Locus 5225

Sequence ID	2R_DroMel_CAF1
Location	17,009,569 – 17,009,728
Length	159
Max. P	0.990784

overview

Window 4

Location	17,009,569 – 17,009,688
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.73
Mean single sequence MFE	-31.84
Consensus MFE	-23.30
Energy contribution	-23.06
Covariance contribution	-0.24
Combinations/Pair	1.11
Mean z-score	-2.97
Structure conservation index	0.73
SVM decision value	2.11
SVM RNA-class probability	0.988154
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17009569 119 + 20766785
UUUGAUAAGCGACGAUGUAUCGCUGGUCGGCGAUACUAUUUCUAAAAUAUCGGCUAGC-UCGAUAGCACCUAUAUGAAAACAUCGAUUCCCGAUGCAUCGAUGUUUCUCCCCAUCACUAU
...((.(((((.((((((((((..(((((((((((............)))))((((..-....))))...............))))))..)))))))))).))))).))........... ( -31.80)
>DroSec_CAF1 105831 118 + 1
UUUGAAAAGCAACGAUGUAUCGCUGGGCUGCGAUACUAUUUCUAAAAUAUCGGCUAGCCUCGAUAGCAUCU--UUGAAAACAUCGAUUUCCGAUGCAUCGAUGUUUCUGCCCAUCACUAU
.............((((((((((......)))))))...............(((.(((.(((((.(((((.--..((((.......)))).)))))))))).)))...))).)))..... ( -31.30)
>DroSim_CAF1 112666 118 + 1
UUUGAAAAAUAACGAUGUAUCGCUGGGCUGCGAUACUAUUUCUAAAAUAUCGGCUAGCCUCGAUACCAUCU--UUGAAAACAUCGAUUCCCGAUGCAUCGAUGUUUCCGCCCAUCACUAU
..(((........(((((((((..(((((((((((............)))).)).)))))))))).)))).--..(.((((((((((.(.....).)))))))))).).....))).... ( -29.70)
>DroEre_CAF1 107996 115 + 1
UUUGAAAAUCAACGAUGUAUCGCUGGUCGGCGAUA---UUACAGAAAUAUCGGCUAACAUCGAUAACAUCU--UUGAAAACAUCGAUUCUCGAUGCAUCGAUGUUUUUUCACAUCACUAU
..(((((.((((.(((((((((.((...(.(((((---((.....))))))).)...)).)))).))))).--))))((((((((((.(.....).)))))))))))))))......... ( -35.50)
>DroYak_CAF1 114714 115 + 1
UUUUAAAAUCUACGAUGUAUCGUUGGUCAGCGAUA---UUACAGAAAUAACGGCCAACAUCGAUAGCAGCU--UUCAGAACAUCGAUUCUCGAUGCAUCGAUGUGCCUUCACAUCACUAG
.............((((((((((((((...((.((---((.....)))).))))))))((((((..(....--....)...))))))....))))))))((((((....))))))..... ( -30.90)
>consensus
UUUGAAAAGCAACGAUGUAUCGCUGGUCGGCGAUACUAUUUCUAAAAUAUCGGCUAGCAUCGAUAGCAUCU__UUGAAAACAUCGAUUCCCGAUGCAUCGAUGUUUCUGCCCAUCACUAU
