Locus 6365

Sequence ID	3L_DroMel_CAF1
Location	17,039,415 – 17,039,555
Length	140
Max. P	0.806262

overview

Window 6

Location	17,039,415 – 17,039,518
Length	103
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	72.07
Mean single sequence MFE	-30.98
Consensus MFE	-18.63
Energy contribution	-19.27
Covariance contribution	0.64
Combinations/Pair	1.12
Mean z-score	-1.24
Structure conservation index	0.60
SVM decision value	0.06
SVM RNA-class probability	0.565525
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17039415 103 + 23771897
UGUGGUUGUGUCUAUUUG-----------GCAAUGAGCCGCACUUACCAGUUGGAUAGGGCAGUCCAAAACUGGGAUAGCCCGAGUAUCCGCGACCAGCGGCAUAAGCAGCAUA
..((((((((..((((((-----------((.....))).......((....))...((((.((((.......)))).)))))))))..))))))))((.((....)).))... ( -37.20)
>DroVir_CAF1 1578 114 + 1
UGGAGGUGUGUCUGUGAGAGAGUAGAAGAGCAGUUAAACAAACUUACCAGUUGGAUAGGGUAGUCCGAAGCUCGGAUAGCCGGAGUAGCCGCGACCUGCGGCAUAGGCAGCAUA
.....(((((((((((.....((((....((.((((..(.......((....))....(((.(((((.....))))).))))...)))).))...))))..)))))))).))). ( -34.60)
>DroPse_CAF1 7030 87 + 1
UA--------------UG-----------G--GUGAACGGGACUUACCAGUUGGAUAGGGGAGUCCGAAGGAGGGAUAGCCCGAAUAUCCGCGACCAGCGGCAUAGGCAGCAUA
..--------------.(-----------(--(((..((((.((..((..((((((......))))))....))...))))))..)))))((..((.........))..))... ( -26.10)
>DroMoj_CAF1 7343 98 + 1
AGAGGGAGAGU--GAGAUAGAGU---------GUU-----GACUUACCAGUUGGAUAGGGUAGUCCGAAGCUGGGAUAACCCGAAUAGCCGCGACCAGCGGCAUAAGCAGCAUA
...........--........((---------(((-----(.((((((....))...((((.((((.......)))).)))).....(((((.....))))).)))))))))). ( -32.30)
>DroAna_CAF1 6134 91 + 1
UGUGU------------G-----------GGUGUGCGUCGGACUUACCAGUUGGAUAGGGCAGACCGAAGCUGGGAUAGCCCGAGUAGCCACGACCAGCGGCAUAAGCAGCAUA
(((((------------.-----------(((.((((((.((((....)))).)))...))).)))...((((((....))).....(((.(.....).)))...))).))))) ( -29.60)
>DroPer_CAF1 697 87 + 1
UA--------------UG-----------G--GUGAACGGGACUUACCAGUUGGAUAGGGGAGUCCGAAGGAGGGAUAGCCCGAAUAUCCGCGACCAGCGGCAUAGGCAGCAUA
..--------------.(-----------(--(((..((((.((..((..((((((......))))))....))...))))))..)))))((..((.........))..))... ( -26.10)
>consensus
UG_GG___________UG___________G__GUGAACCGGACUUACCAGUUGGAUAGGGCAGUCCGAAGCUGGGAUAGCCCGAAUAGCCGCGACCAGCGGCAUAAGCAGCAUA
.................................................((((....((((.((((.......)))).))))......((((.....))))......))))... (-18.63 = -19.27 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	17,039,415 – 17,039,518
Length	103
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	72.07
Mean single sequence MFE	-25.23
Consensus MFE	-14.97
Energy contribution	-14.83
Covariance contribution	-0.13
Combinations/Pair	1.29
Mean z-score	-1.27
Structure conservation index	0.59
SVM decision value	0.05
SVM RNA-class probability	0.557839
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17039415 103 - 23771897
UAUGCUGCUUAUGCCGCUGGUCGCGGAUACUCGGGCUAUCCCAGUUUUGGACUGCCCUAUCCAACUGGUAAGUGCGGCUCAUUGC-----------CAAAUAGACACAACCACA
...((.((....)).))((((((((((((...((((..(((.......)))..))))))))).(((....)))))(((.....))-----------).....))).))...... ( -32.20)
>DroVir_CAF1 1578 114 - 1
UAUGCUGCCUAUGCCGCAGGUCGCGGCUACUCCGGCUAUCCGAGCUUCGGACUACCCUAUCCAACUGGUAAGUUUGUUUAACUGCUCUUCUACUCUCUCACAGACACACCUCCA
...((((.....(((((.....))))).....)))).....((((..((((((..((.........))..)))))).......))))........................... ( -25.50)
>DroPse_CAF1 7030 87 - 1
UAUGCUGCCUAUGCCGCUGGUCGCGGAUAUUCGGGCUAUCCCUCCUUCGGACUCCCCUAUCCAACUGGUAAGUCCCGUUCAC--C-----------CA--------------UA
((((..(((((((((((.....)))).)))..))))............(((((..((.........))..))))).......--.-----------))--------------)) ( -21.60)
>DroMoj_CAF1 7343 98 - 1
UAUGCUGCUUAUGCCGCUGGUCGCGGCUAUUCGGGUUAUCCCAGCUUCGGACUACCCUAUCCAACUGGUAAGUC-----AAC---------ACUCUAUCUC--ACUCUCCCUCU
..((.((((((((((((.....))))).....((((..(((.......)))..))))..........))))).)-----).)---------).........--........... ( -23.50)
>DroAna_CAF1 6134 91 - 1
UAUGCUGCUUAUGCCGCUGGUCGUGGCUACUCGGGCUAUCCCAGCUUCGGUCUGCCCUAUCCAACUGGUAAGUCCGACGCACACC-----------C------------ACACA
..((.(((.......(((((..((((((.....)))))).))))).((((.((..((.........))..)).)))).)))))..-----------.------------..... ( -27.00)
>DroPer_CAF1 697 87 - 1
UAUGCUGCCUAUGCCGCUGGUCGCGGAUAUUCGGGCUAUCCCUCCUUCGGACUCCCCUAUCCAACUGGUAAGUCCCGUUCAC--C-----------CA--------------UA
((((..(((((((((((.....)))).)))..))))............(((((..((.........))..))))).......--.-----------))--------------)) ( -21.60)
>consensus
UAUGCUGCCUAUGCCGCUGGUCGCGGAUACUCGGGCUAUCCCAGCUUCGGACUACCCUAUCCAACUGGUAAGUCCGGUUCAC__C___________CA___________CC_CA
.............((((.....))))......(((....)))......(((((..((.........))..)))))....................................... (-14.97 = -14.83 +  -0.13)

