Locus 2493

Sequence ID	2L_DroMel_CAF1
Location	6,862,377 – 6,862,597
Length	220
Max. P	0.938434

overview

Window 9

Location	6,862,377 – 6,862,488
Length	111
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	78.97
Mean single sequence MFE	-36.41
Consensus MFE	-24.83
Energy contribution	-25.13
Covariance contribution	0.31
Combinations/Pair	1.32
Mean z-score	-1.63
Structure conservation index	0.68
SVM decision value	0.71
SVM RNA-class probability	0.829618
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6862377 111 - 22407834
CCUGGUCGUUCUCACUGUGGCCGCCAAUUUCGGUGGCUACCUAAUAUCGCUGACCACCUUGCCACGUCUCAUUGGCAUGCUCCUGGUGGGCAUACUCUUCCAGGUGAGUUU--
(((((...........(((((((((......)))))))))........(((.((((...(((((........)))))......)))).)))........))))).......-- ( -40.00)
>DroVir_CAF1 97088 112 - 1
CCUGGUGGUGCUGACCGUGGCCGCCAAUUUCGGUGGCUAUCUGAUAUCGUUGACCACCCUGCCACGUCUGAUUGGUAUGCUGCUGGUGGGCAUACUCUUCCAGGUGAGUC-GC
(((((..(((((.((((..((.(((((((...(((((....((...........))....)))))....)))))))..))..).))).)))))......)))))......-.. ( -40.70)
>DroPse_CAF1 84174 101 - 1
CCUGGUCGUCCUAACUGUGGCAGCCAACUUUGGCGGCUACCUGAUAUCUCUGACCACCCUGCCUCGUCUGAUUGGCAUGCUCCUGGUGGGCAUACUCUUUC------------
..((((((........(((((.((((....)))).)))))..........))))))....(((..........)))((((.((....))))))........------------ ( -28.67)
>DroWil_CAF1 53224 109 - 1
UCUUGUUGUGCUGACUGUGGCAGCCAAUUUCGGUGGCUAUUUGAUAUCAUUGACCACAUUACCAAGAUUAAUUGGUAUGCUCAUGGUGGGCAUAUUAUUUCAGGUAAGA----
.((((.((((((.(((((((((..........(((((....((....))..).))))..((((((......))))))))).)))))).))))))......)))).....---- ( -31.40)
>DroMoj_CAF1 98593 111 - 1
CCUGGUGGUGCUCACGGUGGCCGCCAAUUUCGGUGGCUACAUAAUAUCACUGACCACUCUGCCUCGUCUCAUUGGCAUGCUGCUGGUGGGCAUACUCUUUCAGGUGAGA--AC
..((((((((......(((((((((......))))))))).......)))).))))(((.((((.(((.(((..((.....))..))))))..........))))))).--.. ( -39.82)
>DroAna_CAF1 61441 111 - 1
UCUCGUCGUCCUUACUGUGGCCGCCAACUUUGGCGGCUACGUGAUAUCGCUGACUACCCUUCCCCGACUAAUUGGCAUGCUCCUUGUGGGCAUCCUAUUCCAGGUGAGUGU--
.(((..((((......((((((((((....))))))))))(((....)))...............))).....((.((((.((....)))))))).......)..)))...-- ( -37.90)
>consensus
CCUGGUCGUGCUCACUGUGGCCGCCAAUUUCGGUGGCUACCUGAUAUCGCUGACCACCCUGCCACGUCUAAUUGGCAUGCUCCUGGUGGGCAUACUCUUCCAGGUGAGU____
(((((...........(((((((((......)))))))))..........((.(((((.((((..........)))).......))))).)).......)))))......... (-24.83 = -25.13 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	6,862,408 – 6,862,528
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.06
Mean single sequence MFE	-43.45
Consensus MFE	-27.51
Energy contribution	-26.57
Covariance contribution	-0.94
Combinations/Pair	1.48
Mean z-score	-1.54
Structure conservation index	0.63
SVM decision value	0.17
SVM RNA-class probability	0.615515
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6862408 120 - 22407834
UCAUCGGCGAUUCGGCAGCCCCUGGUGGGCAGCUCUUUGGCCUGGUCGUUCUCACUGUGGCCGCCAAUUUCGGUGGCUACCUAAUAUCGCUGACCACCUUGCCACGUCUCAUUGGCAUGC
...((((((((.((((.((((.....)))).(((....)))...))))........(((((((((......))))))))).....))))))))......(((((........)))))... ( -44.80)
>DroVir_CAF1 97120 120 - 1
UUAUCGGGGACACAGCUGCGCCGGGCGGUCAACUGUUUAGCCUGGUGGUGCUGACCGUGGCCGCCAAUUUCGGUGGCUAUCUGAUAUCGUUGACCACCCUGCCACGUCUGAUUGGUAUGC
.(((((....).((((((.((.(((.(((((((.(((..(((....)))...))).(((((((((......)))))))))........))))))).))).)))).).)))...))))... ( -47.70)
>DroGri_CAF1 85169 120 - 1
UUAUUGGGGACACCGCUGCCCCUGGCGGGCAGCUCUUCAGUCUAGUGGUGCUUACAGUAGCUGCCAAUUUUGGUGGUUAUCUGAUAUCAUUGACCACCCUGCCAAGGUUGAUUGGUAUGC
.....((((.....(((((((.....)))))))......(((.(((((((....(((((((..(((....)))..)))).))).))))))))))..))))(((((......))))).... ( -44.80)
>DroWil_CAF1 53253 120 - 1
UCAUUGGAGACUCAGCUGCCCCUGGUGGACAGCUUUUUGGUCUUGUUGUGCUGACUGUGGCAGCCAAUUUCGGUGGCUAUUUGAUAUCAUUGACCACAUUACCAAGAUUAAUUGGUAUGC
......((((((.(((((((......)).)))))....))))))((((.((((.(....)))))))))....(((((....((....))..).))))..((((((......))))))... ( -32.10)
>DroMoj_CAF1 98624 120 - 1
UCAUUGGGGACACAGCUGCCCCGGGUGGGCAGCUCUUCAGCCUGGUGGUGCUCACGGUGGCCGCCAAUUUCGGUGGCUACAUAAUAUCACUGACCACUCUGCCUCGUCUCAUUGGCAUGC
(((...(((((..((((((((.....))))))))...(((..((((((((......(((((((((......))))))))).......)))).))))..)))....)))))..)))..... ( -50.22)
>DroAna_CAF1 61472 120 - 1
UCAUUGGCGACUCGGCUGCCCCUGGCGGACAGCUCUUCGGUCUCGUCGUCCUUACUGUGGCCGCCAACUUUGGCGGCUACGUGAUAUCGCUGACUACCCUUCCCCGACUAAUUGGCAUGC
....((.(((.(((((((((...))))).((((.....((.(.....).))((((.((((((((((....))))))))))))))....))))...........))))....))).))... ( -41.10)
>consensus
UCAUUGGGGACACAGCUGCCCCUGGCGGGCAGCUCUUCAGCCUGGUGGUGCUCACUGUGGCCGCCAAUUUCGGUGGCUACCUGAUAUCACUGACCACCCUGCCACGUCUAAUUGGCAUGC
.....((......(((((.(((....))))))))..(((((......((....)).(((((((((......)))))))))........)))))))....(((((........)))))... (-27.51 = -26.57 +  -0.94)

