Locus 5799

Sequence ID	3L_DroMel_CAF1
Location	15,696,834 – 15,697,076
Length	242
Max. P	0.956177

overview

Window 2

Location	15,696,834 – 15,696,942
Length	108
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	88.01
Mean single sequence MFE	-25.68
Consensus MFE	-20.32
Energy contribution	-21.07
Covariance contribution	0.75
Combinations/Pair	1.12
Mean z-score	-2.01
Structure conservation index	0.79
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696834 108 + 23771897
CAGCAGGCCACACAUAACAUGCAAAAGUGAUUUUCCAUUCGCCGUGUCCGCAUGCCAUCAAUGGCAAAUUAUGCAUUUAAUGGCCAAAUGCAAUUAGCAUCU----CC----UUUC
.....(((((......(((((.....((((........)))))))))..((((((((....))))).....)))......)))))..((((.....))))..----..----.... ( -25.00)
>DroSec_CAF1 12570 108 + 1
CAGCAGGCCACACAUAACAUGCAAAAGUGAUUUUCCAUUCGCCGUGUCCGAAUGCCAUCAAUGGCAAAUUAUGCAUUUAAUGGCCAAAUGCAAUUAGCAUCU----CC----UUUC
.....(((((....(((.(((((...((((........))))..........(((((....))))).....)))))))).)))))..((((.....))))..----..----.... ( -24.70)
>DroSim_CAF1 12502 108 + 1
CAGCAGGCCACACAUAACAUGCAAAAGUGAUUUUCCAUUCGCCGUGUCCGAAUGCCAUCAAUGGCAAAUUAUGCAUUUAAUGGCCAAAUGCAAUUAGCAUCU----CC----UUUC
.....(((((....(((.(((((...((((........))))..........(((((....))))).....)))))))).)))))..((((.....))))..----..----.... ( -24.70)
>DroEre_CAF1 3850 108 + 1
AAGCAGGCCGCACAUAACAUGCAAAAGUGAUUUUCCAUUCGCCGUGUCCGCAUGCCAUCAAUGGCAAAUUAUGCAUUUAAUGGCCAAAUGCAAUUAGCAUCU----CC----UUUC
.....((((((((.....(((.((((....)))).))).....))))..((((((((....))))).....))).......))))..((((.....))))..----..----.... ( -24.80)
>DroYak_CAF1 48594 108 + 1
AAGCAGGCCACACAUAACAUGCAAAAGUGAUUUUCCAUUCGCCGUGUCCGCAUGCCAUCAAUGGCAAAUUAUGCAUUUAAUGGCCAAAUGCAAUUAGCAUCU----CC----UUUC
.....(((((......(((((.....((((........)))))))))..((((((((....))))).....)))......)))))..((((.....))))..----..----.... ( -25.00)
>DroAna_CAF1 10671 103 + 1
CAGCUGGCCAC----AACAUGCAAAAGUGAUUUGCGAAUCAUCAUGCC---------UCCAUGGCAAAUUAUGCAUUUAAUGGCCAGAUGCAAUUACCAUCCAGUGCCUGCCAGUG
...(((((((.----...(((((...((((((....))))))..((((---------.....)))).....)))))....)))))))..(((..(((......)))..)))..... ( -29.90)
>consensus
CAGCAGGCCACACAUAACAUGCAAAAGUGAUUUUCCAUUCGCCGUGUCCGCAUGCCAUCAAUGGCAAAUUAUGCAUUUAAUGGCCAAAUGCAAUUAGCAUCU____CC____UUUC
.....(((((....(((.(((((...((((........))))..........(((((....))))).....)))))))).)))))..((((.....))))................ (-20.32 = -21.07 +   0.75)

