Locus 4422

Sequence ID	3R_DroMel_CAF1
Location	11,658,606 – 11,658,803
Length	197
Max. P	0.825046

overview

Window 5

Location	11,658,606 – 11,658,723
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.37
Mean single sequence MFE	-36.13
Consensus MFE	-17.25
Energy contribution	-17.91
Covariance contribution	0.67
Combinations/Pair	1.27
Mean z-score	-2.40
Structure conservation index	0.48
SVM decision value	0.49
SVM RNA-class probability	0.754939
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11658606 117 + 27905053
AAAUGUUUCCAACACUUUUAUCUCCUCGUUCUCAUCAGUG---GGCUGCACGGCCUUUAGUUCAUGUAGUAAUUCGGUGCAGCCGUCGAGGAGCAUCACCUGCUUCAGGUGAAGCUUAAG
......................((((((....((....))---((((((((.(...(((.(......).)))..).))))))))..))))))((.(((((((...))))))).))..... ( -37.20)
>DroSec_CAF1 3338 116 + 1
AAAUGUUUCCAACACUUUUAUCUCCUCUU-CUCAUUAGUG---GGCUGCACGGCAUUAAGUUCAUGCAGUAAUUCGGUGCAGCCGUCGAGGAGCAUCACCUGCUUCAGGUGAAGCUUAAG
......................(((((..-..((....))---((((((((.(.((((.((....))..)))).).))))))))...)))))((.(((((((...))))))).))..... ( -37.40)
>DroSim_CAF1 4667 117 + 1
AAAAGUUUCCAACACUUUUAGCUCCUCGUCCUCAUUAGUG---GGCUGCACUGCAUUAAGUUCAUGCAGUAAUUCGGUGCAGCCGUCGAGGAGCAUCACCUGCUUCAGGUGAAGCUUAAG
..(((((.............((((((((.(..((....))---((((((((((.((((.((....))..)))).))))))))))).)))))))).(((((((...))))))))))))... ( -48.00)
>DroEre_CAF1 7185 117 + 1
AAAUGUUUCCAAAACUAUUUUCUCCUCGCAGUCAUCAGUC---GGCUGAACGUUAUUCAGUUCAUGCAGGAAAUCGGCGCAGCCGUCGAGGAGCAACAUCUGCUUCAGGUGAAGCUUGAA
...((((((.............((((.((((((.......---)))(((((........))))))))))))..((((((....))))))))))))...((.(((((....)))))..)). ( -32.10)
>DroWil_CAF1 3305 117 + 1
AAAUGUCUCAAACACAAUUUUCCCCUC---CUCAUCGGUCUGCGGCUUAACGGUCUUAAGCUCUUGAAUAAAUUCGAUGCAGCCAUCGAGAUGGCGUAUUUGCUCCAUCUGCAAAUUAUU
...(((.....................---......((.(((((((((((.....))))))).(((((....))))).))))))....((((((.((....)).)))))))))....... ( -25.10)
>DroYak_CAF1 4708 117 + 1
AAAUGUUUCCAAAACAAUUUUCUCCUCGCAGUCAUUAGUC---GGCUGAACGGCAUUAAGUUCCUGGAGGAAAUCUGCGCAGCCGUCGAGGAGAAACAUCUGCUUCAGGUGAAGCUUAAA
...((((.....))))..(((((((((((((((.......---))))).(((((....((((((....))))..)).....))))))))))))))).....(((((....)))))..... ( -37.00)
>consensus
AAAUGUUUCCAACACUAUUAUCUCCUCGU_CUCAUCAGUC___GGCUGAACGGCAUUAAGUUCAUGCAGUAAUUCGGUGCAGCCGUCGAGGAGCAUCACCUGCUUCAGGUGAAGCUUAAG
.....................((((((........((((.....)))).(((((...........................))))).))))))..(((((((...)))))))........ (-17.25 = -17.91 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	11,658,606 – 11,658,723
