Locus 3548

Sequence ID	2L_DroMel_CAF1
Location	10,342,756 – 10,342,952
Length	196
Max. P	0.967616

overview

Window 2

Location	10,342,756 – 10,342,876
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	91.94
Mean single sequence MFE	-31.63
Consensus MFE	-27.08
Energy contribution	-27.58
Covariance contribution	0.50
Combinations/Pair	1.11
Mean z-score	-1.81
Structure conservation index	0.86
SVM decision value	0.59
SVM RNA-class probability	0.791845
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10342756 120 + 22407834
CAAUGUUUCAACCCGAAAAACAUGGGCUUGAGCCCGACUUUCAGCUUACUAAGUUUACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAA
..((((((.........))))))((((....))))((.(((((((((.....(....)(((((.....))))))))))).))).))((((.....(((((.....)))))....)))).. ( -33.20)
>DroSec_CAF1 4359 120 + 1
CAAUGUUUCAACCAGAAAAACAUGGGCUUGAGCCCGACUUUCAGCUUACUAAGUUUACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAA
..((((((.........))))))((((....))))((.(((((((((.....(....)(((((.....))))))))))).))).))((((.....(((((.....)))))....)))).. ( -33.20)
>DroSim_CAF1 2597 120 + 1
CAAUGUUUCAACCAGAAAAACAUGGGCUUUCGCCCGACUUUCAGCUUACUAAGUUUACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAA
..((((((.........))))))((((....))))((.(((((((((.....(....)(((((.....))))))))))).))).))((((.....(((((.....)))))....)))).. ( -32.90)
>DroEre_CAF1 4411 120 + 1
CGAUGUUUCAGCCGGAAAAACAUGGUCUUGAGCCCGACUUUCAGCUAACUAAGUUCACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAAAAGUACCUAAGGGGAA
....((((.(((((........))).)).)))).((((((..((((.....))))...(((((.....))))))))))).....(((((......(((((.....)))))....))))). ( -30.40)
>DroYak_CAF1 3234 120 + 1
CUAUGUUUCAGCCAGAAAAACACGGCCUUGAGCCCGACUUUCAGCUAACUAAGUUCACCACCCAUACCGGGUGAAGUUGCAAAAUCCCCCAGAAAGUACUGGAGAAGUACCUAAGGGGAA
...(((..((((..((((.....(((.....)))....)))).)))............(((((.....)))))..)..)))...(((((......(((((.....)))))....))))). ( -30.00)
>DroAna_CAF1 4442 120 + 1
AAAUGUUCGAACCGGAGAAACAUGGGCUAGCGCCCGAUUUUCAGCUAACUAAGUUUACAACGCACACCGGAUGAAGUUGCAAAAUCCCCCAAAAAGUACUUGAAAAGUACCUACGGGGAA
.....((((..((((.((((..(((((....)))))..))))((((.....))))...........)))).)))).........(((((......(((((.....)))))....))))). ( -30.10)
>consensus
CAAUGUUUCAACCAGAAAAACAUGGGCUUGAGCCCGACUUUCAGCUAACUAAGUUUACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAA
........((((..((((....(((((....)))))..))))................(((((.....)))))..)))).....(((((......(((((.....)))))....))))). (-27.08 = -27.58 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	10,342,756 – 10,342,876
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	91.94
Mean single sequence MFE	-39.32
Consensus MFE	-34.50
Energy contribution	-34.78
Covariance contribution	0.28
Combinations/Pair	1.11
Mean z-score	-2.15
Structure conservation index	0.88
SVM decision value	1.61
SVM RNA-class probability	0.967616
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10342756 120 - 22407834
UUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUAAACUUAGUAAGCUGAAAGUCGGGCUCAAGCCCAUGUUUUUCGGGUUGAAACAUUG
.((((((.(((((((.....)))))))...)))))).....((((.((((((.....)))))).............(((((((..((((....))))....)))))))))))........ ( -41.20)
>DroSec_CAF1 4359 120 - 1
UUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUAAACUUAGUAAGCUGAAAGUCGGGCUCAAGCCCAUGUUUUUCUGGUUGAAACAUUG
.((((((.(((((((.....)))))))...)))))).....(((((((((((.....)))))).((((((((....)))).....((((....))))..))))....)))))........ ( -38.90)
>DroSim_CAF1 2597 120 - 1
UUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUAAACUUAGUAAGCUGAAAGUCGGGCGAAAGCCCAUGUUUUUCUGGUUGAAACAUUG
.((((((.(((((((.....)))))))...)))))).....(((((((((((.....)))))).((((((((....)))).....((((....))))..))))....)))))........ ( -42.40)
>DroEre_CAF1 4411 120 - 1
UUCCCCUUAGGUACUUUUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUGAACUUAGUUAGCUGAAAGUCGGGCUCAAGACCAUGUUUUUCCGGCUGAAACAUCG
.((((((.(((((((.....)))))))...))))))(((.((((((((((((.....)))))).......)))).)).)))(((((((...(((((...))))))))))))......... ( -36.81)
>DroYak_CAF1 3234 120 - 1
UUCCCCUUAGGUACUUCUCCAGUACUUUCUGGGGGAUUUUGCAACUUCACCCGGUAUGGGUGGUGAACUUAGUUAGCUGAAAGUCGGGCUCAAGGCCGUGUUUUUCUGGCUGAAACAUAG
.((((((.(((((((.....)))))))...))))))...........(((((.....)))))(((...((((((((..(((...(((.(....).)))..)))..))))))))..))).. ( -40.20)
>DroAna_CAF1 4442 120 - 1
UUCCCCGUAGGUACUUUUCAAGUACUUUUUGGGGGAUUUUGCAACUUCAUCCGGUGUGCGUUGUAAACUUAGUUAGCUGAAAAUCGGGCGCUAGCCCAUGUUUCUCCGGUUCGAACAUUU
(((((((.(((((((.....)))))))..))))))).........(((..((((.(.((((.......((((....)))).....((((....))))))))..).))))...)))..... ( -36.40)
>consensus
UUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUAAACUUAGUAAGCUGAAAGUCGGGCUCAAGCCCAUGUUUUUCUGGUUGAAACAUUG
..((((..(((((((.....)))))))...))))((((((......((((((.....))))))......(((....)))))))))((((....))))(((((((.......))))))).. (-34.50 = -34.78 +   0.28)