alignment

secondary structure

dotplot

Window 3

Location	15,696,874 – 15,696,979
Length	105
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	81.76
Mean single sequence MFE	-34.55
Consensus MFE	-22.93
Energy contribution	-24.47
Covariance contribution	1.53
Combinations/Pair	1.18
Mean z-score	-1.74
Structure conservation index	0.66
SVM decision value	0.24
SVM RNA-class probability	0.647348
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696874 105 - 23771897
UUG---GGGGCUGGGAUCGUGGAAAGGACCUCUCUCCUUCGAAA----GG----AGAUGCUAAUUGCAUUUGGCCAUUAAAUGCAUAAUUUGCCAUUGAUGGCAUGCGGACACGGC
..(---((((..(((.((.(....).)))))..)))))((....----))----((((((.....)))))).((((((((..(((.....)))..))))))))...((....)).. ( -32.60)
>DroSec_CAF1 12610 105 - 1
UUG---GGGGCUGGGGUCGUGGCAAGGACCUCUCUUCUUCGAAA----GG----AGAUGCUAAUUGCAUUUGGCCAUUAAAUGCAUAAUUUGCCAUUGAUGGCAUUCGGACACGGC
...---((((..((((((.(....).)))))).))))((((((.----..----((((((.....)))))).((((((((..(((.....)))..)))))))).))))))...... ( -35.30)
>DroSim_CAF1 12542 104 - 1
-UG---GGGGCUGGGGUCGUGGAAAGGACCUCUCUCCUUCGAAA----GG----AGAUGCUAAUUGCAUUUGGCCAUUAAAUGCAUAAUUUGCCAUUGAUGGCAUUCGGACACGGC
-..---((((..((((((.(....).)))))).))))((((((.----..----((((((.....)))))).((((((((..(((.....)))..)))))))).))))))...... ( -39.60)
>DroEre_CAF1 3890 100 - 1
CUG---GGAGCUGGGG-----GAAAGGACCUCUCUCCUUUGAAA----GG----AGAUGCUAAUUGCAUUUGGCCAUUAAAUGCAUAAUUUGCCAUUGAUGGCAUGCGGACACGGC
(((---..(((.((((-----.......))))((((((.....)----))----))).)))..((((((...((((((((..(((.....)))..))))))))))))))...))). ( -32.40)
>DroYak_CAF1 48634 108 - 1
UUGAGGGGGGCUGGGGUCGUGAAAAGGACCUCUCUCCUGCGAAA----GG----AGAUGCUAAUUGCAUUUGGCCAUUAAAUGCAUAAUUUGCCAUUGAUGGCAUGCGGACACGGC
.....(((((..((((((.(....).)))))).)))))(((...----..----((((((.....)))))).((((((((..(((.....)))..)))))))).)))......... ( -39.00)
>DroAna_CAF1 10707 99 - 1
------GUGGCCAGGACCUU--AAAGGACCUUUAUUCCACCACUGGCAGGCACUGGAUGGUAAUUGCAUCUGGCCAUUAAAUGCAUAAUUUGCCAUGGA---------GGCAUGAU
------...((((((.((..--...)).)))........(((.(((((((((...((((((...........))))))...))).....))))))))).---------)))..... ( -28.40)
>consensus
UUG___GGGGCUGGGGUCGUGGAAAGGACCUCUCUCCUUCGAAA____GG____AGAUGCUAAUUGCAUUUGGCCAUUAAAUGCAUAAUUUGCCAUUGAUGGCAUGCGGACACGGC
......((((..((((((.(....).)))))).)))).................((((((.....)))))).((((((((..(((.....)))..))))))))............. (-22.93 = -24.47 +   1.53)