alignment

secondary structure

dotplot

Window 8

Location	17,039,438 – 17,039,555
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.52
Mean single sequence MFE	-35.47
Consensus MFE	-22.02
Energy contribution	-22.22
Covariance contribution	0.19
Combinations/Pair	1.17
Mean z-score	-1.75
Structure conservation index	0.62
SVM decision value	0.63
SVM RNA-class probability	0.806262
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17039438 117 + 23771897
GAGCCGCACUUACCAGUUGGAUAGGGCAGUCCAAAACUGGGAUAGCCCGAGUAUCCGCGACCAGCGGCAUAAGCAGCAUAGGCAGCUGCCGGAAAACCUAAUCGAAAAAG---UAUAGAA
..((((((((....))).(((((((((.((((.......)))).))))...))))).......)))))....(((((.......))))).((....))............---....... ( -35.90)
>DroVir_CAF1 1612 114 + 1
UAAACAAACUUACCAGUUGGAUAGGGUAGUCCGAAGCUCGGAUAGCCGGAGUAGCCGCGACCUGCGGCAUAGGCAGCAUACGCAGCUGCCGGAAAGCCUGCGAGAAAGAA-----AAC-A
........(((.((....))...((((..(((...((((((....)).)))).(((((.....)))))...((((((.......)))))))))..))))..)))......-----...-. ( -38.40)
>DroGri_CAF1 7097 113 + 1
UGAGC-AACUUACCAGUUGGAUAGGGUAGUCCAAAGCUAGGAUAGCCGGAGUAACCGCGACCAGAGGCAUAAGCAGCAUACGCAGCUGCCUGAAAGCCUGUGGAAGAAAU------GAAA
...((-......((....))...((.((.(((...((((...)))).))).)).))))..(((.((((.((.(((((.......))))).))...)))).))).......------.... ( -32.50)
>DroEre_CAF1 6927 105 + 1
GAGCCGCACUUACCAGUUGGAUAGGGCAGUCCAAAACUGGGAUAGCCCGAGUAUCCGCGACCAGCGGCAUAGGCAGCGUAGGCAGCUGCCGGAAAACCUA---------------UGGAA
..((((((((....))).(((((((((.((((.......)))).))))...))))).......)))))...((((((.......))))))((....))..---------------..... ( -40.80)
>DroWil_CAF1 10458 120 + 1
GGAUAGAACUUACCAGUUGGAUAGGGUAGACCAAAGCUAGGAUAGCCGGAAUAUCCGCGACCAGCGGCAUAGGCAGCAUAAGCAGCUGCUGGAAAGCCUAAAAGAGAAUGAUGAAAAGAA
........(((....(((((...(((((..((...((((...)))).))..)))))....)))))(((...((((((.......)))))).....))).....))).............. ( -31.50)
>DroAna_CAF1 6145 112 + 1
GCGUCGGACUUACCAGUUGGAUAGGGCAGACCGAAGCUGGGAUAGCCCGAGUAGCCACGACCAGCGGCAUAAGCAGCAUAGGCAGCUGCCGGAAAACCUGCACA--AAAU------AAAA
((.((((.((..((((((.....((.....))..))))))...)).))))...(((.(.....).)))....)).(((..(((....)))((....)))))...--....------.... ( -33.70)
>consensus
GAACCGAACUUACCAGUUGGAUAGGGCAGUCCAAAGCUGGGAUAGCCCGAGUAUCCGCGACCAGCGGCAUAAGCAGCAUAGGCAGCUGCCGGAAAACCUAAAAGA_AAAG______AGAA
............((....)).((((((.((((.......)))).))(((.....((((.....)))).....(((((.......))))))))....)))).................... (-22.02 = -22.22 +   0.19)