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.37
Mean single sequence MFE	-37.34
Consensus MFE	-18.38
Energy contribution	-19.08
Covariance contribution	0.70
Combinations/Pair	1.18
Mean z-score	-2.46
Structure conservation index	0.49
SVM decision value	0.69
SVM RNA-class probability	0.825046
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11658606 117 - 27905053
CUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCUGCACCGAAUUACUACAUGAACUAAAGGCCGUGCAGCC---CACUGAUGAGAACGAGGAGAUAAAAGUGUUGGAAACAUUU
.....((.(((((((...))))))).))((((((..((((((((.(..((.............))..).))))))))---..((....))..))))))...........((....))... ( -37.62)
>DroSec_CAF1 3338 116 - 1
CUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCUGCACCGAAUUACUGCAUGAACUUAAUGCCGUGCAGCC---CACUAAUGAG-AAGAGGAGAUAAAAGUGUUGGAAACAUUU
.....((.(((((((...))))))).))(((((...((((((((.........((((.......)))).))))))))---..((....))-..)))))...........((....))... ( -37.30)
>DroSim_CAF1 4667 117 - 1
CUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCUGCACCGAAUUACUGCAUGAACUUAAUGCAGUGCAGCC---CACUAAUGAGGACGAGGAGCUAAAAGUGUUGGAAACUUUU
........(((((((...))))))).((((((((..((((((((........(((((.......)))))))))))))---..((....))..)))))))).((((((.......)))))) ( -44.90)
>DroEre_CAF1 7185 117 - 1
UUCAAGCUUCACCUGAAGCAGAUGUUGCUCCUCGACGGCUGCGCCGAUUUCCUGCAUGAACUGAAUAACGUUCAGCC---GACUGAUGACUGCGAGGAGAAAAUAGUUUUGGAAACAUUU
.....(((((....)))))...((((.(((((((.((((...)))).....(.((.(((((........))))))).---)...........)))))))..))))....((....))... ( -33.00)
>DroWil_CAF1 3305 117 - 1
AAUAAUUUGCAGAUGGAGCAAAUACGCCAUCUCGAUGGCUGCAUCGAAUUUAUUCAAGAGCUUAAGACCGUUAAGCCGCAGACCGAUGAG---GAGGGGAAAAUUGUGUUUGAGACAUUU
..........(((((...((((((((((..((((.(((((((...(((....)))..(.((((((.....))))))))))).))).))))---..)).......))))))))...))))) ( -31.81)
>DroYak_CAF1 4708 117 - 1
UUUAAGCUUCACCUGAAGCAGAUGUUUCUCCUCGACGGCUGCGCAGAUUUCCUCCAGGAACUUAAUGCCGUUCAGCC---GACUAAUGACUGCGAGGAGAAAAUUGUUUUGGAAACAUUU
.....(((((....))))).....((((((((((.((((((.(((...((((....)))).....)))....)))))---).(....)....)))))))))).......((....))... ( -39.40)
>consensus
CUUAAGCUUCACCUGAAGCAGAUGAUGCUCCUCGACGGCUGCACCGAAUUACUGCAUGAACUUAAUGCCGUGCAGCC___CACUAAUGAG_ACGAGGAGAAAAAAGUGUUGGAAACAUUU
.....(((((....)))))........(((((((..(((((.((.........................)).))))).....(....)....)))))))..........((....))... (-18.38 = -19.08 +   0.70)

