 174718 119 + 1
GAAGUGAGUACUAAAUGCACCCAGCUGGCGCUCAUAUU-UGUAUGUUCGCUAAUUUGCAGCUGAAUGGCGCUUAAAUGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUU
..((((((((.....(((.(.(((((((((..((((..-..))))..))))..((((((((((.((.........)).))))))))))......))))).)))).......)))).)))) ( -36.40)
>DroEre_CAF1 170215 120 + 1
GAAGUGAGUACUAAAUGCGCCCAGCUGGCGUUCAUACUCCGUGUGUUCGCUAAUUUGCAGCUGAAUGGCGCUUAGACGCAGCUGCGGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUU
..((((((((....((..((((((((((((..(((((...)))))..))))..((((((((((.....(.....)...))))))))))......))))).)))..))....)))).)))) ( -40.70)
>DroYak_CAF1 171042 120 + 1
GAAGUGAGUACUAAAUGCGCCCAGCUGGCGCUCAUAUUUUGUAUGUUCGCUAAUUUGCAGCUGAAUGGCGCUUAAGCGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUU
..((((((((....((..((((((((((((..(((((...)))))..))))..(((((((((.....((((....)))))))))))))......))))).)))..))....)))).)))) ( -42.60)
>consensus
GAAGUGAGUACUAAAUGCACCCAGCUGGCGCUCAUAUU_UGUAUGUUCGCUAAUUUGCAGCUGAAUGGCGCUUAAACGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUU
..((((((((.....(((.(.(((((((((..(((((...)))))..))))..((((((((((...............))))))))))......))))).)))).......)))).)))) (-36.70 = -36.22 +  -0.48)

