Locus 8676

Sequence ID	3L_DroMel_CAF1
Location	22,506,339 – 22,506,478
Length	139
Max. P	0.993480

overview

Window 9

Location	22,506,339 – 22,506,446
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	69.07
Mean single sequence MFE	-30.87
Consensus MFE	-12.94
Energy contribution	-14.12
Covariance contribution	1.17
Combinations/Pair	1.27
Mean z-score	-2.23
Structure conservation index	0.42
SVM decision value	1.70
SVM RNA-class probability	0.973014
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22506339 107 + 23771897
UAUGCGCAAUAAGUGCUCGCAGGGGUUGCAAUGUUA--ACAGAAAUUAUCUAACUACCCCUGAGGAGGCAGGGG-AAAAGAAAACUUGACGAAGUUUCUGCAAG----AGCAAA------
.............(((((((((..(((((((.(((.--..(((.....))).....((((((......))))))-.......)))))).)))..)..))))..)----))))..------ ( -28.90)
>DroVir_CAF1 20534 108 + 1
UAAGCC--------GUUUACAGAUAUCCUUAUGUUA--UUUAACAUUAUCUAACCGCCCCUGUCACGGAAGGGGUAGUUUAUAACUUAACGAUACUUCUGCAAAGU--AGCAGAGAUAAG
.....(--------(((...(((((.....(((((.--...))))))))))(((..(((((........)))))..)))........))))....((((((.....--.))))))..... ( -25.40)
>DroSec_CAF1 14403 107 + 1
UAUGCACAAUAAGGGCUCUCAGGGGUUGCAAUGUUA--ACAGAAUUUAUCUAACUACCCCUGAGCAGACAGGGG-AAAAGAAAACUUGACGAAGUUUCUGCAAG----AGCAAA------
..............((((((((((((......((((--............)))).))))))))(((((((((..-.........))))........)))))..)----)))...------ ( -27.00)
>DroSim_CAF1 14755 107 + 1
UAUGCACAAUAAGGGCUCGCAGGGGUUGCAAUGUUA--ACAGAAUUUAUCUAACUACCCCUGAGCAGGCAGGGG-AAAAGAAAACUUGACGAAGUUUCUGCAAG----AGCAAA------
..............((((((((..(((((((.(((.--..(((.....))).....((((((......))))))-.......)))))).)))..)..))))..)----)))...------ ( -28.00)
>DroEre_CAF1 16531 111 + 1
UGUGCAUAAUAGGGGUUCGCAGGGGUUGCAAUGCUA--ACAGAAUUUAUCUGACUACCCCUGCGCAGGCAGGGG-AAGAGAAAACUUGACGAAGCUUCUGCAAGUUACAGCAAA------
((((.....((((((((((((((..((.........--.((((.....)))).((.(((((((....)))))))-.))..))..)))).)).)))))))).....)))).....------ ( -34.40)
>DroMoj_CAF1 27429 110 + 1
CAUGCC--------CCUUGCAGCGUCUGUUAUGUUAUGUUUAACAUUAUCUAGUUACCCCUUAUACAGAAGGGGUGGCAAAAAACUUGACGAAACUCCUGCAAAGC--AGGAGGCGGCUG
...(((--------....((..((((.(((((((((....))))))......((((((((((......))))))))))....)))..))))...(((((((...))--)))))))))).. ( -41.50)
>consensus
UAUGCACAAUAAGGGCUCGCAGGGGUUGCAAUGUUA__ACAGAAAUUAUCUAACUACCCCUGAGCAGGCAGGGG_AAAAGAAAACUUGACGAAGCUUCUGCAAG____AGCAAA______
..............(((.(((((((((....(((((....(((.....))).....((((((......))))))............))))).))))))))).......)))......... (-12.94 = -14.12 +   1.17)