alignment

secondary structure

dotplot

Window 9

Location	17,039,438 – 17,039,555
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.52
Mean single sequence MFE	-35.58
Consensus MFE	-21.25
Energy contribution	-21.67
Covariance contribution	0.42
Combinations/Pair	1.33
Mean z-score	-1.84
Structure conservation index	0.60
SVM decision value	0.61
SVM RNA-class probability	0.799775
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17039438 117 - 23771897
UUCUAUA---CUUUUUCGAUUAGGUUUUCCGGCAGCUGCCUAUGCUGCUUAUGCCGCUGGUCGCGGAUACUCGGGCUAUCCCAGUUUUGGACUGCCCUAUCCAACUGGUAAGUGCGGCUC
.......---............(((.....((((((.......))))))...)))...(((((((((((...((((..(((.......)))..))))))))).(((....))))))))). ( -38.40)
>DroVir_CAF1 1612 114 - 1
U-GUU-----UUCUUUCUCGCAGGCUUUCCGGCAGCUGCGUAUGCUGCCUAUGCCGCAGGUCGCGGCUACUCCGGCUAUCCGAGCUUCGGACUACCCUAUCCAACUGGUAAGUUUGUUUA
.-...-----.........((((((((.((((((((.......))))))...(((((.....)))))......((.((((((.....)))).)).)).........)).))))))))... ( -38.40)
>DroGri_CAF1 7097 113 - 1
UUUC------AUUUCUUCCACAGGCUUUCAGGCAGCUGCGUAUGCUGCUUAUGCCUCUGGUCGCGGUUACUCCGGCUAUCCUAGCUUUGGACUACCCUAUCCAACUGGUAAGUU-GCUCA
....------.......(((.((((....(((((((.......)))))))..)))).)))....(((...((((((((...)))))..)))..))).....(((((....))))-).... ( -32.50)
>DroEre_CAF1 6927 105 - 1
UUCCA---------------UAGGUUUUCCGGCAGCUGCCUACGCUGCCUAUGCCGCUGGUCGCGGAUACUCGGGCUAUCCCAGUUUUGGACUGCCCUAUCCAACUGGUAAGUGCGGCUC
.....---------------..(((.....((((((.......))))))...)))...(((((((((((...((((..(((.......)))..))))))))).(((....))))))))). ( -39.70)
>DroWil_CAF1 10458 120 - 1
UUCUUUUCAUCAUUCUCUUUUAGGCUUUCCAGCAGCUGCUUAUGCUGCCUAUGCCGCUGGUCGCGGAUAUUCCGGCUAUCCUAGCUUUGGUCUACCCUAUCCAACUGGUAAGUUCUAUCC
....................(((((((.((((.(((((.....((((...(((((((.....)))).)))..)))).....)))))((((..........)))))))).))).))))... ( -27.40)
>DroAna_CAF1 6145 112 - 1
UUUU------AUUU--UGUGCAGGUUUUCCGGCAGCUGCCUAUGCUGCUUAUGCCGCUGGUCGUGGCUACUCGGGCUAUCCCAGCUUCGGUCUGCCCUAUCCAACUGGUAAGUCCGACGC
....------....--...((.(((.....((((((.......))))))...)))(((((..((((((.....)))))).))))).((((.((..((.........))..)).)))).)) ( -37.10)
>consensus
UUCU______AUUU_UCGCGCAGGCUUUCCGGCAGCUGCCUAUGCUGCCUAUGCCGCUGGUCGCGGAUACUCCGGCUAUCCCAGCUUUGGACUACCCUAUCCAACUGGUAAGUUCGACUC
......................(((.....((((((.......))))))...)))(((((..((..........))....)))))..((((((..((.........))..)))))).... (-21.25 = -21.67 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:38 2006