alignment

secondary structure

dotplot

Window 7

Location	11,658,646 – 11,658,763
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.11
Mean single sequence MFE	-41.82
Consensus MFE	-20.80
Energy contribution	-21.75
Covariance contribution	0.95
Combinations/Pair	1.16
Mean z-score	-2.16
Structure conservation index	0.50
SVM decision value	0.04
SVM RNA-class probability	0.556158
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11658646 117 + 27905053
---GGCUGCACGGCCUUUAGUUCAUGUAGUAAUUCGGUGCAGCCGUCGAGGAGCAUCACCUGCUUCAGGUGAAGCUUAAGCAGCUCCUGCUGAAUUGUCUUGAUGCACUGGAUUUGUUGG
---.((((((.(..(....)..).))))))(((((((((((....(((((((((.(((((((...))))))).))))...((((....))))......))))))))))))))))...... ( -44.70)
>DroSec_CAF1 3377 117 + 1
---GGCUGCACGGCAUUAAGUUCAUGCAGUAAUUCGGUGCAGCCGUCGAGGAGCAUCACCUGCUUCAGGUGAAGCUUAAGCAGCUCCUGCUGAAUGGUCUUGAUGCACUGGAUUUGGUGG
---((((((((.(.((((.((....))..)))).).))))))))((((((((((.(((((((...))))))).))))...((((....))))......)))))).((((......)))). ( -48.40)
>DroSim_CAF1 4707 117 + 1
---GGCUGCACUGCAUUAAGUUCAUGCAGUAAUUCGGUGCAGCCGUCGAGGAGCAUCACCUGCUUCAGGUGAAGCUUAAGCAGCUCCUGCUGAAUUGUCUUGAUGCUCUGGAUUUGGUGG
---((((((((((.((((.((....))..)))).))))))))))(((..(((((((((...(((((....))))).....((((....))))........))))))))).)))....... ( -48.20)
>DroEre_CAF1 7225 117 + 1
---GGCUGAACGUUAUUCAGUUCAUGCAGGAAAUCGGCGCAGCCGUCGAGGAGCAACAUCUGCUUCAGGUGAAGCUUGAAGAGCUCCUGCUGAAGAGUUUUGAUACACUGGAUUUGGUAA
---.((..(.....((((((((((.((((((..((((((....)))))).((((..((((((...))))))..)))).......)))))))))...((......))))))))))..)).. ( -36.40)
>DroYak_CAF1 4748 117 + 1
---GGCUGAACGGCAUUAAGUUCCUGGAGGAAAUCUGCGCAGCCGUCGAGGAGAAACAUCUGCUUCAGGUGAAGCUUAAAGAGCUCCUGCUGAAGAGCCUUGAUGCACCGGAUUUGGUGA
---(((((....(((.....((((....))))...))).)))))((((((((((....))).((((((..(.(((((...))))).)..))))))..))))))).(((((....))))). ( -39.90)
>DroAna_CAF1 16100 120 + 1
CGCGGCUGGGCGCCAUUCAACUCCUGAAGGAUGUCAAUGCACCCAUCCAGCAGCGUCACCUGCCGCAUCUGCAACUGCAACAACUCCUUCUGGACACUCUUGAUGCUCUCGAUUUGCUCA
.(((((..(((((..((((.....))))(((((..........)))))....)))))....)))((((((((....))).....(((....))).......))))).........))... ( -33.30)
>consensus
___GGCUGCACGGCAUUAAGUUCAUGCAGGAAUUCGGUGCAGCCGUCGAGGAGCAUCACCUGCUUCAGGUGAAGCUUAAACAGCUCCUGCUGAAUAGUCUUGAUGCACUGGAUUUGGUGA
...(((((...............................)))))((((((((((..((((((...))))))..))))...((((....))))......))))))................ (-20.80 = -21.75 +   0.95)

alignment

secondary structure

dotplot

Window 8

Location	11,658,646 – 11,658,763
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.11
Mean single sequence MFE	-37.92
Consensus MFE	-19.38
Energy contribution	-19.91
Covariance contribution	0.53
Combinations/Pair	1.25
Mean z-score	-2.31
Structure conservation index	0.51
SVM decision value	0.38
SVM RNA-class probability	0.714927
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11658646 117 - 27905053
CCAACAAAUCCAGUGCAUCAAGACAAUUCAGCAGGAGCUGCUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCUGCACCGAAUUACUACAUGAACUAAAGGCCGUGCAGCC---
........((.((.((((((......(((((..((((((.....))))))..))))).....))))))..)).)).((((((((.(..((.............))..).))))))))--- ( -36.42)
>DroSec_CAF1 3377 117 - 1
CCACCAAAUCCAGUGCAUCAAGACCAUUCAGCAGGAGCUGCUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCUGCACCGAAUUACUGCAUGAACUUAAUGCCGUGCAGCC---
........((.((.((((((......(((((..((((((.....))))))..))))).....))))))..)).)).((((((((.........((((.......)))).))))))))--- ( -38.30)
>DroSim_CAF1 4707 117 - 1
CCACCAAAUCCAGAGCAUCAAGACAAUUCAGCAGGAGCUGCUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCUGCACCGAAUUACUGCAUGAACUUAAUGCAGUGCAGCC---
............((((((((......(((((..((((((.....))))))..))))).....))))))))......((((((((........(((((.......)))))))))))))--- ( -44.20)
>DroEre_CAF1 7225 117 - 1
UUACCAAAUCCAGUGUAUCAAAACUCUUCAGCAGGAGCUCUUCAAGCUUCACCUGAAGCAGAUGUUGCUCCUCGACGGCUGCGCCGAUUUCCUGCAUGAACUGAAUAACGUUCAGCC---
..........................(((((((((((.((.....(((((....)))))....((((.....))))(((...))))).))))))).))))((((((...))))))..--- ( -29.90)
>DroYak_CAF1 4748 117 - 1
UCACCAAAUCCGGUGCAUCAAGGCUCUUCAGCAGGAGCUCUUUAAGCUUCACCUGAAGCAGAUGUUUCUCCUCGACGGCUGCGCAGAUUUCCUCCAGGAACUUAAUGCCGUUCAGCC---
.((((......))))((((((((((((......))))).)))...(((((....))))).))))............(((((.(((...((((....)))).....)))....)))))--- ( -34.90)
>DroAna_CAF1 16100 120 - 1
UGAGCAAAUCGAGAGCAUCAAGAGUGUCCAGAAGGAGUUGUUGCAGUUGCAGAUGCGGCAGGUGACGCUGCUGGAUGGGUGCAUUGACAUCCUUCAGGAGUUGAAUGGCGCCCAGCCGCG
...((.........(((((.......(((....))).....(((....))))))))(((((......)))))((.(((((((.(..((.(((....)))))..)...))))))).)))). ( -43.80)
>consensus
CCACCAAAUCCAGUGCAUCAAGACUAUUCAGCAGGAGCUGCUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCUGCACCGAAUUACUGCAUGAACUUAAUGCCGUGCAGCC___
........((.((.((((((......(((((..((((((.....))))))..))))).....))))))..)).)).(((((.((.........................)).)))))... (-19.38 = -19.91 +   0.53)

