Locus 2958

Sequence ID	2R_DroMel_CAF1
Location	10,201,473 – 10,201,633
Length	160
Max. P	0.915584

overview

Window 7

Location	10,201,473 – 10,201,571
Length	98
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	74.58
Mean single sequence MFE	-13.77
Consensus MFE	-6.63
Energy contribution	-6.80
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.48
SVM decision value	1.10
SVM RNA-class probability	0.915584
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10201473 98 + 20766785
AAAUAGAAUGGCACAUG-UACAUACAUACAUAUGUAUAUGUUUAAACCAAACG---CAACGGUCAAUCAAUUACAGAAUGGCCACAGAAUAAGCAUAAUAAA
..........(((((((-((((((......)))))))))))............---....(((((.((.......)).))))).........))........ ( -20.50)
>DroSec_CAF1 31179 75 + 1
AAAUAGAAUG--------UACA----------------UAUAUAAACCAAACG---CAACGGUCAAUCAAUUACAGAAUGGCCACAGAAUAAGCAUAAUAAA
..........--------....----------------...............---....(((((.((.......)).)))))................... (  -7.70)
>DroSim_CAF1 30983 87 + 1
AAAUAGAAUG--------UACAUAUGUACAUACA----UAUAUAAACCAAACG---CAACGGUCAAUCAAUUACAGAAUGGCCACAGAAUAAGCAUAAUAAA
.....(.(((--------(((....)))))).).----...............---....(((((.((.......)).)))))................... ( -13.60)
>DroEre_CAF1 34158 94 + 1
AAAUAGAAUGGCACAUG-UACCUACAUACAUGUA----UGCAUAAAGCGAACG---CAGCGGUCAAUCAAUUACAGAAUGGCCACAGAAUCAGCAUAAUAAA
............(((((-((......)))))))(----(((.....((....)---).(.(((((.((.......)).))))).).......))))...... ( -20.20)
>DroYak_CAF1 30456 87 + 1
AAACAGAAUGGCAUAUA-UA----CACACAUAUC----UACAUAUACCAAACG---CAUCGGUCAAUC---UACAGAAUGGCCGCAGAAUAAGCAUAAUAAA
........(((.((((.-((----..........----)).)))).)))....---....(((((.((---....)).)))))((.......))........ ( -10.90)
>DroAna_CAF1 31573 89 + 1
AAA-AGAA---CACAUUAUAC-AACACACAU--A----AACAUUAAG--AGUGUAAUAUCGGUCAAUCAAUUACGAAAUGGCCGCAGAAUAAGCAUAAUAAA
...-....---...(((((.(-...((((..--.----.........--.)))).....((((((.((......))..))))))........).)))))... (  -9.72)
>consensus
AAAUAGAAUG_CACAU__UACAUACAUACAUAUA____UACAUAAACCAAACG___CAACGGUCAAUCAAUUACAGAAUGGCCACAGAAUAAGCAUAAUAAA
............................................................(((((.((.......)).)))))................... ( -6.63 =  -6.80 +   0.17)

alignment

secondary structure

dotplot

Window 8

Location	10,201,512 – 10,201,611
Length	99
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	79.09
Mean single sequence MFE	-21.14
Consensus MFE	-11.88
Energy contribution	-12.52
Covariance contribution	0.64
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.56
SVM decision value	0.55
SVM RNA-class probability	0.779057
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10201512 99 + 20766785
UUUAAAC--C---AAACG---CA-ACGGUCAAUCAAUUACAGAAUGGCCACAGAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGUUUCCCGA
...((((--(---(...(---(.-..(((((.((.......)).)))))((((..(((((((.................)))))))..))))))...))))))..... ( -21.63)
>DroPse_CAF1 13339 103 + 1
UGGAGAC--UCUGGAGAG---CUUCUGUUCAAUCAAUUACCGAAUGGCCACAAAAUAGGCAUAAUAAAUUCGCAAUUAAAUGCUUAAAUUGUGCAAAUGGCUGUCCAA
.(....)--..((((.((---((..(((.((((........((((.(((........))).......))))(((......)))....)))).)))...)))).)))). ( -24.20)
>DroEre_CAF1 34193 99 + 1
CAUAAAG--C---GAACG---CA-GCGGUCAAUCAAUUACAGAAUGGCCACAGAAUCAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGCUUCCCGA
......(--(---....)---)(-(((((((.((.......)).))))).........(((((((......(((......)))....))))))).....)))...... ( -20.60)
>DroWil_CAF1 33380 98 + 1
CAUAAACACUGUG---------A-ACAGUCAAUCAAUUACAAAAUGGCCACAAAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGUUUGCCAA
.......((((..---------.-.))))...............(((((((((..(((((((.................)))))))..)))))..........)))). ( -17.43)
>DroAna_CAF1 31602 100 + 1
CAUUAAG-------AGUGUAAUA-UCGGUCAAUCAAUUACGAAAUGGCCGCAGAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGUUUACCAA
.......-------.(..((((.-.((((((.((......))..)))))).....(((((((.................))))))).))))..)...(((....))). ( -18.43)
>DroPer_CAF1 13177 103 + 1
UGGAGGC--UCUGGAGAG---CUUCUGUUCAAUCAAUUACCGAAUGCCCACAAAAUAGGCAUAAUAAAUUCGUAAUUAAAUGCUUAAAUUGUGCAAAUGGCUGUCCAA
.((((((--((....)))---)))))...............((..((((((((..(((((((.................)))))))..))))).....)))..))... ( -24.53)
>consensus
CAUAAAC__U___GAGAG___CA_ACGGUCAAUCAAUUACAGAAUGGCCACAAAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGCUUCCCAA
..........................(((((.((.......)).))))).........(((((((......(((......)))....)))))))...(((....))). (-11.88 = -12.52 +   0.64)

