Locus 555

Sequence ID	2L_DroMel_CAF1
Location	1,727,019 – 1,727,375
Length	356
Max. P	0.999292

overview

Window 3

Location	1,727,019 – 1,727,123
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	81.29
Mean single sequence MFE	-22.45
Consensus MFE	-14.18
Energy contribution	-14.26
Covariance contribution	0.08
Combinations/Pair	1.12
Mean z-score	-1.68
Structure conservation index	0.63
SVM decision value	-0.02
SVM RNA-class probability	0.524363
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1727019 104 - 22407834
ACCGUGGAGAAAGUCACACCCGAAUGGGGAUAUAUGUAUAAGUUUACACCACUCACAGCUCAAAUUGCAAGUGACUUACAUGCUCACAGCUACAAUUCUUUGCA
...(..(((((((((((.(((.....))).....((((......)))).........((.......))..)))))))....((.....))......))))..). ( -24.80)
>DroSec_CAF1 9154 104 - 1
UCCGCGGAGAAAGUCACACCCGAAUGGGGAUAUAUGUAUAACUUUACACCACUUACCGCUCAAAUUGCAAGUGACUUUCAUGCUCACAGCUAUAGUUCUUUGCA
...((((((((((((((.(((.....))).....((((......)))).........((.......))..)))))))))..((.....))........))))). ( -26.40)
>DroSim_CAF1 9359 95 - 1
UCCGUGGAGAAAGUCACACCCGAAUGGGGAUAUAUGUAUAACUUUACACCACUCACCGCUCAAAUUGCAAGU---------GCUCACAGCUACAAUUCUUUGCA
...(..(((((..........((.(((.((....((((......))))....)).))).)).........((---------((.....)).))..)))))..). ( -17.50)
>DroEre_CAF1 9169 95 - 1
UCCGUGGAGAAAGUCACACCCAAGUGGGGAUACA-----AAACUUACACCACUCGCCGCUCAAAUUGCAAGUGA----CAUGCUCACGCCUACAAUUCUCUGCA
...(..(((((.(((((.....(((((.......-----.........)))))....((.......))..))))----)..((....))......)))))..). ( -24.79)
>DroYak_CAF1 9941 85 - 1
UCCGUGGAGAAAGUCACACCCAAGUGGGGAUACA----UAAACUUACACCACUCGCCACUCAAAUUGCAAGUGA---------------UUACAAUUCUUUGCA
...(..(((((((((((...(((((((.((....----..............)).))))).....))...))))---------------))....)))))..). ( -18.77)
>consensus
UCCGUGGAGAAAGUCACACCCGAAUGGGGAUAUAUGUAUAAAUUUACACCACUCACCGCUCAAAUUGCAAGUGA____CAUGCUCACAGCUACAAUUCUUUGCA
...((((((((.......(((....))).....................((((....((.......)).))))......................)))))))). (-14.18 = -14.26 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	1,727,123 – 1,727,234
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.82
Mean single sequence MFE	-25.48
Consensus MFE	-22.00
Energy contribution	-22.28
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-2.71
Structure conservation index	0.86
SVM decision value	3.49
SVM RNA-class probability	0.999292
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1727123 111 + 22407834
AUA------AUCUCGAAAUGCCCCUCCUGAGUUUUCUAUAUUUAAUUUGUCUUCAAAUUUCAGUUAAAUAUUUCUAUAAUAAUUUAGAGUCACUGACACUGGCGGCAUUUCCCGCUU---
...------.....((((((((((...((..............((((((....))))))(((((.......(((((........)))))..)))))))..)).))))))))......--- ( -21.70)
>DroSec_CAF1 9258 111 + 1
AUA------AUGUCGAAACGCCCCUCCUGCGUUUUCUAUAUUUAAUUUGUCUUCAGAUUUCAGUUAAAUAUUUCUAUAAUUAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU---
...------.(((((((((((.......)))))))..((((((((((.(((....)))...))))))))))(((((........))))).....)))).((((((......))))))--- ( -24.40)
>DroSim_CAF1 9454 111 + 1
AUA------AUGUCGAAAUGCCCCUCCUGCGUUUUCUAUAUUUAAUUUGUCUUCAGAUUUCAGUUAAAUAUUUCUAUAAUUAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU---
...------.....((((((((...((((.(((....((((((((((.(((....)))...))))))))))(((((........))))).....))).)))).))))))))......--- ( -26.40)
>DroEre_CAF1 9264 114 + 1
AUA------GUCUCGAAAUGCCCCCACUGCGAUUUCUAUAUUUAAUUUGUCUUCAGAUUUCAGUUAAAUAUUUCUAAAAUUAUUUGGAGUCACUGACACGGGCGGCAUUUCCCGCUUUGC
..(------((...(((((((((((............((((((((((.(((....)))...))))))))))(((((((....)))))))..........))).))))))))..))).... ( -27.70)
>DroYak_CAF1 10026 120 + 1
AUACUCGUAUUCUCGAAAUGCCCCCUCUGCGUUUUCUAUAUUUAAUUUGUCUUAAGAUUUCAGUUAAAUAUUUCUAAAAUUAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUUUGC
..............(((((((((((............((((((((((.(((....)))...))))))))))(((((((....)))))))..........))).))))))))......... ( -27.20)
>consensus
AUA______AUCUCGAAAUGCCCCUCCUGCGUUUUCUAUAUUUAAUUUGUCUUCAGAUUUCAGUUAAAUAUUUCUAUAAUUAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU___
..............(((((((((((............((((((((((.(((....)))...))))))))))(((((........)))))..........))).))))))))......... (-22.00 = -22.28 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	1,727,157 – 1,727,262
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.25
Mean single sequence MFE	-26.16
Consensus MFE	-19.88
Energy contribution	-19.96
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-2.17
Structure conservation index	0.76
SVM decision value	1.00
SVM RNA-class probability	0.897315
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1727157 105 + 22407834
UUUAAUUUGUCUUCAAAUUUCAGUUAAAUAUUUCUAUAAUAAUUUAGAGUCACUGACACUGGCGGCAUUUCCCGCUU--------UUCCGCUUAUCUCAGUGGGAGAGUUUUC-------
.......((((.(((....(((((.......(((((........)))))..)))))...))).))))......((((--------(((((((......)))))))))))....------- ( -23.10)
>DroSec_CAF1 9292 104 + 1
UUUAAUUUGUCUUCAGAUUUCAGUUAAAUAUUUCUAUAAUUAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU--------UUCCGCUU-UCUCAGUGGGAGAGUUUUC-------
...((((((....))))))(((((.......(((((........)))))..)))))...(((........)))((((--------(((((((.-....)))))))))))....------- ( -23.50)
>DroSim_CAF1 9488 104 + 1
UUUAAUUUGUCUUCAGAUUUCAGUUAAAUAUUUCUAUAAUUAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU--------UUCCGCUU-UCUCAGUGGGAGAGUUUUC-------
...((((((....))))))(((((.......(((((........)))))..)))))...(((........)))((((--------(((((((.-....)))))))))))....------- ( -23.50)
>DroEre_CAF1 9298 112 + 1
UUUAAUUUGUCUUCAGAUUUCAGUUAAAUAUUUCUAAAAUUAUUUGGAGUCACUGACACGGGCGGCAUUUCCCGCUUUGCCGCUUUUCCGCUG-UCUCAGUGGGAGAGUUUUC-------
.......((((....((((((((.(((............))).))))))))...)))).((((((......))))))....((((((((((((-...))))))))))))....------- ( -30.70)
>DroYak_CAF1 10066 119 + 1
UUUAAUUUGUCUUAAGAUUUCAGUUAAAUAUUUCUAAAAUUAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUUUGCCGCUUUUCCGCUU-UCUCAGUGGGAGAGUUUUCAGUUUUC
(((((((.(((....)))...)))))))...(((((((....)))))))..(((((...((((((......))))))....(((((((((((.-....)))))))))))..))))).... ( -30.00)
>consensus
UUUAAUUUGUCUUCAGAUUUCAGUUAAAUAUUUCUAUAAUUAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU________UUCCGCUU_UCUCAGUGGGAGAGUUUUC_______
...((((((....))))))(((((.......(((((........)))))..)))))...((((((......))))))........(((((((......)))))))............... (-19.88 = -19.96 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	1,727,197 – 1,727,302
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.25
Mean single sequence MFE	-32.65
Consensus MFE	-25.58
Energy contribution	-25.82
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.94
Structure conservation index	0.78
SVM decision value	0.94
SVM RNA-class probability	0.887105
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1727197 105 + 22407834
AAUUUAGAGUCACUGACACUGGCGGCAUUUCCCGCUU--------UUCCGCUUAUCUCAGUGGGAGAGUUUUC-------AGUUUGCUCUCGCCGAACAACCGAAUGACCUCUAAGCUAC
..((((((((((..........((((...........--------..(((((......)))))((((((....-------.....))))))))))..........))).))))))).... ( -29.25)
>DroSec_CAF1 9332 104 + 1
UAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU--------UUCCGCUU-UCUCAGUGGGAGAGUUUUC-------AGUUUGCUCUCGCCGAACAACCGAAUGACCUCUAAGCUAC
..((((((((((......(((.((((...........--------..(((((.-....)))))((((((....-------.....)))))))))).....)))..))).))))))).... ( -30.80)
>DroSim_CAF1 9528 104 + 1
UAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU--------UUCCGCUU-UCUCAGUGGGAGAGUUUUC-------AGUUUGCUCUCGCCGAACAACCGAAUGACCUCUAAGCUAC
..((((((((((......(((.((((...........--------..(((((.-....)))))((((((....-------.....)))))))))).....)))..))).))))))).... ( -30.80)
>DroEre_CAF1 9338 112 + 1
UAUUUGGAGUCACUGACACGGGCGGCAUUUCCCGCUUUGCCGCUUUUCCGCUG-UCUCAGUGGGAGAGUUUUC-------AGUUUUCUCUCGCCGAACAACCGAAUGACCUCUAAGCUAC
..((((((((((..(((((((((((((..........))))))....))).))-))((.(((((((((.....-------....))))))))).)).........))).))))))).... ( -37.70)
>DroYak_CAF1 10106 119 + 1
UAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUUUGCCGCUUUUCCGCUU-UCUCAGUGGGAGAGUUUUCAGUUUUCAGUUUUCUCUCUGCGAACAACCGAAUGACCUCUAAGCUAC
..((((((((((......(((((((((..........))))))(((((((((.-....))))))))).......((((.(((........))).))))..)))..))).))))))).... ( -34.70)
>consensus
UAUUUAGAGUCACUGACACGGGCGGCAUUUCCCGCUU________UUCCGCUU_UCUCAGUGGGAGAGUUUUC_______AGUUUGCUCUCGCCGAACAACCGAAUGACCUCUAAGCUAC
..((((((((((((((...((((((......................))))))...)))))))(((((..................)))))..................))))))).... (-25.58 = -25.82 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	1,727,197 – 1,727,302
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.25
Mean single sequence MFE	-35.07
Consensus MFE	-25.53
Energy contribution	-26.13
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.73
SVM decision value	0.48
SVM RNA-class probability	0.751336
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1727197 105 - 22407834
GUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU-------GAAAACUCUCCCACUGAGAUAAGCGGAA--------AAGCGGGAAAUGCCGCCAGUGUCAGUGACUCUAAAUU
.....((((((....(((((((((((.....)))).))))-------)))........((((((.((..((((..--------............))))..)).)))))).))))))... ( -33.04)
>DroSec_CAF1 9332 104 - 1
GUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU-------GAAAACUCUCCCACUGAGA-AAGCGGAA--------AAGCGGGAAAUGCCGCCCGUGUCAGUGACUCUAAAUA
.....((((((....(((((((((((.....)))).))))-------)))........((((((..-..((((..--------..((((......)))))))).)))))).))))))... ( -35.70)
>DroSim_CAF1 9528 104 - 1
GUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU-------GAAAACUCUCCCACUGAGA-AAGCGGAA--------AAGCGGGAAAUGCCGCCCGUGUCAGUGACUCUAAAUA
.....((((((....(((((((((((.....)))).))))-------)))........((((((..-..((((..--------..((((......)))))))).)))))).))))))... ( -35.70)
>DroEre_CAF1 9338 112 - 1
GUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGAAAACU-------GAAAACUCUCCCACUGAGA-CAGCGGAAAAGCGGCAAAGCGGGAAAUGCCGCCCGUGUCAGUGACUCCAAAUA
........(..((((((((((.....((.(((((......-------.....))))))))))))((-((.(((....((((((..........))))))))))))).)))))..)..... ( -34.80)
>DroYak_CAF1 10106 119 - 1
GUAGCUUAGAGGUCAUUCGGUUGUUCGCAGAGAGAAAACUGAAAACUGAAAACUCUCCCACUGAGA-AAGCGGAAAAGCGGCAAAGCGGGAAAUGCCGCCCGUGUCAGUGACUCUAAAUA
.....((((((....(((((((.....(((........)))..)))))))........((((((..-..((((....((((((..........)))))))))).)))))).))))))... ( -36.10)
>consensus
GUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU_______GAAAACUCUCCCACUGAGA_AAGCGGAA________AAGCGGGAAAUGCCGCCCGUGUCAGUGACUCUAAAUA
.....((((((.((((((.(((.(((((.(((((..................)))))...)))))...))).))...........(((((........)))))....))))))))))... (-25.53 = -26.13 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	1,727,234 – 1,727,339
Length	105
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	91.33
Mean single sequence MFE	-35.44
Consensus MFE	-30.77
Energy contribution	-30.33
Covariance contribution	-0.44
Combinations/Pair	1.09
Mean z-score	-2.23
Structure conservation index	0.87
SVM decision value	2.72
SVM RNA-class probability	0.996579
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1727234 105 - 22407834
UUCGCUGGACGCCUCACUUUGGGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU-------GAAAACUCUCCCACUGAGAUAAGCGGAA-----
((((((......((((...((((..((((((((((.......))))))))))(((((((((((.....)))).))))-------)))......)))).))))...)))))).----- ( -36.70)
>DroSec_CAF1 9369 104 - 1
UUCGCUGGACGCCUCACUUUGAGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU-------GAAAACUCUCCCACUGAGA-AAGCGGAA-----
((((((......((((....((((.((((((((((.......))))))))))(((((((((((.....)))).))))-------))).))))......)))).-.)))))).----- ( -34.10)
>DroSim_CAF1 9565 104 - 1
UUCGCUGGACGCCUCACUUUGAGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU-------GAAAACUCUCCCACUGAGA-AAGCGGAA-----
((((((......((((....((((.((((((((((.......))))))))))(((((((((((.....)))).))))-------))).))))......)))).-.)))))).----- ( -34.10)
>DroEre_CAF1 9378 109 - 1
UCUGCUGGACGCCUCACUUUGGGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGAAAACU-------GAAAACUCUCCCACUGAGA-CAGCGGAAAAGCG
((((((((((.((.......)))))((((((((((.......))))))))))((((((.....((.(((((......-------.....))))))))))))).-)))))))...... ( -37.40)
>DroYak_CAF1 10146 116 - 1
UUUGCUGGACGCCUCACUUUGGGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGCAGAGAGAAAACUGAAAACUGAAAACUCUCCCACUGAGA-AAGCGGAAAAGCG
...(((...(((((((...((((..((((((((((.......))))))))))(((((((.....(((........)))..)))))))......)))).)))).-..)))....))). ( -34.90)
>consensus
UUCGCUGGACGCCUCACUUUGGGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU_______GAAAACUCUCCCACUGAGA_AAGCGGAA_____
(((((((((((((((.....))(..((((((((((.......))))))))))..))).)))))((.(((((..................))))))).........))))))...... (-30.77 = -30.33 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	1,727,262 – 1,727,375
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	94.51
Mean single sequence MFE	-34.03
Consensus MFE	-27.52
Energy contribution	-27.68
Covariance contribution	0.16
Combinations/Pair	1.10
Mean z-score	-1.71
Structure conservation index	0.81
SVM decision value	0.60
SVM RNA-class probability	0.796351
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1727262 113 - 22407834
ACUUCCGUUUUUCGCAACUUUUCCACGUACUGCGGCUUCGCUGGACGCCUCACUUUGGGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU
......((((..((((((........))..))))((((((((((((((((......)))).((((((((((.......)))))))))).......))))))))).))))))). ( -35.80)
>DroSec_CAF1 9396 113 - 1
ACUUCCGUUUUUUGCAACUUUUCCACGUACUUCGGCUUCGCUGGACGCCUCACUUUGAGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU
..........(((((..........((.....))..(((((((((((((((.....))(..((((((((((.......))))))))))..))).))))))))))).))))).. ( -33.80)
>DroSim_CAF1 9592 113 - 1
ACUUCCGUUUUUUGCAACUUUUCCACGUACUUCGGCUUCGCUGGACGCCUCACUUUGAGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU
..........(((((..........((.....))..(((((((((((((((.....))(..((((((((((.......))))))))))..))).))))))))))).))))).. ( -33.80)
>DroEre_CAF1 9410 113 - 1
ACUUUCCUUUUUCGCAACUUUUCCACGUCGUGCGGCUCUGCUGGACGCCUCACUUUGGGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGAAAACU
.......((((((((.......((.((..(((.(((((.....)).))).)))..)).(..((((((((((.......))))))))))..))).......))))))))..... ( -33.84)
>DroYak_CAF1 10185 113 - 1
ACUUUCGUUUUUCGCAACUUUUCCACGUAGUGCGGCUUUGCUGGACGCCUCACUUUGGGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGCAGAGAGAAAACU
.(((((.......((((((...(((...((((.(((..........))).)))).)))(..((((((((((.......))))))))))..))))))).....)))))...... ( -32.90)
>consensus
ACUUCCGUUUUUCGCAACUUUUCCACGUACUGCGGCUUCGCUGGACGCCUCACUUUGGGUCUGACCUUUAAAAGUAGCUUAGAGGUCAUUCGGUUGUUCGGCGAGAGCAAACU
.........................((.....))(((((((((((((((((.....))(..((((((((((.......))))))))))..))).))))))))).))))..... (-27.52 = -27.68 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:36 2006