alignment

secondary structure

dotplot

Window 0

Location	22,506,339 – 22,506,446
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	69.07
Mean single sequence MFE	-28.67
Consensus MFE	-17.86
Energy contribution	-17.28
Covariance contribution	-0.58
Combinations/Pair	1.47
Mean z-score	-2.07
Structure conservation index	0.62
SVM decision value	2.08
SVM RNA-class probability	0.987542
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22506339 107 - 23771897
------UUUGCU----CUUGCAGAAACUUCGUCAAGUUUUCUUUU-CCCCUGCCUCCUCAGGGGUAGUUAGAUAAUUUCUGU--UAACAUUGCAACCCCUGCGAGCACUUAUUGCGCAUA
------..((((----(..((((((((((....))))..(((...-((((((......)))))).....)))....))))))--.......(((.....))))))))............. ( -25.90)
>DroVir_CAF1 20534 108 - 1
CUUAUCUCUGCU--ACUUUGCAGAAGUAUCGUUAAGUUAUAAACUACCCCUUCCGUGACAGGGGCGGUUAGAUAAUGUUAAA--UAACAUAAGGAUAUCUGUAAAC--------GGCUUA
.........(((--..((((((((..((((.(((.(((((.(((..(((((........)))))..))).(((...)))..)--)))).))).)))))))))))).--------)))... ( -28.10)
>DroSec_CAF1 14403 107 - 1
------UUUGCU----CUUGCAGAAACUUCGUCAAGUUUUCUUUU-CCCCUGUCUGCUCAGGGGUAGUUAGAUAAAUUCUGU--UAACAUUGCAACCCCUGAGAGCCCUUAUUGUGCAUA
------...(((----(..(((((......(..(((....)))..-).....)))))((((((((.((((((.....)))).--.......)).)))))))))))).............. ( -27.60)
>DroSim_CAF1 14755 107 - 1
------UUUGCU----CUUGCAGAAACUUCGUCAAGUUUUCUUUU-CCCCUGCCUGCUCAGGGGUAGUUAGAUAAAUUCUGU--UAACAUUGCAACCCCUGCGAGCCCUUAUUGUGCAUA
------...(((----(..((((((((((....))))..(((...-((((((......)))))).....)))....))))))--.......(((.....))))))).............. ( -24.50)
>DroEre_CAF1 16531 111 - 1
------UUUGCUGUAACUUGCAGAAGCUUCGUCAAGUUUUCUCUU-CCCCUGCCUGCGCAGGGGUAGUCAGAUAAAUUCUGU--UAGCAUUGCAACCCCUGCGAACCCCUAUUAUGCACA
------..(((((.((((((..((....))..))))))....((.-(((((((....))))))).)).((((.....)))).--)))))(((((.....)))))................ ( -29.10)
>DroMoj_CAF1 27429 110 - 1
CAGCCGCCUCCU--GCUUUGCAGGAGUUUCGUCAAGUUUUUUGCCACCCCUUCUGUAUAAGGGGUAACUAGAUAAUGUUAAACAUAACAUAACAGACGCUGCAAGG--------GGCAUG
..(((.((((((--((...))))))((..((((............(((((((......))))))).........((((((....))))))....))))..))..))--------)))... ( -36.80)
>consensus
______UUUGCU____CUUGCAGAAACUUCGUCAAGUUUUCUUUU_CCCCUGCCUGCUCAGGGGUAGUUAGAUAAAUUCUGU__UAACAUUGCAACCCCUGCGAGCCCUUAUUGUGCAUA
................(((((((.......................((((((......))))))....((((.....)))).................)))))))............... (-17.86 = -17.28 +  -0.58)

alignment

secondary structure

dotplot

Window 1

Location	22,506,377 – 22,506,478
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	69.93
Mean single sequence MFE	-29.17
Consensus MFE	-13.45
Energy contribution	-12.87
Covariance contribution	-0.58
Combinations/Pair	1.35
Mean z-score	-2.20
Structure conservation index	0.46
SVM decision value	1.78
SVM RNA-class probability	0.976904
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22506377 101 + 23771897
AGAAAUUAUCUAACUACCCCUGAGGAGGCAGGGG-AAAAGAAAACUUGACGAAGUUUCUGCAAG----AGCAAA--------------UAGGGGUAGCUUACAGACGCCCAGAGAGAGUG
....(((.(((..(((((((((......))))))-...(((((.(((....))))))))((...----.))...--------------)))((((..(.....)..))))..))).))). ( -23.90)
>DroGri_CAF1 19160 110 + 1
UAACAUUAUCUAACCACCCCUGAUGCAGUAGGGGUAAUCAGAAACUUGACGAAACUUCUGCAAAGA--GUCAAAAUUGAGAGUA-CAGGAGGGGUAGUA----AAUGA---GAGAGAGAG
...((((..(((.((.((((((.(((.((((((((..((((....))))....)))))))).....--.(((....)))..)))-)))).)))))))..----)))).---......... ( -26.80)
>DroSec_CAF1 14441 101 + 1
AGAAUUUAUCUAACUACCCCUGAGCAGACAGGGG-AAAAGAAAACUUGACGAAGUUUCUGCAAG----AGCAAA--------------UAGGGGAAGCUUACAGACGUCCAGAGAGAGUG
........(((.....((((((......))))))-.........((.((((((((((((.(...----......--------------..).)))))))).....)))).)))))..... ( -25.00)
>DroSim_CAF1 14793 101 + 1
AGAAUUUAUCUAACUACCCCUGAGCAGGCAGGGG-AAAAGAAAACUUGACGAAGUUUCUGCAAG----AGCAAA--------------UAGGGGAAGCUUACAGACGUCCAGAGAGAGUG
........(((.....((((((......))))))-.........((.((((((((((((.(...----......--------------..).)))))))).....)))).)))))..... ( -25.20)
>DroEre_CAF1 16569 105 + 1
AGAAUUUAUCUGACUACCCCUGCGCAGGCAGGGG-AAGAGAAAACUUGACGAAGCUUCUGCAAGUUACAGCAAA--------------UAGGGGUAGUUUGCAGACGCGCAGAGAGAGUG
...((((.((((.((.(((((((....)))))))-.))...............((.(((((((..(((..(...--------------..)..)))..))))))).)).))))..)))). ( -37.40)
>DroMoj_CAF1 27461 111 + 1
UAACAUUAUCUAGUUACCCCUUAUACAGAAGGGGUGGCAAAAAACUUGACGAAACUCCUGCAAAGC--AGGAGGCGGCUGGCUAUUAUGAGGGGAGGUC----AAUGC---GAGAGAGAG
........(((.((((((((((......))))))))))......((((.((...(((((((...))--)))))..((((..((........))..))))----..)))---))))))... ( -36.70)
>consensus
AGAAAUUAUCUAACUACCCCUGAGCAGGCAGGGG_AAAAGAAAACUUGACGAAGCUUCUGCAAG____AGCAAA______________UAGGGGAAGCUUACAGACGCCCAGAGAGAGUG
........(((.....((((((......)))))).................(((((.((.(.............................).)).)))))............)))..... (-13.45 = -12.87 +  -0.58)