alignment

secondary structure

dotplot

Window 4

Location	15,696,910 – 15,697,013
Length	103
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	82.30
Mean single sequence MFE	-18.58
Consensus MFE	-15.08
Energy contribution	-15.72
Covariance contribution	0.64
Combinations/Pair	1.05
Mean z-score	-1.65
Structure conservation index	0.81
SVM decision value	0.39
SVM RNA-class probability	0.715468
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696910 103 + 23771897
UUAAUGGCCAAAUGCAAUUAGCAUCUCCUUUCGAAGGAGAGAGGUCCUUUCCACGAUCCCAGCCCC---CAACCCACCAAUCCAAGCCCAUAUAGCAUA-----CCAUAGC
...((((....((((.((..((.((((((.....))))))(.((((........)))).)......---................))....)).)))).-----))))... ( -17.10)
>DroSec_CAF1 12646 100 + 1
UUAAUGGCCAAAUGCAAUUAGCAUCUCCUUUCGAAGAAGAGAGGUCCUUGCCACGACCCCAGCCCC---CAACCC--------AACCCCAUAUAGCAUACCAUACCAUAGC
...((((....((((.....(((...((((((......))))))....)))...(....)......---......--------...........)))).))))........ ( -15.80)
>DroSim_CAF1 12578 95 + 1
UUAAUGGCCAAAUGCAAUUAGCAUCUCCUUUCGAAGGAGAGAGGUCCUUUCCACGACCCCAGCCCC---CA-------------ACCCCAUAUAGCAUACCAUACCAUAGC
...((((....((((........((((((.....))))))(.((((........)))).)......---..-------------..........)))).))))........ ( -19.30)
>DroEre_CAF1 3926 91 + 1
UUAAUGGCCAAAUGCAAUUAGCAUCUCCUUUCAAAGGAGAGAGGUCCUUUC-----CCCCAGCUCC---CAGCCC-------CAGCUCCAUGUAGCAUA-----CCACAGC
.....((((...(((.....)))((((((.....))))))..)))).....-----.....((((.---.(((..-------..)))....).)))...-----....... ( -18.00)
>DroYak_CAF1 48670 99 + 1
UUAAUGGCCAAAUGCAAUUAGCAUCUCCUUUCGCAGGAGAGAGGUCCUUUUCACGACCCCAGCCCCCCUCAACCC-------CCAUUCCAUAUUGCAUA-----CCAUUGC
.((((((....(((((((.....((((((.....))))))(.((((........)))).)...............-------.........))))))).-----)))))). ( -22.70)
>consensus
UUAAUGGCCAAAUGCAAUUAGCAUCUCCUUUCGAAGGAGAGAGGUCCUUUCCACGACCCCAGCCCC___CAACCC_______CAACCCCAUAUAGCAUA_____CCAUAGC
...((((....((((........((((((.....))))))(.((((........)))).)..................................))))......))))... (-15.08 = -15.72 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	15,696,910 – 15,697,013
Length	103
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	82.30
Mean single sequence MFE	-30.81
Consensus MFE	-21.22
Energy contribution	-21.94
Covariance contribution	0.72
Combinations/Pair	1.12
Mean z-score	-1.59
Structure conservation index	0.69
SVM decision value	-0.00
SVM RNA-class probability	0.531477
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696910 103 - 23771897
GCUAUGG-----UAUGCUAUAUGGGCUUGGAUUGGUGGGUUG---GGGGCUGGGAUCGUGGAAAGGACCUCUCUCCUUCGAAAGGAGAUGCUAAUUGCAUUUGGCCAUUAA
..(((((-----....)))))..(((((((((((((.....(---((((..(((.((.(....).))))))))))((((....))))..))))))).))...))))..... ( -28.20)
>DroSec_CAF1 12646 100 - 1
GCUAUGGUAUGGUAUGCUAUAUGGGGUU--------GGGUUG---GGGGCUGGGGUCGUGGCAAGGACCUCUCUUCUUCGAAAGGAGAUGCUAAUUGCAUUUGGCCAUUAA
....(.((((((....)))))).)(((.--------.(((..---..(((.((((((.(....).))))))...(((((....))))).)))......)))..)))..... ( -31.80)
>DroSim_CAF1 12578 95 - 1
GCUAUGGUAUGGUAUGCUAUAUGGGGU-------------UG---GGGGCUGGGGUCGUGGAAAGGACCUCUCUCCUUCGAAAGGAGAUGCUAAUUGCAUUUGGCCAUUAA
....(.((((((....)))))).)(((-------------..---((.((.((((((.(....).))))))((((((.....))))))........)).))..)))..... ( -32.50)
>DroEre_CAF1 3926 91 - 1
GCUGUGG-----UAUGCUACAUGGAGCUG-------GGGCUG---GGAGCUGGGG-----GAAAGGACCUCUCUCCUUUGAAAGGAGAUGCUAAUUGCAUUUGGCCAUUAA
(((((((-----....))))....)))..-------.(((((---((((..((((-----.......)))).)))))........((((((.....))))))))))..... ( -27.90)
>DroYak_CAF1 48670 99 - 1
GCAAUGG-----UAUGCAAUAUGGAAUGG-------GGGUUGAGGGGGGCUGGGGUCGUGAAAAGGACCUCUCUCCUGCGAAAGGAGAUGCUAAUUGCAUUUGGCCAUUAA
..(((((-----((((((((.(((.....-------...(((.((((((..((((((.(....).)))))))))))).))).........))))))))))...)))))).. ( -33.63)
>consensus
GCUAUGG_____UAUGCUAUAUGGGGUUG_______GGGUUG___GGGGCUGGGGUCGUGGAAAGGACCUCUCUCCUUCGAAAGGAGAUGCUAAUUGCAUUUGGCCAUUAA
.(((((.............))))).......................((((((((((.(....).))))))((((((.....))))))(((.....)))...))))..... (-21.22 = -21.94 +   0.72)