alignment

secondary structure

dotplot

Window 1

Location	6,862,448 – 6,862,568
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.05
Mean single sequence MFE	-37.27
Consensus MFE	-22.16
Energy contribution	-22.38
Covariance contribution	0.22
Combinations/Pair	1.32
Mean z-score	-1.85
Structure conservation index	0.59
SVM decision value	0.52
SVM RNA-class probability	0.769405
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6862448 120 + 22407834
GUAGCCACCGAAAUUGGCGGCCACAGUGAGAACGACCAGGCCAAAGAGCUGCCCACCAGGGGCUGCCGAAUCGCCGAUGAUCACAAAGGCGGUGACCCAGAUAAGGACACCUAUUAUUAA
...(((...((.((((((((((...((....)).....))))...(.((.((((.....)))).))).....))))))..)).....)))((((.((.......)).))))......... ( -37.80)
>DroVir_CAF1 97160 117 + 1
AUAGCCACCGAAAUUGGCGGCCACGGUCAGCACCACCAGGCUAAACAGUUGACCGCCCGGCGCAGCUGUGUCCCCGAUAAUCACAAAUGCCACAAUCCAAAGUAGCAAACCUGCAAG---
...((((.......)))).(((.((((((((................))))))))...)))((((.((((...........))))..(((.((........)).)))...))))...--- ( -31.19)
>DroSim_CAF1 59405 120 + 1
AUAGCCACCGAAAUUGGCGGCCACAGUGAGAACGACCAGGCCAAAGAGCUGCCCGCCAGGGGCAGCCGAGUCGCCGAUGAUCACAAAGGCGGUGACCCAGAUAAGGACACCUAUUAUUAA
...(((...((.((((((((((...((....)).....))))...(.(((((((.....)))))))).....))))))..)).....)))((((.((.......)).))))......... ( -42.60)
>DroWil_CAF1 53293 117 + 1
AUAGCCACCGAAAUUGGCUGCCACAGUCAGCACAACAAGACCAAAAAGCUGUCCACCAGGGGCAGCUGAGUCUCCAAUGAUCACAAAGGCCGUGACCCAUAUUAGGACACCUACAAA---
.((((((.......)))))).....(((.........((((.....((((((((.....))))))))..))))...(((.((((.......))))..))).....))).........--- ( -29.70)
>DroMoj_CAF1 98664 115 + 1
GUAGCCACCGAAAUUGGCGGCCACCGUGAGCACCACCAGGCUGAAGAGCUGCCCACCCGGGGCAGCUGUGUCCCCAAUGAUCACAAAGGCUACAAUCCAGAGUAGUAGACCU--AAG---
((((((...((.((((((((((...(((.....)))..))))).(.((((((((.....)))))))).)....)))))..)).....))))))...................--...--- ( -39.90)
>DroAna_CAF1 61512 118 + 1
GUAGCCGCCAAAGUUGGCGGCCACAGUAAGGACGACGAGACCGAAGAGCUGUCCGCCAGGGGCAGCCGAGUCGCCAAUGAUUACAAAGGCUGUUAUCCAAAUAAGGACACCUGUAAA--A
((.(((((((....))))))).)).....(((..(((.(((((....(((((((.....))))))))).)))(((..((....))..))))))..))).....(((...))).....--. ( -42.40)
>consensus
AUAGCCACCGAAAUUGGCGGCCACAGUGAGCACGACCAGGCCAAAGAGCUGCCCACCAGGGGCAGCCGAGUCGCCAAUGAUCACAAAGGCCGUGACCCAGAUAAGGACACCUAUAAA___
...((((.......)))).(((...((((.........(((....(.(((((((.....))))))))..)))........))))...))).............................. (-22.16 = -22.38 +   0.22)