alignment

secondary structure

dotplot

Window 4

Location	10,342,796 – 10,342,916
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.06
Mean single sequence MFE	-25.65
Consensus MFE	-22.08
Energy contribution	-22.17
Covariance contribution	0.09
Combinations/Pair	1.20
Mean z-score	-1.46
Structure conservation index	0.86
SVM decision value	0.06
SVM RNA-class probability	0.563982
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10342796 120 + 22407834
UCAGCUUACUAAGUUUACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAAUAAUGAUGGAUACCUUAUCGG
.((((((.....(....)(((((.....))))))))))).....(((((......(((((.....)))))....))))).......................((((((.....)))))). ( -25.10)
>DroSec_CAF1 4399 120 + 1
UCAGCUUACUAAGUUUACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAACAACGAUGGAUACCUUAUCGG
............((((..(((((.....)))))...........(((((......(((((.....)))))....))))).................))))..((((((.....)))))). ( -27.50)
>DroSim_CAF1 2637 120 + 1
UCAGCUUACUAAGUUUACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAACAAUGAUGGAUACCUUAUCGG
............((((..(((((.....)))))...........(((((......(((((.....)))))....))))).................))))..((((((.....)))))). ( -25.30)
>DroEre_CAF1 4451 114 + 1
UCAGCUAACUAAGUUCACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAAAAGUACCUAAGGGGAACAG------AAAAUAAGAACAAUGAUGGAUACCUUAUCGG
............((((..(((((.....)))))...........(((((......(((((.....)))))....)))))....------.......))))..((((((.....)))))). ( -27.80)
>DroYak_CAF1 3274 120 + 1
UCAGCUAACUAAGUUCACCACCCAUACCGGGUGAAGUUGCAAAAUCCCCCAGAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAAAAAUGAUGGAUACCUUAUCGG
........(((..(((..(((((.....)))))...........(((((......(((((.....)))))....)))))...))).))).............((((((.....)))))). ( -25.60)
>DroAna_CAF1 4482 120 + 1
UCAGCUAACUAAGUUUACAACGCACACCGGAUGAAGUUGCAAAAUCCCCCAAAAAGUACUUGAAAAGUACCUACGGGGAACAGACAUAGCUAAUACAAACAAUGAAGGAUAUCUUAUUGG
..(((((..............(((.((........)))))....(((((......(((((.....)))))....))))).......)))))........((((((........)))))). ( -22.60)
>consensus
UCAGCUAACUAAGUUUACCACCCACACCGGGUGAAGUUGCAAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAACAAUGAUGGAUACCUUAUCGG
............((((..(((((.....)))))...........(((((......(((((.....)))))....))))).................))))..((((((.....)))))). (-22.08 = -22.17 +   0.09)