alignment

secondary structure

dotplot

Window 4

Location	19,989,363 – 19,989,482
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.41
Mean single sequence MFE	-36.06
Consensus MFE	-33.92
Energy contribution	-34.28
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.75
Structure conservation index	0.94
SVM decision value	2.46
SVM RNA-class probability	0.994264
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19989363 119 - 22407834
AAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCGUUUAAGCUCCAUUCAGCUGCAAAUUAGCGAACAUACA-AAUAUGAGCGCCAGCUGGGUGCAUUUAGUACUCACUUC
..((.(((((......((((((((((....(((.((((((((.((.........)).)))))))).))).(((..((((..-..))))..))).))))))).)))....))))))).... ( -35.60)
>DroSec_CAF1 172148 119 - 1
AAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCAUUUAAGCGACAUUCAGCUGCAAAUUAGCGAACAUACA-AAUAUGAGCGCCAGCUGGGUGCAUUUAGUACUCACUUC
..((.(((((......((((((((((....(((.((((((((.((.........)).)))))))).))).(((..((((..-..))))..))).))))))).)))....))))))).... ( -35.30)
>DroSim_CAF1 174718 119 - 1
AAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCAUUUAAGCGCCAUUCAGCUGCAAAUUAGCGAACAUACA-AAUAUGAGCGCCAGCUGGGUGCAUUUAGUACUCACUUC
((((((((.((.((...(((.(((...)))))).))))))))))))...(((((...((((((.......(((..((((..-..))))..))))))))))))))................ ( -35.31)
>DroEre_CAF1 170215 120 - 1
AAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCCGCAGCUGCGUCUAAGCGCCAUUCAGCUGCAAAUUAGCGAACACACGGAGUAUGAACGCCAGCUGGGCGCAUUUAGUACUCACUUC
..((.(((((......((((((((((.........((((((((((....)))).....))))))................((.((....)).))))))))).)))....))))))).... ( -33.80)
>DroYak_CAF1 171042 120 - 1
AAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCGCUUAAGCGCCAUUCAGCUGCAAAUUAGCGAACAUACAAAAUAUGAGCGCCAGCUGGGCGCAUUUAGUACUCACUUC
..((.(((((......((((((((((....(((.(((((((((((....)))).....))))))).))).(((..((((.....))))..))).))))))).)))....))))))).... ( -40.30)
>consensus
AAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCGUUUAAGCGCCAUUCAGCUGCAAAUUAGCGAACAUACA_AAUAUGAGCGCCAGCUGGGUGCAUUUAGUACUCACUUC
..((.(((((......((((((((((....(((.((((((((.((.........)).)))))))).))).(((..((((.....))))..))).))))))).)))....))))))).... (-33.92 = -34.28 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	19,989,402 – 19,989,520
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.54
Mean single sequence MFE	-39.22
Consensus MFE	-33.56
Energy contribution	-33.60
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.04
Structure conservation index	0.86
SVM decision value	1.95
SVM RNA-class probability	0.983576
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19989402 118 + 22407834
GUAUGUUCGCUAAUUUGCAGCUGAAUGGAGCUUAAACGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAAAAGCAGGCUA-ACUGGGGAAAAUGUGGUGG-
.......(((((.((((((((((..(.........)..))))))))))(((((.((((....(((((((......)))))))(((.....))).)))).-.))))).......))))).- ( -40.00)
>DroSec_CAF1 172187 119 + 1
GUAUGUUCGCUAAUUUGCAGCUGAAUGUCGCUUAAAUGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAAAAGCAGGCUA-ACUGGGGAAAAUCGGGUGGG
......(((((..((((((((((.((.........)).))))))))))(((((.((((....(((((((......)))))))(((.....))).)))).-.)))))........))))). ( -40.20)
>DroSim_CAF1 174757 119 + 1
GUAUGUUCGCUAAUUUGCAGCUGAAUGGCGCUUAAAUGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAAAAGCAGGCUA-ACUGGGGAAAAUCGGGUGGG
......(((((..((((((((((.((.........)).))))))))))(((((.((((....(((((((......)))))))(((.....))).)))).-.)))))........))))). ( -40.20)
>DroEre_CAF1 170255 110 + 1
GUGUGUUCGCUAAUUUGCAGCUGAAUGGCGCUUAGACGCAGCUGCGGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAA-AGCAGGCUAGACUGGGUGGAA---------
(((....)))....(((((((((.....(.....)...)))))))))((((((.((((....(((((((......)))))))(((....-))).))))...))))))....--------- ( -38.10)
>DroYak_CAF1 171082 111 + 1
GUAUGUUCGCUAAUUUGCAGCUGAAUGGCGCUUAAGCGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGAAACACCAGGCUAGACUGGGAAAAA---------
.............(((((((((.....((((....)))))))))))))(((((.((((.((.(((((((......))))))).))(......).))))...))))).....--------- ( -37.60)
>consensus
GUAUGUUCGCUAAUUUGCAGCUGAAUGGCGCUUAAACGCAGCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAAAAGCAGGCUA_ACUGGGGAAAAU__GGUGG_
.............((((((((((...............))))))))))(((((.((((....(((((((......)))))))(((.....))).))))...))))).............. (-33.56 = -33.60 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	19,989,402 – 19,989,520
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.54
Mean single sequence MFE	-30.58
Consensus MFE	-26.78
Energy contribution	-26.74
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.86
Structure conservation index	0.88
SVM decision value	1.72
SVM RNA-class probability	0.973779
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19989402 118 - 22407834
-CCACCACAUUUUCCCCAGU-UAGCCUGCUUUUCCAGCCAAAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCGUUUAAGCUCCAUUCAGCUGCAAAUUAGCGAACAUAC
-.............(((((.-.(((..(((.....))).....((((........))))....))).)))))..((((((((.((.........)).))))))))............... ( -28.40)
>DroSec_CAF1 172187 119 - 1
CCCACCCGAUUUUCCCCAGU-UAGCCUGCUUUUCCAGCCAAAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCAUUUAAGCGACAUUCAGCUGCAAAUUAGCGAACAUAC
......((......(((((.-.(((..(((.....))).....((((........))))....))).)))))..((((((((.((.........)).))))))))......))....... ( -28.60)
>DroSim_CAF1 174757 119 - 1
CCCACCCGAUUUUCCCCAGU-UAGCCUGCUUUUCCAGCCAAAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCAUUUAAGCGCCAUUCAGCUGCAAAUUAGCGAACAUAC
......((......(((((.-.(((..(((.....))).....((((........))))....))).)))))..((((((((.((.........)).))))))))......))....... ( -28.60)
>DroEre_CAF1 170255 110 - 1
---------UUCCACCCAGUCUAGCCUGCU-UUCCAGCCAAAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCCGCAGCUGCGUCUAAGCGCCAUUCAGCUGCAAAUUAGCGAACACAC
---------((((((((((...(((..(((-....))).....((((........))))....))).))))))..((((((((((....)))).....))))))......).)))..... ( -31.50)
>DroYak_CAF1 171082 111 - 1
---------UUUUUCCCAGUCUAGCCUGGUGUUUCAGCCAAAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCGCUUAAGCGCCAUUCAGCUGCAAAUUAGCGAACAUAC
---------.....(((((...(((.((((......))))...((((........))))....))).)))))..(((((((((((....)))).....)))))))............... ( -35.80)
>consensus
_CCACC__AUUUUCCCCAGU_UAGCCUGCUUUUCCAGCCAAAUGCAGUAUGACAUCUGCCUCAGCUUCUGGGUCUGCAGCUGCGUUUAAGCGCCAUUCAGCUGCAAAUUAGCGAACAUAC
..............(((((...((((((......)))......((((........))))....))).)))))...(((((((.((.........)).)))))))................ (-26.78 = -26.74 +  -0.04)

