Locus 7611

Sequence ID	3L_DroMel_CAF1
Location	20,484,226 – 20,484,470
Length	244
Max. P	0.865014

overview

Window 6

Location	20,484,226 – 20,484,338
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.00
Mean single sequence MFE	-23.10
Consensus MFE	-19.74
Energy contribution	-19.47
Covariance contribution	-0.28
Combinations/Pair	1.10
Mean z-score	-1.90
Structure conservation index	0.85
SVM decision value	0.71
SVM RNA-class probability	0.829055
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20484226 112 - 23771897
UUUAAUUGAACAAUUUGUAACAAUCAUGCGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGAUGCAACUGGC--GAAAAUUAAUAUCGUCGAUUAAAG------UCU
(((((((((.(((.((((........(((((........))))))))).)))(((......((((((...))))))......)))--..............))))))))).------... ( -22.50)
>DroPse_CAF1 30626 111 - 1
UUUAAUUGAACAAUUUGUAACAAUCAUGUGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGGAGCUGCAACUGGCUGCAAAAUGAAUAUCAUCGAUUAAAG---------
(((((((((.(((.((((........(((((........))))))))).)))............((((.((.((((......)))).))...)))).....))))))))).--------- ( -22.50)
>DroSim_CAF1 26707 112 - 1
UUUAAUUGAACAAUUUGUAACAAUCAUGCGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGAUGCAACUGGC--GAAAAUUAAUAUCGUCGAUUAAAG------UCU
(((((((((.(((.((((........(((((........))))))))).)))(((......((((((...))))))......)))--..............))))))))).------... ( -22.50)
>DroEre_CAF1 28674 118 - 1
UUUAAUUGAACAAUUUGUAACAAUCAUGCGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGAUGCAACUGGC--GAAAAUUAAUAUCCUCGAUUAAAGUGCAAGUGU
............(((((((..((((.(((((........)))))....(((.(((......((((((...))))))......)))--.)))............))))....))))))).. ( -22.80)
>DroAna_CAF1 25320 112 - 1
UUUAAUUGAACAAUUUGUAACAAUCAUGUGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGACGCAACUGGC--CAAAAUUAAUAACAUCGAUUAAAG------UUU
(((((((((.................(((((........)))))....(((((((......((((((...))))))......)))--))))..........))))))))).------... ( -25.80)
>DroPer_CAF1 29249 111 - 1
UUUAAUUGAACAAUUUGUAACAAUCAUGUGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGGAGCUGCAACUGGCUGCAAAAUGAAUAUCAUCGAUUAAAG---------
(((((((((.(((.((((........(((((........))))))))).)))............((((.((.((((......)))).))...)))).....))))))))).--------- ( -22.50)
>consensus
UUUAAUUGAACAAUUUGUAACAAUCAUGCGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGAUGCAACUGGC__CAAAAUUAAUAUCAUCGAUUAAAG______U_U
(((((((((.(((.((((........(((((........))))))))).)))(((......((((((...))))))......)))................))))))))).......... (-19.74 = -19.47 +  -0.28)