alignment

secondary structure

dotplot

Window 9

Location	10,201,543 – 10,201,633
Length	90
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	79.53
Mean single sequence MFE	-19.76
Consensus MFE	-13.63
Energy contribution	-13.05
Covariance contribution	-0.58
Combinations/Pair	1.28
Mean z-score	-1.51
Structure conservation index	0.69
SVM decision value	0.49
SVM RNA-class probability	0.758139
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10201543 90 + 20766785
AGAAUGGCCACAGAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGUUUCCCGAUAUGGUGAC-------GCGGUUUGAGUUC
.((((...(((((..(((((((.................)))))))..)))))(((((.((.((((.....)).)).-------)).))))).)))) ( -19.13)
>DroPse_CAF1 13374 90 + 1
CGAAUGGCCACAAAAUAGGCAUAAUAAAUUCGCAAUUAAAUGCUUAAAUUGUGCAAAUGGCUGUCCAAUAUGGCGACCGCCGCGGCGGUC-------
......((((........(((((((......(((......)))....)))))))...(((....)))...))))((((((....))))))------- ( -26.20)
>DroSim_CAF1 31042 90 + 1
AGAAUGGCCACAGAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGUUUCCCGAUAUGGUGAC-------GCGGUUUGAGUUC
.((((...(((((..(((((((.................)))))))..)))))(((((.((.((((.....)).)).-------)).))))).)))) ( -19.13)
>DroWil_CAF1 33410 81 + 1
AAAAUGGCCACAAAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGUUUGCCAAUAUCGGAAGAG-----AG-----------
....(((((((((..(((((((.................)))))))..)))))..........))))...((....)).-----..----------- ( -15.93)
>DroYak_CAF1 30515 90 + 1
AGAAUGGCCGCAGAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGCUUCCCGAUAUGGUGAC-------GCGGUUCGAGCAC
.....((((((.......(((((((......(((......)))....))))))).................(....)-------))))))....... ( -19.50)
>DroAna_CAF1 31634 79 + 1
GAAAUGGCCGCAGAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGUUUACCAAUCCGGCGGG-------GG-----------
.......((((.......(((((((......(((......)))....)))))))...(((....))).....)))).-------..----------- ( -18.70)
>consensus
AGAAUGGCCACAGAAUAAGCAUAAUAAAUUUGCAAUUAAAUGCUUAAAUUGUGCAAAUGGUUUCCCAAUAUGGUGAC_______GCGGUU_______
....(.((((........(((((((......(((......)))....)))))))...(((....)))...)))).)..................... (-13.63 = -13.05 +  -0.58)

alignment

secondary structure

dotplot

Window 0

Location	10,201,543 – 10,201,633
Length	90
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	79.53
Mean single sequence MFE	-18.95
Consensus MFE	-11.22
Energy contribution	-11.72
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.59
SVM decision value	0.77
SVM RNA-class probability	0.845239
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10201543 90 - 20766785
GAACUCAAACCGC-------GUCACCAUAUCGGGAAACCAUUUGCACAAUUUAAGCAUUUAAUUGCAAAUUUAUUAUGCUUAUUCUGUGGCCAUUCU
...........((-------...........((....)).....((((...(((((((.(((........)))..)))))))...))))))...... ( -17.80)
>DroPse_CAF1 13374 90 - 1
-------GACCGCCGCGGCGGUCGCCAUAUUGGACAGCCAUUUGCACAAUUUAAGCAUUUAAUUGCGAAUUUAUUAUGCCUAUUUUGUGGCCAUUCG
-------((((((....))))))((((((.(((....)))...(((.(((....(((......)))......))).)))......))))))...... ( -27.50)
>DroSim_CAF1 31042 90 - 1
GAACUCAAACCGC-------GUCACCAUAUCGGGAAACCAUUUGCACAAUUUAAGCAUUUAAUUGCAAAUUUAUUAUGCUUAUUCUGUGGCCAUUCU
...........((-------...........((....)).....((((...(((((((.(((........)))..)))))))...))))))...... ( -17.80)
>DroWil_CAF1 33410 81 - 1
-----------CU-----CUCUUCCGAUAUUGGCAAACCAUUUGCACAAUUUAAGCAUUUAAUUGCAAAUUUAUUAUGCUUAUUUUGUGGCCAUUUU
-----------..-----............((((....(....)(((((..(((((((.(((........)))..)))))))..))))))))).... ( -17.20)
>DroYak_CAF1 30515 90 - 1
GUGCUCGAACCGC-------GUCACCAUAUCGGGAAGCCAUUUGCACAAUUUAAGCAUUUAAUUGCAAAUUUAUUAUGCUUAUUCUGCGGCCAUUCU
......(((((((-------...........((....))............(((((((.(((........)))..)))))))....))))...))). ( -16.10)
>DroAna_CAF1 31634 79 - 1
-----------CC-------CCCGCCGGAUUGGUAAACCAUUUGCACAAUUUAAGCAUUUAAUUGCAAAUUUAUUAUGCUUAUUCUGCGGCCAUUUC
-----------..-------...(((((((((((((.....)))).)))))(((((((.(((........)))..))))))).....))))...... ( -17.30)
>consensus
_______AACCGC_______GUCACCAUAUCGGGAAACCAUUUGCACAAUUUAAGCAUUUAAUUGCAAAUUUAUUAUGCUUAUUCUGUGGCCAUUCU
...............................((....)).....((((...(((((((.(((........)))..)))))))...))))........ (-11.22 = -11.72 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:57 2006