Locus 7819

Sequence ID	X_DroMel_CAF1
Location	19,482,618 – 19,482,861
Length	243
Max. P	0.958417

overview

Window 4

Location	19,482,618 – 19,482,738
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-48.12
Consensus MFE	-43.84
Energy contribution	-44.28
Covariance contribution	0.44
Combinations/Pair	1.08
Mean z-score	-1.13
Structure conservation index	0.91
SVM decision value	-0.04
SVM RNA-class probability	0.514961
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19482618 120 + 22224390
AGCUGAGCCCAUCAGGUGGUAGCAACCCUCGGUGACCAUCAUCAUGAAGGUCUGCAUCUUUUCGAAGGCCGUCGGUUCGCUGCGGAUGGUCGUGUCCAAGGGGUCGGUGGGCAGAGCGCA
.(((..(((((((.....(((((((((..((((((((.((.....)).)))).....(((....)))))))..)))).)))))((((......))))........)))))))..)))... ( -48.40)
>DroSec_CAF1 4601 120 + 1
AGCUGAGCCCAUCAGAUGGUAGCAACCCUCGGUGACCAUCAUCAUGAAGGUCUGCAUCUUUUCGAAGGCCGUCGGUUCGCUGCGGAUGGUCGCGUCCAAGGGGUCGGUGGGCAGAGCGCA
.(((..(((((((.(((.(((((((((..((((((((.((.....)).)))).....(((....)))))))..)))).)))))(((((....))))).....))))))))))..)))... ( -51.30)
>DroSim_CAF1 4665 120 + 1
AGCUGAGCCCAUCAGAUGGUAGCAACCCUCGGUGACCAUCAUCAUGAAGGUCUGCAUCUUUUCGAAGGCCGUCGGUUCGCUGCGGAUGGUCGUGUCCAAGGGGUCGGUGGGCAGAGCGCA
.(((..(((((((.(((.(((((((((..((((((((.((.....)).)))).....(((....)))))))..)))).)))))((((......)))).....))))))))))..)))... ( -49.40)
>DroEre_CAF1 4284 120 + 1
UGCUGAGCCCAUCAGAUGGUAGCAACCCUCGGUGACCAUCAUCAUGAAUGUCUGCAUCUUUUCGAAGGCCGUCGGCUCGCUGCGGAUGGUGGUGUCCAAGGGGUCGGUGGGCAGAGCGCA
.(((..(((((((.((((....)..((((.((..(((((((((......((((.(........).))))((.(((....))))))))))))))..)).))))))))))))))..)))... ( -46.70)
>DroYak_CAF1 3839 120 + 1
UGCUGAGCCCAUCAGAUGAUAGCAACCCUCGGUGACCAUCAUCAUGAAUGUCUGCAUCUUUUCAAAGGCUGUCGGCUCGCUGCGGAUGGUGGUGUCCAAGGGGUCGGUGGGCAGUGCGCA
.((...(((((((.((((....)..((((.((..(((((((((..(...(((.(((((((....)))).))).)))...)....)))))))))..)).))))))))))))))...))... ( -44.80)
>consensus
AGCUGAGCCCAUCAGAUGGUAGCAACCCUCGGUGACCAUCAUCAUGAAGGUCUGCAUCUUUUCGAAGGCCGUCGGUUCGCUGCGGAUGGUCGUGUCCAAGGGGUCGGUGGGCAGAGCGCA
.(((..(((((((.((((((....(((...))).)))))).............(.(((((((.((.(((((((.((.....)).)))))))...)).)))))))))))))))..)))... (-43.84 = -44.28 +   0.44)