alignment

secondary structure

dotplot

Window 5

Location	10,342,796 – 10,342,916
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.06
Mean single sequence MFE	-30.17
Consensus MFE	-26.16
Energy contribution	-26.10
Covariance contribution	-0.05
Combinations/Pair	1.13
Mean z-score	-1.61
Structure conservation index	0.87
SVM decision value	0.45
SVM RNA-class probability	0.739554
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10342796 120 - 22407834
CCGAUAAGGUAUCCAUCAUUAUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUAAACUUAGUAAGCUGA
..(((((((((........)).)))))))..........(((((((..(((((((.....)))))))...))))))).........((((((.....)))))).....((((....)))) ( -28.60)
>DroSec_CAF1 4399 120 - 1
CCGAUAAGGUAUCCAUCGUUGUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUAAACUUAGUAAGCUGA
....((((....((((((((((.................(((((((..(((((((.....)))))))...)))))))...)))))..(((.....))))))))....))))......... ( -31.15)
>DroSim_CAF1 2637 120 - 1
CCGAUAAGGUAUCCAUCAUUGUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUAAACUUAGUAAGCUGA
..(((((((.............)))))))..........(((((((..(((((((.....)))))))...))))))).........((((((.....)))))).....((((....)))) ( -28.52)
>DroEre_CAF1 4451 114 - 1
CCGAUAAGGUAUCCAUCAUUGUUCUUAUUUU------CUGUUCCCCUUAGGUACUUUUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUGAACUUAGUUAGCUGA
..(((((((.............)))))))..------..(((((((..(((((((.....)))))))...)))))))...((((((((((((.....)))))).......)))).))... ( -30.13)
>DroYak_CAF1 3274 120 - 1
CCGAUAAGGUAUCCAUCAUUUUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUCUGGGGGAUUUUGCAACUUCACCCGGUAUGGGUGGUGAACUUAGUUAGCUGA
..(((((((.............)))))))..........(((((((..(((((((.....)))))))...)))))))...((((((((((((.....)))))).......)))).))... ( -30.13)
>DroAna_CAF1 4482 120 - 1
CCAAUAAGAUAUCCUUCAUUGUUUGUAUUAGCUAUGUCUGUUCCCCGUAGGUACUUUUCAAGUACUUUUUGGGGGAUUUUGCAACUUCAUCCGGUGUGCGUUGUAAACUUAGUUAGCUGA
.(((((((.....))).))))......(((((((...((((((((((.(((((((.....)))))))..))))))).((((((((..(((.....))).))))))))..))).))))))) ( -32.50)
>consensus
CCGAUAAGGUAUCCAUCAUUGUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUUGCAACUUCACCCGGUGUGGGUGGUAAACUUAGUAAGCUGA
..(((((((.............)))))))..........(((((((..(((((((.....)))))))...))))))).........((((((.....)))))).....((((....)))) (-26.16 = -26.10 +  -0.05)

alignment

secondary structure

dotplot

Window 6

Location	10,342,836 – 10,342,952
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.02
Mean single sequence MFE	-23.48
Consensus MFE	-15.71
Energy contribution	-15.43
Covariance contribution	-0.28
Combinations/Pair	1.14
Mean z-score	-2.10
Structure conservation index	0.67
SVM decision value	0.22
SVM RNA-class probability	0.640181
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10342836 116 + 22407834
AAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAAUAAUGAUGGAUACCUUAUCGGUGAGAGAUAUUACUUUGUAUAAUCAGCAG----AUCUCGA
....(((((......(((((.....)))))....)))))..............................((((.....)))).(((((......(((......)))...----))))).. ( -20.40)
>DroSec_CAF1 4439 109 + 1
AAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAACAACGAUGGAUACCUUAUCGGUGAGAGAUAGUACU-------AUCAGCAG----AUCUGGG
....(((((......(((((.....)))))....))))).((((...............((.((((((.....)))))).))...((((....)-------))).....----.)))).. ( -24.60)
>DroSim_CAF1 2677 109 + 1
AAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAACAAUGAUGGAUACCUUAUCGGUGAGAGAUAGUACU-------AUCAGCAG----AUCUGGG
....(((((......(((((.....)))))....))))).((((..((.....)).......((((((.(((..((((.......)))))))))-------))))....----.)))).. ( -23.80)
>DroEre_CAF1 4491 102 + 1
AAAAUCCCCCAAAAAGUACUGGAAAAGUACCUAAGGGGAACAG------AAAAUAAGAACAAUGAUGGAUACCUUAUCGGUGAGAGAUAGUGUU-------UUCAUCA-----CUAUCGG
....(((((......(((((.....)))))....)))))....------.............(((((((.((.(((((.......))))).)).-------)))))))-----....... ( -25.10)
>DroYak_CAF1 3314 109 + 1
AAAAUCCCCCAGAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAAAAAUGAUGGAUACCUUAUCGGUGAGAGAUAGUACU-------AUCUGCAG----AUCUUGG
....(((((......(((((.....)))))....)))))..............(((((.....(((((.(((..((((.......)))))))))-------))).....----.))))). ( -23.20)
>DroAna_CAF1 4522 113 + 1
AAAAUCCCCCAAAAAGUACUUGAAAAGUACCUACGGGGAACAGACAUAGCUAAUACAAACAAUGAAGGAUAUCUUAUUGGUAAGAAAUAAUGAU-------UUAUUUAUGUUAUGUUCAA
....(((((......(((((.....)))))....)))))...((((((((.........((((((........)))))).....((((((....-------))))))..))))))))... ( -23.80)
>consensus
AAAAUCCCCCAAAAAGUACUGGAGAAGUACCUAAGGGGAACAGAAAUAGAAAAUAAGAACAAUGAUGGAUACCUUAUCGGUGAGAGAUAGUACU_______AUCAGCAG____AUCUCGG
....(((((......(((((.....)))))....)))))..............................((((.....))))...................................... (-15.71 = -15.43 +  -0.28)