.............((((((((((......))))))............((((((......))))))............((((((((((.(.....).)))))))))).....))))..... (-23.30 = -23.06 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	17,009,569 – 17,009,688
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.73
Mean single sequence MFE	-36.70
Consensus MFE	-24.21
Energy contribution	-25.25
Covariance contribution	1.04
Combinations/Pair	1.18
Mean z-score	-3.19
Structure conservation index	0.66
SVM decision value	1.77
SVM RNA-class probability	0.976202
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17009569 119 - 20766785
AUAGUGAUGGGGAGAAACAUCGAUGCAUCGGGAAUCGAUGUUUUCAUAUAGGUGCUAUCGA-GCUAGCCGAUAUUUUAGAAAUAGUAUCGCCGACCAGCGAUACAUCGUCGCUUAUCAAA
..((((((((.(((((.(((((((.........))))))))))))((((.((((((....)-))..))).))))..........(((((((......))))))).))))))))....... ( -35.50)
>DroSec_CAF1 105831 118 - 1
AUAGUGAUGGGCAGAAACAUCGAUGCAUCGGAAAUCGAUGUUUUCAA--AGAUGCUAUCGAGGCUAGCCGAUAUUUUAGAAAUAGUAUCGCAGCCCAGCGAUACAUCGUUGCUUUUCAAA
....(((..(((((((((((((((.........)))))))))))...--.((((.(((((.((((.((.((((((........))))))))))))...)))))))))..))))..))).. ( -42.10)
>DroSim_CAF1 112666 118 - 1
AUAGUGAUGGGCGGAAACAUCGAUGCAUCGGGAAUCGAUGUUUUCAA--AGAUGGUAUCGAGGCUAGCCGAUAUUUUAGAAAUAGUAUCGCAGCCCAGCGAUACAUCGUUAUUUUUCAAA
..((((((((..((((((((((((.........))))))))))))..--.....((((((.((((.((.((((((........))))))))))))...)))))).))))))))....... ( -40.30)
>DroEre_CAF1 107996 115 - 1
AUAGUGAUGUGAAAAAACAUCGAUGCAUCGAGAAUCGAUGUUUUCAA--AGAUGUUAUCGAUGUUAGCCGAUAUUUCUGUAA---UAUCGCCGACCAGCGAUACAUCGUUGAUUUUCAAA
.........(((((((((((((((.........))))))))).((((--.(((((.((((..((..((.((((((.....))---))))))..))...))))))))).)))))))))).. ( -34.90)
>DroYak_CAF1 114714 115 - 1
CUAGUGAUGUGAAGGCACAUCGAUGCAUCGAGAAUCGAUGUUCUGAA--AGCUGCUAUCGAUGUUGGCCGUUAUUUCUGUAA---UAUCGCUGACCAACGAUACAUCGUAGAUUUUAAAA
.....((((((....))))))((.((((((.....))))))))((((--(.(((((((((..((..((.(((((....))))---)...))..))...)))))....)))).)))))... ( -30.70)
>consensus
AUAGUGAUGGGAAGAAACAUCGAUGCAUCGGGAAUCGAUGUUUUCAA__AGAUGCUAUCGAGGCUAGCCGAUAUUUUAGAAAUAGUAUCGCAGACCAGCGAUACAUCGUUGAUUUUCAAA
..((((((.....(((((((((((.........)))))))))))......((((.(((((........(((((((........)))))))........)))))))))))))))....... (-24.21 = -25.25 +   1.04)

