Locus 5508

Sequence ID	2R_DroMel_CAF1
Location	17,656,330 – 17,656,603
Length	273
Max. P	0.999932

overview

Window 3

Location	17,656,330 – 17,656,449
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.31
Mean single sequence MFE	-38.34
Consensus MFE	-36.08
Energy contribution	-35.72
Covariance contribution	-0.36
Combinations/Pair	1.09
Mean z-score	-1.50
Structure conservation index	0.94
SVM decision value	1.49
SVM RNA-class probability	0.958847
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17656330 119 + 20766785
CUAAUUGGAGUUGGCCAAGUCGGAAAAUGCGGUAACUGCAGCGCAGGCGGGAUUCUCGCCGAGAAACGAGAAAUCUUCGCAUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAA
....((((......))))..........(((.(((((....(((.((((((...)))))).............((((((((......-))))))))...)))..)))))..)))...... ( -35.80)
>DroSec_CAF1 9873 119 + 1
CUAAUUGGAGUUGGCCAAGUCGGAAAAUGCGGUAACUGCAGCGCUGGCGGGAUUCUCGGCGAGAAACGAGAAAUCUCCGCAUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAA
....((((......))))(((((....(((((...)))))...)))))....((((((........)))))).((((((((......-))))))))((((((.........))))))... ( -40.40)
>DroSim_CAF1 15826 119 + 1
CUAAUUGGAGUUGGCCAAGUCGGAAAAUGCGGUAACUGCAGCGCUGGCGGGAUUCUCGGCGAGAAACGAGAAAUCUCCGCAUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAA
....((((......))))(((((....(((((...)))))...)))))....((((((........)))))).((((((((......-))))))))((((((.........))))))... ( -40.40)
>DroEre_CAF1 10114 119 + 1
CUAAUUGGAGUUGGCCAAGUCGGAAAAUGCGGUAACUGCAAUGCAGGCGGGAUUCUCGGCGAGAAACGUGCAAUCUCCGCAUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAA
((.((((.(((((.((..((......))..))))))).))))..))(((.(.(((((...))))).).)))..((((((((......-))))))))((((((.........))))))... ( -36.50)
>DroYak_CAF1 21565 120 + 1
CUAAUUGGAGUUGGCCAAGUCGGAAAAUGCGGUAACUGCCGUGCAGGCGGGAUUCUUGGCGAGAAACGAGAAAUCUCCGCAUCUCCUUUGCGGAGGAAAGCGAAAGUUAGACGCUUUAAA
....(((...((.(((((((((.......)))...(((((.....)))))....)))))).))...)))....((((((((.......))))))))((((((.........))))))... ( -38.60)
>consensus
CUAAUUGGAGUUGGCCAAGUCGGAAAAUGCGGUAACUGCAGCGCAGGCGGGAUUCUCGGCGAGAAACGAGAAAUCUCCGCAUCUCCU_UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAA
....((((......))))..........(((.(((((....(((..((((((((((((........)))).)))).)))).(((((.....)))))...)))..)))))..)))...... (-36.08 = -35.72 +  -0.36)

