Locus 3000

Sequence ID	3R_DroMel_CAF1
Location	8,032,269 – 8,032,401
Length	132
Max. P	0.987775

overview

Window 7

Location	8,032,269 – 8,032,377
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.49
Mean single sequence MFE	-35.59
Consensus MFE	-28.29
Energy contribution	-28.07
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-1.45
Structure conservation index	0.79
SVM decision value	1.38
SVM RNA-class probability	0.948017
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8032269 108 + 27905053
G--------GCUUUUUUGCCGCCAUCAAAAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAAGAGGCAUAUAAGG----UC
(--------(((((..(((((((((.......(((((.......)))))))))).(.((.(((((.......)))))..)))(((((.......)))))....))))...))))----)) ( -37.51)
>DroGri_CAF1 149932 105 + 1
UUAUUCUCGAGUUCUUUGG----CCCAAAAUGUGCGCCUCUUUAGCUCAGAGGCAGAGCACUGGUCUUGUAAACCAGCGGUCGUGAGUUCAAUUCUCACAGGAGGCAU----------A-
....((((.........((----(((.....((((((((((.......))))))...))))((((.......))))).))))(((((.......)))))..))))...----------.- ( -31.00)
>DroSim_CAF1 99670 109 + 1
G--------GCUUUUUUGCCGCCAUCAAAACGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGUCGUGAGUUCAAUCCUCACAGGAGGCAUU---UGUAACGA
(--------((......)))(((.((.......((.((......((((.......)))).(((((.......))))))).))(((((.......)))))..)))))...---........ ( -33.60)
>DroWil_CAF1 136041 101 + 1
U--------AGUUAUGGAACUCACAUUAAAUGUGAGCCUCUUUAGCUCAGUGGUAGAGCACUGGUCUUGUAAACCAGGGGUCGUGAGUUCAAUCCUCACAGGAGGCAUC-----------
.--------.......((((((((........(((((.......)))))......((.(.(((((.......))))).).))))))))))...((((....))))....----------- ( -32.00)
>DroMoj_CAF1 169412 111 + 1
UUAUGCCAGAGCUGUGCGA----UCCCAAUCGCCGGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAAU-AGGG----AC
...(((((....)).))).----((((.((.((((((((.....((((.......)))).(((((.......))))))))))(((((.......)))))....))).))-.)))----). ( -41.90)
>DroAna_CAF1 106473 108 + 1
G--------ACUUUUGGGCCGCCCUCGAUAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAAGAGGCAACUGGGG----CC
.--------.......((((.((.(((.....)))(((((((..((((.......))))...((((((........))))))(((((.......))))))))))))....))))----)) ( -37.50)
>consensus
G________ACUUUUGUGCCGCCCUCAAAAUGUGAGCCUCUUUAGCUCAGUGGCAGAGCACUGGUCUUGUAAACCAGGGGCCGUGAGUUCAAUUCUCACAGGAGGCAUC___GG____AC
...................................(((((((..((((.......)))).(((((.......))))).....(((((.......)))))))))))).............. (-28.29 = -28.07 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	8,032,269 – 8,032,377
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.49
Mean single sequence MFE	-36.00
Consensus MFE	-26.90
Energy contribution	-26.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.75
SVM decision value	2.09
SVM RNA-class probability	0.987775
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8032269 108 - 27905053
GA----CCUUAUAUGCCUCUUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUUUUGAUGGCGGCAAAAAAGC--------C
(.----((......((((((((((((.......))))).....((((((.....)))))).((((.......))))..)))))))(((.....))).)))(((......))--------) ( -32.30)
>DroGri_CAF1 149932 105 - 1
-U----------AUGCCUCCUGUGAGAAUUGAACUCACGACCGCUGGUUUACAAGACCAGUGCUCUGCCUCUGAGCUAAAGAGGCGCACAUUUUGGG----CCAAAGAACUCGAGAAUAA
-.----------.(((.....(((((.......)))))((.((((((((.....)))))))).)).((((((.......)))))))))..(((((((----........))))))).... ( -35.10)
>DroSim_CAF1 99670 109 - 1
UCGUUACA---AAUGCCUCCUGUGAGGAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACGUUUUGAUGGCGGCAAAAAAGC--------C