alignment

secondary structure

dotplot

Window 5

Location	19,482,698 – 19,482,796
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	96.33
Mean single sequence MFE	-38.08
Consensus MFE	-32.61
Energy contribution	-33.01
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.86
SVM decision value	1.49
SVM RNA-class probability	0.958417
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19482698 98 + 22224390
UGCGGAUGGUCGUGUCCAAGGGGUCGGUGGGCAGAGCGCAUAUGCCCAUUAGAAGCUUCUUCUCGUGCUCCAUCAUCCCAUGGAUUCCACGAUAACCC
...((...((((((((((.(((((.(((((((((((.((....)).)....((((...)))))).))).)))))))))).))))...))))))..)). ( -35.70)
>DroSec_CAF1 4681 98 + 1
UGCGGAUGGUCGCGUCCAAGGGGUCGGUGGGCAGAGCGCAUAUGCCCAUUAGAAGCUUCUUCUCGUGCUCCAUCAUCCCAUGGAUUCCGCGAUAACCC
...((...((((((((((.(((((.(((((((((((.((....)).)....((((...)))))).))).)))))))))).))))...))))))..)). ( -37.20)
>DroSim_CAF1 4745 98 + 1
UGCGGAUGGUCGUGUCCAAGGGGUCGGUGGGCAGAGCGCAUAUGCCCAUUAGAAGCUUCUUCUCGUGCUCCAUCAUCCCAUGGAUUCCGCGAUAGCCC
...((...((((((((((.(((((.(((((((((((.((....)).)....((((...)))))).))).)))))))))).))))...))))))..)). ( -36.40)
>DroEre_CAF1 4364 98 + 1
UGCGGAUGGUGGUGUCCAAGGGGUCGGUGGGCAGAGCGCAAAUGCCCAUUAGAAGCUUCUUCUCGUUCUCCAUCAUCCCAUGGAUUCCGCGAUAUCCC
...(((((((((.(((((.(((((.(((((..(((((((....)).....(((((...))))).))))))))))))))).))))).))))..))))). ( -39.90)
>DroYak_CAF1 3919 98 + 1
UGCGGAUGGUGGUGUCCAAGGGGUCGGUGGGCAGUGCGCAAAUGCCCAUUAGAAGCUUCUUCUCGUGCUCCAUCAUCCCAUGGAUUCCGCGAUAUCCC
...(((((((((.(((((.(((((.(((((((((((.((....)).))))(((((...)))))...)).)))))))))).))))).))))..))))). ( -41.20)
>consensus
UGCGGAUGGUCGUGUCCAAGGGGUCGGUGGGCAGAGCGCAUAUGCCCAUUAGAAGCUUCUUCUCGUGCUCCAUCAUCCCAUGGAUUCCGCGAUAACCC
.(((((.......(((((.(((((.((((((((..(.((....)).)...(((((...)))))..))).)))))))))).))))))))))........ (-32.61 = -33.01 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	19,482,758 – 19,482,861
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.51
Mean single sequence MFE	-29.05
Consensus MFE	-16.33
Energy contribution	-17.08
Covariance contribution	0.76
Combinations/Pair	1.26
Mean z-score	-1.88
Structure conservation index	0.56
SVM decision value	0.26
SVM RNA-class probability	0.656037
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19482758 103 + 22224390
UCUCGUG--CUCCAUCAUCCCAUGGAUUCCACGAUAACCCUCGGAGAGCGCUUGCA-GAGCCUCCGGAGCAAACAGCUCAUUAAGCAC-ACGCAUCAAGCUCAGCAC-------------
....(((--((((((......))))).((..(((......)))..)))))).(((.-((((.....((((.....)))).....((..-..)).....)))).))).------------- ( -28.30)
>DroSec_CAF1 4741 103 + 1
UCUCGUG--CUCCAUCAUCCCAUGGAUUCCGCGAUAACCCUCGGAGAGCGCGUGCA-GAGCCUCCGGAGCAAACAGCUCAUUUAGCAC-ACGCAUCAAGCUCAGCAC-------------
....(((--(((....((((...))))((((.(......).))))))))))((((.-((((.....((((.....)))).....((..-..)).....)))).))))------------- ( -33.80)
>DroSim_CAF1 4805 103 + 1
UCUCGUG--CUCCAUCAUCCCAUGGAUUCCGCGAUAGCCCUCGGAGAGCGCGUGCA-GAGCCUCCGGAGCAAACAGCUCAUUUAGCAC-ACGCAUCAAGCUCAGCAC-------------
....(((--(((....((((...))))((((.(......).))))))))))((((.-((((.....((((.....)))).....((..-..)).....)))).))))------------- ( -33.80)
>DroEre_CAF1 4424 103 + 1
UCUCGUU--CUCCAUCAUCCCAUGGAUUCCGCGAUAUCCCUCGGAAAGUGCUUGCA-GAGCCUCCGGAGCAAACAGCUCGUUGAGCAC-ACGCAUCAAGCUCAGCAC-------------
.......--.(((((......)))))(((((.(......).))))).(((((....-((((.....((((.....)))).((((((..-..)).)))))))))))))------------- ( -28.70)
>DroYak_CAF1 3979 103 + 1
UCUCGUG--CUCCAUCAUCCCAUGGAUUCCGCGAUAUCCCUCGGAGAGUGCUUGCA-AAGCCUCCGGAGCAAACAGCUCAUUGAGCAC-ACGCAUCAAGCUCAGCAC-------------
.....((--((((....(((...((((........))))...)))(((.(((....-.)))))).))))))....(((..((((((..-..)).))))....)))..------------- ( -29.80)
>DroPer_CAF1 8271 108 + 1
UCUCUUUAUAUGUAACAUCCCAUGUAU----CGAUAAC--------AGAAUCUGCAUCAGCUGUCGCAGCAAAUCGCAGAUUUACCACCACUAAUCAAUAUCAACAUUUCUGGUCGUCAA
..((..((((((........)))))).----.))....--------.((((((((((..((((...))))..)).))))))))((.((((..(((..........)))..)))).))... ( -19.90)
>consensus
UCUCGUG__CUCCAUCAUCCCAUGGAUUCCGCGAUAACCCUCGGAGAGCGCUUGCA_GAGCCUCCGGAGCAAACAGCUCAUUUAGCAC_ACGCAUCAAGCUCAGCAC_____________
..(((((...(((((......)))))...)))))...........((((...(((....((.....((((.....)))).....)).....)))....)))).................. (-16.33 = -17.08 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:17 2006