alignment

secondary structure

dotplot

Window 4

Location	17,656,330 – 17,656,449
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.31
Mean single sequence MFE	-33.62
Consensus MFE	-27.26
Energy contribution	-28.26
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.81
SVM decision value	0.14
SVM RNA-class probability	0.602666
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17656330 119 - 20766785
UUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAUGCGAAGAUUUCUCGUUUCUCGGCGAGAAUCCCGCCUGCGCUGCAGUUACCGCAUUUUCCGACUUGGCCAACUCCAAUUAG
......(((..(((((..(((....((((...-.))))..(((..((((.(((((......))))))))).)))..)))....))))).)))..........((((......)))).... ( -32.50)
>DroSec_CAF1 9873 119 - 1
UUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAUGCGGAGAUUUCUCGUUUCUCGCCGAGAAUCCCGCCAGCGCUGCAGUUACCGCAUUUUCCGACUUGGCCAACUCCAAUUAG
......(((..(((((..((((...((((...-.))))..((((.((((.((((........)))))))))))).))))....))))).)))..........((((......)))).... ( -36.10)
>DroSim_CAF1 15826 119 - 1
UUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAUGCGGAGAUUUCUCGUUUCUCGCCGAGAAUCCCGCCAGCGCUGCAGUUACCGCAUUUUCCGACUUGGCCAACUCCAAUUAG
......(((..(((((..((((...((((...-.))))..((((.((((.((((........)))))))))))).))))....))))).)))..........((((......)))).... ( -36.10)
>DroEre_CAF1 10114 119 - 1
UUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAUGCGGAGAUUGCACGUUUCUCGCCGAGAAUCCCGCCUGCAUUGCAGUUACCGCAUUUUCCGACUUGGCCAACUCCAAUUAG
...((((((.........)))))).((((...-.))))((((((.(((((((...(((((...)))))....(....)..))))))).))))))........((((......)))).... ( -33.90)
>DroYak_CAF1 21565 120 - 1
UUUAAAGCGUCUAACUUUCGCUUUCCUCCGCAAAGGAGAUGCGGAGAUUUCUCGUUUCUCGCCAAGAAUCCCGCCUGCACGGCAGUUACCGCAUUUUCCGACUUGGCCAACUCCAAUUAG
....(((((...((.((((((((((((......)))))).)))))).))...)))))...((((((......(((.....))).((....)).........))))))............. ( -29.50)
>consensus
UUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA_AGGAGAUGCGGAGAUUUCUCGUUUCUCGCCGAGAAUCCCGCCUGCGCUGCAGUUACCGCAUUUUCCGACUUGGCCAACUCCAAUUAG
......(((..(((((..(((....((((.....))))..((((.((((.((((........))))))))))))..)))....))))).)))..........((((......)))).... (-27.26 = -28.26 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	17,656,370 – 17,656,489
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.64
Mean single sequence MFE	-42.00
Consensus MFE	-38.90
Energy contribution	-39.18
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.93
Structure conservation index	0.93
SVM decision value	4.64
SVM RNA-class probability	0.999932
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17656370 119 + 20766785
GCGCAGGCGGGAUUCUCGCCGAGAAACGAGAAAUCUUCGCAUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAG
.....((((((...))))))(((((((((((((((((((((......-))))))))((((((.........))))))................)))))))))))))(((.....)))... ( -45.00)
>DroSec_CAF1 9913 119 + 1
GCGCUGGCGGGAUUCUCGGCGAGAAACGAGAAAUCUCCGCAUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAG
((....))......(((((((((((((((((((((((((((......-))))))))((((((.........))))))................)))))))))))))........)))))) ( -44.30)
>DroSim_CAF1 15866 119 + 1
GCGCUGGCGGGAUUCUCGGCGAGAAACGAGAAAUCUCCGCAUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAG
((....))......(((((((((((((((((((((((((((......-))))))))((((((.........))))))................)))))))))))))........)))))) ( -44.30)
>DroEre_CAF1 10154 119 + 1
AUGCAGGCGGGAUUCUCGGCGAGAAACGUGCAAUCUCCGCAUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUAAAAUUGAAAUUUCUUGUUUCUCGGCUUAUGGCCGAG
.......((((...))))((((((((....(((((((((((......-))))))))((((((.........))))))..........)))...))))))))..((((((.....)))))) ( -38.20)
>DroYak_CAF1 21605 120 + 1
GUGCAGGCGGGAUUCUUGGCGAGAAACGAGAAAUCUCCGCAUCUCCUUUGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUACUCGGUUUAUGGCCGAG
.....(((.(.......(.((((.(((((((((((((((((.......))))))))((((((.........))))))................))))))))).)))).)...).)))... ( -38.20)
>consensus
GCGCAGGCGGGAUUCUCGGCGAGAAACGAGAAAUCUCCGCAUCUCCU_UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAG
.....((((((...)))..((((((((((((((((((((((.......))))))))((((((.........))))))................)))))))))))))).......)))... (-38.90 = -39.18 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	17,656,370 – 17,656,489
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.64
Mean single sequence MFE	-37.60
Consensus MFE	-32.84
Energy contribution	-34.04
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-3.69
Structure conservation index	0.87
SVM decision value	3.97
SVM RNA-class probability	0.999735
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17656370 119 - 20766785
CUCGGCCAUAAACCGAGAAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAUGCGAAGAUUUCUCGUUUCUCGGCGAGAAUCCCGCCUGCGC
....((........(((((((.(((((((((............((((((.........)))))).((((...-.))))....).)))))))).)))))))((((.......)))).)).. ( -38.00)
>DroSec_CAF1 9913 119 - 1
CUCGGCCAUAAACCGAGAAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAUGCGGAGAUUUCUCGUUUCUCGCCGAGAAUCCCGCCAGCGC
((((((........(((((((.(((((((((............((((((.........)))))).((((...-.)))).....))))))))).))))))))))))).............. ( -42.00)
>DroSim_CAF1 15866 119 - 1
CUCGGCCAUAAACCGAGAAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAUGCGGAGAUUUCUCGUUUCUCGCCGAGAAUCCCGCCAGCGC
((((((........(((((((.(((((((((............((((((.........)))))).((((...-.)))).....))))))))).))))))))))))).............. ( -42.00)
>DroEre_CAF1 10154 119 - 1
CUCGGCCAUAAGCCGAGAAACAAGAAAUUUCAAUUUUAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAUGCGGAGAUUGCACGUUUCUCGCCGAGAAUCCCGCCUGCAU
((((((........(((((((....((((((............((((((.........)))))).((((...-.)))).....))))))....))))))))))))).............. ( -35.80)
>DroYak_CAF1 21605 120 - 1
CUCGGCCAUAAACCGAGUAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCAAAGGAGAUGCGGAGAUUUCUCGUUUCUCGCCAAGAAUCCCGCCUGCAC
...(((.......((((.(((.(((((((((............((((((.........)))))).((((.....)))).....))))))))).))).))))....(.....))))..... ( -30.20)
>consensus
CUCGGCCAUAAACCGAGAAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA_AGGAGAUGCGGAGAUUUCUCGUUUCUCGCCGAGAAUCCCGCCUGCGC
((((((........(((((((.(((((((((............((((((.........)))))).((((.....)))).....))))))))).))))))))))))).............. (-32.84 = -34.04 +   1.20)