alignment

secondary structure

dotplot

Window 9

Location	11,658,683 – 11,658,803
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.33
Mean single sequence MFE	-37.24
Consensus MFE	-21.46
Energy contribution	-21.27
Covariance contribution	-0.19
Combinations/Pair	1.38
Mean z-score	-1.96
Structure conservation index	0.58
SVM decision value	0.07
SVM RNA-class probability	0.568761
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11658683 120 - 27905053
AGCAAAUGUUGGCUCUUUCCACGAUUCCACUGCGCAUGGACCAACAAAUCCAGUGCAUCAAGACAAUUCAGCAGGAGCUGCUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCU
(((....(((((((................(((((.((((........)))))))))....((....)))))((((((.((....)).(((((((...))))))).)))))))))).))) ( -35.40)
>DroSec_CAF1 3414 120 - 1
AGCAAAUGUUGGCCGUUUCGACAAUUCCACUGCGCUUGGACCACCAAAUCCAGUGCAUCAAGACCAUUCAGCAGGAGCUGCUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCU
..........(((((((.............((((((.(((........))))))))).............(.((((((.((....)).(((((((...))))))).)))))))))))))) ( -39.80)
>DroSim_CAF1 4744 120 - 1
AGCAAAUGUUGGCCGUUUCGACAAUUCCACUGCGCUUGGACCACCAAAUCCAGAGCAUCAAGACAAUUCAGCAGGAGCUGCUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCU
..........(((((..((((...............((((........))))((((((((......(((((..((((((.....))))))..))))).....)))))))).))))))))) ( -39.40)
>DroEre_CAF1 7262 120 - 1
ACCAGAUGUCAGCUCUUUCCACAAUGCCACUGCGUUUGGAUUACCAAAUCCAGUGUAUCAAAACUCUUCAGCAGGAGCUCUUCAAGCUUCACCUGAAGCAGAUGUUGCUCCUCGACGGCU
...((.((((.(((.............(((((.((((((....)))))).)))))..............)))((((((...((..(((((....))))).))....)))))).)))).)) ( -34.53)
>DroYak_CAF1 4785 120 - 1
ACCAGAUGUUGGCUCUUUCCACAAUGCCACUGCGUUUGGAUCACCAAAUCCGGUGCAUCAAGGCUCUUCAGCAGGAGCUCUUUAAGCUUCACCUGAAGCAGAUGUUUCUCCUCGACGGCU
.((((((((((((............))))..))))))))..((((......))))((((((((((((......))))).)))...(((((....))))).))))................ ( -36.90)
>DroAna_CAF1 16140 120 - 1
AGCAAAUGGCAGCGAUUGAAAAUAUACCACUUCGCCUGGAUGAGCAAAUCGAGAGCAUCAAGAGUGUCCAGAAGGAGUUGUUGCAGUUGCAGAUGCGGCAGGUGACGCUGCUGGAUGGGU
..((..((((((((..(....)..(((((((((..(((((((..(..(((....).))...)..)))))))..)))))(((((((........))))))))))).))))))))..))... ( -37.40)
>consensus
AGCAAAUGUUGGCUCUUUCCACAAUUCCACUGCGCUUGGACCACCAAAUCCAGUGCAUCAAGACUAUUCAGCAGGAGCUGCUUAAGCUUCACCUGAAGCAGGUGAUGCUCCUCGACGGCU
..........((((................(((((.((((........)))))))))...............((((((.......(((((....))))).......))))))....)))) (-21.46 = -21.27 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:52 2006