alignment

secondary structure

dotplot

Window 2

Location	6,862,448 – 6,862,568
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.05
Mean single sequence MFE	-45.82
Consensus MFE	-29.30
Energy contribution	-29.72
Covariance contribution	0.42
Combinations/Pair	1.42
Mean z-score	-2.29
Structure conservation index	0.64
SVM decision value	1.29
SVM RNA-class probability	0.938434
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6862448 120 - 22407834
UUAAUAAUAGGUGUCCUUAUCUGGGUCACCGCCUUUGUGAUCAUCGGCGAUUCGGCAGCCCCUGGUGGGCAGCUCUUUGGCCUGGUCGUUCUCACUGUGGCCGCCAAUUUCGGUGGCUAC
.........((((.......(..(((((.((((..((....))..))))....(((.((((.....)))).)))...)))))..).......))))(((((((((......))))))))) ( -46.94)
>DroVir_CAF1 97160 117 - 1
---CUUGCAGGUUUGCUACUUUGGAUUGUGGCAUUUGUGAUUAUCGGGGACACAGCUGCGCCGGGCGGUCAACUGUUUAGCCUGGUGGUGCUGACCGUGGCCGCCAAUUUCGGUGGCUAU
---.(..((((..((((((........))))))))))..).....(....).((((..((((((((.............))))))))..))))...(((((((((......))))))))) ( -47.62)
>DroSim_CAF1 59405 120 - 1
UUAAUAAUAGGUGUCCUUAUCUGGGUCACCGCCUUUGUGAUCAUCGGCGACUCGGCUGCCCCUGGCGGGCAGCUCUUUGGCCUGGUCGUUCUCACUGUGGCCGCCAAUUUCGGUGGCUAU
.........((((.......(..(((((.((((..((....))..))))....((((((((.....))))))))...)))))..).......))))(((((((((......))))))))) ( -51.24)
>DroWil_CAF1 53293 117 - 1
---UUUGUAGGUGUCCUAAUAUGGGUCACGGCCUUUGUGAUCAUUGGAGACUCAGCUGCCCCUGGUGGACAGCUUUUUGGUCUUGUUGUGCUGACUGUGGCAGCCAAUUUCGGUGGCUAU
---.......(((.(((.....))).))).(((...((.(.(((..((((((.(((((((......)).)))))....))))))...))).).))...)))(((((.......))))).. ( -36.00)
>DroMoj_CAF1 98664 115 - 1
---CUU--AGGUCUACUACUCUGGAUUGUAGCCUUUGUGAUCAUUGGGGACACAGCUGCCCCGGGUGGGCAGCUCUUCAGCCUGGUGGUGCUCACGGUGGCCGCCAAUUUCGGUGGCUAC
---...--(((.((((...........))))))).(((((((((..((.....((((((((.....))))))))......))..))))...)))))(((((((((......))))))))) ( -48.40)
>DroAna_CAF1 61512 118 - 1
U--UUUACAGGUGUCCUUAUUUGGAUAACAGCCUUUGUAAUCAUUGGCGACUCGGCUGCCCCUGGCGGACAGCUCUUCGGUCUCGUCGUCCUUACUGUGGCCGCCAACUUUGGCGGCUAC
.--....(((((((((......))))).(((((.((((........))))...)))))..))))..((((.((.(....)....)).)))).....((((((((((....)))))))))) ( -44.70)
>consensus
___AUUAUAGGUGUCCUAAUCUGGAUCACAGCCUUUGUGAUCAUCGGCGACUCAGCUGCCCCUGGCGGGCAGCUCUUUGGCCUGGUCGUGCUCACUGUGGCCGCCAAUUUCGGUGGCUAC
.........((((.......((((((((...((..((....))..))......(((((.(((....))))))))...)))))))).......))))(((((((((......))))))))) (-29.30 = -29.72 +   0.42)