alignment

secondary structure

dotplot

Window 7

Location	20,484,258 – 20,484,376
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.34
Mean single sequence MFE	-28.40
Consensus MFE	-21.42
Energy contribution	-21.86
Covariance contribution	0.44
Combinations/Pair	1.12
Mean z-score	-3.16
Structure conservation index	0.75
SVM decision value	0.26
SVM RNA-class probability	0.658166
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20484258 118 - 23771897
--UCUUGCCUUUCCUCUGCCCAUUGAGCGUCUUUUAAGCCUUUAAUUGAACAAUUUGUAACAAUCAUGCGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGAUGCAA
--...(((......(((...(((((((..(..((((((((...(((((.((.....))........(((((........))))).))))).))))))))..)..))))))).))).))). ( -29.30)
>DroPse_CAF1 30657 108 - 1
--ACUCGGCUUUCCUCU----------CCUCUUUUAAGCCUUUAAUUGAACAAUUUGUAACAAUCAUGUGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGGAGCUGCAA
--...(((((((.....----------...((((((((((...(((((.((.....))........(((((........))))).))))).)))))))).))........)))))))... ( -25.09)
>DroSec_CAF1 26903 118 - 1
--UCUUGCCUUUUCUAUGCCCAUUGAGCGUCUUUUAAGCCUUUAAUUGAACAAUUUGUAACAAUCAUGCGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGAUGCAA
--...(((.(((((.......((((((..(..((((((((...(((((.((.....))........(((((........))))).))))).))))))))..)..))))))))))).))). ( -29.41)
>DroEre_CAF1 28712 118 - 1
--UCUUGCCUUUCCUCUGCCCAUUGAGCGUCUUUUAAGCCUUUAAUUGAACAAUUUGUAACAAUCAUGCGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGAUGCAA
--...(((......(((...(((((((..(..((((((((...(((((.((.....))........(((((........))))).))))).))))))))..)..))))))).))).))). ( -29.30)
>DroAna_CAF1 25352 120 - 1
CCUCCUGGCUUUCCUCUGGCCAUUGAGCGUCUUUUAAGCCUUUAAUUGAACAAUUUGUAACAAUCAUGUGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGACGCAA
.....(((((.......)))))....((((((((((((((...(((((.((.....))........(((((........))))).))))).)))))).............)))))))).. ( -32.21)
>DroPer_CAF1 29280 108 - 1
--ACUCGGCUUUCCUCU----------CCUCUUUUAAGCCUUUAAUUGAACAAUUUGUAACAAUCAUGUGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGGAGCUGCAA
--...(((((((.....----------...((((((((((...(((((.((.....))........(((((........))))).))))).)))))))).))........)))))))... ( -25.09)
>consensus
__UCUUGCCUUUCCUCUGCCCAUUGAGCGUCUUUUAAGCCUUUAAUUGAACAAUUUGUAACAAUCAUGCGCACAAAAUAGCGCAACAAUUUGGCUUAAAUAGUUUUCAAUGAAGAUGCAA
..........................((((((((((((((...(((((.((.....))........(((((........))))).))))).)))))).............)))))))).. (-21.42 = -21.86 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	20,484,376 – 20,484,470
Length	94
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	89.22
Mean single sequence MFE	-42.50
Consensus MFE	-33.26
Energy contribution	-34.77
Covariance contribution	1.50
Combinations/Pair	1.03
Mean z-score	-2.06
Structure conservation index	0.78
SVM decision value	0.84
SVM RNA-class probability	0.865014
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20484376 94 + 23771897
CCGGGUUCCAAGACACCCAGAACCC--------CAGAUGCCCAGAUCCCAGGUUCUCCUGACUCCGAUCUGCGGUUCGGAGCUGGGAGUUUCGAGUCUGGGU
..((((((...........))))))--------.....((((((((....((..(((((..((((((........))))))..)))))..))..)))))))) ( -41.00)
>DroSec_CAF1 27021 102 + 1
CCGGGUUCCAAGACACCCAGAACCCCCGAUGCCCAGAUGCCCAGAUCCCAGGUUCUACUGGCUCCGAUCUGCGGUCCGGAGCUGGGUGCUUCGAGUCUGGGU
..((((((...........)))))).....(((((((((((((((((((((......))))....)))))).))).((((((.....)))))).)))))))) ( -44.90)
>DroSim_CAF1 26857 102 + 1
CCGGGUUCCAAGACACCCAGAACCCCCGAUGCCCAGAUGCCCAGAUCCCAGGUUCUCCUGGCUCCGAUCUGCGGUCCGGAGCUGGGUGCUUCGAGUCUGGGU
..((((((...........)))))).....((((((((((((((((((((((....)))))....)))))).))).((((((.....)))))).)))))))) ( -47.10)
>DroEre_CAF1 28830 102 + 1
CCGGGUUCCAAGACACCCAGAGCCCCAGAUGCCCAGAUCCCCAGAUCCCAGGUUCUCCUGGCUCCGAUCUGCAGCGCAGAGCUGGGAGUUUCGAGGCUGGCU
((((((........))))..((((...((.((((.......(((((((((((....)))))....))))))((((.....)))))).)).))..)))))).. ( -37.00)
>consensus
CCGGGUUCCAAGACACCCAGAACCCCCGAUGCCCAGAUGCCCAGAUCCCAGGUUCUCCUGGCUCCGAUCUGCGGUCCGGAGCUGGGAGCUUCGAGUCUGGGU
((((..((.(((.(((((((..((..............((((((((((((((....)))))....)))))).)))..))..)))))))))).))..)))).. (-33.26 = -34.77 +   1.50)

alignment

secondary structure

dotplot

Window 9

Location	20,484,376 – 20,484,470
Length	94
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	89.22
Mean single sequence MFE	-43.08
Consensus MFE	-36.17
Energy contribution	-37.42
Covariance contribution	1.25
Combinations/Pair	1.10
Mean z-score	-1.47
Structure conservation index	0.84
SVM decision value	0.17
SVM RNA-class probability	0.617040
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20484376 94 - 23771897
ACCCAGACUCGAAACUCCCAGCUCCGAACCGCAGAUCGGAGUCAGGAGAACCUGGGAUCUGGGCAUCUG--------GGGUUCUGGGUGUCUUGGAACCCGG
.((((((((((...((((..(((((((........)))))))..))))....)))).))))))......--------((((((..((...))..)))))).. ( -43.90)
>DroSec_CAF1 27021 102 - 1
ACCCAGACUCGAAGCACCCAGCUCCGGACCGCAGAUCGGAGCCAGUAGAACCUGGGAUCUGGGCAUCUGGGCAUCGGGGGUUCUGGGUGUCUUGGAACCCGG
..((.(..((.((((((((((((((((.((.(((((((((.((((......))))..))))...)))))))..))))))...))))))).))).))..).)) ( -41.50)
>DroSim_CAF1 26857 102 - 1
ACCCAGACUCGAAGCACCCAGCUCCGGACCGCAGAUCGGAGCCAGGAGAACCUGGGAUCUGGGCAUCUGGGCAUCGGGGGUUCUGGGUGUCUUGGAACCCGG
..((.(..((.((((((((((((((((.((.(((((((((.(((((....)))))..))))...)))))))..))))))...))))))).))).))..).)) ( -44.70)
>DroEre_CAF1 28830 102 - 1
AGCCAGCCUCGAAACUCCCAGCUCUGCGCUGCAGAUCGGAGCCAGGAGAACCUGGGAUCUGGGGAUCUGGGCAUCUGGGGCUCUGGGUGUCUUGGAACCCGG
....(((((((.....(((((.(((((...)))))(((((.(((((....)))))..)))))....)))))....)))))))((((((........)))))) ( -42.20)
>consensus
ACCCAGACUCGAAACACCCAGCUCCGGACCGCAGAUCGGAGCCAGGAGAACCUGGGAUCUGGGCAUCUGGGCAUCGGGGGUUCUGGGUGUCUUGGAACCCGG
.((((((((((...((((..(((((((.(....).)))))))..))))....)))).))))))..............((((((..((...))..)))))).. (-36.17 = -37.42 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:38 2006