alignment

secondary structure

dotplot

Window 6

Location	17,009,609 – 17,009,728
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.39
Mean single sequence MFE	-28.46
Consensus MFE	-20.84
Energy contribution	-21.48
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.16
Structure conservation index	0.73
SVM decision value	0.67
SVM RNA-class probability	0.819234
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17009609 119 + 20766785
UCUAAAAUAUCGGCUAGC-UCGAUAGCACCUAUAUGAAAACAUCGAUUCCCGAUGCAUCGAUGUUUCUCCCCAUCACUAUCAAAUUUGCUUUGCGCUGCAUCGAGACCGAGAAUUAAAGA
(((..(((.((((....(-(((((.(((.......((((((((((((.(.....).)))))))))).))..................((.....))))))))))).))))..)))..))) ( -26.60)
>DroSec_CAF1 105871 118 + 1
UCUAAAAUAUCGGCUAGCCUCGAUAGCAUCU--UUGAAAACAUCGAUUUCCGAUGCAUCGAUGUUUCUGCCCAUCACUAUCAAAUUUGCUUUGCGCUGCAUCGAGACCGAGAAUUAAAGA
(((..(((.((((((.((..((..((((..(--((((...(((((.....)))))....((((........))))....)))))..))))...))..))....)).))))..)))..))) ( -27.30)
>DroSim_CAF1 112706 118 + 1
UCUAAAAUAUCGGCUAGCCUCGAUACCAUCU--UUGAAAACAUCGAUUCCCGAUGCAUCGAUGUUUCCGCCCAUCACUAUCAAAUUUGCUUUGCGCUGCAUCGAGACCGAGAAUUAAAGA
.......((((((......))))))...(((--((((.....(((..((.(((((((..((((........))))............((.....))))))))).)).)))...))))))) ( -25.00)
>DroEre_CAF1 108033 118 + 1
ACAGAAAUAUCGGCUAACAUCGAUAACAUCU--UUGAAAACAUCGAUUCUCGAUGCAUCGAUGUUUUUUCACAUCACUAUCAAAUUUGCUUUACGCUGCAUCGAGACCGAGAAUUAAAGA
.......((((((......))))))...(((--((((.....(((..((((((((((..(((((......)))))............((.....)))))))))))).)))...))))))) ( -31.50)
>DroYak_CAF1 114751 118 + 1
ACAGAAAUAACGGCCAACAUCGAUAGCAGCU--UUCAGAACAUCGAUUCUCGAUGCAUCGAUGUGCCUUCACAUCACUAGAAAAUUUGCUUUGCGCUGCAUCGAGACCGAGAAUUAAAGA
..........(((......(((((.((((((--(((.((.(((((.....)))))..))((((((....))))))....))))....((...))))))))))))..)))........... ( -31.90)
>consensus
UCUAAAAUAUCGGCUAGCAUCGAUAGCAUCU__UUGAAAACAUCGAUUCCCGAUGCAUCGAUGUUUCUGCCCAUCACUAUCAAAUUUGCUUUGCGCUGCAUCGAGACCGAGAAUUAAAGA
.........((((......(((((....((.....))....))))).((.(((((((..((((........))))............((.....))))))))).)))))).......... (-20.84 = -21.48 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	17,009,609 – 17,009,728
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.39
Mean single sequence MFE	-35.96
Consensus MFE	-29.22
Energy contribution	-29.66
Covariance contribution	0.44
Combinations/Pair	1.07
Mean z-score	-2.49
Structure conservation index	0.81
SVM decision value	2.23
SVM RNA-class probability	0.990784
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17009609 119 - 20766785
UCUUUAAUUCUCGGUCUCGAUGCAGCGCAAAGCAAAUUUGAUAGUGAUGGGGAGAAACAUCGAUGCAUCGGGAAUCGAUGUUUUCAUAUAGGUGCUAUCGA-GCUAGCCGAUAUUUUAGA
(((..(((..((((((((((((((.(.((((.....))))...........(((((.(((((((.........)))))))))))).....).))).)))))-)...))))).)))..))) ( -33.60)
>DroSec_CAF1 105871 118 - 1
UCUUUAAUUCUCGGUCUCGAUGCAGCGCAAAGCAAAUUUGAUAGUGAUGGGCAGAAACAUCGAUGCAUCGGAAAUCGAUGUUUUCAA--AGAUGCUAUCGAGGCUAGCCGAUAUUUUAGA
(((..(((..((((((((((((((((.((..((..........))..)).)).(((((((((((.........)))))))))))...--...))).))))))....))))).)))..))) ( -35.00)
>DroSim_CAF1 112706 118 - 1
UCUUUAAUUCUCGGUCUCGAUGCAGCGCAAAGCAAAUUUGAUAGUGAUGGGCGGAAACAUCGAUGCAUCGGGAAUCGAUGUUUUCAA--AGAUGGUAUCGAGGCUAGCCGAUAUUUUAGA
(((..(((..(((((((((((((.((.((..((..........))..)).))((((((((((((.........))))))))))))..--.....))))))))....))))).)))..))) ( -39.40)
>DroEre_CAF1 108033 118 - 1
UCUUUAAUUCUCGGUCUCGAUGCAGCGUAAAGCAAAUUUGAUAGUGAUGUGAAAAAACAUCGAUGCAUCGAGAAUCGAUGUUUUCAA--AGAUGUUAUCGAUGUUAGCCGAUAUUUCUGU
..........((((((((((((((((.....))...........((((((......)))))).))))))))))(((((((...((..--.))...))))))).....))))......... ( -34.60)
>DroYak_CAF1 114751 118 - 1
UCUUUAAUUCUCGGUCUCGAUGCAGCGCAAAGCAAAUUUUCUAGUGAUGUGAAGGCACAUCGAUGCAUCGAGAAUCGAUGUUCUGAA--AGCUGCUAUCGAUGUUGGCCGUUAUUUCUGU
...........(((((((((((((((((...))....((((....((((((....))))))((.((((((.....)))))))).)))--)))))).)))))....))))).......... ( -37.20)
>consensus
UCUUUAAUUCUCGGUCUCGAUGCAGCGCAAAGCAAAUUUGAUAGUGAUGGGAAGAAACAUCGAUGCAUCGGGAAUCGAUGUUUUCAA__AGAUGCUAUCGAGGCUAGCCGAUAUUUUAGA
..........((((((((((((((((.....))...........(((((........))))).)))))))))..((((((...((.....))...)))))).....)))))......... (-29.22 = -29.66 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:34 2006