alignment

secondary structure

dotplot

Window 3

Location	6,862,488 – 6,862,597
Length	109
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	76.55
Mean single sequence MFE	-27.20
Consensus MFE	-19.91
Energy contribution	-20.13
Covariance contribution	0.23
Combinations/Pair	1.21
Mean z-score	-1.60
Structure conservation index	0.73
SVM decision value	1.26
SVM RNA-class probability	0.936855
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6862488 109 + 22407834
CCAAAGAGCUGCCCACCAGGGGCUGCCGAAUCGCCGAUGAUCACAAAGGCGGUGACCCAGAUAAGGACACCUAUUAUUAAGGAA---AUAGUUAACACAAUUAU---AAUGUAUG
((...(.((.((((.....)))).))).....(((..((....))..)))((((.((.......)).)))).........))..---((((((.....))))))---........ ( -24.00)
>DroSec_CAF1 66818 106 + 1
CCAAAGAGCUGCCCACCAGGGGCAGCCGAGUCGCCGAUGAUCACAAAGGCGGUGACCCAGAUAAGGACUCCUAUUAUUAAGAAA---AUAGUUAAUACAAUUAU---AA---CUU
.....(.(((((((.....))))))))((((((((..((....))..)))(....).........)))))(((((........)---)))).............---..---... ( -29.50)
>DroEre_CAF1 66630 108 + 1
CCAAAGAGCUGCCCUCCAGGGGCAGCCGAGUCGCCGAUGAUCACAAAGGCGGUGACCCAGAUGAGGACACCUGUGAUUUAGGAA---AUAAUU-ACACAAUUAU---AACCCCAU
((...(.(((((((.....))))))))((((((((..((....))..)))((((.(((....).)).))))...))))).))..---((((((-....))))))---........ ( -33.30)
>DroWil_CAF1 53333 97 + 1
CCAAAAAGCUGUCCACCAGGGGCAGCUGAGUCUCCAAUGAUCACAAAGGCCGUGACCCAUAUUAGGACACCUACAAA------C---AAAGUUUUGCCAAUUAU---UA------
.(((((((((((((.....))))))))..((((...(((.((((.......))))..)))....)))).........------.---....)))))........---..------ ( -22.20)
>DroYak_CAF1 64647 107 + 1
CCAAAGAGCUGCCCUCCAGGGGCAGCCGAGUCGCCGAUGAUCACGAAGGCGGUGACCCAGAUAAGGACACCUGUAAUUCAGAA----AAAUUU-AUAUAUUUAU---AACCUCAA
.....(.(((((((.....))))))))(.(((((((.(........)..))))))).).....(((....(((.....)))..----....((-(((....)))---)))))... ( -29.80)
>DroAna_CAF1 61552 113 + 1
CCGAAGAGCUGUCCGCCAGGGGCAGCCGAGUCGCCAAUGAUUACAAAGGCUGUUAUCCAAAUAAGGACACCUGUAAA--AGGGUAUUAUAAUAAAUUAAAUUAGAGAAAACUAAA
..((.(.(((((((.....))))))))...))(((..((....))..)))((((((((......))).((((.....--.))))....))))).......((((......)))). ( -24.40)
>consensus
CCAAAGAGCUGCCCACCAGGGGCAGCCGAGUCGCCGAUGAUCACAAAGGCGGUGACCCAGAUAAGGACACCUAUAAUU_AGGAA___AUAGUUAAUACAAUUAU___AA_CUCAA
.....(.(((((((.....)))))))).....(((..((....))..)))((((.((.......)).))))............................................ (-19.91 = -20.13 +   0.23)