alignment

secondary structure

dotplot

Window 7

Location	17,656,410 – 17,656,527
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.04
Mean single sequence MFE	-33.10
Consensus MFE	-29.76
Energy contribution	-30.00
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.28
Structure conservation index	0.90
SVM decision value	0.19
SVM RNA-class probability	0.627154
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17656410 117 + 20766785
AUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGGUUC--GAGACUCCAGCCAAGUG
.((((.(-(((((.....(((....)))....(((((......(((((....)))))....((((((((.....))))))))))))).....))))))...--))))............. ( -32.10)
>DroSec_CAF1 9953 117 + 1
AUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGGUUC--GAGACUCCAGCCAAGUG
.((((.(-(((((.....(((....)))....(((((......(((((....)))))....((((((((.....))))))))))))).....))))))...--))))............. ( -32.10)
>DroSim_CAF1 15906 117 + 1
AUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGGCUC--GAGACUCCAGCCAAGUG
.......-.((((.....(((....)))....(((((......(((((....)))))....((((((((.....))))))))))))).....))))((((.--(.....).))))..... ( -34.30)
>DroEre_CAF1 10194 117 + 1
AUCUCCU-UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUAAAAUUGAAAUUUCUUGUUUCUCGGCUUAUGGCCGAGGAAAAGCAAAAGCCGCGUUUC--GAGACUCCAGCCAAGUG
.....((-(((((((...(((....)))((((((..........................(((((((((.....)))))))))..((....)).)))))).--....)))).).)))).. ( -33.30)
>DroYak_CAF1 21645 120 + 1
AUCUCCUUUGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUACUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGAUUCGCGAGACUCCAGCCAAGUG
.....(((.((((((...(((....)))....(((((.(((..(((((....)))))..))).((((((.....))))))..)))))......((((...))))...)))).)).))).. ( -33.70)
>consensus
AUCUCCU_UGCGGAGGAAAGCGAAAGUUAGACGCUUUAAAUUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGGUUC__GAGACUCCAGCCAAGUG
.((((...(((((.....(((....)))....(((((......(((((....)))))....((((((((.....))))))))))))).....)))))......))))............. (-29.76 = -30.00 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	17,656,410 – 17,656,527
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.04
Mean single sequence MFE	-32.86
Consensus MFE	-27.86
Energy contribution	-27.86
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.44
Structure conservation index	0.85
SVM decision value	2.15
SVM RNA-class probability	0.989219
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17656410 117 - 20766785
CACUUGGCUGGAGUCUC--GAACCGCGGCUUUUGCUUUUCCUCGGCCAUAAACCGAGAAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAU
..((((((..(((((.(--(...)).)))))..)).....(((((.......)))))...))))...................((((((.........)))))).((((...-.)))).. ( -32.60)
>DroSec_CAF1 9953 117 - 1
CACUUGGCUGGAGUCUC--GAACCGCGGCUUUUGCUUUUCCUCGGCCAUAAACCGAGAAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAU
..((((((..(((((.(--(...)).)))))..)).....(((((.......)))))...))))...................((((((.........)))))).((((...-.)))).. ( -32.60)
>DroSim_CAF1 15906 117 - 1
CACUUGGCUGGAGUCUC--GAGCCGCGGCUUUUGCUUUUCCUCGGCCAUAAACCGAGAAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAU
.....((((.(.....)--.))))((((....((((((..(((((.......)))))......(((((....)))))......))))))........))))....((((...-.)))).. ( -32.80)
>DroEre_CAF1 10194 117 - 1
CACUUGGCUGGAGUCUC--GAAACGCGGCUUUUGCUUUUCCUCGGCCAUAAGCCGAGAAACAAGAAAUUUCAAUUUUAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA-AGGAGAU
..((((((..(((((.(--(...)).)))))..)).....((((((.....))))))...))))...................((((((.........)))))).((((...-.)))).. ( -36.20)
>DroYak_CAF1 21645 120 - 1
CACUUGGCUGGAGUCUCGCGAAUCGCGGCUUUUGCUUUUCCUCGGCCAUAAACCGAGUAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCAAAGGAGAU
..((((((..((((..((((...))))))))..)).....(((((.......)))))...))))...................((((((.........)))))).((((.....)))).. ( -30.10)
>consensus
CACUUGGCUGGAGUCUC__GAACCGCGGCUUUUGCUUUUCCUCGGCCAUAAACCGAGAAACAAGAAAUUUCAAUUUCAAAUUUAAAGCGUCUAACUUUCGCUUUCCUCCGCA_AGGAGAU
..((((((..(((((...........)))))..)).....(((((.......)))))...))))...................((((((.........)))))).((((.....)))).. (-27.86 = -27.86 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	17,656,449 – 17,656,563
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.45
Mean single sequence MFE	-35.52
Consensus MFE	-30.82
Energy contribution	-31.14
Covariance contribution	0.32
Combinations/Pair	1.06
Mean z-score	-1.31
Structure conservation index	0.87
SVM decision value	0.23
SVM RNA-class probability	0.644979
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17656449 114 + 20766785
UUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGGUUC--GAGACUCCAGCCAAGUGCACGUU-CGGUUUGGGCCAU---AAACUGUGGCCUGCCAU
....((((((((.((((((.(((((((((.....)))))))))))).))).(((..((((.--(.....).))))..).))...))-))))))(((((((---.....)))))))..... ( -34.30)
>DroSec_CAF1 9992 117 + 1
UUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGGUUC--GAGACUCCAGCCAAGUGCACGUU-CGGUUUGGGCCAUAAUAAACUGUGGCCUGCCAU
....((((((((.((((((.(((((((((.....)))))))))))).))).(((..((((.--(.....).))))..).))...))-))))))((((((((......))))))))..... ( -35.50)
>DroSim_CAF1 15945 114 + 1
UUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGGCUC--GAGACUCCAGCCAAGUGCACGUU-CGGUUUGGGCCAU---AAACUGUGGCCUGCCAU
....((((((((.((((((.(((((((((.....)))))))))))).))).(((..((((.--(.....).))))..).))...))-))))))(((((((---.....)))))))..... ( -36.70)
>DroEre_CAF1 10233 114 + 1
UUUAAAAUUGAAAUUUCUUGUUUCUCGGCUUAUGGCCGAGGAAAAGCAAAAGCCGCGUUUC--GAGACUCCAGCCAAGUGCACGUU-UGGUUUGGGCCAU---AAACUGUGGCCUGCCAU
.......(((((((......(((((((((.....)))))))))..((.......)))))))--))......(((((((......))-))))).(((((((---.....)))))))..... ( -34.90)
>DroYak_CAF1 21685 117 + 1
UUUGAAAUUGAAAUUUCUUGUUACUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGAUUCGCGAGACUCCAGCCAAGUGCACGUUUUGGUUUGGGCCAU---AAACUGUGGCCUGCCAU
...(((((....)))))........((((((((((((..(((...((....))((((...))))....)))(((((((.......)))))))..))))))---))))))(((....))). ( -36.20)
>consensus
UUUGAAAUUGAAAUUUCUUGUUUCUCGGUUUAUGGCCGAGGAAAAGCAAAAGCCGCGGUUC__GAGACUCCAGCCAAGUGCACGUU_CGGUUUGGGCCAU___AAACUGUGGCCUGCCAU
...(((((....)))))...(((((((((.....)))))))))..(((...((.(.((.((....)).))).))....))).......(((..(((((((........)))))))))).. (-30.82 = -31.14 +   0.32)