alignment

secondary structure

dotplot

Window 2

Location	22,506,377 – 22,506,478
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	69.93
Mean single sequence MFE	-25.72
Consensus MFE	-14.35
Energy contribution	-14.35
Covariance contribution	0.00
Combinations/Pair	1.38
Mean z-score	-2.36
Structure conservation index	0.56
SVM decision value	2.40
SVM RNA-class probability	0.993480
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22506377 101 - 23771897
CACUCUCUCUGGGCGUCUGUAAGCUACCCCUA--------------UUUGCU----CUUGCAGAAACUUCGUCAAGUUUUCUUUU-CCCCUGCCUCCUCAGGGGUAGUUAGAUAAUUUCU
..(((.....))).(((((...(((((((((.--------------..(((.----...)))(((((((....))))))).....-.............))))))))))))))....... ( -25.20)
>DroGri_CAF1 19160 110 - 1
CUCUCUCUC---UCAUU----UACUACCCCUCCUG-UACUCUCAAUUUUGAC--UCUUUGCAGAAGUUUCGUCAAGUUUCUGAUUACCCCUACUGCAUCAGGGGUGGUUAGAUAAUGUUA
.........---..(((----((((((((((....-.....(((....))).--....(((((.((....((((......)))).....)).)))))..)))))))).)))))....... ( -23.50)
>DroSec_CAF1 14441 101 - 1
CACUCUCUCUGGACGUCUGUAAGCUUCCCCUA--------------UUUGCU----CUUGCAGAAACUUCGUCAAGUUUUCUUUU-CCCCUGUCUGCUCAGGGGUAGUUAGAUAAAUUCU
...(((..((((((((((((((((........--------------...)))----..)))))).....))))............-((((((......)))))))))..)))........ ( -25.20)
>DroSim_CAF1 14793 101 - 1
CACUCUCUCUGGACGUCUGUAAGCUUCCCCUA--------------UUUGCU----CUUGCAGAAACUUCGUCAAGUUUUCUUUU-CCCCUGCCUGCUCAGGGGUAGUUAGAUAAAUUCU
...(((..((((((((((((((((........--------------...)))----..)))))).....))))............-((((((......)))))))))..)))........ ( -24.20)
>DroEre_CAF1 16569 105 - 1
CACUCUCUCUGCGCGUCUGCAAACUACCCCUA--------------UUUGCUGUAACUUGCAGAAGCUUCGUCAAGUUUUCUCUU-CCCCUGCCUGCGCAGGGGUAGUCAGAUAAAUUCU
...(((..((((((.(((((((..(((..(..--------------...)..)))..))))))).))..................-.((((((....))))))))))..)))........ ( -30.40)
>DroMoj_CAF1 27461 111 - 1
CUCUCUCUC---GCAUU----GACCUCCCCUCAUAAUAGCCAGCCGCCUCCU--GCUUUGCAGGAGUUUCGUCAAGUUUUUUGCCACCCCUUCUGUAUAAGGGGUAACUAGAUAAUGUUA
.........---(((((----(((..............((.....))(((((--((...)))))))....)))))......))).(((((((......)))))))............... ( -25.80)
>consensus
CACUCUCUCUGGGCGUCUGUAAACUACCCCUA______________UUUGCU____CUUGCAGAAACUUCGUCAAGUUUUCUUUU_CCCCUGCCUGCUCAGGGGUAGUUAGAUAAAUUCU
..............(((((...........................(((((........)))))......................((((((......))))))....)))))....... (-14.35 = -14.35 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:05 2006