alignment

secondary structure

dotplot

Window 4

Location	6,862,488 – 6,862,597
Length	109
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.55
Mean single sequence MFE	-28.95
Consensus MFE	-21.37
Energy contribution	-22.90
Covariance contribution	1.53
Combinations/Pair	1.05
Mean z-score	-0.89
Structure conservation index	0.74
SVM decision value	0.13
SVM RNA-class probability	0.598148
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6862488 109 - 22407834
CAUACAUU---AUAAUUGUGUUAACUAU---UUCCUUAAUAAUAGGUGUCCUUAUCUGGGUCACCGCCUUUGUGAUCAUCGGCGAUUCGGCAGCCCCUGGUGGGCAGCUCUUUGG
.(((((..---.....))))).......---.............((((.(((.....))).))))(((..((....))..))).....(((.((((.....)))).)))...... ( -27.80)
>DroSec_CAF1 66818 106 - 1
AAG---UU---AUAAUUGUAUUAACUAU---UUUCUUAAUAAUAGGAGUCCUUAUCUGGGUCACCGCCUUUGUGAUCAUCGGCGACUCGGCUGCCCCUGGUGGGCAGCUCUUUGG
...---..---.............((((---(........)))))(((((.......((....))(((..((....))..))))))))((((((((.....))))))))...... ( -32.00)
>DroEre_CAF1 66630 108 - 1
AUGGGGUU---AUAAUUGUGU-AAUUAU---UUCCUAAAUCACAGGUGUCCUCAUCUGGGUCACCGCCUUUGUGAUCAUCGGCGACUCGGCUGCCCCUGGAGGGCAGCUCUUUGG
.(((((..---((((((....-))))))---.)))))..((...((((.(((.....))).))))(((..((....))..)))))...((((((((.....))))))))...... ( -36.50)
>DroWil_CAF1 53333 97 - 1
------UA---AUAAUUGGCAAAACUUU---G------UUUGUAGGUGUCCUAAUAUGGGUCACGGCCUUUGUGAUCAUUGGAGACUCAGCUGCCCCUGGUGGACAGCUUUUUGG
------..---.......(((((.....---.------))))).(((.(((.......(((((((.....)))))))...))).))).(((((((......)).)))))...... ( -22.80)
>DroYak_CAF1 64647 107 - 1
UUGAGGUU---AUAAAUAUAU-AAAUUU----UUCUGAAUUACAGGUGUCCUUAUCUGGGUCACCGCCUUCGUGAUCAUCGGCGACUCGGCUGCCCCUGGAGGGCAGCUCUUUGG
..(((...---..........-......----............((((.(((.....))).))))(((............)))..)))((((((((.....))))))))...... ( -32.60)
>DroAna_CAF1 61552 113 - 1
UUUAGUUUUCUCUAAUUUAAUUUAUUAUAAUACCCU--UUUACAGGUGUCCUUAUUUGGAUAACAGCCUUUGUAAUCAUUGGCGACUCGGCUGCCCCUGGCGGACAGCUCUUCGG
.((((......))))..................(((--.....)))(((((......)))))...(((..((....))..)))((...(((((((......)).)))))..)).. ( -22.00)
>consensus
AUGAG_UU___AUAAUUGUAUUAACUAU___UUCCU_AAUUACAGGUGUCCUUAUCUGGGUCACCGCCUUUGUGAUCAUCGGCGACUCGGCUGCCCCUGGUGGGCAGCUCUUUGG
............................................((((.(((.....))).))))(((..((....))..))).....((((((((.....))))))))...... (-21.37 = -22.90 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:13 2006