alignment

secondary structure

dotplot

Window 0

Location	17,656,489 – 17,656,603
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.80
Mean single sequence MFE	-42.44
Consensus MFE	-35.29
Energy contribution	-36.09
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.80
Structure conservation index	0.83
SVM decision value	1.23
SVM RNA-class probability	0.932991
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17656489 114 + 20766785
GAAAAGCAAAAGCCGCGGUUC--GAGACUCCAGCCAAGUGCACGUU-CGGUUUGGGCCAU---AAACUGUGGCCUGCCAUUAUGAGCUAACUUGGCCAGGGCGGCGAAGAAGGGGUUUCU
(((..((.......))..)))--((((((((...(((((((.(((.-.(((..(((((((---.....))))))))))...))).))..)))))(((.....)))......)))))))). ( -42.30)
>DroSec_CAF1 10032 114 + 1
GAAAAGCAAAAGCCGCGGUUC--GAGACUCCAGCCAAGUGCACGUU-CGGUUUGGGCCAUAAUAAACUGUGGCCUGCCAUUAUGAGCUAACUUGGCCAGGGCGGCGGAGA---GGUUUCU
((((.......(((((((((.--..))))((.(((((((((.(((.-.(((..((((((((......)))))))))))...))).))..)))))))..))))))).....---..)))). ( -43.44)
>DroSim_CAF1 15985 111 + 1
GAAAAGCAAAAGCCGCGGCUC--GAGACUCCAGCCAAGUGCACGUU-CGGUUUGGGCCAU---AAACUGUGGCCUGCCAUUAUGAGCUAACUUGGCCAGGGCGGCGGAGA---GGUUUCU
...((((.....((((.((((--(......).(((((((((.(((.-.(((..(((((((---.....))))))))))...))).))..)))))))..)))).))))...---.)))).. ( -43.80)
>DroEre_CAF1 10273 111 + 1
GAAAAGCAAAAGCCGCGUUUC--GAGACUCCAGCCAAGUGCACGUU-UGGUUUGGGCCAU---AAACUGUGGCCUGCCAUUAUGAGCUAACGUGGCCAGGGCGGCGGAGA---GGUUUCU
((((.......((((((((..--..))).((.((((.((((.(((.-((((..(((((((---.....)))))))))))..))).))..)).))))..))))))).....---..)))). ( -40.54)
>DroYak_CAF1 21725 114 + 1
GAAAAGCAAAAGCCGCGAUUCGCGAGACUCCAGCCAAGUGCACGUUUUGGUUUGGGCCAU---AAACUGUGGCCUGCCAUUAUGAGCUAACGCGGCCAGGGCGACGGAGA---GGUUUCU
.........((((((((...)))....((((.(((..(.((.(((..((((..(((((((---.....)))))))))))..))).((....)).)))..)))...)))).---))))).. ( -42.10)
>consensus
GAAAAGCAAAAGCCGCGGUUC__GAGACUCCAGCCAAGUGCACGUU_CGGUUUGGGCCAU___AAACUGUGGCCUGCCAUUAUGAGCUAACUUGGCCAGGGCGGCGGAGA___GGUUUCU
((((.......(((((...((....))..((.(((((((((.(((...(((..(((((((........))))))))))...))).))..)))))))..)))))))..........)))). (-35.29 = -36.09 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:09 2006