alignment

secondary structure

dotplot

Window 7

Location	19,989,442 – 19,989,555
Length	113
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	81.93
Mean single sequence MFE	-34.98
Consensus MFE	-23.24
Energy contribution	-23.36
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-1.59
Structure conservation index	0.66
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19989442 113 + 22407834
GCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAAAAGCAGGCUA-ACUGGGGAAAAUGUGGUGG-GAAAUGGGGGAGGGGAGGAGGUAGCUUUUCCACCA
((..((..(((((.((((....(((((((......)))))))(((.....))).)))).-.))))).....))..))..-...........(((((((((....))))))).)). ( -37.60)
>DroSec_CAF1 172227 112 + 1
GCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAAAAGCAGGCUA-ACUGGGGAAAAUCGGGUGGGGAAAUACGG--GGAGAGGAGGCAGCUUUUCCACCA
.(..(.(((((((.((((....(((((((......)))))))(((.....))).)))).-.))))).....))..)..)........((--(((((((......))))))).)). ( -34.30)
>DroSim_CAF1 174797 112 + 1
GCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAAAAGCAGGCUA-ACUGGGGAAAAUCGGGUGGGGAAAUGGGG--GGAGAGCAGGCAGCUUUUCCACCA
.(..(.(((((((.((((....(((((((......)))))))(((.....))).)))).-.))))).....))..)..).....(((.(--(((((((.....)))))))).))) ( -37.50)
>DroEre_CAF1 170295 95 + 1
GCUGCGGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAA-AGCAGGCUAGACUGGGUGGAA---------------AGG--GGAGG--AGGCUGCUUUUCCCCCA
.......((((((.((((....(((((((......)))))))(((....-))).))))...))))))....---------------.((--(((((--((....))))))))).. ( -37.60)
>DroYak_CAF1 171122 98 + 1
GCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGAAACACCAGGCUAGACUGGGAAAAA---------------GGG--GGAGACCAGGCAAUCUUUUCACCA
(((......((...(((..((((((........)))).))..)))......((((......))))......---------------))(--(....)).)))............. ( -27.90)
>consensus
GCUGCAGACCCAGAAGCUGAGGCAGAUGUCAUACUGCAUUUGGCUGGAAAAGCAGGCUA_ACUGGGGAAAAU__GGUGG_GAAAU_GGG__GGAGAGCAGGCAGCUUUUCCACCA
........(((((.((((....(((((((......)))))))(((.....))).))))...))))).........................((((((........)))))).... (-23.24 = -23.36 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:16 2006