alignment

secondary structure

dotplot

Window 6

Location	15,696,979 – 15,697,076
Length	97
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	76.21
Mean single sequence MFE	-20.78
Consensus MFE	-12.20
Energy contribution	-12.87
Covariance contribution	0.67
Combinations/Pair	1.12
Mean z-score	-2.13
Structure conservation index	0.59
SVM decision value	1.46
SVM RNA-class probability	0.956177
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696979 97 + 23771897
CCCACCAAUCCAAGCCCAUAUAGCAUA-----CCAUAGCAAUUGGGUGCGUGUCCAGCAUAAUUGCCCAAGAUUAACAUAAAUCAAUCAAAGGGCAUAAAGC
.............(((((....((...-----.....))...)))))..((((((.(((....)))....((((......)))).......))))))..... ( -20.30)
>DroSec_CAF1 12715 94 + 1
CCC--------AACCCCAUAUAGCAUACCAUACCAUAGCAAUUGGGUGCGUGUCCGGCAUAAUUGCCCAAGAUUAACAUAAAUCAAUCAAAGGCCAUAAAGC
...--------...........((((.(((............)))))))(((.((((((....))))...((((......)))).......)).)))..... ( -17.30)
>DroSim_CAF1 12646 90 + 1
------------ACCCCAUAUAGCAUACCAUACCAUAGCAAUUGGGUGCGUGUCCGGCAUAAUUGCCCAAGAUUAACAUAAAUCAAUCAAAGGCCAUAAAGC
------------..........((((.(((............)))))))(((.((((((....))))...((((......)))).......)).)))..... ( -17.30)
>DroEre_CAF1 3990 90 + 1
CCC-------CAGCUCCAUGUAGCAUA-----CCACAGCAAUUGGGUGCGUGUCCGGCAUAAUUGCCCGAGAUUAACAUAAAUCAAUCAAAGGGCAUGAGGC
...-------..((..(((((.((((.-----(((.......)))))))....((((((....))))...((((......)))).......)))))))..)) ( -24.00)
>DroYak_CAF1 48742 90 + 1
CCC-------CCAUUCCAUAUUGCAUA-----CCAUUGCAAUUGGGUGCGUGUCCGGCAUAAUUGCCCAAGAUUAACAUAAAUCAAUCAAAGGGCAUAAAGC
...-------.(((.(((.((((((..-----....)))))))))))).((((((((((....))))...((((......)))).......))))))..... ( -25.10)
>DroPer_CAF1 32720 79 + 1
UCC-------CAGCUGCAUGGAAAACA-----UUACC-----------AGCUUCUGGCAUAAUUGCCAAAGAUUAAUAUAAAUCAAUCAGCGGGAAGAAAGU
(((-------((((((.(((.....))-----)...)-----------))))..(((((....)))))..((((......)))).......))))....... ( -20.70)
>consensus
CCC_______CAACCCCAUAUAGCAUA_____CCAUAGCAAUUGGGUGCGUGUCCGGCAUAAUUGCCCAAGAUUAACAUAAAUCAAUCAAAGGGCAUAAAGC
.....................................(((......)))((((((((((....))))...((((......)))).......))))))..... (-12.20 = -12.87 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	15,696,979 – 15,697,076