..((((((---((.(((((.((((((.......))))))....((((((.....)))))).((((.......))))....)))))......)))).))))(((......))--------) ( -33.80)
>DroWil_CAF1 136041 101 - 1
-----------GAUGCCUCCUGUGAGGAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUACCACUGAGCUAAAGAGGCUCACAUUUAAUGUGAGUUCCAUAACU--------A
-----------....((((....))))...((((((((((.(.((((((.....)))))).).))......((((((.....))))))........)))))))).......--------. ( -31.90)
>DroMoj_CAF1 169412 111 - 1
GU----CCCU-AUUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCCGGCGAUUGGGA----UCGCACAGCUCUGGCAUAA
((----(((.-((((((....(((((.......)))))((((.((((((.....)))))).((((.......))))......)))))))))).))))----).((.((....)))).... ( -45.10)
>DroAna_CAF1 106473 108 - 1
GG----CCCCAGUUGCCUCUUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUAUCGAGGGCGGCCCAAAAGU--------C
((----((((....((((((((((((.......))))).....((((((.....)))))).((((.......))))..)))))))((.......)).)).)))).......--------. ( -37.80)
>consensus
GU____CC___AAUGCCUCCUGUGAGAAUUGAACUCACGACCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAAGAGGCUCACAUUUUGAGGGCGGCAAAAAACU________A
..............(((((.((((((.......))))))....((((((.....)))))).((((.......))))....)))))................................... (-26.90 = -26.90 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	8,032,301 – 8,032,401
Length	100
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	78.80
Mean single sequence MFE	-23.87
Consensus MFE	-20.00
Energy contribution	-20.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.43
Structure conservation index	0.84
SVM decision value	0.80
SVM RNA-class probability	0.852953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8032301 100 - 27905053
-------ACAGACAGAACAAAAAA-UGCUGUUGACCUUAUAUGCCUCUUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAA
-------...(((((.........-..)))))..........(((....(((((.......))))))))..((((((.....)))))).((((.......)))).... ( -22.90)
>DroPse_CAF1 116441 82 - 1
-----------ACCAAAA-AAAAG-U-------------CAUGCCUCUUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAA
-----------.......-.....-.-------------...(((....(((((.......))))))))..((((((.....)))))).((((.......)))).... ( -20.00)
>DroSec_CAF1 98461 93 - 1
-----------ACAGAACAAAAAG-UGCAGUUGUCC---UAUGCCUCUUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAA
-----------...........((-(.((((.....---..........(((((.......)))))(((.(((((((.....)))))).)....))))))).)))... ( -22.30)
>DroEre_CAF1 101520 97 - 1
-------AAAAAUGCAUGCAAAAA-UGCGGUUGACC---UAUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAA
-------......((((......)-)))(((.....---...)))..(((((((.......)))))))...((((((.....)))))).((((.......)))).... ( -27.10)
>DroMoj_CAF1 169448 84 - 1
-----------------A-AAAAAGU-----CGUCCCU-AUUGCCUCCUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAA
-----------------.-.......-----.......-........(((((((.......)))))))...((((((.....)))))).((((.......)))).... ( -20.30)
>DroAna_CAF1 106505 100 - 1
AAAAUUG----ACAAA---AAUAA-GGGGCUUGGCCCCAGUUGCCUCUUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAA
.......----((...---....(-((((((.(((.......)))....(((((.......))))))))))))((((.....)))).))((((.......)))).... ( -30.60)
>consensus
___________ACAAAAA_AAAAA_UGC_GUUGACC___UAUGCCUCUUGUGAGAAUUGAACUCACGGCCCCUGGUUUACAAGACCAGUGCUCUGCCACUGAGCUAAA
..........................................(((....(((((.......))))))))..((((((.....)))))).((((.......)))).... (-20.00 = -20.00 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:50 2006