alignment

secondary structure

dotplot

Window 7

Location	10,342,836 – 10,342,952
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.02
Mean single sequence MFE	-25.41
Consensus MFE	-19.39
Energy contribution	-19.14
Covariance contribution	-0.25
Combinations/Pair	1.14
Mean z-score	-3.13
Structure conservation index	0.76
SVM decision value	1.14
SVM RNA-class probability	0.921484
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10342836 116 - 22407834
UCGAGAU----CUGCUGAUUAUACAAAGUAAUAUCUCUCACCGAUAAGGUAUCCAUCAUUAUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUU
..(((((----.((((..........))))..)))))..(((.....))).............................(((((((..(((((((.....)))))))...)))))))... ( -26.20)
>DroSec_CAF1 4439 109 - 1
CCCAGAU----CUGCUGAU-------AGUACUAUCUCUCACCGAUAAGGUAUCCAUCGUUGUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUU
..((((.----.....(((-------(....))))....(((.....)))..........................)))).((((((.(((((((.....)))))))...)))))).... ( -24.40)
>DroSim_CAF1 2677 109 - 1
CCCAGAU----CUGCUGAU-------AGUACUAUCUCUCACCGAUAAGGUAUCCAUCAUUGUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUU
..((((.----.....(((-------(....))))....(((.....)))..........................)))).((((((.(((((((.....)))))))...)))))).... ( -24.40)
>DroEre_CAF1 4491 102 - 1
CCGAUAG-----UGAUGAA-------AACACUAUCUCUCACCGAUAAGGUAUCCAUCAUUGUUCUUAUUUU------CUGUUCCCCUUAGGUACUUUUCCAGUACUUUUUGGGGGAUUUU
..(((((-----(((((..-------.((..((((.......))))..))...))))))))))........------..(((((((..(((((((.....)))))))...)))))))... ( -29.50)
>DroYak_CAF1 3314 109 - 1
CCAAGAU----CUGCAGAU-------AGUACUAUCUCUCACCGAUAAGGUAUCCAUCAUUUUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUCUGGGGGAUUUU
..((((.----....((((-------(....)))))...(((.....)))............)))).............(((((((..(((((((.....)))))))...)))))))... ( -23.90)
>DroAna_CAF1 4522 113 - 1
UUGAACAUAACAUAAAUAA-------AUCAUUAUUUCUUACCAAUAAGAUAUCCUUCAUUGUUUGUAUUAGCUAUGUCUGUUCCCCGUAGGUACUUUUCAAGUACUUUUUGGGGGAUUUU
....(((((.(((((((((-------.........(((((....))))).........))))))))....).)))))..((((((((.(((((((.....)))))))..))))))))... ( -24.07)
>consensus
CCGAGAU____CUGCUGAU_______AGUACUAUCUCUCACCGAUAAGGUAUCCAUCAUUGUUCUUAUUUUCUAUUUCUGUUCCCCUUAGGUACUUCUCCAGUACUUUUUGGGGGAUUUU
..........................................(((((((.............)))))))..........(((((((..(((((((.....)))))))...)))))))... (-19.39 = -19.14 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:15 2006