Length	97
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	76.21
Mean single sequence MFE	-27.27
Consensus MFE	-11.92
Energy contribution	-12.15
Covariance contribution	0.23
Combinations/Pair	1.33
Mean z-score	-2.16
Structure conservation index	0.44
SVM decision value	0.51
SVM RNA-class probability	0.763406
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696979 97 - 23771897
GCUUUAUGCCCUUUGAUUGAUUUAUGUUAAUCUUGGGCAAUUAUGCUGGACACGCACCCAAUUGCUAUGG-----UAUGCUAUAUGGGCUUGGAUUGGUGGG
((....(((((...(((((((....)))))))..))))).....))....(((.((.((((.(.((((((-----....))))).).).))))..))))).. ( -26.90)
>DroSec_CAF1 12715 94 - 1
GCUUUAUGGCCUUUGAUUGAUUUAUGUUAAUCUUGGGCAAUUAUGCCGGACACGCACCCAAUUGCUAUGGUAUGGUAUGCUAUAUGGGGUU--------GGG
((......((((..(((((((....)))))))..))))......))..........(((((((.(((((((((...)))))))).).))))--------))) ( -30.30)
>DroSim_CAF1 12646 90 - 1
GCUUUAUGGCCUUUGAUUGAUUUAUGUUAAUCUUGGGCAAUUAUGCCGGACACGCACCCAAUUGCUAUGGUAUGGUAUGCUAUAUGGGGU------------
((((((((((((..(((((((....)))))))..)))).(((((((((.....(((......)))..)))))))))......))))))))------------ ( -27.40)
>DroEre_CAF1 3990 90 - 1
GCCUCAUGCCCUUUGAUUGAUUUAUGUUAAUCUCGGGCAAUUAUGCCGGACACGCACCCAAUUGCUGUGG-----UAUGCUACAUGGAGCUG-------GGG
.((((((((((...(((((((....)))))))..)))))...(((((..(((.(((......))))))))-----)))(((......)))))-------))) ( -28.60)
>DroYak_CAF1 48742 90 - 1
GCUUUAUGCCCUUUGAUUGAUUUAUGUUAAUCUUGGGCAAUUAUGCCGGACACGCACCCAAUUGCAAUGG-----UAUGCAAUAUGGAAUGG-------GGG
......(((((...(((((((....)))))))..)))))....(((.(....))))((((((((((....-----..))))))......)))-------).. ( -25.90)
>DroPer_CAF1 32720 79 - 1
ACUUUCUUCCCGCUGAUUGAUUUAUAUUAAUCUUUGGCAAUUAUGCCAGAAGCU-----------GGUAA-----UGUUUUCCAUGCAGCUG-------GGA
.......((((((((((((((....)))))))(((((((....))))))).(((-----------((...-----......))).))))).)-------))) ( -24.50)
>consensus
GCUUUAUGCCCUUUGAUUGAUUUAUGUUAAUCUUGGGCAAUUAUGCCGGACACGCACCCAAUUGCUAUGG_____UAUGCUAUAUGGAGUUG_______GGG
((((((((......(((((((....)))))))((.((((....)))).))................................))))))))............ (-11.92 = -12.15 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:17 2006